Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008102.1 Hibiscus syriacus cultivar Beakdansim tig00110632_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: 143535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7297 original size:53 final size:53
Alignment explanation
Indices: 7217--7325 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
7207 GGTAGTGATG
7217 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
1 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
7270 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
1 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
7323 CCC
1 CCC
7326 GCTATGCCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (53 bp):
CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
Found at i:8647 original size:18 final size:18
Alignment explanation
Indices: 8626--8660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8616 CTCTCTCTAT
8626 CCTTCTCCCTTTCCTTTG
1 CCTTCTCCCTTTCCTTTG
* *
8644 CCTTGTCTCTTTCCTTT
1 CCTTCTCCCTTTCCTTT
8661 TCTCTGTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.06, T:0.54
Consensus pattern (18 bp):
CCTTCTCCCTTTCCTTTG
Found at i:10873 original size:19 final size:19
Alignment explanation
Indices: 10828--10867 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
10818 CCTTTTCATG
10828 ATTAAATTTGACTCCATCT
1 ATTAAATTTGACTCCATCT
*
10847 ATTAAATTTGATTCCATCT
1 ATTAAATTTGACTCCATCT
10866 AT
1 AT
10868 GTAATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTAAATTTGACTCCATCT
Found at i:11272 original size:25 final size:25
Alignment explanation
Indices: 11238--11292 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
11228 GCCCCGAGGG
11238 AGCGCCTTAGGCCACCTAGGAGTAT
1 AGCGCCTTAGGCCACCTAGGAGTAT
11263 AGCGCCTTAGGCCACCTAGGAGTAT
1 AGCGCCTTAGGCCACCTAGGAGTAT
11288 AGCGC
1 AGCGC
11293 AGTTAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (25 bp):
AGCGCCTTAGGCCACCTAGGAGTAT
Found at i:14117 original size:9 final size:9
Alignment explanation
Indices: 14103--14136 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
14093 TAAGTAAAAT
14103 ATTAAATAA
1 ATTAAATAA
14112 ATTAAAT-A
1 ATTAAATAA
*
14120 CTTAAATAA
1 ATTAAATAA
14129 ATTAAATA
1 ATTAAATA
14137 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:14135 original size:17 final size:17
Alignment explanation
Indices: 14099--14137 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
14089 TAATTAAGTA
14099 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
14115 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
14132 AAATAC
1 AAATAC
14138 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:14203 original size:10 final size:10
Alignment explanation
Indices: 14190--14218 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
14180 ATAAGAGTAT
14190 TTGAGAGAAG
1 TTGAGAGAAG
14200 TTGAGAGAAG
1 TTGAGAGAAG
14210 TTGAGAGAA
1 TTGAGAGAA
14219 TTTAGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:15185 original size:72 final size:71
Alignment explanation
Indices: 15052--15251 Score: 185
Period size: 72 Copynumber: 2.7 Consensus size: 71
15042 TTAATATAGT
* * * *
15052 ATAGTTTTTGAAAATATTTTTTTAAAAATATAATATATAATTTTTAGAAAACGATTTTTGAAAAT
1 ATAGTTTTTGAAAAAATTTTTTAAAAAATATAATATATAAGTTTTAGAAAACAATTTTTGAAAAT
15117 ATATAC
66 ATATAC
*
15123 ATAG-TTTTGAAAACAATTTTTTGAAAATAAGTATATTATAT-AGTTTT-GAAAACAATTTTTGA
1 ATAGTTTTTGAAAA-AATTTTTT-AAAA-AA-TATAATATATAAGTTTTAGAAAACAATTTTTGA
*
15185 AAATATATAT
62 AAATATATAC
* *
15195 ATTATTTAATTTCGAAAATAATTTTTGAAAAATATATATATCATATAA-TTTTA-AAAA
1 A-TAGTT--TTT-GAAAA-AATTTTTTAAAAA-ATATA-AT-ATATAAGTTTTAGAAAA
15252 TGTTTGTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
70 9 0.09
71 11 0.10
72 27 0.26
73 9 0.09
74 10 0.10
75 5 0.05
76 9 0.09
77 24 0.23
78 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (71 bp):
ATAGTTTTTGAAAAAATTTTTTAAAAAATATAATATATAAGTTTTAGAAAACAATTTTTGAAAAT
ATATAC
Found at i:15252 original size:39 final size:38
Alignment explanation
Indices: 15057--15251 Score: 174
Period size: 39 Copynumber: 5.2 Consensus size: 38
15047 ATAGTATAGT
* * *
15057 TTTTGAAAATATTTTTTTAAAA-ATATA-AT-ATATAA
1 TTTTGAAAACAATTTTTGAAAATATATATATCATATAA
* *
15092 TTTTTAGAAAACGATTTTTG-AAA-ATATATA-C--ATAG
1 -TTTT-GAAAACAATTTTTGAAAATATATATATCATATAA
* *
15127 TTTTGAAAACAATTTTTTGAAAATA-AGTATATTATATAG
1 TTTTGAAAACAA-TTTTTGAAAATATA-TATATCATATAA
* *
15166 TTTTGAAAACAATTTTTGAAAATATATATATTATTTAA
1 TTTTGAAAACAATTTTTGAAAATATATATATCATATAA
* *
15204 TTTCGAAAATAATTTTTGAAAAATATATATATCATATAA
1 TTTTGAAAACAATTTTTG-AAAATATATATATCATATAA
*
15243 TTTTAAAAA
1 TTTTGAAAA
15252 TGTTTGTTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
33 7 0.05
34 10 0.08
35 7 0.05
36 17 0.13
37 11 0.08
38 38 0.29
39 42 0.32
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (38 bp):
TTTTGAAAACAATTTTTGAAAATATATATATCATATAA
Found at i:15341 original size:11 final size:11
Alignment explanation
Indices: 15318--15347 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15308 TCTCATTACA
15318 TTATTTA-TAT
1 TTATTTATTAT
15328 TTATTTATTAT
1 TTATTTATTAT
15339 TTATTTATT
1 TTATTTATT
15348 TTATGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:16136 original size:158 final size:158
Alignment explanation
Indices: 15848--16145 Score: 506
Period size: 158 Copynumber: 1.9 Consensus size: 158
15838 CGGAAAAAGC
* * *
15848 AAGGTGAACACTAGCGTTGGATCAAAGGAGGAACAACTACCAGAAAGTTAGAAAATCATCATTGG
1 AAGGTGAACACTAGCGTTGGATCAAAGGAGGAACAACTACCAAAAAGTTAGAAAATCACCATCGG
* *
15913 TAGAGGTAAAACCCCGAAACTTTGGGCGTAGATATACACTTTTCTGGGCTTTTTTGTGGGATTTA
66 TAGAGGTAAAACCCCGAAACTTTGGGCGTAAATATACACTTTTATGGGCTTTTTTGTGGGATTTA
*
15978 GCCTCGGATTCGGGCTCACTAGGTTGGG
131 GCCTCAGATTCGGGCTCACTAGGTTGGG
* * * *
16006 AAGGTGAACACTGGCGTTGGATCAAATGAGGAACAACTACCAAAAAGTTGGAAAGTCACCATCGG
1 AAGGTGAACACTAGCGTTGGATCAAAGGAGGAACAACTACCAAAAAGTTAGAAAATCACCATCGG
16071 TAGAGGTAAAACCCCGAAACTTTGGGCGTAAATATACACTTTTATGGGCTTTTTTGTGGGATTTA
66 TAGAGGTAAAACCCCGAAACTTTGGGCGTAAATATACACTTTTATGGGCTTTTTTGTGGGATTTA
16136 GCCTCAGATT
131 GCCTCAGATT
16146 TTGTTGGACG
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
158 130 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (158 bp):
AAGGTGAACACTAGCGTTGGATCAAAGGAGGAACAACTACCAAAAAGTTAGAAAATCACCATCGG
TAGAGGTAAAACCCCGAAACTTTGGGCGTAAATATACACTTTTATGGGCTTTTTTGTGGGATTTA
GCCTCAGATTCGGGCTCACTAGGTTGGG
Found at i:16931 original size:27 final size:27
Alignment explanation
Indices: 16841--16910 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
16831 TTTATATATG
*
16841 TTAACTTAAAAA-A-TTTA-TATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
*
16865 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
16890 TTAATTTAAAAATATTTTATT
1 TTAATTTAAAAATATTTTATT
16911 TTTATTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 6 0.15
25 9 0.23
26 1 0.03
27 15 0.38
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAAC
Found at i:17081 original size:31 final size:31
Alignment explanation
Indices: 17038--17110 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
17028 CATATTTTTG
* * * *
17038 ACCACATCTTAATTAAATAAAACCGAAAGTG
1 ACCATATCTTAATTAAATAAAAACAAAAGTA
*
17069 GCCATATCTTAATTAAATAAAAACAAAAGTA
1 ACCATATCTTAATTAAATAAAAACAAAAGTA
17100 ACCATATCTTA
1 ACCATATCTTA
17111 TGTTTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACAAAAGTA
Found at i:35201 original size:15 final size:17
Alignment explanation
Indices: 35167--35203 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
35157 TTTCCCACGA
35167 GAAAAACAAACAAAAAT
1 GAAAAACAAACAAAAAT
*
35184 GAAAAA-AAA-AAAACT
1 GAAAAACAAACAAAAAT
35199 GAAAA
1 GAAAA
35204 TTAGCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.05
Consensus pattern (17 bp):
GAAAAACAAACAAAAAT
Found at i:37514 original size:29 final size:28
Alignment explanation
Indices: 37421--37514 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 28
37411 TTCACGATCT
*
37421 AATTAAATAATTAAA-AT-TAATATATTA
1 AATTAAA-AATTAAATATATAATATATAA
* *
37448 AATT-TAAATTAAAT-TGATAAATATTTAA
1 AATTAAAAATTAAATAT-AT-AATATATAA
* *
37476 AAATAGAAATTAAATATATAATGATATAA
1 AATTAAAAATTAAATATATAAT-ATATAA
37505 AATTAAAAAT
1 AATTAAAAAT
37515 AATTAATAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 8 0.15
26 1 0.02
27 5 0.10
28 13 0.25
29 24 0.46
30 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AATTAAAAATTAAATATATAATATATAA
Found at i:40499 original size:201 final size:201
Alignment explanation
Indices: 40126--40534 Score: 617
Period size: 201 Copynumber: 2.0 Consensus size: 201
40116 TGGGAGAGAA
*
40126 TGGAGGGAGCTCCCAAATGAAGAAAAATATGTAGCAAGAATCCCGATTTTGAATTACAAAACTAA
1 TGGAGGGAGCTCCCAAAAGAAGAAAAATATGTAGCAAGAATCCCGATTTTGAATTACAAAACTAA
* * * *
40191 ATCTAAAATCCAATGATCACAATAATGTTTGTATTTATAGTTGCAGCAAATGTTACTCAAACTTG
66 ATCTAAAATCCAATAATCACAATAATGTATGTATTTATAGTAGCAGAAAATGTTACTCAAACTTG
* * * *
40256 GTTGTCAGTATTTAATATGAGTATGTTATTAACACGAATATGATAAATTTTTCCCACGTTCTTCC
131 GTTGTCAGTATTGAATATGAGTATGTGATTAACACAAATATGATAAA-TTTTCCCAAGTTCTTCC
40321 -TAGTCTT
195 AT-GTCTT
* * *
40328 TGGAGGGAGCTCGCAAACAG-AG-AAAATATGTAGCAAGAGTCCCGATTTTTAATTACAAAACTA
1 TGGAGGGAGCTCCCAAA-AGAAGAAAAATATGTAGCAAGAATCCCGATTTTGAATTACAAAACTA
* *
40391 AATCTAAAATCCAATAATCACAATAATGTATGTATTTATTGTAGTAGAAAATGTTACTCAAACTT
65 AATCTAAAATCCAATAATCACAATAATGTATGTATTTATAGTAGCAGAAAATGTTACTCAAACTT
* * *
40456 GGTTGTGAGTATTGAATATGAGTATGTGATTTACACAAATATGATAAATTTTCCCAAGTTTTTCC
130 GGTTGTCAGTATTGAATATGAGTATGTGATTAACACAAATATGATAAATTTTCCCAAGTTCTTCC
40521 ATGTCTT
195 ATGTCTT
40528 TGGAGGG
1 TGGAGGG
40535 TCATTAGCAT
Statistics
Matches: 188, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
200 27 0.14
201 142 0.76
202 18 0.10
203 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (201 bp):
TGGAGGGAGCTCCCAAAAGAAGAAAAATATGTAGCAAGAATCCCGATTTTGAATTACAAAACTAA
ATCTAAAATCCAATAATCACAATAATGTATGTATTTATAGTAGCAGAAAATGTTACTCAAACTTG
GTTGTCAGTATTGAATATGAGTATGTGATTAACACAAATATGATAAATTTTCCCAAGTTCTTCCA
TGTCTT
Found at i:43630 original size:24 final size:23
Alignment explanation
Indices: 43598--43654 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
43588 CCACAAGTAT
* * *
43598 TGTGTCACAAGAGCAGAGAAAACA
1 TGTGTCACAACAACAAAGAAAA-A
*
43622 TGTGTCACAACAATAAAGAAAAA
1 TGTGTCACAACAACAAAGAAAAA
43645 TGTGTCACAA
1 TGTGTCACAA
43655 TGATAGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (23 bp):
TGTGTCACAACAACAAAGAAAAA
Found at i:45443 original size:48 final size:47
Alignment explanation
Indices: 45378--45556 Score: 163
Period size: 53 Copynumber: 3.8 Consensus size: 47
45368 TATAAAATCC
*
45378 CTTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
45423 TTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATAATTTTTTTTCCAATATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGC-T-T-A---TTTTACCAAAATA
* *
45477 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTA-TTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
45523 CTTGCCA-TT--ATTCCAAAAGCTCATAAGCTTATTT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
45557 GTATGCTTAC
Statistics
Matches: 112, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
43 20 0.18
44 2 0.02
45 10 0.09
46 16 0.14
48 18 0.16
49 1 0.01
50 2 0.02
51 2 0.02
52 1 0.01
53 21 0.19
54 19 0.17
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:45705 original size:40 final size:40
Alignment explanation
Indices: 45661--45742 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
45651 ACCGTAGTGC
45661 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
*
45701 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
45741 TA
1 TA
45743 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
Found at i:48392 original size:20 final size:20
Alignment explanation
Indices: 48367--48435 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
48357 CTCGAGATCG
*
48367 ACTAGTCTCAATACCAAAGA
1 ACTAGTCTCTATACCAAAGA
*
48387 ACTAGTATCTATACCAAAGA
1 ACTAGTCTCTATACCAAAGA
* **
48407 ACTGGTCTCTATACTGAAGA
1 ACTAGTCTCTATACCAAAGA
*
48427 ACTGGTCTC
1 ACTAGTCTC
48436 CATATCAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (20 bp):
ACTAGTCTCTATACCAAAGA
Found at i:50698 original size:29 final size:28
Alignment explanation
Indices: 50666--50761 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
50656 AAATAAGTCT
50666 TTAAATTTTTAAACATTCTAATTTCATCC
1 TTAAATTTTTAAACATTCTAATTT-ATCC
** ** *
50695 TTAAACTATGGCT-CTCATTCTAAATTAGTCC
1 TTAAA-T-T-TTTAAACATTCTAATTTA-TCC
*
50726 TTAAATTTTTAAACATTCCAATTTTATCC
1 TTAAATTTTTAAACATTCTAA-TTTATCC
50755 TTAAATT
1 TTAAATT
50762 ATGAATCTCA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
28 1 0.02
29 23 0.46
30 6 0.12
31 19 0.38
32 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (28 bp):
TTAAATTTTTAAACATTCTAATTTATCC
Found at i:50739 original size:60 final size:60
Alignment explanation
Indices: 50636--50814 Score: 223
Period size: 60 Copynumber: 3.0 Consensus size: 60
50626 CATATGTTTC
* * * *
50636 TAAATTATGTCTCTCATTCTAAATAAGTCTTTAAATTTTTAAACATTCTAATTTCATCCT
1 TAAATTATGACTCTCATTCTAAATTAGTCCTTAAATTTTTAAACATTCCAATTTCATCCT
* * *
50696 TAAACTATGGCTCTCATTCTAAATTAGTCCTTAAATTTTTAAACATTCCAATTTTATCCT
1 TAAATTATGACTCTCATTCTAAATTAGTCCTTAAATTTTTAAACATTCCAATTTCATCCT
* * * * * * * *
50756 TAAATTATGAATCTCATTCTAAATTGGTCCCTAAACTTTTAGATATTCCATTTTAATCC
1 TAAATTATGACTCTCATTCTAAATTAGTCCTTAAATTTTTAAACATTCCAATTTCATCC
50815 CAAAATTCAT
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 103 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAATTATGACTCTCATTCTAAATTAGTCCTTAAATTTTTAAACATTCCAATTTCATCCT
Found at i:50884 original size:32 final size:32
Alignment explanation
Indices: 50842--50915 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
50832 TGTAATCAAT
*
50842 TTCAACCATAGTTTAACCTAAATTTCATTCTC
1 TTCAAACATAGTTTAACCTAAATTTCATTCTC
50874 TTCAAACATAGTTTAACCTAAATTTCATTCTC
1 TTCAAACATAGTTTAACCTAAATTTCATTCTC
50906 TTCAAACATA
1 TTCAAACATA
50916 TAATAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (32 bp):
TTCAAACATAGTTTAACCTAAATTTCATTCTC
Found at i:51947 original size:60 final size:59
Alignment explanation
Indices: 51844--51957 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
51834 AATTATGATC
** * * * * *
51844 CTCATCCTAAATTAGTCTCAAATTTTTAAACATTCTAATTTCATCTTTAAACTACTGTT
1 CTCATCCTAAATTAACCTCAAATTGTTAAACATTCCAAATTCATCCTCAAACTACTGTT
* *
51903 CTCATTCTAAATTAACCTCTAAATTGTTGAACATTCCAAATTCATCCTCAAACTA
1 CTCATCCTAAATTAACCTC-AAATTGTTAAACATTCCAAATTCATCCTCAAACTA
51958 TGACCCTTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 16 0.36
60 29 0.64
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
CTCATCCTAAATTAACCTCAAATTGTTAAACATTCCAAATTCATCCTCAAACTACTGTT
Found at i:54026 original size:17 final size:19
Alignment explanation
Indices: 54004--54039 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53994 TATTTCTTCC
54004 TATAATG-TTCT-TTTTCT
1 TATAATGTTTCTCTTTTCT
54021 TATAATGTTTCTCTTTTCT
1 TATAATGTTTCTCTTTTCT
54040 GTCTTGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.64
Consensus pattern (19 bp):
TATAATGTTTCTCTTTTCT
Found at i:54388 original size:66 final size:66
Alignment explanation
Indices: 54287--54565 Score: 294
Period size: 66 Copynumber: 4.2 Consensus size: 66
54277 TCATATAGTG
* * ** * *
54287 ACTCCACCTTATGCACCACAAAGGTACACAAGTCTCATTGAGAGATCAGTATAATATTCAATTAT
1 ACTCCACCTCATGCACAACAAAGGTACATGAGTCTCATTGAGTGATCAGTACAATATTCAATTAT
*
54352 T
66 C
* * * * * *
54353 ATTCCTCCTCATACACTACAAAGGTACATGAGTCTCATTGAGTGATTC-GTGCAGTATTCAATTA
1 ACTCCACCTCATGCACAACAAAGGTACATGAGTCTCATTGAGTGA-TCAGTACAATATTCAATTA
54417 TC
65 TC
* * * *
54419 ACTCCACCTCATGCACCACAAAGGTACATGAGTCTCATTGGGTGAT-ATGTGA-AGTAATCAATT
1 ACTCCACCTCATGCACAACAAAGGTACATGAGTCTCATTGAGTGATCA-GT-ACAATATTCAATT
54482 ATC
64 ATC
* * * * **
54485 ACTCCACCTCATGCACAAAAAAAGTACATGAGTCTCATTGAGTGATCTGTACAATATTAAACAAT
1 ACTCCACCTCATGCACAACAAAGGTACATGAGTCTCATTGAGTGATCAGTACAATATTCAATTAT
54550 C
66 C
*
54551 ACTCCACCTCGTGCA
1 ACTCCACCTCATGCA
54566 TCATTTACTC
Statistics
Matches: 177, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.01
66 173 0.98
67 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (66 bp):
ACTCCACCTCATGCACAACAAAGGTACATGAGTCTCATTGAGTGATCAGTACAATATTCAATTAT
C
Found at i:54524 original size:132 final size:132
Alignment explanation
Indices: 54287--54565 Score: 330
Period size: 132 Copynumber: 2.1 Consensus size: 132
54277 TCATATAGTG
* *
54287 ACTCCACCTTATGCACCACAAAGGTACACAAGTCTCATTGAGAGATCAGTATAATATTCAATTAT
1 ACTCCACCTCATGCACCACAAAGGTACACAAGTCTCATTGAGAGATCAGTATAATAATCAATTAT
* * * * * * * * * **
54352 TATTCCTCCTCATACACTACAAAGGTACATGAGTCTCATTGAGTGAT-TCGTGCAGTATTCAATT
66 CACTCCACCTCATACACAAAAAAAGTACATGAGTCTCATTGAGTGATCT-GTACAATATTAAACA
54416 ATC
130 ATC
** * * *
54419 ACTCCACCTCATGCACCACAAAGGTACATGAGTCTCATTGGGTGAT-ATGTGA-AGTAATCAATT
1 ACTCCACCTCATGCACCACAAAGGTACACAAGTCTCATTGAGAGATCA-GT-ATAATAATCAATT
*
54482 ATCACTCCACCTCATGCACAAAAAAAGTACATGAGTCTCATTGAGTGATCTGTACAATATTAAAC
64 ATCACTCCACCTCATACACAAAAAAAGTACATGAGTCTCATTGAGTGATCTGTACAATATTAAAC
54547 AATC
129 AATC
*
54551 ACTCCACCTCGTGCA
1 ACTCCACCTCATGCA
54566 TCATTTACTC
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
131 1 0.01
132 121 0.98
133 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (132 bp):
ACTCCACCTCATGCACCACAAAGGTACACAAGTCTCATTGAGAGATCAGTATAATAATCAATTAT
CACTCCACCTCATACACAAAAAAAGTACATGAGTCTCATTGAGTGATCTGTACAATATTAAACAA
TC
Found at i:57153 original size:37 final size:36
Alignment explanation
Indices: 57094--57213 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
57084 ATCCCATTAT
* *
57094 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
57130 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
57166 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
57201 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
57214 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:57169 original size:21 final size:21
Alignment explanation
Indices: 57145--57205 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
57135 TTCAAAGAAA
57145 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
57166 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
57180 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
57201 CATTT
1 CATTT
57206 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:57222 original size:35 final size:36
Alignment explanation
Indices: 57096--57240 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
57086 CCCATTATCA
*
57096 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
57131 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
57168 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
57204 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
57238 TTT
1 TTT
57241 AATAATTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:61304 original size:16 final size:17
Alignment explanation
Indices: 61273--61306 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
61263 TGTATCGCCG
*
61273 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
61290 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
61306 A
1 A
61307 TATGGAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:61767 original size:37 final size:37
Alignment explanation
Indices: 61708--61824 Score: 161
Period size: 37 Copynumber: 3.2 Consensus size: 37
61698 CCATTATCAG
* *
61708 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACTAT
* *
61744 TTTTCAAAGAAACATTTAACAAACTTTGAAAATC-A-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACTAT
61779 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACTATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACTA-T
61816 TTTTCAAAG
1 TTTTCAAAG
61825 TTGGTTACCA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
34 4 0.06
35 28 0.39
36 6 0.08
37 33 0.46
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.33
Consensus pattern (37 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACTAT
Found at i:61817 original size:35 final size:35
Alignment explanation
Indices: 61708--61817 Score: 152
Period size: 35 Copynumber: 3.1 Consensus size: 35
61698 CCATTATCAG
* *
61708 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACTA
*
61743 TTTTTCAAAGAAACATTTAACAAACTTTGAAAA-TCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACT-A
61779 TTTTCAAAGAAACATTTACCAAACTTTGAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACTA
61814 TTTT
1 TTTT
61818 TTCAAAGTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
35 37 0.55
36 11 0.16
37 19 0.28
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACTA
Found at i:66984 original size:39 final size:39
Alignment explanation
Indices: 66897--66986 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
66887 ATTTCAGTAC
* *
66897 CAAAGAGAAAATCAGATGATTCTTATGATATTTTAGGGA
1 CAAAGAGAAAATCAGAAGATTCTTATGATATTCTAGGGA
* * * *
66936 CAAAAAGAAAATCCGAAGATTCTTCTGATGTCTCT-GGTG-
1 CAAAGAGAAAATCAGAAGATTCTTATGATAT-TCTAGG-GA
66975 CAAAGAGAAAAT
1 CAAAGAGAAAAT
66987 ATGGAAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 39 0.93
40 3 0.07
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (39 bp):
CAAAGAGAAAATCAGAAGATTCTTATGATATTCTAGGGA
Found at i:68496 original size:34 final size:34
Alignment explanation
Indices: 68429--68566 Score: 174
Period size: 34 Copynumber: 4.0 Consensus size: 34
68419 GCCCCGCCCC
* *
68429 AATTATATATATAAAATATTTTTTTATTTTTTATATT
1 AATTATATATAT---ATAATTTTATATTTTTTATATT
*
68466 AATTATATATATATAACTTTATATTTTTTATATT
1 AATTATATATATATAATTTTATATTTTTTATATT
68500 AATTATATATATATAATTTTTTATATTTTTTATATT
1 AATTATATATATATAA--TTTTATATTTTTTATATT
*
68536 AATTATATGTA-AT-ATTTTATA-TTTTTATATT
1 AATTATATATATATAATTTTATATTTTTTATATT
68567 TTTTCTATTT
Statistics
Matches: 94, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
31 10 0.11
32 7 0.07
34 36 0.38
35 2 0.02
36 27 0.29
37 12 0.13
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.62
Consensus pattern (34 bp):
AATTATATATATATAATTTTATATTTTTTATATT
Found at i:68529 original size:10 final size:9
Alignment explanation
Indices: 68444--68580 Score: 68
Period size: 9 Copynumber: 15.1 Consensus size: 9
68434 TATATATAAA
68444 ATATTTTTT
1 ATATTTTTT
68453 -TATTTTTT
1 ATATTTTTT
**
68461 ATATTAATT
1 ATATTTTTT
* *
68470 ATA-TATAT
1 ATATTTTTT
**
68478 ATA-ACTTT
1 ATATTTTTT
68486 ATATTTTTT
1 ATATTTTTT
**
68495 ATATTAATT
1 ATATTTTTT
* *
68504 ATA-TATAT
1 ATATTTTTT
68512 ATAATTTTTT
1 AT-ATTTTTT
68522 ATATTTTTT
1 ATATTTTTT
**
68531 ATATTAATT
1 ATATTTTTT
68540 ATATGTAATATTT
1 ATAT-T--T-TTT
68553 -TATATTTTT
1 ATAT-TTTTT
68562 ATATTTTTT
1 ATATTTTTT
*
68571 CTATTTTTT
1 ATATTTTTT
68580 A
1 A
68581 ATGAAAAATA
Statistics
Matches: 97, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
8 24 0.25
9 57 0.59
10 10 0.10
12 4 0.04
13 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
ATATTTTTT
Found at i:69724 original size:158 final size:158
Alignment explanation
Indices: 69485--69859 Score: 560
Period size: 158 Copynumber: 2.4 Consensus size: 158
69475 TCTGATTTTA
* *
69485 TTATTTCTTCAATTC--C-TCCATTTTAAG-TCCATTTTTTACCAAATTTGAACCACATGCTCCT
1 TTATTTCTTCAATTCGTCATTCATTTTAAGTTCC-TTTTTTACCAAATTTGAACCACAAGCTCCT
*
69546 AAACAATAGTAGAATACATGTGTACTTTCAATTCCACTTTTTGATGACAAATTTTATATTTTTCA
65 AAACAATAGTAGAATACATGTGTACTTTCAATTCCACTTTTTGATAACAAATTTTATATTTTTCA
* *
69611 ATTTAGTCTTTCAATTTTTCATAATCTTC
130 ATTTAGTCCTTCAATTTTTCATAATCTCC
* *
69640 TTATTTCTTCAATTCGTCATTCATTTTAAGTTCCTTTTTTACCAAATTTGAGCCATAAGCTCCTA
1 TTATTTCTTCAATTCGTCATTCATTTTAAGTTCCTTTTTTACCAAATTTGAACCACAAGCTCCTA
* * * *
69705 AACTATAGTAGATTACATGTGTACTTTCAATTCCTCTTTTTGATAACAAATTTTTTATTTTTCAA
66 AACAATAGTAGAATACATGTGTACTTTCAATTCCACTTTTTGATAACAAATTTTATATTTTTCAA
69770 TTTAGTCCTTCAATTTTTCATAATCTCC
131 TTTAGTCCTTCAATTTTTCATAATCTCC
* * * * * *
69798 TTATTCCTTCAATTTGTGATTTATTTTAAGTTACTTTTTTACCAAATTTGAACCACATGCTC
1 TTATTTCTTCAATTCGTCATTCATTTTAAGTTCCTTTTTTACCAAATTTGAACCACAAGCTC
69860 ATATACTACA
Statistics
Matches: 197, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
155 15 0.08
157 1 0.01
158 178 0.90
159 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (158 bp):
TTATTTCTTCAATTCGTCATTCATTTTAAGTTCCTTTTTTACCAAATTTGAACCACAAGCTCCTA
AACAATAGTAGAATACATGTGTACTTTCAATTCCACTTTTTGATAACAAATTTTATATTTTTCAA
TTTAGTCCTTCAATTTTTCATAATCTCC
Found at i:71380 original size:68 final size:68
Alignment explanation
Indices: 71305--71439 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
71295 AAAACCTCTA
** *
71305 TTCCTAAAAGTTGAAGAAAAAGAGTATACCCTAGCCAATGATCAATGGAAAAGACCATTATCAAA
1 TTCCTAAAAGGGGAAGAAAAAGAGTATACCCTAGCCAATAATCAATGGAAAAGACCATTATCAAA
71370 ACG
66 ACG
* * *
71373 TTCCTAAAAGGGGAAGAAAAAGAGTGTACCTTAGCCAATAATCAATGGAAAAGATCATTATCAAA
1 TTCCTAAAAGGGGAAGAAAAAGAGTATACCCTAGCCAATAATCAATGGAAAAGACCATTATCAAA
71438 AC
66 AC
71440 AAAAGAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (68 bp):
TTCCTAAAAGGGGAAGAAAAAGAGTATACCCTAGCCAATAATCAATGGAAAAGACCATTATCAAA
ACG
Found at i:71463 original size:44 final size:44
Alignment explanation
Indices: 71413--71505 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
71403 TTAGCCAATA
*
71413 ATCAATGGAAAAGATCATTATCAAAACAAAAGAAAATATCAGTG
1 ATCAATGGAAAAGATCATTATCAAAACAAAAGAAAAGATCAGTG
* *
71457 ATCAATGGAAGAGATCATTATTAAAACAAAAGAAAAGATCAGTG
1 ATCAATGGAAAAGATCATTATCAAAACAAAAGAAAAGATCAGTG
71501 ATCAA
1 ATCAA
71506 AACAGGAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (44 bp):
ATCAATGGAAAAGATCATTATCAAAACAAAAGAAAAGATCAGTG
Found at i:80740 original size:24 final size:24
Alignment explanation
Indices: 80687--80742 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
80677 TGAACGTTTG
* *
80687 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
*
80711 GCTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
80735 TTTATGTT
1 GTTATGTT
80743 TAACTCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:81698 original size:16 final size:16
Alignment explanation
Indices: 81674--81705 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
81664 TCTTAAATTT
*
81674 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
81690 TTTTCGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
81706 GAGTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:81801 original size:61 final size:61
Alignment explanation
Indices: 81706--81827 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
81696 AGTTCGAGTC
* *
81706 GAGTTTTAATATTATATTTTGAGTTCGAGTCGAGCTTGATAATTTTAAGCTCGCGAGTTTT
1 GAGTTTCAATATTATATTTCGAGTTCGAGTCGAGCTTGATAATTTTAAGCTCGCGAGTTTT
*
81767 GAGTTTCAATATTATATTTCGAGTTCGAGTCGAGCTTGATAATTTTAATCTCGCGAGTTTT
1 GAGTTTCAATATTATATTTCGAGTTCGAGTCGAGCTTGATAATTTTAAGCTCGCGAGTTTT
81828 CGAATCGAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (61 bp):
GAGTTTCAATATTATATTTCGAGTTCGAGTCGAGCTTGATAATTTTAAGCTCGCGAGTTTT
Found at i:81945 original size:10 final size:10
Alignment explanation
Indices: 81932--81974 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
81922 TTTATGTTCG
*
81932 TGTTCGTTTA
1 TGTTTGTTTA
*
81942 TGTTTATGTTTG
1 TG-TT-TGTTTA
81954 TGTTTGTTTA
1 TGTTTGTTTA
81964 TGTTTGTTTA
1 TGTTTGTTTA
81974 T
1 T
81975 TTATTAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 18 0.64
11 4 0.14
12 6 0.21
ACGTcount: A:0.09, C:0.02, G:0.21, T:0.67
Consensus pattern (10 bp):
TGTTTGTTTA
Found at i:81947 original size:22 final size:22
Alignment explanation
Indices: 81922--81968 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
81912 TTTGTGTTAA
81922 TTTATGTTCGTGTTCGTTTATG
1 TTTATGTTCGTGTTCGTTTATG
* *
81944 TTTATGTTTGTGTTTGTTTATG
1 TTTATGTTCGTGTTCGTTTATG
81966 TTT
1 TTT
81969 GTTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (22 bp):
TTTATGTTCGTGTTCGTTTATG
Found at i:81961 original size:16 final size:16
Alignment explanation
Indices: 81897--81974 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 16
81887 GAGCTCAATA
81897 TTATGTTCGTTTATGT
1 TTATGTTCGTTTATGT
* **
81913 TTGTGTTAATTTATGT
1 TTATGTTCGTTTATGT
**
81929 TCGTGTTCGTTTATGT
1 TTATGTTCGTTTATGT
*
81945 TTATGTTTGTGTT-TGT
1 TTATGTTCGT-TTATGT
*
81961 TTATGTTTGTTTAT
1 TTATGTTCGTTTAT
81975 TTATTAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
15 2 0.04
16 47 0.92
17 2 0.04
ACGTcount: A:0.12, C:0.04, G:0.21, T:0.64
Consensus pattern (16 bp):
TTATGTTCGTTTATGT
Found at i:81973 original size:32 final size:32
Alignment explanation
Indices: 81897--81974 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
81887 GAGCTCAATA
*
81897 TTATGTTCGTTTATGTTTGTGTTAATTTATGT
1 TTATGTTCGTTTATGTTTATGTTAATTTATGT
** **
81929 TCGTGTTCGTTTATGTTTATGTTTGTGTT-TGT
1 TTATGTTCGTTTATGTTTATGTTAAT-TTATGT
*
81961 TTATGTTTGTTTAT
1 TTATGTTCGTTTAT
81975 TTATTAAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.12, C:0.04, G:0.21, T:0.64
Consensus pattern (32 bp):
TTATGTTCGTTTATGTTTATGTTAATTTATGT
Found at i:82638 original size:11 final size:11
Alignment explanation
Indices: 82622--82669 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
82612 ATTAGCACAG
82622 AACCGGCTGAA
1 AACCGGCTGAA
82633 AACCGG--GAA
1 AACCGGCTGAA
*
82642 AACCGGGGTG--
1 AACC-GGCTGAA
82652 AACCGGCTGAA
1 AACCGGCTGAA
82663 AACCGGC
1 AACCGGC
82670 AAAACCGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
9 11 0.35
10 6 0.19
11 13 0.42
12 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.33, T:0.06
Consensus pattern (11 bp):
AACCGGCTGAA
Found at i:82685 original size:30 final size:30
Alignment explanation
Indices: 82621--82677 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
82611 GATTAGCACA
* *
82621 GAACCGGCTGAAAACCGGGAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACCGAGGT
82651 GAACCGGCTGAAAACCGGCAAAACCGA
1 GAACCGGCTGAAAACCGGCAAAACCGA
82678 TTTGAACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.32, T:0.05
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACCGAGGT
Found at i:83464 original size:10 final size:10
Alignment explanation
Indices: 83437--83478 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
83427 TATATAAAAT
*
83437 CCGGTTCAAC
1 CCGGTTGAAC
83447 CGCGGTTGAAC
1 C-CGGTTGAAC
83458 CCGGTTGAAC
1 CCGGTTGAAC
83468 CCGGTTGAAC
1 CCGGTTGAAC
83478 C
1 C
83479 AGTGAACCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (10 bp):
CCGGTTGAAC
Found at i:88592 original size:22 final size:22
Alignment explanation
Indices: 88562--88610 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
88552 GTTACATGAA
* *
88562 TTATTTGATTTAATTCCAGGG-G
1 TTATATGATATAATTCC-GGGAG
88584 TTATATGATATAATTCCGGGAG
1 TTATATGATATAATTCCGGGAG
88606 TTATA
1 TTATA
88611 ACAGCTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (22 bp):
TTATATGATATAATTCCGGGAG
Found at i:93466 original size:5 final size:5
Alignment explanation
Indices: 93456--93484 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
93446 CGCCGTCCAT
93456 CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
93485 TGGTCCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.38, T:0.21
Consensus pattern (5 bp):
CTCGG
Found at i:98355 original size:16 final size:16
Alignment explanation
Indices: 98334--98367 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
98324 GTTGCAATAA
98334 CTTCTAATACGGATAG
1 CTTCTAATACGGATAG
98350 CTTCTAATACGGATAG
1 CTTCTAATACGGATAG
98366 CT
1 CT
98368 CCCACTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (16 bp):
CTTCTAATACGGATAG
Found at i:103653 original size:42 final size:42
Alignment explanation
Indices: 103510--103754 Score: 264
Period size: 42 Copynumber: 5.7 Consensus size: 42
103500 ACAGGTCGGC
* *
103510 TCTATAGTGGCGTTTTTCGGAACAAACGCCGCAATAA-GTCGAGC
1 TCTATAGCGGCGTTTTT-GGAACAAACGCCGCAA-AAGGTC-AGA
*
103554 TCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGA
1 TCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AGA
* * *
103597 TCTATAACGGCGTTTTCTATG-A-AAACGCCGCAAAATGTCAGA
1 TCTATAGCGGCGTTTT-T-GGAACAAACGCCGCAAAAGGTCAGA
**
103639 TCTATAGCGGCGTTTTTGGAGA-AAACGTTGCAAAAGGTCAGA
1 TCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTCAGA
* * * **
103681 TTTATAGCGGCGTTTTTGGAATAAACGCCGTAAAATTTCAGA
1 TCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGA
*
103723 TCTATAGCGGCGTTTTTGGATGCAAACGCCGC
1 TCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
103755 TAATTATCGT
Statistics
Matches: 172, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 2 0.01
42 90 0.52
43 60 0.35
44 18 0.10
45 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
TCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAGA
Found at i:108477 original size:41 final size:41
Alignment explanation
Indices: 108423--108809 Score: 272
Period size: 41 Copynumber: 9.4 Consensus size: 41
108413 TTGTAAACAC
* * *
108423 AAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTATGACTCTATTGCGGCGTTTGTATAA
* * * * * *
108464 AAATGCCGCTAAAGAACGTA-TTTATAGCGGCGTTTGAATAAA
1 AAACGCCGCTAAAGTATG-ACTCTATTGCGGCGTTTGTAT-AA
* ** * *
108506 AAACGCCACTAAAGTATGTGTCTATAGCGGCTTTTGTATAA
1 AAACGCCGCTAAAGTATGACTCTATTGCGGCGTTTGTATAA
* *
108547 AAACGCCGCTAAAGTACT-ACTCTTTTGCGGTGTTTGTATAAA
1 AAACGCCGCTAAAGTA-TGACTCTATTGCGGCGTTTGTAT-AA
* * *
108589 AAACGCCGCTAAAGTACT-ACTCTGTTGCGGCGTTTAT-TGA
1 AAACGCCGCTAAAGTA-TGACTCTATTGCGGCGTTTGTATAA
* * * * *
108629 AAATGCC-ATAATA-TATGAACCCTATTGCGGCGTTTTTATTA
1 AAACGCCGCTAA-AGTATG-ACTCTATTGCGGCGTTTGTATAA
* * * ** *
108670 AAACACCGCTAAAGTACT-ACTATGTCACGGCGTTTGTTTAAA
1 AAACGCCGCTAAAGTA-TGACTCTATTGCGGCGTTTGTAT-AA
* * *
108712 AAACGCCACT-ATGGATGAAC-CTATTGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTATG-ACTCTATTGCGGCGTTTGTATAA
* *
108752 AAACGCCACTAAAGTACT-ACTCTGTTGCGGCGTTTTGTATAAA
1 AAACGCCGCTAAAGTA-TGACTCTATTGCGGCG-TTTGTAT-AA
108795 AAACGCCGCTAAAGT
1 AAACGCCGCTAAAGT
108810 TACTATTTTG
Statistics
Matches: 271, Mismatches: 55, Indels: 38
0.74 0.15 0.10
Matches are distributed among these distances:
38 1 0.00
39 5 0.02
40 39 0.14
41 115 0.42
42 94 0.35
43 17 0.06
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTAAAGTATGACTCTATTGCGGCGTTTGTATAA
Found at i:108619 original size:83 final size:82
Alignment explanation
Indices: 108423--108814 Score: 302
Period size: 83 Copynumber: 4.7 Consensus size: 82
108413 TTGTAAACAC
* * * * *
108423 AAACGCCACTAAAGTA-TGAGTCTATAGCGGCGTTTGTATAAAAATGCCGCTAAAGAACGTA-TT
1 AAACGCCACTAAAGTACT-ACTCTGTAGCGGCGTTTGTATAAAAACGCCGCTAAAGTAC-TACTC
* *
108486 TATAGCGGCGTTTGAATAAA
64 TATTGCGGCGTTTGTAT-AA
** * *
108506 AAACGCCACTAAAGTA-TGTGTCTATAGCGGCTTTTGTATAAAAACGCCGCTAAAGTACTACTCT
1 AAACGCCACTAAAGTACT-ACTCTGTAGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCT
* *
108570 TTTGCGGTGTTTGTATAAA
65 ATTGCGGCGTTTGTAT-AA
* * * * * * *
108589 AAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTAT-TGAAAATGCC-ATAATA-TA-TGAACC
1 AAACGCCACTAAAGTACTACTCTGTAGCGGCGTTTGTATAAAAACGCCGCTAA-AGTACT--ACT
* *
108650 CTATTGCGGCGTTTTTATTA
63 CTATTGCGGCGTTTGTATAA
* * * * * * *
108670 AAACACCGCTAAAGTACTACTATGTCA-CGGCGTTTGTTTAAAAAACGCCACT-ATGGA-TGAAC
1 AAACGCCACTAAAGTACTACTCTGT-AGCGGCGTTTGTAT-AAAAACGCCGCTAAAGTACT--AC
108732 -CTATTGCGGCGTTTGTATAA
62 TCTATTGCGGCGTTTGTATAA
*
108752 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGTATAAAAAACGCCGCTAAAGTTACTA
1 AAACGCCACTAAAGTACTACTCTGTAGCGGCG-TTTGTAT-AAAAACGCCGCTAAAG-TACTA
108815 TTTTGTGGCG
Statistics
Matches: 251, Mismatches: 43, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
80 1 0.00
81 38 0.15
82 74 0.29
83 131 0.52
84 5 0.02
85 1 0.00
86 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (82 bp):
AAACGCCACTAAAGTACTACTCTGTAGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTA
TTGCGGCGTTTGTATAA
Found at i:108825 original size:123 final size:122
Alignment explanation
Indices: 108451--108828 Score: 310
Period size: 123 Copynumber: 3.1 Consensus size: 122
108441 AGTCTATAGC
* * * * * *
108451 GGCGTTTGTAT-AAAAATGCCGCTAAAGAACGTA-TTTATAGCGGCGTTTGAATAAAAAACGCCA
1 GGCGTTTGTATAAAAAACGCCACTAAAGTAC--ACTCTATTGCGGCGTTTGTAT-AAAAACGCCA
** * * *
108514 CTAAAGTATGTGTCTATAGCGGC-TTTTGTATAAAAACGCCGCTAAAGTACTACTCTTTTGC
63 CTAAAGTATGACTCTATTGCGGCGTTTTGTATAAAAACGCCGCTAAAGT--TACTATTTTGT
* * * * * *
108575 GGTGTTTGTATAAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTAT-TGAAAATGCCA-T
1 GGCGTTTGTATAAAAAACGCCACTAAAGTAC-ACTCTATTGCGGCGTTTGTATAAAAACGCCACT
* * * * *
108638 AATA-TATGAACCCTATTGCGGCGTTTT-TATTAAAACACCGCTAAAG-TACTACTATGT
65 AA-AGTATG-ACTCTATTGCGGCGTTTTGTATAAAAACGCCGCTAAAGTTACTATTTTGT
* **
108695 CACGGCGTTTGTTTAAAAAACGCCACTATGGATGA-AC-CTATTGCGGCGTTTGTATAAAAACGC
1 ---GGCGTTTGTATAAAAAACGCCACTAAAG-T-ACACTCTATTGCGGCGTTTGTATAAAAACGC
*
108758 CACTAAAGTACT-ACTCTGTTGCGGCGTTTTGTATAAAAAACGCCGCTAAAGTTACTATTTTGT
61 CACTAAAGTA-TGACTCTATTGCGGCGTTTTGTAT-AAAAACGCCGCTAAAGTTACTATTTTGT
108821 GGCGTTTG
1 GGCGTTTG
108829 AAGTGTAAAC
Statistics
Matches: 202, Mismatches: 35, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
120 7 0.03
122 21 0.10
123 94 0.47
124 26 0.13
125 45 0.22
126 9 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (122 bp):
GGCGTTTGTATAAAAAACGCCACTAAAGTACACTCTATTGCGGCGTTTGTATAAAAACGCCACTA
AAGTATGACTCTATTGCGGCGTTTTGTATAAAAACGCCGCTAAAGTTACTATTTTGT
Found at i:110713 original size:23 final size:24
Alignment explanation
Indices: 110676--110725 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
110666 CGTCCGATAA
* *
110676 TATGTTTGTTTATGTTCATTTATT
1 TATGTTTGTTAATGTTCATTCATT
110700 TATG-TTGTTAATGTTCATTCATT
1 TATGTTTGTTAATGTTCATTCATT
110723 TAT
1 TAT
110726 ATTCATTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.20, C:0.06, G:0.12, T:0.62
Consensus pattern (24 bp):
TATGTTTGTTAATGTTCATTCATT
Found at i:111150 original size:10 final size:10
Alignment explanation
Indices: 111126--111173 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
111116 TGTTGTTGTG
*
111126 GTTTATGTTA
1 GTTTATGTTT
*
111136 ATTTATGTTT
1 GTTTATGTTT
111146 GTTTATTGTATT
1 GTTTA-TGT-TT
111158 CGTTTATGTTT
1 -GTTTATGTTT
111169 GTTTA
1 GTTTA
111174 CGTTCATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 17 0.53
11 5 0.16
12 5 0.16
13 5 0.16
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.65
Consensus pattern (10 bp):
GTTTATGTTT
Found at i:117111 original size:27 final size:27
Alignment explanation
Indices: 117073--117151 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
117063 TTTCTACTGG
* *
117073 TTTTGATATTATTGGGCGCTTTACCAA
1 TTTTGTTATTATTGGACGCTTTACCAA
* *
117100 TTTTGTTATTATTGGATGCTTTACCAG
1 TTTTGTTATTATTGGACGCTTTACCAA
* * *
117127 TTTTGTTATTGTTAGACACTTTACC
1 TTTTGTTATTATTGGACGCTTTACC
117152 GGAAATGTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.49
Consensus pattern (27 bp):
TTTTGTTATTATTGGACGCTTTACCAA
Found at i:120444 original size:17 final size:17
Alignment explanation
Indices: 120422--120482 Score: 122
Period size: 17 Copynumber: 3.6 Consensus size: 17
120412 TACCCGATTA
120422 CCGGGTACCCTCAAAAT
1 CCGGGTACCCTCAAAAT
120439 CCGGGTACCCTCAAAAT
1 CCGGGTACCCTCAAAAT
120456 CCGGGTACCCTCAAAAT
1 CCGGGTACCCTCAAAAT
120473 CCGGGTACCC
1 CCGGGTACCC
120483 GATTACCGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.26, C:0.38, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGGGTACCCTCAAAAT
Found at i:128394 original size:23 final size:22
Alignment explanation
Indices: 128351--128398 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
128341 TATTTAATAT
*
128351 TTTTATTTTTAATGTACTATTGA
1 TTTTATTTTTAATATACTATT-A
*
128374 TTTTATTTATTTATATA-TATTA
1 TTTTATTT-TTAATATACTATTA
128396 TTT
1 TTT
128399 CAAGTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTAATATACTATTA
Found at i:129098 original size:29 final size:30
Alignment explanation
Indices: 129056--129112 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
129046 CCCTTTTTTT
*
129056 AGTTTAGTGCCTAACG-TTTATTTCGTTCC
1 AGTTTAGTGCCTAACGTTTTATTCCGTTCC
* *
129085 AGTTTGGTGCCTAATGTTTTATTCCGTT
1 AGTTTAGTGCCTAACGTTTTATTCCGTT
129113 ACTCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGCCTAACGTTTTATTCCGTTCC
Found at i:130260 original size:23 final size:23
Alignment explanation
Indices: 130202--130289 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
130192 CCAATTAATT
*
130202 TTATGTTCGCTCGTTTATGTTC-
1 TTATGTTCGTTCGTTTATGTTCG
*
130224 --AT-TTACGTTTGTTTATGTTCG
1 TTATGTT-CGTTCGTTTATGTTCG
*
130245 TTATGTTCGTTCGTTTGTGTTCG
1 TTATGTTCGTTCGTTTATGTTCG
*
130268 TTATGTTCGTTCGTTTGTGTTC
1 TTATGTTCGTTCGTTTATGTTC
130290 ATTCATTTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.04
20 15 0.26
23 38 0.67
24 2 0.04
ACGTcount: A:0.08, C:0.14, G:0.22, T:0.57
Consensus pattern (23 bp):
TTATGTTCGTTCGTTTATGTTCG
Found at i:130265 original size:14 final size:13
Alignment explanation
Indices: 130240--130306 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
130230 GTTTGTTTAT
*
130240 GTTCGTTATGTTC
1 GTTCGTTGTGTTC
130253 GTTCGTT-TG-T-
1 GTTCGTTGTGTTC
*
130263 GTTCGTTATGTTC
1 GTTCGTTGTGTTC
130276 GTTCGTTTGTGTTC
1 GTTCG-TTGTGTTC
* *
130290 ATTCATTTGTGTTC
1 GTTC-GTTGTGTTC
130304 GTT
1 GTT
130307 TATCATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 7 0.16
11 3 0.07
12 3 0.07
13 12 0.27
14 20 0.44
ACGTcount: A:0.06, C:0.13, G:0.24, T:0.57
Consensus pattern (13 bp):
GTTCGTTGTGTTC
Found at i:139663 original size:33 final size:33
Alignment explanation
Indices: 139621--139688 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
139611 AAAGCACTGC
139621 GAGAAGCAACATATTTGATAGGAATAGATTCAT
1 GAGAAGCAACATATTTGATAGGAATAGATTCAT
139654 GAGAAGCAACATATTTGATAGGAATAGATTCAT
1 GAGAAGCAACATATTTGATAGGAATAGATTCAT
139687 GA
1 GA
139689 AATAAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (33 bp):
GAGAAGCAACATATTTGATAGGAATAGATTCAT
Done.