Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006615.1 Hibiscus syriacus cultivar Beakdansim tig00016237_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: 123328
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1526 original size:43 final size:42
Alignment explanation
Indices: 1461--1545 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
1451 TGGCTTTAGA
*
1461 GAAGTTAGGAGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
*
1502 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGA--GAAAGTTATCCCCTACATGTAAAAGTTTTGTT
1546 TGATGCACCG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 10 0.26
43 18 0.46
44 11 0.28
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (42 bp):
GAAGTTAGGAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:1786 original size:14 final size:13
Alignment explanation
Indices: 1727--1788 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
1717 CATCTTTGTA
1727 TTTGCATTTGCAT
1 TTTGCATTTGCAT
1740 TTT-CATCTTGCATT
1 TTTGCAT-TTGCA-T
** *
1754 TTTAAATTTTCAT
1 TTTGCATTTGCAT
1767 TGTTGCATTTGCAT
1 T-TTGCATTTGCAT
1781 CTTTGCAT
1 -TTTGCAT
1789 AATTACATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
12 3 0.08
13 10 0.26
14 23 0.59
15 3 0.08
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (13 bp):
TTTGCATTTGCAT
Found at i:3635 original size:10 final size:10
Alignment explanation
Indices: 3622--3661 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
3612 ACTCAATCAA
*
3622 AAAAAGAAAAA
1 AAAAA-AAAAG
3633 AAAAAAAGAAG
1 AAAAAAA-AAG
3644 AAAAAAAAAG
1 AAAAAAAAAG
3654 AAAAAAAA
1 AAAAAAAA
3662 TTCAAGATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3638 original size:13 final size:13
Alignment explanation
Indices: 3620--3661 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
3610 ATACTCAATC
3620 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
*
3633 AAAAAAAGAAGAA
1 AAAAAAAGAAAAA
3646 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
3659 AAA
1 AAA
3662 TTCAAGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:3644 original size:16 final size:15
Alignment explanation
Indices: 3620--3658 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3610 ATACTCAATC
3620 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
3635 AAAAAGAAGAAAAAAA
1 AAAAA-AAGAAAAAAA
3651 AAGAAAAA
1 AA-AAAAA
3659 AAATTCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 14 0.64
17 3 0.14
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:6306 original size:75 final size:75
Alignment explanation
Indices: 6183--6427 Score: 330
Period size: 75 Copynumber: 3.3 Consensus size: 75
6173 AGCTAGAAAA
* * *
6183 AAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAAAAATTGGAATATTGATGTATTTTGAACGT
1 AAATGTTAGGGCATACTGAAAGCCCATTTCAATCAGAAATTGGAATATTGATGCATTTTGAACGT
*
6248 TTGTATTAGC
66 TTGTATCAGC
* * * * *
6258 AAATGTTGGGGCATGCTGAAAGCCCATTTGAATCAGAAATTGGAATATTGACGCATTTTAAACGT
1 AAATGTTAGGGCATACTGAAAGCCCATTTCAATCAGAAATTGGAATATTGATGCATTTTGAACGT
6323 TTGTATCAGC
66 TTGTATCAGC
* * * * *
6333 AAATGTTGGGGCATACTGAAAGCCCCTTTCAATCAG-AATCAGGAATGTTGGTGCATTTTGAACG
1 AAATGTTAGGGCATACTGAAAGCCCATTTCAATCAGAAAT-TGGAATATTGATGCATTTTGAACG
* *
6397 TATGTATCAAC
65 TTTGTATCAGC
6408 AAATGTTAGGGCATACTGAA
1 AAATGTTAGGGCATACTGAA
6428 GACCCACATC
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 3 0.02
75 148 0.98
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (75 bp):
AAATGTTAGGGCATACTGAAAGCCCATTTCAATCAGAAATTGGAATATTGATGCATTTTGAACGT
TTGTATCAGC
Found at i:7358 original size:54 final size:54
Alignment explanation
Indices: 7293--7504 Score: 361
Period size: 54 Copynumber: 3.9 Consensus size: 54
7283 TTGACCAGAA
* **
7293 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTATGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
*
7347 ATCTGGACAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
**
7401 ATCTGGGCAGAAGCCACAGGAAATTATGAATGTGTTGTCAAATGTTTTACAAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
*
7455 ATCTGGGCAGAAGCCACGGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
7505 GAACCAATGA
Statistics
Matches: 148, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 148 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
Found at i:7903 original size:22 final size:22
Alignment explanation
Indices: 7878--7938 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
7868 ATCTACATTC
7878 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
7900 TTCAAATATGATAAATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
7922 TTCAAAGATGAAAGATT
1 TTCAAAGATGATAGATT
7939 TATTGGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:8498 original size:118 final size:121
Alignment explanation
Indices: 8287--8536 Score: 341
Period size: 120 Copynumber: 2.1 Consensus size: 121
8277 CACTCAATGG
*
8287 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGTAGAAGAGAAGAAGTTCATAAT
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGTTCATAAT
* * *
8352 GAGAAGAACTTGTTCAACTTTTTGCTCGATTTTATCCCA-AAAGA-ATAGATCAGC
66 GAGAAGAACTTATTCAACTTTTTGCTCGATTATATCCCAGAAAGATATAAATCAGC
* * * *
8406 ATCAACTTTTCCAGAGAAATTTCATAATGAGAAGAACTTATCTGAAG-AG-GAAGAAG-TCTGTA
1 ATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGTTC-ATA
*
8468 ATGAGAAGAACTTATTCAACCTTTTT-CTCGATTATATCCCAGAAGGATATAAATCAGC
64 ATGAGAAGAACTTATTCAA-CTTTTTGCTCGATTATATCCCAGAAAGATATAAATCAGC
*
8526 ACCAACATTTC
1 ATCAACATTTC
8537 ACTACAAGAA
Statistics
Matches: 115, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
117 2 0.02
118 41 0.36
119 26 0.23
120 46 0.40
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (121 bp):
ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGTTCATAAT
GAGAAGAACTTATTCAACTTTTTGCTCGATTATATCCCAGAAAGATATAAATCAGC
Found at i:9146 original size:32 final size:33
Alignment explanation
Indices: 9110--9239 Score: 102
Period size: 32 Copynumber: 4.0 Consensus size: 33
9100 ACTAAATAAT
* *
9110 TTTGTTACAATTTGTTATTGTGA-AAAATATTA
1 TTTGTCACAATTTGTTATTTTGAGAAAATATTA
* ** * *
9142 TTTGTCACAATTTTTTTATAATGAGAAATTAATA
1 TTTGTCACAA-TTTGTTATTTTGAGAAAATATTA
* * * ** *
9176 TTTGTTATAAATTGTTATTTTGATTAAATA-AA
1 TTTGTCACAATTTGTTATTTTGAGAAAATATTA
* *
9208 TTTGTCAAAAGTTGTTATTTTGAGAAAATATT
1 TTTGTCACAATTTGTTATTTTGAGAAAATATT
9240 GAGACGAAAT
Statistics
Matches: 73, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
32 35 0.48
33 23 0.32
34 15 0.21
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (33 bp):
TTTGTCACAATTTGTTATTTTGAGAAAATATTA
Found at i:9328 original size:16 final size:16
Alignment explanation
Indices: 9307--9384 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
9297 GACTAAATAA
9307 ATTTGTTATAATTGATT
1 ATTTGTTATAATT-ATT
* *
9324 A-TTGTGAAAATATATT
1 ATTTGTTATAAT-TATT
*
9340 ATTTGTTATAATTTTT
1 ATTTGTTATAATTATT
** *
9356 ATATTGAGA-AATTAAT
1 AT-TTGTTATAATTATT
*
9372 ATTTATTATAATT
1 ATTTGTTATAATT
9385 TGTTATTATA
Statistics
Matches: 45, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
15 3 0.07
16 28 0.62
17 14 0.31
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTGTTATAATTATT
Found at i:13193 original size:276 final size:277
Alignment explanation
Indices: 12700--13478 Score: 1425
Period size: 277 Copynumber: 2.8 Consensus size: 277
12690 AATGATTAAC
12700 ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
1 ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
12765 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAACAAAAAAG
66 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAACAAAAAAG
* *
12830 TGGAGAAAAATAGTCATGACAATATACGCGATCACTATAGTTAAACTTTATAACTACAAATATAA
131 TGGAGAAAAATAGTCATGACAATATATGCTATCACTATAGTTAAACTTTATAACTACAAATATAA
* *
12895 TTTATCACAAAAACGTGAATATCATTATTTTTTGTGATAATATTTTTT-TAATAATTATTAACAC
196 TTTGTCACAAAAACGTGAATATCATTATTTTTTGTGACAATATTTTTTGTAATAATTATTAACAC
12959 TTATAGTTACAAAAAAA
261 TTATAGTTACAAAAAAA
* *
12976 ATATATAAGTACAAAAAAAATTTATTATAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
1 ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
*
13041 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAATAAAAAAG
66 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAACAAAAAAG
* *
13106 TGGAGAAAAATAGTCATGATAATTTATGCTATCACTATAGTTAAACTTTATAACTACAAATATAA
131 TGGAGAAAAATAGTCATGACAATATATGCTATCACTATAGTTAAACTTTATAACTACAAATATAA
13171 TTTGTCACAAAAACGTGAATATCATTATTTTTTGTGACAATATTTTTTGTAATAATTATTAACAC
196 TTTGTCACAAAAACGTGAATATCATTATTTTTTGTGACAATATTTTTTGTAATAATTATTAACAC
*
13236 TTATAGTTACAAAAATA
261 TTATAGTTACAAAAAAA
*
13253 ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAGTTTT
1 ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
* *
13318 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCGATACAACTTTTGAAACAAAAAAG
66 TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAACAAAAAAG
*
13383 TGGAGAAAAATAGTCATGACAATATATGTTATCACTATAGTTAAACTTTATAACTACAAATATAA
131 TGGAGAAAAATAGTCATGACAATATATGCTATCACTATAGTTAAACTTTATAACTACAAATATAA
13448 TTTGTCACAAAAACGTGAATATCATTATTTT
196 TTTGTCACAAAAACGTGAATATCATTATTTT
13479 GTAATAATTA
Statistics
Matches: 483, Mismatches: 19, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
276 234 0.48
277 249 0.52
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (277 bp):
ATATATAAGTACAAAAATAATTTATTACAAAAAACTTGAATTTTATTATTTGATGTGATAATTTT
TTCTATAAAAATAACTATAAATTATAATTATAAAAATTATCAATATAACTTTTGAAACAAAAAAG
TGGAGAAAAATAGTCATGACAATATATGCTATCACTATAGTTAAACTTTATAACTACAAATATAA
TTTGTCACAAAAACGTGAATATCATTATTTTTTGTGACAATATTTTTTGTAATAATTATTAACAC
TTATAGTTACAAAAAAA
Found at i:13281 original size:16 final size:19
Alignment explanation
Indices: 13237--13285 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
13227 TATTAACACT
*
13237 TATAGTTACAAAAATAATA
1 TATAATTACAAAAATAATA
*
13256 TATAAGTACAAAAATAAT-
1 TATAATTACAAAAATAATA
13274 T-T-ATTACAAAAA
1 TATAATTACAAAAA
13286 ACTTGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 1 0.04
19 16 0.59
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (19 bp):
TATAATTACAAAAATAATA
Found at i:14468 original size:139 final size:137
Alignment explanation
Indices: 14261--14621 Score: 478
Period size: 137 Copynumber: 2.6 Consensus size: 137
14251 ATATCAGCAC
** *
14261 CAACATTTCCAGATAAAGTTCATAATGAGAAGAA-TTATCTGAAGAGGAAGAAAAAGTTCATAAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAAT
* * * * * *
14325 GAGAAGAATTTGTTCGACCTTAG-CTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACCTC
66 GAGAAGAACTTGTTCAACCTT-GCCTTAATTCATCACATATGAAGTTGAATCAAAG-A-AACCTC
*
14389 TCTTGAGGAT
128 TCTTAAGGAT
* * * *
14399 CAACATTTTCAGAGGAAGTTCATAATGAGAATAACTCATCTGAATAGGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAAT
* * *
14464 GAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAACGATACCTTTCT
66 GAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAGAAACCTCTCT
14529 TAAGGAT
131 TAAGGAT
14536 CAACATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-AAACAAGTTCATA
1 CAACATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAA-AAGTTCATA
* *
14599 ATGAGAAGAACTTATTTAACCTT
64 ATGAGAAGAACTTGTTCAACCTT
14622 TTGCTAGATT
Statistics
Matches: 196, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
136 2 0.01
137 86 0.44
138 35 0.18
139 73 0.37
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (137 bp):
CAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAGAAACCTCTCT
TAAGGAT
Found at i:14877 original size:3 final size:3
Alignment explanation
Indices: 14847--14930 Score: 86
Period size: 3 Copynumber: 29.0 Consensus size: 3
14837 TGTCTCGTTT
* * * * *
14847 TTA TTT TTA TTA CT- TTA ATA TT- TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14893 TTA TTA TTA TTA TTA TTA TTA TGT- TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
14931 ATAAATAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 6 0.09
3 60 0.90
4 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:16569 original size:133 final size:131
Alignment explanation
Indices: 16419--16671 Score: 346
Period size: 133 Copynumber: 1.9 Consensus size: 131
16409 TATTTGCTTT
* *
16419 AATTTTATATAAATTA-TTTTAATTATGTTTTTATTTATTTATTTATTTTTTAAATATTAAGAAA
1 AATTATATATAAATTATTTTTAATTAT-TTTTTA-ATATTTATTTATTTTTT-AATATTAAGAAA
* * * * * * *
16483 GGGGTTGTCTTAAAGCAACTAGAAGTCTTTTTCTTATATTTTTAAATAAATAAATATCCTACTTT
63 GAGGATGTATTAAAGCAAATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATCCTACTTT
16548 TATA
128 TATA
*
16552 AATTATATATAATTTATTTTTTTAATTATTTTTTAATATTTATTTATTTTTTAATATTAAGAAAG
1 AATTATATATAAATTA--TTTTTAATTATTTTTTAATATTTATTTATTTTTTAATATTAAGAAAG
* *
16617 ATGATGTATTAAAGCAAATAGAAGTCATTTTCTGATATTTCTAAGTAAATAAATA
64 AGGATGTATTAAAGCAAATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATA
16672 ACTTATTTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
133 73 0.70
134 16 0.15
135 6 0.06
136 10 0.10
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (131 bp):
AATTATATATAAATTATTTTTAATTATTTTTTAATATTTATTTATTTTTTAATATTAAGAAAGAG
GATGTATTAAAGCAAATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATCCTACTTTTAT
A
Found at i:16591 original size:10 final size:10
Alignment explanation
Indices: 16569--16609 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
16559 TATAATTTAT
16569 TTTTTTAATTA
1 TTTTTTAA-TA
16580 TTTTTTAATA
1 TTTTTTAATA
*
16590 TTTATT--TA
1 TTTTTTAATA
16598 TTTTTTAATA
1 TTTTTTAATA
16608 TT
1 TT
16610 AAGAAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.27
10 11 0.42
11 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:16598 original size:18 final size:18
Alignment explanation
Indices: 16572--16609 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16562 AATTTATTTT
16572 TTTAATTATTTTTTAATA
1 TTTAATTATTTTTTAATA
*
16590 TTTATTTATTTTTTAATA
1 TTTAATTATTTTTTAATA
16608 TT
1 TT
16610 AAGAAAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTATTTTTTAATA
Found at i:16703 original size:133 final size:136
Alignment explanation
Indices: 16435--16703 Score: 341
Period size: 133 Copynumber: 2.0 Consensus size: 136
16425 ATATAAATTA
* * * *
16435 TTTTAATTATGTTTTTATTTATTTATTTATTTTTTAAATATTAAGAAAGGGGTTGTCTTAAAGCA
1 TTTTAATTATGTTTTTATATATTTATTTATTTTTTAAATATTAAGAAAGAGGATGTATTAAAGCA
* * * * * * *
16500 ACTAGAAGTCTTTTTCTTATATTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATAAT
66 AATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATAACCTACTTTTATAAATAAAATATAAT
*
16565 TTATTT
131 ATATTT
*
16571 TTTTAATTAT-TTTTTA-ATATTTATTTATTTTTT-AATATTAAGAAAGATGATGTATTAAAGCA
1 TTTTAATTATGTTTTTATATATTTATTTATTTTTTAAATATTAAGAAAGAGGATGTATTAAAGCA
* * *
16633 AATAGAAGTCATTTTCTGATATTTCTAAGTAAATAAATAACTTATTTATTA-AAATAAAA-ATTA
66 AATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATAACCTACTT-TTATAAATAAAATA-TA
16696 ATATATTT
129 ATATATTT
16704 ATAAAAATTA
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
132 1 0.01
133 79 0.69
134 19 0.17
135 6 0.05
136 10 0.09
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (136 bp):
TTTTAATTATGTTTTTATATATTTATTTATTTTTTAAATATTAAGAAAGAGGATGTATTAAAGCA
AATAGAAGTCATTTTCTGATATTTCTAAATAAATAAATAACCTACTTTTATAAATAAAATATAAT
ATATTT
Found at i:16709 original size:18 final size:18
Alignment explanation
Indices: 16686--16721 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16676 ATTTATTAAA
16686 ATAAAAATTAATATATTT
1 ATAAAAATTAATATATTT
16704 ATAAAAATTAATATATTT
1 ATAAAAATTAATATATTT
16722 TCTTGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAAATTAATATATTT
Found at i:17495 original size:16 final size:17
Alignment explanation
Indices: 17468--17501 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17458 TTCTTCATTA
17468 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
17485 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
17501 T
1 T
17502 GACACATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:23914 original size:22 final size:22
Alignment explanation
Indices: 23889--23941 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
23879 GCTCTTGTTT
* *
23889 TAATGTTG-TCTTATTTTCTGGA
1 TAATGTTGAT-TTATCTTCTAGA
* *
23911 TAATCTAGATTTATCTTCTAGA
1 TAATGTTGATTTATCTTCTAGA
23933 TAATGTTGA
1 TAATGTTGA
23942 ACTAATCCCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.49
Consensus pattern (22 bp):
TAATGTTGATTTATCTTCTAGA
Found at i:27401 original size:16 final size:17
Alignment explanation
Indices: 27372--27405 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27362 TTTAAAAAGA
*
27372 TGTAGTCAATAATTAAT
1 TGTAGTCAAAAATTAAT
27389 TGTA-TCAAAAATTAAT
1 TGTAGTCAAAAATTAAT
27405 T
1 T
27406 TTTAAGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (17 bp):
TGTAGTCAAAAATTAAT
Found at i:30054 original size:103 final size:103
Alignment explanation
Indices: 29919--30228 Score: 410
Period size: 103 Copynumber: 3.0 Consensus size: 103
29909 ATATAGAAGT
* *
29919 AGTACCGATACTGTCAAAATAGAATGCTAAAATGGTACTGATACCATATATGATATCGATATTGA
1 AGTACCGATACTGTCAAAACATAATGCTAAAATGGTACTGATACCATATATGATATCGATATTGA
29984 AACCCAAAATAATGAAGTAGTACCGATACTTCTTAGGC
66 AACCCAAAATAATGAAGTAGTACCGATACTTCTTAGGC
* * *
30022 AGTACCGATATTTTTAAAACATAATGCTAAAATGGTACTGATACCATATATGATATCGATATTGA
1 AGTACCGATACTGTCAAAACATAATGCTAAAATGGTACTGATACCATATATGATATCGATATTGA
* * * *
30087 AACCCAAAATAATAAAGTAGTACCAATAC-T-GTAGGTAT
66 AACCCAAAATAATGAAGTAGTACCGATACTTCTTAGG--C
* * * * *
30125 AGTACTGATACTGTCAAAACATAATCCTAAAATGGTA-TCGATGCCATATATAATATCGATACTG
1 AGTACCGATACTGTCAAAACATAATGCTAAAATGGTACT-GATACCATATATGATATCGATATTG
* ** *
30189 AAGCCCAAAATAATGAAGTAGTATTGATACTTCTGAGGC
65 AAACCCAAAATAATGAAGTAGTACCGATACTTCTTAGGC
30228 A
1 A
30229 AACTGTCAAA
Statistics
Matches: 177, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
101 4 0.02
102 2 0.01
103 167 0.94
104 1 0.01
105 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (103 bp):
AGTACCGATACTGTCAAAACATAATGCTAAAATGGTACTGATACCATATATGATATCGATATTGA
AACCCAAAATAATGAAGTAGTACCGATACTTCTTAGGC
Found at i:30099 original size:53 final size:53
Alignment explanation
Indices: 29941--30099 Score: 145
Period size: 53 Copynumber: 3.1 Consensus size: 53
29931 GTCAAAATAG
29941 AATGCTAAAATGGTACTGATACCATATATGATATCGATATTGAAACCCAAAAT
1 AATGCTAAAATGGTACTGATACCATATATGATATCGATATTGAAACCCAAAAT
* * * * * ** *
29994 AATG---AAGTAGTACCGATACTTC-T-TAGGCAGTACCGATATTTTTAA---AACAT
1 AATGCTAAAATGGTACTGATAC--CATATATG-A-TATCGATA-TTGAAACCCAAAAT
30044 AATGCTAAAATGGTACTGATACCATATATGATATCGATATTGAAACCCAAAAT
1 AATGCTAAAATGGTACTGATACCATATATGATATCGATATTGAAACCCAAAAT
30097 AAT
1 AAT
30100 AAAGTAGTAC
Statistics
Matches: 77, Mismatches: 16, Indels: 26
0.65 0.13 0.22
Matches are distributed among these distances:
50 27 0.35
51 10 0.13
52 10 0.13
53 30 0.39
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (53 bp):
AATGCTAAAATGGTACTGATACCATATATGATATCGATATTGAAACCCAAAAT
Found at i:30953 original size:2 final size:2
Alignment explanation
Indices: 30946--30971 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30936 ATTTAGACAA
30946 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
30972 TCACTTTTAA
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:31432 original size:17 final size:18
Alignment explanation
Indices: 31412--31455 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
31402 AAAAACATAT
*
31412 TTAAAATAGTAAA-AATA
1 TTAAAATAATAAAGAATA
31429 TTAAAATAATAAAGAATA
1 TTAAAATAATAAAGAATA
31447 -TAAAA-AATA
1 TTAAAATAATA
31456 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
TTAAAATAATAAAGAATA
Found at i:31469 original size:28 final size:27
Alignment explanation
Indices: 31422--31478 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
31412 TTAAAATAGT
*
31422 AAAAATATTAAAATAATAAAGAATATA
1 AAAAATATTAAAATAATAAACAATATA
* * *
31449 AAAAATATTTAAATTATTAAACAATTTA
1 AAAAATA-TTAAAATAATAAACAATATA
31477 AA
1 AA
31479 TTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAATATTAAAATAATAAACAATATA
Found at i:31477 original size:17 final size:17
Alignment explanation
Indices: 31455--31489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31445 TATAAAAAAT
31455 ATTTAAATT-ATTAAACA
1 ATTTAAATTCA-TAAACA
31472 ATTTAAATTCATAAACA
1 ATTTAAATTCATAAACA
31489 A
1 A
31490 ATAAAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAAATTCATAAACA
Found at i:31478 original size:45 final size:45
Alignment explanation
Indices: 31401--31495 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
31391 TACTTTAACC
*
31401 TAAAAACATATTTAAAATAGTAAAAATATTAAAATAATAAAGAATA
1 TAAAAACATATTTAAAATAGTAAAAATATTAAAATAATAAACAA-A
* * * *
31447 TAAAAA-ATATTTAAATTATTAAACAAT-TTAAATTCATAAACAAA
1 TAAAAACATATTTAAAATAGTAAA-AATATTAAAATAATAAACAAA
31491 TAAAA
1 TAAAA
31496 GAATTATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 6 0.14
45 28 0.65
46 9 0.21
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (45 bp):
TAAAAACATATTTAAAATAGTAAAAATATTAAAATAATAAACAAA
Found at i:37947 original size:79 final size:77
Alignment explanation
Indices: 37791--37948 Score: 237
Period size: 77 Copynumber: 2.0 Consensus size: 77
37781 TTAATATTTT
* *
37791 TTTAACATTTACGGTAAAGTGCTACCTAAAACATTATTTTTTGCGAGAAATGTTAATATTGGGCG
1 TTTAACATTTACAGTAAAGTGCTACCTAAAACATTATTTTTTCCGAGAAATGTTAATATTGGGCG
*
37856 CTACCTAAAATG
66 CAACCTAAAATG
* *
37868 TTTAACATTTCCAGTAAAGTGCTACCTAAAACATTATATTTTCTACCG-GAGATGTTAATATTGG
1 TTTAACATTTACAGTAAAGTGCTACCTAAAACATTAT-TTTT-T-CCGAGAAATGTTAATATTGG
37932 GCGCAACCTAAAATG
63 GCGCAACCTAAAATG
37947 TT
1 TT
37949 ATTTTTTTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
77 35 0.48
78 4 0.05
79 32 0.44
80 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (77 bp):
TTTAACATTTACAGTAAAGTGCTACCTAAAACATTATTTTTTCCGAGAAATGTTAATATTGGGCG
CAACCTAAAATG
Found at i:38427 original size:21 final size:21
Alignment explanation
Indices: 38401--38453 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
38391 GTTTCCAGAT
*
38401 TCGCAACGCGAACATCGACTA
1 TCGCAATGCGAACATCGACTA
*
38422 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACATCGACTA
38443 TCGCAATGCGA
1 TCGCAATGCGA
38454 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAACATCGACTA
Found at i:38485 original size:19 final size:19
Alignment explanation
Indices: 38457--38519 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
38447 AATGCGATTT
38457 TCCAAATTCGTTGCAATAG
1 TCCAAATTCGTTGCAATAG
* * *
38476 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGC-A-ATAG
*
38499 TCCAAATTTGTTGCAATAG
1 TCCAAATTCGTTGCAATAG
38518 TC
1 TC
38520 GAAGTTCGCG
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 11 0.33
20 1 0.03
21 11 0.33
22 1 0.03
23 9 0.27
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (19 bp):
TCCAAATTCGTTGCAATAG
Found at i:38491 original size:21 final size:21
Alignment explanation
Indices: 38465--38533 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
38455 TTTCCAAATT
38465 CGTTGCAATAGTCCAAGTTCG
1 CGTTGCAATAGTCCAAGTTCG
* * *
38486 CGTTGCGATTTATTCCAAATT--
1 CGTTGC-A-ATAGTCCAAGTTCG
* *
38507 TGTTGCAATAGTCGAAGTTCG
1 CGTTGCAATAGTCCAAGTTCG
38528 CGTTGC
1 CGTTGC
38534 GATTTATTCT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
21 16 0.46
22 1 0.03
23 9 0.26
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
CGTTGCAATAGTCCAAGTTCG
Found at i:38505 original size:42 final size:42
Alignment explanation
Indices: 38449--38570 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 42
38439 ACTATCGCAA
*
38449 TGCGA-TT-TTCCAAATTCGTTGCAATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCAATAGTCGAAGTTCGCGT
*
38489 TGCGATTTATTCCAAATTTGTTGCAATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCAATAGTCGAAGTTCGCGT
** *
38531 TGCGATTTATTCTGAATTCGTTGCGATAGTCGAAGTTCGC
1 TGCGATTTATTCCAAATTCGTTGCAATAGTCGAAGTTCGC
38571 AACGACTGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
40 5 0.07
41 2 0.03
42 67 0.91
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCAATAGTCGAAGTTCGCGT
Found at i:40214 original size:2 final size:2
Alignment explanation
Indices: 40170--40200 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40160 AATTTTGTTT
*
40170 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40201 TAAAAAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40478 original size:2 final size:2
Alignment explanation
Indices: 40471--40495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40461 ATGAAATTTC
40471 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40496 TATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42418 original size:22 final size:22
Alignment explanation
Indices: 42393--42434 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42383 ATTGGTTTAA
42393 AAAAGAGTAATGAGTATAAATC
1 AAAAGAGTAATGAGTATAAATC
*
42415 AAAATAGTAATGAGTATAAA
1 AAAAGAGTAATGAGTATAAA
42435 ATGAAACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (22 bp):
AAAAGAGTAATGAGTATAAATC
Found at i:44733 original size:22 final size:22
Alignment explanation
Indices: 44701--44745 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
44691 ACGAACACGT
*
44701 TCGGATTGTTTCAAAATCGCGA
1 TCGGATCGTTTCAAAATCGCGA
*
44723 TCGGATCGTTTTAAAATCGCGA
1 TCGGATCGTTTCAAAATCGCGA
44745 T
1 T
44746 TCGGTACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (22 bp):
TCGGATCGTTTCAAAATCGCGA
Found at i:53372 original size:3 final size:3
Alignment explanation
Indices: 53364--53396 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53354 TGCAGAAAGG
53364 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
53397 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:53401 original size:2 final size:2
Alignment explanation
Indices: 53394--53422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53384 AAGAAGAAGA
53394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
53423 AGGGCCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66639 original size:21 final size:21
Alignment explanation
Indices: 66597--66639 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
66587 TTTCTGGGTT
* * *
66597 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
66618 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
66639 A
1 A
66640 CAATATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:66699 original size:66 final size:68
Alignment explanation
Indices: 66619--66769 Score: 243
Period size: 67 Copynumber: 2.2 Consensus size: 68
66609 ACCCATTCAA
* *
66619 GGGGAACCGATACCCCCTCAAC-AATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
66683 -GG
66 GGG
* *
66685 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
66750 GGG
66 GGG
*
66753 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
66770 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
66 22 0.28
67 38 0.49
68 18 0.23
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
GGG
Found at i:67439 original size:149 final size:149
Alignment explanation
Indices: 67248--67551 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
67238 GGGTAGAGGG
67248 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
67313 ACTTGATCCCTAGTATATGTATATGAGTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGAGTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
67378 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
67397 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
67462 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGAGTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
67527 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
67546 TCTACG
1 TCTACG
67552 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGAGTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:67574 original size:23 final size:23
Alignment explanation
Indices: 67530--67574 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
67520 ATCATTATAT
*
67530 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
67553 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
67575 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:69227 original size:14 final size:14
Alignment explanation
Indices: 69191--69232 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
69181 CGTTTCTGTC
69191 TATATGCA-GAGATT
1 TATATGCATG-GATT
* *
69205 TTTACGCATGGATT
1 TATATGCATGGATT
69219 TATATGCATGGATT
1 TATATGCATGGATT
69233 AATTCCCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (14 bp):
TATATGCATGGATT
Found at i:74766 original size:78 final size:79
Alignment explanation
Indices: 74618--74775 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 79
74608 CTGTCCTCTA
* *
74618 ATTTGTGCATACACTTGTAGCAGTAAATGGCAATGAAAACAGGTATTTACAAAGGTTACCATGCA
1 ATTTGTGCATACACTTGTAGCAGTAAATAGCAATGAAAACAGGGATTTACAAAGGTTACCATGCA
74683 AAAGTGACTCCACC
66 AAAGTGACTCCACC
* *
74697 ATTTGTGCATACACTTGTAGCAGTGAATAGCAATG-AAACAGGGATTTATAAAGGTTACCATGCA
1 ATTTGTGCATACACTTGTAGCAGTAAATAGCAATGAAAACAGGGATTTACAAAGGTTACCATGCA
74761 AAAGTGACTCCACC
66 AAAGTGACTCCACC
74775 A
1 A
74776 CCCTGTCCCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 42 0.56
79 33 0.44
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (79 bp):
ATTTGTGCATACACTTGTAGCAGTAAATAGCAATGAAAACAGGGATTTACAAAGGTTACCATGCA
AAAGTGACTCCACC
Found at i:78417 original size:20 final size:20
Alignment explanation
Indices: 78388--78439 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
78378 TATCTCTAAT
78388 AATA-GAATTTAAGAATTCG
1 AATATGAATTTAAGAATTCG
78407 AATATGAATTTAAGAATTCG
1 AATATGAATTTAAGAATTCG
78427 AATATGAATTTAA
1 AATATGAATTTAA
78440 TTTACATTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (20 bp):
AATATGAATTTAAGAATTCG
Found at i:78499 original size:2 final size:2
Alignment explanation
Indices: 78492--78518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
78482 GAAAATATTT
78492 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
78519 GGTTTTGTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78967 original size:3 final size:3
Alignment explanation
Indices: 78950--79009 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
78940 CTAAGATGAA
* *
78950 AAT AAT AAC AA- AAT AAT AATT AAA ACAT AAAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT A-AT -AAT -AAT AAT AAT AAT AAT
78998 AAT AAT -AT AAT A
1 AAT AAT AAT AAT A
79010 TTGCAAATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.08
3 34 0.69
4 10 0.20
5 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:78990 original size:11 final size:11
Alignment explanation
Indices: 78949--79009 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
78939 ACTAAGATGA
78949 AAATAATAACA-
1 AAATAATAA-AT
*
78960 AAATAATAATT
1 AAATAATAAAT
78971 AAA-ACATAAAT
1 AAATA-ATAAAT
78982 AAATAAT-AAT
1 AAATAATAAAT
78992 -AATAAT-AAT
1 AAATAATAAAT
79001 AATATAATA
1 AA-ATAATA
79010 TTGCAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.21
10 5 0.12
11 27 0.64
12 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:80448 original size:3 final size:3
Alignment explanation
Indices: 80442--80485 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
80432 TTTTTTTATT
*
80442 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
80486 TGATAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:80801 original size:45 final size:45
Alignment explanation
Indices: 80737--81402 Score: 1071
Period size: 45 Copynumber: 14.8 Consensus size: 45
80727 TAATATCTCA
* * * * ** *
80737 TTTGAAAACATCCTGCACTGTATGTCTTATGGATAACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
80782 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGAT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* **
80827 TTTGAAAACATCATGCACTGAAAGGCTTACAGATGACTTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
80872 TTTGAAAACATCATGCACTGAAGGGCTTGCAGGTGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
80917 TTTGAAAATATCATGCACTGAAGGGCTTATAGGTGACCTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
80962 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
81007 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
81052 TTTGAAAACATAATGCACTGAAGGGCTTACAGATGACCAGAAAGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
81097 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGGCCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
81142 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
81187 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
81232 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
81277 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
*
81323 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
81368 TTTGAAAACATCATGCACTGAAGGGATAACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
81403 TGGGAAATAG
Statistics
Matches: 576, Mismatches: 44, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
45 532 0.92
46 44 0.08
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:82103 original size:22 final size:22
Alignment explanation
Indices: 82078--82154 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
82068 AATAAGGCTT
82078 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* *
82100 TCATCTTTGAAAAGATAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * * **
82122 TCATCTTTGAAGAGTGTGTCTA
1 TCATCTTTAAAAAGAGAATCTA
82144 TCATCTTTAAA
1 TCATCTTTAAA
82155 GAATGTAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:86700 original size:20 final size:20
Alignment explanation
Indices: 86677--86715 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
86667 GTCCAATTTC
86677 ACATTCTAACATCAAATTCA
1 ACATTCTAACATCAAATTCA
*
86697 ACATTCTAACATTAAATTC
1 ACATTCTAACATCAAATTC
86716 CAGATTTGTG
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:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
ACATTCTAACATCAAATTCA
Found at i:93572 original size:2 final size:2
Alignment explanation
Indices: 93565--93596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
93555 GTTGCATACG
93565 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
93597 CAAAAAACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94747 original size:23 final size:23
Alignment explanation
Indices: 94717--94766 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
94707 TATGGTACTG
94717 ATACCAAGGTAAGGGAAGTATCA
1 ATACCAAGGTAAGGGAAGTATCA
*
94740 ATACCAAGGTAAGGGAAGTATCG
1 ATACCAAGGTAAGGGAAGTATCA
94763 ATAC
1 ATAC
94767 TCACTAGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (23 bp):
ATACCAAGGTAAGGGAAGTATCA
Found at i:107344 original size:59 final size:59
Alignment explanation
Indices: 107267--107394 Score: 193
Period size: 59 Copynumber: 2.2 Consensus size: 59
107257 CAGCAGGCTG
* * * *
107267 CATATTCGGGATTGCACTAATGTATAACTAGTGCATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGACTACACTAAAGTATAACTAGTGCAGATGGTGGGCACGACCTTATGTGT
**
107326 CATATTCGGGACTACACTAAAGTATAACTAGTGCAGATGGTGGGCATTACCTTATGTGT
1 CATATTCGGGACTACACTAAAGTATAACTAGTGCAGATGGTGGGCACGACCTTATGTGT
*
107385 CATACTCGGG
1 CATATTCGGG
107395 TTAGCACACG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (59 bp):
CATATTCGGGACTACACTAAAGTATAACTAGTGCAGATGGTGGGCACGACCTTATGTGT
Found at i:114771 original size:19 final size:19
Alignment explanation
Indices: 114735--114770 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
114725 CTTGCAACAC
*
114735 AATCCTCAATTTCATTTTA
1 AATCCTAAATTTCATTTTA
114754 AATCCTAAATTTC-TTTT
1 AATCCTAAATTTCATTTT
114771 TGATCTCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (19 bp):
AATCCTAAATTTCATTTTA
Found at i:116619 original size:28 final size:28
Alignment explanation
Indices: 116574--116627 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
116564 CTCGTGAACG
*
116574 TTCGTTTATGTTCGTTCAGTTATGTTCT
1 TTCGTTTATGTTCATTCAGTTATGTTCT
* *
116602 TTCGTTTATTTTCATTCATTTATGTT
1 TTCGTTTATGTTCATTCAGTTATGTT
116628 TAAGCCAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (28 bp):
TTCGTTTATGTTCATTCAGTTATGTTCT
Found at i:117353 original size:16 final size:16
Alignment explanation
Indices: 117329--117371 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
117319 CCAACGTTTA
*
117329 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
117345 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
117361 TGTTCGTTTAT
1 TGTTCGTTTAT
117372 TATTAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.07, C:0.09, G:0.23, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:118427 original size:42 final size:42
Alignment explanation
Indices: 118339--118680 Score: 267
Period size: 42 Copynumber: 8.2 Consensus size: 42
118329 TGAGAACAAA
*
118339 AAACGCCGCAATAGGTCAATATCTATTA-C-GCGTTTTT-GAAC
1 AAACGCCGCAAAAGGTC-ATATCTA-TAGCGGCGTTTTTGGAAC
*
118380 AAACGCCGCAAAAGGTCGATATCTATAGTGGCGTTTTTGGAA-
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* * * * * *
118422 TAACGCCGCAAAAAGT--TATGATATAGCGGCGTTTCTAGAAA
1 AAACGCCGCAAAAGGTCATAT-CTATAGCGGCGTTTTTGGAAC
* *
118463 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
* * * * * *
118506 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTGTAGAAC
1 AAACGCCGCAAAAGGTCATATCTATAGC-GGCGTTTTTGGAAC
* * * * *
118548 AAAC-CCGTAAAATGTCAGACCTATAGTGGCG-TTTTGGACAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
* * * *
118589 AAATGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
* * *
118632 AAACGCCACAAAA-GTCAGA--TATAGCGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGA-AC
118672 AAACGCCGC
1 AAACGCCGC
118681 TAATTACCAT
Statistics
Matches: 251, Mismatches: 37, Indels: 27
0.80 0.12 0.09
Matches are distributed among these distances:
39 3 0.01
40 50 0.20
41 63 0.25
42 76 0.30
43 59 0.24
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
Found at i:118610 original size:83 final size:85
Alignment explanation
Indices: 118380--118680 Score: 291
Period size: 83 Copynumber: 3.6 Consensus size: 85
118370 GTTTTTGAAC
* * * * * * *
118380 AAACGCCGCAAAAGGTCGATATCTATAGTGGCGTTTTTGGA-A-TAACGCCGCAAAAAGTTATGA
1 AAACGCCGCAAAATGTC-AGACCTATAGCGGCGTTTTTGGACACAAACGCCGC-AAAAGATAAGA
118443 --TATAGCGGCGTTTCTAGAAA
64 CCTATAGCGGCGTTTCTAGAAA
* *
118463 AAACGCCGCAAAATGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATAAGACC
1 AAACGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGATAAGACC
* *
118528 TATA-CTGGCGTTTGTAGAAC
66 TATAGC-GGCGTTTCTAGAAA
* * * *
118548 AAAC-CCGTAAAATGTCAGACCTATAGTGGCG-TTTTGGACACAAATGCCGCAAAATG-TCAGAC
1 AAACGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAA-GATAAGAC
* * *
118610 CTATAGCGGCGTTTTTGGACAC
65 CTATAGCGGCGTTTCTAGA-AA
* * *
118632 AAACGCCACAAAA-GTCAGA--TATAGCGGCATTTTTGGATACAAACGCCGC
1 AAACGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGC
118681 TAATTACCAT
Statistics
Matches: 186, Mismatches: 22, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
82 29 0.16
83 84 0.45
84 47 0.25
85 26 0.14
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (85 bp):
AAACGCCGCAAAATGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGATAAGACC
TATAGCGGCGTTTCTAGAAA
Found at i:121294 original size:41 final size:41
Alignment explanation
Indices: 121249--121710 Score: 415
Period size: 41 Copynumber: 11.4 Consensus size: 41
121239 TTTGCGGTAC
* * *
121249 AAACGCCACTAAAGTACGAGTCTTTTGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * * *
121290 AAACGCCACTAGCGTACGAGTCTTTTGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
121331 AAACGCCACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* * *
121374 AAACGCCACT-AAGTACAAGTCTATAGCGACGTTTGTAAACAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT--ATAA
* * * *
121416 AAATGCCACTAAAGTACGAGTCTATAGCGACGTTTTTAAACA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A
* * *
121458 AAACGCCACTAAAGTATGAGT-TATAGCAGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
121498 AAACG-CAGTAAAGTATGAGT-TATAGCAGCGCTTT-TATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATAA
*
121537 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
121577 AAA-GCCCCTAAAGAACGATTCTATACCGGCGTTTGTGTAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
121617 AAACGCCACTACAA-TACTAATCTTTAGCAGCGTTT-T-TAC
1 AAACGCCACTA-AAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
121656 AAACGCCACTAAAGTAAGA-TCTTTTGCGGCATTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
121696 AAACGCCTCTAAAGT
1 AAACGCCACTAAAGT
121711 TAGTTTTTTG
Statistics
Matches: 361, Mismatches: 46, Indels: 29
0.83 0.11 0.07
Matches are distributed among these distances:
38 14 0.04
39 80 0.22
40 51 0.14
41 116 0.32
42 63 0.17
43 37 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:121622 original size:80 final size:80
Alignment explanation
Indices: 121253--121710 Score: 381
Period size: 80 Copynumber: 5.7 Consensus size: 80
121243 CGGTACAAAC
* * ** ** *
121253 GCCACTAAAGTACGAGTCTTTTGCGGTGTTTGTATAAAAACGCCACTAGCGTACGAGTCTTTTGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
121318 GGCGTTTTTATAAAAA
66 GGCGTTTTTAT-AAAA
* * * *
121334 CGCCACTAAAGTACAAGTCTATAGCGACGTTTGTAAACAAAAACGCCACT-AAGTACAAGTCTAT
1 -GCCACTAAAGTACGAGTCTATAGCGACGTTTGT--ATAAAAACGCCACTAAAGTACGAGTCTTT
* * *
121398 AGCGACGTTTGTAAACAAAAA
63 AGCGGCGTTT-T-TA-TAAAA
* * * *
121419 TGCCACTAAAGTACGAGTCTATAGCGACGTTTTTAAACAAAACGCCACTAAAGTATGAGT-TATA
1 -GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATA-AAAACGCCACTAAAGTACGAGTCTTTA
*
121483 GCAGCGTTTTTATAAAA
64 GCGGCGTTTTTATAAAA
* * *
121500 ACGCAGTAAAGTATGAGT-TATAGC-AGCGCTTT-TATAAAAACGCCACTAAAGTACGAGTCTTT
1 GC-CACTAAAGTACGAGTCTATAGCGA-CG-TTTGTATAAAAACGCCACTAAAGTACGAGTCTTT
*
121562 AGCGGCGTTTGTATAAAA
63 AGCGGCGTTTTTATAAAA
* * * * * * * *
121580 GCCCCTAAAGAACGATTCTATACCGGCGTTTGTGTAAAAACGCCACTACAA-TACTAATCTTTAG
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTA-AAGTACGAGTCTTTAG
* * *
121644 CAGCGTTTTTACAAAC
65 CGGCGTTTTTATAAAA
* * * * * * *
121660 GCCACTAAAGTAAGA-TCTTTTGCGGCATTTGTATACAAACGCCTCTAAAGT
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAAAGT
121711 TAGTTTTTTG
Statistics
Matches: 303, Mismatches: 57, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
78 2 0.01
79 61 0.20
80 88 0.29
81 22 0.07
82 29 0.10
83 21 0.07
84 36 0.12
85 44 0.15
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (80 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC
GGCGTTTTTATAAAA
Found at i:122375 original size:25 final size:24
Alignment explanation
Indices: 122328--122375 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
122318 TTTACGTCTT
122328 TTAAATGATTTTTTCTAAAATTTG
1 TTAAATGATTTTTTCTAAAATTTG
*
122352 TTAAAGTGACTTTTTT-TAATATTT
1 TTAAA-TGA-TTTTTTCTAAAATTT
122376 AATCTACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (24 bp):
TTAAATGATTTTTTCTAAAATTTG
Found at i:122804 original size:13 final size:15
Alignment explanation
Indices: 122783--122817 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
122773 ATATAACGTG
122783 TTATATATA-TTTATA
1 TTATATA-AGTTTATA
122798 TTATATAAGTTTATA
1 TTATATAAGTTTATA
122813 TTATA
1 TTATA
122818 GAAAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATATAAGTTTATA
Found at i:122891 original size:3 final size:3
Alignment explanation
Indices: 122883--122925 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
122873 ATGACGACAA
122883 AAT AAT AAT AAAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
122926 AAGAGTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:122901 original size:13 final size:13
Alignment explanation
Indices: 122882--122922 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
122872 GATGACGACA
122882 AAATAATAATAA-
1 AAATAATAATAAT
122894 ATAATAATAATAAT
1 A-AATAATAATAAT
122908 AAATAATAATAAT
1 AAATAATAATAAT
122921 AA
1 AA
122923 TAAAAGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:122904 original size:16 final size:16
Alignment explanation
Indices: 122883--122926 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
122873 ATGACGACAA
122883 AATAATAATAAATAAT
1 AATAATAATAAATAAT
122899 AATAATAATAAATAAT
1 AATAATAATAAATAAT
122915 AATAATAATAAA
1 AATAATAATAAA
122927 AGAGTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAAATAAT
Done.