Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 7 of 12
Found at i:4318068 original size:33 final size:33
Alignment explanation
Indices: 4318031--4318100 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
4318021 ATCATGTAAA
* * * **
4318031 ATTAACATATCACGTTATTATTTATTATAATAT
1 ATTAACATATCACATCATCATCAATTATAATAT
*
4318064 ATTAACATATTACATCATCATCAATTATAATAT
1 ATTAACATATCACATCATCATCAATTATAATAT
4318097 ATTA
1 ATTA
4318101 CCATGTTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.44
Consensus pattern (33 bp):
ATTAACATATCACATCATCATCAATTATAATAT
Found at i:4321210 original size:29 final size:29
Alignment explanation
Indices: 4321168--4321242 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
4321158 TCAGCCCAAG
4321168 GCACTTGTAAACTCAACTTCCATTTTATA
1 GCACTTGTAAACTCAACTTCCATTTTATA
4321197 GCACTTGTAAACTCAACTTCCATTTTATA
1 GCACTTGTAAACTCAACTTCCATTTTATA
4321226 GCACTTGTAAACTCAAC
1 GCACTTGTAAACTCAAC
4321243 ATATCATGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (29 bp):
GCACTTGTAAACTCAACTTCCATTTTATA
Found at i:4333503 original size:30 final size:32
Alignment explanation
Indices: 4333451--4333510 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
4333441 TTAAAAATAG
4333451 TTAAATAAAGTAATATTAAAAATAAATATTTT
1 TTAAATAAAGTAATATTAAAAATAAATATTTT
*
4333483 TTAAA-AAAGT-ATATTCAAAATAAATATT
1 TTAAATAAAGTAATATTAAAAATAAATATT
4333511 ATTAGACTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 17 0.63
31 5 0.19
32 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (32 bp):
TTAAATAAAGTAATATTAAAAATAAATATTTT
Found at i:4335302 original size:4 final size:4
Alignment explanation
Indices: 4335293--4335317 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4335283 CTTAAAAGTG
4335293 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
4335318 AGTTTCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:4335689 original size:5 final size:5
Alignment explanation
Indices: 4335667--4335780 Score: 56
Period size: 5 Copynumber: 22.4 Consensus size: 5
4335657 ATGTTATAAT
* * * *
4335667 TAAAA TAAAA -ATAT TAAAA TAAAA T-ATA TAATA TAAGAA TCAAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA T--AAAA
* ** * *
4335713 TTAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAGA
1 -TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA
*
4335759 TAAAA TAAAT TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TA
4335781 TATAATATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
4 9 0.11
5 57 0.69
6 12 0.14
7 2 0.02
8 3 0.04
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:4335717 original size:33 final size:31
Alignment explanation
Indices: 4335661--4335803 Score: 117
Period size: 33 Copynumber: 4.7 Consensus size: 31
4335651 TTTATAATGT
4335661 TATAAT-TAAAATAAAAATATTAAAATAAAATA
1 TATAATATAAAA-AAAAA-ATTAAAATAAAATA
*
4335693 TATAATATAAGAATCAAAAATTAAAATAAAATA
1 TATAATATAA-AA-AAAAAATTAAAATAAAATA
*
4335726 -A-AATAT----AAAAAATTAAAAT---TTA
1 TATAATATAAAAAAAAAATTAAAATAAAATA
*
4335748 TATAATATAGATAAAATAAATTAAAATAAAATA
1 TATAATATA-A-AAAAAAAATTAAAATAAAATA
**
4335781 TATAATATAAAAATTAAATTAAA
1 TATAATATAAAAAAAAAATTAAA
4335804 GAAATGAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 27
0.74 0.05 0.22
Matches are distributed among these distances:
22 2 0.02
23 1 0.01
24 5 0.05
25 12 0.13
30 12 0.13
31 17 0.18
32 8 0.09
33 28 0.30
34 7 0.08
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (31 bp):
TATAATATAAAAAAAAAATTAAAATAAAATA
Found at i:4335754 original size:24 final size:25
Alignment explanation
Indices: 4335726--4335803 Score: 52
Period size: 26 Copynumber: 2.9 Consensus size: 25
4335716 AAATAAAATA
4335726 AAATATAAAAAATTAAAATTTATATAATA
1 AAATATAAAAAATTAAAA--TA-A-AATA
*
4335755 TAGATA-AAATAAATTAAAATAAAATA
1 -AAATATAAA-AAATTAAAATAAAATA
*
4335781 TATAATAT-AAAAATTAAATTAAA
1 -A-AATATAAAAAATTAAAATAAA
4335804 GAAATGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
26 18 0.43
27 6 0.14
28 2 0.05
29 3 0.07
30 13 0.31
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (25 bp):
AAATATAAAAAATTAAAATAAAATA
Found at i:4335773 original size:50 final size:52
Alignment explanation
Indices: 4335664--4335851 Score: 148
Period size: 50 Copynumber: 3.6 Consensus size: 52
4335654 ATAATGTTAT
*
4335664 AATTAAAATAAAA-ATATTAAAATAAAATATATAATATAAGAATCAAAAATTA
1 AATTAAAATAAAATATATAAAAATAAAATATATAATATAAGAAT-AAAAATTA
*
4335716 AAATAAAATAAAATATA-AAAAATTAAAATTTATATAATAT-AG-AT-AAAA-TA
1 AATTAAAATAAAATATATAAAAA-TAAAA--TATATAATATAAGAATAAAAATTA
*
4335766 AATTAAAATAAAATATAT-AATATAAAA-AT-TAA-ATTAAAGAAATGAAAAAATATAA
1 AATTAAAATAAAATATATAAAAATAAAATATATAATA-T-AAG-AAT--AAAAAT-T-A
* *
4335821 AATTATAAT--AATAAATAAAAATAAAATATAT
1 AATTAAAATAAAATATATAAAAATAAAATATAT
4335852 GACATTAAAA
Statistics
Matches: 110, Mismatches: 7, Indels: 34
0.73 0.05 0.23
Matches are distributed among these distances:
44 1 0.01
45 4 0.04
46 2 0.02
47 2 0.02
49 7 0.06
50 21 0.19
51 4 0.04
52 20 0.18
53 16 0.15
54 11 0.10
55 21 0.19
56 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (52 bp):
AATTAAAATAAAATATATAAAAATAAAATATATAATATAAGAATAAAAATTA
Found at i:4335824 original size:55 final size:56
Alignment explanation
Indices: 4335709--4335846 Score: 137
Period size: 55 Copynumber: 2.5 Consensus size: 56
4335699 ATAAGAATCA
* * *
4335709 AAAATTAAAATAAAATAAAATATAAAAAATTAAAATTTATATAATATAGATAAAAT
1 AAAATTAAAATAAAATAAAATATAAAAAATTAAAATTTAAAGAATATAGAAAAAAT
4335765 -AAATTAAAATAAAATATATAATAT-AAAAATT-AAA-TTAAAGAA-AT-GAAAAAATAT
1 AAAATTAAAATAAAATA-A-AATATAAAAAATTAAAATTTAAAGAATATAG-AAAAA-AT
*
4335819 AAAATTATAATAATAAATAAAA-ATAAAA
1 AAAATTAAAAT-A-AAATAAAATATAAAA
4335847 TATATGACAT
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
52 1 0.01
53 6 0.09
54 10 0.14
55 33 0.47
56 10 0.14
57 10 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (56 bp):
AAAATTAAAATAAAATAAAATATAAAAAATTAAAATTTAAAGAATATAGAAAAAAT
Found at i:4335834 original size:68 final size:68
Alignment explanation
Indices: 4335758--4335916 Score: 177
Period size: 68 Copynumber: 2.4 Consensus size: 68
4335748 TATAATATAG
*
4335758 ATAA-AATAAATTAAAATAAAATATAT-A-ATATAAAAATTAAATTAAAGAAATGAAAAAATATA
1 ATAATAATAAATAAAAATAAAATATATGACAT-TAAAAA-TAAATTAAAGAAATGAAAAAATATA
*
4335820 AAATT
64 AAAAT
* * * * **
4335825 ATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGATATTATATAAA
1 ATAATAATAAATAAAAATAAAATATATGACATTAAAAATAAATTAAAGAAATGAAAAAATATAAA
4335890 AAT
66 AAT
*
4335893 -TAATAATAAA-AAATAT-AAATATAT
1 ATAATAATAAATAAAAATAAAATATAT
4335917 TAAATTTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
65 8 0.10
66 5 0.06
67 14 0.17
68 44 0.55
69 7 0.09
70 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (68 bp):
ATAATAATAAATAAAAATAAAATATATGACATTAAAAATAAATTAAAGAAATGAAAAAATATAAA
AAT
Found at i:4335844 original size:24 final size:24
Alignment explanation
Indices: 4335758--4335847 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
4335748 TATAATATAG
*
4335758 ATAA-AATAAATTAAAATAAAA-T
1 ATAATAATAAATAAAAATAAAATT
*
4335780 AT-ATAAT--ATAAAAATTAAATT
1 ATAATAATAAATAAAAATAAAATT
* *
4335801 A-AAGAAATGAAA-AAATATAAAATT
1 ATAA-TAAT-AAATAAAAATAAAATT
4335825 ATAATAATAAATAAAAATAAAAT
1 ATAATAATAAATAAAAATAAAAT
4335848 ATATGACATT
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
20 10 0.19
21 4 0.08
22 8 0.15
23 3 0.06
24 24 0.46
25 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
ATAATAATAAATAAAAATAAAATT
Found at i:4336409 original size:6 final size:6
Alignment explanation
Indices: 4336398--4336422 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4336388 GAAGAGAACC
4336398 AAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG A
4336423 GACAGAGAGA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:4341081 original size:15 final size:16
Alignment explanation
Indices: 4341057--4341096 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
4341047 TAATTTAATA
*
4341057 ATAATAAAAAAAT-TT
1 ATAATTAAAAAATGTT
4341072 ATAATTAAAAAATGTT
1 ATAATTAAAAAATGTT
4341088 A-AA-TAAAAA
1 ATAATTAAAAA
4341097 GGTCAAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 14 0.61
16 3 0.13
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAATTAAAAAATGTT
Found at i:4355626 original size:2 final size:2
Alignment explanation
Indices: 4355621--4355667 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4355611 AAACTAATTT
* *
4355621 TA TA TA TA TA CA TA T- TA TA TA TA TA TA TA AA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4355661 TA TA TA T
1 TA TA TA T
4355668 TAAGAAGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4355658 original size:23 final size:23
Alignment explanation
Indices: 4355621--4355667 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4355611 AAACTAATTT
*
4355621 TATATATATACATATTATATATA
1 TATATAAATACATATTATATATA
*
4355644 TATATAAATATATATTATATATA
1 TATATAAATACATATTATATATA
4355667 T
1 T
4355668 TAAGAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATAAATACATATTATATATA
Found at i:4356182 original size:214 final size:215
Alignment explanation
Indices: 4355930--4356430 Score: 565
Period size: 214 Copynumber: 2.3 Consensus size: 215
4355920 GATGTTATGA
* * * *
4355930 ATATATATAATTATA-TAA-ATAATATATGTATATATATTTAATTTATATATAAGTATTACTATA
1 ATATATATAA-TA-AGTAATATATTATATATACATATATTTAATTTATACATAAGTATTACTATA
* * * *
4355993 ATTTATAATAAACTTTATTTATATGATTACACTTAATAACCTTATTAATTA-CACCTTAGTTTTC
64 ATTTATAATAAACTTTATCTATATGATTAAACTTAATAACCTTATTAATCATCACCTTAATTTTC
* * * *
4356057 ATAACATGTTGCTTGTAATTAGTTATTA-TTATATAAATTTT-GT-T-A-TAAAATATTATAACA
129 ATAACATATTGCTTATAATTAGTTATTATTTATACAAATTTTAATATAATTAAAATATTATAACA
4356117 TATAAATTGTGTCATTAATTTC
194 TATAAATTGTGTCATTAATTTC
4356139 ATATATATATAATAAAGTAATATATTATACATATACATATATTTAATTTATACATAAGTATTACT
1 --ATATATATAAT-AAGTAATATATTAT--ATATACATATATTTAATTTATACATAAGTATTACT
* * * * * ** * **
4356204 CTAACTTATAATAGACTTTATCTATATTATTAAATTTAATAATTTTATTAGTCATCGTCTTAATT
61 ATAATTTATAATAAACTTTATCTATATGATTAAACTTAATAACCTTATTAATCATCACCTTAATT
* * **
4356269 TTTATAATATATTTTTTATAATTAGTTATTATTTATACAAATTTTAATATAAAAATTAAAATATT
126 TTCATAACATATTGCTTATAATTAGTTATTATTTATACAAATTTTAATAT---AATTAAAATATT
*
4356334 ATAACATATAAGTTGTGTCATTAATTTC
188 ATAACATATAAATTGTGTCATTAATTTC
* * *
4356362 ATATATATGATAAGTAATATATTATTTATACATATATTTAATTTATACATAA--ATTA-TATATT
1 ATATATATAATAAGTAATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAAT
4356424 TTATAAT
66 TTATAAT
4356431 TATGAATAAA
Statistics
Matches: 244, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
210 2 0.01
211 14 0.06
212 6 0.02
214 75 0.31
215 42 0.17
216 16 0.07
217 1 0.00
218 27 0.11
220 14 0.06
221 10 0.04
222 1 0.00
223 36 0.15
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (215 bp):
ATATATATAATAAGTAATATATTATATATACATATATTTAATTTATACATAAGTATTACTATAAT
TTATAATAAACTTTATCTATATGATTAAACTTAATAACCTTATTAATCATCACCTTAATTTTCAT
AACATATTGCTTATAATTAGTTATTATTTATACAAATTTTAATATAATTAAAATATTATAACATA
TAAATTGTGTCATTAATTTC
Found at i:4360538 original size:2 final size:2
Alignment explanation
Indices: 4360531--4360557 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4360521 ACGATTTGAT
4360531 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4360558 GGCTTCCTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4364498 original size:15 final size:16
Alignment explanation
Indices: 4364478--4364517 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
4364468 TCTAATTTAA
4364478 TATAATAAAAAAAT-T
1 TATAATAAAAAAATGT
4364493 TATAAT-AAAAAATGT
1 TATAATAAAAAAATGT
4364508 TA-AATAAAAA
1 TATAATAAAAA
4364518 GGTCAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TATAATAAAAAAATGT
Found at i:4364504 original size:14 final size:15
Alignment explanation
Indices: 4364478--4364517 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
4364468 TCTAATTTAA
4364478 TATAATAAAAAAAT-T
1 TATAAT-AAAAAATGT
4364493 TATAATAAAAAATGT
1 TATAATAAAAAATGT
4364508 TA-AATAAAAA
1 TATAATAAAAA
4364518 GGTCAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TATAATAAAAAATGT
Found at i:4365460 original size:2 final size:2
Alignment explanation
Indices: 4365449--4365479 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4365439 ATATATATAT
*
4365449 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4365480 ATGATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4370787 original size:13 final size:13
Alignment explanation
Indices: 4370760--4370793 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4370750 GACCAAAGTG
4370760 AAATCAAAACCAAA
1 AAAT-AAAACCAAA
*
4370774 AAATAAAACTAAA
1 AAATAAAACCAAA
4370787 AAATAAA
1 AAATAAA
4370794 GTCTCCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (13 bp):
AAATAAAACCAAA
Found at i:4372273 original size:2 final size:2
Alignment explanation
Indices: 4372266--4372310 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4372256 AGGACAAGTT
* *
4372266 GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4372308 GA G
1 GA G
4372311 CACTACGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4372844 original size:2 final size:2
Alignment explanation
Indices: 4372837--4372862 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4372827 ACTTCAGATG
4372837 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
4372863 TTGTGATTCC
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:4378108 original size:59 final size:60
Alignment explanation
Indices: 4377998--4378219 Score: 184
Period size: 60 Copynumber: 3.7 Consensus size: 60
4377988 CATAAAGCCC
* * * * * **
4377998 CGATTTATATTTGGTGACGTGGGCAATTTCCATGACTAGGTAAAGTAGGACT--AGAGCTT
1 CGATTTATATTTGGTGACATGGGCAGTTTCCACGAGTAAGTAAAGGGGGACTGAAGA-CTT
*
4378057 CGATTTATATTTGGTGACATGGGTAGTTTCCACGAGTAAGTAAAGGGGGACTTGAAGAC-T
1 CGATTTATATTTGGTGACATGGGCAGTTTCCACGAGTAAGTAAAGGGGGAC-TGAAGACTT
* * * * * * * *
4378117 CAATATATATTTGGTGGCGTGGACA-ATTCTCACGAGTAAGTAAAAGGGGATCTGAAGTCTT
1 CGATTTATATTTGGTGACATGGGCAGTTTC-CACGAGTAAGTAAAGGGGGA-CTGAAGACTT
* ** * *
4378178 -GATTTATATCTGGTGGTATGGGCAGTTCCCACGAGTAGGTAA
1 CGATTTATATTTGGTGACATGGGCAGTTTCCACGAGTAAGTAA
4378220 CGATGTTATT
Statistics
Matches: 130, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
59 46 0.35
60 76 0.58
61 5 0.04
62 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (60 bp):
CGATTTATATTTGGTGACATGGGCAGTTTCCACGAGTAAGTAAAGGGGGACTGAAGACTT
Found at i:4378546 original size:27 final size:28
Alignment explanation
Indices: 4378512--4378570 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
4378502 TAATTGGAGG
4378512 AGGGGATTCAAACCCTACTCTTTAGG-A
1 AGGGGATTCAAACCCTACTCTTTAGGTA
*
4378539 AGGGGATTCAAACCTTACTCTTTAGGTA
1 AGGGGATTCAAACCCTACTCTTTAGGTA
4378567 AGGG
1 AGGG
4378571 ATAATACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (28 bp):
AGGGGATTCAAACCCTACTCTTTAGGTA
Found at i:4379035 original size:20 final size:20
Alignment explanation
Indices: 4379010--4379050 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4379000 ACTTGTAAAA
4379010 TAAATTATGTGTAAAAGGGG
1 TAAATTATGTGTAAAAGGGG
4379030 TAAATTATGTGTAAAAGGGG
1 TAAATTATGTGTAAAAGGGG
4379050 T
1 T
4379051 GTCGAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (20 bp):
TAAATTATGTGTAAAAGGGG
Found at i:4395716 original size:32 final size:32
Alignment explanation
Indices: 4395677--4395742 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
4395667 AATCCAAATA
4395677 TATATATAAACCAAAACAAATGTTGAGATATT
1 TATATATAAACCAAAACAAATGTTGAGATATT
* *
4395709 TATATATAAACCAAACCAAATGTTGAGATCTT
1 TATATATAAACCAAAACAAATGTTGAGATATT
4395741 TA
1 TA
4395743 GCTCTCATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (32 bp):
TATATATAAACCAAAACAAATGTTGAGATATT
Found at i:4409717 original size:19 final size:19
Alignment explanation
Indices: 4409680--4409716 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4409670 AATATTTTAA
*
4409680 AAAAAATTTAAATTATTTT
1 AAAAAATTTAAATAATTTT
4409699 AAAAAA-TTAAATAATTTT
1 AAAAAATTTAAATAATTTT
4409717 TTATTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAAATTTAAATAATTTT
Found at i:4410824 original size:13 final size:13
Alignment explanation
Indices: 4410790--4410824 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4410780 TATTATTTAT
4410790 TATAATATATTAA
1 TATAATATATTAA
**
4410803 TATGTTATATTAA
1 TATAATATATTAA
4410816 TATAATATA
1 TATAATATA
4410825 ATATAAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TATAATATATTAA
Found at i:4418436 original size:17 final size:17
Alignment explanation
Indices: 4418414--4418447 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4418404 ATTTGGCAGC
4418414 ATCTCAACACGGATAAT
1 ATCTCAACACGGATAAT
4418431 ATCTCAACACGGATAAT
1 ATCTCAACACGGATAAT
4418448 CTTAAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
ATCTCAACACGGATAAT
Found at i:4422946 original size:49 final size:49
Alignment explanation
Indices: 4422873--4422967 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
4422863 AAGAGGCTAT
* * * * *
4422873 TTATAATAATCAATTAAACCTAAACCTACTTGGTGTGTAAGTAAAGTAA
1 TTATAATAACCAACTAAACCTAAACCTACTTGATGTGCAAGAAAAGTAA
* *
4422922 TTATAATAGCCAACTAAACTTAAACCTACTTGATGTGCAAGAAAAG
1 TTATAATAACCAACTAAACCTAAACCTACTTGATGTGCAAGAAAAG
4422968 AAAATAACAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (49 bp):
TTATAATAACCAACTAAACCTAAACCTACTTGATGTGCAAGAAAAGTAA
Found at i:4437567 original size:20 final size:21
Alignment explanation
Indices: 4437542--4437586 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4437532 AAAACTTATG
*
4437542 TTTATTTGAAAAATAAAA-AT
1 TTTATTTCAAAAATAAAATAT
*
4437562 TTTATTTCAAATATAAAATAT
1 TTTATTTCAAAAATAAAATAT
4437583 TTTA
1 TTTA
4437587 CATGTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTATTTCAAAAATAAAATAT
Found at i:4457179 original size:21 final size:20
Alignment explanation
Indices: 4457141--4457179 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4457131 CTTTTGTTTC
*
4457141 TTTTCTTCTTTTCTTTCCTT
1 TTTTCTTCTTTTCCTTCCTT
*
4457161 TTTTTTTCTTTCTCCTTCC
1 TTTTCTTCTTT-TCCTTCC
4457180 ACTTTCTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCTTCTTTTCCTTCCTT
Found at i:4457535 original size:26 final size:26
Alignment explanation
Indices: 4457503--4457554 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4457493 AAAATAAATA
**
4457503 ATTTTAAAATTAAAGATTTAAATTAT
1 ATTTTAAAATTAAAGAGCTAAATTAT
4457529 ATTTTAAAATTAAAGAGCTAAATTAT
1 ATTTTAAAATTAAAGAGCTAAATTAT
4457555 TACGATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (26 bp):
ATTTTAAAATTAAAGAGCTAAATTAT
Found at i:4458838 original size:2 final size:2
Alignment explanation
Indices: 4458831--4458855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4458821 TTAAAGCAGC
4458831 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
4458856 CTCATCTCCT
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:4459559 original size:6 final size:6
Alignment explanation
Indices: 4459548--4459576 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4459538 TTGCTGACTT
4459548 TACATG TACATG TACATG TACATG TACAT
1 TACATG TACATG TACATG TACATG TACAT
4459577 TTCTTGACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
TACATG
Found at i:4460363 original size:2 final size:2
Alignment explanation
Indices: 4460356--4460388 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4460346 TGAATAGTTA
*
4460356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4460389 GGTTTCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4471557 original size:66 final size:66
Alignment explanation
Indices: 4471443--4471569 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
4471433 CTTGTGAGAT
* ** *
4471443 TCTTTTTATGAGACAAAATCATAAGATTAGTGAACTAAAATCGATAATACCTTACAAAGAAAAGA
1 TCTTTTTATGAGACAAAATCATAAGATCAGAAAACCAAAATCGATAATACCTTACAAAGAAAAGA
4471508 C
66 C
* * *
4471509 TCTTTTTATGATACAAAATCATGAA-ATCAGAAAACCAAAA-CTGCTAATACTTTACAAAGAA
1 TCTTTTTATGAGACAAAATCAT-AAGATCAGAAAACCAAAATC-GATAATACCTTACAAAGAA
4471570 TGATATGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 1 0.02
66 49 0.94
67 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (66 bp):
TCTTTTTATGAGACAAAATCATAAGATCAGAAAACCAAAATCGATAATACCTTACAAAGAAAAGA
C
Found at i:4472566 original size:13 final size:14
Alignment explanation
Indices: 4472542--4472571 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4472532 AAATATTAAT
4472542 ATATTATCTTAAAA
1 ATATTATCTTAAAA
4472556 ATATTAT-TTAAAA
1 ATATTATCTTAAAA
4472569 ATA
1 ATA
4472572 ATTAAAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTATCTTAAAA
Found at i:4472575 original size:14 final size:15
Alignment explanation
Indices: 4472539--4472575 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
4472529 TAAAAATATT
4472539 AATATATTATCTTAAA
1 AATA-ATTATCTTAAA
4472555 AAT-ATTAT-TTAAA
1 AATAATTATCTTAAA
4472568 AATAATTA
1 AATAATTA
4472576 AAAGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.40
14 9 0.45
16 3 0.15
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATTATCTTAAA
Found at i:4492108 original size:17 final size:16
Alignment explanation
Indices: 4492086--4492119 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4492076 CAAAACATAG
4492086 GGAGAGATGAGGGAGAA
1 GGAGAGAT-AGGGAGAA
*
4492103 GGAGAGCTAGGGAGAA
1 GGAGAGATAGGGAGAA
4492119 G
1 G
4492120 CTGGAGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.03, G:0.53, T:0.06
Consensus pattern (16 bp):
GGAGAGATAGGGAGAA
Found at i:4492711 original size:16 final size:15
Alignment explanation
Indices: 4492692--4492732 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
4492682 GAGAGAGAGA
4492692 GAGAGAGAAGGGGGG
1 GAGAGAGAAGGGGGG
*
4492707 TGAGAGAGGAAGGGTGG
1 -GAGAGA-GAAGGGGGG
4492724 GAGAGAGAA
1 GAGAGAGAA
4492733 AGAGCTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.59, T:0.05
Consensus pattern (15 bp):
GAGAGAGAAGGGGGG
Found at i:4492713 original size:18 final size:17
Alignment explanation
Indices: 4492690--4492731 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4492680 GAGAGAGAGA
4492690 GAGAGAGAGAAGGGGGG
1 GAGAGAGAGAAGGGGGG
*
4492707 TGAGAGAG-GAAGGGTGG
1 -GAGAGAGAGAAGGGGGG
4492724 GAGAGAGA
1 GAGAGAGA
4492732 AAGAGCTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 8 0.36
18 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.60, T:0.05
Consensus pattern (17 bp):
GAGAGAGAGAAGGGGGG
Found at i:4495676 original size:56 final size:56
Alignment explanation
Indices: 4495615--4495729 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 56
4495605 AATTTTTAAT
* * * * *
4495615 AAATTTGAAAATATTTTGAGAAAAAATTGT-GTTTTTGATGTCGAAAATTGAGAGAG
1 AAATTTGAAAATATTTTGAAAAAAAATTATAG-TTTTGATGCCAAAAACTGAGAGAG
* * *
4495671 AAATTTGACAGTGTTTTGAAAAAAAATTATAGTTTTGATGCCAAAAACTGAGAGAG
1 AAATTTGAAAATATTTTGAAAAAAAATTATAGTTTTGATGCCAAAAACTGAGAGAG
4495727 AAA
1 AAA
4495730 CACCTTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
56 49 0.98
57 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.32
Consensus pattern (56 bp):
AAATTTGAAAATATTTTGAAAAAAAATTATAGTTTTGATGCCAAAAACTGAGAGAG
Found at i:4495788 original size:22 final size:22
Alignment explanation
Indices: 4495745--4495785 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4495735 TAAATAGTTT
*
4495745 TTAAAAAAAATTTGCTAAGGAG
1 TTAAAAAAAATTTGCAAAGGAG
4495767 TTAAAAAAAATTTG-AAAGG
1 TTAAAAAAAATTTGCAAAGG
4495786 GAGAAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (22 bp):
TTAAAAAAAATTTGCAAAGGAG
Found at i:4501008 original size:24 final size:24
Alignment explanation
Indices: 4500981--4501027 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4500971 TACTTTTTGG
*
4500981 ATTATTATTATTGTTGTTGTTATC
1 ATTATTATTATTGTTCTTGTTATC
4501005 ATTATTATTATTGTTCTTGTTAT
1 ATTATTATTATTGTTCTTGTTAT
4501028 TTAACAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.64
Consensus pattern (24 bp):
ATTATTATTATTGTTCTTGTTATC
Found at i:4502065 original size:51 final size:51
Alignment explanation
Indices: 4501989--4502134 Score: 211
Period size: 51 Copynumber: 2.9 Consensus size: 51
4501979 CAAAATAACA
4501989 GAGTGATACAGGTTGGTGTGCCCTAATGAATGTCATAATAACACATACTAT
1 GAGTGATACAGGTTGGTGTGCCCTAATGAATGTCATAATAACACATACTAT
** *
4502040 GAGTGATACAGGTTGGTGCACCCTAATGAATGTCATAGTAACACATACTAT
1 GAGTGATACAGGTTGGTGTGCCCTAATGAATGTCATAATAACACATACTAT
* * * * * *
4502091 GAGCGATACAAGTTCGTATGGCCTAGTGAATGTCATAATAACAC
1 GAGTGATACAGGTTGGTGTGCCCTAATGAATGTCATAATAACAC
4502135 CTATTACAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 83 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (51 bp):
GAGTGATACAGGTTGGTGTGCCCTAATGAATGTCATAATAACACATACTAT
Found at i:4502959 original size:20 final size:20
Alignment explanation
Indices: 4502934--4502977 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4502924 TTCTCAACTC
*
4502934 TTAATATTTCATAGAATAAA
1 TTAATATTTCATAGAACAAA
4502954 TTAATATTTCATAGAACAAA
1 TTAATATTTCATAGAACAAA
4502974 TTAA
1 TTAA
4502978 AAACATGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
TTAATATTTCATAGAACAAA
Found at i:4503992 original size:27 final size:27
Alignment explanation
Indices: 4503962--4504015 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4503952 TTTTTGTAAG
*
4503962 TTTTA-TTTTCATCAAAATAATATATTA
1 TTTTACTTTT-ATCAAAATAATACATTA
4503989 TTTTACTTTTATCAAAATAATACATTA
1 TTTTACTTTTATCAAAATAATACATTA
4504016 CTTTCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTTACTTTTATCAAAATAATACATTA
Found at i:4513512 original size:2 final size:2
Alignment explanation
Indices: 4513507--4513537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4513497 GGGGATATAT
4513507 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4513538 TCTGTTGCAT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4514963 original size:29 final size:29
Alignment explanation
Indices: 4514930--4514986 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4514920 TTGCTAATGA
4514930 TGTTTGCTAAAGGCAGTTATTGATGGTAT
1 TGTTTGCTAAAGGCAGTTATTGATGGTAT
* *
4514959 TGTTTGCTAATGGTAGTTATTGATGGTA
1 TGTTTGCTAAAGGCAGTTATTGATGGTA
4514987 ATGATGCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (29 bp):
TGTTTGCTAAAGGCAGTTATTGATGGTAT
Found at i:4521653 original size:18 final size:18
Alignment explanation
Indices: 4521630--4521666 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4521620 GGTTATAGCA
4521630 CACCATTTCCAACAGAGC
1 CACCATTTCCAACAGAGC
4521648 CACCATTTCCAACAGAGC
1 CACCATTTCCAACAGAGC
4521666 C
1 C
4521667 GGTCTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.41, G:0.11, T:0.16
Consensus pattern (18 bp):
CACCATTTCCAACAGAGC
Found at i:4559124 original size:18 final size:19
Alignment explanation
Indices: 4559103--4559145 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4559093 AAATCAAAAG
4559103 AAAAATTGAA-CTAAATAA
1 AAAAATTGAATCTAAATAA
* *
4559121 AAAAATTGAATGTGAATAA
1 AAAAATTGAATCTAAATAA
4559140 AAAAAT
1 AAAAAT
4559146 AATTTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAAATTGAATCTAAATAA
Found at i:4560929 original size:3 final size:3
Alignment explanation
Indices: 4560923--4560947 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4560913 CCTCCTCCTC
4560923 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
4560948 ACCTGCTTTA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:4573889 original size:69 final size:70
Alignment explanation
Indices: 4573778--4573918 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 70
4573768 GGGGGGTGTT
4573778 AGGGTACAGATCCTCATGTCATAGTGCTCTGTCATGCACC-AAAAACTAAATCTCCCATAAAGGT
1 AGGGTACAGATCCTCATGTCATAGTGCTCTGTCATGCACCAAAAAACTAAATCTCCCATAAAGGT
4573842 TCTAG
66 TCTAG
* * * * *
4573847 AGGGTGCAGATCTTCATGTCATGGTGCTCTGTCTTGTACCAAAAAACTAAATCTCCCATAAAGGT
1 AGGGTACAGATCCTCATGTCATAGTGCTCTGTCATGCACCAAAAAACTAAATCTCCCATAAAGGT
4573912 TCTAG
66 TCTAG
4573917 AG
1 AG
4573919 ATGGTCAAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 35 0.53
70 31 0.47
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (70 bp):
AGGGTACAGATCCTCATGTCATAGTGCTCTGTCATGCACCAAAAAACTAAATCTCCCATAAAGGT
TCTAG
Found at i:4575087 original size:25 final size:24
Alignment explanation
Indices: 4575048--4575097 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
4575038 TGCTCGCTTC
*
4575048 TTTCTTCTTTCTTTTCTTTTCTTTT
1 TTTCTTCTTTCTTTTCCTTT-TTTT
4575073 TTTCTT-TTTCTTTTTCCTTTTTTT
1 TTTCTTCTTTC-TTTTCCTTTTTTT
4575097 T
1 T
4575098 CTCTGTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTCTTCTTTCTTTTCCTTTTTTT
Found at i:4575095 original size:8 final size:6
Alignment explanation
Indices: 4575048--4575094 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
4575038 TGCTCGCTTC
*
4575048 TTTCTT CTTTC-T TTTCTT TTCTTTT TTTCTT TTTCTT TTTCCTT TTT
1 TTTCTT -TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTT-CTT TTT
4575095 TTTCTCTGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 16 0.46
7 15 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:4575095 original size:14 final size:14
Alignment explanation
Indices: 4575045--4575087 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
4575035 CACTGCTCGC
4575045 TTCTTTCTTCTTTCTT
1 TTCTTT-TTCTTT-TT
4575061 TTC-TTTTCTTTTT
1 TTCTTTTTCTTTTT
4575074 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
4575088 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 16 0.62
15 2 0.08
16 3 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:4589255 original size:66 final size:65
Alignment explanation
Indices: 4589147--4589279 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 65
4589137 TACAGAACTT
* *
4589147 AAAAAATATCATAAGATCTTAGTTTAACTTGATGCCAGGGGAAATAAAGCAAATTGGTACTAGGA
1 AAAAAATACCATAAGATCTTAGTTTAACTTGATGCCAAGGGAAATAAAGCAAATTGGTACTAGGA
*
4589212 AAAATAATACCATAAGATCTTAGTTTAACTTGATGCCAAGGGAAATAAAGCAAATTGGTATTAGG
1 AAAA-AATACCATAAGATCTTAGTTTAACTTGATGCCAAGGGAAATAAAGCAAATTGGTACTAGG
4589277 A
65 A
4589278 AA
1 AA
4589280 GTCATTATCA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 4 0.06
66 60 0.94
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (65 bp):
AAAAAATACCATAAGATCTTAGTTTAACTTGATGCCAAGGGAAATAAAGCAAATTGGTACTAGGA
Found at i:4597647 original size:3 final size:3
Alignment explanation
Indices: 4597639--4597671 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4597629 TGCCGTTTTC
4597639 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4597672 TGGATTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4603334 original size:105 final size:105
Alignment explanation
Indices: 4603152--4603361 Score: 384
Period size: 105 Copynumber: 2.0 Consensus size: 105
4603142 GGGGCAAGAC
*
4603152 TTTGATTCATAACTTGATTCAAATTATAATAAACAATTAAAATGTTGGAATGAGAGAAATAATAA
1 TTTGATTCATAACTTGATTCAAATTATAATAAACAATTAAAATGTTGGAATGAGAGAAATAAGAA
* *
4603217 GAGTAGTATTTCTATACATGCCACTTGTTGAAAAAGATGG
66 GAGTAGTATTTCTACACATGCCACTTGTTGAAAAAAATGG
4603257 TTTGATTCATAACTTGATTCAAATTATAATAAACAATTAAAATGTTGGAATGAGAGAAATAAGAA
1 TTTGATTCATAACTTGATTCAAATTATAATAAACAATTAAAATGTTGGAATGAGAGAAATAAGAA
*
4603322 GAGTAGTATTTCTACACATGTCACTTGTTGAAAAAAATGG
66 GAGTAGTATTTCTACACATGCCACTTGTTGAAAAAAATGG
4603362 AAAGATGGTG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (105 bp):
TTTGATTCATAACTTGATTCAAATTATAATAAACAATTAAAATGTTGGAATGAGAGAAATAAGAA
GAGTAGTATTTCTACACATGCCACTTGTTGAAAAAAATGG
Found at i:4606619 original size:21 final size:22
Alignment explanation
Indices: 4606589--4606631 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4606579 CAGATTGGAC
*
4606589 AATTTGAGTT-ATTTATTTAAA
1 AATTTAAGTTAATTTATTTAAA
*
4606610 AATTTAAGTTAATTTTTTTAAA
1 AATTTAAGTTAATTTATTTAAA
4606632 TTTTGAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
AATTTAAGTTAATTTATTTAAA
Found at i:4617290 original size:18 final size:18
Alignment explanation
Indices: 4617253--4617299 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
4617243 TTTTATTGAC
* * *
4617253 ATAATTTTTTAAATATAT
1 ATAATTATTTAAACAGAT
4617271 ATAATTATTTAAACAGAT
1 ATAATTATTTAAACAGAT
*
4617289 ATTA-TATTTAA
1 ATAATTATTTAA
4617300 CATGCATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
ATAATTATTTAAACAGAT
Found at i:4620561 original size:32 final size:32
Alignment explanation
Indices: 4620525--4620589 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4620515 AAAGTCCTCA
4620525 ATGTAAAATTAAATGAACATAATTGTATTCAT
1 ATGTAAAATTAAATGAACATAATTGTATTCAT
4620557 ATGTAAAATTAAATGAACATAATTGTATTCAT
1 ATGTAAAATTAAATGAACATAATTGTATTCAT
4620589 A
1 A
4620590 GAAACACTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (32 bp):
ATGTAAAATTAAATGAACATAATTGTATTCAT
Found at i:4627391 original size:18 final size:19
Alignment explanation
Indices: 4627370--4627417 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4627360 TATTTAACAT
*
4627370 TTTTAAATAATT-TAATGA
1 TTTTAAATAATTATAATAA
*
4627388 TTTTAAA-ACATTATATTAA
1 TTTTAAATA-ATTATAATAA
4627407 TTTTAAATAAT
1 TTTTAAATAAT
4627418 AAATTTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 10 0.40
19 13 0.52
20 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAAATAATTATAATAA
Found at i:4628365 original size:20 final size:20
Alignment explanation
Indices: 4628340--4628396 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
4628330 CATGAATAAT
4628340 ACAATTAAAATACGATTAAC
1 ACAATTAAAATACGATTAAC
*
4628360 ACAATTAATAA-ATGATTAAC
1 ACAATTAA-AATACGATTAAC
* *
4628380 ACATTTATAATAC-ATTA
1 ACAATTAAAATACGATTA
4628397 TAAAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 23 0.74
21 2 0.06
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (20 bp):
ACAATTAAAATACGATTAAC
Found at i:4628815 original size:23 final size:23
Alignment explanation
Indices: 4628781--4628826 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4628771 TTTCCAATTT
* *
4628781 TTTTTTCTACTTACGTGCATGAA
1 TTTTTTCGACTTACATGCATGAA
4628804 TTTTTTCGACTTACATGCATGAA
1 TTTTTTCGACTTACATGCATGAA
4628827 GTTGAAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (23 bp):
TTTTTTCGACTTACATGCATGAA
Found at i:4637027 original size:7 final size:7
Alignment explanation
Indices: 4637015--4637054 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
4637005 CTACAAGCAG
4637015 CATCACT
1 CATCACT
4637022 CATCACT
1 CATCACT
4637029 CATCACT
1 CATCACT
4637036 CATCACT
1 CATCACT
4637043 CATCACT
1 CATCACT
4637050 CATCA
1 CATCA
4637055 TCCCCCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (7 bp):
CATCACT
Found at i:4641144 original size:20 final size:21
Alignment explanation
Indices: 4641110--4641148 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4641100 ATATTGAAGA
4641110 AAAAAATACACTACATGTCAG
1 AAAAAATACACTACATGTCAG
*
4641131 AAAAAATATA-TACATGTC
1 AAAAAATACACTACATGTC
4641149 TACCCAAAAC
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (21 bp):
AAAAAATACACTACATGTCAG
Found at i:4646863 original size:325 final size:328
Alignment explanation
Indices: 4646342--4647432 Score: 1210
Period size: 339 Copynumber: 3.3 Consensus size: 328
4646332 TATATATATA
* * * *
4646342 TATATATATACTTTTAGTACAAATATATTTACTTTCTATTTTGTGTTAATATTACAAAAATTATA
1 TATATATATACTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTAC-AAAATTATA
* * * *
4646407 ATTTATAAAATTATTAATTATAATAT--ATATACCATTATTTATATAAACTTATAATATATGTAC
65 ACTTATAAAATTATTAATTATAATATACATATACCTTTGTTTATATAAA-TCAT-ATA-A--TA-
* * * * * ** * ** *
4646470 TTAAAGAAAGCTTTTGAAATTAAAATAGTTTTGGAACCTAACTATTTTTTTTAATTTTATGAAAT
124 --AAAGGAAGC-TCTGAGATTAGAATAATTTTAAAATCTAGTTATTTTTTTTAATTTCATGAAAT
*
4646535 TAAGGACAAA-TCCATATAGTTAATTAAATTAATTCAAGAAACTATAATTATTAATTAACTTGTA
186 TAAGGA-AAACT-CATATAATTAATTAAATTAATTCAAGAAACTATAATTATTAATTAACTTGTA
* * *
4646599 ATGTCTTTTAATATATAGAGTTTATATATTGTGTTAATTTATAAGAAATATAATTGTTATTATAT
249 ATGTCTTTTAATATATATAGTTTATATATTGTGTTCATTTATAAAAAATATAATT-TTATTATAT
4646664 ATACTAAAATATTTTTAG
313 ATA-TAAAATA-TTTTAG
* * * *
4646682 TGTATATATACTTCAAATATAAATATATTTACTTTCTTTTTTGTGTTAATATTACAAAACTTATA
1 TATATATATACTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAA-TTATA
*
4646747 ACTTAT-AGATTATTAATTATAATATACATA-A-CTTTGTTTATATAAA-C-T-T-A-AAAA-GA
65 ACTTATAAAATTATTAATTATAATATACATATACCTTTGTTTATATAAATCATATAATAAAAGGA
* * * * *
4646803 AGCTGTGAGATTATAATAGTTTTAAAATCTGGTTTTTTTTTTTAAATTTCATGAAATTAAGGATA
130 AGCTCTGAGATTAGAATAATTTTAAAATCTAGTTATTTTTTTT-AATTTCATGAAATTAAGGA-A
* *
4646868 AACTCATATAATTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGCCTTTT
193 AACTCATATAATTAATTAAATTAATTCAAGAAACTATAATTATTAATTAACTTGTAATGTCTTTT
* * *
4646933 AATGTATATACTTTATATATAT-TAAGTTCATTTATAAAAAATATAA--TTACTATATAT-TAAA
258 AATATATATAGTTTATATAT-TGT--GTTCATTTATAAAAAATATAATTTTATTATATATATAAA
*
4646994 ATACTTTTAA
320 ATA-TTTTAG
* *
4647004 TATATATATACTTTAAATATAAACATATTTACTTTCTATTTTATGTTAACATTATCAAAATTATA
1 TATATATATACTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTA-CAAAATTATA
* *
4647069 ACTTATAAAATTATTTATTATAATATATATATACCTTTGTTTATATAAACTTCTAATATAGAAAT
65 ACTTATAAAATTATTAATTATAATATACATATACCTTTGTTTATATAAA--TC--ATAT---AA-
* *
4647134 CTAAAAGGAAGCTCTGAGATTAGAATAATTTTGAAATCTAGTTATTTTTTTTAATTTCATGTAAT
122 -TAAAAGGAAGCTCTGAGATTAGAATAATTTTAAAATCTAGTTATTTTTTTTAATTTCATGAAAT
* * *
4647199 TAAGGAAACACTCATATAATTAATTAAATTAATT-AATGAAATTATGATTATTAATTTACTTGTA
186 TAAGGAAA-ACTCATATAATTAATTAAATTAATTCAA-GAAACTATAATTATTAATTAACTTGTA
*
4647263 ATGTCTTTTAATATATATAGTTTATATACATTG-GATTCATTCATAAAAAATATAATTATTATTA
249 ATGTCTTTTAATATATATAGTTTATAT--ATTGTG-TTCATTTATAAAAAATATAATT-TTATTA
*
4647327 TATATATTAAAAGTATTTTCG
310 TATATA-TAAAA-TATTTTAG
* * *
4647348 TATATATACACTTTATATATAAATATATTTGCTTTCTATTTTGTGTTAACATTACAAAAATTATA
1 TATATATATACTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTAC-AAAATTATA
4647413 ACTTATAAAATTATTAATTA
65 ACTTATAAAATTATTAATTA
4647433 AGTTTGAGAT
Statistics
Matches: 643, Mismatches: 68, Indels: 76
0.82 0.09 0.10
Matches are distributed among these distances:
322 71 0.11
323 26 0.04
324 41 0.06
325 116 0.18
326 5 0.01
327 19 0.03
328 1 0.00
329 1 0.00
331 1 0.00
332 2 0.00
334 1 0.00
336 2 0.00
338 4 0.01
339 149 0.23
340 100 0.16
341 5 0.01
342 10 0.02
343 1 0.00
344 86 0.13
345 2 0.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (328 bp):
TATATATATACTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAATTATAA
CTTATAAAATTATTAATTATAATATACATATACCTTTGTTTATATAAATCATATAATAAAAGGAA
GCTCTGAGATTAGAATAATTTTAAAATCTAGTTATTTTTTTTAATTTCATGAAATTAAGGAAAAC
TCATATAATTAATTAAATTAATTCAAGAAACTATAATTATTAATTAACTTGTAATGTCTTTTAAT
ATATATAGTTTATATATTGTGTTCATTTATAAAAAATATAATTTTATTATATATATAAAATATTT
TAG
Found at i:4647080 original size:15 final size:17
Alignment explanation
Indices: 4647050--4647082 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4647040 TATTTTATGT
4647050 TAACATTATCAAAATTA
1 TAACATTATCAAAATTA
4647067 TAAC-TTAT-AAAATTA
1 TAACATTATCAAAATTA
4647082 T
1 T
4647083 TTATTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATCAAAATTA
Found at i:4661730 original size:14 final size:13
Alignment explanation
Indices: 4661709--4661743 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
4661699 TAAAAAATAT
4661709 ATTAAAAAACTTA
1 ATTAAAAAACTTA
*
4661722 ATTATAAAAATTTA
1 ATTA-AAAAACTTA
4661736 ATTAAAAA
1 ATTAAAAA
4661744 TTTTACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTAAAAAACTTA
Found at i:4668362 original size:22 final size:23
Alignment explanation
Indices: 4668300--4668364 Score: 60
Period size: 26 Copynumber: 2.7 Consensus size: 23
4668290 CCAAATGAAA
* *
4668300 AAAATTAATAATTTTAGTTAATGT
1 AAAATTAATAA-TTTAATTAATAT
*
4668324 AATAATTTTATATATTTAATT-ATAT
1 AA-AA-TTAATA-ATTTAATTAATAT
4668349 AAAATTAATAATTTAA
1 AAAATTAATAATTTAA
4668365 CTATTGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 4 0.12
25 7 0.21
26 11 0.32
27 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
AAAATTAATAATTTAATTAATAT
Found at i:4679510 original size:28 final size:28
Alignment explanation
Indices: 4679470--4679537 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
4679460 TCCCCAATTT
*
4679470 TTCTT-TTCTCCTTCCTACCTTCTTAACC
1 TTCTTCTT-TCCTTCCCACCTTCTTAACC
**
4679498 TTCTTCTTTCCTTCCCACCTTCTTCTCC
1 TTCTTCTTTCCTTCCCACCTTCTTAACC
4679526 TTCTTCTTTCCT
1 TTCTTCTTTCCT
4679538 GTCTTTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 34 0.94
29 2 0.06
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (28 bp):
TTCTTCTTTCCTTCCCACCTTCTTAACC
Found at i:4680347 original size:15 final size:15
Alignment explanation
Indices: 4680327--4680359 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4680317 AATACTAAAA
*
4680327 AATTATATTTTCAAT
1 AATTATATTCTCAAT
4680342 AATTATATTCTCAAT
1 AATTATATTCTCAAT
4680357 AAT
1 AAT
4680360 AATACAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATATTCTCAAT
Found at i:4683760 original size:20 final size:21
Alignment explanation
Indices: 4683737--4683780 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4683727 ATTAATTTTA
* *
4683737 AAAATTT-AATTATTTAATTC
1 AAAATTTAAATTAATGAATTC
4683757 AAAATTTAAATTAATGAATTC
1 AAAATTTAAATTAATGAATTC
4683778 AAA
1 AAA
4683781 TTTGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATTTAAATTAATGAATTC
Found at i:4683760 original size:21 final size:20
Alignment explanation
Indices: 4683721--4683780 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
4683711 ATAATATTAA
*
4683721 TTAATTATTAATTTTAAAAAT
1 TTAATTATTAA-TTCAAAAAT
4683742 TTAATTATTTAATTC-AAAAT
1 TTAATTA-TTAATTCAAAAAT
*
4683762 TTAAATTAATGAATTCAAA
1 TT-AATT-ATTAATTCAAA
4683781 TTTGAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 7 0.21
21 19 0.58
22 7 0.21
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAATTATTAATTCAAAAAT
Found at i:4684508 original size:16 final size:16
Alignment explanation
Indices: 4684484--4684517 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4684474 GTTTTTCCAT
4684484 CCACCCAATCCCACCA
1 CCACCCAATCCCACCA
* *
4684500 CCACGCAATCCCAGCA
1 CCACCCAATCCCACCA
4684516 CC
1 CC
4684518 GGTGGGATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.59, G:0.06, T:0.06
Consensus pattern (16 bp):
CCACCCAATCCCACCA
Found at i:4688247 original size:22 final size:22
Alignment explanation
Indices: 4688205--4688247 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4688195 ATACTATTAG
**
4688205 TAATTAAATTATTAATTTTATA
1 TAATTAAATTATTAAAATTATA
4688227 TAATTAAA-TATATAAAATTAT
1 TAATTAAATTAT-TAAAATTAT
4688248 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATTAAATTATTAAAATTATA
Found at i:4695023 original size:30 final size:28
Alignment explanation
Indices: 4694989--4695045 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
4694979 GATGAGAGTG
*
4694989 ATATTTGATATTGATTTTAAAAGTCAATTA
1 ATATTTGACA-TGATTTTAAAAG-CAATTA
* *
4695019 ATATTTTACATGTTTTTAAAAGCAATT
1 ATATTTGACATGATTTTAAAAGCAATT
4695046 TAAAATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 11 0.46
30 8 0.33
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (28 bp):
ATATTTGACATGATTTTAAAAGCAATTA
Found at i:4703211 original size:57 final size:57
Alignment explanation
Indices: 4703135--4703246 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
4703125 AATATAATAC
* * *
4703135 CTATGTATGTATAAAAATTAATATCATAAT-GTGTGTGTTTGTAAATTAATATCAATT
1 CTATGTATGTATAAAAATTAATACCA-AATCGTGTATGTTTGGAAATTAATATCAATT
* * * *
4703192 CTATGTATGTCTGAGAATTAATACCAAATCGGTGTATGTTTGGAAGTTAATATCA
1 CTATGTATGTATAAAAATTAATACCAAATC-GTGTATGTTTGGAAATTAATATCA
4703247 TTCCTGTGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
56 3 0.07
57 22 0.48
58 21 0.46
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (57 bp):
CTATGTATGTATAAAAATTAATACCAAATCGTGTATGTTTGGAAATTAATATCAATT
Found at i:4713230 original size:22 final size:22
Alignment explanation
Indices: 4713205--4713250 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4713195 GCTATAATGC
* *
4713205 TTCAACCTTATCTTACATCATT
1 TTCAACCTTATCTCACATAATT
4713227 TTCAACCTTATCTCACATAATT
1 TTCAACCTTATCTCACATAATT
4713249 TT
1 TT
4713251 ATTGAGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (22 bp):
TTCAACCTTATCTCACATAATT
Found at i:4716689 original size:50 final size:51
Alignment explanation
Indices: 4716635--4716747 Score: 160
Period size: 52 Copynumber: 2.2 Consensus size: 51
4716625 AATAAAGGTT
4716635 ATTTTGAGGAGACTCATTAA-AAA-ATATATAATAAATAAAAATTTTTAAAA
1 ATTTTGAGGAGA-TCATTAAGAAATATATATAATAAATAAAAATTTTTAAAA
*
4716685 ATTTT-ATGGAGATCATTAATGAAATATATATAATAAATAAATATTTTTAAAA
1 ATTTTGA-GGAGATCATTAA-GAAATATATATAATAAATAAAAATTTTTAAAA
*
4716737 ATCTTGAGGAG
1 ATTTTGAGGAG
4716748 GCCTTTACGC
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
49 8 0.14
50 10 0.18
51 3 0.05
52 34 0.61
53 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (51 bp):
ATTTTGAGGAGATCATTAAGAAATATATATAATAAATAAAAATTTTTAAAA
Found at i:4740592 original size:15 final size:15
Alignment explanation
Indices: 4740572--4740626 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
4740562 AAAAAATATT
4740572 AATATTTAAATTTAA
1 AATATTTAAATTTAA
* *
4740587 AATATTTTTAACTTAA
1 AATA-TTTAAATTTAA
4740603 AATA-TTAATATTTAA
1 AATATTTAA-ATTTAA
*
4740618 ATTATTTAA
1 AATATTTAA
4740627 TACTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.09
15 12 0.38
16 17 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTTAAATTTAA
Found at i:4740618 original size:37 final size:38
Alignment explanation
Indices: 4740528--4740621 Score: 129
Period size: 37 Copynumber: 2.5 Consensus size: 38
4740518 TAAGTTTGAT
4740528 AAATATTAATATTT-AATTAAAAATATTTAAAAATAAA
1 AAATATTAATATTTAAATTAAAAATATTTAAAAATAAA
* ** * *
4740565 AAATATTAATATTTAAATTTAAAATATTTTTAACT-TA
1 AAATATTAATATTTAAATTAAAAATATTTAAAAATAAA
4740602 AAATATTAATATTTAAATTA
1 AAATATTAATATTTAAATTA
4740622 TTTAATACTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
37 34 0.68
38 16 0.32
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (38 bp):
AAATATTAATATTTAAATTAAAAATATTTAAAAATAAA
Found at i:4741373 original size:16 final size:14
Alignment explanation
Indices: 4741330--4741365 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
4741320 ATCTTTTTTT
*
4741330 ATTTTTTTATAA-A
1 ATTTTTTAATAATA
4741343 ATTTTTTAATAATA
1 ATTTTTTAATAATA
4741357 ATTTTTTAA
1 ATTTTTTAA
4741366 ATTAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTTAATAATA
Found at i:4759316 original size:18 final size:18
Alignment explanation
Indices: 4759293--4759353 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
4759283 AAAAATATCT
4759293 TTAAATATTTATAATATA
1 TTAAATATTTATAATATA
*
4759311 TTAAATATTAAT-ATATA
1 TTAAATATTTATAATATA
*
4759328 ATATAATATATT-TAATATTA
1 TTA-AATAT-TTATAATA-TA
4759348 TTAAAT
1 TTAAAT
4759354 CGTAAACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.20
18 17 0.49
19 7 0.20
20 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATATTTATAATATA
Found at i:4763924 original size:19 final size:19
Alignment explanation
Indices: 4763902--4763945 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4763892 AATTTTATTC
4763902 AATTTCATTCAAATTTTTA
1 AATTTCATTCAAATTTTTA
* **
4763921 AATTTTATTTGAATTTTTA
1 AATTTCATTCAAATTTTTA
4763940 AATTTC
1 AATTTC
4763946 TCCACCCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTCATTCAAATTTTTA
Found at i:4764055 original size:26 final size:24
Alignment explanation
Indices: 4764001--4764065 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
4763991 AAAAAGGTAA
4764001 AATT-TTATTTTATTTATTTATTT
1 AATTATTATTTTATTTATTTATTT
4764024 ATATTATTATTATTATTTATGTT-TTT
1 A-ATTATTATT-TTATTTAT-TTATTT
*
4764050 CAATTA-TATTCTATTT
1 -AATTATTATTTTATTT
4764066 GCTCATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 1 0.03
24 8 0.22
25 9 0.25
26 15 0.42
27 3 0.08
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.68
Consensus pattern (24 bp):
AATTATTATTTTATTTATTTATTT
Found at i:4764207 original size:15 final size:16
Alignment explanation
Indices: 4764187--4764216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4764177 CTGTTATGTA
4764187 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAT
4764202 AATTTTAATTTTTAA
1 AATTTTAATTTTTAA
4764217 AAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTAATTTTTAAT
Found at i:4767698 original size:15 final size:15
Alignment explanation
Indices: 4767678--4767707 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4767668 GACTAACCTC
4767678 TCTCTAACTCTTCCA
1 TCTCTAACTCTTCCA
4767693 TCTCTAACTCTTCCA
1 TCTCTAACTCTTCCA
4767708 GAGATTGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (15 bp):
TCTCTAACTCTTCCA
Found at i:4768365 original size:30 final size:30
Alignment explanation
Indices: 4768329--4768390 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
4768319 TAATATACAC
4768329 AAGTTTGTAATGTAAGAGATGTCTAATTAT
1 AAGTTTGTAATGTAAGAGATGTCTAATTAT
4768359 AAGTTTGTAATGTAAGAGATGTCTAATTAT
1 AAGTTTGTAATGTAAGAGATGTCTAATTAT
4768389 AA
1 AA
4768391 CACAGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (30 bp):
AAGTTTGTAATGTAAGAGATGTCTAATTAT
Found at i:4772044 original size:20 final size:19
Alignment explanation
Indices: 4772006--4772044 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4771996 GTAAAATTAA
*
4772006 ATATTTAATAATTATATAT
1 ATATTTAATAATTAAATAT
*
4772025 ATATTTAAATATTTAAATAT
1 ATATTT-AATAATTAAATAT
4772045 TATGTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTAATAATTAAATAT
Found at i:4772064 original size:14 final size:15
Alignment explanation
Indices: 4772042--4772076 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
4772032 AATATTTAAA
4772042 TATTATGTTATT-TT
1 TATTATGTTATTATT
*
4772056 TATTTTGTTATTATT
1 TATTATGTTATTATT
4772071 TATTAT
1 TATTAT
4772077 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TATTATGTTATTATT
Found at i:4772864 original size:2 final size:2
Alignment explanation
Indices: 4772857--4772886 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4772847 ATATTTTACG
4772857 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
4772887 AAACTCAAAA
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:4782042 original size:15 final size:15
Alignment explanation
Indices: 4782019--4782059 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4782009 CTTTACTATA
* *
4782019 TAATATGATTACAGG
1 TAATGTGATTACAAG
*
4782034 TAATGTGATTGCAAG
1 TAATGTGATTACAAG
4782049 TAATGTGATTA
1 TAATGTGATTA
4782060 TAAGAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (15 bp):
TAATGTGATTACAAG
Found at i:4782285 original size:20 final size:20
Alignment explanation
Indices: 4782260--4782335 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
4782250 TTTTAAAATA
4782260 TTATTTTTTATATTATATAT
1 TTATTTTTTATATTATATAT
4782280 TTATTTTTTAT-TTAT-TAT
1 TTATTTTTTATATTATATAT
* *
4782298 TATATTTTATTATATTTTATTT
1 T-TATTTT-TTATATTATATAT
4782320 TTATTTCTTTA-ATTAT
1 TTATTT-TTTATATTAT
4782336 TTATATTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.08
19 10 0.21
20 19 0.40
21 11 0.23
22 4 0.08
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTTTATATTATATAT
Found at i:4782296 original size:34 final size:34
Alignment explanation
Indices: 4782208--4782352 Score: 138
Period size: 33 Copynumber: 4.3 Consensus size: 34
4782198 TATAAGTTTA
* *
4782208 ATATATTTAATTTT-TTTATTAATTTTTTATATA
1 ATATATTTATTTTTATTTATTAATTTTTTATATT
* * * **
4782241 ATACATTTCTTTTAAAATATT-ATTTTTTATATT
1 ATATATTTATTTTTATTTATTAATTTTTTATATT
4782274 ATATATTTATTTTTTATTTATT-ATTATATTT-TATT
1 ATATATTTA-TTTTTATTTATTAATT-T-TTTATATT
* *
4782309 ATAT-TTTATTTTTATTTCTTTAATTATTTATATT
1 ATATATTTATTTTTATTT-ATTAATTTTTTATATT
4782343 ATATATTTAT
1 ATATATTTAT
4782353 AATTTGTTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
33 40 0.44
34 30 0.33
35 17 0.19
36 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (34 bp):
ATATATTTATTTTTATTTATTAATTTTTTATATT
Found at i:4782311 original size:40 final size:40
Alignment explanation
Indices: 4782261--4782336 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
4782251 TTTAAAATAT
*
4782261 TATTTTTTATATTATATATTTATTT-TTTATTTATTATTA
1 TATTTTTTATATTATATATTTATTTCTTTAATTATTATTA
* *
4782300 TATTTTATTATATTTTATTTTTATTTCTTTAATTATT
1 TATTTT-TTATATTATATATTTATTTCTTTAATTATT
4782337 TATATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 6 0.19
40 17 0.53
41 9 0.28
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (40 bp):
TATTTTTTATATTATATATTTATTTCTTTAATTATTATTA
Found at i:4782355 original size:23 final size:23
Alignment explanation
Indices: 4782266--4782356 Score: 73
Period size: 24 Copynumber: 4.0 Consensus size: 23
4782256 AATATTATTT
**
4782266 TTTATATTATATATTTATTTTTTA
1 TTTATATTATATATTTA-TAATTA
*
4782290 TTTATTATTATAT-TTTATTA-TA
1 TTTA-TATTATATATTTATAATTA
* *
4782312 TTT-TATT-TTTATTTCTTTAATTA
1 TTTATATTATATA-TT-TATAATTA
4782335 TTTATATTATATATTTATAATT
1 TTTATATTATATATTTATAATT
4782357 TGTTTACCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
19 2 0.04
20 4 0.07
21 2 0.04
22 8 0.15
23 13 0.24
24 14 0.26
25 11 0.20
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATATTATATATTTATAATTA
Found at i:4782396 original size:5 final size:5
Alignment explanation
Indices: 4782386--4782448 Score: 60
Period size: 5 Copynumber: 12.4 Consensus size: 5
4782376 TAATTTTTTA
4782386 TATTT TATTT TATTT TAATTT TATTCT TA--T TATTT ATATTT TATTT
1 TATTT TATTT TATTT T-ATTT TATT-T TATTT TATTT -TATTT TATTT
*
4782432 TAATAT T-TTT TATTT TA
1 T-ATTT TATTT TATTT TA
4782449 ATTATAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 26 0.53
6 17 0.35
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:4782420 original size:20 final size:20
Alignment explanation
Indices: 4782381--4782448 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
4782371 TAAATTAATT
4782381 TTTTATATTTTA--TT-TTA
1 TTTTATATTTTATTTTATTA
4782398 TTTTA-ATTTTATTCTTATTA
1 TTTTATATTTTATT-TTATTA
*
4782418 -TTTATATTTTATTTTAATA
1 TTTTATATTTTATTTTATTA
*
4782437 TTTTTTATTTTA
1 TTTTATATTTTA
4782449 ATTATAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 6 0.14
17 5 0.12
19 11 0.26
20 21 0.49
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTTTATTTTATTA
Found at i:4782454 original size:31 final size:30
Alignment explanation
Indices: 4782381--4782454 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
4782371 TAAATTAATT
* *
4782381 TTTTATATTTTATTTTATTTTAATTTTATTC
1 TTTTA-ATTATATTTTATTTTAATTTTATTA
* *
4782412 TTATTATTTATATTTTATTTTAATATTTTTTA
1 TT-TTAATTATATTTTATTTTAAT-TTTATTA
4782444 TTTTAATTATA
1 TTTTAATTATA
4782455 ATAATATAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 26 0.72
32 10 0.28
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTAATTATATTTTATTTTAATTTTATTA
Found at i:4811174 original size:2 final size:2
Alignment explanation
Indices: 4811167--4811197 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4811157 ATGCCATAAA
4811167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4811198 CTTTTTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4818760 original size:2 final size:2
Alignment explanation
Indices: 4818753--4818784 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4818743 TTTCACAAAG
4818753 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
4818785 AATAATCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4824425 original size:23 final size:24
Alignment explanation
Indices: 4824399--4824446 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
4824389 TGAAAAGGTA
4824399 AAATTGATACT-AAAAATATGAAT
1 AAATTGATACTCAAAAATATGAAT
* *
4824422 AAATTGGTATTGCAAAAATATGAAT
1 AAATTGATACT-CAAAAATATGAAT
4824447 CACGTTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (24 bp):
AAATTGATACTCAAAAATATGAAT
Found at i:4836078 original size:12 final size:11
Alignment explanation
Indices: 4836054--4836087 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4836044 ATTTATTAAA
4836054 AAATATAATAT
1 AAATATAATAT
4836065 AAATATATATAT
1 AAATATA-ATAT
*
4836077 AAATAAAATAT
1 AAATATAATAT
4836088 TTATCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:4846951 original size:2 final size:2
Alignment explanation
Indices: 4846944--4846970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4846934 GGTATGCGTT
4846944 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 A
4846971 AGAAAATGTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4857054 original size:32 final size:32
Alignment explanation
Indices: 4857005--4857067 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4856995 AAGTTCAGTG
*
4857005 TTAAATTGACTCGTTACTTTAATGCCTCATTT
1 TTAAATTGACTCATTACTTTAATGCCTCATTT
*
4857037 TTAAATTGATTCATTACTTTAATGCCTCATT
1 TTAAATTGACTCATTACTTTAATGCCTCATT
4857068 CCAAATTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (32 bp):
TTAAATTGACTCATTACTTTAATGCCTCATTT
Found at i:4857066 original size:16 final size:16
Alignment explanation
Indices: 4857018--4857067 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4857008 AATTGACTCG
4857018 TTACTTTAATGCCTCA
1 TTACTTTAATGCCTCA
**
4857034 TT--TTTAAATTGATTCA
1 TTACTTT-AA-TGCCTCA
4857050 TTACTTTAATGCCTCA
1 TTACTTTAATGCCTCA
4857066 TT
1 TT
4857068 CCAAATTACG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 16 0.62
17 2 0.08
18 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (16 bp):
TTACTTTAATGCCTCA
Found at i:4860110 original size:14 final size:14
Alignment explanation
Indices: 4860093--4860121 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4860083 AATTTATTTA
4860093 ATTAAAAAAATAAG
1 ATTAAAAAAATAAG
4860107 ATTAAAAAAATAAG
1 ATTAAAAAAATAAG
4860121 A
1 A
4860122 AATGACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
ATTAAAAAAATAAG
Found at i:4860675 original size:16 final size:17
Alignment explanation
Indices: 4860654--4860694 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
4860644 ATTCTTTTCA
4860654 TTTATATATATAAT-TT
1 TTTATATATATAATATT
4860670 TTTATA-A-ATAATATT
1 TTTATATATATAATATT
4860685 TTTATATATA
1 TTTATATATA
4860695 AAGTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 7 0.32
17 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATATATAATATT
Found at i:4863615 original size:2 final size:2
Alignment explanation
Indices: 4863608--4863635 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4863598 AAAATGAGAA
4863608 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
4863636 TTTAGTATAA
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:4869108 original size:2 final size:2
Alignment explanation
Indices: 4869097--4869132 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
4869087 GAAAAAGATA
4869097 AT AT -T AT AT AT AT A- 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 AT AT AT A
4869133 CACACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4869123 original size:17 final size:16
Alignment explanation
Indices: 4869097--4869132 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4869087 GAAAAAGATA
4869097 ATATTATATATATAAT
1 ATATTATATATATAAT
*
4869113 ATATATATATATATATT
1 ATAT-TATATATATAAT
4869130 ATA
1 ATA
4869133 CACACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTATATATATAAT
Found at i:4876593 original size:10 final size:10
Alignment explanation
Indices: 4876572--4876612 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
4876562 TGTAAATAAG
4876572 TTATTATAATT
1 TTATTAT-ATT
4876583 TTATTATATT
1 TTATTATATT
*
4876593 TAATTA-ATT
1 TTATTATATT
4876602 TT-TTATATT
1 TTATTATATT
4876611 TT
1 TT
4876613 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 3 0.11
9 9 0.33
10 8 0.30
11 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATATT
Found at i:4876608 original size:29 final size:28
Alignment explanation
Indices: 4876575--4876655 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 28
4876565 AAATAAGTTA
*
4876575 TTATAATTTTATTATATTTAATTAATTTT
1 TTATAATTTTATT-TATTTAATTAAATTT
* * *
4876604 TTATATTTTTATTTTTAATTAAATAAATTT
1 TTATAATTTTA--TTTATTTAATTAAATTT
*
4876634 TTATAATTAATATTTATTTAAT
1 TTATAATT-TTATTTATTTAAT
4876656 AAAAATATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
29 18 0.44
30 19 0.46
31 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TTATAATTTTATTTATTTAATTAAATTT
Found at i:4876637 original size:30 final size:29
Alignment explanation
Indices: 4876564--4876641 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 29
4876554 TGGAGAAATG
* * *
4876564 TAAATAAGTTATTATAATTTTATTATATT
1 TAAATAAATTTTTATAATTTTATTATAAT
* * * *
4876593 TAATTAATTTTTTATATTTTTATTTTTAAT
1 TAAATAAATTTTTATAATTTTA-TTATAAT
4876623 TAAATAAATTTTTATAATT
1 TAAATAAATTTTTATAATT
4876642 AATATTTATT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TAAATAAATTTTTATAATTTTATTATAAT
Found at i:4876719 original size:18 final size:17
Alignment explanation
Indices: 4876687--4876727 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
4876677 ATATACATGA
*
4876687 CATATCATAATTAATAT
1 CATATAATAATTAATAT
*
4876704 CATATAATATATTAATTT
1 CATATAATA-ATTAATAT
4876722 CATATA
1 CATATA
4876728 TAAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
CATATAATAATTAATAT
Found at i:4876848 original size:17 final size:18
Alignment explanation
Indices: 4876796--4876851 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
4876786 AAATATAAAA
**
4876796 TAATAAATAATATTTTTAT
1 TAAT-AATAATAAATTTAT
*
4876815 TAATAATAATTAA-TTAT
1 TAATAATAATAAATTTAT
*
4876832 TAATTATAA-AAATTTAT
1 TAATAATAATAAATTTAT
4876849 TAA
1 TAA
4876852 ATTTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 2 0.06
17 19 0.61
18 6 0.19
19 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATAATAAATTTAT
Done.