Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003037.1 Hibiscus syriacus cultivar Beakdansim tig00006318_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: 69096
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1384 original size:182 final size:182
Alignment explanation
Indices: 986--1514 Score: 731
Period size: 178 Copynumber: 3.0 Consensus size: 182
976 TGATACAAAT
* * * * *
986 TAAAAATGTATCGATCCATAGCAATATAACATGTAA-AATATGATAAAACCGGTGTC-ATTATGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTATCGA-AATGA
* ** * *
1049 T-AAACCGTTAAAGCGCTACCAGATATA-TGAAAGTGTCGATAAATTAATATAAGTGTCGACAC-
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
1111 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCAATACTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCAATACTTTA
* *
1164 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTATCGAAATGAT
1229 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* *
1294 TTGTAATTTAAAAGGAAGAAGAAGTTATAG-G-TTGAAAA-GTGTCGATACTTTA
131 TTGTAATTTAAAA-G-AGAAGAAGTTATAGCGCCT-AAAAGGTGTCAATACTTTA
* * * * *
1346 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGAGGTATCG-AA--AT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTATCGAAATGAT
*
1408 AAAACCGGTAAAAAGATACCGGATATATTGAAAGTG-CGATAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* * *
1472 TCGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTC
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTC
1515 GACCATACAA
Statistics
Matches: 316, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
176 13 0.04
177 6 0.02
178 80 0.25
179 59 0.19
180 23 0.07
181 36 0.11
182 79 0.25
183 6 0.02
184 14 0.04
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (182 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTATCGAAATGAT
AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCAATACTTTA
Found at i:3226 original size:87 final size:86
Alignment explanation
Indices: 3122--3281 Score: 266
Period size: 87 Copynumber: 1.8 Consensus size: 86
3112 AAAATAGTCA
*
3122 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
3187 CCGGTTAAATGCCTATTTTATT
66 -CGGTTAAATGCCTATTTTATT
* * * *
3209 ATATAAGCGCTTCCTATTACATTATCTAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
3274 CGGTTAAA
66 CGGTTAAA
3282 GATATAACTA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 8 0.12
87 60 0.88
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CGGTTAAATGCCTATTTTATT
Found at i:3256 original size:23 final size:23
Alignment explanation
Indices: 3206--3250 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3196 TGCCTATTTT
* *
3206 ATTATATAAGCGCTTCCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
3229 ATTATCTAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
3251 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:8059 original size:64 final size:64
Alignment explanation
Indices: 7945--8065 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
7935 AACTGGTGTT
* * * *
7945 GACCTGAACCCGAGTTGGACCTGGAAATTGTGGATCTGAACCCGACCTGCATCCGACCTGAGAAC
1 GACCTGAACCCGAATTGAACC-GGAAATTATGGATCTGAACCCGAACTGCATCCGACCTGAGAAC
8010 GACCTGAACCCGAATTGAACC-GAAATTAT-GATACCTGAACCCGAACTGCATCCGAC
1 GACCTGAACCCGAATTGAACCGGAAATTATGGAT--CTGAACCCGAACTGCATCCGAC
8066 TGATATGAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 3 0.06
63 7 0.14
64 21 0.42
65 19 0.38
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (64 bp):
GACCTGAACCCGAATTGAACCGGAAATTATGGATCTGAACCCGAACTGCATCCGACCTGAGAAC
Found at i:8137 original size:16 final size:16
Alignment explanation
Indices: 8116--8154 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
8106 GGTATTACCC
*
8116 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
8132 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
8148 GACCTGT
1 GACCTGT
8155 AATTGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:9132 original size:24 final size:24
Alignment explanation
Indices: 9105--9151 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9095 AGTCAAAGGA
9105 AAAGATGTATT-AATAAACAATTTG
1 AAAGATGTATTAAAT-AACAATTTG
* *
9129 AAAGTTTTATTAAATAACAATTT
1 AAAGATGTATTAAATAACAATTT
9152 AGATTACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
AAAGATGTATTAAATAACAATTTG
Found at i:11810 original size:20 final size:20
Alignment explanation
Indices: 11785--11832 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
11775 TTAATTGGGT
11785 TGCTCGAGTGATGTCGGGCG
1 TGCTCGAGTGATGTCGGGCG
11805 TGCTCGAGTGATGTCGGGCG
1 TGCTCGAGTGATGTCGGGCG
*
11825 TGCACGAG
1 TGCTCGAG
11833 CAGGGCGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.44, T:0.23
Consensus pattern (20 bp):
TGCTCGAGTGATGTCGGGCG
Found at i:12254 original size:60 final size:60
Alignment explanation
Indices: 12175--12309 Score: 193
Period size: 60 Copynumber: 2.2 Consensus size: 60
12165 TTCTAGTTTT
* *
12175 AAATTTGTTCAATTTAGTCCAAATTTAATAATT-CAATATATTAATTTAAGCTTCATATTTC
1 AAATTTGTTCAATTTAGTCCAAATTTAAT-ATTACAATATATTAA-TTAAACTTCATATTTA
* * *
12236 AACTTT-TTCAATTTAGTCCAAATTTAATATTACAGTTTATTAATTAAACTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATATTACAATATATTAATTAAACTTCATATTTA
12295 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
12310 GATCTTTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 22 0.33
60 39 0.59
61 5 0.08
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.47
Consensus pattern (60 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATATTACAATATATTAATTAAACTTCATATTTA
Found at i:12717 original size:20 final size:20
Alignment explanation
Indices: 12685--12754 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
12675 TATAAACAAT
12685 ATAGTAT-TATAGTTTATAC
1 ATAGTATATATAGTTTATAC
*
12704 ATGGTATATATAGTTTATAC
1 ATAGTATATATAGTTTATAC
* *
12724 ATAATATATATA-TTATATAT
1 ATAGTATATATAGTT-TATAC
12744 ATA-TATATATA
1 ATAGTATATATA
12755 TATATATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
ATAGTATATATAGTTTATAC
Found at i:12843 original size:2 final size:2
Alignment explanation
Indices: 12708--12833 Score: 89
Period size: 2 Copynumber: 62.0 Consensus size: 2
12698 TTATACATGG
* *
12708 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
12749 TA TA TA TA TA TA TA TA TA AA CCA TA TA GT- TA GTT TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA -TA TA TA TA TA
* * *
12791 -A TA CA TA TA CTT TA TA TA TA TA TA TA TA GTT TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
12834 AACAATATAT
Statistics
Matches: 98, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
1 4 0.04
2 88 0.90
3 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12901 original size:22 final size:22
Alignment explanation
Indices: 12866--12923 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
12856 ACCCTAACAC
12866 ATATA-TTCTATATATATATAAACT
1 ATATACTT-TATAT-TA-ATAAACT
12890 ATATACTTTATATTAATAAACT
1 ATATACTTTATATTAATAAACT
*
12912 ATATAATTTATA
1 ATATACTTTATA
12924 CAATATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 18 0.56
23 2 0.06
24 10 0.31
25 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATACTTTATATTAATAAACT
Found at i:13002 original size:9 final size:10
Alignment explanation
Indices: 12926--13007 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 10
12916 AATTTATACA
12926 ATATAT-ATT
1 ATATATAATT
*
12935 ATTTATAATT
1 ATATATAATT
*
12945 ATACATAATAT
1 ATATATAAT-T
12956 ATAAATATAAATT
1 AT--ATAT-AATT
*
12969 GTATAGT--TT
1 ATATA-TAATT
12978 ATATATAATT
1 ATATATAATT
12988 CATATATAATTT
1 -ATATATAA-TT
13000 ATATATAA
1 ATATATAA
13008 ACTATGCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 11 0.19
10 12 0.21
11 22 0.39
12 3 0.05
13 5 0.09
14 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATATAATT
Found at i:13005 original size:13 final size:11
Alignment explanation
Indices: 12970--13007 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
12960 ATATAAATTG
*
12970 TATAGTTTATA
1 TATAATTTATA
*
12981 TATAATTCATA
1 TATAATTTATA
12992 TATAATTTATA
1 TATAATTTATA
13003 TATAA
1 TATAA
13008 ACTATGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:13087 original size:20 final size:19
Alignment explanation
Indices: 13055--13093 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
13045 AAACTATATA
13055 GTATTATAATTTATACATG
1 GTATTATAATTTATACATG
*
13074 GTATATATAGTTTATACATG
1 GTAT-TATAATTTATACATG
13094 TAACCCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (19 bp):
GTATTATAATTTATACATG
Found at i:13809 original size:35 final size:35
Alignment explanation
Indices: 13736--13810 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
13726 CGTCACTAAC
**
13736 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
13771 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
13806 AGTAA
1 AGTAA
13811 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:13948 original size:23 final size:23
Alignment explanation
Indices: 13888--13962 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
13878 CATAATTCAA
*
13888 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
13912 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
13936 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
13959 GTCA
1 GTCA
13963 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:13968 original size:23 final size:23
Alignment explanation
Indices: 13892--13977 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
13882 ATTCAAGTCA
*
13892 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
13915 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
13939 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
13962 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
13978 TCAAGTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:13995 original size:47 final size:47
Alignment explanation
Indices: 13871--13984 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
13861 TATATCAAAA
* * * * *
13871 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
13919 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
* *
13965 ATCATAACAGAATTCAAGTC
1 ATCAGAACAGAATCCAAGTC
13985 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 17 0.31
47 21 0.38
48 17 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:15141 original size:18 final size:18
Alignment explanation
Indices: 15120--15155 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15110 CTTCCATCCG
*
15120 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
15138 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
15156 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:16472 original size:8 final size:8
Alignment explanation
Indices: 16453--16506 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
16443 GTCAACGCCA
16453 GTCAAC-G
1 GTCAACGG
16460 GTCAACGG
1 GTCAACGG
16468 GTCAAC-G
1 GTCAACGG
16475 GTCAACGG
1 GTCAACGG
*
16483 GTCAATGG
1 GTCAACGG
16491 GT---CGG
1 GTCAACGG
16496 GTCAACGG
1 GTCAACGG
16504 GTC
1 GTC
16507 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 23 0.57
ACGTcount: A:0.22, C:0.24, G:0.37, T:0.17
Consensus pattern (8 bp):
GTCAACGG
Found at i:16473 original size:15 final size:15
Alignment explanation
Indices: 16453--16487 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
16443 GTCAACGCCA
16453 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
16468 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
16483 GTCAA
1 GTCAA
16488 TGGGTCGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.31, T:0.14
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:16498 original size:13 final size:13
Alignment explanation
Indices: 16480--16511 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16470 CAACGGTCAA
*
16480 CGGGTCAATGGGT
1 CGGGTCAACGGGT
16493 CGGGTCAACGGGT
1 CGGGTCAACGGGT
16506 CGGGTC
1 CGGGTC
16512 GGGTCAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:16512 original size:18 final size:18
Alignment explanation
Indices: 16474--16526 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
16464 ACGGGTCAAC
16474 GGTCAACGGGTCAATGGGTCG
1 GGTCAACGGGTC---GGGTCG
16495 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
16513 GGTCAACTGGTCGG
1 GGTCAACGGGTCGG
16527 ATAAACGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 19 0.61
21 12 0.39
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:16518 original size:31 final size:31
Alignment explanation
Indices: 16480--16541 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
16470 CAACGGTCAA
* *
16480 CGGGTCAA-TGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACT-GGTCGGATAAACGGGTCGGGT
16511 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
16542 AAACTGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGATAAACGGGTCGGGT
Found at i:16524 original size:13 final size:13
Alignment explanation
Indices: 16508--16554 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
16498 CAACGGGTCG
*
16508 GGTCGGGTCAACT
1 GGTCGGGTAAACT
* *
16521 GGTCGGATAAACG
1 GGTCGGGTAAACT
16534 GGTCGGGTAAACT
1 GGTCGGGTAAACT
16547 GGTCGGGT
1 GGTCGGGT
16555 CGGGTCGGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (13 bp):
GGTCGGGTAAACT
Found at i:17344 original size:2 final size:2
Alignment explanation
Indices: 17337--17422 Score: 99
Period size: 2 Copynumber: 43.5 Consensus size: 2
17327 ACAATACATA
17337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
17379 AT AA ACT AT AT AGT -T AT -T AT AT A- AT AT AGT TT AT A- AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
17418 AT AT A
1 AT AT A
17423 AAACTACATA
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
1 4 0.05
2 66 0.90
3 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17459 original size:14 final size:14
Alignment explanation
Indices: 17437--17482 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
17427 TACATATTTC
*
17437 TAAACCATAAACCT
1 TAAATCATAAACCT
17451 TAAATCATAAACCT
1 TAAATCATAAACCT
* * *
17465 TGAATCCTAAACCC
1 TAAATCATAAACCT
17479 TAAA
1 TAAA
17483 CCCTAACTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAATCATAAACCT
Found at i:17620 original size:39 final size:39
Alignment explanation
Indices: 17577--17676 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 39
17567 TAATATATAA
* * *
17577 ATATAAATTGTATAGTTTATATATA-TTCATATAATTTAT
1 ATATAAACTATATAGTTTATATATAGTTCA-ATAATTCAT
* * *
17616 ATATAAACTATTTAGTTTCTATATAGTTCAATAGTTCAT
1 ATATAAACTATATAGTTTATATATAGTTCAATAATTCAT
17655 ATATAAACTATATAGTATTATA
1 ATATAAACTATATAGT-TTATA
17677 GTTTATACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 43 0.84
40 8 0.16
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (39 bp):
ATATAAACTATATAGTTTATATATAGTTCAATAATTCAT
Found at i:17698 original size:20 final size:19
Alignment explanation
Indices: 17669--17706 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
17659 AAACTATATA
17669 GTATTATAGTTTATACATG
1 GTATTATAGTTTATACATG
17688 GTATATATAGTTTATACAT
1 GTAT-TATAGTTTATACAT
17707 ACATACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (19 bp):
GTATTATAGTTTATACATG
Found at i:17785 original size:2 final size:2
Alignment explanation
Indices: 17689--17776 Score: 88
Period size: 2 Copynumber: 43.0 Consensus size: 2
17679 TTATACATGG
* * * *
17689 TA TA TA TA GTT TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
17732 TA TA TA TA TA TA TA GT- TA TA TA TA TA TA CA TA TA CTT TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
17775 TA
1 TA
17777 AACTATATAG
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
1 1 0.01
2 66 0.94
3 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:18201 original size:205 final size:205
Alignment explanation
Indices: 17793--18258 Score: 677
Period size: 205 Copynumber: 2.2 Consensus size: 205
17783 ATAGTTTACA
17793 TTGAT-CCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATT
1 TTGATCCCTCATCAA-GTGTGTTGTTTAATTTATTTAAA----T-TTT-T-A--T-ATATTTATT
* * *
17857 CAATTTTATCCTCCAAATTTTATTTGCATCTGAAATTGACCCGTACTTATTACTTATTTCTATTT
55 CAATTTTATCCTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTT
* * *
17922 TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATC
120 TTAAATTAGCCCATAACCTTTTAAATGGGTATAATTTAGTACTTTTTTATATTAATTTCAACATC
17987 ACAATTTAAAATTATTTCGAT
185 ACAATTTAAAATTATTTCGAT
*
18008 TTGATCCCTCATCAA-TGTGTTGTTTAATTTATTTAAATTTTTATATATTTGTTCAA-TTTAGTC
1 TTGATCCCTCATCAAGTGTGTTGTTTAATTTATTTAAATTTTTATATATTTATTCAATTTTA-TC
* *
18071 CTCCAAATTTTATTTGCATATGAAATTGATCCATACTTATTACTTAATTCTATTTTTTTAATTAG
65 CTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTA-TTTTTAAATTAG
* *
18136 CCCATAACCTTTTAAATGGGTATAATTTAGTACTTTTTTATATTAATTTCAACCTCTCAATTTAA
129 CCCATAACCTTTTAAATGGGTATAATTTAGTACTTTTTTATATTAATTTCAACATCACAATTTAA
*
18201 AATTATTTTGAT
194 AATTATTTCGAT
18213 TTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTAT
1 TTGATCCCTCATCAA-GTGTGTTGTTTAATTTATTTAAATTTTTAT
18259 TTGTAATTTC
Statistics
Matches: 234, Mismatches: 12, Indels: 18
0.89 0.05 0.07
Matches are distributed among these distances:
203 4 0.02
204 61 0.26
205 98 0.42
207 30 0.13
208 1 0.00
209 3 0.01
210 1 0.00
214 22 0.09
215 5 0.02
216 9 0.04
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (205 bp):
TTGATCCCTCATCAAGTGTGTTGTTTAATTTATTTAAATTTTTATATATTTATTCAATTTTATCC
TCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTCTATTTTTAAATTAGCC
CATAACCTTTTAAATGGGTATAATTTAGTACTTTTTTATATTAATTTCAACATCACAATTTAAAA
TTATTTCGAT
Found at i:20722 original size:21 final size:23
Alignment explanation
Indices: 20649--20711 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
20639 TCGAGGGTTT
*
20649 TATGTGGTTCTTCGGGACAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
20672 TATGTGGTCCTTCGGGACAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
20695 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
20712 GAAATATGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAC
Found at i:28090 original size:16 final size:16
Alignment explanation
Indices: 28069--28104 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28059 TTTGAATCTG
28069 TGAAGGAATTGAAATC
1 TGAAGGAATTGAAATC
28085 TGAAGGAATTGAAATC
1 TGAAGGAATTGAAATC
28101 TGAA
1 TGAA
28105 TCTGAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
TGAAGGAATTGAAATC
Found at i:37440 original size:9 final size:9
Alignment explanation
Indices: 37419--37512 Score: 99
Period size: 9 Copynumber: 10.8 Consensus size: 9
37409 TTAAAGATAA
37419 AAAAAAATG
1 AAAAAAATG
37428 --AAAAATG
1 AAAAAAATG
37435 -AAAAAATG
1 AAAAAAATG
37443 AAAAAAATG
1 AAAAAAATG
37452 AAAAAAATG
1 AAAAAAATG
37461 AAAAAAAT-
1 AAAAAAATG
*
37469 AGAAAAAT-
1 AAAAAAATG
37477 AGAAAAAATG
1 A-AAAAAATG
* *
37487 GAAAAAATAA
1 AAAAAAAT-G
*
37497 AAAAAAAAG
1 AAAAAAATG
37506 AAAAAAA
1 AAAAAAA
37513 AGAAGAAGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
7 7 0.10
8 15 0.21
9 45 0.62
10 6 0.08
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:37440 original size:18 final size:18
Alignment explanation
Indices: 37417--37513 Score: 55
Period size: 17 Copynumber: 5.4 Consensus size: 18
37407 GCTTAAAGAT
37417 AAAAAAAAATGAAAAATG
1 AAAAAAAAATGAAAAATG
*
37435 AAAAAATGAA--AAAAATG
1 AAAAAA-AAATGAAAAATG
37452 --AAAAAAATGAAAAA--
1 AAAAAAAAATGAAAAATG
*
37466 AATAGAAAAATAGAAAAAATGG
1 AA-AAAAAAAT-G-AAAAAT-G
* *
37488 AAAAAATAAA-AAAAAAAG
1 AAAAAA-AAATGAAAAATG
37506 AAAAAAAA
1 AAAAAAAA
37514 GAAGAAGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 25
0.66 0.07 0.27
Matches are distributed among these distances:
14 2 0.03
15 4 0.07
16 5 0.08
17 16 0.26
18 14 0.23
19 12 0.20
21 3 0.05
22 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.09
Consensus pattern (18 bp):
AAAAAAAAATGAAAAATG
Found at i:37457 original size:26 final size:26
Alignment explanation
Indices: 37419--37540 Score: 98
Period size: 26 Copynumber: 4.8 Consensus size: 26
37409 TTAAAGATAA
37419 AAAAAAATG--AAAAATGAAAAAATG
1 AAAAAAATGAAAAAAATGAAAAAATG
37443 AAAAAAATGAAAAAAATGAAAAAAAT-
1 AAAAAAATGAAAAAAATG-AAAAAATG
* *
37469 AGAAAAAT-AGAAAAAATGGAAAAAATAA
1 AAAAAAATGA-AAAAAAT-GAAAAAAT-G
* * *
37497 AAAAAAAAGAAAAAAAAG-AAGAA-G
1 AAAAAAATGAAAAAAATGAAAAAATG
*
37521 AAAAAAA-CAAAAAAAT-AAAA
1 AAAAAAATGAAAAAAATGAAAA
37541 GGGGGGTTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
23 9 0.11
24 16 0.20
25 1 0.01
26 32 0.40
27 9 0.11
28 12 0.15
29 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.11, T:0.08
Consensus pattern (26 bp):
AAAAAAATGAAAAAAATGAAAAAATG
Found at i:37501 original size:8 final size:8
Alignment explanation
Indices: 37419--37540 Score: 95
Period size: 9 Copynumber: 14.5 Consensus size: 8
37409 TTAAAGATAA
37419 AAAAAAAT
1 AAAAAAAT
*
37427 -GAAAAAT
1 AAAAAAAT
*
37434 GAAAAAAT
1 AAAAAAAT
37442 GAAAAAAAT
1 -AAAAAAAT
37451 GAAAAAAAT
1 -AAAAAAAT
37460 GAAAAAAAT
1 -AAAAAAAT
*
37469 AGAAAAAT
1 AAAAAAAT
37477 AGAAAAAAT
1 A-AAAAAAT
*
37486 GGAAAAAAT
1 -AAAAAAAT
37495 AAAAAAA-
1 AAAAAAAT
*
37502 AAAGAAAAA
1 AAA-AAAAT
*
37511 AAAGAAGAAG
1 AAA-AA-AAT
*
37521 AAAAAAAC
1 AAAAAAAT
37529 AAAAAAAT
1 AAAAAAAT
37537 AAAA
1 AAAA
37541 GGGGGGTTCA
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
7 9 0.09
8 37 0.38
9 46 0.47
10 5 0.05
ACGTcount: A:0.80, C:0.01, G:0.11, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:38778 original size:55 final size:55
Alignment explanation
Indices: 38694--38973 Score: 456
Period size: 55 Copynumber: 5.1 Consensus size: 55
38684 TGAAGCAAAA
*
38694 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
38749 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
38804 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
38857 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCATACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
38912 GAAGATTGTTCGAGTCTTATACTCTATGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
38967 GGAGATT
1 GAAGATT
38974 ATTGTTCGAG
Statistics
Matches: 206, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
53 47 0.23
54 6 0.03
55 153 0.74
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:38897 original size:108 final size:110
Alignment explanation
Indices: 38694--38976 Score: 480
Period size: 108 Copynumber: 2.6 Consensus size: 110
38684 TGAAGCAAAA
*
38694 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
38759 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
38804 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* * *
38867 CGAGTCTTATACTCTCTGAATAAATAGGGGGCATACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
38912 GAAGATTGTTCGAGTCTTATACTCTATGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
38977 GTTCGAGTTC
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
108 99 0.61
109 6 0.04
110 56 0.35
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:39028 original size:52 final size:52
Alignment explanation
Indices: 38969--39573 Score: 1003
Period size: 52 Copynumber: 11.6 Consensus size: 52
38959 CGATCGTTGG
38969 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
39021 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
39073 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
39125 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
39177 AGATTATTGTTCGAGTTCTAGTCACTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
39229 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
39281 AGATTATTGTTCGAGTTATAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * ** * * *
39333 AGATTATTTTTCGAGTTCTAGTCCCTGAAAAAAATTGAACAGTCTCGTAAGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
39385 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTCGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
39437 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
39489 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
39541 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
39574 TAGAGAGCGA
Statistics
Matches: 515, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 515 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:43110 original size:25 final size:25
Alignment explanation
Indices: 43081--43183 Score: 206
Period size: 25 Copynumber: 4.1 Consensus size: 25
43071 TTTGGCTTAG
43081 TTTCAATCTTTCCTTTATTATTTTC
1 TTTCAATCTTTCCTTTATTATTTTC
43106 TTTCAATCTTTCCTTTATTATTTTC
1 TTTCAATCTTTCCTTTATTATTTTC
43131 TTTCAATCTTTCCTTTATTATTTTC
1 TTTCAATCTTTCCTTTATTATTTTC
43156 TTTCAATCTTTCCTTTATTATTTTC
1 TTTCAATCTTTCCTTTATTATTTTC
43181 TTT
1 TTT
43184 ATTTTCAATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 78 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTCAATCTTTCCTTTATTATTTTC
Found at i:43121 original size:13 final size:13
Alignment explanation
Indices: 43081--43171 Score: 80
Period size: 13 Copynumber: 7.2 Consensus size: 13
43071 TTTGGCTTAG
43081 TTTCAATCTTTCC
1 TTTCAATCTTTCC
* * *
43094 TTT-ATTATTTTC
1 TTTCAATCTTTCC
43106 TTTCAATCTTTCC
1 TTTCAATCTTTCC
* * *
43119 TTT-ATTATTTTC
1 TTTCAATCTTTCC
43131 TTTCAATCTTTCC
1 TTTCAATCTTTCC
* * *
43144 TTT-ATTATTTTC
1 TTTCAATCTTTCC
43156 TTTCAATCTTTCC
1 TTTCAATCTTTCC
43169 TTT
1 TTT
43172 ATTATTTTCT
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
12 27 0.47
13 30 0.53
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCAATCTTTCC
Found at i:43183 original size:12 final size:12
Alignment explanation
Indices: 43093--43186 Score: 80
Period size: 12 Copynumber: 7.6 Consensus size: 12
43083 TCAATCTTTC
43093 CTTTATTATTTT
1 CTTTATTATTTT
* * *
43105 CTTTCAATCTTTC
1 CTTT-ATTATTTT
43118 CTTTATTATTTT
1 CTTTATTATTTT
* * *
43130 CTTTCAATCTTTC
1 CTTT-ATTATTTT
43143 CTTTATTATTTT
1 CTTTATTATTTT
* * *
43155 CTTTCAATCTTTC
1 CTTT-ATTATTTT
43168 CTTTATTATTTT
1 CTTTATTATTTT
43180 CTTTATT
1 CTTTATT
43187 TTCAATTTAG
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
12 34 0.56
13 27 0.44
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (12 bp):
CTTTATTATTTT
Found at i:49819 original size:15 final size:15
Alignment explanation
Indices: 49799--49827 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49789 GAGCCTGCAA
49799 ATGTACATCTCATAT
1 ATGTACATCTCATAT
49814 ATGTACATCTCATA
1 ATGTACATCTCATA
49828 AAGAGCCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (15 bp):
ATGTACATCTCATAT
Found at i:58694 original size:21 final size:21
Alignment explanation
Indices: 58662--58760 Score: 128
Period size: 21 Copynumber: 4.7 Consensus size: 21
58652 ATAGAATTTG
*
58662 TCCC-AAATGACCACATATATA
1 TCCCGAAA-GACCACTTATATA
*
58683 TCCCGAAAGACCACTTATATG
1 TCCCGAAAGACCACTTATATA
* *
58704 TCCCGAAGGACCACTTATATG
1 TCCCGAAAGACCACTTATATA
*
58725 TCCCGAAGGACCACTTATATA
1 TCCCGAAAGACCACTTATATA
*
58746 TCCCGAATGACCACT
1 TCCCGAAAGACCACT
58761 CCTTAAGAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
21 69 0.96
22 3 0.04
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (21 bp):
TCCCGAAAGACCACTTATATA
Found at i:58723 original size:42 final size:42
Alignment explanation
Indices: 58660--58760 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
58650 ACATAGAATT
* *
58660 TGTCCCAAATGACCACATATATATCCCGAAAGACCACTTATA
1 TGTCCCGAATGACCACTTATATATCCCGAAAGACCACTTATA
* * *
58702 TGTCCCGAAGGACCACTTATATGTCCCGAAGGACCACTTATA
1 TGTCCCGAATGACCACTTATATATCCCGAAAGACCACTTATA
*
58744 TATCCCGAATGACCACT
1 TGTCCCGAATGACCACT
58761 CCTTAAGAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.24
Consensus pattern (42 bp):
TGTCCCGAATGACCACTTATATATCCCGAAAGACCACTTATA
Found at i:60145 original size:13 final size:13
Alignment explanation
Indices: 60127--60151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60117 ATAGAGTTGA
60127 TAAGTTGAATTTT
1 TAAGTTGAATTTT
60140 TAAGTTGAATTT
1 TAAGTTGAATTT
60152 GACTTGTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TAAGTTGAATTTT
Found at i:60356 original size:12 final size:12
Alignment explanation
Indices: 60339--60370 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
60329 GTTTAAAATA
60339 GAAGAATTAAGT
1 GAAGAATTAAGT
60351 GAAGAATTAAGT
1 GAAGAATTAAGT
60363 GAAGAATT
1 GAAGAATT
60371 GATGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
GAAGAATTAAGT
Found at i:60590 original size:37 final size:36
Alignment explanation
Indices: 60480--60585 Score: 169
Period size: 37 Copynumber: 2.9 Consensus size: 36
60470 TATGTGCAGG
*
60480 GGGAAGAGATTTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTT-CCCCTGGGGGGGTATCGATTCCCC
*
60517 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATT-TCCCCTGGGGGGGTATCGATTCCCC
60554 GGGAACAGATTTCCCCT-GGGGGGTATCGATTC
1 GGGAACAGATTTCCCCTGGGGGGGTATCGATTC
60586 TCCCCTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
35 15 0.23
36 5 0.08
37 45 0.69
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.22
Consensus pattern (36 bp):
GGGAACAGATTTCCCCTGGGGGGGTATCGATTCCCC
Found at i:66887 original size:35 final size:36
Alignment explanation
Indices: 66829--66899 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
66819 TATGTGCAGG
66829 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
66865 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
66900 CCTAAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 24 0.69
36 11 0.31
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
Done.