Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006866.1 Hibiscus syriacus cultivar Beakdansim tig00017472_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: 85904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3197 original size:23 final size:22
Alignment explanation
Indices: 3154--3198 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3144 TAACATACCT
3154 TGAATCTTCAAAAGAGCAGAAGG
1 TGAATCTTCAAAAGA-CAGAAGG
3177 TGAATCCTTCAACAAGA-AGAAG
1 TGAAT-CTTCAA-AAGACAGAAG
3199 CGGATCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (22 bp):
TGAATCTTCAAAAGACAGAAGG
Found at i:3271 original size:52 final size:53
Alignment explanation
Indices: 3193--3304 Score: 208
Period size: 52 Copynumber: 2.1 Consensus size: 53
3183 CTTCAACAAG
*
3193 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCC-AATGGAGACTTTAAA
1 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
3245 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
1 AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
3298 AAGAAGC
1 AAGAAGC
3305 AGTGCCGACT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 37 0.64
53 21 0.36
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (53 bp):
AAGAAGCGGATCCCATTCCCTCCTTATTTTTTCTGCCAAACGGAGACTTTAAA
Found at i:9838 original size:216 final size:216
Alignment explanation
Indices: 9448--9877 Score: 808
Period size: 215 Copynumber: 2.0 Consensus size: 216
9438 AAGGCAATGG
9448 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
1 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
9513 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
66 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
9578 TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
131 TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
*
9643 GCTTCCGTAAGAGACCTCCGA
196 GCTTCCGTAAAAGACCTCCGA
9664 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGG-ATTCAAACATTTGACCTTACTTAAG
1 CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
* *
9728 TGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGCTTACCCTTAT
66 GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
*
9793 TCCCATATGTAATGGGGTAAGGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAGC
131 TCCCATATGTAATGGGGTAA-GGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAAC
9858 AGCTTCCGTAAAAGACCTCC
195 AGCTTCCGTAAAAGACCTCC
9878 AAATTATGAA
Statistics
Matches: 209, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
215 108 0.52
216 101 0.48
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (216 bp):
CAACCCTCAACCATGTTTACTACATTCAAAATCATCAGGTATTCAAACATTTGACCTTACTTAAG
GGATTCAATACTTCATTTCACTAAACTAACTGGTTGTTGATATTTTAAAATTAGATTACCCTTAT
TCCCATATGTAATGGGGTAAGGGGAGGTAGGATAGTAGGCTGCCCCCAACGCCAGGTTGAGAACA
GCTTCCGTAAAAGACCTCCGA
Found at i:12815 original size:2 final size:2
Alignment explanation
Indices: 12810--12879 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
12800 TACACACATC
12810 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
12852 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
12880 CTTCTAGTCC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12913 original size:18 final size:18
Alignment explanation
Indices: 12890--12925 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12880 CTTCTAGTCC
12890 TAGTAATAAATT-TTTTGT
1 TAGTAAT-AATTATTTTGT
12908 TAGTAATAATTATTTTGT
1 TAGTAATAATTATTTTGT
12926 ATTATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
TAGTAATAATTATTTTGT
Found at i:15797 original size:38 final size:38
Alignment explanation
Indices: 15754--15830 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
15744 CTAAAAAATC
* *
15754 GGGTCGAGTCAGAGTTGG-TG-AAGAATATATATTTTTTT
1 GGGTCGAGTC-GAGTCGGATGTAAG-ATATAAATTTTTTT
15792 GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTTT
1 GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTTT
15830 G
1 G
15831 ACCGGATCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 6 0.17
38 26 0.74
39 3 0.09
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (38 bp):
GGGTCGAGTCGAGTCGGATGTAAGATATAAATTTTTTT
Found at i:22046 original size:21 final size:21
Alignment explanation
Indices: 21994--22040 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21984 GTTTCCAGAT
*
21994 TCGCAACACGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
22015 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
22036 TCGCA
1 TCGCA
22041 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:22081 original size:21 final size:21
Alignment explanation
Indices: 22055--22109 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
22045 GATTTACATA
*
22055 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCAAAG
*
22076 TTCGCATTACGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
*
22097 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
22110 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCAAAG
Found at i:22196 original size:21 final size:21
Alignment explanation
Indices: 22166--22239 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
22156 GATTTACATA
* *
22166 TTCGCATTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
22187 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
22208 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
22227 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
22240 TTATTCCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 15 0.37
21 26 0.63
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:22225 original size:40 final size:42
Alignment explanation
Indices: 22172--22264 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 42
22162 CATATTCGCA
*
22172 TTGCAATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
22212 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
22254 TTGCGATAGTC
1 TTGCGATAGTC
22265 CAAAATCACA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 26 0.52
41 2 0.04
42 22 0.44
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:22255 original size:21 final size:20
Alignment explanation
Indices: 22191--22260 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
22181 TCGAAGTTCG
22191 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
22210 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
22229 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
22252 CGTTGCGAT
1 CGTTGCGAT
22261 AGTCCAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.03
19 14 0.35
20 1 0.03
21 16 0.40
23 8 0.20
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:22268 original size:19 final size:19
Alignment explanation
Indices: 22191--22268 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
22181 TCGAAGTTCG
**
22191 CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
* *
22210 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATAGTCCAAATT
*
22229 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA--TAGTCCAAATT
22252 CGTTGCGATAGTCCAAA
1 CGTTGCGATAGTCCAAA
22269 ATCACAACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 23 0.49
21 16 0.34
23 8 0.17
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:28207 original size:36 final size:36
Alignment explanation
Indices: 28133--28423 Score: 325
Period size: 36 Copynumber: 7.8 Consensus size: 36
28123 TTTATTTAGA
* *
28133 ATATATATTATATAATTTTGAAAACATTTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACA-TTTTGAAAAC
28170 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
*
28206 ATATATATTATATAGTTTTTAAAACATTTTGAAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
28242 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
* * *
28278 ATATATATATTATATAATTTTTAAAACGTTTTTGAAAAT
1 --ATATATATTATATAGTTTTTAAAAC-ATTTTGAAAAC
* * * *
28317 ATAAATATAATATATGGTTTTTAAAACAATTTTTTGAATAT
1 AT--ATATATTATATAGTTTTTAAAAC-A--TTTTGAAAAC
* * * ***
28358 ATATATAATATATAGTTTTAAAAATTATTTTTTTTAAC
1 ATATATATTATATAGTTTTTAAAA-CA-TTTTGAAAAC
28396 ATATATATTATATAG-TTTTAAAA-ATTTT
1 ATATATATTATATAGTTTTTAAAACATTTT
28424 TCATTGTATT
Statistics
Matches: 223, Mismatches: 23, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
34 4 0.02
35 1 0.00
36 80 0.36
37 33 0.15
38 44 0.20
39 50 0.22
41 11 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
Found at i:28441 original size:3 final size:3
Alignment explanation
Indices: 28433--28494 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
28423 TTCATTGTAT
*
28433 TTA TTA TTA TTA TTA TTA TTA TT- TCTC TT- TT- TTA -TA TATA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA -TTA
28477 TTA CTTA TTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TT
28495 TTTTTGTTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
2 7 0.13
3 36 0.69
4 8 0.15
5 1 0.02
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35099 original size:85 final size:85
Alignment explanation
Indices: 34956--35665 Score: 1135
Period size: 85 Copynumber: 8.4 Consensus size: 85
34946 TAAACAAACT
34956 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35021 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
35041 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35106 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
* ** * *
35126 ATTTACAGCATAACTCAAGACTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
* *
35191 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * * * * * *
35210 ATTTGCAGCATAGCTTAAGTCGAGAAGCGCTATC--TG-CC-AAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35271 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
35291 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35356 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
35376 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35441 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
35461 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
35526 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCGAGGGCACATC
** * * *
35546 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
* *
35611 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCGAGGGCACATC
* * * * * *
35630 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
35666 CTAAAGACCT
Statistics
Matches: 580, Mismatches: 40, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
80 25 0.04
81 40 0.07
82 2 0.00
83 2 0.00
84 81 0.14
85 430 0.74
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (85 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
CTCAGCTTCGAGGGCACATC
Found at i:36388 original size:36 final size:36
Alignment explanation
Indices: 36314--36603 Score: 332
Period size: 36 Copynumber: 7.8 Consensus size: 36
36304 TTTATTTAGA
* *
36314 ATATATATTATATAATTTTGAAAACATTTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACA-TTTTGAAAAC
36351 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
*
36387 ATATATATTATATAGTTTTTAAAACATTTTGAAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
36423 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
* * *
36459 ATATATATATTATATAATTTTTAAAACGTTTTTGAAAAT
1 --ATATATATTATATAGTTTTTAAAAC-ATTTTGAAAAC
* * * *
36498 ATAAATATAATATATGGTTTTTAAAACAATTTTTTGAATAT
1 AT--ATATATTATATAGTTTTTAAAAC-A--TTTTGAAAAC
* * * ***
36539 ATATATAATATATAGTTTTAAAAATTATTTTTTTAAC
1 ATATATATTATATAGTTTTTAAAA-CATTTTGAAAAC
36576 ATATATATTATATAG-TTTTAAAA-ATTTT
1 ATATATATTATATAGTTTTTAAAACATTTT
36604 TCATTGTATT
Statistics
Matches: 222, Mismatches: 23, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.02
36 87 0.39
37 45 0.20
38 24 0.11
39 50 0.23
41 11 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAAC
Found at i:36621 original size:3 final size:3
Alignment explanation
Indices: 36613--36676 Score: 53
Period size: 3 Copynumber: 20.7 Consensus size: 3
36603 TTCATTGTAT
*
36613 TTA TTA TTA TTA TTA TTA TTA TT- TCTC TT- TT- TTA TATA TATA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA T-TA -TTA
36659 TTA CTTA TTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TT
36677 TTTTTTGTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 5 0.09
3 37 0.67
4 12 0.22
5 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39611 original size:14 final size:14
Alignment explanation
Indices: 39592--39623 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39582 AGCTATAGTA
39592 TATTATCATAAATT
1 TATTATCATAAATT
*
39606 TATTATCATAACTT
1 TATTATCATAAATT
39620 TATT
1 TATT
39624 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:44334 original size:13 final size:13
Alignment explanation
Indices: 44316--44346 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44306 TTTTTTAAAA
44316 TAAAATATTTTTT
1 TAAAATATTTTTT
44329 TAAAATATTTTTT
1 TAAAATATTTTTT
44342 TAAAA
1 TAAAA
44347 AAATCTGAAC
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAAAATATTTTTT
Found at i:45232 original size:36 final size:36
Alignment explanation
Indices: 45189--45258 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
45179 ACTAATTACA
45189 ATCTATGGACACAACTTATTACCATGTATGGACACC
1 ATCTATGGACACAACTTATTACCATGTATGGACACC
45225 ATCTATGGACACAACTTATTACCATGTATGGACA
1 ATCTATGGACACAACTTATTACCATGTATGGACA
45259 ACTTATTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (36 bp):
ATCTATGGACACAACTTATTACCATGTATGGACACC
Found at i:45254 original size:23 final size:23
Alignment explanation
Indices: 45222--45284 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
45212 ATGTATGGAC
45222 ACCATCTATGGACACAACTTATT
1 ACCATCTATGGACACAACTTATT
*
45245 ACCATGTATGG--ACAACTTATT
1 ACCATCTATGGACACAACTTATT
*
45266 ACCATCTATGAACACAACT
1 ACCATCTATGGACACAACT
45285 GAATTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.29
Consensus pattern (23 bp):
ACCATCTATGGACACAACTTATT
Found at i:53124 original size:13 final size:14
Alignment explanation
Indices: 53108--53143 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53098 GATATTATGG
53108 AATTATATAT-AAA
1 AATTATATATAAAA
53121 AATTATATATAAAA
1 AATTATATATAAAA
53135 AATTATATA
1 AATTATATA
53144 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATATATAAAA
Found at i:53249 original size:13 final size:12
Alignment explanation
Indices: 53223--53276 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
53213 AGAATGAAAA
*
53223 ATATTTAATTTG
1 ATATTTAATATG
53235 ATATTATAATATG
1 ATATT-TAATATG
*
53248 ATTATTTATTAT-
1 A-TATTTAATATG
53260 ATATTTAA-AT-
1 ATATTTAATATG
53270 ATATTTA
1 ATATTTA
53277 TAATCAGGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.24
11 6 0.16
12 6 0.16
13 12 0.32
14 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (12 bp):
ATATTTAATATG
Found at i:54751 original size:19 final size:19
Alignment explanation
Indices: 54716--54752 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54706 CGTTACACTT
*
54716 GTTTAAATTACATAAATTG
1 GTTTAAATTACAGAAATTG
*
54735 GTTTAAATTTCAGAAATT
1 GTTTAAATTACAGAAATT
54753 AAAACGACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (19 bp):
GTTTAAATTACAGAAATTG
Found at i:61397 original size:21 final size:21
Alignment explanation
Indices: 61373--61421 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
61363 CATATTCGTA
61373 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
61394 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
61415 TTGCGAT
1 TTGCGAT
61422 TTATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:61485 original size:42 final size:42
Alignment explanation
Indices: 61392--61532 Score: 210
Period size: 42 Copynumber: 3.2 Consensus size: 42
61382 TCGAAGTTCG
61392 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCG------ATTTATTCCAAATT
61440 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
61482 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
61524 CGTTGCGAT
1 CGTTGCGAT
61533 TTGTTTCTTA
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
42 62 0.69
48 28 0.31
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:61527 original size:21 final size:21
Alignment explanation
Indices: 61426--61534 Score: 100
Period size: 21 Copynumber: 5.2 Consensus size: 21
61416 TGCGATTTAT
61426 ATTTATTCCAAATTCGTTGCG
1 ATTTATTCCAAATTCGTTGCG
* * *
61447 A--TAGTCGAAGTTCGCGTTGCG
1 ATTTATTCCAAATT--CGTTGCG
*
61468 ATTTATTCCAAATTCGTTGTG
1 ATTTATTCCAAATTCGTTGCG
* *
61489 A--TAGTCCAAGTTCGCGTTGCG
1 ATTTATTCCAAATT--CGTTGCG
61510 ATTTATTCCAAATTCGTTGCG
1 ATTTATTCCAAATTCGTTGCG
61531 ATTT
1 ATTT
61535 GTTTCTTAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
19 17 0.25
21 34 0.50
23 17 0.25
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
ATTTATTCCAAATTCGTTGCG
Found at i:62130 original size:11 final size:11
Alignment explanation
Indices: 62108--62138 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
62098 CGTTCGTCTC
62108 GGGTCG-GGTT
1 GGGTCGTGGTT
62118 GGGTCGTGGTT
1 GGGTCGTGGTT
62129 GGGTCGTGGT
1 GGGTCGTGGT
62139 CGTTGCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.00, C:0.10, G:0.58, T:0.32
Consensus pattern (11 bp):
GGGTCGTGGTT
Found at i:62244 original size:21 final size:21
Alignment explanation
Indices: 62218--62333 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
62208 GATTTACATA
62218 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
62239 TTCGCATTGCGATAGTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* * *
62260 TTCGCATTGGGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
62280 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
62301 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
62322 TTCGCATTGCGA
1 TTCGCATTGCGA
62334 ATCTGGAAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.21
21 62 0.77
22 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:62244 original size:41 final size:41
Alignment explanation
Indices: 62199--62333 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
62189 ACTTCGACTA
62199 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
* * * * * *
62240 TCGCATTGCGATAGTCCAAATTCGCATTGGGATAGT-CGACT
1 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGT
*
62281 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
62323 TCGCATTGCGA
1 TCGCATTGCGA
62334 ATCTGGAAAC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
41 45 0.58
42 33 0.42
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (41 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:63531 original size:29 final size:29
Alignment explanation
Indices: 63498--63557 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
63488 ATAGTCGTGT
* * *
63498 GACCATTTTGTTACTTTTAATATTTGAGG
1 GACCATTTTATAACTTTTAATAGTTGAGG
63527 GACCATTTTATAACTTTTAATAGTTGAGG
1 GACCATTTTATAACTTTTAATAGTTGAGG
63556 GA
1 GA
63558 TTTAATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (29 bp):
GACCATTTTATAACTTTTAATAGTTGAGG
Found at i:64612 original size:13 final size:13
Alignment explanation
Indices: 64596--64620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64586 ATAATCTATT
64596 TATTTTAATTTTA
1 TATTTTAATTTTA
64609 TATTTTAATTTT
1 TATTTTAATTTT
64621 TTTAATTTAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:67530 original size:20 final size:19
Alignment explanation
Indices: 67505--67558 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
67495 ACAAAATAAA
67505 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
*
67525 AATCGCAAAC-CAGTTCCCAG
1 AATCGC-AACGC-GATCCCAG
*
67545 AATCGCAATGCGAT
1 AATCGCAACGCGAT
67559 AGTACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:67592 original size:21 final size:21
Alignment explanation
Indices: 67541--67594 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
67531 AAACCAGTTC
67541 CCAGAATCGCAATGCGATAGT
1 CCAGAATCGCAATGCGATAGT
* * **
67562 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATAGT
67583 CCAGAATCGCAA
1 CCAGAATCGCAA
67595 CGTGAATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATAGT
Found at i:67612 original size:20 final size:20
Alignment explanation
Indices: 67587--67639 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
67577 GATTTTCCAG
* *
67587 AATCGCAACGTGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
67607 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
67627 AATCGCAACGCGA
1 AATCGCAACGCGA
67640 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:67671 original size:20 final size:20
Alignment explanation
Indices: 67648--67717 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
67638 GATTCTGACT
67648 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
67668 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
67689 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
*
67709 ATTGCAACG
1 ATCGCAACG
67718 CGATCGATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:67841 original size:21 final size:21
Alignment explanation
Indices: 67817--67903 Score: 83
Period size: 20 Copynumber: 4.3 Consensus size: 21
67807 AATTTGCGTT
* * *
67817 GCGATTTTCTTAATTCGCAAC
1 GCGATTTACGTAAATCGCAAC
67838 GCGA-TTACGTAAATCGCAAC
1 GCGATTTACGTAAATCGCAAC
*
67858 GCGA-TTACGTAAATCGCAAT
1 GCGATTTACGTAAATCGCAAC
*
67878 GCGA-AT-CTGTAAATCGCAAC
1 GCGATTTAC-GTAAATCGCAAC
*
67898 GAGATT
1 GCGATT
67904 CTGACTATCG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 51 0.91
21 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (21 bp):
GCGATTTACGTAAATCGCAAC
Found at i:67906 original size:20 final size:20
Alignment explanation
Indices: 67831--67903 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
67821 TTTTCTTAAT
67831 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
67851 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
* *
67871 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGATTAC-GTAAA
*
67891 TCGCAACGAGATT
1 TCGCAACGCGATT
67904 CTGACTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGATTACGTAAA
Found at i:68781 original size:24 final size:24
Alignment explanation
Indices: 68754--68807 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
68744 GTATTCGAAA
68754 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
68778 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
68802 TTTGAT
1 TTTGAT
68808 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:71253 original size:20 final size:20
Alignment explanation
Indices: 71228--71316 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
71218 CAACGTGGAA
71228 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
71248 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
71268 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
71288 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
71308 ATCGCAACG
1 ATCGCAACG
71317 AGAGAATCGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:71353 original size:19 final size:19
Alignment explanation
Indices: 71321--71483 Score: 221
Period size: 19 Copynumber: 8.8 Consensus size: 19
71311 GCAACGAGAG
*
71321 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
71340 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
71359 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
71378 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
71397 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
71415 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
71434 AATCGCAA--CG-GGTG--
1 AATCGCAATGCGAAATGAA
71448 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
71468 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
71484 CGTTGCGATT
Statistics
Matches: 127, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
14 8 0.06
16 4 0.03
17 2 0.02
18 20 0.16
19 82 0.65
20 11 0.09
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:71656 original size:14 final size:14
Alignment explanation
Indices: 71637--71673 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
71627 CAACAATTAA
71637 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
71651 ACAAATCATCTTTT
1 ACAAATCAACATTT
71665 ACAAATCAA
1 ACAAATCAA
71674 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:73623 original size:20 final size:20
Alignment explanation
Indices: 73597--73683 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
73587 GAAACTTAAA
*
73597 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
73617 ATTGCAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
73637 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
73657 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAAAATGACT
73677 ATCGCAA
1 ATCGCAA
73684 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:73740 original size:19 final size:19
Alignment explanation
Indices: 73718--73761 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
73708 AAATCGCAAC
*
73718 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCATT
* *
73737 GCGATTTTGGTTTCGCATT
1 GCGATTATAGTTTCGCATT
73756 GCGATT
1 GCGATT
73762 TTGTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCATT
Found at i:73762 original size:19 final size:19
Alignment explanation
Indices: 73727--73764 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
73717 CGCGATTATA
*
73727 GTTTCGCGTTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
73746 GTTTCGCATTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
73765 TCGTTGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
GTTTCGCATTGCGATTTTG
Found at i:73802 original size:33 final size:33
Alignment explanation
Indices: 73733--73824 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
73723 TATAGTTTCG
** * * *
73733 CGTTGCGATTTTGGTTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
73766 CGTTGCAATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
73799 CGTTACGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
73825 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.35
33 33 0.65
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:73824 original size:17 final size:17
Alignment explanation
Indices: 73776--73824 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
73766 CGTTGCAATT
73776 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
* *
73793 TTC---TCTCGTTACGA
1 TTCATTTCGCGTTGCGA
73807 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
73824 T
1 T
73825 AGTCATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (17 bp):
TTCATTTCGCGTTGCGA
Found at i:74089 original size:92 final size:93
Alignment explanation
Indices: 73912--74286 Score: 584
Period size: 92 Copynumber: 4.1 Consensus size: 93
73902 ATGGATTGCA
* * *
73912 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTGT-AGAGTATTAAAGAATACATAG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACT-TCACAG-GTTAAAGAATACACAG
*
73975 TTTATCAGAATTGGCAGCAACCGAACAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
74005 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACA-GTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGGTTAAAGAATACACAGTT
74069 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74097 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAG-GTTAAAGAATACACAGT
*
74162 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
74191 TTAC-TTCAACC-AAA-ACAAAACAAAAGACAAATACT-ACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAG-GTTAAAGAATACACAG
* *
74252 TTTAGCAGTATTGGCAGCAACCGAATAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
74282 TTACT
1 TTACT
74287 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 7, Indels: 13
0.93 0.02 0.04
Matches are distributed among these distances:
91 65 0.24
92 105 0.39
93 12 0.04
94 87 0.32
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:80994 original size:34 final size:34
Alignment explanation
Indices: 80944--81020 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
80934 AATGTTATTG
80944 AACTGCATCTCGTTGGAAATTT-TCAGTGTCATTC
1 AACTGCATCTCGTTGG-AATTTATCAGTGTCATTC
* * * *
80978 AACTGCGTCTCTTTGGAATTTATCAGTGTTATTG
1 AACTGCATCTCGTTGGAATTTATCAGTGTCATTC
81012 AACTGCATC
1 AACTGCATC
81021 CCCATTCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (34 bp):
AACTGCATCTCGTTGGAATTTATCAGTGTCATTC
Found at i:82483 original size:26 final size:26
Alignment explanation
Indices: 82445--82497 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
82435 AATTTTTATT
*
82445 TGTTTAAAGTGATAATTTAATATATA
1 TGTTTAAAGTGATAATGTAATATATA
* *
82471 TGTTATAAA-TGATGATGTGATATATA
1 TGTT-TAAAGTGATAATGTAATATATA
82497 T
1 T
82498 CATGTGCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (26 bp):
TGTTTAAAGTGATAATGTAATATATA
Found at i:82718 original size:32 final size:33
Alignment explanation
Indices: 82658--82723 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
82648 AAATGCATGT
* * *
82658 TATATATACATGAGTGATGATGTGACATG-CAC
1 TATATATACATGAGTGATAATATCACATGTCAC
82690 TATATATACAT-AGGTGATAATATCACATGTCAC
1 TATATATACATGA-GTGATAATATCACATGTCAC
82723 T
1 T
82724 TGTACATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 24 0.83
33 4 0.14
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (33 bp):
TATATATACATGAGTGATAATATCACATGTCAC
Found at i:83750 original size:2 final size:2
Alignment explanation
Indices: 83692--83735 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
83682 TTTTATACCA
83692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83733 AT A
1 AT A
83736 ACATTATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85841 original size:9 final size:10
Alignment explanation
Indices: 85823--85883 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 10
85813 GTCTTTTTTA
85823 TATTATTTAAT
1 TATTA-TTAAT
85834 T-TTATTAAT
1 TATTATTAAT
85843 TATTATT-AT
1 TATTATTAAT
85852 TATTATATATAT
1 TATTAT-TA-AT
85864 TATTATTAAAT
1 TATTATT-AAT
85875 TATATATTA
1 TAT-TATTA
85884 CAAATTTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 14 0.32
10 9 0.20
11 8 0.18
12 13 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATTAAT
Found at i:85847 original size:3 final size:3
Alignment explanation
Indices: 85823--85871 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
85813 GTCTTTTTTA
*
85823 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TA- TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TAT
85867 TAT TA
1 TAT TA
85872 AATTATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 5 0.13
3 28 0.72
4 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:85882 original size:18 final size:17
Alignment explanation
Indices: 85835--85883 Score: 68
Period size: 15 Copynumber: 3.0 Consensus size: 17
85825 TTATTTAATT
85835 TTATTAATTAT-TATTA
1 TTATTAATTATATATTA
85851 TTATT-A-TATATATTA
1 TTATTAATTATATATTA
85866 TTATTAAATTATATATTA
1 TTATT-AATTATATATTA
85884 CAAATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.10
15 11 0.38
16 5 0.17
17 1 0.03
18 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAATTATATATTA
Done.