Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397290.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1682.0, 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: 649016
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Warning! 4074 characters in sequence are not A, C, G, or T
Found at i:2270 original size:17 final size:17
Alignment explanation
Indices: 2248--2284 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2238 CTAACCAAAG
*
2248 ATTCAAATGTAAAGATT
1 ATTCAAATGTAAAAATT
*
2265 ATTCAATTGTAAAAATT
1 ATTCAAATGTAAAAATT
2282 ATT
1 ATT
2285 TAGAAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTCAAATGTAAAAATT
Found at i:9716 original size:31 final size:32
Alignment explanation
Indices: 9669--9729 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
9659 ATTTATTCAA
*
9669 TTTTGTATCTTTTTATTTTAAATCAAATAAAC
1 TTTTGTATCTTTTTATTTTAAATAAAATAAAC
*
9701 TTTTGTAT-TTTTTATTTTAAGTAAAATAA
1 TTTTGTATCTTTTTATTTTAAATAAAATAA
9730 GTTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTTGTATCTTTTTATTTTAAATAAAATAAAC
Found at i:13500 original size:60 final size:60
Alignment explanation
Indices: 13421--13542 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
13411 AGGACAAGAA
*
13421 GATGATGAAGAAGAAGATTATAACTATCAGGAAGAAGGAGAAGATAGTGTA-CTGGAGATG
1 GATGATGAAGAAGAAGATTATAACTATCAGGAAGAAGGAGAAGACAGTG-AGCTGGAGATG
* * * ** *
13481 GATGATGATGATGATGATTATGGCTATCTGGAAGAAGGAGAAGACAGTGAGCTGGAGATG
1 GATGATGAAGAAGAAGATTATAACTATCAGGAAGAAGGAGAAGACAGTGAGCTGGAGATG
13541 GA
1 GA
13543 GAAAGAGGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (60 bp):
GATGATGAAGAAGAAGATTATAACTATCAGGAAGAAGGAGAAGACAGTGAGCTGGAGATG
Found at i:34729 original size:26 final size:26
Alignment explanation
Indices: 34677--34729 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
34667 TCAAATCAAA
* *
34677 TTAATTTAACTAACTTAATCGACTTT
1 TTAATTGAACTAACTTAATCGAATTT
* * *
34703 TTAATTGAATTAATTTAATCTAATTT
1 TTAATTGAACTAACTTAATCGAATTT
34729 T
1 T
34730 GTTGATTAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTGAACTAACTTAATCGAATTT
Found at i:35169 original size:18 final size:19
Alignment explanation
Indices: 35146--35186 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
35136 AATCAAATTG
*
35146 AATCGATTTAAGT-AACTT
1 AATCGAATTAAGTAAACTT
*
35164 AATCGAATTAATTAAACTT
1 AATCGAATTAAGTAAACTT
35183 AATC
1 AATC
35187 TTATTGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (19 bp):
AATCGAATTAAGTAAACTT
Found at i:71005 original size:40 final size:40
Alignment explanation
Indices: 70942--71021 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
70932 TTATCTATTA
* *
70942 AATATATTTTTAATGTTAAATATTTT-TTTTCATTTCTTT
1 AATATATTTTTAATATTAAATATTTTATTTTAATTTCTTT
* *
70981 AATATAATTTTTGATATTATATATTTTATTTTAATTTCTTT
1 AATAT-ATTTTTAATATTAAATATTTTATTTTAATTTCTTT
71022 TACCTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.14
40 18 0.51
41 12 0.34
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (40 bp):
AATATATTTTTAATATTAAATATTTTATTTTAATTTCTTT
Found at i:71065 original size:21 final size:20
Alignment explanation
Indices: 71039--71078 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
71029 ATTATATAAA
71039 TTTTAATTTTTTATATTTTAT
1 TTTTAATTTTTT-TATTTTAT
71060 TTTTAATTTTTTTATTTTA
1 TTTTAATTTTTTTATTTTA
71079 ATTATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTAATTTTTTTATTTTAT
Found at i:71086 original size:20 final size:21
Alignment explanation
Indices: 71037--71086 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
71027 ATATTATATA
71037 AATTTTAATTTTTTATATTTT
1 AATTTTAATTTTTTATATTTT
*
71058 ATTTTTAATTTTTT-TATTTT
1 AATTTTAATTTTTTATATTTT
*
71078 AATTATAAT
1 AATTTTAAT
71087 ATTATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
AATTTTAATTTTTTATATTTT
Found at i:80207 original size:29 final size:28
Alignment explanation
Indices: 80153--80207 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
80143 ATACAATTAA
**
80153 TTTTTAATTTTTTATTATATTTAAATAG
1 TTTTTAATTTTTTATTATATAAAAATAG
* *
80181 TTTTTTATTTTTTATTTTAATAAAAAT
1 TTTTTAATTTTTTATTAT-ATAAAAAT
80208 TTAATAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.73
29 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTTAATTTTTTATTATATAAAAATAG
Found at i:83217 original size:35 final size:35
Alignment explanation
Indices: 83178--83244 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
83168 TGTCACGGGC
*
83178 CACAGTCCAGACCCACCAGGAGGCTCAAGAGGTGA
1 CACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGA
* *
83213 CACAGTCCGGACCCGCCAGGAGGCCCAAGAGG
1 CACAGTCCAGACCCACCAGGAGGCCCAAGAGG
83245 GTGCCAGCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.31, T:0.06
Consensus pattern (35 bp):
CACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGA
Found at i:83386 original size:14 final size:14
Alignment explanation
Indices: 83331--83430 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
83321 TCCCAAATGT
*
83331 TTTGGAGGGAAATC
1 TTTGGAGGGAAAAC
* *
83345 TTTTGGGGGGGAATAC
1 -TTT-GGAGGGAAAAC
* **
83361 TTTGAATTGAAAAC
1 TTTGGAGGGAAAAC
*
83375 TTTGGAGGGAAATC
1 TTTGGAGGGAAAAC
* *
83389 TTTTGGGGGGAATAC
1 -TTTGGAGGGAAAAC
* ***
83404 TTTGAATTAAAAAC
1 TTTGGAGGGAAAAC
83418 TTTGGAGGGAAAA
1 TTTGGAGGGAAAA
83431 GTGGGTGGGG
Statistics
Matches: 58, Mismatches: 25, Indels: 5
0.66 0.28 0.06
Matches are distributed among these distances:
14 33 0.57
15 17 0.29
16 8 0.14
ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31
Consensus pattern (14 bp):
TTTGGAGGGAAAAC
Found at i:83406 original size:15 final size:15
Alignment explanation
Indices: 83325--83400 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
83315 AGAACCTCCC
*
83325 AAATGTTTTGGAGGG
1 AAATCTTTTGGAGGG
*
83340 AAATCTTTTGGGGGG
1 AAATCTTTTGGAGGG
* * **
83355 GAATAC-TTTGAATTG
1 AAAT-CTTTTGGAGGG
*
83370 AAAAC-TTTGGAGGG
1 AAATCTTTTGGAGGG
*
83384 AAATCTTTTGGGGGG
1 AAATCTTTTGGAGGG
83399 AA
1 AA
83401 TACTTTGAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
14 11 0.24
15 33 0.73
16 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (15 bp):
AAATCTTTTGGAGGG
Found at i:83411 original size:43 final size:44
Alignment explanation
Indices: 83331--83429 Score: 182
Period size: 43 Copynumber: 2.3 Consensus size: 44
83321 TCCCAAATGT
*
83331 TTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTGAAAAC
1 TTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
83375 TTTGGAGGGAAATCTTTT-GGGGGGAATACTTTGAATTAAAAAC
1 TTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
83418 TTTGGAGGGAAA
1 TTTGGAGGGAAA
83430 AGTGGGTGGG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 36 0.67
44 18 0.33
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (44 bp):
TTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
Found at i:85672 original size:27 final size:29
Alignment explanation
Indices: 85619--85675 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
85609 AATTCGAAGA
* *
85619 ATAAACTATTAATAATATATTTTAAATAT
1 ATAAACTATTAATAATAAATTTAAAATAT
*
85648 ATAAA-TATTATTAA-AAATTTAAAATAT
1 ATAAACTATTAATAATAAATTTAAAATAT
85675 A
1 A
85676 CCTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 8 0.32
29 5 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAAACTATTAATAATAAATTTAAAATAT
Found at i:95437 original size:17 final size:17
Alignment explanation
Indices: 95392--95438 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
95382 CCCAAACTTG
*
95392 ACATCGATC-CGACCTG
1 ACATCGATCTCGACCTA
*
95408 ACATCG-GCATCGACCTA
1 ACATCGATC-TCGACCTA
95425 ACATCGATCTCGAC
1 ACATCGATCTCGAC
95439 TTGACGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 6 0.24
17 17 0.68
18 1 0.04
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (17 bp):
ACATCGATCTCGACCTA
Found at i:97939 original size:6 final size:6
Alignment explanation
Indices: 97928--97954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
97918 ATTTTCCGAG
97928 CTTTCT CTTTCT CTTTCT CTTTCT CTT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTT
97955 CTCCAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
CTTTCT
Found at i:117426 original size:20 final size:20
Alignment explanation
Indices: 117403--117460 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
117393 AAAGTTATAT
117403 TCATATTTCAAAATCAAATA
1 TCATATTTCAAAATCAAATA
*
117423 TCATATTTCACAA--AAAT-
1 TCATATTTCAAAATCAAATA
* *
117440 TCACATTTCAAAATCCAATA
1 TCATATTTCAAAATCAAATA
117460 T
1 T
117461 ACAAAAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 11 0.35
18 4 0.13
19 3 0.10
20 13 0.42
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (20 bp):
TCATATTTCAAAATCAAATA
Found at i:125167 original size:19 final size:19
Alignment explanation
Indices: 125143--125180 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
125133 AAGGCCAGCG
125143 TTGTTCCCTCCCAGAATCC
1 TTGTTCCCTCCCAGAATCC
125162 TTGTTCCCTCCCAGAATCC
1 TTGTTCCCTCCCAGAATCC
125181 AAACTCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.42, G:0.11, T:0.32
Consensus pattern (19 bp):
TTGTTCCCTCCCAGAATCC
Found at i:125696 original size:2 final size:2
Alignment explanation
Indices: 125691--125743 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
125681 ATTACATTAA
125691 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
125733 AT AT AT AT AT A
1 AT AT AT AT AT A
125744 GCCAGCCTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:132878 original size:3 final size:3
Alignment explanation
Indices: 132870--132925 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
132860 AGTTTCTCCA
* *
132870 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCCC TCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT
*
132915 TCT GCT TCT TC
1 TCT TCT TCT TC
132926 AACTGCTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.94
4 1 0.02
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:133322 original size:10 final size:10
Alignment explanation
Indices: 133307--133333 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
133297 TGGAAAAGTA
133307 AGACAGAGAG
1 AGACAGAGAG
133317 AGACAGAGAG
1 AGACAGAGAG
133327 AGACAGA
1 AGACAGA
133334 AGAAGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.11, G:0.37, T:0.00
Consensus pattern (10 bp):
AGACAGAGAG
Found at i:138777 original size:139 final size:138
Alignment explanation
Indices: 138527--138839 Score: 464
Period size: 139 Copynumber: 2.2 Consensus size: 138
138517 TATTGACGAA
* *
138527 CACTTTTGTAATTAAAAAATAAATTACAATAAATAAATAAAATTTATTATTTAATTATTTGCAAA
1 CACTTTTGTAATTAAAAAATAAATTA-AATAAATAAATAAAAATTATTATTTAATTATGTGCAAA
* * *
138592 TACACATATCATGTGTATAATGGCAAAGTGCCATTATAATTAAATATTATTAATTTAATTAATTC
65 GACACATATCACGTGTACAATGGCAAAGTGCCATTATAATTAAATATTATTAATTTAATTAATTC
138657 CAAAAACAT
130 CAAAAACAT
* *
138666 CACTTTTATAATTAAAAAATAAATTTAAATAAATAAATAAAAATTATTATTTAATTATGTGCACA
1 CACTTTTGTAATTAAAAAATAAA-TTAAATAAATAAATAAAAATTATTATTTAATTATGTGCAAA
* * * * *
138731 GGCACATATCACGTGTCCAATTGCAAAGTGTCATTATAATTAAATATTATTAATTTAATTAATTT
65 GACACATATCACGTGTACAATGGCAAAGTGCCATTATAATTAAATATTATTAATTTAATTAATTC
*
138796 CAAAAATAT
130 CAAAAACAT
* *
138805 CACTTCTGTAGTTAAAAAATAAAATTAAATAAATA
1 CACTTTTGTAATTAAAAAAT-AAATTAAATAAATA
138840 TAATTTATTA
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
139 150 0.96
140 6 0.04
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (138 bp):
CACTTTTGTAATTAAAAAATAAATTAAATAAATAAATAAAAATTATTATTTAATTATGTGCAAAG
ACACATATCACGTGTACAATGGCAAAGTGCCATTATAATTAAATATTATTAATTTAATTAATTCC
AAAAACAT
Found at i:143481 original size:18 final size:18
Alignment explanation
Indices: 143458--143498 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
143448 ACCAGGAAAC
143458 AAGACACAATTTTGAGAA
1 AAGACACAATTTTGAGAA
143476 AAGACACAATTTTGAGAA
1 AAGACACAATTTTGAGAA
143494 AAGAC
1 AAGAC
143499 CCAAAGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.20
Consensus pattern (18 bp):
AAGACACAATTTTGAGAA
Found at i:153956 original size:29 final size:31
Alignment explanation
Indices: 153918--153986 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 31
153908 TTGAGTGGGG
*
153918 GAGGCGGAATTGGGACTCGTGGGA-GGGGGCC
1 GAGG-GGAATTCGGACTCGTGGGAGGGGGGCC
153949 G-GGGGAA-TCGGACTCGTGGGAGGGGGGCC
1 GAGGGGAATTCGGACTCGTGGGAGGGGGGCC
153978 GAGGGGAAT
1 GAGGGGAAT
153987 CAGGTCGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 13 0.38
29 12 0.35
30 8 0.24
31 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.57, T:0.12
Consensus pattern (31 bp):
GAGGGGAATTCGGACTCGTGGGAGGGGGGCC
Found at i:156074 original size:17 final size:16
Alignment explanation
Indices: 156036--156074 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
156026 AAAGAGATAA
156036 TATTTTAATTAAATTT
1 TATTTTAATTAAATTT
*
156052 TAATTTTAATTTAATTT
1 T-ATTTTAATTAAATTT
156069 GTATTT
1 -TATTT
156075 AAATACATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTTAATTAAATTT
Found at i:162960 original size:30 final size:30
Alignment explanation
Indices: 162924--162992 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
162914 CGATGCAAAT
*
162924 ATGATGCCTGCGGGATACAGTGCTCCCAAC
1 ATGATGCCTGAGGGATACAGTGCTCCCAAC
*
162954 ATGATGCCTGAGGGATTCAGTGCTCCCAAC
1 ATGATGCCTGAGGGATACAGTGCTCCCAAC
162984 ATGATGCCT
1 ATGATGCCT
162993 CCTCCTCCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (30 bp):
ATGATGCCTGAGGGATACAGTGCTCCCAAC
Found at i:169721 original size:23 final size:23
Alignment explanation
Indices: 169691--169751 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
169681 AACAGAGGTT
169691 TGAAAACGACAAAGGTAGAAAAG
1 TGAAAACGACAAAGGTAGAAAAG
*
169714 -GAAAAACGACAAAGCTAGAAAAG
1 TG-AAAACGACAAAGGTAGAAAAG
*
169737 TGTAAACGACAAAGG
1 TGAAAACGACAAAGG
169752 ATCAGCATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.25, T:0.08
Consensus pattern (23 bp):
TGAAAACGACAAAGGTAGAAAAG
Found at i:178285 original size:33 final size:33
Alignment explanation
Indices: 178135--178304 Score: 214
Period size: 33 Copynumber: 5.2 Consensus size: 33
178125 TTGCTCTTCT
* * **
178135 TCTTCTTCATGTTTACTCACTTCTTCCTGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
* *
178168 ACTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCG
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
* * * *
178201 TCTTCCTCATGTTTGCTAGCTTCTTCCAGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
*
178234 TCTTCTTCGTGTTTGCTTGCTTCTTCCAGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
** *
178267 TCTTCTTCGTGTTTGCTTGCGCCTTCTTGCTCC
1 TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
178300 TCTTC
1 TCTTC
178305 CTCAAGCCTC
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 118 1.00
ACGTcount: A:0.05, C:0.34, G:0.14, T:0.48
Consensus pattern (33 bp):
TCTTCTTCGTGTTTGCTTGCTTCTTCCTGCTCC
Found at i:178320 original size:99 final size:99
Alignment explanation
Indices: 178135--178321 Score: 241
Period size: 99 Copynumber: 1.9 Consensus size: 99
178125 TTGCTCTTCT
* **
178135 TCTTCTTCATGTTTACTCACTTCTTCCTGCTCCACTTCTTCGTGTTTGCTTGCTTCTTCCTGCTC
1 TCTTCTTCATGTTTACTCACTTCTTCCAGCTCCACTTCTTCGTGTTTGCTTGCGCCTTCCTGCTC
* * **
178200 GTCTTCCTCATGTTTGCTAGCTTCTTCCAGCTCC
66 CTCTTCCTCAAGCCTGCTAGCTTCTTCCAGCTCC
* * ** * *
178234 TCTTCTTCGTGTTTGCTTGCTTCTTCCAGCTCCTCTTCTTCGTGTTTGCTTGCGCCTTCTTGCTC
1 TCTTCTTCATGTTTACTCACTTCTTCCAGCTCCACTTCTTCGTGTTTGCTTGCGCCTTCCTGCTC
178299 CTCTTCCTCAAGCCT-CTTAGCTT
66 CTCTTCCTCAAGCCTGC-TAGCTT
178322 TTTCTTCCAG
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
98 1 0.01
99 73 0.99
ACGTcount: A:0.06, C:0.34, G:0.13, T:0.47
Consensus pattern (99 bp):
TCTTCTTCATGTTTACTCACTTCTTCCAGCTCCACTTCTTCGTGTTTGCTTGCGCCTTCCTGCTC
CTCTTCCTCAAGCCTGCTAGCTTCTTCCAGCTCC
Found at i:183299 original size:17 final size:17
Alignment explanation
Indices: 183257--183299 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
183247 AGCATCTTTC
183257 TCTCTTGTTTCTCCATT
1 TCTCTTGTTTCTCCATT
183274 T-TCTGTGTTTCTCC-TT
1 TCTCT-TGTTTCTCCATT
183290 TGCTCTTGTT
1 T-CTCTTGTT
183300 CGATTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.26
17 14 0.61
18 3 0.13
ACGTcount: A:0.02, C:0.26, G:0.12, T:0.60
Consensus pattern (17 bp):
TCTCTTGTTTCTCCATT
Found at i:184329 original size:2 final size:2
Alignment explanation
Indices: 184322--184353 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
184312 CTCAAACATT
*
184322 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
184354 ATCTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:185831 original size:12 final size:12
Alignment explanation
Indices: 185814--185844 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
185804 AACAGAATCA
*
185814 GATGATAGCAGT
1 GATGATAGCAAT
185826 GATGATAGCAAT
1 GATGATAGCAAT
185838 GATGATA
1 GATGATA
185845 ATGAGGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (12 bp):
GATGATAGCAAT
Found at i:195762 original size:3 final size:3
Alignment explanation
Indices: 195754--195783 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
195744 TCATGGTTGC
195754 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
195784 GCTTTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:203143 original size:54 final size:54
Alignment explanation
Indices: 203061--203168 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
203051 ACCAAGTGAT
*
203061 TAACCAGTCAAGATAATGAGCAATGTTCTAAAAATACTGACAATGAGAGGAATA
1 TAACCAGTCAAGATAATGAACAATGTTCTAAAAATACTGACAATGAGAGGAATA
203115 TAACCAGTCAAGATAATGAACAATGTTCTAAAAATACTGACAATGAGAGGAATA
1 TAACCAGTCAAGATAATGAACAATGTTCTAAAAATACTGACAATGAGAGGAATA
203169 AATAATGTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (54 bp):
TAACCAGTCAAGATAATGAACAATGTTCTAAAAATACTGACAATGAGAGGAATA
Found at i:208160 original size:29 final size:28
Alignment explanation
Indices: 208115--208233 Score: 130
Period size: 29 Copynumber: 4.1 Consensus size: 28
208105 GAGTTAATAA
* *
208115 AGAAAAGCTGTATATGAACGGGTACAAG
1 AGAAAAGCTGTACATGAACAGGTACAAG
*
208143 AGAAAAGGTTGTACATGAACAGGTACAAG
1 AGAAAA-GCTGTACATGAACAGGTACAAG
* *
208172 AGAGGAAGCTGTACATGAACAGGTATAAG
1 AGA-AAAGCTGTACATGAACAGGTACAAG
* * * *
208201 AGAAAAAGATGTACGTGAACAAGTATAAG
1 AG-AAAAGCTGTACATGAACAGGTACAAG
208230 AGAA
1 AGAA
208234 TAAAGAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.10
29 67 0.86
30 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.28, T:0.17
Consensus pattern (28 bp):
AGAAAAGCTGTACATGAACAGGTACAAG
Found at i:208214 original size:58 final size:58
Alignment explanation
Indices: 208119--208232 Score: 156
Period size: 58 Copynumber: 2.0 Consensus size: 58
208109 TAATAAAGAA
* * * * *
208119 AAGCTGTATATGAACGGGTACAAGAGAAAAGGTTGTACATGAACAGGTACAAGAGAGG
1 AAGCTGTACATGAACAGGTACAAGAGAAAAAGATGTACATGAACAAGTACAAGAGAGG
* * *
208177 AAGCTGTACATGAACAGGTATAAGAGAAAAAGATGTACGTGAACAAGTATAAGAGA
1 AAGCTGTACATGAACAGGTACAAGAGAAAAAGATGTACATGAACAAGTACAAGAGA
208233 ATAAAGAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.18
Consensus pattern (58 bp):
AAGCTGTACATGAACAGGTACAAGAGAAAAAGATGTACATGAACAAGTACAAGAGAGG
Found at i:215146 original size:40 final size:40
Alignment explanation
Indices: 215102--215181 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
215092 CACCAGACAA
*
215102 AGAAAAAAATATTAATTAAAAAAAGATGCAGGTTGCATAT
1 AGAAAAAAAGATTAATTAAAAAAAGATGCAGGTTGCATAT
*
215142 AGAAAAAAAGATTAATTAAAAACAGATGCAGGTTGCATAT
1 AGAAAAAAAGATTAATTAAAAAAAGATGCAGGTTGCATAT
215182 CCAGCTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (40 bp):
AGAAAAAAAGATTAATTAAAAAAAGATGCAGGTTGCATAT
Found at i:221951 original size:18 final size:18
Alignment explanation
Indices: 221921--221955 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
221911 AAAAAATAAT
221921 AAATATTATATTAATTAA
1 AAATATTATATTAATTAA
221939 AAATAATTA-ATTAATTA
1 AAAT-ATTATATTAATTA
221956 TTGATCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTATATTAATTAA
Found at i:222776 original size:29 final size:31
Alignment explanation
Indices: 222736--222811 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
222726 ATAATTGATT
* *
222736 ATAAAAATTTATTTAATTT-AAAT-AAAAAT
1 ATAAAATTTTATTTAATTTAAAATAAAAAAA
* *
222765 ATCAAATTTTATTTGATTTAAAATAAAAAAA
1 ATAAAATTTTATTTAATTTAAAATAAAAAAA
*
222796 ATAAAATTTTAATTAA
1 ATAAAATTTTATTTAA
222812 ATATAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 16 0.42
30 4 0.11
31 18 0.47
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
ATAAAATTTTATTTAATTTAAAATAAAAAAA
Found at i:232189 original size:3 final size:3
Alignment explanation
Indices: 232181--232212 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
232171 TAGTGCCTTG
232181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
232213 GCAATACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:239198 original size:26 final size:26
Alignment explanation
Indices: 239167--239221 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
239157 TTTTTCATAT
*
239167 TAAAAATCATCAAATATTT-ATATTATA
1 TAAAAATC-TCAAA-ATTTAATATAATA
239194 TAAAAATCTCAAAATTTAATATAATA
1 TAAAAATCTCAAAATTTAATATAATA
239220 TA
1 TA
239222 TCAAGGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 14 0.54
27 8 0.31
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAAAATCTCAAAATTTAATATAATA
Found at i:253144 original size:18 final size:19
Alignment explanation
Indices: 253108--253154 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
253098 CTTGATTTTT
253108 ATATGAAAAATGAATTAAATA
1 ATAT-AAAAATGAATTAAA-A
*
253129 AT-TAAAAATTAA-TAAAA
1 ATATAAAAATGAATTAAAA
253146 ATATAAAAA
1 ATATAAAAA
253155 AGATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 8 0.33
20 1 0.04
21 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
ATATAAAAATGAATTAAAA
Found at i:253209 original size:12 final size:12
Alignment explanation
Indices: 253192--253216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253182 ATAAAATAAA
253192 TAAATATTTTAT
1 TAAATATTTTAT
253204 TAAATATTTTAT
1 TAAATATTTTAT
253216 T
1 T
253217 TTTTGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATATTTTAT
Found at i:253209 original size:25 final size:25
Alignment explanation
Indices: 253157--253209 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
253147 TATAAAAAAG
** *
253157 ATAAAATAAATACTTATTAGATTTA
1 ATAAAATAAATAAATATTAGATTAA
**
253182 ATAAAATAAATAAATATTTTATTAA
1 ATAAAATAAATAAATATTAGATTAA
253207 ATA
1 ATA
253210 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAAAATAAATAAATATTAGATTAA
Found at i:254172 original size:27 final size:27
Alignment explanation
Indices: 254111--254169 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
254101 AAAAATTGAT
* * *
254111 AAATTAATTTTTTATTAATTAATGTAT
1 AAATTAATTATTTATTAATTAATGAAC
*
254138 AAATTAATTATTTATTAATTTATTGAAC
1 AAATTAATTATTTATTAA-TTAATGAAC
254166 AAAT
1 AAAT
254170 AATATCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (27 bp):
AAATTAATTATTTATTAATTAATGAAC
Found at i:271924 original size:26 final size:26
Alignment explanation
Indices: 271888--271938 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
271878 TCTCTACTTA
271888 ATAAATATATTTTTTGA-ATTAAAAAT
1 ATAAATATATTTTTT-ATATTAAAAAT
*
271914 ATAAATTTATTTTTTATATTAAAAA
1 ATAAATATATTTTTTATATTAAAAA
271939 GCATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
ATAAATATATTTTTTATATTAAAAAT
Found at i:281507 original size:104 final size:104
Alignment explanation
Indices: 281327--282022 Score: 933
Period size: 104 Copynumber: 6.7 Consensus size: 104
281317 NNNNNNNNNN
* *
281327 TTGACATGATCACGTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATAACATGCTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
*
281392 GTGCTATAATGACATAACATGGCATGTTGTCATGGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
* * *
281431 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAATAAATTATAACATGACATACTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
*
281496 GTGCTGTAATGACATAACATGACATGTTGTCATGGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
********** * *
281535 TTGACATNNNNNNNNNNTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGATATGTTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
* *
281600 GTGTTATAATGACATAACATGACATGTTGTCATCGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
* **********
281639 TTGACATGATCACGTTTTTGTGACNNNNNNNNNNATTATAGTAAATGATAACATGACATGCTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
* *
281704 GTGCTATAATAACATAACATGGCATGTTGTCATGGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
* ** * * *
281743 TTGACATGATCACTTTTTTGTAATTAGTTGACTTATTATAGTAAATAATAACATGACATGTTAAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
*
281808 GTGTTATAATGACATAACATGACATGTTGTCATGGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
* * * *
281847 TTGACATAATCACTTTTTTGTGACAAGTTGACGTATTATAGTAAATAATAACATGACATACTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
* *
281912 GTGCTATAATGACATAACATGATATGTTGTTATGGCATA
66 GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
* * **
281951 TTGACATGATCACTTTTTTGTAACAAGTTGACTTATTATAGTAAATGATAACATGATACACTGAT
1 TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
282016 GTGCTAT
66 GTGCTAT
282023 GATAACATTA
Statistics
Matches: 505, Mismatches: 87, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 505 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.36
Consensus pattern (104 bp):
TTGACATGATCACTTTTTTGTGACAAGTTGACTTATTATAGTAAATGATAACATGACATGCTGAT
GTGCTATAATGACATAACATGACATGTTGTCATGGCATA
Found at i:282605 original size:19 final size:21
Alignment explanation
Indices: 282558--282606 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
282548 TTTACTCTTC
282558 ATTAATTTTTATAATTATTATT
1 ATTAA-TTTTATAATTATTATT
*
282580 ATATAATTTTATTATT-TT-TT
1 AT-TAATTTTATAATTATTATT
282600 ATTAATT
1 ATTAATT
282607 AAAAANNNNN
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 4 0.16
21 2 0.08
22 11 0.44
23 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTAATTTTATAATTATTATT
Found at i:282787 original size:15 final size:15
Alignment explanation
Indices: 282767--282806 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
282757 TTTTTTCTGT
*
282767 AATCACATTGCTTGC
1 AATCACATTACTTGC
282782 AATCACATTACTTGC
1 AATCACATTACTTGC
282797 AATCACATTA
1 AATCACATTA
282807 TCTATAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:283255 original size:33 final size:33
Alignment explanation
Indices: 283218--283283 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
283208 ATCATATTAA
* *
283218 ATTAATATATCACATCATCATTAATTGTAATAT
1 ATTAACATATCACATCATCATTAATTATAATAT
*
283251 ATTAACATATCATATCATCATTAATTATAATAT
1 ATTAACATATCACATCATCATTAATTATAATAT
283284 GACAATATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (33 bp):
ATTAACATATCACATCATCATTAATTATAATAT
Found at i:284561 original size:17 final size:16
Alignment explanation
Indices: 284538--284582 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
284528 TTTGAAAAGT
**
284538 TTTTTTAAAAAATAGC
1 TTTTTTAAAAAATAAA
*
284554 TATTTTTAAAGAATAAA
1 T-TTTTTAAAAAATAAA
284571 TTTTTTAAAAAA
1 TTTTTTAAAAAA
284583 AGAGCTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (16 bp):
TTTTTTAAAAAATAAA
Found at i:286736 original size:12 final size:12
Alignment explanation
Indices: 286711--286747 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
286701 ATAATTCATT
286711 TTTTAAAAATAAA
1 TTTTAAAAA-AAA
286724 TTTTAAAAAAAA
1 TTTTAAAAAAAA
286736 TTTATAAAAAAA
1 TTT-TAAAAAAA
286748 GGGGGTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:307613 original size:2 final size:2
Alignment explanation
Indices: 307606--307631 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
307596 ATTAAAAGAG
307606 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
307632 NNNNNNNNNN
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:309723 original size:10 final size:11
Alignment explanation
Indices: 309700--309725 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
309690 ATTCAAACAT
309700 AAATTTTAAAA
1 AAATTTTAAAA
309711 AAATTTTAAAA
1 AAATTTTAAAA
309722 AAAT
1 AAAT
309726 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTTTAAAA
Found at i:309746 original size:17 final size:17
Alignment explanation
Indices: 309709--309747 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
309699 TAAATTTTAA
*
309709 AAAAATTTTAAAAAAAT
1 AAAATTTTTAAAAAAAT
*
309726 -AAATTTTTTAAAAAAT
1 AAAATTTTTAAAAAAAT
309742 AAAATT
1 AAAATT
309748 AAAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTTTTAAAAAAAT
Found at i:316286 original size:2 final size:2
Alignment explanation
Indices: 316279--316318 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
316269 AAGTTGTGTA
316279 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
316319 TTTGCTCAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320698 original size:95 final size:95
Alignment explanation
Indices: 320532--320716 Score: 244
Period size: 95 Copynumber: 1.9 Consensus size: 95
320522 CGTTACTCTC
* * * * * * *
320532 TTCCCGTAAACGCCGCTTATAAAAAGTTCAGGATTTTCCGTTCCTGTTTGATGTGGGATGGAGAT
1 TTCCCATAAACGCCGCTTATAAAAAGCTCAAGATTTTCCGTTCCTGTTCGATGTGAGATAGAGAC
320597 ACTTTTCTCGTGACACTCTCTCTCACGTAA
66 ACTTTTCTCGTGACACTCTCTCTCACGTAA
* * * *
320627 TTCCCATAAACGCTGTTTATAAAGAGCTCAAGATTTTCTGTTCCTGTTCGATGTGAGATAGAGAC
1 TTCCCATAAACGCCGCTTATAAAAAGCTCAAGATTTTCCGTTCCTGTTCGATGTGAGATAGAGAC
* * *
320692 ATTTTTCTCTTGAGACTCTCTCTCA
66 ACTTTTCTCGTGACACTCTCTCTCA
320717 TCCAATTCCG
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (95 bp):
TTCCCATAAACGCCGCTTATAAAAAGCTCAAGATTTTCCGTTCCTGTTCGATGTGAGATAGAGAC
ACTTTTCTCGTGACACTCTCTCTCACGTAA
Found at i:326715 original size:30 final size:30
Alignment explanation
Indices: 326681--326738 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
326671 AATACCGGTG
* **
326681 GAGAAGTTTGGATTGTTGGTGAAGGTGCCT
1 GAGAAGATTGGACAGTTGGTGAAGGTGCCT
326711 GAGAAGATTGGACAGTTGGTGAAGGTGC
1 GAGAAGATTGGACAGTTGGTGAAGGTGC
326739 ATTAGATGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.28
Consensus pattern (30 bp):
GAGAAGATTGGACAGTTGGTGAAGGTGCCT
Found at i:328604 original size:14 final size:15
Alignment explanation
Indices: 328569--328605 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
328559 TTGGGCCAAA
328569 GATATACAAAGAAGT
1 GATATACAAAGAAGT
*
328584 GATATACAAAGCAGT
1 GATATACAAAGAAGT
328599 -ATATACA
1 GATATACA
328606 GTGCAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (15 bp):
GATATACAAAGAAGT
Found at i:346363 original size:2 final size:2
Alignment explanation
Indices: 346358--346388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
346348 GTGGGTTGTA
346358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
346389 CACACATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:350197 original size:2 final size:2
Alignment explanation
Indices: 350185--350230 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
350175 GTCCTGATAA
* *
350185 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT -T GGT 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
350227 AT AT
1 AT AT
350231 TTTCAGAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355804 original size:40 final size:40
Alignment explanation
Indices: 355749--355826 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
355739 GTGACGTTAC
355749 AGAACTTGTCTAACGGAGGTGATTGAAGTATTCGACTTAA
1 AGAACTTGTCTAACGGAGGTGATTGAAGTATTCGACTTAA
355789 AGAACTTGTCTAACGGAGGTGATTGAAGTATTCGACTT
1 AGAACTTGTCTAACGGAGGTGATTGAAGTATTCGACTT
355827 CAGTAATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (40 bp):
AGAACTTGTCTAACGGAGGTGATTGAAGTATTCGACTTAA
Found at i:375971 original size:19 final size:19
Alignment explanation
Indices: 375935--375970 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
375925 TTAAGTAATT
375935 TTTTTAATATTTAATTTTA
1 TTTTTAATATTTAATTTTA
*
375954 TTTTTATTA-TTAATTTT
1 TTTTTAATATTTAATTTT
375971 TTGTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTAATATTTAATTTTA
Found at i:380808 original size:7 final size:7
Alignment explanation
Indices: 380796--380823 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
380786 TGCCAATGCT
380796 TTGGCAA
1 TTGGCAA
380803 TTGGCAA
1 TTGGCAA
380810 TTGGCAA
1 TTGGCAA
380817 TTGGCAA
1 TTGGCAA
380824 ATGACCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TTGGCAA
Found at i:389104 original size:2 final size:2
Alignment explanation
Indices: 389097--389124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
389087 CCCAAAAAGC
389097 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
389125 GGTAGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:410961 original size:75 final size:77
Alignment explanation
Indices: 410825--410977 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 77
410815 TCTCTCACCC
* *
410825 CTTTGAATGAAGCAAAATTACAGGGGCTCTCCTTTTCTTTTACATCAATAAAACTTCTTTTACTG
1 CTTTGAATGAAGCAAAATTACAGAGACTCTCCTTTTCTTTTACATCAATAAAACTTCTTTTACTG
410890 TTAA-TTTACCA
66 TTAATTTTACCA
*
410901 CTTTGAATGAAGCAAAATTACAGAGACTTTCC-TTTCTTTTACATCAATAAAACTTCTTTTACTG
1 CTTTGAATGAAGCAAAATTACAGAGACTCTCCTTTTCTTTTACATCAATAAAACTTCTTTTACTG
410965 TTAATTTTACCA
66 TTAATTTTACCA
410977 C
1 C
410978 CGTTTGCAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
75 36 0.49
76 37 0.51
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (77 bp):
CTTTGAATGAAGCAAAATTACAGAGACTCTCCTTTTCTTTTACATCAATAAAACTTCTTTTACTG
TTAATTTTACCA
Found at i:423035 original size:70 final size:68
Alignment explanation
Indices: 422921--423054 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 68
422911 CTTAAAACTC
* * * * *
422921 AGGAATCTATAGATATAGAATCTGTTTTAGCTCTCTAAATACAAGAACACAGCATGTCAGGATGC
1 AGGAATCAATAGATATAGAACCTGTTTTAGCTCTCTAAAGACAAGAACACAACATGCCAGGATGC
422986 CTG
66 CTG
* *
422989 AGGAATCAATAGATTATAGAGCCTGTCTTTAGCTCTCTAAAGACAAGAAGACAACATGCCAGGAT
1 AGGAATCAATAGA-TATAGAACCTGT-TTTAGCTCTCTAAAGACAAGAACACAACATGCCAGGAT
423054 G
64 G
423055 GCCGAGCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 12 0.21
69 10 0.18
70 35 0.61
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (68 bp):
AGGAATCAATAGATATAGAACCTGTTTTAGCTCTCTAAAGACAAGAACACAACATGCCAGGATGC
CTG
Found at i:428277 original size:3 final size:3
Alignment explanation
Indices: 428269--428299 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
428259 CTTAAAACAT
428269 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
428300 ATGGGGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:439005 original size:17 final size:17
Alignment explanation
Indices: 438983--439018 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
438973 TAATTAAGAA
438983 AATAATGAATAAGGAAG
1 AATAATGAATAAGGAAG
* *
439000 AATAATTAATAAGTAAG
1 AATAATGAATAAGGAAG
439017 AA
1 AA
439019 AATCTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (17 bp):
AATAATGAATAAGGAAG
Found at i:444921 original size:6 final size:6
Alignment explanation
Indices: 444903--444955 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
444893 AAGCGAAGAG
* *
444903 CATGGT CACGGT CATGGT CATGGT CACGGT CATGGT CATGGT CATGGT
1 CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT
444951 CATGG
1 CATGG
444956 GGTCCATGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (6 bp):
CATGGT
Found at i:444926 original size:18 final size:18
Alignment explanation
Indices: 444903--444955 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
444893 AAGCGAAGAG
444903 CATGGTCACGGTCATGGT
1 CATGGTCACGGTCATGGT
444921 CATGGTCACGGTCATGGT
1 CATGGTCACGGTCATGGT
*
444939 CATGGTCATGGTCATGG
1 CATGGTCACGGTCATGG
444956 GGTCCATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (18 bp):
CATGGTCACGGTCATGGT
Found at i:457513 original size:73 final size:74
Alignment explanation
Indices: 457378--457522 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 74
457368 GCAACGTTTT
*
457378 AGTTTGCATTCATAAGGATACCAATTATCCTGAAAAGTTGTTAACATTGATCATCGGTAATAGCA
1 AGTTTGCATTCATAAGGATACCAATCATCCTGAAAAGTTGTTAACATTGATCATCGGTAATAGCA
457443 AAATTGATG
66 AAATTGATG
* *
457452 AGTTTGCATTCATAAGGATATCAATCATCCTG-AAAGTTGTTAACATTGTTCATCGGTAATAGCA
1 AGTTTGCATTCATAAGGATACCAATCATCCTGAAAAGTTGTTAACATTGATCATCGGTAATAGCA
457516 AAATTGA
66 AAATTGA
457523 CGAATAACTT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
73 38 0.56
74 30 0.44
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (74 bp):
AGTTTGCATTCATAAGGATACCAATCATCCTGAAAAGTTGTTAACATTGATCATCGGTAATAGCA
AAATTGATG
Found at i:462519 original size:11 final size:11
Alignment explanation
Indices: 462503--462528 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
462493 GTAGTTGGGT
462503 ATGCCATGAAC
1 ATGCCATGAAC
462514 ATGCCATGAAC
1 ATGCCATGAAC
462525 ATGC
1 ATGC
462529 TTAATGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (11 bp):
ATGCCATGAAC
Found at i:463813 original size:2 final size:2
Alignment explanation
Indices: 463806--463836 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
463796 CATATTTTGT
463806 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
463837 TGAATGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:466606 original size:18 final size:19
Alignment explanation
Indices: 466585--466622 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
466575 CTGATTCTAG
466585 TCTTCTCTC-TTTTTCTTT
1 TCTTCTCTCTTTTTTCTTT
* *
466603 TCTTGTTTCTTTTTTCTTT
1 TCTTCTCTCTTTTTTCTTT
466622 T
1 T
466623 TGCCTGCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (19 bp):
TCTTCTCTCTTTTTTCTTT
Found at i:466993 original size:2 final size:2
Alignment explanation
Indices: 466986--467012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
466976 TTCTAGGAAA
466986 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
467013 AAAGCTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:468601 original size:2 final size:2
Alignment explanation
Indices: 468594--468628 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
468584 ATCCTATCTG
* *
468594 TA TA TA TA TA TA TA CA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
468629 GTTTACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:469725 original size:45 final size:45
Alignment explanation
Indices: 469660--469745 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
469650 TTATACACCG
* * * *
469660 TGTACAGAAACATGTTACACGTCATGGTTAGGTTGTTACACATCA
1 TGTACAAAAACATGTGACACGTCATGGTTAGATTGTGACACATCA
*
469705 TGTACAAAAACGTGTGACACGTCATGGTTAGATTGTGACAC
1 TGTACAAAAACATGTGACACGTCATGGTTAGATTGTGACAC
469746 GGTTAGGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (45 bp):
TGTACAAAAACATGTGACACGTCATGGTTAGATTGTGACACATCA
Found at i:469807 original size:61 final size:61
Alignment explanation
Indices: 469685--469807 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 61
469675 TACACGTCAT
* * * * * *
469685 GGTTAGGTTGTTACACATCATGTACAAAAACGTGTGACACGTCATGGTTAGATTGTGACAC
1 GGTTAGGTTGTTACACACCATGTAAAAAAACGTGTAACACGTCATGATTAGAGTATGACAC
* * *
469746 GGTTAGGTTGTTACACGCCATGTAAAAAAACGTGTAACACG-CTATGATTAGGGTATTACAC
1 GGTTAGGTTGTTACACACCATGTAAAAAAACGTGTAACACGTC-ATGATTAGAGTATGACAC
469807 G
1 G
469808 TCATGTACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 1 0.02
61 51 0.98
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (61 bp):
GGTTAGGTTGTTACACACCATGTAAAAAAACGTGTAACACGTCATGATTAGAGTATGACAC
Found at i:469838 original size:45 final size:45
Alignment explanation
Indices: 469756--469866 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 45
469746 GGTTAGGTTG
* * *
469756 TTACACGCCATGTAAAAAAACGTGTAACACGCTATGATTAGGGTA
1 TTACACGCCATGTACAAAAACATGTAACACGCCATGATTAGGGTA
* * * * * *
469801 TTACACGTCATGTACAAAAATATGTTACACTCCATGATTAGGTTG
1 TTACACGCCATGTACAAAAACATGTAACACGCCATGATTAGGGTA
* *
469846 TTACACACCGTGTACAAAAAC
1 TTACACGCCATGTACAAAAAC
469867 GTATGACACG
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (45 bp):
TTACACGCCATGTACAAAAACATGTAACACGCCATGATTAGGGTA
Found at i:469904 original size:90 final size:88
Alignment explanation
Indices: 469748--469915 Score: 194
Period size: 90 Copynumber: 1.9 Consensus size: 88
469738 TGTGACACGG
* * *
469748 TTAGGTTGTTACACGCCATGTAAAAAAACGTGTAACACGCTATGATTAGGGTATTACACGTCATG
1 TTAGGTTGTTACACACCATGTAAAAAAACGTATAACACGCTATGATTAAGGTATTACACGTCATG
469813 TACAAAAATATGTTACACTCCATGA
66 TAC--AAATATGTTACACTCCATGA
* * * * * * * * *
469838 TTAGGTTGTTACACACCGTGTACAAAAACGTATGACACGTTATGGTTAAGTTGTTATATG-CTAT
1 TTAGGTTGTTACACACCATGTAAAAAAACGTATAACACGCTATGATTAAGGTATTACACGTC-AT
469902 GTACAAATATGTTA
65 GTACAAATATGTTA
469916 TACGTCATGT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 10 0.15
89 1 0.02
90 54 0.83
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (88 bp):
TTAGGTTGTTACACACCATGTAAAAAAACGTATAACACGCTATGATTAAGGTATTACACGTCATG
TACAAATATGTTACACTCCATGA
Found at i:469971 original size:28 final size:27
Alignment explanation
Indices: 469911--470002 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
469901 TGTACAAATA
* *
469911 TGTTATACGTCATGTTAAAAAAAATACTGT
1 TGTTACACGTCATGTT--AAAAAATA-TTT
*
469941 TGTTACACGTCATGTTGAAAAATATTAT
1 TGTTACACGTCATGTTAAAAAATATT-T
* * *
469969 TGTTACACGTCATATTCAAAAACATTT
1 TGTTACACGTCATGTTAAAAAATATTT
469996 TGTTACA
1 TGTTACA
470003 GTTTAATGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 9 0.16
28 31 0.56
30 15 0.27
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (27 bp):
TGTTACACGTCATGTTAAAAAATATTT
Found at i:495463 original size:4 final size:4
Alignment explanation
Indices: 495454--495481 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
495444 ATACTTCTAT
495454 TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA
495482 CAGAGCAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:519019 original size:2 final size:2
Alignment explanation
Indices: 519012--519036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
519002 TTTATTTTTC
519012 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
519037 AAATCAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:556266 original size:3 final size:3
Alignment explanation
Indices: 556258--556283 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
556248 ACGGATGTCC
556258 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
556284 TTGTCGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:557710 original size:17 final size:17
Alignment explanation
Indices: 557663--557713 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
557653 TATTAAATAG
*
557663 TTATATTATGAAAAGAAA
1 TTATATTAT-AAAAAAAA
**
557681 -TA-ATTATTTAAAAAA
1 TTATATTATAAAAAAAA
557696 TTATATTATAAAAAAAA
1 TTATATTATAAAAAAAA
557713 T
1 T
557714 AAATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
TTATATTATAAAAAAAA
Found at i:557714 original size:32 final size:32
Alignment explanation
Indices: 557650--557715 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
557640 TATTAGATAC
* * *
557650 AATTATTAAATAGTTATATTATGAAAAGAAAT
1 AATTATTAAAAAATTATATTATGAAAAAAAAT
557682 AATTATTTAAAAAATTATATTAT-AAAAAAAAT
1 AATTA-TTAAAAAATTATATTATGAAAAAAAAT
557714 AA
1 AA
557716 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (32 bp):
AATTATTAAAAAATTATATTATGAAAAAAAAT
Found at i:557937 original size:23 final size:23
Alignment explanation
Indices: 557902--557947 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
557892 AAAGTCATAC
557902 TCTTCTTTCTTCTCAAAATATTCT
1 TCTTCTTTCTTCTCAAAAT-TTCT
557926 TCTT-TTTCTTCTCAAAATTTCT
1 TCTTCTTTCTTCTCAAAATTTCT
557948 AACAATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.57
Consensus pattern (23 bp):
TCTTCTTTCTTCTCAAAATTTCT
Found at i:562102 original size:6 final size:6
Alignment explanation
Indices: 562091--562117 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
562081 TCAAACAAAC
562091 GTCCAT GTCCAT GTCCAT GTCCAT GTC
1 GTCCAT GTCCAT GTCCAT GTCCAT GTC
562118 GAAACATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.19, T:0.33
Consensus pattern (6 bp):
GTCCAT
Found at i:570920 original size:2 final size:2
Alignment explanation
Indices: 570913--570937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
570903 TAAATGCATT
570913 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
570938 TAGTACAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:588803 original size:23 final size:23
Alignment explanation
Indices: 588753--588805 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
588743 TTGGACTTTG
**
588753 TCTTGATCACGAACTTCGTTGTC
1 TCTTGATCACGAACTTCGCCGTC
*
588776 GCTTGATCACGAACTTCGCCGTC
1 TCTTGATCACGAACTTCGCCGTC
588799 TCTTGAT
1 TCTTGAT
588806 TTTCACTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (23 bp):
TCTTGATCACGAACTTCGCCGTC
Found at i:589158 original size:80 final size:80
Alignment explanation
Indices: 589059--589280 Score: 293
Period size: 81 Copynumber: 2.8 Consensus size: 80
589049 AATACAATTA
* ** * * * *
589059 TTAGAGATAATTTAAATGACCAATAATTAAATTTTGATTGGTCAAAATATGAAGATTATCTCTAA
1 TTAGAGATAAATTGGATGACTAATAATTAATTTTTGATTGGTCAAAATATAAAGATTATCTCCAA
*
589124 ATTATTTTGGTTTAT
66 ATTATTTTAGTTTAT
** * *
589139 TTAGAGATAAATTGGATGACTAATACCTAATTTTTTGATTGGTTAAAATATAAATATTATCTCCA
1 TTAGAGATAAATTGGATGACTAATAATTAA-TTTTTGATTGGTCAAAATATAAAGATTATCTCCA
589204 AATTATTTTAGTTTAT
65 AATTATTTTAGTTTAT
* * *
589220 TTAGAGATAAATTGGATGACTAATAATTAATTTTTGATTGGTC-CAATTTAAATATTATCTC
1 TTAGAGATAAATTGGATGACTAATAATTAATTTTTGATTGGTCAAAATATAAAGATTATCTC
589281 ATGGGATAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 16 0.13
80 36 0.29
81 72 0.58
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (80 bp):
TTAGAGATAAATTGGATGACTAATAATTAATTTTTGATTGGTCAAAATATAAAGATTATCTCCAA
ATTATTTTAGTTTAT
Found at i:589678 original size:33 final size:32
Alignment explanation
Indices: 589593--589681 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 32
589583 ATAAGTAAGA
*
589593 AAATTATAATTTTAGAAGATGTATATTGCAAT
1 AAATTATAATTTTAGAAGAAGTATATTGCAAT
589625 AAA--ACT-A-TTT-GAAGAAGTATATTGCAAT
1 AAATTA-TAATTTTAGAAGAAGTATATTGCAAT
*
589653 AGAATTATAATTTTAAAAGAAGTATATTG
1 A-AATTATAATTTTAGAAGAAGTATATTG
589682 TAATTGGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
28 18 0.38
29 5 0.10
30 3 0.06
31 3 0.06
32 6 0.12
33 13 0.27
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.37
Consensus pattern (32 bp):
AAATTATAATTTTAGAAGAAGTATATTGCAAT
Found at i:589716 original size:23 final size:23
Alignment explanation
Indices: 589690--589738 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
589680 TGTAATTGGT
*
589690 ATTGCATTCCTTAATTGACTAGG
1 ATTGCATTCCTTAATTAACTAGG
*
589713 ATTGCATTCCTTGATTAACTAGG
1 ATTGCATTCCTTAATTAACTAGG
589736 ATT
1 ATT
589739 CTACTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
ATTGCATTCCTTAATTAACTAGG
Found at i:593919 original size:23 final size:23
Alignment explanation
Indices: 593893--593963 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
593883 CTTTGTCTTA
* **
593893 ATCACGAACTTCGTTATCGCTTG
1 ATCACAAACTTCGCCATCGCTTG
* *
593916 ATCACAAACTTCACCGTCGCTTG
1 ATCACAAACTTCGCCATCGCTTG
*
593939 ATCACAAACTTCGCCGTCGCTTG
1 ATCACAAACTTCGCCATCGCTTG
593962 AT
1 AT
593964 ATTCACTCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (23 bp):
ATCACAAACTTCGCCATCGCTTG
Found at i:594028 original size:18 final size:18
Alignment explanation
Indices: 594002--594044 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
593992 TGATCTCTGA
594002 AATGC-TCTCAATCTTCG
1 AATGCTTCTCAATCTTCG
*
594019 AATGCTTCTCAATTTTCG
1 AATGCTTCTCAATCTTCG
594037 AATGCTTC
1 AATGCTTC
594045 CGAATGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (18 bp):
AATGCTTCTCAATCTTCG
Found at i:594457 original size:81 final size:80
Alignment explanation
Indices: 594333--594538 Score: 279
Period size: 81 Copynumber: 2.6 Consensus size: 80
594323 GCTAATTTAA
* * * * * **
594333 ATGACCAATAATTAAATTTTGATTGCTCAAAATATGAAGATTATTTTTAAATTATTTTAGTTTAT
1 ATGACCAATAACTAATTTTTGATTGGTCAAAATATAAAGATTATCTCCAAATTATTTTAGTTTAT
594398 TTAGAGATAAATTGG
66 TTAGAGATAAATTGG
* * *
594413 ATGACCAATAACTAATTTTTTGATTGGTTAAAATATAAATATTATCTCCAAATTATTTTGGTTTA
1 ATGACCAATAACTAA-TTTTTGATTGGTCAAAATATAAAGATTATCTCCAAATTATTTTAGTTTA
594478 TTTAGAGATAAATTGG
65 TTTAGAGATAAATTGG
* * *
594494 ATGACCAATAACTAATTTTTGATTGGTC-CAATTTAAATATTATCT
1 ATGACCAATAACTAATTTTTGATTGGTCAAAATATAAAGATTATCT
594539 TAAGAGATTA
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 15 0.13
80 26 0.23
81 71 0.63
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (80 bp):
ATGACCAATAACTAATTTTTGATTGGTCAAAATATAAAGATTATCTCCAAATTATTTTAGTTTAT
TTAGAGATAAATTGG
Found at i:595236 original size:8 final size:8
Alignment explanation
Indices: 595223--595263 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
595213 GTGAATGTGA
595223 ATACATAT
1 ATACATAT
595231 ATACATAT
1 ATACATAT
595239 ATACATAT
1 ATACATAT
*
595247 ATATATAT
1 ATACATAT
*
595255 ATATATAT
1 ATACATAT
595263 A
1 A
595264 CACGTTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (8 bp):
ATACATAT
Found at i:595240 original size:2 final size:2
Alignment explanation
Indices: 595227--595263 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
595217 ATGTGAATAC
* *
595227 AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
595264 CACGTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:596833 original size:3 final size:3
Alignment explanation
Indices: 596825--596849 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
596815 AATAAAATCT
596825 TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG T
596850 TATAATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:597958 original size:2 final size:2
Alignment explanation
Indices: 597951--597980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
597941 CTTTACCCTT
597951 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
597981 AAAGAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:621671 original size:7 final size:7
Alignment explanation
Indices: 621659--621687 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
621649 AAGAATCAAC
621659 ACTCATG
1 ACTCATG
621666 ACTCATG
1 ACTCATG
621673 ACTCATG
1 ACTCATG
621680 ACTCATG
1 ACTCATG
621687 A
1 A
621688 GAGGCAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (7 bp):
ACTCATG
Found at i:623814 original size:22 final size:22
Alignment explanation
Indices: 623772--623814 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
623762 ACGTCACTGG
*
623772 ATATTAAGTAATGTATAACTAA
1 ATATTAAGTAATGCATAACTAA
* *
623794 ATATTAAGTATTGCATGACTA
1 ATATTAAGTAATGCATAACTA
623815 GTTGTTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (22 bp):
ATATTAAGTAATGCATAACTAA
Found at i:624917 original size:22 final size:23
Alignment explanation
Indices: 624863--624917 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
624853 TTGTTTATAA
*
624863 GCATTACGT-AACTGGATATTAG
1 GCATTACGTGAACTGGATATTAC
**
624885 GCATTGTGTGAA-TGGATATTAC
1 GCATTACGTGAACTGGATATTAC
*
624907 GTATTACGTGA
1 GCATTACGTGA
624918 CTGATTGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (23 bp):
GCATTACGTGAACTGGATATTAC
Found at i:631552 original size:69 final size:69
Alignment explanation
Indices: 631467--631619 Score: 191
Period size: 69 Copynumber: 2.2 Consensus size: 69
631457 ATTTTCGTCT
*
631467 CATATAATAGCAACTTAACAAACATTATGTGCTCATTCTTATCTCATATAGTATATGAAATCTAC
1 CATATAATAGCAACTTAACAAACATCATGTGCTCATTCTTATCTCATATAGTATATGAAATCTAC
631532 ATCA
66 ATCA
* * * * * * * * * *
631536 TATATAATAGCAACTTAGCATATATCATGTGTTTATTCTTATCTCTTGTAGTATGTGGAATCTAC
1 CATATAATAGCAACTTAACAAACATCATGTGCTCATTCTTATCTCATATAGTATATGAAATCTAC
631601 ATCA
66 ATCA
*
631605 CATACAATA-CAACTT
1 CATATAATAGCAACTT
631620 GGCAGACATG
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
68 6 0.08
69 65 0.92
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (69 bp):
CATATAATAGCAACTTAACAAACATCATGTGCTCATTCTTATCTCATATAGTATATGAAATCTAC
ATCA
Found at i:637147 original size:2 final size:2
Alignment explanation
Indices: 637140--637171 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
637130 AACGTACTAC
637140 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
637172 TGCTAAGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:639811 original size:2 final size:2
Alignment explanation
Indices: 639804--639837 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
639794 TGATAGCCAA
639804 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
639838 TAGCAGTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:648970 original size:7 final size:7
Alignment explanation
Indices: 648958--649000 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
648948 AAGTAAGTTC
648958 TCAGGGT
1 TCAGGGT
648965 TCAGGGT
1 TCAGGGT
648972 TCAGGGT
1 TCAGGGT
*
648979 TCGGGGT
1 TCAGGGT
*
648986 TCGGGGT
1 TCAGGGT
*
648993 TCGGGGT
1 TCAGGGT
649000 T
1 T
649001 TTGAGTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.07, C:0.14, G:0.49, T:0.30
Consensus pattern (7 bp):
TCAGGGT
Found at i:648977 original size:14 final size:14
Alignment explanation
Indices: 648958--649000 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
648948 AAGTAAGTTC
*
648958 TCAGGGTTCAGGGT
1 TCAGGGTTCGGGGT
648972 TCAGGGTTCGGGGT
1 TCAGGGTTCGGGGT
*
648986 TCGGGGTTCGGGGT
1 TCAGGGTTCGGGGT
649000 T
1 T
649001 TTGAGTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.14, G:0.49, T:0.30
Consensus pattern (14 bp):
TCAGGGTTCGGGGT
Done.