Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003285.1 Kokia drynarioides strain JFW-HI SEQ_115955, 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: 264210
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:5174 original size:57 final size:57
Alignment explanation
Indices: 5086--5197 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 57
5076 GCAATGATCA
* *
5086 GAAATTGAGTGAGGTAAATAAGTAAGTGAAAACTGAGGGAATGTTAACCATCATGTT
1 GAAATCGAGTGAGGTAAATAAGTAAGTGAAAACTGAGGGAATGTTAACCACCATGTT
* *
5143 GAAATCGATTGAGGTAAATGAGTAAGTGAAAACTGAGGGAATGTTAACCACCATG
1 GAAATCGAGTGAGGTAAATAAGTAAGTGAAAACTGAGGGAATGTTAACCACCATG
5198 CTGACTTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (57 bp):
GAAATCGAGTGAGGTAAATAAGTAAGTGAAAACTGAGGGAATGTTAACCACCATGTT
Found at i:15733 original size:18 final size:19
Alignment explanation
Indices: 15710--15748 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
15700 TTAGTAATGC
*
15710 TTTTATCTCAAAAGTG-TT
1 TTTTATCCCAAAAGTGCTT
15728 TTTTATCCCAAAAGTGCTT
1 TTTTATCCCAAAAGTGCTT
15747 TT
1 TT
15749 GAGAAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (19 bp):
TTTTATCCCAAAAGTGCTT
Found at i:21809 original size:4 final size:4
Alignment explanation
Indices: 21800--21849 Score: 68
Period size: 4 Copynumber: 12.8 Consensus size: 4
21790 AGAACACTAG
*
21800 AAAT AAAT AAAAT AAAT GAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
21847 AAA
1 AAA
21850 CATAAGGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
3 4 0.10
4 34 0.81
5 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:21837 original size:22 final size:23
Alignment explanation
Indices: 21800--21845 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
21790 AGAACACTAG
*
21800 AAATAAATAAAATAAATGAATAA
1 AAATAAATAAAATAAATAAATAA
21823 AAATAAAT-AAATAAATAAATAA
1 AAATAAATAAAATAAATAAATAA
21845 A
1 A
21846 TAAACATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (23 bp):
AAATAAATAAAATAAATAAATAA
Found at i:21847 original size:26 final size:27
Alignment explanation
Indices: 21800--21854 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
21790 AGAACACTAG
*
21800 AAATAAATAAAATAAATGAATAAAAAT
1 AAATAAATAAAATAAATAAATAAAAAT
*
21827 AAATAAAT-AAATAAATAAATAAACAT
1 AAATAAATAAAATAAATAAATAAAAAT
21853 AA
1 AA
21855 GGTAAAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (27 bp):
AAATAAATAAAATAAATAAATAAAAAT
Found at i:22008 original size:25 final size:25
Alignment explanation
Indices: 21969--22017 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21959 TAAACAAAAA
*
21969 TTAAAGTATAAATTAAAA-AAAATG
1 TTAAAGGATAAATTAAAATAAAATG
21993 TTAAAGGATTAAATTAAAATAAAAT
1 TTAAAGGA-TAAATTAAAATAAAAT
22018 AAAAAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAAAGGATAAATTAAAATAAAATG
Found at i:26312 original size:17 final size:17
Alignment explanation
Indices: 26290--26346 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
26280 ATAATAATAG
26290 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
* *
26307 TTTAATACTTATTTTAA
1 TTTAATATTTAATTTAA
* *
26324 --TAGTATTTTA-TTAA
1 TTTAATATTTAATTTAA
26338 TTTAATATT
1 TTTAATATT
26347 AAAGTGATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
14 4 0.13
15 6 0.19
16 6 0.19
17 15 0.48
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAATATTTAATTTAA
Found at i:26325 original size:37 final size:40
Alignment explanation
Indices: 26284--26380 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 40
26274 CTAAAAATAA
26284 TAATAGTTTAATATTTAATTTAAT-TT-AA-T-ACTTATTT
1 TAATAGTTTAATATTTAATTTAATATTAAAGTGA-TTATTT
*
26321 TAATAGTATT-TTA-TTAATTTAATATTAAAGTGATTATTT
1 TAATAGT-TTAATATTTAATTTAATATTAAAGTGATTATTT
*
26360 T-ATTG-TTAA-ATTTAATTTAAT
1 TAATAGTTTAATATTTAATTTAAT
26381 GTTTATATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
36 13 0.26
37 21 0.42
38 7 0.14
39 8 0.16
40 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (40 bp):
TAATAGTTTAATATTTAATTTAATATTAAAGTGATTATTT
Found at i:26346 original size:11 final size:11
Alignment explanation
Indices: 26296--26348 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
26286 ATAGTTTAAT
26296 ATTTAAT-TTA
1 ATTTAATATTA
26306 ATTTAATACTTA
1 ATTTAATA-TTA
* *
26318 TTTTAATAGT-
1 ATTTAATATTA
26328 ATTT--TATTA
1 ATTTAATATTA
26337 ATTTAATATTA
1 ATTTAATATTA
26348 A
1 A
26349 AGTGATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.09
9 4 0.12
10 10 0.29
11 7 0.21
12 10 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTAATATTA
Found at i:28938 original size:21 final size:20
Alignment explanation
Indices: 28907--28948 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
28897 AGTATAAAAG
28907 TAAAAAAAAAA-TTATTCTAT
1 TAAAAAAAAAATTTATT-TAT
28927 TAAAAAATAAAATTTATTTAT
1 TAAAAAA-AAAATTTATTTAT
28948 T
1 T
28949 TTCACTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAAAAAATTTATTTAT
Found at i:35130 original size:12 final size:12
Alignment explanation
Indices: 35115--35140 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35105 GGGTCCCTGA
35115 AAAATCCCCTCT
1 AAAATCCCCTCT
35127 AAAATCCCCTCT
1 AAAATCCCCTCT
35139 AA
1 AA
35141 TGTTCTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATCCCCTCT
Found at i:41639 original size:6 final size:7
Alignment explanation
Indices: 41623--41647 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41613 TTAAAAGTAT
41623 AAAAGGA
1 AAAAGGA
41630 AAAAGGA
1 AAAAGGA
41637 AAAAGGA
1 AAAAGGA
41644 AAAA
1 AAAA
41648 AAAGCATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:50795 original size:52 final size:52
Alignment explanation
Indices: 50738--50845 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
50728 GAAAGTAAAA
50738 AAGCAAAAACCCAGTAAAAATGAGCCTATATATATTCCAATAGGAACAGTAT
1 AAGCAAAAACCCAGTAAAAATGAGCCTATATATATTCCAATAGGAACAGTAT
50790 AAGCAAAAACCCAGTAAAAATGAGCCTATATATATTCCAATAGGAACAGTAT
1 AAGCAAAAACCCAGTAAAAATGAGCCTATATATATTCCAATAGGAACAGTAT
50842 AAGC
1 AAGC
50846 TTAGTCAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (52 bp):
AAGCAAAAACCCAGTAAAAATGAGCCTATATATATTCCAATAGGAACAGTAT
Found at i:62733 original size:33 final size:31
Alignment explanation
Indices: 62676--62739 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
62666 TGTAATTCTT
* *
62676 ATATATCATTTTGAATTTTTAAAAATTATAA
1 ATATATCATTTTAAATTTTTAAAAATAATAA
62707 ATATAT-ATTTTAAAATTTTATAAAAAATAATAA
1 ATATATCATTTT-AAATTTT-T-AAAAATAATAA
62740 TTTTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 5 0.18
31 12 0.43
32 1 0.04
33 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
ATATATCATTTTAAATTTTTAAAAATAATAA
Found at i:65072 original size:20 final size:20
Alignment explanation
Indices: 65029--65072 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
65019 TTAAAAATGT
* * * *
65029 TTTTTTTTATATTTTTATAC
1 TTTTTTTAACATTTTAATAA
65049 TTTTTTTAACATTTTAATAA
1 TTTTTTTAACATTTTAATAA
65069 TTTT
1 TTTT
65073 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTTAACATTTTAATAA
Found at i:78103 original size:23 final size:23
Alignment explanation
Indices: 78077--78124 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
78067 AACGAAGAAG
78077 GAGA-AATTCAAA-GAAGAAAAA
1 GAGAGAATTCAAATGAAGAAAAA
*
78098 GAGAGAATTCAAATGAAGAAGAA
1 GAGAGAATTCAAATGAAGAAAAA
78121 GAGA
1 GAGA
78125 AACTGTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 12 0.50
ACGTcount: A:0.60, C:0.04, G:0.25, T:0.10
Consensus pattern (23 bp):
GAGAGAATTCAAATGAAGAAAAA
Found at i:80407 original size:28 final size:28
Alignment explanation
Indices: 80334--80408 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
80324 GTTGAGCTTG
* *
80334 AATTTTAAATTTTGAAA-AGAGTGACTA
1 AATTTTAAATTTTAAAATAGAATGACTA
** * *
80361 AATTTTTAAAAATAAAAATATAATGACTA
1 AA-TTTTAAATTTTAAAATAGAATGACTA
*
80390 AATTTTAAATTTTTAAATA
1 AATTTTAAATTTTAAAATA
80409 ATACATGTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
27 2 0.06
28 24 0.67
29 10 0.28
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.40
Consensus pattern (28 bp):
AATTTTAAATTTTAAAATAGAATGACTA
Found at i:80851 original size:30 final size:30
Alignment explanation
Indices: 80808--80869 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
80798 TTTTTTATAA
80808 TTTTATTGCTTTTAAAATTTTTAAAAA-TAT
1 TTTTATTGCTTTTAAAA-TTTTAAAAATTAT
80838 TTTTAATTG-TTTTAAAATTTTAAAAATTAT
1 TTTT-ATTGCTTTTAAAATTTTAAAAATTAT
80868 TT
1 TT
80870 AAATGATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 9 0.30
30 17 0.57
31 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTATTGCTTTTAAAATTTTAAAAATTAT
Found at i:82633 original size:15 final size:16
Alignment explanation
Indices: 82598--82638 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
82588 GGCATGGGTG
82598 AAAA-AATTTTATATA
1 AAAATAATTTTATATA
82613 ACAAATAATTTTATA-A
1 A-AAATAATTTTATATA
*
82629 AAAATTATTT
1 AAAATAATTT
82639 AAAAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 5 0.22
17 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATAATTTTATATA
Found at i:84141 original size:23 final size:23
Alignment explanation
Indices: 84097--84141 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
84087 TTAATGTTCA
**
84097 CGAACATGTTCATTTAACTTAAT
1 CGAACATGTTCATCCAACTTAAT
84120 CGAACATGTTCA-CCAACATTAA
1 CGAACATGTTCATCCAAC-TTAA
84142 ACAAAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATCCAACTTAAT
Found at i:84702 original size:31 final size:31
Alignment explanation
Indices: 84666--84732 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
84656 TTTTTTAGTT
84666 AAATTTG-GCACTCAAC-TTTTAAAAATGAGTC
1 AAATTTGAGCA-TCAACATTTTAAAAA-GAGTC
* *
84697 GAATTTGATCATCAACATTTTAAAAAGAGTC
1 AAATTTGAGCATCAACATTTTAAAAAGAGTC
84728 AAATT
1 AAATT
84733 GTTGTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (31 bp):
AAATTTGAGCATCAACATTTTAAAAAGAGTC
Found at i:87121 original size:14 final size:14
Alignment explanation
Indices: 87102--87130 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
87092 AAATTAGTGT
87102 TAATAGTGATTTTG
1 TAATAGTGATTTTG
87116 TAATAGTGATTTTG
1 TAATAGTGATTTTG
87130 T
1 T
87131 TTAATTTGCA
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:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TAATAGTGATTTTG
Found at i:87519 original size:13 final size:13
Alignment explanation
Indices: 87501--87525 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87491 AAATAATAAT
87501 TTTATAAATTTTG
1 TTTATAAATTTTG
87514 TTTATAAATTTT
1 TTTATAAATTTT
87526 ATGATTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTATAAATTTTG
Found at i:87553 original size:21 final size:22
Alignment explanation
Indices: 87494--87553 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
87484 AGTTGAAAAA
87494 TAATAATTTTATA-AATTTTGTT
1 TAATAATTTT-TAGAATTTTGTT
*
87516 T-ATAAATTTTATG-ATTTT-TT
1 TAATAATTTTTA-GAATTTTGTT
87536 TAATAATTTTTAGAATTT
1 TAATAATTTTTAGAATTT
87554 AAAAAGACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 6 0.19
21 25 0.78
22 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TAATAATTTTTAGAATTTTGTT
Found at i:88349 original size:36 final size:37
Alignment explanation
Indices: 88309--88379 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
88299 AACAAGTGTT
* *
88309 ATATAATATTCAAATATTAACAAAAA-AATAATAAGA
1 ATATAATAGTCAAATAGTAACAAAAACAATAATAAGA
* *
88345 ATATAATAGTGAAATAGTAACAAAAACAGTAATAA
1 ATATAATAGTCAAATAGTAACAAAAACAATAATAA
88380 AAAGTGGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.25
Consensus pattern (37 bp):
ATATAATAGTCAAATAGTAACAAAAACAATAATAAGA
Found at i:89129 original size:21 final size:21
Alignment explanation
Indices: 89105--89150 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
89095 TTGAACCCTG
89105 AATCCTGAATCC-CGAACCCAA
1 AATCCTGAA-CCTCGAACCCAA
* *
89126 AATCTTGAACCTTGAACCCAA
1 AATCCTGAACCTCGAACCCAA
89147 AATC
1 AATC
89151 TCAAATCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.20
Consensus pattern (21 bp):
AATCCTGAACCTCGAACCCAA
Found at i:94440 original size:24 final size:23
Alignment explanation
Indices: 94413--94461 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
94403 CTCAAATAAA
*
94413 TAAATAGAATTTAATTGAAACAAT
1 TAAACAGAATTTAATTGAAA-AAT
94437 TAAACAGAATTTAATTGAAAAAT
1 TAAACAGAATTTAATTGAAAAAT
94460 TA
1 TA
94462 TTTCTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (23 bp):
TAAACAGAATTTAATTGAAAAAT
Found at i:94460 original size:139 final size:139
Alignment explanation
Indices: 94205--94484 Score: 398
Period size: 139 Copynumber: 2.0 Consensus size: 139
94195 AGAGCCTATT
* * * *
94205 TATAGGCTAAATTCCAAAGTTAAATAATAATAAAATAATCTAAATTAATAAAAGTTTGATTCAAA
1 TATAAGCTAAATTCCAAAGTTAAATAATAATAAAATAATCTAAACTAATAAAAATTTGACTCAAA
* * * *
94270 CAAATAAACAAAATTTAATTGAAATAATTAAACAGAGTTTAACTAAAAAATTATTTTTCAAATTT
66 CAAATAAACAAAATTTAATTGAAACAATTAAACAGAATTTAACTAAAAAATTATTTCTCAAATCT
*
94335 GACTTGAAA
131 AACTTGAAA
** * *
94344 TATAAGCTAAATTCTTAAGTTAAATAATGATAAAATAATCTAGACTAATAAAAATTTGACTCAAA
1 TATAAGCTAAATTCCAAAGTTAAATAATAATAAAATAATCTAAACTAATAAAAATTTGACTCAAA
* * * * *
94409 TAAATAAATAGAATTTAATTGAAACAATTAAACAGAATTTAATTGAAAAATTATTTCTCAAATCT
66 CAAATAAACAAAATTTAATTGAAACAATTAAACAGAATTTAACTAAAAAATTATTTCTCAAATCT
94474 AACTTGAAA
131 AACTTGAAA
94483 TA
1 TA
94485 AAAATCATAA
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
139 123 1.00
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.33
Consensus pattern (139 bp):
TATAAGCTAAATTCCAAAGTTAAATAATAATAAAATAATCTAAACTAATAAAAATTTGACTCAAA
CAAATAAACAAAATTTAATTGAAACAATTAAACAGAATTTAACTAAAAAATTATTTCTCAAATCT
AACTTGAAA
Found at i:106387 original size:12 final size:12
Alignment explanation
Indices: 106356--106390 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
106346 TAAGCTTTGA
*
106356 TTTTAAAATTAG
1 TTTTAAATTTAG
*
106368 TTTTAAATTTAT
1 TTTTAAATTTAG
106380 TTTTAAATTTA
1 TTTTAAATTTA
106391 AATTTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTAAATTTAG
Found at i:106520 original size:25 final size:24
Alignment explanation
Indices: 106467--106520 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
106457 ACTTAATATT
* *
106467 AAAATTAAAAGCCCAAATAAAAAT
1 AAAATTAAAAGCCAAAATAAAAAC
* *
106491 TAAATTAAAAGTCCAAAATAAATAC
1 AAAATTAAAAG-CCAAAATAAAAAC
106516 AAAAT
1 AAAAT
106521 CCAAATTACA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAATTAAAAGCCAAAATAAAAAC
Found at i:106757 original size:21 final size:22
Alignment explanation
Indices: 106732--106776 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
106722 AGTACCACCT
*
106732 CCAG-CTTCAATTGCACTGCCA
1 CCAGACTTCAATCGCACTGCCA
106753 CCAGCTACTTCAATCGCACTGCCA
1 CCAG--ACTTCAATCGCACTGCCA
106777 TCGCCGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
24 16 0.80
ACGTcount: A:0.24, C:0.40, G:0.13, T:0.22
Consensus pattern (22 bp):
CCAGACTTCAATCGCACTGCCA
Found at i:108409 original size:30 final size:29
Alignment explanation
Indices: 108351--108635 Score: 315
Period size: 30 Copynumber: 9.7 Consensus size: 29
108341 CTAAACTATT
108351 CAAAAA-TCCTATTTTTACCCCCAAACTTC
1 CAAAAATTCC-ATTTTTACCCCCAAACTTC
**
108380 CAAAAATTCCATTTTTGACCCTAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
108410 CCAAAATTCCATTTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* *
108439 CAAAAATTTCATTTTTTACCCCGAAACTTCC
1 CAAAAATTCCA-TTTTTACCCCCAAACTT-C
* * *
108470 CAAAAA-TCCAATTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * *
108498 AAAAAATTCCATTATTAACCCCAAAACTTC
1 CAAAAATTCCATT-TTTACCCCCAAACTTC
* *
108528 CAAAAACTCCATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
108557 C-AAAATACCATTTTTACCCCCCAAACTTC
1 CAAAAATTCCATTTTTA-CCCCCAAACTTC
* * * *
108586 CAAGAATTTCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
108616 CAAAAATTCCATTTTTACCC
1 CAAAAATTCCATTTTTACCC
108636 TTGATTTCCA
Statistics
Matches: 211, Mismatches: 36, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
28 19 0.09
29 79 0.37
30 105 0.50
31 8 0.04
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCAAACTTC
Found at i:108431 original size:59 final size:58
Alignment explanation
Indices: 108351--108635 Score: 324
Period size: 59 Copynumber: 4.8 Consensus size: 58
108341 CTAAACTATT
*
108351 CAAAAATCCTATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCC
1 CAAAAATCC-ATTTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCC
* * * *
108411 CAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTTCATTTTTTACCCCGAAACTTCC
1 CAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCC
* * * * *
108470 CAAAAATCCAATTTTACCCTCGAACTTCAAAAAATTCCATTATTAACCCCAAAACTT-C
1 CAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTCCATT-TTTACCCCAAAACTTCC
* * *
108528 CAAAAACTCCATTTTTACCCCTAAACTTCC-AAAATACCATTTTTACCCCCCAAACTT-C
1 CAAAAA-TCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTA-CCCCAAAACTTCC
* * * *
108586 CAAGAATTTCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCC
1 CAA-AAATCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCC
108636 TTGATTTCCA
Statistics
Matches: 193, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
57 3 0.02
58 41 0.21
59 122 0.63
60 27 0.14
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (58 bp):
CAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCC
Found at i:110062 original size:12 final size:12
Alignment explanation
Indices: 110045--110069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110035 GCAATCAACT
110045 TAGAAGTGTTTA
1 TAGAAGTGTTTA
110057 TAGAAGTGTTTA
1 TAGAAGTGTTTA
110069 T
1 T
110070 GGATTAAGTT
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:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TAGAAGTGTTTA
Found at i:117706 original size:6 final size:6
Alignment explanation
Indices: 117695--117729 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
117685 TTGGTGGGTT
117695 GATTCG GATTCG GATTCG GATTCG GATTCG GATTC
1 GATTCG GATTCG GATTCG GATTCG GATTCG GATTC
117730 AGCCTCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (6 bp):
GATTCG
Found at i:125184 original size:11 final size:11
Alignment explanation
Indices: 125170--125212 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
125160 AGTTAAATAT
125170 TATTTTATTAA
1 TATTTTATTAA
125181 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
125194 TA-TTTATTAT
1 TATTTTATTAA
125204 TATTTTATT
1 TATTTTATT
125213 TAGATAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:125199 original size:23 final size:23
Alignment explanation
Indices: 125173--125218 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
125163 TAAATATTAT
125173 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
125196 TTTATTATTATTTTATTTAGATA
1 TTTATTAATATTTTACTTAGATA
125219 ATGGTAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:125710 original size:21 final size:21
Alignment explanation
Indices: 125670--125710 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
125660 TTCATTTATA
* *
125670 TTTTAATTAATCATATTTTAG
1 TTTTAATCAATCATAATTTAG
*
125691 TTTTAATCAATCTTAATTTA
1 TTTTAATCAATCATAATTTA
125711 CTTAATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAATCAATCATAATTTAG
Found at i:126231 original size:37 final size:36
Alignment explanation
Indices: 126165--126254 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 36
126155 AAAAAAGAGG
* *
126165 TTTAAG-ATTGAATTATAGAATAAAAAAATTT-GCT
1 TTTAAGAATTAAATTATAGAATAAAAAAATTTGGAT
* *
126199 TTTGAAGAATTAAATTGTAGAATAGTAAAAATTTGGAT
1 TTT-AAGAATTAAATTATAGAATA-AAAAAATTTGGAT
*
126237 TTTAAGGATTAAATTATA
1 TTTAAGAATTAAATTATA
126255 AAAAATATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
34 3 0.07
35 3 0.07
36 14 0.30
37 21 0.46
38 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTAAGAATTAAATTATAGAATAAAAAAATTTGGAT
Found at i:128009 original size:28 final size:28
Alignment explanation
Indices: 127963--128019 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
127953 GGGTATAAGT
127963 TTTGTAGGTGATAGCGTAGGGATGAAGA
1 TTTGTAGGTGATAGCGTAGGGATGAAGA
* *
127991 TTTGTAGGTGTTAGGGTAGGGATGAAGA
1 TTTGTAGGTGATAGCGTAGGGATGAAGA
128019 T
1 T
128020 AAAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.40, T:0.32
Consensus pattern (28 bp):
TTTGTAGGTGATAGCGTAGGGATGAAGA
Found at i:128291 original size:12 final size:12
Alignment explanation
Indices: 128283--128309 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
128273 AAATTTAATC
128283 TAATGTTTATAT
1 TAATGTTTATAT
128295 TAATGTTTATAT
1 TAATGTTTATAT
128307 TAA
1 TAA
128310 AGTGATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (12 bp):
TAATGTTTATAT
Found at i:130360 original size:206 final size:206
Alignment explanation
Indices: 130006--130416 Score: 752
Period size: 206 Copynumber: 2.0 Consensus size: 206
129996 CCTTCCTCCT
* *
130006 CTAGATCCTTCAATCGTCCCTCCCCTGTATCAGGTAATTTACCCAACAACTTAAGCTGTTCAGTT
1 CTAGATCCTTCAATCGTCCCTCCCCTCTATCAGGTAATTTACCCAACAACTTAAGCTGTTCAATT
*
130071 GATCAATCCATCTGATATTTTTCTTTGTCTTTCCAGGATAAGTATGAGAACCCCAGTTCCAGAAA
66 GATCAATCCATCCGATATTTTTCTTTGTCTTTCCAGGATAAGTATGAGAACCCCAGTTCCAGAAA
130136 TCAACCTATTGTCGCGAATCCAAGCTCCGAATTCCATCGGAAAACTGATTCTGCTGACGGAAATT
131 TCAACCTATTGTCGCGAATCCAAGCTCCGAATTCCATCGGAAAACTGATTCTGCTGACGGAAATT
130201 CAAGACCGGGA
196 CAAGACCGGGA
*
130212 CTAGATCCTTCAATCGTCCCTTCCCTCTATCAGGTAATTTACCCAACAACTTAAGCTGTTCAATT
1 CTAGATCCTTCAATCGTCCCTCCCCTCTATCAGGTAATTTACCCAACAACTTAAGCTGTTCAATT
*
130277 GATCAATCCATCCGAT-TTTTGTCTTTGTTTTTCCAGGATAAGTATGAGAACCCCAGTTCCAGAA
66 GATCAATCCATCCGATATTTT-TCTTTGTCTTTCCAGGATAAGTATGAGAACCCCAGTTCCAGAA
*
130341 ATCAACCTATTGTCGCGAATCCAAGCTCCGAATTCCATCGGAAAACTGATTCTGCTGACGGAGAT
130 ATCAACCTATTGTCGCGAATCCAAGCTCCGAATTCCATCGGAAAACTGATTCTGCTGACGGAAAT
130406 TCAAGACCGGG
195 TCAAGACCGGG
130417 TCTGGAGGTT
Statistics
Matches: 198, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
205 4 0.02
206 194 0.98
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (206 bp):
CTAGATCCTTCAATCGTCCCTCCCCTCTATCAGGTAATTTACCCAACAACTTAAGCTGTTCAATT
GATCAATCCATCCGATATTTTTCTTTGTCTTTCCAGGATAAGTATGAGAACCCCAGTTCCAGAAA
TCAACCTATTGTCGCGAATCCAAGCTCCGAATTCCATCGGAAAACTGATTCTGCTGACGGAAATT
CAAGACCGGGA
Found at i:132389 original size:21 final size:21
Alignment explanation
Indices: 132359--132398 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
132349 AAAATAATTT
132359 AAATTA-TTTTAAATTTTTAA
1 AAATTATTTTTAAATTTTTAA
*
132379 AAATATATTTTTTAATTTTT
1 AAAT-TATTTTTAAATTTTT
132399 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 2 0.12
22 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTATTTTTAAATTTTTAA
Found at i:141851 original size:9 final size:9
Alignment explanation
Indices: 141839--141874 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
141829 CCAATGAAAT
141839 GGATGATGA
1 GGATGATGA
*
141848 GGATGAGGA
1 GGATGATGA
141857 GGATGATGA
1 GGATGATGA
*
141866 TGATGATGA
1 GGATGATGA
141875 AATATTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.22
Consensus pattern (9 bp):
GGATGATGA
Found at i:142641 original size:18 final size:20
Alignment explanation
Indices: 142609--142651 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
142599 AATACTGAAA
*
142609 AAATTCAAAGGT-AA-AATT
1 AAATTCAAAGATAAATAATT
*
142627 AAATTCAAATATAAATAATT
1 AAATTCAAAGATAAATAATT
142647 AAATT
1 AAATT
142652 TAAAATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATTCAAAGATAAATAATT
Found at i:143018 original size:2 final size:2
Alignment explanation
Indices: 143011--143047 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
143001 CACCGGTAAT
143011 TC TC TC 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 TC TC TC T
143048 GTCTATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:152738 original size:24 final size:24
Alignment explanation
Indices: 152678--152738 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 24
152668 CTCAGGAGCT
*
152678 AGAGGAGAAAAAGAAGCACGAAGA
1 AGAGGAGAAAAAGAAGCAAGAAGA
*
152702 AGAAGAAATGAAAAAGAAGCAAGAAGA
1 AG-AG-GA-GAAAAAGAAGCAAGAAGA
152729 AGAGGAGAAA
1 AGAGGAGAAA
152739 GATAAAGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 3 0.10
27 19 0.61
ACGTcount: A:0.62, C:0.05, G:0.31, T:0.02
Consensus pattern (24 bp):
AGAGGAGAAAAAGAAGCAAGAAGA
Found at i:153600 original size:18 final size:18
Alignment explanation
Indices: 153560--153611 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
153550 TTTTCAGTTG
*
153560 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
153578 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
153596 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
153612 CTTATTCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:158246 original size:73 final size:72
Alignment explanation
Indices: 158127--158346 Score: 293
Period size: 73 Copynumber: 3.0 Consensus size: 72
158117 AATGTACTTC
* ** * *
158127 TATAATTCATTTGGCTTTGTTTGCCTGA-TGGGAAAAAAAGAGAAAGCAAGGCGAAAGCTTTGGA
1 TATAATCCATTTGGCTTTGTTTGGTTGATTGAG-AAACAAGAGAAAGCAAGGC-AAAGCTTTGGA
*
158191 TTTTGGCGT
64 TTTTGGCAT
* *
158200 TATAATCCATTTGGCTTTGTTTGGTTGATTGAGAAACAAGAGAAAGCAAGGCAAAAGGTTCGGAT
1 TATAATCCATTTGGCTTTGTTTGGTTGATTGAGAAACAAGAGAAAGCAAGGC-AAAGCTTTGGAT
158265 TTTGGCAT
65 TTTGGCAT
*
158273 TATAATCCATTTGGCTTTGTTTGGTTGATGTGA-AAAC-AGAGAAAGCAAAGCAAATGCTTTGGA
1 TATAATCCATTTGGCTTTGTTTGGTTGAT-TGAGAAACAAGAGAAAGCAAGGCAAA-GCTTTGGA
158336 TTTTGGCAT
64 TTTTGGCAT
158345 TA
1 TA
158347 GAAGTTTCCT
Statistics
Matches: 132, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
71 3 0.02
72 30 0.23
73 93 0.70
74 6 0.05
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (72 bp):
TATAATCCATTTGGCTTTGTTTGGTTGATTGAGAAACAAGAGAAAGCAAGGCAAAGCTTTGGATT
TTGGCAT
Found at i:165001 original size:39 final size:38
Alignment explanation
Indices: 164957--165055 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 38
164947 CCGTATGTAA
164957 AATTTTTAATGAATACCAAAATCTCTAATCAAATATCAAT
1 AATTTTTAATGAATACCAAAATCTCTAA-CAAATA-CAAT
* * * *
164997 -ATTTTTAATTGAGTACCAAAATTTCTAACAGATACCAT
1 AATTTTTAA-TGAATACCAAAATCTCTAACAAATACAAT
*
165035 AATTTTTAA-CAATACCAAAAT
1 AATTTTTAATGAATACCAAAAT
165056 TTCGTTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
37 10 0.20
38 3 0.06
39 21 0.41
40 17 0.33
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.35
Consensus pattern (38 bp):
AATTTTTAATGAATACCAAAATCTCTAACAAATACAAT
Found at i:165020 original size:20 final size:20
Alignment explanation
Indices: 164955--165057 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
164945 GCCCGTATGT
164955 AAAATTTTTAA-TGAATACC
1 AAAATTTTTAATTGAATACC
* * ** *
164974 AAAATCTCTAATCAAATATC
1 AAAATTTTTAATTGAATACC
* *
164994 AATATTTTTAATTGAGTACC
1 AAAATTTTTAATTGAATACC
* **
165014 AAAATTTCTAACAG-ATACC
1 AAAATTTTTAATTGAATACC
* *
165033 ATAATTTTTAA--CAATACC
1 AAAATTTTTAATTGAATACC
165051 AAAATTT
1 AAAATTT
165058 CGTTTATTTT
Statistics
Matches: 61, Mismatches: 21, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
18 11 0.18
19 22 0.36
20 28 0.46
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (20 bp):
AAAATTTTTAATTGAATACC
Found at i:165038 original size:19 final size:18
Alignment explanation
Indices: 165010--165058 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
165000 TTTAATTGAG
165010 TACCAAAATTTCTAACAGA
1 TACCAAAATTTCTAACA-A
* *
165029 TACCATAATTTTTAACAA
1 TACCAAAATTTCTAACAA
165047 TACCAAAATTTC
1 TACCAAAATTTC
165059 GTTTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (18 bp):
TACCAAAATTTCTAACAA
Found at i:165051 original size:18 final size:19
Alignment explanation
Indices: 164969--165058 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 19
164959 TTTTTAATGA
* *
164969 ATACCAAAATCTCTAATCAA
1 ATACCAAAATTTCTAA-CAG
* * * **
164989 ATATCAATATTTTTAATTG
1 ATACCAAAATTTCTAACAG
165008 AGTACCAAAATTTCTAACAG
1 A-TACCAAAATTTCTAACAG
* *
165028 ATACCATAATTTTTAACA-
1 ATACCAAAATTTCTAACAG
165046 ATACCAAAATTTC
1 ATACCAAAATTTC
165059 GTTTATTTTA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
18 11 0.21
19 16 0.30
20 26 0.49
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.34
Consensus pattern (19 bp):
ATACCAAAATTTCTAACAG
Found at i:165462 original size:20 final size:20
Alignment explanation
Indices: 165415--165470 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
165405 TTCAAATGCT
* * *
165415 ATACCGAAATCTCT-AGCAT
1 ATACCAAAATCTCTAATCAA
*
165434 ATACAAAAATCTCTAATCAA
1 ATACCAAAATCTCTAATCAA
*
165454 ATACCAAAATTTCTAAT
1 ATACCAAAATCTCTAAT
165471 GAAAGATGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (20 bp):
ATACCAAAATCTCTAATCAA
Found at i:171501 original size:23 final size:23
Alignment explanation
Indices: 171431--171503 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
171421 CATAAAGCAG
* * *
171431 AAACATGCCACAAGAAAAAAGAA
1 AAACGTGCCACAAGACATAAGAA
*
171454 AAACGTGCCACAAGACATAGGAA
1 AAACGTGCCACAAGACATAAGAA
* *
171477 AAATGTGCCACAGAGACA-AATAA
1 AAACGTGCCACA-AGACATAAGAA
171500 AAAC
1 AAAC
171504 TAGAAGAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 36 0.88
24 5 0.12
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.08
Consensus pattern (23 bp):
AAACGTGCCACAAGACATAAGAA
Found at i:173547 original size:58 final size:60
Alignment explanation
Indices: 173479--173640 Score: 159
Period size: 58 Copynumber: 2.7 Consensus size: 60
173469 TTGGTACTTG
* * *
173479 AACTTGATACTTTTTAT-TAATTTAGTAATTAAAC-TTTTTT-GACCCAATTTAGTAGCTA
1 AACTTGATACTTTTT-TCTAATTTAGTAACTAAACTTTTTTTGGAACCAATTTAGTACCTA
* * * *
173537 AACTTGATACTTTTTTCTAATTTGGTACCTAAACTTTTTTTGGAACCAATTTGGTACCTG
1 AACTTGATACTTTTTTCTAATTTAGTAACTAAACTTTTTTTGGAACCAATTTAGTACCTA
** * * *
173597 AACTTGACATTTTTTTTTCTTAATTTGGTACCTAAGCTTTTTTT
1 AACTTG--ATACTTTTTTC-TAATTTAGTAACTAAACTTTTTTT
173641 AAGATTCAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 29 0.33
59 6 0.07
60 20 0.23
62 9 0.10
63 23 0.26
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (60 bp):
AACTTGATACTTTTTTCTAATTTAGTAACTAAACTTTTTTTGGAACCAATTTAGTACCTA
Found at i:173862 original size:31 final size:31
Alignment explanation
Indices: 173809--173944 Score: 102
Period size: 31 Copynumber: 4.5 Consensus size: 31
173799 ACCCCAAAAC
* * *
173809 GTTTAAGTACCAACTTA-AAAAAAGTGTCAA
1 GTTTGAGTACCAAATTAGGAAAAAGTGTCAA
* *
173839 GTTT-AGGTATCAAATTAGGAAAAAGTGTTAA
1 GTTTGA-GTACCAAATTAGGAAAAAGTGTCAA
** ***
173870 GTTTGAGTACCAAATTA-GACTAAG-AAAAA
1 GTTTGAGTACCAAATTAGGAAAAAGTGTCAA
* * *
173899 ATTTGAGTACCAAATTAAGAAAAAGTATCAA
1 GTTTGAGTACCAAATTAGGAAAAAGTGTCAA
173930 GTTT-AGATACCAAAT
1 GTTTGAG-TACCAAAT
173945 ATTATATTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
29 19 0.23
30 25 0.30
31 39 0.46
32 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (31 bp):
GTTTGAGTACCAAATTAGGAAAAAGTGTCAA
Found at i:175460 original size:17 final size:18
Alignment explanation
Indices: 175438--175479 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
175428 GTTCAAGATA
*
175438 TAATTAATTTAATTT-TT
1 TAATTAATTAAATTTATT
175455 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
175473 TAATTAA
1 TAATTAA
175480 AAATCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:175483 original size:16 final size:17
Alignment explanation
Indices: 175438--175489 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
175428 GTTCAAGATA
*
175438 TAATTAATTTAATTT-TT
1 TAATTAA-TAAATTTATT
175455 TAATTAATTAAATTTATT
1 TAATTAA-TAAATTTATT
*
175473 TAATTAA-AAATCTATT
1 TAATTAATAAATTTATT
175489 T
1 T
175490 TTATCTCAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 9 0.28
17 14 0.44
18 9 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTAATAAATTTATT
Found at i:176814 original size:1 final size:1
Alignment explanation
Indices: 176808--176833 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
176798 CTTAAATTTG
176808 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
176834 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:188791 original size:26 final size:26
Alignment explanation
Indices: 188726--188797 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
188716 TTAAGATTTT
*
188726 AATTAAGATAATTAGAAGTTTGAATTG
1 AATTAAGATAATTAG-AGTTTAAATTG
* * *
188753 AATTATGACAATTAGAGTTTAAATTT
1 AATTAAGATAATTAGAGTTTAAATTG
188779 AGA-TAAGATAATTAG-GTTT
1 A-ATTAAGATAATTAGAGTTT
188798 TTAAACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 4 0.11
26 20 0.53
27 14 0.37
ACGTcount: A:0.43, C:0.01, G:0.17, T:0.39
Consensus pattern (26 bp):
AATTAAGATAATTAGAGTTTAAATTG
Found at i:190015 original size:27 final size:26
Alignment explanation
Indices: 189976--190029 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
189966 TTTAGATTTT
* * *
189976 AATTAAGATAATTTGGATTTTAAATTG
1 AATTAAGACAA-TTAGAGTTTAAATTG
*
190003 AATTATGACAATTAGAGTTTAAATTG
1 AATTAAGACAATTAGAGTTTAAATTG
190029 A
1 A
190030 GATAAGTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.41
Consensus pattern (26 bp):
AATTAAGACAATTAGAGTTTAAATTG
Found at i:190046 original size:48 final size:47
Alignment explanation
Indices: 189967--190074 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
189957 AGATAATAGT
* * * *
189967 TTAGA-TTTTAATTAAGATAATTTGGATTTTAAATTGAATTATGACAA
1 TTAGAGTTTTAATTAAGATAAGTAGGAGTTTAAATTAAATTA-GACAA
* * *
190014 TTAGAGTTTAAATTGAGATAAGTAGGAGTTTAAATTAAATTAGATAA
1 TTAGAGTTTTAATTAAGATAAGTAGGAGTTTAAATTAAATTAGACAA
190061 TTAGAGTTTTAATT
1 TTAGAGTTTTAATT
190075 TATTTAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 22 0.42
48 30 0.58
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.43
Consensus pattern (47 bp):
TTAGAGTTTTAATTAAGATAAGTAGGAGTTTAAATTAAATTAGACAA
Found at i:190071 original size:26 final size:27
Alignment explanation
Indices: 190021--190074 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
190011 CAATTAGAGT
190021 TTAAATTGAGATAAGTAGGAGTTTAAA
1 TTAAATTGAGATAAGTAGGAGTTTAAA
* *
190048 TTAAATT-AGATAATTA-GAGTTTTAA
1 TTAAATTGAGATAAGTAGGAGTTTAAA
190073 TT
1 TT
190075 TATTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 8 0.32
27 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.41
Consensus pattern (27 bp):
TTAAATTGAGATAAGTAGGAGTTTAAA
Found at i:190134 original size:53 final size:51
Alignment explanation
Indices: 190077--190193 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 51
190067 TTTTAATTTA
* * *
190077 TTTAAATTAATATGTTAGATAATAGTTTAGATTTTA-ATTAAGATAATTAGGAT
1 TTTAAATTAATATGATA-ATAAGAGTTTAGA-TTTAGA-TAAGATAATTAGGAG
* *
190130 TTTAAATTTAATTATGATAATTAGAGTTTATATTTAGATAAGATAATTAGGAG
1 TTTAAA-TTAA-TATGATAATAAGAGTTTAGATTTAGATAAGATAATTAGGAG
*
190183 TTTAAACTAAT
1 TTTAAATTAAT
190194 TTAGAAAGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
51 1 0.02
52 3 0.05
53 30 0.55
54 15 0.27
55 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (51 bp):
TTTAAATTAATATGATAATAAGAGTTTAGATTTAGATAAGATAATTAGGAG
Found at i:190174 original size:26 final size:27
Alignment explanation
Indices: 190100--190188 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
190090 GTTAGATAAT
*
190100 AGTTTAGATTTTAATTAAGATAATTAGG
1 AGTTTA-AATTTAATTAAGATAATTAGG
* *
190128 ATTTTAAATTTAATTATGATAATTA-G
1 AGTTTAAATTTAATTAAGATAATTAGG
*
190154 AGTTTATATTTAGA-TAAGATAATTAGG
1 AGTTTAAATTTA-ATTAAGATAATTAGG
190181 AGTTTAAA
1 AGTTTAAA
190189 CTAATTTAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
26 21 0.40
27 26 0.50
28 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (27 bp):
AGTTTAAATTTAATTAAGATAATTAGG
Found at i:190188 original size:136 final size:136
Alignment explanation
Indices: 189780--190188 Score: 593
Period size: 136 Copynumber: 3.0 Consensus size: 136
189770 GCATATTTAA
*
189780 TTAAATTAGGATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGAATTT
1 TTAAATTA-GATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTT
* * * * **
189845 AATTAAGATAAGTAGGAGTTGAAATTGAATTATGATAATTAGAATTTAAAAAGAGATAAGATAAT
65 AATTAAGATAATTAGGATTTTAAATTGAATTATGATAATTAGAGTTTAAATTGAGATAAGATAAT
189910 TAGGAGT
130 TAGGAGT
189917 TTAAA-T---T-ATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTTA
1 TTAAATTAGATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTTA
* *
189977 ATTAAGATAATTTGGATTTTAAATTGAATTATGACAATTAGAGTTTAAATTGAGATAAG-TAGGA
66 ATTAAGATAATTAGGATTTTAAATTGAATTATGATAATTAGAGTTTAAATTGAGATAAGATA--A
*
190041 GTTTA--A-A
129 --TTAGGAGT
190048 TTAAATTAGATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTTA
1 TTAAATTAGATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTTA
* * *
190113 ATTAAGATAATTAGGATTTTAAATTTAATTATGATAATTAGAGTTTATATTTAGATAAGATAATT
66 ATTAAGATAATTAGGATTTTAAATTGAATTATGATAATTAGAGTTTAAATTGAGATAAGATAATT
190178 AGGAGT
131 AGGAGT
190184 TTAAA
1 TTAAA
190189 CTAATTTAGA
Statistics
Matches: 243, Mismatches: 16, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
130 2 0.01
131 108 0.44
132 4 0.02
133 3 0.01
134 3 0.01
135 3 0.01
136 113 0.47
137 7 0.03
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (136 bp):
TTAAATTAGATAATTAGAGTTTTAATTTATTTAAATTAATATGTTAGATAATAGTTTAGATTTTA
ATTAAGATAATTAGGATTTTAAATTGAATTATGATAATTAGAGTTTAAATTGAGATAAGATAATT
AGGAGT
Found at i:193212 original size:15 final size:15
Alignment explanation
Indices: 193163--193222 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
193153 TCTTACATAA
193163 TTATATTATTTTTAAT
1 TTATA-TATTTTTAAT
*
193179 TTA-ATATTTAATAATT
1 TTATATATTT-TTAA-T
*
193195 TTATATATTTTTTAT
1 TTATATATTTTTAAT
193210 TTACTAATATTTT
1 TTA-T-ATATTTT
193223 ACATATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 13 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATATTTTTAAT
Found at i:210150 original size:18 final size:18
Alignment explanation
Indices: 210129--210163 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
210119 TTTAAAGTTT
210129 TATAAAA-ATCATAAAAAA
1 TATAAAAGA-CATAAAAAA
210147 TATAAAAGACATAAAAA
1 TATAAAAGACATAAAAA
210164 TGACCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
TATAAAAGACATAAAAAA
Found at i:210518 original size:20 final size:20
Alignment explanation
Indices: 210493--210549 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
210483 GTATGATAAT
210493 TTTTATAATTTTTTTACGAA
1 TTTTATAATTTTTTTACGAA
* * *
210513 TTTTAT-ATTTCTTT-CCAT
1 TTTTATAATTTTTTTACGAA
*
210531 TTTTATAATTTTCTTACGA
1 TTTTATAATTTTTTTACGA
210550 GTTTATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 8 0.28
19 13 0.45
20 8 0.28
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAA
Found at i:212518 original size:72 final size:72
Alignment explanation
Indices: 212401--212544 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
212391 GAATGATCTT
*
212401 GATAGAACTATTTTTGTTTTGTTTGAAGCCATTGACTTATGAAGGAATTGTCTTGTCTGTTTATG
1 GATAGAACTATTTTTGTTTTGTTTGAAACCATTGACTTATGAAGGAATTGTCTTGTCTGTTTATG
212466 AATCTAG
66 AATCTAG
212473 GATAGAACTATTTTTGTTTTGTTTGAAACCATTGACTTATGAAGGAATTGTCTTGTCTGTTTATG
1 GATAGAACTATTTTTGTTTTGTTTGAAACCATTGACTTATGAAGGAATTGTCTTGTCTGTTTATG
212538 AATCTAG
66 AATCTAG
212545 AACTTTGACA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (72 bp):
GATAGAACTATTTTTGTTTTGTTTGAAACCATTGACTTATGAAGGAATTGTCTTGTCTGTTTATG
AATCTAG
Found at i:228687 original size:2 final size:2
Alignment explanation
Indices: 228680--228712 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
228670 TGAAATTCAA
228680 AT 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 AT A
228713 AAGTGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238463 original size:30 final size:30
Alignment explanation
Indices: 238397--238468 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
238387 AATAGCATAT
*
238397 ATTTTTATTATTTTTAAAGAGTTAAATTAA
1 ATTTTTATTATTTTTAAAGAGTCAAATTAA
238427 ATTTTTATTATTTTT-AAGAGGTCAAAGTGT-A
1 ATTTTTATTATTTTTAAAGA-GTCAAA-T-TAA
238458 A-TTTTATTATT
1 ATTTTTATTATT
238469 ACTCATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
29 4 0.11
30 30 0.79
31 3 0.08
32 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAGAGTCAAATTAA
Found at i:241267 original size:76 final size:76
Alignment explanation
Indices: 241175--241329 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
241165 TGTCGATTTA
241175 ATGATTCGAGGTCTCATTAATTCTAAAACTCCCAATCGTTTCATAAATACCAACACAAACCCATA
1 ATGATTCGAGGTCTCATTAATTCTAAAACTCCCAATCGTTTCATAAATACCAACACAAACCCATA
241240 TTAATACGCTC
66 TTAATACGCTC
* *
241251 ATGATTCGAGGTCTCATTAATTCTAAAACTCCCAATTGTTTCATAAATACCAACACAAACCCCTA
1 ATGATTCGAGGTCTCATTAATTCTAAAACTCCCAATCGTTTCATAAATACCAACACAAACCCATA
*
241316 TTGATACGCTC
66 TTAATACGCTC
241327 ATG
1 ATG
241330 TCACACATAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (76 bp):
ATGATTCGAGGTCTCATTAATTCTAAAACTCCCAATCGTTTCATAAATACCAACACAAACCCATA
TTAATACGCTC
Found at i:251483 original size:24 final size:23
Alignment explanation
Indices: 251456--251516 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
251446 TAATGGATTG
*
251456 AAAATTAAAATATATTCAAATTT
1 AAAATTAAAATAAATTCAAATTT
* * *
251479 AAAAATCAACATAAATTTAAATTT
1 -AAAATTAAAATAAATTCAAATTT
*
251503 TAAATCTAAAATAA
1 AAAAT-TAAAATAA
251517 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATTAAAATAAATTCAAATTT
Found at i:251854 original size:22 final size:22
Alignment explanation
Indices: 251813--251859 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
251803 GATTTACATA
** *
251813 TTTTTTTATTATTATGATATTT
1 TTTTTTTATTAAAATGATATAT
*
251835 TTTTTTTATTAAAATTATATAT
1 TTTTTTTATTAAAATGATATAT
251857 TTT
1 TTT
251860 GTTATCTAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTTTATTAAAATGATATAT
Found at i:252975 original size:20 final size:20
Alignment explanation
Indices: 252950--252987 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
252940 CACGTAGGAG
* *
252950 GGATGTCTTTGATGGGATGA
1 GGATGTCTATGATAGGATGA
252970 GGATGTCTATGATAGGAT
1 GGATGTCTATGATAGGAT
252988 TGATTATGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.37, T:0.34
Consensus pattern (20 bp):
GGATGTCTATGATAGGATGA
Found at i:253659 original size:340 final size:340
Alignment explanation
Indices: 253029--253710 Score: 1319
Period size: 340 Copynumber: 2.0 Consensus size: 340
253019 ATAAAGCAGT
* *
253029 TGAGCTCACGTGATGTTTGGTAATCAACAACTTCATGTTCCCAATGAAAATTAGGCCATTTGTTG
1 TGAGCCCACATGATGTTTGGTAATCAACAACTTCATGTTCCCAATGAAAATTAGGCCATTTGTTG
253094 CTTGGGTAGTCATCCCAAAAGGGTGAGCTTGCAGGTGACTCTCGGTCTGCTGGTGGCAAGCTTAC
66 CTTGGGTAGTCATCCCAAAAGGGTGAGCTTGCAGGTGACTCTCGGTCTGCTGGTGGCAAGCTTAC
253159 TATTCAGGTGTCTTCTTGGCTTGCCACATGTCTATAAGGTTTTACACTCTTTAAAAGAATACTAA
131 TATTCAGGTGTCTTCTTGGCTTGCCACATGTCTATAAGGTTTTACACTCTTTAAAAGAATACTAA
* *
253224 GCTTACATGTTGTCAACATTATAAAATGTTGACAAAGCAGATGGGGTATAACAATATCTCCCTTT
196 GCTTACATGTTGTCAACATTATAAAATGTTGACAAAGCAGATAGGGTATAACAATATCTCCCTCT
253289 AAGTCAAGAGGAGGGTTATAAAGTGGCTTTCCTCAAGATGCTTTGATTTGATAACTTCCCCTTTT
261 AAGTCAAGAGGAGGGTTATAAAGTGGCTTTCCTCAAGATGCTTTGATTTGATAACTTCCCCTTTT
253354 CCAAGTTGTTCCAAA
326 CCAAGTTGTTCCAAA
253369 TGAGCCCACATGATGTTTGGTAATCAACAACTTCATGTTCCCAATGAAAATTAGGCCATTTGTTG
1 TGAGCCCACATGATGTTTGGTAATCAACAACTTCATGTTCCCAATGAAAATTAGGCCATTTGTTG
253434 CTTGGGTAGTCATCCCAAAAGGGTGAGCTTGCAGGTGACTCTCGGTCTGCTGGTGGCAAGCTTAC
66 CTTGGGTAGTCATCCCAAAAGGGTGAGCTTGCAGGTGACTCTCGGTCTGCTGGTGGCAAGCTTAC
253499 TATTCAGGTGTCTTCTTGGCTTGCCACATGTCTATAAGGTTTTACACTCTTTAAAAGAATACTAA
131 TATTCAGGTGTCTTCTTGGCTTGCCACATGTCTATAAGGTTTTACACTCTTTAAAAGAATACTAA
*
253564 GCTTACATGTTGTCAACATTATAGAATGTTGACAAAGCAGATAGGGTATAACAATATCTCCCTCT
196 GCTTACATGTTGTCAACATTATAAAATGTTGACAAAGCAGATAGGGTATAACAATATCTCCCTCT
253629 AAGTCAAGAGGAGGGTTATAAAGTGGCTTTCCTCAAGATGCTTTGATTTGATAACTTCCCCTTTT
261 AAGTCAAGAGGAGGGTTATAAAGTGGCTTTCCTCAAGATGCTTTGATTTGATAACTTCCCCTTTT
253694 CCAAGTTGTTCCAAA
326 CCAAGTTGTTCCAAA
253709 TG
1 TG
253711 GTAGCTTTAT
Statistics
Matches: 337, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
340 337 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (340 bp):
TGAGCCCACATGATGTTTGGTAATCAACAACTTCATGTTCCCAATGAAAATTAGGCCATTTGTTG
CTTGGGTAGTCATCCCAAAAGGGTGAGCTTGCAGGTGACTCTCGGTCTGCTGGTGGCAAGCTTAC
TATTCAGGTGTCTTCTTGGCTTGCCACATGTCTATAAGGTTTTACACTCTTTAAAAGAATACTAA
GCTTACATGTTGTCAACATTATAAAATGTTGACAAAGCAGATAGGGTATAACAATATCTCCCTCT
AAGTCAAGAGGAGGGTTATAAAGTGGCTTTCCTCAAGATGCTTTGATTTGATAACTTCCCCTTTT
CCAAGTTGTTCCAAA
Found at i:257654 original size:2 final size:2
Alignment explanation
Indices: 257647--257701 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
257637 TAAACCCTTT
257647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257689 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
257702 TTGTGAAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:264147 original size:2 final size:2
Alignment explanation
Indices: 264134--264209 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
264124 CTTAATGCAG
*
264134 AT AT AC 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
264176 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
264210 G
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.