Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 65
Found at i:3357432 original size:120 final size:118
Alignment explanation
Indices: 3357201--3357436 Score: 262
Period size: 120 Copynumber: 2.0 Consensus size: 118
3357191 ATTTTAATCC
* * *
3357201 TGTTTTAATATTTATTTATTTTTCAATATTAAGAAATGACAGTCTTAAAACAATAGGATGTCCAT
1 TGTTTTAATATTTATTTATTTTTCAATATGAAGAAAAGACAGTCTTAAAACAATAGGAAGTCCAT
* * *
3357266 TTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATAATAAT
66 TTTATGATATTTCTAAATAAAAAAATATCCTATTTTATAAATTATATAATAAT
* ** ** *
3357319 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGTTGTCTTAAGGCACCTA-GAAGT
1 TGTTTTAA-TATTTATTTATTTTTCAATAT-GAAGAAAAGA-CAGTCTTAAAACA-ATAGGAAGT
**
3357383 CC-TTTTATGATATTTCTAAATAAAAAAAAATATTTTA-TTTATAAATATATATAA
62 CCATTTTATGATATTTCTAAAT--AAAAAAATATCCTATTTTATAAAT-TATATAA
3357437 ATTAATATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
118 8 0.08
119 20 0.21
120 25 0.26
121 24 0.25
122 20 0.21
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (118 bp):
TGTTTTAATATTTATTTATTTTTCAATATGAAGAAAAGACAGTCTTAAAACAATAGGAAGTCCAT
TTTATGATATTTCTAAATAAAAAAATATCCTATTTTATAAATTATATAATAAT
Found at i:3357927 original size:20 final size:21
Alignment explanation
Indices: 3357904--3357944 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3357894 AGAAATTAAA
3357904 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTCAATTTTT
* *
3357924 AATTCTTTTCTTTCAATTTTT
1 AATTCATTTATTTCAATTTTT
3357945 TATGATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTCATTTATTTCAATTTTT
Found at i:3360482 original size:3 final size:3
Alignment explanation
Indices: 3360469--3360558 Score: 121
Period size: 3 Copynumber: 30.3 Consensus size: 3
3360459 TTACCCATTT
* * *
3360469 TTA TT- TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3360516 TTA TTA TTA -TA ATA TATA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
3360559 AAAAAAAATA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
2 4 0.05
3 70 0.91
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3362164 original size:126 final size:118
Alignment explanation
Indices: 3362034--3362407 Score: 346
Period size: 126 Copynumber: 3.1 Consensus size: 118
3362024 TTTCCTATTT
*
3362034 ATAAATTTAATTTTATAAATTACTTTTAAGAAAAATAATCATATTTTGATATTTATTTATTTTTA
1 ATAAA-TT-ATTTTATAAATTA-TTTTAA-AATAA-AAT-AT-TTTTGATATTTATTTATTTTTA
* * *
3362099 ATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTATGATATTTTTAAATAA
59 ATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCC-TTTTCTGATATTTATAAATAA
* * ** * * * *
3362160 ATAAATATCTTATTAAAATAAATTTTTATTTTAAGAAAATGTTTTGGTTATTTATTTATTTTTCA
1 ATAAAT-TATT-TT---ATAAATTATT-TTAAAATAAAATATTTTTGATATTTATTTATTTTT-A
* * *
3362225 ATATCAAAGAAAAGAGCTTTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTATGAATAA
59 ATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGC-CTTTTCTGATATTTATAAATAA
* *
3362286 ATAAA-TATCTTACT--A-TA--TTAAAATAAAATGTTTTTGATATTTATTTATTTTTTAATATC
1 ATAAATTATTTTA-TAAATTATTTTAAAATAAAATATTTTTGATATTTATTTA-TTTTTAATATC
* *
3362345 AAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCTTTTTTCTGATATTTCTAAATAA
64 AAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCC--TTTTCTGATATTTATAAATAA
*
3362402 GTAAAT
1 ATAAAT
3362408 ATCTTATTTA
Statistics
Matches: 207, Mismatches: 28, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
114 1 0.00
115 61 0.29
116 28 0.14
118 1 0.00
119 1 0.00
120 1 0.00
121 1 0.00
123 2 0.01
124 2 0.01
125 22 0.11
126 68 0.33
127 4 0.02
128 6 0.03
129 9 0.04
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (118 bp):
ATAAATTATTTTATAAATTATTTTAAAATAAAATATTTTTGATATTTATTTATTTTTAATATCAA
AGAAAAGAGCTGTCTTAAGGCACCTAGAAGCCTTTTCTGATATTTATAAATAA
Found at i:3362327 original size:115 final size:116
Alignment explanation
Indices: 3362195--3362413 Score: 341
Period size: 115 Copynumber: 1.9 Consensus size: 116
3362185 TTATTTTAAG
* * * *
3362195 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTTTCTTAAGGTACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
*
3362260 AG-CTCTTTTCTGATATTTATGAATAAATAAATATCTTACTATATTAAAAT
66 AGCCTCTTTTCTGATATTTATAAATAAATAAATATCTTACTATATTAAAAT
* *
3362310 AAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
* * *
3362375 AGCCTTTTTTCTGATATTTCTAAATAAGTAAATATCTTA
66 AGCCTCTTTTCTGATATTTATAAATAAATAAATATCTTA
3362414 TTTATGTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
115 61 0.66
116 32 0.34
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (116 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
AGCCTCTTTTCTGATATTTATAAATAAATAAATATCTTACTATATTAAAAT
Found at i:3362457 original size:115 final size:113
Alignment explanation
Indices: 3362224--3362457 Score: 247
Period size: 115 Copynumber: 2.0 Consensus size: 113
3362214 TTTATTTTTC
* * * *
3362224 AATATCAAAGAAAAGAGCTTTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTATGAATAAATA
1 AATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCTCTTTTCTGATATTTATAAATAAATA
* * * **
3362289 AATATCTTACTATATTAAAATAAAATGTTTTTGATATTTATTTATTTTTT
66 AATATCTTACTATATTAAAATAAAATATTTTTGAAAATTATTTA--TAAT
* * *
3362339 AATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCTTTTTTCTGATATTTCTAAATAAGT
1 AATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAG-CTCTTTTCTGATATTTATAAATAAAT
* * * * *
3362404 AAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAATTATTTGA-AAT
65 AAATATCTTACTATAT-TAAAATAAAATATTTT-TGAAAATTATTT-ATAAT
3362454 AATA
1 AATA
3362458 GAATTATGAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
115 44 0.45
116 44 0.45
117 9 0.09
118 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (113 bp):
AATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCTCTTTTCTGATATTTATAAATAAATA
AATATCTTACTATATTAAAATAAAATATTTTTGAAAATTATTTATAAT
Found at i:3366290 original size:15 final size:15
Alignment explanation
Indices: 3366261--3366304 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3366251 TTTGGGATCA
*
3366261 ATACCTTTTTGCATAC
1 ATACATTTTT-CATAC
3366277 ATACATTTTTCATAC
1 ATACATTTTTCATAC
* *
3366292 ATTCATTATTCAT
1 ATACATTTTTCAT
3366305 TTCATGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (15 bp):
ATACATTTTTCATAC
Found at i:3373653 original size:10 final size:10
Alignment explanation
Indices: 3373638--3373681 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
3373628 ATGCTTGAAG
3373638 AAAAAAAG-A
1 AAAAAAAGAA
*
3373647 AAAAAAAGATG
1 AAAAAAAGA-A
3373658 AAAAAAAGAA
1 AAAAAAAGAA
3373668 AAAAAAAGAA
1 AAAAAAAGAA
3373678 AAAA
1 AAAA
3373682 GGAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 8 0.26
10 14 0.45
11 9 0.29
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:3373662 original size:20 final size:19
Alignment explanation
Indices: 3373636--3373692 Score: 89
Period size: 20 Copynumber: 3.0 Consensus size: 19
3373626 TTATGCTTGA
3373636 AGAAAAAAAGAAAAAAAAG
1 AGAAAAAAAGAAAAAAAAG
3373655 ATGAAAAAAAGAAAAAAAA-
1 A-GAAAAAAAGAAAAAAAAG
*
3373674 AGAAAAAAGGAAAAAAAAG
1 AGAAAAAAAGAAAAAAAAG
3373693 GGTCAAGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 16 0.46
19 2 0.06
20 17 0.49
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (19 bp):
AGAAAAAAAGAAAAAAAAG
Found at i:3373693 original size:10 final size:9
Alignment explanation
Indices: 3373638--3373692 Score: 67
Period size: 9 Copynumber: 5.9 Consensus size: 9
3373628 ATGCTTGAAG
3373638 AAAAAAAGA
1 AAAAAAAGA
3373647 AAAAAAAGA
1 AAAAAAAGA
3373656 TGAAAAAAAGA
1 --AAAAAAAGA
3373667 AAAAAAA-A
1 AAAAAAAGA
*
3373675 GAAAAAAGGA
1 -AAAAAAAGA
3373685 AAAAAAAG
1 AAAAAAAG
3373693 GGTCAAGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 1 0.03
9 29 0.73
10 1 0.03
11 9 0.22
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:3375157 original size:115 final size:115
Alignment explanation
Indices: 3374955--3375302 Score: 599
Period size: 115 Copynumber: 3.0 Consensus size: 115
3374945 TTGGAGCAAG
3374955 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3375020 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGA
*
3375070 TGAATGTGCTCATAGTAGAAATAAGAGGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
3375135 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGA
*
3375185 TGAATGTGCTCATAATAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * * * * * *
3375250 ATGATCTGGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGA
3375299 TGAA
1 TGAA
3375303 CTGCATGATC
Statistics
Matches: 221, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 25 0.11
115 196 0.89
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (115 bp):
TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGA
Found at i:3376201 original size:112 final size:113
Alignment explanation
Indices: 3375986--3376269 Score: 482
Period size: 112 Copynumber: 2.5 Consensus size: 113
3375976 TAGCAAAGAT
* *
3375986 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCGTCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCA-AGAAAAGTTCATAATGAGAAGAACTCATCTG
*
3376051 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
3376100 TCAAATCCATCATTTGATGGATCAGCTTTTCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAAGAAAAGTTCATAATGAGAAGAACTCATCTGA
3376165 A-AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
3376212 TCAAATCCATCATTTGATGGATCAACTTTTCC-AGAAAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAAG-AAAAGTTCATAATGAGAAGAACT
3376270 TGTTCAACTT
Statistics
Matches: 161, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
111 2 0.01
112 97 0.60
113 29 0.18
114 33 0.20
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAAGAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:3376298 original size:73 final size:73
Alignment explanation
Indices: 3376171--3376308 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
3376161 CTGAAAAAGA
* **
3376171 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
3376236 ACTTTTCC
66 ACTTTTCC
* ** *
3376244 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
3376308 A
65 A
3376309 GCATTACCAG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 3 0.05
73 54 0.95
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (73 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACTTTTCC
Found at i:3376327 original size:73 final size:73
Alignment explanation
Indices: 3376171--3376342 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
3376161 CTGAAAAAGA
* **
3376171 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* *
3376235 AACTTTTCC
65 AACATTACC
* ** *
3376244 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
*
3376309 GCATTACC
66 ACATTACC
**** *
3376317 AGTTCGAGTTCATAATAAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
3376343 CATCTGAAGA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 3 0.04
73 80 0.96
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACATTACC
Found at i:3376451 original size:113 final size:112
Alignment explanation
Indices: 3376244--3376582 Score: 441
Period size: 109 Copynumber: 3.0 Consensus size: 112
3376234 CAACTTTTCC
* * * * **
3376244 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
* **** *
3376309 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
66 ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
* * *
3376357 AGAAGAAGTTCATAATGAGAAGAATTTGCTCAACCTTTTGTTTAAATTCATCATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
* *
3376422 ACATTGCCAGGGAAAGTTCATAATGAGAAGAACTCATCT--A-AAGA
66 ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
* * * *
3376466 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
* *
3376531 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
66 ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
3376578 AGAAG
1 AGAAG
3376583 TTCACAATGA
Statistics
Matches: 197, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
109 96 0.49
110 2 0.01
111 2 0.01
112 9 0.05
113 88 0.45
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:3376452 original size:186 final size:185
Alignment explanation
Indices: 3376062--3376455 Score: 558
Period size: 186 Copynumber: 2.1 Consensus size: 185
3376052 AGAAGGAAGA
* **
3376062 AGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGC
1 AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGC
* * *
3376126 TTTTCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGA
66 ATTACCAAGTAGAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGA
* * *
3376191 AGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCCAG
131 AGAATTTGCTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
* * ** *
3376246 AAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGC
1 AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGC
* * *
3376311 ATTACC-AGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
66 ATTACCAAG-TAGAGTTCATAATAAGAAGAACTCATCTGAA-AAAGAAGAAGAAATTCATAATGA
* * * *
3376375 GAAGAATTTGCTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG
129 GAAGAATTTGCTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
*
3376432 GGAAAGTTCATAATGAGAAGAACT
1 AGAAAGTTCATAATGAGAAGAACT
3376456 CATCTAAAGA
Statistics
Matches: 184, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
184 6 0.03
185 85 0.46
186 93 0.51
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (185 bp):
AGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGC
ATTACCAAGTAGAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGA
AGAATTTGCTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTGCCAG
Found at i:3376774 original size:124 final size:124
Alignment explanation
Indices: 3376527--3376826 Score: 321
Period size: 124 Copynumber: 2.5 Consensus size: 124
3376517 CACTTGATGG
* *
3376527 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAGAAGTTCAC
1 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCAC
* * * * * * * *
3376588 AATGAGAAAAGCTTGTTCGACCTTTTACATAATTTTATCATAGAAGAAGATATATTAGC
66 AATGAGAAAAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGAAGATAGATCAAC
* *
3376647 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAACAACTCATCTGAAAAAGAAAGAAAAAGTTCAT
1 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCAC
** * *
3376712 AATGAGAGGAGCTTATTCAACCTTTTGA-ATGACTCTATCACAGAAGGAA-ATAGGTCAAC
66 AATGAGAAAAGCTTATTCAACCTTTT-ACATAACTCTATCACAGAA-GAAGATAGATCAAC
* * *
3376771 ATCATCC---CCAGCGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAAGAGAAGAA
1 ATCAACCTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
3376827 TTTACTCAAC
Statistics
Matches: 151, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
120 42 0.28
121 5 0.03
122 28 0.19
123 8 0.05
124 64 0.42
125 4 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (124 bp):
ATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCAC
AATGAGAAAAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGAAGATAGATCAAC
Found at i:3376978 original size:3 final size:3
Alignment explanation
Indices: 3376965--3377062 Score: 128
Period size: 3 Copynumber: 33.0 Consensus size: 3
3376955 TTACCCATTT
* * *
3376965 TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3377012 TAA TTA TTA TTA TTA -TA ATA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
3377057 TTA TTA
1 TTA TTA
3377063 AAAATAATAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
2 4 0.05
3 78 0.92
4 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3376988 original size:15 final size:15
Alignment explanation
Indices: 3376970--3377062 Score: 143
Period size: 15 Copynumber: 6.2 Consensus size: 15
3376960 CATTTTTATT
*
3376970 TTATTATTATAATAA
1 TTATTATTATTATAA
3376985 TTATTATTATTATAA
1 TTATTATTATTATAA
3377000 TTATTATTATTATAA
1 TTATTATTATTATAA
3377015 TTATTATTATTATAA
1 TTATTATTATTATAA
*
3377030 -TATATATTATTATTA
1 TTAT-TATTATTATAA
*
3377045 TTATTATTATTATTA
1 TTATTATTATTATAA
3377060 TTA
1 TTA
3377063 AAAATAATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
14 3 0.04
15 68 0.92
16 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:3378591 original size:126 final size:126
Alignment explanation
Indices: 3378484--3378838 Score: 287
Period size: 126 Copynumber: 2.9 Consensus size: 126
3378474 TATAAATTAC
* * * * *
3378484 TTTTAAGAAAAATAATCATATTTT-GATATTTATTTATTTTT-AATATCGAAGAAAATAGTTGTC
1 TTTTAAGAAAAAGAA-AATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTC
* *
3378547 TTAAGGCACCTAGAAGC-CATTTTATGATATTTTTAAATAAATAAATATCTTATTAAAATAAA
65 TTAAGGCACCTAGAAGCTC-TTTTATGATATTTGTAAATAAATAAATATATTATTAAAATAAA
* **** * *
3378609 TTTTTATTTTAAGAAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
1 TTTTAAGAAAAAGAAAATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
* * * * *
3378674 TAAGGTACCTAGAAGCTCTTTTCTGATATTTGTGAATAAATAAATATCTTACT---AT--A
66 TAAGGCACCTAGAAGCTCTTTTATGATATTTGTAAATAAATAAATATATTATTAAAATAAA
* * ** * *
3378730 --TT----AAAATAAAATGTTTTTTATATTTATTTATTTTTTAATATCAAAGAAAAGAGTTGTCT
1 TTTTAAGAAAAAGAAAATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
* * * * *
3378789 T-A---ACCTAGAAGCCCTTTTTCTGATATTTCTAAATAAGTAAATATCTTATT
66 TAAGGCACCTAGAAGCTC-TTTTATGATATTTGTAAATAAATAAATATATTATT
3378839 TATGTATATT
Statistics
Matches: 196, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
111 11 0.06
112 31 0.16
114 1 0.01
115 50 0.26
119 2 0.01
121 1 0.01
123 2 0.01
124 6 0.03
125 25 0.13
126 66 0.34
127 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (126 bp):
TTTTAAGAAAAAGAAAATATTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCT
TAAGGCACCTAGAAGCTCTTTTATGATATTTGTAAATAAATAAATATATTATTAAAATAAA
Found at i:3378760 original size:115 final size:112
Alignment explanation
Indices: 3378622--3378836 Score: 308
Period size: 115 Copynumber: 1.9 Consensus size: 112
3378612 TTATTTTAAG
3378622 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGA
1 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTT-A---ACCTAGA
* * *
3378687 AGCTC-TTTTCTGATATTTGTGAATAAATAAATATCTTACTATATTAAAAT
62 AGCCCTTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
* * *
3378737 AAAATGTTTT-TTATATTTATTTATTTTTTAATATCAAAGAAAAGAGTTGTCTTAACCTAGAAGC
1 AAAATGTTTTGGT-TATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAACCTAGAAGC
*
3378801 CCTTTTTCTGATATTTCTAAATAAGTAAATATCTTA
65 CCTTTTTCTGATATTTCTAAATAAATAAATATCTTA
3378837 TTTATGTATA
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
111 11 0.12
112 30 0.33
114 2 0.02
115 48 0.53
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (112 bp):
AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAACCTAGAAGCC
CTTTTTCTGATATTTCTAAATAAATAAATATCTTACTATATTAAAAT
Found at i:3382011 original size:11 final size:11
Alignment explanation
Indices: 3381995--3382033 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3381985 TTATACTTGA
3381995 AAAAAAAGAGG
1 AAAAAAAGAGG
* **
3382006 AAAAAATGAAA
1 AAAAAAAGAGG
3382017 AAAAAAAGAGG
1 AAAAAAAGAGG
3382028 AAAAAA
1 AAAAAA
3382034 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAGG
Found at i:3382022 original size:22 final size:21
Alignment explanation
Indices: 3381994--3382041 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 21
3381984 ATTATACTTG
3381994 AAAAAAAAGAGGAAAAAATGAA
1 AAAAAAAAGAGGAAAAAA-GAA
3382016 AAAAAAAAGAGGAAAAAAGAA
1 AAAAAAAAGAGGAAAAAAGAA
3382037 AAAAA
1 AAAAA
3382042 TTAAACCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAGGAAAAAAGAA
Found at i:3386844 original size:22 final size:22
Alignment explanation
Indices: 3386815--3386869 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3386805 ATCTACACTC
3386815 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
3386837 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3386859 TTCAAAGATGA
1 TTCAAAGATGA
3386870 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3387644 original size:76 final size:76
Alignment explanation
Indices: 3387545--3388258 Score: 1329
Period size: 76 Copynumber: 9.4 Consensus size: 76
3387535 CTATTTCCCA
3387545 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3387610 AGCCATAGGGT
66 AGCCTTAGGGT
3387621 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3387686 AACCTTAGGGT
66 AGCCTTAGGGT
3387697 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3387762 AGCCTTAGGGT
66 AGCCTTAGGGT
3387773 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
3387838 AGTCTTAGGGT
66 AGCCTTAGGGT
3387849 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3387914 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3387925 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3387990 AGCCTTAGGGT
66 AGCCTTAGGGT
*
3388001 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAATAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3388066 AGCCTTAGGGT
66 AGCCTTAGGGT
* * **
3388077 TATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAAACTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3388142 AGCCTTAGGGT
66 AGCCTTAGGGT
3388153 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3388218 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3388229 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
3388259 ATAAGACCTC
Statistics
Matches: 619, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 619 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3388427 original size:3 final size:3
Alignment explanation
Indices: 3388406--3388490 Score: 93
Period size: 3 Copynumber: 28.7 Consensus size: 3
3388396 TTTTTCATTC
* * * * *
3388406 TAT TAT TTT TAT TAA TAT TAT TAT TAT TAT TAT TA- AAT AAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3388452 TAT TAT TAT TAT TAT TCT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
3388491 AATTAAATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
2 3 0.04
3 65 0.93
4 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3388485 original size:22 final size:22
Alignment explanation
Indices: 3388406--3388490 Score: 102
Period size: 22 Copynumber: 3.9 Consensus size: 22
3388396 TTTTTCATTC
* *
3388406 TATTATTTTTATTAATATTAT-
1 TATTATTATTATTATTATTATA
* *
3388427 TATTATTATTATTA-AATAAATA
1 TATTATTATTATTATTAT-TATA
*
3388449 TATTATTATTATTATTATTCTA
1 TATTATTATTATTATTATTATA
3388471 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
3388491 AATTAAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 2 0.04
21 15 0.28
22 35 0.65
23 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTATTATTATTATA
Found at i:3390049 original size:120 final size:120
Alignment explanation
Indices: 3389932--3390164 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 120
3389922 ATTTTAATCC
* * * *
3389932 TGTTTTAA-TATTTATTTATTTTTCAATAT-TAAGAAATGA-CAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* *
3389994 TATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
66 -ATTTTCTGATATTTATAAATAAAAAAATATCCTA-TTTATAAATATATATATTAAT
* * ** **
3390050 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCGCCTAGAAGTC
1 TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
3390115 CTTTTCTGATATTTATAAATAAAAAAATATTTTATTTATAAATATATATA
66 ATTTTCTGATATTTATAAATAAAAAAATATCCTATTTATAAATATATATA
3390165 AATTAATATT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.30
120 43 0.45
121 16 0.17
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (120 bp):
TGTTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
ATTTTCTGATATTTATAAATAAAAAAATATCCTATTTATAAATATATATATTAAT
Found at i:3390061 original size:20 final size:19
Alignment explanation
Indices: 3390036--3390077 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3390026 CTATTTTATA
3390036 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
3390056 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
3390075 AAT
1 AAT
3390078 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:3390165 original size:29 final size:29
Alignment explanation
Indices: 3390128--3390190 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3390118 TTCTGATATT
3390128 TATAAATAAAAAAATATTTTAT-TTATAAA
1 TATAAATAAAAAAATATTTT-TGTTATAAA
* ** *
3390157 TATATATAAATTAATATTTTTGTTATAAT
1 TATAAATAAAAAAATATTTTTGTTATAAA
3390186 TATAA
1 TATAA
3390191 TTTTGAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TATAAATAAAAAAATATTTTTGTTATAAA
Found at i:3394861 original size:24 final size:25
Alignment explanation
Indices: 3394834--3394893 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
3394824 TAAAATAATT
3394834 TTTTAATAATTTAAT-T-TTGTAGTA
1 TTTTAATAATTTAATGTATTG-AGTA
* *
3394858 TTTTTAT-ATTTATTGTATTGAGTA
1 TTTTAATAATTTAATGTATTGAGTA
*
3394882 TCTTAATAATTT
1 TTTTAATAATTT
3394894 TTTTTATCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 6 0.21
24 16 0.55
25 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTTAATAATTTAATGTATTGAGTA
Found at i:3394950 original size:26 final size:25
Alignment explanation
Indices: 3394904--3394952 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3394894 TTTTTATCTC
**
3394904 TTTTATATTTTTAATCTAAATAAAT
1 TTTTATATTTTTAAAATAAATAAAT
*
3394929 TTTTATTTTTTTAAAATGAAATAA
1 TTTTATATTTTTAAAAT-AAATAA
3394953 GTCCTCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTATATTTTTAAAATAAATAAAT
Found at i:3405698 original size:18 final size:19
Alignment explanation
Indices: 3405663--3405699 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3405653 CACGGAATGT
3405663 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3405683 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3405700 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3407923 original size:56 final size:57
Alignment explanation
Indices: 3407837--3407950 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
3407827 ATTACCTAAA
3407837 GGATCTTCACAAGATCTTGGACCAGGATCAGATTCTTGG-TTTGCTGCAGAGGTGCT
1 GGATCTTCACAAGATCTTGGACCAGGATCAGATTCTTGGTTTTGCTGCAGAGGTGCT
*
3407893 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTGCTGCAGAGGTGCT
1 GGATCTTCACAAGATCTTGGACCAGGATCAGATTCTTGGTTTTGCTGCAGAGGTGCT
3407950 G
1 G
3407951 AAGGTTCCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 38 0.68
57 18 0.32
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (57 bp):
GGATCTTCACAAGATCTTGGACCAGGATCAGATTCTTGGTTTTGCTGCAGAGGTGCT
Found at i:3414284 original size:2 final size:2
Alignment explanation
Indices: 3414277--3414305 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3414267 ACCATATAAG
3414277 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3414306 TATTTTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3414641 original size:19 final size:18
Alignment explanation
Indices: 3414619--3414684 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 18
3414609 AAACAGACTT
3414619 AAAATAAAGGATGAATTGA
1 AAAATAAAGGAT-AATTGA
3414638 AAAATAAA-GA-AATTATGA
1 AAAATAAAGGATAA-T-TGA
*
3414656 AAAATTAAGGGACTAAATTGA
1 AAAA-TAAAGGA-T-AATTGA
3414677 AAAATAAA
1 AAAATAAA
3414685 AAATTATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
16 2 0.05
17 1 0.03
18 9 0.24
19 11 0.29
20 5 0.13
21 7 0.18
22 1 0.03
23 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (18 bp):
AAAATAAAGGATAATTGA
Found at i:3419251 original size:23 final size:23
Alignment explanation
Indices: 3419225--3419299 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
3419215 GTCGAAGGTT
3419225 CTATGTGGTCCTTCGAGACAAAA
1 CTATGTGGTCCTTCGAGACAAAA
* *
3419248 CTATGTGGTCTTTCGGGACAAAA
1 CTATGTGGTCCTTCGAGACAAAA
3419271 CTATGTGGTCCTTC-AGGAC-AAA
1 CTATGTGGTCCTTCGA-GACAAAA
3419293 -TATGTGG
1 CTATGTGG
3419300 CACTTCGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.15
22 3 0.06
23 37 0.79
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGAGACAAAA
Found at i:3425664 original size:44 final size:44
Alignment explanation
Indices: 3425616--3425717 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 44
3425606 ATATTTTATA
*
3425616 AACATGTATCGATATATGATAATTTAAAAAAATTGTAATAATAT
1 AACATGTATCGATATATGATAATTTAAAAAAATTGCAATAATAT
* *
3425660 AACATATATTGATATATGATAATTTAAAAAAATTGCAATAATAT
1 AACATGTATCGATATATGATAATTTAAAAAAATTGCAATAATAT
3425704 AACATGTATCGATA
1 AACATGTATCGATA
3425718 CATCATAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (44 bp):
AACATGTATCGATATATGATAATTTAAAAAAATTGCAATAATAT
Found at i:3428164 original size:18 final size:19
Alignment explanation
Indices: 3428122--3428165 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3428112 TTATTTAACT
* *
3428122 TTATTTATAATTTTTTATA
1 TTATTTATAATTTTTAAAA
3428141 TATATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
3428160 TTATTT
1 TTATTT
3428166 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:3429939 original size:18 final size:18
Alignment explanation
Indices: 3429916--3429984 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
3429906 ACGTAGAATT
*
3429916 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3429934 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
3429952 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3429970 TGTCCCAAAGGACCA
1 TGTCCCGAAGGACCA
3429985 TTGATAATCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3432642 original size:2 final size:2
Alignment explanation
Indices: 3432635--3432664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3432625 CTGACTTTAG
3432635 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
3432665 CTTATACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3433954 original size:18 final size:18
Alignment explanation
Indices: 3433933--3434011 Score: 122
Period size: 18 Copynumber: 4.4 Consensus size: 18
3433923 TGTCCCATAA
*
3433933 GACCACTATGTCTCGAAG
1 GACCACTATGTCCCGAAG
* *
3433951 GACCACTGTGTCTCGAAG
1 GACCACTATGTCCCGAAG
*
3433969 GACCACTATGTCCCAAAG
1 GACCACTATGTCCCGAAG
3433987 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
3434005 GACCACT
1 GACCACT
3434012 GATAATCCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
GACCACTATGTCCCGAAG
Found at i:3435996 original size:21 final size:21
Alignment explanation
Indices: 3435970--3436011 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3435960 TTATTATTAT
3435970 TATATATATAATTATAATAAATG
1 TATATA-AT-ATTATAATAAATG
*
3435993 TATATAATATTATATTAAA
1 TATATAATATTATAATAAA
3436012 CATATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATATAATATTATAATAAATG
Found at i:3436117 original size:16 final size:16
Alignment explanation
Indices: 3436096--3436139 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3436086 TGAGTATGTA
*
3436096 ATTTATTATTATATAT
1 ATTTATTAATATATAT
3436112 ATTTATTAATATATAT
1 ATTTATTAATATATAT
*
3436128 ATATATATAATA
1 ATTTAT-TAATA
3436140 AATTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATTAATATATAT
Found at i:3436146 original size:20 final size:21
Alignment explanation
Indices: 3436100--3436146 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
3436090 TATGTAATTT
* *
3436100 ATTAT-TATATATATTTATTA
1 ATTATATATATATATTAATAA
3436120 A-TATATATATATATATAATAA
1 ATTATATATATATAT-TAATAA
3436141 ATTATA
1 ATTATA
3436147 ATTTAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 10 0.45
21 5 0.23
22 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATATATATATATTAATAA
Found at i:3439192 original size:31 final size:31
Alignment explanation
Indices: 3439157--3439219 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3439147 ACACGAAAGC
*
3439157 CAAATTCGCAACACAGATTTCGAATTCGCAA
1 CAAATTCGCAACACAGATTTCAAATTCGCAA
* *
3439188 CAAATTCGCAACTCAGTTTTCAAATTCGCAA
1 CAAATTCGCAACACAGATTTCAAATTCGCAA
3439219 C
1 C
3439220 TCGAATTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (31 bp):
CAAATTCGCAACACAGATTTCAAATTCGCAA
Found at i:3441155 original size:40 final size:40
Alignment explanation
Indices: 3441095--3441216 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
3441085 ACCGTAGTGC
3441095 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
3441135 TACACATAAGGTCGTACCCACCATATATACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
3441175 TACACATAAGGTCGTGCCCACTATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3441215 TA
1 TA
3441217 TAAACCTGCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3442124 original size:29 final size:29
Alignment explanation
Indices: 3442063--3442124 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
3442053 TTCCCAACTT
** * *
3442063 TTTTCAAAATTATGAAATGGTCCACTAAC
1 TTTTCAAAATTACAAAATGGTCCACCAAA
3442092 TTTTCAAAAATTACAAAATGGTCC-CCAAA
1 TTTTC-AAAATTACAAAATGGTCCACCAAA
3442121 TTTT
1 TTTT
3442125 TATAAGGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (29 bp):
TTTTCAAAATTACAAAATGGTCCACCAAA
Found at i:3443445 original size:18 final size:18
Alignment explanation
Indices: 3443422--3443527 Score: 151
Period size: 18 Copynumber: 5.9 Consensus size: 18
3443412 GCATAGAATT
*
3443422 TGTCCCGTAA-GACCACAA
1 TGTCCCG-AAGGACCACTA
* *
3443440 TGTCCCAAAGGACCACTG
1 TGTCCCGAAGGACCACTA
3443458 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3443476 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3443494 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3443512 TATCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
3443528 GTAGACCCTC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
17 2 0.02
18 79 0.98
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3447900 original size:18 final size:17
Alignment explanation
Indices: 3447877--3447928 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 17
3447867 GCGTAGAATT
3447877 TGTCCCGTAAGACCACTA
1 TGTCCCG-AAGACCACTA
3447895 TGTCCCGAAAGACCACTA
1 TGTCCCG-AAGACCACTA
3447913 TGTCCCGAAGGACCAC
1 TGTCCCGAA-GACCAC
3447929 GTAGACCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.06
18 30 0.94
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (17 bp):
TGTCCCGAAGACCACTA
Found at i:3448920 original size:64 final size:63
Alignment explanation
Indices: 3448797--3448937 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
3448787 CCATTGACGG
* * *
3448797 GTGCATCGATGCACTATCTATGCATCGGTGCATAAATCCCATTCGATGTTTGTATTTT-AAGTG
1 GTGCATCGATGCACTATCTATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTTAAAG-A
* **
3448860 GTTGCATCGATGCACT-CCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCT-TCTTTAAA
1 G-TGCATCGATGCACTATC-TATGCATCGATGCA-TAAATCCCATTCGATGTTTCTAT-TTTAAA
3448922 GA
62 GA
3448924 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3448938 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 16 0.24
64 47 0.70
65 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (63 bp):
GTGCATCGATGCACTATCTATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTTAAAGA
Found at i:3452357 original size:18 final size:18
Alignment explanation
Indices: 3452334--3452457 Score: 187
Period size: 18 Copynumber: 6.9 Consensus size: 18
3452324 GCATAGAATT
3452334 TGTCCCGTAA-GACCACTA
1 TGTCCCG-AAGGACCACTA
*
3452352 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* **
3452370 TTTCCCGAAGGACCTTTA
1 TGTCCCGAAGGACCACTA
*
3452388 TATCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3452406 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3452424 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3452442 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
3452458 GTAGACCCTC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
17 2 0.02
18 94 0.98
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3453449 original size:64 final size:63
Alignment explanation
Indices: 3453326--3453466 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
3453316 CCCTTGACGG
* * *
3453326 GTGCATCGATGCACTATCTATGCATCGGTGCATAAATCCCATTCGATGTTTGTATTTT-AAGTG
1 GTGCATCGATGCACTATCTATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTTAAAG-A
* **
3453389 GTTGCATCGATGCACT-CCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCT-TCTTTAAA
1 G-TGCATCGATGCACTATC-TATGCATCGATGCA-TAAATCCCATTCGATGTTTCTAT-TTTAAA
3453451 GA
62 GA
3453453 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3453467 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
63 16 0.24
64 47 0.70
65 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (63 bp):
GTGCATCGATGCACTATCTATGCATCGATGCATAAATCCCATTCGATGTTTCTATTTTAAAGA
Found at i:3455013 original size:34 final size:35
Alignment explanation
Indices: 3454969--3455039 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
3454959 TTCAAAAACA
*
3454969 AATC-ATTTTTCCTAAAAAAAACAATATTTCTTTT
1 AATCAATTTTCCCTAAAAAAAACAATATTTCTTTT
* * *
3455003 AATCAATTTTCCCTCAAAAAAATAATCTTTCTTTT
1 AATCAATTTTCCCTAAAAAAAACAATATTTCTTTT
3455038 AA
1 AA
3455040 AGTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.12
35 28 0.88
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (35 bp):
AATCAATTTTCCCTAAAAAAAACAATATTTCTTTT
Found at i:3455125 original size:23 final size:24
Alignment explanation
Indices: 3455080--3455129 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
3455070 ATCTTTTATA
3455080 TATATTTTAAAATTTTAAGTTAAAT
1 TATATTTTAAAATTTTAAGTT-AAT
3455105 TATA-TTT-AAATTATTAA-TTAAT
1 TATATTTTAAAATT-TTAAGTTAAT
3455127 TAT
1 TAT
3455130 TACATACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 7 0.29
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTTTAAAATTTTAAGTTAAT
Found at i:3467362 original size:42 final size:41
Alignment explanation
Indices: 3467314--3467711 Score: 323
Period size: 42 Copynumber: 9.4 Consensus size: 41
3467304 ATAGGTCAAG
*
3467314 ATCTATAGCGGCGTTTTTGGAATAAACGCCTCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCT-AAAAGGTCAT
* *
3467356 ATCTATAGCGACGTTTTTGGAACAAACG-TTGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCT--AAAAGGTCAT
* * ** *
3467398 ACCTATAGCGACGTTTTTGGAACAAACGTTGTAAAAGATCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACG-CCTAAAAGGTCAT
* * * * * * *
3467440 ACCTATAGCGGCGTTTTTTGAACAAATGCCGCAAAAGATTGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCC-TAAAAG-GTCAT
* * * *
3467483 ATCTATAGCGGCATTTTTAGAACAAACACCGTAAAAGGTTAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCC-TAAAAGGTCAT
* * *
3467525 ATCTATAGCGGTGTTTTTAGAACAAACACAAC-AAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGC--CTAAAAGGTCAT
* * * *
3467567 AACTATAGCGGTGTTTTTGGAACAAACGCCGTAAAAGATCGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCC-TAAAAGGTC-AT
* * * * *
3467610 ATCTATAGAGGCATTTTTGGAACAAATGTCGTAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGAACAAACG-CCTAAAAGGTCAT
** ** *
3467652 ATCTATAGCGGAATTTTTGGAACAAATACCATAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCC-TAAAAGGTCAT
* *
3467694 ATCTATAACGACGTTTTT
1 ATCTATAGCGGCGTTTTT
3467712 TTATACAAAC
Statistics
Matches: 297, Mismatches: 47, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
40 1 0.00
41 2 0.01
42 226 0.76
43 65 0.22
44 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (41 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCTAAAAGGTCAT
Found at i:3467585 original size:169 final size:168
Alignment explanation
Indices: 3467298--3467711 Score: 497
Period size: 169 Copynumber: 2.4 Consensus size: 168
3467288 AACAAAAAAA
* * * *
3467298 GCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGAATAAACGCCTCAAAAGGTCATATCTATA
1 GCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTGGAACAAACACCT-AAAAGGTCATATCTATA
* **** * **
3467363 GCGACGTTTTTGGAACAAACGTTGCAAAAGGTCATACCTATAGCGACGTTTTTGGAACAAACGTT
64 GCGACGTTTTTAGAACAAACACAACAAAAGGTCATAACTATAGCGACGTTTTTGGAACAAACGCC
* * * *
3467428 GTAAAAGATC-ATACCTATAGCGGCGTTTTTTGAACAAAT
129 GTAAAAGATCGAGACCTATAGAGGCATTTTTGGAACAAAT
* * * *
3467467 GCCGCAAAAGATTGAGATCTATAGCGGCATTTTTAGAACAAACACCGTAAAAGGTTATATCTATA
1 GCCGCAAAAG-GTCAGATCTATAGCGGCATTTTTGGAACAAACACC-TAAAAGGTCATATCTATA
** **
3467532 GCGGTGTTTTTAGAACAAACACAACAAAAGGTCATAACTATAGCGGTGTTTTTGGAACAAACGCC
64 GCGACGTTTTTAGAACAAACACAACAAAAGGTCATAACTATAGCGACGTTTTTGGAACAAACGCC
*
3467597 GTAAAAGATCGAGATCTATAGAGGCATTTTTGGAACAAAT
129 GTAAAAGATCGAGACCTATAGAGGCATTTTTGGAACAAAT
* * * * * *
3467637 GTCGTAAAAGGTCAGATCTATAGCGGAATTTTTGGAACAAATACCATAAAAGGTCAGATCTATAA
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGAACAAACACC-TAAAAGGTCATATCTATAG
3467702 CGACGTTTTT
65 CGACGTTTTT
3467712 TTATACAAAC
Statistics
Matches: 204, Mismatches: 38, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
169 170 0.83
170 34 0.17
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (168 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGGAACAAACACCTAAAAGGTCATATCTATAGC
GACGTTTTTAGAACAAACACAACAAAAGGTCATAACTATAGCGACGTTTTTGGAACAAACGCCGT
AAAAGATCGAGACCTATAGAGGCATTTTTGGAACAAAT
Found at i:3467688 original size:127 final size:127
Alignment explanation
Indices: 3467316--3467725 Score: 430
Period size: 127 Copynumber: 3.2 Consensus size: 127
3467306 AGGTCAAGAT
* * * * *
3467316 CTATAGCGGCGTTTTTGGAATAAACGCC-TCAAAAGGTC-ATATCTATAGCGACGTTTTTGGAAC
1 CTATAGCGGCGTTTTTGGAACAAACGCCGT-AAAAGATCGAGATCTATAGCGGCATTTTTGGAAC
* * * **** * *
3467379 AAACGTTGCAAAAGGTCATACCTATAGC-GACGTTTTTGGAACAAACGTTGTAAAAGATCATAC
65 AAACGTCGTAAAAGGTCATATCTATAGCGGA-GTTTTTGGAACAAACACAATAAAAGGTCATAA
* * * * *
3467442 CTATAGCGGCGTTTTTTGAACAAATGCCGCAAAAGATTGAGATCTATAGCGGCATTTTTAGAACA
1 CTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGATCGAGATCTATAGCGGCATTTTTGGAACA
** * * * *
3467507 AACACCGTAAAAGGTTATATCTATAGCGGTGTTTTTAGAACAAACACAACAAAAGGTCATAA
66 AACGTCGTAAAAGGTCATATCTATAGCGGAGTTTTTGGAACAAACACAATAAAAGGTCATAA
* *
3467569 CTATAGCGGTGTTTTTGGAACAAACGCCGTAAAAGATCGAGATCTATAGAGGCATTTTTGGAACA
1 CTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGATCGAGATCTATAGCGGCATTTTTGGAACA
* * * * * * *
3467634 AATGTCGTAAAAGGTCAGATCTATAGCGGAATTTTTGGAACAAATACCATAAAAGGTCAGAT
66 AACGTCGTAAAAGGTCATATCTATAGCGGAGTTTTTGGAACAAACACAATAAAAGGTCATAA
* * **
3467696 CTATAACGACGTTTTTTTATACAAACGCCG
1 CTATAGCGGCGTTTTTGGA-ACAAACGCCG
3467726 CTAATTACCT
Statistics
Matches: 230, Mismatches: 50, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
126 31 0.13
127 188 0.82
128 11 0.05
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (127 bp):
CTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGATCGAGATCTATAGCGGCATTTTTGGAACA
AACGTCGTAAAAGGTCATATCTATAGCGGAGTTTTTGGAACAAACACAATAAAAGGTCATAA
Found at i:3471837 original size:20 final size:21
Alignment explanation
Indices: 3471812--3471863 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3471802 TTTTCCCAAT
*
3471812 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3471832 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3471853 TCGCAATGCGA
1 TCGCAATGCGA
3471864 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3471877 original size:20 final size:20
Alignment explanation
Indices: 3471852--3471986 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
3471842 AATTGGGAAA
3471852 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3471872 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3471892 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3471913 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
3471933 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
3471953 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
3471973 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3471987 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3471896 original size:61 final size:61
Alignment explanation
Indices: 3471849--3471980 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
3471839 GCGAATTGGG
* * * * *
3471849 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
3471910 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3471971 ATAATCGCAA
1 AAAATCGCAA
3471981 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3472183 original size:22 final size:22
Alignment explanation
Indices: 3472155--3472198 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3472145 ACTCTCTCAC
*
3472155 CCATCTCTGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
3472177 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
3472199 ATCTCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.25
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:3472204 original size:20 final size:21
Alignment explanation
Indices: 3472156--3472204 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3472146 CTCTCTCACC
* *
3472156 CATCTCTGACGAAATCCGTCT
1 CATCTCCGGCGAAATCCGTCT
3472177 CCATCTCCGGCGAAATCCGTCT
1 -CATCTCCGGCGAAATCCGTCT
3472199 -ATCTCC
1 CATCTCC
3472205 ATCTCTCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.24
22 19 0.76
ACGTcount: A:0.20, C:0.39, G:0.14, T:0.27
Consensus pattern (21 bp):
CATCTCCGGCGAAATCCGTCT
Found at i:3472515 original size:20 final size:20
Alignment explanation
Indices: 3472461--3472519 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3472451 GCGATTCTCT
**
3472461 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
3472481 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
3472501 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
3472520 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3472710 original size:25 final size:24
Alignment explanation
Indices: 3472656--3472710 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
3472646 TGTTTATTAT
* *
3472656 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTGCACAGTA
**
3472680 TAGTTTTTGGTATATCTAGCTTAGTA
1 T-GTTTTTGGTATATCT-GCACAGTA
3472706 TGTTT
1 TGTTT
3472711 ATTGTTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTGCACAGTA
Found at i:3473855 original size:18 final size:18
Alignment explanation
Indices: 3473834--3473878 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3473824 TCCACTTCGG
*
3473834 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3473852 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3473870 GAGCCATCA
1 GAGCCATCA
3473879 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3474266 original size:12 final size:13
Alignment explanation
Indices: 3474249--3474277 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3474239 GTTGTTAGTA
3474249 TTTGTTTTTGT-T
1 TTTGTTTTTGTCT
3474261 TTTGTTTTTGTCT
1 TTTGTTTTTGTCT
3474274 TTTG
1 TTTG
3474278 GTTGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.79
Consensus pattern (13 bp):
TTTGTTTTTGTCT
Found at i:3474359 original size:20 final size:20
Alignment explanation
Indices: 3474334--3474379 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3474324 TAGTTTACTT
*
3474334 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
3474354 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3474374 TCGCAA
1 TCGCAA
3474380 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3474388 original size:19 final size:20
Alignment explanation
Indices: 3474345--3474389 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3474335 CGCAACATGA
3474345 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
3474365 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
3474384 AAATGA
1 AAATGA
3474390 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:3474427 original size:19 final size:19
Alignment explanation
Indices: 3474373--3474469 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
3474363 GGAAATGGCT
3474373 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3474392 ATCACAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
3474406 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3474425 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3474439 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3474458 GTCGCAATGCGA
1 ATCGCAATGCGA
3474470 TTTGTGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 19 0.31
15 3 0.05
16 4 0.06
17 4 0.06
18 3 0.05
19 29 0.47
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3474463 original size:33 final size:33
Alignment explanation
Indices: 3474373--3474464 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
3474363 GGAAATGGCT
* *
3474373 ATCGCAATGCGAAATGAAAATCACAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3474406 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
3474439 ATCGCAATACGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3474465 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3474541 original size:20 final size:19
Alignment explanation
Indices: 3474507--3474562 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3474497 TTGCGATTTG
*
3474507 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3474526 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
3474546 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3474563 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3475021 original size:41 final size:41
Alignment explanation
Indices: 3474925--3475012 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
3474915 GACTCACCTG
* * *
3474925 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
3474967 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
3475008 TCATC
1 TCATC
3475013 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:3476566 original size:14 final size:14
Alignment explanation
Indices: 3476544--3476578 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3476534 GAAACTGACT
*
3476544 ATCGTAACGAGAAA
1 ATCGCAACGAGAAA
3476558 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
3476572 ATCGCAA
1 ATCGCAA
3476579 TGCGATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:3476633 original size:20 final size:20
Alignment explanation
Indices: 3476610--3476697 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
3476600 CGCTTTTCTA
3476610 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
3476630 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
3476650 ATTGCGATAGCCATTTTCAC
1 GTTGCGATAGCCATTTTCGC
*
3476670 TTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3476690 GTTGCGAT
1 GTTGCGAT
3476698 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 3 0.06
20 47 0.89
21 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:3476933 original size:20 final size:20
Alignment explanation
Indices: 3476908--3476999 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
3476898 TTGAAGATGA
3476908 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
*** *
3476928 TTGCGAAAGTCAGAATCTTG
1 TTGCGATTTTCAGAATCTCG
* **
3476948 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
3476969 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
3476989 TTGCGATTTTC
1 TTGCGATTTTC
3477000 CAAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:3478046 original size:13 final size:13
Alignment explanation
Indices: 3478024--3478057 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3478014 ATATAATCCT
3478024 GAAG-AAAAAGAA
1 GAAGAAAAAAGAA
3478036 GAAGAAAAAAGAA
1 GAAGAAAAAAGAA
3478049 GAAGAAAAA
1 GAAGAAAAA
3478058 GTCCCCGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAGAA
Found at i:3480340 original size:19 final size:18
Alignment explanation
Indices: 3480318--3480409 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 18
3480308 GGAAATTACT
3480318 ATCGCAATGCAAAATGAAA
1 ATCGCAATGC-AAATGAAA
*
3480337 ATCGCAATG---A-GAGA
1 ATCGCAATGCAAATGAAA
3480351 ATCGCAATGCGAAATGAAA
1 ATCGCAATGC-AAATGAAA
* * *
3480370 ATCACAACGC----GAAT
1 ATCGCAATGCAAATGAAA
*
3480384 TTCGCAATGCGAAATGAAA
1 ATCGCAATGC-AAATGAAA
3480403 ATCGCAA
1 ATCGCAA
3480410 CGAGGGAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 22 0.42
15 1 0.02
18 1 0.02
19 29 0.55
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (18 bp):
ATCGCAATGCAAATGAAA
Found at i:3480360 original size:33 final size:33
Alignment explanation
Indices: 3480318--3480431 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
3480308 GGAAATTACT
* *
3480318 ATCGCAATGCAAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3480351 ATCGCAATGCGAAATGAAAATCACAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3480383 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3480417 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
3480432 TAAATTCGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.01
33 68 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3480484 original size:19 final size:19
Alignment explanation
Indices: 3480462--3480520 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
3480452 GATTCCCTCG
*
3480462 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
3480481 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
3480495 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3480514 TTGCGAT
1 TTGCGAT
3480521 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
16 3 0.09
17 3 0.09
19 17 0.53
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3480484 original size:33 final size:33
Alignment explanation
Indices: 3480442--3480520 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
3480432 TAAATTCGTG
*
3480442 TTCGCGTTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTCCCTCATTGCGATTTTCAT
*
3480475 TTCGCGTTGCGATTCTCTCATTGCGATTTTCAT
1 TTCGCGTTGCGATTCCCTCATTGCGATTTTCAT
*
3480508 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
3480521 AGTACTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.43
Consensus pattern (33 bp):
TTCGCGTTGCGATTCCCTCATTGCGATTTTCAT
Found at i:3480646 original size:14 final size:14
Alignment explanation
Indices: 3480627--3480663 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3480617 CATCAATTAA
3480627 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3480641 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3480655 ACAAATCAA
1 ACAAATCAA
3480664 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3482070 original size:21 final size:21
Alignment explanation
Indices: 3482004--3482070 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3481994 GTGAATCGGG
*
3482004 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3482024 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3482046 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3482067 CTCT
1 CTCT
3482071 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3482465 original size:95 final size:84
Alignment explanation
Indices: 3482343--3482522 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 84
3482333 ATTTCAAACT
*
3482343 TTCAACCAAAACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAG
1 TTCAACCAAAACAAAACAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGC--
3482408 AATTGGCAGCAACCGAATAAATTTAC
60 -ATTGGCAGCAACCGAATAAATTTAC
3482434 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAT
1 TTCAACC-AAA-ACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAT
3482499 TGGCAGCAACCGAATAAATTTAC
62 TGGCAGCAACCGAATAAATTTAC
3482522 T
1 T
3482523 AACAATCTAA
Statistics
Matches: 84, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
88 26 0.31
91 21 0.25
92 3 0.04
93 7 0.08
95 27 0.32
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (84 bp):
TTCAACCAAAACAAAACAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCATTGGC
AGCAACCGAATAAATTTAC
Found at i:3484255 original size:19 final size:19
Alignment explanation
Indices: 3484208--3484280 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
3484198 TTGCAATGCG
3484208 GAAATGACTATCGCAA--C
1 GAAATGACTATCGCAACGC
*
3484225 GAGA-GA--ATCGCAACGC
1 GAAATGACTATCGCAACGC
3484241 GAAATGACTATCGCAACGC
1 GAAATGACTATCGCAACGC
** *
3484260 GAAATGAAAATCGCAATGC
1 GAAATGACTATCGCAACGC
3484279 GA
1 GA
3484281 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.15
16 6 0.13
17 5 0.11
19 28 0.61
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGACTATCGCAACGC
Found at i:3484892 original size:20 final size:21
Alignment explanation
Indices: 3484867--3484920 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
3484857 TGCTAGTAAG
*
3484867 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
*
3484887 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
3484908 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3484921 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACCTA
Found at i:3484934 original size:21 final size:21
Alignment explanation
Indices: 3484910--3485085 Score: 69
Period size: 21 Copynumber: 8.5 Consensus size: 21
3484900 TTTTCCTAAT
3484910 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTATGAAAA
** * *
3484931 TCGCAACGCGAA-TACGTAAA
1 TCGCATTGCGAATTATGAAAA
* * *
3484951 TCGCAATGCAAATTAGGAAAA
1 TCGCATTGCGAATTATGAAAA
* * **
3484972 TTGCATTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTA-TGAAAA
* * *
3484992 TCGCATTGCG-ATTTTCCAAAT
1 TCGCATTGCGAATTAT-GAAAA
* * *
3485013 TCGCATTGCGATTTACT--TAT
1 TCGCATTGCGAATTA-TGAAAA
**
3485033 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTATGAAAA
** *
3485054 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTATGAAAA
3485075 TCGCATTGCGA
1 TCGCATTGCGA
3485086 TAGTCATAAT
Statistics
Matches: 114, Mismatches: 32, Indels: 19
0.69 0.19 0.12
Matches are distributed among these distances:
19 2 0.02
20 46 0.40
21 59 0.52
22 6 0.05
23 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGAATTATGAAAA
Found at i:3484955 original size:41 final size:41
Alignment explanation
Indices: 3484910--3485085 Score: 106
Period size: 41 Copynumber: 4.3 Consensus size: 41
3484900 TTTTCCTAAT
*
3484910 TCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
* * * ** *
3484951 TCGCAATGCAAATTAGGAAAATTGCATTGCG-ATA-GTCAGTA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGT-A-AA
* *** * ** * * *
3484992 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTAC-TTAT
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGA-ATACGTAAA
* ** *
3485033 TCGCATTGCGAATTGGGAAAATCGCAACGCGAAATTGGAAAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCG-AATACGTAAA
3485075 TCGCATTGCGA
1 TCGCATTGCGA
3485086 TAGTCATAAT
Statistics
Matches: 96, Mismatches: 32, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
41 74 0.77
42 13 0.14
43 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (41 bp):
TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
Found at i:3485036 original size:20 final size:21
Alignment explanation
Indices: 3484992--3485043 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3484982 ATAGTCAGTA
*
3484992 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
3485013 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
3485033 TCGCATTGCGA
1 TCGCATTGCGA
3485044 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:3485055 original size:103 final size:102
Alignment explanation
Indices: 3484889--3485107 Score: 264
Period size: 103 Copynumber: 2.1 Consensus size: 102
3484879 ATTTACGTAT
* *
3484889 TCGCATTGCGATTTTCCTAATTCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAATCG
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGAATTAT-AAAATCGCAACGCGAATACGAAAATCG
* *
3484954 CAATGC-AAATTAGGAAAATTGCATTGCGATAGTCAGT-A
65 CAACGCGAAATT-GGAAAATCGCATTGCGATAGTCA-TAA
* * * ** **
3484992 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACT-TATTCGCATTGCGAATTGGGAAAATC
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGAATTA-TAAAATCGCAACGCGAA-TACGAAAATC
3485056 GCAACGCGAAATTGGAAAATCGCATTGCGATAGTCATAA
64 GCAACGCGAAATTGGAAAATCGCATTGCGATAGTCATAA
*
3485095 TCGCGTTGCGATT
1 TCGCATTGCGATT
3485108 CTGGAAACTG
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
102 12 0.12
103 82 0.82
104 6 0.06
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (102 bp):
TCGCATTGCGATTTTCCAAATTCGCATTGCGAATTATAAAATCGCAACGCGAATACGAAAATCGC
AACGCGAAATTGGAAAATCGCATTGCGATAGTCATAA
Found at i:3485389 original size:13 final size:13
Alignment explanation
Indices: 3485357--3485397 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
3485347 TATAAGGACT
3485357 AAAATATAAATATAC
1 AAAAT-TAAA-ATAC
3485372 AAAATTAAAATAC
1 AAAATTAAAATAC
*
3485385 CAAATTAAAATAC
1 AAAATTAAAATAC
3485398 GAATAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 16 0.64
14 4 0.16
15 5 0.20
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTAAAATAC
Found at i:3486525 original size:10 final size:10
Alignment explanation
Indices: 3486507--3486545 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
3486497 TCCATTTGTA
*
3486507 ATAAAAATAT
1 ATAATAATAT
3486517 ATAATAATAT
1 ATAATAATAT
*
3486527 ATATTAATAT
1 ATAATAATAT
3486537 ATAATAATA
1 ATAATAATA
3486546 ATACCAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:3486555 original size:20 final size:20
Alignment explanation
Indices: 3486511--3486557 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3486501 TTTGTAATAA
*
3486511 AAATATATAATAATATATAT
1 AAATATATAATAATATATAC
*
3486531 TAATATATAATAATA-ATACC
1 AAATATATAATAATATATA-C
3486551 AAATATA
1 AAATATA
3486558 CATTAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATATAATAATATATAC
Found at i:3490899 original size:21 final size:21
Alignment explanation
Indices: 3490870--3490909 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3490860 ATTTTATACT
3490870 GAGTATACCGATACACCTAGA
1 GAGTATACCGATACACCTAGA
*
3490891 GAGTGTACCGATACACCTA
1 GAGTATACCGATACACCTA
3490910 CGCTCCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
GAGTATACCGATACACCTAGA
Found at i:3500619 original size:21 final size:21
Alignment explanation
Indices: 3500580--3500619 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3500570 CATTTTTTTA
*
3500580 ATTTTGAAATATAATTTTTGT
1 ATTTTGAAATATAAGTTTTGT
3500601 ATTTTGAAA-ATAAAGTTTT
1 ATTTTGAAATAT-AAGTTTT
3500620 ATAATCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTTGAAATATAAGTTTTGT
Found at i:3506582 original size:13 final size:13
Alignment explanation
Indices: 3506559--3506597 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3506549 TAAACTACAT
*
3506559 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAA
3506573 ATTGTTTTCAAAA
1 ATTGTTTTCAAAA
*
3506586 ATAGTTTTCAAA
1 ATTGTTTTCAAA
3506598 TTTACCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAA
Found at i:3507403 original size:180 final size:180
Alignment explanation
Indices: 3507101--3507435 Score: 562
Period size: 180 Copynumber: 1.9 Consensus size: 180
3507091 ATAGGTATTC
* * *
3507101 GGTCTTATCTCTTAGGCCAATTTGTTTATATTGACTCTGACATAATCGTTAATATTTTTGGATCA
1 GGTCTTATCTCTTAGGCCAATTTGTTTATATTGACTCCGACACAATCGCTAATATTTTTGGATCA
* * * *
3507166 GATAACAACGGTTTAGATAATGAAAAAAATATTGTGGCTACCCAATATAAGGCTAAGGCAAGTGC
66 GATAACAACGATTTAGATAACGAAAAAAAGATTATGGCTACCCAATATAAGGCTAAGGCAAGTGC
3507231 GAGTACTTTATTGACTTATCACGAGCGATTCCTCCACTTGATTATCTCTT
131 GAGTACTTTATTGACTTATCACGAGCGATTCCTCCACTTGATTATCTCTT
* *
3507281 GGTCTTATCTCTTAGGCCAATTTGTTTTTATTGACTCCGACACAATCGCTAATATTTTTGGATTA
1 GGTCTTATCTCTTAGGCCAATTTGTTTATATTGACTCCGACACAATCGCTAATATTTTTGGATCA
* * *
3507346 GATAACAACGATTTAGATAACGAATAAAAGATTATGGCTACCCGATATAAGGCTAAGGCGAGTGC
66 GATAACAACGATTTAGATAACGAAAAAAAGATTATGGCTACCCAATATAAGGCTAAGGCAAGTGC
3507411 GAGTACTTTATTGACTTATCACGAG
131 GAGTACTTTATTGACTTATCACGAG
3507436 TTATAGATTT
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
180 143 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (180 bp):
GGTCTTATCTCTTAGGCCAATTTGTTTATATTGACTCCGACACAATCGCTAATATTTTTGGATCA
GATAACAACGATTTAGATAACGAAAAAAAGATTATGGCTACCCAATATAAGGCTAAGGCAAGTGC
GAGTACTTTATTGACTTATCACGAGCGATTCCTCCACTTGATTATCTCTT
Found at i:3508503 original size:20 final size:20
Alignment explanation
Indices: 3508480--3508518 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3508470 AATTTTTATC
3508480 CTTGTATGTACCGATACACT
1 CTTGTATGTACCGATACACT
*
3508500 CTTGTATGTATCGATACAC
1 CTTGTATGTACCGATACAC
3508519 CCCTACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
CTTGTATGTACCGATACACT
Found at i:3508701 original size:21 final size:21
Alignment explanation
Indices: 3508675--3508714 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3508665 ATTTTATACT
*
3508675 GAGTGTACCGATACACCTAGA
1 GAGTGTACCAATACACCTAGA
*
3508696 GAGTGTACTAATACACCTA
1 GAGTGTACCAATACACCTA
3508715 CGCTCCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
GAGTGTACCAATACACCTAGA
Found at i:3516512 original size:20 final size:20
Alignment explanation
Indices: 3516487--3516527 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3516477 TAATAACGGC
3516487 TAGACATAGTATCGATACCA
1 TAGACATAGTATCGATACCA
*
3516507 TAGACATAGTATTGATACCA
1 TAGACATAGTATCGATACCA
3516527 T
1 T
3516528 CAGGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
TAGACATAGTATCGATACCA
Found at i:3520798 original size:34 final size:33
Alignment explanation
Indices: 3520735--3520805 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
3520725 CCTTTACAAC
* *
3520735 TCCCTAGTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACACGAGATAAACTAGAACCTT
* *
3520768 TCCCTAGCTTTTACACGAGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTACACGAGATAAACTAGAACCTT
3520802 TCCC
1 TCCC
3520806 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (33 bp):
TCCCTAGTTTTACACGAGATAAACTAGAACCTT
Found at i:3521226 original size:19 final size:18
Alignment explanation
Indices: 3521161--3521228 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 18
3521151 GTTGCAGCTA
3521161 GGGGGTATGGATACCCCT
1 GGGGGTATGGATACCCCT
3521179 GGGGGTATCGG-TA-CCC-
1 GGGGGTAT-GGATACCCCT
*
3521195 -GGGCTATGGATACCCCT
1 GGGGGTATGGATACCCCT
*
3521212 AGGGGGTATGTATACCC
1 -GGGGGTATGGATACCC
3521229 TTTCTGCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.05
15 8 0.20
16 3 0.07
17 3 0.07
18 10 0.24
19 15 0.37
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.22
Consensus pattern (18 bp):
GGGGGTATGGATACCCCT
Found at i:3521546 original size:18 final size:18
Alignment explanation
Indices: 3521499--3521556 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
3521489 ATGTTTAATG
*
3521499 AAAAATATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
3521517 AACAAAATGATATCAATTGTT
1 -A-AAAA-GATACCAATTGTT
3521538 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
3521556 A
1 A
3521557 CAAATTGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 5 0.15
21 11 0.32
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:3522594 original size:20 final size:20
Alignment explanation
Indices: 3522569--3522618 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3522559 TCTAAATCAT
*
3522569 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTCGA
3522589 TTTTCAAAATTTCATTTCGA
1 TTTTCAAAATTTCATTTCGA
3522609 TTTTCAAAAT
1 TTTTCAAAAT
3522619 CAACTCTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTCGA
Found at i:3522690 original size:20 final size:20
Alignment explanation
Indices: 3522665--3522708 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3522655 TGAGTTTTGA
3522665 AATTAATTTCGTATAATTGG
1 AATTAATTTCGTATAATTGG
3522685 AATTAATTTCGTATAATTGG
1 AATTAATTTCGTATAATTGG
3522705 AATT
1 AATT
3522709 CATGGTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
AATTAATTTCGTATAATTGG
Found at i:3523536 original size:35 final size:35
Alignment explanation
Indices: 3523495--3523566 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3523485 TTTTTCAAGG
*
3523495 ACAAAGAGATAACCTTTATAACTCCCTAGTTTTTC
1 ACAAAGAGATAACCTTTACAACTCCCTAGTTTTTC
3523530 ACAAAGAGATAACCTTTACAACTCCCTAGTTTTTC
1 ACAAAGAGATAACCTTTACAACTCCCTAGTTTTTC
3523565 AC
1 AC
3523567 GTGATAAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (35 bp):
ACAAAGAGATAACCTTTACAACTCCCTAGTTTTTC
Found at i:3529283 original size:11 final size:10
Alignment explanation
Indices: 3529269--3529309 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
3529259 TTGCAATTCA
3529269 TTTATCTTTT
1 TTTATCTTTT
3529279 CTTTATCTTTT
1 -TTTATCTTTT
3529290 TTTAATCTTATT
1 TTT-ATCTT-TT
3529302 TTTATCTT
1 TTTATCTT
3529310 GTTTCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 20 0.71
12 5 0.18
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:3529537 original size:19 final size:19
Alignment explanation
Indices: 3529513--3529581 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
3529503 GTTGCAGCTA
3529513 GGGGGTATGGATACCCCTT
1 GGGGGTATGGATACCCCTT
3529532 GGGGGTATCGG-TA---C-T
1 GGGGGTAT-GGATACCCCTT
* *
3529547 CGGGGTATGGATACCCCTA
1 GGGGGTATGGATACCCCTT
*
3529566 GGGGGTACGGATACCC
1 GGGGGTATGGATACCC
3529582 TTTCTGCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 2 0.05
15 10 0.25
16 1 0.03
18 1 0.03
19 24 0.60
20 2 0.05
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (19 bp):
GGGGGTATGGATACCCCTT
Found at i:3531269 original size:24 final size:25
Alignment explanation
Indices: 3531242--3531303 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
3531232 TAATTTGCAT
3531242 CGAAGTG-CCACGTAGAATTTGTCC
1 CGAAGTGACCACGTAGAATTTGTCC
*
3531266 CGAAG-GACCGCGTAGAATTTGTCC
1 CGAAGTGACCACGTAGAATTTGTCC
3531290 CGAA-TGACCACGTA
1 CGAAGTGACCACGTA
3531304 AAAAAGTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (25 bp):
CGAAGTGACCACGTAGAATTTGTCC
Found at i:3538195 original size:81 final size:80
Alignment explanation
Indices: 3538062--3538221 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 80
3538052 ACTACTCTAG
* * * *
3538062 TGTAGACTCTGCAGACATGATGTAAGTCATCATCTATTTTGTTAATTAATGAGAAATCAGAGGAG
1 TGTAGACCCGGCAGACATGATGTAAGTCATCATCCATTTTGTTAATTAATGAGAAACCAGAGGAG
3538127 CTTGAAT-GGAATTT
66 CTTGAATGGGAATTT
*
3538141 TGTAGACCCGGCAGACATGGTGTAA-TGCAAGTCATCCATTTTGTTAATTAATGAGAAACCAGAG
1 TGTAGACCCGGCAGACATGATGTAAGT-C-A-TCATCCATTTTGTTAATTAATGAGAAACCAGAG
*
3538205 GCGCTTGAATGGGAATT
63 GAGCTTGAATGGGAATT
3538222 CTATATACCC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.01
79 23 0.32
80 1 0.01
81 40 0.56
82 6 0.08
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (80 bp):
TGTAGACCCGGCAGACATGATGTAAGTCATCATCCATTTTGTTAATTAATGAGAAACCAGAGGAG
CTTGAATGGGAATTT
Found at i:3538401 original size:23 final size:23
Alignment explanation
Indices: 3538354--3538403 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3538344 AATAACATAT
**
3538354 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
3538377 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
3538400 TAGG
1 TAGG
3538404 CATTTAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:3538458 original size:23 final size:23
Alignment explanation
Indices: 3538432--3538479 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3538422 ATCAAGTACA
3538432 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
3538455 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
3538478 AT
1 AT
3538480 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:3539576 original size:20 final size:20
Alignment explanation
Indices: 3539532--3539580 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3539522 CGGTAGCTTT
*
3539532 TTACCGGTTTTATCATTTCGA
1 TTACCTGTTTTATCATTTC-A
3539553 -TACCTGTTTTATCATATT-A
1 TTACCTGTTTTATCAT-TTCA
3539572 TTACCTGTT
1 TTACCTGTT
3539581 ATATTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.51
Consensus pattern (20 bp):
TTACCTGTTTTATCATTTCA
Found at i:3540700 original size:182 final size:181
Alignment explanation
Indices: 3539328--3540686 Score: 2007
Period size: 182 Copynumber: 7.6 Consensus size: 181
3539318 ATTAAAGTAC
* ** * *
3539328 CGACACTTTCAACATA-CCGGTAGCGCTTTACCGG-TTTGTCATTTCGATACC-GTTTT-T--TA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * *
3539387 TTTTTACCTATTATATTGTTATGGATCGATACATTT-TCATAAAGTATCGACACTTTTTAGGCGC
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
* *
3539451 TATAATTTCTTCTCTTTTAAATTACTAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTA-AAAAGTGTCGATACTTATATTAATTTAT
* * * *
3539504 CGATACTTTTAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGATACCTGTTTTATCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * *
3539569 TTATTACCTGTTATATTGTTATGGATCGATACATTTGTATAAAATATCGATACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
3539634 ATAACTTCTTCTCTTTTAAATATAAAAAGTGTCGATAATTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TAAAAAGTGTCGATACTTATATTAATTTAT
*
3539686 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGCTTTATCATTTCGAGA-C----TTG---T-
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
*
3539742 TTGTTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
3539807 ATAACTTCTTCTCTTTTAAATTAAAAAATGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTAAAAAGTGTCGATACTTATATTAATTTAT
*
3539858 CGACACTTTCAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* *
3539923 TTATTATCTGTTATATTGCTATAGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
3539988 ATAACTTCTTCTCTTTTAAATATAAAAAGTGTCGATAATTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TAAAAAGTGTCGATACTTATATTAATTTAT
* *
3540040 CGACACTTTCAATATATCTGGTAGCTTTTTACCGGTTTTATCATTTCGATACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* * *
3540105 TTATTACCTGTTATATTGATATGGATTGATACATTTGTATAAAGTATAGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
3540170 ATAACTTCTTCTCTTTTAAATATCAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAAT-TAAAAAGTGTCGATACTTATATTAATTTAT
* * * * * *
3540222 AGACACTTTCAATATATCTGGTATCTTTGTACCAGTTTTATCATTTCGAGACCTGTTTTGTTATA
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
* *
3540287 TTATTACCTGTTATATTGTTATGGATCGATACATTAGTATAAAGTATCGACACTTTTTAGGCGCT
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
*
3540352 ATAACTTCTTCTCTTTTAAATTAAAAAAGTGTCGATACTTACATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATT-AAAAAGTGTCGATACTTATATTAATTTAT
** * * * *
3540404 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACATCGGTTTTGTCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
*
3540468 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTATAGGCGC
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGC
*
3540533 TATAACTTCTTCTCTTTTAAATTACAAAAGTGACGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTA-AAAAGTGTCGATACTTATATTAATTTAT
** * * * *
3540586 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCAT
* *
3540650 ATTTTTACTTGTTATATTGCTATGGATCGATACATTT
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTT
3540687 TTCATTTGTA
Statistics
Matches: 1088, Mismatches: 74, Indels: 36
0.91 0.06 0.03
Matches are distributed among these distances:
172 77 0.07
173 83 0.08
174 1 0.00
176 13 0.01
177 21 0.02
178 16 0.01
179 5 0.00
180 2 0.00
181 86 0.08
182 780 0.72
183 4 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
CGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
TTATTACCTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTCTTCTCTTTTAAATTAAAAAGTGTCGATACTTATATTAATTTAT
Found at i:3545526 original size:2 final size:2
Alignment explanation
Indices: 3545519--3545601 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
3545509 TTGTAATGTG
3545519 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3545558 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
3545600 AT
1 AT
3545602 TATGGTTAGA
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 75 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3547728 original size:27 final size:27
Alignment explanation
Indices: 3547664--3547735 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
3547654 TCTACTTTGT
*
3547664 TTACTTTAATTATTTTTCATTATTTTCCA
1 TTACTTTCATTATTTTT-ATTATTTT-CA
*
3547693 TT--TTCCATTTATTTTTATTATTTT-A
1 TTACTTTCA-TTATTTTTATTATTTTCA
3547718 TTACTTTCATTATTTTTA
1 TTACTTTCATTATTTTTA
3547736 AACCCCCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 3 0.08
26 9 0.24
27 15 0.41
28 8 0.22
29 2 0.05
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (27 bp):
TTACTTTCATTATTTTTATTATTTTCA
Found at i:3555740 original size:20 final size:20
Alignment explanation
Indices: 3555697--3555733 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3555687 TTTAAATATG
*
3555697 TTGAGTTTCTGTTGAATACC
1 TTGAGTTTCTGTTGAACACC
3555717 TTGAGTTT-TGTTGAACA
1 TTGAGTTTCTGTTGAACA
3555734 TCTTTGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (20 bp):
TTGAGTTTCTGTTGAACACC
Found at i:3555762 original size:47 final size:47
Alignment explanation
Indices: 3555723--3555821 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
3555713 TACCTTGAGT
* *
3555723 TTTGTTGAACATCTTTGAATGCCATGAAAGTCTTGAATACATTTCTG
1 TTTGATGAACATCTTTGAATGCCATGAAAGTCTTGAATACATTACTG
* *
3555770 TTTGATGAACATCTTTGATTGCCATGAAAGTCTTGAATACATTTCTG
1 TTTGATGAACATCTTTGAATGCCATGAAAGTCTTGAATACATTACTG
3555817 TTTGA
1 TTTGA
3555822 ATTAAGATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (47 bp):
TTTGATGAACATCTTTGAATGCCATGAAAGTCTTGAATACATTACTG
Found at i:3565111 original size:34 final size:35
Alignment explanation
Indices: 3565073--3565139 Score: 111
Period size: 34 Copynumber: 1.9 Consensus size: 35
3565063 GTAGGTGTTG
3565073 CCTTGAGTAAGAGAAATT-ATCG-TAGGAATGTCTT
1 CCTTGAGTAAGAGAAATTAAT-GATAGGAATGTCTT
3565107 CCTTGAGTAAGAGAAATTAATGATAGGAATGTC
1 CCTTGAGTAAGAGAAATTAATGATAGGAATGTC
3565140 CGGTCTCGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 19 0.61
35 12 0.39
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (35 bp):
CCTTGAGTAAGAGAAATTAATGATAGGAATGTCTT
Found at i:3568835 original size:21 final size:21
Alignment explanation
Indices: 3568811--3568858 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3568801 TGAAGCAAGG
3568811 GAAGCAAAGAGAGCAGCAGCA
1 GAAGCAAAGAGAGCAGCAGCA
*** *
3568832 GAAGCAGCTAGAGCAGCAGTA
1 GAAGCAAAGAGAGCAGCAGCA
3568853 GAAGCA
1 GAAGCA
3568859 GTGGCAGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.33, T:0.04
Consensus pattern (21 bp):
GAAGCAAAGAGAGCAGCAGCA
Done.