Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003445.1 Hibiscus syriacus cultivar Beakdansim tig00007267_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: 55113
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2649 original size:59 final size:59
Alignment explanation
Indices: 2581--2729 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 59
2571 CACCATCTGT
* * * *
2581 ACTAGTTATATTTTAGTACAGTCCCAAATATGAA-AAATAAGGTCGCGCCCACTATACGC
1 ACTAGTTATACTTTAGTACAATCCCAAATAT-AACAAATAAGGTCACGCCCACCATACGC
* * * * *
2640 ACTACTTATACTTTAGTACAATCCCGAATATAACACATAAGGTCATGCCCACCATATGC
1 ACTAGTTATACTTTAGTACAATCCCAAATATAACAAATAAGGTCACGCCCACCATACGC
* * *
2699 ACTAGTTATACTTCAGTGCAATCCCGAATAT
1 ACTAGTTATACTTTAGTACAATCCCAAATAT
2730 GCAGCCTGCT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 2 0.03
59 75 0.97
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (59 bp):
ACTAGTTATACTTTAGTACAATCCCAAATATAACAAATAAGGTCACGCCCACCATACGC
Found at i:12523 original size:85 final size:85
Alignment explanation
Indices: 12367--12526 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 85
12357 TTAAACATTG
* *
12367 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAGGG
1 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAAGA
12432 TATTATTTTAAATAGTATTT
66 TATTATTTTAAATAGTATTT
*
12452 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG-T-TTCAAGTATTTTC-ATTAGGATTTA
1 TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGATGTT--AGTA-TTTCAATTAGGATTTA
*
12514 AGATGTTATTTTA
63 AGATATTATTTTA
12527 GGAATTATCT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 1 0.01
85 61 0.90
86 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (85 bp):
TATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAAGA
TATTATTTTAAATAGTATTT
Found at i:17922 original size:6 final size:6
Alignment explanation
Indices: 17911--17967 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
17901 TTTAACACCT
17911 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA
17959 TTTGCA TTT
1 TTTGCA TTT
17968 TTATTATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTGCA
Found at i:19747 original size:6 final size:6
Alignment explanation
Indices: 19733--19771 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
19723 AATGACACCT
* *
19733 TTTGTA TTTGCA TTTAGCA TTTGTA TTTGCA TTTGCA TT
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA TT
19772 GTATGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGCA
Found at i:19757 original size:19 final size:18
Alignment explanation
Indices: 19733--19775 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
19723 AATGACACCT
19733 TTTGTATTTGCATTTAGCA
1 TTTGTATTTGCATTT-GCA
19752 TTTGTATTTGCATTTGCA
1 TTTGTATTTGCATTTGCA
19770 -TTGTAT
1 TTTGTAT
19776 GTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (18 bp):
TTTGTATTTGCATTTGCA
Found at i:24112 original size:41 final size:42
Alignment explanation
Indices: 24011--24122 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
24001 TCACTATTTG
* * * * * *
24011 TAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGCCATCCGTAAGCCTTTAGAGCAGGATGCA
* * *
24053 TAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGTAGGATG-A
1 TAAGTCCTTCGGGCCATCCGTAAGCCTTTAGAGCAGGATGCA
* *
24094 TAAGTCCTTTGGGCCATCCATAAGACCTT
1 TAAGTCCTTCGGGCCATCCGTAAG-CCTT
24123 CGGGTAGGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 20 0.36
42 36 0.64
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCGTAAGCCTTTAGAGCAGGATGCA
Found at i:24757 original size:41 final size:42
Alignment explanation
Indices: 24656--24767 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
24646 TCACAATTTA
* * * * *
24656 TAAGTCCTCCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGCT
* *
24698 TAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-T
1 TAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGCT
*
24739 TAAGTCCTTCGGGCCATCTATAAGACCTT
1 TAAGTCCTTCGGGCCATCTGTAAG-CCTT
24768 CGGGTAGGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 22 0.37
42 37 0.63
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGCT
Found at i:24980 original size:216 final size:215
Alignment explanation
Indices: 23902--25213 Score: 2056
Period size: 214 Copynumber: 6.1 Consensus size: 215
23892 GTGAAGCAAA
* * * *
23902 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACAA-GGATTTAAAAATGAAAAAATGATG---T
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCA-AATGAATTTGAAAATGAAAAAATGATGTTTT
* * * *
23963 -------TGGAATTTTTGAAAATGAAGAATGAGATTTTCAAAATTTCACTATTTGTAAGTTCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
*
24021 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* * *
24086 TAGGATGATAAGTCCTTTGGG
195 CAAGATGATAAGTCCTTCGGG
* *
24107 CCATCCATAAGACCTTCGGGTAGGATGTTTTAAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
24171 ATAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
* * *
24236 GCCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
24301 AAGAAGATAAGTCTTTCGGG
196 AAGATGATAAGTCCTTCGGG
* *
24321 CCATCAATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTAAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
24385 AGAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACGATTTGTATGTCCTTTG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
* *
24450 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGA
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
24515 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
*
24535 CCATCCATAAGACCTTCAGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AAAAAATGATGTTTT
* * *
24600 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCACGATTTGTAAGTCCTT
24665 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
*
24730 GCAAGATGTTAAGTCCTTCGGG
194 GCAAGATGATAAGTCCTTCGGG
*
24752 CCATCTATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AAAAAATGATGTTTT
* * *
24817 AAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTC
24882 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
24947 CAAGATGATAAGTCATTCGGG
195 CAAGATGATAAGTCCTTCGGG
*
24968 CCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * * *
25033 AGAAGATGGAATTTTTTATAACGAAGAATACGATTTTCAAAATTTCATGATTTGTAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
*
25098 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
25163 AGGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * * *
25183 TCATCCATAAGTCCTTCAGGCAGGATGTTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTTT
25214 TCACCAGGAT
Statistics
Matches: 1030, Mismatches: 63, Indels: 18
0.93 0.06 0.02
Matches are distributed among these distances:
204 12 0.01
205 42 0.04
207 1 0.00
214 380 0.37
215 182 0.18
216 208 0.20
217 205 0.20
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (215 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTGTAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:25113 original size:431 final size:429
Alignment explanation
Indices: 23963--25213 Score: 2047
Period size: 431 Copynumber: 2.9 Consensus size: 429
23953 AAAATGATGT
* * *
23963 TGGAATTTTTGAAAATGAAGAATGAGATTTTCAAAATTTCACTATTTGTAAGTTCTTCGGGCCAT
1 TGGAATTTTTGAAAACGAAGAATGAGATTTTCAAAATTTCACAATTTGTAAGTCCTTCGGGCCAT
* * *
24028 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGTAGGATG
66 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG
* * * *
24093 ATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTAAAATGAATTTAAAAATG-A
131 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAA
* *
24157 AAAATGATGTTTTAATAAGATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACGAT
196 AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGAT
* *
24222 TTGTAAGTCCTTCGGCCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTG
261 TTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
* * *
24287 TAAGTCTTTAGAGCAAGAAGATAAGTCTTTCGGGCCATCAATAAGACCTTCGGGTAGGATGTTTT
326 TAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCAATAAGACCTTCGGGTAGGATGTTTT
24352 CAAATGAATTTAAAAATGAAAAATGATGTTTTAAGAAGA
391 CAAATGAATTTAAAAATGAAAAATGATGTTTTAAGAAGA
* * * * *
24391 TGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACGATTTGTATGTCCTTTGGGCCAT
1 TGGAATTTTTGAAAACGAAGAATGAGATTTTCAAAATTTCACAATTTGTAAGTCCTTCGGGCCAT
*
24456 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGAAAGATG
66 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG
24521 ATAAGTCCTTCGGGCCATCCATAAGACCTTC-AGGTAGGATGTTTTCAAATGAATTTGAAAATGA
131 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGA-GTAGGATGTTTTCAAATGAATTTGAAAATG-
24585 AAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCAC
194 AAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCAC
* * *
24650 AATTTATAAGTCCTCCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
258 GATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
* *
24715 CTGTAAGCCTTTAGAGCAAGATGTTAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGT
323 CTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCAATAAGACCTTCGGGTAGGATGT
*
24780 TTTCAAATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGA
388 TTTCAAATGAATTTAAAAATG--AAAAATGATGTTTTAAGAAGA
* *
24824 TGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCAT
1 TGGAATTTTTGAAAACGAAGAATGAGATTTTCAAAATTTCACAATTTGTAAGTCCTTCGGGCCAT
*
24889 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
66 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG
*
24954 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAA
131 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAA
* * * *
25019 AAAATGATGTTTTAAGAAGATGGAATTTTTTATAACGAAGAATACGATTTTCAAAATTTCATGAT
196 AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGAT
*
25084 TTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCG
261 TTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
* * * * * *
25149 TAAGCCTTTAGAGCAGGATGATAAGTCCTTCGGGTCATCCATAAGTCCTTCAGGCAGGATGTTTT
326 TAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCAATAAGACCTTCGGGTAGGATGTTTT
25214 TCACCAGGAT
Statistics
Matches: 764, Mismatches: 52, Indels: 11
0.92 0.06 0.01
Matches are distributed among these distances:
428 177 0.23
430 55 0.07
431 273 0.36
432 55 0.07
433 203 0.27
434 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (429 bp):
TGGAATTTTTGAAAACGAAGAATGAGATTTTCAAAATTTCACAATTTGTAAGTCCTTCGGGCCAT
CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGAAAGATG
ATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGTAGGATGTTTTCAAATGAATTTGAAAATGAA
AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGAT
TTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTG
TAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCAATAAGACCTTCGGGTAGGATGTTTT
CAAATGAATTTAAAAATGAAAAATGATGTTTTAAGAAGA
Found at i:25183 original size:41 final size:42
Alignment explanation
Indices: 25087--25209 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
25077 TCATGATTTG
* * * * * *
25087 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
*
25129 TAAATCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATG-A
1 TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
* *
25170 TAAGTCCTTCGGGTCATCCATAAGTCCTTCAG-GCAGGATG
1 TAAGTCCTTCGGGTCATCCGTAAG-CCTTTAGAGCAGGATG
25210 TTTTTCACCA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 30 0.43
42 40 0.57
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (42 bp):
TAAGTCCTTCGGGTCATCCGTAAGCCTTTAGAGCAGGATGCA
Found at i:37684 original size:17 final size:17
Alignment explanation
Indices: 37662--37694 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37652 CTGAGCGTAC
37662 TTTTCAAAACAAAAAGA
1 TTTTCAAAACAAAAAGA
*
37679 TTTTCAAAACCAAAAG
1 TTTTCAAAACAAAAAG
37695 TTGATGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
TTTTCAAAACAAAAAGA
Found at i:38001 original size:17 final size:17
Alignment explanation
Indices: 37976--38009 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
37966 CTCTATCCCA
*
37976 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
37993 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
38010 TTATATCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:49033 original size:22 final size:22
Alignment explanation
Indices: 49008--49067 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
48998 AATGGTTGAG
*
49008 ATAATAGCTAGAAATAGAAACA
1 ATAATAGTTAGAAATAGAAACA
* * *
49030 ATAACAATTAGAAATAGTAACA
1 ATAATAGTTAGAAATAGAAACA
*
49052 GTAATAGTTAGAAATA
1 ATAATAGTTAGAAATA
49068 ATAACAACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (22 bp):
ATAATAGTTAGAAATAGAAACA
Found at i:49072 original size:22 final size:22
Alignment explanation
Indices: 49008--49074 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
48998 AATGGTTGAG
*
49008 ATAATAGCTAGAAATAGA-AACA
1 ATAATAGTTAGAAATA-ATAACA
* * *
49030 ATAACAATTAGAAATAGTAACA
1 ATAATAGTTAGAAATAATAACA
*
49052 GTAATAGTTAGAAATAATAACA
1 ATAATAGTTAGAAATAATAACA
49074 A
1 A
49075 CTACGATGTC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.22
Consensus pattern (22 bp):
ATAATAGTTAGAAATAATAACA
Found at i:49481 original size:32 final size:32
Alignment explanation
Indices: 49445--49546 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
49435 ACTTGTGTGT
*
49445 TGCATAGTAGTA-TCATCATTGCATTCAGATAG
1 TGCATAGAAGTACTCAT-ATTGCATTCAGATAG
* * *
49477 TGCATA-AAATATTCAATATTGCATTCAAATAG
1 TGCATAGAAGTACTC-ATATTGCATTCAGATAG
* * *
49509 TGCATAGCAG-ACTCAGTATCGCATTCAGATAA
1 TGCATAGAAGTACTCA-TATTGCATTCAGATAG
49541 TGCATA
1 TGCATA
49547 ACAAGGTTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
31 4 0.07
32 50 0.88
33 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (32 bp):
TGCATAGAAGTACTCATATTGCATTCAGATAG
Found at i:52260 original size:46 final size:46
Alignment explanation
Indices: 52208--52297 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
52198 AGAATTAACT
** * *
52208 CAAAAATATAAAGGTTGGA-CTGAACCAAAACCAACTCGAGTTGAGC
1 CAAAAATATAAAGGTT-GATCCAAACCAAAACCAACCCGAATTGAGC
*
52254 CAAAAATCTAAAGGTTGATCCAAACCAAAACCAACCCGAATTGA
1 CAAAAATATAAAGGTTGATCCAAACCAAAACCAACCCGAATTGA
52298 CATGAAACGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.17
Consensus pattern (46 bp):
CAAAAATATAAAGGTTGATCCAAACCAAAACCAACCCGAATTGAGC
Found at i:52353 original size:32 final size:31
Alignment explanation
Indices: 52305--52381 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
52295 TGACATGAAA
*
52305 CGAAACCAACCGATTCGAGATTAACCCAACC
1 CGAAACCAACCAATTCGAGATTAACCCAACC
** *
52336 CGAACACCAACCAATTCGATTTTGACCCAACC
1 CGAA-ACCAACCAATTCGAGATTAACCCAACC
*
52368 CAAAAACCAACCAA
1 C-GAAACCAACCAA
52382 CTCAGTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.10
32 33 0.85
33 2 0.05
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.13
Consensus pattern (31 bp):
CGAAACCAACCAATTCGAGATTAACCCAACC
Done.