Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001383.1 Hibiscus syriacus cultivar Beakdansim tig00002699_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: 80217
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1206 original size:44 final size:44
Alignment explanation
Indices: 1128--1245 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
1118 CGACGAGTGT
* * * *
1128 ATCGGTACACT-GCAGAGTGTATAGATACACATTCAAGGAATGC
1 ATCGGTACACTAACATAGTGTATCGATGCACATTCAAGGAATGC
* ** ** *
1171 ATCTGTGTACTTTCATAGTGTATCGATGCACATTCAATGAATGC
1 ATCGGTACACTAACATAGTGTATCGATGCACATTCAAGGAATGC
1215 ATCGGTACACTAACATAGTGTATCGATGCAC
1 ATCGGTACACTAACATAGTGTATCGATGCAC
1246 TGTACAAAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
43 8 0.13
44 53 0.87
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
ATCGGTACACTAACATAGTGTATCGATGCACATTCAAGGAATGC
Found at i:7069 original size:65 final size:64
Alignment explanation
Indices: 7000--7180 Score: 213
Period size: 64 Copynumber: 2.8 Consensus size: 64
6990 TACACTTGGG
* * * **
7000 GTGCATCGGTACACT-AATTACATTCAATGTTTCAA-AAGAGTCAGGAGTGTATCGTTGCATGGT
1 GTGCATCGGTACA-TAAAATACATTCAATGTTT-AATAA-AATAAGGAGTGTATCAATGCATGGT
7063 CT
63 CT
* *
7065 GTGCATCGGTACATAAAATGCATTCGATGTTTAATAAAATAAGGAGTGTATCAATGCATGGTCT
1 GTGCATCGGTACATAAAATACATTCAATGTTTAATAAAATAAGGAGTGTATCAATGCATGGTCT
* * * * *
7129 GTTCATTGGTACATAAAATGCATTCGATGTTTAATATAATAAGGAGTGTATC
1 GTGCATCGGTACATAAAATACATTCAATGTTTAATAAAATAAGGAGTGTATC
7181 GACGCATCCA
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
64 75 0.72
65 29 0.28
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCAATGTTTAATAAAATAAGGAGTGTATCAATGCATGGTCT
Found at i:7140 original size:64 final size:64
Alignment explanation
Indices: 7042--7180 Score: 233
Period size: 64 Copynumber: 2.2 Consensus size: 64
7032 CAAAAGAGTC
**
7042 AGGAGTGTATCGTTGCATGGTCTGTGCATCGGTACATAAAATGCATTCGATGTTTAATAAAATA
1 AGGAGTGTATCAATGCATGGTCTGTGCATCGGTACATAAAATGCATTCGATGTTTAATAAAATA
* * *
7106 AGGAGTGTATCAATGCATGGTCTGTTCATTGGTACATAAAATGCATTCGATGTTTAATATAATA
1 AGGAGTGTATCAATGCATGGTCTGTGCATCGGTACATAAAATGCATTCGATGTTTAATAAAATA
7170 AGGAGTGTATC
1 AGGAGTGTATC
7181 GACGCATCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (64 bp):
AGGAGTGTATCAATGCATGGTCTGTGCATCGGTACATAAAATGCATTCGATGTTTAATAAAATA
Found at i:7628 original size:39 final size:39
Alignment explanation
Indices: 7582--7698 Score: 157
Period size: 39 Copynumber: 3.0 Consensus size: 39
7572 AAGTGGGAGA
*
7582 TTGTTGGTGAAACTTGCAGGTGCATCCTTTGTTGAAATAT
1 TTGTTGGTCAAACTTGCAGGTGCATCCTTTGTTGAAAT-T
** *
7622 TT-TTGGTCAAACTTATAAGTGCATCCTTTGTTGAAATT
1 TTGTTGGTCAAACTTGCAGGTGCATCCTTTGTTGAAATT
*
7660 TTGTTGGTCAAACTTGTC-GATGCATCCTTTGTTGAAATT
1 TTGTTGGTCAAACTTG-CAGGTGCATCCTTTGTTGAAATT
7699 GGTTGCAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.04
39 62 0.93
40 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.43
Consensus pattern (39 bp):
TTGTTGGTCAAACTTGCAGGTGCATCCTTTGTTGAAATT
Found at i:9665 original size:41 final size:41
Alignment explanation
Indices: 9549--9672 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 41
9539 CTAATGGTGT
* ** *
9549 TAGTTTATATAGGCATAGTAGAGAATTTAGATTATATTTGC
1 TAGTTTATATAGGAATAGTAGAGTGTTTAGACTATATTTGC
* *
9590 TTAGTTTATATAGGAATA-TA-TGTGTTTAGGCTATATTTGC
1 -TAGTTTATATAGGAATAGTAGAGTGTTTAGACTATATTTGC
*
9630 TAGTTTATATAGGTATAGTAGAGTGTTTAGACTATATTTGC
1 TAGTTTATATAGGAATAGTAGAGTGTTTAGACTATATTTGC
9671 TA
1 TA
9673 ACAATGTGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
39 16 0.23
40 17 0.24
41 22 0.31
42 16 0.23
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (41 bp):
TAGTTTATATAGGAATAGTAGAGTGTTTAGACTATATTTGC
Found at i:11571 original size:12 final size:12
Alignment explanation
Indices: 11554--11588 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
11544 TATGATATAG
11554 TTTTTGAAAATA
1 TTTTTGAAAATA
11566 TTTTTGAAAATA
1 TTTTTGAAAATA
*
11578 TATATTGAAAA
1 T-TTTTGAAAA
11589 CATATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (12 bp):
TTTTTGAAAATA
Found at i:11585 original size:13 final size:13
Alignment explanation
Indices: 11557--11594 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11547 GATATAGTTT
*
11557 TTGAAAATAT-TT
1 TTGAAAATATATA
11569 TTGAAAATATATA
1 TTGAAAATATATA
*
11582 TTGAAAACATATA
1 TTGAAAATATATA
11595 ATATATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (13 bp):
TTGAAAATATATA
Found at i:11695 original size:74 final size:75
Alignment explanation
Indices: 11569--11752 Score: 248
Period size: 74 Copynumber: 2.5 Consensus size: 75
11559 GAAAATATTT
*
11569 TTGAAAATATA-TATTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACATATA
1 TTGAAAATATATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACATATA
11633 TAATAT-GATA
66 TAATATAG-TA
* * * *
11643 TTGAAAATATATTTTTGAAAACGTATAATATATAGTTT-TAAAAAACGGTTTTTGAAAACGTGTA
1 TTGAAAATATATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACATATA
*
11707 TAATATAGTG
66 TAATATAGTA
* *
11717 TTGAAAACATATTTTTGAAATATATATATATATATA
1 TTGAAAATATATTTTTGAAA-ACATATA-ATATATA
11753 TATATATATA
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
74 60 0.62
75 30 0.31
76 7 0.07
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.39
Consensus pattern (75 bp):
TTGAAAATATATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACATATA
TAATATAGTA
Found at i:11703 original size:37 final size:37
Alignment explanation
Indices: 11582--11701 Score: 131
Period size: 37 Copynumber: 3.2 Consensus size: 37
11572 AAAATATATA
11582 TTGAAAACATATAATATATAGTTTAAAAAAAACGGTTT
1 TTGAAAACATATAATATATAGTTT-AAAAAAACGGTTT
* *
11620 TTGAAAACATATATAATATGATA-TTGAAAATATA---TTT
1 TTGAAAAC--ATATAATAT-ATAGTTTAAAA-AAACGGTTT
* *
11657 TTGAAAACGTATAATATATAGTTTTAAAAAACGGTTT
1 TTGAAAACATATAATATATAGTTTAAAAAAACGGTTT
11694 TTGAAAAC
1 TTGAAAAC
11702 GTGTATAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
34 5 0.07
35 13 0.19
37 22 0.32
38 8 0.12
39 4 0.06
40 13 0.19
41 3 0.04
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (37 bp):
TTGAAAACATATAATATATAGTTTAAAAAAACGGTTT
Found at i:11732 original size:37 final size:36
Alignment explanation
Indices: 11568--11736 Score: 123
Period size: 37 Copynumber: 4.6 Consensus size: 36
11558 TGAAAATATT
* * *
11568 TTTGAAAATATA-TATTGAAAACATATA-ATATATAG
1 TTTGAAAAAATATTTTTGAAAACGTATATA-ATATAG
* *
11603 TTT-AAAAAAAACGGTTTTTGAAAACATATATAATAT-G
1 TTTGAAAAAATA---TTTTTGAAAACGTATATAATATAG
*
11640 ATATTGAAAATATATTTTTGAAAACGTATA-ATATATAG
1 -T-TTGAAAAAATATTTTTGAAAACGTATATA-ATATAG
* ** *
11678 TTTTAAAAAACGGTTTTTGAAAACGTGTATAATATAG
1 TTTGAAAAAA-TATTTTTGAAAACGTATATAATATAG
*
11715 TGTTGAAAACATATTTTTGAAA
1 T-TTGAAAAAATATTTTTGAAA
11737 TATATATATA
Statistics
Matches: 106, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
34 6 0.06
35 3 0.03
36 8 0.08
37 52 0.49
38 28 0.26
39 3 0.03
40 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTGAAAAAATATTTTTGAAAACGTATATAATATAG
Found at i:11743 original size:2 final size:2
Alignment explanation
Indices: 11736--11774 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11726 TATTTTTGAA
11736 AT 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 AT A
11775 GTTTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11833 original size:22 final size:22
Alignment explanation
Indices: 11807--11856 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
11797 ACATATAAAT
11807 ATATATAATTTTCGAAAACATA
1 ATATATAATTTTCGAAAACATA
* * * *
11829 TTATATAGTTTTTGAAAATATA
1 ATATATAATTTTCGAAAACATA
11851 ATATAT
1 ATATAT
11857 GTTATATAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (22 bp):
ATATATAATTTTCGAAAACATA
Found at i:11865 original size:29 final size:26
Alignment explanation
Indices: 11829--11881 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 26
11819 CGAAAACATA
11829 TTATATAGTTTTTGAAAATATAATATATG
1 TTATATAGTTTTT--AAATA-AATATATG
11858 TTATATAGTTTTTAAATAAATATA
1 TTATATAGTTTTTAAATAAATATA
11882 GTGTACGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.25
27 5 0.21
29 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TTATATAGTTTTTAAATAAATATATG
Found at i:11906 original size:9 final size:9
Alignment explanation
Indices: 11892--11961 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 9
11882 GTGTACGTAT
11892 TATATTATA
1 TATATTATA
11901 TATA-T-TA
1 TATATTATA
*
11908 TATATTATT
1 TATATTATA
11917 TATATTAT-
1 TATATTATA
11925 TAT-TTAT-
1 TATATTATA
*
11932 TATTTTATA
1 TATATTATA
*
11941 TTTATTATA
1 TATATTATA
*
11950 TTAGATTATA
1 -TATATTATA
11960 TA
1 TA
11962 ATTTATTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 13 0.25
8 9 0.18
9 22 0.43
10 7 0.14
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (9 bp):
TATATTATA
Found at i:11906 original size:14 final size:14
Alignment explanation
Indices: 11889--11952 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
11879 ATAGTGTACG
11889 TATTATATTATATA
1 TATTATATTATATA
11903 TATTATA-TAT-TA
1 TATTATATTATATA
*
11915 T-TTATATTATTATT
1 TATTATATTA-TATA
* *
11929 TATTATTTTATATT
1 TATTATATTATATA
11943 TATTATATTA
1 TATTATATTA
11953 GATTATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
11 5 0.12
12 5 0.12
13 4 0.09
14 22 0.51
15 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATATTATATA
Found at i:11909 original size:7 final size:7
Alignment explanation
Indices: 11889--11952 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
11879 ATAGTGTACG
11889 TATTATA
1 TATTATA
11896 T-TATATA
1 TAT-TATA
11903 TATTATA
1 TATTATA
*
11910 TATTATT
1 TATTATA
11917 TA-TAT-
1 TATTATA
*
11922 TATTATT
1 TATTATA
11929 TATTAT-
1 TATTATA
11935 T-TTATA
1 TATTATA
11941 T-TTATTA
1 TATTA-TA
11948 TATTA
1 TATTA
11953 GATTATATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
5 6 0.12
6 12 0.24
7 27 0.55
8 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATTATA
Found at i:11968 original size:40 final size:40
Alignment explanation
Indices: 11889--11972 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
11879 ATAGTGTACG
* *
11889 TATTATATTATATATATTATATATTATTTATATTATTATT
1 TATTATATTATATATATTATATATTAATTATATAATTATT
11929 TATTAT-TT-TATAT-TTATTATATTAGATTATATAATTTATT
1 TATTATATTATATATATTA-TATATTA-ATTATATAA-TTATT
11969 TATT
1 TATT
11973 TAATTTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 3 0.08
38 12 0.31
39 9 0.23
40 15 0.38
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (40 bp):
TATTATATTATATATATTATATATTAATTATATAATTATT
Found at i:16845 original size:24 final size:24
Alignment explanation
Indices: 16818--16891 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
16808 TCAAGAAGAC
* *
16818 TCATCTGCTGCAAAACCACAAGTT
1 TCATCTGCTACAAAACCACAAGCT
* *
16842 TCATATGCTACAAAAGCACAAGCT
1 TCATCTGCTACAAAACCACAAGCT
* *
16866 TCATC-GACTACAAAAGCATAAGCT
1 TCATCTG-CTACAAAACCACAAGCT
16890 TC
1 TC
16892 TGTAACTAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (24 bp):
TCATCTGCTACAAAACCACAAGCT
Found at i:20796 original size:18 final size:18
Alignment explanation
Indices: 20755--20798 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20745 TCGATGGTTA
20755 AAAGTGGTCCTTCAGGAC
1 AAAGTGGTCCTTCAGGAC
**
20773 GTAGTGGTCCTTCAGGAC
1 AAAGTGGTCCTTCAGGAC
20791 AAAGTGGT
1 AAAGTGGT
20799 TATTCGGGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (18 bp):
AAAGTGGTCCTTCAGGAC
Found at i:26208 original size:22 final size:22
Alignment explanation
Indices: 26165--26209 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26155 CAACATCGGG
* *
26165 TTAGTGACTAAATTATAAAATT
1 TTAGTGACTAAAGTAGAAAATT
*
26187 TTAGTGACTAAAGTAGATAATT
1 TTAGTGACTAAAGTAGAAAATT
26209 T
1 T
26210 GAAAAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (22 bp):
TTAGTGACTAAAGTAGAAAATT
Found at i:28575 original size:12 final size:12
Alignment explanation
Indices: 28560--28585 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28550 AATTTATATT
28560 AAAATGTCATGA
1 AAAATGTCATGA
28572 AAAATGTCATGA
1 AAAATGTCATGA
28584 AA
1 AA
28586 GACCAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AAAATGTCATGA
Found at i:29753 original size:20 final size:20
Alignment explanation
Indices: 29730--29781 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
29720 AACGCGATCC
29730 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
29750 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
29770 CCAAAATCGCAA
1 CCAGAATCGCAA
29782 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:29862 original size:20 final size:20
Alignment explanation
Indices: 29837--30030 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
29827 GATTTTCCAT
* *
29837 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
29857 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
29877 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
29897 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
29917 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
29937 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
29957 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
29977 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
29998 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
30018 AATCGCAACGCGA
1 AATCGCAACGCGA
30031 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:29882 original size:40 final size:39
Alignment explanation
Indices: 29833--30030 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
29823 TTGCGATTTT
* ** *
29833 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
29871 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
29912 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
29952 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
29991 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
30031 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:29920 original size:60 final size:60
Alignment explanation
Indices: 29837--30029 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
29827 GATTTTCCAT
* ** * *
29837 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
29897 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
29957 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
30018 AATCGCAACGCG
1 AATCGCAACGCG
30030 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:30448 original size:33 final size:33
Alignment explanation
Indices: 30409--30479 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
30399 TTCACTTAGA
*
30409 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
30442 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
30475 TTTCA
1 TTTCA
30480 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:30683 original size:19 final size:19
Alignment explanation
Indices: 30659--30720 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
30649 ACATGAAAAT
30659 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
30678 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
30692 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
30711 CGTTGCGATT
1 CGTTGCGATT
30721 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.28
16 3 0.08
17 3 0.08
19 20 0.56
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:30700 original size:33 final size:33
Alignment explanation
Indices: 30658--30775 Score: 209
Period size: 33 Copynumber: 3.6 Consensus size: 33
30648 AACATGAAAA
30658 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
30691 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
* * *
30724 TCGTTGCGATTGTCATCTCGCATTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
30757 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
30776 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGTTGCGATTTTCATTTCGCGTTGCGATTCTC
Found at i:30749 original size:19 final size:17
Alignment explanation
Indices: 30661--30768 Score: 81
Period size: 14 Copynumber: 6.5 Consensus size: 17
30651 ATGAAAATCG
*
30661 TTGCGATTTTCATTTCGC
1 TTGCGA-TTTCATCTCGC
30679 GTTGCGA-TTC-TCTCG-
1 -TTGCGATTTCATCTCGC
*
30694 TTGCGATTTTCATTTCGC
1 TTGCGA-TTTCATCTCGC
30712 GTTGCGA-TTC-TCTCG-
1 -TTGCGATTTCATCTCGC
30727 TTGCGATTGTCATCTCGC
1 TTGCGATT-TCATCTCGC
30745 ATTGCGA-TTC-TCTCG-
1 -TTGCGATTTCATCTCGC
30760 TTGCGATTT
1 TTGCGATTT
30769 TCATTTCAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
14 18 0.24
15 3 0.04
16 18 0.24
17 17 0.23
18 1 0.01
19 18 0.24
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.44
Consensus pattern (17 bp):
TTGCGATTTCATCTCGC
Found at i:32775 original size:92 final size:92
Alignment explanation
Indices: 32473--32756 Score: 527
Period size: 92 Copynumber: 3.1 Consensus size: 92
32463 TAGATTGCTT
*
32473 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
32538 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
32565 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
32629 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32657 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
32722 TTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
32748 AGTAAATTT
1 AGTAAATTT
32757 ATCCATTCAA
Statistics
Matches: 187, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
91 35 0.19
92 136 0.73
93 16 0.09
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32840 original size:19 final size:19
Alignment explanation
Indices: 32800--32928 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
32790 TAGTTTACTT
* *
32800 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
32820 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
32839 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
32858 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
32872 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
32891 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
32905 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
32924 TCGCA
1 TCGCA
32929 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:32879 original size:33 final size:32
Alignment explanation
Indices: 32836--32928 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
32826 CGCGAAACCA
**
32836 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
32868 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
32901 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
32929 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:32926 original size:52 final size:52
Alignment explanation
Indices: 32800--32928 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
32790 TAGTTTACTT
**
32800 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
32852 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
32905 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
32929 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:32946 original size:19 final size:19
Alignment explanation
Indices: 32924--33058 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
32914 GAAACCAAAA
*
32924 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32943 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
32959 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
32976 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
32992 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
33009 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
33028 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
33048 TCGTGTTGCGA
1 TCGCGTTGCGA
33059 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32965 original size:14 final size:14
Alignment explanation
Indices: 32946--33002 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32936 TTTCATTTCG
32946 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
32960 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
32977 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
32993 CGTTGCGATT
1 CGTTGCGATT
33003 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:32971 original size:33 final size:33
Alignment explanation
Indices: 32929--33021 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
32919 CAAAATCGCA
*
32929 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
32962 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
32995 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
33022 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:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:34977 original size:14 final size:14
Alignment explanation
Indices: 34958--34993 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34948 ATTGTTTAAT
34958 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34972 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34986 TGATTTGT
1 TGATTTGT
34994 GTAATTGATG
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:35116 original size:19 final size:19
Alignment explanation
Indices: 35100--35201 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
35090 AAAAATGACT
35100 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35119 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35138 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35152 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35171 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35191 ATCGCAATGCG
1 ATCGCAATGCG
35202 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35254 original size:19 final size:19
Alignment explanation
Indices: 35230--35503 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
35220 GATTATCTCG
35230 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35249 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
35263 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35282 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35301 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35320 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35339 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35358 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35377 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
35391 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35410 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35429 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
35443 TTGCGATTTTCACTTCCGCA
1 TTGCGATTTTCA-TTTCGCA
35463 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
35477 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
35496 TTGCGATT
1 TTGCGATT
35504 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 18 0.08
18 3 0.01
19 138 0.62
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:35286 original size:52 final size:53
Alignment explanation
Indices: 35230--35503 Score: 277
Period size: 52 Copynumber: 5.2 Consensus size: 53
35220 GATTATCTCG
35230 TTGCGATTTTCATTTCGCATTGCGA-TTCTTTCG-TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTGCGATTTTCATTTCGC
35281 ATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC
1 -TTGCGATTTTCATTTCGCATTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGC
* *
35338 ATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG-
1 -TTGCGATTTTCATTTCGCATTGCGA-TTT-CTTTCG-ATTGCGATTTTCATTTCGC
*
35391 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGCATTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGC
* * *
35443 TTGCGATTTTCACTTCCGCATTGCGATTT-TCAT-G-TTGGGATTTTCATTTCGC
1 TTGCGATTTTCA-TTTCGCATTGCGATTTCT-TTCGATTGCGATTTTCATTTCGC
35495 GTTGCGATT
1 -TTGCGATT
35504 GTATTTTCCG
Statistics
Matches: 200, Mismatches: 8, Indels: 27
0.85 0.03 0.11
Matches are distributed among these distances:
48 5 0.03
50 5 0.03
51 5 0.03
52 89 0.44
53 20 0.10
54 7 0.04
55 8 0.04
57 61 0.31
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTGCGATTTTCATTTCGC
Found at i:37802 original size:12 final size:12
Alignment explanation
Indices: 37785--37809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37775 TCTTCGGGGA
37785 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37797 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37809 C
1 C
37810 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:38739 original size:20 final size:20
Alignment explanation
Indices: 38711--39079 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
38701 AAATTTAAGT
* * * *
38711 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
38731 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
38751 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
38771 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
38791 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38811 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
38831 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
38851 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38871 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
38891 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
38911 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
*
38931 GTTGCGATTTACGGATATGC
1 GTTGCGATTTACGGATACGC
*
38951 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
38971 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
38991 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
39011 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
39031 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
39051 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
39071 GTTGCGATT
1 GTTGCGATT
39080 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 295 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:40327 original size:42 final size:43
Alignment explanation
Indices: 40281--40361 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
40271 AAACTACCCG
*
40281 AAGGATTTAATCATCATGCTCG-AAAGACTTACTGATGGACTA
1 AAGGACTTAATCATCATGCTCGAAAAGACTTACTGATGGACTA
*
40323 AAGGACTTCATCATCATGCTCGAAAAGACTTACTGATGG
1 AAGGACTTAATCATCATGCTCGAAAAGACTTACTGATGG
40362 CACTTACTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 20 0.56
43 16 0.44
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (43 bp):
AAGGACTTAATCATCATGCTCGAAAAGACTTACTGATGGACTA
Found at i:40463 original size:136 final size:135
Alignment explanation
Indices: 40142--40466 Score: 465
Period size: 136 Copynumber: 2.4 Consensus size: 135
40132 CTTATGGATG
* ** * ** * *
40142 ACCCAAAGGATTT-ATCATTTTGCTCGAAAGACTCACAAATGACCCGAAGGATTTCATCATCATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATG
* * *
40206 CTCGAAAGACTTACTGATGGTACTTCCTGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAC
66 CTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAC
40271 AAACT
131 AAACT
* **
40276 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACTAAAGGACTTCATCATCATG
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATG
40341 CTCGAAAAGACTTACTGATGGCACTTACTGAT-GAGTTTGCTTCACTACTCTTCCGTGAAGGCTT
66 CTCG-AAAGACTTACTGATGGCACTTACTGATGGA-TTTGCTTCACTACTCTTCCGTGAAGGCTT
* *
40405 ATAAATT
129 ACAAACT
*
40412 ACCCGAGGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
1 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
40467 ACTAAGTGTG
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
134 12 0.07
135 47 0.28
136 109 0.65
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (135 bp):
ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATG
CTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAC
AAACT
Found at i:40849 original size:215 final size:215
Alignment explanation
Indices: 40398--41539 Score: 1530
Period size: 215 Copynumber: 5.3 Consensus size: 215
40388 CTCTTCCGTG
* * * * *
40398 AAGGCTTATAAATTACCCGAGGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
* * *
40463 ACTTACTAAGTGTGAAATTTTGGAAATTGCCTTCTTAG-TTTCAAAGATTTCATTTTCTTAAAAC
66 ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
40527 ATCACTTTCTCATTTTCTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCG
131 ATCACTTTCTCA-TTT-TCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCG
*
40592 AAGGACTTATCATCTTACTTTA
194 AAGGACTTATCATCTTACTCTA
* * * * *
40614 AAGGCTTACATATTACCCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
* *
40679 ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTTAAAAATTTCACCTTCTTAAAAC
66 ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
* * *
40744 AGCA-TTATCTCATTTTCAAATTCATGTGGAAACATCCTACCCGAAGGTCTTATAGATGGCCCGA
131 ATCACTT-TCTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGA
*
40808 AAGACTTATCATCTTACTCTA
195 AGGACTTATCATCTTACTCTA
* * * * *
40829 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTATTAATGGCCCGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
*
40894 ACTTACTAAGTGTGAAATTTTGTAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
66 ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
*
40959 ATCATTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAA
131 ATCACTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAA
* *
41024 GGATTTATCATCTTGCTCTA
196 GGACTTATCATCTTACTCTA
** * * * * * *
41044 AAGATTTACAGATGACCTAAAGGATTTACTCATCATACTCAAAAGACTTAATGATGGCCTGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
* * * * * ** * *
41109 ACTTA-TATGGTGCGAAATTTTGGAAATTGCATTCTTACTCCTCAAAGATTTCAT-TTTTTAAAA
66 ACTTACTA-AGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAA
* *
41172 CATCACTTTCTCATTCTTCAAATTC-----AAAACATCTTACCCAAAGGTCTTATGGATGGCCCG
130 CATCACTTTCTCATT-TTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCG
41232 AAGGACTTATCATCTTACTCTA
194 AAGGACTTATCATCTTACTCTA
* * * * *
41254 AAGACTTACAAATGACCCAAATGATTTACTCATCACGCTCGAAATACTTAATGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
* * * *
41319 ACTTACTAAGTGCGAAA-TTTGGAAATCACCTTCTTACTTTTCAAAAATTTAAATCTTCTTAAAA
66 ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTT-CATCTTCTTAAAA
* * * *
41383 CATAACTTTCTCATTTCTCTAATTCATGTGCAAACATCTTACCCGAAGGTCTTATGGATGGCCCG
130 CATCACTTTCTCATTT-TCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCG
* *
41448 AAGGACTTATCATCTTGCTCAA
194 AAGGACTTATCATCTTACTCTA
* * * * * *
41470 AACGCTTACAGATAACCCAAAGGATTTAATCATCATGCCCGAAAGACTTACTAATGGCCCGAAGG
1 AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
41535 ACTTA
66 ACTTA
41540 ATTTGATTGC
Statistics
Matches: 822, Mismatches: 90, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
209 27 0.03
210 125 0.15
211 31 0.04
214 24 0.03
215 369 0.45
216 216 0.26
217 30 0.04
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (215 bp):
AAGGCTTACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGG
ACTTACTAAGTGTGAAATTTTGGAAATCGCCTTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
ATCACTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAA
GGACTTATCATCTTACTCTA
Found at i:41109 original size:42 final size:41
Alignment explanation
Indices: 41013--41114 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
41003 AGGTCTTATG
* * * * *
41013 GATGGCCCGAAGGATTTATCATCTTGCTCTAAAGATTTACA
1 GATGGCCTGAAGGATTTATCATCATACTCAAAAGACTTACA
* *
41054 GATGACCTAAAGGATTTACTCATCATACTCAAAAGACTTA-A
1 GATGGCCTGAAGGATTTA-TCATCATACTCAAAAGACTTACA
*
41095 TGATGGCCTGAAGGACTTAT
1 -GATGGCCTGAAGGATTTAT
41115 ATGGTGCGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 17 0.35
42 32 0.65
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
GATGGCCTGAAGGATTTATCATCATACTCAAAAGACTTACA
Found at i:43049 original size:125 final size:125
Alignment explanation
Indices: 42827--43079 Score: 454
Period size: 125 Copynumber: 2.0 Consensus size: 125
42817 CCTTCACTAG
42827 TGCCCCAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCCCAACACCTCAAATTGCAAGGC
1 TGCCCCAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCCCAACACCTCAAATTGCAAGGC
**
42892 TCATTCTCAATGCCTTTTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCGA-TCA
66 TCATTCTCAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTC-ATTCA
*
42952 TGCCCCAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGC
1 TGCCCCAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCCCAACACCTCAAATTGCAAGGC
*
43017 TCATTCTTAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCATTCA
66 TCATTCTCAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCATTCA
43077 TGC
1 TGC
43080 TCCGATGTGT
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
124 1 0.01
125 122 0.99
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (125 bp):
TGCCCCAACATTATCTTATACTGGTATGGGCCTTCAAAATGCCCCAACACCTCAAATTGCAAGGC
TCATTCTCAATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCATTCA
Found at i:49949 original size:111 final size:112
Alignment explanation
Indices: 49612--50073 Score: 721
Period size: 111 Copynumber: 4.1 Consensus size: 112
49602 TTGTCGGTTT
* * *
49612 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
49676 GGTCTAAAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
**
49723 GTGTCGATACTTTATAAAAATGTATTTATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
**
49788 AATCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
*
49835 GTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
49899 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
49946 GTGTCGATACTTTATAAAAATGTATCGATCCATAATAATAAAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* * * * * *
50011 CGGTCTATAAATGACAAAATAGGTAAAGCTCTATCAAATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
50059 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
50074 TATAAGTATC
Statistics
Matches: 323, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
111 149 0.46
112 104 0.32
113 70 0.22
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:50000 original size:223 final size:224
Alignment explanation
Indices: 49612--50073 Score: 755
Period size: 223 Copynumber: 2.1 Consensus size: 224
49602 TTGTCGGTTT
**
49612 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATAGCGATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
*
49677 GTCTAAAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTAAAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
** *
49742 ATGTATTTATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCAATCTATAAATGACAAAA
131 ATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCAATCTATAAATGACAAAA
*
49806 CAGGTAAAGCGCTACCAGATATATTGAAA
196 CAGGTAAAGCGCTACCAAATATATTGAAA
* *
49835 GTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATAGCGATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
*
49900 GTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTAAAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* **
49965 ATGTATCGATCCATAATAATAAAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
131 ATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCAATCTATAAATGACAAAA
* * * * *
50030 TAGGTAAAGCTCTATCAAATATGTTGATA
196 CAGGTAAAGCGCTACCAAATATATTGAAA
50059 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
50074 TATAAGTATC
Statistics
Matches: 220, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
223 149 0.68
224 71 0.32
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATAGCGATCCATAACAATATAACAAGTAAAAAATGACAAAACCG
GTCTAAAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATGTATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCAATCTATAAATGACAAAA
CAGGTAAAGCGCTACCAAATATATTGAAA
Found at i:50995 original size:23 final size:23
Alignment explanation
Indices: 50949--50996 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
50939 AAATAAGTCA
*
50949 ATATAAGCGCTACATATTACATT
1 ATATAAGCGCTACATAATACATT
* *
50972 ATATAAGCGCTACTTAATATATT
1 ATATAAGCGCTACATAATACATT
50995 AT
1 AT
50997 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACATAATACATT
Found at i:52568 original size:18 final size:18
Alignment explanation
Indices: 52543--52595 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
52533 TCGAGGGTTA
52543 AAAGTGGTCCTTCGGGAC
1 AAAGTGGTCCTTCGGGAC
* *
52561 ATAGTGGTCCTTCGCGAC
1 AAAGTGGTCCTTCGGGAC
*
52579 AAAGTGGTCATTCGGGA
1 AAAGTGGTCCTTCGGGA
52596 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (18 bp):
AAAGTGGTCCTTCGGGAC
Found at i:58929 original size:64 final size:64
Alignment explanation
Indices: 58822--58942 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
58812 TGAGCTAGAT
* *
58822 TTCAACTTCACAACGAAGGATATCACGCACTATTGACTCAACTTCATGACGAAGGGGCCACAAC
1 TTCAACTTCACAACAAAGGATATCACGCACAATTGACTCAACTTCATGACGAAGGGGCCACAAC
* * * *
58886 TTCAACTTCACAACAAAGGATATCACGCTCAATTGGCTTAACTTCATGATGAAGGGG
1 TTCAACTTCACAACAAAGGATATCACGCACAATTGACTCAACTTCATGACGAAGGGG
58943 TCAACCAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (64 bp):
TTCAACTTCACAACAAAGGATATCACGCACAATTGACTCAACTTCATGACGAAGGGGCCACAAC
Found at i:59461 original size:73 final size:72
Alignment explanation
Indices: 59334--59477 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 72
59324 ATAGTATAGT
59334 TTTTGAAAATATTTTTGAAAACATATAATATATAATTTTTAGAAAACAGTTTTTGAAAACATATA
1 TTTTGAAAATATTTTTGAAAACATATAATATATAATTTTTA-AAAACAGTTTTTGAAAACATATA
59399 TAATATGG
65 TAATATGG
* *
59407 TTTTGAAAACATATTTTTGAAAACGTATAATATATAGTTTTT-AAAAC-GATTTTTGAAAACATA
1 TTTTG-AAA-ATATTTTTGAAAACATATAATATATAATTTTTAAAAACAG-TTTTTGAAAACATA
59470 TATAATAT
63 TATAATAT
59478 TTATAATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
72 1 0.02
73 32 0.48
74 3 0.05
75 30 0.45
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (72 bp):
TTTTGAAAATATTTTTGAAAACATATAATATATAATTTTTAAAAACAGTTTTTGAAAACATATAT
AATATGG
Found at i:59466 original size:36 final size:37
Alignment explanation
Indices: 59328--59499 Score: 183
Period size: 37 Copynumber: 4.5 Consensus size: 37
59318 TGATAGATAG
59328 TATAGTTTTTGAAAA-TATTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAACTATTTTTGAAAACATATAATA
*
59364 TATAATTTTTAGAAAAC-AGTTTTTGAAAACATAT-ATA
1 TATAGTTTTT-GAAAACTA-TTTTTGAAAACATATAATA
* *
59401 -ATATGGTTTTGAAAACATATTTTTGAAAACGTATAATA
1 TATA-GTTTTTGAAAAC-TATTTTTGAAAACATATAATA
*
59439 TATAGTTTTT-AAAACGATTTTTGAAAACATATATAATA
1 TATAGTTTTTGAAAACTATTTTTGAAAAC--ATATAATA
*
59477 TTTATAATTTTTGAAAACATATT
1 --TATAGTTTTTGAAAAC-TATT
59500 ATATAGTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 22
0.78 0.06 0.15
Matches are distributed among these distances:
36 30 0.27
37 32 0.28
38 31 0.27
39 3 0.03
40 9 0.08
41 5 0.04
42 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (37 bp):
TATAGTTTTTGAAAACTATTTTTGAAAACATATAATA
Found at i:59509 original size:22 final size:22
Alignment explanation
Indices: 59474--59525 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
59464 AACATATATA
59474 ATATT-TATAATTTTTGAAAAC
1 ATATTATATAATTTTTGAAAAC
* *
59495 ATATTATATAGTTTTTGAAAAT
1 ATATTATATAATTTTTGAAAAC
*
59517 ATAATATAT
1 ATATTATAT
59526 GTTATATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
ATATTATATAATTTTTGAAAAC
Found at i:59568 original size:5 final size:5
Alignment explanation
Indices: 59558--59611 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
59548 ATAGTGTACT
* *
59558 TATTA TATTA TATATA TATTA GATTA TATTA GATTA TATTA TTATT- TATT-
1 TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA
59608 TATT
1 TATT
59612 TAATTTCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
4 8 0.19
5 26 0.60
6 9 0.21
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:68633 original size:17 final size:17
Alignment explanation
Indices: 68592--68663 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
68582 ATTCATGCAT
68592 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
68609 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
68627 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* * *
68644 ATAGTTTATTTATTAAA
1 CTAGTTCATTAATTAAA
68661 CTA
1 CTA
68664 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:70175 original size:20 final size:20
Alignment explanation
Indices: 70150--70193 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
70140 CCAGGTTAGT
*
70150 AAAAAATTAAAAAAAAAACA
1 AAAAAATGAAAAAAAAAACA
* *
70170 AAAAAATGAAAAAAGAAAGA
1 AAAAAATGAAAAAAAAAACA
70190 AAAA
1 AAAA
70194 TTTTAAAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAAACA
Found at i:70545 original size:22 final size:22
Alignment explanation
Indices: 70520--70563 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
70510 TTTCTTTGGA
*
70520 TTGTATTGGTGAGATTTTTTTT
1 TTGTATTGGTGAGATTTATTTT
* *
70542 TTGTGTTGGTGAGGTTTATTTT
1 TTGTATTGGTGAGATTTATTTT
70564 CATCTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.61
Consensus pattern (22 bp):
TTGTATTGGTGAGATTTATTTT
Found at i:72669 original size:24 final size:24
Alignment explanation
Indices: 72642--72695 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
72632 CACCATTGCT
*
72642 CATATAATTTACACCGAAGTGCCA
1 CATAGAATTTACACCGAAGTGCCA
* * *
72666 CATAGATTTTGCACTGAAGTGCCA
1 CATAGAATTTACACCGAAGTGCCA
*
72690 CGTAGA
1 CATAGA
72696 TTTGTCCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (24 bp):
CATAGAATTTACACCGAAGTGCCA
Found at i:72759 original size:25 final size:23
Alignment explanation
Indices: 72687--72759 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
72677 CACTGAAGTG
72687 CCACGTAG-ATTTGTCCCGAAGGA
1 CCACGTAGAATTT-TCCCGAAGGA
*
72710 CTACGTAGAATTTTCCCGAAGGA
1 CCACGTAGAATTTTCCCGAAGGA
*
72733 CCACGTAGAAATTTATCCCGAATGA
1 CCACGTAG-AATTT-TCCCGAAGGA
72758 CC
1 CC
72760 GTGTAGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 24 0.55
24 9 0.20
25 11 0.25
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CCACGTAGAATTTTCCCGAAGGA
Found at i:75387 original size:15 final size:15
Alignment explanation
Indices: 75362--75397 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
75352 GGAGAAATGA
*
75362 AATAAGGTATGTGAT
1 AATAAGATATGTGAT
*
75377 TATAAGATATGTGAT
1 AATAAGATATGTGAT
75392 AATAAG
1 AATAAG
75398 TTTGTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
AATAAGATATGTGAT
Done.