Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005157.1 Hibiscus syriacus cultivar Beakdansim tig00011628_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 191923
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:914 original size:25 final size:25
Alignment explanation
Indices: 886--941 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
876 GACAGGAAGA
886 TACCAAAGCCTCGATTGTCAGATTG
1 TACCAAAGCCTCGATTGTCAGATTG
911 TACCAAAGCCTCGATTGTCAGATTG
1 TACCAAAGCCTCGATTGTCAGATTG
936 TACCAA
1 TACCAA
942 GATATGGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (25 bp):
TACCAAAGCCTCGATTGTCAGATTG
Found at i:5134 original size:14 final size:14
Alignment explanation
Indices: 5117--5280 Score: 51
Period size: 14 Copynumber: 11.3 Consensus size: 14
5107 AAGAAGAAAT
5117 AAAAGAGAAAATGA
1 AAAAGAGAAAATGA
5131 AAAA-ATGAAAA--A
1 AAAAGA-GAAAATGA
*
5143 AATAATA-AAAATGA
1 AA-AAGAGAAAATGA
5157 GAAGAAGA-AAAA-GA
1 -AA-AAGAGAAAATGA
5171 AGAAA-AGAAAAATGA
1 A-AAAGAG-AAAATGA
*
5186 GAAAAAAGAAAAATGA
1 -AAAAGAG-AAAATGA
*
5202 TGGAAAAAATGAAAA-GA
1 ---AAAAGA-GAAAATGA
*
5219 AAATGGAAGAAAAATGA
1 AAA-AGA-GAA-AATGA
*
5236 AAGAGA-AAAAT-A
1 AAAAGAGAAAATGA
**
5248 AAAAGAGAAAAACA
1 AAAAGAGAAAATGA
5262 AAAAGAGAAAAATGA
1 AAAAGAG-AAAATGA
5277 AAAA
1 AAAA
5281 AATAAAGAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 41
0.69 0.06 0.24
Matches are distributed among these distances:
12 14 0.12
13 13 0.11
14 31 0.26
15 27 0.23
16 15 0.13
17 6 0.05
18 11 0.09
19 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (14 bp):
AAAAGAGAAAATGA
Found at i:5144 original size:9 final size:9
Alignment explanation
Indices: 5124--5237 Score: 58
Period size: 9 Copynumber: 12.0 Consensus size: 9
5114 AATAAAAGAG
5124 AAAATG-AA
1 AAAATGAAA
5132 AAAATGAAA
1 AAAATGAAA
5141 AAAAT-AATA
1 AAAATGAA-A
*
5150 AAAATGAGA
1 AAAATGAAA
*
5159 AGAA-GAAA
1 AAAATGAAA
5167 AAGAA-GAAAAGA
1 AA-AATG--AA-A
5179 AAAATGAGAA
1 AAAATGA-AA
5189 AAAA-GAAA
1 AAAATGAAA
* *
5197 AATGATGGAA
1 AA-AATGAAA
5207 AAAATGAAAA
1 AAAATG-AAA
5217 GAAAATGGAAGA
1 -AAAAT-GAA-A
5229 AAAATGAAA
1 AAAATGAAA
5238 GAGAAAAATA
Statistics
Matches: 83, Mismatches: 8, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
8 16 0.19
9 27 0.33
10 17 0.20
11 17 0.20
12 6 0.07
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (9 bp):
AAAATGAAA
Found at i:5252 original size:75 final size:75
Alignment explanation
Indices: 5129--5276 Score: 173
Period size: 75 Copynumber: 2.0 Consensus size: 75
5119 AAGAGAAAAT
* *
5129 GAAAAAATGAAAAAAATAATAAAAATGAGAAGAAGAAAAAGAAGAAAAGA-AAAATGAGAAAAA-
1 GAAAAAATGAAAAAAATAAGAAAAATGAGAAGAAGAAAAAGAAGAAAAGAGAAAA--ACAAAAAG
5192 AGAAAAATGATG
64 AGAAAAATGATG
*
5204 GAAAAAATGAAAAGAAAATGGAAGAAAAATGA-AAG-AGAAAAA-TA-AAAAGAGAAAAACAAAA
1 GAAAAAATG-AAA-AAAAT--AAGAAAAATGAGAAGAAGAAAAAGAAGAAAAGAGAAAAACAAAA
5265 AGAGAAAAATGA
62 AGAGAAAAATGA
5277 AAAAAATAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
74 6 0.09
75 25 0.39
76 8 0.12
77 12 0.19
78 3 0.05
79 10 0.16
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.08
Consensus pattern (75 bp):
GAAAAAATGAAAAAAATAAGAAAAATGAGAAGAAGAAAAAGAAGAAAAGAGAAAAACAAAAAGAG
AAAAATGATG
Found at i:6928 original size:165 final size:166
Alignment explanation
Indices: 6639--6964 Score: 462
Period size: 165 Copynumber: 2.0 Consensus size: 166
6629 GAAGCAAATA
* *
6639 CGTTTGATGAAGATTGTTCGAGTTCTATACTCACTGAATGAATAGGGAGCGGACCCGTTTGTATG
1 CGTTTGATGAAGATTGTTCGAGTTCTATACTCACTGAAGGAATAGAGAGCGGACCCGTTTGTATG
* * ** * * *
6704 AAGATTGTTTGAGTTCTATACTCTCTGATGGAATAGGGAGCAGACCCGTTTTATGAAGATTGTTC
66 AAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAAACACATTTTATGAAGATTGTTC
6769 GAGT-TCTATAC-TCTCTGAAAGAATAGAGAGCGGACC
131 GAGTCT-TATACTTC-CTGAAAGAATAGAGAGCGGACC
* * *
6805 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTGT-TG
1 CGTTTGATGAAGATTGTTCGAGTTCTATACTCACTGAAGGAATAGAGAGCGGACCCGTTTGTATG
*
6869 AAGATTGTTCGAG-TCTGATACTCCCTGAACGAATAGGGAGCAAACATATTTTATGAAGATTGTT
66 AAGATTGTTCGAGTTCT-ATACTCCCTGAACGAATAGGGAGCAAACACATTTTATGAAGATTGTT
* *
6933 CGAGTCTTATACTTCCTGAACGAATAGGGAGC
130 CGAGTCTTATACTTCCTGAAAGAATAGAGAGC
6965 AGGCTCGTCA
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
164 3 0.02
165 79 0.56
166 60 0.42
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (166 bp):
CGTTTGATGAAGATTGTTCGAGTTCTATACTCACTGAAGGAATAGAGAGCGGACCCGTTTGTATG
AAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAAACACATTTTATGAAGATTGTTC
GAGTCTTATACTTCCTGAAAGAATAGAGAGCGGACC
Found at i:6984 original size:55 final size:55
Alignment explanation
Indices: 6639--6964 Score: 417
Period size: 55 Copynumber: 5.9 Consensus size: 55
6629 GAAGCAAATA
* * *
6639 CGTTTGATGAAGATTGTTCGAGTTCTATACTCACTGAATGAATAGGGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACC
* ** *
6694 CGTTTGTATGAAGATTGTTTGAGTTCTATACTCTCTGATGGAATAGGGAGCAGACC
1 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACC
* *
6750 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACC
* *
6805 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACC
* * ** *
6860 TGTTTGT-TGAAGATTGTTCGAG-TCTGATACTCCCTGAACGAATAGGGAGCAAACA
1 CGTTT-TATGAAGATTGTTCGAGTTCT-ATACTCTCTGAACGAATAGGGAGCGGACC
**
6915 TATTTTATGAAGATTGTTCGAG-TCTTATACT-TCCTGAACGAATAGGGAGC
1 CGTTTTATGAAGATTGTTCGAGTTC-TATACTCT-CTGAACGAATAGGGAGC
6965 AGGCTCGTCA
Statistics
Matches: 244, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
54 4 0.02
55 189 0.77
56 51 0.21
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (55 bp):
CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACC
Found at i:11764 original size:2 final size:2
Alignment explanation
Indices: 11757--11796 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
11747 GGAGCCAAAA
*
11757 AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11797 ATTCAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12003 original size:2 final size:2
Alignment explanation
Indices: 11996--12041 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11986 GATTTGACCC
11996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12038 AT AT
1 AT AT
12042 GTATTTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19300 original size:2 final size:2
Alignment explanation
Indices: 19293--19346 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
19283 TTTACACTTA
19293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19335 AT AT AT AT AT AT
1 AT AT AT AT AT AT
19347 CCAAGGCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21181 original size:67 final size:66
Alignment explanation
Indices: 20853--21414 Score: 682
Period size: 67 Copynumber: 8.5 Consensus size: 66
20843 AGGGATAATG
* * *
20853 GTTTCAAGAGAAACCGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAACA-ACCTCAATG-TT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGA-CTCAAAGATT
20915 TAT
65 T-T
* * *
20918 GTTTTAAG-GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACATACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAGATTT
20981 GT
66 -T
* *
20983 GTTTCAAGAGAAACTATCTCAAG-GAAGACAAAAC-TTATTTC-AAGAGAAACAGACTCAAAGAT
1 GTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAACTTTGTTTCAAAG-GAAACAGACTCAAAGAT
21045 TTT
64 TTT
*
21048 -TTTCAAGAAAAACTGTCTCAAGAGAGAC-AAACTTTGTTTC-AAGAGAAACAGACTCAAAGACT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAG-GAAACAGACTCAAAGA-T
21110 TTT
64 TTT
* * * * *
21113 GTTTCAAGAGAAACTGTCTCGAGAGAGACAAAACTTTGTTTTAAAGGAAACGGATTCAAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAGA-TT
21178 TT
65 TT
* *
21180 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTC-AAGAGAAACAAACTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAG-GAAACAGACTCAAAGA-T
21244 TTT
64 TTT
* * * * *
21247 ATTTCAAGAGAAACTATCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAATATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAGATTT
21312 T
66 T
* * * *
21313 CTTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATT
1 -GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAGATT
21378 TT
65 TT
* * *
21380 -TTTTAAAAGGAACTGTCTCAAGAGAGACAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
21415 ATTTTTAGAA
Statistics
Matches: 438, Mismatches: 43, Indels: 32
0.85 0.08 0.06
Matches are distributed among these distances:
63 4 0.01
64 96 0.22
65 59 0.13
66 78 0.18
67 196 0.45
68 5 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (66 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAGATTT
T
Found at i:21238 original size:37 final size:36
Alignment explanation
Indices: 21171--21306 Score: 104
Period size: 37 Copynumber: 3.9 Consensus size: 36
21161 AACGGATTCA
****
21171 AAAACTTTTGTTTCAAGAGAAATTGTCTCAAGAGAGAC
1 AAAAC-TTTGTTTCAAGAGAAACAAACTCAA-AGAGAC
21209 AAAACTTTGTTTCAAGAGAAACAAACTC-AA-AG--
1 AAAACTTTGTTTCAAGAGAAACAAACTCAAAGAGAC
** * * *
21241 --ATTTTTATTTCAAGAGAAACTATCTCAAAAGAGAC
1 AAAACTTTGTTTCAAGAGAAACAAACTC-AAAGAGAC
* *
21276 AAAACTTTGTTTCAAGGGAAACAGACTCAAA
1 AAAACTTTGTTTCAAGAGAAACAAACTCAAA
21307 TATTTTCTTT
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
30 21 0.28
32 2 0.03
33 2 0.03
34 2 0.03
35 1 0.01
36 4 0.05
37 38 0.51
38 5 0.07
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (36 bp):
AAAACTTTGTTTCAAGAGAAACAAACTCAAAGAGAC
Found at i:26759 original size:2 final size:2
Alignment explanation
Indices: 26747--26784 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
26737 TTTACACTTA
*
26747 AT AT GT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26785 CCAAGGCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27786 original size:3 final size:3
Alignment explanation
Indices: 27774--27838 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
27764 GATGATGATG
*
27774 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27822 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
27839 TTTAAGCCCC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31436 original size:19 final size:19
Alignment explanation
Indices: 31412--31449 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31402 CTTTCGGTGG
*
31412 AATGTGCAGCCGATTTGGA
1 AATGTGCAGCCAATTTGGA
31431 AATGTGCAGCCAATTTGGA
1 AATGTGCAGCCAATTTGGA
31450 CTTTGGAATT
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:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (19 bp):
AATGTGCAGCCAATTTGGA
Found at i:32974 original size:19 final size:19
Alignment explanation
Indices: 32911--32973 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
32901 TACCTCTCCA
*
32911 CTTGATCGTAACCATTTCG
1 CTTGATCGTCACCATTTCG
32930 CTTGATCGTCACCATTTCG
1 CTTGATCGTCACCATTTCG
*
32949 CTTGATTGTCACCATTTCG
1 CTTGATCGTCACCATTTCG
32968 CTTGAT
1 CTTGAT
32974 TTTGAAGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.17, C:0.27, G:0.16, T:0.40
Consensus pattern (19 bp):
CTTGATCGTCACCATTTCG
Found at i:42376 original size:14 final size:14
Alignment explanation
Indices: 42353--42390 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42343 TCTGTCTATA
*
42353 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
42366 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
42381 TGCAGGGATT
1 TGCAGGGATT
42391 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:43011 original size:15 final size:14
Alignment explanation
Indices: 42976--43031 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 14
42966 AAGACAATGA
*
42976 AAAATAAGGATAAT
1 AAAATAAAGATAAT
42990 -AAA-AAAGATGAAT
1 AAAATAAAGAT-AAT
*
43003 AAAATAAAGATAAG
1 AAAATAAAGATAAT
43017 AATATATAAAGATAA
1 AA-A-ATAAAGATAA
43032 AATAGAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 7 0.20
15 7 0.20
16 10 0.29
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (14 bp):
AAAATAAAGATAAT
Found at i:43027 original size:16 final size:15
Alignment explanation
Indices: 43006--43035 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42996 GATGAATAAA
43006 ATAAAGATAAGAATAT
1 ATAAAGATAA-AATAT
43022 ATAAAGATAAAATA
1 ATAAAGATAAAATA
43036 GAGATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
ATAAAGATAAAATAT
Found at i:44018 original size:47 final size:48
Alignment explanation
Indices: 43882--44027 Score: 181
Period size: 47 Copynumber: 3.1 Consensus size: 48
43872 AAACTACTAG
* * * * *
43882 TAACAATATGACACATTCAATGCCTAGTATTCAGTATAAACTATCA-T
1 TAACAGTATGACACATTCAGTGCCCAGTATGCAGTATAAACTGTCAGT
* *
43929 TAACAGTATGACACATTCAGTTCCCAATATGCAGTATAAACTGTCAGT
1 TAACAGTATGACACATTCAGTGCCCAGTATGCAGTATAAACTGTCAGT
* * *
43977 T-ACAGTATGGCACATTTAGTGCCCAGTATGCAGTATAAACTGCCAG-
1 TAACAGTATGACACATTCAGTGCCCAGTATGCAGTATAAACTGTCAGT
44023 TAACA
1 TAACA
44028 TATCGTACAT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 1 0.01
47 82 0.96
48 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (48 bp):
TAACAGTATGACACATTCAGTGCCCAGTATGCAGTATAAACTGTCAGT
Found at i:44654 original size:19 final size:19
Alignment explanation
Indices: 44630--44667 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44620 AACTAACCCA
44630 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
44649 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
44668 TGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:45220 original size:20 final size:22
Alignment explanation
Indices: 45197--45242 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
45187 GTCCAATTTC
*
45197 ACATTTTAACATAT-AATT-CA
1 ACATTCTAACATATAAATTCCA
*
45217 ACATTCTAACATCTAAATTCCA
1 ACATTCTAACATATAAATTCCA
45239 ACAT
1 ACAT
45243 AGTACTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (22 bp):
ACATTCTAACATATAAATTCCA
Found at i:47352 original size:20 final size:20
Alignment explanation
Indices: 47323--47375 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
47313 TAAGCCTTAT
*
47323 AGTATTGATATTGACCCTTG
1 AGTATCGATATTGACCCTTG
47343 AGTATCGATACTT-ACCCTTG
1 AGTATCGATA-TTGACCCTTG
47363 -GTA-CTGATATTGA
1 AGTATC-GATATTGA
47376 TTTTACCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.10
19 8 0.28
20 16 0.55
21 2 0.07
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (20 bp):
AGTATCGATATTGACCCTTG
Found at i:51637 original size:31 final size:33
Alignment explanation
Indices: 51560--51647 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
51550 TGGAAATTTT
* * *
51560 ATCTTGGTTGATGGCCAACTTATTAGAAAATTC
1 ATCTTGGTAGGTGGCCAACTTATTAGAAAAATC
*
51593 ATCTTGGTTGGTGGCCAACTTATT-GTAAAAATC
1 ATCTTGGTAGGTGGCCAACTTATTAG-AAAAATC
*
51626 -T-TTGGTAGGTGGCCAATTTATT
1 ATCTTGGTAGGTGGCCAACTTATT
51648 TTTCATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.38
32 2 0.04
33 29 0.58
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (33 bp):
ATCTTGGTAGGTGGCCAACTTATTAGAAAAATC
Found at i:56237 original size:33 final size:32
Alignment explanation
Indices: 56200--56298 Score: 130
Period size: 33 Copynumber: 3.1 Consensus size: 32
56190 GTTTGGCAAG
*
56200 TTGGAAATTTTATCTTGGTTGGTGGCCAACTTA
1 TTGGAAA-TTAATCTTGGTTGGTGGCCAACTTA
*
56233 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGG-AAATTAATCTTGGTTGGTGGCCAACTTA
*
56266 TTGGAAA--AATCTTTGGTAGGTGGCCAACTTA
1 TTGGAAATTAATC-TTGGTTGGTGGCCAACTTA
56297 TT
1 TT
56299 TTTCATCTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
30 3 0.05
31 20 0.33
32 3 0.05
33 32 0.52
34 3 0.05
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (32 bp):
TTGGAAATTAATCTTGGTTGGTGGCCAACTTA
Found at i:56288 original size:31 final size:33
Alignment explanation
Indices: 56211--56298 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
56201 TGGAAATTTT
*
56211 ATCTTGGTTGGTGGCCAACTTATTGGAAAATTC
1 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
56244 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
1 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
*
56277 -T-TTGGTAGGTGGCCAACTTATT
1 ATCTTGGTTGGTGGCCAACTTATT
56299 TTTCATCTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
31 20 0.38
32 1 0.02
33 32 0.60
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (33 bp):
ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
Found at i:58872 original size:4 final size:4
Alignment explanation
Indices: 58863--58922 Score: 50
Period size: 4 Copynumber: 14.2 Consensus size: 4
58853 TGTCTAGTTG
** *
58863 TTAT TTAT TTAT TTAT TTACAT ACAT TT-T TTACT TTAT TTAT TTAA TTATT
1 TTAT TTAT TTAT TTAT TT--AT TTAT TTAT TTA-T TTAT TTAT TTAT TTA-T
58914 TTAT TTAT T
1 TTAT TTAT T
58923 CGTTTGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
3 3 0.07
4 33 0.73
5 7 0.16
6 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:59899 original size:4 final size:4
Alignment explanation
Indices: 59892--59921 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
59882 TTCTTTCGTC
59892 ATTT ATTT ATTT ATTT ATTT ATTT ACTTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT A
59922 CTAACATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:60558 original size:22 final size:23
Alignment explanation
Indices: 60524--60567 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 23
60514 GGTAGTGGGG
60524 AAGGAATTGAATG-GAACCACAT
1 AAGGAATTGAATGAGAACCACAT
60546 AAGGCAATT-AATGAAGAACCAC
1 AAGG-AATTGAATG-AGAACCAC
60568 CCTGATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (23 bp):
AAGGAATTGAATGAGAACCACAT
Found at i:70547 original size:105 final size:104
Alignment explanation
Indices: 70125--70645 Score: 517
Period size: 105 Copynumber: 5.0 Consensus size: 104
70115 TCGTGCCACT
* *
70125 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTTCCAAT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-TTTCCCAG
* ** * * *
70190 TTCAAAGCTGATTTCAACTCCAC-GACGGAGGATATCGTGCTACC
64 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-GACC
*
70234 CAAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAACAA-TTCCCAGCT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAG-T
* *
70298 TCAG-GACCAATTTCAACTTCACAACGGAGGATATTGGACC
65 TCAGAG-CCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * **
70338 CAAGACAACACAAGCTCAACTTCGCAGCGAAAGGG-CGGCTGACTGTCAACAAACAATTT--C-G
1 CAAGACAACACAAGTTCAACTTCACAACG-AAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAG
* * *
70399 ----GAGCCAATCTCAACTTCACAACGAAGGATATTGGACT
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* *
70436 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAGTT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
* * *
70501 CCAGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACC
66 -CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * * * ** * *
70541 CAAGACAGCACAAGCTCAACTTCGCAGCGAAGGGGCGGCTGACTGTCAATAAACAATTTCCCGGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTCCCAGT
* *
70606 TCCAGAACCAATCTCAACTTCACAGC-AGAGGATATTGGAC
65 T-CAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGGAC
70646 TCAGAACAAT
Statistics
Matches: 347, Mismatches: 47, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
97 13 0.04
98 69 0.20
99 2 0.01
100 1 0.00
103 1 0.00
104 42 0.12
105 84 0.24
106 54 0.16
107 27 0.08
108 5 0.01
109 49 0.14
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (104 bp):
CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
Found at i:70561 original size:203 final size:204
Alignment explanation
Indices: 70236--70679 Score: 619
Period size: 203 Copynumber: 2.2 Consensus size: 204
70226 GTGCTACCCA
*
70236 AGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAACAATTCCCAGCTTCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTCCCAGCTTCA
*
70301 GGACCAATTTCAACTTCACAACGGAGGATATTGGACCCAAGACAACACAAGCTCAACTTCGCAGC
66 GGACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCGCAGC
70366 GAAAGGGCGGCTGACTGTCAACAAACAATTT-CGG-AG-CCAATCTCAACTTCACAAC-GAAGGA
131 GAAAGGGCGGCTGACTGTCAACAAACAATTTCCGGCAGACCAATCTCAACTTCACAACAG-AGGA
70427 TATTGGACTC
195 TATTGGACTC
*
70437 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAACAATTTCCCAG-TT
1 -AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAA-TTCCCAGCTT
* * * * *
70501 CCAGGGCCAGTTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCGC
64 -CAGGACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCGC
* * *
70566 AGCGAAGGGGCGGCTGACTGTCAATAAACAATTTCCCGGTTCCAGAACCAATCTCAACTTCACAG
128 AGCGAAAGGGCGGCTGACTGTCAACAAACAATTT-CCGG---CAG-ACCAATCTCAACTTCACAA
70631 CAGAGGATATTGGACTC
188 CAGAGGATATTGGACTC
* * * * *
70648 AGAACAATACTACTTAAACTTCACTACGAAGG
1 AG-ACAACACAAGTTCAACTTCACAACGAAGG
70680 ATATCCAATT
Statistics
Matches: 214, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
202 53 0.25
203 97 0.45
205 3 0.01
209 2 0.01
210 2 0.01
211 56 0.26
212 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (204 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTCCCAGCTTCA
GGACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCGCAGC
GAAAGGGCGGCTGACTGTCAACAAACAATTTCCGGCAGACCAATCTCAACTTCACAACAGAGGAT
ATTGGACTC
Found at i:72472 original size:4 final size:4
Alignment explanation
Indices: 72463--72538 Score: 82
Period size: 4 Copynumber: 18.2 Consensus size: 4
72453 TGTCTAGTTG
**
72463 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTACAT ACAT TT-T TTACT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT--AT TTAT TTAT TTA-T
*
72513 TTAT TTAT TTAA TTATT TTAT TTAT T
1 TTAT TTAT TTAT TTA-T TTAT TTAT T
72539 CGTTTGTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
3 3 0.05
4 49 0.80
5 7 0.11
6 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:74708 original size:17 final size:17
Alignment explanation
Indices: 74686--74731 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
74676 TTTCTCTATC
74686 AAATTAAATAAATGAGT
1 AAATTAAATAAATGAGT
* *
74703 AAATTAAATGAAGGAGT
1 AAATTAAATAAATGAGT
*
74720 -AATAAAATAAAT
1 AAATTAAATAAAT
74732 TTATTTATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
AAATTAAATAAATGAGT
Found at i:77631 original size:3 final size:3
Alignment explanation
Indices: 77623--77680 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
77613 CAGTTTACTT
* * *
77623 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTG TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
77669 TTA TTA TTA TTA
1 TTA TTA TTA TTA
77681 AATAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:79156 original size:12 final size:12
Alignment explanation
Indices: 79126--79163 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
79116 ATTACTTTTA
79126 TATTTTAATTAT
1 TATTTTAATTAT
**
79138 TGCTTTAATTAT
1 TATTTTAATTAT
79150 TATTTT-ATTAT
1 TATTTTAATTAT
79161 TAT
1 TAT
79164 CTTAGTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:79468 original size:124 final size:124
Alignment explanation
Indices: 79280--79506 Score: 312
Period size: 124 Copynumber: 1.8 Consensus size: 124
79270 TATTTTAAGA
* ** *
79280 AAATATTTTAGTTATTTATTTATTTTTTTAATGTTGAAGGAAAGAGCTGTCTTAAAACAACTAGA
1 AAATATTTTAGTTATTTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGA
**
79345 AGCCCTTTTCTAAATATTTTTAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
66 AGCCCTTTTCT-AATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
* * ** *
79405 AAATGTTTTAGTTATTTATTTA-TTTTTTAATATCAAAGAAAAGAGTTGTCTTAAAGTACCTAGA
1 AAATATTTTAGTTATTTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGA
* * *
79469 AGCCCTTTTCTGATATTTCCAAGTAATTAAATATCTTA
66 AGCCCTTTTCTAATATTTCCAAATAAATAAATATCTTA
79507 TTTATAAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 22 0.25
124 45 0.51
125 21 0.24
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (124 bp):
AAATATTTTAGTTATTTATTTATTTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGA
AGCCCTTTTCTAATATTTCCAAATAAATAAATATCTTACTATATTAAAATAAATTTTTT
Found at i:82383 original size:7 final size:7
Alignment explanation
Indices: 82348--82388 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
82338 TTTTCATATA
82348 TGCATTT
1 TGCATTT
82355 T-CATTT
1 TGCATTT
82361 TGCATCTT
1 TGCAT-TT
82369 TGCATTT
1 TGCATTT
*
82376 TTCATTT
1 TGCATTT
82383 TGCATT
1 TGCATT
82389 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:87887 original size:74 final size:75
Alignment explanation
Indices: 87800--87971 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 75
87790 ATTAACAAGA
* *
87800 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAA
*
87865 TA-TT-TATC
66 CACTTGTATC
* * ** *
87873 AGCAAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGA
*
87938 ACACTTGTATT
65 ACACTTGTATC
*
87949 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
87972 GGCCCACAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 3 0.03
74 56 0.65
75 21 0.24
76 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:89302 original size:22 final size:22
Alignment explanation
Indices: 89270--89343 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
89260 TACACTCTTC
*
89270 AAAGATGATAGATTCTTTTTTT
1 AAAGATGATAGATTCTCTTTTT
*
89292 AAAGATAATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
*
89314 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTT
89336 AAAGATGA
1 AAAGATGA
89344 AAGCTTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:90119 original size:76 final size:76
Alignment explanation
Indices: 90020--90706 Score: 1266
Period size: 76 Copynumber: 9.0 Consensus size: 76
90010 CTATTTCCCA
*
90020 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90085 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90096 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90161 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90172 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90237 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90248 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90313 ACCCTCAGGGT
66 ACCCTCAGGGT
* * *
90324 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90389 ACCCTCAGGGT
66 ACCCTCAGGGT
90400 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90465 ACCCTCAGGGT
66 ACCCTCAGGGT
*
90476 CATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90541 ACCCTCAGGGT
66 ACCCTCAGGGT
90552 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
90617 ACCCTCAGGGT
66 ACCCTCAGGGT
* * *
90628 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
90693 ACGCTCAGGGT
66 ACCCTCAGGGT
90704 CAT
1 CAT
90707 TCATAAGACC
Statistics
Matches: 592, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 592 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCCTCAGGGT
Found at i:90870 original size:3 final size:3
Alignment explanation
Indices: 90862--90925 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
90852 CAGTTTACTT
* *
90862 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
90908 TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
90926 AATAAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:95590 original size:20 final size:20
Alignment explanation
Indices: 95560--95606 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
95550 CGAAATCGAT
*
95560 AATTATTATGTAACAAGTAA
1 AATTATAATGTAACAAGTAA
* *
95580 ATTTATAATGTAACCAGTAA
1 AATTATAATGTAACAAGTAA
95600 AATTATA
1 AATTATA
95607 TTGGTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (20 bp):
AATTATAATGTAACAAGTAA
Found at i:95855 original size:23 final size:23
Alignment explanation
Indices: 95829--95876 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
95819 AAATAGGCCA
* *
95829 ATATAAGCGTTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
95852 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATATATT
95875 AT
1 AT
95877 TGTACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:110669 original size:11 final size:11
Alignment explanation
Indices: 110637--110662 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
110627 ATCTTCGGAA
110637 GCTTAGGTTAT
1 GCTTAGGTTAT
110648 GCTTAGGTTAT
1 GCTTAGGTTAT
110659 GCTT
1 GCTT
110663 TGTTTATTCT
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:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (11 bp):
GCTTAGGTTAT
Found at i:111147 original size:43 final size:43
Alignment explanation
Indices: 111033--111128 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
111023 GACTTACCGT
* * * * * *
111033 TAAATAAACTAACTTTTTCCGGCGTTTGTATCTAAAACGCCGC
1 TAAATAACCTAACATTTTACAGCATTTGTATCTAAAACGCCGA
111076 TAAATAACCTAACATTTTACAGCATTTGTATCTAAAACGCCGA
1 TAAATAACCTAACATTTTACAGCATTTGTATCTAAAACGCCGA
111119 TAAATAACCT
1 TAAATAACCT
111129 GATTTTTTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (43 bp):
TAAATAACCTAACATTTTACAGCATTTGTATCTAAAACGCCGA
Found at i:112974 original size:23 final size:23
Alignment explanation
Indices: 112947--112996 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
112937 AATTTTGGGG
*
112947 TGAAATGAAATAATTATTTTTCA
1 TGAAAAGAAATAATTATTTTTCA
**
112970 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAAATAATTATTTTTCA
112993 TGAA
1 TGAA
112997 TAGTCATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (23 bp):
TGAAAAGAAATAATTATTTTTCA
Found at i:114844 original size:20 final size:20
Alignment explanation
Indices: 114819--114856 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
114809 CAATTTATTC
114819 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
114839 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
114857 TCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:122219 original size:21 final size:21
Alignment explanation
Indices: 122193--122255 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
122183 TTTGGTGCAG
* *
122193 AGGGAATCGATCCCCCCCATA
1 AGGGAACCGATTCCCCCCATA
**
122214 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCAT-A
122236 AGAGGAACCGATTCCCCCCA
1 AG-GGAACCGATTCCCCCCA
122256 CTGGGGAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 3 0.09
23 15 0.44
ACGTcount: A:0.27, C:0.37, G:0.21, T:0.16
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCATA
Found at i:127085 original size:23 final size:23
Alignment explanation
Indices: 127057--127138 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
127047 GCATGGCTTT
127057 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
127080 GTGCATCGATGAATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
127102 -TGTATCGATGCACATACAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
127124 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
127139 TGTTCAGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 3 0.07
23 17 0.37
24 13 0.28
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:127153 original size:44 final size:43
Alignment explanation
Indices: 127056--127157 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 43
127046 TGCATGGCTT
*
127056 TGTGCATCGATGCACATTCAAGGAGTGCATCGATGAATCTTCA
1 TGTGCATCGATGCACATACAAGGAGTGCATCGATGAATCTTCA
* * *
127099 TGATGTATCGATGCACATACAAAGG-GATGCATCGATGCACTGTTCA
1 TG-TGCATCGATGCACATAC-AAGGAG-TGCATCGATG-AATCTTCA
127145 -GTGCATCGATGCA
1 TGTGCATCGATGCA
127158 TTAAGCACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 2 0.04
44 27 0.54
45 15 0.30
46 6 0.12
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
TGTGCATCGATGCACATACAAGGAGTGCATCGATGAATCTTCA
Found at i:133067 original size:20 final size:20
Alignment explanation
Indices: 133031--133068 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
133021 CAATTTATTC
*
133031 ATTGGTGCATTGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
133051 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
133069 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:134362 original size:21 final size:21
Alignment explanation
Indices: 134338--134389 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
134328 GATTTTTGCA
134338 TGATGGAATCAATTTCACTCT
1 TGATGGAATCAATTTCACTCT
134359 TGATGGAATCAATTTCACTCT
1 TGATGGAATCAATTTCACTCT
134380 TGATGGAATC
1 TGATGGAATC
134390 TTTCCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
TGATGGAATCAATTTCACTCT
Found at i:140182 original size:25 final size:25
Alignment explanation
Indices: 140154--140216 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
140144 TGAGTGTTAA
* *
140154 TTTATATTTATGAATATTTTTTATT
1 TTTATATTTATGAATAGTTTTAATT
* **
140179 TTTATTTTTAAAAATAGTTTTAATT
1 TTTATATTTATGAATAGTTTTAATT
*
140204 TTTA-ATTTTTGAA
1 TTTATATTTATGAA
140217 AACTAAAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (25 bp):
TTTATATTTATGAATAGTTTTAATT
Found at i:140827 original size:32 final size:32
Alignment explanation
Indices: 140786--140862 Score: 129
Period size: 31 Copynumber: 2.4 Consensus size: 32
140776 TAGATGAACT
* *
140786 TAATTGATTTTTTTGGGTTAAGTTTGATGGTG
1 TAATTGATTTTTTTGGGCTAAGTTTGATAGTG
140818 TAATTGA-TTTTTTGGGCTAAGTTTGATAGTG
1 TAATTGATTTTTTTGGGCTAAGTTTGATAGTG
140849 TAATTGATTTTTTT
1 TAATTGATTTTTTT
140863 AGAAAGTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.21, C:0.01, G:0.23, T:0.55
Consensus pattern (32 bp):
TAATTGATTTTTTTGGGCTAAGTTTGATAGTG
Found at i:142033 original size:33 final size:33
Alignment explanation
Indices: 141979--142041 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
141969 TCTATTTATC
*
141979 TTATATTATTATTAATGATAGAAAAATAAAGTT
1 TTATACTATTATTAATGATAGAAAAATAAAGTT
*
142012 TTATACTATT-TTCAATTATAGAAAAATAAA
1 TTATACTATTATT-AATGATAGAAAAATAAA
142042 AAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (33 bp):
TTATACTATTATTAATGATAGAAAAATAAAGTT
Found at i:142133 original size:16 final size:16
Alignment explanation
Indices: 142112--142144 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
142102 AAACTAATAA
142112 AAAATATAATAT-TTTT
1 AAAATA-AATATATTTT
142128 AAAATAAATATATTTT
1 AAAATAAATATATTTT
142144 A
1 A
142145 TATATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAAATATATTTT
Found at i:142309 original size:45 final size:46
Alignment explanation
Indices: 142260--142378 Score: 132
Period size: 46 Copynumber: 2.6 Consensus size: 46
142250 AAAAATACCA
* **
142260 AATTTAATTTAGAATTATAAAAAATTTAATA-AAAATATCAAATTT
1 AATTTAAATTAGAAAAATAAAAAATTTAATATAAAATATCAAATTT
* ** **
142305 AATTTAAATTATAAAAATAGTAAATTTAATATAAAATATTGAATTT
1 AATTTAAATTAGAAAAATAAAAAATTTAATATAAAATATCAAATTT
* * *
142351 AATTTAAAATATAAAAATAATAAATTTA
1 AATTTAAATTAGAAAAATAAAAAATTTA
142379 TTTTTTTAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 25 0.40
46 38 0.60
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (46 bp):
AATTTAAATTAGAAAAATAAAAAATTTAATATAAAATATCAAATTT
Found at i:142313 original size:18 final size:18
Alignment explanation
Indices: 142252--142313 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
142242 AAATATGAAA
*
142252 AAATACCAAATTTAATTT
1 AAATATCAAATTTAATTT
* **
142270 AGAATTATAAAAAATTTAATAA
1 A-AA-TAT--CAAATTTAATTT
142292 AAATATCAAATTTAATTT
1 AAATATCAAATTTAATTT
142310 AAAT
1 AAAT
142314 TATAAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
18 14 0.42
19 2 0.06
20 5 0.15
21 2 0.06
22 10 0.30
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATATCAAATTTAATTT
Found at i:142319 original size:27 final size:27
Alignment explanation
Indices: 142288--142339 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
142278 AAAAAATTTA
*
142288 ATAAAAATA-TCAAATTTAATTTAAATT
1 ATAAAAATAGT-AAATTTAATATAAATT
142315 ATAAAAATAGTAAATTTAATATAAA
1 ATAAAAATAGTAAATTTAATATAAA
142340 ATATTGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
ATAAAAATAGTAAATTTAATATAAATT
Found at i:142336 original size:39 final size:39
Alignment explanation
Indices: 142250--142329 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
142240 ATAAATATGA
* * *
142250 AAAAATACCAAATTTAATTTAGAATTATAAAAAATTTAAT
1 AAAAATATCAAATTTAATTTA-AATTATAAAAAAGTAAAT
142290 AAAAATATCAAATTTAATTTAAATTATAAAAATAGTAAAT
1 AAAAATATCAAATTTAATTTAAATTATAAAAA-AGTAAAT
142330 TTAATATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 11 0.31
40 25 0.69
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (39 bp):
AAAAATATCAAATTTAATTTAAATTATAAAAAAGTAAAT
Found at i:142342 original size:19 final size:18
Alignment explanation
Indices: 142318--142365 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
142308 TTAAATTATA
142318 AAAATAGTAAATTTAATAT
1 AAAATA-TAAATTTAATAT
* *
142337 AAAATATTGAATTTAATTT
1 AAAATA-TAAATTTAATAT
142356 AAAATATAAA
1 AAAATATAAA
142366 AATAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AAAATATAAATTTAATAT
Found at i:142355 original size:46 final size:45
Alignment explanation
Indices: 142276--142378 Score: 152
Period size: 46 Copynumber: 2.3 Consensus size: 45
142266 ATTTAGAATT
* *
142276 ATAAAAAATTTAATAAAAATATCAAATTTAATTTAAATTATAAAA
1 ATAATAAATTTAATAAAAATATCAAATTTAATTTAAAATATAAAA
* **
142321 ATAGTAAATTTAATATAAAATATTGAATTTAATTTAAAATATAAAA
1 ATAATAAATTTAATA-AAAATATCAAATTTAATTTAAAATATAAAA
142367 ATAATAAATTTA
1 ATAATAAATTTA
142379 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.25
46 38 0.75
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (45 bp):
ATAATAAATTTAATAAAAATATCAAATTTAATTTAAAATATAAAA
Found at i:142376 original size:27 final size:27
Alignment explanation
Indices: 142288--142378 Score: 74
Period size: 27 Copynumber: 3.7 Consensus size: 27
142278 AAAAAATTTA
*
142288 ATAAAAAT-ATCAAATTTAATTTAAATT
1 ATAAAAATAAT-AAATTTAATTTAAAAT
*
142315 ATAAAAATAGT--A---AATTT--AAT
1 ATAAAAATAATAAATTTAATTTAAAAT
* *
142335 AT-AAAATATTGAATTTAATTTAAAAT
1 ATAAAAATAATAAATTTAATTTAAAAT
142361 ATAAAAATAATAAATTTA
1 ATAAAAATAATAAATTTA
142379 TTTTTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
19 7 0.14
20 4 0.08
21 1 0.02
22 5 0.10
24 5 0.10
25 1 0.02
26 5 0.10
27 21 0.42
28 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAAAAATAATAAATTTAATTTAAAAT
Found at i:145747 original size:3 final size:3
Alignment explanation
Indices: 145739--145790 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
145729 TATTTATATA
* * * * *
145739 ATT ATT ATT ATT ATT ATA ATT ATA ATA ATA ATT ATT ATT AAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
145785 ATT ATT
1 ATT ATT
145791 TAATATTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:151269 original size:15 final size:15
Alignment explanation
Indices: 151249--151280 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
151239 ATCAATACCT
151249 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
151264 TTTTGCATACATTCA
1 TTTTGCATACATGCA
151279 TT
1 TT
151281 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:158624 original size:12 final size:11
Alignment explanation
Indices: 158606--158636 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
158596 TATTATGCTT
158606 GAAAAAAAAAA
1 GAAAAAAAAAA
158617 GAAAAAAAAAA
1 GAAAAAAAAAA
158628 GAAAAAAAA
1 GAAAAAAAA
158637 GGGGGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:159925 original size:83 final size:83
Alignment explanation
Indices: 159791--160501 Score: 1314
Period size: 83 Copynumber: 8.6 Consensus size: 83
159781 TGCAATGTAC
* *
159791 TCATAGCATCTTCTGGAAGTGTTCTTTGATTTATCTGATCTGGTTTAGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
159856 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
159874 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
159939 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
*
159957 TCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
160022 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
160040 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
160105 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
160123 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
*
160188 TTTGAAAGATGAATGTGC
66 TTTGAAAGATGAATGTGA
*
160206 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
160271 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
160289 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
160354 TTTGAAAGATGAATGTGA
66 TTTGAAAGATGAATGTGA
* * *
160372 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAGTTATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
* * *
160437 TTTGGAAGAGGAATGTGC
66 TTTGAAAGATGAATGTGA
*
160455 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
160502 ATATGAAACC
Statistics
Matches: 613, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 613 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
TTTGAAAGATGAATGTGA
Found at i:161764 original size:20 final size:20
Alignment explanation
Indices: 161700--161765 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
161690 TTCCAGAGAA
161700 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * * * **
161720 CGTCTGAAAAAG-GAAGAAGA
1 AGT-TCATAATGAGAAGAACT
161740 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
161760 TGTTCA
1 AGTTCA
161766 ACCTTTTGCC
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:161789 original size:113 final size:113
Alignment explanation
Indices: 161440--162220 Score: 1234
Period size: 113 Copynumber: 6.9 Consensus size: 113
161430 GATTTAAATC
161440 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * **
161505 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
* *** *
161553 CATCA-TGTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACTTGAAG
1 CATCACT-TGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCA-T-C-TGAAG
* * *
161616 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATT
61 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
* *
161669 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCTGAAAAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
161734 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
161782 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
161847 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
*
161895 CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
161960 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
162008 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
162073 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
* * * *
162120 CATCACTTAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-
1 CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
162183 AG-A-ATGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
162221 AATGACTCTA
Statistics
Matches: 625, Mismatches: 35, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
108 25 0.04
109 7 0.01
110 2 0.00
111 1 0.00
112 73 0.12
113 415 0.66
114 2 0.00
115 2 0.00
116 96 0.15
117 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATT
Found at i:162466 original size:15 final size:15
Alignment explanation
Indices: 162448--162512 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
162438 TATTTTAATG
162448 TTATTTATATAATAA
1 TTATTTATATAATAA
*
162463 TTA-TTATTATTATAA
1 TTATTTA-TATAATAA
*
162478 TTA-TAATAATAATAA
1 TTATTTAT-ATAATAA
*
162493 TTATTAATAT-AT-A
1 TTATTTATATAATAA
162506 TTATTTA
1 TTATTTA
162513 ATATTACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 7 0.16
14 6 0.14
15 26 0.60
16 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTTATATAATAA
Found at i:174739 original size:19 final size:19
Alignment explanation
Indices: 174715--174751 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
174705 TAATTTCTGT
*
174715 TCTGATCTCTGATCTCTAC
1 TCTGATCTCTGATATCTAC
*
174734 TCTGATTTCTGATATCTA
1 TCTGATCTCTGATATCTA
174752 TGTTTACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (19 bp):
TCTGATCTCTGATATCTAC
Found at i:185242 original size:39 final size:38
Alignment explanation
Indices: 185178--185375 Score: 245
Period size: 39 Copynumber: 5.1 Consensus size: 38
185168 AGGAAAAACG
* *
185178 TTTTTAGGTTGCAACCTGATATTTCATATAGAAATCAAA
1 TTTTTAGGTTGCAACCTGAT-TTTCATATAGAAACCAGA
*
185217 TTTTTAGGTTGCAAACTGAGTTTTCATATAGAAACCAGA
1 TTTTTAGGTTGCAACCTGA-TTTTCATATAGAAACCAGA
*
185256 TTTTTAGGTTGCAACCTGATATTTCACATAGAAACCAGA
1 TTTTTAGGTTGCAACCTGAT-TTTCATATAGAAACCAGA
* *
185295 TTTTT-GGTTTCAACCTGATTTTTCATATAAAAACCAGA
1 TTTTTAGGTTGCAACCTGA-TTTTCATATAGAAACCAGA
* * * * *
185333 TTTCTAGGTTACAACCTGCTTTTTCATGTAGAAACTAGA
1 TTTTTAGGTTGCAACCTG-ATTTTCATATAGAAACCAGA
185372 TTTT
1 TTTT
185376 AGTTTGAAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
38 33 0.24
39 105 0.76
40 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (38 bp):
TTTTTAGGTTGCAACCTGATTTTCATATAGAAACCAGA
Found at i:185259 original size:19 final size:19
Alignment explanation
Indices: 185237--185298 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
185227 GCAAACTGAG
*
185237 TTTTCATATAGAAACCAGA
1 TTTTCACATAGAAACCAGA
* ** * * *
185256 TTTTTAGGTTGCAACCTGA
1 TTTTCACATAGAAACCAGA
185275 TATTTCACATAGAAACCAGA
1 T-TTTCACATAGAAACCAGA
185295 TTTT
1 TTTT
185299 TGGTTTCAAC
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
TTTTCACATAGAAACCAGA
Found at i:185358 original size:77 final size:78
Alignment explanation
Indices: 185182--185375 Score: 264
Period size: 77 Copynumber: 2.5 Consensus size: 78
185172 AAAACGTTTT
* *
185182 TAGGTTGCAACCTGATATTTCATATAGAAATCAAATTTTTAGGTTGCAAACTGAGTTTTCATATA
1 TAGGTTGCAACCTGATATTTCATATAGAAACCAGATTTTTAGGTTGCAAACTGAGTTTTCATATA
* *
185247 GAAACCAGATTTT
66 AAAACCAGATTTC
* * * *
185260 TAGGTTGCAACCTGATATTTCACATAGAAACCAGATTTTT-GGTTTCAACCTGATTTTTCATATA
1 TAGGTTGCAACCTGATATTTCATATAGAAACCAGATTTTTAGGTTGCAAACTGAGTTTTCATATA
185324 AAAACCAGATTTC
66 AAAACCAGATTTC
* * * * *
185337 TAGGTTACAACCTGCTTTTTCATGTAGAAACTAGATTTT
1 TAGGTTGCAACCTGATATTTCATATAGAAACCAGATTTT
185376 AGTTTGAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 65 0.64
78 37 0.36
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (78 bp):
TAGGTTGCAACCTGATATTTCATATAGAAACCAGATTTTTAGGTTGCAAACTGAGTTTTCATATA
AAAACCAGATTTC
Found at i:185401 original size:77 final size:77
Alignment explanation
Indices: 185182--185418 Score: 230
Period size: 77 Copynumber: 3.1 Consensus size: 77
185172 AAAACGTTTT
* * * * * *
185182 TAGGTTGCAACCTGATATTTCATATAGAAATCAAATTTTTAGGTTGCAAA-CTGAGTTTTCATAT
1 TAGGTTACAACCTGATATTTCACATAGAAACCAGATTTTTA-GTT-TAAACCTGATTTTTCATAT
* *
185246 AGAAACCAGATTTT
64 AAAAACCAGATTTC
* * *
185260 TAGGTTGCAACCTGATATTTCACATAGAAACCAGATTTTTGGTTTCAACCTGATTTTTCATATAA
1 TAGGTTACAACCTGATATTTCACATAGAAACCAGATTTTTAGTTTAAACCTGATTTTTCATATAA
185325 AAACCAGATTTC
66 AAACCAGATTTC
* * ** * * *
185337 TAGGTTACAACCTGCTTTTTCATGTAGAAACTAGA-TTTTAGTTTGAAAACCTTATTTTT-GTAT
1 TAGGTTACAACCTGATATTTCACATAGAAACCAGATTTTTAGTTT--AAACCTGATTTTTCATAT
* *
185400 AATAACCAGAATTC
64 AAAAACCAGATTTC
185414 T-GGTT
1 TAGGTT
185419 GGAACATATT
Statistics
Matches: 135, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
76 14 0.10
77 73 0.54
78 48 0.36
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (77 bp):
TAGGTTACAACCTGATATTTCACATAGAAACCAGATTTTTAGTTTAAACCTGATTTTTCATATAA
AAACCAGATTTC
Done.