Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:2981451 original size:9 final size:9
Alignment explanation
Indices: 2981368--2981470 Score: 76
Period size: 9 Copynumber: 11.6 Consensus size: 9
2981358 AAGAATATAG
2981368 AAATAAAGA-
1 AAATAAA-AT
2981377 AAATAGAAAT
1 AAATA-AAAT
**
2981387 AAAGCAAA-
1 AAATAAAAT
2981395 AAATAAAA-
1 AAATAAAAT
2981403 AAAGT-AAAT
1 AAA-TAAAAT
2981412 AAGAT-AAAT
1 AA-ATAAAAT
2981421 AAAGTAAAAT
1 AAA-TAAAAT
*
2981431 AAAGAAAA-
1 AAATAAAAT
2981439 AAATAAAAT
1 AAATAAAAT
2981448 AAAT-AAAT
1 AAATAAAAT
2981456 AAATGAAAAT
1 AAAT-AAAAT
2981466 AAATA
1 AAATA
2981471 TGAACAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
8 28 0.36
9 29 0.37
10 21 0.27
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2981453 original size:4 final size:4
Alignment explanation
Indices: 2981395--2981470 Score: 62
Period size: 4 Copynumber: 17.2 Consensus size: 4
2981385 ATAAAGCAAA
* * *
2981395 AAAT AAAA AAAGT AAAT AAGAT AAAT AAAGT AAAAT AAAG AAAA AAAT
1 AAAT AAAT AAA-T AAAT AA-AT AAAT AAA-T -AAAT AAAT AAAT AAAT
2981443 AAAAT AAAT AAAT AAAT GAAAAT AAAT A
1 -AAAT AAAT AAAT AAAT --AAAT AAAT A
2981471 TGAACAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
4 40 0.67
5 13 0.22
6 7 0.12
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:2981454 original size:35 final size:34
Alignment explanation
Indices: 2981383--2981468 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2981373 AAGAAAATAG
* *
2981383 AAATAAAGCAAAA-AATAAAAAAAGTAAATAAGAT
1 AAATAAAGTAAAATAA-AAAAAAAATAAATAAGAT
2981417 AAATAAAGTAAAATAAAGAAAAAAATAAAATAA-AT
1 AAATAAAGTAAAATAAA-AAAAAAAT-AAATAAGAT
2981452 AAATAAA-TGAAAATAAA
1 AAATAAAGT-AAAATAAA
2981469 TATGAACAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 14 0.30
35 26 0.57
36 6 0.13
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (34 bp):
AAATAAAGTAAAATAAAAAAAAAATAAATAAGAT
Found at i:2981480 original size:40 final size:42
Alignment explanation
Indices: 2981368--2981481 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 42
2981358 AAGAATATAG
2981368 AAATAAA-GAAAATAGAAATAAAGCAAAAAATAAAAAAAGTAAAT
1 AAATAAATGAAAATA-AAATAAAGCAAAAAAT--AAAAAGTAAAT
* *
2981412 AAGATAAAT-AAAGTAAAATAAAGAAAAAAAT-AAAA-TAAAT
1 AA-ATAAATGAAAATAAAATAAAGCAAAAAATAAAAAGTAAAT
*
2981452 AAATAAATGAAAATAAATATGAA-CAAAAAA
1 AAATAAATGAAAATAAA-ATAAAGCAAAAAA
2981482 GACAGTAACA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
39 6 0.10
40 20 0.33
41 8 0.13
44 17 0.28
45 10 0.16
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (42 bp):
AAATAAATGAAAATAAAATAAAGCAAAAAATAAAAAGTAAAT
Found at i:2981584 original size:17 final size:15
Alignment explanation
Indices: 2981544--2981578 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2981534 GTACTTAAAT
2981544 AAAAATAAATAAGAG
1 AAAAATAAATAAGAG
2981559 AAAAATAAATAAGAG
1 AAAAATAAATAAGAG
2981574 AAAAA
1 AAAAA
2981579 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAATAAATAAGAG
Found at i:2981597 original size:18 final size:17
Alignment explanation
Indices: 2981544--2981591 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
2981534 GTACTTAAAT
*
2981544 AAAAATAAAT--AAGAG
1 AAAAATAAATAAAAGAA
*
2981559 AAAAATAAATAAGAGAA
1 AAAAATAAATAAAAGAA
2981576 AAAAATAAA-AAAAGAA
1 AAAAATAAATAAAAGAA
2981592 TTAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.36
16 6 0.21
17 12 0.43
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAATAAATAAAAGAA
Found at i:2981676 original size:49 final size:51
Alignment explanation
Indices: 2981613--2981709 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 51
2981603 GAGAAAGAAA
* * *
2981613 AATAAGAAATAAAATAAAACAT-ATATATAATAA-AATACTAAAAAAATAT
1 AATAAGAAATAAAATAAAAAATAAAAAATAATAATAATACTAAAAAAATAT
*
2981662 AATAAGGAAA-AAAATAAAAAATAAAAAATAATAATAATGCTAAAAAAA
1 AATAA-GAAATAAAATAAAAAATAAAAAATAATAATAATACTAAAAAAA
2981710 GAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 16 0.39
50 13 0.32
51 12 0.29
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (51 bp):
AATAAGAAATAAAATAAAAAATAAAAAATAATAATAATACTAAAAAAATAT
Found at i:2981743 original size:21 final size:22
Alignment explanation
Indices: 2981705--2981751 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2981695 ATAATGCTAA
*
2981705 AAAAAGAATTAAATAAAATGAT
1 AAAAAGAATTAAATAAAATAAT
2981727 AAAAAGAA-T-AATAAAAATAAT
1 AAAAAGAATTAAAT-AAAATAAT
2981748 AAAA
1 AAAA
2981752 GAAACAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAAAGAATTAAATAAAATAAT
Found at i:2981761 original size:42 final size:42
Alignment explanation
Indices: 2981654--2981761 Score: 94
Period size: 42 Copynumber: 2.5 Consensus size: 42
2981644 AAAATACTAA
*
2981654 AAAAAT-ATAATAAGGAAAAAAATAAAAAATAAAAAATAATAAT
1 AAAAATAATAA-AA-GAAAAAAATAAAAAATAAAAAAGAATAAT
*** * ** *
2981697 AATGCTAAAAAAAGAATTAAATAAAATGAT-AAAAAGAATAAT
1 AAAAATAATAAAAGAAAAAAATAAAA-AATAAAAAAGAATAAT
*
2981739 AAAAATAATAAAAGAAACAAATA
1 AAAAATAATAAAAGAAAAAAATA
2981762 TACATATATA
Statistics
Matches: 49, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
42 39 0.80
43 7 0.14
44 3 0.06
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (42 bp):
AAAAATAATAAAAGAAAAAAATAAAAAATAAAAAAGAATAAT
Found at i:2983603 original size:121 final size:121
Alignment explanation
Indices: 2983386--2983968 Score: 918
Period size: 121 Copynumber: 4.8 Consensus size: 121
2983376 TCTTTCGGGT
* * * * * * * *
2983386 ACGATATCCTTCGTCGTGAAGTCGAAACCATAGATGGCTCCTTTGTCGTGAAGTTGAGCTTTTGA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCGTTGTGAAGTTGAGC-TTTGA
* * *
2983451 ATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATGGTTGCATTGCTTCTTGTGGGC
65 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
* *
2983508 ACGATATCCTTCGTCGCGAAGTTGAAATCTTGGATGACTCATTCGTTGTGAAGTTGAGCTTTGAA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCGTTGTGAAGTTGAGCTTTGAA
**
2983573 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGC
66 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
2983629 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGAT-AGCTCATTCGTTGTGAAGTTGAGCTTTGA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGA-CTCATTCGTTGTGAAGTTGAGCTTTGA
2983693 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
65 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
*
2983750 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGAT-AGCTCATTCGTTGTGAAGTTGAGCTATGA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGA-CTCATTCGTTGTGAAGTTGAGCTTTGA
* *
2983814 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAAGGTTGCATTGATGCTTGTGGGC
65 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
* * *
2983871 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCCTTCGTTGTTAAGTTGAGCTTTAAA
1 ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCGTTGTGAAGTTGAGCTTTGAA
* *
2983936 TTGGATATTCTTCGTTGTGAAGTTGAAATCCAA
66 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
2983969 TCTTGTGTTG
Statistics
Matches: 434, Mismatches: 25, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
120 1 0.00
121 382 0.88
122 51 0.12
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (121 bp):
ACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCATTCGTTGTGAAGTTGAGCTTTGAA
TTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGC
Found at i:2983645 original size:55 final size:55
Alignment explanation
Indices: 2983576--2983899 Score: 188
Period size: 55 Copynumber: 5.5 Consensus size: 55
2983566 CTTTGAATTG
2983576 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGCAC
** * * ** *
2983631 GATATCCTTCGTCGTGAAGTTGAAAT-CGTGGATAGCTCATT-CGTTGTGAAGTTGAGCTTTGAA
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTG--CATTGC-TT-T----TT--G-TGGGCA
*
2983694 TTG
55 --C
**
2983697 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGCAC
** * * ** *
2983752 GATATCCTTCGTCGTGAAGTTGAAAT-CGTGGATAGCTCATT-CGTTGTGAAGTTGAGCTATGAA
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTG--CATTGC-TT-T----TT--G-TGGGCA
*
2983815 TTG
55 --C
* * **
2983818 GATATCCTTCGTCGTGAAGTTGAAATCCAAAGGTTGCATTGATGCTTGTGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGCAC
2983873 GATATCCTTCGTCGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
2983900 GTGGATGACT
Statistics
Matches: 199, Mismatches: 40, Indels: 60
0.67 0.13 0.20
Matches are distributed among these distances:
54 10 0.05
55 81 0.41
56 11 0.06
57 7 0.04
58 2 0.01
60 4 0.02
61 4 0.02
63 2 0.01
64 6 0.03
65 10 0.05
66 53 0.27
67 9 0.05
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (55 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTTTTGTGGGCAC
Found at i:2984188 original size:147 final size:147
Alignment explanation
Indices: 2983921--2984368 Score: 711
Period size: 147 Copynumber: 3.0 Consensus size: 147
2983911 CTTCGTTGTT
*
2983921 AAGTTGAGCTTTAAATTGGATATTCTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
1 AAGTTGAGCTTTAAATTGGATATACTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
**
2983986 TCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTTG-C
66 TCCAATATCCTTCGCAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG-TTGAC
*
2984050 ATACGCTCATTCACTGTG
130 AGACGCTCATTCACTGTG
* * *
2984068 AAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTTGAG
1 AAGTTGAGCTTTAAATTGGATATACTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
* *
2984133 TCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAATGAAACTTGAAAGTTGTTTGTTGACA
66 TCCAATATCCTTCGCAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACA
*
2984198 GACGCTTC-TTCACTGTA
131 GACGC-TCATTCACTGTG
* * *
2984215 AAGTTGAGCTTTTAATTGGATATATTTCGTTATGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
1 AAGTTGAGCTTTAAATTGGATATACTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
* * *
2984280 TCTAATATCCTTCACAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGCTGACA
66 TCCAATATCCTTCGCAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACA
*
2984345 GACGCTCATTCGCTGTG
131 GACGCTCATTCACTGTG
2984362 AAGTTGA
1 AAGTTGA
2984369 ACAACCACCA
Statistics
Matches: 278, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
146 5 0.02
147 271 0.97
148 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (147 bp):
AAGTTGAGCTTTAAATTGGATATACTTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTCGAG
TCCAATATCCTTCGCAGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACA
GACGCTCATTCACTGTG
Found at i:2987971 original size:15 final size:16
Alignment explanation
Indices: 2987951--2987983 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2987941 AGTGAAAATG
2987951 AATAGAAATAAAG-AA
1 AATAGAAATAAAGCAA
2987966 AATAGAAATAAAGCAA
1 AATAGAAATAAAGCAA
2987982 AA
1 AA
2987984 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AATAGAAATAAAGCAA
Found at i:2988001 original size:40 final size:40
Alignment explanation
Indices: 2987956--2988067 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 40
2987946 AAATGAATAG
**
2987956 AAATAAAGAAAATAGAAATAAAGCAAA-AAAATAAA-AAAGT
1 AAATAAAGAAAATA-AAATAAAAAAAAGAAAATAAATAAA-T
*
2987996 AAAT-AAGATAAATAAAGTAAAAAAAAGAAAATAAATAAAT
1 AAATAAAGA-AAATAAAATAAAAAAAAGAAAATAAATAAAT
2988036 AAATAAATGAAAATAAATATGAACAAAAAAGA
1 AAATAAA-GAAAATAAA-AT-AA-AAAAAAGA
2988068 CAGTAACAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
39 13 0.22
40 22 0.37
41 12 0.20
42 3 0.05
43 2 0.03
44 8 0.13
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (40 bp):
AAATAAAGAAAATAAAATAAAAAAAAGAAAATAAATAAAT
Found at i:2988031 original size:4 final size:4
Alignment explanation
Indices: 2987984--2988054 Score: 60
Period size: 4 Copynumber: 17.2 Consensus size: 4
2987974 TAAAGCAAAA
2987984 AAAT AAA- AAAGT AAAT AAGAT AAAT AAAGT AAA- AAA- AAGA- AAAT
1 AAAT AAAT AAA-T AAAT AA-AT AAAT AAA-T AAAT AAAT AA-AT AAAT
2988028 AAAT AAAT AAAT AAAT GAAAAT AAAT A
1 AAAT AAAT AAAT AAAT --AAAT AAAT A
2988055 TGAACAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
3 9 0.15
4 35 0.59
5 11 0.19
6 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:2988048 original size:27 final size:28
Alignment explanation
Indices: 2987988--2988042 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2987978 GCAAAAAAAT
*
2987988 AAAAAAGTAAATAAGATAAATAAAGTAA
1 AAAAAAGAAAATAAGATAAATAAAGTAA
2988016 AAAAAAGAAAATAA-ATAAATAAA-TAA
1 AAAAAAGAAAATAAGATAAATAAAGTAA
2988042 A
1 A
2988043 TGAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 9 0.35
28 13 0.50
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (28 bp):
AAAAAAGAAAATAAGATAAATAAAGTAA
Found at i:2988067 original size:44 final size:43
Alignment explanation
Indices: 2987951--2988054 Score: 102
Period size: 45 Copynumber: 2.3 Consensus size: 43
2987941 AGTGAAAATG
* * * *
2987951 AATAGAAATAAAGAAAATAGAAATAAAGCAAAAAAATAAAAAAGTA
1 AATA-AAATAAATAAAGTA-AAAAAAAGAAAAA-AATAAAAAAGTA
*
2987997 AATAAGATAAATAAAGTAAAAAAAAGAAAATAAATAAATAAA-TA
1 AATAAAATAAATAAAGTAAAAAAAAGAAAA-AAATAAA-AAAGTA
2988041 AATGAAAATAAATA
1 AAT-AAAATAAATA
2988055 TGAACAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
44 21 0.43
45 24 0.49
46 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (43 bp):
AATAAAATAAATAAAGTAAAAAAAAGAAAAAAATAAAAAAGTA
Found at i:2988171 original size:13 final size:13
Alignment explanation
Indices: 2988155--2988200 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
2988145 CAAAAATAAA
*
2988155 AAAAATAAGAATT
1 AAAAATAAGAAAT
2988168 AAAATATTAGAGAAAT
1 AAAA-A-TA-AGAAAT
2988184 AAAAATAAGAAAT
1 AAAAATAAGAAAT
2988197 AAAA
1 AAAA
2988201 TAAAACATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 14 0.48
14 3 0.10
15 3 0.10
16 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (13 bp):
AAAAATAAGAAAT
Found at i:2988315 original size:21 final size:22
Alignment explanation
Indices: 2988277--2988323 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2988267 AATAATGCTA
*
2988277 AAAAAGAATTAAAGAAAATGAT
1 AAAAAGAATTAAAGAAAATAAT
2988299 AAAAAGAA-TAATA-AAAATAAT
1 AAAAAGAATTAA-AGAAAATAAT
2988320 AAAA
1 AAAA
2988324 GAAACAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAAGAATTAAAGAAAATAAT
Found at i:2988332 original size:21 final size:21
Alignment explanation
Indices: 2988291--2988332 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2988281 AGAATTAAAG
* *
2988291 AAAATGATAAAAAGAATAATA
1 AAAATAATAAAAAGAACAATA
2988312 AAAATAAT-AAAAGAAACAATA
1 AAAATAATAAAAAG-AACAATA
2988333 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAATAATAAAAAGAACAATA
Found at i:2988337 original size:2 final size:2
Alignment explanation
Indices: 2988330--2988386 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2988320 AAAAGAAACA
2988330 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
2988372 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2988387 ATAATAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2989550 original size:22 final size:23
Alignment explanation
Indices: 2989517--2989561 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2989507 AAATTGTATA
2989517 TATATATATTATATAAAATAATT
1 TATATATATTATATAAAATAATT
*
2989540 TATA-ATATTATATAAATTAATT
1 TATATATATTATATAAAATAATT
2989562 AAGGCGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATATATTATATAAAATAATT
Found at i:2990742 original size:82 final size:82
Alignment explanation
Indices: 2990602--2991214 Score: 838
Period size: 82 Copynumber: 7.5 Consensus size: 82
2990592 TGATATATCA
* ** * *
2990602 CTGAAAAGTTGTTGAAGATGATAAAACACCACTATTTCACCCATTATCTAAAATGTTGTTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
2990667 TATGCATTGAATGACCT
66 TATGCATTGAATGACCT
* *
2990684 CTGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTAAAAAGTTGTTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
*
2990749 TATGCATTGAATGGCCT
66 TATGCATTGAATGACCT
* * * * * *
2990766 CTGAAAAGTTGCAGAAGGTGATAATGCACCACTATTTCACTCGTTTTCTGAAAAGTTTTTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
2990831 TATGCATTGAATGACCT
66 TATGCATTGAATGACCT
* * *
2990848 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTTTT-TGAAAAGTTATTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
*
2990912 TATTCATTGAATGACCT
66 TATGCATTGAATGACCT
** * * * *
2990929 CTGAAAAGTTACAGAAGATGATAATGAACCCCTATTTCACCCATTTGT-TGAAAAATTATATTTA
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTT-TCT-AAAAAGT-TGTTTA
2990993 AATTATGCATTGAATGACCT
63 AATTATGCATTGAATGACCT
* * *
2991013 CCGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAATTGCTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
* *
2991078 TATACATTGAAAGACCT
66 TATGCATTGAATGACCT
** * **
2991095 CTG-AAAGTTGTAGAAGATGATAATAAACCACTATTTCACCCATTTTCTGAAACTTTGTTTAAAT
1 CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
2991159 TATGCATTGAATGACCT
66 TATGCATTGAATGACCT
2991176 CTGAAAAAAGTTAG-AGAAGATGATAATGCACCACTATTT
1 CTG--AAAAGTT-GTAGAAGATGATAATGCACCACTATTT
2991215 TTGGGCCTAC
Statistics
Matches: 476, Mismatches: 47, Indels: 14
0.89 0.09 0.03
Matches are distributed among these distances:
81 146 0.31
82 221 0.46
83 12 0.03
84 96 0.20
85 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (82 bp):
CTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATTTTCTAAAAAGTTGTTTAAAT
TATGCATTGAATGACCT
Found at i:2991045 original size:165 final size:164
Alignment explanation
Indices: 2990602--2991214 Score: 855
Period size: 165 Copynumber: 3.7 Consensus size: 164
2990592 TGATATATCA
** * *
2990602 CTGAAAAGTTGTTGAAGATGATAA-AACACCACTATTTCACCCATTATCT--AAAATGTTGTTTA
1 CTGAAAAGTTGCAGAAGATGATAATGA-ACCACTATTTCACCCATTTTCTGAAAAAT-TT-TTTA
*
2990664 AATTATGCATTGAATGACCTCTGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTT
63 AATTATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTT
* *
2990729 TTCTAAAAAGTTGTTTAAATTATGCATTGAATGGCCT
128 TTCTAAAAAGTTGTTTAAATTATACATTGAATGACCT
* * * * *
2990766 CTGAAAAGTTGCAGAAGGTGATAATGCACCACTATTTCACTCGTTTTCTGAAAAGTTTTTTAAAT
1 CTGAAAAGTTGCAGAAGATGATAATGAACCACTATTTCACCCATTTTCTGAAAAATTTTTTAAAT
2990831 TATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTTTT-
66 TATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTTTTC
* * *
2990895 TGAAAAGTTATTTAAATTATTCATTGAATGACCT
131 TAAAAAGTTGTTTAAATTATACATTGAATGACCT
* *
2990929 CTGAAAAGTTACAGAAGATGATAATGAACCCCTATTTCACCCATTTGT-TGAAAAATTATATTTA
1 CTGAAAAGTTGCAGAAGATGATAATGAACCACTATTTCACCCATTT-TCTGAAAAATT-T-TTTA
* *
2990993 AATTATGCATTGAATGACCTCCGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCATT
63 AATTATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTT
* * *
2991058 TTCTAAAAAATTGCTTAAATTATACATTGAAAGACCT
128 TTCTAAAAAGTTGTTTAAATTATACATTGAATGACCT
* * *
2991095 CTG-AAAGTTGTAGAAGATGATAATAAACCACTATTTCACCCATTTTCTG-AAACTTTGTTTAAA
1 CTGAAAAGTTGCAGAAGATGATAATGAACCACTATTTCACCCATTTTCTGAAAAATTT-TTTAAA
2991158 TTATGCATTGAATGACCTCTGAAAAAAGTTAG-AGAAGATGATAATGCACCACTATTT
65 TTATGCATTGAATGACCTCTG--AAAAGTT-GTAGAAGATGATAATGCACCACTATTT
2991215 TTGGGCCTAC
Statistics
Matches: 402, Mismatches: 36, Indels: 21
0.88 0.08 0.05
Matches are distributed among these distances:
163 105 0.26
164 118 0.29
165 143 0.36
166 36 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (164 bp):
CTGAAAAGTTGCAGAAGATGATAATGAACCACTATTTCACCCATTTTCTGAAAAATTTTTTAAAT
TATGCATTGAATGACCTCTGAAAAGTTGTAGAAGATGATAATGCACCACTATTTCACCCGTTTTC
TAAAAAGTTGTTTAAATTATACATTGAATGACCT
Found at i:2997007 original size:15 final size:15
Alignment explanation
Indices: 2996984--2997017 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2996974 CCATCCCTAG
*
2996984 TTACTTACTAAGTTA
1 TTACATACTAAGTTA
2996999 TTACATACTAAGTTA
1 TTACATACTAAGTTA
2997014 TTAC
1 TTAC
2997018 TCTCACCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (15 bp):
TTACATACTAAGTTA
Found at i:3001116 original size:11 final size:10
Alignment explanation
Indices: 3001100--3001134 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
3001090 ATTTTATGTT
3001100 AATTTGATTA
1 AATTTGATTA
3001110 AAGTTTGATTA
1 AA-TTTGATTA
3001121 ATATTTGATTA
1 A-ATTTGATTA
3001132 AAT
1 AAT
3001135 AGATTGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 18 0.78
12 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (10 bp):
AATTTGATTA
Found at i:3001870 original size:31 final size:31
Alignment explanation
Indices: 3001771--3001873 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
3001761 CGAGCTCGAT
*
3001771 TCGAGCTTCAATTTTTTATTTCAAGTTTGAG
1 TCGAGCTTCAATTTTTTATTTCGAGTTTGAG
* * * ** * *
3001802 TCAATCTTGAAAACTTTAAATTCGTGAGCTTTCGAG
1 TCGAGCTT-CAATTTTTTATTTC--GAG-TTT-GAG
3001838 TCGAGCTTCAATTTTTTATTTCGAGTTTGAG
1 TCGAGCTTCAATTTTTTATTTCGAGTTTGAG
3001869 TCGAG
1 TCGAG
3001874 ATTGATAATT
Statistics
Matches: 52, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
31 14 0.27
32 12 0.23
33 3 0.06
34 2 0.04
35 12 0.23
36 9 0.17
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (31 bp):
TCGAGCTTCAATTTTTTATTTCGAGTTTGAG
Found at i:3002065 original size:2 final size:2
Alignment explanation
Indices: 3002058--3002090 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3002048 TTTATTTCAA
3002058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3002091 AGTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3007707 original size:58 final size:58
Alignment explanation
Indices: 3007628--3007743 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
3007618 AATATTCAAT
** *
3007628 TTTTTATTTTAATAATAATAAATGTTGTATCACAAAAATGATTAATAAAATAAATTAA
1 TTTTTATTTTAATAATAATAAATGTCATATCACAAAAATCATTAATAAAATAAATTAA
*
3007686 TTTTTATTTTAATGATAATAAATGTCATATCACAAAAATCATTAATAAAATAAATTAA
1 TTTTTATTTTAATAATAATAAATGTCATATCACAAAAATCATTAATAAAATAAATTAA
3007744 AGTGATTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (58 bp):
TTTTTATTTTAATAATAATAAATGTCATATCACAAAAATCATTAATAAAATAAATTAA
Found at i:3009324 original size:7 final size:7
Alignment explanation
Indices: 3009312--3009337 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3009302 TATTGTGTAT
3009312 ATCCATA
1 ATCCATA
3009319 ATCCATA
1 ATCCATA
3009326 ATCCATA
1 ATCCATA
3009333 ATCCA
1 ATCCA
3009338 ACGAAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (7 bp):
ATCCATA
Found at i:3012629 original size:22 final size:22
Alignment explanation
Indices: 3012603--3012649 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3012593 TTATAGTTTA
*
3012603 TAATATATATTAT-ATATTTCTT
1 TAATAT-TATTATAATATATCTT
*
3012625 TAATATTATTTTAATATATCTT
1 TAATATTATTATAATATATCTT
3012647 TAA
1 TAA
3012650 AGTTTCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATATTATTATAATATATCTT
Found at i:3013396 original size:19 final size:19
Alignment explanation
Indices: 3013372--3013410 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3013362 TCACCAGCTA
3013372 CCACTCACCACCATCACCG
1 CCACTCACCACCATCACCG
* *
3013391 CCACTCATCACCATCGCCG
1 CCACTCACCACCATCACCG
3013410 C
1 C
3013411 TGATCACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.56, G:0.08, T:0.13
Consensus pattern (19 bp):
CCACTCACCACCATCACCG
Found at i:3013761 original size:16 final size:16
Alignment explanation
Indices: 3013740--3013773 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3013730 CAATGCAAAC
*
3013740 AACCCTATCGCAAGAA
1 AACCCTAACGCAAGAA
3013756 AACCCTAACGCAAGAA
1 AACCCTAACGCAAGAA
3013772 AA
1 AA
3013774 GTTCAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.09
Consensus pattern (16 bp):
AACCCTAACGCAAGAA
Found at i:3016491 original size:5 final size:5
Alignment explanation
Indices: 3016477--3016528 Score: 70
Period size: 5 Copynumber: 10.6 Consensus size: 5
3016467 CCGCCGCCGC
* * *
3016477 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGGCT CGGCT CGGCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
3016526 CGT
1 CGT
3016529 GGTCGTGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.00, C:0.40, G:0.27, T:0.33
Consensus pattern (5 bp):
CGTCT
Found at i:3020729 original size:19 final size:19
Alignment explanation
Indices: 3020705--3020743 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3020695 GTCCATGATT
*
3020705 ATAGGGTGTTACTTTGTGG
1 ATAGGGTGTTACTTTATGG
3020724 ATAGGGTGTTACTTTATGG
1 ATAGGGTGTTACTTTATGG
3020743 A
1 A
3020744 GTATACGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (19 bp):
ATAGGGTGTTACTTTATGG
Found at i:3023250 original size:20 final size:20
Alignment explanation
Indices: 3023225--3023266 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3023215 GAAGGCTACC
3023225 ATATATACAGCAACTGGCGT
1 ATATATACAGCAACTGGCGT
3023245 ATATATACAGCAACTGGCGT
1 ATATATACAGCAACTGGCGT
3023265 AT
1 AT
3023267 TACAATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (20 bp):
ATATATACAGCAACTGGCGT
Found at i:3023492 original size:30 final size:31
Alignment explanation
Indices: 3023435--3023493 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
3023425 TAATTAACCG
* * *
3023435 AACTTTTTTTCTTTAACCGTTAGCTGAACTA
1 AACTTTTTTTCTTTAAACATTAACTGAACTA
*
3023466 AACTTTTTTT-TTTAAATATTAACTGAAC
1 AACTTTTTTTCTTTAAACATTAACTGAAC
3023494 CGAATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (31 bp):
AACTTTTTTTCTTTAAACATTAACTGAACTA
Found at i:3029804 original size:22 final size:22
Alignment explanation
Indices: 3029772--3029813 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3029762 ACGGTCAACA
3029772 GTCAACAGTCGGGTCGGGTCGG
1 GTCAACAGTCGGGTCGGGTCGG
* *
3029794 GTCAACGGTCGGGTTGGGTC
1 GTCAACAGTCGGGTCGGGTC
3029814 AAACCGGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.45, T:0.21
Consensus pattern (22 bp):
GTCAACAGTCGGGTCGGGTCGG
Found at i:3029805 original size:17 final size:17
Alignment explanation
Indices: 3029783--3029815 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3029773 TCAACAGTCG
3029783 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
3029800 GGTCGGGTTGGGTCAA
1 GGTCGGGTCGGGTCAA
3029816 ACCGGTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.18, G:0.48, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:3029867 original size:20 final size:19
Alignment explanation
Indices: 3029814--3029889 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
3029804 GGGTTGGGTC
*
3029814 AAACCGGTCAAACCGG-TC
1 AAACCGGTCAAACCGGTTG
3029832 AAACCGGTCAAACCGGTTG
1 AAACCGGTCAAACCGGTTG
*
3029851 AAACCGGTTAGAACCGGTTG
1 AAACCGGTCA-AACCGGTTG
*
3029871 AAAACCGGTTAAACCGGTT
1 -AAACCGGTCAAACCGGTT
3029890 TCCAACAGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 16 0.30
19 10 0.19
20 17 0.32
21 10 0.19
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (19 bp):
AAACCGGTCAAACCGGTTG
Found at i:3029889 original size:9 final size:9
Alignment explanation
Indices: 3029814--3029889 Score: 89
Period size: 9 Copynumber: 8.0 Consensus size: 9
3029804 GGGTTGGGTC
*
3029814 AAACCGGTC
1 AAACCGGTT
*
3029823 AAACCGGTC
1 AAACCGGTT
*
3029832 AAACCGGTC
1 AAACCGGTT
3029841 AAACCGGTT
1 AAACCGGTT
3029850 GAAACCGGTT
1 -AAACCGGTT
3029860 AGAACCGGTT
1 A-AACCGGTT
3029870 GAAAACCGGTT
1 --AAACCGGTT
3029881 AAACCGGTT
1 AAACCGGTT
3029890 TCCAACAGCC
Statistics
Matches: 62, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
9 36 0.58
10 17 0.27
11 8 0.13
12 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (9 bp):
AAACCGGTT
Found at i:3037078 original size:7 final size:7
Alignment explanation
Indices: 3037068--3037104 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3037058 AAGTCAACAA
3037068 TCAACGG
1 TCAACGG
3037075 TCAACGG
1 TCAACGG
*
3037082 TCAACTG
1 TCAACGG
3037089 TCAACGG
1 TCAACGG
3037096 TCAACGG
1 TCAACGG
3037103 TC
1 TC
3037105 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (7 bp):
TCAACGG
Found at i:3037086 original size:21 final size:21
Alignment explanation
Indices: 3037060--3037104 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3037050 GTCAAAGAAA
3037060 GTCAACAATCAACGGTCAACG
1 GTCAACAATCAACGGTCAACG
**
3037081 GTCAACTGTCAACGGTCAACG
1 GTCAACAATCAACGGTCAACG
3037102 GTC
1 GTC
3037105 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
GTCAACAATCAACGGTCAACG
Found at i:3037129 original size:9 final size:9
Alignment explanation
Indices: 3037111--3037209 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
3037101 GGTCGGGTCG
*
3037111 GGTCAGACC
1 GGTCAAACC
3037120 GGTCAAACC
1 GGTCAAACC
**
3037129 GGTTCGGACC
1 GG-TCAAACC
3037139 GGTCAAACC
1 GGTCAAACC
*
3037148 GGTTCGAACC
1 GG-TCAAACC
*
3037158 GGTTGAAACC
1 GG-TCAAACC
3037168 GGTCAAACC
1 GGTCAAACC
3037177 GGTCAGAACC
1 GGTCA-AACC
*
3037187 GGTTGGAAACC
1 GG-T-CAAACC
*
3037198 GGTTAAACC
1 GGTCAAACC
3037207 GGT
1 GGT
3037210 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3037138 original size:19 final size:19
Alignment explanation
Indices: 3037116--3037210 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
3037106 GGTCGGGTCA
3037116 GACCGGTCAAACCGGTTCG
1 GACCGGTCAAACCGGTTCG
3037135 GACCGGTCAAACCGGTTCG
1 GACCGGTCAAACCGGTTCG
* * *
3037154 AACCGGTTGAAACCGG-TCA
1 GACCGG-TCAAACCGGTTCG
*
3037173 AACCGGTCAGAACCGGTT-G
1 GACCGGTCA-AACCGGTTCG
*
3037192 GAAACCGGTTAAACCGGTT
1 G--ACCGGTCAAACCGGTT
3037211 TCCAGCAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.03
19 38 0.59
20 17 0.27
21 7 0.11
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCG
Found at i:3037141 original size:10 final size:10
Alignment explanation
Indices: 3037125--3037210 Score: 65
Period size: 10 Copynumber: 8.8 Consensus size: 10
3037115 AGACCGGTCA
3037125 AACCGGTTCG
1 AACCGGTTCG
* *
3037135 GACCGG-TCA
1 AACCGGTTCG
3037144 AACCGGTTCG
1 AACCGGTTCG
3037154 AACCGGTT-G
1 AACCGGTTCG
*
3037163 AAACCGG-TCA
1 -AACCGGTTCG
3037173 AACCGG-TCAG
1 AACCGGTTC-G
*
3037183 AACCGGTTGG
1 AACCGGTTCG
*
3037193 AAACCGGTT-A
1 -AACCGGTTCG
3037203 AACCGGTT
1 AACCGGTT
3037211 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
9 25 0.40
10 28 0.45
11 9 0.15
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:3037158 original size:29 final size:28
Alignment explanation
Indices: 3037136--3037210 Score: 55
Period size: 29 Copynumber: 2.6 Consensus size: 28
3037126 ACCGGTTCGG
*
3037136 ACCGGTCAAACCGGTTCG-AACCGGTTGAA
1 ACCGGTCAAACCGGTT-GAAACCGG-TCAA
* *
3037165 ACCGGTCAAACCGG-TCAGAACCGGTTGGAA
1 ACCGGTCAAACCGGTTGA-AACCGG-T-CAA
*
3037195 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3037211 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 1 0.03
29 22 0.55
30 16 0.40
31 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTGAAACCGGTCAA
Found at i:3039081 original size:9 final size:9
Alignment explanation
Indices: 3039059--3039092 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3039049 TATTTAAAAT
3039059 TTAATTTCGG
1 TTAATTT-GG
3039069 TTAATTTGG
1 TTAATTTGG
*
3039078 TTAATTCGG
1 TTAATTTGG
3039087 TTAATT
1 TTAATT
3039093 AAACTATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (9 bp):
TTAATTTGG
Found at i:3046620 original size:12 final size:12
Alignment explanation
Indices: 3046598--3046636 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3046588 AAATTATAAC
*
3046598 TAATAATATTAAT
1 TAAT-ATATTAAA
*
3046611 TATTATATTAAA
1 TAATATATTAAA
3046623 TAATATATTAAA
1 TAATATATTAAA
3046635 TA
1 TA
3046637 TATTTATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATATTAAA
Found at i:3049649 original size:8 final size:8
Alignment explanation
Indices: 3049636--3049676 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3049626 CTCATTTTCA
3049636 GAGAATTT
1 GAGAATTT
3049644 GAGAATTT
1 GAGAATTT
*
3049652 -AGAGTTT
1 GAGAATTT
*
3049659 GGGAATTT
1 GAGAATTT
3049667 GAGAATTT
1 GAGAATTT
3049675 GA
1 GA
3049677 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:3049857 original size:34 final size:33
Alignment explanation
Indices: 3049819--3049924 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
3049809 TAAGTTGAAA
*
3049819 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
* *
3049853 TTTAAATTTAAATTT-GAATAATATTATTTTTATT
1 TTT-AATTTAAATTTCGAATAATATAATTTATA-T
* *
3049887 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
3049920 TTTAA
1 TTTAA
3049925 AAACATTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
33 29 0.47
34 30 0.48
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:3049887 original size:33 final size:34
Alignment explanation
Indices: 3049826--3049925 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
3049816 AAATTTAATG
*
3049826 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
3049860 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
3049893 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
3049926 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:3050473 original size:21 final size:21
Alignment explanation
Indices: 3050443--3050536 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
3050433 TATGGTATAA
*
3050443 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
3050464 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
3050485 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
*
3050506 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
3050527 AATCCTGCGG
1 AACCCTGCGG
3050537 AGATGGCATA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
20 3 0.05
21 59 0.89
22 4 0.06
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:3050566 original size:21 final size:21
Alignment explanation
Indices: 3050540--3050587 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3050530 CCTGCGGAGA
*
3050540 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
3050561 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
3050582 GGGCAT
1 TGGCAT
3050588 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:3052358 original size:34 final size:31
Alignment explanation
Indices: 3052314--3052402 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
3052304 TTAATAATTC
*
3052314 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
3052348 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
3052379 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
3052403 AAAAATACTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:3052359 original size:31 final size:33
Alignment explanation
Indices: 3052317--3052391 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
3052307 ATAATTCTAA
* * *
3052317 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
3052349 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
3052380 ATAAAAAATAAT
1 ATAAAAAATAAT
3052392 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:3052419 original size:35 final size:34
Alignment explanation
Indices: 3052349--3052426 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
3052339 TTATTTTAAT
* * * *
3052349 AAAAAAATAATATTTACATAAATATATTAATATA
1 AAAAAAATAATATTTACAAAAAAATACTAACATA
3052383 AAAAATAATAACTATTTA-AAAAAAATACTAACATA
1 AAAAA-AATAA-TATTTACAAAAAAATACTAACATA
3052418 AAAATAAAT
1 AAAA-AAAT
3052427 TTCTTACCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 25 0.68
36 7 0.19
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (34 bp):
AAAAAAATAATATTTACAAAAAAATACTAACATA
Found at i:3057285 original size:30 final size:30
Alignment explanation
Indices: 3057240--3057306 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3057230 GAACTGGCAA
* *
3057240 TGAACCGGCTGAAAACCGGTAAAACCGGGG
1 TGAACCGGCTAAAAACCGGCAAAACCGGGG
* * **
3057270 TGAACTGGCTAAAAACTGGCAAAACCGGTT
1 TGAACCGGCTAAAAACCGGCAAAACCGGGG
3057300 TGAACCG
1 TGAACCG
3057307 CCGGTTCACT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.15
Consensus pattern (30 bp):
TGAACCGGCTAAAAACCGGCAAAACCGGGG
Found at i:3061301 original size:32 final size:30
Alignment explanation
Indices: 3061235--3061321 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 30
3061225 AGTAGGCCCC
* *
3061235 TAATAATAAATATTAAAAAAATTGAGCCTA
1 TAATAATAAATATTAAAAAAATTGAACATA
* *
3061265 TAATAATAAATATTAGGATAAAATTGAACATT
1 TAATAATAAATATTA--AAAAAATTGAACATA
* *
3061297 TAATAACAAGTATTAAAAATAATTG
1 TAATAATAAATATTAAAAA-AATTG
3061322 GACCCTATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 18 0.38
31 5 0.11
32 24 0.51
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (30 bp):
TAATAATAAATATTAAAAAAATTGAACATA
Found at i:3069124 original size:23 final size:22
Alignment explanation
Indices: 3069088--3069147 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
3069078 CGTCCGAGAC
3069088 TATATATTATTATTATATTATAA
1 TATAT-TTATTATTATATTATAA
*
3069111 T-TACTCTTATTATTATATTTTAA
1 TATA-T-TTATTATTATATTATAA
3069134 TATATTTATTATTA
1 TATATTTATTATTA
3069148 CAAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 11 0.33
23 20 0.61
24 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTTATTATTATATTATAA
Found at i:3069818 original size:20 final size:21
Alignment explanation
Indices: 3069793--3069857 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
3069783 ATAATGACTG
*
3069793 GAATAGTAACCGCCGATAGT-
1 GAATAGTGACCGCCGATAGTC
* *
3069813 GAATAGTGACCGGCGGTAGTC
1 GAATAGTGACCGCCGATAGTC
*
3069834 GAATAGTGATCGACCGATAGTC
1 GAATAGTGACCG-CCGATAGTC
3069856 GA
1 GA
3069858 TCGGTAACCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 11 0.30
22 9 0.24
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (21 bp):
GAATAGTGACCGCCGATAGTC
Found at i:3071155 original size:21 final size:21
Alignment explanation
Indices: 3071127--3071176 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3071117 AATTAATCAA
3071127 TTGTTTGATAGGCTTTTTAAT
1 TTGTTTGATAGGCTTTTTAAT
* *
3071148 TTTTTTGATAGGTTTTTTAAT
1 TTGTTTGATAGGCTTTTTAAT
3071169 TTGTTTGA
1 TTGTTTGA
3071177 CTTTTGCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.62
Consensus pattern (21 bp):
TTGTTTGATAGGCTTTTTAAT
Found at i:3072561 original size:46 final size:47
Alignment explanation
Indices: 3072470--3072562 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 47
3072460 TTAATTTTAC
* * * * **
3072470 TTTATTTTCCGAACAAATGTATGCGATCTAGAAATCATGCGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAAGTTAGG
3072517 TTTATTTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAAGTTAGG
1 TTTA-TTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAAGTTAGG
3072563 ATACTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
46 19 0.49
47 8 0.21
48 12 0.31
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAAGTTAGG
Found at i:3076858 original size:7 final size:7
Alignment explanation
Indices: 3076846--3076908 Score: 69
Period size: 7 Copynumber: 9.1 Consensus size: 7
3076836 GAAATGAAAG
3076846 AGAAAAA
1 AGAAAAA
3076853 AGAAAAA
1 AGAAAAA
3076860 AGAGATAAA
1 AGA-A-AAA
*
3076869 A-AGAAA
1 AGAAAAA
3076875 AG-AAAA
1 AGAAAAA
3076881 AG-AAAA
1 AGAAAAA
3076887 AGAAAAA
1 AGAAAAA
*
3076894 AGAGAAA
1 AGAAAAA
3076901 AGAAAAA
1 AGAAAAA
3076908 A
1 A
3076909 AAAGAAATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
6 15 0.31
7 27 0.56
8 2 0.04
9 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:3076871 original size:10 final size:9
Alignment explanation
Indices: 3076842--3076913 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 9
3076832 TTCTGAAATG
3076842 AAAGAG-AA
1 AAAGAGAAA
3076850 AAA-AGAAA
1 AAAGAGAAA
3076858 AAAGAGATAA
1 AAAGAGA-AA
3076868 AAAGA-AAA
1 AAAGAGAAA
*
3076876 GAAA-A-AGA
1 -AAAGAGAAA
3076884 AAA-AGAAA
1 AAAGAGAAA
3076892 AAAGAGAAA
1 AAAGAGAAA
3076901 AGAA-A-AAA
1 A-AAGAGAAA
3076909 AAAGA
1 AAAGA
3076914 AATTGAATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
7 8 0.15
8 23 0.43
9 14 0.26
10 9 0.17
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (9 bp):
AAAGAGAAA
Found at i:3076871 original size:26 final size:24
Alignment explanation
Indices: 3076842--3076915 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 24
3076832 TTCTGAAATG
3076842 AAAGAGAAAAAAGAAAAAAGAGATAA
1 AAAGAGAAAAAA-AAAAAAGAGA-AA
3076868 AAAGA-AAAGAAAAAGAAAA-AGAAA
1 AAAGAGAAA-AAAAA-AAAAGAGAAA
3076892 AAAGAGAAAAGAAAAAAAA-AGAAA
1 AAAGAGAAAA-AAAAAAAAGAGAAA
3076916 TTGAATCAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
24 17 0.39
25 15 0.34
26 12 0.27
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (24 bp):
AAAGAGAAAAAAAAAAAAGAGAAA
Found at i:3076892 original size:34 final size:30
Alignment explanation
Indices: 3076849--3076915 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 30
3076839 ATGAAAGAGA
3076849 AAAAAGAAAAAAGAGATAAAAAGAAAAGAAAAAG
1 AAAAAGAAAAAAGAG---AAAAGAAAA-AAAAAG
3076883 AAAAAGAAAAAAGAGAAAAGAAAAAAAAAG
1 AAAAAGAAAAAAGAGAAAAGAAAAAAAAAG
3076913 AAA
1 AAA
3076916 TTGAATCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 9 0.27
31 9 0.27
34 15 0.45
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (30 bp):
AAAAAGAAAAAAGAGAAAAGAAAAAAAAAG
Found at i:3080025 original size:119 final size:119
Alignment explanation
Indices: 3079872--3080144 Score: 413
Period size: 119 Copynumber: 2.3 Consensus size: 119
3079862 CACACATTTG
* *
3079872 TAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTA
1 TAAAACCCCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTA
* * *
3079937 ATGTTCAAGAAAATTAAAACCTCCTGGTAATTTGTAAATCCTTCGGATCATCTA
66 ATGTTCAAGAAAATTAAAACCTCCGGGTAATTTGTAAAACCTCCGGATCATCTA
* *
3079991 TAAAACCCCATGGTAAGATGTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTA
1 TAAAACCCCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTA
* * * * *
3080056 ATTTTCAAGAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTG
66 ATGTTCAAGAAAATTAAAACCTCCGGGTAATTTGTAAAACCTCCGGATCATCTA
*
3080110 TAAAACCTCC-GGGTAGGATGTTTTCTCATGAAAAT
1 TAAAACC-CCAGGGTAGGATGTTTTCGCATGAAAAT
3080145 TAAAACCTCC
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
119 136 0.99
120 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (119 bp):
TAAAACCCCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTA
ATGTTCAAGAAAATTAAAACCTCCGGGTAATTTGTAAAACCTCCGGATCATCTA
Found at i:3080098 original size:20 final size:20
Alignment explanation
Indices: 3080070--3080123 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3080060 TCAAGAAAAT
* * *
3080070 TAAATCCTCCGGGTGATTTG
1 TAAAACCTCCGGGTCATCTG
3080090 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
3080110 TAAAACCTCCGGGT
1 TAAAACCTCCGGGT
3080124 AGGATGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTG
Found at i:3080188 original size:20 final size:20
Alignment explanation
Indices: 3080145--3080198 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3080135 TCATGAAAAT
* * *
3080145 TAAAACCTCCGGGTGATTTG
1 TAAAACCTCCGGGTCATCTA
*
3080165 TAAATCCTCCGGGTCATCTA
1 TAAAACCTCCGGGTCATCTA
*
3080185 TAAAACCTCAGGGT
1 TAAAACCTCCGGGT
3080199 AGGATGTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTA
Found at i:3080189 original size:75 final size:75
Alignment explanation
Indices: 3080064--3080219 Score: 267
Period size: 75 Copynumber: 2.1 Consensus size: 75
3080054 TAATTTTCAA
* * *
3080064 GAAAATTAAATCCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCCGGGTAGGAT
1 GAAAATTAAAACCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
*
3080129 GTTTTCTCAT
66 GTTTTCGCAT
*
3080139 GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
1 GAAAATTAAAACCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
3080204 GTTTTCGCAT
66 GTTTTCGCAT
3080214 GAAAAT
1 GAAAAT
3080220 GAGAAAGCAA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (75 bp):
GAAAATTAAAACCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
GTTTTCGCAT
Found at i:3080279 original size:194 final size:194
Alignment explanation
Indices: 3079945--3080338 Score: 635
Period size: 194 Copynumber: 2.0 Consensus size: 194
3079935 TAATGTTCAA
* * *
3079945 GAAAATTAAAACCTCCTGGTAATTTGTAAATCCTTCGGATCATCTATAAAACCCCATGGTAAGAT
1 GAAAATTAAAACCTCCGGGTAATTTGTAAATCCTCCGGATCATCTATAAAACCCCAGGGTAAGAT
* * *
3080010 GTTTTCGCATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATTTTCAAGAAAATTAAAT
66 GTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAA
* * *
3080075 CCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCCGGGTAGGATGTTTTCTCAT
131 CCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGATGTTTTCGCAT
* * * *
3080139 GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
1 GAAAATTAAAACCTCCGGGTAATTTGTAAATCCTCCGGATCATCTATAAAACCCCAGGGTAAGAT
3080204 GTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAA
66 GTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAA
* * *
3080269 CCTTCGGGTGATTTGTAAATCCTCTGGGTCATCTATAAAACCTCAGGGTAGGATGTTTTCGCAT
131 CCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGATGTTTTCGCAT
*
3080333 AAAAAT
1 GAAAAT
3080339 GAGAAAGCGA
Statistics
Matches: 183, Mismatches: 17, Indels: 0
0.92 0.09 0.00
Matches are distributed among these distances:
194 183 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (194 bp):
GAAAATTAAAACCTCCGGGTAATTTGTAAATCCTCCGGATCATCTATAAAACCCCAGGGTAAGAT
GTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAA
CCTCCGGGTGATTTGTAAAACCTCCGGGTCATCTATAAAACCTCAGGGTAGGATGTTTTCGCAT
Found at i:3080362 original size:119 final size:119
Alignment explanation
Indices: 3080139--3080413 Score: 435
Period size: 119 Copynumber: 2.3 Consensus size: 119
3080129 GTTTTCTCAT
*
3080139 GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCCGGGTCATCTATAAAACCTCAGGGTAGGAT
1 GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCTGGGTCATCTATAAAACCTCAGGGTAGGAT
* **
3080204 GTTTTCGCATGAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTCAA
66 GTTTTCGCATAAAAATGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTCAA
*
3080258 GAAAATTAAAACCTTCGGGTGATTTGTAAATCCTCTGGGTCATCTATAAAACCTCAGGGTAGGAT
1 GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCTGGGTCATCTATAAAACCTCAGGGTAGGAT
* * *
3080323 GTTTTCGCATAAAAATGAGAAAGCGATTACCAAATTTTCTCATTTAATGTTCTA
66 GTTTTCGCATAAAAATGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTCAA
* * *
3080377 GAAAATTAAATCCTCCGGGTTG-TCTGTAAAACCTCTG
1 GAAAATTAAAACCTCCGGG-TGATTTGTAAATCCTCTG
3080414 AGTAGGATGT
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
119 141 0.99
120 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (119 bp):
GAAAATTAAAACCTCCGGGTGATTTGTAAATCCTCTGGGTCATCTATAAAACCTCAGGGTAGGAT
GTTTTCGCATAAAAATGAGAAAGCAATTACCAAAGTTTCTCATTTAATGTTCAA
Found at i:3080583 original size:17 final size:17
Alignment explanation
Indices: 3080575--3080609 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3080565 TTATATTACA
*
3080575 ATTACTATTACTATTAT
1 ATTACAATTACTATTAT
*
3080592 ATTATAATTACTATTAT
1 ATTACAATTACTATTAT
3080609 A
1 A
3080610 ATTATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTACAATTACTATTAT
Found at i:3080589 original size:23 final size:22
Alignment explanation
Indices: 3080557--3080641 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 22
3080547 CGAGACTATA
3080557 TATTATTATTATATTACAATTAC
1 TATTA-TATTATATTACAATTAC
*
3080580 TATTACTATTATATTATAATTAC
1 TATTA-TATTATATTACAATTAC
**
3080603 TATTATAATTATATTTTAA-TA-
1 TATTAT-ATTATATTACAATTAC
3080624 TATT-TATTATTATTACAA
1 TATTATATTA-TATTACAA
3080642 ATAATACAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
19 4 0.07
20 7 0.13
21 4 0.07
22 3 0.05
23 37 0.67
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATATTATATTACAATTAC
Found at i:3083505 original size:54 final size:54
Alignment explanation
Indices: 3083426--3083744 Score: 419
Period size: 54 Copynumber: 5.9 Consensus size: 54
3083416 CAGTGCCCAT
* * * * *
3083426 ACGGTCATTCATAAACATATAATGAATTCTGTGGTTTGCACACATAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAA
* * *
3083480 ATGGTTACTCATCAACATATGATGAATT-TCGTGCTTTGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATATGATGAATTCT-GTGATTTGCACACTTAGTGTCGAA
* * *
3083534 ACAGTTATTGATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAA
*** * *
3083588 ATAATTATTCATCAACATATGATGAATTTTGTGATTTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAA
3083642 ACGGTTATTCATCAACATATGATGAATTCCT-TGATTTGCACACTTAGT-TCCGAA
1 ACGGTTATTCATCAACATATGATGAATT-CTGTGATTTGCACACTTAGTGT-CGAA
* * *
3083696 ACGGTTATTCATCAACATATGATGAACTCTGTGATTTTCATACTTAGTG
1 ACGGTTATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTG
3083745 CCGTCAACAT
Statistics
Matches: 234, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.01
54 229 0.98
55 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (54 bp):
ACGGTTATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAA
Found at i:3083600 original size:108 final size:106
Alignment explanation
Indices: 3083439--3083837 Score: 466
Period size: 108 Copynumber: 3.8 Consensus size: 106
3083429 GTCATTCATA
* * * * *
3083439 AACATATAATGAATTCTGTGGTTTGCACACATAGTGTCGAAATGGTTACTCATCAACATATGATG
1 AACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATG
*
3083504 AATTTCGTGCTTTGCACACTTAGTGTCGAAACAGTTATTGATC
66 AATTTCGTGATTTGCACACTTAGTG-CGAAAC-GTTATTGATC
**
3083547 AACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAAATAATTATTCATCAACATATGATG
1 AACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATG
* *
3083612 AATTTTGTGATTTGCACACTTAGTGCCGAAACGGTTATTCATC
66 AATTTCGTGATTTGCACACTTAGTG-CGAAAC-GTTATTGATC
* *
3083655 AACATATGATGAATTCCT-TGATTTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGAT
1 AACATATGATGAATT-CTGTGATTTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGAT
* * *
3083719 GAA-CTCTGTGATTTTCATACTTAGTGC----C------G-TC
65 GAATTTC-GTGATTTGCACACTTAGTGCGAAACGTTATTGATC
* * *
3083750 AACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACT-GTTATTCATCAACGTATGAT
1 AACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAAA-TGGTTATTCATCAACATATGAT
*
3083814 GAATTCCGTGATTTGCACACTTAG
65 GAATTTCGTGATTTGCACACTTAG
3083838 CGCCTATTTG
Statistics
Matches: 256, Mismatches: 30, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
94 1 0.00
95 76 0.30
96 1 0.00
103 1 0.00
107 2 0.01
108 173 0.68
109 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (106 bp):
AACATATGATGAATTCTGTGATTTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATGATG
AATTTCGTGATTTGCACACTTAGTGCGAAACGTTATTGATC
Found at i:3083712 original size:162 final size:154
Alignment explanation
Indices: 3083432--3083837 Score: 518
Period size: 162 Copynumber: 2.6 Consensus size: 154
3083422 CCATACGGTC
* * * * * *
3083432 ATTCATAAACATATAATGAATTCTGTGGTTTGCACACATAGTGTCGAAATGGTTACTCATCAACA
1 ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAAACGGTTATTCATCAACA
* * * *
3083497 TATGATGAATTTCGTGCTTTGCACACTTAGTGTCGAAACAGTTATTGATCAACATATGATGAATT
66 TATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAACT
3083562 CTGTGATTTGCACACTTAGTGCCG
131 CTGTGATTTGCACACTTAGTGCCG
* *
3083586 AAATAATTATTCATCAACATATGATGAATTTTGTGATTTGCACACTTAGTGCCGAAACGGTTATT
1 --------ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAAACGGTTATT
* *
3083651 CATCAACATATGATGAATTCCTTGATTTGCACACTTAGT-TCCGAAACGGTTATTCATCAACATA
58 CATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGT-CGAAACAGTTATTCATCAACATA
* *
3083715 TGATGAACTCTGTGATTTTCATACTTAGTGCCG
122 TGATGAACTCTGTGATTTGCACACTTAGTGCCG
* * *
3083748 -----TCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACTGTTATTCATCAACG
1 ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAAACGGTTATTCATCAACA
3083808 TATGATGAATTCCGTGATTTGCACACTTAG
66 TATGATGAATTCCGTGATTTGCACACTTAG
3083838 CGCCTATTTG
Statistics
Matches: 221, Mismatches: 22, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
149 84 0.38
161 1 0.00
162 136 0.62
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (154 bp):
ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTGTCGAAACGGTTATTCATCAACA
TATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAACT
CTGTGATTTGCACACTTAGTGCCG
Found at i:3083771 original size:41 final size:41
Alignment explanation
Indices: 3083707--3083785 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
3083697 CGGTTATTCA
* * *
3083707 TCAACATATGATGAACTCTGTGATTTTCATACTTAGTGCCG
1 TCAACATATGATGAACTCCGTGATTTGCACACTTAGTGCCG
*
3083748 TCAACATATGATGAATTCCGTGATTTGCACACTTAGTG
1 TCAACATATGATGAACTCCGTGATTTGCACACTTAGTG
3083786 TCGAAACTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (41 bp):
TCAACATATGATGAACTCCGTGATTTGCACACTTAGTGCCG
Found at i:3083816 original size:95 final size:95
Alignment explanation
Indices: 3083653--3083837 Score: 291
Period size: 95 Copynumber: 1.9 Consensus size: 95
3083643 CGGTTATTCA
*
3083653 TCAACATATGATGAATTCCTTGATTTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGA
1 TCAACATATGATGAATTCCGTGATTTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGA
* * *
3083718 TGAACTCTGTGATTTTCATACTTAGTGCCG
66 TGAACTCCGTGATTTGCACACTTAGTGCCG
* *
3083748 TCAACATATGATGAATTCCGTGATTTGCACACTTAGTGT-CGAAACTGTTATTCATCAACGTATG
1 TCAACATATGATGAATTCCGTGATTTGCACACTTAGT-TCCGAAACGGTTATTCATCAACATATG
*
3083812 ATGAATTCCGTGATTTGCACACTTAG
65 ATGAACTCCGTGATTTGCACACTTAG
3083838 CGCCTATTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 81 0.99
96 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (95 bp):
TCAACATATGATGAATTCCGTGATTTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGA
TGAACTCCGTGATTTGCACACTTAGTGCCG
Found at i:3090458 original size:54 final size:54
Alignment explanation
Indices: 3090416--3090892 Score: 616
Period size: 54 Copynumber: 8.8 Consensus size: 54
3090406 CCATACGATC
* * *** * * *
3090416 ATTCATAAACATATTATGAATTTTTTGGTTTGCACACATAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* ** *
3090470 AGTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTTTCGAAACGATT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* * *
3090524 ATTCATAAACATATGATGAATTTCGTAATTTGCACACTTAGTGCCGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* * *
3090578 ATTCATCAACATATGATGAATTCTGTGATTTGCACACTTAGTACCAAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* * * **
3090632 ATTCATCAACATATGATGAATTACGT-ACTTTGAACACTTAGAGTTGAAACGGTT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCGAAACGGTT
* * * *
3090686 ATTTATCAATATATGATGAATTCCATGATTTGCACACTTAGTGCCGAAACGGCT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
* ** *
3090740 ATTCATCAACATATGATGAATTCTGT-ACTTTGCACACTTAGTGTTGAAACGATT
1 ATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTTAGTGCCGAAACGGTT
* *
3090794 ATTCATCAACATATGATGAATTCCCTGATTTGCACACTTAGTGCCGAAACGTTT
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
*
3090848 ATTCATCAACATATGATGAATTCCTTGATTTGCACACTTAGTGCC
1 ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCC
3090893 TATTTGGTAA
Statistics
Matches: 363, Mismatches: 56, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 359 0.99
55 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGCCGAAACGGTT
Found at i:3100561 original size:16 final size:16
Alignment explanation
Indices: 3100536--3100566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3100526 ATAAATAAAT
3100536 GAACAAAAACGAACAC
1 GAACAAAAACGAACAC
*
3100552 GAACATAAACGAACA
1 GAACAAAAACGAACA
3100567 AAATTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.23, G:0.13, T:0.03
Consensus pattern (16 bp):
GAACAAAAACGAACAC
Found at i:3100637 original size:10 final size:10
Alignment explanation
Indices: 3100622--3100709 Score: 68
Period size: 10 Copynumber: 8.1 Consensus size: 10
3100612 CATTTAAATG
3100622 ATAAACGAAC
1 ATAAACGAAC
3100632 ATAAACGAAC
1 ATAAACGAAC
* *
3100642 GTAACCGAGCAC
1 ATAAACGA--AC
*
3100654 AAACGAACGAAC
1 ATA--AACGAAC
3100666 ATAAACGAAC
1 ATAAACGAAC
*
3100676 ATAATAAATGAAC
1 ---ATAAACGAAC
3100689 ATAAACGAAC
1 ATAAACGAAC
*
3100699 ATAAATGAAC
1 ATAAACGAAC
3100709 A
1 A
3100710 ACACAAACAC
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 42 0.68
12 7 0.11
13 9 0.15
14 4 0.06
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3100712 original size:23 final size:22
Alignment explanation
Indices: 3100658--3100717 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
3100648 GAGCACAAAC
3100658 GAACGAACATAAACGAACATAAT
1 GAAC-AACATAAACGAACATAAT
* *
3100681 AAATGAACATAAACGAACATAAAT
1 GAA-CAACATAAACGAACAT-AAT
*
3100705 GAACAACACAAAC
1 GAACAACATAAAC
3100718 ACAAAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (22 bp):
GAACAACATAAACGAACATAAT
Found at i:3106987 original size:29 final size:30
Alignment explanation
Indices: 3106949--3107022 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
3106939 TTTATGTGGA
*
3106949 GTGAACTTGAATTTTTAAAATTTT-AGGGG
1 GTGAAATTGAATTTTTAAAATTTTAAGGGG
* *
3106978 GTGAAATTGAACTTATAAAATTTTAAGGGG
1 GTGAAATTGAATTTTTAAAATTTTAAGGGG
* * *
3107008 GCGAAAATAAATTTT
1 GTGAAATTGAATTTT
3107023 CAACGGAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (30 bp):
GTGAAATTGAATTTTTAAAATTTTAAGGGG
Found at i:3107785 original size:15 final size:15
Alignment explanation
Indices: 3107743--3107789 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3107733 ATTGAAATTG
3107743 AGAATTAGAGA-TTT
1 AGAATTAGAGATTTT
* * *
3107757 GGATATTGGGGATTTT
1 AGA-ATTAGAGATTTT
3107773 AGAATTAGAGATTTT
1 AGAATTAGAGATTTT
3107788 AG
1 AG
3107790 GTGACGATAG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (15 bp):
AGAATTAGAGATTTT
Found at i:3107961 original size:8 final size:9
Alignment explanation
Indices: 3107943--3107975 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3107933 TAAAATAAAC
3107943 TTTTTATTT
1 TTTTTATTT
3107952 TTTTTATTT
1 TTTTTATTT
3107961 TTTTT-TTAT
1 TTTTTATT-T
3107970 TTTTTA
1 TTTTTA
3107976 ATTAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 20 0.91
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3107965 original size:11 final size:11
Alignment explanation
Indices: 3107949--3107974 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3107939 AAACTTTTTA
3107949 TTTTTTTTATT
1 TTTTTTTTATT
3107960 TTTTTTTTATT
1 TTTTTTTTATT
3107971 TTTT
1 TTTT
3107975 AATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:3107989 original size:20 final size:21
Alignment explanation
Indices: 3107966--3108005 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3107956 TATTTTTTTT
3107966 TTATTTTT-TAATTAAAAATG
1 TTATTTTTATAATTAAAAATG
*
3107986 TTATTTTTATTATTAAAAAT
1 TTATTTTTATAATTAAAAAT
3108006 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATTTTTATAATTAAAAATG
Found at i:3113154 original size:21 final size:20
Alignment explanation
Indices: 3113130--3113206 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
3113120 CATTGCAATT
3113130 TTTCAAATTCGCAACACTGAA
1 TTTCAAATTCGCAACAC-GAA
* *
3113151 TTTCAAATTCGCAACTCGAT
1 TTTCAAATTCGCAACACGAA
*
3113171 TTTCGAATTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
* *
3113191 TTTTAATTTCGCAACA
1 TTTCAAATTCGCAACA
3113207 GGTTTTAGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:3113174 original size:41 final size:40
Alignment explanation
Indices: 3113129--3113205 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
3113119 GCATTGCAAT
3113129 TTTTCAAATTCGCAACACTGAATTTCAAATTCGCAACTCGA
1 TTTTCAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGA
* * *
3113170 TTTTCGAATTCGCAACACGAATTTTAATTTCGCAAC
1 TTTTCAAATTCGCAACACGAATTTCAAATTCGCAAC
3113206 AGGTTTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 16 0.48
41 17 0.52
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.34
Consensus pattern (40 bp):
TTTTCAAATTCGCAACACGAATTTCAAATTCGCAACTCGA
Found at i:3117030 original size:64 final size:64
Alignment explanation
Indices: 3116928--3117079 Score: 243
Period size: 64 Copynumber: 2.4 Consensus size: 64
3116918 AATTTAAAAC
3116928 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
*** * *
3116992 AACAAATCAACTTTTACAAATCAATTAAACAAGA-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAA-ACAAAAAATAAGAATTATTTACACATCAATTA
3117056 AACAAATCAACTTTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
3117080 CTTTTACAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 81 0.99
65 1 0.01
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAAGAATTATTTACACATCAATTA
Found at i:3117076 original size:14 final size:14
Alignment explanation
Indices: 3117057--3117093 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3117047 CATCAATTAA
3117057 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3117071 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3117085 ACAAATCAA
1 ACAAATCAA
3117094 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3118476 original size:21 final size:21
Alignment explanation
Indices: 3118450--3118561 Score: 109
Period size: 21 Copynumber: 5.3 Consensus size: 21
3118440 AATCGGGCTT
*
3118450 TTGAACGGTGGGAGAGACCTC
1 TTGAACGGTGGGAGAGGCCTC
* ** *
3118471 TTGAACGATGACAGGGGCCTC
1 TTGAACGGTGGGAGAGGCCTC
3118492 TTGAACGGTGGGAGAGGCCTC
1 TTGAACGGTGGGAGAGGCCTC
** *
3118513 TTGAA-GGATGATAGGGGCCTC
1 TTGAACGG-TGGGAGAGGCCTC
* * *
3118534 TTGAACGATAGGATAGGCCTC
1 TTGAACGGTGGGAGAGGCCTC
3118555 TTGAACG
1 TTGAACG
3118562 ATGATAGGTG
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
20 2 0.03
21 68 0.96
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
TTGAACGGTGGGAGAGGCCTC
Found at i:3118513 original size:42 final size:42
Alignment explanation
Indices: 3118450--3118565 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 42
3118440 AATCGGGCTT
*
3118450 TTGAACGGTGGGAGAGACCTCTTGAACGATGACAGGGGCCTC
1 TTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGCCTC
* *
3118492 TTGAACGGTGGGAGAGGCCTCTTGAAGGATGATAGGGGCCTC
1 TTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGCCTC
* * *
3118534 TTGAACGATAGGATAGGCCTCTTGAACGATGA
1 TTGAACGGTGGGAGAGGCCTCTTGAACGATGA
3118566 TAGGTGCTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (42 bp):
TTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGCCTC
Found at i:3118871 original size:21 final size:21
Alignment explanation
Indices: 3118847--3118900 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3118837 TGCAACAATC
* *
3118847 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
3118868 TCACGTAAAGCAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
3118889 CCACGTAAAGCA
1 TCACGTAAAGCA
3118901 CCATTGTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:3120736 original size:19 final size:19
Alignment explanation
Indices: 3120685--3120738 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
3120675 AAGACTATTT
3120685 GAAACTTAAAATCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
3120705 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
3120725 GAAACTAAAATCGC
1 GAAACTAAAATCGC
3120739 GTTGCGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:3120921 original size:22 final size:22
Alignment explanation
Indices: 3120864--3120921 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3120854 GATGGAGATA
*
3120864 GACGGATTTCGCTGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* * *
3120886 GATGAATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3120908 GACGGATGTCGCCG
1 GACGGATTTCGCCG
3120922 TAGAGAGTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.16, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3121036 original size:19 final size:20
Alignment explanation
Indices: 3121014--3121051 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3121004 AATATTGTGT
3121014 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
3121033 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
3121052 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:3124603 original size:13 final size:13
Alignment explanation
Indices: 3124566--3124605 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3124556 TCGATATTGA
3124566 AAAATAAATA-TT
1 AAAATAAATATTT
*
3124578 AAAATAATTTATTT
1 AAAATAA-ATATTT
3124592 AAAATAAATATTT
1 AAAATAAATATTT
3124605 A
1 A
3124606 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:3126012 original size:3 final size:3
Alignment explanation
Indices: 3126004--3126057 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
3125994 GGCCTGGTTG
* *
3126004 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
3126050 TAA TAA TA
1 TAA TAA TA
3126058 TAAATAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3126021 original size:12 final size:11
Alignment explanation
Indices: 3126004--3126060 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
3125994 GGCCTGGTTG
3126004 TAATAATAATA
1 TAATAATAATA
3126015 TTAATAATAA-A
1 -TAATAATAATA
3126026 -AATATATAATA
1 TAATA-ATAATA
3126037 -AATAAT-ATAA
1 TAATAATAAT-A
3126047 TAATAATAATA
1 TAATAATAATA
3126058 TAA
1 TAA
3126061 ATAAAACCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.15
10 7 0.17
11 16 0.40
12 11 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAATAATA
Found at i:3126064 original size:12 final size:14
Alignment explanation
Indices: 3126004--3126060 Score: 80
Period size: 14 Copynumber: 4.0 Consensus size: 14
3125994 GGCCTGGTTG
3126004 TAATAATAATATTAA
1 TAATAATAATA-TAA
*
3126019 TAATAAAAATAT-A
1 TAATAATAATATAA
3126032 TAATAAATAATATAA
1 TAAT-AATAATATAA
3126047 TAATAATAATATAA
1 TAATAATAATATAA
3126061 ATAAAACCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
13 5 0.13
14 18 0.47
15 15 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:3126458 original size:20 final size:20
Alignment explanation
Indices: 3126435--3126500 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
3126425 TATGAACTTC
3126435 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
* **
3126455 TTCTT-CTTATT-ATGAACT-TC
1 TTCTTCCTTCTTCA-G-A-TGAG
3126475 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
3126495 TTCTTC
1 TTCTTC
3126501 TCATTATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 18 0.53
21 7 0.21
22 1 0.03
ACGTcount: A:0.15, C:0.24, G:0.11, T:0.50
Consensus pattern (20 bp):
TTCTTCCTTCTTCAGATGAG
Found at i:3126470 original size:40 final size:40
Alignment explanation
Indices: 3126415--3126513 Score: 189
Period size: 40 Copynumber: 2.5 Consensus size: 40
3126405 GTTGAACAAA
3126415 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
3126455 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
3126495 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
3126514 TCTCTGGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.49
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:3126507 original size:153 final size:153
Alignment explanation
Indices: 3126307--3126628 Score: 544
Period size: 153 Copynumber: 2.1 Consensus size: 153
3126297 CTGAACAAAC
*
3126307 TCTTCTCATTGTGAA---CTTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
3126369 AAAGTTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
66 AAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
3126434 CTTCTTCC-TTCTTCAGATGAGT
131 CTTCTTCCTTTCTTCAGATGAGT
* *
3126456 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
3126521 AAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
65 AAAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
3126586 TCTTCTTCCTTTTTTTCAGATGAGT
130 TCTTCTTCC-TTTCTTCAGATGAGT
3126611 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
3126629 TCTCTGGAAA
Statistics
Matches: 160, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
149 13 0.08
152 6 0.04
153 111 0.69
155 30 0.19
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.42
Consensus pattern (153 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAGTGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTTCTTCAGATGAGT
Found at i:3126628 original size:115 final size:113
Alignment explanation
Indices: 3126455--3126751 Score: 479
Period size: 115 Copynumber: 2.6 Consensus size: 113
3126445 TTCAGATGAG
*
3126455 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
3126520 GAAAAGCTGATCCATCAAGTGATGGATTT-GAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTTAG-ACAAAAGGTTAAACAAA
*
3126568 TTCTTCTCATTATGAACTTCTTCTTCCTTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 TTCTTCTCATTATGAACTTCTTCTTCC--TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
3126633 TGGAAAAGTTGATCCATCAAGTGATGAATTTAGGCAAAAGGTTAAACAAG
64 TGGAAAAGCTGATCCATCAAGTGATGAATTTAGACAAAAGGTTAAACAAA
* *
3126683 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
3126748 GAAA
66 GAAA
3126752 TGTCAATCTA
Statistics
Matches: 171, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
113 65 0.38
115 105 0.61
116 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTTAGACAAAAGGTTAAACAAA
Found at i:3127935 original size:83 final size:83
Alignment explanation
Indices: 3127460--3127920 Score: 852
Period size: 83 Copynumber: 5.6 Consensus size: 83
3127450 GTAGTTCTTA
*
3127460 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
3127525 ATTCAATGATTAGTTCTG
66 ATTCAATGATTGGTTCTG
3127543 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3127608 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
3127626 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3127691 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
3127709 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTTTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
3127773 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
3127792 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
3127857 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
3127875 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
3127921 TGGCAAATTC
Statistics
Matches: 367, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
82 2 0.01
83 363 0.99
84 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:3129075 original size:1 final size:1
Alignment explanation
Indices: 3129071--3129160 Score: 54
Period size: 1 Copynumber: 90.0 Consensus size: 1
3129061 CTTGACCCCC
* * * * * * * * * *
3129071 TTTTTCTTTTTTCTTTTTTTTTCTTTTTCTCTCTTTCTTTTTTTTTCTTTTTTTTTCTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
3129136 TCTTTTTTCTTTCTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3129161 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:3129092 original size:10 final size:10
Alignment explanation
Indices: 3129077--3129158 Score: 101
Period size: 10 Copynumber: 7.6 Consensus size: 10
3129067 CCCCTTTTTC
3129077 TTTTTTCTTT
1 TTTTTTCTTT
3129087 TTTTTTCTTTT
1 TTTTTTC-TTT
3129098 TCTCTCTTTCTTT
1 T-T-T-TTTCTTT
3129111 TTTTTTCTTT
1 TTTTTTCTTT
3129121 TTTTTTCTTT
1 TTTTTTCTTT
*
3129131 TTCTTTCTTT
1 TTTTTTCTTT
3129141 TTTCTTTCTTCT
1 TTT-TTTCTT-T
3129153 TTTTTT
1 TTTTTT
3129159 TTCTTCAAGC
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
10 35 0.55
11 14 0.22
12 6 0.09
13 5 0.08
14 4 0.06
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:3129120 original size:34 final size:34
Alignment explanation
Indices: 3129071--3129163 Score: 152
Period size: 34 Copynumber: 2.7 Consensus size: 34
3129061 CTTGACCCCC
3129071 TTTTTCTTTTTTCTTTTTTTTTCTTTTTCTCTCT
1 TTTTTCTTTTTTCTTTTTTTTTCTTTTTCTCTCT
*
3129105 TTCTTT-TTTTTTCTTTTTTTTTCTTTTTCTTTCT
1 TT-TTTCTTTTTTCTTTTTTTTTCTTTTTCTCTCT
*
3129139 TTTTTCTTTCTTCTTTTTTTTTCTT
1 TTTTTCTTTTTTCTTTTTTTTTCTT
3129164 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 3 0.05
34 49 0.89
35 3 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (34 bp):
TTTTTCTTTTTTCTTTTTTTTTCTTTTTCTCTCT
Found at i:3129140 original size:44 final size:44
Alignment explanation
Indices: 3129077--3129163 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
3129067 CCCCTTTTTC
*
3129077 TTTTTTCTTTTTTTTTC-TTTTTCTCTCTTTCTTTTTTTTTCTTT
1 TTTTTTCTTTTTCTTTCTTTTTTCTCTC-TTCTTTTTTTTTCTTT
*
3129121 TTTTTTCTTTTTCTTTCTTTTTTCTTTCTTCTTTTTTTTTCTT
1 TTTTTTCTTTTTCTTTCTTTTTTCTCTCTTCTTTTTTTTTCTT
3129164 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 31 0.77
45 9 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (44 bp):
TTTTTTCTTTTTCTTTCTTTTTTCTCTCTTCTTTTTTTTTCTTT
Found at i:3140310 original size:12 final size:12
Alignment explanation
Indices: 3140293--3140317 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3140283 TCTATTATTA
3140293 AAAATTCAAAAT
1 AAAATTCAAAAT
3140305 AAAATTCAAAAT
1 AAAATTCAAAAT
3140317 A
1 A
3140318 TATTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTCAAAAT
Found at i:3140562 original size:13 final size:13
Alignment explanation
Indices: 3140525--3140564 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3140515 TCGATATTGA
3140525 AAAATAAATA-TT
1 AAAATAAATATTT
*
3140537 AAAATAATTTATTT
1 AAAATAA-ATATTT
3140551 AAAATAAATATTT
1 AAAATAAATATTT
3140564 A
1 A
3140565 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:3141972 original size:3 final size:3
Alignment explanation
Indices: 3141964--3142020 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
3141954 GGCCTGGTTG
* *
3141964 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
3142010 TAA TAA TAA TA
1 TAA TAA TAA TA
3142021 TAAATAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3141981 original size:9 final size:9
Alignment explanation
Indices: 3141967--3142027 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
3141957 CTGGTTGTAA
3141967 TAATAATAT
1 TAATAATAT
*
3141976 TAATAATAA
1 TAATAATAT
*
3141985 AAATATATAAT
1 TAATA-AT-AT
*
3141996 AAATAATA-
1 TAATAATAT
*
3142004 TAATAATAA
1 TAATAATAT
3142013 TAATAATAT
1 TAATAATAT
*
3142022 AAATAA
1 TAATAA
3142028 AACCGGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
9 26 0.60
10 4 0.09
11 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAATAATAT
Found at i:3142026 original size:12 final size:12
Alignment explanation
Indices: 3141965--3142027 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
3141955 GCCTGGTTGT
*
3141965 AATAATAATATT
1 AATAATAATATA
*
3141977 AATAATAAAAATA
1 AATAAT-AATATA
*
3141990 TATAATAA-AT-
1 AATAATAATATA
3142000 AAT-ATAATA-A
1 AATAATAATATA
3142010 TAATAATAATATA
1 -AATAATAATATA
3142023 AATAA
1 AATAA
3142028 AACCGGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 5 0.12
12 19 0.46
13 10 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATAATATA
Found at i:3144452 original size:21 final size:21
Alignment explanation
Indices: 3144426--3144477 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
3144416 GCAGGTGCAT
3144426 CGATGCACTATGAGTGTGTAC
1 CGATGCACTATGAGTGTGTAC
3144447 CGATGCACTATGAGTGTGTAC
1 CGATGCACTATGAGTGTGTAC
3144468 CGATGCACTA
1 CGATGCACTA
3144478 AGACAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (21 bp):
CGATGCACTATGAGTGTGTAC
Found at i:3146733 original size:46 final size:44
Alignment explanation
Indices: 3146639--3146770 Score: 158
Period size: 46 Copynumber: 2.9 Consensus size: 44
3146629 GTAACCATGC
* * **
3146639 AAATAAGCTTATGAGCTTACGGA-ATAATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATA-AATGGTAAGTATATTGGTA
3146683 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-A-TAAATGGTAAGTATATTGGTA
* * *
3146729 AAATATGCTTACAAGCTTATGGGATAAATGGTAAGTAAATTG
1 AAATAAGCTTACGAGCTTAT-GGATAAATGGTAAGTATATTG
3146771 ATAAGAAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
44 20 0.26
45 18 0.23
46 36 0.47
47 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGATAAATGGTAAGTATATTGGTA
Found at i:3147634 original size:5 final size:5
Alignment explanation
Indices: 3147591--3147615 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3147581 CCGAGTAAAA
3147591 CGGTT CGGTT CGGTT CGGTT CGGTT
1 CGGTT CGGTT CGGTT CGGTT CGGTT
3147616 TGGCTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
CGGTT
Done.