Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:3684880 original size:47 final size:47
Alignment explanation
Indices: 3684807--3684897 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
3684797 GCATCCCAAC
*
3684807 TTACTTCTATAAATAATAGAGGTAATTTGACATTTAAAATCATGGAG
1 TTACTTCTATAAATAATAGAGATAATTTGACATTTAAAATCATGGAG
3684854 TTACTTCTATAAATAATAGAGATAATTTGACATTTAAAATCATG
1 TTACTTCTATAAATAATAGAGATAATTTGACATTTAAAATCATG
3684898 AAGCCTTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (47 bp):
TTACTTCTATAAATAATAGAGATAATTTGACATTTAAAATCATGGAG
Found at i:3685230 original size:21 final size:22
Alignment explanation
Indices: 3685206--3685246 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3685196 ACCGATTTTG
3685206 CCGA-TTTTCAGCCGGTTCTCC
1 CCGATTTTTCAGCCGGTTCTCC
*
3685227 CCGATTTTTCCGCCGGTTCT
1 CCGATTTTTCAGCCGGTTCT
3685247 TCCGGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.07, C:0.37, G:0.20, T:0.37
Consensus pattern (22 bp):
CCGATTTTTCAGCCGGTTCTCC
Found at i:3696774 original size:13 final size:13
Alignment explanation
Indices: 3696758--3696811 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
3696748 CTATGACGCG
3696758 CATTTATGACACA
1 CATTTATGACACA
*
3696771 CATTTAAGACACA
1 CATTTATGACACA
*
3696784 CATTTA--AGACA
1 CATTTATGACACA
* *
3696795 TATTTATGACGCA
1 CATTTATGACACA
3696808 CATT
1 CATT
3696812 GCACGTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 9 0.27
13 24 0.73
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:3699209 original size:91 final size:91
Alignment explanation
Indices: 3699054--3699270 Score: 312
Period size: 91 Copynumber: 2.4 Consensus size: 91
3699044 GTAAGTATGC
* * *
3699054 AAATAAGCTTACGAGCATATGGAATAAATGGTAAGTATTTTGGTAGAATAAACTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGTAAAATAAACTTACGAGCTTAT
3699119 GGGATTAAATGGGT-AGCATATTGGTA
66 GGGATTAAAT-GGTAAGCATATTGGTA
*** **
3699145 AAATAAG-TTTTTAGCTTATGGGATTAAATGGTAAGTATTTTGGTAAAATACGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATTTTGGTAAAATAAACTTACGAGCTTA
* *
3699209 TGGGATTAAATGGTAAGTATTTTGGTA
65 TGGGATTAAATGGTAAGCATATTGGTA
3699236 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
3699271 AGATTTTATC
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 14 0.13
91 83 0.75
92 13 0.12
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (91 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGTAAAATAAACTTACGAGCTTAT
GGGATTAAATGGTAAGCATATTGGTA
Found at i:3699277 original size:46 final size:46
Alignment explanation
Indices: 3699054--3699270 Score: 307
Period size: 46 Copynumber: 4.8 Consensus size: 46
3699044 GTAAGTATGC
* *
3699054 AAATAAGCTTACGAGCATAT-GGAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
* * * *
3699099 GAATAAACTTACGAGCTTATGGGATTAAATGGGT-AGCATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAAT-GGTAAGTATTTTGGTA
***
3699145 AAATAAG-TTTTTAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
*
3699190 AAATACGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
3699236 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
3699271 AGATTTTATC
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
44 3 0.02
45 63 0.42
46 81 0.54
47 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
Found at i:3702140 original size:29 final size:27
Alignment explanation
Indices: 3702114--3702259 Score: 104
Period size: 29 Copynumber: 5.1 Consensus size: 27
3702104 TAAAAAACAC
3702114 AAAAAGAAAAGAAGAAAAGAAGAAAACAAA
1 AAAAAGAAAA-AAGAAAAGAAG-AAA-AAA
3702144 AAGAAAGAAGAAAAAGAGAAAG-AGAAAGAGAAA
1 AA-AAAG-A-AAAAAGA-AAAGAAG-AA-A-AAA
*
3702177 AAAAAGAAAAAAGAAAA-AAGAAAGAAT
1 AAAAAGAAAAAAGAAAAGAAGAAA-AAA
*
3702204 AAAAAG-AAAAAGAAAACAAAGAAGAAAA
1 AAAAAGAAAAAAGAAAA-GAAGAA-AAAA
*
3702232 AAAATAG-AAAAAGAAAAGAA-AAGAAA
1 AAAA-AGAAAAAAGAAAAGAAGAAAAAA
3702258 AA
1 AA
3702260 GGGAAAAAAA
Statistics
Matches: 101, Mismatches: 5, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
26 15 0.15
27 12 0.12
28 15 0.15
29 18 0.18
30 9 0.09
31 5 0.05
32 14 0.14
33 13 0.13
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (27 bp):
AAAAAGAAAAAAGAAAAGAAGAAAAAA
Found at i:3702148 original size:27 final size:26
Alignment explanation
Indices: 3702112--3702268 Score: 133
Period size: 26 Copynumber: 5.8 Consensus size: 26
3702102 TATAAAAAAC
*
3702112 ACAAAAAGAAAAGAAGAAAAGAAGAAA
1 ACAAAAAGAAAAAAAGAAAA-AAGAAA
*
3702139 ACAAAAAG-AAAGAAGAAAAAGAGAAA
1 ACAAAAAGAAAAAAAGAAAAA-AGAAA
* *
3702165 GAGAAAGAGAAAAAAAAGAAAAAAGAAA
1 -ACAAAAAG-AAAAAAAGAAAAAAGAAA
3702193 A-AAGAAAGAATAAAAAG-AAAAAGAAA
1 ACAA-AAAGAA-AAAAAGAAAAAAGAAA
*
3702219 ACAAAGAAGAAAAAAAATAGAAAAAGAAA
1 ACAAA-AAG-AAAAAAAGA-AAAAAGAAA
* **
3702248 A-GAAAAGAAAAAGGGAAAAAA
1 ACAAAAAGAAAAAAAGAAAAAA
3702269 ATGAGAGATG
Statistics
Matches: 110, Mismatches: 9, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
25 6 0.05
26 37 0.34
27 37 0.34
28 9 0.08
29 21 0.19
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.01
Consensus pattern (26 bp):
ACAAAAAGAAAAAAAGAAAAAAGAAA
Found at i:3702159 original size:35 final size:34
Alignment explanation
Indices: 3702120--3702257 Score: 127
Period size: 36 Copynumber: 3.9 Consensus size: 34
3702110 ACACAAAAAG
3702120 AAAAGAAGAAAAGAAGAAAACAAAAAGAAAGAAGA
1 AAAAGAAGAAAAGAAGAAAA-AAAAAGAAAGAAGA
*
3702155 AAAAG-AGAAAGAGAAAGAGAAAAAAAAGAAAAAAGAA
1 AAAAGAAGAAA-AG-AAGA-AAAAAAAAGAAAGAAG-A
* *
3702192 AAAAGAAAGAATAAAAAGAAAAAGAAAACAAAGAAGA
1 AAAAG-AAGAA-AAGAAGAAAAA-AAAAGAAAGAAGA
* * *
3702229 AAAAAAATAGAAA-AAGAAAAGAAAAGAAA
1 AAAAGAAGA-AAAGAAGAAAAAAAAAGAAA
3702258 AAGGGAAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
34 12 0.14
35 14 0.16
36 21 0.24
37 19 0.22
38 14 0.16
39 5 0.06
40 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (34 bp):
AAAAGAAGAAAAGAAGAAAAAAAAAGAAAGAAGA
Found at i:3702160 original size:6 final size:6
Alignment explanation
Indices: 3702114--3702260 Score: 112
Period size: 6 Copynumber: 25.0 Consensus size: 6
3702104 TAAAAAACAC
* * *
3702114 AAAAAG -AAAAG AAGAA- AAGAAG -AAAAC AAAAAG AAAGAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG
* * * *
3702160 AGAAAG AGAAAG AGAAA- AAAAAG AAAAAAG AAAAAAG AAAGAAT AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG -AAAAAG AAA-AAG AAAAAG
* *
3702210 AAAAAG AAAACA- AAGAAG AAAAA- AAATAG AAAAAG -AAAAG -AAAAG
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
3702255 AAAAAG
1 AAAAAG
3702261 GGAAAAAAAT
Statistics
Matches: 118, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
5 32 0.27
6 61 0.52
7 25 0.21
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:3702195 original size:77 final size:72
Alignment explanation
Indices: 3702105--3702268 Score: 181
Period size: 74 Copynumber: 2.2 Consensus size: 72
3702095 AAAACAATAT
* *
3702105 AAAAAACACAAAAAGAAAAGAAGAAAAGAAGAAAACA-AAAAGAAAGAAGAAAAAGAGAA-AGAG
1 AAAAAAGA-AAAAAG-AAAGAA-AAAA-AAGAAAA-AGAAAACAAAGAAGAAAAA-A-AATAGA-
3702168 AAAGAGAAAA-AAAAG
58 AAA-AGAAAAGAAAAG
*
3702183 AAAAAAGAAAAAAGAAAGAATAAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAGAAAAAGAAA
1 AAAAAAGAAAAAAGAAAGAAAAAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAGAAAAAGAAA
3702248 AGAAAAG
66 AGAAAAG
*
3702255 AAAAAGGGAAAAAA
1 AAAAA-AGAAAAAA
3702269 ATGAGAGATG
Statistics
Matches: 78, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
71 6 0.08
72 15 0.19
73 12 0.15
74 23 0.29
75 3 0.04
76 6 0.08
77 6 0.08
78 7 0.09
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.01
Consensus pattern (72 bp):
AAAAAAGAAAAAAGAAAGAAAAAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAGAAAAAGAAA
AGAAAAG
Found at i:3702225 original size:65 final size:61
Alignment explanation
Indices: 3702114--3702259 Score: 154
Period size: 65 Copynumber: 2.3 Consensus size: 61
3702104 TAAAAAACAC
*
3702114 AAAAAGAAAAGAAGAAAAGAAGAAAACAAAAAGAAAGAAGAAAAAG-AGAAAGAGAAAGAGAAA
1 AAAAAGAAAA-AAGAAAA-AAGAAAACAAAAAGAAAGAAGAAAAAGAAGAAA-AAAAAGAGAAA
* *
3702177 AAAAAGAAAAAAGAAAAAAGAAAGAATAAAAAGAAA-AAGAAAACAAAGAAGAAAAAAAATAGAA
1 AAAAAGAAAAAAGAAAAAAG-AA-AACAAAAAGAAAGAAG--AA-AAAGAAGAAAAAAAAGAGAA
3702241 A
61 A
*
3702242 AAGAAA-AGAAAAGAAAAA
1 AA-AAAGAAAAAAGAAAAA
3702260 GGGAAAAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
61 3 0.04
62 12 0.17
63 21 0.29
64 2 0.03
65 26 0.36
66 8 0.11
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (61 bp):
AAAAAGAAAAAAGAAAAAAGAAAACAAAAAGAAAGAAGAAAAAGAAGAAAAAAAAGAGAAA
Found at i:3702267 original size:34 final size:35
Alignment explanation
Indices: 3702204--3702270 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
3702194 AAGAAAGAAT
3702204 AAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAG
1 AAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAG
* *
3702239 AAAAAG-AAAAGAAAAGAAA-AAGGGAAAAAAAT
1 AAAAAGAAAAAGAAAACAAAGAA-GAAAAAAAAT
3702271 GAGAGATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 2 0.07
34 21 0.72
35 6 0.21
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (35 bp):
AAAAAGAAAAAGAAAACAAAGAAGAAAAAAAATAG
Found at i:3702268 original size:54 final size:55
Alignment explanation
Indices: 3702115--3702256 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 55
3702105 AAAAAACACA
* * *
3702115 AAAAGAAAAGAAGAAAAGAAGAAAACAAA-AAGAAAGAAGAAAAAGAGAAAGAGAAAGAG
1 AAAA-AAAAGAA-AAAAGAA-AAAAGAAAGAATAAA-AAGAAAAA-AGAAAGACAAAGAG
3702174 AAAAAAAAGAAAAAAGAAAAAAGAAAGAATAAAAAG-AAAAAGAAA-ACAAAGAAG
1 AAAAAAAAGAAAAAAGAAAAAAGAAAGAATAAAAAGAAAAAAGAAAGACAAAG-AG
* *
3702228 AAAAAAAATAGAAAAAGAAAAGA-AAAGAA
1 AAAAAAAAGA-AAAAAGAAAAAAGAAAGAA
3702257 AAAGGGAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 11
0.82 0.05 0.12
Matches are distributed among these distances:
53 5 0.07
54 22 0.29
55 15 0.20
56 10 0.13
57 12 0.16
58 7 0.09
59 4 0.05
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (55 bp):
AAAAAAAAGAAAAAAGAAAAAAGAAAGAATAAAAAGAAAAAAGAAAGACAAAGAG
Found at i:3702269 original size:16 final size:15
Alignment explanation
Indices: 3702114--3702260 Score: 117
Period size: 15 Copynumber: 9.8 Consensus size: 15
3702104 TAAAAAACAC
3702114 AAAAAG-AAAAGAAGA
1 AAAAAGAAAAAGAA-A
*
3702129 AAAGAAGAAAACAAAAA
1 AAA-AAGAAAA-AGAAA
*
3702146 GAAAGAAGAAAAAG-AG
1 -AAA-AAGAAAAAGAAA
* *
3702162 AAAGAGAAAGAGAAA
1 AAAAAGAAAAAGAAA
*
3702177 AAAAAGAAAAA-AGA
1 AAAAAGAAAAAGAAA
*
3702191 AAAAAG--AAAGAAT
1 AAAAAGAAAAAGAAA
3702204 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
* *
3702219 ACAAAGAAGAA-AAA
1 AAAAAGAAAAAGAAA
*
3702233 AAATAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
3702248 AGAAAAGAAAAAG
1 A-AAAAGAAAAAG
3702261 GGAAAAAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.03
13 7 0.07
14 26 0.25
15 35 0.34
16 14 0.13
17 5 0.05
18 14 0.13
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:3704678 original size:39 final size:39
Alignment explanation
Indices: 3704644--3704732 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
3704634 CTCCTTCTTT
* *
3704644 TCTTTCTTTTTCCCTCTTCAGTGTCCCTTCTCCTTTGTCC
1 TCTTCCTTTTTCCAT-TTCAGTGTCCCTTCTCCTTTGTCC
* * *
3704684 TCTTCCTTTTTCCATTTCGGTGTCCCTTCTCCTTTCTCA
1 TCTTCCTTTTTCCATTTCAGTGTCCCTTCTCCTTTGTCC
3704723 TCTTCCTTTT
1 TCTTCCTTTT
3704733 CAACAAGTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.03, C:0.36, G:0.07, T:0.54
Consensus pattern (39 bp):
TCTTCCTTTTTCCATTTCAGTGTCCCTTCTCCTTTGTCC
Found at i:3705195 original size:39 final size:40
Alignment explanation
Indices: 3705136--3705218 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 40
3705126 TTTTCTTTCT
* * *
3705136 TTTTTCCCTCTTCAGTGTCCCTTCTCCTTTGTCCTCTTCC
1 TTTTTCCATCTTCAGTGTCCCTTCTCCTTTCTCATCTTCC
*
3705176 TTTTTCCAT-TTCGGTGTCCCTTCTCCTTTCTCATCTTCC
1 TTTTTCCATCTTCAGTGTCCCTTCTCCTTTCTCATCTTCC
3705215 TTTT
1 TTTT
3705219 CAACAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.04, C:0.36, G:0.07, T:0.53
Consensus pattern (40 bp):
TTTTTCCATCTTCAGTGTCCCTTCTCCTTTCTCATCTTCC
Found at i:3709780 original size:15 final size:15
Alignment explanation
Indices: 3709757--3709812 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3709747 GATGCTTTCT
*
3709757 TTTTCCTTCTTTGACT
1 TTTT-CTTCTTTGACG
3709773 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
3709788 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
3709803 TTGTCTTCTT
1 TTTTCTTCTT
3709813 ACCACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.07, C:0.21, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:3713384 original size:2 final size:2
Alignment explanation
Indices: 3713377--3713408 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3713367 AAAATCTGGA
3713377 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3713409 CATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3713415 original size:2 final size:2
Alignment explanation
Indices: 3713410--3713471 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3713400 CACACACACC
3713410 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
3713452 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3713472 GGTAAAGCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3713887 original size:26 final size:28
Alignment explanation
Indices: 3713840--3713898 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
3713830 AATTAATTTA
* *
3713840 AAATAAAAATAAATAAATCAATG-A-CC
1 AAATTAAAATAAAGAAATCAATGTATCC
3713866 AAATTAAAATAAACGAAA-CAATGTATCC
1 AAATTAAAATAAA-GAAATCAATGTATCC
3713894 AAATT
1 AAATT
3713899 CGAAACAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 17 0.61
27 4 0.14
28 7 0.25
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (28 bp):
AAATTAAAATAAAGAAATCAATGTATCC
Found at i:3715455 original size:139 final size:138
Alignment explanation
Indices: 3715212--3715698 Score: 683
Period size: 139 Copynumber: 3.5 Consensus size: 138
3715202 AAAAAGTTTT
* *
3715212 TCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAA
1 TCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAA
* * *
3715277 TGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATATGATGAATCAAGCAAAGGTTAA
66 TGTTGATCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGATGAATCAAGCAAAGGTTGA
*
3715342 ACAAGTTC
131 ATAAGTTC
* * * * *
3715350 ATCTCATTATGAACTTGTTCTCCCTCATCGAATGAGCTCTTGTCATCATGAACTCTCCACTAGAA
1 -TCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
* *
3715415 ATGTTGATCCCTCGAGTGAGATGTTGTTGATTCAACTCCATATGTGATGAATCAAACAAAGGTTG
65 ATGTTGATCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGATGAATCAAGCAAAGGTTG
3715480 AATAAGTTC
130 AATAAGTTC
*
3715489 TTCTCATTATGAACTTGTTCTCCCTCATC-AGATGAGTTCTTCTCATTATGAACTCTCCACTGGA
1 -TCTCATTATGAACTTCTTCTCCCTCATCGA-ATGAGTTCTTCTCATTATGAACTCTCCACTGGA
* * * * * **
3715553 AATATTGATCCCTCAAGTGAGGTATT-TCTGATTCAACTCCATATGTGATAAATCGAGTTAAGGT
64 AATGTTGATCCCTCGAGTGAGGTGTTGT-TGATTCAACTCCATATGTGATGAATCAAGCAAAGGT
*
3715617 TGAATAACTTTC
128 TGAATAA-GTTC
* * *
3715629 TCTCATTATGAACTTCTTCTCCCTCAT-GGATGAGTTATTCTCATTATGAACTCTCCAATGGAAA
1 TCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAA
3715693 TGTTGA
66 TGTTGA
3715699 CTGGTTTACC
Statistics
Matches: 311, Mismatches: 33, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
138 40 0.13
139 268 0.86
140 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (138 bp):
TCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCACTGGAAA
TGTTGATCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGATGAATCAAGCAAAGGTTGA
ATAAGTTC
Found at i:3716133 original size:36 final size:36
Alignment explanation
Indices: 3716022--3716286 Score: 170
Period size: 36 Copynumber: 7.2 Consensus size: 36
3716012 ATTGTCTCTG
* *
3716022 GTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGA
1 GTGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAA
* * ** ***
3716058 GTGAGATAAATTTCTTGTTTCGAGTAAAATTTATCTCAA
1 GTGAGATGAA-GT-TTGTTTTAAG-AAAAACAATCTCAA
*
3716097 GTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAA
1 GTGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAA
* ****** * * ***
3716133 GTGAGATAAACAAAAAATTTGAGTGAAAATTGTCTCAA
1 GTGAGATGAA-GTTTGTTTTAAG-AAAAACAATCTCAA
* *
3716171 GCGAGATGAAGTTTGTTTTAAGAAAAATAATCTCAA
1 GTGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAA
* * ** ** **
3716207 GTGAGATAAAATTTTGTTTCGAGTGAAACTGTCTCAA
1 GTGAGAT-GAAGTTTGTTTTAAGAAAAACAATCTCAA
* *
3716244 GCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCGA
1 GTGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAA
3716280 GTGAGAT
1 GTGAGAT
3716287 AAAATTTTGT
Statistics
Matches: 160, Mismatches: 63, Indels: 12
0.68 0.27 0.05
Matches are distributed among these distances:
36 70 0.44
37 45 0.28
38 27 0.17
39 18 0.11
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (36 bp):
GTGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAA
Found at i:3716276 original size:73 final size:73
Alignment explanation
Indices: 3716024--3716324 Score: 406
Period size: 74 Copynumber: 4.1 Consensus size: 73
3716014 TGTCTCTGGT
* * *
3716024 GAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAATTTCTTGTTTCGAGTAAAATT
1 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT-TTGTTTCGAGTAAAA-T
*
3716089 TATCTCAAGT
64 TATCTCAAGC
* *****
3716099 GAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACAAAAAATTT-GAGTGAAAAT
1 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA-ATTTTGTTTCGAGT-AAAAT
*
3716163 TGTCTCAAGC
64 TATCTCAAGC
* * * *
3716173 GAGATGAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACTG
1 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTAAAATTA
3716238 TCTCAAGC
66 TCTCAAGC
*
3716246 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTTGTTTCGAGTAAAAATT
1 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGT-AAAATT
3716311 ATCTCAAGC
65 ATCTCAAGC
3716320 GAGAT
1 GAGAT
3716325 AAAGATCCCT
Statistics
Matches: 199, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
73 73 0.37
74 76 0.38
75 50 0.25
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (73 bp):
GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTAAAATTA
TCTCAAGC
Found at i:3716309 original size:147 final size:149
Alignment explanation
Indices: 3716010--3716324 Score: 420
Period size: 147 Copynumber: 2.1 Consensus size: 149
3716000 AAATTTAGGG
** * * * *
3716010 AAATTGTCTCTGGTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAATTTCTTG
1 AAATTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTCTTG
* *
3716075 TTTCGAGTAAAATTTATCTCAAGTGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
66 TTTCGAGTAAAATCTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
*
3716140 AAACAAAAAATTTGAGTGA
131 AAACAAAAAATTTGAGTAA
*
3716159 AAATTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATT-TTG
1 AAATTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTCTTG
* * * *
3716223 TTTCGAGTGAAA-CTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCGAGTGAGAT
66 TTTCGAGTAAAATCTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
*****
3716287 AAA-ATTTTGTTTCGAGTAA
131 AAACAAAAAATTT-GAGTAA
*
3716306 AAATTATCTCAAGCGAGAT
1 AAATTGTCTCAAGCGAGAT
3716325 AAAGATCCCT
Statistics
Matches: 145, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
146 4 0.03
147 73 0.50
148 14 0.10
149 54 0.37
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (149 bp):
AAATTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTCTTG
TTTCGAGTAAAATCTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAACAAAAAATTTGAGTAA
Found at i:3716616 original size:145 final size:144
Alignment explanation
Indices: 3716342--3716721 Score: 481
Period size: 145 Copynumber: 2.6 Consensus size: 144
3716332 CCTCAAGTGA
* * * * * *
3716342 GGCGTTGTTGATTTGAAATGTCGTGAATCAAGAAAAGGAAATGTTGAAAACATCGTACCTGAAGG
1 GGCGTTGATGATTTG-AATGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCATACCCGAAGG
* * * * **
3716407 TCTTATAGATAGCCCGAAGGACTTAAGCTGATTTGAATTGTTGTGAATCAAGAAATATGGAATGT
65 TCTTATGGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCAAGAAATATAAAATGT
* *
3716472 TAACCTCTCTGGTGG
130 TAACCCCTCTGGTAG
* * * *
3716487 GGTGTTGATGATTTGCAATGTTGTGAATCGAGCAAAGGAAATGTTAAAAACATCATGCCCAAAGG
1 GGCGTTGATGATTTG-AATGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCATACCCGAAGG
* * *
3716552 TCTTATGGATGGCCCGAAGGACTTCAGCTGATTCGAAGTGTTGTGAATCGAGCAATATAAAATGT
65 TCTTATGGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCAAGAAATATAAAATGT
3716617 TAACCCCTCTGGTAG
130 TAACCCCTCTGGTAG
* * * *
3716632 GGCATTGCTGATTTGAAGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAACATCCTACCCGAAGG
1 GGCGTTGATGATTTGAA-TGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCATACCCGAAGG
* * *
3716697 TCTTATGGATGTCCCAAATGACTTA
65 TCTTATGGATGGCCCGAAGGACTTA
3716722 TCCTCTTGCT
Statistics
Matches: 200, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
144 2 0.01
145 198 0.99
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (144 bp):
GGCGTTGATGATTTGAATGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCATACCCGAAGGT
CTTATGGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCAAGAAATATAAAATGTT
AACCCCTCTGGTAG
Found at i:3717041 original size:53 final size:53
Alignment explanation
Indices: 3716866--3717282 Score: 506
Period size: 53 Copynumber: 7.9 Consensus size: 53
3716856 TTACAATTAT
* **
3716866 CATCAAGAAACCCCTAAAAATTAGGATTAGCTTCTATAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCT-TTCAAATTCATTTGAAAA
* * ** * * *
3716920 CATCAAAAAACCCCTAAAAATCAGGCTTAATTTCTTTGAAAGATCA----AATA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAA-TTCATTTGAAAA
* ** * *
3716970 -ATCAAGAAACTTCC-AAAAATTCA-TTTTAGTTTCTTTCAAATTCATTTGAAGA
1 CATCAAGAAAC-CCCTAAAAATT-AGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* **
3717022 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTCCCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
3717075 CATCAAGAAACCCCTAAAAATTAGTCTTAGCTTCTTTTAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
3717128 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCATTTGAAAT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
3717181 CATCAAGAAACTCCTAAAAATTAGGCTTCGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* *
3717234 CATCAAGAAACCCGCTAAAAATTAGACTTAGCTTCTTTCAAATTAATTT
1 CATCAAGAAACCC-CTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTT
3717283 TGTCAATAAA
Statistics
Matches: 310, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
48 3 0.01
49 28 0.09
50 6 0.02
52 6 0.02
53 202 0.65
54 65 0.21
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
Found at i:3717382 original size:55 final size:55
Alignment explanation
Indices: 3717295--3717539 Score: 321
Period size: 55 Copynumber: 4.5 Consensus size: 55
3717285 TCAATAAATA
** * * *
3717295 TCTAAAAATTAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
1 TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACT
* * *
3717350 TC-ATAAAATCAAACTTAGTTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACT
1 TCTA-AAAACCAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACT
* * *
3717405 TCTAAAAGCCAGACTTAGTTTCTTTAAAATCTCATTTGAAAATCATCAAGAATCT
1 TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACT
* * * ** *
3717460 TTTAAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTGAAAATTGTCAAGAATCT
1 TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACT
3717515 TCTAAAAACCAGACTTAGTTTCTTT
1 TCTAAAAACCAGACTTAGTTTCTTT
3717540 CAAATTCATT
Statistics
Matches: 167, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
54 1 0.01
55 165 0.99
56 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (55 bp):
TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACT
Found at i:3717427 original size:110 final size:110
Alignment explanation
Indices: 3717295--3717539 Score: 357
Period size: 110 Copynumber: 2.2 Consensus size: 110
3717285 TCAATAAATA
** * *
3717295 TCTAAAAATTAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCAT-AAAAT
1 TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCATCAAGAAACTT-ATAAAAAT
3717359 CAAACTTAGTTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACT
65 CAAACTTAGTTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACT
* * * * *
3717405 TCTAAAAGCCAGACTTAGTTTCTTTAAAATCTCATTTGAAAATCATCAAGAATCTTTTAAAAATC
1 TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCATCAAGAAACTTATAAAAATC
* * * *
3717470 AGACTTAGTTTCTTTGAAAGCTCATTTGAAAATTGTCAAGAATCT
66 AAACTTAGTTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACT
3717515 TCTAAAAACCAGACTTAGTTTCTTT
1 TCTAAAAACCAGACTTAGTTTCTTT
3717540 CAAATTCATT
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
109 1 0.01
110 119 0.99
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (110 bp):
TCTAAAAACCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCATCAAGAAACTTATAAAAATC
AAACTTAGTTTCTTTAAAAGCTCATTTGAAAATCGTCAAGAAACT
Found at i:3718777 original size:28 final size:28
Alignment explanation
Indices: 3718737--3718817 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
3718727 TTAGGATGTC
3718737 TTGT-GAAGGTAATGTGTTTCAGGTTAAT
1 TTGTGGAA-GTAATGTGTTTCAGGTTAAT
3718765 TTGTGGAAGTAATGTGTTTCAGGTTAAT
1 TTGTGGAAGTAATGTGTTTCAGGTTAAT
* *
3718793 TTGGGGAGGTAATGTGTTTCAGGTT
1 TTGTGGAAGTAATGTGTTTCAGGTT
3718818 TGCTTATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 47 0.94
29 3 0.06
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.42
Consensus pattern (28 bp):
TTGTGGAAGTAATGTGTTTCAGGTTAAT
Found at i:3719473 original size:7 final size:7
Alignment explanation
Indices: 3719452--3719583 Score: 180
Period size: 7 Copynumber: 18.9 Consensus size: 7
3719442 GTTTTATTTC
*
3719452 TTCTTTA
1 TTCTTTT
3719459 TT-TTTT
1 TTCTTTT
3719465 TTCTTTT
1 TTCTTTT
3719472 TT-TTTT
1 TTCTTTT
3719478 TT-TTTT
1 TTCTTTT
*
3719484 TTTTTTT
1 TTCTTTT
*
3719491 TTTTTTT
1 TTCTTTT
3719498 TCTCTTTT
1 T-TCTTTT
3719506 TTCTTTT
1 TTCTTTT
3719513 TTCTTTT
1 TTCTTTT
3719520 TTCTTTT
1 TTCTTTT
3719527 TTCTTTT
1 TTCTTTT
3719534 TTCTTTT
1 TTCTTTT
*
3719541 TTTTTTT
1 TTCTTTT
3719548 TTCTTTT
1 TTCTTTT
3719555 TTCTTTT
1 TTCTTTT
3719562 TTCTTTT
1 TTCTTTT
3719569 CTATCTTTT
1 -T-TCTTTT
3719578 TTCTTT
1 TTCTTT
3719584 ACTTTTTTTA
Statistics
Matches: 116, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
6 17 0.15
7 85 0.73
8 8 0.07
9 6 0.05
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (7 bp):
TTCTTTT
Found at i:3719579 original size:1 final size:1
Alignment explanation
Indices: 3719459--3719568 Score: 121
Period size: 1 Copynumber: 110.0 Consensus size: 1
3719449 TTCTTCTTTA
* * * * * *
3719459 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTCTTTTTTCTTTTTTCTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
3719524 TTTTTCTTTTTTCTTTTTTTTTTTTTCTTTTTTCTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3719569 CTATCTTTTT
Statistics
Matches: 87, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 87 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:3720972 original size:20 final size:20
Alignment explanation
Indices: 3720944--3720989 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3720934 AAAAGATGTG
*
3720944 AAGAAGCACATACAAATGCA
1 AAGATGCACATACAAATGCA
3720964 AAGATGCACATACAAATGCA
1 AAGATGCACATACAAATGCA
3720984 AAGATG
1 AAGATG
3720990 AAAAAATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.13
Consensus pattern (20 bp):
AAGATGCACATACAAATGCA
Found at i:3724649 original size:26 final size:28
Alignment explanation
Indices: 3724602--3724660 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
3724592 AATTAATTTA
* * *
3724602 AAATAAAAATAAATAAATCAATG-A-CC
1 AAATTAAAATAAACAAAGCAATGTATCC
*
3724628 AAATTAAAATAAACGAAGCAATGTATCC
1 AAATTAAAATAAACAAAGCAATGTATCC
3724656 AAATT
1 AAATT
3724661 CGAAACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.70
27 1 0.04
28 7 0.26
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (28 bp):
AAATTAAAATAAACAAAGCAATGTATCC
Found at i:3724976 original size:591 final size:587
Alignment explanation
Indices: 3723850--3724985 Score: 1784
Period size: 591 Copynumber: 1.9 Consensus size: 587
3723840 ATAAATACTA
3723850 AAATGAAATATTGCAAAAGTTAAAGTGCTAAATAAACAAGATTAAATAATAAAGAGCCAGAAGAA
1 AAATGAAATATTGCAAAAGTTAAAGTGCTAAATAAACAAGATTAAATAATAAAGAGCCAGAAGAA
*
3723915 ACTTACAATAAATAAAAGACACTCAAATGTAAATAAAAGGAACTAAGGTGCTCAAATTAAAAATA
66 ACTTACAATAAATAAAAGACACTCAAATGTAAATAAAAGGAACTAAGGTGCTCAAATTAAAAAAA
3723980 TGGAAGAAAATAAAAGTGAGAAATTAATTTAAAATAAAAAAACATAAATCAATGACCAAATTAAA
131 TGGAAGAAAATAAAAGTGAGAAATTAATTTAAAATAAAAAAACATAAATCAATGACCAAATTAAA
* *
3724045 ATAAAAGAAACAATGCATCCAAATTCGAAAAAAATAAATTAAAAGAACTTCACTGACCAATGTGC
196 ATAAAAGAAACAATGCATCCAAATTCGAAAAAAATAAAATAAAAGAACTTCACTGACCAATATGC
3724110 TAAAACAAGATAAACATAAAGGGATTATTTCATAATTTTCCCTATTTTAAATGATTAAAATGCAG
261 TAAAACAAGATAAACATAAAGGGATTATTTCATAATTTTCCCTATTTTAAATGATTAAAATGCAG
* *
3724175 AGAAACTCTAAATAGTTAAGGACCTAAAGATGATTTAACCTAGGATTAGTGAAAAAAATGTAAAA
326 AGAAACTCTAAATAGTGAAGGACATAAAGATGATTTAACCTAGGATTAGTGAAAAAAATGTAAAA
* *
3724240 TCACGCCTAAAGTATGGGGGGTAACAAGTGGTTTTACCTCTAAATCAGTGACATAAACGTAAAAT
391 TCACGCCTAAAGTATGGGGGCTAACAAGTGGTTTTACCTCTAAATCAGTGACATAAACATAAAAT
* * *
3724305 CAAGCTAAAGTTACAGGGACCTTATCAGAATTTACCCTAAAGTCTAAATATGTTAGTTGTTTCTT
456 CAAGCTAAAGTTACAGGGACCTTATCAGAATTTACCATAAAGTCTAAATATGTAAGTCGTTTCTT
*
3724370 CCTATTATGGTAAAAAAATTACAAAAGTTAAATGAAATAAAAAAAATCAAGCACTTTAACTTTTC
521 CCTATTATAGTAAAAAAATTA-AAAAGTTAAATGAAATAAAAAAAATCAAGCACTTTAACTTTTC
3724435 AAT
585 AAT
* * *
3724438 AAATGAAATATTGTAAAAGTTAAAGTGCTAAATAAACAAGATTAAATAATAAAGATCCATAAGTA
1 AAATGAAATATTGCAAAAGTTAAAGTGCTAAATAAACAAGATTAAATAATAAAGAGCCAGAAG-A
*
3724503 AA-TTACAATAAATAAAAGATACTCAAATGTAAATAAAAGGAACTAAGGTGCTCAAATTAAAAAA
65 AACTTACAATAAATAAAAGACACTCAAATGTAAATAAAAGGAACTAAGGTGCTCAAATTAAAAAA
*
3724567 ATGGAAGAAAATAAAAAAAGTGAGCAATTAATTTAAAATAAAAATAA-ATAAATCAATGACCAAA
130 ATGGAAGAAAAT---AAAAGTGAGAAATTAATTTAAAATAAAAA-AACATAAATCAATGACCAAA
* * * *
3724631 TTAAAATAAACGAAGCAATGTATCCAAATTCGAAACAAAATAAAAT-AAAGAACTTCAGTGACCA
191 TTAAAATAAAAGAAACAATGCATCCAAATTCGAAA-AAAATAAAATAAAAGAACTTCACTGACCA
* * * *
3724695 ATATGCTAAAACAAGCTAAACATAAAGGGGTTGA-TTCATAATTTTCCCTATTTTAAATGGTTAG
255 ATATGCTAAAACAAGATAAACATAAAGGGATT-ATTTCATAATTTTCCCTATTTTAAATGATTAA
* * * * * * *
3724759 AATGCATAGAGACTCTAAATAGTGGAGGATATAAAGGTGGTTTAACCTAGGATTAGTGATAAAAA
319 AATGCAGAGAAACTCTAAATAGTGAAGGACATAAAGATGATTTAACCTAGGATTAGTGAAAAAAA
* *
3724824 TGTAAAATCACGCCTAAAGTATGGGTGCTAAC-TGATGGTTTTACC-CTTAAATCAGTGATC-TA
384 TGTAAAATCACGCCTAAAGTATGGGGGCTAACAAG-TGGTTTTACCTC-TAAATCAGTGA-CATA
* *
3724886 AACATAAAATCAAGCTAAAGTTATAGGGACCTTATCATAATTTACCATAAAGTCTAAATATGTAA
446 AACATAAAATCAAGCTAAAGTTACAGGGACCTTATCAGAATTTACCATAAAGTCTAAATATGTAA
*
3724951 GTCG-TTCATTCCTATTCTAGTAAAAAAATTAAAAA
511 GTCGTTTC-TTCCTATTATAGTAAAAAAATTAAAAA
3724986 CCAAAAAAAG
Statistics
Matches: 501, Mismatches: 36, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
588 132 0.26
589 3 0.01
590 9 0.02
591 344 0.69
592 13 0.03
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (587 bp):
AAATGAAATATTGCAAAAGTTAAAGTGCTAAATAAACAAGATTAAATAATAAAGAGCCAGAAGAA
ACTTACAATAAATAAAAGACACTCAAATGTAAATAAAAGGAACTAAGGTGCTCAAATTAAAAAAA
TGGAAGAAAATAAAAGTGAGAAATTAATTTAAAATAAAAAAACATAAATCAATGACCAAATTAAA
ATAAAAGAAACAATGCATCCAAATTCGAAAAAAATAAAATAAAAGAACTTCACTGACCAATATGC
TAAAACAAGATAAACATAAAGGGATTATTTCATAATTTTCCCTATTTTAAATGATTAAAATGCAG
AGAAACTCTAAATAGTGAAGGACATAAAGATGATTTAACCTAGGATTAGTGAAAAAAATGTAAAA
TCACGCCTAAAGTATGGGGGCTAACAAGTGGTTTTACCTCTAAATCAGTGACATAAACATAAAAT
CAAGCTAAAGTTACAGGGACCTTATCAGAATTTACCATAAAGTCTAAATATGTAAGTCGTTTCTT
CCTATTATAGTAAAAAAATTAAAAAGTTAAATGAAATAAAAAAAATCAAGCACTTTAACTTTTCA
AT
Found at i:3740539 original size:46 final size:49
Alignment explanation
Indices: 3740471--3740565 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 49
3740461 ATAATCATAT
* * * *
3740471 CCTAACCTCATGCTTTCTAGTTC-CAT-CCTTTATTCAGGAAA-AATAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCATTTATTCAGAAAATAATAA
*
3740517 CCTAACCGCATGATTTTTAGTTCGCATGCATTTATTCAGAAAATAATAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCATTTATTCAGAAAATAATAA
3740566 TAAATAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 20 0.49
47 3 0.07
48 13 0.32
49 5 0.12
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (49 bp):
CCTAACCGCATGATTTCTAGTTCGCATGCATTTATTCAGAAAATAATAA
Found at i:3742990 original size:16 final size:15
Alignment explanation
Indices: 3742969--3743012 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
3742959 GCCTTCGGTC
3742969 TATATAAATAATAAT
1 TATATAAATAATAAT
*
3742984 ATATATAATATAATTAT
1 -TATATAA-ATAATAAT
3743001 TATATACAATAA
1 TATATA-AATAA
3743013 CGTATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAAATAATAAT
Found at i:3743004 original size:18 final size:17
Alignment explanation
Indices: 3742969--3743006 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3742959 GCCTTCGGTC
3742969 TATATAA-ATAATAATA
1 TATATAATATAATAATA
*
3742985 TATATAATATAATTAT-
1 TATATAATATAATAATA
3743001 TATATA
1 TATATA
3743007 CAATAACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATAATATAATAATA
Found at i:3748754 original size:31 final size:31
Alignment explanation
Indices: 3748719--3748790 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
3748709 TATATTGGGT
* *
3748719 TGGGTCAGGCCCCCTACAGGGCTTACTGTGC
1 TGGGTAAGGCCCCCTACAGGGCCTACTGTGC
* * *
3748750 TGGGTTAGGCCCCCTACCGGGCCTGCTGTGC
1 TGGGTAAGGCCCCCTACAGGGCCTACTGTGC
3748781 TGGGTAAGGC
1 TGGGTAAGGC
3748791 TAGTATGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (31 bp):
TGGGTAAGGCCCCCTACAGGGCCTACTGTGC
Found at i:3748893 original size:19 final size:19
Alignment explanation
Indices: 3748849--3748885 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3748839 AAAGAAAAAA
*
3748849 GAAAAATAAATGAATAAAT
1 GAAAAATAAATAAATAAAT
3748868 GAAAAATAAATAAATAAA
1 GAAAAATAAATAAATAAA
3748886 ATGTAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
GAAAAATAAATAAATAAAT
Found at i:3748967 original size:37 final size:36
Alignment explanation
Indices: 3748909--3749014 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 36
3748899 TGAAAATTAC
*
3748909 ATATTACATATATTTTAAAAATGTTTTCAAAATCAT
1 ATATTATATATATTTTAAAAATGTTTTCAAAATCAT
* * *
3748945 ATATTATATATAGTTTTGAAAATGTTTTCTAAATTAT
1 ATATTATATATA-TTTTAAAAATGTTTTCAAAATCAT
*
3748982 ATATTATATATATTTTTCAAAATGTTTTCAAAA
1 ATATTATATATA-TTTTAAAAATGTTTTCAAAA
3749015 ATGTGTTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 11 0.18
37 51 0.82
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (36 bp):
ATATTATATATATTTTAAAAATGTTTTCAAAATCAT
Found at i:3749047 original size:49 final size:50
Alignment explanation
Indices: 3748967--3749064 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 50
3748957 GTTTTGAAAA
* *
3748967 TGTTTTCTAAATTATATATTATATATATTTTTCAAA-ATGTTTTCAAAAATG
1 TGTTTTCAAAATTATATA-TATATATATTTTT-AAACATATTTTCAAAAATG
*
3749018 TGTTTTCAAAATTATATA-ATATATGTTTTTAAATCATATTTTCAAAA
1 TGTTTTCAAAATTATATATATATATATTTTTAAA-CATATTTTCAAAA
3749065 CCATATTATG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 3 0.07
49 11 0.26
50 11 0.26
51 17 0.40
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (50 bp):
TGTTTTCAAAATTATATATATATATATTTTTAAACATATTTTCAAAAATG
Found at i:3754501 original size:15 final size:15
Alignment explanation
Indices: 3754468--3754499 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3754458 TCAATATTTG
3754468 TTTT-TTTTTAATAT
1 TTTTATTTTTAATAT
3754482 TTTTATTTTTAA-AT
1 TTTTATTTTTAATAT
3754496 TTTT
1 TTTT
3754500 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTAATAT
Found at i:3773073 original size:37 final size:37
Alignment explanation
Indices: 3773020--3773123 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 37
3773010 CATTTTCGTC
3773020 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3773057 TTGCTAGGATTCAAACTCC-AAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3773093 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3773124 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 29 0.52
37 27 0.48
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3773518 original size:18 final size:17
Alignment explanation
Indices: 3773479--3773521 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3773469 ATTATATGGA
*
3773479 TATT-TTATTTATTTAT
1 TATTATTATTCATTTAT
*
3773495 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
3773513 TATTATTAT
1 TATTATTAT
3773522 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:3774026 original size:38 final size:40
Alignment explanation
Indices: 3773975--3774051 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
3773965 ATTGGGAGGG
*
3773975 TAGCTTTTCTA-TTT-TTAAGTA-TTTGGTATATATATATA
1 TAGCTTTTCTATTTTATTAA-TACTTTGATATATATATATA
3774013 TAGCTTATT-TATTTTATTAATACTTTGATATATATATAT
1 TAGCTT-TTCTATTTTATTAATACTTTGATATATATATAT
3774052 TTATATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
38 8 0.24
39 7 0.21
40 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATTAATACTTTGATATATATATATA
Found at i:3779352 original size:72 final size:75
Alignment explanation
Indices: 3779260--3779434 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 75
3779250 ATGCAGATGA
* * * *
3779260 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTATTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCATTTTCACTC
3779322 GAAAGAA-G-AT
64 GAAAGAAGGCAT
* * *
3779332 TTATTTCACTCAAGATTGTTTTTCTTAAAATAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCATTTTCACTCGA
3779397 AAGAAGGCAT
66 AAGAAGGCAT
**
3779407 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
3779435 GAAGATTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 48 0.55
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.22
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCATTTTCACTCGA
AAGAAGGCAT
Found at i:3779469 original size:73 final size:72
Alignment explanation
Indices: 3779276--3779471 Score: 170
Period size: 73 Copynumber: 2.7 Consensus size: 72
3779266 CACTCAAATT
* * * *
3779276 TGTTTTTCTTAAA-ACATACTTTGTCTCACTTGAGACTA-TTTT-TCTCGAAAGAAGATTTATTT
1 TGTTTTTCTTAAAGA-AGA-TTTATCTCGCTTGAGAC-AGTTTTCACTCGAAAGAAGATTTATTT
*
3779338 CACTCAAGAT
63 CACTCAAGAC
* * *
3779348 TGTTTTTCTTAAAATAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAAGAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
3779413 TCACTCAAGGC
62 TCACTCAAGAC
* * *
3779424 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAAGAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
3779472 CAGAAAATTT
Statistics
Matches: 104, Mismatches: 12, Indels: 15
0.79 0.09 0.11
Matches are distributed among these distances:
72 30 0.29
73 32 0.31
74 17 0.16
75 6 0.06
76 19 0.18
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAAGAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:3779493 original size:39 final size:39
Alignment explanation
Indices: 3779450--3779602 Score: 128
Period size: 39 Copynumber: 3.6 Consensus size: 39
3779440 TTTTATCTTG
3779450 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * *
3779489 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGATAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
3779541 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
3779579 CTTGAGATAGTTTCTCTTGAAACA
1 CTTGAGATAGTTTCCCTCGAAACA
3779603 TAAACATTGA
Statistics
Matches: 90, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
38 2 0.02
39 46 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 24 0.27
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:3779688 original size:106 final size:105
Alignment explanation
Indices: 3779505--3779824 Score: 488
Period size: 106 Copynumber: 3.1 Consensus size: 105
3779495 ACAGTTTCTC
* *
3779505 TTGAAAACATTTCCCTTGAAATTA-ATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
3779569 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
3779609 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-TATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
*
3779674 ATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
3779715 TTGAAAACATTTCCCTTGAAATGA-ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA-TG--AA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
** *
3779776 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
3779816 TTGAAAACA
1 TTGAAAACA
3779825 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 52 0.26
106 100 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:3779771 original size:36 final size:36
Alignment explanation
Indices: 3779724--3779799 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
3779714 ATTGAAAACA
* *
3779724 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
*
3779760 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
3779796 TTTC
1 TTTC
3779800 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
Found at i:3780201 original size:105 final size:106
Alignment explanation
Indices: 3779999--3780419 Score: 586
Period size: 105 Copynumber: 4.0 Consensus size: 106
3779989 ATATCGTGAC
* ** * *
3779999 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCTC
3780064 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3780105 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AATAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCTC
3780169 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3780210 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGTTGCTTGTCAAC-AA-AA-TT-TC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCTC
* *
3780271 -A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * *
3780310 ACTAGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCTC
* * * *
3780375 GATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3780416 ACTC
1 ACTC
3780420 GGAACAATGC
Statistics
Matches: 283, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
100 81 0.29
101 3 0.01
102 4 0.01
103 4 0.01
104 3 0.01
105 105 0.37
106 83 0.29
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3780311 original size:205 final size:212
Alignment explanation
Indices: 3779999--3780419 Score: 595
Period size: 205 Copynumber: 2.0 Consensus size: 212
3779989 ATATCGTGAC
* * ** *
3779999 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTCCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
* *
3780064 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACACAAGTTCAACT
* * *
3780129 TCACGACGAAGGGACCGCTGCTTGTCAAC-AATAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCCCAATTCCAGAGCCAATTTCAACTTC
3780193 ACAACGAAGGATATTGG
196 ACAACGAAGGATATTGG
* * *
3780210 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGTTGCTTGTCAAC-AA-AA-TT-TC
1 ACTCCAGACAACACAAGTTCAACTCCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
* * *
3780271 -A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTAGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACACAAGTTCAACT
* * * *
3780334 TCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCCCAATTCCAGAGCCAATTTCAACTTC
* *
3780399 ACGACGGAGGATATTGG
196 ACAACGAAGGATATTGG
3780416 ACTC
1 ACTC
3780420 GGAACAATGC
Statistics
Matches: 187, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
205 83 0.44
206 51 0.27
207 2 0.01
208 2 0.01
209 2 0.01
210 2 0.01
211 45 0.24
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (212 bp):
ACTCCAGACAACACAAGTTCAACTCCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACACAAGTTCAACT
TCACAACGAAGGGACCGCTGCTTGTCAACAAATAACTTCCCAATTCCAGAGCCAATTTCAACTTC
ACAACGAAGGATATTGG
Found at i:3781014 original size:37 final size:37
Alignment explanation
Indices: 3780961--3781065 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3780951 CATTTTCGTC
3780961 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3780998 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3781035 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3781066 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3781448 original size:18 final size:17
Alignment explanation
Indices: 3781409--3781451 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3781399 ATTATATGGA
*
3781409 TATT-TTATTTATTTAT
1 TATTATTATTCATTTAT
*
3781425 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
3781443 TATTATTAT
1 TATTATTAT
3781452 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:3782566 original size:29 final size:31
Alignment explanation
Indices: 3782498--3782563 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
3782488 TGTTCAAAGT
* *
3782498 TTGGCCATCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
*
3782531 TTGGCCACCAACCAAGATGAAATTTTC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
3782561 TTG
1 TTG
3782564 CCAACTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:3784966 original size:23 final size:23
Alignment explanation
Indices: 3784940--3785010 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
3784930 GTTTAGGGTA
* *
3784940 GGCTCTGGGTCGGGTTCAGTTTG
1 GGCTCTGGTTCAGGTTCAGTTTG
*
3784963 GGCTCTGGTTCAGGTT-TGATTTG
1 GGCTCTGGTTCAGGTTCAG-TTTG
* *
3784986 GGCTCCGGTTCAGGTTCGGTTTG
1 GGCTCTGGTTCAGGTTCAGTTTG
3785009 GG
1 GG
3785011 TTTTAGGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.95
24 1 0.02
ACGTcount: A:0.06, C:0.17, G:0.41, T:0.37
Consensus pattern (23 bp):
GGCTCTGGTTCAGGTTCAGTTTG
Found at i:3785030 original size:23 final size:22
Alignment explanation
Indices: 3785004--3785046 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3784994 TTCAGGTTCG
*
3785004 GTTTGGGTTTTAGGTTGTGGCCT
1 GTTTGGGTTGTAGGTT-TGGCCT
3785027 GTTTGGGTTGTAGGTTTGGC
1 GTTTGGGTTGTAGGTTTGGC
3785047 TTGTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.05, C:0.07, G:0.42, T:0.47
Consensus pattern (22 bp):
GTTTGGGTTGTAGGTTTGGCCT
Found at i:3785853 original size:240 final size:239
Alignment explanation
Indices: 3785512--3786208 Score: 871
Period size: 240 Copynumber: 2.9 Consensus size: 239
3785502 CAAATGACGA
* *
3785512 ACTAAGTAAGAAACTTTGGAAAT-AGTTTTCTTACTCTTCAGAAAAATCAATTTTCAGAAAATAT
1 ACTAAGTAAGAAACTTTGGAAATCA-TTTTCTTACTTTTCAGAAAAATCAATTTTCAGAAAAGAT
* * *
3785576 TTAAATGAGAAACTTTGGAATTCTCTTTCTCATTTTTCAAAAATCATGTGTAAACATTCTACCCG
65 TTAAATGAGAAACTTTGGAAATC-ATTTCTCATTTTTCAAAAATCATGTGAAAACATTCTACCCG
* * * * *
3785641 AAGATCATATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGGAGG
129 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGG
***
3785706 ATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCAAAGGACTT
194 ATTTAAACATCATGCTCGAAAGACTTACCAATGGCCCAAAGGACTT
* * *** *
3785752 ACTAAATAAGAAACTTTGGAAATCATTTTCTTACTTTTCAGAAAAGTTTGTTTTCATAAAAGATT
1 ACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAGAAAAATCAATTTTCAGAAAAGATT
* * * *
3785817 TAAATGAGAAACTTTGGAAATCGATTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCTGA
66 TAAATGAGAAACTTTGGAAATC-ATTTCTCATTTTTCAAAAATCATGTGAAAACATTCTACCCGA
* *
3785882 AGGTCTTATGGATGGCTCGAAGGACTTATCATCTTACTCGAAAGACTTATAAATGACCCGAAGGA
130 AGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGA
* * * *
3785947 TTTATACATCATGCTCAAAAGACTTACCAATGGCCCGAATGACTT
195 TTTAAACATCATGCTCGAAAGACTTACCAATGGCCCAAAGGACTT
** ** * * *
3785992 ACCCAGTAAGAATA-TTTGGAAATCGCTTTCTTACTTTTCAAGAAAAATCAATTTTGAGACATGA
1 ACTAAGTAAGAA-ACTTTGGAAATCATTTTCTTACTTTTC-AGAAAAATCAATTTTCAGAAAAGA
* ** * *
3786056 TTTAAATGAGAAACATTGGAAATCACTTTCTCATTTTT-TGAAATCATGTCAAAACA-TCTTTCC
64 TTTAAATGAGAAACTTTGGAAATCA-TTTCTCATTTTTCAAAAATCATGTGAAAACATTC-TACC
* * * * * *
3786119 CGAAGGTCTTACGGATGACCCAAAGGACTTATCATTTTGCTCAAAAGACTTATATATGACCCGAA
127 CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAA
*
3786184 GGATTTAAGCATCATGCTCGAAAGA
192 GGATTTAAACATCATGCTCGAAAGA
3786209 TGAGAAACTT
Statistics
Matches: 391, Mismatches: 61, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
239 1 0.00
240 337 0.86
241 53 0.14
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (239 bp):
ACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAGAAAAATCAATTTTCAGAAAAGATT
TAAATGAGAAACTTTGGAAATCATTTCTCATTTTTCAAAAATCATGTGAAAACATTCTACCCGAA
GGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGAT
TTAAACATCATGCTCGAAAGACTTACCAATGGCCCAAAGGACTT
Found at i:3785984 original size:42 final size:41
Alignment explanation
Indices: 3785893--3785992 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
3785883 GGTCTTATGG
* * * *
3785893 ATGGCTCGAAGGACTTATCATCTTACTCGAAAGACTTATAA
1 ATGGCCCGAAGGACTTATCATCATACTCAAAAGACTTACAA
* * * *
3785934 ATGACCCGAAGGATTTATACATCATGCTCAAAAGACTTACCA
1 ATGGCCCGAAGGACTTAT-CATCATACTCAAAAGACTTACAA
*
3785976 ATGGCCCGAATGACTTA
1 ATGGCCCGAAGGACTTA
3785993 CCCAGTAAGA
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (41 bp):
ATGGCCCGAAGGACTTATCATCATACTCAAAAGACTTACAA
Found at i:3786242 original size:147 final size:148
Alignment explanation
Indices: 3786061--3786356 Score: 432
Period size: 148 Copynumber: 2.0 Consensus size: 148
3786051 CATGATTTAA
* *
3786061 ATGAGAAACATTGGAAATCACTTTCTCATTTTTTG-AAATCATGTCAAAACATCTTTCCCGAAGG
1 ATGAGAAACATTGGAAATCACTTTCTCATTTTTTGAAAATCATGTCAAAACATCATGCCCGAAGG
* * * *
3786125 TCTTACGGATGACCCAAAGGACTTATCATTTTGCTCAAAAGACTTATATATGACCCGAAGGATTT
66 TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACCTATAGATGACCCGAAGAATTT
*
3786190 AAGCATCATGCTCGAAAG
131 AAACATCATGCTCGAAAG
* * *
3786208 ATGAGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCTGAAGG
1 ATGAGAAACATTGGAAATCACTTTCTCATTTTTTGAAAATCATGTCAAAACATCATGCCCGAAGG
* * * ** *
3786273 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGCCCTATAGATGACCCGAAGAATTT
66 TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACCTATAGATGACCCGAAGAATTT
*
3786338 AAACATCTTGCTCGAAAG
131 AAACATCATGCTCGAAAG
3786356 A
1 A
3786357 CTTATTGATG
Statistics
Matches: 131, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
147 34 0.26
148 97 0.74
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (148 bp):
ATGAGAAACATTGGAAATCACTTTCTCATTTTTTGAAAATCATGTCAAAACATCATGCCCGAAGG
TCTTACGGATGACCCAAAGGACTTATCATCTTGCTCAAAAGACCTATAGATGACCCGAAGAATTT
AAACATCATGCTCGAAAG
Found at i:3786330 original size:41 final size:41
Alignment explanation
Indices: 3786280--3786385 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
3786270 AGGTCTTATG
* *
3786280 GATGGCCCGAAGGACTTATCATCTTGCTTGAAAGCCCTATA
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACCTATA
* * * * * *
3786321 GATGACCCGAAGAATTTAAACATCTTGCTCGAAAGACTTATT
1 GATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACCTATA
*
3786363 GATGGCCTGAAGGACTTACTCAT
1 GATGGCCCGAAGGACTTA-TCAT
3786386 AAAGAAACCC
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACCTATA
Found at i:3786567 original size:57 final size:56
Alignment explanation
Indices: 3786439--3786650 Score: 298
Period size: 56 Copynumber: 3.8 Consensus size: 56
3786429 GTTTACAGTT
* * ** * * * *
3786439 ATCATCAAGAAACCCCTTAAAATTAAACCTAACTTCATTAAAAATCATTAGAAATA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTAGAAATA
*
3786495 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTGAAAATTCATTGGAAATA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAATTCATTAGAAATA
* * *
3786552 ATCATCAAGAAACCCCAGAAAATTAGGCTTAGATTCTTTAAAATTCATTAGAAATA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTAGAAATA
*
3786608 ATCATCAAGAAACCCCTGAAAGTCAGGCTTAGCTTCTTTAAAA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAA
3786651 ATTTATCATG
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
56 87 0.63
57 51 0.37
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.27
Consensus pattern (56 bp):
ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTAGAAATA
Found at i:3786593 original size:113 final size:113
Alignment explanation
Indices: 3786439--3786653 Score: 333
Period size: 113 Copynumber: 1.9 Consensus size: 113
3786429 GTTTACAGTT
**
3786439 ATCATCAAGAAACCCCTTAAAATTAAACCTAACTTCATTAAAAATCATTAGAAATAATCATCAAG
1 ATCATCAAGAAACCCCAGAAAATTAAACCTAACTTCATTAAAAATCATTAGAAATAATCATCAAG
*
3786504 AAACCCCTGAAAATCAGGCTTAGCTTCTTTGAAAATTCATTGGAAATA
66 AAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
** * * *
3786552 ATCATCAAGAAACCCCAGAAAATTAGGCTTAGA-TTCTTTAAAATTCATTAGAAATAATCATCAA
1 ATCATCAAGAAACCCCAGAAAATTAAACCTA-ACTTCATTAAAAATCATTAGAAATAATCATCAA
*
3786616 GAAACCCCTGAAAGTCAGGCTTAGCTTCTTTAAAAATT
65 GAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATT
3786654 TATCATGTCA
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 91 0.99
114 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (113 bp):
ATCATCAAGAAACCCCAGAAAATTAAACCTAACTTCATTAAAAATCATTAGAAATAATCATCAAG
AAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
Found at i:3790559 original size:13 final size:13
Alignment explanation
Indices: 3790541--3790572 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3790531 TCAAGGTGAG
3790541 TGAAATACATGCA
1 TGAAATACATGCA
3790554 TGAAATACATGCA
1 TGAAATACATGCA
3790567 TGAAAT
1 TGAAAT
3790573 TATACATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (13 bp):
TGAAATACATGCA
Found at i:3790933 original size:40 final size:40
Alignment explanation
Indices: 3790877--3791038 Score: 252
Period size: 40 Copynumber: 4.0 Consensus size: 40
3790867 TGCAGGTTTA
3790877 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
* * *
3790917 TAATACACTACAGTGTATATGGTGGGTACGACCTTATCTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
* * *
3790957 TAATACACTTCGATGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
* *
3790997 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
3791037 TA
1 TA
3791039 GCACTACGGT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATCTG
Found at i:3794467 original size:56 final size:56
Alignment explanation
Indices: 3794405--3794512 Score: 207
Period size: 56 Copynumber: 1.9 Consensus size: 56
3794395 ACTTGACATA
3794405 AAATCTTAAAAATTATTTGTTAAATTTACAAGTATCAATTCGAATAAAGGGTCTGT
1 AAATCTTAAAAATTATTTGTTAAATTTACAAGTATCAATTCGAATAAAGGGTCTGT
*
3794461 AAATCTTCAAAATTATTTGTTAAATTTACAAGTATCAATTCGAATAAAGGGT
1 AAATCTTAAAAATTATTTGTTAAATTTACAAGTATCAATTCGAATAAAGGGT
3794513 GCTATGAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (56 bp):
AAATCTTAAAAATTATTTGTTAAATTTACAAGTATCAATTCGAATAAAGGGTCTGT
Found at i:3799768 original size:14 final size:13
Alignment explanation
Indices: 3799732--3799779 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
3799722 TAATCTAATT
*
3799732 AAAATAATAAA-A
1 AAAATAAAAAATA
*
3799744 AAAAGAAAAAATA
1 AAAATAAAAAATA
*
3799757 CAACATAAAAAATA
1 -AAAATAAAAAATA
3799771 AAAATAAAA
1 AAAATAAAA
3799780 TAAGCATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 9 0.31
13 9 0.31
14 11 0.38
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:3799787 original size:24 final size:23
Alignment explanation
Indices: 3799738--3799789 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
3799728 AATTAAAATA
*
3799738 ATAAAAAAAAGAAAAAATACAAC
1 ATAAAAAAAAAAAAAAATACAAC
*
3799761 ATAAAAAATAAAAATAAAATA-AGC
1 ATAAAAAA-AAAAA-AAAATACAAC
3799785 ATAAA
1 ATAAA
3799790 CACAAGGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 11 0.44
25 6 0.24
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (23 bp):
ATAAAAAAAAAAAAAAATACAAC
Found at i:3805749 original size:90 final size:89
Alignment explanation
Indices: 3805640--3805814 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 89
3805630 TCCTGAATAT
* *
3805640 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
3805705 GGTAACTTGGAAATAAAAGGATTA
66 GGTAACTTGGAAATAAAAGGATTA
3805729 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
* **
3805794 GGGTAATTTGGCTATAAAAGG
65 GGGTAACTTGGAAATAAAAGG
3805815 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 73 0.91
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAG
GGTAACTTGGAAATAAAAGGATTA
Found at i:3812326 original size:89 final size:90
Alignment explanation
Indices: 3812208--3812384 Score: 293
Period size: 89 Copynumber: 2.0 Consensus size: 90
3812198 TAATCCTGAA
* * *
3812208 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAAT-ATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
3812272 AAGGGTAACTTGGATATAAAAGGAT
66 AAGGGTAACTTGGATATAAAAGGAT
*
3812297 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCTTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
3812362 TAGGGTAACTTGGCTATAAAAGG
66 AAGGGTAACTTGGATATAAAAGG
3812385 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 43 0.53
90 38 0.47
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
AAGGGTAACTTGGATATAAAAGGAT
Found at i:3829121 original size:21 final size:21
Alignment explanation
Indices: 3829095--3829155 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
3829085 ACTCGGGGTC
3829095 CAGTATCGATACTTAGGTAAT
1 CAGTATCGATACTTAGGTAAT
* *
3829116 CAGTATCGATACTTACGTAGT
1 CAGTATCGATACTTAGGTAAT
*
3829137 CAGTATCGATACTGAGGTA
1 CAGTATCGATACTTAGGTA
3829156 TTTTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (21 bp):
CAGTATCGATACTTAGGTAAT
Found at i:3835259 original size:19 final size:17
Alignment explanation
Indices: 3835223--3835267 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3835213 CTCCTCATTG
*
3835223 AATTTTTTATTAATTTT
1 AATTTTTTATTAAATTT
3835240 AATTTATTTAATTAAATTT
1 AATTT-TTT-ATTAAATTT
3835259 -ATTTTTTAT
1 AATTTTTTAT
3835268 CCAATCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 7 0.28
19 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTATTAAATTT
Found at i:3836114 original size:14 final size:14
Alignment explanation
Indices: 3836079--3836106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3836069 AACTAGATAA
3836079 AAATAAATTTAATT
1 AAATAAATTTAATT
3836093 AAATAAATTTAATT
1 AAATAAATTTAATT
3836107 TTATAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATAAATTTAATT
Found at i:3837188 original size:108 final size:111
Alignment explanation
Indices: 3836993--3837218 Score: 325
Period size: 108 Copynumber: 2.0 Consensus size: 111
3836983 CATTTAAGTG
* * *
3836993 AAAAAAATATTAATTTAATTTATGACATGACAATGATTCTGTGAAATTGTGTTTAAATTTAATTA
1 AAAAAAATATCAATTTAATTTATGACAGGACAATGATTCCGTGAAATTGTGTTT--ATTTAATTA
*
3837058 AAATATACCAATTTAATTTGTGATGGAATAATCATTCTGTCGGAAATA
64 AAATATACCAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATA
*
3837106 AAAAAAATATCAATTTAATTTATGACAGGACAATGATTCCGTCGTAA-T-T-TTT-TTTAATTAA
1 AAAAAAATATCAATTTAATTTATGACAGGACAATGATTCCGT-GAAATTGTGTTTATTTAATTAA
* * *
3837167 AATATAGCAATTTAATTTGTGATGTAATATTCATTCCGTCGGAAATA
65 AATATACCAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATA
3837214 AAAAA
1 AAAAA
3837219 TATACATTTA
Statistics
Matches: 104, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
108 57 0.55
111 3 0.03
112 1 0.01
113 40 0.38
114 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (111 bp):
AAAAAAATATCAATTTAATTTATGACAGGACAATGATTCCGTGAAATTGTGTTTATTTAATTAAA
ATATACCAATTTAATTTGTGATGGAATAATCATTCCGTCGGAAATA
Found at i:3839261 original size:25 final size:26
Alignment explanation
Indices: 3839223--3839274 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
3839213 ACGGATTTTA
3839223 AATTTTCCGTCAGTAATATACTGACG
1 AATTTTCCGTCAGTAATATACTGACG
* *
3839249 AATTTT-CGTCAGTAATCTTCTGACG
1 AATTTTCCGTCAGTAATATACTGACG
3839274 A
1 A
3839275 CTTACTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (26 bp):
AATTTTCCGTCAGTAATATACTGACG
Found at i:3839946 original size:2 final size:2
Alignment explanation
Indices: 3839939--3839984 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3839929 TTTGTTGCTT
3839939 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
3839981 TA TA
1 TA TA
3839985 AAAGCTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3846506 original size:21 final size:21
Alignment explanation
Indices: 3846480--3846520 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3846470 ATATATACTT
*
3846480 TAATAAAAAATATAATAATAA
1 TAATAAAAAATAAAATAATAA
*
3846501 TAATAATAAATAAAATAATA
1 TAATAAAAAATAAAATAATA
3846521 TTTTTGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAATAAAAAATAAAATAATAA
Found at i:3852932 original size:2 final size:2
Alignment explanation
Indices: 3852925--3852959 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3852915 TGCCTAAGTA
3852925 AT 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 AT A
3852960 ATCCCTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3854612 original size:3 final size:3
Alignment explanation
Indices: 3854604--3854671 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
3854594 AAATGTAAAT
3854604 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3854652 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
3854672 TTAAAATAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3855918 original size:46 final size:46
Alignment explanation
Indices: 3855852--3856206 Score: 599
Period size: 46 Copynumber: 7.8 Consensus size: 46
3855842 GATAAAATCT
3855852 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
3855897 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3855943 CTTGCCATTTAATCCCATAAGCTCGTAAGTTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3855989 CTTGCCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3856035 CTTACCATTTAATCCCATAAGCTCGTAAGTTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3856081 CTTTCCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATG
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3856127 CTTACCATTTAATCCCATAAGCTCATAAGCTTATGTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3856173 CTTTCCA-TT-ATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
3856207 GCCAGTTTAT
Statistics
Matches: 293, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
44 22 0.08
45 12 0.04
46 259 0.88
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3857667 original size:30 final size:30
Alignment explanation
Indices: 3857633--3857700 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3857623 GAAAACAATA
*
3857633 TTGGT-ACCTAAACTTT-CCAAAGTTAATACT
1 TTGGTCACC-AAACTTTACCAAA-TTAATAAT
*
3857663 TTGGTCACCAAACTTTACCAAATTTATAAT
1 TTGGTCACCAAACTTTACCAAATTAATAAT
3857693 TTGGTCAC
1 TTGGTCAC
3857701 TAAATAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (30 bp):
TTGGTCACCAAACTTTACCAAATTAATAAT
Found at i:3857948 original size:43 final size:43
Alignment explanation
Indices: 3857901--3858031 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 43
3857891 AATGAGGAAG
*
3857901 TCTGGCTATTTAAGGATGACGTTGCTCCTACGTGATGAAGAGA
1 TCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGA
* * ** * *
3857944 TCTGG-TCA-GT--GGATGACACTATTCCTACGCGATGATGATG-
1 TCTGGCT-ATTTAAGGATGACATTGCTCCTACGTGATGAAGA-GA
*
3857984 TATGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGA
1 TCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGA
3858027 TCTGG
1 TCTGG
3858032 TCGGTGGATG
Statistics
Matches: 66, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
40 27 0.41
41 3 0.05
42 3 0.05
43 33 0.50
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
TCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGA
Found at i:3857970 original size:40 final size:40
Alignment explanation
Indices: 3857926--3858061 Score: 123
Period size: 40 Copynumber: 3.3 Consensus size: 40
3857916 ATGACGTTGC
*
3857926 TCCTACGTGATGAAGAGATCTGGTCAGTGGATGACACTAT
1 TCCTACGCGATGAAGAGATCTGGTCAGTGGATGACACTAT
* * * * **
3857966 TCCTACGCGATGATGATG-TATGG-CTATTTAAGGATGACATTGC
1 TCCTACGCGATGAAGA-GATCTGGTC-A-GT--GGATGACACTAT
* *
3858009 TCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACTAT
1 TCCTACGCGATGAAGAGATCTGGTCAGTGGATGACACTAT
*
3858049 TCCTTCGCGATGA
1 TCCTACGCGATGA
3858062 TGATGTCTGG
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
39 1 0.01
40 39 0.54
41 2 0.03
42 2 0.03
43 27 0.38
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (40 bp):
TCCTACGCGATGAAGAGATCTGGTCAGTGGATGACACTAT
Found at i:3858021 original size:83 final size:83
Alignment explanation
Indices: 3857882--3858072 Score: 319
Period size: 83 Copynumber: 2.3 Consensus size: 83
3857872 GATAACTCGG
* * * *
3857882 TTCCTACGCAATGAGGAAGTCTGGCTATTTAAGGATGACGTTGCTCCTACGTGATGAAGAGATCT
1 TTCCTACGCGATGATGATGTCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGATCT
3857947 GGTCAGTGGATGACACTA
66 GGTCAGTGGATGACACTA
*
3857965 TTCCTACGCGATGATGATGTATGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGATCT
1 TTCCTACGCGATGATGATGTCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGATCT
*
3858030 GGTCGGTGGATGACACTA
66 GGTCAGTGGATGACACTA
*
3858048 TTCCTTCGCGATGATGATGTCTGGC
1 TTCCTACGCGATGATGATGTCTGGC
3858073 CATATTTAGG
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (83 bp):
TTCCTACGCGATGATGATGTCTGGCTATTTAAGGATGACATTGCTCCTACGTGATGAAGAGATCT
GGTCAGTGGATGACACTA
Found at i:3859166 original size:6 final size:6
Alignment explanation
Indices: 3859155--3859240 Score: 93
Period size: 6 Copynumber: 13.3 Consensus size: 6
3859145 TTATTTATTT
3859155 TTTTTC TTTTTC TTTTTTTC TTTTTTC TTTTTC TTTTTTC TTTTTC TTTTTCC
1 TTTTTC TTTTTC --TTTTTC -TTTTTC TTTTTC -TTTTTC TTTTTC TTTTT-C
*
3859208 TTTTTC TTTTTCC ATTTTT- ATTTTC TTTTTC TT
1 TTTTTC TTTTT-C -TTTTTC TTTTTC TTTTTC TT
3859241 CTCATTCAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
5 4 0.06
6 36 0.51
7 20 0.28
8 11 0.15
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:3859172 original size:13 final size:13
Alignment explanation
Indices: 3859155--3859240 Score: 111
Period size: 13 Copynumber: 6.6 Consensus size: 13
3859145 TTATTTATTT
*
3859155 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TC
3859169 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
3859182 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
3859195 TTTTTCTTTTTCC
1 TTTTTCTTTTTTC
*
3859208 TTTTTCTTTTTCC
1 TTTTTCTTTTTTC
* *
3859221 ATTTT-TATTTTC
1 TTTTTCTTTTTTC
3859233 TTTTTCTT
1 TTTTTCTT
3859241 CTCATTCAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
12 9 0.14
13 44 0.69
14 11 0.17
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:3859191 original size:19 final size:19
Alignment explanation
Indices: 3859155--3859240 Score: 111
Period size: 19 Copynumber: 4.4 Consensus size: 19
3859145 TTATTTATTT
3859155 TTTTTCTTTTTCTTTTTTTC
1 TTTTTCTTTTTC-TTTTTTC
3859175 TTTTTTCTTTTTCTTTTTTC
1 -TTTTTCTTTTTCTTTTTTC
*
3859195 TTTTTCTTTTTCCTTTTTC
1 TTTTTCTTTTTCTTTTTTC
* *
3859214 TTTTTCCATTTT-TATTTTC
1 TTTTT-CTTTTTCTTTTTTC
3859233 TTTTTCTT
1 TTTTTCTT
3859241 CTCATTCAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.03
19 33 0.56
20 12 0.20
21 12 0.20
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTTTC
Found at i:3865640 original size:17 final size:17
Alignment explanation
Indices: 3865618--3865653 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3865608 AGTATCACAT
*
3865618 TTACTTTTCCAAAACAA
1 TTACTTTTACAAAACAA
*
3865635 TTACTTTTACAAAATAA
1 TTACTTTTACAAAACAA
3865652 TT
1 TT
3865654 GAAAATTCAA
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:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TTACTTTTACAAAACAA
Found at i:3866175 original size:23 final size:21
Alignment explanation
Indices: 3866149--3866202 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3866139 AAATTACACT
3866149 GAAGGACCTCATAGGATTGTCTC
1 GAAGGACCTCATA-GA-TGTCTC
* *
3866172 GAAGGACCACATATATGTCTC
1 GAAGGACCTCATAGATGTCTC
*
3866193 GAAGAACCTC
1 GAAGGACCTC
3866203 GTATAACCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 14 0.52
22 1 0.04
23 12 0.44
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
GAAGGACCTCATAGATGTCTC
Found at i:3878191 original size:72 final size:72
Alignment explanation
Indices: 3878109--3878324 Score: 333
Period size: 72 Copynumber: 3.0 Consensus size: 72
3878099 TATCCAAATA
** * *
3878109 AAATTCATCAAAAATCGTCCTACCCAAACATGCTCTCTACCCTTCTATATTTATCTAATTTAAAC
1 AAATTCATCAAAAAGGGTCCTACCCAAATATGCTCTCTACCCTCCTATATTTATCTAATTTAAAC
3878174 CTAATTG
66 CTAATTG
* *
3878181 AAATTTATCAAAAAGGGTCCTACCTAAATATGCTCTCTACCCTCCTATATTTATCTAATTTAAAC
1 AAATTCATCAAAAAGGGTCCTACCCAAATATGCTCTCTACCCTCCTATATTTATCTAATTTAAAC
3878246 CTAATTG
66 CTAATTG
** * * *
3878253 AAATTCATCAAAAAGGGTCCTACCCAAATATGCTCTCTACCGACCTACATTTATCCAATTAAAAC
1 AAATTCATCAAAAAGGGTCCTACCCAAATATGCTCTCTACCCTCCTATATTTATCTAATTTAAAC
3878318 CTAATTG
66 CTAATTG
3878325 CACATAAATT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 131 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (72 bp):
AAATTCATCAAAAAGGGTCCTACCCAAATATGCTCTCTACCCTCCTATATTTATCTAATTTAAAC
CTAATTG
Found at i:3879175 original size:19 final size:18
Alignment explanation
Indices: 3879130--3879175 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
3879120 AATTATGAAT
*
3879130 TTTTGAATAAATTTAAAA
1 TTTTGAATTAATTTAAAA
3879148 TTTTGAATTAATTTAAAAA
1 TTTTGAATTAATTT-AAAA
3879167 TTTTGAATT
1 TTTTGAATT
3879176 GGAGTCGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTTGAATTAATTTAAAA
Found at i:3879736 original size:14 final size:14
Alignment explanation
Indices: 3879717--3879746 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3879707 AATAAAGAAT
*
3879717 TAAAATAAATAAAA
1 TAAAATAAAAAAAA
3879731 TAAAATAAAAAAAA
1 TAAAATAAAAAAAA
3879745 TA
1 TA
3879747 TAATGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:3880169 original size:15 final size:16
Alignment explanation
Indices: 3880131--3880173 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3880121 ACAGAGCCTC
*
3880131 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
3880147 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
3880163 T-AATCATTCAG
1 TGAATCATTCAG
3880174 AGGTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:3890571 original size:5 final size:6
Alignment explanation
Indices: 3890521--3890586 Score: 60
Period size: 6 Copynumber: 10.0 Consensus size: 6
3890511 TTAATATAAC
* *
3890521 AAAATA AAATTA AAATTA AAACATTA AACATTATA AAAATAA AAAATA
1 AAAATA AAAATA AAAATA AAA-A-TA AA-A--ATA AAAAT-A AAAATA
3890569 AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA
3890587 TAATGATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
6 35 0.67
7 6 0.12
8 5 0.10
9 5 0.10
10 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:3890607 original size:42 final size:42
Alignment explanation
Indices: 3890506--3890607 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 42
3890496 CATTAATACC
* * * *
3890506 AACA-TTTAATATAACAAAATAAAATTAAAATTAAAACATTA
1 AACATTTTAATAAAAAAAAATAAAAATAAAAATAAAACATTA
*
3890547 AACATTATAA-AAATAAAAAATAAAAATAAAAATAAAA-ATATA
1 AACATTTTAATAAA-AAAAAATAAAAATAAAAATAAAACAT-TA
**
3890589 ATGATTTTAATAAAAAAAA
1 AACATTTTAATAAAAAAAA
3890608 TTTGCTCTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
41 8 0.16
42 38 0.78
43 3 0.06
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (42 bp):
AACATTTTAATAAAAAAAAATAAAAATAAAAATAAAACATTA
Found at i:3891336 original size:46 final size:46
Alignment explanation
Indices: 3891284--3891594 Score: 444
Period size: 46 Copynumber: 6.6 Consensus size: 46
3891274 TTATTTGTTA
*
3891284 ATTTTAGTTGTGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
*
3891330 ATTTTAGTTATGGCATCCTTTCATG-ACTTAATGCATCCTTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCA-TTAATGCATCCTTTCATGC
* * * *
3891376 ATTTTAGTTATAGCGTCCTTTCAAGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
* * * *
3891422 ATTTTACTTATAGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
*
3891468 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
3891514 ATTTTAGTTATGGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCA--TTA---AT-GCATCCTTTCATGC
*
3891566 ATTTTAGTTAGGGCATCCTTTCATGCATT
1 ATTTTAGTTATGGCATCCTTTCATGCATT
3891595 TTAGTTAGGT
Statistics
Matches: 241, Mismatches: 16, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
45 1 0.00
46 193 0.80
48 3 0.01
50 2 0.01
51 2 0.01
52 40 0.17
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCATTAATGCATCCTTTCATGC
Found at i:3891603 original size:26 final size:26
Alignment explanation
Indices: 3891284--3891601 Score: 309
Period size: 26 Copynumber: 13.4 Consensus size: 26
3891274 TTATTTGTTA
*
3891284 ATTTTAGTTGTGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891310 A--TTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891330 ATTTTAGTTATGGCATCCTTTCATG-
1 ATTTTAGTTATGGCATCCTTTCATGC
* *
3891355 A-CTTA---AT-GCATCCTTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGC
* * *
3891376 ATTTTAGTTATAGCGTCCTTTCAAGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
3891402 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
* * *
3891422 ATTTTACTTATAGTATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
3891448 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891468 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
3891494 --CTTA---AT-GCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891514 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891540 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
*
3891566 ATTTTAGTTAGGGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC
3891592 ATTTTAGTTA
1 ATTTTAGTTA
3891602 GGTGATTAAA
Statistics
Matches: 245, Mismatches: 17, Indels: 60
0.76 0.05 0.19
Matches are distributed among these distances:
20 67 0.27
21 10 0.04
22 15 0.06
24 15 0.06
25 11 0.04
26 127 0.52
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (26 bp):
ATTTTAGTTATGGCATCCTTTCATGC
Found at i:3899269 original size:24 final size:24
Alignment explanation
Indices: 3899242--3899290 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3899232 AGTCTTTCTG
*
3899242 ATGATGTATAACACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
3899266 ATGATGTATAAAACATCTATTTAC
1 ATGATGTATAAAACATCTATGTAC
3899290 A
1 A
3899291 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:3901375 original size:17 final size:17
Alignment explanation
Indices: 3901353--3901396 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3901343 TGATACCCCC
*
3901353 TTTCAATATTGATATCA
1 TTTCAATATTGATACCA
3901370 TTTCAATATTGATACCA
1 TTTCAATATTGATACCA
*
3901387 TTTCTATATT
1 TTTCAATATT
3901397 ATGTGTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTCAATATTGATACCA
Found at i:3905046 original size:34 final size:33
Alignment explanation
Indices: 3905002--3905090 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
3904992 CCCGTGTGCA
**
3905002 AAGTTGGCCACTTACCAAAGATAGATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATA-ATTTTCCAAT
*
3905036 AAGTTAGCCACCAACC-AAGATTAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGA-TAATTTTCCAAT
3905069 AAGTTGGCCACCAACCAAAGAT
1 AAGTTGGCCACCAACCAAAGAT
3905091 GTCAACTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 30 0.61
34 19 0.39
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAAGATAATTTTCCAAT
Found at i:3905113 original size:16 final size:16
Alignment explanation
Indices: 3905092--3905127 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3905082 ACCAAAGATG
3905092 TCAACTTTGCAAACTT
1 TCAACTTTGCAAACTT
*
3905108 TCAACTTTGCCAACTT
1 TCAACTTTGCAAACTT
3905124 TCAA
1 TCAA
3905128 GCCAAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (16 bp):
TCAACTTTGCAAACTT
Found at i:3907061 original size:21 final size:21
Alignment explanation
Indices: 3907023--3907062 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3907013 TTTGCTGAAA
* *
3907023 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGTAGAGTATG
*
3907044 CTCCACTTGTTGTAGAGTA
1 CTCCACCTGTTGTAGAGTA
3907063 CTACTTGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (21 bp):
CTCCACCTGTTGTAGAGTATG
Found at i:3909795 original size:34 final size:33
Alignment explanation
Indices: 3909750--3909839 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
3909740 CCCATGTGTA
**
3909750 AAGTTGGCCACCTGTCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACC-AACAAAGATGAATTTTCCAAT
* *
3909784 AAGTTGACCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACAAAGATGAATTTTCCAAT
3909817 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAA-CAAAGATG
3909840 TCAACTTTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 31 0.63
34 18 0.37
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (33 bp):
AAGTTGGCCACCAACAAAGATGAATTTTCCAAT
Found at i:3909809 original size:33 final size:34
Alignment explanation
Indices: 3909765--3909839 Score: 134
Period size: 33 Copynumber: 2.2 Consensus size: 34
3909755 GGCCACCTGT
3909765 CAAAGATGAATTTTCCAATAAGTTGACCACCAAC
1 CAAAGATGAATTTTCCAATAAGTTGACCACCAAC
*
3909799 C-AAGATGAATTTTCCAATAAGTTGGCCACCAAC
1 CAAAGATGAATTTTCCAATAAGTTGACCACCAAC
3909832 CAAAGATG
1 CAAAGATG
3909840 TCAACTTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (34 bp):
CAAAGATGAATTTTCCAATAAGTTGACCACCAAC
Found at i:3910131 original size:27 final size:26
Alignment explanation
Indices: 3910084--3910134 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
3910074 CCTAACGGTT
*
3910084 TGGTCGATTTTACTCCCATCAAATAA
1 TGGTCGATTTCACTCCCATCAAATAA
*
3910110 TGGTCGACTTTCACTCCTATCAAAT
1 TGGTCGA-TTTCACTCCCATCAAAT
3910135 TAATATTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (26 bp):
TGGTCGATTTCACTCCCATCAAATAA
Found at i:3910988 original size:3 final size:3
Alignment explanation
Indices: 3910982--3911065 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
3910972 CGACGACGAC
3910982 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3911030 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3911066 AATAATAATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3915021 original size:4 final size:4
Alignment explanation
Indices: 3915012--3915036 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3915002 TATTCTTTTA
3915012 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
3915037 GATATAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:3920223 original size:20 final size:20
Alignment explanation
Indices: 3920198--3920235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3920188 TACATGTTAA
3920198 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
3920218 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
3920236 TCAAGGGAAA
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:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:3920746 original size:30 final size:30
Alignment explanation
Indices: 3920710--3920769 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3920700 GTATTTGCGG
3920710 ATATATATATATGAATAAGATATGATATAT
1 ATATATATATATGAATAAGATATGATATAT
*
3920740 ATATATATATATGAATAAGTTATGATATAT
1 ATATATATATATGAATAAGATATGATATAT
3920770 GTTTATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (30 bp):
ATATATATATATGAATAAGATATGATATAT
Found at i:3929139 original size:31 final size:31
Alignment explanation
Indices: 3929095--3929167 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
3929085 ATTTGTATGC
**
3929095 TTTTGGT-ACTTATGTTATTGTTTTATTAAG
1 TTTTGGTCACTTATGTTATCATTTTATTAAG
3929125 TTTTGGTCACTTATGTTATCATTTTATTAAG
1 TTTTGGTCACTTATGTTATCATTTTATTAAG
3929156 TTTTGGTCACTT
1 TTTTGGTCACTT
3929168 GGAGGTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 7 0.17
31 33 0.82
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (31 bp):
TTTTGGTCACTTATGTTATCATTTTATTAAG
Found at i:3930413 original size:3 final size:3
Alignment explanation
Indices: 3930407--3930442 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
3930397 TTTTTCATCA
3930407 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
3930443 AATAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3930430 original size:16 final size:16
Alignment explanation
Indices: 3930409--3930441 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3930399 TTTCATCATA
3930409 TTATTATTATTATTAT
1 TTATTATTATTATTAT
3930425 TTATTATTATTATTAT
1 TTATTATTATTATTAT
3930441 T
1 T
3930442 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:3930826 original size:19 final size:18
Alignment explanation
Indices: 3930798--3930833 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3930788 ACCATTTTTT
*
3930798 GGTGAGTCACCACAAGTTC
1 GGTGACTCACCA-AAGTTC
3930817 GGTGACTCACCAAAGTT
1 GGTGACTCACCAAAGTT
3930834 TGCTCCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (18 bp):
GGTGACTCACCAAAGTTC
Found at i:3932804 original size:15 final size:16
Alignment explanation
Indices: 3932784--3932813 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3932774 TTCTTTCAAT
3932784 TTTTTATACT-TATAG
1 TTTTTATACTATATAG
3932799 TTTTTATACTATATA
1 TTTTTATACTATATA
3932814 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTATACTATATAG
Found at i:3932815 original size:2 final size:2
Alignment explanation
Indices: 3932803--3932854 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
3932793 TTATAGTTTT
3932803 TA TA CTA 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
3932846 TA TA TA TA T
1 TA TA TA TA T
3932855 TCTTCTTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3937222 original size:122 final size:121
Alignment explanation
Indices: 3937004--3937245 Score: 412
Period size: 122 Copynumber: 2.0 Consensus size: 121
3936994 AAGTTCTTAT
*
3937004 AAAAAAAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGTAGTTCGGTGTTTGCTCCAC
1 AAAAAAAGTCATATATTCAAAACATGACCTTGATCGGATATTTGGTAGTTCGGTGTTTGCTCCAC
* * *
3937069 TGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATA
66 TATGATTGTCAAGTCAAAGACATTGTAATGAGTTGAACCCTTTAATTAGTCCAATA
*
3937125 AAAAAAGAGTCATATATTCAAAACATGACCTTGATCGGATATTTGGTAGTTCGGTGTTTGCTCTA
1 AAAAAA-AGTCATATATTCAAAACATGACCTTGATCGGATATTTGGTAGTTCGGTGTTTGCTCCA
* *
3937190 CTATGATTGTCAAGTCGAAGACATTGTAATGAGTTGAACCGTTTAATTAGTCCAAT
65 CTATGATTGTCAAGTCAAAGACATTGTAATGAGTTGAACCCTTTAATTAGTCCAAT
3937246 GAAGGCTAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 6 0.05
122 107 0.95
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (121 bp):
AAAAAAAGTCATATATTCAAAACATGACCTTGATCGGATATTTGGTAGTTCGGTGTTTGCTCCAC
TATGATTGTCAAGTCAAAGACATTGTAATGAGTTGAACCCTTTAATTAGTCCAATA
Found at i:3940102 original size:75 final size:74
Alignment explanation
Indices: 3939979--3940194 Score: 324
Period size: 75 Copynumber: 2.9 Consensus size: 74
3939969 ATCAACAAGA
* ***
3939979 AGCAAATGCTGAGGCATGCTGAAAGCCCGTTTCAATCAGAAGGTGGAATATTAATGCATTTTGAA
1 AGCAAATGCTG-GGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATTAATGCATTTTGAA
3940044 CATTTGTATC
65 CATTTGTATC
3940054 AGCAAATGCTCGGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATTAATGCATTTTGAA
1 AGCAAATGCT-GGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATTAATGCATTTTGAA
3940119 CATTTGTATC
65 CATTTGTATC
* * * * *
3940129 AGTAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTAACGCATTTTGAA
1 AGCAAATGCT-GGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATTAATGCATTTTGAA
3940194 C
65 C
3940195 GTTGGGGCAT
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 129 0.99
76 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (74 bp):
AGCAAATGCTGGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATTAATGCATTTTGAAC
ATTTGTATC
Found at i:3941213 original size:54 final size:54
Alignment explanation
Indices: 3941154--3941372 Score: 210
Period size: 54 Copynumber: 4.0 Consensus size: 54
3941144 TAAATGATTG
* * *
3941154 AACATCTAAGTAGTAGCCATAGGAAATGATGAATATGTTGTCAAATGTTTACGA
1 AACATCTAAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGTTTACGA
* * *
3941208 AACATCTGAGCAGAAACCACAGAAAATGATGAATATGTTGTCAAATGTTTTAC-A
1 AACATCTAAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATG-TTTACGA
** * * * * *
3941262 AACATCTGTGCAGAAGTCACATGAAAAGATGAATGTGTTGTCAAATACTTTACG-
1 AACATCTAAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAAT-GTTTACGA
* * * * * *
3941316 AACATCT-AGCCAGAAGCCACAAGAAAGGATTAATGTGTTATCAAAAGCTTTACGA
1 AACATCTAAG-CAGAAGCCACAGGAAATGATGAATATGTTGTCAAATG-TTTACGA
3941371 AA
1 AA
3941373 ATCCATGAGA
Statistics
Matches: 137, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
53 1 0.01
54 129 0.94
55 7 0.05
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (54 bp):
AACATCTAAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGTTTACGA
Found at i:3941827 original size:22 final size:23
Alignment explanation
Indices: 3941780--3941856 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 23
3941770 ATCTACATTC
** * *
3941780 TTCAAAGATGATAGACACAC-TC
1 TTCAAAGATGATAGATTCTCTTT
3941802 TTCAAAGATGATAGATTCT-TTT
1 TTCAAAGATGATAGATTCTCTTT
3941824 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGATAGATTCTCTTT
3941847 TT-AAAGATGA
1 TTCAAAGATGA
3941857 AATCCTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
22 44 0.90
23 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGATAGATTCTCTTT
Found at i:3942592 original size:45 final size:45
Alignment explanation
Indices: 3942528--3942615 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
3942518 TATTTCCCAC
3942528 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTT
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTT
*
3942573 ATCTGTAAGCCCTTCAGTGCGTGATGTTTTCAAAACCTTCGGG
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
3942616 GTCATCCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (45 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTT
Done.