Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004145.1 Hibiscus syriacus cultivar Beakdansim tig00009063_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: 63114
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2752 original size:24 final size:23
Alignment explanation
Indices: 2712--2769 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
2702 CATTACCTGA
*
2712 ATTCTGTTTGATTTCTGATCTGG
1 ATTCTGTTTGATATCTGATCTGG
**
2735 ATTCTGTTATGATATCTGATCTAA
1 ATTCTGTT-TGATATCTGATCTGG
2759 ATTCT-TTTGAT
1 ATTCTGTTTGAT
2770 TTTGATATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 10 0.32
24 17 0.55
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.52
Consensus pattern (23 bp):
ATTCTGTTTGATATCTGATCTGG
Found at i:3703 original size:30 final size:31
Alignment explanation
Indices: 3660--3718 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
3650 CAAATTTAAG
3660 CAAAATGGTTTTT-GACTTGAATTGAATTTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTTA
3691 CAAAAT-GTTTTTGGACTTAATTGAATTT
1 CAAAATGGTTTTTGGACTTAATTGAATTT
3719 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTTA
Found at i:3825 original size:21 final size:20
Alignment explanation
Indices: 3799--3897 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
3789 AGGGTGTCAA
3799 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
3820 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
3841 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* * *
3862 TAGTGCATCGATGCATCATGC
1 -AGTGCATCCATGCACCCTGC
3883 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3898 TCAAACACCG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.52
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:3833 original size:13 final size:14
Alignment explanation
Indices: 3830--3897 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
3820 AGTGCATCCA
*
3830 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
3843 TGCATCCATGCACC
1 TGCATCCATGCACG
*
3857 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
3872 ATGCAT-CATGCA-G
1 -TGCATCCATGCACG
3885 TGCATCCATGCAC
1 TGCATCCATGCAC
3898 TCAAACACCG
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
12 5 0.12
13 20 0.47
14 8 0.19
15 5 0.12
16 5 0.12
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.24
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:3888 original size:20 final size:20
Alignment explanation
Indices: 3799--3992 Score: 93
Period size: 21 Copynumber: 9.8 Consensus size: 20
3789 AGGGTGTCAA
* *
3799 AGTGCATCCATGCACCCCTGC
1 AGTGCATCGATGCA-TCCTGC
*
3820 AGTGCATCCATGCATCCCTGC
1 AGTGCATCGATGCAT-CCTGC
*
3841 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCGATGCATCCTG--C
*
3862 TAGTGCATCGATGCATCATGC
1 -AGTGCATCGATGCATCCTGC
*
3883 AGTGCATCCATGCA--CT-C
1 AGTGCATCGATGCATCCTGC
** * *
3900 A-AACACCGAATACAAT--T--
1 AGTGCATCG-ATGC-ATCCTGC
*
3917 AGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCATCCTGC
**
3937 TA-TGCATCGATGCATCAAGGC
1 -AGTGCATCGATGCATC-CTGC
*
3958 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
3978 TGTGCATCCATGCAT
1 AGTGCATCGATGCAT
3993 AAAGGCTGTA
Statistics
Matches: 136, Mismatches: 21, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.04
17 9 0.07
18 8 0.06
19 4 0.03
20 43 0.32
21 51 0.38
22 13 0.10
23 3 0.02
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTGC
Found at i:3965 original size:21 final size:21
Alignment explanation
Indices: 3939--4001 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
3929 CATCCTTCTA
3939 TGCATCGATGCATCAAGGCTG
1 TGCATCGATGCATCAAGGCTG
**
3960 TGCATCGATGCATC-CTGCTG
1 TGCATCGATGCATCAAGGCTG
* *
3980 TGCATCCATGCATAAAGGCTG
1 TGCATCGATGCATCAAGGCTG
4001 T
1 T
4002 AACGGCTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCAAGGCTG
Found at i:3965 original size:41 final size:41
Alignment explanation
Indices: 3918--4001 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
3908 AATACAATTA
* * *
3918 GTGCATCGATGCATCCTTCTATGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTATGCATCCATGCATAAAGGCT
*
3959 GTGCATCGATGCATCCTGCTGTGCATCCATGCATAAAGGCT
1 GTGCATCGATGCATCCTGCTATGCATCCATGCATAAAGGCT
4000 GT
1 GT
4002 AACGGCTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTATGCATCCATGCATAAAGGCT
Found at i:4398 original size:34 final size:32
Alignment explanation
Indices: 4359--4428 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
4349 TTTTGTAAAG
* *
4359 GGGAAATGTTCTAGCTAATCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
4393 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
4425 GGGA
1 GGGA
4429 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:6639 original size:29 final size:30
Alignment explanation
Indices: 6569--6628 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
6559 AAATTTAAGG
*
6569 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
6600 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
6629 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:6734 original size:21 final size:21
Alignment explanation
Indices: 6708--6765 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
6698 AGGGTGTTAA
6708 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
6729 AGTGCATCCATGCATCCTTGC
1 AGTGCATCCATGCACCCCTGC
6750 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
6766 TGCACTAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:6793 original size:42 final size:41
Alignment explanation
Indices: 6708--6806 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
6698 AGGGTGTTAA
*
6708 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCATCCTTGC
1 AGTGCATCCATGCACCCCT-CAGTGCATCCATGCATCCATGC
*
6750 AGTGCATCCATGCACCTGCACT-AGTGCATCGATGCAT-CATGC
1 AGTGCATCCATGCACC--C-CTCAGTGCATCCATGCATCCATGC
*
6792 AGTGCATTCATGCAC
1 AGTGCATCCATGCAC
6807 TCAAACACCG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
42 34 0.67
43 14 0.27
44 1 0.02
45 2 0.04
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (41 bp):
AGTGCATCCATGCACCCCTCAGTGCATCCATGCATCCATGC
Found at i:6797 original size:20 final size:20
Alignment explanation
Indices: 6726--6900 Score: 80
Period size: 20 Copynumber: 8.8 Consensus size: 20
6716 CATGCACCCC
* *
6726 TGCAGTGCATCCATGCATCCT
1 TGCAGTGCATCGATGCAT-CA
* *
6747 TGCAGTGCATCCATGCA-CC
1 TGCAGTGCATCGATGCATCA
6766 TGCACTAGTGCATCGATGCATCA
1 TG--C-AGTGCATCGATGCATCA
6789 TGCAGTGCATTC-ATGCA-C-
1 TGCAGTGCA-TCGATGCATCA
** *
6807 T-CA-AACACCGAATGCA--A
1 TGCAGTGCATCG-ATGCATCA
* *
6824 T-TAGTGCATCGATGCATCC
1 TGCAGTGCATCGATGCATCA
* *
6843 TTCTGTGCATCGATGCATCAA
1 TGCAGTGCATCGATGCATC-A
* * *
6864 GGCTGTGCATCGATGCATCC
1 TGCAGTGCATCGATGCATCA
* *
6884 TGCTGTGCATCCATGCA
1 TGCAGTGCATCGATGCA
6901 CGAAGGCTGC
Statistics
Matches: 122, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
15 1 0.01
16 2 0.02
17 14 0.11
18 5 0.04
19 5 0.04
20 41 0.34
21 38 0.31
22 13 0.11
23 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCAGTGCATCGATGCATCA
Found at i:6872 original size:41 final size:41
Alignment explanation
Indices: 6827--6909 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
6817 AATGCAATTA
* *
6827 GTGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCA-CGAAGGCT
6868 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
6909 G
1 G
6910 CAATGGCTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
Found at i:8724 original size:66 final size:66
Alignment explanation
Indices: 8618--8926 Score: 512
Period size: 66 Copynumber: 4.7 Consensus size: 66
8608 TTGTATCTAA
* * *
8618 ATGTAATTATGTTTGAGGTGAGAAAAGTTAGCAACAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
8683 G
66 G
* *
8684 ATGTAATTATGTATGAGATTAGAAAAGTTAGCAATAGGTTGTTGTACATATTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
8749 G
66 G
*
8750 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACAT-ATTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
8814 G
66 G
* *
8815 ATGTAATTATGTATGAGATGAGACAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
8880 G
66 G
* * *
8881 ATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTA
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTA
8927 TCTAAATGTA
Statistics
Matches: 229, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
65 62 0.27
66 167 0.73
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (66 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
G
Found at i:8857 original size:131 final size:132
Alignment explanation
Indices: 8618--8926 Score: 512
Period size: 131 Copynumber: 2.3 Consensus size: 132
8608 TTGTATCTAA
* * *
8618 ATGTAATTATGTTTGAGGTGAGAAAAGTTAGCAACAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
* * *
8683 GATGTAATTATGTATGAGATTAGAAAAGTTAGCAATAGGTTGTTGTACATATTTCTTATACATGT
66 GATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGT
8748 TG
131 TG
*
8750 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACAT-ATTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
*
8814 GATGTAATTATGTATGAGATGAGACAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGT
66 GATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGT
8879 TG
131 TG
* * *
8881 ATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTA
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTA
8927 TCTAAATGTA
Statistics
Matches: 166, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
131 120 0.72
132 46 0.28
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (132 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
GATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGT
TG
Found at i:9029 original size:184 final size:183
Alignment explanation
Indices: 8750--9241 Score: 776
Period size: 184 Copynumber: 2.7 Consensus size: 183
8740 ATACATGTTG
* * *
8750 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACAT-ATTCTTATACAT-GT
1 ATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATAGG-TGTTCTACATGTTTCTTATACATAGT
* * *
8813 -TGATGTAATTATGTATGAGATGAGACAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACAT
65 CGGA-GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACAT
*
8877 GTTGATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTATCTAA
129 ATTGATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTATCTAA
* * *
8932 ATGTAATTATGTGTGAGATGAGAAAAATTAGCAATATAGTGTTCTACATGTTTCTTATATATAGT
1 ATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATA-GGTGTTCTACATGTTTCTTATACATAGT
*
8997 CGGAGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTATTGTACATGTTTCTTATACATA
65 CGGAGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATA
* * *
9062 TTGATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTATCTGA
130 TTGATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTATCTAA
9116 ATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATAGGGTGTTCTACATGTTTCTTATACATAGT
1 ATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATA-GGTGTTCTACATGTTTCTTATACATAGT
*
9181 CGGAGTAATTATGTATGAGATGAGAAAA-TATAGCAATAGGTTGTTGTACATGTTTATTATA
65 CGGAGTAATTATGTATGAGATGAGAAAAGT-TAGCAATAGGTTGTTGTACATGTTTCTTATA
9242 TTTAGGTATG
Statistics
Matches: 285, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
182 43 0.15
183 12 0.04
184 228 0.80
185 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (183 bp):
ATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATAGGTGTTCTACATGTTTCTTATACATAGTC
GGAGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATAT
TGATGTAATTATGAATGAGATGAGAAAAGCTAGCAATAGATTGTTGTATCTAA
Found at i:9091 original size:66 final size:68
Alignment explanation
Indices: 8932--9110 Score: 249
Period size: 67 Copynumber: 2.7 Consensus size: 68
8922 TTGTATCTAA
* * * * *
8932 ATGTAATTATGTGTGAGATGAGAAAAATTAGCAATATAG-TGTTCTACATGTTTCTTATATATAG
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATA-GGTTGTTGTACATGTTTCTTATACATAG
8996 TCGG
65 TCGG
*
9000 A-GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTATTGTACATGTTTCTTATACATA-T
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATAGT
*
9063 -TG
66 CGG
*
9065 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTA
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTA
9111 TCTGAATGTA
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 44 0.44
67 53 0.53
68 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (68 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATAGT
CGG
Found at i:9143 original size:117 final size:118
Alignment explanation
Indices: 9001--9228 Score: 363
Period size: 117 Copynumber: 1.9 Consensus size: 118
8991 TATAGTCGGA
* * *
9001 GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTATTGTACATGTTTCTTATACATA-T-T
1 GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGGTATTCTACATGTTTCTTATACATAGTCG
9064 GATGTAATTATGTATGAGATGAGAAAAGT-TAGCAATAGATTGTTGTATCTGAAT
66 GA-GTAATTATGTATGAGATGAGAAAA-TATAGCAATAGATTGTTGTATCTGAAT
* *
9118 GTAATTATGTGTGAGATGAGAAAAGTTAGCAATAGGGTGTTCTACATGTTTCTTATACATAGTCG
1 GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGGTATTCTACATGTTTCTTATACATAGTCG
*
9183 GAGTAATTATGTATGAGATGAGAAAATATAGCAATAGGTTGTTGTA
66 GAGTAATTATGTATGAGATGAGAAAATATAGCAATAGATTGTTGTA
9229 CATGTTTATT
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
117 58 0.57
118 42 0.41
119 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (118 bp):
GTAATTATGTATGAGATGAGAAAAGTTAGCAATAGGGTATTCTACATGTTTCTTATACATAGTCG
GAGTAATTATGTATGAGATGAGAAAATATAGCAATAGATTGTTGTATCTGAAT
Found at i:10091 original size:20 final size:19
Alignment explanation
Indices: 10053--10091 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
10043 CAAAATCGAT
*
10053 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
10072 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
10092 GAAATCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:10108 original size:199 final size:197
Alignment explanation
Indices: 9489--10565 Score: 1131
Period size: 199 Copynumber: 5.4 Consensus size: 197
9479 TAAAGTAATA
** * * *
9489 GGTA-AAATATACATGTTTAATGACAAAATAGGTCTACATAATGTATCGAGACATTTTAAATTTG
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAATTTG
* * * *
9553 TGTCGATACATTTTGTCCAGAATGAATGTCAAACTAGGTGCACGCATAAAGTGTCGATATATTTA
66 TGTCGATACTTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTA
* * * * *
9618 TAAAACATATCGATCCTAAAAACATCGAAACCCTTAATTATAATATAATAGGTAATTTTACAATG
131 T-AAATATATCGATCCTAAAAACATCGAAA--CATAATTACAATGTAATAGGTAAATTTACAATG
9683 TAACC
193 TAACC
* * * * * * *
9688 GGTATAAATATAACGGTTTAATTAGAAAACAAGTCAACATAATGTATCGACACTTTTTAAATTTG
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAATTTG
* * * *
9753 TGTCGATACTTTTTGTCCATAATGAGTGCCCAAACGAGGTGCACGCATAAAGGGTCGATACATTT
66 TGTCGATACTTTTTGTCCAGAATGAATG-CCAAACAAGGTGCACGCATAAAGTGTCGATACATTT
* * * *
9818 ATAAAAAGTATCGATCAC-AAAAACATCGAAACACATAATTATAATGTAATAGGTAATTTTGCAA
130 ATAAATA-TATCGATC-CTAAAAACATCG-AA-ACATAATTACAATGTAATAGGTAAATTTACAA
9882 TGTAACC
191 TGTAACC
* * * * * * * * *
9889 GATATAAATACATCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGATACTTTTTTATTTTT
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAATTTG
* * ** *
9954 TGTCGAAACTTTTTATCCAGAATGAATGAAAAACAAGGCGCACGCATAAAGTGTCGATACATTTA
66 TGTCGATACTTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTA
* * * *
10019 -AAATTATATCGATCCCAAAAATATCAAAATCGATAATTACAATGTAATAGGTAAATTAACAATG
131 TAAA-TATATCGATCCTAAAAACATCGAAA-C-ATAATTACAATGTAATAGGTAAATTTACAATG
10083 TAACC
193 TAACC
* * ** * * *
10088 GGTAGAAATCTATTGGTTTTATGAAAAAATAGGTCTACATAATGTATCAACACAAATTTAGAA--
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACAC-ATTTTA-AATT
* * *
10151 AGTGTCGAT-CATTTTTGTCCACAATG-ATGCCAAAACTAA-GTACACGCATAAAGTGTCGATAC
64 TGTGTCGATAC-TTTTTGTCCAGAATGAATGCC-AAAC-AAGGTGCACGCATAAAGTGTCGATAC
*
10213 ATTTA-AAATTATATCGATCCTAAAAACATCGAAACTAATAATTACAATGTAATAGGTAAAATTA
126 ATTTATAAA-TATATCGATCCTAAAAACATCGAAAC--ATAATTACAATGTAATAGGTAAATTTA
10277 CAATGTAACC
188 CAATGTAACC
* * * * * *
10287 AGTATAAATATACCAGTTTTATGAGGAAGTAGGTCTACATAAAGTATCGACACAAATTTCGAAA-
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACAC--ATTT-TAAAT
* * * * *
10351 --GTGTCGATACTTTTTATCCAGAATGAATGCCCAACGAGGTGCACGAATAAAGTGTTGATACAT
63 TTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACAT
10414 TTATTAAA-AGTATCGATCCTAAAAACATCGAAACCTATAATTACAATGTAATAGGTAAATTTAC
128 TTA-TAAATA-TATCGATCCTAAAAACATCGAAA-C-ATAATTACAATGTAATAGGTAAATTTAC
*
10478 GATGT-ACTC
189 AATGTAAC-C
* * * *
10487 GGTAGAAATATGCCAGTTTTATGAGAAAATAGGTCTACATAAAGTATCGACAC-TTTATAAATTT
1 GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTT-TAAATTT
10551 GTGTCGATACTTTTT
65 GTGTCGATACTTTTT
10566 TGAAATTACG
Statistics
Matches: 743, Mismatches: 106, Indels: 57
0.82 0.12 0.06
Matches are distributed among these distances:
197 7 0.01
198 10 0.01
199 304 0.41
200 247 0.33
201 171 0.23
202 3 0.00
203 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (197 bp):
GGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAATTTG
TGTCGATACTTTTTGTCCAGAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTA
TAAATATATCGATCCTAAAAACATCGAAACATAATTACAATGTAATAGGTAAATTTACAATGTAA
CC
Found at i:14951 original size:20 final size:20
Alignment explanation
Indices: 14926--14976 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
14916 AAACACATAA
14926 TTATAATGTAATAGGTAAAT
1 TTATAATGTAATAGGTAAAT
14946 TTATAATGTAATAGGTAAAT
1 TTATAATGTAATAGGTAAAT
*
14966 TTACAATGTAA
1 TTATAATGTAA
14977 CCGATAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (20 bp):
TTATAATGTAATAGGTAAAT
Found at i:15517 original size:199 final size:197
Alignment explanation
Indices: 14946--16069 Score: 1246
Period size: 199 Copynumber: 5.6 Consensus size: 197
14936 ATAGGTAAAT
* * * *
14946 TTATAATGTAATAGGTAAATTTACAATGTAACCGATAGATATATACCAGTTTTATGAGAAAATAG
1 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTAGAAATATACC-GTTTAATGAGAAAATAG
** * * * * * *
15011 GTTTACATAATGTACCGACACTTTCTAAATTTATGTTGATACTTTCTGTCCAGAATGAATACCCA
65 GTCAACATAATGTATCGACACTTTCTAAA-TTGTGTCGATACTTTTTGTCCAGAATGAATGCCAA
* * * *
15076 ACGAGCTGTACGCATAAAGTGTCGATACATTTAAAATTGTATTGATCCCAAAAACATCGAAACCG
129 ACGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACTG
15141 ATAA
194 ATAA
* * ** * * *
15145 TTATAATGTAATAGGCAACTTTAA-AATGTAACCGACATAAATATACCGGTTAATTAGAAAATAG
1 TTATAATGTAATAGGTAA-ATTAACAATGTAACCGGTAGAAATATACCGTTTAATGAGAAAATAG
* * *
15209 GTCAATATAATGTATCGATACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAA
65 GTCAACATAATGTATCGACACTTTCTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAA
* * *
15274 CGAGGTGCACGTATAAAGTGTCGATACATGTAAAATTGTATCGATCCCAAAAACATCAAAACTGA
130 CGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACTGA
15339 TAA
195 TAA
* * *
15342 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAATAG
1 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTAGAAATATACC-GTTTAATGAGAAAATAG
* * * * * * *
15407 GTCTACACAATGTATCGACACTTTCTAAATATGTGTCGATACTTTCTGCCCATAATAAATGCCCA
65 GTCAACATAATGTATCGACACTTTCTAAAT-TGTGTCGATACTTTTTGTCCAGAATGAATGCCAA
* *
15472 ATGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACTG
129 ACGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACTG
15537 ATAA
194 ATAA
15541 TTATAATGTAATAGGTAACTTTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATATA
1 TTATAATGTAATAGG--------T-A---AAT---T-A----ACAATGTAACCGGTAGAAATATA
* * * * * * * *
15606 CCGGTTAATTAGAAAATAAGTCAATATAATGTATCTATACTTTTTAAATTGTGTCGAAACTTTTT
46 CCGTTTAATGAGAAAATAGGTCAACATAATGTATCGACACTTTCTAAATTGTGTCGATACTTTTT
* * * *
15671 GTCCATAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATTGATG
111 GTCCAGAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATC
**
15736 CTTAAAACATCGAAACTGATAA
176 CCAAAAACATCGAAACTGATAA
* * * *
15758 TTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAG
1 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTAGAAATATA-CCGTTTAATGAGAAAATAG
* * * * * *
15823 GCCTACACAATGTATCGACACTTTGTAAATTTATGTCGATACTTTTTGTCCAGAATGAAAGCCAA
65 GTCAACATAATGTATCGACACTTTCTAAA-TTGTGTCGATACTTTTTGTCCAGAATGAATGCCAA
* **
15888 ACGAGGTGCACGCATAAAGTGTCGATACATATATTAAATT-TATCGATCCCAAAGGCATCGAAAC
129 ACGAGGTGCACGCATAAAGTGTCGATACAT-T-TAAAATTGTATCGATCCCAAAAACATCGAAAC
**
15952 CCATAA
192 TGATAA
* * * * *
15958 TTATAATGTAATAAGTAAATTTACAATGTAACCGGTAGAAACATACCGATATAATTAGAAAATAG
1 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTAGAAATATACCG-TTTAATGAGAAAATAG
* *
16023 GTCAACATAATGTATCGACACTTT-TAAAATTTGTATCGATATTTTTT
65 GTCAACATAATGTATCGACACTTTCT-AAA-TTGTGTCGATACTTTTT
16070 TAAATCATGC
Statistics
Matches: 778, Mismatches: 117, Indels: 59
0.82 0.12 0.06
Matches are distributed among these distances:
196 4 0.01
197 152 0.20
198 111 0.14
199 208 0.27
200 118 0.15
201 7 0.01
202 1 0.00
205 3 0.00
207 1 0.00
208 2 0.00
209 1 0.00
211 3 0.00
214 1 0.00
215 1 0.00
217 105 0.13
218 36 0.05
219 24 0.03
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (197 bp):
TTATAATGTAATAGGTAAATTAACAATGTAACCGGTAGAAATATACCGTTTAATGAGAAAATAGG
TCAACATAATGTATCGACACTTTCTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAC
GAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACTGAT
AA
Found at i:15566 original size:20 final size:20
Alignment explanation
Indices: 15541--15591 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
15531 AAACTGATAA
15541 TTATAATGTAATAGGTAACT
1 TTATAATGTAATAGGTAACT
15561 TTATAATGTAATAGGTAACT
1 TTATAATGTAATAGGTAACT
*
15581 TTACAATGTAA
1 TTATAATGTAA
15592 CCGGTAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (20 bp):
TTATAATGTAATAGGTAACT
Found at i:15597 original size:20 final size:20
Alignment explanation
Indices: 15545--15597 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
15535 TGATAATTAT
* *
15545 AATGTAATAGGTAACTTTAT
1 AATGTAACAGGTAACTTTAC
*
15565 AATGTAATAGGTAACTTTAC
1 AATGTAACAGGTAACTTTAC
*
15585 AATGTAACCGGTA
1 AATGTAACAGGTA
15598 GAAATATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (20 bp):
AATGTAACAGGTAACTTTAC
Found at i:15672 original size:416 final size:417
Alignment explanation
Indices: 15145--15988 Score: 1298
Period size: 416 Copynumber: 2.0 Consensus size: 417
15135 AAACCGATAA
* *
15145 TTATAATGTAATAGGCAACTTTAAAATGTAACCGACATAAATATACCGGTTAATTAGAAAATAGG
1 TTATAATGTAATAGGCAACTTTAAAATGTAACCGACAGAAATATACCGGTTAATTAGAAAATAAG
*
15210 TCAATATAATGTATCGATACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAC
66 TCAATATAATGTATCGATACTTTTTAAATTGTGTCGAAACTTTTTGTCCAGAATGAATGCCAAAC
*
15275 GAGGTGCACGTATAAAGTGTCGATACATGTAAAATTGTATCGATCCCAAAAACATCAAAACTGAT
131 GAGGTGCACGCATAAAGTGTCGATACATGTAAAATTGTATCGATCCCAAAAACATCAAAACTGAT
*
15340 AATTATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAAT
196 AATTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAAT
* * *
15405 AGGTCTACACAATGTATCGACACTTTCTAAATATGTGTCGATACTTTCTGCCCATAAT-AAATGC
261 AGGCCTACACAATGTATCGACACTTTCTAAATATATGTCGATACTTTCTGCCCAGAATGAAA-GC
* * *
15469 CCAATGAGGTGCACGCATAAAGTGTCGATACAT-T-TAAAATTGTATCGATCCCAAAAATATCGA
325 CAAACGAGGTGCACGCATAAAGTGTCGATACATATATAAAATT-TATCGATCCCAAAAACATCGA
** * *
15532 AACTGATAATTATAATGTAATAGGTAACT
389 AACCCATAATTATAATGTAATAAGTAAAT
* * **
15561 TTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAAG
1 TTATAATGTAATAGGCAACTTTAAAATGTAACCGACAGAAATATACCGGTTAATTAGAAAATAAG
* *
15626 TCAATATAATGTATCTATACTTTTTAAATTGTGTCGAAACTTTTTGTCCATAATGAATGCCAAAC
66 TCAATATAATGTATCGATACTTTTTAAATTGTGTCGAAACTTTTTGTCCAGAATGAATGCCAAAC
* * * * ** *
15691 GAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATTGATGCTTAAAACATCGAAACTGAT
131 GAGGTGCACGCATAAAGTGTCGATACATGTAAAATTGTATCGATCCCAAAAACATCAAAACTGAT
* **
15756 AATTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAAT
196 AATTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAAT
* * * *
15821 AGGCCTACACAATGTATCGACACTTTGTAAATTTATGTCGATACTTTTTGTCCAGAATGAAAGCC
261 AGGCCTACACAATGTATCGACACTTTCTAAATATATGTCGATACTTTCTGCCCAGAATGAAAGCC
* **
15886 AAACGAGGTGCACGCATAAAGTGTCGATACATATATTAAATTTATCGATCCCAAAGGCATCGAAA
326 AAACGAGGTGCACGCATAAAGTGTCGATACATATATAAAATTTATCGATCCCAAAAACATCGAAA
15951 CCCATAATTATAATGTAATAAGTAAAT
391 CCCATAATTATAATGTAATAAGTAAAT
*
15978 TTACAATGTAA
1 TTATAATGTAA
15989 CCGGTAGAAA
Statistics
Matches: 386, Mismatches: 39, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
416 323 0.84
417 57 0.15
418 6 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (417 bp):
TTATAATGTAATAGGCAACTTTAAAATGTAACCGACAGAAATATACCGGTTAATTAGAAAATAAG
TCAATATAATGTATCGATACTTTTTAAATTGTGTCGAAACTTTTTGTCCAGAATGAATGCCAAAC
GAGGTGCACGCATAAAGTGTCGATACATGTAAAATTGTATCGATCCCAAAAACATCAAAACTGAT
AATTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAAT
AGGCCTACACAATGTATCGACACTTTCTAAATATATGTCGATACTTTCTGCCCAGAATGAAAGCC
AAACGAGGTGCACGCATAAAGTGTCGATACATATATAAAATTTATCGATCCCAAAAACATCGAAA
CCCATAATTATAATGTAATAAGTAAAT
Found at i:15723 original size:217 final size:214
Alignment explanation
Indices: 15342--15988 Score: 711
Period size: 217 Copynumber: 3.1 Consensus size: 214
15332 AAACTGATAA
**
15342 TTATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATACCAATTTTATGAGAAAATAG
1 TTATAATGTAATAGGT-AATT-ACAATGTAACCGGTATAAATATACC-GGTTTATGAGAAAATAG
* * * *
15407 GTCTACACAATGTATCGACACTTTCTAAATATGTGTCGATACTTTCTGCCCATAATAAATGCCCA
63 GTCTACACAATGTATCGACACTTTCTAAAT-TGTGTCGATACTTTTTGTCCATAATGAATGCCAA
* * *
15472 ATGAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACTG
127 ACGAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATCGATCCCAAAAACATCGAAACTG
15537 ATAATTATAATGTAATAGGTAACT
192 ATAATTATAATGTAATAGGTAA-T
* * * *
15561 TTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAAG
1 TTATAATGTAATAGGTAA--TTACAATGTAACCGGTATAAATATACCGGTTTATGAGAAAATAGG
* * * * * * *
15626 TCAATATAATGTATCTATACTTTTTAAATTGTGTCGAAACTTTTTGTCCATAATGAATGCCAAAC
64 TCTACACAATGTATCGACACTTTCTAAATTGTGTCGATACTTTTTGTCCATAATGAATGCCAAAC
* * **
15691 GAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATTGATGCTTAAAACATCGAAACTGAT
129 GAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATCGATCCCAAAAACATCGAAACTGAT
*
15756 AATTACAATGTAATAGG----
194 AATTATAATGTAATAGGTAAT
* *
15773 ---T-A---AAT---T-A--ACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGC
1 TTATAATGTAATAGGTAATTACAATGTAACCGGTATAAATATACCGG-TTTATGAGAAAATAGGT
* * * *
15825 CTACACAATGTATCGACACTTTGTAAATTTATGTCGATACTTTTTGTCCAGAATGAAAGCCAAAC
65 CTACACAATGTATCGACACTTTCTAAA-TTGTGTCGATACTTTTTGTCCATAATGAATGCCAAAC
** *
15890 GAGGTGCACGCATAAAGTGTCGATACATATATT-AAATT-TATCGATCCCAAAGGCATCGAAACC
129 GAGGTGCACGCATAAAGTGTCGAT--ATAT-TTAAAATTGTATCGATCCCAAAAACATCGAAACT
* *
15953 CATAATTATAATGTAATAAGTAAAT
191 GATAATTATAATGTAATAGGT-AAT
*
15978 TTACAATGTAA
1 TTATAATGTAA
15989 CCGGTAGAAA
Statistics
Matches: 357, Mismatches: 52, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
197 25 0.07
198 34 0.10
199 57 0.16
200 35 0.10
201 10 0.03
202 3 0.01
205 3 0.01
208 1 0.00
209 2 0.01
212 2 0.01
217 105 0.29
218 38 0.11
219 40 0.11
220 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (214 bp):
TTATAATGTAATAGGTAATTACAATGTAACCGGTATAAATATACCGGTTTATGAGAAAATAGGTC
TACACAATGTATCGACACTTTCTAAATTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGA
GGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATCGATCCCAAAAACATCGAAACTGATAA
TTATAATGTAATAGGTAAT
Found at i:15794 original size:20 final size:19
Alignment explanation
Indices: 15756--15794 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
15746 CGAAACTGAT
*
15756 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
15775 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
15795 TAAATATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:15991 original size:200 final size:198
Alignment explanation
Indices: 15561--16069 Score: 650
Period size: 200 Copynumber: 2.6 Consensus size: 198
15551 ATAGGTAACT
* *
15561 TTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAA
1 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAG
* * * * * *
15625 GTCAATATAATGTATCTATACTTTTTAAA-TTGTGTCGAAACTTTTTGTCCATAATGAATGCCAA
66 GTCAACATAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAAGCCAA
* ** **
15689 ACGAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATTGATGCTTAAAACATCGAAACTG
130 ACGAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATCGATGCCCAAAACATCGAAACCC
15754 ATAA
195 ATAA
* * * * * *
15758 TTACAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAG
1 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAG
* * * *
15823 GCCTACACAATGTATCGACACTTTGTAAATTTATGTCGATACTTTTTGTCCAGAATGAAAGCCAA
66 GTCAACATAATGTATCGACACTTT-TAAATTTGTGTCGATACTTTTTGTCCAGAATGAAAGCCAA
*
15888 ACGAGGTGCACGCATAAAGTGTCGATACATATATT-AAATT-TATCGAT-CCCAAAGGCATCGAA
130 ACGAGGTGCACGCATAAAGTGTCGAT--ATAT-TTAAAATTGTATCGATGCCCAAA-ACATCGAA
15950 ACCCATAA
191 ACCCATAA
* * * *
15958 TTATAATGTAATAAGTAAATTTACAATGTAACCGGTAGAAACATACCGATATAATTAGAAAATAG
1 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAG
* *
16023 GTCAACATAATGTATCGACACTTTTAAAATTTGTATCGATATTTTTT
66 GTCAACATAATGTATCGACACTTTT-AAATTTGTGTCGATACTTTTT
16070 TAAATCATGC
Statistics
Matches: 264, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
197 47 0.18
198 31 0.12
199 62 0.23
200 113 0.43
201 9 0.03
202 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
TTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAG
GTCAACATAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAAGCCAAA
CGAGGTGCACGCATAAAGTGTCGATATATTTAAAATTGTATCGATGCCCAAAACATCGAAACCCA
TAA
Found at i:16843 original size:20 final size:20
Alignment explanation
Indices: 16818--16862 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
16808 TCAAAGAAAT
16818 CTTACCTTACCAATTCCTAG
1 CTTACCTTACCAATTCCTAG
16838 CTTACCTTACCAATTCCTAG
1 CTTACCTTACCAATTCCTAG
16858 CTTAC
1 CTTAC
16863 TATTTGGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (20 bp):
CTTACCTTACCAATTCCTAG
Found at i:17140 original size:19 final size:19
Alignment explanation
Indices: 17116--17163 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
17106 ATGTAGGGGA
17116 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
17135 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
17154 AATTTTGTAT
1 AATTTTGTAT
17164 GTCAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:20278 original size:199 final size:200
Alignment explanation
Indices: 19889--20290 Score: 567
Period size: 199 Copynumber: 2.0 Consensus size: 200
19879 GTAAACATAT
*
19889 GTGTCAATACATTTTATAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCAATACATTTTATAAAAGCATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
19954 AGTAAATTAACAATGTAACCAGTATAAATATACCGGTTAATTCGAAAACATGTCAACATAATGTA
66 AGTAAATTAACAATATAACCAGTATAAATATACCGGTTAATTAGAAAACAGGTCAACATAATGTA
* * * * *
20019 TCGACACATTTGGAATTTGTGTTGATACTTTTTGTCCAGAATGAAAGCCCAACCGAGGTGCACGC
131 TCGACACATTTGAAATTTGTGTCGATACATTTTGTCCAGAATGAAAGCCCAAACGAGGTGCACAC
20084 ATAAA
196 ATAAA
* * *
20089 GTGTCGATACA-TTTATAAAAGCATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCAATACATTTTATAAAAGCATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * *
20153 GGTAAATTTACAATATAACCGGTATAAATATACTGGTTTAATTAGAAAAGC-GGTCAATATAATG
66 AGTAAATTAACAATATAACCAGTATAAATATACCGG-TTAATTAGAAAA-CAGGTCAACATAATG
* * * * *
20217 TATCGACACTTTTTAAATTTGTGTCGATACATTTTGTCTAGAATGAATG-CCAAATGAGGTGCAC
129 TATCGACACATTTGAAATTTGTGTCGATACATTTTGTCCAGAATGAAAGCCCAAACGAGGTGCAC
20281 ACATAAA
194 ACATAAA
20288 GTG
1 GTG
20291 CCCAAAAACA
Statistics
Matches: 178, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
199 103 0.58
200 74 0.42
201 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (200 bp):
GTGTCAATACATTTTATAAAAGCATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
AGTAAATTAACAATATAACCAGTATAAATATACCGGTTAATTAGAAAACAGGTCAACATAATGTA
TCGACACATTTGAAATTTGTGTCGATACATTTTGTCCAGAATGAAAGCCCAAACGAGGTGCACAC
ATAAA
Found at i:20493 original size:23 final size:23
Alignment explanation
Indices: 20443--20487 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20433 TGTCTATTTT
* *
20443 ATTATACAAGTGCTACCTATTAC
1 ATTATACAAGCGCTACCTAATAC
*
20466 ATTATATAAGCGCTACCTAATA
1 ATTATACAAGCGCTACCTAATA
20488 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATACAAGCGCTACCTAATAC
Found at i:27665 original size:19 final size:18
Alignment explanation
Indices: 27621--27680 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
27611 AACAACATAA
27621 AAAATAAA-A-AAATGAT
1 AAAATAAATAGAAATGAT
* *
27637 AAAGTAAATAGAAATGAAC
1 AAAATAAATAGAAATG-AT
27656 AAAATAAATAG-AATGAT
1 AAAATAAATAGAAATGAT
27673 AAAATAAA
1 AAAATAAA
27681 CAAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 7 0.19
17 10 0.27
18 9 0.24
19 11 0.30
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAATAAATAGAAATGAT
Found at i:27691 original size:15 final size:14
Alignment explanation
Indices: 27671--27743 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 14
27661 AAATAGAATG
27671 ATAAAATAAACAAAA
1 ATAAAA-AAACAAAA
*
27686 ATAAAACATAC-AAA
1 ATAAAA-AAACAAAA
27700 ATAAAAAAAGCAATAA
1 ATAAAAAAA-CAA-AA
*
27716 ACAAAAACAA-AATAA
1 ATAAAAA-AACAA-AA
27731 ATAAAAAAACAAA
1 ATAAAAAAACAAA
27744 TGAAAAAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.04
14 13 0.27
15 23 0.48
16 8 0.17
17 2 0.04
ACGTcount: A:0.78, C:0.10, G:0.01, T:0.11
Consensus pattern (14 bp):
ATAAAAAAACAAAA
Found at i:27892 original size:20 final size:21
Alignment explanation
Indices: 27859--27902 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27849 AAAATGTAAG
27859 AAAAACAAATAATA-AAAAATC
1 AAAAACAAATAATAGAAAAA-C
*
27880 AAAAAGAAA-AATAGAAAAAC
1 AAAAACAAATAATAGAAAAAC
27900 AAA
1 AAA
27903 TAATAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.09
Consensus pattern (21 bp):
AAAAACAAATAATAGAAAAAC
Found at i:28834 original size:16 final size:15
Alignment explanation
Indices: 28808--28838 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28798 ATGTGTGACC
28808 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
28823 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
28839 TTCGGTCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:29078 original size:5 final size:5
Alignment explanation
Indices: 29045--29095 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
29035 CCTGGATCAC
* * *
29045 AAAAT AAAAC AAAAT -AAAT TAAAT -TAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
29093 AAA
1 AAA
29096 TATTAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
4 7 0.17
5 33 0.82
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:29081 original size:23 final size:23
Alignment explanation
Indices: 29047--29090 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29037 TGGATCACAA
*
29047 AATAAAACAAAATAAATTAAATT
1 AATAAAACAAAATAAAATAAATT
*
29070 AATAAAATAAAATAAAATAAA
1 AATAAAACAAAATAAAATAAA
29091 ATAAATATTA
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:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AATAAAACAAAATAAAATAAATT
Found at i:29103 original size:15 final size:14
Alignment explanation
Indices: 29060--29109 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
29050 AAAACAAAAT
*
29060 AAATTAAATTAATA
1 AAATAAAATTAATA
*
29074 AAATAAAATAAAATA
1 AAATAAAAT-TAATA
29089 AAATAAATATTAATA
1 AAATAAA-ATTAATA
29104 ATAATA
1 A-AATA
29110 TAGATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.27
15 16 0.53
16 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAATTAATA
Found at i:29195 original size:34 final size:34
Alignment explanation
Indices: 29138--29229 Score: 81
Period size: 34 Copynumber: 2.8 Consensus size: 34
29128 TGTTTCAAAA
29138 AAAACTATA-TAT-TA-TATTT-AAAAA-CATTTT
1 AAAACTATATTATATAGT-TTTCAAAAATCATTTT
*
29168 CAAAACTATATTATATAGTTTTCAAAAATGATTTT
1 -AAAACTATATTATATAGTTTTCAAAAATCATTTT
*
29203 AAAA--ACATTATATAAGTTTTCCAAAAA
1 AAAACTATATTATAT-AGTTTT-CAAAAA
29230 AAATTAAAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
31 9 0.17
32 11 0.21
33 11 0.21
34 16 0.31
35 5 0.10
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (34 bp):
AAAACTATATTATATAGTTTTCAAAAATCATTTT
Found at i:29248 original size:33 final size:35
Alignment explanation
Indices: 29137--29248 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 35
29127 ATGTTTCAAA
* **
29137 AAAAACTATATAT-TATA--TTT-AAAAACATTTT
1 AAAAACTATATATATATAGTTTTCAAAAAGAAATT
* **
29168 CAAAACTATAT-TATATAGTTTTCAAAAATGATTTT
1 AAAAACTATATATATATAGTTTTCAAAAA-GAAATT
29203 AAAAAC-AT-TATATA-AGTTTTCCAAAAA-AAATT
1 AAAAACTATATATATATAGTTTT-CAAAAAGAAATT
29235 -AAAACTATATATAT
1 AAAAACTATATATAT
29249 TATTATATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
30 1 0.01
31 19 0.28
32 5 0.07
33 15 0.22
34 17 0.25
35 10 0.15
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (35 bp):
AAAAACTATATATATATAGTTTTCAAAAAGAAATT
Found at i:29304 original size:34 final size:36
Alignment explanation
Indices: 29252--29348 Score: 112
Period size: 35 Copynumber: 2.7 Consensus size: 36
29242 TATATATTAT
*
29252 TATATAAATTTCCAAAAATGTTTTTAAAAAACTATATA-
1 TATAT-AATTTTC-AAAATG-TTTTAAAAAACTATATAC
* *
29290 T-TAT-ATTTTCAAAATGATTT-CAAAACTATATAC
1 TATATAATTTTCAAAATGTTTTAAAAAACTATATAC
29323 TATATAATTTTCAAAATGTTTTAAAA
1 TATATAATTTTCAAAATGTTTTAAAA
29349 CTTATATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
32 11 0.22
33 4 0.08
34 9 0.18
35 20 0.40
36 2 0.04
37 3 0.06
38 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (36 bp):
TATATAATTTTCAAAATGTTTTAAAAAACTATATAC
Found at i:30329 original size:164 final size:164
Alignment explanation
Indices: 30111--30911 Score: 1278
Period size: 164 Copynumber: 4.8 Consensus size: 164
30101 TGAGCTGAAC
* * *
30111 GTAATCGAACTCGGAGGTCTCTGGTTGGCAGATAACCCTTCTCAACTTAAGCTATACTGTAAATG
1 GTAATCGAACTC-GAGG-GTCT--TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACG
* * * *
30176 ATGTGCCTTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
62 ATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
30241 TAAGTTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
127 TAAGTTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
30279 GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
1 GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
*
30344 ACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTAAG
66 ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTAAG
*
30409 TTATGCTATAAATGATGTGCCCTCGAAGCTGAGT
131 TTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
30443 GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
1 GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
* * *
30508 ACCTTGGAGCTGAGCGTAGTTGAACTTGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
66 ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTAAG
*
30573 TTATGCTGTAAATGATGTGCCCTCGAAGTTGAGT
131 TTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
* *
30607 GTAATCGAACTTGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAACGATAT
1 GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
*
30672 ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACATATAACCCTTCTAGCCTTAAG
66 ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTAAG
* *
30737 TTATGCTGTAAATGATGTTCCCTCGAAGTTGAGT
131 TTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
* * * * *
30771 GTAATCGAACTCGAAGGTCTTTGGTTACCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 GTAATCGAACTCGAGGGTCTTTGG----CAGATAACCCTTCTCGACTTAAGCTATACTGTAAACG
* * * *
30836 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAACCT
62 ATATACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
*
30901 TGAGTTATGCT
127 TAAGTTATGCT
30912 GCAAATGTTG
Statistics
Matches: 598, Mismatches: 31, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
164 475 0.79
166 3 0.01
167 4 0.01
168 116 0.19
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (164 bp):
GTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAACGATAT
ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTAAG
TTATGCTATAAATGATGTGCCCTCGAAGTTGAGT
Found at i:30912 original size:83 final size:83
Alignment explanation
Indices: 30102--30918 Score: 735
Period size: 83 Copynumber: 9.9 Consensus size: 83
30092 GTTTGCCACT
* * * * *
30102 GAGCTGAACGTAATCGAACTCGGAGGTCTCTGGTTGGCAGATAACCCTTCTCAACTTAAGCTATA
1 GAGCTGAGCGTAATCGAACTCGAAGGTCT-TTGTTGGCAGATAACCCTTCTCAACTTAAGTTATG
*
30167 CTGTAAATGATGTGCCTTG
65 CTGTAAATGATATGCCTTG
* * * * * *
30186 GAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCT-AGCCTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* * *
30250 CTATAAATGATGTGCCCTCG
65 CTGTAAATGATATG-CCTTG
* * * * * * *
30270 AAGTTGAGTGTAATCGAACTCGAGGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATAC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
* *
30332 TGTAAACGATATACCTTG
66 TGTAAATGATATGCCTTG
* * * * *
30350 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCT-AGCCTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* * *
30414 CTATAAATGATGTGCCCTCG
65 CTGTAAATGATATG-CCTTG
* * * * * *
30434 AAGCTGAGTGTAATCGAACTCGAGGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATAC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
* *
30496 TGTAAACGATATACCTTG
66 TGTAAATGATATGCCTTG
* * * * * * *
30514 GAGCTGAGCGTAGTTGAACTTGAAGGTCTTTGGTGACAGATAACCCTTCT-AGCCTTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* *
30578 CTGTAAATGATGTGCCCTCG
65 CTGTAAATGATATG-CCTTG
* * * * * * * *
30598 AAGTTGAGTGTAATCGAACTTGAGGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATAC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
* * *
30660 TGCAAACGATATACCTTG
66 TGTAAATGATATGCCTTG
* * * * *
30678 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACATATAACCCTTCT-AGCCTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCA-ACTTAAGTTATG
* * *
30742 CTGTAAATGATGTTCCCTCG
65 CTGTAAATGAT-ATGCCTTG
* * * ** *
30762 AAGTTGAGTGTAATCGAACTCGAAGGTCTTTGGTTACCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCAACTTAAGTTATG
*
30827 CTGCAAATGATATGCCTTG
65 CTGTAAATGATATGCCTTG
* *
30846 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT-AACCTTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAA-CTTAAGTTATG
*
30910 CTGCAAATG
65 CTGTAAATG
30919 TTGTCTTAAA
Statistics
Matches: 571, Mismatches: 139, Indels: 47
0.75 0.18 0.06
Matches are distributed among these distances:
80 78 0.14
81 104 0.18
82 8 0.01
83 179 0.31
84 166 0.29
85 36 0.06
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (83 bp):
GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
TGTAAATGATATGCCTTG
Found at i:36129 original size:21 final size:22
Alignment explanation
Indices: 36095--36136 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
36085 AAAATGTAAG
36095 AAAAACAAATAATAAAAAAACC
1 AAAAACAAATAATAAAAAAACC
* *
36117 AAAAAGAAA-AATAGAAAAAC
1 AAAAACAAATAATAAAAAAAC
36137 AAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.79, C:0.10, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAACAAATAATAAAAAAACC
Found at i:36155 original size:35 final size:36
Alignment explanation
Indices: 36093--36178 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
36083 TAAAAATGTA
36093 AGAAAAACAAATAATAAAAAAACCAAAAAGAAAAAT
1 AGAAAAACAAATAATAAAAAAACCAAAAAGAAAAAT
* *
36129 AGAAAAACAAATAAT-AAAAAGCCAAAATGAAAAAT
1 AGAAAAACAAATAATAAAAAAACCAAAAAGAAAAAT
36164 AGTAAAATA-AAATAA
1 AG-AAAA-ACAAATAA
36179 AGTATATACA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 20 0.43
36 25 0.54
37 1 0.02
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (36 bp):
AGAAAAACAAATAATAAAAAAACCAAAAAGAAAAAT
Found at i:38761 original size:18 final size:18
Alignment explanation
Indices: 38738--38772 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38728 TTCCATCCGG
*
38738 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
38756 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
38773 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:41608 original size:16 final size:15
Alignment explanation
Indices: 41582--41612 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
41572 ATGTGTGACC
41582 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
41597 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
41613 TTCGACCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:41861 original size:19 final size:19
Alignment explanation
Indices: 41824--41900 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
41814 ATCACAAAAC
* *
41824 AAAACAAAATAAATTAAAT
1 AAAATAAAATAAAATAAAT
* *
41843 TAAAT-TAATAAAATGAAAT
1 AAAATAAAATAAAAT-AAAT
41862 AAAATAAAATAAAATAAAT
1 AAAATAAAATAAAATAAAT
*
41881 ATTAATAATAATAATAATAA
1 A-AAATAA-AATAA-AATAA
41901 TATAGATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 7 0.15
19 16 0.35
20 13 0.28
21 5 0.11
22 5 0.11
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (19 bp):
AAAATAAAATAAAATAAAT
Found at i:41869 original size:15 final size:15
Alignment explanation
Indices: 41819--41902 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 15
41809 CCTAGATCAC
* *
41819 AAAACAAAACAAAAT
1 AAAATAAAATAAAAT
* *
41834 -AAATTAAATTAAAT
1 AAAATAAAATAAAAT
* *
41848 -TAATAAAATGAAAT
1 AAAATAAAATAAAAT
41862 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
41877 AAATATTAATAATAATAAT
1 AAA-A-TAA-AATAA-AAT
41896 AATAATA
1 AA-AATA
41903 TAGATTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
14 21 0.39
15 15 0.28
16 1 0.02
17 3 0.06
18 7 0.13
19 6 0.11
20 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.26
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:42000 original size:35 final size:35
Alignment explanation
Indices: 41955--42146 Score: 136
Period size: 35 Copynumber: 5.5 Consensus size: 35
41945 ATTTAAAAAC
* *
41955 ATTTTCAAAACTATATTATATAGTTTTCAAAAATG
1 ATTTTAAAAACTATATTATATAATTTTCAAAAATG
*
41990 ATTTTAAAAAC---ATTATATAAGTTTTCCAAAAA-A
1 ATTTTAAAAACTATATTATATAA-TTTT-CAAAAATG
* *
42023 AATTTAAAACTATATATATTATATAAATTTTCCAAAAATG
1 ATTTTAAAA--A-CTATATTATAT-AATTTT-CAAAAATG
*
42063 TTTTTTAAAAACTATA-TAT-TATATTTTC-AAAATG
1 -ATTTTAAAAACTATATTATATA-ATTTTCAAAAATG
*
42097 A-TTTCAAAACTATATACTATATAATTTTC-AAAATG
1 ATTTTAAAAACTATAT--TATATAATTTTCAAAAATG
42132 --TTTAAAAACTTATAT
1 ATTTTAAAAAC-TATAT
42147 ATTGTATATA
Statistics
Matches: 128, Mismatches: 12, Indels: 34
0.74 0.07 0.20
Matches are distributed among these distances:
32 20 0.16
33 12 0.09
34 20 0.16
35 33 0.26
36 8 0.06
37 3 0.02
38 4 0.03
39 19 0.15
40 2 0.02
41 7 0.05
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (35 bp):
ATTTTAAAAACTATATTATATAATTTTCAAAAATG
Found at i:42029 original size:33 final size:32
Alignment explanation
Indices: 41969--42031 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
41959 TCAAAACTAT
* *
41969 ATTATATAGTTTTCAAAAATGATTTTAAAAAC
1 ATTATATAGTTTTCAAAAATAAATTTAAAAAC
42001 ATTATATAAGTTTTCCAAAAA-AAATTTAAAA
1 ATTATAT-AGTTTT-CAAAAATAAATTTAAAA
42032 CTATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 14 0.52
34 6 0.22
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (32 bp):
ATTATATAGTTTTCAAAAATAAATTTAAAAAC
Found at i:42032 original size:32 final size:33
Alignment explanation
Indices: 41968--42041 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 33
41958 TTCAAAACTA
* *
41968 TATTATATAGTTTTCAAAAATGATTTTAAAAAC
1 TATTATATAGTTTTCAAAAATAAATTTAAAAAC
42001 -ATTATATAAGTTTTCCAAAAA-AAATTT-AAAAC
1 TATTATAT-AGTTTT-CAAAAATAAATTTAAAAAC
42033 TATATATAT
1 TAT-TATAT
42042 TATATAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
32 12 0.34
33 12 0.34
34 11 0.31
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.41
Consensus pattern (33 bp):
TATTATATAGTTTTCAAAAATAAATTTAAAAAC
Found at i:42107 original size:32 final size:32
Alignment explanation
Indices: 41929--42149 Score: 116
Period size: 35 Copynumber: 6.4 Consensus size: 32
41919 TATGTTTAAA
**
41929 AAAAACTATATATTAT-ATTTAAAAACAT-TTT
1 AAAAACTATATATTATAATTTTCAAA-ATGTTT
* *
41960 CAAAACTATAT-TATATAGTTTTCAAAAATGATTTT
1 AAAAACTATATAT-TATAATTTTC-AAAATG--TTT
**
41995 AAAAAC-AT-TA-TATAAGTTTTCCAAAAAAAATTT
1 AAAAACTATATATTATAA-TTTT-C--AAAATGTTT
42028 -AAAACTATATATATTATATAAATTTTCCAAAAATGTTTTTT
1 AAAAAC--TATATA-T-TAT-AATTTT-C-AAAATG---TTT
42069 AAAAACTATATATTAT-ATTTTCAAAATGATTT
1 AAAAACTATATATTATAATTTTCAAAATG-TTT
*
42101 CAAAACTATATACTATATAATTTTCAAAATGTTT
1 AAAAACTATATA-T-TATAATTTTCAAAATGTTT
42135 AAAAACTTATATATT
1 AAAAAC-TATATATT
42150 GTATATAAGA
Statistics
Matches: 151, Mismatches: 13, Indels: 50
0.71 0.06 0.23
Matches are distributed among these distances:
30 1 0.01
31 13 0.09
32 28 0.19
33 13 0.09
34 21 0.14
35 34 0.23
36 7 0.05
38 8 0.05
39 10 0.07
40 8 0.05
41 3 0.02
42 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (32 bp):
AAAAACTATATATTATAATTTTCAAAATGTTT
Found at i:42147 original size:35 final size:34
Alignment explanation
Indices: 41929--42148 Score: 140
Period size: 34 Copynumber: 6.4 Consensus size: 34
41919 TATGTTTAAA
* **
41929 AAAAACTATATAT-TAT-A-TTTAAAAACATTTT
1 AAAAACTATATATATATAATTTTCAAAATGTTTT
* *
41960 CAAAACTATAT-TATATAGTTTTCAAAAATGATTTT
1 AAAAACTATATATATATAATTTTC-AAAATG-TTTT
* ***
41995 AAAAAC-AT-TATATA-AGTTTTCCAAAAAAAATTT
1 AAAAACTATATATATATAATTTT-C-AAAATGTTTT
42028 -AAAACTATATATATTATATAAATTTTCCAAAAATGTTTTTT
1 AAAAAC--TATATA-TATAT-AATTTT-C-AAAATG--TTTT
*
42069 AAAAACTATATAT-TAT-ATTTTCAAAATGATTT
1 AAAAACTATATATATATAATTTTCAAAATGTTTT
*
42101 CAAAACTATATACTATATAATTTTCAAAATG-TTT
1 AAAAACTATATA-TATATAATTTTCAAAATGTTTT
42135 AAAAACT-TATATAT
1 AAAAACTATATATAT
42149 TGTATATAAG
Statistics
Matches: 153, Mismatches: 16, Indels: 39
0.74 0.08 0.19
Matches are distributed among these distances:
30 1 0.01
31 13 0.08
32 22 0.14
33 18 0.12
34 34 0.22
35 24 0.16
36 7 0.05
37 4 0.03
38 3 0.02
39 13 0.08
40 6 0.04
41 3 0.02
42 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (34 bp):
AAAAACTATATATATATAATTTTCAAAATGTTTT
Found at i:42213 original size:37 final size:38
Alignment explanation
Indices: 42172--42278 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 38
42162 TAAGTTTTTT
*
42172 AAAAACGTTTTAAAAAAACTATATA-A-TATATATTTC
1 AAAAACATTTTAAAAAAACTATATATATTATATATTTC
* *** *
42208 GAAAAATATTTTTTGAAAACTATATATATTATATTTTTC
1 -AAAAACATTTTAAAAAAACTATATATATTATATATTTC
*
42247 AAAAACATTTTCAAAAAAATTATACTATATTA
1 AAAAACATTTT-AAAAAAACTATA-TATATTA
42279 CTAAAATAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
37 20 0.36
38 11 0.20
39 17 0.31
40 7 0.13
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (38 bp):
AAAAACATTTTAAAAAAACTATATATATTATATATTTC
Found at i:45085 original size:20 final size:20
Alignment explanation
Indices: 45062--45101 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
45052 CAAATTGGTT
*
45062 GCGAATTTGAAAATCGCAAC
1 GCGAATCTGAAAATCGCAAC
* *
45082 GCGAATCTGTAATTCGCAAC
1 GCGAATCTGAAAATCGCAAC
45102 ACAGAAGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGAATCTGAAAATCGCAAC
Found at i:45115 original size:20 final size:20
Alignment explanation
Indices: 45092--45140 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
45082 GCGAATCTGT
*
45092 AATTCGCAACACAGAAGTCA
1 AATTCACAACACAGAAGTCA
45112 AATTCACAACACAGAAGTCA
1 AATTCACAACACAGAAGTCA
45132 AATTCACAA
1 AATTCACAA
45141 AGCGCTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.16
Consensus pattern (20 bp):
AATTCACAACACAGAAGTCA
Found at i:45300 original size:22 final size:22
Alignment explanation
Indices: 45275--45321 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
45265 CTACGGCGAC
*
45275 ATCCGTCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
*
45297 ATCCATCCCCATCTCCGGCGAA
1 ATCCATCCCCATCTCCGACGAA
45319 ATC
1 ATC
45322 TGTCTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.45, G:0.13, T:0.19
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:45649 original size:20 final size:19
Alignment explanation
Indices: 45599--45649 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
45589 TTTGTATTGT
45599 ATTTTAGTTTCGCGTTGCG
1 ATTTTAGTTTCGCGTTGCG
*
45618 ATTTTCATTTTCGCGTTGCG
1 ATTTT-AGTTTCGCGTTGCG
45638 ATTTTAAGTTTC
1 ATTTT-AGTTTC
45650 AGAAACTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.51
Consensus pattern (19 bp):
ATTTTAGTTTCGCGTTGCG
Found at i:47330 original size:21 final size:21
Alignment explanation
Indices: 47304--47354 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
47294 GTTAGGGGAG
* *
47304 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGATCGGTACT
47325 TTACGTGATGAGATCGGTACT
1 TTACGTGATGAGATCGGTACT
47346 TTACGTGAT
1 TTACGTGAT
47355 AACAATGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TTACGTGATGAGATCGGTACT
Found at i:47411 original size:21 final size:21
Alignment explanation
Indices: 47370--47465 Score: 56
Period size: 21 Copynumber: 4.6 Consensus size: 21
47360 TGGTGCATGG
*
47370 CGTGATGAGGTACTGTCTTTA
1 CGTGATGAGGTAATGTCTTTA
*
47391 CGTGGTGAGGTAGATGT-TTTA
1 CGTGATGAGGTA-ATGTCTTTA
* * *
47412 TGCGATGA--CAATGGTGCTTTA
1 CGTGATGAGGTAAT-GT-CTTTA
* * *
47433 TGTGGTGAGGT-ATCTACTTTA
1 CGTGATGAGGTAATGT-CTTTA
47454 CGTGATGAGGTA
1 CGTGATGAGGTA
47466 GCCGCTCTAC
Statistics
Matches: 55, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
21 45 0.82
22 5 0.09
ACGTcount: A:0.21, C:0.10, G:0.32, T:0.36
Consensus pattern (21 bp):
CGTGATGAGGTAATGTCTTTA
Found at i:47801 original size:21 final size:21
Alignment explanation
Indices: 47784--47858 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
47774 TGTCCCTCCT
* *
47784 ATCGTTCAAAAGGACCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
47805 ATCGTTCAAGAGGCCCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
*
47826 ATCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCCCCTCTC
*
47847 ACCGTTCAAGAG
1 ATCGTTCAAGAG
47859 CCCGATTCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:47823 original size:42 final size:42
Alignment explanation
Indices: 47761--47858 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
47751 GATTCACCTG
* * *
47761 TCATCGTTCAATATGTCCCTC-CTATCGTTCAAAAGGACCCTC
1 TCATCGTTCAAGAGGCCCCTCTC-ATCGTTCAAAAGGACCCTC
* *
47803 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAAAGGACCCTC
* *
47845 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
47859 CCCGATTCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCTCATCGTTCAAAAGGACCCTC
Found at i:49380 original size:20 final size:20
Alignment explanation
Indices: 49355--49402 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
49345 TTCGCGTTGC
*
49355 GATTTTTGTGTTGCGAATTT
1 GATTTTCGTGTTGCGAATTT
49375 GATTTTCGTGTTGCGAATTT
1 GATTTTCGTGTTGCGAATTT
*
49395 GACTTTCG
1 GATTTTCG
49403 CAACAATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
GATTTTCGTGTTGCGAATTT
Found at i:49429 original size:29 final size:29
Alignment explanation
Indices: 49387--49445 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
49377 TTTTCGTGTT
*
49387 GCGAATTTGACTTTCGCAACAATTGCAAC
1 GCGAATTTGACTTTCGCAACAATCGCAAC
49416 GCGAATTTGACTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCGCAACAATCGCAAC
49445 G
1 G
49446 TTTATATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (29 bp):
GCGAATTTGACTTTCGCAACAATCGCAAC
Found at i:51516 original size:21 final size:20
Alignment explanation
Indices: 51489--51585 Score: 104
Period size: 21 Copynumber: 4.7 Consensus size: 20
51479 AAGCACCTGT
51489 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCC-CTCC
*
51510 TATCGTTCAAGAGGCCCTTCC
1 CATCGTTCAAGAGGCCC-TCC
* * *
51531 CACCATTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGG-CCCTCC
*
51552 CATCGTTCAGGAGGTCCCTCC
1 CATCGTTCAAGAGG-CCCTCC
*
51573 CACCGTTCAAGAG
1 CATCGTTCAAGAG
51586 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.94
22 3 0.05
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCTCC
Found at i:51557 original size:42 final size:42
Alignment explanation
Indices: 51494--51585 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
51484 CCTGTCATCG
*
51494 TTCAAGAGGCCTCTCCTATCGTTCAAGAGG-CCCTTCCCACCA
1 TTCAAGAGGCCCCTCCTATCGTTCAAGAGGTCCC-TCCCACCA
* *
51536 TTCAAGAGGCCCCT-CTCATCGTTCAGGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCT-ATCGTTCAAGAGGTCCCTCCCACCA
51578 TTCAAGAG
1 TTCAAGAG
51586 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 2 0.04
42 40 0.89
43 3 0.07
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCTATCGTTCAAGAGGTCCCTCCCACCA
Found at i:52740 original size:22 final size:22
Alignment explanation
Indices: 52715--52771 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
52705 AACAGTGAAC
52715 AGTGGGGGAATCGATTCCCTGT
1 AGTGGGGGAATCGATTCCCTGT
52737 AGTGGGGGAATCGATTCCCTGT
1 AGTGGGGGAATCGATTCCCTGT
**
52759 AGCAGGGGAATCG
1 AGTGGGGGAATCG
52772 GTACCCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.23
Consensus pattern (22 bp):
AGTGGGGGAATCGATTCCCTGT
Found at i:53503 original size:59 final size:59
Alignment explanation
Indices: 53409--53530 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
53399 CTATCTCGAG
* *
53409 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGTACTAGGTATCCTTAAGTACAGTCCCGAA
* ** *
53468 TATGACACATAAGGTCGTGCCCACCATATAG-ACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATAT-GTACTAGGTATCCTTAAGTACAGTCCCGAA
53527 TATG
1 TATG
53531 CAGCCTGCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGTACTAGGTATCCTTAAGTACAGTCCCGAA
Found at i:56212 original size:14 final size:14
Alignment explanation
Indices: 56190--56223 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
56180 TGTTTAATTT
*
56190 ATTTATAAAAGTTG
1 ATTTGTAAAAGTTG
56204 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
56218 ATTTGT
1 ATTTGT
56224 TTAATTGATG
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:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:56220 original size:78 final size:77
Alignment explanation
Indices: 56123--56286 Score: 240
Period size: 78 Copynumber: 2.1 Consensus size: 77
56113 GCTTGTTTAA
56123 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGA-TTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTT-ACTTGTTTAA
*
56187 TTTATTTATAAAAG
64 TTGATTTATAAAAG
* * ***
56201 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTACTTGTTTAATT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTACTTGTTTAATT
*
56266 GATTTGTAAAAG
66 GATTTATAAAAG
56278 TTGATTTGT
1 TTGATTTGT
56287 TGTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 34 0.44
78 43 0.55
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (77 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTACTTGTTTAATT
GATTTATAAAAG
Found at i:56410 original size:20 final size:20
Alignment explanation
Indices: 56359--56410 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
56349 CAATGCGATT
*
56359 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGAAAGTCAAA
***
56379 TTCGCAACGCGAAAGTCAAA
1 TTCGCGTTGCGAAAGTCAAA
56399 TTCGCGTTGCGA
1 TTCGCGTTGCGA
56411 TTTTCGCGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TTCGCGTTGCGAAAGTCAAA
Found at i:58994 original size:23 final size:24
Alignment explanation
Indices: 58961--59013 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58951 CTGAAACATC
58961 ATCAAAATCCGAGTA-TGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
58984 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
59008 ATCAAA
1 ATCAAA
59014 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:59027 original size:24 final size:24
Alignment explanation
Indices: 58961--59027 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
58951 CTGAAACATC
* *
58961 ATCAAAATCCGAGTA-TGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
58984 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
59008 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
59028 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 13 0.36
24 23 0.64
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:60041 original size:39 final size:39
Alignment explanation
Indices: 59978--60106 Score: 170
Period size: 39 Copynumber: 3.3 Consensus size: 39
59968 ACTAAAACCT
59978 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCGAAA-TAAAATTCGTGTTGCGAATTCAAAAATCGA
* *
60018 GTTGCGAAATAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATAAAATTCGTGTTGCGAATTCAAAAATCGA
* ** *
60057 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGAAAATCGT
1 GTTGCGAA-ATAAAATTC-GTGTTGCGAATTCAAAAATCGA
60098 GTTGC-AAAT
1 GTTGCGAAAT
60107 TTATTGGTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 37 0.47
40 19 0.24
41 22 0.28
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (39 bp):
GTTGCGAAATAAAATTCGTGTTGCGAATTCAAAAATCGA
Found at i:60108 original size:20 final size:19
Alignment explanation
Indices: 59958--60109 Score: 128
Period size: 20 Copynumber: 7.7 Consensus size: 19
59948 TAAAATATTT
**
59958 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAATTTAAAATC
* *
59976 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAATTTAAAA-TC
*
59996 GTGTTGCGAATTCAAAAATC
1 GTGTTGCGAATT-TAAAATC
* *
60016 GAGTTGCGAA-ATAAAATTC
1 GTGTTGCGAATTTAAAA-TC
* *
60035 GCGTTGCGAATTCAGAAATC
1 GTGTTGCGAATTTA-AAATC
*
60055 GAGTTGCGAATTTAAAATTC
1 GTGTTGCGAATTTAAAA-TC
60075 AGTGTTGCGAATTTGAAAATC
1 -GTGTTGCGAATTT-AAAATC
*
60096 GTGTTGCAAATTTA
1 GTGTTGCGAATTTA
60110 TTGGTCATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
18 19 0.17
19 15 0.14
20 51 0.46
21 21 0.19
22 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (19 bp):
GTGTTGCGAATTTAAAATC
Done.