Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 62 of 226
Found at i:24273075 original size:98 final size:98
Alignment explanation
Indices: 24272945--24273141 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
24272935 TAAAAAATAA
* * *
24272945 TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATTGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
24273010 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
24273043 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
*
24273108 TTAAATCTTGGTTAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
24273141 T
1 T
24273142 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:24273599 original size:14 final size:14
Alignment explanation
Indices: 24273580--24273609 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24273570 ATAGTGGGTA
*
24273580 TCTCTTTTTCTTCT
1 TCTCTTTTGCTTCT
24273594 TCTCTTTTGCTTCT
1 TCTCTTTTGCTTCT
24273608 TC
1 TC
24273610 CAACAGCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (14 bp):
TCTCTTTTGCTTCT
Found at i:24273791 original size:25 final size:25
Alignment explanation
Indices: 24273761--24273811 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
24273751 TTAATGATAA
24273761 TTTTATTATTTTAATTAAAATTGAG
1 TTTTATTATTTTAATTAAAATTGAG
24273786 TTTTATTATTTTAATTAAAATTGAG
1 TTTTATTATTTTAATTAAAATTGAG
24273811 T
1 T
24273812 AATCATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (25 bp):
TTTTATTATTTTAATTAAAATTGAG
Found at i:24274173 original size:24 final size:24
Alignment explanation
Indices: 24274145--24274196 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
24274135 TTTTTAGAAG
* *
24274145 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
24274169 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
24274193 ATTT
1 ATTT
24274197 GACCTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:24278367 original size:47 final size:47
Alignment explanation
Indices: 24278316--24278455 Score: 219
Period size: 47 Copynumber: 3.0 Consensus size: 47
24278306 CCTAAAAATA
* *
24278316 CTATCTATACTTAGTATTGGACAAAGCAGAAAATCAGGGAGATCGAT
1 CTATCTATACTTAGTATCGGACAAAGAAGAAAATCAGGGAGATCGAT
24278363 CTATCTATACTTAGTATCGGACAACA-AAGAAAATCAGGGAGATCGAT
1 CTATCTATACTTAGTATCGGACAA-AGAAGAAAATCAGGGAGATCGAT
** *
24278410 CTATCTATACTTAGTATCGGACATCGAAAAAAATCAGGGAGATCGA
1 CTATCTATACTTAGTATCGGACAAAGAAGAAAATCAGGGAGATCGA
24278456 ATTGCAATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
47 85 0.99
48 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (47 bp):
CTATCTATACTTAGTATCGGACAAAGAAGAAAATCAGGGAGATCGAT
Found at i:24284162 original size:18 final size:19
Alignment explanation
Indices: 24284141--24284199 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
24284131 AATATTTTCT
24284141 TTAAATAATTA-AAAATAG
1 TTAAATAATTATAAAATAG
* *
24284159 TTAATTAATTATTATAATA-
1 TTAAATAATTA-TAAAATAG
24284178 TTAAAT-ATTAATAAAATAG
1 TTAAATAATT-ATAAAATAG
24284197 TTA
1 TTA
24284200 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 19 0.58
19 9 0.27
20 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAAATAATTATAAAATAG
Found at i:24284511 original size:29 final size:29
Alignment explanation
Indices: 24284477--24284532 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
24284467 TTTGATTCTT
* *
24284477 TTTAATAGTATAAGAACTAAATTGATCCA
1 TTTAATACTAGAAGAACTAAATTGATCCA
* *
24284506 TTTAATACTAGAAGGACTAATTTGATC
1 TTTAATACTAGAAGAACTAAATTGATC
24284533 TAATTCCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (29 bp):
TTTAATACTAGAAGAACTAAATTGATCCA
Found at i:24286891 original size:2 final size:2
Alignment explanation
Indices: 24286886--24286937 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
24286876 CTCCCTTCGT
24286886 TC TC TC TC TC TC TC TC TC TC TC TC TC 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 TC TC TC TC
24286928 TC TC TC TC TC
1 TC TC TC TC TC
24286938 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:24287760 original size:2 final size:2
Alignment explanation
Indices: 24287753--24287788 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24287743 NNNNNNTCCT
24287753 TC TC TC TC TC TC TC TC TC TC 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 TC
24287789 CATGTACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:24287824 original size:4 final size:4
Alignment explanation
Indices: 24287809--24287869 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
24287799 TTTCTTTGGG
*
24287809 TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24287857 TGTA TGTA TGTA T
1 TGTA TGTA TGTA T
24287870 ATAAAACTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:24289344 original size:2 final size:2
Alignment explanation
Indices: 24289337--24289364 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24289327 ACATGATTTG
24289337 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
24289365 TTATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:24290248 original size:206 final size:206
Alignment explanation
Indices: 24289894--24290307 Score: 828
Period size: 206 Copynumber: 2.0 Consensus size: 206
24289884 CAATAAAAAG
24289894 TTAACGGGTTTTATTTTTGTTATTTCTTTGGGTAGTATTGGATGAAAAAGCAGCATTATCGATGG
1 TTAACGGGTTTTATTTTTGTTATTTCTTTGGGTAGTATTGGATGAAAAAGCAGCATTATCGATGG
24289959 GTGCTGGTGTTTGTGCTTGAATCCACACATAGGGTCAAGGTTCGTCATTGTTGGTTCGTGTTTGA
66 GTGCTGGTGTTTGTGCTTGAATCCACACATAGGGTCAAGGTTCGTCATTGTTGGTTCGTGTTTGA
24290024 TTCTTTGACATTAGGTCAAGAGACCGCTCTTCTTGAGTCTTAAGGGAAAGGGTTTTGATCGAATC
131 TTCTTTGACATTAGGTCAAGAGACCGCTCTTCTTGAGTCTTAAGGGAAAGGGTTTTGATCGAATC
24290089 TGATTTGGGGT
196 TGATTTGGGGT
24290100 TTAACGGGTTTTATTTTTGTTATTTCTTTGGGTAGTATTGGATGAAAAAGCAGCATTATCGATGG
1 TTAACGGGTTTTATTTTTGTTATTTCTTTGGGTAGTATTGGATGAAAAAGCAGCATTATCGATGG
24290165 GTGCTGGTGTTTGTGCTTGAATCCACACATAGGGTCAAGGTTCGTCATTGTTGGTTCGTGTTTGA
66 GTGCTGGTGTTTGTGCTTGAATCCACACATAGGGTCAAGGTTCGTCATTGTTGGTTCGTGTTTGA
24290230 TTCTTTGACATTAGGTCAAGAGACCGCTCTTCTTGAGTCTTAAGGGAAAGGGTTTTGATCGAATC
131 TTCTTTGACATTAGGTCAAGAGACCGCTCTTCTTGAGTCTTAAGGGAAAGGGTTTTGATCGAATC
24290295 TGATTTGGGGT
196 TGATTTGGGGT
24290306 TT
1 TT
24290308 GAAGACCTTG
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 208 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.39
Consensus pattern (206 bp):
TTAACGGGTTTTATTTTTGTTATTTCTTTGGGTAGTATTGGATGAAAAAGCAGCATTATCGATGG
GTGCTGGTGTTTGTGCTTGAATCCACACATAGGGTCAAGGTTCGTCATTGTTGGTTCGTGTTTGA
TTCTTTGACATTAGGTCAAGAGACCGCTCTTCTTGAGTCTTAAGGGAAAGGGTTTTGATCGAATC
TGATTTGGGGT
Found at i:24295934 original size:54 final size:54
Alignment explanation
Indices: 24295870--24295981 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
24295860 TGACCAAAAC
*
24295870 ATAAACTTACTAATCGTTTAGTGACTTTAGGTGTAATTTACCCTTTATTTTATA
1 ATAAACTTACTAATAGTTTAGTGACTTTAGGTGTAATTTACCCTTTATTTTATA
24295924 ATAAACTTACTAATAGTTTAGTGACTTTAGGTGTAATTTACCCTTTATTTTATA
1 ATAAACTTACTAATAGTTTAGTGACTTTAGGTGTAATTTACCCTTTATTTTATA
24295978 ATAA
1 ATAA
24295982 GATAATATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (54 bp):
ATAAACTTACTAATAGTTTAGTGACTTTAGGTGTAATTTACCCTTTATTTTATA
Found at i:24296155 original size:22 final size:23
Alignment explanation
Indices: 24296128--24296183 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
24296118 TTATCCTTTA
*
24296128 ATTAAATATTCATA-TTTATATT
1 ATTAAATATTCATATTTTATAAT
*
24296150 ATTAAATATTTTATATTTTATAAT
1 ATTAAATA-TTCATATTTTATAAT
*
24296174 ATAAAATATT
1 ATTAAATATT
24296184 TTTACTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.28
23 7 0.24
24 14 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTAAATATTCATATTTTATAAT
Found at i:24296164 original size:17 final size:17
Alignment explanation
Indices: 24296142--24296175 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
24296132 AATATTCATA
24296142 TTTATATTATTA-AATAT
1 TTTATATT-TTATAATAT
24296159 TTTATATTTTATAATAT
1 TTTATATTTTATAATAT
24296176 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATTTTATAATAT
Found at i:24297195 original size:21 final size:20
Alignment explanation
Indices: 24297169--24297207 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24297159 TATAATATAA
24297169 TTTTAAAATAAATATTTTATC
1 TTTTAAAATAAAT-TTTTATC
*
24297190 TTTTAAAATGAATTTTTA
1 TTTTAAAATAAATTTTTA
24297208 ACATCACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTAAAATAAATTTTTATC
Found at i:24297573 original size:109 final size:110
Alignment explanation
Indices: 24297426--24297639 Score: 297
Period size: 110 Copynumber: 2.0 Consensus size: 110
24297416 TTATATCTTC
* * * * * *
24297426 ATAATTTTTAAAGGGTTTAATAAAATTTTTATCGTTTTT-GAGAGGTAAAGTACAATTTTACCAT
1 ATAATTTTTAAAGAGTTTAATAAAATTTTTATCATTTTTAAAAAAGTAAAGTAAAATTTTACCAT
*
24297490 TACTAATTTAAAGTTTTATAAATTATAAAAGGTTTAAATTGATTT
66 TACTAATTTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTT
** * *
24297535 ATAATTTTTAAAGAG-TTAGATCGAATTTTTATCATTTTTAAAAAATTAAAGTAAAATTTTATCA
1 ATAATTTTTAAAGAGTTTA-ATAAAATTTTTATCATTTTTAAAAAAGTAAAGTAAAATTTTACCA
*
24297599 TTACTAATTTAAAATTTTATAAATTATAAAATGTTTAAATT
65 TTACTAATTTAAAATTTTATAAATTATAAAAGGTTTAAATT
24297640 ACAATTTTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
108 3 0.03
109 31 0.34
110 57 0.63
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (110 bp):
ATAATTTTTAAAGAGTTTAATAAAATTTTTATCATTTTTAAAAAAGTAAAGTAAAATTTTACCAT
TACTAATTTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTT
Found at i:24297637 original size:16 final size:17
Alignment explanation
Indices: 24297604--24297640 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
24297594 TATCATTACT
*
24297604 AATT-TAAAATTTTATA
1 AATTATAAAATGTTATA
24297620 AATTATAAAATGTT-TA
1 AATTATAAAATGTTATA
24297636 AATTA
1 AATTA
24297641 CAATTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTATAAAATGTTATA
Found at i:24297910 original size:17 final size:17
Alignment explanation
Indices: 24297888--24297920 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24297878 ATATAATAAA
24297888 TATTTTTATT-ATTTTAT
1 TATTTTT-TTAATTTTAT
24297905 TATTTTTTTAATTTTA
1 TATTTTTTTAATTTTA
24297921 AAATACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTTAATTTTAT
Found at i:24297930 original size:11 final size:11
Alignment explanation
Indices: 24297916--24298021 Score: 61
Period size: 11 Copynumber: 10.4 Consensus size: 11
24297906 ATTTTTTTAA
24297916 TTTTAAAATAC
1 TTTTAAAATAC
24297927 TTTTAAAATAC
1 TTTTAAAATAC
24297938 TTTTATTAAAT--
1 TTTTA--AAATAC
*
24297949 TTTT-TAA-A-
1 TTTTAAAATAC
**
24297957 TTTTAAAATTT
1 TTTTAAAATAC
24297968 TTTTAAAATAC
1 TTTTAAAATAC
*
24297979 TTTTTAAAT--
1 TTTTAAAATAC
* *
24297988 TTTT---TTAA
1 TTTTAAAATAC
*
24297996 TTTTAAAATAT
1 TTTTAAAATAC
24298007 TTTTAAAATAC
1 TTTTAAAATAC
24298018 TTTT
1 TTTT
24298022 TTTAATTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
6 1 0.01
8 10 0.14
9 6 0.08
11 53 0.72
13 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:24297962 original size:30 final size:29
Alignment explanation
Indices: 24297927--24298013 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 29
24297917 TTTAAAATAC
24297927 TTTTAAAATACTTTTATT-AAAT-TTTTTAAA
1 TTTTAAAAT--TTTT-TTAAAATATTTTTAAA
24297957 TTTTAAAATTTTTTTAAAATACTTTTTAAA
1 TTTTAAAATTTTTTTAAAATA-TTTTTAAA
24297987 TTTT----TTTAATTTTAAAATATTTTTAAA
1 TTTTAAAATTT--TTTTAAAATATTTTTAAA
24298014 ATACTTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
26 3 0.06
27 10 0.19
28 18 0.35
30 21 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAAAATTTTTTTAAAATATTTTTAAA
Found at i:24297986 original size:39 final size:40
Alignment explanation
Indices: 24297906--24298055 Score: 203
Period size: 41 Copynumber: 3.6 Consensus size: 40
24297896 TTATTTTATT
*
24297906 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTATTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT-TTAA
* *
24297947 ATTTTTTAAATTTTAAAATTTTTTTAAAATAC-TTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
24297986 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAA
*
24298027 TTTTTATTTTAATTTTTAAAATAATTTTT
1 -ATTT-TTTTAA-TTTTAAAAT-ATTTTT
24298056 TGGTATTTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
39 34 0.35
40 3 0.03
41 36 0.37
42 3 0.03
43 6 0.06
44 9 0.09
45 6 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:24303532 original size:18 final size:18
Alignment explanation
Indices: 24303509--24303546 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
24303499 AAACTCGTAG
24303509 ATAGTGTCTACCTCTTTA
1 ATAGTGTCTACCTCTTTA
24303527 ATAGTGTCTACCTCTTTA
1 ATAGTGTCTACCTCTTTA
24303545 AT
1 AT
24303547 GGACCTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.45
Consensus pattern (18 bp):
ATAGTGTCTACCTCTTTA
Found at i:24307185 original size:85 final size:86
Alignment explanation
Indices: 24307018--24307185 Score: 185
Period size: 85 Copynumber: 2.0 Consensus size: 86
24307008 CTATATAATT
* * * * * *
24307018 AATATATAATTTTGATAATCTTTTTTACCTGAACCCCAAACCTCAAAGTCAAATCCAAAATCTTG
1 AATACATAATTTTAACAATCTTTTTAACCTGAACCCCAAACCTCAAAATCAAATCCAAAATCTTA
* * * *
24307083 AACCTTGAACTCGAACCCCTA
66 AACCCTAAACCCAAACCCCTA
* ** * * *
24307104 AATACATAATTTTAACAA-CTTTTTAACTTGAACCCTGAACCTCAAAATTAAATCTAAAATTTTA
1 AATACATAATTTTAACAATCTTTTTAACCTGAACCCCAAACCTCAAAATCAAATCCAAAATCTTA
24307168 AACCCTAAACCCAAACCC
66 AACCCTAAACCCAAACCC
24307186 AAACCTAGAA
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
85 51 0.77
86 15 0.23
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (86 bp):
AATACATAATTTTAACAATCTTTTTAACCTGAACCCCAAACCTCAAAATCAAATCCAAAATCTTA
AACCCTAAACCCAAACCCCTA
Found at i:24308033 original size:4 final size:4
Alignment explanation
Indices: 24308024--24308053 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
24308014 GAATGAACAT
24308024 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
24308054 GAACATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:24308400 original size:2 final size:2
Alignment explanation
Indices: 24308395--24308427 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24308385 ATATGTATGC
24308395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24308428 ACAAAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24327586 original size:2 final size:2
Alignment explanation
Indices: 24327579--24327619 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
24327569 AACCGAAGTA
24327579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24327620 AATGTGTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24328897 original size:14 final size:15
Alignment explanation
Indices: 24328867--24328904 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
24328857 AAACAACATG
24328867 ATATTTAATAATTAAA
1 ATATTTAATAA-TAAA
*
24328883 ATTTTTAATAA-AAA
1 ATATTTAATAATAAA
24328897 ATATTTAA
1 ATATTTAA
24328905 ATTATAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 10 0.50
16 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTAATAATAAA
Found at i:24333423 original size:20 final size:20
Alignment explanation
Indices: 24333398--24333439 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
24333388 CCTTTCTAAA
24333398 TATATGGTTCTTAATTGACT
1 TATATGGTTCTTAATTGACT
*
24333418 TATATGTTTCTTAATTGACT
1 TATATGGTTCTTAATTGACT
24333438 TA
1 TA
24333440 ATAACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TATATGGTTCTTAATTGACT
Found at i:24341226 original size:8 final size:8
Alignment explanation
Indices: 24341212--24341257 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
24341202 TCTTTTGCTC
24341212 TCTTTTTT
1 TCTTTTTT
*
24341220 CCTTTTTT
1 TCTTTTTT
24341228 TCTTTCTTT
1 TCTTT-TTT
*
24341237 TC-TGTTT
1 TCTTTTTT
24341244 TCTTTTTT
1 TCTTTTTT
24341252 TCTTTT
1 TCTTTT
24341258 ATTTTCTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 5 0.16
8 22 0.69
9 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:24341262 original size:25 final size:25
Alignment explanation
Indices: 24341216--24341264 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
24341206 TTGCTCTCTT
*
24341216 TTTTCCTTTTTTTCTTTCTTTTCTG
1 TTTTCCTTTTTTTCTTTATTTTCTG
24341241 TTTT-CTTTTTTTCTTTTATTTTCT
1 TTTTCCTTTTTTTC-TTTATTTTCT
24341265 CTAATCCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTTCCTTTTTTTCTTTATTTTCTG
Found at i:24341599 original size:25 final size:22
Alignment explanation
Indices: 24341571--24341625 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 22
24341561 TCCTTTTTAA
*
24341571 TTCTTTCTCTGATTTTTTGCTTTGC
1 TTCTTTCTCT-ATCTTTTGC-TT-C
24341596 TTCTTGCTCTCTATCTTTTGCTTC
1 TTCTT--TCTCTATCTTTTGCTTC
24341620 TTCTTT
1 TTCTTT
24341626 TTTTAATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 1 0.04
24 6 0.22
25 7 0.26
26 8 0.30
27 5 0.19
ACGTcount: A:0.04, C:0.24, G:0.09, T:0.64
Consensus pattern (22 bp):
TTCTTTCTCTATCTTTTGCTTC
Found at i:24343503 original size:24 final size:24
Alignment explanation
Indices: 24343476--24343521 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24343466 CTAATTAAAT
* *
24343476 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
24343500 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
24343522 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:24345249 original size:17 final size:18
Alignment explanation
Indices: 24345200--24345240 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24345190 TATTTTTTTT
* * *
24345200 AAAAAGACATAGAACACA
1 AAAAAGATATAAAATACA
24345218 AAAAAGATATAAAATACA
1 AAAAAGATATAAAATACA
24345236 AAAAA
1 AAAAA
24345241 TTATTAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAAAGATATAAAATACA
Found at i:24345623 original size:28 final size:29
Alignment explanation
Indices: 24345589--24345647 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
24345579 CATTCACATG
*
24345589 TTTTAAAGCTTTTCATA-TTTTTCTGAAT
1 TTTTAAAGCTTTTCAGATTTTTTCTGAAT
** *
24345617 TTTTAAATTTTTTGAGATTTTTTCTGAAT
1 TTTTAAAGCTTTTCAGATTTTTTCTGAAT
24345646 TT
1 TT
24345648 GTTTTGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.61
Consensus pattern (29 bp):
TTTTAAAGCTTTTCAGATTTTTTCTGAAT
Found at i:24346861 original size:70 final size:70
Alignment explanation
Indices: 24346777--24346925 Score: 289
Period size: 70 Copynumber: 2.1 Consensus size: 70
24346767 ATTTATTTTT
24346777 TAAAATATTTATTTATTTTACATATTTTATTATACAATTATAAGGCACTTGTCAACTCCTATTTG
1 TAAAA-ATTTATTTATTTTACATATTTTATTATACAATTATAAGGCACTTGTCAACTCCTATTTG
24346842 TGAGTC
65 TGAGTC
24346848 TAAAAATTTATTTATTTTACATATTTTATTATACAATTATAAGGCACTTGTCAACTCCTATTTGT
1 TAAAAATTTATTTATTTTACATATTTTATTATACAATTATAAGGCACTTGTCAACTCCTATTTGT
24346913 GAGTC
66 GAGTC
24346918 TAAAAATT
1 TAAAAATT
24346926 CACTAACAGT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 73 0.94
71 5 0.06
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (70 bp):
TAAAAATTTATTTATTTTACATATTTTATTATACAATTATAAGGCACTTGTCAACTCCTATTTGT
GAGTC
Found at i:24346948 original size:70 final size:70
Alignment explanation
Indices: 24346804--24346949 Score: 195
Period size: 70 Copynumber: 2.1 Consensus size: 70
24346794 TTACATATTT
* * * ***
24346804 TATTATACAATTATAAGGCACTTGTCAACTCCTATTTGTGAGTCTAAAAATTTATTTATTTTACA
1 TATTATACAATTATAAGGCACTTGTCAACTCCTATTTGTGAGTCTAAAAATTCACTAACAGTACA
* **
24346869 TATTT
66 CATAA
24346874 TATTATACAATTATAAGGCACTTGTCAACTCCTATTTGTGAGTCTAAAAATTCACTAACAGTACA
1 TATTATACAATTATAAGGCACTTGTCAACTCCTATTTGTGAGTCTAAAAATTCACTAACAGTACA
24346939 CCA-AA
66 -CATAA
24346944 TATTAT
1 TATTAT
24346950 GTTAAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
70 65 0.98
71 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (70 bp):
TATTATACAATTATAAGGCACTTGTCAACTCCTATTTGTGAGTCTAAAAATTCACTAACAGTACA
CATAA
Found at i:24358944 original size:24 final size:24
Alignment explanation
Indices: 24358917--24358966 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
24358907 AAAGTTGAAT
24358917 TCTTACCAAATAGCACATTGACTA
1 TCTTACCAAATAGCACATTGACTA
24358941 TCTTACCAAATAGCACATTGACTA
1 TCTTACCAAATAGCACATTGACTA
24358965 TC
1 TC
24358967 ACAAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (24 bp):
TCTTACCAAATAGCACATTGACTA
Found at i:24362767 original size:43 final size:43
Alignment explanation
Indices: 24362706--24362908 Score: 268
Period size: 43 Copynumber: 4.7 Consensus size: 43
24362696 CTGATAAGTG
*
24362706 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCTATTTGTA
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTA
*
24362749 TTTTCGTGTAAGACCACGTCTAGGACGATGGCATCGATTTGTA
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTA
24362792 TTTTCGTGT-AGACCACGTCTGGGACGATGGCATCGATTTGTA
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTA
* ** * * * *
24362834 TTTTCGAGTAAGACCTTGTCTAGGAC-AGTGGCATCAATGTGCGA
1 TTTTCGTGTAAGACCACGTCTGGGACGA-TGGCATCGATTTG-TA
* *
24362878 -TTACATGTAAGACCACGTCTGGGACGATGGC
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGC
24362909 GTTGTATGAA
Statistics
Matches: 140, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
42 41 0.29
43 97 0.69
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (43 bp):
TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTA
Found at i:24362816 original size:85 final size:87
Alignment explanation
Indices: 24362706--24362908 Score: 288
Period size: 85 Copynumber: 2.4 Consensus size: 87
24362696 CTGATAAGTG
* *
24362706 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCTATTTGTATTTTCGTGTAAGACCACGTCTA
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTATTTTCGAGTAAGACCACGTCTA
* * *
24362771 GGAC-GATGGCATCGATTTG-TA
66 GGACAG-TGGCATCAATGTGCGA
**
24362792 TTTTCGTGT-AGACCACGTCTGGGACGATGGCATCGATTTGTATTTTCGAGTAAGACCTTGTCTA
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTATTTTCGAGTAAGACCACGTCTA
24362856 GGACAGTGGCATCAATGTGCGA
66 GGACAGTGGCATCAATGTGCGA
* *
24362878 -TTACATGTAAGACCACGTCTGGGACGATGGC
1 TTTTCGTGTAAGACCACGTCTGGGACGATGGC
24362909 GTTGTATGAA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
85 72 0.69
86 33 0.31
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (87 bp):
TTTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTATTTTCGAGTAAGACCACGTCTA
GGACAGTGGCATCAATGTGCGA
Found at i:24363113 original size:2 final size:2
Alignment explanation
Indices: 24363106--24363132 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24363096 TTGTTATGGT
24363106 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
24363133 TTTACNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24364312 original size:2 final size:2
Alignment explanation
Indices: 24364305--24364332 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24364295 TTTTATTTAA
24364305 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
24364333 TTGAGAAATA
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:24364595 original size:24 final size:24
Alignment explanation
Indices: 24364568--24364621 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
24364558 TGAGCATGCA
24364568 AATTTAGTATAATTGTTTCGTCTT
1 AATTTAGTATAATTGTTTCGTCTT
24364592 AATTTAGTATAATTGTTTCGTCTT
1 AATTTAGTATAATTGTTTCGTCTT
24364616 AATTTA
1 AATTTA
24364622 AGCATGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (24 bp):
AATTTAGTATAATTGTTTCGTCTT
Found at i:24368469 original size:18 final size:17
Alignment explanation
Indices: 24368448--24368481 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24368438 GTCTAAAATA
24368448 TATATATTTAATAAAAAG
1 TATAT-TTTAATAAAAAG
*
24368466 TATATTTTATTAAAAA
1 TATATTTTAATAAAAA
24368482 ATAAAAATAT
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TATATTTTAATAAAAAG
Found at i:24368491 original size:43 final size:40
Alignment explanation
Indices: 24368385--24368503 Score: 125
Period size: 43 Copynumber: 2.9 Consensus size: 40
24368375 GGCCCGGCCC
* *
24368385 ATATTTGATTAAAAATAAAAAGATATATATTTAAT-ATAT
1 ATATTTGATTAAAAATAAAAATATATATATTTAATAAAAT
* *
24368424 A-ATTCTGATTAAAAGTCTAAAATATATATATTTAATAAAAAGT
1 ATATT-TGATTAAAAAT-AAAAATATATATATTTAAT-AAAA-T
* *
24368467 ATATTTTATTAAAAAATAAAAATATATGTATTTAATA
1 ATATTTGATT-AAAAATAAAAATATATATATTTAATA
24368504 TATAATTCAG
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 3 0.05
39 11 0.17
40 17 0.26
42 3 0.05
43 23 0.35
44 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (40 bp):
ATATTTGATTAAAAATAAAAATATATATATTTAATAAAAT
Found at i:24368501 original size:23 final size:24
Alignment explanation
Indices: 24368457--24368501 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
24368447 ATATATATTT
*
24368457 AATAAAAAGTATATTTTATTAAAA
1 AATAAAAAGTATATTATATTAAAA
24368481 AATAAAAA-TATATGTAT-TTAA
1 AATAAAAAGTATAT-TATATTAA
24368502 TATATAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AATAAAAAGTATATTATATTAAAA
Found at i:24371016 original size:28 final size:27
Alignment explanation
Indices: 24370985--24371050 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
24370975 AAGTTAAATG
24370985 TAAATTTAACTAAAAAATAA-ATTAAA-AC
1 TAAATTTAA--AAAAAA-AATATTAAAGAC
*
24371013 TAAATTGAGAAAAAAAAATATTAAAGAC
1 TAAATTTA-AAAAAAAAATATTAAAGAC
24371041 TAAATTTAAA
1 TAAATTTAAA
24371051 GTTATAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 2 0.06
27 14 0.42
28 16 0.48
29 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (27 bp):
TAAATTTAAAAAAAAAATATTAAAGAC
Found at i:24386914 original size:3 final size:3
Alignment explanation
Indices: 24386901--24386997 Score: 126
Period size: 3 Copynumber: 32.7 Consensus size: 3
24386891 TTAGTAATTC
24386901 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
24386948 TAT TAT TAT TAT TAC TA- TATT TGT TAG TAT TAT TAC TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
24386993 TAT TA
1 TAT TA
24386998 CTAATTTATA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 4 0.05
3 78 0.94
4 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:24387576 original size:67 final size:61
Alignment explanation
Indices: 24387473--24387599 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 61
24387463 TTTGTTAGTC
*
24387473 TTGTTCGTTTATTTATGTACATGTTTGTTTTTCTTGCTTTAGTTTTTATC-TGTTTATCATT
1 TTGTTCGTTTATTTATGTACATGTTTGTTTTTCTTGCTTTAGTTTTT-GCATGTTTATCATT
24387534 TTGTTCGTTTATTTATGTACATGTTTGTTATTGTTTTTCTTGCTTTAGTTTTTGCATGTTTATCA
1 TTGTTCGTTTATTTATGTACA----TG-T-TTGTTTTTCTTGCTTTAGTTTTTGCATGTTTATCA
24387599 T
60 T
24387600 CTGTCATGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
61 21 0.36
65 2 0.03
66 2 0.03
67 33 0.57
ACGTcount: A:0.13, C:0.09, G:0.14, T:0.63
Consensus pattern (61 bp):
TTGTTCGTTTATTTATGTACATGTTTGTTTTTCTTGCTTTAGTTTTTGCATGTTTATCATT
Found at i:24388061 original size:110 final size:111
Alignment explanation
Indices: 24387947--24388255 Score: 457
Period size: 110 Copynumber: 2.8 Consensus size: 111
24387937 TTTCTAAAAA
* * * **
24387947 AAAAAAATTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACATGTCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCT
24388012 GGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATAT-CTTTTT
66 GGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* *
24388057 AAAAAATTTCAAAATATGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATACCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCT
*
24388122 GGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATGTCCTTTTT
66 GGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* * * *
24388168 -AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTACCCTAAGGTGTT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCT
* *
24388231 GGGTTTCGA--TTTCTCGTTTAACCAA
66 GGGTATCGATTTTTCTCGTTCAACCAA
24388256 GTTGCCAAAT
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
107 15 0.08
109 24 0.13
110 137 0.75
111 6 0.03
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (111 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCT
GGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
Found at i:24389345 original size:31 final size:30
Alignment explanation
Indices: 24389272--24389353 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
24389262 AATGTATAAT
*
24389272 TATATACAT-AAACTTTAATTTGGTGCAAT
1 TATATACATGAAACTTTAATTTGGTGCAAA
* * * *
24389301 TATACACGTGAAACTCTAATTATGGTTCAAA
1 TATATACATGAAACTTTAATT-TGGTGCAAA
*
24389332 TATATACTTGAAACTTTAATTT
1 TATATACATGAAACTTTAATTT
24389354 TGATTTAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 7 0.16
30 11 0.26
31 25 0.58
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
TATATACATGAAACTTTAATTTGGTGCAAA
Found at i:24389530 original size:30 final size:29
Alignment explanation
Indices: 24389496--24389552 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
24389486 TAATTGGGTC
*
24389496 AAATCAATATTTCATGTATAAAATTACACA
1 AAATCAA-AGTTCATGTATAAAATTACACA
24389526 AAATCAAAGTTCATGTATAAAATTACA
1 AAATCAAAGTTCATGTATAAAATTACA
24389553 TTATACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTACACA
Found at i:24391034 original size:31 final size:29
Alignment explanation
Indices: 24390964--24391035 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
24390954 TTGTATATAT
* *
24390964 AAATTTTAATTTGGTGAATTATATACGTG
1 AAATTTTAATTTGGTCAAATATATACGTG
* * **
24390993 AAACTCTAATTGTGGTTCAAATATATATTTG
1 AAATTTTAATT-TGG-TCAAATATATACGTG
24391024 AAATTTTAATTT
1 AAATTTTAATTT
24391036 TGATTTAATC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
29 9 0.27
30 4 0.12
31 20 0.61
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (29 bp):
AAATTTTAATTTGGTCAAATATATACGTG
Found at i:24391498 original size:2 final size:2
Alignment explanation
Indices: 24391491--24391528 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24391481 TAGAAAGTTA
24391491 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
24391529 CAATTAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24394381 original size:36 final size:36
Alignment explanation
Indices: 24394340--24394530 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
24394330 GGTAGCATTA
24394340 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
24394376 GCTACACTTATCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
24394421 AGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
24394458 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
24394494 GCTATACTTATCTGATCAAGTGACAAAGTAATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
24394530 G
1 G
24394531 GTAGCCTTAG
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 99 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:24394407 original size:82 final size:82
Alignment explanation
Indices: 24394304--24394619 Score: 353
Period size: 82 Copynumber: 3.9 Consensus size: 82
24394294 TTTGAGTACT
24394304 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
24394369 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* * *
24394386 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
24394451 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * * * * ** *
24394468 TCTGATCAAGTGAAAAAGTGATAAGTGCTA-TACTTATCT-GA-TCAAGTGA-CAAAGT-AATAA
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCA-TTAGCTACACTTATCTGATC-AAGTGAAAAA
*
24394528 GTGGT-AGCCTTAGCTACACTTA
64 GTGATAAG---T-GCTACACTTA
* * * *
24394550 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
24394612 GATAAGTG
66 GATAAGTG
24394620 ATCATATGTA
Statistics
Matches: 192, Mismatches: 30, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
78 2 0.01
79 9 0.05
80 10 0.05
81 6 0.03
82 157 0.82
83 7 0.04
84 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:24394478 original size:21 final size:20
Alignment explanation
Indices: 24394450--24394515 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
24394440 AGTGAGAAAG
24394450 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
24394470 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
24394486 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
24394506 TGATCAAGTG
1 TGAT-AAGTG
24394516 ACAAAGTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:24394553 original size:118 final size:118
Alignment explanation
Indices: 24394340--24394576 Score: 411
Period size: 118 Copynumber: 2.0 Consensus size: 118
24394330 GGTAGCATTA
*
24394340 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGATAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
* * *
24394405 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGT
66 AATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
* * *
24394458 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
24394523 AATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
66 AATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
24394576 G
1 G
24394577 GTAGCCTAGC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 112 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (118 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
AATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:24394602 original size:45 final size:46
Alignment explanation
Indices: 24394494--24394619 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
24394484 AGTGATAAGT
* *
24394494 GCTATACTTATCTGATCAAGTGACAAAGTAATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
24394540 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
24394585 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
24394620 ATCATATGTA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
43 12 0.16
44 5 0.06
45 19 0.25
46 41 0.53
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:24395422 original size:13 final size:13
Alignment explanation
Indices: 24395404--24395453 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
24395394 ATATTTTTTT
24395404 AATTAAAATTATA
1 AATTAAAATTATA
*
24395417 AATTAAAATAATA
1 AATTAAAATTATA
* *
24395430 ATTCTAAAAATTATC
1 AAT-T-AAAATTATA
24395445 AATTAAAAT
1 AATTAAAAT
24395454 GTTATTAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 19 0.63
14 2 0.07
15 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:24396926 original size:29 final size:30
Alignment explanation
Indices: 24396893--24396981 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
24396883 TTGATTTAAT
*
24396893 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTATATACATGAAACTTTAATTTG
* *
24396922 GTGCAATTATACACATGAAACTCTAATTATG
1 GTGCAATTATATACATGAAACTTTAATT-TG
* * * *
24396953 GTTCAAATATATACTTGAAACTTTGATTT
1 GTGCAATTATATACATGAAACTTTAATTT
24396982 TGATTTAATC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.31
30 10 0.20
31 24 0.49
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (30 bp):
GTGCAATTATATACATGAAACTTTAATTTG
Found at i:24402189 original size:8 final size:8
Alignment explanation
Indices: 24402176--24402212 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
24402166 CTGTCAAATT
24402176 TTATAAAA
1 TTATAAAA
24402184 TTATAAAA
1 TTATAAAA
*
24402192 TTATATAA
1 TTATAAAA
*
24402200 TAATAAAA
1 TTATAAAA
24402208 TTATA
1 TTATA
24402213 TTTTAAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:24402837 original size:29 final size:29
Alignment explanation
Indices: 24402805--24402860 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
24402795 AGCAAATGAT
*
24402805 AAATT-AATATCTATAATAATCTAATATCC
1 AAATTCAATATCTATAA-AAACTAATATCC
* *
24402834 AAATTCATTATTTATAAAAACTAATAT
1 AAATTCAATATCTATAAAAACTAATAT
24402861 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATTCAATATCTATAAAAACTAATATCC
Found at i:24410554 original size:68 final size:68
Alignment explanation
Indices: 24410421--24410550 Score: 178
Period size: 68 Copynumber: 1.9 Consensus size: 68
24410411 AAAGTCTTAA
* *
24410421 CTGCTCATAACATCATGGTGGGGTATAACAGATTGTTACTAATAATAATGAAAACGCTAGAAAAG
1 CTGCTCATAACATCATGGTGGGGTATAAAAGATTGTTACTAATAATAAAGAAAACGCTAGAAAAG
24410486 TGT
66 TGT
* *
24410489 CTGCTCA-AATCATTATGGTGGGGTGTAAAAGATTGTTACTAA-AA-AAAGAAAACG-TCAGAAA
1 CTGCTCATAA-CATCATGGTGGGGTATAAAAGATTGTTACTAATAATAAAGAAAACGCT-AGAAA
24410550 A
64 A
24410551 AAGTAGTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 1 0.02
66 15 0.27
67 4 0.07
68 36 0.64
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (68 bp):
CTGCTCATAACATCATGGTGGGGTATAAAAGATTGTTACTAATAATAAAGAAAACGCTAGAAAAG
TGT
Found at i:24415003 original size:20 final size:20
Alignment explanation
Indices: 24414978--24415015 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24414968 ATTAATTAAA
24414978 TAAATA-TATAAAACAAATCT
1 TAAATATTATAAAA-AAATCT
24414998 TAAATATTATAAAAAAAT
1 TAAATATTATAAAAAAAT
24415016 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATATTATAAAAAAATCT
Found at i:24420294 original size:21 final size:21
Alignment explanation
Indices: 24420242--24420303 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
24420232 TAAAAAATGT
24420242 ATTTTT-TATATTTT-AAATA
1 ATTTTTATATATTTTAAAATA
*
24420261 ATTTTAATA-ATTTTAAAATA
1 ATTTTTATATATTTTAAAATA
*
24420281 ATTTTTATATATTTAAAAATA
1 ATTTTTATATATTTTAAAATA
24420302 AT
1 AT
24420304 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 10 0.27
20 15 0.41
21 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTATATATTTTAAAATA
Found at i:24420321 original size:38 final size:38
Alignment explanation
Indices: 24420213--24420321 Score: 118
Period size: 38 Copynumber: 2.8 Consensus size: 38
24420203 TTAATTAATG
* * *
24420213 TTTTAAAAATTAAAAAATTTAAAAAATGTATTTTTTATA
1 TTTTAAAAATTAATAATTTTAAAAAA-GTAATTTTTATA
24420252 TTTTAAATAATTTTAATAATTTT--AAAA-TAATTTTTATA
1 TTTTAAA-AA--TTAATAATTTTAAAAAAGTAATTTTTATA
24420290 TATTTAAAAA-TAATAATTTTAAAAAAGTAATT
1 T-TTTAAAAATTAATAATTTTAAAAAAGTAATT
24420322 AATTGTTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
35 10 0.17
37 4 0.07
38 18 0.30
39 13 0.22
40 6 0.10
42 9 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (38 bp):
TTTTAAAAATTAATAATTTTAAAAAAGTAATTTTTATA
Found at i:24420933 original size:89 final size:87
Alignment explanation
Indices: 24420863--24421024 Score: 292
Period size: 88 Copynumber: 1.9 Consensus size: 87
24420853 CTTTTTGTTT
24420863 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAA-AGCCCTCAAATCTTAAAAAAAAAA
1 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGA-CCCTCAAA-CTTAAAAAAAAAA
24420927 GCAATTAAGCCCTTACAATTTTTA
64 GCAATTAAGCCCTTACAATTTTTA
24420951 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAAA-C
1 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAAAGC
24421015 AATTAAGCCC
66 AATTAAGCCC
24421025 CTACTTTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
86 11 0.15
87 13 0.18
88 48 0.66
89 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (87 bp):
CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAAAGC
AATTAAGCCCTTACAATTTTTA
Found at i:24421185 original size:36 final size:36
Alignment explanation
Indices: 24421145--24421255 Score: 98
Period size: 38 Copynumber: 3.0 Consensus size: 36
24421135 ATAAAAATCG
24421145 TAAAAAATTATAAAGTACAT-AGAAATATAAAAAATA
1 TAAAAAATTATAAAGT-CATAAGAAATATAAAAAATA
** * * *
24421181 TAAAATTTTATAAAGTCGTAAGAAAAGTATACAAAATG
1 TAAAAAATTATAAAGTCATAAG-AAA-TATAAAAAATA
* * *
24421219 TAAAAAAATATAAATTTCATAAAAAATATATAAAAAT
1 TAAAAAATTATAAA-GTCATAAGAAATATA-AAAAAT
24421256 TATTGTATCA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
35 2 0.03
36 16 0.28
37 7 0.12
38 28 0.48
39 5 0.09
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (36 bp):
TAAAAAATTATAAAGTCATAAGAAATATAAAAAATA
Found at i:24422324 original size:80 final size:82
Alignment explanation
Indices: 24422192--24422344 Score: 222
Period size: 80 Copynumber: 1.9 Consensus size: 82
24422182 GACTTTGGTC
* * *
24422192 CCCTCAAAATGAAAATTTTCAATTCATTCTTATTATAAATAAAAAATCTATAAATTAAT-T-TAG
1 CCCTCAAAATAAAAATTTTCAATTCAGTCTTATTATAAATAAAAAATCTATAAAGTAATATATAG
*
24422255 TGAAATTATATTCTAGT
66 TAAAATTATATTCTAGT
* *
24422272 CCCTTAAAATAAAAATTTTCAATTCAGTCTTCTTATAAATAGAAAAAT-TATAAAGTAATATATA
1 CCCTCAAAATAAAAATTTTCAATTCAGTCTTATTATAAATA-AAAAATCTATAAAGTAATATATA
24422336 GTAAAATTA
65 GTAAAATTA
24422345 CATTTTAACT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 47 0.73
81 7 0.11
82 10 0.16
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (82 bp):
CCCTCAAAATAAAAATTTTCAATTCAGTCTTATTATAAATAAAAAATCTATAAAGTAATATATAG
TAAAATTATATTCTAGT
Found at i:24423785 original size:15 final size:16
Alignment explanation
Indices: 24423760--24423790 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
24423750 AGCTTTTGTT
24423760 GTTTCTGTTTTGTATG
1 GTTTCTGTTTTGTATG
24423776 GTTT-TGTTTTGTATG
1 GTTTCTGTTTTGTATG
24423791 TTTGTATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.06, C:0.03, G:0.26, T:0.65
Consensus pattern (16 bp):
GTTTCTGTTTTGTATG
Found at i:24426539 original size:16 final size:16
Alignment explanation
Indices: 24426518--24426559 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
24426508 TTATTAAATT
*
24426518 ATATATTTTAATTATA
1 ATATATTTTAATAATA
24426534 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
24426549 AT-TATGTTTAA
1 ATATAT-TTTAA
24426560 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:24426544 original size:15 final size:15
Alignment explanation
Indices: 24426509--24426550 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24426499 TTAAGAATTT
*
24426509 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24426523 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24426537 TATTTAATAATAAT
1 TATTTAATTATAAT
24426551 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24431002 original size:20 final size:21
Alignment explanation
Indices: 24430977--24431018 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
24430967 ATAATTTTTT
24430977 ATTTTTAATAATGTTT-TAAA
1 ATTTTTAATAATGTTTATAAA
*
24430997 ATTTTTAATAGTGTTTATAAA
1 ATTTTTAATAATGTTTATAAA
24431018 A
1 A
24431019 ATAAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTTTAATAATGTTTATAAA
Found at i:24431137 original size:19 final size:18
Alignment explanation
Indices: 24431106--24431142 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24431096 GTTTTTTTAA
24431106 AAATTTTGTATAAATTTT
1 AAATTTTGTATAAATTTT
*
24431124 AAATTTTTTAATAAATTTT
1 AAATTTTGT-ATAAATTTT
24431143 TTAAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AAATTTTGTATAAATTTT
Found at i:24439771 original size:29 final size:29
Alignment explanation
Indices: 24439721--24439776 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
24439711 CAAATAGGGA
24439721 TTAAATTGAGAAATATGAAAAT-TATGTG
1 TTAAATTGAGAAATATGAAAATGTATGTG
*
24439749 TTAAATGTGAGAAAT-TGTGAAATGTATG
1 TTAAAT-TGAGAAATATG-AAAATGTATG
24439777 GGCTGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (29 bp):
TTAAATTGAGAAATATGAAAATGTATGTG
Found at i:24441597 original size:43 final size:43
Alignment explanation
Indices: 24441531--24441613 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
24441521 GTATGGACAT
* *
24441531 GGGCTGGGACACGGCCGTGTGTCCCCATTTTGAATGCCTACAC
1 GGGCTGGGACACGGCCGTATGTCCCCATTTTAAATGCCTACAC
*
24441574 GGGCTGGGACACGTCCGTATGTCCCCATTTTAAATGCCTA
1 GGGCTGGGACACGGCCGTATGTCCCCATTTTAAATGCCTA
24441614 TTTTGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (43 bp):
GGGCTGGGACACGGCCGTATGTCCCCATTTTAAATGCCTACAC
Found at i:24446225 original size:2 final size:2
Alignment explanation
Indices: 24446153--24446211 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
24446143 TAAATGTTAA
* ** * *
24446153 AT AT GT AT AT AT GG AT AT AT AT AA AT AT AA 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
24446195 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
24446212 GAAGCAGTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:24447866 original size:132 final size:132
Alignment explanation
Indices: 24447628--24448280 Score: 910
Period size: 132 Copynumber: 4.8 Consensus size: 132
24447618 GTCTACTCCA
* * * * * *
24447628 CATCTTTGATCTGCTCCTCTACTGCTTATGGGGGACAGAAACTGCAATCTTTAACCTATTCCACT
1 CATCTTCGATCTGCTCCACTACTGCTTA-GGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
* * *
24447693 ACTGCTTAGGGTGATAGGACTAATGGCATAAATCTGCTTCTCCGCTGTATTGGGAAGATAAAAGT
65 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAAATT
24447758 CAC
130 CAC
* * *
24447761 CATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCTACCCCACTG
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
*
24447826 CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTC
66 CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAAATTC
24447891 AC
131 AC
*
24447893 CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTGCTCCACTA
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
* * * *
24447958 CTGTTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCATTGTATTGGAAAGATAAGATTC
66 CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAAATTC
24448023 AC
131 AC
24448025 CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
1 CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
24448090 CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCCTCCCACTTGTATTTGGGGAAGATAA
66 CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTT-CT-CCAC-TGTA-TT-GGGAAGATAA
24448155 GAATTCACC
126 -AATTCA-C
24448164 CATCCTTCGATCCTGCTCCCACTTACTGCTTTAGGGGTGAACAGAATCTGCAATCTTCCAACCCT
1 CAT-CTTCGAT-CTGCT-CCAC-TACTGC-TTA-GGGTG-ACAGAATCTGCAATCTT-CAA-CCT
*
24448229 ACCTCCACCTACTGGCTTAGGGGGTGAAAAGGAACTAATGGCTTAATATCTG
57 A-CTCCA-CTACT-GCTTA--GGGTG-ATAGG-ACTAATGGCTTAA-ATCTG
24448281 GTTTCCGCCC
Statistics
Matches: 470, Mismatches: 26, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
132 320 0.68
133 27 0.06
134 3 0.01
135 4 0.01
136 2 0.00
137 9 0.02
138 5 0.01
139 4 0.01
140 7 0.01
141 5 0.01
142 4 0.01
143 6 0.01
144 3 0.01
145 5 0.01
146 17 0.04
147 3 0.01
148 4 0.01
149 5 0.01
150 5 0.01
151 5 0.01
153 5 0.01
154 4 0.01
155 13 0.03
156 5 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
CATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
CTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAAATTC
AC
Found at i:24447951 original size:44 final size:44
Alignment explanation
Indices: 24447762--24448102 Score: 180
Period size: 44 Copynumber: 7.8 Consensus size: 44
24447752 AAAAGTCACC
* *
24447762 ATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * *
24447806 ATCTTCAACCTACCCCACTGCTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * * * * * *
24447847 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACC
1 AT--CTTCAATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
*
24447894 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
24447938 ATCTTCAACCTGCTCCACTACTGTTTAGGGTGATAGGA-CT--A
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * * ** * * * *
24447979 ATGGCTTAAATCTGCTTCTCCATTG-TATTGGAAAGATAAGATTC-ACC
1 AT--CTTCAATCTGCTCCACTACTGCT-TAGG-GTGA-CAGAATCTGCA
*
24448026 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
24448070 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1 ATCTTCAATCTGCTCCACTACTGCTTAGGGTGA
24448103 TAGGACTAAT
Statistics
Matches: 210, Mismatches: 67, Indels: 40
0.66 0.21 0.13
Matches are distributed among these distances:
41 6 0.03
42 2 0.01
43 49 0.23
44 103 0.49
45 42 0.20
46 4 0.02
47 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:24448387 original size:157 final size:142
Alignment explanation
Indices: 24447628--24448398 Score: 739
Period size: 132 Copynumber: 5.5 Consensus size: 142
24447618 GTCTACTCCA
* * * * * *
24447628 CATCTTTGATCTGCT-CCTC-TACTGCTTATGGG-GGACAGAAACTGCAATCTTTAACCTA-TTC
1 CATCTTCGATCTGCTCCCACTTACTGCTTA-GGGTGAACAGAATCTGCAATCTTAAACCTACCTC
* * * * *
24447689 CA-CTACTGCTTAGGGTGATAGGACTAATGGCATAAATCTGCTT-C-TCCGCT-GTATTG-GGAA
65 CACCTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCCGCCCACTGGTATTGTGAAA
*
24447749 GATAA-AAGTCAC
130 GATAAGAATTCAC
* *
24447761 CATCTTCGATCTGCT-CCAC-TACTACTTAGGGTG-ACAGAATCTGCAATCTTCAACCTACC-CC
1 CATCTTCGATCTGCTCCCACTTACTGCTTAGGGTGAACAGAATCTGCAATCTTAAACCTACCTCC
* * * *
24447822 A-CTGCTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTT-C-TCCACT-GTATTG-GGAAG
66 ACCTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCCGCCCACTGGTATTGTGAAAG
24447882 ATAAG-ATTCAC
131 ATAAGAATTCAC
* *
24447893 CATCTTCGATCTGCT-CCAC-TACTGCTTAGGGTG-ACAGAATCTGCAATCTTCAACCT-GCTCC
1 CATCTTCGATCTGCTCCCACTTACTGCTTAGGGTGAACAGAATCTGCAATCTTAAACCTACCTCC
* * * *
24447954 A-CTACTGTTTAGGGTGATAGGACTAATGGCTTAAATCTGCTT-C-TCCA-TTGTATTG-GAAAG
66 ACCTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCCGCCCACTGGTATTGTGAAAG
24448014 ATAAG-ATTCAC
131 ATAAGAATTCAC
*
24448025 CATCTTCGATCTGCT-CCAC-TACTGCTTAGGGTG-ACAGAATCTGCAATCTTCAACCTA-CTCC
1 CATCTTCGATCTGCTCCCACTTACTGCTTAGGGTGAACAGAATCTGCAATCTTAAACCTACCTCC
* * * * *
24448086 A-CTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCCTCCCACTTGTATTTGGGGAA
66 ACCTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCCGCCCACTGGTA-TTGTGAAA
24448150 GATAAGAATTCACC
130 GATAAGAATTCA-C
*
24448164 CATCCTTCGATCCTGCTCCCACTTACTGCTTTAGGGGTGAACAGAATCTGCAATCTTCCAACCCT
1 CAT-CTTCGAT-CTGCTCCCACTTACTGC-TTA-GGGTGAACAGAATCTGCAATCTT--AAACCT
*
24448229 ACCTCCACCTACTGGCTTAGGGGGTGAAAAGGAACTAATGGCTTAATATCTGGTTTCCGCCCACT
60 ACCTCCACCTACT-GCTTA--GGGTG-AAAGG-ACTAATGGCTTAA-ATCT-GCTTCCGCCCACT
24448294 GGTATTGTGAAAAGAATAAGAATTCAC
118 GGTATTGTG-AAAG-ATAAGAATTCAC
* * * * *
24448321 AATCTTTGACTCTGGCTCCCACTTACTGGCTTAAGGTGAAAAGAATCTGGAGATGCTGTAAACCT
1 CATCTTCGA-TCT-GCTCCCACTTACT-GCTTAGGGTGAACAGAATCTGCA-AT-CT-TAAACCT
*
24448386 ACCTCCACTTACT
60 ACCTCCACCTACT
24448399 NNNNNNNNNN
Statistics
Matches: 566, Mismatches: 33, Indels: 54
0.87 0.05 0.08
Matches are distributed among these distances:
131 2 0.00
132 317 0.56
133 27 0.05
134 3 0.01
135 5 0.01
136 3 0.01
137 9 0.02
138 5 0.01
139 4 0.01
140 7 0.01
141 5 0.01
142 4 0.01
143 6 0.01
144 3 0.01
145 5 0.01
146 17 0.03
148 5 0.01
149 5 0.01
150 5 0.01
151 5 0.01
153 5 0.01
154 4 0.01
155 13 0.02
156 30 0.05
157 56 0.10
158 15 0.03
159 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (142 bp):
CATCTTCGATCTGCTCCCACTTACTGCTTAGGGTGAACAGAATCTGCAATCTTAAACCTACCTCC
ACCTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCCGCCCACTGGTATTGTGAAAG
ATAAGAATTCAC
Found at i:24448568 original size:46 final size:46
Alignment explanation
Indices: 24448499--24449022 Score: 778
Period size: 46 Copynumber: 11.4 Consensus size: 46
24448489 NNNNNNNNNN
* *
24448499 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCGAAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* * *
24448545 ATAAGATCTACTATCTTCGATCCCCTCTGCTGCCAAATACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* * *
24448591 ACAAGATCTGCTATCTTTGATCCCTTCCGCTGCCAAATACAGAAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
*
24448637 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCTAAATACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* **
24448683 ACAAGATCTACTATCTTTAATCCCCTCCGCTGCCAAATACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
*
24448729 ACAAGATCTGCTATCTTCGATCCCCTCCGCTACCAAATACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
*
24448775 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAATTACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* *
24448821 ACAAGATCTACTATCTTCGATCCCCTCCGCTGCCAAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* * *
24448867 ACAAGATCTGCTATCTTCGATCCCGTCTGCTGCCAATTACAGGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* * * * *
24448913 ACAAGATCTGCTATCCTCGATCTCTTCCGCTGCCAAATACATGAAA
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
* ** * *
24448959 ATAAGATCTGCTATCTTCGATCTTCTCCGCTGCCAAATGCAAGAAG
1 ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
*
24449005 ACAAGATATGCTATCTTC
1 ACAAGATCTGCTATCTTC
24449023 ATTGATCTGT
Statistics
Matches: 429, Mismatches: 49, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 429 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (46 bp):
ACAAGATCTGCTATCTTCGATCCCCTCCGCTGCCAAATACAGGAAG
Found at i:24450197 original size:13 final size:13
Alignment explanation
Indices: 24450181--24450216 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
24450171 TTTTTCATTT
24450181 TTCATTTTTTTCA
1 TTCATTTTTTTCA
24450194 TTCATTTTTTTCA
1 TTCATTTTTTTCA
24450207 TT--TTTTTTTC
1 TTCATTTTTTTC
24450217 TTTTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
13 15 0.65
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (13 bp):
TTCATTTTTTTCA
Found at i:24450232 original size:19 final size:19
Alignment explanation
Indices: 24450198--24450234 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24450188 TTTTCATTCA
**
24450198 TTTTTTTCATTTTTTTTTC
1 TTTTTTTCATCATTTTTTC
24450217 TTTTTTTCATCATTTTTT
1 TTTTTTTCATCATTTTTT
24450235 TGTTTGAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTCATCATTTTTTC
Found at i:24450235 original size:22 final size:21
Alignment explanation
Indices: 24450178--24450226 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
24450168 TACTTTTTCA
24450178 TTTTTCATTTTTTTCATTCATT
1 TTTTTCATTTTTTT-ATTCATT
24450200 TTTTTCATTTTTTT-TTC-TT
1 TTTTTCATTTTTTTATTCATT
24450219 TTTTTCAT
1 TTTTTCAT
24450227 CATTTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
22 14 0.52
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCATTTTTTTATTCATT
Found at i:24451074 original size:10 final size:10
Alignment explanation
Indices: 24451059--24451087 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
24451049 AATTTTTGAC
24451059 TTTGATTTTT
1 TTTGATTTTT
24451069 TTTGA-TTTT
1 TTTGATTTTT
24451078 TTTGATTTTT
1 TTTGATTTTT
24451088 GATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (10 bp):
TTTGATTTTT
Found at i:24458481 original size:101 final size:100
Alignment explanation
Indices: 24458308--24458567 Score: 333
Period size: 101 Copynumber: 2.6 Consensus size: 100
24458298 CGTTTTCTTT
* * ** * * *
24458308 ATGCCATAGTCCAACTATGGTCTTACACATGCAT-TGCCATGGCCCAGCCATGGTCTTACATTCG
1 ATGCCATAGCCCAACTATGGTCTTACATATAAATATGCCATGGTCCAACCATGGTCTTACATTCA
* * * *
24458372 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
66 AAGTGCCATAACCCAGATATGGTATTATCATCAAA
* * *
24458407 ATGCCATAGCCCAGCTATGGTCTTACTTATAAATACTGCCATGGTCCAACCATGGTCTTACGTTC
1 ATGCCATAGCCCAACTATGGTCTTACATATAAATA-TGCCATGGTCCAACCATGGTCTTACATTC
* *
24458472 AAAGTGCCATAACCCAGATATGGTATTTTCATTAAA
65 AAAGTGCCATAACCCAGATATGGTATTATCATCAAA
* *
24458508 ATGCCATAGCCCAACTATGGTTTTACATATAAACATTGCCATGGTCCAACCATGGTCTTA
1 ATGCCATAGCCCAACTATGGTCTTACATATAAATA-TGCCATGGTCCAACCATGGTCTTA
24458568 TCCGTCAATT
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 28 0.20
101 110 0.80
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (100 bp):
ATGCCATAGCCCAACTATGGTCTTACATATAAATATGCCATGGTCCAACCATGGTCTTACATTCA
AAGTGCCATAACCCAGATATGGTATTATCATCAAA
Found at i:24458549 original size:35 final size:32
Alignment explanation
Indices: 24458308--24458567 Score: 135
Period size: 33 Copynumber: 7.8 Consensus size: 32
24458298 CGTTTTCTTT
* * **
24458308 ATGCCATAGTCCAACTATGGTCTTACACATGCA
1 ATGCCATAGCCCAACTATGGTCTTACA-TTAAA
* * * * **
24458341 TTGCCATGGCCCAGCCATGGTCTTACATTCGTA
1 ATGCCATAGCCCAACTATGGTCTTACATT-AAA
* * ** * *
24458374 GTGCCATAACCCAGTTATGGTCTTATCATCAGA
1 ATGCCATAGCCCAACTATGGTCTTA-CATTAAA
* *
24458407 ATGCCATAGCCCAGCTATGGTCTTACTTATAAA
1 ATGCCATAGCCCAACTATGGTCTTACAT-TAAA
* * * *
24458440 TACTGCCATGGTCCAACCATGGTCTTACGTTCAAA
1 -A-TGCCATAGCCCAACTATGGTCTTACATT-AAA
* * * *
24458475 GTGCCATAACCCAGA-TATGGTATTTTCATTAAA
1 ATGCCATAGCCCA-ACTATGGT-CTTACATTAAA
*
24458508 ATGCCATAGCCCAACTATGGTTTTACATATAAA
1 ATGCCATAGCCCAACTATGGTCTTACAT-TAAA
* * *
24458541 CATTGCCATGGTCCAACCATGGTCTTA
1 -A-TGCCATAGCCCAACTATGGTCTTA
24458568 TCCGTCAATT
Statistics
Matches: 174, Mismatches: 41, Indels: 22
0.73 0.17 0.09
Matches are distributed among these distances:
32 10 0.06
33 107 0.61
34 12 0.07
35 45 0.26
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (32 bp):
ATGCCATAGCCCAACTATGGTCTTACATTAAA
Found at i:24461399 original size:3 final size:3
Alignment explanation
Indices: 24461393--24461432 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
24461383 TTATTTAACC
* *
24461393 TTA TTA TTG TTA TTA TTA TTA CTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
24461433 GTTTTGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:24464250 original size:14 final size:14
Alignment explanation
Indices: 24464231--24464273 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
24464221 TTACGTTTAA
24464231 TTTAAAATTTAATT
1 TTTAAAATTTAATT
*
24464245 TTT-AAACTTAATTT
1 TTTAAAATTTAA-TT
24464259 TTTAAAATTT-ATT
1 TTTAAAATTTAATT
24464272 TT
1 TT
24464274 GGTACCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.44
14 9 0.36
15 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAAAATTTAATT
Found at i:24464273 original size:13 final size:13
Alignment explanation
Indices: 24464231--24464273 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
24464221 TTACGTTTAA
24464231 TTTAAAATTTAATT
1 TTTAAAATTT-ATT
* *
24464245 TTTAAACTTAATTT
1 TTTAAAATTTA-TT
24464259 TTTAAAATTTATT
1 TTTAAAATTTATT
24464272 TT
1 TT
24464274 GGTACCTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAAAATTTATT
Found at i:24465398 original size:11 final size:11
Alignment explanation
Indices: 24465382--24465442 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
24465372 AATCAAAGAA
24465382 GAAAAAGAAAG
1 GAAAAAGAAAG
24465393 GAAAAACAAGAAA-
1 G--AAA-AAGAAAG
24465406 GAAAAAGAAA-
1 GAAAAAGAAAG
24465416 GAGAAAAGAAATG
1 GA-AAAAGAAA-G
*
24465429 GAAAAGGAAAG
1 GAAAAAGAAAG
24465440 GAA
1 GAA
24465443 TACGTTAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 8 0.19
11 16 0.37
12 7 0.16
13 6 0.14
14 6 0.14
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (11 bp):
GAAAAAGAAAG
Found at i:24465413 original size:10 final size:10
Alignment explanation
Indices: 24465376--24465426 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
24465366 TAACGAAATC
24465376 AAAG-AAGAA
1 AAAGAAAGAA
24465385 AAAGAAAGGAAAA
1 AAAGAAA-G--AA
24465398 ACAAGAAAGAA
1 A-AAGAAAGAA
24465409 AAAGAAAGAGA
1 AAAGAAAGA-A
24465420 AAAGAAA
1 AAAGAAA
24465427 TGGAAAAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.11
10 10 0.28
11 12 0.33
13 4 0.11
14 6 0.17
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:24467800 original size:43 final size:43
Alignment explanation
Indices: 24467744--24467859 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
24467734 CGTGTATTAC
* * *
24467744 TTTCC-GTTTAGCTCTTACGAGCTTCTGTTTAACTCATAT-GAG
1 TTTCCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATAG-G
* *
24467786 TTTCCTGTTCAGCTCTTTCGAGCTTCTGTTCAACCCTTATAGG
1 TTTCCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATAGG
* *
24467829 TTT-CTGTTCAACTCTTACGAGCTACTGTTCA
1 TTTCCTGTTCAGCTCTTACGAGCTTCTGTTCA
24467860 GCTTTCAAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 30 0.47
43 33 0.52
44 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (43 bp):
TTTCCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCATATAGG
Found at i:24467816 original size:21 final size:21
Alignment explanation
Indices: 24467755--24467859 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
24467745 TTCCGTTTAG
* *
24467755 CTCTTACGAGCTTCTGTTTAA
1 CTCTTTCGAGCTTCTGTTCAA
* * *
24467776 CTCATAT-GAGTTTCCTGTTCAG
1 CTC-TTTCGAGCTT-CTGTTCAA
24467798 CTCTTTCGAGCTTCTGTTCAA
1 CTCTTTCGAGCTTCTGTTCAA
* * *
24467819 CCCTTATAG-GTTTCTGTTCAA
1 CTCTT-TCGAGCTTCTGTTCAA
* *
24467840 CTCTTACGAGCTACTGTTCA
1 CTCTTTCGAGCTTCTGTTCA
24467860 GCTTTCAAGC
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.02
21 45 0.71
22 17 0.27
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (21 bp):
CTCTTTCGAGCTTCTGTTCAA
Found at i:24469286 original size:43 final size:43
Alignment explanation
Indices: 24469211--24469340 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 43
24469201 TAGGATCTTC
* *
24469211 GATATGTGCTTT-CGTGTAAGACCACGTTTGGGACGTTGGCATT
1 GATATGTG-TTTACGTGTAAGACCACGTCTGGGACGTTGACATT
*
24469254 GACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGACATC
1 GA-TATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGACATT
* * * *
24469297 GATATGTGATTACATGTAAGACCACGTCTGAGACGTTGCCATT
1 GATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGACATT
24469340 G
1 G
24469341 TACGAGCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
42 6 0.08
43 63 0.88
44 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
GATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGACATT
Found at i:24473028 original size:9 final size:9
Alignment explanation
Indices: 24473002--24473105 Score: 65
Period size: 9 Copynumber: 11.7 Consensus size: 9
24472992 ATTTAAGATT
24473002 TTATT-TAA
1 TTATTATAA
24473010 GTTATATATAA
1 -TTAT-TATAA
*
24473021 ATATTAT-A
1 TTATTATAA
24473029 TGTA-TATAA
1 T-TATTATAA
24473038 TTATTATAA
1 TTATTATAA
*
24473047 TTATTAAACA
1 TTATTATA-A
**
24473057 TTATTATGG
1 TTATTATAA
24473066 TT-TTAT-A
1 TTATTATAA
*
24473073 TTATTATTA
1 TTATTATAA
* *
24473082 CTATTATTA
1 TTATTATAA
*
24473091 TTATTATTA
1 TTATTATAA
24473100 TTATTA
1 TTATTA
24473106 AATAAACCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
7 2 0.03
8 14 0.18
9 48 0.62
10 11 0.14
11 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (9 bp):
TTATTATAA
Found at i:24473052 original size:3 final size:3
Alignment explanation
Indices: 24473037--24473105 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
24473027 TATGTATATA
* ** * *
24473037 ATT ATT ATA ATT ATT AAAC ATT ATT ATG GTT -TT AT- ATT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
24473081 ACT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
24473106 AATAAACCAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 4 0.08
3 47 0.90
4 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:24478861 original size:56 final size:56
Alignment explanation
Indices: 24478775--24478888 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
24478765 TCATATCTCT
*
24478775 AAAAAAACTCCTTCCATATTATTATGGAATTAGTTATCCATTTTGACTTAAATTTC
1 AAAAAAACTCCTTCCATATCATTATGGAATTAGTTATCCATTTTGACTTAAATTTC
24478831 AAAAAAACTCCTTCCATATCATTATGGAATTAGTTATCCATTTTGACTTAAATTTC
1 AAAAAAACTCCTTCCATATCATTATGGAATTAGTTATCCATTTTGACTTAAATTTC
24478887 AA
1 AA
24478889 GTGCATGTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (56 bp):
AAAAAAACTCCTTCCATATCATTATGGAATTAGTTATCCATTTTGACTTAAATTTC
Found at i:24481813 original size:5 final size:6
Alignment explanation
Indices: 24481790--24481822 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
24481780 TTACCTCTTC
*
24481790 TTTTAA TTTTAA TTTTAA -TTTAA TTTTAC TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
24481823 TTAAATCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:24481813 original size:11 final size:12
Alignment explanation
Indices: 24481790--24481822 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
24481780 TTACCTCTTC
24481790 TTTTAATTTTAA
1 TTTTAATTTTAA
24481802 TTTTAA-TTTAA
1 TTTTAATTTTAA
*
24481813 TTTTACTTTT
1 TTTTAATTTT
24481823 TTAAATCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:24484126 original size:13 final size:13
Alignment explanation
Indices: 24484108--24484132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24484098 TTCTATTTTT
24484108 TCTCTATTTAAAC
1 TCTCTATTTAAAC
24484121 TCTCTATTTAAA
1 TCTCTATTTAAA
24484133 TTATATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTCTATTTAAAC
Found at i:24486084 original size:24 final size:24
Alignment explanation
Indices: 24486057--24486102 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24486047 ATTATTCATT
*
24486057 ATATTATTGAATTTTTTATTTTAA
1 ATATTATTGAATTATTTATTTTAA
* *
24486081 ATATTTTTTAATTATTTATTTT
1 ATATTATTGAATTATTTATTTT
24486103 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATTATTGAATTATTTATTTTAA
Found at i:24487293 original size:14 final size:15
Alignment explanation
Indices: 24487264--24487296 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
24487254 TATTCGTGTA
*
24487264 TTAAATATTTTTTTT
1 TTAAATATTTTATTT
24487279 TTAAAT-TTTTATTT
1 TTAAATATTTTATTT
24487293 TTAA
1 TTAA
24487297 TCTACCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAAATATTTTATTT
Found at i:24487343 original size:2 final size:2
Alignment explanation
Indices: 24487336--24487365 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24487326 CACTTTGGAA
24487336 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
24487366 CTCCAAATAC
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:24487507 original size:31 final size:31
Alignment explanation
Indices: 24487471--24487532 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24487461 ATAATCATTG
*
24487471 AATTATTCGAAAGTTGTCATTTAAGTCACTA
1 AATTATTCGAAAGTTGTCAGTTAAGTCACTA
* * *
24487502 AATTATTTGAAAGTTTTTAGTTAAGTCACTA
1 AATTATTCGAAAGTTGTCAGTTAAGTCACTA
24487533 GACTATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (31 bp):
AATTATTCGAAAGTTGTCAGTTAAGTCACTA
Found at i:24489377 original size:42 final size:42
Alignment explanation
Indices: 24489324--24489404 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
24489314 TAATTTTATA
*
24489324 TATATGTTGATGACAGTCTACTCATTGGGAATGATGTAATTT
1 TATATGTTGATGAAAGTCTACTCATTGGGAATGATGTAATTT
*
24489366 TATATGTTGATGAAATTCTACTCATTGGGAATGATGTAA
1 TATATGTTGATGAAAGTCTACTCATTGGGAATGATGTAA
24489405 GGACATTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (42 bp):
TATATGTTGATGAAAGTCTACTCATTGGGAATGATGTAATTT
Found at i:24498857 original size:12 final size:12
Alignment explanation
Indices: 24498840--24498864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24498830 ACCAGTCTCT
24498840 TTCTTCTTTTTC
1 TTCTTCTTTTTC
24498852 TTCTTCTTTTTC
1 TTCTTCTTTTTC
24498864 T
1 T
24498865 CCACCAAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:24502765 original size:20 final size:20
Alignment explanation
Indices: 24502740--24502784 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
24502730 ATTTAATGAC
* *
24502740 TTAATGGCTTTTCCATGCAT
1 TTAATGGATTTTCCATACAT
* *
24502760 TTAATGTATTTTCCCTACAT
1 TTAATGGATTTTCCATACAT
24502780 TTAAT
1 TTAAT
24502785 TTTTTTTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (20 bp):
TTAATGGATTTTCCATACAT
Found at i:24502791 original size:20 final size:20
Alignment explanation
Indices: 24502757--24502804 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
24502747 CTTTTCCATG
24502757 CATTTAATGTATTTTCCCTA
1 CATTTAATGTATTTTCCCTA
* * *
24502777 CATTTAATTTTTTTTCTCTA
1 CATTTAATGTATTTTCCCTA
24502797 CATTTAAT
1 CATTTAAT
24502805 CCTTAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.02, T:0.56
Consensus pattern (20 bp):
CATTTAATGTATTTTCCCTA
Found at i:24505956 original size:23 final size:23
Alignment explanation
Indices: 24505930--24506120 Score: 274
Period size: 23 Copynumber: 8.3 Consensus size: 23
24505920 ATAAGTGCCA
24505930 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
24505953 CACTAATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
24505976 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
** *
24505999 CACTGATATGTATTCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
24506022 CACTGAAATGTATCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
24506045 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
24506068 CACTGATATGTAGCCAAAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
24506091 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
24506114 CACTGAT
1 CACTGAT
24506121 CAATAACACT
Statistics
Matches: 149, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 149 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:24509955 original size:31 final size:32
Alignment explanation
Indices: 24509911--24509973 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
24509901 TTCCTAAAAG
*
24509911 AAAAGTTACCAAGCCACAAACCAA-AAATAATT
1 AAAAATTACCAAGCCA-AAACCAATAAATAATT
24509943 AAAAATTA-CAAGCCAAAACCAATAAATAATT
1 AAAAATTACCAAGCCAAAACCAATAAATAATT
24509974 CATAATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 15 0.52
32 7 0.24
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.17
Consensus pattern (32 bp):
AAAAATTACCAAGCCAAAACCAATAAATAATT
Found at i:24511845 original size:21 final size:21
Alignment explanation
Indices: 24511787--24511845 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
24511777 CAAGGCTAAT
*
24511787 TTAAAAATGATTTAAAGATCCA
1 TTAAAAAT-ATTTAAAAATCCA
**
24511809 TTAAAAATATGGAAAAATACC-
1 TTAAAAATATTTAAAAAT-CCA
*
24511830 TTTAAAATATTTAAAA
1 TTAAAAATATTTAAAA
24511846 TTCTCATAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
TTAAAAATATTTAAAAATCCA
Found at i:24533828 original size:50 final size:50
Alignment explanation
Indices: 24533720--24533966 Score: 217
Period size: 50 Copynumber: 4.8 Consensus size: 50
24533710 ATTTGGGTAA
* * *
24533720 AGAGATCCCATGTAAGACCATGTCTCGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATG
* **
24533776 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * *
24533826 AGAGGTCCCGCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * * * * *
24533876 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCAGT-ACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* ** * *
24533925 AAACATCCCATGTAAGACCATGTGTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
24533967 TGTTATTATC
Statistics
Matches: 157, Mismatches: 34, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
49 37 0.24
50 79 0.50
53 4 0.03
55 1 0.01
56 36 0.23
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:24537965 original size:19 final size:18
Alignment explanation
Indices: 24537924--24537971 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
24537914 CATTTCAAAT
24537924 TAATT-TTTCTAAAAATAA
1 TAATTATTT-TAAAAATAA
24537942 T-ATTATTTTAAAAATTAA
1 TAATTATTTTAAAAA-TAA
*
24537960 TAATTAATTTAA
1 TAATTATTTTAA
24537972 TTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTATTTTAAAAATAA
Found at i:24538794 original size:21 final size:21
Alignment explanation
Indices: 24538764--24538806 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
24538754 TACACATAAA
* *
24538764 TTAATTTTTATAATTTAACTT
1 TTAATATTTATAATATAACTT
24538785 TTAATATTTATAATATAACTT
1 TTAATATTTATAATATAACTT
24538806 T
1 T
24538807 AGAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATATTTATAATATAACTT
Found at i:24539891 original size:21 final size:21
Alignment explanation
Indices: 24539865--24539920 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
24539855 AACAGCGGTG
*
24539865 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
24539886 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
24539907 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
24539921 AACAATAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:24540177 original size:20 final size:20
Alignment explanation
Indices: 24540140--24540178 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24540130 TTTAATAAAC
* * *
24540140 TATATAATCAATTTAAATTA
1 TATATAATAAAATAAAATTA
24540160 TATATAATAAAATAAAATT
1 TATATAATAAAATAAAATT
24540179 TTATCTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAATAAAATAAAATTA
Found at i:24540218 original size:24 final size:25
Alignment explanation
Indices: 24540167--24540218 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
24540157 TTATATATAA
* *
24540167 TAAAATAAAATTTTATCTAATTTTT
1 TAAAATAAAATTGTATCTAATTTAT
* *
24540192 TAAAATAAAGTTGTA-CTTATTTAT
1 TAAAATAAAATTGTATCTAATTTAT
24540216 TAA
1 TAA
24540219 CTATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAAATAAAATTGTATCTAATTTAT
Found at i:24540342 original size:15 final size:16
Alignment explanation
Indices: 24540310--24540352 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
24540300 TATATTTATT
24540310 AAATTATATAAAATTAA
1 AAATTAT-TAAAATTAA
*
24540327 ATATTATTAAAA-TAA
1 AAATTATTAAAATTAA
24540342 AAATTATTAAA
1 AAATTATTAAA
24540353 TAAGTATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 5 0.21
17 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTATTAAAATTAA
Done.