Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007405.1 Hibiscus syriacus cultivar Beakdansim tig00020009_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: 96709
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5729 original size:46 final size:47
Alignment explanation
Indices: 5662--5761 Score: 166
Period size: 47 Copynumber: 2.1 Consensus size: 47
5652 CCATGCATCG
* *
5662 GACATGCTCCCTAAAGGGTA-CCCAAACGTTGGCATTTGGTTCAAAA
1 GACATGGTCCCTAAAGGGTACCCCAAACATTGGCATTTGGTTCAAAA
5708 GACATGGTCCCTAAAGGGTACCCCAAACATTGGCATTTGGTTCAAAA
1 GACATGGTCCCTAAAGGGTACCCCAAACATTGGCATTTGGTTCAAAA
*
5755 GGCATGG
1 GACATGG
5762 GAACAACTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
46 19 0.38
47 31 0.62
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (47 bp):
GACATGGTCCCTAAAGGGTACCCCAAACATTGGCATTTGGTTCAAAA
Found at i:10077 original size:18 final size:19
Alignment explanation
Indices: 10043--10084 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
10033 TCACTTCTGG
*
10043 TCAA-CAATCCCACCATCT
1 TCAACCAATCCCACCATCA
*
10061 TCAACCAATCCC-TCATCA
1 TCAACCAATCCCACCATCA
10079 TCAACC
1 TCAACC
10085 TCGACCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (19 bp):
TCAACCAATCCCACCATCA
Found at i:11074 original size:10 final size:10
Alignment explanation
Indices: 11055--11088 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
11045 ATATTTATTA
11055 AATATAAAAT
1 AATATAAAAT
*
11065 AATTTAAAAT
1 AATATAAAAT
11075 AA-ATAAAAT
1 AATATAAAAT
11084 AATAT
1 AATAT
11089 TTTATTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATATAAAAT
Found at i:14644 original size:23 final size:24
Alignment explanation
Indices: 14617--14661 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
14607 ACACGTTTAG
14617 TATTTAAACTA-TT-AATTTTTATC
1 TATTTAAA-TATTTAAATTTTTATC
*
14640 TATTTTAATATTTAAATTTTTA
1 TATTTAAATATTTAAATTTTTA
14662 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 9 0.47
24 8 0.42
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTAAATATTTAAATTTTTATC
Found at i:17252 original size:5 final size:5
Alignment explanation
Indices: 17244--17269 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17234 TTTTTTTATT
17244 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
17270 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:18230 original size:2 final size:2
Alignment explanation
Indices: 18225--18253 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18215 GATTTTTTTA
18225 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
18254 ATAAGGCTTT
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:21914 original size:41 final size:41
Alignment explanation
Indices: 21867--21956 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
21857 CGATCTCTGG
*
21867 TATCGCAAATCAGTTTCCAGATTTGCAACGCGAACTTCGAC
1 TATCGCAAATCAGTTTCCAGATTCGCAACGCGAACTTCGAC
21908 TATCGCAAATCAGTTTCCAGATTCGCAACGCGAACTTCGAC
1 TATCGCAAATCAGTTTCCAGATTCGCAACGCGAACTTCGAC
21949 TATCGCAA
1 TATCGCAA
21957 TGCGAACTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (41 bp):
TATCGCAAATCAGTTTCCAGATTCGCAACGCGAACTTCGAC
Found at i:21996 original size:42 final size:42
Alignment explanation
Indices: 21950--22113 Score: 267
Period size: 42 Copynumber: 3.9 Consensus size: 42
21940 AACTTCGACT
* * *
21950 ATCGCAATGCGAACTT-GAACTATCGCAATGAATTTGGAATAA
1 ATCGCAACGCGAACTTCG-ACTATCGCAACGAACTTGGAATAA
21992 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* *
22034 ATCTCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
22076 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
22114 CTATCGCAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
42 113 0.99
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:22080 original size:63 final size:61
Alignment explanation
Indices: 22013--22170 Score: 167
Period size: 63 Copynumber: 2.5 Consensus size: 61
22003 AACTTCGACT
*
22013 ATCGCAACGAACTTGGAATAAATCTCAACGCGAACTTCGACTATCGC-A-ACGAACTTAGAATAA
1 ATCGCAACGAACTTGGAAT--ATCGCAA--CGAACTTCGACTATCGCAATACGAACTTAGAATAA
* * * * *
22076 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAATACGAATTTGGAATAA
1 ATCGCAA--CGAACTTGGAATATCGCAACGAACTTCGACTATCGCAATACGAACTTAGAATAA
*
22139 ATCGCAACACGAACTTGGACTATCGCAACGAA
1 ATCGC-A-ACGAACTTGGAATATCGCAACGAA
22171 TTTAGAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
61 16 0.20
62 1 0.01
63 53 0.65
64 1 0.01
65 11 0.13
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAACTTGGAATATCGCAACGAACTTCGACTATCGCAATACGAACTTAGAATAA
Found at i:22143 original size:84 final size:81
Alignment explanation
Indices: 21938--22146 Score: 265
Period size: 84 Copynumber: 2.5 Consensus size: 81
21928 ATTCGCAACG
* * * *
21938 CGAACTTCGACTATCGCAATGCGAACTTGAACTATCGCAATGAATTTGGAATAAATCGCAACGCG
1 CGAACTTGGACTATCGCAATGCGAACTTGAA-TATCGCAACGAACTTAGAATAAATCGCAACGCG
22003 AACTTCGACTATCGCAA
65 AACTTCGACTATCGCAA
* * * *
22020 CGAACTTGGAATAAATCTCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAAATCGCAACG
1 CGAACTTGGACT--ATCGCAATGCGAACTT-GAATATCGCAACGAACTTAGAATAAATCGCAACG
22085 CGAACTTCGACTATCGCAA
63 CGAACTTCGACTATCGCAA
* *
22104 CGAACTTGGACTATCGCAATACGAATTTGGAATAAATCGCAAC
1 CGAACTTGGACTATCGCAATGCGAACTT-GAAT--ATCGCAAC
22147 ACGAACTTGG
Statistics
Matches: 107, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
82 25 0.23
84 80 0.75
85 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (81 bp):
CGAACTTGGACTATCGCAATGCGAACTTGAATATCGCAACGAACTTAGAATAAATCGCAACGCGA
ACTTCGACTATCGCAA
Found at i:22164 original size:84 final size:82
Alignment explanation
Indices: 21950--22168 Score: 219
Period size: 84 Copynumber: 2.6 Consensus size: 82
21940 AACTTCGACT
** * * *
21950 ATCGCAATGCGAACTT-GAACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 ATCGCAACACGAACTTCGAA-TATCGCAACGAACTTAGAAT-AATCGCAACGCGAACTTCGACTA
22014 TCGCAACGAACTTGGAATAA
64 TCGCAACGAACTTGGAAT-A
* * *
22034 ATCTCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTCGACTAT
1 ATCGCAACACGAACTTCGAATATCGCAACGAACTTAGAAT-AATCGCAACGCGAACTTCGACTAT
*
22099 CGCAACGAACTTGGACT-
65 CGCAACGAACTTGGAATA
* * * * *
22116 ATCGCAATACGAATTTGGAATAAATCGCAACACGAACTTGGACT-ATCGCAACG
1 ATCGCAACACGAACTTCGAAT--ATCGC-A-ACGAACTTAGAATAATCGCAACG
22169 AATTTAGAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
82 15 0.13
84 86 0.75
85 3 0.03
86 11 0.10
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (82 bp):
ATCGCAACACGAACTTCGAATATCGCAACGAACTTAGAATAATCGCAACGCGAACTTCGACTATC
GCAACGAACTTGGAATA
Found at i:22183 original size:63 final size:63
Alignment explanation
Indices: 22061--22184 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
22051 GACTATCGCA
* * **
22061 ACGAACTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAAT
1 ACGAACTTAGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTAGAAAATCGCAAT
* * * *
22124 ACGAATTTGGAATAAATCGCAACACGAACTTGGACTATCGCAACGAATTTAGAAAATCGCA
1 ACGAACTTAGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTAGAAAATCGCA
22185 TTGCGATAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (63 bp):
ACGAACTTAGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTAGAAAATCGCAAT
Found at i:22209 original size:21 final size:21
Alignment explanation
Indices: 22180--22232 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
22170 ATTTAGAAAA
*
22180 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
22201 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
22222 TCGCGTTGCGA
1 TCGCGTTGCGA
22233 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:28309 original size:51 final size:51
Alignment explanation
Indices: 28233--28334 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
28223 GAGATACAAG
28233 CATTACTCATGGAAACCAAGCCTTAAATCCTGAATCCTAAATCAATAAAAA
1 CATTACTCATGGAAACCAAGCCTTAAATCCTGAATCCTAAATCAATAAAAA
28284 CATTACTCATGGAAACCAAGCCTTAAATCCTGAATCCTAAATCAATAAAAA
1 CATTACTCATGGAAACCAAGCCTTAAATCCTGAATCCTAAATCAATAAAAA
28335 TACGACTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (51 bp):
CATTACTCATGGAAACCAAGCCTTAAATCCTGAATCCTAAATCAATAAAAA
Found at i:34582 original size:7 final size:7
Alignment explanation
Indices: 34570--34600 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
34560 GTCAAAGAAA
34570 GTCAACG
1 GTCAACG
34577 GTCAACG
1 GTCAACG
34584 GTCAACG
1 GTCAACG
34591 GTCAACG
1 GTCAACG
34598 GTC
1 GTC
34601 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:34607 original size:5 final size:5
Alignment explanation
Indices: 34597--34654 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
34587 AACGGTCAAC
* *
34597 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
34646 GGTCG GGTC
1 GGTCG GGTC
34655 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:34618 original size:22 final size:22
Alignment explanation
Indices: 34590--34654 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
34580 AACGGTCAAC
34590 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
34612 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
34634 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
34655 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:34674 original size:19 final size:18
Alignment explanation
Indices: 34651--34729 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
34641 GGTCGGGTCG
34651 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
34669 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
34688 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
34708 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
34727 GGT
1 GGT
34730 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:34708 original size:29 final size:31
Alignment explanation
Indices: 34676--34750 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
34666 ACCGAGTCAG
34676 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
34705 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
34735 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
34751 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:34750 original size:9 final size:9
Alignment explanation
Indices: 34651--34749 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
34641 GGTCGGGTCG
*
34651 GGTCAGACC
1 GGTCAAACC
34660 GGTCAAACC
1 GGTCAAACC
*
34669 GAGTCAGACC
1 G-GTCAAACC
34679 GGTCAAACC
1 GGTCAAACC
*
34688 GGTTCGAACC
1 GG-TCAAACC
*
34698 GGTTGAAACC
1 GG-TCAAACC
34708 GGTCAAACC
1 GGTCAAACC
34717 GGTCAGAACC
1 GGTCA-AACC
*
34727 GGTTGAAAACC
1 GG-T-CAAACC
*
34738 GGTTAAACC
1 GGTCAAACC
34747 GGT
1 GGT
34750 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:41917 original size:7 final size:7
Alignment explanation
Indices: 41905--41942 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
41895 GTCAAAGAAA
41905 GTCAACG
1 GTCAACG
41912 GTCAACG
1 GTCAACG
41919 GTCAACG
1 GTCAACG
41926 GTCAACG
1 GTCAACG
41933 GTCAACG
1 GTCAACG
41940 GTC
1 GTC
41943 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:41949 original size:5 final size:5
Alignment explanation
Indices: 41939--41996 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
41929 AACGGTCAAC
* *
41939 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
41988 GGTCG GGTC
1 GGTCG GGTC
41997 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:41960 original size:22 final size:22
Alignment explanation
Indices: 41932--41996 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
41922 AACGGTCAAC
41932 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
41954 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
41976 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
41997 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:42016 original size:19 final size:18
Alignment explanation
Indices: 41993--42071 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
41983 GGTCGGGTCG
41993 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
42011 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
42030 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
42050 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
42069 GGT
1 GGT
42072 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:42050 original size:29 final size:31
Alignment explanation
Indices: 42018--42092 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
42008 ACCGAGTCAG
42018 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
42047 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
42077 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
42093 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:42092 original size:9 final size:9
Alignment explanation
Indices: 41993--42091 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
41983 GGTCGGGTCG
*
41993 GGTCAGACC
1 GGTCAAACC
42002 GGTCAAACC
1 GGTCAAACC
*
42011 GAGTCAGACC
1 G-GTCAAACC
42021 GGTCAAACC
1 GGTCAAACC
*
42030 GGTTCGAACC
1 GG-TCAAACC
*
42040 GGTTGAAACC
1 GG-TCAAACC
42050 GGTCAAACC
1 GGTCAAACC
42059 GGTCAGAACC
1 GGTCA-AACC
*
42069 GGTTGAAAACC
1 GG-T-CAAACC
*
42080 GGTTAAACC
1 GGTCAAACC
42089 GGT
1 GGT
42092 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:60958 original size:42 final size:41
Alignment explanation
Indices: 60892--60998 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
60882 TTCACAATTT
* * * *
60892 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
60933 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* *
60975 ATAAGTCCTTCGGGCCATCCGTAA
1 ATAAATCCTTCGGGCCATCAGTAA
60999 AACCTTCGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:61162 original size:214 final size:214
Alignment explanation
Indices: 60775--61176 Score: 660
Period size: 214 Copynumber: 1.9 Consensus size: 214
60765 GTGAAGCAAA
* * * *
60775 CCATCCATAAGACCTTCGGGTAAGATGTTTTCAATAGAATTTGAAAATAAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAAAATTTGAAAATAAAAAACGATGTTTTAA
* *
60840 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
60905 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATCTGTAAGCCTTTAGAGCA
60970 AGATGATAAGTCCTTCGGG
196 AGATGATAAGTCCTTCGGG
* * *
60989 CCATCCGTAAAACCTTCGGGTAAGATGTTTTCAAAAAAATTTGAAAATGAAAAACGATGTTTTGA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAAAATTTGAAAATAAAAAACGATGTTTTAA
*
61054 GAAGATGAAATTTTTGAAAACAAATAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
61119 TCCATCAGTAAGTCTTTCGAGCATGATGATTAATTCATTCGGGTAATTTGTAAGCCTT
131 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATCTGTAAGCCTT
61177 CACCGAAGAG
Statistics
Matches: 172, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
214 172 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (214 bp):
CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAAAATTTGAAAATAAAAAACGATGTTTTAA
GAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGGG
Found at i:61218 original size:13 final size:13
Alignment explanation
Indices: 61200--61224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61190 TGAAGCAAAC
61200 CCATCAGTAAGTG
1 CCATCAGTAAGTG
61213 CCATCAGTAAGT
1 CCATCAGTAAGT
61225 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:61271 original size:20 final size:20
Alignment explanation
Indices: 61212--61275 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
61202 ATCAGTAAGT
61212 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
* * *
61232 G-CATGATGATGAAATCTTTCGG
1 GCCATCA-G-T-AAGTCTTTCGA
61254 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
61274 GC
1 GC
61276 ATGATGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:61295 original size:42 final size:42
Alignment explanation
Indices: 61212--61296 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
61202 ATCAGTAAGT
*
61212 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
* *
61254 GCCATCAGTAAGTCTTTCGAGCATGATGATTAATTCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
61296 G
1 G
61297 TAATTTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCATTCGG
Found at i:61404 original size:42 final size:41
Alignment explanation
Indices: 61341--61432 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 41
61331 AAATCCATCA
*
61341 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGCCATTT
* *
61383 GTAAGTCTTTCGAGTGA-GATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAG-CATGATGATAAATCCTTCGGGCCATTT
*
61424 -TAAGCCTTT
1 GTAAGTCTTT
61433 TCAGAATAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 8 0.18
41 16 0.36
42 20 0.44
43 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGCCATTT
Found at i:61404 original size:122 final size:120
Alignment explanation
Indices: 61213--61431 Score: 323
Period size: 122 Copynumber: 1.8 Consensus size: 120
61203 TCAGTAAGTG
*
61213 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
61278 GATGATTAATTCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGA-TAAGTCATTCGGGCAATTT-TAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* ** *
61335 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAGTCTTTCGAGTGA
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAG-CA
* *
61400 -GATGATAAGTCCTTCGGGCCATTTTAAGCCTT
65 TGATGATAAGTCATTCGGGCAATTTTAAGCCTT
61432 TTCAGAATAG
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
120 8 0.09
121 15 0.17
122 63 0.72
123 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (120 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATAAGTCATTCGGGCAATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:61882 original size:53 final size:53
Alignment explanation
Indices: 61799--62006 Score: 296
Period size: 53 Copynumber: 3.9 Consensus size: 53
61789 AGAATCACAC
* *
61799 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * * * *
61852 CAAAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
*
61905 CAGAAGATTATTCAAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTA-A
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
*
61957 GCAGAAGATTATTCAAATTCTACTCCCTGAA-CAAGAGGGAGC-AGACCCGT
1 -CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGA-ACCCGT
62007 CATTCGAAGA
Statistics
Matches: 142, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
51 1 0.01
52 16 0.11
53 125 0.88
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (53 bp):
CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
Found at i:64641 original size:3 final size:3
Alignment explanation
Indices: 64635--64717 Score: 73
Period size: 3 Copynumber: 27.0 Consensus size: 3
64625 TATTTTTTAT
*
64635 TAA TAA TAA TAA TAA TAAA TAA TAA TAA -ATA TTA TAA TAA -ATA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA
* *
64681 TAA TAA T-A TAA TAGA TTAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
64718 AAACAAATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
2 4 0.06
3 54 0.82
4 6 0.09
5 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:64711 original size:37 final size:34
Alignment explanation
Indices: 64636--64717 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
64626 ATTTTTTATT
* * *
64636 AATAATAATAATAATAAATAATAATAAATATTAT
1 AATAAAAATAATAATAAATAATAATAAATATAAA
* *
64670 AATAAATATAATAATAATATAATAGATTAATAATAAA
1 AATAAAAATAATAATAA-ATAATA-ATAAAT-ATAAA
64707 AATAAAAATAA
1 AATAAAAATAA
64718 AAACAAATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
34 15 0.38
35 6 0.15
36 5 0.13
37 13 0.33
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (34 bp):
AATAAAAATAATAATAAATAATAATAAATATAAA
Found at i:64717 original size:43 final size:43
Alignment explanation
Indices: 64635--64718 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
64625 TATTTTTTAT
* * *
64635 TAATAATAATAATAATAAATAATAATAAATATTATAATAAATA
1 TAATAATAATAATAATAAATAATAATAAAAATAAAAATAAATA
*
64678 TAATAATAAT-ATAATAGATTAATAATAAAAATAAAAATAAA
1 TAATAATAATAATAATA-AATAATAATAAAAATAAAAATAAA
64719 AACAAATGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 6 0.17
43 30 0.83
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (43 bp):
TAATAATAATAATAATAAATAATAATAAAAATAAAAATAAATA
Found at i:65249 original size:124 final size:124
Alignment explanation
Indices: 65046--65483 Score: 729
Period size: 123 Copynumber: 3.6 Consensus size: 124
65036 TTAAACAAAT
* *
65046 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
* *
65111 AAAAATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGAAAAAGGTTGAACAAGC
66 AAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
*
65170 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
*
65235 AAAGGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
66 AAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
*
65294 TCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * *
65358 AAATGTTGGTGATGATTTATCTCCTTCTGCGATAGAGTCATGCAAAAGGTTGAACAAGC
66 AAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
* *
65417 TCTTCTCATTATGAACTTTTTCTTCC-TCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCT-G
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
65480 AAAA
66 AAAA
65484 TGTCGATCCA
Statistics
Matches: 298, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
122 4 0.01
123 150 0.50
124 144 0.48
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (124 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
Found at i:66101 original size:19 final size:18
Alignment explanation
Indices: 66077--66137 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
66067 AGATGTATCA
66077 ATGCAATGCATGATCTGTT
1 ATGCAATGCATGAT-TGTT
*
66096 ATGCAAATG-ATG-TTCTT
1 ATGC-AATGCATGATTGTT
*
66113 ATG-AATGCATGAATGTT
1 ATGCAATGCATGATTGTT
66130 GATGCAAT
1 -ATGCAAT
66138 CTTCATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 9 0.26
18 4 0.12
19 10 0.29
20 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (18 bp):
ATGCAATGCATGATTGTT
Found at i:66446 original size:22 final size:22
Alignment explanation
Indices: 66421--66471 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
66411 TAAAGCGTTT
66421 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
* * *
66443 ATCTTTGGAGAGTGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
66465 ATCTTTG
1 ATCTTTG
66472 TAGATGTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:72690 original size:32 final size:31
Alignment explanation
Indices: 72654--72730 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
72644 CGGGGCCGTG
*
72654 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
72686 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
72717 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
72731 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:72713 original size:63 final size:63
Alignment explanation
Indices: 72607--72730 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
72597 CCCTAAGGGA
* * ** *
72607 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
72670 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
72731 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:73635 original size:17 final size:17
Alignment explanation
Indices: 73613--73650 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
73603 AACGGTCAAC
73613 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
73630 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
73647 GGTC
1 GGTC
73651 GGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:73674 original size:19 final size:19
Alignment explanation
Indices: 73652--73735 Score: 100
Period size: 19 Copynumber: 4.4 Consensus size: 19
73642 GGTCGGGTCG
*
73652 GACCGGTCAAACCGGCTCA
1 GACCGGTCAAACCGGTTCA
*
73671 GACCGGTCAAACCGATTCA
1 GACCGGTCAAACCGGTTCA
73690 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
73708 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
73728 GAACCGGT
1 G-ACCGGT
73736 TGAAAACCGG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.02
19 42 0.72
20 15 0.26
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:73694 original size:10 final size:9
Alignment explanation
Indices: 73647--73705 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
73637 GGTCGGGTCG
*
73647 GGTCGGACC
1 GGTCAGACC
*
73656 GGTCAAACC
1 GGTCAGACC
73665 GGCTCAGACC
1 GG-TCAGACC
*
73675 GGTCAAACC
1 GGTCAGACC
*
73684 GATTCAGACC
1 G-GTCAGACC
*
73694 GGTCAAACC
1 GGTCAGACC
73703 GGT
1 GGT
73706 TCGAACCGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 25 0.62
10 15 0.38
ACGTcount: A:0.25, C:0.32, G:0.29, T:0.14
Consensus pattern (9 bp):
GGTCAGACC
Found at i:73723 original size:20 final size:21
Alignment explanation
Indices: 73698--73756 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
73688 CAGACCGGTC
73698 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCGAACCGGTTGA
73718 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTC-GAACCGGTTGA
*
73739 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCGAACCGGTT
73757 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 2 0.06
20 25 0.71
21 7 0.20
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:80033 original size:32 final size:31
Alignment explanation
Indices: 79997--80073 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
79987 CGGGGCCGTG
*
79997 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
80029 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
80060 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
80074 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:80056 original size:63 final size:63
Alignment explanation
Indices: 79950--80073 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
79940 CCCTAAGGGA
* * ** *
79950 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
80013 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
80074 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:80978 original size:17 final size:17
Alignment explanation
Indices: 80956--80993 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
80946 AACGGTCAAC
80956 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
80973 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
80990 GGTC
1 GGTC
80994 GGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:81017 original size:19 final size:19
Alignment explanation
Indices: 80995--81108 Score: 106
Period size: 19 Copynumber: 5.9 Consensus size: 19
80985 GGTCGGGTCG
*
80995 GACCGGTCAAACCGGCTCA
1 GACCGGTCAAACCGGTTCA
*
81014 GACCGGTCAAACCGATTCA
1 GACCGGTCAAACCGGTTCA
*
81033 GACCGGTCAAACCGATTC-
1 GACCGGTCAAACCGGTTCA
*
81051 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
81071 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
81092 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
81109 TCCAGCAGCC
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.04
19 53 0.65
20 16 0.20
21 9 0.11
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:81083 original size:29 final size:29
Alignment explanation
Indices: 81003--81107 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
80993 CGGACCGGTC
* * *
81003 AAACCGGCTCAGACCGGTCA-AACCGATTC
1 AAACCGG-TCAAACCGGTCAGAACCGGTTG
* *
81032 AGACCGGTCAAACCGATTC-GAACCGGTTG
1 AAACCGGTCAAACCG-GTCAGAACCGGTTG
81061 AAACCGGTCAAACCGGTCAGAACCGGTTG
1 AAACCGGTCAAACCGGTCAGAACCGGTTG
*
81090 AAAACCGGTTAAACCGGT
1 -AAACCGGTCAAACCGGT
81108 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 9 0.14
29 39 0.61
30 16 0.25
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (29 bp):
AAACCGGTCAAACCGGTCAGAACCGGTTG
Found at i:81108 original size:9 final size:9
Alignment explanation
Indices: 80996--81107 Score: 89
Period size: 9 Copynumber: 11.7 Consensus size: 9
80986 GTCGGGTCGG
80996 ACCGGTCAA
1 ACCGGTCAA
*
81005 ACCGGCTCAG
1 ACCGG-TCAA
81015 ACCGGTCAA
1 ACCGGTCAA
* *
81024 ACCGATTCAG
1 ACCG-GTCAA
81034 ACCGGTCAA
1 ACCGGTCAA
* *
81043 ACCGATTCGA
1 ACCG-GTCAA
*
81053 ACCGGTTGAA
1 ACCGG-TCAA
81063 ACCGGTCAA
1 ACCGGTCAA
81072 ACCGGTCAGA
1 ACCGGTCA-A
*
81082 ACCGGTTGAAA
1 ACCGG-T-CAA
*
81093 ACCGGTTAA
1 ACCGGTCAA
81102 ACCGGT
1 ACCGGT
81108 TTCCAGCAGC
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
9 38 0.46
10 36 0.44
11 7 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:84979 original size:46 final size:49
Alignment explanation
Indices: 84912--85003 Score: 145
Period size: 46 Copynumber: 1.9 Consensus size: 49
84902 AGGTATAAAT
* *
84912 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAATTAA
84958 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAAT
1 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAAT
85004 AAAATAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 21 0.51
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAATTAA
Found at i:85560 original size:2 final size:2
Alignment explanation
Indices: 85501--85542 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
85491 ATACAAAATA
*
85501 AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85541 AT
1 AT
85543 GAAGAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86288 original size:14 final size:14
Alignment explanation
Indices: 86265--86302 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
86255 TCTGTCTATA
*
86265 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
86278 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
86293 TGCAGGGATT
1 TGCAGGGATT
86303 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:87927 original size:19 final size:19
Alignment explanation
Indices: 87887--87928 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
87877 CGGTGGTAAG
* *
87887 TCTCTCGGTTTTTTTCTTT
1 TCTCTCGGTTTTATTCTGT
87906 TCTCTCGGTTTGTATT-TGT
1 TCTCTCGGTTT-TATTCTGT
87925 TCTC
1 TCTC
87929 GGGTTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.02, C:0.21, G:0.14, T:0.62
Consensus pattern (19 bp):
TCTCTCGGTTTTATTCTGT
Found at i:88513 original size:3 final size:3
Alignment explanation
Indices: 88507--88573 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
88497 TTATTATTAT
88507 TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAA T-A TAA TAGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A
* *
88552 TTAA TAA TAA AAA TAA AAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA
88574 AAACAAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 3 0.05
3 47 0.85
4 3 0.05
5 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:96117 original size:81 final size:83
Alignment explanation
Indices: 95964--96129 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 83
95954 ATACATATCT
95964 ATTCTGAGATTTTTTTTTATAATTTGAAGAAGCAAGTATAAATAGGATGAGGGGATCTCTTCATT
1 ATTCTGAGATTTTTTTTTATAATTTGAAGAAGCAAGTATAAATAGGAT-AGGGGATCTCTTCATT
96029 ATAAAGTAATATCTCAATG
65 ATAAAGTAATATCTCAATG
96048 ATTCTGAGATTTTTTTTTATAATTTGAAGAAGCAAGTATAAATA-GAT-GGGGATCTCTTCATTA
1 ATTCTGAGATTTTTTTTTATAATTTGAAGAAGCAAGTATAAATAGGATAGGGGATCTCTTCATTA
96111 TAAAGTAATATCTCAATG
66 TAAAGTAATATCTCAATG
96129 A
1 A
96130 AGTAAGACAT
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
81 35 0.43
83 3 0.04
84 44 0.54
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (83 bp):
ATTCTGAGATTTTTTTTTATAATTTGAAGAAGCAAGTATAAATAGGATAGGGGATCTCTTCATTA
TAAAGTAATATCTCAATG
Found at i:96384 original size:59 final size:58
Alignment explanation
Indices: 96285--96464 Score: 186
Period size: 59 Copynumber: 3.1 Consensus size: 58
96275 TCATATGTTT
* * **
96285 TAAATTATAACTCTTATTTTAAATTGGTCCTTAATTTTTTGAATATTCTAATTTCATTCC
1 TAAATTATGACT-TTA-TTTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATTCC
* * * *
96345 TAAATTATGACTTTATTCTAAATTAGTTCTTAAACTTTTGGACATTCTAATTTCATCCC
1 TAAATTATGACTTTATT-TAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATTCC
* ** * *
96404 TAAACTATGACACT-TTTAAATTGGTTC-TAAAGTTTTGAATATTCTCATTTCA-TCC
1 TAAATTATGACTTTATTTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATTCC
*
96459 TGAATT
1 TAAATT
96465 TCACCAATAT
Statistics
Matches: 100, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
55 6 0.06
56 21 0.21
57 10 0.10
58 4 0.04
59 48 0.48
60 11 0.11
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (58 bp):
TAAATTATGACTTTATTTAAATTGGTTCTTAAACTTTTGAATATTCTAATTTCATTCC
Done.