Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 41
Found at i:5045829 original size:99 final size:99
Alignment explanation
Indices: 5045657--5045838 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 99
5045647 GTTGCTCTTG
* *** * * * * *
5045657 AAATGTTACAAAAGTTTAAGTTGATGGGGTCTTATAAATCTCACGATAATAAAATAGATTAATTA
1 AAATGTTACAAAAGTTTAAGCTGATGGAAACTTAGAAATCACACGACAACAAAATAGATTAAATA
* *
5045722 TTTGTTTTGTTATAAATATTATCATCTGTCACTA
66 ATTATTTTGTTATAAATATTATCATCTGTCACTA
5045756 AAATGTTACTAAAA-TTTAAGCTGATGGAAACTTAGAAATCACACGACAACAAAATA-AGTTAAA
1 AAATGTTAC-AAAAGTTTAAGCTGATGGAAACTTAGAAATCACACGACAACAAAATAGA-TTAAA
5045819 TAATTATTTTGTTATAAATA
64 TAATTATTTTGTTATAAATA
5045839 AATATAACAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
98 1 0.01
99 65 0.93
100 4 0.06
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (99 bp):
AAATGTTACAAAAGTTTAAGCTGATGGAAACTTAGAAATCACACGACAACAAAATAGATTAAATA
ATTATTTTGTTATAAATATTATCATCTGTCACTA
Found at i:5046323 original size:20 final size:20
Alignment explanation
Indices: 5046298--5046340 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5046288 TCTAATAGCT
*
5046298 CATTTAGGACCATGTAGATG
1 CATTTAGGACCATATAGATG
* *
5046318 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
5046338 CAT
1 CAT
5046341 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:5048411 original size:100 final size:100
Alignment explanation
Indices: 5048252--5048444 Score: 316
Period size: 100 Copynumber: 1.9 Consensus size: 100
5048242 TCAAACGGTC
**
5048252 AAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGGTAGCTAGTTTAA
1 AAGTTGTAAATATTTTACCGTTTACACCATTATTATACCTTTAAACAAATCGGTAGCTAGTTTAA
*
5048317 CGTAATAGGTTGCGTCTATTTTATTTTAACCAGTT
66 CGTAATAGGTTGCGCCTATTTTATTTTAACCAGTT
* *
5048352 AAGTTGTAAATATTTTACCGTTTACACCATTATTATACTTTTAAACAAA-CATGTAGCTAGTTTA
1 AAGTTGTAAATATTTTACCGTTTACACCATTATTATACCTTTAAACAAATC-GGTAGCTAGTTTA
*
5048416 ACGTAATAGGTTGTGCCTATTTTATTTTA
65 ACGTAATAGGTTGCGCCTATTTTATTTTA
5048445 CCTTTTACAT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
99 1 0.01
100 85 0.99
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (100 bp):
AAGTTGTAAATATTTTACCGTTTACACCATTATTATACCTTTAAACAAATCGGTAGCTAGTTTAA
CGTAATAGGTTGCGCCTATTTTATTTTAACCAGTT
Found at i:5048462 original size:76 final size:76
Alignment explanation
Indices: 5048362--5048596 Score: 346
Period size: 76 Copynumber: 3.1 Consensus size: 76
5048352 AAGTTGTAAA
* ** *
5048362 TATTTTACCGTTTACACCATTATTATACTTTTAAACAAA-CATGTAGCTAGTTTAACGTAATAGG
1 TATTTTACCATTTACATTATTATTATACATTTAAACAAACCA-GTAGCTAGTTTAACGTAATAGG
*
5048426 TTGTGCCTATTT
65 TTGCGCCTATTT
* * * *
5048438 TATTTTACCTTTTACATTATTATTATACATTTAAACAAACCAATAGCTAGTTTAACGTAACAGTT
1 TATTTTACCATTTACATTATTATTATACATTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGT
*
5048503 TGCGTCTATTT
66 TGCGCCTATTT
*
5048514 TATTTTACCATTTACATTATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCATTTACATTATTATTATACATTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGT
*
5048579 TGCACCTATTT
66 TGCGCCTATTT
5048590 TATTTTA
1 TATTTTA
5048597 ACTGGTTATG
Statistics
Matches: 142, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
76 140 0.99
77 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (76 bp):
TATTTTACCATTTACATTATTATTATACATTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGT
TGCGCCTATTT
Found at i:5049769 original size:23 final size:23
Alignment explanation
Indices: 5049726--5049770 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5049716 TTGTGAAACT
* *
5049726 TTTTAATTTTTTATTAGTTTATA
1 TTTTAATTTTATACTAGTTTATA
5049749 TTTTAATTTATATACTA-TTTAT
1 TTTTAATTT-TATACTAGTTTAT
5049771 TTAATTAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTAATTTTATACTAGTTTATA
Found at i:5052465 original size:19 final size:19
Alignment explanation
Indices: 5052426--5052466 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5052416 ATTAAAGATG
*
5052426 AATTGATTTTGAAAGTAAA
1 AATTGATTTTGAAAATAAA
*
5052445 AATTGATTTTGAAAATCAA
1 AATTGATTTTGAAAATAAA
5052464 AAT
1 AAT
5052467 GAAATTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (19 bp):
AATTGATTTTGAAAATAAA
Found at i:5053971 original size:36 final size:36
Alignment explanation
Indices: 5053924--5053992 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
5053914 ATGTAATTAG
*
5053924 TGTACCGATACACCCTGTAGTGTATCCATACACTAC
1 TGTACCGATACACCCTGCAGTGTATCCATACACTAC
* *
5053960 TGTACTGATACACTCTGCAGTGTATCCATACAC
1 TGTACCGATACACCCTGCAGTGTATCCATACAC
5053993 CCTGGTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (36 bp):
TGTACCGATACACCCTGCAGTGTATCCATACACTAC
Found at i:5056022 original size:20 final size:20
Alignment explanation
Indices: 5055997--5056034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5055987 GTATTGGAGC
*
5055997 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGCTGTGGG
*
5056017 ATGCATGTGGGAGCTGTG
1 ATGCATGGGGGAGCTGTG
5056035 CATGGGACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.50, T:0.26
Consensus pattern (20 bp):
ATGCATGGGGGAGCTGTGGG
Found at i:5056046 original size:20 final size:20
Alignment explanation
Indices: 5056023--5056060 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5056013 TGGGATGCAT
*
5056023 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
*
5056043 GTGGGAATTGTGCATGGG
1 GTGGGAACTGTGCATGGG
5056061 CCATGCACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.11, G:0.50, T:0.24
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:5056113 original size:30 final size:30
Alignment explanation
Indices: 5056079--5056148 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
5056069 GTCGAACGGT
* *
5056079 GTAGGTTGCCATGGAGTCACTGCGAGCTTG
1 GTAGGTCGCCATGGAGTCACGGCGAGCTTG
5056109 GTAGGTCGCCATGGAGTCACGGCGAGCTTG
1 GTAGGTCGCCATGGAGTCACGGCGAGCTTG
5056139 GTAGGTCGCC
1 GTAGGTCGCC
5056149 GTGTAGGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (30 bp):
GTAGGTCGCCATGGAGTCACGGCGAGCTTG
Found at i:5056247 original size:14 final size:14
Alignment explanation
Indices: 5056230--5056257 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5056220 AACGCATCCA
5056230 TAGCTGGGAGATTC
1 TAGCTGGGAGATTC
5056244 TAGCTGGGAGATTC
1 TAGCTGGGAGATTC
5056258 CTGCATCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
TAGCTGGGAGATTC
Found at i:5056307 original size:44 final size:44
Alignment explanation
Indices: 5056244--5056334 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
5056234 TGGGAGATTC
5056244 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
1 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
* *
5056288 TAGCTGGGAGATTCCTGCATCCGTAGCTGTATGTGTTGCATCCA
1 TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
5056332 TAG
1 TAG
5056335 TTGCGTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (44 bp):
TAGCTGGGAGATTCCTGCATCCGTAGCTGCATGCGTTGCATCCA
Found at i:5056308 original size:23 final size:23
Alignment explanation
Indices: 5056244--5056316 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
5056234 TGGGAGATTC
5056244 TAGCTGGGAGATTCCTGCATCCG
1 TAGCTGGGAGATTCCTGCATCCG
* * * *
5056267 TAGCT--G-CATGCGTTGCATCCA
1 TAGCTGGGAGATTC-CTGCATCCG
5056288 TAGCTGGGAGATTCCTGCATCCG
1 TAGCTGGGAGATTCCTGCATCCG
5056311 TAGCTG
1 TAGCTG
5056317 TATGTGTTGC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 13 0.34
23 19 0.50
24 3 0.08
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (23 bp):
TAGCTGGGAGATTCCTGCATCCG
Found at i:5056329 original size:21 final size:21
Alignment explanation
Indices: 5056259--5056330 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
5056249 GGGAGATTCC
*
5056259 TGCATCCGTAGCTGCATGCGT
1 TGCATCCGTAGCTGCATGTGT
* *
5056280 TGCATCCATAGCTGGGA-GAT-T
1 TGCATCCGTAGCT-GCATG-TGT
*
5056301 CCTGCATCCGTAGCTGTATGTGT
1 --TGCATCCGTAGCTGCATGTGT
5056324 TGCATCC
1 TGCATCC
5056331 ATAGTTGCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 21 0.52
22 5 0.12
23 14 0.35
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
TGCATCCGTAGCTGCATGTGT
Found at i:5056729 original size:21 final size:21
Alignment explanation
Indices: 5056704--5056747 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5056694 AATCTAGTTA
5056704 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5056725 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5056746 AT
1 AT
5056748 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5056757 original size:28 final size:30
Alignment explanation
Indices: 5056724--5056786 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
5056714 TAGTATAAAT
*
5056724 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5056752 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5056782 TATTA
1 TATTA
5056787 TATAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:5056956 original size:33 final size:33
Alignment explanation
Indices: 5056914--5057061 Score: 191
Period size: 33 Copynumber: 4.5 Consensus size: 33
5056904 TTATAAAAAA
5056914 TTATATATTATATTATTAGTTTGTTAGTTTAAG
1 TTATATATTATATTATTAGTTTGTTAGTTTAAG
5056947 TTATATATTATATTAGTATA-TTAGTGTCTTAGTTTAAG
1 TTATATATTATATTA-T-TAGTT--TG--TTAGTTTAAG
5056985 TTATATATTATATTATTAGTTTGTTAGTTTAAG
1 TTATATATTATATTATTAGTTTGTTAGTTTAAG
*
5057018 -T-TATA-T-TA-TATTAGTTTATTAGTTTAAG
1 TTATATATTATATTATTAGTTTGTTAGTTTAAG
5057046 TTATATATTATATTAT
1 TTATATATTATATTAT
5057062 ATAAAAAAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 24
0.80 0.01 0.19
Matches are distributed among these distances:
28 19 0.19
29 3 0.03
30 5 0.05
31 5 0.05
32 3 0.03
33 28 0.27
34 3 0.03
35 4 0.04
36 4 0.04
37 3 0.03
38 25 0.25
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.57
Consensus pattern (33 bp):
TTATATATTATATTATTAGTTTGTTAGTTTAAG
Found at i:5056969 original size:38 final size:37
Alignment explanation
Indices: 5056917--5057064 Score: 160
Period size: 38 Copynumber: 4.3 Consensus size: 37
5056907 TAAAAAATTA
5056917 TATATTATATTATTAGTTTGTTAGTTTAAGTTATATAT
1 TATATTATA-TATTAGTTTGTTAGTTTAAGTTATATAT
* *
5056955 TATATTAGTATATTAGTGTCTTAGTTTAAGTTATATA-
1 TATATTA-TATATTAGTTTGTTAGTTTAAGTTATATAT
5056992 T-TA-TAT-TATTAGTTTGTTAGTTTAAG-------T
1 TATATTATATATTAGTTTGTTAGTTTAAGTTATATAT
*
5057019 TATA-T-TATATTAGTTTATTAGTTTAAGTTATATAT
1 TATATTATATATTAGTTTGTTAGTTTAAGTTATATAT
5057054 TATATTATATA
1 TATATTATATA
5057065 AAAAAATTAG
Statistics
Matches: 92, Mismatches: 5, Indels: 27
0.74 0.04 0.22
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
33 18 0.20
34 1 0.01
35 7 0.08
36 3 0.03
37 5 0.05
38 32 0.35
39 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (37 bp):
TATATTATATATTAGTTTGTTAGTTTAAGTTATATAT
Found at i:5057039 original size:8 final size:8
Alignment explanation
Indices: 5056926--5057043 Score: 51
Period size: 8 Copynumber: 15.4 Consensus size: 8
5056916 ATATATTATA
5056926 TTATTAGT
1 TTATTAGT
*
5056934 TTGTTAGT
1 TTATTAGT
5056942 TTA--AG-
1 TTATTAGT
5056947 TTATATA-T
1 TTAT-TAGT
5056955 TATATTAGT
1 T-TATTAGT
*
5056964 ATATTAGT
1 TTATTAGT
* *
5056972 GTCTTAGT
1 TTATTAGT
5056980 TTAAGTTA-T
1 TT-A-TTAGT
*
5056989 ATATTA-T
1 TTATTAGT
5056996 ATTATTAGT
1 -TTATTAGT
*
5057005 TTGTTAGT
1 TTATTAGT
5057013 TTA--AG-
1 TTATTAGT
5057018 TTA-TA-T
1 TTATTAGT
5057024 TATATTAGT
1 T-TATTAGT
5057033 TTATTAGT
1 TTATTAGT
5057041 TTA
1 TTA
5057044 AGTTATATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
5 6 0.07
6 6 0.07
7 6 0.07
8 54 0.64
9 9 0.11
10 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (8 bp):
TTATTAGT
Found at i:5057039 original size:28 final size:30
Alignment explanation
Indices: 5056954--5057060 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 30
5056944 AAGTTATATA
* * *
5056954 TTATATTAGTATATTAGTGTCTTAGTTTAAG
1 TTATA-TATTATATTAGTTTATTAGTTTAAG
*
5056985 TTATATATTATATTATTAGTTTGTTAGTTTAAG
1 TTATATA-T-TA-TATTAGTTTATTAGTTTAAG
5057018 -T-TATATTATATTAGTTTATTAGTTTAAG
1 TTATATATTATATTAGTTTATTAGTTTAAG
5057046 TTATATATTATATTA
1 TTATATATTATATTA
5057061 TATAAAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
28 19 0.28
29 3 0.04
30 15 0.22
31 9 0.13
32 3 0.04
33 18 0.27
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (30 bp):
TTATATATTATATTAGTTTATTAGTTTAAG
Found at i:5057074 original size:71 final size:71
Alignment explanation
Indices: 5056914--5057085 Score: 174
Period size: 71 Copynumber: 2.4 Consensus size: 71
5056904 TTATAAAAAA
* ** *
5056914 TTATATATTATATTATTAGTTTGTTAGTTTAAGTTATATATTATATTAGTATATTAGTGTCTTAG
1 TTATATATTAAAAAATTAGTTTGTTAGTTTAAGTTATATATTATATTAGTATATTAGTGTCTAAG
5056979 TTTAAG
66 TTTAAG
* ** *
5056985 TTATATATTATATTATTAGTTTGTTAGTTTAAG-T-TATATTATATTAGTTTATTAGT-T-TAAG
1 TTATATATTAAAAAATTAGTTTGTTAGTTTAAGTTATATATTATATTAGTATATTAGTGTCTAAG
5057046 TTATATA-
66 TT-TA-AG
**
5057053 TTATATTATATAAAAAAATTAGTTAATTAGTTT
1 TTATA-TAT-T-AAAAAATTAGTTTGTTAGTTT
5057086 CTTAGTTTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
67 5 0.06
68 8 0.09
69 25 0.28
70 2 0.02
71 49 0.55
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (71 bp):
TTATATATTAAAAAATTAGTTTGTTAGTTTAAGTTATATATTATATTAGTATATTAGTGTCTAAG
TTTAAG
Found at i:5057123 original size:38 final size:38
Alignment explanation
Indices: 5056913--5057124 Score: 144
Period size: 38 Copynumber: 5.7 Consensus size: 38
5056903 ATTATAAAAA
* *
5056913 ATTATA-TAT-TATATTATTAGTTTGTTAGTTTAAGTT
1 ATTATATTATATATTTTATTAGTTTCTTAGTTTAAGTT
* * *
5056949 A-TATATTATATTAGTATATTAGTGTCTTAGTTTAAGTT
1 ATTATATTATA-TATTTTATTAGTTTCTTAGTTTAAGTT
*
5056987 A-TATA-T-TATA--TTATTAGTTTGTTAGTTTAAG--
1 ATTATATTATATATTTTATTAGTTTCTTAGTTTAAGTT
* * *
5057018 -TTATATTATATTAGTTTATTAG-TT-TAAGTTATATATTAT
1 ATTATATTATA-TATTTTATTAGTTTCTTAGTT-TA-AGT-T
* * *
5057057 ATTATATAAAAAAATTAGTTAATTAGTTTCTTAGTTTAAGTT
1 ATTATAT-TATATATT--TT-ATTAGTTTCTTAGTTTAAGTT
5057099 ATTATATTATATATTTTATTAGTTTC
1 ATTATATTATATATTTTATTAGTTTC
5057125 GGATTTCTTA
Statistics
Matches: 136, Mismatches: 19, Indels: 40
0.70 0.10 0.21
Matches are distributed among these distances:
31 4 0.03
32 1 0.01
33 20 0.15
34 7 0.05
35 10 0.07
36 14 0.10
37 1 0.01
38 36 0.26
39 2 0.01
40 8 0.06
41 7 0.05
42 10 0.07
43 7 0.05
44 4 0.03
45 5 0.04
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.55
Consensus pattern (38 bp):
ATTATATTATATATTTTATTAGTTTCTTAGTTTAAGTT
Found at i:5057360 original size:21 final size:21
Alignment explanation
Indices: 5057335--5057378 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5057325 AATCTAGTTA
5057335 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5057356 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5057377 AT
1 AT
5057379 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5057388 original size:28 final size:30
Alignment explanation
Indices: 5057355--5057417 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
5057345 TAGTATAAAT
*
5057355 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5057383 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5057413 TATTA
1 TATTA
5057418 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:5057967 original size:20 final size:21
Alignment explanation
Indices: 5057923--5057967 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5057913 AAATATTGTG
**
5057923 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
5057944 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
5057964 TTTA
1 TTTA
5057968 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:5058257 original size:26 final size:25
Alignment explanation
Indices: 5058228--5058286 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
5058218 AAATCATATT
*
5058228 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
5058254 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
5058280 ATTATTA
1 ATTATTA
5058287 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:5061207 original size:26 final size:26
Alignment explanation
Indices: 5061181--5061434 Score: 226
Period size: 26 Copynumber: 10.2 Consensus size: 26
5061171 GATGATTTAG
*
5061181 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
5061207 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
5061233 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
5061259 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
5061282 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
5061305 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
5061331 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
5061357 TAATGATTTTATAATAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
5061382 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
5061406 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
5061431 TAAT
1 TAAT
5061435 TATTACTAAT
Statistics
Matches: 187, Mismatches: 28, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.02
22 3 0.02
23 14 0.07
24 22 0.12
25 30 0.16
26 113 0.60
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:5061343 original size:124 final size:124
Alignment explanation
Indices: 5061123--5061374 Score: 479
Period size: 124 Copynumber: 2.0 Consensus size: 124
5061113 ATGTATTTAT
5061123 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
5061188 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTTA-TAA
5061247 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
5061312 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTTATAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTTATAA
5061371 TAAT
1 TAAT
5061375 TATTTAGTTA
Statistics
Matches: 126, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
124 122 0.97
125 4 0.03
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTTATAA
Found at i:5061403 original size:35 final size:37
Alignment explanation
Indices: 5061181--5061418 Score: 80
Period size: 35 Copynumber: 6.4 Consensus size: 37
5061171 GATGATTTAG
* * * * *
5061181 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAA
1 TAATGATTTAATAATTAT--TTATAATAATTATTTAAT-A
* * *
5061221 TAATCATTATAATAATGATTTAGTAATAATCATTATAA-A
1 TAATGATT-TAATAATTATTTA-TAATAATTATT-TAATA
* * * * *
5061260 -AATGATTTAATAATGATTTA-AATATTTA-ATGATT
1 TAATGATTTAATAATTATTTATAATAATTATTTAATA
* * * *
5061294 TGATGATTTAGTAATGATTTGATAATAATCA-TT-ATAA
1 TAATGATTTAATAATTATTT-ATAATAATTATTTAAT-A
* * * *
5061331 TAATGATTTGATAATAATCATTATAATAATGATTTTATAA
1 TAATGATTTAATAATTAT--TTATAATAATTATTTAAT-A
* * * *
5061371 TAATTATTTAGTTATTA-TT-TAGTAATTATTT-ATAA
1 TAATGATTTAATAATTATTTATAATAATTATTTAAT-A
5061406 TAATGATTTAATA
1 TAATGATTTAATA
5061419 CTAATGATTT
Statistics
Matches: 153, Mismatches: 33, Indels: 29
0.71 0.15 0.13
Matches are distributed among these distances:
33 2 0.01
35 37 0.24
36 13 0.08
37 36 0.24
38 15 0.10
39 8 0.05
40 32 0.21
41 10 0.07
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (37 bp):
TAATGATTTAATAATTATTTATAATAATTATTTAATA
Found at i:5061425 original size:14 final size:14
Alignment explanation
Indices: 5061181--5061434 Score: 125
Period size: 14 Copynumber: 19.1 Consensus size: 14
5061171 GATGATTTAG
*
5061181 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
5061195 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
5061207 TAATGATTTGATAA
1 TAATGATTTAATAA
*
5061221 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
5061233 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
5061247 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
5061259 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
5061270 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
5061286 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
5061305 TAATGATTTGATAA
1 TAATGATTTAATAA
*
5061319 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
5061331 TAATGATTTGATAA
1 TAATGATTTAATAA
*
5061345 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
5061357 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
5061371 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
5061383 T-ATTATTTAGTAA
1 TAATGATTTAATAA
5061396 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
5061406 TAATGATTTAATAC
1 TAATGATTTAATAA
5061420 TAATGATTTAATAA
1 TAATGATTTAATAA
5061434 T
1 T
5061435 TATTACTAAT
Statistics
Matches: 190, Mismatches: 27, Indels: 46
0.72 0.10 0.17
Matches are distributed among these distances:
10 4 0.02
11 22 0.12
12 49 0.26
13 23 0.12
14 67 0.35
15 2 0.01
16 11 0.06
18 1 0.01
19 9 0.05
20 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:5061457 original size:38 final size:38
Alignment explanation
Indices: 5061387--5061460 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
5061377 TTTAGTTATT
* **
5061387 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
5061425 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
5061461 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:5061668 original size:17 final size:17
Alignment explanation
Indices: 5061643--5061675 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5061633 ACTAAATATT
*
5061643 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
5061660 TAATGATTTGATACTA
1 TAATGATTTGATACTA
5061676 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:5061668 original size:25 final size:23
Alignment explanation
Indices: 5061589--5061668 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
5061579 GATTTATTGT
5061589 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
5061610 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
5061637 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
5061659 GTAATGATTT
1 -TAAT-ATTT
5061669 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:5063848 original size:15 final size:14
Alignment explanation
Indices: 5063825--5063855 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5063815 TACAACACTA
5063825 AACTTTAATATAAT
1 AACTTTAATATAAT
5063839 AACTTATAATATAAT
1 AACTT-TAATATAAT
5063854 AA
1 AA
5063856 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:5063863 original size:16 final size:16
Alignment explanation
Indices: 5063830--5063876 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5063820 CACTAAACTT
*
5063830 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
5063845 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
5063861 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
5063877 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:5064115 original size:45 final size:45
Alignment explanation
Indices: 5064038--5064170 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
5064028 TCAACAAACA
*
5064038 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
5064086 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
5064130 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
5064171 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:5064198 original size:41 final size:40
Alignment explanation
Indices: 5064110--5064198 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
5064100 TTAACAAAAC
* *
5064110 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
5064151 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
5064192 AAACTAA
1 AAACTAA
5064199 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:5064769 original size:29 final size:29
Alignment explanation
Indices: 5064727--5064831 Score: 156
Period size: 29 Copynumber: 3.6 Consensus size: 29
5064717 GGACTACATG
**
5064727 GGGACTACATGGCGACCTACTTGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
5064756 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
*
5064785 GGGACTACATGGTGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
** *
5064814 CAGACTGCATGGCGACCT
1 GGGACTACATGGCGACCT
5064832 CTCCATTGGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.22, C:0.30, G:0.30, T:0.17
Consensus pattern (29 bp):
GGGACTACATGGCGACCTACAAGGTCGCC
Found at i:5064867 original size:20 final size:20
Alignment explanation
Indices: 5064838--5064899 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5064828 ACCTCTCCAT
5064838 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
* *
5064858 TGGCTTGTATGGCTCGTATG
1 TGGCTCGTATGGCTCGTATA
** *
5064878 TCACCCCGTATGGCTCGTATA
1 T-GGCTCGTATGGCTCGTATA
5064899 T
1 T
5064900 CACCCCGTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:5064890 original size:21 final size:21
Alignment explanation
Indices: 5064864--5064910 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
5064854 TATATGGCTT
*
5064864 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATATCACCCC
5064885 GTATGGCTCGTATATCACCCC
1 GTATGGCTCGTATATCACCCC
5064906 GTATG
1 GTATG
5064911 TCACCCGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATATCACCCC
Found at i:5064896 original size:9 final size:9
Alignment explanation
Indices: 5064838--5064877 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
5064828 ACCTCTCCAT
5064838 TGGCTCGTA
1 TGGCTCGTA
5064847 TGGCTCGTATA
1 TGGCTCG--TA
*
5064858 TGGCTTGTA
1 TGGCTCGTA
5064867 TGGCTCGTA
1 TGGCTCGTA
5064876 TG
1 TG
5064878 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:5072291 original size:23 final size:25
Alignment explanation
Indices: 5072248--5072293 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
5072238 CATTTTACAT
*
5072248 TCATTGCCTTAAATCTGGATTTTGA
1 TCATTGCCTTAAATCTCGATTTTGA
5072273 TCATTGCC-T-AATCTCGATTTT
1 TCATTGCCTTAAATCTCGATTTT
5072294 TTTCGATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 1 0.05
25 8 0.40
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (25 bp):
TCATTGCCTTAAATCTCGATTTTGA
Found at i:5080439 original size:27 final size:27
Alignment explanation
Indices: 5080401--5080463 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
5080391 CCAAGTGAAT
5080401 AAGCGTAAATCATGCTTGCACGCTTTG
1 AAGCGTAAATCATGCTTGCACGCTTTG
5080428 AAGCGTAAATCATGCTTGCACGCTTTG
1 AAGCGTAAATCATGCTTGCACGCTTTG
5080455 AAGCGTAAA
1 AAGCGTAAA
5080464 CAACAGCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (27 bp):
AAGCGTAAATCATGCTTGCACGCTTTG
Found at i:5080475 original size:27 final size:27
Alignment explanation
Indices: 5080401--5080485 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
5080391 CCAAGTGAAT
* *
5080401 AAGCGTAAATCATGCTTGCACGCTTTG
1 AAGCGTAAATCAAGCTAGCACGCTTTG
* *
5080428 AAGCGTAAATCATGCTTGCACGCTTTG
1 AAGCGTAAATCAAGCTAGCACGCTTTG
*
5080455 AAGCGTAAA-CAACAGC-AGCACGCTTCG
1 AAGCGTAAATC-A-AGCTAGCACGCTTTG
5080482 AAGC
1 AAGC
5080486 CAGTGGCCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.02
27 50 0.94
28 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (27 bp):
AAGCGTAAATCAAGCTAGCACGCTTTG
Found at i:5082965 original size:2 final size:2
Alignment explanation
Indices: 5082958--5082998 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5082948 TAATCTAAGA
5082958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5082999 TATTATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5090301 original size:34 final size:31
Alignment explanation
Indices: 5090262--5090347 Score: 84
Period size: 34 Copynumber: 2.6 Consensus size: 31
5090252 AAGAAATAAT
5090262 AAATAAATATTAAATAAATCAAAGAAAAATATAG
1 AAATAAA-ATTAAATAAATCAAAG-AAAA-ATAG
* *
5090296 AAATAAAATAAAAATAAAAATAAAAGAAAAATAG
1 AAATAAAAT-TAAAT--AAATCAAAGAAAAATAG
*
5090330 AAAGAAAA-TAAATAAATC
1 AAATAAAATTAAATAAATC
5090348 GAAGGGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
30 4 0.09
32 4 0.09
33 2 0.05
34 22 0.50
35 4 0.09
36 8 0.18
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (31 bp):
AAATAAAATTAAATAAATCAAAGAAAAATAG
Found at i:5090318 original size:17 final size:17
Alignment explanation
Indices: 5090286--5090341 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
5090276 TAAATCAAAG
5090286 AAAAATATAGAAATAAAAT
1 AAAAATA-A-AAATAAAAT
*
5090305 AAAAATAAAAATAAAAG
1 AAAAATAAAAATAAAAT
* *
5090322 AAAAATAGAAAGAAAAT
1 AAAAATAAAAATAAAAT
5090339 AAA
1 AAA
5090342 TAAATCGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 25 0.76
18 1 0.03
19 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAATAAAAT
Found at i:5090380 original size:9 final size:9
Alignment explanation
Indices: 5090366--5090404 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
5090356 AAAATGAGAT
5090366 AAAAAATAA
1 AAAAAATAA
5090375 AAAAAATAA
1 AAAAAATAA
*
5090384 AGAAAATGAAA
1 AAAAAAT--AA
5090395 AAAAAATAA
1 AAAAAATAA
5090404 A
1 A
5090405 TCAAAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:5090501 original size:12 final size:12
Alignment explanation
Indices: 5090486--5090516 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
5090476 TAATTTAAAA
5090486 AATAAAAAAAGG
1 AATAAAAAAAGG
5090498 AAT-AAAAAAGG
1 AATAAAAAAAGG
5090509 AATAAAAA
1 AATAAAAA
5090517 TGTAAGGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (12 bp):
AATAAAAAAAGG
Found at i:5092161 original size:37 final size:36
Alignment explanation
Indices: 5092042--5092462 Score: 357
Period size: 36 Copynumber: 12.1 Consensus size: 36
5092032 ATGTTTTTTG
* *
5092042 TGTTTCAAGAGAAACTGTCCCAAGAGAGAC-AACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
5092077 TGTTTCAAGGGAAACTGTCAC-A-AGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
5092111 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * **
5092148 TGTTCCAAAAGAAACTGTCTCGAGAGAGACGGAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
5092184 TGTTTAAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
5092213 TGTTTCAAGGGAAACTGTCTGAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
5092249 TGATTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
5092285 TGTTTCAAGAGAAACTGTCTAAAAAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
5092322 AGTTCCAAAAGAAACTGTCTCAAGGGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
5092358 TGTTTCAAG-GAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
5092387 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
5092421 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
5092458 TGTTT
1 TGTTT
5092463 TGAGTAAATT
Statistics
Matches: 313, Mismatches: 45, Indels: 54
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.01
29 34 0.11
30 4 0.01
31 2 0.01
32 4 0.01
33 10 0.03
34 56 0.18
35 24 0.08
36 106 0.34
37 70 0.22
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:5092311 original size:102 final size:100
Alignment explanation
Indices: 5092045--5092461 Score: 300
Period size: 102 Copynumber: 4.0 Consensus size: 100
5092035 TTTTTTGTGT
* * * *
5092045 TTCAAGAGAAACTGTCCCAAGAGAGACAACTTTGTTTCAAGGGAAACTGTCACAAGAGACAAAAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTCAA-GGAAACTGTC-TAA-A-A-AGAAT
5092110 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
61 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
* * * * * * *
5092150 TTCCAAAAGAAACTGTCTCGAGAGAGACGGAATTTGTTTAAAGGAAAACATAT-T-CAAAGATTT
1 TT-CAAGAGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGG-AAAC-TGTCTAAAAAGAATT
* *
5092213 TGTTTCAAGGGAAACTGTCTGAAGAGAGACAAAA-TTTG
62 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
*
5092251 ATTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGATA
1 -TTCAAGAGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAG-GAAACTGTCTAAAAAGA-AT-
* * * *
5092316 AAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGA-AAAAATTTG
61 ----TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
** * *
5092360 TTTCAAG-GAAAACAAAT-TC-A-A-AG---ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 -TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAATTTGTTTCAA-GGAAACTGTCT-AA-A-A-AG
*
5092417 AATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
58 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
5092460 TT
1 TT
5092462 TTGAGTAAAT
Statistics
Matches: 251, Mismatches: 37, Indels: 54
0.73 0.11 0.16
Matches are distributed among these distances:
99 26 0.10
100 12 0.05
101 43 0.17
102 65 0.26
103 5 0.02
104 2 0.01
105 5 0.02
106 28 0.11
107 15 0.06
108 10 0.04
109 39 0.16
110 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (100 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGAAACTGTCTAAAAAGAATTTGTT
TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
Found at i:5092329 original size:174 final size:173
Alignment explanation
Indices: 5092042--5092462 Score: 632
Period size: 174 Copynumber: 2.4 Consensus size: 173
5092032 ATGTTTTTTG
* * * *
5092042 TGTTTCAAGAGAAACTGTCCCAAGAGAGACAACTTTGTTTCAAGGGAAACTGTCAC-A-AGAGAC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * * *
5092105 AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCG
66 AAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCA
*** *
5092170 AGAGAGACGGAATTTGTTTAAAGGAAAACATATTCAAAGATTT
131 AGAGAGAAAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTT
* *
5092213 TGTTTCAAGGGAAACTGTCTGAAGAGAGACAAAATTTGATTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
5092278 CAAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTC
65 CAAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
* *
5092343 AAGGGAGAAAAAATTTGTTTCAAGGAAAACAAATTCAAAGATTT
130 AAGAGAGAAAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTT
* *
5092387 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AATTTGTTTTAAGAGAAACTGTCTCAAGAGAGAC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
5092451 AAAACTTTGTTT
66 AAAA-TTTGTTT
5092463 TGAGTAAATT
Statistics
Matches: 225, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
171 27 0.12
172 58 0.26
173 8 0.04
174 132 0.59
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (173 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
AAAATTTGTTTCAAGAGAAACTGTCTAAAAAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCA
AGAGAGAAAAAATTTGTTTAAAGGAAAACAAATTCAAAGATTT
Found at i:5092363 original size:73 final size:71
Alignment explanation
Indices: 5092211--5092370 Score: 205
Period size: 73 Copynumber: 2.2 Consensus size: 71
5092201 ATTCAAAGAT
* * * **
5092211 TTTGTTTCAAGGGAAACTGTCTGAAGAGAGACAAAATTTGATTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAA-GGAAACTGTCTAAAAAGAGACAAAATTAGATTCAAAAGAAACTGTCTCAAGAGA
*
5092276 GACAAAA
65 GAAAAAA
* *
5092283 TTTGTTTCAAGAGAAACTGTCTAAAAAGAGATAAAACTTAG-TTCCAAAAGAAACTGTCTCAAGG
1 TTTGTTTCAAG-GAAACTGTCTAAAAAGAGACAAAA-TTAGATT-CAAAAGAAACTGTCTCAAGA
5092347 GAGAAAAAA
63 GAGAAAAAA
5092356 TTTGTTTCAAGGAAA
1 TTTGTTTCAAGGAAA
5092371 ACAAATTCAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
71 1 0.01
72 37 0.48
73 39 0.51
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (71 bp):
TTTGTTTCAAGGAAACTGTCTAAAAAGAGACAAAATTAGATTCAAAAGAAACTGTCTCAAGAGAG
AAAAAA
Found at i:5093887 original size:17 final size:16
Alignment explanation
Indices: 5093865--5093918 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
5093855 AACCGGGTAT
5093865 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
5093882 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
5093897 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
5093914 CGGGT
1 CGGGT
5093919 CGGGACACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 16 0.52
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:5096211 original size:29 final size:29
Alignment explanation
Indices: 5096179--5096251 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 29
5096169 AAAAATATAG
5096179 TAATAAAAAATAAAAATAGAAAGAAAAAA
1 TAATAAAAAATAAAAATAGAAAGAAAAAA
* * *
5096208 TAAT-AAAAAT--AAATTGAAGGGAAAAA
1 TAATAAAAAATAAAAATAGAAAGAAAAAA
5096234 TGAGATAAAAAATAAAAA
1 T-A-ATAAAAAATAAAAA
5096252 AATGAGATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 14 0.39
27 1 0.03
28 8 0.22
29 10 0.28
31 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (29 bp):
TAATAAAAAATAAAAATAGAAAGAAAAAA
Found at i:5096221 original size:26 final size:29
Alignment explanation
Indices: 5096156--5096249 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 29
5096146 AATAAATATT
*
5096156 AAATAAAT-CAAAGAAAAATAT-AGTAATAAA
1 AAATAAATAGAAAGAAAAA-ATGAG--ATAAA
5096186 AAATAAAAATAGAAAGAAAAAAT-A-AT-AA
1 AAAT--AAATAGAAAGAAAAAATGAGATAAA
* * *
5096214 AAATAAATTGAAGGGAAAAATGAGATAAA
1 AAATAAATAGAAAGAAAAAATGAGATAAA
5096243 AAATAAA
1 AAATAAA
5096250 AAAATGAGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
26 14 0.26
27 1 0.02
28 8 0.15
29 11 0.20
30 4 0.07
32 7 0.13
33 9 0.17
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.17
Consensus pattern (29 bp):
AAATAAATAGAAAGAAAAAATGAGATAAA
Found at i:5096254 original size:20 final size:22
Alignment explanation
Indices: 5096229--5096273 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
5096219 AATTGAAGGG
5096229 AAAAATGAGAT-AA-AAAATAA
1 AAAAATGAGATAAATAAAATAA
5096249 AAAAATGAGATGAAATAAAATAA
1 AAAAATGAGAT-AAATAAAATAA
5096272 AA
1 AA
5096274 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAATGAGATAAATAAAATAA
Found at i:5097386 original size:13 final size:13
Alignment explanation
Indices: 5097370--5097414 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
5097360 TAAAAAAATC
5097370 ATAACAAAATTAT
1 ATAACAAAATTAT
5097383 ATAACAAAATTAT
1 ATAACAAAATTAT
*
5097396 ATAACTATAATTAT
1 ATAAC-AAAATTAT
5097410 ATAAC
1 ATAAC
5097415 TATTCTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAACAAAATTAT
Found at i:5097391 original size:27 final size:27
Alignment explanation
Indices: 5097361--5097414 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5097351 ATTTGGGGTT
5097361 AAAAAAATCATAAC-AAAATTATATAAC
1 AAAAAAAT-ATAACTAAAATTATATAAC
** *
5097388 AAAATTATATAACTATAATTATATAAC
1 AAAAAAATATAACTAAAATTATATAAC
5097415 TATTCTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAAAATATAACTAAAATTATATAAC
Found at i:5097409 original size:14 final size:14
Alignment explanation
Indices: 5097377--5097417 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
5097367 ATCATAACAA
*
5097377 AATTATATAAC-AA
1 AATTATATAACTAT
5097390 AATTATATAACTAT
1 AATTATATAACTAT
5097404 AATTATATAACTAT
1 AATTATATAACTAT
5097418 TCTTTCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:5097901 original size:307 final size:310
Alignment explanation
Indices: 5097279--5097905 Score: 1057
Period size: 307 Copynumber: 2.0 Consensus size: 310
5097269 ATTCAAATTA
5097279 ACTACAACATAATATTTAAGGTAAAACATATTAAATAATAAATATAATTATATAACTATAATTAA
1 ACTACAACATAATATTTAAGGTAAAACATATTAAATAATAAATATAATTATATAACTATAATTAA
5097344 AAAATAAATTTGGGGTTAAAAAAATCATAACAAAATTATATAACAAAATTATATAACTATAATTA
66 AAAATAAATTTGGGGTTAAAAAAA-CAT-AC------A-ATAACAAAATTATATAACTATAATTA
5097409 TATAACTATTCTTTCACTTCAATCAAGCTCGAATTTTAGGCTTCAATCGAACTTTTAATATTTTT
122 TATAACTATTCTTTCACTTCAATCAAGCTCGAATTTTAGGCTTCAATCGAACTTTTAATATTTTT
*
5097474 TTTTGAGTTCAAGCCTTTTTGAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTGAACTTAA
187 TTTTGAGTTCAAGCCTTTTTAAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTGAACTTAA
5097539 TAATTTTTAGCTTGTGAATTTGAGTTGAGTTGAACTTACTTTTAAAGTTTTCAAGTTCG
252 TAATTTTTAGCTTGTGAATTTGAGTTGAGTTGAACTTACTTTTAAAGTTTTCAAGTTCG
5097598 ACTACAACATAATATTTAAGGTAAAACATATTAAATAATAAATATAATTATATAACTATAATTAA
1 ACTACAACATAATATTTAAGGTAAAACATATTAAATAATAAATATAATTATATAACTATAATTAA
*
5097663 AAAATAAATTTGGGGTT-AAAAAA-AT-C-ATAACAAAATTATATAACTATAATTATATAATTAT
66 AAAATAAATTTGGGGTTAAAAAAACATACAATAACAAAATTATATAACTATAATTATATAACTAT
* *
5097724 TCTTTCACTTCAATCAAGCTCGAATTTTAGGTTTCAATCGAACTTTTAATTTTTTTTTTTTGAGT
131 TCTTTCACTTCAATCAAGCTCGAATTTTAGGCTTCAATCGAACTTTTAA-TATTTTTTTTTGAGT
* * *
5097789 TTAAGCCTTTTTAAGTTTAAGTTTTAATATTATATTTCGAGTTTGAGTTGAACTTAATAATTTTT
195 TCAAGCCTTTTTAAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTGAACTTAATAATTTTT
5097854 AGCTTGT-AAGTTTGAGTTGAGTTGAACTTACTTTTAAAGTTTTCAAGTTCG
260 AGCTTGTGAA-TTTGAGTTGAGTTGAACTTACTTTTAAAGTTTTCAAGTTCG
5097905 A
1 A
5097906 GTCGAGCTCA
Statistics
Matches: 299, Mismatches: 7, Indels: 16
0.93 0.02 0.05
Matches are distributed among these distances:
306 84 0.28
307 124 0.41
314 1 0.00
316 2 0.01
318 6 0.02
319 82 0.27
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (310 bp):
ACTACAACATAATATTTAAGGTAAAACATATTAAATAATAAATATAATTATATAACTATAATTAA
AAAATAAATTTGGGGTTAAAAAAACATACAATAACAAAATTATATAACTATAATTATATAACTAT
TCTTTCACTTCAATCAAGCTCGAATTTTAGGCTTCAATCGAACTTTTAATATTTTTTTTTGAGTT
CAAGCCTTTTTAAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTGAACTTAATAATTTTTA
GCTTGTGAATTTGAGTTGAGTTGAACTTACTTTTAAAGTTTTCAAGTTCG
Found at i:5108885 original size:111 final size:111
Alignment explanation
Indices: 5108663--5109441 Score: 1113
Period size: 111 Copynumber: 7.0 Consensus size: 111
5108653 GGGAAAATTA
* ** * * * * * **
5108663 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATATGGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
** *
5108728 TCTGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGA-TCTATTG
65 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATTC-ATTG
* * *
5108775 AATCAGGGTAGACTTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * * *
5108840 CCGCTTCCTCTGAGGGAATATCATATATGGGAAAGTTGATTTATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
5108886 AATCAAGGTAGATTTGTTCCGTTGTCATTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
5108949 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
5108995 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
5109060 CCACTTCATCTGAGGAAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
5109106 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
5109169 CCACTTCATCTGAGGGAATATCAGATCTGTGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* *
5109215 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGAGAATATCAAATCTTGAAAGAGAGGGGTCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * * * *
5109280 CCATTTCTTTTAAGGGAATATCAGATCTGGGAAAGTTGATTCACTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
5109326 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * *
5109391 CCACTTCTTCTAAGGGAATATCAAATCTGGGAAAGTTGA-TCTATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC-ATTG
5109437 AATCA
1 AATCA
5109442 GGGTTGAACC
Statistics
Matches: 610, Mismatches: 50, Indels: 15
0.90 0.07 0.02
Matches are distributed among these distances:
109 202 0.33
110 10 0.02
111 347 0.57
112 51 0.08
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (111 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:5109074 original size:220 final size:220
Alignment explanation
Indices: 5108663--5109441 Score: 1114
Period size: 220 Copynumber: 3.5 Consensus size: 220
5108653 GGGAAAATTA
* ** * * * * *
5108663 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATATGGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAG---GGATCTGT
** * *
5108728 TCTGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCTATTGAATCAGGGTAGACTTGT
63 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCAAGGTAGACTTGT
* * * *
5108792 TCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCCTCTGAGGGA
127 TCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGA
* * *
5108857 ATATCATATATGGGAAAGTTGATTTATTG
192 ATATCAGATCTGGGAAAGTTGATTCATTG
* * * *
5108886 AATCAAGGTAGATTTGTTCCGTTGTCATTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTCC
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTCC
5108951 ACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGAT-TCATTGAATCAAGGTAGACTTGTTCC
66 ACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCT-ATTGAATCAAGGTAGACTTGTTCC
* *
5109015 GCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCATCTGAGGAAATA
130 GCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAATA
5109080 TCAGATCTGGGAAAGTTGATTCATTG
195 TCAGATCTGGGAAAGTTGATTCATTG
5109106 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTCC
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTCC
* *
5109171 ACTTCATCTGAGGGAATATCAGATCTGTGAAAGTTGAT-TCATTGAATCAAGGTAGACTTGTTCC
66 ACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCT-ATTGAATCAAGGTAGACTTGTTCC
* * * * * *
5109235 GCTGTCACTCAGAGAATATCAAATCTTGAAAGAGAGGGGTCTGTTCCATTTCTTTTAAGGGAATA
130 GCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAATA
*
5109300 TCAGATCTGGGAAAGTTGATTCACTG
195 TCAGATCTGGGAAAGTTGATTCATTG
* *
5109326 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
* * *
5109391 CCACTTCTTCTAAGGGAATATCAAATCTGGGAAAGTTGATCTATTGAATCA
64 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCA
5109442 GGGTTGAACC
Statistics
Matches: 507, Mismatches: 44, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
219 1 0.00
220 399 0.79
221 4 0.01
222 57 0.11
223 46 0.09
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (220 bp):
AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTCC
ACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCAAGGTAGACTTGTTCCG
CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAATAT
CAGATCTGGGAAAGTTGATTCATTG
Found at i:5109298 original size:331 final size:330
Alignment explanation
Indices: 5108663--5109441 Score: 1132
Period size: 331 Copynumber: 2.3 Consensus size: 330
5108653 GGGAAAATTA
* ** * * * * * **
5108663 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATATGGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
** * *
5108728 TCTGCTTCTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCTATTGAATCAGGGTAGACTTGTT
65 TCCACTTCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCAAGGTAGACTTGTT
* * * *
5108793 CCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCCTCTGAGGGAA
129 CCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAA
* * * * * *
5108858 TATCATATATGGGAAAGTTGATTTATTGAATCAAGGTAGATTTGTTCCGTTGTCATTCAGGGAAT
194 TATCAGATATGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGAGAAT
*
5108923 ATCAAATCTTGAAAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGA
259 ATCAAATCTTGAAAGAGGGATCTGTTCCACTTCCTCTAAGGGAATATCAGATCTGGGAAAGTTGA
*
5108988 TTCATTG
324 TTCACTG
*
5108995 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
5109060 CCACTTCATCTGAGGAAATATCAGATCTGGGAAAGTTGAT-TCATTGAATCAAGGTAGACTTGTT
66 CCACTTC-TCTGAGGGAATATCAGATCTGGGAAAGTTGATCT-ATTGAATCAAGGTAGACTTGTT
*
5109124 CCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTTCCACTTCATCTGAGGGAA
129 CCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAA
* *
5109187 TATCAGATCTGTGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGAGAAT
194 TATCAGATATGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGAGAAT
* * * *
5109252 ATCAAATCTTGAAAGAGAGGGGTCTGTTCCATTTCTTTTAAGGGAATATCAGATCTGGGAAAGTT
259 ATCAAATCTTG-AA-AGAGGGATCTGTTCCACTTCCTCTAAGGGAATATCAGATCTGGGAAAGTT
5109317 GATTCACTG
322 GATTCACTG
*
5109326 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
5109391 CCACTTCTTCTAAGGGAATATCAAATCTGGGAAAGTTGATCTATTGAATCA
66 CCACTTC-TCTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCA
5109442 GGGTTGAACC
Statistics
Matches: 401, Mismatches: 41, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
329 97 0.24
330 5 0.01
331 250 0.62
332 49 0.12
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (330 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCTATTGAATCAAGGTAGACTTGTTCC
ACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCATCTGAGGGAATA
TCAGATATGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGAGAATAT
CAAATCTTGAAAGAGGGATCTGTTCCACTTCCTCTAAGGGAATATCAGATCTGGGAAAGTTGATT
CACTG
Found at i:5110589 original size:17 final size:16
Alignment explanation
Indices: 5110556--5110607 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
5110546 CATCCTTTTA
5110556 TTTTTTTC-TTTTC-T
1 TTTTTTTCTTTTTCAT
5110570 TTTTTTTCATTTTTCAT
1 TTTTTTTC-TTTTTCAT
*
5110587 TTTTTAGTCTTTTTCAT
1 TTTTT-TTCTTTTTCAT
5110604 TTTT
1 TTTT
5110608 AGGCGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 8 0.24
16 5 0.15
17 18 0.55
18 2 0.06
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTTTCAT
Found at i:5114168 original size:21 final size:24
Alignment explanation
Indices: 5114126--5114168 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
5114116 GATCTAACCC
5114126 ATATCAAAATAGAATGAAATAATA
1 ATATCAAAATAGAATGAAATAATA
5114150 ATAT-AAAATA-AAT-AAATAA
1 ATATCAAAATAGAATGAAATAA
5114169 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 6 0.32
24 4 0.21
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (24 bp):
ATATCAAAATAGAATGAAATAATA
Found at i:5114184 original size:17 final size:18
Alignment explanation
Indices: 5114142--5114178 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5114132 AAATAGAATG
5114142 AAAT-AATAATATAAAAT
1 AAATAAATAATATAAAAT
5114159 AAATAAATAA-ATAAAA-
1 AAATAAATAATATAAAAT
5114175 AAAT
1 AAAT
5114179 GCAATAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAATAATATAAAAT
Found at i:5117791 original size:11 final size:11
Alignment explanation
Indices: 5117777--5117806 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5117767 TGCAATGTAG
5117777 ATGCAATATGA
1 ATGCAATATGA
*
5117788 ATGCAAGATGA
1 ATGCAATATGA
5117799 ATGCAATA
1 ATGCAATA
5117807 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:5128898 original size:21 final size:21
Alignment explanation
Indices: 5128855--5128899 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5128845 TTAAAATTAT
*
5128855 AAATTAAATATATCGAAATAA
1 AAATTAAATATATCGAAACAA
*
5128876 AAATTAAATAATAT-TAAACAA
1 AAATTAAAT-ATATCGAAACAA
5128897 AAA
1 AAA
5128900 CCCAAACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAAATATATCGAAACAA
Found at i:5134019 original size:16 final size:16
Alignment explanation
Indices: 5133998--5134035 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5133988 TGGAGAGATA
*
5133998 ATATCATAACATGAAC
1 ATATCAGAACATGAAC
5134014 ATATCAGAACATGAAC
1 ATATCAGAACATGAAC
5134030 ATATCA
1 ATATCA
5134036 CTGCTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (16 bp):
ATATCAGAACATGAAC
Found at i:5134311 original size:12 final size:12
Alignment explanation
Indices: 5134294--5134326 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5134284 GGTAAAAACT
5134294 TCAATAATAACA
1 TCAATAATAACA
5134306 TCAATAATAACA
1 TCAATAATAACA
5134318 TCAATAATA
1 TCAATAATA
5134327 GGGGTAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (12 bp):
TCAATAATAACA
Found at i:5146448 original size:129 final size:127
Alignment explanation
Indices: 5146244--5146616 Score: 395
Period size: 129 Copynumber: 2.9 Consensus size: 127
5146234 ATCGAACCAA
* * * * * *
5146244 AATTTATTTGAAAATTAATAACCGAACTGAATTAACTGAATTTTTTTGAAAATTATTTACCAAAT
1 AATTAATTTGAAAATTATTAAACGAACCGAATTAACTG-A--TTTTTAAAAATTATTAACCAAAT
*
5146309 TAAGC-AAAGCAAAAATTTGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTAACCGAA-A
63 TAA-CTGAAGCAAAAATTTGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTAACCGAACA
5146372 TG
127 -G
* * *
5146374 AATTAATTTGAAAATTATTAATCGGACCGAATTAACCGATTTTTAAAAAAATTATTAACCAAATT
1 AATTAATTTGAAAATTATTAAACGAACCGAATTAACTGATTTTT--AAAAATTATTAACCAAATT
* *
5146439 AACTGAAGCAAAAATTCT-ATTAATTCGGTTCGGTTAATTTG----AAAA-TTATTAACCGAACA
64 AACTGAAGCAAAAATT-TGGTTAATTCGGTTCGGTTAA-TCGAACCAAAATTTATTAACCGAACA
5146498 G
127 G
* ** * *
5146499 AATTAATTTGAAAATTATTAAAAGAAACCGAATTAACTGATTTTTTTAAATTATTAATCGAATTA
1 AATTAATTTGAAAATTATTAAACG-AACCGAATTAACTGATTTTTAAAAATTATTAACCAAATTA
* * * *
5146564 A-TCGAAGTAAAAATTCGGTTAATTCCGTTTGGTTAATCGAACCAAAATTTATT
65 ACT-GAAGCAAAAATTTGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATT
5146617 TGAAAATTAT
Statistics
Matches: 204, Mismatches: 25, Indels: 30
0.79 0.10 0.12
Matches are distributed among these distances:
123 3 0.01
124 44 0.22
125 35 0.17
126 23 0.11
127 9 0.04
128 6 0.03
129 49 0.24
130 35 0.17
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (127 bp):
AATTAATTTGAAAATTATTAAACGAACCGAATTAACTGATTTTTAAAAATTATTAACCAAATTAA
CTGAAGCAAAAATTTGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTAACCGAACAG
Found at i:5146534 original size:30 final size:29
Alignment explanation
Indices: 5146472--5146534 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
5146462 TTCGGTTCGG
**
5146472 TTAATTTGAAAATTATTAACCGAACAGAA
1 TTAATTTGAAAATTATTAAAAGAACAGAA
*
5146501 TTAATTTGAAAATTATTAAAAGAAACCGAA
1 TTAATTTGAAAATTATTAAAAG-AACAGAA
5146531 TTAA
1 TTAA
5146535 CTGATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAATTTGAAAATTATTAAAAGAACAGAA
Found at i:5148360 original size:28 final size:28
Alignment explanation
Indices: 5148320--5148387 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
5148310 CTACATGATT
*
5148320 CTTCGGGACATATGTGTTTTATGTGGTC
1 CTTCGGGACATATGCGTTTTATGTGGTC
5148348 CTTCGGGACATATGCGTTTTATGTGGTC
1 CTTCGGGACATATGCGTTTTATGTGGTC
5148376 CTTCGGGACATA
1 CTTCGGGACATA
5148388 GTGGTCTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (28 bp):
CTTCGGGACATATGCGTTTTATGTGGTC
Found at i:5148393 original size:18 final size:18
Alignment explanation
Indices: 5148370--5148421 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
5148360 TGCGTTTTAT
*
5148370 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
*
5148388 GTGGTCTTTCGGGACATA
1 GTGGTCATTCGGGACATA
5148406 GTGGTCATTCGGGACA
1 GTGGTCATTCGGGACA
5148422 AATTCTACGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:5151683 original size:15 final size:15
Alignment explanation
Indices: 5151650--5151680 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5151640 CATAGTTACC
5151650 AATAAAACTAAACTA
1 AATAAAACTAAACTA
5151665 AATAAAA-TAAACTA
1 AATAAAACTAAACTA
5151679 AA
1 AA
5151681 ATAGTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACTAAACTA
Found at i:5152153 original size:17 final size:16
Alignment explanation
Indices: 5152131--5152164 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5152121 TAAAAACAGT
5152131 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
5152148 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
5152164 A
1 A
5152165 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:5153104 original size:9 final size:9
Alignment explanation
Indices: 5153090--5153115 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5153080 TGGGTGCAAA
5153090 ATACCCCTC
1 ATACCCCTC
5153099 ATACCCCTC
1 ATACCCCTC
5153108 ATACCCCT
1 ATACCCCT
5153116 AGAATCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (9 bp):
ATACCCCTC
Found at i:5153704 original size:18 final size:17
Alignment explanation
Indices: 5153671--5153704 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5153661 GAATAATTAA
5153671 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
5153688 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
5153705 AAACAGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:5161724 original size:15 final size:15
Alignment explanation
Indices: 5161691--5161721 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5161681 CATAGTTACC
5161691 AATAAAACTAAACTA
1 AATAAAACTAAACTA
5161706 AATAAAA-TAAACTA
1 AATAAAACTAAACTA
5161720 AA
1 AA
5161722 ATAGTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACTAAACTA
Found at i:5162014 original size:18 final size:17
Alignment explanation
Indices: 5161981--5162014 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5161971 GAATAATTAA
5161981 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
5161998 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
5162015 AAATAGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:5167164 original size:2 final size:2
Alignment explanation
Indices: 5167157--5167184 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5167147 TGTTTACATG
5167157 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
5167185 GCGTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5167370 original size:6 final size:6
Alignment explanation
Indices: 5167359--5167392 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5167349 TTTTTTTGTA
5167359 ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
5167393 AACGTTGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:5169098 original size:64 final size:64
Alignment explanation
Indices: 5169030--5169152 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
5169020 AATTTTTCAA
* * * * *
5169030 GGTGTATCGATGCACATGAAGTGCATCGGTGCACTCCTTTAAAATAAAAACATCGAATGTCATC
1 GGTGTATCGATGCACAAGAACTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATC
* * *
5169094 GGTGTATCGATGCACAAGTACTGCATCGATGCACCCCCTTAAAATACAACCATCGAATG
1 GGTGTATCGATGCACAAGAACTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
5169153 GGATTTATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (64 bp):
GGTGTATCGATGCACAAGAACTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATC
Found at i:5169169 original size:64 final size:64
Alignment explanation
Indices: 5169032--5169193 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 64
5169022 TTTTTCAAGG
* * * * * * *
5169032 TGTATCGATGCACATGAAGTGCATCGGTGCACTCCTTTAAAATAAAAACATCGAATGTCATCGG
1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATCGA
* * * * **
5169096 TGTATCGATGCACAAGTACTGCATCGATGCACCCCCTTAAAATACAACCATCGAATGGGATTTA
1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATCGA
* * *
5169160 TGTACCGATGCA-TAGATAGTGCATCGATACACCC
1 TGTATCGATGCACAAG-TAGTGCATCGATGCACCC
5169194 ATCAAGGGAT
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 2 0.03
64 78 0.98
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (64 bp):
TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGGCATCGA
Found at i:5169901 original size:23 final size:23
Alignment explanation
Indices: 5169833--5169893 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
5169823 ACATCTTATA
*
5169833 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
5169856 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
5169879 TGGTACTTCGGTGCA
1 TGGCACTTCGGTGCA
5169894 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5173148 original size:18 final size:18
Alignment explanation
Indices: 5173121--5173176 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
5173111 ATGTTTTATT
* *
5173121 TGGTCATTCGACACATAG
1 TGGTCCTTCGAAACATAG
*
5173139 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGAAACATAG
*
5173157 TGATCCTTCGAAACATAG
1 TGGTCCTTCGAAACATAG
5173175 TG
1 TG
5173177 ATCATTCGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCGAAACATAG
Found at i:5173177 original size:18 final size:18
Alignment explanation
Indices: 5173127--5173189 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
5173117 TATTTGGTCA
* *
5173127 TTCGACACATAGTGGTCC
1 TTCGAAACATAGTGATCC
*
5173145 TTCGAGACATAGTGATCC
1 TTCGAAACATAGTGATCC
*
5173163 TTCGAAACATAGTGATCA
1 TTCGAAACATAGTGATCC
*
5173181 TTCGGAACA
1 TTCGAAACA
5173190 AATTCTACGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (18 bp):
TTCGAAACATAGTGATCC
Found at i:5173757 original size:65 final size:65
Alignment explanation
Indices: 5173624--5173764 Score: 212
Period size: 65 Copynumber: 2.2 Consensus size: 65
5173614 AATTTTAATG
* * *
5173624 AACATCGAATGCTTTTGATGTACCGATGCACATACCATGCATCGATGCACTACAGGTTTTCTTAA
1 AACATCGAATGCTTTTGATGTACCAATGCACAAACCATGCATCGATGCACTACAGGTCTTCTTAA
* * *
5173689 AACATCGAATGCTTTTGATGTACCAATGCACAAACCATGCATCGATGCACTCCTGGCTCTT-TTG
1 AACATCGAATGCTTTTGATGTACCAATGCACAAACCATGCATCGATGCACTACAGG-TCTTCTTA
5173753 A
65 A
5173754 AACATCGAATG
1 AACATCGAATG
5173765 TAATTAGTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
65 66 0.96
66 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCTTTTGATGTACCAATGCACAAACCATGCATCGATGCACTACAGGTCTTCTTAA
Found at i:5176373 original size:103 final size:103
Alignment explanation
Indices: 5176148--5176365 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
5176138 GTCGAGGGTC
5176148 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGCGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGCGAGACACATAC
** *
5176213 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
**
5176251 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGCGAGACACATAC
*
5176316 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
5176354 TATGTGGTCCTT
1 TATGTGGTCCTT
5176366 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGCGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:5176448 original size:23 final size:23
Alignment explanation
Indices: 5176372--5176449 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
5176362 CCTTATGGAC
*
5176372 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
5176396 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
5176419 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
5176442 GTTATATG
1 ATTATATG
5176450 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:5179491 original size:23 final size:23
Alignment explanation
Indices: 5179464--5179517 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5179454 CACTACGGTG
*
5179464 CAATTATACGTGGCATTTTGGTA
1 CAATTATACGTGGCACTTTGGTA
* *
5179487 CAATTCTACGTGGCACTTTGGTG
1 CAATTATACGTGGCACTTTGGTA
*
5179510 CATTTATA
1 CAATTATA
5179518 TGAGCTGTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
CAATTATACGTGGCACTTTGGTA
Found at i:5198025 original size:20 final size:20
Alignment explanation
Indices: 5198000--5198038 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5197990 TTTATGCACA
5198000 ATGCATCGATACACTATGAT
1 ATGCATCGATACACTATGAT
5198020 ATGCATCGATACACTATGA
1 ATGCATCGATACACTATGA
5198039 AGGTGCACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGCATCGATACACTATGAT
Found at i:5199652 original size:15 final size:16
Alignment explanation
Indices: 5199615--5199652 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5199605 TTTTAACATT
5199615 TTGA-ATGTTTTTGGA
1 TTGATATGTTTTTGGA
*
5199630 TTGTTATGTTTTTGGA
1 TTGATATGTTTTTGGA
5199646 TT-ATATG
1 TTGATATG
5199653 GATGTTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (16 bp):
TTGATATGTTTTTGGA
Found at i:5204104 original size:4 final size:4
Alignment explanation
Indices: 5204095--5204151 Score: 105
Period size: 4 Copynumber: 14.2 Consensus size: 4
5204085 AGGTAAGTTG
*
5204095 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5204143 ATGT ATGT A
1 ATGT ATGT A
5204152 AGTTATTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:5209104 original size:20 final size:19
Alignment explanation
Indices: 5209069--5209109 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
5209059 TTTTTTGTAA
5209069 TTTTTCTGATTTTTTAAAT
1 TTTTTCTGATTTTTTAAAT
5209088 TTTTTCTGATTTTTTTAAAT
1 TTTTTCTGA-TTTTTTAAAT
5209108 TT
1 TT
5209110 GTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTCTGATTTTTTAAAT
Found at i:5213342 original size:21 final size:21
Alignment explanation
Indices: 5213316--5213357 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5213306 AATAATTAAT
*
5213316 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
5213337 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
5213358 TAATAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:5213763 original size:16 final size:16
Alignment explanation
Indices: 5213742--5213773 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5213732 AAACCTAAAT
5213742 TCGCTCCATCTTTAAC
1 TCGCTCCATCTTTAAC
5213758 TCGCTCCATCTTTAAC
1 TCGCTCCATCTTTAAC
5213774 ACACATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.38
Consensus pattern (16 bp):
TCGCTCCATCTTTAAC
Found at i:5217797 original size:17 final size:18
Alignment explanation
Indices: 5217777--5217810 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5217767 AAGAAAATAT
5217777 AATAA-ATAAGTAAAAAC
1 AATAACATAAGTAAAAAC
5217794 AATAACATAAGTAAAAA
1 AATAACATAAGTAAAAA
5217811 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAACATAAGTAAAAAC
Found at i:5218840 original size:35 final size:33
Alignment explanation
Indices: 5218791--5218866 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 33
5218781 TTCTTTTTCC
*
5218791 CTTTTCTTTCCTTTC-TATTTCTCTCCCCTTTTTT
1 CTTTTTTTTCCTTTCTTATTT-TCTCCCC-TTTTT
* *
5218825 CTGTTTTTTTTCTTTCTTATTTTCTCTCCTTTTT
1 CT-TTTTTTTCCTTTCTTATTTTCTCCCCTTTTT
5218859 CTTTTTTT
1 CTTTTTTT
5218867 CCTGTAAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.16
34 9 0.24
35 17 0.46
36 5 0.14
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (33 bp):
CTTTTTTTTCCTTTCTTATTTTCTCCCCTTTTT
Found at i:5219459 original size:3 final size:3
Alignment explanation
Indices: 5219451--5219490 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
5219441 TAAAATTAAA
*
5219451 AAT AAT AAT AAT AAT AGTT AAT AAT AATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT AAT AA-T AAT AAT AAT AA
5219491 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.85
4 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5219474 original size:10 final size:10
Alignment explanation
Indices: 5219451--5219488 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
5219441 TAAAATTAAA
5219451 AATAATAA-T
1 AATAATAATT
*
5219460 AATAATAGTT
1 AATAATAATT
5219470 AATAATAATT
1 AATAATAATT
5219480 AATAATAAT
1 AATAATAAT
5219489 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
AATAATAATT
Found at i:5219490 original size:13 final size:12
Alignment explanation
Indices: 5219451--5219490 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
5219441 TAAAATTAAA
5219451 AATAATAATAAT
1 AATAATAATAAT
*
5219463 AATAGTTAATAAT
1 AATA-ATAATAAT
5219476 AATTAATAATAAT
1 AA-TAATAATAAT
5219489 AA
1 AA
5219491 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 18 0.75
14 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:5219714 original size:43 final size:40
Alignment explanation
Indices: 5219649--5219764 Score: 126
Period size: 43 Copynumber: 2.8 Consensus size: 40
5219639 TTGGTTGTTG
*
5219649 GGGATGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAA
1 GGGATGACACGGCTCATACGTGATGAAGAGTTCGGGTCG----A
* * ** *
5219693 GGG-TGACACGGTTCATACGTGATGATGAAATCTGGTCGA
1 GGGATGACACGGCTCATACGTGATGAAGAGTTCGGGTCGA
*
5219732 GGGATGACACGACTCATACGTGATGAAGAGTTC
1 GGGATGACACGGCTCATACGTGATGAAGAGTTC
5219765 TTGGCCATCT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
39 4 0.07
40 24 0.40
43 29 0.48
44 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (40 bp):
GGGATGACACGGCTCATACGTGATGAAGAGTTCGGGTCGA
Found at i:5219976 original size:130 final size:133
Alignment explanation
Indices: 5219688--5219990 Score: 368
Period size: 135 Copynumber: 2.3 Consensus size: 133
5219678 GTTCGGGTCG
** * * * **
5219688 TCTAAGGGTGACACGGTTCATACGTGATGATGAAATCTGGTC-GAGGGATGACACGACTCATACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAG-GGGATGACACGACTCATACG
*
5219752 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGGC
65 TGATGAAGAGTTCTTGGCCATCTTTA-GAA-GGTGATAACTCAGTTCCTACGCAATGAGGACGGC
5219817 TGGTTA
128 TGGTTA
*
5219823 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACTG-TTCATACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACAC-GACTCATACG
* *
5219887 TGATGAAGAGTTCTTGGCCAT-TTTA-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGCT
65 TGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGCT
5219948 GGTTA
129 GGTTA
* * **
5219953 TCTAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCT
1 TCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAGATCT
5219991 GGTCAGCTGA
Statistics
Matches: 149, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
130 67 0.45
131 2 0.01
132 1 0.01
134 4 0.03
135 73 0.49
136 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (133 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACGACTCATACGT
GATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTGG
TTA
Found at i:5230780 original size:5 final size:5
Alignment explanation
Indices: 5230767--5230806 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
5230757 ATGCAGTATG
*
5230767 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC -AAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC A
5230807 GTTAGTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5232798 original size:17 final size:18
Alignment explanation
Indices: 5232778--5232811 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5232768 AAGAAAATAT
5232778 AATAA-ATAAGTAAAAAC
1 AATAACATAAGTAAAAAC
5232795 AATAACATAAGTAAAAA
1 AATAACATAAGTAAAAA
5232812 TAAATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AATAACATAAGTAAAAAC
Found at i:5233861 original size:35 final size:33
Alignment explanation
Indices: 5233794--5233869 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
5233784 TTCTTTTTCC
* *
5233794 CTTTTCTTTCCTTTCTATTTCTCTCCCCTTTTTT
1 CTTTTTTTTCCTTTCTATTTCTCT-CCCATTTTT
* *
5233828 CTGTTTTTTTTCTTTCTTATTT-TCTCTCATTTTT
1 CT-TTTTTTTCCTTTC-TATTTCTCTCCCATTTTT
5233862 CTTTTTTT
1 CTTTTTTT
5233870 CCTGTAAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 6 0.17
34 11 0.31
35 14 0.39
36 5 0.14
ACGTcount: A:0.04, C:0.24, G:0.01, T:0.71
Consensus pattern (33 bp):
CTTTTTTTTCCTTTCTATTTCTCTCCCATTTTT
Found at i:5234466 original size:16 final size:16
Alignment explanation
Indices: 5234447--5234477 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5234437 TAATATGTAA
5234447 AATTAAAAATAATAAT
1 AATTAAAAATAATAAT
*
5234463 AATTAATAATAATAA
1 AATTAAAAATAATAA
5234478 AAAAATAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTAAAAATAATAAT
Found at i:5237883 original size:14 final size:15
Alignment explanation
Indices: 5237859--5237888 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5237849 TTTTCATCTT
5237859 TATTTTATTTAAAAA
1 TATTTTATTTAAAAA
5237874 TATTTT-TTTAAAAA
1 TATTTTATTTAAAAA
5237888 T
1 T
5237889 TCCTTCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTTATTTAAAAA
Found at i:5246588 original size:24 final size:24
Alignment explanation
Indices: 5246529--5246595 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
5246519 TTTTATTTGG
* * *
5246529 ATTCTGATTTGATACTT-ACCTGT
1 ATTCTGATATGATACTTGACATGC
* *
5246552 ATTCTGAAATGATATTTGACATGC
1 ATTCTGATATGATACTTGACATGC
*
5246576 ATTCTGATCTGATACTTGAC
1 ATTCTGATATGATACTTGAC
5246596 CTGAATTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGC
Found at i:5246786 original size:2 final size:2
Alignment explanation
Indices: 5246779--5246817 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5246769 GAGATTGTGT
5246779 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
5246818 GTTTTAAAAG
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:5247692 original size:24 final size:22
Alignment explanation
Indices: 5247652--5247712 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 22
5247642 AAGGGTTGTA
*
5247652 TTTTTTTAAAAAAATTA-TAGTG
1 TTTTTTTAAAAAAATTATTA-AG
5247674 TTTTTTTAAAATAATATTATTAAG
1 TTTTTTTAAAA-AA-ATTATTAAG
5247698 TTTTTTTAAATAAAA
1 TTTTTTTAAA-AAAA
5247713 ATTCAAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 11 0.32
23 3 0.09
24 17 0.50
25 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTTTTAAAAAAATTATTAAG
Found at i:5257517 original size:2 final size:2
Alignment explanation
Indices: 5257510--5257541 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5257500 TAATTTATCA
5257510 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
5257542 GTGTGTGTGT
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:5257729 original size:12 final size:12
Alignment explanation
Indices: 5257712--5257745 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
5257702 CTATCGCAAA
5257712 TTCGCGTTGCAT
1 TTCGCGTTGCAT
5257724 TTCGCGTTGCAT
1 TTCGCGTTGCAT
5257736 TTCGCGTTGC
1 TTCGCGTTGC
5257746 GATAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:5257826 original size:19 final size:19
Alignment explanation
Indices: 5257802--5257848 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
5257792 TCTACAGTTG
5257802 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
5257821 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
5257840 TCGTTGCGA
1 TCGTTGCGA
5257849 AAATTCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:5257943 original size:6 final size:6
Alignment explanation
Indices: 5257932--5257956 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5257922 GTGTCGAAGA
5257932 CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC C
5257957 CGAGACGAGA
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:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:5258829 original size:6 final size:6
Alignment explanation
Indices: 5258818--5258850 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5258808 TCTCGTCTCG
5258818 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5258851 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:5259005 original size:20 final size:20
Alignment explanation
Indices: 5258980--5259094 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
5258970 AACTGTAGAC
5258980 TATCGCAACGCGAAATGGAA
1 TATCGCAACGCGAAATGGAA
* ** **
5259000 TATCGCAACGCTATTTTCAA
1 TATCGCAACGCGAAATGGAA
5259020 CTATCGCAACGCGAAATGGAA
1 -TATCGCAACGCGAAATGGAA
* ** **
5259041 AATCGCAACGCGATTTTTAA
1 TATCGCAACGCGAAATGGAA
5259061 CTATCGCAACGCGAAATGGAA
1 -TATCGCAACGCGAAATGGAA
*
5259082 AATCGCAACGCGA
1 TATCGCAACGCGA
5259095 TTTTCAACTA
Statistics
Matches: 72, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 42 0.58
21 30 0.42
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
TATCGCAACGCGAAATGGAA
Found at i:5259023 original size:41 final size:41
Alignment explanation
Indices: 5258978--5259116 Score: 251
Period size: 41 Copynumber: 3.4 Consensus size: 41
5258968 GCAACTGTAG
* *
5258978 ACTATCGCAACGCGAAATGGAATATCGCAACGCTATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
5259019 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTTA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
5259060 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
5259101 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
5259117 TTTGCGATAA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Done.