Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 69 of 208
Found at i:25508672 original size:29 final size:28
Alignment explanation
Indices: 25508606--25508673 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
25508596 GTTTTTAAAA
25508606 TTAAAAT-ATTTAATATATTTTATACTT
1 TTAAAATAATTTAATATATTTTATACTT
* *
25508633 TTTAAACAATTTAA-ATCATTTTTATA-TT
1 TTAAAATAATTTAATAT-A-TTTTATACTT
25508661 TTAAAAATAATTT
1 TT-AAAATAATTT
25508674 TTGTACTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.21
28 11 0.33
29 15 0.45
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAAAATAATTTAATATATTTTATACTT
Found at i:25508716 original size:33 final size:31
Alignment explanation
Indices: 25508650--25508716 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
25508640 AATTTAAATC
*
25508650 ATTTTTATATTTTAAAAATAATTTTTGTACTT
1 ATTTTTATATTTTAAAAATAATTGTTG-ACTT
25508682 ATTTTTATATTTTAAAAAATTAATTAGTTG-CTT
1 ATTTTTATATTTT-AAAAA-TAATT-GTTGACTT
25508715 AT
1 AT
25508717 ATGACAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 5 0.16
35 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (31 bp):
ATTTTTATATTTTAAAAATAATTGTTGACTT
Found at i:25509838 original size:9 final size:9
Alignment explanation
Indices: 25509824--25509908 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
25509814 GTAGTGATTC
25509824 AATTCGGTT
1 AATTCGGTT
*
25509833 AATTCGGGT
1 AATTCGGTT
*
25509842 AATTCGGGT
1 AATTCGGTT
*
25509851 AATTTGGTT
1 AATTCGGTT
*
25509860 AATTCGGGT
1 AATTCGGTT
25509869 AATTCGGTT
1 AATTCGGTT
*
25509878 AATTCGATT
1 AATTCGGTT
*
25509887 AATTCGATT
1 AATTCGGTT
25509896 AATTCGGTT
1 AATTCGGTT
25509905 AATT
1 AATT
25509909 TTCAACCAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 68 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:25514068 original size:3 final size:3
Alignment explanation
Indices: 25514060--25514090 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25514050 GTGGAGAAAT
25514060 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
25514091 GCACCTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:25514796 original size:14 final size:14
Alignment explanation
Indices: 25514777--25514808 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25514767 CTCCTTCATA
*
25514777 TCAAGATGAATGTC
1 TCAAGATGAATATC
25514791 TCAAGATGAATATC
1 TCAAGATGAATATC
25514805 TCAA
1 TCAA
25514809 TTGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (14 bp):
TCAAGATGAATATC
Found at i:25514836 original size:19 final size:21
Alignment explanation
Indices: 25514812--25514851 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
25514802 ATCTCAATTG
25514812 ATTTAAT-TTTTTT-ACTTTA
1 ATTTAATATTTTTTAACTTTA
25514831 ATTTAATGATTTTTTAACTTT
1 ATTTAAT-ATTTTTTAACTTT
25514852 TAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTAATATTTTTTAACTTTA
Found at i:25515315 original size:2 final size:2
Alignment explanation
Indices: 25515308--25515333 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25515298 TGTTCACGTT
25515308 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
25515334 AAGCCTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:25520562 original size:6 final size:6
Alignment explanation
Indices: 25520551--25520583 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
25520541 AAGTAGTAGT
25520551 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTC
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTC
25520584 TATAGGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.36, G:0.30, T:0.18
Consensus pattern (6 bp):
CTCAGG
Found at i:25523977 original size:15 final size:15
Alignment explanation
Indices: 25523957--25523985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25523947 TATATATATA
25523957 TTTTTTAATATTTAT
1 TTTTTTAATATTTAT
25523972 TTTTTTAATATTTA
1 TTTTTTAATATTTA
25523986 CTATACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTAATATTTAT
Found at i:25526675 original size:21 final size:21
Alignment explanation
Indices: 25526634--25526675 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25526624 TATATATAGG
*
25526634 TATAATAATATTAATATCTAA
1 TATAATAATAATAATATCTAA
25526655 TATAATAATAAATAATA-CTAA
1 TATAATAAT-AATAATATCTAA
25526676 CAATAAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAATAATAATATCTAA
Found at i:25529854 original size:19 final size:19
Alignment explanation
Indices: 25529830--25529867 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25529820 GATTTCTAGA
25529830 AAATGATTGACTTTTCTGG
1 AAATGATTGACTTTTCTGG
*
25529849 AAATGATTTACTTTTCTGG
1 AAATGATTGACTTTTCTGG
25529868 TGTTTGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (19 bp):
AAATGATTGACTTTTCTGG
Found at i:25529969 original size:18 final size:18
Alignment explanation
Indices: 25529943--25529985 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
25529933 AAAAGCTGTT
*
25529943 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
25529961 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
25529979 TTTATAT
1 TTTATAT
25529986 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:25532259 original size:8 final size:8
Alignment explanation
Indices: 25532246--25532271 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
25532236 CGTTACAGGC
25532246 AACAAAGA
1 AACAAAGA
25532254 AACAAAGA
1 AACAAAGA
25532262 AACAAAGA
1 AACAAAGA
25532270 AA
1 AA
25532272 GGCAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AACAAAGA
Found at i:25536882 original size:17 final size:17
Alignment explanation
Indices: 25536860--25536898 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
25536850 CAGTTTAATT
25536860 TTTTAAAAATTATAAGC
1 TTTTAAAAATTATAAGC
* *
25536877 TTTTAAAATTTCTAAGC
1 TTTTAAAAATTATAAGC
25536894 TTTTA
1 TTTTA
25536899 TTTAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTTAAAAATTATAAGC
Found at i:25541459 original size:21 final size:20
Alignment explanation
Indices: 25541425--25541476 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
25541415 GGGGGTGAAG
25541425 AAATAAAATAATGACATA-A-A
1 AAAT-AAATAATGA-ATAGAGA
25541445 TAAATAAATAGATGAATAGAGA
1 -AAATAAATA-ATGAATAGAGA
25541467 AAATAAATAA
1 AAATAAATAA
25541477 AAGGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 9 0.32
21 18 0.64
22 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (20 bp):
AAATAAATAATGAATAGAGA
Found at i:25541810 original size:65 final size:64
Alignment explanation
Indices: 25541638--25541831 Score: 194
Period size: 67 Copynumber: 3.0 Consensus size: 64
25541628 AATGAAAATA
* * * * * *
25541638 AAATATAAATAATATCAAATTTAAATATTTTAAAGGT-GAAAGAATAACAAATAAATAGATATAA
1 AAATATAAATAATATAAAACTAAAATATTTAAAAAGTAAAAAGAA-AA-AAATAAATAG--ATAA
25541702 AAC
62 AAC
* * * *
25541705 AAATATAAATAATATTAAATTTAAATGTTTAAAAAGT-AAAAGAAAAAAATAAATAGATAAAAC
1 AAATATAAATAATATAAAACTAAAATATTTAAAAAGTAAAAAGAAAAAAATAAATAGATAAAAC
* * * *
25541768 AAATATTAGTAATATCAAAACTAAAATATTTAAAAATGTAAAAAGTAAAAAATAAATAAATAAA
1 AAATATAAATAATAT-AAAACTAAAATATTTAAAAA-GTAAAAAGAAAAAAATAAATAGATAAA
25541832 TAAATAGATA
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
63 20 0.18
64 16 0.14
65 12 0.11
66 24 0.22
67 39 0.35
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (64 bp):
AAATATAAATAATATAAAACTAAAATATTTAAAAAGTAAAAAGAAAAAAATAAATAGATAAAAC
Found at i:25541946 original size:35 final size:34
Alignment explanation
Indices: 25541907--25542015 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 34
25541897 AATAAATAAA
25541907 TAAATAGATAAAACAAAAATAGATAATATCAAATT
1 TAAATAGATAAAACAAAAATA-ATAATATCAAATT
** ** * * * **
25541942 TAAATATTTAAAAGTAAAAGAATAACA-AAAAAA
1 TAAATAGATAAAACAAAAATAATAATATCAAATT
* *
25541975 TAAATAGATATAACAAATATAAATAATATCAAATT
1 TAAATAGATAAAACAAAAAT-AATAATATCAAATT
25542010 TAAATA
1 TAAATA
25542016 TTTACAAGTA
Statistics
Matches: 52, Mismatches: 20, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
33 16 0.31
34 11 0.21
35 25 0.48
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (34 bp):
TAAATAGATAAAACAAAAATAATAATATCAAATT
Found at i:25541978 original size:19 final size:21
Alignment explanation
Indices: 25541951--25542000 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
25541941 TTAAATATTT
*
25541951 AAAAGTAAA-AGA-ATAACAA
1 AAAAATAAATAGATATAACAA
25541970 AAAAATAAATAGATATAACAA
1 AAAAATAAATAGATATAACAA
25541991 ATATAAATAA
1 A-A-AAATAA
25542001 TATCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 3 0.12
21 8 0.31
22 1 0.04
23 6 0.23
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAAATAAATAGATATAACAA
Found at i:25541981 original size:68 final size:67
Alignment explanation
Indices: 25541638--25542123 Score: 481
Period size: 68 Copynumber: 7.0 Consensus size: 67
25541628 AATGAAAATA
* * * *
25541638 AAATATAAATAATATCAAATTTAAATATTTTAAAGGTGAAAGAATAACAAATAAATAGAT--ATA
1 AAATATAAATAATATCAAATTTAAATA-TTTAAAAGTAAAAGAATAA-AAAAAAATAAATAGATA
25541701 AAAC
64 AAAC
* *
25541705 AAATATAAATAATATTAAATTTAAATGTTTAAAAAGTAAAAG-----AAAAAAATAAATAGATAA
1 AAATATAAATAATATCAAATTTAAATATTT-AAAAGTAAAAGAATAAAAAAAAATAAATAGATAA
25541765 AAC
65 AAC
* * * *
25541768 AAATATTAGTAATATCAAAACTAAAATATTTAAAAATGTAAAAAGTAAAAAATAAATAAATAAAT
1 AAATATAAATAATATC-AAATTTAAATATTT-AAAA-GT-AAAAG-----AATAAA-AAA-AAAT
25541833 AAATAGATAAAAC
55 AAATAGATAAAAC
* * *
25541846 AAATATAAATAATATCAAATTTTAAGTATTAAAAAGAGCAAAAGAATAACGAATAAATAAATAAA
1 AAATATAAATAATATCAAA-TTTAAATATT-TAAA-AGTAAAAGAAT-A--AA-AAA-AAATAAA
25541911 TAGATAAAAC
58 TAGATAAAAC
* * *
25541921 AAAAATAGATAATATCAAATTTAAATATTTAAAAGTAAAAGAATAACAAAAAAATAAATAGATAT
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGTAAAAGAATAA-AAAAAAATAAATAGATAA
25541986 AAC
65 AAC
*
25541989 AAATATAAATAATATCAAATTTAAATATTTACAAGTAAAAGAATAAAAAATAAATAAATAGATAA
1 AAATATAAATAATATCAAATTTAAATATTTAAAAGTAAAAGAATAAAAAA-AAATAAATAGATAA
25542054 ATA-
65 A-AC
* * *
25542057 AAATATAAATAAAATCAAATTTAAATATTAAAAAAGTAAAAGAAT---AATAAATAAATAGATAA
1 AAATATAAATAATATCAAATTTAAATATT-TAAAAGTAAAAGAATAAAAAAAAATAAATAGATAA
25542119 AAC
65 AAC
25542122 AA
1 AA
25542124 CTCATAAAAG
Statistics
Matches: 357, Mismatches: 33, Indels: 60
0.79 0.07 0.13
Matches are distributed among these distances:
61 10 0.03
63 20 0.06
64 17 0.05
65 19 0.05
66 10 0.03
67 38 0.11
68 101 0.28
69 18 0.05
70 1 0.00
71 1 0.00
72 13 0.04
73 4 0.01
74 9 0.03
75 41 0.11
76 1 0.00
77 11 0.03
78 42 0.12
79 1 0.00
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (67 bp):
AAATATAAATAATATCAAATTTAAATATTTAAAAGTAAAAGAATAAAAAAAAATAAATAGATAAA
AC
Found at i:25542057 original size:16 final size:16
Alignment explanation
Indices: 25542036--25542119 Score: 52
Period size: 16 Copynumber: 5.2 Consensus size: 16
25542026 AAAGAATAAA
25542036 AAATAAATAAATAGAT
1 AAATAAATAAATAGAT
* *
25542052 AAATAAA-ATATAAAT
1 AAATAAATAAATAGAT
*
25542067 AAAATCAAATTTAAATA-TT
1 -AAAT-AAA--TAAATAGAT
25542086 AAA-AAAGTAAA-AGA-
1 AAATAAA-TAAATAGAT
25542100 ATAATAAATAAATAGAT
1 A-AATAAATAAATAGAT
25542117 AAA
1 AAA
25542120 ACAACTCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
14 2 0.04
15 16 0.31
16 22 0.42
17 4 0.08
18 3 0.06
19 1 0.02
20 4 0.08
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATAAATAAATAGAT
Found at i:25542071 original size:11 final size:11
Alignment explanation
Indices: 25542030--25542071 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
25542020 CAAGTAAAAG
*
25542030 AATAAAAAATA
1 AATAAAATATA
*
25542041 AATAAATAGATA
1 AATAAA-ATATA
25542053 AATAAAATATA
1 AATAAAATATA
25542064 AATAAAAT
1 AATAAAAT
25542072 CAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAAAATATA
Found at i:25545760 original size:17 final size:17
Alignment explanation
Indices: 25545740--25545802 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
25545730 GTTATTTTTC
25545740 AAATATAAAAATTTAAA
1 AAATATAAAAATTTAAA
* *
25545757 AAATATAATCATTATTAAA
1 AAATATAA-AAAT-TTAAA
*
25545776 AAATATTTAAAATTTATAA
1 AAATA-TAAAAATTTA-AA
25545795 AAAT-TAAA
1 AAATATAAA
25545803 TGAATGATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 11 0.31
18 5 0.14
19 18 0.50
20 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATAAAAATTTAAA
Found at i:25550893 original size:18 final size:18
Alignment explanation
Indices: 25550870--25550959 Score: 135
Period size: 18 Copynumber: 5.0 Consensus size: 18
25550860 CCCAACTACT
*
25550870 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
25550888 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
25550906 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
**
25550924 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
25550942 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
25550960 ATAAACGGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:25550922 original size:36 final size:36
Alignment explanation
Indices: 25550870--25550959 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
25550860 CCCAACTACT
*
25550870 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
* *
25550906 GTATATGTGAATAGTACCGTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
25550942 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
25550960 ATAAACGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:25553821 original size:22 final size:19
Alignment explanation
Indices: 25553784--25553824 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25553774 ATGACTTTTA
25553784 AATAATTTTTTTATTAAGT
1 AATAATTTTTTTATTAAGT
* *
25553803 AATAA-TATTTTATTAATT
1 AATAATTTTTTTATTAAGT
25553821 AATA
1 AATA
25553825 TTATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATAATTTTTTTATTAAGT
Found at i:25557667 original size:18 final size:19
Alignment explanation
Indices: 25557641--25557696 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
25557631 AAGGTTTATA
*
25557641 AAGAGATAT-ATATATAAT
1 AAGACATATAATATATAAT
25557659 AAGACATATAGATATATAAT
1 AAGACATATA-ATATATAAT
* *
25557679 AAGATATAAAGATATATA
1 AAGACATATA-ATATATA
25557697 GATATAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 8 0.24
20 25 0.76
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (19 bp):
AAGACATATAATATATAAT
Found at i:25557675 original size:20 final size:20
Alignment explanation
Indices: 25557650--25557696 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
25557640 AAAGAGATAT
*
25557650 ATATATAATAAGACATATAG
1 ATATATAATAAGACATAAAG
*
25557670 ATATATAATAAGATATAAAG
1 ATATATAATAAGACATAAAG
25557690 ATATATA
1 ATATATA
25557697 GATATAAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGACATAAAG
Found at i:25557711 original size:15 final size:15
Alignment explanation
Indices: 25557644--25557717 Score: 64
Period size: 15 Copynumber: 5.0 Consensus size: 15
25557634 GTTTATAAAG
*
25557644 AGATATATATATAATA
1 AGATATATAGAT-ATA
*
25557660 AGACATATAGATAT-
1 AGATATATAGATATA
*
25557674 ATA-ATA-AGATATAA
1 AGATATATAGATAT-A
25557688 AGATATATAGATATA
1 AGATATATAGATATA
* *
25557703 AGGTATATATATATA
1 AGATATATAGATATA
25557718 CGTATACGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.12
13 3 0.06
14 4 0.08
15 19 0.40
16 16 0.33
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.34
Consensus pattern (15 bp):
AGATATATAGATATA
Found at i:25557717 original size:8 final size:8
Alignment explanation
Indices: 25557644--25557717 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
25557634 GTTTATAAAG
25557644 AGATATAT
1 AGATATAT
*
25557652 ATATA-AT
1 AGATATAT
*
25557659 AAGACATAT
1 -AGATATAT
25557668 AGATATAT
1 AGATATAT
25557676 --A-ATA-
1 AGATATAT
*
25557680 AGATATAA
1 AGATATAT
25557688 AGATATAT
1 AGATATAT
25557696 AGATATA-
1 AGATATAT
*
25557703 AGGTATAT
1 AGATATAT
*
25557711 ATATATA
1 AGATATA
25557718 CGTATACGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
5 3 0.06
6 2 0.04
7 11 0.22
8 33 0.65
9 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.34
Consensus pattern (8 bp):
AGATATAT
Found at i:25563132 original size:15 final size:15
Alignment explanation
Indices: 25563109--25563138 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25563099 AAAAAAGAAA
*
25563109 GGTTTTCTTTTCTTC
1 GGTTCTCTTTTCTTC
25563124 GGTTCTCTTTTCTTC
1 GGTTCTCTTTTCTTC
25563139 TCCGATGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.13, T:0.63
Consensus pattern (15 bp):
GGTTCTCTTTTCTTC
Found at i:25568917 original size:13 final size:13
Alignment explanation
Indices: 25568901--25568973 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 13
25568891 GATCAAAACG
*
25568901 AAAAGAAAAATAA
1 AAAAGAAAAATCA
** *
25568914 AAAATCAAAGTCA
1 AAAAGAAAAATCA
* *
25568927 AAATG-AAAATGA
1 AAAAGAAAAATCA
25568939 AAAAGAGAAAA-CA
1 AAAAGA-AAAATCA
**
25568952 AAAAGAAAAAGGA
1 AAAAGAAAAATCA
25568965 AAAAGAAAA
1 AAAAGAAAA
25568974 GGAGAGGTCA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
12 13 0.28
13 29 0.63
14 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAAGAAAAATCA
Found at i:25568919 original size:31 final size:32
Alignment explanation
Indices: 25568872--25568942 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
25568862 GGGTTCATAT
*
25568872 TGAAAATAAAAAAAATC-AAGATCAAAACGAAAA
1 TGAAAA-ATAAAAAATCAAAG-TCAAAACGAAAA
*
25568905 -GAAAAATAAAAAATCAAAGTCAAAATGAAAA
1 TGAAAAATAAAAAATCAAAGTCAAAACGAAAA
25568936 TGAAAAA
1 TGAAAAA
25568943 GAGAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (32 bp):
TGAAAAATAAAAAATCAAAGTCAAAACGAAAA
Found at i:25568962 original size:6 final size:6
Alignment explanation
Indices: 25568926--25568973 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
25568916 AATCAAAGTC
* * *
25568926 AAAATG AAAATG AAAAAG AGAAAAC AAAAAG AAAAAGG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA-G AAAAAG AAAA
25568974 GGAGAGGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:25568968 original size:19 final size:19
Alignment explanation
Indices: 25568932--25568967 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25568922 AGTCAAAATG
*
25568932 AAAATGAAAAAGAGAAAAC
1 AAAAAGAAAAAGAGAAAAC
25568951 AAAAAGAAAAAG-GAAAA
1 AAAAAGAAAAAGAGAAAA
25568968 AGAAAAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAGAGAAAAC
Found at i:25568973 original size:19 final size:18
Alignment explanation
Indices: 25568926--25568973 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
25568916 AATCAAAGTC
* *
25568926 AAAATGAAAATGAAAAAG
1 AAAAAGAAAAAGAAAAAG
*
25568944 AGAAAACAAAAAGAAAAAGG
1 A-AAAAGAAAAAGAAAAA-G
25568964 AAAAAGAAAA
1 AAAAAGAAAA
25568974 GGAGAGGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:25570695 original size:43 final size:43
Alignment explanation
Indices: 25570562--25570696 Score: 100
Period size: 43 Copynumber: 3.2 Consensus size: 43
25570552 AAAACAAAGC
* * * *
25570562 CTTGCCTCCATCGATTGCAGTGGAGCTAGTTAAAGAAGTAGAT
1 CTTGCCTCCATCAATTGCAGTGAAGCTGGTTAAAGAAGCAGAT
* * * ** * *
25570605 CTTGCCTTCC-TACAGA-T-CAGCGAAGCAGATCGAA-AA-CAAAGC
1 CTTGCC-TCCAT-CA-ATTGCAGTGAAGCTGGTTAAAGAAGCAGA-T
25570647 CTTGCCTCCATCAATTGCAGTGAAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCCATCAATTGCAGTGAAGCTGGTTAAAGAAGCAGAT
25570690 CTTGCCT
1 CTTGCCT
25570697 TCCTACAGAT
Statistics
Matches: 65, Mismatches: 18, Indels: 18
0.64 0.18 0.18
Matches are distributed among these distances:
40 1 0.02
41 8 0.12
42 21 0.32
43 26 0.40
44 8 0.12
45 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (43 bp):
CTTGCCTCCATCAATTGCAGTGAAGCTGGTTAAAGAAGCAGAT
Found at i:25570695 original size:85 final size:85
Alignment explanation
Indices: 25570552--25570786 Score: 380
Period size: 85 Copynumber: 2.8 Consensus size: 85
25570542 GTGAAGATAA
* *
25570552 AAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTAGTTAAAGAAGTAGATCTTGCCTTCCTA
1 AAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTA
25570617 CAGATCAGCGAAGCAGATCG
66 CAGATCAGCGAAGCAGATCG
* *
25570637 AAAACAAAGCCTTGCCTCCATCAATTGCAGTGAAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTA
1 AAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTA
25570702 CAGATCAGCGAAGCAGATCG
66 CAGATCAGCGAAGCAGATCG
* * * * *
25570722 AAAACAAAGCCTTACCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATGTTGCCCTCCT
1 AAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCT
25570787 GCGTCGACAG
Statistics
Matches: 138, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 123 0.89
86 15 0.11
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (85 bp):
AAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTA
CAGATCAGCGAAGCAGATCG
Found at i:25570715 original size:43 final size:43
Alignment explanation
Indices: 25570585--25570715 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
25570575 ATTGCAGTGG
* *
25570585 AGCTAGTTAAAGAAGTAGATCTTGCCTTCCTACAGATCAGCGA
1 AGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACAGATCAGCGA
* * ** * * *
25570628 AGCAGATCGAA-AA-CAAAGCCTTGCC-TCC-ATCA-ATTGCAGTGA
1 AGCTGGTTAAAGAAGCAGA-TCTTGCCTTCCTA-CAGA-T-CAGCGA
25570670 AGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACAGATCAGCGA
1 AGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACAGATCAGCGA
25570713 AGC
1 AGC
25570716 AGATCGAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 18
0.65 0.16 0.19
Matches are distributed among these distances:
40 2 0.03
41 8 0.13
42 20 0.32
43 22 0.35
44 9 0.14
45 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (43 bp):
AGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACAGATCAGCGA
Found at i:25575169 original size:129 final size:131
Alignment explanation
Indices: 25574854--25575190 Score: 495
Period size: 129 Copynumber: 2.6 Consensus size: 131
25574844 GTTTAATGAG
* * ** **
25574854 AAAAATCGAAACCCCGTAAGTTAGGGTAC-AATTTCTCGAATCACCCAAAAAGCGAAATG--TTA
1 AAAAATCGAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAAT-GGCCAAAAAGC-AAA-GCATGG
*
25574916 CCTTATAACGAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTAA
63 CCTTATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTAA
25574981 CAAA
128 CAAA
* * *
25574985 AAAAACCAAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAATGGCCAAAATGCAAAGCATGGCCT
1 AAAAATCGAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAATGGCCAAAAAGCAAAGCATGGCCT
*
25575050 TATAACAAAATTTCTTTT-TTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTGGGCCTAAC-A
66 TATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTAACAA
25575113 A
131 A
* *
25575114 AAAAATCGAAACCCCGTAAGTTAGGGTTCGATTTTCTCAAATGGCCAAAACGCAAAGCATGGCCT
1 AAAAATCGAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAATGGCCAAAAAGCAAAGCATGGCCT
25575179 TATAACAAAATT
66 TATAACAAAATT
25575191 CTTACTTTGC
Statistics
Matches: 188, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
129 76 0.40
130 46 0.24
131 55 0.29
132 11 0.06
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (131 bp):
AAAAATCGAAACCCCGTAAGTTAGGGTTCGATTTTCTCGAATGGCCAAAAAGCAAAGCATGGCCT
TATAACAAAATTTCTTTTATTATTTTGAAATTCAAAAAGGGTTCTTTGCTATTTAGGCCTAACAA
A
Found at i:25577523 original size:18 final size:18
Alignment explanation
Indices: 25577502--25577957 Score: 210
Period size: 18 Copynumber: 25.5 Consensus size: 18
25577492 AACAATTTTT
**
25577502 ATTTTTGAGCACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25577520 ATTTTTTAAAACACGAGA
1 ATTTTTGAAAACACGAAA
* *
25577538 ATTTTAG-AGACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25577555 ATTCTTAAAAACACGAAA
1 ATTTTTGAAAACACGAAA
*
25577573 ATTTTTGAAAACACGACA
1 ATTTTTGAAAACACGAAA
*
25577591 A-TTTTG-AAACACGAGA
1 ATTTTTGAAAACACGAAA
25577607 A-TTTT-AAAACACGAGAA
1 ATTTTTGAAAACACGA-AA
* **
25577624 TTGTTTTTTTGAAAACACGATT
1 ----ATTTTTGAAAACACGAAA
* *
25577646 TTTTTTG-AAACTCGAAA
1 ATTTTTGAAAACACGAAA
* *
25577663 A--TTTGAGAAATACGAGA
1 ATTTTTGA-AAACACGAAA
* * *
25577680 GTTGTTGAAAACAAGAAA
1 ATTTTTGAAAACACGAAA
* **
25577698 ACTCAT-AAAACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25577715 ATTTTTG-AAACATGGAA
1 ATTTTTGAAAACACGAAA
* *
25577732 GTTTTTAGAAAACAGGAAAA
1 ATTTTT-GAAAACACG-AAA
* *
25577752 ATTTCTTTG--ATCATC-AGA
1 A-TT-TTTGAAAACA-CGAAA
25577770 ATTTTTGAAAACACGAAA
1 ATTTTTGAAAACACGAAA
25577788 ATTTTTG-AAACACG-AA
1 ATTTTTGAAAACACGAAA
* * **
25577804 AGTTTTAAAAACACGAGG
1 ATTTTTGAAAACACGAAA
*
25577822 ATTTTTGAAACACATG-AA
1 ATTTTTGAAA-ACACGAAA
* * *
25577840 TTTTTTAAAAACATGAAA
1 ATTTTTGAAAACACGAAA
* ***
25577858 AATTTTGAAAATTTG-AA
1 ATTTTTGAAAACACGAAA
* *
25577875 TTTTTTGAAAACACGGGAATT
1 ATTTTTGAAAACAC--GAA-A
* *
25577896 TTTTTTGAAAACATGAAA
1 ATTTTTGAAAACACGAAA
**
25577914 ATTTTTG-AAACACGGGA
1 ATTTTTGAAAACACGAAA
*
25577931 ATTTTTGAAAACACGAAT
1 ATTTTTGAAAACACGAAA
*
25577949 TTTTTTGAA
1 ATTTTTGAA
25577958 TTTTTGTTAA
Statistics
Matches: 323, Mismatches: 83, Indels: 64
0.69 0.18 0.14
Matches are distributed among these distances:
15 4 0.01
16 33 0.10
17 105 0.33
18 125 0.39
19 21 0.07
20 3 0.01
21 16 0.05
22 7 0.02
23 9 0.03
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAA
Found at i:25577575 original size:53 final size:50
Alignment explanation
Indices: 25577512--25577630 Score: 157
Period size: 53 Copynumber: 2.3 Consensus size: 50
25577502 ATTTTTGAGC
* *
25577512 ACACGAAAATTTTTTAAAACACGAGAATTTTAGAGACACGAAAATTCTTAAAA
1 ACACGAAAATTTTTTAAAACACGACAATTTT-GAAACACGAAAATT-TT-AAA
* *
25577565 ACACGAAAATTTTTGAAAACACGACAATTTTGAAACACGAGAATTTTAAA
1 ACACGAAAATTTTTTAAAACACGACAATTTTGAAACACGAAAATTTTAAA
*
25577615 ACACGAGAATTGTTTT
1 ACACGAAAATT-TTTT
25577631 TTTGAAAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 13 0.22
51 5 0.08
52 12 0.20
53 29 0.49
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (50 bp):
ACACGAAAATTTTTTAAAACACGACAATTTTGAAACACGAAAATTTTAAA
Found at i:25577602 original size:16 final size:16
Alignment explanation
Indices: 25577523--25577625 Score: 116
Period size: 16 Copynumber: 6.1 Consensus size: 16
25577513 CACGAAAATT
25577523 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
* *
25577539 TTTTAGAGACACGAAAA
1 TTTTA-AAACACGAGAA
*
25577556 TTCTTAAAAACACGAAAA
1 TT-TT-AAAACACGAGAA
*
25577574 TTTTTGAAAACACGACAA
1 -TTTT-AAAACACGAGAA
*
25577592 TTTTGAAACACGAGAA
1 TTTTAAAACACGAGAA
25577608 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
25577624 TT
1 TT
25577626 GTTTTTTTGA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
16 32 0.43
17 15 0.20
18 25 0.33
19 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (16 bp):
TTTTAAAACACGAGAA
Found at i:25577610 original size:34 final size:34
Alignment explanation
Indices: 25577502--25577947 Score: 161
Period size: 35 Copynumber: 12.5 Consensus size: 34
25577492 AACAATTTTT
**
25577502 ATTTTTGAGCACACGAAAATTTTTTAAAACACGAGA
1 ATTTTTGAAAACACGAAAA--TTTTAAAACACGAGA
* * *
25577538 ATTTTAG-AGACACGAAAATTCTTAAAAACACGAAA
1 ATTTTTGAAAACACGAAAATT-TT-AAAACACGAGA
* *
25577573 ATTTTTGAAAACACGACAATTTTGAAACACGAGA
1 ATTTTTGAAAACACGAAAATTTTAAAACACGAGA
* **
25577607 A-TTTT-AAAACACGAGAATTGTTTTTTTGAAAACACGATT
1 ATTTTTGAAAACACGA-AA-----ATTTT-AAAACACGAGA
* * * *
25577646 TTTTTTG-AAACTCGAAAATTTGAGAAATACGAGA
1 ATTTTTGAAAACACGAAAATTTTA-AAACACGAGA
* * * ** *
25577680 GTTGTTGAAAACAAGAAAACTCATAAAACACGAAA
1 ATTTTTGAAAACACGAAAA-TTTTAAAACACGAGA
* ** * *
25577715 ATTTTTG-AAACATGGAAGTTTTTAGAAAACAGGAAAA
1 ATTTTTGAAAACA-CGAAAATTTT--AAAACACG-AGA
* * * *
25577752 ATTTCTTTGATCATCA-G-AATTTTTGAAAACACGAAA
1 A-TT-TTTGA-AAACACGAAAATTTT-AAAACACGAGA
* *
25577788 ATTTTTG-AAACACGAAAGTTTTAAAAACACGAGG
1 ATTTTTGAAAACACGAAAATTTT-AAAACACGAGA
* ** * *
25577822 ATTTTTGAAACACATGAATTTTTTAAAAACATGAAA
1 ATTTTTGAAA-ACACGAAAATTTT-AAAACACGAGA
* *** ** *
25577858 AATTTTGAAAATTTGAATTTTTTGAAAACACGGGA
1 ATTTTTGAAAACACGAAAATTTT-AAAACACGAGA
* * *
25577893 ATTTTTTTTGAAAACATGAAAATTTTTGAAACACGGGA
1 A---TTTTTGAAAACACGAAAA-TTTTAAAACACGAGA
25577931 ATTTTTGAAAACACGAA
1 ATTTTTGAAAACACGAA
25577948 TTTTTTTGAA
Statistics
Matches: 311, Mismatches: 68, Indels: 63
0.70 0.15 0.14
Matches are distributed among these distances:
32 12 0.04
33 9 0.03
34 60 0.19
35 91 0.29
36 58 0.19
37 12 0.04
38 36 0.12
39 19 0.06
40 11 0.04
41 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (34 bp):
ATTTTTGAAAACACGAAAATTTTAAAACACGAGA
Found at i:25577725 original size:17 final size:17
Alignment explanation
Indices: 25577502--25577957 Score: 152
Period size: 17 Copynumber: 25.5 Consensus size: 17
25577492 AACAATTTTT
*
25577502 ATTTTTGAGCACACGAAA
1 ATTTTTGA-AACACGAAA
* *
25577520 ATTTTTTAAAACACGAGA
1 A-TTTTTGAAACACGAAA
* *
25577538 ATTTTAGAGACACGAAA
1 ATTTTTGAAACACGAAA
**
25577555 ATTCTTAAAAACACGAAA
1 ATT-TTTGAAACACGAAA
*
25577573 ATTTTTGAAAACACGACA
1 ATTTTTG-AAACACGAAA
*
25577591 A-TTTTGAAACACGAGA
1 ATTTTTGAAACACGAAA
*
25577607 A-TTTTAAAACACGAGAA
1 ATTTTTGAAACACGA-AA
* **
25577624 TTGTTTTTTTGAAAACACGATT
1 ----ATTTTTG-AAACACGAAA
* *
25577646 TTTTTTGAAACTCGAAA
1 ATTTTTGAAACACGAAA
** * *
25577663 ATTTGAGAAATACGAGA
1 ATTTTTGAAACACGAAA
* * *
25577680 GTTGTTGAAAACAAGAAA
1 ATTTTTG-AAACACGAAA
* ** *
25577698 ACTCATAAAACACGAAA
1 ATTTTTGAAACACGAAA
* *
25577715 ATTTTTGAAACATGGAA
1 ATTTTTGAAACACGAAA
* *
25577732 GTTTTTAGAAAACAGGAAAA
1 ATTTTT-G-AAACACG-AAA
* *
25577752 ATTTCTTTG-ATCATC-AGA
1 A-TT-TTTGAAACA-CGAAA
25577770 ATTTTTGAAAACACGAAA
1 ATTTTTG-AAACACGAAA
25577788 ATTTTTGAAACACGAAA
1 ATTTTTGAAACACGAAA
* ** **
25577805 GTTTTAAAAACACGAGG
1 ATTTTTGAAACACGAAA
25577822 ATTTTTGAAACAC-ATGAA
1 ATTTTTGAAACACGA--AA
* * *
25577840 TTTTTTAAAAACATGAAA
1 ATTTTT-GAAACACGAAA
* *
25577858 AATTTTGAAA-ATTTG-AA
1 ATTTTTGAAACA--CGAAA
* *
25577875 TTTTTTGAAAACACGGGAATT
1 ATTTTTG-AAACAC--GAA-A
* *
25577896 TTTTTTGAAAACATGAAA
1 ATTTTTG-AAACACGAAA
**
25577914 ATTTTTGAAACACGGGA
1 ATTTTTGAAACACGAAA
*
25577931 ATTTTTGAAAACACGAAT
1 ATTTTTG-AAACACGAAA
*
25577949 TTTTTTGAA
1 ATTTTTGAA
25577958 TTTTTGTTAA
Statistics
Matches: 319, Mismatches: 86, Indels: 67
0.68 0.18 0.14
Matches are distributed among these distances:
16 28 0.09
17 130 0.41
18 101 0.32
19 25 0.08
20 4 0.01
21 16 0.05
22 7 0.02
23 8 0.03
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (17 bp):
ATTTTTGAAACACGAAA
Found at i:25577911 original size:56 final size:54
Alignment explanation
Indices: 25577768--25577954 Score: 163
Period size: 56 Copynumber: 3.5 Consensus size: 54
25577758 TTGATCATCA
** * * * *
25577768 GAATTTTTGAAAACACGAA-AATTTTT-GAAACACG-AAAGTTTTAAAAACACGAG
1 GAATTTTTGAAAACACGAATTTTTTTTAAAAACATGAAAAATTTT-GAAACACG-G
* ***
25577821 G-ATTTTTGAAACACATGAA--TTTTTTAAAAACATGAAAAATTTTGAAA-ATTT
1 GAATTTTTGAAA-ACACGAATTTTTTTTAAAAACATGAAAAATTTTGAAACACGG
* *
25577872 GAATTTTTTGAAAACACGGGAATTTTTTTTGAAAACATGAAAATTTTTGAAACACGG
1 GAA-TTTTTGAAAACAC--GAATTTTTTTTAAAAACATGAAAAATTTTGAAACACGG
25577929 GAATTTTTGAAAACACGAATTTTTTT
1 GAATTTTTGAAAACACGAATTTTTTT
25577955 GAATTTTTGT
Statistics
Matches: 109, Mismatches: 15, Indels: 19
0.76 0.10 0.13
Matches are distributed among these distances:
51 1 0.01
52 20 0.18
53 25 0.23
54 20 0.18
56 39 0.36
57 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (54 bp):
GAATTTTTGAAAACACGAATTTTTTTTAAAAACATGAAAAATTTTGAAACACGG
Found at i:25578513 original size:17 final size:17
Alignment explanation
Indices: 25578491--25578526 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25578481 CGAGCCTTCC
25578491 TTTTTTCCTTTTTCCCT
1 TTTTTTCCTTTTTCCCT
* *
25578508 TTTTTTTCTTTTTCTCT
1 TTTTTTCCTTTTTCCCT
25578525 TT
1 TT
25578527 CCCTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCCTTTTTCCCT
Found at i:25578527 original size:23 final size:24
Alignment explanation
Indices: 25578492--25578547 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
25578482 GAGCCTTCCT
*
25578492 TTTTTCCTTTTTCCC-TTTTTTTTC
1 TTTTT-CTCTTTCCCTTTTTTTTTC
25578516 TTTTTCTCTTTCCCTTTTTTTTTC
1 TTTTTCTCTTTCCCTTTTTTTTTC
25578540 TCTTTTCT
1 T-TTTTCT
25578548 TTTTTTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 8 0.28
24 15 0.52
25 6 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTCTTTCCCTTTTTTTTTC
Found at i:25578537 original size:18 final size:17
Alignment explanation
Indices: 25578511--25578567 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
25578501 TTTCCCTTTT
25578511 TTTTCTTTTTCTCTTTCCC
1 TTTT-TTTTTCTCTTT-CC
*
25578530 TTTTTTTTTCTCTTTTC
1 TTTTTTTTTCTCTTTCC
*
25578547 TTTTTTTCATTCTTTTTCC
1 TTTTTTT--TTCTCTTTCC
25578566 TT
1 TT
25578568 CGGCCTGCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.24
18 11 0.33
19 14 0.42
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTTTCTCTTTCC
Found at i:25578758 original size:14 final size:13
Alignment explanation
Indices: 25578726--25578765 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
25578716 GGGGGTTTTC
25578726 TCTTTTTTTTGGG
1 TCTTTTTTTTGGG
*
25578739 TCTTTTTTATTTGG
1 TCTTTTTT-TTGGG
25578753 T-TTTTTTTTGGG
1 TCTTTTTTTTGGG
25578765 T
1 T
25578766 AGGGTTCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.03, C:0.05, G:0.20, T:0.72
Consensus pattern (13 bp):
TCTTTTTTTTGGG
Found at i:25578895 original size:13 final size:12
Alignment explanation
Indices: 25578851--25578908 Score: 55
Period size: 13 Copynumber: 4.6 Consensus size: 12
25578841 TAAAAATTTA
25578851 TTTTCTTTCTTC
1 TTTTCTTTCTTC
*
25578863 TTCCTCTTTTCTT-
1 TT-TTC-TTTCTTC
*
25578876 ATTTCTTTCTTTC
1 TTTTCTTTC-TTC
25578889 TTTTCTTTCTTC
1 TTTTCTTTCTTC
25578901 TTCTTCTT
1 TT-TTCTT
25578909 CTCCGTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 4 0.11
12 11 0.30
13 16 0.43
14 6 0.16
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTCTTTCTTC
Found at i:25579332 original size:28 final size:29
Alignment explanation
Indices: 25579255--25579346 Score: 98
Period size: 28 Copynumber: 3.1 Consensus size: 29
25579245 AGTTTTGAGG
*
25579255 CAAAAGTGTAATTTTGAGAAAGTTTAGGGGT
1 CAAAA-TGTAATTTT-AGAAAATTTAGGGGT
* * *
25579286 TAAAATGAAATTTTA-AAAATGTAGGGGT
1 CAAAATGTAATTTTAGAAAATTTAGGGGT
*
25579314 CAAAATGTAA-TTTAGAAAAGTTTAGGAGT
1 CAAAATGTAATTTTAGAAAA-TTTAGGGGT
25579343 CAAA
1 CAAA
25579347 TTACAATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
27 4 0.08
28 23 0.45
29 12 0.24
30 8 0.16
31 4 0.08
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (29 bp):
CAAAATGTAATTTTAGAAAATTTAGGGGT
Found at i:25579344 original size:29 final size:29
Alignment explanation
Indices: 25579242--25579346 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 29
25579232 TAAATGCAGC
* * *
25579242 AAAAGTTT-TGAGGCAAAAGTGTAATTTTG
1 AAAAGTTTAGGAGTCAAAA-TGTAATTTAG
* * *
25579271 AGAAAGTTTAGGGGTTAAAATGAAATTTTA-
1 A-AAAGTTTAGGAGTCAAAATGTAA-TTTAG
* *
25579301 AAAA-TGTAGGGGTCAAAATGTAATTTAG
1 AAAAGTTTAGGAGTCAAAATGTAATTTAG
25579329 AAAAGTTTAGGAGTCAAA
1 AAAAGTTTAGGAGTCAAA
25579347 TTACAATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.07
28 20 0.33
29 15 0.25
30 12 0.20
31 9 0.15
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (29 bp):
AAAAGTTTAGGAGTCAAAATGTAATTTAG
Found at i:25579695 original size:74 final size:74
Alignment explanation
Indices: 25579502--25580127 Score: 719
Period size: 74 Copynumber: 8.3 Consensus size: 74
25579492 TTCTTTTTAC
* * * * * * *
25579502 TTGAAAAACAGAAATCG-AGAATAGCTCGGCGTGCAACCCGAGGCCCAACTCACCTCTAGCAATA
1 TTGAAAAACAGAAATTGAAAAATACCTCGACGTG--ACTCGAGGCTCAACTCACCTCTCGCAATA
*
25579566 TGAGTTAATTTTT
64 TGAGTTGA--TTT
* *
25579579 TTGAAAAGCA-AGAATTGAAAAATATCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGA-AATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
25579643 GAGTTGATTT
65 GAGTTGATTT
* *
25579653 TGGAAAAATAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACC-CTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATG
25579717 AGTTGATTT
66 AGTTGATTT
* *
25579726 TTGAAAAACAGAAATT-TAAAATACCTC-AGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTGAAAAATACCTCGA-CGT--GACTCGAGGCTCAACTCACCTCTCGCAAT
* *
25579789 ATAAGTTGCTTTTT
63 ATGAGTTG--ATTT
* * *
25579803 TTGAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCAGCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATG
25579868 AGTTGATTT
66 AGTTGATTT
* * *
25579877 TTGAAAAACAAAAATT-TAAAATACCTC-AGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTGAAAAATACCTCGA-CGT--GACTCGAGGCTCAACTCACCTCTCGCAAT
25579940 ATGAGTTGATTT
63 ATGAGTTGATTT
* * * * *
25579952 TTGAAAAACAGAAATTTAAAAATACCTTGACATGAGTCGAGGCTCAACTCACCTCTAGCAATATG
1 TTGAAAAACAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATG
25580017 AGTTGATTT
66 AGTTGATTT
* * * * *
25580026 TTGAAGAACAGAAATTTAAAAGAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACATCTCGCA
1 TTGAAAAACAGAAA-TT-GAA-AAATACCTCGAC--GTGACTCGAGGCTCAACTCACCTCTCGCA
25580091 ATATGAGTTGATTT
61 ATATGAGTTGATTT
* * *
25580105 TTTAAAAAAAG-AATTAAAAAATA
1 TTGAAAAACAGAAATTGAAAAATA
25580128 AAATAAAATA
Statistics
Matches: 479, Mismatches: 49, Indels: 44
0.84 0.09 0.08
Matches are distributed among these distances:
71 1 0.00
72 14 0.03
73 47 0.10
74 138 0.29
75 77 0.16
76 84 0.18
77 43 0.09
78 28 0.06
79 47 0.10
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAATACCTCGACGTGACTCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTT
Found at i:25580261 original size:79 final size:75
Alignment explanation
Indices: 25580137--25580424 Score: 357
Period size: 79 Copynumber: 3.8 Consensus size: 75
25580127 AAAATAAAAT
* * *
25580137 AAAATACCTCGGCATGCGACCCGAGGCTCAACTCACCCCTTGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
25580202 ACATAAACTTAAA
66 ACA-AAA-TT-GA
* * * * * *
25580215 AGAAATACATCGGCGTGTGACCCAAGGCTCAACCCATCTCTCGCAATATGAGTTGATTTTTGAAC
1 A-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
25580280 AACAGAAATTGA
65 AACA-AAATTGA
** *
25580292 AAAATACCTTAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAGAA
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
25580354 ACAAAAATTGA
66 AC-AAAATTGA
* * *
25580365 AAAATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTT
1 AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
25580425 TTTTGAAAAA
Statistics
Matches: 181, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
73 26 0.14
74 38 0.21
75 38 0.21
76 13 0.07
77 2 0.01
78 3 0.02
79 61 0.34
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (75 bp):
AAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
ACAAAATTGA
Found at i:25580321 original size:243 final size:242
Alignment explanation
Indices: 25579893--25580348 Score: 641
Period size: 243 Copynumber: 1.9 Consensus size: 242
25579883 AACAAAAATT
* *
25579893 TAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 TAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTGAAA
* * * ** * *
25579958 AACAGAAATTTAAAAATACCTTGACATGAGTCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA
66 AACAGAAATTAAAAAATACATCGACATGACCCAAGGCTCAACCCACCTCTAGCAATATGAGTTGA
* *
25580023 TTTTTGAAGAACAGAAATTTAAAAGAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACATCTC
131 TTTTTGAACAACAGAAATTTAAAAGAAATACCTCAGCG-GTGACCCGAGGCTCAACTCACATCTC
25580088 GCAATATGAGTTGATTTTTTAAAAAAAGAATTAAAAAATAAAATAAAA
195 GCAATATGAGTTGATTTTTTAAAAAAAGAATTAAAAAATAAAATAAAA
* *
25580136 TAAAATACCTCGGCATGCGACCCGAGGCTCAACTCACCCCTTGCAATATGAGTTGATTTTTGAAA
1 TAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTGAAA
* * * * *
25580201 AACATAAACTTAAAAGAAATACATCGGCGTGTGACCCAAGGCTCAACCCATCTCTCGCAATATGA
66 AACAGAAA-TT-AAA-AAATACATCGAC--ATGACCCAAGGCTCAACCCACCTCTAGCAATATGA
* * *
25580266 GTTGATTTTTGAACAACAGAAA-TT-GAA-AAATACCTTAGC-GTGACCCGAGGCTCAACTCACC
126 GTTGATTTTTGAACAACAGAAATTTAAAAGAAATACCTCAGCGGTGACCCGAGGCTCAACTCACA
25580327 TCTCGCAATATGAGTTGATTTT
191 TCTCGCAATATGAGTTGATTTT
25580349 GAGAAACAAA
Statistics
Matches: 187, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
243 111 0.59
244 2 0.01
245 12 0.06
246 11 0.06
247 2 0.01
248 49 0.26
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (242 bp):
TAAAATACCTCAGCATGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTGAAA
AACAGAAATTAAAAAATACATCGACATGACCCAAGGCTCAACCCACCTCTAGCAATATGAGTTGA
TTTTTGAACAACAGAAATTTAAAAGAAATACCTCAGCGGTGACCCGAGGCTCAACTCACATCTCG
CAATATGAGTTGATTTTTTAAAAAAAGAATTAAAAAATAAAATAAAA
Found at i:25581331 original size:6 final size:6
Alignment explanation
Indices: 25581330--25581377 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
25581320 CTTTTTTGTT
*
25581330 TTTTTG TTTTTG TTTTGTT TTTTTG TTTTTG TTTTT- TTGTTTG TTTTT
1 TTTTTG TTTTTG TTTT-TG TTTTTG TTTTTG TTTTTG TT-TTTG TTTTT
25581378 TAGGCATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 2 0.05
6 28 0.76
7 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:25581331 original size:14 final size:13
Alignment explanation
Indices: 25581321--25581378 Score: 80
Period size: 14 Copynumber: 4.2 Consensus size: 13
25581311 TTTTTTTTAC
25581321 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
*
25581334 TGTTTTTGTTTTGT
1 T-TTTTTGTTTTTT
25581348 TTTTTTGTTTTTGT
1 TTTTTTGTTTTT-T
25581362 TTTTTTGTTTGTTT
1 TTTTTTGTTT-TTT
25581376 TTT
1 TTT
25581379 AGGCATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 11 0.28
14 27 0.68
15 2 0.05
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:25581332 original size:8 final size:8
Alignment explanation
Indices: 25581321--25581376 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
25581311 TTTTTTTTAC
25581321 TTTTTTGT
1 TTTTTTGT
25581329 TTTTTTGT
1 TTTTTTGT
25581337 TTTTGTT-T
1 TTTT-TTGT
25581345 TGTTTTT-T
1 T-TTTTTGT
25581353 TGTTTTTGT
1 T-TTTTTGT
25581362 TTTTTTGT
1 TTTTTTGT
25581370 TTGTTTT
1 TT-TTTT
25581377 TTAGGCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
8 33 0.75
9 11 0.25
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (8 bp):
TTTTTTGT
Found at i:25581334 original size:19 final size:19
Alignment explanation
Indices: 25581323--25581377 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
25581313 TTTTTTACTT
25581323 TTTTGTTTTTTTGTTTTTG
1 TTTTGTTTTTTTGTTTTTG
25581342 TTTTGTTTTTTTGTTTTTG
1 TTTTGTTTTTTTGTTTTTG
*
25581361 TTTT-TTTGTTTGTTTTT
1 TTTTGTTTTTTTGTTTTT
25581378 TAGGCATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 12 0.34
19 23 0.66
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
TTTTGTTTTTTTGTTTTTG
Found at i:25587442 original size:18 final size:18
Alignment explanation
Indices: 25587421--25587870 Score: 202
Period size: 18 Copynumber: 25.3 Consensus size: 18
25587411 AACAATTTTT
**
25587421 ATTTTTGAGCACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25587439 ATTTTTTAAAACACGAGA
1 ATTTTTGAAAACACGAAA
* *
25587457 ATTTTAG-AGACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25587474 ATTCTTAAAAACACGAAA
1 ATTTTTGAAAACACGAAA
*
25587492 ATTTTTGAAAACACGACA
1 ATTTTTGAAAACACGAAA
*
25587510 A-TTTTG-AAACACGAGA
1 ATTTTTGAAAACACGAAA
25587526 A-TTTT-AAAACACGAGAA
1 ATTTTTGAAAACACGA-AA
* **
25587543 TTGTTTTTTGAAAACACGATT
1 ---ATTTTTGAAAACACGAAA
* *
25587564 TTTTTTG-AAACTCGAAA
1 ATTTTTGAAAACACGAAA
* *
25587581 A--TTTGAGAAATACGAGA
1 ATTTTTGA-AAACACGAAA
* * *
25587598 GTTGTTGAAAACAAGAAA
1 ATTTTTGAAAACACGAAA
* **
25587616 ACTCAT--AAACACGAAA
1 ATTTTTGAAAACACGAAA
* *
25587632 ATTTTTG-AAACATGGAA
1 ATTTTTGAAAACACGAAA
* *
25587649 GTTTTTAGAAAACAGGAAAA
1 ATTTTT-GAAAACACG-AAA
* *
25587669 ATTTCTTTG--ATCATCG-GA
1 A-TT-TTTGAAAACA-CGAAA
* *
25587687 ATTTTTGAAAATACAAAA
1 ATTTTTGAAAACACGAAA
25587705 ATTTTTG-AAACACG-AA
1 ATTTTTGAAAACACGAAA
* * **
25587721 AGTTTTAAAAACACGAGG
1 ATTTTTGAAAACACGAAA
*
25587739 ATTTTTG-AAACACGGGAA
1 ATTTTTGAAAACAC-GAAA
* *
25587757 TTTTTTGAAAACATGAAA
1 ATTTTTGAAAACACGAAA
* ***
25587775 AATTTTGAAAATTTG-AA
1 ATTTTTGAAAACACGAAA
*
25587792 TTTTTTGAAAACACGGGAAA
1 ATTTTTGAAAACAC--GAAA
* *
25587812 TTTTTTTGAAAACATGAAA
1 -ATTTTTGAAAACACGAAA
* **
25587831 ATATTTG-AAACACGGGA
1 ATTTTTGAAAACACGAAA
25587848 ATTTTTGAAAACACG-AA
1 ATTTTTGAAAACACGAAA
25587865 ATTTTT
1 ATTTTT
25587871 TTGATTTTTT
Statistics
Matches: 317, Mismatches: 84, Indels: 63
0.68 0.18 0.14
Matches are distributed among these distances:
15 4 0.01
16 45 0.14
17 97 0.31
18 111 0.35
19 23 0.07
20 5 0.02
21 20 0.06
22 12 0.04
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAA
Found at i:25587494 original size:53 final size:50
Alignment explanation
Indices: 25587431--25587549 Score: 157
Period size: 53 Copynumber: 2.3 Consensus size: 50
25587421 ATTTTTGAGC
* *
25587431 ACACGAAAATTTTTTAAAACACGAGAATTTTAGAGACACGAAAATTCTTAAAA
1 ACACGAAAATTTTTTAAAACACGACAATTTT-GAAACACGAAAATT-TT-AAA
* *
25587484 ACACGAAAATTTTTGAAAACACGACAATTTTGAAACACGAGAATTTTAAA
1 ACACGAAAATTTTTTAAAACACGACAATTTTGAAACACGAAAATTTTAAA
*
25587534 ACACGAGAATTGTTTT
1 ACACGAAAATT-TTTT
25587550 TTGAAAACAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 13 0.22
51 5 0.08
52 12 0.20
53 29 0.49
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (50 bp):
ACACGAAAATTTTTTAAAACACGACAATTTTGAAACACGAAAATTTTAAA
Found at i:25587521 original size:16 final size:16
Alignment explanation
Indices: 25587442--25587544 Score: 116
Period size: 16 Copynumber: 6.1 Consensus size: 16
25587432 CACGAAAATT
25587442 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
* *
25587458 TTTTAGAGACACGAAAA
1 TTTTA-AAACACGAGAA
*
25587475 TTCTTAAAAACACGAAAA
1 TT-TT-AAAACACGAGAA
*
25587493 TTTTTGAAAACACGACAA
1 -TTTT-AAAACACGAGAA
*
25587511 TTTTGAAACACGAGAA
1 TTTTAAAACACGAGAA
25587527 TTTTAAAACACGAGAA
1 TTTTAAAACACGAGAA
25587543 TT
1 TT
25587545 GTTTTTTGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
16 32 0.43
17 15 0.20
18 25 0.33
19 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (16 bp):
TTTTAAAACACGAGAA
Found at i:25587726 original size:17 final size:17
Alignment explanation
Indices: 25587421--25587870 Score: 160
Period size: 17 Copynumber: 25.4 Consensus size: 17
25587411 AACAATTTTT
*
25587421 ATTTTTGAGCACACGAAA
1 ATTTTTGA-AACACGAAA
* *
25587439 ATTTTTTAAAACACGAGA
1 A-TTTTTGAAACACGAAA
* *
25587457 ATTTTAGAGACACGAAA
1 ATTTTTGAAACACGAAA
**
25587474 ATTCTTAAAAACACGAAA
1 ATT-TTTGAAACACGAAA
*
25587492 ATTTTTGAAAACACGACA
1 ATTTTTG-AAACACGAAA
*
25587510 A-TTTTGAAACACGAGA
1 ATTTTTGAAACACGAAA
*
25587526 A-TTTTAAAACACGAGAA
1 ATTTTTGAAACACGA-AA
* **
25587543 TTGTTTTTTGAAAACACGATT
1 ---ATTTTTG-AAACACGAAA
* *
25587564 TTTTTTGAAACTCGAAA
1 ATTTTTGAAACACGAAA
** * *
25587581 ATTTGAGAAATACGAGA
1 ATTTTTGAAACACGAAA
* * *
25587598 GTTGTTGAAAACAAGAAA
1 ATTTTTG-AAACACGAAA
* **
25587616 ACTCAT-AAACACGAAA
1 ATTTTTGAAACACGAAA
* *
25587632 ATTTTTGAAACATGGAA
1 ATTTTTGAAACACGAAA
* *
25587649 GTTTTTAGAAAACAGGAAAA
1 ATTTTT-G-AAACACG-AAA
* *
25587669 ATTTCTTTG-ATCATCG-GA
1 A-TT-TTTGAAACA-CGAAA
* *
25587687 ATTTTTGAAAATACAAAA
1 ATTTTTG-AAACACGAAA
25587705 ATTTTTGAAACACGAAA
1 ATTTTTGAAACACGAAA
* ** **
25587722 GTTTTAAAAACACGAGG
1 ATTTTTGAAACACGAAA
*
25587739 ATTTTTGAAACACGGGAA
1 ATTTTTGAAACAC-GAAA
* *
25587757 TTTTTTGAAAACATGAAA
1 ATTTTTG-AAACACGAAA
* *
25587775 AATTTTGAAA-ATTTG-AA
1 ATTTTTGAAACA--CGAAA
*
25587792 TTTTTTGAAAACACGGGAAA
1 ATTTTTG-AAACAC--GAAA
* *
25587812 TTTTTTTGAAAACATGAAA
1 -ATTTTTG-AAACACGAAA
* **
25587831 ATATTTGAAACACGGGA
1 ATTTTTGAAACACGAAA
25587848 ATTTTTGAAAACACG-AA
1 ATTTTTG-AAACACGAAA
25587865 ATTTTT
1 ATTTTT
25587871 TTGATTTTTT
Statistics
Matches: 316, Mismatches: 85, Indels: 63
0.68 0.18 0.14
Matches are distributed among these distances:
16 39 0.12
17 120 0.38
18 95 0.30
19 26 0.08
20 5 0.02
21 20 0.06
22 11 0.03
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (17 bp):
ATTTTTGAAACACGAAA
Found at i:25587828 original size:56 final size:56
Alignment explanation
Indices: 25587729--25587874 Score: 182
Period size: 56 Copynumber: 2.7 Consensus size: 56
25587719 AAAGTTTTAA
25587729 AAACACGAGG-ATTTTTG-AAACACGGG-AA-TTTTTTGAAAACATGAAAA-ATTTTG
1 AAACACG-GGAATTTTTGAAAACACGGGAAATTTTTTTGAAAACATGAAAATA-TTTG
***
25587782 AAA-ATTTGAATTTTTTGAAAACACGGGAAATTTTTTTGAAAACATGAAAATATTTG
1 AAACACGGGAA-TTTTTGAAAACACGGGAAATTTTTTTGAAAACATGAAAATATTTG
25587838 AAACACGGGAATTTTTGAAAACAC--GAAATTTTTTTGA
1 AAACACGGGAATTTTTGAAAACACGGGAAATTTTTTTGA
25587875 TTTTTTATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
51 1 0.01
52 2 0.03
53 9 0.11
54 22 0.28
55 2 0.03
56 39 0.49
57 5 0.06
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (56 bp):
AAACACGGGAATTTTTGAAAACACGGGAAATTTTTTTGAAAACATGAAAATATTTG
Found at i:25587842 original size:38 final size:36
Alignment explanation
Indices: 25587704--25587865 Score: 102
Period size: 35 Copynumber: 4.5 Consensus size: 36
25587694 AAAATACAAA
* *
25587704 AATTTTTG-AAACACGAAAGT-TTTAAAAACACGAGG
1 AATTTTTGAAAACACGAAAATATTTGAAAACACG-GG
* * * * **
25587739 -ATTTTTG-AAACACGGGAATTTTTTGAAAACATGAA
1 AATTTTTGAAAACAC-GAAAATATTTGAAAACACGGG
* *** * *
25587774 AAATTTTGAAAATTTG-AATTTTTTGAAAACACGGG
1 AATTTTTGAAAACACGAAAATATTTGAAAACACGGG
*
25587809 AAATTTTTTTGAAAACATGAAAATATTTG-AAACACGGG
1 -AA--TTTTTGAAAACACGAAAATATTTGAAAACACGGG
25587847 AATTTTTGAAAACACGAAA
1 AATTTTTGAAAACACGAAA
25587866 TTTTTTTGAT
Statistics
Matches: 100, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
34 13 0.13
35 36 0.36
36 19 0.19
37 5 0.05
38 20 0.20
39 7 0.07
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (36 bp):
AATTTTTGAAAACACGAAAATATTTGAAAACACGGG
Found at i:25588427 original size:16 final size:16
Alignment explanation
Indices: 25588406--25588472 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
25588396 GACTCGAGCC
25588406 TTCCTTTTTTCTTTTT
1 TTCCTTTTTTCTTTTT
25588422 TTCCTTTTTT-TTCTTT
1 TTCCTTTTTTCTT-TTT
**
25588438 TT-CTCTTTCCCTTTTT
1 TTCCT-TTTTTCTTTTT
* *
25588454 TTTCTCTTTTCTTTTT
1 TTCCTTTTTTCTTTTT
25588470 TTC
1 TTC
25588473 ATTCTTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
15 4 0.10
16 33 0.80
17 4 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTCCTTTTTTCTTTTT
Found at i:25588432 original size:17 final size:17
Alignment explanation
Indices: 25588406--25588482 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 17
25588396 GACTCGAGCC
25588406 TTCC-TTTTTTCTTTTT
1 TTCCTTTTTTTCTTTTT
*
25588422 TTCCTTTTTTT-TCTTT
1 TTCCTTTTTTTCTTTTT
* **
25588438 TT-CTCTTTCCCTTTTT
1 TTCCTTTTTTTCTTTTT
* *
25588454 TTTC-TCTTTTCTTTTT
1 TTCCTTTTTTTCTTTTT
*
25588470 TTCATTCTTTTTC
1 TTCCTT-TTTTTC
25588483 CTTCGGCCTG
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
15 5 0.11
16 26 0.59
17 8 0.18
18 5 0.11
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCCTTTTTTTCTTTTT
Found at i:25588480 original size:24 final size:24
Alignment explanation
Indices: 25588411--25588480 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
25588401 GAGCCTTCCT
* *
25588411 TTTTTCTTTTTTTCCTTTTTTTTC
1 TTTTTCTTTTTTTCATTTTTTCTC
* * * *
25588435 TTTTTC-TCTTTCCCTTTTTTTTC
1 TTTTTCTTTTTTTCATTTTTTCTC
25588458 TCTTTTCTTTTTTTCATTCTTTT
1 T-TTTTCTTTTTTTCATT-TTTT
25588481 TCCTTCGGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 16 0.42
24 11 0.29
25 7 0.18
26 4 0.11
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTCTTTTTTTCATTTTTTCTC
Found at i:25588630 original size:24 final size:24
Alignment explanation
Indices: 25588603--25588651 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
25588593 TGGGCTGGTC
25588603 TGCTGCGGGCTTCTTCTTTTTTTT
1 TGCTGCGGGCTTCTTCTTTTTTTT
** * *
25588627 TGCTTTGGGGTTTTTCTTTTTTTT
1 TGCTGCGGGCTTCTTCTTTTTTTT
25588651 T
1 T
25588652 TGGGTCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.20, T:0.65
Consensus pattern (24 bp):
TGCTGCGGGCTTCTTCTTTTTTTT
Found at i:25588673 original size:21 final size:20
Alignment explanation
Indices: 25588617--25588673 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
25588607 GCGGGCTTCT
*
25588617 TCTTTTTTTTTGCTTTGGGG
1 TCTTTTTTTTTGCTTTTGGG
*
25588637 T-TTTTCTTTTT-TTTTTGGG
1 TCTTTT-TTTTTGCTTTTGGG
*
25588656 TCTTTTTTATTTGGTTTT
1 TCTTTTTT-TTTGCTTTT
25588674 TTTTGGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.02, C:0.07, G:0.18, T:0.74
Consensus pattern (20 bp):
TCTTTTTTTTTGCTTTTGGG
Found at i:25589223 original size:29 final size:29
Alignment explanation
Indices: 25589174--25589258 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
25589164 GGTAAAAGTG
* *
25589174 TAATTTTGAGAAAGTTTAGGGGTTAAAATA
1 TAATTTT-AGAAAATTTAGGGGTCAAAATA
* *
25589204 TAATTTTAAAAAATTTAGGGGTCAAAATG
1 TAATTTTAGAAAATTTAGGGGTCAAAATA
*
25589233 TAA-TTTAGAAAATTTTAGGAGTCAAA
1 TAATTTTAGAAAA-TTTAGGGGTCAAA
25589259 TTGCAATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.17
29 33 0.69
30 7 0.15
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (29 bp):
TAATTTTAGAAAATTTAGGGGTCAAAATA
Found at i:25589266 original size:29 final size:28
Alignment explanation
Indices: 25589208--25589267 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
25589198 AAAATATAAT
* *
25589208 TTTAAAAAATTTAGGGGTCAAAATGTAA
1 TTTAAAAAATTTAGGAGTCAAAATGCAA
* *
25589236 TTTAGAAAATTTTAGGAGTCAAATTGCAA
1 TTTA-AAAAATTTAGGAGTCAAAATGCAA
25589265 TTT
1 TTT
25589268 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (28 bp):
TTTAAAAAATTTAGGAGTCAAAATGCAA
Found at i:25589414 original size:30 final size:32
Alignment explanation
Indices: 25589380--25589441 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
25589370 CCTCAAGCAA
25589380 TTTAGTTTT-CTTTT-ATATGTTT-TTTTTATT
1 TTTAGTTTTGCTTTTAATAT-TTTGTTTTTATT
*
25589410 TTTAGTTTTGTTTTTAATATTTTGTTTTTATT
1 TTTAGTTTTGCTTTTAATATTTTGTTTTTATT
25589442 AGTTTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 7 0.25
32 12 0.43
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.76
Consensus pattern (32 bp):
TTTAGTTTTGCTTTTAATATTTTGTTTTTATT
Found at i:25589423 original size:17 final size:19
Alignment explanation
Indices: 25589384--25589423 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
25589374 AAGCAATTTA
*
25589384 GTTTTCTTTTATATGTTTT
1 GTTTTATTTTATATGTTTT
25589403 -TTTTATTTT-TA-GTTTT
1 GTTTTATTTTATATGTTTT
25589419 GTTTT
1 GTTTT
25589424 TAATATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.78
Consensus pattern (19 bp):
GTTTTATTTTATATGTTTT
Found at i:25591561 original size:20 final size:20
Alignment explanation
Indices: 25591528--25591577 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
25591518 GCAACTACAA
* *
25591528 TAATAATGAGAATACCAAAT
1 TAATAATAATAATACCAAAT
* *
25591548 TAATAATAATAATATCAATT
1 TAATAATAATAATACCAAAT
*
25591568 TTATAATAAT
1 TAATAATAAT
25591578 GGTACTAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAATAATAATACCAAAT
Found at i:25592358 original size:28 final size:27
Alignment explanation
Indices: 25592304--25592356 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
25592294 TGTATCCGTT
25592304 ACATAGTTTTTTTGTTTTGGCTTTTTA
1 ACATAGTTTTTTTGTTTTGGCTTTTTA
25592331 ACATAGTTTTTTTGTTTTGGCTTTTT
1 ACATAGTTTTTTTGTTTTGGCTTTTT
25592357 TATAGCCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (27 bp):
ACATAGTTTTTTTGTTTTGGCTTTTTA
Found at i:25592815 original size:16 final size:16
Alignment explanation
Indices: 25592794--25592829 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25592784 GGAAATTAAT
25592794 TATTAAAAATAAAAAA
1 TATTAAAAATAAAAAA
* *
25592810 TATTAAAAATTATAAA
1 TATTAAAAATAAAAAA
25592826 TATT
1 TATT
25592830 GGTTCGGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTAAAAATAAAAAA
Found at i:25597416 original size:79 final size:80
Alignment explanation
Indices: 25597324--25597490 Score: 239
Period size: 79 Copynumber: 2.1 Consensus size: 80
25597314 GCAAAATTAA
* * ** *
25597324 ATAAATTCGCAATCAACACT-AAATTTATTTTTTAAAATCATGAAAAATTCAAACCTAATAGTAT
1 ATAAATTCACAATCAACA-TGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTAT
25597388 TAGCAA-TTAACTTTC
65 TAGCAATTTAACTTTC
*
25597403 ATAAATTCACAATCAACATGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAGTAGTATT
1 ATAAATTCACAATCAACATGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTATT
*
25597468 AGTAATTTAACTTTC
66 AGCAATTTAACTTTC
25597483 ATCAAATT
1 AT-AAATT
25597491 AATCTTAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 61 0.78
80 11 0.14
81 5 0.06
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (80 bp):
ATAAATTCACAATCAACATGAAATTTATTCTACAAAATCATGAAAAATTCAAACATAATAGTATT
AGCAATTTAACTTTC
Found at i:25599084 original size:31 final size:32
Alignment explanation
Indices: 25599046--25599108 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
25599036 AGGCAAATTA
25599046 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
25599077 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
25599109 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:25602704 original size:15 final size:16
Alignment explanation
Indices: 25602679--25602712 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
25602669 TGCAAAAGAT
25602679 CAACAAAACAACTAGG
1 CAACAAAACAACTAGG
25602695 CAAC-AAACAACTAGG
1 CAACAAAACAACTAGG
25602710 CAA
1 CAA
25602713 ATATGTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.56, C:0.26, G:0.12, T:0.06
Consensus pattern (16 bp):
CAACAAAACAACTAGG
Found at i:25605558 original size:28 final size:27
Alignment explanation
Indices: 25605507--25605565 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
25605497 AAGAAAAACA
25605507 AAAATTAGAAATAAAATGAGAATAAAT
1 AAAATTAGAAATAAAATGAGAATAAAT
25605534 AAAATTAGTTAAATAATAAT-A-AATAAAT
1 AAAATTAG--AAATAA-AATGAGAATAAAT
25605562 AAAA
1 AAAA
25605566 GAAAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 8 0.28
28 11 0.38
29 7 0.24
30 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATTAGAAATAAAATGAGAATAAAT
Found at i:25606441 original size:43 final size:43
Alignment explanation
Indices: 25606246--25606475 Score: 208
Period size: 43 Copynumber: 5.3 Consensus size: 43
25606236 CAGCAGCGAC
* * * * * * *
25606246 TTCCCCATAAACACCGCTATAGAATATGACCTTTAACAGCGCT
1 TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
* * * * * * *
25606289 TTCCCGACAATCACCGATAAAGAATATGACCTTTAACGGCGCT
1 TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
* * * *
25606332 TTCCCCACAAACGTCGTTAAAGAACATGGCCTTTAGCGACACT
1 TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
* * *
25606375 ATCCCCACAAACGCCGCTGAAGAACATGACCTTTAGTGGCACT
1 TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
* * * * **
25606418 TTCCCCACAAATGCCACTAAAGAACATGGCTTTTAGCGGTGCT
1 TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
*
25606461 TTTCCCACAAACGCC
1 TTCCCCACAAACGCC
25606476 ATTAACTTTA
Statistics
Matches: 153, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 153 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
TTCCCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACT
Found at i:25607193 original size:24 final size:24
Alignment explanation
Indices: 25607166--25607211 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
25607156 GAGTTAGAAA
25607166 CGAAATATATAATCAAAACAAGAG
1 CGAAATATATAATCAAAACAAGAG
*
25607190 CGAAATTTATAATCAAAACAAG
1 CGAAATATATAATCAAAACAAG
25607212 TGCAACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (24 bp):
CGAAATATATAATCAAAACAAGAG
Found at i:25608587 original size:17 final size:18
Alignment explanation
Indices: 25608565--25608601 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
25608555 ATGAAGTGTA
25608565 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
25608582 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
25608600 AA
1 AA
25608602 AATAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:25608761 original size:3 final size:3
Alignment explanation
Indices: 25608693--25608741 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
25608683 CAAGACATAG
* * * *
25608693 ATA ATA ACA ACA ACA ATA ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25608741 A
1 A
25608742 CTTATTAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:25611725 original size:29 final size:29
Alignment explanation
Indices: 25611693--25611750 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
25611683 GATTTGTTAA
*
25611693 AACGTAGAATTTTAT-TTGTAAAATTTATT
1 AACGAAGAATTTTATATT-TAAAATTTATT
*
25611722 AACGAATAATTTTATATTTAAAATTTATT
1 AACGAAGAATTTTATATTTAAAATTTATT
25611751 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
AACGAAGAATTTTATATTTAAAATTTATT
Found at i:25613649 original size:3 final size:3
Alignment explanation
Indices: 25613641--25613666 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25613631 CCAGAAGCTG
25613641 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
25613667 ACGTTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:25621301 original size:18 final size:18
Alignment explanation
Indices: 25621286--25621322 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25621276 TGTAAAATCA
25621286 AATAATTATTTCAAATAT
1 AATAATTATTTCAAATAT
* *
25621304 CATTATTATTTCAAATAT
1 AATAATTATTTCAAATAT
25621322 A
1 A
25621323 GTTGATTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAATTATTTCAAATAT
Found at i:25622093 original size:6 final size:6
Alignment explanation
Indices: 25622061--25622108 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
25622051 ACGCCTTCTT
* * *
25622061 TTCCCC TTTCCCC TTTCCCC TTTCCC TTCCCC TTCCCT TTTCCC TTCC
1 TTCCCC -TTCCCC -TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCC
25622109 ATTTGGGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
6 22 0.63
7 13 0.37
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (6 bp):
TTCCCC
Found at i:25622106 original size:7 final size:7
Alignment explanation
Indices: 25622060--25622104 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
25622050 GACGCCTTCT
25622060 TTTCCCC
1 TTTCCCC
25622067 TTTCCCC
1 TTTCCCC
25622074 TTTCCCC
1 TTTCCCC
25622081 TTT-CCC
1 TTTCCCC
25622087 -TTCCCC
1 TTTCCCC
*
25622093 -TTCCCT
1 TTTCCCC
25622099 TTTCCC
1 TTTCCC
25622105 TTCCATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 2 0.06
6 11 0.31
7 22 0.63
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTCCCC
Found at i:25622477 original size:11 final size:11
Alignment explanation
Indices: 25622461--25622486 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25622451 TTGCTGGATG
25622461 ATATTTTGGTT
1 ATATTTTGGTT
25622472 ATATTTTGGTT
1 ATATTTTGGTT
25622483 ATAT
1 ATAT
25622487 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:25624910 original size:22 final size:20
Alignment explanation
Indices: 25624867--25624905 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25624857 TAATTTAAAA
25624867 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
25624887 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
25624906 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:25625029 original size:20 final size:20
Alignment explanation
Indices: 25625004--25625043 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25624994 AATATTTTCC
*
25625004 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25625024 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
25625044 CCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25625050 original size:14 final size:14
Alignment explanation
Indices: 25625027--25625066 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25625017 ACAGAAAAGT
*
25625027 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
25625041 AAACCATTTTACGG
1 AAAACATTTTACAG
25625055 AAAACATTTTAC
1 AAAACATTTTAC
25625067 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:25625058 original size:34 final size:35
Alignment explanation
Indices: 25624992--25625058 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25624982 CAAACACCAA
* *
25624992 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAACCATTTTACAGAAAAGT
*
25625027 AAAACATTTTCCAG-AAACCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAACCATTTTACAGAAAA
25625059 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAACCATTTTACAGAAAAGT
Found at i:25625356 original size:21 final size:20
Alignment explanation
Indices: 25625307--25625356 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
25625297 GGCCCGGCCC
* *
25625307 ATATTAAATATATATATTTG
1 ATATAAAATATATATATTTA
25625327 AT-TAGAAATAATATATATTTA
1 ATATA-AAAT-ATATATATTTA
25625348 ATATAAAAT
1 ATATAAAAT
25625357 TCGAGCCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 6 0.24
21 16 0.64
22 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATAAAATATATATATTTA
Found at i:25627213 original size:115 final size:117
Alignment explanation
Indices: 25627005--25627236 Score: 308
Period size: 115 Copynumber: 2.0 Consensus size: 117
25626995 TTGACATCAT
**
25627005 CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTTGATATTAAAATCAAAGGCTTTC
1 CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTCAATATTAAAATCAAAGGCTTTC
* *
25627070 ATGAGTAAAAATTACAGGTCATAAGCTTATTTAACTA-AAAAA-A-CATAAG
66 ATGAGTAAAAATTACAAGTCACAAGCTTATTTAACTATAAAAATAGCATAAG
* * * *
25627119 CATAAAATGTAAATTAGTTTGAAGTTTTAAAATATTTTTACTTCAATATTAAAATCAAATGCTTT
1 CATAAAATGCAAATTAGTTTAAAATTTT-AAATATTTTTACTTCAATATTAAAATCAAAGGCTTT
* * ** **
25627184 CATGATTAAAAATTATAAGTTGCGGGCTTATTTAACTATAAAAATAGCATAAG
65 CATGAGTAAAAATTACAAGTCACAAGCTTATTTAACTATAAAAATAGCATAAG
25627237 GACTAGTTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
114 25 0.25
115 63 0.63
116 5 0.05
117 1 0.01
118 6 0.06
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (117 bp):
CATAAAATGCAAATTAGTTTAAAATTTTAAATATTTTTACTTCAATATTAAAATCAAAGGCTTTC
ATGAGTAAAAATTACAAGTCACAAGCTTATTTAACTATAAAAATAGCATAAG
Found at i:25628547 original size:31 final size:31
Alignment explanation
Indices: 25628511--25628573 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
25628501 TGTCATTCAC
* *
25628511 CATCTATGACGAGTGTTTGTTATTATTTTCT
1 CATCTATGACGAGTCTTTATTATTATTTTCT
25628542 CATCTATGACGAGTCTTTATTATTATTTTCT
1 CATCTATGACGAGTCTTTATTATTATTTTCT
25628573 C
1 C
25628574 CCTAAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.51
Consensus pattern (31 bp):
CATCTATGACGAGTCTTTATTATTATTTTCT
Found at i:25628984 original size:25 final size:25
Alignment explanation
Indices: 25628956--25629016 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
25628946 AATTAAAATT
*
25628956 AAAATTACA-TAGTAAAATTTAATAA
1 AAAATTA-AGTAGCAAAATTTAATAA
* * *
25628981 AAAATCAAGTGGCAAAATTTAATAT
1 AAAATTAAGTAGCAAAATTTAATAA
25629006 AAAATTGAAGT
1 AAAATT-AAGT
25629017 GGAATGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 24 0.83
26 4 0.14
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.30
Consensus pattern (25 bp):
AAAATTAAGTAGCAAAATTTAATAA
Found at i:25635900 original size:18 final size:18
Alignment explanation
Indices: 25635879--25635917 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25635869 GATTGAGAGT
* *
25635879 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
25635897 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
25635915 GAA
1 GAA
25635918 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:25647291 original size:19 final size:19
Alignment explanation
Indices: 25647267--25647327 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
25647257 GGAAATTTTT
25647267 ATTTAAACATAAATTTATA
1 ATTTAAACATAAATTTATA
* *
25647286 ATTTAAACAAAAAATTT-TT
1 ATTTAAAC-ATAAATTTATA
25647305 ATTTAAACATAAATTTATA
1 ATTTAAACATAAATTTATA
25647324 ATTT
1 ATTT
25647328 TCTGTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.19
19 22 0.61
20 7 0.19
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAACATAAATTTATA
Found at i:25651834 original size:57 final size:59
Alignment explanation
Indices: 25651722--25651862 Score: 198
Period size: 57 Copynumber: 2.4 Consensus size: 59
25651712 AATTGACGGT
25651722 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
25651785 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
25651841 AAAATAGATTTAGTCCGGACGG
1 AAAA-AGATCTAGCCCGGACGG
25651863 ATAATCCGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
56 5 0.07
57 42 0.56
59 1 0.01
61 1 0.01
62 21 0.28
63 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:25653305 original size:21 final size:21
Alignment explanation
Indices: 25653265--25653313 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
25653255 ATAAATAAAA
*
25653265 TCATTCA-TGTCAATTCCCTG
1 TCATTCATTGACAATTCCCTG
*
25653285 TCATTCATTGACAATTTCCTG
1 TCATTCATTGACAATTCCCTG
25653306 TCATTCAT
1 TCATTCAT
25653314 AACTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (21 bp):
TCATTCATTGACAATTCCCTG
Found at i:25653512 original size:21 final size:21
Alignment explanation
Indices: 25653486--25653595 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
25653476 TGAATACACC
25653486 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* *
25653507 AACAGAAGCTTG-AA-AGCTA
1 AACAGAAGCTCGTAAGAGCTG
* *
25653526 AATAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTG
* * *
25653547 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
* **
25653568 AACAGAAGCTCATAAGAATTG
1 AACAGAAGCTCGTAAGAGCTG
25653589 AACAGAA
1 AACAGAA
25653596 AGTAAAATAC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.18
20 4 0.05
21 58 0.76
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:25662643 original size:12 final size:11
Alignment explanation
Indices: 25662611--25662644 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
25662601 TTAAAAAATA
25662611 AAAATATTTTT
1 AAAATATTTTT
*
25662622 AAAATGTTTTT
1 AAAATATTTTT
25662633 AAAATACTTTTT
1 AAAATA-TTTTT
25662645 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:25671093 original size:9 final size:8
Alignment explanation
Indices: 25671064--25671094 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
25671054 CAACATTTAA
25671064 TTAAAATT
1 TTAAAATT
25671072 TTAAAATT
1 TTAAAATT
25671080 TTAAAATAT
1 TTAAAAT-T
25671089 TTAAAA
1 TTAAAA
25671095 ACGCTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTAAAATT
Found at i:25671129 original size:19 final size:19
Alignment explanation
Indices: 25671105--25671151 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
25671095 ACGCTTTTAT
25671105 ATTTTTAATA-ATTTTAATA
1 ATTTTTAATATATTTTAA-A
*
25671124 ATTTTTAATATTATTTTTAA
1 ATTTTTAATA-TATTTTAAA
25671144 ATTTTTAA
1 ATTTTTAA
25671152 ATTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 9 0.36
21 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTAATATATTTTAAA
Found at i:25671139 original size:12 final size:10
Alignment explanation
Indices: 25671105--25671151 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
25671095 ACGCTTTTAT
25671105 ATTTTTAATA
1 ATTTTTAATA
25671115 A-TTTTAATA
1 ATTTTTAATA
25671124 ATTTTTAATA
1 ATTTTTAATA
25671134 TTATTTTT-A-A
1 --ATTTTTAATA
25671144 ATTTTTAA
1 ATTTTTAA
25671152 ATTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.18
9 10 0.30
10 10 0.30
11 1 0.03
12 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:25671936 original size:28 final size:29
Alignment explanation
Indices: 25671905--25671962 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
25671895 TAAAAAGTTC
* *
25671905 AAAAATTATTA-ATTTTAACAAAAGTAAA
1 AAAAATTATTACATTTAAAAAAAAGTAAA
* *
25671933 AAAAGTTATTACATTTAAAAAAAATTAAA
1 AAAAATTATTACATTTAAAAAAAAGTAAA
25671962 A
1 A
25671963 TTATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAAATTATTACATTTAAAAAAAAGTAAA
Found at i:25672882 original size:21 final size:22
Alignment explanation
Indices: 25672843--25672891 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
25672833 TCCTATTTAG
* * *
25672843 TATATTTTAAATTCTAATATAC
1 TATATTTAAAATTCAAATAAAC
*
25672865 TATATTTAAAATT-AAATAAAT
1 TATATTTAAAATTCAAATAAAC
25672886 TATATT
1 TATATT
25672892 AGTATCATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATTTAAAATTCAAATAAAC
Found at i:25675234 original size:44 final size:44
Alignment explanation
Indices: 25675186--25675376 Score: 206
Period size: 44 Copynumber: 4.3 Consensus size: 44
25675176 GTATTGGCGT
* * * * *
25675186 GAAGTAGATCGAATATAGCAGGTCATGTCTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATACTGGTAGC
* * *
25675230 GAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
** *** *
25675274 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGTAG-
1 GAAGTAGATCGAAG-ATGCAGATCTTGTCTTCCCATACTGGTAGC
* *
25675318 GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
25675362 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
25675377 AAACAGATCT
Statistics
Matches: 118, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
43 43 0.36
44 54 0.46
45 21 0.18
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (44 bp):
GAAGTAGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTAGC
Found at i:25675335 original size:88 final size:88
Alignment explanation
Indices: 25675186--25675387 Score: 332
Period size: 88 Copynumber: 2.3 Consensus size: 88
25675176 GTATTGGCGT
* * * * * *
25675186 GAAGTAGATCGAATATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAAA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
25675251 TCTTGTCTTCCCATACTGGTGGC
66 TCTTGTCTTCCCATACTGGTGGC
* *
25675274 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGTAGGAAGTGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
25675339 TCTTGTCTTCCCATACTGGTGGC
66 TCTTGTCTTCCCATACTGGTGGC
25675362 GAAGTAGATCGAAGAAAACAGATCTT
1 GAAGTAGATCGAAGAAAACAGATCTT
25675388 ATCTCTCTAA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 106 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (88 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGTAGGAAGTGGATCGAAGATGCAAA
TCTTGTCTTCCCATACTGGTGGC
Found at i:25675534 original size:50 final size:50
Alignment explanation
Indices: 25675471--25675934 Score: 263
Period size: 50 Copynumber: 9.3 Consensus size: 50
25675461 GCTACGACGA
* * *
25675471 CGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * * * ** * **
25675521 CGAATCTTACTTCCCTGGCAGTACAGTGGAACTGATTAAAGCTACAACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * ** * **
25675571 TGAATCTTGCTTCCCCAACATTGCAATTTAAAAGATTGAAGCCGCAACAA
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* **** *** * ** * **
25675621 CGAATCTTACTTCCTTGGTGGTGCAGCGGGACTGATTAAAGCTACAACGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * *
25675671 TGAATCTTACTTTCCC-GATATTGCAATTTAAAAGATTGAAGCCGCAATGG
1 CGAATCTTAC-TTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * * ** * * **
25675721 CGAATCTTACTTCCATGGCGA-TGCAGTGGAGCATATTAAAGCTACAACGG
1 CGAATCTTACTTCCCTGAC-ATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * *
25675771 TGAATCTTGCTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAATGG
1 CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * ** * **
25675821 CGAATCTTACTTCCCT-AGCGA-TACAGTGGAGCAGATTAAAGCTACAACGG
1 CGAATCTTACTTCCCTGA-C-ATTGCAATTGAAAAGATTGAAGCCGCAACGG
* * * **
25675871 CGAATCTTACTT-CCTCGACATTGTAATTTAAAAGATTGAAGCCGTAACAA
1 CGAATCTTACTTCCCT-GACATTGCAATTGAAAAGATTGAAGCCGCAACGG
25675921 CGAATCTTACTTCC
1 CGAATCTTACTTCC
25675935 TTGGTGGTGC
Statistics
Matches: 284, Mismatches: 120, Indels: 19
0.67 0.28 0.04
Matches are distributed among these distances:
49 10 0.04
50 266 0.94
51 8 0.03
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (50 bp):
CGAATCTTACTTCCCTGACATTGCAATTGAAAAGATTGAAGCCGCAACGG
Found at i:25676007 original size:100 final size:100
Alignment explanation
Indices: 25675435--25675995 Score: 692
Period size: 100 Copynumber: 5.6 Consensus size: 100
25675425 CCTTATCTCT
* * * * * * *
25675435 CTGGCGGTACAGTGGAGCAGATTAAAGCTACGACGACGAATCTTGCTTCCCTGATATTGCAATTT
1 CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
25675500 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
66 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
* * * *
25675535 CTGGCAGTACAGTGGAACTGATTAAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGCAATTT
1 CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
**
25675600 AAAAGATTGAAGCCGCAACAACGAATCTTACTTCC
66 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
* * * * * * * *
25675635 TTGGTGGTGCAGCGGGACTGATTAAAGCTACAACGGTGAATCTTACTTTCCCGATATTGCAATTT
1 CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
*
25675700 AAAAGATTGAAGCCGCAATGGCGAATCTTACTTCC
66 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
* * * * *
25675735 ATGGCGATGCAGTGGAGCAT-ATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCAATT
1 CTGGCGGTGCAGTGGAAC-TGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATT
* *
25675799 AAAAAGATTGAAGCCGCAATGGCGAATCTTACTTCC
65 TAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
* * * * * * * *
25675835 CTAGCGATACAGTGGAGCAGATTAAAGCTACAACGGCGAATCTTACTTCCTCGACATTGTAATTT
1 CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
* **
25675900 AAAAGATTGAAGCCGTAACAACGAATCTTACTTCC
66 AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
* * * ** *
25675935 TTGGTGGTGCAGCGGAACTGATTAAAGCTACAACAACGAATCTTGCTTCCCCGACAATGCA
1 CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
25675996 GTTAATCAGA
Statistics
Matches: 396, Mismatches: 63, Indels: 4
0.86 0.14 0.01
Matches are distributed among these distances:
100 395 1.00
101 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (100 bp):
CTGGCGGTGCAGTGGAACTGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTT
AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
Found at i:25676063 original size:40 final size:40
Alignment explanation
Indices: 25676009--25676475 Score: 296
Period size: 40 Copynumber: 11.1 Consensus size: 40
25675999 AATCAGATTA
25676009 AAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 AAACCA-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
** *
25676051 GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-C
1 AAACCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* ** * ** *
25676090 GAAAAAAACCAA-TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTA
1 -----AAACCAAGTCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TC
25676136 AAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 AAACCA-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * * *
25676178 ACATCAAGTTTTATCTCCCTAAGCAGTAGTGGAGCAGACC
1 AAACCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* ** * * * *
25676218 GAAAAATACCAA-TCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTA
1 ----AA-ACCAAGTCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TC
25676264 AAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 AAACCA-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
** * * *
25676306 GCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACTGAAAA
1 AAACCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-T----C
* ** * * * *
25676351 AAACCAA-TCCTATCTCCCTAAAGTTGCAGTGGAACGGATTA
1 AAACCAAGTCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TC
* * *
25676392 AAACCACAGATCTTACCTCTCTAAGCAGTAGTGGAGCATATC
1 AAACCA-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
25676434 ACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-C
1 AAACCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
25676473 AAA
1 AAA
25676476 AGAAACCAAT
Statistics
Matches: 321, Mismatches: 74, Indels: 63
0.70 0.16 0.14
Matches are distributed among these distances:
39 4 0.01
40 116 0.36
41 26 0.08
42 22 0.07
43 49 0.15
44 70 0.22
45 34 0.11
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (40 bp):
AAACCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
Found at i:25676304 original size:128 final size:127
Alignment explanation
Indices: 25676004--25676523 Score: 898
Period size: 128 Copynumber: 4.1 Consensus size: 127
25675994 CAGTTAATCA
*
25676004 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCC
*
25676069 CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTG
66 CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
*
25676131 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCC
* *
25676196 CTAAGCAGTAGTGGAGCAGACCGAAAAATACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCG
66 CTAAGCAGTAGTGGAGCAGA-CGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
*
25676259 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCC
* * *
25676324 CTAAGCAGTAGTGGAGTAGACTGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAACG
66 CTAAGCAGTAGTGGAGCAGAC-GAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
* * *
25676387 GATTAAAACCACAGATCTTACCTCTCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCC
25676452 CTAAGCAGTAGTGGAGCAGAC-AAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
66 CTAAGCAGTAGTGGAGCAGACGAAAA-AAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
25676514 GATTAAAACC
1 GATTAAAACC
25676524 CAATCTCATC
Statistics
Matches: 371, Mismatches: 19, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
126 4 0.01
127 128 0.35
128 239 0.64
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (127 bp):
GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCC
CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
Found at i:25676486 original size:255 final size:255
Alignment explanation
Indices: 25676004--25676523 Score: 918
Period size: 255 Copynumber: 2.0 Consensus size: 255
25675994 CAGTTAATCA
25676004 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
* **
25676069 CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
66 CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAACGGAT
* *
25676134 TAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTTTTATCTCCCTA
131 TAAAACCACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTA
*
25676199 AGCAGTAGTGGAGCAGACCGAAAAATACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCG
196 AGCAGTAGTGGAGCAGACCGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCG
25676259 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
1 GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
*
25676324 CTAAGCAGTAGTGGAGTAGACTGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAACGGA
66 CTAAGCAGTAGTGGAGCAGAC-GAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAACGGA
* *
25676389 TTAAAACCACAGATCTTACCTCTCTAAGCAGTAGTGGAGCATATCACATCAAGTCTTATCTCCCT
130 TTAAAACCACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCT
*
25676454 AAGCAGTAGTGGAGCAGA-C-AAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCG
195 AAGCAGTAGTGGAGCAGACCGAAAA-AAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCG
25676514 GATTAAAACC
1 GATTAAAACC
25676524 CAATCTCATC
Statistics
Matches: 253, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
254 4 0.02
255 130 0.51
256 119 0.47
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (255 bp):
GATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCC
CTAAGCAGTAGTGGAGCAGACGAAAAAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAACGGAT
TAAAACCACAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTA
AGCAGTAGTGGAGCAGACCGAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCG
Found at i:25688619 original size:15 final size:16
Alignment explanation
Indices: 25688573--25688625 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
25688563 GAGATATCAA
25688573 ATCTAATTTAATATTT
1 ATCTAATTTAATATTT
25688589 ATCTAGA--TAATA-TT
1 ATCTA-ATTTAATATTT
25688603 AT-TAATTTAATATTT
1 ATCTAATTTAATATTT
*
25688618 ATGTAATT
1 ATCTAATT
25688626 AATTCTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 9 0.28
15 9 0.28
16 10 0.31
17 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
ATCTAATTTAATATTT
Found at i:25690301 original size:23 final size:23
Alignment explanation
Indices: 25690252--25690301 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
25690242 CCTTCCGCTT
* * *
25690252 GTAATATCCTGAAAATTACAACT
1 GTAATACCCCGAAAATTACAACA
*
25690275 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACAACA
25690298 GTAA
1 GTAA
25690302 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACAACA
Found at i:25694676 original size:9 final size:9
Alignment explanation
Indices: 25694662--25694686 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25694652 TTCGATGTAT
25694662 TACAATCTA
1 TACAATCTA
25694671 TACAATCTA
1 TACAATCTA
25694680 TACAATC
1 TACAATC
25694687 ACACATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (9 bp):
TACAATCTA
Done.