Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2295895 original size:3 final size:3
Alignment explanation
Indices: 2295887--2295927 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
2295877 TGTATAGGTC
2295887 TTA TTA TTA TTA TTA TTA CTTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT-A TTA TTA
2295928 CTTACATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2295911 original size:16 final size:16
Alignment explanation
Indices: 2295889--2295927 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2295879 TATAGGTCTT
2295889 ATTATTATTATTATTA
1 ATTATTATTATTATTA
*
2295905 CTTATTATTATTATTA
1 ATTATTATTATTATTA
2295921 ATTATTA
1 ATTATTA
2295928 CTTACATTAT
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:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:2301812 original size:31 final size:31
Alignment explanation
Indices: 2301774--2301848 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
2301764 TTTTTTTAAG
*
2301774 TTTAGGTACTAAAATGGACCAAAATTGATAA
1 TTTAGGTACTAAAATGGACCAAAATTAATAA
*
2301805 TTTAGGTACTAAAATGGACCAAAATTAATAG
1 TTTAGGTACTAAAATGGACCAAAATTAATAA
*
2301836 TTTAAGTACTAAA
1 TTTAGGTACTAAA
2301849 CTTATAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (31 bp):
TTTAGGTACTAAAATGGACCAAAATTAATAA
Found at i:2308930 original size:23 final size:23
Alignment explanation
Indices: 2308904--2308964 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2308894 CTCGTATAAA
2308904 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
* *
2308927 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
**
2308950 TGCACTTTAGTGCCA
1 TGCACTGAAGTGCCA
2308965 AATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACTGAAGTGCCACGTAGAAT
Found at i:2313859 original size:30 final size:30
Alignment explanation
Indices: 2313825--2313884 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2313815 TTACTCGTAG
*
2313825 CTTCTAAGGGAATCCTCAATTCTTTTACTA
1 CTTCTAAGGGAATCCTCAATTCCTTTACTA
2313855 CTTCTAAGGGAATCCTCAATTCCTTTACTA
1 CTTCTAAGGGAATCCTCAATTCCTTTACTA
2313885 ACATACTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
CTTCTAAGGGAATCCTCAATTCCTTTACTA
Found at i:2315932 original size:23 final size:23
Alignment explanation
Indices: 2315906--2315950 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2315896 CACCACAGCT
*
2315906 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
2315929 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
2315951 GCATAGAATT
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:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:2315957 original size:23 final size:23
Alignment explanation
Indices: 2315916--2315974 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2315906 CGTATAAATA
*
2315916 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACATAGAATTG
*
2315939 CACCGAAGTGCCGCATAGAATTG
1 CACCGAAGTGCCACATAGAATTG
* *
2315962 CACTGTAGTGCCA
1 CACCGAAGTGCCA
2315975 TATAAGATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGAATTG
Found at i:2316687 original size:63 final size:64
Alignment explanation
Indices: 2316615--2316776 Score: 168
Period size: 63 Copynumber: 2.5 Consensus size: 64
2316605 ATCCCTTGAC
* * * *
2316615 GGGTGCATCGATGCACTA-TCTATACATCGGTGCA-TAAATCCCATTCGATGTTTATA-TTTAAT
1 GGGTGCATCGATGCACTACT-TATACATCGATACACT-AATCACATTCGATGTTTATATTTTAAA
2316677 G
64 G
* * * *
2316678 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTATACATCGATACACTAATCACATTCGATGTTTATATTTTAAAG
* * * * *
2316742 GAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTATACATCGATACAC
2316777 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 45 0.53
64 40 0.47
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATACATCGATACACTAATCACATTCGATGTTTATATTTTAAAG
Found at i:2316766 original size:64 final size:63
Alignment explanation
Indices: 2316656--2316776 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 63
2316646 GCATAAATCC
* * *
2316656 CATTCGATGTTTATATTTAATGGGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTATATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTAATGA
* *
2316719 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 CATTCGATGTTTATA-TTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACAC
2316777 CTTGAACAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
63 14 0.27
64 38 0.73
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
CATTCGATGTTTATATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTAATGA
Found at i:2318879 original size:20 final size:20
Alignment explanation
Indices: 2318856--2318927 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
2318846 GGATTATCAA
2318856 TGGTCCTCCGGGACAAACAG
1 TGGTCCTCCGGGACAAACAG
2318876 TGGTCCTCCGGGACAAACAG
1 TGGTCCTCCGGGACAAACAG
* *
2318896 TGGTCCTTCGGGAC--ATAG
1 TGGTCCTCCGGGACAAACAG
*
2318914 TGGTCCTTCGGGAC
1 TGGTCCTCCGGGAC
2318928 CAATATTCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.34
20 33 0.66
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (20 bp):
TGGTCCTCCGGGACAAACAG
Found at i:2319309 original size:4 final size:4
Alignment explanation
Indices: 2319302--2319331 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2319292 TGATAATGAC
*
2319302 ATGT ATGT ATGT ATGT ATGT ATAT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2319332 TGTTAGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2332671 original size:41 final size:41
Alignment explanation
Indices: 2332586--2332761 Score: 119
Period size: 41 Copynumber: 4.3 Consensus size: 41
2332576 CGTTTCTTCT
* * *
2332586 CAAACGCCACAATATGGTTCATCTATAGTGGCG-TTTGT-ATA
1 CAAACGCCGCAATA-GGTACATCTATAGTGGCGTTTTTTCA-A
* *
2332627 CAAACGCCGCAATAGGTCCATCTATAGTGTCGTTTTTTCAA
1 CAAACGCCGCAATAGGTACATCTATAGTGGCGTTTTTTCAA
* * * * * * *
2332668 CAAACGACGCAA-AGGAGTA-GTTTTTAGCGGCATTTTTATTAA
1 CAAACGCCGCAATA-G-GTACATCTATAGTGGCGTTTTT-TCAA
* * * *
2332710 -AAACGTCGCAATAGGTATATTTATAGTGTCGTTTTTTCAA
1 CAAACGCCGCAATAGGTACATCTATAGTGGCGTTTTTTCAA
*
2332750 AAAACGCCGCAA
1 CAAACGCCGCAA
2332762 AGGAATACTA
Statistics
Matches: 106, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
40 23 0.22
41 76 0.72
42 7 0.07
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (41 bp):
CAAACGCCGCAATAGGTACATCTATAGTGGCGTTTTTTCAA
Found at i:2332735 original size:82 final size:81
Alignment explanation
Indices: 2332623--2332864 Score: 270
Period size: 82 Copynumber: 2.9 Consensus size: 81
2332613 GTGGCGTTTG
* * * * *
2332623 TATACAAACGCCGCAATAGGTCCATCTATAGTGTCGTTTTTTCAACAAACGACGCAAAGGAGTAG
1 TATAAAAACGCCGCAATAGGT-TATCTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAGTAC
*
2332688 T-TTTTAGCGGCATTTT
65 TATTTTAGCGGCATATT
* * *
2332704 TATTAAAAACGTCGCAATAGGTATATTTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAATA
1 TA-TAAAAACGCCGCAATAGGT-TATCTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAGTA
*
2332769 CTACTTTAGCGGCATATT
64 CTATTTTAGCGGCATATT
* ** * * * * *
2332787 TATACAAACGCCGTGATATGGTTCACCTATAGTGACATTTTTTCAATAAAGGCCGCAAAGGAGTA
1 TATAAAAACGCCGCAATA-GGTT-ATCTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAGTA
2332852 CTATTTTAGCGGC
64 CTATTTTAGCGGC
2332865 GTTGTTATAC
Statistics
Matches: 134, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
81 2 0.01
82 68 0.51
83 64 0.48
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (81 bp):
TATAAAAACGCCGCAATAGGTTATCTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAGTACT
ATTTTAGCGGCATATT
Found at i:2332828 original size:83 final size:81
Alignment explanation
Indices: 2332623--2332929 Score: 296
Period size: 83 Copynumber: 3.7 Consensus size: 81
2332613 GTGGCGTTTG
* * * * *
2332623 TATACAAACGCCGCAATAGGTCCATCTATAGTGTCGTTTTTTCAACAAACGACGCAAAGGAGTAG
1 TATACAAACGCCGCAATAGGTTCACCTATAGTGTCATTTTTTCAACAAACGCCGCAAAGGAGTAC
2332688 T-TTTTAGCGGCATTTT
66 TATTTTAGCGGCA-TTT
* * ** * * *
2332704 TATTAAAAACGTCGCAATAGGTAT-ATTTATAGTGTCGTTTTTTCAAAAAACGCCGCAAAGGAAT
1 TA-TACAAACGCCGCAATAGGT-TCACCTATAGTGTCATTTTTTCAACAAACGCCGCAAAGGAGT
*
2332768 ACTACTTTAGCGGCATATT
64 ACTATTTTAGCGGCAT-TT
** * * *
2332787 TATACAAACGCCGTGATATGGTTCACCTATAGTGACATTTTTTCAATAAAGGCCGCAAAGGAGTA
1 TATACAAACGCCGCAATA-GGTTCACCTATAGTGTCATTTTTTCAACAAACGCCGCAAAGGAGTA
*
2332852 CTATTTTAGCGGCGTTGT
65 CTATTTTAGCGGCATT-T
* * * * *
2332870 TATACAAATGTCC-TAATAGGGTTAACCTATAGTGGCATTTTTTCTAACGAACGCCGCAAA
1 TATACAAACG-CCGCAATA-GGTTCACCTATAGTGTCATTTTTTC-AACAAACGCCGCAAA
2332930 AGTTTAGTAC
Statistics
Matches: 187, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
81 2 0.01
82 70 0.37
83 101 0.54
84 14 0.07
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (81 bp):
TATACAAACGCCGCAATAGGTTCACCTATAGTGTCATTTTTTCAACAAACGCCGCAAAGGAGTAC
TATTTTAGCGGCATTT
Found at i:2334915 original size:16 final size:18
Alignment explanation
Indices: 2334899--2334943 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2334889 ATATTCGATT
2334899 ATTTT-AATCGAATATTA
1 ATTTTAAATCGAATATTA
*
2334916 ATTTTGAAATCGAATATAAA
1 ATTTT-AAATCGAATAT-TA
2334936 ATTTTAAA
1 ATTTTAAA
2334944 ATTCATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (18 bp):
ATTTTAAATCGAATATTA
Found at i:2334940 original size:20 final size:19
Alignment explanation
Indices: 2334904--2334945 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2334894 CGATTATTTT
* *
2334904 AATCGAATATTAATTTTGA
1 AATCGAATATAAATTTTAA
2334923 AATCGAATATAAAATTTTAA
1 AATCGAATAT-AAATTTTAA
2334943 AAT
1 AAT
2334946 TCATTTACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (19 bp):
AATCGAATATAAATTTTAA
Found at i:2344621 original size:3 final size:3
Alignment explanation
Indices: 2344615--2344645 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2344605 GGCAAAAAAA
2344615 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2344646 TGTTGGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2352777 original size:46 final size:46
Alignment explanation
Indices: 2352615--2352785 Score: 197
Period size: 47 Copynumber: 3.8 Consensus size: 46
2352605 TCATCCACCG
*
2352615 ACCAGCCGTCCTCATCACGTAGGAACCGTG---TC-ACCCCAGATA
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAACCTCAGATA
** * * * *
2352657 ACCAGCCGTCCTCATCATATAGGAACCATGTTATCACCCTTTAGATG
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAACC-TCAGATA
* *
2352704 ACCAGCCATCCTCATCATGTAGGAACCGTGTTATCAACCTCAGATA
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAACCTCAGATA
* * *
2352750 ACCAACCGTCCTCATCACGTAGAAACCGAGTTATCA
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
2352786 CCATTCTAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
42 27 0.25
45 2 0.02
46 38 0.36
47 39 0.37
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (46 bp):
ACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAACCTCAGATA
Found at i:2352786 original size:93 final size:89
Alignment explanation
Indices: 2352614--2352787 Score: 233
Period size: 93 Copynumber: 1.9 Consensus size: 89
2352604 ATCATCCACC
* * *
2352614 GACCAGCCGTCCTCATCACGTAGGAACCGTGTCACCCCAGATAACCAGCCGTCCTCATCATATAG
1 GACCAGCCATCCTCATCACGTAGGAACCGTGTCACCCCAGATAACCAACCGTCCTCATCACATAG
*
2352679 GAACCATGTTATCACCCTTTAGAT
66 AAACCATGTTATCACCCTTTAGAT
* *
2352703 GACCAGCCATCCTCATCATGTAGGAACCGTGTTATCAACCTCAGATAACCAACCGTCCTCATCAC
1 GACCAGCCATCCTCATCACGTAGGAACCGTG---TC-ACCCCAGATAACCAACCGTCCTCATCAC
*
2352768 GTAGAAACCGA-GTTATCACC
62 ATAGAAACC-ATGTTATCACC
2352788 ATTCTAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
89 29 0.40
92 2 0.03
93 41 0.56
94 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (89 bp):
GACCAGCCATCCTCATCACGTAGGAACCGTGTCACCCCAGATAACCAACCGTCCTCATCACATAG
AAACCATGTTATCACCCTTTAGAT
Found at i:2352995 original size:3 final size:3
Alignment explanation
Indices: 2352982--2353021 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
2352972 GGCCAAAAAA
2352982 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
2353022 TGTTGGGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2355999 original size:19 final size:19
Alignment explanation
Indices: 2355972--2356023 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2355962 ATGCATTTCA
*
2355972 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
2355991 TGCACCGATTCACTCTTAG
1 TGCACCGATGCACTCTTAG
2356010 TGCACCGATGCACT
1 TGCACCGATGCACT
2356024 AAGGGTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:2359733 original size:12 final size:12
Alignment explanation
Indices: 2359716--2359740 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2359706 TTATAAATAC
2359716 AAATGACGTTGG
1 AAATGACGTTGG
2359728 AAATGACGTTGG
1 AAATGACGTTGG
2359740 A
1 A
2359741 GAACCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
AAATGACGTTGG
Found at i:2363802 original size:29 final size:28
Alignment explanation
Indices: 2363770--2363827 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
2363760 AGATGTTTAA
2363770 ATTTGATGGTTAT-TGGATGTTTTGAACTT
1 ATTT-ATGGTTATATGGAT-TTTTGAACTT
* * *
2363799 ATTTTTTGTTTTATGGATTTTTGAACTT
1 ATTTATGGTTATATGGATTTTTGAACTT
2363827 A
1 A
2363828 ATATTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.21, C:0.03, G:0.19, T:0.57
Consensus pattern (28 bp):
ATTTATGGTTATATGGATTTTTGAACTT
Found at i:2364693 original size:64 final size:63
Alignment explanation
Indices: 2364489--2364696 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
2364479 TTTCAAAGTG
* ** *
2364489 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATT-GAACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGG--TATTTTAAAACATCGAATGCATT
2364552 TC
62 TC
* * *
2364554 ATGCATCGATGCA-CATACTATGCATCGATACACTCAGAGT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCTG-GTATTT-T-AAAACATCGAATGCATT
*
2364617 TG
62 TC
*
2364619 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTAAAACATCGAATGCATTTC
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCTGG-TATTTTAAAACATCGAATGCATTTC
2364683 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2364697 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 50 0.41
65 63 0.52
66 5 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCTGGTATTTTAAAACATCGAATGCATTTC
Found at i:2364714 original size:64 final size:64
Alignment explanation
Indices: 2364537--2364716 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 64
2364527 GAATAAATTG
*
2364537 AACATCGAATGCATTTCATGCATCGATGCACATACTA-TGCATCGATACACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CTAGTGCATCGATGCACTCAGAGTTTTATGA
2364601 A
64 A
* *
2364602 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCTG-GCTATTT-
1 AACATCGAATGCATTTCATGCATCGATGCACTCTAG---TGCATCGATGCACTCAGAG-T-TTTA
2364663 T-AA
61 TGAA
* *
2364666 AACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCACCAATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TAGTGCATCGATGCACT
2364717 AACGGTCCAA
Statistics
Matches: 100, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 45 0.45
65 48 0.48
66 3 0.03
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTAGTGCATCGATGCACTCAGAGTTTTATGAA
Found at i:2369908 original size:14 final size:13
Alignment explanation
Indices: 2369891--2369923 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2369881 GGTTTGGGGT
2369891 TTATAGTTTAGAGG
1 TTATAGTTTAG-GG
2369905 TTATAGTTTAGGG
1 TTATAGTTTAGGG
2369918 TT-TAGT
1 TTATAGT
2369924 GTTATCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 4 0.21
14 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (13 bp):
TTATAGTTTAGGG
Found at i:2370567 original size:41 final size:41
Alignment explanation
Indices: 2370522--2370645 Score: 95
Period size: 41 Copynumber: 3.1 Consensus size: 41
2370512 AACAAGTGTT
2370522 ATTACCACACTAGTTGTATTTCTCGTTCAATAAATTAATTA
1 ATTACCACACTAGTTGTATTTCTCGTTCAATAAATTAATTA
* * * *
2370563 ATTACTGCAACCACT--TTCGTA-TGC-C-TT-AA-CAAGT-GTT-
1 ATTAC--C-A-CACTAGTT-GTATTTCTCGTTCAATAAATTAATTA
*
2370600 ATTACCAGACTAGTTGTATTTCTCGTTCAATAAATTAATTA
1 ATTACCACACTAGTTGTATTTCTCGTTCAATAAATTAATTA
2370641 ATTAC
1 ATTAC
2370646 TGCAGCATAC
Statistics
Matches: 60, Mismatches: 9, Indels: 28
0.62 0.09 0.29
Matches are distributed among these distances:
33 3 0.05
34 4 0.07
35 5 0.08
36 1 0.02
37 7 0.12
38 4 0.07
39 6 0.10
40 4 0.07
41 12 0.20
42 1 0.02
43 5 0.08
44 4 0.07
45 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (41 bp):
ATTACCACACTAGTTGTATTTCTCGTTCAATAAATTAATTA
Found at i:2374765 original size:16 final size:16
Alignment explanation
Indices: 2374743--2374781 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2374733 ACCTGATCCG
*
2374743 AACCGTTGACTGGTCT
1 AACCGTTGACCGGTCT
* *
2374759 GACCGTTTACCGGTCT
1 AACCGTTGACCGGTCT
2374775 AACCGTT
1 AACCGTT
2374782 AACTTTGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (16 bp):
AACCGTTGACCGGTCT
Found at i:2379530 original size:33 final size:33
Alignment explanation
Indices: 2379491--2379561 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2379481 ATAAATACTA
*
2379491 AATATTTAATA-TAAATATTAT-TAATACTAT-TAT
1 AATATTTAAAATTAAA-ATTATATAA-ACTATGT-T
2379524 AATATTTAAAATTAAAATTATATAAACTATGTT
1 AATATTTAAAATTAAAATTATATAAACTATGTT
2379557 AATAT
1 AATAT
2379562 GTTATAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (33 bp):
AATATTTAAAATTAAAATTATATAAACTATGTT
Found at i:2380960 original size:11 final size:12
Alignment explanation
Indices: 2380934--2380971 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
2380924 ACTATTAAGA
2380934 ATAATAATAATA-
1 ATAAT-ATAATAT
2380946 ATAATATAA-AT
1 ATAATATAATAT
2380957 ATAATATAATAT
1 ATAATATAATAT
2380969 ATA
1 ATA
2380972 TTATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:2381228 original size:36 final size:36
Alignment explanation
Indices: 2381166--2381306 Score: 248
Period size: 36 Copynumber: 3.9 Consensus size: 36
2381156 TGATCTGATC
2381166 TTGCTTCACTACTCTTTTTGTGAAGGC-TGAATTTGCA
1 TTGCTTCACTACTC-TTTTGTGAAGGCTTG-ATTTGCA
2381203 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
*
2381239 TTGCTTCACTAATCTTTTGTGAAGGCTTGATTTGCA
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
2381275 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
1 TTGCTTCACTACTCTTTTGTGAAGGCTTGATT
2381307 GACTTGAGAA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
36 85 0.84
37 16 0.16
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (36 bp):
TTGCTTCACTACTCTTTTGTGAAGGCTTGATTTGCA
Found at i:2391855 original size:90 final size:90
Alignment explanation
Indices: 2391694--2391869 Score: 291
Period size: 90 Copynumber: 1.9 Consensus size: 90
2391684 CTAACACACC
*
2391694 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATA-CCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATAT
* *
2391759 TTAATTAATTGGAATTTAATAATCCT
65 TTAATTAATTGAAATTAAATAATCCT
*
2391785 CTTTTAT-CCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATATATAT
1 CTTTTATACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATAT
2391849 TTAATTAATTGAAATTAAATA
65 TTAATTAATTGAAATTAAATA
2391870 TTCAAGATTA
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 25 0.31
90 48 0.60
91 7 0.09
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (90 bp):
CTTTTATACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATT
TAATTAATTGAAATTAAATAATCCT
Found at i:2391856 original size:20 final size:21
Alignment explanation
Indices: 2391831--2391900 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
2391821 TATTATTTGA
2391831 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
2391851 AATTAATTGAAATTAAATATTCA
1 AATTAATT-AAAATATATATT-T
*
2391874 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAATATATATTT
2391895 AATTAA
1 AATTAA
2391901 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 18 0.47
23 4 0.11
24 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:2398627 original size:90 final size:90
Alignment explanation
Indices: 2398464--2398641 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
2398454 ACCTAACACA
2398464 CTCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATAT
1 CTCTTTTATA-CCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATAT
* *
2398529 ATTTAATTAATTGGAATTTAATAATC
65 ATTTAATTAATTGAAATTAAATAATC
* *
2398555 CTCTTTTAT-CCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTAT
1 CTCTTTTATACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
2398619 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
2398642 TTCAGGATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
89 25 0.30
90 48 0.59
91 9 0.11
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (90 bp):
CTCTTTTATACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAAATAATC
Found at i:2399172 original size:3 final size:3
Alignment explanation
Indices: 2399164--2399216 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2399154 TTGTTTTTAA
* *
2399164 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
2399209 TAT TAT TA
1 TAT TAT TA
2399217 CAAACAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2399189 original size:25 final size:27
Alignment explanation
Indices: 2399161--2399214 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2399151 CATTTGTTTT
2399161 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
2399186 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
2399214 T
1 T
2399215 TACAAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:2399209 original size:10 final size:10
Alignment explanation
Indices: 2399167--2399214 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
2399157 TTTTTAATAT
2399167 TATTATTAATA
1 TATTATT-ATA
2399178 TATTATTATA
1 TATTATTATA
*
2399188 -ATT-TTATT
1 TATTATTATA
2399196 TATTATTATA
1 TATTATTATA
2399206 TATTATTAT
1 TATTATTAT
2399215 TACAAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:2404701 original size:15 final size:15
Alignment explanation
Indices: 2404681--2404712 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2404671 GATCAATACC
2404681 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2404696 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2404711 TT
1 TT
2404713 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2412049 original size:22 final size:21
Alignment explanation
Indices: 2412014--2412068 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
2412004 ATTATGCTTG
2412014 AAGAAAAAATGAAAAGAAAAAAA
1 AAGAAAAAA-GAAAAG-AAAAAA
* *
2412037 AAGAAAAAAGAAAAGAAGAAG
1 AAGAAAAAAGAAAAGAAAAAA
2412058 AAGAAAAAAGA
1 AAGAAAAAAGA
2412069 GGGGGTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 15 0.50
22 6 0.20
23 9 0.30
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAGAAAAGAAAAAA
Found at i:2412460 original size:19 final size:18
Alignment explanation
Indices: 2412418--2412466 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
2412408 TATTTTCTCT
2412418 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
2412434 AGATTCAATTTATTTTTG
1 AAATTCAATTTATTTTTG
*
2412452 AAAATTCAAATTATT
1 -AAATTCAATTTATT
2412467 CTGTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
18 4 0.15
19 12 0.44
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Done.