Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 89 of 144
Found at i:20739830 original size:34 final size:34
Alignment explanation
Indices: 20739787--20739853 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
20739777 TTTTTAAATA
*
20739787 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* *
20739821 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT
20739854 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:20740568 original size:15 final size:15
Alignment explanation
Indices: 20740533--20740612 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
20740523 ACAATTTCAT
* *
20740533 TAATAATATTAACAG
1 TAATAATATTAATAA
*
20740548 TGATAATATTAATAA
1 TAATAATATTAATAA
* *
20740563 TAATAATTTTATTAA
1 TAATAATATTAATAA
* *
20740578 TAATGACATTAATTAA
1 TAATAATATTAA-TAA
20740594 TAAATAATATTAATAA
1 T-AATAATATTAATAA
20740610 TAA
1 TAA
20740613 CAAAAAAAAG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
15 34 0.67
16 8 0.16
17 9 0.18
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (15 bp):
TAATAATATTAATAA
Found at i:20744503 original size:6 final size:6
Alignment explanation
Indices: 20744478--20744516 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
20744468 ACAATTCATA
* * *
20744478 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
20744517 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:20747750 original size:18 final size:19
Alignment explanation
Indices: 20747723--20747770 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
20747713 TATTATATAA
* *
20747723 TATTTAAATTTATAT-TTT
1 TATTTTAATTTATATATTC
*
20747741 TATTTTAATTAATATATTC
1 TATTTTAATTTATATATTC
20747760 TATTTTAATTT
1 TATTTTAATTT
20747771 TTAAAACTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTAATTTATATATTC
Found at i:20747926 original size:25 final size:26
Alignment explanation
Indices: 20747898--20747959 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
20747888 TGTATTTTAC
*
20747898 ATATTTTAATTTT-AAATTTTCAAAT
1 ATATTTTAATTTTAAAATTGTCAAAT
*
20747923 ATATTTTAATTTTAAAATTGTCAAGT
1 ATATTTTAATTTTAAAATTGTCAAAT
20747949 ATATTTTAATT
1 ATATTTTAATT
20747960 GTCATGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
ATATTTTAATTTTAAAATTGTCAAAT
Found at i:20747956 original size:20 final size:20
Alignment explanation
Indices: 20747931--20747975 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
20747921 ATATATTTTA
20747931 ATTTTAAAATTGTCAAGTAT
1 ATTTTAAAATTGTCAAGTAT
*
20747951 ATTTT--AATTGTCATGTAT
1 ATTTTAAAATTGTCAAGTAT
20747969 ATTTTAA
1 ATTTTAA
20747976 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.77
20 5 0.23
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATTGTCAAGTAT
Found at i:20747959 original size:18 final size:18
Alignment explanation
Indices: 20747938--20747977 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
20747928 TTAATTTTAA
20747938 AATTGTCAAGTATATTTT
1 AATTGTCAAGTATATTTT
*
20747956 AATTGTCATGTATATTTT
1 AATTGTCAAGTATATTTT
20747974 AATT
1 AATT
20747978 TTTTTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (18 bp):
AATTGTCAAGTATATTTT
Found at i:20757021 original size:19 final size:21
Alignment explanation
Indices: 20756983--20757023 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20756973 CAGCAAATGA
*
20756983 TTTTAAAATTATTAAAATTAT
1 TTTTAAAAATATTAAAATTAT
20757004 TTTTAAAAATA-T-AAATTAT
1 TTTTAAAAATATTAAAATTAT
20757023 T
1 T
20757024 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAAATATTAAAATTAT
Found at i:20757036 original size:29 final size:27
Alignment explanation
Indices: 20756986--20757055 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 27
20756976 CAAATGATTT
20756986 TAAAATTATTAAAATTATTTTTAAAAA
1 TAAAATTATTAAAATTATTTTTAAAAA
**
20757013 TATAAATTATTAAAATTATTTTTTTGAAA
1 TA-AAATTATTAAAATTA-TTTTTAAAAA
20757042 TAATAATTATTAAA
1 TAA-AATTATTAAA
20757056 TAATTATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 2 0.05
28 16 0.42
29 20 0.53
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
TAAAATTATTAAAATTATTTTTAAAAA
Found at i:20757480 original size:14 final size:13
Alignment explanation
Indices: 20757447--20757492 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
20757437 TTATCAATTT
20757447 AAAATAAA-AATA
1 AAAATAAATAATA
*
20757459 ATAATAAATAACTA
1 AAAATAAATAA-TA
20757473 AAAATAAATAA-A
1 AAAATAAATAATA
*
20757485 TAAATAAA
1 AAAATAAA
20757493 AACTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 15 0.52
13 2 0.07
14 12 0.41
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:20757484 original size:18 final size:20
Alignment explanation
Indices: 20757448--20757494 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
20757438 TATCAATTTA
20757448 AAATAAAAATAATAATAAAT
1 AAATAAAAATAATAATAAAT
*
20757468 AACTAAAAAT-A-AATAAAT
1 AAATAAAAATAATAATAAAT
20757486 AAATAAAAA
1 AAATAAAAA
20757495 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 9 0.36
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAAAAATAATAATAAAT
Found at i:20770012 original size:21 final size:21
Alignment explanation
Indices: 20769985--20770038 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20769975 AGAGTTTTTA
*
20769985 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTC-TCACTT
*
20770006 GTTTCGGTAGAAGTCTCACTT
1 GTATCGGTAGAAGTCTCACTT
20770027 GTATCGGTAGAA
1 GTATCGGTAGAA
20770039 CTATCTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCTCACTT
Found at i:20770912 original size:243 final size:243
Alignment explanation
Indices: 20770484--20770973 Score: 962
Period size: 243 Copynumber: 2.0 Consensus size: 243
20770474 TGTTCTTGAA
*
20770484 CCTATTCTCTGATACAACCAAATGTAACACCAAATACCCAGCCCGATTGTCTAGCCCGAATACTA
1 CCTATTCTCTGATACAACCAAATGTAACACCAAATACCCAGCCAGATTGTCTAGCCCGAATACTA
20770549 GGATGTCACACCACCGTCTCACATCATACTTACCTCATTTTAAACGTTTTATTTCAAATGAAAAT
66 GGATGTCACACCACCGTCTCACATCATACTTACCTCATTTTAAACGTTTTATTTCAAATGAAAAT
20770614 TTTTCTTTTAAGGGAAAAACCAAAGAAGTGATTGTGAACTGTGCACCGTGCACCAGGTAAAGTCC
131 TTTTCTTTTAAGGGAAAAACCAAAGAAGTGATTGTGAACTGTGCACCGTGCACCAGGTAAAGTCC
20770679 TAGGAAAGGGAGGTGAGTCAAATTTGACCGCTTAAAAACTAAGCCTTT
196 TAGGAAAGGGAGGTGAGTCAAATTTGACCGCTTAAAAACTAAGCCTTT
*
20770727 CCTATTCTCTGATACAACCAAATGTAACACTAAATACCCAGCCAGATTGTCTAGCCCGAATACTA
1 CCTATTCTCTGATACAACCAAATGTAACACCAAATACCCAGCCAGATTGTCTAGCCCGAATACTA
20770792 GGATGTCACACCACCGTCTCACATCATACTTACCTCATTTTAAACGTTTTATTTCAAATGAAAAT
66 GGATGTCACACCACCGTCTCACATCATACTTACCTCATTTTAAACGTTTTATTTCAAATGAAAAT
20770857 TTTTCTTTTAAGGGAAAAACCAAAGAAGTGATTGTGAACTGTGCACCGTGCACCAGGTAAAGTCC
131 TTTTCTTTTAAGGGAAAAACCAAAGAAGTGATTGTGAACTGTGCACCGTGCACCAGGTAAAGTCC
20770922 TAGGAAAGGGAGGTGAGTCAAATTTGACCGCTTAAAAACTAAGCCTTT
196 TAGGAAAGGGAGGTGAGTCAAATTTGACCGCTTAAAAACTAAGCCTTT
20770970 CCTA
1 CCTA
20770974 GCCAGAGTCA
Statistics
Matches: 245, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
243 245 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (243 bp):
CCTATTCTCTGATACAACCAAATGTAACACCAAATACCCAGCCAGATTGTCTAGCCCGAATACTA
GGATGTCACACCACCGTCTCACATCATACTTACCTCATTTTAAACGTTTTATTTCAAATGAAAAT
TTTTCTTTTAAGGGAAAAACCAAAGAAGTGATTGTGAACTGTGCACCGTGCACCAGGTAAAGTCC
TAGGAAAGGGAGGTGAGTCAAATTTGACCGCTTAAAAACTAAGCCTTT
Found at i:20776255 original size:23 final size:23
Alignment explanation
Indices: 20776198--20776255 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
20776188 CTCATAACAC
**
20776198 TTTTGGAGAATTTTGTGTTTACG
1 TTTTGGAGTTTTTTGTGTTTACG
* *
20776221 TTTTGAGGGTTTTTTGT-TTTAAGG
1 TTTTG-GAGTTTTTTGTGTTT-ACG
20776245 TTTTGGAGTTT
1 TTTTGGAGTTT
20776256 AATTTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.14, C:0.02, G:0.28, T:0.57
Consensus pattern (23 bp):
TTTTGGAGTTTTTTGTGTTTACG
Found at i:20777609 original size:20 final size:20
Alignment explanation
Indices: 20777573--20777611 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20777563 GCAACAACAC
*
20777573 TATTCTGTTATTGTTATTAT
1 TATTCTGTGATTGTTATTAT
20777593 TATTCATGTGATT-TTATTA
1 TATTC-TGTGATTGTTATTA
20777612 CTGCATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (20 bp):
TATTCTGTGATTGTTATTAT
Found at i:20781759 original size:29 final size:29
Alignment explanation
Indices: 20781697--20781788 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 29
20781687 GCATAACAAT
** *
20781697 CCACGCATATATATATATATAACACCAAAAC
1 CCACGCATATATAT-TATATAA-AATAAAGC
*
20781728 CCATGCATATATATTATATAAAATAAAGC
1 CCACGCATATATATTATATAAAATAAAGC
** *
20781757 CCACATATATATATTATCTATATAATAAAGC
1 CCACGCATATATATTA--TATAAAATAAAGC
20781788 C
1 C
20781789 AGGCCTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.35
30 7 0.14
31 26 0.51
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (29 bp):
CCACGCATATATATTATATAAAATAAAGC
Found at i:20786772 original size:24 final size:24
Alignment explanation
Indices: 20786734--20786779 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20786724 GAAGATTTAA
*
20786734 TATTTATTAATATAATATATTTTG
1 TATTTATTAACATAATATATTTTG
* *
20786758 TATTTATTAGCATAATTTATTT
1 TATTTATTAACATAATATATTT
20786780 GACTTGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
TATTTATTAACATAATATATTTTG
Found at i:20791094 original size:27 final size:27
Alignment explanation
Indices: 20791064--20791153 Score: 72
Period size: 31 Copynumber: 3.1 Consensus size: 27
20791054 AAACTTACTT
20791064 ATTTATTTGTTATATCAATTTTATTAA
1 ATTTATTTGTTATATCAATTTTATTAA
* *** * *
20791091 ATTTATTTTTTATCATTTCAATAAAAATCAT
1 ATTTATTTGTTAT-A--TCAAT-TTTATTAA
*
20791122 ATTTAATTGTTATATCAATTTTTATTAA
1 ATTTATTTGTTATATCAA-TTTTATTAA
20791150 ATTT
1 ATTT
20791154 TCACTTATGA
Statistics
Matches: 45, Mismatches: 13, Indels: 9
0.67 0.19 0.13
Matches are distributed among these distances:
27 12 0.27
28 12 0.27
29 1 0.02
30 6 0.13
31 14 0.31
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTATTTGTTATATCAATTTTATTAA
Found at i:20791858 original size:15 final size:15
Alignment explanation
Indices: 20791825--20791856 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
20791815 ATAACTTAAA
20791825 TTTAATATTTAATTT
1 TTTAATATTTAATTT
20791840 TTTAATA-TTAATTT
1 TTTAATATTTAATTT
20791854 TTT
1 TTT
20791857 TAGCATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTAATATTTAATTT
Found at i:20793001 original size:48 final size:48
Alignment explanation
Indices: 20792930--20793026 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
20792920 GCTCGAATCT
20792930 ATGTCTTATTAATTGTTGCAACAACAATAATACCAATTGAACTAAGGC
1 ATGTCTTATTAATTGTTGCAACAACAATAATACCAATTGAACTAAGGC
20792978 ATGTCTTATTAATTGTTGCAACAACAATAATACCAATTGAACTAAGGC
1 ATGTCTTATTAATTGTTGCAACAACAATAATACCAATTGAACTAAGGC
20793026 A
1 A
20793027 GTGGCGGAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (48 bp):
ATGTCTTATTAATTGTTGCAACAACAATAATACCAATTGAACTAAGGC
Found at i:20793891 original size:23 final size:24
Alignment explanation
Indices: 20793846--20793892 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
20793836 ATACTTTGTT
***
20793846 AACTTGAAAATAATTTGTTTTTAA
1 AACTTGAAAATAATTTAAATTTAA
20793870 AACTT-AAAATAATTTAAATTTAA
1 AACTTGAAAATAATTTAAATTTAA
20793893 TTATTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AACTTGAAAATAATTTAAATTTAA
Found at i:20795632 original size:13 final size:13
Alignment explanation
Indices: 20795614--20795639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20795604 TATAAATGTG
20795614 TTAAAATAATTAA
1 TTAAAATAATTAA
20795627 TTAAAATAATTAA
1 TTAAAATAATTAA
20795640 AAACATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAATAATTAA
Found at i:20796181 original size:21 final size:21
Alignment explanation
Indices: 20796157--20796202 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20796147 TACAAATGTA
20796157 TTAAT-ATCTAATTATAAATAT
1 TTAATGAT-TAATTATAAATAT
* *
20796178 TTAATGATTATTTTTAAATAT
1 TTAATGATTAATTATAAATAT
20796199 TTAA
1 TTAA
20796203 AATATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATGATTAATTATAAATAT
Found at i:20796246 original size:20 final size:20
Alignment explanation
Indices: 20796221--20796272 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
20796211 TTATATATTC
20796221 TAATTAAT-TTTTTATAAAAA
1 TAATTAATATTTTT-TAAAAA
20796241 TAATTAATATTTTTTAAAAA
1 TAATTAATATTTTTTAAAAA
* *
20796261 TATTTAAAATTT
1 TAATTAATATTT
20796273 ATATTTCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTAATATTTTTTAAAAA
Found at i:20796829 original size:29 final size:28
Alignment explanation
Indices: 20796796--20796858 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
20796786 TATTTTATCC
20796796 ATTTAACTA-AAAAAATAATTACAAAAATG
1 ATTTAACTATAAAAAAT--TTACAAAAATG
* * *
20796825 ATTTAGCTATAATAAATTTACTAAAATG
1 ATTTAACTATAAAAAATTTACAAAAATG
20796853 ATTTAA
1 ATTTAA
20796859 AATGAGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 15 0.52
29 8 0.28
30 6 0.21
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTTAACTATAAAAAATTTACAAAAATG
Found at i:20797557 original size:17 final size:17
Alignment explanation
Indices: 20797524--20797556 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
20797514 AATTAAAATT
20797524 TTAAAGTTTATTTAAAA
1 TTAAAGTTTATTTAAAA
20797541 TTAAA-TTTATTTAAAA
1 TTAAAGTTTATTTAAAA
20797557 AAATTCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTAAAGTTTATTTAAAA
Found at i:20798596 original size:24 final size:23
Alignment explanation
Indices: 20798564--20798613 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
20798554 GACTTAAAAT
20798564 AAATTTAATTATAAATAAACTTTA
1 AAATTTAATTATAAATAAAC-TTA
* *
20798588 AAATTTAATTTTAAGTAAACTTA
1 AAATTTAATTATAAATAAACTTA
20798611 AAA
1 AAA
20798614 CCCCCAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTTAATTATAAATAAACTTA
Found at i:20799791 original size:15 final size:16
Alignment explanation
Indices: 20799749--20799791 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
20799739 TAAAAAATGC
20799749 AAAAGGATTAAAATAT
1 AAAAGGATTAAAATAT
* *
20799765 AAAAGAAATAAAA-AT
1 AAAAGGATTAAAATAT
*
20799780 AAAAGGGTTAAA
1 AAAAGGATTAAA
20799792 TTTTAACAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAAGGATTAAAATAT
Found at i:20799812 original size:32 final size:30
Alignment explanation
Indices: 20799749--20799834 Score: 100
Period size: 32 Copynumber: 2.8 Consensus size: 30
20799739 TAAAAAATGC
* *
20799749 AAAAGGATTAAAATATAAAAGAAATAAAAAT
1 AAAAGGATT-AAATTTAAAAAAAATAAAAAT
* *
20799780 AAAAGGGTTAAATTTTAACAAAAAATACAAAT
1 AAAAGGATTAAA-TTTAA-AAAAAATAAAAAT
*
20799812 AAAAGGATTTAATTTAAAAAAAA
1 AAAAGGATTAAATTTAAAAAAAA
20799835 GAATAAATGG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
30 9 0.19
31 17 0.36
32 21 0.45
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (30 bp):
AAAAGGATTAAATTTAAAAAAAATAAAAAT
Found at i:20799830 original size:62 final size:63
Alignment explanation
Indices: 20799749--20799891 Score: 150
Period size: 62 Copynumber: 2.3 Consensus size: 63
20799739 TAAAAAATGC
* * * * *
20799749 AAAAGGATTAAAATATAAAAGAAATAAAAATAAAAGGGTTAAA-TTTTAACAAAAA-ATACA-AA
1 AAAAGGATT-AAATTTAAAA-AAA-AAAAATAAAAGGGTAAAATTTTTAAAAAAAAGAAAAACAA
20799811 T
63 T
* * *
20799812 AAAAGGATTTAATTT-AAAAAAAAGAATAAATGGGTAAAATTTTTAAAAAAAAGAAAAACAAT
1 AAAAGGATTAAATTTAAAAAAAAAAAATAAAAGGGTAAAATTTTTAAAAAAAAGAAAAACAAT
*
20799874 AAGAGGATTAAATTTAAA
1 AAAAGGATTAAATTTAAA
20799892 TTAAAATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
59 15 0.23
60 14 0.21
61 6 0.09
62 20 0.30
63 11 0.17
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (63 bp):
AAAAGGATTAAATTTAAAAAAAAAAAATAAAAGGGTAAAATTTTTAAAAAAAAGAAAAACAAT
Found at i:20801831 original size:42 final size:42
Alignment explanation
Indices: 20801761--20803478 Score: 1732
Period size: 42 Copynumber: 40.8 Consensus size: 42
20801751 TTCTAGATTA
* *
20801761 GGGTAAAAGATTGGATGA--TCTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
20801801 GGGTAAGAGATTGGATAATGTCTTTAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20801843 GGGTAAAAGATTTGATGGTAG-CTTCAATCTGCCCCAT-AGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGA-TCG
*
20801885 GGGTAAGAGATTGGATGA--TCTTCAATCTGCCCCATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
20801925 GGGTAAGAGATTAGATGATGTCTTCAATCTG-CCCGTGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
20801966 GGATAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * *
20802008 GGGTAAGAGATTAGATGGTGTCTTCAATCTACCCCATTATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
20802050 GGGTAAGAGGTTGGATGATGTCCTCAATCTACCCCATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * *
20802092 AGGTAAGAGATTGGATAATGTCTTCAATCTGCCCTATGGTTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
20802134 GGGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* * **
20802176 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCTTCTTGACTTAA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC--CATGA--TCG
*
20802222 GGGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* * * **
20802264 GCGTAAGAGATTGGATGATGTCTTCAATTTACCTTATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20802306 GGGTAAGAGATTTGATGGTAG-CTTCAATCTGCCTCATGATCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* * * *
20802348 GGGTAAGAGATTGGATGA--TCTTTAATCT-ACCTAT-AGTCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGA-TCG
* * * * **
20802387 AGGTAAGAGATTGGATGATGTCTTAAATCTGCCCTTCTTAACTTAA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC--CATGA--TCG
* **
20802433 GGGTAAGAGATTGGATGATAG-CTTCAATCTGCCTCATGATTA
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
*
20802475 GGGTAAGAGATTAGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
20802517 GGGTAAGAGATTTGATGATAG-CTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* **
20802559 GGGTAAGAGATTGAATGA--TCTTCAATCTGCCCCATGATTT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
20802599 GGGTAAAAGATTGGATGATATCTTCAATCTG-CCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
20802640 GGATAAAAGATTGAATGATGTTTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
20802682 GGGTAAGAGATTAGATGGTGTCTTCAATCTGCCACATGATTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20802724 TGATAAGAGGTTGGATGATGTCTTCAATCTGCCCCAT-AGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGA-TCG
* * *
20802766 AGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
20802808 GGGTAGGAGATTCGATGGTAG-CTTCAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* * * * **
20802850 GGGCAAGAGATTGGATGATGTCTTCAATTTGCCCTTCTTAACTTAA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC--CATGA--TCG
* * * * **
20802896 TGGTAAGAGATTGGATGATAG-CTTCAATCTACCCTTCTTAACTTAA
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCC--CATGA--TCG
* *
20802942 GGGTAAGAGATTGGATGATAG-CTTCAATCTGCCTCATGGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* *
20802984 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
** * * * *
20803026 GGGTAAGAGATTTAATGGTATCTTGAATCTGCCCCATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
20803068 AGGTAAGAGATTAGATGA--TCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20803108 AGGTAGGAGATTAGATGATGTCTTCAATCTG-CCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20803149 GGATAAGAGATTAGATGATGTCTTCAATCTACCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * * *
20803191 AGATAAGAGATTAGATGGTGTCTTCAATTTGCCCCATGATTG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * *
20803233 TGGTAAGAGGTTGGATGATGTCCTCGATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * ** * *
20803275 AGGTAAGAGATTGAATGATGTCTTCAATCTATCCTATGGTCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * *
20803317 GGGTAATAGATTGGATGATAG-CTTCAATCTGTCCCATGGTCG
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
* **
20803359 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTTCTTGACTTAA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC--CATGA--TCG
* *
20803405 GGGTAAGAGATTGGATGATAG-CTTCAATCTACCCCATGGTC-
1 GGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATCG
*
20803446 GGG-AAGAGATTGGATGATGTCTTCAATCCGCCC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCC
20803479 TTCTTGACTT
Statistics
Matches: 1408, Mismatches: 215, Indels: 110
0.81 0.12 0.06
Matches are distributed among these distances:
38 1 0.00
39 23 0.02
40 156 0.11
41 130 0.09
42 900 0.64
43 6 0.00
44 21 0.01
45 1 0.00
46 166 0.12
47 4 0.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
Found at i:20802934 original size:509 final size:505
Alignment explanation
Indices: 20801762--20803438 Score: 2069
Period size: 509 Copynumber: 3.3 Consensus size: 505
20801752 TCTAGATTAG
* * * *
20801762 GGTAAAAGATTGGATGA--TCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATAAT-GTCT
1 GGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGGTCGGGGTAAGAGATTGGATGATAG-CT
* * * * * **
20801824 TTAATCTGCCCCATGATCGGGGTAAAAGATTTGATGGTAG-CTTCAATCTGCCC-CATA-GTCGG
65 TCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCTCATACTTAAG
* * * * *
20801886 GGTAAGAGATTGGATGAT-CTTCAATCTGCCC--CATGA--TCAGGGTAAGAGATTAGATGAT-G
129 GGTAAGAGATTGGATGATGCTTCAATCTACCCTTCTTAACTTAAGGGTAAGAGATTGGATGATAG
* *
20801945 TCTTCAATCTGCC-CGTGA-TCGGGATAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
194 -CTTCAATCTGCCTCATGATTAGGG-TAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * ** * * *
20802008 GGGTAAGAGATTAGATGGT-GTCTTCAATCTACCCCATTATCAGGGTAAGAGGTTGGATGATGTC
257 GGGTAAGAGATTTGATGGTAG-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGA--TC
* * * * * * *
20802072 CTCAATCTACCCCATGGTCGAGGTAAGAGATTGGATAATGTCTTCAATCTGCCCTATGGTTGGGG
319 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-ATGATCGGGA
* * *
20802137 TAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTC
383 TAAGAGATTGAATGAT-GTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTAGATGGTGTCTTC
* * * *
20802201 AATCTACCCTTCTTGACTTAAG-GGTAAGAGATTGGATGATAG-CTTCAATCTGCCCCATGGTCG
447 AATCT-GCC-ACATGA-TT--GTGGTAAGAGGTTGGATGAT-GTCTTCAATCTGCCCCAT-GTCG
20802264 -
505 A
* * * * *
20802264 GCGTAAGAGATTGGATGATGTCTTCAATTTACCTTATGATCGGGGTAAGAGATTTGATGGTAGCT
1 G-GTAAGAGATTGGATGATGTCTTCAATCTACCCTATGGTCGGGGTAAGAGATTGGATGATAGCT
* * * *
20802329 TCAATCTGCCTCATGATCGGGGTAAGAGATTGGATGA--TCTTTAATCT-ACCT-ATAGTCT-A-
65 TCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTCATACT-TAAG
* *
20802388 GGTAAGAGATTGGATGATGTCTTAAATCTGCCCTTCTTAACTTAAGGGTAAGAGATTGGATGATA
129 GGTAAGAGATTGGATGATG-CTTCAATCTACCCTTCTTAACTTAAGGGTAAGAGATTGGATGATA
*
20802453 GCTTCAATCTGCCTCATGATTAGGGTAAGAGATTAGATGATGTCTTCAATCTGCCCCATGATCGG
193 GCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGG
*
20802518 GGTAAGAGATTTGATGATAGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATCTTCA
258 GGTAAGAGATTTGATGGTAGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATCTTCA
* * * *
20802583 ATCTGCCCCATGATTTG-GGTAAAAGATTGGATGATATCTTCAATCTGCCCATGATCGGGATAAA
323 ATCTGCCCCATGA-TCGAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCATGATCGGGATAAG
*
20802647 AGATTGAATGATGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATTAGATGGTGTCTTCAATCT
387 AGATTGAATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTAGATGGTGTCTTCAATCT
*
20802712 GCCACATGATTGTGATAAGAGGTTGGATGATGTCTTCAATCTGCCCCATAGTCGA
452 GCCACATGATTGTGGTAAGAGGTTGGATGATGTCTTCAATCTGCCCCAT-GTCGA
* * * *
20802767 GGTAAGAGATTGGATGATGTCTTCAATCTGCCCTATGGTCGGGGTAGGAGATTCGATGGTAGCTT
1 GGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGGTCGGGGTAAGAGATTGGATGATAGCTT
* * * * *
20802832 CAATCTGCCCCATGGTCGGGGCAAGAGATTGGATGATGTCTTCAATTTGCCCTTCTTAACTTAAT
66 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-TCAT-ACTTAAG
20802897 GGTAAGAGATTGGATGATAGCTTCAATCTACCCTTCTTAACTTAAGGGTAAGAGATTGGATGATA
129 GGTAAGAGATTGGATGAT-GCTTCAATCTACCCTTCTTAACTTAAGGGTAAGAGATTGGATGATA
* ** * *
20802962 GCTTCAATCTGCCTCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGATCGG
193 GCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGG
* * * *
20803027 GGTAAGAGATTTAATGGTATCTTGAATCTGCCCCATGGTCGAGGTAAGAGATT-AGATGATCTTC
258 GGTAAGAGATTTGATGGTAGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGA-ATGATCTTC
* *
20803091 AATCTGCCCCATGATCGAGGTAGGAGATTAGATGATGTCTTCAATCTGCCCATGATCGGGATAAG
322 AATCTGCCCCATGATCGAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCATGATCGGGATAAG
* * * *
20803156 AGATT-AGATGATGTCTTCAATCTACCCCATGATCGAGATAAGAGATTAGATGGTGTCTTCAATT
387 AGATTGA-ATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTAGATGGTGTCTTCAATC
* * *
20803220 TGCCCCATGATTGTGGTAAGAGGTTGGATGATGTCCTCGATCTGCCCCATGATCGA
451 TGCCACATGATTGTGGTAAGAGGTTGGATGATGTCTTCAATCTGCCCCATG-TCGA
* * *
20803276 GGTAAGAGATTGAATGATGTCTTCAATCTATCCTATGGTCGGGGTAATAGATTGGATGATAGCTT
1 GGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGGTCGGGGTAAGAGATTGGATGATAGCTT
* * *
20803341 CAATCTGTCCCATGGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTTCTTGACTTAAG
66 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-TCAT-ACTTAAG
20803406 GGTAAGAGATTGGATGATAGCTTCAATCTACCC
129 GGTAAGAGATTGGATGAT-GCTTCAATCTACCC
20803439 CATGGTCGGG
Statistics
Matches: 1030, Mismatches: 109, Indels: 65
0.86 0.09 0.05
Matches are distributed among these distances:
501 2 0.00
502 151 0.15
503 26 0.03
504 25 0.02
505 72 0.07
506 74 0.07
507 48 0.05
508 42 0.04
509 584 0.57
510 6 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (505 bp):
GGTAAGAGATTGGATGATGTCTTCAATCTACCCTATGGTCGGGGTAAGAGATTGGATGATAGCTT
CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTCATACTTAAGGG
TAAGAGATTGGATGATGCTTCAATCTACCCTTCTTAACTTAAGGGTAAGAGATTGGATGATAGCT
TCAATCTGCCTCATGATTAGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGT
AAGAGATTTGATGGTAGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATCTTCAATC
TGCCCCATGATCGAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCATGATCGGGATAAGAGAT
TGAATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTAGATGGTGTCTTCAATCTGCCA
CATGATTGTGGTAAGAGGTTGGATGATGTCTTCAATCTGCCCCATGTCGA
Found at i:20803805 original size:40 final size:40
Alignment explanation
Indices: 20803709--20803811 Score: 145
Period size: 40 Copynumber: 2.6 Consensus size: 40
20803699 CAGTCTATCT
* * * *
20803709 CATGGTCGAGGTAAGAGATTGGTGCGTCTTTAATCTGCCC
1 CATGGTCGGGGTAAGATATTGGTGCATCTTTAATCTGCAC
*
20803749 CATGGTCGGGGTAAGATATTGGTGCATCTTTAATCTGTAC
1 CATGGTCGGGGTAAGATATTGGTGCATCTTTAATCTGCAC
*
20803789 CATGGTTGGGGTAAGAT-TTGGTG
1 CATGGTCGGGGTAAGATATTGGTG
20803812 AGTAGTTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 6 0.11
40 51 0.89
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (40 bp):
CATGGTCGGGGTAAGATATTGGTGCATCTTTAATCTGCAC
Found at i:20804309 original size:146 final size:146
Alignment explanation
Indices: 20804068--20804582 Score: 444
Period size: 146 Copynumber: 3.5 Consensus size: 146
20804058 TTGCCCTTAT
* * *
20804068 GGCTTCAATCTAACCCTCTTATTTCTAAGGTATAAGGTTCACTATTGCGGCCTCAACCTTTCCCT
1 GGCTTCAATCTAACCCTCTTATTTCTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCT
* * * * * * * * * * *
20804133 TCATATCTCTAGGGTATAAGGTTCGCCGTTGCGGTATCGATCGCTCTTTTCACATTTTTAGGGTT
66 TCACATCTTTAGGGTACAAGATTCGCCGTTGCGGCATCAATCGCTCCTTTCACAATTCTAAGGTA
**
20804198 TAAGATTCGTCATTAC
131 TAAGATTCACCATTAC
* *
20804214 GGCTTCAATCTAGCCCTCTTATTTTTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCT
1 GGCTTCAATCTAACCCTCTTATTTCTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCT
* * * * **
20804279 TCACATCTTTAGGGTACAAGATTTGTCGTTGTGGCGTCAATCTTTCCTTTCACAATTCTAAGGTA
66 TCACATCTTTAGGGTACAAGATTCGCCGTTGCGGCATCAATCGCTCCTTTCACAATTCTAAGGTA
* *
20804344 TAAGGTTCACCATTGC
131 TAAGATTCACCATTAC
* * * ** ** * ** * *
20804360 AGCCTCAACCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGCCATTATGACCTCGACCTTTCCC
1 GGCTTCAATCTAACCC-TCTTATTTCTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCC
* * * * * *
20804425 TTCACATCTTTAGGGTTCAAGATTCGCCATTGCAGCTTCAATCTTGC-CCTTT--TATTTCTAAG
65 TTCACATCTTTAGGGTACAAGATTCGCCGTTGCGGCATCAATC--GCTCCTTTCACAATTCTAAG
* * *
20804487 GTATAAGGTTCACCGTTTC
128 GTATAAGATTCACCATTAC
* * ** * * * * *
20804506 GGCCTCAACCTTTCCCT-TTACATCTCTAGGGTATAAGATTTGCCGTTGCGGCCTCAAACTTTCC
1 GGCTTCAATCTAACCCTCTT--ATTTCTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCC
*
20804570 TTTCACATCTTTA
64 CTTCACATCTTTA
20804583 AGGAATAGTA
Statistics
Matches: 300, Mismatches: 64, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
145 1 0.00
146 218 0.73
147 76 0.25
148 5 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (146 bp):
GGCTTCAATCTAACCCTCTTATTTCTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCT
TCACATCTTTAGGGTACAAGATTCGCCGTTGCGGCATCAATCGCTCCTTTCACAATTCTAAGGTA
TAAGATTCACCATTAC
Found at i:20804324 original size:49 final size:49
Alignment explanation
Indices: 20804096--20804582 Score: 345
Period size: 49 Copynumber: 10.0 Consensus size: 49
20804086 TTATTTCTAA
* * * * *
20804096 GGTATAAGGTTCACTATTGCGGCCTCAACCTTTCCCTTCATATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* * ** * * ** ** *
20804145 GGTATAAGGTTCGCCGTTGCGGTATCGATCGCTCTTTTCACATTTTTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* * * * * ** ** *
20804194 GGTTTAAGATTCGTCATTACGGCTTCAATCTAGCCC-TCTTATTTTTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
*
20804242 GGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* * * * * * * * * *
20804291 GGTACAAGATTTGTCGTTGTGGCGTCAATCTTTCCTTTCACAAT-TCTAA
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCAC-ATCTTTAG
* * * *
20804340 GGTATAAGGTTCACCATTGCAGCCTCAACCTTTCCCTTCACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* ** * *
20804389 GGTATAAGGTTCGCCATTATGACCTCGACCTTTCCCTTCACATCTTTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* * * * ** *
20804438 GGT-TCAAGATTCGCCATTGCAGCTTCAATCTTGCCCTT-TTAT-TTCTAA
1 GGTAT-AAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTT-TAG
* * * * * *
20804486 GGTATAAGGTTCACCGTTTCGGCCTCAACCTTTCCCTTTACATCTCTAG
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
* * * *
20804535 GGTATAAGATTTGCCGTTGCGGCCTCAAACTTTCCTTTCACATCTTTA
1 GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTA
20804583 AGGAATAGTA
Statistics
Matches: 328, Mismatches: 102, Indels: 16
0.74 0.23 0.04
Matches are distributed among these distances:
47 2 0.01
48 73 0.22
49 250 0.76
50 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (49 bp):
GGTATAAGATTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAG
Found at i:20804431 original size:244 final size:244
Alignment explanation
Indices: 20803994--20804576 Score: 711
Period size: 244 Copynumber: 2.4 Consensus size: 244
20803984 CCTTTACATC
* * * * * *
20803994 TCTAGGGTATAAGGTTCATCGTTGTC-GCCTCGACCTTTCCCTTCACGTCATTAGGGTTCAACAT
1 TCTAGGGTATAAGGTTCACCGTTG-CGGCCTCAACCTTTCCCTTCACATCTTTAGGGTACAAGAT
* * * ** * ** * * *
20804058 TTGCCCTTATGGCTTCAATCTAACC-CTCTTATTTCTAAGGTATAAGGTTCACTATTGCGGCCTC
65 TTGCCGTTGTGGCCTCAATCTTTCCTTTCACAATTCTAAGGTATAAGGTTCACCATTGCAGCCTC
* * * ** * **
20804122 AACCTTTCCCTTCATATCTCTAGGGTATAAGGTTCGCCGTTGCGGTATCGATCGCTCTTTTCACA
130 AACCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGCCATTACGACATCGACCGCTCCCTTCACA
* * * *
20804187 TTTTTAGGGTTTAAGATTCGTCATTACGGCTTCAATCTAGCCCTCTTATT
195 TCTTTAGGGTTCAAGATTCGCCATTACAGCTTCAATCTAGCCCTCTTATT
* * *
20804237 TTTAGGGTATAAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCACATCTTTAGGGTACAAGATT
1 TCTAGGGTATAAGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTAGGGTACAAGATT
* *
20804302 TGTCGTTGTGGCGTCAATCTTTCCTTTCACAATTCTAAGGTATAAGGTTCACCATTGCAGCCTCA
66 TGCCGTTGTGGCCTCAATCTTTCCTTTCACAATTCTAAGGTATAAGGTTCACCATTGCAGCCTCA
* * **
20804367 ACCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGCCATTATGACCTCGACCTTTCCCTTCACAT
131 ACCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGCCATTACGACATCGACCGCTCCCTTCACAT
* * *
20804432 CTTTAGGGTTCAAGATTCGCCATTGCAGCTTCAATCTTGCCCTTTTATT
196 CTTTAGGGTTCAAGATTCGCCATTACAGCTTCAATCTAGCCCTCTTATT
* * * * *
20804481 TCTAAGGTATAAGGTTCACCGTTTCGGCCTCAACCTTTCCCTTTACATCTCTAGGGTATAAGATT
1 TCTAGGGTATAAGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTAGGGTACAAGATT
* *
20804546 TGCCGTTGCGGCCTCAAACTTTCCTTTCACA
66 TGCCGTTGTGGCCTCAATCTTTCCTTTCACA
20804577 TCTTTAAGGA
Statistics
Matches: 286, Mismatches: 52, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
242 1 0.00
243 72 0.25
244 213 0.74
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (244 bp):
TCTAGGGTATAAGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTTAGGGTACAAGATT
TGCCGTTGTGGCCTCAATCTTTCCTTTCACAATTCTAAGGTATAAGGTTCACCATTGCAGCCTCA
ACCTTTCCCTTCACATCTCTAGGGTATAAGGTTCGCCATTACGACATCGACCGCTCCCTTCACAT
CTTTAGGGTTCAAGATTCGCCATTACAGCTTCAATCTAGCCCTCTTATT
Found at i:20805229 original size:112 final size:111
Alignment explanation
Indices: 20805043--20805247 Score: 329
Period size: 112 Copynumber: 1.8 Consensus size: 111
20805033 CACTAATCGC
*
20805043 TATTTCAATGCAAAAATGTTTGAACAAGAATGTAAGATGGATAAAATTGAGTTTTATTGAAGGCA
1 TATTTCAATGCAAAAATGATTGAACAAGAATGTAAGATGGATAAAATTGAGTTTTATTGAAGGCA
*
20805108 AAGCTCGCATGAATGAAAAGTTTAAAAATCATTGGTCCACTAACAGT
66 AAGCTCGCATGAATGAAAAG-ATAAAAATCATTGGTCCACTAACAGT
* * ** * *
20805155 TATTTCAATTCAAAAATGATTGAATAAGGTTGTAAGGTGGATAAAATTGAGTTTTATTGGAGGCA
1 TATTTCAATGCAAAAATGATTGAACAAGAATGTAAGATGGATAAAATTGAGTTTTATTGAAGGCA
20805220 AAGCTCGCATGAATGAAAAGATAAAAAT
66 AAGCTCGCATGAATGAAAAGATAAAAAT
20805248 AACGAATATT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 7 0.08
112 78 0.92
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (111 bp):
TATTTCAATGCAAAAATGATTGAACAAGAATGTAAGATGGATAAAATTGAGTTTTATTGAAGGCA
AAGCTCGCATGAATGAAAAGATAAAAATCATTGGTCCACTAACAGT
Found at i:20805569 original size:6 final size:6
Alignment explanation
Indices: 20805560--20805611 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
20805550 CGACCTCTCC
* * * *
20805560 TTTTCT TTTTCCT TCTT-T TTTTCT TTTTCT TTTCCA TTTCCT TTTTCT
1 TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
20805608 TTTT
1 TTTT
20805612 TTTCTCTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
7 5 0.13
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:20805587 original size:24 final size:22
Alignment explanation
Indices: 20805560--20805641 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 22
20805550 CGACCTCTCC
20805560 TTTTCTTTTTCCTTCTTTTTTTCT
1 TTTTC-TTTTCCTTCTTTTTTT-T
20805584 TTTTCTTTTCCATTTCCTTTTTCTTTT
1 TTTTCTTTTCC--TT-C-TTTT-TTTT
*
20805611 TTTTCTCTTCCTT-TTTTTTATT
1 TTTTCTTTTCCTTCTTTTTT-TT
*
20805633 TTTTATTTT
1 TTTTCTTTT
20805642 TTGGCGGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.04
22 13 0.27
23 6 0.12
24 5 0.10
25 4 0.08
26 1 0.02
27 15 0.31
28 3 0.06
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTCCTTCTTTTTTTT
Found at i:20805601 original size:29 final size:27
Alignment explanation
Indices: 20805567--20805636 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 27
20805557 TCCTTTTCTT
* *
20805567 TTTCCTTCTTTTTTTCTTTTTCTTTTCCA
1 TTTCCTT-TTTCTTT-TTTTTCTCTTCCA
20805596 TTTCCTTTTTCTTTTTTTTCTCTTCC-
1 TTTCCTTTTTCTTTTTTTTCTCTTCCA
*
20805622 TTT--TTTTTATTTTTT
1 TTTCCTTTTTCTTTTTT
20805637 ATTTTTTGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 11 0.29
26 3 0.08
27 11 0.29
28 6 0.16
29 7 0.18
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTCCTTTTTCTTTTTTTTCTCTTCCA
Found at i:20810186 original size:106 final size:108
Alignment explanation
Indices: 20809988--20810200 Score: 272
Period size: 107 Copynumber: 2.0 Consensus size: 108
20809978 CACAAATAAA
* *
20809988 GAACATTGATTAATTTAAAATAGGATACTCAATTATTTAGGTTTTAAAAAAATCACACCCAGTAC
1 GAACATTGATTAATTTAAAATAGGATACTCAATTATTTAGGTTTAAAAAAAATCACACCCAATAC
* * *
20810053 GTTTGAGCACAATTTTTTGAATTCCCT-AAATAAAAGAACATC
66 GTTAGAGCACAATTTATCGAATTCCCTAAAATAAAAGAACATC
* * * ** *
20810095 GAACATTTATTCATTTTAAATAGGATACTTGATTATTTAGG-TTAAAAAAAA-CTATACCCAATA
1 GAACATTGATTAATTTAAAATAGGATACTCAATTATTTAGGTTTAAAAAAAATC-ACACCCAATA
*
20810158 CGTTA-AGGCACAATTTATCGAATTCCCTAAAATAAAATAACAT
65 CGTTAGA-GCACAATTTATCGAATTCCCTAAAATAAAAGAACAT
20810201 TGCATCGAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
105 2 0.02
106 40 0.44
107 49 0.54
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (108 bp):
GAACATTGATTAATTTAAAATAGGATACTCAATTATTTAGGTTTAAAAAAAATCACACCCAATAC
GTTAGAGCACAATTTATCGAATTCCCTAAAATAAAAGAACATC
Found at i:20810564 original size:30 final size:30
Alignment explanation
Indices: 20810521--20810597 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
20810511 TTAAAATATA
* *
20810521 AAAAATAGAATAAAAGGG-TAATTTTTAA-
1 AAAAATAAAATAAAAGGGTTAAATTTTAAC
20810549 AAGAAATAAAAATAAAAGGGTTAAATTTTAAC
1 AA-AAAT-AAAATAAAAGGGTTAAATTTTAAC
20810581 AAAAATAAAATAAAAGG
1 AAAAATAAAATAAAAGG
20810598 ATTTAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 2 0.05
29 4 0.09
30 22 0.51
31 13 0.30
32 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.13, T:0.23
Consensus pattern (30 bp):
AAAAATAAAATAAAAGGGTTAAATTTTAAC
Found at i:20810626 original size:51 final size:52
Alignment explanation
Indices: 20810556--20810657 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
20810546 TAAAAGAAAT
* * * * *
20810556 AAAAATAAAAGGGTTAAATTTTAACAAA-AATAA-AATAAAAGGATTTAATTA
1 AAAAATAAAAGAG-TAAAATTTAAAAAAGAAAAACAATAAAAGGATTAAATTA
*
20810607 AAAAATAAATGAGTAAAATTTAAAAAAGAAAAACAATAAAAGGATTAAATT
1 AAAAATAAAAGAGTAAAATTTAAAAAAGAAAAACAATAAAAGGATTAAATT
20810658 TAAATTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 12 0.28
51 15 0.35
52 16 0.37
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.25
Consensus pattern (52 bp):
AAAAATAAAAGAGTAAAATTTAAAAAAGAAAAACAATAAAAGGATTAAATTA
Found at i:20817170 original size:12 final size:13
Alignment explanation
Indices: 20817125--20817167 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
20817115 GAGTCATAAA
20817125 AATTAATATAAAAT
1 AATTAAT-TAAAAT
*
20817139 GAATTAATT-AATT
1 -AATTAATTAAAAT
20817152 AATTAATTAAAAT
1 AATTAATTAAAAT
20817165 AAT
1 AAT
20817168 AATAATCAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 1 0.04
15 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AATTAATTAAAAT
Found at i:20818130 original size:34 final size:35
Alignment explanation
Indices: 20818059--20818131 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
20818049 TGTTATACCA
* * *
20818059 TGTGCGAACCTATGTTATTATGCGAACTTTTACAT
1 TGTGCGAACCCATGTTATTATGCGAACTGTAACAT
*
20818094 TGTGCGAACCCATGTT-TTATGCGAACTGTAATAT
1 TGTGCGAACCCATGTTATTATGCGAACTGTAACAT
20818128 TGTG
1 TGTG
20818132 AACTCTGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (35 bp):
TGTGCGAACCCATGTTATTATGCGAACTGTAACAT
Found at i:20819507 original size:27 final size:27
Alignment explanation
Indices: 20819469--20819527 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
20819459 TAGGAGATGG
* *
20819469 CAGGGTAAGTTGCGAACTA-GTGGTTCA
1 CAGGGCAAGTTGCAAACTAGGT-GTTCA
20819496 CAGGGCAAGTTGCAAACTAGGTGTTCA
1 CAGGGCAAGTTGCAAACTAGGTGTTCA
20819523 CAGGG
1 CAGGG
20819528 TAGGTCGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (27 bp):
CAGGGCAAGTTGCAAACTAGGTGTTCA
Found at i:20820819 original size:13 final size:13
Alignment explanation
Indices: 20820798--20820839 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20820788 TTTTAATCGA
20820798 TTATTTATTT-TT
1 TTATTTATTTATT
*
20820810 CTTGTTTATTTATT
1 -TTATTTATTTATT
20820824 TTATTTATTTAATT
1 TTATTTATTT-ATT
20820838 TT
1 TT
20820840 CTATCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:20832295 original size:15 final size:16
Alignment explanation
Indices: 20832275--20832308 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20832265 GTGTTCATTA
*
20832275 GTCAGA-TCGGGCTGG
1 GTCAGATTCGGACTGG
20832290 GTCAGATTCGGACTGG
1 GTCAGATTCGGACTGG
20832306 GTC
1 GTC
20832309 TAAGCATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.21, G:0.41, T:0.24
Consensus pattern (16 bp):
GTCAGATTCGGACTGG
Found at i:20832502 original size:16 final size:17
Alignment explanation
Indices: 20832483--20832517 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20832473 ATATTTAATA
20832483 ATTTTGT-AAATTTTTT
1 ATTTTGTAAAATTTTTT
*
20832499 ATTTTTTAAAATTTTTT
1 ATTTTGTAAAATTTTTT
20832516 AT
1 AT
20832518 ATTATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTTGTAAAATTTTTT
Found at i:20835659 original size:10 final size:9
Alignment explanation
Indices: 20835641--20835673 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
20835631 AGGCTTAAAA
20835641 TATTTATAT
1 TATTTATAT
20835650 TATATTATAT
1 TAT-TTATAT
20835660 TATTT-TAT
1 TATTTATAT
20835668 TATTTA
1 TATTTA
20835674 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTATAT
Found at i:20835680 original size:16 final size:18
Alignment explanation
Indices: 20835642--20835683 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
20835632 GGCTTAAAAT
*
20835642 ATTTATATTATATTATATT
1 ATTT-TATTATATTATATA
20835661 ATTTTATTAT-TTA-ATA
1 ATTTTATTATATTATATA
20835677 ATTTTAT
1 ATTTTAT
20835684 ACATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 3 0.14
18 6 0.27
19 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTATTATATTATATA
Found at i:20846856 original size:17 final size:17
Alignment explanation
Indices: 20846834--20846866 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20846824 TTTAAAAGCA
*
20846834 TAAAATAAAAGATAAAC
1 TAAAATAAAAAATAAAC
20846851 TAAAATAAAAAATAAA
1 TAAAATAAAAAATAAA
20846867 GGAGAAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAATAAAAAATAAAC
Found at i:20847437 original size:13 final size:13
Alignment explanation
Indices: 20847411--20847444 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20847401 CTCGTTTTAC
*
20847411 AACTGAAAATTAAA
1 AACT-AAAACTAAA
20847425 AACTAAAACTAAA
1 AACTAAAACTAAA
20847438 AACTAAA
1 AACTAAA
20847445 GTCTAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.18
Consensus pattern (13 bp):
AACTAAAACTAAA
Found at i:20850019 original size:19 final size:22
Alignment explanation
Indices: 20849990--20850029 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20849980 TTTTAATTAA
20849990 TTCTATTATGG-T-TTTGGACT
1 TTCTATTATGGATATTTGGACT
20850010 TTCT-TTATGGATATTTGGAC
1 TTCTATTATGGATATTTGGAC
20850030 GCATGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (22 bp):
TTCTATTATGGATATTTGGACT
Found at i:20862823 original size:27 final size:26
Alignment explanation
Indices: 20862785--20862841 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
20862775 AAAAATATTG
*
20862785 AAATAAAGGATTGT-ATTTAAAATAA-A
1 AAATAAAAGATT-TAATTTAAAA-AACA
20862811 AAATAAAAAGATTTAATTTAAAAAACA
1 AAAT-AAAAGATTTAATTTAAAAAACA
20862838 AAAT
1 AAAT
20862842 GAATGAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (26 bp):
AAATAAAAGATTTAATTTAAAAAACA
Found at i:20864815 original size:39 final size:39
Alignment explanation
Indices: 20864769--20865057 Score: 269
Period size: 39 Copynumber: 7.2 Consensus size: 39
20864759 AAGGTAAAAA
20864769 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAG
1 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAG
** * *
20864808 ATTGGATGATATATTCAATATGCCCCATGATCAGGGTAAGAT
1 ATTGGATG---GCTTCAATCTGCCCCATGATCAGGGTAAGAG
* *
20864850 ATTGGATGGCTTCAATCTGCCCCATCATCGGGGTAAGAG
1 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAG
* * * * *
20864889 ATTAGATGATGTCTTTAATTTGCCCCATAATCGGGGTAAGAG
1 ATT-G--GATGGCTTCAATCTGCCCCATGATCAGGGTAAGAG
* * * *
20864931 ATCGGGTGGCTGT-GATCTGCCCCATGATTTA-GGTAAGAG
1 ATTGGATGGCT-TCAATCTGCCCCATGA-TCAGGGTAAGAG
* * * *
20864970 ATCGGATGGTTTTCAATCTGGCCCATGATCGGGGTAAGAG
1 ATTGGATGG-CTTCAATCTGCCCCATGATCAGGGTAAGAG
* * *
20865010 ATTAGATGG-TTGCGATCTGCCCTATGATCAGGGTAAGAG
1 ATTGGATGGCTT-CAATCTGCCCCATGATCAGGGTAAGAG
20865049 ATTGGATGG
1 ATTGGATGG
20865058 TTGATGTAGC
Statistics
Matches: 203, Mismatches: 35, Indels: 24
0.77 0.13 0.09
Matches are distributed among these distances:
38 2 0.01
39 101 0.50
40 31 0.15
41 1 0.00
42 68 0.33
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (39 bp):
ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAG
Found at i:20864859 original size:81 final size:79
Alignment explanation
Indices: 20864769--20865056 Score: 321
Period size: 81 Copynumber: 3.6 Consensus size: 79
20864759 AAGGTAAAAA
20864769 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATATATTCAATATGCCCC
1 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGAT-T-TTCAATATGCCCC
* *
20864834 ATGATCAGGGTAAGAT
64 ATGATCGGGGTAAGAG
* * * * *
20864850 ATTGGATGGCTTCAATCTGCCCCATCATCGGGGTAAGAGATTAGATGATGTCTTTAATTTGCCCC
1 ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGAT-T-TTCAATATGCCCC
*
20864915 ATAATCGGGGTAAGAG
64 ATGATCGGGGTAAGAG
* * * * * * * *
20864931 ATCGGGTGGCTGT-GATCTGCCCCATGATTTA-GGTAAGAGATCGGATGGTTTTCAATCTGGCCC
1 ATTGGATGGCT-TCAATCTGCCCCATGA-TCAGGGTAAGAGATTGGATGATTTTCAATATGCCCC
20864994 ATGATCGGGGTAAGAG
64 ATGATCGGGGTAAGAG
* * *
20865010 ATTAGATGG-TTGCGATCTGCCCTATGATCAGGGTAAGAGATTGGATG
1 ATTGGATGGCTT-CAATCTGCCCCATGATCAGGGTAAGAGATTGGATG
20865057 GTTGATGTAG
Statistics
Matches: 173, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
77 1 0.01
78 3 0.02
79 59 0.34
80 1 0.01
81 107 0.62
82 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (79 bp):
ATTGGATGGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATTTTCAATATGCCCCAT
GATCGGGGTAAGAG
Found at i:20865473 original size:50 final size:50
Alignment explanation
Indices: 20865335--20865628 Score: 190
Period size: 50 Copynumber: 5.9 Consensus size: 50
20865325 ATCCTTCCCA
* * *
20865335 TCACATCTTC-ATGGTACCGGGTTTGT-CATTGCAGCCTCAACCTTTCCCA
1 TCACATCTTCTAAGGTACCGGGTTT-TCCATTGCAGCCTCAACCTTTCTCT
* ** ** * *
20865384 TCACATCTTCTAAGGTATCGGGTTCACTGTTGCAACCTCAACATTTCTCT
1 TCACATCTTCTAAGGTACCGGGTTTTCCATTGCAGCCTCAACCTTTCTCT
* *
20865434 TCACATCTTTTAAGGTACCGGGTTTTCCATTGCGGCCTCAACCTTTCTC-
1 TCACATCTTCTAAGGTACCGGGTTTTCCATTGCAGCCTCAACCTTTCTCT
* * * * * * * * *
20865483 T-ACATTTTTTTCATGGTACCAGATTTGT-CATTGCGGCCTCAA-TTCTTCCCA
1 TCACA-TCTTCT-AAGGTACCGGGTTT-TCCATTGCAGCCTCAACCT-TTCTCT
* * * ** *
20865534 TCACATTTTCTAAGGTATCAGGTTCGCCGTTGCAGCCTCAACCTTTC-CT
1 TCACATCTTCTAAGGTACCGGGTTTTCCATTGCAGCCTCAACCTTTCTCT
* * ** * *
20865583 TCAAATCTTC-ATGGTACCGGGTTCGCCGTTGCAGCCTCGACCTTTC
1 TCACATCTTCTAAGGTACCGGGTTTTCCATTGCAGCCTCAACCTTTC
20865629 CCATCGCATT
Statistics
Matches: 194, Mismatches: 41, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
48 35 0.18
49 26 0.13
50 122 0.63
51 8 0.04
52 3 0.02
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.35
Consensus pattern (50 bp):
TCACATCTTCTAAGGTACCGGGTTTTCCATTGCAGCCTCAACCTTTCTCT
Found at i:20865639 original size:150 final size:150
Alignment explanation
Indices: 20865342--20865630 Score: 377
Period size: 150 Copynumber: 1.9 Consensus size: 150
20865332 CCATCACATC
* * *
20865342 TTCATGGTACCGGGTTTGTCATTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGT
1 TTCATGGTACCAGATTTGTCATTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCAGGT
* * * ** *
20865407 TCACTGTTGCAACCTCAACATTTCTCTTCACATCTTTTAAGGTACCGGGTTTTCCATTGCGGCCT
66 TCACCGTTGCAACCTCAACATTTCTCTTCAAATCTTTCAAGGTACCGGGTTCGCCATTGCAGCCT
*
20865472 CAACCTTTCTCTACATTTTT
131 CAACCTTTCCCTACATTTTT
* * *
20865492 TTCATGGTACCAGATTTGTCATTGCGGCCTCAA-TTCTTCCCATCACATTTTCTAAGGTATCAGG
1 TTCATGGTACCAGATTTGTCATTGCAGCCTCAACCT-TTCCCATCACATCTTCTAAGGTATCAGG
* * * * *
20865556 TTCGCCGTTGCAGCCTCAACCTTTC-CTTCAAATC-TTCATGGTACCGGGTTCGCCGTTGCAGCC
65 TTCACCGTTGCAACCTCAACATTTCTCTTCAAATCTTTCAAGGTACCGGGTTCGCCATTGCAGCC
*
20865619 TCGACCTTTCCC
130 TCAACCTTTCCC
20865631 ATCGCATTTC
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
148 33 0.28
149 9 0.08
150 77 0.65
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (150 bp):
TTCATGGTACCAGATTTGTCATTGCAGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCAGGT
TCACCGTTGCAACCTCAACATTTCTCTTCAAATCTTTCAAGGTACCGGGTTCGCCATTGCAGCCT
CAACCTTTCCCTACATTTTT
Found at i:20866652 original size:13 final size:13
Alignment explanation
Indices: 20866618--20866660 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
20866608 CCTTTTCTCT
*
20866618 TTTTTCTTTCTT-
1 TTTTTCTTTTTTA
*
20866630 TTTCTCTTTTTTA
1 TTTTTCTTTTTTA
20866643 TTTTTCTTTTTTA
1 TTTTTCTTTTTTA
20866656 TTTTT
1 TTTTT
20866661 TGGGTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTTA
Found at i:20871435 original size:3 final size:3
Alignment explanation
Indices: 20871427--20871467 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20871417 AAAATGGACC
20871427 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20871468 ATAAAGGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20872631 original size:17 final size:17
Alignment explanation
Indices: 20872610--20872733 Score: 142
Period size: 17 Copynumber: 7.2 Consensus size: 17
20872600 CTCAATCCAT
20872610 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
20872628 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
20872644 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
20872661 TTTAAATTTATTCTAAAA
1 TTTAAATTTATT-TTAAA
* *
20872679 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
20872696 TTTAATTTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
** *
20872714 TTTAAAACTATTATAAA
1 TTTAAATTTATTTTAAA
20872731 TTT
1 TTT
20872734 GAATGTCTAG
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.01
17 61 0.68
18 28 0.31
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:20872664 original size:6 final size:6
Alignment explanation
Indices: 20872610--20872719 Score: 81
Period size: 6 Copynumber: 19.0 Consensus size: 6
20872600 CTCAATCCAT
* * * *
20872610 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTGAA TTT-AT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
20872655 TTTAAA TTTAAA TTT--A TTCTAAAA TTTAAA TTT-AA TTTAAG TTTAAT
1 TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTAAA TTTAAA TTTAAA
*
20872702 TTTATA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
20872720 ACTATTATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
4 3 0.04
5 19 0.23
6 56 0.68
7 1 0.01
8 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:20872687 original size:35 final size:34
Alignment explanation
Indices: 20872610--20872733 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 34
20872600 CTCAATCCAT
20872610 TTTAAATTTATTTTAAGA-TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTTAAA
* *
20872644 TTTGAATTTATTTTAAATTTAAATTTATTCTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATT-TTAAA
* * *
20872679 TTTAAATTTAATTTAAGTTTAATTTTATATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTAT-TTTAAA
** *
20872714 TTTAAAACTATTATAAATTT
1 TTTAAATTTATTTTAAATTT
20872734 GAATGTCTAG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.01
34 26 0.35
35 47 0.63
36 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Found at i:20874630 original size:29 final size:29
Alignment explanation
Indices: 20874588--20874678 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
20874578 TAAACTGTCC
** *
20874588 AAAAATTGTATTTTGACCCCTGAACTTCT
1 AAAAATTACATTTTAACCCCTGAACTTCT
* *
20874617 AAAAATTCCATTTTTAACCCC-GAAACTTCC
1 AAAAATTACA-TTTTAACCCCTG-AACTTCT
*
20874647 AAAAATTACATTTTTA-CCCTCGAACTTCT
1 AAAAATTACATTTTAACCCCT-GAACTTCT
20874676 AAA
1 AAA
20874679 CTTCCAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 23 0.45
30 25 0.49
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCTGAACTTCT
Found at i:20874644 original size:30 final size:29
Alignment explanation
Indices: 20874605--20874678 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
20874595 GTATTTTGAC
*
20874605 CCCT-GAACTTCTAAAAATTCCATTTTTAA
1 CCCTCGAACTTCTAAAAATTACATTTTT-A
*
20874634 CCC-CGAAACTTCCAAAAATTACATTTTTA
1 CCCTCG-AACTTCTAAAAATTACATTTTTA
20874663 CCCTCGAACTTCTAAA
1 CCCTCGAACTTCTAAA
20874679 CTTCCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCTCGAACTTCTAAAAATTACATTTTTA
Found at i:20874740 original size:67 final size:67
Alignment explanation
Indices: 20874610--20874741 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 67
20874600 TTGACCCCTG
* * * **
20874610 AACTTCTAAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTC
1 AACTTCCAAAAATTACATTTTTAACCCCGAAAATTCCAAAAATTACATTTTTACCCTAAAACTTC
20874675 TA
66 TA
* * * *
20874677 AACTTCCAAAAATTATATTTTT-ACCCCTAAAATTCCAAAAATTTCATTTTTGACCTTAAAACTT
1 AACTTCCAAAAATTACATTTTTAACCCCGAAAATTCCAAAAATTACATTTTT-ACCCTAAAACTT
20874741 C
65 C
20874742 CAAAAATTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 26 0.47
67 29 0.53
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (67 bp):
AACTTCCAAAAATTACATTTTTAACCCCGAAAATTCCAAAAATTACATTTTTACCCTAAAACTTC
TA
Found at i:20874749 original size:96 final size:96
Alignment explanation
Indices: 20874577--20874761 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
20874567 ATGAAGGTCC
* * * * *
20874577 CTAAACTGTCCAAAAATTGTATTTTGACCCCTGAACTTCTAAAAATTCCATTTTTAACCCCGAAA
1 CTAAACTGTCCAAAAATTATATTTTGACCCCTAAAATTCCAAAAATTCCATTTTTAACCCCAAAA
20874642 CTTCCAAAAATTACATTTTTACCCTCGAACTT
66 CTTCCAAAAATTACA-TTTTACCCTCGAACTT
* * * **
20874674 CTAAACT-TCCAAAAATTATATTTTTACCCCTAAAATTCCAAAAATTTCATTTTTGACCTTAAAA
1 CTAAACTGTCCAAAAATTATATTTTGACCCCTAAAATTCCAAAAATTCCATTTTTAACCCCAAAA
20874738 CTTCCAAAAATTACATTTTACCCT
66 CTTCCAAAAATTACATTTTACCCT
20874762 TGAAACTACA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 9 0.12
96 62 0.79
97 7 0.09
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (96 bp):
CTAAACTGTCCAAAAATTATATTTTGACCCCTAAAATTCCAAAAATTCCATTTTTAACCCCAAAA
CTTCCAAAAATTACATTTTACCCTCGAACTT
Found at i:20874762 original size:29 final size:30
Alignment explanation
Indices: 20874676--20874785 Score: 120
Period size: 29 Copynumber: 3.8 Consensus size: 30
20874666 TCGAACTTCT
* *
20874676 AAACTTCCAAAAATTATATTTTTACCCCTA
1 AAACTTCCAAAAATTACATTTTTACCCTTA
*
20874706 AAA-TTCCAAAAATTTCATTTTTGA-CCTTA
1 AAACTTCCAAAAATTACATTTTT-ACCCTTA
*
20874735 AAACTTCCAAAAATTACA-TTTTACCCTTG
1 AAACTTCCAAAAATTACATTTTTACCCTTA
* * *
20874764 AAAC-TACAGAAATTCCATTTTT
1 AAACTTCCAAAAATTACATTTTT
20874786 GACTTCAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 11 0.16
29 40 0.59
30 17 0.25
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTACCCTTA
Found at i:20874785 original size:58 final size:58
Alignment explanation
Indices: 20874676--20874820 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 58
20874666 TCGAACTTCT
* * * *
20874676 AAACTTCCAAAAATTATATTTTTACCCCTAAAATTCCAAAAATTTCATTTTTGACCTT-A
1 AAACTTCCAAAAATTACA-TTTTACCCCTAAAACTACAAAAATTCCATTTTTGA-CTTAA
* * *
20874735 AAACTTCCAAAAATTACATTTTACCCTTGAAACTACAGAAATTCCATTTTTGACTTCAA
1 AAACTTCCAAAAATTACATTTTACCCCTAAAACTACAAAAATTCCATTTTTGACTT-AA
*
20874794 AAAATT-CAAAAATTACCATTTTACCCC
1 AAACTTCCAAAAATTA-CATTTTACCCC
20874821 GAATGTCCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 3 0.04
58 38 0.51
59 33 0.45
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTACCCCTAAAACTACAAAAATTCCATTTTTGACTTAA
Found at i:20874947 original size:28 final size:28
Alignment explanation
Indices: 20874914--20874989 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
20874904 TCCAAATTTT
* * * *
20874914 TCCAAAACTACCATTTTGCCCTCGAGAG
1 TCCAAAATTACCATTTTACCCCCGAAAG
20874942 TCCAAAATTACCATTTTACCCCCGAAAG
1 TCCAAAATTACCATTTTACCCCCGAAAG
*
20874970 TCCAAAATTACCATATTACC
1 TCCAAAATTACCATTTTACC
20874990 TACGGGCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCCGAAAG
Found at i:20881532 original size:50 final size:49
Alignment explanation
Indices: 20881341--20881639 Score: 185
Period size: 50 Copynumber: 5.9 Consensus size: 49
20881331 ACATGACGAA
* * *
20881341 AAAGATCTAAGATCGCAATGACGGATCCAGTACCG--TAAAGACATAAGGG
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCGCAAAAAGACA-AAGGG
* ** * *
20881390 AAAGATCTAAGCTGCAACGGTGGATCTAGTACCATGTAAAAAGACAAAAGGG
1 AAAGATCTAAGCCGCAACGACGGATCCAGTACC--GCAAAAAGAC-AAAGGG
* * * * * * * * * *
20881442 AAAGGTCTAAGTCACAACGGCAGA-CCGTGTACCTCAAAAAATACGACGGG
1 AAAGATCTAAGCCGCAACGACGGATCC-AGTACCGC-AAAAAGACAAAGGG
20881492 AAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGG
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCGCAAAAAGAC-AAAGGG
* * * * * * * *
20881543 AAAGGTCTAAGTCGCAACAACAGA-CCGTGTACCTC-AGAAGACATTACGGG
1 AAAGATCTAAGCCGCAACGACGGATCC-AGTACCGCAAAAAGACA--AAGGG
* **
20881593 AAAGATCTAAGACCGCAACGGCGGATCCAGTACCTTAAAAAGACAAA
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCGCAAAAAGACAAA
20881640 AAGGAAATGT
Statistics
Matches: 187, Mismatches: 47, Indels: 31
0.71 0.18 0.12
Matches are distributed among these distances:
48 17 0.09
49 19 0.10
50 53 0.28
51 52 0.28
52 45 0.24
53 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (49 bp):
AAAGATCTAAGCCGCAACGACGGATCCAGTACCGCAAAAAGACAAAGGG
Found at i:20881538 original size:101 final size:101
Alignment explanation
Indices: 20881387--20881646 Score: 360
Period size: 101 Copynumber: 2.6 Consensus size: 101
20881377 AAAGACATAA
* * *
20881387 GGGAAAGATCTAAG-CTGCAACGGTGGATCTAGTACCATGTAAAAAGACAAAAGGGAAAGGTCTA
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC--GTAAAAAGACAAAAGGGAAAGGTCTA
** *
20881451 AGTCACAACGGCAGACCGTGTACCTCAAAAAATACGAC
64 AGTCACAACAACAGACCGTGTACCTCAAAAAACACGAC
* *
20881489 GGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAAAGACAAAAGGGAAAGGTCTAAG
* * * **
20881554 TCGCAACAACAGACCGTGTACCTCAGAAGACATTAC
66 TCACAACAACAGACCGTGTACCTCAAAAAACACGAC
* *
20881590 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCTTAAAAAGACAAAAAGGAAA
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAAAGACAAAAGGGAAA
20881647 TGTTTTTATC
Statistics
Matches: 140, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
101 108 0.77
102 14 0.10
103 18 0.13
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (101 bp):
GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAAAGACAAAAGGGAAAGGTCTAAG
TCACAACAACAGACCGTGTACCTCAAAAAACACGAC
Found at i:20881646 original size:51 final size:50
Alignment explanation
Indices: 20881341--20881646 Score: 210
Period size: 51 Copynumber: 6.1 Consensus size: 50
20881331 ACATGACGAA
* * * *
20881341 AAAGATCTAAGATCGCAATGACGGATCCAGTACCGT--AAAGACATAAGGG
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCTTAAAAAGACAAAAGGG
* ** *
20881390 AAAGATCTAAGCTGCAACGGTGGATCTAGTACCATGTAAAAAGACAAAAGGG
1 AAAGATCTAAGCCGCAACGACGGATCCAGTACC-T-TAAAAAGACAAAAGGG
* * * * * * * * * *
20881442 AAAGGTCTAAGTCACAACGGCAGA-CCGTGTACCTCAAAAA-ATACGACGGG
1 AAAGATCTAAGCCGCAACGACGGATCC-AGTACCTTAAAAAGACA-AAAGGG
**
20881492 AAAGATCTAAGACCGCAACGACGGATCCAGTACCGCAAAAAGACAAAAGGG
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCTTAAAAAGACAAAAGGG
* * * * * * * * *
20881543 AAAGGTCTAAGTCGCAACAACAGA-CCGTGTACC-TCAGAAGACATTACGGG
1 AAAGATCTAAGCCGCAACGACGGATCC-AGTACCTTAAAAAGACA-AAAGGG
* *
20881593 AAAGATCTAAGACCGCAACGGCGGATCCAGTACCTTAAAAAGACAAAAAGG
1 AAAGATCTAAG-CCGCAACGACGGATCCAGTACCTTAAAAAGACAAAAGGG
20881644 AAA
1 AAA
20881647 TGTTTTTATC
Statistics
Matches: 192, Mismatches: 51, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
48 16 0.08
49 22 0.11
50 49 0.26
51 56 0.29
52 49 0.26
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (50 bp):
AAAGATCTAAGCCGCAACGACGGATCCAGTACCTTAAAAAGACAAAAGGG
Found at i:20881739 original size:52 final size:52
Alignment explanation
Indices: 20881656--20881774 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
20881646 ATGTTTTTAT
* *
20881656 CTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCGATTCCTATC
1 CTCT-TGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATC
*
20881709 CT-TATGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAAGCATCAATTCCTATC
1 CTCT-TGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATC
20881761 CTCTTGAAGTTGCA
1 CTCTTGAAGTTGCA
20881775 ATAAAAGCTG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
52 58 0.95
53 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (52 bp):
CTCTTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATC
Found at i:20881961 original size:38 final size:38
Alignment explanation
Indices: 20881919--20881992 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
20881909 GATTCAAGAA
20881919 GGGCAAAATGAAG-ATTCTGAT-TTCTTACCCCGAGCAAG
1 GGGCAAAATGAAGCATT-TGATCTT-TTACCCCGAGCAAG
* *
20881957 GGGCATATTGAAGCCATTTGATCTTTTACCCCGAGC
1 GGGCAAAATGAAG-CATTTGATCTTTTACCCCGAGC
20881993 TTGGGGCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 11 0.35
39 15 0.48
40 5 0.16
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (38 bp):
GGGCAAAATGAAGCATTTGATCTTTTACCCCGAGCAAG
Found at i:20882020 original size:39 final size:38
Alignment explanation
Indices: 20881977--20882185 Score: 152
Period size: 39 Copynumber: 5.4 Consensus size: 38
20881967 AAGCCATTTG
20881977 ATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATC-TCATCAACCA
** * ****
20882016 ATCTTTTACCCCGAGCCAGGGGTAGAT-TGCAGTCATTTG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCT-CA-TCAACCA
* * * *
20882055 ATTTTTTACCCCGAGCCTGGGGCAGATCGTCGTCAATCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATC-TCATCAACCA
** * * * *
20882094 ATCTCCTACCCCGAGCTAGGGGCAGAT-TGCAACCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCT-C-ATCAACCA
* * *
20882133 ACCTTTTACTCCGAGCTTGGAGCAGATCATCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATC-TCATCAACCA
*
20882172 ATCTTCTACCCCGA
1 ATCTTTTACCCCGA
20882186 TCACGGGGCA
Statistics
Matches: 126, Mismatches: 36, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
37 2 0.02
38 3 0.02
39 117 0.93
40 2 0.02
41 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (38 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCTCATCAACCA
Found at i:20882037 original size:78 final size:78
Alignment explanation
Indices: 20881944--20882199 Score: 316
Period size: 78 Copynumber: 3.3 Consensus size: 78
20881934 TCTGATTTCT
*
20881944 TACCCCGAGCAAGGGGCATATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATCA
1 TACCCCGAGCAAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATCA
*
20882009 TCAACCAATCTTT
66 TCAACCAATCTTC
* * * * * * * *
20882022 TACCCCGAGCCAGGGGTAGATTGCAGTCATTTGATTTTTTACCCCGAGCCTGGGGCAGATCGTCG
1 TACCCCGAGCAAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATCA
* *
20882087 TCAATCAATCTCC
66 TCAACCAATCTTC
* ** * * *
20882100 TACCCCGAGCTAGGGGCAGATTGCAA-CCATCCGACCTTTTACTCCGAGCTTGGAGCAGATCATC
1 TACCCCGAGCAAGGGGCAGATTG-AAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATC
20882164 ATCAACCAATCTTC
65 ATCAACCAATCTTC
* *
20882178 TACCCCGATCACGGGGCAGATT
1 TACCCCGAGCAAGGGGCAGATT
20882200 TCGATTATTG
Statistics
Matches: 147, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
78 146 0.99
79 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (78 bp):
TACCCCGAGCAAGGGGCAGATTGAAGCCATTTGATCTTTTACCCCGAGCTTGGGGCAGATCATCA
TCAACCAATCTTC
Found at i:20882563 original size:201 final size:200
Alignment explanation
Indices: 20882223--20883186 Score: 1300
Period size: 201 Copynumber: 4.8 Consensus size: 200
20882213 CAAACGATGC
* * * * **
20882223 GGTCATCTTCTTGATGAGATACTGAGAAGAAAACCAAATCAAATCCACGCTCGATATGAGCAAAT
1 GGTCATCTTCCTGATGAGATACAGAGAAGTATACC-AA-C---T-CACGCTCGATGCGAGCAAAT
* * * * *
20882288 ATTTGAACCCCAGCTTCTTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAAATGGTTTGCTTC
60 CTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
* * * * *
20882353 CTAATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGACACAGAGAAGCGGATTGAA
125 CTGATGAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAA
* *
20882418 ATAATTGAGGA
190 ACAAGTGAGGA
* * * *
20882429 GGTCCTCTTCCTGATGAGATACAGAGAAGTATGCCAACTCGACGCTCGATACGAGTAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-ACGCTCGATGCGAGCAAATCTTCG
* * * * * *
20882494 AACCCTAGCTTCCTGATGAGATATTGAGAAGCAAGTCGAAGAAATAAAATGGTTAGCCTCCTGAT
65 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
* * * *
20882559 GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGACATACAGAGAAGCGAATTGAAATAAT
130 GAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAG
20882624 TGAGGA
195 TGAGGA
*
20882630 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGCGCTTGATGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCA-CGCTCGATGCGAGCAAATCTTCG
* * *
20882695 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGTTCGAAGTAATAAAATGGTTAGCTTCTTGAT
65 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
* * * * *
20882760 GAGATGCGGAGAAGTGGACCAAATTCGTCTTCCTGATTAGATACGGAGAAGTGAATTAAAACAAG
130 GAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAG
*
20882825 TGAGGC
195 TGAGGA
*
20882831 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGCGCTTGATGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCA-CGCTCGATGCGAGCAAATCTTCG
*
20882896 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGAT
65 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
* * *
20882961 GAGATACGGAGAAGTGGACCAAATTCATCTTCCTGATAAGATACGGAGAAGCGAATTGAAACAAG
130 GAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAG
* *
20883026 AGAGGC
195 TGAGGA
* * *
20883032 GATCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCGACACTCGATGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-ACGCTCGATGCGAGCAAATCTTCG
* * *
20883097 AACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTT-CTGAA
65 AACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG-A
* * *
20883161 TGAGACACAGAGAAGTGAACCAAATT
129 TGAGATACGGAGAAGTGGACCAAATT
20883187 TGCTTTTCTA
Statistics
Matches: 688, Mismatches: 66, Indels: 13
0.90 0.09 0.02
Matches are distributed among these distances:
200 5 0.01
201 650 0.94
202 1 0.00
204 1 0.00
205 2 0.00
206 29 0.04
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (200 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCACGCTCGATGCGAGCAAATCTTCGA
ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
AGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGT
GAGGA
Found at i:20883621 original size:6 final size:6
Alignment explanation
Indices: 20883601--20883676 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
20883591 CTCAATCCAT
*
20883601 TTTAAA TTT-AT TTTAAA TTTAAA TTT--A TTCTAAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTAAA
* *
20883647 TTTAAG TTTAAA TTTATA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
20883677 ACTATTATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.05
5 10 0.17
6 41 0.71
7 1 0.02
8 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:20883636 original size:18 final size:17
Alignment explanation
Indices: 20883601--20883690 Score: 108
Period size: 17 Copynumber: 5.2 Consensus size: 17
20883591 CTCAATCCAT
20883601 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
20883618 TTTAAATTTATTCTAAAA
1 TTTAAATTTATT-TTAAA
* *
20883636 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
20883653 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
** *
20883671 TTTAAAACTATTATAAA
1 TTTAAATTTATTTTAAA
20883688 TTT
1 TTT
20883691 GAATGTCCAG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 33 0.53
18 29 0.47
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:20883640 original size:35 final size:35
Alignment explanation
Indices: 20883601--20883690 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
20883591 CTCAATCCAT
20883601 TTTAAATTTATTTTAAATTTAAATTTAT-TCTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATAT-TAAAA
* * *
20883636 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTATATTAAAA
** *
20883671 TTTAAAACTATTATAAATTT
1 TTTAAATTTATTTTAAATTT
20883691 GAATGTCCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 45 0.98
36 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATATTAAAA
Found at i:20884414 original size:15 final size:15
Alignment explanation
Indices: 20884394--20884463 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
20884384 AATATTACTA
20884394 AATATTAATAATAAT
1 AATATTAATAATAAT
20884409 AATATTTATAATAAATAGCATT
1 AATA--T-TAAT-AATA--A-T
20884431 AATGATTAATAATAAT
1 AAT-ATTAATAATAAT
* *
20884447 ATTATTATTAATAAT
1 AATATTAATAATAAT
20884462 AA
1 AA
20884464 AAGAAAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
15 16 0.36
16 3 0.07
17 2 0.05
18 4 0.09
19 8 0.18
20 4 0.09
21 2 0.05
22 4 0.09
23 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (15 bp):
AATATTAATAATAAT
Found at i:20885635 original size:58 final size:58
Alignment explanation
Indices: 20885535--20885795 Score: 294
Period size: 58 Copynumber: 4.4 Consensus size: 58
20885525 GGAGGTCCCT
** *
20885535 AAACTGTCCAAAAATTGTATTTTGACCCTCAAACTTCTAAAAATTCCA-TTTTAACCCCA
1 AAACT-TCCAAAAATTACATTTT-ACCCTTAAACTTCTAAAAATTCCATTTTTAACCCCA
* * * *
20885594 AAACTTCCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTTCATTTTTGACCCTA
1 AAACTTCCAAAAATTACA-TTTTACCCTTAAACTTCTAAAAATTCCATTTTTAACCCCA
* * * *
20885653 AAACTTCTAAAAATTATATTTTACCCTTGAACTTCTAAAAATTCCATTTTTAACTCCA
1 AAACTTCCAAAAATTACATTTTACCCTTAAACTTCTAAAAATTCCATTTTTAACCCCA
* * * * *
20885711 AAACTTCCAAAAATCACATTTTACCCTTGAAACTT-TAGAAATTCCATTTTTGACTTCAA
1 AAACTTCCAAAAATTACATTTTACCCTT-AAACTTCTAAAAATTCCATTTTTAAC-CCCA
*
20885770 AAAATT-CAAAAATTACCATTTTACCC
1 AAACTTCCAAAAATTA-CATTTTACCC
20885796 GATGTCTAAA
Statistics
Matches: 173, Mismatches: 24, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
58 116 0.67
59 57 0.33
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTACCCTTAAACTTCTAAAAATTCCATTTTTAACCCCA
Found at i:20885743 original size:29 final size:30
Alignment explanation
Indices: 20885535--20885745 Score: 179
Period size: 29 Copynumber: 7.2 Consensus size: 30
20885525 GGAGGTCCCT
** * *
20885535 AAACTGTCCAAAAATTGTATTTTGACCC-TC
1 AAACT-TCCAAAAATTACATTTTTACCCTTA
* * * *
20885565 AAACTTCTAAAAATTCCATTTTAACCC-CA
1 AAACTTCCAAAAATTACATTTTTACCCTTA
20885594 AAACTTCCAAAAATTACATTTTTACCCTT-
1 AAACTTCCAAAAATTACATTTTTACCCTTA
*
20885623 AAACTTCCAAAAATTTCATTTTTGACCC-TA
1 AAACTTCCAAAAATTACATTTTT-ACCCTTA
* *
20885653 AAACTTCTAAAAATTATA-TTTTACCCTT-
1 AAACTTCCAAAAATTACATTTTTACCCTTA
* * *
20885681 GAACTTCTAAAAATTCCATTTTTAACTCC--A
1 AAACTTCCAAAAATTACATTTTT-AC-CCTTA
* *
20885711 AAACTTCCAAAAATCACA-TTTTACCCTTG
1 AAACTTCCAAAAATTACATTTTTACCCTTA
20885740 AAACTT
1 AAACTT
20885746 TAGAAATTCC
Statistics
Matches: 149, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 21 0.14
29 84 0.56
30 40 0.27
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTACCCTTA
Found at i:20885761 original size:29 final size:30
Alignment explanation
Indices: 20885565--20885761 Score: 182
Period size: 29 Copynumber: 6.8 Consensus size: 30
20885555 TTTGACCCTC
* *
20885565 AAACTTCTAAAAATTCCATTTTAACCC-CA
1 AAACTTCTAAAAATTCCATTTTTACCCTTA
* *
20885594 AAACTTCCAAAAATTACATTTTTACCCTT-
1 AAACTTCTAAAAATTCCATTTTTACCCTTA
* *
20885623 AAACTTCCAAAAATTTCATTTTTGACCC-TA
1 AAACTTCTAAAAATTCCATTTTT-ACCCTTA
20885653 AAACTTCTAAAAATT--ATATTTTACCCTT-
1 AAACTTCTAAAAATTCCAT-TTTTACCCTTA
*
20885681 GAACTTCTAAAAATTCCATTTTTAACTCC--A
1 AAACTTCTAAAAATTCCATTTTT-AC-CCTTA
* *
20885711 AAACTTCCAAAAA-TCACA-TTTTACCCTTG
1 AAACTTCTAAAAATTC-CATTTTTACCCTTA
*
20885740 AAACTT-TAGAAATTCCATTTTT
1 AAACTTCTAAAAATTCCATTTTT
20885762 GACTTCAAAA
Statistics
Matches: 141, Mismatches: 12, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
27 2 0.01
28 28 0.20
29 74 0.52
30 35 0.25
31 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAACTTCTAAAAATTCCATTTTTACCCTTA
Found at i:20885927 original size:28 final size:28
Alignment explanation
Indices: 20885889--20885960 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
20885879 CCAAATTTTC
* * * *
20885889 CCAAAACTACCATTTTTCCCTCGAGAGT
1 CCAAAATTACCATTTTACCCCCGAAAGT
20885917 CCAAAATTACCATTTTACCCCCGAAAGT
1 CCAAAATTACCATTTTACCCCCGAAAGT
20885945 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
20885961 GCCTTCGGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAAAGT
Found at i:20889998 original size:14 final size:14
Alignment explanation
Indices: 20889981--20890010 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20889971 TATAGACTAA
20889981 ATTGAAAATTTTTT
1 ATTGAAAATTTTTT
20889995 ATTGAAAATTTTTT
1 ATTGAAAATTTTTT
20890009 AT
1 AT
20890011 AGTTGGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTGAAAATTTTTT
Found at i:20906105 original size:29 final size:30
Alignment explanation
Indices: 20906064--20906121 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
20906054 CCTTATTGCT
* * *
20906064 TTTTTCCCAAAAA-TTTTACTCCTTCCCAC
1 TTTTCCCCAAAAACTTTTACCCCCTCCCAC
*
20906093 TTTTCCCCTAAAACTTTTACCCCCTCCCA
1 TTTTCCCCAAAAACTTTTACCCCCTCCCA
20906122 TCCCACCCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (30 bp):
TTTTCCCCAAAAACTTTTACCCCCTCCCAC
Found at i:20906414 original size:20 final size:20
Alignment explanation
Indices: 20906378--20906415 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20906368 AAAACGTCCA
*
20906378 AAACTTTTTATTTTCACCTC
1 AAACTTTTTATTCTCACCTC
20906398 AAAC-TTTTACTTCTCACC
1 AAACTTTTTA-TTCTCACC
20906416 CCTTACCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
AAACTTTTTATTCTCACCTC
Found at i:20909205 original size:53 final size:53
Alignment explanation
Indices: 20909092--20909279 Score: 220
Period size: 52 Copynumber: 3.6 Consensus size: 53
20909082 ATGAAAAAGG
* * * * *
20909092 GGTCTGATGATTAAGTGTCATCGTGAGTAAATG-AATCCTTTATGGA-TTATGA
1 GGTCCGATGACTAAGTGTCATCATGAGTATATGAAATCCTTTATGGATTTA-AA
* *
20909144 CGTCCGATGACTAAGTGTCATCATGAGTTTATGAAATCCTTTATGGATTTAAA
1 GGTCCGATGACTAAGTGTCATCATGAGTATATGAAATCCTTTATGGATTTAAA
* * *
20909197 GGTCCGATGACTAAGTGTCATCATGAGTATAT-AGATCCTTTACGGATTAAAA
1 GGTCCGATGACTAAGTGTCATCATGAGTATATGAAATCCTTTATGGATTTAAA
* ** *
20909249 GGTCTGATGACTCTGTGTCATCGTGAGTATA
1 GGTCCGATGACTAAGTGTCATCATGAGTATA
20909280 CAAATCCCAC
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
52 71 0.60
53 44 0.37
54 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (53 bp):
GGTCCGATGACTAAGTGTCATCATGAGTATATGAAATCCTTTATGGATTTAAA
Found at i:20933751 original size:90 final size:91
Alignment explanation
Indices: 20933624--20933864 Score: 233
Period size: 90 Copynumber: 2.7 Consensus size: 91
20933614 CAAAAAGATT
* * *
20933624 AATTAAG-CCC-TTTTTTTCCACTCAATTTG-ATATTTGAACTTTCAAAATGCATAAAAAAAGCC
1 AATTAAGCCCCTTTTTTTTGCACTCAA-TTGAATACTTGAACTTTCAAAATGCATAAAAAAAGAC
*
20933686 CTT-AAGCTTTTTCAAAAAAAAAAAAC
65 CTTCAAACTTTTTCAAAAAAAAAAAAC
** *
20933712 AATTAAGCCCCTTTTTTTTGCACTCAATTGAATACTTGAACTTTCAAAATAAAT-CAAAAAGACC
1 AATTAAGCCCCTTTTTTTTGCACTCAATTGAATACTTGAACTTTCAAAATGCATAAAAAAAGACC
* ** **
20933776 TTCAAATTTTTTCAAAAAAAGCAATT
66 TTCAAACTTTTTCAAAAAAAAAAAAC
** *** *
20933802 AAGTCTCTGCTTTTTTTTTGTTGCACTCAATTGAGTACTTGAA-TTGTCAAAATGCATAAAAAA
1 AA-T-TAAGCCCCTTTTTT-TTGCACTCAATTGAATACTTGAACTT-TCAAAATGCATAAAAAA
20933865 GGCTCTTTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
88 7 0.06
89 16 0.13
90 53 0.43
91 1 0.01
92 11 0.09
93 31 0.25
94 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (91 bp):
AATTAAGCCCCTTTTTTTTGCACTCAATTGAATACTTGAACTTTCAAAATGCATAAAAAAAGACC
TTCAAACTTTTTCAAAAAAAAAAAAC
Found at i:20934526 original size:12 final size:12
Alignment explanation
Indices: 20934505--20934610 Score: 67
Period size: 12 Copynumber: 9.2 Consensus size: 12
20934495 ATAACATCCA
*
20934505 AACAACAAAAAT
1 AACAATAAAAAT
*
20934517 AACAATAAAAAC
1 AACAATAAAAAT
* **
20934529 AGCAGCAAAAAT
1 AACAATAAAAAT
*
20934541 AACAGT-AAAAT
1 AACAATAAAAAT
*
20934552 AAC-AT-TAAA-
1 AACAATAAAAAT
*
20934561 AACAACAAAAAT
1 AACAATAAAAAT
*
20934573 AGCAATAAAAAT
1 AACAATAAAAAT
** *
20934585 AGTAACAAAAAT
1 AACAATAAAAAT
*
20934597 AACAGTAAAAAT
1 AACAATAAAAAT
20934609 AA
1 AA
20934611 TACGAAAATA
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
9 3 0.04
10 5 0.07
11 11 0.15
12 52 0.73
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (12 bp):
AACAATAAAAAT
Found at i:20934618 original size:24 final size:23
Alignment explanation
Indices: 20934547--20934640 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 23
20934537 AAATAACAGT
* *
20934547 AAAATAACATTAAAAA-CA-ACA
1 AAAATAACAATAAAAATAATACA
* *
20934568 AAAATAGCAATAAAAATAGTAACA
1 AAAATAACAATAAAAATAAT-ACA
* *
20934592 AAAATAACAGTAAAAATAATACG
1 AAAATAACAATAAAAATAATACA
* * *
20934615 AAAATAGCAATCAAAACAATA-A
1 AAAATAACAATAAAAATAATACA
20934637 AAAA
1 AAAA
20934641 CAACTCAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
21 14 0.25
22 4 0.07
23 19 0.33
24 20 0.35
ACGTcount: A:0.69, C:0.11, G:0.05, T:0.15
Consensus pattern (23 bp):
AAAATAACAATAAAAATAATACA
Found at i:20934630 original size:23 final size:23
Alignment explanation
Indices: 20934565--20934640 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 23
20934555 ATTAAAAACA
*
20934565 ACAAAAATAGCAATAAAAATAGT
1 ACAAAAATAGCAATAAAAATAAT
* *
20934588 AACAAAAATAACAGTAAAAATAAT
1 -ACAAAAATAGCAATAAAAATAAT
* * *
20934612 ACGAAAATAGCAATCAAAACAAT
1 ACAAAAATAGCAATAAAAATAAT
20934635 A-AAAAA
1 ACAAAAA
20934641 CAACTCAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 4 0.09
23 19 0.44
24 20 0.47
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (23 bp):
ACAAAAATAGCAATAAAAATAAT
Found at i:20934683 original size:21 final size:22
Alignment explanation
Indices: 20934625--20934684 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
20934615 AAAATAGCAA
*
20934625 TCAAAACAAT-AAAAAA-CAAC
1 TCAAAACAGTAAAAAAATCAAC
20934645 TCAAAAACAGTAAAAAAATCAAC
1 TC-AAAACAGTAAAAAAATCAAC
20934668 -CAAAACAGTAAAAAAAT
1 TCAAAACAGTAAAAAAAT
20934685 TATATTAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 2 0.06
21 23 0.64
22 7 0.19
23 4 0.11
ACGTcount: A:0.68, C:0.17, G:0.03, T:0.12
Consensus pattern (22 bp):
TCAAAACAGTAAAAAAATCAAC
Found at i:20934829 original size:12 final size:12
Alignment explanation
Indices: 20934808--20934913 Score: 85
Period size: 12 Copynumber: 9.2 Consensus size: 12
20934798 AAAACATCCA
*
20934808 AACAACAAAAAT
1 AACAATAAAAAT
20934820 AACAATAAAAAT
1 AACAATAAAAAT
* **
20934832 AGCAGCAAAAAT
1 AACAATAAAAAT
*
20934844 AACAGT-AAAAT
1 AACAATAAAAAT
*
20934855 AAC-AT-TAAA-
1 AACAATAAAAAT
20934864 AACAATAAAAAT
1 AACAATAAAAAT
* *
20934876 AGCAATAAAAAC
1 AACAATAAAAAT
* *
20934888 AGCAACAAAAAT
1 AACAATAAAAAT
*
20934900 AACAGTAAAAAT
1 AACAATAAAAAT
20934912 AA
1 AA
20934914 TACGAAAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
9 3 0.04
10 6 0.08
11 11 0.15
12 55 0.73
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (12 bp):
AACAATAAAAAT
Found at i:20934897 original size:303 final size:305
Alignment explanation
Indices: 20934373--20934985 Score: 1149
Period size: 303 Copynumber: 2.0 Consensus size: 305
20934363 AAAATACATT
*
20934373 AAAAAATTATATTAAGATAGTTGTAACTAAATTAATAAAAAAATTAACAATAAAACATAAGTTCT
1 AAAAAATTATATTAAGATAGTTGTAACTAAATTAATAAAAAAATTAACAATAAAACATAAGTCCT
20934438 ACAATATTCAAATAATATTTAAAAAGACAGTGAAACAATAGTAAAAACGCATAAAAAATAACATC
66 ACAATATTCAAATAATATTTAAAAAGACAGTGAAACAATAGTAAAAACGCATAAAAAATAACATC
20934503 CAAACAACAAAAATAACAATAAAAACAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACA
131 CAAACAACAAAAATAACAATAAAAACAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACA
* *
20934568 AAAATAGCAATAAAAATAGTAACAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACA
196 AAAATAGCAATAAAAACAGCAACAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACA
*
20934633 ATAAAAAACAACTCAAAAACAGTAAAAAAATCAACCAAAACAGTA
261 ATAAAAAACAACTCAAAAACAGTAAAAAAATCAACAAAAACAGTA
*
20934678 AAAAAATTATATTAAGATAGTTGTAACTAAATTAGTAAAAAAATTAACAATAAAACATAAGTCCT
1 AAAAAATTATATTAAGATAGTTGTAACTAAATTAATAAAAAAATTAACAATAAAACATAAGTCCT
20934743 ACAATATTCAAATAATATTTAAAAAGACAGTGAAACAATAGTAAAAACGCAT-AAAAA-AACATC
66 ACAATATTCAAATAATATTTAAAAAGACAGTGAAACAATAGTAAAAACGCATAAAAAATAACATC
* *
20934806 CAAACAACAAAAATAACAATAAAAATAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAATA
131 CAAACAACAAAAATAACAATAAAAACAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACA
20934871 AAAATAGCAATAAAAACAGCAACAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACA
196 AAAATAGCAATAAAAACAGCAACAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACA
20934936 ATAAAAAACAACTCAAAAACAGTAAAAAAATCAACAAAAACAGTA
261 ATAAAAAACAACTCAAAAACAGTAAAAAAATCAACAAAAACAGTA
20934981 AAAAA
1 AAAAA
20934986 GCACTAAAAC
Statistics
Matches: 301, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
303 181 0.60
304 5 0.02
305 115 0.38
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.18
Consensus pattern (305 bp):
AAAAAATTATATTAAGATAGTTGTAACTAAATTAATAAAAAAATTAACAATAAAACATAAGTCCT
ACAATATTCAAATAATATTTAAAAAGACAGTGAAACAATAGTAAAAACGCATAAAAAATAACATC
CAAACAACAAAAATAACAATAAAAACAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACA
AAAATAGCAATAAAAACAGCAACAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACA
ATAAAAAACAACTCAAAAACAGTAAAAAAATCAACAAAAACAGTA
Found at i:20934900 original size:68 final size:67
Alignment explanation
Indices: 20934826--20934971 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 67
20934816 AAATAACAAT
* *
20934826 AAAAATAGCAGCAAAAATAACA-GTAAAATAACATTAAAAACAATAAAAATAGCAA-T-AAAAAC
1 AAAAATAACAGCAAAAATAACACG-AAAATAACAATAAAAACAATAAAAA-A-CAACTCAAAAAC
20934888 AGCAA
63 AGCAA
* * * *
20934893 CAAAAATAACAGTAAAAATAATACGAAAATAGCAATCAAAACAATAAAAAACAACTCAAAAACAG
1 -AAAAATAACAGCAAAAATAACACGAAAATAACAATAAAAACAATAAAAAACAACTCAAAAACAG
*
20934958 TAA
65 CAA
20934961 AAAAATCAACA
1 AAAAAT-AACA
20934972 AAAACAGTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
66 3 0.04
67 8 0.12
68 55 0.82
69 1 0.01
ACGTcount: A:0.67, C:0.14, G:0.06, T:0.13
Consensus pattern (67 bp):
AAAAATAACAGCAAAAATAACACGAAAATAACAATAAAAACAATAAAAAACAACTCAAAAACAGC
AA
Found at i:20934938 original size:56 final size:54
Alignment explanation
Indices: 20934794--20934994 Score: 148
Period size: 56 Copynumber: 3.7 Consensus size: 54
20934784 TAAAAACGCA
* * *
20934794 TAAAAA-AACATCCAAACAACAA-AAATAACAATAAAAATAGCAGCAAAAATAACAG
1 TAAAAATAACA-CGAAA-AACAATAAAAAACAATAAAAA-AGCAACAAAAATAACAG
**
20934849 T-AAAATAACATTAAAAACAATAAAAATAGCAATAAAAACAGCAACAAAAATAACAG
1 TAAAAATAACACGAAAAACAATAAAAA-A-CAATAAAAA-AGCAACAAAAATAACAG
* * **
20934905 TAAAAATAATACGAAAATAGCAAT-CAAAACAATAAAAAA-CAACTCAAA-AACAG
1 TAAAAATAACACGAAAA-A-CAATAAAAAACAATAAAAAAGCAACAAAAATAACAG
* *
20934958 TAAAAA-AATCAAC-AAAAACAGTAAAAAAGCACTAAAA
1 TAAAAATAA-C-ACGAAAAACAATAAAAAA-CAATAAAA
20934995 CAACAATATA
Statistics
Matches: 120, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
51 3 0.03
52 7 0.06
53 27 0.22
54 20 0.17
55 7 0.06
56 35 0.29
57 13 0.11
58 4 0.03
59 4 0.03
ACGTcount: A:0.68, C:0.14, G:0.05, T:0.12
Consensus pattern (54 bp):
TAAAAATAACACGAAAAACAATAAAAAACAATAAAAAAGCAACAAAAATAACAG
Found at i:20934943 original size:45 final size:44
Alignment explanation
Indices: 20934820--20934935 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 44
20934810 CAACAAAAAT
** * *
20934820 AACAATAAAAATAGC-AGCAAAA-ATAACAGTAAAATAACATTAAA
1 AACAATAAAAATAGCAATAAAAACACAACA--AAAATAACAGTAAA
20934864 AACAATAAAAATAGCAATAAAAACAGCAACAAAAATAACAGTAAA
1 AACAATAAAAATAGCAATAAAAACA-CAACAAAAATAACAGTAAA
* *
20934909 AATAATACGAAAATAGCAATCAAAACA
1 AACAATA--AAAATAGCAATAAAAACA
20934936 ATAAAAAACA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
44 15 0.25
45 24 0.39
46 1 0.02
47 21 0.34
ACGTcount: A:0.66, C:0.13, G:0.07, T:0.14
Consensus pattern (44 bp):
AACAATAAAAATAGCAATAAAAACACAACAAAAATAACAGTAAA
Found at i:20934954 original size:21 final size:22
Alignment explanation
Indices: 20934918--20935002 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 22
20934908 AAATAATACG
*
20934918 AAAATAGCAA-TC-AAAACAAT
1 AAAAAAGCAACTCAAAAACAAT
*
20934938 AAAAAA-CAACTCAAAAACAGT
1 AAAAAAGCAACTCAAAAACAAT
* *
20934959 AAAAAAATCAA--CAAAAACAGT
1 -AAAAAAGCAACTCAAAAACAAT
*
20934980 AAAAAAGC-ACTAAAACAACAAT
1 AAAAAAGCAACTCAAA-AACAAT
20935002 A
1 A
20935003 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
19 4 0.08
20 14 0.26
21 20 0.38
22 12 0.23
23 3 0.06
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (22 bp):
AAAAAAGCAACTCAAAAACAAT
Found at i:20935390 original size:20 final size:20
Alignment explanation
Indices: 20935365--20935429 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
20935355 GTGTGATAAT
20935365 TTTTATAATTTTTTTACGAA
1 TTTTATAATTTTTTTACGAA
* *
20935385 TTTTAT-ATTTCTTTAC-AT
1 TTTTATAATTTTTTTACGAA
*
20935403 TTTTATAATTTTCTTACG-A
1 TTTTATAATTTTTTTACGAA
20935422 TTTTATAA
1 TTTTATAA
20935430 AATTTTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.18
19 25 0.66
20 6 0.16
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAA
Found at i:20935462 original size:19 final size:20
Alignment explanation
Indices: 20935432--20935483 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
20935422 TTTTATAAAA
*
20935432 TTTTATAATTTTTCTA-TAT
1 TTTTATATTTTTTCTACTAT
20935451 ATTTTAT-TTTTTT-TACTAT
1 -TTTTATATTTTTTCTACTAT
20935470 TTTTATATTTTTTC
1 TTTTATATTTTTTC
20935484 CTAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.29
19 14 0.50
20 6 0.21
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATATTTTTTCTACTAT
Found at i:20935492 original size:20 final size:19
Alignment explanation
Indices: 20935432--20935499 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
20935422 TTTTATAAAA
* *
20935432 TTTTATAATTTTTCTATATA
1 TTTTATATTTTTTCTA-ATT
*
20935452 TTTTAT-TTTTTT-TACTAT
1 TTTTATATTTTTTCTAAT-T
20935470 TTTTATATTTTTTCCTAATT
1 TTTTATATTTTTT-CTAATT
*
20935490 TTTAATATTT
1 TTTTATATTT
20935500 GAATATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 8 0.21
19 11 0.28
20 16 0.41
21 3 0.08
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTTTCTAATT
Found at i:20935546 original size:10 final size:9
Alignment explanation
Indices: 20935360--20935567 Score: 70
Period size: 9 Copynumber: 22.2 Consensus size: 9
20935350 TTTTGGTGTG
20935360 ATAATTTTT
1 ATAATTTTT
20935369 ATAATTTTT
1 ATAATTTTT
* *
20935378 TTACGAATTTT
1 ATA--ATTTTT
20935389 AT-ATTTCTT
1 ATAATTT-TT
20935398 -TACATTTTT
1 ATA-ATTTTT
20935407 ATAATTTTCT
1 ATAATTTT-T
20935417 -TACGA-TTTT
1 ATA--ATTTTT
*
20935426 ATAAAATTTT
1 AT-AATTTTT
20935436 ATAATTTTT
1 ATAATTTTT
*
20935445 CTATATATTTT
1 ATA-AT-TTTT
**
20935456 ATTTTTTTT
1 ATAATTTTT
20935465 ACT-ATTTTT
1 A-TAATTTTT
*
20935474 ATATTTTTT
1 ATAATTTTT
*
20935483 CCTAATTTTT
1 -ATAATTTTT
**
20935493 A-ATATTTGA
1 ATA-ATTTTT
20935502 AT-ATTTTT
1 ATAATTTTT
***
20935510 ATTAAAAATT
1 A-TAATTTTT
* * *
20935520 AAAAATTTA
1 ATAATTTTT
20935529 ATAATTTTT
1 ATAATTTTT
20935538 ATAATTTTT
1 ATAATTTTT
*
20935547 ATTGATTTTT
1 A-TAATTTTT
*
20935557 ATTATTTTT
1 ATAATTTTT
20935566 AT
1 AT
20935568 CACATGTCAT
Statistics
Matches: 147, Mismatches: 30, Indels: 44
0.67 0.14 0.20
Matches are distributed among these distances:
8 11 0.07
9 83 0.56
10 40 0.27
11 13 0.09
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:20946498 original size:16 final size:16
Alignment explanation
Indices: 20946474--20946506 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20946464 TATTATATAC
20946474 TTTACATAATATAAATA
1 TTTACATAATA-AAATA
20946491 TTTA-ATAATAAAATA
1 TTTACATAATAAAATA
20946506 T
1 T
20946507 CACATTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTACATAATAAAATA
Found at i:20946632 original size:15 final size:14
Alignment explanation
Indices: 20946605--20946631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20946595 GAATATAGTA
20946605 AAATATTAAAAAAT
1 AAATATTAAAAAAT
20946619 AAATATTAAAAAA
1 AAATATTAAAAAA
20946632 AAAACGTGTC
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:20950292 original size:2 final size:2
Alignment explanation
Indices: 20950285--20950331 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
20950275 ATTTATTTTA
*
20950285 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20950325 A- AT AT AT
1 AT AT AT AT
20950332 CAATTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20953036 original size:13 final size:13
Alignment explanation
Indices: 20953018--20953043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20953008 AATATGTTTT
20953018 TGTTGTTGTAAAA
1 TGTTGTTGTAAAA
20953031 TGTTGTTGTAAAA
1 TGTTGTTGTAAAA
20953044 GTATATGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTTGTTGTAAAA
Found at i:20953146 original size:14 final size:14
Alignment explanation
Indices: 20953127--20953174 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
20953117 ATAAACTGTT
*
20953127 CATCAAAATACAAC
1 CATCAAAATAAAAC
* *
20953141 CATCAAAAT-GATC
1 CATCAAAATAAAAC
*
20953154 CAACAAAATAAAAC
1 CATCAAAATAAAAC
20953168 CATCAAA
1 CATCAAA
20953175 TTATCCATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.58, C:0.25, G:0.02, T:0.15
Consensus pattern (14 bp):
CATCAAAATAAAAC
Found at i:20953227 original size:81 final size:80
Alignment explanation
Indices: 20953127--20953287 Score: 241
Period size: 81 Copynumber: 2.0 Consensus size: 80
20953117 ATAAACTGTT
* * *
20953127 CATCAAAATACAACCATCAAAATGATCCAACAAAATAAAACCATCAAATTATCCATCATATGTTA
1 CATCAAAATACAACAATCAAAATAACCCAACAAAATAAAACCATCAAATTATCCATCATATGTTA
20953192 ACAAAATAAAACCATC
66 ACAAAA-AAAACCATC
* * * *
20953208 CATCAAAATACAACAATCAAAATAACCCAATAGAATAAAACCATCAAGTTATCCATCGTATGTTA
1 CATCAAAATACAACAATCAAAATAACCCAACAAAATAAAACCATCAAATTATCCATCATATGTTA
*
20953273 ACAAAAAGAACCATC
66 ACAAAAAAAACCATC
20953288 AAACTTTCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 8 0.11
81 64 0.89
ACGTcount: A:0.52, C:0.23, G:0.04, T:0.20
Consensus pattern (80 bp):
CATCAAAATACAACAATCAAAATAACCCAACAAAATAAAACCATCAAATTATCCATCATATGTTA
ACAAAAAAAACCATC
Found at i:20959346 original size:456 final size:456
Alignment explanation
Indices: 20958493--20959847 Score: 2613
Period size: 456 Copynumber: 3.0 Consensus size: 456
20958483 ATGTTTCTAG
20958493 TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
1 TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
20958558 CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
66 CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
20958623 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
131 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
* * *
20958688 TTTCAAATTAACTCCTTTTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGAATTTGGAAC
196 TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGGATTTGGAAC
20958753 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
261 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
20958818 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
326 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
20958883 AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATATTAAAGGGTCAG
391 AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATATTAAAGGGTCAG
20958948 T
456 T
20958949 TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
1 TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
20959014 CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
66 CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
20959079 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
131 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
20959144 TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGGATTTGGAAC
196 TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGGATTTGGAAC
20959209 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
261 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
*
20959274 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTTGAGTTTTGAGGGACTACAAGAA
326 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
20959339 AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATATTAAAGGGTCAG
391 AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATATTAAAGGGTCAG
20959404 T
456 T
*
20959405 TATTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
1 TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
* *
20959470 CCCTTTTGTGTAGCAGTTTAGATCTTGAAAGTATGGAAAAATTAGAAGAATTAATGAAATTTAAA
66 CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
20959535 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
131 GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
*
20959600 TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTT-TAGGCTTCGGATTTAGAAC
196 TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGGATTTGGAAC
*
20959664 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGAAAACACTTTACCAGTGATT
261 TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
20959729 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
326 GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
*
20959794 AGTGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATAT
391 AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATAT
20959848 GCACAAAATA
Statistics
Matches: 888, Mismatches: 11, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
455 199 0.22
456 689 0.78
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (456 bp):
TGTTGATGTTGTTGAACCACTAACGAATTTGCATTTTGAATGTTGTGAGGTAGACGAGTTACAAA
CCCTTTTGTGTAGCAGTTTAGATATTGAAAGTATGGAAAAATTAGAAGAATTAATGACATTTAAA
GATCCAGTTCGTGAAGCCATTTTTCTTATGGAGGCTCCGAAATTTCCTTGAAGTCAAGGCAAGTA
TTTCGAATTAACTCCTTCTAAAACTAAATTGTTGCCTTCGATTTTATAGGCTTCGGATTTGGAAC
TCAAGCCTCTACCTGAACACCTTAAGTGCGCATTCCTAAGAGACGGAAACACTTTACCAGTGATT
GTTTCGAGTAAGCTTTCGAAGTTGGAGGAAGAAAATGTAGTTCGAGTTTTGAGGGACTACAAGAA
AGCGATCGAATGGTCAATTGTCGATATTAAAGGGTTAAGTCCCTCAACCTATATTAAAGGGTCAG
T
Found at i:20967159 original size:6 final size:6
Alignment explanation
Indices: 20967137--20967204 Score: 56
Period size: 6 Copynumber: 12.2 Consensus size: 6
20967127 GTTTAAATTG
* * * *
20967137 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
20967183 A-TTAA ATTTGA A-TT-A ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
20967205 ACTTAATATT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
4 4 0.08
5 11 0.23
6 33 0.69
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:20967203 original size:16 final size:17
Alignment explanation
Indices: 20967137--20967204 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 17
20967127 GTTTAAATTG
*
20967137 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-ATTTAA
**
20967155 ATTTAAATTTGCTTTAA
1 ATTTAAATTTAATTTAA
20967172 ATTTAAATTTAA-TTAA
1 ATTTAAATTTAATTTAA
*
20967188 ATTTGAA-TTAATTTAA
1 ATTTAAATTTAATTTAA
20967204 A
1 A
20967205 ACTTAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
15 4 0.09
16 15 0.34
17 15 0.34
18 10 0.23
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:20967210 original size:27 final size:27
Alignment explanation
Indices: 20967157--20967211 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
20967147 ATTTTTAAAT
** *
20967157 TTAAATTTGCTTTAAATTTAAATTTAA
1 TTAAATTTGAATTAAATTTAAACTTAA
20967184 TTAAATTTGAATT-AATTTAAAACTTAA
1 TTAAATTTGAATTAAATTT-AAACTTAA
20967211 T
1 T
20967212 ATTAAAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
TTAAATTTGAATTAAATTTAAACTTAA
Found at i:20969077 original size:30 final size:29
Alignment explanation
Indices: 20969039--20969306 Score: 150
Period size: 29 Copynumber: 9.2 Consensus size: 29
20969029 CCTTGAAAGT
*
20969039 CCCT-AAACTATCCAAAAATTATATTTTGA
1 CCCTCAAACT-TCCAAAAATTACATTTTGA
*
20969068 CCCTCAAACTTTTTC-AAAATTACAATTTT-A
1 CCCTCAAAC--TTCCAAAAATTAC-ATTTTGA
* *
20969098 ACCTCAAAACTTCTAAAAATTACATTTTG-
1 CCCTC-AAACTTCCAAAAATTACATTTTGA
*
20969127 -CCTCCAAACTTCCAAAAATTACATTTTTA
1 CCCT-CAAACTTCCAAAAATTACATTTTGA
* * *
20969156 CCCCCAAA-TATCCAAAAAATCCATTTTTGA
1 CCCTCAAACT-TCCAAAAATTACA-TTTTGA
* ** *
20969186 TCC-CAATTTTTCTAAAAATTAGCATTTT-A
1 CCCTCAA-ACTTCCAAAAATTA-CATTTTGA
* *
20969215 CCCCCGAA-TGTCCAAAAATT-CTATTTTTGA
1 CCCTCAAACT-TCCAAAAATTAC-A-TTTTGA
*
20969245 CCC-CGAAA-TTCCAAAAATTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTGA
*
20969273 CCC-CTAAAATTCCAAAAATTACCATTTT-A
1 CCCTC-AAACTTCCAAAAATTA-CATTTTGA
20969302 CCCTC
1 CCCTC
20969307 GGATGTCCAA
Statistics
Matches: 191, Mismatches: 23, Indels: 49
0.73 0.09 0.19
Matches are distributed among these distances:
27 1 0.01
28 39 0.20
29 74 0.39
30 62 0.32
31 14 0.07
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTGA
Found at i:20969096 original size:31 final size:30
Alignment explanation
Indices: 20969043--20969153 Score: 104
Period size: 30 Copynumber: 3.7 Consensus size: 30
20969033 GAAAGTCCCT
* * *
20969043 AAACTATCCAAAAATTATATTTTGACCCTC-
1 AAACT-TCTAAAAATTACATTTTGAACCTCA
* *
20969073 AAACTTTTTCAAAATTACAATTTT-AACCTCA
1 AAAC-TTCTAAAAATTAC-ATTTTGAACCTCA
*
20969104 AAACTTCTAAAAATTACATTTTG--CCTCC
1 AAACTTCTAAAAATTACATTTTGAACCTCA
*
20969132 AAACTTCCAAAAATTACATTTT
1 AAACTTCTAAAAATTACATTTT
20969154 TACCCCCAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
28 25 0.37
29 5 0.07
30 28 0.41
31 10 0.15
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTCTAAAAATTACATTTTGAACCTCA
Found at i:20969214 original size:59 final size:58
Alignment explanation
Indices: 20969112--20969300 Score: 192
Period size: 59 Copynumber: 3.2 Consensus size: 58
20969102 CAAAACTTCT
*
20969112 AAAAATTACA-TTTTG-CCTCC-AAACTTCCAAAAATTACATTTTTACCCCCAAATATCC
1 AAAAATTCCATTTTTGACC-CCGAAA-TTCCAAAAATTACATTTTTACCCCCAAATATCC
* * * * * *
20969169 AAAAAATCCATTTTTGATCCC-AATTTTTCTAAAAATTAGCA-TTTTACCCCCGAATGTCC
1 AAAAATTCCATTTTTGACCCCGAA--ATTCCAAAAATTA-CATTTTTACCCCCAAATATCC
* *
20969228 AAAAATTCTATTTTTGACCCCGAAATTCCAAAAATTACATTTTTACCCCTAAA-ATTCC
1 AAAAATTCCATTTTTGACCCCGAAATTCCAAAAATTACATTTTTACCCCCAAATA-TCC
20969286 AAAAATTACCATTTT
1 AAAAATT-CCATTTT
20969301 ACCCTCGGAT
Statistics
Matches: 107, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
57 10 0.09
58 41 0.38
59 52 0.49
60 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTGACCCCGAAATTCCAAAAATTACATTTTTACCCCCAAATATCC
Found at i:20969301 original size:29 final size:29
Alignment explanation
Indices: 20969083--20969304 Score: 163
Period size: 29 Copynumber: 7.7 Consensus size: 29
20969073 AAACTTTTTC
* * * *
20969083 AAAATTACAATTTTAACCTCAAAACTTCTA
1 AAAATTACCATTTTTACCCCAAAA-TTCCA
* *
20969113 AAAATTA-CA-TTTTGCCTCCAAACTTCCA
1 AAAATTACCATTTTTACC-CCAAAATTCCA
*
20969141 AAAATTA-CATTTTTACCCCCAAATATCCA
1 AAAATTACCATTTTTACCCCAAAAT-TCCA
* * ** *
20969170 AAAAAT-CCATTTTTGATCCCAATTTTTCTA
1 AAAATTACCATTTTT-ACCCCAA-AATTCCA
* **
20969200 AAAATTAGCA-TTTTACCCCCGAATGTCCA
1 AAAATTACCATTTTTACCCCAAAAT-TCCA
* *
20969229 AAAATT-CTATTTTTGACCCCGAAATTCCA
1 AAAATTACCATTTTT-ACCCCAAAATTCCA
20969258 AAAATTA-CATTTTTACCCCTAAAATTCCA
1 AAAATTACCATTTTTACCCC-AAAATTCCA
20969287 AAAATTACCA-TTTTACCC
1 AAAATTACCATTTTTACCC
20969305 TCGGATGTCC
Statistics
Matches: 150, Mismatches: 29, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
28 30 0.20
29 83 0.55
30 34 0.23
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTTACCCCAAAATTCCA
Done.