Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002497.1 Hibiscus syriacus cultivar Beakdansim tig00005091_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: 101296
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:415 original size:14 final size:15
Alignment explanation
Indices: 398--439 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
388 TTTAAGATAA
*
398 TTTATTAATAAAT-T
1 TTTATTAAAAAATAT
412 TTTATATAAAAAATAT
1 TTTAT-TAAAAAATAT
428 TTTATTAAAAAA
1 TTTATTAAAAAA
440 GTATAATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.20
15 14 0.56
16 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTATTAAAAAATAT
Found at i:4070 original size:20 final size:20
Alignment explanation
Indices: 4047--4089 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4037 ATCACAAAGT
4047 GAATTTGACTTTCACGTTGC
1 GAATTTGACTTTCACGTTGC
*
4067 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACGTTGC
4087 GAA
1 GAA
4090 AGTGTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
GAATTTGACTTTCACGTTGC
Found at i:5590 original size:21 final size:21
Alignment explanation
Indices: 5564--5678 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
5554 GTGAATCGGG
* *
5564 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
5585 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
5606 CTCTTGAACAGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
** *
5627 CTCTTGAA-GGATGATAGGGCC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
5648 CTCTTGAATGATAGGG-GAGGC
1 CTCTTGAACGGT-GGGAGGGGC
5669 CTCTTGAACG
1 CTCTTGAACG
5679 ATGACAGATG
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
20 1 0.01
21 69 0.96
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:5630 original size:42 final size:42
Alignment explanation
Indices: 5564--5682 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 42
5554 GTGAATCGGG
* * *
5564 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
* *
5606 CTCTTGAACAGTGGGAGGGGCCTCTTGAAGGATGATAGGGCC
1 CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
*
5648 CTCTTGAA-TGATAGGG-GAGGCCTCTTGAACGATGA
1 CTCTTGAACAG-T-GGGAGAGGCCTCTTGAACGATGA
5683 CAGATGAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 63 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACAGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
Found at i:5846 original size:12 final size:12
Alignment explanation
Indices: 5827--5868 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5817 GGGCCGCTAA
*
5827 AAATAAATTAAT
1 AAATAAATCAAT
*
5839 ACATAAATCAAT
1 AAATAAATCAAT
5851 AAATAAA-CAAAT
1 AAATAAATC-AAT
5863 AAATAA
1 AAATAA
5869 CGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:5990 original size:21 final size:21
Alignment explanation
Indices: 5965--6018 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5955 TGCAATAATT
* *
5965 CCACGTAGAGCAACTACCTCA
1 CCACGTAAAGCAAATACCTCA
* * *
5986 TCACGCAAAGTAAATACCTCA
1 CCACGTAAAGCAAATACCTCA
6007 CCACGTAAAGCA
1 CCACGTAAAGCA
6019 GCATTGTCAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.33, G:0.13, T:0.15
Consensus pattern (21 bp):
CCACGTAAAGCAAATACCTCA
Found at i:8215 original size:22 final size:22
Alignment explanation
Indices: 8190--8245 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
8180 GATTTTACCA
8190 GAGATGGGGACGAATTTCGTCG
1 GAGATGGGGACGAATTTCGTCG
*
8212 GAGATTGGGACGAATTTCGTCG
1 GAGATGGGGACGAATTTCGTCG
8234 GAGATGGGGACG
1 GAGATGGGGACG
8246 GATGTCGCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.12, G:0.43, T:0.21
Consensus pattern (22 bp):
GAGATGGGGACGAATTTCGTCG
Found at i:8445 original size:20 final size:20
Alignment explanation
Indices: 8422--8471 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
8412 TGACTTCTGT
*
8422 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
*
8442 GTTGCGATTTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
8462 GTTGCGAATT
1 GTTGCGAATT
8472 TAGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:10878 original size:16 final size:14
Alignment explanation
Indices: 10842--10869 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10832 ATGTAATATT
10842 TTAAATATTGATAC
1 TTAAATATTGATAC
10856 TTAAATATTGATAC
1 TTAAATATTGATAC
10870 AATTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAAATATTGATAC
Found at i:11432 original size:14 final size:14
Alignment explanation
Indices: 11411--11448 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
11401 ACATTTCTAA
11411 TAAC-ATATTTCCT
1 TAACTATATTTCCT
11424 TAACTATATATTTCCT
1 TAAC--TATATTTCCT
11440 TAACTATAT
1 TAACTATAT
11449 ATTAAGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
16 13 0.59
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (14 bp):
TAACTATATTTCCT
Found at i:11436 original size:16 final size:16
Alignment explanation
Indices: 11415--11451 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
11405 TTCTAATAAC
11415 ATATTTCCTTAACTAT
1 ATATTTCCTTAACTAT
11431 ATATTTCCTTAACTAT
1 ATATTTCCTTAACTAT
11447 ATATT
1 ATATT
11452 AAGACTGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTCCTTAACTAT
Found at i:14905 original size:31 final size:31
Alignment explanation
Indices: 14859--14938 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
14849 TTTATTTAAA
*
14859 TTTTAAA-AATTATAAAACAACCATTAAGTT
1 TTTTAAATAATTATAAAACAACCATTAAATT
* * **
14889 TTTTAAATGATTATAAAATATTCATTAAATT
1 TTTTAAATAATTATAAAACAACCATTAAATT
* *
14920 TTATCAAATTATTATAAAA
1 TT-TTAAATAATTATAAAA
14939 TGATCATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.17
31 20 0.49
32 14 0.34
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTTAAATAATTATAAAACAACCATTAAATT
Found at i:14939 original size:32 final size:32
Alignment explanation
Indices: 14880--14968 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
14870 ATAAAACAAC
* * *
14880 CATTAAGTTTT-TTAAATGATTATAAAAT-ATT
1 CATTAAATTTTATCAAATTATTATAAAATGA-T
14911 CATTAAATTTTATCAAATTATTATAAAATGAT
1 CATTAAATTTTATCAAATTATTATAAAATGAT
* *
14943 CATTAAA-CTTATCAAATTTTTATAAA
1 CATTAAATTTTATCAAATTATTATAAA
14969 TTAGTCTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 27 0.53
32 23 0.45
33 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (32 bp):
CATTAAATTTTATCAAATTATTATAAAATGAT
Found at i:14958 original size:31 final size:32
Alignment explanation
Indices: 14893--14968 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
14883 TAAGTTTTTT
* *
14893 AAATGATTATAAAATATTCATTAAATTTTATC
1 AAATTATTATAAAATATTCATTAAATCTTATC
14925 AAATTATTATAAAATGA-TCATTAAA-CTTATC
1 AAATTATTATAAAAT-ATTCATTAAATCTTATC
*
14956 AAATTTTTATAAA
1 AAATTATTATAAA
14969 TTAGTCTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 17 0.43
32 22 0.55
33 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (32 bp):
AAATTATTATAAAATATTCATTAAATCTTATC
Found at i:18945 original size:48 final size:48
Alignment explanation
Indices: 18874--18970 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
18864 CGATAATGTC
18874 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
1 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
* *
18922 GGAAGAAAGTATGATGTTGATGTGTGAAAAGTTGGCATTATTTGTACG
1 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
18970 G
1 G
18971 CTCTGTAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (48 bp):
GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
Found at i:19107 original size:16 final size:16
Alignment explanation
Indices: 19086--19117 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19076 TATGTATATA
19086 AGATAAATATATTTAT
1 AGATAAATATATTTAT
19102 AGATAAATATATTTAT
1 AGATAAATATATTTAT
19118 GTTTATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
AGATAAATATATTTAT
Found at i:28748 original size:51 final size:52
Alignment explanation
Indices: 28654--28753 Score: 166
Period size: 51 Copynumber: 1.9 Consensus size: 52
28644 ATTATAATAT
* *
28654 CCTTGTGATTAGTTGTAATCTCCTAACTTTAGGCTAGTCTCCTATTTATGTG
1 CCTTGTAATTAGTTGTAATCTCCTAACTCTAGGCTAGTCTCCTATTTATGTG
*
28706 CCTTGTAATTAGTTGTAATC-CCTAACTCTAGGCTAGTTTCCTATTTAT
1 CCTTGTAATTAGTTGTAATCTCCTAACTCTAGGCTAGTCTCCTATTTAT
28754 ATATGCCCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 26 0.58
52 19 0.42
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCTCCTAACTCTAGGCTAGTCTCCTATTTATGTG
Found at i:32537 original size:15 final size:15
Alignment explanation
Indices: 32519--32577 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
32509 GAAAAGATGA
*
32519 TATTAGAAATATTAT
1 TATTATAAATATTAT
* *
32534 TATTTTAAATATTTT
1 TATTATAAATATTAT
*
32549 TTTTATAAA-A-TAT
1 TATTATAAATATTAT
32562 TATT-TAAAATATTAT
1 TATTAT-AAATATTAT
32577 T
1 T
32578 TTTTTATCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 2 0.06
15 23 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTATAAATATTAT
Found at i:32571 original size:28 final size:32
Alignment explanation
Indices: 32531--32595 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 32
32521 TTAGAAATAT
*
32531 TATTATTTTAAATA-T-TTTTTTTAT-A-AAA
1 TATTATTTAAAATATTATTTTTTTATCATAAA
32559 TATTATTTAAAATATTATTTTTTTATCATAAA
1 TATTATTTAAAATATTATTTTTTTATCATAAA
32591 TATTA
1 TATTA
32596 ATATTAGACG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 13 0.41
29 1 0.03
30 9 0.28
31 1 0.03
32 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTAAAATATTATTTTTTTATCATAAA
Found at i:32666 original size:45 final size:45
Alignment explanation
Indices: 32562--32679 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 45
32552 TATAAAATAT
* *
32562 TATTTAAAATATTATTTTTTTATCATAAATATTAATATTAGACGT
1 TATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAGACGC
* * *
32607 TACTT-AAATATTATTTTTTTATTAAAAATATTAATATT-GAATGC
1 TATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAG-ACGC
*
32651 TATTTAAAAAATTA-TTTTTTATCAAAAAT
1 TATTTAAAATATTATTTTTTTATCAAAAAT
32680 TAGTTAACAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 51 0.81
45 11 0.17
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (45 bp):
TATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAGACGC
Found at i:33072 original size:16 final size:16
Alignment explanation
Indices: 33035--33094 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
33025 GTTTACGAAA
*
33035 GAATTAGAATCTGTAAAG
1 GAATTAGAAT-T-TATAG
33053 GAATTAGAATTTATAG
1 GAATTAGAATTTATAG
* * *
33069 GAATTGGAATATGTAG
1 GAATTAGAATTTATAG
*
33085 GAATTGGAAT
1 GAATTAGAAT
33095 CCAATTCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 27 0.71
17 1 0.03
18 10 0.26
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (16 bp):
GAATTAGAATTTATAG
Found at i:33726 original size:36 final size:38
Alignment explanation
Indices: 33642--33731 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
33632 TTTTCACCCT
*
33642 AAACCCGAACCCGACCTGACTCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCTGACCCGAATATCACACTTAAAA
33681 AAACCCGACCCGA-CTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
33718 AAA-CCGACCCGACC
1 AAACCCGACCCGACC
33732 CAAACAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
36 9 0.19
37 9 0.19
38 23 0.48
39 7 0.15
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (38 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:34072 original size:207 final size:206
Alignment explanation
Indices: 33688--34119 Score: 649
Period size: 205 Copynumber: 2.1 Consensus size: 206
33678 AAAAAACCCG
* *
33688 ACCCGACTCGACCCGAATATCACACTTAAAAAACCGACCCGACCCAAACAAAATAAAGTTTCATC
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA-C-ACCCGACCCAAACAAAATAAAATTTCATC
*
33753 CGACCTGACCCGAATATATGAATTAGAAATCCGACCCGACCAGACCCGAAATAATAAAAAAAAAT
64 CGACCTGACCCGAATATATGAATTAAAAATCCGA-CC-ACCAGACCCGAAATAATAAAAAAAAAT
* *
33818 TATTTAATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCG
127 TATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCG
*
33883 ATTTTTTTCACCCTAA
192 -GTTTTTTCACCCTAA
* *
33899 ACCCGACCCAACCCGAATATCACACTT-AAAAA-ACCCGACCCGAACAAAATAAAATTTCATCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAACACCCGACCCAAACAAAATAAAATTTCATCCG
* * *
33962 ACCTGACCCGAATATATGAATTAAAAATTCGA-C-CC-GATCCGAAATAATAAAAAAATATTTTT
66 ACCTGACCCGAATATATGAATTAAAAATCCGACCACCAGACCCGAAATAATAAAAAAA-A--ATT
34024 ATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGG
128 ATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGG
34089 TTTTTTCACCCTAA
193 TTTTTTCACCCTAA
34103 ACCCGAACCCGACCCGA
1 ACCCG-ACCCGACCCGA
34120 CCCGACCCAA
Statistics
Matches: 205, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
202 19 0.09
203 3 0.01
204 19 0.09
205 75 0.37
207 59 0.29
210 5 0.02
211 25 0.12
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (206 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAACACCCGACCCAAACAAAATAAAATTTCATCCG
ACCTGACCCGAATATATGAATTAAAAATCCGACCACCAGACCCGAAATAATAAAAAAAAATTATT
TAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTT
TTTCACCCTAA
Found at i:34170 original size:37 final size:37
Alignment explanation
Indices: 34108--34195 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
34098 CCTAAACCCG
*
34108 AACCCGACCCGACCCGACCCAAATATCACACTTAAAA
1 AACCCGACCCGACCCAACCCAAATATCACACTTAAAA
* * * *
34145 AACCCGACCCGACTCAACCCGAATATCATACTTTAAA
1 AACCCGACCCGACCCAACCCAAATATCACACTTAAAA
34182 AACCCGACCCGACC
1 AACCCGACCCGACC
34196 TAAACAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.38, C:0.41, G:0.09, T:0.12
Consensus pattern (37 bp):
AACCCGACCCGACCCAACCCAAATATCACACTTAAAA
Found at i:34171 original size:252 final size:253
Alignment explanation
Indices: 33899--34418 Score: 773
Period size: 257 Copynumber: 2.0 Consensus size: 253
33889 TTCACCCTAA
33899 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCGACCCG-AACAAAATAAAATTTCATCCGA
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCGACCCGAAACAAAATAAAATTTCAT----
*
33963 CCTGACCCGAATATATGAATTAAAAATTCGACCCGA-T-CC-GAAATAATAAAAAAATATTTTTA
62 CC-GACCCGAATATATGAATTAAAAATTCAACCCGACTACCTGAAATAATAAAAAAATATTTTTA
34025 TTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCG-G
126 TTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGAG
34089 TTTTTTCACCCTAAACCCGAACCCGACCCGACCCGACCCAAATATCACACTT-AAAAAACCCG
191 TTTTTTCACCCTAAACCCGAACCCGACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
* * * *
34151 ACCCGACTCAACCCGAATATCATACTTTAAAAACCCGACCCGACCTAAACAAAATAAAGTTTCAT
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCGACCCG----AAACAAAATAAAATTTCAT
* *
34216 CCGACCCGAATATATGAATTAGAAATTCAACCCGACCTGACCTGAAATAATAAAAAATTATTTTT
62 CCGACCCGAATATATGAATTAAAAATTCAACCCGA-CT-ACCTGAAATAATAAAAAAATATTTTT
* * *
34281 ATTTAATAAAAACAGTGACTTAATCCGATCCGACCTGAATTATATATATTTTCGGGTCGGTCCGA
125 ATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGA
* * *
34346 TTTTTTTCACTCTAAACCCGAACTCGACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
190 GTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
*
34410 ATCCGACCC
1 ACCCGACCC
34419 GACCAAAATA
Statistics
Matches: 241, Mismatches: 15, Indels: 17
0.88 0.05 0.06
Matches are distributed among these distances:
252 70 0.29
253 2 0.01
254 1 0.00
256 2 0.01
257 99 0.41
258 50 0.21
259 17 0.07
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.24
Consensus pattern (253 bp):
ACCCGACCCAACCCGAATATCACACTTAAAAAACCCGACCCGAAACAAAATAAAATTTCATCCGA
CCCGAATATATGAATTAAAAATTCAACCCGACTACCTGAAATAATAAAAAAATATTTTTATTTAA
TAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGAGTTTTT
TCACCCTAAACCCGAACCCGACCCGACCCGACCCAAATATCACACTTAAAAAAACCCG
Found at i:37083 original size:24 final size:25
Alignment explanation
Indices: 37043--37089 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
37033 ATTTTAAATT
37043 TATATACTTTTTAATAAAATTTATA
1 TATATACTTTTTAATAAAATTTATA
*
37068 TATATA-TTTTTTATAAAATTTA
1 TATATACTTTTTAATAAAATTTA
37090 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATACTTTTTAATAAAATTTATA
Found at i:41560 original size:20 final size:20
Alignment explanation
Indices: 41481--41581 Score: 109
Period size: 20 Copynumber: 5.0 Consensus size: 20
41471 AGGGTAATTA
*
41481 TATCCGTAAAATCGCAACACG
1 TATCCGT-AAATCGCAACGCG
41502 TATCCGTAAATCGCAACGAC-
1 TATCCGTAAATCGCAACG-CG
* *
41522 AATACGTAAAATCGCAACGCG
1 TATCCGT-AAATCGCAACGCG
41543 TATCCGTAAATCGCAACGCG
1 TATCCGTAAATCGCAACGCG
*
41563 -AT-CGATAATTCGCAACGCG
1 TATCCG-TAAATCGCAACGCG
41582 ATCTCCGGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
19 15 0.21
20 29 0.41
21 24 0.34
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (20 bp):
TATCCGTAAATCGCAACGCG
Found at i:41637 original size:20 final size:20
Alignment explanation
Indices: 41612--41677 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
41602 GTTTCCAGAT
*
41612 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
41632 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
41652 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
41672 TCGCAA
1 TCGCAA
41678 CAAGATTCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:45051 original size:33 final size:34
Alignment explanation
Indices: 45001--45069 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
44991 GCAACACAGA
45001 ATTTTCATTTTCGCATTGCGATTCACTCGTTGCG
1 ATTTTCATTTTCGCATTGCGATTCACTCGTTGCG
*
45035 ATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTTCATTTTCGCATTGCGATTCACTCGTTGCG
45068 AT
1 AT
45070 CAAAATCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (34 bp):
ATTTTCATTTTCGCATTGCGATTCACTCGTTGCG
Found at i:45301 original size:20 final size:20
Alignment explanation
Indices: 45276--45364 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
45266 TAACGCGGAA
45276 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
45296 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
45316 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGAAAATGACT
*
45336 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
45356 ATCGCAACG
1 ATCGCAACG
45365 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:45335 original size:40 final size:40
Alignment explanation
Indices: 45276--45364 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
45266 TAACGCGGAA
45276 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACT
* * *
45316 ATCGCAATGCGGAATTGACTATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACT
45356 ATCGCAACG
1 ATCGCAACG
45365 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACT
Found at i:45424 original size:34 final size:34
Alignment explanation
Indices: 45336--45431 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
45326 GGAATTGACT
** **
45336 ATCGCAACACGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
45370 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
45403 ATCGTAATGCGAAAATGAAAATCGTAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
45432 CGAAATTGCG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:45598 original size:14 final size:14
Alignment explanation
Indices: 45579--45615 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45569 CATCAATTAA
45579 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
45593 ACAAATCATCTTTT
1 ACAAATCAACATTT
45607 ACAAATCAA
1 ACAAATCAA
45616 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:47075 original size:42 final size:42
Alignment explanation
Indices: 46968--47079 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
46958 TCTAGAATGT
* * * *
46968 TGGGAG-GGACCTCTTCAACGATGACAGTGGCGTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
47010 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
47052 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
47080 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:47582 original size:20 final size:20
Alignment explanation
Indices: 47559--47645 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
47549 GAAACTTAAA
*
47559 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
47579 ATCGCAATGCGAAAATGACC
1 ATCGCAATGCGAAAATGACT
*
47599 ATCGTAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
47619 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
47639 ATCGCAA
1 ATCGCAA
47646 CGAGAGAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:47702 original size:19 final size:19
Alignment explanation
Indices: 47689--47758 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
47679 CGCGATTATA
47689 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
47708 GTTTCACGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
47726 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
47741 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
47759 CATTTCTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.64
ACGTcount: A:0.07, C:0.16, G:0.29, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:47733 original size:14 final size:14
Alignment explanation
Indices: 47714--47740 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47704 TTTGGTTTCA
47714 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
47728 CGTTGCGATTTTG
1 CGTTGCGATTTTG
47741 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:47737 original size:33 final size:33
Alignment explanation
Indices: 47695--47758 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
47685 TATAGTTTCG
47695 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
*
47728 CGTTGCGATTTTGGTTTCGCGTTGCGATTTT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTT
47759 CATTTCTCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
Found at i:47745 original size:52 final size:51
Alignment explanation
Indices: 47680--47829 Score: 160
Period size: 52 Copynumber: 2.9 Consensus size: 51
47670 AAATCGCAAC
* * *
47680 GCGATTATAGTTTCGCGTTGCGATTTTGGTTTCACGTTGCGATTTTGTCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTT-ATTTCACGTTGCGATTTTCTCGTT
* * * *
47732 GCGATTTTGGTTTCGCGTTGCGATTTTCATTTCTCGTTACGATTCTCTCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTT-ATTTCACGTTGCGATTTTCTCGTT
* *
47784 GCGA-TTCA-TTTCGCGTTGCGATAGTTATTTTTCACGTTGCGATTTT
1 GCGATTTTAGTTTCGCGTTGCGAT--TT-TATTTCACGTTGCGATTTT
47830 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
50 14 0.17
51 2 0.02
52 64 0.79
53 1 0.01
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (51 bp):
GCGATTTTAGTTTCGCGTTGCGATTTTATTTCACGTTGCGATTTTCTCGTT
Found at i:47764 original size:19 final size:19
Alignment explanation
Indices: 47690--47845 Score: 68
Period size: 19 Copynumber: 8.7 Consensus size: 19
47680 GCGATTATAG
**
47690 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
*
47709 TTTCACGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
* **
47725 TGT--CGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
47742 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
47761 TTTCTCGTTACGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
47777 --TCTCGTTGCGA--TTCA
1 TTTCGCGTTGCGATTTTCA
*
47792 TTTCGCGTTGCGATAGTTAT-T
1 TTTCGCGTTGCGAT--TT-TCA
* *
47813 TTTCACGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
47832 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
47846 AAGTAAACTA
Statistics
Matches: 108, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
14 21 0.19
15 3 0.03
16 2 0.02
17 15 0.14
18 4 0.04
19 37 0.34
20 11 0.10
21 14 0.13
22 1 0.01
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:48039 original size:94 final size:94
Alignment explanation
Indices: 47893--48272 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
47883 ATGGATTGCA
* * * *
47893 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACGCAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
47957 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
47986 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
48051 TTAGCAGAATTGGCAGCAACAGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
48080 TTACTTTCAACCAAAAGATAAAACAAAGGCAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
48145 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
48174 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
48238 TTTAGCAGTATTGGCAGTAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
48268 TTACT
1 TTACT
48273 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 22 0.08
94 248 0.92
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:49533 original size:11 final size:11
Alignment explanation
Indices: 49492--49534 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
49482 TTATAAGATA
49492 ATCATTAAATT
1 ATCATTAAATT
*
49503 -TTATTAAATT
1 ATCATTAAATT
* *
49513 ATAATAAAATT
1 ATCATTAAATT
49524 ATCATTAAATT
1 ATCATTAAATT
49535 TAGGGTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
ATCATTAAATT
Found at i:50241 original size:2 final size:2
Alignment explanation
Indices: 50234--50287 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
50224 TTTAAAAATC
50234 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
50276 AT AT AT AT AT AT
1 AT AT AT AT AT AT
50288 TGATATACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61273 original size:16 final size:16
Alignment explanation
Indices: 61252--61282 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61242 TCGCCGACAA
61252 AAATTTACTATTCACG
1 AAATTTACTATTCACG
61268 AAATTTACTATTCAC
1 AAATTTACTATTCAC
61283 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATTTACTATTCACG
Found at i:61550 original size:30 final size:30
Alignment explanation
Indices: 61514--61574 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
61504 GAGAAAATTT
61514 ACAGGTGTTTACTAAACACTCACTACTCAC
1 ACAGGTGTTTACTAAACACTCACTACTCAC
61544 ACAGGTGTTTACTAAACACTCACTACTCAC
1 ACAGGTGTTTACTAAACACTCACTACTCAC
61574 A
1 A
61575 AGAAACTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (30 bp):
ACAGGTGTTTACTAAACACTCACTACTCAC
Found at i:67628 original size:30 final size:30
Alignment explanation
Indices: 67594--67695 Score: 168
Period size: 30 Copynumber: 3.4 Consensus size: 30
67584 CCGAATGACT
67594 TATCCAGAGGTCATAAAGATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
*
67624 TATCCAGAGGTCATAAAAATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
*
67654 TATCCAGAGGTCATAAAGATCCTCGGTATC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
* *
67684 TGTCCATAGGTC
1 TATCCAGAGGTC
67696 CCGAAGAACC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (30 bp):
TATCCAGAGGTCATAAAGATCCTCGGTAAC
Found at i:67712 original size:60 final size:60
Alignment explanation
Indices: 67594--67712 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
67584 CCGAATGACT
* *
67594 TATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCAGAAAAATCCTAGGTAAC
* * * * *
67654 TATCCAGAGGTCATAAAGATCCTCGGTATCTGTCCATAGGTCCCGAAGAA-CCTAGGTAA
1 TATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGT-CAGAAAAATCCTAGGTAA
67713 ACTGTCCATA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 46 0.90
61 5 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (60 bp):
TATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCAGAAAAATCCTAGGTAAC
Found at i:68658 original size:20 final size:22
Alignment explanation
Indices: 68633--68690 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
68623 TTCCCCTTGA
68633 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
68653 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
68676 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
68691 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:72202 original size:30 final size:30
Alignment explanation
Indices: 72168--72240 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
72158 CCCGAAGGAC
72168 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
72198 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
72228 CTGTCCATAGGTC
1 CTATCCAGAGGTC
72241 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:72264 original size:31 final size:31
Alignment explanation
Indices: 72226--72290 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
72216 GATCCTCGGT
* *
72226 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTACCGAAGAACATAGGTA
* **
72257 AACTGTCCATATGTACCTTAGAACATAGGTA
1 AACTGTCCATAGGTACCGAAGAACATAGGTA
72288 AAC
1 AAC
72291 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTACCGAAGAACATAGGTA
Found at i:73209 original size:20 final size:22
Alignment explanation
Indices: 73184--73241 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
73174 TTCCCCTTGA
73184 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
73204 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
73227 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
73242 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:73299 original size:64 final size:63
Alignment explanation
Indices: 73229--73390 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 63
73219 TCTTTAACAT
* * *
73229 GTGCATCGATGCACTACTCATGCATCTATACACAAATTACCTTCGATG-TT-TTCATTTAAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTC-TTT-AAAGA
* * * * *
73292 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
*
73356 GTGCATCGATGCA-TATTCAATATGCATCGATACAC
1 GTGCATCGATGCACTACTC---ATGCATCGATACAC
73391 CTTGCCCAGA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
62 2 0.02
63 13 0.16
64 45 0.56
65 18 0.22
66 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:81216 original size:15 final size:15
Alignment explanation
Indices: 81176--81206 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
81166 TGTATGGCTT
81176 TTTA-AATATTTAAA
1 TTTATAATATTTAAA
81190 TTTATAATATTTAAA
1 TTTATAATATTTAAA
81205 TT
1 TT
81207 ATATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATATTTAAA
Found at i:82045 original size:21 final size:21
Alignment explanation
Indices: 82016--82060 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
82006 AAATAGGAGT
* *
82016 AATTTAAAAATTTAATAAGT-A
1 AATTGAAAAAATTAA-AAGTGA
82037 AATTGAAAAAATTAAAAGTGA
1 AATTGAAAAAATTAAAAGTGA
82058 AAT
1 AAT
82061 AAGAAAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (21 bp):
AATTGAAAAAATTAAAAGTGA
Found at i:86166 original size:14 final size:14
Alignment explanation
Indices: 86149--86185 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
86139 AAAAGTATCG
86149 AATTAAACAAATCC
1 AATTAAACAAATCC
86163 AATTAAACAAATCC
1 AATTAAACAAATCC
86177 AATTAAACA
1 AATTAAACA
86186 GCAAGACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (14 bp):
AATTAAACAAATCC
Found at i:92358 original size:2 final size:2
Alignment explanation
Indices: 92351--92412 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
92341 GTGTACTTTC
92351 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
92393 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
92413 GTGTTTCATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.