Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 45 of 89
Found at i:9957049 original size:46 final size:46
Alignment explanation
Indices: 9956979--9957322 Score: 508
Period size: 46 Copynumber: 7.5 Consensus size: 46
9956969 AAATGAATGA
** ** * *
9956979 ATAAATGAAAAAACATAACAGTGCATTATCAGCATTAAAGGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
9957025 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * *
9957071 ATAAATGAAAATACATAATGGTGAATTGTCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* *
9957117 ATAAATGAAAATGCATAAAGGTGCATTATCGGCATGAAAGAATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
9957163 ATAAATGAAAATGCAAAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * *
9957209 ATAAATGAAAATGTATAACGGTGCATTATCGGCATGAAAGGATTCT
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
9957255 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGGC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* *
9957301 ACAAATGAAAATACATAATGGT
1 ATAAATGAAAATGCATAATGGT
9957323 ATATTAACGA
Statistics
Matches: 267, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 267 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
Found at i:9965102 original size:17 final size:18
Alignment explanation
Indices: 9965067--9965103 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9965057 GGATTAATAA
9965067 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
9965085 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
9965102 AT
1 AT
9965104 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:9968291 original size:53 final size:53
Alignment explanation
Indices: 9968213--9968434 Score: 284
Period size: 53 Copynumber: 4.2 Consensus size: 53
9968203 TTTGCACCTA
* * * * *
9968213 AGTGCCGAAATTGTAATTCACAAACTCATTATGAATTCCATGGATGCACATAT
1 AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACAT
* * * * * *
9968266 AGTGTCGAAATGGTAATTGATAAACTCAATATAAATTCCATGGATGCACACAT
1 AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACAT
* *
9968319 AATGCCAAAATGGTAATTCATAAACTCATTATGAATACCATATG-TGCACACAT
1 AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCAT-GGATGCACACAT
* * *
9968372 AGTGTCAAAATGGTAATTCAGAAACTCATTATGAATACCATGGGTGCACACAT
1 AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACAT
9968425 AGTGCCAAAA
1 AGTGCCAAAA
9968435 GTACACATAG
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
52 1 0.01
53 145 0.99
54 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACAT
Found at i:9972478 original size:7 final size:7
Alignment explanation
Indices: 9972466--9972495 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
9972456 AAATATCCTC
9972466 ATCTTTA
1 ATCTTTA
9972473 ATCTTTA
1 ATCTTTA
9972480 ATCTTTA
1 ATCTTTA
9972487 ATCTTTA
1 ATCTTTA
9972494 AT
1 AT
9972496 TGAAGGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (7 bp):
ATCTTTA
Found at i:9975272 original size:53 final size:53
Alignment explanation
Indices: 9975189--9975383 Score: 255
Period size: 53 Copynumber: 3.7 Consensus size: 53
9975179 GTTGCACTTA
* *
9975189 AGTGTCGAAATGGTAGTTCACAAACTCATTATGAATTCCATGGATGCACACAT
1 AGTGTCGAAATGGTAATTCATAAACTCATTATGAATTCCATGGATGCACACAT
* * * * **
9975242 AATGTCGAAATGGTAATTCATAAACACATTATGAATTCTATGAATTAACACAT
1 AGTGTCGAAATGGTAATTCATAAACTCATTATGAATTCCATGGATGCACACAT
* * * *
9975295 AGTGCCAAAATGGTAATTCATAAACTCATTATGAATACCATGGGTGCACACAT
1 AGTGTCGAAATGGTAATTCATAAACTCATTATGAATTCCATGGATGCACACAT
* * *
9975348 AGTGTCGAAATGGTAATTTAGAAATTCATTATGAAT
1 AGTGTCGAAATGGTAATTCATAAACTCATTATGAAT
9975384 CATTGGTACA
Statistics
Matches: 119, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (53 bp):
AGTGTCGAAATGGTAATTCATAAACTCATTATGAATTCCATGGATGCACACAT
Found at i:9981143 original size:28 final size:28
Alignment explanation
Indices: 9981109--9981169 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
9981099 GTTAAACTGT
9981109 ATTACATTTCACTTAAATATTGAACTAC
1 ATTACATTTCACTTAAATATTGAACTAC
* *
9981137 ATTACATTTCACTTGAATGTTGAACTAC
1 ATTACATTTCACTTAAATATTGAACTAC
9981165 ATTAC
1 ATTAC
9981170 TTGAATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (28 bp):
ATTACATTTCACTTAAATATTGAACTAC
Found at i:9981552 original size:131 final size:131
Alignment explanation
Indices: 9981313--9981579 Score: 331
Period size: 131 Copynumber: 2.0 Consensus size: 131
9981303 ATTAACATCA
* * * * *
9981313 TTTTAAGATGAAAAAACCATTAAAGCACTACACATTTGCGGCATTTTTTGTTCTCAAACGTTGCT
1 TTTTAAGATGAAAAAACCACTAAAGCACTACACAATTGCAGCATTTTTTGTTCTCAAACATCGCT
* ** * * * * *
9981378 ATATTGCTTAACATTTAGTGGCGTTTGTGTACGAAATGCCACTAAATATCATGGTATATAGCGTC
66 ATATAGCTTAACATTTAACGACATTTGTGTACAAAACGCCACTAAATATCATGGTATATAGCGAC
9981443 G
131 G
* * *
9981444 TTTTAAGATG-AAAAACGCACTAAAGGACTACATAATTGTAGCATTTTTTGCTT-TCAAACATCG
1 TTTTAAGATGAAAAAAC-CACTAAAGCACTACACAATTGCAGCATTTTTTG-TTCTCAAACATCG
* * *
9981507 CTATATAGCTTAACATTTAACGACATTTGTGTACAAAACGTCACTAAATATTATTGTATATAGCG
64 CTATATAGCTTAACATTTAACGACATTTGTGTACAAAACGCCACTAAATATCATGGTATATAGCG
9981572 ACG
129 ACG
9981575 TTTTA
1 TTTTA
9981580 TTCACAAACG
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
130 6 0.05
131 107 0.93
132 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (131 bp):
TTTTAAGATGAAAAAACCACTAAAGCACTACACAATTGCAGCATTTTTTGTTCTCAAACATCGCT
ATATAGCTTAACATTTAACGACATTTGTGTACAAAACGCCACTAAATATCATGGTATATAGCGAC
G
Found at i:9982717 original size:63 final size:64
Alignment explanation
Indices: 9982647--9982786 Score: 221
Period size: 63 Copynumber: 2.2 Consensus size: 64
9982637 GAATAATTTC
* * *
9982647 TATTAGATTTTAATATATATCATTTTAATTTAATAT-TAAAAATATTAAATTGTGAGCAGTAAA
1 TATTAGATTTTAATATATAGCATTTTAACTTAATATCAAAAAATATTAAATTGTGAGCAGTAAA
*
9982710 TATTAGATTTTAATATATAGCATTTTAACTTAATATCAAAAAATATTAAATTGTGAGCGGTAAA
1 TATTAGATTTTAATATATAGCATTTTAACTTAATATCAAAAAATATTAAATTGTGAGCAGTAAA
9982774 TA-TATGATTTTAA
1 TATTA-GATTTTAA
9982787 AAAGTATGAC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
63 36 0.51
64 35 0.49
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (64 bp):
TATTAGATTTTAATATATAGCATTTTAACTTAATATCAAAAAATATTAAATTGTGAGCAGTAAA
Found at i:9986806 original size:88 final size:86
Alignment explanation
Indices: 9986702--9986862 Score: 277
Period size: 88 Copynumber: 1.8 Consensus size: 86
9986692 TAATTTCAAT
9986702 TAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAATCCCCAATATGATTAGGGTAAC
1 TAATTAATTAAATATAGATTTAATTAATTTAAAATAAT-AAAA-CCCCAATATGATTAGGGTAAC
9986767 TTGGATATAAGAGGATTATTAAA
64 TTGGATATAAGAGGATTATTAAA
* *
9986790 TAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTT
1 TAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCCAATATGATTAGGGTAACTT
*
9986855 GGCTATAA
66 GGATATAA
9986863 AAGGGTGTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
86 29 0.41
87 4 0.06
88 37 0.53
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (86 bp):
TAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCCAATATGATTAGGGTAACTT
GGATATAAGAGGATTATTAAA
Found at i:9994583 original size:22 final size:21
Alignment explanation
Indices: 9994565--9994646 Score: 83
Period size: 23 Copynumber: 3.7 Consensus size: 21
9994555 TTAATTTTCC
9994565 TTTTTTCCTTTTTTTATTTTT
1 TTTTTTCCTTTTTTTATTTTT
* *
9994586 TTTCCTTTTCTTTTTTAATTTTT
1 TTT--TTTCCTTTTTTTATTTTT
**
9994609 TTATTTTTATTTTTTTATTTTTAT
1 TT-TTTTCCTTTTTTTA-TTTT-T
9994633 TTTTTTCCTTTTTT
1 TTTTTTCCTTTTTT
9994647 CTTTCTTCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 3 0.06
22 11 0.22
23 32 0.64
24 4 0.08
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTCCTTTTTTTATTTTT
Found at i:9994608 original size:9 final size:8
Alignment explanation
Indices: 9994573--9994638 Score: 61
Period size: 8 Copynumber: 8.9 Consensus size: 8
9994563 CCTTTTTTCC
9994573 TTTTTTTA
1 TTTTTTTA
9994581 TTTTTTT-
1 TTTTTTTA
** *
9994588 TCCTTTTC
1 TTTTTTTA
*
9994596 TTTTTTAA
1 TTTTTTTA
9994604 TTTTTTTA
1 TTTTTTTA
9994612 --TTTTTA
1 TTTTTTTA
9994618 TTTTTTTA
1 TTTTTTTA
9994626 --TTTTTA
1 TTTTTTTA
9994632 TTTTTTT
1 TTTTTTT
9994639 CCTTTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 12 0.26
7 5 0.11
8 29 0.63
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:9994645 original size:15 final size:14
Alignment explanation
Indices: 9994573--9994638 Score: 80
Period size: 14 Copynumber: 4.5 Consensus size: 14
9994563 CCTTTTTTCC
9994573 TTTTTTTATTTTT-
1 TTTTTTTATTTTTA
*
9994586 TTTCCTTTTCTTTTTTAA
1 TTT--TTTT-ATTTTT-A
9994604 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
9994618 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
9994632 TTTTTTT
1 TTTTTTT
9994639 CCTTTTTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
13 3 0.07
14 22 0.48
15 9 0.20
16 9 0.20
18 3 0.07
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:9997985 original size:14 final size:14
Alignment explanation
Indices: 9997934--9997999 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
9997924 GTGCAAAAGT
* *
9997934 AAATATAAAAATAC
1 AAATGTAAAAATGC
* *
9997948 AAATGCAAAGATGCC
1 AAATGTAAAAATG-C
*
9997963 AAATGTAAATATGC
1 AAATGTAAAAATGC
* *
9997977 AAATATAAAAATGT
1 AAATGTAAAAATGC
9997991 AAATGTAAA
1 AAATGTAAA
9998000 TTATTTAACA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
14 29 0.71
15 12 0.29
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.23
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:10001805 original size:3 final size:3
Alignment explanation
Indices: 10001797--10001849 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
10001787 ATTATTTATT
* *
10001797 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10001841 TAA TAA TAA
1 TAA TAA TAA
10001850 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:10001821 original size:19 final size:18
Alignment explanation
Indices: 10001797--10001852 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
10001787 ATTATTTATT
10001797 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
10001816 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
10001835 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
10001853 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:10001825 original size:22 final size:22
Alignment explanation
Indices: 10001797--10001859 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
10001787 ATTATTTATT
* * *
10001797 TAATAATAATAATATAATATAA
1 TAATAATAATAAAACAAAATAA
*
10001819 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAACAAAATAA
10001841 TAATAATAAATAAAACAAA
1 TAATAAT-AATAAAACAAA
10001860 TGAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 25 0.71
23 10 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
TAATAATAATAAAACAAAATAA
Found at i:10001957 original size:37 final size:37
Alignment explanation
Indices: 10001913--10001986 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
10001903 TTTTGAAACT
10001913 TCTTTAAAATAATCTATATAAGATGTGTCGGTTTTGC
1 TCTTTAAAATAATCTATATAAGATGTGTCGGTTTTGC
10001950 TCTTTAAAATAATCTATATAAGATGTGTCGGTTTTGC
1 TCTTTAAAATAATCTATATAAGATGTGTCGGTTTTGC
10001987 AATATATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (37 bp):
TCTTTAAAATAATCTATATAAGATGTGTCGGTTTTGC
Found at i:10003236 original size:2 final size:2
Alignment explanation
Indices: 10003208--10003356 Score: 61
Period size: 2 Copynumber: 77.0 Consensus size: 2
10003198 AATACTTACT
*
10003208 TA TA TA TCA TA TA -A TCA TA TA -A TA TA TA TA T- TA TA AA TA T-
1 TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
10003248 TA T- TCA TA CTA TA TA -A TA CA CA CA CA TA TA TA TA TA TA AA TA
1 TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
10003290 CTA TA CTA TA TA TA GA TA -A TA TA -A TT TA -A TA TA -A TG TA TA
1 -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
10003330 TA GTA TA TA -A TA TA TA AA TA -A TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
10003357 ACGCATGTAG
Statistics
Matches: 114, Mismatches: 14, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
1 12 0.11
2 89 0.78
3 13 0.11
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (2 bp):
TA
Found at i:10003302 original size:22 final size:22
Alignment explanation
Indices: 10003186--10003308 Score: 71
Period size: 22 Copynumber: 5.6 Consensus size: 22
10003176 TACAAATATT
10003186 TATATATA-ATATAATACT-TAC
1 TATATATATATA-AATACTATAC
*
10003207 T-TATATATCATATAAT-CATATAA
1 TATATATAT-ATA-AATAC-TATAC
* *
10003230 TATATATATTATAAATATTATTC
1 TATATATA-TATAAATACTATAC
* * *
10003253 -ATA-CTATAT-AATACACACAC
1 TATATATATATAAATAC-TATAC
10003273 ATATATATATATAAATACTATAC
1 -TATATATATATAAATACTATAC
*
10003296 TATATATAGATAA
1 TATATATATATAA
10003309 TATAATTTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
19 4 0.05
20 11 0.14
21 4 0.05
22 26 0.34
23 17 0.22
24 14 0.18
25 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.41
Consensus pattern (22 bp):
TATATATATATAAATACTATAC
Found at i:10003357 original size:94 final size:88
Alignment explanation
Indices: 10003186--10003357 Score: 195
Period size: 94 Copynumber: 1.9 Consensus size: 88
10003176 TACAAATATT
* * *
10003186 TATATATAATATAATACTTACTTATATATCATATAATCATATAATATATATATTATAAATATTAT
1 TATATATAATATAATACTTACTTATATATAATATAATAATATAATATATATAGTATAAATATTAT
** *
10003251 TCATACTATATAATACACACACA
66 AAATAATATATAATACACACACA
*
10003274 TATATAT-ATATAAATACTATACTATATATAGATAATATAATTTAATATAATGTATATAGTATAT
1 TATATATAATAT-AATACT-TACT-TATAT--ATAATATAA--TAATATAATATATATAGTATA-
10003338 AATA-TATAAATAATATATAA
58 AATATTATAAATAATATATAA
10003358 CGCATGTAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
87 4 0.06
88 13 0.19
89 4 0.06
90 5 0.07
92 8 0.12
94 31 0.45
95 4 0.06
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (88 bp):
TATATATAATATAATACTTACTTATATATAATATAATAATATAATATATATAGTATAAATATTAT
AAATAATATATAATACACACACA
Found at i:10003556 original size:38 final size:38
Alignment explanation
Indices: 10003499--10003573 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
10003489 CACCTATGAT
* *
10003499 CATCAAAGTAGAGGAACATTAGGGTTCATGATTAGGAC
1 CATCAAAGTAGAAGAACATTAGGGTTCATGAGTAGGAC
* *
10003537 CATCAAAGTATAAGCACATTAGGGTTCATGAGTAGGA
1 CATCAAAGTAGAAGAACATTAGGGTTCATGAGTAGGA
10003574 ACACTCTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (38 bp):
CATCAAAGTAGAAGAACATTAGGGTTCATGAGTAGGAC
Found at i:10012563 original size:31 final size:31
Alignment explanation
Indices: 10012528--10012591 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
10012518 AAGGGAGTAC
10012528 CTTGGGGCCTGAGAGCCTACCCAAGAAAAAT
1 CTTGGGGCCTGAGAGCCTACCCAAGAAAAAT
*
10012559 CTTGGGGCCTGAGAGCTTACCCAAGAAAAAT
1 CTTGGGGCCTGAGAGCCTACCCAAGAAAAAT
10012590 CT
1 CT
10012592 CGGAGTCGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (31 bp):
CTTGGGGCCTGAGAGCCTACCCAAGAAAAAT
Found at i:10012609 original size:31 final size:31
Alignment explanation
Indices: 10012531--10012614 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
10012521 GGAGTACCTT
* * *
10012531 GGGGCCTGAGAGCCTACCCAAGAAAAATCTT
1 GGGGCCTGAGAACTTACCCAAGAAAAATCTC
*
10012562 GGGGCCTGAGAGCTTACCCAAGAAAAATCTC
1 GGGGCCTGAGAACTTACCCAAGAAAAATCTC
* *
10012593 GGAGTC-GTAGAACTTACCCAAG
1 GGGGCCTG-AGAACTTACCCAAG
10012615 CTTGACTTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.02
31 46 0.98
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (31 bp):
GGGGCCTGAGAACTTACCCAAGAAAAATCTC
Found at i:10014202 original size:2 final size:2
Alignment explanation
Indices: 10014151--10014186 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10014141 AAAACGAATA
10014151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10014187 TATTTTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10033763 original size:16 final size:16
Alignment explanation
Indices: 10033744--10033779 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10033734 GTATTTTACC
10033744 TAAAGAAAAAGAAGAA
1 TAAAGAAAAAGAAGAA
* *
10033760 TAAAGAAAAATAATAA
1 TAAAGAAAAAGAAGAA
10033776 TAAA
1 TAAA
10033780 ATAAAATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
TAAAGAAAAAGAAGAA
Found at i:10034789 original size:82 final size:82
Alignment explanation
Indices: 10034644--10035430 Score: 951
Period size: 82 Copynumber: 9.6 Consensus size: 82
10034634 AAATATCCGG
*
10034644 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATTA-TGGAGCACAAC-CGTCTTCCAAA
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAA-TAGTGGAGCA-GACTCGTCTTCCAAA
*
10034707 ATTGATCAGACTACCCGAA
64 ATTGATCTGACTACCCGAA
* * * * * *
10034726 AAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAAGAATAGTAGAGCAGACTCATCTTTCAAAAT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
*
10034791 TGATCTGGCTACCCGAA
66 TGATCTGACTACCCGAA
* * * *
10034808 AAAGAGGAACAAATCAAGTTTGATGTCCCCTGAAAGATTTGTGGAGCAGAAC-CGTCTTCCAAAA
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAG-ACTCGTCTTCCAAAA
* * * *
10034872 TTGATTTGAATTCCTGAA
65 TTGATCTGACTACCCGAA
* * * * *
10034890 AAAGAGGAACATATCAAGTATAATCTACCCTTAAATAATAGTGGAGCAGACTCGTCTTCCAAAAT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
*
10034955 TGATCTGACTACCCCAA
66 TGATCTGACTACCCGAA
* * ** * * *
10034972 AAAGTGAAACGGATCAAGTTTGATCTCCCCT-ATAATAATAGTGGAGCAAACTCCTCTTCCAAAA
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGA-AAGAATAGTGGAGCAGACTCGTCTTCCAAAA
* *
10035036 TTGA-AT-AGCAGACCCGAAA
65 TTGATCTGA-C-TACCCG-AA
* * *
10035055 AAAGAGGAACATATCAAGTTTGATCTTCCCTGAAAGAATAGTGGAGCAGACCCATCTTCCAAAAT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
10035120 TGATCTGACTACCCGAA
66 TGATCTGACTACCCGAA
* * * * * * * *
10035137 AAAAATGAACATATCAAGTCTAATTTCCCCTGAAATAATAGTGGAGTAGACTCATCTTCCAAAAT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
10035202 TGATCTGACTACCCG-A
66 TGATCTGACTACCCGAA
* * * *
10035218 AAAGTGAAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAAACCCGTCTTCCAAAAT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
*
10035283 TGATTTGACTACCCGAA
66 TGATCTGACTACCCGAA
* * *
10035300 AAAGAGGAACATATCAAGTTTGATCTCCCCTAAAAGAATAGTGGAGCAGACCCGTCTTCCAAATT
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
*
10035365 TGATCTGACTACCCGAC
66 TGATCTGACTACCCGAA
* * **
10035382 AAA-ATGAACATAACAAGTTTGATCTCCCCTGAAAGACGAGTGGAGCAGA
1 AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGA
10035431 TTTACCATCA
Statistics
Matches: 599, Mismatches: 94, Indels: 25
0.83 0.13 0.03
Matches are distributed among these distances:
80 1 0.00
81 118 0.20
82 410 0.68
83 66 0.11
84 3 0.01
85 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (82 bp):
AAAGAGGAACATATCAAGTTTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAAT
TGATCTGACTACCCGAA
Found at i:10035591 original size:27 final size:27
Alignment explanation
Indices: 10035552--10035603 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
10035542 CCGTCCATAC
*
10035552 ATATATTATTATTATTATTATTATTTT
1 ATATATTACTATTATTATTATTATTTT
*
10035579 ATATATTACTATTATTATTGTTATT
1 ATATATTACTATTATTATTATTATT
10035604 AAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
ATATATTACTATTATTATTATTATTTT
Found at i:10035612 original size:3 final size:3
Alignment explanation
Indices: 10035555--10035604 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
10035545 TCCATACATA
* *
10035555 TAT TAT TAT TAT TAT TAT TAT T-T TAT ATAT TAC TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
10035600 TAT TA
1 TAT TA
10035605 AATTATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:10038520 original size:17 final size:17
Alignment explanation
Indices: 10038498--10038537 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
10038488 TCTTGGAATC
10038498 TCAACGATTCCCATAAA
1 TCAACGATTCCCATAAA
*
10038515 TCAACGATTCCCATATA
1 TCAACGATTCCCATAAA
10038532 TCAACG
1 TCAACG
10038538 CCTGGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.30, G:0.07, T:0.25
Consensus pattern (17 bp):
TCAACGATTCCCATAAA
Found at i:10046474 original size:6 final size:6
Alignment explanation
Indices: 10046465--10046504 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
10046455 ACATTCACAT
* * *
10046465 ATTTAC ATTTGC ATTTAC ATTTGC ATTTAC ATTTGC ATTT
1 ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTT
10046505 TTTTACGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (6 bp):
ATTTAC
Found at i:10046482 original size:12 final size:12
Alignment explanation
Indices: 10046465--10046504 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
10046455 ACATTCACAT
10046465 ATTTACATTTGC
1 ATTTACATTTGC
10046477 ATTTACATTTGC
1 ATTTACATTTGC
10046489 ATTTACATTTGC
1 ATTTACATTTGC
10046501 ATTT
1 ATTT
10046505 TTTTACGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:10046515 original size:28 final size:28
Alignment explanation
Indices: 10046478--10046534 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
10046468 TACATTTGCA
*
10046478 TTTACATTTGCATTTACATTTGCATTTT
1 TTTACATTTGCATTTAAATTTGCATTTT
* * *
10046506 TTTACGTTTGTATTTAAATTTTCATTTT
1 TTTACATTTGCATTTAAATTTGCATTTT
10046534 T
1 T
10046535 ACATAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (28 bp):
TTTACATTTGCATTTAAATTTGCATTTT
Found at i:10048626 original size:2 final size:2
Alignment explanation
Indices: 10048619--10048686 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
10048609 TTATCCTTTA
10048619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10048661 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
10048687 CCTTTGTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10049012 original size:26 final size:28
Alignment explanation
Indices: 10048976--10049027 Score: 90
Period size: 26 Copynumber: 1.9 Consensus size: 28
10048966 TATACTCATC
10048976 CAGCAAAGAAA-GAAAAAAG-AAAAATA
1 CAGCAAAGAAAGGAAAAAAGTAAAAATA
10049002 CAGCAAAGAAAGGAAAAAAGTAAAAA
1 CAGCAAAGAAAGGAAAAAAGTAAAAA
10049028 AGAGGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 11 0.46
27 8 0.33
28 5 0.21
ACGTcount: A:0.71, C:0.08, G:0.17, T:0.04
Consensus pattern (28 bp):
CAGCAAAGAAAGGAAAAAAGTAAAAATA
Found at i:10049035 original size:18 final size:16
Alignment explanation
Indices: 10049010--10049096 Score: 102
Period size: 17 Copynumber: 5.2 Consensus size: 16
10049000 TACAGCAAAG
10049010 AAAGGAAAAAAGTAAAA
1 AAAGGAAAAAA-TAAAA
10049027 AAGAGGAAAAAATAAAA
1 AA-AGGAAAAAATAAAA
**
10049044 AAATAAAAAAATAAAAA
1 AAAGGAAAAAAT-AAAA
10049061 AAAGGAAAGAAATAAAA
1 AAAGGAAA-AAATAAAA
**
10049078 AAATAAAAAAATAAAA
1 AAAGGAAAAAATAAAA
10049094 AAA
1 AAA
10049097 TAAAAAGGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
16 19 0.31
17 29 0.48
18 13 0.21
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (16 bp):
AAAGGAAAAAATAAAA
Found at i:10049037 original size:1 final size:1
Alignment explanation
Indices: 10049033--10049125 Score: 51
Period size: 1 Copynumber: 93.0 Consensus size: 1
10049023 AAAAAAGAGG
* * * ** * * * * *
10049033 AAAAAATAAAAAAATAAAAAAATAAAAAAAAGGAAAGAAATAAAAAAATAAAAAAATAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** ** *
10049098 AAAAAGGAAAAGGAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
10049126 TTGAATCAAG
Statistics
Matches: 68, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.08
Consensus pattern (1 bp):
A
Found at i:10049044 original size:8 final size:8
Alignment explanation
Indices: 10049033--10049102 Score: 106
Period size: 8 Copynumber: 8.5 Consensus size: 8
10049023 AAAAAAGAGG
10049033 AAAAAATA
1 AAAAAATA
10049041 AAAAAATA
1 AAAAAATA
10049049 AAAAAATA
1 AAAAAATA
10049057 AAAAAA-A
1 AAAAAATA
10049064 GGAAAGAAATA
1 --AAA-AAATA
10049075 AAAAAATA
1 AAAAAATA
10049083 AAAAAATA
1 AAAAAATA
10049091 AAAAAATA
1 AAAAAATA
10049099 AAAA
1 AAAA
10049103 GGAAAAGGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.02
8 47 0.81
9 6 0.10
10 3 0.05
11 1 0.02
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:10049053 original size:34 final size:34
Alignment explanation
Indices: 10049015--10049096 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
10049005 CAAAGAAAGG
* *
10049015 AAAAAAGTAAAAAAGAGGAAA-AAATAAAAAAAT
1 AAAAAAATAAAAAAAAGGAAAGAAATAAAAAAAT
10049048 AAAAAAATAAAAAAAAGGAAAGAAATAAAAAAAT
1 AAAAAAATAAAAAAAAGGAAAGAAATAAAAAAAT
10049082 AAAAAAATAAAAAAA
1 AAAAAAATAAAAAAA
10049097 TAAAAAGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 19 0.41
34 27 0.59
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (34 bp):
AAAAAAATAAAAAAAAGGAAAGAAATAAAAAAAT
Found at i:10049062 original size:42 final size:42
Alignment explanation
Indices: 10049015--10049126 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
10049005 CAAAGAAAGG
*
10049015 AAAAAAGTAAA-AAAGAGGAAAAAATAAAAAAATAAAAAAATAA
1 AAAAAAGGAAAGAAAGA--AAAAAATAAAAAAATAAAAAAATAA
*
10049058 AAAAAAGGAAAGAAATAAAAAAATAAAAAAATAAAAAAATAAA
1 AAAAAAGGAAAGAAAGAAAAAAATAAAAAAATAAAAAAAT-AA
*
10049101 AAGGAAAAGGAAAAAAAGAAAAAAAT
1 AA--AAAAGGAAAGAAAGAAAAAAAT
10049127 TGAATCAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 23 0.38
43 14 0.23
44 4 0.07
45 20 0.33
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (42 bp):
AAAAAAGGAAAGAAAGAAAAAAATAAAAAAATAAAAAAATAA
Found at i:10049117 original size:9 final size:8
Alignment explanation
Indices: 10048984--10049125 Score: 76
Period size: 8 Copynumber: 17.4 Consensus size: 8
10048974 TCCAGCAAAG
10048984 AAAG-AAA
1 AAAGAAAA
10048991 AAAGAAAA
1 AAAGAAAA
*
10048999 ATACAGCAAAG
1 A-A-AG-AAAA
*
10049010 AAAGGAAA
1 AAAGAAAA
10049018 AAAGTAAAA
1 AAAG-AAAA
*
10049027 AAGAGGAAA
1 AA-AGAAAA
*
10049036 AAATAAAA
1 AAAGAAAA
*
10049044 AAATAAAA
1 AAAGAAAA
*
10049052 AAATAAAAA
1 AAA-GAAAA
*
10049061 AAAGGAAAG
1 AAA-GAAAA
*
10049070 AAATAAAA
1 AAAGAAAA
*
10049078 AAATAAAA
1 AAAGAAAA
*
10049086 AAA-TAAA
1 AAAGAAAA
*
10049093 AAA-ATAA
1 AAAGAAAA
*
10049100 AAAG-GAA
1 AAAGAAAA
*
10049107 AAGGAAAA
1 AAAGAAAA
10049115 AAAGAAAA
1 AAAGAAAA
10049123 AAA
1 AAA
10049126 TTGAATCAAG
Statistics
Matches: 106, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
7 20 0.19
8 51 0.48
9 26 0.25
10 5 0.05
11 4 0.04
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (8 bp):
AAAGAAAA
Found at i:10049767 original size:32 final size:32
Alignment explanation
Indices: 10049731--10049793 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10049721 GTCAGACACA
*
10049731 AGAAGTATCTCTACCAGATGAGCATAACAATG
1 AGAAGTATCTCTACAAGATGAGCATAACAATG
10049763 AGAAGTATCTCTACAAGATGAGCATAACAAT
1 AGAAGTATCTCTACAAGATGAGCATAACAAT
10049794 CATTTCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAATG
Found at i:10051615 original size:114 final size:114
Alignment explanation
Indices: 10051415--10051637 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 114
10051405 TGCCATGTTC
10051415 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGA
* * *
10051480 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGT
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGT
* *
10051529 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGA
* *
10051594 TTCGGTAGGAACCCCAGAACCAATTATTGGAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
10051638 CTGCATGATC
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGT
Found at i:10052541 original size:54 final size:54
Alignment explanation
Indices: 10052456--10052579 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
10052446 TTCCCCCTTG
* * ** *
10052456 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAACTGTTTA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACCATTCA
* * *
10052510 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCA
1 GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACCATTCA
10052564 GGGGGGAATCGGTTCC
1 GGGGGGAATCGGTTCC
10052580 TCCTATGGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.22
Consensus pattern (54 bp):
GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAACCATTCA
Found at i:10055221 original size:21 final size:21
Alignment explanation
Indices: 10055195--10055234 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10055185 CAGAACCCCA
*
10055195 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
10055216 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
10055235 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:10061247 original size:76 final size:76
Alignment explanation
Indices: 10061041--10061249 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
10061031 GACCGTTGAA
* * * *
10061041 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTC
1 CAGGGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTC
**
10061104 GGAACAAAACTGTT
63 GGAACAAAACCATT
* *
10061118 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGA
* *
10061182 GCCAAACCATT
66 ACAAAACCATT
*
10061193 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
10061250 TTTTTGGCTT
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
75 65 0.56
76 31 0.27
77 19 0.16
78 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGA
ACAAAACCATT
Found at i:10063905 original size:22 final size:22
Alignment explanation
Indices: 10063876--10063930 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
10063866 ATCTACACTC
**
10063876 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAAATTCTCTT
*
10063898 TTTAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
*
10063920 TTCAAATATGA
1 TTCAAAGATGA
10063931 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:10064732 original size:76 final size:76
Alignment explanation
Indices: 10064606--10064787 Score: 303
Period size: 76 Copynumber: 2.4 Consensus size: 76
10064596 CTATTTCTCA
*
10064606 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
10064671 AGCCTTAGGGT
66 AACCTTAGGGT
10064682 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
10064747 AACCTTCGGGT
66 AACCTTAGGGT
* *
10064758 CAGCTGTAAGCCCTACAGTGCA-GAATGTTT
1 CATCTGTAAGTCCTACAGTGCATG-ATGTTT
10064788 TTTCTTAAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 1 0.01
76 99 0.99
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:10065350 original size:113 final size:113
Alignment explanation
Indices: 10064798--10065547 Score: 1073
Period size: 113 Copynumber: 6.6 Consensus size: 113
10064788 TTTCTTAAAA
*
10064798 CATTTCCAG-GTATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 CATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ** *
10064862 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCGATGGATCAG
65 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAG
*
10064911 CATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
10064975 GAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAA
66 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* * *
10065023 CATTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGA
1 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
10065087 GAAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTTGATGGATTAA
66 GAAGAACTTGTTCAACCTTTTGCTC-AAATCCATCACTTGATGGATCAG
* * *
10065135 CTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAAGGAAGAAGAAGTTCATACTG
1 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGGAAGAAGAAGTTCATAATG
* *
10065200 AGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGTATCAG
65 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* *
10065249 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGA
1 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
10065314 GAAGAGCTTGTTTAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* * *
10065362 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAATGAAGAAGAAGTTCATAATGA
1 CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
10065427 GAA-AAGCTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
66 GAAGAA-CTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* * * *
10065475 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAACAAATTCATAATG
1 CATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
10065539 AGAAGAACT
65 AGAAGAACT
10065548 CATCTGAAGA
Statistics
Matches: 586, Mismatches: 41, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
111 1 0.00
112 207 0.35
113 275 0.47
114 102 0.17
115 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
Found at i:10065525 original size:20 final size:20
Alignment explanation
Indices: 10065500--10065565 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
10065490 TTCATAATGA
10065500 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
**
10065520 GAAGAACAAATTCAT-AATG-A-
1 GAAGAACTCA-TC-TGAA-GAAG
10065540 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
10065560 GAAGAA
1 GAAGAA
10065566 GAATAAGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 22 0.61
21 5 0.14
22 2 0.06
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAGAACTCATCTGAAGAAG
Found at i:10065581 original size:43 final size:41
Alignment explanation
Indices: 10065488--10065629 Score: 220
Period size: 40 Copynumber: 3.5 Consensus size: 41
10065478 TGCCAGGTAG
*
10065488 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAACAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
10065529 A-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-A-A
10065571 AGTTCATAATGAGAAGAACTCATCTTG-AG-AGGAAGAAG-A
1 AGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAA
10065610 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
10065630 TGTTCGACCT
Statistics
Matches: 96, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
39 21 0.22
40 36 0.38
41 2 0.02
42 11 0.11
43 24 0.25
44 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.20
Consensus pattern (41 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
Found at i:10069635 original size:27 final size:27
Alignment explanation
Indices: 10069605--10069660 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
10069595 TTTTAGTGAC
10069605 ATAATATAAATGTTACCTAATAATATT
1 ATAATATAAATGTTACCTAATAATATT
10069632 ATAATATAAATGTTACCTAATAATATT
1 ATAATATAAATGTTACCTAATAATATT
10069659 AT
1 AT
10069661 GAATGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
ATAATATAAATGTTACCTAATAATATT
Found at i:10069932 original size:14 final size:14
Alignment explanation
Indices: 10069913--10069942 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
10069903 AACTAAAAAT
10069913 TGTCACTTTTTTAA
1 TGTCACTTTTTTAA
10069927 TGTCACTTTTTTAA
1 TGTCACTTTTTTAA
10069941 TG
1 TG
10069943 ACAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (14 bp):
TGTCACTTTTTTAA
Found at i:10070789 original size:317 final size:316
Alignment explanation
Indices: 10069960--10070916 Score: 1776
Period size: 317 Copynumber: 3.0 Consensus size: 316
10069950 ATATTAAAAT
10069960 AAAATTACTTATACAAATCTAAAT-AAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
1 AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
10070024 AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
66 AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
10070089 AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
131 AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
10070154 CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCAACTGGAGTTGATTGCAA
196 CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCAACTGGAGTTGATTGCAA
10070219 CTTCACCATTTTCTCCTAAAAAAAA-TCATTCATAAATAAAATAATCCTTAGATGA
261 CTTCACCATTTTCTCCTAAAAAAAAGTCATTCATAAATAAAATAATCCTTAGATGA
*
10070274 AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATATTAAGATTTAAACA
1 AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
10070339 AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
66 AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
10070404 AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
131 AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
*
10070469 CCTTGAGTCGATTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCAACTGGAGTTGATTGCAA
196 CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCAACTGGAGTTGATTGCAA
*
10070534 CTTCACCATTTTCTCCTTAAAAAAAAGTCATTCATAAATAAAATAATCCTTGGATGA
261 CTTCACCATTTTCTCC-TAAAAAAAAGTCATTCATAAATAAAATAATCCTTAGATGA
10070591 AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
1 AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
*
10070656 AACATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
66 AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
* *
10070721 AAATAAAAATAATATGATAATAATATTACTTGTGGAATATTTCGTAGTAGCAATCTCAATCCAAA
131 AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
*
10070786 CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCTTCAACTGAAGTTGATTG
196 CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTG---CTTCTTCAACTGGAGTTGATTG
* *
10070851 CAACTCCACCATTTTCTCCT-AAAAAACGTCATTCATAAATAAAATAATCCTTAGATGA
258 CAACTTCACCATTTTCTCCTAAAAAAAAGTCATTCATAAATAAAATAATCCTTAGATGA
10070909 AAAATTAC
1 AAAATTAC
10070917 AATTTAATAC
Statistics
Matches: 625, Mismatches: 12, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
314 24 0.04
315 249 0.40
316 9 0.01
317 259 0.41
318 44 0.07
319 1 0.00
320 39 0.06
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (316 bp):
AAAATTACTTATACAAATCTAAATAAAAAATAATTCACTTATTGCAAAATAATAAGATTTAAACA
AATATTTCAATAAAAACATAATAATTTCATTTCTATAAATATAAAAATGTTTAAATGTTTACAGA
AAATAAAAATAATATGATAATAATATGACTTGTGGAATATTTCGTAGTAACAATCTCAATCCAAA
CCTTGAGTCGGTTGTGATTTCAAGGCTTACATATTTTCTGCTTCTTCAACTGGAGTTGATTGCAA
CTTCACCATTTTCTCCTAAAAAAAAGTCATTCATAAATAAAATAATCCTTAGATGA
Found at i:10071095 original size:18 final size:19
Alignment explanation
Indices: 10071060--10071104 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
10071050 ATGATTTCAA
*
10071060 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
10071079 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
10071097 ATAATAAA
1 AAAATAAA
10071105 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:10073212 original size:17 final size:17
Alignment explanation
Indices: 10073178--10073213 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
10073168 TCAATTTTTA
10073178 ATTTTTTTTAAAATAAT
1 ATTTTTTTTAAAATAAT
10073195 ATTTTATTTTAAAA-AAT
1 ATTTT-TTTTAAAATAAT
10073212 AT
1 AT
10073214 AAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTTTTAAAATAAT
Found at i:10076475 original size:3 final size:3
Alignment explanation
Indices: 10076467--10076544 Score: 140
Period size: 3 Copynumber: 26.0 Consensus size: 3
10076457 ATATATATAT
10076467 ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
10076513 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10076545 TGGTATTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 68 0.93
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10079177 original size:66 final size:64
Alignment explanation
Indices: 10079071--10079192 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 64
10079061 TTGTTGAAGG
* *
10079071 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTAAATGAACATCGAATGCCATGG
1 TGCATCAATGCATAAGGAGTGCATCGATGCACTCATTTAAAATAAA--AACATCGAATGCCATGG
10079136 A
64 A
* *
10079137 TGCATCAATGCATAAGGAGTGCATCGATGCTC-CTTCTTAAAATAAAAACATCGAAT
1 TGCATCAATGCATAAGGAGTGCATCGATGCACTCAT-TTAAAATAAAAACATCGAAT
10079193 AAGATTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
64 10 0.20
65 2 0.04
66 39 0.76
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
TGCATCAATGCATAAGGAGTGCATCGATGCACTCATTTAAAATAAAAACATCGAATGCCATGGA
Found at i:10080567 original size:22 final size:22
Alignment explanation
Indices: 10080542--10080729 Score: 304
Period size: 22 Copynumber: 8.5 Consensus size: 22
10080532 GGGTATATTA
*
10080542 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
10080564 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* * *
10080586 GTCATTCAGGACGTATCCAGTT
1 GTCCTTCGGGACGTATCCAGTG
* *
10080608 GTCATTCGAGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
10080630 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
10080652 GTCCTTCGAGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
10080674 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
10080696 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
10080718 GTCCTTCGGGAC
1 GTCCTTCGGGAC
10080730 ATAATAGTCC
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 154 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:10088797 original size:3 final size:3
Alignment explanation
Indices: 10088789--10088820 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
10088779 ATACACATAT
10088789 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10088821 TGTTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:10096221 original size:24 final size:24
Alignment explanation
Indices: 10096177--10096246 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
10096167 ATAGTGCTAG
*
10096177 GAGTACACAAATGT-CTAAATACAA
1 GAGTACACGAATGTACT-AATACAA
* **
10096201 GAGTACAC-AGTGGTACTAATATGA
1 GAGTACACGAAT-GTACTAATACAA
10096225 GAGTACACGAATGTACTAATAC
1 GAGTACACGAATGTACTAATAC
10096247 GATAGCGCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 2 0.05
24 32 0.84
25 4 0.11
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (24 bp):
GAGTACACGAATGTACTAATACAA
Found at i:10098846 original size:4 final size:4
Alignment explanation
Indices: 10098837--10098911 Score: 53
Period size: 4 Copynumber: 18.2 Consensus size: 4
10098827 TTCTTTAACA
* * * * * *
10098837 TTAT TTAT TTAT CTT-G TTAT TCAT TCAT TCAT TCAT TCAT TTATT TTAT
1 TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT
*
10098886 ATTAT TTAT TTAT TTAT CTAT TTAT T
1 -TTAT TTAT TTAT TTAT TTAT TTAT T
10098912 ATAGAAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
3 2 0.03
4 49 0.80
5 10 0.16
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:10100757 original size:13 final size:13
Alignment explanation
Indices: 10100739--10100786 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
10100729 TGCGTCATAA
10100739 ATTTATGACGCGC
1 ATTTATGACGCGC
*
10100752 ATTTATGACACGC
1 ATTTATGACGCGC
10100765 ATTTATGACGCGC
1 ATTTATGACGCGC
10100778 ATTTATGAC
1 ATTTATGAC
10100787 ATTTGTGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:10100907 original size:2 final size:2
Alignment explanation
Indices: 10100900--10100942 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10100890 TTTCGTAAAT
10100900 TA TA TA TA TA TA TA TA 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
10100942 T
1 T
10100943 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10101600 original size:32 final size:32
Alignment explanation
Indices: 10101554--10101624 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
10101544 TTATATAGAA
10101554 TTTCATTATCATACGCTTAAATTAAGTTTCTTT
1 TTTC-TTATCATACGCTTAAATTAAGTTTCTTT
10101587 TTTCTTATCATACGCTTAAATTAAGTTTCTTT
1 TTTCTTATCATACGCTTAAATTAAGTTTCTTT
10101619 TTTCTT
1 TTTCTT
10101625 CAGAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 34 0.89
33 4 0.11
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (32 bp):
TTTCTTATCATACGCTTAAATTAAGTTTCTTT
Found at i:10105648 original size:53 final size:53
Alignment explanation
Indices: 10105583--10105798 Score: 270
Period size: 53 Copynumber: 4.1 Consensus size: 53
10105573 CCTAAGTGTA
* * * *
10105583 GAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACATATAGTGCT
1 GAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* * * *
10105636 GAAATAGTAATTCATAAACTCAATATGAATTCCATGGATGCACACATACTGCC
1 GAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* * * **
10105689 AAAATGGTAATTCATAAACTCATTATGAATACCACGGGTGCACACATAGTATC
1 GAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* * * * *
10105742 GAAATGTTAATTCAGAAACTCATTTTGAATACCATGGGTGCACATATAGTGCC
1 GAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGCC
10105795 GAAA
1 GAAA
10105799 GTACATATAG
Statistics
Matches: 140, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 140 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (53 bp):
GAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGCC
Found at i:10107134 original size:9 final size:9
Alignment explanation
Indices: 10107120--10107248 Score: 114
Period size: 10 Copynumber: 13.3 Consensus size: 9
10107110 GCTGCTGGAA
10107120 ACCGGTTTG
1 ACCGGTTTG
*
10107129 ACCGGTTTTCA
1 ACCGG-TTT-G
10107140 ACCGGTTCTG
1 ACCGGTT-TG
10107150 ACCGGTTTG
1 ACCGGTTTG
*
10107159 ACCGGTTTTCA
1 ACCGG-TTT-G
10107170 ACCGGTTCTG
1 ACCGGTT-TG
10107180 ACCGGTTTG
1 ACCGGTTTG
*
10107189 ACCGGTTTCA
1 ACCGGTTT-G
*
10107199 ACCGGTTCG
1 ACCGGTTTG
10107208 AACCGGTTTG
1 -ACCGGTTTG
*
10107218 ACCGGTCTG
1 ACCGGTTTG
*
10107227 AATCGGTTTG
1 -ACCGGTTTG
*
10107237 ACCGGTCTG
1 ACCGGTTTG
10107246 ACC
1 ACC
10107249 CGACCCGACC
Statistics
Matches: 98, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
9 40 0.41
10 46 0.47
11 12 0.12
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:10107156 original size:30 final size:29
Alignment explanation
Indices: 10107120--10107248 Score: 181
Period size: 30 Copynumber: 4.4 Consensus size: 29
10107110 GCTGCTGGAA
10107120 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
10107150 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
10107180 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
10107208 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
10107237 ACCGGTCTGACC
1 ACCGGTTTGACC
10107249 CGACCCGACC
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
28 12 0.13
29 37 0.40
30 44 0.47
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:10107164 original size:19 final size:19
Alignment explanation
Indices: 10107120--10107248 Score: 115
Period size: 19 Copynumber: 6.7 Consensus size: 19
10107110 GCTGCTGGAA
*
10107120 ACCGGTT-TGACCGGTTTTCA
1 ACCGGTTCTGACCGG-TTT-G
10107140 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
* *
10107159 ACCGGTTTTCAACCGGTTCTG
1 ACCGGTTCT-GACCGGTT-TG
*
10107180 ACCGGTT-TGACCGGTTTCA
1 ACCGGTTCTGACCGGTTT-G
10107199 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
*
10107218 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
10107237 ACCGG-TCTGACC
1 ACCGGTTCTGACC
10107249 CGACCCGACC
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
18 5 0.05
19 47 0.50
20 26 0.28
21 16 0.17
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:10107275 original size:22 final size:22
Alignment explanation
Indices: 10107245--10107309 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
10107235 TGACCGGTCT
10107245 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
10107267 GACTCGACCCGACCGTTAACCC
1 GACCCGACCCGACCGTTGACCC
10107289 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
10107310 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.48, G:0.22, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:10108275 original size:32 final size:32
Alignment explanation
Indices: 10108239--10108315 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
10108229 GTAGGCCCTG
*
10108239 CGGCCCTAAGATGTGTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGGCTCTCA
* * *
10108271 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 CGG-CCCTAAGATGTATCTTAGGTAGGCTCTCA
10108303 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
10108316 TCCCTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
30 5 0.14
31 16 0.44
32 10 0.28
33 5 0.14
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
Found at i:10108275 original size:63 final size:62
Alignment explanation
Indices: 10108192--10108315 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 62
10108182 CTAATGTGAC
* * *
10108192 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTATC-GGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCCGAAATC--TATCTGGGTAGGCCCT-CAGGCCCTAAGATGTGT
*
10108255 TCTTAGGTAGGC-CTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCTATC-TGGGTAGGCCCTCAGGCCCTAAGATGT
10108316 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
61 4 0.08
62 3 0.06
63 46 0.87
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (62 bp):
TCTTAGGTAGGCTCTACGGCCCCGAAATCTATCTGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:10114492 original size:9 final size:9
Alignment explanation
Indices: 10114478--10114576 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
10114468 GCTGCTGGAA
10114478 ACCGGTTTG
1 ACCGGTTTG
*
10114487 ACCGGTTTTCA
1 ACCGG-TTT-G
10114498 ACCGGTTCTG
1 ACCGGTT-TG
10114508 ACCGGTTTG
1 ACCGGTTTG
*
10114517 ACCGGTTTCA
1 ACCGGTTT-G
*
10114527 ACCGGTTCG
1 ACCGGTTTG
10114536 AACCGGTTTG
1 -ACCGGTTTG
*
10114546 ACCGGTCTG
1 ACCGGTTTG
*
10114555 AATCGGTTTG
1 -ACCGGTTTG
*
10114565 ACCGGTCTG
1 ACCGGTTTG
10114574 ACC
1 ACC
10114577 CCACCAGACC
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.47
11 6 0.08
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:10114522 original size:19 final size:19
Alignment explanation
Indices: 10114478--10114576 Score: 89
Period size: 19 Copynumber: 5.2 Consensus size: 19
10114468 GCTGCTGGAA
* *
10114478 ACCGGTTTGACCGGTTTTCA
1 ACCGGTTTGACCGGTTCT-G
10114498 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
10114517 ACCGGTTTCAACCGGTTC-G
1 ACCGGTTT-GACCGGTTCTG
10114536 AACCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
*
10114555 AATCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
10114574 ACC
1 ACC
10114577 CCACCAGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.57
20 16 0.23
21 9 0.13
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:10114540 original size:29 final size:30
Alignment explanation
Indices: 10114477--10114576 Score: 127
Period size: 29 Copynumber: 3.4 Consensus size: 30
10114467 GGCTGCTGGA
10114477 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
10114508 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
10114536 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
10114565 -ACCGGTCTGACC
1 AACCGGTTTGACC
10114577 CCACCAGACC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.59
30 14 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:10114611 original size:22 final size:22
Alignment explanation
Indices: 10114573--10114637 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
10114563 TGACCGGTCT
* *
10114573 GACCCCACCAGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
10114595 GACTCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
10114617 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
10114638 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.48, G:0.22, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:10114639 original size:7 final size:7
Alignment explanation
Indices: 10114627--10114657 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
10114617 GACCCGACCC
10114627 GACCGTT
1 GACCGTT
10114634 GACCGTT
1 GACCGTT
10114641 GACCGTT
1 GACCGTT
10114648 GACCGTT
1 GACCGTT
10114655 GAC
1 GAC
10114658 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:10115604 original size:32 final size:32
Alignment explanation
Indices: 10115568--10115644 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
10115558 GTAGGCCCTG
*
10115568 CGGCCCTAAGATGTGTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGGCTCTCA
* * *
10115600 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 CGG-CCCTAAGATGTATCTTAGGTAGGCTCTCA
10115632 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
10115645 TCCCTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
30 5 0.14
31 16 0.44
32 10 0.28
33 5 0.14
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
Found at i:10115604 original size:63 final size:62
Alignment explanation
Indices: 10115521--10115644 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 62
10115511 CTAATGTGAC
* * *
10115521 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTATC-GGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCCGAAATC--TATCTGGGTAGGCCCT-CAGGCCCTAAGATGTGT
*
10115584 TCTTAGGTAGGC-CTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCTATC-TGGGTAGGCCCTCAGGCCCTAAGATGT
10115645 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
61 4 0.08
62 3 0.06
63 46 0.87
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (62 bp):
TCTTAGGTAGGCTCTACGGCCCCGAAATCTATCTGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:10122052 original size:3 final size:3
Alignment explanation
Indices: 10122044--10122092 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
10122034 AAAACATTTT
10122044 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10122092 A
1 A
10122093 AACGTTCGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10122770 original size:52 final size:53
Alignment explanation
Indices: 10122609--10122817 Score: 235
Period size: 53 Copynumber: 4.0 Consensus size: 53
10122599 TAAGTGTCAG
* * *
10122609 AATGGTAATTCAAAAACTCATTATCAATTCCATGGATGCAAACATAGTGCCGA
1 AATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGCCGA
* * * * * *
10122662 AGTGGTAAGT-AATAAACTCATTATGAATTCCATGGATGAACTCATAGTGCCAA
1 AATGGTAATTCAA-AAACTCATTATGAATACCATGGATGCACACATAGTGCCGA
* * * *
10122715 AAT-GTAATTCATAAACTCATTATGAATACCAT-AAGTGCACACATACTGTCGA
1 AATGGTAATTCAAAAACTCATTATGAATACCATGGA-TGCACACATAGTGCCGA
* * *
10122767 AATGGTAACTCAAAAACTCATTATGAATACCATGGATGCAGACATGGTGCC
1 AATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGCC
10122818 AAAAGTACAC
Statistics
Matches: 127, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
51 1 0.01
52 41 0.32
53 84 0.66
54 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
AATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGCCGA
Found at i:10122800 original size:105 final size:105
Alignment explanation
Indices: 10122613--10122804 Score: 262
Period size: 105 Copynumber: 1.8 Consensus size: 105
10122603 TGTCAGAATG
* * * * *
10122613 GTAATTCAAAAACTCATTATCAATTCCATGGATGCAAACATAGTGCCGAAGTGGTAAGTAATAAA
1 GTAATTCAAAAACTCATTATCAATACCATAGATGCAAACATACTGCCGAAATGGTAACTAATAAA
*
10122678 CTCATTATGAATTCCATGGATGAACTCATAGTGCCAAAAT
66 CTCATTATGAATACCATGGATGAACTCATAGTGCCAAAAT
* * * *
10122718 GTAATTCATAAACTCATTATGAATACCATA-AGTGCACACATACTGTCGAAATGGTAACTCAA-A
1 GTAATTCAAAAACTCATTATCAATACCATAGA-TGCAAACATACTGCCGAAATGGTAACT-AATA
10122781 AACTCATTATGAATACCATGGATG
64 AACTCATTATGAATACCATGGATG
10122805 CAGACATGGT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
104 1 0.01
105 72 0.96
106 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (105 bp):
GTAATTCAAAAACTCATTATCAATACCATAGATGCAAACATACTGCCGAAATGGTAACTAATAAA
CTCATTATGAATACCATGGATGAACTCATAGTGCCAAAAT
Found at i:10126447 original size:132 final size:131
Alignment explanation
Indices: 10126205--10126450 Score: 309
Period size: 132 Copynumber: 1.9 Consensus size: 131
10126195 ATTAGCAGGG
* **
10126205 TTTTAAGATGAAAACGCCATTAAAGCACCACACATTTGTGACATTTTTTGTTCTCAAACATTGCT
1 TTTTAAGATGAAAACGCCACTAAAGCACCACACATTTGTGACATTTTTTGTTCTCAAACATCACT
* * ** *
10126270 ATATTGCTTATCATTTAGCGTCGTTTGTGTACAAAACGCCACTAAATATCATGGTATATAACGTC
66 ATATAGCTTAACATTTAAAGTCGTTTGTGTACAAAACACCACTAAATATCATGGTATATAACGTC
10126335 A
131 A
* * * *
10126336 TTTTAAGATGAAAAACGTCACTAAAGGACTACACATTTGT-AGCATTTTTT-TCTTTCAAACATC
1 TTTTAAGATG-AAAACGCCACTAAAGCACCACACATTTGTGA-CATTTTTTGT-TCTCAAACATC
* *
10126399 ACTATATAGCTTAACATTTAAAGAT-GTTTGTGTACAAAACATCGCTAAATAT
63 ACTATATAGCTTAACATTTAAAG-TCGTTTGTGTACAAAACACCACTAAATAT
10126451 TATTATATAT
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
131 12 0.12
132 84 0.87
133 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (131 bp):
TTTTAAGATGAAAACGCCACTAAAGCACCACACATTTGTGACATTTTTTGTTCTCAAACATCACT
ATATAGCTTAACATTTAAAGTCGTTTGTGTACAAAACACCACTAAATATCATGGTATATAACGTC
A
Found at i:10128050 original size:83 final size:80
Alignment explanation
Indices: 10127963--10128226 Score: 194
Period size: 83 Copynumber: 3.2 Consensus size: 80
10127953 TTTAGTGGAT
* *
10127963 TTTTTTTTATAAAAACGCCAGGATAGAGTAGTAATTTAGCGGCG-TTTTATACAAACACCGCAAT
1 TTTTTTTCA-AAAAACGCCA--AAAGAGTAGTAATTTAGCGGCGTTTTTATACAAACACCGCAAT
*
10128027 AGGTTCATCCATAGTGGCG
63 AGGGTCATCCATAGTGG-G
* * * * * * * *
10128046 -TTTTTTGAAAAAATGTCGCAACAGAGTAGTATTTTAGCGGCGTTTTTATATAAATATCGTAATA
1 TTTTTTTCAAAAAACG-C-CAAAAGAGTAGTAATTTAGCGGCGTTTTTATACAAACACCGCAATA
* *
10128110 GGGTCATCTATAGTTGG
64 GGGTCATCCATAGTGGG
* * *** *
10128127 TGTTTTTTCAACAAACACCAATAAAGAGTAGT-ATTGTAGCGGCGTTTTTATACAAATGTCGGAA
1 T-TTTTTTCAAAAAACGCC-A-AAAGAGTAGTAATT-TAGCGGCGTTTTTATACAAACACCGCAA
* ** *
10128191 TAGGGTAATGTATAGTGGC
62 TAGGGTCATCCATAGTGGG
*
10128210 TTTTTTT-GAAAAACGCC
1 TTTTTTTCAAAAAACGCC
10128227 GCTATAGACT
Statistics
Matches: 146, Mismatches: 27, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
81 35 0.24
82 48 0.33
83 63 0.43
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (80 bp):
TTTTTTTCAAAAAACGCCAAAAGAGTAGTAATTTAGCGGCGTTTTTATACAAACACCGCAATAGG
GTCATCCATAGTGGG
Found at i:10128133 original size:82 final size:82
Alignment explanation
Indices: 10127987--10128222 Score: 246
Period size: 83 Copynumber: 2.9 Consensus size: 82
10127977 ACGCCAGGAT
* * * * * *
10127987 AGAGTAGTAATTTAGCGGCG-TTTTATACAAACACCGCAATAGGTTCATCCATAGTGGCGTTTTT
1 AGAGTAGTATTTTAGCGGCGTTTTTATACAAATATCGCAATAGGGTCATCTATAGTGGTGTTTTT
** *
10128051 TGAAAAAATGTCGC-A-AC
66 TGAAAAAA-CAC-CAATAA
* *
10128068 AGAGTAGTATTTTAGCGGCGTTTTTATATAAATATCGTAATAGGGTCATCTATAGTTGGTGTTTT
1 AGAGTAGTATTTTAGCGGCGTTTTTATACAAATATCGCAATAGGGTCATCTATAG-TGGTGTTTT
* *
10128133 TTCAACAAACACCAATAA
65 TTGAAAAAACACCAATAA
* * * * *
10128151 AGAGTAGTATTGTAGCGGCGTTTTTATACAAATGTCGGAATAGGGTAATGTATAGTGGCT-TTTT
1 AGAGTAGTATTTTAGCGGCGTTTTTATACAAATATCGCAATAGGGTCATCTATAGTGG-TGTTTT
10128215 TTGAAAAA
65 TTGAAAAA
10128223 CGCCGCTATA
Statistics
Matches: 129, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
81 20 0.16
82 43 0.33
83 66 0.51
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (82 bp):
AGAGTAGTATTTTAGCGGCGTTTTTATACAAATATCGCAATAGGGTCATCTATAGTGGTGTTTTT
TGAAAAAACACCAATAA
Found at i:10128248 original size:41 final size:40
Alignment explanation
Indices: 10128203--10128435 Score: 171
Period size: 41 Copynumber: 5.6 Consensus size: 40
10128193 GGGTAATGTA
*
10128203 TAGTGGCTTTTTTTGAAAAACGCCGCTATAGACTCGTATTT
1 TAGTGGCTTTTTTT-AAAAACGCCGCTATAGACTCGTACTT
* **
10128244 TAGTGGTTTTTTTATAAAAACATCGCTATAGACTCGTACTT
1 TAGTGGCTTTTTT-TAAAAACGCCGCTATAGACTCGTACTT
* * * * * *
10128285 TAGTGG-TGTTTGTATACAAATGCCGTTACAGACTCATACTT
1 TAGTGGCT-TTT-TTTAAAAACGCCGCTATAGACTCGTACTT
* * * * * * *
10128326 TATTGACTTTTTTATACAAACGCCGCTGTAAACTTGTATTT
1 TAGTGGCTTTTTT-TAAAAACGCCGCTATAGACTCGTACTT
* * * * *
10128367 TAGCGGCGTTTTTAAACAAATGCCACTATAGACTCGTACTT
1 TAGTGGCTTTTTTTAA-AAACGCCGCTATAGACTCGTACTT
*
10128408 TAGTGGCGTTTATGTTTACAAACGCCGC
1 TAGTGGC-TTT-T-TTTAAAAACGCCGC
10128436 AAGTTTATAA
Statistics
Matches: 142, Mismatches: 41, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
40 3 0.02
41 123 0.87
42 5 0.04
43 8 0.06
44 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (40 bp):
TAGTGGCTTTTTTTAAAAACGCCGCTATAGACTCGTACTT
Found at i:10131480 original size:43 final size:43
Alignment explanation
Indices: 10131393--10131760 Score: 262
Period size: 42 Copynumber: 8.8 Consensus size: 43
10131383 AGCGTTTGAA
* * * * * **
10131393 TCCAAAAATGCCGCTATAGATCT-GGCCTTTTCCAGCATTTGT
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
* *
10131435 TCCAAAAACGCCACTGTAGATCTCGATCTTTTGCGGTGTTTGT
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
* *
10131478 TCCAAAACCGCCTA-TATAGATCT-GAACTTTT---GTGTTTGT
1 TCCAAAAACGCC-ACTATAGATCTCGACCTTTTGCGGTGTTTGT
* * ** * *
10131517 TTCAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTG-
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
* * * ** * *
10131559 TCCCAAAACGTCGCTATAGAAATCGACCTTTTGCGGCGTTTAT
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
*
10131602 TCC-AAAACTGCCTA-TATAGATCT-GAACTTTT---GTGTTTGT
1 TCCAAAAAC-GCC-ACTATAGATCTCGACCTTTTGCGGTGTTTGT
* ** ** *
10131641 TTCAAAAACGCTGCTATAGATCTATACCTTTTACGGTGTTTG-
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
* * * *
10131683 TCCCAAAACGTCACTATAGATATCGACCTTTTGCGGCGTTTGT
1 TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
* *
10131726 TCCAAAAATGCCACTATAGA-CATCGACCGTTTGCG
1 TCCAAAAACGCCACTATAGATC-TCGACCTTTTGCG
10131761 ACGTTTAGAT
Statistics
Matches: 252, Mismatches: 56, Indels: 35
0.73 0.16 0.10
Matches are distributed among these distances:
39 44 0.17
40 18 0.07
42 102 0.40
43 87 0.35
44 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (43 bp):
TCCAAAAACGCCACTATAGATCTCGACCTTTTGCGGTGTTTGT
Found at i:10131607 original size:124 final size:124
Alignment explanation
Indices: 10131395--10131732 Score: 498
Period size: 124 Copynumber: 2.7 Consensus size: 124
10131385 CGTTTGAATC
* * * * ** * * * *
10131395 CAAAAATGCCGCTATAGATCT-GGCCTTTTCCAGCATTTGTTCCAAAAACGCCACTGTAGATCTC
1 CAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTG-TCCCAAAACGTCACTATAGATATC
* *
10131459 GATCTTTTGCGGTGTTTGTTCCAAAACCGCCTATATAGATCTGAACTTTTGTGTTTGTTT
65 GACCTTTTGCGGCGTTTGTTCCAAAACCGCCTATATAGATCTGAACTTTTGTGTTTGTTT
* *
10131519 CAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTGTCCCAAAACGTCGCTATAGAAATCG
1 CAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTGTCCCAAAACGTCACTATAGATATCG
* *
10131584 ACCTTTTGCGGCGTTTATTCCAAAACTGCCTATATAGATCTGAACTTTTGTGTTTGTTT
66 ACCTTTTGCGGCGTTTGTTCCAAAACCGCCTATATAGATCTGAACTTTTGTGTTTGTTT
* *
10131643 CAAAAACGCTGCTATAGATCTATACCTTTTACGGTGTTTGTCCCAAAACGTCACTATAGATATCG
1 CAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTGTCCCAAAACGTCACTATAGATATCG
10131708 ACCTTTTGCGGCGTTTGTTCCAAAA
66 ACCTTTTGCGGCGTTTGTTCCAAAA
10131733 ATGCCACTAT
Statistics
Matches: 192, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
124 179 0.93
125 13 0.07
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (124 bp):
CAAAAATGCTGCTATAGATCTAGACCTTTTACGGTGTTTGTCCCAAAACGTCACTATAGATATCG
ACCTTTTGCGGCGTTTGTTCCAAAACCGCCTATATAGATCTGAACTTTTGTGTTTGTTT
Found at i:10134591 original size:19 final size:20
Alignment explanation
Indices: 10134549--10134593 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
10134539 GCTATGCTAT
* *
10134549 AAATTAATGTTAGAGTGTTG
1 AAATTGATGTTAGAATGTTG
10134569 AAATTGATGTTAGAATG-TG
1 AAATTGATGTTAGAATGTTG
10134588 AAATTG
1 AAATTG
10134594 GGCAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (20 bp):
AAATTGATGTTAGAATGTTG
Found at i:10145890 original size:6 final size:6
Alignment explanation
Indices: 10145879--10145927 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
10145869 TGGTATGCTA
10145879 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
10145927 G
1 G
10145928 CTTTAGTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:10147032 original size:17 final size:17
Alignment explanation
Indices: 10147012--10147175 Score: 159
Period size: 17 Copynumber: 9.5 Consensus size: 17
10147002 TTTAACTAAG
*
10147012 TAGTTCATTCATTAAAC
1 TAGTTCATTCATCAAAC
10147029 TAGTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
*
10147046 TACTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
*
10147063 TACTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
*
10147080 TACTTCATTCATCAAAC
1 TAGTTCATTCATCAAAC
** *
10147097 TAGTTCATTCAAGATTAC
1 TAGTTCATTCATCA-AAC
* * *
10147115 AAGTTCATTGAAT-AAATT
1 TAGTTCATT-CATCAAA-C
* * * *
10147133 TAATGCATTAATTAAAC
1 TAGTTCATTCATCAAAC
*
10147150 TAGTCCATTCATCAAAC
1 TAGTTCATTCATCAAAC
10147167 TAGTTCATT
1 TAGTTCATT
10147176 TATTAACATA
Statistics
Matches: 123, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
17 102 0.83
18 20 0.16
19 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:10147051 original size:51 final size:51
Alignment explanation
Indices: 10146996--10147108 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
10146986 TTAGCTATGC
* * * * * *
10146996 ACTTCATTTAACTAAGTAGTTCATTCATTAAACTAGTTCATTCATCAAACT
1 ACTTCATTCAACAAACTACTTCATTCATCAAACTACTTCATTCATCAAACT
*
10147047 ACTTCATTCATCAAACTACTTCATTCATCAAACTACTTCATTCATCAAACT
1 ACTTCATTCAACAAACTACTTCATTCATCAAACTACTTCATTCATCAAACT
*
10147098 AGTTCATTCAA
1 ACTTCATTCAA
10147109 GATTACAAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (51 bp):
ACTTCATTCAACAAACTACTTCATTCATCAAACTACTTCATTCATCAAACT
Found at i:10152300 original size:22 final size:22
Alignment explanation
Indices: 10152278--10152365 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 22
10152268 AGAACCCCAG
*
10152278 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTACAA
* *
10152299 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTAC-AA
* *
10152322 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTACAA
* *
10152344 GGGAGTATCGATTCCCTCTACA
1 GGGGGAATCGATTCCC-CTACA
10152366 CTAAAATGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 17 0.30
22 15 0.26
23 25 0.44
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTACAA
Found at i:10152324 original size:23 final size:23
Alignment explanation
Indices: 10152298--10152343 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
10152288 ATTCCCCTAC
10152298 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
10152321 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
10152344 GGGAGTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:10157481 original size:11 final size:12
Alignment explanation
Indices: 10157449--10157481 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10157439 AAATGGTTCG
10157449 AAATATTTTGTA
1 AAATATTTTGTA
10157461 AAATTATTTTG-A
1 AAA-TATTTTGTA
10157473 AAATATTTT
1 AAATATTTT
10157482 AAGATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 7 0.35
13 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
AAATATTTTGTA
Found at i:10160299 original size:17 final size:17
Alignment explanation
Indices: 10160258--10160300 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10160248 ATTTAAACAT
* *
10160258 GTAGTTCATTTAGCTAT
1 GTAGTTCATTTAACTAA
* *
10160275 GCACTTCATTTAACTAA
1 GTAGTTCATTTAACTAA
10160292 GTAGTTCAT
1 GTAGTTCAT
10160301 CCATTAAACT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (17 bp):
GTAGTTCATTTAACTAA
Found at i:10160317 original size:34 final size:35
Alignment explanation
Indices: 10160279--10160355 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 35
10160269 AGCTATGCAC
* * *
10160279 TTCATTTAACT-AAGTAGTTCATCCATTAAACTAG
1 TTCATTCAACTAAACTAGTTCATCCATCAAACTAG
* * *
10160313 TTCA-TCCATTAAACTAGTTCATTCATCAAACTAG
1 TTCATTCAACTAAACTAGTTCATCCATCAAACTAG
10160347 TTCATTCAA
1 TTCATTCAA
10160356 GATTACAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
33 3 0.09
34 28 0.82
35 3 0.09
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (35 bp):
TTCATTCAACTAAACTAGTTCATCCATCAAACTAG
Found at i:10160352 original size:17 final size:17
Alignment explanation
Indices: 10160293--10160432 Score: 120
Period size: 17 Copynumber: 8.1 Consensus size: 17
10160283 TTTAACTAAG
*
10160293 TAGTTCATCCATTAAAC
1 TAGTTCATTCATTAAAC
*
10160310 TAGTTCATCCATTAAAC
1 TAGTTCATTCATTAAAC
*
10160327 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
** *
10160344 TAGTTCATTCAAGATTAC
1 TAGTTCATTCATTA-AAC
* * * * *
10160362 AAGTACATTGAATAAAGT
1 TAGTTCATTCATTAAA-C
*
10160380 TAGTTCATTAATTAAAC
1 TAGTTCATTCATTAAAC
*
10160397 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
*
10160414 TA-TCTCATTTATTAAAC
1 TAGT-TCATTCATTAAAC
10160431 TA
1 TA
10160433 ACTATTAATT
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
16 1 0.01
17 75 0.75
18 24 0.24
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (17 bp):
TAGTTCATTCATTAAAC
Found at i:10162466 original size:20 final size:20
Alignment explanation
Indices: 10162430--10162467 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10162420 TTCCACATTA
**
10162430 AATATTAATATTTTTTATTT
1 AATATTAATATAATTTATTT
10162450 AATATTAATATAATTTAT
1 AATATTAATATAATTTAT
10162468 CATGTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTAATATAATTTATTT
Found at i:10165404 original size:17 final size:17
Alignment explanation
Indices: 10165382--10165469 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
10165372 AATTGAAAAA
10165382 ATATAATATATATATAT
1 ATATAATATATATATAT
*
10165399 ATATAATATA-AGTTTAT
1 ATATAATATATA-TATAT
*
10165416 ATATAA-ACTATATTTAT
1 ATATAATA-TATATATAT
10165433 ATTATAA-ACTATATA-ATT
1 A-TATAATA-TATATATA-T
10165451 ATTATAAGT-TATATATAT
1 A-TATAA-TATATATATAT
10165469 A
1 A
10165470 AATTATGTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.03
17 29 0.48
18 29 0.48
19 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:10165433 original size:15 final size:15
Alignment explanation
Indices: 10165415--10165532 Score: 50
Period size: 15 Copynumber: 7.9 Consensus size: 15
10165405 TATAAGTTTA
10165415 TATATAAACTATATTT
1 TATATAAACTATA-TT
10165431 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
* *
10165450 TAT-TATAAGT-TATA
1 TATATA-AACTATATT
* *
10165464 TATATAAATTATGTT
1 TATATAAACTATATT
*
10165479 TATATGAACTATA--
1 TATATAAACTATATT
*
10165492 TCTATAAACTATA--
1 TATATAAACTATATT
* * *
10165505 TATGTAAGCTATATA
1 TATATAAACTATATT
*
10165520 TGTATAAACTATA
1 TATATAAACTATA
10165533 AAAAGTATAT
Statistics
Matches: 77, Mismatches: 16, Indels: 18
0.69 0.14 0.16
Matches are distributed among these distances:
13 21 0.27
14 6 0.08
15 24 0.31
16 5 0.06
17 7 0.09
18 13 0.17
19 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:10165452 original size:20 final size:17
Alignment explanation
Indices: 10165388--10165446 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
10165378 AAAAATATAA
*
10165388 TATATATATATATATAA-
1 TATATTTATATATA-AAC
10165405 TATAAGTTTATATATAAAC
1 TAT-A-TTTATATATAAAC
10165424 TATATTTATATTATAAAC
1 TATATTTATA-TATAAAC
10165442 TATAT
1 TATAT
10165447 AATTATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 9 0.24
18 16 0.43
19 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATTTATATATAAAC
Found at i:10165453 original size:18 final size:17
Alignment explanation
Indices: 10165412--10165457 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
10165402 TAATATAAGT
*
10165412 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
10165430 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
10165449 TTATTATAA
1 TTATTATAA
10165458 GTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:10165532 original size:13 final size:13
Alignment explanation
Indices: 10165460--10165532 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
10165450 TATTATAAGT
*
10165460 TATATATATAAAT
1 TATATATATAAAC
* *
10165473 TATGTTTATATGAAC
1 TA--TATATATAAAC
*
10165488 TATATCTATAAAC
1 TATATATATAAAC
* *
10165501 TATATATGTAAGC
1 TATATATATAAAC
10165514 TATATATGTATAAAC
1 TATATA--TATAAAC
10165529 TATA
1 TATA
10165533 AAAAGTATAT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
13 26 0.58
15 19 0.42
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:10165699 original size:39 final size:39
Alignment explanation
Indices: 10165656--10165731 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
10165646 TTTATTTGGG
*
10165656 AATTTAGAGGGAAATTG-AGAATTTAGAGGGAAATTGAAA
1 AATTTAGAGGG-AATAGAAGAATTTAGAGGGAAATTGAAA
*
10165695 AATTTAGAGGGAATAGAAGATTTTAGAGGGAAATTGA
1 AATTTAGAGGGAATAGAAGAATTTAGAGGGAAATTGA
10165732 GAATTGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (39 bp):
AATTTAGAGGGAATAGAAGAATTTAGAGGGAAATTGAAA
Found at i:10165700 original size:20 final size:20
Alignment explanation
Indices: 10165655--10165736 Score: 116
Period size: 19 Copynumber: 4.2 Consensus size: 20
10165645 TTTTATTTGG
10165655 GAATTTAGAGGGAAATTG-A
1 GAATTTAGAGGGAAATTGAA
10165674 GAATTTAGAGGGAAATTGAA
1 GAATTTAGAGGGAAATTGAA
* *
10165694 AAATTTAGAGGG-AATAGAA
1 GAATTTAGAGGGAAATTGAA
*
10165713 GATTTTAGAGGGAAATTG-A
1 GAATTTAGAGGGAAATTGAA
10165732 GAATT
1 GAATT
10165737 GAGATTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 39 0.71
20 16 0.29
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (20 bp):
GAATTTAGAGGGAAATTGAA
Found at i:10166195 original size:27 final size:28
Alignment explanation
Indices: 10166165--10166238 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
10166155 AGTTTTATAG
* *
10166165 AAACCTTAAACCTTAAATCATAAACA-T
1 AAACCCTAAACCTTAAACCATAAACACT
*
10166192 AAACCCTAAACTTTAAACCATAAACACT
1 AAACCCTAAACCTTAAACCATAAACACT
*
10166220 AAACACTAAACAC-TAAACC
1 AAACCCTAAAC-CTTAAACC
10166239 CTAATGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (28 bp):
AAACCCTAAACCTTAAACCATAAACACT
Found at i:10166208 original size:14 final size:14
Alignment explanation
Indices: 10166185--10166242 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
10166175 CCTTAAATCA
10166185 TAAACA-TAAACCC
1 TAAACACTAAACCC
** *
10166198 TAAACTTTAAACCA
1 TAAACACTAAACCC
*
10166212 TAAACACTAAACAC
1 TAAACACTAAACCC
10166226 TAAACACTAAACCC
1 TAAACACTAAACCC
10166240 TAA
1 TAA
10166243 TGTAAATGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
13 5 0.14
14 32 0.86
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACACTAAACCC
Found at i:10166215 original size:21 final size:20
Alignment explanation
Indices: 10166171--10166242 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
10166161 ATAGAAACCT
*
10166171 TAAACCTTAAATCA-TAAACA
1 TAAACCCTAAA-CACTAAACA
**
10166191 TAAACCCTAAACTTTAAACCA
1 TAAACCCTAAACACTAAA-CA
*
10166212 TAAACACTAAACACTAAACA
1 TAAACCCTAAACACTAAACA
10166232 CTAAACCCTAA
1 -TAAACCCTAA
10166243 TGTAAATGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 16 0.37
21 26 0.60
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAACCCTAAACACTAAACA
Found at i:10166222 original size:7 final size:7
Alignment explanation
Indices: 10166185--10166242 Score: 57
Period size: 7 Copynumber: 8.4 Consensus size: 7
10166175 CCTTAAATCA
10166185 TAAACA-
1 TAAACAC
*
10166191 TAAACCC
1 TAAACAC
**
10166198 TAAACTT
1 TAAACAC
10166205 TAAAC-C
1 TAAACAC
10166211 ATAAACAC
1 -TAAACAC
10166219 TAAACAC
1 TAAACAC
10166226 TAAACAC
1 TAAACAC
*
10166233 TAAACCC
1 TAAACAC
10166240 TAA
1 TAA
10166243 TGTAAATGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
6 5 0.11
7 38 0.86
8 1 0.02
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACAC
Found at i:10166646 original size:2 final size:2
Alignment explanation
Indices: 10166601--10166637 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
10166591 ATAAAACATC
10166601 TA TA GTA TA TA 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
10166638 AACTATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10166963 original size:14 final size:14
Alignment explanation
Indices: 10166944--10166990 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
10166934 ATTTTTTCTT
10166944 TATATAAATTAAAC
1 TATATAAATTAAAC
10166958 TATAT-AATT----
1 TATATAAATTAAAC
10166967 TATATAAATTAAAC
1 TATATAAATTAAAC
*
10166981 TATATTAATT
1 TATATAAATT
10166991 TTCCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:10166968 original size:23 final size:24
Alignment explanation
Indices: 10166942--10166991 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
10166932 TTATTTTTTC
10166942 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
10166965 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
10166989 TTT
1 TTT
10166992 TCCTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:10176632 original size:21 final size:21
Alignment explanation
Indices: 10176578--10176640 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
10176568 ATTCCCCTGT
10176578 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
10176601 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
* *
10176622 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
10176641 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:10183247 original size:16 final size:16
Alignment explanation
Indices: 10183217--10183257 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
10183207 ATTAAATTAA
*
10183217 AAAAATAAAAATGCAT
1 AAAATTAAAAATGCAT
* *
10183233 AAATTTAAAAGTGCAT
1 AAAATTAAAAATGCAT
10183249 AAAATTAAA
1 AAAATTAAA
10183258 TAACATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (16 bp):
AAAATTAAAAATGCAT
Found at i:10183470 original size:16 final size:16
Alignment explanation
Indices: 10183428--10183470 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
10183418 CAGTTAGTAA
*
10183428 TTAGCGGTTAGAAATG
1 TTAGCGGTTAGAAAAG
**
10183444 TTAGCTATTAGAAAAG
1 TTAGCGGTTAGAAAAG
10183460 TTAGCGGTTAG
1 TTAGCGGTTAG
10183471 CATAGTCTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:10183805 original size:4 final size:4
Alignment explanation
Indices: 10183796--10183827 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
10183786 TATTAAAAAC
10183796 AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA
10183828 GTGGTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:10183843 original size:29 final size:28
Alignment explanation
Indices: 10183826--10183904 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
10183816 AATAAATAAA
10183826 TAGTGGTTAAAGTGAAATAAAATAAAAGT
1 TAGTGGTTAAA-TGAAATAAAATAAAAGT
*
10183855 TAGTGGTTAATATGCAATAAAATAAAAGT
1 TAGTGGTTAA-ATGAAATAAAATAAAAGT
* *
10183884 TAGTAGTTAACTTGAAATAAA
1 TAGTGGTTAA-ATGAAATAAA
10183905 TAACATATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (28 bp):
TAGTGGTTAAATGAAATAAAATAAAAGT
Found at i:10186026 original size:18 final size:19
Alignment explanation
Indices: 10185978--10186026 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
10185968 TTGGACCCTT
10185978 AGTGCATCGATGCACTAAG
1 AGTGCATCGATGCACTAAG
*
10185997 AGTACATCGATGCA-TAA-
1 AGTGCATCGATGCACTAAG
10186014 AGTGCATTCGATG
1 AGTGCA-TCGATG
10186027 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 13 0.48
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:10186065 original size:45 final size:47
Alignment explanation
Indices: 10185996--10186119 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 47
10185986 GATGCACTAA
*
10185996 GAGTACATCGATGCA-TAAAGTGCATTCGATG-TTTCA-AAATAGC-C
1 GAGTGCATCGATGCATTAAAGTGCATTCGATGTTTTCATAAATA-CTC
*
10186040 TGAGTGCATCGATGCATTAAA-TGCATTCGATGTTTTCATTAATACTC
1 -GAGTGCATCGATGCATTAAAGTGCATTCGATGTTTTCATAAATACTC
* *
10186087 GAGTGCATCGATGCATGGAGAGTGCA-TCGATGT
1 GAGTGCATCGATGCAT-TAAAGTGCATTCGATGT
10186120 ATGAACTGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 25 0.36
46 26 0.38
47 14 0.20
48 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (47 bp):
GAGTGCATCGATGCATTAAAGTGCATTCGATGTTTTCATAAATACTC
Found at i:10186094 original size:46 final size:46
Alignment explanation
Indices: 10185996--10186119 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 46
10185986 GATGCACTAA
*
10185996 GAGTACATCGATGCA-TAAAGTGCATTCGATGTTTCAAAATAGCCT
1 GAGTGCATCGATGCATTAAAGTGCATTCGATGTTTCAAAATAGCCT
*
10186041 GAGTGCATCGATGCATTAAA-TGCATTCGATGTTTTCATTAATA--CT
1 GAGTGCATCGATGCATTAAAGTGCATTCGATG-TTTCA-AAATAGCCT
* *
10186086 CGAGTGCATCGATGCATGGAGAGTGCA-TCGATGT
1 -GAGTGCATCGATGCAT-TAAAGTGCATTCGATGT
10186120 ATGAACTGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
45 27 0.39
46 26 0.38
47 12 0.17
48 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATTAAAGTGCATTCGATGTTTCAAAATAGCCT
Done.