Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004414.1 Hibiscus syriacus cultivar Beakdansim tig00009679_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: 56552
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:130 original size:18 final size:18
Alignment explanation
Indices: 107--154 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
97 TCGGTCGATT
107 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
125 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
143 AGGTGATGGCTC
1 AGGTGATGGCTC
155 CCGAAGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1497 original size:20 final size:20
Alignment explanation
Indices: 1449--1507 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1439 AATAGTTTCT
** *
1449 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1469 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1489 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1508 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1783 original size:20 final size:21
Alignment explanation
Indices: 1758--1805 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1748 GCTCTGAGAT
1758 GGAGAT-AGACGAATTTCGTC
1 GGAGATGAGACGAATTTCGTC
* *
1778 GGAGATGGGACGGATTTCGTC
1 GGAGATGAGACGAATTTCGTC
1799 GGAGATG
1 GGAGATG
1806 GGTGAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.25, C:0.12, G:0.40, T:0.23
Consensus pattern (21 bp):
GGAGATGAGACGAATTTCGTC
Found at i:1794 original size:21 final size:21
Alignment explanation
Indices: 1765--1807 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1755 GATGGAGATA
1765 GACGAATTTCGTCGGAGATGG
1 GACGAATTTCGTCGGAGATGG
*
1786 GACGGATTTCGTCGGAGATGG
1 GACGAATTTCGTCGGAGATGG
1807 G
1 G
1808 TGAAAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (21 bp):
GACGAATTTCGTCGGAGATGG
Found at i:2092 original size:41 final size:41
Alignment explanation
Indices: 1973--2110 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
1963 CGCTTTGAAA
* * *
1973 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * * *
2014 ATTGCGTTGCAAAATT-AAGTATCGAGTTACGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
2054 ATCGTGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
2095 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
2111 CCAATTCGCA
Statistics
Matches: 74, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 30 0.41
41 44 0.59
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2107 original size:20 final size:20
Alignment explanation
Indices: 1993--2106 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
1983 GATTATGTAT
*
1993 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
2013 TATTGCGTTGCAAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
* *
2033 TATCGAGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
2053 TATCGTGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2074 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2094 TATCGCGTTGCGA
1 TATCGCGTTGCGA
2107 TTTTCCAATT
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
19 3 0.04
20 54 0.75
21 13 0.18
22 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2139 original size:21 final size:20
Alignment explanation
Indices: 2096--2167 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
2086 ATAGTCAGTA
*
2096 TCGCGTTGCGATTTTCCAAT
1 TCGCATTGCGATTTTCCAAT
2116 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCC-AAT
* **
2137 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAT
2157 TCGCATTGCGA
1 TCGCATTGCGA
2168 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCAAT
Found at i:2182 original size:41 final size:41
Alignment explanation
Indices: 2095--2182 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
2085 GATAGTCAGT
* * * *
2095 ATCGCGTTGCGATTTTCCAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTACCAATTCGCATTGCGAATTGCCAAA
* ** **
2136 TTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTACCAATTCGCATTGCGAATTGCCAAA
2177 ATCGCA
1 ATCGCA
2183 ACGCGAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTACCAATTCGCATTGCGAATTGCCAAA
Found at i:2209 original size:21 final size:22
Alignment explanation
Indices: 2157--2209 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2147 ATTTACTTAT
2157 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2178 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2199 TCGCATTGCGA
1 TCGCATTGCGA
2210 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2734 original size:22 final size:21
Alignment explanation
Indices: 2700--2740 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2690 ATAATTATTT
2700 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
2721 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
2741 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:3227 original size:15 final size:16
Alignment explanation
Indices: 3193--3227 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3183 GCTTCTAAAT
*
3193 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
3209 TTTTTCGAGTTCAAG-
1 TTTTTCGAGTTCAAGC
3224 TTTT
1 TTTT
3228 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:4730 original size:180 final size:180
Alignment explanation
Indices: 4454--4875 Score: 631
Period size: 180 Copynumber: 2.4 Consensus size: 180
4444 TCGAGATCGA
* * *
4454 TTTGTCATATTTTTACATGTTATA---TCATGGATCGATACATTTTTATAAAGTATCGATA-TTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
4515 ATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAGTATCGACA
66 ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAGTATCGACA
* * * * * *
4580 CTTTCAACATATCTGGTAGCTCTTTA-CTGGTTTTGT-TTTTTGAGACCGGT
131 CTATCAACATATCTGGTAGCGCTTTACCT-GTTTTATATTTAT-AAACCGAT
*
4630 TTTGTCATATATTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
4695 ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAGTATCGACA
66 ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAGTATCGACA
4760 CTATCAACATATCTGGTAGCGCTTTACCTGTTTTATCATTTATAAACCGAT
131 CTATCAACATATCTGGTAGCGCTTTACCTGTTTTAT-ATTTATAAACCGAT
* * * *
4811 TGTGTCATTTTTTTACCTGTTATATTGTTATGAATCGATACATTTTTATAAAGTATCAACACTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
4876 CAATATATCC
Statistics
Matches: 222, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
176 22 0.10
179 32 0.14
180 96 0.43
181 68 0.31
182 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (180 bp):
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
ATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAGTATCGACA
CTATCAACATATCTGGTAGCGCTTTACCTGTTTTATATTTATAAACCGAT
Found at i:4977 original size:112 final size:112
Alignment explanation
Indices: 4749--5199 Score: 645
Period size: 112 Copynumber: 4.1 Consensus size: 112
4739 TACTTATAAT
* * * * * * *
4749 AAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTATCATTTATAAACCGATTGT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
* * *
4814 GTCATTTTTTTACCTGTTATATTGTTATGAATCGATACATTTTTATA
66 GTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
* *
4861 AAGTATCAACACTTTCAATATATCCGGTAGTGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
4926 GTCATTTTTTTTACATGTTATATTGTTATGGATCAATACATTTTTAT-
66 GTCA-TTTTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
*
4973 AAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
*
5038 GTCA-TTTTTTACATG-T-TATTGTTATGGATC----GATTTTTATA
66 GTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
* * *
5078 AAGTATCGACACTTTC-ATATATCCGGCAGCGGTTTACCTGTTTTGTCATTTATAGATCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
*
5142 GTCA-TTTTTTATC-TGTTATATTGTTATGGATCAATATATTTTTATA
66 GTCATTTTTTTA-CATGTTATATTGTTATGGATCAATACATTTTTATA
5188 AAGTATCGACAC
1 AAGTATCGACAC
5200 AAACCGACAA
Statistics
Matches: 309, Mismatches: 21, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
104 65 0.21
105 18 0.06
106 14 0.05
108 14 0.05
109 1 0.00
110 32 0.10
112 126 0.41
113 39 0.13
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.45
Consensus pattern (112 bp):
AAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTT
GTCATTTTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
Found at i:5744 original size:60 final size:60
Alignment explanation
Indices: 5675--5787 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
5665 CTATGACCCT
* * *
5675 CATTTTAAATTGGTCCCTAAACTTTTAAATATTATAATTTCAT-CCTCAAACTACAAATCC
1 CATTCTAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCCT-AAACTACAAATCC
* *
5735 CATTCTAAATTAGTCCTTAAACTTTTGAACATTATAATTTCATCCCTAAACTA
1 CATTCTAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCCTAAACTA
5788 TGACTATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (60 bp):
CATTCTAAATTAGTCCCTAAACTTTTAAACATTATAATTTCATCCCTAAACTACAAATCC
Found at i:5827 original size:29 final size:28
Alignment explanation
Indices: 5753--5841 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
5743 ATTAGTCCTT
* * * *
5753 AAACTTTTGAACATTATAATTTCATCCCT
1 AAACTTTTGAATATTCTAA-TTAATCCCC
* * *
5782 AAAC-TATGACTATTTCTAAGTTGATCCCC
1 AAACTTTTGAATA-TTCTAA-TTAATCCCC
5811 AAACTTTTGAATATTCTAATTAATCCCC
1 AAACTTTTGAATATTCTAATTAATCCCC
5839 AAA
1 AAA
5842 TTCATCCAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
28 16 0.33
29 26 0.54
30 6 0.12
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (28 bp):
AAACTTTTGAATATTCTAATTAATCCCC
Found at i:6343 original size:2 final size:2
Alignment explanation
Indices: 6336--6382 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
6326 TTCATTTGTG
* *
6336 TA TA TA TA TA TA TC TA TA -A TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6377 TA TA TA
1 TA TA TA
6383 CAATAATCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11268 original size:14 final size:14
Alignment explanation
Indices: 11251--11283 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11241 ATTTCTATGT
*
11251 AGGGAATTATTTGC
1 AGGGAATTATTTAC
11265 AGGGAATTATTTAC
1 AGGGAATTATTTAC
11279 AGGGA
1 AGGGA
11284 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:15877 original size:17 final size:17
Alignment explanation
Indices: 15846--15915 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
15836 AAATTGAAAA
15846 AATATATAA-TATATAT
1 AATATATAATTATATAT
*
15862 AATATAAAATTATATAT
1 AATATATAATTATATAT
*
15879 AA-ACTATATTTATATTAT
1 AATA-TATAATTATA-TAT
15897 AAATATATAATTAT-TAT
1 -AATATATAATTATATAT
15914 AA
1 AA
15916 ACTATATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
16 11 0.24
17 20 0.44
18 3 0.07
19 10 0.22
20 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATATAATTATATAT
Found at i:15916 original size:17 final size:17
Alignment explanation
Indices: 15845--15933 Score: 76
Period size: 19 Copynumber: 5.1 Consensus size: 17
15835 AAAATTGAAA
15845 AAATATATAA-TA-TAT
1 AAATATATAATTATTAT
*
15860 ATAATATAAAATTATATAT
1 A-AATATATAATTAT-TAT
*
15879 AAACTATAT-TTATATTAT
1 AAA-TATATAAT-TATTAT
15897 AAATATATAATTATTAT
1 AAATATATAATTATTAT
*
15914 AAACTATATATATAATTAT
1 AAA-TATATA-ATTATTAT
15933 A
1 A
15934 TTTATGTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.02
16 8 0.13
17 16 0.27
18 16 0.27
19 19 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATAATTATTAT
Found at i:15950 original size:47 final size:44
Alignment explanation
Indices: 15850--15952 Score: 113
Period size: 47 Copynumber: 2.3 Consensus size: 44
15840 TGAAAAAATA
* *
15850 TATAATATATATAATATAAAATTATATATAAACTATATTTATAT
1 TATAATATATATAATATAAAACTATATATAAACTATATTTATAG
*
15894 TATAA-ATATATAATTATTATAAACTATATATATAATTATATTTAT-G
1 TATAATATATATAA-TA-TA-AAACTATATATA-AACTATATTTATAG
15940 TA-AACTATATATA
1 TATAA-TATATATA
15953 TAAACTATGT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
43 8 0.16
44 7 0.14
45 4 0.08
46 13 0.26
47 18 0.36
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (44 bp):
TATAATATATATAATATAAAACTATATATAAACTATATTTATAG
Found at i:15958 original size:13 final size:13
Alignment explanation
Indices: 15847--16069 Score: 126
Period size: 13 Copynumber: 17.1 Consensus size: 13
15837 AATTGAAAAA
15847 ATATATAATA-TAT
1 ATATATAA-ACTAT
*
15860 ATAATATAAAAT-T
1 AT-ATATAAACTAT
15873 ATATATAAACTAT
1 ATATATAAACTAT
* *
15886 AT-T-TATATTAT
1 ATATATAAACTAT
*
15897 AAATATATAA-T-T
1 ATATATA-AACTAT
15909 AT-TATAAACTAT
1 ATATATAAACTAT
15921 ATATATAATTA-TAT
1 ATATATAA--ACTAT
* *
15935 TTATGTAAACTAT
1 ATATATAAACTAT
15948 ATATATAAACTAT
1 ATATATAAACTAT
* *
15961 GTATATAAAATTAT
1 ATATAT-AAACTAT
*
15975 AAACTATATAA-T-T
1 ATA-TATA-AACTAT
*
15988 AT-TATAAGCTAT
1 ATATATAAACTAT
*
16000 ATATATAAATTATGT
1 ATATATAAACTA--T
* * *
16015 TTATGTGAACTAT
1 ATATATAAACTAT
16028 ATATATAAACTAT
1 ATATATAAACTAT
*
16041 GTATATAAACTAT
1 ATATATAAACTAT
16054 ATATGTATAAACTAT
1 ATA--TATAAACTAT
16069 A
1 A
16070 AAAAGTACAT
Statistics
Matches: 161, Mismatches: 27, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.02
11 17 0.11
12 19 0.12
13 70 0.43
14 26 0.16
15 26 0.16
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:16041 original size:80 final size:78
Alignment explanation
Indices: 15847--16049 Score: 272
Period size: 80 Copynumber: 2.6 Consensus size: 78
15837 AATTGAAAAA
* * * * *
15847 ATATATAA-TATATATAATATAAAAT-TATATATAAACTA--TAT-TTATATTATAAATATATAA
1 ATATATAATTATAT-TTATGTAAACTATATATATAAACTATGTATATAAAATTATAAATATATAA
15907 TTATTATAAACTAT
65 TTATTATAAACTAT
15921 ATATATAATTATATTTATGTAAACTATATATATAAACTATGTATATAAAATTATAAACTATATAA
1 ATATATAATTATATTTATGTAAACTATATATATAAACTATGTATATAAAATTATAAA-TATATAA
*
15986 TTATTATAAGCTAT
65 TTATTATAAACTAT
* *
16000 ATATATAAATTATGTTTATGTGAACTATATATATAAACTATGTATATAAA
1 ATATAT-AATTATATTTATGTAAACTATATATATAAACTATGTATATAAA
16050 CTATATATGT
Statistics
Matches: 114, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
74 16 0.14
75 18 0.16
77 3 0.03
78 10 0.09
79 26 0.23
80 41 0.36
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (78 bp):
ATATATAATTATATTTATGTAAACTATATATATAAACTATGTATATAAAATTATAAATATATAAT
TATTATAAACTAT
Found at i:16204 original size:75 final size:76
Alignment explanation
Indices: 16042--16190 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 76
16032 ATAAACTATG
* *
16042 TATATAAACTATATATGTATAAACTATAAAAAGTACATAGTTTATAAAATATTATTTATATTAAT
1 TATATAAACTATATATGTATAAACTATAAAAAGTA-ATAGTTTATAAAATATAATTTATAATAAT
16107 ATAGTATATGTA
65 ATAGTATATGTA
***
16119 TATATAAACTATATATGTATAAACTATATAAAA-T-ATAGTTTATATGTTATAATTTATAATAAT
1 TATATAAACTATATATGTATAAACTATA-AAAAGTAATAGTTTATAAAATATAATTTATAATAAT
*
16182 ATATTATAT
65 ATAGTATAT
16191 ACGATGTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 32 0.49
77 29 0.45
78 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (76 bp):
TATATAAACTATATATGTATAAACTATAAAAAGTAATAGTTTATAAAATATAATTTATAATAATA
TAGTATATGTA
Found at i:16524 original size:2 final size:2
Alignment explanation
Indices: 16517--16593 Score: 133
Period size: 2 Copynumber: 40.0 Consensus size: 2
16507 TATAACTATG
16517 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16557 TA T- TA TA TA TA 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 TA TA TA TA TA TA
16594 ATTATACAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16719 original size:20 final size:21
Alignment explanation
Indices: 16694--16734 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
16684 AACTTCAAAT
16694 CCTAAAATATAAA-CCTAAAC
1 CCTAAAATATAAACCCTAAAC
*
16714 CCTAAAATTTAAACCCTAAAC
1 CCTAAAATATAAACCCTAAAC
16735 ATATGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
CCTAAAATATAAACCCTAAAC
Found at i:16805 original size:14 final size:14
Alignment explanation
Indices: 16786--16818 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
16776 TAAAAGGGAT
16786 ATTTATGGTTTAGG
1 ATTTATGGTTTAGG
16800 ATTTATGGTTTAGG
1 ATTTATGGTTTAGG
16814 ATTTA
1 ATTTA
16819 AGAATCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
ATTTATGGTTTAGG
Found at i:16890 original size:12 final size:12
Alignment explanation
Indices: 16869--16916 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
16859 TAAGGTTTGA
*
16869 TTTATGATTTAGG
1 TTTAT-ATTTATG
* *
16882 TGTATATTTATA
1 TTTATATTTATG
16894 TTTATATTTATG
1 TTTATATTTATG
16906 TTTATATTTAT
1 TTTATATTTAT
16917 ATAAACTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 26 0.87
13 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:16895 original size:6 final size:6
Alignment explanation
Indices: 16884--16918 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16874 GATTTAGGTG
*
16884 TATATT TATATT TATATT TATGTT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
16919 AAACTGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:17010 original size:20 final size:19
Alignment explanation
Indices: 16987--17297 Score: 115
Period size: 20 Copynumber: 15.7 Consensus size: 19
16977 AGTTTATATT
16987 TATATACTATATATATGAAC
1 TATATA-TATATATATGAAC
* *
17007 TATAGAT-TATATATAAAC
1 TATATATATATATATGAAC
*
17025 TATATAGTTTATATACT-AAC
1 TATATA-TATATATA-TGAAC
* *
17045 TATAGT-T-TACATATAAAC
1 TATA-TATATATATATGAAC
* *
17063 TATAGTATTTACATATGAA-
1 TATA-TATATATATATGAAC
* *
17082 T-TATAGTTTACATATGAAC
1 TATATA-TATATATATGAAC
* *
17101 TATATATAAACTATATAGTTAC
1 TATATATATA-TATAT-G-AAC
*
17123 -ATATGACCTATATATATAAAC
1 TATAT-A--TATATATATGAAC
* * *
17144 TATATAGTTTACATATGACC
1 TATATA-TATATATATGAAC
17164 TATATATATATATAT-ATAC
1 TATATATATATATATGA-AC
*
17183 TATAGT-TGATATTTAT-ATAC
1 TATA-TAT-ATATATATGA-AC
* * * *
17203 TATATGGTTTACATATGACC
1 TATAT-ATATATATATGAAC
*
17223 TATATATATATACTAT-AGTC
1 TATATATATATA-TATGA-AC
*
17243 TATATTTATATACTAT-ATAC
1 TATATATATATA-TATGA-AC
*
17263 TATATATTATATATATAAAC
1 TATATA-TATATATATGAAC
17283 TATATATACTATATA
1 TATATATA-TATATA
17298 GTTTAGTTTA
Statistics
Matches: 230, Mismatches: 33, Indels: 56
0.72 0.10 0.18
Matches are distributed among these distances:
17 3 0.01
18 44 0.19
19 29 0.13
20 120 0.52
21 19 0.08
22 7 0.03
23 5 0.02
24 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (19 bp):
TATATATATATATATGAAC
Found at i:17017 original size:18 final size:18
Alignment explanation
Indices: 16999--17104 Score: 106
Period size: 18 Copynumber: 5.7 Consensus size: 18
16989 TATACTATAT
* *
16999 ATATGAACTATAGATTAT
1 ATATGAACTATAGTTTAC
* *
17017 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
17037 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
17055 ATATAAACTATAGTATTTAC
1 ATATGAACTATAG--TTTAC
*
17075 ATATGAATTATAGTTTAC
1 ATATGAACTATAGTTTAC
17093 ATATGAACTATA
1 ATATGAACTATA
17105 TATAAACTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.01
18 43 0.57
20 31 0.41
21 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:17021 original size:44 final size:44
Alignment explanation
Indices: 16930--17022 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
16920 AACTGCATAC
**
16930 TATAATTTATATCTATATACTATATTATATACTATTTATATAAA
1 TATAATTTATATCTATATACTATATTATATACTATAGATATAAA
* * *
16974 TATAGTTTATATTTATATACTATA-TATATGAACTATAGAT-TATA
1 TATAATTTATATCTATATACTATATTATAT--ACTATAGATATAAA
17018 TATAA
1 TATAA
17023 ACTATATAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
43 5 0.12
44 29 0.71
45 7 0.17
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (44 bp):
TATAATTTATATCTATATACTATATTATATACTATAGATATAAA
Found at i:17171 original size:2 final size:2
Alignment explanation
Indices: 17164--17297 Score: 65
Period size: 2 Copynumber: 62.0 Consensus size: 2
17154 ACATATGACC
*
17164 TA TA TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA
* * * ** * *
17207 TGG TT TA CA TA TGA CC TA TA TA TA TA TA CTA TA GTC TA TA TT TA
1 T-A TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
*
17251 TA TA CTA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
17294 TA TA
1 TA TA
17298 GTTTAGTTTA
Statistics
Matches: 101, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
1 2 0.02
2 81 0.80
3 18 0.18
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:17224 original size:59 final size:58
Alignment explanation
Indices: 16987--17297 Score: 221
Period size: 59 Copynumber: 5.2 Consensus size: 58
16977 AGTTTATATT
* * *
16987 TATATACTATATATAT-GAACTATAGATTATATATA-A-ACTATATAGTTTATATACT-AAC
1 TATATA-TATATATATAGTACTAT--ATTATATATATATACTATATAGTTTACATA-TGACC
* * * * * * *
17045 TATAGT-T-TACATATA-AACTATAGTATTTACATATGAAT-TATAGTTTACATATGAAC
1 TATA-TATATATATATAGTACTATATTATATATATAT-ACTATATAGTTTACATATGACC
* * *
17101 TATATATAAACTATATAGTTACATATGACCTATATATATAAACTATATAGTTTACATATGACC
1 TATATATATA-TATATAG-TAC-TAT-A-TTATATATATATACTATATAGTTTACATATGACC
* *
17164 TATATATATATATATA-TACTATAGTTGATATTTATATACTATATGGTTTACATATGACC
1 TATATATATATATATAGTACTATA-TT-ATATATATATACTATATAGTTTACATATGACC
* * *
17223 TATATATATATACTATAGT-CTATATTTATATACTATATACTATATA-TTATATATATAAAC
1 TATATATATATA-TATAGTACTATA-TTATATA-TATATACTATATAGTT-TACATATGACC
17283 TATATATACTATATA
1 TATATATA-TATATA
17298 GTTTAGTTTA
Statistics
Matches: 205, Mismatches: 27, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
54 7 0.03
55 3 0.01
56 32 0.16
57 4 0.02
58 11 0.05
59 51 0.25
60 46 0.22
61 8 0.04
62 9 0.04
63 34 0.17
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (58 bp):
TATATATATATATATAGTACTATATTATATATATATACTATATAGTTTACATATGACC
Found at i:17295 original size:27 final size:28
Alignment explanation
Indices: 17227--17296 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
17217 ATGACCTATA
* *
17227 TATATATACTATAGTCTATATTTATATAC
1 TATATATACTATA-TCTATATATATAAAC
17256 TATATACTA-TATAT-TATATATATAAAC
1 TATATA-TACTATATCTATATATATAAAC
17283 TATATATACTATAT
1 TATATATACTATAT
17297 AGTTTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 2 0.05
27 22 0.59
28 1 0.03
29 10 0.27
30 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (28 bp):
TATATATACTATATCTATATATATAAAC
Found at i:17540 original size:13 final size:12
Alignment explanation
Indices: 17512--17552 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
17502 ATTTAAACAG
*
17512 AACCCAAACCCA
1 AACCTAAACCCA
17524 AACCTAAACCTCA
1 AACCTAAACC-CA
17537 AACCTTAAACCCA
1 AACC-TAAACCCA
17550 AAC
1 AAC
17553 TTTAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 11 0.42
14 6 0.23
ACGTcount: A:0.49, C:0.41, G:0.00, T:0.10
Consensus pattern (12 bp):
AACCTAAACCCA
Found at i:17557 original size:13 final size:12
Alignment explanation
Indices: 17517--17559 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
17507 AACAGAACCC
*
17517 AAACCCAAACCT
1 AAACCCAAACTT
17529 AAACCTCAAACCTT
1 AAACC-CAAA-CTT
17543 AAACCCAAACTTT
1 AAACCCAAAC-TT
17556 AAAC
1 AAAC
17560 TCTAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.22
13 14 0.52
14 7 0.26
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (12 bp):
AAACCCAAACTT
Found at i:20215 original size:10 final size:10
Alignment explanation
Indices: 20200--20291 Score: 62
Period size: 10 Copynumber: 8.8 Consensus size: 10
20190 CTTCTATTGC
*
20200 TGCTTGTTGT
1 TGCTTGCTGT
20210 TGCTTGCTGT
1 TGCTTGCTGT
* *
20220 TGCCTGTTGT
1 TGCTTGCTGT
20230 TGCTTGCTGTT
1 TGCTTGCTG-T
*
20241 TCCTGTTGCCTGT
1 TGC--TTG-CTGT
*
20254 TGCTTGCTGC
1 TGCTTGCTGT
*
20264 TGCTTGTTGTT
1 TGCTTGCTG-T
20275 TG-TTGCCTGT
1 TGCTTG-CTGT
20285 TG-TTGCT
1 TGCTTGCT
20292 TTGTATTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 2 0.03
10 44 0.68
11 10 0.15
13 6 0.09
14 3 0.05
ACGTcount: A:0.00, C:0.20, G:0.28, T:0.52
Consensus pattern (10 bp):
TGCTTGCTGT
Found at i:20229 original size:20 final size:20
Alignment explanation
Indices: 20204--20292 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
20194 TATTGCTGCT
20204 TGTTGTTGCTTGCTGTTGCC
1 TGTTGTTGCTTGCTGTTGCC
*
20224 TGTTGTTGCTTGCTGTTTCC
1 TGTTGTTGCTTGCTGTTGCC
* *
20244 TGTTGCCTG-TTGCTTGCTG-C
1 TGTTG-TTGCTTGC-TGTTGCC
20264 TGCTTGTTG-TT--TGTTGCC
1 TG-TTGTTGCTTGCTGTTGCC
20282 TGTTGTTGCTT
1 TGTTGTTGCTT
20293 TGTATTTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.17
18 5 0.09
20 35 0.60
21 8 0.14
ACGTcount: A:0.00, C:0.19, G:0.28, T:0.53
Consensus pattern (20 bp):
TGTTGTTGCTTGCTGTTGCC
Found at i:20278 original size:24 final size:24
Alignment explanation
Indices: 20226--20280 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20216 CTGTTGCCTG
* *
20226 TTGTTGCTTGCTGTTTCCTGTTGC
1 TTGTTGCTTGCTGCTGCCTGTTGC
* * *
20250 CTGTTGCTTGCTGCTGCTTGTTGT
1 TTGTTGCTTGCTGCTGCCTGTTGC
20274 TTGTTGC
1 TTGTTGC
20281 CTGTTGTTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.27, T:0.53
Consensus pattern (24 bp):
TTGTTGCTTGCTGCTGCCTGTTGC
Found at i:20761 original size:23 final size:22
Alignment explanation
Indices: 20728--20779 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
20718 TTAAAATTCA
20728 TTTATTATCAAATTAATTA-TTAT
1 TTTATTATCAAA--AATTATTTAT
*
20751 TTTATTGTCAAAAATTATTTAT
1 TTTATTATCAAAAATTATTTAT
*
20773 ATTATTA
1 TTTATTA
20780 ATGTAAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATTATCAAAAATTATTTAT
Found at i:21194 original size:16 final size:16
Alignment explanation
Indices: 21134--21194 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
21124 TTTACAGGTT
*
21134 AGGTTAAAAACAAATC
1 AGGTTAAAAACAGATC
21150 AGGTTAAAAACATG-TC
1 AGGTTAAAAACA-GATC
* * *
21166 AAGTTGAAAACAGATT
1 AGGTTAAAAACAGATC
*
21182 AGGTTGAAAACAG
1 AGGTTAAAAACAG
21195 GTCGGGTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 37 0.97
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (16 bp):
AGGTTAAAAACAGATC
Found at i:31214 original size:19 final size:21
Alignment explanation
Indices: 31180--31234 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
31170 ATGTAATATT
*
31180 ATAAATGATAATAATT-TTTA
1 ATAAATGATAAAAATTATTTA
31200 ATAAAT-ATAAAAATTATTTATA
1 ATAAATGATAAAAATTA-TT-TA
31222 ATAATATGATAAA
1 ATAA-ATGATAAA
31235 TTTAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 8 0.28
20 6 0.21
21 2 0.07
22 6 0.21
23 2 0.07
24 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
ATAAATGATAAAAATTATTTA
Found at i:31235 original size:22 final size:22
Alignment explanation
Indices: 31180--31236 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
31170 ATGTAATATT
* *
31180 ATAA-ATGAT-AATAATTTTTA
1 ATAATATGATAAATTATTTATA
*
31200 ATAAATAT-AAAAATTATTTATA
1 AT-AATATGATAAATTATTTATA
31222 ATAATATGATAAATT
1 ATAATATGATAAATT
31237 TAATAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 8 0.28
22 19 0.66
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATAATATGATAAATTATTTATA
Found at i:31245 original size:30 final size:31
Alignment explanation
Indices: 31198--31268 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
31188 TAATAATTTT
*
31198 TAATAAATATAAAAATTA-TTTATAATAATA
1 TAATAAATTTAAAAATTATTTTATAATAATA
* * * *
31228 TGATAAATTTAATAATTATTTTATAATGATT
1 TAATAAATTTAAAAATTATTTTATAATAATA
31259 TAATAAATTT
1 TAATAAATTT
31269 TATTGACCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TAATAAATTTAAAAATTATTTTATAATAATA
Found at i:32223 original size:2 final size:2
Alignment explanation
Indices: 32218--32395 Score: 77
Period size: 2 Copynumber: 94.5 Consensus size: 2
32208 AGTAGTGTGT
32218 TA TA TA TA TA GTA T- TA TGA TA T- TA TA TA TA TA GTA TA TA -A
1 TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA TA
* *
32258 TGG TA T- TA TA T- TA T- TA TA TA GTA TT TA T- TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
32298 TA TA -A TA T- TA TA CA -A TA TT TA CA CA -A TA TG TCA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* *
32336 TA TA T- TA TG TT TA TA TA T- TA T- TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
32374 TA TA T- TT TA T- TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA T
32396 TTGTATAGTA
Statistics
Matches: 137, Mismatches: 14, Indels: 50
0.68 0.07 0.25
Matches are distributed among these distances:
1 18 0.13
2 107 0.78
3 12 0.09
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32242 original size:8 final size:7
Alignment explanation
Indices: 32217--32395 Score: 85
Period size: 7 Copynumber: 25.9 Consensus size: 7
32207 TAGTAGTGTG
32217 TTATATA
1 TTATATA
32224 -TATAGTA
1 TTATA-TA
32231 TTATGATA
1 TTAT-ATA
32239 TTATATA
1 TTATATA
32246 TATAGTATA
1 T-TA-TATA
* *
32255 TAATGGTA
1 TTAT-ATA
32263 TTATATTA
1 TTATA-TA
32271 TTATATA
1 TTATATA
* *
32278 GTATTTA
1 TTATATA
32285 TTATATA
1 TTATATA
32292 -TATATA
1 TTATATA
32298 -TATAATA
1 TTAT-ATA
*
32305 TTATACA
1 TTATATA
32312 --ATAT-
1 TTATATA
* *
32316 TTACACA
1 TTATATA
* *
32323 ATATGTCA
1 TTATAT-A
32331 TATATTATA
1 T-TA-TATA
*
32340 TTATGT-
1 TTATATA
32346 TTATATA
1 TTATATA
32353 TTAT-TA
1 TTATATA
32359 -TATATA
1 TTATATA
32365 TTATATA
1 TTATATA
32372 -TATATA
1 TTATATA
32378 TT-T-TA
1 TTATATA
32383 TTATATA
1 TTATATA
*
32390 GTATAT
1 TTATAT
32396 TTGTATAGTA
Statistics
Matches: 130, Mismatches: 21, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
5 10 0.08
6 32 0.25
7 46 0.35
8 30 0.23
9 10 0.08
10 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (7 bp):
TTATATA
Found at i:32264 original size:24 final size:23
Alignment explanation
Indices: 32218--32378 Score: 91
Period size: 24 Copynumber: 7.5 Consensus size: 23
32208 AGTAGTGTGT
*
32218 TATATATATAGTATTATGATATTA
1 TATATATATA-TATAATGATATTA
*
32242 TATATATAGTATATAATGGTATTA
1 TATATATA-TATATAATGATATTA
*
32266 TAT-TAT-TATATAGT-AT-TTA
1 TATATATATATATAATGATATTA
*
32285 T-TATATATATATATATAATATTA
1 TATATATATATATA-ATGATATTA
* * * * * *
32308 TACAATATTTACACAAT-ATGTCA
1 TA-TATATATATATAATGATATTA
32331 TATAT-TATAT-T-ATG-T-TTA
1 TATATATATATATAATGATATTA
32349 TATAT-TAT-TAT-AT-ATATTA
1 TATATATATATATAATGATATTA
32368 TATATATATAT
1 TATATATATAT
32379 TTTATTATAT
Statistics
Matches: 107, Mismatches: 16, Indels: 31
0.69 0.10 0.20
Matches are distributed among these distances:
17 1 0.01
18 15 0.14
19 18 0.17
20 10 0.09
21 12 0.11
22 4 0.04
23 13 0.12
24 24 0.22
25 10 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
TATATATATATATAATGATATTA
Found at i:32306 original size:37 final size:35
Alignment explanation
Indices: 32218--32389 Score: 107
Period size: 39 Copynumber: 4.7 Consensus size: 35
32208 AGTAGTGTGT
* * *
32218 TATATATATAGTATTATGATAT-TATATATATAGTA
1 TATATATATAATATTATTATATATATTTATATA-TA
* *
32253 TATAATGGTATTATATTATTATATAGTATTTATTATATA
1 TAT-AT-ATATAATATTATTATATA-TATTTA-TATATA
* * *
32292 TATATATATAATATTA-TACA-ATATTTACACAATA
1 TATATATATAATATTATTATATATATTTATA-TATA
* * *
32326 TGTCATATATTATATTATGTTTATATATTATTATATATA
1 TAT-ATATATAATATTAT-TATATATA-T-TTATATATA
*
32365 TTATATATATATATTTTATTATATA
1 -TATATATATA-ATATTATTATATA
32390 GTATATTTGT
Statistics
Matches: 103, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
33 1 0.01
34 11 0.11
35 16 0.16
36 5 0.05
37 24 0.23
38 5 0.05
39 25 0.24
40 16 0.16
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (35 bp):
TATATATATAATATTATTATATATATTTATATATA
Found at i:32354 original size:13 final size:12
Alignment explanation
Indices: 32331--32388 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
32321 CAATATGTCA
32331 TATATTATATTAT
1 TATA-TATATTAT
*
32344 GTTTATATATTAT
1 -TATATATATTAT
32357 TATATATATTAT
1 TATATATATTAT
32369 ATATATATATT-T
1 -TATATATATTAT
32381 TAT-TATAT
1 TATATATAT
32389 AGTATATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 5 0.12
11 3 0.07
12 12 0.29
13 18 0.44
14 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TATATATATTAT
Found at i:32402 original size:25 final size:25
Alignment explanation
Indices: 32333--32402 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
32323 ATATGTCATA
*
32333 TATTATAT-TATGTTTATATATTAT
1 TATTATATATATATTTATATATTAT
*
32357 TA-TATATATTATATATATATATT-T
1 TATTATATA-TATATTTATATATTAT
*
32381 TATTATATAGTATATTTGTATA
1 TATTATATA-TATATTTATATA
32403 GTATAGTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 5 0.13
24 5 0.13
25 28 0.74
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TATTATATATATATTTATATATTAT
Found at i:32402 original size:27 final size:26
Alignment explanation
Indices: 32330--32421 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
32320 ACAATATGTC
*
32330 ATATATTATATTATGTTTATATATTATT
1 ATATA-TATATT-TGTATATATATTATT
* * *
32358 ATATATATTATATATATATATTTTATT
1 ATATATA-TATTTGTATATATATTATT
* *
32385 ATATAGTATATTTGTATAGTATAGTGTT
1 ATATA-TATATTTGTATA-TATATTATT
32413 ATAT-TATAT
1 ATATATATAT
32422 GTAACATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 5 0.10
27 27 0.52
28 20 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (26 bp):
ATATATATATTTGTATATATATTATT
Found at i:32407 original size:18 final size:16
Alignment explanation
Indices: 32345--32409 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
32335 TTATATTATG
*
32345 TTTATATATTATTATAT
1 TTTATATA-TAGTATAT
32362 ATATTATATATA-TATAT
1 -T-TTATATATAGTATAT
32379 TTTATTATATAGTATAT
1 TTTA-TATATAGTATAT
32396 TTGTATAGTATAGT
1 TT-TATA-TATAGT
32410 GTTATATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.07
16 7 0.17
17 14 0.33
18 11 0.26
19 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTATATATAGTATAT
Found at i:36516 original size:24 final size:24
Alignment explanation
Indices: 36485--36576 Score: 107
Period size: 24 Copynumber: 3.8 Consensus size: 24
36475 TTCGATTTGA
36485 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* *
36509 A-TCTTGATCTGATA-TCTGACATAG
1 ATTC-TGATATGATACT-TGACATGG
*
36533 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
36557 ATTCTAATCTGATACTTGAC
1 ATTCTGATATGATACTTGAC
36577 CTGATTTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 3 0.05
24 51 0.89
25 3 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:36795 original size:2 final size:2
Alignment explanation
Indices: 36788--36832 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
36778 TGGATGAGGG
*
36788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36830 TA T
1 TA T
36833 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41750 original size:24 final size:24
Alignment explanation
Indices: 41723--41838 Score: 148
Period size: 24 Copynumber: 4.8 Consensus size: 24
41713 TTGGATTTGA
*
41723 ATTCTGATCTGATACTTGGCATGG
1 ATTCTGATCTGATACTTGACATGG
*
41747 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
41771 ATTCTGATCTGATACTTGAC-TGGG
1 ATTCTGATCTGATACTTGACAT-GG
*
41795 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
41819 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
41839 CTGATTTATG
Statistics
Matches: 83, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
23 2 0.02
24 77 0.93
25 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:48433 original size:35 final size:36
Alignment explanation
Indices: 48394--48492 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 36
48384 GAGGGGTAAC
*
48394 TCGCATGGCTTGCCATGCGTCTCCCAA-GGGGGGAG
1 TCGCATGACTTGCCATGCGTCTCCCAAGGGGGGGAG
48429 TCGCATGACTTGCCATGCGTCTCCCAAGGGGGGGGGGAG
1 TCGCATGACTTGCCATGCGTCTCCCAA---GGGGGGGAG
48468 TCGCATGACTTGCCATGCGTCTCCC
1 TCGCATGACTTGCCATGCGTCTCCC
48493 CGGGGTCCTC
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
35 26 0.44
39 33 0.56
ACGTcount: A:0.14, C:0.30, G:0.34, T:0.21
Consensus pattern (36 bp):
TCGCATGACTTGCCATGCGTCTCCCAAGGGGGGGAG
Found at i:53543 original size:28 final size:28
Alignment explanation
Indices: 53510--53593 Score: 107
Period size: 29 Copynumber: 3.0 Consensus size: 28
53500 ATAATAATTA
53510 ACTTGATTTTATAATAATTTATGTATAT
1 ACTTGATTTTATAATAATTTATGTATAT
* * * *
53538 ATTTGATTTTATAGTAATTAACT-TAATTT
1 ACTTGATTTTATAATAATTTA-TGT-ATAT
53567 ACTTGATTTTATAATAATTTATGTATA
1 ACTTGATTTTATAATAATTTATGTATA
53594 ATAATTAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
ACTTGATTTTATAATAATTTATGTATAT
Found at i:53578 original size:29 final size:29
Alignment explanation
Indices: 53504--53619 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 29
53494 TTTTTTATAA
* *
53504 TAATTAACTTGATTTTATAATAATTTATG
1 TAATTTACTTGATTTTATAATAATTAATG
* * *
53533 T-ATATATTTGATTTTATAGTAATTAACT-
1 TAATTTACTTGATTTTATAATAATTAA-TG
*
53561 TAATTTACTTGATTTTATAATAATTTATG
1 TAATTTACTTGATTTTATAATAATTAATG
*
53590 TATAATAATTAACTTTATTTTATAATAATT
1 --TAAT--TT-ACTTGATTTTATAATAATT
53620 TATGCATTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
28 22 0.32
29 23 0.33
31 4 0.06
33 2 0.03
34 18 0.26
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TAATTTACTTGATTTTATAATAATTAATG
Found at i:53584 original size:20 final size:20
Alignment explanation
Indices: 53561--53621 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
53551 GTAATTAACT
53561 TAATTTACTTGATTTTATAA
1 TAATTTACTTGATTTTATAA
53581 TAATTTA--TG----TATAA
1 TAATTTACTTGATTTTATAA
* *
53595 TAATTAACTTTATTTTATAA
1 TAATTTACTTGATTTTATAA
53615 TAATTTA
1 TAATTTA
53622 TGCATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
18 2 0.06
20 18 0.56
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TAATTTACTTGATTTTATAA
Found at i:53749 original size:26 final size:29
Alignment explanation
Indices: 53714--53790 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 29
53704 ATTATTAAAA
*
53714 TAACAATAAAATATATATTTTATT-TTATT
1 TAAC-ATAAAATATATATTTTATTATTATC
**
53743 TATTA-AAAATATA-ATTTT-TTATTATC
1 TAACATAAAATATATATTTTATTATTATC
53769 TAACATAAAATATATATTTTAT
1 TAACATAAAATATATATTTTAT
53791 CTCATCTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.05
26 12 0.31
27 16 0.41
28 6 0.15
29 3 0.08
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TAACATAAAATATATATTTTATTATTATC
Found at i:53782 original size:54 final size:58
Alignment explanation
Indices: 53662--53800 Score: 155
Period size: 54 Copynumber: 2.4 Consensus size: 58
53652 TTTAAAGTTG
*
53662 AAAA-ATATATTTTATTTTTATCTTAAATTATGAAATAAATTTATTATTAAAATAACAAT
1 AAAATATATATTTTA-TTTTATCTT-AATTATAAAATAAATTTATTATTAAAATAACAAT
* **
53721 AAAATATATATTTTATTTTAT-TT-ATTA-AAAATATAATTTTTTATT-ATCTAAC-AT
1 AAAATATATATTTTATTTTATCTTAATTATAAAATA-AATTTATTATTAAAATAACAAT
* *
53775 AAAATATATATTTTATCTCATCTTAA
1 AAAATATATATTTTATTTTATCTTAA
53801 CTTTTAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
54 21 0.30
55 12 0.17
56 15 0.21
58 2 0.03
59 10 0.14
60 10 0.14
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (58 bp):
AAAATATATATTTTATTTTATCTTAATTATAAAATAAATTTATTATTAAAATAACAAT
Found at i:53797 original size:28 final size:26
Alignment explanation
Indices: 53714--53790 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
53704 ATTATTAAAA
*
53714 TAACAATAAAATATATATTTTATTTTATT
1 TAAC-ATAAAATATATATTTTA--TTATC
** *
53743 TATTA-AAAATATAATTTTTTATTATC
1 TAACATAAAATAT-ATATTTTATTATC
53769 TAACATAAAATATATATTTTAT
1 TAACATAAAATATATATTTTAT
53791 CTCATCTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
26 15 0.38
27 14 0.36
28 8 0.21
29 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TAACATAAAATATATATTTTATTATC
Found at i:54976 original size:36 final size:37
Alignment explanation
Indices: 54924--54996 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
54914 TATGTGCAGG
*
54924 GGGAGCAGATTCCCCCT-GGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGGTATCGATTCCCC
54960 GGGAACAGATTCCCCCTGGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGGTATCGATTCCCC
54997 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 16 0.46
37 19 0.54
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.19
Consensus pattern (37 bp):
GGGAACAGATTCCCCCTGGGGGGGGTATCGATTCCCC
Found at i:56377 original size:30 final size:29
Alignment explanation
Indices: 56334--56404 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 29
56324 CCCGCTGGAC
*
56334 CTATCCAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAGGTCATAAAGATCCTCGGCAA
56363 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCA-AGGTCATAAAGATCCTCGGCAA
56393 CTATCCATAGGT
1 CTATCCA-AGGT
56405 TCCAAAGAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 7 0.18
30 32 0.82
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (29 bp):
CTATCCAAGGTCATAAAGATCCTCGGCAA
Found at i:56412 original size:30 final size:30
Alignment explanation
Indices: 56334--56412 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
56324 CCCGCTGGAC
* *
56334 CTATCCA-AGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGCAA
*
56363 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGATCCTCGGCAA
*
56393 CTATCCATAGGTTC-CAAAGA
1 CTATCCAGAGG-TCACAAAGA
56413 ACCTAGGTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.16
30 36 0.80
31 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGCAA
Found at i:56489 original size:31 final size:32
Alignment explanation
Indices: 56396--56510 Score: 95
Period size: 31 Copynumber: 3.8 Consensus size: 32
56386 TCGGCAACTA
* * *
56396 TCCATAGGTTCCAAAGAACCTAGGTGAA--CTG
1 TCCATATGTTCCGAAGAACATAGGT-AATTCTG
**
56427 TCCATATGTTCCTTAGAACATA--T-A--CTG
1 TCCATATGTTCCGAAGAACATAGGTAATTCTG
56454 TCCATATG-TCTCGAAG-ACATAGGTAATTCTG
1 TCCATATGTTC-CGAAGAACATAGGTAATTCTG
*
56485 TCCATATGTTCCGTAGAACATAGGTA
1 TCCATATGTTCCGAAGAACATAGGTA
56511 CCCTTGACTC
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
26 7 0.10
27 15 0.22
28 1 0.01
29 2 0.03
31 33 0.48
32 11 0.16
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (32 bp):
TCCATATGTTCCGAAGAACATAGGTAATTCTG
Done.