Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 87 of 144
Found at i:20131452 original size:22 final size:22
Alignment explanation
Indices: 20131390--20131449 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
20131380 ATTTCCATTA
*
20131390 TTTAATTTT--TTATAATTTTCC
1 TTTAATTTTGATTTTAA-TTTCC
* *
20131411 TTTATTTTTTATTTTAATTTCC
1 TTTAATTTTGATTTTAATTTCC
20131433 TTCTAATTTTGATTTTA
1 TT-TAATTTTGATTTTA
20131450 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.25
22 7 0.22
23 17 0.53
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTAATTTTGATTTTAATTTCC
Found at i:20145215 original size:8 final size:8
Alignment explanation
Indices: 20145202--20145232 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
20145192 TATGTGAAAA
20145202 TGACAAAT
1 TGACAAAT
20145210 TGACAAAT
1 TGACAAAT
20145218 TGACAAAT
1 TGACAAAT
20145226 TGA-AAAT
1 TGACAAAT
20145233 GGCAAGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (8 bp):
TGACAAAT
Found at i:20145223 original size:16 final size:15
Alignment explanation
Indices: 20145196--20145232 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
20145186 AATACGTATG
20145196 TGAAAA-TGACAAAT
1 TGAAAATTGACAAAT
20145210 TGACAAATTGACAAAT
1 TGA-AAATTGACAAAT
20145226 TGAAAAT
1 TGAAAAT
20145233 GGCAAGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 7 0.33
16 11 0.52
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (15 bp):
TGAAAATTGACAAAT
Found at i:20146191 original size:32 final size:32
Alignment explanation
Indices: 20146154--20146214 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
20146144 ATGAGCCTTT
*
20146154 AAATCAATTTGAATAG-AATCAAATCAAATAAA
1 AAATCAATTT-AATAGAAAACAAATCAAATAAA
*
20146186 AAATCAATTTAATTGAAAACAAATCAAAT
1 AAATCAATTTAATAGAAAACAAATCAAAT
20146215 CGAGATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (32 bp):
AAATCAATTTAATAGAAAACAAATCAAATAAA
Found at i:20147942 original size:21 final size:21
Alignment explanation
Indices: 20147917--20147968 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
20147907 GTGTAGACTC
20147917 CTACCGATACAAGTGAC-T-CTT
1 CTACCGATACAAGT--CTTACTT
20147938 CTACCGATACAAGTCTTACTT
1 CTACCGATACAAGTCTTACTT
20147959 CTACCGATAC
1 CTACCGATAC
20147969 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 27 0.93
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCTTACTT
Found at i:20152587 original size:19 final size:20
Alignment explanation
Indices: 20152553--20152590 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20152543 ATCCCCTTCC
20152553 CACATAAAGCCTATATCAGG
1 CACATAAAGCCTATATCAGG
*
20152573 CACAT-AAGTCTATATCAG
1 CACATAAAGCCTATATCAG
20152591 ACACTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (20 bp):
CACATAAAGCCTATATCAGG
Found at i:20154041 original size:78 final size:80
Alignment explanation
Indices: 20153921--20154152 Score: 210
Period size: 77 Copynumber: 3.0 Consensus size: 80
20153911 TAATTTTTTG
*
20153921 TTTGGAAACTAAATCAAAATCAATCAAATCTGTTGAACGACGGGAATAAATCCCGAAA-AAAATT
1 TTTGGAAACTAAATCAAAATCAA-CAAATCTGTTGAACGACGGGAATAAATCCCAAAACAAAATT
*
20153985 ATTTAATTCTAATTCTCA
65 ATTCAA-T-TAATTCTCA
* * **
20154003 TTTGGAAACTAAATCAGAAT-AA-AATAT-T-TTGAATGACGGGAATAAATTTCAAAACAAAATT
1 TTTGGAAACTAAATCAAAATCAACAA-ATCTGTTGAACGACGGGAATAAATCCCAAAACAAAATT
* *
20154064 ATTCAATTAGTTCTTA
65 ATTCAATTAATTCTCA
* * * * * * * * * *
20154080 TTTGGAAACAAAATCCAAAT---CAATTCTGCTAAACAACAGGAATAAATTCTAAAACAGAATTA
1 TTTGGAAACTAAATCAAAATCAACAAATCTGTTGAACGACGGGAATAAATCCCAAAACAAAATTA
20154142 TTCAATTAATT
66 TTCAATTAATT
20154153 ATTATAAAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
75 1 0.01
76 3 0.02
77 60 0.48
78 23 0.19
79 14 0.11
80 2 0.02
81 2 0.02
82 19 0.15
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (80 bp):
TTTGGAAACTAAATCAAAATCAACAAATCTGTTGAACGACGGGAATAAATCCCAAAACAAAATTA
TTCAATTAATTCTCA
Found at i:20154122 original size:77 final size:76
Alignment explanation
Indices: 20154041--20154303 Score: 237
Period size: 76 Copynumber: 3.4 Consensus size: 76
20154031 TTGAATGACG
20154041 GGAATAAATT-TCAAAACAAAATTATTCAATTAGTTCTTATTTGGAAACAAAATCCAAATCAATT
1 GGAATAAATTCT-AAAACAAAATTATTCAATTA-TTCTTATTTGGAAACAAAATCCAAATCAATT
20154105 CTGCTAAACAACA
64 CTGCTAAACAACA
* * * * ** * *
20154118 GGAATAAATTCTAAAACAGAATTATTCAATTA--ATTATTAT-AAAATCCAAATATAGAATAAAA
1 GGAATAAATTCTAAAACAAAATTATTCAATTATTCTTATT-TGGAAA-CAAAATCCA-AATCAAT
* * ***
20154180 TATGTTAAATGGCA
63 TCTGCTAAACAACA
* * * * * *
20154194 GGAAAAAATCCTGAAAGAAATTTATTCAACTTATTCTTGTTTTGGAAACAAAATCCAAATCAATT
1 GGAATAAATTCTAAAACAAAATTATTCAA-TTATTCTT-ATTTGGAAACAAAATCCAAATCAATT
* *
20154259 CTGCTAAACTATA
64 CTGCTAAACAACA
*
20154272 GGAATAAATTCTAAAACAGAATTATTCAATTA
1 GGAATAAATTCTAAAACAAAATTATTCAATTA
20154304 ATTATTATAA
Statistics
Matches: 138, Mismatches: 39, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
74 8 0.06
75 7 0.05
76 37 0.27
77 35 0.25
78 37 0.27
79 9 0.07
80 5 0.04
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (76 bp):
GGAATAAATTCTAAAACAAAATTATTCAATTATTCTTATTTGGAAACAAAATCCAAATCAATTCT
GCTAAACAACA
Found at i:20154221 original size:76 final size:75
Alignment explanation
Indices: 20154139--20154376 Score: 230
Period size: 76 Copynumber: 3.1 Consensus size: 75
20154129 TAAAACAGAA
*
20154139 TTATTCAATTAATTATTATAAAATCCAAATATAGAATAAAATATGTTAAATGGCAGGAAAAAATC
1 TTATTCAATTAATTATTATAAAATCCAAATATA-AATAAAATCTGTTAAATGGCAGGAAAAAATC
20154204 CTGAAAGAAAT
65 CTGAAAGAAAT
* * * * * ** * * * ** *
20154215 TTATTCAACTTATTCTTGTTTTGGAAA-CAAAATCCAAATCAATTCTGCTAAACT-ATAGGAATA
1 TTATTCAA-TTA--ATTATTAT-AAAATCCAAATATAAATAAAATCTGTTAAA-TGGCAGGAAAA
* * *
20154278 AATTCTAAAACAGAA-
61 AATCCTGAAAGA-AAT
20154293 TTATTCAATTAATTATTATAAAATCCAAATATAAAATAAAATCTGTTAAATGGCAGGAAAAAATC
1 TTATTCAATTAATTATTATAAAATCCAAATAT-AAATAAAATCTGTTAAATGGCAGGAAAAAATC
20154358 CTGAAAGAAAT
65 CTGAAAGAAAT
20154369 TTATTCAA
1 TTATTCAA
20154377 CTTATTCTTG
Statistics
Matches: 119, Mismatches: 33, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
74 3 0.03
75 13 0.11
76 45 0.38
77 6 0.05
78 35 0.29
79 14 0.12
80 3 0.03
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (75 bp):
TTATTCAATTAATTATTATAAAATCCAAATATAAATAAAATCTGTTAAATGGCAGGAAAAAATCC
TGAAAGAAAT
Found at i:20154253 original size:154 final size:154
Alignment explanation
Indices: 20154062--20154407 Score: 615
Period size: 154 Copynumber: 2.3 Consensus size: 154
20154052 CAAAACAAAA
*
20154062 TTATTCAA-TTAGTTCTT-ATTTGGAAACAAAATCCAAATCAATTCTGCTAAACAACAGGAATAA
1 TTATTCAACTTA-TTCTTGTTTTGGAAACAAAATCCAAATCAATTCTGCTAAACAACAGGAATAA
*
20154125 ATTCTAAAACAGAATTATTCAATTAATTATTATAAAATCCAAATATAGAATAAAATATGTTAAAT
65 ATTCTAAAACAGAATTATTCAATTAATTATTATAAAATCCAAATATAAAATAAAATATGTTAAAT
20154190 GGCAGGAAAAAATCCTGAAAGAAAT
130 GGCAGGAAAAAATCCTGAAAGAAAT
* *
20154215 TTATTCAACTTATTCTTGTTTTGGAAACAAAATCCAAATCAATTCTGCTAAACTATAGGAATAAA
1 TTATTCAACTTATTCTTGTTTTGGAAACAAAATCCAAATCAATTCTGCTAAACAACAGGAATAAA
*
20154280 TTCTAAAACAGAATTATTCAATTAATTATTATAAAATCCAAATATAAAATAAAATCTGTTAAATG
66 TTCTAAAACAGAATTATTCAATTAATTATTATAAAATCCAAATATAAAATAAAATATGTTAAATG
20154345 GCAGGAAAAAATCCTGAAAGAAAT
131 GCAGGAAAAAATCCTGAAAGAAAT
*
20154369 TTATTCAACTTATTCTTGTTTTGGAAACAAAATCAAAAT
1 TTATTCAACTTATTCTTGTTTTGGAAACAAAATCCAAAT
20154408 AGAATAACAT
Statistics
Matches: 185, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
153 13 0.07
154 172 0.93
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (154 bp):
TTATTCAACTTATTCTTGTTTTGGAAACAAAATCCAAATCAATTCTGCTAAACAACAGGAATAAA
TTCTAAAACAGAATTATTCAATTAATTATTATAAAATCCAAATATAAAATAAAATATGTTAAATG
GCAGGAAAAAATCCTGAAAGAAAT
Found at i:20154435 original size:83 final size:83
Alignment explanation
Indices: 20154312--20154500 Score: 222
Period size: 83 Copynumber: 2.3 Consensus size: 83
20154302 TAATTATTAT
* * * * *
20154312 AAAATCCAAATATAAAATAAAATCTGTTAAATGGCAGGAAA-AAATCCTGAAAGAA-ATTTATTC
1 AAAAT-CAAA-ATAGAATAAAATATGTTAAACGGCAGGAAATAAATCCCGAAA-AAGAATTATTC
*
20154375 AACTT-ATTCTTGTTTTGGAAAC
63 -ACTTAATTCTT-ATTTGGAAAC
* **
20154397 AAAATCAAAATAGAATAACATATGTTAAACGGTGGGAAATAAATCCCGAAAAAGAATTATTCACT
1 AAAATCAAAATAGAATAAAATATGTTAAACGGCAGGAAATAAATCCCGAAAAAGAATTATTCACT
20154462 TAATTCTTATTTGGAAAC
66 TAATTCTTATTTGGAAAC
*
20154480 AAAATCAAAATAGAATCAAAT
1 AAAATCAAAATAGAATAAAAT
20154501 CAATTGAACG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
83 58 0.64
84 27 0.30
85 5 0.06
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (83 bp):
AAAATCAAAATAGAATAAAATATGTTAAACGGCAGGAAATAAATCCCGAAAAAGAATTATTCACT
TAATTCTTATTTGGAAAC
Found at i:20155282 original size:32 final size:32
Alignment explanation
Indices: 20155221--20155282 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
20155211 AAGAGCCTTT
** *
20155221 AAATCAATTTAAATAGAATTAAATTAAATCAA
1 AAATCAATTTAAATAGAAACAAATCAAATCAA
*
20155253 AAATCAATTTAATTAGAAACAAATCAAATC
1 AAATCAATTTAAATAGAAACAAATCAAATC
20155283 GAGATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATCAATTTAAATAGAAACAAATCAAATCAA
Found at i:20158167 original size:16 final size:16
Alignment explanation
Indices: 20158146--20158199 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
20158136 TAAAATTATT
20158146 TTTTTAAAATATAAAA
1 TTTTTAAAATATAAAA
20158162 TTTTTAAAAT-T---A
1 TTTTTAAAATATAAAA
*
20158174 TTTTTTAAATATAAAA
1 TTTTTAAAATATAAAA
*
20158190 TTATTAAAAT
1 TTTTTAAAAT
20158200 TATTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
15 1 0.03
16 19 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTAAAATATAAAA
Found at i:20158186 original size:28 final size:29
Alignment explanation
Indices: 20158127--20158227 Score: 159
Period size: 30 Copynumber: 3.4 Consensus size: 29
20158117 TAGATGATTT
20158127 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTTAAAATA
*
20158157 TAAAATTTTTAAAATTATTTTTT-AAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
20158185 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAT-A
20158215 TAAAATTATTAAA
1 TAAAATTATTAAA
20158228 TAAATTTAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 27 0.40
29 10 0.15
30 30 0.45
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:20159421 original size:19 final size:19
Alignment explanation
Indices: 20159375--20159421 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
20159365 GTCTAAAAAA
*
20159375 AATTTAAA-TGTTTTTTTT
1 AATTTAAATTGTTTTTTAT
*
20159393 AATTTTAATTG-TTTTTAT
1 AATTTAAATTGTTTTTTAT
20159411 AAGTTTAAATT
1 AA-TTTAAATT
20159422 TATTTGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (19 bp):
AATTTAAATTGTTTTTTAT
Found at i:20161831 original size:12 final size:12
Alignment explanation
Indices: 20161809--20161914 Score: 58
Period size: 12 Copynumber: 9.1 Consensus size: 12
20161799 ATAACATCCA
20161809 AACAA-CAAAAT
1 AACAACCAAAAT
20161820 AACAACCAAAAT
1 AACAACCAAAAT
*
20161832 AGCAA-CAAGAAT
1 AACAACCAA-AAT
** *
20161844 AAC-AGGAAAAC
1 AACAACCAAAAT
*
20161855 AACAACAAAAAT
1 AACAACCAAAAT
* *
20161867 AGCAACAAAAAT
1 AACAACCAAAAT
* * *
20161879 AATAGCAAAAAT
1 AACAACCAAAAT
* * *
20161891 AGC-ACTAAAAC
1 AACAACCAAAAT
20161902 AACAACCAAAAT
1 AACAACCAAAAT
20161914 A
1 A
20161915 GTAAAAAAGC
Statistics
Matches: 71, Mismatches: 19, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
11 21 0.30
12 50 0.70
ACGTcount: A:0.66, C:0.19, G:0.07, T:0.08
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:20161874 original size:15 final size:15
Alignment explanation
Indices: 20161854--20161886 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20161844 AACAGGAAAA
20161854 CAACAACAAA-AATAG
1 CAACAA-AAATAATAG
20161869 CAACAAAAATAATAG
1 CAACAAAAATAATAG
20161884 CAA
1 CAA
20161887 AAATAGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (15 bp):
CAACAAAAATAATAG
Found at i:20161911 original size:24 final size:24
Alignment explanation
Indices: 20161850--20161915 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
20161840 GAATAACAGG
20161850 AAAACAACAACAAAAATAGCAACA
1 AAAACAACAACAAAAATAGCAACA
* * * *
20161874 AAAATAATAGCAAAAATAGC-ACT
1 AAAACAACAACAAAAATAGCAACA
*
20161897 AAAACAACAACCAAAATAG
1 AAAACAACAACAAAAATAG
20161916 TAAAAAAGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (24 bp):
AAAACAACAACAAAAATAGCAACA
Found at i:20165329 original size:26 final size:26
Alignment explanation
Indices: 20165300--20165422 Score: 133
Period size: 26 Copynumber: 4.8 Consensus size: 26
20165290 TCTCATTTCT
* * *
20165300 ATTTTACCTCGAGTAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTATGATG
*
20165326 ATTTTACCCCTAGTAAAATTATGACG
1 ATTTTACCCCTAGTAAAATTATGATG
*
20165352 ATTTTACCCCTAATAAAATTATGATG
1 ATTTTACCCCTAGTAAAATTATGATG
* *
20165378 GTTTTACCCCTA-TAAAATTTTGA-G
1 ATTTTACCCCTAGTAAAATTATGATG
* **
20165402 AAATTTACCCCCGGTAAAATT
1 -ATTTTACCCCTAGTAAAATT
20165423 TCAAGAAAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
24 1 0.01
25 18 0.22
26 64 0.77
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTATGATG
Found at i:20165527 original size:26 final size:25
Alignment explanation
Indices: 20165496--20165578 Score: 121
Period size: 26 Copynumber: 3.2 Consensus size: 25
20165486 AATTTTCGAG
20165496 AAAATTATGATGATTTTACCCCTAGT
1 AAAATTATGATGATTTTACCCCTA-T
20165522 AAAATTATGATGATTTTACCCCTAAT
1 AAAATTATGATGATTTTACCCCT-AT
* * *
20165548 AAAATTATAACGATTTTACCCATAT
1 AAAATTATGATGATTTTACCCCTAT
20165573 AAAATT
1 AAAATT
20165579 TTGACAAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
25 8 0.15
26 44 0.83
27 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (25 bp):
AAAATTATGATGATTTTACCCCTAT
Found at i:20165628 original size:182 final size:182
Alignment explanation
Indices: 20165308--20165676 Score: 605
Period size: 182 Copynumber: 2.0 Consensus size: 182
20165298 CTATTTTACC
*
20165308 TCGAGTAAAATTTTGATGATTTTACCCCTAGTAAAATTATGACGATTTTACCCCTAATAAAATTA
1 TCGAGTAAAATTATGATGATTTTACCCCTAGTAAAATTATGACGATTTTACCCCTAATAAAATTA
* * * * * *
20165373 TGATGGTTTTACCCCTATAAAATTTTGAGAAATTTACCCCCGGTAAAATTTCAAGAAAATATGTT
66 TAACGATTTTACCCATATAAAATTTTGACAAACTTACCCCCGGTAAAATTTCAAGAAAATATGTT
* * *
20165438 TAATATTTCATAACTCAATATTCCCACTGTAATTGGATGATTTATTTTAATTT
131 TAATATTTCATAACTCAACATTCCCACTGTAACTGAATGATTT-TTTTAATTT
*
20165491 TCGAG-AAAATTATGATGATTTTACCCCTAGTAAAATTATGATGATTTTACCCCTAATAAAATTA
1 TCGAGTAAAATTATGATGATTTTACCCCTAGTAAAATTATGACGATTTTACCCCTAATAAAATTA
20165555 TAACGATTTTACCCATATAAAATTTTGACAAACTTACCCCCGGTAAAATTTCAAGAAAATATGTT
66 TAACGATTTTACCCATATAAAATTTTGACAAACTTACCCCCGGTAAAATTTCAAGAAAATATGTT
* *
20165620 TAATATTTCATAACTCAACATTCTCACTGTAACTGAATGGTTTTTTTAATTT
131 TAATATTTCATAACTCAACATTCCCACTGTAACTGAATGATTTTTTTAATTT
20165672 TCGAG
1 TCGAG
20165677 CTTCAAAACA
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
181 14 0.08
182 154 0.89
183 5 0.03
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (182 bp):
TCGAGTAAAATTATGATGATTTTACCCCTAGTAAAATTATGACGATTTTACCCCTAATAAAATTA
TAACGATTTTACCCATATAAAATTTTGACAAACTTACCCCCGGTAAAATTTCAAGAAAATATGTT
TAATATTTCATAACTCAACATTCCCACTGTAACTGAATGATTTTTTTAATTT
Found at i:20169057 original size:25 final size:25
Alignment explanation
Indices: 20169023--20169113 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
20169013 TAGCTCATAT
*
20169023 GAGCCTAGACAGAATCA-CACTGTTAC
1 GAGCC-AGACAGAAT-ATCACTCTTAC
* * *
20169049 GAGGCAGACAAAATATTACTCTTAC
1 GAGCCAGACAGAATATCACTCTTAC
* *
20169074 GAGCCAGACAGTATATCACTCTTAT
1 GAGCCAGACAGAATATCACTCTTAC
*
20169099 GAGCCCAAACAGAAT
1 GAG-CCAGACAGAAT
20169114 TTAACCAGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 1 0.02
25 38 0.73
26 13 0.25
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (25 bp):
GAGCCAGACAGAATATCACTCTTAC
Found at i:20177885 original size:16 final size:15
Alignment explanation
Indices: 20177858--20177896 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
20177848 AACAATATAC
20177858 TTCTTTTTCC-TTCTT
1 TTCTTTTTCCTTTC-T
20177873 TTCTTTTTACCTTTCT
1 TTCTTTTT-CCTTTCT
20177889 TTCTTTTT
1 TTCTTTTT
20177897 TTTAATAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTTTTCCTTTCT
Found at i:20178229 original size:10 final size:10
Alignment explanation
Indices: 20178214--20178250 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
20178204 GAAGAGCTCA
20178214 ATATTCATTC
1 ATATTCATTC
20178224 ATATTCATTC
1 ATATTCATTC
20178234 ATATTCATTC
1 ATATTCATTC
20178244 A-ATTCAT
1 ATATTCAT
20178251 ATATCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.22
10 21 0.78
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATTCATTC
Found at i:20178990 original size:15 final size:16
Alignment explanation
Indices: 20178954--20178991 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
20178944 CTCTTCCTTC
20178954 TCTTCTTCAAGGTCCT
1 TCTTCTTCAAGGTCCT
*
20178970 T-ATCTTC-AGGTCCT
1 TCTTCTTCAAGGTCCT
20178984 TCTTCTTC
1 TCTTCTTC
20178992 TCCTTCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 8 0.42
15 10 0.53
16 1 0.05
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.47
Consensus pattern (16 bp):
TCTTCTTCAAGGTCCT
Found at i:20181767 original size:17 final size:17
Alignment explanation
Indices: 20181742--20181775 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20181732 ACGAAACAGG
* *
20181742 GGAAGAAGAAAAGGGAA
1 GGAAAAAGAAAAAGGAA
20181759 GGAAAAAGAAAAAGGAA
1 GGAAAAAGAAAAAGGAA
20181776 AAACTAGGAT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GGAAAAAGAAAAAGGAA
Found at i:20188860 original size:17 final size:17
Alignment explanation
Indices: 20188835--20188868 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20188825 ACGAAACAGG
* *
20188835 GGAAGAAGAAAAGGGAA
1 GGAAAAAGAAAAAGGAA
20188852 GGAAAAAGAAAAAGGAA
1 GGAAAAAGAAAAAGGAA
20188869 AAACTAGGAT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GGAAAAAGAAAAAGGAA
Found at i:20208184 original size:18 final size:19
Alignment explanation
Indices: 20208158--20208195 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20208148 CGGTTGGTTC
*
20208158 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
20208176 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
20208195 G
1 G
20208196 TGAATAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:20208906 original size:3 final size:3
Alignment explanation
Indices: 20208893--20208926 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
20208883 TCTCAGTCAT
20208893 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20208927 ATGTTGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20216687 original size:21 final size:21
Alignment explanation
Indices: 20216642--20216685 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
20216632 CTTCATGTCA
**
20216642 TTCTCTTCTTTTTTTTCTTCT
1 TTCTCTTCTTTTCCTTCTTCT
20216663 TTCTCTTCCTTTTCCTTCTTCT
1 TTCTCTT-CTTTTCCTTCTTCT
20216685 T
1 T
20216686 CTTCTGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTCTTCTTTTCCTTCTTCT
Found at i:20231781 original size:31 final size:31
Alignment explanation
Indices: 20231730--20231800 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
20231720 TATTCAAGTT
*
20231730 AAGACTAAAATTTCGAAATTCAAAAAGTATA
1 AAGACTAAAATTTCGAAATTCAAAAAGTACA
*
20231761 AAGACTAAAA-TT-GACCAATTCTAAAAGTACA
1 AAGACTAAAATTTCGA--AATTCAAAAAGTACA
*
20231792 ATGACTAAA
1 AAGACTAAA
20231801 TTTAATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 31 0.89
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.24
Consensus pattern (31 bp):
AAGACTAAAATTTCGAAATTCAAAAAGTACA
Found at i:20232250 original size:20 final size:20
Alignment explanation
Indices: 20232218--20232258 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
20232208 TAAAGAAATT
20232218 TATATATTAAAATATTTTCA
1 TATATATTAAAATATTTTCA
20232238 TATA-ATTACAAATATTTTCA
1 TATATATTA-AAATATTTTCA
20232258 T
1 T
20232259 CTCTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATATTAAAATATTTTCA
Found at i:20233338 original size:2 final size:2
Alignment explanation
Indices: 20233331--20233372 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20233321 TCACAACCAA
20233331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20233373 GTATGTAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20238011 original size:33 final size:34
Alignment explanation
Indices: 20237962--20238025 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
20237952 TAATATAAAT
* * *
20237962 ATAAGTAGTCCTTTAAC-AAACTTTCAAGCAAAC
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCAAAC
20237995 ATAAGTAATCCCTTAACAAAACTTGCAAGCA
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCA
20238026 TAATATAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (34 bp):
ATAAGTAATCCCTTAACAAAACTTGCAAGCAAAC
Found at i:20238535 original size:32 final size:34
Alignment explanation
Indices: 20238493--20238557 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
20238483 ATATGAAAGT
* *
20238493 TTAAGGAAGATGGAAGG-TAAGA-TCAAGGGAGG
1 TTAAGAAAGATGGAAGGTTAAAAGTCAAGGGAGG
20238525 TTAAGAAAGATGGAAGGTTAAAAGTCAAGGGAG
1 TTAAGAAAGATGGAAGGTTAAAAGTCAAGGGAG
20238558 ATGAAAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 16 0.55
33 4 0.14
34 9 0.31
ACGTcount: A:0.43, C:0.03, G:0.37, T:0.17
Consensus pattern (34 bp):
TTAAGAAAGATGGAAGGTTAAAAGTCAAGGGAGG
Found at i:20238713 original size:30 final size:30
Alignment explanation
Indices: 20238677--20238750 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
20238667 TTATAATAGG
* *
20238677 TTTTTTTAATTTGGTATTTGAATTTAATAT
1 TTTTTTTAATTTGGTATTTGAACTTAACAT
* *
20238707 TTTTTTTAAGTTCGTATTTGAACTTAACAT
1 TTTTTTTAATTTGGTATTTGAACTTAACAT
20238737 TTATTTTTAATTTG
1 TT-TTTTTAATTTG
20238751 ATACTTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 28 0.76
31 9 0.24
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (30 bp):
TTTTTTTAATTTGGTATTTGAACTTAACAT
Found at i:20239898 original size:25 final size:24
Alignment explanation
Indices: 20239828--20239902 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 24
20239818 TAAACTTAGG
20239828 AAAAAGTTAGGTACCAAATTAGGAA
1 AAAAAGTTAGGTACCAAA-TAGGAA
*
20239853 AAAGTGTTAAGTTCATGTACCAAATAGGACA
1 AAA-----AAGTT-AGGTACCAAATAGGA-A
20239884 AAAAAGTTAGGTACCAAAT
1 AAAAAGTTAGGTACCAAAT
20239903 TAAGAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
25 13 0.32
26 5 0.12
30 10 0.24
31 13 0.32
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.23
Consensus pattern (24 bp):
AAAAAGTTAGGTACCAAATAGGAA
Found at i:20242539 original size:21 final size:21
Alignment explanation
Indices: 20242504--20242550 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
20242494 CATACAAGGA
*
20242504 CACATGTTAACATACAAGGTTT
1 CACATGTTAACATAC-AGGGTT
*
20242526 CACATG-TCACATACAGGGTT
1 CACATGTTAACATACAGGGTT
20242546 CACAT
1 CACAT
20242551 ATTATACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
CACATGTTAACATACAGGGTT
Found at i:20245513 original size:13 final size:13
Alignment explanation
Indices: 20245495--20245525 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20245485 TTTTATCGTA
*
20245495 TAATTATAGTAAT
1 TAATTATAATAAT
20245508 TAATTATAATAAT
1 TAATTATAATAAT
20245521 TAATT
1 TAATT
20245526 TTATCGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
TAATTATAATAAT
Found at i:20247663 original size:24 final size:25
Alignment explanation
Indices: 20247631--20247677 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
20247621 TATTAAAAGA
*
20247631 ATAATATTTAATGCATCATTATTTC
1 ATAATATTTAATGCACCATTATTTC
* *
20247656 ATAA-ATTTGATGTACCATTATT
1 ATAATATTTAATGCACCATTATT
20247678 GAACAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (25 bp):
ATAATATTTAATGCACCATTATTTC
Found at i:20251590 original size:73 final size:73
Alignment explanation
Indices: 20251499--20251644 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
20251489 ATGAAATATG
20251499 ATAATTCTTGGTTAATAATCAAACGATATAACTTTTGATTACTTATAACTTTTCATTTGCAACAA
1 ATAATTCTTGGTTAATAATCAAACGATATAACTTTTGATTACTTATAACTTTTCATTTGCAACAA
20251564 TTGAAACA
66 TTGAAACA
* *
20251572 ATAATTCTTGGTTAATAATCAAATGATATAACTTTTGGTTACTTATAACTTTTCATTTGCAACAA
1 ATAATTCTTGGTTAATAATCAAACGATATAACTTTTGATTACTTATAACTTTTCATTTGCAACAA
20251637 TTGAAACA
66 TTGAAACA
20251645 CTATATATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (73 bp):
ATAATTCTTGGTTAATAATCAAACGATATAACTTTTGATTACTTATAACTTTTCATTTGCAACAA
TTGAAACA
Found at i:20260481 original size:29 final size:29
Alignment explanation
Indices: 20260441--20260499 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20260431 CTGTGGAAGA
* * *
20260441 GGTGGAGAACTTGTTCGTTGAGAGTTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
*
20260470 GGTGAAGAACTTGTTTGTAGAGAATTCGT
1 GGTGAAGAACTTGTTCGTAGAGAATTCGT
20260499 G
1 G
20260500 TCAAGGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTAGAGAATTCGT
Found at i:20265043 original size:52 final size:53
Alignment explanation
Indices: 20264980--20265092 Score: 210
Period size: 52 Copynumber: 2.2 Consensus size: 53
20264970 TTAGTCTTTG
20264980 TTAAAAATAATAATTTAAAATTTTTTTAAAGTTGATGATTAAATTCAACA-TT
1 TTAAAAATAATAATTTAAAATTTTTTTAAAGTTGATGATTAAATTCAACATTT
*
20265032 TTAAAAATAATAATTTAAATTTTTTTTAAAGTTGATGATTAAATTCAACATTT
1 TTAAAAATAATAATTTAAAATTTTTTTAAAGTTGATGATTAAATTCAACATTT
20265085 TTAAAAAT
1 TTAAAAAT
20265093 TTAACTAGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 49 0.83
53 10 0.17
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (53 bp):
TTAAAAATAATAATTTAAAATTTTTTTAAAGTTGATGATTAAATTCAACATTT
Found at i:20265073 original size:24 final size:24
Alignment explanation
Indices: 20264994--20265076 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
20264984 AAATAATAAT
*
20264994 TTAAAATTTTTTTAAAGTTGATGA
1 TTAAATTTTTTTTAAAGTTGATGA
** ** * *
20265018 TTAAATTCAACATTTTAAAAATAATAA
1 TTAAATT---TTTTTTAAAGTTGATGA
20265045 TTTAAATTTTTTTTAAAGTTGATGA
1 -TTAAATTTTTTTTAAAGTTGATGA
20265070 TTAAATT
1 TTAAATT
20265077 CAACATTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
24 13 0.31
25 11 0.26
27 11 0.26
28 7 0.17
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (24 bp):
TTAAATTTTTTTTAAAGTTGATGA
Found at i:20272763 original size:40 final size:40
Alignment explanation
Indices: 20272710--20272849 Score: 235
Period size: 40 Copynumber: 3.5 Consensus size: 40
20272700 GAGGATATGT
*
20272710 TTAAAAAGGAAGACCTATGACTCGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACATATGACTCGGTAGAGCATAAGATTG
* * *
20272750 TTAAAAGGGAAGACTTATGACTTGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACATATGACTCGGTAGAGCATAAGATTG
*
20272790 TTAAAAAGGAAGACGTATGACTCGGTAGAGCATAAGATTG
1 TTAAAAAGGAAGACATATGACTCGGTAGAGCATAAGATTG
20272830 TTAAAAAGGAAGACATATGA
1 TTAAAAAGGAAGACATATGA
20272850 ACCTGTGTAA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (40 bp):
TTAAAAAGGAAGACATATGACTCGGTAGAGCATAAGATTG
Found at i:20273539 original size:21 final size:21
Alignment explanation
Indices: 20273513--20273581 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
20273503 GGAGTTTTTA
* *
20273513 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAACTAACACTT
* **
20273534 GTATCGATAGAACTGTCACTT
1 GTATCGGTAGAACTAACACTT
**
20273555 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAACTAACACTT
20273576 GTATCG
1 GTATCG
20273582 ATAGTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAACTAACACTT
Found at i:20292015 original size:19 final size:19
Alignment explanation
Indices: 20291972--20292015 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
20291962 CAAGGACAAG
* *
20291972 AAAAGAAAAAGGTAGGACA
1 AAAAGAAAAAGGAAGCACA
20291991 AAAAGAAAAA-GAAGCACA
1 AAAAGAAAAAGGAAGCACA
20292009 AAGAAGA
1 AA-AAGA
20292016 GTGCCTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.68, C:0.07, G:0.23, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAGGAAGCACA
Found at i:20305517 original size:23 final size:22
Alignment explanation
Indices: 20305491--20305557 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 22
20305481 GTCCCTGTAT
20305491 TTTTATATTGTTTTAATTTAATC
1 TTTTAT-TTGTTTTAATTTAATC
20305514 TTTTATTCTGTTTTTTAATTTTAATC
1 TTTTATT-TG--TTTTAA-TTTAATC
*
20305540 TTTAATTTGTTTTAATTT
1 TTTTATTTGTTTTAATTT
20305558 TAATTAACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 4 0.10
23 14 0.36
25 8 0.21
26 13 0.33
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTTGTTTTAATTTAATC
Found at i:20305558 original size:23 final size:23
Alignment explanation
Indices: 20305498--20305561 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
20305488 TATTTTTATA
*
20305498 TTGTTTTAA-TTTAATCTTTTAT
1 TTGTTTTAATTTTAATCTTTAAT
20305520 TCTGTTTTTTAATTTTAATCTTTAAT
1 T-TG--TTTTAATTTTAATCTTTAAT
20305546 TTGTTTTAATTTTAAT
1 TTGTTTTAATTTTAAT
20305562 TAACTCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.41
25 8 0.22
26 13 0.35
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (23 bp):
TTGTTTTAATTTTAATCTTTAAT
Found at i:20305664 original size:7 final size:6
Alignment explanation
Indices: 20305652--20305712 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 6
20305642 ATTTAGTCCA
* * *
20305652 TTTATT GTTTATT TTTATTT TTTATA TTTATT TATTATT TTATGTT TATTATG
1 TTTATT -TTTATT TTTA-TT TTTATT TTTATT T-TTATT TT-TATT T-TTATT
20305705 TTTATT TT
1 TTTATT TT
20305713 CTGTAGTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 18 0.41
7 25 0.57
8 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:20305670 original size:13 final size:13
Alignment explanation
Indices: 20305652--20305701 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
20305642 ATTTAGTCCA
20305652 TTTATTGTTTATT
1 TTTATTGTTTATT
* *
20305665 TTTATTTTTTATA
1 TTTATTGTTTATT
20305678 TTTATT-TATTA-T
1 TTTATTGT-TTATT
20305690 TTTA-TGTTTATT
1 TTTATTGTTTATT
20305702 ATGTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.13
12 7 0.23
13 20 0.65
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTATTGTTTATT
Found at i:20305680 original size:26 final size:27
Alignment explanation
Indices: 20305651--20305711 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
20305641 AATTTAGTCC
20305651 ATTTATTGT-TTATTTTTAT-TTT-TTAT
1 ATTTATT-TATTA-TTTTATGTTTATTAT
20305677 ATTTATTTATTATTTTATGTTTATTAT
1 ATTTATTTATTATTTTATGTTTATTAT
*
20305704 GTTTATTT
1 ATTTATTT
20305712 TCTGTAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 13 0.42
27 11 0.35
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (27 bp):
ATTTATTTATTATTTTATGTTTATTAT
Found at i:20305694 original size:18 final size:17
Alignment explanation
Indices: 20305665--20305701 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
20305655 ATTGTTTATT
20305665 TTTATTTTTTATATTTA
1 TTTATTTTTTATATTTA
*
20305682 TTTATTATTTTATGTTTA
1 TTTATT-TTTTATATTTA
20305700 TT
1 TT
20305702 ATGTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTATATTTA
Found at i:20309523 original size:15 final size:13
Alignment explanation
Indices: 20309499--20309537 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
20309489 TGCATATGCA
20309499 TACATGCATTCAT
1 TACATGCATTCAT
20309512 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
20309528 TACATGCATT
1 TACATGCATT
20309538 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:20311674 original size:5 final size:5
Alignment explanation
Indices: 20311660--20311704 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
20311650 AATTTCACCC
20311660 AAAA- AAAAG AAAAG AAAAG AAAAG -AAA- AAAAG AAAA- AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
20311705 AAGAGAGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
4 14 0.38
5 23 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:20311689 original size:17 final size:17
Alignment explanation
Indices: 20311660--20311706 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
20311650 AATTTCACCC
*
20311660 AAAAAA-AAGAAAAGAA
1 AAAAAAGAAAAAAAGAA
20311676 AAGAAAAGAAAAAAAGAA
1 AA-AAAAGAAAAAAAGAA
20311694 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
20311707 GAGAGGTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 2 0.07
17 15 0.54
18 11 0.39
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGAA
Found at i:20311698 original size:9 final size:9
Alignment explanation
Indices: 20311660--20311706 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
20311650 AATTTCACCC
20311660 AAAAA-AAA
1 AAAAAGAAA
*
20311668 GAAAAGAAA
1 AAAAAGAAA
20311677 AGAAAAG-AA
1 A-AAAAGAAA
20311686 AAAAAGAAA
1 AAAAAGAAA
20311695 AAAAAGAAA
1 AAAAAGAAA
20311704 AAA
1 AAA
20311707 GAGAGGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 9 0.26
9 20 0.59
10 5 0.15
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:20311705 original size:23 final size:23
Alignment explanation
Indices: 20311661--20311704 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20311651 ATTTCACCCA
20311661 AAAAAAAGAAAAGAAAAGAAAAG
1 AAAAAAAGAAAAGAAAAGAAAAG
20311684 AAAAAAAGAAAA-AAAAGAAAA
1 AAAAAAAGAAAAGAAAAGAAAA
20311705 AAGAGAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAGAAAAGAAAAG
Found at i:20312750 original size:102 final size:102
Alignment explanation
Indices: 20312571--20313199 Score: 706
Period size: 102 Copynumber: 6.2 Consensus size: 102
20312561 AAACAACTCT
* * * **
20312571 TATATCTCTGAAGTTGCAGTGGAAT-AGAGTAAAAC-AATAGTAGCAGATCTCAATCTCTTTGAA
1 TATATCCCTGAAGTTGCAGTGG-ATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAA
* * * *
20312634 GTTACATTGAAATGGAGTGAAGCCACAACACCAAATTC
65 GTTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
* * * * * *
20312672 TATATTCCTAAAGTTACAGTGGATTAGATTAAAACTAATAGTAGCAGATCTCAATCTTCCTGAAG
1 TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
*
20312737 TTACATTGGAATGGAGTGAAGTCACAACACCAAATCC
66 TTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
* * * * *
20312774 TATATCCCTGAAGTTGCAATAGATCAGATTAAAACTAGCAGTAGTAGATCTTAATCTCCCTGAAG
1 TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
** *
20312839 TTGTAATGGAATGGAGTGAAGCCACAACACCAAATCC
66 TTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
** * * ** *
20312876 TATATCCCTGAAGTTGTTGTGGATCGGATCAAAACTAATGGTAGCAAATCTCAATCTCCCTGAAG
1 TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
* * * *
20312941 TTACAGTGGAATGGAGTGAAATTACAACACCAAAACC
66 TTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
* * * *
20312978 TATGTCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAAACTCCCTGAAG
1 TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
* * *
20313043 TTGCAATGGAATAGAGTGAAGTTACAACACCAAATCC
66 TTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
* * * * * * *
20313080 TATATCCTTGAGGTTGTAGTGGATTAGATTAAAACTCACAATAGCGGATCTCAATCTCCCTGAAG
1 TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
* ** * * *
20313145 CTGTAGTGGAATGAAGTGAAGTTACAA-ACCCAAATCC
66 TTACAATGGAATGGAGTGAAGTCACAACA-CCAAATCC
* *
20313182 TATATTCTTGAAGTTGCA
1 TATATCCCTGAAGTTGCA
20313200 TAAATAAGAT
Statistics
Matches: 451, Mismatches: 74, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
100 2 0.00
101 28 0.06
102 421 0.93
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (102 bp):
TATATCCCTGAAGTTGCAGTGGATCAGATTAAAACTAACAGTAGCAGATCTCAATCTCCCTGAAG
TTACAATGGAATGGAGTGAAGTCACAACACCAAATCC
Found at i:20312787 original size:50 final size:50
Alignment explanation
Indices: 20312630--20312788 Score: 129
Period size: 50 Copynumber: 3.1 Consensus size: 50
20312620 TCAATCTCTT
* * *
20312630 TGAAGTTACATTGAAATGGAGTGAAGCCACAACACCAAATTCTATATTCC
1 TGAAGTTACATTGGAATGGAGTGAAGTCACAACACCAAATCCTATATTCC
* * * * * * * * * ** * * * *
20312680 TAAAGTTACAGTGGATTAGATTAAAACTAATAGTAGCAGATCTCAATCTTCC
1 TGAAGTTACATTGGAATGGAGT-GAAGTCACAACACCAAATC-CTATATTCC
*
20312732 TGAAGTTACATTGGAATGGAGTGAAGTCACAACACCAAATCCTATATCCC
1 TGAAGTTACATTGGAATGGAGTGAAGTCACAACACCAAATCCTATATTCC
20312782 TGAAGTT
1 TGAAGTT
20312789 GCAATAGATC
Statistics
Matches: 73, Mismatches: 34, Indels: 4
0.66 0.31 0.04
Matches are distributed among these distances:
50 29 0.40
51 20 0.27
52 24 0.33
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (50 bp):
TGAAGTTACATTGGAATGGAGTGAAGTCACAACACCAAATCCTATATTCC
Found at i:20312999 original size:50 final size:48
Alignment explanation
Indices: 20312830--20313102 Score: 142
Period size: 50 Copynumber: 5.4 Consensus size: 48
20312820 GATCTTAATC
* *
20312830 TCCCTGAAGTTGTAATGGAATGGAGTGAAGCCACAACACCAAATCCTATA
1 TCCCTGAAGTTGTAGTGGAATGGAGTGAA--AACAACACCAAATCCTATA
* * * * * *
20312880 TCCCTGAAGTTGTTGTGG-ATCGGA-TCAAAACTAATGGTAGCAAATCTCAATC
1 TCCCTGAAGTTGTAGTGGAAT-GGAGTGAAAAC-AA---CACCAAATC-CTATA
** * *
20312932 TCCCTGAAGTTACAGTGGAATGGAGTGAAATTACAACACCAAAACCTATG
1 TCCCTGAAGTTGTAGTGGAATGGAGTGAAA--ACAACACCAAATCCTATA
* * * *
20312982 TCCCTGAAGTTGTAGTGG-ATCGGA-TTAAAACTAACAGTAGCAGAT-CTCAAA
1 TCCCTGAAGTTGTAGTGGAAT-GGAGTGAAAAC-AAC---ACCAAATCCT-ATA
* * * *
20313033 CTCCCTGAAGTTGCAATGGAATAGAGTGAAGTTACAACACCAAATCCTATA
1 -TCCCTGAAGTTGTAGTGGAATGGAGTGAA--AACAACACCAAATCCTATA
* *
20313084 TCCTTGAGGTTGTAGTGGA
1 TCCCTGAAGTTGTAGTGGA
20313103 TTAGATTAAA
Statistics
Matches: 164, Mismatches: 37, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
47 4 0.02
48 5 0.03
49 11 0.07
50 58 0.35
51 25 0.15
52 41 0.25
53 11 0.07
54 5 0.03
55 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (48 bp):
TCCCTGAAGTTGTAGTGGAATGGAGTGAAAACAACACCAAATCCTATA
Found at i:20313043 original size:52 final size:52
Alignment explanation
Indices: 20312778--20313045 Score: 161
Period size: 52 Copynumber: 5.2 Consensus size: 52
20312768 AAATCCTATA
* * * * * * * *
20312778 TCCCTGAAGTTGCAATAGATCAGATTAAAACTAGCAGTAGTAGATCTTAATC
1 TCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAATC
* * * * * ** * * *
20312830 TCCCTGAAGTTGTAATGGAAT-GGAGTGAAGC-CACAACACCAAATC-CTATA
1 TCCCTGAAGTTGTAGTGG-ATCGGATTAAAACTAACAGTAGCAAATCTCAATC
* * **
20312880 TCCCTGAAGTTGTTGTGGATCGGATCAAAACTAATGGTAGCAAATCTCAATC
1 TCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAATC
** * * * ** * * * *
20312932 TCCCTGAAGTTACAGTGGAAT-GGAGTGAAA-TTACAACACCAAAAC-CTATG
1 TCCCTGAAGTTGTAGTGG-ATCGGATTAAAACTAACAGTAGCAAATCTCAATC
* *
20312982 TCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAGATCTCAAAC
1 TCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAATC
20313034 TCCCTGAAGTTG
1 TCCCTGAAGTTG
20313046 CAATGGAATA
Statistics
Matches: 150, Mismatches: 58, Indels: 16
0.67 0.26 0.07
Matches are distributed among these distances:
49 4 0.03
50 50 0.33
51 32 0.21
52 60 0.40
53 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (52 bp):
TCCCTGAAGTTGTAGTGGATCGGATTAAAACTAACAGTAGCAAATCTCAATC
Found at i:20313832 original size:13 final size:13
Alignment explanation
Indices: 20313814--20313865 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
20313804 CTCAAACACC
20313814 CAAACCCAAAATA
1 CAAACCCAAAATA
*
20313827 CAAACCC-AAATT
1 CAAACCCAAAATA
20313839 CAAAACCCAAAATTA
1 C-AAACCCAAAA-TA
20313854 CACAAGCCCAAA
1 CA-AA-CCCAAA
20313866 TTTAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 13 0.41
14 4 0.12
15 4 0.12
16 6 0.19
ACGTcount: A:0.56, C:0.33, G:0.02, T:0.10
Consensus pattern (13 bp):
CAAACCCAAAATA
Found at i:20313866 original size:29 final size:26
Alignment explanation
Indices: 20313815--20313872 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
20313805 TCAAACACCC
20313815 AAACCCAAAATACAAACCCAAATTCA
1 AAACCCAAAATACAAACCCAAATTCA
*
20313841 AAACCCAAAATTACACAAGCCCAAATTTA
1 AAACCCAAAA-TACA-AA-CCCAAATTCA
20313870 AAA
1 AAA
20313873 AGACAAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.36
27 4 0.14
28 2 0.07
29 12 0.43
ACGTcount: A:0.57, C:0.28, G:0.02, T:0.14
Consensus pattern (26 bp):
AAACCCAAAATACAAACCCAAATTCA
Found at i:20316883 original size:24 final size:25
Alignment explanation
Indices: 20316840--20316886 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20316830 ATTTAATTAT
*
20316840 TTTATTTTGTTTTTTAATTTTAACC
1 TTTAATTTGTTTTTTAATTTTAACC
20316865 TTTAATTTGTTTTTT-ATTTTAA
1 TTTAATTTGTTTTTTAATTTTAA
20316887 TTAAGTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTAATTTGTTTTTTAATTTTAACC
Found at i:20318870 original size:37 final size:36
Alignment explanation
Indices: 20318791--20318870 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 36
20318781 ATTTTAAAAT
* *
20318791 TAATTTTTTAAATATAAAATTATTAATATTACTATA
1 TAATTTTTTAAATATAAAATTATTAAAATTACTAAA
* *
20318827 TTATTTTTTAAAATATAAAATTATTAAAATTATTAAA
1 TAATTTTTT-AAATATAAAATTATTAAAATTACTAAA
20318864 TAATTTT
1 TAATTTT
20318871 AATTTCATCG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
36 8 0.21
37 30 0.79
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
TAATTTTTTAAATATAAAATTATTAAAATTACTAAA
Found at i:20322102 original size:38 final size:38
Alignment explanation
Indices: 20322060--20322135 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
20322050 GAACAAAGAA
20322060 AACCTGAAATGCCAATATCATATCCAAACATCAAGCCT
1 AACCTGAAATGCCAATATCATATCCAAACATCAAGCCT
20322098 AACCTGAAATGCCAATATCATATCCAAACATCAAGCCT
1 AACCTGAAATGCCAATATCATATCCAAACATCAAGCCT
20322136 CCAAAGGCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (38 bp):
AACCTGAAATGCCAATATCATATCCAAACATCAAGCCT
Found at i:20325494 original size:29 final size:29
Alignment explanation
Indices: 20325395--20325683 Score: 164
Period size: 29 Copynumber: 9.8 Consensus size: 29
20325385 AACGAAGTCA
* ** *
20325395 AAAAT-GTAATTTTTGGATGCCCAGGGGT
1 AAAATGGTAATTTTTGGAAGTTCGGGGGT
* * * *
20325423 AAAACGGTAATTTTTGGAAAATT-TGAGGT
1 AAAATGGTAATTTTTGG-AAGTTCGGGGGT
*
20325452 CAAAAATGAT-ATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGT
* **
20325482 AAAATGGTAATTTTTGGAGGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAGTTCGGGGGT
*
20325511 AAAATGGTAATTTTTGAGGAGTTC-GGGGT
1 AAAATGGTAATTTTTG-GAAGTTCGGGGGT
* *
20325540 CAAAAATGG-AATTTTTGGAAATTCGAGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGT
* ***
20325570 AAAATGGTAATTTTTGGAAATTTC-AAAGT
1 AAAATGGTAATTTTTGG-AAGTTCGGGGGT
**
20325599 CAAAAAT-GTAATTTTTGTGAAGTTCGGGAGCC
1 --AAAATGGTAATTTTTG-GAAGTTCGGG-GGT
* *
20325631 AAAAT-ATAAATTTTGGGAAGTTCGGGGGT
1 AAAATGGT-AATTTTTGGAAGTTCGGGGGT
* *
20325660 CAAAAT-ATAATTTTTAGAAAGTTC
1 -AAAATGGTAATTTTT-GGAAGTTC
20325684 AGGGACCTTC
Statistics
Matches: 204, Mismatches: 37, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
28 18 0.09
29 81 0.40
30 79 0.39
31 26 0.13
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGGT
Found at i:20325534 original size:59 final size:55
Alignment explanation
Indices: 20325395--20325588 Score: 169
Period size: 59 Copynumber: 3.3 Consensus size: 55
20325385 AACGAAGTCA
* ** * *
20325395 AAAAT-GTAATTTTTGGATGCCCAGGGGTAAAACGGTAATTTTTGGAAAATTTGAGGT
1 AAAATGGTAATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGG--AATTTGGGGT
* *
20325452 CAAAAATGAT-ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAGGTTTAGGGGT
1 --AAAATGGTAATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGGA-ATTT-GGGGT
* *
20325511 AAAATGGTAATTTTTGAGGAGTTCGGGGTCAAAAATGG-AATTTTTGGAAATTCGAGGGT
1 AAAATGGTAATTTTTG-GAAGTTCGGGGT--AAAATGGTAATTTTTGG-AATTTG-GGGT
20325570 AAAATGGTAATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
20325589 ATTTCAAAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
57 8 0.07
58 18 0.16
59 78 0.69
60 9 0.08
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (55 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTGGAATTTGGGGT
Found at i:20325601 original size:59 final size:60
Alignment explanation
Indices: 20325507--20325624 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
20325497 GGAGGTTTAG
* ***
20325507 GGGTAAAATGGTAATTTTTGAGGAGTTCGGGGTCAAAAATGGAATTTTTG-GAAATTCGA
1 GGGTAAAATGGTAATTTTTGAGAAGTTCAAAGTCAAAAATGGAATTTTTGTGAAATTCGA
* * *
20325566 GGGTAAAATGGTAATTTTTG-GAAATTTCAAAGTCAAAAATGTAATTTTTGTGAAGTTCG
1 GGGTAAAATGGTAATTTTTGAG-AAGTTCAAAGTCAAAAATGGAATTTTTGTGAAATTCG
20325625 GGAGCCAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.02
59 42 0.84
60 7 0.14
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (60 bp):
GGGTAAAATGGTAATTTTTGAGAAGTTCAAAGTCAAAAATGGAATTTTTGTGAAATTCGA
Found at i:20325612 original size:30 final size:30
Alignment explanation
Indices: 20325538--20325624 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
20325528 GGAGTTCGGG
* **
20325538 GTCAAAAATGGAATTTTTGGAAATTCGAGG
1 GTCAAAAATGTAATTTTTGGAAATTCGAAA
20325568 GT--AAAATGGTAATTTTTGGAAATTTC-AAA
1 GTCAAAAAT-GTAATTTTTGGAAA-TTCGAAA
*
20325597 GTCAAAAATGTAATTTTTGTGAAGTTCG
1 GTCAAAAATGTAATTTTTG-GAAATTCG
20325625 GGAGCCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 18 0.38
31 8 0.17
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (30 bp):
GTCAAAAATGTAATTTTTGGAAATTCGAAA
Found at i:20325635 original size:30 final size:30
Alignment explanation
Indices: 20325601--20325688 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
20325591 TTCAAAGTCA
* *
20325601 AAAATGTAATTTTTGTGAAGTTCGGGAGCC
1 AAAATATAATTTTTGGGAAGTTCGGGAGCC
* * *
20325631 AAAATATAAATTTTGGGAAGTTCGGGGGTC
1 AAAATATAATTTTTGGGAAGTTCGGGAGCC
* *
20325661 AAAATATAATTTTTAGAAAGTTCAGGGA
1 AAAATATAATTTTTGGGAAGTTC-GGGA
20325689 CCTTCTGGGA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 45 0.94
31 3 0.06
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAATATAATTTTTGGGAAGTTCGGGAGCC
Found at i:20326699 original size:3 final size:3
Alignment explanation
Indices: 20326691--20326779 Score: 72
Period size: 3 Copynumber: 29.0 Consensus size: 3
20326681 CATTTCCTTT
* * *
20326691 TTA TTA TTA ATA TT- TTA TTAA TTAA TTA TTG TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA TTA
* * * * *
20326737 ATA ATA TTA TTA CTA TTA TTA ATG TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
20326780 ATCGTTTTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
2 2 0.03
3 57 0.83
4 10 0.14
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:20326742 original size:40 final size:40
Alignment explanation
Indices: 20326691--20326781 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
20326681 CATTTCCTTT
* *
20326691 TTATTATTAATATT-TTATTAATTAATTATTGTTA-TTAATA
1 TTATTATTAATATTATTACT-ATT-ATTAATGTTATTTAATA
* *
20326731 TTATTAATAATATTATTACTATTATTAATGTTATTTATTA
1 TTATTATTAATATTATTACTATTATTAATGTTATTTAATA
20326771 TTATTATTAAT
1 TTATTATTAAT
20326782 CGTTTTAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 9 0.20
40 31 0.70
41 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (40 bp):
TTATTATTAATATTATTACTATTATTAATGTTATTTAATA
Found at i:20327451 original size:6 final size:6
Alignment explanation
Indices: 20327440--20327529 Score: 80
Period size: 6 Copynumber: 15.7 Consensus size: 6
20327430 TGGACTTTTA
* * * * *
20327440 TTAAAT TTAAA- TTAATT TTAAAT TTAAAA GTAAAC TTAAAC TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** *
20327486 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
20327530 TCTTAGAATA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
5 15 0.22
6 52 0.78
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:20327459 original size:11 final size:11
Alignment explanation
Indices: 20327439--20327529 Score: 67
Period size: 11 Copynumber: 8.0 Consensus size: 11
20327429 CTGGACTTTT
20327439 ATTAAATTTAA
1 ATTAAATTTAA
*
20327450 ATTAATTTTAA
1 ATTAAATTTAA
**
20327461 ATTTAAAAGTAA
1 A-TTAAATTTAA
*
20327473 ACTTAAACTTAA
1 A-TTAAATTTAA
*
20327485 TTTAAATTTAA
1 ATTAAATTTAA
**
20327496 ATTTAAA-ACAA
1 A-TTAAATTTAA
20327507 ATTTAAATTTAA
1 A-TTAAATTTAA
*
20327519 AATAAATTTAA
1 ATTAAATTTAA
20327530 TCTTAGAATA
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
11 38 0.61
12 24 0.39
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:20327462 original size:17 final size:17
Alignment explanation
Indices: 20327440--20327547 Score: 119
Period size: 17 Copynumber: 6.3 Consensus size: 17
20327430 TGGACTTTTA
* *
20327440 TTAAATTTAAATTAATT
1 TTAAATTTAAAATAAAT
*
20327457 TTAAATTTAAAAGTAAAC
1 TTAAATTTAAAA-TAAAT
* **
20327475 TTAAACTTAATTTAAAT
1 TTAAATTTAAAATAAAT
*
20327492 TTAAATTTAAAACAAAT
1 TTAAATTTAAAATAAAT
20327509 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
20327526 TT-AATCTTAGAATAAAT
1 TTAAAT-TTAAAATAAAT
20327543 TTAAA
1 TTAAA
20327548 AAAGGTCTAG
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
16 3 0.04
17 58 0.77
18 14 0.19
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:20327478 original size:29 final size:29
Alignment explanation
Indices: 20327441--20327496 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
20327431 GGACTTTTAT
*
20327441 TAAATTTAAA-TTAATTTTAAATTTAAAAG
1 TAAACTTAAACTTAA-TTTAAATTTAAAAG
20327470 TAAACTTAAACTTAATTTAAATTTAAA
1 TAAACTTAAACTTAATTTAAATTTAAA
20327497 TTTAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
TAAACTTAAACTTAATTTAAATTTAAAAG
Found at i:20327502 original size:29 final size:29
Alignment explanation
Indices: 20327439--20327502 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
20327429 CTGGACTTTT
*
20327439 ATTAAATTTAAATTAATTTTAAATTTAAA
1 ATTAAACTTAAATTAATTTTAAATTTAAA
*
20327468 AGTAAACTTAAACTTAA-TTTAAATTTAAA
1 ATTAAACTTAAA-TTAATTTTAAATTTAAA
*
20327497 TTTAAA
1 ATTAAA
20327503 ACAAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTAAACTTAAATTAATTTTAAATTTAAA
Found at i:20328166 original size:209 final size:209
Alignment explanation
Indices: 20327868--20328526 Score: 789
Period size: 209 Copynumber: 3.1 Consensus size: 209
20327858 TGGTTTGGCC
* *
20327868 TACTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTTTGTTTTGATCACTTCTCTGTGTCTC
1 TACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC-TTGTTTTGATCACTTCTCTGTATCTC
20327933 ATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAACCGCTTTATTGCTTC
65 ATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAACCGCTTTATTGCTTC
* *
20327998 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCACATCGAGCTTTGAC
130 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC-CTGAC
*
20328063 TTCATTGATTTGGT-T
194 TTCATTGACTTGGTCT
* * *
20328078 TACTTCTCAATATCTCATCAGGAAGATGACTC-CA-C-CTCTGTTTTGATCCACTTTTCTATATC
1 TACTTCTCAGTATCTCATCAGGAAGATGAC-CGCATCACT-TGTTTTGAT-CACTTCTCTGTATC
* * *
20328140 TCATCAGGAAGACGGATCCGGTTCACTTCTCTGTATCTCAT-TAGAAAGGTAACCGCTTTATTGC
63 TCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAG-AAGGTAACCGCTTTATTGC
* * *
20328204 TTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTAGAAGATTTGCTCACTTCGAGCCTG
127 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTG
** *
20328269 GTTTTATTGACTTGGTCT
192 ACTTCATTGACTTGGTCT
* ** *
20328287 T-CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATTCGCTTCTCTGTATCTC
1 TACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGA-TCACTTCTCTGTATCTC
* * * * * * * * * * **
20328351 ATCAAGAAGATGAATTTGGTCCACATCT-TAGTGTTTCATCAGGAAGCTAACCATTTTATTGCTT
65 ATCAGGAAGACGGATCTGGTTCACTTCTCTA-TATCTCATCAAGAAGGTAACCGCTTTATTGCTT
* * *
20328415 CGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACTTTTGAGCCT-A
129 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC-ATCGAGCCTGA
* * *
20328479 GTTTC-TTCAATTTGGTCT
193 -CTTCATT-GACTTGGTCT
*
20328497 T-CTTCTCAGTATCTCATCTGGAAGATGACC
1 TACTTCTCAGTATCTCATCAGGAAGATGACC
20328527 ATATTTTTTT
Statistics
Matches: 387, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
207 2 0.01
208 56 0.14
209 246 0.64
210 82 0.21
211 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (209 bp):
TACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCACTTCTCTGTATCTCA
TCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAACCGCTTTATTGCTTCG
ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGACTT
CATTGACTTGGTCT
Found at i:20340801 original size:59 final size:58
Alignment explanation
Indices: 20340651--20340876 Score: 149
Period size: 59 Copynumber: 3.9 Consensus size: 58
20340641 AAACGGAGAC
* * * * * * *
20340651 AAAAAT-GTGATTTTT-GGATGCTCGAGGGTAAAATGGCAATTTTTGGAAAATTCGAGGTC
1 AAAAATGGTAATTTTTGGGAAGCTCGAGGATAAAATGG-AATTATTGGAAAGTT-AAGG-G
* * * * * * *
20340710 AAAAATGAT-ACTTTT-GGAAGTTCTG-GGGTAAAATGATAATTATT-GAAGGTTCAGGG
1 AAAAATGGTAATTTTTGGGAAGCTC-GAGGATAAAATG-GAATTATTGGAAAGTTAAGGG
* *
20340766 CAAAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGG
1 -AAAAATGGTAATTTTTGGGAAGCTCGAGGAT-AAAATGGAATTATTGGAAAGTTAAGGG
* * * * *
20340826 TAAAATGGTAATTTTTGGGGAGTTCGAGGTTAAAAATGGAATTTTTGGAAA
1 AAAAATGGTAATTTTTGGGAAGCTCGAGGAT-AAAATGGAATTATTGGAAA
20340877 TTTAGGGGTC
Statistics
Matches: 135, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
57 11 0.08
58 11 0.08
59 96 0.71
60 17 0.13
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (58 bp):
AAAAATGGTAATTTTTGGGAAGCTCGAGGATAAAATGGAATTATTGGAAAGTTAAGGG
Found at i:20340812 original size:30 final size:31
Alignment explanation
Indices: 20340651--20340873 Score: 125
Period size: 29 Copynumber: 7.6 Consensus size: 31
20340641 AAACGGAGAC
* * * *
20340651 AAAAAT-GTGATTTTT-GGATGCTCGAGGGT
1 AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
* * *
20340680 -AAAATGGCAATTTTTGGAAAATTCGAGG-T
1 AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
* * *
20340709 CAAAAATGAT-ACTTTT-GGAAGTTCTG-GGGT
1 -AAAAATGGTAATTTTTGGGAAGTTC-GAGGAT
* * **
20340739 -AAAATGATAATTATT--GAAGGTTC-AGGGC
1 AAAAATGGTAATTTTTGGGAA-GTTCGAGGAT
*
20340767 AAAAATGGTAATTTTTGGGAAGCTCGAGGAT
1 AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
* ** *
20340798 AAAAATGG-AATTTTT-GGAAATTTAAGGGT
1 AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
* *
20340827 -AAAATGGTAATTTTTGGGGAGTTCGAGGTT
1 AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
20340857 AAAAATGG-AATTTTTGG
1 AAAAATGGTAATTTTTGG
20340874 AAATTTAGGG
Statistics
Matches: 149, Mismatches: 29, Indels: 31
0.71 0.14 0.15
Matches are distributed among these distances:
28 26 0.17
29 53 0.36
30 43 0.29
31 27 0.18
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (31 bp):
AAAAATGGTAATTTTTGGGAAGTTCGAGGAT
Found at i:20340829 original size:29 final size:29
Alignment explanation
Indices: 20340797--20340885 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
20340787 AGCTCGAGGA
20340797 TAAAAATGGAATTTTTGGAAATTTAAGGG
1 TAAAAATGGAATTTTTGGAAATTTAAGGG
* * ** *
20340826 T-AAAATGGTAATTTTTGGGGAGTTCGAGGT
1 TAAAAATGG-AATTTTT-GGAAATTTAAGGG
*
20340856 TAAAAATGGAATTTTTGGAAATTTAGGGG
1 TAAAAATGGAATTTTTGGAAATTTAAGGG
20340885 T
1 T
20340886 CAACATATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
28 7 0.15
29 16 0.35
30 16 0.35
31 7 0.15
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAATTTAAGGG
Found at i:20340877 original size:59 final size:59
Alignment explanation
Indices: 20340768--20340885 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
20340758 GTTCAGGGCA
20340768 AAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
1 AAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
* * * *
20340827 AAAATGGTAATTTTTGGGGAGTTCGAGGTTAAAAATGGAATTTTTGGAAATTTAGGGGT
1 AAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
20340886 CAACATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
Found at i:20340897 original size:59 final size:59
Alignment explanation
Indices: 20340768--20340899 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 59
20340758 GTTCAGGGCA
*
20340768 AAAATGGTAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
1 AAAATGATAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
* * * * *
20340827 AAAATGGTAATTTTTGGGGAGTTCGAGGTTAAAAATGGAATTTTTGGAAATTTAGGGGT
1 AAAATGATAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
*
20340886 CAACAT-ATAATTTT
1 -AAAATGATAATTTT
20340900 AAGAAAGTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 62 0.94
60 4 0.06
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAATGATAATTTTTGGGAAGCTCGAGGATAAAAATGGAATTTTTGGAAATTTAAGGGT
Found at i:20341924 original size:3 final size:3
Alignment explanation
Indices: 20341916--20341998 Score: 69
Period size: 3 Copynumber: 27.0 Consensus size: 3
20341906 CATTTCCTTT
* * * *
20341916 TTA TTA TTA ATA TT- TTA GTAA TTAA TTA TTG TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * *
20341962 TTA CTA TTA TTA ATG TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
20341999 ATCGTTTTAA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
2 2 0.03
3 52 0.84
4 8 0.13
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:20342676 original size:97 final size:98
Alignment explanation
Indices: 20342499--20342766 Score: 328
Period size: 97 Copynumber: 2.8 Consensus size: 98
20342489 GAGAAGAAGA
* * * * *
20342499 TATTCGATTA-TCGTGATTTGAAGAAAAGTTGCACCTGGTAAGTTAAGGCACAAA-TTTAAAAAA
1 TATTCGATTATTC-AGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAAT
* * * *
20342562 CCAGAGATAAAGAAACATTGCCTAGATTTAAGGG
65 TCAGAAATAAAGAAACATTGCCTAGATTGAAAGG
* * *
20342596 TATTCGATTATTCAGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAATT
1 TATTCGATTATTCAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATT
* * *
20342661 CA-AAATGAAGTAACATTGCCTCGATTGAAAGG
66 CAGAAATAAAGAAACATTGCCTAGATTGAAAGG
* * *
20342693 TATTCAATTATTCCGATTTGAAGAAAAATTGCACCTAGTTAGTTAAGGCACAAATTTTCAAAATT
1 TATTCGATTATTCAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATT
*
20342758 -TGAAATAAA
66 CAGAAATAAA
20342767 AGAATATTGC
Statistics
Matches: 145, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
97 134 0.92
98 11 0.08
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (98 bp):
TATTCGATTATTCAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATT
CAGAAATAAAGAAACATTGCCTAGATTGAAAGG
Found at i:20343327 original size:59 final size:59
Alignment explanation
Indices: 20343008--20343353 Score: 236
Period size: 59 Copynumber: 5.9 Consensus size: 59
20342998 GGATGCCCAG
** * * *
20343008 GGGTAAAACAGTAA-TTTTGGACACTTCAGGGT-AAAATGGTAATTTTTGGAAA-TTTCA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAAT-GTAATTTTTGGAAAGTTTGA
* * * * *
20343065 GTGTCAAAAATGGGATTTTTTGGACA-TTTAGGGGGT-AAAATGGTAATTTTT-GAAAGTTT-A
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCA--GGGTCAAAAT-GTAATTTTTGGAAAGTTTGA
* * * *
20343125 GGGGTAAAATGGAAATTTTTGG-AAGTTTTAAGGTCAAAAATGGAATTTTTGG-AAGTTTTGA
1 -GGGTAAAATGGTAATTTTTGGAAAG-TTCAGGGTC-AAAATGTAATTTTTGGAAAG-TTTGA
* ** * * *
20343186 -GGTTAAATGGTAATTTTTGG-AAGTTTTGGGGCCAAAAATG-AAGTTTTTTG-AAGTTTAA
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCAGGGTC-AAAATGTAA-TTTTTGGAAAGTTTGA
** *
20343244 GGGTAAAATGGT-ATTTTTTTAAAGTTCGGGGTCAAAATGTAATTTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAATGTAATTTTTGGAAAGTTTGA
*
20343302 GGGTCAAAAT-GTAATTTTTGGAAAGTTCAAGGGTCAAAATGTGATTTTTGGA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTC-AGGGTCAAAATGTAATTTTTGGA
20343354 CAATTTAAGG
Statistics
Matches: 237, Mismatches: 30, Indels: 41
0.77 0.10 0.13
Matches are distributed among these distances:
57 15 0.06
58 38 0.16
59 110 0.46
60 48 0.20
61 26 0.11
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAATGTAATTTTTGGAAAGTTTGA
Found at i:20343343 original size:30 final size:31
Alignment explanation
Indices: 20343035--20343363 Score: 236
Period size: 30 Copynumber: 11.1 Consensus size: 31
20343025 TGGACACTTC
*
20343035 AGGGT-AAAATGGTAATTTTTGGAAA-TTTC
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
* * * *
20343064 AGTGTCAAAAATGGGATTTTTTGGACA-TTTA
1 AGGGTC-AAAATGGTAATTTTTGGAAAGTTTA
*
20343095 GGGGGT-AAAATGGTAATTTTT-GAAAGTTTA
1 -AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
* *
20343125 GGGGT-AAAATGGAAATTTTTGG-AAGTTTTA
1 AGGGTCAAAATGGTAATTTTTGGAAAG-TTTA
20343155 A-GGTCAAAAATGG-AATTTTTGG-AAGTTT-
1 AGGGTC-AAAATGGTAATTTTTGGAAAGTTTA
* * *
20343183 TGAGGT-TAAATGGTAATTTTTGG-AAGTTTT
1 AG-GGTCAAAATGGTAATTTTTGGAAAGTTTA
* * *
20343213 GGGGCCAAAAAT-G-AAGTTTTTTG-AAGTTTA
1 AGGGTC-AAAATGGTAA-TTTTTGGAAAGTTTA
** *
20343243 AGGGT-AAAATGGT-ATTTTTTTAAAG-TTC
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
* *
20343271 GGGGTCAAAAT-GTAATTTTTGGAAAGTTTG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
*
20343301 AGGGTCAAAAT-GTAATTTTTGGAAAGTTCA
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
*
20343331 AGGGTCAAAAT-GTGATTTTTGGACAA-TTTA
1 AGGGTCAAAATGGTAATTTTTGGA-AAGTTTA
20343361 AGG
1 AGG
20343364 ACCTTCAAGG
Statistics
Matches: 246, Mismatches: 32, Indels: 43
0.77 0.10 0.13
Matches are distributed among these distances:
28 25 0.10
29 74 0.30
30 111 0.45
31 33 0.13
32 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (31 bp):
AGGGTCAAAATGGTAATTTTTGGAAAGTTTA
Found at i:20345233 original size:23 final size:22
Alignment explanation
Indices: 20345207--20345249 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20345197 ACTAAATTTA
20345207 AATTTAGAAATAAATTTAAAACC
1 AATTTA-AAATAAATTTAAAACC
* *
20345230 AATTTAAACTTAATTTAAAA
1 AATTTAAAATAAATTTAAAA
20345250 ATCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (22 bp):
AATTTAAAATAAATTTAAAACC
Found at i:20345973 original size:18 final size:18
Alignment explanation
Indices: 20345935--20345979 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
20345925 TGGACTTTTA
**
20345935 TTAAATTT-AAAGTAATT
1 TTAAATTTAAAAGTAAAC
20345952 TTAAATTTAAAAGTAAAC
1 TTAAATTTAAAAGTAAAC
*
20345970 TTAAACTTAA
1 TTAAATTTAA
20345980 TTTAAGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
TTAAATTTAAAAGTAAAC
Found at i:20346013 original size:17 final size:18
Alignment explanation
Indices: 20345991--20346034 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
20345981 TTAAGTGTTT
20345991 TAAATTTAAAT-TTAAAA
1 TAAATTTAAATCTTAAAA
*
20346008 TAAATTT-AATCTTATAA
1 TAAATTTAAATCTTAAAA
20346025 TAAATTTAAA
1 TAAATTTAAA
20346035 AAAGATCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 19 0.79
18 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTTAAATCTTAAAA
Found at i:20346660 original size:209 final size:207
Alignment explanation
Indices: 20346335--20347019 Score: 856
Period size: 209 Copynumber: 3.3 Consensus size: 207
20346325 CTTCAGTGAT
* * *
20346335 TTGGTGTT-ATTGATTTGGCCTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCATTTGTTT
1 TTGGT-TTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC-TCTGTTT
* * * * * *
20346399 TGATCCACTTCTCTGTGTCACATGAGGAAGACGGATCTGGTTCGCTTCTCTGTATCTCATCAAGA
64 TGATCCACTTCTCTATATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGA
**
20346464 AGGTAATCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTA-GAATATGGGGTTCGAAGA
129 AGGTAA-CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC-AGGAAGCTGGGGTTCGAAGA
* *
20346528 TTCGCTCACATCGAGC
192 TTTGCTCACTTCGAGC
*
20346544 TTTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTCTGTTTT
1 -TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTCTGTTTT
*
20346609 GATCCACTTTTCTATATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAA
65 GATCCACTTCTCTATATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAA
* * *
20346674 GGTAACCACTTTATTGCTTCGACTTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
130 GGTAA-CGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
20346739 TGCTCACTTCGAGC
194 TGCTCACTTCGAGC
* * * * * * * *
20346753 TTGGTTTTATTGACTTGGTCTTCTTCTCAGTATCTCATCAGGTAGATGACCACATCACTTGCTTC
1 TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTC-TGTTTT
* * * * * * *
20346818 AATCCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAA
65 GATCCACTTCTCTATATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAA
** * * *
20346883 TCTAACGATTTTATTGGTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATT
130 GGTAACG-CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATT
*
20346948 TGCTCACTTTTGAGC
194 TGCTCAC-TTCGAGC
* * * *
20346963 CTGGTTTC-TTCGATTTGGTCTTCTTCTCAGTATCCCATCTA-GAAGATGATCGCATCT
1 TTGGTTTCATT-GATTTGGTCTACTTCTCAGTATCTCATC-AGGAAGATGACCGCATCT
20347020 ATTTTGGATA
Statistics
Matches: 415, Mismatches: 53, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
208 53 0.13
209 261 0.63
210 100 0.24
211 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (207 bp):
TTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTCTGTTTTG
ATCCACTTCTCTATATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAG
GTAACGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
CTCACTTCGAGC
Found at i:20358244 original size:30 final size:29
Alignment explanation
Indices: 20358208--20358398 Score: 110
Period size: 30 Copynumber: 6.4 Consensus size: 29
20358198 TAAAACGGTA
*
20358208 ATTTTTGGAAAATTCGGAGTCAAAAATGAT
1 ATTTTTGG-AAATTCGGGGTCAAAAATGAT
*
20358238 ATTTTTGGAAGTTCGAGGGT-AAAAA-GAT
1 ATTTTTGGAAATTCG-GGGTCAAAAATGAT
* *
20358266 AATTTTTGGGAAGTTCGGGGACAAAAATTGA-
1 -ATTTTT-GGAAATTCGGGGTCAAAAA-TGAT
* *
20358297 ATTTCTGGAAATTCGAGGGT--AAAATGGT
1 ATTTTTGGAAATTCG-GGGTCAAAAATGAT
* **
20358325 AATTTTTTAGG-AGTTTAGGGTCAAAAATGGA-
1 -A-TTTTT-GGAAATTCGGGGTCAAAAAT-GAT
* * *
20358356 ATTTTTGAGGAGTTCGGTGTCAAAAATGGA-
1 ATTTTTG-GAAATTCGGGGTCAAAAAT-GAT
20358386 ATTTTTGGAAATT
1 ATTTTTGGAAATT
20358399 TAGGAGTAAA
Statistics
Matches: 128, Mismatches: 17, Indels: 33
0.72 0.10 0.19
Matches are distributed among these distances:
27 2 0.02
28 8 0.06
29 43 0.34
30 65 0.51
31 7 0.05
32 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAATTCGGGGTCAAAAATGAT
Found at i:20358258 original size:59 final size:59
Alignment explanation
Indices: 20358195--20358331 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
20358185 TTATGCTTGG
* * * *
20358195 GGGTAAAACGGTAATTTTTGGAAAATTCGGAGTCAAAAA-TGATATTTTTGGAAGTTCGA
1 GGGTAAAAAGGTAATTTTTGGAAAATTCGGAGACAAAAATTGA-ATTTCTGGAAATTCGA
* * * *
20358254 GGGTAAAAAGATAATTTTTGGGAAGTTCGGGGACAAAAATTGAATTTCTGGAAATTCGA
1 GGGTAAAAAGGTAATTTTTGGAAAATTCGGAGACAAAAATTGAATTTCTGGAAATTCGA
*
20358313 GGGTAAAATGGTAATTTTT
1 GGGTAAAAAGGTAATTTTT
20358332 TAGGAGTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 64 0.96
60 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (59 bp):
GGGTAAAAAGGTAATTTTTGGAAAATTCGGAGACAAAAATTGAATTTCTGGAAATTCGA
Found at i:20358350 original size:59 final size:59
Alignment explanation
Indices: 20358195--20358359 Score: 158
Period size: 59 Copynumber: 2.8 Consensus size: 59
20358185 TTATGCTTGG
* * * * *
20358195 GGGTAAAACGGTAATTTTT-GGAAAATTC-GGAGTCAAAAA-TGATATTTTTGGAAGTTCGA
1 GGGTAAAAAGATAATTTTTAGG-AAGTTCAGG-GTCAAAAATTGA-ATTTCTGGAAATTCGA
* * *
20358254 GGGTAAAAAGATAATTTTTGGGAAGTTCGGGGACAAAAATTGAATTTCTGGAAATTCGA
1 GGGTAAAAAGATAATTTTTAGGAAGTTCAGGGTCAAAAATTGAATTTCTGGAAATTCGA
* * * *
20358313 GGGTAAAATGGTAATTTTTTAGG-AGTTTAGGGTCAAAAATGGAATTT
1 GGGTAAAAAGATAA-TTTTTAGGAAGTTCAGGGTCAAAAATTGAATTT
20358360 TTGAGGAGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 75 0.84
60 14 0.16
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
GGGTAAAAAGATAATTTTTAGGAAGTTCAGGGTCAAAAATTGAATTTCTGGAAATTCGA
Found at i:20358419 original size:28 final size:29
Alignment explanation
Indices: 20358378--20358445 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
20358368 TTCGGTGTCA
20358378 AAAATGG-AATTTTTGG-AAATTTAGGAGT
1 AAAATGGTAA-TTTTGGAAAATTTAGGAGT
*
20358406 AAAATGGTAATTTTGGAAAATTTAGGATT
1 AAAATGGTAATTTTGGAAAATTTAGGAGT
*
20358435 AAAATTGTAAT
1 AAAATGGTAAT
20358446 GTTTTGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAATTTAGGAGT
Found at i:20358451 original size:89 final size:89
Alignment explanation
Indices: 20358265--20358463 Score: 215
Period size: 89 Copynumber: 2.2 Consensus size: 89
20358255 GGTAAAAAGA
*
20358265 TAATTTTTGGGAAGTTCGGGGACAAAAATTGAATTTCTGGAAATTCGAGGGTAAAATGGTAATTT
1 TAATTTTTGGGAAGTTCGGGGACAAAAATGGAATTTCTGGAAATTCGAGGGTAAAATGGTAATTT
** * * *
20358330 TTTAGGAGTTTAGGGTCAAAAATG
66 TGGAGAAATTTAGGATCAAAAATG
* * * * *
20358354 GAATTTTTGAGG-AGTTCGGTGTCAAAAATGGAATTTTTGGAAATT-TAGGAGTAAAATGGTAAT
1 TAATTTTTG-GGAAGTTCGGGGACAAAAATGGAATTTCTGGAAATTCGAGG-GTAAAATGGTAAT
* *
20358417 TTTGGA-AAATTTAGGATTAAAATTG
64 TTTGGAGAAATTTAGGATCAAAAATG
* *
20358442 TAATGTTTTGTGAAGTTTGGGG
1 TAAT-TTTTGGGAAGTTCGGGG
20358464 GCCAAATTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
88 21 0.24
89 66 0.74
90 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (89 bp):
TAATTTTTGGGAAGTTCGGGGACAAAAATGGAATTTCTGGAAATTCGAGGGTAAAATGGTAATTT
TGGAGAAATTTAGGATCAAAAATG
Found at i:20358487 original size:30 final size:30
Alignment explanation
Indices: 20358447--20358510 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
20358437 AATTGTAATG
* * *
20358447 TTTTGTGAAGTTTGGGGGCCAAATTAAAAT
1 TTTTGGGAAGTTTGAGGGCCAAAATAAAAT
* *
20358477 TTTTGGGAAGTTTGAGGGTCAAAATATAAT
1 TTTTGGGAAGTTTGAGGGCCAAAATAAAAT
20358507 TTTT
1 TTTT
20358511 AAAAAGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.41
Consensus pattern (30 bp):
TTTTGGGAAGTTTGAGGGCCAAAATAAAAT
Found at i:20359541 original size:3 final size:3
Alignment explanation
Indices: 20359533--20359626 Score: 84
Period size: 3 Copynumber: 30.7 Consensus size: 3
20359523 CATTTCTTTT
* * * *
20359533 TTA TTA TTA ATA GT- TTA TTAA TTAA TTA TTG TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA TTA
* *
20359579 ATA TTA TTA TTA CTA TTA TTAA TGT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA
20359625 TT
1 TT
20359627 CGTTTTAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 63 0.84
4 9 0.12
5 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:20360335 original size:17 final size:17
Alignment explanation
Indices: 20360315--20360355 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20360305 CAACATAATT
20360315 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
20360332 TAAATTTAATTTTAGAA
1 TAAATTTAAATTTAAAA
20360349 TAAATTT
1 TAAATTT
20360356 TAAAAAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20365098 original size:21 final size:20
Alignment explanation
Indices: 20365066--20365104 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20365056 GAGCATGAAA
20365066 ATATAACTGAAATTGTGATTC
1 ATATAACTGAAATT-TGATTC
20365087 ATAT-ACTCGAAATTTGAT
1 ATATAACT-GAAATTTGAT
20365105 ACATGATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
ATATAACTGAAATTTGATTC
Found at i:20365463 original size:15 final size:15
Alignment explanation
Indices: 20365443--20365472 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20365433 GCTAAGTGAT
20365443 AACATGATGATTGAA
1 AACATGATGATTGAA
*
20365458 AACATGGTGATTGAA
1 AACATGATGATTGAA
20365473 GCAAGAAATT
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:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
AACATGATGATTGAA
Found at i:20369501 original size:21 final size:21
Alignment explanation
Indices: 20369468--20369517 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
20369458 GCAGTAGACT
* *
20369468 TCTACCGATACAAGTGATACA
1 TCTACCGAAACAAGTCATACA
* *
20369489 TCTACTGAAACAAGTCATACT
1 TCTACCGAAACAAGTCATACA
20369510 TCTACCGA
1 TCTACCGA
20369518 TACTAAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (21 bp):
TCTACCGAAACAAGTCATACA
Found at i:20370248 original size:18 final size:18
Alignment explanation
Indices: 20370219--20370265 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
20370209 CTTCTGTGAT
**
20370219 CCAGTAATGCTCTTACGAG
1 CCAGT-ATGCTCAAACGAG
*
20370238 CCAGTATGCTCAAACGTG
1 CCAGTATGCTCAAACGAG
20370256 CCAGTATGCT
1 CCAGTATGCT
20370266 ATTCATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:20371723 original size:51 final size:51
Alignment explanation
Indices: 20371646--20371826 Score: 281
Period size: 51 Copynumber: 3.5 Consensus size: 51
20371636 TAAACGAAAG
* *
20371646 GGTCCGATGACTAAGTGTCATCGTGAGAAAATGAATCCTTTATGGAGTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
* *
20371697 GGTCCGATGACTAAGTGTCATTGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
* * *
20371748 GGTCCGATGACTAAGTGTCATCGTGAGTAAATAAATCTTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
* *
20371799 GGTCCAATGACTAAGTGCCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
20371827 TTATGGATTC
Statistics
Matches: 119, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 119 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAT
Found at i:20378517 original size:51 final size:51
Alignment explanation
Indices: 20378441--20378624 Score: 253
Period size: 51 Copynumber: 3.6 Consensus size: 51
20378431 TAAATGAAAG
* *
20378441 GGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
20378492 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
** * * **
20378543 GGTCCGATGACTAAGTGTCATCGTGAGTTTATGGATTCCTATATGGAACAAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAAT-GAATCCTTTATGGATTAA-A
*
20378596 GGTCCGATGACTATA-TATCATCGTGAGTA
1 GGTCCGATGACTA-AGTGTCATCGTGAGTA
20378625 TTAAATGAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
51 79 0.66
52 14 0.12
53 26 0.22
54 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:20379912 original size:117 final size:117
Alignment explanation
Indices: 20379706--20379945 Score: 462
Period size: 117 Copynumber: 2.1 Consensus size: 117
20379696 AGAAATTACC
20379706 AATTTCTTCTTTAAATTTTTACTTATATAACAATAGCAATTTTGTAGATTTTAAGACTTCTATCA
1 AATTTCTTCTTTAAATTTTTACTTATATAACAATAGCAATTTTGTAGATTTTAAGACTTCTATCA
20379771 TTAGCTTTAATGAACCCCTTTTTACCTTAATTAATCTCACCCATAATCACTT
66 TTAGCTTTAATGAACCCCTTTTTACCTTAATTAATCTCACCCATAATCACTT
*
20379823 AATTTCTTCTTTAAATTTTTACTTATATAACAATAGCAATTTTGTATATTTTAAGACTTCTATCA
1 AATTTCTTCTTTAAATTTTTACTTATATAACAATAGCAATTTTGTAGATTTTAAGACTTCTATCA
20379888 TTAGCTTTAATGAACCCCTTTTTACCTTAATTAATCTCACCCATAATCACTT
66 TTAGCTTTAATGAACCCCTTTTTACCTTAATTAATCTCACCCATAATCACTT
*
20379940 TATTTC
1 AATTTC
20379946 ATGACATTGC
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 121 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (117 bp):
AATTTCTTCTTTAAATTTTTACTTATATAACAATAGCAATTTTGTAGATTTTAAGACTTCTATCA
TTAGCTTTAATGAACCCCTTTTTACCTTAATTAATCTCACCCATAATCACTT
Found at i:20381421 original size:9 final size:11
Alignment explanation
Indices: 20381392--20381425 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
20381382 TTGAAAATCC
*
20381392 TTTTTAGAGAA
1 TTTTGAGAGAA
20381403 TTTTGAGAGAA
1 TTTTGAGAGAA
*
20381414 TTTGGAGAGAA
1 TTTTGAGAGAA
20381425 T
1 T
20381426 ATGATATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (11 bp):
TTTTGAGAGAA
Found at i:20383512 original size:24 final size:26
Alignment explanation
Indices: 20383478--20383527 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
20383468 TCCTTAAAAC
*
20383478 GAAAATGAAAA-TACTAAAACCTAAA
1 GAAAATGAAAACAACTAAAACCTAAA
*
20383503 GAAAA-GAAAACAACTAAAACTTAAA
1 GAAAATGAAAACAACTAAAACCTAAA
20383528 TTACAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.66, C:0.12, G:0.08, T:0.14
Consensus pattern (26 bp):
GAAAATGAAAACAACTAAAACCTAAA
Found at i:20385400 original size:13 final size:13
Alignment explanation
Indices: 20385384--20385414 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20385374 ACGAAAAATG
20385384 AAAATAAAAAACA
1 AAAATAAAAAACA
*
20385397 AAAATGAAAAACA
1 AAAATAAAAAACA
20385410 AAAAT
1 AAAAT
20385415 TTCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.10
Consensus pattern (13 bp):
AAAATAAAAAACA
Found at i:20389217 original size:22 final size:23
Alignment explanation
Indices: 20389192--20389239 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
20389182 ACCAATGGCC
*
20389192 TTTACA-TAATTACTCAATTAA-A
1 TTTACATTAATCACT-AATTAATA
*
20389214 TTTATATTAATCACTAATTAATA
1 TTTACATTAATCACTAATTAATA
20389237 TTT
1 TTT
20389240 CAGGCGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTACATTAATCACTAATTAATA
Found at i:20409849 original size:17 final size:17
Alignment explanation
Indices: 20409818--20409859 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20409808 TTATTTATCA
20409818 TTGCATTTGATTTGTTAG
1 TTGCATTTGATTTG-TAG
20409836 -TGCATTTG-TATTGTAG
1 TTGCATTTGAT-TTGTAG
20409852 TTGCATTT
1 TTGCATTT
20409860 CCATTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (17 bp):
TTGCATTTGATTTGTAG
Found at i:20410442 original size:10 final size:11
Alignment explanation
Indices: 20410429--20410474 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
20410419 AAAAATTCAC
20410429 AAAAAG-AAAG
1 AAAAAGAAAAG
20410439 AAAAAG-AAAG
1 AAAAAGAAAAG
*
20410449 AAGAAGAAAAG
1 AAAAAGAAAAG
20410460 AGAAAAGAAAAG
1 A-AAAAGAAAAG
20410472 AAA
1 AAA
20410475 TAGATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:20414600 original size:15 final size:16
Alignment explanation
Indices: 20414572--20414605 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
20414562 AAAAACTTCC
20414572 TCTTTCTCTCCTTCTT
1 TCTTTCTCTCCTTCTT
*
20414588 TCTTT-TCTTCTTCTT
1 TCTTTCTCTCCTTCTT
20414603 TCT
1 TCT
20414606 CCTCTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTCTCTCCTTCTT
Found at i:20419609 original size:30 final size:29
Alignment explanation
Indices: 20419574--20419892 Score: 118
Period size: 29 Copynumber: 10.8 Consensus size: 29
20419564 TCTAGTCCCC
20419574 AAACTTTCCAAAATTCCATTTTTGACC-CAA
1 AAACTTTCCAAAATTCCATTTTT-ACCTC-A
*
20419604 AAAC-TTCCAAAAATTACC-GTTTTACCTCA
1 AAACTTTCC-AAAATT-CCATTTTTACCTCA
* * *
20419633 AAATTTTCCAAAATTCCATTTTTAACAC-
1 AAACTTTCCAAAATTCCATTTTTACCTCA
* *
20419661 GAA-TTTCACCCAAAATTACCA-TTTTATCC-CC
1 AAACTTT---CCAAAATT-CCATTTTTA-CCTCA
20419692 AAACTTTCCAAAATTCCATTTTTAACCTC-
1 AAACTTTCCAAAATTCCATTTTT-ACCTCA
* * * *
20419721 -AA-TTTCACCCAAAAATTACAATTTTACCCCC
1 AAACTTT---CC-AAAATTCCATTTTTACCTCA
*
20419752 AAACTTTCTAAAATTCCATTTTTGACC-C-
1 AAACTTTCCAAAATTCCATTTTT-ACCTCA
**
20419780 CGA-TTTCACCCAAAATTACCA-TTTTATCCTC-
1 AAACTTT---CCAAAATT-CCATTTTTA-CCTCA
20419811 AAACTTTCC-AAATTCCATTTTTAACC-C-
1 AAACTTTCCAAAATTCCATTTTT-ACCTCA
**** * *
20419838 CGGTTTTACCCAAAATTACCA-TTTTACCCCC
1 AAACTTT--CCAAAATT-CCATTTTTACCTCA
20419869 AAACTTTCCAAAATTCCATTTTTA
1 AAACTTTCCAAAATTCCATTTTTA
20419893 ACCTTGATTT
Statistics
Matches: 223, Mismatches: 27, Indels: 79
0.68 0.08 0.24
Matches are distributed among these distances:
27 16 0.07
28 24 0.11
29 73 0.33
30 68 0.30
31 31 0.14
32 8 0.04
33 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTACCTCA
Found at i:20419613 original size:29 final size:29
Alignment explanation
Indices: 20419574--20419656 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
20419564 TCTAGTCCCC
20419574 AAACTTTCCAAAATTCCATTTTTGACC-CAA
1 AAAC-TTCCAAAATTCCATTTTT-ACCTCAA
*
20419604 AAACTTCCAAAAATTACC-GTTTTACCTCAA
1 AAACTTCC-AAAATT-CCATTTTTACCTCAA
**
20419634 AATTTTCCAAAATTCCATTTTTA
1 AAACTTCCAAAATTCCATTTTTA
20419657 ACACGAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.40
30 23 0.51
31 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAATTCCATTTTTACCTCAA
Found at i:20419877 original size:177 final size:173
Alignment explanation
Indices: 20419570--20420038 Score: 568
Period size: 177 Copynumber: 2.6 Consensus size: 173
20419560 GCTATCTAGT
* ** * *
20419570 CCCCAAACTTTCCAAAATTCCATTTTTGACCCAAAAACTT--CCAAAAATTACCGTTTTACCTCA
1 CCCCAAACTTTCTAAAATTCCATTTTTGACCC--CGATTTCACCAAAAATTACCATTTTACCTC-
* *
20419633 AAATTTTCCAAAATTCCATTTTTAACACGAATTTCACCCAAAATTACCATTTTATCCCCAAACTT
63 AAA-TTTCC-AAATTCCATTTTTAACACG-ATTTTACCCAAAATTACCATTTTACCCCCAAACTT
20419698 TCCAAAATTCCATTTTTAACCTCAATTTCACCCAAAAATTACAATTTTAC
125 TCCAAAATTCCATTTTTAACCTCAATTTCACCC-AAAATTACAATTTTAC
*
20419748 CCCCAAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTATCCTCAA
1 CCCCAAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTA-CCTCAA
* *
20419813 ACTTTCCAAATTCCATTTTTAACCCCGGTTTTACCCAAAATTACCATTTTACCCCCAAACTTTCC
65 A-TTTCCAAATTCCATTTTTAA-CACGATTTTACCCAAAATTACCATTTTACCCCCAAACTTTCC
** *
20419878 AAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTAC
128 AAAATTCCATTTTTAACCTCAATTTCACCCAAAATTACAATTTTAC
* * * * * * *
20419924 CCCCGAACCTTCTAAAATTCTATTTTTAACCTCGATTTCACAAAAAATTACCATTTTACCCCCAA
1 CCCCAAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTA-CCTCAA
* * *
20419989 ATCTTCTAAAATCCCATTTTTAA-ACTTGATTTTTCCCAAAATTA-CATTTT
65 AT-TTC-CAAATTCCATTTTTAACAC--GATTTTACCCAAAATTACCATTTT
20420039 TACCACGAGA
Statistics
Matches: 255, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
175 2 0.01
176 84 0.33
177 107 0.42
178 58 0.23
179 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (173 bp):
CCCCAAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCTCAAA
TTTCCAAATTCCATTTTTAACACGATTTTACCCAAAATTACCATTTTACCCCCAAACTTTCCAAA
ATTCCATTTTTAACCTCAATTTCACCCAAAATTACAATTTTAC
Found at i:20420000 original size:118 final size:117
Alignment explanation
Indices: 20419569--20420038 Score: 545
Period size: 118 Copynumber: 4.0 Consensus size: 117
20419559 TGCTATCTAG
* * *** * * * *
20419569 TCCCCAAACTTTCCAAAATTCCATTTTTGACC-CAAAAACTTCCAAAAATTACCGTTTTACCTCA
1 TCCCCAAACTTT-CAAAATTCCATTTTTAACCTCGATTTC-ACCAAAAATTACCATTTTACCCCC
*
20419633 AAATTTTCCAAAATTCCATTTTTAACAC--GAATTTCACCCAAAATTACCATTTTA
64 AAACTTTCCAAAATTCCATTTTTAAC-CTTG-ATTTCACCCAAAATTACCATTTTA
* *
20419687 TCCCCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACCCAAAAATTACAATTTTACCCCC
1 TCCCCAAACTTT-CAAAATTCCATTTTTAACCTCGATTTCA-CCAAAAATTACCATTTTACCCCC
* * **
20419752 AAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTA
64 AAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTA
* * * * * *
20419806 TCCTCAAACTTTCCAAATTCCATTTTTAACCCCGGTTTTACCCAAAATTACCATTTTACCCCCAA
1 TCCCCAAACTTTCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAA
20419871 ACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTA
66 ACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTA
* * * * *
20419923 CCCCCGAACCTTCTAAAATTCTATTTTTAACCTCGATTTCACAAAAAATTACCATTTTACCCCCA
1 TCCCCAAACTTTC-AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCA
* * * **
20419988 AA-TCTTCTAAAATCCCATTTTTAAACTTGATTTTTCCCAAAATTA-CATTTT
65 AACT-TTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTT
20420039 TACCACGAGA
Statistics
Matches: 306, Mismatches: 40, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
117 87 0.28
118 137 0.45
119 81 0.26
120 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (117 bp):
TCCCCAAACTTTCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCAA
ACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTA
Found at i:20420042 original size:59 final size:58
Alignment explanation
Indices: 20419613--20420038 Score: 489
Period size: 59 Copynumber: 7.2 Consensus size: 58
20419603 AAAACTTCCA
* * * * * *
20419613 AAAATTACCGTTTTACCTCAAAATTTTCCAAAATTCCATTTTTAA-CACGAATTTCACCC
1 AAAATTACCATTTTACCCCCAAA-CTTCTAAAATTCCATTTTTAACCTCG-ATTTCACCC
* * *
20419672 AAAATTACCATTTTATCCCCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACCC
1 AAAATTACCATTTTACCCCCAAAC-TTCTAAAATTCCATTTTTAACCTCGATTTCACCC
* * *
20419731 AAAAATTACAATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCC
1 -AAAATTACCATTTTACCCCCAAAC-TTCTAAAATTCCATTTTTAACCTCGATTTCACCC
* * * * * *
20419791 AAAATTACCATTTTATCCTCAAACTT-TCCAAATTCCATTTTTAACCCCGGTTTTACCC
1 AAAATTACCATTTTACCCCCAAACTTCT-AAAATTCCATTTTTAACCTCGATTTCACCC
* *
20419849 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCC
1 AAAATTACCATTTTACCCCCAAAC-TTCTAAAATTCCATTTTTAACCTCGATTTCACCC
* * **
20419908 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCTATTTTTAACCTCGATTTCACAA
1 AAAATTACCATTTTACCCCC-AAACTTCTAAAATTCCATTTTTAACCTCGATTTCACCC
* * * **
20419967 AAAATTACCATTTTACCCCCAAATCTTCTAAAATCCCATTTTTAAACTTGATTTTTCCC
1 AAAATTACCATTTTACCCCCAAA-CTTCTAAAATTCCATTTTTAACCTCGATTTCACCC
20420026 AAAATTA-CATTTT
1 AAAATTACCATTTT
20420039 TACCACGAGA
Statistics
Matches: 316, Mismatches: 43, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.00
58 58 0.18
59 199 0.63
60 58 0.18
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTCTAAAATTCCATTTTTAACCTCGATTTCACCC
Done.