Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000236.1 Hibiscus syriacus cultivar Beakdansim tig00000408_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: 104120
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2686 original size:18 final size:19
Alignment explanation
Indices: 2665--2706 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
2655 AAATTCTTTT
2665 ATAAT-TATTCCAAAAATC
1 ATAATATATTCCAAAAATC
*
2683 ATAATCAATATTCTAAAAATC
1 ATAAT--ATATTCCAAAAATC
2704 ATA
1 ATA
2707 TAAACCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
21 15 0.75
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATATTCCAAAAATC
Found at i:10172 original size:26 final size:26
Alignment explanation
Indices: 10143--10193 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
10133 TTTATATTTC
10143 AGACTTCAGTTCTTATCATTTTAGGA
1 AGACTTCAGTTCTTATCATTTTAGGA
10169 AGACTTCAGTTCTTATCATTTTAGG
1 AGACTTCAGTTCTTATCATTTTAGG
10194 CCCTCACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (26 bp):
AGACTTCAGTTCTTATCATTTTAGGA
Found at i:15168 original size:21 final size:21
Alignment explanation
Indices: 15144--15192 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
15134 TTCAAGGGTT
15144 CTCTTTTGGAAATAATCAAAA
1 CTCTTTTGGAAATAATCAAAA
15165 CTCTTTTGGAAATAATCAAAA
1 CTCTTTTGGAAATAATCAAAA
*
15186 CACTTTT
1 CTCTTTT
15193 AATTCGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
CTCTTTTGGAAATAATCAAAA
Found at i:15951 original size:22 final size:22
Alignment explanation
Indices: 15923--15969 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
15913 CATTAAGGAT
15923 GATGCCATTGGAGGTTGTCTTA
1 GATGCCATTGGAGGTTGTCTTA
15945 GATGCCATTGGAGGTTGTCTTA
1 GATGCCATTGGAGGTTGTCTTA
15967 GAT
1 GAT
15970 CTCATGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.36
Consensus pattern (22 bp):
GATGCCATTGGAGGTTGTCTTA
Found at i:21783 original size:16 final size:16
Alignment explanation
Indices: 21762--21794 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21752 TACCATGTTT
21762 AAAAAT-AAAACTTAAA
1 AAAAATGAAAA-TTAAA
21778 AAAAATGAAAATTAAA
1 AAAAATGAAAATTAAA
21794 A
1 A
21795 CTTGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATGAAAATTAAA
Found at i:21788 original size:23 final size:25
Alignment explanation
Indices: 21762--21812 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
21752 TACCATGTTT
*
21762 AAAAATAAAACTT-AAAA-AAAATG
1 AAAAATAAAACTTGAAAAGAAAAGG
*
21785 AAAATTAAAACTTGAAAAGAAAAGG
1 AAAAATAAAACTTGAAAAGAAAAGG
21810 AAA
1 AAA
21813 GAAAGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 4 0.17
25 8 0.33
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.16
Consensus pattern (25 bp):
AAAAATAAAACTTGAAAAGAAAAGG
Found at i:27274 original size:16 final size:16
Alignment explanation
Indices: 27253--27284 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27243 CAGATGAAAA
*
27253 AAATATGATTTTCTTT
1 AAATATGATTTACTTT
27269 AAATATGATTTACTTT
1 AAATATGATTTACTTT
27285 GGCTCTCGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
AAATATGATTTACTTT
Found at i:33975 original size:16 final size:16
Alignment explanation
Indices: 33934--33976 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
33924 CAATTAGTAA
* *
33934 TTAGTGGTTAGAAATG
1 TTAGAGGTTAGAAAAG
*
33950 TTAGATGTTAGAAAAG
1 TTAGAGGTTAGAAAAG
*
33966 TTAGCGGTTAG
1 TTAGAGGTTAG
33977 CAGAATCCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (16 bp):
TTAGAGGTTAGAAAAG
Found at i:34193 original size:4 final size:4
Alignment explanation
Indices: 34184--34208 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34174 TATTAGAAAC
34184 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
34209 CAATGGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:34243 original size:138 final size:136
Alignment explanation
Indices: 33961--34331 Score: 509
Period size: 138 Copynumber: 2.7 Consensus size: 136
33951 TAGATGTTAG
** * * * * * *
33961 AAAAGTTAGCGGTTAGCAGAATCCAAACTATAGTAATACGGATCATACCCCGAATCGGGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCA
34026 CAAGGTCGAATCAA-ATT-AAAAAT-AATAAATAAATAAATAAATAACCAATGGTTAGAATGCAA
66 CAAGGTCGAATCAATATTAAAAAATAAATAAATAAATAAATAAATAACCAATGGTTAGAATGCAA
34088 TAAAAT
131 TAAAAT
* * *
34094 AAAAGTCAGTAGTTAACAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGAGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCA
34159 CAAGGTCGAATCGAATATTAGAAACAATAAATAAATAAATAAATAAATAA-CAATGGTTA-AAGT
66 CAAGGTCGAATC-AATATTA-AAA-AATAAATAAATAAATAAATAAATAACCAATGGTTAGAA-T
34222 GCAATAAAAT
127 GCAATAAAAT
* **
34232 AAAAGTTAGTAGTTAGTAGAGTCCGAACCATAATAATGTAGATCATACCCCGGATCGGGTCACCA
1 AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCA
*
34297 CAAGGTCGAAACAAATATTATAAATAATAAATAAA
66 CAAGGTCGAATC-AATATTA-AAA-AATAAATAAA
34332 CAATGGTTAA
Statistics
Matches: 210, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
133 66 0.31
134 2 0.01
135 3 0.01
137 5 0.02
138 113 0.54
139 21 0.10
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (136 bp):
AAAAGTTAGTAGTTAGCAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCA
CAAGGTCGAATCAATATTAAAAAATAAATAAATAAATAAATAAATAACCAATGGTTAGAATGCAA
TAAAAT
Found at i:36158 original size:2 final size:2
Alignment explanation
Indices: 36142--36182 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
36132 TTGGTTAAAC
36142 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36182 T
1 T
36183 CAATTTCGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44130 original size:21 final size:21
Alignment explanation
Indices: 44104--44144 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44094 ATAAGAAGCG
44104 AGTTAGTTTCTTTCTTTTTAA
1 AGTTAGTTTCTTTCTTTTTAA
44125 AGTTAGTTTCTTTCTTTTTA
1 AGTTAGTTTCTTTCTTTTTA
44145 CCATTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (21 bp):
AGTTAGTTTCTTTCTTTTTAA
Found at i:52674 original size:27 final size:29
Alignment explanation
Indices: 52618--52674 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 29
52608 GTACTAATAT
* *
52618 ATATATATATATATTAATATATTTTTAAA
1 ATATATATATATATTAATATAATTTAAAA
52647 ATATATATA-AT-TTAA-ATACATTTAAAA
1 ATATATATATATATTAATATA-ATTTAAAA
52674 A
1 A
52675 AAACAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.12
27 11 0.44
28 2 0.08
29 9 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATATATATATATTAATATAATTTAAAA
Found at i:52860 original size:39 final size:39
Alignment explanation
Indices: 52817--52893 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
52807 TACTATGTAA
52817 ACATGTAATACGTGACATCATCTATATAATACAAAATGG
1 ACATGTAATACGTGACATCATCTATATAATACAAAATGG
** *
52856 ACATGTAATATTTGATATCATCTATATAATACAAAATG
1 ACATGTAATACGTGACATCATCTATATAATACAAAATG
52894 AACCTGGACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.32
Consensus pattern (39 bp):
ACATGTAATACGTGACATCATCTATATAATACAAAATGG
Found at i:53208 original size:34 final size:35
Alignment explanation
Indices: 53152--53223 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
53142 TCAAGGCAAT
53152 TTTGTTTCTAAATTCTCTCTTC-TACCAT-GACAAA
1 TTTGTTTCTAAATTCTCTCTTCTTACCATGGA-AAA
* *
53186 TTTGTTTCTAGATTAT-TCCTTCTTACCATGGAAAA
1 TTTGTTTCTAAATTCTCT-CTTCTTACCATGGAAAA
53221 TTT
1 TTT
53224 CCATCTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 1 0.03
34 18 0.55
35 12 0.36
36 2 0.06
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (35 bp):
TTTGTTTCTAAATTCTCTCTTCTTACCATGGAAAA
Found at i:55334 original size:13 final size:13
Alignment explanation
Indices: 55293--55336 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
55283 ACTACACTGC
55293 TGACCGTCACCGT
1 TGACCGTCACCGT
*
55306 TGA-CGTCCCCGTT
1 TGACCGTCACCG-T
*
55319 TGACCGTCACTGT
1 TGACCGTCACCGT
55332 TGACC
1 TGACC
55337 ATTGACCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 7 0.27
13 13 0.50
14 6 0.23
ACGTcount: A:0.14, C:0.36, G:0.23, T:0.27
Consensus pattern (13 bp):
TGACCGTCACCGT
Found at i:59761 original size:60 final size:60
Alignment explanation
Indices: 59631--59764 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
59621 TAATGAATAA
* * * * *
59631 TCGGGTGATCATTTTGTAACTTTTCATAGTCGAGGGATTTAACAACGCAACATTCTATAG
1 TCGGGTGATCATTTTATAACTTTTAATAGTCGAGAGATTTAACAAAGCAACACTCTATAG
* * * *
59691 TCAGATGATCATTTTATAACTTTTAATAGTCGAGAGATTTAATAAAGCAATAC-CTTATAG
1 TCGGGTGATCATTTTATAACTTTTAATAGTCGAGAGATTTAACAAAGCAACACTC-TATAG
*
59751 TCGGGGGATCATTT
1 TCGGGTGATCATTT
59765 GTGTACTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.02
60 60 0.98
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (60 bp):
TCGGGTGATCATTTTATAACTTTTAATAGTCGAGAGATTTAACAAAGCAACACTCTATAG
Found at i:60087 original size:24 final size:24
Alignment explanation
Indices: 60041--60087 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
60031 ATTATAAGAT
**
60041 AATTTTTTTAATTATACCTTTATG
1 AATTTTTTTAATTATACAATTATG
60065 AATTTTTTT-ATTCATACAATTAT
1 AATTTTTTTAATT-ATACAATTAT
60088 TTTATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (24 bp):
AATTTTTTTAATTATACAATTATG
Found at i:60212 original size:59 final size:61
Alignment explanation
Indices: 60118--60236 Score: 215
Period size: 59 Copynumber: 2.0 Consensus size: 61
60108 ATTATGATTA
60118 AATTTATAAAATTAATATCACCTTATCTTCTCAAGAAATGAATAATCTTATCCCACAAAGG
1 AATTTATAAAATTAATATCACCTTATCTTCTCAAGAAATGAATAATCTTATCCCACAAAGG
*
60179 AATTTA-AAAA-TATTATCACCTTATCTTCTCAAGAAATGAATAATCTTATCCCACAAAG
1 AATTTATAAAATTAATATCACCTTATCTTCTCAAGAAATGAATAATCTTATCCCACAAAG
60237 AAAAATTGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 47 0.82
60 4 0.07
61 6 0.11
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (61 bp):
AATTTATAAAATTAATATCACCTTATCTTCTCAAGAAATGAATAATCTTATCCCACAAAGG
Found at i:69863 original size:29 final size:30
Alignment explanation
Indices: 69803--69864 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
69793 TTTTTGGTCC
** * *
69803 CTAAACATTTCAAAATTTATATTTTAGCCA
1 CTAAACATTTCAAAAAATACATTTTAACCA
*
69833 CTAAAC-TTTCAAAAAATACATTTTAATCA
1 CTAAACATTTCAAAAAATACATTTTAACCA
69862 CTA
1 CTA
69865 GCCAGAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.37
Consensus pattern (30 bp):
CTAAACATTTCAAAAAATACATTTTAACCA
Found at i:70646 original size:26 final size:25
Alignment explanation
Indices: 70593--70651 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
70583 TCAAATTTCA
*
70593 AAAATAATTATTTTTAAAAAAACTT
1 AAAATAATTATTTTTAAAAAAACCT
* *
70618 AAAATTATTATTTTTATAAAAATCCT
1 AAAATAATTATTTTTA-AAAAAACCT
70644 AAAA-AATT
1 AAAATAATT
70652 GAAATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATAATTATTTTTAAAAAAACCT
Found at i:71060 original size:14 final size:15
Alignment explanation
Indices: 71037--71069 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
71027 TCGATTTTTT
*
71037 TTTTTTAAAAAAT-C
1 TTTTTAAAAAAATAC
71051 TTTTTAAAAAAATAC
1 TTTTTAAAAAAATAC
71066 TTTT
1 TTTT
71070 ATTATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTTAAAAAAATAC
Found at i:77154 original size:22 final size:23
Alignment explanation
Indices: 77125--77182 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
77115 ACAAGTAATT
*
77125 AAAA-ATATAAATGATAAAT-C-C
1 AAAAGATATAAATG-TAAATGCAA
*
77146 AAAAGATATGAAAAGTAAATGCAA
1 AAAAGATAT-AAATGTAAATGCAA
77170 AAAAGATATAAAT
1 AAAAGATATAAAT
77183 AACAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.13
22 9 0.30
23 8 0.27
24 9 0.30
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (23 bp):
AAAAGATATAAATGTAAATGCAA
Found at i:77223 original size:16 final size:16
Alignment explanation
Indices: 77195--77251 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
77185 CAAATTTATC
*
77195 AAAAATAATTAAATATT
1 AAAAATAA-TAAATAGT
77212 AAAAATAATAAATAGT
1 AAAAATAATAAATAGT
77228 AAAAAT-ATAAA-AG-
1 AAAAATAATAAATAGT
*
77241 GAAAATAATAA
1 AAAAATAATAA
77252 GTAATAAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.14
14 6 0.16
15 5 0.14
16 13 0.35
17 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAAAATAATAAATAGT
Found at i:77411 original size:2 final size:2
Alignment explanation
Indices: 77404--77435 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77394 GATATACCAA
77404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77436 TAGATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77961 original size:20 final size:21
Alignment explanation
Indices: 77936--77987 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
77926 TTTTCCCAAT
*
77936 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
77956 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
77977 TCGCAATGCGA
1 TCGCAATGCGA
77988 TAATGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:78001 original size:20 final size:20
Alignment explanation
Indices: 77976--78110 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
77966 AATTGGGAAA
77976 ATCGCAATGCGATAATGACT
1 ATCGCAATGCGATAATGACT
* *
77996 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATGACT
*
78016 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATAATGAC--T
* * *
78037 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATAATGACT
* * **
78057 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATGACT
* *
78077 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATAATGAC-T
*
78097 AATCGTAATGCGAT
1 -ATCGCAATGCGAT
78111 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATAATGACT
Found at i:78020 original size:61 final size:61
Alignment explanation
Indices: 77973--78101 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 61
77963 GCGAATTGGG
* * * * *
77973 AAAATCGCAATGCGATAATGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
78034 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
78095 ATAATCG
1 AAAATCG
78102 TAATGCGATT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:78041 original size:41 final size:40
Alignment explanation
Indices: 77976--78069 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
77966 AATTGGGAAA
* * * *
77976 ATCGCAATGCGATAATGACTATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATGACAATCGCAACGAGATACTGACT
78016 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAATGCGATAATGAC--AATCGCAACGAGATACTGACT
* *
78057 TTCGCAACGCGAT
1 ATCGCAATGCGAT
78070 TCTGACTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.04
40 16 0.35
41 28 0.61
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGATAATGACAATCGCAACGAGATACTGACT
Found at i:78306 original size:22 final size:22
Alignment explanation
Indices: 78278--78321 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
78268 CACTCTCTCA
78278 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
78300 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
78322 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:78604 original size:20 final size:20
Alignment explanation
Indices: 78567--78623 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
78557 GATTCTCTCG
**
78567 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
78587 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
**
78607 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
78624 AGAAACTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:78814 original size:25 final size:24
Alignment explanation
Indices: 78760--78814 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
78750 TGTTTATTAT
* *
78760 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
78784 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
78810 TGTTT
1 TGTTT
78815 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:79964 original size:18 final size:18
Alignment explanation
Indices: 79943--79987 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
79933 TCCACTTCGG
*
79943 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
79961 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
79979 GAGCCATCA
1 GAGCCATCA
79988 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:80494 original size:20 final size:20
Alignment explanation
Indices: 80469--80514 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
80459 TAGTTTACTT
80469 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
80489 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
80509 TCGCAA
1 TCGCAA
80515 AGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:80523 original size:19 final size:20
Alignment explanation
Indices: 80480--80524 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
80470 CGCAACACGA
*
80480 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAAAGCAG
*
80500 AAATGGCTATCGCAAAGC-G
1 AAATGACTATCGCAAAGCAG
80519 AAATGA
1 AAATGA
80525 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAAAGCAG
Found at i:80530 original size:19 final size:19
Alignment explanation
Indices: 80508--80604 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
80498 AGAAATGGCT
80508 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
80527 ATCGC-AA-CG--A-CAAA
1 ATCGCAAAGCGAAATGAAA
*
80541 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
80560 ATCGC-AA-CG--AT-AAA
1 ATCGCAAAGCGAAATGAAA
*
80574 ATCGCAACGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
80593 ATCGCAATGCGA
1 ATCGCAAAGCGA
80605 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 16 0.26
15 5 0.08
16 4 0.06
17 4 0.06
18 6 0.10
19 27 0.44
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:80543 original size:14 final size:14
Alignment explanation
Indices: 80524--80582 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
80514 AAGCGAAATG
80524 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
80538 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
80557 AAAATCGCAACGAT
1 AAAATCGCAACGAC
80571 AAAATCGCAACG
1 AAAATCGCAACG
80583 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:80553 original size:33 final size:33
Alignment explanation
Indices: 80508--80599 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
80498 AGAAATGGCT
80508 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
* *
80541 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
80574 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAAAGCGAAATGAAAATCGCAA
80600 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:80635 original size:14 final size:14
Alignment explanation
Indices: 80616--80706 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
80606 TTGTGTTTCG
80616 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
80630 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
80646 CGCATTGCGCTTTTGT
1 CG--TTGCGATTTTGT
*
80662 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
80679 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
80695 CGTTGTGATTTT
1 CGTTGCGATTTT
80707 CATTTCGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 25 0.41
15 3 0.05
16 12 0.20
17 4 0.07
18 11 0.18
19 6 0.10
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:80680 original size:33 final size:33
Alignment explanation
Indices: 80611--80722 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
80601 GCGATTTGTG
*
80611 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
80643 TTTCGCATTGCGCTTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
80676 TTTCGCATTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
80709 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
80723 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 25 0.33
33 50 0.67
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:80741 original size:20 final size:19
Alignment explanation
Indices: 80707--80762 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
80697 TTGTGATTTT
*
80707 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
80726 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
80746 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
80763 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:81217 original size:41 final size:42
Alignment explanation
Indices: 81121--81208 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
81111 GACTCACTTG
* * *
81121 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
* *
81163 TCTTCCCTCAAGAGTCCCCCCCACT-GTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
81204 TCATC
1 TCATC
81209 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 18 0.45
42 22 0.55
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCACTCGTTCAAGAGGCCACTA
Found at i:82653 original size:14 final size:14
Alignment explanation
Indices: 82619--82657 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
82609 TTGATTGTTT
82619 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
82633 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
82647 TGTTGATTTGT
1 AATTGATTTGT
82658 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:82803 original size:14 final size:14
Alignment explanation
Indices: 82784--82839 Score: 67
Period size: 14 Copynumber: 3.6 Consensus size: 14
82774 GAAACTGACT
82784 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
82798 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
82817 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
82831 ATCGCAACG
1 ATCGCAACG
82840 CGATTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 20 0.54
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:82830 original size:19 final size:19
Alignment explanation
Indices: 82794--82830 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
82784 ATCGCAACGA
* *
82794 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
82813 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
82831 ATCGCAACGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:82855 original size:33 final size:33
Alignment explanation
Indices: 82764--82842 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
82754 AAAACAGACT
* **
82764 ATCGCAACACGAAACTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAACGAGAAA
*
82798 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
82831 ATCGCAACGCGA
1 ATCGCAACGCGA
82843 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
Found at i:83923 original size:24 final size:24
Alignment explanation
Indices: 83896--83949 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
83886 GTATTCGAAA
*
83896 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
83920 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
83944 TTTGAT
1 TTTGAT
83950 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:84141 original size:12 final size:12
Alignment explanation
Indices: 84124--84158 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
84114 ATATAATCCT
84124 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84136 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84148 GAAGAAGAAAA
1 GAAGAAGAAAA
84159 GTCCCCGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:86469 original size:19 final size:19
Alignment explanation
Indices: 86447--86577 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
86437 GGAAATTACT
86447 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
86466 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
86480 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
86499 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
86513 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
86532 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
86546 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
86565 ATCACAACGCGAA
1 ATCGCAATGCGAA
86578 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 39 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:86489 original size:33 final size:33
Alignment explanation
Indices: 86447--86573 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
86437 GGAAATTACT
86447 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
86480 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
86512 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
86546 ATCGCAATGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
86574 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:86554 original size:66 final size:66
Alignment explanation
Indices: 86448--86580 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
86438 GAAATTACTA
*
86448 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
86513 T
66 T
*
86514 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
86579 T
66 T
86580 T
1 T
86581 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
T
Found at i:86595 original size:19 final size:19
Alignment explanation
Indices: 86573--86614 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
86563 AAATCACAAC
*
86573 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
86592 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
86611 GCGA
1 GCGA
86615 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:86741 original size:14 final size:14
Alignment explanation
Indices: 86722--86755 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
86712 CATCAATTAA
86722 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
86736 ACAAATCACCTTTT
1 ACAAATCAACTTTT
86750 ACAAAT
1 ACAAAT
86756 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:88139 original size:21 final size:20
Alignment explanation
Indices: 88111--88175 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
88101 CCATGTGAAT
*
88111 AGGG-CTCTTGAATGGTGGG
1 AGGGCCTCTTGAACGGTGGG
* * **
88130 AGGGACCTCTTCAACGATGAC
1 AGGG-CCTCTTGAACGGTGGG
88151 AGTGGCCTCTTGAACGGTGGG
1 AG-GGCCTCTTGAACGGTGGG
88172 AGGG
1 AGGG
88176 GACTCTCGAG
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 26 0.76
22 2 0.06
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (20 bp):
AGGGCCTCTTGAACGGTGGG
Found at i:88200 original size:42 final size:41
Alignment explanation
Indices: 88115--88237 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
88105 GTGAATAGGG
* * * *
88115 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
88157 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
88199 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
88238 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:88630 original size:91 final size:90
Alignment explanation
Indices: 88455--88639 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
88445 ATTTCAAACT
*
88455 TTCAACCAAAACACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAACACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
88520 AAAATTGGCAGCAACCGAATAAATTTAC
63 AAAATTGGCAGCAACCGAATAAATTTAC
* *
88548 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCATAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAACACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
**
88612 GTATTGGCAGCAACCGAATAAATTTAC
64 AAATTGGCAGCAACCGAATAAATTTAC
88639 T
1 T
88640 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 26 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAACACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAAA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:90370 original size:40 final size:36
Alignment explanation
Indices: 90326--90447 Score: 139
Period size: 33 Copynumber: 3.4 Consensus size: 36
90316 TCTTTTGGTT
*
90326 GAAATGAAAATCACAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAG--AA-GAGAATCGCAACGC
**
90365 GGAAATGACTATCGCAAC--G-AGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAAGAGAATCGCAACGC
90399 GAAATGAAAATCGCAAC--G-AGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAGAGAATCGCAACGC
90432 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
90448 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
33 47 0.61
34 14 0.18
35 1 0.01
38 1 0.01
40 14 0.18
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGAGAAGAGAATCGCAACGC
Found at i:90371 original size:20 final size:19
Alignment explanation
Indices: 90326--90452 Score: 94
Period size: 19 Copynumber: 7.1 Consensus size: 19
90316 TCTTTTGGTT
* *
90326 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
*
90345 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
90365 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
90383 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
90399 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
90416 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
90432 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
90451 GA
1 GA
90453 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 3 0.04
18 3 0.04
19 26 0.31
20 26 0.31
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:90394 original size:14 final size:14
Alignment explanation
Indices: 90375--90430 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
90365 GGAAATGACT
90375 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
90389 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
90408 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
90422 ATCGCAACG
1 ATCGCAACG
90431 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:90412 original size:33 final size:33
Alignment explanation
Indices: 90351--90447 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
90341 ACGAGATAAT
**
90351 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
90385 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
90418 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
90448 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:90481 original size:19 final size:19
Alignment explanation
Indices: 90448--90514 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
90438 AAAATCGCAA
**
90448 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
90467 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
90486 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
90506 TGCGATTTT
1 TGCGATTTT
90515 CAATCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:91100 original size:21 final size:20
Alignment explanation
Indices: 91036--91127 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
91026 GCTATGTAAA
* *
91036 TCGCATTGCGATAGTA-AGAT
1 TCGCATTGCGAT-TTACATAT
*
91056 TCACATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
91076 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACAT-AT
*
91097 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
91117 TCGCATTGCGA
1 TCGCATTGCGA
91128 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.03
20 42 0.68
21 18 0.29
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:91142 original size:41 final size:41
Alignment explanation
Indices: 91059--91262 Score: 148
Period size: 41 Copynumber: 5.0 Consensus size: 41
91049 GTAAGATTCA
* * ** *
91059 CATTGCGATTTACATATTCGCATTGCG-ATTTTCCTAATTCG
1 CATTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCG
91100 CATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCG
1 CATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCG
** * * ** * *
91141 CAACGCGA-ATACGTAAATCGCAAGGCGAATTAGGAAAATTG
1 CATTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAATCG
* * * *
91182 CATTGCGATAGT-CAGTA-TCGCATTGCG-ATTTTCCAAATTCG
1 CATTGCGAT-TTAC-GTATTCGCATTGCGAATTAT-GAAAATCG
* **
91223 CATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATC
1 CATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATC
91263 ACAACGCGAA
Statistics
Matches: 125, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
40 11 0.09
41 102 0.82
42 9 0.07
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
CATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCG
Found at i:91148 original size:21 final size:21
Alignment explanation
Indices: 91124--91179 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
91114 TATTCGCATT
*
91124 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
91145 GCGAA-TACGTAAATCGCAAG
1 GCGAATTACGAAAATCGCAAC
*
91165 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
91180 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:91189 original size:21 final size:21
Alignment explanation
Indices: 91117--91189 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
91107 ATTTACGTAT
* *
91117 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
91138 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
* *
91158 TCGCAAGGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
91179 TTGCATTGCGA
1 TCGCAATGCGA
91190 TAGTCAGTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:91243 original size:20 final size:21
Alignment explanation
Indices: 91199--91250 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
91189 ATAGTCAGTA
*
91199 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
91220 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
91240 TCGCATTGCGA
1 TCGCATTGCGA
91251 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:91292 original size:21 final size:22
Alignment explanation
Indices: 91240--91292 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
91230 ATTTACTTAT
91240 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
91261 TCACAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
91282 TCGCATTGCGA
1 TCGCATTGCGA
91293 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:91308 original size:123 final size:122
Alignment explanation
Indices: 91033--91312 Score: 332
Period size: 123 Copynumber: 2.3 Consensus size: 122
91023 GGCGCTATGT
* * * * *
91033 AAATCGCATTGCGATAGTAAGATTCACATTGCGATTTACATATTCGCATTGCGATTTTCCTAATT
1 AAATCGCATTGCGATAGTAAAAATCGCATTGCGATGTACATATTCGCATTGCGATTTTCCAAATT
* * *
91098 CGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGAATACGT
66 CGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCACAACGCGAATACGA
** * *
91155 AAATCGCAAGGCGAATTAG-GAAAATTGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCA
1 AAATCGCATTGCG-A-TAGTAAAAATCGCATTGCGAT-GTACA-TATTCGCATTGCGATTTTCCA
* * **
91217 AATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATCACAACGCGAAATTGGA
62 AATTCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCACAACGCG-AATACGA
* *
91279 AAATCGCATTGCGATAGTCATAATCGCATTGCGA
1 AAATCGCATTGCGATAGTAAAAATCGCATTGCGA
91313 ATCTGGAAAC
Statistics
Matches: 131, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
122 14 0.11
123 96 0.73
124 21 0.16
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (122 bp):
AAATCGCATTGCGATAGTAAAAATCGCATTGCGATGTACATATTCGCATTGCGATTTTCCAAATT
CGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATCACAACGCGAATACGA
Found at i:97017 original size:46 final size:47
Alignment explanation
Indices: 96963--97052 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
96953 TCGAATAAAT
* *
96963 GCATGCGAACTAGATATCACGTGGTTAGG-TTTATTTTTTTGAACAA
1 GCATGCGAACTAGATATCACGCGGTTAGGATTTATTTTTGTGAACAA
* *
97009 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCACGCGGTTAGGATTTATTTTTGTGAA
97053 TAACAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 26 0.67
47 13 0.33
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (47 bp):
GCATGCGAACTAGATATCACGCGGTTAGGATTTATTTTTGTGAACAA
Done.