Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007912.1 Hibiscus syriacus cultivar Beakdansim tig00110313_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: 1361188
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 6
Found at i:367015 original size:20 final size:20
Alignment explanation
Indices: 366990--367032 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
366980 TATCTACCCG
366990 ACCTGTTTGACCCAACCCAA
1 ACCTGTTTGACCCAACCCAA
**
367010 ACCTGTTTGACCTGACCCAA
1 ACCTGTTTGACCCAACCCAA
367030 ACC
1 ACC
367033 ATTGACCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.40, G:0.12, T:0.21
Consensus pattern (20 bp):
ACCTGTTTGACCCAACCCAA
Found at i:367097 original size:22 final size:22
Alignment explanation
Indices: 367072--367118 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
367062 CGGTCAGACA
*
367072 TTGACTGGTCAAACCATTAACT
1 TTGACCGGTCAAACCATTAACT
** *
367094 TTGACCGGTCTGACCATTGACT
1 TTGACCGGTCAAACCATTAACT
367116 TTG
1 TTG
367119 TCTTTGACCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (22 bp):
TTGACCGGTCAAACCATTAACT
Found at i:369052 original size:22 final size:23
Alignment explanation
Indices: 369005--369066 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
368995 CGATTCCCCT
369005 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
369028 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
369050 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
369067 TCTGCCCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:377595 original size:22 final size:23
Alignment explanation
Indices: 377544--377606 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
377534 CGATTCCCCT
377544 AGGGTGGAATCGGTTCCCCTTCAA
1 AGGG-GGAATCGGTTCCCCTTCAA
377568 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
377590 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
377607 TCTGCTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.43
23 17 0.46
24 4 0.11
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:381455 original size:20 final size:21
Alignment explanation
Indices: 381417--381462 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
381407 AGTTTATTTT
381417 CATTTTTCAATTTTGAAAAAC
1 CATTTTTCAATTTTGAAAAAC
381438 CATTTTT-ATATTTT-AAAAAC
1 CATTTTTCA-ATTTTGAAAAAC
*
381458 AATTT
1 CATTT
381463 CTCATAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (21 bp):
CATTTTTCAATTTTGAAAAAC
Found at i:383350 original size:20 final size:21
Alignment explanation
Indices: 383305--383357 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
383295 GCTTGGAGCG
383305 TGGGGGAATCGGTACCCCTCA
1 TGGGGGAATCGGTACCCCTCA
*
383326 T-GGGGAATGGGTACCCC-C-
1 TGGGGGAATCGGTACCCCTCA
383344 TGGGGGGAATCGGT
1 T-GGGGGAATCGGT
383358 TCCCTCCGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 25 0.89
21 1 0.04
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.19
Consensus pattern (21 bp):
TGGGGGAATCGGTACCCCTCA
Found at i:386041 original size:19 final size:19
Alignment explanation
Indices: 386017--386054 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
386007 CCAGAACTCC
*
386017 AGGGGGTATCGATTCCCCT
1 AGGGGGAATCGATTCCCCT
*
386036 AGGGGGAATCGGTTCCCCT
1 AGGGGGAATCGATTCCCCT
386055 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (19 bp):
AGGGGGAATCGATTCCCCT
Found at i:386083 original size:22 final size:23
Alignment explanation
Indices: 386036--386102 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
386026 CGATTCCCCT
386036 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
386059 AGGGGGAATTGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
386081 AGGGGGTATCGATTCCCTCTTC
1 AGGGGGAATCGGTTCCC-CTTC
386103 CCTATAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:396990 original size:2 final size:2
Alignment explanation
Indices: 396983--397014 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
396973 CTTTCACCTC
396983 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
397015 CAAAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401325 original size:22 final size:22
Alignment explanation
Indices: 401297--401390 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
401287 TTTCATTTCG
401297 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
401319 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
401338 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
401360 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
401382 CATTGCGAT
1 CGTTGCGAT
401391 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.17
20 5 0.09
21 5 0.09
22 38 0.66
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:401331 original size:41 final size:43
Alignment explanation
Indices: 401248--401368 Score: 144
Period size: 41 Copynumber: 2.9 Consensus size: 43
401238 TCCACTATCG
* * * *
401248 CAAATTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTT
1 CAAATTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTC
*
401290 C-ATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CAAATTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
*
401332 CAAATT--CGTTGCGATAGTCTACAGTTGTTGTTGCGAT
1 CAAATTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT
401369 AGTCTACAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
41 51 0.74
42 15 0.22
43 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (43 bp):
CAAATTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
Found at i:402021 original size:5 final size:5
Alignment explanation
Indices: 402007--402052 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
401997 CCGCCGCCGC
402007 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
402053 GGTCGTGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.10
5 37 0.90
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:402064 original size:6 final size:6
Alignment explanation
Indices: 402053--402085 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
402043 TCTCGTCTCG
402053 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
402086 AATACATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:402241 original size:42 final size:41
Alignment explanation
Indices: 402192--402273 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
402182 GCAACGAATT
402192 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
402234 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAA
402274 TTTGCGATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 20 0.56
42 16 0.44
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:403881 original size:20 final size:20
Alignment explanation
Indices: 403856--403952 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
403846 ATTAACGGTT
* * *
403856 GACCGGTTCAGTTCGGGCTA
1 GACCGATTCGGTTCGGGCTG
* * *
403876 GACCGGTTTGGTTCGGGTTG
1 GACCGATTCGGTTCGGGCTG
*
403896 GACCGATTCGGTTCGGGTTG
1 GACCGATTCGGTTCGGGCTG
*
403916 GACCGATTCGGTTCAGGCTG
1 GACCGATTCGGTTCGGGCTG
*
403936 GACCGATTCGGATCGGG
1 GACCGATTCGGTTCGGG
403953 TCTGATCGAG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.12, C:0.22, G:0.39, T:0.27
Consensus pattern (20 bp):
GACCGATTCGGTTCGGGCTG
Found at i:403910 original size:40 final size:40
Alignment explanation
Indices: 403852--403971 Score: 118
Period size: 40 Copynumber: 3.0 Consensus size: 40
403842 AACGATTAAC
* * * * *
403852 GGTT-GACCGGTTCAGTTCGGGCTAGACCGGTTTGGTTCG
1 GGTTGGACCGATTCGGTTCGGGCTAGACCGATTCGGTTCA
* *
403891 GGTTGGACCGATTCGGTTCGGGTTGGACCGATTCGGTTCA
1 GGTTGGACCGATTCGGTTCGGGCTAGACCGATTCGGTTCA
* * * *
403931 GGCTGGACCGATTCGGATCGGGTCT-GATCGAGTCGGTTCA
1 GGTTGGACCGATTCGGTTCGGG-CTAGACCGATTCGGTTCA
403971 G
1 G
403972 ATCGGGTAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
39 4 0.06
40 62 0.93
41 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.38, T:0.28
Consensus pattern (40 bp):
GGTTGGACCGATTCGGTTCGGGCTAGACCGATTCGGTTCA
Found at i:404485 original size:11 final size:12
Alignment explanation
Indices: 404458--404489 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
404448 TTAGTTACTT
404458 TCTAAATTTAGA
1 TCTAAATTTAGA
404470 TCTAAATTTA-A
1 TCTAAATTTAGA
404481 TCTAAATTT
1 TCTAAATTT
404490 CAATTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (12 bp):
TCTAAATTTAGA
Found at i:407917 original size:18 final size:19
Alignment explanation
Indices: 407872--407917 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
407862 AACCGACTCG
* *
407872 TTGACTTTGACTCGATCCG
1 TTGACTTTGACTCGACCCA
*
407891 TTAACTTTGAC-CGACCCA
1 TTGACTTTGACTCGACCCA
407909 TTGACTTTG
1 TTGACTTTG
407918 GCCATAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGACTTTGACTCGACCCA
Found at i:415901 original size:23 final size:23
Alignment explanation
Indices: 415839--415916 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 23
415829 TGATCTTATA
* *
415839 ATATCATATGATATGTTTTGTATT
1 ATATCAT-TGATATGTTTTATTTT
* *
415863 -T-TCACT-ATATGATTTATTTT
1 ATATCATTGATATGTTTTATTTT
*
415883 ATATCATTGATATGTTTTACTTT
1 ATATCATTGATATGTTTTATTTT
* *
415906 GTATTATTGAT
1 ATATCATTGAT
415917 TACGTCTCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 11 0.26
21 2 0.05
22 7 0.17
23 22 0.52
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (23 bp):
ATATCATTGATATGTTTTATTTT
Found at i:418682 original size:31 final size:31
Alignment explanation
Indices: 418643--418753 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
418633 TTAGGTCCAT
418643 AAGGAATTACCAGTCGGTGCTGAACCTATAC
1 AAGGAATTACCAGTCGGTGCTGAACCTATAC
* ** * * * *
418674 AAGAAATTATTAG-CAGCGACTGAACCTGCCAGAG
1 AAGGAATTACCAGTCGGTG-CTGAACCT---ATAC
*
418708 ATAGGAATTACCAGTCGGTGTTGAACCTATAC
1 A-AGGAATTACCAGTCGGTGCTGAACCTATAC
418740 AAGGAATTACCAGT
1 AAGGAATTACCAGT
418754 AGCAACTAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
30 3 0.05
31 31 0.53
32 3 0.05
34 3 0.05
35 16 0.27
36 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (31 bp):
AAGGAATTACCAGTCGGTGCTGAACCTATAC
Found at i:418721 original size:66 final size:66
Alignment explanation
Indices: 418644--418773 Score: 197
Period size: 66 Copynumber: 2.0 Consensus size: 66
418634 TAGGTCCATA
** * *
418644 AGGAATTACCAGTCGGTGCTGAACCTATACAAGAAATTATTAGCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGGTGCTGAACCTATACAAGAAATTACCAGCAGCAACTAAACCTGCCAGAGA
418709 T
66 T
* * *
418710 AGGAATTACCAGTCGGTGTTGAACCTATACAAGGAATTACCAGTAGCAACTAAACCTGCCAGAG
1 AGGAATTACCAGTCGGTGCTGAACCTATACAAGAAATTACCAGCAGCAACTAAACCTGCCAGAG
418774 TCTTCATACT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (66 bp):
AGGAATTACCAGTCGGTGCTGAACCTATACAAGAAATTACCAGCAGCAACTAAACCTGCCAGAGA
T
Found at i:420900 original size:22 final size:22
Alignment explanation
Indices: 420854--420907 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
420844 TCAATAGTCA
* * *
420854 GACCAATCAAAGTCAACTAGCT
1 GACCGATCAAAGTCAACGAGAT
*
420876 GACCGATCAAAGTCAACGATAT
1 GACCGATCAAAGTCAACGAGAT
*
420898 GACTGATCAA
1 GACCGATCAA
420908 TGGTTCGGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
GACCGATCAAAGTCAACGAGAT
Found at i:420903 original size:26 final size:22
Alignment explanation
Indices: 420838--420892 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
420828 CTTTTTTCGG
*
420838 TCAAAGTCAA-TAGTCAGACCAA
1 TCAAAGTCAACTAG-CTGACCAA
*
420860 TCAAAGTCAACTAGCTGACCGA
1 TCAAAGTCAACTAGCTGACCAA
420882 TCAAAGTCAAC
1 TCAAAGTCAAC
420893 GATATGACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (22 bp):
TCAAAGTCAACTAGCTGACCAA
Found at i:420937 original size:20 final size:20
Alignment explanation
Indices: 420909--420947 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
420899 ACTGATCAAT
420909 GGTTCGGGTCAAGTTAAACA
1 GGTTCGGGTCAAGTTAAACA
* **
420929 GGTTTGGGTTGAGTTAAAC
1 GGTTCGGGTCAAGTTAAAC
420948 GAATCGGGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (20 bp):
GGTTCGGGTCAAGTTAAACA
Found at i:422450 original size:17 final size:18
Alignment explanation
Indices: 422428--422467 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
422418 AACTTTTTGT
422428 TAAAAC-ACTTAAAATCA
1 TAAAACAACTTAAAATCA
* *
422445 TAAAACAATTTAAAATCC
1 TAAAACAACTTAAAATCA
422463 TAAAA
1 TAAAA
422468 AGGTGAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAACAACTTAAAATCA
Found at i:423208 original size:66 final size:66
Alignment explanation
Indices: 423088--423217 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
423078 TAGGTCCATA
* * * * * *
423088 AGGAATTAACAGTCGGTGCTGAACCTATACAATGAATTACTAGTAGTGACTGAACCTGCCAGAGA
1 AGGAATTAACAATCAGTGCTGAACATATACAATGAATTACCAGCAGCGACTGAACCTGCCAGAGA
423153 T
66 T
* * *
423154 AGGAATTACCAATCAGTGTTGAACATATACAATGAATTACCAGCAGCGATTGAACCTGCCAGAG
1 AGGAATTAACAATCAGTGCTGAACATATACAATGAATTACCAGCAGCGACTGAACCTGCCAGAG
423218 TCTTATACCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (66 bp):
AGGAATTAACAATCAGTGCTGAACATATACAATGAATTACCAGCAGCGACTGAACCTGCCAGAGA
T
Found at i:444126 original size:43 final size:43
Alignment explanation
Indices: 444061--444147 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
444051 AAAGATTAAG
* *
444061 ATGGGGATATAGCACTCCATAGAGGATCCCAATCATAATCAGA
1 ATGGGGATATAGCACTCCATAGAGGATCCCAAGCAGAATCAGA
* * *
444104 ATGGGGATATCGCCCTCTATAGAGGATCCCAAGCAGAATCAGA
1 ATGGGGATATAGCACTCCATAGAGGATCCCAAGCAGAATCAGA
444147 A
1 A
444148 ATCAGAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (43 bp):
ATGGGGATATAGCACTCCATAGAGGATCCCAAGCAGAATCAGA
Found at i:445387 original size:46 final size:46
Alignment explanation
Indices: 445320--445506 Score: 284
Period size: 46 Copynumber: 4.0 Consensus size: 46
445310 GGGAAGAAAC
445320 ATTGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
1 ATTGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
*
445366 ATTGACGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
1 ATTGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
* *
445412 ATGGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGA
1 ATTGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
** ** * *
445458 ACAGATGCATTAAGTTAGGAAAGTATGCCATAACTAAAAATGCATGA
1 ATTGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAATGCATGA
445505 AT
1 AT
445507 GAATGTATTA
Statistics
Matches: 128, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
46 116 0.91
47 12 0.09
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATTGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA
Found at i:445438 original size:20 final size:20
Alignment explanation
Indices: 445322--445439 Score: 58
Period size: 20 Copynumber: 5.3 Consensus size: 20
445312 GAAGAAACAT
445322 TGATGCATTAAGGCATGAAA
1 TGATGCATTAAGGCATGAAA
* * *
445342 GGATGCCATAACTAAAATGCATGAAT
1 TGATG-CAT---T--AAGGCATGAAA
*
445368 TGACGCATTAAGGCATGAAA
1 TGATGCATTAAGGCATGAAA
* *
445388 GGATGCCATAACTAAAATGCATG-AA
1 TGATG-CAT---T--AAGGCATGAAA
445413 TGGATGCATTAAGGCATGAAA
1 T-GATGCATTAAGGCATGAAA
445434 TGATGC
1 TGATGC
445440 CATAACTAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
20 28 0.39
21 9 0.12
22 2 0.03
24 2 0.03
25 8 0.11
26 23 0.32
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (20 bp):
TGATGCATTAAGGCATGAAA
Found at i:445465 original size:26 final size:26
Alignment explanation
Indices: 445334--445458 Score: 103
Period size: 26 Copynumber: 5.3 Consensus size: 26
445324 ATGCATTAAG
445334 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
** * *
445360 GCATGAATTGACG-CAT---T--AAG
1 GCATGAAAGGATGCCATAACTAAAAT
445380 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
* *
445406 GCATGAATGGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAACTAAAAT
*
445426 GCATGAAATGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
445452 GCATGAA
1 GCATGAA
445459 CAGATGCATT
Statistics
Matches: 74, Mismatches: 13, Indels: 24
0.67 0.12 0.22
Matches are distributed among these distances:
20 25 0.34
21 6 0.08
22 2 0.03
24 2 0.03
25 6 0.08
26 33 0.45
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAACTAAAAT
Found at i:445480 original size:92 final size:93
Alignment explanation
Indices: 445323--445527 Score: 295
Period size: 92 Copynumber: 2.2 Consensus size: 93
445313 AAGAAACATT
** *
445323 GATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAATTGACGCATTAAGGCATGAAA
1 GATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACAGACGCATTAAGGCAGGAAA
445388 GGATGCCATAACT-AAAATGCATGAATG
66 GGATGCCATAACTAAAAATGCATGAATG
* * **
445415 GATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAACAGATGCATTAAGTTAGGAAA
1 GATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACAGACGCATTAAGGCAGGAAA
*
445480 GTATGCCATAACTAAAAATGCATGAATG
66 GGATGCCATAACTAAAAATGCATGAATG
* * * *
445508 AATGTATTAAAGCATAAAAG
1 GATGCATTAAGGCATGAAAG
445528 AGGCTATAAC
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
92 70 0.71
93 29 0.29
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (93 bp):
GATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACAGACGCATTAAGGCAGGAAA
GGATGCCATAACTAAAAATGCATGAATG
Found at i:445537 original size:46 final size:46
Alignment explanation
Indices: 445324--445543 Score: 225
Period size: 46 Copynumber: 4.8 Consensus size: 46
445314 AGAAACATTG
* *
445324 ATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAATTG-
1 ATGCATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAA-TGA
* * * *
445370 ACGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAATGG
1 ATGCATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAATGA
* * *
445416 ATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAA-CA
1 ATGCATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAATGA
* *
445461 GATGCATT-AAG-TTAGGAAAGTATGCCATAACTAAAAATGCATGAATGA
1 -ATGCATTAAAGCAT-GAAAAG-ATGCCATAACT-AAAATGCATGAATGA
* * * *
445509 ATGTATTAAAGCAT-AAAAGAGGCTATAACTGAAAT
1 ATGCATTAAAGCATGAAAAGATGCCATAACTAAAAT
445544 TAATTAATTA
Statistics
Matches: 150, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.01
45 12 0.08
46 110 0.73
47 22 0.15
48 4 0.03
49 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
ATGCATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAATGA
Found at i:455420 original size:8 final size:8
Alignment explanation
Indices: 455407--455447 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
455397 GGTCGACGCT
455407 GGTCAACG
1 GGTCAACG
455415 GGTCAACG
1 GGTCAACG
455423 GGTCAACG
1 GGTCAACG
455431 GGT---CG
1 GGTCAACG
455436 GGTCAACG
1 GGTCAACG
455444 GGTC
1 GGTC
455448 GGGTAAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
8 25 0.83
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:455439 original size:13 final size:13
Alignment explanation
Indices: 455407--455465 Score: 82
Period size: 13 Copynumber: 4.3 Consensus size: 13
455397 GGTCGACGCT
455407 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
455423 GGTCAACGGGTCG
1 GGTCAACGGGTCG
455436 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
455449 GGTAAACGGGTCG
1 GGTCAACGGGTCG
455462 GGTC
1 GGTC
455466 GGGTCGGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
13 30 0.73
16 11 0.27
ACGTcount: A:0.19, C:0.22, G:0.44, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:457752 original size:46 final size:45
Alignment explanation
Indices: 457615--457784 Score: 252
Period size: 45 Copynumber: 3.8 Consensus size: 45
457605 GGTAATCATG
* *
457615 AAAATAAGCTTATGAGCTTATGGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
457659 AAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* ** *
457704 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACGTTAGT
1 AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGT
*
457750 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAA
457785 ATATTTTGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 24 0.21
45 50 0.44
46 40 0.35
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:457768 original size:91 final size:89
Alignment explanation
Indices: 457615--457784 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 89
457605 GGTAATCATG
* * *
457615 AAAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTACATTAGTAAAATAAGCTTACGAGCTTAT
457680 GGAACAAATGGTAAGTATATTGGT
66 GGAACAAATGGTAAGTATATTGGT
* * *
457704 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACGTTAGTAAAATAAGCTTACGAGCTT
1 AAAATAAGCTTACGAGCTTAT-GGAAT-AATGGCAAGTACATTAGTAAAATAAGCTTACGAGCTT
* *
457769 ATGGGATAAATGGTAA
64 ATGGAACAAATGGTAA
457785 ATATTTTGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 20 0.28
90 4 0.06
91 47 0.66
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.29
Consensus pattern (89 bp):
AAAATAAGCTTACGAGCTTATGGAATAATGGCAAGTACATTAGTAAAATAAGCTTACGAGCTTAT
GGAACAAATGGTAAGTATATTGGT
Found at i:462668 original size:29 final size:29
Alignment explanation
Indices: 462626--462700 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
462616 ATTACGATAA
*
462626 TCATAAGTCAAATACATTCTAGAGTATTT
1 TCATAAGTCAAATACATTCCAGAGTATTT
462655 TCATAAGTCAAATACATTCCAGAGTATTT
1 TCATAAGTCAAATACATTCCAGAGTATTT
*
462684 TCATAAGTCCAATACAT
1 TCATAAGTCAAATACAT
462701 GCCATCTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (29 bp):
TCATAAGTCAAATACATTCCAGAGTATTT
Found at i:463368 original size:140 final size:140
Alignment explanation
Indices: 463109--463368 Score: 355
Period size: 140 Copynumber: 1.9 Consensus size: 140
463099 TCAAAATGGA
* * * * *
463109 AATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGCCGAAAGTACATATAGTATTGA
1 AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACATAGTACTAA
** * * *
463174 TACAAAAATGCACCGTTATGCATTTAACAAAATCGATCGATAACTTTTTCATACATAATTGTATA
66 TACAAAAATGCACCAATATGCATTTAACAAAATAGATCGATAACATTATCATACATAATTGTATA
463239 TCGAAGTGGT
131 TCGAAGTGGT
* *
463249 AATTCACAAACTCATTATGAATACCATGGTTGCATATC-TAGTGCCAAAAGTACACATAGTACTA
1 AATTCACAAACTCATTATGAATACCATGGATGCACA-CATAGTGCCAAAAGTACACATAGTACTA
*
463313 ATACAAAAATGCACCAATATGCA-TTACACAAAATAGATTGATAACCATTAT-ATACA
65 ATACAAAAATGCACCAATATGCATTTA-ACAAAATAGATCGATAA-CATTATCATACA
463369 ATTTATGTCG
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
139 3 0.03
140 96 0.92
141 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (140 bp):
AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACATAGTACTAA
TACAAAAATGCACCAATATGCATTTAACAAAATAGATCGATAACATTATCATACATAATTGTATA
TCGAAGTGGT
Found at i:473465 original size:26 final size:28
Alignment explanation
Indices: 473408--473467 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
473398 TACAAGTCTC
**
473408 CTTCATTGATTTTCAAGCTTCTTTCATT
1 CTTCATTGATTTTCAAGCTTCTTTCAAG
473436 CTTC-TTGA-TTTCAAGTCTTC-TTCAAG
1 CTTCATTGATTTTCAAG-CTTCTTTCAAG
473462 CTTCAT
1 CTTCAT
473468 CATCTCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 15 0.54
27 9 0.32
28 4 0.14
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.50
Consensus pattern (28 bp):
CTTCATTGATTTTCAAGCTTCTTTCAAG
Found at i:475546 original size:15 final size:15
Alignment explanation
Indices: 475526--475555 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
475516 TAGAGCTTAA
475526 ATGGTTGATCGATAT
1 ATGGTTGATCGATAT
475541 ATGGTTGATCGATAT
1 ATGGTTGATCGATAT
475556 GGCACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
ATGGTTGATCGATAT
Found at i:479930 original size:22 final size:22
Alignment explanation
Indices: 479860--479930 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
479850 GATCAGTCTG
* *
479860 TTGATCGGTCAGACCTTTGACT
1 TTGACCGGTCAGACCATTGACT
* *
479882 TTGACTGGGT-AGACCGTTGACT
1 TTGAC-CGGTCAGACCATTGACT
*
479904 TTGACCGGTCTGACCATTGACT
1 TTGACCGGTCAGACCATTGACT
479926 TTGAC
1 TTGAC
479931 TTTGACCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.07
22 35 0.85
23 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (22 bp):
TTGACCGGTCAGACCATTGACT
Found at i:482664 original size:19 final size:19
Alignment explanation
Indices: 482583--482662 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 19
482573 TGATGACCAC
* *
482583 TGATTTCTGTTATGAACTT
1 TGATATCTGTTATGATCTT
*
482602 TGATATCTGTTATGATCTC
1 TGATATCTGTTATGATCTT
* * *
482621 TGATATTTGATCTGATCTT
1 TGATATCTGTTATGATCTT
* *
482640 TGATCTCTGTTATGATTTT
1 TGATATCTGTTATGATCTT
482659 TGAT
1 TGAT
482663 CTGTATTTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.53
Consensus pattern (19 bp):
TGATATCTGTTATGATCTT
Found at i:486751 original size:22 final size:22
Alignment explanation
Indices: 486726--486791 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
486716 AAAAGATAGC
*
486726 TTCCTTACGAGACAAAGTTGTA
1 TTCCTTAAGAGACAAAGTTGTA
486748 TTCCTTAAGAGACAAAGTTGTA
1 TTCCTTAAGAGACAAAGTTGTA
* *
486770 TTCCTTAAGAGGCAAGGTTGTA
1 TTCCTTAAGAGACAAAGTTGTA
486792 GTATCTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (22 bp):
TTCCTTAAGAGACAAAGTTGTA
Found at i:490199 original size:25 final size:25
Alignment explanation
Indices: 490165--490214 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
490155 TAATCCGAAC
490165 TGAACCGATCCAACCTAAATTGAAT
1 TGAACCGATCCAACCTAAATTGAAT
* * *
490190 TGAATCGATCCAACTTAACTTGAAT
1 TGAACCGATCCAACCTAAATTGAAT
490215 CAAACTGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (25 bp):
TGAACCGATCCAACCTAAATTGAAT
Found at i:491735 original size:3 final size:3
Alignment explanation
Indices: 491727--491769 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
491717 TTATCATAAT
491727 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
491770 AACCCTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:499030 original size:36 final size:36
Alignment explanation
Indices: 498987--499070 Score: 134
Period size: 36 Copynumber: 2.3 Consensus size: 36
498977 TATAAATTCG
* *
498987 ACTCGACTCGAAAACTCGCG-AGCTTAAAATTTTTAA
1 ACTCGACTCGAAAACTCG-GAAGCCTAAAATTTTCAA
499023 ACTCGACTCGAAAACTCGGAAGCCTAAAATTTTCAA
1 ACTCGACTCGAAAACTCGGAAGCCTAAAATTTTCAA
499059 ACTCGACTCGAA
1 ACTCGACTCGAA
499071 CTCGAAAGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (36 bp):
ACTCGACTCGAAAACTCGGAAGCCTAAAATTTTCAA
Found at i:499092 original size:31 final size:33
Alignment explanation
Indices: 498987--499108 Score: 113
Period size: 36 Copynumber: 3.6 Consensus size: 33
498977 TATAAATTCG
** *
498987 ACTCGACTCGAAAACTCGCGAGCTTAAAATTTTTAA
1 ACTCGACTCG--AACTCGAAAGCATAAAA-TTTTAA
* *
499023 ACTCGACTCGAAAACTCGGAAGCCTAAAATTTTCAA
1 ACTCGACTCG--AACTCGAAAGCATAAAATTTT-AA
*
499059 ACTCGACTCGAACTCGAAAG-ATAATA-TTTAA
1 ACTCGACTCGAACTCGAAAGCATAAAATTTTAA
*
499090 ACTCGATTCGAACTCGAAA
1 ACTCGACTCGAACTCGAAA
499109 AAACTCGAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
31 20 0.26
32 3 0.04
33 4 0.05
34 9 0.12
35 4 0.05
36 38 0.49
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (33 bp):
ACTCGACTCGAACTCGAAAGCATAAAATTTTAA
Found at i:501352 original size:7 final size:7
Alignment explanation
Indices: 501313--501353 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
501303 TTTTAAGATA
*
501313 TTTAAGG
1 TTTAGGG
*
501320 TTTAGTG
1 TTTAGGG
501327 TTTAGGG
1 TTTAGGG
*
501334 GTTAGGG
1 TTTAGGG
501341 TTTAGGG
1 TTTAGGG
501348 TTTAGG
1 TTTAGG
501354 ATTTTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:508448 original size:113 final size:113
Alignment explanation
Indices: 508249--508469 Score: 397
Period size: 113 Copynumber: 2.0 Consensus size: 113
508239 AATGAACACC
508249 ATAAAAATATATTCTTGAATTAATTTCATATTCAAATCTCAAATAAATAAGCAAAAATGCTAAAA
1 ATAAAAATATATTCTTGAATTAATTTCATATTCAAATCTCAAATAAATAAGCAAAAATGCTAAAA
* *
508314 ATACTAAGCATTTTCGAATTAACAGGTTTGATTAGGGACTTTCAGGTT
66 ATACTAAGCATTTTCGAATTAACAGGCTCGATTAGGGACTTTCAGGTT
*
508362 ATAAAAATGTATTCTTGAATTAATTTCATATTCAAATCTCAAATAAATAAGCAAAAATGCTAAAA
1 ATAAAAATATATTCTTGAATTAATTTCATATTCAAATCTCAAATAAATAAGCAAAAATGCTAAAA
* *
508427 ATACTAAGCATTTTCGGATTAACATGCTCGATTAGGGACTTTC
66 ATACTAAGCATTTTCGAATTAACAGGCTCGATTAGGGACTTTC
508470 GGGTCAGAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (113 bp):
ATAAAAATATATTCTTGAATTAATTTCATATTCAAATCTCAAATAAATAAGCAAAAATGCTAAAA
ATACTAAGCATTTTCGAATTAACAGGCTCGATTAGGGACTTTCAGGTT
Found at i:509107 original size:36 final size:36
Alignment explanation
Indices: 509060--509132 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
509050 TAGGATATGA
509060 ATGTTTATTGATGTTTACTAGTAGATTTGACTTGTC
1 ATGTTTATTGATGTTTACTAGTAGATTTGACTTGTC
*
509096 ATGTTTATTGATGTTTACTAGTATATTTGACTTGTC
1 ATGTTTATTGATGTTTACTAGTAGATTTGACTTGTC
509132 A
1 A
509133 ATGAAGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (36 bp):
ATGTTTATTGATGTTTACTAGTAGATTTGACTTGTC
Found at i:509395 original size:20 final size:20
Alignment explanation
Indices: 509370--509424 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
509360 CTGGGTAATG
*
509370 GTATCGGTACTGATAGAACA
1 GTATCGATACTGATAGAACA
*
509390 GTATCGATACTGATAGAATA
1 GTATCGATACTGATAGAACA
509410 GTATCGATACT-ATAG
1 GTATCGATACTGATAG
509425 GCTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACTGATAGAACA
Found at i:510241 original size:18 final size:18
Alignment explanation
Indices: 510218--510260 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
510208 TTATGAATGT
510218 TGGCATTGGTAATGTGTG
1 TGGCATTGGTAATGTGTG
510236 TGGCATTGGTAATGTGTG
1 TGGCATTGGTAATGTGTG
*
510254 TGCCATT
1 TGGCATT
510261 TACGTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (18 bp):
TGGCATTGGTAATGTGTG
Found at i:510554 original size:81 final size:80
Alignment explanation
Indices: 510386--510640 Score: 359
Period size: 81 Copynumber: 3.2 Consensus size: 80
510376 CTATTCCAAA
*
510386 AGTAAAATACTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAA
1 AGTAAAAGACTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAA
510451 GGTTAAATACCTTTG
66 GGTTAAATACCTTTG
* * *
510466 AGTAAAAGACTAATGGCCTAGTTGTGCATTTGACAAAAATGTTTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGACTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAA
510531 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * * * * *
510547 AGTAAAAGATTAATAGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCAAGTTAAATGAA
1 AGTAAAAGACTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGC-AGTTAGATGAA
* * *
510612 ATGCTAAATGCCTTTG
65 AGGTTAAATACCTTTG
510628 -GATAAAAGACTAA
1 AG-TAAAAGACTAA
510641 AGGAATTAAA
Statistics
Matches: 155, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
80 50 0.32
81 105 0.68
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (80 bp):
AGTAAAAGACTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAA
GGTTAAATACCTTTG
Found at i:513249 original size:2 final size:2
Alignment explanation
Indices: 513242--513269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
513232 GATTTCAGAA
513242 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
513270 TCTGGCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515937 original size:81 final size:81
Alignment explanation
Indices: 515802--516219 Score: 552
Period size: 81 Copynumber: 5.2 Consensus size: 81
515792 CTATTCTAAA
* * *
515802 AGTAAAATACTAATGGTCTAG-TAGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGACTAATGGCCTAGCT-GTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
515866 AATGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * *
515883 AGTAAAAGACTAATGACCTAGCTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGACTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
515948 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
** * *
515964 AGTAAAAGTTTAATGGCCTAGCTGTGCATTTAATAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGACTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
516029 AGGTTAAATACCTTAG
66 AGGTTAAATACCTTTG
*
516045 -GATAAAAGACTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGA
1 AG-TAAAAGACTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
516109 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * * * * * * * ** * *
516126 AGTAAAATATTAATAGCCTAGATGTGTATTTGGCATAAAGGTATCAAGCATGCAAGTTAAATGAA
1 AGTAAAAGACTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
516191 AGGATAAATGCCTTTG
66 AGGTTAAATACCTTTG
*
516207 GGTAAAAGACTAA
1 AGTAAAAGACTAA
516220 AGGAATTAAA
Statistics
Matches: 297, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.00
81 294 0.99
82 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (81 bp):
AGTAAAAGACTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:522984 original size:30 final size:30
Alignment explanation
Indices: 522924--522994 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
522914 AAATTTAGAT
* * *
522924 CTAAATTTAATCAAAATTTTACTTTGGTCC
1 CTAAATTTAATCAAAATTTCAATTTAGTCC
* *
522954 CTAAATTTAGTTAAAATTTCAATTTAGTCC
1 CTAAATTTAATCAAAATTTCAATTTAGTCC
* *
522984 CCAAAATTAAT
1 CTAAATTTAAT
522995 TTTAAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (30 bp):
CTAAATTTAATCAAAATTTCAATTTAGTCC
Found at i:525363 original size:19 final size:19
Alignment explanation
Indices: 525339--525377 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
525329 TGAGTCAACC
* *
525339 TGACCTGACCCGTTGGCTT
1 TGACCTAACCCGTTGACTT
*
525358 TGACCTAACCTGTTGACTT
1 TGACCTAACCCGTTGACTT
525377 T
1 T
525378 AACACGACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (19 bp):
TGACCTAACCCGTTGACTT
Found at i:526065 original size:20 final size:20
Alignment explanation
Indices: 526040--526083 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
526030 TGGCTATAGC
526040 TGACCGTTAACATTAACCGT
1 TGACCGTTAACATTAACCGT
526060 TGACCGTTAACATTAACCGT
1 TGACCGTTAACATTAACCGT
526080 TGAC
1 TGAC
526084 TTTGACCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (20 bp):
TGACCGTTAACATTAACCGT
Found at i:530347 original size:43 final size:44
Alignment explanation
Indices: 530225--530350 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 44
530215 TATAAAATCT
530225 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAT-TCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
530270 TTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATT-CATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
530317 CTTGCCA-TTATTCATAAGCTTGTAAGCTTATTTT
1 CTTACCATTTATTCATAAGCTCGTAAGCTTATTTT
530351 CATACTTACC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
43 20 0.29
44 3 0.04
45 9 0.13
46 3 0.04
47 35 0.50
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (44 bp):
CTTACCATTTATTCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:531502 original size:283 final size:283
Alignment explanation
Indices: 530995--531569 Score: 1132
Period size: 283 Copynumber: 2.0 Consensus size: 283
530985 GATCTGTATA
530995 AATCACAAATTTATAACAATACATATGTTAGTATTGTACTAACATAAACATATCCCAAAATAATT
1 AATCACAAATTTATAACAATACATATGTTAGTATTGTACTAACATAAACATATCCCAAAATAATT
*
531060 CCATAGTATATTTGATACTCATTATCTATCAGAATACTTAATACTTAATAATTTCCTTTTAACAT
66 CCATAGTATATTTGATACTCATTATCTATCAAAATACTTAATACTTAATAATTTCCTTTTAACAT
*
531125 TGGAACCAACTTTTCCAATTTACACAAAATGGTCCTTCACTATTTTATCACTTAGAATTTCAATA
131 TGGAACCAACTTTTCCAATTTACACAAAATGGTCCTTCACCATTTTATCACTTAGAATTTCAATA
531190 CAAAAATTCCAGTATTGAAATTATTATCAACCAAGTACACAAAGGTATAATTACAATAACACTCC
196 CAAAAATTCCAGTATTGAAATTATTATCAACCAAGTACACAAAGGTATAATTACAATAACACTCC
531255 CATCAATTCAAAATTTGTATTAC
261 CATCAATTCAAAATTTGTATTAC
531278 AATCACAAATTTATAACAATACATATGTTAGTATTGTACTAACATAAACATATCCCAAAATAATT
1 AATCACAAATTTATAACAATACATATGTTAGTATTGTACTAACATAAACATATCCCAAAATAATT
531343 CCATAGTATATTTGATACTCATTATCTATCAAAATACTTAATACTTAATAATTTCCTTTTAACAT
66 CCATAGTATATTTGATACTCATTATCTATCAAAATACTTAATACTTAATAATTTCCTTTTAACAT
531408 TGGAACCAACTTTTCCAATTTACACAAAATGGTCCTTCACCATTTTATCACTTAGAATTTCAATA
131 TGGAACCAACTTTTCCAATTTACACAAAATGGTCCTTCACCATTTTATCACTTAGAATTTCAATA
531473 CAAAAATTCCAGTATTGAAATTATTATCAACCAAGTACACAAAGGTATAATTACAATAACACTCC
196 CAAAAATTCCAGTATTGAAATTATTATCAACCAAGTACACAAAGGTATAATTACAATAACACTCC
531538 CATCAATTCAAAATTTGTATTAC
261 CATCAATTCAAAATTTGTATTAC
531561 AATCACAAA
1 AATCACAAA
531570 ACTTTCTAAA
Statistics
Matches: 290, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
283 290 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (283 bp):
AATCACAAATTTATAACAATACATATGTTAGTATTGTACTAACATAAACATATCCCAAAATAATT
CCATAGTATATTTGATACTCATTATCTATCAAAATACTTAATACTTAATAATTTCCTTTTAACAT
TGGAACCAACTTTTCCAATTTACACAAAATGGTCCTTCACCATTTTATCACTTAGAATTTCAATA
CAAAAATTCCAGTATTGAAATTATTATCAACCAAGTACACAAAGGTATAATTACAATAACACTCC
CATCAATTCAAAATTTGTATTAC
Found at i:540570 original size:19 final size:19
Alignment explanation
Indices: 540546--540643 Score: 135
Period size: 19 Copynumber: 5.2 Consensus size: 19
540536 AATTTAACTC
*
540546 GACCCGACCCGTTAACTTT
1 GACCCGACCCGTTGACTTT
*
540565 GACCCGACCTGTTGACTTT
1 GACCCGACCCGTTGACTTT
* *
540584 GACCTGATCCGTTGACTTT
1 GACCCGACCCGTTGACTTT
* *
540603 GACTCGACACGTTGACTTT
1 GACCCGACCCGTTGACTTT
540622 GA-CCGACCCGTTGACTTT
1 GACCCGACCCGTTGACTTT
540640 GACC
1 GACC
540644 ATAGTTGACG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
18 16 0.24
19 51 0.76
ACGTcount: A:0.18, C:0.32, G:0.20, T:0.30
Consensus pattern (19 bp):
GACCCGACCCGTTGACTTT
Found at i:542885 original size:25 final size:23
Alignment explanation
Indices: 542807--542915 Score: 166
Period size: 23 Copynumber: 4.7 Consensus size: 23
542797 CTTAATTGTT
542807 CCAAAG-GACCACATAGGTTTGCA
1 CCAAAGTG-CCACATAGGTTTGCA
542830 CCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTGCCACATAGGTTTGCA
542853 CCAAAGTGCCACATAGGTTTGCACA
1 CCAAAGTGCCACATAGGTTTG--CA
542878 CCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTGCCACATAGGTTTGCA
* *
542901 CCGAAGTACCACATA
1 CCAAAGTGCCACATA
542916 TTTATCCCGA
Statistics
Matches: 81, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
23 57 0.70
24 1 0.01
25 23 0.28
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (23 bp):
CCAAAGTGCCACATAGGTTTGCA
Found at i:542897 original size:48 final size:46
Alignment explanation
Indices: 542807--542915 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 46
542797 CTTAATTGTT
542807 CCAAAG-GACCACATAGGTTTGCACCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTG-CCACATAGGTTTGCACCAAAGTGCCACATAGGTTTGCA
542853 CCAAAGTGCCACATAGGTTTGCACACCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTGCCACATAGGTTTG--CACCAAAGTGCCACATAGGTTTGCA
* *
542901 CCGAAGTACCACATA
1 CCAAAGTGCCACATA
542916 TTTATCCCGA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
46 19 0.33
47 1 0.02
48 38 0.66
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (46 bp):
CCAAAGTGCCACATAGGTTTGCACCAAAGTGCCACATAGGTTTGCA
Found at i:543589 original size:20 final size:20
Alignment explanation
Indices: 543564--543615 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
543554 ATGATTTAAG
*
543564 GGTATCGATACCATCCTT-C
1 GGTATCGATACCACCCTTAC
543583 AGGTATCGATACCACCCTTAC
1 -GGTATCGATACCACCCTTAC
543604 GGTATCGATACC
1 GGTATCGATACC
543616 TCTATCAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCACCCTTAC
Found at i:544219 original size:19 final size:20
Alignment explanation
Indices: 544195--544245 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
544185 CAGCCAAGAG
*
544195 CATGTATTTTCGTT-AAAGT
1 CATGTATTTTCATTAAAAGT
*
544214 CATGTATTTTCATTAAAATT
1 CATGTATTTTCATTAAAAGT
544234 CATGTATTTTCA
1 CATGTATTTTCA
544246 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAGT
Found at i:548162 original size:20 final size:20
Alignment explanation
Indices: 548119--548170 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
548109 CGGCCAAGAG
* * *
548119 CATGTATTTTC-GTTAAAGT
1 CATGTATTTTCAATAAAAAT
548138 CATGTATTTTCAATAAAAAT
1 CATGTATTTTCAATAAAAAT
548158 CATGTATTTTCAA
1 CATGTATTTTCAA
548171 AGGGATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCAATAAAAAT
Found at i:548869 original size:20 final size:20
Alignment explanation
Indices: 548828--548879 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
548818 CGGCCAAGAG
* *
548828 CATGTATTTTC-ATTAAAGT
1 CATGTATTTTCAATAAAAAT
*
548847 CATGTAATTTCAATAAAAAT
1 CATGTATTTTCAATAAAAAT
548867 CATGTATTTTCAA
1 CATGTATTTTCAA
548880 AGGGATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCAATAAAAAT
Found at i:549283 original size:709 final size:709
Alignment explanation
Indices: 547926--549349 Score: 2672
Period size: 709 Copynumber: 2.0 Consensus size: 709
547916 GACCCATGTG
* * * *
547926 CATTCAAGTAGGTTGCCATGTGCATCATTCAAGCATGTGCACTCTATGTGACATCAAATAGGCGT
1 CATTCAAGTAGGCTACCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGC
*
547991 CAAAACACCAAGGGATGCTTCCTATTCGGACAAAGACTTATTCCTCTTCATTTTTGGCGCCAAGT
66 CAAAACACCAAGGGATGCTTCCTATTCGGACAAAGACTTATTCCTCTTCATTTTCGGCGCCAAGT
548056 AACTTCCAAAAACATTCAAAACACCCTTAGGGCCGAACCAACACCTTACCATTCGGCCAAGAGCA
131 AACTTCCAAAAACATTCAAAACACCCTTAGGGCCGAACCAACACCTTACCATTCGGCCAAGAGCA
* *
548121 TGTATTTTCGTTAAAGTCATGTATTTTCAATAAAAATCATGTATTTTCAAAGGGATTTCATCCTT
196 TGTATTTTCATTAAAGTCATGTAATTTCAATAAAAATCATGTATTTTCAAAGGGATTTCATCCTT
548186 GGCCGAACCATCATGTATCTATGCAGCCTAAACCCTTTGAAAACTATAAATAGGCTATCACAATT
261 GGCCGAACCATCATGTATCTATGCAGCCTAAACCCTTTGAAAACTATAAATAGGCTATCACAATT
548251 CATTTGTAATGAGACCTTTTGATTAATTAAAGTGAGATTATTCTATTTCCTTAGTCCTGGTGACT
326 CATTTGTAATGAGACCTTTTGATTAATTAAAGTGAGATTATTCTATTTCCTTAGTCCTGGTGACT
548316 TTTATCGACTTATCAAGTATTTTAATACTTGTGGCGTCAACCCCTTCCCCTTGATACTTCTGGTT
391 TTTATCGACTTATCAAGTATTTTAATACTTGTGGCGTCAACCCCTTCCCCTTGATACTTCTGGTT
*
548381 CCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAATACCACCCCTTAGAGAAGCAATAGAAAGTC
456 CCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAATACCACCCCTTAAAGAAGCAATAGAAAGTC
*
548446 TGGGTCTTTCCTCTCTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATATTATCCTCACAAC
521 TGGGTCTTTCCTCTCTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATACTATCCTCACAAC
* *
548511 CATTCCATTGTTTCATCAACCAAACCCATAGCCAAATAAACATCCTTATGCTACCATCTCTCAAT
586 CATTCCATTGTTTCATCAACCAAACCCATAACCAAATAAACATCCTTATGCTACCATCTCTCAAA
548576 TTATAAATAACCTACCTATTCACCTTTACATTTACCACCCTTAACCATCTGTTTTGAGC
651 TTATAAATAACCTACCTATTCACCTTTACATTTACCACCCTTAACCATCTGTTTTGAGC
548635 CATTCAAGTAGGCTACCATGT-CTATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCG
1 CATTCAAGTAGGCTACCATGTGC-ATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCG
548699 CCAAAACACCAAGGGATGCTTCCTATTCGGACAAAGACTTATTCCTCTTCATTTTCGGCGCCAAG
65 CCAAAACACCAAGGGATGCTTCCTATTCGGACAAAGACTTATTCCTCTTCATTTTCGGCGCCAAG
548764 TAACTTCCAAAAACATTCAAAACACCCTTAGGGCCGAACCAACACCTTACCATTCGGCCAAGAGC
130 TAACTTCCAAAAACATTCAAAACACCCTTAGGGCCGAACCAACACCTTACCATTCGGCCAAGAGC
548829 ATGTATTTTCATTAAAGTCATGTAATTTCAATAAAAATCATGTATTTTCAAAGGGATTTCATCCT
195 ATGTATTTTCATTAAAGTCATGTAATTTCAATAAAAATCATGTATTTTCAAAGGGATTTCATCCT
*
548894 TGGCCGAACCATCATGTATCTAT-TAGGCCTAAACCCTTTGAAAACTATAAATAGGCTATCACAA
260 TGGCCGAACCATCATGTATCTATGCA-GCCTAAACCCTTTGAAAACTATAAATAGGCTATCACAA
548958 TTCATTTGTAATGAGACCTTTTGATTAATTAAAGTGAGATTATTCTATTTCCTTAGTCCTGGTGA
324 TTCATTTGTAATGAGACCTTTTGATTAATTAAAGTGAGATTATTCTATTTCCTTAGTCCTGGTGA
*
549023 CTTTTATCGACTTATCAAGTATTTTAATACTTGTGGCGTCAACCTCTTCCCCTTGATACTTCTGG
389 CTTTTATCGACTTATCAAGTATTTTAATACTTGTGGCGTCAACCCCTTCCCCTTGATACTTCTGG
549088 TTCCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAATACCACCCCTTAAAGAAGCAATAGAAAG
454 TTCCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAATACCACCCCTTAAAGAAGCAATAGAAAG
549153 TCTGGGTCTTTCCTCTCTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATACTATCCTCACA
519 TCTGGGTCTTTCCTCTCTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATACTATCCTCACA
* *
549218 ACCATTCCATTGTTTCATCAACCAAACCCATAACCAAATCAACATCCTTCTGCTACCATCTCTCA
584 ACCATTCCATTGTTTCATCAACCAAACCCATAACCAAATAAACATCCTTATGCTACCATCTCTCA
*
549283 AATTATAAATAGCCTACCTATTCACCTTTACATTTACCACCCTTAACCATCTGTTTTGAGC
649 AATTATAAATAACCTACCTATTCACCTTTACATTTACCACCCTTAACCATCTGTTTTGAGC
549344 CATTCA
1 CATTCA
549350 CTTATGCAGG
Statistics
Matches: 697, Mismatches: 16, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
708 2 0.00
709 695 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (709 bp):
CATTCAAGTAGGCTACCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGC
CAAAACACCAAGGGATGCTTCCTATTCGGACAAAGACTTATTCCTCTTCATTTTCGGCGCCAAGT
AACTTCCAAAAACATTCAAAACACCCTTAGGGCCGAACCAACACCTTACCATTCGGCCAAGAGCA
TGTATTTTCATTAAAGTCATGTAATTTCAATAAAAATCATGTATTTTCAAAGGGATTTCATCCTT
GGCCGAACCATCATGTATCTATGCAGCCTAAACCCTTTGAAAACTATAAATAGGCTATCACAATT
CATTTGTAATGAGACCTTTTGATTAATTAAAGTGAGATTATTCTATTTCCTTAGTCCTGGTGACT
TTTATCGACTTATCAAGTATTTTAATACTTGTGGCGTCAACCCCTTCCCCTTGATACTTCTGGTT
CCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAATACCACCCCTTAAAGAAGCAATAGAAAGTC
TGGGTCTTTCCTCTCTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATACTATCCTCACAAC
CATTCCATTGTTTCATCAACCAAACCCATAACCAAATAAACATCCTTATGCTACCATCTCTCAAA
TTATAAATAACCTACCTATTCACCTTTACATTTACCACCCTTAACCATCTGTTTTGAGC
Found at i:549805 original size:63 final size:66
Alignment explanation
Indices: 549738--549878 Score: 216
Period size: 66 Copynumber: 2.2 Consensus size: 66
549728 TTTGATATTT
* * *
549738 AACGTCTACACCTTTAAATCTCAAAAAAT-A-A-CAATCATTTTACCATATAACCATTTGACACC
1 AACGTTTACACCTTTAAATCTCAAAAAATAACACCAATCATTTTACCAGACAACCATTTGACACC
549800 A
66 A
*
549801 AACGTTTACACCTTTAAATCTCAAAAAATAACACCAATCATTTTACCAGACAACCATTTGACATC
1 AACGTTTACACCTTTAAATCTCAAAAAATAACACCAATCATTTTACCAGACAACCATTTGACACC
549866 A
66 A
*
549867 AACATTTACACC
1 AACGTTTACACC
549879 CGTAACCTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 28 0.40
64 1 0.01
65 1 0.01
66 40 0.57
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.28
Consensus pattern (66 bp):
AACGTTTACACCTTTAAATCTCAAAAAATAACACCAATCATTTTACCAGACAACCATTTGACACC
A
Found at i:554569 original size:54 final size:56
Alignment explanation
Indices: 554499--554650 Score: 168
Period size: 55 Copynumber: 2.8 Consensus size: 56
554489 CTATACGAGA
* * ** * *
554499 ATTCATCAACCCATGATAAATTCCGTGGGCTACACATACAATG-TC-TATACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGGAATACACACACAAAGTTCTTATACGGTG
* ** *
554553 ATTCATCAACTTATGATGAATTCCGT-GAATATGCACACAAAGTTCTTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGGAATACACACACAAAGTTCTTATACGGTG
**
554608 ATTCATCAACTCATGATGAATTCCGT-GAATATGCACACAAAGT
1 ATTCATCAACTCATGATGAATTCCGTGGAATACACACACAAAGT
554651 GCCTATAGTA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 10 0.12
54 25 0.29
55 50 0.59
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (56 bp):
ATTCATCAACTCATGATGAATTCCGTGGAATACACACACAAAGTTCTTATACGGTG
Found at i:554616 original size:55 final size:55
Alignment explanation
Indices: 554546--554650 Score: 201
Period size: 55 Copynumber: 1.9 Consensus size: 55
554536 ACAATGTCTA
*
554546 TACGGTGATTCATCAACTTATGATGAATTCCGTGAATATGCACACAAAGTTCTTG
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTTCTTG
554601 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGT
1 TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGT
554651 GCCTATAGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
TACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTTCTTG
Found at i:554793 original size:21 final size:21
Alignment explanation
Indices: 554767--554810 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
554757 TAGCCTATAA
*
554767 TATCAGCACTGTTCTTAGCAG
1 TATCAGCACTATTCTTAGCAG
*
554788 TATCAGTACTATTCTTAGCAG
1 TATCAGCACTATTCTTAGCAG
554809 TA
1 TA
554811 CCGATACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
TATCAGCACTATTCTTAGCAG
Found at i:561030 original size:55 final size:56
Alignment explanation
Indices: 560823--561030 Score: 259
Period size: 55 Copynumber: 3.8 Consensus size: 56
560813 CTATACGAGA
* ***
560823 ATTCATCAACCCATGATGAA-TTCTGTG-GGCTGCACACACAA-TG-CATGTACGGTG
1 ATTCATCAACTCATGATGAATTTC-GTGAATATGCACACA-AAGTGTCATGTACGGTG
560877 ATTCATCAACTCATGATGAATTTCGTGAATATGCACACAAAGT-TCATGTACGGTG
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCACACAAAGTGTCATGTACGGTG
* * * * *
560932 ATTCATCAACTCATGATGAATTCCATTAATATGCACACAAAGTGT-TTGTATGGTG
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCACACAAAGTGTCATGTACGGTG
560987 ATTCATCAACTCATGATGAATTTCGTGAATATGC-CTACAAAGTG
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCAC-ACAAAGTG
561031 CCTGTAGTAC
Statistics
Matches: 136, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
54 25 0.18
55 110 0.81
56 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (56 bp):
ATTCATCAACTCATGATGAATTTCGTGAATATGCACACAAAGTGTCATGTACGGTG
Found at i:566283 original size:617 final size:617
Alignment explanation
Indices: 565328--566567 Score: 2446
Period size: 617 Copynumber: 2.0 Consensus size: 617
565318 TCTTATATTT
565328 TTCTATTTTTATGTCAATCTAGTTTCGTGTAAAACAAACGATGACTAATTTCAAAGTCTATATTA
1 TTCTATTTTTATGTCAATCTAGTTTCGTGTAAAACAAACGATGACTAATTTCAAAGTCTATATTA
*
565393 GAAGATGTGAATATTTTATTGATGATATGTCAGAAAATAGGGCAACAAATTATGCTCTAGACAGA
66 GAAGATGTGAATATTTTATTGATGATAGGTCAGAAAATAGGGCAACAAATTATGCTCTAGACAGA
565458 TTCTGGAAATTGGATTAGAAATTTCACCATAAATTGTACAAATTGAACTAAAAGGATTAATTTAT
131 TTCTGGAAATTGGATTAGAAATTTCACCATAAATTGTACAAATTGAACTAAAAGGATTAATTTAT
565523 ATGGATGAGTATGTATTTGAATCTAGTTTCTAATAGAGAAAACGTAGTTAAATTATAGTGTGTAT
196 ATGGATGAGTATGTATTTGAATCTAGTTTCTAATAGAGAAAACGTAGTTAAATTATAGTGTGTAT
565588 ATTAATACATAAAAATAATTCGTTAAAGGTAGTGCATGCTATTAGAATAGAAAAATGAGTGGCAA
261 ATTAATACATAAAAATAATTCGTTAAAGGTAGTGCATGCTATTAGAATAGAAAAATGAGTGGCAA
565653 GTCATGCATTTTATGTTACCTTTTTGTTATATGGCATTGTAAAGGCTTGAGAAGAGCCAAATCTA
326 GTCATGCATTTTATGTTACCTTTTTGTTATATGGCATTGTAAAGGCTTGAGAAGAGCCAAATCTA
565718 TTATATTGAAATGATTATTATGATATTTATCATATGAGGGACATATTGTTCACATGTTAAAAAGG
391 TTATATTGAAATGATTATTATGATATTTATCATATGAGGGACATATTGTTCACATGTTAAAAAGG
565783 TAAGTGACTAATGACATTTTCATGATATATTCATGTTATGTGGAAATGAAATTATATGTGGGGTA
456 TAAGTGACTAATGACATTTTCATGATATATTCATGTTATGTGGAAATGAAATTATATGTGGGGTA
565848 TGAATTGTCCATTGTACTATTATATGAAATGTTCGATATATTGTTATCTTTGATAATTGATTAAC
521 TGAATTGTCCATTGTACTATTATATGAAATGTTCGATATATTGTTATCTTTGATAATTGATTAAC
565913 AGGTAATAATTAATGGAAATACCCATTATATG
586 AGGTAATAATTAATGGAAATACCCATTATATG
565945 TTCTATTTTTATGTCAATCTAGTTTCGTGTAAAACAAACGATGACTAATTTCAAAGTCTATATTA
1 TTCTATTTTTATGTCAATCTAGTTTCGTGTAAAACAAACGATGACTAATTTCAAAGTCTATATTA
566010 GAAGATGTGAATATTTTATTGATGATAGGTCAGAAAATAGGGCAACAAATTATGCTCTAGACAGA
66 GAAGATGTGAATATTTTATTGATGATAGGTCAGAAAATAGGGCAACAAATTATGCTCTAGACAGA
566075 TTCTGGAAATTGGATTAGAAATTTCACCATAAATTGTACAAATTGAACTAAAAGGATTAATTTAT
131 TTCTGGAAATTGGATTAGAAATTTCACCATAAATTGTACAAATTGAACTAAAAGGATTAATTTAT
566140 ATGGATGAGTATGTATTTGAATCTAGTTTCTAATAGAGAAAACGTAGTTAAATTATAGTGTGTAT
196 ATGGATGAGTATGTATTTGAATCTAGTTTCTAATAGAGAAAACGTAGTTAAATTATAGTGTGTAT
566205 ATTAATACATAAAAATAATTCGTTAAAGGTAGTGCATGCTATTAGAATAGAAAAATGAGTGGCAA
261 ATTAATACATAAAAATAATTCGTTAAAGGTAGTGCATGCTATTAGAATAGAAAAATGAGTGGCAA
566270 GTCATGCATTTTATGTTACCTTTTTGTTATATGGCATTGTAAAGGCTTGAGAAGAGCCAAATCTA
326 GTCATGCATTTTATGTTACCTTTTTGTTATATGGCATTGTAAAGGCTTGAGAAGAGCCAAATCTA
*
566335 TTATATTGAAATGATTATTATGATATTTATCATATGATGGACATATTGTTCACATGTTAAAAAGG
391 TTATATTGAAATGATTATTATGATATTTATCATATGAGGGACATATTGTTCACATGTTAAAAAGG
566400 TAAGTGACTAATGACATTTTCATGATATATTCATGTTATGTGGAAATGAAATTATATGTGGGGTA
456 TAAGTGACTAATGACATTTTCATGATATATTCATGTTATGTGGAAATGAAATTATATGTGGGGTA
566465 TGAATTGTCCATTGTACTATTATATGAAATGTTCGATATATTGTTATCTTTGATAATTGATTAAC
521 TGAATTGTCCATTGTACTATTATATGAAATGTTCGATATATTGTTATCTTTGATAATTGATTAAC
*
566530 AGGTAATAATTAATGGAAATGCCCATTATATG
586 AGGTAATAATTAATGGAAATACCCATTATATG
566562 TT-TATT
1 TTCTATT
566568 GAGAGCCCTT
Statistics
Matches: 620, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
616 4 0.01
617 616 0.99
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (617 bp):
TTCTATTTTTATGTCAATCTAGTTTCGTGTAAAACAAACGATGACTAATTTCAAAGTCTATATTA
GAAGATGTGAATATTTTATTGATGATAGGTCAGAAAATAGGGCAACAAATTATGCTCTAGACAGA
TTCTGGAAATTGGATTAGAAATTTCACCATAAATTGTACAAATTGAACTAAAAGGATTAATTTAT
ATGGATGAGTATGTATTTGAATCTAGTTTCTAATAGAGAAAACGTAGTTAAATTATAGTGTGTAT
ATTAATACATAAAAATAATTCGTTAAAGGTAGTGCATGCTATTAGAATAGAAAAATGAGTGGCAA
GTCATGCATTTTATGTTACCTTTTTGTTATATGGCATTGTAAAGGCTTGAGAAGAGCCAAATCTA
TTATATTGAAATGATTATTATGATATTTATCATATGAGGGACATATTGTTCACATGTTAAAAAGG
TAAGTGACTAATGACATTTTCATGATATATTCATGTTATGTGGAAATGAAATTATATGTGGGGTA
TGAATTGTCCATTGTACTATTATATGAAATGTTCGATATATTGTTATCTTTGATAATTGATTAAC
AGGTAATAATTAATGGAAATACCCATTATATG
Found at i:566785 original size:26 final size:26
Alignment explanation
Indices: 566749--566799 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
566739 ATACATTGAC
*
566749 TGGCACTAAAAGTGCATCTCACTAAG
1 TGGCACTAAAAGTACATCTCACTAAG
* *
566775 TGGCATTAAAAGTACATCTTACTAA
1 TGGCACTAAAAGTACATCTCACTAA
566800 CTCGTTAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (26 bp):
TGGCACTAAAAGTACATCTCACTAAG
Found at i:569973 original size:255 final size:255
Alignment explanation
Indices: 569522--570031 Score: 1020
Period size: 255 Copynumber: 2.0 Consensus size: 255
569512 AAATATAATC
569522 TCATAATCTAAAAAATCATCATATTTCAATTAACAATTTAACATATAACTTAGACTGTTGTCAAA
1 TCATAATCTAAAAAATCATCATATTTCAATTAACAATTTAACATATAACTTAGACTGTTGTCAAA
569587 ATTTAACAAAAAAATAAGTTTGAAACATACTAAATAATCGACTGACTTTTTTACAACTTTTAATA
66 ATTTAACAAAAAAATAAGTTTGAAACATACTAAATAATCGACTGACTTTTTTACAACTTTTAATA
569652 ATGAGAAACTCAACAAAGCAAACATCTTATAATCGAAAAATTATTTTGTAACTTTCAATAATAAA
131 ATGAGAAACTCAACAAAGCAAACATCTTATAATCGAAAAATTATTTTGTAACTTTCAATAATAAA
569717 GGGACTCACATTCGACAAAACATCACCCTATATATAATCAAATGATTATTTGTTTACTTG
196 GGGACTCACATTCGACAAAACATCACCCTATATATAATCAAATGATTATTTGTTTACTTG
569777 TCATAATCTAAAAAATCATCATATTTCAATTAACAATTTAACATATAACTTAGACTGTTGTCAAA
1 TCATAATCTAAAAAATCATCATATTTCAATTAACAATTTAACATATAACTTAGACTGTTGTCAAA
569842 ATTTAACAAAAAAATAAGTTTGAAACATACTAAATAATCGACTGACTTTTTTACAACTTTTAATA
66 ATTTAACAAAAAAATAAGTTTGAAACATACTAAATAATCGACTGACTTTTTTACAACTTTTAATA
569907 ATGAGAAACTCAACAAAGCAAACATCTTATAATCGAAAAATTATTTTGTAACTTTCAATAATAAA
131 ATGAGAAACTCAACAAAGCAAACATCTTATAATCGAAAAATTATTTTGTAACTTTCAATAATAAA
569972 GGGACTCACATTCGACAAAACATCACCCTATATATAATCAAATGATTATTTGTTTACTTG
196 GGGACTCACATTCGACAAAACATCACCCTATATATAATCAAATGATTATTTGTTTACTTG
570032 ACCTAAAATA
Statistics
Matches: 255, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 255 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (255 bp):
TCATAATCTAAAAAATCATCATATTTCAATTAACAATTTAACATATAACTTAGACTGTTGTCAAA
ATTTAACAAAAAAATAAGTTTGAAACATACTAAATAATCGACTGACTTTTTTACAACTTTTAATA
ATGAGAAACTCAACAAAGCAAACATCTTATAATCGAAAAATTATTTTGTAACTTTCAATAATAAA
GGGACTCACATTCGACAAAACATCACCCTATATATAATCAAATGATTATTTGTTTACTTG
Found at i:575078 original size:15 final size:15
Alignment explanation
Indices: 575058--575104 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 15
575048 TAACCGGTTT
575058 TGGTTTTAAAAAAAC
1 TGGTTTTAAAAAAAC
575073 TGGTTTTTTTAAAAAAAC
1 TGG---TTTTAAAAAAAC
*
575091 -GGTTATAAAAAAAC
1 TGGTTTTAAAAAAAC
575105 CGATTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 11 0.39
15 3 0.11
17 2 0.07
18 12 0.43
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (15 bp):
TGGTTTTAAAAAAAC
Found at i:575094 original size:17 final size:18
Alignment explanation
Indices: 575061--575094 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
575051 CCGGTTTTGG
575061 TTTTAAAAAAACTGGTTT
1 TTTTAAAAAAACTGGTTT
575079 TTTTAAAAAAAC-GGTT
1 TTTTAAAAAAACTGGTT
575095 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
TTTTAAAAAAACTGGTTT
Found at i:575307 original size:21 final size:21
Alignment explanation
Indices: 575283--575335 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
575273 ACACTTAGGG
575283 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
575304 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
575325 TACCGATTCCC
1 AACCGATTCCC
575336 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:575667 original size:32 final size:33
Alignment explanation
Indices: 575571--575669 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
575561 AACTCAACAT
* * *
575571 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
575604 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
575637 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
575669 A
1 A
575670 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:575688 original size:21 final size:21
Alignment explanation
Indices: 575664--575703 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
575654 ACTTCAAGTT
575664 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
575685 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
575704 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:578011 original size:12 final size:12
Alignment explanation
Indices: 577994--578039 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
577984 TTCGGATAAA
577994 AACCGGTTTTTT
1 AACCGGTTTTTT
578006 AACCGGTTTTTTT
1 AACCGG-TTTTTT
578019 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
578033 ATCCGGT
1 AACCGGT
578040 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:578024 original size:15 final size:14
Alignment explanation
Indices: 577993--578032 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
577983 TTTCGGATAA
577993 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
578006 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
578019 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
578033 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:578109 original size:20 final size:20
Alignment explanation
Indices: 578084--578123 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
578074 GTTAAAATAA
* *
578084 CCGGTTTAAAAAAATCCGAT
1 CCGGTTAAAAAAAAACCGAT
578104 CCGGTTAAAAAAAAACCGAT
1 CCGGTTAAAAAAAAACCGAT
578124 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
CCGGTTAAAAAAAAACCGAT
Found at i:582644 original size:28 final size:28
Alignment explanation
Indices: 582604--582676 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
582594 CCATGAGGAA
582604 AAATTCAAAAAATCATTTGTATCTGATG
1 AAATTCAAAAAATCATTTGTATCTGATG
582632 AAATTCAAAAAATCATTTGTATCTGATG
1 AAATTCAAAAAATCATTTGTATCTGATG
582660 AAATTCATAAAAA-CATT
1 AAATTCA-AAAAATCATT
582677 CAAGATAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 39 0.89
29 5 0.11
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATTCAAAAAATCATTTGTATCTGATG
Found at i:583129 original size:103 final size:104
Alignment explanation
Indices: 582824--583130 Score: 301
Period size: 103 Copynumber: 3.0 Consensus size: 104
582814 AGCAAAGAAC
* * * *
582824 AAATTTTATCTCACTTGATACAGTTTTCCTTGAAACACAAATTTTAAAATTGTTTCACTCGAAAC
1 AAATTTTATCTCACTTGAGACAGTTTCCCTTGAAACATAAAATTTAAAATTGTTTCACTCGAAAC
* *
582889 AAAATTTTTTATCTCACTTGAGAT-TGTTT-TCTTAAAAT-
66 -AAATTTTTTATCTCACTTGATATGT-TTTCTCTTGAAATA
* * * * * * ** *
582927 AAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAATTTTAATATCATTAT-ACTC--TA
1 AAATTTTATCTCACTTGAGACAGTTTCCCTTGAAACATAAAATTTAAAATTGTT-TCACTCGAAA
** * * *
582989 -ATTTTTTTTATCTCATTTGAGGT-TG-CTTCCCTTGAAATA
65 CAAATTTTTTATCTCACTTGA--TATGTTTTCTCTTGAAATA
* *
583028 AAATTTCATCTCACTTGA-ACAGTTTCCCTTGAAACATAAAATTTGAAATTGTTTCACTCGAAAC
1 AAATTTTATCTCACTTGAGACAGTTTCCCTTGAAACATAAAATTTAAAATTGTTTCACTCGAAAC
583092 AAATTTTTTATCTCACTTGATATGTTTTCTCTTGAAATA
66 AAATTTTTTATCTCACTTGATATGTTTTCTCTTGAAATA
583131 CGAATTTTGA
Statistics
Matches: 158, Mismatches: 34, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
99 20 0.13
100 40 0.25
101 17 0.11
102 3 0.02
103 77 0.49
104 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (104 bp):
AAATTTTATCTCACTTGAGACAGTTTCCCTTGAAACATAAAATTTAAAATTGTTTCACTCGAAAC
AAATTTTTTATCTCACTTGATATGTTTTCTCTTGAAATA
Found at i:585409 original size:36 final size:36
Alignment explanation
Indices: 585362--585434 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
585352 AGTTCTGAAA
*
585362 TTAAGTGATAAAAGAATCAGCCATGGATATATAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
585398 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
585434 T
1 T
585435 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
Found at i:587250 original size:12 final size:12
Alignment explanation
Indices: 587235--587291 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
587225 GATACATGAC
587235 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
587247 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
587259 CTGGATTTTGTT
1 CTGAATTCTGTT
587271 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
587283 CTGAATTCT
1 CTGAATTCT
587292 ATTTTGATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:587270 original size:24 final size:24
Alignment explanation
Indices: 587235--587306 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
587225 GATACATGAC
587235 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* * * *
587259 CTGGATTTTGTTCTGATATCTGTT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
587283 CTGAATTCTATTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
587307 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:593755 original size:21 final size:21
Alignment explanation
Indices: 593680--593749 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 21
593670 TTTTGGTGCA
*
593680 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
593700 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
593721 GAAGGGGAACCGATTCCCCCCAT
1 G-A-GGGAACCGATTCCCCCCAT
593744 -AGGGAA
1 GAGGGAA
593750 ATCGATACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 15 0.36
21 9 0.21
22 1 0.02
23 17 0.40
ACGTcount: A:0.26, C:0.31, G:0.27, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:598379 original size:23 final size:23
Alignment explanation
Indices: 598334--598379 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
598324 GACCGGTTCT
* * *
598334 AACCCCACCTGACCCTTTTACCC
1 AACCCCACCCGACCCGTTGACCC
*
598357 AACCCGACCCGACCCGTTGACCC
1 AACCCCACCCGACCCGTTGACCC
598380 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.52, G:0.11, T:0.15
Consensus pattern (23 bp):
AACCCCACCCGACCCGTTGACCC
Found at i:599083 original size:36 final size:36
Alignment explanation
Indices: 599036--599108 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
599026 AGTTTTGGAA
*
599036 TTAAGTGATAAAAGAATCAGCCATGGATATATAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
*
599072 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
599108 T
1 T
599109 ATAACTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
Found at i:600931 original size:24 final size:24
Alignment explanation
Indices: 600894--600962 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
600884 GATACATGAC
*
600894 CTGAATTCTATTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * * *
600918 CTGGATTTTGTTATGATATCTGTT
1 CTGAATTCTGTTATGATTTCTGAT
*
600942 CTGAATTCTGTTTTGATTTCT
1 CTGAATTCTGTTATGATTTCT
600963 AATATCTCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.54
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:603171 original size:17 final size:17
Alignment explanation
Indices: 603146--603180 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
603136 ATGATTTTAA
*
603146 AAATAATAAAAGTAAAT
1 AAATAATAAAAATAAAT
*
603163 AAATCATAAAAATAAAT
1 AAATAATAAAAATAAAT
603180 A
1 A
603181 CCGAATAAAA
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:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAATAATAAAAATAAAT
Found at i:603455 original size:17 final size:17
Alignment explanation
Indices: 603435--603468 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
603425 CACTGATAGA
603435 TCCAAATCAACTTTAAG
1 TCCAAATCAACTTTAAG
603452 TCCAAATCAACTTTAAG
1 TCCAAATCAACTTTAAG
603469 CTTTGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
TCCAAATCAACTTTAAG
Found at i:604765 original size:20 final size:18
Alignment explanation
Indices: 604732--604770 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
604722 TTTTCCTTTC
604732 ATTTTTTTATTTTTTACAA
1 ATTTTTTTATTTTTT-CAA
*
604751 ATTTTTTTTTGTTTTTCAA
1 ATTTTTTTAT-TTTTTCAA
604770 A
1 A
604771 ATTCCTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTTTTATTTTTTCAA
Found at i:604772 original size:20 final size:21
Alignment explanation
Indices: 604733--604773 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
604723 TTTCCTTTCA
*
604733 TTTTTTTATTTTTTACAAATT
1 TTTTTTTATTTTTCACAAATT
*
604754 TTTTTTTGTTTTTCA-AAATT
1 TTTTTTTATTTTTCACAAATT
604774 CCTCCCCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTTATTTTTCACAAATT
Found at i:611292 original size:21 final size:21
Alignment explanation
Indices: 611266--611322 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
611256 TTGTGCATAA
611266 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
611287 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
611311 TGCATCGATACA
1 TGCATCGATACA
611323 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:611341 original size:45 final size:44
Alignment explanation
Indices: 611266--611363 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 44
611256 TTGTGCATAA
*
611266 TGCATCGATACACTATGAAAGTGCATCGATGC-ATCCCTTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCAAT-CC-TTGAATG
611311 TGCATCGATACA-TCATG-AAGATGCACCGATGCAATCCTTGAATG
1 TGCATCGATACACT-ATGAAAG-TGCACCGATGCAATCCTTGAATG
611355 TGCATCGAT
1 TGCATCGAT
611364 GCATAAGGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
44 20 0.41
45 27 0.55
46 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCAATCCTTGAATG
Found at i:611566 original size:19 final size:20
Alignment explanation
Indices: 611542--611579 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
611532 TTACTTCTCC
*
611542 AAATCATGC-TAACATCATT
1 AAATCATGCAAAACATCATT
611561 AAATCATGCAAAACATCAT
1 AAATCATGCAAAACATCAT
611580 CACATTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATCATGCAAAACATCATT
Found at i:611698 original size:14 final size:14
Alignment explanation
Indices: 611679--611705 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
611669 TCTAGGACGA
611679 ATATATATGTATAT
1 ATATATATGTATAT
611693 ATATATATGTATA
1 ATATATATGTATA
611706 AGGGGATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:614501 original size:20 final size:20
Alignment explanation
Indices: 614444--614504 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
614434 TTACTTTGCT
* *
614444 TTTGATTTTGATTCTTTCCC
1 TTTGCTTTTGATTCTTTTCC
* *
614464 TTTACTTTTGATTATTTTCC
1 TTTGCTTTTGATTCTTTTCC
614484 TTTGCTTTTGATTCTTTTCC
1 TTTGCTTTTGATTCTTTTCC
614504 T
1 T
614505 GGTAGTCTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTGCTTTTGATTCTTTTCC
Found at i:616035 original size:25 final size:25
Alignment explanation
Indices: 616007--616057 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
615997 AACACACTTT
*
616007 ACTTATGGTTTTGATGATTAAACTA
1 ACTTATGGTTTAGATGATTAAACTA
*
616032 ACTTGTGGTTTAGATGATTAAACTA
1 ACTTATGGTTTAGATGATTAAACTA
616057 A
1 A
616058 ACTGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (25 bp):
ACTTATGGTTTAGATGATTAAACTA
Found at i:623305 original size:3 final size:3
Alignment explanation
Indices: 623297--623346 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
623287 ATGTTTATGT
*
623297 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
623345 TT
1 TT
623347 TGTTCTTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:623442 original size:13 final size:13
Alignment explanation
Indices: 623424--623450 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
623414 TCCTTGACCC
623424 TTGTATATTTATA
1 TTGTATATTTATA
623437 TTGTATATTTATA
1 TTGTATATTTATA
623450 T
1 T
623451 ATATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTGTATATTTATA
Found at i:629156 original size:31 final size:31
Alignment explanation
Indices: 629058--629148 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
629048 CAATTTAAGG
629058 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
629089 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
629120 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
629149 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:629410 original size:21 final size:21
Alignment explanation
Indices: 629377--629416 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
629367 TTTGAGTAGA
*
629377 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
629399 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
629417 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:630919 original size:6 final size:6
Alignment explanation
Indices: 630910--630941 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
630900 CTTATCTTTA
630910 ATACAT ATACAT ATACAT ATACAT AT-CAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATA
630942 ACATCACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATACAT
Found at i:631111 original size:23 final size:23
Alignment explanation
Indices: 631085--631145 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
631075 CTCATATAAA
631085 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
631108 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
631131 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
631146 TATAAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:631617 original size:15 final size:15
Alignment explanation
Indices: 631593--631627 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
631583 ACTCATATAA
* *
631593 CTTATTATCACATAT
1 CTTATAATCACATAC
631608 CTTATAATCACATAC
1 CTTATAATCACATAC
631623 CTTAT
1 CTTAT
631628 TTCAGTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTATAATCACATAC
Found at i:633814 original size:22 final size:23
Alignment explanation
Indices: 633771--633816 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
633761 TTAATATTAT
*
633771 TTTAATAATATATTTTTTAAATA
1 TTTAATAATATATTTTTAAAATA
*
633794 TTTATTAATA-ATTTTTAAAATA
1 TTTAATAATATATTTTTAAAATA
633816 T
1 T
633817 AATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAATAATATATTTTTAAAATA
Found at i:633824 original size:22 final size:22
Alignment explanation
Indices: 633775--633826 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
633765 TATTATTTTA
* *
633775 ATAATATATTTTTTAAATATTT
1 ATAATATATTTTTAAAATATAT
633797 ATTAATA-ATTTTTAAAATATAAT
1 A-TAATATATTTTTAAAATAT-AT
633820 ATAATAT
1 ATAATAT
633827 TCTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATATTTTTAAAATATAT
Found at i:634175 original size:16 final size:16
Alignment explanation
Indices: 634131--634168 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
634121 TTAAAAATCT
*
634131 AAATATAAT-TTAATTA
1 AAATATAATATTTA-TA
634147 AAATATAATATTTATA
1 AAATATAATATTTATA
634163 AAATAT
1 AAATAT
634169 TAAATTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATTTATA
Found at i:634742 original size:2 final size:2
Alignment explanation
Indices: 634735--634759 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
634725 TATGAAAATA
634735 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 A
634760 ATTGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:640382 original size:63 final size:65
Alignment explanation
Indices: 640235--640385 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 65
640225 ACACTTGGTG
* * *
640235 TGCATCGGTACACT-AATTGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTTT
1 TGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAACCAAGAGTGCATCGATGCATGGTCT
*
640299 G
65 A
* * *
640300 TGCATCGGTACATAGAATGCATTCGATGTTT-AATAA-AACTATGAGTGCATCGATGCATGG-CT
1 TGCATCGGTACATAAAATGCATTCGATGTTTCAA-AAGAACCAAGAGTGCATCGATGCATGGTCT
640362 A
65 A
*
640363 TGCATCGATACATAAAATGCATT
1 TGCATCGGTACATAAAATGCATT
640386 TGAATTAGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 22 0.29
64 24 0.32
65 29 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (65 bp):
TGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAACCAAGAGTGCATCGATGCATGGTCTA
Found at i:640747 original size:13 final size:13
Alignment explanation
Indices: 640729--640762 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
640719 TAAGATTTTG
*
640729 TTTGAAAATCATT
1 TTTGAAAATCAAT
640742 TTTG-AAATCAAT
1 TTTGAAAATCAAT
640754 TTTGAAAAT
1 TTTGAAAAT
640763 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:646123 original size:3 final size:3
Alignment explanation
Indices: 646115--646139 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
646105 AACTCCAACG
646115 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
646140 CCGTCTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:647681 original size:65 final size:64
Alignment explanation
Indices: 647607--647746 Score: 185
Period size: 65 Copynumber: 2.2 Consensus size: 64
647597 ATACACTTGG
* * *
647607 TGTGCATCGGTACACTA-ATTGCATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGG
1 TGTGCATCGGTACA-TAGAATGCATTCGATGTTTCAATAA-AACAAGGAGTGCATCGATGCATGG
647670 CC
64 -C
* * *
647672 TGTGCATCGGTAGATAGAATGCATTCGATGTTTCAATAAAACAATGAGTGCATCGATGCATGGT
1 TGTGCATCGGTACATAGAATGCATTCGATGTTTCAATAAAACAAGGAGTGCATCGATGCATGGC
647736 TGTGCATCGGT
1 TGTGCATCGGT
647747 GCATTTGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 13 0.19
65 52 0.78
66 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (64 bp):
TGTGCATCGGTACATAGAATGCATTCGATGTTTCAATAAAACAAGGAGTGCATCGATGCATGGC
Found at i:663064 original size:17 final size:17
Alignment explanation
Indices: 663042--663086 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
663032 AAAGTGTTTG
*
663042 TTTCTCGAACGAGAGTT
1 TTTCTCGAACGAGAATT
*
663059 TTTCTCGAAAGAGAATT
1 TTTCTCGAACGAGAATT
*
663076 TCTCTC-AACGA
1 TTTCTCGAACGA
663087 AATGGAAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (17 bp):
TTTCTCGAACGAGAATT
Found at i:664894 original size:40 final size:39
Alignment explanation
Indices: 664789--664909 Score: 158
Period size: 40 Copynumber: 3.1 Consensus size: 39
664779 GAGTAATATC
*
664789 TACACCATAGTGC--TACACATAAGGTCGTGCCCACCACA
1 TACACCA-AGTGCATTACACATAAGGTCGTGCCCACCATA
* *
664827 TACA-CTAGTGCATTACACATAAGGTCGTGCCCACCATT
1 TACACCAAGTGCATTACACATAAGGTCGTGCCCACCATA
* *
664865 TACACCGAAGTGTATTACACATAACGTCGTGCCCACCATA
1 TACACC-AAGTGCATTACACATAAGGTCGTGCCCACCATA
664905 TACAC
1 TACAC
664910 TTAGTGTCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
36 5 0.07
37 1 0.01
38 31 0.43
39 1 0.01
40 34 0.47
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.22
Consensus pattern (39 bp):
TACACCAAGTGCATTACACATAAGGTCGTGCCCACCATA
Done.