Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002401.1 Hibiscus syriacus cultivar Beakdansim tig00004911_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: 94049
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1150 original size:3 final size:3
Alignment explanation
Indices: 1142--1182 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1132 GATGTATAAA
1142 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1183 ATAACTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3033 original size:32 final size:32
Alignment explanation
Indices: 2997--3065 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
2987 TCTAAATGTG
* *
2997 ACACTAACACTCCTATGCATTATATGAATGCA
1 ACACTAACACTCATAAGCATTATATGAATGCA
* * * *
3029 ACACTGACTCTGATAAGCATTATTTGAATGCA
1 ACACTAACACTCATAAGCATTATATGAATGCA
3061 ACACT
1 ACACT
3066 GTTAGTATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (32 bp):
ACACTAACACTCATAAGCATTATATGAATGCA
Found at i:3965 original size:19 final size:20
Alignment explanation
Indices: 3941--4001 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
3931 AAAAATTTAT
3941 AATAGTATTG-TACTGTATG
1 AATAGTATTGATACTGTATG
* *
3960 AATAGTATTGATATTGTATT
1 AATAGTATTGATACTGTATG
** *
3980 AATAGTACCGATACTGTGTG
1 AATAGTATTGATACTGTATG
4000 AA
1 AA
4002 CAGTGGTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 10 0.29
20 24 0.71
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (20 bp):
AATAGTATTGATACTGTATG
Found at i:4108 original size:21 final size:21
Alignment explanation
Indices: 4078--4131 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
4068 ACTGCTACAA
* *
4078 TAGTACCGATACCATGAATAG
1 TAGTATCGATACCATGAACAG
4099 TAGTATCGATACCATGAACAG
1 TAGTATCGATACCATGAACAG
4120 TAGTATCGATAC
1 TAGTATCGATAC
4132 TATCAAGCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
TAGTATCGATACCATGAACAG
Found at i:5897 original size:20 final size:20
Alignment explanation
Indices: 5883--5932 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5873 TGACCTGGGT
5883 TGACCCGACCCGACCCGGTC
1 TGACCCGACCCGACCCGGTC
5903 TGACCCGACCCGACCC-GT-
1 TGACCCGACCCGACCCGGTC
*
5921 TGACCCAACCCG
1 TGACCCGACCCG
5933 TTGACCGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 11 0.38
19 2 0.07
20 16 0.55
ACGTcount: A:0.18, C:0.50, G:0.22, T:0.10
Consensus pattern (20 bp):
TGACCCGACCCGACCCGGTC
Found at i:5931 original size:13 final size:13
Alignment explanation
Indices: 5909--5938 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5899 GGTCTGACCC
*
5909 GACCCGACCCGTT
1 GACCCAACCCGTT
5922 GACCCAACCCGTT
1 GACCCAACCCGTT
5935 GACC
1 GACC
5939 GTTAACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:6182 original size:135 final size:135
Alignment explanation
Indices: 5927--6170 Score: 321
Period size: 135 Copynumber: 1.8 Consensus size: 135
5917 CCGTTGACCC
* * * *
5927 AACCCGTTGACCGTTAACTTTGACCAAAAAGTAAATTTTTCGAAAAGTCACATTTTAAGTTTTTT
1 AACCCGTTGACCGTTAACTTTGAACAAAAAGTAAAATTTTCAAAAAGTCACATTTTAAGTTTTTC
* *
5992 GATATCCTGAGTCCGAATCTGAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCGAAATTATT
66 GACATCCTGAGTCCGAATCCGAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCGAAATTATT
6057 AGTCA
131 AGTCA
* * * * *
6062 AACCCGTTGA-CTTTGACTTTGAACAAAAAGTCAAAATTTTCAAAAAGTTATATTTTATGTTTTT
1 AACCCGTTGACCGTTAACTTTGAACAAAAAGT-AAAATTTTCAAAAAGTCACATTTTAAGTTTTT
* * * *
6126 CGACGTCCTGAG-CCTGATTCCGAAGTCTGTTTTGCCAGATTCAAA
65 CGACATCCTGAGTCC-GAATCCGAAGTCCGTTTTGCCAAATTCAAA
6171 TTTGAAAGCC
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
134 20 0.22
135 72 0.78
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (135 bp):
AACCCGTTGACCGTTAACTTTGAACAAAAAGTAAAATTTTCAAAAAGTCACATTTTAAGTTTTTC
GACATCCTGAGTCCGAATCCGAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCGAAATTATT
AGTCA
Found at i:7631 original size:19 final size:20
Alignment explanation
Indices: 7607--7654 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
7597 AGTGATTTTC
* *
7607 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
7626 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
7646 TTTTGAAAA
1 TTTTGAAAA
7655 AGGATTTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:7701 original size:21 final size:21
Alignment explanation
Indices: 7626--7701 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 21
7616 CAAAAATGGA
** *
7626 TTTTGAAAACCAAAATGAAA-
1 TTTTGAAAAAGAAATTGAAAG
* * *
7646 TTTTGAAAAAG-GATTTACAG
1 TTTTGAAAAAGAAATTGAAAG
* *
7666 ATTTCAAAAATGAAATTGAAAG
1 TTTTGAAAAA-GAAATTGAAAG
7688 TTTTGAAAAAGAAA
1 TTTTGAAAAAGAAA
7702 ATTTTGATTT
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
19 4 0.10
20 17 0.43
21 5 0.12
22 14 0.35
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.29
Consensus pattern (21 bp):
TTTTGAAAAAGAAATTGAAAG
Found at i:9006 original size:21 final size:21
Alignment explanation
Indices: 8980--9026 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
8970 ATTGTATTGT
8980 ATGAACAATAGTATCAATACC
1 ATGAACAATAGTATCAATACC
*
9001 ATGAACAATAGTATCGATACC
1 ATGAACAATAGTATCAATACC
9022 ATGAA
1 ATGAA
9027 TAGTATCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (21 bp):
ATGAACAATAGTATCAATACC
Found at i:9030 original size:18 final size:19
Alignment explanation
Indices: 8986--9036 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
8976 TTGTATGAAC
*
8986 AATAGTATCAATACCATGAA
1 AATAGTATCGATACCATG-A
9006 CAATAGTATCGATACCATG-
1 -AATAGTATCGATACCATGA
9025 AATAGTATCGAT
1 AATAGTATCGAT
9037 GCTAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.41
21 17 0.59
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (19 bp):
AATAGTATCGATACCATGA
Found at i:10711 original size:21 final size:21
Alignment explanation
Indices: 10685--10732 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
10675 GGCATCCCAC
* *
10685 GGTGTTGTCCAG-ACGCACCGG
1 GGTGTTATCCAGCA-GCACCAG
10706 GGTGTTATCCAGCAGCACCAG
1 GGTGTTATCCAGCAGCACCAG
10727 GGTGTT
1 GGTGTT
10733 CCCTAGCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGTGTTATCCAGCAGCACCAG
Found at i:12214 original size:13 final size:13
Alignment explanation
Indices: 12196--12228 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12186 AACTCAGCTA
12196 GGCTCGATGACTC
1 GGCTCGATGACTC
12209 GGCTCGATGACTC
1 GGCTCGATGACTC
12222 GGCTCGA
1 GGCTCGA
12229 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.21
Consensus pattern (13 bp):
GGCTCGATGACTC
Found at i:13962 original size:20 final size:18
Alignment explanation
Indices: 13936--13987 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 18
13926 TTCGTCCAAG
13936 AGCATGTATTTTCACTTAA
1 AGCATGTATTTTCA-TTAA
13955 AGGCATGTATTTTCATTAA
1 A-GCATGTATTTTCATTAA
* *
13974 ATCATATATTTTCA
1 AGCATGTATTTTCA
13988 AAGGCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 6 0.20
20 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
AGCATGTATTTTCATTAA
Found at i:14779 original size:178 final size:178
Alignment explanation
Indices: 14468--14801 Score: 488
Period size: 178 Copynumber: 1.9 Consensus size: 178
14458 ATTTCTTTTA
* * ** *
14468 TTACTTGTCATTACATCATTCTAACTTAAACTTTTCTTATTTGTATCCCAAGCTTTCAAAGTGGG
1 TTACTTATAATTACATCATTCTAACTTAAACTTTTCTTATTTACAACCCAAGCTTTCAAAGTGGG
* * * * * *
14533 AATAACACTTATTGTTCGTCCTAGATCGGGAAACAATAAAGGTATCCCATTCTTCTTCATCCTTG
66 AACAAAACTTATTGTTCATCCTAGATCGGGAAACAATAAAGGCATCACATCCTTCTTCATCCTTG
*
14598 GAGGAGTGTGGACGGTCCTTTATCAAAACCTTATCCATCAGAATGCAT
131 GAGGAGTGTGGACGATCCTTTATCAAAACCTTATCCATCAGAATGCAT
* *
14646 TTACTTATAATTACATCATTCTAACTTAAATTTTTCTTATTTACAACCCAAGTTTTCAAAGTGGG
1 TTACTTATAATTACATCATTCTAACTTAAACTTTTCTTATTTACAACCCAAGCTTTCAAAGTGGG
* * * * **
14711 AACAAAACTTATTGTTTATCCTAGATTGGGAAACAATCAAGGCATTACATCCTTCTTCATTGTTG
66 AACAAAACTTATTGTTCATCCTAGATCGGGAAACAATAAAGGCATCACATCCTTCTTCATCCTTG
14776 GAGGAGTGTGGACGATCCTTTATCAA
131 GAGGAGTGTGGACGATCCTTTATCAA
14802 GTAGAATCAG
Statistics
Matches: 136, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
178 136 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (178 bp):
TTACTTATAATTACATCATTCTAACTTAAACTTTTCTTATTTACAACCCAAGCTTTCAAAGTGGG
AACAAAACTTATTGTTCATCCTAGATCGGGAAACAATAAAGGCATCACATCCTTCTTCATCCTTG
GAGGAGTGTGGACGATCCTTTATCAAAACCTTATCCATCAGAATGCAT
Found at i:18102 original size:20 final size:20
Alignment explanation
Indices: 18073--18110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18063 TTTCAAAGTG
18073 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
18093 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
18111 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:18186 original size:91 final size:92
Alignment explanation
Indices: 18071--18252 Score: 228
Period size: 91 Copynumber: 2.0 Consensus size: 92
18061 TTTTTCAAAG
* *
18071 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CAATTAATTTTTC-AAACATCGAAGGCA
1 TGATGCACCGATGCACCAAACCATGCATCGATGCACTC-A-GAATTTTTCAAAACATCGAAGGCA
*
18134 TTTAATGCATCGTTGCA-CTTAGTGCATT
64 TTTAATGCATCGATGCACCTTAGTGCATT
* ** *
18162 TGATGCATCGATGCA-CAAGACCATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCAT
1 TGATGCACCGATGCACCAA-ACCATGCATCGATGCACTCAGAATTTTTCAAAACATCGAAGGCAT
*
18226 TTTATGCATCGATGCACTCTTAGTGCA
65 TTAATGCATCGATGCAC-CTTAGTGCA
18253 CCGATGCATT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
90 9 0.12
91 59 0.76
92 1 0.01
93 9 0.12
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (92 bp):
TGATGCACCGATGCACCAAACCATGCATCGATGCACTCAGAATTTTTCAAAACATCGAAGGCATT
TAATGCATCGATGCACCTTAGTGCATT
Found at i:26773 original size:20 final size:20
Alignment explanation
Indices: 26744--26781 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26734 TTTCAAAGTG
*
26744 ATGCACCGATGTACCAATCC
1 ATGCACCGATGCACCAATCC
*
26764 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
26782 TAATTTTTCA
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:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:26858 original size:45 final size:46
Alignment explanation
Indices: 26804--26891 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
26794 CATCGAATGA
* *
26804 ATTTTATGCATCGATGCAC-ATACCATGCATCCATGCACTCAGTGC
1 ATTTGATGCATCGATGCACAAGACCATGCATCCATGCACTCAGTGC
*
26849 ATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 ATTTGATGCATCGATGCACAAGACCATGCATCCATGCACTCAG
26892 GCTTTTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (46 bp):
ATTTGATGCATCGATGCACAAGACCATGCATCCATGCACTCAGTGC
Found at i:28262 original size:21 final size:20
Alignment explanation
Indices: 28218--28272 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
28208 TTGCAGCCTT
*
28218 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
28238 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGC-AG
28259 GATGCATCGATGCA
1 GATGCATCGATGCA
28273 CTAATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:28361 original size:21 final size:21
Alignment explanation
Indices: 28292--28392 Score: 118
Period size: 21 Copynumber: 4.8 Consensus size: 21
28282 TTCGATGTTT
*
28292 GGATGCATGGATGCATTGCA-
1 GGATGCATGGATGCACTGCAG
* * *
28312 TGATGCATCGATGCA-T-TAG
1 GGATGCATGGATGCACTGCAG
28331 TGCAGATGCATGGATGCACTGCAG
1 -G--GATGCATGGATGCACTGCAG
28355 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCACTGCAG
28376 GGATGCATGGATGCACT
1 GGATGCATGGATGCACT
28393 TTGACACCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 13 0.19
21 37 0.54
22 13 0.19
23 2 0.03
24 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
GGATGCATGGATGCACTGCAG
Found at i:28493 original size:29 final size:29
Alignment explanation
Indices: 28472--28529 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
28462 AAACTTTGAA
28472 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
28501 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
28530 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:28519 original size:30 final size:30
Alignment explanation
Indices: 28472--28531 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
28462 AAACTTTGAA
28472 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
28501 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
28532 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:29793 original size:23 final size:22
Alignment explanation
Indices: 29751--29809 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
29741 TCAAATCAAT
29751 ATTTTCTTTTTCAAAACTCTCA
1 ATTTTCTTTTTCAAAACTCTCA
* *
29773 ATTTTCATTTTTGAAAGCTCT-A
1 ATTTTC-TTTTTCAAAACTCTCA
* *
29795 A-ATCCTTTTTCAAAA
1 ATTTTCTTTTTCAAAA
29810 TTTCATTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 8 0.27
21 2 0.07
22 8 0.27
23 12 0.40
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTTTCTTTTTCAAAACTCTCA
Found at i:29837 original size:19 final size:20
Alignment explanation
Indices: 29801--29848 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
29791 TCTAAATCCT
*
29801 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
*
29821 TTTTCAAAA-TCCATTTTTG
1 TTTTCAAAATTCCATTTTGG
*
29840 CTTTCAAAA
1 TTTTCAAAA
29849 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:31246 original size:64 final size:64
Alignment explanation
Indices: 31193--31355 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
31183 CGGTGCACCA
*
31193 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
31257 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
31322 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
31356 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:31327 original size:19 final size:19
Alignment explanation
Indices: 31303--31353 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
31293 GAAAATATTC
31303 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
31322 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
31341 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
31354 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:36979 original size:26 final size:27
Alignment explanation
Indices: 36908--37038 Score: 90
Period size: 27 Copynumber: 4.9 Consensus size: 27
36898 AATCTTAGTT
* ** *
36908 TTGAGGGTATTTAGGTCATTCCAAAAC
1 TTGAGGGTATTTTGGTCATTTTAAAGC
* **
36935 TCGAGGGTATTTTTATCATTTTAAAGC
1 TTGAGGGTATTTTGGTCATTTTAAAGC
36962 TTGA-GGTATTTTGGTCATTTTAAAG-
1 TTGAGGGTATTTTGGTCATTTTAAAGC
* * *
36987 TTTAGGGGTA-ATTGAGTTATTTTAAAG-
1 TTGA-GGGTATTTTG-GTCATTTTAAAGC
* * * *
37014 TTTAGGGGAATTTGATCATTTTAAA
1 TTGAGGGTATTTTGGTCATTTTAAA
37039 AAATTCATTC
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
25 3 0.04
26 35 0.42
27 45 0.54
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (27 bp):
TTGAGGGTATTTTGGTCATTTTAAAGC
Found at i:37008 original size:27 final size:26
Alignment explanation
Indices: 36949--37038 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 26
36939 GGGTATTTTT
* * *
36949 ATCATTTTAAAGCTT-GAGGTATTTTG
1 ATCATTTTAAAGTTTAG-GGGAATTTG
*
36975 GTCATTTTAAAGTTTAGGGGTAA-TTG
1 ATCATTTTAAAGTTTAGGGG-AATTTG
*
37001 AGTTATTTTAAAGTTTAGGGGAATTTG
1 A-TCATTTTAAAGTTTAGGGGAATTTG
37028 ATCATTTTAAA
1 ATCATTTTAAA
37039 AAATTCATTC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 29 0.55
27 24 0.45
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.44
Consensus pattern (26 bp):
ATCATTTTAAAGTTTAGGGGAATTTG
Found at i:47328 original size:2 final size:2
Alignment explanation
Indices: 47321--47349 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47311 AGTCGGATGA
47321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47350 GGTTGGATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48771 original size:31 final size:31
Alignment explanation
Indices: 48734--48796 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
48724 TTTTTTCTAT
48734 TAGTTTTCTTCGTAGTATGGGATTCTACATG
1 TAGTTTTCTTCGTAGTATGGGATTCTACATG
*
48765 TAGTTTTCTTCGTAGTATGGGTTTCTACATG
1 TAGTTTTCTTCGTAGTATGGGATTCTACATG
48796 T
1 T
48797 TTCGTTGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.48
Consensus pattern (31 bp):
TAGTTTTCTTCGTAGTATGGGATTCTACATG
Found at i:50096 original size:2 final size:2
Alignment explanation
Indices: 50024--50078 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
50014 TTTATAATGG
50024 TA TA TA TA TA TA 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
50066 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
50079 CCATCCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50102 original size:20 final size:21
Alignment explanation
Indices: 50069--50110 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
50059 ATATATATAT
50069 ATATATATATCCATCCAAAAC
1 ATATATATATCCATCCAAAAC
50090 ATATATA-ATCCATCCAAAAC
1 ATATATATATCCATCCAAAAC
50110 A
1 A
50111 ACATAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (21 bp):
ATATATATATCCATCCAAAAC
Found at i:50370 original size:16 final size:16
Alignment explanation
Indices: 50345--50380 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
50335 TTCAGTCAAT
*
50345 GTTTATTCATTATTTA
1 GTTTACTCATTATTTA
50361 GTTTACTCATTATTTA
1 GTTTACTCATTATTTA
50377 GTTT
1 GTTT
50381 TGTTATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.61
Consensus pattern (16 bp):
GTTTACTCATTATTTA
Found at i:55127 original size:25 final size:28
Alignment explanation
Indices: 55097--55150 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
55087 AAGGGCACTA
55097 TTTTTCAA-A-AC-TTCATCAAACATTT
1 TTTTTCAACATACTTTCATCAAACATTT
*
55122 TTTTTCAACATTCTTTCATCAAACATTT
1 TTTTTCAACATACTTTCATCAAACATTT
55150 T
1 T
55151 CAAAACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 1 0.04
27 1 0.04
28 15 0.60
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTTCAACATACTTTCATCAAACATTT
Found at i:55143 original size:14 final size:14
Alignment explanation
Indices: 55108--55174 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 14
55098 TTTTCAAAAC
55108 TTCATCAAACATTT
1 TTCATCAAACATTT
**
55122 TTTTTC-AACATTCT
1 TTCATCAAACATT-T
55136 TTCATCAAACA-TT
1 TTCATCAAACATTT
*
55149 TTCA--AAAC-TTA
1 TTCATCAAACATTT
*
55160 TTCATTAAACATTT
1 TTCATCAAACATTT
55174 T
1 T
55175 CACCTTTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
11 9 0.22
13 15 0.37
14 13 0.32
15 4 0.10
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.46
Consensus pattern (14 bp):
TTCATCAAACATTT
Found at i:55575 original size:30 final size:30
Alignment explanation
Indices: 55539--55606 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
55529 GGCCACTAAT
55539 GTTAAATAGTA-AAGGAAGTTGGACACCAAG
1 GTTAAATAGTAGAA-GAAGTTGGACACCAAG
* * *
55569 GTTAAATAGTAGAAGAAGTTGGCCATCAAT
1 GTTAAATAGTAGAAGAAGTTGGACACCAAG
55599 GTTAAATA
1 GTTAAATA
55607 ACACATGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.25
Consensus pattern (30 bp):
GTTAAATAGTAGAAGAAGTTGGACACCAAG
Found at i:56289 original size:231 final size:232
Alignment explanation
Indices: 55862--56316 Score: 529
Period size: 231 Copynumber: 2.0 Consensus size: 232
55852 TTTCAATTAT
** * * *
55862 GACTAAACCTCCTCAAACGTGAATGAACAATGTCATCATCAAATTTGACATCGAGCAAATCACCC
1 GACTAAACCTCCTCAAACGCAAAGGAACAATGTCATCATCAAATTTAACATCAAGCAAATCACCC
* * * * * * * *
55927 AAAAGCGATCAGATCTCTTTAGCATGTAGGGGAAATTTCATTTACAAAATCAAATTATCTCTAGA
66 AAAAGCGACCAAATCTCTTCAACACGTAAGGGAAATATCATTTACAAAATCAAATTATCTATAGA
* * * * *
55992 TAATAAGACTTCCTTAACGTGAAAGAACAATGTTGTCTTCCCAGGTACAATTATCCAAATATGAC
131 CAATAAGACTTCCTCAACGTGAAAGAAAAATGTTGTCTTCACAGGCACAATTATCCAAATATGAC
*
56057 TAGATGTACTCAACACGAAGGAACAATGTCGTCTATA
196 TAGACGTACTCAACACGAAGGAACAATGTCGTCTATA
* * * *
56094 GACTAGACCTCCTC-AACGCAAAGGAACAATGTCATCATCAGATTTAATATCAAGCAAATCACTC
1 GACTAAACCTCCTCAAACGCAAAGGAACAATGTCATCATCAAATTTAACATCAAGCAAATCACCC
** * * *
56158 TGAAGTGACCAAATCTCTTCAACACG-AAGGGACAATATCATTTCCAAAGTCAAATTATCTATAG
66 AAAAGCGACCAAATCTCTTCAACACGTAAGGGA-AATATCATTTACAAAATCAAATTATCTATAG
* * ** * * * * *
56222 GCAATCAGGTTTCCTCAACGTGAAGGAAAAATGTTGTCTTCAGATGCACAATCTTTGC-AATATG
130 ACAATAAGACTTCCTCAACGTGAAAGAAAAATGTTGTCTTCACAGGCACAAT-TATCCAAATATG
*
56286 ACTAGACGTCCTCAACACGAAGGAACAATGT
194 ACTAGACGTACTCAACACGAAGGAACAATGT
56317 TGTCAGTAAA
Statistics
Matches: 183, Mismatches: 38, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
230 5 0.03
231 162 0.89
232 16 0.09
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (232 bp):
GACTAAACCTCCTCAAACGCAAAGGAACAATGTCATCATCAAATTTAACATCAAGCAAATCACCC
AAAAGCGACCAAATCTCTTCAACACGTAAGGGAAATATCATTTACAAAATCAAATTATCTATAGA
CAATAAGACTTCCTCAACGTGAAAGAAAAATGTTGTCTTCACAGGCACAATTATCCAAATATGAC
TAGACGTACTCAACACGAAGGAACAATGTCGTCTATA
Found at i:59292 original size:12 final size:13
Alignment explanation
Indices: 59274--59307 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
59264 AAAATCATAC
59274 TTCAAATTTAAAA
1 TTCAAATTTAAAA
*
59287 TT-AAATTAAAAA
1 TTCAAATTTAAAA
59299 TTCAAATTT
1 TTCAAATTT
59308 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
TTCAAATTTAAAA
Found at i:67301 original size:20 final size:21
Alignment explanation
Indices: 67262--67301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
67252 TTTCATCGAG
* *
67262 CTCTTTTTTTTTTGCATAAAC
1 CTCTTTTCTTTTAGCATAAAC
67283 CTCTTTTCTTTTAGC-TAAA
1 CTCTTTTCTTTTAGCATAAA
67302 GCTGCTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (21 bp):
CTCTTTTCTTTTAGCATAAAC
Found at i:69298 original size:24 final size:24
Alignment explanation
Indices: 69271--69342 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
69261 GTAAACGGAT
69271 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
69295 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
* *
69319 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
69342 A
1 A
69343 GGTAACGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:69343 original size:12 final size:12
Alignment explanation
Indices: 69275--69366 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
69265 ACGGATATAT
* *
69275 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
69287 CAGAATTCATAT
1 CAGAATTCAGAA
*
69299 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
69311 CAGAATCCAGAT
1 CAGAATTCAGAA
69323 CAGAA-TCAGAA
1 CAGAATTCAGAA
69334 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
69348 C-GTA-TCAGAA
1 CAGAATTCAGAA
69358 CAGAATTCA
1 CAGAATTCA
69367 ATTCAGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:69354 original size:47 final size:47
Alignment explanation
Indices: 69273--69380 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 47
69263 AAACGGATAT
* * *
69273 ATCAGAAATCAAAACAGAATTCATATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCATAACAGATATCAGAACAGAATCCA
*
69320 GATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCA--TAACAGATATCAGAACAGAATCCA
69367 ATTCAGAAATCAGA
1 A-TCAGAAATCAGA
69381 TAAAATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
46 1 0.02
47 35 0.67
48 13 0.25
49 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCATAACAGATATCAGAACAGAATCCA
Found at i:69378 original size:24 final size:24
Alignment explanation
Indices: 69274--69380 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
69264 AACGGATATA
*
69274 TCAGAAATCAAAACAGAATTC-AT
1 TCAGAAATCAGAACAGAATTCAAT
* * *
69297 ATCAGATATCATAACAGAATCCAGA-
1 -TCAGAAATCAGAACAGAATTCA-AT
**
69322 TCAG-AATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAT
* *
69345 TAACG-TATCAGAACAGAATTCAAT
1 TCA-GAAATCAGAACAGAATTCAAT
69369 TCAGAAATCAGA
1 TCAGAAATCAGA
69381 TAAAATATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 17 0.26
24 47 0.72
26 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAT
Found at i:70089 original size:18 final size:18
Alignment explanation
Indices: 70079--70119 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
70069 GTCGGGTCAA
70079 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
70097 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
70115 CGGGT
1 CGGGT
70120 TATGACTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:70119 original size:13 final size:13
Alignment explanation
Indices: 70060--70102 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
70050 GCTGGTCAAC
70060 GGTCAACGGGTCG
1 GGTCAACGGGTCG
70073 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
70086 GGTCAACAGGTCG
1 GGTCAACGGGTCG
70099 GGTC
1 GGTC
70103 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:72139 original size:24 final size:24
Alignment explanation
Indices: 72112--72183 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
72102 GTAAACGGAG
*
72112 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
72136 ATATAAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
72160 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
72183 A
1 A
72184 GGTAACGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 15 0.38
24 25 0.62
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:72178 original size:11 final size:11
Alignment explanation
Indices: 72145--72180 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
72135 CATATAAGAT
72145 ATCAGAACAGA
1 ATCAGAACAGA
*
72156 ATCCAGATCAGA
1 AT-CAGAACAGA
72168 ATCAGAACAGA
1 ATCAGAACAGA
72179 AT
1 AT
72181 TCAGGTAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (11 bp):
ATCAGAACAGA
Found at i:72184 original size:12 final size:12
Alignment explanation
Indices: 72116--72184 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
72106 ACGGAGATAT
* *
72116 CAGAAATCAAAA
1 CAGAATTCAGAA
*
72128 CAGAATTCATATA
1 CAGAATTCAGA-A
72141 -AG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
72152 CAGAATCCAGAT
1 CAGAATTCAGAA
72164 CAGAA-TCAGAA
1 CAGAATTCAGAA
72175 CAGAATTCAG
1 CAGAATTCAG
72185 GTAACGTATC
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 12 0.27
12 30 0.67
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:72214 original size:47 final size:48
Alignment explanation
Indices: 72114--72221 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 48
72104 AAACGGAGAT
* *
72114 ATCAGAAATCAAAACAGAATTCATATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
* * * *
72162 ATCAG-AATCAGAACAGAATTCAGGTAACG-TATCAGAATATAATTCA-
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCAG
72208 ATTCAGAAATCAGA
1 A-TCAGAAATCAGA
72222 TAAAATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
46 1 0.02
47 37 0.73
48 13 0.25
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:74657 original size:18 final size:18
Alignment explanation
Indices: 74636--74676 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
74626 CGCCGATCAA
74636 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
74654 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
74672 CGGGT
1 CGGGT
74677 TATGACTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:76777 original size:24 final size:24
Alignment explanation
Indices: 76750--76821 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
76740 GTAAACGGAG
* *
76750 ATATAAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
76774 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
* *
76798 AGATCAG-AATCAGAATAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
76821 A
1 A
76822 GGTAACGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 14 0.35
24 26 0.65
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:76793 original size:12 final size:11
Alignment explanation
Indices: 76758--76818 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
76748 AGATATAAGA
*
76758 AATCAAAACAG
1 AATCAGAACAG
* *
76769 AATTCATATCAG
1 AA-TCAGAACAG
76781 ATATCAGAACAG
1 A-ATCAGAACAG
*
76793 AATCCAGATCAG
1 AAT-CAGAACAG
*
76805 AATCAGAATAG
1 AATCAGAACAG
76816 AAT
1 AAT
76819 TCAGGTAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
11 13 0.32
12 26 0.65
13 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:85561 original size:8 final size:7
Alignment explanation
Indices: 85542--85597 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
85532 AGGTAAAGCC
85542 TTTCTTT
1 TTTCTTT
85549 CTTTCCTTT
1 -TTT-CTTT
85558 TTTCTTT
1 TTTCTTT
* *
85565 GTTGTTT
1 TTTCTTT
85572 TTTCTTCT
1 TTTCTT-T
85580 TTTCGTTT
1 TTTC-TTT
85588 TTTCTTT
1 TTTCTTT
85595 TTT
1 TTT
85598 TTTCTCTCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 19 0.46
8 16 0.39
9 6 0.15
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:85598 original size:16 final size:16
Alignment explanation
Indices: 85542--85598 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
85532 AGGTAAAGCC
* *
85542 TTTCTTTCTTTCCTTT
1 TTTCTTTTTTTCGTTT
*
85558 TTTC-TTTGTT-GTTT
1 TTTCTTTTTTTCGTTT
*
85572 TTTCTTCTTTTCGTTT
1 TTTCTTTTTTTCGTTT
85588 TTTCTTTTTTT
1 TTTCTTTTTTT
85599 TTCTCTCCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 18 0.55
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTTCGTTT
Found at i:88259 original size:17 final size:17
Alignment explanation
Indices: 88229--88261 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
88219 TTATTGATAA
88229 ATTATGATTTATTTAAG
1 ATTATGATTTATTTAAG
88246 ATTAT-ATTTGATTTAA
1 ATTATGATTT-ATTTAA
88262 TATTGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
ATTATGATTTATTTAAG
Found at i:93189 original size:22 final size:23
Alignment explanation
Indices: 93159--93206 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
93149 AAATGACCGA
*
93159 AAAACATGTGA-AAAGACAGAAG
1 AAAACATGTCATAAAGACAGAAG
* *
93181 AAAATATGTCATAAAGACAGATG
1 AAAACATGTCATAAAGACAGAAG
93204 AAA
1 AAA
93207 GTGTGTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.15
Consensus pattern (23 bp):
AAAACATGTCATAAAGACAGAAG
Found at i:93196 original size:23 final size:23
Alignment explanation
Indices: 93170--93216 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
93160 AAACATGTGA
93170 AAAGACAGAAGAAAATATGTCAT
1 AAAGACAGAAGAAAATATGTCAT
* * *
93193 AAAGACAGATGAAAGTGTGTCAT
1 AAAGACAGAAGAAAATATGTCAT
93216 A
1 A
93217 CATATAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (23 bp):
AAAGACAGAAGAAAATATGTCAT
Done.