Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000409.1 Hibiscus syriacus cultivar Beakdansim tig00000755_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: 92435
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:17768 original size:2 final size:2
Alignment explanation
Indices: 17761--17796 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17751 AACCACTGAT
17761 TA TA TA TA TA TA TA TA TA 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
17797 GCAATTCCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20773 original size:29 final size:30
Alignment explanation
Indices: 20731--20803 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
20721 TCCTTTGTTG
**
20731 AGTCACTTTACTATC-AAAAGTTATAAAAT
1 AGTCACTCGACTATCAAAAAGTTATAAAAT
20760 AGTCACTCGACTATCAAAAAGTTATAAAAT
1 AGTCACTCGACTATCAAAAAGTTATAAAAT
20790 AGTCACTCGACTAT
1 AGTCACTCGACTAT
20804 TAATTATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (30 bp):
AGTCACTCGACTATCAAAAAGTTATAAAAT
Found at i:21595 original size:41 final size:42
Alignment explanation
Indices: 21508--21622 Score: 178
Period size: 41 Copynumber: 2.8 Consensus size: 42
21498 CCCGAAATCT
* * * *
21508 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATATTTTTT
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATAGTTTTC
21550 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAT-GTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATAGTTTTC
*
21591 CGTGTTTGTTTCACGTAATTTGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
21623 TGTAATTCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 35 0.51
42 33 0.49
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATAGTTTTC
Found at i:21979 original size:28 final size:27
Alignment explanation
Indices: 21897--21986 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 27
21887 TTATAATAAT
* *
21897 ATAAGATATTATATTTTT-TAT-TTTA
1 ATAATATATAATATTTTTATATATTTA
21922 ATAATATATAATAATTTTTTATATATTTA
1 ATAATATATAAT-A-TTTTTATATATTTA
21951 ATAATGA-ATAATATTATTTATATATTTAA
1 ATAAT-ATATAATATT-TTTATATATTT-A
21980 ATAATAT
1 ATAATAT
21987 TTTAGTAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 7 0.13
28 16 0.29
29 20 0.36
30 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATAATATATAATATTTTTATATATTTA
Found at i:22155 original size:18 final size:20
Alignment explanation
Indices: 22128--22165 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
22118 TAACAAAATT
22128 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
22146 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
22166 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:22344 original size:20 final size:20
Alignment explanation
Indices: 22315--22361 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
22305 TTTCCAGATG
22315 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
22335 TTTTCTAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
22355 TTTTCCA
1 TTTTCCA
22362 TAATTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.45
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:22382 original size:15 final size:15
Alignment explanation
Indices: 22347--22413 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
22337 TTCTAGAAAT
**
22347 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
22362 -TAATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
22376 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
22391 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
22406 GTAATTCA
1 GTAATTCA
22414 TTTTCTGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:22396 original size:30 final size:29
Alignment explanation
Indices: 22347--22418 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
22337 TTCTAGAAAT
22347 GTAATTCATTTTCCATAATTCAAATTCCA
1 GTAATTCATTTTCCATAATTCAAATTCCA
*
22376 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCA-TAATTCAAATTCCA
22406 GTAATTCATTTTC
1 GTAATTCATTTTC
22419 TGAAAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (29 bp):
GTAATTCATTTTCCATAATTCAAATTCCA
Found at i:22431 original size:29 final size:30
Alignment explanation
Indices: 22367--22431 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
22357 TTCCATAATT
* **
22367 CAAATTCCAGTAATTCATTTTTCAGTAATT
1 CAAATTCCAGTAATTCATTTTTCAGAAAAA
*
22397 CAAATTCCAGTAATTCA-TTTTCTGAAAAA
1 CAAATTCCAGTAATTCATTTTTCAGAAAAA
*
22426 CTAATT
1 CAAATT
22432 ACAGGCAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (30 bp):
CAAATTCCAGTAATTCATTTTTCAGAAAAA
Found at i:22781 original size:22 final size:22
Alignment explanation
Indices: 22753--22795 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
22743 TCGAAAATGT
* *
22753 TAAAAAATATTAATGTTTTAAG
1 TAAAAAATAATAATATTTTAAG
22775 TAAAAAATAATAATATTTTAA
1 TAAAAAATAATAATATTTTAA
22796 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAAAAATAATAATATTTTAAG
Found at i:25856 original size:32 final size:31
Alignment explanation
Indices: 25820--25895 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
25810 GGGGCCGTGA
*
25820 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
25852 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
25883 AGCCTACCTAAGA
1 GGCCTACCTAAGA
25896 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:25878 original size:63 final size:63
Alignment explanation
Indices: 25772--25895 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
25762 CCCTAAGGGA
* * * *
25772 ACATCTTAGGGCCTGAGAGTCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
25835 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
25896 GTCACATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 2 0.04
63 48 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:26777 original size:7 final size:7
Alignment explanation
Indices: 26765--26795 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
26755 GTCAAAGGAA
26765 GTCAACG
1 GTCAACG
26772 GTCAACG
1 GTCAACG
26779 GTCAACG
1 GTCAACG
26786 GTCAACG
1 GTCAACG
26793 GTC
1 GTC
26796 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:26807 original size:17 final size:17
Alignment explanation
Indices: 26785--26841 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
26775 AACGGTCAAC
*
26785 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
26802 GGTCAACAGTCAGGTCG
1 GGTCAACAGTCGGGTCG
26819 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
26836 GGTCAA
1 GGTCAA
26842 ACCGGTTCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.23, G:0.40, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:26857 original size:10 final size:10
Alignment explanation
Indices: 26838--26925 Score: 94
Period size: 9 Copynumber: 9.1 Consensus size: 10
26828 TCGGGTCGGG
26838 TCAAACCGGT
1 TCAAACCGGT
*
26848 TCAGACCGG-
1 TCAAACCGGT
26857 TCAAACCGGT
1 TCAAACCGGT
*
26867 TCAGACCGG-
1 TCAAACCGGT
26876 TCAAACCGGT
1 TCAAACCGGT
*
26886 TCGAACCGG-
1 TCAAACCGGT
*
26895 TCAAATCGGT
1 TCAAACCGGT
*
26905 TCAAAACTGG-
1 TC-AAACCGGT
26915 TCAAACCGGT
1 TCAAACCGGT
26925 T
1 T
26926 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 29 0.46
10 29 0.46
11 5 0.08
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:26860 original size:19 final size:19
Alignment explanation
Indices: 26836--26925 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
26826 AGTCGGGTCG
26836 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
26855 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
26874 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
26893 GGTCAAATCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
26913 GGTCAAACCGGTT
1 GGTCAAACCGGTT
26926 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.77
20 14 0.22
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:26892 original size:29 final size:30
Alignment explanation
Indices: 26852--26925 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
26842 ACCGGTTCAG
26852 ACCGG-TCAAACCGGTTCAGACCGGTC-AA
1 ACCGGTTCAAACCGGTTCAGACCGGTCAAA
* * *
26880 ACCGGTTCGAACCGG-TCAAATCGGTTCAAA
1 ACCGGTTCAAACCGGTTCAGACCGG-TCAAA
*
26910 ACTGG-TCAAACCGGTT
1 ACCGGTTCAAACCGGTT
26926 TTCCAGCAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 12 0.32
29 18 0.49
30 7 0.19
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.19
Consensus pattern (30 bp):
ACCGGTTCAAACCGGTTCAGACCGGTCAAA
Found at i:37030 original size:19 final size:20
Alignment explanation
Indices: 36982--37033 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
36972 ATCGCACGTG
36982 TCGAAGTTCGCGTTGCGATTTAT
1 TCGAAGTT--CGTTGCGA-TTAT
*
37005 TCTAAGTTCGTTGCGA-TAT
1 TCGAAGTTCGTTGCGATTAT
37024 TCGAAGTTCG
1 TCGAAGTTCG
37034 CATTTGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.44
21 8 0.30
23 7 0.26
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGAAGTTCGTTGCGATTAT
Found at i:37735 original size:16 final size:18
Alignment explanation
Indices: 37703--37737 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
37693 ATATAAAAAC
37703 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
37721 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
37737 A
1 A
37738 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:37773 original size:20 final size:20
Alignment explanation
Indices: 37748--37785 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37738 AATGAGTAAA
37748 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
37768 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
37786 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:37790 original size:42 final size:43
Alignment explanation
Indices: 37744--37842 Score: 96
Period size: 42 Copynumber: 2.3 Consensus size: 43
37734 AATAAATGAG
* *
37744 TAAAATATATAAAAAAGTAA-A-AGCATATATATATAAGTAAAA
1 TAAAATATATAAAAAAGTAATATA-CATATATATACAAGCAAAA
* * * *
37786 TAAAAAAAAT-CAAAAGTAATATACATATATATACATGCAAAA
1 TAAAATATATAAAAAAGTAATATACATATATATACAAGCAAAA
37828 TAGGAAATATATAAA
1 TA--AAATATATAAA
37843 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
41 8 0.19
42 27 0.63
43 1 0.02
44 6 0.14
45 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.25
Consensus pattern (43 bp):
TAAAATATATAAAAAAGTAATATACATATATATACAAGCAAAA
Found at i:37808 original size:36 final size:37
Alignment explanation
Indices: 37742--37814 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
37732 TAAATAAATG
* *
37742 AGTAAAATATATAAAAAAGTAAAAGCATATATATATA
1 AGTAAAATATATAAAAAAGTAAAAGAATATACATATA
37779 AGTAAAATA-A-AAAAAA-TCAAAAGTAATATACATATA
1 AGTAAAATATATAAAAAAGT-AAAAG-AATATACATATA
37815 TATACATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 1 0.03
35 11 0.34
36 11 0.34
37 9 0.28
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (37 bp):
AGTAAAATATATAAAAAAGTAAAAGAATATACATATA
Found at i:37937 original size:30 final size:31
Alignment explanation
Indices: 37841--37934 Score: 75
Period size: 32 Copynumber: 2.9 Consensus size: 31
37831 GAAATATATA
* **
37841 AATATATATATATAATAACACTAATAA-AAAAAC
1 AATATACATATATAATAA-A--AATAATAAAAGT
*
37874 ATATATACATATATAATAAAATTAATAGAAAGT
1 A-ATATACATATATAATAAAAATAATA-AAAGT
*
37907 AATATGCATATATAA-AAAGAATAATAAA
1 AATATACATATATAATAAA-AATAATAAA
37935 GTAGGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.18
32 20 0.39
33 6 0.12
34 16 0.31
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (31 bp):
AATATACATATATAATAAAAATAATAAAAGT
Found at i:38347 original size:36 final size:37
Alignment explanation
Indices: 38269--38366 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 37
38259 GTGCTTGTGG
* * **
38269 ATCCTATCTTTAGGAGTTT-AAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCA-AGCAAAATTCT
*
38306 ATCCTATTTTTAAGAG-TTGAATCCAAGCAGAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCAAGCAAAATTCT
*
38342 ATCCTATTTTTGAGAGTTTGAATCC
1 ATCCTATTTTTAAGAGTTTGAATCC
38367 TAGTAGGACG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.51
37 26 0.49
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCAAGCAAAATTCT
Found at i:39141 original size:106 final size:107
Alignment explanation
Indices: 38830--39459 Score: 561
Period size: 109 Copynumber: 5.9 Consensus size: 107
38820 AATATTGTTC
* * * *
38830 CGAGTC-CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGA
1 CGAGTCACAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATCTGGAAATTGTTTGTTGA
** * * * *
38893 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
38936 CGAGTC-TAATATCCTTCG-CTATGAAGTTGAAATTGACTCTG-AA-C--GAAA-T-CTTGTTGA
1 CGAGTCACAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATCTGGAAATTGTTTGTTGA
* *
38993 CAATCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
39036 CGAGTC-CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGAC
1 CGAGTCACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATCTGGAAATTGTTTGTTGAC
* * *
39100 AACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTATTGTCT
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * *
39142 CGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAA-TCGCGGATGAAA-CTGAAAAGTTGTTCGT
1 CGAGT--CACAATATCCTCCGTCGTGAAGTTGAAATTGGC-TCTGAAATCTGGAAA-TTGTTTGT
* * * * *
39205 TGACAATCAGCCATCCCTTCGTTGTGAAGTTGGACTTTTGTTTTCT
62 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
39251 CGGGTATCACGATATCCTCCGTCGTGGAGTTGAAATTGGTTCTGGAATATGGAAGTTGTTCGTTG
1 CGAG--TCACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATCTGGAAATTGTTTGTTG
39316 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
39360 CGGGTAGCACGATATCTTCCATCGTGGAGTTGAAATCGGTTCCGAAAT-TGGGAAATTG-TTGTT
1 CGAGT--CACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATCT-GGAAATTGTTTGTT
* *
39423 GGCAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTG
63 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
39460 ACTCTAGCTA
Statistics
Matches: 440, Mismatches: 65, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
100 80 0.18
101 3 0.01
102 4 0.01
104 4 0.01
105 3 0.01
106 86 0.20
107 1 0.00
108 50 0.11
109 202 0.46
110 6 0.01
111 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (107 bp):
CGAGTCACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATCTGGAAATTGTTTGTTGAC
AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:40119 original size:67 final size:67
Alignment explanation
Indices: 40039--40197 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
40029 GAAACGAAAT
* *
40039 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTATCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGAC
40102 AAAA
64 AAAA
* * *
40106 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAA
40171 AA
66 AA
**
40173 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
40198 GAGAGACGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAA
AA
Found at i:40196 original size:36 final size:36
Alignment explanation
Indices: 40072--40548 Score: 250
Period size: 36 Copynumber: 13.9 Consensus size: 36
40062 AAAGATTTTG
* * * *
40072 TGTTTCAAGAGAAACTATCTCATGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** **
40108 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
40138 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
40175 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * *
40211 CATTTC-AGAGGAAA-TGTTTTC-A-A-TG-C----TT
1 TGTTTCAAG-GGAAACTG-TCTCAAGAGAGACAAAATT
40239 ATGTTTC-AGGAGAAACTGTCTCAA-AGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGA-GAGACAAAA-TT
*
40277 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
40313 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
40341 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAATT
* *
40379 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
40415 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
40443 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
40481 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
40517 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
40549 TGGTGAGCAC
Statistics
Matches: 329, Mismatches: 67, Indels: 90
0.68 0.14 0.19
Matches are distributed among these distances:
28 6 0.02
29 38 0.12
30 15 0.05
31 19 0.06
32 5 0.02
33 5 0.02
34 4 0.01
35 12 0.04
36 131 0.40
37 84 0.26
38 10 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:40291 original size:37 final size:36
Alignment explanation
Indices: 40240--40548 Score: 210
Period size: 37 Copynumber: 8.9 Consensus size: 36
40230 TCAATGCTTA
40240 TGTTTC-AGGAGAAACTGTCTCAAAGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTC-AAGGAGACAAAATTT
*
40277 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
** * **
40313 CATTTCAAGGGAAA-TGTTTC-------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATTT
* * *
40341 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
* *
40379 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
** * *
40415 CATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATTT
* *
40443 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
*
40481 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
40517 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
40549 TGGTGAGCAC
Statistics
Matches: 210, Mismatches: 33, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 27 0.13
30 7 0.03
32 1 0.00
33 1 0.00
35 5 0.02
36 72 0.34
37 81 0.39
38 10 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATTT
Found at i:40314 original size:102 final size:102
Alignment explanation
Indices: 40072--40530 Score: 643
Period size: 102 Copynumber: 4.5 Consensus size: 102
40062 AAAGATTTTG
* * * ** * *** * *
40072 TGTTTCAAGAGAAACTATCTCATGGGAGACAAAATTTGTTTCGAGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC-AATG-TT
* *
40137 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
64 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* * *
40175 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCATTTC-AGAGGAAATGTTTTCAATGCTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAG-GGAAATGTTTTCAATGTTT
* * *
40239 ATGTTTCAGGAGAAACTGTCTCAAAGGAGACAAAATTT
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
*
40277 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
40342 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
*
40379 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
40444 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* * **
40481 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
40531 CTGTCTCAAG
Statistics
Matches: 321, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
101 34 0.11
102 242 0.75
103 45 0.14
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
Found at i:42055 original size:13 final size:12
Alignment explanation
Indices: 42039--42102 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
42029 CCCTTTTTTA
42039 TTTTTGTTCTTTCT
1 TTTTTGTTC-TT-T
42053 TTTTTGTTC-TT
1 TTTTTGTTCTTT
* *
42064 GTTTT-TTCCTT
1 TTTTTGTTCTTT
42075 TTTTTGCTTCTTT
1 TTTTTG-TTCTTT
*
42088 TCTTTTTTTCTTT
1 T-TTTTGTTCTTT
42101 TT
1 TT
42103 GCCCTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 3 0.07
11 11 0.26
12 2 0.05
13 13 0.31
14 13 0.31
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:42056 original size:20 final size:21
Alignment explanation
Indices: 42030--42078 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
42020 CTTTTTGTTC
*
42030 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
42051 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
42071 CCTTTTTT
1 CCTTTTTT
42079 TGCTTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:42079 original size:9 final size:8
Alignment explanation
Indices: 42032--42102 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
42022 TTTTGTTCCC
*
42032 TTTTTTAT
1 TTTTTTCT
42040 TTTTGTTCT
1 TTTT-TTCT
42049 TTCTTTT-T
1 TT-TTTTCT
* *
42057 TGTTCTTGT
1 T-TTTTTCT
*
42066 TTTTTCCT
1 TTTTTTCT
42074 TTTTTTGCT
1 TTTTTT-CT
*
42083 TCTTTTCT
1 TTTTTTCT
42091 TTTTTTCT
1 TTTTTTCT
42099 TTTT
1 TTTT
42103 GCCCTTTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
8 31 0.62
9 17 0.34
10 2 0.04
ACGTcount: A:0.01, C:0.13, G:0.06, T:0.80
Consensus pattern (8 bp):
TTTTTTCT
Found at i:42096 original size:20 final size:20
Alignment explanation
Indices: 42032--42096 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
42022 TTTTGTTCCC
* * *
42032 TTTTTTATTTTTGTTCTTTC
1 TTTTTTGTTCTTGTTCTTTT
*
42052 TTTTTTGTTCTTGTTTTTTCCT
1 TTTTTTGTTCTTGTTCTTT--T
42074 TTTTTTGCTTCTT-TTCTTTT
1 TTTTTTG-TTCTTGTTCTTTT
42094 TTT
1 TTT
42097 CTTTTTGCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 20 0.54
22 12 0.32
23 5 0.14
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (20 bp):
TTTTTTGTTCTTGTTCTTTT
Found at i:45327 original size:16 final size:18
Alignment explanation
Indices: 45296--45328 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
45286 TATAAAAACA
45296 TAAAATATAGGATAAATG
1 TAAAATATAGGATAAATG
45314 TAAAA-ATA-GATAAAT
1 TAAAATATAGGATAAAT
45329 AAATGAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (18 bp):
TAAAATATAGGATAAATG
Found at i:45354 original size:17 final size:17
Alignment explanation
Indices: 45262--45357 Score: 50
Period size: 19 Copynumber: 5.2 Consensus size: 17
45252 TAATGCAAAT
*
45262 AAATAAATAAAACAAGTA
1 AAATATATAAAA-AAGTA
*
45280 AAAGAATATAAAAACA-TA
1 AAA-TATATAAAAA-AGTA
* * *
45298 AAATATAGGATAAATGTAA
1 AAATATA-TAAAAAAGT-A
*
45317 AAATAGATAAATAAATGAGTA
1 AAATATAT-AA-AAA--AGTA
45338 AAATATATAAAAAAGTA
1 AAATATATAAAAAAGTA
45355 AAA
1 AAA
45358 GCATATATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 19
0.66 0.12 0.22
Matches are distributed among these distances:
17 10 0.17
18 14 0.24
19 19 0.33
20 5 0.09
21 8 0.14
22 2 0.03
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.21
Consensus pattern (17 bp):
AAATATATAAAAAAGTA
Found at i:45961 original size:36 final size:38
Alignment explanation
Indices: 45906--45978 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 38
45896 TTTAAAACAT
45906 AGCAAAATTCTATCATATTTTTAG-GAG-TTGAATCCA
1 AGCAAAATTCTATCATATTTTTAGAGAGTTTGAATCCA
* * * *
45942 AGCAGAATTTTATCCTATTTTTTGAGAGTTTGAATCC
1 AGCAAAATTCTATCATATTTTTAGAGAGTTTGAATCC
45979 TAGTAGGACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 20 0.65
37 3 0.10
38 8 0.26
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (38 bp):
AGCAAAATTCTATCATATTTTTAGAGAGTTTGAATCCA
Found at i:46848 original size:103 final size:102
Alignment explanation
Indices: 46648--46852 Score: 254
Period size: 103 Copynumber: 2.0 Consensus size: 102
46638 CGTTGCGATT
* *
46648 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATTGCAACGAACTTTG
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTTG
** * *
46713 ACTATCGCAACGAATTTGTAATAAATCGCAATGCGAAC
66 AAAATCGCAACGAATTCGTAAT-AATCACAATGCGAAC
* * *
46751 TTGGACTATCGCAATAAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAA-TTTG
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTT-
*
46815 GAAAATCGCAACGCGAACTTCG-ACT-ATCACAATGCGAA
65 GAAAATCGCAA--CGAA-TTCGTAATAATCACAATGCGAA
46853 TATGTAAATC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
102 3 0.03
103 76 0.86
105 6 0.07
106 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (102 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTTG
AAAATCGCAACGAATTCGTAATAATCACAATGCGAAC
Found at i:46853 original size:42 final size:41
Alignment explanation
Indices: 46704--46842 Score: 199
Period size: 42 Copynumber: 3.4 Consensus size: 41
46694 ACTATTGCAA
* * *
46704 CGAACTTTGACTATCGCAACGAATTTGTAATAAATCGCAATG
1 CGAACTTGGACTATCGCAACGAATTTG-GATAAATCGCAACG
**
46746 CGAACTTGGACTATCGCAATAAATTTGGAATAAATCGCAACG
1 CGAACTTGGACTATCGCAACGAATTTGG-ATAAATCGCAACG
46788 CGAACTTGGACTATCGCAACGAATTTGGA-AAATCGCAACG
1 CGAACTTGGACTATCGCAACGAATTTGGATAAATCGCAACG
*
46828 CGAACTTCGACTATC
1 CGAACTTGGACTATC
46843 ACAATGCGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 25 0.28
41 1 0.01
42 62 0.70
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (41 bp):
CGAACTTGGACTATCGCAACGAATTTGGATAAATCGCAACG
Found at i:46891 original size:21 final size:21
Alignment explanation
Indices: 46867--46913 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
46857 TAAATCGCAA
46867 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
46888 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
46909 TGCGA
1 TGCGA
46914 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:48290 original size:38 final size:38
Alignment explanation
Indices: 48232--48383 Score: 218
Period size: 38 Copynumber: 4.0 Consensus size: 38
48222 TTTCGATTTC
* * *
48232 ATTTGAGTATTTTGACGAATTTGTTTTTAGGATTCTTT
1 ATTTGTGTATTTTCACGAATTTGTTTTTAGGGTTCTTT
* *
48270 ATTTG-GATATTTTCATGAATTTATTTTTAGGGTTCTTT
1 ATTTGTG-TATTTTCACGAATTTGTTTTTAGGGTTCTTT
*
48308 ATTTGTGTATTTTCACGAATTTGTTTTTAGGGTTCTTC
1 ATTTGTGTATTTTCACGAATTTGTTTTTAGGGTTCTTT
48346 ATTTGTGTATTTTCACGAATTTGTTTCTT-GGGTTCTTT
1 ATTTGTGTATTTTCACGAATTTGTTT-TTAGGGTTCTTT
48384 TCGATTTCAT
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
37 1 0.01
38 99 0.96
39 3 0.03
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.57
Consensus pattern (38 bp):
ATTTGTGTATTTTCACGAATTTGTTTTTAGGGTTCTTT
Found at i:56287 original size:23 final size:22
Alignment explanation
Indices: 56239--56288 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
56229 GTGTTTTATT
**
56239 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
56261 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
56284 ATATT
1 ATATT
56289 ATATTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:56320 original size:27 final size:27
Alignment explanation
Indices: 56282--56370 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
56272 ATCTTTATTA
*
56282 AAATATTA-TATTAATATTAAATATAT
1 AAATAATATTATTAATATTAAATATAT
* *
56308 AAATAATATTATTCATTATTAAA-ATTT
1 AAATAATATTATT-AATATTAAATATAT
* ** *
56335 TAATAATATTATTTCTATAAAAT-TAAT
1 AAATAATATTATTAATATTAAATAT-AT
56362 AAATAATAT
1 AAATAATAT
56371 AAATTTTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
26 14 0.28
27 28 0.56
28 8 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATAATATTATTAATATTAAATATAT
Found at i:56415 original size:43 final size:42
Alignment explanation
Indices: 56329--56415 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 42
56319 TTCATTATTA
*
56329 AAATTTTAATAATATTATTTCTATAAAATTAATAAATAATAT
1 AAATTTTAATAATATTATTTATATAAAATTAATAAATAATAT
**
56371 AAATTTTAATAATAATT-TATTATATATTATTAA-AATATAATAT
1 AAATTTTAATAAT-ATTAT-TTATATAAAATTAATAA-ATAATAT
56414 AA
1 AA
56416 TATCTCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (42 bp):
AAATTTTAATAATATTATTTATATAAAATTAATAAATAATAT
Found at i:56417 original size:33 final size:35
Alignment explanation
Indices: 56379--56456 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 35
56369 ATAAATTTTA
56379 ATAATAATTTAT-TATATATTATTA-AAATA-TAAT
1 ATAATAATTTATAT-TATATTATTAGAAATATTAAT
*
56412 ATAAT-ATCTCATATTATATTATTAGAAATATTAAT
1 ATAATAAT-TTATATTATATTATTAGAAATATTAAT
56447 A-AATATATTT
1 ATAATA-ATTT
56457 TAAATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
32 2 0.05
33 18 0.49
34 9 0.24
35 6 0.16
36 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
ATAATAATTTATATTATATTATTAGAAATATTAAT
Found at i:63891 original size:18 final size:17
Alignment explanation
Indices: 63868--63910 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
63858 TCTATTTTCC
63868 TTTAAAATCAAATTCTCT
1 TTTAAAATCAAA-TCTCT
* *
63886 TTTAAATTCGAATCTCT
1 TTTAAAATCAAATCTCT
63903 TTTAAAAT
1 TTTAAAAT
63911 TTAACATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTAAAATCAAATCTCT
Found at i:73054 original size:15 final size:15
Alignment explanation
Indices: 73034--73062 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73024 GCAAATTATT
73034 TGACATTAACATTAG
1 TGACATTAACATTAG
73049 TGACATTAACATTA
1 TGACATTAACATTA
73063 ACTTTATATG
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:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (15 bp):
TGACATTAACATTAG
Found at i:73264 original size:263 final size:263
Alignment explanation
Indices: 72797--73314 Score: 1000
Period size: 263 Copynumber: 2.0 Consensus size: 263
72787 CCACTATTGT
72797 TTAACTTTATATGAGAGCTCCTCAACCTATTGCTTCTTAAGGCGGTTCGGGTCTGTTCAGTGGTA
1 TTAACTTTATATGAGAGCTCCTCAACCTATTGCTTCTTAAGGCGGTTCGGGTCTGTTCAGTGGTA
72862 TGGTGTTAGGCAAAGATAAGGGTTCCTTTATGCTATCTCATATGCAATTTGCAGATGACCTCATT
66 TGGTGTTAGGCAAAGATAAGGGTTCCTTTATGCTATCTCATATGCAATTTGCAGATGACCTCATT
*
72927 ATTTTTTGTAATGCATCCAAGACGTAAATTTTAAATGTTAAGAGAGTTTTACGAGTTTTTGAAGT
131 ATTTTTTGTAATGCATCCAAGAAGTAAATTTTAAATGTTAAGAGAGTTTTACGAGTTTTTGAAGT
72992 AATGTCCGGCCTTCAACTTAATCTTAGAAAAAGCAAATTATTTGACATTAACATTAGTGACATTA
196 AATGTCCGGCCTTCAACTTAATCTTAGAAAAAGCAAATTATTTGACATTAACATTAGTGACATTA
73057 ACA
261 ACA
* *
73060 TTAACTTTATATGAGAGCTCCTCAACCTATTGCTTCTTAAGGCGGTTCGGGTTTGTTCTGTGGTA
1 TTAACTTTATATGAGAGCTCCTCAACCTATTGCTTCTTAAGGCGGTTCGGGTCTGTTCAGTGGTA
*
73125 TGGTGTTAGGCAAAGATAAGGGTTCCTTTATGCTATCTCATCTGCAATTTGCAGATGACCTCATT
66 TGGTGTTAGGCAAAGATAAGGGTTCCTTTATGCTATCTCATATGCAATTTGCAGATGACCTCATT
73190 ATTTTTTGTAATGCATCCAAGAAGTAAATTTTAAATGTTAAGAGAGTTTTACGAGTTTTTGAAGT
131 ATTTTTTGTAATGCATCCAAGAAGTAAATTTTAAATGTTAAGAGAGTTTTACGAGTTTTTGAAGT
73255 AATGTCCGGCCTTCAACTTAATCTTAGAAAAAGCAAATTATTTGACATTAACATTAGTGA
196 AATGTCCGGCCTTCAACTTAATCTTAGAAAAAGCAAATTATTTGACATTAACATTAGTGA
73315 GGAAGAGGTT
Statistics
Matches: 251, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
263 251 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (263 bp):
TTAACTTTATATGAGAGCTCCTCAACCTATTGCTTCTTAAGGCGGTTCGGGTCTGTTCAGTGGTA
TGGTGTTAGGCAAAGATAAGGGTTCCTTTATGCTATCTCATATGCAATTTGCAGATGACCTCATT
ATTTTTTGTAATGCATCCAAGAAGTAAATTTTAAATGTTAAGAGAGTTTTACGAGTTTTTGAAGT
AATGTCCGGCCTTCAACTTAATCTTAGAAAAAGCAAATTATTTGACATTAACATTAGTGACATTA
ACA
Found at i:80290 original size:19 final size:21
Alignment explanation
Indices: 80266--80323 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
80256 CAATATCAGC
80266 AACTTAA-A-GAACCAAAGCT
1 AACTTAACAGGAACCAAAGCT
80285 AACTTAATGCAGGAACCAAAGCT
1 AACTTAA--CAGGAACCAAAGCT
80308 AACTTAATGCAGGAAC
1 AACTTAA--CAGGAAC
80324 AAATACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.20
22 1 0.03
23 27 0.77
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.17
Consensus pattern (21 bp):
AACTTAACAGGAACCAAAGCT
Found at i:80304 original size:23 final size:23
Alignment explanation
Indices: 80274--80323 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
80264 GCAACTTAAA
80274 GAACCAAAGCTAACTTAATGCAG
1 GAACCAAAGCTAACTTAATGCAG
80297 GAACCAAAGCTAACTTAATGCAG
1 GAACCAAAGCTAACTTAATGCAG
80320 GAAC
1 GAAC
80324 AAATACAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (23 bp):
GAACCAAAGCTAACTTAATGCAG
Found at i:80334 original size:23 final size:23
Alignment explanation
Indices: 80274--80334 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
80264 GCAACTTAAA
* *
80274 GAACCAAAGCTAACTTAATGCAG
1 GAACCAAAACAAACTTAATGCAG
* *
80297 GAACCAAAGCTAACTTAATGCAG
1 GAACCAAAACAAACTTAATGCAG
80320 GAA-CAAATACAAACT
1 GAACCAAA-ACAAACT
80335 CATTCAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.11
23 31 0.89
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.16
Consensus pattern (23 bp):
GAACCAAAACAAACTTAATGCAG
Found at i:92252 original size:42 final size:43
Alignment explanation
Indices: 92200--92292 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
92190 TTAGATTCTT
** *
92200 ATTTTTTTAATCTTA-TTTTTACCTTTATAATTAAGGCT-CATG
1 ATTTTTTTAATCCCACTTTTTACCTTTATAATTAA-GCTCCATA
* *
92242 ATTTTTTTAATCCCACTTTTTACTTTTATAATTGAGCTCCATA
1 ATTTTTTTAATCCCACTTTTTACCTTTATAATTAAGCTCCATA
92285 ATTTTTTT
1 ATTTTTTT
92293 TAGTTTCACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 16 0.36
43 28 0.64
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.56
Consensus pattern (43 bp):
ATTTTTTTAATCCCACTTTTTACCTTTATAATTAAGCTCCATA
Done.