Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001687.1 Hibiscus syriacus cultivar Beakdansim tig00003369_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: 87376
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4263 original size:34 final size:31
Alignment explanation
Indices: 4225--4289 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 31
4215 AATTGGTATA
*
4225 TTTTTTAAAATAGTTTTATATTTTTTTTATAAAT
1 TTTTTTAAAATA-TTTTAT-TTTTTGTTA-AAAT
4259 TTTTTTAAAATATTTTATTTTTTGTTAAAAT
1 TTTTTTAAAATATTTTATTTTTTGTTAAAAT
4290 AAGATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.13
32 8 0.27
33 6 0.20
34 12 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTTTTAAAATATTTTATTTTTTGTTAAAAT
Found at i:6109 original size:42 final size:42
Alignment explanation
Indices: 6041--6146 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
6031 GATGATGCAA
* *
6041 CAAGGGTACATGCCCAGCCCACCAGTTCAAATGTCATCTCCG
1 CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
* * * *
6083 CAATGTTATATGCCAAGCCCACCAGTTCATATGTCATCTCCT
1 CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
* *
6125 CAAGGTTACATTCCTAGCCCAC
1 CAAGGTTACATGCCAAGCCCAC
6147 AGGGGTACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (42 bp):
CAAGGTTACATGCCAAGCCCACCAGTTCAAATGTCATCTCCG
Found at i:6194 original size:21 final size:21
Alignment explanation
Indices: 6128--6194 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
6118 ATCTCCTCAA
* *
6128 GGTTACATTCCTAGCCCACAG
1 GGTTACATACCCAGCCCACAG
* *
6149 GGGTACATACCCAGCCCACAA
1 GGTTACATACCCAGCCCACAG
* * *
6170 GGTTACATGCCCAGCTCGCAG
1 GGTTACATACCCAGCCCACAG
6191 GGTT
1 GGTT
6195 TTATGACACC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (21 bp):
GGTTACATACCCAGCCCACAG
Found at i:7587 original size:140 final size:138
Alignment explanation
Indices: 7202--7825 Score: 757
Period size: 139 Copynumber: 4.5 Consensus size: 138
7192 AATTTCAAGA
* * **
7202 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAGGGAAGACGTGCCCCCTGAAACGTACT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCCTGAAACGCGCT
* * * * *
7267 TTCACCACTTTGTTGTGTCCTCTCAAACATGATAGATACTGACATGAATAGTGCCCCGCCAGGAG
66 TTCACCACTTTGCTGCGTCC-CTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGG
*
7332 ACATTACAC
130 ACATCACAC
*** * * * **
7341 ATAATAAAACAATTATAACCTATTCTCTG--ATAAAAAAGGAAGGCACGCCCCCTGAAACGCATT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCCTGAAACGCGCT
* * * * * *
7404 TTCACTACTTTACTACGTCTCTTCAAACATTATAGGTACTGACATGAATAGTGCCCCACCGGGGG
66 TTCACCACTTTGCTGCGTC-CCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGG
7469 ACATCACAC
130 ACATCACAC
* * * * *
7478 ATAATAGGGTAATTATAACATATTCTCTGACACAAAAAAAAGAAGGCGCACCCCCTGAAACGCGC
1 ATAATAGGGCAATTATAACCTATTCTCTGACA-AAAAAAAGGAAGACGCGCCCCCTGAAACGCGC
* * * *
7543 TTTCATCACTTTGCTGCGTCCACACAAACATGATAGGTACTGACATAAATAGTGACCCGCCGGGG
65 TTTCACCACTTTGCTGCGTCC-CTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGG
*
7608 AACATCACAC
129 GACATCACAC
* * * *
7618 ATAATAGGGTAATTATAACCTATTCTCTAACAAAAAAAGGGAAGACGCGCGCCCTGAAACGCGCT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCCTGAAACGCGCT
* * ** * * *
7683 TTCACCAATTTGTTGTATCCCCTCAAACATGATAGGTACTGATATGAATAGTACCCTGCCGGGGG
66 TTCACCACTTTGCTGCGT-CCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGG
*
7748 ACATCGCAC
130 ACATCACAC
* *
7757 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCTTGAAACGCGTT
1 ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCCTGAAACGCGCT
7822 TTCA
66 TTCA
7826 TATGAATAGT
Statistics
Matches: 409, Mismatches: 70, Indels: 12
0.83 0.14 0.02
Matches are distributed among these distances:
137 111 0.27
138 1 0.00
139 177 0.43
140 120 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (138 bp):
ATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAAGGAAGACGCGCCCCCTGAAACGCGCT
TTCACCACTTTGCTGCGTCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCGCCGGGGGA
CATCACAC
Found at i:13149 original size:20 final size:20
Alignment explanation
Indices: 13119--13171 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
13109 CTGATTCAGT
* *
13119 AGGTATGGATACCTAAGGG-
1 AGGTATCGATACCGAAGGGA
*
13138 GGAGTATCGATACCGAAGGGA
1 AG-GTATCGATACCGAAGGGA
13159 AGGTATCGATACC
1 AGGTATCGATACC
13172 ATTTCAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.19
Consensus pattern (20 bp):
AGGTATCGATACCGAAGGGA
Found at i:13220 original size:19 final size:20
Alignment explanation
Indices: 13196--13249 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
13186 TGCAAAATCG
13196 GTATCGATACCATAGCA-TA
1 GTATCGATACCATAGCAGTA
* *
13215 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGCA--GTA
13237 GTATCGATACCAT
1 GTATCGATACCAT
13250 GGTATGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 15 0.52
22 14 0.48
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATAGCAGTA
Found at i:13241 original size:22 final size:22
Alignment explanation
Indices: 13196--13266 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
13186 TGCAAAATCG
*
13196 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGTATGGTA
*
13215 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
13237 GTATCGATACCATGGTATGG--
1 GTATCGATACCATAGTATGGTA
13257 GTATCGATAC
1 GTATCGATAC
13267 TGAAGTGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 15 0.33
20 10 0.22
22 20 0.44
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:13651 original size:54 final size:54
Alignment explanation
Indices: 13589--13887 Score: 411
Period size: 54 Copynumber: 5.5 Consensus size: 54
13579 TACCAAATAA
*
13589 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTTG
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
13643 GCACTAAGTGTGCATTTCAC-AGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGA-AATTCATCCTATGTGGATGAATAACCGTTTCG
* *
13697 GCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * * * * **
13751 GTATTAAGTGTACATTTCATGGAATTCATTCTATGTGGATGAATAATTGTTTCG
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
* * *
13805 GCTCTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
* * ***
13859 ACACTATGTGTGCAAAACACGAAATTCAT
1 GCACTAAGTGTGCATTTCACGAAATTCAT
13888 AATTTGTTTA
Statistics
Matches: 220, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 219 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCG
Found at i:15393 original size:13 final size:13
Alignment explanation
Indices: 15375--15400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15365 CAGAGTGTGC
15375 AAACATGAAAAAT
1 AAACATGAAAAAT
15388 AAACATGAAAAAT
1 AAACATGAAAAAT
15401 GATTAGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAACATGAAAAAT
Found at i:19983 original size:20 final size:19
Alignment explanation
Indices: 19938--19989 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
19928 CTGATTCAAT
* *
19938 AGGTATCGATAACTAAGGG
1 AGGTATCGATACCGAAGGG
*
19957 GGGTATCGATACCGAAGGG
1 AGGTATCGATACCGAAGGG
19976 AAGGTATCGATACC
1 -AGGTATCGATACC
19990 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (19 bp):
AGGTATCGATACCGAAGGG
Found at i:20065 original size:22 final size:22
Alignment explanation
Indices: 20014--20073 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
20004 TGCAAAAATG
*
20014 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGTATGGTA
*
20033 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
* *
20055 GTATTGATACCATGGTATG
1 GTATCGATACCATAGTATG
20074 CATATCGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 15 0.45
22 18 0.55
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:20475 original size:54 final size:54
Alignment explanation
Indices: 20409--20856 Score: 542
Period size: 54 Copynumber: 8.3 Consensus size: 54
20399 TTACCAAATA
* * *
20409 GGCACTAAGTGTGCATTT-ATCGGAATCCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCA-CGGAATTCATTCTATGTGGATGAATAACCGTTTC
* * *
20463 GGAACTAAGTGTGTATTTCACGGAATTTATTCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* *
20517 GGCACTACGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* * * ***
20571 GGCACTAAGTGTGCATTTCACGAAATTTA-TCATATGTGCATGAATAATTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTC-TATGTGGATGAATAACCGTTTC
* * *
20625 GGCACTAAGTGTACATTTCACGAAATTCATTCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* * *
20679 GACACTTAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* * *
20733 GACACTTAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* *** ** ** * *
20787 GGCACTATGTGTGCAAAGCACGGAATTCATAATATGTTTATGAATGACCGTAT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* *
20840 GGCACTACGGGTGCATT
1 GGCACTAAGTGTGCATT
20857 ACAACGAAAT
Statistics
Matches: 344, Mismatches: 47, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
53 14 0.04
54 327 0.95
55 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
Found at i:23510 original size:22 final size:22
Alignment explanation
Indices: 23485--23535 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
23475 TTAGAATTTT
*
23485 TTTTATATATTTTCTATTAAAA
1 TTTTATATATTTTCTACTAAAA
* * * *
23507 TTTTATTTTTTTTCTCCTGAAA
1 TTTTATATATTTTCTACTAAAA
23529 TTTTATA
1 TTTTATA
23536 AATTAAGTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTATATATTTTCTACTAAAA
Found at i:24915 original size:20 final size:20
Alignment explanation
Indices: 24890--24954 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
24880 TTATATTTTG
*
24890 TATCGATACTGCAAGAACGA
1 TATCGATATTGCAAGAACGA
* * * *
24910 TATCGATATTGTAAGTATGG
1 TATCGATATTGCAAGAACGA
* *
24930 TATCGGTATTGCAAGAACAA
1 TATCGATATTGCAAGAACGA
24950 TATCG
1 TATCG
24955 GTAATTCTTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
TATCGATATTGCAAGAACGA
Found at i:30167 original size:24 final size:24
Alignment explanation
Indices: 30135--30182 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30125 AAGCATGATC
30135 CTCTTTTAAGAGGATAAATGTTAG
1 CTCTTTTAAGAGGATAAATGTTAG
30159 CTCTTTTAAGAGGATAAATGTTAG
1 CTCTTTTAAGAGGATAAATGTTAG
30183 ATTTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (24 bp):
CTCTTTTAAGAGGATAAATGTTAG
Found at i:30775 original size:42 final size:40
Alignment explanation
Indices: 30729--30808 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
30719 ATTAGCGGCA
*
30729 TTTGTATAAAAAAACGCCGCCAAAGAATGTACTTTAGTGGAG
1 TTTGTAT--AAAAACGCCGCCAAAGAATATACTTTAGTGGAG
* * *
30771 TTTGTATAAAACCGCCGCTAAAGACTATACTTTAGTGG
1 TTTGTATAAAAACGCCGCCAAAGAATATACTTTAGTGG
30809 CATTTTAGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 27 0.79
42 7 0.21
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (40 bp):
TTTGTATAAAAACGCCGCCAAAGAATATACTTTAGTGGAG
Found at i:30863 original size:41 final size:41
Alignment explanation
Indices: 30740--31060 Score: 380
Period size: 41 Copynumber: 7.9 Consensus size: 41
30730 TTGTATAAAA
* * * * *
30740 AAACGCCGCCAAAGAAT-GTACTTTAGTGGAGTTTGTATA-
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * *
30779 AAACCGCCGCTAAAGACT-ATACTTTAGTGGC-ATTTTAGAC
1 AAA-CGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
** *
30819 AAACGCTACTATAGACTCGTACTTTAGTGGCGTTTTTAGAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
30860 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
30901 AAACGCCGATATAGACTCGTACTTTAGTGGTGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
30942 AAACGCCTCTACAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
30983 AAACGCCGCTAAAGACTCGTACTTTAATGGCGTTTGTGTTTAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT-T-TATAC
* * *
31026 AAACGCCGCTAAAGACTTGTATTTTAGTGGCGTTT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
31061 GTAATAGACT
Statistics
Matches: 246, Mismatches: 30, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
39 19 0.08
40 38 0.15
41 152 0.62
42 1 0.00
43 36 0.15
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:34767 original size:85 final size:84
Alignment explanation
Indices: 34636--34970 Score: 384
Period size: 85 Copynumber: 3.9 Consensus size: 84
34626 TAATGAGCTT
* * * * * *
34636 TTTTGCGGCGTTTGTATCAAAAAACGCCGCTACAGATATGAGCTTTTGCGGCGTTTATATCCAAA
1 TTTTGCGGCGTTTAT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAA
34701 AACGCCGCTATAGATATGACC
64 AACGCCGCTATAGATATGACC
* * *
34722 ATTTGCGGTGTTTATTCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAA
1 TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAA
*
34787 CGCCGCTATAGATCTGACC
66 CGCCGCTATAGATATGACC
* * * * *
34806 TTTTGGCGGCGTTTCTTCCAAAAACGCTGCTATAGATCTGACATTTTGCGGCATTT-TTCCAGAA
1 TTTT-GCGGCGTTTATTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAA
34870 ACGCCGCTATAGATATCGACC
65 ACGCCGCTATAGATAT-GACC
* * * * * * * * *
34891 TTTTGCGACGTTTTTTTCTAGAAACACCGCGATAGGTCTTGACCTATTGTGGCGTTTGTTCCAAA
1 TTTTGCGGCG-TTTATTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAA
*
34956 AACGCCGCGATAGAT
64 AACGCCGCTATAGAT
34971 CTTGATCTAT
Statistics
Matches: 211, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
84 56 0.27
85 109 0.52
86 26 0.12
87 20 0.09
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (84 bp):
TTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAA
CGCCGCTATAGATATGACC
Found at i:34974 original size:43 final size:42
Alignment explanation
Indices: 34636--34989 Score: 379
Period size: 43 Copynumber: 8.3 Consensus size: 42
34626 TAATGAGCTT
* * * *
34636 TTTTGCGGCGTTTGTATCAAAAAACGCCGCTACAGATATGAGC
1 TTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACC
* *
34679 TTTTGCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACC
1 TTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACC
* * * *
34722 ATTTGCGGTGTTTATTCCAAAAATGCCGCTATAGATCTGACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
34764 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
* * *
34806 TTTTGGCGGCGTTTCTTCCAAAAACGCTGCTATAGATCTGACA
1 TTTT-GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
* * *
34849 TTTTGCGGCATTT-TTCCAGAAACGCCGCTATAGATATCGACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACC
* * * * * * *
34891 TTTTGCGACGTTTTTTTCTAGAAACACCGCGATAGGTCTTGACC
1 TTTTGCGGCG-TTTGTTCCAAAAACGCCGCTATAGATC-TGACC
* * * *
34935 TATTGTGGCGTTTGTTCCAAAAACGCCGCGATAGATCTTGATC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACC
*
34978 -TATGCGGCGTTT
1 TTTTGCGGCGTTT
34990 TTTGTTCTCA
Statistics
Matches: 267, Mismatches: 39, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
41 21 0.08
42 95 0.36
43 121 0.45
44 29 0.11
45 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (42 bp):
TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACC
Found at i:38626 original size:23 final size:22
Alignment explanation
Indices: 38599--38643 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
38589 ATAATCAATA
*
38599 ATATAAAGTAAAACATATTGATG
1 ATATAAAATAAAACATA-TGATG
*
38622 ATATAAAATAAATCATATGATG
1 ATATAAAATAAAACATATGATG
38644 GAAATACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (22 bp):
ATATAAAATAAAACATATGATG
Found at i:39765 original size:51 final size:50
Alignment explanation
Indices: 39701--39814 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 50
39691 AGCAGTAAAA
* ** *
39701 CGCGCCCCATGCACCACACTATACGATGATTTGGCGCCACGTGGGGTATAG
1 CGCGCCCCCTGCACCACACTATACGATGAGCTGACGCCACGT-GGGTATAG
* * *
39752 CGCGCCCCCTGCACCGCGCTATACGGTGAGCTGACGCCACGTGGGTATAG
1 CGCGCCCCCTGCACCACACTATACGATGAGCTGACGCCACGTGGGTATAG
*
39802 CGCGACCCCTGCA
1 CGCGCCCCCTGCA
39815 GCGCGCTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 20 0.36
51 35 0.64
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (50 bp):
CGCGCCCCCTGCACCACACTATACGATGAGCTGACGCCACGTGGGTATAG
Found at i:39848 original size:50 final size:49
Alignment explanation
Indices: 39737--39855 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 49
39727 TGATTTGGCG
*
39737 CCACGTGGGGTATAGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGA
1 CCACGTGGGGTATAGCGCGACCCCTGCACCGCGCTATACGGTGAGCTGA
* * * *
39786 CGCCACGT-GGGTATAGCGCGACCCCTGCAGCGCGCTATACATGTATATCTGA
1 --CCACGTGGGGTATAGCGCGACCCCTGCACCGCGCTATAC-GGT-GAGCTGA
39838 -CACGTGGGGTATAGCGCG
1 CCACGTGGGGTATAGCGCG
39856 GTACAGGGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 5 0.08
50 42 0.70
51 8 0.13
52 5 0.08
ACGTcount: A:0.18, C:0.31, G:0.32, T:0.18
Consensus pattern (49 bp):
CCACGTGGGGTATAGCGCGACCCCTGCACCGCGCTATACGGTGAGCTGA
Found at i:39987 original size:12 final size:10
Alignment explanation
Indices: 39945--39986 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
39935 TTTTATCACA
39945 TCAAATTCTC
1 TCAAATTCTC
39955 TCAAATTCTC
1 TCAAATTCTC
39965 T-AAATTTCTC
1 TCAAA-TTCTC
*
39975 TCAAATACTC
1 TCAAATTCTC
39985 TC
1 TC
39987 TTTTTAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.10
10 23 0.79
11 3 0.10
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:43027 original size:51 final size:46
Alignment explanation
Indices: 42917--43032 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 46
42907 ACAAAACGCG
* *
42917 GTACCTGATCCGCGCTATATAAAATTATGTTTAAAGGTATGTCGCG
1 GTACCTGATCCGCGCTATATAAAATTATGTGTAAAGGTATGTCGCA
**
42963 GTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAG-CGCA
1 GTACCTGATCCGCGCTATATAAAATTATGT-----GTAAAGGTAT-GTCGCA
43014 GTACCTGATCCGCGCTATA
1 GTACCTGATCCGCGCTATA
43033 CCCCTACGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
46 28 0.48
51 29 0.50
52 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
GTACCTGATCCGCGCTATATAAAATTATGTGTAAAGGTATGTCGCA
Found at i:43153 original size:51 final size:50
Alignment explanation
Indices: 43046--43171 Score: 135
Period size: 51 Copynumber: 2.5 Consensus size: 50
43036 CTACGTGGCG
* * ** * ** *
43046 TATAGCGCGCTGCAGGGGTCGCATTATACCCACGTGGCGCCAGCTCACCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACCA
* *
43096 TATAGCGCGGTGCAGGGGGCGCGCTATATCTCACGTGGCACCAAATCATCA
1 TATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGGCACCAAATCACCA
* *
43147 TATAGCGCGGTACAGGGGGTGCGCT
1 TATAGCGCGGTGCAGGGGGCGCGCT
43172 TTACTACTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 24 0.38
51 39 0.62
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.19
Consensus pattern (50 bp):
TATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACCA
Found at i:46191 original size:23 final size:23
Alignment explanation
Indices: 46156--46200 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46146 AAAAAAGATA
*
46156 AGTGAAATGTGAACATTTTGATG
1 AGTGAAATATGAACATTTTGATG
*
46179 AGTGGAATATGAACATTTTGAT
1 AGTGAAATATGAACATTTTGAT
46201 ATCGATATTG
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:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (23 bp):
AGTGAAATATGAACATTTTGATG
Found at i:47450 original size:33 final size:33
Alignment explanation
Indices: 47413--47486 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 33
47403 TATCGGATCG
*
47413 GTTGATTTTTTAGGTCTGGTCAAGATTGGATAT
1 GTTGATTTTTTAGGTCGGGTCAAGATTGGATAT
47446 GTTGA-TTTTTAGGTCGGGTCAAGATTGGATAT
1 GTTGATTTTTTAGGTCGGGTCAAGATTGGATAT
47478 GTTGATTTT
1 GTTGATTTT
47487 CGAGTCGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.20, C:0.05, G:0.28, T:0.46
Consensus pattern (33 bp):
GTTGATTTTTTAGGTCGGGTCAAGATTGGATAT
Found at i:47494 original size:32 final size:32
Alignment explanation
Indices: 47413--47496 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
47403 TATCGGATCG
* *
47413 GTTGATTTTTTAGGTCTGGTCAAGATTGGATAT
1 GTTGA-TTTTGAGGTCGGGTCAAGATTGGATAT
*
47446 GTTGATTTTTAGGTCGGGTCAAGATTGGATAT
1 GTTGATTTTGAGGTCGGGTCAAGATTGGATAT
47478 GTTGATTTTCGA-GTCGGGT
1 GTTGATTTT-GAGGTCGGGT
47497 TAATACTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
32 42 0.88
33 6 0.12
ACGTcount: A:0.19, C:0.07, G:0.31, T:0.43
Consensus pattern (32 bp):
GTTGATTTTGAGGTCGGGTCAAGATTGGATAT
Found at i:48355 original size:16 final size:15
Alignment explanation
Indices: 48334--48377 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
48324 AAATTTTGTA
48334 TTGGGTATGGTTCGGG
1 TTGGGTATGGTT-GGG
48350 TTGGGTATGGGTTGGG
1 TTGGGTAT-GGTTGGG
*
48366 TATGAGTATGGT
1 T-TGGGTATGGT
48378 AAATCAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.11, C:0.02, G:0.48, T:0.39
Consensus pattern (15 bp):
TTGGGTATGGTTGGG
Found at i:48986 original size:33 final size:34
Alignment explanation
Indices: 48949--49025 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
48939 GGTAAGAAAT
*
48949 TTATTTTTATATTAGTAT-TTT-T-TAAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAAA-A-TTA
48982 TTATTTTTTATATTAATATATTTATGTAAAAATTA
1 TTA-TTTTTATATTAATATATTTATGTAAAAATTA
49017 TT-TTTTTAT
1 TTATTTTTAT
49026 TAAAATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
33 10 0.26
34 14 0.36
35 8 0.21
36 2 0.05
37 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAAAATTA
Found at i:49037 original size:34 final size:31
Alignment explanation
Indices: 48981--49058 Score: 84
Period size: 34 Copynumber: 2.4 Consensus size: 31
48971 TAAAATAGTT
*
48981 ATTATTTTTTATATTAATATATTTATGTAAAA
1 ATTATTTTTT-TATTAATATATTTATATAAAA
**
49013 ATTATTTTTTTATTAAAATAATATTTATATAATT
1 ATTATTTTTTTATT--AAT-ATATTTATATAAAA
*
49047 ATTATTTATTTA
1 ATTATTTTTTTA
49059 GAATTATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 4 0.10
32 10 0.26
33 3 0.08
34 22 0.56
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTATTTTTTTATTAATATATTTATATAAAA
Found at i:49047 original size:31 final size:32
Alignment explanation
Indices: 48981--49055 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
48971 TAAAATAGTT
* *
48981 ATTATTTTTTATATTAATATATTTATGTAAAA
1 ATTATTTTTTATATTAAAATATATATGTAAAA
* *
49013 ATTATTTTTT-TATTAAAATA-ATATTTATATA
1 ATTATTTTTTATATTAAAATATATATGTA-AAA
*
49044 ATTATTATTTAT
1 ATTATTTTTTAT
49056 TTAGAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 5 0.14
31 20 0.56
32 11 0.31
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
ATTATTTTTTATATTAAAATATATATGTAAAA
Found at i:50809 original size:21 final size:21
Alignment explanation
Indices: 50779--50826 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50769 GCAGGGGTAC
* *
50779 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
50800 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
50821 ATGCCA
1 ATGCCA
50827 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:50856 original size:21 final size:21
Alignment explanation
Indices: 50830--50923 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
50820 TATGCCATCT
*
50830 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
50851 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
50872 CCGCCA-GGTTACATACCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
50893 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
50914 CCGCAGGGTT
1 CCGCAGGGTT
50924 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:51505 original size:33 final size:34
Alignment explanation
Indices: 51446--51542 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
51436 AAATGTTTTT
*
51446 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
51480 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
51513 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
51543 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:51549 original size:34 final size:33
Alignment explanation
Indices: 51444--51549 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
51434 ATAAATGTTT
*
51444 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
51478 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
51510 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
51545 TTAAA
1 TTAAA
51550 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:52570 original size:127 final size:128
Alignment explanation
Indices: 51930--52921 Score: 1863
Period size: 127 Copynumber: 7.8 Consensus size: 128
51920 TTTAAGTTAT
*
51930 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
51993 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
52056 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
52121 GCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
* *
52184 TCCCCGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTTTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
52249 GCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
52311 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
52375 GCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
52437 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
52502 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
52565 T-CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
52629 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT-TCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
52691 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
52756 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
52819 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
* *
52884 GCGCGCCCCCAGGAACGCGTCTTCATGTGAATAGTGAA
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
52922 CCGATTATAG
Statistics
Matches: 848, Mismatches: 12, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
126 182 0.21
127 359 0.42
128 307 0.36
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:53002 original size:8 final size:8
Alignment explanation
Indices: 52989--53029 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
52979 TCACAATCTT
52989 TCAAATTC
1 TCAAATTC
52997 TCAAATTC
1 TCAAATTC
* *
53005 CCAAACTC
1 TCAAATTC
53013 T-AAATTC
1 TCAAATTC
53020 TCAAATTC
1 TCAAATTC
53028 TC
1 TC
53030 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:56056 original size:20 final size:22
Alignment explanation
Indices: 56009--56054 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
55999 AATACAAAAT
*
56009 ATATTTAATATATTATTTAATA
1 ATATTTAATATATTAGTTAATA
56031 ATATTTAATATTATTAGTT-ATA
1 ATATTTAATA-TATTAGTTAATA
56053 AT
1 AT
56055 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATTTAATATATTAGTTAATA
Found at i:59381 original size:28 final size:27
Alignment explanation
Indices: 59350--59409 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
59340 ATACTGACAC
* *
59350 AAAATTTTATGTTATATGATAATT-TTAT
1 AAAATTATATATTATA-GA-AATTATTAT
59378 AAAATTATATATTATAGAAATTAATTAT
1 AAAATTATATATTATAGAAATT-ATTAT
59406 AAAA
1 AAAA
59410 AAAAATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 2 0.07
28 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (27 bp):
AAAATTATATATTATAGAAATTATTAT
Found at i:63036 original size:21 final size:20
Alignment explanation
Indices: 62996--63036 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
62986 AAATTAATTT
62996 TATAATTATTTTTTAGAAAAA
1 TATAATTATTTTTTA-AAAAA
63017 TATAATTAACTTTTTTAAAA
1 TATAATT-A-TTTTTTAAAA
63037 GTGTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATTATTTTTTAAAAAA
Found at i:77765 original size:20 final size:20
Alignment explanation
Indices: 77727--77891 Score: 143
Period size: 20 Copynumber: 8.2 Consensus size: 20
77717 GACCAAAGGA
* * * *
77727 TTTACAAATTACTCAGAGGT
1 TTTACAAATGACCCGGAGGC
77747 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
77767 TTTAAAAATGAGCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
77787 TTTATAAAATGACCCGGAGGC
1 TTTA-CAAATGACCCGGAGGC
* *
77808 TTTACAAATGAACCGAAGGC
1 TTTACAAATGACCCGGAGGC
* * *
77828 TTTGCAAATGACTCGAAGGC
1 TTTACAAATGACCCGGAGGC
* * **
77848 TTTGCAAATGACTCAAAGGC
1 TTTACAAATGACCCGGAGGC
* *
77868 TTTACAAAT-AACCGAAGGC
1 TTTACAAATGACCCGGAGGC
77887 TTTAC
1 TTTAC
77892 TTAAATGAGA
Statistics
Matches: 124, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
19 12 0.10
20 94 0.76
21 18 0.15
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (20 bp):
TTTACAAATGACCCGGAGGC
Found at i:77785 original size:40 final size:39
Alignment explanation
Indices: 77722--77891 Score: 164
Period size: 40 Copynumber: 4.3 Consensus size: 39
77712 CAGATGACCA
* * *
77722 AAGGATTTACAAATTACTCAGAGGTTTTACAAATGACCCG
1 AAGGCTTTACAAATGAC-CAGAGGCTTTACAAATGACCCG
* * *
77762 GAGGCTTTAAAAATGAGCCAGAGGCTTTATAAAATGACCCG
1 AAGGCTTTACAAATGA-CCAGAGGCTTTA-CAAATGACCCG
* * *
77803 GAGGCTTTACAAATGAACC-GAAGGCTTTGCAAATGACTCG
1 AAGGCTTTACAAATG-ACCAG-AGGCTTTACAAATGACCCG
* * *
77843 AAGGCTTTGCAAATGACTCAAAGGCTTTACAAAT-AACCG
1 AAGGCTTTACAAATGAC-CAGAGGCTTTACAAATGACCCG
77882 AAGGCTTTAC
1 AAGGCTTTAC
77892 TTAAATGAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
39 14 0.13
40 58 0.54
41 34 0.32
42 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (39 bp):
AAGGCTTTACAAATGACCAGAGGCTTTACAAATGACCCG
Found at i:83745 original size:45 final size:45
Alignment explanation
Indices: 83657--83746 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
83647 AAAATCATAT
* * * *
83657 CCTAACCTCATGTTTTCTAGTTCCATGCTTTGTTTGGAAAAATAA
1 CCTAACCGCATGATTTCTAGTTCCATGCTTTGATTGCAAAAATAA
*
83702 CCTAACCGCATGATTTCTAGTTCGCATGCATTT-ATT-CAGAAATAA
1 CCTAACCGCATGATTTCTAGTTC-CATGC-TTTGATTGCAAAAATAA
83747 AATAATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
45 28 0.74
46 7 0.18
47 3 0.08
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (45 bp):
CCTAACCGCATGATTTCTAGTTCCATGCTTTGATTGCAAAAATAA
Found at i:84708 original size:20 final size:22
Alignment explanation
Indices: 84683--84734 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
84673 ATTAAAATAA
84683 AAATATTAAATAAT-TT-TTAT
1 AAATATTAAATAATCTTATTAT
*
84703 AAATATT-AATAGTCTTATTAT
1 AAATATTAAATAATCTTATTAT
84724 -AATATTAAATA
1 AAATATTAAATA
84735 TTAAAACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.18
20 15 0.54
21 8 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATATTAAATAATCTTATTAT
Found at i:84939 original size:15 final size:16
Alignment explanation
Indices: 84903--84939 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
84893 TATAATTCAG
84903 GACTAAAATATAAATA
1 GACTAAAATATAAATA
*
84919 -ATTAAAATATAAA-A
1 GACTAAAATATAAATA
84933 GACTAAA
1 GACTAAA
84940 TAGGTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (16 bp):
GACTAAAATATAAATA
Found at i:86011 original size:34 final size:30
Alignment explanation
Indices: 85973--86041 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
85963 TCGATATAAC
85973 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
86007 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
86036 AATTTA
1 AATTTA
86042 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:86054 original size:30 final size:30
Alignment explanation
Indices: 85982--86041 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
85972 CAATTTAAGG
85982 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
86013 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
86042 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:86167 original size:22 final size:21
Alignment explanation
Indices: 86131--86172 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
86121 TTCAAGATTG
* *
86131 CCCAGGGGTATAGATTCCCCC
1 CCCAGGGGTACAGATACCCCC
86152 CCCAGGGGGTACAGATACCCC
1 CCCA-GGGGTACAGATACCCC
86173 GGGTACAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.14
Consensus pattern (21 bp):
CCCAGGGGTACAGATACCCCC
Found at i:86197 original size:19 final size:18
Alignment explanation
Indices: 86151--86206 Score: 82
Period size: 15 Copynumber: 3.2 Consensus size: 18
86141 TAGATTCCCC
86151 CCCCAGGGGGTACAGATA
1 CCCCAGGGGGTACAGATA
86169 CCCC---GGGTACAGATA
1 CCCCAGGGGGTACAGATA
86184 CACCCAGGGGGTACAGATA
1 C-CCCAGGGGGTACAGATA
86203 CCCC
1 CCCC
86207 CTGCAGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.35
16 3 0.09
18 7 0.21
19 12 0.35
ACGTcount: A:0.27, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
CCCCAGGGGGTACAGATA
Found at i:86205 original size:17 final size:17
Alignment explanation
Indices: 86152--86205 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
86142 AGATTCCCCC
86152 CCCAGGGGGTACAGATA
1 CCCAGGGGGTACAGATA
*
86169 CCC--CGGGTACAGATACA
1 CCCAGGGGGTACAGAT--A
86186 CCCAGGGGGTACAGATA
1 CCCAGGGGGTACAGATA
86203 CCC
1 CCC
86206 CCTGCAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 10 0.32
17 11 0.35
19 10 0.32
ACGTcount: A:0.28, C:0.31, G:0.30, T:0.11
Consensus pattern (17 bp):
CCCAGGGGGTACAGATA
Found at i:86265 original size:20 final size:20
Alignment explanation
Indices: 86240--86279 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
86230 AAACAGAATG
86240 TCCAGGGGGTACCGATTCCC
1 TCCAGGGGGTACCGATTCCC
86260 TCCAGGGGGTACCGATTCCC
1 TCCAGGGGGTACCGATTCCC
86280 CCCCTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (20 bp):
TCCAGGGGGTACCGATTCCC
Found at i:86345 original size:21 final size:21
Alignment explanation
Indices: 86319--86361 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
86309 ATTTGAATAT
*
86319 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
86340 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
86361 T
1 T
86362 CTATTCTGGT
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:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:86676 original size:33 final size:31
Alignment explanation
Indices: 86633--86702 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
86623 CCTTTTGTAA
*
86633 AGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGG-AAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
86667 AGGGAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAGGTTCTAGCTTAGCCCGGAAAAACT
86698 AGGGA
1 AGGGA
86703 GTTTGTAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 11 0.32
32 1 0.03
33 18 0.53
34 4 0.12
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (31 bp):
AGGGAAGGTTCTAGCTTAGCCCGGAAAAACT
Done.