Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002686.1 Hibiscus syriacus cultivar Beakdansim tig00005550_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: 141164
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1866 original size:20 final size:20
Alignment explanation
Indices: 1841--1879 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1831 GGCAGGTTCT
1841 AATTCCCAGCCTGTAGTGCA
1 AATTCCCAGCCTGTAGTGCA
1861 AATTCCCAGCCTGTAGTGC
1 AATTCCCAGCCTGTAGTGC
1880 CATTTGCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (20 bp):
AATTCCCAGCCTGTAGTGCA
Found at i:3803 original size:41 final size:41
Alignment explanation
Indices: 3635--3855 Score: 159
Period size: 43 Copynumber: 5.3 Consensus size: 41
3625 CTTTAAGCTT
** * *
3635 TAGCGGCGTTT-T-TAAATAACGCCACTAAAGTACGAGTTTA
1 TAGCGGCGTTTGTATAAA-AAAACCACTAAAGTATGAGTCTA
* * *
3675 TAGCTGCATTT-T-TAAACACAAACGCCACTAAATTATGAGTCTA
1 TAGCGGCGTTTGTATAAA-A-AAA--CCACTAAAGTATGAGTCTA
*
3718 TAGCGGCGTTT-TA-AAACATAAACGCCACTAAAGTATGAGCCTA
1 TAGCGGCGTTTGTATAAA-A-AAA--CCACTAAAGTATGAGTCTA
* *
3761 TAGCGGCGTTTGTATAAAAATACCATTAAAGTATGAGTCTA
1 TAGCGGCGTTTGTATAAAAAAACCACTAAAGTATGAGTCTA
* * ** *
3802 TAGCGGCGTTTATATATAAACGCCACTAAAGTACT-ACTCTA
1 TAGCGGCGTTTGTATAAAAAAACCACTAAAGTA-TGAGTCTA
*
3843 TTGCGGCGTTTGT
1 TAGCGGCGTTTGT
3856 TGAAAATCCA
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
40 15 0.10
41 62 0.41
42 1 0.01
43 66 0.44
44 3 0.02
45 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAAAACCACTAAAGTATGAGTCTA
Found at i:3849 original size:82 final size:84
Alignment explanation
Indices: 3703--3855 Score: 224
Period size: 82 Copynumber: 1.8 Consensus size: 84
3693 CAAACGCCAC
*
3703 TAAATTATGAGTCTATAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGC
1 TAAAGTATGAGTCTATAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGC
3768 GTTTGTATAAAAATACCAT
66 GTTTGTATAAAAATACCAT
* * *
3787 TAAAGTATGAGTCTATAGCGGCG-TTT-ATATATAAACGCCACTAAAGTACT-A-CTCTATTGCG
1 TAAAGTATGAGTCTATAGCGGCGTTTTAAAACATAAACGCCACTAAAGTA-TGAGC-CTATAGCG
3848 GCGTTTGT
64 GCGTTTGT
3856 TGAAAATCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
81 1 0.02
82 36 0.57
83 4 0.06
84 22 0.35
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (84 bp):
TAAAGTATGAGTCTATAGCGGCGTTTTAAAACATAAACGCCACTAAAGTATGAGCCTATAGCGGC
GTTTGTATAAAAATACCAT
Found at i:3883 original size:39 final size:40
Alignment explanation
Indices: 3840--3941 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
3830 AAGTACTACT
* * * *
3840 CTATTGCGGCGTTTGTTGAAAAT-CCACTATAGATGAATC
1 CTATTACGGCGTTTATTAAAAATGCCACTATAGATGAACC
* *
3879 CTATTACGACGTTTATTAAAAATGCCACTATAGATTAACC
1 CTATTACGGCGTTTATTAAAAATGCCACTATAGATGAACC
*
3919 CTATTACGGCATTTATATAAAAA
1 CTATTACGGCGTTTAT-TAAAAA
3942 CGCCGCTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.36
40 28 0.53
41 6 0.11
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (40 bp):
CTATTACGGCGTTTATTAAAAATGCCACTATAGATGAACC
Found at i:13202 original size:2 final size:2
Alignment explanation
Indices: 13195--13255 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
13185 CTATCCTAAA
13195 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
13237 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
13256 AACAGGAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19610 original size:47 final size:45
Alignment explanation
Indices: 19542--19667 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
19532 ATAAAATCTA
*
19542 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
19587 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* ** *
19634 TTGCCA-TTATTCTGTAAGCTCATAAGCTTATTTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
19668 TATGGTTACC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:26944 original size:47 final size:45
Alignment explanation
Indices: 26874--27000 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
26864 TATAAAATCT
*
26874 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
26919 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
26966 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
27001 TATGGTTACC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.33
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:31214 original size:21 final size:20
Alignment explanation
Indices: 31179--31322 Score: 92
Period size: 21 Copynumber: 6.8 Consensus size: 20
31169 CATAAAATGT
*
31179 TCCGAAGGACAACATATATG
1 TCCGAAGGACCACATATATG
* *
31199 TCCTGAATGACCACATAGAATTG
1 TCC-GAAGGACCACATA-TA-TG
*
31222 TCCTGTAGGACCACATATATG
1 TCC-GAAGGACCACATATATG
*
31243 TTCCAAAGGACCAAACATATAT-
1 -TCCGAAGGACC--ACATATATG
* *
31265 CCCGAAGGATCACATATATG
1 TCCGAAGGACCACATATATG
* **
31285 TTCCCAAGGATTACATATATG
1 -TCCGAAGGACCACATATATG
* *
31306 TCCCGAATGACCGCATA
1 T-CCGAAGGACCACATA
31323 GAGCCCTCGA
Statistics
Matches: 96, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
19 8 0.08
20 4 0.04
21 54 0.56
22 5 0.05
23 25 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
TCCGAAGGACCACATATATG
Found at i:36133 original size:98 final size:99
Alignment explanation
Indices: 35960--36145 Score: 338
Period size: 98 Copynumber: 1.9 Consensus size: 99
35950 AAAAAATTTA
*
35960 AAATATTTGGTTTGATTTTATAATTGGTAAAAGTTGAAGAATCATGTTGGGAATAATTATTTATG
1 AAATATTTGGTTTGATTTTATAAATGGTAAAAGTTGAAGAATCATGTTGGGAATAATTATTTATG
36025 GAATTAAATAAGTATTTT-ATAATGAAATTGCAT
66 GAATTAAATAAGTATTTTGATAATGAAATTGCAT
*
36058 AAATATTTGGTTTGATTTTATAAATGGTAAAAGTTGAAGAATCGTGTTGGGAATAATTATTTATG
1 AAATATTTGGTTTGATTTTATAAATGGTAAAAGTTGAAGAATCATGTTGGGAATAATTATTTATG
*
36123 GAATTGAATAAGTATTTTGATAA
66 GAATTAAATAAGTATTTTGATAA
36146 GTTTGAAGTT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
98 80 0.95
99 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (99 bp):
AAATATTTGGTTTGATTTTATAAATGGTAAAAGTTGAAGAATCATGTTGGGAATAATTATTTATG
GAATTAAATAAGTATTTTGATAATGAAATTGCAT
Found at i:38908 original size:38 final size:38
Alignment explanation
Indices: 38837--38930 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
38827 CACTGAATAT
* *
38837 TTGTCCCGAATGACCACTATGTCTCGAATGACCAATGA
1 TTGTCCCGAAAGACCACTATGTCTCGAAAGACCAATGA
* * *
38875 TTGTTCCG-AAGAACCACTATGTC-CTGAAAGACCACTGT
1 TTGTCCCGAAAG-ACCACTATGTCTC-GAAAGACCAATGA
38913 TTGTCCCGAAAGACCACT
1 TTGTCCCGAAAGACCACT
38931 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
37 3 0.06
38 41 0.87
39 3 0.06
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (38 bp):
TTGTCCCGAAAGACCACTATGTCTCGAAAGACCAATGA
Found at i:38910 original size:18 final size:18
Alignment explanation
Indices: 38838--38930 Score: 71
Period size: 18 Copynumber: 4.9 Consensus size: 18
38828 ACTGAATATT
*
38838 TGTCCCGAATGACCACTA
1 TGTCCCGAAAGACCACTA
* * *
38856 TGTCTCGAATGACCAATGA
1 TGTCCCGAAAGACCACT-A
*
38875 TTGTTCCG-AAGAACCACTA
1 -TGTCCCGAAAG-ACCACTA
* *
38894 TGTCCTGAAAGACCACTGTT
1 TGTCCCGAAAGACCAC--TA
38914 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
38931 GATAATCCCT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 26 0.44
19 7 0.12
20 26 0.44
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:38923 original size:20 final size:20
Alignment explanation
Indices: 38894--38931 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38884 AGAACCACTA
*
38894 TGTCCTGAAAGACCACTGTT
1 TGTCCCGAAAGACCACTGTT
38914 TGTCCCGAAAGACCACTG
1 TGTCCCGAAAGACCACTG
38932 ATAATCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
TGTCCCGAAAGACCACTGTT
Found at i:38939 original size:20 final size:20
Alignment explanation
Indices: 38900--38939 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38890 ACTATGTCCT
* **
38900 GAAAGACCACTGTTTGTCCC
1 GAAAGACCACTGATAATCCC
38920 GAAAGACCACTGATAATCCC
1 GAAAGACCACTGATAATCCC
38940 TCGACTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (20 bp):
GAAAGACCACTGATAATCCC
Found at i:39349 original size:12 final size:12
Alignment explanation
Indices: 39327--39360 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
39317 TCATATATAA
39327 TCATATA-TACT
1 TCATATAGTACT
39338 TCATATAGTACT
1 TCATATAGTACT
39350 TCATATAGTAC
1 TCATATAGTAC
39361 ATAGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (12 bp):
TCATATAGTACT
Found at i:45047 original size:13 final size:13
Alignment explanation
Indices: 45029--45059 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
45019 TCCTTTAATA
45029 GTATTTTATTTAT
1 GTATTTTATTTAT
45042 GTATTTTATTTAT
1 GTATTTTATTTAT
45055 GTATT
1 GTATT
45060 AATTTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (13 bp):
GTATTTTATTTAT
Found at i:46278 original size:24 final size:24
Alignment explanation
Indices: 46244--46352 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
46234 AAACGAAGAT
* *
46244 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
46268 AACAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
46292 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
46316 GTCATATATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
46339 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
46353 TAAAATAATT
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:46279 original size:12 final size:12
Alignment explanation
Indices: 46246--46334 Score: 72
Period size: 12 Copynumber: 7.4 Consensus size: 12
46236 ACGAAGATAT
*
46246 CAGAAATCAAAA
1 CAGAAATCAGAA
* *
46258 TAGAATTCAGAA
1 CAGAAATCAGAA
*
46270 CAGATATCAGAA
1 CAGAAATCAGAA
*
46282 CA-AAATCCAGAT
1 CAGAAAT-CAGAA
46294 CAGAAATCAGAA
1 CAGAAATCAGAA
* **
46306 CAGAATTCAGGT
1 CAGAAATCAGAA
* *
46318 CATATATCAGAA
1 CAGAAATCAGAA
46330 CAGAA
1 CAGAA
46335 TTCAAGTCGG
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
11 3 0.05
12 49 0.88
13 4 0.07
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:46348 original size:48 final size:48
Alignment explanation
Indices: 46244--46352 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
46234 AAACGAAGAT
* * *
46244 ATCAGAAATCAAAATAGAATTCAGAACAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
** * *
46292 ATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACA-AAATCAAG
*
46341 -TCGGAAATCAGA
1 ATCAGAAATCAGA
46353 TAAAATAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 46 0.88
49 6 0.12
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
Found at i:48676 original size:14 final size:13
Alignment explanation
Indices: 48657--48700 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
48647 GGTCAACGCC
48657 GGTCAACGGGTCGG
1 GGTCAACGGGTC-G
48671 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
48684 GGTAAACGGGTAG
1 GGTCAACGGGTCG
48697 GGTC
1 GGTC
48701 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.18, C:0.18, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:50519 original size:19 final size:21
Alignment explanation
Indices: 50478--50517 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50468 ATATTTTAAT
*
50478 TTTTTTCCTTGCAAATGACCC
1 TTTTTTCCTTGCAAATCACCC
*
50499 TTTTTTCCTT-CAATTCACC
1 TTTTTTCCTTGCAAATCACC
50518 TTATAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.17, C:0.30, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTTTTCCTTGCAAATCACCC
Found at i:53777 original size:2 final size:2
Alignment explanation
Indices: 53770--53819 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
53760 TATGTTGAGT
53770 TA TA TA 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 TA TA TA
53812 TA TA TA TA
1 TA TA TA TA
53820 GTACTACTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56604 original size:24 final size:24
Alignment explanation
Indices: 56559--56608 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
56549 TGGTGGTTGG
56559 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
56583 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
56607 TT
1 TT
56609 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:62489 original size:307 final size:302
Alignment explanation
Indices: 61924--62533 Score: 1125
Period size: 307 Copynumber: 2.0 Consensus size: 302
61914 AAATGTCCAT
61924 TCTTAGATGAAGGTAGGTGTTCGAAAGAATCCTAAGCTAAAATTACTTGTAAGTATTCGGAAGAA
1 TCTTAGATGAAGGTAGGTGTTCGAAAGAATCCTAAGCTAAAATTACTTGTAAGTATTCGGAAGAA
61989 ACGCAAGACAAGATCCTAAGCAATGGGTTATAGTATTTTCAAGGGGCTTTGAACCGGCTAGGGTA
66 ACGCAAGACAAGATCCTAAGCAATGGG-T-TAGTATTTTCAAGGGGCTTTGAACCGGCTAGGGTA
62054 TTATAACCTAATCCCTTAGATCTCGGAAGAGACTAGGATAGGATTTCAACGACTAAAAGGGTGTC
129 TTATAACCTAATCCCTTAGATCTCGGAAGAGACTAGGATAGGATTTCAACGACTAAAAGGGTGTC
62119 TTTATCAATAGGGTAGGTTGTCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTATTCTG
194 TTTATCAATAGGGTAGGTTGTCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTATTCTG
62184 TTAGGTTCCTGTGAGAACATTTTAGGAAAGCCCTGTCGAGTAAA
259 TTAGGTTCCTGTGAGAACATTTTAGGAAAGCCCTGTCGAGTAAA
62228 TCTTAGATGAAGGTTAGGTGTTCGAAAGAATCCTAAGCTAAAATTACTTGTAAGTATTCGGAAGA
1 TCTTAGATGAAGG-TAGGTGTTCGAAAGAATCCTAAGCTAAAATTACTTGTAAGTATTCGGAAGA
62293 AACGCAAGACAAGATCCTCATAAGCAATGGG-TAGTATTTTCAAGGGGCTTTGAACCGGCCTAGG
65 AACGCAAGACAAGAT-C-C-TAAGCAATGGGTTAGTATTTTCAAGGGGCTTTGAACCGG-CTAGG
62357 AGTATTATAACCTAATCCCTTAGATCTCGGAAGAGACTAGGATAGGA-TTCAACGACTAAAAAGG
126 -GTATTATAACCTAATCCCTTAGATCTCGGAAGAGACTAGGATAGGATTTCAACGACT-AAAAGG
62421 GTGTCTTTATCAATAGGGTAGGTTGTCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTA
189 GTGTCTTTATCAATAGGGTAGGTTGTCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTA
62486 TTCTGTTAGGTTCCTGTGAGAACATTTTAGGAAAGCCCTGTCGAGTAA
254 TTCTGTTAGGTTCCTGTGAGAACATTTTAGGAAAGCCCTGTCGAGTAA
62534 GTAACGACCA
Statistics
Matches: 299, Mismatches: 0, Indels: 11
0.96 0.00 0.04
Matches are distributed among these distances:
304 13 0.04
305 93 0.31
306 16 0.05
307 166 0.56
308 11 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (302 bp):
TCTTAGATGAAGGTAGGTGTTCGAAAGAATCCTAAGCTAAAATTACTTGTAAGTATTCGGAAGAA
ACGCAAGACAAGATCCTAAGCAATGGGTTAGTATTTTCAAGGGGCTTTGAACCGGCTAGGGTATT
ATAACCTAATCCCTTAGATCTCGGAAGAGACTAGGATAGGATTTCAACGACTAAAAGGGTGTCTT
TATCAATAGGGTAGGTTGTCCAACATCGTTGAGTGAGAGCAGATGCCTTGGCATCCTATTCTGTT
AGGTTCCTGTGAGAACATTTTAGGAAAGCCCTGTCGAGTAAA
Found at i:64464 original size:20 final size:20
Alignment explanation
Indices: 64427--64465 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
64417 AGATTGAGTG
* * *
64427 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
64447 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
64466 AGTTTATGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:64659 original size:20 final size:20
Alignment explanation
Indices: 64636--64673 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
64626 TTCCCCTGTG
64636 GGGGGAATC-AGTTCCCTCAA
1 GGGGGAATCGA-TTCCCTCAA
*
64656 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
64674 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:73657 original size:36 final size:36
Alignment explanation
Indices: 73616--73714 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
73606 GAGTATTATT
*
73616 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
73652 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
* *
73688 AGCTTTGGTATATCCGTGTATCAATGT
1 AGCTTTGGTACATTCGTGTATCAATGT
73715 CCAGCACCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (36 bp):
AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
Found at i:78583 original size:21 final size:21
Alignment explanation
Indices: 78558--78699 Score: 67
Period size: 21 Copynumber: 6.7 Consensus size: 21
78548 GCCACATAGA
78558 ATGTCCCGAAGGACAACATAT
1 ATGTCCCGAAGGACAACATAT
* * *
78579 ATGTCCTGAAGGACCACATAGA
1 ATGTCCCGAAGGACAACATA-T
** * *
78601 ATTGTCATGTAGGACCACATAT
1 A-TGTCCCGAAGGACAACATAT
* * *
78623 ATGTTCCAAAGCACCGAACATAT
1 ATGTCCCGAAGGA-C-AACATAT
* * **
78646 AT-T-CTGAAAGATTACATAT
1 ATGTCCCGAAGGACAACATAT
78665 ATGTTCCC-AAGGATC-ACATAT
1 ATG-TCCCGAAGGA-CAACATAT
*
78686 ATGTCCCAAAGGAC
1 ATGTCCCGAAGGAC
78700 CGCGTAGACC
Statistics
Matches: 90, Mismatches: 22, Indels: 19
0.69 0.17 0.15
Matches are distributed among these distances:
19 8 0.09
20 5 0.06
21 47 0.52
22 5 0.06
23 25 0.28
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (21 bp):
ATGTCCCGAAGGACAACATAT
Found at i:81242 original size:20 final size:21
Alignment explanation
Indices: 81219--81263 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
81209 AAATTATGGG
*
81219 AACTATTGAA-TTACTATGA-A
1 AACTA-TGAAGTTACCATGATA
81239 AACTATGAAGTTACCATGATA
1 AACTATGAAGTTACCATGATA
81260 AACT
1 AACT
81264 TGACTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (21 bp):
AACTATGAAGTTACCATGATA
Found at i:92574 original size:4 final size:4
Alignment explanation
Indices: 92565--92821 Score: 471
Period size: 4 Copynumber: 64.2 Consensus size: 4
92555 ATCAACTGTG
92565 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92613 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92661 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92709 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
92757 CATA CATA CATA CATA CATA CATA CATA CATA CACT- CATA CATA CAAA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA
* *
92805 TATA CGTA CATA CATA C
1 CATA CATA CATA CATA C
92822 CTCGATGATG
Statistics
Matches: 245, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
3 1 0.00
4 243 0.99
5 1 0.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:95797 original size:189 final size:189
Alignment explanation
Indices: 95468--96223 Score: 1145
Period size: 189 Copynumber: 4.0 Consensus size: 189
95458 AGCAAAATTT
* * **
95468 GGCAAGCAATATAAACTCAGACGATAGCTAATTCAACGAGATATCTTAAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * ** * *
95533 CACAATGAAACTCATATTCAAAAATGAAATTCTGGATAACTCGAAAATGTAGTTCATACTCCCTA
66 CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
* * *
95598 GCAATTTAATCTATGATTCATGGTCTAGAATGGTAAAAATATATAACATCAATATGATA
131 GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
* * *
95657 GGCAAGCAATATAAACTCAGACGATAGCTAATCCAATGAGATATTTTAAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
*
95722 CACAATGAAACTCATATTCGAAAACGAAATTCCGGAGAACTCGAAAATGTAGTCCATACTCCCTA
66 CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
* * * * * *
95787 GTAGTTTAATCTCTTATTCAAGGTCTATAATGGTACAAGTATATAACATCAATATGATG
131 GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
* *
95846 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATCTCTTAAACAGAATCATAGCTAC
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * *
95911 CACATTGGAACTCATATTTGAAAACGAAAATT-CAGAGAACTCGAAAATGTAGTCCATACTCCCT
66 CACAATGAAACTCATATTCGAAAACG-AAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCT
* *
95975 AGCGGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATG
130 AGCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
* *
96035 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATCTCTTGAACAGAATCATAGCTAT
1 GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
* * * * * *
96100 CACAAAGGAACTCATATTCTAAAACGAAATTTCAGAGAACTCGAAAATGCAATCCATACTCCCTA
66 CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
*
96165 GCAGTTTAACCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
131 GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
96224 TAGGCAACAC
Statistics
Matches: 522, Mismatches: 43, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
188 5 0.01
189 512 0.98
190 5 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (189 bp):
GGCAAGCAACATAAACTCAGACGATAGCTAATCCAATAAGATATCTTAAACAGAATCATAGCTAT
CACAATGAAACTCATATTCGAAAACGAAATTCCAGAGAACTCGAAAATGTAGTCCATACTCCCTA
GCAGTTTAATCTATGATTCATGGTCTAGAATGGTACAAGTATATAACATCAATATGATA
Found at i:97829 original size:12 final size:12
Alignment explanation
Indices: 97814--97838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
97804 AAAATTTAAA
97814 ATATAAAAAATT
1 ATATAAAAAATT
97826 ATATAAAAAATT
1 ATATAAAAAATT
97838 A
1 A
97839 AATGTTTTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAAAAATT
Found at i:98760 original size:28 final size:29
Alignment explanation
Indices: 98716--98777 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
98706 AGTCTTTATT
* *
98716 TTTAAAAAATATGATCAAATGAACCCTTG
1 TTTAAAAAATAGGATCAAATCAACCCTTG
98745 TTTAAAAAA-AGGATCAAATCAACCCTTG
1 TTTAAAAAATAGGATCAAATCAACCCTTG
98773 TTTAA
1 TTTAA
98778 TAATTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.31
Consensus pattern (29 bp):
TTTAAAAAATAGGATCAAATCAACCCTTG
Found at i:99651 original size:31 final size:29
Alignment explanation
Indices: 99605--99701 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 29
99595 CATTGAAGTT
*
99605 TCAAAAGTTATAAAATAATTATTAAATTTA
1 TCAAAA-TTACAAAATAATTATTAAATTTA
* * *
99635 TCAAACTATTACAAAATGATCATTAATATTTT
1 TCAAA--ATTACAAAATAATTATTAA-ATTTA
*** *
99667 TCCAAAATTTTTAAATAATTATTAAATTCA
1 T-CAAAATTACAAAATAATTATTAAATTTA
99697 TCAAA
1 TCAAA
99702 TTTTATGATA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
29 4 0.08
30 9 0.17
31 29 0.56
32 6 0.12
33 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.40
Consensus pattern (29 bp):
TCAAAATTACAAAATAATTATTAAATTTA
Found at i:110747 original size:17 final size:17
Alignment explanation
Indices: 110727--110759 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
110717 TTCAAAGTTA
110727 TAATTATATAAAAAATG
1 TAATTATATAAAAAATG
*
110744 TAATTATATATAAAAT
1 TAATTATATAAAAAAT
110760 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATTATATAAAAAATG
Found at i:110999 original size:126 final size:130
Alignment explanation
Indices: 110771--111007 Score: 288
Period size: 130 Copynumber: 1.9 Consensus size: 130
110761 TAAAAAAAAA
* * * * *
110771 TATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGTCTTAAGACAGCTCTTTTCTTTGATATT
1 TATTTATTTAAAAATATCAGAAAATGAATTCCAGGTGTCTTAAGACAGCTCCTTTCTTTAATATT
**
110836 AAAAAATAAATAAATAATTAAAACATTTTTCTAAAAATAATATATAATTTCAAAAATAGGATATT
66 AAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATATAATTTCAAAAATAGGATATT
* * * *
110901 TATTTATTTAAAAATATTTAGAAAATGAATATCCAGTTGTTTTAAGACTGC-CCTTTC-TTAATA
1 TATTTATTTAAAAATA-TCAGAAAATGAAT-TCCAGGTGTCTTAAGACAGCTCCTTTCTTTAATA
* * *
110964 TTGAAAAATAAAT-AATTATTAAAACA-TGAT-T-AAAATAATTTATA
64 TTAAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATATA
111008 TTAAAAATAA
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
126 12 0.13
127 1 0.01
128 2 0.02
129 12 0.13
130 32 0.35
131 16 0.18
132 16 0.18
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (130 bp):
TATTTATTTAAAAATATCAGAAAATGAATTCCAGGTGTCTTAAGACAGCTCCTTTCTTTAATATT
AAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATATAATTTCAAAAATAGGATATT
Found at i:112435 original size:3 final size:3
Alignment explanation
Indices: 112429--112483 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
112419 AATAATTATT
**
112429 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
112472 TAA TAA TAA TAA
1 TAA TAA TAA TAA
112484 ATTAAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:112740 original size:76 final size:76
Alignment explanation
Indices: 112640--113504 Score: 1525
Period size: 76 Copynumber: 11.4 Consensus size: 76
112630 TAGGTCTTAA
** * * *
112640 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* **
112705 TGGCTTTTTAA
66 AGGCTTTTTGG
112716 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
112781 AGGCTTTTTGG
66 AGGCTTTTTGG
112792 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
112857 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * * * *
112868 AAACATCATGTACTGTAGGACTTACAAATGACCCGAATG-TTTGAAAACATCAAAAACCTCCAGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
112932 AGGCTTTTTGG
66 AGGCTTTTTGG
*
112943 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCAGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
113008 AGGCTTTTTAG
66 AGGCTTTTTGG
113019 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113084 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
113095 AAACATCATGCACTGTAGGGCTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113160 AGGCTTTTTGG
66 AGGCTTTTTGG
113171 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113236 AGGCTTTTTGG
66 AGGCTTTTTGG
*
113247 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113312 AGGCTTTTTGG
66 AGGCTTTTTGG
*
113323 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113388 AGGCTTTTTGG
66 AGGCTTTTTGG
*
113399 AAACATCATGCACTGTAGGACTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
113464 AGGCTTTTTGG
66 AGGCTTTTTGG
*
113475 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
113505 TGGGAAATAG
Statistics
Matches: 757, Mismatches: 31, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 69 0.09
76 688 0.91
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:114206 original size:22 final size:22
Alignment explanation
Indices: 114178--114276 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
114168 AATAAAGCTT
114178 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
114200 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
114222 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
114244 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
114266 TCATCTTTGAA
1 TCATCTTTGAA
114277 GAATGTAGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:114241 original size:44 final size:44
Alignment explanation
Indices: 114178--114278 Score: 193
Period size: 44 Copynumber: 2.3 Consensus size: 44
114168 AATAAAGCTT
*
114178 TCATCTTTGAAAAGAGAATCTATCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
114222 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
114266 TCATCTTTGAAGA
1 TCATCTTTGAAGA
114279 ATGTAGATGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (44 bp):
TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATCTA
Found at i:118976 original size:17 final size:16
Alignment explanation
Indices: 118970--119060 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
118960 TCTTTTTCCC
118970 TTTT-TTTTTCCTTTT
1 TTTTCTTTTTCCTTTT
*
118985 TTCTCATTTTTCCTTTT
1 TTTTC-TTTTTCCTTTT
** *
119002 TCATCTTTTTTCTTTT
1 TTTTCTTTTTCCTTTT
* **
119018 TTTTCTTTTTTCTCAT
1 TTTTCTTTTTCCTTTT
* *
119034 TTTTCTTTTTTCATCTT
1 TTTTC-TTTTTCCTTTT
119051 TTTTCTTTTT
1 TTTTCTTTTT
119061 TTCTTTATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
15 3 0.05
16 32 0.52
17 27 0.44
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCCTTTT
Found at i:118987 original size:26 final size:25
Alignment explanation
Indices: 118956--119066 Score: 77
Period size: 25 Copynumber: 4.4 Consensus size: 25
118946 ATTTCTCCCA
118956 TTTTTCTTTTTCCCTTTTTTTTTCCTT
1 TTTTTCTTTTT-CCTTTTTTTTTCC-T
**
118983 TTTTCTCATTTTTCC-TTTTTCAT-CT
1 TTTT-TC-TTTTTCCTTTTTTTTTCCT
*
119008 TTTTTCTTTTT--TTTCTTTTTTCTCA
1 TTTTTCTTTTTCCTTT-TTTTTTC-CT
* * * *
119033 TTTTTCTTTTTTCATCTTTTTTCTT
1 TTTTTCTTTTTCCTTTTTTTTTCCT
119058 TTTTTCTTT
1 TTTTTCTTT
119067 ATTTGCTGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
22 2 0.03
23 9 0.13
24 2 0.03
25 26 0.39
26 8 0.12
27 11 0.16
28 4 0.06
29 5 0.07
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTTTCCTTTTTTTTTCCT
Found at i:118994 original size:16 final size:14
Alignment explanation
Indices: 118975--119066 Score: 57
Period size: 17 Copynumber: 6.2 Consensus size: 14
118965 TTCCCTTTTT
118975 TTTTCCTTTTTTCTC
1 TTTT-CTTTTTTCTC
*
118990 ATTTTTCCTTTTTCATC
1 --TTTTCTTTTTTC-TC
*
119007 TTTT-TTCTTT-T-
1 TTTTCTTTTTTCTC
119018 TTTTCTTTTTTCTC
1 TTTTCTTTTTTCTC
119032 ATTTTTCTTTTTTCATC
1 --TTTTCTTTTTTC-TC
119049 TTTTTTCTTTTTT-TC
1 --TTTTCTTTTTTCTC
119064 TTT
1 TTT
119067 ATTTGCTGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.06
12 6 0.10
13 4 0.06
14 4 0.06
15 6 0.10
16 19 0.30
17 20 0.32
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTTTCTC
Found at i:119003 original size:42 final size:42
Alignment explanation
Indices: 118956--119066 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
118946 ATTTCTCCCA
118956 TTTTTC-T-TTTTCCCTTTTTTTTTCCTTTTTTCTCATTTTTCC
1 TTTTTCATCTTTTCCC-TTTTTTTT-CTTTTTTCTCATTTTTCC
** *
118998 TTTTTCATCTTTTTTCTTTTTTTTCTTTTTTCTCATTTTTCT
1 TTTTTCATCTTTTCCCTTTTTTTTCTTTTTTCTCATTTTTCC
**
119040 TTTTTCATCTTTTTTC-TTTTTTTCTTT
1 TTTTTCATCTTTTCCCTTTTTTTTCTTT
119067 ATTTGCTGGA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
41 11 0.17
42 39 0.61
43 9 0.14
44 5 0.08
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (42 bp):
TTTTTCATCTTTTCCCTTTTTTTTCTTTTTTCTCATTTTTCC
Found at i:119009 original size:9 final size:8
Alignment explanation
Indices: 118982--119066 Score: 70
Period size: 9 Copynumber: 10.4 Consensus size: 8
118972 TTTTTTTCCT
118982 TTTTTCTC
1 TTTTTCTC
118990 ATTTTTC-C
1 -TTTTTCTC
118998 TTTTTCATC
1 TTTTTC-TC
119007 TTTTT-TC
1 TTTTTCTC
*
119014 TTTTTTTTC
1 -TTTTTCTC
119023 TTTTTTCTC
1 -TTTTTCTC
119032 ATTTTTCT-
1 -TTTTTCTC
119040 TTTTTCATC
1 TTTTTC-TC
119049 TTTTT-TC
1 TTTTTCTC
*
119056 TTTTTTTC
1 TTTTTCTC
119064 TTT
1 TTT
119067 ATTTGCTGGA
Statistics
Matches: 67, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
7 21 0.31
8 12 0.18
9 34 0.51
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCTC
Found at i:119080 original size:27 final size:27
Alignment explanation
Indices: 119050--119104 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
119040 TTTTTCATCT
*
119050 TTTTTCTTTTTTTCTTTATTTGCTGGA
1 TTTTTATTTTTTTCTTTATTTGCTGGA
*
119077 TTTTTATTTTTTTCTTTCTTTGCTGGA
1 TTTTTATTTTTTTCTTTATTTGCTGGA
119104 T
1 T
119105 GAGTATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.71
Consensus pattern (27 bp):
TTTTTATTTTTTTCTTTATTTGCTGGA
Found at i:119093 original size:42 final size:41
Alignment explanation
Indices: 118971--119093 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 41
118961 CTTTTTCCCT
* *
118971 TTTTTTTTCCTTTTTTCTCATTTTTCCTTTTTCATCTTTTTTC
1 TTTTTTTT-CTTTTTTCTCATTTTT-ATTTTTTATCTTTTTTC
*
119014 TTTTTTTTCTTTTTTCTCATTTTTCTTTTTTCATCTTTTTTC
1 TTTTTTTTCTTTTTTCTCATTTTTATTTTTT-ATCTTTTTTC
*
119056 -TTTTTTTCTTTATTTGCTGGATTTTTATTTTTT-TCTTT
1 TTTTTTTTCTTT-TTT-CT-CATTTTTATTTTTTATCTTT
119094 CTTTGCTGGA
Statistics
Matches: 73, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
41 17 0.23
42 34 0.47
43 10 0.14
44 12 0.16
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.76
Consensus pattern (41 bp):
TTTTTTTTCTTTTTTCTCATTTTTATTTTTTATCTTTTTTC
Found at i:122295 original size:20 final size:20
Alignment explanation
Indices: 122272--122310 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
122262 CGAACGTAAA
*
122272 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
122292 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
122311 AAATTATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:124680 original size:126 final size:128
Alignment explanation
Indices: 124451--124695 Score: 286
Period size: 130 Copynumber: 1.9 Consensus size: 128
124441 ATAAAAAAAA
* * * * *
124451 TTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGTCTTAAGACAGCTCTTTTCTTTGATAT
1 TTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGTCTTAAGACAGCTCCTTTCTTTAATAT
**
124516 TAAAAAATAAATAAATAATTAAAACATTTTTCTAAAAATAATATATAATTTAAAAAATAGGATAT
66 TAAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATAT-A-TTAAAAAATAGGATAT
* * * *
124581 TTATTTATTTAAAAATATTTAGAAAATAGACATCCAGTTGTTTTAAGACTGC-CCTTTC-TTAAT
1 TTATTTATTTAAAAATA-TCAGAAAAT-GACATCCAGGTGTCTTAAGACAGCTCCTTTCTTTAAT
* * *
124644 ATTGAAAAATAAAT-AATTATTAAAACA-TGAT-T-AAAATAATTTATATTAAAAA
64 ATTAAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATATATTAAAAA
124696 TAAAATAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
124 7 0.07
125 1 0.01
126 11 0.11
127 1 0.01
128 2 0.02
129 12 0.12
130 33 0.33
131 13 0.13
132 19 0.19
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (128 bp):
TTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGTCTTAAGACAGCTCCTTTCTTTAATAT
TAAAAAATAAATAAATAATTAAAACATTGATCTAAAAATAATATATATTAAAAAATAGGATAT
Found at i:124771 original size:30 final size:30
Alignment explanation
Indices: 124737--124797 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
124727 ATATAAATAA
124737 ATAATGACTAAAATA-AATAAA-AATAAAACT
1 ATAATG-CTAAAATATAA-AAACAATAAAACT
*
124767 ATAATGTTAAAATATAAAAAGCAATAAAACT
1 ATAATGCTAAAATATAAAAA-CAATAAAACT
124798 TGCAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.37
30 8 0.30
31 9 0.33
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (30 bp):
ATAATGCTAAAATATAAAAACAATAAAACT
Found at i:126092 original size:3 final size:3
Alignment explanation
Indices: 126086--126164 Score: 101
Period size: 3 Copynumber: 27.0 Consensus size: 3
126076 AATAATTATT
*
126086 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
126129 TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
126165 ATTAAGTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 6 0.09
3 57 0.86
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:126127 original size:12 final size:12
Alignment explanation
Indices: 126075--126162 Score: 82
Period size: 12 Copynumber: 7.8 Consensus size: 12
126065 TCTGGGCTTG
*
126075 TAATAATTATT-
1 TAATAATAATTA
126086 TAATAATAA-TA
1 TAATAATAATTA
*
126097 TAAT-ATATATAA
1 TAATAATA-ATTA
126109 T-ATAATAATTA
1 TAATAATAATTA
126120 TAATAAT-A--A
1 TAATAATAATTA
*
126129 TAATAATAATAA
1 TAATAATAATTA
*
126141 TAATAATAATTT
1 TAATAATAATTA
126153 TAATAATAAT
1 TAATAATAAT
126163 AAATTAAGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.12
10 5 0.08
11 20 0.31
12 31 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:130128 original size:23 final size:22
Alignment explanation
Indices: 130102--130165 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
130092 TAAATGTTAA
*
130102 ATATAATTTAAAAAATAAAATTT
1 ATATAATTTAAAAAATAAAA-AT
**
130125 ATATACCTTAATAAAATAAAAAT
1 ATATAATTTAA-AAAATAAAAAT
*
130148 A-ATAATTTAAATAATAAA
1 ATATAATTTAAAAAATAAA
130166 CGTGTAGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 11 0.32
24 9 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAATTTAAAAAATAAAAAT
Found at i:130777 original size:23 final size:21
Alignment explanation
Indices: 130741--130792 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
130731 CGGTTCAACC
130741 TAAATTTTTT--TATTTTTTAT
1 TAAATTTTTTGGTA-TTTTTAT
130761 TAAATATTTTTGGTATTTTTAT
1 TAAAT-TTTTTGGTATTTTTAT
*
130783 TTAATTTTTT
1 TAAATTTTTT
130793 AAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 10 0.36
22 11 0.39
23 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TAAATTTTTTGGTATTTTTAT
Found at i:140192 original size:23 final size:23
Alignment explanation
Indices: 140163--140206 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
140153 AACACAAACG
*
140163 AACGAAC-CTAATAAATGAACATA
1 AACGAACAC-AATAAACGAACATA
140186 AACGAACACAATAAACGAACA
1 AACGAACACAATAAACGAACA
140207 ACACAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:140484 original size:14 final size:14
Alignment explanation
Indices: 140465--140493 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
140455 ACCCTTTGTT
140465 CGAACATAAATGAA
1 CGAACATAAATGAA
140479 CGAACATAAATGAA
1 CGAACATAAATGAA
140493 C
1 C
140494 ATAAACGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:140514 original size:12 final size:11
Alignment explanation
Indices: 140464--140515 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 11
140454 TACCCTTTGT
140464 TCGAACATAAA
1 TCGAACATAAA
140475 TGAACGAACATAAA
1 T---CGAACATAAA
140489 T-GAACATAAA
1 TCGAACATAAA
140499 -CGAACATATAA
1 TCGAACATA-AA
140510 TCGAAC
1 TCGAAC
140516 GCTCACGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
10 16 0.46
11 3 0.09
12 5 0.14
14 11 0.31
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (11 bp):
TCGAACATAAA
Done.