Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004676.1 Hibiscus syriacus cultivar Beakdansim tig00010483_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: 69816
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:584 original size:25 final size:24
Alignment explanation
Indices: 542--588 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
532 AAATTATATC
542 TTTAATTTAAATTATTAATTTTGA
1 TTTAATTTAAATTATTAATTTTGA
* *
566 TTTATTTTAATATTTTTAATTTT
1 TTTAATTTAA-ATTATTAATTTT
589 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTAATTTAAATTATTAATTTTGA
Found at i:4738 original size:40 final size:41
Alignment explanation
Indices: 4673--4836 Score: 126
Period size: 40 Copynumber: 4.2 Consensus size: 41
4663 AATCATAAAA
* * *
4673 CAATAATTCACCATTCGACTCAATTCGATCATGATA-CATG
1 CAATAATTCACAATTCGACTCAATTCAATCATGACAGCATG
* * * * * *
4713 CAATAATTCACAATTTGATTTAATTCAATCATGGCAGTATT
1 CAATAATTCACAATTCGACTCAATTCAATCATGACAGCATG
*
4754 CAATAATTCACAA-T----TCAATTCAATCATGACAACATG
1 CAATAATTCACAATTCGACTCAATTCAATCATGACAGCATG
* * * * ** *
4790 AAATAATTCATAATTCAACTTAATTTGATCATGGCAGCATG
1 CAATAATTCACAATTCGACTCAATTCAATCATGACAGCATG
4831 C-ATAAT
1 CAATAAT
4837 CCATAATTGA
Statistics
Matches: 96, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
36 28 0.29
37 1 0.01
40 35 0.36
41 32 0.33
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (41 bp):
CAATAATTCACAATTCGACTCAATTCAATCATGACAGCATG
Found at i:5054 original size:41 final size:40
Alignment explanation
Indices: 4996--5087 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 40
4986 GCTTTTCTTT
* * * *
4996 CAATTCAATTTGGTCATGGCAACATGCATTTATTCACAAAC
1 CAATTCAATTAGATCATGACAACATGCATTAATTCAC-AAC
* * *
5037 CAATTCAATTAGATCATGATAACATGTATTAATTCACATC
1 CAATTCAATTAGATCATGACAACATGCATTAATTCACAAC
*
5077 CAATACAATTA
1 CAATTCAATTA
5088 AAATCAACGC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 12 0.28
41 31 0.72
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (40 bp):
CAATTCAATTAGATCATGACAACATGCATTAATTCACAAC
Found at i:12883 original size:41 final size:41
Alignment explanation
Indices: 12838--13066 Score: 243
Period size: 41 Copynumber: 5.6 Consensus size: 41
12828 TTCGATCTTG
* *
12838 GCAACATGCACTAATTCACAATTCGATTCAGTTCAATCATA
1 GCAACATGCAATAATTCACAATTCGATTCAATTCAATCATA
* *
12879 GCAACATGCAATAATTCACCATTCGACTCAATTCGAA-CATGA
1 GCAACATGCAATAATTCACAATTCGATTCAATTC-AATCAT-A
* *
12921 G-AGCATGCAATAATTCACAATTCGATTCAATTCAATCATG
1 GCAACATGCAATAATTCACAATTCGATTCAATTCAATCATA
*
12961 GCAACATGCAATAATTCACAATTCGATTCAATTCAATCATG
1 GCAACATGCAATAATTCACAATTCGATTCAATTCAATCATA
* ** * *
13002 GTTCCACA--CAATAATTCACAATTTAACTT-AATTCGATCATG
1 G--CAACATGCAATAATTCACAATTCGA-TTCAATTCAATCATA
* * *
13043 GCAGCATGCAATAATCCATAATTC
1 GCAACATGCAATAATTCACAATTC
13067 AATCATGGAA
Statistics
Matches: 161, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.02
40 3 0.02
41 145 0.90
42 6 0.04
43 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (41 bp):
GCAACATGCAATAATTCACAATTCGATTCAATTCAATCATA
Found at i:13035 original size:123 final size:122
Alignment explanation
Indices: 12836--13066 Score: 313
Period size: 123 Copynumber: 1.9 Consensus size: 122
12826 AGTTCGATCT
* * *
12836 TGGCAACATGCACTAATTCACAATTCGATTCAGTTCAATCATAGCAACATGCAATAATTCACCAT
1 TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCATAGCAACA-GCAATAATTCACAAT
* *
12901 TCGACTCAATTCGAACATGAG-AGCATGCAATAATTCACAATTCGATTCAATTCAATCA
65 TCAACTCAATTCGAACATG-GCAGCATGCAATAATCCACAATTCGATTCAATTCAATCA
* *
12959 TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCATGGTTCCACA-CAATAATTCACAA
1 TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCATAG--CAACAGCAATAATTCACAA
* * * *
13023 TTTAACTTAATTCGATCATGGCAGCATGCAATAATCCATAATTC
64 TTCAACTCAATTCGAACATGGCAGCATGCAATAATCCACAATTC
13067 AATCATGGAA
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
122 1 0.01
123 89 0.95
125 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (122 bp):
TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCATAGCAACAGCAATAATTCACAATT
CAACTCAATTCGAACATGGCAGCATGCAATAATCCACAATTCGATTCAATTCAATCA
Found at i:21566 original size:20 final size:19
Alignment explanation
Indices: 21536--21586 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
21526 AGGCACTTGG
21536 AGAGAAAGAAGAAAAAATAA
1 AGAG-AAGAAGAAAAAATAA
* * *
21556 ATAGGAAGAAGGAAAAATGA
1 AGA-GAAGAAGAAAAAATAA
21576 AGAGAAGAAGA
1 AGAGAAGAAGA
21587 GAAGAAGAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (19 bp):
AGAGAAGAAGAAAAAATAA
Found at i:22715 original size:22 final size:22
Alignment explanation
Indices: 22687--22731 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22677 GCTCATGCTC
22687 ATATACCAACACGATAATAATA
1 ATATACCAACACGATAATAATA
22709 ATATACCAACACGATAATAATA
1 ATATACCAACACGATAATAATA
22731 A
1 A
22732 GGATGAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (22 bp):
ATATACCAACACGATAATAATA
Found at i:24689 original size:20 final size:20
Alignment explanation
Indices: 24664--24702 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
24654 AGAAAATTTT
24664 TAGGTTAACCATTTTAATGA
1 TAGGTTAACCATTTTAATGA
*
24684 TAGGTTAACTATTTTAATG
1 TAGGTTAACCATTTTAATG
24703 GTCCCGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGGTTAACCATTTTAATGA
Found at i:26652 original size:37 final size:37
Alignment explanation
Indices: 26576--26652 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
26566 TTTTTATATT
*
26576 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
26613 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
26650 TTT
1 TTT
26653 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:31814 original size:56 final size:55
Alignment explanation
Indices: 31738--31847 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 55
31728 AAAATGAACC
* *
31738 AAAGATTCACAAAGTTATCATTTTCTTAGCCAAGAAAACACAGATATGAATACAT
1 AAAGATTAACAAAGTAATCATTTTCTTAGCCAAGAAAACACAGATATGAATACAT
* *
31793 AAAGAATTAACAAAGTAATCATTTTCTTATCCAAGAAAACACAGATTTGAATACA
1 AAAG-ATTAACAAAGTAATCATTTTCTTAGCCAAGAAAACACAGATATGAATACA
31848 GAAAAAAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 4 0.08
56 46 0.92
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (55 bp):
AAAGATTAACAAAGTAATCATTTTCTTAGCCAAGAAAACACAGATATGAATACAT
Found at i:34078 original size:18 final size:18
Alignment explanation
Indices: 34057--34104 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
34047 ATACATTTTT
34057 GGTATCGATACTCATAGG
1 GGTATCGATACTCATAGG
34075 GGTATCGATACTCATAGG
1 GGTATCGATACTCATAGG
*
34093 GGTATCAATACT
1 GGTATCGATACT
34105 TAACCCTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (18 bp):
GGTATCGATACTCATAGG
Found at i:37322 original size:12 final size:11
Alignment explanation
Indices: 37283--37328 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
37273 GCATCGATGC
37283 ACTGCTACAGT
1 ACTGCTACAGT
*
37294 AAC-GCTTCAGT
1 -ACTGCTACAGT
37305 ACTGCTACAGT
1 ACTGCTACAGT
37316 GACTGCTACAGT
1 -ACTGCTACAGT
37328 A
1 A
37329 ATTTCAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 2 0.07
11 15 0.50
12 13 0.43
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (11 bp):
ACTGCTACAGT
Found at i:37705 original size:46 final size:45
Alignment explanation
Indices: 37653--37777 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
37643 ATCCAATATT
*
37653 TTACCATTTATTTCCGTAAGCTCGTAAGCTTATTTTACCAAAATAA
1 TTACCATTTA-TTCCATAAGCTCGTAAGCTTATTTTACCAAAATAA
* * * * *
37699 TTACCATTTGTCCCATAAGCTCGTAAGCTTATTTTTACCCATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTTACCAAAATAA
* * *
37745 TTGCCA-ATATTCCATAAGCTCGTAAGATTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
37778 GCATGCTTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 3 0.04
45 39 0.58
46 25 0.37
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAA
Found at i:37937 original size:40 final size:40
Alignment explanation
Indices: 37882--37963 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
37872 ACCGTAGTGC
*
37882 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
37922 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
37962 TA
1 TA
37964 TGAACCTACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:41594 original size:21 final size:20
Alignment explanation
Indices: 41568--41607 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
41558 TCTGGGTTCG
41568 AATATCGATACTAGAATGAAC
1 AATATCGATACTAG-ATGAAC
41589 AATATCGATACTAGATGAA
1 AATATCGATACTAGATGAA
41608 TTAGGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (20 bp):
AATATCGATACTAGATGAAC
Found at i:42077 original size:16 final size:16
Alignment explanation
Indices: 42056--42088 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42046 TAATAAATAG
42056 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42072 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42088 A
1 A
42089 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:42169 original size:10 final size:10
Alignment explanation
Indices: 42154--42228 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
42144 CATTTAATAA
42154 ATAAACGAAC
1 ATAAACGAAC
42164 ATAAACGAAC
1 ATAAACGAAC
42174 ----ACGAAC
1 ATAAACGAAC
42180 ATAAACGAAC
1 ATAAACGAAC
** *
42190 ACGAAC-ATAA
1 ATAAACGA-AC
42200 ATGAACACGAAC
1 AT-AA-ACGAAC
42212 ATAAACGAAC
1 ATAAACGAAC
42222 ATAAACG
1 ATAAACG
42229 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:42179 original size:16 final size:16
Alignment explanation
Indices: 42158--42222 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
42148 TAATAAATAA
42158 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42174 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
42190 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
42206 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42222 A
1 A
42223 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:42997 original size:24 final size:24
Alignment explanation
Indices: 42970--43030 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
42960 TAAATGAATG
*
42970 AACATAAACGAACATAATCGAACA
1 AACATAAACGAACATAACCGAACA
*
42994 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACA
*
43018 AACATAACCGAAC
1 AACATAAACGAAC
43031 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.56, C:0.25, G:0.10, T:0.10
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACA
Found at i:43017 original size:14 final size:14
Alignment explanation
Indices: 42976--43031 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
42966 AATGAACATA
*
42976 AACGAACATAATCG
1 AACGAACATAACCG
*
42990 AACAAACAT-A---
1 AACGAACATAACCG
43000 AACGAACATAACCG
1 AACGAACATAACCG
43014 AACGAACATAACCG
1 AACGAACATAACCG
43028 AACG
1 AACG
43032 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:43651 original size:39 final size:40
Alignment explanation
Indices: 43608--43695 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
43598 AATTAAACTT
* * *
43608 AAAATATTATC-TTTTTCATAATATTTTAAGTTATATCCG
1 AAAATATTATCATTTTTCATAATAATTTAAGTTATAACCA
* *
43647 AAAATATTA-CATTTTTCCTAATAATTTAAGTTATAACTA
1 AAAATATTATCATTTTTCATAATAATTTAAGTTATAACCA
43686 AAAATATTAT
1 AAAATATTAT
43696 ATATAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.02
39 41 0.98
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (40 bp):
AAAATATTATCATTTTTCATAATAATTTAAGTTATAACCA
Found at i:44003 original size:22 final size:22
Alignment explanation
Indices: 43978--44020 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43968 TGGTATTTTC
43978 TTTTAAATAATTTAATTTTTAT
1 TTTTAAATAATTTAATTTTTAT
*
44000 TTTTAATTAATTTAATTTTTA
1 TTTTAAATAATTTAATTTTTA
44021 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAAATAATTTAATTTTTAT
Found at i:50024 original size:28 final size:28
Alignment explanation
Indices: 49967--50068 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
49957 GAAAAGTCTG
* * *
49967 AATAGTTTAGGTACCTATTTTG-GCATAA
1 AATACTTTAGATACCTATTTTGACCA-AA
49995 AATACTTTAGATACCTATTTTGACCAAAAAA
1 AATACTTTAGATACCTATTTTGACC---AAA
* ** *
50026 AATAATTTTAGATATTTATTTTGATCAAAA
1 AAT-ACTTTAGATACCTATTTTGA-CCAAA
50056 AATACTTTAGATA
1 AATACTTTAGATA
50069 ATTGAATGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
28 20 0.33
29 10 0.17
30 6 0.10
31 5 0.08
32 18 0.30
33 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (28 bp):
AATACTTTAGATACCTATTTTGACCAAA
Found at i:58095 original size:20 final size:19
Alignment explanation
Indices: 58070--58123 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
58060 GCGAAATAAA
58070 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
58090 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
58110 AATCGCAACGCGAT
1 AATCGCAACGCGAT
58124 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:58134 original size:21 final size:20
Alignment explanation
Indices: 58110--58222 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
58100 CAGTTCCCAG
58110 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
58130 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
58151 AATTCGCATTGCGATTTTTCAT
1 AA-TCGCAACGCGA-TTATGAA
*
58173 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
* *
58193 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
58213 TATCGCAACG
1 AATCGCAACG
58223 AGTATCCGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 34 0.48
21 32 0.45
22 2 0.03
23 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:58198 original size:20 final size:20
Alignment explanation
Indices: 58173--58465 Score: 243
Period size: 20 Copynumber: 14.5 Consensus size: 20
58163 GATTTTTCAT
* *
58173 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
*
58193 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
58212 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* * *
58234 AATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACGT-A
* *
58255 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
58275 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
58296 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
58316 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
58336 AATCGCAACGCGTATATGTA
1 AATCGCAACGCGAATACGTA
* *
58356 AATCGCAACGAGATTACGTA
1 AATCGCAACGCGAATACGTA
* * *
58376 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
58396 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
58416 AATCGCAACACGAACACGTA
1 AATCGCAACGCGAATACGTA
*
58436 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
58456 AATCGTAACG
1 AATCGCAACG
58466 AGATTCTGAC
Statistics
Matches: 225, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.02
20 161 0.72
21 58 0.26
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:58350 original size:40 final size:40
Alignment explanation
Indices: 58214--58465 Score: 301
Period size: 40 Copynumber: 6.2 Consensus size: 40
58204 GATTCTGACT
* * *
58214 ATCGCAACGAGTATCCGTAAAATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATACGT-AA
*
58256 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
*
58297 ATCGCAACGCGTATCCGTAAATCGTAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
** *
58337 ATCGCAACGCGTATATGTAAATCGCAACGAGATTACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * *
58377 ATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * * *
58417 ATCGCAACACG-AACACGTAAATCGCAATGCGAAT-CTGTAA
1 ATCGCAACGCGTATC-CGTAAATCGCAACGAGAATAC-GTAA
*
58457 ATCGTAACG
1 ATCGCAACG
58466 AGATTCTGAC
Statistics
Matches: 187, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 3 0.02
40 111 0.59
41 56 0.30
42 17 0.09
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:58530 original size:19 final size:17
Alignment explanation
Indices: 58496--58544 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
58486 CTGAATTTCA
*
58496 AATTCGCAACTCGTTTCT
1 AATTCGCAACACGTTT-T
*
58514 GAATTCGCAACAGGTTTT
1 -AATTCGCAACACGTTTT
58532 AATTTCGCAACAC
1 AA-TTCGCAACAC
58545 AAATGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.08
18 10 0.38
19 14 0.54
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTCGCAACACGTTTT
Found at i:59836 original size:54 final size:51
Alignment explanation
Indices: 59775--59878 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
59765 GCTCATAAGC
59775 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTA
*** * * *
59829 TTATTTTTTTTAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
59879 TGCATGGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 23 0.52
53 2 0.05
54 19 0.43
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (51 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTA
Found at i:62540 original size:24 final size:24
Alignment explanation
Indices: 62513--62566 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
62503 GTATTCGAAA
62513 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
62537 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
62561 TTTGAT
1 TTTGAT
62567 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:65116 original size:19 final size:19
Alignment explanation
Indices: 65092--65204 Score: 111
Period size: 19 Copynumber: 6.4 Consensus size: 19
65082 GCAACGAGAG
65092 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
65111 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
* *
65125 AATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
65145 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
65164 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
65178 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
65197 AATCGCAA
1 AATCGCAA
65205 CGAGGGAATC
Statistics
Matches: 76, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 3 0.04
17 5 0.07
18 1 0.01
19 32 0.42
20 12 0.16
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:65116 original size:33 final size:34
Alignment explanation
Indices: 65059--65152 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
65049 CTTAATGTCT
* ** *
65059 ATCGCAACGCGGAAATTACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
* *
65093 ATCGCAATGC-GAAATGAAAATCGCAACGTGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
**
65126 ATCGCAACGCGGAAATGACTATCGCAA
1 ATCGCAACGCGGAAATGAAAATCGCAA
65153 TGCGAAATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAAA
Found at i:65126 original size:14 final size:14
Alignment explanation
Indices: 65107--65134 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
65097 CAATGCGAAA
65107 TGAAAATCGCAACG
1 TGAAAATCGCAACG
65121 TGAAAATCGCAACG
1 TGAAAATCGCAACG
65135 CGGAAATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:65141 original size:14 final size:14
Alignment explanation
Indices: 65108--65141 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
65098 AATGCGAAAT
*
65108 GAAAATCGCAACGT
1 GAAAATCGCAACGC
65122 GAAAATCGCAACGC
1 GAAAATCGCAACGC
*
65136 GGAAAT
1 GAAAAT
65142 GACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:65150 original size:53 final size:52
Alignment explanation
Indices: 65092--65204 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 52
65082 GCAACGAGAG
* *
65092 AATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGCAACGCGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAATGAA
* * *
65145 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
65197 AATCGCAA
1 AATCGCAA
65205 CGAGGGAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
52 14 0.26
53 40 0.74
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
Found at i:65185 original size:33 final size:33
Alignment explanation
Indices: 65146--65239 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
65136 GGAAATGACT
65146 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
65179 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
65212 ATCACAATGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
65240 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:65421 original size:14 final size:14
Alignment explanation
Indices: 65402--65438 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
65392 CATCAATTAA
65402 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
65416 ACAAATCATCTTTT
1 ACAAATCAACTTTT
65430 ACAAATCAA
1 ACAAATCAA
65439 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:68896 original size:20 final size:20
Alignment explanation
Indices: 68871--68952 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
68861 TTTTGGTTGA
68871 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
68891 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
68910 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
68930 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
68950 AAT
1 AAT
68953 CGCAATGCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.32
20 36 0.68
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:68913 original size:40 final size:39
Alignment explanation
Indices: 68869--68945 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
68859 TCTTTTGGTT
68869 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAACGCG
** *
68909 GAAATGACTATCGCAACGCGAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACG
68946 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 16 0.47
40 18 0.53
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGCG
Found at i:68933 original size:19 final size:19
Alignment explanation
Indices: 68869--68981 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
68859 TCTTTTGGTT
*
68869 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
68888 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
68908 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
68928 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
68945 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
*
68961 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
68980 GA
1 GA
68982 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 31 0.39
20 31 0.39
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:69010 original size:19 final size:19
Alignment explanation
Indices: 68977--69021 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
68967 AAAATCGCAA
**
68977 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
68996 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
69015 TGCGATT
1 TGCGATT
69022 CTCTCATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:69073 original size:20 final size:20
Alignment explanation
Indices: 69048--69085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
69038 CATTTCTCTC
69048 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
69068 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
69086 AATATTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:69567 original size:20 final size:20
Alignment explanation
Indices: 69542--69713 Score: 211
Period size: 20 Copynumber: 8.6 Consensus size: 20
69532 CTTTAAAAAT
69542 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
69562 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
69582 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
69603 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
69623 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
69643 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
69663 CTCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
69683 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
69703 CTCGTTGCGAT
1 CGCGTTGCGAT
69714 AGTCAGAAGC
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
20 109 0.87
21 17 0.13
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:69628 original size:40 final size:40
Alignment explanation
Indices: 69544--69771 Score: 277
Period size: 40 Copynumber: 5.8 Consensus size: 40
69534 TTAAAAATCG
*
69544 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
69585 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
69625 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
69665 CGTTGCAATTTACGGATACGCGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
69705 CGTTGCGATAGT-CAGA-A-GCGTTGCGATTTA--TAGTTCG
1 CGTTGCGAT-TTACGGATACGCGTTGCGATTTACGTA-TTCT
* ** *
69742 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
69772 ATGGAAAATC
Statistics
Matches: 165, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
36 2 0.01
37 14 0.08
38 13 0.08
39 12 0.07
40 96 0.58
41 28 0.17
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:69746 original size:19 final size:19
Alignment explanation
Indices: 69722--69771 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
69712 ATAGTCAGAA
69722 GCGTTGCGATTT-ATAGTTC
1 GCGTTGCGATTTCATA-TTC
69741 GCGTTGCGATTTTCATATTC
1 GCGTTGCGA-TTTCATATTC
69761 GCGTTGCGATT
1 GCGTTGCGATT
69772 ATGGAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.38
20 15 0.52
21 3 0.10
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (19 bp):
GCGTTGCGATTTCATATTC
Done.