Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001209.1 Hibiscus syriacus cultivar Beakdansim tig00002390_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: 162536
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:7364 original size:14 final size:14
Alignment explanation
Indices: 7345--7373 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7335 TGTAATGCTT
7345 GTTTACAAAGTAAA
1 GTTTACAAAGTAAA
7359 GTTTACAAAGTAAA
1 GTTTACAAAGTAAA
7373 G
1 G
7374 CTCACAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (14 bp):
GTTTACAAAGTAAA
Found at i:20238 original size:22 final size:22
Alignment explanation
Indices: 20195--20238 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20185 TCTTATTTTT
* *
20195 ACTTTAATTACTTTATTTAATC
1 ACTTTAATTACTTTACTAAATC
20217 ACTTT-ATTATCTTTACTAAATC
1 ACTTTAATTA-CTTTACTAAATC
20239 CCCCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (22 bp):
ACTTTAATTACTTTACTAAATC
Found at i:25748 original size:6 final size:6
Alignment explanation
Indices: 25737--25770 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
25727 ATTCCGTTAC
25737 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
25771 TTACTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:36117 original size:39 final size:39
Alignment explanation
Indices: 36063--36141 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
36053 TGGTAATCCA
36063 TTTCATATTAACATATTTTAGAGAAGATTAAAATCTTCT
1 TTTCATATTAACATATTTTAGAGAAGATTAAAATCTTCT
*
36102 TTTCATATTAACATATTTTAGAGAAGATTATAATCTTCT
1 TTTCATATTAACATATTTTAGAGAAGATTAAAATCTTCT
36141 T
1 T
36142 ACACGTGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (39 bp):
TTTCATATTAACATATTTTAGAGAAGATTAAAATCTTCT
Found at i:38611 original size:16 final size:17
Alignment explanation
Indices: 38576--38611 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
38566 TTAAACTTAA
*
38576 TTTGATGCTATAATAAT
1 TTTGATGCTAAAATAAT
38593 TTTG-TGCTAAAATAAT
1 TTTGATGCTAAAATAAT
38609 TTT
1 TTT
38612 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTGATGCTAAAATAAT
Found at i:42077 original size:2 final size:2
Alignment explanation
Indices: 42070--42095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42060 ACTAAAAATA
42070 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
42096 GAGAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54993 original size:55 final size:55
Alignment explanation
Indices: 54935--55451 Score: 461
Period size: 55 Copynumber: 9.6 Consensus size: 55
54925 TGACGAGCCT
* * * **
54935 GCTCCCTATTCCTTCAG-GAAGTATAAGGCTCGAACAATCTTCATAAAATGTGTAT
1 GCTCTCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACGTGTCC
** * * * *
54990 GCTCTCTATTTATTCAGAAAGTATAAGACTTGACCAATCTTCAATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-ATAAAACGTGTCC
*
55046 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGGAA-AATCTTTA-ATAAACAG-GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAG-ACTC-GAACAATCTTCATA-AAAC-GTGTCC
* * * *
55101 GCTCCCTATTCTTTCAGAGAGTATATGACT----CAATCTTTA-ACAAACGTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCC
* * * *
55152 GCTCCCTATTCCTTCAGAGAGTATATA-ACTCGAGCAATCTTTATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCATAAAACGTGTCC
55207 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCA-ACAAACGTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAACGTGTCC
** *
55262 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATGCAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATAAAACGTGTCC
* *
55317 GCTCTCTATTCCTTCAGAGAGTA-AAGGACT----CAATCTTTA-ACAAACATGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAA-GACTCGAACAATCTTCATA-AAACGTGTCC
* * * * *
55368 GCTCCCTATTCTTTCAGAGAGTATAGGACTCG----ATCTTTATAAAATGTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGTGTCC
* *
55419 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGA
1 GCTCTCTATTCCTTCAGAGAGTATAAGACTCGA
55452 TCTTCATAAA
Statistics
Matches: 393, Mismatches: 42, Indels: 57
0.80 0.09 0.12
Matches are distributed among these distances:
50 1 0.00
51 130 0.33
52 2 0.01
53 1 0.00
54 2 0.01
55 212 0.54
56 43 0.11
57 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (55 bp):
GCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGTGTCC
Found at i:55212 original size:161 final size:157
Alignment explanation
Indices: 55002--55459 Score: 499
Period size: 161 Copynumber: 2.9 Consensus size: 157
54992 TCTCTATTTA
* *
55002 TTCAGAAAGTATAAGACTTGACCAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAG
1 TTCAGAGAGTATAA-AC-TGA-CAATCTT-TATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAG
*
55067 TATAGAACTCGGAAAATCTTTAATAAACAG-GTCCGCTCCCTATTCTTTCAGAGAGTATATGACT
62 TATAGAACTC-GAAAATCTTTAATAAACAGTGTCCGCTCCCTATTCCTTCAGAGAGTATA-GACT
* *
55131 CAATCTTTA-ACAAACGTGTCCGCTCCCTATTCC
125 CAATCTTCATAC-AACGGGTCCGCTCCCTATTCC
55164 TTCAGAGAGTATATAACTCGAGCAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGT
1 TTCAGAGAGTATA-AACT-GA-CAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGT
* * *
55229 ATAGAACTCGAACAATCTTCAACAAAC-GTGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTC
63 ATAGAACTCGAA-AATCTTTAATAAACAGTGTCCGCTCCCTATTCCTTCAGAGAGTATAG-ACT-
* *
55293 GAACAATCTTCATGCAACGGGTCCGCTCTCTATTCC
125 ---CAATCTTCATACAACGGGTCCGCTCCCTATTCC
** * *
55329 TTCAGAGAGTA-AAGGACT--CAATCTTTA-ACAAACATGTCCGCTCCCTATTCTTTCAGAGAGT
1 TTCAGAGAGTATAA--ACTGACAATCTTTATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGT
*
55390 ATAGGACTCG---ATCTTT-ATAAA-ATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
63 ATAGAACTCGAAAATCTTTAATAAACA-GTGTCCGCTCCCTATTCCTTCAGAGAGTATA-GACTC
*
55450 GATCTTCATA
126 AATCTTCATA
55460 AAATGAGTTT
Statistics
Matches: 259, Mismatches: 21, Indels: 41
0.81 0.07 0.13
Matches are distributed among these distances:
153 9 0.03
156 4 0.02
157 38 0.15
158 1 0.00
160 6 0.02
161 133 0.51
162 23 0.09
163 2 0.01
164 1 0.00
165 41 0.16
166 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (157 bp):
TTCAGAGAGTATAAACTGACAATCTTTATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
GAACTCGAAAATCTTTAATAAACAGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGACTCAATCT
TCATACAACGGGTCCGCTCCCTATTCC
Found at i:55507 original size:37 final size:36
Alignment explanation
Indices: 55466--55537 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
55456 CATAAAATGA
55466 GTTTGCTTCACTAATCTACCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTACCGTGAAGGCTTA-AGATG
* *
55503 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTACCGTGAAGGCTTAAGAT
55538 TGACCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTACCGTGAAGGCTTAAGATG
Found at i:56846 original size:16 final size:16
Alignment explanation
Indices: 56827--57022 Score: 110
Period size: 16 Copynumber: 12.2 Consensus size: 16
56817 TATTTCTTTT
56827 TTTTTTCATTTTTCTC
1 TTTTTTCATTTTTCTC
*
56843 TTTTTTCATTTTTCATT
1 TTTTTTCATTTTTC-TC
56860 TTTTCTTC-TATTTTC-C
1 TTTT-TTCAT-TTTTCTC
* *
56876 ATTTTTC--TCTTCTC
1 TTTTTTCATTTTTCTC
* * *
56890 TTTTTTTCTTTTTGTTTT
1 -TTTTTTCATTTT-TCTC
56908 TTTTTCATCATTTTTCT-
1 TTTTT--TCATTTTTCTC
56925 TTTTTCTCATTTTTCT-
1 TTTTT-TCATTTTTCTC
*
56941 TTTCTTC-TTTTTCT-
1 TTTTTTCATTTTTCTC
* * *
56955 TCTTCTCATTTTTAT-
1 TTTTTTCATTTTTCTC
56970 TATTTTTCATTTTT-TC
1 T-TTTTTCATTTTTCTC
56986 ATTTTTTCATTTTT-TC
1 -TTTTTTCATTTTTCTC
57002 ATTTTTCTC-TTTTTCTC
1 -TTTTT-TCATTTTTCTC
57019 TTTT
1 TTTT
57023 ATTTCTTCTT
Statistics
Matches: 146, Mismatches: 18, Indels: 32
0.74 0.09 0.16
Matches are distributed among these distances:
13 4 0.03
14 12 0.08
15 19 0.13
16 70 0.48
17 23 0.16
18 12 0.08
19 6 0.04
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTTTCATTTTTCTC
Found at i:56902 original size:47 final size:50
Alignment explanation
Indices: 56838--56953 Score: 125
Period size: 48 Copynumber: 2.4 Consensus size: 50
56828 TTTTTCATTT
56838 TTCTC-TTTTTTCATTTTTCATTTTTTCTTC-T-ATTTTCCATTTTTCTC-
1 TTCTCTTTTTTTC-TTTTTCATTTTTTCTTCATCATTTTCCATTTTTCTCA
* * * *
56885 TTCTCTTTTTTTCTTTTT-GTTTTTTTTTCATCATTTTTCTTTTTTCTCA
1 TTCTCTTTTTTTCTTTTTCATTTTTTCTTCATCATTTTCCATTTTTCTCA
* *
56934 TTTTTCTTTTCTTCTTTTTC
1 -TTCTCTTTTTTTCTTTTTC
56954 TTCTTCTCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
46 9 0.16
47 11 0.19
48 21 0.37
50 16 0.28
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (50 bp):
TTCTCTTTTTTTCTTTTTCATTTTTTCTTCATCATTTTCCATTTTTCTCA
Found at i:56980 original size:45 final size:42
Alignment explanation
Indices: 56819--56983 Score: 121
Period size: 42 Copynumber: 3.9 Consensus size: 42
56809 CCTCCTTTTA
*
56819 TTTCTTTTTTTTT--TCATTTTTCTCTTTTT-TCATTTTTCATTT
1 TTTCTTTTTTTTTCATCATTTTTAT-TTTTTCTCATTTTTC--TT
* * * * * *
56861 TTTCTTCTATTTTC--CATTTTTCTCTTCTCT-TTTTTTCTT
1 TTTCTTTTTTTTTCATCATTTTTATTTTTTCTCATTTTTCTT
* *
56900 TTTGTTTTTTTTTCATCATTTTTCTTTTTTCTCATTTTTCTTT
1 TTTCTTTTTTTTTCATCATTTTTATTTTTTCTCATTTTTC-TT
56943 TCTTCTTTTTCTTCTTC-TCATTTTTATTATTTT-TCATTTTT
1 T-TTCTTTTT-TT-TTCATCATTTTTATT-TTTTCTCATTTTT
56984 TCATTTTTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
39 13 0.13
41 23 0.23
42 27 0.27
43 3 0.03
44 7 0.07
45 20 0.20
46 7 0.07
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (42 bp):
TTTCTTTTTTTTTCATCATTTTTATTTTTTCTCATTTTTCTT
Found at i:57014 original size:7 final size:8
Alignment explanation
Indices: 56835--57022 Score: 73
Period size: 8 Copynumber: 23.5 Consensus size: 8
56825 TTTTTTTTCA
56835 TTTTTCTC
1 TTTTTCTC
56843 TTTTT-TC
1 TTTTTCTC
56850 ATTTTTCAT-
1 -TTTTTC-TC
56859 TTTTTCTTC
1 TTTTTC-TC
56868 TATTTTC-C
1 T-TTTTCTC
56876 ATTTTTCTC
1 -TTTTTCTC
* *
56885 -TTCTCTT
1 TTTTTCTC
56892 TTTTTCT-
1 TTTTTCTC
* *
56899 TTTTGTTTT
1 TTTT-TCTC
56908 TTTTTCATC
1 TTTTTC-TC
56917 ATTTTTCT-
1 -TTTTTCTC
56925 TTTTTCTC
1 TTTTTCTC
*
56933 ATTTT-TC
1 TTTTTCTC
56940 -TTTTCT-
1 TTTTTCTC
56946 TCTTTT-TC
1 T-TTTTCTC
*
56954 TTCTTCTC
1 TTTTTCTC
*
56962 ATTTTTAT-
1 -TTTTTCTC
56970 TATTTT-TC
1 T-TTTTCTC
56978 ATTTTT-TC
1 -TTTTTCTC
56986 ATTTTT-TC
1 -TTTTTCTC
56994 ATTTTT-TC
1 -TTTTTCTC
57002 ATTTTTCTC
1 -TTTTTCTC
57011 TTTTTCTC
1 TTTTTCTC
57019 TTTT
1 TTTT
57023 ATTTCTTCTT
Statistics
Matches: 146, Mismatches: 11, Indels: 46
0.72 0.05 0.23
Matches are distributed among these distances:
6 4 0.03
7 27 0.18
8 86 0.59
9 17 0.12
10 12 0.08
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTCTC
Found at i:57022 original size:15 final size:15
Alignment explanation
Indices: 56835--57022 Score: 55
Period size: 15 Copynumber: 12.8 Consensus size: 15
56825 TTTTTTTTCA
*
56835 TTTTTCTCTTTTTTC
1 TTTTTCTCTTTTCTC
* *
56850 ATTTT-TCATTT-T-
1 TTTTTCTCTTTTCTC
* *
56862 TTCTTCTATTTTC-C
1 TTTTTCTCTTTTCTC
56876 ATTTTTCTC--TTCTC
1 -TTTTTCTCTTTTCTC
*
56890 TTTTTTTCTTTT-T-
1 TTTTTCTCTTTTCTC
*
56903 GTTTT-T-TTTTCATC
1 TTTTTCTCTTTTC-TC
*
56917 ATTTTTCTTTTTTCTC
1 -TTTTTCTCTTTTCTC
*
56933 ATTTT-TCTTTTCTTC
1 TTTTTCTCTTTTC-TC
*
56948 TTTTTCT-TCTTCTC
1 TTTTTCTCTTTTCTC
* *
56962 ATTTTTAT-TATTTTTC
1 -TTTTTCTCT-TTTCTC
*
56978 ATTTTT-TCATTTTTTC
1 -TTTTTCTC-TTTTCTC
56994 ATTTTT-TCATTTTTCTC
1 -TTTTTCTC--TTTTCTC
57011 TTTTTCTCTTTT
1 TTTTTCTCTTTT
57023 ATTTCTTCTT
Statistics
Matches: 132, Mismatches: 20, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
11 4 0.03
12 4 0.03
13 20 0.15
14 15 0.11
15 42 0.32
16 33 0.25
17 14 0.11
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTTTCTCTTTTCTC
Found at i:66797 original size:44 final size:45
Alignment explanation
Indices: 66678--66810 Score: 196
Period size: 44 Copynumber: 2.9 Consensus size: 45
66668 CCATGCTTTG
*
66678 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATAC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATAC
* *
66725 TTATTCAAAAAATAAACCTAACCACATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
* *
66770 TTGTT-GAAAAATAAACCTAACCGCATGATATCTAGTTCGCA
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCA
66811 AGCATTTATT
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 34 0.43
45 30 0.38
46 9 0.11
47 7 0.09
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
Found at i:72366 original size:21 final size:21
Alignment explanation
Indices: 72330--72382 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
72320 TTCTCCTTCG
* *
72330 TCATCATCCCCATCATCTGCCATG
1 TCATCATCCTCATCA-C--CCATA
72354 TCATCATCCTCATCACCCATA
1 TCATCATCCTCATCACCCATA
72375 TCATCATC
1 TCATCATC
72383 TGCCCTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
23 1 0.04
24 14 0.52
ACGTcount: A:0.25, C:0.42, G:0.04, T:0.30
Consensus pattern (21 bp):
TCATCATCCTCATCACCCATA
Found at i:73703 original size:19 final size:21
Alignment explanation
Indices: 73664--73704 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
73654 ATAATCCTAT
73664 TATTTCAAAATTATAAAAAAA
1 TATTTCAAAATTATAAAAAAA
*
73685 TATTT-AAAA-TATCAAAAAA
1 TATTTCAAAATTATAAAAAAA
73704 T
1 T
73705 GACTTCTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
TATTTCAAAATTATAAAAAAA
Found at i:74562 original size:15 final size:15
Alignment explanation
Indices: 74542--74581 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
74532 CCGGCAACCG
74542 TCTGCCGCCGCGAAT
1 TCTGCCGCCGCGAAT
*
74557 TCTGCCACCGCGAAT
1 TCTGCCGCCGCGAAT
74572 TCTGCCGCCG
1 TCTGCCGCCG
74582 ACCACCGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.12, C:0.42, G:0.25, T:0.20
Consensus pattern (15 bp):
TCTGCCGCCGCGAAT
Found at i:75323 original size:12 final size:11
Alignment explanation
Indices: 75305--75389 Score: 69
Period size: 9 Copynumber: 8.2 Consensus size: 11
75295 TTATATATGT
75305 ATTTAAT-AT-
1 ATTTAATAATA
75314 ATTTAATAATA
1 ATTTAATAATA
75325 A--TAATAATA
1 ATTTAATAATA
*
75334 ATAATAATAATA
1 AT-TTAATAATA
*
75346 ATACTAATAATA
1 AT-TTAATAATA
75358 A-TT-ATAATA
1 ATTTAATAATA
75367 A--TAATAATA
1 ATTTAATAATA
75376 ATTATAATAATA
1 ATT-TAATAATA
75388 AT
1 AT
75390 AATAAGAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
8 1 0.02
9 30 0.46
10 3 0.05
11 1 0.02
12 30 0.46
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:75325 original size:3 final size:3
Alignment explanation
Indices: 75317--75394 Score: 129
Period size: 3 Copynumber: 26.0 Consensus size: 3
75307 TTAATATATT
* *
75317 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
75365 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75395 GAAATCCATA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:75712 original size:36 final size:38
Alignment explanation
Indices: 75671--75774 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 38
75661 AAGGTTAAAC
*
75671 AAGTTCTTCTCGTTATGAACTTC-CTT-TTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTCTTCTTCTTCAGAT
*
75707 GAGTTCTTCTCATTATGAACTCTCTTCTTCCTTCTTCAGAT
1 AAGTTCTTCTCATTATGAACT-TC-TCTT-CTTCTTCAGAT
*
75748 AAATTCTTCTCATTATGAACTTTCTCT
1 AAGTTCTTCTCATTATGAAC-TTCTCT
75775 GGAAAAGTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
36 19 0.33
37 2 0.03
39 3 0.05
40 3 0.05
41 30 0.52
42 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (38 bp):
AAGTTCTTCTCATTATGAACTTCTCTTCTTCTTCAGAT
Found at i:76086 original size:113 final size:113
Alignment explanation
Indices: 75809--76476 Score: 819
Period size: 113 Copynumber: 5.9 Consensus size: 113
75799 AAAGTCGAAT
*
75809 AAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGATGAGTTCTTCTCATTATGAACTC
1 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAAC-C
* * * * * * *
75874 TT-CCTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTG-AC
62 TTATCTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC
*
75924 AAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAT
1 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAT
* *
75989 CTGGAAAAGCTGATCCATCTAA-TGATGGATTTGAGCAAAAGGTTGAAC
66 CTGGAAAAGCTAATCCATC-AAGTGATGGATTTAAGCAAAAGGTTGAAC
** * * *
76037 AAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAT
* * * *
76102 TTGGAAAAGCTGATCCATTGAA-TGATGGATTTAAGCATAAGGTTGAAC
66 CTGGAAAAGCTAATCCA-TCAAGTGATGGATTTAAGCAAAAGGTTGAAC
* * *
76150 AAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAT
* * *
76215 CTGGCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAAC
66 CTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC
*
76263 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCGA
1 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCT-TA
* * * * *
76327 ACTGGAAAAGCTAATCCATCAAGTGATGGGTTTGAGCAAAAAGTTGAAT
65 TCTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC
** ** *
76376 AAATTCTTCAAGAGAAATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 AAATTCTTC-TCA-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT
* * * *
76441 CTCT-GACAATGTTAATCCATTGAA-TGATGGATTTAA
64 ATCTGGA-AAAGCTAATCCA-TCAAGTGATGGATTTAA
76477 ATCTTTGCTA
Statistics
Matches: 488, Mismatches: 54, Indels: 22
0.87 0.10 0.04
Matches are distributed among these distances:
111 3 0.01
112 62 0.13
113 314 0.64
114 4 0.01
115 101 0.21
116 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAT
CTGGAAAAGCTAATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC
Found at i:76442 original size:341 final size:338
Alignment explanation
Indices: 75721--76477 Score: 997
Period size: 341 Copynumber: 2.3 Consensus size: 338
75711 TCTTCTCATT
* *
75721 ATGAACTCTCTTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGGAAAA--G--
1 ATGAACT-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGAT
* * *
75782 ---TTG-ATG-TTGA-TTAAACTAAAGTCGAATAAATTCTTCTCATTATGAACTTCTTCTTCTTT
65 CCATTGAATGATGGATTTAAACTAAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
* * *
75841 CTTCAGATGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTAATCCATCAATTGATGAA
130 CTTCA-ATGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAAAGCTAATCCATCAAGTGATGAA
* *
75906 TTTAAACAAAAGGTTGACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCT
194 TTCAAACAAAAGGTTGACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
75971 TCTCATTATGAACCTTATCTGGAAAAGCTGATCCATCTAATGATGGATTTGAGCAAAAGGTTGAA
259 TCTCATTATGAACCTGAACTGGAAAAGCTAATCCATCTAATGATGGATTTGAGCAAAAAGTTGAA
* * **
76036 CAAGCTCTTCTCATT
324 CAAACTCTTCACAAA
* *
76051 ATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAGCTGAT
1 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-TGAT
* * * *
76116 CCATTGAATGATGGATTTAAGCATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCT
65 CCATTGAATGATGGATTTAAAC-TAAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCT
*
76181 TCTTC-A-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGCAAAGCTAATCCATCAAGTGATGG
129 TCTTCAATGATGAGTTCTTCTCATTATGAACTCTTC-CTGGCAAAGCTAATCCATCAAGTGATGA
**
76243 ATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
193 ATTCAAACAAAAGGTTG-ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
*
76308 CTTCTCATTATGAA-CTCGAACTGGAAAAGCTAATCCATC-AAGTGATGGGTTTGAGCAAAAAGT
257 CTTCTCATTATGAACCT-GAACTGGAAAAGCTAATCCATCTAA-TGATGGATTTGAGCAAAAAGT
* * *
76371 TGAATAAATTCTTCAAGAGAA
320 TGAACAAACTCTTC-ACA-AA
* *
76392 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-GACAATGTTAA
1 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA-AAAG-TGA
76456 TCCATTGAATGATGGATTTAAA
64 TCCATTGAATGATGGATTTAAA
76478 TCTTTGCTAA
Statistics
Matches: 371, Mismatches: 37, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
329 48 0.13
330 7 0.02
332 1 0.00
337 6 0.02
338 69 0.19
339 113 0.30
340 8 0.02
341 119 0.32
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (338 bp):
ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATC
CATTGAATGATGGATTTAAACTAAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
TTCAATGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAAAGCTAATCCATCAAGTGATGAATT
CAAACAAAAGGTTGACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTGAACTGGAAAAGCTAATCCATCTAATGATGGATTTGAGCAAAAAGTTGAACA
AACTCTTCACAAA
Found at i:77576 original size:83 final size:84
Alignment explanation
Indices: 77295--77851 Score: 812
Period size: 85 Copynumber: 6.5 Consensus size: 84
77285 GGGGTTCATA
* *
77295 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCGTCTTTCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTTCA
*
77360 AATTCAATGATTGGTTTTGGTTCATA
66 AATTCAATGA------TTGGTTC-TG
* * *
77386 CCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCGTCTTTCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTTCA
* * *
77451 AATTCAATGATTAGTTTTA
66 AATTCAATGATTGGTTCTG
* * *
77470 CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTA-TGAGCATATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTTCA
77534 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* *
77553 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCCTTCTTCATCTTTC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGG-CATATTCATCTTTC
*
77618 AAATTTAATGATTGGTTCTG
65 AAATTCAATGATTGGTTCTG
* *
77638 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTTCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTTCA
*
77702 ACTTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* * *
77721 CCAAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGGGCCTTCTTCATCTTTC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGG-CATATTCATCTTTC
*
77786 AAATTTAATGATTGGTTCTG
65 AAATTCAATGATTGGTTCTG
*
77806 CCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
77852 GAGCACATGG
Statistics
Matches: 429, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
83 148 0.34
84 54 0.13
85 153 0.36
91 74 0.17
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTTCA
AATTCAATGATTGGTTCTG
Found at i:77658 original size:168 final size:168
Alignment explanation
Indices: 77295--77856 Score: 876
Period size: 168 Copynumber: 3.3 Consensus size: 168
77285 GGGGTTCATA
* * *
77295 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCGTCTTTCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTTCA
* *
77360 AATTCAATGATTGGTTTTGGTTCATACCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAG
65 AATTCAATGA------TTGGTTC-TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * * * * *
77425 ATGCTATTGGGCAC--ATTCGTCTTTCAAATTCAATGATTAGTTTTA
123 ATGCTATTGGGC-CTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
* * *
77470 CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCATATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTTCAA
77535 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
77600 GGGCCTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
131 GGGCCTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
77638 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTTCAA
* *
77703 CTTCAATGATTGGTTCTGCCAAACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATT
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
77768 GGGCCTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
131 GGGCCTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
*
77806 CCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
77857 CATGGCATTT
Statistics
Matches: 366, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
166 1 0.00
167 51 0.14
168 245 0.67
174 25 0.07
175 44 0.12
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (168 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTTCAA
ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
GGGCCTTCTTCATCTTTCAAATTTAATGATTGGTTCTG
Found at i:79036 original size:10 final size:10
Alignment explanation
Indices: 79001--79042 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
78991 ATTGACCCCC
79001 TTTTTTTTCT
1 TTTTTTTTCT
*
79011 TTTTTCTCTCT
1 TTTTT-TTTCT
79022 TTTTTTTTCT
1 TTTTTTTTCT
79032 TTTTTTTTCT
1 TTTTTTTTCT
79042 T
1 T
79043 CAAGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:90266 original size:20 final size:21
Alignment explanation
Indices: 90229--90269 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
90219 ATAATCCTAT
90229 TATTTCAAAATTATAAAAAAA
1 TATTTCAAAATTATAAAAAAA
90250 TATTT-AAAA-TATCAAAAAAA
1 TATTTCAAAATTAT-AAAAAAA
90270 GGACTTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
TATTTCAAAATTATAAAAAAA
Found at i:91858 original size:3 final size:3
Alignment explanation
Indices: 91850--91933 Score: 114
Period size: 3 Copynumber: 28.0 Consensus size: 3
91840 TTAATATATT
* *
91850 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
91898 TTA TAA TAA TAA TTA TTA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
91934 GAAATCCATA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:91859 original size:15 final size:15
Alignment explanation
Indices: 91841--91929 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 15
91831 TATATGTATT
91841 TAATATATTTAATAA
1 TAATATATTTAATAA
*
91856 TAATA-ATAATAATAA
1 TAATATAT-TTAATAA
*
91871 TAATAATGATAATAATAA
1 TAAT-AT-AT-TTAATAA
91889 TAATAATTATTATAATAA
1 TAAT-A-TATT-TAATAA
91907 TAATTATTATTATAATAA
1 TAA-TA-TATT-TAATAA
91925 TAATA
1 TAATA
91930 ATAAGAAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.03
15 15 0.23
16 1 0.02
17 2 0.03
18 43 0.66
19 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
TAATATATTTAATAA
Found at i:95209 original size:21 final size:21
Alignment explanation
Indices: 95093--95247 Score: 88
Period size: 21 Copynumber: 7.5 Consensus size: 21
95083 ATTATGACTA
95093 TCGCAATGCGATTTTC-TAATT
1 TCGCAATGCGATTTTCATAA-T
** **
95114 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
95135 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
** *
95155 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
95175 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
95196 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
95216 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
95237 TCGCAATGCGA
1 TCGCAATGCGA
95248 ATACGTAAAT
Statistics
Matches: 100, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.02
20 43 0.43
21 50 0.50
22 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:95262 original size:20 final size:20
Alignment explanation
Indices: 95237--95324 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
95227 TTTTCATAAT
95237 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
95257 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
95277 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
95298 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
95318 TCGCAAT
1 TCGCAAT
95325 TGGGAATCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 39 0.70
21 17 0.30
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:95268 original size:41 final size:41
Alignment explanation
Indices: 95155--95269 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 41
95145 AATAAGTAAA
* *
95155 TCGCAATGCGATACTGAC-T-ATCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATA-T-ACGTAATCGCAATGCGATTTTCATAAT
* * * **
95196 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATATACGTAATCGCAATGCGATTTTCATAAT
*
95237 TCGCAATGCGA-ATACGTAAATCGCAACGCGATT
1 TCGCAATGCGATATACGT-AATCGCAATGCGATT
95270 AAGTAAATCG
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
39 2 0.03
40 7 0.12
41 49 0.84
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (41 bp):
TCGCAATGCGATATACGTAATCGCAATGCGATTTTCATAAT
Found at i:95299 original size:41 final size:40
Alignment explanation
Indices: 95237--95324 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 40
95227 TTTTCATAAT
* *
95237 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
* * * *
95277 TCGCAATGCGAATTAGGAAAATCGTAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGAATAAGTAAA
95318 TCGCAAT
1 TCGCAAT
95325 TGGGAATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 12 0.29
41 29 0.71
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
Found at i:95895 original size:19 final size:20
Alignment explanation
Indices: 95848--95900 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
95838 GTTTCGAGAC
95848 TGAAAATCGCAACGCGGAAA
1 TGAAAATCGCAACGCGGAAA
*
95868 T-AACTATCGCAACGC-GAAA
1 TGAA-AATCGCAACGCGGAAA
95887 TGAAAATCGCAACG
1 TGAAAATCGCAACG
95901 AGATAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGGAAA
Found at i:95948 original size:19 final size:19
Alignment explanation
Indices: 95926--96071 Score: 69
Period size: 19 Copynumber: 8.1 Consensus size: 19
95916 GAAACCAAAA
* *
95926 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTGTCATT
* *
95945 TCGCGTTGCGATAGTCATT
1 TCGCATTGCGATTGTCATT
* *
95964 TCGCATTGTGA-T-TC-TC
1 TCGCATTGCGATTGTCATT
*
95980 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTGTCATT
* *
95997 TCGCGTTGCGA-T-TC-TC
1 TCGCATTGCGATTGTCATT
*
96013 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTGTCATT
* *
96030 TCCGCGTTGCGATTTTCATT
1 T-CGCATTGCGATTGTCATT
* * *
96050 ATCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTGTCATT
96070 TC
1 TC
96072 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
14 11 0.11
16 12 0.12
17 10 0.10
18 2 0.02
19 32 0.33
20 29 0.30
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTGTCATT
Found at i:95990 original size:33 final size:33
Alignment explanation
Indices: 95948--96043 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
95938 TTTTATTTCG
*
95948 CGTTGCGATAGTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
*
95981 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
*
96014 CGTTGCGATAGTCATTTCCGCGTTGCGATT
1 CGTTGCGATAGTCATTT-CGCATTGCGATT
96044 TTCATTATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.80
34 12 0.20
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
Found at i:96048 original size:20 final size:20
Alignment explanation
Indices: 96014--96071 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
96004 GCGATTCTCT
**
96014 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
96034 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
96054 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
96072 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:99654 original size:14 final size:14
Alignment explanation
Indices: 99635--99670 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
99625 ATTGTTTAAT
99635 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
99649 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
99663 TGATTTGT
1 TGATTTGT
99671 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:99819 original size:33 final size:33
Alignment explanation
Indices: 99777--99868 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
99767 AAAAATTACT
* *
99777 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
99810 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
99843 ATCGCAACGCGAAACT-AAAATCGCAA
1 ATCGCAATGCGAAA-TGAAAATCGCAA
99869 TGCGAAACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:99876 original size:19 final size:18
Alignment explanation
Indices: 99777--99885 Score: 90
Period size: 19 Copynumber: 6.3 Consensus size: 18
99767 AAAAATTACT
99777 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
*
99796 ATCGCAA--CGAGAT--A
1 ATCGCAATGCGAAATAAA
99810 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
*
99829 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAATAAA
*
99843 ATCGCAACGCGAAACTAAA
1 ATCGCAATGCGAAA-TAAA
99862 ATCGCAATGCGAAACTAAA
1 ATCGCAATGCGAAA-TAAA
*
99881 TTCGC
1 ATCGC
99886 GTTGCGATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.24
15 1 0.01
16 7 0.09
17 7 0.09
18 1 0.01
19 40 0.54
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:99909 original size:19 final size:19
Alignment explanation
Indices: 99887--100011 Score: 73
Period size: 19 Copynumber: 7.4 Consensus size: 19
99877 TAAATTCGCG
*
99887 TTGCGATTTTCATTTCTCT
1 TTGCGATTTTCATTTCTCA
* *
99906 TTGCGA--TTC---CCTCG
1 TTGCGATTTTCATTTCTCA
*
99920 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCTCA
*
99939 TTGCGA--TT-A--TCTCG
1 TTGCGATTTTCATTTCTCA
*
99953 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCTCA
*
99972 TTGCGA--TT-A--TCTCG
1 TTGCGATTTTCATTTCTCA
*
99986 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCTCA
100005 TTGCGAT
1 TTGCGAT
100012 AGTAATTTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 30
0.64 0.11 0.25
Matches are distributed among these distances:
14 27 0.35
16 9 0.12
17 9 0.12
19 33 0.42
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCA
Found at i:99927 original size:33 final size:33
Alignment explanation
Indices: 99885--100011 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
99875 ACTAAATTCG
* * **
99885 CGTTGCGATTTTCATTTCTCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
99918 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
99951 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
99984 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
100012 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:99958 original size:14 final size:14
Alignment explanation
Indices: 99939--99993 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
99929 TCATTTCGCA
99939 TTGCGATTATCTCG
1 TTGCGATTATCTCG
*
99953 TTGCGATTTTCATTTCG
1 TTGCGA--TT-ATCTCG
99970 CATTGCGATTATCTCG
1 --TTGCGATTATCTCG
99986 TTGCGATT
1 TTGCGATT
99994 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTATCTCG
Found at i:103406 original size:20 final size:21
Alignment explanation
Indices: 103381--103432 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
103371 TTTTCCCAAT
*
103381 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
*
103401 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTAAGAAAA
103422 TCGCAATGCGA
1 TCGCAATGCGA
103433 TACTGACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:103445 original size:41 final size:42
Alignment explanation
Indices: 103400--103493 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 42
103390 GAATAAGTAA
* * * *
103400 ATCGCAATGCGAAT-TTAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
103441 ATCGCAACGCG-ATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
*
103482 TTCGCAACGCGA
1 ATCGCAACGCGA
103494 TTCTGACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.04
41 44 0.96
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAATAATACAAAATCGCAACGCGATACTGACT
Found at i:103446 original size:20 final size:20
Alignment explanation
Indices: 103421--103530 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
103411 AATTTAGAAA
*
103421 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
103441 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
103462 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
103482 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
103502 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
103522 TTCGCAACG
1 ATCGCAACG
103531 AGATTCTGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:103547 original size:40 final size:40
Alignment explanation
Indices: 103417--103548 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
103407 TGCGAATTTA
* * **
103417 GAAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
*
103457 ACAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
*** * * *
103498 GACTTTCGCAACGAGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
103538 GAAAATCGCAA
1 GAAAATCGCAA
103549 TCATCTTCAA
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 41 0.54
41 35 0.46
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
Found at i:103548 original size:20 final size:20
Alignment explanation
Indices: 103463--103539 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
103453 TAATACAAAA
* *
103463 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATTCTGACTT
*
103483 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
103503 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
103523 TCGCAACGAGATTCTGA
1 TCGCAACGAGATTCTGA
103540 AAATCGCAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:103840 original size:33 final size:33
Alignment explanation
Indices: 103803--103873 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
103793 AAAATCGCAA
*
103803 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
103836 TGCGATTTTTATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
103869 TGCGA
1 TGCGA
103874 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:105483 original size:43 final size:42
Alignment explanation
Indices: 105436--105529 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
105426 CCTCTTCAAC
* *
105436 GATGACAGTGG-CCTCTTGAACGGTGGGGGGGGGACTCTTGAGG
1 GATGACAG-GGTCCTCTTGAACGAT-GGGAGGGGACTCTTGAGG
* *
105479 GATGATAGGGTCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGTCCTCTTGAACGATGGGAGGGGACTCTTGAGG
105521 GATGACAGG
1 GATGACAGG
105530 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 26 0.58
43 19 0.42
ACGTcount: A:0.20, C:0.15, G:0.43, T:0.22
Consensus pattern (42 bp):
GATGACAGGGTCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:105946 original size:20 final size:20
Alignment explanation
Indices: 105892--105945 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
105882 AAACTTACTT
105892 TCGCAACGCAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
**
105912 TCGCAACGCGGAAATGACTA
1 TCGCAACGCAAAAATGACTA
105932 TCGCAACGACAAAA
1 TCGCAACG-CAAAA
105946 TCGCAATGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:105950 original size:14 final size:14
Alignment explanation
Indices: 105931--105986 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
105921 GGAAATGACT
105931 ATCGCAACGACAAA
1 ATCGCAACGACAAA
*
105945 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-CAAA
105964 ATCGCAACGACAAA
1 ATCGCAACGACAAA
105978 ATCGCAACG
1 ATCGCAACG
105987 CGAAACACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (14 bp):
ATCGCAACGACAAA
Found at i:105961 original size:33 final size:33
Alignment explanation
Indices: 105911--105991 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 33
105901 AAAAATGACT
**
105911 ATCGCAACGCGGAAATGACTATCGCAACGACAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGACAAA
*
105945 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
105978 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
105992 CACAAATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.79
34 9 0.21
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:106025 original size:19 final size:19
Alignment explanation
Indices: 106000--106050 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
105990 AACACAAATT
106000 GCATTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
*
106019 GCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
106038 GCATTGCGATTTT
1 GCATTGCGATTTT
106051 GTCGTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
GCATTGCGATTTTCATTTC
Found at i:106100 original size:20 final size:20
Alignment explanation
Indices: 106075--106119 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
106065 CATTTCGCAG
106075 TGCGATAGCCATTTCCGCGT
1 TGCGATAGCCATTTCCGCGT
* * *
106095 TGCGATAGTCATTTTCGTGT
1 TGCGATAGCCATTTCCGCGT
106115 TGCGA
1 TGCGA
106120 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.36
Consensus pattern (20 bp):
TGCGATAGCCATTTCCGCGT
Found at i:106683 original size:18 final size:18
Alignment explanation
Indices: 106660--106707 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
106650 CAGGTCGATC
106660 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
106678 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
106696 AGGTGATGGCTC
1 AGGTGATGGCTC
106708 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:108054 original size:20 final size:20
Alignment explanation
Indices: 108029--108070 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
108019 ATAGTTTCTA
108029 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACACG
* * *
108049 AAAATGACAATCTCAACGCG
1 AAAATGAAAATCGCAACACG
108069 AA
1 AA
108071 TTTGACTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATGAAAATCGCAACACG
Found at i:108377 original size:22 final size:22
Alignment explanation
Indices: 108350--108393 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
108340 GATGGAGATA
108350 GATGGATTTCGCCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
*
108372 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
108394 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.25
Consensus pattern (22 bp):
GATGGATTTCGCCGGAGATGGG
Found at i:108632 original size:40 final size:41
Alignment explanation
Indices: 108580--108690 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 41
108570 GATTATGTAT
*
108580 TATCTCGTTGCGAAAGTCAGTATTGCGTTGAGAAATT-AAG
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTGAGAAATTGAAG
* * * ** * *
108620 TATCGCGTTGCGAAAGTCAGTATCGAGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTGAGAAATTGAAG
*
108661 TATCGCGTTGCGATAGTCAGTATTGCGTTG
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTG
108691 CGATTTTCCA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 31 0.53
41 28 0.47
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATTGCGTTGAGAAATTGAAG
Found at i:108679 original size:41 final size:41
Alignment explanation
Indices: 108566--108697 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
108556 GAAAATCGTA
* *
108566 TTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATTGCG
* ** * * * *
108607 TTGAGAAATT-AAGTATCGCGTTGCGAAAGTCAGTATCGAG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATTGCG
*
108647 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATTGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATTGCG
108688 TTGCGATTTT
1 TTGCGATTTT
108698 CCAAATTCGC
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
40 32 0.44
41 41 0.56
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATTGCG
Found at i:108694 original size:20 final size:20
Alignment explanation
Indices: 108580--108693 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
108570 GATTATGTAT
*
108580 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
108600 TATTGCGTTGAGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
108620 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
108640 TATCGAGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
108661 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
108681 TATTGCGTTGCGA
1 TATCGCGTTGCGA
108694 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.04
20 56 0.76
21 13 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:108714 original size:21 final size:21
Alignment explanation
Indices: 108688--108755 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
108678 CAGTATTGCG
108688 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
108709 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
108730 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
108750 TTGCGA
1 TTGCGA
108756 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:108715 original size:41 final size:40
Alignment explanation
Indices: 108580--108714 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 40
108570 GATTATGTAT
* * ** *
108580 TATCTCGTTGCGAAAGTCAGTATTGCGTTGAGAAATTAAG
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTGCGATTTTAAA
* * * *
108620 TATCGCGTTGCGAAAGTCAGTATCGAGTTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTGCGATTTT-AAA
*
108661 TATCGCGTTGCGATAGTCAGTATTGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGAAAGTCAGTATTGCGTTGCGATTTT--AAA
*
108703 T-TCGCATTGCGA
1 TATCGCGTTGCGA
108715 TTTTCCAAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 31 0.40
41 45 0.58
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (40 bp):
TATCGCGTTGCGAAAGTCAGTATTGCGTTGCGATTTTAAA
Found at i:108797 original size:21 final size:22
Alignment explanation
Indices: 108745--108797 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
108735 ATTTACTTAT
108745 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
108766 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
108787 TCGCATTGCGA
1 TCGCATTGCGA
108798 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:112125 original size:74 final size:74
Alignment explanation
Indices: 112031--112168 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 74
112021 AAGTCTCCTC
* * *
112031 ATAGAACCATTTCTAGTAAAATTATTTTGTTCACTTTTCAACAATCAATCTCTAAGCCAAATAGC
1 ATAGAACCATTTCTAGTAAAAATATTTTGTTCACCTTTCAACAATCAATCTCTAAACCAAATAGC
112096 TATTACTTA
66 TATTACTTA
112105 ATAGAACCATTTC-AGGTAAAAATATTTTGTTCACCTTTCAACAATCAATCTCTAAACCAAATAG
1 ATAGAACCATTTCTA-GTAAAAATATTTTGTTCACCTTTCAACAATCAATCTCTAAACCAAATAG
112169 TTATCATAGC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 1 0.02
74 59 0.98
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (74 bp):
ATAGAACCATTTCTAGTAAAAATATTTTGTTCACCTTTCAACAATCAATCTCTAAACCAAATAGC
TATTACTTA
Found at i:115282 original size:14 final size:14
Alignment explanation
Indices: 115263--115291 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
115253 TCGATTATAT
115263 GTTCATTTATGTTC
1 GTTCATTTATGTTC
115277 GTTCATTTATGTTC
1 GTTCATTTATGTTC
115291 G
1 G
115292 AACAGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:115597 original size:14 final size:14
Alignment explanation
Indices: 115578--115608 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
115568 CATTTATTAA
115578 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
115592 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
115606 GTT
1 GTT
115609 TACGTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:115704 original size:16 final size:16
Alignment explanation
Indices: 115683--115714 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
115673 AACAAAAAAA
115683 ATTGTTCGTTTATGTT
1 ATTGTTCGTTTATGTT
115699 ATTGTTCGTTTATGTT
1 ATTGTTCGTTTATGTT
115715 CTTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.19, T:0.62
Consensus pattern (16 bp):
ATTGTTCGTTTATGTT
Found at i:117731 original size:5 final size:5
Alignment explanation
Indices: 117721--117745 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
117711 TAATACATAA
117721 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
117746 AATTGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:118544 original size:22 final size:22
Alignment explanation
Indices: 118506--118548 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
118496 AAGTCCGAAT
*
118506 TTTGAAAGATCAAAAAAGAAAGC
1 TTTGAAAGAACAAAAAA-AAAGC
118529 TTTGAAA-AACAAAAAAAAAG
1 TTTGAAAGAACAAAAAAAAAG
118549 GCGGCGGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 8 0.42
23 7 0.37
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (22 bp):
TTTGAAAGAACAAAAAAAAAGC
Found at i:119187 original size:24 final size:25
Alignment explanation
Indices: 119128--119195 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
119118 TATTCTTGTT
*
119128 TTAT-TTTAGTTTCA-TTTTTAATC
1 TTATATTTATTTTCATTTTTTAATC
*
119151 TTATTTTTATTTTCATTTTTTATAT-
1 TTATATTTATTTTCATTTTTTA-ATC
*
119176 TTATATTT-TTTTCTTTTTTT
1 TTATATTTATTTTCATTTTTT
119196 TCTTCTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.10
24 20 0.51
25 13 0.33
26 2 0.05
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (25 bp):
TTATATTTATTTTCATTTTTTAATC
Found at i:120294 original size:21 final size:19
Alignment explanation
Indices: 120261--120304 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
120251 TTTTTTCGTT
*
120261 TTTTCTTTCATCATTTATTTA
1 TTTTATTTCATCA-TT-TTTA
*
120282 TTTTATTTTATCATTTTTA
1 TTTTATTTCATCATTTTTA
120301 TTTT
1 TTTT
120305 GCTAACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTTCATCATTTTTA
Found at i:123305 original size:95 final size:94
Alignment explanation
Indices: 123184--123378 Score: 286
Period size: 95 Copynumber: 2.1 Consensus size: 94
123174 CACATTATAA
*
123184 TATTAT-TTATATGCAATAAAGCTTGAGTTGTCCCTCT-AGAGTAATTGGTTAAACGCCCCGACT
1 TATTATATTATA--CAATAAAGCTTGAGTTGTCCCTCTAAG-GCAATTGGTTAAACGCCCCGACT
* *
123247 TTATGGATAATATTCAACTAGCCTGATAAAGG
63 TTATGGATAAGATTCAACTAACCTGATAAAGG
*
123279 TGATTATATTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTT
1 T-ATTATATTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTT
* *
123344 ATGGATAAGATTCAGCTAACTTGATAAAGG
65 ATGGATAAGATTCAACTAACCTGATAAAGG
123374 TATTA
1 TATTA
123379 CATATTGAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
94 4 0.04
95 75 0.82
96 7 0.08
97 5 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (94 bp):
TATTATATTATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGACTTTA
TGGATAAGATTCAACTAACCTGATAAAGG
Found at i:124701 original size:65 final size:65
Alignment explanation
Indices: 124595--125049 Score: 371
Period size: 65 Copynumber: 6.9 Consensus size: 65
124585 TATCGATCAG
* *
124595 CTTTGAGATA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 CTTTGA-ATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
124659 T
65 T
* ** *
124660 CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATT
1 CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA--
*
124725 TTGTCT
64 ----AT
* *
124731 CTCTTGAGATA--TTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 CT-TTGA-ATATGTTTTC-CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
124791 AAT
63 AAT
* * * * *
124794 CTTTGAATCTATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAT
1 CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * * * ** *
124859 ATTTGAATATGTTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGATTCTTTTAAAACAAATT
1 CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA--
*
124924 TTGTCT
64 ----AT
* * *
124930 CTCTTGAGACA--TTTTCTCTT--AA-AAA-TT-GTCTCTCTTGAGATAGTTCCCCTTGAAACAA
1 CT-TTGA-ATATGTTTTC-CTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
124988 AAT
63 AAT
* * * *
124991 CTTTTAATTTGTTTTCCTTTAAACAAATTTCGTCTCT-TTCGAGACAGTTTCTCTTGAAA
1 CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTT-GAGACAGTTTCCCTTGAAA
125050 AAATTTGTCT
Statistics
Matches: 310, Mismatches: 48, Indels: 64
0.73 0.11 0.15
Matches are distributed among these distances:
59 1 0.00
60 6 0.02
61 10 0.03
62 9 0.03
63 10 0.03
64 9 0.03
65 165 0.53
67 24 0.08
68 2 0.01
69 36 0.12
70 4 0.01
71 15 0.05
72 14 0.05
73 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (65 bp):
CTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:124731 original size:36 final size:35
Alignment explanation
Indices: 124672--124791 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 35
124662 TTGAATATGT
* * *
124672 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTT-AAACAAATTTTGTCTCTCTTGAGATAG
* *
124707 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGATAT
1 TTTCTCTT-AAACAAATTTTGTCTCTCTTGAGATAG
124743 TTTCTCTT-AA-AAATTTTGTCTCTCTTGAGATAG
1 TTTCTCTTAAACAAATTTTGTCTCTCTTGAGATAG
*
124776 TTTCCCTTGAAACAAA
1 TTTCTCTT-AAACAAA
124792 ATCTTTGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
33 29 0.40
34 2 0.03
35 6 0.08
36 35 0.49
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTCTCTTAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:124946 original size:199 final size:197
Alignment explanation
Indices: 124606--125049 Score: 737
Period size: 199 Copynumber: 2.2 Consensus size: 197
124596 TTTGAGATAG
*
124606 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATG
* *
124671 TTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTT
66 TTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGATTCTTTTAAAACAAATTTTGTCTCTCTT
* *
124736 GAGATATTTTCTCTTAAAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTTGAA
131 GAGACATTTTCTCTTAAAAA--TTGTCTCTCTTGAGATAGTTCCCCTTGAAACAAAATCTTTGAA
124801 TCTA
194 TCTA
*
124805 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAATATTTGAATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATG
124870 TTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGATTCTTTTAAAACAAATTTTGTCTCTCTT
66 TTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGATTCTTTTAAAACAAATTTTGTCTCTCTT
* *
124935 GAGACATTTTCTCTTAAAAATTGTCTCTCTTGAGATAGTTCCCCTTGAAACAAAATCTTTTAATT
131 GAGACATTTTCTCTTAAAAATTGTCTCTCTTGAGATAGTTCCCCTTGAAACAAAATCTTTGAATC
*
125000 TG
196 TA
* * * *
125002 TTTTCCTTTAAACAAATTTCGTCTCT-TTCGAGACAGTTTCTCTTGAAA
1 TTTCCCTTGAAACAAATTTTGTCTCTCTT-GAGACAGTTTCCCTTGAAA
125050 AAATTTGTCT
Statistics
Matches: 230, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
196 2 0.01
197 83 0.36
199 145 0.63
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (197 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATG
TTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGATTCTTTTAAAACAAATTTTGTCTCTCTT
GAGACATTTTCTCTTAAAAATTGTCTCTCTTGAGATAGTTCCCCTTGAAACAAAATCTTTGAATC
TA
Found at i:124952 original size:36 final size:36
Alignment explanation
Indices: 124870--124953 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 36
124860 TTTGAATATG
*
124870 TTTTC-CTTGAAACAAATTTCATCTCCCTTGAGACA
1 TTTTCTCTTAAAACAAATTTCATCTCCCTTGAGACA
** * ** *
124905 GATTCTTTTAAAACAAATTTTGTCTCTCTTGAGACA
1 TTTTCTCTTAAAACAAATTTCATCTCCCTTGAGACA
124941 TTTTCTCTTAAAA
1 TTTTCTCTTAAAA
124954 ATTGTCTCTC
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (36 bp):
TTTTCTCTTAAAACAAATTTCATCTCCCTTGAGACA
Found at i:124985 original size:132 final size:130
Alignment explanation
Indices: 124823--125079 Score: 345
Period size: 132 Copynumber: 2.0 Consensus size: 130
124813 GAAACAAATT
* *
124823 TTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTCCCCTTGAAACAAAATATTTGAATATGTTTTCCTTGAAACAAATT
* * * *
124888 TCATCTCCCTT-GAGACAGATTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAA
66 TCATCT-CCTTCGAGACAGATTCTCTTAAAA-AAA-TTTGTCTCCCTTGAGACAGTTCCTCTTAA
124952 AAA
128 AAA
* * * * *
124955 TTGTCTCTCTTGAGATAGTTCCCCTTGAAACAAAATCTTTTAATTTGTTTTCCTTTAAACAAATT
1 TTGTCTCTCTTGAGACAGTTCCCCTTGAAACAAAATATTTGAATATGTTTTCCTTGAAACAAATT
* * * *
125020 TCGTCTCTTTCGAGACAGTTTCTCTTGAAAAAATTTGTCTCCCTTGAGACAGTTCCTCTT
66 TCATCTCCTTCGAGACAGATTCTCTTAAAAAAATTTGTCTCCCTTGAGACAGTTCCTCTT
125080 GAGACAATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
130 24 0.22
131 6 0.06
132 79 0.72
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (130 bp):
TTGTCTCTCTTGAGACAGTTCCCCTTGAAACAAAATATTTGAATATGTTTTCCTTGAAACAAATT
TCATCTCCTTCGAGACAGATTCTCTTAAAAAAATTTGTCTCCCTTGAGACAGTTCCTCTTAAAAA
Found at i:125082 original size:15 final size:15
Alignment explanation
Indices: 125062--125096 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
125052 ATTTGTCTCC
*
125062 CTTGAGACAGTTCCT
1 CTTGAGACAATTCCT
*
125077 CTTGAGACAATTTCT
1 CTTGAGACAATTCCT
125092 CTTGA
1 CTTGA
125097 AACACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (15 bp):
CTTGAGACAATTCCT
Found at i:127026 original size:6 final size:6
Alignment explanation
Indices: 126990--127041 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
126980 TTTATTCTTG
* * * *
126990 TTTTA- TTTTAG TTTCAT TTTTAA TCTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
127037 ATTTT
1 -TTTT
127042 TTTCTTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 5 0.13
6 29 0.76
7 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:127036 original size:18 final size:17
Alignment explanation
Indices: 126962--127033 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 17
126952 TATTATTTTC
* *
126962 TTTATTTTTTTTCTTTGT
1 TTTATTTTTATT-TTTAT
* *
126980 TTTATTCTT-GTTTTAT
1 TTTATTTTTATTTTTAT
* *
126996 TTTAGTTTCATTTTTAAT
1 TTTATTTTTATTTTT-AT
*
127014 CTTATTTTTATTTTTAT
1 TTTATTTTTATTTTTAT
127031 TTT
1 TTT
127034 TATATTTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
16 10 0.24
17 9 0.22
18 22 0.54
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTATTTTTATTTTTAT
Found at i:131802 original size:17 final size:17
Alignment explanation
Indices: 131780--131812 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
131770 GGGAAAGAGA
131780 GAAGGGAATTAGGGATC
1 GAAGGGAATTAGGGATC
*
131797 GAAGGGGATTAGGGAT
1 GAAGGGAATTAGGGAT
131813 TGCAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.45, T:0.18
Consensus pattern (17 bp):
GAAGGGAATTAGGGATC
Found at i:144366 original size:21 final size:21
Alignment explanation
Indices: 144342--144384 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
144332 ATGCCCTGAG
144342 ATTGCTTATGGGTCTAAGCAA
1 ATTGCTTATGGGTCTAAGCAA
*
144363 ATTGCTTCTGGGTCTAAGCAA
1 ATTGCTTATGGGTCTAAGCAA
144384 A
1 A
144385 GCTTTCCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (21 bp):
ATTGCTTATGGGTCTAAGCAA
Found at i:154032 original size:33 final size:31
Alignment explanation
Indices: 153972--154068 Score: 97
Period size: 33 Copynumber: 3.0 Consensus size: 31
153962 AGTGATAAGG
*
153972 TGATAATTAAAATTT-TTAAACAGTTATAAAA
1 TGATAATTAAAATTTATTAAATA-TTATAAAA
154003 TGATAATTAAAATTTTATTAAATTATTATAAAA
1 TGATAATTAAAA-TTTATTAAA-TATTATAAAA
* * * * *
154036 TAATCATTAAACTTTATCAAACTATTAAAAAA
1 TGATAATTAAAATTTATTAAA-TATTATAAAA
154068 T
1 T
154069 ACCTTTAGAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 12 0.21
32 21 0.38
33 22 0.39
34 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (31 bp):
TGATAATTAAAATTTATTAAATATTATAAAA
Found at i:154062 original size:32 final size:33
Alignment explanation
Indices: 153974--154069 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 33
153964 TGATAAGGTG
* *
153974 ATAATTAAAA-TTT-TTAAAC-AGTTATAAAATG
1 ATAATTAAAACTTTATCAAACTA-TTATAAAATA
* * *
154005 ATAATTAAAATTTTATTAAATTATTATAAAATA
1 ATAATTAAAACTTTATCAAACTATTATAAAATA
* *
154038 ATCATT-AAACTTTATCAAACTATTAAAAAATA
1 ATAATTAAAACTTTATCAAACTATTATAAAATA
154070 CCTTTAGACT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 10 0.18
32 25 0.45
33 19 0.35
34 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (33 bp):
ATAATTAAAACTTTATCAAACTATTATAAAATA
Done.