Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 15 of 20
Found at i:6098305 original size:13 final size:13
Alignment explanation
Indices: 6098273--6098333 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
6098263 TTCAAGTTTA
* *
6098273 AAATTTAACATTCA
1 AAATTTAAGATT-T
*
6098287 AAATTTAAGTTTT
1 AAATTTAAGATTT
6098300 AAATTTAAGATTT
1 AAATTTAAGATTT
* *
6098313 ATAATATAAGAGTT
1 A-AATTTAAGATTT
6098327 AAGATTT
1 AA-ATTT
6098334 TTTGTTGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 14 0.37
14 24 0.63
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (13 bp):
AAATTTAAGATTT
Found at i:6098322 original size:27 final size:27
Alignment explanation
Indices: 6098266--6098322 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6098256 TATTTATTTC
*
6098266 AAGTTTAAAATTTAACATTCAAAATTT
1 AAGTTTAAAATTTAACATTCAAAATAT
* * * *
6098293 AAGTTTTAAATTTAAGATTTATAATAT
1 AAGTTTAAAATTTAACATTCAAAATAT
6098320 AAG
1 AAG
6098323 AGTTAAGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (27 bp):
AAGTTTAAAATTTAACATTCAAAATAT
Found at i:6103181 original size:15 final size:15
Alignment explanation
Indices: 6103161--6103195 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6103151 ACCTGAAATG
6103161 CCACCTCCACCTCCA
1 CCACCTCCACCTCCA
* *
6103176 CCACCTCTATCTCCA
1 CCACCTCCACCTCCA
6103191 CCACC
1 CCACC
6103196 ATTGCCACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.63, G:0.00, T:0.17
Consensus pattern (15 bp):
CCACCTCCACCTCCA
Found at i:6105761 original size:42 final size:42
Alignment explanation
Indices: 6105711--6105794 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
6105701 AAGTATAAAA
*
6105711 AATGT-TTAAAAT-TATAAAATTAAATATTTATTAATAGATG
1 AATGTATTTAAATATATAAAATTAAATATTTATTAATAGATG
*
6105751 AATGTATTTAATTATATAAAATTAAATATTTATTAATAGATG
1 AATGTATTTAAATATATAAAATTAAATATTTATTAATAGATG
6105793 AA
1 AA
6105795 AATATCTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 5 0.12
41 5 0.12
42 30 0.75
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (42 bp):
AATGTATTTAAATATATAAAATTAAATATTTATTAATAGATG
Found at i:6105799 original size:20 final size:20
Alignment explanation
Indices: 6105732--6105804 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
6105722 TTATAAAATT
6105732 AAATATTTATTAATAGATGA
1 AAATATTTATTAATAGATGA
** * *
6105752 ATGTATTTAATTATATAAAAT-T
1 AAATATTT-ATTA-AT-AGATGA
6105774 AAATATTTATTAATAGATGA
1 AAATATTTATTAATAGATGA
*
6105794 AAATATCTATT
1 AAATATTTATT
6105805 TATATATTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.08
20 18 0.45
21 8 0.20
22 8 0.20
23 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (20 bp):
AAATATTTATTAATAGATGA
Found at i:6105808 original size:42 final size:42
Alignment explanation
Indices: 6105723--6105810 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
6105713 TGTTTAAAAT
** *
6105723 TATAAAATTAAATATTTATTAATAGATGAATGTATTTAATTA
1 TATAAAATTAAATATTTATTAATAGATGAAAATATCTAATTA
*
6105765 TATAAAATTAAATATTTATTAATAGATGAAAATATCTATTTA
1 TATAAAATTAAATATTTATTAATAGATGAAAATATCTAATTA
6105807 TATA
1 TATA
6105811 TTACGTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (42 bp):
TATAAAATTAAATATTTATTAATAGATGAAAATATCTAATTA
Found at i:6105953 original size:17 final size:18
Alignment explanation
Indices: 6105928--6105968 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6105918 ATAATTAATA
*
6105928 TAAAATATTT-TATTATT
1 TAAAATATTTAAATTATT
*
6105945 TAAATTATTTAAATTATT
1 TAAAATATTTAAATTATT
6105963 TAAAAT
1 TAAAAT
6105969 TAAAAAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAATATTTAAATTATT
Found at i:6105970 original size:10 final size:9
Alignment explanation
Indices: 6105939--6105966 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6105929 AAAATATTTT
6105939 ATTATTTAA
1 ATTATTTAA
6105948 ATTATTTAA
1 ATTATTTAA
6105957 ATTATTTAA
1 ATTATTTAA
6105966 A
1 A
6105967 ATTAAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTATTTAA
Found at i:6105990 original size:17 final size:19
Alignment explanation
Indices: 6105968--6106007 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
6105958 TTATTTAAAA
6105968 TTAAAAAGT-TAAATTT-T
1 TTAAAAAGTATAAATTTAT
*
6105985 TTAAAAATTATAAATTTAT
1 TTAAAAAGTATAAATTTAT
6106004 TTAA
1 TTAA
6106008 TATATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TTAAAAAGTATAAATTTAT
Found at i:6117688 original size:39 final size:39
Alignment explanation
Indices: 6117634--6117711 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
6117624 GAAGAAACAG
6117634 CTTCATCAAGATTTGTTGTGTTGTCCAAAAATAGTGTAA
1 CTTCATCAAGATTTGTTGTGTTGTCCAAAAATAGTGTAA
6117673 CTTCATCAAGATTTGTTGTGTTGTCCAAAAATAGTGTAA
1 CTTCATCAAGATTTGTTGTGTTGTCCAAAAATAGTGTAA
6117712 GGAAAAAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (39 bp):
CTTCATCAAGATTTGTTGTGTTGTCCAAAAATAGTGTAA
Found at i:6149638 original size:31 final size:30
Alignment explanation
Indices: 6149580--6149640 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
6149570 TGTTAGTAAT
* *
6149580 TAAAAATAAATATAATTTACTATTTAATTA
1 TAAAAATAAAAATAATATACTATTTAATTA
*
6149610 TAAAAATAAAAATAAATATATTATTTAATTA
1 TAAAAATAAAAAT-AATATACTATTTAATTA
6149641 AGTACTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAAATAAAAATAATATACTATTTAATTA
Found at i:6179591 original size:13 final size:13
Alignment explanation
Indices: 6179573--6179597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6179563 TCTATCATTC
6179573 TTTTTATTTTTTA
1 TTTTTATTTTTTA
6179586 TTTTTATTTTTT
1 TTTTTATTTTTT
6179598 TTGAAATTTC
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:6191948 original size:15 final size:16
Alignment explanation
Indices: 6191909--6191950 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6191899 GAAGGTCGGG
6191909 AAGAAGAAGAAATGGAA
1 AAGAAGAA-AAATGGAA
*
6191926 AAGCAAGAAAAA-GGAC
1 AAG-AAGAAAAATGGAA
6191942 AAGAAGAAA
1 AAGAAGAAA
6191951 CAGAAAGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 6 0.26
17 6 0.26
18 5 0.22
ACGTcount: A:0.67, C:0.05, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAAATGGAA
Found at i:6198942 original size:261 final size:262
Alignment explanation
Indices: 6198452--6198943 Score: 606
Period size: 261 Copynumber: 1.9 Consensus size: 262
6198442 AATTTAATAA
* * *
6198452 TTTAAGATAATTTATTTTTTAATTAATTAAAGTTTATTTGGAATATAATTTTGTTATGTTACATG
1 TTTAAGATAATTTATTTTTTAATTAATTAAAGTTAATTTGGAAAATAATTTTGTTATATTACATG
*
6198517 TTTCTAATTTTGTTTTGTCCTAATTTACATCCATTAATATCTACTTGAAATTTAGTTTATTTTTC
66 TTTCTAATTTTGTTTTGTCCTAATTTACATCCATTAACATCTACTTGAAATTTAGTTTATTTTTC
* * *
6198582 TTATTTTAAACTTTAAAAAAGTGTAAAAAGTAAAGCTTTAATGAATATTGCAAATGTATTTTTTT
131 TTATTTTAAACTTTAAAAAAGCGTAAAAAGTAAAGCTTTAATAAATATTACAAATGTATTTTTTT
* * * *
6198647 TCTATACTTGGCATTTTCAATTATTAAGGTTAGTTTTGTTGCAAACATTAACTAAGAAGTTTAAT
196 ACTATACTTAGCATTTTCAATGATTAAAGTTAGTTTTGTTGCAAACATTAACTAAGAAGTTTAAT
6198712 GT
261 GT
* *
6198714 TTTAGGATAGTTTATTTTTTAATTAATT-AAGATTAATTTGGAAAAT-ATTTTGTTGA-ATTACA
1 TTTAAGATAATTTATTTTTTAATTAATTAAAG-TTAATTTGGAAAATAATTTTGTT-ATATTACA
* * ** ** *
6198776 TGTTTCTAATTTTGTTTTGTTCTAGTTTAGGTTTATTAACATCTAATTATTTGAGAGATTTAG-T
64 TGTTTCTAATTTTGTTTTGTCCTAATTTACATCCATTAACATC----TACTTGA-A-ATTTAGTT
* * * *
6198840 T-TTTTT-TTGTTTTGATCTTT-AAACAGCGT-AAAAGTAAAGCTTTAATAAATATTACAAATG-
123 TATTTTTCTTATTTTAAACTTTAAAAAAGCGTAAAAAGTAAAGCTTTAATAAATATTACAAATGT
* * *
6198900 ATTTTTTTACTATTCTTAGCTTTTTGAATGATTAAAGTTAGTTT
188 ATTTTTTTACTATACTTAGCATTTTCAATGATTAAAGTTAGTTT
6198944 ATATTTGTGT
Statistics
Matches: 195, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
261 89 0.46
262 68 0.35
263 7 0.04
264 11 0.06
265 11 0.06
266 3 0.02
267 6 0.03
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.50
Consensus pattern (262 bp):
TTTAAGATAATTTATTTTTTAATTAATTAAAGTTAATTTGGAAAATAATTTTGTTATATTACATG
TTTCTAATTTTGTTTTGTCCTAATTTACATCCATTAACATCTACTTGAAATTTAGTTTATTTTTC
TTATTTTAAACTTTAAAAAAGCGTAAAAAGTAAAGCTTTAATAAATATTACAAATGTATTTTTTT
ACTATACTTAGCATTTTCAATGATTAAAGTTAGTTTTGTTGCAAACATTAACTAAGAAGTTTAAT
GT
Found at i:6209146 original size:2 final size:2
Alignment explanation
Indices: 6209139--6209167 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6209129 AGAGATTATG
6209139 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6209168 GACTGGGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6228730 original size:2 final size:2
Alignment explanation
Indices: 6228723--6228752 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6228713 CGGTATGAAA
6228723 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
6228753 TTTAGGTTTA
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:6239614 original size:2 final size:2
Alignment explanation
Indices: 6239607--6239639 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6239597 TTTCAGGGTC
6239607 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
6239640 CTGGTCATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6240045 original size:16 final size:17
Alignment explanation
Indices: 6240024--6240058 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6240014 CTCATCCCGG
6240024 TTTTTCT-TTCCTTTTT
1 TTTTTCTCTTCCTTTTT
*
6240040 TTTTTCTCTTTCTTTTT
1 TTTTTCTCTTCCTTTTT
6240057 TT
1 TT
6240059 GGATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTCTTCCTTTTT
Found at i:6240705 original size:16 final size:18
Alignment explanation
Indices: 6240684--6240722 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6240674 CTTATATTTT
6240684 ATTTTA-AATTAA-ATTA
1 ATTTTATAATTAATATTA
6240700 ATTTTATAATTAATTATTA
1 ATTTTATAATTAA-TATTA
6240719 ATTT
1 ATTT
6240723 AATCAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
19 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTATAATTAATATTA
Found at i:6240969 original size:21 final size:21
Alignment explanation
Indices: 6240945--6240993 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 21
6240935 AAATTTATTT
6240945 AATTTAAAATAAAAATATAA-A
1 AATTTAAAAT-AAAATATAATA
6240966 AATTT--AATAAAATATAATA
1 AATTTAAAATAAAATATAATA
*
6240985 AATGTAAAA
1 AATTTAAAA
6240994 ATTTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
21 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTTAAAATAAAATATAATA
Found at i:6241005 original size:27 final size:26
Alignment explanation
Indices: 6240941--6241006 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
6240931 ATAAAAATTT
6240941 ATTTAATTTAAA-ATAAAAATATAAAA
1 ATTT-ATTTAAATATAAAAATATAAAA
* * *
6240967 ATTTAATAAAATATAATAAATGTAAAA
1 ATTTATTTAAATATAA-AAATATAAAA
6240994 ATTTATTTAAATA
1 ATTTATTTAAATA
6241007 ATTTAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 5 0.15
26 8 0.24
27 20 0.61
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTTATTTAAATATAAAAATATAAAA
Found at i:6241016 original size:20 final size:21
Alignment explanation
Indices: 6240989--6241029 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6240979 ATAATAAATG
*
6240989 TAAAAATTTATTTAAATAATT
1 TAAAATTTTATTTAAATAATT
*
6241010 TAAAATTTTATTTGAATAAT
1 TAAAATTTTATTTAAATAAT
6241030 AATACCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAAATTTTATTTAAATAATT
Found at i:6246833 original size:2 final size:2
Alignment explanation
Indices: 6246828--6246852 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6246818 TTCTATAGAT
6246828 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
6246853 TAACCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6255675 original size:18 final size:15
Alignment explanation
Indices: 6255633--6255677 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
6255623 AAATAATAAA
6255633 TATTATATTAATTAAT
1 TATTAT-TTAATTAAT
6255649 TATTA-TTAATTAAT
1 TATTATTTAATTAAT
*
6255663 TA-TATTTATTTAAT
1 TATTATTTAATTAAT
6255677 T
1 T
6255678 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 20 0.74
16 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTTAATTAAT
Found at i:6255698 original size:21 final size:21
Alignment explanation
Indices: 6255674--6255725 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
6255664 ATATTTATTT
*
6255674 AATTTAAAATAAAAATATAAA
1 AATTTAAAATAAAAATAAAAA
* *
6255695 AATTT-AATTAAACATAAAAA
1 AATTTAAAATAAAAATAAAAA
6255715 AATTTTAAAAT
1 AA-TTTAAAAT
6255726 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 14 0.56
21 8 0.32
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAAATAAAAATAAAAA
Found at i:6267511 original size:22 final size:22
Alignment explanation
Indices: 6267467--6267512 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6267457 AGAGATTGAG
* *
6267467 AATTTAAGTTTTATAAAACTTT
1 AATTTAAATTTTATAAAAATTT
6267489 AATTTAAATTTT-TAAGAAATTT
1 AATTTAAATTTTATAA-AAATTT
6267511 AA
1 AA
6267513 AAATGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTTAAATTTTATAAAAATTT
Found at i:6267680 original size:16 final size:15
Alignment explanation
Indices: 6267659--6267691 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
6267649 ACTCTTGAAT
6267659 ATCTATTGATAGTATA
1 ATCTATTGATAG-ATA
6267675 ATCTATTGATAGATA
1 ATCTATTGATAGATA
6267690 AT
1 AT
6267692 ATGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (15 bp):
ATCTATTGATAGATA
Found at i:6267811 original size:37 final size:39
Alignment explanation
Indices: 6267769--6267843 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
6267759 TTAAAGTTGA
*
6267769 AAATAAATAGT-TAATAATATTATA-T-TTTTTAATATTT
1 AAATAAATAATATAA-AATATTATATTATTTTTAATATTT
*
6267806 AAATAATTAATATAAAATATTATATTATTTTTAATATT
1 AAATAAATAATATAAAATATTATATTATTTTTAATATT
6267844 ATTATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 18 0.55
38 4 0.12
39 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (39 bp):
AAATAAATAATATAAAATATTATATTATTTTTAATATTT
Found at i:6281789 original size:16 final size:16
Alignment explanation
Indices: 6281764--6281799 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6281754 ATTTGTTCGA
6281764 TTAATATTTTTAATTT
1 TTAATATTTTTAATTT
* *
6281780 TTAATTTTTTTATTTT
1 TTAATATTTTTAATTT
6281796 TTAA
1 TTAA
6281800 ATATCTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATATTTTTAATTT
Found at i:6285979 original size:63 final size:63
Alignment explanation
Indices: 6285872--6286056 Score: 275
Period size: 63 Copynumber: 3.0 Consensus size: 63
6285862 TAGCACAGTT
* * * *
6285872 TTGTAATGGGTCCGCCCCGA-TGGTGCAT-TAAGTGCAGCATTTTCTTCATTTATCAAAAAGTC
1 TTGTAATGGGTCAGCACC-ATTGGTGCCTCTTAGTGCAGCATTTTCTTCATTTATCAAAAAGTC
* *
6285934 TTGTAATGGTTCAGCACCATTGGTGCCTCTTAGTGCAGCATTTTCTTCATTTATCAAAATGTC
1 TTGTAATGGGTCAGCACCATTGGTGCCTCTTAGTGCAGCATTTTCTTCATTTATCAAAAAGTC
* *
6285997 TTGTAATGGGTCAGCACCATTGGTGTCTCTTAGTGCAGCATTTTCTTCATTTGTCAAAAA
1 TTGTAATGGGTCAGCACCATTGGTGCCTCTTAGTGCAGCATTTTCTTCATTTATCAAAAA
6286057 TAATAATAGC
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
61 1 0.01
62 22 0.20
63 88 0.79
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (63 bp):
TTGTAATGGGTCAGCACCATTGGTGCCTCTTAGTGCAGCATTTTCTTCATTTATCAAAAAGTC
Found at i:6315426 original size:24 final size:24
Alignment explanation
Indices: 6315395--6315459 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
6315385 CATTTTAATG
*
6315395 ATAAAATTATTACATATAAAT-ATA
1 ATAAAATTATTA-ATATAAATCAAA
6315419 ATAAAATT-TTATATATAAATCAAA
1 ATAAAATTATTA-ATATAAATCAAA
*
6315443 ATAAATTTA-TAATATAA
1 ATAAAATTATTAATATAA
6315460 GATTGTAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAATTATTAATATAAATCAAA
Found at i:6315438 original size:23 final size:24
Alignment explanation
Indices: 6315395--6315459 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
6315385 CATTTTAATG
* *
6315395 ATAAAATTATTACATATAAAT-ATA
1 ATAAAATT-TTATATATAAATCAAA
6315419 ATAAAATTTTATATATAAATCAAA
1 ATAAAATTTTATATATAAATCAAA
6315443 AT-AAA-TTTATAATATAA
1 ATAAAATTTTAT-ATATAA
6315460 GATTGTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 5 0.14
23 20 0.54
24 12 0.32
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAATTTTATATATAAATCAAA
Found at i:6315833 original size:2 final size:2
Alignment explanation
Indices: 6315793--6315818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6315783 AATCAATTAA
6315793 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
6315819 GTAGTGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6317426 original size:2 final size:2
Alignment explanation
Indices: 6317419--6317446 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6317409 CTGATTCAAT
6317419 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
6317447 AGGCACGACT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6330053 original size:2 final size:2
Alignment explanation
Indices: 6330039--6330071 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
6330029 AAAATAATTG
6330039 GA GA GA CGA -A GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA G
6330072 GCAATGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6338430 original size:2 final size:2
Alignment explanation
Indices: 6338423--6338454 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6338413 GAGGTTACAC
6338423 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
6338455 TTGACTCAGC
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:6355909 original size:2 final size:2
Alignment explanation
Indices: 6355897--6355934 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
6355887 TGTTCTCTTT
* *
6355897 AG AG CG AG AG AG AC AG AG AG AG AG AG AG A- AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6355935 TTGCATAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.05, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6358373 original size:6 final size:7
Alignment explanation
Indices: 6358355--6358382 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
6358345 TCATGTGCTG
6358355 ATTTTTT
1 ATTTTTT
6358362 ATTTTTT
1 ATTTTTT
6358369 ATTTTTT
1 ATTTTTT
6358376 ATTTTTT
1 ATTTTTT
6358383 GGATAGGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:6383190 original size:18 final size:18
Alignment explanation
Indices: 6383167--6383204 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6383157 ACTTAACCAT
*
6383167 TAATAATCAA-AATATTTA
1 TAATAAACAATAAT-TTTA
6383185 TAATAAACAATAATTTTA
1 TAATAAACAATAATTTTA
6383203 TA
1 TA
6383205 TAACATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAAACAATAATTTTA
Found at i:6392327 original size:16 final size:16
Alignment explanation
Indices: 6392306--6392340 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6392296 GCTGACATGG
*
6392306 AATTATTGCTAAGGGT
1 AATTATTGCTAAAGGT
6392322 AATTATTGCTAAAGGT
1 AATTATTGCTAAAGGT
6392338 AAT
1 AAT
6392341 ATATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
AATTATTGCTAAAGGT
Found at i:6402981 original size:11 final size:11
Alignment explanation
Indices: 6402956--6402993 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
6402946 TTATTTCCTC
6402956 GAAAAA-AAAA
1 GAAAAAGAAAA
6402966 -AAAAAGGAAAA
1 GAAAAA-GAAAA
6402977 GAAAAAGAAAA
1 GAAAAAGAAAA
6402988 GAAAAA
1 GAAAAA
6402994 TCCGAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:6411640 original size:36 final size:36
Alignment explanation
Indices: 6411588--6411675 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
6411578 ATTTCTAGTT
*
6411588 CTAGTCTTGTAGCTCCAACACAAGCTGAAATGCCTA
1 CTAGCCTTGTAGCTCCAACACAAGCTGAAATGCCTA
6411624 CTAGCCTTGTAGCTCCAACACAAGCTGAAATGCCTA
1 CTAGCCTTGTAGCTCCAACACAAGCTGAAATGCCTA
6411660 CTAGCCTTGTAGCTCC
1 CTAGCCTTGTAGCTCC
6411676 GTTGGTATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (36 bp):
CTAGCCTTGTAGCTCCAACACAAGCTGAAATGCCTA
Found at i:6418966 original size:31 final size:30
Alignment explanation
Indices: 6418906--6418971 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
6418896 CCCACGTGAC
* *
6418906 AAACTTAGAGGTTTTTTACCTAAAAAAAAAA
1 AAACTTAGAGGTTTTGTA-CAAAAAAAAAAA
*
6418937 AAACTTAGAGGTTTTGTAAAAAATGAAAAAAA
1 AAACTTAGAGGTTTTGTACAAAA--AAAAAAA
6418969 AAA
1 AAA
6418972 GGGTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 3 0.10
31 17 0.57
32 10 0.33
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (30 bp):
AAACTTAGAGGTTTTGTACAAAAAAAAAAA
Found at i:6431470 original size:133 final size:131
Alignment explanation
Indices: 6431305--6431570 Score: 433
Period size: 133 Copynumber: 2.0 Consensus size: 131
6431295 CTTTCTCTTC
* *
6431305 ATCGGTTTCTTCTCTCTGTTCTCTCTCTAGGGTTTAGCAGAGAGGATAGATTAATGGTCTGTAAT
1 ATCGGTTTCTTCTCTCTGTTCTCTCTCTAGGGTTTAGCACAGAGGATAGATTAATGGGCTGTAAT
* * * *
6431370 TGGATCTTTTGGGCCTAATTCAACCGAAGGAGTCTGGGTTTAATTGGGCTTTTTTGGGTCGGAAA
66 TGGATCTTTTGGGCCTAATTCAACAGAAAGAATCTGGGTTTAATTGGGCTATTTTGGGTCGGAAA
6431435 A
131 A
* *
6431436 ATCGGTTTCTTCTCTCTTTTATCTCTCTCTAGGGTTTAGCACAGAGGATCGATTAATGGGCTGTA
1 ATCGGTTTCTTCTCTC-TGT-TCTCTCTCTAGGGTTTAGCACAGAGGATAGATTAATGGGCTGTA
*
6431501 ATTGGATCTTTTGGGCCTAGTTCAACAGAAAGAATCTGGGTTTAATTGGGCTATTTTGGGTCGGA
64 ATTGGATCTTTTGGGCCTAATTCAACAGAAAGAATCTGGGTTTAATTGGGCTATTTTGGGTCGGA
6431566 AAA
129 AAA
6431569 AT
1 AT
6431571 TGAGAAAACG
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 16 0.13
132 2 0.02
133 106 0.85
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (131 bp):
ATCGGTTTCTTCTCTCTGTTCTCTCTCTAGGGTTTAGCACAGAGGATAGATTAATGGGCTGTAAT
TGGATCTTTTGGGCCTAATTCAACAGAAAGAATCTGGGTTTAATTGGGCTATTTTGGGTCGGAAA
A
Found at i:6432427 original size:2 final size:2
Alignment explanation
Indices: 6432420--6432450 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6432410 TGCATTTTAA
6432420 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 A
6432451 ACCAAGACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6446697 original size:32 final size:32
Alignment explanation
Indices: 6446650--6446711 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
6446640 ACATGATTTT
*
6446650 GTGTTTGGGACGAAGATAATATCTATAAAATA
1 GTGTTTGGGACGAAGAAAATATCTATAAAATA
**
6446682 GTGTTTGGGGTGAAGAAAATATCTATAAAA
1 GTGTTTGGGACGAAGAAAATATCTATAAAA
6446712 GAGTCATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (32 bp):
GTGTTTGGGACGAAGAAAATATCTATAAAATA
Found at i:6450487 original size:26 final size:26
Alignment explanation
Indices: 6450434--6450489 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
6450424 TAGAACTGAC
**
6450434 CAAACTTAAAAGAAAATCAAACTGAT
1 CAAACTTAAAAGAAAATCAAACCAAT
* *
6450460 CAAACTTAAAAGAAGATGAAACCAAT
1 CAAACTTAAAAGAAAATCAAACCAAT
6450486 CAAA
1 CAAA
6450490 TATTAAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (26 bp):
CAAACTTAAAAGAAAATCAAACCAAT
Found at i:6453145 original size:72 final size:74
Alignment explanation
Indices: 6453029--6453164 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 74
6453019 TTCCATTTAA
* *
6453029 ACCATCGAAGTTAAGCTTAGGATAAAAAAAGGATATCAAATCTTGAACCTACGTCTATTTCTTAT
1 ACCATCGAAGTTAAACTTAAGATAAAAAAAGGATATCAAATCTTGAACCTACGTCTATTTCTTAT
6453094 TACCATTCC
66 TACCATTCC
* * * *
6453103 ACCATTGAAGTTAAACTTAAGA-AAAGAAA-GATATTAAATCTTGAACCTATGTCTATTTCTTA
1 ACCATCGAAGTTAAACTTAAGATAAAAAAAGGATATCAAATCTTGAACCTACGTCTATTTCTTA
6453165 CAAGGTGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 31 0.55
73 6 0.11
74 19 0.34
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (74 bp):
ACCATCGAAGTTAAACTTAAGATAAAAAAAGGATATCAAATCTTGAACCTACGTCTATTTCTTAT
TACCATTCC
Found at i:6453529 original size:2 final size:2
Alignment explanation
Indices: 6453522--6453559 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6453512 TCCACTTAAC
6453522 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
6453560 CCAAATGAAG
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:6457854 original size:24 final size:24
Alignment explanation
Indices: 6457820--6457865 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
6457810 GTTTGAAGAC
6457820 ATTAATGCCAAGCAATTAATATAA
1 ATTAATGCCAAGCAATTAATATAA
*
6457844 ATTAATTCCAAGCAATTAATAT
1 ATTAATGCCAAGCAATTAATAT
6457866 TTGTATGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTAATGCCAAGCAATTAATATAA
Found at i:6459522 original size:21 final size:21
Alignment explanation
Indices: 6459498--6459550 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
6459488 TCCAAAATTA
*
6459498 AAAATTTTTTACATATTATAT
1 AAAATTTTTTAAATATTATAT
* * *
6459519 AAAAATTTTTAAATTTTTTAT
1 AAAATTTTTTAAATATTATAT
6459540 -AAATTTTTTAA
1 AAAATTTTTTAA
6459551 TAGCCTCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATTTTTTAAATATTATAT
Found at i:6459684 original size:21 final size:18
Alignment explanation
Indices: 6459658--6459700 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
6459648 TTTTCTTTCA
6459658 ATTTATATGATTATAATTTTT
1 ATTTAT-TGATT-T-ATTTTT
*
6459679 ATTTATTTATTTATTTTT
1 ATTTATTGATTTATTTTT
6459697 ATTT
1 ATTT
6459701 TATTTACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 4 0.19
21 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTATTGATTTATTTTT
Found at i:6460805 original size:18 final size:18
Alignment explanation
Indices: 6460782--6460819 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6460772 GACTTCAAAA
6460782 TTATGAGACATTGAGCCT
1 TTATGAGACATTGAGCCT
6460800 TTATGAGACATTGAGCCT
1 TTATGAGACATTGAGCCT
6460818 TT
1 TT
6460820 GGTTTTGCTC
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:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (18 bp):
TTATGAGACATTGAGCCT
Found at i:6463500 original size:4 final size:4
Alignment explanation
Indices: 6463491--6463518 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6463481 GATAAATTAA
6463491 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
6463519 TTAATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:6463673 original size:19 final size:18
Alignment explanation
Indices: 6463646--6463705 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
6463636 GTACTTAAAG
*
6463646 TTAACTATTACTTTTTTAT
1 TTAAATATTACTTTTTT-T
6463665 TTAAATATTACGTTTTTTT
1 TTAAATATTAC-TTTTTTT
*
6463684 TCTAAAAATTA-TTTTTTT
1 T-TAAATATTACTTTTTTT
6463702 TTAA
1 TTAA
6463706 TTTTTATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 3 0.08
18 8 0.22
19 12 0.32
20 14 0.38
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTAAATATTACTTTTTTT
Found at i:6474634 original size:2 final size:2
Alignment explanation
Indices: 6474627--6474661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6474617 AAAATGATTG
6474627 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 A
6474662 GATCCAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6493339 original size:6 final size:6
Alignment explanation
Indices: 6493305--6493340 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
6493295 ACTACTACTG
6493305 CTACAA CTACAA CTACAA CTACAA CTACAA CTACAA
1 CTACAA CTACAA CTACAA CTACAA CTACAA CTACAA
6493341 ACACAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
CTACAA
Found at i:6502376 original size:27 final size:27
Alignment explanation
Indices: 6502352--6502409 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
6502342 GCATTTCTGT
*
6502352 GCTTGGAACACTCTGAACGCTTTCTAC
1 GCTTGGAACACCCTGAACGCTTTCTAC
* *
6502379 GCTTGGAATACCCTGAACGCTTTTTAC
1 GCTTGGAACACCCTGAACGCTTTCTAC
6502406 GCTT
1 GCTT
6502410 TAAACACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (27 bp):
GCTTGGAACACCCTGAACGCTTTCTAC
Found at i:6517037 original size:24 final size:24
Alignment explanation
Indices: 6517014--6517073 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 24
6517004 ATTAATTATA
6517014 AAAATTA-TAAATAAAAATAATAT
1 AAAATTATTAAATAAAAATAATAT
*
6517037 AAAATTATTAAATTAAAATTTAATATT
1 AAAATTATTAAA-TAAAA-ATAATA-T
*
6517064 AAATTTATTA
1 AAAATTATTA
6517074 TTTATAGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 7 0.23
24 4 0.13
25 5 0.16
26 5 0.16
27 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTATTAAATAAAAATAATAT
Found at i:6523177 original size:13 final size:13
Alignment explanation
Indices: 6523159--6523185 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6523149 GCAATGGCTT
6523159 ATACATGCACCTA
1 ATACATGCACCTA
6523172 ATACATGCACCTA
1 ATACATGCACCTA
6523185 A
1 A
6523186 AGAACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (13 bp):
ATACATGCACCTA
Found at i:6525494 original size:15 final size:16
Alignment explanation
Indices: 6525471--6525504 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6525461 AAATAAATTT
6525471 TTAATAATATTATTAA
1 TTAATAATATTATTAA
*
6525487 TTAA-AATATTATTTA
1 TTAATAATATTATTAA
6525502 TTA
1 TTA
6525505 TTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATAATATTATTAA
Found at i:6525563 original size:18 final size:17
Alignment explanation
Indices: 6525542--6525577 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6525532 AAGGAAATAT
6525542 TTTATAATAATATTATTA
1 TTTATAATAATA-TATTA
*
6525560 TTTATTATAATATATTA
1 TTTATAATAATATATTA
6525577 T
1 T
6525578 AATATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATAATAATATATTA
Found at i:6525565 original size:10 final size:10
Alignment explanation
Indices: 6525537--6525593 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
6525527 GAAATAAGGA
*
6525537 AATATTTTAT
1 AATATATTAT
6525547 AATAATATTAT
1 AAT-ATATTAT
* *
6525558 TATTTATTAT
1 AATATATTAT
6525568 AATATATTAT
1 AATATATTAT
6525578 AATAT-TATAT
1 AATATAT-TAT
6525588 AATATA
1 AATATA
6525594 AAATAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 1 0.03
10 30 0.77
11 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATATTAT
Found at i:6525583 original size:18 final size:18
Alignment explanation
Indices: 6525548--6525586 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6525538 ATATTTTATA
*
6525548 ATAATATTATTATTTATT
1 ATAATATTATTATATATT
6525566 ATAATA-TATTATAATATT
1 ATAATATTATTAT-ATATT
6525584 ATA
1 ATA
6525587 TAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATATTATTATATATT
Found at i:6525615 original size:25 final size:25
Alignment explanation
Indices: 6525576--6525649 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 25
6525566 ATAATATATT
*
6525576 ATAATATTATATAATATAAAATAATAA
1 ATAATATT-T-TAATATAAAAAAATAA
*
6525603 ATAATATTTTAAT-TAATAAAAATTA
1 ATAATATTTTAATATAA-AAAAATAA
* *
6525628 ATTATATATTAATCATAAAAAA
1 ATAATATTTTAAT-ATAAAAAA
6525650 TTTTTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.08
25 21 0.52
26 5 0.12
27 11 0.28
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATATTTTAATATAAAAAAATAA
Found at i:6531001 original size:23 final size:24
Alignment explanation
Indices: 6530962--6531006 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
6530952 TGATGTCATA
*
6530962 TTTTAAGAAAATTAATAATATTTG
1 TTTTAAGAAAATAAATAATATTTG
*
6530986 TTTTAA-AAAATAAATAGTATT
1 TTTTAAGAAAATAAATAATATT
6531007 AATTTTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (24 bp):
TTTTAAGAAAATAAATAATATTTG
Found at i:6531012 original size:23 final size:24
Alignment explanation
Indices: 6530961--6531012 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
6530951 CTGATGTCAT
* *
6530961 ATTTTAAGAAAATTAATAATATTT
1 ATTTTAAGAAAATAAATAATATTA
* *
6530985 GTTTTAA-AAAATAAATAGTATTA
1 ATTTTAAGAAAATAAATAATATTA
6531008 ATTTT
1 ATTTT
6531013 GAAGTCTGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTTTAAGAAAATAAATAATATTA
Found at i:6532021 original size:11 final size:10
Alignment explanation
Indices: 6532003--6532029 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6531993 GATTTAATTT
6532003 TTTTAAAAAA
1 TTTTAAAAAA
6532013 TTTTAAAAAA
1 TTTTAAAAAA
6532023 TTTTAAA
1 TTTTAAA
6532030 CGTTATGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:6548771 original size:38 final size:38
Alignment explanation
Indices: 6548715--6548790 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
6548705 GGTTTATTAC
*
6548715 TTTTCTAGTGATAAGTAATGAGTTATTATTCAATATTT
1 TTTTCTAGTGATAAGTAATGAGTTATCATTCAATATTT
* * *
6548753 TTTTCTAGTTATAGGTAATGAGTTATCATTTAATATTT
1 TTTTCTAGTGATAAGTAATGAGTTATCATTCAATATTT
6548791 AATATTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.51
Consensus pattern (38 bp):
TTTTCTAGTGATAAGTAATGAGTTATCATTCAATATTT
Found at i:6548847 original size:24 final size:23
Alignment explanation
Indices: 6548806--6548851 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
6548796 TTGTAAAAAA
* *
6548806 ATTTAAAATTGTTTATTAATTAT
1 ATTTAAAATTGATAATTAATTAT
6548829 ATTTAATAATTGATAATTAATTA
1 ATTTAA-AATTGATAATTAATTA
6548852 ACTGTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
ATTTAAAATTGATAATTAATTAT
Found at i:6549875 original size:14 final size:15
Alignment explanation
Indices: 6549851--6549900 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
6549841 TAAAAATTTT
*
6549851 TAATAAATTTTTATA
1 TAATTAATTTTTATA
*
6549866 T-TTTAA-TTTTATA
1 TAATTAATTTTTATA
6549879 TAATTAATTTTT-TA
1 TAATTAATTTTTATA
*
6549893 TGATTAAT
1 TAATTAAT
6549901 AGTTGATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 8 0.28
14 16 0.55
15 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TAATTAATTTTTATA
Found at i:6550138 original size:21 final size:21
Alignment explanation
Indices: 6550114--6550158 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6550104 AAAAATATTT
6550114 AATTTAAAATAAA-AATATAAA
1 AATTT-AAATAAATAATATAAA
* *
6550135 AATTTAATTAAATATTATAAA
1 AATTTAAATAAATAATATAAA
6550156 AAT
1 AAT
6550159 AGTGACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTAAATAAATAATATAAA
Found at i:6555557 original size:58 final size:58
Alignment explanation
Indices: 6555492--6555607 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
6555482 TAAAAGTTAA
6555492 GAAGGAAACTATTTTGACTTACATAAACATTTGGATTGAATGAGGCTTCAATAGACTG
1 GAAGGAAACTATTTTGACTTACATAAACATTTGGATTGAATGAGGCTTCAATAGACTG
6555550 GAAGGAAACTATTTTGACTTACATAAACATTTGGATTGAATGAGGCTTCAATAGACTG
1 GAAGGAAACTATTTTGACTTACATAAACATTTGGATTGAATGAGGCTTCAATAGACTG
6555608 TGATACGTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (58 bp):
GAAGGAAACTATTTTGACTTACATAAACATTTGGATTGAATGAGGCTTCAATAGACTG
Found at i:6558191 original size:2 final size:2
Alignment explanation
Indices: 6558186--6558218 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6558176 ATATCATATA
6558186 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6558219 TTAAAGTTAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6581718 original size:14 final size:14
Alignment explanation
Indices: 6581683--6581950 Score: 51
Period size: 13 Copynumber: 18.9 Consensus size: 14
6581673 TCATTAAAAT
6581683 AAATAATAATAT-AA
1 AAATAA-AATATAAA
*
6581697 GAAT-AAAT-TAATA
1 AAATAAAATATAA-A
6581710 AAATAAAATATAAA
1 AAATAAAATATAAA
* * *
6581724 AAATTAATATTTATA
1 AAA-TAAAATATAAA
* * *
6581739 TAATATAGATA-AAC
1 AAATA-AAATATAAA
*
6581753 AAATTAAA-ATAAA
1 AAATAAAATATAAA
* *
6581766 ATATATAATATAAA
1 AAATAAAATATAAA
*
6581780 AAAT-ATAT-TAAA
1 AAATAAAATATAAA
*
6581792 GAAA-GAAA-ATAAA
1 -AAATAAAATATAAA
* *
6581805 ATATAAAATAT-TA
1 AAATAAAATATAAA
*
6581818 TAATAATAA-AT-AA
1 AAATAA-AATATAAA
**
6581831 AAATAAAATATATG
1 AAATAAAATATAAA
*
6581845 AATTAAAATATATTTAA
1 AAATAAAATATA---AA
**
6581862 GAATGATATTATATAAA
1 -AA--ATAAAATATAAA
*
6581879 AATTAATAATAT--A
1 AAATAA-AATATAAA
* *
6581892 ATATAAAATATATTA
1 AAATAAAATATA-AA
6581907 AAATAAAATATAAA
1 AAATAAAATATAAA
* *
6581921 TATTATAATAATAAATAA
1 -A-AATAA-AATATA-AA
6581939 AAATAAAATATA
1 AAATAAAATATA
6581951 TGATATTAAA
Statistics
Matches: 177, Mismatches: 47, Indels: 59
0.63 0.17 0.21
Matches are distributed among these distances:
11 1 0.01
12 18 0.10
13 48 0.27
14 43 0.24
15 38 0.21
16 10 0.06
17 8 0.05
18 4 0.02
20 7 0.04
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAATAAAATATAAA
Found at i:6581808 original size:32 final size:33
Alignment explanation
Indices: 6581759--6581842 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
6581749 AAACAAATTA
* *
6581759 AAATAAAATATATAATATAAAA-AATATATTAA-
1 AAATAAAA-ATAAAATATAAAATAATATAATAAT
*
6581791 AGAA-AGAAAATAAAATATAAAATATTATAATAAT
1 A-AATA-AAAATAAAATATAAAATAATATAATAAT
6581825 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
6581843 TGAATTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 14 0.32
33 28 0.64
34 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAATAATATAATAAT
Found at i:6581892 original size:72 final size:71
Alignment explanation
Indices: 6581738--6581923 Score: 175
Period size: 72 Copynumber: 2.5 Consensus size: 71
6581728 TAATATTTAT
*
6581738 ATAATATAGATAAACAAATTAAAATAAAATATATAATATAAAAAATATATTAAAGAAAGAAAATA
1 ATAATATA-ATAAA-AAATAAAAATAAAATATATAATAT-AAAAATATATTAAAGAAAGAAAATA
6581803 AAATATAAA
63 AAATATAAA
* * * *
6581812 ATATTATAATAATAAATAAAAATAAAATATATGAAT-T-AAAATATATTTAAGAATGATATTATA
1 ATAATATAATAAAAAATAAAAATAAAATATAT-AATATAAAAATATATTAAAGAAAGA-A--A-A
*
6581875 TAAAA-AT-TA
61 TAAAATATAAA
6581884 ATAATATAATATAAAATATATTAAAATAAAATATA-AATAT
1 ATAATATAATA-AAAA-ATA--AAAATAAAATATATAATAT
6581924 TATAATAATA
Statistics
Matches: 94, Mismatches: 8, Indels: 19
0.78 0.07 0.16
Matches are distributed among these distances:
70 17 0.18
71 1 0.01
72 30 0.32
73 13 0.14
74 19 0.20
75 1 0.01
76 13 0.14
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (71 bp):
ATAATATAATAAAAAATAAAAATAAAATATATAATATAAAAATATATTAAAGAAAGAAAATAAAA
TATAAA
Found at i:6581901 original size:15 final size:15
Alignment explanation
Indices: 6581883--6582013 Score: 55
Period size: 15 Copynumber: 8.9 Consensus size: 15
6581873 TATAAAAATT
6581883 AATAATATAATATAA
1 AATAATATAATATAA
*
6581898 AAT-ATATTAAAATAA
1 AATAATA-TAATATAA
* *
6581913 AATATAAATATTATAA
1 AATA-ATATAATATAA
*
6581929 TAATAA-ATAAAAATAA
1 -AATAATAT-AATATAA
* *
6581945 AAT-ATATGATATTA
1 AATAATATAATATAA
*
6581959 AA-AATAT-ATTTAA
1 AATAATATAATATAA
* * *
6581972 GA-AATGATATTATAT
1 AATAAT-ATAATATAA
6581987 AA-AAT-TAATAATAA
1 AATAATATAAT-ATAA
6582001 AA-AATATAATATA
1 AATAATATAATATA
6582014 TTAAACTTAT
Statistics
Matches: 87, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
13 11 0.13
14 27 0.31
15 31 0.36
16 12 0.14
17 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
AATAATATAATATAA
Found at i:6581926 original size:108 final size:111
Alignment explanation
Indices: 6581797--6582018 Score: 380
Period size: 110 Copynumber: 2.0 Consensus size: 111
6581787 TTAAAGAAAG
6581797 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGA-ATT-AAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
* *
6581860 AAG-AATGATATTATATAAAAATTAATAATATAATATAAAATATATT
66 AAGAAATGATATTATAT-AAAATTAATAATAAAAAATAAAATATATT
6581906 AAAATAAAATAT-AAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
*
6581970 AAGAAATGATATTATATAAAATTAATAATAAAAAATATAATATATT
66 AAGAAATGATATTATATAAAATTAATAATAAAAAATAAAATATATT
6582016 AAA
1 AAA
6582019 CTTATATTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
108 36 0.34
109 15 0.14
110 43 0.40
111 13 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (111 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
AAGAAATGATATTATATAAAATTAATAATAAAAAATAAAATATATT
Found at i:6581947 original size:32 final size:32
Alignment explanation
Indices: 6581884--6581950 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
6581874 ATAAAAATTA
* *
6581884 ATAATATAATATAAAATATATTAAAATAAAAT
1 ATAATATAATATAAAATAAATAAAAATAAAAT
*
6581916 ATAA-ATATTATAATAATAAATAAAAATAAAAT
1 ATAATATAATATAA-AATAAATAAAAATAAAAT
6581948 ATA
1 ATA
6581951 TGATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (32 bp):
ATAATATAATATAAAATAAATAAAAATAAAAT
Found at i:6582187 original size:15 final size:15
Alignment explanation
Indices: 6582167--6582220 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
6582157 TTTTCTCTGT
*
6582167 AATCACATTGCTTGC
1 AATCACATTACTTGC
6582182 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
6582197 AATCACATTACCTGT
1 AATCACATTACTTGC
6582212 AATCACATT
1 AATCACATT
6582221 GCATTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:6582355 original size:20 final size:20
Alignment explanation
Indices: 6582335--6582372 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6582325 TATGAAAAAT
*
6582335 TTAAAAA-TATTTTTATTAA
1 TTAAAAATTATTATTATTAA
6582354 TTAAAAATTATTATTATTA
1 TTAAAAATTATTATTATTA
6582373 TTATTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAAATTATTATTATTAA
Found at i:6587052 original size:21 final size:21
Alignment explanation
Indices: 6587026--6587069 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6587016 ATTAAATAGG
*
6587026 TTCACTCACCACTATGTCTTA
1 TTCACTCACCACTATATCTTA
* *
6587047 TTCACTCAGCAGTATATCTTA
1 TTCACTCACCACTATATCTTA
6587068 TT
1 TT
6587070 TCAACAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (21 bp):
TTCACTCACCACTATATCTTA
Found at i:6604006 original size:2 final size:2
Alignment explanation
Indices: 6603999--6604031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6603989 ATCTAAACTT
6603999 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6604032 GAAGCGAGAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6609460 original size:18 final size:18
Alignment explanation
Indices: 6609447--6609490 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6609437 AATTTTCATA
6609447 AATAT-AATTTTTTTAAT
1 AATATAAATTTTTTTAAT
*
6609464 AATTTAAATTTTTTTATAT
1 AATATAAATTTTTTTA-AT
*
6609483 ATTATAAA
1 AATATAAA
6609491 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATAAATTTTTTTAAT
Found at i:6616389 original size:28 final size:28
Alignment explanation
Indices: 6616355--6616413 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
6616345 AATATGTTAC
*
6616355 AAACAAAGAACTTACATAAAATATAAAT
1 AAACAAAGAAATTACATAAAATATAAAT
* *
6616383 AAACAAATAAATTACATCAAATATAAAT
1 AAACAAAGAAATTACATAAAATATAAAT
6616411 AAA
1 AAA
6616414 ATTTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (28 bp):
AAACAAAGAAATTACATAAAATATAAAT
Found at i:6616625 original size:119 final size:118
Alignment explanation
Indices: 6616452--6616689 Score: 399
Period size: 119 Copynumber: 2.0 Consensus size: 118
6616442 CTATAACTAT
*
6616452 ACGTATATAATTAAATAAATAAAAACTTCAAGACTCATTTATATCTTCCACAATTCTTATTTTCA
1 ACGTATATAATCAAATAAATAAAAACTTCAAGACTCATTTATATCTTCCACAATTCTTATTTTCA
*
6616517 AGCAAATCATTTAAATCTTATTTAGACAGTAATGATG-TCTGAATGTCTGAATA
66 AGCAAATCATTTAAATCTTATTTAGACAGTAATGATGTTATGAAT-TCTGAATA
* *
6616570 ACGTATATAATCAATTAAAATAAGAAACTTCAAGACTTATTTATAT-TTCCACAATTCTTATTTT
1 ACGTATATAATCAAAT-AAATAA-AAACTTCAAGACTCATTTATATCTTCCACAATTCTTATTTT
6616634 CAAGCAAATCATTTAAATCTTATTTAGACAGTAATGATGTTATGAATTCTGAATA
64 CAAGCAAATCATTTAAATCTTATTTAGACAGTAATGATGTTATGAATTCTGAATA
6616689 A
1 A
6616690 TTATCAATTT
Statistics
Matches: 113, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
118 14 0.12
119 72 0.64
120 27 0.24
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (118 bp):
ACGTATATAATCAAATAAATAAAAACTTCAAGACTCATTTATATCTTCCACAATTCTTATTTTCA
AGCAAATCATTTAAATCTTATTTAGACAGTAATGATGTTATGAATTCTGAATA
Found at i:6624443 original size:4 final size:4
Alignment explanation
Indices: 6624434--6624464 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
6624424 TGAATTGATT
6624434 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
6624465 TGGAACTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:6628279 original size:3 final size:3
Alignment explanation
Indices: 6628273--6628301 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6628263 GAGCCTTTTT
6628273 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
6628302 AAGACTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:6629657 original size:2 final size:2
Alignment explanation
Indices: 6629650--6629693 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
6629640 TGATCACCTC
*
6629650 AT AT AT AT AT AT AT A- AGG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
6629692 AT
1 AT
6629694 GCCTACACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6630877 original size:18 final size:17
Alignment explanation
Indices: 6630838--6630881 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
6630828 AGAGATAGAG
*
6630838 GGAAAAAAGAAAGCAAA
1 GGAAAAAAAAAAGCAAA
* *
6630855 AGAAAAGAAAAAAGCCAA
1 GGAAAA-AAAAAAGCAAA
6630873 GGAAAAAAA
1 GGAAAAAAA
6630882 GATAGGATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (17 bp):
GGAAAAAAAAAAGCAAA
Found at i:6633713 original size:2 final size:2
Alignment explanation
Indices: 6633706--6633733 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6633696 GTTGTAAAGC
6633706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6633734 CATACATGGC
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):
TA
Found at i:6634105 original size:2 final size:2
Alignment explanation
Indices: 6634088--6634126 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6634078 CCATAGTAAA
*
6634088 AG AG AG -G A- AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6634127 CTAGGGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:6635109 original size:2 final size:2
Alignment explanation
Indices: 6635102--6635131 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6635092 TATTAAGTTC
6635102 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
6635132 TTCCCACATT
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:6637301 original size:2 final size:2
Alignment explanation
Indices: 6637294--6637333 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
6637284 ATAGTCCATA
* * *
6637294 AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6637334 GCCCTGCAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6641647 original size:36 final size:36
Alignment explanation
Indices: 6641600--6641672 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
6641590 AACCTCTGTA
6641600 CTGGAAGCTTAATACTGACATTTCCTACCCACTAGC
1 CTGGAAGCTTAATACTGACATTTCCTACCCACTAGC
6641636 CTGGAAGCTTAATACTGACATTTCCTACCCACTAGC
1 CTGGAAGCTTAATACTGACATTTCCTACCCACTAGC
6641672 C
1 C
6641673 CAACATCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (36 bp):
CTGGAAGCTTAATACTGACATTTCCTACCCACTAGC
Found at i:6656227 original size:13 final size:13
Alignment explanation
Indices: 6656211--6656235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6656201 TTTAACTTAC
6656211 AAAGCCCACTTCA
1 AAAGCCCACTTCA
6656224 AAAGCCCACTTC
1 AAAGCCCACTTC
6656236 GACCCTATCT
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:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAGCCCACTTCA
Found at i:6656472 original size:12 final size:12
Alignment explanation
Indices: 6656455--6656490 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
6656445 TCTACAGAGG
6656455 GAAGCTGAAGCC
1 GAAGCTGAAGCC
6656467 GAAGCTGAAGCC
1 GAAGCTGAAGCC
* *
6656479 GAGGCGGAAGCC
1 GAAGCTGAAGCC
6656491 ATGGCCATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.39, T:0.06
Consensus pattern (12 bp):
GAAGCTGAAGCC
Found at i:6662811 original size:38 final size:38
Alignment explanation
Indices: 6662760--6662870 Score: 204
Period size: 38 Copynumber: 2.9 Consensus size: 38
6662750 TTAGTTTATT
6662760 TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTAATG
1 TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTAATG
6662798 TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTAATG
1 TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTAATG
**
6662836 TCTCTTTGTATTGACTGCAGTGTAAACTCTATGTA
1 TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTA
6662871 CTTAAAATAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (38 bp):
TCTCTTTGTATTGACTAAAGTGTAAACTCTATGTAATG
Found at i:6668282 original size:2 final size:2
Alignment explanation
Indices: 6668277--6668348 Score: 54
Period size: 2 Copynumber: 36.0 Consensus size: 2
6668267 CTCTCTCTCT
* * * * *
6668277 CA CA CA CA CA CA CA CA AA CA CA CT CA CA CA CG CA CA AA CA CG
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* * ** *
6668319 CA CG CT GG CA CA CA CA CA CA CA CA CG CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
6668349 TTTTTACATG
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.43, C:0.46, G:0.08, T:0.03
Consensus pattern (2 bp):
CA
Found at i:6699359 original size:5 final size:5
Alignment explanation
Indices: 6699351--6699396 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
6699341 CCAACCTGAC
6699351 CCCTT CCCTT CCCTT CCCTT CCCTGAGT CCC-T CCCTT -CCTT CCCTT
1 CCCTT CCCTT CCCTT CCCTT CCCT---T CCCTT CCCTT CCCTT CCCTT
6699397 TGTTTTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 8 0.22
5 24 0.67
8 4 0.11
ACGTcount: A:0.02, C:0.57, G:0.04, T:0.37
Consensus pattern (5 bp):
CCCTT
Found at i:6699889 original size:12 final size:12
Alignment explanation
Indices: 6699872--6699903 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6699862 TTCTGCAAAA
6699872 TTGTTCTTCTTC
1 TTGTTCTTCTTC
6699884 TTGTTCTTCTTC
1 TTGTTCTTCTTC
*
6699896 TTCTTCTT
1 TTGTTCTT
6699904 TTACCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (12 bp):
TTGTTCTTCTTC
Found at i:6726809 original size:2 final size:2
Alignment explanation
Indices: 6726802--6726826 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6726792 TAGGGAGGGG
6726802 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
6726827 TGTTACTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6727310 original size:13 final size:13
Alignment explanation
Indices: 6727294--6727318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6727284 CTCGGCATAA
6727294 TCATCATCATCAT
1 TCATCATCATCAT
6727307 TCATCATCATCA
1 TCATCATCATCA
6727319 ACACCTATCT
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:0.32, G:0.00, T:0.36
Consensus pattern (13 bp):
TCATCATCATCAT
Found at i:6739762 original size:6 final size:7
Alignment explanation
Indices: 6739733--6739763 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6739723 GATCCATGAT
6739733 CCATTCC
1 CCATTCC
6739740 CCATTCC
1 CCATTCC
6739747 CCATTCC
1 CCATTCC
6739754 CCA-TCC
1 CCATTCC
6739760 CCAT
1 CCAT
6739764 GCATGCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.26
Consensus pattern (7 bp):
CCATTCC
Found at i:6762220 original size:18 final size:18
Alignment explanation
Indices: 6762197--6762234 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6762187 AAAAGTTTTC
* *
6762197 TCTTTTATGAGTAAAGAG
1 TCTTTTACGAATAAAGAG
6762215 TCTTTTACGAATAAAGAG
1 TCTTTTACGAATAAAGAG
6762233 TC
1 TC
6762235 ATTGTAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (18 bp):
TCTTTTACGAATAAAGAG
Found at i:6762691 original size:2 final size:2
Alignment explanation
Indices: 6762684--6762713 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6762674 TCCTGATTGC
6762684 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6762714 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6765688 original size:25 final size:25
Alignment explanation
Indices: 6765660--6765711 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
6765650 CTCGGAATTT
*
6765660 TCTCTCAGAACAGTCAAAAGGAAAA
1 TCTCTCAGAACAGTCAAAAGAAAAA
6765685 TCTCTCAGAACAGTCAAAAGAAAAA
1 TCTCTCAGAACAGTCAAAAGAAAAA
6765710 TC
1 TC
6765712 GTGGGTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (25 bp):
TCTCTCAGAACAGTCAAAAGAAAAA
Found at i:6792785 original size:2 final size:2
Alignment explanation
Indices: 6792778--6792802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6792768 CCAACATTAT
6792778 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
6792803 AAGGGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6796310 original size:30 final size:29
Alignment explanation
Indices: 6796239--6796310 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
6796229 TGCATTCAAT
*
6796239 TAAACTCTTATATTTTTGTTTTAAGCTAA
1 TAAACTCTTATATTTTTATTTTAAGCTAA
*
6796268 TAAAATCTTTATATTTTTATTTTAAG-TGAAA
1 TAAACTC-TTATATTTTTATTTTAAGCT--AA
6796299 TAAACTCTTATA
1 TAAACTCTTATA
6796311 ACTAATGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 7 0.19
30 22 0.59
31 8 0.22
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (29 bp):
TAAACTCTTATATTTTTATTTTAAGCTAA
Found at i:6799002 original size:17 final size:18
Alignment explanation
Indices: 6798980--6799013 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6798970 AAGATATAAT
6798980 ATTTATGAT-AAACTTAG
1 ATTTATGATAAAACTTAG
*
6798997 ATTTATGTTAAAACTTA
1 ATTTATGATAAAACTTA
6799014 ATGAGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTTATGATAAAACTTAG
Found at i:6800179 original size:20 final size:18
Alignment explanation
Indices: 6800153--6800198 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
6800143 ATATATGAGT
6800153 AAATAAAATAGAAATAAAA
1 AAATAAAATA-AAATAAAA
*
6800172 ATAATAAAATAAATTAAAA
1 A-AATAAAATAAAATAAAA
6800191 AAATAAAA
1 AAATAAAA
6800199 ACAACATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAATAAAA
Found at i:6800207 original size:20 final size:19
Alignment explanation
Indices: 6800167--6800210 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6800157 AAAATAGAAA
*
6800167 TAAAAATAATAAAATAAAT
1 TAAAAATAATAAAACAAAT
6800186 TAAAAA-AATAAAAACAACAT
1 TAAAAATAAT-AAAACAA-AT
6800206 TAAAA
1 TAAAA
6800211 TGGAGTCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (19 bp):
TAAAAATAATAAAACAAAT
Found at i:6816111 original size:6 final size:6
Alignment explanation
Indices: 6816100--6816133 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6816090 AACTTTCTAC
6816100 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTG
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTG
6816134 ATTCCCTTCG
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:0.00, C:0.15, G:0.18, T:0.68
Consensus pattern (6 bp):
TTTGCT
Found at i:6821446 original size:6 final size:6
Alignment explanation
Indices: 6821437--6821464 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6821427 TTACGTTCGT
6821437 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
6821465 GAGCTTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:6828284 original size:50 final size:51
Alignment explanation
Indices: 6828225--6828330 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 51
6828215 TCCAGGCAAG
6828225 TTATTAATGTTTCCTTTTCTTCCTCTCCTACATTAATGTAAGGGTATGA-T
1 TTATTAATGTTTCCTTTTCTTCCTCTCCTACATTAATGTAAGGGTATGAGT
* * *
6828275 TTATTAATGTTTCCTTTTCTTTCTTTCCTACATTAATGTCAGGGTATGAGT
1 TTATTAATGTTTCCTTTTCTTCCTCTCCTACATTAATGTAAGGGTATGAGT
6828326 TTATT
1 TTATT
6828331 TTCTTCTGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 46 0.88
51 6 0.12
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (51 bp):
TTATTAATGTTTCCTTTTCTTCCTCTCCTACATTAATGTAAGGGTATGAGT
Found at i:6832533 original size:7 final size:7
Alignment explanation
Indices: 6832521--6832545 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6832511 GACAACAGTA
6832521 AAACCCT
1 AAACCCT
6832528 AAACCCT
1 AAACCCT
6832535 AAACCCT
1 AAACCCT
6832542 AAAC
1 AAAC
6832546 TTTCGACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:6891182 original size:2 final size:2
Alignment explanation
Indices: 6891175--6891219 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6891165 TGGCAGTACT
6891175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6891217 TA T
1 TA T
6891220 CATCTGAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6904963 original size:23 final size:22
Alignment explanation
Indices: 6904935--6905001 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
6904925 CAAAATATCG
6904935 TTTATAAATTTGAAAAATTACATA
1 TTTATAAATTT-AAAAATTA-ATA
* *
6904959 -TTATATATTATAAAAAATAATA
1 TTTATAAATT-TAAAAATTAATA
*
6904981 TTTTTAAATTTAAAAATTAAT
1 TTTATAAATTTAAAAATTAAT
6905002 TAAAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 13 0.36
23 22 0.61
24 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (22 bp):
TTTATAAATTTAAAAATTAATA
Found at i:6905130 original size:156 final size:155
Alignment explanation
Indices: 6904958--6905245 Score: 452
Period size: 156 Copynumber: 1.9 Consensus size: 155
6904948 AAAATTACAT
* * *
6904958 ATTATATATTATAAAAAATAATATTTTTAAATTTAAAAATTAATTAAAATTATTAATATTTGAAT
1 ATTATATATTATAAAAAATAACATTTTGAAATTTAAAAATTAATTAAAATTATTAATATTTGAAC
* *
6905023 CATAATAACATTTAAATTATAAATAAATTATTAATATT-TAAAAATGTTAATGATTAAATTATAA
66 CATAATAACA-TTAAATTATAAATAAAATATTAATATTGT-AAAATGTTAATAATTAAATTATAA
6905087 ATAAAAAGAAAAAAGTTTAAATTTTTA
129 ATAAAAAGAAAAAAGTTTAAATTTTTA
* * * * *
6905114 ATTATATATTATAAAAAATACCATTTTGAATTTTAAAAATTAATTTAAATTATTTATATTTTAAC
1 ATTATATATTATAAAAAATAACATTTTGAAATTTAAAAATTAATTAAAATTATTAATATTTGAAC
*
6905179 CATAATAACATTCAATTATAAATAAAATATTAATATTGTAAAATGTTAATAATTAAATTATAAAT
66 CATAATAACATTAAATTATAAATAAAATATTAATATTGTAAAATGTTAATAATTAAATTATAAAT
6905244 AA
131 AA
6905246 CATATTCATA
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
155 52 0.43
156 68 0.57
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (155 bp):
ATTATATATTATAAAAAATAACATTTTGAAATTTAAAAATTAATTAAAATTATTAATATTTGAAC
CATAATAACATTAAATTATAAATAAAATATTAATATTGTAAAATGTTAATAATTAAATTATAAAT
AAAAAGAAAAAAGTTTAAATTTTTA
Done.