Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001717.1 Hibiscus syriacus cultivar Beakdansim tig00003477_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: 119204
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1810 original size:17 final size:18
Alignment explanation
Indices: 1773--1817 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1763 TTTATAAGTT
*
1773 AATTAGAATTTGTGAAGG
1 AATTAGAATCTGTGAAGG
*
1791 AATTAGAATCTGT-CAGG
1 AATTAGAATCTGTGAAGG
1808 AATTAGAATC
1 AATTAGAATC
1818 CAATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (18 bp):
AATTAGAATCTGTGAAGG
Found at i:3383 original size:18 final size:18
Alignment explanation
Indices: 3343--3384 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3333 CGTTCCTAAA
3343 ATTTTTAAATTCTTATAT
1 ATTTTTAAATTCTTATAT
* *
3361 A-TTTTAAATTTTTATGT
1 ATTTTTAAATTCTTATAT
3378 ATTTTTA
1 ATTTTTA
3385 TTAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTTAAATTCTTATAT
Found at i:3436 original size:26 final size:27
Alignment explanation
Indices: 3390--3442 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3380 TTTTATTAAT
3390 AATTTATTTATTCTCTAAAATTTTATA
1 AATTTATTTATTCTCTAAAATTTTATA
3417 AATTTATATTA-TCTCT-AAATTTTATA
1 AATTTAT-TTATTCTCTAAAATTTTATA
3443 CGTTCGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.40
27 12 0.48
28 3 0.12
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTATTTATTCTCTAAAATTTTATA
Found at i:10916 original size:3 final size:3
Alignment explanation
Indices: 10908--10933 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10898 TTTCCCCCTT
10908 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
10934 TTGTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19282 original size:60 final size:60
Alignment explanation
Indices: 19218--19355 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
19208 ACTAGTTGGG
* * *
19218 TGACCATTTTGTAACTTTTAATAGTTGAGGGACTCTACAAAATAATATCCTATAATTGAA
1 TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCCTATAATAGAA
* * * * * *
19278 TGACCATTTTGTAACTTTTAGTAGTTTAGAGATTCAATAAAGTAATATCTTATAATAGAA
1 TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCCTATAATAGAA
19338 TGACCATTTGTGT-ACTTT
1 TGACCATTT-TGTAACTTT
19356 ACCCTAAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 65 0.96
61 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAATAATATCCTATAATAGAA
Found at i:22694 original size:22 final size:22
Alignment explanation
Indices: 22664--22711 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
22654 GAAATATGGT
* *
22664 TTAATTGATATTTTTG-TAATAA
1 TTAAATGATATGTTTGATAA-AA
22686 TTAAATGATATGTTTGATAAAA
1 TTAAATGATATGTTTGATAAAA
22708 TTAA
1 TTAA
22712 TAGTTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TTAAATGATATGTTTGATAAAA
Found at i:24671 original size:27 final size:28
Alignment explanation
Indices: 24641--24700 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
24631 ATAATTTTTA
*
24641 TTTAAAA-TATAGGATTTAGAGTATA-AG
1 TTTAAAAGT-TAGGATTTAAAGTATATAG
* *
24668 TTTAAAAGTTAGGGTTTAAAGTTTATAG
1 TTTAAAAGTTAGGATTTAAAGTATATAG
24696 TTTAA
1 TTTAA
24701 GATACATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (28 bp):
TTTAAAAGTTAGGATTTAAAGTATATAG
Found at i:36921 original size:21 final size:20
Alignment explanation
Indices: 36835--36992 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
36825 AAATGACCAA
**
36835 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
36854 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
36874 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
36894 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
36915 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
36936 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
36956 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
36977 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
36993 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:37054 original size:20 final size:20
Alignment explanation
Indices: 36960--37152 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
36950 GATTTTCCAG
* ** *
36960 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
36980 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37000 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37020 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37040 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37060 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37080 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
37100 AATCGTAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
37121 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37141 AATCGCAACGCG
1 AATCGCAACGCG
37153 ATTTTTAAAA
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 130 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:37571 original size:33 final size:33
Alignment explanation
Indices: 37532--37602 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
37522 TTCACTTAGA
37532 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
37565 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
37598 TTTCA
1 TTTCA
37603 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:37708 original size:21 final size:21
Alignment explanation
Indices: 37682--37757 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
37672 TGCAGAAGAG
37682 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
37703 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
37723 TCTGCAACGAGAAAAATG-AAA
1 TC-GCAACGAGAGAAATGAAAA
37744 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
37758 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 20 0.43
21 21 0.46
22 5 0.11
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:37799 original size:19 final size:19
Alignment explanation
Indices: 37777--37904 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
37767 GAAACCAAAA
*
37777 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37796 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
37810 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
37829 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
37843 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
37863 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
37883 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
37903 TC
1 TC
37905 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:37818 original size:14 final size:14
Alignment explanation
Indices: 37799--37855 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37789 TTTCATTTCG
37799 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37813 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
37832 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37846 CGTTGCGATT
1 CGTTGCGATT
37856 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37824 original size:33 final size:33
Alignment explanation
Indices: 37782--37905 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
37772 CAAAATCGCA
*
37782 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
37815 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
37848 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
37889 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
37906 ACCAAAAGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:37866 original size:21 final size:21
Alignment explanation
Indices: 37840--37904 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
37830 CACGTTGCGA
37840 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
37861 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
37881 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
37902 TTC
1 TTC
37905 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:39851 original size:14 final size:14
Alignment explanation
Indices: 39832--39888 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
39822 CGAAACTTAA
39832 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
39846 AATCGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
*
39865 AATCGCAACGACAG
1 AATCGCAACGAGAG
39879 AATCGCAACG
1 AATCGCAACG
39889 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:39869 original size:33 final size:33
Alignment explanation
Indices: 39814--39937 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
39804 TAGTTTACTT
* * *
39814 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
39848 TCGCAACGTGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
39881 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
39914 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
39938 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:39903 original size:19 final size:19
Alignment explanation
Indices: 39879--39937 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
39869 GCAACGACAG
39879 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
39898 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
39912 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
39931 AATCGCA
1 AATCGCA
39938 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:39914 original size:14 final size:14
Alignment explanation
Indices: 39863--39921 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
39853 ACGTGAAATG
39863 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
39877 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
39896 AAAATCGCAACGAC
1 AAAATCGCAACGAC
39910 AAAATCGCAACG
1 AAAATCGCAACG
39922 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:39955 original size:19 final size:19
Alignment explanation
Indices: 39933--40105 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
39923 GAAACCAAAA
*
39933 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39952 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
39966 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
39985 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
40001 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
40018 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
40037 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* * *
40056 TCTCGTTGCTATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
40075 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
40095 TCGTGTTGCGA
1 TCGCGTTGCGA
40106 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
19 79 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:39974 original size:14 final size:14
Alignment explanation
Indices: 39955--40011 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
39945 TTTCATTTCG
39955 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
39969 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
39986 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
40002 CGTTGCGATT
1 CGTTGCGATT
40012 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:39980 original size:33 final size:33
Alignment explanation
Indices: 39938--40030 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
39928 CAAAATCGCA
39938 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
39971 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
40004 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
40031 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:40063 original size:38 final size:38
Alignment explanation
Indices: 39933--40105 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
39923 GAAACCAAAA
*
39933 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
39968 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
40001 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** * *
40037 TCGCGTTGCGATTTTGGTTTCTCGTTGCTATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
40075 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
40106 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.46
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.38
39 10 0.09
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:42046 original size:14 final size:14
Alignment explanation
Indices: 42027--42062 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
42017 ATTGTTTAAT
42027 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
42041 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
42055 TGATTTGT
1 TGATTTGT
42063 GTACTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:42204 original size:19 final size:19
Alignment explanation
Indices: 42169--42267 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
42159 AAAAATGACT
*
42169 ATCGCAATACGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
42189 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
42208 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
42222 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
42241 ATCGCAAAGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
42261 ATCGCAA
1 ATCGCAA
42268 CGATAGAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 26 0.40
20 24 0.37
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:42299 original size:53 final size:53
Alignment explanation
Indices: 42169--42286 Score: 175
Period size: 53 Copynumber: 2.2 Consensus size: 53
42159 AAAAATGACT
* * *
42169 ATCGCAATACGGAAATGAAAATCACAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAAAGCGGAAATGAAAATCGCAACGAGAGA
* *
42222 ATCGTAATGCGAAATGAAAATCGCAAAGCGGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAAAGCGGAAATGAAAATCGCAACGAGAGA
42275 ATCGCAATGCGA
1 ATCGCAATGCGA
42287 TTTTCATTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 17 0.29
53 41 0.71
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAAAGCGGAAATGAAAATCGCAACGAGAGA
Found at i:42368 original size:72 final size:70
Alignment explanation
Indices: 42277--42571 Score: 268
Period size: 72 Copynumber: 4.2 Consensus size: 70
42267 ACGATAGAAT
*
42277 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTCATTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
42342 TTCATTT-
63 TTCATTTC
* * * * *
42349 CGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCG
1 CGCATTGCGATTTTCATTT-CG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCG
42411 ATTTTCATTTC
60 ATTTTCATTTC
* * *
42422 CGCATTGCGA--TTC-TCTCGTTGCAATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGA
42484 TTTTCATTTC
61 TTTTCATTTC
* * *
42494 CGCATTGCGATTTTCA--T-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
42556 ATTTC
66 ATTTC
**
42561 CGTGTTGCGAT
1 CGCATTGCGAT
42572 AGTCAAATGC
Statistics
Matches: 186, Mismatches: 21, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 30 0.16
68 2 0.01
69 6 0.03
70 7 0.04
71 3 0.02
72 86 0.46
73 27 0.15
74 9 0.05
75 4 0.02
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (70 bp):
CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
ATTTC
Found at i:42567 original size:53 final size:53
Alignment explanation
Indices: 42282--42552 Score: 412
Period size: 53 Copynumber: 5.1 Consensus size: 53
42272 AGAATCGCAA
42282 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
42335 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
42388 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
42441 TGCAATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--T
*
42499 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
42546 TGCGATT
1 TGCGATT
42553 GTAATTTCCG
Statistics
Matches: 207, Mismatches: 5, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 10 0.05
53 162 0.78
54 3 0.01
55 3 0.01
56 3 0.01
58 11 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:44850 original size:12 final size:12
Alignment explanation
Indices: 44833--44857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44823 TCTTCGGGGA
44833 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44845 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44857 C
1 C
44858 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:45065 original size:24 final size:24
Alignment explanation
Indices: 45031--45077 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45021 CTGAAACATC
45031 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
45055 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
45078 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:45772 original size:20 final size:20
Alignment explanation
Indices: 45744--45972 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
45734 AAATTTCAGT
* * *
45744 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
45764 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
45784 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
45804 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
45824 GTTGGGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
45844 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
45864 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
45884 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
45904 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
45924 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
45944 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
45964 GTTGCGATT
1 GTTGCGATT
45973 CTGGAAAATC
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:51131 original size:64 final size:64
Alignment explanation
Indices: 51028--51151 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
51018 GGGGGACCCT
* * * * *
51028 TTGAGTCCTTATCTTTTTCTAATTTGTGCAGAAGGATTGTCGTTTTTGCTTAATTTGGCTCCCG
1 TTGAGTCCTTATCTTTTTATAATTCGTGCAGAAGCATTGTCGTCTTTGCTCAATTTGGCTCCCG
51092 TTGAGTCCTTATCTTTTTATAATTCGTGCAGAAGCATTGTCGTCTTTGCTCAATTTGGCT
1 TTGAGTCCTTATCTTTTTATAATTCGTGCAGAAGCATTGTCGTCTTTGCTCAATTTGGCT
51152 AAACACTCTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (64 bp):
TTGAGTCCTTATCTTTTTATAATTCGTGCAGAAGCATTGTCGTCTTTGCTCAATTTGGCTCCCG
Found at i:53716 original size:58 final size:57
Alignment explanation
Indices: 53647--53790 Score: 159
Period size: 59 Copynumber: 2.5 Consensus size: 57
53637 CAATTTAGGG
*
53647 TAAAA-TATATAAATAATCTACAACTATA-AGATATTATTTTATTGAGTCCCCTGATTAT
1 TAAAAGTATA-AAATAATCTACAACTATAGA-ATATTATTTTATTGAGT-CCCTGACTAT
* * * *
53705 TAAAAGTTATAAAATGA-CCATCGACTATAGAATATTATTTTATTGAGTCTCTGACTAT
1 TAAAAG-TATAAAATAATCTA-CAACTATAGAATATTATTTTATTGAGTCCCTGACTAT
*
53763 TAAAAGTATAAAATAATCATCCAACTAT
1 TAAAAGTATAAAATAATC-TACAACTAT
53791 TCATATATTC
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
57 9 0.13
58 28 0.39
59 29 0.41
60 5 0.07
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (57 bp):
TAAAAGTATAAAATAATCTACAACTATAGAATATTATTTTATTGAGTCCCTGACTAT
Found at i:53971 original size:28 final size:28
Alignment explanation
Indices: 53929--53982 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
53919 CTCTCCGTTT
*
53929 ACATTATGTCATCGAGTCAATGCTTGGA
1 ACATTAGGTCATCGAGTCAATGCTTGGA
* *
53957 ACATTAGGTCGTCGAGTCAGTGCTTG
1 ACATTAGGTCATCGAGTCAATGCTTG
53983 AAAGCAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (28 bp):
ACATTAGGTCATCGAGTCAATGCTTGGA
Found at i:62081 original size:15 final size:14
Alignment explanation
Indices: 62063--62109 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
62053 ATTATATGAA
*
62063 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
62078 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
62091 ATGTGATATGAAC-
1 ATGTGATAAGAACT
62104 ATGTGA
1 ATGTGA
62110 ATGTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 17 0.59
14 6 0.21
15 6 0.21
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:62240 original size:21 final size:21
Alignment explanation
Indices: 62191--62250 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
62181 GAGTCGAGGG
*
62191 TCTACGCGGTCCTTCGGG--A
1 TCTACGTGGTCCTTCGGGACA
*
62210 TATA-GTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
62230 TCTACGTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
62251 AATTCTACGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.34
19 3 0.09
20 4 0.11
21 16 0.46
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (21 bp):
TCTACGTGGTCCTTCGGGACA
Found at i:62266 original size:24 final size:21
Alignment explanation
Indices: 62218--62266 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
62208 GATATAGTGG
* *
62218 TCCTTCGGGACATCTACGTGG
1 TCCTTCGGGACATCTACGCGC
62239 TCCTTCGGGACAAATTCTACGCGC
1 TCCTTCGGGAC--A-TCTACGCGC
62263 TCCT
1 TCCT
62267 AGTGAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
23 1 0.04
24 11 0.48
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (21 bp):
TCCTTCGGGACATCTACGCGC
Found at i:62513 original size:2 final size:2
Alignment explanation
Indices: 62508--62547 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
62498 ATATATGTTA
62508 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
62548 GAATGAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64919 original size:2 final size:2
Alignment explanation
Indices: 64912--64963 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
64902 ATATTCAGAC
64912 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
64954 AT AT AT AT AT
1 AT AT AT AT AT
64964 CCGACACGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67707 original size:20 final size:20
Alignment explanation
Indices: 67682--67727 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
67672 TCATTCTCTT
67682 CAACCACATCTCCGCTTCAC
1 CAACCACATCTCCGCTTCAC
67702 CAACCACATCTCCGCTTCAC
1 CAACCACATCTCCGCTTCAC
67722 CAACCA
1 CAACCA
67728 AGCCAGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.50, G:0.04, T:0.17
Consensus pattern (20 bp):
CAACCACATCTCCGCTTCAC
Found at i:69881 original size:30 final size:28
Alignment explanation
Indices: 69847--69903 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
69837 TTGGTATTAT
69847 ATTTTTCAAAATTTTAGAGATTTTATAAAG
1 ATTTTTCAAAATTTT-G-GATTTTATAAAG
* *
69877 ATTTTTGAAAATTTTGGATTTTTTAAA
1 ATTTTTCAAAATTTTGGATTTTATAAA
69904 ATATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 1 0.04
30 14 0.56
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (28 bp):
ATTTTTCAAAATTTTGGATTTTATAAAG
Found at i:70630 original size:2 final size:2
Alignment explanation
Indices: 70623--70659 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
70613 ATCATTAAAA
70623 AT AT AT AT AT AT AT AT 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 AT AT A
70660 ATTAGACAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82495 original size:50 final size:49
Alignment explanation
Indices: 82421--82576 Score: 124
Period size: 50 Copynumber: 3.1 Consensus size: 49
82411 GTAGCAGTAA
*
82421 AGCGCGCCCCCTGACCCGCACTATATGTTGATTTGGCGTCACGTGGGGTAT
1 AGCGCGCCCCCT-ACCCGCGCTATA-GTTGATTTGGCGTCACGTGGGGTAT
* * *
82472 AGCGCG-CCCCTACACCGCGCTATACGCTGA-CTGG-GTTACACGT-GGCTAT
1 AGCGCGCCCCCTAC-CCGCGCTATA-GTTGATTTGGCG-T-CACGTGGGGTAT
* * ** *
82521 AGCGCGCCCCCTGCTCCGCGCTATACTT-ATTTATCTGACACGTGGGGTAT
1 AGCGCGCCCCCTAC-CCGCGCTATAGTTGATTTGGC-GTCACGTGGGGTAT
82571 AGCGCG
1 AGCGCG
82577 GTGCAGGGGA
Statistics
Matches: 83, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
48 2 0.02
49 24 0.29
50 50 0.60
51 7 0.08
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.24
Consensus pattern (49 bp):
AGCGCGCCCCCTACCCGCGCTATAGTTGATTTGGCGTCACGTGGGGTAT
Found at i:82687 original size:10 final size:10
Alignment explanation
Indices: 82668--82698 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
82658 TTCATCACAC
*
82668 CAAATTCTCT
1 CAAATACTCT
82678 CAAATACTCT
1 CAAATACTCT
82688 CAAATACTCT
1 CAAATACTCT
82698 C
1 C
82699 TCGTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (10 bp):
CAAATACTCT
Found at i:83536 original size:14 final size:14
Alignment explanation
Indices: 83519--83550 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
83509 ATTCAGTTGG
83519 GGCTCGACAGTTTT
1 GGCTCGACAGTTTT
83533 GGCTCGACAGTTTT
1 GGCTCGACAGTTTT
83547 GGCT
1 GGCT
83551 TTGCTGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.31, T:0.34
Consensus pattern (14 bp):
GGCTCGACAGTTTT
Found at i:89786 original size:21 final size:21
Alignment explanation
Indices: 89760--89822 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
89750 TTTTGGTGCA
*
89760 GAGGGAATCGATCCCCCCAAT
1 GAGGGAACCGATCCCCCCAAT
* **
89781 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCAAT
*
89802 GAAGGGGAACCGATTCCCCCA
1 G-A-GGGAACCGATCCCCCCA
89823 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCAAT
Found at i:89847 original size:19 final size:20
Alignment explanation
Indices: 89804--89841 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
89794 CCCCCTTTGA
*
89804 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
89824 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
89842 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:96368 original size:23 final size:23
Alignment explanation
Indices: 96334--96402 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
96324 CACCACAGCT
*
96334 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
96357 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
96380 CGTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
96403 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:99590 original size:15 final size:15
Alignment explanation
Indices: 99570--99602 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
99560 GCTTCTTCTT
99570 TGCTTGAAAACTCCA
1 TGCTTGAAAACTCCA
*
99585 TGCTTGAAAACTTCA
1 TGCTTGAAAACTCCA
99600 TGC
1 TGC
99603 CTAAAGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (15 bp):
TGCTTGAAAACTCCA
Found at i:100868 original size:14 final size:15
Alignment explanation
Indices: 100834--100872 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
100824 TCAAATAATC
100834 ATAATAAATAATAAGT
1 ATAATAAA-AATAAGT
*
100850 ATAATAAAAA-AATT
1 ATAATAAAAATAAGT
100864 ATAATAAAA
1 ATAATAAAA
100873 TTACCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:111159 original size:108 final size:110
Alignment explanation
Indices: 110929--111170 Score: 326
Period size: 108 Copynumber: 2.2 Consensus size: 110
110919 GGGGCATATG
* **
110929 TGCTTTTATGTTCTGTTTCTCTTAGCTTGGCATCTAGCTACCCAAGTATGTTGAAACGCAACTAC
1 TGCTTTGATGTTCTGTTTCTCTTAGCTTGGCATCTAGCTACCCAAGTATGTCCAAACG-AACTAC
* * * *
110994 TGACTATATATTAGAGAATACAGACTGAACTGTTGACGGGGTATCG
65 TGACCATATATTAGAGAATACAGACTGAACTGCTGACAGGGTATCA
* * * * *
111040 TGCTATGATGTTCTGTTTCTCTTAGCTTGGCATCTGGCTATCCAAGTATGTCCTAA-G-GCTACT
1 TGCTTTGATGTTCTGTTTCTCTTAGCTTGGCATCTAGCTACCCAAGTATGTCCAAACGAACTACT
* * *
111103 GACCATTTATTAGAGAATACAGATTGAATTGCTGACAGGGTATCA
66 GACCATATATTAGAGAATACAGACTGAACTGCTGACAGGGTATCA
111148 TGCTTTGATGTTCTGTTTCTCTT
1 TGCTTTGATGTTCTGTTTCTCTT
111171 CCTATCAAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
108 65 0.57
110 1 0.01
111 49 0.43
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (110 bp):
TGCTTTGATGTTCTGTTTCTCTTAGCTTGGCATCTAGCTACCCAAGTATGTCCAAACGAACTACT
GACCATATATTAGAGAATACAGACTGAACTGCTGACAGGGTATCA
Found at i:113360 original size:16 final size:16
Alignment explanation
Indices: 113313--113362 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
113303 ATTATTGATT
113313 TTAAATTCAATAATAA
1 TTAAATTCAATAATAA
*
113329 TT-TA-TCAA-AA-AA
1 TTAAATTCAATAATAA
113341 TTAAATTCAATAATAA
1 TTAAATTCAATAATAA
113357 TTAAAT
1 TTAAAT
113363 AAAAACAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 8 0.29
15 3 0.11
16 10 0.36
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTCAATAATAA
Found at i:113366 original size:28 final size:28
Alignment explanation
Indices: 113313--113375 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
113303 ATTATTGATT
*
113313 TTAAATTCAATAATAATTTATCAAAAAA
1 TTAAATTCAATAATAATTAATCAAAAAA
*
113341 TTAAATTCAATAATAATTAAATAAAAACAA
1 TTAAATTCAATAATAATT-AATCAAAA-AA
113371 TTAAA
1 TTAAA
113376 ATATTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 6 0.19
30 7 0.23
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (28 bp):
TTAAATTCAATAATAATTAATCAAAAAA
Done.