Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005924.1 Hibiscus syriacus cultivar Beakdansim tig00013908_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: 85062
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:698 original size:108 final size:108
Alignment explanation
Indices: 506--710 Score: 250
Period size: 108 Copynumber: 1.9 Consensus size: 108
496 AAAAAGGGTA
** * * * * * *
506 AATAATGTGGTTGAGCAAACTGTAATTTTGGAGGATATTCATGCTGTAGAGGAAGTAAGTACGAT
1 AATAATGTGCCTGAGCAAACTGAAAATATGGAGGATATTCATGCCGTAGAGGAAGCAAGTACGAA
* *
571 ATGGCCGAGCCAGAGGAGACCCTGTGATGGAAAAAATATGGTG
66 ATGGACGAGCCAGAGGAGACCCTGTAATGGAAAAAATATGGTG
* * * *
614 AATAATGTGCCTGGGCAAACTGAAAATATGGAGGATATTCATGCCGTAGGGGCAGCAGGTACGGA
1 AATAATGTGCCTGAGCAAACTGAAAATATGGAGGATATTCATGCCGTAGAGGAAGCAAGTAC-GA
* *
679 AATGGACGAGGCTGA-GAGACCCTGTAATGGAA
65 AATGGACGAGCCAGAGGAGACCCTGTAATGGAA
711 GAGGAATGGA
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
108 67 0.84
109 13 0.16
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (108 bp):
AATAATGTGCCTGAGCAAACTGAAAATATGGAGGATATTCATGCCGTAGAGGAAGCAAGTACGAA
ATGGACGAGCCAGAGGAGACCCTGTAATGGAAAAAATATGGTG
Found at i:11993 original size:29 final size:31
Alignment explanation
Indices: 11925--12012 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 31
11915 AGTAACCGTA
11925 ATAACTTTTTTTTCATTTTAATACCTATCTG
1 ATAACTTTTTTTTCATTTTAATACCTATCTG
*
11956 ATAACTTTTTATTTCATTTTAGT-CC-ATCTG
1 ATAACTTTTT-TTTCATTTTAATACCTATCTG
*
11986 -TCAA-TTTTTGTTTCATTTTAACACCTA
1 AT-AACTTTTT-TTTCATTTTAATACCTA
12013 AATTTTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 16 0.33
30 9 0.18
31 13 0.27
32 11 0.22
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (31 bp):
ATAACTTTTTTTTCATTTTAATACCTATCTG
Found at i:14836 original size:38 final size:38
Alignment explanation
Indices: 14748--14836 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 38
14738 GATGTGTTTG
* * *
14748 GTTCGTTTATATTTACGAACAACCTCGTTTATTGACTT
1 GTTCATTTATGTTTACGAACAACCTCGTTTATCGACTT
* * ** * *
14786 ATTCATTCATGTTTACGAACAAGTTTGTTTATCGATTT
1 GTTCATTTATGTTTACGAACAACCTCGTTTATCGACTT
*
14824 GTTCTTTTATGTT
1 GTTCATTTATGTT
14837 CATGAATAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.49
Consensus pattern (38 bp):
GTTCATTTATGTTTACGAACAACCTCGTTTATCGACTT
Found at i:15104 original size:23 final size:23
Alignment explanation
Indices: 15061--15104 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
15051 ACATCAATAG
*
15061 AATATATTCGTGAACATTAAACT
1 AATATATTCGTGAACAATAAACT
*
15084 AATATATTCGTGAATAATAAA
1 AATATATTCGTGAACAATAAA
15105 TAAACGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (23 bp):
AATATATTCGTGAACAATAAACT
Found at i:15627 original size:32 final size:30
Alignment explanation
Indices: 15590--15662 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
15580 TTAAAGATAT
15590 TTTGTAATAATTTGAGAAAATTTAATGATTA
1 TTTGTAATAATTTGAG-AAATTTAATGATTA
** * *
15621 GTTTGTAACCATTTGAGAGATTTAATGGTTA
1 -TTTGTAATAATTTGAGAAATTTAATGATTA
15652 TTT-T-ATAATTT
1 TTTGTAATAATTT
15663 ATGGAACTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 1 0.03
30 3 0.09
31 12 0.34
32 14 0.40
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (30 bp):
TTTGTAATAATTTGAGAAATTTAATGATTA
Found at i:22100 original size:21 final size:22
Alignment explanation
Indices: 22054--22112 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
22044 CAAAAGAGAA
*
22054 AAGGGGTCGATCA-TTTCTTTC
1 AAGGGATCGATCATTTTCTTTC
*
22075 GAGGGATCGATCATTTTC-TTC
1 AAGGGATCGATCATTTTCTTTC
*
22096 AAGGGATCAATCATTTT
1 AAGGGATCGATCATTTT
22113 GAAAATGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (22 bp):
AAGGGATCGATCATTTTCTTTC
Found at i:22684 original size:64 final size:63
Alignment explanation
Indices: 22613--22791 Score: 157
Period size: 65 Copynumber: 2.8 Consensus size: 63
22603 TGGACTCTTT
* *
22613 GTGCATCGGTGCA-CTAAGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCA
1 GTGCATCGGTGCAGCT--G-GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-AGCCA
*
22675 GA
62 CA
* * *
22677 GTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAATCCTCA
1 GTGCATCGGTGCA--GCTGGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCACA
* * * * * *
22742 GTGCATCGGTGCATGGTATGTGCATCGATGAATGAAATACATTCGATGTT
1 GTGCATCGGTGCA-GCT-GGTGCATCGATGCATCAAATGCATTCAATGTT
22792 CAATTTAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 41 0.43
65 49 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (63 bp):
GTGCATCGGTGCAGCTGGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCACA
Found at i:22765 original size:65 final size:65
Alignment explanation
Indices: 22632--22791 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
22622 TGCACTAAGA
* *
22632 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
22696 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
22759 AT
65 -G
* * *
22761 GTGCATCGATGAATGAAATACATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
22792 CAATTTAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.34
65 51 0.62
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:23847 original size:21 final size:21
Alignment explanation
Indices: 23822--23865 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
23812 TCGTAGTAGG
*
23822 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
** *
23843 AGGAGCAGCTTGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
23864 AG
1 AG
23866 CTCCTGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.41, T:0.11
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:27091 original size:20 final size:20
Alignment explanation
Indices: 27066--27160 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
27056 ACACAGGTTC
*
27066 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
27086 CAAATTCACAACGCGGAAGT
1 CAAATTCGCAACGCGAAAGT
**
27106 CGAAATTCGCAACGCG-ATTT
1 C-AAATTCGCAACGCGAAAGT
* * *
27126 TAAGATTTGCAACGCGATAGT
1 CAA-ATTCGCAACGCGAAAGT
27147 CAAAATTCGCAACG
1 C-AAATTCGCAACG
27161 TGATTTAAGA
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.03
20 31 0.53
21 23 0.40
22 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:27160 original size:21 final size:21
Alignment explanation
Indices: 27067--27198 Score: 96
Period size: 21 Copynumber: 6.5 Consensus size: 21
27057 CACAGGTTCC
* *
27067 AAATTCGTAACGCGAAAGTC-
1 AAATTCGCAACGCGATAGTCA
* *
27087 AAATTCACAACGCGGA-AGTCG
1 AAATTCGCAACGC-GATAGTCA
* *
27108 AAATTCGCAACGCGAT-TTTA
1 AAATTCGCAACGCGATAGTCA
* *
27128 AGATTTGCAACGCGATAGTCA
1 AAATTCGCAACGCGATAGTCA
* *
27149 AAATTCGCAACGTGAT--TTA
1 AAATTCGCAACGCGATAGTCA
* *
27168 AGATTCGCAACGCGATACTCCA
1 AAATTCGCAACGCGATAGT-CA
27190 AAA-TCGCAA
1 AAATTCGCAA
27199 TGCATTTGTT
Statistics
Matches: 87, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
19 16 0.18
20 32 0.37
21 36 0.41
22 3 0.03
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
AAATTCGCAACGCGATAGTCA
Found at i:27179 original size:40 final size:41
Alignment explanation
Indices: 27089--27198 Score: 136
Period size: 41 Copynumber: 2.7 Consensus size: 41
27079 CGAAAGTCAA
* *
27089 ATTCACAACGCGGA-AGTCGAAATTCGCAACGCGATTTTAAG
1 ATTCGCAACGC-GATAGTCAAAATTCGCAACGCGATTTTAAG
* *
27130 ATTTGCAACGCGATAGTCAAAATTCGCAACGTGA-TTTAAG
1 ATTCGCAACGCGATAGTCAAAATTCGCAACGCGATTTTAAG
*
27170 ATTCGCAACGCGATACTCCAAAA-TCGCAA
1 ATTCGCAACGCGATAGT-CAAAATTCGCAA
27199 TGCATTTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 29 0.48
41 32 0.52
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (41 bp):
ATTCGCAACGCGATAGTCAAAATTCGCAACGCGATTTTAAG
Found at i:28057 original size:21 final size:21
Alignment explanation
Indices: 28031--28087 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
28021 TCCCATCTTG
* *
28031 TCGCGTTGTGAATTTTGACTA
1 TCGCGTTGCGAATTTCGACTA
*
28052 TCGCGTTGCGAATTTCGACTT
1 TCGCGTTGCGAATTTCGACTA
*
28073 TTGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
28088 GGAACCTGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGAATTTCGACTA
Found at i:30080 original size:21 final size:21
Alignment explanation
Indices: 30056--30107 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 21
30046 GAATGTACAT
30056 CGATACACCATGAAGGTGCAC
1 CGATACACCATGAAGGTGCAC
* * * *
30077 CGATGCACGCCTTGAATGTGCAT
1 CGAT--ACACCATGAAGGTGCAC
30100 CGATACAC
1 CGATACAC
30108 AAGGTCATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.29
23 17 0.71
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (21 bp):
CGATACACCATGAAGGTGCAC
Found at i:30101 original size:44 final size:42
Alignment explanation
Indices: 30009--30107 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 42
29999 TTGTACTTAA
* * *
30009 TGCATCGATACACCTAACAGTGTATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
* *
30051 TACATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATG
30095 TGCATCGATACAC
1 TGCATCGATACAC
30108 AAGGTCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 13 0.27
43 12 0.25
44 23 0.48
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
Found at i:30124 original size:43 final size:42
Alignment explanation
Indices: 30027--30126 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 42
30017 TACACCTAAC
* * * *
30027 AGTGTATCGATGCATCCTTGAATGTACATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTACATCGATACACAAGGA
* * *
30069 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATACACAAGGTC
1 A-GTGCATCGATGCA-GCCTTGAATGTACATCGATACACAAGG-A
30114 A-TGCATCGATGCA
1 AGTGCATCGATGCA
30127 TCGATCGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 22 0.47
44 23 0.49
45 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTACATCGATACACAAGGA
Found at i:32049 original size:14 final size:15
Alignment explanation
Indices: 32024--32052 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
32014 TTGATTTTAA
32024 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
32039 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
32053 AAATGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:34944 original size:13 final size:13
Alignment explanation
Indices: 34926--34951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34916 AATATATTGA
34926 AATAATTAATTTT
1 AATAATTAATTTT
34939 AATAATTAATTTT
1 AATAATTAATTTT
34952 TTAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATAATTAATTTT
Found at i:34960 original size:16 final size:14
Alignment explanation
Indices: 34925--34962 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
34915 AAATATATTG
34925 AAATAATTAATTTT
1 AAATAATTAATTTT
34939 -AATAATTAATTTTTT
1 AAATAATTAA--TTTT
34954 AAATAATTA
1 AAATAATTA
34963 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATAATTAATTTT
Found at i:57116 original size:3 final size:3
Alignment explanation
Indices: 57103--57152 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
57093 GTGAAGCTGA
*
57103 AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57151 AA
1 AA
57153 TGGGTGTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:64772 original size:21 final size:21
Alignment explanation
Indices: 64723--64773 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
64713 TATGACTATT
*
64723 GCAATGCAATTTTCCAATTTC
1 GCAATGCGATTTTCCAATTTC
**
64744 GCGTTGCGATTTTCCCAA-TTC
1 GCAATGCGATTTT-CCAATTTC
64765 GCAATGCGA
1 GCAATGCGA
64774 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (21 bp):
GCAATGCGATTTTCCAATTTC
Found at i:64837 original size:21 final size:21
Alignment explanation
Indices: 64803--64875 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
64793 ATACTGACTA
* *
64803 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
64824 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
64844 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
64865 TCGCAATGCGA
1 TCGCAATGCGA
64876 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:64890 original size:20 final size:20
Alignment explanation
Indices: 64865--64974 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
64855 TTTTCATAAT
64865 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
64885 TCGCAACGCGATTAAGTAAC
1 TCGCAATGCGAATACGTAAA
* *
64905 TCGCAAT--GAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
64924 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* *
64944 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
64964 TCGCAATGCGA
1 TCGCAATGCGA
64975 TTTACATAGC
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
18 2 0.03
19 15 0.21
20 52 0.72
21 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:64896 original size:41 final size:41
Alignment explanation
Indices: 64783--64897 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 41
64773 AATAAGTAAA
* *
64783 TCGCAATGCGATACTGAC-T-ATCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATA-T-ACGTAATCGCAATGCGATTTTCATAAT
* * * **
64824 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATATACGTAATCGCAATGCGATTTTCATAAT
*
64865 TCGCAATGCGA-ATACGTAAATCGCAACGCGATT
1 TCGCAATGCGATATACGT-AATCGCAATGCGATT
64898 AAGTAACTCG
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
39 2 0.03
40 7 0.12
41 49 0.84
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (41 bp):
TCGCAATGCGATATACGTAATCGCAATGCGATTTTCATAAT
Found at i:65556 original size:19 final size:19
Alignment explanation
Indices: 65492--65565 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
65482 TAGTTTCGAG
65492 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
65512 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
65528 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
65545 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
65564 AA
1 AA
65566 CCAAAATCGT
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
14 7 0.16
15 2 0.05
16 2 0.05
17 1 0.02
18 2 0.05
19 19 0.44
20 10 0.23
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:65571 original size:19 final size:19
Alignment explanation
Indices: 65532--65574 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
65522 GCAACGAGAG
**
65532 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
65551 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
65570 AATCG
1 AATCG
65575 TATTGCGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:65623 original size:33 final size:33
Alignment explanation
Indices: 65586--65648 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
65576 ATTGCGCTTT
*
65586 TCATTTCGCGTTGTGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
65619 TCATTTCGCGTTGCGATTCTCTCGTTGCGA
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGA
65649 CTCTCTCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:65646 original size:14 final size:14
Alignment explanation
Indices: 65594--65663 Score: 68
Period size: 14 Copynumber: 4.6 Consensus size: 14
65584 TTTCATTTCG
*
65594 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
65608 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
65627 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
65641 CGTTGCGACTCTCT
1 CGTTGCGATTCTCT
65655 CGTTGCGAT
1 CGTTGCGAT
65664 AGTCATTTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 31 0.67
16 2 0.04
17 2 0.04
19 11 0.24
ACGTcount: A:0.10, C:0.26, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:65663 original size:47 final size:48
Alignment explanation
Indices: 65594--65684 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 48
65584 TTTCATTTCG
* *
65594 CGTTGTGATTCTCTCGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGACTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
65641 CGTTGCGACTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATT
1 CGTTGCGACTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATT
65685 TTCATTATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 29 0.71
48 12 0.29
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (48 bp):
CGTTGCGACTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:65689 original size:20 final size:20
Alignment explanation
Indices: 65655--65712 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
65645 GCGACTCTCT
**
65655 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
65675 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
65695 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
65713 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:67883 original size:42 final size:42
Alignment explanation
Indices: 67837--67925 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
67827 CCTATCGTTG
* *
67837 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCTTTC
1 AAGAGGCCACTATC-TTCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
67879 AAGAGGCCACTGTCTTCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCTTCCTCGAAGAGGTCCCTCCCACCATTC
67921 AAGAG
1 AAGAG
67926 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.12
42 33 0.82
43 2 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
AAGAGGCCACTATCTTCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:69293 original size:14 final size:14
Alignment explanation
Indices: 69273--69309 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
69263 TATTGTTTAA
69273 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
69286 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
69301 TTGATTTGT
1 TTGATTTGT
69310 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:69438 original size:19 final size:19
Alignment explanation
Indices: 69416--69533 Score: 87
Period size: 19 Copynumber: 6.7 Consensus size: 19
69406 AAAAATTACT
69416 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
69435 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
69449 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
69468 ATTGCAA--C--TA-GAGA
1 ATCGCAATGCGAAATGAAA
*
69482 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
69501 ATCGCAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
*
69520 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
69534 CTAAATTCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 48 0.62
20 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:69458 original size:33 final size:33
Alignment explanation
Indices: 69416--69509 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
69406 AAAAATTACT
*
69416 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
69449 ATCGCAATGCGAAATGAAAATTGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
69482 ATCGCAATGCGAAATAAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
69510 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:69550 original size:19 final size:19
Alignment explanation
Indices: 69481--69543 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
69471 GCAACTAGAG
*
69481 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
69500 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
69519 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
69538 ATTCGC
1 AATCGC
69544 GTTGCGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:69585 original size:33 final size:33
Alignment explanation
Indices: 69543--69702 Score: 275
Period size: 33 Copynumber: 4.8 Consensus size: 33
69533 ACTAAATTCG
*
69543 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
69576 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
69609 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
**
69642 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
69675 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
69703 AGTAATTTTC
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 124 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:69649 original size:14 final size:14
Alignment explanation
Indices: 69564--69684 Score: 53
Period size: 14 Copynumber: 7.6 Consensus size: 14
69554 TCATTTCGCT
*
69564 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
69578 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
69595 CTTTGCGATTCCCTCG
1 --TTGCGATTCTCTCG
*
69611 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
69628 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
69644 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
69661 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
69677 TTGCGATT
1 TTGCGATT
69685 TTCATTTCGC
Statistics
Matches: 82, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 26 0.32
16 20 0.24
17 18 0.22
19 18 0.22
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:69768 original size:20 final size:20
Alignment explanation
Indices: 69696--69768 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
69686 TCATTTCGCA
* *
69696 TTGCGATAGTAATTTTCGCG
1 TTGCGATAGTCATTTTCGTG
* **
69716 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTTCG-TG
69736 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTTCGTG
69757 TTGCGATAGTCA
1 TTGCGATAGTCA
69769 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:72043 original size:12 final size:12
Alignment explanation
Indices: 72026--72050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72016 TCTTCGGGGA
72026 CTTTTTCTTCTT
1 CTTTTTCTTCTT
72038 CTTTTTCTTCTT
1 CTTTTTCTTCTT
72050 C
1 C
72051 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:73022 original size:20 final size:20
Alignment explanation
Indices: 72997--73113 Score: 153
Period size: 20 Copynumber: 5.8 Consensus size: 20
72987 ACTTTGAAAA
*
72997 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
* *
73017 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
* * *
73037 TCGTAATGCAATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
73057 CCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
73077 TCGCAACGAGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
73097 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
73114 AAATCGCAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:73121 original size:40 final size:40
Alignment explanation
Indices: 72991--73122 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 40
72981 TTGCGAACTT
* * * *
72991 TGAAAATCGCAACGCGATACTGACTTTCGCAATGCGATAC
1 TGAAAATCGCAACGAGATTCTGACTTTCGCAACGCGATTC
*** * * *
73031 TGACTTTCGTAATGCA-ATTCTGACTTCCGCAACGCGATTC
1 TGAAAATCGCAACG-AGATTCTGACTTTCGCAACGCGATTC
*** *
73071 TGACTTTCGCAACGAGATTCTGACTTTCGCAACGAGATTC
1 TGAAAATCGCAACGAGATTCTGACTTTCGCAACGCGATTC
73111 TGAAAATCGCAA
1 TGAAAATCGCAA
73123 TCATCTTCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (40 bp):
TGAAAATCGCAACGAGATTCTGACTTTCGCAACGCGATTC
Found at i:73122 original size:60 final size:60
Alignment explanation
Indices: 72991--73122 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
72981 TTGCGAACTT
* * * *
72991 TGAAAATCGCAACGCGATACTGACTTTCGCAATGCGATACTGACTTTCGTAATGCAATTC
1 TGAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACTGACTTTCGCAACGCAATTC
** * *
73051 TG-ACTTCCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGACTTTCGCAACG-AGATTC
1 TGAAAAT-CGCAACGCGATACTGACTTTCGCAACGAGATACTGACTTTCGCAACGCA-ATTC
73111 TGAAAATCGCAA
1 TGAAAATCGCAA
73123 TCATCTTCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.05
60 54 0.92
61 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (60 bp):
TGAAAATCGCAACGCGATACTGACTTTCGCAACGAGATACTGACTTTCGCAACGCAATTC
Found at i:73344 original size:20 final size:20
Alignment explanation
Indices: 73319--73376 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
73309 ATTCATTTGA
73319 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
73339 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
73359 CTATCGCAACGCGAAAAT
1 CTATCGCAACGCGAAAAT
73377 CGCAATGCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:75047 original size:41 final size:42
Alignment explanation
Indices: 74993--75084 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
74983 CCTCTTCAAC
* *
74993 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
75034 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
75076 GATGACAGG
1 GATGACAGG
75085 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:75049 original size:21 final size:21
Alignment explanation
Indices: 75020--75080 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
75010 GAACGGTGGG
*
75020 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
75041 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
75062 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
75081 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:75446 original size:20 final size:20
Alignment explanation
Indices: 75421--75493 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
75411 GAAGAATAGT
*
75421 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
75441 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
75461 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
75481 TGACTATCGCAAC
1 TTACTTTCGCAAC
75494 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:75471 original size:40 final size:40
Alignment explanation
Indices: 75427--75512 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
75417 TAGTTTACTT
* *
75427 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
75467 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
75507 TCGCAA
1 TCGCAA
75513 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:75494 original size:20 final size:20
Alignment explanation
Indices: 75447--75533 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
75437 AAACTTACTT
*
75447 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
75467 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
75487 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
75507 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
75526 TCGCAACG
1 TCGCAACG
75534 ACAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:75586 original size:19 final size:19
Alignment explanation
Indices: 75564--75642 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
75554 ACAAATTGCA
75564 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
75583 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
75597 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
75616 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
75636 TTGCGAT
1 TTGCGAT
75643 AATCATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 8 0.17
15 3 0.06
16 2 0.04
17 2 0.04
18 3 0.06
19 19 0.40
20 10 0.21
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:75649 original size:20 final size:19
Alignment explanation
Indices: 75595--75650 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
75585 GCGATTTTGT
**
75595 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAATCATTTCG
* **
75614 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAATCATTT-CG
75634 CGTTGCGATAATCATTT
1 CGTTGCGATAATCATTT
75651 TCTTGTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAATCATTTCG
Found at i:76229 original size:18 final size:18
Alignment explanation
Indices: 76206--76253 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
76196 AGGGTCGATC
76206 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
76224 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
76242 AGGTGATGGCTC
1 AGGTGATGGCTC
76254 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:77911 original size:22 final size:22
Alignment explanation
Indices: 77884--77927 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
77874 GATGGAGATA
77884 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
77906 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
77928 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:78198 original size:21 final size:22
Alignment explanation
Indices: 78169--78252 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 22
78159 AGTTGTGAAA
78169 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
* *
78191 GT-ATTATCGCGTTGCGA--TA
1 GTCAGTATCGCGTTGCGATTTT
78210 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
* *
78232 -CCA-AATTCGCGTTGCGATTTT
1 GTCAGTA-TCGCGTTGCGATTTT
78253 CAAAATTCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.60
22 3 0.06
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (22 bp):
GTCAGTATCGCGTTGCGATTTT
Found at i:78217 original size:41 final size:41
Alignment explanation
Indices: 78094--78231 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
78084 CGCTTTGAAA
* * *
78094 ATCGCATTGCGATTATGTATTATCTCATTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCTCGTTGCGAAAGTCAGT
* ** * * * *
78135 ATTGCGTTGCGAAATT-AAGTATCTAGTTGTGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCTCGTTGCGAAAGTCAGT
* *
78175 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCTCGTTGCGAAAGTCAGT
78216 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
78232 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCTCGTTGCGAAAGTCAGT
Found at i:78228 original size:20 final size:20
Alignment explanation
Indices: 78121--78227 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
78111 TATTATCTCA
*
78121 TTGCGAAAGTCAGTATTGCG
1 TTGCGAAAGTCAGTATCGCG
* * **
78141 TTGCGAAATTAAGTATCTAG
1 TTGCGAAAGTCAGTATCGCG
*
78161 TTGTGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
** *
78181 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--AAGTCAGTATCGCG
*
78202 TTGCGATAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
78222 TTGCGA
1 TTGCGA
78228 TTTTCCAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
19 3 0.04
20 49 0.72
21 14 0.21
22 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCG
Found at i:78242 original size:41 final size:41
Alignment explanation
Indices: 78121--78249 Score: 127
Period size: 41 Copynumber: 3.2 Consensus size: 41
78111 TATTATCTCA
* * ** * **
78121 TTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAGTATCTAG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCG
* * ** *
78161 TTGTGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCG
78202 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCG
78243 TTGCGAT
1 TTGCGAT
78250 TTTCAAAATT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
40 26 0.35
41 46 0.62
42 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCG
Found at i:78253 original size:21 final size:21
Alignment explanation
Indices: 78217--78272 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
78207 ATAGTCAGTA
*
78217 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCAAAAT
78238 TCGCGTTGCGATTTTCAAAAT
1 TCGCGTTGCGATTTTCAAAAT
*
78259 TCGCATTGCGATTT
1 TCGCGTTGCGATTT
78273 ACTTATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAT
Found at i:78331 original size:21 final size:22
Alignment explanation
Indices: 78279--78331 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
78269 ATTTACTTAT
78279 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
78300 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
78321 TCGCATTGCGA
1 TCGCATTGCGA
78332 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:80991 original size:19 final size:20
Alignment explanation
Indices: 80948--80995 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
80938 AAGCAGTCAA
*
80948 TATCGATACTGAGAGTTAGG
1 TATCGATACTCAGAGTTAGG
*
80968 TATCGATACTCAGGGTTA-G
1 TATCGATACTCAGAGTTAGG
80987 TATCGATAC
1 TATCGATAC
80996 CAACGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGATACTCAGAGTTAGG
Found at i:82136 original size:2 final size:2
Alignment explanation
Indices: 82129--82156 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82119 TAAATTCTTA
82129 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
82157 TAATTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85001 original size:2 final size:2
Alignment explanation
Indices: 84994--85021 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84984 AGAGGAAACC
84994 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
85022 GATTAGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.