Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 105 of 109
Found at i:21484870 original size:24 final size:24
Alignment explanation
Indices: 21484843--21484888 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21484833 ATTAAATTAA
* *
21484843 ATAAATTTATTCGTGAACATATTT
1 ATAAATATATTCATGAACATATTT
21484867 ATAAATATATTCATGAACATAT
1 ATAAATATATTCATGAACATAT
21484889 ATAAACGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (24 bp):
ATAAATATATTCATGAACATATTT
Found at i:21484958 original size:10 final size:10
Alignment explanation
Indices: 21484905--21484976 Score: 58
Period size: 10 Copynumber: 7.2 Consensus size: 10
21484895 GAACGTATTC
21484905 ATAAATAATAA
1 ATAAAT-ATAA
21484916 ATAAATTATAA
1 ATAAA-TATAA
* *
21484927 CT-AA-ACAA
1 ATAAATATAA
* *
21484935 ATAAATTTAG
1 ATAAATATAA
*
21484945 ATAAACATAA
1 ATAAATATAA
*
21484955 ATAAATTTAA
1 ATAAATATAA
21484965 ATAAATATAA
1 ATAAATATAA
21484975 AT
1 AT
21484977 GAATCTTAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
8 4 0.09
9 2 0.04
10 29 0.63
11 10 0.22
12 1 0.02
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (10 bp):
ATAAATATAA
Found at i:21484958 original size:20 final size:19
Alignment explanation
Indices: 21484912--21484976 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
21484902 TTCATAAATA
21484912 ATAAATAAATTATAACTAAAC
1 ATAAATAAATT-TAA-TAAAC
21484933 --AAATAAATTTAGATAAAC
1 ATAAATAAATTTA-ATAAAC
*
21484951 ATAAATAAATTTAAATAAAT
1 ATAAATAAATTT-AATAAAC
21484971 ATAAAT
1 ATAAAT
21484977 GAATCTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 21 0.54
21 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAATAAATTTAATAAAC
Found at i:21485451 original size:13 final size:14
Alignment explanation
Indices: 21485433--21485461 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21485423 AATTTTAATC
21485433 AAATT-AATTGATT
1 AAATTAAATTGATT
21485446 AAATTAAATTGATT
1 AAATTAAATTGATT
21485460 AA
1 AA
21485462 TTGATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATTAAATTGATT
Found at i:21485849 original size:28 final size:27
Alignment explanation
Indices: 21485799--21485854 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
21485789 AATTAATTTT
* * *
21485799 TAAAATTAAAAAATTTAATTCAATTAA
1 TAAAAATAAAAAATATAACTCAATTAA
21485826 TAAAAATAAAACAATATAACTCAATTAA
1 TAAAAATAAAA-AATATAACTCAATTAA
21485854 T
1 T
21485855 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (27 bp):
TAAAAATAAAAAATATAACTCAATTAA
Found at i:21488232 original size:2 final size:2
Alignment explanation
Indices: 21488225--21488249 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21488215 CGTGTGCGTG
21488225 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 T
21488250 TACTTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21488368 original size:2 final size:2
Alignment explanation
Indices: 21488361--21488391 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21488351 TCTAATCATA
21488361 TC TC 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 TC TC T
21488392 ATCCTAAAAA
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21494161 original size:2 final size:2
Alignment explanation
Indices: 21494154--21494180 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21494144 CTCAGCCTTT
21494154 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21494181 GAAAGAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21502328 original size:2 final size:2
Alignment explanation
Indices: 21502315--21502347 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21502305 TCTTTTGTAG
*
21502315 TA TA TA TG 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 TA TA T
21502348 GGATCTTAAT
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21503348 original size:2 final size:2
Alignment explanation
Indices: 21503341--21503370 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21503331 AGGATTATGT
*
21503341 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21503371 GATCTAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21503491 original size:30 final size:30
Alignment explanation
Indices: 21503455--21503540 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
21503445 CAATTATATC
* *
21503455 CAAATAAGTTTTTAATTTTTAATTTGTATT
1 CAAATAAATTTTTAAATTTTAATTTGTATT
21503485 CAAATAAATTTTTAAATTTTAATTTGTATT
1 CAAATAAATTTTTAAATTTTAATTTGTATT
* *
21503515 CAAATAAATTCTTAACTTTTAATTTG
1 CAAATAAATTTTTAAATTTTAATTTG
21503541 CACCTAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (30 bp):
CAAATAAATTTTTAAATTTTAATTTGTATT
Found at i:21503550 original size:30 final size:30
Alignment explanation
Indices: 21503455--21503551 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
21503445 CAATTATATC
* * * * *
21503455 CAAATAAGTTTTTAATTTTTAATTTGTATT
1 CAAATAAATTCTTAAATTTTAATTTGCACT
* * *
21503485 CAAATAAATTTTTAAATTTTAATTTGTATT
1 CAAATAAATTCTTAAATTTTAATTTGCACT
*
21503515 CAAATAAATTCTTAACTTTTAATTTGCAC-
1 CAAATAAATTCTTAAATTTTAATTTGCACT
21503544 CTAAATAA
1 C-AAATAA
21503552 GAATTTATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 1 0.02
30 59 0.98
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.48
Consensus pattern (30 bp):
CAAATAAATTCTTAAATTTTAATTTGCACT
Found at i:21504141 original size:18 final size:17
Alignment explanation
Indices: 21504116--21504153 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
21504106 TTTTTGATTA
* *
21504116 AAAT-AAAATTTTATTT
1 AAATAAAAAATTTACTT
21504132 AAATAAAAAATTTACTT
1 AAATAAAAAATTTACTT
21504149 AAATA
1 AAATA
21504154 CAATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAAAAAATTTACTT
Found at i:21507067 original size:11 final size:11
Alignment explanation
Indices: 21507036--21507089 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
21507026 ATAGTTATAT
21507036 AATATATATT-
1 AATATATATTA
21507046 AA-A-AT-TTA
1 AATATATATTA
21507054 AATATATATTA
1 AATATATATTA
*
21507065 AATACATATTA
1 AATATATATTA
**
21507076 AATAGGTATTA
1 AATATATATTA
21507087 AAT
1 AAT
21507090 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 2 0.05
8 4 0.11
9 2 0.05
10 4 0.11
11 25 0.68
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (11 bp):
AATATATATTA
Found at i:21507239 original size:10 final size:10
Alignment explanation
Indices: 21507195--21507269 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
21507185 TGTTTATATA
21507195 TATTCAT-AT
1 TATTCATGAT
* *
21507204 TAATCGTGAT
1 TATTCATGAT
*
21507214 TATTCGTG-T
1 TATTCATGAT
*
21507223 TAGTCATGAT
1 TATTCATGAT
21507233 TATTCAT-ATT
1 TATTCATGA-T
* *
21507243 TATCCGT-AT
1 TATTCATGAT
*
21507252 TATTCATGTT
1 TATTCATGAT
21507262 TATTCATG
1 TATTCATG
21507270 TTGTGTTTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 19 0.37
10 32 0.63
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (10 bp):
TATTCATGAT
Found at i:21507245 original size:29 final size:29
Alignment explanation
Indices: 21507213--21507268 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
21507203 TTAATCGTGA
* *
21507213 TTATTCGTGTTAGTCATGATTATTCATAT
1 TTATCCGTATTAGTCATGATTATTCATAT
* *
21507242 TTATCCGTATTATTCATGTTTATTCAT
1 TTATCCGTATTAGTCATGATTATTCAT
21507269 GTTGTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (29 bp):
TTATCCGTATTAGTCATGATTATTCATAT
Found at i:21507364 original size:14 final size:15
Alignment explanation
Indices: 21507347--21507376 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21507337 TATGTCATAA
21507347 CATGTTTT-ATAATT
1 CATGTTTTAATAATT
21507361 CATGTTTTAATAATT
1 CATGTTTTAATAATT
21507376 C
1 C
21507377 GTGCCATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (15 bp):
CATGTTTTAATAATT
Found at i:21508690 original size:18 final size:19
Alignment explanation
Indices: 21508667--21508703 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21508657 ATTTATTTTA
21508667 TTATTTT-AAGTTTTTATT
1 TTATTTTCAAGTTTTTATT
*
21508685 TTATTTTCAATTTTTTATT
1 TTATTTTCAAGTTTTTATT
21508704 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (19 bp):
TTATTTTCAAGTTTTTATT
Found at i:21508712 original size:22 final size:23
Alignment explanation
Indices: 21508680--21508727 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
21508670 TTTTAAGTTT
*
21508680 TTATTTTATTTT-CAATTTTTTA
1 TTATTTAATTTTACAATTTTTTA
*
21508702 TTATTTAATTTTACTATTTTTTA
1 TTATTTAATTTTACAATTTTTTA
21508725 TTA
1 TTA
21508728 AAAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTTAATTTTACAATTTTTTA
Found at i:21508791 original size:13 final size:15
Alignment explanation
Indices: 21508761--21508793 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21508751 TAGAAGAAGC
21508761 AAATAATAAGATAAAA
1 AAATAATAAGAT-AAA
21508777 AAATAATAA-ATAAA
1 AAATAATAAGATAAA
21508791 AAA
1 AAA
21508794 ATTTTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 2 0.12
16 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAATAAGATAAA
Found at i:21508791 original size:15 final size:16
Alignment explanation
Indices: 21508761--21508795 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
21508751 TAGAAGAAGC
21508761 AAATAATAAGATAAAA
1 AAATAATAAGATAAAA
21508777 AAATAATAA-ATAAAA
1 AAATAATAAGATAAAA
21508792 AAAT
1 AAAT
21508796 TTTTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATAATAAGATAAAA
Found at i:21509787 original size:2 final size:2
Alignment explanation
Indices: 21509780--21509805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21509770 TCAATTTCTC
21509780 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
21509806 TGGAATTTCC
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:21518986 original size:17 final size:17
Alignment explanation
Indices: 21518966--21518999 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21518956 TATCTATGGC
* *
21518966 TTTCTTTCTTTAATCTT
1 TTTCATTCTTAAATCTT
21518983 TTTCATTCTTAAATCTT
1 TTTCATTCTTAAATCTT
21519000 AAAAGAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCATTCTTAAATCTT
Found at i:21519036 original size:58 final size:60
Alignment explanation
Indices: 21518960--21519076 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
21518950 TTCTTTTATC
* * * *
21518960 TATGGCTTTCTTTCTTTAAT-CTTTTTCATTCTTAAATCTTAAAAGAATAAGATAAACCA
1 TATGGCTTTCTTTCTTTAATAATTTTTCATTCTTAAATCCTAAAAGAACAAGACAAACCA
* *
21519019 TATGG-TTTCTTTTTTTAATAATTTTTCATTCTTCAATCCTAAAAGAACAAGACAAACC
1 TATGGCTTTCTTTCTTTAATAATTTTTCATTCTTAAATCCTAAAAGAACAAGACAAACC
21519077 CTGTAATCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 13 0.25
59 38 0.75
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (60 bp):
TATGGCTTTCTTTCTTTAATAATTTTTCATTCTTAAATCCTAAAAGAACAAGACAAACCA
Found at i:21519134 original size:162 final size:156
Alignment explanation
Indices: 21518861--21519147 Score: 396
Period size: 162 Copynumber: 1.8 Consensus size: 156
21518851 TTTTATCATT
* *
21518861 CATATGTTTATTTATTTAATATTTTTAATCTTCAATCCTAAAAAATAAACAAATCATATAACCTC
1 CATATGTTTATTTATTTAATATTTTTAATCTTCAATCCTAAAAAACAAACAAACCATATAACCTC
* * * *
21518926 ATCTTTTTAAACAAAGTTCTATTTTTCTTTTATCTATGGCTTTCTTTCTTTAATCTTTTTCATTC
66 ACCTTTTTAAACAAAGTTATATTTTTCTTCTATCTATGGCTTTCTTTCTTTAATATTTTTCATTC
21518991 TTAAATCTTAAAAGAATAAGATAAAC
131 TTAAATCTTAAAAGAATAAGATAAAC
* * * * *
21519017 CATATGGTTTCTTTTTTTAATAATTTTTCATTCTTCAATCCTAAAAGAACAAGACAAACCCTGTA
1 CATAT-GTTTATTTATTTAAT-ATTTTT-AATCTTCAATCCTAAAA-AACAA-ACAAACCATATA
*
21519082 ATCCTCACCTTTTTAAACAAAGTTATATTTTTCTTCTATTTATAGG-TTTCTTTCTTTAATATTT
61 A-CCTCACCTTTTTAAACAAAGTTATATTTTTCTTCTATCTAT-GGCTTTCTTTCTTTAATATTT
21519146 TT
124 TT
21519148 TTTCATTCTT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
156 5 0.04
157 13 0.12
158 6 0.05
159 16 0.14
160 4 0.04
161 10 0.09
162 56 0.50
163 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (156 bp):
CATATGTTTATTTATTTAATATTTTTAATCTTCAATCCTAAAAAACAAACAAACCATATAACCTC
ACCTTTTTAAACAAAGTTATATTTTTCTTCTATCTATGGCTTTCTTTCTTTAATATTTTTCATTC
TTAAATCTTAAAAGAATAAGATAAAC
Found at i:21519622 original size:60 final size:60
Alignment explanation
Indices: 21519555--21519731 Score: 250
Period size: 60 Copynumber: 3.0 Consensus size: 60
21519545 GGGTTACATG
* * * *
21519555 GTTTGTCTTATTTTTTTAAGATTGAAGAATAAAAAATTATTAAAGAAAGTAAGCCATAC-
1 GTTTGTCTTATTCTTTTAGGATTGAAGAATGAAAAATTATTAAAGAAAGAAAGCCATACA
* * *
21519614 GATTTGTCTTGTGCTTTTAGGATTGAAGAATGAAAAATTATTAAAGAAAGGAAGCCATACA
1 G-TTTGTCTTATTCTTTTAGGATTGAAGAATGAAAAATTATTAAAGAAAGAAAGCCATACA
* *
21519675 GTTTGTCTTATTCTTTTAGGATTGAAGAATGAAAGA-TATTAAAGAAAGAAAGTCATA
1 GTTTGTCTTATTCTTTTAGGATTGAAGAATGAAAAATTATTAAAGAAAGAAAGCCATA
21519732 GATAAAAGAA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 20 0.19
60 84 0.80
61 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (60 bp):
GTTTGTCTTATTCTTTTAGGATTGAAGAATGAAAAATTATTAAAGAAAGAAAGCCATACA
Found at i:21520624 original size:3 final size:3
Alignment explanation
Indices: 21520616--21520653 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21520606 GATCATACAA
21520616 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21520654 CAACGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21522532 original size:62 final size:62
Alignment explanation
Indices: 21522421--21522682 Score: 187
Period size: 62 Copynumber: 4.2 Consensus size: 62
21522411 ATCAAAAACA
* * * * * *
21522421 CTTAAAGTAATCTCATTCAATTTTTTGTAATG-GATTATTTAAGATGTTTTTGGCTAGAAATCT
1 CTTAAA-TAATCTCAGTCAATTTTTTGCAA-GAGATTATTCAATACGTTTTTGGCTAAAAATCT
* * *
21522484 CTTCAATAATCTCAGTCAATTTTTTGCAAGAGATTATTCAATACGTTTTTTTGGGC-AAAAACCC
1 CTTAAATAATCTCAGTCAATTTTTTGCAAGAGATTATTCAATACG--TTTTT-GGCTAAAAATCT
* **** * * *
21522548 CTTAAATAATCTC-TTCATAAAAATTG-AAGAGGATTATTCAA-GCTGTTTTTTGCTAAAAATAT
1 CTTAAATAATCTCAGTCA-ATTTTTTGCAAGA-GATTATTCAATAC-GTTTTTGGCTAAAAATCT
* * * *
21522610 CTTTAATAACCCCAGTCAATTTTTTGCAAGGGATTATTCAATACGTTTTTTGGGC-AAAAATGC-
1 CTTAAATAATCTCAGTCAATTTTTTGCAAGAGATTATTCAATACG-TTTTT-GGCTAAAAAT-CT
21522673 CTTAAATAAT
1 CTTAAATAAT
21522683 TTCTTCATAA
Statistics
Matches: 151, Mismatches: 34, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
61 3 0.02
62 67 0.44
63 39 0.26
64 39 0.26
65 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (62 bp):
CTTAAATAATCTCAGTCAATTTTTTGCAAGAGATTATTCAATACGTTTTTGGCTAAAAATCT
Found at i:21522630 original size:126 final size:123
Alignment explanation
Indices: 21522452--21522722 Score: 389
Period size: 126 Copynumber: 2.2 Consensus size: 123
21522442 TTTTTGTAAT
* * * * * *
21522452 GGATTATTTAAGATGTTTTTGGCTAGAAATCTCTTCAATAATCTCAGTCAATTTTTTGCAAGAGA
1 GGATTATTCAAG-TGTTTTTTGCTAAAAATATCTTCAATAACCCCAGTCAATTTTTTGCAAGAGA
21522517 TTATTCAATACGTTTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAATTGAAGA
65 TTATTCAATACG-TTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAA-TGAAGA
* *
21522578 GGATTATTCAAGCTGTTTTTTGCTAAAAATATCTTTAATAACCCCAGTCAATTTTTTGCAAGGGA
1 GGATTATTCAAG-TGTTTTTTGCTAAAAATATCTTCAATAACCCCAGTCAATTTTTTGCAAGAGA
** * *
21522643 TTATTCAATACGTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAATGAAGG
65 TTATTCAATACGTTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAATGAAGA
*
21522702 GGATTATTCAAGTGGTTTTTG
1 GGATTATTCAAGTGTTTTTTG
21522723 GCCACAAATG
Statistics
Matches: 131, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
123 8 0.06
124 17 0.13
125 38 0.29
126 68 0.52
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (123 bp):
GGATTATTCAAGTGTTTTTTGCTAAAAATATCTTCAATAACCCCAGTCAATTTTTTGCAAGAGAT
TATTCAATACGTTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAATGAAGA
Found at i:21522705 original size:62 final size:62
Alignment explanation
Indices: 21522515--21522712 Score: 163
Period size: 62 Copynumber: 3.2 Consensus size: 62
21522505 TTTTGCAAGA
** *
21522515 GATTATTCAATACGTTTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAATTGAAGAG
1 GATTATTCAATACG-TTTTTTGGGCAAAAATACCTTAAATAATCTCTTCATAAAAA-TGAAGGG
* * * * * * ****
21522579 GATTATTCAA-GCTGTTTTTT--GCTAAAAATATCTTTAATAACCCCAGTCA-ATTTTTTGCAA-
1 GATTATTCAATAC-GTTTTTTGGGC-AAAAATACCTTAAATAATCTC-TTCATA-AAAATG-AAG
21522639 GG
61 GG
* *
21522641 GATTATTCAATACGTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAATGAAGGG
1 GATTATTCAATACGTTTTTTGGGCAAAAATACCTTAAATAATCTCTTCATAAAAATGAAGGG
21522703 GATTATTCAA
1 GATTATTCAA
21522713 GTGGTTTTTG
Statistics
Matches: 99, Mismatches: 25, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
61 4 0.04
62 53 0.54
63 29 0.29
64 13 0.13
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (62 bp):
GATTATTCAATACGTTTTTTGGGCAAAAATACCTTAAATAATCTCTTCATAAAAATGAAGGG
Found at i:21522785 original size:125 final size:124
Alignment explanation
Indices: 21522452--21522773 Score: 346
Period size: 126 Copynumber: 2.6 Consensus size: 124
21522442 TTTTTGTAAT
* * * * * * *
21522452 GGATTATTTAAGATGTTTTTGGCTAGAAAT-CTCTTCAATAATCTCAGTCAATTTTTTGCAAGAG
1 GGATTATTCAAGCTGTTTTTGGCCAAAAATAC-CTTCAATAACCCCAGTCAATTTTTT-CAAGAA
** *
21522516 ATTATTCAATACGTTTTTTTGGGCAAAAACCCCTTAAATAATCTCTTCATAAAAATTGAAGA
64 ATTATTCAATAC-TTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAATTGAAGA
* * * * **
21522578 GGATTATTCAAGCTGTTTTTTGCTAAAAATATCTTTAATAACCCCAGTCAATTTTTTGCAAGGGA
1 GGATTATTCAAGCTGTTTTTGGCCAAAAATACCTTCAATAACCCCAGTCAATTTTTT-CAAGAAA
* *
21522643 TTATTCAATACGTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAA-TGAAGG
65 TTATTCAATACTTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAATTGAAGA
* * * * * *
21522702 GGATTATTCAAG-TGGTTTTTGGCCACAAATGCCTTCACTAACCTCATTTAATTTTTAT-AAGAA
1 GGATTATTCAAGCT-GTTTTTGGCCAAAAATACCTTCAATAACCCCAGTCAATTTTT-TCAAGAA
21522765 ATTATTCAA
64 ATTATTCAA
21522774 GGTATTTTTT
Statistics
Matches: 167, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
123 13 0.08
124 49 0.29
125 39 0.23
126 66 0.40
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (124 bp):
GGATTATTCAAGCTGTTTTTGGCCAAAAATACCTTCAATAACCCCAGTCAATTTTTTCAAGAAAT
TATTCAATACTTTTTTTGGGCAAAAATGCCTTAAATAATTTCTTCATAAAAATTGAAGA
Found at i:21523235 original size:62 final size:62
Alignment explanation
Indices: 21523160--21523298 Score: 156
Period size: 62 Copynumber: 2.2 Consensus size: 62
21523150 AAATTTTTGT
* ** * *
21523160 AAGGGGTTATTCAAAGGGTTTACT-GAGCAGAAATC-CCTTGAATAATCTACTCATAAAAATTG
1 AAGGGATTATTCAAAGCCTTT-CTGGAGCA-AAAACGCCTTAAATAATCTACTCATAAAAATTG
* * * *
21523222 AAGGGATTATTCAATGCCTTTTTGGAGCAAAAACGTCTTAAATAATCTTCTCATAAAAATTG
1 AAGGGATTATTCAAAGCCTTTCTGGAGCAAAAACGCCTTAAATAATCTACTCATAAAAATTG
21523284 AAGGGAATTATTCAA
1 AAGGG-ATTATTCAA
21523299 GTGGTTTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
61 5 0.08
62 51 0.78
63 9 0.14
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (62 bp):
AAGGGATTATTCAAAGCCTTTCTGGAGCAAAAACGCCTTAAATAATCTACTCATAAAAATTG
Found at i:21523747 original size:252 final size:251
Alignment explanation
Indices: 21523458--21523950 Score: 855
Period size: 252 Copynumber: 2.0 Consensus size: 251
21523448 AATAATCCCC
* * *
21523458 TCAAAAAAATTTAAGGGAATTAGTCAAGGCATTTTTTGTCAGAAACGCCTTGAGTAATGCTATAC
1 TCAAAAAAATTTAAGGGAATTAGTCAAGGCATTTTTTGTCAGAAACACCTTGAGTAATCCCATAC
*
21523523 TTTTTTTTATAAGTGATTATTCAAGGCG-TTTTTTGTCAGAAACCCCTTCAATAACCCATTCAAA
66 TTTTTTTTATAAGTGATTATTCAAGGCGTTTTTTTG-CAAAAACCCCTTCAATAACCCATTCAAA
*
21523587 TTTTTTTCATATAAAAAATTTAAAATTGAAAAGGATTATTTAAGGCGTTTTTTGTTAAAAACGCT
130 -TTTTTTCATATAAAAAATTAAAAATTGAAAAGGATTATTTAAGGCGTTTTTTGTTAAAAACGCT
* *
21523652 TTAATAATCTTCTCAAAAAAATTGAA-GAGGGTTAGTCAAGATGTTTTTAAGGGATTAG
194 TCAATAATCTTCTCAAAAAAATTGAAGGA-GATTAGTCAAGATGTTTTTAAGGGATTAG
*
21523710 TCAAAAAAATTTAAGGGAATTAGTCAAGGCGTTTTTTGTCAGAAACACCTTGAGTAATCCCATAC
1 TCAAAAAAATTTAAGGGAATTAGTCAAGGCATTTTTTGTCAGAAACACCTTGAGTAATCCCATAC
21523775 TTTTTTTTATAAGTGATTATTCAAGGCGTTTTTTTGCAAAAACCCCTTCAATAACCCATTCAAAT
66 TTTTTTTTATAAGTGATTATTCAAGGCGTTTTTTTGCAAAAACCCCTTCAATAACCCATTCAAAT
*
21523840 TTTTTCATATAAAAAATTAAAAATTGAAAGGGATTATTTAAGGCGTTTTTTGTTAAAAACGCTTC
131 TTTTTCATATAAAAAATTAAAAATTGAAAAGGATTATTTAAGGCGTTTTTTGTTAAAAACGCTTC
*
21523905 AATAATCTTTTCAAAAAAATTGAAGGAGATTAGTCAAGATGTTTTT
196 AATAATCTTCTCAAAAAAATTGAAGGAGATTAGTCAAGATGTTTTT
21523951 GATCAGAGAT
Statistics
Matches: 229, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
251 104 0.45
252 118 0.52
253 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (251 bp):
TCAAAAAAATTTAAGGGAATTAGTCAAGGCATTTTTTGTCAGAAACACCTTGAGTAATCCCATAC
TTTTTTTTATAAGTGATTATTCAAGGCGTTTTTTTGCAAAAACCCCTTCAATAACCCATTCAAAT
TTTTTCATATAAAAAATTAAAAATTGAAAAGGATTATTTAAGGCGTTTTTTGTTAAAAACGCTTC
AATAATCTTCTCAAAAAAATTGAAGGAGATTAGTCAAGATGTTTTTAAGGGATTAG
Found at i:21532742 original size:6 final size:6
Alignment explanation
Indices: 21532727--21532763 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
21532717 AGAATTTATG
*
21532727 GGTGGA GGTGGG GGTGGA GGTGGA GGTGGA GGTGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G
21532764 AAGGCACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.70, T:0.16
Consensus pattern (6 bp):
GGTGGA
Found at i:21539862 original size:26 final size:26
Alignment explanation
Indices: 21539816--21539870 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
21539806 TACCCTCCTG
* *
21539816 TCTAGCAATTATCATTTTCCTTTCTT
1 TCTAGCAATTATCAGTGTCCTTTCTT
*
21539842 TCTAGCAATTCTCAGTGTCCTTTCTT
1 TCTAGCAATTATCAGTGTCCTTTCTT
21539868 TCT
1 TCT
21539871 TGCTTAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.07, T:0.51
Consensus pattern (26 bp):
TCTAGCAATTATCAGTGTCCTTTCTT
Found at i:21544185 original size:2 final size:2
Alignment explanation
Indices: 21544178--21544207 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21544168 TACCAAAATT
*
21544178 TA TA TA TA CA 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
21544208 AACGCAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21550728 original size:27 final size:28
Alignment explanation
Indices: 21550698--21550757 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
21550688 GAGCTTACGA
*
21550698 ATTTAAATATTAATTTTTGTA-AAATTT
1 ATTTAAATATAAATTTTTGTATAAATTT
*
21550725 ATTT-AATATAAATTTTTTTATAAATTT
1 ATTTAAATATAAATTTTTGTATAAATTT
*
21550752 TTTTAA
1 ATTTAA
21550758 TTACAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.50
27 13 0.46
28 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTAAATATAAATTTTTGTATAAATTT
Found at i:21550732 original size:26 final size:27
Alignment explanation
Indices: 21550698--21550758 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
21550688 GAGCTTACGA
*
21550698 ATTTAAATATTAATTTTTGTA-AAATTT
1 ATTT-AATATAAATTTTTGTATAAATTT
*
21550725 ATTTAATATAAATTTTTTTATAAATTT
1 ATTTAATATAAATTTTTGTATAAATTT
*
21550752 TTTTAAT
1 ATTTAAT
21550759 TACAATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTAATATAAATTTTTGTATAAATTT
Found at i:21550748 original size:12 final size:12
Alignment explanation
Indices: 21550709--21550756 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
21550699 TTTAAATATT
*
21550709 AATTTTTGTA-A
1 AATTTTTTTATA
21550720 AATTTATTTAATATA
1 AATTT-TTT--TATA
21550735 AATTTTTTTATA
1 AATTTTTTTATA
21550747 AATTTTTTTA
1 AATTTTTTTA
21550757 ATTACAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
14 5 0.16
15 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
AATTTTTTTATA
Found at i:21550765 original size:15 final size:14
Alignment explanation
Indices: 21550719--21550765 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
21550709 AATTTTTGTA
*
21550719 AAATTTATTTAATAT
1 AAATTTTTTTAAT-T
21550734 AAATTTTTTT-A-T
1 AAATTTTTTTAATT
21550746 AAATTTTTTTAATT
1 AAATTTTTTTAATT
21550760 ACAATT
1 A-AATT
21550766 ATAATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 11 0.39
13 1 0.04
14 3 0.11
15 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
AAATTTTTTTAATT
Found at i:21550780 original size:27 final size:29
Alignment explanation
Indices: 21550750--21550812 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
21550740 TTTTATAAAT
*
21550750 TTTTTTAATTACAATTATAA-TAA-TTTA
1 TTTTTTAATCACAATTATAATTAATTTTA
* *
21550777 TTTTTCAATCATAATTATAATTAATTTTA
1 TTTTTTAATCACAATTATAATTAATTTTA
21550806 TTATTTT
1 TT-TTTT
21550813 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 17 0.59
28 3 0.10
29 6 0.21
30 3 0.10
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTTAATCACAATTATAATTAATTTTA
Found at i:21553335 original size:11 final size:11
Alignment explanation
Indices: 21553319--21553344 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21553309 TCGATTGTGG
21553319 ATTATTTTGAT
1 ATTATTTTGAT
21553330 ATTATTTTGAT
1 ATTATTTTGAT
21553341 ATTA
1 ATTA
21553345 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
ATTATTTTGAT
Found at i:21553599 original size:25 final size:25
Alignment explanation
Indices: 21553565--21553614 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21553555 TTATGTGTGA
21553565 TATCACCGACTCCCACTGTACGATT
1 TATCACCGACTCCCACTGTACGATT
21553590 TATCACCGACTCCCACTGTACGATT
1 TATCACCGACTCCCACTGTACGATT
21553615 CACCGACCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.28
Consensus pattern (25 bp):
TATCACCGACTCCCACTGTACGATT
Found at i:21553620 original size:22 final size:24
Alignment explanation
Indices: 21553565--21553621 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
21553555 TTATGTGTGA
21553565 TATCACCGACTCCCACTGTACGATT
1 TATCACCGACTCCCACTGTACGA-T
21553590 TATCACCGACTCCCACTGTACGA-
1 TATCACCGACTCCCACTGTACGAT
21553613 T-TCACCGAC
1 TATCACCGAC
21553622 CGCAGATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.25
23 1 0.03
25 23 0.72
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.25
Consensus pattern (24 bp):
TATCACCGACTCCCACTGTACGAT
Found at i:21560270 original size:14 final size:13
Alignment explanation
Indices: 21560251--21560293 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
21560241 ATATATCAAC
21560251 TTCAATAAAATTT
1 TTCAATAAAATTT
21560264 ATTCAATATAAATTT
1 -TTCAATA-AAATTT
* *
21560279 TTTATTAAAATTT
1 TTCAATAAAATTT
21560292 TT
1 TT
21560294 TTTCAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.31
14 12 0.46
15 6 0.23
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (13 bp):
TTCAATAAAATTT
Found at i:21560325 original size:24 final size:24
Alignment explanation
Indices: 21560282--21560343 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
21560272 TAAATTTTTT
21560282 ATTAAAAT-TTTTTTTCAATCATA
1 ATTAAAATATTTTTTTCAATCATA
* *
21560305 ATTAAAATATTTTTTTTAATCGTA
1 ATTAAAATATTTTTTTCAATCATA
* *
21560329 ATTATAATAATTTTT
1 ATTAAAATATTTTTT
21560344 ATTATAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 8 0.24
24 26 0.76
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTAAAATATTTTTTTCAATCATA
Found at i:21560341 original size:25 final size:26
Alignment explanation
Indices: 21560287--21560343 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
21560277 TTTTTATTAA
21560287 AATTTTTTTTCAATCATAATTAAAAT
1 AATTTTTTTTCAATCATAATTAAAAT
* *
21560313 -ATTTTTTTT-AATCGTAATTATAAT
1 AATTTTTTTTCAATCATAATTAAAAT
21560337 AATTTTT
1 AATTTTT
21560344 ATTATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (26 bp):
AATTTTTTTTCAATCATAATTAAAAT
Found at i:21561793 original size:7 final size:7
Alignment explanation
Indices: 21561778--21561809 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
21561768 ATCCTGTCGA
*
21561778 AAAAGAC
1 AAAACAC
21561785 AAAACAC
1 AAAACAC
21561792 AAAACAC
1 AAAACAC
21561799 AAAACAC
1 AAAACAC
21561806 AAAA
1 AAAA
21561810 ATACCCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.22, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAACAC
Found at i:21563064 original size:31 final size:31
Alignment explanation
Indices: 21563026--21563094 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
21563016 TATATTTTAT
*
21563026 ATTTTTATATCAACA-ATAAT-TATAATATATA
1 ATTTTTATAT-AAAATATAATATA-AATATATA
21563057 ATTTTTATATAAAATATAATATAAATATATA
1 ATTTTTATATAAAATATAATATAAATATATA
*
21563088 AATTTTA
1 ATTTTTA
21563095 ACATTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 29 0.85
32 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTTTTATATAAAATATAATATAAATATATA
Found at i:21563723 original size:21 final size:21
Alignment explanation
Indices: 21563676--21563734 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
21563666 TTTAACGTAA
*
21563676 TATTTAA-ATTATAAATTTAT
1 TATTTAATATAATAAATTTAT
*
21563696 TAATTAATATAATAATATTTAT
1 TATTTAATATAATAA-ATTTAT
*
21563718 T-TTTAATATAATTAATT
1 TATTTAATATAATAAATT
21563735 ATAAATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.27
21 17 0.52
22 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTAATATAATAAATTTAT
Found at i:21563844 original size:12 final size:12
Alignment explanation
Indices: 21563827--21563854 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21563817 AATTATTAAA
21563827 ATTAAATATTTT
1 ATTAAATATTTT
21563839 ATTAAATATTTT
1 ATTAAATATTTT
21563851 ATTA
1 ATTA
21563855 TAATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTAAATATTTT
Found at i:21572002 original size:2 final size:2
Alignment explanation
Indices: 21571995--21572040 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
21571985 CTCATTTTTC
*
21571995 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21572037 AT AT
1 AT AT
21572041 TGTTTACCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21572612 original size:2 final size:2
Alignment explanation
Indices: 21572605--21572636 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21572595 TAAACAATAA
21572605 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
21572637 TCTCACGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21575349 original size:12 final size:12
Alignment explanation
Indices: 21575332--21575357 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21575322 TTTCTCTTCT
21575332 AAAATTCATTGA
1 AAAATTCATTGA
21575344 AAAATTCATTGA
1 AAAATTCATTGA
21575356 AA
1 AA
21575358 TCTCAACACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAATTCATTGA
Found at i:21576844 original size:26 final size:26
Alignment explanation
Indices: 21576763--21576867 Score: 83
Period size: 26 Copynumber: 4.1 Consensus size: 26
21576753 AAAGGATATT
* * *
21576763 TATTTTTTTATT-TTTTATTACATAGT
1 TATTTATTTATTAATTTATTACATA-A
** *
21576789 TATTTATTTTAGTTAAAATAATA-ATAA
1 TATTTA-TTTA-TTAATTTATTACATAA
* *
21576816 T-TTTATTT-TTAGTTTATTATATAA
1 TATTTATTTATTAATTTATTACATAA
21576840 TATTTATTTATTAATTTATTACATAA
1 TATTTATTTATTAATTTATTACATAA
21576866 TA
1 TA
21576868 ATAAAATTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
23 7 0.11
24 5 0.08
25 10 0.16
26 25 0.41
27 5 0.08
28 5 0.08
29 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (26 bp):
TATTTATTTATTAATTTATTACATAA
Found at i:21576868 original size:29 final size:26
Alignment explanation
Indices: 21576809--21576870 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 26
21576799 AGTTAAAATA
*
21576809 ATAATAAT-TTTATTTTTAGTTTATT
1 ATAATAATATTTATTTTTAATTTATT
21576834 AT-ATAATATTTATTTATTAATTTATT
1 ATAATAATATTTATTT-TTAATTTATT
21576860 ACATAATAATA
1 --ATAATAATA
21576871 AAATTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 5 0.16
25 9 0.29
26 9 0.29
28 2 0.06
29 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
ATAATAATATTTATTTTTAATTTATT
Found at i:21583046 original size:18 final size:18
Alignment explanation
Indices: 21583006--21583056 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
21582996 ATTGAATTCG
*
21583006 AATTTAAAT-AATTTATT
1 AATTTAAGTAAATTTATT
21583023 AATTTAAGTAAATTT-TT
1 AATTTAAGTAAATTTATT
*
21583040 AATTTTAATTAAATTTA
1 AA-TTTAAGTAAATTTA
21583057 AATAATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATTTAAGTAAATTTATT
Found at i:21583250 original size:36 final size:36
Alignment explanation
Indices: 21583168--21583285 Score: 84
Period size: 36 Copynumber: 3.2 Consensus size: 36
21583158 TTTAATCGAA
* *
21583168 TAAATTTTAATAATTTAAAATTTATCTTTAATTAAACT
1 TAAATTTTAA-AAATTAAAATTTATC-TAAATTAAACT
*
21583206 CAAA-TTTAAAAATTAAAATTTTATC-AAATTTAAA-T
1 TAAATTTTAAAAATTAAAA-TTTATCTAAA-TTAAACT
* * *
21583241 TAAATTTTAAATAA-TAAATTTTGA-ATGAATTCAAACT
1 TAAATTTTAAA-AATTAAAATTT-ATCTAAATT-AAACT
21583278 TAAATTTT
1 TAAATTTT
21583286 TTTATTATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
35 11 0.17
36 29 0.45
37 22 0.34
38 3 0.05
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (36 bp):
TAAATTTTAAAAATTAAAATTTATCTAAATTAAACT
Found at i:21586159 original size:23 final size:24
Alignment explanation
Indices: 21586119--21586163 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
21586109 ATTATCATAT
* *
21586119 GATTGATAGGATTCTGTTTGGTCA
1 GATTGAGAGGATTATGTTTGGTCA
21586143 GATTGAGA-GATTATGTTTGGT
1 GATTGAGAGGATTATGTTTGGT
21586164 TTTGAGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.42
Consensus pattern (24 bp):
GATTGAGAGGATTATGTTTGGTCA
Found at i:21588958 original size:23 final size:24
Alignment explanation
Indices: 21588890--21588958 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
21588880 TTTTATTCAA
* **
21588890 ATTTAAATTTAAATTTTAAATATTT
1 ATTTAAATATAAAAATTAAATA-TT
* *
21588915 ATTTAATTA-AAATAATAAAATA-T
1 ATTTAAATATAAA-AATTAAATATT
21588938 ATTTAAATATAAAAATTAAAT
1 ATTTAAATATAAAAATTAAAT
21588959 TAAATTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
23 16 0.46
24 6 0.17
25 13 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTAAATATAAAAATTAAATATT
Found at i:21588998 original size:21 final size:21
Alignment explanation
Indices: 21588940--21589001 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
21588930 TAAAATATAT
21588940 TTAAAT-ATAAAA-A-TTAAA
1 TTAAATCATAAAATATTTAAA
*
21588958 TTAAATTCATAAACTATTTAAA
1 TTAAA-TCATAAAATATTTAAA
21588980 TTAAA-CATAAAAATATTTAAA
1 TTAAATCAT-AAAATATTTAAA
21589001 T
1 T
21589002 ATAATTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 8 0.22
21 13 0.35
22 10 0.27
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAATCATAAAATATTTAAA
Found at i:21589056 original size:26 final size:29
Alignment explanation
Indices: 21588994--21589062 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
21588984 ACATAAAAAT
*
21588994 ATTTAAATATAATTTAATCAATAAATTAA
1 ATTTAAATTTAATTTAATCAATAAATTAA
*
21589023 ATTTTTAATTTTAATTTAAT-AAT-AATTAA
1 A--TTTAAATTTAATTTAATCAATAAATTAA
21589052 A-TTAAATTTAA
1 ATTTAAATTTAA
21589063 ATAATTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 9 0.26
29 8 0.23
30 3 0.09
31 15 0.43
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTAAATTTAATTTAATCAATAAATTAA
Found at i:21589309 original size:1 final size:1
Alignment explanation
Indices: 21589303--21589327 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21589293 AGAAAGAATG
21589303 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
21589328 CCGATCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21593858 original size:20 final size:21
Alignment explanation
Indices: 21593813--21593858 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21593803 TACTTTTAAG
*
21593813 ATTAAAAACTATTAACTAAAA
1 ATTAAAAAATATTAACTAAAA
*
21593834 ATTAAAAAAT-TTAACTTAAA
1 ATTAAAAAATATTAACTAAAA
*
21593854 TTTAA
1 ATTAA
21593859 TTTTTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAATATTAACTAAAA
Found at i:21597193 original size:19 final size:18
Alignment explanation
Indices: 21597169--21597207 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21597159 TATGGTTATT
21597169 ATCCACTATAAAATGTATC
1 ATCCAC-ATAAAATGTATC
* *
21597188 ATCCACCTCAAATGTATC
1 ATCCACATAAAATGTATC
21597206 AT
1 AT
21597208 TTACCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (18 bp):
ATCCACATAAAATGTATC
Found at i:21597202 original size:18 final size:18
Alignment explanation
Indices: 21597179--21597292 Score: 67
Period size: 18 Copynumber: 6.4 Consensus size: 18
21597169 ATCCACTATA
21597179 AAATGTATCATCCACCTC
1 AAATGTATCATCCACCTC
**
21597197 AAATGTATCATTTACCAT-
1 AAATGTATCATCCACC-TC
* * *
21597215 ATATATATATC-CCTCACCAC
1 A-A-ATGTATCATC-CACCTC
* * *
21597235 AAACGTATCATGCACCAC
1 AAATGTATCATCCACCTC
*
21597253 AGATGTATCAT---CCTC
1 AAATGTATCATCCACCTC
*
21597268 AAATATATCATCCACCTC
1 AAATGTATCATCCACCTC
21597286 AAATGTA
1 AAATGTA
21597293 CTAAAAACAA
Statistics
Matches: 70, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
15 12 0.17
18 45 0.64
19 3 0.04
20 10 0.14
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATGTATCATCCACCTC
Found at i:21597453 original size:31 final size:31
Alignment explanation
Indices: 21597415--21597478 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
21597405 TCAATAATTG
21597415 TAGTTGAT-AGAATTTGAAATTATTATATTTT
1 TAGTTGATGA-AATTTGAAATTATTATATTTT
21597446 TAGTTGATGAAATTTGAAATTATTATATTTT
1 TAGTTGATGAAATTTGAAATTATTATATTTT
21597477 TA
1 TA
21597479 AGTTTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (31 bp):
TAGTTGATGAAATTTGAAATTATTATATTTT
Found at i:21601865 original size:22 final size:20
Alignment explanation
Indices: 21601824--21601871 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
21601814 TTTCAAGCTT
21601824 AAATTTATTTAATATATTAA
1 AAATTTATTTAATATATTAA
*
21601844 AAATTATATTTAA-ATAATTTA
1 AAATT-TATTTAATAT-ATTAA
21601865 AAATTTA
1 AAATTTA
21601872 ATGAATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTATTTAATATATTAA
Found at i:21602549 original size:18 final size:17
Alignment explanation
Indices: 21602503--21602562 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
21602493 GATTAAATTT
*
21602503 ATTATATTATTAATTTTA
1 ATTAT-TTATTAATTATA
*
21602521 ATAAAATTTATTTAA-TATAA
1 AT--TATTTA-TTAATTAT-A
21602541 ATTATTTATTAATTATA
1 ATTATTTATTAATTATA
21602558 ATTAT
1 ATTAT
21602563 AATTATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
17 10 0.29
18 10 0.29
19 5 0.15
20 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTATTAATTATA
Found at i:21602950 original size:31 final size:31
Alignment explanation
Indices: 21602915--21602981 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
21602905 ACCAAGATCA
* * *
21602915 ATAAATTTAATAATTTA-AAATATAATATAAT
1 ATAAAATTAAAAATATATAAATA-AATATAAT
*
21602946 ATAAAATTAAAAATATATAAATAAATTTAAT
1 ATAAAATTAAAAATATATAAATAAATATAAT
21602977 -TAAAA
1 ATAAAA
21602982 ATATTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
ATAAAATTAAAAATATATAAATAAATATAAT
Found at i:21602953 original size:24 final size:20
Alignment explanation
Indices: 21602926--21602975 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
21602916 TAAATTTAAT
21602926 AATTTAAAATATAATATAATATA
1 AATTTAAAA-AT-ATATAA-ATA
*
21602949 AAATTAAAAATATATAAATA
1 AATTTAAAAATATATAAATA
21602969 AATTTAA
1 AATTTAA
21602976 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 6 0.24
22 2 0.08
23 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTAAAAATATATAAATA
Found at i:21603044 original size:12 final size:12
Alignment explanation
Indices: 21603001--21603051 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
21602991 ATTATTATAT
*
21603001 TAATATAAATTA
1 TAATATAAAATA
* * *
21603013 TAATACATAATT
1 TAATATAAAATA
*
21603025 TTATATAAAATA
1 TAATATAAAATA
21603037 TAATATAAAATA
1 TAATATAAAATA
21603049 TAA
1 TAA
21603052 CTTATTAATA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:21607410 original size:27 final size:27
Alignment explanation
Indices: 21607380--21607450 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
21607370 AATTTTTTAA
*
21607380 AAATCAAATTTTAAGTTAAATAAAATT
1 AAATCAAATTTTAAGTTAAATAAAATC
* *
21607407 AAATC-AA--TTAA-TAAAAAAAAATC
1 AAATCAAATTTTAAGTTAAATAAAATC
21607430 AAGATCAAATTTTAAG-TAAAT
1 AA-ATCAAATTTTAAGTTAAAT
21607451 TTATATGACT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
23 11 0.32
24 7 0.21
25 2 0.06
26 2 0.06
27 12 0.35
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (27 bp):
AAATCAAATTTTAAGTTAAATAAAATC
Found at i:21608530 original size:2 final size:2
Alignment explanation
Indices: 21608525--21608554 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21608515 TGTGTGTGTG
21608525 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21608555 TAACTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21608546 original size:13 final size:13
Alignment explanation
Indices: 21608528--21608553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21608518 GTGTGTGTAT
21608528 ATATATATATATA
1 ATATATATATATA
21608541 ATATATATATATA
1 ATATATATATATA
21608554 TTAACTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:21608546 original size:15 final size:15
Alignment explanation
Indices: 21608526--21608554 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21608516 GTGTGTGTGT
21608526 ATATATATATATATA
1 ATATATATATATATA
21608541 ATATATATATATAT
1 ATATATATATATAT
21608555 TAACTTCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:21614894 original size:11 final size:11
Alignment explanation
Indices: 21614846--21614896 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
21614836 CTTCAATTTG
*
21614846 ATTTGATTTAA
1 ATTTAATTTAA
21614857 ATTT--TTTAA
1 ATTTAATTTAA
* *
21614866 TTTTTATTTAAA
1 ATTTAATTT-AA
21614878 ATTTAATTTAA
1 ATTTAATTTAA
21614889 ATTTAATT
1 ATTTAATT
21614897 GGAATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.24
11 17 0.50
12 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:21619808 original size:42 final size:42
Alignment explanation
Indices: 21619745--21619827 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
21619735 GAAACTAAAA
* *
21619745 GTCAGTCGTGATCAGACTCTGGATTTGAGATGATTCTTGTTC
1 GTCAGTCATGATCAGACTCTGGATTTGAGATCATTCTTGTTC
*
21619787 GTCAGTCATGATCAGATTCTGGATTTGAGATCATTCTTGTT
1 GTCAGTCATGATCAGACTCTGGATTTGAGATCATTCTTGTT
21619828 TGGCCACTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (42 bp):
GTCAGTCATGATCAGACTCTGGATTTGAGATCATTCTTGTTC
Found at i:21625610 original size:24 final size:24
Alignment explanation
Indices: 21625583--21625655 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
21625573 ATAAATTTAT
* *
21625583 ATTTGATATCTTATTAATATATAA
1 ATTTAATATCTTATTAATAAATAA
* *
21625607 ATTTTATATATTA-TAAGTAAATTAA
1 ATTTAATATCTTATTAA-TAAA-TAA
21625632 A--TAATATCTTATTAATAAATAA
1 ATTTAATATCTTATTAATAAATAA
21625654 AT
1 AT
21625656 ATCTATCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.10
23 15 0.38
24 17 0.43
25 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTTAATATCTTATTAATAAATAA
Found at i:21625643 original size:23 final size:22
Alignment explanation
Indices: 21625588--21625679 Score: 59
Period size: 23 Copynumber: 4.2 Consensus size: 22
21625578 TTTATATTTG
* * *
21625588 ATATCTTATTAATATATAAATTTT
1 ATATATTATTAATAAATAAA--TA
21625612 ATATATTA-TAAGTAAATTAAATA
1 ATATATTATTAA-TAAA-TAAATA
*
21625635 ATATCTTATTAATAAATAAAT-
1 ATATATTATTAATAAATAAATA
* *
21625656 ATCTATCATT-A-AAATAAAT-
1 ATATATTATTAATAAATAAATA
21625675 ATATA
1 ATATA
21625680 AAAATAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
19 12 0.21
20 1 0.02
21 7 0.12
22 5 0.09
23 15 0.26
24 13 0.23
25 4 0.07
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
ATATATTATTAATAAATAAATA
Found at i:21625658 original size:19 final size:20
Alignment explanation
Indices: 21625629--21625676 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
21625619 ATAAGTAAAT
21625629 TAAAT-AATATCT-T-ATTAA
1 TAAATAAATATCTATCATT-A
21625647 TAAATAAATATCTATCATTA
1 TAAATAAATATCTATCATTA
21625667 -AAATAAATAT
1 TAAATAAATAT
21625677 ATAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 17 0.63
20 2 0.07
21 3 0.11
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAATATCTATCATTA
Found at i:21625774 original size:24 final size:23
Alignment explanation
Indices: 21625747--21625801 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
21625737 TTATTCACTG
* *
21625747 ATAATATATTAAATTTATATATTA
1 ATAATATATTAAATATAAAT-TTA
*
21625771 ATAATACATTAAATATAAATTTA
1 ATAATATATTAAATATAAATTTA
21625794 ATTAATAT
1 A-TAATAT
21625802 TAGTTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAATATATTAAATATAAATTTA
Found at i:21627168 original size:6 final size:6
Alignment explanation
Indices: 21627157--21627191 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
21627147 TAAATTATAA
*
21627157 AATTTT AATTTT AATTTT AATTTT AA-ATT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
21627192 TTAAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:21627192 original size:18 final size:18
Alignment explanation
Indices: 21627157--21627191 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21627147 TAAATTATAA
*
21627157 AATTTTAATTTTAATTTT
1 AATTTTAATATTAATTTT
21627175 AATTTTAA-ATTAATTTT
1 AATTTTAATATTAATTTT
21627192 TTAAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTAATATTAATTTT
Found at i:21627495 original size:20 final size:20
Alignment explanation
Indices: 21627458--21627497 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21627448 ATTGAACAAT
*
21627458 AAATTTTTATTTTAATTTTC
1 AAATTTTTAATTTAATTTTC
21627478 AAATTTTTAGATTT-ATTTTC
1 AAATTTTTA-ATTTAATTTTC
21627498 TTAGACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
AAATTTTTAATTTAATTTTC
Found at i:21632881 original size:51 final size:51
Alignment explanation
Indices: 21632826--21633226 Score: 184
Period size: 51 Copynumber: 7.9 Consensus size: 51
21632816 AAGCATAATG
*
21632826 GAGGAGGAA-ATTGAAAGGGAAAGA-G-AGGAAGAGGAAGAAGCCAGGAAGAAA
1 GAGGAGGAAGA-TGAAA--GAAAGAGGAAGGAAGAAGAAGAAGCCAGGAAGAAA
*
21632877 GAGGAGGAAGATGACAGAAAGAGGAAGGAAGAAGAAGAAGCCAGGAAGAAA
1 GAGGAGGAAGATGAAAGAAAGAGGAAGGAAGAAGAAGAAGCCAGGAAGAAA
* ** *
21632928 GAGGAGGAAGAGGCCAGAAAGA-GAGAGGAAG-AG--GAGGCC----AGAAA
1 GAGGAGGAAGATGAAAGAAAGAGGA-AGGAAGAAGAAGAAGCCAGGAAGAAA
* * * * *
21632972 GAGGAAGGAAGA-GGACG-AAGCCAGGAAGAAACAGGAGGAAGAAGCCAGAAAGAGAGA
1 GAGG-AGGAAGATGAAAGAAAG--AGGAAG-GA-A-GAAGAAGAAGCCAGGAAGA-A-A
* * * * * *
21633029 GGAAGAGGAAGAAGCCAAG-AAGAGGGAGGAGGAGGAGGAAGAAGCCCGGAAGAAA
1 -GAGGAGGAAGATG-AAAGAAAGA-GGA--AGGAAGAAGAAGAAGCCAGGAAGAAA
* * ** *
21633084 GAGGAGGGAGAAGCCAGAAAGA-GAGAGGAAG-AGAAAGAAGCCAGGAGGAAA
1 GAGGAGGAAGATGAAAGAAAGAGGA-AGGAAGAAG-AAGAAGCCAGGAAGAAA
** * * **
21633135 GAGGAGGAAGCA-GCCAGAAAGA-GAGAGGAAGAGGAAGAAGCCAAGAAGAGG
1 GAGGAGGAAG-ATGAAAGAAAGAGGA-AGGAAGAAGAAGAAGCCAGGAAGAAA
*
21633186 GAGGAGGAAGA--AAAG-AAGA-GAA-G-AGAAGAAGAAGCAAGGAA
1 GAGGAGGAAGATGAAAGAAAGAGGAAGGAAGAAGAAGAAGCCAGGAA
21633227 AGAGCAAGAG
Statistics
Matches: 284, Mismatches: 36, Indels: 66
0.74 0.09 0.17
Matches are distributed among these distances:
43 3 0.01
44 11 0.04
45 25 0.09
46 4 0.01
47 2 0.01
48 12 0.04
49 9 0.03
50 7 0.02
51 141 0.50
52 5 0.02
53 3 0.01
54 15 0.05
55 4 0.01
56 2 0.01
57 26 0.09
58 7 0.02
59 6 0.02
60 2 0.01
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.01
Consensus pattern (51 bp):
GAGGAGGAAGATGAAAGAAAGAGGAAGGAAGAAGAAGAAGCCAGGAAGAAA
Found at i:21632898 original size:24 final size:24
Alignment explanation
Indices: 21632856--21633197 Score: 236
Period size: 24 Copynumber: 13.4 Consensus size: 24
21632846 AAGAGAGGAA
*
21632856 GAGGAAGAAGCCAGGAAGAAAGAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
* * *
21632880 GAGGAAGATGACAGAAAGAGGAAGGAA
1 GAGGAAGAAGCCAGAAAGA--AA-GAG
* *
21632907 GAAGAAGAAGCCAGGAAGAAAGAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
* *
21632931 GAGGAAGAGGCCAGAAAGAGAGAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
* * * *
21632955 GAAGAGGAGGCCAGAAAGAGGAAGGAA
1 GAGGAAGAAGCCAGAAAGA--AA-GAG
* * *
21632982 GAGGACGAAGCCAGGAAGAAACAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
*
21633006 GAGGAAGAAGCCAGAAAGAGAGAGGAA
1 GAGGAAGAAGCCAGAAAGA-A-A-GAG
*
21633033 GAGGAAGAAGCCAAGAAGAGGGAGGAGGAG
1 GAGGAAGAAGCC-AGAA-A--GA--AAGAG
* *
21633063 GAGGAAGAAGCCCGGAAGAAAGAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
* *
21633087 GAGGGAGAAGCCAGAAAGAGAGAG
1 GAGGAAGAAGCCAGAAAGAAAGAG
* *
21633111 GAAGAGAAAGAAGCCAGGAGGAAAGAG
1 G-AG-G-AAGAAGCCAGAAAGAAAGAG
* *
21633138 GAGGAAGCAGCCAGAAAGAGAGAGGAA
1 GAGGAAGAAGCCAGAAAGA-A-A-GAG
**
21633165 GAGGAAGAAGCCA-AGAAGAGGGAG
1 GAGGAAGAAGCCAGA-AAGAAAGAG
21633189 GAGGAAGAA
1 GAGGAAGAA
21633198 AAGAAGAGAA
Statistics
Matches: 249, Mismatches: 48, Indels: 42
0.73 0.14 0.12
Matches are distributed among these distances:
24 121 0.49
25 9 0.04
26 11 0.04
27 82 0.33
28 5 0.02
29 3 0.01
30 14 0.06
31 2 0.01
32 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.43, T:0.00
Consensus pattern (24 bp):
GAGGAAGAAGCCAGAAAGAAAGAG
Found at i:21632915 original size:20 final size:19
Alignment explanation
Indices: 21632870--21632915 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
21632860 AAGAAGCCAG
*
21632870 GAAGAAAGAGGAGGAAGAT
1 GAAGAAAGAGGAGGAAGAA
21632889 GACAGAAAGAGGAAGGAAGAA
1 GA-AGAAAGAGG-AGGAAGAA
21632910 GAAGAA
1 GAAGAA
21632916 GCCAGGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.39, T:0.02
Consensus pattern (19 bp):
GAAGAAAGAGGAGGAAGAA
Found at i:21632937 original size:21 final size:19
Alignment explanation
Indices: 21632854--21633041 Score: 83
Period size: 21 Copynumber: 9.1 Consensus size: 19
21632844 GAAAGAGAGG
*
21632854 AAGAGGAAGAAGCCAGGAAGA
1 AAGAGGAGGAAG--AGGAAGA
*
21632875 AAGAGGAGGAAGATGACAGA
1 AAGAGGAGGAAGAGGA-AGA
*
21632895 AAGAGGAAGGAAGAAGAAG-
1 AAGAGG-AGGAAGAGGAAGA
* *
21632914 AAGCCAGGAAGAAAGAGG-AGG
1 AAG--AGG-AGGAAGAGGAAGA
* *
21632935 AAGAGGCCAGAAAGAGAGAGGA
1 AAGAGG--AGGAAGAG-GAAGA
* *
21632957 AGAGGAGGCCAGAAAGAGGAAGG
1 A-A-GAGG--AGGAAGAGGAAGA
*
21632980 AAGAGGACGAAGCCAGGAAGA
1 AAGAGGAGGAAG--AGGAAGA
* **
21633001 AACAGGAGGAAGAAGCCAGA
1 AAGAGGAGGAAG-AGGAAGA
21633021 AAGAGAGAGGAAGAGGAAGA
1 AAGAG-GAGGAAGAGGAAGA
21633041 A
1 A
21633042 GCCAAGAAGA
Statistics
Matches: 133, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.10
20 36 0.27
21 62 0.47
22 3 0.02
23 5 0.04
24 14 0.11
ACGTcount: A:0.51, C:0.08, G:0.41, T:0.01
Consensus pattern (19 bp):
AAGAGGAGGAAGAGGAAGA
Found at i:21632944 original size:75 final size:75
Alignment explanation
Indices: 21632856--21633197 Score: 316
Period size: 75 Copynumber: 4.4 Consensus size: 75
21632846 AAGAGAGGAA
* * * *
21632856 GAGGAAGAAGCCAGGAAGAAAGAGGAGGAAGATGACAGAAAGAGGAAGGAAGAAGAAGAAGCCAG
1 GAGGAAGAAGCCAGAAAGAAAGAGGAGGAAGAAGCCAGAAAGAGGAAGGAAGAGGAAGAAGCCAG
21632921 GAAGAAAGAG
66 GAAGAAAGAG
* * * * * *
21632931 GAGGAAGAGGCCAGAAAGAGAGAGGAAGAGGAGGCCAGAAAGAGGAAGGAAGAGGACGAAGCCAG
1 GAGGAAGAAGCCAGAAAGAAAGAGGAGGAAGAAGCCAGAAAGAGGAAGGAAGAGGAAGAAGCCAG
*
21632996 GAAGAAACAG
66 GAAGAAAGAG
* *
21633006 GAGGAAGAAGCCAGAAAGAGAGAGGAAGAGGAAGAAGCCA-AGAAGAGGGAGGAGGAGGAGGAAG
1 GAGGAAGAAGCCAGAAAGA-A-A-GAGGAGGAAGAAGCCAGA-AAGA-GGA--AGGAAGAGGAAG
*
21633070 AAGCCCGGAAGAAAGAG
59 AAGCCAGGAAGAAAGAG
* * * * *
21633087 GAGGGAGAAGCCAGAAAGAGAGAGGAAGAGAAAGAAGCCAG---GAGGAAAGAGGAGGAAGCAGC
1 GAGGAAGAAGCCAGAAAGAAAGAGG-AG-G-AAGAAGCCAGAAAGAGGAAGGAAGAGGAAGAAGC
* *
21633149 CAGAAAGAGAGAGGAA
63 CAGGAAGA-A-A-GAG
**
21633165 GAGGAAGAAGCCA-AGAAGAGGGAGGAGGAAGAA
1 GAGGAAGAAGCCAGA-AAGAAAGAGGAGGAAGAA
21633198 AAGAAGAGAA
Statistics
Matches: 222, Mismatches: 30, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
75 108 0.49
76 2 0.01
77 9 0.04
78 44 0.20
79 6 0.03
80 1 0.00
81 52 0.23
ACGTcount: A:0.49, C:0.08, G:0.43, T:0.00
Consensus pattern (75 bp):
GAGGAAGAAGCCAGAAAGAAAGAGGAGGAAGAAGCCAGAAAGAGGAAGGAAGAGGAAGAAGCCAG
GAAGAAAGAG
Found at i:21633122 original size:81 final size:82
Alignment explanation
Indices: 21632972--21633126 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 82
21632962 AGGCCAGAAA
* *
21632972 GAGGAAGGAAGAGGACGAAGCCAGGAAGAAACAGGAGGAAGAAGCCAGAAAGAGAGAGGAAGAGG
1 GAGGAAGGAAGAGGAAGAAGCCAGGAAGAAACAGGAGGAAGAAGCCAGAAAGAGAGAGGAAGAGA
21633037 AAGAAGCCAAGAAGAGG
66 AAGAAGCCAAGAAGAGG
* * * *
21633054 GAGG-AGGAGGAGGAAGAAGCCCGGAAGAAAGAGGAGGGAGAAGCCAGAAAGAGAGAGGAAGAGA
1 GAGGAAGGAAGAGGAAGAAGCCAGGAAGAAACAGGAGGAAGAAGCCAGAAAGAGAGAGGAAGAGA
21633118 AAGAAGCCA
66 AAGAAGCCA
21633127 GGAGGAAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 63 0.94
82 4 0.06
ACGTcount: A:0.48, C:0.10, G:0.43, T:0.00
Consensus pattern (82 bp):
GAGGAAGGAAGAGGAAGAAGCCAGGAAGAAACAGGAGGAAGAAGCCAGAAAGAGAGAGGAAGAGA
AAGAAGCCAAGAAGAGG
Found at i:21633173 original size:20 final size:20
Alignment explanation
Indices: 21633120--21633173 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
21633110 GGAAGAGAAA
*
21633120 GAAGCCAGGAGGAAAGAGGAG
1 GAAG-CAGGAAGAAAGAGGAG
**
21633141 GAAGCAGCCAGAAAGAGAGAG
1 GAAGCAGGAAGAAAGAG-GAG
21633162 GAAG-AGGAAGAA
1 GAAGCAGGAAGAA
21633174 GCCAAGAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.48, C:0.09, G:0.43, T:0.00
Consensus pattern (20 bp):
GAAGCAGGAAGAAAGAGGAG
Found at i:21633190 original size:21 final size:21
Alignment explanation
Indices: 21633165--21633218 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
21633155 GAGAGAGGAA
**
21633165 GAGGAAGAAGCCAAGAAGAGG
1 GAGGAAGAAGAAAAGAAGAGG
*
21633186 GAGGAGGAAGAAAAGAAGA-G
1 GAGGAAGAAGAAAAGAAGAGG
*
21633206 AAGAGAAGAAGAA
1 GAG-GAAGAAGAA
21633219 GCAAGGAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.56, C:0.04, G:0.41, T:0.00
Consensus pattern (21 bp):
GAGGAAGAAGAAAAGAAGAGG
Found at i:21633335 original size:26 final size:26
Alignment explanation
Indices: 21633284--21633341 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
21633274 CGAGACAGGA
21633284 AGAAGAAGAAAGGAAACGACAAGAAG
1 AGAAGAAGAAAGGAAACGACAAGAAG
*
21633310 AGAAGGAGAAA-GAAA-GACGAAGGAAG
1 AGAAGAAGAAAGGAAACGAC-AA-GAAG
21633336 -GAAGAA
1 AGAAGAA
21633342 CAAGAGCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 11 0.39
26 14 0.50
ACGTcount: A:0.60, C:0.05, G:0.34, T:0.00
Consensus pattern (26 bp):
AGAAGAAGAAAGGAAACGACAAGAAG
Found at i:21637765 original size:20 final size:20
Alignment explanation
Indices: 21637740--21637778 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21637730 CAATTAATTT
*
21637740 GATTTTAGATAATTCGATTC
1 GATTTTAAATAATTCGATTC
21637760 GATTTTAAATAATTCGATT
1 GATTTTAAATAATTCGATT
21637779 TGAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
GATTTTAAATAATTCGATTC
Found at i:21637774 original size:15 final size:16
Alignment explanation
Indices: 21637756--21637789 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21637746 AGATAATTCG
*
21637756 ATTCGATTTTAAA-TA
1 ATTCGATTTGAAATTA
21637771 ATTCGATTTGAAATTA
1 ATTCGATTTGAAATTA
21637787 ATT
1 ATT
21637790 AAACTGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
ATTCGATTTGAAATTA
Found at i:21637787 original size:20 final size:20
Alignment explanation
Indices: 21637748--21637787 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21637738 TTGATTTTAG
**
21637748 ATAATTCGATTCGATTTTAA
1 ATAATTCGATTCGAAATTAA
*
21637768 ATAATTCGATTTGAAATTAA
1 ATAATTCGATTCGAAATTAA
21637788 TTAAACTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (20 bp):
ATAATTCGATTCGAAATTAA
Found at i:21637909 original size:106 final size:106
Alignment explanation
Indices: 21637711--21637911 Score: 305
Period size: 106 Copynumber: 1.9 Consensus size: 106
21637701 TCTGTTAACA
*
21637711 AAAATAAATTAATACAATTCAATTAATTTGATTTTAGATAATTCGATTCGATTTTAAATAATTCG
1 AAAATAAATTAATACAATTCAATTAATTCGATTTTAGATAATTCGATTCGATTTTAAATAATTCG
* * **
21637776 ATTTGAAATTAATTAAACTGATGATATATCTATGATTAATG
66 ATTTGAAATTAATCAAACAGACAATATATCTATGATTAATG
* * *
21637817 AAAATAAATTAATATAATTCAATTAATTCGATTTTAGATAATTTGATTTGATTTTGAAA-AATTC
1 AAAATAAATTAATACAATTCAATTAATTCGATTTTAGATAATTCGATTCGATTTT-AAATAATTC
*
21637881 GATTTGAAATTAATCATACAGACAATATATC
65 GATTTGAAATTAATCAAACAGACAATATATC
21637912 AACCCTTACT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 82 0.96
107 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (106 bp):
AAAATAAATTAATACAATTCAATTAATTCGATTTTAGATAATTCGATTCGATTTTAAATAATTCG
ATTTGAAATTAATCAAACAGACAATATATCTATGATTAATG
Found at i:21639982 original size:6 final size:6
Alignment explanation
Indices: 21639968--21640001 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
21639958 GAGCTGGTGC
* *
21639968 AGCTGG AGTTGG AGTTGG AGCTGG AGCTGG AGCT
1 AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AGCT
21640002 TGCACTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.12, G:0.47, T:0.24
Consensus pattern (6 bp):
AGCTGG
Found at i:21640009 original size:18 final size:18
Alignment explanation
Indices: 21639965--21640009 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
21639955 GCAGAGCTGG
*
21639965 TGCAGCTGGAGTTGGAGT
1 TGCAGCTGGAGCTGGAGT
*
21639983 TGGAGCTGGAGCTGGAGCT
1 TGCAGCTGGAGCTGGAG-T
21640002 TGCA-CTGG
1 TGCAGCTGG
21640010 TGGTGGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.16, C:0.16, G:0.44, T:0.24
Consensus pattern (18 bp):
TGCAGCTGGAGCTGGAGT
Found at i:21641725 original size:26 final size:27
Alignment explanation
Indices: 21641679--21641729 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
21641669 TTAATTTTTT
21641679 TTATATTACTCTTTTTAAAATTTATCA
1 TTATATTACTCTTTTTAAAATTTATCA
* *
21641706 TTATGTTACT-TTTTTTAAATTTAT
1 TTATATTACTCTTTTTAAAATTTAT
21641730 TATGTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATATTACTCTTTTTAAAATTTATCA
Found at i:21642018 original size:18 final size:18
Alignment explanation
Indices: 21641997--21642043 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
21641987 AAAATAAAAG
21641997 TATTTTATATTTAATAAA
1 TATTTTATATTTAATAAA
* *
21642015 TATTTAATATTT--TATA
1 TATTTTATATTTAATAAA
21642031 -ATTTTATATTTAA
1 TATTTTATATTTAA
21642044 ATTAAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 10 0.42
16 3 0.12
18 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATATTTAATAAA
Found at i:21642714 original size:21 final size:22
Alignment explanation
Indices: 21642671--21642716 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
21642661 TTTTTTTATG
*
21642671 TATTTATTTAATAATTAATATT
1 TATTTATTTAATAAATAATATT
21642693 TATTTA-TTAATAAAATAA-ATT
1 TATTTATTTAAT-AAATAATATT
21642714 TAT
1 TAT
21642717 ATTCGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATTTAATAAATAATATT
Found at i:21643103 original size:33 final size:34
Alignment explanation
Indices: 21643065--21643140 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
21643055 TAAATAATGA
* * *
21643065 CTAAATCAAT-TTTTATAATCACTTAATCAATAT
1 CTAAATCAATATTTAATAATCACTAAATCAAAAT
* *
21643098 CTAAATCAATATTTAATATTCTCTAAATCAAAAT
1 CTAAATCAATATTTAATAATCACTAAATCAAAAT
21643132 -TAAATCAAT
1 CTAAATCAAT
21643141 CTAAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (34 bp):
CTAAATCAATATTTAATAATCACTAAATCAAAAT
Found at i:21643176 original size:30 final size:31
Alignment explanation
Indices: 21643135--21643196 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
21643125 TCAAAATTAA
*
21643135 ATCAATCTAAAATATTATTAGAATA-TTATT
1 ATCAATCTAAAATATTATCAGAATATTTATT
*
21643165 ATCAATTTAAAATATTATCAGAATATTTATT
1 ATCAATCTAAAATATTATCAGAATATTTATT
21643196 A
1 A
21643197 CTAGAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
ATCAATCTAAAATATTATCAGAATATTTATT
Found at i:21645171 original size:22 final size:21
Alignment explanation
Indices: 21645146--21645208 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
21645136 AATTAATATC
21645146 AAATCAATCTAAAATATTACT
1 AAATCAATCTAAAATATTACT
*
21645167 GAAAT-ATTAT-TAAAATAATA-T
1 -AAATCA--ATCTAAAATATTACT
*
21645188 -CATCAATCTAAAATATTACT
1 AAATCAATCTAAAATATTACT
21645208 A
1 A
21645209 TAATATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 13
0.67 0.06 0.27
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 2 0.06
21 2 0.06
22 13 0.41
23 2 0.06
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATCAATCTAAAATATTACT
Found at i:21645196 original size:41 final size:42
Alignment explanation
Indices: 21645122--21645218 Score: 135
Period size: 41 Copynumber: 2.3 Consensus size: 42
21645112 CTAATCAATA
* *
21645122 TATAATATTCTCTAAATTAATATCAAATCAATCTAAAATATTAC
1 TATAATATTAT-TAAAATAATATC-AATCAATCTAAAATATTAC
21645166 TGA-AATATTATTAAAATAATATC-ATCAATCTAAAATATTAC
1 T-ATAATATTATTAAAATAATATCAATCAATCTAAAATATTAC
21645207 TATAATATTATT
1 TATAATATTATT
21645219 GACACACATC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
40 1 0.02
41 28 0.57
43 11 0.22
44 8 0.16
45 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.40
Consensus pattern (42 bp):
TATAATATTATTAAAATAATATCAATCAATCTAAAATATTAC
Found at i:21648075 original size:22 final size:23
Alignment explanation
Indices: 21648024--21648074 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
21648014 TAAAAATTTT
21648024 AAAAAATCTTTAAAATAAATACA
1 AAAAAATCTTTAAAATAAATACA
21648047 AAAAAATCTTTAAAATAAATACA
1 AAAAAATCTTTAAAATAAATACA
21648070 AAAAA
1 AAAAA
21648075 TAAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAAATCTTTAAAATAAATACA
Found at i:21648136 original size:15 final size:15
Alignment explanation
Indices: 21648101--21648138 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
21648091 TATACTTACA
*
21648101 TAATTATA-ATATTT
1 TAATTATATATAATT
21648115 TAATTATATATAATT
1 TAATTATATATAATT
*
21648130 TATTTATAT
1 TAATTATAT
21648139 TGAGTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTATATATAATT
Found at i:21659288 original size:16 final size:17
Alignment explanation
Indices: 21659267--21659308 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
21659257 AATATTTAAT
21659267 TTTAAATAATTT-TTTA
1 TTTAAATAATTTATTTA
*
21659283 TTTAAATGATTTATTTA
1 TTTAAATAATTTATTTA
21659300 TTTAAATAA
1 TTTAAATAA
21659309 ATAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAATAATTTATTTA
Found at i:21659803 original size:16 final size:16
Alignment explanation
Indices: 21659774--21659819 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
21659764 TTAACTTGAA
*
21659774 TTAAAATCTAAAATAAT
1 TTAAAATC-GAAATAAT
21659791 TTAAAATCGAAATAAT
1 TTAAAATCGAAATAAT
* *
21659807 TCAAATTCGAAAT
1 TTAAAATCGAAAT
21659820 GCTTGAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (16 bp):
TTAAAATCGAAATAAT
Found at i:21664286 original size:17 final size:17
Alignment explanation
Indices: 21664253--21664285 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21664243 AATATAAAAA
*
21664253 ATAAATTATTTTATTTT
1 ATAAATTATTATATTTT
21664270 ATAAATTATTA-ATTTT
1 ATAAATTATTATATTTT
21664286 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAAATTATTATATTTT
Found at i:21664387 original size:12 final size:13
Alignment explanation
Indices: 21664355--21664379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21664345 TTAATATGAA
21664355 AAATTAAAATTTT
1 AAATTAAAATTTT
21664368 AAATTAAAATTT
1 AAATTAAAATTT
21664380 AATTTAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:21665837 original size:4 final size:4
Alignment explanation
Indices: 21665828--21665866 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
21665818 AAGAATCTAT
** *
21665828 TATG TATG TACA TATG TATG TATG TATG TTTG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
21665867 ATGGATATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:21668835 original size:19 final size:19
Alignment explanation
Indices: 21668811--21668851 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
21668801 CCTAACCAAT
* *
21668811 AAGAAACAAAGAAAATAAA
1 AAGAAAAAAAGAAAAAAAA
21668830 AAGAAAAAAAGAAAAAAAA
1 AAGAAAAAAAGAAAAAAAA
21668849 AAG
1 AAG
21668852 GTGAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAAA
Found at i:21668872 original size:12 final size:12
Alignment explanation
Indices: 21668831--21668882 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
21668821 GAAAATAAAA
21668831 AGAAAAAAAGA-
1 AGAAAAAAAGAG
*
21668842 AAAAAAAAAG-G
1 AGAAAAAAAGAG
* *
21668853 TGAGAAAAAGAG
1 AGAAAAAAAGAG
*
21668865 AGAAAAAAATAG
1 AGAAAAAAAGAG
21668877 AGAAAA
1 AGAAAA
21668883 TTGAAATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (12 bp):
AGAAAAAAAGAG
Found at i:21668879 original size:22 final size:21
Alignment explanation
Indices: 21668819--21668882 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
21668809 ATAAGAAACA
* *
21668819 AAGAAAATAAAAAGAAAAAAAG
1 AAGAAAA-AAATAGAGAAAAAG
*
21668841 AAAAAAAAAAGGT-GAGAAAAAG
1 AAGAAAAAAA--TAGAGAAAAAG
21668863 AGAGAAAAAAATAGAGAAAA
1 A-AGAAAAAAATAGAGAAAA
21668883 TTGAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.12
22 22 0.65
23 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (21 bp):
AAGAAAAAAATAGAGAAAAAG
Found at i:21677969 original size:2 final size:2
Alignment explanation
Indices: 21677962--21677989 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21677952 ACCTTTTCCT
21677962 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21677990 AGGCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:21678841 original size:27 final size:27
Alignment explanation
Indices: 21678811--21678891 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
21678801 ACCCAAAAGC
* *
21678811 TCACCATCACCGCCACCACCGCCACCT
1 TCACCATCACCACCACCACCGCCACCA
* * * **
21678838 TCACCGTCCCCACCACCTCCGCCAAAA
1 TCACCATCACCACCACCACCGCCACCA
* *
21678865 TCATCATCATCACCACCACCGCCACCA
1 TCACCATCACCACCACCACCGCCACCA
21678892 GCTGATAATA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.56, G:0.06, T:0.12
Consensus pattern (27 bp):
TCACCATCACCACCACCACCGCCACCA
Found at i:21684930 original size:212 final size:213
Alignment explanation
Indices: 21684559--21684980 Score: 729
Period size: 212 Copynumber: 2.0 Consensus size: 213
21684549 GGTGATCTTC
*
21684559 TACTCTTTAGGTATTGTTCTACCATTAAGAATCATCCTATAAAGGTATCTGTGGTAAGGGGCTGA
1 TACTCTTTAGGTATTGTTCTACCATTAAGAATCATCCTATAAAGGTATCCGTGGTAAGGGGCTGA
* * *
21684624 TTACTTTTTTTCTCAATCCCCAATATTTTTACAATTCCAAAGATGTTGCTTCATCCTGCACAGCA
66 TTACTCTGTTTCCCAATCCCCAATATTTTTACAATTCCAAAGATGTTGCTTCATCCTGCACAGCA
* *
21684689 AAGCTGAAAAACTATGTTGAGCAGATAAGTTGTGCGTTGAGCCTTTTTGGCCTTTA-TTTCGAGC
131 AAGCTGAAAAACTATATTGAGCAGATAAGTTGTGCGTCGAGCCTTTTTGGCCTTTATTTTCGAGC
* * *
21684753 GACGTAAGGTGGCTGACA
196 AACATAAGCTGGCTGACA
*
21684771 TACTCTTTAGGTATTGTTCTACCATTAAGAATTATCCTATAAAGGTATCCGTGGTAAGGGGCTGA
1 TACTCTTTAGGTATTGTTCTACCATTAAGAATCATCCTATAAAGGTATCCGTGGTAAGGGGCTGA
21684836 TTACTCTGTTTCCCAATCCCCAATATTTTTACAATTCCAAAGATGTTGCTTCATCCTGCACAGCA
66 TTACTCTGTTTCCCAATCCCCAATATTTTTACAATTCCAAAGATGTTGCTTCATCCTGCACAGCA
**
21684901 AAGCTGAAAAACTATATTGAGTGGATAAGTTGTGCGTCGAGCCTTTTTGGCCTTTATTTTCGAGC
131 AAGCTGAAAAACTATATTGAGCAGATAAGTTGTGCGTCGAGCCTTTTTGGCCTTTATTTTCGAGC
21684966 AACATAAGCTGGCTG
196 AACATAAGCTGGCTG
21684981 GCATCTGTTC
Statistics
Matches: 197, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
212 177 0.90
213 20 0.10
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (213 bp):
TACTCTTTAGGTATTGTTCTACCATTAAGAATCATCCTATAAAGGTATCCGTGGTAAGGGGCTGA
TTACTCTGTTTCCCAATCCCCAATATTTTTACAATTCCAAAGATGTTGCTTCATCCTGCACAGCA
AAGCTGAAAAACTATATTGAGCAGATAAGTTGTGCGTCGAGCCTTTTTGGCCTTTATTTTCGAGC
AACATAAGCTGGCTGACA
Done.