Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002503.1 Hibiscus syriacus cultivar Beakdansim tig00005101_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: 65022
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1717 original size:35 final size:33
Alignment explanation
Indices: 1645--1717 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1635 AAATAATATA
* * *
1645 TATATATATATATATAATTAAAAATATAACAAT
1 TATATATATATATATAATTAAAAATAAAAAAAG
* *
1678 TATATATATATATATGGATTAAATATAGAAAAAAG
1 TATATATATATATAT-AATTAAAAATA-AAAAAAG
1713 TATAT
1 TATAT
1718 TAATTGTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 15 0.45
34 9 0.27
35 9 0.27
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (33 bp):
TATATATATATATATAATTAAAAATAAAAAAAG
Found at i:2985 original size:78 final size:79
Alignment explanation
Indices: 2885--3066 Score: 199
Period size: 78 Copynumber: 2.3 Consensus size: 79
2875 ATGTTTCATC
* * * * * * *
2885 TATAGTGGCGTTTTGTCGACAAACGGCACAACCGAGTAGTATTTTTGC-GTGTTTTTATAC-AAT
1 TATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAG--TTTTAGCAGAGTTTTTATACAAAC
*
2948 GCCACAATAGGTACA-
64 GCCACAATAGGCACAT
* * **
2963 TCTAGTGTCGTTTTTTCAACAAACGCCTCAAGGGAGTAGTTTTAGCAGAGTTTTTATACAAACGC
1 TATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAGTTTTAGCAGAGTTTTTATACAAACGC
*
3028 CACAATAGGCCCAT
66 CACAATAGGCACAT
3042 TATAGTGTCGTTTTTTTCAACAAAC
1 TATAGTGTCG-TTTTTTCAACAAAC
3067 ATCGCAAAGG
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
76 6 0.07
77 11 0.13
78 46 0.53
79 9 0.10
80 14 0.16
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (79 bp):
TATAGTGTCGTTTTTTCAACAAACGCCACAACCGAGTAGTTTTAGCAGAGTTTTTATACAAACGC
CACAATAGGCACAT
Found at i:3110 original size:82 final size:79
Alignment explanation
Indices: 2935--3190 Score: 259
Period size: 82 Copynumber: 3.2 Consensus size: 79
2925 ATTTTTGCGT
* * * *
2935 GTTTTTATAC-AATGCCACAATAGGTACATCTAGTGTCGTTTTTTCAACAAACGCCTCAAGGGAG
1 GTTTTTATACAAACGCCACAATAGGTACATATAGTGTCGTTTTTTCAACAAAC-CCGCAAAGGAG
* * *
2999 TAGT--TTTAGCAGA
65 TACTACTTTAGCGGC
** *
3012 GTTTTTATACAAACGCCACAATAGGCCCATTATAGTGTCGTTTTTTTCAACAAACATCGCAAAGG
1 GTTTTTATACAAACGCCACAATAGGTACA-TATAGTGTCG-TTTTTTCAACAAAC-CCGCAAAGG
3077 AGTACTACTTTAGCGGC
63 AGTACTACTTTAGCGGC
* * * * * * *
3094 GTATTTATACAAACGCCGCGATATGGTTCACCTATAGTGACGTTTTTT-AATAAACGCTGCAAAG
1 GTTTTTATACAAACGCCACAATA-GG-T-ACATATAGTGTCGTTTTTTCAACAAAC-CCGCAAAG
3158 GAGTACTACTTTAGCGGC
62 GAGTACTACTTTAGCGGC
3176 GTTTTTATACAAACG
1 GTTTTTATACAAACG
3191 TCATAATATG
Statistics
Matches: 148, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
77 10 0.07
78 15 0.10
79 9 0.06
80 25 0.17
82 71 0.48
83 8 0.05
84 9 0.06
85 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (79 bp):
GTTTTTATACAAACGCCACAATAGGTACATATAGTGTCGTTTTTTCAACAAACCCGCAAAGGAGT
ACTACTTTAGCGGC
Found at i:3190 original size:41 final size:41
Alignment explanation
Indices: 3069--3190 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
3059 CAACAAACAT
*
3069 CGCAAAGGAGTACTACTTTAGCGGCGTATTTATACAAACGC
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
* * * * * * *
3110 CGCGATATG-GTTC-ACCTATAGTGACGTTTTT-TAATAAACGC
1 CGC-AAAGGAGTACTA-CTTTAGCGGCGTTTTTAT-ACAAACGC
*
3151 TGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
3191 TCATAATATG
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
40 5 0.08
41 49 0.83
42 5 0.08
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (41 bp):
CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
Found at i:8048 original size:2 final size:2
Alignment explanation
Indices: 8043--8074 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8033 TTTCACACAA
*
8043 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8075 TAAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8223 original size:16 final size:16
Alignment explanation
Indices: 8202--8232 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8192 AAAAATATAT
8202 AAATTATATAAAAATA
1 AAATTATATAAAAATA
*
8218 AAATTATATTAAAAT
1 AAATTATATAAAAAT
8233 TATTTAGAGA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATATAAAAATA
Found at i:8838 original size:14 final size:14
Alignment explanation
Indices: 8819--8845 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8809 AAATGAACAT
8819 AAACGAACATAAAC
1 AAACGAACATAAAC
8833 AAACGAACATAAA
1 AAACGAACATAAA
8846 TTTAATTGGG
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:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:8966 original size:23 final size:23
Alignment explanation
Indices: 8938--8981 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8928 TTATTTGGGT
8938 TTAAAATATTAATAGGT-TTAAGG
1 TTAAAAT-TTAATAGGTCTTAAGG
*
8961 TTAAAATTTATTAGGTCTTAA
1 TTAAAATTTAATAGGTCTTAA
8982 TATTTCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (23 bp):
TTAAAATTTAATAGGTCTTAAGG
Found at i:9043 original size:10 final size:10
Alignment explanation
Indices: 9025--9099 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 10
9015 TAAACGAACG
9025 AACGAACATA
1 AACGAACATA
* *
9035 TATGAACATA
1 AACGAACATA
9045 AACGAACATAAA
1 AACGAACAT--A
9057 TAAGCGAACATA
1 -AA-CGAACATA
*
9069 AACAAACATATA
1 AACGAAC--ATA
9081 CGAACGAACATA
1 --AACGAACATA
9093 AACGAAC
1 AACGAAC
9100 GGTTCACGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
10 26 0.51
11 2 0.04
12 8 0.16
13 2 0.04
14 13 0.25
ACGTcount: A:0.57, C:0.19, G:0.11, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:9065 original size:24 final size:24
Alignment explanation
Indices: 9038--9099 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
9028 GAACATATAT
*
9038 GAACATAAACGAACATA-AATAAGC
1 GAACATAAACGAACATATAAGAA-C
* *
9062 GAACATAAACAAACATATACGAAC
1 GAACATAAACGAACATATAAGAAC
9086 GAACATAAACGAAC
1 GAACATAAACGAAC
9100 GGTTCACGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATATAAGAAC
Found at i:9092 original size:14 final size:14
Alignment explanation
Indices: 9045--9100 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
9035 TATGAACATA
*
9045 AACGAACATAAA-T
1 AACGAACATAAACG
9058 AAGCGAACATAAAC-
1 AA-CGAACATAAACG
*
9072 -A--AACATATACG
1 AACGAACATAAACG
9083 AACGAACATAAACG
1 AACGAACATAAACG
9097 AACG
1 AACG
9101 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
10 8 0.23
12 1 0.03
13 3 0.09
14 23 0.66
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:25092 original size:27 final size:26
Alignment explanation
Indices: 25056--25108 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
25046 AACTGAATTA
* *
25056 AGAAATAAAATATTAGATACCAAACT
1 AGAAATAAAAAATTAGACACCAAACT
25082 AGAATATAAAAAATTAGACACCAAACT
1 AGAA-ATAAAAAATTAGACACCAAACT
25109 GTAACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (26 bp):
AGAAATAAAAAATTAGACACCAAACT
Found at i:25119 original size:27 final size:27
Alignment explanation
Indices: 25062--25122 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
25052 ATTAAGAAAT
* * * *
25062 AAAATATTAGATACCAAACTAGAATAT
1 AAAAAATTAGACACCAAACTAGAACAA
25089 AAAAAATTAGACACCAAACT-GTAACAA
1 AAAAAATTAGACACCAAACTAG-AACAA
25116 AAAAAAT
1 AAAAAAT
25123 ACGTTTGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.20
Consensus pattern (27 bp):
AAAAAATTAGACACCAAACTAGAACAA
Found at i:26280 original size:18 final size:17
Alignment explanation
Indices: 26251--26287 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
26241 ATATTTTTTT
26251 ATTTAATAAAAATAATA
1 ATTTAATAAAAATAATA
26268 ATTTAATTAAAAATAATA
1 ATTTAA-TAAAAATAATA
26286 AT
1 AT
26288 ATATATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAATAAAAATAATA
Found at i:29048 original size:27 final size:27
Alignment explanation
Indices: 29014--29077 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
29004 AGGGTAAAAT
29014 ATTGATGAGAGTATAATGAGTCAATGA
1 ATTGATGAGAGTATAATGAGTCAATGA
* *
29041 ATTGATGAGGGTATAATGAGTTAATGA
1 ATTGATGAGAGTATAATGAGTCAATGA
29068 ATTGATGAGA
1 ATTGATGAGA
29078 AGAAAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (27 bp):
ATTGATGAGAGTATAATGAGTCAATGA
Found at i:29460 original size:158 final size:156
Alignment explanation
Indices: 29229--29578 Score: 402
Period size: 158 Copynumber: 2.2 Consensus size: 156
29219 GCATGTGATT
* * *
29229 CAAATTTGGTAAAAAAATTGACTTAAAGTAAATCACAAATTGAAGAAATAAGGAGATTATAATAA
1 CAAATTTGGT--AAAAA-GGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATAATAA
* * *
29294 GTTGAAGGACTAAATTTAAAAATAAAAAAATGG-TATAAAAAAAGAGGAATTGAAAGTACACATG
63 ATTAAAGGACTAAATTGAAAAATAAAAAAATGGTTAT-AAAAAAGAGGAATTGAAAGTACACATG
* *
29358 CATTCTACTAATG-TTTAGGAGCATGT-GTCA
127 CATTCTAC-AATGATTTAAGAGCATATAGT-A
* *
29388 CAAATTTGGTAAAAACGGACTTAAAAATAAATGACGAATTGAATAAATAAGGAGATTATGAA-AA
1 CAAATTTGGTAAAAA-GGACTT-AAAATAAATGACAAATTGAAGAAATAAGGAGATTAT-AATAA
* * * * * * *
29452 ATTAAAGGATTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGGATTGAAAGTACATATGT
63 ATTAAAGGACTAAATTGAAAAATAAAAAAATGGTTATAAAAAAGAGGAATTGAAAGTACACATGC
* *
29517 ATTCTACGATGATTTAAGAGCATATAGTT
128 ATTCTACAATGATTTAAGAGCATATAGTA
*
29546 TAAATTTGGTAAAAAGAGACTTAAAATAAATGA
1 CAAATTTGGTAAAAAG-GACTTAAAATAAATGA
29579 GGGGTTGAAA
Statistics
Matches: 164, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
157 25 0.15
158 122 0.74
159 17 0.10
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.27
Consensus pattern (156 bp):
CAAATTTGGTAAAAAGGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGATTATAATAAATT
AAAGGACTAAATTGAAAAATAAAAAAATGGTTATAAAAAAGAGGAATTGAAAGTACACATGCATT
CTACAATGATTTAAGAGCATATAGTA
Found at i:31925 original size:20 final size:20
Alignment explanation
Indices: 31877--31938 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
31867 AACTTAAATC
*
31877 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
31897 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
31915 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
31934 AAAAT
1 AAAAT
31939 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:32001 original size:64 final size:65
Alignment explanation
Indices: 31933--32093 Score: 263
Period size: 63 Copynumber: 2.5 Consensus size: 65
31923 TTATATGATA
31933 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
31997 TAAAATT-AATATCTATAATATAATATTAAAATATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
* *
32061 TAAAATTAAAATATAATATAATATAAAATTAAA
1 TAAAATT-AAATAT-CTATAATATAATATTAAA
32094 TAAAACCTCT
Statistics
Matches: 90, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
63 43 0.48
64 26 0.29
66 5 0.06
67 16 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:32041 original size:26 final size:25
Alignment explanation
Indices: 31988--32069 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 25
31978 TTTATTTAAA
31988 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-TAT
32013 AATATAATATTAAAATATTAATATT-T
1 AAT-TAATATTAAAA-ATTAATATTAT
* *
32039 AATTTAT-TTAAAAAATTAATATTAA
1 AATTAATATT-AAAAATTAATATTAT
32064 AATTAA
1 AATTAA
32070 AATATAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 11 0.22
25 15 0.31
26 11 0.22
27 4 0.08
28 8 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAATATTAAAAATTAATATTAT
Found at i:32056 original size:24 final size:27
Alignment explanation
Indices: 31991--32062 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 27
31981 ATTTAAAAAT
31991 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATAT-TATAATA
*
32017 TAATATTAAAATATTAATATT-TAAT-
1 TAATATTAAAAAATTAATATTATAATA
*
32042 TTAT-TTAAAAAATTAATATTA
1 TAATATTAAAAAATTAATATTA
32063 AAATTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 15 0.38
25 3 0.08
26 11 0.28
27 1 0.03
28 10 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATATTAAAAAATTAATATTATAATA
Found at i:34707 original size:18 final size:18
Alignment explanation
Indices: 34681--34777 Score: 54
Period size: 18 Copynumber: 5.3 Consensus size: 18
34671 ATACATATAG
*
34681 TATAATTTTAAATAATAT
1 TATATTTTTAAATAATAT
*
34699 TATATTTTT-AATATTAT
1 TATATTTTTAAATAATAT
* *
34716 TAATATATACTCAAAT-ATAT
1 T-ATAT-T-TTTAAATAATAT
* ** * *
34736 TATAATGATATATGATAT
1 TATATTTTTAAATAATAT
*
34754 TATATTTTTAAATTAATAC
1 TATATTTTTAAA-TAATAT
34773 TATAT
1 TATAT
34778 AATAAATTAT
Statistics
Matches: 57, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
17 11 0.19
18 25 0.44
19 13 0.23
20 5 0.09
21 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATTTTTAAATAATAT
Found at i:34740 original size:55 final size:54
Alignment explanation
Indices: 34675--34778 Score: 136
Period size: 55 Copynumber: 1.9 Consensus size: 54
34665 TGTAATATAC
** *
34675 ATATAGTATAATTTTAAATAATATTATATTTTTAATATTATTAATATATACTCAA
1 ATATAGTATAATGATAAATAATATTATATTTTTAA-ATTAATAATATATACTCAA
* * * *
34730 ATATATTATAATGATATATGATATTATATTTTTAAATTAATACTATATA
1 ATATAGTATAATGATAAATAATATTATATTTTTAAATTAATAATATATA
34779 ATAAATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
54 12 0.29
55 30 0.71
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (54 bp):
ATATAGTATAATGATAAATAATATTATATTTTTAAATTAATAATATATACTCAA
Found at i:35165 original size:30 final size:30
Alignment explanation
Indices: 35100--35207 Score: 146
Period size: 30 Copynumber: 3.6 Consensus size: 30
35090 CCCAGAAAAT
* * *
35100 GTAATTTATTTTACCTAAAACACTTTT-AA
1 GTAATTCATTTTACGTAAAACAATTTTCAA
* *
35129 GTAATTCATTTTAAGTAAAACAATTTTCAT
1 GTAATTCATTTTACGTAAAACAATTTTCAA
35159 GTAATTCATTTTACGTAAAACAATTTTCAA
1 GTAATTCATTTTACGTAAAACAATTTTCAA
* *
35189 GTTATCCATTTTACGTAAA
1 GTAATTCATTTTACGTAAA
35208 TTATTTTCCA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
29 23 0.33
30 46 0.67
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAATTTTCAA
Found at i:35169 original size:15 final size:14
Alignment explanation
Indices: 35123--35176 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
35113 CCTAAAACAC
35123 TTTTAAGTAATTCA
1 TTTTAAGTAATTCA
**
35137 TTTTAAGTAAAACAA
1 TTTTAAGTAATTC-A
*
35152 TTTTCATGTAATTCA
1 TTTT-AAGTAATTCA
*
35167 TTTTACGTAA
1 TTTTAAGTAA
35177 AACAATTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 16 0.50
15 10 0.31
16 6 0.19
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (14 bp):
TTTTAAGTAATTCA
Found at i:35184 original size:15 final size:15
Alignment explanation
Indices: 35115--35190 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
35105 TTATTTTACC
*
35115 TAAAACACTTTTAAG
1 TAAAACAATTTTAAG
**
35130 TAATTC-ATTTTAAG
1 TAAAACAATTTTAAG
*
35144 TAAAACAATTTTCATG
1 TAAAACAATTTT-AAG
** *
35160 TAATTC-ATTTTACG
1 TAAAACAATTTTAAG
35174 TAAAACAATTTTCAAG
1 TAAAACAATTTT-AAG
35190 T
1 T
35191 TATCCATTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
14 17 0.38
15 19 0.42
16 9 0.20
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (15 bp):
TAAAACAATTTTAAG
Found at i:51231 original size:223 final size:224
Alignment explanation
Indices: 50832--51292 Score: 753
Period size: 223 Copynumber: 2.1 Consensus size: 224
50822 TGTCAGTTTA
* *
50832 TGTCGATACTTTATAAAAATATATTGATCCATAATAATATAATAAGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
50897 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* * *
50962 ATGTATCTATCCATAATAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGTCAAAAC
131 ATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAATCGGTCTAGAAATGACAAAAC
* *
51027 AGGTAAAGCGCTACCGGATATATTGAAAG
196 AGGTAAAGAGCTACCAGATATATTGAAAG
* * *
51056 TGTCAATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGT-AAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
* *
51120 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* * *
51185 ATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATGACAAAAC
131 ATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAATCGGTCTAGAAATGACAAAAC
* * *
51250 CGGTAAAGAGCTACCAGATATGTTGATAG
196 AGGTAAAGAGCTACCAGATATATTGAAAG
51279 TGTCGATACTTTAT
1 TGTCGATACTTTAT
51293 TATAAGTATC
Statistics
Matches: 218, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
223 176 0.81
224 42 0.19
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (224 bp):
TGTCGATACTTTATAAAAATATATCGATCCATAATAATATAACAAGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAATCGGTCTAGAAATGACAAAAC
AGGTAAAGAGCTACCAGATATATTGAAAG
Found at i:51304 original size:111 final size:112
Alignment explanation
Indices: 50832--51292 Score: 735
Period size: 112 Copynumber: 4.1 Consensus size: 112
50822 TGTCAGTTTA
* * * *
50832 TGTCGATACTTTATAAAAATATATTGATCCATAATAATATAATAAGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
50897 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
* *
50944 TGTCGATACTTTATAAAAATGTATCTATCCATAATAATATAACAGGTAAAAAAATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
*
51009 GTCTATAAATGTCAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
*
51056 TGTCAATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGT-AAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
* *
51120 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAG
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
* * *
51167 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
** * * * * *
51232 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAG
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
51279 TGTCGATACTTTAT
1 TGTCGATACTTTAT
51293 TATAAGTATC
Statistics
Matches: 326, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 106 0.33
112 220 0.67
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (112 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
Found at i:51472 original size:182 final size:182
Alignment explanation
Indices: 51165--51616 Score: 787
Period size: 182 Copynumber: 2.5 Consensus size: 182
51155 ATATGTTGAT
51165 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
51230 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
* * *
51295 TAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAA
131 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
*
51347 AGTGTCGATATTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
*
51412 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
51477 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
131 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
* * * * *
51529 AGTGTCGACACTTTATAAAAATGTATCAATCCATAACAATATAATAGGTAAAAATATGACAAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGA-TAAAA
* *
51594 TCGATCCCGAAATGACAAAACCG
65 TCGGTCTCGAAATGACAAAACCG
51617 ATAGTAAAAA
Statistics
Matches: 256, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
182 231 0.90
183 25 0.10
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAAAT
CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAATTATAGCGTCAATAA
Found at i:52267 original size:23 final size:23
Alignment explanation
Indices: 52238--52285 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
52228 AAATAGGTCA
*
52238 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
52261 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
52284 AT
1 AT
52286 TATACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:54382 original size:31 final size:32
Alignment explanation
Indices: 54339--54431 Score: 107
Period size: 36 Copynumber: 2.8 Consensus size: 32
54329 AATTGAATCA
*
54339 AAAGTGCGGATGCTTCCTTCCGTTCACT-TCG
1 AAAGTGCCGATGCTTCCTTCCGTTCACTATCG
* **
54370 AAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAATCG
1 AAAGTGCCGATGCTTCCTTCCGTTC--ACT--ATCG
54406 AAAGTGCCGATGCTTCCTTCCGTTCA
1 AAAGTGCCGATGCTTCCTTCCGTTCA
54432 TTTTGAATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 23 0.45
33 1 0.02
36 27 0.53
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (32 bp):
AAAGTGCCGATGCTTCCTTCCGTTCACTATCG
Found at i:54414 original size:36 final size:36
Alignment explanation
Indices: 54367--54468 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
54357 TCCGTTCACT
54367 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
* *
54403 TCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAA
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
* *
54439 TCGAAAGTGCTGATGTTTCCTTTCGTTCTT
1 TCGAAAGTGCCGATGCTTCCTTTCGTTCTT
54469 CTTATTCACC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (36 bp):
TCGAAAGTGCCGATGCTTCCTTTCGTTCTTTTTGAA
Found at i:56912 original size:13 final size:13
Alignment explanation
Indices: 56879--56905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56869 AAAACTTCTT
56879 AATAAACACTTCA
1 AATAAACACTTCA
56892 AATAAACACTTCA
1 AATAAACACTTCA
56905 A
1 A
56906 CAAAACAATT
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAACACTTCA
Found at i:60492 original size:9 final size:9
Alignment explanation
Indices: 60473--60504 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
60463 CCTTATGGGC
60473 CATTT-TTT
1 CATTTCTTT
60481 CATTTCTTT
1 CATTTCTTT
60490 CATTTCTTT
1 CATTTCTTT
60499 C-TTTCT
1 CATTTCT
60505 CTGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 10 0.43
9 13 0.57
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (9 bp):
CATTTCTTT
Found at i:61301 original size:3 final size:3
Alignment explanation
Indices: 61293--61343 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
61283 TAAAATTATT
* * * *
61293 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61339 TAA TA
1 TAA TA
61344 GAACCGGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:61896 original size:112 final size:111
Alignment explanation
Indices: 61647--62310 Score: 795
Period size: 112 Copynumber: 5.9 Consensus size: 111
61637 AAATTAAGGC
* * *
61647 AAGGTTGAACAAATTCTT-TCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
* * *** ** *
61710 TGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGA-TAGAGTCAAACA
65 TGAACATTTCTGG-AA-----ATGTTGATCCATCAAGTGATG-AATTAGAG-C--A-A
* * *
61767 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * **
61832 GAACTTTCTCTGGAAAAGTTAATTTATCAAGTGATGAATTCAG-GCAA
66 GAACATT-TCTGGAAATGTTGATCCATCAAGTGATGAATT-AGAGCAA
* *
61879 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
61944 GAAC-TTTCTGGAAATGTTGATCTATCAAGTGATGAATTAGAGCAA
66 GAACATTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
* * *
61989 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC--CTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
*
62052 GAACACTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
66 GAACATTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
* * *
62098 AAGCTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAA-TTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGAT-AAGTTCTTCTCATT
* * *
62162 ATGAACACTTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAA
64 ATGAACATTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
*
62210 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * *
62275 GAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATG
66 GAAC-ATTTCTGGAAATGTTGATCCATCAAGTGATG
62311 GATTTGAATC
Statistics
Matches: 491, Mismatches: 40, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
108 29 0.06
109 76 0.15
110 68 0.14
111 29 0.06
112 197 0.40
113 2 0.00
115 2 0.00
116 15 0.03
117 2 0.00
120 18 0.04
121 46 0.09
122 7 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (111 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACATTTCTGGAAATGTTGATCCATCAAGTGATGAATTAGAGCAA
Found at i:62195 original size:331 final size:338
Alignment explanation
Indices: 61647--62310 Score: 884
Period size: 331 Copynumber: 2.0 Consensus size: 338
61637 AAATTAAGGC
* *
61647 AAGGTTGAACAAATTCTTTCATTATGAATTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATG
1 AAGGTTAAACAAATTCTTTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATG
* ** ** * * *
61712 AACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAACAAAGGTTGAAC
66 AACACTTCTGGAAA---T-ATGTTGATCCATCAACTGATGTAATAGAGTC-AACAAAGCTTAAAC
* **
61777 AAATTCTTCTTATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
126 AAATTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACACTCTC
** *
61842 TGGAAAAGTTAATTTATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATG
191 TGGAAAAGTTAATCCATCAAGTGATGAATT-AGAGCAAAAGGTTGAACAAACTCTTCTCATTATG
* * * *
61906 AATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TTTCTGGAAATGTTGATCTATC
255 AACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTCTGGAAAAGCTGATCCATC
61970 AAGTGATGAATTAGAGCAA
320 AAGTGATGAATTAGAGCAA
*
61989 AAGGTTAAACAAGTTCTTCTCATTATGAACTTC-T-TCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTAAACAAATTCTT-TCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* *
62052 GAACACTTCTGG-AA-ATGTTGATCCATCAAGTGATG-AATTAGAG-C-A-AAAGCTTAAACAAG
65 GAACACTTCTGGAAATATGTTGATCCATCAACTGATGTAA-TAGAGTCAACAAAGCTTAAACAAA
*
62111 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAA-TTCTTCTCATTATGAACACT-TCT
129 TTCTTCTCATTATGAACTTCTTCTTC-ATCTTCAGAT-AAGTTCTTCTCATTATGAACACTCTCT
* * * * *
62174 GGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
192 GGAAAAGTTAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAA
62239 CTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCA
257 CTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TTTTCTGGAAAAGCTGATCCATCA
62304 AGTGATG
321 AGTGATG
62311 GATTTGAATC
Statistics
Matches: 286, Mismatches: 29, Indels: 23
0.85 0.09 0.07
Matches are distributed among these distances:
330 1 0.00
331 133 0.47
332 28 0.10
333 29 0.10
334 2 0.01
335 20 0.07
340 2 0.01
341 41 0.14
342 17 0.06
343 13 0.05
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (338 bp):
AAGGTTAAACAAATTCTTTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATG
AACACTTCTGGAAATATGTTGATCCATCAACTGATGTAATAGAGTCAACAAAGCTTAAACAAATT
CTTCTCATTATGAACTTCTTCTTCATCTTCAGATAAGTTCTTCTCATTATGAACACTCTCTGGAA
AAGTTAATCCATCAAGTGATGAATTAGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTCTGGAAAAGCTGATCCATCAAGTGA
TGAATTAGAGCAA
Found at i:62764 original size:21 final size:22
Alignment explanation
Indices: 62713--62769 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
62703 CATAAAGCTT
* *
62713 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
62735 TCATCTTTGAAGAGGGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
62757 TC-TCTTTGAAGAG
1 TCATCTTTGAAGAG
62770 TGTAGATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:63211 original size:49 final size:50
Alignment explanation
Indices: 63125--63321 Score: 199
Period size: 49 Copynumber: 3.9 Consensus size: 50
63115 AGAATAGCAG
*
63125 GTTCGT-AAACATTTGACAAATATTCATCTTTTCTGTGGTTTCTGTCGA-
1 GTTCGTAAAACATTTGACAAACATTCATCTTTTCTGTGGTTTCTGTCGAC
* * * *
63173 GTT-GTAAAACACTTGACAACACATTCATCCTTTT-TGTGGCTTGCT-TAGAT
1 GTTCGTAAAACATTTGACAA-ACATTCAT-CTTTTCTGTGG-TTTCTGTCGAC
63223 GTTCGTAAAACATTTGAC-AACATTCATCTTTTCCTGTGGTTTCTGCTCAGAC
1 GTTCGTAAAACATTTGACAAACATTCATCTTTT-CTGTGGTTTCTG-TC-GAC
* * * *
63275 GTTCGTAAAGCGTTTGACAACACATTTATCCTTTTCTGTGGCTTCTG
1 GTTCGTAAAACATTTGACAA-ACATTCAT-CTTTTCTGTGGTTTCTG
63322 CCAAGATTCT
Statistics
Matches: 123, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
47 2 0.02
48 20 0.16
49 27 0.22
50 18 0.15
51 14 0.11
52 18 0.15
53 1 0.01
54 18 0.15
55 5 0.04
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (50 bp):
GTTCGTAAAACATTTGACAAACATTCATCTTTTCTGTGGTTTCTGTCGAC
Found at i:63291 original size:52 final size:53
Alignment explanation
Indices: 63125--63322 Score: 213
Period size: 52 Copynumber: 3.9 Consensus size: 53
63115 AGAATAGCAG
*
63125 GTTCGT-AAACATTTGACAA-ATATTCAT-CTTTTCTGTGGTTTCTG-TC-GA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGA
* * *
63173 GTT-GTAAAACACTTGACAACACATTCATCCTTTT-TGTGG-CT-TGCTTAGA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGA
63222 TGTTCGTAAAACATTTGAC-A-ACATTCAT-CTTTTCCTGTGGTTTCTGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCATCCTTTT-CTGTGGTTTCTGCTCAGA
* * * *
63274 CGTTCGTAAAGCGTTTGACAACACATTTATCCTTTTCTGTGGCTTCTGC
1 -GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGC
63323 CAAGATTCTT
Statistics
Matches: 124, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
47 4 0.03
48 22 0.18
49 22 0.18
50 14 0.11
51 14 0.11
52 23 0.19
53 1 0.01
54 19 0.15
55 5 0.04
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGA
Done.