Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004198.1 Hibiscus syriacus cultivar Beakdansim tig00009181_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: 71792
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1831 original size:34 final size:34
Alignment explanation
Indices: 1793--1871 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
1783 TGAACATATA
* * * *
1793 TAAACGAATATGTTCGCGAACGTTATACGAACAC
1 TAAACGAACATGTTCACGAACGTTAAACAAACAC
* *
1827 TAAACGAACATGTTCATGAATGTTAAACAAACAC
1 TAAACGAACATGTTCACGAACGTTAAACAAACAC
1861 TAAACGAACAT
1 TAAACGAACAT
1872 TAAACGAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (34 bp):
TAAACGAACATGTTCACGAACGTTAAACAAACAC
Found at i:1870 original size:11 final size:11
Alignment explanation
Indices: 1850--1892 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1840 TCATGAATGT
*
1850 TAAACAAACAC
1 TAAACGAACAC
*
1861 TAAACGAACAT
1 TAAACGAACAC
**
1872 TAAACGAATGC
1 TAAACGAACAC
1883 TAAACGAACA
1 TAAACGAACA
1893 TGTTAGTGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:2455 original size:36 final size:36
Alignment explanation
Indices: 2402--2483 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
2392 TATATCCCTA
* *
2402 AAATCAATCTTAGCCTTCACAGAAGAGTAGTGAAGC
1 AAATCAATCTTAACCTTCACAGAAGAATAGTGAAGC
*
2438 AAATCAAT-TTAAACCTTCACGGAAGAATAGTGAAGC
1 AAATCAATCTT-AACCTTCACAGAAGAATAGTGAAGC
2474 AAATCAATCT
1 AAATCAATCT
2484 CAAGTCTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 2 0.05
36 38 0.93
37 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (36 bp):
AAATCAATCTTAACCTTCACAGAAGAATAGTGAAGC
Found at i:2615 original size:47 final size:47
Alignment explanation
Indices: 2546--3073 Score: 360
Period size: 47 Copynumber: 10.6 Consensus size: 47
2536 TCTCGAGTCT
*
2546 TATCTCCCTAAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * * *
2593 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C----ACTTA--GA-TCA
* * * *
2648 TATCTCCCTAAAAGAAGAGTGGAGAAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * * *
2695 TATCTCCCTGAAAGAATAGTGGACCAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * * * * *
2742 TATCTCCCTGAAAGAAGAGTGGAGCATATCCTTTTTACAAAGATTTATCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C----ACTTA--GA-TCA
* * * *
2797 TATCTCCCTGAAAGAAGAGTAGAGAAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* *
2844 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGAT-A
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * * * * *
2890 GTATCTCCCTTAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCT
1 -TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C----A-CT-TAGA-TCA
* * * * * *
2946 TATCTCACTGGAAGAAGAGTGGAGCATATCCGTTTTACAAAGATTTCTTA-AGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C----A---CTTAGA-TCA
* * *
3001 TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTTTTCCCTT-GAATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAG-ATCA
3048 TATCTCCCTGAAAGAAGAGTGGAGCA
1 TATCTCCCTGAAAGAAGAGTGGAGCA
3074 TATCCATTTT
Statistics
Matches: 391, Mismatches: 60, Indels: 60
0.77 0.12 0.12
Matches are distributed among these distances:
46 1 0.00
47 216 0.55
48 8 0.02
50 4 0.01
52 6 0.02
53 1 0.00
54 10 0.03
55 142 0.36
56 1 0.00
57 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (47 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
Found at i:2667 original size:102 final size:101
Alignment explanation
Indices: 2491--2971 Score: 434
Period size: 102 Copynumber: 4.8 Consensus size: 101
2481 TCTCAAGTCT
* * * *
2491 TATCTCCCTAAAAGAAGAGTGGAGAATATTCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTT-TCGAGTCTTATCTCCCTG
2556 AAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
65 AAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* *
2593 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTT-TCGAGTCTTATCTCCCTG
* * *
2658 AAAGAAGAGTGGAGAAGATTCGTCTTCCCTTGGATCA
65 AAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * * ** * *
2695 TATCTCCCTGAAAGAATAGTGGACCAGATTCGTCTT-C-----CCTTGGA-TCATATCTCCCTGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTTTCGAGTCTTATCTCCCTGA
* * * * * *
2753 AAGAAGAGTGGAGCATATCCTTTTTACAAAGATTTATCGAGTCT
66 AAGAAGAGTGGAGCAGATTCGTCTT-C----ACTTA--GA-TCA
* * * ** * *
2797 TATCTCCCTGAAAGAAGAGTAGAGAAGATTCGTCTT-C-----CCTTGGA-TCATATCTCCCTGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTTTCGAGTCTTATCTCCCTGA
* *
2855 AAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGAT-A
66 AAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
* * *
2890 GTATCTCCCTTAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCACT
1 -TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTT-TCGAGTCTTATCTCCCT
*
2955 GGAAGAAGAGTGGAGCA
64 GAAAGAAGAGTGGAGCA
2972 TATCCGTTTT
Statistics
Matches: 313, Mismatches: 49, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
94 64 0.20
95 7 0.02
96 1 0.00
97 2 0.01
99 2 0.01
100 1 0.00
101 7 0.02
102 229 0.73
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (101 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTTTTACAAAGATTTTCGAGTCTTATCTCCCTGA
AAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCA
Found at i:2764 original size:149 final size:149
Alignment explanation
Indices: 2546--3182 Score: 857
Period size: 149 Copynumber: 4.2 Consensus size: 149
2536 TCTCGAGTCT
* * *
2546 TATCTCCCTAAAAGAAGAGTGGAGCAGATTCGTCTTCACTTAGATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
2611 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGAAGA
66 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGAAGA
2676 TTCGTCTTCCCTTGGATCA
131 TTCGTCTTCCCTTGGATCA
* *
2695 TATCTCCCTGAAAGAATAGTGGACCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
* * * *
2760 GTGGAGCATATCCTTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTAGAGAAGA
66 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGAAGA
2825 TTCGTCTTCCCTTGGATCA
131 TTCGTCTTCCCTTGGATCA
*
2844 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGAT-AGTATCTCCCTTAAAGAAG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA-TATCTCCCTGAAAGAAG
* * ** * *
2908 AGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCACTGGAAGAAGAGTGGAGCAT
65 AGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGAAG
* * * * *
2973 ATCCGTTTTACAAAGATTTCTT-AAGTCT
130 ATTCGTCTT-C-------CCTTGGA-TCA
* * *
3001 TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTTTTCCCTTGAATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
* * * *
3066 GTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCTTATCTCCCTAAAAGAAGCA-TGGAGCAG
66 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAG-AGTGGAGAAG
*
3130 ATTCGTCTTCCCTTGGATCT
130 ATTCGTCTTCCCTTGGATCA
* * * *
3150 TATCTTCCTAAAAAAAGAGTGGAGCAGACTCGT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGT
3183 TTTCTAAAGA
Statistics
Matches: 431, Mismatches: 44, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
148 1 0.00
149 297 0.69
150 2 0.00
156 2 0.00
157 127 0.29
158 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (149 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGAAGA
TTCGTCTTCCCTTGGATCA
Found at i:3072 original size:102 final size:102
Alignment explanation
Indices: 2695--3243 Score: 437
Period size: 102 Copynumber: 5.4 Consensus size: 102
2685 CCTTGGATCA
* *
2695 TATCTCCCTGAAAGAATAGTGGACCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
* * **
2760 GTGGAGCATATCCTTTTTACAAAGATTTATCGAGTCT
66 GTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
*
2797 TATCTCCCTGAAAGAAGAGTAGAGA-AGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAG
1 TATCTCCCTGAAAGAAGAGTGGA-ACAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAG
* * * ** ***
2861 AGTGGAGCAGATTCGTCTT-C---CCTTGGAT-AG---
65 AGTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
** ** * * * * *
2891 TATCTCCCTTAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGAT-TT--C-TCGAGTCTTATCTC
1 TATCTCCC-T---GAA-AGAAGAGTGGAACAG-ATT-C---G-TCTTCCCTTGGA-TCATATCTC
* *
2952 ACTGGAAGAAGAGTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
54 CCTGAAAGAAGAGTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
* *
3001 TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTTTTCCCTTGAATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
* **
3066 GTGGAGCATATCCATTTTACAAAGATTTCTCGAGTCT
66 GTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
* * * * * *
3103 TATCTCCCTAAAAGAAGCA-TGGAGCAGATTCGTCTTCCCTTGGATCTTATCTTCCTAAAAAAAG
1 TATCTCCCTGAAAGAAG-AGTGGAACAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAG
*
3167 AGTGGAGCAGA-CTCGTTTT-CTAAAGATTTCTTAAGTCT
65 AGTGGAGCATATC-CGTTTTAC-AAAGATTTCTTAAGTCT
* * * * * *
3205 GATCTCCCCTGAATGAATAGTGGAGCAGACTCATCTTCC
1 TATCT-CCCTGAAAGAAGAGTGGAACAGATTCGTCTTCC
3244 AAAATTGATC
Statistics
Matches: 352, Mismatches: 64, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
94 8 0.02
95 1 0.00
97 2 0.01
98 5 0.01
99 10 0.03
100 5 0.01
101 7 0.02
102 251 0.71
103 31 0.09
104 5 0.01
105 10 0.03
106 6 0.02
107 2 0.01
109 1 0.00
110 8 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (102 bp):
TATCTCCCTGAAAGAAGAGTGGAACAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
GTGGAGCATATCCGTTTTACAAAGATTTCTTAAGTCT
Found at i:5692 original size:34 final size:34
Alignment explanation
Indices: 5654--5754 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 34
5644 TGAACATATA
* *
5654 TAAACGAATATGTTCACGAACGTTATACGAACAC
1 TAAACGAACATGTTCACGAACGTTAAACGAACAC
* * * *
5688 TAAACGAACAAGTTCATGAATGTTAAACAAACAC
1 TAAACGAACATGTTCACGAACGTTAAACGAACAC
*
5722 TAAAC-ACACATGTTTACGAACGTTAAACGAACA
1 TAAACGA-ACATGTTCACGAACGTTAAACGAACA
5755 TGTTTACGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 1 0.02
34 54 0.98
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (34 bp):
TAAACGAACATGTTCACGAACGTTAAACGAACAC
Found at i:5824 original size:23 final size:23
Alignment explanation
Indices: 5729--5818 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
5719 CACTAAACAC
*
5729 ACATGTTTACGAACGTTAAACGA
1 ACATGTTCACGAACGTTAAACGA
*
5752 ACATGTTTACGAACGTTAAACGA
1 ACATGTTCACGAACGTTAAACGA
* * *
5775 ACATATTCACTAACATATAAACGA
1 ACATGTTCACGAACGT-TAAACGA
*
5799 ACATGTTCATGAACGTTAAA
1 ACATGTTCACGAACGTTAAA
5819 TAAACAAACA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 39 0.67
24 19 0.33
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (23 bp):
ACATGTTCACGAACGTTAAACGA
Found at i:12709 original size:40 final size:40
Alignment explanation
Indices: 12650--12752 Score: 181
Period size: 40 Copynumber: 2.6 Consensus size: 40
12640 TTGACCATTC
*
12650 ATTT-TTATTATATAATAAATTTTCTGAAAATTATTTTTAA
1 ATTTATTA-TATATAATAAATTTTCTAAAAATTATTTTTAA
12690 ATTTATTATATATAATAAATTTTCTAAAAATTATTTTTAA
1 ATTTATTATATATAATAAATTTTCTAAAAATTATTTTTAA
12730 ATTTATTATATATAATAAATTTT
1 ATTTATTATATATAATAAATTTT
12753 TACGAGTCCA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 58 0.95
41 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (40 bp):
ATTTATTATATATAATAAATTTTCTAAAAATTATTTTTAA
Found at i:12710 original size:18 final size:18
Alignment explanation
Indices: 12687--12751 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
12677 AAATTATTTT
12687 TAAATTTATTATATATAA
1 TAAATTTATTATATATAA
* **
12705 TAAATTT-TCTAAAAATTATTTT
1 TAAATTTAT-T--ATA-TA-TAA
12727 TAAATTTATTATATATAA
1 TAAATTTATTATATATAA
12745 TAAATTT
1 TAAATTT
12752 TTACGAGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
17 1 0.03
18 16 0.46
19 2 0.06
20 4 0.11
21 2 0.06
22 9 0.26
23 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAATTTATTATATATAA
Found at i:13677 original size:20 final size:20
Alignment explanation
Indices: 13624--13679 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
13614 TTCGAATTCG
*
13624 AGTTGCGAATTTGAAAACTA
1 AGTTGCGAATTTGGAAACTA
*
13644 AGTTGCGAATTTGGAAACTG
1 AGTTGCGAATTTGGAAACTA
* *
13664 TGTTGCGAAATTGGAA
1 AGTTGCGAATTTGGAA
13680 TTCATGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (20 bp):
AGTTGCGAATTTGGAAACTA
Found at i:22087 original size:29 final size:29
Alignment explanation
Indices: 22050--22110 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
22040 TCTGTTTTCT
22050 CCCCTGAAATTTTATAAATTCAAGTCCGC
1 CCCCTGAAATTTTATAAATTCAAGTCCGC
*
22079 CCCCTGAAATTTTATAAATTCAAGTTCGC
1 CCCCTGAAATTTTATAAATTCAAGTCCGC
22108 CCC
1 CCC
22111 TAACTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.31
Consensus pattern (29 bp):
CCCCTGAAATTTTATAAATTCAAGTCCGC
Found at i:23601 original size:2 final size:2
Alignment explanation
Indices: 23594--23619 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23584 GATTAACTAT
23594 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23620 AACTAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24990 original size:20 final size:18
Alignment explanation
Indices: 24953--24987 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24943 ATATCATGTT
*
24953 TCTTGTTTTATATGTATG
1 TCTTATTTTATATGTATG
24971 TCTTATTTTATATGTAT
1 TCTTATTTTATATGTAT
24988 ATGTACCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (18 bp):
TCTTATTTTATATGTATG
Found at i:25639 original size:23 final size:23
Alignment explanation
Indices: 25588--25641 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
25578 GAAAAACATG
* * *
25588 TCACAAAGGCAGAGATAAACGTT
1 TCACAAAGGAAAAGATAAACGTA
* *
25611 TTACAAAGGAAAAGATAATCGTA
1 TCACAAAGGAAAAGATAAACGTA
25634 TCACAAAG
1 TCACAAAG
25642 ACATAATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (23 bp):
TCACAAAGGAAAAGATAAACGTA
Found at i:26861 original size:40 final size:40
Alignment explanation
Indices: 26806--26895 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
26796 ATAGCAATCT
26806 CCGTCCCCATTTCTCTTTGAGCTTTGGGGATAAAACCTCC
1 CCGTCCCCATTTCTCTTTGAGCTTTGGGGATAAAACCTCC
26846 CCGTCCCCATTTCTCTTTGAGCTTTGGGGATAAAACCTCC
1 CCGTCCCCATTTCTCTTTGAGCTTTGGGGATAAAACCTCC
26886 CCGTCCCCAT
1 CCGTCCCCAT
26896 CTCAAAGGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.17, C:0.36, G:0.17, T:0.31
Consensus pattern (40 bp):
CCGTCCCCATTTCTCTTTGAGCTTTGGGGATAAAACCTCC
Found at i:27651 original size:21 final size:20
Alignment explanation
Indices: 27605--27738 Score: 119
Period size: 20 Copynumber: 6.5 Consensus size: 20
27595 TTTTCCCAAT
*
27605 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
27625 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
27645 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
**
27666 TCGCAACT-CGAATTGGGAAAA
1 TCGCAA-TGCGAATAAGG-AAA
*
27687 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
**
27707 TCGCAACT-CGAATTGGGAAAA
1 TCGCAA-TGCGAATAAGG-AAA
27728 TCGCAATGCGA
1 TCGCAATGCGA
27739 TACTGACTAT
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
20 45 0.50
21 45 0.50
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:27752 original size:20 final size:20
Alignment explanation
Indices: 27727--27820 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
27717 AATTGGGAAA
*
27727 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
27747 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
27768 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
27788 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
27808 TTCGCAACGCGAT
1 ATCGCAACGCGAT
27821 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:27753 original size:41 final size:41
Alignment explanation
Indices: 27605--27738 Score: 250
Period size: 41 Copynumber: 3.3 Consensus size: 41
27595 TTTTCCCAAT
* *
27605 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAT
1 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
27646 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
27687 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
27728 TCGCAATGCGA
1 TCGCAATGCGA
27739 TACTGACTAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACTCGAATTGGGAAAA
Found at i:27801 original size:41 final size:41
Alignment explanation
Indices: 27724--27801 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
27714 TCGAATTGGG
* * **
27724 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
27765 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
27802 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:28401 original size:19 final size:19
Alignment explanation
Indices: 28377--28417 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28367 CGAGATAATA
*
28377 GCAACGCGAAATAAAAATC
1 GCAACGCGAAACAAAAATC
*
28396 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACAAAAATC
28415 GCA
1 GCA
28418 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (19 bp):
GCAACGCGAAACAAAAATC
Found at i:28435 original size:19 final size:19
Alignment explanation
Indices: 28413--28558 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
28403 GAAACCAAAA
*
28413 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28432 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28451 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
28467 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
28484 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28498 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
28517 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
28537 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
28557 TC
1 TC
28559 AACCAAAAGA
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 20 0.20
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.41
20 31 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28483 original size:33 final size:33
Alignment explanation
Indices: 28446--28533 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
28436 GTTGCGATTT
* *
28446 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
28479 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
28512 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
28534 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:28535 original size:20 final size:20
Alignment explanation
Indices: 28501--28558 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28491 GCGATTCTCT
**
28501 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
28521 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
28541 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
28559 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:30617 original size:42 final size:42
Alignment explanation
Indices: 30557--30679 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
30547 GCTCGACTCG
* * *
30557 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
30599 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
30641 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
30680 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:30637 original size:21 final size:21
Alignment explanation
Indices: 30613--30679 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30603 TCATTCCTCG
30613 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
30634 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
30655 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
30676 AGAG
1 AGAG
30680 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:31154 original size:14 final size:14
Alignment explanation
Indices: 31137--31173 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31127 ACATCATTAA
31137 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
31151 ACAAATCATCTTTT
1 ACAAATCAACATTT
31165 ACAAATCAA
1 ACAAATCAA
31174 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:31559 original size:20 final size:20
Alignment explanation
Indices: 31534--31584 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
31524 ATTCATTTGA
*
31534 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
31554 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
31574 TTATCACAACG
1 CTATCGCAACG
31585 AGAATATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:31651 original size:19 final size:19
Alignment explanation
Indices: 31610--31676 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
31600 GAAATGAAAA
31610 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
31626 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
31643 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
31661 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
31677 TCGTTGCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:31812 original size:14 final size:14
Alignment explanation
Indices: 31793--31829 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31783 CATCAATTAA
31793 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
31807 ACAAATCATCTTTT
1 ACAAATCAACATTT
31821 ACAAATCAA
1 ACAAATCAA
31830 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:33733 original size:20 final size:19
Alignment explanation
Indices: 33698--33764 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
33688 GAAACTTAAA
33698 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
33717 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
33737 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
33756 ATCGCAACG
1 ATCGCAACG
33765 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:33772 original size:14 final size:14
Alignment explanation
Indices: 33753--33810 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
33743 ATGCGAAATG
33753 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
33767 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
33783 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
33799 AAAATCGCAACG
1 AAAATCGCAACG
33811 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:33795 original size:32 final size:33
Alignment explanation
Indices: 33737--33815 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
33727 GGAAATGGCT
*
33737 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
33770 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
33802 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
33816 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:33844 original size:19 final size:19
Alignment explanation
Indices: 33822--33903 Score: 86
Period size: 18 Copynumber: 4.6 Consensus size: 19
33812 GAAACACAAA
33822 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
33841 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
33859 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
33875 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
33892 TCGCATTACGAT
1 TCGCATTGCGAT
33904 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 21 0.39
19 16 0.30
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:33910 original size:19 final size:20
Alignment explanation
Indices: 33888--33931 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
33878 TTGCGATTTT
33888 CATTT-CGCATTACGATAGC
1 CATTTCCGCATTACGATAGC
* * *
33907 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTACGATAGC
33927 CATTT
1 CATTT
33932 TTCGTGTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:34442 original size:18 final size:18
Alignment explanation
Indices: 34416--34460 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
34406 GTCGATCAGA
*
34416 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
34434 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
34452 TGATGGCTC
1 TGATGGCTC
34461 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:35804 original size:20 final size:20
Alignment explanation
Indices: 35779--35816 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35769 AATAGTTTCT
35779 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
35799 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
35817 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:36098 original size:23 final size:23
Alignment explanation
Indices: 36071--36115 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
36061 GATTTAGATA
*
36071 GACGGATTTCGCCGGAGATGGGG
1 GACGGATTTCGCCGAAGATGGGG
*
36094 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
36116 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.44, T:0.20
Consensus pattern (23 bp):
GACGGATTTCGCCGAAGATGGGG
Found at i:36328 original size:20 final size:20
Alignment explanation
Indices: 36303--36396 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
36293 GATTATGTAT
36303 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
36323 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
36343 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
36364 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
36384 TATCGCATTGCGA
1 TATCGCGTTGCGA
36397 TTTTCCCAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:36397 original size:20 final size:20
Alignment explanation
Indices: 36283--36397 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
36273 CGATTTGAAA
*
36283 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
36304 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
36324 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
36344 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
36365 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
36385 ATCGCATTGCGAT
1 ATCGCATTGCGAT
36398 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
19 2 0.03
20 51 0.66
21 24 0.31
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:36416 original size:41 final size:41
Alignment explanation
Indices: 36325--36459 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
36315 AAAGTCAGTA
* * * ** *
36325 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
*
36365 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
* * *
36407 TCGCGTTGCGAT--TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAAT
36448 TCGCGTTGCGAT
1 TCGCGTTGCGAT
36460 TTACTTATTC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 74 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
Found at i:36430 original size:20 final size:20
Alignment explanation
Indices: 36386--36478 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
36376 ATAGTCAGTA
* **
36386 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
36407 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
36427 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
36448 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
36468 TCGCATTGCGA
1 TCGCATTGCGA
36479 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:36460 original size:41 final size:41
Alignment explanation
Indices: 36386--36481 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
36376 ATAGTCAGTA
*
36386 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
36427 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
36468 TCGCATTGCGAATT
1 TCGCATTGCGAATT
36482 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:38939 original size:2 final size:2
Alignment explanation
Indices: 38932--38980 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38922 TTTGAGGTTA
38932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38974 AT AT AT A
1 AT AT AT A
38981 ATTTCGGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44713 original size:30 final size:31
Alignment explanation
Indices: 44646--44713 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
44636 CACACCTAGA
44646 CATTTGGAGATCCTTAATTAAATAAATATGC
1 CATTTGGAGATCCTTAATTAAATAAATATGC
*
44677 CA-TTGGAGATCGTTAATTAAATAAATA-GC
1 CATTTGGAGATCCTTAATTAAATAAATATGC
44706 CATTTGGA
1 CATTTGGA
44714 CCTTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 4 0.11
30 29 0.83
31 2 0.06
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
CATTTGGAGATCCTTAATTAAATAAATATGC
Found at i:47888 original size:29 final size:29
Alignment explanation
Indices: 47838--47893 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
47828 GCTTTGCACT
* * *
47838 TTTGTAGTAATTTTTGACAAAATTATTAA
1 TTTGTAGTAATTATTAAAAAAATTATTAA
*
47867 TTTGTTGTAATTATTAAAAAAATTATT
1 TTTGTAGTAATTATTAAAAAAATTATT
47894 CAACCAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (29 bp):
TTTGTAGTAATTATTAAAAAAATTATTAA
Found at i:52525 original size:23 final size:23
Alignment explanation
Indices: 52458--52543 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
52448 TCGTATAAAT
*
52458 TTGCACCGAAGTGCCACATAGAA
1 TTGCACCGAAGTGCCACGTAGAA
**
52481 TTTGTC-CCGAAG-GACCGTGTAGGAA
1 -TTG-CACCGAAGTG-CCACGTA-GAA
52506 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
52528 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
52544 TATAATATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.08
23 28 0.56
24 14 0.28
25 4 0.08
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:52834 original size:31 final size:31
Alignment explanation
Indices: 52785--52878 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
52775 TTATATCGCT
52785 TAGACATATCA-TTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
52815 TAGACATATCATTTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
52846 TAGACATATCATTTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
52877 TA
1 TA
52879 ACTTATATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 11 0.17
31 52 0.83
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (31 bp):
TAGACATATCATTTTCCATACCTTTATCACA
Found at i:54202 original size:31 final size:31
Alignment explanation
Indices: 54160--54300 Score: 169
Period size: 31 Copynumber: 4.5 Consensus size: 31
54150 AGAGTCGAGG
54160 GTTTACCTATGTTCTTCGGGATATATAGACT
1 GTTTACCTATGTTCTTCGGGATATATAGACT
* *
54191 GTTTACTTATGTTCTTCGGG-TCATATGGACT
1 GTTTACCTATGTTCTTCGGGAT-ATATAGACT
* *
54222 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATAGACT
* * * *
54253 GATTACCTATGTTCTTAGAGATATATAAACT
1 GTTTACCTATGTTCTTCGGGATATATAGACT
*
54284 -TATTACCTAGGTTCTTC
1 GT-TTACCTATGTTCTTC
54301 AGAGTCTATG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.01
31 93 0.99
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATATATAGACT
Found at i:55024 original size:21 final size:21
Alignment explanation
Indices: 54998--55041 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
54988 TGCCGAAATT
*
54998 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
55019 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
55040 AC
1 AC
55042 AATTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:58022 original size:44 final size:42
Alignment explanation
Indices: 57959--58048 Score: 103
Period size: 45 Copynumber: 2.1 Consensus size: 42
57949 ATCGGTACAC
57959 ATGCAATATGTACCGATGCA-CTCTTAA-ATAAATAAACATCGA
1 ATGCAATATGTACCGATGCACCTCTTAAGAT-AA-AAACATCGA
* *
58001 ATGCAATGAGTGTATCGATGCACCCTCTTAAGATGAAAACATCGA
1 ATGCAAT-A-TGTACCGATGCA-CCTCTTAAGATAAAAACATCGA
58046 ATG
1 ATG
58049 TAATTTGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
42 7 0.17
43 1 0.02
44 11 0.27
45 12 0.29
46 8 0.20
47 2 0.05
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCAATATGTACCGATGCACCTCTTAAGATAAAAACATCGA
Found at i:67980 original size:64 final size:65
Alignment explanation
Indices: 67867--68001 Score: 175
Period size: 64 Copynumber: 2.1 Consensus size: 65
67857 CACTAATTAT
* * *
67867 ATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTTTGTGCATCGGTACACAAAATGC
1 ATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGATATATGCATCGGTACACAAAATGC
** * **
67932 ATTCGATGTTTCAATAA-A-CCCTGAGTGCATTGATGCATGATATATGCATCGGTACACTTAATG
1 ATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGATATATGCATCGGTACACAAAATG
67995 C
65 C
67996 ATTCGA
1 ATTCGA
68002 AATAGGGTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 44 0.72
65 15 0.25
66 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (65 bp):
ATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGATATATGCATCGGTACACAAAATGC
Found at i:68761 original size:31 final size:31
Alignment explanation
Indices: 68703--68856 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
68693 AGAGTCGAGG
68703 GTTTACCTATGTTCTTCGGG--ATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
68732 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
68763 GTTTACCTATGTTCTTCGGGACATATGGACC
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
68794 GATTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
68825 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
68856 G
1 G
68857 GTCCTTCGAG
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
29 20 0.17
31 94 0.82
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:69563 original size:21 final size:21
Alignment explanation
Indices: 69537--69581 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
69527 TGCCGAAATT
* *
69537 ACTGTAGTAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGATAC
69558 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
69579 ACT
1 ACT
69582 ATTCATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Done.