Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000836.1 Hibiscus syriacus cultivar Beakdansim tig00001617_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: 98063
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4502 original size:27 final size:27
Alignment explanation
Indices: 4462--4535 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
4452 ATTGGATCTT
* *
4462 AAAATGATCGAAATACCCTCGAGT-TCC
1 AAAATGACCAAAATACCCTCGAGTAT-C
* *
4489 AAAATGACTAAAATAACCC-CGAGTATT
1 AAAATGACCAAAAT-ACCCTCGAGTATC
*
4516 AAAATGACCCAAATACCCTC
1 AAAATGACCAAAATACCCTC
4536 ATGATATGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.11
27 29 0.76
28 5 0.13
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATACCCTCGAGTATC
Found at i:8376 original size:21 final size:21
Alignment explanation
Indices: 8313--8376 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
8303 TCGTCTCTGG
*
8313 AATTTTTCATGGGATGCAACC
1 AATTTTTCATGGGATGAAACC
** *
8334 AACGTTTCTTGGGAT-AAGACC
1 AATTTTTCATGGGATGAA-ACC
*
8355 AATTTTTCATGGGATGTAACC
1 AATTTTTCATGGGATGAAACC
8376 A
1 A
8377 TCTTTTCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
AATTTTTCATGGGATGAAACC
Found at i:8382 original size:21 final size:21
Alignment explanation
Indices: 8316--8383 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
8306 TCTCTGGAAT
* *
8316 TTTTCATGGGATGCAACCAAC
1 TTTTCATGGGATGAAACCATC
* *
8337 GTTTCTTGGGAT-AAGACCAAT-
1 TTTTCATGGGATGAA-ACC-ATC
*
8358 TTTTCATGGGATGTAACCATC
1 TTTTCATGGGATGAAACCATC
8379 TTTTC
1 TTTTC
8384 TTGTGAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 3 0.08
21 31 0.86
22 2 0.06
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTTCATGGGATGAAACCATC
Found at i:10777 original size:21 final size:23
Alignment explanation
Indices: 10727--10779 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
10717 ATAGCCTTCA
10727 AAATCCTAAAAACAAAGTAAAGAT
1 AAATCCT-AAAACAAAGTAAAGAT
*
10751 -AATCCTAAAATAAAG-AAA-AT
1 AAATCCTAAAACAAAGTAAAGAT
10771 AAATCCTAA
1 AAATCCTAA
10780 TTAAAATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 11 0.41
22 8 0.30
23 6 0.22
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (23 bp):
AAATCCTAAAACAAAGTAAAGAT
Found at i:10882 original size:5 final size:5
Alignment explanation
Indices: 10821--10876 Score: 112
Period size: 5 Copynumber: 11.2 Consensus size: 5
10811 ACCTAATACA
10821 AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT
1 AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT AAGAT
10871 AAGAT A
1 AAGAT A
10877 TAATATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
AAGAT
Found at i:15167 original size:22 final size:22
Alignment explanation
Indices: 15119--15167 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
15109 TGTGTTGTAC
15119 GTTTTCATTATCTTTATAGCAT
1 GTTTTCATTATCTTTATAGCAT
* * *
15141 ATTTTC-TTATTCTTTTTGGCAT
1 GTTTTCATTA-TCTTTATAGCAT
15163 GTTTT
1 GTTTT
15168 TCAGTTGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.61
Consensus pattern (22 bp):
GTTTTCATTATCTTTATAGCAT
Found at i:15795 original size:19 final size:19
Alignment explanation
Indices: 15747--15797 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
15737 AAGTTTTAAA
15747 AATTAAACAAATTATATGT
1 AATTAAACAAATTATATGT
* *
15766 --TTAAACGAATTATATTT
1 AATTAAACAAATTATATGT
*
15783 AATTAAATAAATTAT
1 AATTAAACAAATTAT
15798 TCACAACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 15 0.58
19 11 0.42
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (19 bp):
AATTAAACAAATTATATGT
Found at i:15978 original size:29 final size:29
Alignment explanation
Indices: 15946--16003 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
15936 AAAAAATCGG
*
15946 TTAATTCGGTTCGGTGAATAATTTTCAAA
1 TTAATTCGGTTCGGTGAATAATTTACAAA
*
15975 TTAATTCGGTTCGGTTAATAATTTACAAA
1 TTAATTCGGTTCGGTGAATAATTTACAAA
16004 AAAATTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (29 bp):
TTAATTCGGTTCGGTGAATAATTTACAAA
Found at i:16009 original size:29 final size:29
Alignment explanation
Indices: 15948--16022 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
15938 AAAATCGGTT
* * **
15948 AATTCGGTTCGGTGAATAATTTTCAAATT
1 AATTCGGTTCGGTTAATAATTTACAAAAA
15977 AATTCGGTTCGGTTAATAATTTACAAAAA
1 AATTCGGTTCGGTTAATAATTTACAAAAA
* *
16006 AATTTGGTTCGATTAAT
1 AATTCGGTTCGGTTAAT
16023 CAAACTGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (29 bp):
AATTCGGTTCGGTTAATAATTTACAAAAA
Found at i:16116 original size:28 final size:29
Alignment explanation
Indices: 16082--16139 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
16072 AAAAAATTGG
*
16082 TTAATTCGGATCGGTT-ATTATTTTCAAA
1 TTAATTCGGATCGGTTAATAATTTTCAAA
16110 TTAATTCGGATCGGTTAATAATTTTCAAA
1 TTAATTCGGATCGGTTAATAATTTTCAAA
16139 T
1 T
16140 AAAATTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAATTCGGATCGGTTAATAATTTTCAAA
Found at i:16251 original size:29 final size:29
Alignment explanation
Indices: 16219--16295 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
16209 AAAAAATCGG
*
16219 TTAATTTGGTTCGGTTAATAATTTTCAAA
1 TTAATTTGGTTCAGTTAATAATTTTCAAA
** *
16248 TTAATTCAGTTCAGTTAATAATTTTCTAA
1 TTAATTTGGTTCAGTTAATAATTTTCAAA
* *
16277 TAAATTTTGGTTCAATTAA
1 TTAA-TTTGGTTCAGTTAA
16296 CCAAACTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (29 bp):
TTAATTTGGTTCAGTTAATAATTTTCAAA
Found at i:16394 original size:29 final size:29
Alignment explanation
Indices: 16359--16515 Score: 143
Period size: 29 Copynumber: 5.2 Consensus size: 29
16349 AAATAATCGG
*
16359 TTAATTCTGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
*
16388 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
* * * * ***
16417 TAAATTTTGGTTCGATTAATGATTAAAAAAATAA
1 TTAA-TTCGGTTCGGTTAATAATT---TTCA-AA
*
16451 GTTAATCCGGTTCGGTTAATAATTTTCAAA
1 -TTAATTCGGTTCGGTTAATAATTTTCAAA
* *
16481 TTAATTCAGTTCGGTTAATAATTTTAAAA
1 TTAATTCGGTTCGGTTAATAATTTTCAAA
*
16510 TAAATT
1 TTAATT
16516 TTGGTTCGAT
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
29 61 0.61
30 17 0.17
31 1 0.01
33 1 0.01
34 17 0.17
35 3 0.03
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.43
Consensus pattern (29 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAA
Found at i:16409 original size:140 final size:137
Alignment explanation
Indices: 15935--16435 Score: 718
Period size: 137 Copynumber: 3.6 Consensus size: 137
15925 ATGGTTAAAG
* * *
15935 AAAAAAATCGGTTAATTCGGTTCGGTGAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTA
1 AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTT
* * * * *
16000 CAAA-AAAATTTGGTTCGATTAATCAAACTGAATTAACCGATTTTTTGCTTCGATTAATTCAATT
66 CAAATAAATTTTGGTTCGATTAACCAAACTGAATTAACCAAATTTTTGCTTCGATTAATTCGATT
16064 AATAATT
131 AATAATT
* * * * *
16071 AAAAAAATTGGTTAATTCGGATCGGTT-ATTATTTTCAAATTAATTCGGATCGGTTAATAATTTT
1 AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTT
* * * * * *
16135 CAAATAAAATTTTGGTTCGATTAACCGAGCCGAATTAATCAAAGTTTTACTTCGATTAATTCGAT
66 CAAAT-AAATTTTGGTTCGATTAACCAAACTGAATTAACCAAATTTTTGCTTCGATTAATTCGAT
16200 TAATAATT
130 TAATAATT
* *
16208 AAAAAAATCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTCAGTTCAGTTAATAATTTT
1 AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTT
* * *
16273 CTAATAAATTTTGGTTCAATTAACCAAACTGAATTAACCAAATTTTTGCTTCGATTAATTCGGTT
66 CAAATAAATTTTGGTTCGATTAACCAAACTGAATTAACCAAATTTTTGCTTCGATTAATTCGATT
16338 AATAATTTT
131 AATAA--TT
* *
16347 CAAAATAATCGGTTAATTCTGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTT
1 -AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTT
16412 TCAAATAAATTTTGGTTCGATTAA
65 TCAAATAAATTTTGGTTCGATTAA
16436 TGATTAAAAA
Statistics
Matches: 320, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
135 38 0.12
136 24 0.08
137 137 0.43
138 37 0.12
139 2 0.01
140 82 0.26
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.41
Consensus pattern (137 bp):
AAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTT
CAAATAAATTTTGGTTCGATTAACCAAACTGAATTAACCAAATTTTTGCTTCGATTAATTCGATT
AATAATT
Found at i:16445 original size:233 final size:234
Alignment explanation
Indices: 16194--16627 Score: 710
Period size: 233 Copynumber: 1.9 Consensus size: 234
16184 CTTCGATTAA
** **
16194 TTCGATTAATAATTAAAAAAATCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTCAGTT
1 TTCGATTAATAATTAAAAAAATAAGTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTT
** *
16259 CAGTTAATAATTTTCTAATAAATTTTGGTTCAATTAACCAAACTGAATTAACCAAATTTTTGCTT
66 CAGTTAATAATTTTAAAATAAATTTTGGTTCAATTAACCAAACCGAATTAACCAAATTTTTGCTT
*
16324 CGATTAATTCGGTTAATAA-TTTTCAAAATAATCGGTTAATTCT-GTTCGGTTAATAATTTTCAA
131 CGATTAATTCGGTTAATAATTTTTCAAAAAAATCGGTTAATT-TGGTTCGGTTAATAATTTTCAA
*
16387 ATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGG
195 ATAAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGG
*
16427 TTCGATTAATGATTAAAAAAATAAGTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTT
1 TTCGATTAATAATTAAAAAAATAAGTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTT
* * *
16492 CGGTTAATAATTTTAAAATAAATTTTGGTTCGATTAACCAAACCGAATTAACCGAATTTTTGCTT
66 CAGTTAATAATTTTAAAATAAATTTTGGTTCAATTAACCAAACCGAATTAACCAAATTTTTGCTT
* *
16557 CGATTAATTCGGTTAATAATTTTTTAAAAAAATTGGTTAATTTGGTTCGGTTAATAATTTTCAAA
131 CGATTAATTCGGTTAATAATTTTTCAAAAAAATCGGTTAATTTGGTTCGGTTAATAATTTTCAAA
16622 TAAATT
196 TAAATT
16628 TTGGTTCAAT
Statistics
Matches: 184, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
233 139 0.76
234 45 0.24
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (234 bp):
TTCGATTAATAATTAAAAAAATAAGTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTT
CAGTTAATAATTTTAAAATAAATTTTGGTTCAATTAACCAAACCGAATTAACCAAATTTTTGCTT
CGATTAATTCGGTTAATAATTTTTCAAAAAAATCGGTTAATTTGGTTCGGTTAATAATTTTCAAA
TAAATTCGGTTCAGTTAATAATTTTCAAATAAATTTTGG
Found at i:16471 original size:93 final size:93
Alignment explanation
Indices: 16358--16528 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
16348 AAAATAATCG
* * * *
16358 GTTAATTCTGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATT
1 GTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTTCAGTTAATAATTTTAAAATAAATT
16423 TTGGTTCGATTAATGATTAAAAAAATAA
66 TTGGTTCGATTAATGATTAAAAAAATAA
*
16451 GTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTTCGGTTAATAATTTTAAAATAAATT
1 GTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTTCAGTTAATAATTTTAAAATAAATT
16516 TTGGTTCGATTAA
66 TTGGTTCGATTAA
16529 CCAAACCGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (93 bp):
GTTAATCCGGTTCGGTTAATAATTTTCAAATTAATTCAGTTCAGTTAATAATTTTAAAATAAATT
TTGGTTCGATTAATGATTAAAAAAATAA
Found at i:16578 original size:103 final size:107
Alignment explanation
Indices: 16461--16665 Score: 265
Period size: 112 Copynumber: 1.9 Consensus size: 107
16451 GTTAATCCGG
*
16461 TTCGGTTAATAA-TTTT-CAAA-TTAATTCAGTTCGGTTAATAATTTTAAAATAAATTTTGGTTC
1 TTCGGTTAATAATTTTTAAAAAGTTAATTCAGTTCGGTTAATAATTTTAAAATAAATTTTGGTTC
* *
16523 GATTAACCAAACCGAATTAACC-GAATTTTTGCTTCGATTAA
66 AATTAACCAAACCGAATTAACCAAAATTTTTGCTTCGATTAA
** *
16564 TTCGGTTAATAATTTTTTAAAAAAATTGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTT
1 TTCGGTTAATAA-TTTTT--AAAAA---GTTAATTCAGTTCGGTTAATAATTTTAAAATAAATTT
*
16629 TGGTTCAATTAACCGAACCGAATTAACCAAAATTTTT
60 TGGTTCAATTAACCAAACCGAATTAACCAAAATTTTT
16666 CTTTAACCGT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
103 12 0.14
105 4 0.05
108 3 0.04
112 59 0.69
113 7 0.08
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (107 bp):
TTCGGTTAATAATTTTTAAAAAGTTAATTCAGTTCGGTTAATAATTTTAAAATAAATTTTGGTTC
AATTAACCAAACCGAATTAACCAAAATTTTTGCTTCGATTAA
Found at i:20283 original size:42 final size:42
Alignment explanation
Indices: 20098--20363 Score: 259
Period size: 43 Copynumber: 6.2 Consensus size: 42
20088 TGAGAACAAA
* * * *
20098 AAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAAGTC-AGATCTA-TAGCGGCGTTTTTGGAAC
* * *
20141 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * * * *
20184 AAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGAAA
1 AAACGCCGCAAAAAGTCA-GATCTATAGCGGCGTTTTTGGAAC
* *
20227 AAACACCGCAAAAAGTCAGATCTATAGCAGCGTTTTTGGATAC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGA-AC
* * * * *
20270 AAACGCCGCAAAAGAG-AAGACCTATA-CTAGTGTTTTTAGAAC
1 AAACGCCGCAAAA-AGTCAGATCTATAGC-GGCGTTTTTGGAAC
*
20312 AAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGA-AC
20355 AAACGCCGC
1 AAACGCCGC
20364 TAATTACCTT
Statistics
Matches: 188, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.01
42 55 0.29
43 129 0.69
44 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:20310 original size:85 final size:85
Alignment explanation
Indices: 20128--20363 Score: 289
Period size: 85 Copynumber: 2.8 Consensus size: 85
20118 ATCTATTACG
* * * *
20128 GCGTTTTTTGAACAAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCG
1 GCGTTTTTAGAACAAACGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTGGATACAAACGCCG
* * *
20192 CAAAAAGTTATGATATATAGCG
65 CAAAAAG-TAAGACATATAGCA
* * * *
20214 GCGTTTCTAGAAAAAACACCGCAAAAAGTCAGATCTATAGCAGCGTTTTTGGATACAAACGCCGC
1 GCGTTTTTAGAACAAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
*
20279 AAAAGAG-AAGACCTATA-CTA
66 AAAA-AGTAAGACATATAGC-A
* *
20299 GTGTTTTTAGAACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 GCGTTTTTAGAACAAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
20364 TAATTACCTT
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 87 0.67
86 39 0.30
87 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (85 bp):
GCGTTTTTAGAACAAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
AAAAAGTAAGACATATAGCA
Found at i:25083 original size:41 final size:42
Alignment explanation
Indices: 25026--25205 Score: 233
Period size: 41 Copynumber: 4.4 Consensus size: 42
25016 GAGGATTGAC
*
25026 AACGCCACTATAGTAC-ATGTGTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTGTATAACGGCGTTTGTATAAA
* *
25067 AACGCCACTATAGTAC-ATGTGTATAACGGTGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTGTATAACGGCGTTTGTATAAA
* *
25108 AACGCCACTAAAGTACAAT-TTTATAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTGTATAACGGCGTTTGTATAAA
** * * * *
25149 AATACCACTAAATTACGA-GTCTTTAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACAATGTGTATAACGGCGTTTGTATAAA
25190 AACGCCACTAAAGTAC
1 AACGCCACTAAAGTAC
25206 TACTCTTTTG
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
41 120 0.98
42 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (42 bp):
AACGCCACTAAAGTACAATGTGTATAACGGCGTTTGTATAAA
Found at i:25213 original size:41 final size:39
Alignment explanation
Indices: 25026--25241 Score: 202
Period size: 41 Copynumber: 5.3 Consensus size: 39
25016 GAGGATTGAC
* *
25026 AACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACATCT-T-TAACGGCGTTTGTATAAA
* * *
25067 AACGCCACTATAGTACATGTGTATAACGGTGTTTGTATAAA
1 AACGCCACTAAAGTACATCT-T-TAACGGCGTTTGTATAAA
25108 AACGCCACTAAAGTACAAT-TTTATAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTAC-ATCTTTA-A-CGGCGTTTGTATAAA
** *
25149 AATACCACTAAATTACGAGTCTTTAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTAC-A-TCTTTAACGGCGTTTGTATAAA
** *
25190 AACGCCACTAAAGTACTACTCTTTTGCGGTGTTTGT-TGAAAA
1 AACGCCACTAAAGTAC-A-TCTTTAACGGCGTTTGTAT--AAA
25232 AACGCCACTA
1 AACGCCACTA
25242 TCGATGAACC
Statistics
Matches: 153, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.01
40 3 0.02
41 127 0.83
42 17 0.11
43 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (39 bp):
AACGCCACTAAAGTACATCTTTAACGGCGTTTGTATAAA
Found at i:26501 original size:131 final size:131
Alignment explanation
Indices: 26262--26506 Score: 341
Period size: 131 Copynumber: 1.9 Consensus size: 131
26252 TCGAGAGGAT
* * * *
26262 ATATCACTATTTCATCTTAAAATTCAATATTGATTCGAAAGTAAATAATAATATCTAATTATTTA
1 ATATAACTATTTCATCTTAAAATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATTTA
* * *
26327 CAATCGAGAATAAATGACCTCCCATGCGTTAAAGCATTCATTTATTACTTTAATCAAAATGAAGA
66 CAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACTTTAATCAAAATGAAGA
26392 G
131 G
* **
26393 ATATAACTATTT-AGTCTTAAAGA-TCAATATTAATTCGAGAGAAAACGGTAATATCTAATTATT
1 ATATAACTATTTCA-TCTTAAA-ATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATT
* **
26456 TTCAATCGAGAATAAATGACCTTTCATGCCTTAAAGCAGTAATTTATTACT
64 TACAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACT
26507 CCAACCGAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
130 1 0.01
131 97 0.98
132 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (131 bp):
ATATAACTATTTCATCTTAAAATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATTTA
CAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACTTTAATCAAAATGAAGA
G
Found at i:26523 original size:131 final size:131
Alignment explanation
Indices: 26262--26535 Score: 327
Period size: 131 Copynumber: 2.1 Consensus size: 131
26252 TCGAGAGGAT
* * * *
26262 ATATCACTATTTCATCTTAAAATTCAATATTGATTCGAAAGTAAATAATAATATCTAATTATTTA
1 ATATAACTATTTCATCTTAAAATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATTTA
* * * ** * **
26327 CAATCGAGAATAAATGACCTCCCATGCGTTAAAGCATTCATTTATTACTTTAATCAAAATGAAGA
66 CAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACTCCAACCAAAACAAAGA
26392 G
131 G
* **
26393 ATATAACTATTT-AGTCTTAAAGA-TCAATATTAATTCGAGAGAAAACGGTAATATCTAATTATT
1 ATATAACTATTTCA-TCTTAAA-ATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATT
* ** *
26456 TTCAATCGAGAATAAATGACCTTTCATGCCTTAAAGCAGTAATTTATTACTCCAACCGAAACAAA
64 TACAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACTCCAACCAAAACAAA
26521 GAG
129 GAG
* *
26524 ATGTTACTATTT
1 ATATAACTATTT
26536 TCAAAATCGA
Statistics
Matches: 120, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
130 1 0.01
131 118 0.98
132 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (131 bp):
ATATAACTATTTCATCTTAAAATTCAATATTAATTCGAAAGAAAACAATAATATCTAATTATTTA
CAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTAATTTATTACTCCAACCAAAACAAAGA
G
Found at i:29596 original size:910 final size:912
Alignment explanation
Indices: 26531--30192 Score: 6734
Period size: 912 Copynumber: 4.0 Consensus size: 912
26521 GAGATGTTAC
26531 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
1 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
26596 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
66 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
*
26661 ATAAGGATGTTCAATTATTTAAATGCGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
131 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
*
26726 TCGGTAAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
196 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
*
26791 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTATTATAC
261 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
*
26856 ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTGA
326 ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTAA
26921 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
391 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
* *
26986 AAAAATTAGAATAAAATAAAATGAAAATAGGATTAAAATATAAACAATCAAATCATCATGTTAAA
456 AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
27051 AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
521 AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
*
27116 ACAAAGGATAAAAATAAATAAAACATGGGAACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
586 ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
*
27181 TAAATTAAATAAAAAATATTATAGTTCAAAATTTAAAGGGACTATTTCCTAATTATTCCTTTTCT
651 TAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCCTTTTCT
*
27246 ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAACA
716 ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAAAA
*
27311 ATTAAATCATCACTACACAAGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
781 ATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
27376 AATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGTG
846 AATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGTG
27441 AA
911 AA
27443 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
1 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
27508 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
66 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
27573 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
131 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
27638 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
196 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
27703 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
261 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
* *
27768 ATTAATATAGTCACTTTACGACAATATTAAAATGAATGAATATTACCCTAGTCAAATTATTTTAA
326 ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTAA
27833 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
391 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
27898 AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
456 AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
27963 AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
521 AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
28028 ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
586 ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
28093 TAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCCTTTTCT
651 TAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCCTTTTCT
*
28158 ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAACA
716 ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAAAA
28223 ATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
781 ATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
28288 AATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGTG
846 AATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGTG
28353 AA
911 AA
28355 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
1 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
28420 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
66 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
28485 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
131 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
28550 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
196 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
28615 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
261 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
*
28680 ATTAAGATAGTCACTTTACGACAATATTAAAATGAATGAATATTACCCTAGTCAAATTATTTTAA
326 ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTAA
28745 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
391 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
28810 AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
456 AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
*
28875 AATTAAAAGAAAATAAAGTGTAAACGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
521 AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
28940 ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
586 ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
*
29005 TAAATTAAAT-AAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCATTTTCT
651 TAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCCTTTTCT
* *
29069 ATGAGACTAAATTATGCTTCTAAAAATGATTAAATTATTAAATCAGTCCAGAAGTATTTTAAAAA
716 ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAAAA
* *
29134 ATTAAATCATCACTACACATGACTAAAATGT-AAAAAAAGCTAAACATGGAGGGATTAAAACGAA
781 ATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
* *
29198 AATAACCATAAAAATATAT-ACTATGCACAAAAGTCGGTAAATTATAAAATCGATCCCTACAGGT
846 AATAACCATAAAAATATATAAC-ATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGT
29262 GAA
910 GAA
29265 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
1 TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
*
29330 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAAAGAGA
66 AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
29395 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
131 ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
*
29460 TCTGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
196 TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
29525 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
261 TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
* *
29590 ATTAAGACAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTGA
326 ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTAA
*
29655 TTCGAAAGAAATGCCTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
391 TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATG-------A---
*
29720 AATAAACATGCAAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAATAATCAAATC
446 AAT-AACATGCAAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATC
*
29785 ATCATGTGAAAAATTAAAAGAAAATAAAGTGT---A---A--AAAATGAACATTTTTAATATTAA
510 ATCATGTCAAAAATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAA
*
29842 GTGCTAAAATTACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAATTTG
575 GTGCTAAAATTACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTG
* *
29907 CATGGCCAAATTAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTACTAATT
640 CATGACCAAATTAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATT
* *
29972 ATTCCTTTCCTATGAGACTAAATCATGCTTCTAAAAAATGATTAAATTACTAAATCAATCCAGAA
705 ATTCCTTTTCTATGAGACTAAATCATGCTTCT-AAAAATGATTAAATTACTAAATCAGTCCAGAA
* * **
30037 GTATTTTAAAAAATTAAATCATCACTACACATGACTAAAATGTAAAATAAAGCTAAACATGGGGG
769 GTATTTTAAAAAATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGG
* * * *
30102 GATTAAAATGCAAATAACCATAAAAATATATAACAAGCACAAAAGTGGGTAAATTATAGAATCAA
834 GATTAAAACGAAAATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGA
*
30167 TCCCTATAGGTGAA
899 TCCCTACAGGTGAA
30181 TATTTTGCAAAA
1 TATTTT-CAAAA
30193 CACGCGCAAG
Statistics
Matches: 2686, Mismatches: 47, Indels: 29
0.97 0.02 0.01
Matches are distributed among these distances:
909 2 0.00
910 531 0.20
911 146 0.05
912 1559 0.58
913 107 0.04
914 71 0.03
915 74 0.03
916 94 0.03
917 8 0.00
920 3 0.00
921 91 0.03
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (912 bp):
TATTTTCAAAATCGATTCGAGTGTTACTACTTTGATAACCCATTGGAAAACACATGCAAAAATAA
AGCAAATTAAAAGCATACCCCAAGCAAGTACAATTAATTATTTATTTTACCAATACTTAATGAGA
ATAAGGATGTTCAATTATTTAAATACGTCGAGACGAGAACTTAGATTTGATCTAACAGTCTTTTC
TCGGTGAATTTAATTAAAAGAACATAATCTTTTTCCCAATCACCAAATTTTAAAATGGATTCAAT
TTAATTCGTGTCACTAAGTGGGATAGACTTTCATTTTAAAACTATCGAAAATAACTTTGTTATAC
ATTAAGATAGTCACTTTACGACAATATTAAAATGAACGAATATTACCCTAGTCAAATTATTTTAA
TTCGAAAGAAATGCTTATGAGGGTATCATGCAAAATCAATTAATGACTAAAATGAAATAACATGC
AAAAATTAGAATAAAATAAAATGAAAATAGGACTAAAATATAAACAATCAAATCATCATGTCAAA
AATTAAAAGAAAATAAAGTGTAAAAGTGACTAAAATGAACATTTTTAATATTAAGTGCTAAAATT
ACAAAGGATAAAAATAAATAAAACATGGGGACCAAATTGAAATAAAAAAAATTGCATGACCAAAT
TAAATTAAATAAAAAATATTATAGTTCAAAATTTACAGGGACTATTTCCTAATTATTCCTTTTCT
ATGAGACTAAATCATGCTTCTAAAAATGATTAAATTACTAAATCAGTCCAGAAGTATTTTAAAAA
ATTAAATCATCACTACACATGACTAAAATGTAAAAAAAAACTAAACATGCAGGGATTAAAACGAA
AATAACCATAAAAATATATAACATGCACAAAAGTGGGTAAATTATAGAATCGATCCCTACAGGTG
AA
Found at i:33294 original size:17 final size:17
Alignment explanation
Indices: 33272--33306 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33262 CTTGTGAATC
33272 CATCGAATGGGTTCACT
1 CATCGAATGGGTTCACT
33289 CATCGAATGGGTTCACT
1 CATCGAATGGGTTCACT
33306 C
1 C
33307 GCAGATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (17 bp):
CATCGAATGGGTTCACT
Found at i:34082 original size:77 final size:77
Alignment explanation
Indices: 33995--34150 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
33985 GAGTCTAATG
33995 GTTTCTCCATATTAAGTTTTGGATTGGATTCTGATTACTGCGATTGTTGTTGCTGTTGTTTTCGC
1 GTTTCTCCATATTAAGTTTTGGATTGGATTCTGATTACTGCGATTGTTGTTGCTGTTGTTTTCGC
34060 CTTTCTTATAGT
66 CTTTCTTATAGT
*
34072 GTTTCTCCATATTAAGTTTTGGATTGGATTCTGATTACTGCGATTGTTGTTGTTGTTGTTTTCGC
1 GTTTCTCCATATTAAGTTTTGGATTGGATTCTGATTACTGCGATTGTTGTTGCTGTTGTTTTCGC
34137 CTTTCTTATAGT
66 CTTTCTTATAGT
34149 GT
1 GT
34151 GTGTGACCGT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.14, C:0.13, G:0.21, T:0.51
Consensus pattern (77 bp):
GTTTCTCCATATTAAGTTTTGGATTGGATTCTGATTACTGCGATTGTTGTTGCTGTTGTTTTCGC
CTTTCTTATAGT
Found at i:39921 original size:18 final size:18
Alignment explanation
Indices: 39898--39932 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39888 AGATGCTTGA
*
39898 TCAATAAGGCTATCAAGT
1 TCAATAAGGCTACCAAGT
39916 TCAATAAGGCTACCAAG
1 TCAATAAGGCTACCAAG
39933 AAGGACCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (18 bp):
TCAATAAGGCTACCAAGT
Found at i:57614 original size:33 final size:33
Alignment explanation
Indices: 57590--57754 Score: 118
Period size: 33 Copynumber: 4.8 Consensus size: 33
57580 ACAAAATTCA
57590 CTATGGAATTATTAATTGAAGTTACAACATATT
1 CTATGGAATTATTAATTGAAGTTACAACATATT
*
57623 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGT
1 CTATGGAATTATTAATTGAAGTTAC---AACATA--T-T
* * * ** * * ****
57662 TTTTCG-ATT-TTTGTGTAAGATGTTACAAAACCCA
1 CTATGGAATTATTAAT-T--GAAGTTACAACATATT
*
57696 CTATGGAATTATTGATTGAAGTTACAACATATT
1 CTATGGAATTATTAATTGAAGTTACAACATATT
57729 CTATGGAATTATTAATTGAAGTTACA
1 CTATGGAATTATTAATTGAAGTTACA
57755 TAAAAATAGT
Statistics
Matches: 98, Mismatches: 23, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
33 60 0.61
34 3 0.03
35 4 0.04
36 8 0.08
37 7 0.07
38 5 0.05
39 4 0.04
40 7 0.07
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (33 bp):
CTATGGAATTATTAATTGAAGTTACAACATATT
Found at i:57636 original size:106 final size:106
Alignment explanation
Indices: 57502--57838 Score: 629
Period size: 106 Copynumber: 3.2 Consensus size: 106
57492 TTTAGGCTAC
* *
57502 AAGTTAGAACATATTCCATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
1 AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
**
57567 TGTGTAAGATGTTACAAAATTCACTATGGAATTATTAATTG
66 TGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATTG
57608 AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
1 AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
*
57673 TGTGTAAGATGTTACAAAACCCACTATGGAATTATTGATTG
66 TGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATTG
57714 AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
1 AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
57779 TGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATTG
66 TGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATTG
57820 AAGTTACAACATATTCTAT
1 AAGTTACAACATATTCTAT
57839 AAAAATAGTT
Statistics
Matches: 225, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 225 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (106 bp):
AAGTTACAACATATTCTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTT
TGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATTG
Found at i:57893 original size:83 final size:83
Alignment explanation
Indices: 57754--57921 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
57744 TTGAAGTTAC
57754 ATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATT
1 ATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATT
*
57819 GAAGTTACAACATATTCT
66 GAAATTACAACATATTCT
*
57837 ATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAATCCACTATGGAATTATTAATT
1 ATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATT
57902 GAAATTACAACATATTCT
66 GAAATTACAACATATTCT
57920 AT
1 AT
57922 GAAATTATTA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (83 bp):
ATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCACTATGGAATTATTAATT
GAAATTACAACATATTCT
Found at i:57910 original size:33 final size:33
Alignment explanation
Indices: 57873--57943 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
57863 GTGTAAGATG
* *
57873 TTACAAAATCCACTATGGAATTATTAATTGAAA
1 TTACAAAATACACTATGAAATTATTAATTGAAA
* ** *
57906 TTACAACATATTCTATGAAATTATTAATTGAAG
1 TTACAAAATACACTATGAAATTATTAATTGAAA
57939 TTACA
1 TTACA
57944 TAAAAATAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (33 bp):
TTACAAAATACACTATGAAATTATTAATTGAAA
Found at i:57968 original size:189 final size:179
Alignment explanation
Indices: 57623--58122 Score: 856
Period size: 189 Copynumber: 2.7 Consensus size: 179
57613 ACAACATATT
*
57623 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
1 CTATGGAATTATTAATTGAAGTTGCATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
* *
57688 AAAACCCACTATGGAATTATTGATTGAAGTTACAACATATTCTATGGAATTATTAATTGAAGTTA
66 AAAATCCACTATGGAATTATTAATTGAAGTTACAACATATTCTATGGAATTATTAATTGAAGTTA
57753 CATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCA
131 CATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCA
*
57802 CTATGGAATTATTAATTGAAGTTACAACATATTCTATAAAAATAGTTGTTTTTCGATTTTTGTGT
1 CTATGGAATTATTAATTGAAG--------T-TGC-ATAAAAATAGTTGTTTTTCGATTTTTGTGT
* *
57867 AAGATGTTACAAAATCCACTATGGAATTATTAATTGAAATTACAACATATTCTATGAAATTATTA
56 AAGATGTTACAAAATCCACTATGGAATTATTAATTGAAGTTACAACATATTCTATGGAATTATTA
57932 ATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCA
121 ATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCA
57991 CTATGGAATTATTAATTGAAGTTGCATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
1 CTATGGAATTATTAATTGAAGTTGCATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
58056 AAAATCCACTATGGAATTATTAATTGAAGTTACAACATATTCTATGGAATTATTAATTGAAGTTA
66 AAAATCCACTATGGAATTATTAATTGAAGTTACAACATATTCTATGGAATTATTAATTGAAGTTA
58121 CA
131 CA
58123 ATATATTCTA
Statistics
Matches: 303, Mismatches: 8, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
179 126 0.42
180 2 0.01
181 1 0.00
187 1 0.00
188 2 0.01
189 171 0.56
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (179 bp):
CTATGGAATTATTAATTGAAGTTGCATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
AAAATCCACTATGGAATTATTAATTGAAGTTACAACATATTCTATGGAATTATTAATTGAAGTTA
CATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTACAAAACCCA
Found at i:58025 original size:73 final size:73
Alignment explanation
Indices: 57918--58207 Score: 355
Period size: 73 Copynumber: 4.1 Consensus size: 73
57908 ACAACATATT
*
57918 CTATGAAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
1 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
*
57983 AAAACCCA
66 AAAATCCA
*
57991 CTATGGAATTATTAATTGAAGTTGCATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
1 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
58056 AAAATCCA
66 AAAATCCA
* * * * * * *
58064 CTATGGAATTATTAATTGAAGTTAC---AACATA--T-TCTATGGA--ATTAT-TAATTGAAGTT
1 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAA--GATGTT
* ***
58120 ACAATATATT
64 ACAAAATCCA
* *
58130 CTATGGAATTATCAATTGAAGTTACATAAAAATAGTTGTTTTTCGTTTTTTGTGTAAGATGTTAC
1 CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
58195 AAAATCCA
66 AAAATCCA
58203 CTATG
1 CTATG
58208 CTCGAGGTTG
Statistics
Matches: 178, Mismatches: 28, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
64 3 0.02
65 3 0.02
66 35 0.20
67 5 0.03
68 1 0.01
69 5 0.03
70 5 0.03
71 1 0.01
72 4 0.02
73 110 0.62
74 3 0.02
75 3 0.02
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (73 bp):
CTATGGAATTATTAATTGAAGTTACATAAAAATAGTTGTTTTTCGATTTTTGTGTAAGATGTTAC
AAAATCCA
Found at i:58088 original size:33 final size:33
Alignment explanation
Indices: 58064--58155 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
58054 ACAAAATCCA
*
58064 CTATGGAATTATTAATTGAAGTTACAACATATT
1 CTATGGAATTATTAATTGAAGTTACAAAATATT
*
58097 CTATGGAATTATTAATTGAAGTTACAATATATT
1 CTATGGAATTATTAATTGAAGTTACAAAATATT
*
58130 CTATGGAATTATCAATTGAAGTTACA
1 CTATGGAATTATTAATTGAAGTTACA
58156 TAAAAATAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (33 bp):
CTATGGAATTATTAATTGAAGTTACAAAATATT
Found at i:62448 original size:161 final size:161
Alignment explanation
Indices: 62183--62509 Score: 609
Period size: 161 Copynumber: 2.0 Consensus size: 161
62173 GAATGCTATT
62183 AAAACAAGAACATAAAGCCATTGAAAACTCCTCCAAAACATTCATATCTCTAACCTCATAAGATC
1 AAAACAAGAACATAAAGCCATTGAAAACTCCTCCAAAACATTCATATCTCTAACCTCATAAGATC
62248 AACAAAATCAAAGGAAAATCAGAAACAGATACTTTGAAGCAAAAGTAAGCAGTCAAAGGAGTTCA
66 AACAAAATCAAAGGAAAATCAGAAACAGATACTTTGAAGCAAAAGTAAGCAGTCAAAGGAGTTCA
* *
62313 ACTTACATGAAGCTCAATGAAAATCAAACCG
131 ACTTAAATGAAGCTCAATAAAAATCAAACCG
*
62344 AAAACAAGAACATAAAGCCATTGAAAACTCCTCCAAAACATTTATATCTCTAACCTCATAAGATC
1 AAAACAAGAACATAAAGCCATTGAAAACTCCTCCAAAACATTCATATCTCTAACCTCATAAGATC
* *
62409 AACAAGATCAAAGGAAAATCAGGAACAGATACTTTGAAGCAAAAGTAAGCAGTCAAAGGAGTTCA
66 AACAAAATCAAAGGAAAATCAGAAACAGATACTTTGAAGCAAAAGTAAGCAGTCAAAGGAGTTCA
62474 ACTTAAATGAAGCTCAATAAAAATCAAACCG
131 ACTTAAATGAAGCTCAATAAAAATCAAACCG
62505 AAAAC
1 AAAAC
62510 CAAGGATTCT
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.19
Consensus pattern (161 bp):
AAAACAAGAACATAAAGCCATTGAAAACTCCTCCAAAACATTCATATCTCTAACCTCATAAGATC
AACAAAATCAAAGGAAAATCAGAAACAGATACTTTGAAGCAAAAGTAAGCAGTCAAAGGAGTTCA
ACTTAAATGAAGCTCAATAAAAATCAAACCG
Found at i:67532 original size:17 final size:17
Alignment explanation
Indices: 67490--67538 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
67480 TTACCATAAA
* * *
67490 AATATATTAATTTAATT
1 AATATATAAATTCAAAT
67507 AA-ATAATAAATTCAAAT
1 AATAT-ATAAATTCAAAT
67524 AATATATAAATTCAA
1 AATATATAAATTCAA
67539 TCAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATATAAATTCAAAT
Found at i:77618 original size:22 final size:23
Alignment explanation
Indices: 77587--77631 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
77577 ACCATAATAA
* *
77587 AAAATCATAAAGCCT-AAACTCT
1 AAAATAATAAACCCTAAAACTCT
77609 AAAATAATAAACCCTAAAACTCT
1 AAAATAATAAACCCTAAAACTCT
77632 TACCCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAATAAACCCTAAAACTCT
Found at i:78610 original size:60 final size:59
Alignment explanation
Indices: 78440--78624 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 59
78430 TTTGGATGAA
* * **
78440 TTTGGGGATAAAATTGGAATATTCAAATGTTTGGGGACCAATTTAGAAA-GAGGGTCATAG
1 TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA-AAATGA-GGTCATAG
* * * * **
78500 TTTAGGGATGAAATTAGAAT-TCTCAAAAGTTTAAGGACTAGTTTTGAATGAGGTTCATAG
1 TTTGGGGATAAAATTAGAATAT-TCAAAAGTTTAAGGACCAATTTAAAATGAGG-TCATAG
* * *
78560 TTTGGGGTTAAAATCAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAA
1 TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAG-GTCATAG
78620 TTTGG
1 TTTGG
78625 AGACATTTGA
Statistics
Matches: 101, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
59 5 0.05
60 94 0.93
61 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (59 bp):
TTTGGGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGTCATAG
Found at i:81286 original size:82 final size:84
Alignment explanation
Indices: 81137--81292 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 84
81127 AAATCTTTTC
* * * *
81137 CACTACTATTCCGTGACGATTTCATACTTTACTAAAAAAATTCGTTTCACTATTCTTTCGTGGAG
1 CACTACTATTCCGTGAAGATTTCATACTTTACTAAAAAAATCCGTTCCACTACTCTTTCGTGGAG
*
81202 TTCAGATTTTCTTTTGCTT
66 TTCAAATTTTCTTTTGCTT
* * *
81221 CACTACTCTTCCGTGAAGATTT-ATACTTTGCT-AAAATATCCGTTCCACTACTCTTTCGTGGAG
1 CACTACTATTCCGTGAAGATTTCATACTTTACTAAAAAAATCCGTTCCACTACTCTTTCGTGGAG
81284 TTCAAATTT
66 TTCAAATTT
81293 CGTTTTGTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 35 0.55
83 9 0.14
84 20 0.31
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (84 bp):
CACTACTATTCCGTGAAGATTTCATACTTTACTAAAAAAATCCGTTCCACTACTCTTTCGTGGAG
TTCAAATTTTCTTTTGCTT
Found at i:81909 original size:22 final size:22
Alignment explanation
Indices: 81884--81931 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
81874 AAAGCTTTGC
*
81884 CTTTGAAAAGAGAATATATCAT
1 CTTTGAAAAGAGAATACATCAT
81906 CTTTGAAAAGAGAATACATCAT
1 CTTTGAAAAGAGAATACATCAT
81928 CTTT
1 CTTT
81932 TCAAAATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
CTTTGAAAAGAGAATACATCAT
Done.