Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 93 of 182
Found at i:30206653 original size:14 final size:15
Alignment explanation
Indices: 30206634--30206664 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
30206624 TTTACTTTAT
30206634 TTTATTTTTAT-CTC
1 TTTATTTTTATCCTC
30206648 TTTATTTTTATCCTC
1 TTTATTTTTATCCTC
30206663 TT
1 TT
30206665 AAAAACACTC
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:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTTTATCCTC
Found at i:30223720 original size:21 final size:21
Alignment explanation
Indices: 30223696--30223744 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
30223686 AGTTTAGCCG
* *
30223696 AAAAGAGAGAAAT-AGT-GAA
1 AAAAAAGAAAAATGAGTAGAA
30223715 AAAAAAGAAAAATGAGTAGAA
1 AAAAAAGAAAAATGAGTAGAA
*
30223736 ACAAAAGAA
1 AAAAAAGAA
30223745 TAGAATCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.44
20 3 0.12
21 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.08
Consensus pattern (21 bp):
AAAAAAGAAAAATGAGTAGAA
Found at i:30242299 original size:6 final size:6
Alignment explanation
Indices: 30242290--30242337 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
30242280 GTTTTGAAAT
* * **
30242290 TTTTAA TTTTCA TTTTTA TTGTTGT TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TT-TTAA TTTTAA TTTTAA TTTTAA TTTTA
30242338 TTTATTATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:30242305 original size:21 final size:21
Alignment explanation
Indices: 30242264--30242305 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30242254 CTGTTAAGAA
**
30242264 GAAATTTTTTAATTTGGTTTT
1 GAAATTTTTTAATTTCATTTT
30242285 GAAA-TTTTTAATTTTCATTTT
1 GAAATTTTTTAA-TTTCATTTT
30242306 TATTGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.26, C:0.02, G:0.10, T:0.62
Consensus pattern (21 bp):
GAAATTTTTTAATTTCATTTT
Found at i:30242351 original size:31 final size:31
Alignment explanation
Indices: 30242290--30242352 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
30242280 GTTTTGAAAT
* * * *
30242290 TTTTAATTTTCATTTTTATTGTTGTTTTTAA
1 TTTTAATTTTAATTTTTATTATTATGTTTAA
30242321 TTTTAATTTTAA-TTTTATTTATTATGTTTAA
1 TTTTAATTTTAATTTTTA-TTATTATGTTTAA
30242352 T
1 T
30242353 AAAGGGGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.70
Consensus pattern (31 bp):
TTTTAATTTTAATTTTTATTATTATGTTTAA
Found at i:30243718 original size:22 final size:25
Alignment explanation
Indices: 30243684--30243747 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 25
30243674 TTCTGATCAT
*
30243684 TTATTGCAGTTCATCTCATAATACCA
1 TTATT-CAATTCATCTCATAATACCA
30243710 TTTCATTCAATTCATCTCATAATACCA
1 -TT-ATTCAATTCATCTCATAATACCA
30243737 TTTCATTCAAT
1 -TT-ATTCAAT
30243748 CATACTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.42
Consensus pattern (25 bp):
TTATTCAATTCATCTCATAATACCA
Found at i:30243723 original size:27 final size:27
Alignment explanation
Indices: 30243693--30243747 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
30243683 TTTATTGCAG
30243693 TTCATCTCATAATACCATTTCATTCAA
1 TTCATCTCATAATACCATTTCATTCAA
30243720 TTCATCTCATAATACCATTTCATTCAA
1 TTCATCTCATAATACCATTTCATTCAA
30243747 T
1 T
30243748 CATACTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (27 bp):
TTCATCTCATAATACCATTTCATTCAA
Found at i:30244886 original size:15 final size:16
Alignment explanation
Indices: 30244868--30244897 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30244858 TTAAAACCTA
30244868 AAAAAAGAAA-AAAAG
1 AAAAAAGAAAGAAAAG
30244883 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
30244898 AGTCAAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAG
Found at i:30245803 original size:7 final size:7
Alignment explanation
Indices: 30245793--30245855 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 7
30245783 ACAAAATTAA
30245793 AAAAAGG
1 AAAAAGG
30245800 AAAAAAGAG
1 -AAAAAG-G
30245809 AAAAAGAG
1 AAAAAG-G
30245817 AAAAA-G
1 AAAAAGG
30245823 -AAAAGG
1 AAAAAGG
30245829 AAAAA-G
1 AAAAAGG
*
30245835 AAGAAACG
1 AA-AAAGG
*
30245843 AAAAAAG
1 AAAAAGG
30245850 AAAAAG
1 AAAAAG
30245856 AGGAGGTCGA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
5 4 0.08
6 5 0.10
7 16 0.33
8 22 0.46
9 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:30245839 original size:21 final size:21
Alignment explanation
Indices: 30245800--30245856 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
30245790 TAAAAAAAGG
30245800 AAAAAAGAGAAAAAG-AGAAA-
1 AAAAAAG-GAAAAAGAAGAAAC
30245820 AAGAAAAGGAAAAAGAAGAAAC
1 AA-AAAAGGAAAAAGAAGAAAC
30245842 GAAAAAA-GAAAAAGA
1 -AAAAAAGGAAAAAGA
30245857 GGAGGTCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 9 0.27
21 18 0.55
22 4 0.12
23 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAAGGAAAAAGAAGAAAC
Found at i:30246811 original size:49 final size:49
Alignment explanation
Indices: 30246739--30246970 Score: 205
Period size: 49 Copynumber: 4.7 Consensus size: 49
30246729 TATACAGGTT
* * *
30246739 TGAAGGGAAAGATTGAAGCCGCAATGGCAAATCTAATACCTTAGAGATA
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCTTAGAGATA
* * * * **
30246788 TGAAGAGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGGGACG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCTTAGAGATA
* * * * * *
30246837 TGATGGGAAAGATTGAAGCCGCGACGGTGAATCTTGTACCCTAGAGCTA
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCTTAGAGATA
* * * * * * * *
30246886 TGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCCTATAGATG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCTTAGAGATA
* * * *
30246935 TGAAGGAAAAGATT-AGGGCCGCAATGACGAATCTTA
1 TGAAGGGAAAGATTGA-AGCCGCAACGGCGAATCTTA
30246971 CATTCTGAAG
Statistics
Matches: 144, Mismatches: 38, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
48 1 0.01
49 143 0.99
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCTTAGAGATA
Found at i:30246967 original size:98 final size:98
Alignment explanation
Indices: 30246739--30246970 Score: 268
Period size: 98 Copynumber: 2.4 Consensus size: 98
30246729 TATACAGGTT
* * *
30246739 TGAAGGGAAAGATTGAAGCCGCAATGGCAAATCTAATACCTTAGAGATATGAAGAGAAAGGTTGA
1 TGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAGAGATATGAAGAGAAAGGTTGA
* * *
30246804 AGCCGCAACGGCGAACCTTATACCTTAGGGACG
66 AGCCGCAACGACGAACCTTATACCCTAGAGACG
* * * * * * * *
30246837 TGATGGGAAAGATTGAAGCCGCGACGGTGAATCTTGTACCCTAGAGCTATGGAGGGAAAGGTTGA
1 TGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAGAGATATGAAGAGAAAGGTTGA
* * *
30246902 AGCCGCAACGACGAACCTTGTACCCTATAGATG
66 AGCCGCAACGACGAACCTTATACCCTAGAGACG
* * *
30246935 TGAAGGAAAAGATT-AGGGCCGCAATGACGAATCTTA
1 TGAAGGGAAAGATTGA-AGCCGCAATGGCGAATCTTA
30246971 CATTCTGAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
97 1 0.01
98 107 0.99
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (98 bp):
TGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTAGAGATATGAAGAGAAAGGTTGA
AGCCGCAACGACGAACCTTATACCCTAGAGACG
Found at i:30247301 original size:40 final size:39
Alignment explanation
Indices: 30247246--30247334 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 39
30247236 TACAATCATC
30247246 CAATCTTTTACCCTAATCAGAGGACAGATTGAAGACCATT
1 CAATCTTTTACCCTAATCAGAGGACAGATTGAAGACCA-T
*
30247286 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACCAT
1 CAATCTTTTACCCTAATCAGAGGACAGATTGAAGACCAT
30247325 CAGATCTTTT
1 CA-ATCTTTT
30247335 TGAAGACCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 3 0.06
40 44 0.94
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (39 bp):
CAATCTTTTACCCTAATCAGAGGACAGATTGAAGACCAT
Found at i:30247339 original size:20 final size:20
Alignment explanation
Indices: 30247314--30247354 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
30247304 AGAGGGCAGA
30247314 TTGAAGACCAT-CAGATCTTT
1 TTGAAGACCATCCA-ATCTTT
30247334 TTGAAGACCATCCAATCTTT
1 TTGAAGACCATCCAATCTTT
30247354 T
1 T
30247355 ACCCTAACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (20 bp):
TTGAAGACCATCCAATCTTT
Found at i:30247388 original size:39 final size:39
Alignment explanation
Indices: 30247334--30247619 Score: 167
Period size: 39 Copynumber: 7.3 Consensus size: 39
30247324 TCAGATCTTT
30247334 TTGAAGACCATCCAATCTTTTACCCTAACCGAGGACAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCGAGGACAGA
* * * *
30247373 TTGAAGACCATCCAATCTCTTA-CCTCGACCATAGTG-CAAA
1 TTGAAGACCATCCAATCTTTTACCCT-AACC-GAG-GACAGA
* * * *
30247413 TTGAAGTA--GTCCAATCTTTTATCCTAACTAGAGGGCAGA
1 TTGAAG-ACCATCCAATCTTTTACCCTAAC-CGAGGACAGA
* * * * ** *
30247452 TTGAAG-TCATCTAATCTCTCACCCCGACC-ATGGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCGA--GGACAGA
* * *
30247491 TTGAAG-CAAACCAATCTTTTACCCTAACCAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACC-GAGGACAGA
* * ** *
30247530 TTGAA-ATCATCTAATCTTTTACCCTAATTAGAGGACAAA
1 TTGAAGACCATCCAATCTTTTACCCTAA-CCGAGGACAGA
* * * *
30247569 TTAAAGACCATTCAATCTTTTACCCTAATC-AGAGAGTAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCGAG-GA-CAGA
30247609 TTGAAGACCAT
1 TTGAAGACCAT
30247620 TAGATCTTTT
Statistics
Matches: 187, Mismatches: 42, Indels: 35
0.71 0.16 0.13
Matches are distributed among these distances:
37 1 0.01
38 6 0.03
39 132 0.71
40 45 0.24
41 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
TTGAAGACCATCCAATCTTTTACCCTAACCGAGGACAGA
Found at i:30247468 original size:78 final size:77
Alignment explanation
Indices: 30247334--30247614 Score: 265
Period size: 78 Copynumber: 3.6 Consensus size: 77
30247324 TCAGATCTTT
* * * * * *
30247334 TTGAAGACCATCCAATCTTTTACCCTAACCGAGGACAGATTGAAGACCATCCAATCTCTTACCTC
1 TTGAAG-CAATCCAATCTTTTACCCTAACAGAGGGCAGATTGAAG-TCATCTAATCTCTTACCCC
*
30247399 GACCATAGTGCAAA
64 GACCATAGGGCAAA
* * * *
30247413 TTGAAGTAGTCCAATCTTTTATCCTAACTAGAGGGCAGATTGAAGTCATCTAATCTCTCACCCCG
1 TTGAAGCAATCCAATCTTTTACCCTAAC-AGAGGGCAGATTGAAGTCATCTAATCTCTTACCCCG
* *
30247478 ACCATGGGGCAGA
65 ACCATAGGGCAAA
* * * **
30247491 TTGAAGCAAACCAATCTTTTACCCTAACCAGAGGGCAGATTGAAATCATCTAATCTTTTACCCTA
1 TTGAAGCAATCCAATCTTTTACCCTAA-CAGAGGGCAGATTGAAGTCATCTAATCTCTTACCCCG
** * *
30247556 ATTAGAGGACAAA
65 ACCATAGGGCAAA
* * * * *
30247569 TTAAAGACCATTCAATCTTTTACCCTAATCAGAGAGTAGATTGAAG
1 TTGAAG-CAATCCAATCTTTTACCCTAA-CAGAGGGCAGATTGAAG
30247615 ACCATTAGAT
Statistics
Matches: 163, Mismatches: 36, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
78 110 0.67
79 53 0.33
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (77 bp):
TTGAAGCAATCCAATCTTTTACCCTAACAGAGGGCAGATTGAAGTCATCTAATCTCTTACCCCGA
CCATAGGGCAAA
Found at i:30247684 original size:40 final size:40
Alignment explanation
Indices: 30247629--30248109 Score: 500
Period size: 40 Copynumber: 12.2 Consensus size: 40
30247619 TTAGATCTTT
* * *
30247629 TTGAAGGCCATCCAATCTTTTACCCTAACTAGAGGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* ** *
30247669 TTGAAGACCATCCAATCTCTTACCCCGACCATG-GGGCAAA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
*
30247709 TTGAAG--CAGTCCAATCTTTTACCCTAACTAGAGGGCAGA
1 TTGAAGACCA-TCCAATCTTTTACCCTAACCAGAGGGCAGA
* * *
30247748 TTGAA-ATCATCCAATCTCTTACCCCAACCATGA-GGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* *
30247787 TTGAAG-CAATCCAATCTTTTATCCTAACCAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
*
30247826 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
*
30247866 TTGAAGACCATCCAATCTTTTACCCTAACTAGAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * *
30247906 TTGAAGACTATCAAATCTTTTACCCTAACTAAAGGGCAGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * *
30247946 TTGAAG-CCATCTAATCTCTTATCC-AGACCATG-GGGTAGA
1 TTGAAGACCATCCAATCTTTTACCCTA-ACCA-GAGGGCAGA
* * **
30247985 TTGAAGACCATCCTATCTCTTACCCCGACCAGAGGGCA-A
1 TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * *
30248024 TTAAAAACCATCCGATCTCTTACCCTAACCATGA-GGCTGA
1 TTGAAGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGA
** *
30248064 TTGAA-ATGATTCAGATCTTTTACCCTAACCAGAGGGCAGA
1 TTGAAGACCATCCA-ATCTTTTACCCTAACCAGAGGGCAGA
30248104 TTGAAG
1 TTGAAG
30248110 TAATCCAGAT
Statistics
Matches: 373, Mismatches: 49, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
38 6 0.02
39 154 0.41
40 212 0.57
41 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (40 bp):
TTGAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGA
Found at i:30247751 original size:139 final size:138
Alignment explanation
Indices: 30247501--30247752 Score: 312
Period size: 139 Copynumber: 1.8 Consensus size: 138
30247491 TTGAAGCAAA
* * * * * **
30247501 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAATCATCTAATCTTTTACCCTAATTAGAGGAC
1 CCAATCTTTTACCCTAACCAGAGGGCAAATTGAAACCATCCAATCTCTTACCCCAACCAGAGGAC
* *
30247566 AAATTAAAGACCATTCAATCTTTTACCCTAATCAGAGAGTAGATTGAAGACCATTAGATCTTTTT
66 AAATTAAAGA-CATCCAATCTTTTACCCTAATCAGAGAGCAGATTGAAGACCATTAGATCTTTTT
30247631 GAAGGCCAT
130 GAAGGCCAT
* *
30247640 CCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCCGACCATG-GG
1 CCAATCTTTTACCCTAACCAGAGGGCAAATTGAA-ACCATCCAATCTCTTACCCCAACCA-GAGG
* * *
30247704 GCAAATTGAAG-CAGTCCAATCTTTTACCCTAA-CTAGAGGGCAGATTGAA
64 ACAAATTAAAGACA-TCCAATCTTTTACCCTAATC-AGAGAGCAGATTGAA
30247753 ATCATCCAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
138 3 0.03
139 62 0.65
140 29 0.31
141 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (138 bp):
CCAATCTTTTACCCTAACCAGAGGGCAAATTGAAACCATCCAATCTCTTACCCCAACCAGAGGAC
AAATTAAAGACATCCAATCTTTTACCCTAATCAGAGAGCAGATTGAAGACCATTAGATCTTTTTG
AAGGCCAT
Found at i:30248143 original size:198 final size:197
Alignment explanation
Indices: 30247636--30248154 Score: 539
Period size: 198 Copynumber: 2.6 Consensus size: 197
30247626 TTTTTGAAGG
* * * * **
30247636 CCATCCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCCGACCAT
1 CCATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACCA-
* * * * * **
30247701 G-GGGCAAATTGAAG-CAGTCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAATCATCCAATC
65 GAGGGCAGATTGAAGACA-TCAAATCTCTTACCCTAACCAAAGGGCAGATTGAAGCCATCCAATC
* * * *
30247764 TCTTACCCCAACCATGAGGCAGATTGAAGCAATCCAATCTTTTATCCTAACCAGAGGGCAGATTG
129 TCTTACCCCAACCATGAGGCAGATTGAAGCAATCCAATCTCTTACCCCAACCAGAGGGCAGATTA
*
30247829 AAGA
194 AAAA
* * *
30247833 CCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACTAG
1 CCATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACCAG
* * *
30247898 AGGGCAGATTGAAGACTATCAAATCTTTTACCCTAACTAAAGGGCAGATTGAAGCCATCTAATCT
66 AGGGCAGATTGAAGAC-ATCAAATCTCTTACCCTAACCAAAGGGCAGATTGAAGCCATCCAATCT
* * * * * *
30247963 CTTA-TCCAGACCATGGGGTAGATTGAAGACCATCCTATCTCTTACCCCGACCAGAGGGCA-ATT
130 CTTACCCCA-ACCATGAGGCAGATTGAAG-CAATCCAATCTCTTACCCCAACCAGAGGGCAGATT
30248026 AAAAA
193 AAAAA
* * ** *
30248031 CCATCCGATCTCTTACCCTAACCATGA-GGCTGATTGAA-ATGATTCAGATCTTTTACCCTAACC
1 CCATCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACCATCCA-ATCTTTTACCCTAACC
* ** * **
30248094 AGAGGGCAGATTGAAGTA-ATCCAGATCTCTTATTCTGACCATGGGGCAGATTGAAGCCATC
64 AGAGGGCAGATTGAAG-ACAT-CAAATCTCTTACCCTAACCAAAGGGCAGATTGAAGCCATC
30248155 AGATTGAAAA
Statistics
Matches: 275, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
196 1 0.00
197 81 0.29
198 164 0.60
199 29 0.11
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (197 bp):
CCATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAACCAG
AGGGCAGATTGAAGACATCAAATCTCTTACCCTAACCAAAGGGCAGATTGAAGCCATCCAATCTC
TTACCCCAACCATGAGGCAGATTGAAGCAATCCAATCTCTTACCCCAACCAGAGGGCAGATTAAA
AA
Found at i:30248158 original size:79 final size:78
Alignment explanation
Indices: 30247629--30248155 Score: 419
Period size: 79 Copynumber: 6.7 Consensus size: 78
30247619 TTAGATCTTT
* * * * * *
30247629 TTGAAGGCCATCCAATCTTTTACCCTAACTA-GAGGGCAAATTGAAGACCATCCAATCTCTTACC
1 TTGAA-GCAATCCAATCTCTTATCCTAACCATG-GGGCAGATTGAAGACCAT-CAATCTTTTACC
** *
30247693 CCGACCATG-GGGCAAA
63 CTAACCA-GAGGGCAGA
* * * * * *
30247709 TTGAAGCAGTCCAATCTTTTACCCTAACTA-GAGGGCAGATTGAA-ATCATCCAATCTCTTACCC
1 TTGAAGCAATCCAATCTCTTATCCTAACCATG-GGGCAGATTGAAGACCAT-CAATCTTTTACCC
*
30247772 CAACCATGA-GGCAGA
64 TAACCA-GAGGGCAGA
*
30247787 TTGAAGCAATCCAATCTTTTATCCTAACCA-GAGGGCAGATTGAAGACCATCCAATCTTTTACCC
1 TTGAAGCAATCCAATCTCTTATCCTAACCATG-GGGCAGATTGAAGACCAT-CAATCTTTTACCC
*
30247851 TAACTAGAGGGCAGA
64 TAACCAGAGGGCAGA
* * * * *
30247866 TTGAAGACCATCCAATCTTTTACCCTAACTA-GAGGGCAGATTGAAGACTATCAAATCTTTTACC
1 TTGAAG-CAATCCAATCTCTTATCCTAACCATG-GGGCAGATTGAAGACCATC-AATCTTTTACC
* *
30247930 CTAACTAAAGGGCAGA
63 CTAACCAGAGGGCAGA
* * * * *
30247946 TTGAAGCCATCTAATCTCTTATCC-AGACCATGGGGTAGATTGAAGACCATCCTATCTCTTACCC
1 TTGAAGCAATCCAATCTCTTATCCTA-ACCATGGGGCAGATTGAAGACCAT-CAATCTTTTACCC
**
30248010 CGACCAGAGGGCA-A
64 TAACCAGAGGGCAGA
* * * * * * * **
30248024 TTAAAAACCATCCGATCTCTTACCCTAACCATGAGGCTGATTGAA-ATGATTCAGATCTTTTACC
1 TT-GAAGCAATCCAATCTCTTATCCTAACCATGGGGCAGATTGAAGACCA-TCA-ATCTTTTACC
30248088 CTAACCAGAGGGCAGA
63 CTAACCAGAGGGCAGA
* * *
30248104 TTGAAGTAATCCAGATCTCTTATTCTGACCATGGGGCAGATTGAAG-CCATCA
1 TTGAAGCAATCCA-ATCTCTTATCCTAACCATGGGGCAGATTGAAGACCATCA
30248156 GATTGAAAAT
Statistics
Matches: 376, Mismatches: 56, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
78 80 0.21
79 186 0.49
80 110 0.29
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (78 bp):
TTGAAGCAATCCAATCTCTTATCCTAACCATGGGGCAGATTGAAGACCATCAATCTTTTACCCTA
ACCAGAGGGCAGA
Found at i:30253895 original size:24 final size:24
Alignment explanation
Indices: 30253808--30253896 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
30253798 TTCCAGGAAT
* * *
30253808 TTAGCTCATACGAGCCTAGACAGAA
1 TTAGCTCTTACGAGCCTAGATAG-G
* *
30253833 TTAGCTCTTACAAGCCCAGATAGG
1 TTAGCTCTTACGAGCCTAGATAGG
30253857 TTAGC-CGTTACGAGCCTAGATAGG
1 TTAGCTC-TTACGAGCCTAGATAGG
*
30253881 TTAGCTCTTATGAGCC
1 TTAGCTCTTACGAGCC
30253897 CAGACAGAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 1 0.02
24 33 0.61
25 20 0.37
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCTAGATAGG
Found at i:30254783 original size:40 final size:40
Alignment explanation
Indices: 30254728--30254804 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
30254718 ACACCTTAAG
*
30254728 CCTTAAGCCTCCTTTGGGTATGATCCTCGGAATACTATTT
1 CCTTAAGCCTCCTTTGGGTATGATCCTCAGAATACTATTT
30254768 CCTTAAGCCTCCTTTGGGTATGATCCTCAGAATACTA
1 CCTTAAGCCTCCTTTGGGTATGATCCTCAGAATACTA
30254805 CCAAGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (40 bp):
CCTTAAGCCTCCTTTGGGTATGATCCTCAGAATACTATTT
Found at i:30268818 original size:29 final size:29
Alignment explanation
Indices: 30268766--30268822 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
30268756 TCAACATGCA
* *
30268766 ATAACACAACACATATTAAAATCACACAG
1 ATAACACAACACAGAATAAAATCACACAG
*
30268795 ATAACACAACACAGAATAATATCACACA
1 ATAACACAACACAGAATAAAATCACACA
30268823 AGATGTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.56, C:0.25, G:0.04, T:0.16
Consensus pattern (29 bp):
ATAACACAACACAGAATAAAATCACACAG
Found at i:30269246 original size:14 final size:13
Alignment explanation
Indices: 30269205--30269239 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
30269195 GTTGTTCGAA
*
30269205 AAAGTCAACAATC
1 AAAGTCAACGATC
30269218 AAAGTCAACGATC
1 AAAGTCAACGATC
30269231 AAAGGTCAA
1 AAA-GTCAA
30269240 TGGTCAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:30273101 original size:12 final size:13
Alignment explanation
Indices: 30273081--30273112 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
30273071 TTAATAGTTC
30273081 AGTCAATGGGTCG
1 AGTCAATGGGTCG
30273094 AG-CAATGGGTCG
1 AGTCAATGGGTCG
30273106 AGTCAAT
1 AGTCAAT
30273113 CAATTGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.22
Consensus pattern (13 bp):
AGTCAATGGGTCG
Found at i:30278024 original size:20 final size:20
Alignment explanation
Indices: 30277999--30278037 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30277989 GATGGGGCTG
30277999 AGGCTTTGTTTGCCAGCAGT
1 AGGCTTTGTTTGCCAGCAGT
*
30278019 AGGCTTTGTTTGGCAGCAG
1 AGGCTTTGTTTGCCAGCAG
30278038 GCTAACTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (20 bp):
AGGCTTTGTTTGCCAGCAGT
Found at i:30279816 original size:12 final size:12
Alignment explanation
Indices: 30279799--30279825 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30279789 GCAACACAAA
30279799 CGTTCTTGTAAT
1 CGTTCTTGTAAT
30279811 CGTTCTTGTAAT
1 CGTTCTTGTAAT
30279823 CGT
1 CGT
30279826 CAATCGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (12 bp):
CGTTCTTGTAAT
Found at i:30279909 original size:26 final size:26
Alignment explanation
Indices: 30279878--30279933 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
30279868 TGCATTTGTA
30279878 TGAACTAGTTTCAAAATTACATATGT
1 TGAACTAGTTTCAAAATTACATATGT
30279904 TGAACTAGTTTCAAAATTACATATGT
1 TGAACTAGTTTCAAAATTACATATGT
30279930 TGAA
1 TGAA
30279934 TGTGATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (26 bp):
TGAACTAGTTTCAAAATTACATATGT
Found at i:30280140 original size:13 final size:14
Alignment explanation
Indices: 30280121--30280153 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30280111 TACCGATTAC
30280121 AATATAATTCTTTT
1 AATATAATTCTTTT
*
30280135 -ATATAATTTTTTT
1 AATATAATTCTTTT
30280148 AATATA
1 AATATA
30280154 CTAGTGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATAATTCTTTT
Found at i:30280717 original size:10 final size:10
Alignment explanation
Indices: 30280704--30280737 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
30280694 TTCAATATTG
30280704 TTTAATAAAT
1 TTTAATAAAT
*
30280714 TTTAATAAAG
1 TTTAATAAAT
30280724 TTTAATAAAGT
1 TTTAATAAA-T
30280735 TTT
1 TTT
30280738 TAATTGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
TTTAATAAAT
Found at i:30281211 original size:16 final size:18
Alignment explanation
Indices: 30281172--30281205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30281162 TAAGTTTATA
30281172 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
30281189 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
30281206 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:30283424 original size:22 final size:21
Alignment explanation
Indices: 30283377--30283421 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
30283367 CTATGTTTAT
*
30283377 AAATGGTGTTTTGAAGAAGAA
1 AAATGGTGTTTGGAAGAAGAA
30283398 AAATGGTGTTTGGCAAG-AGAA
1 AAATGGTGTTTGG-AAGAAGAA
30283419 AAA
1 AAA
30283422 ATGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.24
Consensus pattern (21 bp):
AAATGGTGTTTGGAAGAAGAA
Found at i:30283867 original size:17 final size:19
Alignment explanation
Indices: 30283847--30283888 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
30283837 AACATATTCT
30283847 TATAAAAATT-AA-AAATA
1 TATAAAAATTCAATAAATA
30283864 TATAAAAATTCAATAAATA
1 TATAAAAATTCAATAAATA
*
30283883 CATAAA
1 TATAAA
30283889 TTTTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 2 0.09
19 10 0.45
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
TATAAAAATTCAATAAATA
Found at i:30283887 original size:19 final size:17
Alignment explanation
Indices: 30283848--30283888 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
30283838 ACATATTCTT
*
30283848 ATAAAAATTAAAAATAT
1 ATAAAAATTAAAAATAC
30283865 ATAAAAATTCAATAAATAC
1 ATAAAAATT-AA-AAATAC
30283884 ATAAA
1 ATAAA
30283889 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 10 0.48
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATTAAAAATAC
Found at i:30290665 original size:17 final size:18
Alignment explanation
Indices: 30290643--30290676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30290633 AGAAAACTCT
30290643 TTGTTTA-TTTGTATTTA
1 TTGTTTACTTTGTATTTA
*
30290660 TTGTTTACTTTTTATTT
1 TTGTTTACTTTGTATTT
30290677 GATTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (18 bp):
TTGTTTACTTTGTATTTA
Found at i:30291076 original size:19 final size:19
Alignment explanation
Indices: 30291053--30291091 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
30291043 ATTTAACCAG
30291053 ATTTTTA-ATATTT-TTTTT
1 ATTTTTATA-ATTTATTTTT
30291071 ATTTTTATAATTTATTTTT
1 ATTTTTATAATTTATTTTT
30291090 AT
1 AT
30291092 AAATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTTATAATTTATTTTT
Found at i:30291097 original size:14 final size:13
Alignment explanation
Indices: 30291068--30291093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30291058 TAATATTTTT
30291068 TTTATTTTTATAA
1 TTTATTTTTATAA
30291081 TTTATTTTTATAA
1 TTTATTTTTATAA
30291094 ATTTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTTTATAA
Found at i:30303839 original size:37 final size:37
Alignment explanation
Indices: 30303776--30303860 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
30303766 ACATCCAAAT
* * *
30303776 TTGCGCCCAAAACTATCGTCGCATGAGCACTTCTAGA
1 TTGCACCCAAAACTATCGCCGCATGAGCACTTCCAGA
* * *
30303813 TTGCACTCAAAACTGTCGCCGTATGAGCACTTCCAGA
1 TTGCACCCAAAACTATCGCCGCATGAGCACTTCCAGA
30303850 TTGCACCCAAA
1 TTGCACCCAAA
30303861 GTTATCGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
TTGCACCCAAAACTATCGCCGCATGAGCACTTCCAGA
Found at i:30304790 original size:16 final size:16
Alignment explanation
Indices: 30304769--30304799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30304759 TTGTGGATCC
30304769 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
30304785 CATTTTATCTTTATT
1 CATTTTACCTTTATT
30304800 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:30308407 original size:21 final size:21
Alignment explanation
Indices: 30308381--30308428 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
30308371 ATTTCTCTGT
30308381 AACATCTGGTTGTGCACTGGC
1 AACATCTGGTTGTGCACTGGC
30308402 AACATCTGGTTGTGCACTGGC
1 AACATCTGGTTGTGCACTGGC
*
30308423 ATCATC
1 AACATC
30308429 AACTGTGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
AACATCTGGTTGTGCACTGGC
Found at i:30314101 original size:18 final size:18
Alignment explanation
Indices: 30314065--30314101 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30314055 AGATACCTCA
**
30314065 GGTTGCGTCGACATTTTT
1 GGTTGCGTCGACAGCTTT
30314083 GGTTGCGTCGACAGCTTT
1 GGTTGCGTCGACAGCTTT
30314101 G
1 G
30314102 ATGGTCGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.38
Consensus pattern (18 bp):
GGTTGCGTCGACAGCTTT
Found at i:30323191 original size:17 final size:18
Alignment explanation
Indices: 30323144--30323184 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
30323134 TATATTAATA
30323144 CATTTTATTTTGTCATAG
1 CATTTTATTTTGTCATAG
*
30323162 CATTTTATTTTGTCATTG
1 CATTTTATTTTGTCATAG
30323180 CATTT
1 CATTT
30323185 CTTTTGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (18 bp):
CATTTTATTTTGTCATAG
Found at i:30323812 original size:21 final size:20
Alignment explanation
Indices: 30323783--30323821 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
30323773 TATGAATGAG
30323783 AAAAGGAAAAGAAAAAGAGA
1 AAAAGGAAAAGAAAAAGAGA
30323803 AAAAGAGAAAAGAAAAAGA
1 AAAAG-GAAAAGAAAAAGA
30323822 AATATCGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAGGAAAAGAAAAAGAGA
Found at i:30328841 original size:30 final size:30
Alignment explanation
Indices: 30328786--30328843 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
30328776 AGCTAAAGAA
*
30328786 GAAGAAGAAGATCCAGACGAGGATCCTAAG
1 GAAGAAGAAGATCCAGACGAAGATCCTAAG
*
30328816 GAAGAAGAAGATCCTA-AGGAAGATCCTA
1 GAAGAAGAAGATCC-AGACGAAGATCCTA
30328844 TGGAGATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.28, T:0.12
Consensus pattern (30 bp):
GAAGAAGAAGATCCAGACGAAGATCCTAAG
Found at i:30346150 original size:17 final size:17
Alignment explanation
Indices: 30346111--30346155 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
30346101 TGATATATGG
**
30346111 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
30346128 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
30346145 AAATGCAATGA
1 AAATGCAATGA
30346156 AAAAGGAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:30355896 original size:15 final size:14
Alignment explanation
Indices: 30355876--30355916 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
30355866 GATCAAGAAG
30355876 AAGAAGAAGAAAGA
1 AAGAAGAAGAAAGA
30355890 AAG--GAAGAAGAGA
1 AAGAAGAAGAA-AGA
30355903 AAGAAGAA-AAAGA
1 AAGAAGAAGAAAGA
30355916 A
1 A
30355917 CCTGTCGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.25
13 10 0.42
14 5 0.21
15 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAAGA
Found at i:30355906 original size:21 final size:20
Alignment explanation
Indices: 30355872--30355911 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
30355862 GAAAGATCAA
30355872 GAAGAAGAAGAAGAAAGAAAG
1 GAAGAAGAAGAAG-AAGAAAG
30355893 GAAGAAG-AGAAAGAAGAAA
1 GAAGAAGAAG-AAGAAGAAA
30355912 AAGAACCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAGAAGAAGAAGAAGAAAG
Found at i:30358359 original size:30 final size:30
Alignment explanation
Indices: 30358325--30358387 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
30358315 CAGTGCGCCG
*
30358325 ACATTGAAAATGCGATGACAGGTTGGGTTA
1 ACATTGAAAACGCGATGACAGGTTGGGTTA
30358355 ACATTGAAAACGCGATGACAGGTTGGGTTA
1 ACATTGAAAACGCGATGACAGGTTGGGTTA
30358385 ACA
1 ACA
30358388 AGTAAGTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.24
Consensus pattern (30 bp):
ACATTGAAAACGCGATGACAGGTTGGGTTA
Found at i:30359865 original size:37 final size:37
Alignment explanation
Indices: 30359821--30360033 Score: 284
Period size: 37 Copynumber: 5.8 Consensus size: 37
30359811 TGTTTGCACA
* * * *
30359821 GTATTCAGGGTTTGTGCCTAGTAGGCTTCGTGCCGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
*
30359858 GCATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
30359895 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
* *
30359932 GTATTCAGGCTGTGTGCCTAGCGGGCTTCGTTCTGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
* * * *
30359969 GTATTC-GAGCTATGTGCATAGTAGGCTTCGTGCCGGT
1 GTATTCAG-GCTGTGTGCCTAGCAGGCTTCGTGCTGGT
* * *
30360006 GTATTCGGGCTATGTGCCTAGCAAGCTT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTT
30360034 TATGCCGGTG
Statistics
Matches: 157, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
36 1 0.01
37 155 0.99
38 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.34, T:0.33
Consensus pattern (37 bp):
GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
Found at i:30359903 original size:21 final size:21
Alignment explanation
Indices: 30359879--30359942 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
30359869 GTGTGCCTAG
30359879 CAGGCTTCGTGCTGGTGTATT
1 CAGGCTTCGTGCTGGTGTATT
** *
30359900 CAGGC-T-GTG-T-GCCTA-G
1 CAGGCTTCGTGCTGGTGTATT
30359916 CAGGCTTCGTGCTGGTGTATT
1 CAGGCTTCGTGCTGGTGTATT
30359937 CAGGCT
1 CAGGCT
30359943 GTGTGCCTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
18 4 0.12
19 4 0.12
20 4 0.12
21 11 0.34
ACGTcount: A:0.11, C:0.22, G:0.34, T:0.33
Consensus pattern (21 bp):
CAGGCTTCGTGCTGGTGTATT
Found at i:30367358 original size:37 final size:37
Alignment explanation
Indices: 30367313--30367498 Score: 264
Period size: 37 Copynumber: 5.0 Consensus size: 37
30367303 TGTTTGCACA
* * *
30367313 GTATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCAGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
* *
30367350 GCATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
*
30367387 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCTGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
30367424 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
* * * * **
30367461 GTATTCGGGCTATGTGCATAGCAGACTTTATGCCGGT
1 GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
30367498 G
1 G
30367499 ATCCAAGAAC
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.13, C:0.23, G:0.33, T:0.32
Consensus pattern (37 bp):
GTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGT
Found at i:30367376 original size:16 final size:16
Alignment explanation
Indices: 30367355--30367450 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
30367345 CCAGTGCATT
30367355 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
** *
30367371 CAGGCTTCGTGCTGGTGTATT
1 CAGGC-T-GTG-T-GCCTA-G
30367392 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
*
30367408 CAGGCT-TCGTGCCTGTGTATT
1 CAGGCTGT-GTGCC----TA-G
30367429 CAGGCTGTGTGCCTAG
1 CAGGCTGTGTGCCTAG
30367445 CAGGCT
1 CAGGCT
30367451 TCGTGCCGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
15 1 0.02
16 22 0.37
17 6 0.10
18 4 0.07
19 4 0.07
20 6 0.10
21 16 0.27
22 1 0.02
ACGTcount: A:0.11, C:0.24, G:0.34, T:0.30
Consensus pattern (16 bp):
CAGGCTGTGTGCCTAG
Found at i:30389911 original size:25 final size:25
Alignment explanation
Indices: 30389865--30389912 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30389855 ACTGGATACT
* * *
30389865 TTTAATATTATAATTTATTTATTTA
1 TTTAATATTAGAAATTAATTATTTA
30389890 TTTAATATTAGAAATTAATTATT
1 TTTAATATTAGAAATTAATTATT
30389913 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTAATATTAGAAATTAATTATTTA
Found at i:30391469 original size:30 final size:29
Alignment explanation
Indices: 30391409--30391497 Score: 128
Period size: 30 Copynumber: 3.1 Consensus size: 29
30391399 TAAATGTCTA
* *
30391409 TTAATTAAATTATTTGTATAATAA--AAT
1 TTAATTAAACTATTTTTATAATAATTAAT
30391436 TTAATTCAAACTATTTTTATAATAATTAAT
1 TTAATT-AAACTATTTTTATAATAATTAAT
30391466 TTAATTTAAACTATTTTTATAATAATTAAT
1 TTAA-TTAAACTATTTTTATAATAATTAAT
30391496 TT
1 TT
30391498 GTACTATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 6 0.11
28 16 0.29
30 32 0.57
31 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (29 bp):
TTAATTAAACTATTTTTATAATAATTAAT
Found at i:30394581 original size:83 final size:83
Alignment explanation
Indices: 30394442--30394609 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
30394432 ACATTGCCAA
* * *
30394442 CTTAGTAGCTGCAAAAGTCAACTCTCGCCTTTAGTCAATCAAAACACTAATTTTCATCAAGCTTT
1 CTTAGTAGATGCAAAAGTCAACTCTCGCCTTCAGTCAATCAAAACACTAATCTTCATCAAGCTTT
30394507 ATACCTTTCCGACCTCGT
66 ATACCTTTCCGACCTCGT
**
30394525 CTTAGTAGATGCCGAAGTCAACTCTCGCCTTCAGTCAATCAAAACACTAATCTTCATCAAGCTTT
1 CTTAGTAGATGCAAAAGTCAACTCTCGCCTTCAGTCAATCAAAACACTAATCTTCATCAAGCTTT
30394590 ATACCTTTCCGACCTCGT
66 ATACCTTTCCGACCTCGT
30394608 CT
1 CT
30394610 CACCACAGTC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (83 bp):
CTTAGTAGATGCAAAAGTCAACTCTCGCCTTCAGTCAATCAAAACACTAATCTTCATCAAGCTTT
ATACCTTTCCGACCTCGT
Found at i:30399242 original size:67 final size:64
Alignment explanation
Indices: 30399138--30399312 Score: 271
Period size: 67 Copynumber: 2.7 Consensus size: 64
30399128 TTATTTATTT
*
30399138 ATTTATTTATCTATATTCAT-AAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
*
30399201 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTT
1 ATTTATTTATTTATATTCATA-AA-AAT-AATAAATAAATAATAAAACAAAATTAATATTATTTT
*
30399266 AT
63 AC
*
30399268 ATTTATTTATTTATATTCATAAAAATAATAAATGAATGAATAAAA
1 ATTTATTTATTTATATTCATAAAAATAATAAATAAAT-AATAAAA
30399313 ATAATAAGAA
Statistics
Matches: 103, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
63 19 0.18
64 10 0.10
65 12 0.12
66 5 0.05
67 57 0.55
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (64 bp):
ATTTATTTATTTATATTCATAAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:30401696 original size:31 final size:31
Alignment explanation
Indices: 30401650--30401729 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
30401640 CGTCTTTCTC
30401650 AAACTTT-T-AATGCATGAAAATGCGATGCA
1 AAACTTTATGAATGCATGAAAATGCGATGCA
* *
30401679 AAACTTTATGAATGCATGAAAATGTGATGCG
1 AAACTTTATGAATGCATGAAAATGCGATGCA
*
30401710 AAATTTTATGAATGCATGAA
1 AAACTTTATGAATGCATGAA
30401730 TTCATATGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 7 0.15
30 1 0.02
31 38 0.83
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATGCGATGCA
Found at i:30403887 original size:11 final size:11
Alignment explanation
Indices: 30403871--30403896 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30403861 TCGACAAAGG
30403871 AATGGAAGGGA
1 AATGGAAGGGA
30403882 AATGGAAGGGA
1 AATGGAAGGGA
30403893 AATG
1 AATG
30403897 CTAAAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (11 bp):
AATGGAAGGGA
Found at i:30404346 original size:64 final size:63
Alignment explanation
Indices: 30404210--30404388 Score: 260
Period size: 64 Copynumber: 2.9 Consensus size: 63
30404200 TTATTTTGTT
* *
30404210 TATTTATTTATCTATATTCATAAAATAATAAATAAAT-AATAAA-ACAAAATTAATATTATTTTA
1 TATTTATTTATTTATATTCAT-AAATAATAAATAAATAAATAAATA-AAAATTAATATAATTTTA
*
30404273 CATTTATTTATTTATATTCATACAATAATAAATAAATAAATAAATAAAAATTAATATAATTTTA
1 TATTTATTTATTTATATTCATA-AATAATAAATAAATAAATAAATAAAAATTAATATAATTTTA
*
30404337 TATTTATTTATTTATATTCATAAA-AAT-AATAAATAAATGAATAAAAA-TAATA
1 TATTTATTTATTTATATTCATAAATAATAAATAAATAAATAAATAAAAATTAATA
30404389 AGAAAAATGG
Statistics
Matches: 108, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
60 5 0.05
61 19 0.18
62 4 0.04
63 35 0.32
64 44 0.41
65 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (63 bp):
TATTTATTTATTTATATTCATAAATAATAAATAAATAAATAAATAAAAATTAATATAATTTTA
Found at i:30404573 original size:17 final size:16
Alignment explanation
Indices: 30404551--30404586 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
30404541 ACTTGTATTA
30404551 TTTTTAAAAATGTCTTT
1 TTTTTAAAAATGT-TTT
30404568 TTTTTAAAAATGTTTT
1 TTTTTAAAAATGTTTT
30404584 TTT
1 TTT
30404587 AATTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTTTAAAAATGTTTT
Found at i:30406287 original size:21 final size:21
Alignment explanation
Indices: 30406261--30406317 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
30406251 CAGTAGTTTC
* *
30406261 CTACCGGTAGAAGTGAAGGTT
1 CTACCGATACAAGTGAAGGTT
30406282 CTACCGATACAAGTGAAGGTT
1 CTACCGATACAAGTGAAGGTT
30406303 CTACCGATACAAGTG
1 CTACCGATACAAGTG
30406318 TTCAGACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
CTACCGATACAAGTGAAGGTT
Found at i:30407050 original size:19 final size:19
Alignment explanation
Indices: 30406959--30407051 Score: 114
Period size: 19 Copynumber: 4.9 Consensus size: 19
30406949 TTAGTAATTT
* * *
30406959 GCTCTTATGAGCCAGTATT
1 GCTCTTACGAGCTAGTATC
* *
30406978 GCTCTTACGAGCCAATATC
1 GCTCTTACGAGCTAGTATC
* *
30406997 GCTCCTACGAGCTAGTATA
1 GCTCTTACGAGCTAGTATC
30407016 GCTCTTACGAGCTAGTATC
1 GCTCTTACGAGCTAGTATC
*
30407035 GCTCTTACGAGTTAGTA
1 GCTCTTACGAGCTAGTA
30407052 CAGTAATTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (19 bp):
GCTCTTACGAGCTAGTATC
Found at i:30407382 original size:102 final size:102
Alignment explanation
Indices: 30407199--30407386 Score: 297
Period size: 102 Copynumber: 1.8 Consensus size: 102
30407189 GCTACTCATT
*
30407199 AGTAAGTCATCCAAGACTAGCTCCCGAACTGTATAGCCCCTAATGACACGTCCTTTGAGTCCTGA
1 AGTAAGTCATCCAAGACTAGCTCCCGAACTGTATAGCCCCTAATGACACGTCCTTTGAGTCCCGA
* *
30407264 TTAGTCATGAAGTACATATGCTCAAGTACAGCCCATC
66 TTAGTCACGAAATACATATGCTCAAGTACAGCCCATC
* ** *
30407301 AGTAAGTTATCCAAGACTAGCTCTTGAACTGTATAGCCCCTAATGACACGTCCTTTCTA-TCCCG
1 AGTAAGTCATCCAAGACTAGCTCCCGAACTGTATAGCCCCTAATGACACGTCCTTT-GAGTCCCG
30407365 ATTAGTCACGAAATACATATGC
65 ATTAGTCACGAAATACATATGC
30407387 GTCATATACC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 77 0.99
103 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (102 bp):
AGTAAGTCATCCAAGACTAGCTCCCGAACTGTATAGCCCCTAATGACACGTCCTTTGAGTCCCGA
TTAGTCACGAAATACATATGCTCAAGTACAGCCCATC
Found at i:30411205 original size:18 final size:18
Alignment explanation
Indices: 30411182--30411218 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30411172 CCTATCAAAT
30411182 CCTAAAGATAAGATACTC
1 CCTAAAGATAAGATACTC
30411200 CCTAAAGATAAGATACTC
1 CCTAAAGATAAGATACTC
30411218 C
1 C
30411219 TTTATCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (18 bp):
CCTAAAGATAAGATACTC
Found at i:30417079 original size:17 final size:17
Alignment explanation
Indices: 30417059--30417097 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
30417049 GATAATGTAG
30417059 ATGCAACGACAATAAAA
1 ATGCAACGACAATAAAA
** *
30417076 ATGCAGTGATAATAAAA
1 ATGCAACGACAATAAAA
30417093 ATGCA
1 ATGCA
30417098 GGGACAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (17 bp):
ATGCAACGACAATAAAA
Found at i:30433491 original size:28 final size:28
Alignment explanation
Indices: 30433451--30433520 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
30433441 GGAAATATGT
* *
30433451 ACTTCGGTGCTTACCATTACAAGATTGC
1 ACTTTGGTGCTTACCATCACAAGATTGC
** *
30433479 ACTTTGGTGCTTACTGTCACATGATTGC
1 ACTTTGGTGCTTACCATCACAAGATTGC
30433507 ACTTTGGTGCTTAC
1 ACTTTGGTGCTTAC
30433521 TACTACGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (28 bp):
ACTTTGGTGCTTACCATCACAAGATTGC
Found at i:30433535 original size:28 final size:28
Alignment explanation
Indices: 30433476--30433549 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
30433466 ATTACAAGAT
* *
30433476 TGCACTTTGGTGCTTACTGTCACATGAT
1 TGCACTTTGGTGCTTACTCTCACATGAA
*
30433504 TGCACTTTGGTGCTTACTACT-ACGTGAA
1 TGCACTTTGGTGCTTACT-CTCACATGAA
* *
30433532 TGCACTATGGTGCCTACT
1 TGCACTTTGGTGCTTACT
30433550 GTTCTGCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (28 bp):
TGCACTTTGGTGCTTACTCTCACATGAA
Found at i:30435962 original size:12 final size:12
Alignment explanation
Indices: 30435947--30435993 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
30435937 ATGCAAGAAA
*
30435947 AAAACTAAAACT
1 AAAACTAAAAAT
30435959 AAAACTAAAAAT
1 AAAACTAAAAAT
30435971 -AAA-T-AAAAT
1 AAAACTAAAAAT
30435980 -AAA-TAAAAAT
1 AAAACTAAAAAT
30435990 AAAA
1 AAAA
30435994 AGAAAATTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.28
10 6 0.19
11 6 0.19
12 11 0.34
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAACTAAAAAT
Found at i:30435988 original size:10 final size:10
Alignment explanation
Indices: 30435964--30435992 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
30435954 AAACTAAAAC
30435964 TAAAAATAAA
1 TAAAAATAAA
30435974 T-AAAATAAA
1 TAAAAATAAA
30435983 TAAAAATAAA
1 TAAAAATAAA
30435993 AAGAAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:30439071 original size:26 final size:26
Alignment explanation
Indices: 30439035--30439091 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
30439025 TTTTGGGCGT
*
30439035 AATTCTGGACACGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCAAC
*
30439061 AATTCTGGACATGTTCATGCAGCAAC
1 AATTCTGGACACGTTCATGCAGCAAC
30439087 -ATTCT
1 AATTCT
30439092 TGGGTGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCAAC
Found at i:30439136 original size:36 final size:38
Alignment explanation
Indices: 30439089--30439173 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
30439079 GCAGCAACAT
*
30439089 TCTTGGGTGCAA-TTGAAGAATACTTATGTAGCGATAG
1 TCTTGGGTGCAATTTGAAGAATACTTATGCAGCGATAG
* * *
30439126 T-TTGGATGCAATTTGAGGAATATTTATGCAGCGATAG
1 TCTTGGGTGCAATTTGAAGAATACTTATGCAGCGATAG
30439163 TCTTGGGTGCA
1 TCTTGGGTGCA
30439174 TTCTGAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 9 0.22
37 24 0.59
38 8 0.20
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (38 bp):
TCTTGGGTGCAATTTGAAGAATACTTATGCAGCGATAG
Found at i:30441650 original size:51 final size:51
Alignment explanation
Indices: 30441566--30441707 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 51
30441556 GCTATAAACA
* * * *
30441566 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* *
30441618 AAAGGTCCGATGACTAAGTGCCATCGTAAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* * * *
30441669 AAAGGTCTGATGACTTAGTGTTATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
30441708 TTCTATACGG
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 74 0.95
52 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:30442360 original size:21 final size:24
Alignment explanation
Indices: 30442335--30442391 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 24
30442325 GACTTGAGTT
30442335 GTATCGGTAGTTAAAT-TAT-G-A
1 GTATCGGTAGTTAAATGTATAGAA
*
30442356 GTATCGGTAGTTATATGTATAGAA
1 GTATCGGTAGTTAAATGTATAGAA
30442380 GTATCGGTAGTT
1 GTATCGGTAGTT
30442392 TGCATGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 15 0.47
22 3 0.09
23 1 0.03
24 13 0.41
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTAAATGTATAGAA
Found at i:30447673 original size:15 final size:16
Alignment explanation
Indices: 30447644--30447673 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30447634 GGGTAAAAAT
30447644 GATAATTATTGGAGAA
1 GATAATTATTGGAGAA
30447660 GATAATTA-TGGAGA
1 GATAATTATTGGAGA
30447674 CTTAATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (16 bp):
GATAATTATTGGAGAA
Found at i:30451697 original size:24 final size:24
Alignment explanation
Indices: 30451668--30451718 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
30451658 CTTCCAGAAT
*
30451668 TTAGCTCATGCGAGCCC-AGAAAGG
1 TTAGCTCATACGAGCCCAAG-AAGG
*
30451692 TTAGCTCTTACGAGCCCAAGAAGG
1 TTAGCTCATACGAGCCCAAGAAGG
30451716 TTA
1 TTA
30451719 ACCAGGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAAGAAGG
Found at i:30456639 original size:240 final size:241
Alignment explanation
Indices: 30456193--30456676 Score: 711
Period size: 240 Copynumber: 2.0 Consensus size: 241
30456183 CAGCCAAATA
* *
30456193 TGTCACCACATGAATATTTCTACATTACACCAAAGACTTTATGTTGCTAACATATCCAAAAGTAC
1 TGTCACCAAATGAATATTTCTACATTACACCAAAGACTTTATGCTGCTAACATATCCAAAAGTAC
* * * *
30456258 CAGCGCAGGTGAATGTCAAGTTGTCATAGCAAATAAAAATCTTAATTTTTGTCCAGTAATGTCGC
66 CAACGCAGGAGAATGTCAAGTTGTCATAGCAAATAAAAATCTTAATTTTCGTCCAGCAATGTCGC
* * *
30456323 GACAACCTGCAATTACCTAATGCACAAACCAGATTTGCGTGATTGTACACCTGAAAATAACCAAC
131 GACAACCTGCAATTACCTAATGCACAAACCAGATATGCGTGAGTGTACACATGAAAATAACCAAC
*
30456388 TTGTACAGCTGCTAAAGGGAGTTAGATCTGAGAAGGGCAAGAGACC
196 TTGTACAGCTGCAAAAGGGAGTTAGATCTGAGAAGGGCAAGAGACC
* ** * * * *
30456434 TGTCACTAAATGAATATTTCTA-ATTACACCAGGGATTTTATGCTGCTAACATATCTAGAAGTTC
1 TGTCACCAAATGAATATTTCTACATTACACCAAAGACTTTATGCTGCTAACATATCCAAAAGTAC
* *
30456498 CAACGCAGGAGAATGTCAAGTTGTCGTAGCAAATAAAAATCTTAATTTTCGTCCAGCAATGTTGC
66 CAACGCAGGAGAATGTCAAGTTGTCATAGCAAATAAAAATCTTAATTTTCGTCCAGCAATGTCGC
* * * *
30456563 GACAATCTGTAACTT-CCTAATGCACAAACCAGATATGCGTGAGTGTACAGATGGAAATAACCAA
131 GACAACCTGCAA-TTACCTAATGCACAAACCAGATATGCGTGAGTGTACACATGAAAATAACCAA
* * *
30456627 CTTGTACAGCTGCAAAAGGGAGTTATATCTTAGAAGGGGAAGAGACC
195 CTTGTACAGCTGCAAAAGGGAGTTAGATCTGAGAAGGGCAAGAGACC
30456674 TGT
1 TGT
30456677 ACCTTCTAGT
Statistics
Matches: 216, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
240 194 0.90
241 22 0.10
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (241 bp):
TGTCACCAAATGAATATTTCTACATTACACCAAAGACTTTATGCTGCTAACATATCCAAAAGTAC
CAACGCAGGAGAATGTCAAGTTGTCATAGCAAATAAAAATCTTAATTTTCGTCCAGCAATGTCGC
GACAACCTGCAATTACCTAATGCACAAACCAGATATGCGTGAGTGTACACATGAAAATAACCAAC
TTGTACAGCTGCAAAAGGGAGTTAGATCTGAGAAGGGCAAGAGACC
Found at i:30465072 original size:15 final size:15
Alignment explanation
Indices: 30465036--30465082 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
30465026 AGGAAGAAGA
*
30465036 GAAAAGAGAAGAAGAAG
1 GAAAA-AGAA-AAAAAG
30465053 G-AAAAGAAAAAAAG
1 GAAAAAGAAAAAAAG
30465067 GAAAAAGAAAATAAAG
1 GAAAAAGAAAA-AAAG
30465083 AAGATTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 13 0.48
16 7 0.26
17 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAAG
Found at i:30469541 original size:29 final size:29
Alignment explanation
Indices: 30469508--30469732 Score: 238
Period size: 29 Copynumber: 7.7 Consensus size: 29
30469498 GAACTTTCCA
*
30469508 AAAATCATATTTTAACCCCAAACTTCTCT
1 AAAATTATATTTTAACCCCAAACTTCTCT
* *
30469537 AAAATTACATTTTGACCCCTAAACTT-TCCT
1 AAAATTATATTTTAACCCC-AAACTTCT-CT
* * *
30469567 AAAATTAGATTTTAACCCCTAAACTTTTTT
1 AAAATTATATTTTAACCCC-AAACTTCTCT
* *
30469597 AAAATTATATTTTGACCCCCAAACTTCTCC
1 AAAATTATATTTT-AACCCCAAACTTCTCT
* *
30469627 AAAATCACATTTTAACCCCAAACTTCTCT
1 AAAATTATATTTTAACCCCAAACTTCTCT
** *
30469656 AAAATTATATTTTAACCCTTAACTTTTCT
1 AAAATTATATTTTAACCCCAAACTTCTCT
* *
30469685 AAAATTACATTTTTACCTCCAAACTTC-CT
1 AAAATTATATTTTAACC-CCAAACTTCTCT
* *
30469714 AAAATTATGTTTTGACCCC
1 AAAATTATATTTTAACCCC
30469733 GTATTCTCCA
Statistics
Matches: 163, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.01
29 86 0.53
30 69 0.42
31 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTATATTTTAACCCCAAACTTCTCT
Found at i:30469699 original size:59 final size:59
Alignment explanation
Indices: 30469516--30469728 Score: 268
Period size: 60 Copynumber: 3.6 Consensus size: 59
30469506 CAAAAATCAT
* * * *
30469516 ATTTTAACCCCAAACTTCTCTAAAATTACATTTTGACCCCTAAACTTTCCTAAAATTAG
1 ATTTTAACCCCAAACTTCTCTAAAATTATATTTTGAACCCTAAACTTTTCTAAAATTAC
* * * * * * *
30469575 ATTTTAACCCCTAAACTTTTTTAAAATTATATTTTGACCCCCAAACTTCTCCAAAATCAC
1 ATTTTAACCCC-AAACTTCTCTAAAATTATATTTTGAACCCTAAACTTTTCTAAAATTAC
*
30469635 ATTTTAACCCCAAACTTCTCTAAAATTATATTTT-AACCCTTAACTTTTCTAAAATTAC
1 ATTTTAACCCCAAACTTCTCTAAAATTATATTTTGAACCCTAAACTTTTCTAAAATTAC
* *
30469693 ATTTTTACCTCCAAACTTC-CTAAAATTATGTTTTGA
1 ATTTTAACC-CCAAACTTCTCTAAAATTATATTTTGA
30469729 CCCCGTATTC
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
58 40 0.30
59 42 0.32
60 50 0.38
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (59 bp):
ATTTTAACCCCAAACTTCTCTAAAATTATATTTTGAACCCTAAACTTTTCTAAAATTAC
Found at i:30481323 original size:39 final size:39
Alignment explanation
Indices: 30481274--30481714 Score: 221
Period size: 39 Copynumber: 11.3 Consensus size: 39
30481264 CAGCCATTCG
* *
30481274 ATCTTTTACCCCGAGCTT-GGGAAAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTAGGG-TAGATCACCATCAGCCA
**** * * *
30481313 ATCTCTTACCCCGAGCTTAGGGTAGATTGTAACCATCCG
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
30481352 ATCT-TTCACCCCGAGCTTAGGGTAGATCACCATCAGCCA
1 ATCTCTT-ACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* **** * ** *
30481391 ATCTCTTACCCCGAGCTT-GGGCAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* * * * * *
30481429 ATCTTTTACCCTGATCATAAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* * * * * * * *
30481468 ATCTCTTATCTCAAGCCTAGAGTAGATTA-CAGTCATCCG
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCA-TCAGCCA
* * * * *
30481507 ATCTTTTACTCCTAGCCTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* * * *
30481546 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT---CCT
1 ATCTCTTACCCCGAGCTTAGGGTAGA-T-CA-CCATCAGCCA
* * * * * *
30481585 ATCTTTTTCCCTGAGCTTGGGGCAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* ** * * ** *
30481624 ATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
* * * * * * *
30481663 ATCTTTTACCCCGATCATGGGGCAAATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
30481702 ATCTCTTACCCCG
1 ATCTCTTACCCCG
30481715 CAACAAGGGC
Statistics
Matches: 292, Mismatches: 98, Indels: 24
0.71 0.24 0.06
Matches are distributed among these distances:
36 4 0.01
37 2 0.01
38 30 0.10
39 242 0.83
40 8 0.03
41 2 0.01
42 4 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
Found at i:30481387 original size:78 final size:78
Alignment explanation
Indices: 30481258--30481750 Score: 533
Period size: 78 Copynumber: 6.3 Consensus size: 78
30481248 GGCCTGAGGC
* * *
30481258 AGATTGCAGCCATTCGATCTTTTACCCCGAGCTT-GGGAAAGATCACCATCAGCCAATCTCTTAC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGG-CAGATCACCATCAGCCAATCTCTTAC
30481322 CCCGAGCTTAGGGT
65 CCCGAGCTTAGGGT
* * *
30481336 AGATTGTAACCATCCGATCTTTCACCCCGAGCTTAGGGTAGATCACCATCAGCCAATCTCTTACC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
*
30481401 CCGAGCTT-GGGC
66 CCGAGCTTAGGGT
* * * * * * *
30481413 AGATTGTAACCATTCGATCTTTTACCCTGATCATAAGGCAGATCACCATCAGCCAATCTCTTATC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
* * * *
30481478 TCAAGCCTAGAGT
66 CCGAGCTTAGGGT
* ** * * *
30481491 AGATTACAGTCATCCGATCTTTTACTCCTAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
* * *
30481556 CCGAGCCTGGGGC
66 CCGAGCTTAGGGT
* * * * * *
30481569 AGATTGCAGCCATCCTATCTTTTTCCCTGAGCTTGGGGCAAATCACCATCAGCCAATCTCTTACC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
*
30481634 CCGAGCTTGGGGT
66 CCGAGCTTAGGGT
* * * * * *
30481647 AGATTGCAACCATTCGATCTTTTACCCCGATCATGGGGCAAATCACCGTCAGCCAATCTCTTACC
1 AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
* * *
30481712 CCGCAAC-AAGGGC
66 CCG-AGCTTAGGGT
* * *
30481725 AGATTACAACCATCCAATCTCTTACC
1 AGATTGCAACCATCCGATCTTTTACC
30481751 AAAAAAAAAT
Statistics
Matches: 348, Mismatches: 64, Indels: 6
0.83 0.15 0.01
Matches are distributed among these distances:
77 65 0.19
78 278 0.80
79 5 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (78 bp):
AGATTGCAACCATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACC
CCGAGCTTAGGGT
Found at i:30483292 original size:17 final size:17
Alignment explanation
Indices: 30483259--30483292 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30483249 AGTTTTTTTT
* *
30483259 AGAAAAAATACATAATA
1 AGAAAAAATAAAAAATA
30483276 AGAAAAAATAAAAAATA
1 AGAAAAAATAAAAAATA
30483293 TATACAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AGAAAAAATAAAAAATA
Found at i:30484185 original size:29 final size:29
Alignment explanation
Indices: 30484080--30484365 Score: 299
Period size: 29 Copynumber: 9.7 Consensus size: 29
30484070 TTCGATAAGT
* *
30484080 CCCTAAAC-TTTCCAAAAATCATATTTTAA
1 CCCTAAACTTTTCC-AAAATTACATTTTAA
*
30484109 CCCTCAAACTTCTCCAAAATTACATTTTAA
1 CCCT-AAACTTTTCCAAAATTACATTTTAA
*
30484139 CTCCTAAACTTTCCCAAAATTACATTTTAA
1 C-CCTAAACTTTTCCAAAATTACATTTTAA
* * *
30484169 CCCTAAACTTTTTCAAAATGATATTTTAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* * * *
30484198 CCCTAAATTTTTCTAAAATTATATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* * *
30484227 CCCTAAACTTTCCCAAAATTAAATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* *
30484256 CCCTTAAACTTCTCCAAAATCACATTTTAA
1 CCC-TAAACTTTTCCAAAATTACATTTTAA
*
30484286 CCCTAAACTTCTT-TAAAATTACATTTTAA
1 CCCTAAACTT-TTCCAAAATTACATTTTAA
* * *
30484315 TCCTTAAC-TTTCCTAAAATTACATTTTTA
1 CCCTAAACTTTTCC-AAAATTACATTTTAA
*
30484344 CCTCTAAACTTTTCTAAAATTA
1 CC-CTAAACTTTTCCAAAATTA
30484366 TGTTTTGACC
Statistics
Matches: 215, Mismatches: 33, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.01
28 1 0.00
29 122 0.57
30 79 0.37
31 11 0.05
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:30484283 original size:88 final size:88
Alignment explanation
Indices: 30484083--30484363 Score: 336
Period size: 88 Copynumber: 3.2 Consensus size: 88
30484073 GATAAGTCCC
* * *
30484083 TAAAC-TTTCCAAAAATCATATTTTAACCCTCAAACTTCTCCAAAATTACATTTTAACTCCTAAA
1 TAAACTTTTCC-AAAATCATATTTTAACCCT-AAATTTTTCTAAAATTACATTTTAAC-CCTAAA
30484147 CTTTCCCAAAATTACATTTTAACCC-
63 CTTTCCCAAAATTACATTTTAACCCT
* * * *
30484172 TAAACTTTTTCAAAATGATATTTTAACCCTAAATTTTTCTAAAATTATATTTTGACCCTAAACTT
1 TAAACTTTTCCAAAATCATATTTTAACCCTAAATTTTTCTAAAATTACATTTTAACCCTAAACTT
* *
30484237 TCCCAAAATTAAATTTTGACCCT
66 TCCCAAAATTACATTTTAACCCT
* * * * *
30484260 TAAACTTCTCCAAAATCACATTTTAACCCTAAACTTCTT-TAAAATTACATTTTAATCCTTAACT
1 TAAACTTTTCCAAAATCATATTTTAACCCTAAA-TTTTTCTAAAATTACATTTTAACCCTAAACT
* *
30484324 TTCCTAAAATTACATTTTTA-CCT
65 TTCCCAAAATTACATTTTAACCCT
*
30484347 CTAAACTTTTCTAAAAT
1 -TAAACTTTTCCAAAAT
30484364 TATGTTTTGA
Statistics
Matches: 165, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
87 32 0.19
88 102 0.62
89 27 0.16
90 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (88 bp):
TAAACTTTTCCAAAATCATATTTTAACCCTAAATTTTTCTAAAATTACATTTTAACCCTAAACTT
TCCCAAAATTACATTTTAACCCT
Found at i:30485991 original size:213 final size:213
Alignment explanation
Indices: 30485624--30486038 Score: 794
Period size: 213 Copynumber: 1.9 Consensus size: 213
30485614 AATTCATTTT
30485624 CATTACAAGTAGATTACTAAAAACATGCCTAATTCGGACTACAACATGTTGATACTTAGCTCATT
1 CATTACAAGTAGATTACTAAAAACATGCCTAATTCGGACTACAACATGTTGATACTTAGCTCATT
30485689 ACAAAACACCAAATATATTTGATAGCAAATCTCAAGATAAAATCATTCCAAATAACATTACTCAT
66 ACAAAACACCAAATATATTTGATAGCAAATCTCAAGATAAAATCATTCCAAATAACATTACTCAT
*
30485754 CAAATATTTAGATTTACAATCCTACTACATGGCATATAAGTCAAGTGATACGAGGACTATCGAAC
131 CAAATATTTAGATTTACAATCCTACTACATGACATATAAGTCAAGTGATACGAGGACTATCGAAC
30485819 AAACTCCAAATAAATCTA
196 AAACTCCAAATAAATCTA
* *
30485837 CATTACAAGTAGATTACTAAAAACATGCCTAATTCGGACTATAACATGTTGATACTTAGTTCATT
1 CATTACAAGTAGATTACTAAAAACATGCCTAATTCGGACTACAACATGTTGATACTTAGCTCATT
*
30485902 ACAAAACACCAAATATATTTGATAGCAAGTCTCAAGATAAAATCATTCCAAATAACATTACTCAT
66 ACAAAACACCAAATATATTTGATAGCAAATCTCAAGATAAAATCATTCCAAATAACATTACTCAT
30485967 CAAATATTTAGATTTACAATCCTACTACATGACATATAAGTCAAGTGATACGAGGACTATCGAAC
131 CAAATATTTAGATTTACAATCCTACTACATGACATATAAGTCAAGTGATACGAGGACTATCGAAC
30486032 AAACTCC
196 AAACTCC
30486039 CGAGATAGTG
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
213 198 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (213 bp):
CATTACAAGTAGATTACTAAAAACATGCCTAATTCGGACTACAACATGTTGATACTTAGCTCATT
ACAAAACACCAAATATATTTGATAGCAAATCTCAAGATAAAATCATTCCAAATAACATTACTCAT
CAAATATTTAGATTTACAATCCTACTACATGACATATAAGTCAAGTGATACGAGGACTATCGAAC
AAACTCCAAATAAATCTA
Found at i:30486294 original size:23 final size:23
Alignment explanation
Indices: 30486254--30486327 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
30486244 CTTTCAAAAT
* *
30486254 TTAGCTCATATGAGCCCAGAAGG
1 TTAGCTCTTACGAGCCCAGAAGG
* * *
30486277 TTAGCTCTTACGAACCCATAAAGA
1 TTAGCTCTTACGAGCCCA-GAAGG
30486301 TTAGCTCTTACGAGCCCAGAAAGG
1 TTAGCTCTTACGAGCCCAG-AAGG
30486325 TTA
1 TTA
30486328 ACCAGTATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 15 0.37
24 26 0.63
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (23 bp):
TTAGCTCTTACGAGCCCAGAAGG
Found at i:30491239 original size:7 final size:7
Alignment explanation
Indices: 30491227--30491252 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30491217 CCATTCCTAA
30491227 TCATCCC
1 TCATCCC
30491234 TCATCCC
1 TCATCCC
30491241 TCATCCC
1 TCATCCC
30491248 TCATC
1 TCATC
30491253 TTTCTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:30493087 original size:32 final size:34
Alignment explanation
Indices: 30493013--30493088 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
30493003 TGTGCTTCTT
* * *
30493013 AAAACATGACATTCTAATCTGATATATGTTTATG
1 AAAATATGACATTCTAATCCGATATATGTTTACG
* *
30493047 AAAATATGATATTCTGATCCGATATATG-TT-CG
1 AAAATATGACATTCTAATCCGATATATGTTTACG
30493079 AAAATATGAC
1 AAAATATGAC
30493089 CTTATGATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 10 0.28
33 2 0.06
34 24 0.67
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (34 bp):
AAAATATGACATTCTAATCCGATATATGTTTACG
Found at i:30498392 original size:57 final size:58
Alignment explanation
Indices: 30498266--30498401 Score: 154
Period size: 58 Copynumber: 2.3 Consensus size: 58
30498256 CATTTTTACT
* *
30498266 AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTGTATATTATTTTATTA
1 AATT-ATA-TTTAATAATAATTATATTAAAAATATTAATAAATTGTAAATTATTTTATTA
* *
30498326 AATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAA-T-TAAATT-TTTT-TTA
1 AATTATATTTAATAATAATTATATTAAAA-AT-ATT-AATAAATTGTAAATTATTTTATTA
*
30498383 CATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
30498402 CATTAAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
57 20 0.30
58 25 0.37
59 9 0.13
60 8 0.12
61 5 0.07
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAAATATTAATAAATTGTAAATTATTTTATTA
Found at i:30502033 original size:58 final size:58
Alignment explanation
Indices: 30501945--30502090 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 58
30501935 ATATATTATA
* *
30501945 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
*
30502002 ATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
30502062 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
30502091 CATTAAAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.61
59 12 0.15
60 10 0.13
61 8 0.10
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:30502234 original size:44 final size:46
Alignment explanation
Indices: 30502185--30502278 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
30502175 ATTACAGCAT
* *
30502185 CATTCCATTCAACCAAAC-ATAAGAA-TA-TTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACAAT-AGAATTACTGATTACAGCTCTATTC
*
30502229 CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACAATAGAATTACTGATTACAGCTCTATTC
30502275 CATT
1 CATT
30502279 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 20 0.45
45 4 0.09
46 20 0.45
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (46 bp):
CATTCCAATCAACCAAACAATAGAATTACTGATTACAGCTCTATTC
Found at i:30502281 original size:16 final size:16
Alignment explanation
Indices: 30502260--30502331 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
30502250 TGAATTACTG
30502260 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
30502276 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
30502292 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
30502308 ATTACACCTCTATTTC
1 ATTACAGCTCTATTCC
30502324 ATTACAGC
1 ATTACAGC
30502332 GAACCAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:30512812 original size:25 final size:25
Alignment explanation
Indices: 30512757--30512812 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
30512747 AAATATCCCT
* *
30512757 AGAATAATCAGAGTTTAATTGAGAA
1 AGAATAATCAAAGTTTAACTGAGAA
* *
30512782 AAAATAAT-AAAGTTTAACTGGGAGA
1 AGAATAATCAAAGTTTAACTGAGA-A
30512807 AGAATA
1 AGAATA
30512813 CGAGGCATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.25
Consensus pattern (25 bp):
AGAATAATCAAAGTTTAACTGAGAA
Found at i:30513116 original size:6 final size:6
Alignment explanation
Indices: 30513105--30513129 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30513095 CATCAACTTG
30513105 TATACA TATACA TATACA TATACA T
1 TATACA TATACA TATACA TATACA T
30513130 GTATACTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:30527451 original size:3 final size:3
Alignment explanation
Indices: 30527443--30527473 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30527433 TGACAACAGC
*
30527443 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30527474 TTCCTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30533588 original size:130 final size:126
Alignment explanation
Indices: 30533322--30533720 Score: 388
Period size: 126 Copynumber: 3.0 Consensus size: 126
30533312 ACACTTTTGG
* ** *
30533322 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCAACATACGTTTTGGCCAACTCTTTGTATAA
1 GCCGACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATACACTTTGACCAACTCTTTGTATAA
* * *
30533387 GGGTTGAGATATGCATGCCTAATGCAACGCTTAAATAAGAGTTGGCTTTGTCCAACACTAT
66 GGGTTGAGATATGCATGCCTAAGGCAACACTTAAATAAGAATTGGCTTTGTCCAACACTAT
** * * *
30533448 ATCGATACTTTCCTATGTGTTAGGATAGACTTGTCGACATACACTTTGACCAACTCTTTGTATAA
1 GCCGACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATACACTTTGACCAACTCTTTGTATAA
* *
30533513 GGGCCAATTTG-GATATGCATGCCTAAGGTAACACTTAAATAAGAATTGGTTTTGTCCAACACTA
66 GGG-----TTGAGATATGCATGCCTAAGGCAACACTTAAATAAGAATTGGCTTTGTCCAACACTA
30533577 T
126 T
**
30533578 GCCGACACTTTTGGGCCGACACCTTCATAAGTGTTAGGATAGACTTGTCAACATATGCTTT-AGC
1 GCCGACAC-TTT----------C--C-TAAGTGTTAGGATAGACTTGTCAACATACACTTTGA-C
* * * ** * * *
30533642 CAATTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAATGCTTATATAAGAGTCGGCTTTG
51 CAACTCTTTGTATAAGGGTTGAGATATGCATGCCTAAGGCAACACTTAAATAAGAATTGGCTTTG
30533707 TCCAACACTAT
116 TCCAACACTAT
30533718 GCC
1 GCC
30533721 AACTTTTGTT
Statistics
Matches: 222, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
126 59 0.27
130 54 0.24
131 6 0.03
139 3 0.01
140 50 0.23
141 1 0.00
143 2 0.01
144 47 0.21
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (126 bp):
GCCGACACTTTCCTAAGTGTTAGGATAGACTTGTCAACATACACTTTGACCAACTCTTTGTATAA
GGGTTGAGATATGCATGCCTAAGGCAACACTTAAATAAGAATTGGCTTTGTCCAACACTAT
Found at i:30533720 original size:140 final size:140
Alignment explanation
Indices: 30533464--30533728 Score: 347
Period size: 140 Copynumber: 1.9 Consensus size: 140
30533454 ACTTTCCTAT
* *
30533464 GTGTTAGGATAGACTTGTCGACATACACTTTGACCAACTCTTTGTATAAGGGCCAATTTGGATAT
1 GTGTTAGGATAGACTTGTCAACATACACTTTGACCAACTCTTTGTATAA-GG-CAATTGGGATAT
* * *
30533529 GCATGCCTAAGGTAACACTTAAATAAGAATTGGTTTTGTCCAACACTATGCCGACACTTTTGGGC
64 GCATGCCTAAGGCAACACTTAAATAAGAATCGGCTTTGTCCAACACTATGCC-A-ACTTTTGGGC
30533594 CGACACCTTCATAA
127 CGACACCTTCATAA
** * *
30533608 GTGTTAGGATAGACTTGTCAACATATGCTTT-AGCCAATTCTTTGTATAA-G-AGTTGGGATATG
1 GTGTTAGGATAGACTTGTCAACATACACTTTGA-CCAACTCTTTGTATAAGGCAATTGGGATATG
** * *
30533670 CATGCCTAAGGCAATGCTTATATAAGAGTCGGCTTTGTCCAACACTATGCCAACTTTTG
65 CATGCCTAAGGCAACACTTAAATAAGAATCGGCTTTGTCCAACACTATGCCAACTTTTG
30533729 TTATACCTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
138 7 0.07
139 1 0.01
140 54 0.50
142 1 0.01
143 1 0.01
144 43 0.40
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (140 bp):
GTGTTAGGATAGACTTGTCAACATACACTTTGACCAACTCTTTGTATAAGGCAATTGGGATATGC
ATGCCTAAGGCAACACTTAAATAAGAATCGGCTTTGTCCAACACTATGCCAACTTTTGGGCCGAC
ACCTTCATAA
Found at i:30538141 original size:19 final size:16
Alignment explanation
Indices: 30538113--30538151 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 16
30538103 CTATGTGAAC
30538113 CTTTCTCTCTTTCTTTCT
1 CTTTCTCTC-TTCTTT-T
30538131 CTTTCCTCTCTTCTTTT
1 CTTT-CTCTCTTCTTTT
30538148 CTTT
1 CTTT
30538152 GTTGTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTCTCTCTTCTTTT
Found at i:30544354 original size:19 final size:18
Alignment explanation
Indices: 30544330--30544365 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30544320 ATAACCTAAA
30544330 AATAAAAAGAAATTAAACG
1 AATAAAAAGAAA-TAAACG
*
30544349 AATAAAAATAAATAAAC
1 AATAAAAAGAAATAAAC
30544366 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AATAAAAAGAAATAAACG
Found at i:30544364 original size:10 final size:9
Alignment explanation
Indices: 30544327--30544378 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
30544317 TAAATAACCT
30544327 AAAAATAAA
1 AAAAATAAA
*
30544336 AAGAAATTAA
1 AA-AAATAAA
**
30544346 ACGAATAAA
1 AAAAATAAA
30544355 AATAAATAAA
1 AA-AAATAAA
30544365 CAAAAATAAA
1 -AAAAATAAA
30544375 AAAA
1 AAAA
30544379 TATCGTATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 12 0.35
10 20 0.59
11 2 0.06
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (9 bp):
AAAAATAAA
Found at i:30548237 original size:19 final size:19
Alignment explanation
Indices: 30548213--30548252 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30548203 TGTCATTTTA
* *
30548213 TATTTCTATTAATTGTTAT
1 TATTTCCATTAATTGTAAT
30548232 TATTTCCATTAATTGTAAT
1 TATTTCCATTAATTGTAAT
30548251 TA
1 TA
30548253 GACAGTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTTCCATTAATTGTAAT
Found at i:30549245 original size:35 final size:35
Alignment explanation
Indices: 30549228--30549568 Score: 324
Period size: 35 Copynumber: 9.5 Consensus size: 35
30549218 TTTTAAGCGA
30549228 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
* * ***
30549263 GTCTATCCCAACCTTTTTTAAAGGCTGTCTTAAACAAA
1 GTCTATCCCAACC-TTTTT-AAGGTTGTCTTAGA-TGG
* *
30549301 GTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGATGG
1 GTCTATCCCAA-CCTTTTT-AAGGTTGTCTTAGATGG
* *
30549338 GTCTATCCTC-ACCTTTTTAAGATTGCCTTAGATGG
1 GTCTATCC-CAACCTTTTTAAGGTTGTCTTAGATGG
* * * * * *
30549373 GTCTATTCCAACTTTTTTAAAGTTGCCTTAGACGA
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
* ** * **
30549408 GTTTATCCCAACCTTTTTTAAAGGTTACCTTAAACAAG
1 GTCTATCCCAACC-TTTTT-AAGGTTGTCTTAGA-TGG
** *
30549446 ACCTATCCCAACCTTTTTAAGGTTTTCTTAGATGG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
* *
30549481 TTCTATCCCAACCTTTTTAAGGTAGTCTTAGATGG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
* * *
30549516 GTCTATCCCAACCATTTTAAGGTTGTCTTAAACGG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
*
30549551 GTTTATCCCAACCTTTTT
1 GTCTATCCCAACCTTTTT
30549569 TAAAGATCGA
Statistics
Matches: 249, Mismatches: 48, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
34 1 0.00
35 144 0.58
36 27 0.11
37 37 0.15
38 39 0.16
39 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (35 bp):
GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGG
Found at i:30549476 original size:108 final size:107
Alignment explanation
Indices: 30549230--30549533 Score: 349
Period size: 108 Copynumber: 2.8 Consensus size: 107
30549220 TTAAGCGAGT
*
30549230 CTATCCCAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAACCTTTTTTAAAGGCTGTCTTA
1 CTATCCCAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAA-CTTTTTTAAA-GTTGTCTTA
* * * * * ** **
30549295 AACAAAGTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGATGGGT
64 GAC-GAGTCTATCCCAACCTTTTTTAAAGGTTACCTTAAAAAGAC
* * * *
30549340 CTATCCTC-ACCTTTTTAAGATTGCCTTAGATGGGTCTATTCCAACTTTTTTAAAGTTGCCTTAG
1 CTATCC-CAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAACTTTTTTAAAGTTGTCTTAG
*
30549404 ACGAGTTTATCCCAACCTTTTTTAAAGGTTACCTTAAACAAGAC
65 ACGAGTCTATCCCAACCTTTTTTAAAGGTTACCTTAAA-AAGAC
* * * * *
30549448 CTATCCCAACCTTTTTAAGGTTTTCTTAGATGGTTCTATCCCAACCTTTTTAAGGTAGTCTTAGA
1 CTATCCCAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAACTTTTTTAAAGTTGTCTTAGA
* * *
30549513 TGGGTCTATCCCAACCATTTT
66 CGAGTCTATCCCAACCTTTTT
30549534 AAGGTTGTCT
Statistics
Matches: 163, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
107 32 0.20
108 81 0.50
109 10 0.06
110 39 0.24
111 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (107 bp):
CTATCCCAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAACTTTTTTAAAGTTGTCTTAGA
CGAGTCTATCCCAACCTTTTTTAAAGGTTACCTTAAAAAGAC
Found at i:30549534 original size:143 final size:145
Alignment explanation
Indices: 30549228--30549573 Score: 466
Period size: 143 Copynumber: 2.4 Consensus size: 145
30549218 TTTTAAGCGA
* * **
30549228 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGATGGGTCTATCCCAACCTTTTTTAAAGGCTGTCT
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGGTTTATCCCAACCTTTTTTAAAGGCTACCT
* *
30549293 TAAACAAAGTCTATCCCAATCTTTTTTAAAGGTTGCCTTAGATGGGTCTATCCTCACCTTTTTAA
66 TAAACAAAGCCTATCCCAATCCTTTTTAAAGGTTGCCTTAGATGGGTCTATCCTCACCTTTTTAA
*
30549358 GATTGCCTTAGATGG
131 GATAGCCTTAGATGG
* * * * * *
30549373 GTCTATTCCAACTTTTTTAAAGTTGCCTTAGACGAGTTTATCCCAACCTTTTTTAAAGGTTACCT
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGGTTTATCCCAACCTTTTTTAAAGGCTACCT
** *
30549438 TAAAC-AAGACCTATCCCAA-CCTTTTT-AAGGTTTTCTTAGATGGTTCTATCC-CAACCTTTTT
66 TAAACAAAG-CCTATCCCAATCCTTTTTAAAGGTTGCCTTAGATGGGTCTATCCTC-ACCTTTTT
* *
30549499 AAGGTAGTCTTAGATGG
129 AAGATAGCCTTAGATGG
* *
30549516 GTCTATCCCAACCATTTTAAGGTTGTCTTAAACGGGTTTATCCCAACCTTTTTTAAAG
1 GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGGTTTATCCCAACCTTTTTTAAAG
30549574 ATCGACCTTG
Statistics
Matches: 174, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
142 1 0.01
143 95 0.55
144 9 0.05
145 69 0.40
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (145 bp):
GTCTATCCCAACCTTTTTAAGGTTGTCTTAGACGGGTTTATCCCAACCTTTTTTAAAGGCTACCT
TAAACAAAGCCTATCCCAATCCTTTTTAAAGGTTGCCTTAGATGGGTCTATCCTCACCTTTTTAA
GATAGCCTTAGATGG
Found at i:30551595 original size:116 final size:114
Alignment explanation
Indices: 30551430--30551642 Score: 268
Period size: 116 Copynumber: 1.9 Consensus size: 114
30551420 TTCAAGAAAA
* * *
30551430 TTCAAATCATTTCTTAGCCTTTTCTTCTACCAAGGTCGATTCTTCTTCTCTCTTATCTGAAAAAA
1 TTCAAATCATTTCTCAGCCCTTTCTTCTACCAAGGTCGATTCTTCTTCTCTC-T-TCTCAAAAAA
* **
30551495 ATAGTCTGGTTTCAAGGCTTTATTCTTT-TCCAAAAACTCTTCAAGAAACTT
64 ATAGTCTGG-CTCAAGGCTCCATTCTTTCTCCAAAAACTCTTCAAGAAACTT
* * * * **
30551546 TTCAAATCTTTTCTCAGCCCTTTCTTCTACTAAGGCTGGA-TGTTCTTCTCTCTTCTCAAAAACT
1 TTCAAATCATTTCTCAGCCCTTTCTTCTACCAAGG-TCGATTCTTCTTCTCTCTTCTCAAAAAAA
30551610 TAGTCTGGCTCAAGGCTCCATTCTTTCTCCAAA
65 TAGTCTGGCTCAAGGCTCCATTCTTTCTCCAAA
30551643 TCCATTCGAG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
113 15 0.18
114 22 0.27
115 1 0.01
116 42 0.51
117 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.40
Consensus pattern (114 bp):
TTCAAATCATTTCTCAGCCCTTTCTTCTACCAAGGTCGATTCTTCTTCTCTCTTCTCAAAAAAAT
AGTCTGGCTCAAGGCTCCATTCTTTCTCCAAAAACTCTTCAAGAAACTT
Found at i:30557201 original size:16 final size:16
Alignment explanation
Indices: 30557180--30557229 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
30557170 ACATCTAATC
30557180 ATATAATAAATTATTA
1 ATATAATAAATTATTA
30557196 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
30557209 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
30557226 ATAT
1 ATAT
30557230 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:30557279 original size:16 final size:17
Alignment explanation
Indices: 30557243--30557279 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
30557233 AATTTTATTT
*
30557243 TAATAGTAAGTTTTAAA
1 TAATAATAAGTTTTAAA
30557260 -AATAATAA-TTTTAAA
1 TAATAATAAGTTTTAAA
30557275 TAATA
1 TAATA
30557280 CTATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATAAGTTTTAAA
Found at i:30557352 original size:15 final size:15
Alignment explanation
Indices: 30557334--30557367 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30557324 AATAAATATT
30557334 TATTACAATTATAAA
1 TATTACAATTATAAA
**
30557349 TATTTTAATTATAAA
1 TATTACAATTATAAA
30557364 TATT
1 TATT
30557368 TTGTAGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTACAATTATAAA
Found at i:30557368 original size:15 final size:15
Alignment explanation
Indices: 30557340--30557369 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30557330 TATTTATTAC
30557340 AATTATAAATATTTT
1 AATTATAAATATTTT
30557355 AATTATAAATATTTT
1 AATTATAAATATTTT
30557370 GTAGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATAAATATTTT
Found at i:30564131 original size:5 final size:5
Alignment explanation
Indices: 30564121--30564146 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30564111 ATTCACATTT
30564121 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
30564147 TTATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:30568195 original size:20 final size:20
Alignment explanation
Indices: 30568170--30568238 Score: 138
Period size: 20 Copynumber: 3.5 Consensus size: 20
30568160 TTCTGCATTA
30568170 TTTTCAAAAATTGATTTAAT
1 TTTTCAAAAATTGATTTAAT
30568190 TTTTCAAAAATTGATTTAAT
1 TTTTCAAAAATTGATTTAAT
30568210 TTTTCAAAAATTGATTTAAT
1 TTTTCAAAAATTGATTTAAT
30568230 TTTTCAAAA
1 TTTTCAAAA
30568239 GCTATAGTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTCAAAAATTGATTTAAT
Found at i:30569029 original size:40 final size:34
Alignment explanation
Indices: 30569000--30569070 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
30568990 TTTTAAAAAT
30569000 ATAATAATAAATTTAAATTGATACTAAATATTAAA
1 ATAAT-ATAAATTTAAATTGATACTAAATATTAAA
* * *
30569035 ATCATATAAATTTAAATTTATACTAAACATTCAAA
1 ATAATATAAATTTAAATTGATACTAAATATT-AAA
30569070 A
1 A
30569071 CTTCTAGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAATATAAATTTAAATTGATACTAAATATTAAA
Found at i:30569061 original size:17 final size:17
Alignment explanation
Indices: 30569007--30569061 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
30568997 AATATAATAA
*
30569007 TAAATTTAAATTGATAC
1 TAAATTTAAATTCATAC
*
30569024 TAAATATTAAAATCATA-
1 TAAAT-TTAAATTCATAC
*
30569041 TAAATTTAAATTTATAC
1 TAAATTTAAATTCATAC
30569058 TAAA
1 TAAA
30569062 CATTCAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.28
17 14 0.44
18 9 0.28
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTCATAC
Found at i:30569659 original size:192 final size:190
Alignment explanation
Indices: 30569297--30569672 Score: 472
Period size: 192 Copynumber: 2.0 Consensus size: 190
30569287 ATCTCATAAA
* * ** *
30569297 ATACTTGGAGTTTGTAGCTAAAATTTGTAGTGAATGTACATGATGCATATATTCAACAAAATTTC
1 ATACTTGGAGTTTGAAGCTAAAATTTCTAGTGAATGTACAAAATGCAGATATTCAACAAAATTTC
* ** *
30569362 TTAGATTTTTCCCATTGGGTGTCGCTAACTTGGACAAAAGAAGTAATAAGAAACATATGAAAAAT
66 TTAGACTTTTCCCATTGGGACTCGCTAACTTGGACAAAAGAAATAATAAGAAACATATGAAAAAT
* * * *
30569427 TACTTCAAAAGATGACAAATAAGTGGGTCTAGTAATTTATTACTAGCAAGTCCTCGTAAC
131 GACTTCAAAAGATGACAAAGAAGTGGGCCTAGTAATTTATTACTAGCAACTCCTCGTAAC
* * * *
30569487 ATACTTGGAGTTTGAAGCTATAATTTCTACAGTGAATGTAGAAAATGCAGATCTTCAATAAAATT
1 ATACTTGGAGTTTGAAGCTAAAATTTCT--AGTGAATGTACAAAATGCAGATATTCAACAAAATT
* *
30569552 TCTT-GAACTTTTCCCATTGGGACTCGTTAACTTGGA-AAAAGAAATCATCAA-ATAACATATGA
64 TCTTAG-ACTTTTCCCATTGGGACTCGCTAACTTGGACAAAAGAAATAAT-AAGA-AACATATGA
* * *
30569614 AAAATGATTTCAAAAGAT-ATGAAAGAAGTGGGCCTAGTGATTTATTACTAGCAACTCCT
126 AAAATGACTTCAAAAGATGA-CAAAGAAGTGGGCCTAGTAATTTATTACTAGCAACTCCT
30569673 TTGCATTGTC
Statistics
Matches: 158, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
190 25 0.16
191 13 0.08
192 120 0.76
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (190 bp):
ATACTTGGAGTTTGAAGCTAAAATTTCTAGTGAATGTACAAAATGCAGATATTCAACAAAATTTC
TTAGACTTTTCCCATTGGGACTCGCTAACTTGGACAAAAGAAATAATAAGAAACATATGAAAAAT
GACTTCAAAAGATGACAAAGAAGTGGGCCTAGTAATTTATTACTAGCAACTCCTCGTAAC
Found at i:30571348 original size:7 final size:7
Alignment explanation
Indices: 30571336--30571374 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
30571326 TTATTTAGCC
30571336 ATTTTTA
1 ATTTTTA
30571343 ATTTTTA
1 ATTTTTA
30571350 A-TTTTA
1 ATTTTTA
*
30571356 ATATTTTT
1 AT-TTTTA
30571364 ATTTTTA
1 ATTTTTA
30571371 ATTT
1 ATTT
30571375 AATTTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.57
8 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:30571361 original size:15 final size:15
Alignment explanation
Indices: 30571343--30571372 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30571333 GCCATTTTTA
30571343 ATTTTTAATTTTAAT
1 ATTTTTAATTTTAAT
*
30571358 ATTTTTATTTTTAAT
1 ATTTTTAATTTTAAT
30571373 TTAATTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTAATTTTAAT
Found at i:30571362 original size:21 final size:19
Alignment explanation
Indices: 30571336--30571381 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
30571326 TTATTTAGCC
30571336 ATTTTTAATTTTTAATTTTA
1 ATTTTTAATTTTTAA-TTTA
*
30571356 ATATTTTTATTTTTAATTTA
1 AT-TTTTAATTTTTAATTTA
30571376 ATTTTT
1 ATTTTT
30571382 CTATTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 12 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTAATTTTTAATTTA
Found at i:30571375 original size:20 final size:21
Alignment explanation
Indices: 30571336--30571386 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
30571326 TTATTTAGCC
30571336 ATTTTTAATTTTTAATTTTAAT
1 ATTTTT-ATTTTTAATTTTAAT
30571358 ATTTTTATTTTTAA-TTTAAT
1 ATTTTTATTTTTAATTTTAAT
30571378 -TTTTCTATT
1 ATTTT-TATT
30571387 CAAAATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 8 0.29
22 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTATTTTTAATTTTAAT
Found at i:30573305 original size:20 final size:22
Alignment explanation
Indices: 30573280--30573320 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
30573270 AAAAAGGGGT
30573280 TTGATTGTGTG-TTAA-ATGAA
1 TTGATTGTGTGATTAATATGAA
30573300 TTGATTGTGTGATTAATATGA
1 TTGATTGTGTGATTAATATGA
30573321 GAAATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
TTGATTGTGTGATTAATATGAA
Found at i:30573755 original size:105 final size:103
Alignment explanation
Indices: 30573569--30573808 Score: 277
Period size: 105 Copynumber: 2.3 Consensus size: 103
30573559 GTAAATGAAA
* * *
30573569 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTATGAGGTTTGATGA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAGAGGTCTGATGA
* * * * *
30573634 CTAAGTGTCGTTGTGAGTATATGGAATCCTTTATGGATTT
66 CTAAGTGTCATCGTGAGTATA-CGAATCCCTCATGGA-TT
* * * *
30573674 AAAGGTCCGATGGCTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCTGATGA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAGAGGTCTGATGA
*
30573739 CTCTA-TGTCATCGTGAGTATACGAATCCCTCATGGATT
66 CT-AAGTGTCATCGTGAGTATACGAATCCCTCATGGATT
* * *
30573777 ATAAGGTTCGATGACCATA-TGTCATCATGAGT
1 A-AAGGTCCGATGACTA-AGTGTCATCGTGAGT
30573809 GTTAAATGAA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
103 3 0.03
104 36 0.31
105 75 0.65
106 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (103 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAGAGGTCTGATGA
CTAAGTGTCATCGTGAGTATACGAATCCCTCATGGATT
Done.