Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000446.1 Hibiscus syriacus cultivar Beakdansim tig00000815_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: 71124
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:1342 original size:13 final size:13
Alignment explanation
Indices: 1301--1342 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1291 TTTACTCCTA
1301 TTATAATATT-TT
1 TTATAATATTATT
*
1313 TTA-AATATTAAT
1 TTATAATATTATT
*
1325 TTATAATTTTATT
1 TTATAATATTATT
1338 TTATA
1 TTATA
1343 GGATTTGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 6 0.24
12 7 0.28
13 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATAATATTATT
Found at i:2778 original size:108 final size:105
Alignment explanation
Indices: 2584--2802 Score: 341
Period size: 108 Copynumber: 2.1 Consensus size: 105
2574 TGGTTTCAAA
* * * *
2584 TAATGATATTGTTAATGATGAAAAAATAAAAATAAATCATTCAAATGAGGTTTTAAACCTGGATC
1 TAATAATATTGTTAATGATGAAAAAATAAAAATAAATCATTAAAATGAGGTTTCAAACCTAGATC
*
2649 AATGGTGACATGTGTCACGATTTTATTGGATTGAAAATAAATT
66 AATGGTGACATGTGTCACGATTTGA-T--ATTGAAAATAAATT
*
2692 TAATAATATTGTTAATGATGAAAAAATTAAAAA-AAATCATTAAAATGAGGTTTCAACCCTAGAT
1 TAATAATATTGTTAATGATGAAAAAA-TAAAAATAAATCATTAAAATGAGGTTTCAAACCTAGAT
2756 CAATGGTGACATGTGTCACGATTTGATATTGAAAATAAATT
65 CAATGGTGACATGTGTCACGATTTGATATTGAAAATAAATT
2797 TAATAA
1 TAATAA
2803 ATTAAAATAA
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
105 20 0.19
107 1 0.01
108 77 0.74
109 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (105 bp):
TAATAATATTGTTAATGATGAAAAAATAAAAATAAATCATTAAAATGAGGTTTCAAACCTAGATC
AATGGTGACATGTGTCACGATTTGATATTGAAAATAAATT
Found at i:5808 original size:36 final size:36
Alignment explanation
Indices: 5768--5853 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
5758 TACGAACAAA
* *
5768 CTTGTTTATATGTTCATAAACTAGCTCGTTTAAAAG
1 CTTGTTTATATGTTCATAAACAAGCTCGTTCAAAAG
* * *
5804 CTTGTTTATAAGTTCATGAACAAGCTCGTTCACAAG
1 CTTGTTTATATGTTCATAAACAAGCTCGTTCAAAAG
*
5840 CTCGTTTATATGTT
1 CTTGTTTATATGTT
5854 TTAAGAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTGTTTATATGTTCATAAACAAGCTCGTTCAAAAG
Found at i:7706 original size:24 final size:24
Alignment explanation
Indices: 7679--7724 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
7669 TTGTGTTGAG
* *
7679 TTTTATTTATTATTTATTTAATGT
1 TTTTATTTATTATATAATTAATGT
7703 TTTTATTTATTATATAATTAAT
1 TTTTATTTATTATATAATTAAT
7725 ATTATGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTATTTATTATATAATTAATGT
Found at i:7749 original size:2 final size:2
Alignment explanation
Indices: 7738--7775 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
7728 ATGGCATAGT
7738 TA TA -A 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
7776 TTAATATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9778 original size:14 final size:14
Alignment explanation
Indices: 9759--9790 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
9749 GTATGTTATA
9759 TATGTGTGTGTGTG
1 TATGTGTGTGTGTG
9773 TATGTGTGTGTGTG
1 TATGTGTGTGTGTG
9787 TATG
1 TATG
9791 AGTTGATAAA
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:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (14 bp):
TATGTGTGTGTGTG
Found at i:10059 original size:22 final size:22
Alignment explanation
Indices: 10034--10083 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
10024 GTCCTTTAGA
*
10034 ACATATACACAGGTCCTTCGGG
1 ACATATACACAGGTCATTCGGG
* *
10056 ACATATGCATAGGTCATTCGGG
1 ACATATACACAGGTCATTCGGG
10078 ACATAT
1 ACATAT
10084 TTCATATGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
ACATATACACAGGTCATTCGGG
Found at i:18639 original size:28 final size:28
Alignment explanation
Indices: 18607--18664 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
18597 AACGAATTGT
* *
18607 TTCTTTTGAATTAGCTCTTTTGTATTTA
1 TTCTTTTGAATTAGCTATTTTCTATTTA
* * *
18635 TTCTTTTTAATTTGTTATTTTCTATTTA
1 TTCTTTTGAATTAGCTATTTTCTATTTA
18663 TT
1 TT
18665 TGTAACATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (28 bp):
TTCTTTTGAATTAGCTATTTTCTATTTA
Found at i:18768 original size:23 final size:23
Alignment explanation
Indices: 18685--18785 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 23
18675 TTAACATATA
* * **
18685 TAAACGAATATGTTCACTAACTT
1 TAAACGAACATGTTCACGAACGC
* *
18708 TAAACAAACATGTTCATGAACGC
1 TAAACGAACATGTTCACGAACGC
*
18731 TAAACGAACACGTTCACGAACGC
1 TAAACGAACATGTTCACGAACGC
** * **
18754 TATGCGATCATGTTCACGAACAT
1 TAAACGAACATGTTCACGAACGC
18777 TAAACGAAC
1 TAAACGAAC
18786 GCAAAATGAA
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCACGAACGC
Found at i:18820 original size:24 final size:23
Alignment explanation
Indices: 18793--18854 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
18783 AACGCAAAAT
*
18793 GAACATGTTTGTGAACATTTAAAC
1 GAACATGTTCGTGAACA-TTAAAC
*
18817 GAACATGTTCGCGAACATTAAAC
1 GAACATGTTCGTGAACATTAAAC
*
18840 GAACACGTTCGTGAA
1 GAACATGTTCGTGAA
18855 TGTTAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (23 bp):
GAACATGTTCGTGAACATTAAAC
Found at i:19718 original size:39 final size:39
Alignment explanation
Indices: 19595--19779 Score: 207
Period size: 39 Copynumber: 4.7 Consensus size: 39
19585 ATATATATAG
* *
19595 TATATAATATATATTTTTTTATAAA-ATTTTGAAAACATA
1 TATATAATATATA-GTTTTTAAAAATATTTTGAAAACATA
* *
19634 TATGTAATATATAGTTTTCTAAAAAAGACGTTTTGAAAACATA
1 TATATAATATATAGTTTT-T-AAAAATA--TTTTGAAAACATA
*
19677 TATATAATATATAGTTTTTAAAAATATTTTG--AATATA
1 TATATAATATATAGTTTTTAAAAATATTTTGAAAACATA
* * *
19714 TATATAATATATAGTTTTTGAAAACATTTT-AAGAACACA
1 TATATAATATATAGTTTTTAAAAATATTTTGAA-AACATA
*
19753 TATATAATATATAGTTTTTGAAAATAT
1 TATATAATATATAGTTTTTAAAAATAT
19780 ATATAATATA
Statistics
Matches: 127, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
37 33 0.26
38 4 0.03
39 48 0.38
40 4 0.03
41 7 0.06
42 1 0.01
43 30 0.24
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (39 bp):
TATATAATATATAGTTTTTAAAAATATTTTGAAAACATA
Found at i:19788 original size:76 final size:79
Alignment explanation
Indices: 19595--19791 Score: 210
Period size: 76 Copynumber: 2.5 Consensus size: 79
19585 ATATATATAG
* * *
19595 TATATAATATATATTTTTTTATAAAAT-TT-TGAAAACATATATGTAATATATAGTTTTCTAAAA
1 TATATAATATATA-GTTTTTA-AAAATATTATG--AATATATATATAATATATAGTTTTCT-AAA
* *
19658 AAGACGTTTTGAAAACATA
61 AAGACATTTTGAAAACACA
* *
19677 TATATAATATATAGTTTTTAAAAATATTTTGAATATATATATAATATATAGTTTT-T-GAAA-AC
1 TATATAATATATAGTTTTTAAAAATATTATGAATATATATATAATATATAGTTTTCTAAAAAGAC
19739 ATTTT-AAGAACACA
66 ATTTTGAA-AACACA
*
19753 TATATAATATATAGTTTTTGAAAATATATAT-AATATATA
1 TATATAATATATAGTTTTTAAAAATAT-TATGAATATATA
19792 GTTTTTGAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
75 2 0.02
76 45 0.44
77 5 0.05
79 1 0.01
80 27 0.26
81 8 0.08
82 15 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (79 bp):
TATATAATATATAGTTTTTAAAAATATTATGAATATATATATAATATATAGTTTTCTAAAAAGAC
ATTTTGAAAACACA
Found at i:19819 original size:38 final size:37
Alignment explanation
Indices: 19767--19877 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
19757 TAATATATAG
**
19767 TTTTTGAAAATATATATAATATATAGTTTTTGAATTTT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAA-AAT
*
19805 TTTTTGAAACTATATATAATATATAGTTTTTGAAAAT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* * *
19842 ATTTTGAAAATATATATATTATATAGTTTTTTAAAA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAA
19878 AAAATATTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
37 33 0.50
38 33 0.50
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAAT
Found at i:19840 original size:64 final size:65
Alignment explanation
Indices: 19703--19843 Score: 205
Period size: 64 Copynumber: 2.2 Consensus size: 65
19693 TTTAAAAATA
*
19703 TTTTGAATATATATATAATATATAGTTTTTGAAAACATTTTAAGAACACATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAGAACACATATATAATATATAGT
*** **
19768 TTTTGAAAATATATATAATATATAGTTTTTG-AATTTTTTTTTGAA-ACTATATATAATATATAG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAGAACAC-ATATATAATATATAG
19831 T
65 T
19832 TTTTGAAAATAT
1 TTTTGAAAATAT
19844 TTTGAAAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 2 0.03
64 37 0.54
65 30 0.43
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (65 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAGAACACATATATAATATATAGT
Found at i:19872 original size:64 final size:63
Alignment explanation
Indices: 19703--19873 Score: 150
Period size: 64 Copynumber: 2.7 Consensus size: 63
19693 TTTAAAAATA
* * * * * **
19703 TTTTGAATATATATATAATATATAGTTTTTGAAAACATTTTAAGAACAC-ATATATAATATATAG
1 TTTTGAAAATATATAAAATATATAGTTTAT-AATA-GTTTTTTGAA-ACTATATATAATATATAG
19767 T
63 T
* * **
19768 TTTTGAAAATATATATAATATATAGTTTTTGAATTTTTTTTTGAAACTATATATAATATATAGT
1 TTTTGAAAATATATAAAATATATAGTTTAT-AATAGTTTTTTGAAACTATATATAATATATAGT
*
19832 TTTTGAAAATATTTTGAAAATATATA-TATTAT-ATAGTTTTTT
1 TTTTGAAAATA-TAT-AAAATATATAGT-TTATAATAGTTTTTT
19874 AAAAAAAATA
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 42 0.46
65 35 0.38
66 12 0.13
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (63 bp):
TTTTGAAAATATATAAAATATATAGTTTATAATAGTTTTTTGAAACTATATATAATATATAGT
Found at i:19965 original size:26 final size:27
Alignment explanation
Indices: 19924--19975 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
19914 TTATTTACTA
*
19924 TATTTTTTTCATTTTCATTTTACTTTT
1 TATTTATTTCATTTTCATTTTACTTTT
* *
19951 TATTTATTT-ATTTTCGTTTTTCTTT
1 TATTTATTTCATTTTCATTTTACTTT
19976 CTTTGGTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.13, C:0.10, G:0.02, T:0.75
Consensus pattern (27 bp):
TATTTATTTCATTTTCATTTTACTTTT
Found at i:20836 original size:51 final size:55
Alignment explanation
Indices: 20773--20891 Score: 126
Period size: 55 Copynumber: 2.3 Consensus size: 55
20763 TAATCGTTCT
* *
20773 TTTATCTTTATTTT-TAATT-AT-TTATTTTA-TTTTAATTTTAG-TAATTTTTTC
1 TTTATCTTTATTTTGCAATTGATATTATTTTATTTTTAA-TTTAGTTAACTTTTTC
* *
20824 TTTAT-TTATATTTTGCAATTGATATTTTTTTATTTTTAATTTAGTTGACTTTTTC
1 TTTATCTT-TATTTTGCAATTGATATTATTTTATTTTTAATTTAGTTAACTTTTTC
*
20879 TTTA-CATTATTTT
1 TTTATCTTTATTTT
20892 TCTTTACTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
50 2 0.04
51 11 0.20
52 4 0.07
53 2 0.04
54 18 0.32
55 19 0.34
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (55 bp):
TTTATCTTTATTTTGCAATTGATATTATTTTATTTTTAATTTAGTTAACTTTTTC
Found at i:20893 original size:15 final size:15
Alignment explanation
Indices: 20873--20908 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
20863 TTTAGTTGAC
20873 TTTTTCTTTACATTA
1 TTTTTCTTTACATTA
*
20888 TTTTTCTTTACTTTA
1 TTTTTCTTTACATTA
20903 TATTTT
1 T-TTTT
20909 AAATATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCTTTACATTA
Found at i:23502 original size:23 final size:21
Alignment explanation
Indices: 23452--23530 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 21
23442 AGGGTGTCAA
23452 AGTGCATCCATGCACC--CCTGT
1 AGTGCATCCATGCACCTGCC--T
23473 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTG-C-CT
*
23496 AGTGCATCGATGCACCATG--T
1 AGTGCATCCATGCACC-TGCCT
23516 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
23531 TCCATTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
23 16 0.31
24 3 0.06
25 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGCCT
Found at i:23988 original size:34 final size:32
Alignment explanation
Indices: 23949--24018 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
23939 TTTTGTAAAG
* *
23949 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
23983 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
24015 GGGA
1 GGGA
24019 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:26990 original size:21 final size:21
Alignment explanation
Indices: 26942--27063 Score: 129
Period size: 21 Copynumber: 5.7 Consensus size: 21
26932 AGGGTGTCAA
* *
26942 AGTGCATTCATGCACCCCCTAC
1 AGTGCATCCATGCA-CCCCTGC
26964 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
26985 AATGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* **
27006 AGTGCATCCATACACCTCCCAC
1 AGTGCATCCATGCACC-CCTGC
* * *
27028 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTGC
27049 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
27064 TCCATTTCGA
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
20 13 0.16
21 41 0.49
22 17 0.20
23 12 0.14
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:27058 original size:64 final size:64
Alignment explanation
Indices: 26942--27063 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
26932 AGGGTGTCAA
* * *
26942 AGTGCATTCATGCACCCCCTACAGTGCATCCATGCACCCCTGCAATGCATCCATGCACCCCTGC
1 AGTGCATCCATACACCCCCTACAGTGCATCCATGCACCCATGCAATGCATCCATGCACCCCTGC
* * *
27006 AGTGCATCCATACACCTCCC-ACTAGTGCATCGATGCA-CCATGTAGTGCATCCATGCAC
1 AGTGCATCCATACACC-CCCTAC-AGTGCATCCATGCACCCATGCAATGCATCCATGCAC
27064 TCCATTTCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 34 0.68
65 16 0.32
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (64 bp):
AGTGCATCCATACACCCCCTACAGTGCATCCATGCACCCATGCAATGCATCCATGCACCCCTGC
Found at i:33384 original size:38 final size:38
Alignment explanation
Indices: 33342--33603 Score: 228
Period size: 38 Copynumber: 6.6 Consensus size: 38
33332 ATGTATATAG
33342 TATATAAATATATAGTTTTTTATAAA-A-TTTTGAAAACA
1 TATAT-AATATATAGTTTTTTA-AAACATTTTTGAAAACA
* * *
33380 TATATGTAATATATAGTTTTCTAAAAAAGACGTTTTGAAAACATA
1 TATA--TAATATATAGTTTT-T-TAAAACA-TTTTTGAAAAC--A
* * *
33425 TATATATATAATATAGTTTTTAAAAATATTTTTGAAAATA
1 TATATA-AT-ATATAGTTTTTTAAAACATTTTTGAAAACA
*
33465 TATATAATATATA-TTTTTTGAAAACA-TTTTAAAATACA
1 TATATAATATATAGTTTTTT-AAAACATTTTTGAAA-ACA
* * * *
33503 TATATAATATATAGGTTTTGAAAATATTTTTGAAAATA
1 TATATAATATATAGTTTTTTAAAACATTTTTGAAAACA
* *
33541 TATATAATATATAGTTTTTGAAAACA-TTTTGAAAATATA
1 TATATAATATATAGTTTTTTAAAACATTTTTG-AAA-ACA
*
33580 TATATAATATATAGTTTTTGAAAA
1 TATATAATATATAGTTTTTTAAAA
33604 TATATATAAT
Statistics
Matches: 192, Mismatches: 15, Indels: 33
0.80 0.06 0.14
Matches are distributed among these distances:
37 17 0.09
38 63 0.33
39 53 0.28
40 12 0.06
41 2 0.01
42 9 0.05
43 18 0.09
44 3 0.02
45 15 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (38 bp):
TATATAATATATAGTTTTTTAAAACATTTTTGAAAACA
Found at i:33500 original size:27 final size:26
Alignment explanation
Indices: 33453--33505 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
33443 TTTAAAAATA
* * *
33453 TTTTTGAAAATATATATAATATATAT
1 TTTTTGAAAACATATAAAATACATAT
*
33479 TTTTTGAAAACATTTTAAAATACATAT
1 TTTTTGAAAACA-TATAAAATACATAT
33506 ATAATATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAACATATAAAATACATAT
Found at i:33516 original size:76 final size:77
Alignment explanation
Indices: 33336--33606 Score: 323
Period size: 76 Copynumber: 3.4 Consensus size: 77
33326 TAGTATATGT
* *
33336 ATATAGTATATAAATATATAGTTTTTTATAAA-A-TTTTGAAAACATATATGTAATATATAGTTT
1 ATATA-TATAT-AATATATAG-TTTTTAAAAATATTTTTG-AAA-ATATATATAATATATA-TTT
** *
33399 TCTAAAAAAGACGTTTTGAAA
60 T-T-TGAAA-ACATTTTGAAA
*
33420 ACATATATATATATAATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATATTTTTTG
1 ATATATATATA-AT-ATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATATTTTTTG
33485 AAAACATTTT-AAA
64 AAAACATTTTGAAA
* * * *
33498 ATACATATATAATATATAGGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTTGAA
1 ATATATATATAATATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATATTTTTTGAA
33563 AACATTTTGAAA
66 AACATTTTGAAA
*
33575 ATATATATATAATATATAGTTTTTGAAAATAT
1 ATATATATATAATATATAGTTTTTAAAAATAT
33607 ATATAATATA
Statistics
Matches: 169, Mismatches: 13, Indels: 17
0.85 0.07 0.09
Matches are distributed among these distances:
76 57 0.34
77 35 0.21
78 12 0.07
79 6 0.04
80 3 0.02
81 1 0.01
82 5 0.03
83 31 0.18
84 14 0.08
85 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (77 bp):
ATATATATATAATATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATATTTTTTGAA
AACATTTTGAAA
Found at i:47726 original size:3 final size:3
Alignment explanation
Indices: 47720--47796 Score: 97
Period size: 3 Copynumber: 26.0 Consensus size: 3
47710 ATTATTATTT
*
47720 TAA TAA TAA T-A TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
47764 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47797 ATAAATAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.09
3 53 0.82
4 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:47747 original size:12 final size:12
Alignment explanation
Indices: 47730--47804 Score: 86
Period size: 12 Copynumber: 6.3 Consensus size: 12
47720 TAATAATAAT
47730 ATAATATATATA
1 ATAATATATATA
47742 ATAATATATATA
1 ATAATATATATA
47754 ATAAT-TATAATA
1 ATAATATAT-ATA
47766 ATAATA-ATTATA
1 ATAATATA-TATA
47778 ATAATA-ATAATA
1 ATAATATAT-ATA
*
47790 ATAATAAATA-A
1 ATAATATATATA
47801 ATAA
1 ATAA
47805 AATGGGTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.16
12 46 0.79
13 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATATATA
Found at i:48061 original size:17 final size:17
Alignment explanation
Indices: 48039--48097 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
48029 TTGCACAAGC
48039 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
48056 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
48075 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
48092 CCTTCT
1 TCTTCT
48098 GGAAATGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 4 0.12
19 10 0.30
20 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:48288 original size:113 final size:111
Alignment explanation
Indices: 48141--48515 Score: 450
Period size: 113 Copynumber: 3.3 Consensus size: 111
48131 ATAGAGTCAT
* *
48141 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
* * * * *
48206 ATGATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATAAATTCGA
65 ATTATGAACTCTC-CTGGAAATGTTGATCCATCGAATGATGAATTCAA
* *
48254 GCGAAAAGTTGAACAAGTTCTTCTTATTATGAA---CTTCTTCTTTCTTTAGATGACGAGTTCTT
1 GC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGAT---GAGTTCTT
* * *
48316 CTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAA
62 CTCATTATGAACTCT-CCTGGAAATGTTGATCCATCGAATGATGAATTCAA
* * *
48367 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTT
1 GCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
** * * *
48432 ATTATGAACTCGAACTGGTAATGCTGATCCATTGAATGATGAATTCAA
65 ATTATGAACTC-TCCTGGAAATGTTGATCCATCGAATGATGAATTCAA
*
48480 GAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
1 G-CAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
48516 TCTCTGGAAA
Statistics
Matches: 224, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
110 17 0.08
112 4 0.02
113 177 0.79
114 9 0.04
116 17 0.08
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (111 bp):
GCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCCTGGAAATGTTGATCCATCGAATGATGAATTCAA
Found at i:48510 original size:73 final size:73
Alignment explanation
Indices: 48422--48585 Score: 193
Period size: 73 Copynumber: 2.2 Consensus size: 73
48412 TCTTCAGATG
* * * **
48422 AGTTCTTCTTATTATGAACTCGAACTGGTAATGCTGATCCATTGAATGATGAATTCAAGAAAAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAATGATGAATTCAAGAAAAAA
48487 GTTGAACA
66 GTTGAACA
**** * ** * *
48495 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAATGATGAATTCAAGAAAAAA
48560 GTTGAACA
66 GTTGAACA
*
48568 AATTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
48586 TTTCTTCTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAATGATGAATTCAAGAAAAAA
GTTGAACA
Found at i:48760 original size:300 final size:299
Alignment explanation
Indices: 48196--48817 Score: 818
Period size: 300 Copynumber: 2.1 Consensus size: 299
48186 TCTTCAGATG
* * * * *
48196 AGTTCTTCTCATGATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATAAATTCGAGCGAAAA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATAAATTCGAGCGAAAA
* * * *
48261 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTAGATGACGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTACATGACGAGTTCTTCTCATTATGA
* *
48326 ACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCT
131 ACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCT
* * * *
48391 CATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGC
196 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGC
**
48456 TGATCCATTGAATGATGAATTCAAGAAAAAAGTTGAACA
261 TGATCCATCAAATGATGAATTCAAGAAAAAAGTTGAACA
** *
48495 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATAAATTCGAGCGAAAA
* * *
48559 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTAT
66 -GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-TACATGACGAGTTCTTCTCATTAT
* * *** * * *
48623 GAATTTTTTTTTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
129 GAA-CTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCT
* ****
48688 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAA
193 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAA
* ** * *
48753 AGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACA
258 AGCTGATCCATCAAATGATGAATTCAAGAAAAAAGTTGAACA
*
48795 AATTCTTCTCATTATGAA-TTTCT
1 AGTTCTTCTCATTATGAACTTTCT
48818 TCTTCCTTCT
Statistics
Matches: 278, Mismatches: 42, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
298 4 0.01
299 113 0.41
300 161 0.58
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (299 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATAAATTCGAGCGAAAA
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTACATGACGAGTTCTTCTCATTATGA
ACTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGC
TGATCCATCAAATGATGAATTCAAGAAAAAAGTTGAACA
Found at i:48890 original size:227 final size:227
Alignment explanation
Indices: 48495--49082 Score: 1140
Period size: 227 Copynumber: 2.6 Consensus size: 227
48485 AAGTTGAACA
*
48495 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
48560 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
48625 ATTTTTTTTTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
131 ACTTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
48690 TCATTATGAATTTCTTCTTCCTTCTTCAGATG
196 TCATTATGAATTTCTTCTTCCTTCTTCAGATG
48722 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
48787 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
48852 ACTTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
131 ACTTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
48917 TCATTATGAATTTCTTCTTCCTTCTTCAGATG
196 TCATTATGAATTTCTTCTTCCTTCTTCAGATG
48949 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
*
49014 GTTGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
49079 ACTT
131 ACTT
49083 CAACTGACAC
Statistics
Matches: 357, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
227 357 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (227 bp):
AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTC
TCATTATGAATTTCTTCTTCCTTCTTCAGATG
Found at i:49112 original size:113 final size:113
Alignment explanation
Indices: 48495--49082 Score: 1104
Period size: 113 Copynumber: 5.2 Consensus size: 113
48485 AAGTTGAACA
*
48495 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
48560 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
* * *
48608 AGTTCTTCTCATTATGAATTTTTTTTTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAA
1 AGTTCTTCTCATTATGAA-CTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAA
48673 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
48722 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
48787 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
48835 AGTTCTTCTCATTATGAACTTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAA
1 AGTTCTTCTCATTATGAAC-TTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAA
48900 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
48949 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
*
49014 GTTGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
49062 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
49083 CAACTGACAC
Statistics
Matches: 463, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
113 242 0.52
114 221 0.48
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
Found at i:49599 original size:22 final size:22
Alignment explanation
Indices: 49520--49596 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
49510 GATAAAGCTT
49520 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
49542 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
49564 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
49586 TCATCTTTGAA
1 TCATCTTTGAA
49597 GAGTGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:50045 original size:54 final size:54
Alignment explanation
Indices: 49956--50121 Score: 287
Period size: 54 Copynumber: 3.1 Consensus size: 54
49946 AGAATAGCAG
*
49956 GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGAT
* * *
50010 GTTTGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGAT
*
50064 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGAT
50118 GTTC
1 GTTC
50122 TCAATCATTG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 105 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGAT
Found at i:52448 original size:91 final size:91
Alignment explanation
Indices: 52185--52452 Score: 385
Period size: 92 Copynumber: 2.9 Consensus size: 91
52175 GATCATGCAG
* * *
52185 TTCATCTTTT-AATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATT-CAATGATT-GTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
52249 AACACTTCCAGAAGATGCTATTAGCACA
64 AACACTTCCAGAAGATACTATGAGCACA
* ** * *
52277 TTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATTCAATGA-TTGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
52342 ACACTTCCAGAAGATACTATGAGCACA
65 ACACTTCCAGAAGATACTATGAGCACA
* * *
52369 TTTATCTTTTAAATTCAATGATTGATATGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TTCATCTTTTAAATTCAATGATTGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
52434 CACTTCCAGAAGATACTAT
66 CACTTCCAGAAGATACTAT
52453 TGGGTCTTCT
Statistics
Matches: 156, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
91 60 0.38
92 91 0.58
93 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (91 bp):
TTCATCTTTTAAATTCAATGATTGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATACTATGAGCACA
Found at i:54756 original size:11 final size:11
Alignment explanation
Indices: 54740--54780 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
54730 TCAATTTTCC
54740 TTTTTCTTTTT
1 TTTTTCTTTTT
*
54751 TTTTTCCTTTT
1 TTTTTCTTTTT
*
54762 TTTTCCTTTTT
1 TTTTTCTTTTT
54773 TTTTTCTT
1 TTTTTCTT
54781 CTTTCTTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:54761 original size:10 final size:10
Alignment explanation
Indices: 54734--54775 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
54724 CTTGATTCAA
54734 TTTTCCTTTT
1 TTTTCCTTTT
*
54744 TCTT--TTTT
1 TTTTCCTTTT
54752 TTTTCCTTTT
1 TTTTCCTTTT
54762 TTTTCCTTTT
1 TTTTCCTTTT
54772 TTTT
1 TTTT
54776 TTCTTCTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.25
10 21 0.75
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCCTTTT
Found at i:54771 original size:18 final size:18
Alignment explanation
Indices: 54734--54788 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
54724 CTTGATTCAA
*
54734 TTTTCCTTTTTCTTTTTT
1 TTTTCCTTTTTCTTTCTT
54752 TTTTCCTTTTT-TTTCCTT
1 TTTTCCTTTTTCTTT-CTT
*
54770 TTTT-TTTTCTTCTTTCTT
1 TTTTCCTTT-TTCTTTCTT
54788 T
1 T
54789 GCTGGATGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 6 0.19
18 23 0.72
19 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCCTTTTTCTTTCTT
Found at i:58110 original size:14 final size:14
Alignment explanation
Indices: 58072--58125 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
58062 CATAAAAATA
* *
58072 CAAATGCAAAGATG
1 CAAATGTAAATATG
58086 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
58101 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
58115 TAAATGTAAAT
1 CAAATGTAAAT
58126 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:61723 original size:3 final size:3
Alignment explanation
Indices: 61717--61791 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
61707 TATTATTTTT
61717 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TAA TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
61759 TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61792 ATAAATAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
2 8 0.12
3 55 0.83
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:64332 original size:3 final size:3
Alignment explanation
Indices: 64324--64348 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
64314 TAGATTATAG
64324 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
64349 AAAAGACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:65017 original size:80 final size:82
Alignment explanation
Indices: 64728--65066 Score: 334
Period size: 80 Copynumber: 4.1 Consensus size: 82
64718 ATGGCGTGTA
* * * * *
64728 TTTTCAACAAACGGCTTAACAGAGTAGTACTTTAGCGGCATTTTTATACAAAAACCGCAATA-GG
1 TTTTCAACAAACGCCATAACAAAGTAGTACTTTAGCGGTATTTTTATACAAACACCGCAATAGGG
* *
64792 TTTATCTATAGTGGCGTTT
66 TTCATCTATAGT-G-GATT
* ** * *
64811 TTTTCAATAAACGCCGCAACATAA-TAGTACTTTAGCGGT-GTTTTATAC-AACACTGCAATAGG
1 TTTTCAACAAACGCCATAACA-AAGTAGTACTTTAGCGGTATTTTTATACAAACACCGCAATAGG
*
64873 GTCCATCTATAGTGGTATT
65 GTTCATCTATAGTGG-ATT
* *
64892 GTTTTCAACAAACGTCATAACAGAGTA-TAACTTTAGCGG-AGTTTTTATACAAACACCGCAATA
1 -TTTTCAACAAACGCCATAACAAAGTAGT-ACTTTAGCGGTA-TTTTTATACAAACACCGCAATA
64955 GGGTTCATCTATAGT-G-TT
63 GGGTTCATCTATAGTGGATT
* * * **** *
64973 TTTTCAATAAATGCCATAATAAAGTAGTACTTTAGCGGTATTTTTATACAAATGTTGCAACAGGG
1 TTTTCAACAAACGCCATAACAAAGTAGTACTTTAGCGGTATTTTTATACAAACACCGCAATAGGG
*
65038 TTCATCTATAGTGACATT
66 TTCATCTATAGTG-GATT
65056 TTTTCAACAAA
1 TTTTCAACAAA
65067 TGTGCAACAT
Statistics
Matches: 210, Mismatches: 32, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
80 64 0.30
81 19 0.09
82 49 0.23
83 52 0.25
84 26 0.12
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (82 bp):
TTTTCAACAAACGCCATAACAAAGTAGTACTTTAGCGGTATTTTTATACAAACACCGCAATAGGG
TTCATCTATAGTGGATT
Found at i:66232 original size:31 final size:31
Alignment explanation
Indices: 66191--66250 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
66181 TTTATCTATA
* *
66191 TAAAATTTTCTATTAAGGTCTTTTTCATTAT
1 TAAAATTTTCTATTAAAGTATTTTTCATTAT
*
66222 TAAAGTTTTCTATTAAAGTATTTTTCATT
1 TAAAATTTTCTATTAAAGTATTTTTCATT
66251 TTTTCTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (31 bp):
TAAAATTTTCTATTAAAGTATTTTTCATTAT
Found at i:69703 original size:23 final size:23
Alignment explanation
Indices: 69669--69729 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
69659 ACATCTTATA
*
69669 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
69692 CT-GCACTTCGGTGCAATTCTATG
1 -TGGCACTTCGGTGCAATTCTACG
69715 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
69730 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Done.