Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001774.1 Hibiscus syriacus cultivar Beakdansim tig00003576_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: 78834
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:270 original size:49 final size:48
Alignment explanation
Indices: 133--277 Score: 186
Period size: 47 Copynumber: 3.0 Consensus size: 48
123 TAGTGACATA
* * * *
133 TTTCTGCCAAAAGGCACCGTTAGGCA-TTAACTTGCATTGGTGGCACC
1 TTTCTGCCAAAAAGCACCATTATGCATTTAACTTGCATTAGTGGCACC
* ** *
180 TTTCTACCAAAAAGCGTCATT-TGCATTTAACTTGTATTAGTGGCACC
1 TTTCTGCCAAAAAGCACCATTATGCATTTAACTTGCATTAGTGGCACC
*
227 TTTCTGCCAAAAATGAACCATTATGCATTTAACTTGCATTAGTGGCACC
1 TTTCTGCCAAAAA-GCACCATTATGCATTTAACTTGCATTAGTGGCACC
276 TT
1 TT
278 CATTCTTCCA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
46 3 0.04
47 47 0.57
48 5 0.06
49 27 0.33
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (48 bp):
TTTCTGCCAAAAAGCACCATTATGCATTTAACTTGCATTAGTGGCACC
Found at i:3399 original size:31 final size:31
Alignment explanation
Indices: 3361--3428 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
3351 TTGTTTTCAA
3361 GCTTATGTGATGATTAAAATCACCTAAAAAT
1 GCTTATGTGATGATTAAAATCACCTAAAAAT
3392 GCTTATGTGATGATTAAAATCACCTAAAAAT
1 GCTTATGTGATGATTAAAATCACCTAAAAAT
3423 GCTTAT
1 GCTTAT
3429 ATTTGATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (31 bp):
GCTTATGTGATGATTAAAATCACCTAAAAAT
Found at i:5803 original size:17 final size:17
Alignment explanation
Indices: 5781--5891 Score: 111
Period size: 17 Copynumber: 6.5 Consensus size: 17
5771 AAAATGAATC
*
5781 TAAAAGAAATAGTACAG
1 TAAAAGAAATAGTACAA
5798 TAAAAGTAGAA-A-TACAA
1 TAAAAG-A-AATAGTACAA
*
5815 TAAAATAAATAGTACAA
1 TAAAAGAAATAGTACAA
* *
5832 CAAAAGAAATAGTACAG
1 TAAAAGAAATAGTACAA
* * *
5849 TAAAAGAAATAATATAG
1 TAAAAGAAATAGTACAA
5866 TAAAAGAAATAAGTACAA
1 TAAAAGAAAT-AGTACAA
5884 T-AAAGAAA
1 TAAAAGAAA
5892 CAATACAATG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
15 2 0.03
16 2 0.03
17 65 0.83
18 7 0.09
19 2 0.03
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (17 bp):
TAAAAGAAATAGTACAA
Found at i:5870 original size:51 final size:51
Alignment explanation
Indices: 5782--5891 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
5772 AAATGAATCT
* *
5782 AAAAGAAATAGTACAGTAAAAGTAGAAATACAATAAAATAAAT-AGTACAA
1 AAAAGAAATAGTACAGTAAAAGTAAAAATACAATAAAAGAAATAAGTACAA
* *
5832 CAAAAGAAATAGTACAGTAAAAG-AAATAATATAGTAAAAGAAATAAGTACAA
1 -AAAAGAAATAGTACAGTAAAAGTAAA-AATACAATAAAAGAAATAAGTACAA
*
5884 TAAAGAAA
1 AAAAGAAA
5892 CAATACAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.04
51 43 0.83
52 7 0.13
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.17
Consensus pattern (51 bp):
AAAAGAAATAGTACAGTAAAAGTAAAAATACAATAAAAGAAATAAGTACAA
Found at i:5900 original size:16 final size:16
Alignment explanation
Indices: 5868--5919 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
5858 TAATATAGTA
*
5868 AAAGAAATAAGTACAAT
1 AAAGAAACAA-TACAAT
5885 AAAGAAACAATACAAT
1 AAAGAAACAATACAAT
* *
5901 GAAGGGAACAATAC-AT
1 -AAAGAAACAATACAAT
5917 AAA
1 AAA
5920 TGAGGAACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 8 0.27
17 20 0.67
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAGAAACAATACAAT
Found at i:10662 original size:33 final size:33
Alignment explanation
Indices: 10584--10668 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
10574 TTTTCACCCT
10584 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
**
10618 AAACCATACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
10651 AAACCCGACCCGAGCCCG
1 AAACCCGACCCGA-CCCG
10669 GAATTTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 37 0.80
34 9 0.20
ACGTcount: A:0.41, C:0.38, G:0.11, T:0.11
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:12128 original size:20 final size:20
Alignment explanation
Indices: 12105--12168 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
12095 TAGTATTTAG
12105 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
12125 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
12145 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
12164 TTAAA
1 ATAAA
12169 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:12138 original size:19 final size:20
Alignment explanation
Indices: 12114--12163 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12104 GATAAATTTA
*
12114 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
12133 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
12154 TT-ATAATTTT
1 TTAATAATTTT
12164 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:12166 original size:31 final size:30
Alignment explanation
Indices: 12081--12167 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
12071 TTTGATAATA
* *
12081 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
12112 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
12143 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
12168 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:12938 original size:31 final size:31
Alignment explanation
Indices: 12886--12946 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12876 GAACACTTAT
* *
12886 TAAATTTATTAAAAGATTATAAAATTATTAA
1 TAAATTTATTAAAAGACTATAAAATAATTAA
*
12917 TAAATTTATCT-AAATACTATAAAATAATTA
1 TAAATTTAT-TAAAAGACTATAAAATAATTA
12947 TTATATTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAATTTATTAAAAGACTATAAAATAATTAA
Found at i:14960 original size:21 final size:21
Alignment explanation
Indices: 14936--14990 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
14926 TTATAAGGAC
14936 AGTATTGATACTCTAAACACG
1 AGTATTGATACTCTAAACACG
14957 AGTATTGATACTCTAAACACG
1 AGTATTGATACTCTAAACACG
14978 AGTATTGATACTC
1 AGTATTGATACTC
14991 CCTATTATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (21 bp):
AGTATTGATACTCTAAACACG
Found at i:30832 original size:22 final size:22
Alignment explanation
Indices: 30801--30855 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
30791 GTGAACCTAG
*
30801 AACCCGAACCTAGGTAGAGCCT
1 AACCCAAACCTAGGTAGAGCCT
30823 AACCCAAACCTAGGTAGAGCCT
1 AACCCAAACCTAGGTAGAGCCT
30845 AACCCAAACCT
1 AACCCAAACCT
30856 TAGGAATCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.35, G:0.16, T:0.13
Consensus pattern (22 bp):
AACCCAAACCTAGGTAGAGCCT
Found at i:32067 original size:21 final size:21
Alignment explanation
Indices: 32041--32082 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32031 CCATAATGGG
*
32041 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
32062 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
32083 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:32227 original size:19 final size:19
Alignment explanation
Indices: 32189--32254 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
32179 AGCCTTGGGG
* * *
32189 TACTGTTCAAACAGTGATT
1 TACTATTCAAATAGTAATT
*
32208 TACTATTCAAATATTAATT
1 TACTATTCAAATAGTAATT
* * *
32227 TATTGTTCAAATAGTAAAT
1 TACTATTCAAATAGTAATT
32246 TACTATTCA
1 TACTATTCA
32255 TAAAAACATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (19 bp):
TACTATTCAAATAGTAATT
Found at i:32366 original size:30 final size:30
Alignment explanation
Indices: 32319--32391 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
32309 AATTTTTGAA
32319 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
* * *
32348 TAAATTTAATTCAAGTCCAAATTCGTTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
32378 TAAATTCAATTCAA
1 TAAATTCAATTCAA
32392 CATTTTGCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 10 0.26
30 29 0.74
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACATTTTG
Found at i:34376 original size:21 final size:22
Alignment explanation
Indices: 34331--34377 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
34321 ACCTAGTTTG
*
34331 AGAAAACTTAACAAGAGATACA
1 AGAAAACTTAACAAGAGACACA
* *
34353 AGAAAACTTGAGAA-AGACACA
1 AGAAAACTTAACAAGAGACACA
34374 AGAA
1 AGAA
34378 GATATGCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.11
Consensus pattern (22 bp):
AGAAAACTTAACAAGAGACACA
Found at i:41168 original size:11 final size:11
Alignment explanation
Indices: 41152--41176 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41142 AAAAGGATAA
41152 AAAGAAAAAAG
1 AAAGAAAAAAG
41163 AAAGAAAAAAG
1 AAAGAAAAAAG
41174 AAA
1 AAA
41177 AAAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:41188 original size:4 final size:4
Alignment explanation
Indices: 41181--41207 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41171 AAGAAAAAAG
41181 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
41208 GGGGGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:45019 original size:2 final size:2
Alignment explanation
Indices: 45012--45055 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
45002 AGGAGCTTTC
*
45012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45054 AT
1 AT
45056 GCATGTAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45078 original size:4 final size:4
Alignment explanation
Indices: 45053--45425 Score: 705
Period size: 4 Copynumber: 93.8 Consensus size: 4
45043 TATATATGTA
* * *
45053 TATG CATG TAGG TATA TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45101 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45149 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45197 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45245 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45293 TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45339 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
45387 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
45426 ATATAAAATC
Statistics
Matches: 361, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
2 2 0.01
4 359 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:48093 original size:77 final size:77
Alignment explanation
Indices: 48007--48162 Score: 222
Period size: 77 Copynumber: 2.0 Consensus size: 77
47997 TGGAGTATGA
* * * * *
48007 TGGTTATCGATCGATTTTATTTAATGCATATGTTGGATTTTTGTATCAGTACCTTTGTGTACTTT
1 TGGTTATCGAACAATTTTATTTAATGCATATGTTGCATTTTTGTATCAATACCCTTGTGTACTTT
48072 CGACACTATGTG
66 CGACACTATGTG
* *
48084 TGGTTATCGAACAATTTTGTTTCATGCATATGTTGCATTTTTGTATCAATACCCTTGTGTACTTT
1 TGGTTATCGAACAATTTTATTTAATGCATATGTTGCATTTTTGTATCAATACCCTTGTGTACTTT
* * *
48149 TGGCACTATTTG
66 CGACACTATGTG
48161 TG
1 TG
48163 CATGCATGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (77 bp):
TGGTTATCGAACAATTTTATTTAATGCATATGTTGCATTTTTGTATCAATACCCTTGTGTACTTT
CGACACTATGTG
Found at i:58919 original size:20 final size:20
Alignment explanation
Indices: 58896--58949 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 20
58886 TCTTTATTCC
58896 TTTTTTTTAAAAATATTTTA
1 TTTTTTTTAAAAATATTTTA
58916 TTTTTTTT-AAAATATTTTA
1 TTTTTTTTAAAAATATTTTA
58935 TTTTTTTTAAAAATA
1 TTTTTTTTAAAAATA
58950 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTTAAAAATATTTTA
Found at i:65612 original size:3 final size:3
Alignment explanation
Indices: 65604--65720 Score: 119
Period size: 3 Copynumber: 39.0 Consensus size: 3
65594 ATTTTCATTT
* * *
65604 TTA TTA TTA TTA TAA TTA TT- TTT TTA TTA TTA TTAA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
** * * * * **
65649 TTA TTA AAA TTA TTA TTA TTA ATA ATA ATA ATA TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65697 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
65721 ATAATAAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.02
3 93 0.96
4 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:65629 original size:23 final size:24
Alignment explanation
Indices: 65601--65647 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
65591 TTCATTTTCA
65601 TTTTTATTATTATT-ATAATTATT
1 TTTTTATTATTATTAATAATTATT
65624 TTTTTATTATTATTAATAATTATT
1 TTTTTATTATTATTAATAATTATT
65648 ATTATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTATTATTATTAATAATTATT
Found at i:67076 original size:19 final size:20
Alignment explanation
Indices: 67049--67099 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
67039 ATGTATTTTA
* *
67049 TGCACCGATGCACAG-GTAG
1 TGCATCGATGCACAGTGCAG
* *
67068 TGCATCGATACACTGTGCAG
1 TGCATCGATGCACAGTGCAG
67088 TGCATCGATGCA
1 TGCATCGATGCA
67100 TACCTTCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAGTGCAG
Found at i:67698 original size:31 final size:31
Alignment explanation
Indices: 67660--67724 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
67650 AGAGTCGAGG
*
67660 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
67691 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
67722 GTT
1 GTT
67725 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:67811 original size:29 final size:30
Alignment explanation
Indices: 67710--67808 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
67700 GGTTCTTCGG
*
67710 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
67740 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
67770 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
67799 GACCTCTGGA
1 GACCTCTGGA
67809 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 18 0.28
30 47 0.72
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:68081 original size:2 final size:2
Alignment explanation
Indices: 68074--68104 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
68064 GTATGCGTGG
68074 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68105 GAAAGGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69306 original size:64 final size:64
Alignment explanation
Indices: 69160--69315 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 64
69150 GAAGGTGTAT
* *** * * *
69160 CGATGCACAAGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGTAATTGGTGCAT
1 CGATGCACAGGTAGTGCATCGATGCACTCCAATAATCAAAAAACATCGAATGTAATTGATGCAC
* * * *
69224 CGATGCATAAGGCA-TGCATCGATGCA-TCCCAATAAT-AAACAAACATCGAATGTATTTTATGC
1 CGATGCA-CAGGTAGTGCATCGATGCACT-CCAATAATCAAA-AAACATCGAATGTAATTGATGC
69286 AC
63 AC
*
69288 CGATGCACAGGTAGTGCATCGATACACT
1 CGATGCACAGGTAGTGCATCGATGCACT
69316 GTGCAGTGCA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 7 0.10
64 62 0.85
65 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
CGATGCACAGGTAGTGCATCGATGCACTCCAATAATCAAAAAACATCGAATGTAATTGATGCAC
Found at i:69310 original size:19 final size:20
Alignment explanation
Indices: 69283--69333 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
69273 ATGTATTTTA
* *
69283 TGCACCGATGCACAG-GTAG
1 TGCATCGATGCACAGTGCAG
* *
69302 TGCATCGATACACTGTGCAG
1 TGCATCGATGCACAGTGCAG
69322 TGCATCGATGCA
1 TGCATCGATGCA
69334 TACCTTCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAGTGCAG
Found at i:69951 original size:31 final size:31
Alignment explanation
Indices: 69893--69970 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
69883 AGAGTCGAGG
*
69893 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
* * *
69924 GTTTACCTAGGT-TCTTCGGGACCTATGGATA
1 GTTTACCTAGGTCT-TTCGAGACATATGGACA
*
69955 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
69971 ATGACCTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGACA
Found at i:70038 original size:29 final size:30
Alignment explanation
Indices: 69943--70044 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
69933 GGTTCTTCGG
*
69943 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
69973 GACCTCTTGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
70003 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
70032 GACCTCTGGATAG
1 GACCTCTGGATAG
70045 GTCCTTCGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 21 0.32
30 44 0.68
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:70315 original size:2 final size:2
Alignment explanation
Indices: 70308--70338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
70298 GTATGCGTGG
70308 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70339 GAAAGGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71241 original size:18 final size:18
Alignment explanation
Indices: 71218--71253 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
71208 AATGGTATTT
*
71218 ATACCCTTACCAAAACGA
1 ATACCCTCACCAAAACGA
71236 ATACCCTCACCAAAACGA
1 ATACCCTCACCAAAACGA
71254 CGTCGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.36, G:0.06, T:0.14
Consensus pattern (18 bp):
ATACCCTCACCAAAACGA
Found at i:76087 original size:8 final size:8
Alignment explanation
Indices: 76012--76080 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
76002 TTCATTCATC
76012 AGAAAAAA
1 AGAAAAAA
76020 AGAAAAAA
1 AGAAAAAA
76028 AG--AAAA
1 AGAAAAAA
76034 AGAAAAAA
1 AGAAAAAA
**
76042 TAGATGAAA
1 -AGAAAAAA
*
76051 AGAGAAAA
1 AGAAAAAA
76059 AGAAAAAA
1 AGAAAAAA
76067 AGAAAAAA
1 AGAAAAAA
76075 A-AAAAA
1 AGAAAAA
76081 GAAAAAATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
6 6 0.11
7 5 0.09
8 36 0.68
9 6 0.11
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AGAAAAAA
Found at i:78574 original size:74 final size:75
Alignment explanation
Indices: 78399--78574 Score: 193
Period size: 74 Copynumber: 2.4 Consensus size: 75
78389 CAACAAGAAG
* *
78399 CAAATGTTGAGGCATGTTGAAAGA-CCATTTCAATCAGAAATTGGAATATTGATTCATTTTAAAC
1 CAAATGTTGGGGCATGTTG-AAGACCCATTTCAATCAGAAATTGGAATATTGATGCATTTTAAAC
**
78463 GTTTGTATCAA
65 GTTCATATCAA
* * * * *
78474 CAAATGCTAGGGAATG-TGAA-AGCCCATTTCAATCA-AAATTAGGAATTTTGAATGCA-TTTGA
1 CAAATGTTGGGGCATGTTGAAGA-CCCATTTCAATCAGAAATT-GGAATATTG-ATGCATTTTAA
78535 ACGTTCATATC-A
63 ACGTTCATATCAA
78547 CAAATGTTGGGGCATGTTGAAGACCCAT
1 CAAATGTTGGGGCATGTTGAAGACCCAT
78575 ATCTTATGGA
Statistics
Matches: 83, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
72 1 0.01
73 21 0.25
74 44 0.53
75 17 0.20
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (75 bp):
CAAATGTTGGGGCATGTTGAAGACCCATTTCAATCAGAAATTGGAATATTGATGCATTTTAAACG
TTCATATCAA
Done.