Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007394.1 Hibiscus syriacus cultivar Beakdansim tig00019931_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: 330936
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:852 original size:24 final size:25
Alignment explanation
Indices: 799--845 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
789 AAAGAAAGTG
799 AAGCACTCAAAAGAAAGAAAAAATC
1 AAGCACTCAAAAGAAAGAAAAAATC
* *
824 CAGCACTCAAACG-AAGAAAAAA
1 AAGCACTCAAAAGAAAGAAAAAA
846 CAAAGCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.62, C:0.19, G:0.13, T:0.06
Consensus pattern (25 bp):
AAGCACTCAAAAGAAAGAAAAAATC
Found at i:21298 original size:28 final size:28
Alignment explanation
Indices: 21258--21311 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
21248 CTCACATTCA
21258 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
21286 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
21312 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:25936 original size:11 final size:13
Alignment explanation
Indices: 25904--25933 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25894 TGGCCAAAGA
25904 TGAAAAGGTATGT
1 TGAAAAGGTATGT
25917 TGAAAAGGTATG-
1 TGAAAAGGTATGT
25929 TGAAA
1 TGAAA
25934 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:30375 original size:350 final size:350
Alignment explanation
Indices: 29729--30428 Score: 1328
Period size: 350 Copynumber: 2.0 Consensus size: 350
29719 ACCCCTTTTC
*
29729 TTTCATCTTGATACTTCTGGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAATACCATCC
1 TTTCATCTTGATACTTCTGGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAACACCATCC
* *
29794 CTTGAAGAAACAATATAAAGATTGGGTCTCTGCTCTATATAGCATTGGTTCTTCTTTGAGTTTTC
66 CTTGAAGAAACAATATAAAGATTGGGTCTCTGCTCTATATAGCATTGGTTCTTCTTTGAGATCTC
29859 TTCAAGATACTATCCTCACAACCATCCTTTTATTTCATCACCATAACCATAGCCTTATCAACTAT
131 TTCAAGATACTATCCTCACAACCATCCTTTTATTTCATCACCATAACCATAGCCTTATCAACTAT
29924 CTTCCGCTTCCATTACTCATTATTTAAATAGCCTACCAATTCACCCATACGTCTACCACCCTTAA
196 CTTCCGCTTCCATTACTCATTATTTAAATAGCCTACCAATTCACCCATACGTCTACCACCCTTAA
29989 CCATTCTACTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTT
261 CCATTCTACTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTT
30054 GAAAAGGTACAAGTACCTTACATCA
326 GAAAAGGTACAAGTACCTTACATCA
*
30079 TTTCATCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAGTACTTAACACCATCC
1 TTTCATCTTGATACTTCTGGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAACACCATCC
*
30144 TTTGAAGAAACAATATAAAGATTGGGTCTCTGCTCTATATAGCATTGGTTCTTCTTTGAGATCTC
66 CTTGAAGAAACAATATAAAGATTGGGTCTCTGCTCTATATAGCATTGGTTCTTCTTTGAGATCTC
*
30209 TTCAAGATACTATCCTCACAACCATCCTTTTATTTCATCACCATAACCATAGCCTTATTAACTAT
131 TTCAAGATACTATCCTCACAACCATCCTTTTATTTCATCACCATAACCATAGCCTTATCAACTAT
30274 CTTCCGCTTCCATTACTCATTATTTAAATAGCCTACCAATTCACCCATACGTCTACCACCCTTAA
196 CTTCCGCTTCCATTACTCATTATTTAAATAGCCTACCAATTCACCCATACGTCTACCACCCTTAA
* *
30339 CCATTCTATTTTGAGCCATTCACTTTGCATGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTT
261 CCATTCTACTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTT
30404 GAAAAGGTACAAGTACCTTACATCA
326 GAAAAGGTACAAGTACCTTACATCA
30429 ACTTTACAGC
Statistics
Matches: 342, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
350 342 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (350 bp):
TTTCATCTTGATACTTCTGGTTCCTAGTTCATATAACTAGTGGGTCAAAGTACTTAACACCATCC
CTTGAAGAAACAATATAAAGATTGGGTCTCTGCTCTATATAGCATTGGTTCTTCTTTGAGATCTC
TTCAAGATACTATCCTCACAACCATCCTTTTATTTCATCACCATAACCATAGCCTTATCAACTAT
CTTCCGCTTCCATTACTCATTATTTAAATAGCCTACCAATTCACCCATACGTCTACCACCCTTAA
CCATTCTACTTTGAGCCATTCACTTTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTT
GAAAAGGTACAAGTACCTTACATCA
Found at i:34313 original size:55 final size:55
Alignment explanation
Indices: 34251--34619 Score: 560
Period size: 55 Copynumber: 6.7 Consensus size: 55
34241 ACATGTTCAC
*
34251 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
** * * * *
34306 TCCCTATTTATTTAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
34361 TCCTTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
*
34416 TCCCTATTCCTTCAGAGAGTATGAGACTCGAATAATCTTCAATAATCGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * * *
34471 TCCCTATTCTTTCAGAGAGTATGACACTCCAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
34526 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTTTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
*
34581 TCCCTATTCTTTCAGAGAGTATGAGACTCGAAC-ATCTTC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTC
34620 TTCTTACGGG
Statistics
Matches: 283, Mismatches: 31, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 6 0.02
55 277 0.98
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
Found at i:34639 original size:54 final size:54
Alignment explanation
Indices: 34581--35539 Score: 999
Period size: 54 Copynumber: 18.0 Consensus size: 54
34571 TCGTGTTTGT
* * ** *
34581 TCCCTATTCTTTCAGAGAGTATGAG-ACTCGAACATCTTCTTCTTACGGGTTCAC
1 TCCCTCTT-TTTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * * ** *
34635 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCAAAAAATCGTCTTCTTACGAGTTCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTC-GAACATCTTCTTCAAACGGGTTCGC
* * *
34690 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGAACATCTTTTTCAAACGGGCTCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * * *
34744 TCCCTCTTTCTCTAGGGAGTATG-GAATTTGGACATCTTCTTCAAACGGGTTAGC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
34798 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGAGTTCCC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
34852 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
34906 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGAGTTCCC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * *
34960 TCCCTATTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTCCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * ** *
35014 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
35065 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACA---TCTTCAAACGGGTTTGC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
35116 TCCCTCTTTCTCTAGGGAGTAT-AGAACTCGGACATTTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * ** * *
35170 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCTC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
35221 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
35272 TCCCTCTTTCTCTAGGGAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
35326 TCCCTCTTTCCTT-AGGGAGTATG-GAACTCGAACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT--TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
35380 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
35434 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGAGTTCCC
1 TCCCTCTTTTTC-AGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
35488 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTC
1 TCCCTCTTT-TTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTC
35540 TGATGTAAGG
Statistics
Matches: 780, Mismatches: 88, Indels: 74
0.83 0.09 0.08
Matches are distributed among these distances:
50 4 0.01
51 166 0.21
52 6 0.01
53 16 0.02
54 530 0.68
55 57 0.07
56 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (54 bp):
TCCCTCTTTTTCAGGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
Found at i:34832 original size:108 final size:108
Alignment explanation
Indices: 34597--35539 Score: 1267
Period size: 108 Copynumber: 8.8 Consensus size: 108
34587 TTCTTTCAGA
** *
34597 GAGTAT-GAGACTCGAACATCTTCTTCTTACGGGTTCACTCCCTCTTTCTTCAGGAAGTATAGAA
1 GAGTATGGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAA
** * * ** *
34661 CTCAAAAAATCGTCTTCTTACGAGTTCGCTCCCTCTTTCT-TCAGG
65 CTC-GGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * * *
34706 AAGTATAGAACTCGAACATCTTTTTCAAACGGGCTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
* * *
34770 TTTGGACATCTTCTTCAAACGGGTTAGCTCCCTCTTTCTCTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
34814 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
34879 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
34922 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTATTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
*
34987 TCGGACATCTTCTTCAAACGGGTCCGCTCCCTCTTTCT-TCAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * ** * * *
35030 AAGTATAGAACTC-CA-AT-AACTTCACACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
* *
35091 CTC-GA-A-CATCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
35132 GAGTATAGAACTCGGACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
* ** * *
35197 TC-CA-AT-AACTTCACACGGGTTCTCTCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
35237 GAGTATGGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
35298 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-CTTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC-TAGG
35342 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
35407 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
35450 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
35515 TCGGACATCTTCTTCAAACGGGTTC
66 TCGGACATCTTCTTCAAACGGGTTC
35540 TGATGTAAGG
Statistics
Matches: 744, Mismatches: 68, Indels: 45
0.87 0.08 0.05
Matches are distributed among these distances:
101 2 0.00
102 84 0.11
103 4 0.01
104 9 0.01
105 169 0.23
106 4 0.01
107 2 0.00
108 411 0.55
109 57 0.08
110 2 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (108 bp):
GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:34879 original size:162 final size:161
Alignment explanation
Indices: 34612--35539 Score: 1193
Period size: 162 Copynumber: 5.8 Consensus size: 161
34602 TGAGACTCGA
** * * * * *
34612 ACATCTTCTTCTTACGGGTTCACTCCCTCTTTCT-TCAGGAAGTATAGAACTCAAAAAATCGTCT
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTC-GAACATCTTCT
** * * *
34676 TCTTACGAGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTTTTCAAACGGGCT
64 TCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTT
34741 CGCTCCCTCTTTCTCTAGGGAGTATGGAATTTGG
129 CGCTCCCTCTTTCTCTAGGGAGTATGGAA-TTGG
* *
34775 ACATCTTCTTCAAACGGGTTAGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTC
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTC
*
34840 AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTCG
66 AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCG
* *
34905 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGA
131 CTCCCTCTTTCTCTAGGGAGTATGGAA-TTGG
* * * * *
34937 ACATCTTCTTCAAACGAGTTCCCTCCCTATTTCT-TCAGGAAGTATAGAACTCGGACATCTTCTT
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCTT
* * ** *
35001 CAAACG-GGTCCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-CA-AT-AACTTCACACGGGTT
65 CAAACGAGTTCC-CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTT
* *
35062 CGCTCCCTCTTTCTCTAGGGAGTATGGAACTCG
129 CGCTCCCTCTTTCTCTAGGGAGTATGGAATTGG
* * * *
35095 A-A-CATCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATTTTCTTC
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTC
* * * ** * *
35158 AAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTC-CA-AT-AACTTCACACGGGTTCT
66 AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCG
* *
35220 CTCCCTCTTTCTCTAGGGAGTATGGAACTCG
131 CTCCCTCTTTCTCTAGGGAGTATGGAATTGG
* *
35251 A-A-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTC
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTC
* * * *
35314 AAACGGGTTCGCTCCCTCTTTCCTT-AGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTC
66 AAACGAGTTCCCTCCCTCTTT-CTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTC
* * *
35378 GCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGG
130 GCTCCCTCTTTCTCT-AGGGAGTATGGAA-TTGG
*
35411 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTC
1 ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTC
*
35476 AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGGACATCTTCTTCAAACGGGTTC
66 AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTC
35540 TGATGTAAGG
Statistics
Matches: 685, Mismatches: 66, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
156 234 0.34
157 9 0.01
158 4 0.01
159 77 0.11
160 4 0.01
161 10 0.01
162 302 0.44
163 44 0.06
164 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (161 bp):
ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTC
AAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCG
CTCCCTCTTTCTCTAGGGAGTATGGAATTGG
Found at i:39105 original size:20 final size:21
Alignment explanation
Indices: 39082--39125 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
39072 TTCTTTTCTT
*
39082 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
39102 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
39121 TGCTT
1 TGCTT
39126 CTTTTCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:41156 original size:51 final size:51
Alignment explanation
Indices: 41077--41224 Score: 190
Period size: 51 Copynumber: 2.9 Consensus size: 51
41067 GATCGTATCA
* * * *
41077 GGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCCAATAACTTCACACG
1 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCCAACAACTTCAAACG
* * *
41128 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAATCGAACATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCCAACAACTTCAAACG
* * *
41179 GATTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAACATCTTC
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCCAACAACTTC
41225 TTCTGCTTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 85 0.99
52 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (51 bp):
GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCCAACAACTTCAAACG
Found at i:50304 original size:10 final size:10
Alignment explanation
Indices: 50289--50317 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
50279 GTTTAGACAC
50289 TCCCAAGTGT
1 TCCCAAGTGT
50299 TCCCAAGTGT
1 TCCCAAGTGT
50309 TCCCAAGTG
1 TCCCAAGTG
50318 CTGTGCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (10 bp):
TCCCAAGTGT
Found at i:53715 original size:12 final size:12
Alignment explanation
Indices: 53698--53745 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
53688 TTTTTTTTCA
53698 AAAAAAAAAAAC
1 AAAAAAAAAAAC
**
53710 AAAAAAAAAGGC
1 AAAAAAAAAAAC
**
53722 AAAAAAAAAGGC
1 AAAAAAAAAAAC
53734 AAAAAAACAAAA
1 AAAAAAA-AAAA
53746 AAAGAGCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 29 0.94
13 2 0.06
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:53748 original size:11 final size:12
Alignment explanation
Indices: 53698--53740 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
53688 TTTTTTTTCA
**
53698 AAAAAAAAAAAC
1 AAAAAAAAAGGC
53710 AAAAAAAAAGGC
1 AAAAAAAAAGGC
53722 AAAAAAAAAGGC
1 AAAAAAAAAGGC
53734 AAAAAAA
1 AAAAAAA
53741 CAAAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:53766 original size:20 final size:20
Alignment explanation
Indices: 53713--53766 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
53703 AAAAAACAAA
*
53713 AAAAAAGGCAAAAAAAAAGGC
1 AAAAAA-GCAAAAAAAAAGCC
* *
53734 AAAAAAACAAAAAAAGAGCC
1 AAAAAAGCAAAAAAAAAGCC
53754 AAAAAAGCCAAAA
1 AAAAAAG-CAAAA
53767 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAGCAAAAAAAAAGCC
Found at i:59500 original size:52 final size:52
Alignment explanation
Indices: 59369--59500 Score: 176
Period size: 52 Copynumber: 2.5 Consensus size: 52
59359 TTGCATTTAT
* *
59369 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACAT-ACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
59423 ATTCACATAGCAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATA-CAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* *
59475 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCAC-ATACAGCATGTTTATCATT
59501 ATAACTCATG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
52 37 0.53
53 29 0.41
54 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (52 bp):
ATTCACATACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:61141 original size:4 final size:4
Alignment explanation
Indices: 61132--61156 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
61122 ATTACTTTCA
61132 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
61157 GTCCTTTGAA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:64042 original size:17 final size:17
Alignment explanation
Indices: 64020--64062 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
64010 GTAGGAGTCT
64020 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
64037 TTTTCTTATTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
64055 TTTT-TTTT
1 TTTTCTTTT
64063 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:64505 original size:36 final size:36
Alignment explanation
Indices: 64432--64536 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
64422 ATTTATAAGT
* * *
64432 TGGTGATAATATAGGCGTGAT-ATGGTGATGTAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
64467 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
64503 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
64537 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:68624 original size:36 final size:36
Alignment explanation
Indices: 68551--68655 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
68541 ATTTATAAGT
* * *
68551 TGGTGATAATATAGGCGTGAT-ATGGTGATGTAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
68586 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
68622 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
68656 ATATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:75173 original size:52 final size:52
Alignment explanation
Indices: 75042--75173 Score: 176
Period size: 52 Copynumber: 2.5 Consensus size: 52
75032 TTGCATTTAT
* *
75042 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACAT-ACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
75096 ATTCACATAGCAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATA-CAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* *
75148 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCAC-ATACAGCATGTTTATCATT
75174 ATAACTCATG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
52 37 0.53
53 29 0.41
54 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (52 bp):
ATTCACATACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:76815 original size:4 final size:4
Alignment explanation
Indices: 76806--76830 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
76796 ATTACTTTCA
76806 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
76831 GTCCTTTGAA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:80077 original size:36 final size:36
Alignment explanation
Indices: 80004--80108 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
79994 ATTTATAAGT
* * *
80004 TGGTGATAATATAGGCGTGAT-ATGGTGATGTAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
80039 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
80075 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
80109 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:87429 original size:19 final size:21
Alignment explanation
Indices: 87405--87456 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
87395 CGGCCAAGAG
*
87405 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
87424 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
87445 CATGTATTTTCA
1 CATGTATTTTCA
87457 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:91511 original size:19 final size:21
Alignment explanation
Indices: 91487--91538 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
91477 CGGCCAAGAG
*
91487 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
91506 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
91527 CATGTATTTTCA
1 CATGTATTTTCA
91539 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:93954 original size:20 final size:21
Alignment explanation
Indices: 93931--93974 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
93921 TTCTTTTCTT
*
93931 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
93951 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
93970 TGCTT
1 TGCTT
93975 CTTTTCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:98013 original size:52 final size:53
Alignment explanation
Indices: 97882--98013 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
97872 TTGCATTTAT
* *
97882 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
97936 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
97988 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
98014 ATAACTCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:99629 original size:4 final size:4
Alignment explanation
Indices: 99620--99652 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
99610 ATTACTTTCA
99620 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
99653 GTCCTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:106763 original size:52 final size:53
Alignment explanation
Indices: 106632--106763 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
106622 TTGCATTTAT
* *
106632 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
106686 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
106738 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
106764 ATAACTCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:108355 original size:20 final size:21
Alignment explanation
Indices: 108326--108365 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
108316 TTTTTTTTCA
*
108326 AAAAACAAAAGGCAAAAAAAC
1 AAAAACAAAAGCCAAAAAAAC
108347 AAAAA-AAAAGCCAAAAAAA
1 AAAAACAAAAGCCAAAAAAA
108366 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAGCCAAAAAAAC
Found at i:110043 original size:21 final size:21
Alignment explanation
Indices: 110003--110044 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
109993 TCAGAGAATA
* *
110003 TTACCAAGGTATTTCATCCTC
1 TTACCAAGGTAATCCATCCTC
*
110024 TTACCAAGGTAATCCTTCCTC
1 TTACCAAGGTAATCCATCCTC
110045 ATCTTCTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.36
Consensus pattern (21 bp):
TTACCAAGGTAATCCATCCTC
Found at i:114056 original size:11 final size:11
Alignment explanation
Indices: 114034--114080 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
114024 TTTGAGAATT
114034 TGGTGATGATA
1 TGGTGATGATA
114045 TAGGTG-TGATA
1 T-GGTGATGATA
114056 TGGTGATGGACTA
1 TGGTGAT-GA-TA
114069 TGGTGATGATA
1 TGGTGATGATA
114080 T
1 T
114081 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:114062 original size:22 final size:24
Alignment explanation
Indices: 114034--114080 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
114024 TTTGAGAATT
114034 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
114056 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
114080 T
1 T
114081 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:114080 original size:35 final size:37
Alignment explanation
Indices: 114034--114114 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 37
114024 TTTGAGAATT
* *
114034 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
114069 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
114106 TGGGGATGA
1 TGGTGATGA
114115 AAATAGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.02, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:122163 original size:13 final size:11
Alignment explanation
Indices: 122122--122206 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
122112 ACAATCTGTC
122122 CATCACCATTAT
1 CATCACCA-TAT
*
122134 CA-CGCCTATAT
1 CATCACC-ATAT
122145 CATCACCATAGT
1 CATCACCATA-T
122157 CCATCACCATTAT
1 -CATCACCA-TAT
*
122170 CA-CGCCTATAT
1 CATCACC-ATAT
122181 CATCACCATATT
1 CATCACCATA-T
122193 CCATCACCATAT
1 -CATCACCATAT
122205 CA
1 CA
122207 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:122166 original size:36 final size:36
Alignment explanation
Indices: 122119--122223 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
122109 GATACAATCT
122119 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
122155 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
122191 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
122224 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:126122 original size:19 final size:20
Alignment explanation
Indices: 126102--126137 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
126092 CTTTCTTTAT
126102 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
126120 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
126138 ATTATTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:126140 original size:19 final size:17
Alignment explanation
Indices: 126098--126140 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
126088 TATCCTTTCT
126098 TTAT-TTTATTTCATTC
1 TTATATTTATTTCATTC
126114 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
126134 TTATATT
1 TTATATT
126141 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 4 0.17
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:127937 original size:13 final size:11
Alignment explanation
Indices: 127896--127980 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
127886 ACAATATGTC
127896 CATCACCATTAT
1 CATCACCA-TAT
*
127908 CA-CGCCTATAT
1 CATCACC-ATAT
127919 CATCACCATAGT
1 CATCACCATA-T
127931 CCATCACCATTAT
1 -CATCACCA-TAT
*
127944 CA-CGCCTATAT
1 CATCACC-ATAT
127955 CATCACCATATT
1 CATCACCATA-T
127967 CCATCACCATAT
1 -CATCACCATAT
127979 CA
1 CA
127981 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:127940 original size:36 final size:36
Alignment explanation
Indices: 127893--127997 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
127883 GATACAATAT
127893 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
127929 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
127965 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
127998 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:133369 original size:16 final size:16
Alignment explanation
Indices: 133338--133384 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
133328 TGCTAATGAA
133338 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
133355 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
133372 ATAAAAAAATGAA
1 ATAAAAAAATGAA
133385 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:134040 original size:13 final size:12
Alignment explanation
Indices: 134021--134085 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
134011 ATATAGGCGT
134021 GATATGGTGATG
1 GATATGGTGATG
134033 GAATATGGTGAT-
1 G-ATATGGTGATG
*
134045 GATATAGGCG-T-
1 GATAT-GGTGATG
134056 GATAATGGTGATG
1 GAT-ATGGTGATG
134069 GACTATGGTGAT-
1 GA-TATGGTGATG
134081 GATAT
1 GATAT
134086 AAGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:134076 original size:36 final size:36
Alignment explanation
Indices: 134003--134107 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
133993 ATTTATAAGT
* *
134003 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
134038 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
134074 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
134108 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:145166 original size:13 final size:12
Alignment explanation
Indices: 145147--145232 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
145137 AAATAGGCGT
145147 GATATGGTGATG
1 GATATGGTGATG
145159 GAATATGGTGAT-
1 G-ATATGGTGATG
*
145171 GATATAGGCG-T-
1 GATAT-GGTGATG
145182 GATAATGGTGATG
1 GAT-ATGGTGATG
145195 GACTATGGTGAT-
1 GA-TATGGTGATG
*
145207 GATATAGGCG-T-
1 GATAT-GGTGATG
145218 GATAATGGTGATG
1 GAT-ATGGTGATG
145231 GA
1 GA
145233 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:145202 original size:36 final size:36
Alignment explanation
Indices: 145129--145233 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
145119 ATTTATAAGT
* * *
145129 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
145164 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
145200 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
145234 AGATTGTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:150872 original size:35 final size:37
Alignment explanation
Indices: 150826--150905 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
150816 TTTAAGAATT
*
150826 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
150861 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
150898 TGGGGATG
1 TGGTGATG
150906 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:161630 original size:13 final size:13
Alignment explanation
Indices: 161608--161637 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
161598 ACAAAACACC
161608 TTTC-ACATACCT
1 TTTCAACATACCT
161620 TTTCAACATACCT
1 TTTCAACATACCT
161633 TTTCA
1 TTTCA
161638 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:166280 original size:24 final size:25
Alignment explanation
Indices: 166238--166299 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 25
166228 GTAATGTACT
*
166238 TGGAGCTTCAA-TGATCACAACTTG
1 TGGAACTTCAAGTGATCACAACTTG
* * *
166262 TGGCACTTCAAGTGA-CACATCTTT
1 TGGAACTTCAAGTGATCACAACTTG
*
166286 TTGAACTTCAAGTG
1 TGGAACTTCAAGTG
166300 GCATAACTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (25 bp):
TGGAACTTCAAGTGATCACAACTTG
Found at i:170260 original size:24 final size:25
Alignment explanation
Indices: 170223--170279 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
170213 GTACTTAGAG
*
170223 CTTCAA-TGATCACAACTTGTGGCA
1 CTTCAAGTGATCACAACTTGTGGAA
* * *
170247 CTTCAAGTGA-CACATCTTTTTGAA
1 CTTCAAGTGATCACAACTTGTGGAA
170271 CTTCAAGTG
1 CTTCAAGTG
170280 GCATAACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (25 bp):
CTTCAAGTGATCACAACTTGTGGAA
Found at i:173064 original size:19 final size:20
Alignment explanation
Indices: 173036--173075 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
173026 GGATAATAAT
173036 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
173056 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
173075 A
1 A
173076 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:177147 original size:19 final size:20
Alignment explanation
Indices: 177119--177158 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
177109 GGATAATAAT
177119 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
177139 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
177158 A
1 A
177159 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:179663 original size:35 final size:37
Alignment explanation
Indices: 179602--179674 Score: 123
Period size: 35 Copynumber: 2.0 Consensus size: 37
179592 ATAAGATACA
179602 ATATGTCCATCACCATTATCACGCCTATATCATCACC
1 ATATGTCCATCACCATTATCACGCCTATATCATCACC
*
179639 ATAT-TCCATCACCA-TATCACGCCTATATTATCACC
1 ATATGTCCATCACCATTATCACGCCTATATCATCACC
179674 A
1 A
179675 ACTTCTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 21 0.60
36 10 0.29
37 4 0.11
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCTATATCATCACC
Found at i:180070 original size:21 final size:20
Alignment explanation
Indices: 180044--180093 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
180034 GTGCTACAAC
*
180044 AAAAAAGCAACAAGAAAGAAGA
1 AAAAAAGAAACAA-AAAGAA-A
180066 AAAAAA-AAACAAAAAGAAA
1 AAAAAAGAAACAAAAAGAAA
180085 AGAAAAAGA
1 A-AAAAAGA
180094 CTCCTACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 11 0.44
21 6 0.24
22 6 0.24
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAACAAAAAGAAA
Found at i:180073 original size:24 final size:22
Alignment explanation
Indices: 180044--180091 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
180034 GTGCTACAAC
* *
180044 AAAAAAGCAACAAGAAAGAAGAAA
1 AAAAAAACAAAAAG-AA-AAGAAA
180068 AAAAAAACAAAAAGAAAAGAAA
1 AAAAAAACAAAAAGAAAAGAAA
180090 AA
1 AA
180092 GACTCCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAGAAAAGAAA
Found at i:183493 original size:35 final size:36
Alignment explanation
Indices: 183437--183504 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
183427 ATACAATCTG
183437 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
183473 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
183505 ACTTCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:184159 original size:21 final size:20
Alignment explanation
Indices: 184133--184182 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
184123 GTGCTACAAC
*
184133 AAAAAAGCAACAAGAAAGAAGA
1 AAAAAAGAAACAA-AAAGAA-A
184155 AAAAAA-AAACAAAAAGAAA
1 AAAAAAGAAACAAAAAGAAA
184174 AGAAAAAGA
1 A-AAAAAGA
184183 CTCCTACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 11 0.44
21 6 0.24
22 6 0.24
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAACAAAAAGAAA
Found at i:184162 original size:24 final size:22
Alignment explanation
Indices: 184133--184180 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
184123 GTGCTACAAC
* *
184133 AAAAAAGCAACAAGAAAGAAGAAA
1 AAAAAAACAAAAAG-AA-AAGAAA
184157 AAAAAAACAAAAAGAAAAGAAA
1 AAAAAAACAAAAAGAAAAGAAA
184179 AA
1 AA
184181 GACTCCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAGAAAAGAAA
Found at i:191339 original size:23 final size:25
Alignment explanation
Indices: 191299--191352 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
191289 TTCTTTTCTT
191299 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
191324 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
191347 TTTCTT
1 TTTCTT
191353 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:195494 original size:14 final size:15
Alignment explanation
Indices: 195460--195506 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
195450 AATTTGGAGT
195460 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
195475 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
195489 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
195506 G
1 G
195507 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:195677 original size:12 final size:12
Alignment explanation
Indices: 195662--195693 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
195652 ATTTCATTTC
195662 CTTTTCTTTCAT
1 CTTTTCTTTCAT
195674 CTTTTCTTTCAT
1 CTTTTCTTTCAT
195686 CTTTTCTT
1 CTTTTCTT
195694 ATTCCATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (12 bp):
CTTTTCTTTCAT
Found at i:200706 original size:35 final size:37
Alignment explanation
Indices: 200638--200717 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
200628 ATACTATTTC
* *
200638 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
200675 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
200710 CATCACCA
1 CATCACCA
200718 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:201131 original size:103 final size:103
Alignment explanation
Indices: 200946--201152 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 103
200936 TGTACGGATT
*
200946 ATTTTTCAATTCATGGTGTAGCATTTGGTGTCTTTCCTAGATCGGGAAACAACAAGGTTGCCAAC
1 ATTTTTCAATTCAAGGTGTAGCATTTGGTGTCTTTCCTAGATCGGGAAACAACAAGGTTGCCAAC
201011 TTCTCCATAATTGAAGAAGCCTAGTTAGCCTTACATCA
66 TTCTCCATAATTGAAGAAGCCTAGTTAGCCTTACATCA
201049 ATTTTTCAATTCAAGGTGTAGCATTTGGTGTCTTTCCTAGATCGGGAAACAACAAGGTTGCCAAC
1 ATTTTTCAATTCAAGGTGTAGCATTTGGTGTCTTTCCTAGATCGGGAAACAACAAGGTTGCCAAC
*
201114 TTCTCCATAA-TGTAAGAAGCCTGGTTAGCCTTACATCA
66 TTCTCCATAATTG-AAGAAGCCTAGTTAGCCTTACATCA
201152 A
1 A
201153 GTGGTATCAG
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 2 0.02
103 99 0.98
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (103 bp):
ATTTTTCAATTCAAGGTGTAGCATTTGGTGTCTTTCCTAGATCGGGAAACAACAAGGTTGCCAAC
TTCTCCATAATTGAAGAAGCCTAGTTAGCCTTACATCA
Found at i:201224 original size:12 final size:11
Alignment explanation
Indices: 201207--201240 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
201197 AAATAGCAAC
201207 AAGAAAGAAGAA
1 AAGAAA-AAGAA
201219 AAGAAAAGAGAA
1 AAGAAAA-AGAA
201231 AAGAAAAAGA
1 AAGAAAAAGA
201241 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:201296 original size:14 final size:15
Alignment explanation
Indices: 201262--201308 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
201252 AATTTGGAGT
201262 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
201277 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
201291 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
201308 G
1 G
201309 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:207172 original size:19 final size:20
Alignment explanation
Indices: 207131--207181 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
207121 GAAACCCCTT
*
207131 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
207151 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
207170 TGAAGATACATG
1 TGAAAATACATG
207182 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:210609 original size:11 final size:10
Alignment explanation
Indices: 210558--210609 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
210548 TTTTGAATTC
*
210558 TTTTCTTTTC
1 TTTTCTTTTT
210568 TTTTCTTCTTT
1 TTTTCTT-TTT
*
210579 TCTTCTTCTTT
1 TTTTCTT-TTT
*
210590 TTGTCTTTTT
1 TTTTCTTTTT
*
210600 CTTTCTTTTT
1 TTTTCTTTTT
210610 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:210610 original size:18 final size:18
Alignment explanation
Indices: 210556--210610 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
210546 CTTTTTGAAT
210556 TCTTTTCTTTTCTTTTCT-
1 TCTTTTCTTTTCTTTT-TG
210574 TCTTTTCTTCTTCTTTTTG
1 TCTTTTCTT-TTCTTTTTG
210593 TCTTTT-TCTTTCTTTTTG
1 TCTTTTCT-TTTCTTTTTG
210611 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTTG
Found at i:211358 original size:19 final size:20
Alignment explanation
Indices: 211317--211367 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
211307 GAAACCCCTT
*
211317 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
211337 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
211356 TGAAGATACATG
1 TGAAAATACATG
211368 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:221832 original size:14 final size:14
Alignment explanation
Indices: 221809--221838 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
221799 TTTTTTGAAA
*
221809 TTTTGGCTTTTTTT
1 TTTTGCCTTTTTTT
221823 TTTTGCCTTTTTTT
1 TTTTGCCTTTTTTT
221837 TT
1 TT
221839 GAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (14 bp):
TTTTGCCTTTTTTT
Found at i:227905 original size:35 final size:37
Alignment explanation
Indices: 227861--227930 Score: 117
Period size: 35 Copynumber: 1.9 Consensus size: 37
227851 TAGAAGTTGC
227861 TGATAATATAGGCGTGAT-ATGGTGATGGA-ATATAG
1 TGATAATATAGGCGTGATAATGGTGATGGACATATAG
*
227896 TGATGATATAGGCGTGATAATGGTGATGGACATAT
1 TGATAATATAGGCGTGATAATGGTGATGGACATAT
227931 TGTATCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.53
36 11 0.34
37 4 0.12
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (37 bp):
TGATAATATAGGCGTGATAATGGTGATGGACATATAG
Found at i:232630 original size:35 final size:37
Alignment explanation
Indices: 232584--232662 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
232574 TTTGAGAATT
*
232584 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
232619 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
232656 TGGTGAT
1 TGGTGAT
232663 AGAAATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:233049 original size:19 final size:20
Alignment explanation
Indices: 233002--233052 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
232992 GAAATCCCTT
**
233002 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
233022 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
233041 TGAAGATACATG
1 TGAAAATACATG
233053 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:235571 original size:11 final size:11
Alignment explanation
Indices: 235515--235563 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
235505 TTTGAGAATT
235515 TGGTGATGATA
1 TGGTGATGATA
*
235526 TAGGCG-TGATA
1 T-GGTGATGATA
235537 TGGTGATGGACTA
1 TGGTGAT-GA-TA
235550 TGGTGATGATA
1 TGGTGATGATA
235561 TGG
1 TGG
235564 GCATGATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.09
11 13 0.41
12 7 0.22
13 9 0.28
ACGTcount: A:0.24, C:0.04, G:0.39, T:0.33
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:235980 original size:19 final size:20
Alignment explanation
Indices: 235933--235983 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
235923 GAAATCCCTT
**
235933 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
235953 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
235972 TGAAGATACATG
1 TGAAAATACATG
235984 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:237820 original size:25 final size:25
Alignment explanation
Indices: 237774--237821 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
237764 ATTATAAAGT
*
237774 AATGAAATAAGAAAAGATGAAAGAA
1 AATGAAATAAGAAAAGAAGAAAGAA
*
237799 AATGAAATAA-AATAGTAAGAAAG
1 AATGAAATAAGAAAAG-AAGAAAG
237822 TGAAGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (25 bp):
AATGAAATAAGAAAAGAAGAAAGAA
Found at i:238908 original size:19 final size:20
Alignment explanation
Indices: 238861--238911 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
238851 GAAATCCCTT
**
238861 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
238881 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
238900 TGAAGATACATG
1 TGAAAATACATG
238912 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:247987 original size:35 final size:37
Alignment explanation
Indices: 247941--248019 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
247931 TTTGAGAATT
*
247941 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
247976 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
248013 TGGTGAT
1 TGGTGAT
248020 AGAAATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:248406 original size:19 final size:19
Alignment explanation
Indices: 248359--248411 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
248349 GAAATCCCTT
**
248359 TGAAAATACATGATTTTTGA
1 TGAAAATACATGA-TTTAAA
248379 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
248398 TGAAGATACATGAT
1 TGAAAATACATGAT
248412 CTTGGCCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:255548 original size:19 final size:19
Alignment explanation
Indices: 255524--255573 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
255514 GAAACCCCTT
*
255524 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
255543 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
255562 TGAAGATACATG
1 TGAAAATACATG
255574 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:258964 original size:11 final size:11
Alignment explanation
Indices: 258950--259005 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
258940 TCTTTTTGAA
258950 TTCTTTTTCTT
1 TTCTTTTTCTT
258961 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
258974 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
258987 TGTCTTTTTC-T
1 T-TCTTTTTCTT
258998 TTCTTTTT
1 TTCTTTTT
259006 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:258974 original size:19 final size:18
Alignment explanation
Indices: 258950--259005 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
258940 TCTTTTTGAA
258950 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
258968 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
258987 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
259005 T
1 T
259006 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:259756 original size:19 final size:20
Alignment explanation
Indices: 259715--259765 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
259705 GAAACCCCTT
*
259715 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
259735 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
259754 TGAAGATACATG
1 TGAAAATACATG
259766 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:261032 original size:11 final size:13
Alignment explanation
Indices: 261000--261029 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
260990 TGGCCAAAGA
261000 TGAAAAGGTATGT
1 TGAAAAGGTATGT
261013 TGAAAAGGTATG-
1 TGAAAAGGTATGT
261025 TGAAA
1 TGAAA
261030 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:263564 original size:19 final size:20
Alignment explanation
Indices: 263540--263579 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
263530 TATCCTTTCT
263540 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
263559 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
263579 T
1 T
263580 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:263881 original size:16 final size:16
Alignment explanation
Indices: 263851--263902 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
263841 TTGGAGTGAA
263851 AAAAGAAGAAAAAAATCAG
1 AAAAGAA-AAAAAAA--AG
*
263870 AAAAGAAGAAAAAAAG
1 AAAAGAAAAAAAAAAG
*
263886 AAAAGAAAAGAAAAAG
1 AAAAGAAAAAAAAAAG
263902 A
1 A
263903 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 17 0.57
18 6 0.20
19 7 0.23
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:269060 original size:19 final size:20
Alignment explanation
Indices: 269036--269075 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
269026 TATCCTTTCT
269036 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
269055 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
269075 T
1 T
269076 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:269552 original size:18 final size:19
Alignment explanation
Indices: 269522--269567 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
269512 ATCCTTTCTT
269522 TATTTTATTTCATT-CTTAA
1 TATTTTATTTCATTACTT-A
269541 TATTTT-TTTCATTACTTA
1 TATTTTATTTCATTACTTA
269559 TATTATTAT
1 TATT-TTAT
269568 CCCCTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.50
19 11 0.46
20 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTATTTCATTACTTA
Found at i:271351 original size:19 final size:21
Alignment explanation
Indices: 271308--271359 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
271298 GAAACCCCTT
271308 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
271329 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
271348 TGAAGATACATG
1 TGAAAATACATG
271360 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:272176 original size:26 final size:25
Alignment explanation
Indices: 272147--272195 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
272137 ATAATATCAG
*
272147 ATAAGTATATGAATTATTATAAAGTA
1 ATAAGAATATGAA-TATTATAAAGTA
* *
272173 ATAAGAATGTGCATATTATAAAG
1 ATAAGAATATGAATATTATAAAG
272196 ATGTGAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (25 bp):
ATAAGAATATGAATATTATAAAGTA
Found at i:274220 original size:19 final size:20
Alignment explanation
Indices: 274174--274222 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
274164 TAATAAAGGG
274174 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
274194 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
274213 AATAAAATAA
1 AATAAAATAA
274223 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:274736 original size:20 final size:21
Alignment explanation
Indices: 274699--274737 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
274689 GATGGTCTTG
*
274699 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
274720 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
274738 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:275110 original size:19 final size:20
Alignment explanation
Indices: 275072--275114 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
275062 GAAACCCCTT
*
275072 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
275092 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
275111 TGAA
1 TGAA
275115 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:278603 original size:10 final size:10
Alignment explanation
Indices: 278569--278610 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
278559 TCTTTTTGAA
278569 TTTCTT-TTT
1 TTTCTTCTTT
**
278578 TTTCTGATTCT
1 TTTCTTCTT-T
278589 TTTCTTCTTT
1 TTTCTTCTTT
278599 TTTCTTCTTT
1 TTTCTTCTTT
278609 TT
1 TT
278611 GTACTCCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.18
10 15 0.54
11 8 0.29
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTCTTCTTT
Found at i:278983 original size:20 final size:21
Alignment explanation
Indices: 278946--278984 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
278936 GATGGTCTTG
*
278946 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
278967 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
278985 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:279358 original size:19 final size:20
Alignment explanation
Indices: 279320--279362 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
279310 GAAACCCCTT
*
279320 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
279340 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
279359 TGAA
1 TGAA
279363 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:280320 original size:20 final size:19
Alignment explanation
Indices: 280284--280322 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
280274 AGTAAAGATG
**
280284 TGAAAACATATTTTATGCA
1 TGAAAACATATAGTATGCA
280303 TGAAAATCATATAGTATGCA
1 TGAAAA-CATATAGTATGCA
280323 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (19 bp):
TGAAAACATATAGTATGCA
Found at i:280723 original size:19 final size:21
Alignment explanation
Indices: 280680--280731 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
280670 GAAACCCCTT
280680 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
280701 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
280720 TGAAGATACATG
1 TGAAAATACATG
280732 CTCTTGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:295080 original size:133 final size:133
Alignment explanation
Indices: 294842--295108 Score: 507
Period size: 133 Copynumber: 2.0 Consensus size: 133
294832 TACATATCAT
* *
294842 TTCTTAGGATATTATTATTACATGTTTCCCTTTATCATTTATGAATACCATGTTATATGATATTC
1 TTCTTAGGATATTATTATTACATGTTTCCATTTATCACTTATGAATACCATGTTATATGATATTC
*
294907 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATAGTAGGATAGTC
294972 TTA
131 TTA
294975 TTCTTAGGATATTATTATTACATGTTTCCATTTATCACTTATGAATACCATGTTATATGATATTC
1 TTCTTAGGATATTATTATTACATGTTTCCATTTATCACTTATGAATACCATGTTATATGATATTC
295040 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATAGTAGGATAGTC
66 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATAGTAGGATAGTC
295105 TTA
131 TTA
295108 T
1 T
295109 AATCATATTA
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (133 bp):
TTCTTAGGATATTATTATTACATGTTTCCATTTATCACTTATGAATACCATGTTATATGATATTC
ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATAGTAGGATAGTC
TTA
Found at i:298156 original size:11 final size:11
Alignment explanation
Indices: 298142--298172 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
298132 AATACAAAAA
298142 GAAGTGCAAGT
1 GAAGTGCAAGT
298153 GAAGTGCAAGT
1 GAAGTGCAAGT
298164 GAAGTGCAA
1 GAAGTGCAA
298173 AGTCAAAGAA
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:0.39, C:0.10, G:0.35, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:298262 original size:10 final size:10
Alignment explanation
Indices: 298247--298272 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
298237 ACTCAAAAAG
298247 AAGAAAAGGA
1 AAGAAAAGGA
298257 AAGAAAAGGA
1 AAGAAAAGGA
298267 AAGAAA
1 AAGAAA
298273 GAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:304616 original size:14 final size:13
Alignment explanation
Indices: 304597--304635 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
304587 GTGCTGCAAC
304597 AAAAAGCAAAAAAA
1 AAAAAG-AAAAAAA
304611 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
304624 AGCAAAAGAAAA
1 A--AAAAGAAAA
304636 GACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:310403 original size:19 final size:21
Alignment explanation
Indices: 310360--310411 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
310350 GAAACCCCTT
310360 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
310381 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
310400 TGAAGATACATG
1 TGAAAATACATG
310412 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:314551 original size:19 final size:21
Alignment explanation
Indices: 314508--314559 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
314498 GAAACCCCTT
314508 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
314529 TGAAAATATATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
314548 TGAATATACATG
1 TGAAAATACATG
314560 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:315483 original size:30 final size:31
Alignment explanation
Indices: 315444--315503 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
315434 AGATGCTGCC
**
315444 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
315475 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
315504 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:318682 original size:19 final size:20
Alignment explanation
Indices: 318641--318683 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
318631 GAAACCCCTT
* *
318641 TGAAAATACATGATTTTTGA
1 TGAAAAAACATGATTTTTAA
318661 TGAAAAAACATGA-TTTTAA
1 TGAAAAAACATGATTTTTAA
318680 TGAA
1 TGAA
318684 GATACATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAAAACATGATTTTTAA
Found at i:318690 original size:19 final size:20
Alignment explanation
Indices: 318641--318690 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
318631 GAAACCCCTT
*
318641 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
318661 TGAAAAAACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
318680 TGAAGATACAT
1 TGAAAATACAT
318691 TCTCTTGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:322040 original size:19 final size:19
Alignment explanation
Indices: 321979--322037 Score: 109
Period size: 19 Copynumber: 3.1 Consensus size: 19
321969 TATCCTTTAT
321979 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
321998 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
322017 TTATTTCATTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
322037 T
1 T
322038 ATTATTATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
19 34 0.87
20 5 0.13
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:327147 original size:12 final size:12
Alignment explanation
Indices: 327130--327161 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
327120 ATTTATTACT
327130 TCGGTTTGTCCA
1 TCGGTTTGTCCA
327142 TCGGTTTGTCCA
1 TCGGTTTGTCCA
327154 TCGGTTTG
1 TCGGTTTG
327162 AGGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.22, G:0.28, T:0.44
Consensus pattern (12 bp):
TCGGTTTGTCCA
Done.