Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 74 of 345
Found at i:20283390 original size:17 final size:17
Alignment explanation
Indices: 20283361--20283394 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20283351 TATCAATTTT
20283361 TTATTATTAATATAATA
1 TTATTATTAATATAATA
20283378 TTATT-TTATATATAATA
1 TTATTATTA-ATATAATA
20283395 ATTTGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTATTAATATAATA
Found at i:20284477 original size:2 final size:2
Alignment explanation
Indices: 20284470--20284496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20284460 CAGAAAGTTT
20284470 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
20284497 TGTTTTGTTT
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:20289687 original size:26 final size:26
Alignment explanation
Indices: 20289658--20289741 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
20289648 CATGAAATTC
* *
20289658 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
20289684 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
20289710 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
20289736 TTATCA
1 TTATCA
20289742 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:20290400 original size:45 final size:46
Alignment explanation
Indices: 20290335--20290425 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
20290325 GCTGGAAATC
20290335 CTCCTCCCCCTCCCCTCTCTCTTCCTTCTCTCTCTTTTTTTTTCTT
1 CTCCTCCCCCTCCCCTCTCTCTTCCTTCTCTCTCTTTTTTTTTCTT
20290381 CTCCT-CCCCTCCCCTCTCTCTTCCTTCTCTCTCTTTTTTTTTCTT
1 CTCCTCCCCCTCCCCTCTCTCTTCCTTCTCTCTCTTTTTTTTTCTT
20290426 TCTCTCCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 40 0.89
46 5 0.11
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (46 bp):
CTCCTCCCCCTCCCCTCTCTCTTCCTTCTCTCTCTTTTTTTTTCTT
Found at i:20290911 original size:3 final size:3
Alignment explanation
Indices: 20290905--20291024 Score: 59
Period size: 3 Copynumber: 39.0 Consensus size: 3
20290895 TCATTCCTAA
* * * * *
20290905 TAT TAT TAA TAC TAT TAT T-T CTAT TAT TAT AAT TGT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* ** *
20290950 TAT TCT GGT TAT TAAA TAT TAT TAT T-T TAAT GTAT TAT TAT T-T CTAGT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT -TA-T
*
20290998 TAT TAT TAT T-T CTAG TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT
20291025 ATATAATATT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
2 5 0.06
3 73 0.83
4 8 0.09
5 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:20290985 original size:16 final size:17
Alignment explanation
Indices: 20290966--20291022 Score: 77
Period size: 16 Copynumber: 3.6 Consensus size: 17
20290956 GGTTATTAAA
20290966 TATTATTATTT-TAATG
1 TATTATTATTTCTAATG
*
20290982 TATTATTATTTCTAGT-
1 TATTATTATTTCTAATG
20290998 TATTATTATTTCT-A-G
1 TATTATTATTTCTAATG
20291013 TATTATTATT
1 TATTATTATT
20291023 ATATATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 10 0.27
16 24 0.65
17 3 0.08
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (17 bp):
TATTATTATTTCTAATG
Found at i:20291034 original size:18 final size:18
Alignment explanation
Indices: 20290997--20291035 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20290987 TTATTTCTAG
* * *
20290997 TTATTATTATTTCTAGTA
1 TTATTATTATATATAATA
20291015 TTATTATTATATATAATA
1 TTATTATTATATATAATA
20291033 TTA
1 TTA
20291036 GTGTATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTATTATATATAATA
Found at i:20291300 original size:12 final size:12
Alignment explanation
Indices: 20291283--20291310 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20291273 GAAAGTAAAT
20291283 AATATAATAATA
1 AATATAATAATA
20291295 AATATAATAATA
1 AATATAATAATA
20291307 AATA
1 AATA
20291311 CATATGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATAATA
Found at i:20291391 original size:3 final size:3
Alignment explanation
Indices: 20291378--20291412 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
20291368 ATATCTAAAT
20291378 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20291413 TTTATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20291524 original size:12 final size:12
Alignment explanation
Indices: 20291507--20291534 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20291497 TGTACATATG
20291507 TATTTATTATTA
1 TATTTATTATTA
20291519 TATTTATTATTA
1 TATTTATTATTA
20291531 TATT
1 TATT
20291535 ATTTACTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTATTATTA
Found at i:20291762 original size:35 final size:33
Alignment explanation
Indices: 20291708--20291784 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 33
20291698 TTTTTAAAAA
* * *
20291708 ATATTATATTTTTCATATATTATGTATTTTTTTAT
1 ATATTATATTATTCATATATT-T-TATTGTATTAT
*
20291743 ATATTATATTATTCGTATATTTTATTGTATTAT
1 ATATTATATTATTCATATATTTTATTGTATTAT
20291776 ATA-TATATT
1 ATATTATATT
20291785 TTAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.16
33 12 0.32
34 1 0.03
35 19 0.50
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (33 bp):
ATATTATATTATTCATATATTTTATTGTATTAT
Found at i:20291837 original size:73 final size:74
Alignment explanation
Indices: 20291723--20291859 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 74
20291713 ATATTTTTCA
* * * *
20291723 TATATTATGTATTTTTTTATATATTATATTATTCGTATATTTTATTG-TA-TT-ATATATATATT
1 TATATTATGTATTTTTGTATATATCATACTATTCATATATTTTATTGTTATTTCATATATATATT
20291785 TTAAATAAT
66 TTAAATAAT
20291794 TATATTATGTATATATTTGTA-AGTATCATACTATTCATATATTTTATTGTTATTTCATATATAT
1 TATATTATGTAT-T-TTTGTATA-TATCATACTATTCATATATTTTATTGTTATTTCATATATAT
20291858 AT
63 AT
20291860 ATATATGTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
71 12 0.21
72 2 0.04
73 28 0.50
74 2 0.04
75 2 0.04
76 10 0.18
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.58
Consensus pattern (74 bp):
TATATTATGTATTTTTGTATATATCATACTATTCATATATTTTATTGTTATTTCATATATATATT
TTAAATAAT
Found at i:20291979 original size:25 final size:25
Alignment explanation
Indices: 20291941--20291988 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20291931 ATTATTGTTG
* *
20291941 TTAATATTAGTATATGTATATATCT
1 TTAATATTAGTATAGGTACATATCT
20291966 TTAATATATA-TATAGGTACATAT
1 TTAATAT-TAGTATAGGTACATAT
20291989 TTATGTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
TTAATATTAGTATAGGTACATATCT
Found at i:20304473 original size:75 final size:75
Alignment explanation
Indices: 20304368--20304532 Score: 287
Period size: 75 Copynumber: 2.2 Consensus size: 75
20304358 TAATGTTTTT
* *
20304368 ATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
20304432 GGTATTTTCA
66 GGTATTTTCA
*
20304442 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGGGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
20304507 GGTATTTTCA
66 GGTATTTTCA
*
20304517 ATTTCTGCTTTTCAAA
1 ATTTCTGTTTTTCAAA
20304533 TTATGCTTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 12 0.14
75 74 0.86
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (75 bp):
ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
GGTATTTTCA
Found at i:20304530 original size:14 final size:14
Alignment explanation
Indices: 20304511--20304546 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20304501 CGCTGAGGTA
* *
20304511 TTTTCAATTTCTGC
1 TTTTCAAATTATGC
20304525 TTTTCAAATTATGC
1 TTTTCAAATTATGC
20304539 TTTTCAAA
1 TTTTCAAA
20304547 AAAATCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (14 bp):
TTTTCAAATTATGC
Found at i:20304587 original size:89 final size:89
Alignment explanation
Indices: 20304436--20304811 Score: 587
Period size: 89 Copynumber: 4.2 Consensus size: 89
20304426 CGCTGAGGTA
* * *
20304436 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGGGGTGAGTTGAGCCTCAGGACA
1 TTTTCAAATTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
20304501 CGCTGAGGTATTTTCAATTTCTGC
66 CGCTGAGGTATTTTCAATTTCTGC
* * *
20304525 TTTTCAAATTATGCTTTTCAAAAAAATCAACTCATATTGCGAGGGGTGAGTTGAGCATCAGGACA
1 TTTTCAAATTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
20304590 CGCTGAGGTATTTTCAATTTCTGC
66 CGCTGAGGTATTTTCAATTTCTGC
* *
20304614 TTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAAATTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
20304679 CGCTGAGGTATTTTCAATTT-TCGT
66 CGCTGAGGTATTTTCAATTTCT-GC
* * * * *
20304703 TTTTCAATTTATGCTTTTC--AAAACTCAACTCATATTGCGAGAGGTGGGTTGAGCCTCAGGGCA
1 TTTTCAAATTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
20304766 CGCTGAGGTATTTTCAAATTCTGC
66 CGCTGAGGTATTTTCAATTTCTGC
20304790 TTTTCAAATTCTGCTTTTCAAA
1 TTTTCAAATTCTGCTTTTCAAA
20304812 TTCTACTTTT
Statistics
Matches: 262, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
87 77 0.29
88 2 0.01
89 183 0.70
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (89 bp):
TTTTCAAATTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTTCTGC
Found at i:20304619 original size:14 final size:14
Alignment explanation
Indices: 20304600--20304635 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20304590 CGCTGAGGTA
* *
20304600 TTTTCAATTTCTGC
1 TTTTCAAATTCTAC
20304614 TTTTCAAATTCTAC
1 TTTTCAAATTCTAC
20304628 TTTTCAAA
1 TTTTCAAA
20304636 AAAATCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTTCAAATTCTAC
Found at i:20304795 original size:14 final size:14
Alignment explanation
Indices: 20304776--20304825 Score: 91
Period size: 14 Copynumber: 3.6 Consensus size: 14
20304766 CGCTGAGGTA
20304776 TTTTCAAATTCTGC
1 TTTTCAAATTCTGC
20304790 TTTTCAAATTCTGC
1 TTTTCAAATTCTGC
*
20304804 TTTTCAAATTCTAC
1 TTTTCAAATTCTGC
20304818 TTTTCAAA
1 TTTTCAAA
20304826 AAAATCAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (14 bp):
TTTTCAAATTCTGC
Found at i:20304818 original size:190 final size:190
Alignment explanation
Indices: 20304600--20304983 Score: 687
Period size: 190 Copynumber: 2.0 Consensus size: 190
20304590 CGCTGAGGTA
* * *
20304600 TTTTCAATTTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 TTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGT
* * *
20304665 TGAGCCTCAAGACACGCTGAGGTATTTTCAATTTTCGTTTTTCAATTTATGCTTTTCAAAACTCA
66 TGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAAGTTATGCTTTTCAAAAATCA
*
20304730 ACTCATATTGCGAGAGGTGGGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTCTGC
131 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTCTGC
20304790 TTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGT
1 TTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGT
20304855 TGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAAGTTATGCTTTTCAAAAATCA
66 TGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAAGTTATGCTTTTCAAAAATCA
* *
20304920 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT
131 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTCTGC
20304980 TTTT
1 TTTT
20304984 TCAATTTATA
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
190 185 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (190 bp):
TTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGT
TGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCCGTTTTTCAAGTTATGCTTTTCAAAAATCA
ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTCTGC
Found at i:20304871 original size:103 final size:103
Alignment explanation
Indices: 20304722--20304914 Score: 287
Period size: 103 Copynumber: 1.9 Consensus size: 103
20304712 TATGCTTTTC
* * * * * *
20304722 AAAACTCAACTCATATTGCGAGAGGTGGGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAAATTC
* *
20304787 TGCTTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAA
66 CGCTTTTCAAATTATGCTTTTCAAATTCTACTTTTCAA
*
20304825 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAAATTC
* *
20304890 CGTTTTTCAAGTTATGCTTTTCAAA
66 CGCTTTTCAAATTATGCTTTTCAAA
20304915 AATCAACTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (103 bp):
AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAAATTC
CGCTTTTCAAATTATGCTTTTCAAATTCTACTTTTCAA
Found at i:20305030 original size:88 final size:88
Alignment explanation
Indices: 20304790--20305124 Score: 392
Period size: 88 Copynumber: 3.8 Consensus size: 88
20304780 CAAATTCTGC
* *
20304790 TTTTCAAATTCTGCTTTTCAAATTCTACTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGT
1 TTTTCAAATTCTGCTTTTCAAATTATACTTTTC-AAAAAATCAACTCATATTGCGAGAGATGAGT
* *
20304855 TGAGCCTCAAGACACGCTGAGGTA
65 TGAGCCTCAGGGCACGCTGAGGTA
* * * * * *
20304879 TTTTCAATTTCCGTTTTTCAAGTTATGCTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTT
1 TTTTCAAATTCTGCTTTTCAAATTATACTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTT
20304943 GAGCCTCAGGGCACGCTGAGGTA
66 GAGCCTCAGGGCACGCTGAGGTA
* * * * * *
20304966 TTTTCAATTTCTGTTTTTTCAATTTATATTTTTC-AAAAATCAACTCCTATTGCGAGAGGTGAGT
1 TTTTCAAATTCTG-CTTTTCAAATTATACTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGT
**
20305030 TGAGCCTC-GGGTCACATATCGAGGTA
65 TGAGCCTCAGGG-CAC-GCT-GAGGTA
* * * *
20305056 TTTTCAAAATCTGCTTTTCAAATTA-A-GTTTCAAAAAACCAACTCATATTGCGAGAAATGAGTT
1 TTTTCAAATTCTGCTTTTCAAATTATACTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTT
20305119 GAGCCT
66 GAGCCT
20305125 TGGCTCACGT
Statistics
Matches: 215, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
87 69 0.32
88 91 0.42
89 38 0.18
90 17 0.08
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (88 bp):
TTTTCAAATTCTGCTTTTCAAATTATACTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTT
GAGCCTCAGGGCACGCTGAGGTA
Found at i:20305718 original size:25 final size:25
Alignment explanation
Indices: 20305681--20305728 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20305671 AAAAGTCTTT
*
20305681 ACTCTATTCTCGTCACACGACAACA
1 ACTCTATTATCGTCACACGACAACA
* * *
20305706 ACTCTGTTATCGTTATACGACAA
1 ACTCTATTATCGTCACACGACAA
20305729 TGAGTAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (25 bp):
ACTCTATTATCGTCACACGACAACA
Found at i:20306366 original size:17 final size:19
Alignment explanation
Indices: 20306323--20306360 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20306313 TCATTTTTCC
*
20306323 ACATATATATATATCAAAA
1 ACATATAAATATATCAAAA
20306342 ACATATAAATATAT-AAAA
1 ACATATAAATATATCAAAA
20306360 A
1 A
20306361 GTATAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
ACATATAAATATATCAAAA
Found at i:20306959 original size:3 final size:3
Alignment explanation
Indices: 20306924--20307070 Score: 59
Period size: 3 Copynumber: 48.7 Consensus size: 3
20306914 ATTTATTTAT
* * * * * * * * *
20306924 TTA TT- TTA TTT TTA TTT TTT TTA ATA TTT TTA TTA TCA TTC CTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
20306971 TTA TTA ATA CTA TTA TT- TCTA TTA TTA TTA TTG TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * *
20307016 TTC TGG TTA TTAA ATA TTA TTA TT- TTAA TGTA TTA TTA TT- TCTA GTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TT-A T-TA TTA TTA TTA T-TA TTA
20307063 TTA TTA TT
1 TTA TTA TT
20307071 GTGAAAAATA
Statistics
Matches: 104, Mismatches: 31, Indels: 18
0.68 0.20 0.12
Matches are distributed among these distances:
2 6 0.06
3 91 0.88
4 6 0.06
5 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20311158 original size:3 final size:3
Alignment explanation
Indices: 20311147--20311183 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
20311137 ATTCTAATAA
20311147 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20311184 ATTTAGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20311197 original size:2 final size:2
Alignment explanation
Indices: 20311176--20311225 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
20311166 TTATTATTAT
* *
20311176 TA TA T- TA TA TT TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20311217 TA TG TA TA T
1 TA TA TA TA T
20311226 TTATTTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20311411 original size:7 final size:7
Alignment explanation
Indices: 20311399--20311433 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
20311389 CATTTCTTCA
20311399 TTATTTT
1 TTATTTT
20311406 TTATTTT
1 TTATTTT
20311413 TTA-TTT
1 TTATTTT
20311419 TTATTTTT
1 TTA-TTTT
20311427 TTATTTT
1 TTATTTT
20311434 AATATTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 14 0.54
8 6 0.23
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTATTTT
Found at i:20311479 original size:16 final size:16
Alignment explanation
Indices: 20311460--20311520 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
20311450 TTTTTTTAAA
20311460 ATATTATATTTTTCAT
1 ATATTATATTTTTCAT
*
20311476 ATATTATGTATTTTTTTAT
1 ATATTA--TA-TTTTTCAT
* *
20311495 ATATTATATTATTCGT
1 ATATTATATTTTTCAT
*
20311511 ATATTTTATT
1 ATATTATATT
20311521 GTATTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
16 20 0.54
17 2 0.05
18 2 0.05
19 13 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
ATATTATATTTTTCAT
Found at i:20311499 original size:35 final size:33
Alignment explanation
Indices: 20311450--20311537 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 33
20311440 CTTATTTAGT
* *
20311450 TTTTTTTAAAATATTATATTTTTCATATATTATGTA
1 TTTTTTT-ATATATTATATTATTCATATATT-T-TA
*
20311486 TTTTTTTATATATTATATTATTCGTATATTTTA
1 TTTTTTTATATATTATATTATTCATATATTTTA
* *
20311519 TTGTATTATATATATATAT
1 TTTTTTTATATAT-TATAT
20311538 ATTTAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 13 0.28
34 6 0.13
35 20 0.43
36 7 0.15
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (33 bp):
TTTTTTTATATATTATATTATTCATATATTTTA
Found at i:20311612 original size:2 final size:2
Alignment explanation
Indices: 20311605--20311658 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
20311595 TTGTTATTTC
*
20311605 AT AT AT AT AT AT GT AT AT -T AT -T AGT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
20311645 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
20311659 TTTTATACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 3 0.07
2 42 0.91
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20311625 original size:24 final size:25
Alignment explanation
Indices: 20311598--20311648 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
20311588 TATTTTATTG
*
20311598 TTATT-TCATATATATATATGTATA
1 TTATTATCATATATATATATATATA
*
20311622 TTATTAGTTATATATATATATATATA
1 TTATTA-TCATATATATATATATATA
20311648 T
1 T
20311649 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
26 18 0.78
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TTATTATCATATATATATATATATA
Found at i:20313270 original size:75 final size:75
Alignment explanation
Indices: 20313151--20313322 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
20313141 CATGGCAAAG
** *
20313151 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
20313210 CCATACTGAGC
65 CCATACCGAGC
20313221 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
20313286 CATACCGAGT
66 CATACCGAGC
***
20313296 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
20313323 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:20313289 original size:35 final size:35
Alignment explanation
Indices: 20313154--20313320 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
20313144 GGCAAAGTGT
* **
20313154 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
20313189 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
20313224 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
20313264 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
20313300 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
20313321 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:20313312 original size:36 final size:35
Alignment explanation
Indices: 20313250--20313320 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
20313240 ATTATCAAAT
* *
20313250 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
20313285 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
20313321 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:20317261 original size:379 final size:378
Alignment explanation
Indices: 20316562--20317323 Score: 1506
Period size: 379 Copynumber: 2.0 Consensus size: 378
20316552 CTTAGTAGGT
20316562 GAGTGATCTAGGTCTTTAGATACAAAAGTGAGGTTGCTATGTCAAGAGTATGATAAAACTTAAGT
1 GAGTGATCTAGGTCTTTAGATACAAAAGTGAGGTTGCTATGTCAAGAGTATGATAAAACTTAAGT
*
20316627 CACTTGTTGCAATGGAGATTACAGATAGTGAATCTACTCACTAAGCTAGACTCCCAAATGTAGAG
66 CACTGGTTGCAATGGAGATTACAGATAGTGAATCTACTCACTAAGCTAGACTCCCAAATGTAGAG
20316692 AAATCAAACTACGTAAATAATCTTGTGTACTTTCTTTACCCTGCATTTAGGTTTGTTCATCGCAA
131 AAATCAAACTACGTAAATAATCTTGTGTACTTTCTTTACCCTGCATTTAGGTTTGTTCATCGCAA
20316757 TAGAAACTGAAGTGGCCAATGTAGCTAATCATTTTCATTCAACTCTATTTTCTTAGCAATTAGCA
196 TAGAAACTGAAGTGGCCAATGTAGCTAATCATTTTCATTCAACTCTATTTTCTTAGCAATTAGCA
20316822 GTTGTTTGATTCAACAAATGGTATCAAAACTTCCCACTCAATGCAGCTGCTGGTGTTTCCTAGTG
261 GTTGTTTGATTCAACAAATGGTATCAAAACTTCCCACTCAATGCAGCTGCTGGTGTTTCCTAGTG
20316887 TTGTTTATTGCCAGATATGGGAAAAGATTCGACTACTCGTCCCCCAGTGTCAGA
326 TTGTTTATTGCCAGATATGGGAAAAGATTCGACTACTCGT-CCCCAGTGTCAGA
20316941 GAGTGATCTAGGTCTTTAGATACAAAAGTGAGGTTGCTATGTCAAGAGTATGATAAAACTTAAGT
1 GAGTGATCTAGGTCTTTAGATACAAAAGTGAGGTTGCTATGTCAAGAGTATGATAAAACTTAAGT
20317006 CACTGGTTGCAATGGAGATTACAGATAGTGAATCTACTCACTAAGCTAGACTCCCAAATGTAGAG
66 CACTGGTTGCAATGGAGATTACAGATAGTGAATCTACTCACTAAGCTAGACTCCCAAATGTAGAG
20317071 AAATCAAACTACGTAAATAATCTTGTGTACTTTCTTTACCCTGCATTTAGGTTTGTTCATCGCAA
131 AAATCAAACTACGTAAATAATCTTGTGTACTTTCTTTACCCTGCATTTAGGTTTGTTCATCGCAA
20317136 TAGAAACTGAAGTGGCCAATGTAGCTAATCATTTTCATTCAACTCTATTTTCTTAGCAATTAGCA
196 TAGAAACTGAAGTGGCCAATGTAGCTAATCATTTTCATTCAACTCTATTTTCTTAGCAATTAGCA
20317201 GTTGTTTGATTCAACAAATGGTATCAAAACTTCCCACTCAATGCAGCTGCTGGTGTTTCCTAGTG
261 GTTGTTTGATTCAACAAATGGTATCAAAACTTCCCACTCAATGCAGCTGCTGGTGTTTCCTAGTG
20317266 TTGTTTATTGCCAGATATGGGAAAAGATTCGACTACTCGTCCCCAGTGTCAGA
326 TTGTTTATTGCCAGATATGGGAAAAGATTCGACTACTCGTCCCCAGTGTCAGA
20317319 GAGTG
1 GAGTG
20317324 GCAACTATGC
Statistics
Matches: 382, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
378 18 0.05
379 364 0.95
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (378 bp):
GAGTGATCTAGGTCTTTAGATACAAAAGTGAGGTTGCTATGTCAAGAGTATGATAAAACTTAAGT
CACTGGTTGCAATGGAGATTACAGATAGTGAATCTACTCACTAAGCTAGACTCCCAAATGTAGAG
AAATCAAACTACGTAAATAATCTTGTGTACTTTCTTTACCCTGCATTTAGGTTTGTTCATCGCAA
TAGAAACTGAAGTGGCCAATGTAGCTAATCATTTTCATTCAACTCTATTTTCTTAGCAATTAGCA
GTTGTTTGATTCAACAAATGGTATCAAAACTTCCCACTCAATGCAGCTGCTGGTGTTTCCTAGTG
TTGTTTATTGCCAGATATGGGAAAAGATTCGACTACTCGTCCCCAGTGTCAGA
Found at i:20320543 original size:22 final size:22
Alignment explanation
Indices: 20320502--20320560 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
20320492 GTTTTAATAA
* *
20320502 TTGTTTTAGTA-TCATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
20320523 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
20320545 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
20320561 GATTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.48
22 10 0.30
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:20320559 original size:20 final size:22
Alignment explanation
Indices: 20320515--20320560 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
20320505 TTTTAGTATC
* *
20320515 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
20320537 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
20320557 ATTT
1 ATTT
20320561 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:20320577 original size:26 final size:24
Alignment explanation
Indices: 20320531--20320590 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
20320521 ATTTGTTTTA
*
20320531 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
20320555 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
20320581 TTTTTTATTT
1 ATATTTATTT
20320591 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:20322410 original size:44 final size:44
Alignment explanation
Indices: 20322344--20322432 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
20322334 ATAGCTGGGC
** *
20322344 TATGGCATCGGTGCAATGTGATAATGTGACTCCGTATAAGACCA
1 TATGGCATCGGCACAATATGATAATGTGACTCCGTATAAGACCA
* *
20322388 TATGGCATCGGCATAATATGATAATGTGATTCCGTATAAGACCA
1 TATGGCATCGGCACAATATGATAATGTGACTCCGTATAAGACCA
20322432 T
1 T
20322433 GTCTGGGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
TATGGCATCGGCACAATATGATAATGTGACTCCGTATAAGACCA
Found at i:20322476 original size:46 final size:48
Alignment explanation
Indices: 20322404--20322498 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
20322394 ATCGGCATAA
* * **
20322404 TATGATAATGTGATTCCGTATAAGACCATGTCTGGGATATGGCTTCGG
1 TATGATAATGTGATACCGTATAAGACCATGGCAAGGATATGGCTTCGG
* *
20322452 TATGAT-ATGTGA-ACCGTGTAAGACCATGGCAAGGCTATGGCTTCGG
1 TATGATAATGTGATACCGTATAAGACCATGGCAAGGATATGGCTTCGG
20322498 T
1 T
20322499 GTGTGATGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 29 0.71
47 6 0.15
48 6 0.15
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (48 bp):
TATGATAATGTGATACCGTATAAGACCATGGCAAGGATATGGCTTCGG
Found at i:20329477 original size:53 final size:53
Alignment explanation
Indices: 20329336--20329486 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
20329326 ACAAGTGTGC
* **
20329336 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
20329389 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
20329442 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
20329487 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:20331397 original size:26 final size:26
Alignment explanation
Indices: 20331361--20331412 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20331351 TTGAATAAAA
20331361 GAGATACAGGAATGCAAAGAAGACAT
1 GAGATACAGGAATGCAAAGAAGACAT
*
20331387 GAGATAGAGGAATGCAAAGAAGACAT
1 GAGATACAGGAATGCAAAGAAGACAT
20331413 ACTTGAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.29, T:0.12
Consensus pattern (26 bp):
GAGATACAGGAATGCAAAGAAGACAT
Found at i:20331981 original size:23 final size:21
Alignment explanation
Indices: 20331955--20332001 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
20331945 CGTCTAAATT
20331955 TAAATT-TAAAATATTATTATGTA
1 TAAATTATAAAAT-TTA-TAT-TA
20331978 TAAATTATAAAATTTATATTA
1 TAAATTATAAAATTTATATTA
20331999 TAA
1 TAA
20332002 GCATGATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.22
22 3 0.13
23 9 0.39
24 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAATTATAAAATTTATATTA
Found at i:20332974 original size:19 final size:18
Alignment explanation
Indices: 20332939--20332993 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
20332929 TTTATAAAAA
*
20332939 TATAAATTTTGGAATTTT
1 TATAAATTTTTGAATTTT
20332957 TATAAATATTTTGAA-TTT
1 TATAAAT-TTTTGAATTTT
*
20332975 TAGTAATTTTTTTGAATTT
1 TA-TAA-ATTTTTGAATTT
20332994 CTTTTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 12 0.39
19 16 0.52
20 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TATAAATTTTTGAATTTT
Found at i:20334772 original size:17 final size:17
Alignment explanation
Indices: 20334750--20334783 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20334740 ATGGGGTTTT
* *
20334750 TATTTATTTAATATTTA
1 TATTTATATAAAATTTA
20334767 TATTTATATAAAATTTA
1 TATTTATATAAAATTTA
20334784 AATTAATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTATATAAAATTTA
Found at i:20339836 original size:5 final size:5
Alignment explanation
Indices: 20339826--20339853 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20339816 CTGTGTGTTC
20339826 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
20339854 TACAAGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:20344034 original size:19 final size:18
Alignment explanation
Indices: 20343990--20344041 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
20343980 TGTAAATTTT
20343990 TATTTATTATTTTTTATTA
1 TATTT-TTATTTTTTATTA
20344009 TACTTTTTAGTTTTTTGA-TA
1 TA-TTTTTA-TTTTTT-ATTA
20344029 TATTTTCTATTTT
1 TATTTT-TATTTT
20344042 GGTCAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 13 0.45
20 15 0.52
21 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (18 bp):
TATTTTTATTTTTTATTA
Found at i:20346105 original size:27 final size:27
Alignment explanation
Indices: 20346075--20346182 Score: 110
Period size: 27 Copynumber: 3.9 Consensus size: 27
20346065 AAAGCCAAAT
*
20346075 TATATATGAATA-ATTTTAAAGAAAACA
1 TATATAT-AATAGATTTAAAAGAAAACA
* * *
20346102 TATATATAATAAATTTAGAAGAAAATA
1 TATATATAATAGATTTAAAAGAAAACA
* * *
20346129 TTTACATAACAGATTTGAAAAGAAAACA
1 TATATATAATAGATTT-AAAAGAAAACA
20346157 TATATATTAAATAGATTTAAAAGAAA
1 TATATA-T-AATAGATTTAAAAGAAA
20346183 CTATAAAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
26 4 0.06
27 31 0.48
28 13 0.20
29 9 0.14
30 8 0.12
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (27 bp):
TATATATAATAGATTTAAAAGAAAACA
Found at i:20346197 original size:29 final size:30
Alignment explanation
Indices: 20346139--20346198 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
20346129 TTTACATAAC
* * *
20346139 AGATTTGAAAAGAAAACATATATATTAAAT
1 AGATTTGAAAAGAAAACATAAAAATAAAAT
20346169 AGATTT-AAAAG-AAACTATAAAAATAAAAT
1 AGATTTGAAAAGAAAAC-ATAAAAATAAAAT
20346198 A
1 A
20346199 ACATAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (30 bp):
AGATTTGAAAAGAAAACATAAAAATAAAAT
Found at i:20347877 original size:88 final size:87
Alignment explanation
Indices: 20347752--20348161 Score: 479
Period size: 88 Copynumber: 4.7 Consensus size: 87
20347742 TCCGCTATTA
* * * * * * *
20347752 CTTAGGGAGATATGATTTGTAATCTT-CAGCTTGTTACCTTACTGCTTATGGGGTTAAAGCTTAC
1 CTTA-GGAGATAAGATCTGTAAT-TTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCAC
*
20347816 CGTCTTCGATCTGCTCCACTACTG
64 CGTCTTCGATCCGCTCCACTACTG
* * * *
20347840 CTTAGGAAGATAAGATCTGTAATTTCCAGCCTATTACCCTATTACTTAGGGGGTTAAGGCTCACC
1 CTTAGG-AGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACC
*
20347905 GTCTTCGATCTGCTCCACTACTG
65 GTCTTCGATCCGCTCCACTACTG
* *
20347928 CTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACT
1 CTT-AGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACC
*
20347993 GTCTTCAATCCGCTCCACTACTG
65 GTCTTCGATCCGCTCCACTACTG
* * *
20348016 CTTAGGGAGATAAGATTTGTAATCTT-CAGCCTGTTACCGTACTGCTTAAAGGGTTAAGGCTCAC
1 CTTA-GGAGATAAGATCTGTAAT-TTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCAC
* * *
20348080 TGTCTTAGATCCACTCCACTACTG
64 CGTCTTCGATCCGCTCCACTACTG
* * * * * *
20348104 TTTAGG-G--GAGATCTGTATTTTCCAGCCTGGTACCCTACTACTTAGGGGGTTAAGGCTC
1 CTTAGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTC
20348162 GTATCTTCAA
Statistics
Matches: 282, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
83 2 0.01
84 40 0.14
86 1 0.00
87 7 0.02
88 227 0.80
89 5 0.02
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (87 bp):
CTTAGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACCG
TCTTCGATCCGCTCCACTACTG
Found at i:20348014 original size:44 final size:44
Alignment explanation
Indices: 20347884--20348019 Score: 109
Period size: 44 Copynumber: 3.1 Consensus size: 44
20347874 TACCCTATTA
* * * *
20347884 CTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTG
1 CTTAAGGGGTTAAGGCTCACTGTCTTCAATCCGCTCCACTACTG
* * * * * * *
20347928 CTTAAGGAGATAA-GAT--CTGTAATTTCTAGCCTGTTACC-CTACTG
1 CTTAAGGGGTTAAGGCTCACTGT--CTTCAATCC-GCT-CCACTACTG
20347972 CTTAAGGGGTTAAGGCTCACTGTCTTCAATCCGCTCCACTACTG
1 CTTAAGGGGTTAAGGCTCACTGTCTTCAATCCGCTCCACTACTG
20348016 CTTA
1 CTTA
20348020 GGGAGATAAG
Statistics
Matches: 67, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
41 3 0.04
43 9 0.13
44 41 0.61
45 10 0.15
47 4 0.06
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (44 bp):
CTTAAGGGGTTAAGGCTCACTGTCTTCAATCCGCTCCACTACTG
Found at i:20348459 original size:177 final size:177
Alignment explanation
Indices: 20348112--20348695 Score: 766
Period size: 177 Copynumber: 3.3 Consensus size: 177
20348102 TGTTTAGGGG
* * * * * *
20348112 AGATCTGTA-TTTTCCAGCCTGGTACCCTACTACTTAGGGGGTTAAGGCTCGTATCTTCAACCTG
1 AGATCTGTAGTTTT-CAACCTGTTACCCTACTGCTTAAGGGGTTAAAGCTTGTATCTTCAACCTG
* *
20348176 CTTTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATCTGC-TCTATAGCCGATACATGGA
65 CTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATATGCTTC-ATAGCCGATACATGGA
* * *
20348240 GATAAGACTCACCATTTTCGATCTGCT-TCATAGTCCATACATGGAGATA
129 GATAAGACTCGCCATTTTTGATCTGCTCT-ATAGTCGATACATGGAGATA
* * *
20348289 AGACCTATAGTTTTCAACCTGTTACCTTACTGCTTAAGGGGTTAAAGCTTGTATCTTCAACCTGC
1 AGATCTGTAGTTTTCAACCTGTTACCCTACTGCTTAAGGGGTTAAAGCTTGTATCTTCAACCTGC
* * * * *
20348354 TGTCTTGCTACCTCAGAGAGATAAGGCCGGTAGCTAAAATATGCTTCATAACCAATACATAGAGA
66 TCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATATGCTTCATAGCCGATACATGGAGA
*
20348419 TAAGACTCGCCATTTTTGATCTACTCTATAG-CTGATACATGGAGATA
131 TAAGACTCGCCATTTTTGATCTGCTCTATAGTC-GATACATGGAGATA
* * * *
20348466 AGATCTGTAGTTTTTAGCTTGTTGCCCTACTGCTT-AGGCTGG-TAAAGCTTGTATCTTCAACCT
1 AGATCTGTAGTTTTCAACCTGTTACCCTACTGCTTAAGG--GGTTAAAGCTTGTATCTTCAACCT
* * * *
20348529 GCTCTCTTGCTACCTCAGAGATATAAGGCCGGTGGCTGAAATTTGCTCCATAGCCGATACATGGA
64 GCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATATGCTTCATAGCCGATACATGGA
* * *
20348594 GATAAGACTCGCCATTTTTAATTTGCTCCATAGTCGATACATGGAGATA
129 GATAAGACTCGCCATTTTTGATCTGCTCTATAGTCGATACATGGAGATA
* * *
20348643 AGATCTGTAGTTTTCATCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTA
1 AGATCTGTAGTTTTCAACCTGTTACCCTACTGCTTAAGGGGTTAAAGCTTGTA
20348696 AATTTACCGA
Statistics
Matches: 353, Mismatches: 45, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
176 6 0.02
177 335 0.95
178 12 0.03
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (177 bp):
AGATCTGTAGTTTTCAACCTGTTACCCTACTGCTTAAGGGGTTAAAGCTTGTATCTTCAACCTGC
TCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCTAAAATATGCTTCATAGCCGATACATGGAGA
TAAGACTCGCCATTTTTGATCTGCTCTATAGTCGATACATGGAGATA
Found at i:20353221 original size:19 final size:19
Alignment explanation
Indices: 20353197--20353242 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
20353187 TATGAAGTTT
*
20353197 AATGCACATG-ATGCAATG
1 AATGCAAATGTATGCAATG
*
20353215 CAATGCAAATGTATGGAATG
1 -AATGCAAATGTATGCAATG
20353235 AATGCAAA
1 AATGCAAA
20353243 AGAAAGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (19 bp):
AATGCAAATGTATGCAATG
Found at i:20355508 original size:25 final size:27
Alignment explanation
Indices: 20355468--20355525 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
20355458 AAAAAAAGCC
*
20355468 AAAT-TATATATGAATAATTTTA-AAG
1 AAATATATATATGAATAAATTTAGAAG
20355493 AAATATATATAT-AATAAATTTAGAAG
1 AAATATATATATGAATAAATTTAGAAG
20355519 AAA-ATAT
1 AAATATAT
20355526 TTACATAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (27 bp):
AAATATATATATGAATAAATTTAGAAG
Found at i:20355533 original size:27 final size:25
Alignment explanation
Indices: 20355480--20355533 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
20355470 ATTATATATG
* *
20355480 AATAATTTTAAAGAAATATATATAT
1 AATAAATTTAAAGAAATATATACAT
*
20355505 AATAAATTTAGAAGAAAATATTTACAT
1 AATAAATTTA-AAG-AAATATATACAT
20355532 AA
1 AA
20355534 CAGATTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (25 bp):
AATAAATTTAAAGAAATATATACAT
Found at i:20355593 original size:29 final size:30
Alignment explanation
Indices: 20355535--20355594 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
20355525 TTTACATAAC
* * *
20355535 AGATTTGAAAAGAAAACATATATATTAAAT
1 AGATTTGAAAAGAAAACATAAAAATAAAAT
20355565 AGATTT-AAAAG-AAACTATAAAAATAAAAT
1 AGATTTGAAAAGAAAAC-ATAAAAATAAAAT
20355594 A
1 A
20355595 ACATAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (30 bp):
AGATTTGAAAAGAAAACATAAAAATAAAAT
Found at i:20359029 original size:73 final size:73
Alignment explanation
Indices: 20358952--20359098 Score: 231
Period size: 73 Copynumber: 2.0 Consensus size: 73
20358942 ACATTTAAAC
* * * *
20358952 TTAACCATAAAATAATTATTCTCAATATTCATAATTTGAAATGGGGCTTTTAGTTTCCAAAGTGA
1 TTAACCATAAAATAATCATTCTCAAAATTCATAATTTGAAATGGGACTTTTAGTTTCCAAAGCGA
20359017 ATGAAGTT
66 ATGAAGTT
* * *
20359025 TTAACCATAAAATAATCATTCTCAAAATTCATAATTTTAATTGGGACTTTTGGTTTCCAAAGCGA
1 TTAACCATAAAATAATCATTCTCAAAATTCATAATTTGAAATGGGACTTTTAGTTTCCAAAGCGA
20359090 ATGAAGTT
66 ATGAAGTT
20359098 T
1 T
20359099 ATTCGATAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (73 bp):
TTAACCATAAAATAATCATTCTCAAAATTCATAATTTGAAATGGGACTTTTAGTTTCCAAAGCGA
ATGAAGTT
Found at i:20363885 original size:18 final size:17
Alignment explanation
Indices: 20363842--20363892 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
20363832 GGAAATATAG
*
20363842 ATTTAAAAAATAAGTTT
1 ATTTAAAAAATAAGTTC
* *
20363859 AGGTAAAAAAATAAGATTC
1 A-TTTAAAAAATAAG-TTC
20363878 ATTTAAAAAATAAGT
1 ATTTAAAAAATAAGT
20363893 CAAGTCTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 22 0.81
19 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (17 bp):
ATTTAAAAAATAAGTTC
Found at i:20367971 original size:18 final size:17
Alignment explanation
Indices: 20367930--20367972 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
20367920 ATATTAGAAT
*
20367930 AAAATAATAAGTATAATG
1 AAAAT-ATAAGGATAATG
20367948 ATAAATATAAGGATATATG
1 A-AAATATAAGGATA-ATG
20367967 AAAATA
1 AAAATA
20367973 ATACTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (17 bp):
AAAATATAAGGATAATG
Found at i:20368026 original size:22 final size:21
Alignment explanation
Indices: 20367993--20368040 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
20367983 TAAAAAGTAT
20367993 ATATATATACATGT-ATAATAA
1 ATATATATACAT-TAATAATAA
20368014 A-ATATACTAACATTAATAATAA
1 ATATATA-T-ACATTAATAATAA
20368036 ATATA
1 ATATA
20368041 ATAGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.22
21 3 0.13
22 12 0.52
23 3 0.13
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATATATACATTAATAATAA
Found at i:20368209 original size:22 final size:21
Alignment explanation
Indices: 20368129--20368268 Score: 82
Period size: 22 Copynumber: 6.7 Consensus size: 21
20368119 GAGATGAGAT
20368129 AAAATATATACATGGAATAGTA-A
1 AAAATATATACAT--AATA-TATA
*
20368152 AGAA-ATATACATAATATATA
1 AAAATATATACATAATATATA
*
20368172 AAAATATATA-ACTAATGATATC
1 AAAATATATACA-TAAT-ATATA
*
20368194 AAAATATGTACATAATAATATA
1 AAAATATATACATAAT-ATATA
20368216 TAAAATAT-TA-A-AA-A-A-A
1 -AAAATATATACATAATATATA
* *
20368232 AAACATATGTACATAACATATA
1 AAA-ATATATACATAATATATA
*
20368254 CAAAAAATATACATA
1 -AAAATATATACATA
20368269 TACATACATA
Statistics
Matches: 95, Mismatches: 8, Indels: 29
0.72 0.06 0.22
Matches are distributed among these distances:
15 3 0.03
16 5 0.05
17 3 0.03
18 2 0.02
19 4 0.04
20 12 0.13
21 11 0.12
22 41 0.43
23 14 0.15
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATATATACATAATATATA
Found at i:20368400 original size:2 final size:2
Alignment explanation
Indices: 20368388--20368427 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
20368378 AATTAAAATA
* *
20368388 AT AT CAT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20368428 ATAAAACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:20368489 original size:16 final size:15
Alignment explanation
Indices: 20368454--20368493 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
20368444 TATTATATAT
20368454 ATAATAAT-ACTAGA
1 ATAATAATAACTAGA
20368468 ACTAATAATAACTAGTA
1 A-TAATAATAACTAG-A
20368485 ATAATAATA
1 ATAATAATA
20368494 CATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 7 0.30
16 13 0.57
17 2 0.09
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAACTAGA
Found at i:20368588 original size:3 final size:3
Alignment explanation
Indices: 20368470--20368572 Score: 57
Period size: 3 Copynumber: 33.7 Consensus size: 3
20368460 ATACTAGAAC
* * **
20368470 TAA TAA TAA CTAG TAA TAA TAA TACA TTAA AAA TAA TAA T-A TGT TAA
1 TAA TAA TAA -TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
** * * * *
20368517 TAA CCA GAA TAT TAA TAA TAA CAA TAA TAA TAA TAGA -AA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
20368562 TAT TAA TAA TA
1 TAA TAA TAA TA
20368573 TTAGGAATGA
Statistics
Matches: 75, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
2 3 0.04
3 65 0.87
4 5 0.07
5 2 0.03
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20371219 original size:38 final size:38
Alignment explanation
Indices: 20371120--20371220 Score: 102
Period size: 39 Copynumber: 2.7 Consensus size: 38
20371110 AATAAACCCA
* *
20371120 ACAA-CTAAGCCTCTAAATTGAAAAATAAATGGACCTT
1 ACAATCTAAGCTTCTAAACTGAAAAATAAATGGACCTT
*
20371157 ACAAT-TAGGTCTT-TAAACTAGAAAAAGTAAATGGACCTT
1 ACAATCTAAG-CTTCTAAACT-GAAAAA-TAAATGGACCTT
* *
20371196 GC-ATCTAAGCTTCTATACTGAAAAA
1 ACAATCTAAGCTTCTAAACTGAAAAA
20371221 CAAAATTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
37 12 0.23
38 19 0.37
39 21 0.40
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (38 bp):
ACAATCTAAGCTTCTAAACTGAAAAATAAATGGACCTT
Found at i:20372868 original size:2 final size:2
Alignment explanation
Indices: 20372861--20372886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20372851 ATTAAAGGTT
20372861 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20372887 AGTAATATAG
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):
TA
Found at i:20375942 original size:40 final size:40
Alignment explanation
Indices: 20375887--20376056 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
20375877 AACATTGGAA
20375887 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20375927 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
20375967 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
20376006 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
20376047 CTATATCCGG
1 ATATATCCGG
20376057 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:20384040 original size:40 final size:40
Alignment explanation
Indices: 20383985--20384194 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20383975 AACATTGGAA
20383985 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20384025 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20384065 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
20384105 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
20384144 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
20384185 CTATATCCGG
1 ATATATCCGG
20384195 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:20386035 original size:40 final size:37
Alignment explanation
Indices: 20385936--20386066 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 37
20385926 CCTCATGAAT
** *
20385936 AATACCATACCTACATTTTTCAACTCGGTATGG--GA
1 AATACCATACCTACATTTCACAACTCAGTATGGATGA
* **
20385971 AAT-GCATACCTACATTTCTTAACTCAGTATGGATTTGA
1 AATACCATACCTACATTTCACAACTCAGTATGGA--TGA
20386009 TAATACCATACCTACATTTCACAACTCAGTATGGATG-
1 -AATACCATACCTACATTTCACAACTCAGTATGGATGA
20386046 -ATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
20386067 CTTGCCATGG
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
34 25 0.30
35 24 0.29
38 4 0.05
39 3 0.04
40 27 0.33
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (37 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATGA
Found at i:20390286 original size:49 final size:49
Alignment explanation
Indices: 20390226--20390388 Score: 209
Period size: 49 Copynumber: 3.5 Consensus size: 49
20390216 TACATATGTG
* * *
20390226 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
*
20390275 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAA--G--TG--TA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
*
20390318 --TG-TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
*
20390364 TGTGATAAGGCCTAATGGCTAATGT
1 TGTGATAAGGCCTAATGGCCAATGT
20390389 AAAATATATG
Statistics
Matches: 99, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
40 33 0.33
41 2 0.02
42 1 0.01
43 2 0.02
44 2 0.02
45 2 0.02
46 2 0.02
47 1 0.01
48 2 0.02
49 52 0.53
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:20390324 original size:40 final size:40
Alignment explanation
Indices: 20390280--20390361 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
20390270 GTATATGTGA
20390280 TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATG
1 TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATG
20390320 TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATG
1 TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATG
20390360 TA
1 TA
20390362 TATGTGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (40 bp):
TAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATG
Found at i:20390534 original size:37 final size:37
Alignment explanation
Indices: 20390484--20390568 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
20390474 GGAATATGTT
*
20390484 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
20390521 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
20390558 CCGGGTAAGAC
1 CCGGGTAAGAC
20390569 TTCTTTTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:20394354 original size:40 final size:40
Alignment explanation
Indices: 20394246--20394455 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20394236 CGGGATTTAA
* * * * *
20394246 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
20394286 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20394326 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20394366 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20394406 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20394446 CCGGATATAT
1 CCGGATATAT
20394456 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:20402492 original size:40 final size:40
Alignment explanation
Indices: 20402384--20402593 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20402374 CGGGATTTAA
* * * * *
20402384 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
20402424 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20402464 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20402504 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20402544 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20402584 CCGGATATAT
1 CCGGATATAT
20402594 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:20408118 original size:40 final size:40
Alignment explanation
Indices: 20408020--20408237 Score: 266
Period size: 40 Copynumber: 5.5 Consensus size: 40
20408010 TGGATGATAA
* *
20408020 CCGGGATAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
20408061 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
20408101 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
20408141 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
20408181 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
20408220 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20408238 TACTTGGCTT
Statistics
Matches: 157, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 15 0.10
39 15 0.10
40 101 0.64
41 23 0.15
42 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:20414673 original size:39 final size:39
Alignment explanation
Indices: 20414619--20414771 Score: 243
Period size: 39 Copynumber: 3.9 Consensus size: 39
20414609 GAATGTTCGA
*
20414619 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
20414658 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
20414697 ATGATATTCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
20414736 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
20414772 GGTTACCATA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 87 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:20414787 original size:40 final size:39
Alignment explanation
Indices: 20414620--20414801 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
20414610 AATGTTCGAG
* *
20414620 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
20414659 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
20414698 TGATATTCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
20414737 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
20414777 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
20414802 TGTTTTGAAC
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 86 0.68
40 40 0.32
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:20423568 original size:40 final size:40
Alignment explanation
Indices: 20423513--20423682 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
20423503 AACATTGGAA
20423513 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20423553 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
20423593 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
20423632 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
20423673 CTATATCCGG
1 ATATATCCGG
20423683 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:20431665 original size:40 final size:40
Alignment explanation
Indices: 20431610--20431819 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20431600 AACATTGGAA
20431610 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20431650 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
20431690 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
20431730 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
20431769 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
20431810 CTATATCCGG
1 ATATATCCGG
20431820 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:20433671 original size:40 final size:37
Alignment explanation
Indices: 20433585--20433716 Score: 157
Period size: 35 Copynumber: 3.6 Consensus size: 37
20433575 TTTTCCTCAT
*
20433585 TGAAATACCATACCTACATTT-TTCAACTCGGTATGG-
1 TGAAATACCATACCTACATTTCTT-AACTCAGTATGGA
*
20433621 -GAAATGCCATACCTACATTTCTTAACTCAGTATGGA
1 TGAAATACCATACCTACATTTCTTAACTCAGTATGGA
**
20433657 TTTGATAATACCATACCTACATTTCACAACTCAGTATGGA
1 --TGA-AATACCATACCTACATTTCTTAACTCAGTATGGA
20433697 TG--ATACCATACCTACATTTC
1 TGAAATACCATACCTACATTTC
20433717 ACACTTTGCC
Statistics
Matches: 85, Mismatches: 5, Indels: 13
0.83 0.05 0.13
Matches are distributed among these distances:
35 48 0.56
36 2 0.02
38 2 0.02
39 2 0.02
40 31 0.36
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (37 bp):
TGAAATACCATACCTACATTTCTTAACTCAGTATGGA
Found at i:20438472 original size:33 final size:32
Alignment explanation
Indices: 20438405--20438474 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
20438395 AAATTAAAAA
*
20438405 TAATTTTTTTAAAAATAATTAATTACTAACGT
1 TAATTTTTTTAAAAATAATTAATTACTAAAGT
**
20438437 TAATTTTTCTTAAAAATAATTCTTTGA-TAAAGT
1 TAATTTTT-TTAAAAATAATTAATT-ACTAAAGT
20438470 TAATT
1 TAATT
20438475 CAAAACTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 8 0.24
33 24 0.73
34 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (32 bp):
TAATTTTTTTAAAAATAATTAATTACTAAAGT
Found at i:20439131 original size:16 final size:15
Alignment explanation
Indices: 20439102--20439130 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20439092 GAGTATAATA
20439102 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
20439117 AAATATTAAAAAAA
1 AAATATTAAAAAAA
20439131 AAGAGAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:20452556 original size:25 final size:28
Alignment explanation
Indices: 20452501--20452558 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
20452491 ACTTTTCCCT
*
20452501 CAAAACTTTTACTGCTTCCCACTTTCCTCC
1 CAAAACTTTTACTGC-TCCCAC-TTCATCC
20452531 CAAAACTTTTACT-C-CCCA-TTCATCC
1 CAAAACTTTTACTGCTCCCACTTCATCC
20452556 CAA
1 CAA
20452559 CCCCCCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.33
27 4 0.15
29 1 0.04
30 13 0.48
ACGTcount: A:0.26, C:0.40, G:0.02, T:0.33
Consensus pattern (28 bp):
CAAAACTTTTACTGCTCCCACTTCATCC
Found at i:20453156 original size:19 final size:20
Alignment explanation
Indices: 20453119--20453156 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20453109 AAGTTAATCA
*
20453119 AAATTTTGATTAAGGTGGAC
1 AAATTTTGATTAAGATGGAC
*
20453139 AAATTTT-ATTACGATGGA
1 AAATTTTGATTAAGATGGA
20453157 TGACGGTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (20 bp):
AAATTTTGATTAAGATGGAC
Found at i:20454427 original size:9 final size:9
Alignment explanation
Indices: 20454413--20454443 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20454403 TACCAATCAT
20454413 GTATTTCAG
1 GTATTTCAG
*
20454422 GTATTTCAA
1 GTATTTCAG
20454431 GTATTTCAG
1 GTATTTCAG
20454440 GTAT
1 GTAT
20454444 ATTCGAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (9 bp):
GTATTTCAG
Found at i:20454820 original size:25 final size:24
Alignment explanation
Indices: 20454786--20454836 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
20454776 AAGTTCAAGC
20454786 GAGCCATATCAAGAAGCTCACAAA
1 GAGCCATATCAAGAAGCTCACAAA
* * *
20454810 GAGCCTATATCAATATGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCACAAA
20454835 GA
1 GA
20454837 TCTACGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCACAAA
Found at i:20459799 original size:18 final size:18
Alignment explanation
Indices: 20459776--20459821 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
20459766 ATGAAATAAG
20459776 TTATATGTTGTTGTTCAT
1 TTATATGTTGTTGTTCAT
20459794 TTATATGTTGTTGTTCAT
1 TTATATGTTGTTGTTCAT
*
20459812 TTATAAGTTG
1 TTATATGTTG
20459822 AAGTTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.04, G:0.17, T:0.59
Consensus pattern (18 bp):
TTATATGTTGTTGTTCAT
Found at i:20461825 original size:14 final size:14
Alignment explanation
Indices: 20461806--20461844 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20461796 CCAGAAAAGT
* *
20461806 AAATCATTTTTCAG
1 AAATCATTTTCCAA
20461820 AAATCATTTTCCAA
1 AAATCATTTTCCAA
20461834 AAATCATTTTC
1 AAATCATTTTC
20461845 AGGAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:20465707 original size:30 final size:29
Alignment explanation
Indices: 20465661--20465721 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
20465651 CAAGTAGCCG
20465661 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
*
20465690 AAGCTAGTTTGAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
20465720 AA
1 AA
20465722 ACTTCCGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:20469234 original size:33 final size:33
Alignment explanation
Indices: 20469192--20469322 Score: 174
Period size: 33 Copynumber: 4.0 Consensus size: 33
20469182 GGAGATCATA
*
20469192 GAGATCCAACAGAAATTAGAATGCCTGGAAATG
1 GAGATCCAACAGAAATTAGAATACCTGGAAATG
* * *
20469225 GAGATCCAACAGGAATTGGAATGCCTGGAAATG
1 GAGATCCAACAGAAATTAGAATACCTGGAAATG
* * * *
20469258 GAGCTCCTACAGGAATTAGAATACCTGGAAATA
1 GAGATCCAACAGAAATTAGAATACCTGGAAATG
20469291 GAGATCCAACA-AGAATTAGAATACCTGGAAAT
1 GAGATCCAACAGA-AATTAGAATACCTGGAAAT
20469323 CGGGGTCCCA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (33 bp):
GAGATCCAACAGAAATTAGAATACCTGGAAATG
Found at i:20470304 original size:14 final size:14
Alignment explanation
Indices: 20470281--20470314 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20470271 ATGTTATTTG
*
20470281 CTATTATATTGTTA
1 CTATTTTATTGTTA
20470295 CTATTTTATTGTTA
1 CTATTTTATTGTTA
*
20470309 TTATTT
1 CTATTT
20470315 GGATATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (14 bp):
CTATTTTATTGTTA
Found at i:20473142 original size:18 final size:18
Alignment explanation
Indices: 20473119--20473153 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20473109 TCTTCTATAA
20473119 AGTATTGATACTAATTTT
1 AGTATTGATACTAATTTT
20473137 AGTATTGATACTAATTT
1 AGTATTGATACTAATTT
20473154 GCAGTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (18 bp):
AGTATTGATACTAATTTT
Found at i:20477916 original size:57 final size:58
Alignment explanation
Indices: 20477853--20477970 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 58
20477843 TTTAGGTCAT
* *
20477853 TTTTCATTTTCATTTTAGAGGAAACCACATTCATTTCCAAATTATTT-C-ATTTCTCTA
1 TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAA-TATTTCCTATTTCTCTA
* * *
20477910 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTTCAAATATTTCCTATTTCTCTA
1 TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATATTTCCTATTTCTCTA
20477968 TTT
1 TTT
20477971 CACCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 5 0.09
57 37 0.69
58 12 0.22
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (58 bp):
TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATATTTCCTATTTCTCTA
Found at i:20480245 original size:2 final size:2
Alignment explanation
Indices: 20480238--20480270 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20480228 CACAAAGTGA
20480238 AT AT 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 AT AT
20480271 TTTGTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20482298 original size:46 final size:46
Alignment explanation
Indices: 20482244--20482419 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
20482234 TGGTTGAGCA
*
20482244 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *** * * ** *
20482290 TCCAAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
20482337 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
20482383 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20482420 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 70 0.67
47 34 0.33
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20482400 original size:93 final size:93
Alignment explanation
Indices: 20482241--20482411 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
20482231 GGATGGTTGA
* * *
20482241 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
20482306 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * *
20482334 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
20482399 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20482412 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCATTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:20485354 original size:15 final size:15
Alignment explanation
Indices: 20485316--20485359 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20485306 CATAGTATCG
* *
20485316 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTC
20485331 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTC
20485346 TATCTTGGATTTCT
1 TATCTTGGATTTCT
20485360 TATTCGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:20487799 original size:46 final size:46
Alignment explanation
Indices: 20487749--20487922 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
20487739 TGGTTGAGCA
*
20487749 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * ** *
20487795 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--GATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
20487840 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
20487886 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20487923 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
44 2 0.02
45 33 0.31
46 70 0.65
47 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20487901 original size:91 final size:91
Alignment explanation
Indices: 20487746--20487914 Score: 293
Period size: 91 Copynumber: 1.9 Consensus size: 91
20487736 GGATGGTTGA
* *
20487746 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20487811 TGAGTCCGAGTTCGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGATGTAACTAG
* * *
20487837 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
20487902 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20487915 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGATGTAACTAG
Found at i:20490851 original size:15 final size:14
Alignment explanation
Indices: 20490821--20490886 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
20490811 TCGTATCTTG
20490821 GGTTTCTTTATCTCT
1 GGTTTCTTTAT-TCT
20490836 GGATTTCTTTATTCT
1 GG-TTTCTTTATTCT
*
20490851 GGTTTCTCTA-TCTT
1 GGTTTCTTTATTC-T
20490865 GGATTTCTTTATTC-
1 GG-TTTCTTTATTCT
20490879 GGTTTCTT
1 GGTTTCTT
20490887 GTTATCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 8 0.18
14 12 0.27
15 14 0.31
16 11 0.24
ACGTcount: A:0.09, C:0.17, G:0.15, T:0.59
Consensus pattern (14 bp):
GGTTTCTTTATTCT
Found at i:20490875 original size:29 final size:29
Alignment explanation
Indices: 20490821--20490885 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 29
20490811 TCGTATCTTG
*
20490821 GGTTTCTTTATCTCTGGATTTCTTTATTC
1 GGTTTCTCTATCTCTGGATTTCTTTATTC
20490850 TGGTTTCTCTATCT-TGGATTTCTTTATTC
1 -GGTTTCTCTATCTCTGGATTTCTTTATTC
20490879 GGTTTCT
1 GGTTTCT
20490886 TGTTATCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 7 0.21
29 15 0.44
30 12 0.35
ACGTcount: A:0.09, C:0.17, G:0.15, T:0.58
Consensus pattern (29 bp):
GGTTTCTCTATCTCTGGATTTCTTTATTC
Found at i:20493285 original size:46 final size:46
Alignment explanation
Indices: 20493235--20493410 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
20493225 ATGTTGAGCA
20493235 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20493281 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
20493326 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
20493374 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20493411 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20493391 original size:93 final size:93
Alignment explanation
Indices: 20493232--20493402 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
20493222 AGGATGTTGA
* *
20493232 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20493297 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
20493325 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20493390 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
20493403 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20495655 original size:40 final size:40
Alignment explanation
Indices: 20495547--20495756 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20495537 CGGGATTTAA
* * * * *
20495547 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
20495587 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20495627 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20495667 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20495707 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20495747 CCGGATATAT
1 CCGGATATAT
20495757 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:20503783 original size:40 final size:40
Alignment explanation
Indices: 20503675--20503884 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
20503665 CGGGATTTAA
* * * * *
20503675 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
20503715 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20503755 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20503795 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20503835 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
20503875 CCGGATATAT
1 CCGGATATAT
20503885 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:20511099 original size:93 final size:93
Alignment explanation
Indices: 20510987--20511158 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
20510977 CGCCCATAAG
* *
20510987 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
20511052 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
20511080 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
20511145 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
20511159 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:20511155 original size:46 final size:46
Alignment explanation
Indices: 20510980--20511155 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
20510970 TGTAACCCGC
* * *
20510980 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
20511026 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
20511076 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
20511119 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
20511156 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:20518643 original size:93 final size:93
Alignment explanation
Indices: 20518531--20518702 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
20518521 CGCCCATAAG
* *
20518531 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
20518596 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
20518624 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
20518689 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
20518703 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:20518699 original size:46 final size:46
Alignment explanation
Indices: 20518524--20518699 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
20518514 TGTAACCCGC
* * *
20518524 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
20518570 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
20518620 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
20518663 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
20518700 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:20520734 original size:2 final size:2
Alignment explanation
Indices: 20520727--20520751 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20520717 CATATGTTGG
20520727 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
20520752 GTAGTTATTC
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:20525407 original size:25 final size:25
Alignment explanation
Indices: 20525378--20525425 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20525368 TTATAACATG
* * *
20525378 AAAATGACCGTTTTGCCCCTAGGCA
1 AAAATGACCATTATACCCCTAGGCA
20525403 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
20525426 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGCA
Found at i:20525509 original size:11 final size:11
Alignment explanation
Indices: 20525473--20525528 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
20525463 CATGGTATGT
20525473 ATGATATGCAC
1 ATGATATGCAC
* *
20525484 ATGACATG--T
1 ATGATATGCAC
20525493 ATGATATGCAC
1 ATGATATGCAC
*
20525504 ATGATATG--T
1 ATGATATGCAC
20525513 ATGATATGCAC
1 ATGATATGCAC
20525524 ATGAT
1 ATGAT
20525529 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:20525528 original size:20 final size:20
Alignment explanation
Indices: 20525462--20525528 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
20525452 ATTTTGATAA
*
20525462 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
20525482 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
20525502 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
20525522 ACATGAT
1 ACATGAT
20525529 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:20525646 original size:46 final size:47
Alignment explanation
Indices: 20525579--20525674 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
20525569 AGGAAGTGAA
20525579 AAAGGGCTTACGCCCCAGTTATT-AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTACGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
* **
20525625 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTACGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
20525672 AAA
1 AAA
20525675 AGAGGCTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 22 0.48
47 24 0.52
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (47 bp):
AAAGGGCTTACGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATT
Found at i:20525657 original size:24 final size:24
Alignment explanation
Indices: 20525578--20525681 Score: 158
Period size: 23 Copynumber: 4.4 Consensus size: 24
20525568 GAGGAAGTGA
20525578 AAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTACGCCCCAGTTATT
20525602 -AAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTACGCCCCAGTTATT
*
20525625 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTACGCCCCAGTTATT
**
20525648 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTACGCCCCAGTTATT
20525672 AAAAGAGGCT
1 AAAAG-GGCT
20525682 AGGCTTCCAG
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
23 45 0.59
24 27 0.36
25 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTACGCCCCAGTTATT
Found at i:20525924 original size:31 final size:31
Alignment explanation
Indices: 20525889--20525952 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
20525879 CGTTTACAGT
20525889 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
20525920 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
20525951 AA
1 AA
20525953 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:20529066 original size:15 final size:15
Alignment explanation
Indices: 20529032--20529078 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
20529022 TTTAATTCTA
*
20529032 ATTATTTTAAT-ATT
1 ATTATTTTATTAATT
20529046 -TTATTTTATTAATT
1 ATTATTTTATTAATT
20529060 ATTA-TTTATTGAATT
1 ATTATTTTATT-AATT
20529075 ATTA
1 ATTA
20529079 GCCTAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 9 0.31
14 9 0.31
15 11 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTATTTTATTAATT
Found at i:20532779 original size:27 final size:27
Alignment explanation
Indices: 20532749--20532809 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
20532739 TTCAGAAAAA
*
20532749 AAAAGTTTTTA-GGGTTTAGAAGGAAGT
1 AAAAGTTTTAAGGGGTTT-GAAGGAAGT
* *
20532776 AAAAATTTTAAGGGGTTTGATGGAAGT
1 AAAAGTTTTAAGGGGTTTGAAGGAAGT
20532803 AAAAGTT
1 AAAAGTT
20532810 ATAGGGGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (27 bp):
AAAAGTTTTAAGGGGTTTGAAGGAAGT
Found at i:20532815 original size:26 final size:28
Alignment explanation
Indices: 20532760--20532816 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
20532750 AAAGTTTTTA
*
20532760 GGGTTTAGAAGGAAGTAAAAATTTTAAG
1 GGGTTTAGAAGGAAGTAAAAATTATAAG
* *
20532788 GGGTTT-GATGGAAGTAAAAGTTAT-AG
1 GGGTTTAGAAGGAAGTAAAAATTATAAG
20532814 GGG
1 GGG
20532817 AAAGAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 15 0.58
28 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (28 bp):
GGGTTTAGAAGGAAGTAAAAATTATAAG
Found at i:20539177 original size:13 final size:13
Alignment explanation
Indices: 20539159--20539188 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
20539149 ATTGATGTTG
20539159 TTTTAATTTTATC
1 TTTTAATTTTATC
20539172 TTTTAATTTTATC
1 TTTTAATTTTATC
20539185 TTTT
1 TTTT
20539189 TTTAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTATC
Done.