Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002892.1 Hibiscus syriacus cultivar Beakdansim tig00005976_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: 118533
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5760 original size:45 final size:46
Alignment explanation
Indices: 5673--5764 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
5663 TTGAAAAGCC
* * *
5673 TGAGTGCATCGATGCATGGTCTTGTGCATCGATGCTTCAAATGCAT
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
5719 TGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCAT
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
5764 T
1 T
5765 CGATGTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 23 0.53
46 20 0.47
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (46 bp):
TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
Found at i:6813 original size:20 final size:21
Alignment explanation
Indices: 6775--6815 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6765 TTTTTCATTT
6775 AGGGGGAATCGATACCCCCTC
1 AGGGGGAATCGATACCCCCTC
6796 AGGGGGAATCTG-TACCCCCT
1 AGGGGGAATC-GATACCCCCT
6816 GCACAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (21 bp):
AGGGGGAATCGATACCCCCTC
Found at i:7094 original size:12 final size:12
Alignment explanation
Indices: 7077--7101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7067 AGATGACAAG
7077 TCAAATTCAACT
1 TCAAATTCAACT
7089 TCAAATTCAACT
1 TCAAATTCAACT
7101 T
1 T
7102 ATCAAGTCTA
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAATTCAACT
Found at i:9272 original size:22 final size:22
Alignment explanation
Indices: 9247--9291 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9237 AATGTCAGAG
*
9247 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATACCCCTGCTACA
9269 GGGAACCGATACCCCTGCTACA
1 GGGAACCGATACCCCTGCTACA
9291 G
1 G
9292 TGCTGCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (22 bp):
GGGAACCGATACCCCTGCTACA
Found at i:10121 original size:32 final size:32
Alignment explanation
Indices: 10016--10140 Score: 132
Period size: 31 Copynumber: 4.0 Consensus size: 32
10006 AACCTCGGCA
* * *
10016 ACTGTCCATAGGCCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
* **
10047 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
10078 ACTGTCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGTAA-T
* *
10111 A-TGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAA
10141 ACACTCGACT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.03
31 47 0.60
32 26 0.33
33 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:10135 original size:63 final size:62
Alignment explanation
Indices: 10016--10139 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 62
10006 AACCTCGGCA
* *
10016 ACTGTCCATAGGCCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGCCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
10078 ACTGTCCATATGTCCCGAA-AGACATAGGTAATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGCCCCGAAGA-ACATAGGTAA--ACTGTCCATATGTTCCGTAGAACATAGGTA
10140 AACACTCGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
61 1 0.02
62 26 0.47
63 27 0.49
64 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGCCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:11700 original size:21 final size:21
Alignment explanation
Indices: 11676--11716 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11666 TTTTTCATTT
11676 AGGGGGAAT-TGATACCCCCTC
1 AGGGGGAATCTG-TACCCCCTC
11697 AGGGGGAATCTGTACCCCCT
1 AGGGGGAATCTGTACCCCCT
11717 GCACAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (21 bp):
AGGGGGAATCTGTACCCCCTC
Found at i:11996 original size:12 final size:12
Alignment explanation
Indices: 11979--12003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11969 AGATGACAAG
11979 TCAAATTCAACT
1 TCAAATTCAACT
11991 TCAAATTCAACT
1 TCAAATTCAACT
12003 T
1 T
12004 ATCAACTCTA
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAATTCAACT
Found at i:12612 original size:25 final size:22
Alignment explanation
Indices: 12584--12630 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
12574 GTTTTAACTC
12584 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
12609 AATCTAATCCTAAAAGATAATA
1 AATCTAATCCTAAAAAATAATA
12631 CATCATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 3 0.14
25 4 0.19
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:13862 original size:733 final size:727
Alignment explanation
Indices: 12459--13907 Score: 2336
Period size: 733 Copynumber: 2.0 Consensus size: 727
12449 TCAAAGTTGA
* *
12459 ATGAAACCTTCTTTATATAGGGTGAGAAGTCCTTGTTGTAACATGACTAATGAATAAAGATAATG
1 ATGAAACCTCCTTTATATAGGGTGAGAAGTCCTTGTTGTAACATGACTAATGAATAAAGATAATA
*
12524 TTTCGATTCTATCCTAATTCCTAATAAAATAATAATACACTAAGAATTATGTTTTAACTCAATCT
66 TTTCGATTCTATCCTAATTCCTAATAAAATAATAATACACTAAGAATTATGTTTTAACTCAATAT
12589 TAATTCCTAATAAAATAATAAATCTAATCCTAAAAGATAATACATCATCTATATTAAATTATATT
131 TAATTCCTAATAAAATAATAAATCTAATCCTAAAAGATAATACATCATCTATATTAAATTATATT
* * *
12654 ACAAATAATCAATAAAAATATTGAAAATTCGTAATATTTATAAAATCTCATAGTAATCCCGTATA
196 ACAAATAATCAATAAAAATATTGAAAACTCGTAATATTTATAAAATCTCACAGTAATCCCATATA
* * *
12719 GGAATTTCTGCATGTGTTGTCTTTAGTAAAATGAACGAATCTTGAGTTTCCGATATAGGATTGAT
261 AGAATTTCTGCATGCGTTGTCTTCAGTAAAATGAACGAATCTTGAGTTTCCGATATAGGATTGAT
* * **
12784 GCGATTAAAAAACCGTTGGAAAGCCGGACATATTTCTAGAAGAAATGTTGATTGAATAAGATCAG
326 GCAATTAAAAAACCGTTGGAAAGCCGGACATATCTCTAGAAGAAATGTTGACCGAATAAGATCAG
* * ** *
12849 GATTCCATTCAAAAAGCAGTCGTAATTCTTCTGTTATGCTATTATTTTTTTCCAAGGCTTGTTCG
391 GATCCCATTCAAAAAGAAGTCACAA-T-TTC--TTATGCTATTATTCTTTTCCAAGGCTTGTTCG
*
12914 TGTGGATCAATTGGAAGTGCTACTCTATATTCCTTTGATGTGAGCCTTGTAATGCATGTATCACC
452 TGTGGATCAATTGGAAGTACTACTCTATATTCCTTTGATGTGAGCCTTGTAATGCATGTATCACC
*
12979 TCAATATTCTTGTGTATTTTATTTTCCATTTTATTTTATTTAACCGGGAACGACATCAATCTTAA
517 TCAATATTCTTGTGTATTTTATTTTCCATTTTATTTTATTTAACCAGGAACGACATCAATCTTAA
13044 TATTAGTTGTCGATCGTTGGTGAATATTAGTTCTCTTGGTTTTTCATATTATGTCATTTGTTTTC
582 TATTAGTTGTCGATCGTTGGTGAATATTAGTTCTCTTGGTTTTTCATATTATGTCATTTGTTTTC
* * *
13109 CTTTTTCTTAAGTTTTCCCCCTCTA-TTTTGAATAAGAATC-TGTCCTTGTGACATGTGTTTTCT
647 CTTTTTCTTAAGTTTTCCCCCTC-AGTTTTGAATAAAAATCTTGTCCTTGTGACACGCGTTTTCT
13172 CATATTTGATTTTTCAT
711 CATATTTGATTTTTCAT
* *
13189 ATGAAACCTCCTTTATATATGGTGAGGAGTCCTTGTTGTAACATGACTAATGAATAAAGATAATA
1 ATGAAACCTCCTTTATATAGGGTGAGAAGTCCTTGTTGTAACATGACTAATGAATAAAGATAATA
13254 TTTCGATTCTATCCTAATTCCTAATAAAATAATAATACACTAAGAATTAT-TTTTAACTCAATAT
66 TTTCGATTCTATCCTAATTCCTAATAAAATAATAATACACTAAGAATTATGTTTTAACTCAATAT
*
13318 TAATTCCTAATAAAATAATAAATCTAATCTTAAAAGATAATACATCATCTATATTAAATTATATT
131 TAATTCCTAATAAAATAATAAATCTAATCCTAAAAGATAATACATCATCTATATTAAATTATATT
* *
13383 ACAAATAATCAATAAAAATATTGAAAACTCGTAATATTTATAAAATCTCGCATTAATCCTCATAT
196 ACAAATAATCAATAAAAATATTGAAAACTCGTAATATTTATAAAATCTCACAGTAATCC-CATAT
** *
13448 AAGAATTTCTGCATGCGTTGTCTTCAGTAAAATGAACGTGTCTTGAGTTTCTGATATAGGATTGA
260 AAGAATTTCTGCATGCGTTGTCTTCAGTAAAATGAACGAATCTTGAGTTTCCGATATAGGATTGA
* * *
13513 TGCAATTCAAAAACCTTTGGAAAGTTAAGAGACATCCGGTCATATCTCTAGAAGAAATGTTGACC
325 TGCAATTAAAAAACCGTT-G---G--AA-AG----CCGGACATATCTCTAGAAGAAATGTTGACC
13578 GAATAAGATCAGGATCCCATTCAAAAAGAAGTCACAA-TTC-T-T-CTATTATTCTTTTCCAAGG
379 GAATAAGATCAGGATCCCATTCAAAAAGAAGTCACAATTTCTTATGCTATTATTCTTTTCCAAGG
*
13639 CTTGTTCGTGTGGATCAATTGGAAGTACTACTCTATATTCCTTTGATGTGAGCCTTGTGATGCAT
444 CTTGTTCGTGTGGATCAATTGGAAGTACTACTCTATATTCCTTTGATGTGAGCCTTGTAATGCAT
13704 GTATCACCTCAATATTCTTGTGTATTTTATTTTCCATTTTATTTTATTTAACCAGGAACGACATC
509 GTATCACCTCAATATTCTTGTGTATTTTATTTTCCATTTTATTTTATTTAACCAGGAACGACATC
** *
13769 AATCTTAATATTAGTTGTCGATCGTTGGTGGTTATTAGTTCTCTTGGTTTTTTATATTATGTCAT
574 AATCTTAATATTAGTTGTCGATCGTTGGTGAATATTAGTTCTCTTGGTTTTTCATATTATGTCAT
*
13834 TTGTTTTCCTTTTTCTTGAGTTTTCCCCCTCAGTTTTGAATAAAAATCTTTGTCCTTGTGACACG
639 TTGTTTTCCTTTTTCTTAAGTTTTCCCCCTCAGTTTTGAATAAAAATC-TTGTCCTTGTGACACG
13899 CGTTTTCTC
703 CGTTTTCTC
13908 TGCTCTTGTG
Statistics
Matches: 665, Mismatches: 39, Indels: 25
0.91 0.05 0.03
Matches are distributed among these distances:
729 132 0.20
730 189 0.28
731 1 0.00
732 1 0.00
733 251 0.38
734 2 0.00
735 23 0.03
736 2 0.00
737 2 0.00
738 3 0.00
741 59 0.09
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (727 bp):
ATGAAACCTCCTTTATATAGGGTGAGAAGTCCTTGTTGTAACATGACTAATGAATAAAGATAATA
TTTCGATTCTATCCTAATTCCTAATAAAATAATAATACACTAAGAATTATGTTTTAACTCAATAT
TAATTCCTAATAAAATAATAAATCTAATCCTAAAAGATAATACATCATCTATATTAAATTATATT
ACAAATAATCAATAAAAATATTGAAAACTCGTAATATTTATAAAATCTCACAGTAATCCCATATA
AGAATTTCTGCATGCGTTGTCTTCAGTAAAATGAACGAATCTTGAGTTTCCGATATAGGATTGAT
GCAATTAAAAAACCGTTGGAAAGCCGGACATATCTCTAGAAGAAATGTTGACCGAATAAGATCAG
GATCCCATTCAAAAAGAAGTCACAATTTCTTATGCTATTATTCTTTTCCAAGGCTTGTTCGTGTG
GATCAATTGGAAGTACTACTCTATATTCCTTTGATGTGAGCCTTGTAATGCATGTATCACCTCAA
TATTCTTGTGTATTTTATTTTCCATTTTATTTTATTTAACCAGGAACGACATCAATCTTAATATT
AGTTGTCGATCGTTGGTGAATATTAGTTCTCTTGGTTTTTCATATTATGTCATTTGTTTTCCTTT
TTCTTAAGTTTTCCCCCTCAGTTTTGAATAAAAATCTTGTCCTTGTGACACGCGTTTTCTCATAT
TTGATTTTTCAT
Found at i:13922 original size:24 final size:24
Alignment explanation
Indices: 13888--13946 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
13878 AATCTTTGTC
*
13888 CTTGTGACACGCGTTTTCTCTGCT
1 CTTGTGGCACGCGTTTTCTCTGCT
* *
13912 CTTGTGGCACGTGTTTTTTCTGCT
1 CTTGTGGCACGCGTTTTCTCTGCT
*
13936 TTTGTGGCACG
1 CTTGTGGCACG
13947 ATTCTTATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.07, C:0.24, G:0.25, T:0.44
Consensus pattern (24 bp):
CTTGTGGCACGCGTTTTCTCTGCT
Found at i:15385 original size:7 final size:7
Alignment explanation
Indices: 15370--15403 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
15360 GGTTATTATA
15370 TAAACCC
1 TAAACCC
*
15377 TAAATCC
1 TAAACCC
*
15384 TAAACCG
1 TAAACCC
15391 TAAACCC
1 TAAACCC
15398 TAAACC
1 TAAACC
15404 AACATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:18503 original size:28 final size:28
Alignment explanation
Indices: 18447--18503 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
18437 CTCTTTGTTT
* * * *
18447 ACATTATGTCGTTGAGCCATTGCTTGAA
1 ACATTATGTCGTCGAGCCAGTGATCGAA
*
18475 ACATTATGTTGTCGAGCCAGTGATCGAA
1 ACATTATGTCGTCGAGCCAGTGATCGAA
18503 A
1 A
18504 GTAATGGTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (28 bp):
ACATTATGTCGTCGAGCCAGTGATCGAA
Found at i:19900 original size:60 final size:58
Alignment explanation
Indices: 19817--19957 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 58
19807 TGACCTCCAG
* * *
19817 TTTAAATTGGT-TCTTAAATTTTTGAATATTCAAATTTTATCCTCAAAATATGACTCTCAT
1 TTTAAATTGGTCT-TTAAACTTTTGAATATTCAAATTTCAT-CTCAAAA-ATGACCCTCAT
* ** *
19877 TTTAAATTAGTCTTTAAACTTTTGAATATTCCTATTTCATCTCCAAAATGACCCTCAT
1 TTTAAATTGGTCTTTAAACTTTTGAATATTCAAATTTCATCTCAAAAATGACCCTCAT
**
19935 TTTAAATTGGTCTACAAACTTTT
1 TTTAAATTGGTCTTTAAACTTTT
19958 AAATCTTCCA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 30 0.43
59 6 0.09
60 33 0.47
61 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (58 bp):
TTTAAATTGGTCTTTAAACTTTTGAATATTCAAATTTCATCTCAAAAATGACCCTCAT
Found at i:19954 original size:58 final size:59
Alignment explanation
Indices: 19817--19970 Score: 177
Period size: 58 Copynumber: 2.6 Consensus size: 59
19807 TGACCTCCAG
* * * *
19817 TTTAAATTGGTTCTTAAATTTTTGAATATTCAAATTTTATCCTCAAAATATGACTCTCAT
1 TTTAAATTGG-TCTTAAACTTTTGAATATTCCAATTTCATCCTCAAAATATGACCCTCAT
* * *
19877 TTTAAATTAGTCTTTAAACTTTTGAATATTCCTATTTCAT-CTCCAAA-ATGACCCTCAT
1 TTTAAATTGGTC-TTAAACTTTTGAATATTCCAATTTCATCCTCAAAATATGACCCTCAT
* * *
19935 TTTAAATTGGTCTACAAACTTTTAAATCTTCCAATT
1 TTTAAATTGGTCT-TAAACTTTTGAATATTCCAATT
19971 AATTCTCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
57 1 0.01
58 39 0.49
59 8 0.10
60 32 0.40
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (59 bp):
TTTAAATTGGTCTTAAACTTTTGAATATTCCAATTTCATCCTCAAAATATGACCCTCAT
Found at i:26206 original size:2 final size:2
Alignment explanation
Indices: 26201--26246 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
26191 ATTTTTTTAA
26201 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
26243 AT AT
1 AT AT
26247 TATCAATTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29372 original size:29 final size:29
Alignment explanation
Indices: 29319--29384 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
29309 TCATTTTCAT
*
29319 CATTAAATTTTTAAAATTTATAAAATAAG
1 CATTAAATTTTTAAAATTTACAAAATAAG
* * *
29348 CATTAAATTTATTAAGA-TTACAAAATTAT
1 CATTAAATTT-TTAAAATTTACAAAATAAG
29377 CATTAAAT
1 CATTAAAT
29385 ATAATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (29 bp):
CATTAAATTTTTAAAATTTACAAAATAAG
Found at i:32939 original size:14 final size:14
Alignment explanation
Indices: 32921--32958 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
32911 TTTTCCATTT
*
32921 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
32936 TTTTT-TTTCTCTC
1 TTTTTCTTTCTCTC
32949 TTTTTCTTTC
1 TTTTTCTTTC
32959 GAACAACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:32980 original size:18 final size:17
Alignment explanation
Indices: 32949--32991 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
32939 TTTTTCTCTC
*
32949 TTTTTCTTTCGAACAACT
1 TTTTTTTTTCGAAC-ACT
* *
32967 TTTTTTTTTTGAACTCT
1 TTTTTTTTTCGAACACT
32984 TTTTTTTT
1 TTTTTTTT
32992 CTTCTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTTTTTTCGAACACT
Found at i:40421 original size:19 final size:18
Alignment explanation
Indices: 40388--40448 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
40378 ATTATTTTTT
*
40388 ATATTAATATATTTATGTAA
1 ATATT-ATATTTTTAT-TAA
40408 ATATTATATTTTTATTAA
1 ATATTATATTTTTATTAA
* *
40426 A-ATAATATTTATA-TAA
1 ATATTATATTTTTATTAA
*
40442 TTATTAT
1 ATATTAT
40449 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.09
17 14 0.40
18 4 0.11
19 9 0.26
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTATATTTTTATTAA
Found at i:40454 original size:36 final size:33
Alignment explanation
Indices: 40367--40455 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
40357 AGTATTTTTT
* *
40367 TTTAAATAGTTATTATTT-TTTATATTAATATA
1 TTTATATAATTATTATTTATTTATATTAATATA
* * *
40399 TTTATGTAAATATTATATT-TTTAT-TAAAATAATA
1 TTTATATAATTATTAT-TTATTTATAT-TAAT-ATA
40433 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTATTTA
40456 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 13 0.28
33 12 0.26
34 21 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTATATAATTATTATTTATTTATATTAATATA
Found at i:40618 original size:17 final size:17
Alignment explanation
Indices: 40596--40649 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
40586 AATGTTAATA
40596 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
40613 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
40630 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
40647 TTT
1 TTT
40650 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:45328 original size:18 final size:17
Alignment explanation
Indices: 45274--45322 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
45264 TTGGACTCCT
* *
45274 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
45292 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
45310 AGTGCATTCGATG
1 AGTGCA-TCGATG
45323 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:45407 original size:64 final size:64
Alignment explanation
Indices: 45274--45482 Score: 189
Period size: 64 Copynumber: 3.2 Consensus size: 64
45264 TTGGACTCCT
* * * *
45274 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
* ** * *
45335 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATC
45400 AG
63 AG
* * *
45402 AGTGCATCGATGCATGGAGAGTG-ATTC-AGTGCATGGAATGCATTCGATGTTTCAATTTATTCA
1 AGTGCATCGATGCATGGAGAGTGCA-TCGA-TGCATGAAATGCATTCGATGTTTCAATTAAATCA
45465 TTG
64 --G
45468 A-TGCATCGATGCATG
1 AGTGCATCGATGCATG
45483 CCTTTGAAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 15
0.80 0.11 0.10
Matches are distributed among these distances:
63 3 0.02
64 96 0.79
65 14 0.12
66 6 0.05
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG
Found at i:48039 original size:24 final size:23
Alignment explanation
Indices: 47968--48047 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
47958 CATGGTCTTG
**
47968 TGCATCGATGCACATTCAAGTAA
1 TGCATCGATGCACATTCAAGGGA
* *
47991 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
48012 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
48036 TGCATCGATGCA
1 TGCATCGATGCA
48048 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
23 11 0.24
24 17 0.37
25 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:48060 original size:44 final size:42
Alignment explanation
Indices: 47945--48067 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
47935 AAAACCCGAC
* *
47945 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
** * **
47988 TAATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
48033 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
48068 TTAAGCACAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
43 16 0.26
44 28 0.45
45 18 0.29
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:63626 original size:64 final size:64
Alignment explanation
Indices: 63558--63677 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 64
63548 AAATAGGCTG
** *
63558 GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAAA
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCAAA
* **
63622 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATT
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATT
63678 TATTCATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCAAA
Found at i:63645 original size:19 final size:18
Alignment explanation
Indices: 63620--63669 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
63610 AATTAAATCA
63620 AAGTGCATCGATGCATGG
1 AAGTGCATCGATGCATGG
*
63638 AGAGTGCATCGGTGCATGG
1 A-AGTGCATCGATGCATGG
63657 AA-TGCATTCGATG
1 AAGTGCA-TCGATG
63670 TTTCAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 17 0.61
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
AAGTGCATCGATGCATGG
Found at i:66255 original size:35 final size:34
Alignment explanation
Indices: 66170--66256 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
66160 AAAATAATTT
*
66170 TAAATACAACAAATTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
66204 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
66242 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
66257 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:69370 original size:35 final size:34
Alignment explanation
Indices: 69330--69407 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
69320 AACACAATCC
69330 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTT-ATTCTAAACCCTAAATTTCAAAATAAT
* * * *
69365 TCAATTATATTTTAAACCTTAAATTTTAAAATACT
1 TCAATT-TATTCTAAACCCTAAATTTCAAAATAAT
69400 TCAATTTA
1 TCAATTTA
69408 GGATTTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 35 0.92
36 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (34 bp):
TCAATTTATTCTAAACCCTAAATTTCAAAATAAT
Found at i:69441 original size:35 final size:35
Alignment explanation
Indices: 69402--69476 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
69392 AAAATACTTC
*
69402 AATTTAGGATTTAGAATGTAATT-AAAGTATTTTGG
1 AATTTAGGATTTAGAATGTAATTGAAA-TATTTTAG
* *
69437 AATTTGGGGTTTAGAATGTAATTGAAATATTTTAG
1 AATTTAGGATTTAGAATGTAATTGAAATATTTTAG
69472 AATTT
1 AATTT
69477 TGAACATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 33 0.92
36 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (35 bp):
AATTTAGGATTTAGAATGTAATTGAAATATTTTAG
Found at i:75383 original size:8 final size:8
Alignment explanation
Indices: 75370--75410 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
75360 CTCATTTTCA
75370 GAGAATTT
1 GAGAATTT
75378 GAGAATTT
1 GAGAATTT
*
75386 -AGAGTTT
1 GAGAATTT
*
75393 GGGAATTT
1 GAGAATTT
75401 GAGAATTT
1 GAGAATTT
75409 GA
1 GA
75411 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:75956 original size:125 final size:126
Alignment explanation
Indices: 75478--76205 Score: 1390
Period size: 126 Copynumber: 5.8 Consensus size: 126
75468 CTATAATCGG
75478 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
75543 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
75604 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
75669 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
75730 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
75795 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
75856 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
75920 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
75981 TTCACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
76045 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
76106 TTCACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
76171 TCATTGCCCTATTATGTCACTCATGT-CCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
76206 ATAACTTAAA
Statistics
Matches: 592, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
125 256 0.43
126 336 0.57
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:76141 original size:251 final size:252
Alignment explanation
Indices: 75478--76205 Score: 1417
Period size: 251 Copynumber: 2.9 Consensus size: 252
75468 CTATAATCGG
75478 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
75543 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
75608 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
75673 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
75730 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
75795 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
75860 CTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
*
75924 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
75981 TTCACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
76045 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
*
76110 CTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
76175 TGCCCTATTATGTCACTCATGT-CCTCGGGGA
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
76206 ATAACTTAAA
Statistics
Matches: 473, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
250 128 0.27
251 191 0.40
252 154 0.33
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (252 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
Found at i:76653 original size:33 final size:34
Alignment explanation
Indices: 76592--76691 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
76582 AAATTTAATG
*
76592 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
76626 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
76659 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
76692 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:77298 original size:21 final size:21
Alignment explanation
Indices: 77210--77303 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
77200 TATGGTATAA
*
77210 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
77231 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
77252 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
77273 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
77294 AACCCTGCGG
1 AACCCTGCGG
77304 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:77333 original size:21 final size:21
Alignment explanation
Indices: 77307--77354 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
77297 CCTGCGGAGA
*
77307 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
77328 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
77349 GGGCAT
1 TGGCAT
77355 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:79112 original size:34 final size:32
Alignment explanation
Indices: 79072--79155 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
79062 AATTCTAAAT
79072 AAATAATAATTATATAAATATTATTTAATAAAAA
1 AAATAATAATTATATAAATA-TA-TTAATAAAAA
* * *
79106 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* *
79138 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
79156 AAAATACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 23 0.53
33 2 0.05
34 18 0.42
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:79139 original size:32 final size:34
Alignment explanation
Indices: 79067--79146 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
79057 TTAATAATTC
*
79067 TAAATAAATAATAATTATATAAATATTATTTAATA
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
* *
79102 AAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
79134 TAAAAAATAATAA
1 TAAAAAATAATAA
79147 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
32 17 0.43
33 2 0.05
34 18 0.45
35 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:79171 original size:34 final size:34
Alignment explanation
Indices: 79099--79178 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
79089 ATATTATTTA
* * *
79099 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAAAAATAATATTTACATAAAAATACTAAC
79133 ATAAAAAATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAAAA-AATAA-TATTTACATAAAAATACTAAC
79167 ATAAAAATAAAT
1 ATAAAAA-AAAT
79179 TTTTACCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 27 0.68
35 7 0.17
36 6 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAAAAATAATATTTACATAAAAATACTAAC
Found at i:81905 original size:18 final size:19
Alignment explanation
Indices: 81882--81927 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
81872 GAAATTTAAG
81882 TAATAAATAAACATAT-CA
1 TAATAAATAAACATATACA
*
81900 TAATAAA-CAACATATACA
1 TAATAAATAAACATATACA
81918 TATATAAATA
1 TA-ATAAATA
81928 TGTAAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.30
18 11 0.48
19 5 0.22
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (19 bp):
TAATAAATAAACATATACA
Found at i:81913 original size:17 final size:19
Alignment explanation
Indices: 81891--81925 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
81881 GTAATAAATA
81891 AACATAT-CATA-ATAAAC
1 AACATATACATATATAAAC
81908 AACATATACATATATAAA
1 AACATATACATATATAAA
81926 TATGTAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (19 bp):
AACATATACATATATAAAC
Found at i:83977 original size:40 final size:40
Alignment explanation
Indices: 83914--83990 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
83904 GTTATCTAGG
* * *
83914 GGTGACACGACTCCTACGCGATGAGGAGATCTGGTCAGGA
1 GGTGACAAGACTCATACGCGATGAAGAGATCTGGTCAGGA
* * *
83954 GGTGACAAGGCTCATACGTGATGAAGAGTTCTGGTCA
1 GGTGACAAGACTCATACGCGATGAAGAGATCTGGTCA
83991 TCTTTAGGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (40 bp):
GGTGACAAGACTCATACGCGATGAAGAGATCTGGTCAGGA
Found at i:84030 original size:134 final size:134
Alignment explanation
Indices: 83819--84111 Score: 383
Period size: 134 Copynumber: 2.2 Consensus size: 134
83809 GTTGTCGGGT
* * * *
83819 GGATGACACGACTCATACGTGATGAAGAGTTTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTC
1 GGATGACAAGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACTCGGTTC
* * *
83884 TTGCGTGATGAGGAC-GACTGGTTATCTAGGGGTGACACGACTCCTACGCGATGAGGAGATCTGG
66 CTACGTGATGAGGACAG-CTGGTTATCTAAGGGTGACACGACTCCTACGCGATGAGGAGATCTGG
83948 TCAGG
130 TCAGG
* *
83953 AGG-TGACAAGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAAGTCGGTT
1 -GGATGACAAGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACTCGGTT
* * ** * * *
84017 CCTACTTGGTGAGGACAGCTGGTTATCTAAGTTTGACGCGGCTCCTACGTGATGAGGAGATCTGG
65 CCTACGTGATGAGGACAGCTGGTTATCTAAGGGTGACACGACTCCTACGCGATGAGGAGATCTGG
84082 TCAGG
130 TCAGG
* * *
84087 GGATGACACGGTTCCTACGTGATGA
1 GGATGACAAGGCTCATACGTGATGA
84112 GGACAGCTGG
Statistics
Matches: 137, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
133 2 0.01
134 132 0.96
135 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (134 bp):
GGATGACAAGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACTCGGTTC
CTACGTGATGAGGACAGCTGGTTATCTAAGGGTGACACGACTCCTACGCGATGAGGAGATCTGGT
CAGG
Found at i:84282 original size:35 final size:35
Alignment explanation
Indices: 84237--84309 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
84227 GGAGAGAAAA
*
84237 TTTGTTTCAAGGGAAACAATCTCAAAGATATTTGT
1 TTTGTTTCAAGGGAAACAAACTCAAAGATATTTGT
*
84272 TTTGTTTCAAGGGAAACAAACTCAAAGATTTTTGT
1 TTTGTTTCAAGGGAAACAAACTCAAAGATATTTGT
84307 TTT
1 TTT
84310 AATAGAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (35 bp):
TTTGTTTCAAGGGAAACAAACTCAAAGATATTTGT
Found at i:84361 original size:66 final size:66
Alignment explanation
Indices: 84285--84523 Score: 188
Period size: 66 Copynumber: 3.6 Consensus size: 66
84275 GTTTCAAGGG
* * * *
84285 AAACAAACTCAAAGATTTTTGTTTTAATAGAAATTGTCTCAAAAGA-ACAAAACTTTGTTTTCAT
1 AAACAAACTCAAAGATTTTT-CTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTTCAT
84349 AA
65 AA
* * * *
84351 AAACAGACTCAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGATAAAATTTTG-TTTC-TA
1 AAACAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTTCAT-
84414 AA
65 AA
* * * * * * * *
84416 GAAACATACTCAAATA-TTCT-TTC-AAAGAAACTTTCTCAAAAGAGACGAAATTTTGTTATCAA
1 -AAACAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTTCAT
84478 AA
65 AA
* * *
84480 GAAATAGACTCAAAGATCATTTGT-TTCAAAAGAAA-TGACTCAAA
1 -AAACAAACTCAAAGAT--TTT-TCTTCAAAAGAAACTGTCTCAAA
84524 GATGATGTTT
Statistics
Matches: 140, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
63 28 0.20
64 22 0.16
65 29 0.21
66 41 0.29
67 2 0.01
68 11 0.08
69 7 0.05
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (66 bp):
AAACAAACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAAAGAGACAAAACTTTGTTTTCATA
A
Found at i:84522 original size:30 final size:32
Alignment explanation
Indices: 84467--84526 Score: 106
Period size: 30 Copynumber: 1.9 Consensus size: 32
84457 GAGACGAAAT
84467 TTTGTTATCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTATCAAAAGAAATAGACTCAAAGATCA
84499 TTTGTT-TCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTATCAAAAGAAATAGACTCAAAGAT
84527 GATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 11 0.39
31 11 0.39
32 6 0.21
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (32 bp):
TTTGTTATCAAAAGAAATAGACTCAAAGATCA
Found at i:84609 original size:36 final size:36
Alignment explanation
Indices: 84564--84701 Score: 147
Period size: 36 Copynumber: 3.8 Consensus size: 36
84554 ATAATTTGGA
* *
84564 AAATAGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
84600 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
84636 AAATTGTCTCAAGCGAGACAA-AGTTTATTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
** *
84671 AAAACGATCTCAAGTGAGACCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
84702 AATGTGAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 8 0.09
36 75 0.87
37 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:84988 original size:214 final size:207
Alignment explanation
Indices: 84640--85123 Score: 605
Period size: 212 Copynumber: 2.3 Consensus size: 207
84630 TTAGAGAAAT
*
84640 TGTCTCAAGCGAGAC-AAAGTTTATTTTTGAGAAAACGATCTCAAGTGAGACCAACTTTGTTTAA
1 TGTCTCAAGCGAGACGAAA-TTT-TTTTTGAGAAAACAATCTCAAGTGAGACCAACTTTGTTTAA
*
84704 TGTGAAACAAATTCGAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTT
64 TGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTT
* **
84769 TGAAAGAAATAACAATTCTCAAGAGAGATTAATTTTTGTTTCAAGTGAATCAAATTCAAAATTTG
129 TGAAAGAAACAACAA-TCTCAAGAGAGATTAA-TTTTGTTTCAAGTGAAGAAAATTCAAAATTTG
* *
84834 TATATCAGAGGAAAAAAA
192 CATATCAAAGG--AAAAA
** *
84852 TGTCTCAAGCGAGACGAAATTTTTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTTT
1 TGTCTCAAGCGAGACGAAATTTTTTTTG--AG-AA-AACAATCTCAAGTGAGACCAACTTTG-TT
* * *
84917 TAA-GTGAAGCAAATTCAAAATTTGTA-TCTCAAAGGAAAAATGTCTCAAGCGAGACGAAGTTTG
61 TAATGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTTG
* * *
84980 TTTTGAAAGAGACAACAATCTCAAGTGAGATTAATTTTGTTTTAAGTGAAGAAAATTCAAAATTT
126 TTTTGAAAGAAACAACAATCTCAAGAGAGATTAATTTTGTTTCAAGTGAAGAAAATTCAAAATTT
*
85045 GCATCTCAAAGGAAAAA
191 GCATATCAAAGGAAAAA
* * * * ** * * *
85062 TGTCTCAAGTGAGACGAAGTTTGTTTTAAGATAAATTATCTTAAGTGAGACAAAATTTGTTT
1 TGTCTCAAGCGAGACGAAATTTTTTTTGAGA-AAACAATCTCAAGTGAGACCAACTTTGTTT
85124 TTCAATAACT
Statistics
Matches: 238, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
206 3 0.01
207 21 0.09
208 3 0.01
210 29 0.12
211 6 0.03
212 55 0.23
213 20 0.08
214 53 0.22
215 43 0.18
216 5 0.02
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (207 bp):
TGTCTCAAGCGAGACGAAATTTTTTTTGAGAAAACAATCTCAAGTGAGACCAACTTTGTTTAATG
TGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTG
AAAGAAACAACAATCTCAAGAGAGATTAATTTTGTTTCAAGTGAAGAAAATTCAAAATTTGCATA
TCAAAGGAAAAA
Found at i:84998 original size:105 final size:105
Alignment explanation
Indices: 84640--85088 Score: 602
Period size: 105 Copynumber: 4.3 Consensus size: 105
84630 TTAGAGAAAT
* * * ** *
84640 TGTCTCAAGCGAGACAAAGTTTATTTTTG--AG-AA-AACGATCTCAAGTGAGACCAACTTTG-T
1 TGTCTCAAGCGAGACGAAGTTT-GTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTT
* *
84700 TTAATGTGAAACAAATTCGAAATTTGTATTCTCAAAGGAAAAA
65 TTAA-GTGAAGCAAATTCAAAATTTGTA-TCTCAAAGGAAAAA
* * * *
84743 TGTCTCAAACGAGACGAAATTTGTTTTGAAAGAAATAACAATTCTCAAGAGAGATTAATTTTTGT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTGAAAGAAACAACAA-TCTCAAGTGAGATTAA-TTTTGT
* * * *
84808 TTCAAGTGAATCAAATTCAAAATTTGTATATCAGAGGAAAAAAA
64 TTTAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGG--AAAAA
* *
84852 TGTCTCAAGCGAGACGAAATTTTTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTTT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTTT
84917 TAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGGAAAAA
66 TAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGGAAAAA
*
84957 TGTCTCAAGCGAGACGAAGTTTGTTTTGAAAGAGACAACAATCTCAAGTGAGATTAATTTTGTTT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTTT
* *
85022 TAAGTGAAGAAAATTCAAAATTTGCATCTCAAAGGAAAAA
66 TAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGGAAAAA
*
85062 TGTCTCAAGTGAGACGAAGTTTGTTTT
1 TGTCTCAAGCGAGACGAAGTTTGTTTT
85089 AAGATAAATT
Statistics
Matches: 309, Mismatches: 28, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
102 5 0.02
103 19 0.06
104 2 0.01
105 133 0.43
106 4 0.01
107 59 0.19
108 40 0.13
109 47 0.15
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (105 bp):
TGTCTCAAGCGAGACGAAGTTTGTTTTGAAAGAAACAACAATCTCAAGTGAGATTAATTTTGTTT
TAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGGAAAAA
Found at i:85121 original size:36 final size:35
Alignment explanation
Indices: 85056--85253 Score: 184
Period size: 36 Copynumber: 5.6 Consensus size: 35
85046 CATCTCAAAG
* * *
85056 GAAAAATGTCTCAAGTGAGACGAAGTTTGTTTTAA
1 GAAAACTGTCTCAAGTGAGACAAAATTTGTTTTAA
* * * *
85091 GATAAATTATCTTAAGTGAGACAAAATTTGTTTTTCA
1 GA-AAACTGTCTCAAGTGAGACAAAATTTG-TTTTAA
* * *
85128 -ATAACTGTCTCAAGCGAGACAAAATTTTGTTTCAA
1 GAAAACTGTCTCAAGTGAGACAAAA-TTTGTTTTAA
* * *
85163 GAAAACTGTCTCAAGTTAGACAAAATTTGATTTGA
1 GAAAACTGTCTCAAGTGAGACAAAATTTGTTTTAA
* * *
85198 G-AAATTGTCTCAAGCGAGACAAAGTTTGTTTTTAA
1 GAAAACTGTCTCAAGTGAGACAAAATTTG-TTTTAA
* *
85233 GAAAACTATCTCTAGTGAGAC
1 GAAAACTGTCTCAAGTGAGAC
85254 GACACTTTGT
Statistics
Matches: 128, Mismatches: 29, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
34 23 0.18
35 37 0.29
36 63 0.49
37 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (35 bp):
GAAAACTGTCTCAAGTGAGACAAAATTTGTTTTAA
Found at i:85147 original size:71 final size:70
Alignment explanation
Indices: 85062--85267 Score: 220
Period size: 71 Copynumber: 2.9 Consensus size: 70
85052 AAAGGAAAAA
* * *
85062 TGTCTCAAGTGAGACGAAGTTTGTTTTAAGATAAATTATCTTAAGTGAGACAAAATTTGTTTTTC
1 TGTCTCAAGCGAGACAAAGTTTGTTTTAAGA-AAACTATCTTAAGTGAGACAAAATTTGTTTTTC
85127 A-ATAAC
65 AGA-AAC
* * * * * * *
85133 TGTCTCAAGCGAGACAAAATTTTGTTTCAAGAAAACTGTCTCAAGTTAGACAAAATTTG-ATTTG
1 TGTCTCAAGCGAGAC-AAAGTTTGTTTTAAGAAAACTATCTTAAGTGAGACAAAATTTGTTTTTC
*
85197 AGAAAT
65 AGAAAC
* *
85203 TGTCTCAAGCGAGACAAAGTTTGTTTTTAAGAAAACTATCTCT-AGTGAGACGACACTTTGTTTT
1 TGTCTCAAGCGAGACAAAGTTTG-TTTTAAGAAAACTATCT-TAAGTGAGAC-AAAATTTGTTTT
85267 T
63 T
85268 TTAAGAAAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
69 7 0.06
70 43 0.39
71 44 0.40
72 16 0.15
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (70 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAACTATCTTAAGTGAGACAAAATTTGTTTTTCA
GAAAC
Found at i:85218 original size:70 final size:70
Alignment explanation
Indices: 85062--85253 Score: 226
Period size: 70 Copynumber: 2.7 Consensus size: 70
85052 AAAGGAAAAA
* * * * *
85062 TGTCTCAAGTGAGACGAAGTTTGTTTTAAGATAAATTATCTTAAGTGAGACAAAATTTGTTTTTC
1 TGTCTCAAGCGAGACAAAGTTTGTTTTAAGA-AAACTATCTCAAGTGAGACAAAATTTGTATTTC
85127 AATAAC
65 AATAAC
* * * * *
85133 TGTCTCAAGCGAGACAAAATTTTGTTTCAAGAAAACTGTCTCAAGTTAGACAAAATTTG-ATTTG
1 TGTCTCAAGCGAGAC-AAAGTTTGTTTTAAGAAAACTATCTCAAGTGAGACAAAATTTGTATTTC
*
85197 AGA-AAT
65 A-ATAAC
*
85203 TGTCTCAAGCGAGACAAAGTTTGTTTTTAAGAAAACTATCTCTAGTGAGAC
1 TGTCTCAAGCGAGACAAAGTTTG-TTTTAAGAAAACTATCTCAAGTGAGAC
85254 GACACTTTGT
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
69 7 0.07
70 44 0.43
71 38 0.37
72 13 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (70 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAACTATCTCAAGTGAGACAAAATTTGTATTTCA
ATAAC
Found at i:86799 original size:16 final size:15
Alignment explanation
Indices: 86778--86849 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 15
86768 TTGTATGTGC
86778 TCTTTGTCCTCTTTTT
1 TCTTTGT-CTCTTTTT
86794 TCTTTGT-T-TTTTT
1 TCTTTGTCTCTTTTT
*
86807 TCTTTCTCTCTTTGTT
1 TCTTTGTCTCTTT-TT
*
86823 TCTTTCTCT-TTGATTT
1 TCTTTGTCTCTT--TTT
86839 TCTTTGT-TCTT
1 TCTTTGTCTCTT
86850 CGCTTTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
13 11 0.23
14 2 0.04
15 6 0.12
16 28 0.58
17 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.07, T:0.72
Consensus pattern (15 bp):
TCTTTGTCTCTTTTT
Found at i:88168 original size:20 final size:20
Alignment explanation
Indices: 88145--88183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
88135 CTTAAAAATA
*
88145 AAATGCAGATACAAAAATGC
1 AAATGCAAATACAAAAATGC
*
88165 AAATGCAAATGCAAAAATG
1 AAATGCAAATACAAAAATG
88184 TTGATCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATGCAAATACAAAAATGC
Found at i:96103 original size:20 final size:18
Alignment explanation
Indices: 96065--96117 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
96055 TTATAAATCA
*
96065 TTTTTCAAAATTTAATTTT
1 TTTTTCAAAA-TCAATTTT
96084 GTTTTTCAAAATCAACTTTT
1 -TTTTTCAAAATCAA-TTTT
*
96104 TCTTTCAAAATCAA
1 TTTTTCAAAATCAA
96118 ATCATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTTCAAAATCAATTTT
Found at i:98177 original size:44 final size:44
Alignment explanation
Indices: 98129--98266 Score: 144
Period size: 44 Copynumber: 3.2 Consensus size: 44
98119 ACCTTGAGAG
98129 TATCGATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAA
1 TATCGATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAA
* * *** *
98173 TATCGGA-ACTGT-TC--A--TATAGTATCGGTACTGTAAGAACAA
1 TATC-GATACT-TCTCTTACCTTTAGTATCAGTACCACATGAACAA
* *
98213 TATCAATACTTCTCTTACCTTTGGTATCAGTACCACATGAACAA
1 TATCGATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAA
98257 TATCGATACT
1 TATCGATACT
98267 GTTCATATAA
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
39 2 0.03
40 28 0.39
42 2 0.03
44 36 0.51
45 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (44 bp):
TATCGATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAA
Found at i:98246 original size:84 final size:84
Alignment explanation
Indices: 98129--98308 Score: 299
Period size: 84 Copynumber: 2.1 Consensus size: 84
98119 ACCTTGAGAG
* *
98129 TATCGATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAATATCGGA-ACTGTTCATATAG
1 TATCAATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAATATC-GATACTGTTCATATAA
98193 TATCGGTACTGTAAGAACAA
65 TATCGGTACTGTAAGAACAA
*
98213 TATCAATACTTCTCTTACCTTTGGTATCAGTACCACATGAACAATATCGATACTGTTCATATAAT
1 TATCAATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAATATCGATACTGTTCATATAAT
*
98278 ATCGGTATTGTAAGAACAA
66 ATCGGTACTGTAAGAACAA
*
98297 TATCAGTACTTC
1 TATCAATACTTC
98309 ATACCTAGAA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 2 0.02
84 88 0.98
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (84 bp):
TATCAATACTTCTCTTACCTTTAGTATCAGTACCACATGAACAATATCGATACTGTTCATATAAT
ATCGGTACTGTAAGAACAA
Found at i:100325 original size:6 final size:6
Alignment explanation
Indices: 100314--100356 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
100304 TAATTTAAGA
100314 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT T
100357 TTTATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TAATAT
Found at i:100569 original size:2 final size:2
Alignment explanation
Indices: 100562--100596 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
100552 TGAGATTAAT
100562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
100597 TAATTACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104835 original size:47 final size:47
Alignment explanation
Indices: 104784--104878 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 47
104774 TGTAATTTGA
*
104784 TTATTGAAACTTACCATCTAATAA-AGATGTATCATCATGTAATTCAG
1 TTATTGAAACTTACCATCTAATAAGA-ATGTATCAGCATGTAATTCAG
** * * * *
104831 TTATTGAAGTTTACCATTTGATAAGAATGTATTAGCCTGTAATTCAG
1 TTATTGAAACTTACCATCTAATAAGAATGTATCAGCATGTAATTCAG
104878 T
1 T
104879 GATTCTTCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 39 0.98
48 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (47 bp):
TTATTGAAACTTACCATCTAATAAGAATGTATCAGCATGTAATTCAG
Found at i:107259 original size:2 final size:2
Alignment explanation
Indices: 107254--107335 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
107244 TTGAATTCTC
107254 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
107296 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
107336 CTATTGATAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109546 original size:21 final size:22
Alignment explanation
Indices: 109515--109555 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
109505 TCTTATTGGC
109515 GTCTTATCGAGCAAGATGATAA
1 GTCTTATCGAGCAAGATGATAA
*
109537 GTCTT-TCGAGCATGATGAT
1 GTCTTATCGAGCAAGATGAT
109556 TAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (22 bp):
GTCTTATCGAGCAAGATGATAA
Found at i:110893 original size:42 final size:43
Alignment explanation
Indices: 110813--110916 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 43
110803 CGAAGGTCTT
* * * *
110813 ATAGATGGCCCAAAGGACTT-ATCATCTTGCTCGAAAGAC-TA
1 ATAGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
*
110854 ATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
1 ATAGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
* *
110897 CT-GATGGCCTGAAGGATTTA
1 ATAGATGGCCCGAAGGATTTA
110917 CTAATTTTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 17 0.32
42 33 0.62
43 3 0.06
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (43 bp):
ATAGATGGCCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
Found at i:111099 original size:260 final size:259
Alignment explanation
Indices: 110489--111301 Score: 1155
Period size: 258 Copynumber: 3.1 Consensus size: 259
110479 TTACTGGGTA
* * * *
110489 AGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTGTCTGAAGGTCT
1 AGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCT
* * * * * * * ** * *
110554 CATAGATAGCCCGAACGACTTATAATCCTGCTTGAAAGACTGACAGATGGTCCAAAGGATTTAAT
66 AATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGATTTAAG
* * * * * * * *
110619 CATCATGCTCGAAAGACTTACTAATAGCCCGAATGACTTACCAATTTTGGAAATAGTCTACTAGG
131 CATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTTACTAATTTTGGAAATAATTTACTGGG
* *
110684 TAAGAAACTTT-AAATATCGCTTTCTTACTTTTCAAAAATTTCATTTTATG-AAAACATTAAATA
196 TAAGAAACTTTGAAA-ATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAACATTAAATG
**
110747 AGAAACTTTGAAAATTGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCT
1 AGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCT
* * *
110812 TATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTAATAGATGACCCGAAGGATTTAAG
66 AATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGATTTAAG
* * *
110877 CATCATGCTCGAAAGACTTACTGATGGCCTGAAGGATTTACTAATTTTAGAAATAATTTACTGGG
131 CATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTTACTAATTTTGGAAATAATTTACTGGG
* *
110942 TATGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAAGATTTAAATG
196 TAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAACA-TTAAATG
* * *
111007 AGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATCCTGCCCAAAGGTCT
1 AGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCT
* * *
111072 AATAGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTAAG
66 AATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGATTTAAG
*
111137 CATCATGTTCGAAAGACTTACTGATGGCCAGAAGGACTTACTAATTTTGGAAATAATTTACTGGG
131 CATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTTACTAATTTTGGAAATAATTTACTGGG
* * * *
111202 TAAGAAACTTTGGAAACCACTTTCTTACTTTTCAAAAATTTCATTTTCT-AAACACATTAAATG
196 TAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAACATTAAATG
* *
111265 AGAAAATTTGAAAATCGCTTTCTCATTTTTCGAAAAT
1 AGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAAT
111302 AACTTAATGG
Statistics
Matches: 494, Mismatches: 58, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
258 250 0.51
259 13 0.03
260 231 0.47
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (259 bp):
AGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCT
AATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGATTTAAG
CATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTTACTAATTTTGGAAATAATTTACTGGG
TAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAACATTAAATG
Found at i:112398 original size:14 final size:13
Alignment explanation
Indices: 112372--112396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112362 TTTATTTTCA
112372 AAATTTGAAAAAT
1 AAATTTGAAAAAT
112385 AAATTTGAAAAA
1 AAATTTGAAAAA
112397 ATTCAAAAAT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATTTGAAAAAT
Done.