Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 6 of 22
Found at i:2923883 original size:18 final size:19
Alignment explanation
Indices: 2923852--2923887 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2923842 TTTGATTTTA
*
2923852 GAAAAATGACAAAAAAAAG
1 GAAAAATGAAAAAAAAAAG
2923871 GAAAAA-GAAAAAAAAAA
1 GAAAAATGAAAAAAAAAA
2923888 CCACGAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (19 bp):
GAAAAATGAAAAAAAAAAG
Found at i:2944037 original size:13 final size:13
Alignment explanation
Indices: 2943998--2944038 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2943988 GGTTCGTAAC
2943998 TATCTCTAATT-TT
1 TATCT-TAATTATT
2944011 TAT-TTAATTCATT
1 TATCTTAATT-ATT
2944024 TATCTTAATTATT
1 TATCTTAATTATT
2944037 TA
1 TA
2944039 GTATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.20
12 1 0.04
13 13 0.52
14 6 0.24
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (13 bp):
TATCTTAATTATT
Found at i:2991255 original size:16 final size:16
Alignment explanation
Indices: 2991231--2991261 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2991221 AAATTGTGAG
2991231 TATAATATTTAAAATA
1 TATAATATTTAAAATA
*
2991247 TATATTATTTAAAAT
1 TATAATATTTAAAAT
2991262 TATTTAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAATATTTAAAATA
Found at i:2991541 original size:13 final size:12
Alignment explanation
Indices: 2991514--2991548 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2991504 TTAATGATAA
2991514 TTATTTAATTAT
1 TTATTTAATTAT
*
2991526 TTATTATAATTGT
1 TTATT-TAATTAT
2991539 TTATTTAATT
1 TTATTTAATT
2991549 CAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TTATTTAATTAT
Found at i:3002216 original size:16 final size:17
Alignment explanation
Indices: 3002195--3002229 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3002185 TTTATATTTT
*
3002195 ATTTTTA-ATTAAATAA
1 ATTTTTATAATAAATAA
3002211 ATTTTTATAATAAATAA
1 ATTTTTATAATAAATAA
3002228 AT
1 AT
3002230 AATTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTTATAATAAATAA
Found at i:3002473 original size:21 final size:21
Alignment explanation
Indices: 3002449--3002491 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3002439 AAATTATTTG
3002449 ATTTATAATAAAAAT-ATAAAA
1 ATTTA-AATAAAAATAATAAAA
* *
3002470 ATTTAATTAAATATAATAAAA
1 ATTTAAATAAAAATAATAAAA
3002491 A
1 A
3002492 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAAATAAAAATAATAAAA
Found at i:3013827 original size:33 final size:33
Alignment explanation
Indices: 3013756--3013819 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
3013746 AGGTCTGCTG
*
3013756 CTTCTTCTCCATTTGCAGCAGACGTTTCTCCCC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCCC
3013789 CTTCTTCTCCATTTGCAGCAGACGTTGCTCC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCC
3013820 TCTTTCTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.12, C:0.38, G:0.14, T:0.36
Consensus pattern (33 bp):
CTTCTTCTCCATTTGCAGCAGACGTTGCTCCCC
Found at i:3014556 original size:15 final size:15
Alignment explanation
Indices: 3014536--3014577 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
3014526 TTATCTTCTC
*
3014536 TGCAATCACATTGCT
1 TGCAATCACATTGCA
3014551 TGCAATCACATTGCA
1 TGCAATCACATTGCA
*
3014566 AGCAATCACATT
1 TGCAATCACATT
3014578 ACACTGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (15 bp):
TGCAATCACATTGCA
Found at i:3016041 original size:18 final size:17
Alignment explanation
Indices: 3016003--3016043 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
3015993 GAATTCGTGG
*
3016003 GGAGTAAGTTTTGGAAGA
1 GGAG-AAGTTTTGGAAAA
3016021 GGAGAAGTTTTGGACAAA
1 GGAGAAGTTTTGGA-AAA
3016039 GGAGA
1 GGAGA
3016044 GATAAGCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.37, C:0.02, G:0.39, T:0.22
Consensus pattern (17 bp):
GGAGAAGTTTTGGAAAA
Found at i:3016877 original size:48 final size:48
Alignment explanation
Indices: 3016806--3016904 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
3016796 CTCTCATAAT
3016806 TTTGATATTGGATCATGTAGTGGGATTTGGAGCTGGATGAGCTTGTTA
1 TTTGATATTGGATCATGTAGTGGGATTTGGAGCTGGATGAGCTTGTTA
3016854 TTTGATATTGGATCATGTAGTGGGATTTGGAGCTGGATGAGCTTGTTA
1 TTTGATATTGGATCATGTAGTGGGATTTGGAGCTGGATGAGCTTGTTA
3016902 TTT
1 TTT
3016905 ATTGTGTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.20, C:0.06, G:0.32, T:0.41
Consensus pattern (48 bp):
TTTGATATTGGATCATGTAGTGGGATTTGGAGCTGGATGAGCTTGTTA
Found at i:3018202 original size:15 final size:15
Alignment explanation
Indices: 3018182--3018210 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3018172 TCTGTTGCCT
3018182 TTAACATATTTCACA
1 TTAACATATTTCACA
3018197 TTAACATATTTCAC
1 TTAACATATTTCAC
3018211 TTCACTTATA
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:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAACATATTTCACA
Found at i:3021010 original size:19 final size:18
Alignment explanation
Indices: 3020982--3021020 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
3020972 TCGATATTTA
*
3020982 AATATTTAATTTATTAATT
1 AATATATAATTTATT-ATT
3021001 AATATATAATTTATTATT
1 AATATATAATTTATTATT
3021019 AA
1 AA
3021021 CAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATATAATTTATTATT
Found at i:3022787 original size:2 final size:2
Alignment explanation
Indices: 3022766--3022814 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
3022756 ACCCGTCCTA
*
3022766 TC TC T- TC TC TC -C TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3022806 TC TC TC TC T
1 TC TC TC TC T
3022815 TTTCTTCTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:3030299 original size:2 final size:2
Alignment explanation
Indices: 3030292--3030319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3030282 CATCTTTCCA
3030292 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3030320 ACAAACATTT
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3036202 original size:20 final size:19
Alignment explanation
Indices: 3036177--3036259 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
3036167 AAAATTTTAT
*
3036177 AATATTATAATTAAAATAAA
1 AATATTA-AAATAAAATAAA
*
3036197 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATA-AA
3036217 AATA-TAAGAATAAAA-AATA
1 AATATTAA-AATAAAATAA-A
*
3036236 AATA-TAAAA-AATATAAA
1 AATATTAAAATAAAATAAA
3036253 AA-ATTAA
1 AATATTAA
3036260 CATTTAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.02
17 9 0.17
18 5 0.09
19 20 0.37
20 19 0.35
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:3036243 original size:33 final size:32
Alignment explanation
Indices: 3036177--3036251 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
3036167 AAAATTTTAT
3036177 AATATTATAATTAAAATAAAAATATTAAAATAA
1 AATA-TATAATTAAAATAAAAATATTAAAATAA
3036210 AATATATAATATAAGAATAAAAA-A-TAAATATAA
1 AATATATAAT-TAA-AATAAAAATATTAAA-ATAA
*
3036243 AAAATATAA
1 AATATATAA
3036252 AAAATTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
32 10 0.26
33 20 0.53
34 8 0.21
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (32 bp):
AATATATAATTAAAATAAAAATATTAAAATAA
Found at i:3036295 original size:14 final size:15
Alignment explanation
Indices: 3036190--3036443 Score: 68
Period size: 14 Copynumber: 17.9 Consensus size: 15
3036180 ATTATAATTA
*
3036190 AAATA-AAAAT-ATT
1 AAATATAAAATAAAT
*
3036203 AAA-ATAAAATATAT
1 AAATATAAAATAAAT
3036217 -AATATAAGAATAAA-
1 AAATATAA-AATAAAT
*
3036231 AAATA-AATATAAA-
1 AAATATAAAATAAAT
*
3036244 AAATATAAAA-AATT
1 AAATATAAAATAAAT
* *
3036258 AACATTTAATAT-AAT
1 AA-ATATAAAATAAAT
* **
3036273 ATAGGTAAAATAAAT
1 AAATATAAAATAAAT
*
3036288 AAAT-TAAAATATAT
1 AAATATAAAATAAAT
3036302 AAATAT-AAA-AAAT
1 AAATATAAAATAAAT
* *
3036315 --ATATTAAAGAAAT
1 AAATATAAAATAAAT
*
3036328 GAAA-ATAAAA-ATAT
1 -AAATATAAAATAAAT
*
3036342 ATATTATAATAAT-AAT
1 A-AATATAA-AATAAAT
*
3036358 AAA-ATAAAATATAT
1 AAATATAAAATAAAT
*
3036372 GACAT-T--AA-AAAT
1 -AAATATAAAATAAAT
* * **
3036384 ATATTTAAAATTGAT
1 AAATATAAAATAAAT
* *
3036399 ATTATATAAAATTAAT
1 A-AATATAAAATAAAT
3036415 -AATATAAATATAAAT
1 AAATATAAA-ATAAAT
*
3036430 ATATATAAAATAAA
1 AAATATAAAATAAA
3036444 ATATAAAGTA
Statistics
Matches: 178, Mismatches: 33, Indels: 58
0.66 0.12 0.22
Matches are distributed among these distances:
11 7 0.04
12 8 0.04
13 35 0.20
14 53 0.30
15 50 0.28
16 25 0.14
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATATAAAATAAAT
Found at i:3036432 original size:12 final size:12
Alignment explanation
Indices: 3036415--3036480 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
3036405 TAAAATTAAT
3036415 AATATAAATATA
1 AATATAAATATA
*
3036427 AATATATATA-A
1 AATATAAATATA
3036438 AATA-AAATATA
1 AATATAAATATA
3036449 AAGTATTATAATAATA
1 AA-TA-TA-AAT-ATA
3036465 AATA-AAATA-A
1 AATATAAATATA
3036475 AATATA
1 AATATA
3036481 TGACATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
10 9 0.20
11 10 0.22
12 14 0.31
13 1 0.02
14 1 0.02
15 5 0.11
16 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATAAATATA
Found at i:3036470 original size:32 final size:28
Alignment explanation
Indices: 3036404--3036817 Score: 94
Period size: 32 Copynumber: 14.3 Consensus size: 28
3036394 TTGATATTAT
*
3036404 ATAAAATTAATAATATAAATATAAATATAT
1 ATAAAA-TAA-AATATAAATATAAATATAA
3036434 ATAAAATAAAATATAAAGTATTATAATAATAA
1 ATAAAATAAAATATAAA-TA-TA-AAT-ATAA
* *
3036466 ATAAAATAAAATATATGACATTAAAAATATAT
1 ATAAAATAAAATATA--A-A-TATAAATATAA
* *** * *
3036498 TTAAGAAT-GTTTAT-TATATAAA-ATTA
1 ATAA-AATAAAATATAAATATAAATATAA
* *
3036524 AT--AATAAAATATAAATAT-ATTAAAA
1 ATAAAATAAAATATAAATATAAATATAA
*
3036549 ATAAAATATAAAGTATTATAATAATAAATAAAA
1 ATAAAATA-AAA-TA-TA-AAT-ATAAATATAA
* * *
3036582 ATAAAATATATGATATTAAAAATAAAT-TTA
1 ATAAAATA-A-AATA-TAAATATAAATATAA
* * * *
3036612 A-GAAATAATAT-TAGATA-AAA-ATTA
1 ATAAAATAAAATATAAATATAAATATAA
* *
3036636 ATAATA-AAAATATAAATATATTAA-AGAA
1 ATAAAATAAAATATAAATATA--AATATAA
*
3036664 ATGAAAATAAAA-ATATATATTATAATAATAA
1 AT-AAAATAAAATATAAATA-TA-AAT-ATAA
* *
3036695 ATAAAATAAAATATATGACATTAAAAATATAT
1 ATAAAATAAAATATA--A-A-TATAAATATAA
* ** * * *
3036727 TTAAAATATGATAT-TATATAAAAATTA
1 ATAAAATAAAATATAAATATAAATATAA
* *
3036754 ATAATAT-AAATAT-AATA-ATATA-AA
1 ATAAAATAAAATATAAATATAAATATAA
3036778 ATAAAATATAAAGTATTATAATAATAAATA-AA
1 ATAAAATA-AAA-TA-TA-AAT-ATAAATATAA
3036810 ATAAAATA
1 ATAAAATA
3036818 TATGACATTA
Statistics
Matches: 281, Mismatches: 59, Indels: 86
0.66 0.14 0.20
Matches are distributed among these distances:
23 3 0.01
24 22 0.08
25 22 0.08
26 14 0.05
27 25 0.09
28 21 0.07
29 24 0.09
30 30 0.11
31 21 0.07
32 59 0.21
33 30 0.11
34 5 0.02
35 5 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (28 bp):
ATAAAATAAAATATAAATATAAATATAA
Found at i:3036602 original size:111 final size:111
Alignment explanation
Indices: 3036329--3036998 Score: 956
Period size: 110 Copynumber: 6.0 Consensus size: 111
3036319 TAAAGAAATG
*
3036329 AAAATAAAA-ATATA-TATTATAATAAT-AATAAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
3036391 A-AATTGATATTATAT-AAAATTAATAATATAAATATAAATATA-TA
66 AGAATTGATATTATATAAAAATTAATAATA-AAATATAAATATATTA
3036435 TAAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTT
1 -AAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTT
*
3036500 AAGAA-TGTTTATTATAT-AAAATTAATAATAAAATATAAATATATTA
65 AAGAATTG-ATATTATATAAAAATTAATAATAAAATATAAATATATTA
* *
3036546 AAAATAAAATATAAAGTATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATAAATTT
1 AAAATAAAATATAAAGTATTATAATAATAAAT-AAAATAAAATATATGACATTAAAAATATATTT
* * *
3036611 AAGAAATAATATTAGATAAAAATTAATAATAAAAATATAAATATATTAA
65 AAGAATTGATATTATATAAAAATTAATAAT-AAAATATAAATATATT-A
* *
3036660 AGAAATGAAAATAAAAATATATATTATAATAATAAATAAAATAAAATATATGACATTAAAAATAT
1 A-AAAT-AAAAT-ATAA-A-GTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATAT
3036725 ATTTAA-AATATGATATTATATAAAAATTAATAATATAAATAT-AATA-A-TA
61 ATTTAAGAAT-TGATATTATATAAAAATTAATAATA-AAATATAAATATATTA
3036774 TAAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTT
1 -AAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTT
3036839 AAGAA-TGATATTATATATAAAATTAATAATAAAATATAAATATATTA
65 AAGAATTGATATTATATA-AAAATTAATAATAAAATATAAATATATTA
* *
3036886 AAAATAAAATATAAAGTATTATAATAATAAATAAAAATAAAATATATGATATT-AAAATAAATTT
1 AAAATAAAATATAAAGTATTATAATAATAAAT-AAAATAAAATATATGACATTAAAAATATATTT
* * *
3036950 AAGAAATAATATTAGATAAAAATTATATAA-AAAATATAAATATATTA
65 AAGAATTGATATTATATAAAAATTA-ATAATAAAATATAAATATATTA
3036997 AA
1 AA
3036999 TTTATATTTT
Statistics
Matches: 516, Mismatches: 20, Indels: 50
0.88 0.03 0.09
Matches are distributed among these distances:
107 9 0.02
108 4 0.01
109 30 0.06
110 151 0.29
111 144 0.28
112 51 0.10
113 21 0.04
114 7 0.01
115 6 0.01
116 6 0.01
117 10 0.02
118 61 0.12
119 16 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (111 bp):
AAAATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTA
AGAATTGATATTATATAAAAATTAATAATAAAATATAAATATATTA
Found at i:3036673 original size:31 final size:30
Alignment explanation
Indices: 3036546--3036710 Score: 87
Period size: 31 Copynumber: 5.4 Consensus size: 30
3036536 AAATATATTA
*
3036546 AAAAT-AAAATATAAAGTATTATAATAATAAAT
1 AAAATAAAAATAT-AA--ATTATAATAAGAAAT
* *
3036578 AAAA-ATAAAATAT--ATGATATTAA-AAAT
1 AAAATA-AAAATATAAATTATAATAAGAAAT
* * *
3036605 AAATTTAAGAAATA-ATATTA-GATAA-AAATT
1 AAA-ATAA-AAATATAAATTATAATAAGAAA-T
*
3036635 AATAATAAAAATATAAA-TATATTAAAGAAAT
1 AA-AATAAAAATATAAATTATAAT-AAGAAAT
* *
3036666 GAAAATAAAAATATATATTATAATAATAAAT
1 -AAAATAAAAATATAAATTATAATAAGAAAT
3036697 AAAATAAAATATAT
1 AAAATAAAA-ATAT
3036711 GACATTAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
27 7 0.07
28 9 0.09
29 19 0.18
30 21 0.20
31 27 0.26
32 14 0.13
33 7 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (30 bp):
AAAATAAAAATATAAATTATAATAAGAAAT
Found at i:3036800 original size:20 final size:20
Alignment explanation
Indices: 3036754--3036932 Score: 58
Period size: 18 Copynumber: 9.1 Consensus size: 20
3036744 ATAAAAATTA
3036754 ATAATATAAATATAATAATAT
1 ATAATA-AAATATAATAATAT
* *
3036775 AAAATAAAATATAA-AGTATT
1 ATAATAAAATATAATAATA-T
* *
3036795 ATAATAATAAATAAAATAAAAT
1 ATAAT-A-AAATATAATAATAT
* * *
3036817 AT-ATGACAT-TAAAAATAT
1 ATAATAAAATATAATAATAT
* * * *
3036835 AT-TTAAGA-ATGATATTAT
1 ATAATAAAATATAATAATAT
3036853 AT-ATAAAAT-TAATAATA-
1 ATAATAAAATATAATAATAT
* *
3036870 A-AATATAAATATATTAAAAAT
1 ATAATA-AAATATAAT-AATAT
* *
3036891 AAAATATAAAGTATTATAATA-
1 ATAATA-AAA-TATAATAATAT
3036912 ATAAATAAAA-ATAA-AATAT
1 AT-AATAAAATATAATAATAT
3036931 AT
1 AT
3036933 GATATTAAAA
Statistics
Matches: 115, Mismatches: 28, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
17 4 0.03
18 37 0.32
19 14 0.12
20 16 0.14
21 13 0.11
22 25 0.22
23 6 0.05
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (20 bp):
ATAATAAAATATAATAATAT
Found at i:3036807 original size:339 final size:337
Alignment explanation
Indices: 3036311--3036998 Score: 1278
Period size: 339 Copynumber: 2.0 Consensus size: 337
3036301 TAAATATAAA
3036311 AAATATATTAAAGAAATGAAAATAAAAATATATATTATAATAATAATAAAATAAAATATATGACA
1 AAATATATTAAAGAAATGAAAATAAAAATATATATTATAATAATAATAAAATAAAATATATGACA
3036376 TTAAAAATATATTTAAAATTGATATTATATAAAATTAATAATATAAATATAAATATATATAAAAT
66 TTAAAAATATATTTAAAATTGATATTATATAAAATTAATAATATAAATATAAATATATATAAAAT
3036441 AAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAT
131 AAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAT
3036506 G-T-TTATTATATAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAGTATTATA
196 GATATTA-TATATAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAGTATTATA
3036569 ATAATAAATAAAAATAAAATATATGATATTAAAAATAAATTTAAGAAATAATATTAGATAAAAAT
260 ATAATAAATAAAAATAAAATATATGATATT-AAAATAAATTTAAGAAATAATATTAGATAAAAAT
3036634 TA-ATAATAAAAATAT
324 TATAT-A-AAAAATAT
3036649 AAATATATTAAAGAAATGAAAATAAAAATATATATTATAATAATAAATAAAATAAAATATATGAC
1 AAATATATTAAAGAAATGAAAATAAAAATATATATTATAATAAT-AATAAAATAAAATATATGAC
3036714 ATTAAAAATATATTTAAAATATGATATTATATAAAAATTAATAATATAAATAT-AATA-ATATAA
65 ATTAAAAATATATTTAAAAT-TGATATTATAT-AAAATTAATAATATAAATATAAATATATATAA
3036777 AATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAG
128 AATAAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAG
3036842 AATGATATTATATATAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAGTATTA
193 AATGATATTATATATAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAGTATTA
3036907 TAATAATAAATAAAAATAAAATATATGATATTAAAATAAATTTAAGAAATAATATTAGATAAAAA
258 TAATAATAAATAAAAATAAAATATATGATATTAAAATAAATTTAAGAAATAATATTAGATAAAAA
3036972 TTATATAAAAAATAT
323 TTATATAAAAAATAT
3036987 AAATATATTAAA
1 AAATATATTAAA
3036999 TTTATATTTT
Statistics
Matches: 344, Mismatches: 0, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
338 64 0.19
339 152 0.44
340 105 0.31
341 23 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (337 bp):
AAATATATTAAAGAAATGAAAATAAAAATATATATTATAATAATAATAAAATAAAATATATGACA
TTAAAAATATATTTAAAATTGATATTATATAAAATTAATAATATAAATATAAATATATATAAAAT
AAAATATAAAGTATTATAATAATAAATAAAATAAAATATATGACATTAAAAATATATTTAAGAAT
GATATTATATATAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAGTATTATAA
TAATAAATAAAAATAAAATATATGATATTAAAATAAATTTAAGAAATAATATTAGATAAAAATTA
TATAAAAAATAT
Found at i:3037188 original size:15 final size:15
Alignment explanation
Indices: 3037148--3037180 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3037138 TTTTCCCTGT
*
3037148 AATCACATTGCTTGC
1 AATCACATTACTTGC
3037163 AATCACATTACTTGC
1 AATCACATTACTTGC
3037178 AAT
1 AAT
3037181 TATATTACCT
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:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:3041324 original size:12 final size:11
Alignment explanation
Indices: 3041293--3041343 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
3041283 TTATGTATAT
3041293 TATTTATATTA
1 TATTTATATTA
*
3041304 AATTT-TATTA
1 TATTTATATTA
3041314 TATTTGATATTA
1 TATTT-ATATTA
3041326 TTATTT-TATTA
1 -TATTTATATTA
*
3041337 TAATTAT
1 TATTTAT
3041344 TTTTTATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 13 0.39
11 10 0.30
12 5 0.15
13 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTTATATTA
Found at i:3041350 original size:13 final size:14
Alignment explanation
Indices: 3041325--3041358 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3041315 ATTTGATATT
3041325 ATTATTTTATTATA
1 ATTATTTTATTATA
3041339 ATTATTTT-TTATA
1 ATTATTTTATTATA
*
3041352 ACTATTT
1 ATTATTT
3041359 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATTTTATTATA
Found at i:3041998 original size:16 final size:15
Alignment explanation
Indices: 3041967--3041996 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3041957 AAAACACTTA
*
3041967 ATTTTAAAAATATTT
1 ATTTTAAAAAAATTT
3041982 ATTTTAAAAAAATTT
1 ATTTTAAAAAAATTT
3041997 TAAAATCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAAAAATTT
Found at i:3049745 original size:22 final size:22
Alignment explanation
Indices: 3049719--3049764 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3049709 TATTAAATTA
*
3049719 TATAAAAT-TTAATATATAACAT
1 TATAAAATATAAAT-TATAACAT
*
3049741 TATAATATATAAATTATAACAT
1 TATAAAATATAAATTATAACAT
3049763 TA
1 TA
3049765 ATTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
TATAAAATATAAATTATAACAT
Found at i:3049771 original size:22 final size:23
Alignment explanation
Indices: 3049733--3049795 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
3049723 AAATTTAATA
*
3049733 TATAACATT-ATAATATATAAAT
1 TATAACATTAATATTATATAAAT
*
3049755 TATAACATTAAT-TTATATATAT
1 TATAACATTAATATTATATAAAT
* *
3049777 AATAA-AATAATATTATATA
1 TATAACATTAATATTATATA
3049796 TATTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.14
22 28 0.80
23 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAACATTAATATTATATAAAT
Found at i:3055466 original size:22 final size:21
Alignment explanation
Indices: 3055431--3055475 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3055421 ATTTATATTT
3055431 AAACTTAAAAAATAAAACATA
1 AAACTTAAAAAATAAAACATA
* *
3055452 AAACTATAAAGAATAAAATATA
1 AAACT-TAAAAAATAAAACATA
3055474 AA
1 AA
3055476 TAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACTTAAAAAATAAAACATA
Found at i:3055483 original size:22 final size:21
Alignment explanation
Indices: 3055435--3055483 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3055425 ATATTTAAAC
*
3055435 TTAAAAAATAAAACATAAAAC
1 TTAAAAAATAAAACATAAAAA
* *
3055456 TATAAAGAATAAAATATAAATAA
1 T-TAAAAAATAAAACATAAA-AA
3055479 TTAAA
1 TTAAA
3055484 TACGAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
TTAAAAAATAAAACATAAAAA
Found at i:3070886 original size:18 final size:17
Alignment explanation
Indices: 3070852--3070885 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3070842 GTCACCCTAT
*
3070852 TTTTTTAATAATATATA
1 TTTTTAAATAATATATA
3070869 TTTTTAAATAA-ATATA
1 TTTTTAAATAATATATA
3070885 T
1 T
3070886 AATTTGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAAATAATATATA
Found at i:3073376 original size:30 final size:31
Alignment explanation
Indices: 3073342--3073417 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
3073332 AAAAAAATTT
* *
3073342 AAATAAATTTTTATA-TTTTTATTTTTAATC
1 AAATAAACTTTTATATTTTTTATTTTGAATC
* *
3073372 AAATAAACTTTTATATTTTTTATTTTGAGTT
1 AAATAAACTTTTATATTTTTTATTTTGAATC
3073403 AAATAAACTTTTATA
1 AAATAAACTTTTATA
3073418 ATTAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 14 0.34
31 27 0.66
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (31 bp):
AAATAAACTTTTATATTTTTTATTTTGAATC
Found at i:3081347 original size:2 final size:2
Alignment explanation
Indices: 3081340--3081365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3081330 GCCATATCAA
3081340 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
3081366 CTTTGCACTT
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:3087073 original size:2 final size:2
Alignment explanation
Indices: 3087066--3087093 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3087056 TCTTATTTTA
3087066 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
3087094 TTAACCAGTT
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:3106933 original size:16 final size:16
Alignment explanation
Indices: 3106903--3106947 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3106893 TTATATTTTT
3106903 ATTTTA-AATTAAATAA
1 ATTTTATAATT-AATAA
3106919 ATTTTATAATTAAT-A
1 ATTTTATAATTAATAA
*
3106934 ATTAT-TAATTAATA
1 ATTTTATAATTAATA
3106948 TATCATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 9 0.35
17 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTATAATTAATAA
Found at i:3114651 original size:49 final size:49
Alignment explanation
Indices: 3114544--3114683 Score: 235
Period size: 49 Copynumber: 2.8 Consensus size: 49
3114534 GAGATCTTAA
3114544 ACTTGTAAGGACATCAAGGATTTGAATGGGCATTAAGGATTTGAATGGGTTAG
1 ACTTGTAAGGACATCAAGGATTTGAATGGG---T-AGGATTTGAATGGGTTAG
*
3114597 ACTTGTAAGGACATCAAGAATTTGAATGGGTAGGATTTGAATGGGTTAG
1 ACTTGTAAGGACATCAAGGATTTGAATGGGTAGGATTTGAATGGGTTAG
3114646 ACTTGTAAGGACATCAAGGATTTGAATGGGTAGGATTT
1 ACTTGTAAGGACATCAAGGATTTGAATGGGTAGGATTT
3114684 AAGTGGATGG
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
49 55 0.65
50 1 0.01
53 29 0.34
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (49 bp):
ACTTGTAAGGACATCAAGGATTTGAATGGGTAGGATTTGAATGGGTTAG
Found at i:3114781 original size:15 final size:15
Alignment explanation
Indices: 3114761--3114815 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3114751 AAGGACATCA
*
3114761 AGGATTTAAGTGGGT
1 AGGATTTGAGTGGGT
*
3114776 AGGATTTGAGTGGAT
1 AGGATTTGAGTGGGT
*
3114791 GGGA-TT--GTGGGT
1 AGGATTTGAGTGGGT
3114803 AGGATTTGAGTGG
1 AGGATTTGAGTGG
3114816 ATGGGATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 8 0.25
13 2 0.06
14 2 0.06
15 20 0.62
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGGT
Found at i:3114801 original size:27 final size:27
Alignment explanation
Indices: 3114770--3114826 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3114760 AAGGATTTAA
3114770 GTGGGTAGGATTTGAGTGGATGGGATT
1 GTGGGTAGGATTTGAGTGGATGGGATT
3114797 GTGGGTAGGATTTGAGTGGATGGGATT
1 GTGGGTAGGATTTGAGTGGATGGGATT
3114824 GTG
1 GTG
3114827 ATACCCAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (27 bp):
GTGGGTAGGATTTGAGTGGATGGGATT
Found at i:3114822 original size:15 final size:15
Alignment explanation
Indices: 3114761--3114823 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
3114751 AAGGACATCA
* *
3114761 AGGATTTAAGTGGGT
1 AGGATTTGAGTGGAT
3114776 AGGATTTGAGTGGAT
1 AGGATTTGAGTGGAT
* *
3114791 GGGA-TT--GTGGGT
1 AGGATTTGAGTGGAT
3114803 AGGATTTGAGTGGAT
1 AGGATTTGAGTGGAT
*
3114818 GGGATT
1 AGGATT
3114824 GTGATACCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 2 0.05
15 26 0.68
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGAT
Found at i:3114847 original size:107 final size:107
Alignment explanation
Indices: 3114727--3115238 Score: 392
Period size: 122 Copynumber: 4.5 Consensus size: 107
3114717 CTTTTACATT
* *
3114727 ACTCTGGTGAGATCTTAGACTTGTAAGGACATCAAGGATTTAAGTGGGTAGGATTTGAGTGGATG
1 ACTCTGGTGAGATCTTGGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGATTTGAGTGGATG
3114792 GGATTGTGGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
66 GGATTGTGGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
* * ** * * *
3114834 ACTCTGGTGAGATCTTGGACGATT-TGAGTG-GATGGGATGATTTGAGTGGATGGGATTGTGA-T
1 ACTCTGGTGAGATCTTGGAC--TTGTAAG-GACAT-CAAGGATTTGAGTGGGTAGGATT-TGAGT
**** * * * ***
3114896 --ACCCAACTCT-GGT-GAGATCTTGGACCTGTAAGGACATCAAGGATT-TGAGTTACATT
61 GGATGGGATTGTGGGTAG-GAT-TT-GA---GT--GG--AT--GGGATTGTGA--TACCCA
* * *
3114952 ACTCTGGTAAGATCTTAGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGATTTGAGTAGATG
1 ACTCTGGTGAGATCTTGGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGATTTGAGTGGATG
3115017 GGATTGTGGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
66 GGATTGTGGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
* * * *
3115059 ACTCTGGTGAGATCTTGGACCTGTAAGGACATTAAGAATTTGAGTGGGTAGGATTTAAGTGGGTA
1 ACTCTGGTGAGATCTTGGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGA-TT---TGAGT-
* *
3115124 GGATTTGAGTGGATAGGATTGTGGGTAGGATTTGAGTGAATGGGATTGTGATACCCA
61 GGA--T--G-GGAT-TG-T---GGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
* *
3115181 ACTCTGGTGAGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGTAAGATTTGA
1 ACTCTGGTGAGATCTTGGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGATTTGA
3115239 CCTGTAAGGA
Statistics
Matches: 312, Mismatches: 51, Indels: 73
0.72 0.12 0.17
Matches are distributed among these distances:
105 1 0.00
106 6 0.02
107 76 0.24
108 14 0.04
109 24 0.08
110 5 0.02
111 6 0.02
112 4 0.01
113 2 0.01
114 3 0.01
115 5 0.02
116 26 0.08
117 16 0.05
118 30 0.10
119 7 0.02
120 1 0.00
121 2 0.01
122 84 0.27
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.31
Consensus pattern (107 bp):
ACTCTGGTGAGATCTTGGACTTGTAAGGACATCAAGGATTTGAGTGGGTAGGATTTGAGTGGATG
GGATTGTGGGTAGGATTTGAGTGGATGGGATTGTGATACCCA
Found at i:3114877 original size:18 final size:18
Alignment explanation
Indices: 3114854--3114889 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3114844 GATCTTGGAC
3114854 GATTTGAGTGGATGGGAT
1 GATTTGAGTGGATGGGAT
3114872 GATTTGAGTGGATGGGAT
1 GATTTGAGTGGATGGGAT
3114890 TGTGATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (18 bp):
GATTTGAGTGGATGGGAT
Found at i:3115006 original size:15 final size:15
Alignment explanation
Indices: 3114986--3115040 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3114976 AAGGACATCA
3114986 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
* *
3115001 AGGATTTGAGTAGAT
1 AGGATTTGAGTGGGT
*
3115016 GGGA-TT--GTGGGT
1 AGGATTTGAGTGGGT
3115028 AGGATTTGAGTGG
1 AGGATTTGAGTGG
3115041 ATGGGATTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
12 7 0.23
13 2 0.06
14 2 0.06
15 20 0.65
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGGT
Found at i:3115026 original size:27 final size:27
Alignment explanation
Indices: 3114995--3115051 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
3114985 AAGGATTTGA
3114995 GTGGGTAGGATTTGAGTAGATGGGATT
1 GTGGGTAGGATTTGAGTAGATGGGATT
*
3115022 GTGGGTAGGATTTGAGTGGATGGGATT
1 GTGGGTAGGATTTGAGTAGATGGGATT
3115049 GTG
1 GTG
3115052 ATACCCAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (27 bp):
GTGGGTAGGATTTGAGTAGATGGGATT
Found at i:3115047 original size:15 final size:15
Alignment explanation
Indices: 3114986--3115048 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
3114976 AAGGACATCA
*
3114986 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGAT
*
3115001 AGGATTTGAGTAGAT
1 AGGATTTGAGTGGAT
* *
3115016 GGGA-TT--GTGGGT
1 AGGATTTGAGTGGAT
3115028 AGGATTTGAGTGGAT
1 AGGATTTGAGTGGAT
*
3115043 GGGATT
1 AGGATT
3115049 GTGATACCCA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
12 7 0.19
13 2 0.05
14 2 0.05
15 26 0.70
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGAT
Found at i:3115119 original size:15 final size:15
Alignment explanation
Indices: 3115096--3115161 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
3115086 GACATTAAGA
3115096 ATTTGAGTGGGTAGG
1 ATTTGAGTGGGTAGG
*
3115111 ATTTAAGTGGGTAGG
1 ATTTGAGTGGGTAGG
*
3115126 ATTTGAGTGGATAGG
1 ATTTGAGTGGGTAGG
3115141 A-TT--GTGGGTAGG
1 ATTTGAGTGGGTAGG
3115153 ATTTGAGTG
1 ATTTGAGTG
3115162 AATGGGATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
12 9 0.20
13 2 0.05
14 2 0.05
15 31 0.70
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (15 bp):
ATTTGAGTGGGTAGG
Found at i:3115155 original size:27 final size:27
Alignment explanation
Indices: 3115096--3115173 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
3115086 GACATTAAGA
*
3115096 ATTTGAGTGGGTAGGATTTAAGTGGGTAGG
1 ATTTGAGTGGATAGGA-TT--GTGGGTAGG
3115126 ATTTGAGTGGATAGGATTGTGGGTAGG
1 ATTTGAGTGGATAGGATTGTGGGTAGG
* *
3115153 ATTTGAGTGAATGGGATTGTG
1 ATTTGAGTGGATAGGATTGTG
3115174 ATACCCAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.62
29 2 0.04
30 15 0.33
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (27 bp):
ATTTGAGTGGATAGGATTGTGGGTAGG
Found at i:3115203 original size:122 final size:122
Alignment explanation
Indices: 3114986--3115236 Score: 439
Period size: 122 Copynumber: 2.1 Consensus size: 122
3114976 AAGGACATCA
* * *
3114986 AGGATTTGAGTGGGTAGGATTTGAGTAGATGGGATTGTGGGTAGGATTTGAGTGGATGGGATTGT
1 AGGATTTAAGTGGGTAGGATTTGAGTAGATAGGATTGTGGGTAGGATTTGAGTGAATGGGATTGT
*
3115051 GATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATTAAGAATTTGAGTGGGT
66 GATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATCAAGAATTTGAGTGGGT
*
3115108 AGGATTTAAGTGGGTAGGATTTGAGTGGATAGGATTGTGGGTAGGATTTGAGTGAATGGGATTGT
1 AGGATTTAAGTGGGTAGGATTTGAGTAGATAGGATTGTGGGTAGGATTTGAGTGAATGGGATTGT
*
3115173 GATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
66 GATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATCAAGAATTTGAGTGGGT
*
3115230 AAGATTT
1 AGGATTT
3115237 GACCTGTAAG
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.25, C:0.08, G:0.36, T:0.31
Consensus pattern (122 bp):
AGGATTTAAGTGGGTAGGATTTGAGTAGATAGGATTGTGGGTAGGATTTGAGTGAATGGGATTGT
GATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATCAAGAATTTGAGTGGGT
Found at i:3115252 original size:39 final size:40
Alignment explanation
Indices: 3115190--3115305 Score: 163
Period size: 37 Copynumber: 3.0 Consensus size: 40
3115180 AACTCTGGTG
3115190 AGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
1 AGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
*
3115230 AAGAT-TT-GACCTGTAAGGACATCAAGGACTCT-AGT--G-
1 -AGATCTTGGACCTGTAAGGACATCAAGGA-TTTGAGTGGGT
3115266 AGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
1 AGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
3115306 GGGATTGTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
35 4 0.06
36 4 0.06
37 25 0.38
39 25 0.38
40 4 0.06
41 4 0.06
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (40 bp):
AGATCTTGGACCTGTAAGGACATCAAGGATTTGAGTGGGT
Found at i:3115376 original size:15 final size:15
Alignment explanation
Indices: 3115356--3115391 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3115346 AAGGACATCA
3115356 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
3115371 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
*
3115386 GGGATT
1 AGGATT
3115392 GTGATACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGGT
Found at i:3115424 original size:80 final size:80
Alignment explanation
Indices: 3115291--3115616 Score: 625
Period size: 80 Copynumber: 4.1 Consensus size: 80
3115281 AAGGACATCA
3115291 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
1 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
3115356 AGGATTTGAGTGGGT
66 AGGATTTGAGTGGGT
3115371 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
1 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
3115436 AGGATTTGAGTGGGT
66 AGGATTTGAGTGGGT
3115451 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
1 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
3115516 AGGATTTGAGTGGGT
66 AGGATTTGAGTGGGT
*
3115531 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAAGACATCA
1 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
*
3115596 AGGATTTAAGTGGGT
66 AGGATTTGAGTGGGT
*
3115611 GGGATT
1 AGGATT
3115617 GTTATTCCCA
Statistics
Matches: 243, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 243 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.29
Consensus pattern (80 bp):
AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
AGGATTTGAGTGGGT
Found at i:3115449 original size:141 final size:137
Alignment explanation
Indices: 3115150--3115449 Score: 372
Period size: 141 Copynumber: 2.1 Consensus size: 137
3115140 GATTGTGGGT
*
3115150 AGGATTTGAGTGAATGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTGTAAGGACATCA
1 AGGATTTGAG-G--TGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
* *
3115215 AGGATTTGAGTGGGTAAGATTTGACCTGTAAGGACATCAAGGACTCTAGTGAGATCTTGGACCTG
63 AGGATTTGAGTGGGTAAGATTTGACCTGTAAGGACACCAA-GACTCTAGTGAGATCTTGGACCTA
3115280 TAAGGACATCA
127 TAAGGACATCA
3115291 AGGATTTGAGTGGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
1 AGGATTTGA---GGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCA
* * * * * *
3115356 AGGATTTGAGTGGGTAGGATTTGA-GTGGGTGGGATTGTGATACCCA-ACTCTGGTGAGATCTTG
63 AGGATTTGAGTGGGTAAGATTTGACCT--GT---A-AG-GACACCAAGACTCTAGTGAGATCTTG
3115419 GACCTATAAGGACATCA
121 GACCTATAAGGACATCA
3115436 AGGATTTGA-GTGGG
1 AGGATTTGAGGTGGG
3115450 TAGGATTTGA
Statistics
Matches: 140, Mismatches: 9, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
140 1 0.01
141 87 0.62
142 2 0.01
143 1 0.01
144 1 0.01
145 42 0.30
146 1 0.01
147 5 0.04
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.28
Consensus pattern (137 bp):
AGGATTTGAGGTGGGATTGTGATACCCAACTCTGGTGAGATCTTGGACCTATAAGGACATCAAGG
ATTTGAGTGGGTAAGATTTGACCTGTAAGGACACCAAGACTCTAGTGAGATCTTGGACCTATAAG
GACATCA
Found at i:3115456 original size:15 final size:15
Alignment explanation
Indices: 3115436--3115471 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3115426 AAGGACATCA
3115436 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
3115451 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
*
3115466 GGGATT
1 AGGATT
3115472 GTGATACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGGT
Found at i:3115536 original size:15 final size:15
Alignment explanation
Indices: 3115516--3115551 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3115506 AAGGACATCA
3115516 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
3115531 AGGATTTGAGTGGGT
1 AGGATTTGAGTGGGT
*
3115546 GGGATT
1 AGGATT
3115552 GTGATACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
AGGATTTGAGTGGGT
Found at i:3115681 original size:13 final size:13
Alignment explanation
Indices: 3115663--3115690 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3115653 TTGTTAAAGA
3115663 CCTACATAACAAT
1 CCTACATAACAAT
3115676 CCTACATAACAAT
1 CCTACATAACAAT
3115689 CC
1 CC
3115691 AAATTTGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (13 bp):
CCTACATAACAAT
Found at i:3116345 original size:7 final size:7
Alignment explanation
Indices: 3116333--3116397 Score: 121
Period size: 7 Copynumber: 9.3 Consensus size: 7
3116323 AGCATTGTCT
3116333 GGTCTAA
1 GGTCTAA
3116340 GGTCTAA
1 GGTCTAA
3116347 GGTCTAA
1 GGTCTAA
3116354 GGTCTAA
1 GGTCTAA
3116361 GGTCTAA
1 GGTCTAA
3116368 GGTCTAA
1 GGTCTAA
3116375 GGTCTAA
1 GGTCTAA
*
3116382 GGTCTAT
1 GGTCTAA
3116389 GGTCTAA
1 GGTCTAA
3116396 GG
1 GG
3116398 ATAATGGGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (7 bp):
GGTCTAA
Found at i:3118681 original size:21 final size:21
Alignment explanation
Indices: 3118655--3118699 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3118645 CTTAGAAGAG
3118655 TTACTGTAAATCTAATATCTA
1 TTACTGTAAATCTAATATCTA
*
3118676 TTACTGTAAATCTCATATCTA
1 TTACTGTAAATCTAATATCTA
3118697 TTA
1 TTA
3118700 TTCTCTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (21 bp):
TTACTGTAAATCTAATATCTA
Found at i:3134691 original size:14 final size:13
Alignment explanation
Indices: 3134674--3134718 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
3134664 GGAAATATAA
3134674 AAAAAAATTAAATT
1 AAAAAAATTAAA-T
*
3134688 AAAAAAAATAAAT
1 AAAAAAATTAAAT
*
3134701 AAAAAGCATTAAAT
1 AAAAA-AATTAAAT
3134715 AAAA
1 AAAA
3134719 TAAAGATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:3137029 original size:14 final size:13
Alignment explanation
Indices: 3137003--3137033 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3136993 CAAATTCAAA
3137003 TAACTAAACTAAT
1 TAACTAAACTAAT
3137016 TAACTAATACTAAT
1 TAACTAA-ACTAAT
3137030 TAAC
1 TAAC
3137034 AAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TAACTAAACTAAT
Found at i:3142557 original size:64 final size:64
Alignment explanation
Indices: 3142456--3142576 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
3142446 AAAAGCTGTC
* *
3142456 GGGCTAATGGTTGAATTTGAATTGTTACACTATAAATAAAAGTTGAAGGACTTATTTTGCTGCT
1 GGGCTAATGGTTGAACTTGAATCGTTACACTATAAATAAAAGTTGAAGGACTTATTTTGCTGCT
* * * *
3142520 GGGCTAGTGGTTGGACTTGAGTCGTTACACTATAAATAAAAGTTTAAGGACTTATTT
1 GGGCTAATGGTTGAACTTGAATCGTTACACTATAAATAAAAGTTGAAGGACTTATTT
3142577 GGCTCAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (64 bp):
GGGCTAATGGTTGAACTTGAATCGTTACACTATAAATAAAAGTTGAAGGACTTATTTTGCTGCT
Found at i:3142703 original size:31 final size:31
Alignment explanation
Indices: 3142668--3142726 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3142658 TATAAGAGTT
*
3142668 TATTTGATTCAAAATAAAAATATAAAAAATG
1 TATTTGACTCAAAATAAAAATATAAAAAATG
*
3142699 TATTTGGCTCAAAATAAAAATATAAAAA
1 TATTTGACTCAAAATAAAAATATAAAAA
3142727 CTTAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (31 bp):
TATTTGACTCAAAATAAAAATATAAAAAATG
Found at i:3145758 original size:41 final size:41
Alignment explanation
Indices: 3145701--3145783 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
3145691 TGGATGCAAG
3145701 CCTCTATCATTTTAGTTATATGACAAAGTGATCATGATACT
1 CCTCTATCATTTTAGTTATATGACAAAGTGATCATGATACT
3145742 CCTCTATCATTTTAGTTATATGACAAAGTGATCATGATACT
1 CCTCTATCATTTTAGTTATATGACAAAGTGATCATGATACT
3145783 C
1 C
3145784 ACCTAATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (41 bp):
CCTCTATCATTTTAGTTATATGACAAAGTGATCATGATACT
Found at i:3190497 original size:22 final size:22
Alignment explanation
Indices: 3190455--3190497 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3190445 CTCAAATACG
* *
3190455 ATTAAATACAAAACTTGTTCAA
1 ATTAAATACAAAACATATTCAA
3190477 ATTAAATAC-AAACAATATTCA
1 ATTAAATACAAAAC-ATATTCA
3190498 TGTTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (22 bp):
ATTAAATACAAAACATATTCAA
Found at i:3190723 original size:31 final size:31
Alignment explanation
Indices: 3190687--3190746 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
3190677 ATTTAAAATC
* *
3190687 AATAATTATAAAAACAATTATAACAAAATAA
1 AATAATAATAAAAACAAATATAACAAAATAA
* * *
3190718 AATAATAATAACATCAAATATAATAAAAT
1 AATAATAATAAAAACAAATATAACAAAAT
3190747 TTAACATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (31 bp):
AATAATAATAAAAACAAATATAACAAAATAA
Found at i:3192541 original size:370 final size:373
Alignment explanation
Indices: 3191913--3192684 Score: 884
Period size: 370 Copynumber: 2.0 Consensus size: 373
3191903 CCCTTTTTCA
* * * *
3191913 TATTCATCAAATTAGAAAAATATTTTTTTGTTTTCTCAACCCTTTATTCTCTTTTTTTTTAATCA
1 TATTCATCAAATT--ATAAATATTTTTTTGTTTTCTCAACCCTTTATTCTATTTTTTTTGAATAA
* * **
3191978 CTTGTCTTATTCTCTTTCTTCTTAAATCAATAAAATAATTATCATTTATTAAAGTAAAAAGACTC
64 CTTGTCTTATTCTCTTTCTTCATAAATCAATAAAACAATTATCATTTACCAAAGTAAAAAGAC-C
* * * * * * *
3192043 TTTTTCTTATATTATTTTTTCGTGAATCAATTAATTTTCTATCAAATAATTATCATTCATCAATG
128 ATTTTCTTATATTATTTTTTCATGAATCAATAAATTTCCAATCAAACAATCATCATTCATCAATG
* *
3192108 CTTTTAAAAAAAATATTATTTATCAAATTAGAAAAACCTTATATCCTTTTTTTTTACGAATCAAT
193 CTTTTAAAAAAAATATTATTCATCAAATTAGAAAAACCTTATATACTTTTTTTTTACGAATCAAT
* * * * *
3192173 CAAACAATATTTT-T-TC-TT-C-TTTCTCTTCAAATCAAATAAGATCTTATGTTAAATATACAT
258 AAAACAAT-TTTTGTGTCATTACATTTCTCTTCAAATCAAATAAGATCCTATATAAAAAATACAT
* * *
3192233 CATTTCACAGCTTACCATCTCTAATTTGAAAATCAATCAATTAAACAATTAT
322 CATTTAACAGCTTACAATCTCTAATGTGAAAATCAATCAATTAAACAATTAT
* * * * *
3192285 TATTCATCAAATTATAAAT-TTTTTTCTTTTTTTTCAATCCTTTGTTCTATTTTTTTTGAATAAT
1 TATTCATCAAATTATAAATATTTTTT-TGTTTTCTCAACCCTTTATTCTATTTTTTTTGAATAAC
* * *
3192349 TTGTCTTATTCTCTTTCTTCATAAATCAATTAAACATTTATCATTTACCAAATTAGAAAA-A-CA
65 TTGTCTTATTCTCTTTCTTCATAAATCAATAAAACAATTATCATTTACCAAAGTA-AAAAGACCA
* *
3192412 TTTT-TTAT-TCTCTTTTTTCATGAATCAATAAATTTCCAATCAAACAATCATCATTCATCGATG
129 TTTTCTTATAT-TATTTTTTCATGAATCAATAAATTTCCAATCAAACAATCATCATTCATCAATG
* * *
3192475 CTTTT-AAAAAAATATTATTCATCAAATTAGAAAAACCTTAGTCTTATTTTCTTTTTTCATGAAT
193 CTTTTAAAAAAAATATTATTCATCAAATTAGAAAAACCTTA-T-ATACTTT-TTTTTT-ACGAAT
3192539 CAATAAAACAATTTTTGTGGATCAATTAAACAAAATTTTCTCTTCAAATCAAATAAGATCCTATA
254 CAATAAAACAATTTTTGT-G-TC-ATT--AC---A-TTTCTCTTCAAATCAAATAAGATCCTATA
* * * * *
3192604 TAAAAAATACATTATTTAACAGCTTATAATCTCTAATGTGAAAATCTATTAATTAATCAATTAT
310 TAAAAAATACATCATTTAACAGCTTACAATCTCTAATGTGAAAATCAATCAATTAAACAATTAT
*
3192668 TATTTATCAAATT-TAAA
1 TATTCATCAAATTATAAA
3192685 AGACCCTTCG
Statistics
Matches: 335, Mismatches: 44, Indels: 32
0.82 0.11 0.08
Matches are distributed among these distances:
366 35 0.10
367 55 0.16
368 9 0.03
369 16 0.05
370 101 0.30
371 4 0.01
372 13 0.04
373 2 0.01
375 2 0.01
378 1 0.00
382 4 0.01
383 93 0.28
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.45
Consensus pattern (373 bp):
TATTCATCAAATTATAAATATTTTTTTGTTTTCTCAACCCTTTATTCTATTTTTTTTGAATAACT
TGTCTTATTCTCTTTCTTCATAAATCAATAAAACAATTATCATTTACCAAAGTAAAAAGACCATT
TTCTTATATTATTTTTTCATGAATCAATAAATTTCCAATCAAACAATCATCATTCATCAATGCTT
TTAAAAAAAATATTATTCATCAAATTAGAAAAACCTTATATACTTTTTTTTTACGAATCAATAAA
ACAATTTTTGTGTCATTACATTTCTCTTCAAATCAAATAAGATCCTATATAAAAAATACATCATT
TAACAGCTTACAATCTCTAATGTGAAAATCAATCAATTAAACAATTAT
Found at i:3193302 original size:21 final size:21
Alignment explanation
Indices: 3193256--3193304 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3193246 ACCCAATCTA
* *
3193256 TAACCTTTCATGATTAACTTT
1 TAACCTTTCATGATAAAATTT
3193277 TAACCTTTCATG-TAAAATTT
1 TAACCTTTCATGATAAAATTT
3193297 TGAACCTT
1 T-AACCTT
3193305 ACATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (21 bp):
TAACCTTTCATGATAAAATTT
Found at i:3196738 original size:15 final size:15
Alignment explanation
Indices: 3196718--3196747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3196708 AAATGTAATA
*
3196718 AAATAATAATTTTAT
1 AAATAATAATATTAT
3196733 AAATAATAATATTAT
1 AAATAATAATATTAT
3196748 CATCAGACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAATAATATTAT
Found at i:3217813 original size:20 final size:22
Alignment explanation
Indices: 3217790--3217829 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3217780 TTTTTAAACG
3217790 TATAATAT-T-AAATATAAAAT
1 TATAATATATAAAATATAAAAT
3217810 TATAATATATAAAATATAAA
1 TATAATATATAAAATATAAA
3217830 TAGTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAATATATAAAATATAAAAT
Found at i:3218274 original size:12 final size:12
Alignment explanation
Indices: 3218257--3218284 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3218247 AAAAATAAAC
3218257 AAATAACAATAT
1 AAATAACAATAT
3218269 AAATAACAATAT
1 AAATAACAATAT
3218281 AAAT
1 AAAT
3218285 TAAGAAAAGA
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:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATAACAATAT
Found at i:3218419 original size:9 final size:9
Alignment explanation
Indices: 3218405--3218456 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
3218395 GAAATATATA
3218405 AAAAATTTT
1 AAAAATTTT
3218414 AAAAATTTT
1 AAAAATTTT
** *
3218423 ATAAAACATA
1 A-AAAATTTT
3218433 AAAGAATTTTT
1 AAA-AA-TTTT
3218444 AAAAATTTT
1 AAAAATTTT
3218453 AAAA
1 AAAA
3218457 GCCTATGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 20 0.59
10 10 0.29
11 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:3230535 original size:18 final size:17
Alignment explanation
Indices: 3230514--3230565 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
3230504 ATGCATTATC
3230514 AATATATATTACATAAAA
1 AATAT-TATTACATAAAA
*
3230532 AATATTACTTA-ATTATAA
1 AATATTA-TTACA-TAAAA
*
3230550 AATATTATTTCATAAA
1 AATATTATTACATAAA
3230566 TGAAAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATTATTACATAAAA
Found at i:3248883 original size:31 final size:31
Alignment explanation
Indices: 3248848--3248911 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3248838 AAGGTAAGAA
3248848 TGCTTAATTAATTCTATTATTCTAAGAGTGT
1 TGCTTAATTAATTCTATTATTCTAAGAGTGT
3248879 TGCTTAATTAATTCTATTATTCTAAGAGTGT
1 TGCTTAATTAATTCTATTATTCTAAGAGTGT
3248910 TG
1 TG
3248912 AGTCACTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.48
Consensus pattern (31 bp):
TGCTTAATTAATTCTATTATTCTAAGAGTGT
Found at i:3252594 original size:9 final size:9
Alignment explanation
Indices: 3252582--3252612 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3252572 TGGAGACAAC
3252582 TGATTATGA
1 TGATTATGA
*
3252591 TGATGATGA
1 TGATTATGA
3252600 TGATTATGA
1 TGATTATGA
3252609 TGAT
1 TGAT
3252613 GGATCTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (9 bp):
TGATTATGA
Found at i:3258761 original size:44 final size:42
Alignment explanation
Indices: 3258708--3258809 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 42
3258698 AAGAATCCAA
*
3258708 AAATAAAATAAAATAAAATATAAAAATTTAA-ATT-TATATAAT
1 AAATAAAATAAAATAAAATA-AAAAATATAAGATTATA-ATAAT
* *
3258750 ATAAGTAAAATAAATTAAAATAAAATATATAAGATTATAATAAT
1 A-AA-TAAAATAAAATAAAATAAAAAATATAAGATTATAATAAT
3258794 AAATAAAAATAAAATA
1 AAAT-AAAATAAAATA
3258810 TATAAAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.04
43 22 0.43
44 25 0.49
45 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (42 bp):
AAATAAAATAAAATAAAATAAAAAATATAAGATTATAATAAT
Found at i:3258781 original size:33 final size:33
Alignment explanation
Indices: 3258742--3258814 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
3258732 AATTTAAATT
* *
3258742 TATATAATATAAGTAA-AATAAATTAAAATAAAA
1 TATATAAGATAA-TAATAATAAATAAAAATAAAA
*
3258775 TATATAAGATTATAATAATAAATAAAAATAAAA
1 TATATAAGATAATAATAATAAATAAAAATAAAA
3258808 TATATAA
1 TATATAA
3258815 AATTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (33 bp):
TATATAAGATAATAATAATAAATAAAAATAAAA
Found at i:3258809 original size:15 final size:15
Alignment explanation
Indices: 3258755--3258822 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
3258745 ATAATATAAG
*
3258755 TAAAATAAATTAAAA
1 TAAAATAAATAAAAA
* *
3258770 TAAAATATATAAGATTA
1 TAAAATAAATAA-A-AA
3258787 TAATAATAAATAAAAA
1 TAA-AATAAATAAAAA
* *
3258803 TAAAATATATAAAAT
1 TAAAATAAATAAAAA
3258818 TAAAA
1 TAAAA
3258823 ATATATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 25 0.58
16 5 0.12
17 5 0.12
18 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (15 bp):
TAAAATAAATAAAAA
Found at i:3258874 original size:49 final size:50
Alignment explanation
Indices: 3258755--3258878 Score: 132
Period size: 49 Copynumber: 2.5 Consensus size: 50
3258745 ATAATATAAG
* *
3258755 TAAAATAAATTAAAATAAAATATA--TAAGATTATAATAATAAATAAAAA
1 TAAAATATATAAAAATAAAATATATTTAAGATTATAATAATAAATAAAAA
* * * *
3258803 TAAAATATATAAAATTAAAAATATATTTAAGA-TATGATATTATATAAAAA
1 TAAAATATATAAAAAT-AAAATATATTTAAGATTATAATAATAAATAAAAA
3258853 T-AAATA-ATAAAAAATATAAATATATT
1 TAAAATATAT-AAAAATA-AAATATATT
3258879 AAATTTATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
48 16 0.25
49 27 0.42
50 16 0.25
51 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (50 bp):
TAAAATATATAAAAATAAAATATATTTAAGATTATAATAATAAATAAAAA
Found at i:3263241 original size:15 final size:15
Alignment explanation
Indices: 3263221--3263260 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3263211 ATTACGAATA
3263221 AATATGATTATAGA-T
1 AATATGATTATA-ATT
3263236 AATATGATTATAATT
1 AATATGATTATAATT
*
3263251 AATATTATTA
1 AATATGATTA
3263261 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
AATATGATTATAATT
Found at i:3264048 original size:42 final size:42
Alignment explanation
Indices: 3263989--3264072 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
3263979 AACTTTTTGG
*
3263989 TAATGTAAATCAAGGTTCCATGGGACATGAATACATGTACTA
1 TAATGTAAATCAAGGTTCAATGGGACATGAATACATGTACTA
3264031 TAATGTAAATCAAGGTTCAATGGGACATGAATACATGTACTA
1 TAATGTAAATCAAGGTTCAATGGGACATGAATACATGTACTA
3264073 GGTTTGTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (42 bp):
TAATGTAAATCAAGGTTCAATGGGACATGAATACATGTACTA
Found at i:3267499 original size:18 final size:18
Alignment explanation
Indices: 3267476--3267510 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3267466 ATTACTTCAA
3267476 AAATATATTTT-ATATATT
1 AAATAT-TTTTAATATATT
3267494 AAATATTTTTAATATAT
1 AAATATTTTTAATATAT
3267511 ATCTCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATATTTTTAATATATT
Found at i:3274408 original size:23 final size:22
Alignment explanation
Indices: 3274372--3274432 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
3274362 TAATTATAAA
* *
3274372 AAATAATAATATAATATTTAAT
1 AAATAATAAAATAATAATTAAT
3274394 AAATAAATAAAATAATAATTAA-
1 AAAT-AATAAAATAATAATTAAT
* *
3274416 AATATAAGAAGATAATA
1 AA-ATAATAAAATAATA
3274433 TTACAGTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (22 bp):
AAATAATAAAATAATAATTAAT
Found at i:3274572 original size:60 final size:56
Alignment explanation
Indices: 3274461--3274655 Score: 146
Period size: 60 Copynumber: 3.3 Consensus size: 56
3274451 TTTTGTTGAA
* *
3274461 ATTATTA-TATTAATTTTTA-AAATTAGTTTTATTTATTAAAATAAAAATTTAATATATTTAT
1 ATTATTATTATTAATTTTTATAAA-TA---TTATTT-TT-AAATATAATTTTAATATA-TTAT
* *
3274522 ATTCATTATTATTAATTTTTATAAAATATTATTTCTTAAATATATTTTTAATGTAATATAT
1 ATT-ATTATTATTAATTTTTAT-AAATATTATTT-TTAAATATAATTTTAATAT-AT-TAT
* * ** * *
3274583 TTTATTTTTATTATAACTTTATATATTTTATTTTTAAATATAATTTT-ATATATTAT
1 ATTATTATTATTA-ATTTTTATAAATATTATTTTTAAATATAATTTTAATATATTAT
3274639 ATATATTATT-TTAATTT
1 AT-TATTATTATTAATTT
3274656 ATTTTTAAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
55 2 0.02
56 7 0.06
57 8 0.07
58 3 0.03
59 13 0.12
60 32 0.29
61 23 0.21
62 4 0.04
63 12 0.11
64 2 0.02
65 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (56 bp):
ATTATTATTATTAATTTTTATAAATATTATTTTTAAATATAATTTTAATATATTAT
Found at i:3274607 original size:26 final size:27
Alignment explanation
Indices: 3274577--3274636 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3274567 TTTTAATGTA
*
3274577 ATATATTTTATTTTT-ATTATAACTTT
1 ATATATTTTATTTTTAAATATAACTTT
*
3274603 ATATATTTTATTTTTAAATATAATTTT
1 ATATATTTTATTTTTAAATATAACTTT
3274630 ATATATT
1 ATATATT
3274637 ATATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 15 0.48
27 16 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATATTTTATTTTTAAATATAACTTT
Found at i:3274623 original size:17 final size:18
Alignment explanation
Indices: 3274603--3274645 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3274593 TTATAACTTT
*
3274603 ATATATTTTAT-TTTTAA
1 ATATATTTTATATATTAA
*
3274620 ATATAATTTTATATATTAT
1 ATAT-ATTTTATATATTAA
3274639 ATATATT
1 ATATATT
3274646 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATATTTTATATATTAA
Found at i:3274642 original size:19 final size:18
Alignment explanation
Indices: 3274602--3274643 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3274592 ATTATAACTT
*
3274602 TATAT-ATTTTATTTTTA
1 TATATAATTTTATTATTA
*
3274619 AATATAATTTTATATATTA
1 TATATAATTTTAT-TATTA
3274638 TATATA
1 TATATA
3274644 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATAATTTTATTATTA
Found at i:3287695 original size:22 final size:22
Alignment explanation
Indices: 3287667--3287712 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3287657 AAACATTCGA
3287667 ATTTCATATATTTAAGTATT-TT
1 ATTTCATATATTTAA-TATTATT
*
3287689 ATTTCATATTTTTAATATTATT
1 ATTTCATATATTTAATATTATT
3287711 AT
1 AT
3287713 ATTTATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTCATATATTTAATATTATT
Found at i:3290404 original size:7 final size:7
Alignment explanation
Indices: 3290392--3290427 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
3290382 TTCAATCGTC
3290392 GTTCAAA
1 GTTCAAA
3290399 GTTCAAA
1 GTTCAAA
3290406 GTTCAAA
1 GTTCAAA
*
3290413 CTTCAAA
1 GTTCAAA
*
3290420 CTTCAAA
1 GTTCAAA
3290427 G
1 G
3290428 ATTTGCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (7 bp):
GTTCAAA
Found at i:3299808 original size:6 final size:6
Alignment explanation
Indices: 3299777--3299816 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3299767 ATACACACAC
* * *
3299777 ATATCT ATATCC ATATCT ACATCT ATATCT ATATAT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
3299817 ATATTCTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (6 bp):
ATATCT
Found at i:3321302 original size:2 final size:2
Alignment explanation
Indices: 3321295--3321333 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3321285 ATCCCCAATT
*
3321295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3321334 TCCAGAGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3323311 original size:41 final size:42
Alignment explanation
Indices: 3323258--3323345 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
3323248 TATTAGATTT
3323258 TTTAAATATTAATAATTAATCAT-TT-AAATATAAATATTTCA
1 TTTAAATATTAATAATTAAT-ATATTAAAATATAAATATTTCA
* * *
3323299 TTTATAAT-TTAATCATTAATATATTAAAATATTAATATTTTA
1 TTTA-AATATTAATAATTAATATATTAAAATATAAATATTTCA
3323341 TTTAA
1 TTTAA
3323346 TTAAATATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 2 0.05
41 18 0.44
42 21 0.51
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (42 bp):
TTTAAATATTAATAATTAATATATTAAAATATAAATATTTCA
Found at i:3323411 original size:128 final size:128
Alignment explanation
Indices: 3323256--3323530 Score: 381
Period size: 128 Copynumber: 2.2 Consensus size: 128
3323246 TTTATTAGAT
* *
3323256 TTTTTAAATATTAATAATTAATCATTTAAATATAAATATTTCATTTATAATTTAATCATTAATAT
1 TTTTTAAATATTAATAATTGATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATAT
3323321 ATTAAAATATTAATATTTTATTTAATTAAATATTATTATGA-TCAATTATTTTATTTTATTTTA
66 ATTAAAATATTAATATTTTATTT-ATTAAATATTATTATGATTCAATTATTTTATTTTATTTTA
* * * *
3323384 TTTTCAAATATTAATATTTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATT-ATAT
1 TTTTTAAATATTAATAATTGATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATAT
* * *
3323448 TTTTAAATATTAATA--TT-TTTATTAAATATTATTATGGTT-AATTATTTTATTTTA---T-
66 ATTAAAATATTAATATTTTATTTATTAAATATTATTATGATTCAATTATTTTATTTTATTTTA
*
3323503 TTTTTAAATATTAATAATTGATAGTTTA
1 TTTTTAAATATTAATAATTGATAATTTA
3323531 TTTAAAATAT
Statistics
Matches: 134, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
119 25 0.19
120 1 0.01
123 31 0.23
124 4 0.03
125 2 0.01
127 17 0.13
128 54 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (128 bp):
TTTTTAAATATTAATAATTGATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATAT
ATTAAAATATTAATATTTTATTTATTAAATATTATTATGATTCAATTATTTTATTTTATTTTA
Found at i:3323415 original size:22 final size:21
Alignment explanation
Indices: 3323258--3323478 Score: 92
Period size: 22 Copynumber: 10.5 Consensus size: 21
3323248 TATTAGATTT
* *
3323258 TTTAAATATTAATAATTAATCA
1 TTTAAATATTAAT-ATTTATAA
* *
3323280 TTTAAATATAAATA-TT-TCA
1 TTTAAATATTAATATTTATAA
*
3323299 TTTATAAT-TTAATCATTAATATA
1 TTTA-AATATTAAT-ATTTATA-A
*
3323322 TTAAAATATTAATATTTTATTTAA
1 TTTAAATATTAATA-TTTA--TAA
* *
3323346 -TTAAATATTATTA-TGATCAA
1 TTTAAATATTAATATTTAT-AA
** * *
3323366 -TTATTTTATT-TTATTT-TAT
1 TTTA-AATATTAATATTTATAA
3323385 TTTCAAATATTAATATTTGATAA
1 TTT-AAATATTAATATTT-ATAA
3323408 TTTAAATATTAATATTT-T-A
1 TTTAAATATTAATATTTATAA
*
3323427 TTTATAAT-TTAATCA-TTATATT
1 TTTA-AATATTAAT-ATTTATA-A
*
3323449 TTTAAATATTAATATTT-TTA
1 TTTAAATATTAATATTTATAA
3323469 -TTAAATATTA
1 TTTAAATATTA
3323479 TTATGGTTAA
Statistics
Matches: 154, Mismatches: 21, Indels: 51
0.68 0.09 0.23
Matches are distributed among these distances:
19 35 0.23
20 26 0.17
21 20 0.13
22 42 0.27
23 28 0.18
24 1 0.01
25 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (21 bp):
TTTAAATATTAATATTTATAA
Found at i:3323452 original size:26 final size:27
Alignment explanation
Indices: 3323398--3323450 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
3323388 CAAATATTAA
3323398 TATTTGATAATTTAAATATTAATATTT
1 TATTTGATAATTTAAATATTAATATTT
3323425 TATTT-ATAATTT-AATCATT-ATATTT
1 TATTTGATAATTTAAAT-ATTAATATTT
3323450 T
1 T
3323451 TAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.40
26 10 0.40
27 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATTTGATAATTTAAATATTAATATTT
Found at i:3323536 original size:63 final size:59
Alignment explanation
Indices: 3323325--3323542 Score: 178
Period size: 64 Copynumber: 3.5 Consensus size: 59
3323315 TAATATATTA
* * *
3323325 AAATATTAATATTTTATTTAATTAAATATTATTATGATCAATTATTTTATTTTATTTTATTTT
1 AAATATTAATATTATATTTATTTAAATATTATTATG-TTAATTATTTTATTTTA--TT-TTTT
* * * * *
3323388 CAAATATTAATATT-TGA-TAATTTAAATATTAATATTTTATTTATAATTTAATCATTATATTTT
1 -AAATATTAATATTAT-ATTTATTTAAATATTATTATGTTAATTAT--TTT-AT-TTTAT-TTTT
3323451 T
59 T
3323452 AAATATTAATA-T-T-TTTA-TTAAATATTATTATGGTTAATTATTTTATTTTATTTTTT
1 AAATATTAATATTATATTTATTTAAATATTATTAT-GTTAATTATTTTATTTTATTTTTT
3323508 AAATATTAATAATTGATAGTTTATTTAAAATATTA
1 AAATATTAAT-ATT-ATA-TTTATTT-AAATATTA
3323543 ATAATTGACC
Statistics
Matches: 126, Mismatches: 12, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
56 15 0.12
57 5 0.04
58 3 0.02
59 3 0.02
60 14 0.11
61 9 0.07
62 12 0.10
63 29 0.23
64 30 0.24
65 3 0.02
66 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (59 bp):
AAATATTAATATTATATTTATTTAAATATTATTATGTTAATTATTTTATTTTATTTTTT
Found at i:3323608 original size:21 final size:20
Alignment explanation
Indices: 3323261--3323616 Score: 85
Period size: 21 Copynumber: 17.1 Consensus size: 20
3323251 TAGATTTTTT
3323261 AAATATTAATAATTAATCATTT-
1 AAATATTAAT-ATT-AT-ATTTA
*
3323283 AAATATAAATATT-TCATTTA
1 AAATATTAATATTAT-ATTTA
*
3323303 TAAT-TTAATCATTAATATATTA
1 AAATATTAAT-ATT-ATAT-TTA
*
3323325 AAATATTAATATTTTATTTAA
1 AAATATTAATATTATATTT-A
* * *
3323346 TTAAATATTATTATGATCAATTA
1 --AAATATTAATATTAT-ATTTA
*** * * *
3323369 TTTTATT-TTATTTTATTTTC
1 AAATATTAATATTATA-TTTA
3323389 AAATATTAATATTTGATAATTT-
1 AAATATTAATA-TT-AT-ATTTA
*
3323411 AAATATTAATATTTTATTTA
1 AAATATTAATATTATATTTA
* *
3323431 TAAT-TTAATCATTATATTTTT
1 AAATATTAAT-ATTATA-TTTA
*
3323452 AAATATTAATATT-T-TTATT
1 AAATATTAATATTATATT-TA
**
3323471 AAATA-T--TATTATGGTT-
1 AAATATTAATATTATATTTA
* * * * *
3323487 AATTATTTTATTTTATTTTTT
1 AAATA-TTAATATTATATTTA
3323508 AAATATTAATAATTGATAGTTTATTTA
1 AAATATTAAT-A-T--TA---TATTTA
**
3323535 AAATATTAATAATTGACCTTT-
1 AAATATTAAT-ATT-ATATTTA
3323556 AAATATTAATATT-TATTTA
1 AAATATTAATATTATATTTA
* *
3323575 TAAT-TTAGTTATTAATATTTA
1 AAATATTA-ATATT-ATATTTA
*
3323596 AAATATTAATATTTTATTTA
1 AAATATTAATATTATATTTA
3323616 A
1 A
3323617 TTTAAATATT
Statistics
Matches: 249, Mismatches: 45, Indels: 82
0.66 0.12 0.22
Matches are distributed among these distances:
16 8 0.03
17 2 0.01
18 11 0.04
19 34 0.14
20 50 0.20
21 53 0.21
22 44 0.18
23 22 0.09
24 7 0.03
25 1 0.00
26 1 0.00
27 16 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATATTAATATTATATTTA
Found at i:3323670 original size:24 final size:27
Alignment explanation
Indices: 3323499--3323722 Score: 131
Period size: 31 Copynumber: 7.9 Consensus size: 27
3323489 TTATTTTATT
3323499 TTATTT-TTT-AAATATTAATAATTGA
1 TTATTTATTTAAAATATTAATAATTGA
3323524 -TAGTTTATTTAAAATATTAATAATTGA
1 TTA-TTTATTTAAAATATTAATAATTGA
** * * *
3323551 CCTT-TAAATATTAATATTTATTTATAATTTA
1 --TTATTTAT-TTAA-A-ATATTAATAATTGA
3323582 GTTATTAATATTTAAAATATTAAT-ATT--
1 -TTATT--TATTTAAAATATTAATAATTGA
* **
3323609 TTATTTAATTT-AAATATTATTATGATAAA
1 TTATTT-ATTTAAAATATTA--ATAATTGA
*
3323638 TTATTTTATTTTTAAATATTAATAATTGA
1 TTA-TTTA-TTTAAAATATTAATAATTGA
*
3323667 TTATTTATTTAAAATATTAATAATTTAA
1 TTATTTATTTAAAATATTAATAA-TTGA
*
3323695 TCATTAATATTTTAAAATATTAATAATT
1 TTATT--TA-TTTAAAATATTAATAATT
3323723 TATTTAAGTT
Statistics
Matches: 157, Mismatches: 17, Indels: 45
0.72 0.08 0.21
Matches are distributed among these distances:
24 11 0.07
25 7 0.04
26 10 0.06
27 33 0.21
28 14 0.09
29 19 0.12
30 20 0.13
31 37 0.24
32 4 0.03
33 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (27 bp):
TTATTTATTTAAAATATTAATAATTGA
Found at i:3323677 original size:143 final size:144
Alignment explanation
Indices: 3323380--3323691 Score: 406
Period size: 143 Copynumber: 2.2 Consensus size: 144
3323370 TTTATTTTAT
* *
3323380 TTTATTTTCAAATATTAATATTTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTA
1 TTTA-TTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTA
* *
3323445 TATTTTTAAATATTAATATTTTTATTAAATATTATTATGGTTAATTATTTTATTTTATTTTTTAA
65 TATTTTAAAATATTAATATTTTTATTAAATATTATTATGGATAA-TA-TTTATTTTATTTTTTAA
3323510 ATATTAATAATTGATAG
128 ATATTAATAATTGATAG
** * *
3323527 TTTATTTAAAATATTAATAATTGA-CCTTTAAATATTAATA-TTTATTTATAATTTAGTTATTA-
1 TTTATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAT
3323589 ATATTTAAAATATTAATATTTTATTTAATTTAAATATTATTAT-GATAA-A-TTATTTTA-TTTT
66 AT-TTTAAAATATTAATA--TT-TTT-A-TTAAATATTATTATGGATAATATTTATTTTATTTTT
3323650 TAAATATTAATAATTGATTA-
125 TAAATATTAATAATTGA-TAG
3323670 TTTATTTAAAATATTAATAATT
1 TTTATTTAAAATATTAATAATT
3323692 TAATCATTAA
Statistics
Matches: 150, Mismatches: 8, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
143 45 0.30
144 44 0.29
145 14 0.09
146 21 0.14
147 7 0.05
148 5 0.03
149 14 0.09
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (144 bp):
TTTATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAT
ATTTTAAAATATTAATATTTTTATTAAATATTATTATGGATAATATTTATTTTATTTTTTAAATA
TTAATAATTGATAG
Found at i:3323682 original size:58 final size:56
Alignment explanation
Indices: 3323592--3323761 Score: 190
Period size: 58 Copynumber: 3.1 Consensus size: 56
3323582 GTTATTAATA
*
3323592 TTTAAAATATTAAT-ATTTTATTTAATTTAAATATTATTATGATAAATTATTTTAT
1 TTTAAAATATTAATAATTTTATTTAATTTAAATATTATTATGATTAATTATTTTAT
* * * *
3323647 TTTTAAATATTAATAATTGATTATTT-ATTTAAA-A-TATTAATAATTTAATCATTAATAT
1 TTTAAAATATTAATAATT--TTATTTAATTTAAATATTATT-ATGA-TTAATTATT-TTAT
* *
3323705 TTTAAAATATTAATAA-TTTATTTAAGTTAAATATTATTATGATTCATT-TTTTAT
1 TTTAAAATATTAATAATTTTATTTAATTTAAATATTATTATGATTAATTATTTTAT
3323759 TTT
1 TTT
3323762 CTCTATTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
54 6 0.06
55 25 0.26
56 17 0.18
57 19 0.20
58 28 0.29
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (56 bp):
TTTAAAATATTAATAATTTTATTTAATTTAAATATTATTATGATTAATTATTTTAT
Found at i:3323692 original size:16 final size:16
Alignment explanation
Indices: 3323673--3323724 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
3323663 TTGATTATTT
3323673 ATTTAAAATATTAATA
1 ATTTAAAATATTAATA
3323689 ATTT--AATCATTAATA
1 ATTTAAAAT-ATTAATA
*
3323704 TTTTAAAATATTAATA
1 ATTTAAAATATTAATA
3323720 ATTTA
1 ATTTA
3323725 TTTAAGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 3 0.10
15 10 0.32
16 15 0.48
17 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAAATATTAATA
Found at i:3323704 original size:143 final size:144
Alignment explanation
Indices: 3323380--3323705 Score: 402
Period size: 144 Copynumber: 2.3 Consensus size: 144
3323370 TTTATTTTAT
* *
3323380 TTTATTTTCAAATATTAAT-ATTTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATT
1 TTTA-TTTAAAATATTAATAATTTGATCA-TTAAATATTAATATTTTATTTATAATTTAATCATT
* *
3323444 ATATTTTTAAATATTAATATTTTTATTAAATATTATTATGGTTAATTATTTTATTTTATTTTTTA
64 ATATTTTAAAATATTAATATTTTTATTAAATATTATTATGGATAA-TA-TTTATTTTATTTTTTA
3323509 AATATTAATAATTGATAG
127 AATATTAATAATTGATAG
* * * *
3323527 TTTATTTAAAATATTAATAA-TTGACCTTTAAATATTAATA-TTTATTTATAATTTAGTTATTA-
1 TTTATTTAAAATATTAATAATTTGATCATTAAATATTAATATTTTATTTATAATTTAATCATTAT
3323589 ATATTTAAAATATTAATATTTTATTTAATTTAAATATTATTAT-GATAA-A-TTATTTTA-TTTT
66 AT-TTTAAAATATTAATA--TT-TTT-A-TTAAATATTATTATGGATAATATTTATTTTATTTTT
3323650 TAAATATTAATAATTGATTA-
125 TAAATATTAATAATTGA-TAG
*
3323670 TTTATTTAAAATATTAATAATTTAATCATT-AATATT
1 TTTATTTAAAATATTAATAATTTGATCATTAAATATT
3323706 TTAAAATATT
Statistics
Matches: 159, Mismatches: 11, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
143 49 0.31
144 50 0.31
145 13 0.08
146 20 0.13
147 8 0.05
148 5 0.03
149 14 0.09
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (144 bp):
TTTATTTAAAATATTAATAATTTGATCATTAAATATTAATATTTTATTTATAATTTAATCATTAT
ATTTTAAAATATTAATATTTTTATTAAATATTATTATGGATAATATTTATTTTATTTTTTAAATA
TTAATAATTGATAG
Found at i:3323737 original size:55 final size:55
Alignment explanation
Indices: 3323531--3323740 Score: 185
Period size: 55 Copynumber: 3.7 Consensus size: 55
3323521 TGATAGTTTA
* * *
3323531 TTTAAAATATTAATAATTGACCTTTAAATATTAATATTTATTTATAATTTAGTTATTAATA-
1 TTTAAAATATTAATAATTTA--TTT-AAT-TTAA-A--TATTAATAATTTAATTATTAATAT
* * * *
3323592 TTTAAAATATTAATATTTTATTTAATTTAAATATT-ATTATGATAAATTATT-TTAT
1 TTTAAAATATTAATAATTTATTTAATTTAAATATTAATAAT--TTAATTATTAATAT
* *
3323647 TTTTAAATATTAATAATTGATTATTT-ATTTAAAATATTAATAATTTAATCATTAATAT
1 TTTAAAATATTAATAA-T--TTATTTAATTT-AAATATTAATAATTTAATTATTAATAT
*
3323705 TTTAAAATATTAATAATTTATTTAAGTTAAATATTA
1 TTTAAAATATTAATAATTTATTTAATTTAAATATTA
3323741 TTATGATTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
53 4 0.03
54 6 0.05
55 35 0.28
56 5 0.04
57 16 0.13
58 34 0.27
59 7 0.06
61 18 0.14
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (55 bp):
TTTAAAATATTAATAATTTATTTAATTTAAATATTAATAATTTAATTATTAATAT
Found at i:3328820 original size:27 final size:27
Alignment explanation
Indices: 3328782--3328834 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3328772 TTTGATGAAT
3328782 AGCAATCACACAATTCATTTCCTATTC
1 AGCAATCACACAATTCATTTCCTATTC
*
3328809 AGCAATGACACAATTCATTTCCTATT
1 AGCAATCACACAATTCATTTCCTATT
3328835 ATTCACTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (27 bp):
AGCAATCACACAATTCATTTCCTATTC
Found at i:3334913 original size:27 final size:27
Alignment explanation
Indices: 3334677--3335038 Score: 195
Period size: 27 Copynumber: 13.6 Consensus size: 27
3334667 TGACATAGCA
* *
3334677 TGTAACAATTAAATTATTTAACATGACG
1 TGTAATAACTAAATT-TTTAACATGACG
* * ** *
3334705 TGTAACAATTAAACATTTAACATAACG
1 TGTAATAACTAAATTTTTAACATGACG
* * *
3334732 TATAATAACTAAATATTTAACAT-A-A
1 TGTAATAACTAAATTTTTAACATGACG
* * * **
3334757 TAT-GTGA-TAAA-TTTT--CATGATA
1 TGTAATAACTAAATTTTTAACATGACG
* *
3334779 TGTAATAACTAAAATTTTCAATATGA-G
1 TGTAATAACT-AAATTTTTAACATGACG
* * ** * * * *
3334806 ATGCAACAACGGAATTTTCAATATAACA
1 -TGTAATAACTAAATTTTTAACATGACG
* * * * *
3334834 TGTAACAACCAAATCTTCAACATGATG
1 TGTAATAACTAAATTTTTAACATGACG
* *
3334861 TGTAATAATTATATTTTTCAACATGACG
1 TGTAATAACTAAATTTTT-AACATGACG
* *
3334889 TCTAATAACTAAATTTTTAATATGACG
1 TGTAATAACTAAATTTTTAACATGACG
* * **
3334916 TATAATAACTACATTTTTAACATGATA
1 TGTAATAACTAAATTTTTAACATGACG
*
3334943 TGTAATAACTAAATTTTTAATATGACG
1 TGTAATAACTAAATTTTTAACATGACG
* * **
3334970 TGTAATAATTATATTTTTAACATGATA
1 TGTAATAACTAAATTTTTAACATGACG
* * *
3334997 TGTAATAA-T-TATTTTCAACTTGACG
1 TGTAATAACTAAATTTTTAACATGACG
*
3335022 TATAATAACTAAATTTT
1 TGTAATAACTAAATTTT
3335039 AGAGTATGAC
Statistics
Matches: 258, Mismatches: 63, Indels: 27
0.74 0.18 0.08
Matches are distributed among these distances:
20 3 0.01
21 1 0.00
22 6 0.02
23 6 0.02
24 3 0.01
25 25 0.10
26 6 0.02
27 161 0.62
28 47 0.18
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (27 bp):
TGTAATAACTAAATTTTTAACATGACG
Found at i:3335500 original size:327 final size:331
Alignment explanation
Indices: 3334860--3335521 Score: 798
Period size: 327 Copynumber: 2.0 Consensus size: 331
3334850 TCAACATGAT
* * * * ** *
3334860 GTGTAATAATTATATTTTTCAACATGACGTCTAATAACTAAATTTTTAATATGACGTATAATAAC
1 GTGTAATAATTATATATTTCAACATAACGTATAATAACTAAATATTTAATAAAACGTATAACAAC
* * * * * * * *
3334925 TACATTTTTAACATGATATGTAATAACTAAATTTTTAATATGACGTGTAATAATTATATTTTTAA
66 TACATTTTTAACATGACATGTAACAACTAAATTTTCAACATGACGTATAATAAATACATTTTCAA
* * * * * * *
3334990 CATGATATGTAATAATTATTTTCAACTTGACGTATAATAACTAAATTTTAGAGTATGACATGTAA
131 CATGATATATAACAATCATTTTCAACTTGACGTATAACAACTAAATTTTAAAATATAACATGTAA
* * * *
3335055 CATTGCATTTTTCAACATGACGTTAGCAATATTTTTTGCACAAAAAAATAACAATAAGATTTCCC
196 CATTACATTTTTCAACATGACGTTAACAACATTTTTTGCACAAAAAAATAACAATAACATTTCCC
* * * * *
3335120 AACATATTGTGTAACAAATATTAAGAAAATATTTTTAGCTGCTATGTCATCAGCTCATGTGATTT
261 AACATACTGTGTAACAAATATTAAGAAAATATTTTTAGCTGCCATGCCATCAGCTCACGCGATTT
*
3335185 TTTGTC
326 TTTATC
*
3335191 GTGTAATAATTA-A-ATTTCAACATAACGTATAATAACTAAATATTTAATAAAATGTATAACAAC
1 GTGTAATAATTATATATTTCAACATAACGTATAATAACTAAATATTTAATAAAACGTATAACAAC
*
3335254 TATATTTTTCAACATGACATGTAACAACTAAATTTTCAACA-GA-GTATAATAAATACATTTTCA
66 TACATTTTT-AACATGACATGTAACAACTAAATTTTCAACATGACGTATAATAAATACATTTTCA
* * * * **
3335317 ACATGATTTATAACAATCA-TTTCAATTTGTA-GTGTAACAATTAAATTTTAAAATATAATGTGT
130 ACATGATATATAACAATCATTTTCAACTTG-ACGTATAACAACTAAATTTTAAAATATAACATGT
* * * *
3335380 AACATTACATTTTTCAACATGATGTTAACAACATTTTTTGCA-TAAAAAGTAATAATAACATTTC
194 AACATTACATTTTTCAACATGACGTTAACAACATTTTTTGCACAAAAAAATAACAATAACATTTC
* * * ** *
3335444 TCAACATGCTGTGTAATAAATATTTTGAATATATTTTTGAGCTGCCATGCCATCAGCTCACGCGA
259 CCAACATACTGTGTAACAAATATTAAGAAAATATTTTT-AGCTGCCATGCCATCAGCTCACGCGA
3335509 TTTTTTATC
323 TTTTTTATC
3335518 GTGT
1 GTGT
3335522 GTGATATACG
Statistics
Matches: 278, Mismatches: 50, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
326 49 0.18
327 105 0.38
328 32 0.12
329 52 0.19
330 28 0.10
331 12 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (331 bp):
GTGTAATAATTATATATTTCAACATAACGTATAATAACTAAATATTTAATAAAACGTATAACAAC
TACATTTTTAACATGACATGTAACAACTAAATTTTCAACATGACGTATAATAAATACATTTTCAA
CATGATATATAACAATCATTTTCAACTTGACGTATAACAACTAAATTTTAAAATATAACATGTAA
CATTACATTTTTCAACATGACGTTAACAACATTTTTTGCACAAAAAAATAACAATAACATTTCCC
AACATACTGTGTAACAAATATTAAGAAAATATTTTTAGCTGCCATGCCATCAGCTCACGCGATTT
TTTATC
Found at i:3337335 original size:13 final size:13
Alignment explanation
Indices: 3337317--3337344 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3337307 AATAGTTTTA
3337317 TCCTTTTAATTGG
1 TCCTTTTAATTGG
3337330 TCCTTTTAATTGG
1 TCCTTTTAATTGG
3337343 TC
1 TC
3337345 AGCTCGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.54
Consensus pattern (13 bp):
TCCTTTTAATTGG
Found at i:3341446 original size:3 final size:3
Alignment explanation
Indices: 3341438--3341463 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3341428 TGCCATGAAT
3341438 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
3341464 TTTTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3357179 original size:22 final size:22
Alignment explanation
Indices: 3357151--3357194 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3357141 TAATTAAAAT
*
3357151 TTTTATTTATAAATTA-AATAAA
1 TTTTATTAAT-AATTATAATAAA
3357173 TTTTATTAATAATTATAATAAA
1 TTTTATTAATAATTATAATAAA
3357195 AAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTATTAATAATTATAATAAA
Found at i:3360501 original size:86 final size:86
Alignment explanation
Indices: 3360347--3360537 Score: 220
Period size: 86 Copynumber: 2.2 Consensus size: 86
3360337 ATAAATGAGG
* * * * * * ** * * **
3360347 TGTGAGTTTTCTGAATATATTTTAGAAGAATAAATAAGGAATGACTTATTTTAAGTTTATCTTGA
1 TGTGAGTTTTCTAAATATAATCTAAAAGAATAAACAAGGAATGACCTATGGTAAATTTACCTCAA
* *
3360412 AATCCAAAAGAGTAAACAAGT
66 AATCCAAAAAAGTAAACAAAT
* *
3360433 TGTGAGTTTTTTAAATATAATCTAAAAGAATAAACAAGGTATGACCTATGGTAAATTTACCTCAA
1 TGTGAGTTTTCTAAATATAATCTAAAAGAATAAACAAGGAATGACCTATGGTAAATTTACCTCAA
3360498 AATCCAAAAAAGTAAACAAAT
66 AATCCAAAAAAGTAAACAAAT
* *
3360519 TATGAGTTTCCTAAATATA
1 TGTGAGTTTTCTAAATATA
3360538 TTATAAGTCT
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (86 bp):
TGTGAGTTTTCTAAATATAATCTAAAAGAATAAACAAGGAATGACCTATGGTAAATTTACCTCAA
AATCCAAAAAAGTAAACAAAT
Found at i:3362030 original size:16 final size:15
Alignment explanation
Indices: 3362011--3362102 Score: 66
Period size: 15 Copynumber: 6.1 Consensus size: 15
3362001 TGAAAACTAA
3362011 TAAATAATAAATAAAT
1 TAAA-AATAAATAAAT
3362027 TAAAAAATAACATCAAAT
1 T-AAAAATAA-AT-AAAT
* * * *
3362045 T-AAAGTAACTCACT
1 TAAAAATAAATAAAT
*
3362059 TAAAAATAAATTAAT
1 TAAAAATAAATAAAT
*
3362074 T-ATAA-AAAT-AAT
1 TAAAAATAAATAAAT
3362086 TAAAAATAAATAAAT
1 TAAAAATAAATAAAT
3362101 TA
1 TA
3362103 TAATTGAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 10 0.17
15 16 0.27
16 12 0.20
17 5 0.08
18 5 0.08
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (15 bp):
TAAAAATAAATAAAT
Found at i:3364814 original size:22 final size:21
Alignment explanation
Indices: 3364767--3364815 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
3364757 TAAATAAAAT
* * *
3364767 TTTATAATTAATAATTGACTA
1 TTTATTATTAATAAATAACTA
*
3364788 ATTATTATTAATCAAATAACTA
1 TTTATTATTAAT-AAATAACTA
3364810 TTTATT
1 TTTATT
3364816 GTTTTATCTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATTATTAATAAATAACTA
Found at i:3367566 original size:16 final size:15
Alignment explanation
Indices: 3367542--3367585 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
3367532 AATCATGTCC
3367542 TTTACAAAAAAAAAAGT
1 TTTA-AAAAAAAAAA-T
3367559 TTTAAAAAATAAAAAT
1 TTTAAAAAA-AAAAAT
3367575 TTTAACAAAAA
1 TTTAA-AAAAA
3367586 CTGATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (15 bp):
TTTAAAAAAAAAAAT
Found at i:3367567 original size:17 final size:16
Alignment explanation
Indices: 3367542--3367585 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3367532 AATCATGTCC
*
3367542 TTTACAAAAAAAAAAGT
1 TTTA-AAAAAAAAAAAT
*
3367559 TTTAAAAAATAAAAAT
1 TTTAAAAAAAAAAAAT
3367575 TTTAACAAAAA
1 TTTAA-AAAAA
3367586 CTGATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (16 bp):
TTTAAAAAAAAAAAAT
Found at i:3368885 original size:25 final size:25
Alignment explanation
Indices: 3368857--3368955 Score: 81
Period size: 25 Copynumber: 4.0 Consensus size: 25
3368847 TCACCCTTTT
* **
3368857 CCTGTTGGCTCGCGCGCCTCGTCTG
1 CCTGTTGGCCCGCGCGCCGAGTCTG
* *
3368882 CCTGCTGGCCCGCTCGCCGAGTCTG
1 CCTGTTGGCCCGCGCGCCGAGTCTG
* * * *
3368907 CCTGTTGGCCCGTGTGCCCAGTCTA
1 CCTGTTGGCCCGCGCGCCGAGTCTG
* * * *
3368932 CTTGCTGGCCCGCGCACCCAGTCT
1 CCTGTTGGCCCGCGCGCCGAGTCT
3368956 ACTTTCGAGT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.05, C:0.41, G:0.29, T:0.24
Consensus pattern (25 bp):
CCTGTTGGCCCGCGCGCCGAGTCTG
Found at i:3373686 original size:38 final size:38
Alignment explanation
Indices: 3373632--3373705 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
3373622 ACTTGGTCGC
3373632 AAAGATGATGAATGAGACTCCGGTGAAATTAACAAATA
1 AAAGATGATGAATGAGACTCCGGTGAAATTAACAAATA
* * * *
3373670 AAAGATGATGATTGAGATTCTGGTGAAATTAGCAAA
1 AAAGATGATGAATGAGACTCCGGTGAAATTAACAAA
3373706 ACTATTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (38 bp):
AAAGATGATGAATGAGACTCCGGTGAAATTAACAAATA
Found at i:3381049 original size:2 final size:2
Alignment explanation
Indices: 3381042--3381083 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3381032 GGTATGTATG
3381042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3381084 AATGATTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3388585 original size:42 final size:42
Alignment explanation
Indices: 3388517--3388597 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
3388507 TCATTTATTT
3388517 ATTTATTTATTTATCTTGATTCGACCTAACAAAATCACTCTC
1 ATTTATTTATTTATCTTGATTCGACCTAACAAAATCACTCTC
*
3388559 ATTTATTTATTTATCTT-ATTTTGACCTAACAAAATCACT
1 ATTTATTTATTTATCTTGA-TTCGACCTAACAAAATCACT
3388598 AGACGTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.46
Consensus pattern (42 bp):
ATTTATTTATTTATCTTGATTCGACCTAACAAAATCACTCTC
Found at i:3389416 original size:17 final size:17
Alignment explanation
Indices: 3389383--3389430 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3389373 AATTAAAAAT
3389383 ATTTTATTAATTATTTA
1 ATTTTATTAATTATTTA
*
3389400 ATTTTTTTATATT-TTTA
1 ATTTTATTA-ATTATTTA
* *
3389417 ATATAATTAATTAT
1 ATTTTATTAATTAT
3389431 ATTATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATTAATTATTTA
Found at i:3389426 original size:26 final size:25
Alignment explanation
Indices: 3389389--3389437 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3389379 AAATATTTTA
* * *
3389389 TTAATTATTTAATTTTTTTATATTT
1 TTAATTAATTAATTATATTATATTT
3389414 TTAATATAATTAATTATATTATAT
1 TTAAT-TAATTAATTATATTATAT
3389438 ATAATTAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAATTAATTAATTATATTATATTT
Found at i:3389840 original size:160 final size:159
Alignment explanation
Indices: 3389577--3389889 Score: 536
Period size: 160 Copynumber: 2.0 Consensus size: 159
3389567 AATCTTTGGA
3389577 ATATATATATATCACTTTCTATTCTCTTTTTTTGAATAAGTTTGGAATATTTACTTTTCAATTCA
1 ATATATATATATCACTTTCTATTCTCTTTTTTTGAATAAGTTTGGAATATTTACTTTTCAATTCA
* *
3389642 TATATTTTTTTAAACCTCATTTTTATGAATTACAATAAATCATTTTTATACTCCCTTTGTCCTAT
66 TATATTTTTTTAAACCTCATTTTTATGAATTACAATAAATCAATGTTATACTCCCTTTGTCCTAT
3389707 TTTGTTTATCCTTTATTGATTTTATATAT
131 TTTGTTTATCCTTTATTGATTTTATATAT
* * *
3389736 ATATATATATATTCACTTTTTATTTTCTTTTTTTGCATAAGTTTGGAATATTTACTTTTCAATTC
1 ATATATATATA-TCACTTTCTATTCTCTTTTTTTGAATAAGTTTGGAATATTTACTTTTCAATTC
* * **
3389801 TTATATTTTTTTAAAGCTGGTTTTTATGAATTACAATAAATCAATGTTATACTCCCTTTGTCCTA
65 ATATATTTTTTTAAACCTCATTTTTATGAATTACAATAAATCAATGTTATACTCCCTTTGTCCTA
3389866 TTTTGTTTATCCTTTATTGATTTT
130 TTTTGTTTATCCTTTATTGATTTT
3389890 TTTGATTAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
159 11 0.08
160 133 0.92
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (159 bp):
ATATATATATATCACTTTCTATTCTCTTTTTTTGAATAAGTTTGGAATATTTACTTTTCAATTCA
TATATTTTTTTAAACCTCATTTTTATGAATTACAATAAATCAATGTTATACTCCCTTTGTCCTAT
TTTGTTTATCCTTTATTGATTTTATATAT
Found at i:3392493 original size:22 final size:22
Alignment explanation
Indices: 3392452--3392517 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
3392442 GATAAATATG
* **
3392452 TTATATTTATTATTTTATTTAA
1 TTATATTTTTTATTACATTTAA
*
3392474 TTATATTTTTTATTCCATTT-A
1 TTATATTTTTTATTACATTTAA
*
3392495 TTATGATTTTTTTTTACATTTAA
1 TTAT-ATTTTTTATTACATTTAA
3392518 GTATTTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.14
22 31 0.84
23 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATATTTTTTATTACATTTAA
Done.