Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005509.1 Hibiscus syriacus cultivar Beakdansim tig00012720_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: 93424
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:3075 original size:44 final size:44
Alignment explanation
Indices: 3026--3129 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
3016 TTGTGCTAAG
** *
3026 TGCATCGATACACTATAAAAGTGTATCGATGCATTCATTGAATA
1 TGCATCGATACACTATAAAAGTACACCGATGCATTCATTGAATA
* * * *
3070 TGCATCGATACATTATGAAGGTACACCGATGCATTCCTTGAATA
1 TGCATCGATACACTATAAAAGTACACCGATGCATTCATTGAATA
*
3114 TGTATCGATACACTAT
1 TGCATCGATACACTAT
3130 GCAGTGTACC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (44 bp):
TGCATCGATACACTATAAAAGTACACCGATGCATTCATTGAATA
Found at i:3083 original size:23 final size:23
Alignment explanation
Indices: 3050--3125 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
3040 ATAAAAGTGT
*
3050 ATCGATGCATTCATTGAATATGC
1 ATCGATACATTCATTGAATATGC
** *
3073 ATCGATACATT-A-TGAAGGTAC
1 ATCGATACATTCATTGAATATGC
* * * *
3094 ACCGATGCATTCCTTGAATATGT
1 ATCGATACATTCATTGAATATGC
3117 ATCGATACA
1 ATCGATACA
3126 CTATGCAGTG
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
21 15 0.39
22 1 0.03
23 22 0.58
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (23 bp):
ATCGATACATTCATTGAATATGC
Found at i:3635 original size:13 final size:13
Alignment explanation
Indices: 3612--3650 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3602 AAAACTAAAT
*
3612 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAA
3626 ATTGTTTTCAAAA
1 ATTGTTTTCAAAA
*
3639 ATAGTTTTCAAA
1 ATTGTTTTCAAA
3651 TTTGCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAA
Found at i:7557 original size:46 final size:46
Alignment explanation
Indices: 7488--7851 Score: 524
Period size: 46 Copynumber: 8.0 Consensus size: 46
7478 CTAAAACGAA
* *
7488 GCCATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * * *
7534 GTCATAACTAAAATACATGAAAGGATACATTAAGGCTTGAAAAGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
7580 GCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
7626 GCCATAACTAAAATGCATGAAAGGATGCATTAATGCATGACAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
7672 GCCATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * *
7718 GCCATAACTAAAATGCATAAAAGGATGCCTTAAGGCATGAAATGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
7764 G-CAT---T--AAGGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
7804 GTCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGAT
1 GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
7850 GC
1 GC
7852 ATTAAGGCAT
Statistics
Matches: 282, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
40 32 0.11
41 3 0.01
42 1 0.00
44 1 0.00
45 3 0.01
46 242 0.86
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (46 bp):
GCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
Found at i:7619 original size:20 final size:20
Alignment explanation
Indices: 7594--8008 Score: 263
Period size: 20 Copynumber: 18.6 Consensus size: 20
7584 TAACTAAAAT
*
7594 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
7614 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
7640 GCATGAAAGGATGCATTAAT
1 GCATGAAAGGATGCATTAAG
* *
7660 GCATGACAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
7686 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
7706 GCATAAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
7732 GCATAAAAGGATGCCTTAAG
1 GCATGAAAGGATGCATTAAG
*
7752 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
7772 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
7792 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
7818 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
7838 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
7858 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
7884 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
** *
7904 GCATGAAAATATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
7930 TCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
7950 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
7976 GTATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
7996 GCATGAAAGGATG
1 GCATGAAAGGATG
8009 TCATAAATGA
Statistics
Matches: 320, Mismatches: 33, Indels: 84
0.73 0.08 0.19
Matches are distributed among these distances:
20 165 0.52
21 21 0.07
22 7 0.02
24 7 0.02
25 20 0.06
26 100 0.31
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:7653 original size:26 final size:25
Alignment explanation
Indices: 7490--7563 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 25
7480 AAAACGAAGC
7490 CATAACTAAAATGCATGAAAGGAT-A
1 CATAACTAAAAT-CATGAAAGGATGA
* *
7515 CAT---TAAGA-CATGAAAGGATGT
1 CATAACTAAAATCATGAAAGGATGA
7536 CATAACTAAAATACATGAAAGGAT-A
1 CATAACTAAAAT-CATGAAAGGATGA
7561 CAT
1 CAT
7564 TAAGGCTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 4 0.10
24 4 0.10
25 6 0.15
26 11 0.28
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (25 bp):
CATAACTAAAATCATGAAAGGATGA
Found at i:7718 original size:66 final size:66
Alignment explanation
Indices: 7502--7911 Score: 385
Period size: 66 Copynumber: 6.1 Consensus size: 66
7492 TAACTAAAAT
* * * * * *
7502 GCATGAAAGGATACATTAAGACATGAAAGGATGTCATAACTAAAATACATGAAAGGATACATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
7567 G
66 G
* * * * * *
7568 GCTTGAAAAGATGCCATAACTAAAATGCATGAAATGATG-CAT---T--AAGGCATGAAAGGATG
1 GCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATG
*
7627 CCATAACTAAAAT
60 -CAT---T--AAG
* *
7640 GCATGAAAGGATGCATTAATGCATGACAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
7705 G
66 G
* * * *
7706 GCATAAAAGGATGCCATAACTAAAATGCATAAAAGGATGCC-T---T--AAGGCATGAAATGATG
1 GCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATG
7765 CATTAAG
60 CATTAAG
*
7772 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
7837 G
66 G
*
7838 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
7903 G
66 G
7904 GCATGAAA
1 GCATGAAA
7912 ATATGTCATA
Statistics
Matches: 286, Mismatches: 28, Indels: 60
0.76 0.07 0.16
Matches are distributed among these distances:
60 15 0.05
61 1 0.00
62 1 0.00
64 1 0.00
65 3 0.01
66 179 0.63
67 12 0.04
68 4 0.01
70 4 0.01
71 10 0.03
72 56 0.20
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (66 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
G
Found at i:7888 original size:46 final size:46
Alignment explanation
Indices: 7838--8014 Score: 291
Period size: 46 Copynumber: 3.8 Consensus size: 46
7828 ATGCATTAAG
7838 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
** *
7884 GCATGAAAGGATGCATTAAGGCATGAAAATATGTCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
7930 TCATGAAAAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
7976 GTATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
8015 ATGAAATTAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:7954 original size:66 final size:63
Alignment explanation
Indices: 7502--8013 Score: 272
Period size: 66 Copynumber: 7.6 Consensus size: 63
7492 TAACTAAAAT
* * * ** *
7502 GCATGAAAGGATACATTAA-GACATGAAAGGATGTCATAACTAAAATACATGAAAGGATACATTA
1 GCATGAAAAGATGCATTAATG-CATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATTA
7566 AG
62 AG
* *
7568 GCTTGAAAAGATGCCATAACTAAAATGCATGAAATGATG-CAT-T-AAGGCATGAAAGGATGCCA
1 GCATGAAAAGATG-CAT---T--AATGCATGAAAGGATGCCATATAAAGGCATGAAAGGATG-CA
*
7630 TAACTAAAAT
59 T---T--AAG
* * * *
7640 GCATGAAAGGATGCATTAATGCATGACAGGATGCCATAACTAAAATGCATGAAATGATGCATTAA
1 GCATGAAAAGATGCATTAATGCATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATTAA
7705 G
63 G
* *
7706 GCAT-AAAAGGATGCCATAACTAAAATGCATAAAAGGATGCC-T-T-AAGGCATGAAATGATGCA
1 GCATGAAAA-GATG-CAT---T--AATGCATGAAAGGATGCCATATAAAGGCATGAAAGGATGCA
7767 TTAAG
59 TTAAG
* * * * *
7772 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAA
1 GCATGAAAAGATGCATTAATGCATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATTAA
7837 G
63 G
* * *
7838 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAAGATGCATTAATGCATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATTAA
7903 G
63 G
* * *
7904 GCATGAAAATATGTCATAACTAAAATTCATGAAAAGATG-CAT-T-AAGGCATGAAAGGATGCCA
1 GCATGAAAAGATG-CAT---T--AATGCATGAAAGGATGCCATATAAAGGCATGAAAGGATG-CA
*
7966 TAACTAAAAT
59 T---T--AAG
* * * *
7976 GTATGAAAGGATGCATTAAGGCATGAAAGGATGTCATA
1 GCATGAAAAGATGCATTAATGCATGAAAGGATGCCATA
8014 AATGAAATTA
Statistics
Matches: 360, Mismatches: 39, Indels: 92
0.73 0.08 0.19
Matches are distributed among these distances:
60 15 0.04
61 1 0.00
62 1 0.00
64 1 0.00
65 6 0.02
66 202 0.56
67 24 0.07
68 6 0.02
70 6 0.02
71 16 0.04
72 81 0.22
73 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (63 bp):
GCATGAAAAGATGCATTAATGCATGAAAGGATGCCATATAAAGGCATGAAAGGATGCATTAAG
Found at i:9889 original size:3 final size:3
Alignment explanation
Indices: 9883--9931 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
9873 TTTTTTAAAA
9883 AAT AAT -AT AAAT AA- AAT -AT AAAT AAT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT
9928 AAT A
1 AAT A
9932 TTAACCCAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 6 0.15
3 27 0.68
4 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9902 original size:11 final size:12
Alignment explanation
Indices: 9878--9932 Score: 59
Period size: 11 Copynumber: 5.1 Consensus size: 12
9868 CTATTTTTTT
*
9878 TAAAAAATAATA
1 TAAATAATAATA
9890 TAAATAA-AATA
1 TAAATAATAATA
9901 TAAATAAT-A-A
1 TAAATAATAATA
9911 T-AATAATAA-A
1 TAAATAATAATA
9921 T-AATAATAATA
1 TAAATAATAATA
9932 T
1 T
9933 TAACCCAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
9 6 0.15
10 13 0.33
11 14 0.36
12 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAATAATAATA
Found at i:9903 original size:16 final size:15
Alignment explanation
Indices: 9892--9932 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
9882 AAATAATATA
9892 AATAA-AATATAAAT
1 AATAATAATATAAAT
9906 AATAATAATAATAAAT
1 AATAATAAT-ATAAAT
9922 AATAATAATAT
1 AATAATAATAT
9933 TAACCCAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
16 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATAATATAAAT
Found at i:10193 original size:15 final size:15
Alignment explanation
Indices: 10169--10198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10159 GTCACCGATC
*
10169 AAATTGAATTAGTCA
1 AAATTAAATTAGTCA
10184 AAATTAAATTAGTCA
1 AAATTAAATTAGTCA
10199 TATTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
AAATTAAATTAGTCA
Found at i:20325 original size:21 final size:20
Alignment explanation
Indices: 20285--20326 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
20275 TTAAGTGAAT
**
20285 TCAATTTTAAAAGTATTTGA
1 TCAATTTTAAAAAAATTTGA
20305 TCAATTTTAAATAAAATTTGA
1 TCAATTTTAAA-AAAATTTGA
20326 T
1 T
20327 TTTTGAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
TCAATTTTAAAAAAATTTGA
Found at i:22559 original size:2 final size:2
Alignment explanation
Indices: 22554--22583 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22544 TATAATTAAC
22554 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22584 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39563 original size:20 final size:20
Alignment explanation
Indices: 39534--39585 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
39524 TCTTATGGGG
*
39534 AGTATTGATACTCTACGTAT
1 AGTATCGATACTCTACGTAT
*
39554 AGTATCGATACTCTATGTAT
1 AGTATCGATACTCTACGTAT
39574 AGTATCGATACT
1 AGTATCGATACT
39586 TCTATGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTCTACGTAT
Found at i:42748 original size:36 final size:35
Alignment explanation
Indices: 42633--43013 Score: 110
Period size: 37 Copynumber: 10.7 Consensus size: 35
42623 CTCGAAATAC
* *
42633 AAATTTTATCTCACTTGAGATAGTTTTCCTTAAAAG
1 AAATTTTATCTCACTTGAGATATTTTTCC-TAAAAA
* * * * *
42669 AAA-TTCATCTCACTCGAGACAGTTTCTCTTGAAACAA
1 AAATTTTATCTCACTTGAGATA-TTTTTCCT-AAA-AA
*
42706 AAATTTTATCTCGCTTGAGATATTTTTCCTAAAAA
1 AAATTTTATCTCACTTGAGATATTTTTCCTAAAAA
* ** * * * *
42741 ATAATTTTCATGC-AACTCAAGACAATTTCTCTCGAAACA
1 A-AATTTT-AT-CTCACTTGAGA-TATTTTTC-CTAAAAA
* *
42780 AAATTTTATCGCACTT---AT-TTTTCTCTTAAAATA
1 AAATTTTATCTCACTTGAGATATTTT-TCCTAAAA-A
* * * *
42813 AAA-TTTGTCTCACTTGAGACA-ATCTCCTTGAAACAA
1 AAATTTTATCTCACTTGAGATATTTTTCC-T-AAA-AA
* * * **
42849 AAATTATATCTCACTTAAGA-ATTTTCCCT--TGA
1 AAATTTTATCTCACTTGAGATATTTTTCCTAAAAA
* * * *
42881 AAATTTT-TCTCACTCGAGACAGTTTTACTCAAAACA
1 AAATTTTATCTCACTTGAGATATTTTTCCT-AAAA-A
* * * **
42917 AAATTTCATCTTACTTGAGATATTTTCCCT--TGA
1 AAATTTTATCTCACTTGAGATATTTTTCCTAAAAA
* * *
42950 AAATTGTTGTCTCACTCGAGATAATTTCTT-TTGAAACAA
1 AAATT-TTATCTCACTTGAGAT-ATTT-TTCCT-AAA-AA
*
42989 AAA-TTTATTTCACTTGAGATATTTT
1 AAATTTTATCTCACTTGAGATATTTT
43014 CCCTTGAAAA
Statistics
Matches: 241, Mismatches: 70, Indels: 69
0.63 0.18 0.18
Matches are distributed among these distances:
31 10 0.04
32 29 0.12
33 12 0.05
34 15 0.06
35 28 0.12
36 41 0.17
37 68 0.28
38 28 0.12
39 10 0.04
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (35 bp):
AAATTTTATCTCACTTGAGATATTTTTCCTAAAAA
Found at i:43008 original size:37 final size:37
Alignment explanation
Indices: 42961--43085 Score: 105
Period size: 37 Copynumber: 3.5 Consensus size: 37
42951 AATTGTTGTC
*
42961 TCACTCGAGATAATTTCTTTTGAAACAAAAATTTATT
1 TCACTCGAGATATTTTCTTTTGAAACAAAAATTTATT
* ** * *
42998 TCACTTGAGATATTTTCCCTTG----AAAATTTTCATA
1 TCACTCGAGATATTTTCTTTTGAAACAAAAATTT-ATT
* * * * *
43032 TCAATCGAGATAGTTTCTTTCGAAACAAAAATTCACT
1 TCACTCGAGATATTTTCTTTTGAAACAAAAATTTATT
*
43069 TCACTTGAGATATTTTC
1 TCACTCGAGATATTTTC
43086 CTTGAAATTT
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
33 7 0.11
34 18 0.28
37 33 0.52
38 6 0.09
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (37 bp):
TCACTCGAGATATTTTCTTTTGAAACAAAAATTTATT
Found at i:43153 original size:212 final size:211
Alignment explanation
Indices: 42842--43262 Score: 552
Period size: 212 Copynumber: 2.0 Consensus size: 211
42832 CAATCTCCTT
* *
42842 GAAACAAAAATTATATCTCACTTAAGAATTTTCCCTTGAAAATTTTTCTCACTCGAGACAGTTTT
1 GAAACAAAAATTATATCTCACTTAAGAATTTTCCCTTGAAAATTTTTCTCACTCGAAACAATTTT
*
42907 ACTCAAAACAAAATTTCATCTTACTTGAGATATTTTCCCTTGAAAAT-TGT-TGTCTCACTCGAG
66 ACTCAAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATCT-TCT-TCTCACTCGAG
* * *
42970 ATAATTTCTTTTGAAACAAAAATTTATTTCACTTGAGATATTTTCCCTTGAAAATTTTCATATCA
129 ACAATTTCTCTTGAAACAAAAATTTATCTCACTTGAGATATTTTCCCTTGAAAATTTTCATATCA
43035 ATCGAGATAGTTTCTTTC
194 ATCGAGATAGTTTCTTTC
* *
43053 GAAACAAAAATT-CA-CTTCACTTGAGATATTTT-CCTTG-AAATTTTTCATCTTACTCGAAACA
1 GAAACAAAAATTATATC-TCACTTAAGA-ATTTTCCCTTGAAAATTTTTC-TC--ACTCGAAACA
*
43114 ATTTCT-CTCGAAAA-AAAATTTCATCTCAGTTGAGATATTTTCCCTTGAAAATCTTCTTCTCAC
61 ATTT-TACTC-AAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATCTTCTTCTCAC
* * * **
43177 TCGAGACAATTTCTCTTGAAATAAAATTTTATCTCACTTGAGATATTTTCTCTTGAAAATTTTTG
124 TCGAGACAATTTCTCTTGAAACAAAAATTTATCTCACTTGAGATATTTTCCCTTGAAAATTTTCA
* * *
43242 TCTCACTCGAGATATTTTCTT
189 TATCAATCGAGATAGTTTCTT
43263 GACATGACTT
Statistics
Matches: 184, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
209 10 0.05
210 17 0.09
211 17 0.09
212 133 0.72
213 7 0.04
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (211 bp):
GAAACAAAAATTATATCTCACTTAAGAATTTTCCCTTGAAAATTTTTCTCACTCGAAACAATTTT
ACTCAAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATCTTCTTCTCACTCGAGAC
AATTTCTCTTGAAACAAAAATTTATCTCACTTGAGATATTTTCCCTTGAAAATTTTCATATCAAT
CGAGATAGTTTCTTTC
Found at i:43156 original size:141 final size:141
Alignment explanation
Indices: 42643--43251 Score: 498
Period size: 141 Copynumber: 4.3 Consensus size: 141
42633 AAATTTTATC
* ** * * * *
42643 TCACTTGAGATAGTTTTCCTTAAAAGAAATTCATCTCACTCGAGACAGTTTCTCTTGAAACAAAA
1 TCACTTGAGATA-TTTTCCTTGAAA-ATTTTTATCTCACTCGAAACAATTTCTCTCGAAACAAAA
* * ** * *
42708 ATTTTATCTCGCTTGAGATATTTTTCCTAAAAAATAATTT-TCATGCAACTCAAGACAATTTCT-
64 A-TTTATCTCACTTGAGATATTTTCCCTTGAAAAT--TTTCTC-T-C-ACTCGAGACAGTTTCTA
* *
42771 CTCGAAACAAAATTTTA-T
123 TTCGAAACAAAATTTCACT
* * * * * * *
42789 CGCACTT---AT-TTTTCTCTT-AAAATAAAATTTGTCTCACTTGAGACAATCTC-CTTGAAACA
1 -TCACTTGAGATATTTTC-CTTGAAAAT---TTTTATCTCACTCGAAACAATTTCTCTCGAAACA
* *
42848 AAAATTATATCTCACTTAAGA-ATTTTCCCTTGAAAATTTT-TCTCACTCGAGACAGTTT-TACT
61 AAAATT-TATCTCACTTGAGATATTTTCCCTTGAAAATTTTCTCTCACTCGAGACAGTTTCTATT
*
42910 CAAAACAAAATTTCATCT
125 CGAAACAAAATTTCA-CT
* * * * * *
42928 T-ACTTGAGATATTTTCCCTTGAAAATTGTTGTCTCACTCGAGATAATTTCTTTTGAAACAAAAA
1 TCACTTGAGATATTTT-CCTTGAAAATTTTTATCTCACTCGAAACAATTTCTCTCGAAACAAAAA
* * * *
42992 TTTATTTCACTTGAGATATTTTCCCTTGAAAATTTTCATATCAATCGAGATAGTTTCT-TTCGAA
65 TTTATCTCACTTGAGATATTTTCCCTTGAAAATTTTC-TCTCACTCGAGACAGTTTCTATTCGAA
*
43056 ACAAAAATTCACT
129 ACAAAATTTCACT
*
43069 TCACTTGAGATATTTTCCTTG-AAATTTTTCATCTTACTCGAAACAATTTCTCTCGAAA-AAAAA
1 TCACTTGAGATATTTTCCTTGAAAATTTTT-ATCTCACTCGAAACAATTTCTCTCGAAACAAAAA
* * * *
43132 TTTCATCTCAGTTGAGATATTTTCCCTTGAAAATCTTCTTCTCACTCGAGACAATTTCTCTT-GA
65 TTT-ATCTCACTTGAGATATTTTCCCTTGAAAATTTTC-TCTCACTCGAGACAGTTTCTATTCGA
* *
43196 AATAAAATTTTA-T
128 AACAAAATTTCACT
*
43209 CTCACTTGAGATATTTTCTCTTGAAAATTTTTGTCTCACTCGA
1 -TCACTTGAGATATTTTC-CTTGAAAATTTTTATCTCACTCGA
43252 GATATTTTCT
Statistics
Matches: 385, Mismatches: 51, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
136 1 0.00
137 31 0.08
138 1 0.00
139 33 0.09
140 56 0.15
141 113 0.29
142 87 0.23
143 37 0.10
144 21 0.05
147 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (141 bp):
TCACTTGAGATATTTTCCTTGAAAATTTTTATCTCACTCGAAACAATTTCTCTCGAAACAAAAAT
TTATCTCACTTGAGATATTTTCCCTTGAAAATTTTCTCTCACTCGAGACAGTTTCTATTCGAAAC
AAAATTTCACT
Found at i:43195 original size:34 final size:34
Alignment explanation
Indices: 43082--43253 Score: 107
Period size: 34 Copynumber: 4.9 Consensus size: 34
43072 CTTGAGATAT
* *
43082 TTTC-CTTG-AAATTTTTCATCTTACTCGAAACAA
1 TTTCTCTTGAAAATTTTT-ATCTCACTCGAGACAA
* * * * * * *
43115 TTTCTCTCGAAAAAAAATTTCATCTCAGTTGAGATAT
1 TTTCTCTTG---AAAATTTTTATCTCACTCGAGACAA
* *
43152 TTTCCCTTGAAAATCTTCT-TCTCACTCGAGACAA
1 TTTCTCTTGAAAAT-TTTTATCTCACTCGAGACAA
* * * *
43186 TTTCTCTTGAAATAAAATTTTATCTCACTTGAGATAT
1 TTTCTCTTG--A-AAATTTTTATCTCACTCGAGACAA
*
43223 TTTCTCTTGAAAATTTTTGTCTCACTCGAGA
1 TTTCTCTTGAAAATTTTTATCTCACTCGAGA
43254 TATTTTCTTG
Statistics
Matches: 102, Mismatches: 27, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
33 4 0.04
34 44 0.43
35 3 0.03
36 4 0.04
37 41 0.40
38 6 0.06
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTCTCTTGAAAATTTTTATCTCACTCGAGACAA
Found at i:43261 original size:71 final size:70
Alignment explanation
Indices: 42598--43253 Score: 543
Period size: 71 Copynumber: 9.2 Consensus size: 70
42588 TTAACATAAT
* * *
42598 TTTTTTCCTCA-T-GAGACAATTTTCCCTCGAAATACAAATTTTATCTCACTTGAGATAGTTTT-
1 TTTTTT-CTCACTCGAGACAA-TTTCTCTTGAAACA-AAATTTTATCTCACTTGAGATA-TTTTC
*
42660 CCTTAAAAGAA
62 CCTT-GAA-AA
* ** * * *
42671 ATTCATCTCACTCGAGACAGTTTCTCTTGAAACAAAAATTTTATCTCGCTTGAGATATTTTTCCT
1 TTTTTTCTCACTCGAGACAATTTCTCTTGAAAC-AAAATTTTATCTCACTTGAGATATTTTCCCT
**
42736 AAAAAA
65 TGAAAA
* * * *
42742 TAATTTTCATGCAACTCAAGACAATTTCTCTCGAAACAAAATTTTATCGCACTT---AT-TTTTC
1 T-TTTTTC-T-C-ACTCGAGACAATTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTC
*
42803 TCTT-AAAA
62 CCTTGAAAA
* * * * *
42811 TAAAATTTGTCTCACTTGAGACAATCTC-CTTGAAACAAAAATTATATCTCACTTAAGA-ATTTT
1 T----TTTTTCTCACTCGAGACAATTTCTCTTGAAAC-AAAATTTTATCTCACTTGAGATATTTT
42874 CCCTTGAAAA
61 CCCTTGAAAA
* ** * *
42884 -TTTTTCTCACTCGAGACAGTTT-TACTCAAAACAAAATTTCATCTTACTTGAGATATTTTCCCT
1 TTTTTTCTCACTCGAGACAATTTCT-CTTGAAACAAAATTTTATCTCACTTGAGATATTTTCCCT
42947 TGAAAA
65 TGAAAA
* * * * *
42953 TTGTTGTCTCACTCGAGATAATTTCTTTTGAAACAAAAATTTATTTCACTTGAGATATTTTCCCT
1 TT-TTTTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCCCT
43018 TGAAAA
65 TGAAAA
* * * * * * *
43024 TTTTCATATCAATCGAGATAGTTTCT-TTCGAAACAAAAATTCA-CTTCACTTGAGATATTTT-C
1 TTTT-TTCTCACTCGAGACAATTTCTCTT-GAAACAAAATTTTATC-TCACTTGAGATATTTTCC
43086 CTTG-AAA
63 CTTGAAAA
* * * * * *
43093 TTTTTCATCTTACTCGAAACAATTTCTCTCGAAAAAAAATTTCATCTCAGTTGAGATATTTTCCC
1 TTTTT--TCTCACTCGAGACAATTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCCC
43158 TTGAAAA
64 TTGAAAA
* * *
43165 TCTTCTTCTCACTCGAGACAATTTCTCTTGAAATAAAATTTTATCTCACTTGAGATATTTTCTCT
1 T-TTTTTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCCCT
43230 TGAAAA
65 TGAAAA
43236 TTTTTGTCTCACTCGAGA
1 TTTTT-TCTCACTCGAGA
43254 TATTTTCTTG
Statistics
Matches: 473, Mismatches: 76, Indels: 70
0.76 0.12 0.11
Matches are distributed among these distances:
68 42 0.09
69 60 0.13
70 61 0.13
71 187 0.40
72 33 0.07
73 46 0.10
74 23 0.05
75 21 0.04
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (70 bp):
TTTTTTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTTATCTCACTTGAGATATTTTCCCTT
GAAAA
Found at i:44078 original size:22 final size:21
Alignment explanation
Indices: 44048--44089 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
44038 AGTAGTTTAT
*
44048 GTATTATTTTAAAATATATATA
1 GTATAATTTTAAAAT-TATATA
*
44070 GTATAATTTTAATATTATAT
1 GTATAATTTTAAAATTATAT
44090 GTGTGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
GTATAATTTTAAAATTATATA
Found at i:44165 original size:26 final size:25
Alignment explanation
Indices: 44134--44212 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 25
44124 AAAAAATATT
* *
44134 TATAATATATTTATAATTTTTTAAAA
1 TATAATAT-TATATAATATTTTAAAA
*
44160 TATAATATTATATAGTATTTTAAAA
1 TATAATATTATATAATATTTTAAAA
*
44185 TA-AATATTATAT-ATATATTAAAAA
1 TATAATATTATATAATAT-TTTAAAA
44209 TATA
1 TATA
44213 TGTATTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.07
24 18 0.39
25 17 0.37
26 8 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
TATAATATTATATAATATTTTAAAA
Found at i:46712 original size:12 final size:12
Alignment explanation
Indices: 46695--46721 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46685 TCATATTTGT
46695 ATTATCATTAGA
1 ATTATCATTAGA
46707 ATTATCATTAGA
1 ATTATCATTAGA
46719 ATT
1 ATT
46722 CCCATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (12 bp):
ATTATCATTAGA
Found at i:48791 original size:42 final size:42
Alignment explanation
Indices: 48744--48835 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
48734 TCCGAAATCT
*
48744 CGTGTTTGTTTCACGTAATTCATTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCC
* *
48786 CGTGTTTGTTTTACGTAATTCGTTTTTCGAAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCC
*
48828 AGTGTTTG
1 CGTGTTTG
48836 GTTGGAGGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCATTTTTCGAAAAATGTTTTCC
Found at i:49096 original size:21 final size:21
Alignment explanation
Indices: 49048--49105 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
49038 TAATTATTAA
*
49048 AATATTTAACT-ATAT-TTATT
1 AATATTTAA-TAATATAATATT
49068 AATATTTAATAATATAATATT
1 AATATTTAATAATATAATATT
*
49089 -ATATTTTAATATTATAA
1 AATA-TTTAATAATATAA
49106 AAAACAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 16 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTTAATAATATAATATT
Found at i:49260 original size:23 final size:22
Alignment explanation
Indices: 49234--49277 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
49224 CTAAATATTT
49234 TAATAAAGATATTTAAAATATAC
1 TAATAAAGAT-TTTAAAATATAC
* * *
49257 TAATTAATATTTTTAAATATA
1 TAATAAAGATTTTAAAATATA
49278 ATATAACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATAAAGATTTTAAAATATAC
Found at i:49636 original size:20 final size:20
Alignment explanation
Indices: 49611--49660 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
49601 TCGAAAAACG
*
49611 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATATAATTCA
49631 TTTTCCAGAAATATAATTCA
1 TTTTCCAGAAATATAATTCA
49651 TTTTCCAGAA
1 TTTTCCAGAA
49661 TTCAAATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATATAATTCA
Found at i:49695 original size:30 final size:30
Alignment explanation
Indices: 49644--49717 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
49634 TCCAGAAATA
49644 TAATTCATTTTCC-AGAATTCAAATTCCAG
1 TAATTCATTTTCCAAGAATTCAAATTCCAG
** *
49673 TAATTTTTTTTCCAATAATTCAAATTCCAG
1 TAATTCATTTTCCAAGAATTCAAATTCCAG
49703 TAATTCATTTTCCAA
1 TAATTCATTTTCCAA
49718 AAAAACCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (30 bp):
TAATTCATTTTCCAAGAATTCAAATTCCAG
Found at i:49715 original size:15 final size:15
Alignment explanation
Indices: 49644--49716 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
49634 TCCAGAAATA
49644 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
**
49659 -AATTCAAATTCCAG
1 TAATTCATTTTCCAG
** *
49673 TAATTTTTTTTCCAA
1 TAATTCATTTTCCAG
**
49688 TAATTCAAATTCCAG
1 TAATTCATTTTCCAG
49703 TAATTCATTTTCCA
1 TAATTCATTTTCCA
49717 AAAAAACCAA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:53784 original size:26 final size:26
Alignment explanation
Indices: 53702--53784 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
53692 TTTACATATT
* *
53702 TATATATGAATCATATCAATTTAAAC
1 TATATATGAATTATATCAATTTAAAA
* * * * * *
53728 TATA-ATAAATTTTAAACAAATTATTAT
1 TATATATGAATTAT-ATCAATTTA-AAA
53755 TATATATGAATTATATCAATTTAAAA
1 TATATATGAATTATATCAATTTAAAA
53781 TATA
1 TATA
53785 ATAAAAATAT
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
25 6 0.15
26 16 0.39
27 12 0.29
28 7 0.17
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
TATATATGAATTATATCAATTTAAAA
Found at i:54661 original size:18 final size:18
Alignment explanation
Indices: 54638--54674 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54628 ACCTATATAT
54638 ATATTACAT-ATTTTAAAA
1 ATATTA-ATAATTTTAAAA
54656 ATATTAATAATTTTAAAA
1 ATATTAATAATTTTAAAA
54674 A
1 A
54675 GAATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTAATAATTTTAAAA
Found at i:58669 original size:24 final size:24
Alignment explanation
Indices: 58635--58707 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
58625 ATACATTACC
* *
58635 TGAATTATGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* *
58659 TGGATTCTGTTATGATATT-TGATT
1 TGAATTCTGTTATGAT-TTCTGATA
*
58683 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
58707 T
1 T
58708 CTCATTTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:58874 original size:2 final size:2
Alignment explanation
Indices: 58867--58901 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58857 CGGATGGGGG
58867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58902 GTTTTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63727 original size:48 final size:48
Alignment explanation
Indices: 63671--63781 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
63661 AAATATTTTA
*
63671 TCTGATTTCCGACT-TGAATTCTGTTCTGATA-CATTACCTGAATTCAGT
1 TCTGATTTCCGA-TATGAATTCTGTTCTGATATC-TGACCTGAATTCAGT
* * * * *
63719 TCTGATTTCTGATATGGATTCTGTTCTGGTATCTGATCTGAATTCGGT
1 TCTGATTTCCGATATGAATTCTGTTCTGATATCTGACCTGAATTCAGT
*
63767 TTTGATTTCCGATAT
1 TCTGATTTCCGATAT
63782 CTCATTTCAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTCTGTTCTGATATCTGACCTGAATTCAGT
Found at i:63739 original size:24 final size:24
Alignment explanation
Indices: 63709--63781 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
63699 ATACATTACC
63709 TGAATTCAGTTCTGATTTCTGATA
1 TGAATTCAGTTCTGATTTCTGATA
* * * * *
63733 TGGATTCTGTTCTGGTATCTGATC
1 TGAATTCAGTTCTGATTTCTGATA
* * *
63757 TGAATTCGGTTTTGATTTCCGATA
1 TGAATTCAGTTCTGATTTCTGATA
63781 T
1 T
63782 CTCATTTCAC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (24 bp):
TGAATTCAGTTCTGATTTCTGATA
Found at i:68856 original size:24 final size:24
Alignment explanation
Indices: 68784--68856 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
68774 ATACATTACC
* *
68784 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* * * * *
68808 TGGATGCTGGTATGATATCTAATA
1 TGAATTCTGTTATGATTTCTGATA
* *
68832 TGAATTCTGTTTTGATTTATGATA
1 TGAATTCTGTTATGATTTCTGATA
68856 T
1 T
68857 CTCATTTCAC
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:69023 original size:2 final size:2
Alignment explanation
Indices: 69016--69054 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
69006 ACGGATGGGG
69016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69055 GTTTTTTTAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81112 original size:59 final size:60
Alignment explanation
Indices: 80958--81140 Score: 173
Period size: 60 Copynumber: 3.0 Consensus size: 60
80948 AATTCCATCA
* * * *
80958 CATCCTCA-AATTACGACTTTTATTCTAAA-CTAGTCCTTAGACTTTTAAACA-TTCAAATTT
1 CATCCTCATAA-TATGACCTTTATTCTAAATC-AGTCCTTAAACTTTTGAACATTTC-AATTT
* *
81018 CAT-CTC-TAAATATCGA-CTATCATTCTAAATTAGTCCTTAAACTTTTGAACATTTC-ATTT
1 CATCCTCAT-AATAT-GACCT-TTATTCTAAATCAGTCCTTAAACTTTTGAACATTTCAATTT
* **
81077 CATCCTCATACTATGACCTTTATTCTAAATCAGTCCCCAAACTTCTTGAACATTTCAATTT
1 CATCCTCATAATATGACCTTTATTCTAAATCAGTCCTTAAACTT-TTGAACATTTCAATTT
81138 CAT
1 CAT
81141 AATAAACTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
59 36 0.36
60 54 0.53
61 11 0.11
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
CATCCTCATAATATGACCTTTATTCTAAATCAGTCCTTAAACTTTTGAACATTTCAATTT
Found at i:81896 original size:16 final size:15
Alignment explanation
Indices: 81863--81909 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
81853 TCTTTGAAGT
81863 TTTTTTATAATTTAA
1 TTTTTTATAATTTAA
*
81878 TTTTTTATAGTTT--
1 TTTTTTATAATTTAA
* *
81891 TTATTTATATTTTAA
1 TTTTTTATAATTTAA
81906 TTTT
1 TTTT
81910 ATACCTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTTTATAATTTAA
Found at i:86699 original size:20 final size:20
Alignment explanation
Indices: 86674--86722 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
86664 AATAAAGTAT
86674 AAGAGAATTGTAGAGAAAAG
1 AAGAGAATTGTAGAGAAAAG
86694 AAGAGAATTGTAGAGAAAAG
1 AAGAGAATTGTAGAGAAAAG
86714 AAGA-AATTG
1 AAGAGAATTG
86723 GTCTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (20 bp):
AAGAGAATTGTAGAGAAAAG
Found at i:87438 original size:87 final size:85
Alignment explanation
Indices: 87347--87510 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 85
87337 TCTCAAGTTA
* * * *
87347 GTGAATTCATCAAGTCCTTCTCACTATGACCACTCAAATCCTGAGCTATAAATT-CATTGAGAGT
1 GTGAATTCATCAAGTCCTTCTCAATAGGACCAC-CAAAACCTGAGCTAT-AATTCCATTAAGAG-
**
87411 GTAAAGCTCATCCTTTCACGTCG
63 CAAAAGCTCATCCTTTCACGTCG
* *
87434 GTGAATTTATCAAGTCCTTCTCAATAGGACCACCAAAACCTGGGCTATAATTCCATTAAGAGCAA
1 GTGAATTCATCAAGTCCTTCTCAATAGGACCACCAAAACCTGAGCTATAATTCCATTAAGAGCAA
87499 AAGCTCATCCTT
66 AAGCTCATCCTT
87511 ATGCATGTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 17 0.25
86 21 0.31
87 30 0.44
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (85 bp):
GTGAATTCATCAAGTCCTTCTCAATAGGACCACCAAAACCTGAGCTATAATTCCATTAAGAGCAA
AAGCTCATCCTTTCACGTCG
Done.