Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001385.1 Hibiscus syriacus cultivar Beakdansim tig00002703_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: 48755
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Found at i:9359 original size:36 final size:36
Alignment explanation
Indices: 9283--9420 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
9273 AGTGGAGTAT
* *
9283 TATCAGCTTTGATACATTCGTGTATCAGT-TTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
9318 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
**
9354 TATCAGCTTTGGTACATTTATGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
9390 TATCATCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
9421 CTAGCACCGT
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 27 0.28
36 68 0.72
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:11998 original size:14 final size:13
Alignment explanation
Indices: 11973--12012 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11963 AATTGTTTAG
11973 TTATATTTTAATT
1 TTATATTTTAATT
11986 TTATATGTTTAATT
1 TTATAT-TTTAATT
**
12000 CAATATTTTAATT
1 TTATATTTTAATT
12013 ATGATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:12370 original size:15 final size:15
Alignment explanation
Indices: 12350--12379 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12340 TTTAGAGAAA
12350 TATTTTATTAATATT
1 TATTTTATTAATATT
*
12365 TATTTTTTTAATATT
1 TATTTTATTAATATT
12380 AAGAAAGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:12468 original size:138 final size:142
Alignment explanation
Indices: 12073--12468 Score: 325
Period size: 141 Copynumber: 2.8 Consensus size: 142
12063 TATAAGTTAA
* *
12073 TAATATTTATTTATTTTTTAAAATATTAAGAAAATGCA-GTCTTAAAGCAACTAGATGTCATAT-
1 TAATATTTA-TTATTTTTT--AATATTAAGAAAA-GGATGTCTTAAAGCAACTAGAAGTCAT-TC
* * * * * * * * * *
12136 TCTGGTATTT-TAAAGAATAATAAATATCATGC--TTATAAAAAATATATACA-TTTGCT-TTAA
61 TCTGATATTTCTAAA-TA-AATAAATGTCATACTTTTATATAAATTAAAAATATTTTG-TATTAC
* * *
12196 TTTTATATAAATCATTTTTT
123 TTTTAGAGAAATCATTTTAT
* *
12216 TAATATTTATTTATTTTTTAATATTAAGAAAAGGATGTCTTAAAGCAACTAGATGTCATTTTCTG
1 TAATATTTA-TTATTTTTTAATATTAAGAAAAGGATGTCTTAAAGCAACTAGAAGTCATTCTCTG
* * * * * **
12281 ATATTTTTAAATAAATTAATTTCATACTTTTATATTAATTTAATTTATTTTGTATTACTTTTAGA
65 ATATTTCTAAATAAATAAATGTCATACTTTTATATAAATTAAAAATATTTTGTATTACTTTTAGA
12346 GAAAT-ATTTTAT
130 GAAATCATTTTAT
* * * *
12358 TAATATTTA-T-TTTTTTAATATTAAGAAAGGGCTTTCTTAAAGCAGC-AGAAGTCATTCTCTGA
1 TAATATTTATTATTTTTTAATATTAAGAAAAGGATGTCTTAAAGCAACTAGAAGTCATTCTCTGA
*
12420 TATTTCTAAATAAAATAAATGTCTTA--TTTAT-TAAAATATAAAAATATTT
66 TATTTCTAAAT-AAATAAATGTCATACTTTTATAT-AAAT-TAAAAATATTT
12469 ATTTATAAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
136 1 0.00
137 8 0.04
138 32 0.15
139 43 0.20
140 15 0.07
141 46 0.22
142 31 0.15
143 36 0.17
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (142 bp):
TAATATTTATTATTTTTTAATATTAAGAAAAGGATGTCTTAAAGCAACTAGAAGTCATTCTCTGA
TATTTCTAAATAAATAAATGTCATACTTTTATATAAATTAAAAATATTTTGTATTACTTTTAGAG
AAATCATTTTAT
Found at i:14141 original size:14 final size:14
Alignment explanation
Indices: 14124--14154 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14114 TTTGTATTTA
*
14124 CATTTTCATTTTTG
1 CATTTTCATCTTTG
14138 CATTTTCATCTTTG
1 CATTTTCATCTTTG
14152 CAT
1 CAT
14155 AATTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (14 bp):
CATTTTCATCTTTG
Found at i:20095 original size:75 final size:75
Alignment explanation
Indices: 19959--20137 Score: 223
Period size: 75 Copynumber: 2.4 Consensus size: 75
19949 ATTAAAAAGA
* * * *
19959 AGCAAATGATGGAGCATGCTGAAAGACCATTTCAATCATAATTAGGAATATTGACACATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGACCATTTCAATCAGAATCAGGAATATTGACACATTTTGAA
*
20024 TGTTTATATT
66 CGTTTATATT
* * * * ***
20034 AGCCAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATGTTGATGTATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGACCATTTCAATCAGAATCAGGAATATTGACACATTTTGAA
*
20099 CGTTTGTATT
66 CGTTTATATT
* *
20109 AGCAAATGTTGGGTCATGCTGAAGGACCA
1 AGCAAATGTTGGGGCATGCTGAAAGACCA
20138 CATCATCATG
Statistics
Matches: 86, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGACCATTTCAATCAGAATCAGGAATATTGACACATTTTGAA
CGTTTATATT
Found at i:21049 original size:54 final size:54
Alignment explanation
Indices: 20998--21246 Score: 304
Period size: 54 Copynumber: 4.6 Consensus size: 54
20988 AACCACAAAA
** *
20998 AAAGGATGAATGT-TTGTCAAATATTTTACGAACATCTGTGCAAAAGCCACAAG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAAAAGCCACAAG
* * * *
21051 AAAGGATGAATGTGTTTTCAAATGCTTTACGAACATCTGGGCAGAAGGCACAGG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAAAAGCCACAAG
* *
21105 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAGAAGCCACAGG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAAAAGCCACAAG
* * * * ** *
21159 AAAGAATGAATGTGTTTTCAAATGTTTTACGAACATCTGAG-AAGAAATCACATG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAA-AAGCCACAAG
* * *
21213 AGATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
21247 CAATAATTAT
Statistics
Matches: 173, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
53 14 0.08
54 159 0.92
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (54 bp):
AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAAAAGCCACAAG
Found at i:21126 original size:108 final size:108
Alignment explanation
Indices: 20998--21246 Score: 365
Period size: 108 Copynumber: 2.3 Consensus size: 108
20988 AACCACAAAA
* * *
20998 AAAGGATGAATGT-TTGTCAAATATTTTACGAACATCTGTGCAAAAGCCACAAGAAAGGATGAAT
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGGGCAAAAGCCACAAGAAAGAATGAAT
* * *
21062 GTGTTTTCAAATGCTTTACGAACATCTGGGCAGAAGGCACAGG
66 GTGTTTTCAAATGCTTTACGAACATCTGAGAAGAAAGCACAGG
* * *
21105 AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGGGCAGAAGCCACAGGAAAGAATGAAT
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGGGCAAAAGCCACAAGAAAGAATGAAT
* * *
21170 GTGTTTTCAAATGTTTTACGAACATCTGAGAAGAAATCACATG
66 GTGTTTTCAAATGCTTTACGAACATCTGAGAAGAAAGCACAGG
* *
21213 AGATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
21247 CAATAATTAT
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
107 13 0.10
108 113 0.90
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (108 bp):
AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGGGCAAAAGCCACAAGAAAGAATGAAT
GTGTTTTCAAATGCTTTACGAACATCTGAGAAGAAAGCACAGG
Found at i:21635 original size:22 final size:22
Alignment explanation
Indices: 21610--21707 Score: 160
Period size: 22 Copynumber: 4.5 Consensus size: 22
21600 TCTACACTCA
*
21610 TCAAATATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
*
21632 TCAAATATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
*
21654 TCAAAGATGATAGATTCACTCT
1 TCAAAGATGATAGATTCTCTCT
*
21676 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTCT
21698 TCAAAGATGA
1 TCAAAGATGA
21708 AAGCTTTATT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:22442 original size:45 final size:45
Alignment explanation
Indices: 22378--22602 Score: 378
Period size: 45 Copynumber: 5.0 Consensus size: 45
22368 ATATTTCCCA
* * *
22378 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
22423 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
22468 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
*
22513 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
22558 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGG
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTC-AAAA-CCTTCGG
22603 AAGCTTTTTG
Statistics
Matches: 171, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 160 0.94
46 4 0.02
47 7 0.04
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
Found at i:22622 original size:76 final size:74
Alignment explanation
Indices: 22535--22676 Score: 230
Period size: 76 Copynumber: 1.9 Consensus size: 74
22525 CTTCAGTGCA
* *
22535 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAA-CCTT
22600 CGGAAGCTTTT
64 CGGAAGCTTTT
* *
22611 TGATGTTTTCAAAGCCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCG
22676 G
66 G
22677 GTCATTTGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 7 0.11
75 4 0.06
76 51 0.82
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (74 bp):
TGATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCG
GAAGCTTTT
Found at i:22664 original size:45 final size:45
Alignment explanation
Indices: 22611--22758 Score: 206
Period size: 45 Copynumber: 3.3 Consensus size: 45
22601 GGAAGCTTTT
*
22611 TGATGTTTTCAAAGCCTCCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* * * *
22656 TGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* ** *
22701 TGATGTTTTCAAAGCCTTCGAGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
22746 AGATGTTTTCAAA
1 TGATGTTTTCAAA
22759 TGAGATTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:22706 original size:121 final size:119
Alignment explanation
Indices: 22490--22720 Score: 381
Period size: 121 Copynumber: 1.9 Consensus size: 119
22480 CTTCAGTGCA
* *
22490 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTCCAGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
22555 GGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTT
66 GGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTC--AAAGCCTTCGGAAGCTTTT
* *
22611 TGATGTTTTCAAAGCCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTCCAGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
22676 GGTCATTTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCG
66 GGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAGCCTTCG
22721 AGTCATCCAT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
119 10 0.10
121 93 0.90
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (119 bp):
TGATGTTTTCAAAACCTCCAGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAGCCTTCGGAAGCTTTT
Found at i:22745 original size:166 final size:166
Alignment explanation
Indices: 22446--22758 Score: 509
Period size: 166 Copynumber: 1.9 Consensus size: 166
22436 TTCAGTGCAG
* *
22446 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAG
1 GATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCAG
* ** * *
22511 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGTCATCCATAAGACCTACAG
*
22576 TGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTT
131 TGCAAGATGTTTTCAAAAAGCCTTCGGAAGCTTTTT
* *
22612 GATGTTTTCAAAGCCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGG
1 GATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCAG
* * *
22677 GTCATTTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCGAGTCATCCATAAGACCTACAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGTCATCCATAAGACCTACAG
22742 TGCAAGATGTTTTCAAA
131 TGCAAGATGTTTTCAAA
22759 TGAGATTTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
166 134 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (166 bp):
GATGTTTTCAAAACCTCCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCAG
GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGTCATCCATAAGACCTACAG
TGCAAGATGTTTTCAAAAAGCCTTCGGAAGCTTTTT
Found at i:24853 original size:25 final size:25
Alignment explanation
Indices: 24787--24854 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 25
24777 TTAACATATT
* *
24787 TAAAAACAAAGCTTGAAAATAAAAG
1 TAAAAAGAAAGCTTTAAAATAAAAG
* * *
24812 TAAAATGAAAACTTTTAAAATTAAA-
1 TAAAAAGAAAGC-TTTAAAATAAAAG
24837 TAAAAAAGAAAGCTTTAA
1 T-AAAAAGAAAGCTTTAA
24855 TAAAACTAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (25 bp):
TAAAAAGAAAGCTTTAAAATAAAAG
Found at i:36750 original size:89 final size:89
Alignment explanation
Indices: 36625--36952 Score: 374
Period size: 92 Copynumber: 3.7 Consensus size: 89
36615 ATAGCAAAAG
* * * * * * *
36625 GGGAGCCAACCTAAGAAAATACCTT--GGGCCTATGGGCCCACCCAATGATATCCTTAGATCCGT
1 GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATAGGCCTACCCAATGATATCCTTAGATCCGT
*
36688 AGGGTTACCTTCAACACACAGCGAA
66 AGGGTTACCTT-AACACACAGCAAA
* * * * *
36713 GGGAACCAACCTAAGGATATGCCTT-GGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATTCGT
1 GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATAGGCCTACCCAATGATATCCTTAGATCCGT
*
36777 AGGGTTATCTTAAGCACACAGCAAAA
66 AGGGTTACCTTAA-CACACAGC-AAA
* * * * *
36803 GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATATGCCTACCGAAAGGTATCTTTAGATCCGT
1 GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATAGGCCTACCCAATGATATCCTTAGATCCGT
* *
36868 AGGGTTACCTTAAGAACACAACAAAAA
66 AGGGTTACCTTAA-CACACAGC--AAA
* *
36895 GGGAACCAACCTAAAGATATGCCTTGGGGGCCAATATGCCTACCCAATGATATCCTTA
1 GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATAGGCCTACCCAATGATATCCTTA
36953 AGTCCGCAAG
Statistics
Matches: 210, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
88 23 0.11
89 52 0.25
90 27 0.13
91 51 0.24
92 57 0.27
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (89 bp):
GGGAACCAACCTAAGGATATGCCTTGGGGGCCAATAGGCCTACCCAATGATATCCTTAGATCCGT
AGGGTTACCTTAACACACAGCAAA
Found at i:36869 original size:91 final size:91
Alignment explanation
Indices: 36591--36952 Score: 401
Period size: 91 Copynumber: 4.0 Consensus size: 91
36581 CCAGAACTGC
* * * * * * * *
36591 ATCCGTAGGGCTTACCCTCAGCATATAGCAAAAGGGGAGCCAACCTAAGAAAATACCTT--GGGC
1 ATCCGTAGGG-TTACCTTAAGCACACAGCAAAA-GGGAACCAACCTAAGGATATGCCTTGGGGGC
* ** * * *
36654 CTATGGGCCCACCCAATGATATCCTTAG
64 CAATATGCCTACCCAAAGGTATCCTTAG
*
36682 ATCCGTAGGGTTACCTTCAA-CACACAGC-GAAGGGAACCAACCTAAGGATATGCCTT-GGGGCC
1 ATCCGTAGGGTTACCTT-AAGCACACAGCAAAAGGGAACCAACCTAAGGATATGCCTTGGGGGCC
* ** *
36744 TATGGGCCTACCCAAGGGTATCCTTAG
65 AATATGCCTACCCAAAGGTATCCTTAG
* *
36771 ATTCGTAGGGTTATCTTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATGCCTTGGGGGCCA
1 ATCCGTAGGGTTACCTTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATGCCTTGGGGGCCA
* *
36836 ATATGCCTACCGAAAGGTATCTTTAG
66 ATATGCCTACCCAAAGGTATCCTTAG
* * *
36862 ATCCGTAGGGTTACCTTAAGAACACAACAAAAAGGGAACCAACCTAAAGATATGCCTTGGGGGCC
1 ATCCGTAGGGTTACCTTAAGCACACAGC-AAAAGGGAACCAACCTAAGGATATGCCTTGGGGGCC
* *
36927 AATATGCCTACCCAATGATATCCTTA
65 AATATGCCTACCCAAAGGTATCCTTA
36953 AGTCCGCAAG
Statistics
Matches: 235, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
88 23 0.10
89 54 0.23
90 39 0.17
91 62 0.26
92 57 0.24
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (91 bp):
ATCCGTAGGGTTACCTTAAGCACACAGCAAAAGGGAACCAACCTAAGGATATGCCTTGGGGGCCA
ATATGCCTACCCAAAGGTATCCTTAG
Found at i:37313 original size:15 final size:15
Alignment explanation
Indices: 37293--37322 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37283 ACAAGTGAAA
*
37293 CATAAAACCATAATT
1 CATAAAACAATAATT
37308 CATAAAACAATAATT
1 CATAAAACAATAATT
37323 TTCATGATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (15 bp):
CATAAAACAATAATT
Found at i:39682 original size:17 final size:16
Alignment explanation
Indices: 39660--39691 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
39650 AGTTAACACT
39660 GGTCAACGACGGTCAAC
1 GGTCAACGA-GGTCAAC
39677 GGTCAACGAGGTCAA
1 GGTCAACGAGGTCAA
39692 TGGTTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.25, G:0.31, T:0.12
Consensus pattern (16 bp):
GGTCAACGAGGTCAAC
Found at i:41835 original size:89 final size:88
Alignment explanation
Indices: 41712--42011 Score: 318
Period size: 92 Copynumber: 3.3 Consensus size: 88
41702 ATAGCAAAAG
* * * * **
41712 GGGAGCCAACCTAAGGATATACC-TAGGGCCTATGGGCTTATCCAAGGATATCCTTAGATATGTA
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTATGGGCTTACCCAAGG-TATCCTTAGATCCGTA
* * *
41776 GGGCTACCTTCAGCATACAATGAA
65 GGGCTACCTTAAGCACACAATAAA
* *
41800 GGGAACTAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCCTTAGATCCGTA
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTATGGGCTTACCCAA-GGTATCCTTAGATCCGTA
*
41865 GGGCTACCTTAAGCACACAACAAAAA
65 GGGCTACCTTAAGCACAC-A-ATAAA
* * * * *
41891 GTGAACCAACCTAAGGATATGTCTTGGGGGCCAATAT-GCCTT-CCCAATGGCATCCTTAGTTCC
1 GGGAACCAACCTAAGGATATGCCTT-GGGGCC--TATGGGCTTACCCAA-GGTATCCTTAGATCC
*
41954 GTAGGGTTACCTTAAGCACACAATAAAAA
62 GTAGGGCTACCTTAAGCACACAAT--AAA
*
41983 GGGAACCAACCTAAAGATATGCCTTGGGG
1 GGGAACCAACCTAAGGATATGCCTTGGGG
42012 GCCAATATAC
Statistics
Matches: 178, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
88 20 0.11
89 49 0.28
90 4 0.02
91 30 0.17
92 69 0.39
93 3 0.02
94 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (88 bp):
GGGAACCAACCTAAGGATATGCCTTGGGGCCTATGGGCTTACCCAAGGTATCCTTAGATCCGTAG
GGCTACCTTAAGCACACAATAAA
Found at i:41955 original size:92 final size:92
Alignment explanation
Indices: 41761--42048 Score: 341
Period size: 92 Copynumber: 3.2 Consensus size: 92
41751 ATCCAAGGAT
** * * ** *
41761 ATCCTTAGATATGTAGGGCTACCTTCAGCATAC-A-ATGAAGGGAACTAACCTAAGGATATGCCT
1 ATCCTTAGATCCGTAGGGCTACCTTAAGCACACAACAAAAAGGGAACCAACCTAAGGATATGCCT
* ** *
41824 T-GGGGCCTATGGGCCTACCCAAGGGT
66 TGGGGGCCAATATGCCTACCCAAGGGC
* *
41850 ATCCTTAGATCCGTAGGGCTACCTTAAGCACACAACAAAAAGTGAACCAACCTAAGGATATGTCT
1 ATCCTTAGATCCGTAGGGCTACCTTAAGCACACAACAAAAAGGGAACCAACCTAAGGATATGCCT
* *
41915 TGGGGGCCAATATGCCTTCCCAATGGC
66 TGGGGGCCAATATGCCTACCCAAGGGC
* * * *
41942 ATCCTTAGTTCCGTAGGGTTACCTTAAGCACACAATAAAAAGGGAACCAACCTAAAGATATGCCT
1 ATCCTTAGATCCGTAGGGCTACCTTAAGCACACAACAAAAAGGGAACCAACCTAAGGATATGCCT
* **
42007 TGGGGGCCAATATACCTACCCAAGGAT
66 TGGGGGCCAATATGCCTACCCAAGGGC
42034 ATCCTTA-AGTCCGTA
1 ATCCTTAGA-TCCGTA
42049 AGGTCTCACC
Statistics
Matches: 168, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
89 29 0.17
90 1 0.01
91 25 0.15
92 113 0.67
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (92 bp):
ATCCTTAGATCCGTAGGGCTACCTTAAGCACACAACAAAAAGGGAACCAACCTAAGGATATGCCT
TGGGGGCCAATATGCCTACCCAAGGGC
Found at i:42609 original size:16 final size:16
Alignment explanation
Indices: 42585--42617 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42575 TTCAGTGGAA
42585 AAAAGGGAGAAACTTC
1 AAAAGGGAGAAACTTC
*
42601 AAAATGGAGAAACTTC
1 AAAAGGGAGAAACTTC
42617 A
1 A
42618 GTAACCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (16 bp):
AAAAGGGAGAAACTTC
Found at i:44576 original size:23 final size:23
Alignment explanation
Indices: 44550--44617 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
44540 GACATTATAT
*
44550 GGCACTTCGATGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
44573 GGCACTGCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
44596 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
44618 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:48145 original size:16 final size:18
Alignment explanation
Indices: 48110--48146 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
48100 TGATATGAGT
*
48110 ATATGTGTTTGTATGTTG
1 ATATGTGTTTGTATGATG
48128 ATATGT-TTTGTAT-ATG
1 ATATGTGTTTGTATGATG
48144 ATA
1 ATA
48147 CATGATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (18 bp):
ATATGTGTTTGTATGATG
Done.