Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 101 of 106
Found at i:21447479 original size:23 final size:23
Alignment explanation
Indices: 21447436--21447480 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21447426 TTATTTCTTA
*
21447436 TTGCTTTCTTTTTTCTCTATTTG
1 TTGCTTTCTTTTTTATCTATTTG
*
21447459 TTGCTTTTTTTTGTTAT-TATTT
1 TTGCTTTCTTTT-TTATCTATTT
21447481 AAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.07, C:0.11, G:0.09, T:0.73
Consensus pattern (23 bp):
TTGCTTTCTTTTTTATCTATTTG
Found at i:21454549 original size:24 final size:25
Alignment explanation
Indices: 21454521--21454568 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
21454511 TGAAGTATCT
21454521 TATATTAA-ATAAAA-AAATTATTTG
1 TATA-TAATATAAAAGAAATTATTTG
*
21454545 TATATAATTTAAAAGAAATTATTT
1 TATATAATATAAAAGAAATTATTT
21454569 ATGTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TATATAATATAAAAGAAATTATTTG
Found at i:21457035 original size:29 final size:30
Alignment explanation
Indices: 21456993--21457169 Score: 139
Period size: 30 Copynumber: 5.8 Consensus size: 30
21456983 AGATTTTGTA
21456993 AATTTAT-TT-AAATAAATTTTTATATTTT
1 AATTTATATTCAAATAAATTTTTATATTTT
* * *
21457021 TA-TTAGATTCAAATAAGTTTTT-TATCTTT
1 AATTTATATTCAAATAAATTTTTATAT-TTT
* * *
21457050 AATTTATATTTAAATTAATTTTTAAATTTT
1 AATTTATATTCAAATAAATTTTTATATTTT
*
21457080 AATTTATATTCAAATAAATCTTTA-ACTTTT
1 AATTTATATTCAAATAAATTTTTATA-TTTT
* * **
21457110 AATTTACATTTAAATAAGATTTTAATATAAATT
1 AATTTATATTCAAATAA-ATTTT--TATATTTT
* *
21457143 AATTTATTATTTGAAATAAAATTTTAT
1 AATTTA-TA-TTCAAATAAATTTTTAT
21457170 TTAATATAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
27 3 0.03
28 6 0.05
29 16 0.14
30 59 0.50
31 6 0.05
32 3 0.03
33 10 0.09
34 6 0.05
35 8 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (30 bp):
AATTTATATTCAAATAAATTTTTATATTTT
Found at i:21457070 original size:59 final size:60
Alignment explanation
Indices: 21456997--21457132 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
21456987 TTTGTAAATT
* * * * *
21456997 TATTTAAATAAATTTTTATATTTTTA-TTAGATTCAAATAAGTTTTTTA-TCTTTAATTTA
1 TATTTAAATAAATTTTTAAATTTTAATTTAGATTCAAATAAATCTTTAACT-TTTAATTTA
* *
21457056 TATTTAAATTAATTTTTAAATTTTAATTTATATTCAAATAAATCTTTAACTTTTAATTTA
1 TATTTAAATAAATTTTTAAATTTTAATTTAGATTCAAATAAATCTTTAACTTTTAATTTA
*
21457116 CATTTAAATAAGATTTT
1 TATTTAAATAA-ATTTT
21457133 AATATAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 23 0.35
60 36 0.55
61 6 0.09
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (60 bp):
TATTTAAATAAATTTTTAAATTTTAATTTAGATTCAAATAAATCTTTAACTTTTAATTTA
Found at i:21457204 original size:23 final size:23
Alignment explanation
Indices: 21457160--21457232 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 23
21457150 TATTTGAAAT
* *
21457160 AAAATTTTATTTAATATAAATAA
1 AAAAATTTATTAAATATAAATAA
21457183 ACAAAATTTATTAAATAT-AATAA
1 A-AAAATTTATTAAATATAAATAA
* * *
21457206 AAAAACTTA-T-AATTTAATTAA
1 AAAAATTTATTAAATATAAATAA
21457227 AAAAAT
1 AAAAAT
21457233 AATCCAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.10
21 10 0.24
22 7 0.17
23 7 0.17
24 14 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATTTATTAAATATAAATAA
Found at i:21459046 original size:27 final size:25
Alignment explanation
Indices: 21458987--21459046 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
21458977 GTATATTTGA
*
21458987 TTAATTTTTATAAATATATATTAAT
1 TTAATTTTTATAAAAATATATTAAT
* *
21459012 ATATATTTTTAATAAAAATATATTCATT
1 TTA-ATTTTT-ATAAAAATATATT-AAT
21459040 TTAATTT
1 TTAATTT
21459047 ATATTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.07
26 6 0.21
27 16 0.57
28 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATTTTTATAAAAATATATTAAT
Found at i:21468765 original size:17 final size:17
Alignment explanation
Indices: 21468743--21468819 Score: 56
Period size: 16 Copynumber: 4.7 Consensus size: 17
21468733 ATTTATTTAT
21468743 ATATAATATAAAAATTA
1 ATATAATATAAAAATTA
*
21468760 ATATAA-ATTAAAATT-
1 ATATAATATAAAAATTA
*
21468775 TTA-AACTATAAAAA--A
1 ATATAA-TATAAAAATTA
* *
21468790 ATATAATAAAAAAACTA
1 ATATAATATAAAAATTA
*
21468807 GTATATATATAAA
1 ATATA-ATATAAA
21468820 GTATAACATA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
14 2 0.04
15 11 0.24
16 16 0.35
17 11 0.24
18 6 0.13
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (17 bp):
ATATAATATAAAAATTA
Found at i:21473176 original size:1 final size:1
Alignment explanation
Indices: 21473172--21473196 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21473162 TTGCCTTCTA
21473172 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
21473197 GCAATTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21475805 original size:54 final size:54
Alignment explanation
Indices: 21475690--21475792 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
21475680 TATAAATATT
* * * * *
21475690 ATTTAGAAGAAATATGTTATATTTAATTTCAAATGTATAATTTTTTGTCAGGTA
1 ATTTAAAAGAAACATGTTATATTTAATTTCAAATGTATAATCTCTTATCAGGTA
21475744 ATTTAAAAGAAACATGTTA-AGTTTAATTTCAAATGTATAATCTCTTATC
1 ATTTAAAAGAAACATGTTATA-TTTAATTTCAAATGTATAATCTCTTATC
21475793 CTGTGATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (54 bp):
ATTTAAAAGAAACATGTTATATTTAATTTCAAATGTATAATCTCTTATCAGGTA
Found at i:21479379 original size:2 final size:2
Alignment explanation
Indices: 21479372--21479403 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21479362 TTATAATCTC
21479372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21479404 AAAGGAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21482449 original size:63 final size:63
Alignment explanation
Indices: 21482330--21482449 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
21482320 AGATAGTAAG
*
21482330 AAAAATCAATAATTAATTTTAAATTCAAAATAAACAACATGAAATGGACTTAAAAAGAGCGAA
1 AAAAATCAATAATTAATTTTAAATTCAAAATAAACAACATGAAATGGACTCAAAAAGAGCGAA
* * * *
21482393 AAAAATTAGTAATTAATTTTAAATTCAAATTAAACAACATGAAATGGACTCCAAAAG
1 AAAAATCAATAATTAATTTTAAATTCAAAATAAACAACATGAAATGGACTCAAAAAG
21482450 GTAAAGTTGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (63 bp):
AAAAATCAATAATTAATTTTAAATTCAAAATAAACAACATGAAATGGACTCAAAAAGAGCGAA
Found at i:21484916 original size:16 final size:16
Alignment explanation
Indices: 21484895--21484926 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21484885 GTCTTTCGCC
21484895 CCACCCTTTCAATTTT
1 CCACCCTTTCAATTTT
*
21484911 CCACCCTTTTAATTTT
1 CCACCCTTTCAATTTT
21484927 TGAAATAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (16 bp):
CCACCCTTTCAATTTT
Found at i:21485936 original size:143 final size:137
Alignment explanation
Indices: 21485755--21486055 Score: 315
Period size: 141 Copynumber: 2.2 Consensus size: 137
21485745 GTTTTGTTGA
* *
21485755 AAATTTTTAATTTAATCATAATTTTTCGTAAATTTATTTT-TATTTTAAAAAATAAAAAATATAT
1 AAATTTTTAATTTAATCATAAATTTTC-TAAATTTATTTTCAATTTT-AAAAA-AAAAAA-ATAT
* * * ** * * * *
21485819 TTTACTAATATATCATAGTATAATAAAATATAAATACTAATGGCTTTTAAT-ATGATAAATTATA
62 TTAACTAATAAATCACAACATAATAAAAAATAAATACTAAT--ATATTAATAAT-ATAAATTAAA
21485883 TTAATTACTTTGTT
124 TTAATTACTTTGTT
** * *
21485897 AAATTTTTTAATTTAATGTTAAATTTT-TAAATATATATTTTCAATTTTTAAAAAGAAAAATATT
1 AAA-TTTTTAATTTAATCATAAATTTTCTAAAT-T-TATTTTCAATTTTAAAAAAAAAAAATATT
21485961 TAACTAATAAATCACAACATAATAAAAAATAAATACTAATATATTAATAATATAAATTAAATTAA
63 TAACTAATAAATCACAACATAATAAAAAATAAATACTAATATATTAATAATATAAATTAAATTAA
* *
21486026 TTGCGTTGTT
128 TTACTTTGTT
*
21486036 ACA-TTTTAATTTAAT-ATAAA
1 AAATTTTTAATTTAATCATAAA
21486056 ACAAATATAA
Statistics
Matches: 135, Mismatches: 19, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
136 4 0.03
137 12 0.09
139 29 0.21
140 2 0.01
141 44 0.33
142 9 0.07
143 30 0.22
144 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (137 bp):
AAATTTTTAATTTAATCATAAATTTTCTAAATTTATTTTCAATTTTAAAAAAAAAAAATATTTAA
CTAATAAATCACAACATAATAAAAAATAAATACTAATATATTAATAATATAAATTAAATTAATTA
CTTTGTT
Found at i:21488729 original size:11 final size:10
Alignment explanation
Indices: 21488709--21488733 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21488699 TCACACACAC
21488709 AAAAATAAAA
1 AAAAATAAAA
21488719 AAAAATAAAA
1 AAAAATAAAA
21488729 AAAAA
1 AAAAA
21488734 CCTTCCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:21490047 original size:18 final size:19
Alignment explanation
Indices: 21490015--21490052 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21490005 TAGACATCGA
*
21490015 TTTTATTTGGATTTATTAT
1 TTTTATTTGGATTTAATAT
21490034 TTTTATTTGG-TTTAATAT
1 TTTTATTTGGATTTAATAT
21490052 T
1 T
21490053 AATAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (19 bp):
TTTTATTTGGATTTAATAT
Found at i:21490067 original size:3 final size:3
Alignment explanation
Indices: 21490046--21490107 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
21490036 TTATTTGGTT
* ** *
21490046 TAA TAT TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA T-A TATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
*
21490091 AAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
21490108 TATATTTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:21490120 original size:27 final size:27
Alignment explanation
Indices: 21490046--21490120 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
21490036 TTATTTGGTT
*
21490046 TAATATTAATA-ATTTTAATAATAATAA
1 TAATAATAATATATTTTAA-AATAATAA
*
21490073 TAATAATAATATATTTAAAAATAATAA
1 TAATAATAATATATTTTAAAATAATAA
21490100 TAATAAT-ATATATTTTTAAAA
1 TAATAATAATATA-TTTTAAAA
21490121 AAAAGAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.12
27 32 0.74
28 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATAATAATATATTTTAAAATAATAA
Found at i:21490442 original size:13 final size:14
Alignment explanation
Indices: 21490412--21490443 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21490402 ACCTATATCC
21490412 AAATAGAAACACAA
1 AAATAGAAACACAA
21490426 AAATAGAAACA-AA
1 AAATAGAAACACAA
21490439 AAATA
1 AAATA
21490444 AAGACAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (14 bp):
AAATAGAAACACAA
Found at i:21494565 original size:25 final size:26
Alignment explanation
Indices: 21494512--21494566 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
21494502 AAAAATTGAT
**
21494512 ATTT-ATTTATTAATAAAATATCATT
1 ATTTAATTTATTAATAAAATATCAAA
21494537 ATTTAATTTATTAA-AAATATAT-AAA
1 ATTTAATTTATTAATAAA-ATATCAAA
21494562 ATTTA
1 ATTTA
21494567 TATACAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATTTATTAATAAAATATCAAA
Found at i:21495844 original size:18 final size:18
Alignment explanation
Indices: 21495808--21495846 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21495798 ATGATTATGA
*
21495808 TTATTATTTATTAATTAT
1 TTATTATTTATAAATTAT
21495826 TTATTATTT-TAAATATAT
1 TTATTATTTATAAAT-TAT
21495844 TTA
1 TTA
21495847 CAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATTTATAAATTAT
Found at i:21500612 original size:13 final size:13
Alignment explanation
Indices: 21500594--21500619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21500584 ACCTATCTCC
21500594 ATAAAAAAAATAA
1 ATAAAAAAAATAA
21500607 ATAAAAAAAATAA
1 ATAAAAAAAATAA
21500620 TTTCACAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAAAATAA
Found at i:21508559 original size:30 final size:29
Alignment explanation
Indices: 21508492--21508560 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
21508482 TTTTATTATT
21508492 ATTAAATAAGCCTTCAATTTTTAATTTAC
1 ATTAAATAAGCCTTCAATTTTTAATTTAC
* *
21508521 ATTCAAATAGGCTCTT-AATTTTTAATTTAT
1 ATT-AAATAAGC-CTTCAATTTTTAATTTAC
21508551 ACTTAAATAA
1 A-TTAAATAA
21508561 AATTTTAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 26 0.76
31 5 0.15
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (29 bp):
ATTAAATAAGCCTTCAATTTTTAATTTAC
Found at i:21517304 original size:33 final size:33
Alignment explanation
Indices: 21517261--21517329 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
21517251 CAAACAAATT
* *
21517261 TTAATAGGAAAACCTAAATTAAACAAAAATAAC
1 TTAATAGGAAAACCCAAATTAAACAAAAACAAC
* *
21517294 TTAATGGGAAAACCCAAATTAAATAAAAACAAC
1 TTAATAGGAAAACCCAAATTAAACAAAAACAAC
21517327 TTA
1 TTA
21517330 CGGTTGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.58, C:0.13, G:0.07, T:0.22
Consensus pattern (33 bp):
TTAATAGGAAAACCCAAATTAAACAAAAACAAC
Found at i:21519796 original size:6 final size:7
Alignment explanation
Indices: 21519781--21519808 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21519771 GAACAAAGAT
21519781 AAAATAA
1 AAAATAA
21519788 AAAATAA
1 AAAATAA
21519795 AAAATAA
1 AAAATAA
21519802 AAAATAA
1 AAAATAA
21519809 TACTGTTAAA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:21535734 original size:23 final size:21
Alignment explanation
Indices: 21535708--21535750 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21535698 TCTATTGGTT
21535708 ATTACATTAATTATTTTTATATA
1 ATTACATTAA-T-TTTTTATATA
**
21535731 ATTATTTTAATTTTTTATAT
1 ATTACATTAATTTTTTATAT
21535751 TTTCTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTACATTAATTTTTTATATA
Found at i:21539391 original size:16 final size:17
Alignment explanation
Indices: 21539351--21539394 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
21539341 TCAATTTTTT
*
21539351 TATTTTTTATTTAAATG
1 TATTATTTATTTAAATG
* *
21539368 TTTTATTTATTTAATTG
1 TATTATTTATTTAAATG
21539385 -ATTATTTATT
1 TATTATTTATT
21539395 ATTCTTTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TATTATTTATTTAAATG
Found at i:21540666 original size:20 final size:20
Alignment explanation
Indices: 21540623--21540665 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
21540613 AAAATATATC
*
21540623 AAAATTTATTAAAATTTTTA
1 AAAATGTATTAAAATTTTTA
*
21540643 AAAATGTATT-AATTTTTTA
1 AAAATGTATTAAAATTTTTA
21540662 AAAA
1 AAAA
21540666 AAATTTACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAAATGTATTAAAATTTTTA
Found at i:21541250 original size:37 final size:36
Alignment explanation
Indices: 21541168--21541251 Score: 87
Period size: 37 Copynumber: 2.3 Consensus size: 36
21541158 GACCCGATCT
* * * * * *
21541168 AATATTATATAAAAAATTATTTTTTAATTTTTTAAT
1 AATAATATTTAAAAAATAATATTTTAATTTTTAAAA
*
21541204 TATATATATTTAAAAAATAATATTTTATATTTTTAAAA
1 AATA-ATATTTAAAAAATAATATTTTA-ATTTTTAAAA
21541242 AATAATATTT
1 AATAATATTT
21541252 TATTAATTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
36 3 0.08
37 24 0.63
38 11 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATAATATTTAAAAAATAATATTTTAATTTTTAAAA
Found at i:21541255 original size:21 final size:23
Alignment explanation
Indices: 21541206--21541254 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
21541196 TTTTTAATTA
*
21541206 TATATATTTAAAAAATAATATTT
1 TATATTTTTAAAAAATAATATTT
21541229 TATATTTTTAAAAAATAATATTT
1 TATATTTTTAAAAAATAATATTT
21541252 TAT
1 TAT
21541255 TAATTTCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTTTTAAAAAATAATATTT
Found at i:21549340 original size:18 final size:18
Alignment explanation
Indices: 21549301--21549347 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21549291 TACTAGTAAA
* *
21549301 TTTTATTAGTAATAATAT
1 TTTTATTTGCAATAATAT
*
21549319 TTTTATTTGCAATAATTT
1 TTTTATTTGCAATAATAT
*
21549337 TTTTCTTTGCA
1 TTTTATTTGCA
21549348 GAAGATGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTATTTGCAATAATAT
Found at i:21557013 original size:13 final size:13
Alignment explanation
Indices: 21556995--21557026 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21556985 ATTAAACTAT
21556995 TGATAATATCTCA
1 TGATAATATCTCA
21557008 TGATAATATCTCA
1 TGATAATATCTCA
21557021 T-ATAAT
1 TGATAAT
21557027 CAATGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (13 bp):
TGATAATATCTCA
Found at i:21568576 original size:46 final size:45
Alignment explanation
Indices: 21568412--21568577 Score: 120
Period size: 46 Copynumber: 3.6 Consensus size: 45
21568402 AGATTCATAT
* * * * * *
21568412 CCAAAA-TTCAAATATTCACATTAAAAAATTTTAAAGG-TTCACAT
1 CCAAAATTTCAAAAATTCTCATTAAAAAACTTT-AGGGACTCACAA
* * * * * * *
21568456 TCAAAATTTCAAATATCCTCATTTGAAAAACTTTAGTGATTCACAT
1 CCAAAATTTCAAAAATTCTCA-TTAAAAAACTTTAGGGACTCACAA
* * * *
21568502 CCAATATTTTAAAAATTTTCATTCAAAAAACTTCTAGGGACTCATAA
1 CCAAAATTTCAAAAATTCTCATT-AAAAAACTT-TAGGGACTCACAA
*
21568549 CCAAAATTTCAAAGATTCTCATTAAAAAA
1 CCAAAATTTCAAAAATTCTCATTAAAAAA
21568578 AAAAAAAAAA
Statistics
Matches: 95, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
44 5 0.05
45 16 0.17
46 46 0.48
47 28 0.29
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (45 bp):
CCAAAATTTCAAAAATTCTCATTAAAAAACTTTAGGGACTCACAA
Found at i:21569065 original size:24 final size:25
Alignment explanation
Indices: 21569028--21569075 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
21569018 ATGTTCACTA
*
21569028 CATGATGTAAATGC-ATTACCAAAT
1 CATGATGCAAATGCAATTACCAAAT
* *
21569052 CATGATGCAGATGCAATTATCAAA
1 CATGATGCAAATGCAATTACCAAA
21569076 ACAAAGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (25 bp):
CATGATGCAAATGCAATTACCAAAT
Found at i:21573269 original size:4 final size:4
Alignment explanation
Indices: 21573262--21573288 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21573252 ATAATAAGCA
21573262 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
21573289 AATCTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:21574077 original size:16 final size:16
Alignment explanation
Indices: 21574056--21574086 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21574046 CTCAAAGCCT
*
21574056 TTTTTTTAAATAATTA
1 TTTTTTTAAAAAATTA
21574072 TTTTTTTAAAAAATT
1 TTTTTTTAAAAAATT
21574087 GATACTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTTAAAAAATTA
Found at i:21574104 original size:57 final size:56
Alignment explanation
Indices: 21573945--21574215 Score: 244
Period size: 56 Copynumber: 4.8 Consensus size: 56
21573935 TTTTTTCAAA
* * * * * * * *
21573945 TTTTTT-AAATATTTTTTATTTTAGGAAAATTAATATTTTAAC-TTTCCTTAAAACA
1 TTTTTTAAAATATTTATT-TTTAAGAAAAATTGATACTTCAACTTTTCCTCAAAACT
* * ** *
21574000 TCTTTTAAAATTTTTATTTTTAAGAAAAATTGATAAATCAAC-TTTCCTCAAAGCCT
1 TTTTTTAAAATATTTATTTTTAAGAAAAATTGATACTTCAACTTTTCCTCAAA-ACT
* * * *
21574056 TTTTTTTAAATAATTATTTTTTTA-AAAAATTGATACTTCAACTTTTCCTTAAAACT
1 TTTTTTAAAATATTTA-TTTTTAAGAAAAATTGATACTTCAACTTTTCCTCAAAACT
* * * **
21574112 TTTTTTAAAATTTTTATTTTTAAGAAAAATTAATACTTCAATTTTTTTTCAAAACAT
1 TTTTTTAAAATATTTATTTTTAAGAAAAATTGATACTTCAACTTTTCCTCAAAAC-T
* * * *
21574169 TTTTTGAGAATATTTATTTTTAAGAAAAATTGATTCTTTAACTTTTC
1 TTTTTTAAAATATTTATTTTTAAGAAAAATTGATACTTCAACTTTTC
21574216 AAAATTTTGA
Statistics
Matches: 172, Mismatches: 38, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
55 38 0.22
56 79 0.46
57 55 0.32
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (56 bp):
TTTTTTAAAATATTTATTTTTAAGAAAAATTGATACTTCAACTTTTCCTCAAAACT
Found at i:21574172 original size:112 final size:113
Alignment explanation
Indices: 21573908--21574215 Score: 328
Period size: 112 Copynumber: 2.8 Consensus size: 113
21573898 CGATGCTTTA
* *
21573908 TTTAAGGAAAATTTGATACTTTCAATTTTTTTTC--AA-A-TTTTTTAAAT-ATTTTTTATTTTA
1 TTTAA-GAAAAATTGATAC-TTCAATTTTTTTTCAAAACATTTTTTTAAATAATTATTT-TTTTA
* * *
21573968 GGAAAATTAATATTTTAAC-TTTCCTTAAAACATCTTTTAAAATTTTTATT
63 GAAAAATTGATACTTTAACTTTTCCTTAAAACATCTTTTAAAATTTTTATT
** * ** * *
21574018 TTTAAGAAAAATTGATAAATCAA-CTTTCCTCAAAGCCTTTTTTTTAAATAATTATTTTTTTA-A
1 TTTAAGAAAAATTGATACTTCAATTTTTTTTCAAA-ACATTTTTTTAAATAATTATTTTTTTAGA
* * *
21574081 AAAATTGATACTTCAACTTTTCCTTAAAACTTTTTTTAAAATTTTTATT
65 AAAATTGATACTTTAACTTTTCCTTAAAACATCTTTTAAAATTTTTATT
* * * *
21574130 TTTAAGAAAAATTAATACTTCAATTTTTTTTCAAAACATTTTTTGAGAATATTTA-TTTTTAAGA
1 TTTAAGAAAAATTGATACTTCAATTTTTTTTCAAAACATTTTTTTA-AATAATTATTTTTTTAGA
*
21574194 AAAATTGATTCTTTAACTTTTC
65 AAAATTGATACTTTAACTTTTC
21574216 AAAATTTTGA
Statistics
Matches: 160, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
107 5 0.03
108 4 0.03
109 12 0.08
110 5 0.03
111 14 0.09
112 78 0.49
113 42 0.26
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (113 bp):
TTTAAGAAAAATTGATACTTCAATTTTTTTTCAAAACATTTTTTTAAATAATTATTTTTTTAGAA
AAATTGATACTTTAACTTTTCCTTAAAACATCTTTTAAAATTTTTATT
Found at i:21582983 original size:24 final size:24
Alignment explanation
Indices: 21582951--21583004 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
21582941 TTTGAGGTTG
21582951 AAAAAGGCAAATCAGTTTGAGACC
1 AAAAAGGCAAATCAGTTTGAGACC
*
21582975 AAAAAGGCAAATCAGTTTGAGAGC
1 AAAAAGGCAAATCAGTTTGAGACC
21582999 AAAAAG
1 AAAAAG
21583005 ACAATAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.50, C:0.13, G:0.22, T:0.15
Consensus pattern (24 bp):
AAAAAGGCAAATCAGTTTGAGACC
Found at i:21584046 original size:3 final size:3
Alignment explanation
Indices: 21584033--21584080 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
21584023 AAAAATTTTA
21584033 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
21584078 AAT
1 AAT
21584081 TTCAAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21584517 original size:16 final size:16
Alignment explanation
Indices: 21584498--21584528 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21584488 ACTATCAGGC
21584498 AAAAAAG-CTAAAACA
1 AAAAAAGACTAAAACA
21584513 AAAAAAGACTAAAACA
1 AAAAAAGACTAAAACA
21584529 TGATGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAGACTAAAACA
Found at i:21585459 original size:3 final size:3
Alignment explanation
Indices: 21585451--21585558 Score: 90
Period size: 3 Copynumber: 33.7 Consensus size: 3
21585441 GAATGGTTAA
* * *
21585451 AAT AAT AATT AAA AAT ATAT ATAT AAT AAAT AGT AAT AAAT AAT ATT
1 AAT AAT AA-T AAT AAT A-AT A-AT AAT -AAT AAT AAT -AAT AAT AAT
* * * *
21585498 AAT AAT GAT AAT GAT AAT GAT AAT GAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
21585544 AAT AAAT AAT AAT AA
1 AAT -AAT AAT AAT AA
21585559 AGAAATTGAA
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
3 63 0.74
4 22 0.26
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21585655 original size:3 final size:3
Alignment explanation
Indices: 21585649--21585739 Score: 116
Period size: 3 Copynumber: 30.7 Consensus size: 3
21585639 AAAATTATTA
*
21585649 AAT AAT AAA AAT AA- AAT AAT AA- AAT -AT CAAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT
* *
21585693 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21585740 ATTTAATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
2 6 0.08
3 66 0.86
4 5 0.06
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21588078 original size:16 final size:16
Alignment explanation
Indices: 21588051--21588090 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21588041 GCCTTTTCAC
*
21588051 TCATTCATTCATCCAT
1 TCATTTATTCATCCAT
* *
21588067 TCGTTTATTCATTCAT
1 TCATTTATTCATCCAT
21588083 TCATTTAT
1 TCATTTAT
21588091 GTATCCACTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.53
Consensus pattern (16 bp):
TCATTTATTCATCCAT
Found at i:21589135 original size:21 final size:20
Alignment explanation
Indices: 21589104--21589153 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
21589094 GGAGCATGTC
21589104 AAGAAAAAAAAAAGAACAA-A
1 AAGAAAAAAAAAAGAA-AAGA
21589124 AAGAACAAAAAAAAGAAAAGA
1 AAGAA-AAAAAAAAGAAAAGA
21589145 AAGAAAAAA
1 AAGAAAAAA
21589154 GGACAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAAAGAAAAGA
Found at i:21589142 original size:17 final size:16
Alignment explanation
Indices: 21589104--21589154 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
21589094 GGAGCATGTC
21589104 AAGAAAA-AAAAAAGAA
1 AAGAAAAGAAAAAA-AA
*
21589120 CA-AAAAGAACAAAAAA
1 AAGAAAAGAA-AAAAAA
*
21589136 AAGAAAAGAAAGAAAA
1 AAGAAAAGAAAAAAAA
21589152 AAG
1 AAG
21589155 GACAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 14 0.48
17 11 0.38
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAAAAA
Found at i:21589673 original size:20 final size:17
Alignment explanation
Indices: 21589646--21589687 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 17
21589636 AAGTGAAAAG
21589646 AAAAAGAAAAAGGTGAAGA
1 AAAAAGAAAAA-GTG-AGA
21589665 AAAATAGAAAAAGTGAGA
1 AAAA-AGAAAAAGTGAGA
21589683 AAAAA
1 AAAAA
21589688 AGGAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.32
19 7 0.32
20 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAAAGTGAGA
Found at i:21589688 original size:20 final size:18
Alignment explanation
Indices: 21589636--21589695 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
21589626 TCAATCCACT
21589636 AAGTGAAAAGAAAAAGAAA
1 AAGTGAAAA-AAAAAGAAA
*
21589655 AAGGTGAAGAAAAATAGAAA
1 AA-GTGAA-AAAAAAAGAAA
*
21589675 AAGTGAGAAAAAAAGGAAA
1 AAGTGA-AAAAAAAAGAAA
21589694 AA
1 AA
21589696 TAATAAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 17 0.49
20 16 0.46
21 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (18 bp):
AAGTGAAAAAAAAAGAAA
Found at i:21589694 original size:18 final size:18
Alignment explanation
Indices: 21589636--21589695 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 18
21589626 TCAATCCACT
*
21589636 AAGTGAAAAGAAAAAGAAA
1 AAGTGAGAA-AAAAAGAAA
*
21589655 AAGGTGAAGAAAAATAGAAA
1 AA-GTG-AGAAAAAAAGAAA
21589675 AAGTGAGAAAAAAAGGAAA
1 AAGTGAGAAAAAAA-GAAA
21589694 AA
1 AA
21589696 TAATAAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 8 0.23
19 11 0.31
20 13 0.37
21 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (18 bp):
AAGTGAGAAAAAAAGAAA
Found at i:21590064 original size:10 final size:10
Alignment explanation
Indices: 21590049--21590078 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21590039 TAATTAACAG
21590049 AGAAAAAAAA
1 AGAAAAAAAA
21590059 AG-AAAAAAA
1 AGAAAAAAAA
21590068 AGAAAAAAAA
1 AGAAAAAAAA
21590078 A
1 A
21590079 TAAGAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:21590066 original size:9 final size:9
Alignment explanation
Indices: 21590052--21590077 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21590042 TTAACAGAGA
21590052 AAAAAAAAG
1 AAAAAAAAG
21590061 AAAAAAAAG
1 AAAAAAAAG
21590070 AAAAAAAA
1 AAAAAAAA
21590078 ATAAGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:21591277 original size:25 final size:26
Alignment explanation
Indices: 21591238--21591291 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
21591228 TTGTATAAAA
21591238 CATTTGCATTAG-AAAAAGACATTTG
1 CATTTGCATTAGAAAAAAGACATTTG
*
21591263 CATTTGCATCT-GAAAAAAGATATTTG
1 CATTTGCAT-TAGAAAAAAGACATTTG
21591289 CAT
1 CAT
21591292 ATATGCATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (26 bp):
CATTTGCATTAGAAAAAAGACATTTG
Found at i:21591551 original size:23 final size:23
Alignment explanation
Indices: 21591519--21591562 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21591509 AGATAAGATG
*
21591519 TTTTGAAACAAAGAGTGAAAAAAA
1 TTTTGAAACAAAAAGT-AAAAAAA
21591543 TTTT-AAACAAAAAGTAAAAA
1 TTTTGAAACAAAAAGTAAAAA
21591563 TTTTTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.23
Consensus pattern (23 bp):
TTTTGAAACAAAAAGTAAAAAAA
Found at i:21591577 original size:21 final size:21
Alignment explanation
Indices: 21591519--21591569 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
21591509 AGATAAGATG
*
21591519 TTTTGAAACAAAGAGTGAAAAAAA
1 TTTT-AAACAAAAAGT--AAAAAA
*
21591543 TTTTAAACAAAAAGTAAAAAT
1 TTTTAAACAAAAAGTAAAAAA
21591564 TTTTAA
1 TTTTAA
21591570 GTAAAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
23 10 0.40
24 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (21 bp):
TTTTAAACAAAAAGTAAAAAA
Found at i:21591817 original size:120 final size:120
Alignment explanation
Indices: 21591620--21591958 Score: 286
Period size: 120 Copynumber: 2.8 Consensus size: 120
21591610 GAATGAGAAT
* *
21591620 ATGATTT-TCGAAGACCT-CTGAGCAAAATTTTAGATTTTTGAAT-ATTTTCTAAGACC-CCCAG
1 ATGATTTCTC-AAGACCTAC-GAG-AAAA-TTTA-AATTTTGAATGATTTTC-AAGACCTCCGA-
** * * * * ***
21591681 GTAAAACCTTAAATTTTTTTATCATTTCT-AAAGACCTCCAAGTGAAACCTTAGGTTTTTAA
59 GTAAAATTTTAGATTTTTTGAACATTTCTCAAAGACCTCCAAGTAAAACCTTAAAATTTTAA
*
21591742 ATGA-TT-TCAAGACTTCTAGGA-AAAATATTAAATCTTTGAATGATTTTCAAGACCTCCGAGTA
1 ATGATTTCTCAAGAC--CTACGAGAAAAT-TTAAAT-TTTGAATGATTTTCAAGACCTCCGAGTA
* * * *
21591804 AAATTTTAGA-TTTTTGAACATTTTTCAAAGGCCTCCAAGTAAAATCTTAAAATTTTGA
62 AAATTTTAGATTTTTTGAACATTTCTCAAAGACCTCCAAGTAAAACCTTAAAATTTTAA
* * * * *
21591862 ATGATTTCTCAAGACCTCCGAGAAAATTTAAATTTTCAAAAGATTTTCCAAGATCTTCGAGTAAA
1 ATGATTTCTCAAGACCTACGAGAAAATTTAAATTTT-GAATGATTTT-CAAGACCTCCGAGTAAA
*
21591927 ATTTTAGA-TTTTTGAATATTT-TCAAAGACCTC
64 ATTTTAGATTTTTTGAACATTTCTCAAAGACCTC
21591959 TGGTCAAAAT
Statistics
Matches: 180, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
119 18 0.10
120 92 0.51
121 55 0.31
122 15 0.08
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (120 bp):
ATGATTTCTCAAGACCTACGAGAAAATTTAAATTTTGAATGATTTTCAAGACCTCCGAGTAAAAT
TTTAGATTTTTTGAACATTTCTCAAAGACCTCCAAGTAAAACCTTAAAATTTTAA
Found at i:21592226 original size:41 final size:41
Alignment explanation
Indices: 21591620--21592442 Score: 302
Period size: 41 Copynumber: 20.4 Consensus size: 41
21591610 GAATGAGAAT
* ** * * *
21591620 ATGATTTTCGAAGACCTCTGAGCAAAATTTTAGATTTTTGA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * * * **
21591661 AT-ATTTTCTAAGACCCCCAGGTAAAACCTTAAATTTTTTT
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* ** * **
21591701 ATCA-TTTCTAAAGACCTCCAAGTGAAACCTTAGGTTTTTAA
1 ATGATTTTC-AAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * * * * *
21591742 ATGA-TTTC-AAGACTTCTAGGAAAAATATTAAATCTTTGA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * *
21591781 ATGATTTTC-AAGACCTCCGAGTAAAATTTTAGATTTTTGAA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTT-AA
* * * *
21591822 CAT--TTTTCAAAGGCCTCCAAGTAAAATCTTAAAATTTTGA
1 -ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* *
21591862 ATGATTTCTC-AAGACCTCCGAG-AAAAT-TTAAATTTTCAA
1 ATGATTT-TCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * * * * * * *
21591901 AAGATTTTCCAAGATCTTCGAGTAAAATTTTAGATTTTTGA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
** * *
21591942 AT-ATTTTCAAAGACCT-CTGGTCAAAATCTCATATTTTTAA
1 ATGATTTTCAAAGACCTCCAAG-CAAAATCTTAAATTTTTAA
* * *** *
21591982 ATGA-TTTCAAAAGGCCTCTAAGCAAAATCTTAAAACGTTGA
1 ATGATTTTC-AAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * ** * * * *
21592023 ATGA-TCTCTAAGATCT-CTGGATAAAATTTTAGATTTTTGA
1 ATGATTTTCAAAGACCTCCAAG-CAAAATCTTAAATTTTTAA
* ** * **
21592063 ACGATTTTTGAAGA-CTTCTGGACAAAA-CTTTAAATTTTTAA
1 ATGATTTTCAAAGACCTCCAAG-CAAAATC-TTAAATTTTTAA
* * * *
21592104 ATGATTTCCAAAG---T-CTAGACAAAATTTTAAATTTTCAA
1 ATGATTTTCAAAGACCTCCAAG-CAAAATCTTAAATTTTTAA
* * * *** *
21592142 AAGATTTTTTAAAAACCT-CAAGGTGAA-CTTTCAATTTTTTAA
1 ATGA-TTTTCAAAGACCTCCAAGCAAAATC-TT-AAATTTTTAA
* *
21592184 ATGATTTTCAAAGACCTCCAAGTAAAATCTTAAATTTCTAA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* **** * * * *
21592225 ATGATTTACAAA-ACCTTTGGGCAAAATTTTAGATTTGTGA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * * *
21592265 ATGATTTCCAAAGACCTCCGAGCAAAATCTTACATTTCTAA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * ** * * * *
21592306 ATGA--TTCCATGACCTCTTAGTAAAATTTTATATTTTTGA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
* * *
21592345 GTGATTTTCAAAAACCTCTGAA-CAAAATCTTAAATTTTTAA
1 ATGATTTTCAAAGACCTC-CAAGCAAAATCTTAAATTTTTAA
* * *
21592386 AGGATTTTC-AAGTCCTCCAAACAAAA-CTTCAAATTTTTAA
1 ATGATTTTCAAAGACCTCCAAGCAAAATCTT-AAATTTTTAA
21592426 ATGATTTCTC-AAGACCT
1 ATGATTT-TCAAAGACCT
21592443 GCGAACAAAG
Statistics
Matches: 577, Mismatches: 169, Indels: 72
0.71 0.21 0.09
Matches are distributed among these distances:
38 25 0.04
39 94 0.16
40 186 0.32
41 242 0.42
42 29 0.05
43 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (41 bp):
ATGATTTTCAAAGACCTCCAAGCAAAATCTTAAATTTTTAA
Found at i:21592371 original size:80 final size:79
Alignment explanation
Indices: 21592183--21592391 Score: 222
Period size: 80 Copynumber: 2.6 Consensus size: 79
21592173 CAATTTTTTA
* * *
21592183 AATGATTTTCAAAGACCTCCAAGTAAAATCTTAAATTTCTAAATGATTTACAAAACCTTTGGGCA
1 AATGATTTTCAAAGACCTCGAA-CAAAATCTTAAATTTCTAAATGA-TTACAAAACCTTTGAGCA
21592248 AAATTTTAGATTTGTG
64 AAATTTTAGATTTGTG
* * * * ** *
21592264 AATGATTTCCAAAGACCTCCGAGCAAAATCTTACATTTCTAAATGATTCCATGACCTCTT-AGTA
1 AATGATTTTCAAAGACCT-CGAACAAAATCTTAAATTTCTAAATGATTACAAAACCT-TTGAGCA
* *
21592328 AAATTTTATATTTTTG
64 AAATTTTAGATTTGTG
* * * *
21592344 AGTGATTTTCAAAAACCTCTGAACAAAATCTTAAATTTTTAAAGGATT
1 AATGATTTTCAAAGACCTC-GAACAAAATCTTAAATTTCTAAATGATT
21592392 TTCAAGTCCT
Statistics
Matches: 106, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
79 1 0.01
80 63 0.59
81 40 0.38
82 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (79 bp):
AATGATTTTCAAAGACCTCGAACAAAATCTTAAATTTCTAAATGATTACAAAACCTTTGAGCAAA
ATTTTAGATTTGTG
Found at i:21592710 original size:46 final size:46
Alignment explanation
Indices: 21592659--21592765 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
21592649 AATCTTTTGT
* * * *
21592659 TTTATTTTCTAAAGTCATTGAGCC-TTAGTTTAAAAAAACTTTTAAA
1 TTTATTTTCAAAAATCATTAAGCCTTTA-CTTAAAAAAACTTTTAAA
* ** *
21592705 TTTATTTTCAAAAATTATTAAGCCTTTACTTAAATGAGCTTTTAAA
1 TTTATTTTCAAAAATCATTAAGCCTTTACTTAAAAAAACTTTTAAA
21592751 TTTATTTTCAAAAAT
1 TTTATTTTCAAAAAT
21592766 TGTGGAGCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
46 49 0.94
47 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (46 bp):
TTTATTTTCAAAAATCATTAAGCCTTTACTTAAAAAAACTTTTAAA
Found at i:21592775 original size:46 final size:46
Alignment explanation
Indices: 21592689--21592808 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
21592679 AGCCTTAGTT
* *
21592689 TAAAA-AAACTTTTAAATTTATTTTCAAAAATTATTAAGCCTTTAC
1 TAAAAGAAGCTTTTAAATTTATTTTCAAAAATTATGAAGCCTTTAC
* * * *
21592734 TTAAATG-AGCTTTTAAATTTATTTTCAAAAATTGTGGAGCCTTTGC
1 -TAAAAGAAGCTTTTAAATTTATTTTCAAAAATTATGAAGCCTTTAC
* * *
21592780 TAAAAGAAGTTTTTAAATTCATTTCCAAA
1 TAAAAGAAGCTTTTAAATTTATTTTCAAA
21592809 TGGTCAAGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
45 5 0.08
46 57 0.92
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (46 bp):
TAAAAGAAGCTTTTAAATTTATTTTCAAAAATTATGAAGCCTTTAC
Found at i:21593702 original size:16 final size:15
Alignment explanation
Indices: 21593651--21593703 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
21593641 AAAAAACCAA
*
21593651 AAAAAAAAAAAAACT
1 AAAACAAAAAAAACT
*
21593666 ACTAAACAGAAAAAAATT
1 A--AAACA-AAAAAAACT
21593684 AAAACAAAAAAAGACT
1 AAAACAAAAAAA-ACT
21593700 AAAA
1 AAAA
21593704 GGTGAAGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.23
16 11 0.35
17 4 0.13
18 9 0.29
ACGTcount: A:0.77, C:0.09, G:0.04, T:0.09
Consensus pattern (15 bp):
AAAACAAAAAAAACT
Found at i:21594661 original size:3 final size:3
Alignment explanation
Indices: 21594655--21594740 Score: 61
Period size: 3 Copynumber: 28.7 Consensus size: 3
21594645 AAAAAGTTAA
* * * *
21594655 AAT AAT AAT TA- AAT -AT ATAT AAT AAAT AGT AAT AAAC AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT -AAT AAT AAT -AAT AAT AAT AAT
* **
21594701 AAT GAT AAT GTT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21594741 AGAGATTGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 5 0.08
3 50 0.79
4 8 0.13
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:21594702 original size:26 final size:26
Alignment explanation
Indices: 21594673--21594741 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
21594663 TTAAATATAT
*
21594673 ATAATAAATAGTAATAAACAATATTA
1 ATAATAAATAGTAATAAACAATAATA
* *
21594699 ATAATGATAAT-GTTA-AAATAATAATA
1 ATAAT-A-AATAGTAATAAACAATAATA
*
21594725 ATAAT-AATAATAATAAA
1 ATAATAAATAGTAATAAA
21594742 GAGATTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 3 0.09
26 19 0.56
27 4 0.12
28 3 0.09
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (26 bp):
ATAATAAATAGTAATAAACAATAATA
Found at i:21594839 original size:3 final size:3
Alignment explanation
Indices: 21594831--21594879 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
21594821 AAATTTATTA
*
21594831 AAT AAT AAT AAT AA- AAT AAT AA- AAT -AT CAAT AAAT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT
21594875 AAT AA
1 AAT AA
21594880 AATTTAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 6 0.15
3 28 0.72
4 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21594849 original size:14 final size:15
Alignment explanation
Indices: 21594829--21594876 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
21594819 GAAAATTTAT
21594829 TAAATAATAATAATA
1 TAAATAATAATAATA
21594844 -AAATAATAA-AATA
1 TAAATAATAATAATA
*
21594857 TCAATAAATAATAATTA
1 TAAAT-AATAATAA-TA
21594874 TAA
1 TAA
21594877 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 12 0.44
15 5 0.19
16 2 0.07
17 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAATAATAATA
Found at i:21597369 original size:28 final size:27
Alignment explanation
Indices: 21597312--21597383 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
21597302 AAATACAATC
*
21597312 ATATTA-ATTAATAAATTTATAATTTAA
1 ATATTATATTAA-AATTTTATAATTTAA
* *
21597339 ATATTATATTAAAATTTTTTAATTTTTA
1 ATATTATATTAAAATTTTATAA-TTTAA
*
21597367 ATATTATATTAATATTT
1 ATATTATATTAAAATTT
21597384 ACATAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 14 0.36
28 25 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATTATATTAAAATTTTATAATTTAA
Found at i:21602319 original size:52 final size:52
Alignment explanation
Indices: 21602233--21602356 Score: 176
Period size: 52 Copynumber: 2.4 Consensus size: 52
21602223 TATAACCATA
* *
21602233 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * *
21602285 CAAATTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
21602337 TAAACTTACCTATTAAGAAT
1 CAAACTTGCCTATTAAGAAT
21602357 TCTCTTTCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:21602375 original size:52 final size:52
Alignment explanation
Indices: 21602233--21602389 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 52
21602223 TATAACCATA
* * * * *
21602233 CAAACTTGCCCATTAAGAATCCCTCTCCTCTT-AGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCT-TTGAGAATTCTTCTCTTGCAAGT
* * *
21602285 CAAATTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCCTTTCCTTTGAGAATTCTTCTCTTGCAAGT
* * *
21602337 TAAACTTACCTATTAAGAATTCTCTTT-CTCTTGA-AATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAA-TCCCTTTCCT-TTGAGAATTCTTCTCTTGCAAGT
21602389 C
1 C
21602390 TTCTTGTCCA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 2 0.02
52 79 0.88
53 9 0.10
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCCTTTCCTTTGAGAATTCTTCTCTTGCAAGT
Found at i:21602424 original size:21 final size:22
Alignment explanation
Indices: 21602406--21602452 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
21602396 TCCATCAAGC
*
21602406 AATATCTGACAAATCTCAAACA
1 AATATCTAACAAATCTCAAACA
* *
21602428 AATCTCTAACAAATCTCTAACA
1 AATATCTAACAAATCTCAAACA
21602450 AAT
1 AAT
21602453 CTCTTATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (22 bp):
AATATCTAACAAATCTCAAACA
Found at i:21602430 original size:11 final size:11
Alignment explanation
Indices: 21602414--21602456 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
21602404 GCAATATCTG
*
21602414 ACAAATCTCAA
1 ACAAATCTCTA
21602425 ACAAATCTCTA
1 ACAAATCTCTA
21602436 ACAAATCTCTA
1 ACAAATCTCTA
21602447 ACAAATCTCT
1 ACAAATCTCT
21602457 TATGAGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:21602597 original size:51 final size:51
Alignment explanation
Indices: 21602539--21602641 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
21602529 TATTAAAAGA
* *
21602539 AGAAAATAAAGCATTAACAAGAATTGCAGCTGAGCTTAAGAGGGAAAATGG
1 AGAAAATAAAGCATTAACAAGAATCGCAGCTGAGCTTAAAAGGGAAAATGG
* * *
21602590 AGAAAATAAAGCATTGACAAGAATCGTAGTTGAGCTTAAAAGGGAAAATGG
1 AGAAAATAAAGCATTAACAAGAATCGCAGCTGAGCTTAAAAGGGAAAATGG
21602641 A
1 A
21602642 TGTTTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (51 bp):
AGAAAATAAAGCATTAACAAGAATCGCAGCTGAGCTTAAAAGGGAAAATGG
Found at i:21603445 original size:33 final size:33
Alignment explanation
Indices: 21603403--21603470 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
21603393 TTTGTTAATG
21603403 TACTTTATTGAGTTGAGGTTGGTGTGGAATCCT
1 TACTTTATTGAGTTGAGGTTGGTGTGGAATCCT
21603436 TACTTTATTGAGTTGAGGTTGGTGTGGAATCCT
1 TACTTTATTGAGTTGAGGTTGGTGTGGAATCCT
21603469 TA
1 TA
21603471 GTTATTACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.19, C:0.09, G:0.29, T:0.43
Consensus pattern (33 bp):
TACTTTATTGAGTTGAGGTTGGTGTGGAATCCT
Found at i:21606756 original size:45 final size:45
Alignment explanation
Indices: 21606683--21606768 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
21606673 TATACACTAT
* * * *
21606683 TTGTCCCTCTGTATCTTTGTTACTAATTTATCCTTTATCCCCTAA
1 TTGTCCCTCTATATCTTTGCTACCAATTTATCCTTCATCCCCTAA
*
21606728 TTGTCCCTTTATATCTTTGCTACCAATTTATCCTTCATCCC
1 TTGTCCCTCTATATCTTTGCTACCAATTTATCCTTCATCCC
21606769 ATGTAAACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (45 bp):
TTGTCCCTCTATATCTTTGCTACCAATTTATCCTTCATCCCCTAA
Found at i:21607974 original size:24 final size:25
Alignment explanation
Indices: 21607942--21607988 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
21607932 AAATCTAGAT
21607942 AATACTCACATTTC-AATTCTTTCG
1 AATACTCACATTTCTAATTCTTTCG
* * *
21607966 AATATTCACCTTTCTCATTCTTT
1 AATACTCACATTTCTAATTCTTT
21607989 TTTTATACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (25 bp):
AATACTCACATTTCTAATTCTTTCG
Found at i:21611146 original size:34 final size:34
Alignment explanation
Indices: 21611103--21611167 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
21611093 ATTTCCAAAC
*
21611103 TTTTGAATATTGTTAAAAATCTAACATTTTAGAT
1 TTTTGAATATTATTAAAAATCTAACATTTTAGAT
*
21611137 TTTTGAATATTATTAAAAATCTGACATTTTA
1 TTTTGAATATTATTAAAAATCTAACATTTTA
21611168 TTAGGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (34 bp):
TTTTGAATATTATTAAAAATCTAACATTTTAGAT
Found at i:21622030 original size:24 final size:23
Alignment explanation
Indices: 21621978--21622030 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
21621968 ACAATGTTAA
*
21621978 AATTTTTTATCAAAATAATATCT
1 AATTTTTTATCAAAATAATAACT
* *
21622001 AGTTTTTTACTTAAAA-AATAACTT
1 AATTTTTTA-TCAAAATAATAAC-T
21622025 AATTTT
1 AATTTT
21622031 GTGGCCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTTTTTATCAAAATAATAACT
Found at i:21625735 original size:7 final size:7
Alignment explanation
Indices: 21625725--21625754 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
21625715 TCCCCTTTTT
21625725 CCTTTGC
1 CCTTTGC
21625732 CCTTTGC
1 CCTTTGC
21625739 CCTTTGC
1 CCTTTGC
21625746 CCTTTGC
1 CCTTTGC
21625753 CC
1 CC
21625755 CCCAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.47, G:0.13, T:0.40
Consensus pattern (7 bp):
CCTTTGC
Found at i:21639537 original size:28 final size:28
Alignment explanation
Indices: 21639505--21639558 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21639495 TGAAAGGGTC
* *
21639505 AAACATAGCTTTGCAATTTAGCTAACAA
1 AAACATAACTTTGAAATTTAGCTAACAA
*
21639533 AAACATAACTTTGAAATTTGGCTAAC
1 AAACATAACTTTGAAATTTAGCTAAC
21639559 CAGAGCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (28 bp):
AAACATAACTTTGAAATTTAGCTAACAA
Found at i:21648425 original size:1 final size:1
Alignment explanation
Indices: 21648421--21648454 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
21648411 TTCCTGTGGT
* *
21648421 CCCCCTCCCCTCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
21648455 AAACCAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.94, G:0.00, T:0.06
Consensus pattern (1 bp):
C
Found at i:21653419 original size:28 final size:28
Alignment explanation
Indices: 21653387--21653440 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21653377 TGAAAGGGTC
* *
21653387 AAACATAGCTTTGCAATTTAGCTAACAA
1 AAACATAACTTTGAAATTTAGCTAACAA
*
21653415 AAACATAACTTTGAAATTTGGCTAAC
1 AAACATAACTTTGAAATTTAGCTAAC
21653441 CAGAGCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (28 bp):
AAACATAACTTTGAAATTTAGCTAACAA
Found at i:21660070 original size:18 final size:19
Alignment explanation
Indices: 21660049--21660099 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
21660039 TATTTATGTA
21660049 ATATAAAATATTATA-TTT
1 ATATAAAATATTATATTTT
**
21660067 ATATATTTATATTATATTTT
1 ATATA-AAATATTATATTTT
21660087 ATATAAAA-ATTAT
1 ATATAAAATATTAT
21660100 GTATTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 10 0.37
19 9 0.33
20 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATAAAATATTATATTTT
Found at i:21660783 original size:25 final size:26
Alignment explanation
Indices: 21660749--21660801 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
21660739 ATGAAAGGAG
*
21660749 TTTTAACACAT-ATAT-ATATAATAA
1 TTTTAACACATGATATGATATAAAAA
21660773 TTTTAAACACATGATATGATATAAAAA
1 TTTT-AACACATGATATGATATAAAAA
21660800 TT
1 TT
21660802 ATATAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 7 0.28
26 4 0.16
27 10 0.40
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTTAACACATGATATGATATAAAAA
Found at i:21661689 original size:19 final size:20
Alignment explanation
Indices: 21661665--21661704 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21661655 AATAATAATC
21661665 ATAATAGT-AATAAAATTAA
1 ATAATAGTCAATAAAATTAA
* *
21661684 ATAATATTCAATAAATTTAA
1 ATAATAGTCAATAAAATTAA
21661704 A
1 A
21661705 ATTTAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (20 bp):
ATAATAGTCAATAAAATTAA
Found at i:21663297 original size:2 final size:2
Alignment explanation
Indices: 21663290--21663314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21663280 CCTCTTCCTA
21663290 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 A
21663315 GACACATACA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21663703 original size:55 final size:55
Alignment explanation
Indices: 21663643--21663749 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
21663633 AAAATGAGAA
21663643 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
1 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
21663698 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTT
1 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTT
21663750 GCGATCATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.26
Consensus pattern (55 bp):
AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
Found at i:21665666 original size:35 final size:35
Alignment explanation
Indices: 21665620--21665689 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
21665610 TGTATATATC
* *
21665620 AAGTCAATTGTAGGTTTATGC-CTGAAAAATATTTG
1 AAGTCAATTGTAGATTTATGCAC-AAAAAATATTTG
* *
21665655 AAGTCAGTTGTATATTTATGCACAAAAAATATTTG
1 AAGTCAATTGTAGATTTATGCACAAAAAATATTTG
21665690 GTTTATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (35 bp):
AAGTCAATTGTAGATTTATGCACAAAAAATATTTG
Found at i:21669199 original size:34 final size:34
Alignment explanation
Indices: 21669113--21669222 Score: 85
Period size: 34 Copynumber: 3.2 Consensus size: 34
21669103 ACAAATGTTA
* * * **
21669113 CTAAAATAACAACTTTTTCTAAATACAAACGTGG
1 CTAATATAACAGCATTTTCTAAATACAAACGCCG
* * * *
21669147 TTAATATAGCTGCATTTTCTAAATTCAAACGCCG
1 CTAATATAACAGCATTTTCTAAATACAAACGCCG
* * ** * *
21669181 CTAATATAACAGCCTTTTCCACCTACAAATGTCG
1 CTAATATAACAGCATTTTCTAAATACAAACGCCG
21669215 CTAATATA
1 CTAATATA
21669223 GCGACATTTT
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (34 bp):
CTAATATAACAGCATTTTCTAAATACAAACGCCG
Found at i:21669829 original size:16 final size:18
Alignment explanation
Indices: 21669808--21669846 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21669798 AAAAACATTG
21669808 AAAAAATA-A-ATAAAAC
1 AAAAAATATATATAAAAC
*
21669824 AAAAAATATATATAATAC
1 AAAAAATATATATAAAAC
21669842 AAAAA
1 AAAAA
21669847 GTTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAATATATATAAAAC
Found at i:21670204 original size:39 final size:39
Alignment explanation
Indices: 21670090--21670206 Score: 93
Period size: 39 Copynumber: 3.0 Consensus size: 39
21670080 TCAATAATTC
* *
21670090 ATTATCTAAAAATATTAAATTTAAATAATCTATTAAATA
1 ATTATCTATAAATATTAAATTTAAATAATTTATTAAATA
* * *
21670129 ATT-T-T-TAATTTTTGATAGATTT---TGATTTAAATTTAAATA
1 ATTATCTATAAATATT-A-A-ATTTAAATAATTT--A-TTAAATA
21670168 ATTATCTATAAATATTAAATTTAAATAATTTATTAAATA
1 ATTATCTATAAATATTAAATTTAAATAATTTATTAAATA
21670207 GAATTATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
36 9 0.16
37 2 0.03
38 3 0.05
39 28 0.48
40 3 0.05
41 2 0.03
42 11 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (39 bp):
ATTATCTATAAATATTAAATTTAAATAATTTATTAAATA
Found at i:21670369 original size:26 final size:26
Alignment explanation
Indices: 21670340--21670389 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
21670330 AGATTTTGAT
21670340 TTCAATTTAAATAA-TTATGTAAAATA
1 TTCAATTTAAATAATTTAT-TAAAATA
21670366 TTCAATTTAAATAATTTATTAAAA
1 TTCAATTTAAATAATTTATTAAAA
21670390 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTCAATTTAAATAATTTATTAAAATA
Found at i:21673853 original size:15 final size:16
Alignment explanation
Indices: 21673833--21673866 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21673823 TTAGATAATT
21673833 TAAATAATTTTA-AAA
1 TAAATAATTTTATAAA
*
21673848 TAAATATTTTTATAAA
1 TAAATAATTTTATAAA
21673864 TAA
1 TAA
21673867 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAATTTTATAAA
Found at i:21675145 original size:3 final size:3
Alignment explanation
Indices: 21675139--21675169 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21675129 TATTTTAAAT
21675139 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21675170 CCATCAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21678321 original size:19 final size:19
Alignment explanation
Indices: 21678277--21678346 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
21678267 TTATTTTAAG
*
21678277 TATTTTT-ATATTAACATAA
1 TATTTTTAATATTAA-ATAT
*
21678296 TA-ATTTAATATTAAATAT
1 TATTTTTAATATTAAATAT
* *
21678314 TATTTTTAA-AATATA-AT
1 TATTTTTAATATTAAATAT
21678331 TATGTTTTAATATTAA
1 TAT-TTTTAATATTAA
21678347 TAATTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
17 5 0.12
18 18 0.45
19 17 0.43
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (19 bp):
TATTTTTAATATTAAATAT
Found at i:21678428 original size:14 final size:14
Alignment explanation
Indices: 21678409--21678435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21678399 TTAATATTAC
21678409 TTAAAAAATTAATT
1 TTAAAAAATTAATT
21678423 TTAAAAAATTAAT
1 TTAAAAAATTAAT
21678436 CAAATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAAAATTAATT
Found at i:21680070 original size:21 final size:20
Alignment explanation
Indices: 21680040--21680085 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
21680030 TAAAAAATAC
21680040 AAAAAATTT-ATTATATTATA
1 AAAAAATTTAATTA-ATTATA
*
21680060 AAAATAATTTAATTAATTTTA
1 AAAA-AATTTAATTAATTATA
21680081 AAAAA
1 AAAAA
21680086 TTCCCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAAATTTAATTAATTATA
Found at i:21684017 original size:20 final size:21
Alignment explanation
Indices: 21683981--21684019 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21683971 TTTTGTTTTT
*
21683981 AACTTTTTATAATTTTTATCA
1 AACTTTCTATAATTTTTATCA
21684002 AACTTTCTAT-ATTTTTAT
1 AACTTTCTATAATTTTTAT
21684020 TCTTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
AACTTTCTATAATTTTTATCA
Found at i:21684018 original size:37 final size:37
Alignment explanation
Indices: 21683976--21684056 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
21683966 TAATTTTTTG
*
21683976 TTTTTA-ACTTTTTATAATTTTTATCAAACTTTCTATA
1 TTTTTATACTTTTTATAATTTTTA-CAAAATTTCTATA
* ** *
21684013 TTTTTATTCTTTTTATGTTTTTTAGAAAATTTCTATA
1 TTTTTATACTTTTTATAATTTTTACAAAATTTCTATA
21684050 TTTTTAT
1 TTTTTAT
21684057 TTTTTAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 24 0.63
38 14 0.37
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (37 bp):
TTTTTATACTTTTTATAATTTTTACAAAATTTCTATA
Found at i:21688770 original size:47 final size:47
Alignment explanation
Indices: 21688719--21688828 Score: 118
Period size: 47 Copynumber: 2.3 Consensus size: 47
21688709 AAATTAGGCC
*
21688719 TTTATAAAGGTAATTTGTTGATCCAAGCT-TTTTGATCGAGTT-GAGCT
1 TTTATAAAGGTAATTTGTTAATCCAAGCTCTTTTG-TCGAGTTGGA-CT
* ** *
21688766 TTTATGAAA-GCAATTTGTTAATCTGAGCTCTTTTGTCGAGTTGGATT
1 TTTAT-AAAGGTAATTTGTTAATCCAAGCTCTTTTGTCGAGTTGGACT
*
21688813 TTTATGAAGGTAATTT
1 TTTATAAAGGTAATTT
21688829 ATTTATTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
46 2 0.04
47 40 0.77
48 10 0.19
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (47 bp):
TTTATAAAGGTAATTTGTTAATCCAAGCTCTTTTGTCGAGTTGGACT
Found at i:21689665 original size:22 final size:20
Alignment explanation
Indices: 21689614--21689670 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
21689604 TCACATTGGG
21689614 AATATTTTATATTAATAAAT
1 AATATTTTATATTAATAAAT
21689634 AATATATTTATACTTAATTTAAA-
1 AATAT-TTTATA-TTAA--TAAAT
21689657 AATATTTTAGTATT
1 AATATTTTA-TATT
21689671 TTAATAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 10 0.31
23 7 0.22
24 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AATATTTTATATTAATAAAT
Found at i:21691125 original size:59 final size:57
Alignment explanation
Indices: 21691060--21691210 Score: 187
Period size: 58 Copynumber: 2.6 Consensus size: 57
21691050 TTTATACAAT
* * *
21691060 AAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTTTATTTTCAA
1 AAAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTT-AAAATTTTTATGTTCAA
* **
21691118 GGAAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTTTAATTTTTATGTTCAA
1 -AAAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTAAAATTTTTATGTTCAA
* *
21691176 AAGAAATTGGTACATTCAACTTTC-CTTCAAAAATA
1 AA-AAATTGATACTTTCAACTTTCTC-TCAAAAATA
21691211 AATTTTTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
57 2 0.02
58 42 0.52
59 37 0.46
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTAAAATTTTTATGTTCAA
Found at i:21691194 original size:58 final size:58
Alignment explanation
Indices: 21691061--21691219 Score: 187
Period size: 59 Copynumber: 2.7 Consensus size: 58
21691051 TTATACAATA
* * ** * *
21691061 AAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAATTTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTT-TTAATTTTTATGTTCAAAG
21691120 AAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTTTAATTTTTATGTTCAAA-
1 AAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTTTAATTTTTATGTTCAAAG
* * *
21691177 AGAAATTGGTACATTCAACTTTC-CTTCAAAAATAAATTTTTTT
1 A-AAATTGATACTTTCAACTTTCTC-TCAAAAAT-ATTTTTTTT
21691220 CATATTTTCA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 2 0.02
58 41 0.47
59 45 0.51
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTCTCTCAAAAATATTTTTTTTAATTTTTATGTTCAAAG
Found at i:21691833 original size:18 final size:19
Alignment explanation
Indices: 21691793--21691834 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
21691783 ACCGGTGCAA
* *
21691793 AAAAATTTATCAGAAACTG
1 AAAAATTTATCAAAAAATG
*
21691812 AAAAATTT-TCAAAAAATT
1 AAAAATTTATCAAAAAATG
21691830 AAAAA
1 AAAAA
21691835 AAAATCTGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAATTTATCAAAAAATG
Found at i:21691837 original size:22 final size:22
Alignment explanation
Indices: 21691812--21691862 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
21691802 TCAGAAACTG
*
21691812 AAAAATTTTCAAAAAATTAAAA
1 AAAAATTTGCAAAAAATTAAAA
* * * *
21691834 AAAAATCTGCCAAAATTTCAAA
1 AAAAATTTGCAAAAAATTAAAA
21691856 AAAAATT
1 AAAAATT
21691863 CCTAAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAATTTGCAAAAAATTAAAA
Found at i:21691869 original size:21 final size:22
Alignment explanation
Indices: 21691831--21691873 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
21691821 CAAAAAATTA
21691831 AAAAAAAATCTGCCAAAATTTC
1 AAAAAAAATCTGCCAAAATTTC
21691853 AAAAAAAAT-T-CCTAAAATTTC
1 AAAAAAAATCTGCC-AAAATTTC
21691874 TAAATTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 9 0.45
22 9 0.45
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAAAATCTGCCAAAATTTC
Found at i:21692083 original size:15 final size:15
Alignment explanation
Indices: 21692063--21692092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21692053 TCAACCACAT
*
21692063 TTTTTTTGTTTTTTA
1 TTTTTTTATTTTTTA
21692078 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
21692093 ATTAATATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:21692132 original size:4 final size:5
Alignment explanation
Indices: 21692111--21692148 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
21692101 CTTATTATCT
21692111 TAAAA TAAAA TAAAA T-AAA TAAAA T-AAA TAAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAAA
21692149 CAATTAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 18 0.60
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:21692132 original size:14 final size:15
Alignment explanation
Indices: 21692112--21692148 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
21692102 TTATTATCTT
21692112 AAAATAAAATAAA-A
1 AAAATAAAATAAATA
*
21692126 TAAATAAAATAAATA
1 AAAATAAAATAAATA
21692141 AAAATAAA
1 AAAATAAA
21692149 CAATTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:21692135 original size:19 final size:19
Alignment explanation
Indices: 21692111--21692148 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
21692101 CTTATTATCT
21692111 TAAAATAAA-ATAAAATAAA
1 TAAAATAAATA-AAAATAAA
21692130 TAAAATAAATAAAAATAAA
1 TAAAATAAATAAAAATAAA
21692149 CAATTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAATAAATAAAAATAAA
Found at i:21696108 original size:2 final size:2
Alignment explanation
Indices: 21696101--21696131 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21696091 GGCGATGATG
21696101 GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21696132 AAGGGGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21696120 original size:15 final size:15
Alignment explanation
Indices: 21696100--21696130 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21696090 AGGCGATGAT
21696100 GGAGAGAGAGAGAGA
1 GGAGAGAGAGAGAGA
21696115 GGAGAGAGAGAGAGA
1 GGAGAGAGAGAGAGA
21696130 G
1 G
21696131 AAAGGGGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (15 bp):
GGAGAGAGAGAGAGA
Found at i:21696121 original size:13 final size:13
Alignment explanation
Indices: 21696103--21696128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21696093 CGATGATGGA
21696103 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
21696116 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
21696129 AGAAAGGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:21703653 original size:16 final size:16
Alignment explanation
Indices: 21703632--21703662 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21703622 AGGGAAAACT
21703632 GATTGATTCCTTGCAC
1 GATTGATTCCTTGCAC
21703648 GATTGATTCCTTGCA
1 GATTGATTCCTTGCA
21703663 TTTTCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
GATTGATTCCTTGCAC
Found at i:21704135 original size:5 final size:5
Alignment explanation
Indices: 21704118--21704147 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
21704108 TGTTTGGTAT
21704118 ATAAA ATTAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA A-TAAA ATAAA ATAAA ATAAA ATAA
21704148 GATGATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:21705127 original size:2 final size:2
Alignment explanation
Indices: 21705120--21705155 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21705110 CAACATTGAA
21705120 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
21705156 CACAAAGAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21713112 original size:28 final size:29
Alignment explanation
Indices: 21713064--21713119 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
21713054 ATAAATAAAT
*
21713064 TAATCATGTTTAATTATTTA-TTCGTATA
1 TAATCATGTTTAATCATTTATTTCGTATA
21713092 TAATCATG-TTAATCATATTATTTCGTAT
1 TAATCATGTTTAATCAT-TTATTTCGTAT
21713120 TATATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 11 0.44
29 7 0.28
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (29 bp):
TAATCATGTTTAATCATTTATTTCGTATA
Found at i:21713488 original size:14 final size:13
Alignment explanation
Indices: 21713463--21713492 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21713453 ATATAGAAAA
21713463 TAAAATAAAATTT
1 TAAAATAAAATTT
*
21713476 TAAAATAAAAATT
1 TAAAATAAAATTT
21713489 TAAA
1 TAAA
21713493 GTAGCGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATAAAATTT
Found at i:21713835 original size:18 final size:19
Alignment explanation
Indices: 21713812--21713853 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
21713802 TTACATTCTT
*
21713812 TTATACATGTC-ATATTGA
1 TTATACAAGTCAATATTGA
21713830 TTATACAAGTCAATATTGA
1 TTATACAAGTCAATATTGA
*
21713849 ATATA
1 TTATA
21713854 AAAATAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (19 bp):
TTATACAAGTCAATATTGA
Found at i:21714264 original size:19 final size:19
Alignment explanation
Indices: 21714227--21714265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21714217 TTTTTTTACA
*
21714227 ATTTTATATAATTTCATTT
1 ATTTTATATAATTTAATTT
21714246 ATTTTATAT-ATTTAAATTT
1 ATTTTATATAATTT-AATTT
21714265 A
1 A
21714266 ATATATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTATATAATTTAATTT
Found at i:21714467 original size:25 final size:25
Alignment explanation
Indices: 21714430--21714482 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
21714420 TGTATTGAAT
* *
21714430 ATTTTAAAGATAATGAAATAAATCA
1 ATTTTAAAAATAACGAAATAAATCA
21714455 ATTTTAAAAATAACGAAATAAATCA
1 ATTTTAAAAATAACGAAATAAATCA
21714480 ATT
1 ATT
21714483 GAGTTAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
ATTTTAAAAATAACGAAATAAATCA
Found at i:21716230 original size:21 final size:21
Alignment explanation
Indices: 21716200--21716250 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
21716190 GATATTTTTA
21716200 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
21716220 AATATTTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
21716241 AATATTTTAT
1 AATATTTTAT
21716251 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:21717785 original size:31 final size:31
Alignment explanation
Indices: 21717747--21717808 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
21717737 CATAAGTTTT
*
21717747 CTCTTTACAAATCAAATTAAAAATGCTGGAA
1 CTCTTTACAAATCAAACTAAAAATGCTGGAA
21717778 CTCTTTACAAATCAAACTAAAAATGCTGGAA
1 CTCTTTACAAATCAAACTAAAAATGCTGGAA
21717809 GAGGTAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (31 bp):
CTCTTTACAAATCAAACTAAAAATGCTGGAA
Found at i:21720129 original size:31 final size:32
Alignment explanation
Indices: 21720088--21720163 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
21720078 AATTAATGAA
21720088 ATCAAATGAAATTC-ATGTGCATTAATATTTT
1 ATCAAATGAAATTCAATGTGCATTAATATTTT
*
21720119 ATCAATTGAAA-TCAAATGTGCATTAATATTTT
1 ATCAAATGAAATTC-AATGTGCATTAATATTTT
*
21720151 ACCAAATGAAATT
1 ATCAAATGAAATT
21720164 ATATTTAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 2 0.05
31 10 0.26
32 26 0.67
33 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (32 bp):
ATCAAATGAAATTCAATGTGCATTAATATTTT
Done.