Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 17 of 32
Found at i:9012154 original size:34 final size:33
Alignment explanation
Indices: 9012092--9012179 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
9012082 TAAGTAAAAT
* * *
9012092 AAAATAAAATATATAATATAAAAAATTATATTAAA
1 AAAATAAAA-ATAAAATATATAAAATTATAAT-AA
* *
9012127 AAAATAAAAATAAAATATATTAGATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
* * *
9012160 TACATGAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
9012180 GACATTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 19 0.42
34 17 0.38
35 9 0.20
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:9012450 original size:15 final size:15
Alignment explanation
Indices: 9012410--9012451 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
9012400 TAACATTGGT
* *
9012410 TGCAATCACAATATC
1 TGCAATCACATTATA
9012425 TGCAATCACATTATA
1 TGCAATCACATTATA
*
9012440 TGTAATCACATT
1 TGCAATCACATT
9012452 GTATTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (15 bp):
TGCAATCACATTATA
Found at i:9013310 original size:91 final size:91
Alignment explanation
Indices: 9013145--9013325 Score: 317
Period size: 91 Copynumber: 2.0 Consensus size: 91
9013135 CAGATGGGAA
* * *
9013145 GTTGAACTGACAATGAGACGCTTTCCACCAATCGACCTTGCATCATCTGCCAATTCACCACGTCG
1 GTTGAACTAACAATGAGACGCCTTCCACCAATCGACCTTGCATCATCTGCCAATTCACCACGTCC
*
9013210 CTTGTATATAAATACCCACAAACATG
66 CTTGCATATAAATACCCACAAACATG
*
9013236 GTTGAGCTAACAATGAGACGCCTTCCACCAATCGACCTTGCATCATCTGCCAATTCACCACGTCC
1 GTTGAACTAACAATGAGACGCCTTCCACCAATCGACCTTGCATCATCTGCCAATTCACCACGTCC
9013301 CTTGCATATAAATACCCACAAACAT
66 CTTGCATATAAATACCCACAAACAT
9013326 AGCTTCTTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (91 bp):
GTTGAACTAACAATGAGACGCCTTCCACCAATCGACCTTGCATCATCTGCCAATTCACCACGTCC
CTTGCATATAAATACCCACAAACATG
Found at i:9014640 original size:27 final size:27
Alignment explanation
Indices: 9014610--9014712 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 27
9014600 TTGAACAACA
* *
9014610 AAATTTTTAACATGACGTGTAATAATT
1 AAATTTTCAACATGACATGTAATAATT
* *
9014637 AAATTCTCATCATGACATGTAATAATT
1 AAATTTTCAACATGACATGTAATAATT
* * * *
9014664 AAATCTTCAACATAACATAG-AACAACT
1 AAATTTTCAACATGACAT-GTAATAATT
* *
9014691 ATATTTTTCAACATGTCATGTA
1 A-AATTTTCAACATGACATGTA
9014713 GTAACGAAAG
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
27 44 0.75
28 15 0.25
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (27 bp):
AAATTTTCAACATGACATGTAATAATT
Found at i:9014780 original size:27 final size:27
Alignment explanation
Indices: 9014738--9014856 Score: 123
Period size: 27 Copynumber: 4.4 Consensus size: 27
9014728 ATAACTATAT
*
9014738 TTTTCAACATGGTGTATAATAATTAAA
1 TTTTCAACATGATGTATAATAATTAAA
* *
9014765 TTTTAAACATGATGTATAACAATTAAA
1 TTTTCAACATGATGTATAATAATTAAA
* *
9014792 TTTTCAACAT-AGTGTGTAATAATTATAT
1 TTTTCAACATGA-TGTATAATAATTA-AA
* ** * *
9014820 TTTTCAACATAACATACAACAATTAAA
1 TTTTCAACATGATGTATAATAATTAAA
9014847 TTTTCAACAT
1 TTTTCAACAT
9014857 AACATATAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 55 0.72
28 19 0.25
29 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (27 bp):
TTTTCAACATGATGTATAATAATTAAA
Found at i:9014858 original size:27 final size:27
Alignment explanation
Indices: 9014752--9014993 Score: 169
Period size: 28 Copynumber: 8.8 Consensus size: 27
9014742 CAACATGGTG
* * * **
9014752 TATAATAATTAAATTTTAAACATGATG
1 TATAACAATTAAATTTTCAACATAACA
***
9014779 TATAACAATTAAATTTTCAACATAGTG
1 TATAACAATTAAATTTTCAACATAACA
* * *
9014806 TGTAATAATTATATTTTTCAACATAACA
1 TATAACAATTA-AATTTTCAACATAACA
*
9014834 TACAACAATTAAATTTTCAACATAACA
1 TATAACAATTAAATTTTCAACATAACA
* * *
9014861 TATAACAATTACATTTTTTAACATATCA
1 TATAACAATTA-AATTTTCAACATAACA
***
9014889 CGCAACAAATTAAATTTTCAACATAACA
1 TATAAC-AATTAAATTTTCAACATAACA
* * *
9014917 TATAACAATTACATTTTTTAACATATCA
1 TATAACAATTA-AATTTTCAACATAACA
** * * * **
9014945 CGTAACAAACTAAATTTTCAATATGATG
1 TATAAC-AATTAAATTTTCAACATAACA
* *
9014973 TGTAACAATTATATTTTCAAC
1 TATAACAATTAAATTTTCAAC
9014994 GTAATTTATT
Statistics
Matches: 166, Mismatches: 44, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
27 74 0.45
28 83 0.50
29 9 0.05
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (27 bp):
TATAACAATTAAATTTTCAACATAACA
Found at i:9014882 original size:23 final size:23
Alignment explanation
Indices: 9014856--9014942 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
9014846 ATTTTCAACA
9014856 TAACATATAACAATTACATTTTT
1 TAACATATAACAATTACATTTTT
* *
9014879 TAACATATCACGCAACAAATTAAATTTTCAACA
1 TAACATAT-----AAC-AATTACATTTT----T
9014912 TAACATATAACAATTACATTTTT
1 TAACATATAACAATTACATTTTT
9014935 TAACATAT
1 TAACATAT
9014943 CACGTAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
23 16 0.32
27 10 0.20
28 6 0.12
29 10 0.20
33 8 0.16
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (23 bp):
TAACATATAACAATTACATTTTT
Found at i:9014989 original size:56 final size:56
Alignment explanation
Indices: 9014785--9014965 Score: 247
Period size: 56 Copynumber: 3.2 Consensus size: 56
9014775 GATGTATAAC
*** * * * * * **
9014785 AATTAAATTTTCAACATAGTGTGTAATAATTATATTTTTCAACATAACATACAAC-
1 AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGCAACA
9014840 AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGCAACA
1 AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGCAACA
*
9014896 AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGTAACA
1 AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGCAACA
*
9014952 AACTAAATTTTCAA
1 AATTAAATTTTCAA
9014966 TATGATGTGT
Statistics
Matches: 113, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
55 45 0.40
56 68 0.60
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (56 bp):
AATTAAATTTTCAACATAACATATAACAATTACATTTTTTAACATATCACGCAACA
Found at i:9016954 original size:24 final size:24
Alignment explanation
Indices: 9016921--9016966 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9016911 CCGACCTCGC
*
9016921 CCACTTTGCCTACCG-TACCAAGGG
1 CCACTCTGCCT-CCGCTACCAAGGG
9016945 CCACTCTGCCTCCGCTACCAAG
1 CCACTCTGCCTCCGCTACCAAG
9016967 CATGCCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (24 bp):
CCACTCTGCCTCCGCTACCAAGGG
Found at i:9025097 original size:26 final size:26
Alignment explanation
Indices: 9025078--9025131 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
9025068 TTTATTTTTA
9025078 AAAATTAAATTAAAATTTTAATTATAT
1 AAAA-TAAATTAAAATTTTAATTATAT
9025105 AAAATAATATTTAAAATTTTAATTATA
1 AAAATAA-A-TTAAAATTTTAATTATA
9025132 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 3 0.12
27 5 0.20
28 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATAAATTAAAATTTTAATTATAT
Found at i:9025109 original size:16 final size:16
Alignment explanation
Indices: 9025088--9025131 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 16
9025078 AAAATTAAAT
9025088 TAAAATTTTAATTATA
1 TAAAATTTTAATTATA
*
9025104 TAAAA---TAA-TATT
1 TAAAATTTTAATTATA
9025116 TAAAATTTTAATTATA
1 TAAAATTTTAATTATA
9025132 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 8
0.69 0.06 0.25
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
15 3 0.14
16 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATTTTAATTATA
Found at i:9033781 original size:29 final size:29
Alignment explanation
Indices: 9033699--9033814 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 29
9033689 GTAATGTTAT
*
9033699 AATTAAAAT-AAA-ATATATAATAT-AAG
1 AATTAAAATAAAATATATATAATATAAAA
9033725 AATTAGAAA-ATAAA-ATA-A-AATATAAAA
1 AATTA-AAATA-AAATATATATAATATAAAA
**
9033752 AATTAAAAT-TTATATAATATAAGTA-AAAA
1 AATTAAAATAAAATAT-ATATAA-TATAAAA
9033781 AATTAAAATAAAATATATATAATATAAAA
1 AATTAAAATAAAATATATATAATATAAAA
9033810 AATTA
1 AATTA
9033815 TATTAAACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
25 1 0.01
26 15 0.21
27 12 0.16
28 9 0.12
29 30 0.41
30 6 0.08
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (29 bp):
AATTAAAATAAAATATATATAATATAAAA
Found at i:9033839 original size:34 final size:33
Alignment explanation
Indices: 9033801--9033873 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
9033791 AAATATATAT
*
9033801 AATATAAAAAATTATATTAAACAAATGAAAATAA
1 AATATAAAAAATTATAAT-AACAAATGAAAATAA
** * *
9033835 AATATCTAAGATTATAATAAGAAATGAAAATAA
1 AATATAAAAAATTATAATAACAAATGAAAATAA
9033868 AATATA
1 AATATA
9033874 TGACATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 19 0.58
34 14 0.42
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.27
Consensus pattern (33 bp):
AATATAAAAAATTATAATAACAAATGAAAATAA
Found at i:9034100 original size:15 final size:16
Alignment explanation
Indices: 9034077--9034110 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9034067 ATTTTCGTTA
*
9034077 TAATTACATTAC-TTG
1 TAATCACATTACATTG
9034092 TAATCACATTACATTG
1 TAATCACATTACATTG
9034108 TAA
1 TAA
9034111 AGTATCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (16 bp):
TAATCACATTACATTG
Found at i:9034382 original size:27 final size:27
Alignment explanation
Indices: 9034352--9034433 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
9034342 ATAATATGAG
9034352 AAATTATATTAAGAAATAAAATTTATA
1 AAATTATATTAAGAAATAAAATTTATA
* * *
9034379 AAATTATAATATGAAATGAAA---ATA
1 AAATTATATTAAGAAATAAAATTTATA
* *
9034403 AAA-TATATATAAGAGATAATATTATATA
1 AAATTATAT-TAAGAAATAAAATT-TATA
9034431 AAA
1 AAA
9034434 ATAAAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
23 4 0.10
24 14 0.33
27 18 0.43
28 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (27 bp):
AAATTATATTAAGAAATAAAATTTATA
Found at i:9034435 original size:34 final size:34
Alignment explanation
Indices: 9034330--9034439 Score: 95
Period size: 34 Copynumber: 3.3 Consensus size: 34
9034320 GAAAAAAATT
*
9034330 AAAATAAAATATATAATATGAG--AA-ATTATATTA
1 AAAATAAAATATAT-ATAAGAGATAATATTATA-TA
* * * * *
9034363 AGAAATAAAAT-T-TATAAAATTATAATATGAAATG
1 A-AAATAAAATATATATAAGA-GATAATATTATATA
9034397 AAAATAAAATATATATAAGAGATAATATTATATA
1 AAAATAAAATATATATAAGAGATAATATTATATA
9034431 AAAATAAAA
1 AAAATAAAA
9034440 AATTAATAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
31 4 0.07
32 1 0.02
33 11 0.19
34 33 0.56
35 10 0.17
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (34 bp):
AAAATAAAATATATATAAGAGATAATATTATATA
Found at i:9034457 original size:67 final size:67
Alignment explanation
Indices: 9034325--9034457 Score: 148
Period size: 67 Copynumber: 2.0 Consensus size: 67
9034315 TAAAAGAAAA
* * * * *
9034325 AAATTAAAATAAAATATATAATATGAGAAATTATATTAAGAAATAAAATTTATAAAATTATAATA
1 AAATGAAAATAAAATATATAATAAGAGAAATTATATTAAGAAATAAAAATTATAAAATAAAAATA
9034390 TG
66 TG
*
9034392 AAATGAAAATAAAATATAT-ATAAGAGATAA-TATTATATAA-AAATAAAAAATTA-ATAATAAA
1 AAATGAAAATAAAATATATAATAAGAGA-AATTA-TAT-TAAGAAAT-AAAAATTATAAAATAAA
9034453 AATAT
62 AATAT
9034458 AAAAATATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
66 9 0.16
67 37 0.66
68 10 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (67 bp):
AAATGAAAATAAAATATATAATAAGAGAAATTATATTAAGAAATAAAAATTATAAAATAAAAATA
TG
Found at i:9034464 original size:14 final size:14
Alignment explanation
Indices: 9034426--9034464 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
9034416 AGATAATATT
9034426 ATATAAAAATAAAA
1 ATATAAAAATAAAA
*
9034440 A-ATTAATAATAAAA
1 ATA-TAAAAATAAAA
9034454 ATATAAAAATA
1 ATATAAAAATA
9034465 TATTAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATATAAAAATAAAA
Found at i:9034913 original size:16 final size:17
Alignment explanation
Indices: 9034888--9034921 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9034878 TATATGATGA
9034888 TTAAAATTTATTA-ATT
1 TTAAAATTTATTATATT
*
9034904 TTAAATTTTATTATATT
1 TTAAAATTTATTATATT
9034921 T
1 T
9034922 GATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAAATTTATTATATT
Found at i:9034982 original size:25 final size:25
Alignment explanation
Indices: 9034954--9035001 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
9034944 TTTTATTTCA
9034954 AATTTAAATAA-TATAATTATATTTT
1 AATTT-AATAATTATAATTATATTTT
*
9034979 AATTTAATAATTTTAATTATATT
1 AATTTAATAATTATAATTATATT
9035002 AATCATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTTAATAATTATAATTATATTTT
Found at i:9034991 original size:33 final size:33
Alignment explanation
Indices: 9034937--9035000 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
9034927 ATATTAATAT
* *
9034937 TTATATTTTTTATTTCAAATTTAAATAATATAA
1 TTATATTTTTAATTTAAAATTTAAATAATATAA
* *
9034970 TTATA-TTTTAATTTAATAATTTTAATTATAT
1 TTATATTTTTAATTTAA-AATTTAAATAATAT
9035001 TAATCATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 9 0.35
33 17 0.65
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
TTATATTTTTAATTTAAAATTTAAATAATATAA
Found at i:9036015 original size:3 final size:3
Alignment explanation
Indices: 9036007--9036034 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9035997 GATTAGCCTC
9036007 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9036035 ATGTGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9041562 original size:20 final size:20
Alignment explanation
Indices: 9041539--9041578 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9041529 GTAATCACCT
9041539 GATTAGATTGCTAATGAGTG
1 GATTAGATTGCTAATGAGTG
*
9041559 GATTAGATTGTTAATGAGTG
1 GATTAGATTGCTAATGAGTG
9041579 AATGGCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (20 bp):
GATTAGATTGCTAATGAGTG
Found at i:9055693 original size:29 final size:27
Alignment explanation
Indices: 9055661--9055721 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
9055651 AGAAATGCAT
9055661 CAAAACA-AAAAAAAAATGAAAAATGAAGA
1 CAAAACAGAAAAAAAAA-GAAAAAT-AA-A
* *
9055690 CAAAAGAGAGAAAAAAAGAAAAATAAA
1 CAAAACAGAAAAAAAAAGAAAAATAAA
9055717 CAAAA
1 CAAAA
9055722 TGAGAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 2 0.07
29 13 0.45
30 8 0.28
ACGTcount: A:0.77, C:0.07, G:0.11, T:0.05
Consensus pattern (27 bp):
CAAAACAGAAAAAAAAAGAAAAATAAA
Found at i:9055703 original size:28 final size:28
Alignment explanation
Indices: 9055670--9055726 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
9055660 TCAAAACAAA
9055670 AAAAAAATGAAAAATGAAGACAAAA-GAGAG
1 AAAAAAA-GAAAAAT-AA-ACAAAATGAGAG
9055700 AAAAAAAGAAAAATAAACAAAATGAGA
1 AAAAAAAGAAAAATAAACAAAATGAGA
9055727 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.23
28 6 0.23
29 7 0.27
30 7 0.27
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (28 bp):
AAAAAAAGAAAAATAAACAAAATGAGAG
Found at i:9056577 original size:142 final size:139
Alignment explanation
Indices: 9056168--9056643 Score: 659
Period size: 140 Copynumber: 3.4 Consensus size: 139
9056158 TAGAAATTTC
* *
9056168 CAAGAAACCATCTCTTATAGTATTCTTAAGATTTTATCATCAAAGAATTTTTATTTAA-TGGCGT
1 CAAGAAACCATCTCTTATAGCATTCTTGAGATTTTATCATCAAAGAATTTTTATTTAATTGG-GT
* * * *
9056232 TCTATATTCTTATCAATTTATTTATTTTATTTAATTACTTCTTTTATTAATATTTATGTAAATCC
65 TTTATATTTTTATCAATTTATTTACTTTATTTAATTA-TTTTTTTATTAATATTTATGTAAATCC
9056297 TCTCAAATTCT
129 TCTCAAATTCT
** * * ** * * *
9056308 CAAGAAGTCATCTCTAATAACATTCTTGAGAAATTATCATCAAAGAATATTTGTTTAATAGCGGT
1 CAAGAAACCATCTCTTATAGCATTCTTGAGATTTTATCATCAAAGAATTTTTATTTAATTG-GGT
9056373 TTTATATTTTTATCAATTTATTTACTTTATTTAATTATTTTTTTATTAATATTTATGTAAATCCT
65 TTTATATTTTTATCAATTTATTTACTTTATTTAATTATTTTTTTATTAATATTTATGTAAATCCT
* *
9056438 TTCAAATTTT
130 CTCAAATTCT
* * *
9056448 CAAGAAATCATCTCTTATAGCATTTTTGAGATTTTATTCATCTAAGAATTTTTATTTAATTGGGT
1 CAAGAAACCATCTCTTATAGCATTCTTGAGATTTTA-TCATCAAAGAATTTTTATTTAATTGGG-
9056513 TTTATATATTTTTATCAATTTATTTACTTTATTTAATTATTTTTTTATTAATATTTATGTAAATC
64 TTT-TATATTTTTATCAATTTATTTACTTTATTTAATTATTTTTTTATTAATATTTATGTAAATC
9056578 CTCTCAAATTCT
128 CTCTCAAATTCT
** * *
9056590 CAAGATGCCATCTCTTATAGCATTCTTGAGATGTTATCATCGAAA-AATTCTTAT
1 CAAGAAACCATCTCTTATAGCATTCTTGAGATTTTATCATC-AAAGAATTTTTAT
9056644 AAATTTTGTT
Statistics
Matches: 294, Mismatches: 36, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
140 115 0.39
141 74 0.25
142 105 0.36
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (139 bp):
CAAGAAACCATCTCTTATAGCATTCTTGAGATTTTATCATCAAAGAATTTTTATTTAATTGGGTT
TTATATTTTTATCAATTTATTTACTTTATTTAATTATTTTTTTATTAATATTTATGTAAATCCTC
TCAAATTCT
Found at i:9057462 original size:2 final size:2
Alignment explanation
Indices: 9057455--9057480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9057445 GAGGAAGCAA
9057455 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
9057481 TGAAATTTAG
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:9058741 original size:2 final size:2
Alignment explanation
Indices: 9058729--9058761 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9058719 ACTTGAATGC
*
9058729 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9058762 TTTGGCAGTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9097900 original size:26 final size:27
Alignment explanation
Indices: 9097861--9097911 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9097851 TACTAATATT
9097861 TTATTTATAATTTAAA-TATTATTATGA
1 TTATTTATAATTTAAATTATT-TTATGA
*
9097888 TTATTTAT-TTTTAAATTATTTTAT
1 TTATTTATAATTTAAATTATTTTAT
9097912 TTTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATTTATAATTTAAATTATTTTATGA
Found at i:9097942 original size:41 final size:41
Alignment explanation
Indices: 9097861--9097945 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
9097851 TACTAATATT
* *
9097861 TTATTTATAATTTAAATATTATTATGATTATTTATTTTTAAA
1 TTATTTATAATTTAAATATTATAATGATAATTTA-TTTTAAA
* *
9097903 TTATTT-TATTTTAAATATTAATAATGTATAATTTATTTAAAA
1 TTATTTATAATTTAAATATT-ATAATG-ATAATTTATTTTAAA
9097945 T
1 T
9097946 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 12 0.32
42 18 0.49
43 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (41 bp):
TTATTTATAATTTAAATATTATAATGATAATTTATTTTAAA
Found at i:9097981 original size:158 final size:157
Alignment explanation
Indices: 9097803--9098190 Score: 487
Period size: 158 Copynumber: 2.5 Consensus size: 157
9097793 TTATATTATT
*
9097803 TTTAAATATTAATATTTTATTTATAATCTAATCATTAACATTATAAAATACTAATATTTTATTTA
1 TTTAAATATTAATATTTTATTTATAAT-TAATCATTAA-ATTATAAAATAATAATATTTTATTTA
9097868 TAATTTAAATATTATTATGATTATTTATTTTTAAATTATTTTA-TTTTAAATATTAATAATGTAT
64 TAATTTAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTTAAATATTAATAATGTAT
*
9097932 AATTTATTTAAAATATTAAAAATTGAT-A
129 AATTTACTTAAAATATTAAAAATTGATCA
* * * **
9097960 GTTTAAATATTAATATTTTATTTATACTTTAATCAATAATATTA-AAAACAATAATATTCAATTT
1 -TTTAAATATTAATATTTTATTTATA-ATTAATCATTAA-ATTATAAAATAATAATATTTTATTT
* ** *
9098024 ATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTATTTTTAAATATTAATAATTTA
63 ATAATTTAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTTAAATATTAATAATGTA
* * * *
9098089 TATTTTACTTATAATATTAATAATTTATCA
128 TAATTTACTTAAAATATTAAAAATTGATCA
* * * * * *
9098119 TTTATATA-TAATATTTTATTCATAAATTAATTATTAATTTTTAAAATATTAATATTTTTATTTA
1 TTTAAATATTAATATTTTATTTAT-AATTAATCATTAAATTATAAAATAATAATA-TTTTATTTA
*
9098183 TAGTTTAA
64 TAATTTAA
9098191 TCATTAATAT
Statistics
Matches: 196, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
156 2 0.01
157 90 0.46
158 102 0.52
159 2 0.01
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (157 bp):
TTTAAATATTAATATTTTATTTATAATTAATCATTAAATTATAAAATAATAATATTTTATTTATA
ATTTAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTTAAATATTAATAATGTATAA
TTTACTTAAAATATTAAAAATTGATCA
Found at i:9098104 original size:27 final size:26
Alignment explanation
Indices: 9098057--9098133 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
9098047 ATTTATTTTT
*
9098057 ATTT-TATTTTATTTTTAAATATTAATA
1 ATTTATATTTTA-TTAT-AATATTAATA
9098084 ATTTATATTTTACTTATAATATTAATA
1 ATTTATATTTTA-TTATAATATTAATA
9098111 ATTTATCA-TTTATATATAATATT
1 ATTTAT-ATTTTAT-TATAATATT
9098134 TTATTCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.02
27 33 0.73
28 11 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTATATTTTATTATAATATTAATA
Found at i:9098172 original size:157 final size:156
Alignment explanation
Indices: 9097808--9098174 Score: 452
Period size: 157 Copynumber: 2.3 Consensus size: 156
9097798 TTATTTTTAA
* * * **
9097808 ATAT-TAATATTTTATTTAT-AATCTAATCATTAACATTATAAAATACTAATATTTTATTTATAA
1 ATATATAATATTTTATTTATAAAT-TAATCATTAA-TTTTTAAAATAATAATATTCAATTTATAA
9097871 TTTAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTAAATATTAATAATGTATAATT
64 TTTAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTAAATATTAATAATGTATAATT
*
9097936 TATTTAAAATATTAAAAATTGATAGTTT
129 TACTTAAAATATTAAAAATTGATAGTTT
* ** * * * *
9097964 AAATATTAATATTTTATTTATACTTTAATCAATAATATTAAAAACAATAATATTCAATTTATAAT
1 ATATA-TAATATTTTATTTATAAATTAATCATTAATTTTTAAAATAATAATATTCAATTTATAAT
* ** * *
9098029 TTAAATGTTATTATGATTATTTATTTTTATTTTATTTTATTTTTAAATATTAATAATTTATATTT
65 TTAAATATTATTATGATTATTTATTTTTAAATTATTTTA-TTTTAAATATTAATAATGTATAATT
* * *
9098094 TACTTATAATATTAATAATTTATCA-TTT
129 TACTTAAAATATTAAAAATTGAT-AGTTT
* * *
9098122 ATATATAATATTTTATTCATAAATTAATTATTAATTTTTAAAATATTAATATT
1 ATATATAATATTTTATTTATAAATTAATCATTAATTTTTAAAATAATAATATT
9098175 TTTATTTATA
Statistics
Matches: 175, Mismatches: 31, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
156 3 0.02
157 97 0.55
158 73 0.42
159 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (156 bp):
ATATATAATATTTTATTTATAAATTAATCATTAATTTTTAAAATAATAATATTCAATTTATAATT
TAAATATTATTATGATTATTTATTTTTAAATTATTTTATTTTAAATATTAATAATGTATAATTTA
CTTAAAATATTAAAAATTGATAGTTT
Found at i:9098191 original size:42 final size:41
Alignment explanation
Indices: 9098122--9098211 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 41
9098112 TTTATCATTT
* *
9098122 ATATATAATATTTTATTCATAAATTAATTATTAAT-TTTTAAA
1 ATAT-TAATATTTTATTCATAAATTAATCATTAATATTAT-AA
* **
9098164 ATATTAATATTTTTATTTATAGTTTAATCATTAATATTATAA
1 ATATTAATA-TTTTATTCATAAATTAATCATTAATATTATAA
9098206 ATATTA
1 ATATTA
9098212 TAAATACTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.12
42 33 0.80
43 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (41 bp):
ATATTAATATTTTATTCATAAATTAATCATTAATATTATAA
Found at i:9098504 original size:27 final size:26
Alignment explanation
Indices: 9098477--9098526 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
9098467 AATTTTTAAT
9098477 TTAA-ATTTCACTTAATAATTTAAAAA
1 TTAATATTTCA-TTAATAATTTAAAAA
*
9098503 TTAATATTTCATTTATAATTTAAA
1 TTAATATTTCATTAATAATTTAAA
9098527 TATCTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATTTCATTAATAATTTAAAAA
Found at i:9098536 original size:16 final size:16
Alignment explanation
Indices: 9098515--9098545 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9098505 AATATTTCAT
*
9098515 TTATAATTTAAATATC
1 TTATAATTAAAATATC
9098531 TTATAATTAAAATAT
1 TTATAATTAAAATAT
9098546 GAAAATATCA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAATTAAAATATC
Found at i:9098584 original size:21 final size:22
Alignment explanation
Indices: 9098558--9098599 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
9098548 AAATATCAAT
9098558 AATATTTAATTTT-TAA-TTTAA
1 AATA-TTAATTTTATAAGTTTAA
9098579 AATATTAATTTTATAAGTTTA
1 AATATTAATTTTATAAGTTTA
9098600 TGTTTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATTAATTTTATAAGTTTAA
Found at i:9102934 original size:49 final size:49
Alignment explanation
Indices: 9102862--9102960 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
9102852 TGGTAATTTG
9102862 AGCTTATCAAAAGTTTATAGGCAATCACAATCATCACTATCTTCCAGGC
1 AGCTTATCAAAAGTTTATAGGCAATCACAATCATCACTATCTTCCAGGC
9102911 AGCTTATCAAAAGTTTATAGGCAATCACAATCATCACTATCTTCCAGGC
1 AGCTTATCAAAAGTTTATAGGCAATCACAATCATCACTATCTTCCAGGC
9102960 A
1 A
9102961 TTAACATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.28
Consensus pattern (49 bp):
AGCTTATCAAAAGTTTATAGGCAATCACAATCATCACTATCTTCCAGGC
Found at i:9107114 original size:2 final size:2
Alignment explanation
Indices: 9107107--9107144 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9107097 CTTCTTCCTA
9107107 TC TC TC TC TC TC TC 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
9107145 CTTTTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9118895 original size:2 final size:2
Alignment explanation
Indices: 9118888--9118922 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9118878 GATATGAGTT
*
9118888 TA 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 TA T
9118923 GTTTATGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9119491 original size:16 final size:16
Alignment explanation
Indices: 9119467--9119505 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
9119457 GCTTTGTTGT
*
9119467 AGGGGTGGCAATAAAC
1 AGGGTTGGCAATAAAC
9119483 AGGGTTGGCAATAAAC
1 AGGGTTGGCAATAAAC
9119499 AGGGTTG
1 AGGGTTG
9119506 ATAGTAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.38, T:0.18
Consensus pattern (16 bp):
AGGGTTGGCAATAAAC
Found at i:9129425 original size:105 final size:103
Alignment explanation
Indices: 9129227--9129430 Score: 273
Period size: 105 Copynumber: 2.0 Consensus size: 103
9129217 ATTTTTTAAC
* * ** *
9129227 TGTAAACTTTATCGCTCTTATTTTGGTTGTAATGTTATTGTTGTTTGGTTGCAAGCTTTATCGCT
1 TGTAAACTTTATCACTCTTACTTTGGTTGTAACATTATTGTTGTTTGGTCGCAAGCTTTATCGCT
*
9129292 CATTCTTGGACCATACAATTCATTACTCATATTTTAGT
66 CATTCTTGGACCATACAATTCATCACTCATATTTTAGT
* * *
9129330 TGTAAGCTTTATCACTTTTACTTTGGTTGTAACATTATTGTTGTATTTGGTCGCAAGCTTTATTG
1 TGTAAACTTTATCACTCTTACTTTGGTTGTAACATTATTGTTG--TTTGGTCGCAAGCTTTATCG
* * * *
9129395 CTCATTTTTTGACCATATAATTTATCACTCATATTT
64 CTCATTCTTGGACCATACAATTCATCACTCATATTT
9129431 CAACCACAAG
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
103 37 0.43
105 49 0.57
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (103 bp):
TGTAAACTTTATCACTCTTACTTTGGTTGTAACATTATTGTTGTTTGGTCGCAAGCTTTATCGCT
CATTCTTGGACCATACAATTCATCACTCATATTTTAGT
Found at i:9129460 original size:105 final size:103
Alignment explanation
Indices: 9129248--9129466 Score: 231
Period size: 105 Copynumber: 2.1 Consensus size: 103
9129238 TCGCTCTTAT
** *
9129248 TTTGGTTGTAATGTTATTGTTGTTTGGTTGCAAGCTTTATCGCTCATTCTTGGACCATACAATTC
1 TTTGGTTGTAACATTATTGTTGTTTGGTCGCAAGCTTTATCGCTCATTCTTGGACCATACAATTC
* * ***** * ** *
9129313 ATTACTCATATTTTAGTTGTAAGCTTTATCACTTTTAC
66 ATCACTCATATTTCAACCACAAGCTTTAACACTCATAA
* * * *
9129351 TTTGGTTGTAACATTATTGTTGTATTTGGTCGCAAGCTTTATTGCTCATTTTTTGACCATATAAT
1 TTTGGTTGTAACATTATTGTTG--TTTGGTCGCAAGCTTTATCGCTCATTCTTGGACCATACAAT
* *
9129416 TTATCACTCATATTTCAACCACAAGCTTTAACTCTCATAA
64 TCATCACTCATATTTCAACCACAAGCTTTAACACTCATAA
*
9129456 TTTGGATGTAA
1 TTTGGTTGTAA
9129467 TGATATTATG
Statistics
Matches: 93, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
103 20 0.22
105 73 0.78
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (103 bp):
TTTGGTTGTAACATTATTGTTGTTTGGTCGCAAGCTTTATCGCTCATTCTTGGACCATACAATTC
ATCACTCATATTTCAACCACAAGCTTTAACACTCATAA
Found at i:9130400 original size:44 final size:44
Alignment explanation
Indices: 9130351--9130442 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
9130341 TTCACTAGTC
* *
9130351 CTTCCTACTCGCATTTTATTAGAAAGAGAAGATGTAACAATGTT
1 CTTCCTACTCGCATTTTATTAAAAAGAGAAGATGTAACAATATT
* * *
9130395 CTTCCTACTTGCATTTTCTTAAAAAGAGAAGATGTAGCAATATT
1 CTTCCTACTCGCATTTTATTAAAAAGAGAAGATGTAACAATATT
9130439 CTTC
1 CTTC
9130443 TTCTTTTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (44 bp):
CTTCCTACTCGCATTTTATTAAAAAGAGAAGATGTAACAATATT
Found at i:9130593 original size:17 final size:17
Alignment explanation
Indices: 9130552--9130589 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
9130542 AGCATATAAG
9130552 TATTCATGCATTATCAT
1 TATTCATGCATTATCAT
**
9130569 TGCTCATGCATTA-CAT
1 TATTCATGCATTATCAT
9130585 TATTC
1 TATTC
9130590 CATGTTTGTT
Statistics
Matches: 17, Mismatches: 4, Indels: 1
0.77 0.18 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (17 bp):
TATTCATGCATTATCAT
Found at i:9130988 original size:2 final size:2
Alignment explanation
Indices: 9130981--9131020 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9130971 TGTATGTATG
9130981 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
9131021 CACGAGCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9131117 original size:2 final size:2
Alignment explanation
Indices: 9131110--9131139 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9131100 TTCCCAAATC
9131110 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
9131140 AGCGTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9131637 original size:49 final size:49
Alignment explanation
Indices: 9131557--9131670 Score: 203
Period size: 49 Copynumber: 2.3 Consensus size: 49
9131547 AGCATTACGA
9131557 GTTCCCCCCTGCGGCCCTGCCCCCCCTCCTCCGGCTCCCACGAGTCCCG
1 GTTCCCCCCTGCGGCCCTGCCCCCCCTCCTCCGGCTCCCACGAGTCCCG
9131606 GTTCCCCCCTGCGGCCCTGCCCGCCCC-CCTCCGGCTCCCACGAGTCCCG
1 GTTCCCCCCTGCGGCCCTGCCC-CCCCTCCTCCGGCTCCCACGAGTCCCG
*
9131655 GTTCCCCCATGCGGCC
1 GTTCCCCCCTGCGGCC
9131671 AGTCGGGCTG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
49 59 0.94
50 4 0.06
ACGTcount: A:0.04, C:0.58, G:0.22, T:0.16
Consensus pattern (49 bp):
GTTCCCCCCTGCGGCCCTGCCCCCCCTCCTCCGGCTCCCACGAGTCCCG
Found at i:9133328 original size:16 final size:16
Alignment explanation
Indices: 9133307--9133337 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9133297 ATTCTAGAGA
9133307 AGAAATAATAGTCATC
1 AGAAATAATAGTCATC
9133323 AGAAATAATAGTCAT
1 AGAAATAATAGTCAT
9133338 ATTTTCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (16 bp):
AGAAATAATAGTCATC
Found at i:9135079 original size:18 final size:19
Alignment explanation
Indices: 9135052--9135093 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
9135042 TAAATATTGC
9135052 TTTTATTTCTT-TTCTTTTT
1 TTTTATTTCTTATT-TTTTT
9135071 TTTTA-TTCTTATTTTTTT
1 TTTTATTTCTTATTTTTTT
9135089 TTTTA
1 TTTTA
9135094 CCTTGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTATTTCTTATTTTTTT
Found at i:9153276 original size:25 final size:26
Alignment explanation
Indices: 9153219--9153269 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
9153209 TTATGACCCT
*
9153219 AAAAATTACTTTTTATATTATTTTAA
1 AAAAATTACTTTTTATATTAATTTAA
9153245 AAAAATTA-TTTTT-TATTAAATTTAA
1 AAAAATTACTTTTTATATT-AATTTAA
9153270 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
26 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AAAAATTACTTTTTATATTAATTTAA
Found at i:9165315 original size:22 final size:22
Alignment explanation
Indices: 9165284--9165334 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
9165274 TAAAATTTGA
9165284 ATTTAATTTA-AATATTAATTTT
1 ATTTAATTTATAAT-TTAATTTT
* *
9165306 TTTTATTTTATAATTTAATTTT
1 ATTTAATTTATAATTTAATTTT
9165328 ATTTAAT
1 ATTTAAT
9165335 AAGGAGATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTAATTTATAATTTAATTTT
Found at i:9165790 original size:12 final size:12
Alignment explanation
Indices: 9165775--9165800 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9165765 TGTGAACACT
9165775 TATTCAAAATGG
1 TATTCAAAATGG
9165787 TATTCAAAATGG
1 TATTCAAAATGG
9165799 TA
1 TA
9165801 CTTAATTAAT
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:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
TATTCAAAATGG
Found at i:9166280 original size:17 final size:17
Alignment explanation
Indices: 9166237--9166274 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
9166227 TCACTGGATA
9166237 ATTTTATTTACCCATTT
1 ATTTTATTTACCCATTT
*
9166254 ATTTTATTTACTCATTT
1 ATTTTATTTACCCATTT
9166271 ATTT
1 ATTT
9166275 GTTTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATTTACCCATTT
Found at i:9168420 original size:30 final size:31
Alignment explanation
Indices: 9168384--9168442 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9168374 TTCAATCAAA
*
9168384 TTTTATA-TTTTTATTTTGAATTAAATAAAT
1 TTTTATATTTTTTATTTTGAATCAAATAAAT
9168414 TTTTATATTTTTTATTTTGAATCAAATAA
1 TTTTATATTTTTTATTTTGAATCAAATAA
9168443 TTAATGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTATATTTTTTATTTTGAATCAAATAAAT
Found at i:9168697 original size:21 final size:22
Alignment explanation
Indices: 9168668--9168722 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
9168658 GTATTTTTAC
* *
9168668 TAATGATAATTATTTAATT-AT
1 TAATAATAATAATTTAATTAAT
* *
9168689 TAATAATAAAAATTTATTTAAT
1 TAATAATAATAATTTAATTAAT
9168711 TAA-AATAATAAT
1 TAATAATAATAAT
9168723 ACAAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAATAATAATAATTTAATTAAT
Found at i:9171019 original size:17 final size:18
Alignment explanation
Indices: 9170999--9171037 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9170989 AAATAGAGAA
9170999 AAAAATA-AAATGAAATT
1 AAAAATATAAATGAAATT
* *
9171016 AAAAATATAAATTATATT
1 AAAAATATAAATGAAATT
9171034 AAAA
1 AAAA
9171038 TTTTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATATAAATGAAATT
Found at i:9171076 original size:27 final size:27
Alignment explanation
Indices: 9171042--9171093 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9171032 TTAAAATTTT
*
9171042 AATTATAAAGTGTTAATATTTTAAATA
1 AATTATAAAGTCTTAATATTTTAAATA
**
9171069 AATTATAACTTCTTAATATTTTAAA
1 AATTATAAAGTCTTAATATTTTAAA
9171094 AATAAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (27 bp):
AATTATAAAGTCTTAATATTTTAAATA
Found at i:9171129 original size:17 final size:19
Alignment explanation
Indices: 9171089--9171129 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
9171079 TCTTAATATT
9171089 TTAAAAATAAAACTAGAGA
1 TTAAAAATAAAACTAGAGA
9171108 -T-AAAAT-AAACTAGA-A
1 TTAAAAATAAAACTAGAGA
9171123 TTAAAAA
1 TTAAAAA
9171130 AAATAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.05
16 9 0.45
17 9 0.45
18 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (19 bp):
TTAAAAATAAAACTAGAGA
Found at i:9171893 original size:2 final size:2
Alignment explanation
Indices: 9171886--9171934 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
9171876 TGCTTGTTGA
* *
9171886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9171928 AT AT AT A
1 AT AT AT A
9171935 GACACGCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9172574 original size:32 final size:32
Alignment explanation
Indices: 9172530--9172615 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
9172520 CTTAGAGGGT
* *
9172530 AAATATGTTTTAA-AAGATTATTTAAATAATAGA
1 AAATAT-TTTTAACAA-ATTATCTAAATAATAAA
*
9172563 AAATATTTTTAACAATTTATCTAAATAATAAA
1 AAATATTTTTAACAAATTATCTAAATAATAAA
*
9172595 AAATATTTTTAACAATTTATC
1 AAATATTTTTAACAAATTATC
9172616 AACTTCATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 41 0.84
33 8 0.16
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
AAATATTTTTAACAAATTATCTAAATAATAAA
Found at i:9187601 original size:24 final size:20
Alignment explanation
Indices: 9187571--9187616 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
9187561 ATAAGATCTC
*
9187571 TTCTCTCTCTCTAAATACTTTCT
1 TTCT-TCTCTTTAAATA-TTT-T
9187594 TTCTTCTCTTTAAATATTTT
1 TTCTTCTCTTTAAATATTTT
9187614 TTC
1 TTC
9187617 AAGTTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 11 0.50
23 4 0.18
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCTTCTCTTTAAATATTTT
Found at i:9187628 original size:23 final size:23
Alignment explanation
Indices: 9187600--9187646 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
9187590 TTCTTTCTTC
9187600 TCTTTAAATATTTTTTCAAGTTA
1 TCTTTAAATATTTTTTCAAGTTA
** *
9187623 TCTTTATTTATTTTTTTAAGTTA
1 TCTTTAAATATTTTTTCAAGTTA
9187646 T
1 T
9187647 TTTTCATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (23 bp):
TCTTTAAATATTTTTTCAAGTTA
Found at i:9188793 original size:27 final size:28
Alignment explanation
Indices: 9188749--9188803 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 28
9188739 TCTCACTGTC
9188749 CTCTCTGCTTTCTAATATA-ATATATCT
1 CTCTCTGCTTTCTAATATATATATATCT
*
9188776 CTCTCTTCTCTTCTATATATATATATAT
1 CTCTCTGCT-TTCTA-ATATATATATAT
9188804 ATATATTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 5 0.21
29 5 0.21
30 6 0.25
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (28 bp):
CTCTCTGCTTTCTAATATATATATATCT
Found at i:9196455 original size:15 final size:15
Alignment explanation
Indices: 9196421--9196457 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
9196411 AATTATTATT
*
9196421 ATATATATACTTTTA
1 ATATATATACTTTAA
*
9196436 GTATATATACTTTAA
1 ATATATATACTTTAA
9196451 ATATATA
1 ATATATA
9196458 AACATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:9197423 original size:18 final size:18
Alignment explanation
Indices: 9197402--9197437 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9197392 TAATTTTGAA
9197402 ATAAAATTAAATTAAAAT
1 ATAAAATTAAATTAAAAT
**
9197420 ATAAAATTTCATTAAAAT
1 ATAAAATTAAATTAAAAT
9197438 TTAATCAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAATTAAATTAAAAT
Found at i:9197450 original size:51 final size:52
Alignment explanation
Indices: 9197395--9197493 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 52
9197385 AATTAATTAA
*
9197395 TTTTGAAATAAAATTAAATTAAAATATAAAATTTCATTAA-AATTTAATCAG
1 TTTTGAAATAAAATTAAATTAAAACATAAAATTTCATTAATAATTTAATCAG
* *
9197446 TTTTGAAATAAAATTAAATTATAACATAAATTTTCATTAATAATTTAA
1 TTTTGAAATAAAATTAAATTAAAACATAAAATTTCATTAATAATTTAA
9197494 ATAAAAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 37 0.84
52 7 0.16
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (52 bp):
TTTTGAAATAAAATTAAATTAAAACATAAAATTTCATTAATAATTTAATCAG
Found at i:9197886 original size:30 final size:30
Alignment explanation
Indices: 9197818--9197920 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
9197808 AGAAAAATTC
* * * *
9197818 AAATAAGTTTTTATACGTTTATTAT-ATTT
1 AAATAAATTTTTATACTTTTATTTTGAGTT
*
9197847 AATTAAATTTTTATACTTTTATTTTGAGTT
1 AAATAAATTTTTATACTTTTATTTTGAGTT
* * *
9197877 AAATAAATTTATTTTA-TTTTATTTTGTGTC
1 AAATAAATTT-TTATACTTTTATTTTGAGTT
*
9197907 AAATAAGTTTTTAT
1 AAATAAATTTTTAT
9197921 GATCAATGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
29 24 0.39
30 33 0.54
31 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (30 bp):
AAATAAATTTTTATACTTTTATTTTGAGTT
Found at i:9209508 original size:14 final size:14
Alignment explanation
Indices: 9209486--9209533 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
9209476 TTTAATTAAA
9209486 TTATATTATAATAT
1 TTATATTATAATAT
* *
9209500 TTATTTTATAATAA
1 TTATATTATAATAT
*
9209514 AT-TATTATAATA-
1 TTATATTATAATAT
9209526 TTATATTA
1 TTATATTA
9209534 CAATGTAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 1 0.04
13 14 0.50
14 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATTATAATAT
Found at i:9209689 original size:25 final size:25
Alignment explanation
Indices: 9209657--9209740 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
9209647 TTACTAATTT
* * * *
9209657 ATTAAAAATATTTTATAATATTATA
1 ATTAAAAATAATATATAATATAAAA
*
9209682 ATTAAAAAAAATATATAATATAAAA
1 ATTAAAAATAATATATAATATAAAA
* *
9209707 ATTATAAAATAAAATAAAATATAAAAA
1 ATTA-AAAATAATATATAATAT-AAAA
9209734 ATTAAAA
1 ATTAAAA
9209741 TTTATATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
25 24 0.49
26 17 0.35
27 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATTAAAAATAATATATAATATAAAA
Found at i:9209705 original size:18 final size:18
Alignment explanation
Indices: 9209673--9209707 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9209663 AATATTTTAT
9209673 AATATTATAATTAAAAAA
1 AATATTATAATTAAAAAA
9209691 AATA-TATAATATAAAAA
1 AATATTATAAT-TAAAAA
9209708 TTATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATTATAATTAAAAAA
Found at i:9209718 original size:19 final size:19
Alignment explanation
Indices: 9209696--9209751 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 19
9209686 AAAAAAATAT
9209696 ATAATATAAAAATTATAAA
1 ATAATATAAAAATTATAAA
*
9209715 ATAAAAT-AAAA-TATAAA
1 ATAATATAAAAATTATAAA
* *
9209732 A-AAT-TAAAATTTATATA
1 ATAATATAAAAATTATAAA
9209749 ATA
1 ATA
9209752 CAAGAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.17
17 13 0.43
18 5 0.17
19 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATATAAAAATTATAAA
Found at i:9209741 original size:33 final size:32
Alignment explanation
Indices: 9209676--9209842 Score: 85
Period size: 34 Copynumber: 5.0 Consensus size: 32
9209666 ATTTTATAAT
* * *
9209676 ATTAT-AATTAAAAAAAATATATAATATAAAA
1 ATTATAAAATAAAAAAAATATAAAAAATAAAA
9209707 ATTATAAAATAAAATAAAATATAAAAAATTAAAA
1 ATTATAAAATAAAA-AAAATATAAAAAA-TAAAA
* * * *
9209741 TTTATATAATACAAGAAAAA-AGAATTAGAAT-AAA
1 ATTATAAAATA-AA-AAAAATATAA--AAAATAAAA
* * *
9209775 ATATGTAATATAAAAAATTATATTAAAAAAT-AAA
1 AT-TATAAAATAAAAAA-AATA-TAAAAAATAAAA
9209809 ATATATAAAATTATAATAAAAA-AT-AAAAATAAAA
1 AT-TATAAAA-TA-AA-AAAAATATAAAAAATAAAA
9209843 TATATGACAT
Statistics
Matches: 104, Mismatches: 17, Indels: 27
0.70 0.11 0.18
Matches are distributed among these distances:
31 5 0.05
32 7 0.07
33 20 0.19
34 43 0.41
35 17 0.16
36 9 0.09
37 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (32 bp):
ATTATAAAATAAAAAAAATATAAAAAATAAAA
Found at i:9209804 original size:29 final size:27
Alignment explanation
Indices: 9209687--9209842 Score: 129
Period size: 27 Copynumber: 5.7 Consensus size: 27
9209677 TTATAATTAA
9209687 AAAAAATATATAATAT-AAAAATTATAA-
1 AAAAAATA-A-AATATAAAAAATTATAAT
*
9209714 AATAAAATAAAATATAAAAAATTAAAATTT
1 AA-AAAATAAAATATAAAAAATTATAA--T
* * * * * *
9209744 ATATAATACAAGAAAAAAGAATTAGAAT
1 AAAAAATAAAATATAAAA-AATTATAAT
* ** *
9209772 AAAATATGTAATATAAAAAATTATATT
1 AAAAAATAAAATATAAAAAATTATAAT
*
9209799 AAAAAATAAAATATATAAAATTATAAT
1 AAAAAATAAAATATAAAAAATTATAAT
9209826 AAAAAATAAAA-ATAAAA
1 AAAAAATAAAATATAAAA
9209843 TATATGACAT
Statistics
Matches: 101, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
26 10 0.10
27 53 0.52
28 18 0.18
29 12 0.12
30 8 0.08
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAAATAAAATATAAAAAATTATAAT
Found at i:9209839 original size:13 final size:13
Alignment explanation
Indices: 9209784--9209842 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
9209774 AATATGTAAT
* *
9209784 ATAAAAAATTATA
1 ATAAAAAATAAAA
*
9209797 TTAAAAAATAAAA
1 ATAAAAAATAAAA
* * *
9209810 TATATAAAATTATA
1 -ATAAAAAATAAAA
9209824 ATAAAAAATAAAA
1 ATAAAAAATAAAA
9209837 ATAAAA
1 ATAAAA
9209843 TATATGACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
13 26 0.74
14 9 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:9209869 original size:33 final size:34
Alignment explanation
Indices: 9209769--9209869 Score: 84
Period size: 33 Copynumber: 3.0 Consensus size: 34
9209759 AAAGAATTAG
* * * *
9209769 AATAAAATATGTAATA-TAAAAAATTATATTAAAA
1 AATAAAATATATAAAATTATAAAA-TATATTTAAA
**
9209803 AATAAAATATATAAAATTATAATAA-A-AAATAAA
1 AATAAAATATATAAAATTATAA-AATATATTTAAA
* *
9209836 AATAAAATATATGACATT-TAAAATATATTTAAA
1 AATAAAATATATAAAATTATAAAATATATTTAAA
9209869 A
1 A
9209870 GATGATATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
31 2 0.04
32 4 0.08
33 26 0.49
34 15 0.28
35 4 0.08
36 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (34 bp):
AATAAAATATATAAAATTATAAAATATATTTAAA
Found at i:9218761 original size:68 final size:68
Alignment explanation
Indices: 9218653--9218951 Score: 314
Period size: 68 Copynumber: 4.4 Consensus size: 68
9218643 AGTATATAAA
* * **
9218653 ATATACATAATCTCCT-GCATTTATCATGCTTTTTCAATCATCTCATGTAGTATATAGAATTTAC
1 ATATACATAATCTCATGGCATTTATCATGCATACTCAATCATCTCATGTAGTATATAGAATTTAC
9218717 ATC
66 ATC
* * * * * * *
9218720 ATATACATAACCTCATGGCATTCATCATGCTTTCTCAATCATCTTATGTAGTATATAAAATATAC
1 ATATACATAATCTCATGGCATTTATCATGCATACTCAATCATCTCATGTAGTATATAGAATTTAC
9218785 ATC
66 ATC
* * * * * *
9218788 ATATATATAATCTCATGGCATTTATCATGCATACTTAATCACCTCATATTA-TATATGGAATGTA
1 ATATACATAATCTCATGGCATTTATCATGCATACTCAATCATCTCAT-GTAGTATATAGAATTTA
9218852 CATC
65 CATC
* *** ** * * * * *
9218856 ATATACATAATCTTATAATATACATCATGCATACTTAATCATCTCATATGGTATATGGAAGTTAC
1 ATATACATAATCTCATGGCATTTATCATGCATACTCAATCATCTCATGTAGTATATAGAATTTAC
9218921 ATC
66 ATC
*
9218924 ATATACATAATCTTATGGCATTTATCAT
1 ATATACATAATCTCATGGCATTTATCAT
9218952 ACCGAATATA
Statistics
Matches: 193, Mismatches: 36, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
67 15 0.08
68 176 0.91
69 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (68 bp):
ATATACATAATCTCATGGCATTTATCATGCATACTCAATCATCTCATGTAGTATATAGAATTTAC
ATC
Found at i:9220206 original size:17 final size:17
Alignment explanation
Indices: 9220180--9220221 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
9220170 GGATTCAATA
* *
9220180 AAAATATAAAAAAAATC
1 AAAATCTAAAAAAAACC
*
9220197 AAAATCT-AAAAGAACC
1 AAAATCTAAAAAAAACC
9220213 AAAATCTAA
1 AAAATCTAA
9220222 TTTTTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAATCTAAAAAAAACC
Found at i:9225452 original size:47 final size:47
Alignment explanation
Indices: 9225391--9225485 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
9225381 ATAACTCTCT
*
9225391 TTTACACTAAAAGGAATAATTTGTTATTATAAATAATTTTAACTGAA
1 TTTACACTAAAAGGAATAATTTGTTATTATAAATAATTTTAAATGAA
*
9225438 TTTACACTAAAAGGAATCATTTGTTATTATAAATAATTTTAAATGAA
1 TTTACACTAAAAGGAATAATTTGTTATTATAAATAATTTTAAATGAA
9225485 T
1 T
9225486 GTACGTTGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.41
Consensus pattern (47 bp):
TTTACACTAAAAGGAATAATTTGTTATTATAAATAATTTTAAATGAA
Found at i:9234213 original size:2 final size:2
Alignment explanation
Indices: 9234208--9234236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9234198 TCTCTCTGTC
9234208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9234237 CAGGTAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9235964 original size:102 final size:103
Alignment explanation
Indices: 9235839--9236032 Score: 275
Period size: 103 Copynumber: 1.9 Consensus size: 103
9235829 AAGAGGCAAA
* * **
9235839 TATTATAGTGTACAATCAAATTCATAG-AACATAATA-TTTCTTAGGACTACCATTATGTTTTTC
1 TATTATAGTGTACAATCAAATTCATAGTAACACAATACTTTC-TAAGACTACCATTACATTTTTC
* * *
9235902 TCTTTTTATAGTGTCATTTTCTAAAACTGCCTATGTAAG
65 TATGTTTATAGAGTCATTTTCTAAAACTGCCTATGTAAG
* *
9235941 TATTATAGTGTAGAATCATATTCATAGTAACACAATACTTTCTAAGACTACCATTACATTTTTCT
1 TATTATAGTGTACAATCAAATTCATAGTAACACAATACTTTCTAAGACTACCATTACATTTTTCT
*
9236006 ATGTTTATAGAGTTATTTTCTAAAACT
66 ATGTTTATAGAGTCATTTTCTAAAACT
9236033 ACTCGTGTAG
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
102 25 0.31
103 51 0.64
104 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (103 bp):
TATTATAGTGTACAATCAAATTCATAGTAACACAATACTTTCTAAGACTACCATTACATTTTTCT
ATGTTTATAGAGTCATTTTCTAAAACTGCCTATGTAAG
Found at i:9236240 original size:191 final size:189
Alignment explanation
Indices: 9235916--9236291 Score: 520
Period size: 191 Copynumber: 2.0 Consensus size: 189
9235906 TTTATAGTGT
* * *
9235916 CATTTTCTAAAACTGCCTATGTAAGTATTATAGTGTAGAATCATATTCATAGTAACACAATACTT
1 CATTTTCTAAAACTACCTATGTAAGTATTATAATGTAGAATCAAATTCATAGTAACACAATACTT
*
9235981 TCTAAGACTACCATTACATTTTTCTATGTTTATAGAGTTATTTTCTAAAACTACTCGTGTAGTGT
66 TCTAAGACTACCATTACATTTTTCTATGTTTATAGAGTCATTTTCTAAAACTACTCGTGTAGTGT
* * * *
9236046 CATTTCTACAAGAGGATGTAAGTGTACTTTCTAAGACTATCATTACGTTTTTCTTCAATGA
131 CATTTCCA-AAGAAGATGGAAGTGTACTTTCGAAGACTATCATTACGTTTTT-TTCAATGA
* * * *
9236107 CATTTTCTAAGACTATCTATGTAGGTATTATAATGTAGAGTCAAATTCATAGTAACACAATACTT
1 CATTTTCTAAAACTACCTATGTAAGTATTATAATGTAGAATCAAATTCATAGTAACACAATACTT
* * ** * * * *
9236172 TTTAAGATTACCATTATGTTTTTCTAT-TTTCATAGTGTCATTTTCTAAGACTGCTTGTGTAGTG
66 TCTAAGACTACCATTACATTTTTCTATGTTT-ATAGAGTCATTTTCTAAAACTACTCGTGTAGTG
* *
9236236 TCATTTCCAAATAAGATGGAAGTGTACTTTCGAAGACTATCATTATGTTTTTTTCA
130 TCATTTCCAAAGAAGATGGAAGTGTACTTTCGAAGACTATCATTACGTTTTTTTCA
9236292 TTTTTATAGT
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
189 4 0.02
190 41 0.25
191 117 0.72
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (189 bp):
CATTTTCTAAAACTACCTATGTAAGTATTATAATGTAGAATCAAATTCATAGTAACACAATACTT
TCTAAGACTACCATTACATTTTTCTATGTTTATAGAGTCATTTTCTAAAACTACTCGTGTAGTGT
CATTTCCAAAGAAGATGGAAGTGTACTTTCGAAGACTATCATTACGTTTTTTTCAATGA
Found at i:9237151 original size:16 final size:16
Alignment explanation
Indices: 9237127--9237160 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9237117 ACACAATTGT
*
9237127 CACTTTCTAAGACTAC
1 CACTCTCTAAGACTAC
9237143 CACTCTCTAAGACTAC
1 CACTCTCTAAGACTAC
9237159 CA
1 CA
9237161 GTCTTTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (16 bp):
CACTCTCTAAGACTAC
Found at i:9237223 original size:32 final size:32
Alignment explanation
Indices: 9237162--9237225 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
9237152 AGACTACCAG
* **
9237162 TCTTTCTACACTGGATGTAAGTATCATACACA
1 TCTTTCTACACAGGATGTAAAAATCATACACA
*
9237194 TCTTTCTACACAGGATGTAAAAATTATACACA
1 TCTTTCTACACAGGATGTAAAAATCATACACA
9237226 AATATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (32 bp):
TCTTTCTACACAGGATGTAAAAATCATACACA
Found at i:9243566 original size:2 final size:2
Alignment explanation
Indices: 9243559--9243587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9243549 CTAGCATGTA
9243559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9243588 ATAGCAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9251683 original size:21 final size:22
Alignment explanation
Indices: 9251637--9251683 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
9251627 TACATAATTA
* *
9251637 ATAATTTCTTTTTATACTCAAG
1 ATAATTTCTTTTCATACTAAAG
*
9251659 ATAATTTCTTTTCA-ACTAAAT
1 ATAATTTCTTTTCATACTAAAG
9251680 ATAA
1 ATAA
9251684 AACGTAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAATTTCTTTTCATACTAAAG
Found at i:9251856 original size:15 final size:16
Alignment explanation
Indices: 9251830--9251859 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9251820 TTTTTAACTT
9251830 TTAAAAATTAAAATCA
1 TTAAAAATTAAAATCA
9251846 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
9251860 TACATAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCA
Found at i:9276490 original size:22 final size:22
Alignment explanation
Indices: 9276465--9276513 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
9276455 TACTACATAA
*
9276465 AATATCATATTAATATTGTAAT
1 AATATAATATTAATATTGTAAT
* * * *
9276487 AATAAAATTTTCATATTTTAAT
1 AATATAATATTAATATTGTAAT
9276509 AATAT
1 AATAT
9276514 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
AATATAATATTAATATTGTAAT
Found at i:9307230 original size:22 final size:22
Alignment explanation
Indices: 9307199--9307242 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9307189 GCCATGGCTA
9307199 CTATAAAAAGTAAGATTGTGTG
1 CTATAAAAAGTAAGATTGTGTG
*
9307221 CTATAGAAAGTAAGATTGTGTG
1 CTATAAAAAGTAAGATTGTGTG
9307243 TCTTCTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (22 bp):
CTATAAAAAGTAAGATTGTGTG
Found at i:9314829 original size:44 final size:44
Alignment explanation
Indices: 9314764--9314856 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
9314754 CAAAAAGAAA
* *
9314764 AATAATAGTATACAAAATAATCCCTACTTACTGTTCAAGCATCC
1 AATAATAGCATACAAAATAATCCCCACTTACTGTTCAAGCATCC
*
9314808 AATAATAGCATACAAATTAATCCCCACTTACTGTTCAAGCATCC
1 AATAATAGCATACAAAATAATCCCCACTTACTGTTCAAGCATCC
9314852 AATAA
1 AATAA
9314857 CTGCGCCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (44 bp):
AATAATAGCATACAAAATAATCCCCACTTACTGTTCAAGCATCC
Found at i:9318990 original size:14 final size:14
Alignment explanation
Indices: 9318971--9318997 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9318961 TGAAAATTTT
9318971 AAAAAAAATTAGTA
1 AAAAAAAATTAGTA
9318985 AAAAAAAATTAGT
1 AAAAAAAATTAGT
9318998 TATTTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAAAAAATTAGTA
Found at i:9323110 original size:10 final size:10
Alignment explanation
Indices: 9323095--9323142 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
9323085 TTTTTATGAA
9323095 TGTGTGTATG
1 TGTGTGTATG
*
9323105 TGTGTGTGTG
1 TGTGTGTATG
9323115 TGTGATTGTATG
1 TGTG--TGTATG
9323127 TGT-TGTGATG
1 TGTGTGT-ATG
9323137 TGTGTG
1 TGTGTG
9323143 CATTAAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 3 0.09
10 19 0.59
11 2 0.06
12 8 0.25
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (10 bp):
TGTGTGTATG
Found at i:9323985 original size:2 final size:2
Alignment explanation
Indices: 9323978--9324006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9323968 AGTGCTTTGC
9323978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9324007 CATACATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9343358 original size:2 final size:2
Alignment explanation
Indices: 9343351--9343388 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9343341 GCCCTCTGAA
9343351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9343389 GTAGACTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9350953 original size:20 final size:20
Alignment explanation
Indices: 9350916--9350953 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9350906 CTTTTAATGA
*
9350916 AAAATAAAAAGTATAATCCC
1 AAAATAAAAAATATAATCCC
9350936 AAAATAAAAGAATA-AATC
1 AAAATAAAA-AATATAATC
9350954 TAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATAAAAAATATAATCCC
Found at i:9368496 original size:14 final size:14
Alignment explanation
Indices: 9368479--9368515 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
9368469 AATTTTTGTT
*
9368479 TTTATTTATAATTA
1 TTTATATATAATTA
9368493 TTTATATATAATTA
1 TTTATATATAATTA
9368507 TTTA-ATATA
1 TTTATATATA
9368516 CAGTATTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATATAATTA
Found at i:9375613 original size:21 final size:20
Alignment explanation
Indices: 9375575--9375614 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9375565 TTATGTATGT
*
9375575 TATTTATGTTAATTTTATTA
1 TATTTATGTTAATATTATTA
*
9375595 TATTTGATGTTAGTATTATT
1 TATTT-ATGTTAATATTATT
9375615 TTGTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TATTTATGTTAATATTATTA
Found at i:9381403 original size:19 final size:20
Alignment explanation
Indices: 9381379--9381422 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
9381369 TCATATGCAA
9381379 TTTTAAAA-AG-ATGGAAGGG
1 TTTTAAAATAGAAT-GAAGGG
9381398 TTTTAAAATAGAATGAAGGG
1 TTTTAAAATAGAATGAAGGG
9381418 TTTTA
1 TTTTA
9381423 TGAGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 13 0.57
21 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (20 bp):
TTTTAAAATAGAATGAAGGG
Found at i:9381526 original size:97 final size:96
Alignment explanation
Indices: 9381359--9381553 Score: 297
Period size: 97 Copynumber: 2.0 Consensus size: 96
9381349 AAAACACTCC
9381359 AATTCATATTTCATATGCAATTTTAAAAAGATGGAAGGGTTTTAAAATAGAATGAAGGGTTTTAT
1 AATTCATATTTCATATGCAATTTTAAAAAGATGGAAGGGTTTTAAAATAGAATGAAGGGTTTTAT
* *
9381424 GAGAAAAAACGAAAG-AAAATGAAAAAACAAGG
66 GAGAAAAAA-AAAAGAAAAAAGAAAAAA-AAGG
*
9381456 AATTCATATTTCATATGCAATTTTAAAAAGATGG-AGGGTTTTGAAAA-AGAATGAGGGGTTTCT
1 AATTCATATTTCATATGCAATTTTAAAAAGATGGAAGGGTTTT-AAAATAGAATGAAGGGTTT-T
*
9381519 ATTAGAAAAAAAAAAGAAAAAAGAAAAAAAAGG
64 ATGAGAAAAAAAAAAGAAAAAAGAAAAAAAAGG
9381552 AA
1 AA
9381554 AGATGAGGAG
Statistics
Matches: 91, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
96 31 0.34
97 60 0.66
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (96 bp):
AATTCATATTTCATATGCAATTTTAAAAAGATGGAAGGGTTTTAAAATAGAATGAAGGGTTTTAT
GAGAAAAAAAAAAGAAAAAAGAAAAAAAAGG
Found at i:9381687 original size:19 final size:19
Alignment explanation
Indices: 9381659--9381699 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
9381649 TCATATGTAA
9381659 TTTTAAAAAG-ATGAAGGG
1 TTTTAAAAAGAATGAAGGG
9381677 TTTTAAAAAAGAATGAAGGG
1 TTTT-AAAAAGAATGAAGGG
9381697 TTT
1 TTT
9381700 CTATCAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (19 bp):
TTTTAAAAAGAATGAAGGG
Found at i:9381737 original size:23 final size:23
Alignment explanation
Indices: 9381712--9381756 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
9381702 ATCAGACAAA
*
9381712 AAAAAAGAATA-AAAAAGAAAGG
1 AAAAAAGAAAAGAAAAAGAAAGG
*
9381734 AAAAAAGAAAAGAAAAAGGAAGG
1 AAAAAAGAAAAGAAAAAGAAAGG
9381757 TGAAGGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAGAAAAAGAAAGG
Found at i:9381791 original size:19 final size:19
Alignment explanation
Indices: 9381757--9381813 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
9381747 AAAAGGAAGG
9381757 TGAAGGG-TTT-AAAAAAA
1 TGAAGGGTTTTAAAAAAAA
9381774 TGAAGGGTTTTAAAAAAAA
1 TGAAGGGTTTTAAAAAAAA
*
9381793 TAAAGGGTTTTTATAAAAAAA
1 TGAAGGG-TTTTA-AAAAAAA
9381814 AGGAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
17 7 0.20
18 3 0.09
19 13 0.37
20 5 0.14
21 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (19 bp):
TGAAGGGTTTTAAAAAAAA
Found at i:9381901 original size:19 final size:20
Alignment explanation
Indices: 9381873--9381924 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
9381863 TTTTATGTAA
9381873 TTTT-AAAAAGAA-GAAGGG
1 TTTTAAAAAAGAATGAAGGG
9381891 TTTTAAAAAAGAATGAAGGG
1 TTTTAAAAAAGAATGAAGGG
*
9381911 TTTCAATAAAAGAA
1 TTTTAA-AAAAGAA
9381925 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 11 0.37
21 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.25
Consensus pattern (20 bp):
TTTTAAAAAAGAATGAAGGG
Found at i:9382156 original size:19 final size:19
Alignment explanation
Indices: 9382127--9382167 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
9382117 TACTATACAA
9382127 TTTTAAAAAG-ATGAAAGG
1 TTTTAAAAAGAATGAAAGG
*
9382145 TTTTACAAAAGAATGAAGGG
1 TTTTA-AAAAGAATGAAAGG
9382165 TTT
1 TTT
9382168 CTATTAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (19 bp):
TTTTAAAAAGAATGAAAGG
Found at i:9383073 original size:18 final size:18
Alignment explanation
Indices: 9383032--9383070 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
9383022 ATAAACAATA
9383032 AATTTTAATATTAAATTTT
1 AATTTTAATATT-AATTTT
*
9383051 AATTTTATATATTATTTTT
1 AATTTTA-ATATTAATTTT
9383070 A
1 A
9383071 TTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTAATATTAATTTT
Found at i:9390981 original size:22 final size:22
Alignment explanation
Indices: 9390956--9390999 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9390946 TCCAATTTCT
9390956 TCTTATTTTATTAAAACTCTTA
1 TCTTATTTTATTAAAACTCTTA
9390978 TCTTATTTTATTAAAACTCTTA
1 TCTTATTTTATTAAAACTCTTA
9391000 CTTCAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.55
Consensus pattern (22 bp):
TCTTATTTTATTAAAACTCTTA
Found at i:9391370 original size:28 final size:28
Alignment explanation
Indices: 9391338--9391446 Score: 103
Period size: 28 Copynumber: 3.8 Consensus size: 28
9391328 AATTAAAATA
* * *
9391338 AAACATATTATCTTGTATAAATTGAGAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
*
9391366 AAACAT-GTTTCTTGTCTAAATTAAGAC
1 AAACATATTTTCTTGTCTAAATTAAGAC
* * *
9391393 TAAATATATTTTTCTTCTTTTAAATTAAGAC
1 -AAACATA-TTTTCTT-GTCTAAATTAAGAC
* *
9391424 AAATATGTTTTCTTGTCTAAATT
1 AAACATATTTTCTTGTCTAAATT
9391447 GGAAAAAAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 17 0.26
28 18 0.27
29 7 0.11
30 12 0.18
31 12 0.18
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (28 bp):
AAACATATTTTCTTGTCTAAATTAAGAC
Found at i:9393876 original size:39 final size:39
Alignment explanation
Indices: 9393822--9393899 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
9393812 ATCATGGTAA
* *
9393822 AGATTGCTTTTGAATTCAAAACCACGAGAGTTGTTAGAT
1 AGATTGCTTTTGAATTCAAAACCACGAGAATTGCTAGAT
*
9393861 AGATTGCTTTTGAATTCAAAACCATGAGAATTGCTAGAT
1 AGATTGCTTTTGAATTCAAAACCACGAGAATTGCTAGAT
9393900 GTTGATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (39 bp):
AGATTGCTTTTGAATTCAAAACCACGAGAATTGCTAGAT
Found at i:9395631 original size:15 final size:17
Alignment explanation
Indices: 9395602--9395640 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
9395592 TATAAATATA
9395602 AATA-TAAATATTTTAT
1 AATACTAAATATTTTAT
9395618 AA-ACTAAA-ATTTTAT
1 AATACTAAATATTTTAT
9395633 AATACTAA
1 AATACTAA
9395641 TTTATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATACTAAATATTTTAT
Found at i:9396662 original size:2 final size:2
Alignment explanation
Indices: 9396655--9396680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9396645 GAATTCATCA
9396655 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
9396681 CTTAAACAAG
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:9399939 original size:24 final size:22
Alignment explanation
Indices: 9399912--9399956 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9399902 ATTATACGTA
9399912 ATGTTGAAACAAAAAAGTTGTTAT
1 ATGTTG-AA-AAAAAAGTTGTTAT
*
9399936 ATGTTGAAAAGAAAGTTGTTA
1 ATGTTGAAAAAAAAGTTGTTA
9399957 CATGCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.33
Consensus pattern (22 bp):
ATGTTGAAAAAAAAGTTGTTAT
Found at i:9400198 original size:26 final size:27
Alignment explanation
Indices: 9400169--9400226 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
9400159 AAAAAAAAAC
9400169 TTACAAG-TCATGTT-AAAAAAAAATTA
1 TTACAAGAT-ATGTTGAAAAAAAAATTA
* *
9400195 TTACATGATATGTTGAAAAAAAAATTG
1 TTACAAGATATGTTGAAAAAAAAATTA
9400222 TTACA
1 TTACA
9400227 CATTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (27 bp):
TTACAAGATATGTTGAAAAAAAAATTA
Found at i:9400365 original size:25 final size:26
Alignment explanation
Indices: 9400331--9400386 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
9400321 TTGTTGTTGC
*
9400331 ATGTTCAAAAAAAGTTATTACAAGCT
1 ATGTTCAAAAAAAATTATTACAAGCT
* * *
9400357 ATGTT-AAAAAAAATTGTTACACGTT
1 ATGTTCAAAAAAAATTATTACAAGCT
9400382 ATGTT
1 ATGTT
9400387 TAAGATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (26 bp):
ATGTTCAAAAAAAATTATTACAAGCT
Found at i:9410404 original size:18 final size:18
Alignment explanation
Indices: 9410381--9410417 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9410371 CTTATATGGT
9410381 TGTTGTCGTTGATGTTGC
1 TGTTGTCGTTGATGTTGC
9410399 TGTTGTCGTTGATGTTGC
1 TGTTGTCGTTGATGTTGC
9410417 T
1 T
9410418 TTACCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.32, T:0.51
Consensus pattern (18 bp):
TGTTGTCGTTGATGTTGC
Found at i:9421747 original size:16 final size:16
Alignment explanation
Indices: 9421726--9421763 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9421716 ATCTTATTAG
9421726 AAAAAACCTTA-TAGGA
1 AAAAAACCTTAGT-GGA
*
9421742 AAAAAATCTTAGTGGA
1 AAAAAACCTTAGTGGA
9421758 AAAAAA
1 AAAAAA
9421764 AGAGAGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAAAACCTTAGTGGA
Found at i:9427345 original size:24 final size:24
Alignment explanation
Indices: 9427318--9427383 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
9427308 ATTATTAAAT
9427318 TATTTAATGAAAATTATAATATAA
1 TATTTAATGAAAATTATAATATAA
* ** *
9427342 TA-TTATTAGTTAATTATATTATAA
1 TATTTAAT-GAAAATTATAATATAA
* *
9427366 TGTTTAATTAAAATTATA
1 TATTTAATGAAAATTATA
9427384 TCAAGCTTAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
23 4 0.13
24 23 0.74
25 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
TATTTAATGAAAATTATAATATAA
Found at i:9429157 original size:21 final size:22
Alignment explanation
Indices: 9429109--9429148 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9429099 TATCATTTTT
9429109 TTATTA-A-TTTTAAAAAATTA
1 TTATTATATTTTTAAAAAATTA
*
9429129 TTATTATATTTTTTAAAAAT
1 TTATTATATTTTTAAAAAAT
9429149 ATATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATATTTTTAAAAAATTA
Found at i:9429348 original size:31 final size:32
Alignment explanation
Indices: 9429281--9429348 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
9429271 TTTTTTTAAT
* * *
9429281 TTTTTTAAATTAATAAAAATTATATAATAATAA
1 TTTTTAAAAATAATAAAAA-TATAAAATAATAA
*
9429314 TTTTTAAAAATAATAAAAA-ATAAAATTATAA
1 TTTTTAAAAATAATAAAAATATAAAATAATAA
9429345 TTTT
1 TTTT
9429349 AATATATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.45
33 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTTAAAAATAATAAAAATATAAAATAATAA
Found at i:9441307 original size:17 final size:17
Alignment explanation
Indices: 9441281--9441326 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
9441271 TTACATATTA
9441281 AATTGACTTTGTATGAT
1 AATTGACTTTGTATGAT
*
9441298 AATTGGCTTTGTATGAT
1 AATTGACTTTGTATGAT
*
9441315 -ATTGATTTTGTA
1 AATTGACTTTGTA
9441327 ACTAGTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (17 bp):
AATTGACTTTGTATGAT
Found at i:9486041 original size:18 final size:20
Alignment explanation
Indices: 9486007--9486053 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
9485997 CGGGCCCGGC
*
9486007 CGGCGGCGCCGCGCGGCG-CG
1 CGGCGG-GCCGCCCGGCGCCG
9486027 CGG-GGGCCGCCCGGCGCCG
1 CGGCGGGCCGCCCGGCGCCG
9486046 CGGCGGGC
1 CGGCGGGC
9486054 GGTCGGCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.00, C:0.45, G:0.55, T:0.00
Consensus pattern (20 bp):
CGGCGGGCCGCCCGGCGCCG
Done.