Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 103 of 113
Found at i:20351958 original size:14 final size:14
Alignment explanation
Indices: 20351941--20351991 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 14
20351931 GCCTTTTAGC
20351941 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
*
20351955 TTTTTTC-TTTTTT
1 TTTTCTCTTTTTTT
*
20351968 TTTT-TCTTTTCTT
1 TTTTCTCTTTTTTT
20351981 TTTTCTCTTTT
1 TTTTCTCTTTT
20351992 GCATGAGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 12 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTCTTTTTTT
Found at i:20351960 original size:16 final size:16
Alignment explanation
Indices: 20351941--20351984 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
20351931 GCCTTTTAGC
20351941 TTTTCTCTTTTTTTTT
1 TTTTCTCTTTTTTTTT
20351957 TTTTCT-TTTTTTTTT
1 TTTTCTCTTTTTTTTT
20351972 TCTTT-TCTTTTTT
1 T-TTTCTCTTTTTT
20351985 CTCTTTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTCTCTTTTTTTTT
Found at i:20351965 original size:12 final size:12
Alignment explanation
Indices: 20351950--20351991 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
20351940 CTTTTCTCTT
20351950 TTTTTTTTTTTC
1 TTTTTTTTTTTC
20351962 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
20351974 TTTTCTTTTTTC
1 TTTTTTTTTTTC
20351986 TCTTTT
1 T-TTTT
20351992 GCATGAGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 24 0.89
13 3 0.11
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:20359088 original size:20 final size:19
Alignment explanation
Indices: 20359042--20359081 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
20359032 AAATTATTTA
20359042 TTTATTTGAAAAGACCTTTTT
1 TTTA-TTGAAAAGA-CTTTTT
20359063 TTTATTGAAAAGA-TTTTT
1 TTTATTGAAAAGACTTTTT
20359081 T
1 T
20359082 AATTATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTATTGAAAAGACTTTTT
Found at i:20359234 original size:5 final size:5
Alignment explanation
Indices: 20359226--20359262 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
20359216 TAAAAGGGTT
20359226 AAATA AAATA AAATA AAATTAA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAA-T-A AAATA AAATA AAATA
20359263 GGAAAAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 24 0.80
6 2 0.07
7 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:20362244 original size:43 final size:42
Alignment explanation
Indices: 20362168--20362250 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 42
20362158 AGAAAGAAAG
* *
20362168 AAAAGAAAAAATAAAATAAAGATAATATATTAATAGATAACC
1 AAAAGAAAAAATAAAATAAAGAAAAAATATTAATAGATAACC
* * *
20362210 AAAAGAAAATAATTAGATAAATAAAAAATATTAATAGATAA
1 AAAAGAAAA-AATAAAATAAAGAAAAAATATTAATAGATAA
20362251 ATAATAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 9 0.26
43 26 0.74
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (42 bp):
AAAAGAAAAAATAAAATAAAGAAAAAATATTAATAGATAACC
Found at i:20362249 original size:21 final size:22
Alignment explanation
Indices: 20362194--20362254 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
20362184 TAAAGATAAT
**
20362194 ATATTAATAGATAACCAAAAGA
1 ATATTAATAGATAAATAAAAGA
*
20362216 A-AATAATTAGATAAATAAAA-A
1 ATATTAA-TAGATAAATAAAAGA
20362237 ATATTAATAGATAAATAA
1 ATATTAATAGATAAATAA
20362255 TAATAAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (22 bp):
ATATTAATAGATAAATAAAAGA
Found at i:20362250 original size:17 final size:18
Alignment explanation
Indices: 20362215--20362256 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
20362205 TAACCAAAAG
20362215 AAAATAATTAGATAAATAA
1 AAAAT-ATTAGATAAATAA
*
20362234 AAAATATTA-ATAGATAA
1 AAAATATTAGATAAATAA
*
20362251 ATAATA
1 AAAATA
20362257 ATAAAGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAATATTAGATAAATAA
Found at i:20362258 original size:14 final size:14
Alignment explanation
Indices: 20362229--20362326 Score: 83
Period size: 14 Copynumber: 6.9 Consensus size: 14
20362219 TAATTAGATA
*
20362229 AATAAA-AAATATT
1 AATAAATAAATAAT
*
20362242 AATAGATAAATAAT
1 AATAAATAAATAAT
*
20362256 AATAAAGTATATATATT
1 AATAAA-TA-A-ATAAT
* *
20362273 AACAGATAAATAAT
1 AATAAATAAATAAT
* *
20362287 AATAAATATATATT
1 AATAAATAAATAAT
*
20362301 AATAAAT-AGTAAT
1 AATAAATAAATAAT
20362314 AATAAATAAATAA
1 AATAAATAAATAA
20362327 ATAAGATACA
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
13 15 0.23
14 36 0.55
15 3 0.05
16 3 0.05
17 8 0.12
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (14 bp):
AATAAATAAATAAT
Found at i:20362272 original size:31 final size:29
Alignment explanation
Indices: 20362229--20362319 Score: 109
Period size: 31 Copynumber: 3.2 Consensus size: 29
20362219 TAATTAGATA
20362229 AATAAAA-A-ATATTAATAGATAAATAAT
1 AATAAAATATATATTAATAGATAAATAAT
*
20362256 AATAAAGTATATATATTAACAGATAAATAAT
1 AATAAA--ATATATATTAATAGATAAATAAT
* *
20362287 AAT-AAATATATATTAATAAAT-AGTAAT
1 AATAAAATATATATTAATAGATAAATAAT
20362314 AATAAA
1 AATAAA
20362320 TAAATAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 14 0.25
28 16 0.29
29 1 0.02
30 3 0.05
31 21 0.38
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (29 bp):
AATAAAATATATATTAATAGATAAATAAT
Found at i:20362366 original size:12 final size:13
Alignment explanation
Indices: 20362336--20362371 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20362326 AATAAGATAC
20362336 ACAAAATAAAAAT
1 ACAAAATAAAAAT
20362349 ACAAAATAAAAA-
1 ACAAAATAAAAAT
*
20362361 ATAAAATAAAA
1 ACAAAATAAAA
20362372 TGGGCTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (13 bp):
ACAAAATAAAAAT
Found at i:20364798 original size:3 final size:3
Alignment explanation
Indices: 20364777--20364913 Score: 109
Period size: 3 Copynumber: 44.7 Consensus size: 3
20364767 ATGGGCCCAC
* * *
20364777 ATT ATT -TT ATT TTT TTT ATT ATTT ATTT ATT ATT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT
* ** * *
20364823 -TT TTT CGT -TT GTT ATTT ATA ATT ATT ACTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
* *
20364868 ATC ATT ATTT ATTT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT AT
1 ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20364914 CATTTTTTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
2 5 0.04
3 88 0.78
4 20 0.18
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20364823 original size:35 final size:35
Alignment explanation
Indices: 20364777--20364899 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 35
20364767 ATGGGCCCAC
20364777 ATTATT-TTATTTTTTTTATTATTTATTTATTATT
1 ATTATTATTATTTTTTTTATTATTTATTTATTATT
* *
20364811 ATTAGTATTATTTTTTTCGTTTGTTATTTATAATTATTACTT
1 ATTATTATTA--TTTTT--TTTATTATTTAT--TTATTA-TT
* * *
20364853 ATTATTATTATTATTATCATTATTTATTTATTATT
1 ATTATTATTATTTTTTTTATTATTTATTTATTATT
20364888 ATTATTATTATT
1 ATTATTATTATT
20364900 ACTATTATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
34 5 0.07
35 17 0.23
36 6 0.08
37 5 0.07
38 9 0.12
39 11 0.15
40 4 0.05
41 6 0.08
42 11 0.15
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (35 bp):
ATTATTATTATTTTTTTTATTATTTATTTATTATT
Found at i:20365923 original size:73 final size:72
Alignment explanation
Indices: 20365821--20365955 Score: 220
Period size: 74 Copynumber: 1.9 Consensus size: 72
20365811 TTCAATGATT
*
20365821 TTTCTAAAATAAAATTTCAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTAAA
1 TTTCTAAAATAAAATTTCAAAAAATATTTTTAAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAA
20365885 AGTAAAA
66 AGTAAAA
20365892 TTTCTAAAAATAAAAATTTCCAAAAAA-ATTTTTAAGGAAAAAGTTGAAAGTATCAATTTTTCTT
1 TTTCT-AAAAT-AAAATTT-CAAAAAATATTTTTAAGGAAAAAGTTGAAAGTATCAATTTTTCTT
20365956 TGAAAATAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
71 5 0.08
72 5 0.08
73 16 0.27
74 33 0.56
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (72 bp):
TTTCTAAAATAAAATTTCAAAAAATATTTTTAAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAA
AGTAAAA
Found at i:20365954 original size:58 final size:56
Alignment explanation
Indices: 20365892--20366072 Score: 188
Period size: 59 Copynumber: 3.1 Consensus size: 56
20365882 AAAAGTAAAA
*
20365892 TTTC-TAAAAATAAAAATTTCCAAAAAAAT-TTTTAAGGAAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATTT--AAAAAAATATTTTAA--AGAAAGTTGAAAGTATCAATT
* * *
20365950 TTTCTTTGAAAAT-AAAATGTAAAAAAAATAATTTTAAAGATAGTTGAAAGTATCAATT
1 TTTC-TTAAAAATAAAAAT-TTAAAAAAAT-ATTTTAAAGAAAGTTGAAAGTATCAATT
* *
20366008 TTCCTTTAAAATAAAAAGGTTTAAAAAAATAATTTTAAAGAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAA--TTTAAAAAAAT-ATTTTAAAGAAAGTTGAAAGTATCAATT
*
20366067 TCTCTT
1 TTTCTT
20366073 GTTTGGCGTG
Statistics
Matches: 105, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
57 7 0.07
58 38 0.36
59 46 0.44
60 14 0.13
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (56 bp):
TTTCTTAAAAATAAAAATTTAAAAAAATATTTTAAAGAAAGTTGAAAGTATCAATT
Found at i:20365975 original size:74 final size:73
Alignment explanation
Indices: 20365826--20365983 Score: 209
Period size: 74 Copynumber: 2.2 Consensus size: 73
20365816 TGATTTTTCT
*
20365826 AAAAT-AAAATTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAA
1 AAAATAAAAATTTCAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAA
* *
20365890 AATTTCTA
66 AATGTCAA
20365898 AAAATAAAAATTTCCAAAAAA-ATTTTTAAGGAAAAAGTTGAAAGTATCAATTTTTCTTTGAAAA
1 AAAATAAAAATTT-CAAAAAATATTTTTAAGG-AAAAGTTGAAAGTATCAATTTTTC-TT-AAAA
20365962 -TAAAATGT-AA
62 GTAAAATGTCAA
*
20365972 AAAA-AATAATTT
1 AAAATAAAAATTT
20365984 TAAAGATAGT
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
72 5 0.06
73 23 0.30
74 36 0.47
75 9 0.12
76 4 0.05
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (73 bp):
AAAATAAAAATTTCAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAA
AATGTCAA
Found at i:20366055 original size:59 final size:58
Alignment explanation
Indices: 20365931--20366067 Score: 213
Period size: 59 Copynumber: 2.3 Consensus size: 58
20365921 TTTTAAGGAA
* *
20365931 AAAGTTGAAAGTATCAATTTTTCTTTGAAAATAAAATGTAAAAAAAATAATTTTAAAG
1 AAAGTTGAAAGTATCAATTTTCCTTTGAAAATAAAAGGTAAAAAAAATAATTTTAAAG
* *
20365989 ATAGTTGAAAGTATCAATTTTCCTTT-AAAATAAAAAGGTTTAAAAAAATAATTTTAAAG
1 AAAGTTGAAAGTATCAATTTTCCTTTGAAAAT-AAAAGG-TAAAAAAAATAATTTTAAAG
20366048 AAAGTTGAAAGTATCAATTT
1 AAAGTTGAAAGTATCAATTT
20366068 CTCTTGTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
57 5 0.07
58 29 0.40
59 38 0.53
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (58 bp):
AAAGTTGAAAGTATCAATTTTCCTTTGAAAATAAAAGGTAAAAAAAATAATTTTAAAG
Found at i:20367997 original size:14 final size:15
Alignment explanation
Indices: 20367978--20368008 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
20367968 TCTTGGTGGG
20367978 TTTCCTTTTTT-TTT
1 TTTCCTTTTTTGTTT
20367992 TTTCCTTTTTTGTTT
1 TTTCCTTTTTTGTTT
20368007 TT
1 TT
20368009 GTATGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTCCTTTTTTGTTT
Found at i:20368874 original size:84 final size:84
Alignment explanation
Indices: 20368764--20369132 Score: 318
Period size: 84 Copynumber: 4.4 Consensus size: 84
20368754 GTCCAAAGGT
* * * * * * *
20368764 CTTAAAGATTATGCTCGGAGTTTTTACAAATCTTGACTCTAAAACAAATTTAGCTCGAAAGACTT
1 CTTAGAGATTACGCTCGAAGGTTTTACAAATCTTGACTCTAAAATAAATTCAGCTCAAAAGACTT
20368829 A-CAAGTCTTACCCAGAGGA
66 ATCAA-TCTTACCCAGAGGA
* * * * ***
20368848 CTTAGAGATTACGCTCAAAGGTTTTACAAATCTCGA-TCTTAAAATAGATTCAACTTGCAAGACT
1 CTTAGAGATTACGCTCGAAGGTTTTACAAATCTTGACTC-TAAAATAAATTCAGCTCAAAAGACT
* * * * *
20368912 TATGAATCTTGCCTAAATGA
65 TATCAATCTTACCCAGAGGA
* * * * * *
20368932 CTCACAGATTACACTTGAAGGTGTTACAAATCTTGACTTTAAAATAAATTCAGCTCAAAAGACTT
1 CTTAGAGATTACGCTCGAAGGTTTTACAAATCTTGACTCTAAAATAAATTCAGCTCAAAAGACTT
* **
20368997 ATGAATCTTGTCCA-AGGA
66 ATCAATCTTACCCAGAGGA
* * * * *
20369015 CTTAGAGATTACTCTCGGAGGTTTTATAAATCTCGACTTTAAAATAAATTCAAG-TCAAAAGACT
1 CTTAGAGATTACGCTCGAAGGTTTTACAAATCTTGACTCTAAAATAAATTC-AGCTCAAAAGACT
*
20369079 TA-CGAATCTTACTCAGAGGA
65 TATC-AATCTTACCCAGAGGA
* * *
20369099 CTTGGAGATTATGCGT-GGAGGTTTTACAAATCTT
1 CTTAGAGATTACGC-TCGAAGGTTTTACAAATCTT
20369133 AGAGATTATG
Statistics
Matches: 228, Mismatches: 50, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
83 68 0.30
84 156 0.68
85 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (84 bp):
CTTAGAGATTACGCTCGAAGGTTTTACAAATCTTGACTCTAAAATAAATTCAGCTCAAAAGACTT
ATCAATCTTACCCAGAGGA
Found at i:20369079 original size:167 final size:168
Alignment explanation
Indices: 20368787--20369088 Score: 412
Period size: 167 Copynumber: 1.8 Consensus size: 168
20368777 CTCGGAGTTT
* *
20368787 TTACAAATCTTGACTCTAAAACAAATTTAGCTCGAAAGACTTACAAGTCTTACCCAGAGGACTTA
1 TTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTACAAGTCTTACCCAGAGGACTTA
* *** *
20368852 GAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAGATTCAACTTGCAAGACTTATGA
66 GAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAAATTCAACTCAAAAGACTTACGA
20368917 ATCTTGCCTAAATGACTCACAGATTACACTTGAAGGTG
131 ATCTTGCCTAAATGACTCACAGATTACACTTGAAGGTG
* * * **
20368955 TTACAAATCTTGACTTTAAAATAAATTCAGCTCAAAAGACTTATGAA-TCTTGTCCA-AGGACTT
1 TTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTA-CAAGTCTTACCCAGAGGACTT
* ** * *
20369018 AGAGATTACTCTCGGAGGTTTTATAAATCTCGA-CTTTAAAATAAATTCAAGTCAAAAGACTTAC
65 AGAGATTACGCTCAAAGGTTTTACAAATCTCGATC-TTAAAATAAATTCAACTCAAAAGACTTAC
20369082 GAATCTT
129 GAATCTT
20369089 ACTCAGAGGA
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
166 1 0.01
167 66 0.57
168 46 0.40
169 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (168 bp):
TTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTACAAGTCTTACCCAGAGGACTTA
GAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAAATTCAACTCAAAAGACTTACGA
ATCTTGCCTAAATGACTCACAGATTACACTTGAAGGTG
Found at i:20369128 original size:167 final size:167
Alignment explanation
Indices: 20368769--20369132 Score: 394
Period size: 167 Copynumber: 2.2 Consensus size: 167
20368759 AAGGTCTTAA
* * *
20368769 AGATTATGCTCGGAGTTTTTACAAATCTTGACTCTAAAACAAATTTAGCTCGAAAGACTTACAAG
1 AGATTATGCT-GGAGGTTTTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTACAAG
*
20368834 TCTTACCCAGAGGACTTAGAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAGATTC
65 TCTTACCCAGAGGACTTAGAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAAATTC
*** * * *
20368899 AACTTGCAAGACTTATGAATCTTGCCTAAATGACTCAC
130 AACTCAAAAGACTTACGAATCTTACCTAAAGGACTCAC
** * * * * *
20368937 AGATTACACTTGAAGGTGTTACAAATCTTGACTTTAAAATAAATTCAGCTCAAAAGACTTATGAA
1 AGATTATGC-TGGAGGTTTTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTA-CAA
** * ** *
20369002 -TCTTGTCCA-AGGACTTAGAGATTACTCTCGGAGGTTTTATAAATCTCGA-CTTTAAAATAAAT
64 GTCTTACCCAGAGGACTTAGAGATTACGCTCAAAGGTTTTACAAATCTCGATC-TTAAAATAAAT
* * ***
20369064 TCAAGTCAAAAGACTTACGAATCTTA-CTCAGAGGACTTGG
128 TCAACTCAAAAGACTTACGAATCTTACCT-AAAGGACTCAC
20369104 AGATTATGCGTGGAGGTTTTACAAATCTT
1 AGATTATGC-TGGAGGTTTTACAAATCTT
20369133 AGAGATTATG
Statistics
Matches: 159, Mismatches: 33, Indels: 9
0.79 0.16 0.04
Matches are distributed among these distances:
166 3 0.02
167 96 0.60
168 57 0.36
169 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (167 bp):
AGATTATGCTGGAGGTTTTACAAATCTTGACTCTAAAACAAATTCAGCTCAAAAGACTTACAAGT
CTTACCCAGAGGACTTAGAGATTACGCTCAAAGGTTTTACAAATCTCGATCTTAAAATAAATTCA
ACTCAAAAGACTTACGAATCTTACCTAAAGGACTCAC
Found at i:20369281 original size:84 final size:84
Alignment explanation
Indices: 20369130--20369284 Score: 233
Period size: 84 Copynumber: 1.8 Consensus size: 84
20369120 TTTTACAAAT
* * * *
20369130 CTTAGAGATTATGCCCAAAGGTCTTACAAATCGTAACTCTAAAATAGATTCAGCTTAGAAGATTT
1 CTTAGAGATTATACCCAAAGGTCTGACAAATCGTAACTCTAAAATAGATTCAGCTTAGAAAACTT
20369195 ATGAATATTGACCAAAAGA
66 ATGAATATTGACCAAAAGA
*
20369214 CTTAGAGATTATACCCAAAGGTCTGATAAATC-TCAACTCTAAAATAGATTCAGCTT-GAAAAAC
1 CTTAGAGATTATACCCAAAGGTCTGACAAATCGT-AACTCTAAAATAGATTCAGCTTAG-AAAAC
20369277 TTATGAAT
64 TTATGAAT
20369285 CTTACCAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (84 bp):
CTTAGAGATTATACCCAAAGGTCTGACAAATCGTAACTCTAAAATAGATTCAGCTTAGAAAACTT
ATGAATATTGACCAAAAGA
Found at i:20370620 original size:23 final size:24
Alignment explanation
Indices: 20370593--20370650 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
20370583 CAAAGATGCC
*
20370593 TTTTTTCTTTTC-TCTCTTTTTTT
1 TTTTTTCTTTTCTTCTCTTTTCTT
20370616 CTTTTTTCTTTTCTTCTCTTTTC-T
1 -TTTTTTCTTTTCTTCTCTTTTCTT
20370640 TTTTTTCTTTT
1 TTTTTTCTTTT
20370651 GCATGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 11 0.34
24 13 0.41
25 8 0.25
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTCTTTTCTTCTCTTTTCTT
Found at i:20376584 original size:17 final size:16
Alignment explanation
Indices: 20376562--20376608 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
20376552 CTTATTGAGC
*
20376562 TTTTTTTTTGTTTTGG
1 TTTTTTTTTTTTTTGG
*
20376578 TTTTTTTCCTTTTTTGG
1 TTTTTTT-TTTTTTTGG
20376595 TTTTTTTTGTTTTT
1 TTTTTTTT-TTTTT
20376609 CAATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGG
Found at i:20377792 original size:20 final size:21
Alignment explanation
Indices: 20377753--20377793 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
20377743 AAATTATTTA
20377753 TTTATTTGAAAAGACCTTTTT
1 TTTATTTGAAAAGACCTTTTT
20377774 TTTA-TTGAAAAGA--TTTTT
1 TTTATTTGAAAAGACCTTTTT
20377792 TT
1 TT
20377794 AATCATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTATTTGAAAAGACCTTTTT
Found at i:20377984 original size:19 final size:19
Alignment explanation
Indices: 20377944--20377983 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
20377934 GGGTTAAAAT
20377944 AAAAT-AAAATAAAATTAG
1 AAAATAAAAATAAAATTAG
20377962 AAAATAAAAATAAAA-TAG
1 AAAATAAAAATAAAATTAG
20377980 AAAA
1 AAAA
20377984 AGAAAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAATAAAAATAAAATTAG
Found at i:20377987 original size:24 final size:23
Alignment explanation
Indices: 20377939--20377989 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
20377929 AAAATGGGTT
*
20377939 AAAATAAAATAAAATAAAATTAG
1 AAAATAAAATAAAATAAAATAAG
20377962 AAAATAAAAATAAAATAGAAA-AAG
1 AAAAT-AAAATAAAATA-AAATAAG
20377986 AAAA
1 AAAA
20377990 CTTGCGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 17 0.68
25 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (23 bp):
AAAATAAAATAAAATAAAATAAG
Found at i:20377989 original size:18 final size:18
Alignment explanation
Indices: 20377944--20377989 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
20377934 GGGTTAAAAT
*
20377944 AAAATAAAATAAAATTAG
1 AAAAAAAAATAAAATTAG
20377962 AAAATAAAAATAAAA-TAG
1 AAAA-AAAAATAAAATTAG
20377980 AAAAAGAAAA
1 AAAAA-AAAA
20377990 CTTGCGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
19 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAAAAAATAAAATTAG
Found at i:20377989 original size:19 final size:19
Alignment explanation
Indices: 20377949--20377989 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20377939 AAAATAAAAT
*
20377949 AAAATAAAATTAGAAAATA
1 AAAATAAAATTAGAAAAGA
20377968 AAAATAAAA-TAGAAAAAGA
1 AAAATAAAATTAG-AAAAGA
20377987 AAA
1 AAA
20377990 CTTGCGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAATAAAATTAGAAAAGA
Found at i:20380932 original size:2 final size:2
Alignment explanation
Indices: 20380921--20380955 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20380911 GAAAGCTGTA
20380921 AT AT -T 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
20380956 TTTAAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20381772 original size:24 final size:24
Alignment explanation
Indices: 20381745--20381792 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20381735 ATAAAATCTT
*
20381745 GATATATATAA-TTTTGCTAAATAA
1 GATATATA-AATTTTTGATAAATAA
*
20381769 GATATTTAAATTTTTGATAAATAA
1 GATATATAAATTTTTGATAAATAA
20381793 AGTTACCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (24 bp):
GATATATAAATTTTTGATAAATAA
Found at i:20382057 original size:2 final size:2
Alignment explanation
Indices: 20382050--20382082 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20382040 AATTAGATTC
*
20382050 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20382083 CACACACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20386203 original size:6 final size:6
Alignment explanation
Indices: 20386192--20386228 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
20386182 CCAAAATTTA
* *
20386192 CACCAT CACCAT CACCAT CTCCAT CACCAT CATCAT C
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT C
20386229 TAGACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.30, C:0.49, G:0.00, T:0.22
Consensus pattern (6 bp):
CACCAT
Found at i:20386215 original size:18 final size:18
Alignment explanation
Indices: 20386194--20386229 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20386184 AAAATTTACA
20386194 CCATCACCATCACCATCT
1 CCATCACCATCACCATCT
*
20386212 CCATCACCATCATCATCT
1 CCATCACCATCACCATCT
20386230 AGACTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25
Consensus pattern (18 bp):
CCATCACCATCACCATCT
Found at i:20389932 original size:19 final size:20
Alignment explanation
Indices: 20389908--20389945 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20389898 AACAACAAAA
*
20389908 AAAATTA-AAATTCATATAC
1 AAAATTATAAATTAATATAC
20389927 AAAATTATAAATTAATATA
1 AAAATTATAAATTAATATA
20389946 TAACACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTATAAATTAATATAC
Found at i:20390291 original size:38 final size:40
Alignment explanation
Indices: 20390214--20390296 Score: 134
Period size: 39 Copynumber: 2.1 Consensus size: 40
20390204 CAATCTTTGT
*
20390214 CCACCTTTCCCCCCAACATCCCACCACACCCAATCCCTCC
1 CCACCTTTCCCCCCAACACCCCACCACACCCAATCCCTCC
*
20390254 CCACC-TTCCCCCCAACGCCCCACCACACCCAAT-CCTCC
1 CCACCTTTCCCCCCAACACCCCACCACACCCAATCCCTCC
20390292 CCACC
1 CCACC
20390297 CCATCCAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 10 0.24
39 26 0.63
40 5 0.12
ACGTcount: A:0.22, C:0.65, G:0.01, T:0.12
Consensus pattern (40 bp):
CCACCTTTCCCCCCAACACCCCACCACACCCAATCCCTCC
Found at i:20390293 original size:19 final size:19
Alignment explanation
Indices: 20390233--20390315 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
20390223 CCCCCAACAT
20390233 CCCACCACACCCAATCCCTC
1 CCCACCACACCCAAT-CCTC
* * *
20390253 CCCACCTTCCCCCCAA--CGC
1 CCCACC--ACACCCAATCCTC
20390272 CCCACCACACCCAATCCTC
1 CCCACCACACCCAATCCTC
* *
20390291 CCCACCCCATCCAATCTCTC
1 CCCACCACACCCAATC-CTC
20390311 CCCAC
1 CCCAC
20390316 GTGCCTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 6 0.12
19 24 0.48
20 14 0.28
22 6 0.12
ACGTcount: A:0.22, C:0.65, G:0.01, T:0.12
Consensus pattern (19 bp):
CCCACCACACCCAATCCTC
Found at i:20390315 original size:39 final size:38
Alignment explanation
Indices: 20390233--20390304 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
20390223 CCCCCAACAT
*
20390233 CCCACCACACCCAATCCCTCCCCACCTTCCCCCCAACGC
1 CCCACCACACCCAATCCCTCCCCACC-TCCACCCAACGC
*
20390272 CCCACCACACCCAAT-CCTCCCCACC-CCATCCAA
1 CCCACCACACCCAATCCCTCCCCACCTCCACCCAA
20390305 TCTCTCCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 6 0.19
38 10 0.32
39 15 0.48
ACGTcount: A:0.24, C:0.65, G:0.01, T:0.10
Consensus pattern (38 bp):
CCCACCACACCCAATCCCTCCCCACCTCCACCCAACGC
Found at i:20397685 original size:17 final size:17
Alignment explanation
Indices: 20397652--20397710 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
20397642 CTAGATAAGT
*
20397652 AAAAGACTAAA-ACATAA
1 AAAAGA-TAAATAAATAA
20397669 AAAAGATAAATAAATAA
1 AAAAGATAAATAAATAA
*
20397686 ATAAA-ACAAATAAGATATA
1 A-AAAGATAAATAA-ATA-A
20397705 AAAAGA
1 AAAAGA
20397711 AAAGTTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 4 0.11
17 19 0.54
18 9 0.26
19 3 0.09
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (17 bp):
AAAAGATAAATAAATAA
Found at i:20398680 original size:18 final size:19
Alignment explanation
Indices: 20398647--20398685 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20398637 TTTATTGAGC
*
20398647 TTTTCTTTTTTGTTTTTGT
1 TTTTCTCTTTTGTTTTTGT
20398666 TTTTCTCTTTT-TTTTTGT
1 TTTTCTCTTTTGTTTTTGT
20398684 TT
1 TT
20398686 ATTTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (19 bp):
TTTTCTCTTTTGTTTTTGT
Found at i:20399872 original size:20 final size:21
Alignment explanation
Indices: 20399839--20399877 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20399829 GATAAAAATT
20399839 CTTTATTTATTTGAAAAGACC
1 CTTTATTTATTTGAAAAGACC
*
20399860 CTTTTTTTA-TTGAAAAGA
1 CTTTATTTATTTGAAAAGA
20399878 GTTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (21 bp):
CTTTATTTATTTGAAAAGACC
Found at i:20399929 original size:18 final size:18
Alignment explanation
Indices: 20399908--20399947 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
20399898 ATTTTGAAAA
20399908 TTTTATTTGCAAAA-ATTT
1 TTTTATTTG-AAAAGATTT
*
20399926 TTTTGTTTGAAAAGATTT
1 TTTTATTTGAAAAGATTT
20399944 TTTT
1 TTTT
20399948 TAGAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (18 bp):
TTTTATTTGAAAAGATTT
Found at i:20400032 original size:6 final size:6
Alignment explanation
Indices: 20400023--20400080 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 6
20400013 AAAAATGGGT
*
20400023 TAAAAA T-AAAA T-AAAA T-AAAA TAAAAT TAGAAAA TAAAAA T-AAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA TAAAAA TAAAAA
*
20400068 TAGAAAA GAAAAA
1 TA-AAAA TAAAAA
20400081 ACCTGCGATC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
5 20 0.44
6 15 0.33
7 10 0.22
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:20400033 original size:5 final size:5
Alignment explanation
Indices: 20400025--20400069 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
20400015 AAATGGGTTA
20400025 AAAAT AAAAT AAAAT AAAAT AAAATT AGAAAAT AAAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAA-T --AAAAT -AAAAT AAAAT A
20400070 GAAAAGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 25 0.69
6 6 0.17
7 1 0.03
8 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:20400058 original size:18 final size:17
Alignment explanation
Indices: 20400025--20400079 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
20400015 AAATGGGTTA
20400025 AAAATAAAAT--AAAAT
1 AAAATAAAATAGAAAAT
20400040 AAAATAAAATTAGAAAAT
1 AAAATAAAA-TAGAAAAT
*
20400058 AAAAATAAAATAGAAAAG
1 -AAAATAAAATAGAAAAT
20400076 AAAA
1 AAAA
20400080 AACCTGCGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 4 0.11
18 12 0.34
19 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAGAAAAT
Found at i:20400080 original size:24 final size:22
Alignment explanation
Indices: 20400030--20400079 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
20400020 GGTTAAAAAT
20400030 AAAATAAAATAAAATAAAATTAG
1 AAAATAAAATAAAATAAAA-TAG
20400053 AAAATAAAAATAAAATAGAAA-AG
1 AAAAT-AAAATAAAATA-AAATAG
20400076 AAAA
1 AAAA
20400080 AACCTGCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
24 11 0.44
25 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAG
Found at i:20400081 original size:19 final size:19
Alignment explanation
Indices: 20400035--20400081 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
20400025 AAAATAAAAT
*
20400035 AAAATAAAATAAAATTAGA
1 AAAAAAAAATAAAATTAGA
*
20400054 AAATAAAAATAAAA-TAGA
1 AAAAAAAAATAAAATTAGA
20400072 AAAGAAAAAA
1 AAA-AAAAAA
20400082 CCTGCGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (19 bp):
AAAAAAAAATAAAATTAGA
Found at i:20404151 original size:2 final size:2
Alignment explanation
Indices: 20404144--20404174 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20404134 AATTAGATTC
*
20404144 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20404175 CATACACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20417998 original size:4 final size:4
Alignment explanation
Indices: 20417989--20418013 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20417979 TTTTTATTTG
20417989 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
20418014 TTGTTTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:20419576 original size:18 final size:17
Alignment explanation
Indices: 20419551--20419586 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
20419541 AATTTATTTT
*
20419551 ATTTTATAAAATTTAAA
1 ATTTTATAAAAATTAAA
20419568 ATTTATATAAAAATTAAA
1 ATTT-TATAAAAATTAAA
20419586 A
1 A
20419587 AAATAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTTATAAAAATTAAA
Found at i:20424792 original size:24 final size:24
Alignment explanation
Indices: 20424765--20424820 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 24
20424755 CAATAGTCCA
20424765 ACATCATCTGATCTAATATCCACC
1 ACATCATCTGATCTAATATCCACC
*
20424789 ACATCGGCTTCTGATCTAATATCCACC
1 ACAT---CATCTGATCTAATATCCACC
20424816 ACATC
1 ACATC
20424821 TGCTTCTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.18
27 23 0.82
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.29
Consensus pattern (24 bp):
ACATCATCTGATCTAATATCCACC
Found at i:20424802 original size:27 final size:27
Alignment explanation
Indices: 20424771--20424856 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
20424761 TCCAACATCA
*
20424771 TCTGATCTAATATCCACCACATCGGCT
1 TCTGATCTAATATCCACCACATCTGCT
20424798 TCTGATCTAATATCCACCACATCTGCT
1 TCTGATCTAATATCCACCACATCTGCT
* * * *
20424825 TCTGACCTTATATCCACTACCTCTGCT
1 TCTGATCTAATATCCACCACATCTGCT
20424852 TCTGA
1 TCTGA
20424857 CGTTATATCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (27 bp):
TCTGATCTAATATCCACCACATCTGCT
Found at i:20424857 original size:27 final size:27
Alignment explanation
Indices: 20424771--20424868 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
20424761 TCCAACATCA
* *
20424771 TCTGATCTAATATCCACCACATCGGCT
1 TCTGACCTAATATCCACCACATCTGCT
*
20424798 TCTGATCTAATATCCACCACATCTGCT
1 TCTGACCTAATATCCACCACATCTGCT
* * *
20424825 TCTGACCTTATATCCACTACCTCTGCT
1 TCTGACCTAATATCCACCACATCTGCT
* *
20424852 TCTGACGTTATATCCAC
1 TCTGACCTAATATCCAC
20424869 TATCTCTGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (27 bp):
TCTGACCTAATATCCACCACATCTGCT
Found at i:20424875 original size:27 final size:27
Alignment explanation
Indices: 20424771--20424879 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 27
20424761 TCCAACATCA
* * * * *
20424771 TCTGATCTAATATCCACCACATCGGCT
1 TCTGACCTTATATCCACTACCTCTGCT
* * * *
20424798 TCTGATCTAATATCCACCACATCTGCT
1 TCTGACCTTATATCCACTACCTCTGCT
20424825 TCTGACCTTATATCCACTACCTCTGCT
1 TCTGACCTTATATCCACTACCTCTGCT
* *
20424852 TCTGACGTTATATCCACTATCTCTGCT
1 TCTGACCTTATATCCACTACCTCTGCT
20424879 T
1 T
20424880 TTTTTACCAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.36
Consensus pattern (27 bp):
TCTGACCTTATATCCACTACCTCTGCT
Found at i:20428815 original size:20 final size:21
Alignment explanation
Indices: 20428792--20428831 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
20428782 TATTAAAAAA
20428792 ATAAAATTTT-AATTAAATTT
1 ATAAAATTTTAAATTAAATTT
*
20428812 ATAAACTTTTCAAATTAAAT
1 ATAAAATTTT-AAATTAAAT
20428832 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAATTTTAAATTAAATTT
Found at i:20429759 original size:17 final size:17
Alignment explanation
Indices: 20429724--20429758 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20429714 TAGTAAAATC
*
20429724 ATATTTTAATAATAAAA
1 ATATTTTAAAAATAAAA
20429741 ATATTTTAAAAAATAAAA
1 ATATTTT-AAAAATAAAA
20429759 TTAATTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTTTAAAAATAAAA
Found at i:20432231 original size:2 final size:2
Alignment explanation
Indices: 20432218--20432249 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20432208 GAACCACTCG
*
20432218 AT AT AT AC 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
20432250 CTTTGAGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20434494 original size:38 final size:38
Alignment explanation
Indices: 20434452--20434527 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
20434442 AAAACTTCAT
**
20434452 TAGCAGAATTAGATGGAAGTTGGAAGTTGTTGCTTTGA
1 TAGCAGAATTAGATGGAAGTTGGAAGTAATTGCTTTGA
20434490 TAGCAGAATTAGATGGAAGTTGGAAGTAATTGCTTTGA
1 TAGCAGAATTAGATGGAAGTTGGAAGTAATTGCTTTGA
20434528 ATACGCAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (38 bp):
TAGCAGAATTAGATGGAAGTTGGAAGTAATTGCTTTGA
Found at i:20434824 original size:17 final size:18
Alignment explanation
Indices: 20434802--20434838 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20434792 TTCACGGACA
*
20434802 AAAAAATTATTAAT-TAT
1 AAAAAATTATAAATATAT
20434819 AAAAAATTATAAATATAT
1 AAAAAATTATAAATATAT
20434837 AA
1 AA
20434839 CTATTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAATTATAAATATAT
Found at i:20435393 original size:26 final size:25
Alignment explanation
Indices: 20435335--20435393 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 25
20435325 ATATAAAATT
20435335 ATATTTATTAAGATATTTTAATAAA
1 ATATTTATTAAGATATTTTAATAAA
*
20435360 AT-TATTATTTA-ATATTTTAATTTAAA
1 ATAT-TTATTAAGATATTTTAA--TAAA
20435386 ATATTTAT
1 ATATTTAT
20435394 CATAACATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 10 0.34
25 8 0.28
26 10 0.34
27 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATATTTATTAAGATATTTTAATAAA
Found at i:20435987 original size:57 final size:58
Alignment explanation
Indices: 20435910--20436067 Score: 180
Period size: 57 Copynumber: 2.7 Consensus size: 58
20435900 TGCTTTTGTA
20435910 CAAGAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTCT-G-AAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTCTAGAAAAC-TTAATTT
* * * * *
20435967 CGAGAAAAATTGGTATTTTCAAC-TTTTCCTCAAAA-ATGTTTTTTAGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTTCC-CAAAATAT-TTTTCTAGAAAACTTAATTT
* * *
20436025 CAAGGAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTT
1 CAAGAAAAATTGATACTTTCAACTTTT-TCCCAAAATATTTTT
20436068 TTTGAAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
56 8 0.10
57 30 0.36
58 26 0.31
59 15 0.18
60 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTCTAGAAAACTTAATTT
Found at i:20436035 original size:58 final size:56
Alignment explanation
Indices: 20435910--20436068 Score: 187
Period size: 58 Copynumber: 2.8 Consensus size: 56
20435900 TGCTTTTGTA
*
20435910 CAAGAAAAATTGATACTTTCAACTTTTTCC-CAAAATATTTTTCTGAAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAA-ATTTTTTTGAAACTTTAATTT
* * * *
20435967 CGAGAAAAATTGGTATTTTCAACTTTTCCTCAAAAATGTTTTTTAGAAAAC-TTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTT-G-AAACTTTAATTT
* *
20436025 CAAGGAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTT
20436069 TTGAAATTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
56 8 0.09
57 30 0.34
58 45 0.52
59 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.43
Consensus pattern (56 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAACTTTAATTT
Found at i:20436151 original size:3 final size:3
Alignment explanation
Indices: 20436143--20436177 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20436133 CTAATCAATA
20436143 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20436178 ATAAGAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20436947 original size:3 final size:3
Alignment explanation
Indices: 20436939--20437139 Score: 55
Period size: 3 Copynumber: 63.7 Consensus size: 3
20436929 AACCAACCAA
20436939 AAT AAT AAT AAT AAT AAT AAT ATAT ACATT AAT CAAT AA- ATAT AA-
1 AAT AAT AAT AAT AAT AAT AAT A-AT A-A-T AAT -AAT AAT A-AT AAT
* * *
20436984 AAA AAT ATT GAT AGAT AAAT AAT AAT AAT AAT AGAT AAGT -AT AA- AA-
1 AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT
* *
20437030 AAT -AT ACATT AAT AAAT AAAT AAT AA- AA- AAT AAT ATT AAT GGAT
1 AAT AAT A-A-T AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
20437074 AACT AAT AAA AAT ATAT ATT ATT AGAT -AT AAT ATAT ATAT AAAT AAT
1 AA-T AAT AAT AAT A-AT AAT AAT A-AT AAT AAT A-AT A-AT -AAT AAT
*
20437121 -AT AAA AAT AA- AGAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AA
20437140 AACTAAAAAT
Statistics
Matches: 155, Mismatches: 16, Indels: 54
0.69 0.07 0.24
Matches are distributed among these distances:
2 19 0.12
3 86 0.55
4 44 0.28
5 6 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20437029 original size:44 final size:47
Alignment explanation
Indices: 20436974--20437064 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
20436964 ACATTAATCA
* * *
20436974 ATAAATATAAAAAA-AT-ATTGATAGATAAATAAT-AATAATAATAG
1 ATAAATATAAAAAATATAATTAATAAATAAATAATAAAAAATAATAG
*
20437018 ATAAGTATAAAAAATATACATTAATAAATAAATAATAAAAAATAATA
1 ATAAATATAAAAAATATA-ATTAATAAATAAATAATAAAAAATAATA
20437065 TTAATGGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 13 0.33
45 2 0.05
47 15 0.38
48 9 0.23
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (47 bp):
ATAAATATAAAAAATATAATTAATAAATAAATAATAAAAAATAATAG
Found at i:20437036 original size:71 final size:71
Alignment explanation
Indices: 20436939--20437087 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 71
20436929 AACCAACCAA
* * * *
20436939 AATAATAATAATAATAATAATATATACATTAATCAATAAAT-AT-AAAAA-AATATTGATAGATA
1 AATAATAATAATAATAAAAAAATATACATTAATAAATAAATAATAAAAAATAATATTAATAGATA
20437001 AATAAT
66 AATAAT
*
20437007 AATAATAATAGATAAGTATAAAAAATATACATTAATAAATAAATAATAAAAAATAATATTAATGG
1 AATAATAATA-ATAA-TA-AAAAAATATACATTAATAAATAAATAATAAAAAATAATATTAATAG
*
20437072 ATAACTAAT
63 ATAAATAAT
*
20437081 AAAAATA
1 AATAATA
20437088 TATATTATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
68 10 0.15
69 4 0.06
70 2 0.03
71 22 0.32
72 2 0.03
73 5 0.07
74 23 0.34
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (71 bp):
AATAATAATAATAATAAAAAAATATACATTAATAAATAAATAATAAAAAATAATATTAATAGATA
AATAAT
Found at i:20437048 original size:27 final size:27
Alignment explanation
Indices: 20436998--20437085 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
20436988 ATATTGATAG
* * * * *
20436998 ATAAATAATAATAATAATAGATAAGT-
1 ATAAAAAATAACATTAATAAATAAATA
20437024 ATAAAAAATATACATTAATAAATAAATA
1 ATAAAAAATA-ACATTAATAAATAAATA
* ** *
20437052 ATAAAAAATAATATTAATGGATAACTA
1 ATAAAAAATAACATTAATAAATAAATA
20437079 ATAAAAA
1 ATAAAAA
20437086 TATATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.18
27 32 0.63
28 10 0.20
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (27 bp):
ATAAAAAATAACATTAATAAATAAATA
Found at i:20437075 original size:54 final size:56
Alignment explanation
Indices: 20436998--20437122 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 56
20436988 ATATTGATAG
* * *
20436998 ATAAATAATAATAATAATAGATAAGT-ATAAAAAATATACATTAATAAATA-AATA-
1 ATAAAAAATAATATTAATAGATAACTAAT-AAAAATATACATTAATAAATATAATAT
* * * *
20437052 ATAAAAAATAATATTAATGGATAACTAATAAAAATATATATTATTAGATATAATAT
1 ATAAAAAATAATATTAATAGATAACTAATAAAAATATACATTAATAAATATAATAT
*
20437108 ATATATAAATAATAT
1 ATA-AAAAATAATAT
20437123 AAAAATAAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
54 40 0.68
55 6 0.10
56 3 0.05
57 10 0.17
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (56 bp):
ATAAAAAATAATATTAATAGATAACTAATAAAAATATACATTAATAAATATAATAT
Found at i:20437092 original size:27 final size:27
Alignment explanation
Indices: 20437027--20437141 Score: 85
Period size: 27 Copynumber: 4.1 Consensus size: 27
20437017 GATAAGTATA
*
20437027 AAAAATATACATTAATAAATAAATAAT
1 AAAAATATATATTAATAAATAAATAAT
** *
20437054 AAAAA-ATAATATTAATGGATAACTAAT
1 AAAAATAT-ATATTAATAAATAAATAAT
*
20437081 AAAAATATATATTATTAGATATAATATATAT
1 AAAAATATATATTAATA-A-ATAA-ATA-AT
*
20437112 ATAAATA-ATA-TAA-AAATAAAGATAAT
1 AAAAATATATATTAATAAAT-AA-ATAAT
20437138 AAAA
1 AAAA
20437142 CTAAAAATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
26 9 0.13
27 38 0.55
28 3 0.04
29 6 0.09
30 5 0.07
31 8 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAAATATATATTAATAAATAAATAAT
Found at i:20437329 original size:9 final size:8
Alignment explanation
Indices: 20437299--20437328 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20437289 CAACTGGATA
*
20437299 TTTTTTGT
1 TTTTTTAT
20437307 TTTTTTAT
1 TTTTTTAT
20437315 TTTTTTAT
1 TTTTTTAT
20437323 TTTTTT
1 TTTTTT
20437329 TGTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:20437481 original size:41 final size:41
Alignment explanation
Indices: 20437391--20437710 Score: 330
Period size: 41 Copynumber: 7.8 Consensus size: 41
20437381 AAAAAAACAA
* * *
20437391 AGCTCCTCTAAACAGAGGCTCCATGACCTTG-AAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
20437431 GGCTTCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
20437472 GGCTCCTCTAATCAGAGGCTTAACGATTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
20437513 TGCTCCTCTAAATAAAGGCTCAACGAC-TT---AAA-CAA-
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
20437548 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* *
20437589 AAAGCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAATTAA
1 --AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAA--AT
* * **
20437634 AGCTCCTCTAAACAAAGGCTCAACAACTTTCGAAAGGTAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAAT
* *
20437676 TGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAA
1 AGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAA
20437711 GGTAAATACT
Statistics
Matches: 238, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
35 24 0.10
36 4 0.02
37 3 0.01
39 3 0.01
40 30 0.13
41 67 0.28
42 34 0.14
43 65 0.27
44 7 0.03
45 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (41 bp):
AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:20437607 original size:43 final size:44
Alignment explanation
Indices: 20437541--20437710 Score: 231
Period size: 43 Copynumber: 4.0 Consensus size: 44
20437531 CTCAACGACT
* *
20437541 TAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAA
1 TAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAAAA
**
20437584 TAAATAAAGCTCCTCTAAACAGAGGCTCAATGACTTT-GAAAAA
1 TAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAAAA
* * **
20437627 TAATTAAAGCTCCTCTAAACAAAGGCTCAACAACTTTCGAAAGG
1 TAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAAAA
*
20437671 TAAAT--TGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAA
1 TAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAA
20437711 GGTAAATACT
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 33 0.29
43 74 0.64
44 8 0.07
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (44 bp):
TAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTCGAAAAA
Found at i:20438763 original size:24 final size:25
Alignment explanation
Indices: 20438731--20438783 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
20438721 TGAGTCTTCA
*
20438731 TTTTTCA-TTCACTTTTCCTTTTTT
1 TTTTTCATTTCACTTTTCCTCTTTT
* *
20438755 TTTTTCATTTCATTTTTTCTCTTTT
1 TTTTTCATTTCACTTTTCCTCTTTT
20438780 TTTT
1 TTTT
20438784 CAAGCATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTCATTTCACTTTTCCTCTTTT
Found at i:20462338 original size:31 final size:31
Alignment explanation
Indices: 20462291--20462349 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20462281 AGCTGACTTG
*
20462291 GTAGGAGTAACCTATGTAATAATTTATCATA
1 GTAGGAATAACCTATGTAATAATTTATCATA
* *
20462322 GTAGGAATAACTTATGTAATACTTTATC
1 GTAGGAATAACCTATGTAATAATTTATC
20462350 TTAATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (31 bp):
GTAGGAATAACCTATGTAATAATTTATCATA
Found at i:20463343 original size:189 final size:190
Alignment explanation
Indices: 20463019--20463395 Score: 573
Period size: 189 Copynumber: 2.0 Consensus size: 190
20463009 AATATACAAC
*
20463019 ATATACTCACACCTTTCCTATTTTCTCTCTTCTTCTTTTTTTTGATTTAGAATGATTTCTATTTG
1 ATATACTCACACCTTTCCCATTTTCTCTCTTCTTCTTTTTTTTGATTTAGAATGATTTCTATTTG
* * * **
20463084 TGAATAAGTGTGAAATTTTAACACCTTTCCTATTTTGTTTTCTCACTTTTCTTTCATACAAACCA
66 TCAATAAGTGTGAAAATTTAACACCTTTCCTATTTTGTTTTCTCACTTTTCTTTCAAACAAAAAA
* *
20463149 CATTCACAA-TTCATTTTCTTTCTATATTTCCATTCCCTCTATTCATCCTTTTACTTTTAA
131 CATTCAAAATTTC-TTTTCTTTCTACATTTCCATTCCCTCTATTCATCCTTTTACTTTTAA
* *
20463209 ATATACTCACACCTTTCCCATTTTCTCTCTT-TT-TTTCTTTTTGATTTAGAGTGATTTGTATTT
1 ATATACTCACACCTTTCCCATTTTCTCTCTTCTTCTTT-TTTTTGATTTAGAATGATTTCTATTT
* **
20463272 GTCAATAAGTGTGAAAATTTGACATGTTTCCTATTTT-TTTTCTCACTTTTCTTTCAAACAAAAA
65 GTCAATAAGTGTGAAAATTTAACACCTTTCCTATTTTGTTTTCTCACTTTTCTTTCAAAC-AAAA
*
20463336 AACATTCAAAATTTCTTTTCTTTCTACATTTCCATTTCCTCTATTCATCCTTTTACTTTT
129 AACATTCAAAATTTCTTTTCTTTCTACATTTCCATTCCCTCTATTCATCCTTTTACTTTT
20463396 CCATTATACC
Statistics
Matches: 170, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
188 24 0.14
189 113 0.66
190 33 0.19
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (190 bp):
ATATACTCACACCTTTCCCATTTTCTCTCTTCTTCTTTTTTTTGATTTAGAATGATTTCTATTTG
TCAATAAGTGTGAAAATTTAACACCTTTCCTATTTTGTTTTCTCACTTTTCTTTCAAACAAAAAA
CATTCAAAATTTCTTTTCTTTCTACATTTCCATTCCCTCTATTCATCCTTTTACTTTTAA
Found at i:20465218 original size:3 final size:3
Alignment explanation
Indices: 20465205--20465244 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
20465195 GATTTTATTT
20465205 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20465245 TATACATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:20465230 original size:20 final size:20
Alignment explanation
Indices: 20465205--20465244 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20465195 GATTTTATTT
20465205 ATAATAA-AATAATAATAATA
1 ATAATAATAA-AATAATAATA
20465225 ATAATAATAAAATAATAATA
1 ATAATAATAAAATAATAATA
20465245 TATACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAATAATAAAATAATAATA
Found at i:20465234 original size:23 final size:23
Alignment explanation
Indices: 20465205--20465308 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
20465195 GATTTTATTT
20465205 ATAATAAAATAATAATAATAATA
1 ATAATAAAATAATAATAATAATA
20465228 ATAATAAAATAATAATATATACATTA
1 ATAATAAAATAATAATA-ATA-A-TA
* * * *
20465254 ATCGATAAATATAA-AAAAATATTG
1 AT-AATAAA-ATAATAATAATAATA
*
20465278 ATAGAT-AAATAAAAATAATAATA
1 ATA-ATAAAATAATAATAATAATA
20465301 ATAGATAA
1 ATA-ATAA
20465309 GTATAAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.06
23 32 0.49
24 9 0.14
25 1 0.02
26 7 0.11
27 8 0.12
28 4 0.06
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
ATAATAAAATAATAATAATAATA
Found at i:20465280 original size:20 final size:20
Alignment explanation
Indices: 20465257--20465294 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20465247 TACATTAATC
20465257 GATAAATATAA-AAAAATATT
1 GATAAATA-AATAAAAATATT
*
20465277 GATAGATAAATAAAAATA
1 GATAAATAAATAAAAATA
20465295 ATAATAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
GATAAATAAATAAAAATATT
Found at i:20465314 original size:47 final size:46
Alignment explanation
Indices: 20465229--20465350 Score: 122
Period size: 47 Copynumber: 2.5 Consensus size: 46
20465219 ATAATAATAA
* *
20465229 TAATAAAATAATAATATATACATTAATCGATAAATATAAAAAAATATTG-A-
1 TAAT-AAATAAAAATA-ATA-A-TAATAGATAAATAT-AAAAAATA-TGCAT
*
20465279 TAGATAAATAAAAATAATAATAATAGATAAGTATAAAAAATATGCAT
1 TA-ATAAATAAAAATAATAATAATAGATAAATATAAAAAATATGCAT
*
20465326 TAATAAATAAATAATAAAAATAATA
1 TAATAAATAAA-AATAATAATAATA
20465351 TTAATGGATA
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
45 2 0.03
46 18 0.28
47 26 0.41
48 1 0.02
49 3 0.05
50 12 0.19
51 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (46 bp):
TAATAAATAAAAATAATAATAATAGATAAATATAAAAAATATGCAT
Found at i:20465320 original size:23 final size:23
Alignment explanation
Indices: 20465267--20465320 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
20465257 GATAAATATA
* *
20465267 AAAAAATATTGATAGATAAATA-
1 AAAAAATAATAATAGATAAATAT
*
20465289 AAAATAATAATAATAGATAAGTAT
1 AAAA-AATAATAATAGATAAATAT
20465313 AAAAAATA
1 AAAAAATA
20465321 TGCATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAAATAATAATAGATAAATAT
Found at i:20466929 original size:23 final size:22
Alignment explanation
Indices: 20466885--20466935 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
20466875 TTTTTTTTTA
* *
20466885 CTTTTTATAATTGACCTGCTTT
1 CTTTTTATAATTGAACTACTTT
*
20466907 CTTTCTTATCATTGAACTACTTT
1 CTTT-TTATAATTGAACTACTTT
*
20466930 TTTTTT
1 CTTTTT
20466936 TTTTTCCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (22 bp):
CTTTTTATAATTGAACTACTTT
Found at i:20468253 original size:2 final size:2
Alignment explanation
Indices: 20468246--20468278 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20468236 AACAAGTAGA
20468246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20468279 ATTATCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20469304 original size:31 final size:31
Alignment explanation
Indices: 20469257--20469315 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20469247 CGCTGACTTG
*
20469257 GTAGGAGTAACCTATGTAATAATTTATCATA
1 GTAGGAATAACCTATGTAATAATTTATCATA
* *
20469288 GTAGGAATAACTTATGTAATACTTTATC
1 GTAGGAATAACCTATGTAATAATTTATC
20469316 TTAATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (31 bp):
GTAGGAATAACCTATGTAATAATTTATCATA
Found at i:20469751 original size:14 final size:15
Alignment explanation
Indices: 20469720--20469774 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
20469710 CTTCAAGGCC
20469720 AGATAGAAAATAGAA
1 AGATAGAAAATAGAA
*
20469735 AGATA-AAAATTGGAA
1 AGATAGAAAA-TAGAA
20469750 GAGA-AGAAAAGTAGAA
1 -AGATAGAAAA-TAGAA
20469766 AGAT-GAAAA
1 AGATAGAAAA
20469775 ACATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 4 0.12
15 18 0.55
16 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (15 bp):
AGATAGAAAATAGAA
Found at i:20470175 original size:18 final size:19
Alignment explanation
Indices: 20470154--20470211 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 19
20470144 AAGTATGTAT
*
20470154 AAAATATGAAATACAATAA
1 AAAATATGAAATACAAAAA
*
20470173 AAAATATAAAATAC-AAAA
1 AAAATATGAAATACAAAAA
20470191 AAAATATGAAATA-AAAAA
1 AAAATATGAAATACAAAAA
20470209 AAA
1 AAA
20470212 CAAAACAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAATATGAAATACAAAAA
Found at i:20470178 original size:19 final size:18
Alignment explanation
Indices: 20470154--20470211 Score: 91
Period size: 19 Copynumber: 3.2 Consensus size: 18
20470144 AAGTATGTAT
20470154 AAAATATGAAATACAATAA
1 AAAATATGAAATACAA-AA
*
20470173 AAAATATAAAATACAAAA
1 AAAATATGAAATACAAAA
20470191 AAAATATGAAATA-AAAA
1 AAAATATGAAATACAAAA
20470208 AAAA
1 AAAA
20470212 CAAAACAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.22
18 14 0.38
19 15 0.41
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAATATGAAATACAAAA
Found at i:20470228 original size:37 final size:37
Alignment explanation
Indices: 20470154--20470231 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 37
20470144 AAGTATGTAT
* *
20470154 AAAATATGAAATACAATAAAAAATATAAAATACAAAA
1 AAAATATGAAATACAATAAAAAACATAAAAAACAAAA
20470191 AAAATATGAAATA-AA-AAAAAACA-AAACAGAACAAAA
1 AAAATATGAAATACAATAAAAAACATAAA-A-AACAAAA
20470227 AAAAT
1 AAAAT
20470232 CAAGGATGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 3 0.08
35 8 0.22
36 13 0.35
37 13 0.35
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (37 bp):
AAAATATGAAATACAATAAAAAACATAAAAAACAAAA
Found at i:20470303 original size:29 final size:29
Alignment explanation
Indices: 20470271--20470329 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
20470261 CCACTGCCAC
*
20470271 CACCCCATCCTTCTGATCACCAGACCCTA
1 CACCCCATCCTTCTAATCACCAGACCCTA
*
20470300 CACCCCATCCTTCTAATCACCAGACTCTA
1 CACCCCATCCTTCTAATCACCAGACCCTA
20470329 C
1 C
20470330 CCTCCACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.05, T:0.22
Consensus pattern (29 bp):
CACCCCATCCTTCTAATCACCAGACCCTA
Found at i:20471383 original size:26 final size:27
Alignment explanation
Indices: 20471323--20471373 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
20471313 GTTAATTTTT
20471323 AAAATAAACTTTAAAAACAATAATATA
1 AAAATAAACTTTAAAAACAATAATATA
* *
20471350 AAAATAAA-TTTAATAATAATAATA
1 AAAATAAACTTTAAAAACAATAATA
20471374 AACTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATAAACTTTAAAAACAATAATATA
Found at i:20471809 original size:12 final size:12
Alignment explanation
Indices: 20471789--20471822 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20471779 AATTTTAATT
20471789 TTAATTAAAAAAA
1 TTAA-TAAAAAAA
*
20471802 TTAATAAAACAA
1 TTAATAAAAAAA
20471814 TTAATAAAA
1 TTAATAAAA
20471823 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAATAAAAAAA
Found at i:20472260 original size:195 final size:195
Alignment explanation
Indices: 20471909--20472262 Score: 620
Period size: 195 Copynumber: 1.8 Consensus size: 195
20471899 TTTAGACCTC
* * *
20471909 CCAAAGATTAGATTCTAAAAGTATTTCGAGTAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAGA
1 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGA
*
20471974 ATTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATT
66 ATTCTTTTAATGTTACCAACGTACTGAAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATT
*
20472039 TATTTTTTTTCGAGAATAAATTTTTTTTAACATGACATTTTCTTATGAAAAATAAATTCGAGCCT
131 TATTTTTTCTCGAGAATAAATTTTTTTTAACATGACATTTTCTTATGAAAAATAAATTCGAGCCT
*
20472104 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTATGTGAGAAAGA
1 CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGA
* *
20472169 GTTCTTTTAATGTTACCAACGTACTGAAACATTTTAAGAATTATTTCAATAAAAAGGTTTTGATT
66 ATTCTTTTAATGTTACCAACGTACTGAAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATT
*
20472234 TA-TTTTTCTCGAGAATAATTTTTTTTTAA
131 TATTTTTTCTCGAGAATAAATTTTTTTTAA
20472263 TAAATAAAAA
Statistics
Matches: 150, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
194 25 0.17
195 125 0.83
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (195 bp):
CCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGA
ATTCTTTTAATGTTACCAACGTACTGAAACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATT
TATTTTTTCTCGAGAATAAATTTTTTTTAACATGACATTTTCTTATGAAAAATAAATTCGAGCCT
Found at i:20482355 original size:48 final size:47
Alignment explanation
Indices: 20482177--20482793 Score: 712
Period size: 48 Copynumber: 13.0 Consensus size: 47
20482167 TTTTGAGAGA
* * *
20482177 AAATGAAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTTT
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTC
* * *
20482225 AAGATGAAATTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAACTTTTTC
1 AA-ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
20482273 AGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
*
20482320 AAATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCC
1 AAATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
20482368 AAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTCC
1 AA-ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
20482416 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
1 AA-ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * *
20482465 AAATGAGATTTTAAAGTCGTTGAGCCTTTACTGAAAGGAGCCTTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* * *
20482513 --A--AGATTTTAAAATTGTTGAGCCT-TGTTGAGAGGAGCCCTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
** *
20482556 AAATGAGATTTTAAAGTAATTGAGCCTCTGCTGAAAGGAGCTTTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTC
* *
20482604 --A--AGATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCCTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* * *
20482648 AAATGAGATTTTAAAATCGTTGAGCCTCTACTGAGAGGAGCTTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * * * * * *
20482695 AGATTTTAAATTGTTTAAAGTTGTTAAGCCTCTGTTGAGAGGAGCCCTTTCC
1 A-A-ATGAGA-T-TTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
* *
20482747 AAATGAGATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCTTTTTC
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
20482794 TGATTTTAAA
Statistics
Matches: 486, Mismatches: 62, Indels: 43
0.82 0.10 0.07
Matches are distributed among these distances:
43 16 0.03
44 56 0.12
45 2 0.00
46 3 0.01
47 107 0.22
48 180 0.37
49 85 0.17
50 4 0.01
51 27 0.06
52 6 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (47 bp):
AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:20482451 original size:192 final size:191
Alignment explanation
Indices: 20482177--20482792 Score: 799
Period size: 192 Copynumber: 3.2 Consensus size: 191
20482167 TTTTGAGAGA
* * * *
20482177 AAATGAAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTTTAAGATGAAATTTTAAAG
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAGATTTTAAAG
* * *
20482242 TTGTTAAGCCTCTGCTGAGAGGAACTTTTTCAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGA
66 TTGTTGAGCCTCTGCTGAGAGGAACTTTTTCAAATGAGATTTTAAAGTCGTTGAGCCTCTACTGA
* *
20482307 GATGAGCTTTTTCAAATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCC
131 GAGGAGCTTTTTCAAAT-AGATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTTCC
* *
20482368 AAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGC-TTTTCCAAGATGAGATTTTTAA
1 AA-ATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAGA-TTTTAA
* *
20482432 AGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAATGAGATTTTAAAGTCGTTGAGCCTTTACT
64 AGTTGTTGAGCCTCTGCTGAGAGGAACTTTTTCAAATGAGATTTTAAAGTCGTTGAGCCTCTACT
* *
20482497 GAAAGGAGCCTTTTTC--A-AGA-TTTTAAAATTGTTGAGCCT-TGTTGAGAGGAGCCCTTTT-C
129 GAGAGGAG-CTTTTTCAAATAGATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG-CCTTTTCC
** *
20482556 AAATGAGATTTTAAAGTAATTGAGCCTCTGCTGAAAGGAGCTTTTTTC---A--AGATTTTAAAG
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAGATTTTAAAG
* * * *
20482616 TTGTTGAGCCTCTGTTGAGAGGAGCCCTTTTCAAATGAGATTTTAAAATCGTTGAGCCTCTACTG
66 TTGTTGAGCCTCTGCTGAGAGGA-ACTTTTTCAAATGAGATTTTAAAGTCGTTGAGCCTCTACTG
* * * *
20482681 AGAGGAGCTTTTTCAGATTTTAAATTGTTTAAAGTTGTTAAGCCTCTGTTGAGAGGAGCCCTTTC
130 AGAGGAGCTTTTTCA-A--ATAGATT-TTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTTC
20482746 C
191 C
* *
20482747 AAATGAGATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCTTTTT
1 AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
20482793 CTGATTTTAA
Statistics
Matches: 372, Mismatches: 36, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
182 37 0.10
183 46 0.12
185 1 0.00
187 46 0.12
188 28 0.08
189 9 0.02
190 21 0.06
191 69 0.19
192 108 0.29
193 7 0.02
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (191 bp):
AAATGAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTCAAGATGAGATTTTAAAG
TTGTTGAGCCTCTGCTGAGAGGAACTTTTTCAAATGAGATTTTAAAGTCGTTGAGCCTCTACTGA
GAGGAGCTTTTTCAAATAGATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTTCC
Found at i:20482725 original size:51 final size:50
Alignment explanation
Indices: 20482656--20482845 Score: 170
Period size: 51 Copynumber: 3.8 Consensus size: 50
20482646 TCAAATGAGA
* *
20482656 TTTTAAAATCGTTGAGCCTCTACTGAGAGGAGCTTTTTCAGATTTTAAAT
1 TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAGATTTTAAAT
* ** * * * * *
20482706 TGTTTAAAGTTGTTAAGCCTCTGTTGAGAGGAGCCCTTTCCA-A-ATGAGA-
1 T-TTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-CTTTTTCAGATTTTAAAT
* * * *
20482755 TTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCTTTTTCTGATTTTAAAT
1 TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAGATTTTAAAT
* * * *
20482805 TTTTGAAAGTTGTCGAGCCTCAAGTGAGAGGAGCATTTTCA
1 TTTT-AAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCA
20482846 ATAAAAAAAA
Statistics
Matches: 106, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
47 5 0.05
48 28 0.26
49 4 0.04
50 8 0.08
51 55 0.52
52 6 0.06
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (50 bp):
TTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAGATTTTAAAT
Found at i:20483001 original size:20 final size:19
Alignment explanation
Indices: 20482976--20483038 Score: 110
Period size: 18 Copynumber: 3.3 Consensus size: 19
20482966 AAGTACGTAT
20482976 AAAATATGAAATACAATAAA
1 AAAATATGAAATACAA-AAA
20482996 AAAATATGAAATAC-AAAA
1 AAAATATGAAATACAAAAA
20483014 AAAATATGAAATACAAAAA
1 AAAATATGAAATACAAAAA
20483033 AAAATA
1 AAAATA
20483039 AAACAGAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 17 0.40
19 11 0.26
20 14 0.33
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAATATGAAATACAAAAA
Found at i:20483050 original size:38 final size:38
Alignment explanation
Indices: 20482976--20483056 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 38
20482966 AAGTACGTAT
* *
20482976 AAAATATGAAATACAATAAAAAAATATGAAATACAAAA
1 AAAATATGAAATACAATAAAAAAATATAAAAAACAAAA
20483014 AAAATATGAAATACAA-AAAAAAATA-AAACAGAACAAAA
1 AAAATATGAAATACAATAAAAAAATATAAA-A-AACAAAA
20483052 AAAAT
1 AAAAT
20483057 CAAGGATGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 2 0.05
37 10 0.26
38 27 0.69
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.15
Consensus pattern (38 bp):
AAAATATGAAATACAATAAAAAAATATAAAAAACAAAA
Found at i:20483473 original size:21 final size:21
Alignment explanation
Indices: 20483427--20483474 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
20483417 CTGCACGAAG
***
20483427 AAAAAAAAAAGAGTCAGTTTA
1 AAAAAAAAAAGAGTCAGAACA
20483448 AAAAAAAAAAGAGTCAGAACA
1 AAAAAAAAAAGAGTCAGAACA
*
20483469 CAAAAA
1 AAAAAA
20483475 TATATAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAAGAGTCAGAACA
Found at i:20484185 original size:26 final size:27
Alignment explanation
Indices: 20484147--20484197 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
20484137 GTTAATTTTT
20484147 AAAACAAACTTTAAAAACAATAATATA
1 AAAACAAACTTTAAAAACAATAATATA
* * *
20484174 AAAATAAA-TTTAATAATAATAATA
1 AAAACAAACTTTAAAAACAATAATA
20484198 AACTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAACAAACTTTAAAAACAATAATATA
Found at i:20484641 original size:12 final size:12
Alignment explanation
Indices: 20484621--20484654 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20484611 AATTTTAATT
20484621 TTAATTAAAAAAA
1 TTAA-TAAAAAAA
*
20484634 TTAATAAAACAA
1 TTAATAAAAAAA
20484646 TTAATAAAA
1 TTAATAAAA
20484655 TTTTAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAATAAAAAAA
Found at i:20489218 original size:18 final size:19
Alignment explanation
Indices: 20489195--20489230 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20489185 ATATTTTTTA
*
20489195 GAAAACTTAT-TTTTAAAG
1 GAAAACTGATATTTTAAAG
20489213 GAAAACTGATATTTTAAA
1 GAAAACTGATATTTTAAA
20489231 CTTTTTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (19 bp):
GAAAACTGATATTTTAAAG
Found at i:20489313 original size:60 final size:60
Alignment explanation
Indices: 20489155--20489312 Score: 223
Period size: 59 Copynumber: 2.7 Consensus size: 60
20489145 TTGTACAAGA
* *
20489155 AAAATTGATACTTTTAACTTTTTCTCAAAAATA-TTTTTTAGAAAACTTATTTTTAAAGG
1 AAAATTGATACTTTAAACTTTTCCTCAAAAATATTTTTTTAGAAAACTTATTTTTAAAGG
* * * *
20489214 AAAACTGATATTTTAAACTTTTTCC-CAAAAATATTTTTTTAGAAAACTTA-TTTTCAATG
1 AAAATTGATACTTTAAAC-TTTTCCTCAAAAATATTTTTTTAGAAAACTTATTTTTAAAGG
*
20489273 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAAATTGATACTTTAAACTTTTCCTCAAAAATATTTTTTT
20489313 TTTGGAATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 6 0.07
59 60 0.69
60 21 0.24
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (60 bp):
AAAATTGATACTTTAAACTTTTCCTCAAAAATATTTTTTTAGAAAACTTATTTTTAAAGG
Found at i:20490195 original size:3 final size:3
Alignment explanation
Indices: 20490187--20490223 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20490177 AACCAACCAA
20490187 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20490224 TATACATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20490259 original size:20 final size:20
Alignment explanation
Indices: 20490236--20490273 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20490226 TACATTAATC
20490236 GATAAATATAA-AAAAATATT
1 GATAAATA-AATAAAAATATT
*
20490256 GATAGATAAATAAAAATA
1 GATAAATAAATAAAAATA
20490274 ATAATAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
GATAAATAAATAAAAATATT
Found at i:20490276 original size:23 final size:23
Alignment explanation
Indices: 20490236--20490301 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
20490226 TACATTAATC
*
20490236 GATAAATATAAAAAAATATTGATA
1 GATAAATATAAAATAATA-TGATA
*
20490260 GATAAATA-AAAATAATAATAATA
1 GATAAATATAAAATAAT-ATGATA
*
20490283 GATAAGTATAAAA-AATATG
1 GATAAATATAAAATAATATG
20490302 CATTAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.06
23 21 0.58
24 13 0.36
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
GATAAATATAAAATAATATGATA
Found at i:20490287 original size:47 final size:50
Alignment explanation
Indices: 20490231--20490330 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 50
20490221 ATATATACAT
* * * *
20490231 TAATCGATAAATATAAAAAA-AT-ATTGATAGATAAATAA-AAATAATAA
1 TAATAGATAAATATAAAAAATATCATTAATAAATAAATAATAAAAAATAA
*
20490278 TAATAGATAAGTATAAAAAATATGCATTAATAAATAAATAATAAAAAATAA
1 TAATAGATAAATATAAAAAATAT-CATTAATAAATAAATAATAAAAAATAA
20490329 TA
1 TA
20490331 TTAATGGATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
47 18 0.41
48 2 0.05
50 14 0.32
51 10 0.23
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (50 bp):
TAATAGATAAATATAAAAAATATCATTAATAAATAAATAATAAAAAATAA
Found at i:20490348 original size:74 final size:70
Alignment explanation
Indices: 20490187--20490353 Score: 174
Period size: 74 Copynumber: 2.3 Consensus size: 70
20490177 AACCAACCAA
* **
20490187 AATA-ATAATAATAATAATAATAATAATAATAATAATATATACATTAATCGATAAATATAAAAAA
1 AATAGATAATAATAATAATAATAATAATAATAATAAAATATACATTAATAAATAAATATAAAAAA
20490251 ATATT
66 ATATT
* * * *
20490256 GATAGATAAATAAAAATAATAATAATAGATAAGTATAAAAAATATGCATTAATAAATAAATAATA
1 AATAGAT-AATAATAATAATAATAATA-ATAA-TA-ATAAAATATACATTAATAAATAAAT-AT-
20490321 AAAAATAATATT
60 AAAAA-AATATT
* *
20490333 AATGGATAACTAATAAAAATA
1 AATAGATAA-TAATAATAATA
20490354 TATATATTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
69 3 0.04
70 2 0.03
71 18 0.23
72 4 0.05
73 2 0.03
74 20 0.26
75 2 0.03
76 7 0.09
77 20 0.26
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (70 bp):
AATAGATAATAATAATAATAATAATAATAATAATAAAATATACATTAATAAATAAATATAAAAAA
ATATT
Found at i:20490397 original size:23 final size:23
Alignment explanation
Indices: 20490237--20490399 Score: 63
Period size: 23 Copynumber: 6.8 Consensus size: 23
20490227 ACATTAATCG
*
20490237 ATAAAT-ATAAAAAAATATTGATAG
1 ATAAATAATAAAAAAATA-T-ATAT
*
20490261 ATAAATAA-AAATAATAATA-ATAG
1 ATAAATAATAAA-AA-AATATATAT
* *
20490284 ATAAGT-ATAAAAAATATGCATTAATAA
1 ATAAATAATAAAAAA-AT--A-T-ATAT
20490311 ATAAATAAT-AAAAAATA-ATAT
1 ATAAATAATAAAAAAATATATAT
20490332 -TAATGGATAACTAATAAAAATATATAT
1 ATAA---ATAA-TAA-AAAAATATATAT
* * * *
20490359 ATTATTAGA-CATAAAATATATAT
1 ATAAATA-ATAAAAAAATATATAT
20490382 ATAAATAATAAAAAAATA
1 ATAAATAATAAAAAAATA
20490400 AAGATAATAA
Statistics
Matches: 106, Mismatches: 12, Indels: 43
0.66 0.07 0.27
Matches are distributed among these distances:
20 3 0.03
21 4 0.04
22 6 0.06
23 39 0.37
24 13 0.12
25 6 0.06
26 14 0.13
27 17 0.16
28 4 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
ATAAATAATAAAAAAATATATAT
Found at i:20492003 original size:23 final size:23
Alignment explanation
Indices: 20491968--20492024 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
20491958 TTTTTTTTTT
20491968 TTTTGCTTTTTATAATTGACCTGC
1 TTTT-CTTTTTATAATTGACCTGC
*
20491992 -TTTCTTTCTTATCATTGACCTGC
1 TTTTCTTT-TTATAATTGACCTGC
20492015 TTTTCTTTTT
1 TTTTCTTTTT
20492025 TTTTTCCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 19 0.63
24 7 0.23
ACGTcount: A:0.12, C:0.19, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTTCTTTTTATAATTGACCTGC
Found at i:20494862 original size:31 final size:31
Alignment explanation
Indices: 20494816--20494878 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
20494806 CTGACATTGC
*
20494816 TAGGAGTAACCTATGTAATAATTTATCATAA
1 TAGGAATAACCTATGTAATAATTTATCATAA
* * *
20494847 TAGGAATAACTTATGTAATACTTTATCTTAA
1 TAGGAATAACCTATGTAATAATTTATCATAA
20494878 T
1 T
20494879 TTTGATTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (31 bp):
TAGGAATAACCTATGTAATAATTTATCATAA
Found at i:20495308 original size:14 final size:15
Alignment explanation
Indices: 20495277--20495331 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
20495267 CTTCAAGGCC
20495277 AGATAGAAAATAGAA
1 AGATAGAAAATAGAA
*
20495292 AGATA-AAAATTGGAA
1 AGATAGAAAA-TAGAA
20495307 GAGA-AGAAAAGTAGAA
1 -AGATAGAAAA-TAGAA
20495323 AGAT-GAAAA
1 AGATAGAAAA
20495332 ACATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 4 0.12
15 18 0.55
16 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (15 bp):
AGATAGAAAATAGAA
Found at i:20501516 original size:36 final size:36
Alignment explanation
Indices: 20501483--20501558 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
20501473 CATCCTCAGC
* *
20501483 ACCAATATTA-CTTTCACCACCAGCATTACCCTCACT
1 ACCAATATTACCTTT-ACCACCAACATTAACCTCACT
* * *
20501519 GCCAGTATTACCTTTACCACCAACATTAACCTCATT
1 ACCAATATTACCTTTACCACCAACATTAACCTCACT
20501555 ACCA
1 ACCA
20501559 TCATTGCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
ACCAATATTACCTTTACCACCAACATTAACCTCACT
Found at i:20501517 original size:18 final size:18
Alignment explanation
Indices: 20501446--20501552 Score: 61
Period size: 18 Copynumber: 5.9 Consensus size: 18
20501436 TGACCTTTAT
*
20501446 CACCAGCATTACCCTTAC
1 CACCAGCATTACCCTCAC
* * * * *
20501464 CACTATCATCATCCTCAG
1 CACCAGCATTACCCTCAC
** **
20501482 CACCAATATTACTTTCAC
1 CACCAGCATTACCCTCAC
20501500 CACCAGCATTACCCTCAC
1 CACCAGCATTACCCTCAC
** * * *
20501518 TGCCAGTATTACCTTTAC
1 CACCAGCATTACCCTCAC
* *
20501536 CACCAACATTAACCTCA
1 CACCAGCATTACCCTCA
20501553 TTACCATCAT
Statistics
Matches: 59, Mismatches: 30, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.30, C:0.39, G:0.05, T:0.26
Consensus pattern (18 bp):
CACCAGCATTACCCTCAC
Found at i:20503602 original size:13 final size:13
Alignment explanation
Indices: 20503584--20503609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20503574 CTCAAAAAAA
20503584 ATATTTTATTTTT
1 ATATTTTATTTTT
20503597 ATATTTTATTTTT
1 ATATTTTATTTTT
20503610 TTCCAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATATTTTATTTTT
Found at i:20503674 original size:18 final size:17
Alignment explanation
Indices: 20503653--20503697 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
20503643 ATAAACACAT
20503653 AAATAAAATACTAAAAAA
1 AAATAAAATACT-AAAAA
20503671 AAATTAAAAATACTAAAAA
1 AAA-T-AAAATACTAAAAA
20503690 AAATAAAA
1 AAATAAAA
20503698 ATGGCTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
19 9 0.36
20 8 0.32
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAAATACTAAAAA
Found at i:20503698 original size:18 final size:19
Alignment explanation
Indices: 20503653--20503699 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
20503643 ATAAACACAT
20503653 AAAT-AAAATACTAAAAAA
1 AAATAAAAATACTAAAAAA
20503671 AAATTAAAAATACT-AAAAA
1 AAA-TAAAAATACTAAAAAA
20503690 AAATAAAAAT
1 AAATAAAAAT
20503700 GGCTCAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.37
19 9 0.33
20 8 0.30
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAAAAATACTAAAAAA
Found at i:20504852 original size:43 final size:43
Alignment explanation
Indices: 20504715--20505131 Score: 393
Period size: 43 Copynumber: 9.8 Consensus size: 43
20504705 TCAGATTTCC
* * * *
20504715 TCTAAATAGAGGCTCAACAACTTTGAAAAATAAAATTAAGCTCT
1 TCTAAACAAAGGCTCAACAACTTTGAAAAAT-AAATAAAGCTCA
* * ** *
20504759 TCTAAACAGAGGCTCAACGACTTCAAAAAAAAATAAATAAAGCTCC
1 TCTAAACAAAGGCTCAACAACTT---TGAAAAATAAATAAAGCTCA
**
20504805 TCTAAACAAAGGCTCAATGACTTTGAAAAATAAATAAAGCTCA
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* *
20504848 TCTAATCAAAGGCTCTACAACTTTGAAAAATAAATAAAGCTCA
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* * * * * *
20504891 TCTAATCAGAGGCTCCACAGCTTTGAAAAAT-AA-AAGGCTCC
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* * *
20504932 TCTAAATAAAGGCTCAATAACTTTG--AAA-AAATAAATGCTCT
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAA-GCTCA
* * * * *
20504973 TCTAATCAGAGGCTCAACAACTTTGAAAAAT-AA-AAGGTTCC
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* * * *
20505014 TCTAAATAGAGGCTCAACGACTTTGAAAAAT-AA-AAGGCTCA
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* ** *
20505055 TCTAAACAAAGGCCCAATGACTTTGAAAAATAAATAAAGTTCA
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
* *
20505098 TCTAATCAAAGGCTCCACAACTTTGAAAAATAAA
1 TCTAAACAAAGGCTCAACAACTTTGAAAAATAAA
20505132 GGCTCATCGA
Statistics
Matches: 311, Mismatches: 51, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
39 5 0.02
40 2 0.01
41 116 0.37
42 6 0.02
43 124 0.40
44 21 0.07
46 31 0.10
47 6 0.02
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (43 bp):
TCTAAACAAAGGCTCAACAACTTTGAAAAATAAATAAAGCTCA
Found at i:20504956 original size:41 final size:41
Alignment explanation
Indices: 20504793--20505139 Score: 337
Period size: 41 Copynumber: 8.4 Consensus size: 41
20504783 AAAAAAAAAT
* * **
20504793 AAAT-AAA-GCTCCTCTAAACAAAGGCTCAATGACTTTGAA
1 AAATAAAAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
* *
20504832 AAATAAATAAAGCTCATCTAATCAAAGGCTCTACAACTTTGAA
1 AAAT-AA-AAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
* * * *
20504875 AAATAAATAAAGCTCATCTAATCAGAGGCTCCACAGCTTTGAA
1 AAAT-AA-AAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
* *
20504918 AAATAAAAGGCTCCTCTAAAT-AAAGGCTCAATAACTTTGAA
1 AAATAAAAGGCTCATCT-AATCAAAGGCTCAACAACTTTGAA
* * *
20504959 AAA-ATAAATGCTCTTCTAATCAGAGGCTCAACAACTTTGAA
1 AAATA-AAAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
* * * *
20505000 AAATAAAAGGTTCCTCTAAAT-AGAGGCTCAACGACTTTGAA
1 AAATAAAAGGCTCATCT-AATCAAAGGCTCAACAACTTTGAA
* * **
20505041 AAATAAAAGGCTCATCTAAACAAAGGCCCAATGACTTTGAA
1 AAATAAAAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
* * *
20505082 AAATAAATAAAGTTCATCTAATCAAAGGCTCCACAACTTTGAA
1 AAAT-AA-AAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
20505125 AAAT-AAAGGCTCATC
1 AAATAAAAGGCTCATC
20505140 GACAATCATG
Statistics
Matches: 259, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.02
40 14 0.05
41 125 0.48
42 13 0.05
43 103 0.40
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (41 bp):
AAATAAAAGGCTCATCTAATCAAAGGCTCAACAACTTTGAA
Found at i:20505514 original size:20 final size:20
Alignment explanation
Indices: 20505477--20505514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20505467 AACATCAAAA
* *
20505477 AGTTCAAAGTTTCTCATTTG
1 AGTTCAAAGGTTCACATTTG
20505497 AGTTCAAAGGTTCACATT
1 AGTTCAAAGGTTCACATT
20505515 CAATAAATCT
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:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
AGTTCAAAGGTTCACATTTG
Found at i:20506828 original size:20 final size:19
Alignment explanation
Indices: 20506799--20506841 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
20506789 TTTTCTCTCC
*
20506799 TTTTCATTTTTTTTTATTT
1 TTTTCATTTTTTATTATTT
20506818 TTTTCATTTTTTTATTATTT
1 TTTTCA-TTTTTTATTATTT
20506838 TTTT
1 TTTT
20506842 TTGTTCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTCATTTTTTATTATTT
Done.