Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009062.1 Hibiscus syriacus cultivar Beakdansim tig00112485_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: 60485
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6297 original size:41 final size:41
Alignment explanation
Indices: 6228--6467 Score: 198
Period size: 41 Copynumber: 6.0 Consensus size: 41
6218 AAAATGAAAC
* * * *
6228 TTTAGCGGCGTTTTT-TCAACAAATGCCGCAATAGGGTGGTAA
1 TTTAGCGGCGTTTTTAT--ATAAACGCCGCAATAGAGTTGTAA
6270 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
* * * *
6309 TTATAGTGGCGTTTTCTAAAAAAAC-CCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTT-TATATAAACGCCGCAATAGAGTTGTAA
*
6351 TTTAGCGGCGTTTTTATATAAA-GCTGC-A-AGAGTTGT--
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
* * * *
6387 TTATAGTGGCG-TTTTACAAGAAACGCCGCAA-ATGGGTTGTACA
1 TT-TAGCGGCGTTTTTA-TATAAACGCCGCAATA-GAGTTGTA-A
*
6430 -TTAGTGGCGTTTTTATATAAACGCCGCAATAGAGTTGT
1 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT
6468 TTATAGTGGC
Statistics
Matches: 161, Mismatches: 21, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
36 7 0.04
37 11 0.07
38 11 0.07
39 5 0.03
40 40 0.25
41 62 0.39
42 24 0.15
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTAA
Found at i:6338 original size:40 final size:40
Alignment explanation
Indices: 6276--6482 Score: 221
Period size: 40 Copynumber: 5.2 Consensus size: 40
6266 GTAATTTAGC
6276 GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
1 GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
* * * *
6316 GGCGTTTTCTAAAAAAAC-CCGCAATAGAGTAGTAATT-TAGC
1 GGCGTTTT-TATATAAACGCCGCAATAGAGTTGT--TTATAGT
*
6357 GGCGTTTTTATATAAA-GCTGC-A-AGAGTTGTTTATAGT
1 GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
* * * **
6394 GGCG-TTTTACAAGAAACGCCGCAA-ATGGGTTGTACATTAGT
1 GGCGTTTTTA-TATAAACGCCGCAATA-GAGTTGTTTA-TAGT
6435 GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
1 GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
6475 GGCGTTTT
1 GGCGTTTT
6483 ACAAGAAACG
Statistics
Matches: 135, Mismatches: 20, Indels: 24
0.75 0.11 0.13
Matches are distributed among these distances:
36 7 0.05
37 11 0.08
38 11 0.08
39 3 0.02
40 50 0.37
41 45 0.33
42 8 0.06
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGT
Found at i:6351 original size:81 final size:82
Alignment explanation
Indices: 6234--6498 Score: 350
Period size: 81 Copynumber: 3.3 Consensus size: 82
6224 AAACTTTAGC
* * * *
6234 GGCGTTTTTTCAACAAATGCCGCAATAGGGTGGTAATTTAGCGGCGTTTTTATATAAACGCCGCA
1 GGCGTTTTTACAAAAAACGCCGCAATAGGGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCA
6299 ATAGAGTTGTTTATAGT
66 ATAGAGTTGTTTATAGT
* *
6316 GGCGTTTTCTA-AAAAAAC-CCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAA-GCTGC
1 GGCGTTTT-TACAAAAAACGCCGCAATAGGGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGC
6378 -A-AGAGTTGTTTATAGT
65 AATAGAGTTGTTTATAGT
* * *
6394 GGCG-TTTTACAAGAAACGCCGCAA-ATGGGTTGTACA-TTAGTGGCGTTTTTATATAAACGCCG
1 GGCGTTTTTACAAAAAACGCCGCAATA-GGGTAGTA-ATTTAGCGGCGTTTTTATATAAACGCCG
6456 CAATAGAGTTGTTTATAGT
64 CAATAGAGTTGTTTATAGT
*
6475 GGCG-TTTTACAAGAAACGCCGCAA
1 GGCGTTTTTACAAAAAACGCCGCAA
6499 ATGGGTCGTA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
76 2 0.01
77 10 0.06
78 51 0.31
79 6 0.04
80 5 0.03
81 76 0.46
82 13 0.08
83 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (82 bp):
GGCGTTTTTACAAAAAACGCCGCAATAGGGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCA
ATAGAGTTGTTTATAGT
Found at i:6499 original size:81 final size:81
Alignment explanation
Indices: 6271--6540 Score: 356
Period size: 81 Copynumber: 3.4 Consensus size: 81
6261 GGGTGGTAAT
*
6271 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTT-CTAAAAAAAC-
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTAC--AAGAAACG
*
6334 CCGC-AATAGAGTAGTA-A
64 CCGCAAAT-GGGTAGTACA
*
6351 TTTAGCGGCGTTTTTATATAAA-GCTGC-A-AGAGTTGTTTATAGTGGCGTTTTACAAGAAACGC
1 -TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGC
*
6413 CGCAAATGGGTTGTACA
65 CGCAAATGGGTAGTACA
*
6430 TTAGTGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
1 TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
*
6495 GCAAATGGGTCGTACA
66 GCAAATGGGTAGTACA
** * * *
6511 TTAGTTGCGTTTTTCTGTAAACGCTGCAAT
1 TTAGCGGCGTTTTTATATAAACGCCGCAAT
6541 TAATTTTAAC
Statistics
Matches: 171, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
77 6 0.04
78 53 0.31
79 10 0.06
80 5 0.03
81 97 0.57
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (81 bp):
TTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGTTTATAGTGGCGTTTTACAAGAAACGCC
GCAAATGGGTAGTACA
Found at i:6533 original size:41 final size:41
Alignment explanation
Indices: 6390--6539 Score: 137
Period size: 41 Copynumber: 3.7 Consensus size: 41
6380 GAGTTGTTTA
* *
6390 TAGTGGCGTTTTACAAG-AAACGCCGCAAATGGGTTGTACAT
1 TAGTGGCGTTTTTC-TGTAAACGCCGCAAATGGGTTGTACAT
* * * **
6431 TAGTGGCGTTTTTATATAAACGCCGC-AATAGAGTTGTTTA-
1 TAGTGGCGTTTTTCTGTAAACGCCGCAAAT-GGGTTGTACAT
* * *
6471 TAGTGGCGTTTTACAAG-AAACGCCGCAAATGGGTCGTACAT
1 TAGTGGCGTTTTTC-TGTAAACGCCGCAAATGGGTTGTACAT
* *
6512 TAGTTGCGTTTTTCTGTAAACGCTGCAA
1 TAGTGGCGTTTTTCTGTAAACGCCGCAA
6540 TTAATTTTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
40 31 0.37
41 53 0.63
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
TAGTGGCGTTTTTCTGTAAACGCCGCAAATGGGTTGTACAT
Found at i:15565 original size:21 final size:21
Alignment explanation
Indices: 15547--15632 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
15537 ATGAAGCAAG
15547 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* ** *
15568 GGAAGTAGCTAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
* * *
15589 GAAAGCAGAGAGAGAAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
* *
15610 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
15631 GG
1 GG
15633 CAGAACAGAG
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.37, C:0.16, G:0.42, T:0.05
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:15634 original size:21 final size:21
Alignment explanation
Indices: 15592--15647 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
15582 CAGCAGTGAA
* *
15592 AGCAGAGAGAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAGCGGC
*
15613 AGCACAGAGAGAGGCAGCGGC
1 AGCACAGAGAGAAGCAGCGGC
*
15634 AGAACAGAGAGAAG
1 AGCACAGAGAGAAG
15648 TAATATATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.41, T:0.02
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCGGC
Found at i:16030 original size:43 final size:46
Alignment explanation
Indices: 15983--16123 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 46
15973 CATACATTTA
*
15983 GCGGCGTTTGT-GATAAAAATGCCGCGAAATCTCAAGACATA-T-T
1 GCGGCGTTTGTCGACAAAAATGCCGCGAAATCTCAAGACATATTCT
* * *
16026 GCGGCGTTT-TCGACGAAATTGCCGCTAAATCTCAAGACATATTCT
1 GCGGCGTTTGTCGACAAAAATGCCGCGAAATCTCAAGACATATTCT
** * * * *
16071 GCGGCGTTTGT--AGGAAAACGCCGCTAAATATC-A-ACATCTTCT
1 GCGGCGTTTGTCGACAAAAATGCCGCGAAATCTCAAGACATATTCT
16113 GCGGCGTTTGT
1 GCGGCGTTTGT
16124 AGGAAAAACG
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
42 20 0.24
43 36 0.42
44 18 0.21
45 10 0.12
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (46 bp):
GCGGCGTTTGTCGACAAAAATGCCGCGAAATCTCAAGACATATTCT
Found at i:16245 original size:86 final size:83
Alignment explanation
Indices: 16022--16292 Score: 213
Period size: 86 Copynumber: 3.1 Consensus size: 83
16012 TCTCAAGACA
* * * * *
16022 TATTGCGGCGTTT-TCGACGAAATTGCCGCTAAATCTCAAGACATATTCTGCGGCGTTTGTAGGA
1 TATTGCGGCGTTTGTCG-C-AAAATGCCGCTAAATATCAACACCTA-T-TGCGGCGTTT-TAAGA
16086 AAACGCCGCTAAATATCAACATC
61 AAACGCCGCTAAATATCAACATC
* * * * * * * * *
16109 T-TCTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAATATCTACTGCGGCGTTTATGAAGAA
1 TAT-TGCGGCGTTTGT-CGCAAAATGCCGCTAAATATCAACACCTATTGCGGCGTTT-T-AAGAA
* *
16173 AACGCCGCTAAACATCAACGTC
62 AACGCCGCTAAATATCAACATC
* * **
16195 TATTGCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAACACCTATTGCGGCGTTTTTCTGCAAA
1 TATTGCGGCGTTTGTC-GCAAAATGCCGCTAAATATCAACACCTATTGCGGCG-TTTTAAG-AAA
* *
16260 ACGCCGCTAAATATCAATACC
63 ACGCCGCTAAATATCAACATC
*
16281 TTTTGCGGCGTT
1 TATTGCGGCGTT
16293 ACAAACGCCG
Statistics
Matches: 143, Mismatches: 33, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
85 12 0.08
86 97 0.68
87 32 0.22
88 1 0.01
89 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (83 bp):
TATTGCGGCGTTTGTCGCAAAATGCCGCTAAATATCAACACCTATTGCGGCGTTTTAAGAAAACG
CCGCTAAATATCAACATC
Found at i:16287 original size:43 final size:43
Alignment explanation
Indices: 16070--16292 Score: 209
Period size: 43 Copynumber: 5.2 Consensus size: 43
16060 AGACATATTC
*
16070 TGCGGCGTTTGTA-GGAAAACGCCGCTAAATATCAACATCT-T
1 TGCGGCGTTTGTATGCAAAACGCCGCTAAATATCAACATCTAT
* * * * * * *
16111 CTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAATATCTAC
1 -TGCGGCGTTTGTATGCAAAACGCCGCTAAATATCAACATCTAT
* * * *
16155 TGCGGCGTTTATGAAG-AAAACGCCGCTAAACATCAACGTCTAT
1 TGCGGCGTTTGT-ATGCAAAACGCCGCTAAATATCAACATCTAT
* * * * *
16198 TGCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAACACCTAT
1 TGCGGCGTTTGTATGCAAAACGCCGCTAAATATCAACATCTAT
* * * * *
16241 TGCGGCGTTTTTCTGCAAAACGCCGCTAAATATCAATACCTTT
1 TGCGGCGTTTGTATGCAAAACGCCGCTAAATATCAACATCTAT
16284 TGCGGCGTT
1 TGCGGCGTT
16293 ACAAACGCCG
Statistics
Matches: 148, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
42 14 0.09
43 132 0.89
44 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
TGCGGCGTTTGTATGCAAAACGCCGCTAAATATCAACATCTAT
Found at i:18081 original size:65 final size:65
Alignment explanation
Indices: 18025--18145 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
18015 TTACTCTGAC
*
18025 TAAA-TAAT-TTTGTTACAATTTATTATTGTGAAAT-AATATTATTTGTCACAATTTTTTATAAT
1 TAAATTAATATTTGTTACAATTTATTATT-TGAAATAAATA-AATTTGTCACAATTTTTTATAAT
18087 GA
64 GA
* * * *
18089 TAAATTAATATTTGTTATAATTTGTTATTTTAATTAAATAAATTTGTCACAATTTTT
1 TAAATTAATATTTGTTACAATTTATTATTTGAAATAAATAAATTTGTCACAATTTTT
18146 CATTTTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
64 4 0.08
65 24 0.49
66 21 0.43
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (65 bp):
TAAATTAATATTTGTTACAATTTATTATTTGAAATAAATAAATTTGTCACAATTTTTTATAATGA
Found at i:18101 original size:33 final size:33
Alignment explanation
Indices: 18025--18145 Score: 88
Period size: 33 Copynumber: 3.7 Consensus size: 33
18015 TTACTCTGAC
* * ** *
18025 TAAATAAT-TTTGTTACAATTTATTATTGTGAAA
1 TAAATAATATTTGTCACAATTTTTTATAAT-AAT
* *
18058 T-AATATTATTTGTCACAATTTTTTATAATGA-
1 TAAATAATATTTGTCACAATTTTTTATAATAAT
* * * **
18089 TAAATTAATATTTGTTATAATTTGTTATTTTAAT
1 TAAA-TAATATTTGTCACAATTTTTTATAATAAT
18123 TAAATAA-ATTTGTCACAATTTTT
1 TAAATAATATTTGTCACAATTTTT
18146 CATTTTGATA
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
31 1 0.01
32 21 0.31
33 42 0.62
34 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (33 bp):
TAAATAATATTTGTCACAATTTTTTATAATAAT
Found at i:18389 original size:13 final size:15
Alignment explanation
Indices: 18371--18402 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
18361 CAAAAGTTTT
18371 TATTGTGA-GAAA-A
1 TATTGTGACGAAATA
18384 TATTGTGACGAAATA
1 TATTGTGACGAAATA
18399 TATT
1 TATT
18403 TAACATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (15 bp):
TATTGTGACGAAATA
Found at i:21113 original size:16 final size:16
Alignment explanation
Indices: 21092--21134 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
21082 ATTAAAATCC
21092 CTACCTCTCGCTCTAT
1 CTACCTCTCGCTCTAT
21108 CTACCTCTCGCTCTAT
1 CTACCTCTCGCTCTAT
21124 CTACCTCTCGC
1 CTACCTCTCGC
21135 GGCAGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.12, C:0.47, G:0.07, T:0.35
Consensus pattern (16 bp):
CTACCTCTCGCTCTAT
Found at i:21651 original size:21 final size:21
Alignment explanation
Indices: 21625--21664 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21615 TTTAACTGCA
*
21625 TTTTCACTTTACTTTCAGTAT
1 TTTTCACTTTACGTTCAGTAT
*
21646 TTTTCACTTTTCGTTCAGT
1 TTTTCACTTTACGTTCAGT
21665 GTTTGGGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTCACTTTACGTTCAGTAT
Found at i:28821 original size:2 final size:2
Alignment explanation
Indices: 28814--28858 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28804 GCCATTGAAT
28814 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
28856 TA T
1 TA T
28859 CACAGAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28946 original size:3 final size:3
Alignment explanation
Indices: 28932--29013 Score: 96
Period size: 3 Copynumber: 28.0 Consensus size: 3
28922 TTTATCCATT
* * * * *
28932 TTA TTA TCA TTA TTA TTA ATA TTA TTA TCA TTA TTA ATA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
28980 TTA TTA TT- TTA TTA TTA TTA TTA TT- TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29014 AATATATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29022 original size:20 final size:20
Alignment explanation
Indices: 28932--29014 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 20
28922 TTTATCCATT
*
28932 TTATTATCATTATTATTAATA
1 TTATTATTATT-TTATTAATA
* *
28953 TTATTATCATTATTAATATTATTA
1 TTA-T-T-ATTATT-TTATTAATA
* *
28977 TCATTATTATTTTATTATTA
1 TTATTATTATTTTATTAATA
*
28997 TTATTATTTTTTTATTAA
1 TTATTATTATTTTATTAA
29015 ATATATTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 23 0.45
21 9 0.18
22 2 0.04
23 2 0.04
24 15 0.29
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTTTATTAATA
Found at i:31137 original size:18 final size:18
Alignment explanation
Indices: 31123--31157 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31113 AATTTTTTTT
31123 ATATTTATTATTTTTATA
1 ATATTTATTATTTTTATA
31141 ATATTTA-TATGTTTTAT
1 ATATTTATTAT-TTTTAT
31158 TTGCAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTTATTATTTTTATA
Found at i:41691 original size:18 final size:19
Alignment explanation
Indices: 41668--41706 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
41658 ATTATGCTTG
41668 AAGAAAAAAAAAAAA-AAA
1 AAGAAAAAAAAAAAAGAAA
41686 AAGAAAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAAAGAAA
41705 AA
1 AA
41707 ATAGAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAAAAAGAAA
Found at i:41712 original size:9 final size:9
Alignment explanation
Indices: 41668--41736 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
41658 ATTATGCTTG
41668 AAGAAAAAA
1 AAGAAAAAA
*
41677 AAAAAAAAA
1 AAGAAAAAA
41686 AAGAAAAAA
1 AAGAAAAAA
41695 AA-AAAAGAA
1 AAGAAAA-AA
41704 AA-AATAGAAA
1 AAGAA-A-AAA
*
41714 ATGAAAAAA
1 AAGAAAAAA
* *
41723 GAG-AAGAA
1 AAGAAAAAA
41731 AAGAAA
1 AAGAAA
41737 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 10 0.21
9 30 0.62
10 5 0.10
11 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:41720 original size:22 final size:22
Alignment explanation
Indices: 41671--41736 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
41661 ATGCTTGAAG
41671 AAAAAAAAA-AAAAAAAAGAAA
1 AAAAAAAAAGAAAAAAAAGAAA
*
41692 AAAAAAAAAGAAAAAATAGAAA
1 AAAAAAAAAGAAAAAAAAGAAA
** *
41714 ATGAAAAAAGAGAAGAAAAGAAA
1 AAAAAAAAAGA-AAAAAAAGAAA
41737 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 9 0.24
22 20 0.53
23 9 0.24
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAGAAA
Found at i:41722 original size:1 final size:1
Alignment explanation
Indices: 41671--41707 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
41661 ATGCTTGAAG
* *
41671 AAAAAAAAAAAAAAAAAGAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41708 TAGAAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:42790 original size:52 final size:52
Alignment explanation
Indices: 42671--43119 Score: 759
Period size: 52 Copynumber: 8.8 Consensus size: 52
42661 TATGTGCTCA
* * *
42671 ATAGCATCTTCTGGAA--GTTATTTAAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42720 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42772 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42824 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42876 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42928 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42980 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
43032 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
43080 ATAGCATCTTCTTGAAGTTTTCTTTGAGTTATCTAATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
43120 ATTAGACATA
Statistics
Matches: 385, Mismatches: 10, Indels: 9
0.95 0.02 0.02
Matches are distributed among these distances:
48 44 0.11
49 16 0.04
51 26 0.07
52 299 0.78
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:43972 original size:119 final size:118
Alignment explanation
Indices: 43751--44200 Score: 768
Period size: 119 Copynumber: 3.8 Consensus size: 118
43741 CAAATATTCA
* *
43751 AATTCATCACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
43816 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43869 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
43934 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43988 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
44053 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
44107 AATTCATCAGTTGATGGATCAACA-TTACAG-GTAA-AGTTCATAATGAGAAGAA--C-TCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
*
44166 GAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
44201 CATCAAGAGC
Statistics
Matches: 322, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
112 39 0.12
113 1 0.00
115 18 0.06
116 3 0.01
117 5 0.02
118 22 0.07
119 234 0.73
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (118 bp):
AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:44523 original size:3 final size:3
Alignment explanation
Indices: 44442--44507 Score: 64
Period size: 3 Copynumber: 22.7 Consensus size: 3
44432 TTTTATCCAT
* * * * *
44442 TTA TTA TCA -TA TTA ATA TTA -TA TTA TCA TTA TTA ATA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
44488 TTA TTT TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
44508 TTTTTTTAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
2 3 0.06
3 46 0.94
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:47019 original size:16 final size:18
Alignment explanation
Indices: 46990--47028 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
46980 AATTTCAAGA
46990 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
47008 AAATATA-T-ATTTTTAT
1 AAATATATTAATTTTTAT
47024 AAATA
1 AAATA
47029 AGATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:47034 original size:17 final size:16
Alignment explanation
Indices: 47000--47036 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
46990 AAATATATTA
*
47000 ATTTTTATAAATATAT
1 ATTTTTATAAATAGAT
47016 ATTTTTATAAATAAGAT
1 ATTTTTATAAAT-AGAT
47033 ATTT
1 ATTT
47037 ATTTATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTTTATAAATAGAT
Found at i:47253 original size:140 final size:141
Alignment explanation
Indices: 47047--47331 Score: 414
Period size: 140 Copynumber: 2.0 Consensus size: 141
47037 ATTTATTTAG
*
47047 AAATATCAGAAAAAGGCTTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
1 AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
*
47112 AAATAACTAAAACATTTTCTTAAAATAATAAT-AATAAA-AAAATATTTTAATATAGTAAGATAT
66 AAATAACTAAAACATTTTCTTAAAATAAGAATAAATAAATAAAATATTTTAATATA-TAAGATAT
47175 TTATTTATTTAA
130 TTATTTATTTAA
* * *
47187 AAATATCAGAAAAGGGATTCTAGTTGTTTTAAGACAACTCTTTTCTTCGAT-TTAAAAAAATAAA
1 AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATT-AAAAAATAAA
* * *
47251 TAAATAACTAAAATATTTTCTTAAAATAAGAATAAAATAAATTTAAAATATATATAATTTATAAG
65 TAAATAACTAAAACATTTTCTTAAAATAAGAAT-AAATAAA--TAAAATAT-TTTAATATATAA-
47316 GATATTTATTTATTTA
125 GATATTTATTTATTTA
47332 TTTAAACAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
139 2 0.02
140 88 0.68
142 6 0.05
145 10 0.08
146 23 0.18
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (141 bp):
AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
AAATAACTAAAACATTTTCTTAAAATAAGAATAAATAAATAAAATATTTTAATATATAAGATATT
TATTTATTTAA
Found at i:47391 original size:12 final size:11
Alignment explanation
Indices: 47364--47440 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 11
47354 TATGACTAAG
47364 ATAATAATAAA
1 ATAATAATAAA
47375 ATAAT-A-AAA
1 ATAATAATAAA
* *
47384 GTAATAATTTAA
1 ATAATAA-TAAA
47396 AT-ATATATCAAA
1 ATAATA-AT-AAA
47408 AGTAATAATAAA
1 A-TAATAATAAA
*
47420 ATAATATTACAA
1 ATAATAATA-AA
47432 ATGAATAAT
1 AT-AATAAT
47441 GATCAAAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
9 7 0.14
10 2 0.04
11 16 0.31
12 15 0.29
13 8 0.16
14 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:47432 original size:25 final size:24
Alignment explanation
Indices: 47365--47426 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
47355 ATGACTAAGA
47365 TAATAAT-AAA-ATA-AT-AAAAG
1 TAATAATAAAATATATATCAAAAG
*
47385 TAATAATTTAAATATATATCAAAAG
1 TAATAA-TAAAATATATATCAAAAG
47410 TAATAATAAAATA-ATAT
1 TAATAATAAAATATATAT
47427 TACAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 3 0.08
23 7 0.19
24 8 0.22
25 11 0.31
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
TAATAATAAAATATATATCAAAAG
Found at i:47711 original size:2 final size:2
Alignment explanation
Indices: 47704--47770 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
47694 ACCTAAAATA
47704 AT AT AT AT AT AT AT AT AT -T 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
47745 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
47771 TGCAATGACT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:48580 original size:24 final size:24
Alignment explanation
Indices: 48546--48610 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
48536 GTGCAGCTGC
*
48546 GACGTGTAGGGGCTGCTGGTGAGG
1 GACGTGGAGGGGCTGCTGGTGAGG
* *
48570 GACGTGGAGGGGCTACTGGTGTGG
1 GACGTGGAGGGGCTGCTGGTGAGG
48594 GACGTGGAGGGGCTGCT
1 GACGTGGAGGGGCTGCT
48611 CGGGTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.12, C:0.14, G:0.54, T:0.20
Consensus pattern (24 bp):
GACGTGGAGGGGCTGCTGGTGAGG
Found at i:49116 original size:45 final size:45
Alignment explanation
Indices: 49049--49169 Score: 179
Period size: 45 Copynumber: 2.7 Consensus size: 45
49039 GAGGTCTTAT
* * * *
49049 CATCTTGCACTGTAGGTTTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
*
49094 CATCATGCACTGAAGGACTTACAGATGACCCAAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
* *
49139 CATCATGCACTAAAGGTCTTACAAATGACCC
1 CATCATGCACTGAAGGTCTTACAGATGACCC
49170 TGAGGCTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
Found at i:49293 original size:76 final size:74
Alignment explanation
Indices: 49130--49685 Score: 870
Period size: 76 Copynumber: 7.5 Consensus size: 74
49120 GACCCAAAGG
** *
49130 TTTTGAAAACATCATGCACTAAAGGTCTTACAAATGACCCTGAGGCTTTAAATATC-AAAAGCT-
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
49193 CCGAAGGCT
66 CCGAAGGCT
* * *
49202 TTTTGAAAACATCATGCACTGTAGGTCATACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
**
49267 TCATGAAGGCT
64 TCCCGAAGGCT
* *
49278 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
*
49343 TCCCAAAGGC-
64 TCCCGAAGGCT
49353 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
49418 CCGAAGGCT
66 CCGAAGGCT
*
49427 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
*
49492 TCCCAAAGGCT
64 TCCCGAAGGCT
49503 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGC-TTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
*
49567 CTGAAGGCTT
66 CCGAAGGC-T
*
49577 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAAGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
49642 CCGAAGGC-
66 CCGAAGGCT
*
49650 TTTTGAAAACATCATGCACTATAGGTCTTACAGATG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
49686 TGGGAAATAG
Statistics
Matches: 450, Mismatches: 25, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
72 44 0.10
73 78 0.17
74 101 0.22
75 82 0.18
76 145 0.32
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (74 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCT
Found at i:49467 original size:149 final size:148
Alignment explanation
Indices: 49130--49685 Score: 879
Period size: 149 Copynumber: 3.7 Consensus size: 148
49120 GACCCAAAGG
* * *
49130 TTTTGAAAACATCATGCACTAAAGGTCTTACAAATGACCCTGAGGCTTTAAATATC-AAAAGCT-
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
* * * *
49193 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCATACAGATGACCCTAAGGCTTTAAAAACA
66 CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATA
*
49258 TCAAAAAGCTCATGAAGGCT
129 TCAAAAAGCTCCTGAAGGCT
49278 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTT--AAACATCAAAAAGC
49343 TCCCAAAGGC-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
64 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
*
49407 TCAAAAAGCTCCCGAAGGCT
129 TCAAAAAGCTCCTGAAGGCT
*
49427 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTT--AAACATCAAAAAGC
49492 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGC-TTAAATA
64 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
49556 TCAAAAAGCTCCTGAAGGCTT
129 TCAAAAAGCTCCTGAAGGC-T
* * *
49577 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAAGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
* *
49642 CCGAAGGC-TTTTGAAAACATCATGCACTATAGGTCTTACAGATG
66 CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
49686 TGGGAAATAG
Statistics
Matches: 387, Mismatches: 15, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
147 35 0.09
148 69 0.18
149 121 0.31
150 101 0.26
151 54 0.14
152 7 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (148 bp):
TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
AAAAAGCTCCTGAAGGCT
Found at i:49519 original size:225 final size:222
Alignment explanation
Indices: 49122--49685 Score: 929
Period size: 225 Copynumber: 2.5 Consensus size: 222
49112 TTACAGATGA
** *
49122 CCCAAAGG-TTTTGAAAACATCATGCACTAAAGGTCTTACAAATGACCCTGAGGCTTTAAATATC
1 CCCAAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
*
49186 -AAAAGCT-CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCATACAGATGACCCTAAGGCT
66 AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCT
**
49249 TTAAAAACATCAAAAAGCTCATGAAGGCTTTTTGAAAACATCATGCACTATAGGTCTTACAGATG
131 TTAAAAACATCAAAAAGCTCACAAAGGCTTTTTGAAAACATCATGCACTATAGGTCTTACAGATG
49314 ACCCTGAGGCTTTAAAAACATCAAAAAGCT
196 ACCCTGAGGC-TT--AAACATCAAAAAGCT
49344 CCCAAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
1 CCCAAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
*
49409 AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCT
66 AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCT
* *
49474 TTAAAAACATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
131 TTAAAAACATCAAAAAGCTCACAAAGGCTTTTTGAAAACATCATGCACTATAGGTCTTACAGATG
*
49539 ACCCTGAGGCTTAAATATCAAAAAGCT
196 ACCCTGAGGCTTAAACATCAAAAAGCT
** *
49566 CCTGAAGGCTTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAAGCTTTAAATA
1 CCCAAAGGC--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
*
49631 TCAAAAAGCTCCCGAAGGC-TTTTGAAAACATCATGCACTATAGGTCTTACAGATG
64 TCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
49686 TGGGAAATAG
Statistics
Matches: 323, Mismatches: 14, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
222 29 0.09
223 88 0.27
224 81 0.25
225 125 0.39
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (222 bp):
CCCAAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAAGGCT
TTAAAAACATCAAAAAGCTCACAAAGGCTTTTTGAAAACATCATGCACTATAGGTCTTACAGATG
ACCCTGAGGCTTAAACATCAAAAAGCT
Found at i:56957 original size:13 final size:14
Alignment explanation
Indices: 56921--56960 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
56911 ATGTAAGTGT
56921 AAATACAAACAT--A
1 AAATACAAA-ATGCA
56934 AAATACAAAATGCA
1 AAATACAAAATGCA
56948 AAATAC-AAATGCA
1 AAATACAAAATGCA
56961 TGTATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 16 0.64
14 7 0.28
ACGTcount: A:0.65, C:0.15, G:0.05, T:0.15
Consensus pattern (14 bp):
AAATACAAAATGCA
Found at i:60034 original size:136 final size:133
Alignment explanation
Indices: 59774--60040 Score: 396
Period size: 136 Copynumber: 2.0 Consensus size: 133
59764 TAATTTTTAT
*
59774 AAATATATTTTATAAATAAGTATTTATTTATTTAGAAATATCAGAAAATGGCTTCTATTGCTTTA
1 AAATATATTTTATAAATAAGTATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTATTGCTTTA
* *
59839 AGACAACTCTTTTCTTTGATATTAAAAATAAATAAATAACTAAACATTTTCTTAAAAAATAATAA
66 AGACAACTCATTTCTTCGATATTAAAAATAAATAAATAACTAAACATTTTCTT-AAAAATAATAA
59904 TAAA
130 TAAA
*
59908 AAAT-TATTTTAATATAGTAAGATATTTATTTATTTA-AAATATCAGAAAAGGGCTTCTAGTTGC
1 AAATATATTTT-ATA-AATAAG-TATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTA-TTGC
* *
59971 TTTAAGACAACTCATTTCTTCGATTTTAAAAAATAAATAAATAACTAAAATATTTTCTT-AAAAT
62 TTTAAGACAACTCATTTCTTCGATATT-AAAAATAAATAAATAACT-AAACATTTTCTTAAAAAT
60035 AATAAT
125 AATAAT
60041 GAAATAAAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
133 6 0.05
134 7 0.06
135 26 0.21
136 53 0.44
137 18 0.15
138 11 0.09
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (133 bp):
AAATATATTTTATAAATAAGTATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTATTGCTTTA
AGACAACTCATTTCTTCGATATTAAAAATAAATAAATAACTAAACATTTTCTTAAAAATAATAAT
AAA
Found at i:60461 original size:2 final size:2
Alignment explanation
Indices: 60454--60485 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
60444 TATTTACCTA
60454 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.