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 12 of 20
Found at i:4568045 original size:27 final size:29
Alignment explanation
Indices: 4567996--4568049 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4567986 TTAATATATT
*
4567996 TATATTTTTATATAATATCATATTTTAAA
1 TATATTTTTATATAACATCATATTTTAAA
*
4568025 TATATTTTTA-ATGACAT-ATATTTTA
1 TATATTTTTATATAACATCATATTTTA
4568050 TTTTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 5 0.22
29 10 0.43
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (29 bp):
TATATTTTTATATAACATCATATTTTAAA
Found at i:4568148 original size:73 final size:76
Alignment explanation
Indices: 4568015--4568214 Score: 195
Period size: 73 Copynumber: 2.6 Consensus size: 76
4568005 ATATAATATC
* * *
4568015 ATATTTTAAATATATTTTTAATGA-CATATATTTTATTTTTATTTA--TTACTATAATCTTATAT
1 ATATTTT-AATATATTTTTTAT-ATTATATATTTTATTTTAATTTATTTTACTATAA-CTTATAT
*
4568077 -AT-TTTA-TTTTT
63 AATGTTAATTTTTT
*
4568088 ATTTCTTTAATATATTTTTTATATTATATATTTTATTTTAATTTATTTTACCTAT-A-TTATATA
1 ATAT-TTTAATATATTTTTTATATTATATATTTTATTTTAATTTATTTTA-CTATAACTTATAT-
4568151 AATGTTAATTTTTT
63 AATGTTAATTTTTT
*
4568165 ATATTTTAAT-TTTTATTCTTATATTATATATTTTATTTTAATATT-TTTTA
1 ATATTTTAATATATT-TT-TTATATTATATATTTTATTTTAAT-TTATTTTA
4568215 TTTTAATTAT
Statistics
Matches: 108, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
72 1 0.01
73 41 0.38
74 3 0.03
75 9 0.08
76 15 0.14
77 37 0.34
78 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (76 bp):
ATATTTTAATATATTTTTTATATTATATATTTTATTTTAATTTATTTTACTATAACTTATATAAT
GTTAATTTTTT
Found at i:4568175 original size:15 final size:15
Alignment explanation
Indices: 4568155--4568222 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
4568145 TATATAAATG
4568155 TTAATTTTTTATATT
1 TTAATTTTTTATATT
*
4568170 TTAA-TTTTTAT-TC
1 TTAATTTTTTATATT
*
4568183 TTATATTATATATTTTATT
1 TTA-ATT-T-T-TTATATT
4568202 TTAATATTTTT-TATT
1 TTAAT-TTTTTATATT
4568217 TTAATT
1 TTAATT
4568223 ATAGCATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.09
14 9 0.21
15 14 0.33
16 3 0.07
17 2 0.05
18 6 0.14
19 5 0.12
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (15 bp):
TTAATTTTTTATATT
Found at i:4568219 original size:40 final size:39
Alignment explanation
Indices: 4568071--4568219 Score: 114
Period size: 40 Copynumber: 3.8 Consensus size: 39
4568061 TACTATAATC
* * *
4568071 TTATATATTTTATTTT-TATTTCTTTAATATATTTTTTATA
1 TTATATATTTTATTTTATATTT-TTTATTTTA-TTCTTATA
*
4568111 TTATATATTTTATTTTA-A---TTTATTTTA--CCTATA
1 TTATATATTTTATTTTATATTTTTTATTTTATTCTTATA
* * *
4568144 TTATATAAATGTTAATTTTTTATATTTTAATTTTTATTCTTATA
1 TTATAT--AT-TTTATTTTATAT-TTTTTA-TTTTATTCTTATA
4568188 TTATATATTTTATTTTAATATTTTTTATTTTA
1 TTATATATTTTATTTT-ATATTTTTTATTTTA
4568220 ATTATAGCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
33 10 0.12
35 2 0.02
36 14 0.16
37 1 0.01
40 22 0.26
41 15 0.18
42 10 0.12
44 11 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (39 bp):
TTATATATTTTATTTTATATTTTTTATTTTATTCTTATA
Found at i:4582917 original size:2 final size:2
Alignment explanation
Indices: 4582910--4582942 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4582900 CAAAAATACA
*
4582910 AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4582943 TTGATGCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4586002 original size:5 final size:5
Alignment explanation
Indices: 4585992--4586024 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
4585982 CCACTTTCTT
4585992 TTTTG TTTTG TTTTG TTTTG TTTT- TTTT- TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
4586025 CTAAACCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:4587573 original size:12 final size:12
Alignment explanation
Indices: 4587533--4587582 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
4587523 TAACCACAAC
*
4587533 TACATACATATG
1 TACATACATATA
* *
4587545 TACCTACATACA
1 TACATACATATA
*
4587557 AACATACATATA
1 TACATACATATA
*
4587569 TACATATATATA
1 TACATACATATA
4587581 TA
1 TA
4587583 GTGTAGTTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (12 bp):
TACATACATATA
Found at i:4590272 original size:23 final size:23
Alignment explanation
Indices: 4590246--4590301 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4590236 TAATCTTCAA
4590246 ACTTTATATTTAAAACCATTTGT
1 ACTTTATATTTAAAACCATTTGT
* *
4590269 ACTTTACATTTAAAATCATTTGT
1 ACTTTATATTTAAAACCATTTGT
4590292 ACATTTATAT
1 AC-TTTATAT
4590302 AAATGTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (23 bp):
ACTTTATATTTAAAACCATTTGT
Found at i:4595826 original size:2 final size:2
Alignment explanation
Indices: 4595819--4595847 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4595809 AGGAAGGGGA
4595819 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4595848 TCAGAAATGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4612380 original size:19 final size:19
Alignment explanation
Indices: 4612358--4612413 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
4612348 ATTTTAATTT
*
4612358 TTAATTTATTTTTTA-TAAA
1 TTAATTT-TTATTTATTAAA
*
4612377 TTAACTTTTTATTTATTAAT
1 TTAA-TTTTTATTTATTAAA
4612397 TTAATTTTTA-TTATTAA
1 TTAATTTTTATTTATTAA
4612414 TATATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 7 0.21
19 16 0.48
20 10 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAATTTTTATTTATTAAA
Found at i:4623620 original size:28 final size:29
Alignment explanation
Indices: 4623577--4623633 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
4623567 TTTAATTCAA
4623577 AATAAAAATATAAAAATTAAATTAAATTT
1 AATAAAAATATAAAAATTAAATTAAATTT
* *
4623606 AATAAAAA-CTAAAAATTAATTTAAATTT
1 AATAAAAATATAAAAATTAAATTAAATTT
4623634 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAAAAATATAAAAATTAAATTAAATTT
Found at i:4632942 original size:24 final size:24
Alignment explanation
Indices: 4632910--4632963 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
4632900 AAGGAAACCT
4632910 TTGTACCATCCTGTTCAGTAACAG
1 TTGTACCATCCTGTTCAGTAACAG
*
4632934 TTGTACCATCTTGTTCAGTAACAG
1 TTGTACCATCCTGTTCAGTAACAG
4632958 TTGTAC
1 TTGTAC
4632964 GGTAGCCCAT
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:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (24 bp):
TTGTACCATCCTGTTCAGTAACAG
Found at i:4637072 original size:2 final size:2
Alignment explanation
Indices: 4637065--4637092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4637055 AGAAGAATAA
4637065 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
4637093 TTATCTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4637813 original size:19 final size:18
Alignment explanation
Indices: 4637784--4637824 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
4637774 ACAGACTTTC
4637784 ATATAATATATA-ATTATT
1 ATATAATATATATA-TATT
4637802 ATATATATATATATATATT
1 ATATA-ATATATATATATT
4637821 ATAT
1 ATAT
4637825 GTTTCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATATATATATATT
Found at i:4646668 original size:20 final size:21
Alignment explanation
Indices: 4646643--4646697 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
4646633 ATACAAATTA
4646643 TAATTATATTAATTTA-ATAT
1 TAATTATATTAATTTATATAT
* *
4646663 TAATTATATTTATTTATTTAT
1 TAATTATATTAATTTATATAT
*
4646684 AAATTTATATTAAT
1 TAA-TTATATTAAT
4646698 ATAAAATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.52
21 5 0.17
22 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATTATATTAATTTATATAT
Found at i:4646700 original size:16 final size:16
Alignment explanation
Indices: 4646621--4646702 Score: 53
Period size: 16 Copynumber: 4.9 Consensus size: 16
4646611 TATTAAGGTA
*
4646621 TTATATGTACATATACAAA
1 TTATAT-TA-ATATA-AAT
*
4646640 TTATAATT-ATATTAAT
1 TTAT-ATTAATATAAAT
*
4646656 TTAATATTAAT-TATAT
1 TT-ATATTAATATAAAT
*
4646672 TTAT-TTATTTATAAAT
1 TTATATTA-ATATAAAT
4646688 TTATATTAATATAAA
1 TTATATTAATATAAA
4646703 ATTACAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 26 0.52
17 11 0.22
19 5 0.10
20 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (16 bp):
TTATATTAATATAAAT
Found at i:4647261 original size:214 final size:215
Alignment explanation
Indices: 4646849--4647263 Score: 539
Period size: 214 Copynumber: 1.9 Consensus size: 215
4646839 TATAATTGTA
* * * * *
4646849 TATATATATTATATATATTTAATTTATACATTAGTATTACTATAATTTATAATAGACTTTATTTA
1 TATATATATTACATATATTTAATTTATACATTAGCATGACTATAACTTATAATAAACTTTATTTA
* * * * * * *
4646914 TATGATTACACATAATAACTTTATTAGTTATTACGTTAGATTTTAGAACTTATTGTTTATAATTA
66 TATGATTACACATAATAAATTTATTAGTCATCACATCAGATTTTAGAACATATTGTGTATAATTA
* * * * *
4646979 GTTATTATTTATACAAACTTTGCTATAAAACATTTTAGCATACAATTTGTACCATTAACTTTATA
131 GTTATTATTTATACAAACTTTGCTATAAAACATTATAACATACAAGTTATACAATTAACTTTATA
4647044 TATATAACAAAGTAATATAT
196 TATATAACAAAGTAATATAT
* *
4647064 TATATATA-TACATATATTTAATTTATACA-TACGCATGATTATAACTTATAATAAATTTTATTT
1 TATATATATTACATATATTTAATTTATACATTA-GCATGACTATAACTTATAATAAACTTTATTT
* * *
4647127 ATATGATTACACTTAATAAATTTATTAGTCATCATATCAGATTTTATAACATATTGTGTATAATT
65 ATATGATTACACATAATAAATTTATTAGTCATCACATCAGATTTTAGAACATATTGTGTATAATT
* * * * * *
4647192 AGTTATTATTTATATAAATTTTGTTATAAAATATTATAACATATAAGTTATATAATTAA-TTTCA
130 AGTTATTATTTATACAAACTTTGCTATAAAACATTATAACATACAAGTTATACAATTAACTTT-A
4647256 TATATATA
194 TATATATA
4647264 TAATTATGAA
Statistics
Matches: 170, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
213 5 0.03
214 157 0.92
215 8 0.05
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (215 bp):
TATATATATTACATATATTTAATTTATACATTAGCATGACTATAACTTATAATAAACTTTATTTA
TATGATTACACATAATAAATTTATTAGTCATCACATCAGATTTTAGAACATATTGTGTATAATTA
GTTATTATTTATACAAACTTTGCTATAAAACATTATAACATACAAGTTATACAATTAACTTTATA
TATATAACAAAGTAATATAT
Found at i:4656405 original size:67 final size:67
Alignment explanation
Indices: 4656316--4656449 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 67
4656306 ATTGTAGATG
* * * *
4656316 TAGACTTAGGCAAGACCTCCTATGAGGCTTAGATTCTGAATTTAGTTAACTATTGATTGTTTGTC
1 TAGACTTAGACAAGACCCCCTATGAGGCTCAGATTCTAAATTTAGTTAACTATTGATTGTTTGTC
4656381 TT
66 TT
*
4656383 TAGACTTAGACAAGACCCCCTATGAGGCTCAGATTCTAAATTTAGTTAACTATTTATTGTTTGTC
1 TAGACTTAGACAAGACCCCCTATGAGGCTCAGATTCTAAATTTAGTTAACTATTGATTGTTTGTC
4656448 TT
66 TT
4656450 GTCACTAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (67 bp):
TAGACTTAGACAAGACCCCCTATGAGGCTCAGATTCTAAATTTAGTTAACTATTGATTGTTTGTC
TT
Found at i:4656728 original size:16 final size:16
Alignment explanation
Indices: 4656704--4656734 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4656694 TGTGAAATGA
*
4656704 TTCATGAATGATAGAG
1 TTCAAGAATGATAGAG
4656720 TTCAAGAATGATAGA
1 TTCAAGAATGATAGA
4656735 CTGCAATTGA
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:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (16 bp):
TTCAAGAATGATAGAG
Found at i:4659183 original size:22 final size:22
Alignment explanation
Indices: 4659155--4659198 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4659145 AAGACAGCTC
4659155 AAATGTTTTTTGCTTGCGAAAG
1 AAATGTTTTTTGCTTGCGAAAG
4659177 AAATGTTTTTTGCTTGCGAAAG
1 AAATGTTTTTTGCTTGCGAAAG
4659199 TTAGGTTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (22 bp):
AAATGTTTTTTGCTTGCGAAAG
Found at i:4659779 original size:3 final size:3
Alignment explanation
Indices: 4659771--4659795 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4659761 GTTGTACTTT
4659771 GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA G
4659796 GCCTGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:4659824 original size:2 final size:2
Alignment explanation
Indices: 4659817--4659843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4659807 TTAACACCAG
4659817 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 G
4659844 GATATGCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4664270 original size:28 final size:28
Alignment explanation
Indices: 4664238--4664324 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
4664228 AAAAATTAAA
*
4664238 ATATTTAAATAAATTTTTATATTTTATT
1 ATATTTAAATAAAATTTTATATTTTATT
**
4664266 ATATTT-AATCAAGCTTTTATACTTTTATT
1 ATATTTAAAT-AAAATTTTATA-TTTTATT
* **
4664295 TTAAACTAAATAAAATTTTATATTTT-TT
1 AT-ATTTAAATAAAATTTTATATTTTATT
4664323 AT
1 AT
4664325 TTTGAGTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
27 3 0.06
28 18 0.38
29 12 0.26
30 11 0.23
31 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (28 bp):
ATATTTAAATAAAATTTTATATTTTATT
Found at i:4667661 original size:2 final size:2
Alignment explanation
Indices: 4667654--4667681 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4667644 TTGATTTAGA
4667654 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
4667682 CTTTAGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4669138 original size:12 final size:13
Alignment explanation
Indices: 4669121--4669158 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
4669111 AAATGATATT
4669121 ATAATTAAAAT-A
1 ATAATTAAAATAA
4669133 ATAATTAAAAATAA
1 ATAATT-AAAATAA
4669147 ATATATTAAAAT
1 ATA-ATTAAAAT
4669159 TTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 9 0.39
15 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATTAAAATAA
Found at i:4669145 original size:13 final size:14
Alignment explanation
Indices: 4669121--4669157 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4669111 AAATGATATT
4669121 ATAATT-AAAAT-A
1 ATAATTAAAAATAA
4669133 ATAATTAAAAATAA
1 ATAATTAAAAATAA
4669147 ATATATTAAAA
1 ATA-ATTAAAA
4669158 TTTATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 4 0.18
15 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATTAAAAATAA
Found at i:4670728 original size:19 final size:20
Alignment explanation
Indices: 4670691--4670733 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4670681 TTGAGAAATT
* *
4670691 TATTTTTTGATAATGTTTAA
1 TATTTTTTGAAAATATTTAA
4670711 TATTTTTT-AAAATATTTAA
1 TATTTTTTGAAAATATTTAA
4670730 TATT
1 TATT
4670734 ATTAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTTTTTGAAAATATTTAA
Found at i:4673954 original size:20 final size:21
Alignment explanation
Indices: 4673906--4673956 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
4673896 TTAAGGAAAA
* *
4673906 TTTAAATAAATTGTTTTTTAT
1 TTTAAATTAATTGTTTTTAAT
* *
4673927 ATTCAATTAATT-TTTTTAAT
1 TTTAAATTAATTGTTTTTAAT
4673947 TTTAAATTAA
1 TTTAAATTAA
4673957 ATATATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAAATTAATTGTTTTTAAT
Found at i:4674034 original size:18 final size:18
Alignment explanation
Indices: 4674013--4674070 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
4674003 TTTATATTAA
*
4674013 ATAATATATTAATATATC
1 ATAATAAATTAATATATC
4674031 ATAATAAATT-ATA-A-C
1 ATAATAAATTAATATATC
*
4674046 ATAATACATTAATATGAT-
1 ATAATAAATTAATAT-ATC
4674064 ATAATAA
1 ATAATAA
4674071 CATTCTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.30
16 4 0.12
17 3 0.09
18 16 0.48
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATAAATTAATATATC
Found at i:4674170 original size:26 final size:27
Alignment explanation
Indices: 4674141--4674196 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4674131 AAATAAATTT
*
4674141 ATTTAATTTAA-AATAA-AAATATAAAA
1 ATTTAA-TTAAGAATAATAAAAATAAAA
*
4674167 ATTTAATTAAGTATAATAAAAATAAAA
1 ATTTAATTAAGAATAATAAAAATAAAA
4674194 ATT
1 ATT
4674197 GTTTAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 10 0.38
27 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATTTAATTAAGAATAATAAAAATAAAA
Found at i:4680821 original size:23 final size:23
Alignment explanation
Indices: 4680765--4680817 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
4680755 CTTTATATCT
*
4680765 AATTAT-ATTGAT-AAATTTATA
1 AATTATAATTAATAAAATTTATA
*
4680786 AATTATTATTAATAAAATTT-TA
1 AATTATAATTAATAAAATTTATA
*
4680808 TATTATAATT
1 AATTATAATT
4680818 TAATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 15 0.56
23 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTATAATTAATAAAATTTATA
Found at i:4683889 original size:34 final size:34
Alignment explanation
Indices: 4683848--4683920 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 34
4683838 AAATTTAAAT
4683848 TTAAATAA-TCAAAAAC-AATATTTCAAAT-ATCAAC
1 TTAAATAACT-AAAAACAAATA-TTCAAATAAT-AAC
4683882 TTAAATAACTAAAAACAAATATTCAAATAATAAC
1 TTAAATAACTAAAAACAAATATTCAAATAATAAC
4683916 TTAAA
1 TTAAA
4683921 CAATATTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (34 bp):
TTAAATAACTAAAAACAAATATTCAAATAATAAC
Found at i:4684108 original size:15 final size:17
Alignment explanation
Indices: 4684090--4684122 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4684080 ATTATGATTG
4684090 ATAA-TTTTATAA-ATT
1 ATAAGTTTTATAATATT
4684105 ATAAGTTTTATAATATT
1 ATAAGTTTTATAATATT
4684122 A
1 A
4684123 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATAAGTTTTATAATATT
Found at i:4684437 original size:24 final size:22
Alignment explanation
Indices: 4684373--4684438 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
4684363 TCTTTTTAGG
* *
4684373 TATATATATATATATTATAATTT
1 TATATAAATA-ATATTATAATAT
4684396 TATATAAATAA-ATGTATATATAT
1 TATATAAATAATAT-TATA-ATAT
*
4684419 TATAATTAATAATATTATAA
1 TAT-ATAAATAATATTATAA
4684439 GTTATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.06
22 5 0.14
23 16 0.44
24 11 0.31
25 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATAAATAATATTATAATAT
Found at i:4689819 original size:105 final size:105
Alignment explanation
Indices: 4689695--4689913 Score: 438
Period size: 105 Copynumber: 2.1 Consensus size: 105
4689685 CGTTAAGTAC
4689695 AATATTTTTATATATCACCTCATAATACTGATTATTTTATATATTTGCATATTATTAATTGTAAT
1 AATATTTTTATATATCACCTCATAATACTGATTATTTTATATATTTGCATATTATTAATTGTAAT
4689760 ACTAATTCCTATTCCTGTTATAATGTGCTACTCTTCCATA
66 ACTAATTCCTATTCCTGTTATAATGTGCTACTCTTCCATA
4689800 AATATTTTTATATATCACCTCATAATACTGATTATTTTATATATTTGCATATTATTAATTGTAAT
1 AATATTTTTATATATCACCTCATAATACTGATTATTTTATATATTTGCATATTATTAATTGTAAT
4689865 ACTAATTCCTATTCCTGTTATAATGTGCTACTCTTCCATA
66 ACTAATTCCTATTCCTGTTATAATGTGCTACTCTTCCATA
4689905 AATATTTTT
1 AATATTTTT
4689914 TCATAAGCCA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 114 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (105 bp):
AATATTTTTATATATCACCTCATAATACTGATTATTTTATATATTTGCATATTATTAATTGTAAT
ACTAATTCCTATTCCTGTTATAATGTGCTACTCTTCCATA
Found at i:4691792 original size:2 final size:2
Alignment explanation
Indices: 4691785--4691815 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4691775 AACACATAAC
4691785 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4691816 CCTAGCAGCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4696429 original size:2 final size:2
Alignment explanation
Indices: 4696422--4696451 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4696412 GAGTAGTCTG
4696422 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
4696452 AAATCAAAAG
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):
TA
Found at i:4717905 original size:5 final size:5
Alignment explanation
Indices: 4717895--4717927 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
4717885 GTCCTTTTTC
4717895 TTCCT TTCCT TTCCT TTCCT TTCCT TTCCT TTC
1 TTCCT TTCCT TTCCT TTCCT TTCCT TTCCT TTC
4717928 AAGAGGGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCCT
Found at i:4719158 original size:61 final size:61
Alignment explanation
Indices: 4719043--4719160 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 61
4719033 AATGAATGCG
* * *
4719043 ATTTCTATCGATACATTATTTAAATGTATTGAGAGATTTGAAGAGCAAGACATTCTGGCTGA
1 ATTTCTATCGATACATTATTCAAATGTATCGAGAAATTTGAAGA-CAAGACATTCTGGCTGA
4719105 ATTT-TATCGATACATTATTCAAATGTATCGA-ATAATTTGAAG-CAAAGATCATTCTG
1 ATTTCTATCGATACATTATTCAAATGTATCGAGA-AATTTGAAGAC-AAGA-CATTCTG
4719161 TCTAAAAAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 1 0.02
60 5 0.10
61 40 0.80
62 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (61 bp):
ATTTCTATCGATACATTATTCAAATGTATCGAGAAATTTGAAGACAAGACATTCTGGCTGA
Found at i:4719444 original size:45 final size:45
Alignment explanation
Indices: 4719339--4719535 Score: 149
Period size: 45 Copynumber: 4.4 Consensus size: 45
4719329 TGTCTATTAA
* ** **
4719339 GAGATTACTTCCGATGATGATTACATTG-TGATGTCAT-TCGTT--
1 GAGATTACTTCGGATGATGATTATGTTGATGATACCATCT-GTTAG
* * *
4719381 GAGATTACTTC-AAGTGATGAGTATGTCT-ATGATACCATCTATTAG
1 GAGATTACTTCGGA-TGATGATTATGT-TGATGATACCATCTGTTAG
* * **
4719426 GAGATTACTTCGGATGATGATTATGTTGATGATATCATCCGTCCG
1 GAGATTACTTCGGATGATGATTATGTTGATGATACCATCTGTTAG
* * * *
4719471 GAGATTA-TTCCAGATGTTGATTACGTTGATGACACCATCTGTCTA-
1 GAGATTACTT-CGGATGATGATTATGTTGATGATACCATCTGT-TAG
4719516 GAGATTACTTCGGATGATGA
1 GAGATTACTTCGGATGATGA
4719536 CTTGACTTTT
Statistics
Matches: 120, Mismatches: 24, Indels: 19
0.74 0.15 0.12
Matches are distributed among these distances:
41 1 0.01
42 20 0.17
43 10 0.08
44 4 0.03
45 82 0.68
46 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (45 bp):
GAGATTACTTCGGATGATGATTATGTTGATGATACCATCTGTTAG
Found at i:4724260 original size:55 final size:55
Alignment explanation
Indices: 4724190--4724302 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
4724180 ACAACTGAGC
4724190 AAATTTTGGAGCCATCCCTTTCCTACTTGCTTTTACAAATTCAACTGGAAGCTTG
1 AAATTTTGGAGCCATCCCTTTCCTACTTGCTTTTACAAATTCAACTGGAAGCTTG
4724245 AAATTTTGGAGCCATCCCTTTCCTACTTGCTTTTACAAATTCAACTGGAAGCTTG
1 AAATTTTGGAGCCATCCCTTTCCTACTTGCTTTTACAAATTCAACTGGAAGCTTG
4724300 AAA
1 AAA
4724303 CAAATTTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (55 bp):
AAATTTTGGAGCCATCCCTTTCCTACTTGCTTTTACAAATTCAACTGGAAGCTTG
Found at i:4727534 original size:2 final size:2
Alignment explanation
Indices: 4727527--4727552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4727517 GTTGCATTAC
4727527 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
4727553 TCAACATTAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4729113 original size:22 final size:21
Alignment explanation
Indices: 4729068--4729169 Score: 61
Period size: 21 Copynumber: 4.9 Consensus size: 21
4729058 TTAAACAATT
*
4729068 TTAAAT-AATTTTTATTATAT
1 TTAAATAAATTTTTATTATAA
* * *
4729088 TTAATTATATTTTTATTTTAAA
1 TTAAATAAATTTTTATTAT-AA
4729110 TTAAATAAA-TTTTA-TA-AA
1 TTAAATAAATTTTTATTATAA
* * *
4729128 TATTAATTAATTATTATTATTAA
1 T-TAAATAAATTTTTATTA-TAA
*
4729151 TTAAA-ATATTATTTATTAT
1 TTAAATAAATT-TTTATTAT
4729170 TTTATATTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
18 3 0.05
19 6 0.10
20 10 0.17
21 21 0.35
22 17 0.28
23 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAATAAATTTTTATTATAA
Found at i:4729115 original size:42 final size:42
Alignment explanation
Indices: 4729068--4729184 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
4729058 TTAAACAATT
*
4729068 TTAAATAATTTTTATTATATTTAATTATATTTTTATT-TTAAA
1 TTAAATAATTTTTATTATATTTAATTATATTATTATTATT-AA
* *
4729110 TTAAATAAATTTTA-TAAATATTAATTA-ATTATTATTATTAA
1 TTAAATAATTTTTATTATAT-TTAATTATATTATTATTATTAA
4729151 TTAAA-ATATTATTTATTAT-TTTATATTATATTAT
1 TTAAATA-ATT-TTTATTATATTTA-ATTATATTAT
4729185 GTTATTGTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
40 1 0.02
41 24 0.38
42 31 0.49
43 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (42 bp):
TTAAATAATTTTTATTATATTTAATTATATTATTATTATTAA
Found at i:4729177 original size:29 final size:30
Alignment explanation
Indices: 4729125--4729183 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4729115 TAAATTTTAT
4729125 AAATATTAATTAATTATTATTATTA-ATTA
1 AAATATTAATTAATTATTATTATTATATTA
* *
4729154 AAATATT-ATTTATTATTTTATATTATATTA
1 AAATATTAATTAATTATTAT-TATTATATTA
4729184 TGTTATTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 12 0.46
30 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
AAATATTAATTAATTATTATTATTATATTA
Found at i:4733068 original size:14 final size:16
Alignment explanation
Indices: 4733045--4733086 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
4733035 AACGCGAATC
4733045 TTTCTCTCTCTTATTA
1 TTTCTCTCTCTTATTA
4733061 TTTCTCTCTCTTATTA
1 TTTCTCTCTCTTATTA
4733077 TTTCTCTCTC
1 TTTCTCTCTC
4733087 ATCAGTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.10, C:0.29, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCTCTCTCTTATTA
Found at i:4739306 original size:6 final size:6
Alignment explanation
Indices: 4739295--4739319 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4739285 TTAATCTATG
4739295 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
4739320 ATAGCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:4746558 original size:17 final size:16
Alignment explanation
Indices: 4746514--4746551 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
4746504 ATGAAACTCA
4746514 AAAAATAATTTTAAAC
1 AAAAATAATTTTAAAC
4746530 AAAAATAATTTTAAAC
1 AAAAATAATTTTAAAC
4746546 AAAAAT
1 AAAAAT
4746552 TCATTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAATTTTAAAC
Found at i:4748015 original size:17 final size:19
Alignment explanation
Indices: 4747989--4748032 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4747979 AATTTATATA
4747989 TTTAACAATAAA-TA-TTAT
1 TTTAA-AATAAATTATTTAT
4748007 TTTAAAATAAATTATTTAT
1 TTTAAAATAAATTATTTAT
4748026 TTTAAAA
1 TTTAAAA
4748033 ATTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAAATAAATTATTTAT
Found at i:4751160 original size:16 final size:16
Alignment explanation
Indices: 4751139--4751175 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4751129 GAAAAAGCTG
4751139 AAGAAGAAGAAAAGAA
1 AAGAAGAAGAAAAGAA
* *
4751155 AAGAAGAAGGAAAGAG
1 AAGAAGAAGAAAAGAA
4751171 AAGAA
1 AAGAA
4751176 AAATAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAAAGAA
Found at i:4767085 original size:19 final size:19
Alignment explanation
Indices: 4767063--4767104 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4767053 TAAATTTGAT
4767063 AAAAATAAAATATTAAAATA
1 AAAAAT-AAATATTAAAATA
* *
4767083 AAAAATATATTTTAAAATA
1 AAAAATAAATATTAAAATA
4767102 AAA
1 AAA
4767105 TTTTAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATAAATATTAAAATA
Found at i:4773910 original size:23 final size:23
Alignment explanation
Indices: 4773884--4773929 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4773874 AAATTAAATT
4773884 AAATATAAATTTAAAAAAATAAA
1 AAATATAAATTTAAAAAAATAAA
***
4773907 AAATATTTTTTTAAAAAAATAAA
1 AAATATAAATTTAAAAAAATAAA
4773930 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAATTTAAAAAAATAAA
Found at i:4773936 original size:19 final size:21
Alignment explanation
Indices: 4773893--4773944 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
4773883 TAAATATAAA
4773893 TTTAAAAAAATAAAAAATATTTT
1 TTTAAAAAAAT--AAAATATTTT
4773916 TTTAAAAAAAT-AAAT-TTTT
1 TTTAAAAAAATAAAATATTTT
4773935 TTTAAAAAAA
1 TTTAAAAAAA
4773945 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 14 0.48
20 4 0.14
23 11 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAAAAATAAAATATTTT
Found at i:4773946 original size:20 final size:21
Alignment explanation
Indices: 4773897--4773946 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
4773887 TATAAATTTA
*
4773897 AAAAAATAAAAAATATTTTTTT
1 AAAAAA-AATAAATATTTTTTT
4773919 -AAAAAAATAAAT-TTTTTTT
1 AAAAAAAATAAATATTTTTTT
4773938 AAAAAAAAT
1 AAAAAAAAT
4773947 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAAATAAATATTTTTTT
Found at i:4773968 original size:19 final size:19
Alignment explanation
Indices: 4773911--4773974 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
4773901 AATAAAAAAT
4773911 ATTTTTTTAAAAAAAT-AA
1 ATTTTTTTAAAAAAATAAA
*
4773929 ATTTTTTT--TAAAA-AAA
1 ATTTTTTTAAAAAAATAAA
4773945 A----TTTAAAAAAATAAA
1 ATTTTTTTAAAAAAATAAA
4773960 ATTTTTTTAAAAAAA
1 ATTTTTTTAAAAAAA
4773975 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
12 3 0.08
14 4 0.11
15 4 0.11
16 7 0.19
18 8 0.22
19 10 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTTTTAAAAAAATAAA
Found at i:4773986 original size:31 final size:30
Alignment explanation
Indices: 4773916--4773985 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
4773906 AAAATATTTT
*
4773916 TTTAAAAAAATAAATTTTTTTTAAAAAAAA
1 TTTAAAAAAATAAAATTTTTTTAAAAAAAA
4773946 TTTAAAAAAATAAAATTTTTTTAAAAAAAA
1 TTTAAAAAAATAAAATTTTTTTAAAAAAAA
4773976 TTTAAAAAAA
1 TTTAAAAAAA
4773986 AAACTTAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTAAAAAAATAAAATTTTTTTAAAAAAAA
Found at i:4774509 original size:25 final size:25
Alignment explanation
Indices: 4774457--4774509 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4774447 TCTGTAAAAA
* *
4774457 AATTAATAAATATATTAACATCATT
1 AATTAATAAATATATTAACATAAAT
*
4774482 AATTACATAAA-ATTTTAACATAAAT
1 AATTA-ATAAATATATTAACATAAAT
4774507 AAT
1 AAT
4774510 ATACTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
AATTAATAAATATATTAACATAAAT
Found at i:4786100 original size:15 final size:15
Alignment explanation
Indices: 4786070--4786118 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4786060 CGTTTGGTAC
*
4786070 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
* *
4786086 ATTATAGGTAATGTG
1 ATTACAAGTAATGTG
*
4786101 ATTGCAAGTAATGTG
1 ATTACAAGTAATGTG
4786116 ATT
1 ATT
4786119 GCAGGAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:4786119 original size:15 final size:15
Alignment explanation
Indices: 4786093--4786121 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4786083 GTGATTATAG
4786093 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
4786108 GTAATGTGATTGCA
1 GTAATGTGATTGCA
4786122 GGAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:4786380 original size:14 final size:14
Alignment explanation
Indices: 4786361--4786711 Score: 74
Period size: 14 Copynumber: 23.9 Consensus size: 14
4786351 TATTATTATA
4786361 ATATTTTATATTTT
1 ATATTTTATATTTT
*
4786375 ATATTTAATATATTT
1 ATATTTTATAT-TTT
4786390 ATA-TTTATATTATT
1 ATATTTTATATT-TT
**
4786404 A-ATTTTATATAAT
1 ATATTTTATATTTT
**
4786417 ATTCATTTCT-TA-AAT
1 A-T-ATTT-TATATTTT
*
4786432 ATATTTTA-ATGTCAT
1 ATATTTTATAT-T-TT
4786447 ATATTTTAT-TTTT
1 ATATTTTATATTTT
4786460 ATTTATTATTATAATTTT
1 A--TATT-TTAT-ATTTT
4786478 ATATATTT-TATTTTT
1 ATAT-TTTATA-TTTT
4786493 ATATATTTATA-TTT
1 ATAT-TTTATATTTT
*
4786507 ATATTATTA-CTTTT
1 ATATT-TTATATTTT
**
4786521 ATATAATATCATTTCT
1 ATATTTTAT-ATTT-T
**
4786537 -TA-AATATATTTT
1 ATATTTTATATTTT
* *
4786549 -TAATGTCATATTTT
1 AT-ATTTTATATTTT
* *
4786563 TTATTTTATTTGTTTT
1 ATATTTTA--TATTTT
*
4786579 ATAATTTATATATTT
1 ATATTTTATAT-TTT
*
4786594 AT-TTTAATATATTT
1 ATATTTTATAT-TTT
4786608 ATA-TTTATATTATT
1 ATATTTTATATT-TT
*
4786622 A-ATTTTTATATAATATC
1 ATA-TTTTATAT--T-TT
4786639 ATATTTTAAAATATTTT
1 ATATTTT---ATATTTT
* *
4786656 A-ATGTCATATATTT
1 ATATTTTATAT-TTT
4786670 AT-TTTTATTTATTATT
1 ATATTTTA--TATT-TT
4786686 ATATTTTATATATTT
1 ATATTTTATAT-TTT
4786701 -TATTTT-TATTT
1 ATATTTTATATTT
4786712 CTTTAATATA
Statistics
Matches: 261, Mismatches: 28, Indels: 98
0.67 0.07 0.25
Matches are distributed among these distances:
12 6 0.02
13 27 0.10
14 98 0.38
15 62 0.24
16 40 0.15
17 17 0.07
18 7 0.03
20 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (14 bp):
ATATTTTATATTTT
Found at i:4786497 original size:111 final size:111
Alignment explanation
Indices: 4786266--4786709 Score: 669
Period size: 111 Copynumber: 4.0 Consensus size: 111
4786256 AAAATATAAG
*
4786266 TTTATATATATTATATTTTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTATATAT-TTATA-TTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAAT
* *
4786331 ATCATA-ATTTTATTTCTATTTATTATTATAATATTT-TATATTTTATAT
64 GTCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTAT-T
*
4786379 TTAATATATTTATATTTATATTATTAATTTTATATAATATTCATTTCTTAAATATA-TTTTAATG
1 TTTATATATTTATATTTATATTATTAATTTTATATAATA-TCATTTCTTAAATATATTTTTAATG
4786443 TCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 TCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
*
4786490 TTTATATATTTATATTTATATTATTACTTTTATATAATATCATTTCTTAAATATATTTTTAATGT
1 TTTATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATGT
* *
4786555 CATATTTTTTA-TTTTATTTGTT-TTATAA-TTTATATA-TTTATT
66 CATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
*
4786597 TTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAA-ATA-TTTTAAT
1 TTTATATATTTATATTTATATTATTAA-TTTTATATAATATCAT-TTCTTAAATATATTTTTAAT
4786659 GTCATATA-TTTATTTTTATTTATTATTAT-ATTTTATATATTTTATT
64 GTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
4786705 TTTAT
1 TTTAT
4786710 TTCTTTAATA
Statistics
Matches: 308, Mismatches: 13, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
105 4 0.01
106 25 0.08
107 46 0.15
108 39 0.13
109 8 0.03
110 26 0.08
111 96 0.31
112 56 0.18
113 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (111 bp):
TTTATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATGT
CATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
Found at i:4786534 original size:28 final size:27
Alignment explanation
Indices: 4786266--4786646 Score: 83
Period size: 28 Copynumber: 13.9 Consensus size: 27
4786256 AAAATATAAG
* *
4786266 TTTATATATATTATATTTTTTATTATTAAT
1 TTTATATATA-TATA-TTTATATT-TTACT
* * * *
4786296 TTTATATA-ATATCATTTCTTAAATATATT
1 TTTATATATATAT-ATTT-AT-ATTTTACT
*
4786325 TTTA-ATATCATA-ATTT-TATTTCTATT
1 TTTATATAT-ATATATTTATATTT-TACT
4786351 TATTAT-TATA-ATATTTTATATTTTA-T
1 T-TTATATATATATA-TTTATATTTTACT
* *
4786377 ATTTAATATATTTATATTTATATTATTAAT
1 -TTT-ATATATATATATTTATATT-TTACT
* * *
4786407 TTTATATA-ATATTCATTTCTTAAATATA-T
1 TTTATATATATA-T-ATTT-AT-ATTTTACT
* *
4786436 TTTA-ATGTCATATATTT-TATTTTTATT
1 TTTATATAT-ATATATTTATA-TTTTACT
* *
4786463 TATTAT-TATA-ATTTTATATATTTTATT
1 T-TTATATATATATATT-TATATTTTACT
*
4786490 TTTATATATTTATATTTATATTATTACT
1 TTTATATATATATATTTATATT-TTACT
* * * *
4786518 TTTATATA-ATATCATTTCTTAAATATATT
1 TTTATATATATAT-ATTT-AT-ATTTTACT
* *
4786547 TTTA-ATGTCATAT-TTTTTATTTTA-T
1 TTTATATAT-ATATATTTATATTTTACT
4786572 TTGT-T-T-TATA-ATTTATATATTTA-T
1 TT-TATATATATATATTTATAT-TTTACT
* *
4786596 TTTAATATATTTATATTTATATTATTAAT
1 TTT-ATATATATATATTTATATT-TTACT
*
4786625 TTT-TATATA-ATA-TCATATTTTA
1 TTTATATATATATATTTATATTTTA
4786647 AAATATTTTA
Statistics
Matches: 273, Mismatches: 30, Indels: 102
0.67 0.07 0.25
Matches are distributed among these distances:
23 10 0.04
24 11 0.04
25 15 0.05
26 32 0.12
27 51 0.19
28 84 0.31
29 42 0.15
30 26 0.10
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTATATATATATATTTATATTTTACT
Found at i:4786590 original size:9 final size:8
Alignment explanation
Indices: 4786576--4786742 Score: 58
Period size: 8 Copynumber: 21.6 Consensus size: 8
4786566 TTTTATTTGT
4786576 TTTATA-A
1 TTTATATA
4786583 TTTATATA
1 TTTATATA
4786591 TTTAT-T-
1 TTTATATA
*
4786597 TTAATATA
1 TTTATATA
4786605 -TT-TATA
1 TTTATATA
4786611 TTTATAT-
1 TTTATATA
*
4786618 TATTA-ATT
1 T-TTATATA
4786626 TTTATATA
1 TTTATATA
*
4786634 -ATATCATA
1 TTTAT-ATA
*
4786642 TTTTAAAATA
1 -TTT-ATATA
4786652 TTT-TA-A
1 TTTATATA
*
4786658 TGTCATATA
1 T-TTATATA
4786667 TTTAT-T-
1 TTTATATA
*
4786673 TTTATTTA
1 TTTATATA
4786681 -TTATTATA
1 TTTA-TATA
4786689 TTTTATATA
1 -TTTATATA
*
4786698 TTT-TATT
1 TTTATATA
* *
4786705 TTTATTTC
1 TTTATATA
4786713 TTTAATATA
1 TTT-ATATA
*
4786722 TTT-TTTA
1 TTTATATA
4786729 TCTTATATA
1 T-TTATATA
4786738 TTTAT
1 TTTAT
4786743 TTTAATTTGT
Statistics
Matches: 119, Mismatches: 17, Indels: 47
0.65 0.09 0.26
Matches are distributed among these distances:
6 15 0.13
7 37 0.31
8 40 0.34
9 19 0.16
10 7 0.06
11 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:4786598 original size:20 final size:19
Alignment explanation
Indices: 4786569--4786632 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
4786559 TTTTTTATTT
*
4786569 TATTTGTTTTATAATTTATA
1 TATTTATTTTATAATTT-TA
4786589 TATTTATTTTA-ATATATTTA
1 TATTTATTTTATA-AT-TTTA
*
4786609 TATTTATATTATTAATTTTTA
1 TATTTATTTTA-TAA-TTTTA
4786630 TAT
1 TAT
4786633 AATATCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 24 0.65
21 10 0.27
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTTATTTTATAATTTTA
Found at i:4786674 original size:47 final size:48
Alignment explanation
Indices: 4786593--4786703 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 48
4786583 TTTATATATT
*
4786593 TATTTTAATATA-TTTATATTTATATTATTAATTTTTATATAATATCA
1 TATTTTAATATATTTTATATTCATATTATTAATTTTTATATAATATCA
* * * * *
4786640 TATTTTAAAATATTTTA-ATGTCATA-TATTTATTTTTATTTATTATTA
1 TATTTTAATATATTTTATAT-TCATATTATTAATTTTTATATAATATCA
4786687 TATTTT-ATATATTTTAT
1 TATTTTAATATATTTTAT
4786704 TTTTATTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
46 9 0.17
47 37 0.69
48 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (48 bp):
TATTTTAATATATTTTATATTCATATTATTAATTTTTATATAATATCA
Found at i:4786784 original size:218 final size:221
Alignment explanation
Indices: 4786266--4786851 Score: 651
Period size: 218 Copynumber: 2.7 Consensus size: 221
4786256 AAAATATAAG
* * * * *
4786266 TTTATATATATTATATTTTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTATATAT-TTATA-TATATATTATTACTTTTATATAATATAATTTCTTAAATATATTTTAAAT
*
4786331 ATCATAA-TTTTATTTCTATTTATTATTATAATATTTTATATTTTATATTTAATATATTTATATT
64 AT-ATAATTTTTATTT-TATTTATTATTATAATATTATATATTTTATATTTAATATATTTATATT
4786395 TATATTATTAATTTTATATAATATTCATTTCTTAAATATATTTTAATGTCATATATTTTATTTTT
127 TATATTATTAATTTTATATAATATTCATTTCTTAAATATATTTTAATGTCATATATTTTATTTTT
4786460 ATTTATTATTATAATTTTATATATTTTATT
192 ATTTATTATTATAATTTTATATATTTTATT
* * * *
4786490 TTTATATATTTATATTTATATTATTACTTTTATATAATATCATTTCTTAAATATATTTTTAATGT
1 TTTATATATTTATATATATATTATTACTTTTATATAATATAATTTCTTAAATATATTTTAAATAT
* *
4786555 CATATTTTTTATTTTATTTGTT-TTATAAT-TTATATA-TTTAT-TTTAATATATTTATATTTAT
66 -ATAATTTTTATTTTATTTATTATTATAATATTATATATTTTATATTTAATATATTTATATTTAT
4786616 ATTATTAATTTTTATATAATA-TCATATT-TTAAA-ATATTTTAATGTCATATA-TTTATTTTTA
130 ATTATTAA-TTTTATATAATATTCAT-TTCTTAAATATATTTTAATGTCATATATTTTATTTTTA
4786677 TTTATTATTAT-ATTTTATATATTTTATT
193 TTTATTATTATAATTTTATATATTTTATT
* * * * * * * **
4786705 TTTATTTCTTTA-ATATAT-TTTTTATCTTATATATTTATTTTAATTTGTTTTATCTATATTATA
1 TTTATATATTTATATATATATTATTA-CTT-T-TATATAATATAA-TT-TCTTAAATATATT-T-
*
4786768 TAAATAT-TAATTTTTATATTTA-TT-TTATT-TAAT-TT-TTTATTCTTATA-TT-ATATATTT
59 TAAATATATAATTTTTAT-TTTATTTATTATTATAATATTATATATT-TTATATTTAATATATTT
* *
4786825 AT-TTTA-ATTA-TAATATTATAAAATATT
122 ATATTTATATTATTAATTTTATATAATATT
4786852 TTTAATAAGA
Statistics
Matches: 323, Mismatches: 23, Indels: 42
0.83 0.06 0.11
Matches are distributed among these distances:
213 15 0.05
214 12 0.04
215 32 0.10
216 36 0.11
217 39 0.12
218 66 0.20
219 24 0.07
220 11 0.03
221 7 0.02
222 59 0.18
223 13 0.04
224 9 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (221 bp):
TTTATATATTTATATATATATTATTACTTTTATATAATATAATTTCTTAAATATATTTTAAATAT
ATAATTTTTATTTTATTTATTATTATAATATTATATATTTTATATTTAATATATTTATATTTATA
TTATTAATTTTATATAATATTCATTTCTTAAATATATTTTAATGTCATATATTTTATTTTTATTT
ATTATTATAATTTTATATATTTTATT
Found at i:4786813 original size:23 final size:22
Alignment explanation
Indices: 4786774--4786818 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4786764 TATATAAATA
*
4786774 TTAATTTTTATATTTATTTTAT
1 TTAATTTTTATATTTATATTAT
4786796 TTAATTTTT-TATTCTTATATTAT
1 TTAATTTTTATA-T-TTATATTAT
4786819 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 8 0.40
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTAATTTTTATATTTATATTAT
Found at i:4786829 original size:48 final size:47
Alignment explanation
Indices: 4786675--4786829 Score: 115
Period size: 48 Copynumber: 3.2 Consensus size: 47
4786665 TATTTATTTT
* * *
4786675 TATTTATTATTATATTT-TATATATTT-TATTTTTATTTCTT-TAATATA
1 TATTTATTTTTATATTTAT-TTTATTTAT-TTTTTA-TTCTTATATTATA
* * * *
4786722 TTTTTTATCTTATATATTTATTTTAATT-TGTTTTA-TC-TATATTATA
1 -TATTTAT-TTTTATATTTATTTTATTTATTTTTTATTCTTATATTATA
4786768 TAAATATTAATTTTTATATTTATTTTATTTAATTTTTTATTCTTATATTATA
1 T--AT-TT-ATTTTTATATTTATTTTATTT-ATTTTTTATTCTTATATTATA
4786820 TATTTATTTT
1 TATTTATTTT
4786830 AATTATAATA
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
45 2 0.02
46 8 0.09
47 1 0.01
48 35 0.41
49 18 0.21
50 9 0.11
51 2 0.02
52 10 0.12
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (47 bp):
TATTTATTTTTATATTTATTTTATTTATTTTTTATTCTTATATTATA
Found at i:4787944 original size:28 final size:28
Alignment explanation
Indices: 4787904--4787962 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
4787894 TACTTTTCAC
* *
4787904 ATGGAAATGAAAATGGGGAAAATTAAGA
1 ATGGAAATGAAAATGAGAAAAATTAAGA
*
4787932 ATGGAAATGAAAATGAGAAAAATTAATA
1 ATGGAAATGAAAATGAGAAAAATTAAGA
4787960 ATG
1 ATG
4787963 ATTTTTTCCA
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:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (28 bp):
ATGGAAATGAAAATGAGAAAAATTAAGA
Found at i:4788519 original size:13 final size:14
Alignment explanation
Indices: 4788501--4788529 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4788491 TAAGCATAAA
4788501 TTTT-AAAAATATT
1 TTTTAAAAAATATT
4788514 TTTTAAAAAATATT
1 TTTTAAAAAATATT
4788528 TT
1 TT
4788530 ACATTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAAAAATATT
Found at i:4796905 original size:38 final size:38
Alignment explanation
Indices: 4796861--4796934 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
4796851 AATAATTTCG
* *
4796861 TTTATATCACTTCTTAATCATTTCATAAAAAAATTTTA
1 TTTATATCACTTCCTAATAATTTCATAAAAAAATTTTA
**
4796899 TTTATATCACTTCCTAATAATTTTGTAAAAAAATTT
1 TTTATATCACTTCCTAATAATTTCATAAAAAAATTT
4796935 ATTGGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.47
Consensus pattern (38 bp):
TTTATATCACTTCCTAATAATTTCATAAAAAAATTTTA
Found at i:4797147 original size:25 final size:25
Alignment explanation
Indices: 4797119--4797181 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 25
4797109 AACGTGTAAT
*
4797119 AATTTTTTTTAACATGTTGTATAAC
1 AATTTTTTTTAACATGATGTATAAC
* *
4797144 AATTTTTTTTTAATATGATGTGTAAC
1 AA-TTTTTTTTAACATGATGTATAAC
4797170 AATTTTTTTTAA
1 AATTTTTTTTAA
4797182 TATAACATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 12 0.35
26 22 0.65
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.56
Consensus pattern (25 bp):
AATTTTTTTTAACATGATGTATAAC
Found at i:4797318 original size:27 final size:26
Alignment explanation
Indices: 4797097--4797364 Score: 120
Period size: 25 Copynumber: 10.3 Consensus size: 26
4797087 TATTATAACA
* *
4797097 TTTTTTT-AATATAACGTGTAATAAT
1 TTTTTTTCAATATGATGTGTAATAAT
* * * *
4797122 TTTTTTT-AACATGTTGTATAACAAT
1 TTTTTTTCAATATGATGTGTAATAAT
* *
4797147 TTTTTTTTAATATGATGTGTAACAAT
1 TTTTTTTCAATATGATGTGTAATAAT
* ** *
4797173 TTTTTTT-AATATAACATGTAGTAA-
1 TTTTTTTCAATATGATGTGTAATAAT
** * * * *
4797197 -CATTTTGAACT-TAATATGTAACAAT
1 TTTTTTTCAA-TATGATGTGTAATAAT
** ** *
4797222 GACATTTTTCAATATGACATTTAATAA-
1 --TTTTTTTCAATATGATGTGTAATAAT
*
4797249 TTTTTTT-AATATGATATGTAATAAT
1 TTTTTTTCAATATGATGTGTAATAAT
* *
4797274 TTTTTTTCAACATAATGTGTAATAAT
1 TTTTTTTCAATATGATGTGTAATAAT
* *
4797300 TTTATTTTCAATGTGATGTATAATAATGATT
1 TTT-TTTTCAATATGATGTGTAAT-A--A-T
* * *
4797331 TTTTTTTCAACATGAAGTATAATAAT
1 TTTTTTTCAATATGATGTGTAATAAT
4797357 ATTTTTTT
1 -TTTTTTT
4797365 TTAACATCAT
Statistics
Matches: 187, Mismatches: 40, Indels: 30
0.73 0.16 0.12
Matches are distributed among these distances:
23 4 0.02
24 27 0.14
25 51 0.27
26 41 0.22
27 25 0.13
28 16 0.09
29 1 0.01
30 18 0.10
31 4 0.02
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (26 bp):
TTTTTTTCAATATGATGTGTAATAAT
Found at i:4797338 original size:30 final size:29
Alignment explanation
Indices: 4797267--4797371 Score: 110
Period size: 30 Copynumber: 3.7 Consensus size: 29
4797257 ATATGATATG
* *
4797267 TAATAATTTTTTTTCAACAT-AATGTGTAA
1 TAATATTTTTTTTTCAACATGAA-GTATAA
* ** *
4797296 T-A-ATTTTATTTTCAATGTGATGTATAA
1 TAATATTTTTTTTTCAACATGAAGTATAA
4797323 TAATGATTTTTTTTTCAACATGAAGTATAA
1 TAAT-ATTTTTTTTTCAACATGAAGTATAA
4797353 TAATATTTTTTTTT-AACAT
1 TAATATTTTTTTTTCAACAT
4797372 CATATATAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
27 18 0.29
28 8 0.13
29 11 0.18
30 25 0.40
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (29 bp):
TAATATTTTTTTTTCAACATGAAGTATAA
Found at i:4797388 original size:27 final size:26
Alignment explanation
Indices: 4797249--4797402 Score: 103
Period size: 27 Copynumber: 5.6 Consensus size: 26
4797239 CATTTAATAA
* *
4797249 TTTTTTTAATATGATATGTAATAATT
1 TTTTTTTAACATGATATATAATAATT
* * * *
4797275 TTTTTTCAACATAATGTGTAATAATT
1 TTTTTTTAACATGATATATAATAATT
* ** *
4797301 TTATTTTCAATGTGATGTATAATAATGATT
1 TT-TTTTTAACATGA--TAT-ATAATAATT
4797331 TTTTTTTCAACATGA-AGTATAATAATATT
1 TTTTTTT-AACATGATA-TATAAT-A-ATT
*
4797360 TTTTTTTAACATCATATATAATAACTT
1 TTTTTTTAACATGATATATAATAA-TT
**
4797387 TTTTCCTAACATGATA
1 TTTTTTTAACATGATA
4797403 AAAGTAACAA
Statistics
Matches: 100, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
26 25 0.25
27 31 0.31
28 13 0.13
29 17 0.17
30 14 0.14
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (26 bp):
TTTTTTTAACATGATATATAATAATT
Found at i:4817665 original size:63 final size:64
Alignment explanation
Indices: 4817549--4817675 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 64
4817539 ATTTGGGAGA
* *
4817549 TTATATTTGGACCTTTGAAGACGAAAAGAAAACCAAGATATTAATACAAAAGTAATGAGAAATT
1 TTATAGTTGGACCTTTAAAGACGAAAAGAAAACCAAGATATTAATACAAAAGTAATGAGAAATT
* *
4817613 TTATAGTTGGGCCTTTAAAGACGAAAAG-AAACCAAGATATTATTACAAAAGTAATGAGAAATT
1 TTATAGTTGGACCTTTAAAGACGAAAAGAAAACCAAGATATTAATACAAAAGTAATGAGAAATT
4817676 AATCAAACTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 34 0.58
64 25 0.42
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (64 bp):
TTATAGTTGGACCTTTAAAGACGAAAAGAAAACCAAGATATTAATACAAAAGTAATGAGAAATT
Found at i:4826771 original size:21 final size:21
Alignment explanation
Indices: 4826746--4826791 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4826736 AAAATTTATT
4826746 AAATTTAAA-ATAATAAAATAA
1 AAATTTAAATA-AATAAAATAA
* *
4826767 AAATTTAATTAAATACAATAA
1 AAATTTAAATAAATAAAATAA
4826788 AAAT
1 AAAT
4826792 ATTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTTAAATAAATAAAATAA
Found at i:4830411 original size:2 final size:2
Alignment explanation
Indices: 4830406--4830434 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4830396 TATATATTCT
4830406 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
4830435 TGAGATTCTT
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:4833960 original size:2 final size:2
Alignment explanation
Indices: 4833955--4833998 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
4833945 CCCAACAAGG
4833955 TA TA TA -A TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4833997 TA
1 TA
4833999 AATAAAGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4845142 original size:2 final size:2
Alignment explanation
Indices: 4845135--4845168 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4845125 GGCGAGACAG
4845135 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
4845169 CCCCATGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4846568 original size:18 final size:18
Alignment explanation
Indices: 4846547--4846590 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4846537 TGCAGAAGAT
*
4846547 GAAGAGCCCGAAGATGAA
1 GAAGAGCCAGAAGATGAA
** *
4846565 GAAGAGGAAGAGGATGAA
1 GAAGAGCCAGAAGATGAA
4846583 GAAGAGCC
1 GAAGAGCC
4846591 TGTTCAGCCA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.39, T:0.05
Consensus pattern (18 bp):
GAAGAGCCAGAAGATGAA
Found at i:4850341 original size:17 final size:16
Alignment explanation
Indices: 4850327--4850358 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4850317 AACGCAAATG
4850327 ACTAAAAAACTCAAAA
1 ACTAAAAAACTCAAAA
*
4850343 ACTCAAAAACTCAAAA
1 ACTAAAAAACTCAAAA
4850359 GATTCGAAGA
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:0.66, C:0.22, G:0.00, T:0.12
Consensus pattern (16 bp):
ACTAAAAAACTCAAAA
Found at i:4850350 original size:7 final size:8
Alignment explanation
Indices: 4850331--4850358 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4850321 CAAATGACTA
4850331 AAAAACTC
1 AAAAACTC
4850339 AAAAACTC
1 AAAAACTC
4850347 AAAAACTC
1 AAAAACTC
4850355 AAAA
1 AAAA
4850359 GATTCGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.21, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAACTC
Found at i:4856194 original size:2 final size:2
Alignment explanation
Indices: 4856187--4856217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4856177 CTCTCCCTTA
4856187 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4856218 AAAATCCAAG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4861000 original size:2 final size:2
Alignment explanation
Indices: 4860995--4861041 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4860985 GATCTGTAAG
*
4860995 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4861037 CT CT C
1 CT CT C
4861042 ATTTCCGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4875706 original size:4 final size:4
Alignment explanation
Indices: 4875697--4875731 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
4875687 ATAGGTACAT
4875697 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA- ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4875732 GCAAATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:4883363 original size:8 final size:8
Alignment explanation
Indices: 4883347--4883425 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
4883337 GTATGTGTAC
4883347 ATATACAT
1 ATATACAT
*
4883355 ATATGCAT
1 ATATACAT
* *
4883363 ATGTATAT
1 ATATACAT
*
4883371 GTATACAT
1 ATATACAT
*
4883379 ATAGGTATAT
1 ATA--TACAT
* * *
4883389 ACATATAC
1 ATATACAT
4883397 ATATACAT
1 ATATACAT
**
4883405 ATATAGGT
1 ATATACAT
4883413 ATATACAT
1 ATATACAT
4883421 ATATA
1 ATATA
4883426 AAAAAGCTTG
Statistics
Matches: 51, Mismatches: 18, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
8 45 0.88
10 6 0.12
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:4883363 original size:14 final size:14
Alignment explanation
Indices: 4883346--4883424 Score: 62
Period size: 12 Copynumber: 5.9 Consensus size: 14
4883336 TGTATGTGTA
4883346 CATATACATATATG
1 CATATACATATATG
*
4883360 CATAT--GTATATG
1 CATATACATATATG
*
4883372 --TATACATATAGG
1 CATATACATATATG
*
4883384 TATATACATATA--
1 CATATACATATATG
4883396 CATATACATATATAGG
1 CATATACATATAT--G
*
4883412 TATATACATATAT
1 CATATACATATAT
4883425 AAAAAAGCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.06
12 22 0.42
14 15 0.29
16 12 0.23
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (14 bp):
CATATACATATATG
Found at i:4883388 original size:30 final size:28
Alignment explanation
Indices: 4883325--4883381 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
4883315 GGCAGAATCA
* *
4883325 ATATAGGCATATGTATGTGTACATATAC
1 ATATATGCATATGTATGTATACATATAC
4883353 ATATATGCATATGTATATGTATACATATA
1 ATATATGCATATG--TATGTATACATATA
4883382 GGTATATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
30 13 0.52
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (28 bp):
ATATATGCATATGTATGTATACATATAC
Found at i:4883389 original size:20 final size:20
Alignment explanation
Indices: 4883366--4883415 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
4883356 TATGCATATG
* **
4883366 TATATGTATACATATAGGTA
1 TATACGTATACATATACATA
*
4883386 TATACATATACATATACATA
1 TATACGTATACATATACATA
*
4883406 TATAGGTATA
1 TATACGTATA
4883416 TACATATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (20 bp):
TATACGTATACATATACATA
Found at i:4883394 original size:30 final size:29
Alignment explanation
Indices: 4883338--4883422 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
4883328 TAGGCATATG
* ** *
4883338 TATGTGTACATATACATATATGCATATGTA
1 TATGTATACATATAGGTATATACATAT-TA
4883368 TATGTATACATATAGGTATATACATA-TA
1 TATGTATACATATAGGTATATACATATTA
* * * *
4883396 CATATACATATATAGGTATATACATAT
1 TATGTATACATATAGGTATATACATAT
4883423 ATAAAAAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 24 0.52
30 22 0.48
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (29 bp):
TATGTATACATATAGGTATATACATATTA
Found at i:4916495 original size:17 final size:16
Alignment explanation
Indices: 4916473--4916506 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
4916463 AAAGTTTTTT
4916473 TTATTTATATTATTTAA
1 TTATTTATA-TATTTAA
4916490 TTATTTATATATTTAA
1 TTATTTATATATTTAA
4916506 T
1 T
4916507 AATTCTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTATATATTTAA
Found at i:4927666 original size:2 final size:2
Alignment explanation
Indices: 4927659--4927684 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4927649 ATTCAGTTGA
4927659 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
4927685 TTGGCTCCTT
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:4931449 original size:18 final size:18
Alignment explanation
Indices: 4931400--4931451 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
4931390 ATAATTTATT
4931400 TTTATTAATTTT-AAAAA
1 TTTATTAATTTTAAAAAA
* *
4931417 -TTACT-ATTATAAAAAA
1 TTTATTAATTTTAAAAAA
4931433 TTTATTAATTTTAAAAAA
1 TTTATTAATTTTAAAAAA
4931451 T
1 T
4931452 AAGTGCTCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 4 0.14
18 11 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTATTAATTTTAAAAAA
Found at i:4931527 original size:23 final size:23
Alignment explanation
Indices: 4931479--4931529 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
4931469 TGTGCTCCTT
* *
4931479 ATTTTTTAAAAAATATAATAATA
1 ATTTTTTAAAAAATATAAAAAAA
*
4931502 ATTTTTTAAATTAATA-AAAAAAA
1 ATTTTTTAAA-AAATATAAAAAAA
4931525 ATTTT
1 ATTTT
4931530 AATCTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTTTTAAAAAATATAAAAAAA
Found at i:4931970 original size:28 final size:27
Alignment explanation
Indices: 4931930--4932053 Score: 113
Period size: 28 Copynumber: 4.5 Consensus size: 27
4931920 TTGTAACAAC
*
4931930 TTTTTTATCATAATGTGTAATAACTAAA
1 TTTTTAAT-ATAATGTGTAATAACTAAA
* *
4931958 TTTTTCAATATAATGTATAATAATTAAA
1 TTTTT-AATATAATGTGTAATAACTAAA
* * *
4931986 TTTTTAATATGACGTGTAATAACTATA
1 TTTTTAATATAATGTGTAATAACTAAA
* * * * * *
4932013 TTTGTTAACATGATGTATGATAATTACA
1 TTT-TTAATATAATGTGTAATAACTAAA
4932041 TTTTTAATATAAT
1 TTTTTAATATAAT
4932054 TTTTTATTAC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
27 28 0.36
28 48 0.62
29 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTTAATATAATGTGTAATAACTAAA
Found at i:4932003 original size:55 final size:55
Alignment explanation
Indices: 4931944--4932050 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
4931934 TTATCATAAT
*
4931944 GTGTAATAACTAAATTT-TTCAATATAATGTATAATAATTAAATTTTTAATATGAC
1 GTGTAATAACTAAATTTGTT-AACATAATGTATAATAATTAAATTTTTAATATGAC
* * * *
4931999 GTGTAATAACTATATTTGTTAACATGATGTATGATAATTACATTTTTAATAT
1 GTGTAATAACTAAATTTGTTAACATAATGTATAATAATTAAATTTTTAATAT
4932051 AATTTTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 44 0.96
56 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (55 bp):
GTGTAATAACTAAATTTGTTAACATAATGTATAATAATTAAATTTTTAATATGAC
Found at i:4939620 original size:4 final size:4
Alignment explanation
Indices: 4939583--4939633 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
4939573 ATTTTTGTAC
* * *
4939583 AATA ATTA AATA TATA AATA ACTA AATA ATATA AATA AA-A AATAA AATA
1 AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AAT-A AATA
4939632 AA
1 AA
4939634 ATAATATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 3 0.08
4 27 0.71
5 8 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:4939625 original size:16 final size:17
Alignment explanation
Indices: 4939590--4939633 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
4939580 TACAATAATT
*
4939590 AAAT-ATATAAATAACT
1 AAATAATATAAATAACA
4939606 AAATAATATAAATAA-A
1 AAATAATATAAATAACA
*
4939622 AAATAAAATAAA
1 AAATAATATAAA
4939634 ATAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAATATAAATAACA
Found at i:4951335 original size:14 final size:14
Alignment explanation
Indices: 4951312--4951358 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
4951302 GAATTTGATA
*
4951312 AACGAATAACAGAT
1 AACGAGTAACAGAT
4951326 AACGAGTAACAGAT
1 AACGAGTAACAGAT
*
4951340 AACGAGTAACAGGT
1 AACGAGTAACAGAT
4951354 AACGA
1 AACGA
4951359 TACCTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (14 bp):
AACGAGTAACAGAT
Found at i:4968921 original size:14 final size:15
Alignment explanation
Indices: 4968902--4968930 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4968892 ATAACATTCG
4968902 TAAATATCAT-TTAA
1 TAAATATCATGTTAA
4968916 TAAATATCATGTTAA
1 TAAATATCATGTTAA
4968931 AAACTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAATATCATGTTAA
Found at i:4972358 original size:21 final size:23
Alignment explanation
Indices: 4972334--4972375 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4972324 TATTATTTTT
4972334 TATTTTCATT-T-AATCAAATTG
1 TATTTTCATTGTGAATCAAATTG
*
4972355 TATTTTTATTGTGAATCAAAT
1 TATTTTCATTGTGAATCAAAT
4972376 AAACTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (23 bp):
TATTTTCATTGTGAATCAAATTG
Found at i:4982377 original size:30 final size:31
Alignment explanation
Indices: 4982341--4982406 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4982331 ATTATTAGTC
**
4982341 ATAAAAACTT-ATTTGATTTAA-AATAAAAAT
1 ATAAAAACTTGATTAAATTTAATAA-AAAAAT
*
4982371 ATAAAAACTTGATTAAATTTAATAAAAGAAT
1 ATAAAAACTTGATTAAATTTAATAAAAAAAT
4982402 ATAAA
1 ATAAA
4982407 TTTATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.32
31 19 0.61
32 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (31 bp):
ATAAAAACTTGATTAAATTTAATAAAAAAAT
Found at i:4989913 original size:23 final size:23
Alignment explanation
Indices: 4989846--4989913 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
4989836 AAAATACTCA
* *
4989846 AATAATTAAAATAA-AAATTATAT
1 AATAATT-TAATAATAAATTATTT
4989869 AACTAATTTAAT-ATAAATTATTT
1 AA-TAATTTAATAATAAATTATTT
4989892 AATAATTTAATAATAAATTATT
1 AATAATTTAATAATAAATTATT
4989914 GATGTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.25
23 25 0.62
24 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAATTTAATAATAAATTATTT
Found at i:4989937 original size:134 final size:137
Alignment explanation
Indices: 4989768--4990048 Score: 383
Period size: 134 Copynumber: 2.1 Consensus size: 137
4989758 TTATATCAAT
* *
4989768 TAATAAATTATTAATTTTTAATAAAAATAGAAATTAATAGATT-AGAAAATAAAAAATACAAATA
1 TAATAAATTATTAATGTTTAATAAAAATAGAAATTAAAAGATTAAG-AAATAAAAAATACAAATA
* *
4989832 AAGAAAAAT-ACTCAAATAATTA-AAATAAAAATTATATAACTAATTTAATA-TAAATTATTTAA
65 AAGAAAAATGACTCAAATAATTACAAATAAAAATCATATAACTAATTTAATAGTAAATTATTCAA
*
4989894 TAATTTAA
130 TAATGTAA
* * * *
4989902 TAATAAATTATTGATGTTTAATGAAAAT-GTAAATTAAAAGATTAAGACATGAAAAATACAAATA
1 TAATAAATTATTAATGTTTAATAAAAATAG-AAATTAAAAGATTAAGAAATAAAAAATACAAATA
* * * * *
4989966 GAGATAAATGATTCAAATTATTACAATTAAAAATCATATAACTAATTTAATAGTAAATTATTCAA
65 AAGAAAAATGACTCAAATAATTACAAATAAAAATCATATAACTAATTTAATAGTAAATTATTCAA
4990031 TAATGTAA
130 TAATGTAA
4990039 TAATAAATTA
1 TAATAAATTA
4990049 AAACTATTAA
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
133 1 0.01
134 60 0.47
135 13 0.10
136 26 0.20
137 28 0.22
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (137 bp):
TAATAAATTATTAATGTTTAATAAAAATAGAAATTAAAAGATTAAGAAATAAAAAATACAAATAA
AGAAAAATGACTCAAATAATTACAAATAAAAATCATATAACTAATTTAATAGTAAATTATTCAAT
AATGTAA
Found at i:4990095 original size:27 final size:23
Alignment explanation
Indices: 4990065--4990127 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
4990055 TTAATAATTT
4990065 AATAATAATTTATTGATATTTAATGAA
1 AATAA-AATTTATT--T-TTTAATGAA
* *
4990092 AATAGAATTTATTTTTTTATGAA
1 AATAAAATTTATTTTTTAATGAA
*
4990115 AATAAATTTTATT
1 AATAAAATTTATT
4990128 ATAACAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.59
24 1 0.03
26 8 0.25
27 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
AATAAAATTTATTTTTTAATGAA
Found at i:4991244 original size:28 final size:27
Alignment explanation
Indices: 4991204--4991257 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
4991194 ATGATTCAAA
*
4991204 ATAAAAAATAATAAAATTTAATTAAAT
1 ATAAAAAAGAATAAAATTTAATTAAAT
*
4991231 ATAATAAAAGAATAAAATTTATTTAAA
1 ATAA-AAAAGAATAAAATTTAATTAAA
4991258 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
ATAAAAAAGAATAAAATTTAATTAAAT
Found at i:4996652 original size:2 final size:2
Alignment explanation
Indices: 4996645--4996695 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4996635 TGATGTGATC
4996645 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
4996687 TA TA TA TA T
1 TA TA TA TA T
4996696 GGATGAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4998690 original size:2 final size:2
Alignment explanation
Indices: 4998677--4998710 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4998667 CAAATATGTC
*
4998677 TA TA TA TT 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
4998711 GTATCCAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5005541 original size:21 final size:21
Alignment explanation
Indices: 5005508--5005550 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5005498 AGAAAAGAGA
5005508 AAGAAAGCAAAGGAGAAGGAG
1 AAGAAAGCAAAGGAGAAGGAG
* *
5005529 AAGAGAGCCAAGGAGAAGGAG
1 AAGAAAGCAAAGGAGAAGGAG
5005550 A
1 A
5005551 GAAGGAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.40, T:0.00
Consensus pattern (21 bp):
AAGAAAGCAAAGGAGAAGGAG
Found at i:5006041 original size:16 final size:17
Alignment explanation
Indices: 5006015--5006046 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5006005 TGCCTCGTGG
5006015 CAAATCAAAAAATTTTT
1 CAAATCAAAAAATTTTT
5006032 CAAA-CAAAAAATTTT
1 CAAATCAAAAAATTTT
5006047 ACCATGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (17 bp):
CAAATCAAAAAATTTTT
Found at i:5006091 original size:15 final size:16
Alignment explanation
Indices: 5006063--5006107 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
5006053 TCATAAAGAT
*
5006063 TAAATTGAACAAAAA-
1 TAAATTGAATAAAAAC
* *
5006078 TATATTGTATAAAAAC
1 TAAATTGAATAAAAAC
5006094 TAAATTGAATAAAA
1 TAAATTGAATAAAA
5006108 TTGAGATGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (16 bp):
TAAATTGAATAAAAAC
Found at i:5007637 original size:21 final size:21
Alignment explanation
Indices: 5007610--5007662 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5007600 AGTGGAAGAG
5007610 AGGAAGAGAAGAGAAAGAAA-A
1 AGGAAGAGAAGAG-AAGAAACA
* *
5007631 CGGAAGAGAGGAGAAGAAACA
1 AGGAAGAGAAGAGAAGAAACA
5007652 AGGAAGA-AAGA
1 AGGAAGAGAAGA
5007663 TGAGATAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.60, C:0.04, G:0.36, T:0.00
Consensus pattern (21 bp):
AGGAAGAGAAGAGAAGAAACA
Found at i:5008819 original size:90 final size:90
Alignment explanation
Indices: 5008715--5008883 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
5008705 AAGAGCAAAG
* * *
5008715 AAGAAAAAGAGAAGAAAAGGAGG-AGGAGGAGAAGAAGAAGAAGAGACAAGAGGAGGTTGAGAGG
1 AAGAAAAAGAGAAG-AAAGGAGGAAAGAGAAGAAGAAGAAGAAGAGACAAGAAGAGGTTGAGAGG
5008779 AAACGAGCACAAGAAGACGCGAAGAA
65 AAACGAGCACAAGAAGACGCGAAGAA
** *
5008805 AAGAAAAATG-GAAGAGTGGAGGAAAGAGAAGGAGAAGAAGAAGAGACAAGAAGAGGTTGAGAGG
1 AAGAAAAA-GAGAAGAAAGGAGGAAAGAGAAGAAGAAGAAGAAGAGACAAGAAGAGGTTGAGAGG
5008869 AAACGAGCACAAGAA
65 AAACGAGCACAAGAA
5008884 CGGATGATGA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 6 0.08
90 64 0.90
91 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.37, T:0.04
Consensus pattern (90 bp):
AAGAAAAAGAGAAGAAAGGAGGAAAGAGAAGAAGAAGAAGAAGAGACAAGAAGAGGTTGAGAGGA
AACGAGCACAAGAAGACGCGAAGAA
Found at i:5008866 original size:27 final size:27
Alignment explanation
Indices: 5008836--5008900 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
5008826 GAAAGAGAAG
*
5008836 GAGAAGAAGAAGAG-ACAAGAAGAGGTT
1 GAGAAGAAGAAGAGCACAAGAA-AGGAT
* * *
5008863 GAGAGGAA-ACGAGCACAAGAACGGAT
1 GAGAAGAAGAAGAGCACAAGAAAGGAT
5008889 GATGAAGAAGAA
1 GA-GAAGAAGAA
5008901 AGAAGTAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 9 0.31
27 19 0.66
28 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.35, T:0.06
Consensus pattern (27 bp):
GAGAAGAAGAAGAGCACAAGAAAGGAT
Found at i:5025783 original size:34 final size:32
Alignment explanation
Indices: 5025744--5025835 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 32
5025734 AAATTTGATG
5025744 AATATTAATATTTAACTTAAAATATAAAAAATAA
1 AATATTAATATTTAA-TTAAAATAT-AAAAATAA
* * * ***
5025778 AATATTAGTATTTAATTTTAAAAAATTAGTTTAA
1 AATATTAATATTTAA--TTAAAATATAAAAATAA
*
5025812 AATATTAATATTTAAATAAAATAT
1 AATATTAATATTTAATTAAAATAT
5025836 TTAATATTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
32 7 0.15
34 32 0.68
35 8 0.17
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (32 bp):
AATATTAATATTTAATTAAAATATAAAAATAA
Found at i:5025856 original size:19 final size:20
Alignment explanation
Indices: 5025809--5025850 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
5025799 AAAATTAGTT
5025809 TAAAATA-TTAATATTTAAA
1 TAAAATATTTAATATTTAAA
5025828 TAAAATATTTAATATTT-AA
1 TAAAATATTTAATATTTAAA
5025847 TAAA
1 TAAA
5025851 TCATTTTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATATTTAATATTTAAA
Found at i:5029800 original size:12 final size:12
Alignment explanation
Indices: 5029777--5029846 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
5029767 GAATGAGCAC
*
5029777 GTACCGGGAGCT
1 GTACCAGGAGCT
*
5029789 GTATCAGGAGCT
1 GTACCAGGAGCT
* *
5029801 GTGCCAGGAGCC
1 GTACCAGGAGCT
*
5029813 GCACCAGGAGCT
1 GTACCAGGAGCT
* *
5029825 GTACCTGGAGCC
1 GTACCAGGAGCT
*
5029837 GCACCAGGAG
1 GTACCAGGAG
5029847 ACAAAGAAAC
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.37, T:0.13
Consensus pattern (12 bp):
GTACCAGGAGCT
Found at i:5029810 original size:24 final size:24
Alignment explanation
Indices: 5029793--5029846 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5029783 GGAGCTGTAT
*
5029793 CAGGAGCTGTGCCAGGAGCCGCAC
1 CAGGAGCTGTACCAGGAGCCGCAC
*
5029817 CAGGAGCTGTACCTGGAGCCGCAC
1 CAGGAGCTGTACCAGGAGCCGCAC
5029841 CAGGAG
1 CAGGAG
5029847 ACAAAGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.31, G:0.37, T:0.09
Consensus pattern (24 bp):
CAGGAGCTGTACCAGGAGCCGCAC
Found at i:5031812 original size:3 final size:3
Alignment explanation
Indices: 5031804--5031833 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5031794 TAGTATACTG
5031804 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5031834 AAAAGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.