Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008812.1 Hibiscus syriacus cultivar Beakdansim tig00111973_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 944649
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:296823 original size:23 final size:23
Alignment explanation
Indices: 296782--296839 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
296772 TAAAAAACGG
296782 TTTTTGAAAATATATATAATATATA
1 TTTTT-AAAA-ATATATAATATATA
296807 TTTTTAAAAATATATAATATATA
1 TTTTTAAAAATATATAATATATA
* *
296830 GTTTTGAAAA
1 TTTTTAAAAA
296840 CATCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 22 0.71
24 4 0.13
25 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TTTTTAAAAATATATAATATATA
Found at i:296848 original size:60 final size:61
Alignment explanation
Indices: 296784--297067 Score: 190
Period size: 60 Copynumber: 4.5 Consensus size: 61
296774 AAAAACGGTT
296784 TTTGAAAATATATATAATATATAT-TTTT-AAAA-ATATATAATATATAG-TTTTGAAAACATC
1 TTTG-AAA-ATATATAATATAT-TGTTTTGAAAATATATATAATATATAGTTTTTGAAAACATC
*
296844 TTTGAAAATATATAATATATTGTTTTGAAAATATATATAATATATAGTTTTTGAAAACATA
1 TTTGAAAATATATAATATATTGTTTTGAAAATATATATAATATATAGTTTTTGAAAACATC
* * * * *
296905 TAT-ATAATATAAAAT-TTTTGAAAACATTTTGAAAACATATATATATAATATAG-TTTTGAAAA
1 TTTGAAAATATATAATATATTG------TTTTGAAAATATATATA-AT-ATATAGTTTTTGAAAA
*
296967 CATA
58 CATC
* * * ** * *** *
296971 TAT-ATATTATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAATAT-
1 TTTGAAAATATA--TAAT-ATATTGTTTTGAAAATATATATAATATATAGTTTTTGAAAACATC
* *
297033 TTCGAAAATATATATATTATATAGTTTTGAAAATA
1 TTTGAAAATATATA-A-TATATTGTTTTGAAAATA
297068 ATTTTTGAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
57 1 0.01
58 17 0.10
59 11 0.06
60 29 0.16
61 15 0.08
62 20 0.11
63 20 0.11
64 16 0.09
65 16 0.09
66 25 0.14
67 6 0.03
68 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (61 bp):
TTTGAAAATATATAATATATTGTTTTGAAAATATATATAATATATAGTTTTTGAAAACATC
Found at i:296871 original size:23 final size:24
Alignment explanation
Indices: 296844--296910 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
296834 TGAAAACATC
*
296844 TTTGAAAATATATAATATATTG-T
1 TTTGAAAATATATAATATATAGTT
296867 TTTGAAAATATATATAATATATAGTT
1 TTTG-AAA-ATATATAATATATAGTT
*
296893 TTTGAAAACATAT-ATATA
1 TTTGAAAATATATAATATA
296911 ATATAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.23
24 8 0.21
25 17 0.44
26 5 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (24 bp):
TTTGAAAATATATAATATATAGTT
Found at i:296914 original size:28 final size:28
Alignment explanation
Indices: 296851--296931 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
296841 ATCTTTGAAA
*
296851 ATATATAATATATTG-TTTTG-AAA-AT
1 ATATATAATATATAGTTTTTGAAAACAT
296876 ATATATAATATATAGTTTTTGAAAACAT
1 ATATATAATATATAGTTTTTGAAAACAT
* *
296904 ATATATAATATAAAATTTTTGAAAACAT
1 ATATATAATATATAGTTTTTGAAAACAT
296932 TTTGAAAACA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
25 14 0.28
26 5 0.10
27 3 0.06
28 28 0.56
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (28 bp):
ATATATAATATATAGTTTTTGAAAACAT
Found at i:296945 original size:37 final size:37
Alignment explanation
Indices: 296892--297090 Score: 125
Period size: 37 Copynumber: 5.6 Consensus size: 37
296882 AATATATAGT
296892 TTTTGAAAACATATATATAATATAAAATTTTTGAAAACA
1 TTTTGAAAAC--ATATATAATATAAAATTTTTGAAAACA
* *
296931 TTTTGAAAACATATAT-ATAT--AA----T--ATA-G
1 TTTTGAAAACATATATAATATAAAATTTTTGAAAACA
* *
296958 TTTTGAAAACATATAT-ATATTATAGTTTTTGAAAACA
1 TTTTGAAAACATATATAATA-TAAAATTTTTGAAAACA
* * * *
296995 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAACATATATAATATAAAATTTTTGAAAACA
* * * * * *
297032 TTTCGAAAATATATATATTAT-ATAGTTTTGAAAATAA
1 TTTTGAAAACATATATAATATAAAATTTTTGAAAA-CA
* *
297069 TTTTTGAAAGCATATATCATAT
1 -TTTTGAAAACATATATAATAT
297091 GTAATTTTAA
Statistics
Matches: 128, Mismatches: 19, Indels: 27
0.74 0.11 0.16
Matches are distributed among these distances:
27 19 0.15
28 3 0.02
30 2 0.02
34 3 0.02
36 15 0.12
37 57 0.45
38 19 0.15
39 10 0.08
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATAAAATTTTTGAAAACA
Found at i:296981 original size:25 final size:27
Alignment explanation
Indices: 296931--296995 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
296921 TTTGAAAACA
296931 TTTTGAAAACATATATATATAATATAG-
1 TTTTGAAAACATATATATAT-ATATAGT
296958 TTTTGAAAACATATATATAT-TATAGT
1 TTTTGAAAACATATATATATATATAGT
296984 TTTTGAAAACAT
1 TTTTGAAAACAT
296996 TTTGAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
25 5 0.14
26 12 0.32
27 20 0.54
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTTGAAAACATATATATATATATAGT
Found at i:296989 original size:64 final size:65
Alignment explanation
Indices: 296866--297029 Score: 262
Period size: 64 Copynumber: 2.5 Consensus size: 65
296856 TAATATATTG
296866 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATATATATAATATAAAATTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATATATATAATATAAAATTTTTGAAAACA
* * *
296931 TTTTGAAAACATATATATATAATATAG-TTTTGAAAACATATATAT-AT-TATAGTTTTTGAAAA
1 TTTTGAAAATATATATA-AT-ATATAGTTTTTGAAAACATATATATAATATAAAATTTTTGAAAA
296993 CA
64 CA
296995 TTTTGAAAATATATATAATATATAGTTTTTGAAAA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAA
297030 TATTTCGAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
62 6 0.07
63 11 0.12
64 31 0.34
65 18 0.20
66 20 0.22
67 6 0.07
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (65 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATATATATAATATAAAATTTTTGAAAACA
Found at i:297043 original size:26 final size:26
Alignment explanation
Indices: 296995--297044 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
296985 TTTGAAAACA
* *
296995 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATAGAAAATATAGT
* *
297021 TTTTGAAAATATTTCGAAAATATA
1 TTTTGAAAATATATAGAAAATATA
297045 TATATTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTGAAAATATATAGAAAATATAGT
Found at i:297084 original size:36 final size:36
Alignment explanation
Indices: 296958--297090 Score: 160
Period size: 37 Copynumber: 3.6 Consensus size: 36
296948 TATAATATAG
*
296958 TTTTGAAAACATATATATATTATAGTTTTTGAAAACA
1 TTTTGAAAACATATATATA-TATAGTTTTTGAAAATA
*
296995 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTGAAAACATATAT-ATATATAGTTTTTGAAAATA
* *
297032 TTTCGAAAATATATATATTATATAG-TTTTGAAAATAA
1 TTTTGAAAACATATATA-TATATAGTTTTTGAAAAT-A
*
297069 TTTTTGAAAGCATATATCATAT
1 -TTTTGAAAACATATAT-ATAT
297091 GTAATTTTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
36 11 0.13
37 54 0.64
38 19 0.22
39 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACATATATATATATAGTTTTTGAAAATA
Found at i:297104 original size:74 final size:74
Alignment explanation
Indices: 296962--297105 Score: 168
Period size: 74 Copynumber: 1.9 Consensus size: 74
296952 ATATAGTTTT
* * * *
296962 GAAAACATATATATATTATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGA
1 GAAAACATATATATATTATAGTTTTTGAAAAAATTTTGAAAACATATATAATATATAGATTTTAA
297027 AAATATTTC
66 AAATATTTC
* * * *
297036 GAAAATATATATAT-TATATAG-TTTTGAAAATAATTTTTGAAAGCATATATCATATGTA-ATTT
1 GAAAACATATATATAT-TATAGTTTTTGAAAA-AA-TTTTGAAAACATATATAATATATAGATTT
297098 TAAAAATA
63 TAAAAATA
297106 GTATTTTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
73 10 0.17
74 29 0.49
75 20 0.34
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (74 bp):
GAAAACATATATATATTATAGTTTTTGAAAAAATTTTGAAAACATATATAATATATAGATTTTAA
AAATATTTC
Found at i:298324 original size:15 final size:15
Alignment explanation
Indices: 298304--298338 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
298294 ATCCTTAACT
*
298304 TTTAATTCTTTCTAA
1 TTTAATCCTTTCTAA
*
298319 TTTAATCCTTTTTAA
1 TTTAATCCTTTCTAA
298334 TTTAA
1 TTTAA
298339 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATCCTTTCTAA
Found at i:298371 original size:14 final size:14
Alignment explanation
Indices: 298354--298380 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
298344 CTTTTATTCC
298354 TTTTATTTACTTTT
1 TTTTATTTACTTTT
298368 TTTTATTTACTTT
1 TTTTATTTACTTT
298381 ATTTCGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTACTTTT
Found at i:302590 original size:99 final size:99
Alignment explanation
Indices: 302414--302691 Score: 448
Period size: 99 Copynumber: 2.8 Consensus size: 99
302404 TTATAGTATT
* * * * * *
302414 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTTGTTAAACACCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
302479 ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
*
302513 ATATATATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
* * *
302578 ATAAAATTCAGCTAGCCTGATAAAGGTGATTGTA
66 ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
* *
302612 ATATATATACAATAAAGCTTAAGTTGTTCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATTG
1 ATATATATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
302677 ATAAGATTCAGCTAG
66 ATAAGATTCAGCTAG
302692 ACAGACAATG
Statistics
Matches: 165, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 165 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTGTTCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
Found at i:305103 original size:37 final size:37
Alignment explanation
Indices: 305051--305384 Score: 392
Period size: 37 Copynumber: 8.9 Consensus size: 37
305041 AAAAAAACGG
305051 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
305088 TTTTTAAAAACATATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
305125 TTTTTG-AAA-ATATATAATTTATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
305160 TTTTTTAAAATATATATACTATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAG-TTTTGAAAACA
* ** *
305198 TTCTAAAAACATATATATAATATATAGTTTTCTAAAACA
1 TTTTTGAAA-ATATATATAATATATAGTTTT-GAAAACA
*
305237 -ATTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTTG-AAA-ATATATATAATATATAG-TTTTGAAAACA
305276 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAG-TTTTGAAAACA
* *
305313 -TTTTGAAAATATATAT-ATCATATAGTTTTCAAAATAA
1 TTTTTGAAAATATATATAAT-ATATAGTTTTGAAAA-CA
** ** *
305350 TTTTTGAAAGCATATATCGTATATAGTTTTTAAAA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAA
305385 TGATTTTTTT
Statistics
Matches: 262, Mismatches: 24, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
35 30 0.11
36 16 0.06
37 105 0.40
38 53 0.20
39 54 0.21
40 4 0.02
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:305396 original size:15 final size:16
Alignment explanation
Indices: 305376--305412 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
305366 TCGTATATAG
305376 TTTTTAAA-ATGATT-T
1 TTTTTAAACAT-ATTAT
305391 TTTTTAAACATATTAT
1 TTTTTAAACATATTAT
305407 TTTTTA
1 TTTTTA
305413 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTTAAACATATTAT
Found at i:305541 original size:31 final size:30
Alignment explanation
Indices: 305498--305560 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
305488 GGCCATACTA
305498 GCCTAACCTAGCACAGTAGACCCAGTAAGGG
1 GCCTAACCTAGCACAGTAGACCCAGT-AGGG
* * *
305529 GCCTGACCTAGCACAGTAGGCCCGGTAGGG
1 GCCTAACCTAGCACAGTAGACCCAGTAGGG
305559 GC
1 GC
305561 ATGATCCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.13
Consensus pattern (30 bp):
GCCTAACCTAGCACAGTAGACCCAGTAGGG
Found at i:306706 original size:16 final size:17
Alignment explanation
Indices: 306685--306717 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
306675 CTTTTATTCC
306685 TTTTATTTAC-TTATTT
1 TTTTATTTACTTTATTT
306701 TTTTATTTACTTTATTT
1 TTTTATTTACTTTATTT
306718 CGATCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTACTTTATTT
Found at i:307207 original size:24 final size:21
Alignment explanation
Indices: 307169--307232 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
307159 TTTAAAGGTA
*
307169 AATTATTTAAAATAATTTTAATT
1 AATTATTT-TAATAATTTTAA-T
307192 ACATTATTTTACATAATTTTTAAT
1 A-ATTATTTTA-ATAA-TTTTAAT
307216 AATT-TTTTAATAATTTT
1 AATTATTTTAATAATTTT
307233 TTTAATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 5 0.14
23 5 0.14
24 13 0.35
25 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTATTTTAATAATTTTAAT
Found at i:307233 original size:12 final size:12
Alignment explanation
Indices: 307208--307245 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
307198 TTTTACATAA
307208 TTTTTAATAA-T
1 TTTTTAATAATT
307219 TTTTTAATAATT
1 TTTTTAATAATT
307231 TTTTTAATAATT
1 TTTTTAATAATT
307243 TTT
1 TTT
307246 AAAGGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATAATT
Found at i:307247 original size:10 final size:11
Alignment explanation
Indices: 307184--307245 Score: 72
Period size: 11 Copynumber: 5.3 Consensus size: 11
307174 TTTAAAATAA
307184 TTTTAATTACATT
1 TTTTAA-TA-ATT
307197 ATTTTACATAA-T
1 -TTTTA-ATAATT
307209 TTTTAATAATT
1 TTTTAATAATT
307220 TTTTAATAATTT
1 TTTTAATAA-TT
307232 TTTTAATAATT
1 TTTTAATAATT
307243 TTT
1 TTT
307246 AAAGGTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.09
11 20 0.44
12 12 0.27
13 1 0.02
14 7 0.16
15 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:307833 original size:85 final size:82
Alignment explanation
Indices: 307730--307900 Score: 252
Period size: 85 Copynumber: 2.0 Consensus size: 82
307720 TATAGTAGCT
*
307730 ATTTGAATTATGAATTTATGTCTAAAAACAATAAAAGAGATAATATTAGTGTTACATATTGAAAA
1 ATTTGAATTATAAATTTATGTCTAAAAACAATAAAAGAGATAATATTAGTGTTACATATT-AAAA
307795 ATATTAAATAAATAAAAAGG
65 ATA-TAAATAAATAAAAA-G
* * * * *
307815 ATTTGAATTCTAAATTTATGTCTAAAAATATTAAAAGAGATAATATTAGTTTTATATATTAAAAA
1 ATTTGAATTATAAATTTATGTCTAAAAACAATAAAAGAGATAATATTAGTGTTACATATTAAAAA
*
307880 TATAAATAAATGAAAAG
66 TATAAATAAATAAAAAG
307897 ATTT
1 ATTT
307901 TTATTTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
82 5 0.06
83 13 0.16
84 7 0.09
85 54 0.68
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (82 bp):
ATTTGAATTATAAATTTATGTCTAAAAACAATAAAAGAGATAATATTAGTGTTACATATTAAAAA
TATAAATAAATAAAAAG
Found at i:310900 original size:21 final size:21
Alignment explanation
Indices: 310875--310914 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
310865 AAGACTTTAT
310875 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
310896 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
310915 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:312290 original size:16 final size:16
Alignment explanation
Indices: 312271--312307 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
312261 AATCCTTAGT
*
312271 GTGGATAGTTAAGGTA
1 GTGGATAGTTAAGATA
312287 GTGGATAGTTAAGATA
1 GTGGATAGTTAAGATA
312303 GTGGA
1 GTGGA
312308 CGTGGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (16 bp):
GTGGATAGTTAAGATA
Found at i:320989 original size:31 final size:31
Alignment explanation
Indices: 320954--321026 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
320944 CTCAGGCCTC
*
320954 AGTGACCACATCATT-ATTAAATAAAAACGAA
1 AGTGACCAAATC-TTAATTAAATAAAAACGAA
* *
320985 AGTGATCAAATCTTAATTAAATAAAAATGAA
1 AGTGACCAAATCTTAATTAAATAAAAACGAA
*
321016 AGTGATCAAAT
1 AGTGACCAAAT
321027 ATTATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAATAAAAACGAA
Found at i:321731 original size:22 final size:24
Alignment explanation
Indices: 321697--321773 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 24
321687 AAGTATATTA
** *
321697 ATATTATGAAATTATTTTACAAT-
1 ATATTATTTAATTATTTTAAAATC
321720 AT-TTATTTAA-T-TTTTAAAATC
1 ATATTATTTAATTATTTTAAAATC
* * *
321741 ATATTATTTATTTA-TTTGAAATA
1 ATATTATTTAATTATTTTAAAATC
321764 ATATTATTTA
1 ATATTATTTA
321774 TTTGAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.18
21 3 0.07
22 13 0.30
23 20 0.45
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (24 bp):
ATATTATTTAATTATTTTAAAATC
Found at i:321749 original size:26 final size:23
Alignment explanation
Indices: 321717--321776 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
321707 ATTATTTTAC
*
321717 AATATTTATTTAATT-TTTAAAAT
1 AATA-TTATTTATTTATTTAAAAT
* *
321740 CATATTATTTATTTATTTGAAAT
1 AATATTATTTATTTATTTAAAAT
321763 AATATTATTTATTT
1 AATATTATTTATTT
321777 GAAATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
AATATTATTTATTTATTTAAAAT
Found at i:321762 original size:23 final size:22
Alignment explanation
Indices: 321708--321791 Score: 79
Period size: 19 Copynumber: 3.9 Consensus size: 22
321698 TATTATGAAA
* *
321708 TTATTTTACAATAT-TTATTTAA
1 TTATTTGA-AATATATTATTTAT
*
321730 TT-TTTAAAATCATATTATTTAT
1 TTATTTGAAAT-ATATTATTTAT
321752 TTATTTGAAATA-A-TA-TTAT
1 TTATTTGAAATATATTATTTAT
321771 TTATTTGAAATAATATTATTT
1 TTATTTGAAAT-ATATTATTT
321792 TTAAATTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
19 15 0.29
20 6 0.12
21 8 0.15
22 14 0.27
23 9 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTGAAATATATTATTTAT
Found at i:321772 original size:15 final size:19
Alignment explanation
Indices: 321748--321791 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
321738 ATCATATTAT
321748 TTATTTATTTGAAATAATA
1 TTATTTATTTGAAATAATA
321767 TTATTTATTTGAAATAATA
1 TTATTTATTTGAAATAATA
321786 TTATTT
1 TTATTT
321792 TTAAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTATTTATTTGAAATAATA
Found at i:321797 original size:16 final size:16
Alignment explanation
Indices: 321759--321819 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 16
321749 TATTTATTTG
321759 AAATAATATTATTTATTT
1 AAATAATATTA-TT-TTT
321777 GAAATAATATTATTTTT
1 -AAATAATATTATTTTT
*
321794 AAATTATATATTCAATTTT
1 AAA-TA-ATATT-ATTTTT
321813 AAATAAT
1 AAATAAT
321820 GTTGTGTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 9 0.24
19 19 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATAATATTATTTTT
Found at i:321890 original size:18 final size:20
Alignment explanation
Indices: 321869--321909 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
321859 AACTTACACT
*
321869 AAATTTAAA-A-ATTATTTA
1 AAATTTAAATAGATAATTTA
321887 AAA-TTAAATAGATAATTTA
1 AAATTTAAATAGATAATTTA
321906 AAAT
1 AAAT
321910 AATATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATTTAAATAGATAATTTA
Found at i:324913 original size:29 final size:29
Alignment explanation
Indices: 324825--324913 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
324815 TAAATTTTGG
*
324825 TTAGTGACTAAAATGT-ATGTTTTGAAAGT
1 TTAGTGACTAAAATATAAT-TTTTGAAAGT
* * *
324854 TTAGTGGCTAAAGTATAA-ATTTGAAAAAGT
1 TTAGTGACTAAAATATAATTTTTG--AAAGT
* *
324884 TTAGTGACCAAAATCTAATTTTTGAAAGT
1 TTAGTGACTAAAATATAATTTTTGAAAGT
324913 T
1 T
324914 ATATTTTTGG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
28 4 0.09
29 19 0.40
30 20 0.43
31 4 0.09
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (29 bp):
TTAGTGACTAAAATATAATTTTTGAAAGT
Found at i:334266 original size:34 final size:34
Alignment explanation
Indices: 334214--334343 Score: 140
Period size: 34 Copynumber: 3.6 Consensus size: 34
334204 AAAAATCGGT
* *
334214 TTTTGAAAATATAT--TATATAGTTTACGAAAACA
1 TTTTAAAAATATATAATATATAGTTT-TGAAAACA
334247 TTTT-AAAATATATAATATATAGTTTTTGAAAACA
1 TTTTAAAAATATATAATATATAG-TTTTGAAAACA
334281 TTTTAAAAACATATATATAATATATAGTTTTGAAAACA
1 TTTT--AAA-A-ATATATAATATATAGTTTTGAAAACA
334319 TTTTGAAAACATATATATATATATA
1 TTTT-AAAA-ATATATA-ATATATA
334344 TATATATATA
Statistics
Matches: 85, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
32 9 0.11
33 4 0.05
34 18 0.21
35 3 0.04
36 8 0.09
37 12 0.14
38 16 0.19
39 15 0.18
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (34 bp):
TTTTAAAAATATATAATATATAGTTTTGAAAACA
Found at i:334297 original size:39 final size:39
Alignment explanation
Indices: 334222--334555 Score: 336
Period size: 38 Copynumber: 8.6 Consensus size: 39
334212 GTTTTTGAAA
* **
334222 ATATATTATATAGTTTACGAAAACATTTT---AA-A-AT
1 ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
334256 ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
1 ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
*
334295 ATATAATATATAG-TTTTGAAAACATTTTGAAAACATATATATATATAT
1 ATATAATATATAGTTTTTGAAAACATTTT------A-A-A-A-ACATAT
*
334343 ATATATATATATAATTTTTGAAAACATTTTAAAAACATAT
1 ATATA-ATATATAGTTTTTGAAAACATTTTAAAAACATAT
334383 ATATAATATATAG-TTTTGAAAACATTTTAAAAACATAT
1 ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
*
334421 ATATAATATATAG-TTTTGAAAACATTTTGAAAACATAT
1 ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
* * * *
334459 ATATATTATATAGTTTTTGAAAACA-TTTAGGATATATAT
1 ATATAATATATAGTTTTTGAAAACATTTTA-AAAACATAT
* **
334498 ATATATATATATATTTTTTGAAAACATTTT--TTA-A-AT
1 ATATA-ATATATAGTTTTTGAAAACATTTTAAAAACATAT
334534 ATATAATATATAG-TTTTGAAAA
1 ATATAATATATAGTTTTTGAAAA
334556 TGATTTTTAA
Statistics
Matches: 262, Mismatches: 17, Indels: 42
0.82 0.05 0.13
Matches are distributed among these distances:
34 35 0.13
35 7 0.03
36 7 0.03
37 3 0.01
38 95 0.36
39 44 0.17
40 28 0.11
41 4 0.02
42 1 0.00
43 1 0.00
44 2 0.01
45 1 0.00
46 1 0.00
47 1 0.00
48 10 0.04
49 7 0.03
50 15 0.06
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (39 bp):
ATATAATATATAGTTTTTGAAAACATTTTAAAAACATAT
Found at i:334336 original size:2 final size:2
Alignment explanation
Indices: 334329--334355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
334319 TTTTGAAAAC
334329 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
334356 ATTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:334372 original size:88 final size:84
Alignment explanation
Indices: 334254--334555 Score: 352
Period size: 88 Copynumber: 3.8 Consensus size: 84
334244 ACATTTTAAA
*
334254 ATATATAATATATAGTTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAACA
1 ATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAACA
334319 TTTTGAAAACATATATATATAT
66 TTTTG--AA-ATATATATATAT
334341 ATATATATATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAAC
1 ATATATA-ATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAAC
*
334406 ATTTT---A-A-A-A-ACAT
65 ATTTTGAAATATATATATAT
* * *
334419 ATATATAATATAT-AGTTTTGAAAACATTTTGAAAACATATATATATTATATAGTTTTTGAAAAC
1 ATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAG-TTTTGAAAAC
**
334483 A-TTT--AGGATATATATAT
65 ATTTTGAAATATATATATAT
**
334500 ATATAT-ATATAT--TTTTTGAAAACATTTT--TTA-A-ATATATAATATATAGTTTTGAAAA
1 ATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAA
334556 TGATTTTTAA
Statistics
Matches: 197, Mismatches: 11, Indels: 27
0.84 0.05 0.11
Matches are distributed among these distances:
74 9 0.05
75 14 0.07
76 41 0.21
77 18 0.09
78 11 0.06
79 17 0.09
80 8 0.04
81 10 0.05
82 1 0.01
87 7 0.04
88 61 0.31
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (84 bp):
ATATATAATATATAATTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGAAAACA
TTTTGAAATATATATATAT
Found at i:334496 original size:28 final size:28
Alignment explanation
Indices: 334445--334500 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
334435 TTTGAAAACA
*
334445 TTTTGAAAACATATATATATTATATAGT
1 TTTTGAAAACATATAGATATTATATAGT
*
334473 TTTTGAAAACATTTAGGATATATATATA
1 TTTTGAAAACATATA-GATAT-TATATA
334501 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 4 0.17
30 6 0.25
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (28 bp):
TTTTGAAAACATATAGATATTATATAGT
Found at i:334675 original size:21 final size:20
Alignment explanation
Indices: 334638--334680 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
334628 TTATTTATCA
*
334638 TTTATTTTTTCATTTTTATT
1 TTTATTTTTTCAGTTTTATT
*
334658 TTTATTTTTTTAGGTTTTATT
1 TTTATTTTTTCA-GTTTTATT
334679 TT
1 TT
334681 CAGGTCCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTATTTTTTCAGTTTTATT
Found at i:335439 original size:30 final size:30
Alignment explanation
Indices: 335395--335490 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
335385 GCGGTGACCA
* *
335395 GAGCGTCGATAGGAGACGGATTAGCAACCG
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
* *
335425 GAGCGGCGACAGGAGACGGATTGGCAACCA
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
* * * *
335455 GAGGGGTGATAGGCGACGAATTGGCAACCG
1 GAGCGGCGATAGGAGACGGATTGGCAACCG
*
335485 TAGCGG
1 GAGCGG
335491 TGGCCGACCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.41, T:0.11
Consensus pattern (30 bp):
GAGCGGCGATAGGAGACGGATTGGCAACCG
Found at i:335854 original size:15 final size:15
Alignment explanation
Indices: 335834--335871 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
335824 ATCCCTAACT
335834 TTTAATTCTTTCTAA
1 TTTAATTCTTTCTAA
*
335849 TTTAATCCTTTCTAA
1 TTTAATTCTTTCTAA
335864 TTTGAATT
1 TTT-AATT
335872 TTCTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAATTCTTTCTAA
Found at i:338949 original size:65 final size:65
Alignment explanation
Indices: 338878--339014 Score: 197
Period size: 65 Copynumber: 2.1 Consensus size: 65
338868 CACACCCATT
* *
338878 TCGAATGCATTTTGTGTATC-GAAGCACA-ATCCATGCATCGATGCACTCTTGAATATTTTGAAA
1 TCGAATGCATTTTGTGTA-CAGAAGCACAGA-CCATGCATCAATGCACTCCTGAATATTTTGAAA
338941 CA
64 CA
* * *
338943 TCGAATGCATTTTGTGTACAGATGCACAGACCATGCATCAATGCACTCCTGACTTTTTTGAAACA
1 TCGAATGCATTTTGTGTACAGAAGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
339008 TCGAATG
1 TCGAATG
339015 TAATTAGTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 63 0.97
66 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACAGAAGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
Found at i:339025 original size:65 final size:64
Alignment explanation
Indices: 338878--339033 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
338868 CACACCCATT
* * * * *
338878 TCGAATGCATTTTGTGTATCGAAGCACA-ATCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCAATTAGTGTA-CGATGCACAGA-CCATGCATCAATGCACTCCTGAATATTTTGAAAC
338942 A
64 A
* * * *
338943 TCGAATGCATTTTGTGTACAGATGCACAGACCATGCATCAATGCACTCCTGACTTTTTTGAAACA
1 TCGAATGCAATTAGTGTAC-GATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
*
339008 TCGAATGTAATTAGTGTACGATGCAC
1 TCGAATGCAATTAGTGTACGATGCAC
339034 CCCTAGTGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 8 0.10
65 72 0.89
66 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGCAATTAGTGTACGATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
Found at i:343516 original size:44 final size:43
Alignment explanation
Indices: 343434--343529 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 43
343424 TTATGCACTA
* * *
343434 TGCATCGATACACTAGACAGTGTATCGATGCATCCCTTGAATG
1 TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAATG
*
343477 TGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCA-GACA-GTGCACCGATGCATCCCTTGAATG
343521 TGCATCGAT
1 TGCATCGAT
343530 GCACTCTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 15 0.32
44 32 0.68
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAATG
Found at i:343523 original size:23 final size:22
Alignment explanation
Indices: 343457--343532 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
343447 TAGACAGTGT
343457 ATCGATGCATCCCTTGAATGTGC
1 ATCGATGCAT-CCTTGAATGTGC
* * *
343480 ATCGATACA-CCATGAAGGTGC
1 ATCGATGCATCCTTGAATGTGC
*
343501 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCA-TCCTTGAATGTGC
343524 ATCGATGCA
1 ATCGATGCA
343533 CTCTGTTGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
23 26 0.60
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (22 bp):
ATCGATGCATCCTTGAATGTGC
Found at i:346124 original size:65 final size:65
Alignment explanation
Indices: 346050--346186 Score: 222
Period size: 65 Copynumber: 2.1 Consensus size: 65
346040 CACACCCATT
*
346050 TCGAATGCATTTTGTGTACCGATGCACA-ATCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACATA-CCATGCATCGATGCACTCCTGAATATTTTGAAAC
346114 A
65 A
** *
346115 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTTTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATATTTTGAAACA
346180 TCGAATG
1 TCGAATG
346187 TAATTAGTAG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 66 0.99
66 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:346367 original size:16 final size:16
Alignment explanation
Indices: 346346--346376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
346336 TCTAGTTTTT
*
346346 CCGAGTACCTGGTTAC
1 CCGAGTACCCGGTTAC
346362 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
346377 GTCTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:346598 original size:15 final size:15
Alignment explanation
Indices: 346578--346634 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
346568 AAACGGGTAT
346578 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
346593 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
346610 TGGGTACCCGATTAC
1 CGGGTACCCGATTAC
346625 CGGGTACCCG
1 CGGGTACCCG
346635 TAACATCCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:349078 original size:85 final size:85
Alignment explanation
Indices: 348913--349407 Score: 598
Period size: 85 Copynumber: 5.8 Consensus size: 85
348903 TATAAGAATT
* * * ** * *
348913 ATTTGCAACATAGCTCAAGGCGAGAAGAGCTATTTGCCAACAAAAAACCTTCGAGTTCAATTCCA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAAC-AAAAACCTTCGAGTTCGATTACA
*
348978 TTAAGCTCAAGGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * * *
348999 ATTTACAACATAGCTCAAGGCGAGAAGTGTTATCTTTCAACCAAAACCTTTGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
*
349064 TCAGCTTAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
** * *
349084 ATTTACAACATAGCTCAATACGAAAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
*
349149 TTAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * * *
349169 ATTTACAGCATAGCTCAAGACGAGAAGGTCTATCCGAT-AACAAAAACCTTTGAGTTTGATTACA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTAT-CTATCAACAAAAACCTTCGAGTTCGATTACA
* **
349233 TTCAGCTGAAAAGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* ** *
349254 ATTTACAGA-ATAGCTTAAGGCGAGAAGGGCTATCCGTCAACAAAAAACTTCGAGTTCGATTACA
1 ATTTACA-ACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACA
349318 TTCAGCTCAAGGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * * * * *
349339 ATTTATAGCATAGCTCAAGGCGAGTAGGGTTATCTATCACCAAAAACCTTTGAGTTCGATTCCAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
349404 TCAG
66 TCAG
349408 TTCGATGACA
Statistics
Matches: 348, Mismatches: 57, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.01
85 309 0.89
86 37 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGGCATATCAA
Found at i:349217 original size:170 final size:169
Alignment explanation
Indices: 348913--349407 Score: 679
Period size: 170 Copynumber: 2.9 Consensus size: 169
348903 TATAAGAATT
* * * * * *
348913 ATTTGCAACATAGCTCAAGGCGAGAAGAGCTATTTGCCAACAAAAAACCTTCGAGTTCAATTCCA
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACA
* * *
348978 TTAAGCTCAAGGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGTGTTATCTTTCAACCAA
65 TTAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAG-GTTATCTATCAACAAA
* **
349043 AACCTTTGAGTTCGATTACATTCAGCTTAAGGGCATATCAA
129 AACCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
** *
349084 ATTTACAACATAGCTCAATACGAAAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
349149 TTAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGACGAGAAGGTCTATCCGAT-AACAAA
66 TAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGT-TAT-CTATCAACAAA
*
349213 AACCTTTGAGTTTGATTACATTCAGCTGAAAAGCATATCAA
129 AACCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
* * *
349254 ATTTACAGA-ATAGCTTAAGGCGAGAAGGGCTATCCGTCAACAAAAAACTTCGAGTTCGATTACA
1 ATTTACA-ACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACA
* * * *
349318 TTCAGCTCAAGGGCATATCAAATTTATAGCATAGCTCAAGGCGAGTAGGGTTATCTATCACCAAA
65 TTAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAG-AAGGTTATCTATCAACAAA
*
349383 AACCTTTGAGTTCGATTCCATTCAG
129 AACCTTTGAGTTCGATTACATTCAG
349408 TTCGATGACA
Statistics
Matches: 286, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
169 5 0.02
170 240 0.84
171 41 0.14
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (169 bp):
ATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TAAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGTTATCTATCAACAAAAA
CCTTTGAGTTCGATTACATTCAGCTGAAAAGCATATCAA
Found at i:350140 original size:38 final size:38
Alignment explanation
Indices: 350071--350362 Score: 389
Period size: 38 Copynumber: 7.7 Consensus size: 38
350061 TATTTTGAAA
*
350071 ATATATATAATATATAGTTTTTGTAAACATTTTAAAAAC
1 ATATATATAATATATAG-TTTTGAAAACATTTTAAAAAC
* * *
350110 ATATATATAATATAAAGTTTTGAAAACATTTTGAAATC
1 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
350148 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
1 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
350186 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
1 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
*
350224 ATATATATAATATATAGTTTTGGAAACATTTTAAAAAC
1 ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
* *
350262 ATATATAT--TATATAGTTTTTGAAAACATTTTGAAAAT
1 ATATATATAATATATAG-TTTTGAAAACATTTTAAAAAC
** **
350299 ATATATATATATAATATAGTTTTTTTTAAACATTTT--TTA-
1 ATATATATA-AT-ATATAG--TTTTGAAAACATTTTAAAAAC
350338 A-ATATATAATATATAGTTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAA
350363 TGTTTTTTAA
Statistics
Matches: 230, Mismatches: 17, Indels: 17
0.87 0.06 0.06
Matches are distributed among these distances:
34 7 0.03
36 13 0.06
37 28 0.12
38 143 0.62
39 17 0.07
40 2 0.01
41 6 0.03
42 14 0.06
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTGAAAACATTTTAAAAAC
Found at i:350176 original size:76 final size:75
Alignment explanation
Indices: 350038--350362 Score: 394
Period size: 76 Copynumber: 4.3 Consensus size: 75
350028 ATTTTTGAAA
* * * * *
350038 ATATATTATATTGTTTTCAAAAATATTTTGAAA-ATATATATAATATATAGTTTTTGTAAACATT
1 ATATAATATATAGTTTT-GAAAACATTTTGAAATATATATATAATATATAG-TTTTGAAAACATT
350102 TTAAAAACATAT
64 TTAAAAACATAT
*
350114 ATATAATATAAAGTTTTGAAAACATTTTGAAATCATATATATAATATATAGTTTTGAAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAT-ATATATATAATATATAGTTTTGAAAACATTT
350179 TAAAAACATAT
65 TAAAAACATAT
* * *
350190 ATATAATATATAGTTTTGAAAACATTTTAAAAACATATATATAATATATAGTTTTGGAAACATTT
1 ATATAATATATAGTTTTGAAAACATTTT-GAAATATATATATAATATATAGTTTTGAAAACATTT
350255 TAAAAACATAT
65 TAAAAACATAT
**
350266 ATAT--TATATAGTTTTTGAAAACATTTTGAAAATATATATATATATAATATAGTTTTTTTTAAA
1 ATATAATATATAG-TTTTGAAAACATTTTG-AAATATATATATA-AT-ATATAG--TTTTGAAAA
**
350329 CATTTT--TTA-A-AT
60 CATTTTAAAAACATAT
350341 ATATAATATATAGTTTTGAAAA
1 ATATAATATATAGTTTTGAAAA
350363 TGTTTTTTAA
Statistics
Matches: 222, Mismatches: 16, Indels: 22
0.85 0.06 0.08
Matches are distributed among these distances:
74 7 0.03
75 46 0.21
76 122 0.55
77 34 0.15
79 13 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (75 bp):
ATATAATATATAGTTTTGAAAACATTTTGAAATATATATATAATATATAGTTTTGAAAACATTTT
AAAAACATAT
Found at i:352585 original size:23 final size:23
Alignment explanation
Indices: 352548--352608 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
352538 CAACTCATAT
352548 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
352571 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
352594 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
352609 TCATATAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.28, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:353114 original size:2 final size:2
Alignment explanation
Indices: 353109--353134 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
353099 TACCTTATTC
353109 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
353135 CCGCAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:357208 original size:13 final size:13
Alignment explanation
Indices: 357186--357218 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
357176 CCCTTATTCA
*
357186 TGTAAAAAATCCC
1 TGTAACAAATCCC
357199 TGTAACAAATCCC
1 TGTAACAAATCCC
357212 TGTAACA
1 TGTAACA
357219 CATATGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (13 bp):
TGTAACAAATCCC
Found at i:357590 original size:23 final size:23
Alignment explanation
Indices: 357564--357629 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
357554 CACCACAGCT
*
357564 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
357587 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
357610 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
357630 TCATATAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:360973 original size:2 final size:2
Alignment explanation
Indices: 360966--360998 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
360956 TATTTATCAA
360966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
360999 CGATTCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:363144 original size:18 final size:19
Alignment explanation
Indices: 363121--363168 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
363111 TTCACAATAA
*
363121 TTTTATTCT-TTGATAATC
1 TTTTATTCTACTGATAATC
363139 TTTTATTCCTACTGATAATC
1 TTTTATT-CTACTGATAATC
*
363159 TTATATTCTA
1 TTTTATTCTA
363169 TGAATCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 14 0.54
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTATTCTACTGATAATC
Found at i:365798 original size:19 final size:19
Alignment explanation
Indices: 365774--365811 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
365764 TTATTGGGTG
365774 TTTTACCAATTTTGTTATT
1 TTTTACCAATTTTGTTATT
*
365793 TTTTACCTATTTTGTTATT
1 TTTTACCAATTTTGTTATT
365812 GTTGGACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTACCAATTTTGTTATT
Found at i:367961 original size:36 final size:35
Alignment explanation
Indices: 367870--367973 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 35
367860 AGATGAACAA
* * *
367870 TTGAATCGAAAGTGCTGACGCTTCCTTCCTTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCAC
* *
367905 TTAAATCGAAAGTG-TCGATGCTTCTTTTCGTTCAC
1 TTGAATCGAAAGTGCT-GATGCTTCCTTTCGTTCAC
367940 TTTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
367974 TTCTTATTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.02
35 28 0.47
36 29 0.49
37 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCAC
Found at i:376963 original size:31 final size:31
Alignment explanation
Indices: 376907--376972 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
376897 GGTGGAGATC
* * *
376907 ATATCTTAATTAAATAAAAATGAAAGTGATA
1 ATATCTTAACTAAACAAAAACGAAAGTGATA
* *
376938 ATATTTTAACTAAACAAAAACGAAAGTGATC
1 ATATCTTAACTAAACAAAAACGAAAGTGATA
376969 ATAT
1 ATAT
376973 ATTATGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (31 bp):
ATATCTTAACTAAACAAAAACGAAAGTGATA
Found at i:377382 original size:16 final size:17
Alignment explanation
Indices: 377363--377397 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
377353 AAAATTTCAG
*
377363 AAAATAT-AATTTTTTA
1 AAAATATGAATCTTTTA
377379 AAAATATGAATCTTTTA
1 AAAATATGAATCTTTTA
377396 AA
1 AA
377398 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
AAAATATGAATCTTTTA
Found at i:377958 original size:34 final size:32
Alignment explanation
Indices: 377890--377958 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
377880 CAAACTGTGG
* * *
377890 ATTTTCTTCTCTTTCTCTTCTTCAAACAATCA
1 ATTTTCTTCTATTTCTCTTATTCAAACAACCA
*
377922 ATTTTCTTCTATTTCTCTTATTCTTGAACAACCA
1 ATTTTCTTCTATTTCTCTTATTC--AAACAACCA
377956 ATT
1 ATT
377959 AAGTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 21 0.68
34 10 0.32
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (32 bp):
ATTTTCTTCTATTTCTCTTATTCAAACAACCA
Found at i:378796 original size:33 final size:33
Alignment explanation
Indices: 378750--378821 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
378740 ATTTTGTAGG
* * * *
378750 TGATGAAGGTGGGCTAGTTGAAGATGGGTCAAA
1 TGATGAAGATGGGCCAGTTGAAGATAGGCCAAA
378783 TGATGAAGATGGGCCAGTTGAAGATAGGCCAAA
1 TGATGAAGATGGGCCAGTTGAAGATAGGCCAAA
378816 TGATGA
1 TGATGA
378822 TAATATTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.22
Consensus pattern (33 bp):
TGATGAAGATGGGCCAGTTGAAGATAGGCCAAA
Found at i:381424 original size:21 final size:21
Alignment explanation
Indices: 381381--381425 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
381371 AAATCTTTTC
*
381381 TTTATTTTACTTTAAATCGCT
1 TTTATTTTACTTTAAATAGCT
*
381402 TTTATTATTA-TTTAAATATCT
1 TTTATT-TTACTTTAAATAGCT
381423 TTT
1 TTT
381426 TACCAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTATTTTACTTTAAATAGCT
Found at i:389064 original size:24 final size:24
Alignment explanation
Indices: 389016--389065 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
389006 CCATATCCAT
*
389016 TTTTAACTTTAAATATTTTCTTTA
1 TTTTAACTTTAAATATTTTCATTA
389040 TTTT-ACTTTAAATCAATTTT-ATTA
1 TTTTAACTTTAAAT--ATTTTCATTA
389064 TT
1 TT
389066 ATTTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 9 0.39
24 9 0.39
25 5 0.22
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTAACTTTAAATATTTTCATTA
Found at i:389682 original size:21 final size:21
Alignment explanation
Indices: 389655--389702 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
389645 TATGTCATCT
*
389655 CAGACTGCTTCAGCTTTATCC
1 CAGACTGCTCCAGCTTTATCC
*
389676 TAGACTGCTCCAGCTTTATCC
1 CAGACTGCTCCAGCTTTATCC
389697 CAGACT
1 CAGACT
389703 ACAACATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (21 bp):
CAGACTGCTCCAGCTTTATCC
Found at i:389801 original size:21 final size:21
Alignment explanation
Indices: 389777--389845 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
389767 CAACAAGTTT
* * *
389777 ATCTCATCTTGCATCACCTTC
1 ATCTCAACATGCAACACCTTC
389798 ATCTCAACATGCAACACCTTC
1 ATCTCAACATGCAACACCTTC
*
389819 ATCTCAACATACAACACCTTC
1 ATCTCAACATGCAACACCTTC
389840 ATCTCA
1 ATCTCA
389846 GCCTGTAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.29
Consensus pattern (21 bp):
ATCTCAACATGCAACACCTTC
Found at i:391537 original size:19 final size:18
Alignment explanation
Indices: 391513--391561 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
391503 TAAATTTTTA
*
391513 GTTTTAAATTTTTATTAGT
1 GTTTTAAATTTTTA-AAGT
391532 GTTTT-AATATTTTAAAGT
1 GTTTTAAAT-TTTTAAAGT
*
391550 ATTTTAAATTTT
1 GTTTTAAATTTT
391562 AATAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
GTTTTAAATTTTTAAAGT
Found at i:392048 original size:21 final size:21
Alignment explanation
Indices: 392015--392067 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
392005 ATTTTGACTA
392015 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
392036 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
392057 TCGCAATGCGA
1 TCGCATTGCGA
392068 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:392082 original size:20 final size:20
Alignment explanation
Indices: 392057--392190 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
392047 TTTTCCTAAT
392057 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
392077 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
392098 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
392118 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
392138 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
392158 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
392178 TCGCAATGCGAAT
1 TCGCAATGCGAAT
392191 CTGATTATCG
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
20 88 0.85
21 15 0.15
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:392813 original size:20 final size:19
Alignment explanation
Indices: 392755--392822 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
392745 GCGATTCTGT
**
392755 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
392774 CGTCGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
392794 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
392814 TGTTGCGAT
1 CGTTGCGAT
392823 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.28
20 29 0.73
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:394087 original size:33 final size:33
Alignment explanation
Indices: 394030--394114 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
394020 ACTAATTTCG
394030 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
394064 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* **
394097 CATTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
394115 CACGTTGCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.70
34 14 0.30
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:394127 original size:20 final size:20
Alignment explanation
Indices: 394099--394185 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
394089 GATTCTCTCA
394099 TTGCGATAGTCATTTCCACG
1 TTGCGATAGTCATTTCCACG
* *
394119 TTGCAATAGTCAATTCCACG
1 TTGCGATAGTCATTTCCACG
**
394139 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCACG
*
394159 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCACG
394179 TTGCGAT
1 TTGCGAT
394186 TTCCGCGTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCACG
Found at i:396390 original size:14 final size:14
Alignment explanation
Indices: 396371--396397 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
396361 TCCCGTGGCA
396371 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
396385 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
396398 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:396633 original size:24 final size:24
Alignment explanation
Indices: 396599--396652 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
396589 CTGAAAAATC
396599 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
396623 ATCAAACTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
396647 ATCAAA
1 ATCAAA
396653 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:396666 original size:24 final size:24
Alignment explanation
Indices: 396599--396666 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
396589 CTGAAAAATC
* * *
396599 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAACTCCGAATACTGACCAAG
** *
396623 ATCAAACTCCGGGTATTGACCAAG
1 ATCAAACTCCGAATACTGACCAAG
* *
396647 ATCAAATTTCGAATACTGAC
1 ATCAAACTCCGAATACTGAC
396667 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAACTCCGAATACTGACCAAG
Found at i:397537 original size:20 final size:20
Alignment explanation
Indices: 397501--397538 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
397491 AGTATTGCAA
*
397501 ATAGTCAGAATCTCGTTGTG
1 ATAGTCAGAATCGCGTTGTG
*
397521 ATAGTCAGATTCGCGTTG
1 ATAGTCAGAATCGCGTTG
397539 CGATTTACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
ATAGTCAGAATCGCGTTGTG
Found at i:397552 original size:20 final size:20
Alignment explanation
Indices: 397529--397581 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
397519 TGATAGTCAG
*
397529 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
397549 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
397569 ATTCGCATTGCGA
1 ATTCGCATTGCGA
397582 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:397602 original size:21 final size:21
Alignment explanation
Indices: 397578--397623 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
397568 TATTCGCATT
397578 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
397599 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
397620 GCGA
1 GCGA
397624 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:399343 original size:29 final size:25
Alignment explanation
Indices: 399265--399323 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
399255 TTTGAGTAAC
399265 AGAATGAAACATTAGGCACTAAACT
1 AGAATGAAACATTAGGCACTAAACT
399290 AGAATGAAACATTAGGCACTAAACT
1 AGAATGAAACATTAGGCACTAAACT
399315 AGAATGAAA
1 AGAATGAAA
399324 TAAACGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.19
Consensus pattern (25 bp):
AGAATGAAACATTAGGCACTAAACT
Found at i:399877 original size:23 final size:23
Alignment explanation
Indices: 399851--399903 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
399841 AAAAAAAGGG
* *
399851 AAAAAAGGTTA-ATGCATTAATT
1 AAAAAAGGTTAGATGCAGTAATA
* *
399873 TAAAAAGATTAGATGCAGTAATA
1 AAAAAAGGTTAGATGCAGTAATA
399896 AAAAAAGG
1 AAAAAAGG
399904 ACTTAATTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.25
Consensus pattern (23 bp):
AAAAAAGGTTAGATGCAGTAATA
Found at i:400645 original size:19 final size:17
Alignment explanation
Indices: 400601--400647 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
400591 TTGATTTTCG
*
400601 TTGATTTGTGTTGAATGT
1 TTGATTTG-GTTGAATCT
400619 TT-ATTTGGTTGACATTCT
1 TTGATTTGGTTGA-A-TCT
400637 TTGATTTGGTT
1 TTGATTTGGTT
400648 TTGTTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 6 0.24
19 8 0.32
ACGTcount: A:0.15, C:0.04, G:0.23, T:0.57
Consensus pattern (17 bp):
TTGATTTGGTTGAATCT
Found at i:418034 original size:16 final size:16
Alignment explanation
Indices: 418012--418049 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
418002 AAAATTTATT
418012 TCTTTTTG-GCTTTTC
1 TCTTTTTGTGCTTTTC
418027 TCCTTTTTGTGCTTTTC
1 T-CTTTTTGTGCTTTTC
418044 TCTTTT
1 TCTTTT
418050 GTTTTTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 12 0.57
17 8 0.38
ACGTcount: A:0.00, C:0.21, G:0.11, T:0.68
Consensus pattern (16 bp):
TCTTTTTGTGCTTTTC
Found at i:421558 original size:44 final size:44
Alignment explanation
Indices: 421421--421557 Score: 204
Period size: 44 Copynumber: 3.1 Consensus size: 44
421411 ATAAAATGAG
*
421421 TGGCACATTT-TGCCAATAATGTATTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGTATCGTTATGCATTTTCATTTA
* *
421464 TGGCACATTTCTACCAATAATGTATCGTTATGTATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGTATCGTTATGCATTTTCATTTA
* * *
421508 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGTATCGTTATGCATTTTCATTTA
*
421552 CGGCAC
1 TGGCAC
421558 CGTTATGCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 10 0.12
44 74 0.88
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGTATCGTTATGCATTTTCATTTA
Found at i:421570 original size:69 final size:70
Alignment explanation
Indices: 421489--421635 Score: 206
Period size: 70 Copynumber: 2.1 Consensus size: 70
421479 AATAATGTAT
* * * *
421489 CGTTATGTATTTTCATTTATGGCACCTTTCTGC-CAATAATGCACCGTTATGCATTTTCATTTAC
1 CGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCACCGTTATGCATTTTCATTTAC
*
421553 GGCAC
66 GGAAC
* * *
421558 CGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCATCGTTATGCATTTTTATTTAT
1 CGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCACCGTTATGCATTTTCATTTAC
421623 GGAAC
66 GGAAC
*
421628 CTTTATGC
1 CGTTATGC
421636 CAATAATGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 31 0.46
70 37 0.54
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (70 bp):
CGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCACCGTTATGCATTTTCATTTAC
GGAAC
Found at i:421591 original size:25 final size:25
Alignment explanation
Indices: 421529--421583 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
421519 TGCCAATAAT
421529 GCACCGTTATGCATTTTCATTTACG
1 GCACCGTTATGCATTTTCATTTACG
421554 GCACCGTTATGCATTTTCATTTACG
1 GCACCGTTATGCATTTTCATTTACG
421579 GCACC
1 GCACC
421584 TTTCTGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (25 bp):
GCACCGTTATGCATTTTCATTTACG
Found at i:421630 original size:114 final size:113
Alignment explanation
Indices: 421446--421671 Score: 344
Period size: 114 Copynumber: 2.0 Consensus size: 113
421436 ATAATGTATT
* * * * *
421446 GTTATGCATTTTCATTTATGGCACATTTCTACCAATAATGTATCGTTATGTATTTTCATTTATGG
1 GTTATGCATTTTCATTTACGGCACATTTCTACAAAAAATGCATCGTTATGCATTTTCATTTATGG
* *
421511 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTACGGCACC
66 AACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTACGGCACC
* * *
421559 GTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCATCGTTATGCATTTTTATTTATG
1 GTTATGCATTTTCATTTACGGCACATTTCTAC-AAAAAATGCATCGTTATGCATTTTCATTTATG
*
421624 GAACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC
65 GAACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTACGGCAC
421672 ATTTCTTCCA
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
113 29 0.29
114 72 0.71
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (113 bp):
GTTATGCATTTTCATTTACGGCACATTTCTACAAAAAATGCATCGTTATGCATTTTCATTTATGG
AACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTACGGCACC
Found at i:421659 original size:44 final size:44
Alignment explanation
Indices: 421554--421883 Score: 468
Period size: 44 Copynumber: 7.5 Consensus size: 44
421544 TTCATTTACG
* * *
421554 GCACCGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC-CAATAAT
* * * *
421599 GCATCGTTATGCATTTTTATTTATGGAACCTTTATGCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
* *
421643 GCACCGTTATGCATTTTCATTTATGGCACATTTCTTCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
* ** **
421687 GCATCGTTATGCATTTTCATTTATGGCATATTTCTGTTAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
421731 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
* * *
421775 G---CGTTATGCATTTTCATTTATGCCACCTTTCTACTAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
*
421816 GCACCGTTATGCATTTTCATTTATGACACCTTTCTGCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
421860 GCACCGTTATGCATTTTCATTTAT
1 GCACCGTTATGCATTTTCATTTAT
421884 TTTAGAGTAG
Statistics
Matches: 253, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
41 38 0.15
44 183 0.72
45 32 0.13
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
Found at i:421858 original size:173 final size:175
Alignment explanation
Indices: 421554--421883 Score: 511
Period size: 173 Copynumber: 1.9 Consensus size: 175
421544 TTCATTTACG
*
421554 GCACCGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGCATCGTTATGCATTTTTAT
1 GCACCGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATG-A-CGTTATGCATTTTCAT
* * * *
421619 TTATGGAACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACATTTCTTCCAAT
64 TTATGCAACCTTTATACCAATAATGCACCGTTATGCATTTTCATTTATGACACATTTCTGCCAAT
*
421684 AATGCATCGTTATGCATTTTCATTTATGGCATATTTCTGTTAATAAT
129 AATGCACCGTTATGCATTTTCATTTATGGCATATTTCTGTTAATAAT
* * *
421731 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGC-CAATAATG-CGTTATGCATTTTCATTT
1 GCACCGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGACGTTATGCATTTTCATTT
* * * *
421794 ATGCCACCTTTCTACTAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTCTGCCAATAA
66 ATGCAACCTTTATACCAATAATGCACCGTTATGCATTTTCATTTATGACACATTTCTGCCAATAA
421859 TGCACCGTTATGCATTTTCATTTAT
131 TGCACCGTTATGCATTTTCATTTAT
421884 TTTAGAGTAG
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
173 98 0.70
176 6 0.04
177 36 0.26
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (175 bp):
GCACCGTTATGCATTTTCATTTACGGCACCTTTCTGCAAAAAAATGACGTTATGCATTTTCATTT
ATGCAACCTTTATACCAATAATGCACCGTTATGCATTTTCATTTATGACACATTTCTGCCAATAA
TGCACCGTTATGCATTTTCATTTATGGCATATTTCTGTTAATAAT
Found at i:426847 original size:44 final size:44
Alignment explanation
Indices: 426779--427086 Score: 483
Period size: 44 Copynumber: 7.0 Consensus size: 44
426769 ATACCATGAG
* *
426779 TGGCACCATTCTGACAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
426823 TGACATCTTTCTTCCAAAAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
426867 TGTCACCTTTCTGCCAA-AATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
426910 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
426954 TGGCACATTTCTGCCAATAATGCACCGTTATGAATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
426998 TGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
427042 TGCCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
427086 T
1 T
427087 TTTAGAGTAG
Statistics
Matches: 242, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 39 0.16
44 203 0.84
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:427013 original size:131 final size:132
Alignment explanation
Indices: 426779--427086 Score: 478
Period size: 131 Copynumber: 2.3 Consensus size: 132
426769 ATACCATGAG
* *
426779 TGGCACCA-TTCTGACAATAATGCACCGTTATGCATTTTCATTTATGACATCTTTCTTCCAAAAA
1 TGGCA-CATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACATCTTTCTGCCAAAAA
* * * * *
426843 TGCACTGTTATGCATTTTCATTTATGTCACCTTTCTGCCAA-AATGCATCGTTATGCATTTTCAT
65 TGCACCGTTATGAATTTTCATTTATGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCAT
426907 TTA
130 TTA
* *
426910 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CATTTCTGCCAATAA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACATC-TTTCTGCCAAAAA
426974 TGCACCGTTATGAATTTTCATTTATGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCAT
65 TGCACCGTTATGAATTTTCATTTATGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCAT
427039 TTA
130 TTA
* *
427042 TGCCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
427087 TTTAGAGTAG
Statistics
Matches: 163, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
130 3 0.02
131 93 0.57
132 67 0.41
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (132 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGACATCTTTCTGCCAAAAAT
GCACCGTTATGAATTTTCATTTATGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCATT
TA
Found at i:428677 original size:74 final size:72
Alignment explanation
Indices: 428598--428769 Score: 218
Period size: 75 Copynumber: 2.3 Consensus size: 72
428588 AAATACAAAT
* *
428598 TTTATCTCACTTGTGATAGTTTACCTTAAAACAAAATTCGTCTCACTCGAGACAGTTTCTCTTGA
1 TTTATCTCACTTGAGATAGTTT-CCTTAAAACAAAATTCGTCTCACTCGAGACAATTTCTCTTGA
428663 AACAAAACA
65 AACAAAA-A
* * ** * *
428672 TTTATCTCACTTGAGATAGGTTTCATCGAAAACAATTTTTGTCTCACTCGAGATAATTTCTCTTG
1 TTTATCTCACTTGAGATA-GTTTCCT-TAAAACAAAATTCGTCTCACTCGAGACAATTTCTCTTG
*
428737 AAACAAAAG
64 AAACAAAAA
*
428746 TTTATCTCACTTGAGATATTTTCC
1 TTTATCTCACTTGAGATAGTTTCC
428770 CTTGAACGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
73 4 0.05
74 37 0.44
75 44 0.52
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (72 bp):
TTTATCTCACTTGAGATAGTTTCCTTAAAACAAAATTCGTCTCACTCGAGACAATTTCTCTTGAA
ACAAAAA
Found at i:428754 original size:37 final size:36
Alignment explanation
Indices: 428592--429023 Score: 197
Period size: 37 Copynumber: 12.0 Consensus size: 36
428582 CCCTCAAAAT
* * *
428592 ACAAATTTTATCTCACTTGTGATAGTTTAC-CTTAAA
1 ACAAAATTTATCTCACTTGAGATAGTTT-CTCTTGAA
** * *
428628 ACAAAATTCGTCTCACTCGAGACAGTTTCTCTTGAA
1 ACAAAATTTATCTCACTTGAGATAGTTTCTCTTGAA
428664 ACAAAACATTTATCTCACTTGAGATAGGTTTCATC--GAAA
1 AC-AAA-ATTTATCTCACTTGAGATA-GTTTC-TCTTG-AA
** * * *
428703 ACAATTTTTGTCTCACTCGAGATAATTTCTCTTGAA
1 ACAAAATTTATCTCACTTGAGATAGTTTCTCTTGAA
* *
428739 ACAAAAGTTTATCTCACTTGAGATATTTTCCCTTG-A
1 ACAAAA-TTTATCTCACTTGAGATAGTTTCTCTTGAA
*** * * *
428775 AC-GTTTTTGTCTCACTTGAGATATTTTCCCTTG--
1 ACAAAATTTATCTCACTTGAGATAGTTTCTCTTGAA
* * * ** * * *
428808 A-AAATTTTCGTCTTACCCGAGACAGTTTATCTCGAA
1 ACAAAATTT-ATCTCACTTGAGATAGTTTCTCTTGAA
* * *
428844 ACAAAATTTCATCTCACTTGCGATATTTTCCCTTG-A
1 ACAAAATTT-ATCTCACTTGAGATAGTTTCTCTTGAA
*** * * * * **
428880 A-ATTTTTTGTCTCACTCGAGAAAGTTTTTCTCAAA
1 ACAAAATTTATCTCACTTGAGATAGTTTCTCTTGAA
* * *
428915 ACAAAATTTCATTTCACTTGAGATATTTTCCCTTG--
1 ACAAAATTT-ATCTCACTTGAGATAGTTTCTCTTGAA
** * * * **
428950 A-AATTTTTTTCCTTACTCGAGATAGTTTCTCTCAAA
1 ACAAAATTTAT-CTCACTTGAGATAGTTTCTCTTGAA
* *
428986 ACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAA
1 ACAAAATTT-ATCTCACTTGAGATAGTTTCTCTTGAA
429023 A
1 A
429024 ATTTTCATCT
Statistics
Matches: 284, Mismatches: 90, Indels: 43
0.68 0.22 0.10
Matches are distributed among these distances:
33 6 0.02
34 81 0.29
35 10 0.04
36 50 0.18
37 107 0.38
38 19 0.07
39 9 0.03
40 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
ACAAAATTTATCTCACTTGAGATAGTTTCTCTTGAA
Found at i:428808 original size:71 final size:74
Alignment explanation
Indices: 428637--428810 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 74
428627 AACAAAATTC
* *
428637 GTCTCACTCGAGACAGTTTCTCTTGAAACAAAACATTTATCTCACTTGAGATAGGTTTCATCGAA
1 GTCTCACTCGAGATAATTTCTCTTGAAACAAAACATTTATCTCACTTGAGATAGGTTTCATCG-A
428702 AACAATTTTT
65 AACAATTTTT
* * * *
428712 GTCTCACTCGAGATAATTTCTCTTGAAACAAAA-GTTTATCTCACTTGAGATA-TTTTCCCTTG-
1 GTCTCACTCGAGATAATTTCTCTTGAAACAAAACATTTATCTCACTTGAGATAGGTTT-CATCGA
*
428774 AAC-GTTTTT
65 AACAATTTTT
* * *
428783 GTCTCACTTGAGATATTTTCCCTTGAAA
1 GTCTCACTCGAGATAATTTCTCTTGAAA
428811 ATTTTCGTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
71 30 0.34
72 3 0.03
73 3 0.03
74 21 0.24
75 31 0.35
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (74 bp):
GTCTCACTCGAGATAATTTCTCTTGAAACAAAACATTTATCTCACTTGAGATAGGTTTCATCGAA
ACAATTTTT
Found at i:428859 original size:71 final size:71
Alignment explanation
Indices: 428784--429107 Score: 395
Period size: 71 Copynumber: 4.6 Consensus size: 71
428774 AACGTTTTTG
* * * *
428784 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTTACCCGAGACAGTTTATCTCGAAACAAA
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTCTCAAAACAAA
428849 ATTTCA
66 ATTTCA
* * * * *
428855 TCTCACTTGCGATATTTTCCCTTGAAATTTTTTGTCTCACTCGAGAAAGTTTTTCTCAAAACAAA
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTCTCAAAACAAA
428920 ATTTCA
66 ATTTCA
* ** * *
428926 TTTCACTTGAGATATTTTCCCTTG-AAATTTTTTTCCTTACTCGAGATAGTTTCTCTCAAAACAA
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGT-CTCACTCGAGACAGTTTCTCTCAAAACAA
428990 AATTTCA
65 AATTTCA
* *
428997 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCATCTCATTCGAGACAGTTTCTCTCTAAAA-AA
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTCTC-AAAACAA
429061 AA-TTCA
65 AATTTCA
* * * * ** *
429067 TCTCATTTG-TATGTTTTCTCTTGAAAAAGTTCATCTCACTC
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTC
429108 AAGAGATTTT
Statistics
Matches: 222, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
69 26 0.12
70 20 0.09
71 164 0.74
72 12 0.05
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (71 bp):
TCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTCTCAAAACAAA
ATTTCA
Found at i:428879 original size:142 final size:143
Alignment explanation
Indices: 428713--429024 Score: 330
Period size: 142 Copynumber: 2.2 Consensus size: 143
428703 ACAATTTTTG
* * * * * **
428713 TCTCACTCGAGATAATTTCTCTTGAAACAAAAGTTTATCTCACTTGAGATA-TTTTCC-CTTGAA
1 TCTCACTTGAGATATTTTCCCTTGAAA-AAAAGTTTATCTCACTCGAGAAAGTTTTCCTC-AAAA
** **
428776 C-GTTTTTGTCTCACTTGAGATATTTTCCCTTGAAAATTTTCGT-CTTACCCGAGACAGTTTATC
64 CAAATTTCATCTCACTTGAGATATTTTCCCTTG-AAATTTTCGTCCTTACCCGAGACAGTTTATC
*
428839 TCGAAACAAAATTTCA
128 TCAAAACAAAATTTCA
* *** * *
428855 TCTCACTTGCGATATTTTCCCTTG--AAATTTTTTGTCTCACTCGAGAAAGTTTTTCTCAAAACA
1 TCTCACTTGAGATATTTTCCCTTGAAAAAAAGTTTATCTCACTCGAGAAAGTTTTCCTCAAAAC-
* ** * * *
428918 AAATTTCATTTCACTTGAGATATTTTCCCTTGAAATTTTTTTCCTTACTCGAGATAGTTTCTCTC
65 AAATTTCATCTCACTTGAGATATTTTCCCTTGAAATTTTCGTCCTTACCCGAGACAGTTTATCTC
428983 AAAACAAAATTTCA
130 AAAACAAAATTTCA
428997 TCTCACTTGAGATATTTTCCCTTGAAAA
1 TCTCACTTGAGATATTTTCCCTTGAAAA
429025 TTTTCATCTC
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
139 17 0.12
140 9 0.07
141 9 0.07
142 101 0.73
144 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (143 bp):
TCTCACTTGAGATATTTTCCCTTGAAAAAAAGTTTATCTCACTCGAGAAAGTTTTCCTCAAAACA
AATTTCATCTCACTTGAGATATTTTCCCTTGAAATTTTCGTCCTTACCCGAGACAGTTTATCTCA
AAACAAAATTTCA
Found at i:428894 original size:34 final size:34
Alignment explanation
Indices: 428750--429035 Score: 151
Period size: 34 Copynumber: 8.1 Consensus size: 34
428740 CAAAAGTTTA
** *
428750 TCTCACTTGAGATATTTTCCCTTGAACGTTTTTG
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
428784 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
* ** * * *** * *
428818 TCTTACCCGAGACAGTTTATCTCGAAACAAAATTTCA
1 TCTCACTTGAGATA-TTT-TCCCTTGA-AAATTTTCG
* * *
428855 TCTCACTTGCGATATTTTCCCTTGAAATTTTTTG
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
* * * *** * *
428889 TCTCACTCGAGAAAGTTTTTCTCAAAACAAAATTTCA
1 TCTCACTTGAGATA--TTTTCCCTTGA-AAATTTTCG
* **
428926 TTTCACTTGAGATATTTTCCCTTG-AAATTTTTT
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
* * * *** * *
428959 TCCTTACTCGAGATAGTTTCTCTCAAAACAAAATTTCA
1 T-CTCACTTGAGATA-TTT-TCCCTTGA-AAATTTTCG
*
428997 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCA
1 TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
429031 TCTCA
1 TCTCA
429036 TTCGAGACAG
Statistics
Matches: 177, Mismatches: 64, Indels: 22
0.67 0.24 0.08
Matches are distributed among these distances:
33 7 0.04
34 80 0.45
35 20 0.11
36 20 0.11
37 43 0.24
38 7 0.04
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (34 bp):
TCTCACTTGAGATATTTTCCCTTGAAAATTTTCG
Found at i:429070 original size:36 final size:36
Alignment explanation
Indices: 428966--429073 Score: 107
Period size: 36 Copynumber: 3.0 Consensus size: 36
428956 TTTTCCTTAC
428966 TCGAGATAGTTTCTCTC-AAAACAAAATTTCATCTCACT
1 TCGAGATAGTTTCTCTCTAAAA-AAAA-TTCATCTCA-T
* ** **
429004 T-GAGATA-TTT-TCCCTTGAAAATTTTCATCTCAT
1 TCGAGATAGTTTCTCTCTAAAAAAAATTCATCTCAT
*
429037 TCGAGACAGTTTCTCTCTAAAAAAAATTCATCTCAT
1 TCGAGATAGTTTCTCTCTAAAAAAAATTCATCTCAT
429073 T
1 T
429074 TGTATGTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
33 2 0.04
34 14 0.25
35 8 0.15
36 24 0.44
37 6 0.11
38 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.38
Consensus pattern (36 bp):
TCGAGATAGTTTCTCTCTAAAAAAAATTCATCTCAT
Found at i:430174 original size:241 final size:242
Alignment explanation
Indices: 429855--430402 Score: 633
Period size: 241 Copynumber: 2.3 Consensus size: 242
429845 TTATGACAAG
*
429855 TTAGCTTAACTCAACGACGAGGAGCTATTTCCCAGA-CTAGATTTTGAGTTAGATTTCAACTTCA
1 TTAGCTTAACTCAACGACGAGGAGCTACTTCCCA-ACCTAGATTTTGAGTTAGATTTCAACTTCA
* * * * * **
429919 CGATGAAGGATATCAAGCTCGAATCGCTTAAGATCGACTT-TACTCATTATGGAGGAGTTATCCA
65 CGAAGAAGGATATCAAGCTCGAATCGCCTAAGATCAAATTAAAC-CACAATGGAGGAGTTATCCA
* *
429983 CAACATAACTTAACTTAACAGCGAAGAA-CTATTTTTCAACTAAAGTTTTCAAGTCAAATTTCAA
129 CAACATAACTTAACTCAACAAC-AAGAAGCTATTTTTCAACTAAAGTTTTCAAGTCAAATTT-AA
** * * * * *
430047 CCTCGTGACGAGGGATATT-AGACTATAAGGAGA-TACAAGATTGACTATGAT
192 CCTCGCAACGAGGGACATTGA-ACTAGAAGGAGACT-CAAAATCGACTACGAT
430098 TTAGCTTAACTCAACGACG-GG-GCTACTTCCCAACCTAGATTTTGAGTTAGATTTCAACTTCAC
1 TTAGCTTAACTCAACGACGAGGAGCTACTTCCCAACCTAGATTTTGAGTTAGATTTCAACTTCAC
* * * * **
430161 GAAGAATGATATCAAGCTCGAGTCGCCTAGGGTCAAATTAAACCACAATGGAGGAGTTATCTGCA
66 GAAGAAGGATATCAAGCTCGAATCGCCTAAGATCAAATTAAACCACAATGGAGGAGTTATCCACA
*** * * * *
430226 ACATTGTTTAACTCAACAACAAGAAGTTATTTTTCAACTAAGGTTTTTAAGTCGAATTTAACCTC
131 ACATAACTTAACTCAACAACAAGAAGCTATTTTTCAACTAAAGTTTTCAAGTCAAATTTAACCTC
*
430291 GCAACGAGGGACATTGAACTAGAAGGAGACTCAAAATCGACTACGGT
196 GCAACGAGGGACATTGAACTAGAAGGAGACTCAAAATCGACTACGAT
** * * * * * **
430338 TTAGCTTAACTCAATAATGAGGAGCTACTTTCTAGCCCAGATTCCGAGTTAGATTTCAACTTCAC
1 TTAGCTTAACTCAACGACGAGGAGCTACTTCCCAACCTAGATTTTGAGTTAGATTTCAACTTCAC
430403 AACAAAGGTT
Statistics
Matches: 258, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
240 63 0.24
241 136 0.53
242 40 0.16
243 19 0.07
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (242 bp):
TTAGCTTAACTCAACGACGAGGAGCTACTTCCCAACCTAGATTTTGAGTTAGATTTCAACTTCAC
GAAGAAGGATATCAAGCTCGAATCGCCTAAGATCAAATTAAACCACAATGGAGGAGTTATCCACA
ACATAACTTAACTCAACAACAAGAAGCTATTTTTCAACTAAAGTTTTCAAGTCAAATTTAACCTC
GCAACGAGGGACATTGAACTAGAAGGAGACTCAAAATCGACTACGAT
Found at i:432950 original size:49 final size:49
Alignment explanation
Indices: 432897--433044 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 49
432887 GAACAAGAAG
432897 CAATTCACCACATATGTATTCATGTTATCTATATGGCAATCGGATTAAA
1 CAATTCACCACATATGTATTCATGTTATCTATATGGCAATCGGATTAAA
* ** * * * * * * *
432946 CAATTCAACATGTACGACATTC-TTTTCTCTAT-TCG-AA-CAAGA--AGA
1 CAATTCACCACATATG-TATTCATGTTATCTATATGGCAATC-GGATTAAA
**
432991 -AATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAA
1 CAATTCACCACATATGTATTCATGTTATCTATATGGCAATCGGATTAAA
433039 CAATTC
1 CAATTC
433045 CCAACAGCCT
Statistics
Matches: 68, Mismatches: 22, Indels: 18
0.63 0.20 0.17
Matches are distributed among these distances:
43 4 0.06
44 17 0.25
45 4 0.06
46 5 0.07
47 5 0.07
48 4 0.06
49 25 0.37
50 4 0.06
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (49 bp):
CAATTCACCACATATGTATTCATGTTATCTATATGGCAATCGGATTAAA
Found at i:432954 original size:98 final size:93
Alignment explanation
Indices: 432785--433044 Score: 385
Period size: 98 Copynumber: 2.7 Consensus size: 93
432775 TCTTTCCTCC
* * * *
432785 ATTCGAACAAGAAACAATTCACCACATATGTATTCATGCAATCTATATGGCATTCAGATTAAACG
1 ATTCGAACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAACA
*
432850 ATTCAACATGTATAACATTATTTCCTCTATTCT
66 ATTCAACATGTACAACATTATTT--TC---TCT
**
432883 ATTCGAACAAGAAGCAATTCACCACATATGTATTCATGTTATCTATATGGCAATCGGATTAAACA
1 ATTCGAACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAACA
* *
432948 ATTCAACATGTACGACATTCTTTTCTCT
66 ATTCAACATGTACAACATTATTTTCTCT
*
432976 ATTCGAACAAGAAGAAATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAACA
1 ATTCGAACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAACA
433041 ATTC
66 ATTC
433045 CCAACAGCCT
Statistics
Matches: 150, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
93 69 0.46
96 2 0.01
98 79 0.53
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (93 bp):
ATTCGAACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGCAATCGGATTAAACA
ATTCAACATGTACAACATTATTTTCTCT
Found at i:435432 original size:182 final size:183
Alignment explanation
Indices: 435125--435493 Score: 731
Period size: 182 Copynumber: 2.0 Consensus size: 183
435115 CAACAATTGA
435125 AATTATATCCATAATCAAACTTATAATTTCTAAAGGATCAACTCAATTAAACTCTTAAAATTTCG
1 AATTATATCCATAATCAAACTTATAATTTCTAAAGGATCAACTCAATTAAACTCTTAAAATTTCG
435190 AAAGGAAATAAAGGGAAAGGATTAATTGTAGGCTAGGTGAATTCTTTAGTAATCTAAGCTTGAAA
66 AAAGGAAATAAAGGGAAAGGATTAATTGTAGGCTAGGTGAATTCTTTAGTAATCTAAGCTTGAAA
435255 TCCAAGCATGCATGGCCGAATACTCCCTTTGCATTCTCTCAA-TTTTTTTCTC
131 TCCAAGCATGCATGGCCGAATACTCCCTTTGCATTCTCTCAATTTTTTTTCTC
435307 AATTATATCCATAATCAAACTTATAATTTCTAAAGGATCAACTCAATTAAACTCTTAAAATTTCG
1 AATTATATCCATAATCAAACTTATAATTTCTAAAGGATCAACTCAATTAAACTCTTAAAATTTCG
435372 AAAGGAAATAAAGGGAAAGGATTAATTGTAGGCTAGGTGAATTCTTTAGTAATCTAAGCTTGAAA
66 AAAGGAAATAAAGGGAAAGGATTAATTGTAGGCTAGGTGAATTCTTTAGTAATCTAAGCTTGAAA
435437 TCCAAGCATGCATGGCCGAATACTCCCTTTGCATTCTCTCAATTTTTTTTCTC
131 TCCAAGCATGCATGGCCGAATACTCCCTTTGCATTCTCTCAATTTTTTTTCTC
435490 AATT
1 AATT
435494 TTCTTTCTCA
Statistics
Matches: 186, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 172 0.92
183 14 0.08
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (183 bp):
AATTATATCCATAATCAAACTTATAATTTCTAAAGGATCAACTCAATTAAACTCTTAAAATTTCG
AAAGGAAATAAAGGGAAAGGATTAATTGTAGGCTAGGTGAATTCTTTAGTAATCTAAGCTTGAAA
TCCAAGCATGCATGGCCGAATACTCCCTTTGCATTCTCTCAATTTTTTTTCTC
Found at i:435491 original size:13 final size:13
Alignment explanation
Indices: 435473--435506 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
435463 CTTTGCATTC
*
435473 TCTCAATTTTTTT
1 TCTCAATTTTCTT
435486 TCTCAATTTTCTT
1 TCTCAATTTTCTT
435499 TCTCAATT
1 TCTCAATT
435507 ACGTTCACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCAATTTTCTT
Found at i:437208 original size:16 final size:16
Alignment explanation
Indices: 437189--437230 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
437179 TATATATATA
437189 TATTTATATTTTT-TT
1 TATTTATATTTTTATT
*
437204 CTATTTTTATTTTTATT
1 -TATTTATATTTTTATT
437221 TATTTATATT
1 TATTTATATT
437231 ATATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTATATTTTTATT
Found at i:437220 original size:22 final size:22
Alignment explanation
Indices: 437189--437246 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
437179 TATATATATA
* *
437189 TATTTATATTTTTTTCTATTTT
1 TATTTATATTTATTTATATTTT
* *
437211 TATTTTTATTTATTTATA-TTA
1 TATTTATATTTATTTATATTTT
437232 TA-TTATATTT-TTTAT
1 TATTTATATTTATTTAT
437247 TATACATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 4 0.13
22 15 0.48
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTATATTTATTTATATTTT
Found at i:437240 original size:16 final size:16
Alignment explanation
Indices: 437181--437264 Score: 53
Period size: 17 Copynumber: 5.0 Consensus size: 16
437171 AACATTAATA
437181 TATATATATATTTATAT
1 TATAT-TATATTTATAT
* * * *
437198 TTTTTTCTATTTTTATT
1 TATATTATATTTATA-T
*
437215 TTTATT-TATTTATAT
1 TATATTATATTTATAT
*
437230 TATATTATATTTTTTAT
1 TATATTATA-TTTATAT
*
437247 TATACATATATTTTATAT
1 TATA-TTATA-TTTATAT
437265 CATTATTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
15 6 0.11
16 17 0.32
17 19 0.36
18 11 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTATATTTATAT
Found at i:437589 original size:8 final size:7
Alignment explanation
Indices: 437574--437655 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 7
437564 CTTCGGTTTC
437574 TTTATTT
1 TTTATTT
437581 TTATATTT
1 TT-TATTT
437589 TTTATTT
1 TTTATTT
* *
437596 ATT-TTA
1 TTTATTT
* *
437602 CTTACTAT
1 TTTA-TTT
437610 TTTA-TT
1 TTTATTT
437616 TTTACTTT
1 TTTA-TTT
437624 TTTATCTTT
1 TTTA--TTT
437633 TTTATTT
1 TTTATTT
437640 AATTTATTT
1 --TTTATTT
437649 TTTATTT
1 TTTATTT
437656 ATTTTAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
6 9 0.15
7 19 0.32
8 17 0.28
9 15 0.25
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTATTT
Found at i:437610 original size:23 final size:21
Alignment explanation
Indices: 437574--437661 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 21
437564 CTTCGGTTTC
437574 TTTA-TTT-TTATATTTTTTA
1 TTTATTTTATTATATTTTTTA
437593 TTTATTTTACTTACTATTTTATT-
1 TTTATTTTA-TTA-TATTTT-TTA
*
437616 TTTACTTTT-TTATCTTTTTTA
1 TTTA-TTTTATTATATTTTTTA
437637 TTTA----ATT-TATTTTTTA
1 TTTATTTTATTATATTTTTTA
437653 TTTATTTTA
1 TTTATTTTA
437662 ATTTAATTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 23
0.69 0.03 0.29
Matches are distributed among these distances:
16 12 0.22
17 2 0.04
19 4 0.07
20 6 0.11
21 9 0.16
22 6 0.11
23 10 0.18
24 6 0.11
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTATTATATTTTTTA
Found at i:437645 original size:26 final size:26
Alignment explanation
Indices: 437616--437671 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
437606 CTATTTTATT
437616 TTTACTTTTTTATCTT-TTTT-ATTTAA
1 TTTA-TTTTTTAT-TTATTTTAATTTAA
437642 TTTATTTTTTATTTATTTTAATTTAA
1 TTTATTTTTTATTTATTTTAATTTAA
437668 TTTA
1 TTTA
437672 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.07
25 12 0.43
26 14 0.50
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTATTTTTTATTTATTTTAATTTAA
Found at i:437649 original size:16 final size:16
Alignment explanation
Indices: 437630--437682 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
437620 CTTTTTTATC
437630 TTTTTTATTTAATTTA
1 TTTTTTATTTAATTTA
*
437646 TTTTTTATTTATTTTA
1 TTTTTTATTTAATTTA
* *
437662 -ATTTAATTTAATTTA
1 TTTTTTATTTAATTTA
437677 TTTTTT
1 TTTTTT
437683 TCTTACATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTATTTAATTTA
Found at i:437655 original size:44 final size:43
Alignment explanation
Indices: 437578--437660 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 43
437568 GGTTTCTTTA
*
437578 TTTTTATATTTTTTATTTATTTTACTTACTATTTTATTTTTACT
1 TTTTTATATTTTTTATTTAATTTACTTACTA-TTTATTTTTACT
* * **
437622 TTTTTATCTTTTTTATTTAATTTATTTTTTATTTATTTT
1 TTTTTATATTTTTTATTTAATTTACTTACTATTTATTTT
437661 AATTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 8 0.24
44 26 0.76
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (43 bp):
TTTTTATATTTTTTATTTAATTTACTTACTATTTATTTTTACT
Found at i:441574 original size:43 final size:43
Alignment explanation
Indices: 441513--441633 Score: 179
Period size: 43 Copynumber: 2.8 Consensus size: 43
441503 CGAATGGGCC
*
441513 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCATAA
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACAA
* * *
441556 ATCCACGATTTCAACTCCACGACGGAGGATATCATGCCCACAC
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACAA
* * *
441599 ATCCACAATTTCAACTTCACGACGAAGGATATCGT
1 ATCCACGATTTCAACTCCACGACGGAGGATATCGT
441634 GTCCATCTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACAA
Found at i:441752 original size:125 final size:128
Alignment explanation
Indices: 441605--441838 Score: 314
Period size: 130 Copynumber: 1.8 Consensus size: 128
441595 ACACATCCAC
* * *
441605 AATTTCAACTTCACGACGAAGGATATCGTG-TC-CATC-T-CTAGATTGGATTTCAACTTCACGA
1 AATTTCAACTTCACGACGAAGGATATCG-GATCGAAACATACAAGATTGGATTTCAACTTCACGA
* *
441666 CGAAGGATATTCAATTCAAAGATCAACTTCACGACGAAGGGGCTTCCCAGTTTCATTCAGAGCT
65 CGAAGGATATTCAAGTCAAAGATCAACTTCACAACGAAGGGGCTTCCCAGTTTCATTCAGAGCT
* * *
441730 AATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACG
1 AATTTCAACTTCACGACGAAGGATATCGGA-TCGAAAC-ATACAAGATTGGATTTCAACTTCACG
* * *
441795 ACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGC
64 ACGAAGGATATTCAAGTCAAAGATCAACTTCACAACGAAGGGGC
441839 CATCCACAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
124 1 0.01
125 26 0.28
126 2 0.02
127 2 0.02
129 1 0.01
130 60 0.65
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (128 bp):
AATTTCAACTTCACGACGAAGGATATCGGATCGAAACATACAAGATTGGATTTCAACTTCACGAC
GAAGGATATTCAAGTCAAAGATCAACTTCACAACGAAGGGGCTTCCCAGTTTCATTCAGAGCT
Found at i:442162 original size:116 final size:116
Alignment explanation
Indices: 442023--442256 Score: 351
Period size: 116 Copynumber: 2.0 Consensus size: 116
442013 TAATCTTCAT
* * * * *
442023 ATTGGATTTCAACTTCACGACGAAGGATACCCAATTCAAGGCTTAATTTCACCATGAAAGGGCCA
1 ATTGGATTTCAACTTCACAACGAAGGATACCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCA
*
442088 TCCACGGTTTAAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTC
66 TCCACGGTTTAAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTC
* * *
442139 ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCA
1 ATTGGATTTCAACTTCACAACGAAGGATACCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCA
* * * *
442204 TCTACGGTTTCAACTTCACGACGAAGGGAAACGTGCTCACTAGTAACATTC
66 TCCACGGTTTAAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTC
442255 AT
1 AT
442257 CTTTAGATTG
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (116 bp):
ATTGGATTTCAACTTCACAACGAAGGATACCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCA
TCCACGGTTTAAACTTCACGACGAAGGGAAACGTGCTCACCAGCAACATTC
Found at i:442824 original size:23 final size:23
Alignment explanation
Indices: 442792--442845 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
442782 CTATACAAAT
442792 ATATATTTATATAA-ATTATTATTA
1 ATAT-TTTAT-TAATATTATTATTA
* *
442816 TTATTTTATTAATATTTTTATTA
1 ATATTTTATTAATATTATTATTA
442839 ATATTTT
1 ATATTTT
442846 TGCACCCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTTTATTAATATTATTATTA
Found at i:442836 original size:12 final size:12
Alignment explanation
Indices: 442792--442846 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
442782 CTATACAAAT
*
442792 ATATATTTATATA
1 ATATTTTTAT-TA
*
442805 A-ATTATTATTA
1 ATATTTTTATTA
*
442816 TTA-TTTTATTA
1 ATATTTTTATTA
442827 ATATTTTTATTA
1 ATATTTTTATTA
442839 ATATTTTT
1 ATATTTTT
442847 GCACCCCACT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 11 0.31
12 23 0.66
13 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTTTTATTA
Found at i:451865 original size:30 final size:28
Alignment explanation
Indices: 451818--451903 Score: 109
Period size: 30 Copynumber: 3.0 Consensus size: 28
451808 TATTTAAGTT
451818 TAAAGTATCTTTTTATCAAAATAGATATC
1 TAAAGTAT-TTTTTATCAAAATAGATATC
* *
451847 TAAAGTTATTTTCTTATCAAAATAGTTATT
1 TAAAG-TATTTT-TTATCAAAATAGATATC
* *
451877 TAAAATATTTTTTACCAAAATAGATAT
1 TAAAGTATTTTTTATCAAAATAGATAT
451904 TCAATCATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.28
29 14 0.28
30 22 0.44
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (28 bp):
TAAAGTATTTTTTATCAAAATAGATATC
Found at i:452051 original size:28 final size:29
Alignment explanation
Indices: 451986--452060 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
451976 TGAAAAAATT
* * *
451986 AAATACTTTAAATATTTGTTTTGACAAAA
1 AAATATTTTAAATACTTGTTTTAACAAAA
* *
452015 ATATAATTTTAAATACTT-TTTTAATAAAA
1 AAAT-ATTTTAAATACTTGTTTTAACAAAA
* *
452044 AAATATTTGAGATACTT
1 AAATATTTTAAATACTT
452061 AAATGAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 11 0.30
29 15 0.41
30 11 0.30
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (29 bp):
AAATATTTTAAATACTTGTTTTAACAAAA
Found at i:456640 original size:18 final size:19
Alignment explanation
Indices: 456614--456649 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
456604 CTAAATTATT
*
456614 TTAATAATTA-TAAAAATA
1 TTAAAAATTATTAAAAATA
456632 TTAAAAATTATTAAAAAT
1 TTAAAAATTATTAAAAAT
456650 TATATAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATTATTAAAAATA
Found at i:456643 original size:10 final size:10
Alignment explanation
Indices: 456614--456652 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
456604 CTAAATTATT
*
456614 TTAATAATTA
1 TTAAAAATTA
456624 -TAAAAA-TA
1 TTAAAAATTA
456632 TTAAAAATTA
1 TTAAAAATTA
456642 TTAAAAATTA
1 TTAAAAATTA
456652 T
1 T
456653 ATAGATTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.08
9 11 0.42
10 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:456691 original size:13 final size:13
Alignment explanation
Indices: 456673--456697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
456663 ACAAGAGTAA
456673 TATTTTTTAATAT
1 TATTTTTTAATAT
456686 TATTTTTTAATA
1 TATTTTTTAATA
456698 ATGATGAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTTTAATAT
Done.