Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005937.1 Hibiscus syriacus cultivar Beakdansim tig00013943_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: 100713
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:929 original size:103 final size:102
Alignment explanation
Indices: 731--1043 Score: 511
Period size: 103 Copynumber: 3.1 Consensus size: 102
721 AGTCGAGGGT
*
731 ATATGTGGTCCTTCAGGACATATATGTATTC-TTGGAACATGTGTGAAGTCTGGTGAGGACAC--
1 ATATGTGGTCCTTC-GGGCATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGA-GACACAT
793 ACTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
64 ACTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
832 ATATGTGGTCCTTCGGGCTATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGC-ATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
897 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
935 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGG-CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1000 CTTGATCC----C-TA-GTATATGATTCTTAAGGAA-G
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
1031 ATATGTGGTCCTT
1 ATATGTGGTCCTT
1044 ATGGACATTA
Statistics
Matches: 206, Mismatches: 1, Indels: 15
0.93 0.00 0.07
Matches are distributed among these distances:
96 14 0.07
97 19 0.09
98 2 0.01
99 1 0.00
100 3 0.01
101 31 0.15
102 25 0.12
103 110 0.53
104 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (102 bp):
ATATGTGGTCCTTCGGGCATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
Found at i:4080 original size:13 final size:12
Alignment explanation
Indices: 4062--4118 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
4052 ATTTATAATG
4062 TAAAATGTTATTA
1 TAAAAT-TTATTA
* * *
4075 TAAAATATAATG
1 TAAAATTTATTA
4087 TAAAATATTATTA
1 TAAAAT-TTATTA
* *
4100 TAAAATATAATA
1 TAAAATTTATTA
4112 TAAAATT
1 TAAAATT
4119 ATGTGATTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
12 19 0.56
13 15 0.44
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (12 bp):
TAAAATTTATTA
Found at i:4089 original size:25 final size:25
Alignment explanation
Indices: 4055--4117 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
4045 TGGAGACATT
*
4055 TATAATGTAAAATGTTATTATAAAA
1 TATAATGTAAAATATTATTATAAAA
4080 TATAATGTAAAATATTATTATAAAA
1 TATAATGTAAAATATTATTATAAAA
*
4105 TATAATATAAAAT
1 TATAATGTAAAAT
4118 TATGTGATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (25 bp):
TATAATGTAAAATATTATTATAAAA
Found at i:4092 original size:12 final size:12
Alignment explanation
Indices: 4073--4117 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
4063 AAAATGTTAT
4073 TATAAAATATAA
1 TATAAAATATAA
* *
4085 TGTAAAATATTAT
1 TATAAAATA-TAA
4098 TATAAAATATAA
1 TATAAAATATAA
4110 TATAAAAT
1 TATAAAAT
4118 TATGTGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:5239 original size:30 final size:30
Alignment explanation
Indices: 5202--5424 Score: 374
Period size: 30 Copynumber: 7.4 Consensus size: 30
5192 CCCGAAGGAC
5202 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5232 TTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5262 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
5292 CTATCCATAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
5322 ATATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5352 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5382 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
5412 CTGTCCATAGGTC
1 CTATCCAGAGGTC
5425 CCGAAGAACC
Statistics
Matches: 181, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 181 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6161 original size:64 final size:62
Alignment explanation
Indices: 6090--6250 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 62
6080 TCTTTAGCAT
* * * *
6090 GTGCATCGATGCAGTACCCGTA-CATCGATTCACAAATCACATTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT--CCGTAGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
* * ** *
6153 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAG
1 G-TGCATCGATGCACTCCGTA-GCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
*
6217 GTGCATCGATGCACTTCCTGT-GCATCGATACACA
1 GTGCATCGATGCAC-TCC-GTAGCATCGATGCACA
6251 CTGAACAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
62 4 0.05
63 25 0.31
64 51 0.63
65 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTCCGTAGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
Found at i:8700 original size:30 final size:30
Alignment explanation
Indices: 8664--8826 Score: 245
Period size: 30 Copynumber: 5.4 Consensus size: 30
8654 CCCGAAGGAC
* **
8664 CTATCCAGAGGTCATAAAGATCTTATGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
8694 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
8724 CTATCTATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
8754 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
8784 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
8814 CTGTCCATAGGTC
1 CTATCCAGAGGTC
8827 CCGAAGAACC
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 122 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:8843 original size:90 final size:91
Alignment explanation
Indices: 8664--8851 Score: 261
Period size: 90 Copynumber: 2.1 Consensus size: 91
8654 CCCGAAGGAC
* * * *
8664 CTATCCAGAGGTCATAAAGATCTTATGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAAAGGTCATAAAGATCCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAACTATC
* * * *
8729 TATAGGTCATAAAGATCCTCGGT-AA
66 CATAGGTCACAAAGAACCTAGGTAAA
* *
8754 CTATCCAAAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAACTGTC
1 CTATCCAAAGGTCATAAAGATCCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAACTATC
* *
8819 CATAGGTCCCGAAGAACCTAGGTAAA
66 CATAGGTCACAAAGAACCTAGGTAAA
8845 CTATCCA
1 CTATCCA
8852 TATGTTCCTT
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 76 0.89
91 9 0.11
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (91 bp):
CTATCCAAAGGTCATAAAGATCCTAGGTAACTATCCAGAGGTCATAAAAATCCTCGGTAACTATC
CATAGGTCACAAAGAACCTAGGTAAA
Found at i:8900 original size:31 final size:30
Alignment explanation
Indices: 8809--8904 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
8799 AAAAATCCTC
* * *
8809 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
8839 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
8870 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
8901 GGTA
1 GGTA
8905 GTTCTTTAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:9509 original size:20 final size:20
Alignment explanation
Indices: 9447--9503 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
9437 TTTCCCTTGA
*
9447 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAT
*
9467 AGTGCATTGATGCATTCAAT
1 AGTGCATCGATGCATTCAAT
9487 AGTGCATCGATGCATTC
1 AGTGCATCGATGCATTC
9504 TTTAGTATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAT
Found at i:11036 original size:21 final size:20
Alignment explanation
Indices: 11012--11088 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
11002 AATTATATTA
11012 ATTATTTATTATATTAAAAAT
1 ATTA-TTATTATATTAAAAAT
***
11033 ATTA-TATTA-ATTATTTA-
1 ATTATTATTATATTAAAAAT
* *
11050 ATTATTTATTAAAATAAAAAT
1 ATTA-TTATTATATTAAAAAT
*
11071 ATTATTATAATATTAAAA
1 ATTATTATTATATTAAAA
11089 TTAAAATTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
17 4 0.10
18 5 0.12
19 10 0.24
20 15 0.36
21 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATTATTATATTAAAAAT
Found at i:11037 original size:30 final size:31
Alignment explanation
Indices: 10999--11063 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
10989 ATTAAAATTT
10999 AAAAATTATATTAATTATTT-ATTA-TATTA
1 AAAAATTATATTAATTATTTAATTATTATTA
11028 AAAATATTATATTAATTATTTAATTATTTATTA
1 AAAA-ATTATATTAATTATTTAATTA-TTATTA
11061 AAA
1 AAA
11064 TAAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 4 0.12
30 16 0.50
31 4 0.12
33 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
AAAAATTATATTAATTATTTAATTATTATTA
Found at i:11058 original size:38 final size:39
Alignment explanation
Indices: 10980--11075 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 39
10970 ACTATTATAT
* *
10980 TTTATTAAAATTAAAAT-TTA-A-AAATTATATTAATTA
1 TTTATTAAAATAAAAATATTATATTAATTATATTAATTA
* *
11016 TTTATTATATTAAAAATATTATATTAATTAT-TTAATTA
1 TTTATTAAAATAAAAATATTATATTAATTATATTAATTA
11054 TTTATTAAAATAAAAATATTAT
1 TTTATTAAAATAAAAATATTAT
11076 TATAATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
36 14 0.27
37 3 0.06
38 28 0.55
39 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TTTATTAAAATAAAAATATTATATTAATTATATTAATTA
Found at i:11091 original size:38 final size:38
Alignment explanation
Indices: 10980--11087 Score: 109
Period size: 38 Copynumber: 2.9 Consensus size: 38
10970 ACTATTATAT
* * *
10980 TTTATTAAAATTAAAAT-TTA-A-AAATTATATTAATTA
1 TTTATTAAAATAAAAATATTATATTAATTAT-TAAATTA
* * *
11016 TTTATTATATTAAAAATATTATATTAATTATTTAATTA
1 TTTATTAAAATAAAAATATTATATTAATTATTAAATTA
11054 TTTATTAAAATAAAAATATTAT-TATAA-TATTAAA
1 TTTATTAAAATAAAAATATTATAT-TAATTATTAAA
11088 ATTAAAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
36 14 0.23
37 10 0.16
38 31 0.51
39 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
TTTATTAAAATAAAAATATTATATTAATTATTAAATTA
Found at i:11201 original size:26 final size:30
Alignment explanation
Indices: 11142--11201 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
11132 TTTAAATATT
*
11142 TAATAATTAAATAATAATATTTTATGAGAG
1 TAATAAATAAATAATAATATTTTATGAGAG
*
11172 TAATAAATAAA-AATTA-ATTTTAT-AGA-
1 TAATAAATAAATAATAATATTTTATGAGAG
11198 TAAT
1 TAAT
11202 TTATCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 3 0.11
28 7 0.25
29 4 0.14
30 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (30 bp):
TAATAAATAAATAATAATATTTTATGAGAG
Found at i:11222 original size:42 final size:42
Alignment explanation
Indices: 11176--11258 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
11166 TGAGAGTAAT
* * *
11176 AAATAAAAAT-TAATTTTATAGATAATTTATCATATATTATTA
1 AAATAAAAATATAATATCATAGATAA-TTATAATATATTATTA
* *
11218 AAATAAAAATATAATATCATATATTATTATAATATATTATT
1 AAATAAAAATATAATATCATAGATAATTATAATATATTATT
11259 TTATAAAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 24 0.69
43 11 0.31
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (42 bp):
AAATAAAAATATAATATCATAGATAATTATAATATATTATTA
Found at i:20635 original size:112 final size:112
Alignment explanation
Indices: 20438--20899 Score: 766
Period size: 112 Copynumber: 4.1 Consensus size: 112
20428 TTGTCGGTTT
*
20438 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
20503 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
20550 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
20615 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
20662 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
** * *
20727 CCATCTATAAATGACAAAACAGGTAAAGCGCTA-C-AAAATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
20773 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAACAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
** * *
20838 GGTCTATAAATGACAAAACAAATAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
20885 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
20900 TATAAGTATC
Statistics
Matches: 329, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
110 43 0.13
111 59 0.18
112 180 0.55
113 47 0.14
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:20831 original size:223 final size:224
Alignment explanation
Indices: 20438--20899 Score: 766
Period size: 223 Copynumber: 2.1 Consensus size: 224
20428 TTGTCGGTTT
*
20438 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
** * *
20503 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 CATCTATAAATGACAAAACAGGTAAAGCGCTACCGAAAATATTGAAAGTGTCGATACTTTATAAA
* *
20568 AATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
131 AATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
**
20633 CAGGTAAAGCGCTACCGGATATATTGAAA
196 CAAATAAAGCGCTACCGGATATATTGAAA
*
20662 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
20727 CCATCTATAAATGACAAAACAGGTAAAGCGCTA-C-AAAATATTGAAAGTGTCGATACTTTATAA
65 CCATCTATAAATGACAAAACAGGTAAAGCGCTACCGAAAATATTGAAAGTGTCGATACTTTATAA
* * *
20790 AAATGTATCGATCCATAACAATATAACAGGTAAACAAATGACAAAATCGGTCTATAAATGACAAA
130 AAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
* *
20855 ACAAATAAAGCGCTACCGGATATGTTGATA
195 ACAAATAAAGCGCTACCGGATATATTGAAA
20885 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
20900 TATAAGTATC
Statistics
Matches: 222, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
223 128 0.58
224 47 0.21
225 47 0.21
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
CATCTATAAATGACAAAACAGGTAAAGCGCTACCGAAAATATTGAAAGTGTCGATACTTTATAAA
AATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
CAAATAAAGCGCTACCGGATATATTGAAA
Found at i:22008 original size:182 final size:182
Alignment explanation
Indices: 21700--22051 Score: 634
Period size: 182 Copynumber: 1.9 Consensus size: 182
21690 CAAACACTAT
21700 CAGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAG
1 CAGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAG
* *
21765 AAGTTATAGCGCCAATAAATTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAG
66 AAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
21830 GTAAAAATATGACAAAACCGGTATCGAAATGACAAAACCGGTAAAGAGCTAC
131 GTAAAAATATGACAAAACCGGTATCGAAATGACAAAACCGGTAAAGAGCTAC
* *
21882 CAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACAC-TTTGAGAATTTAAAAGAGAA
1 CAGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTG-GAATTTAAAAGAAAA
21946 GAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
65 GAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* *
22011 GGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACCG
130 GGTAAAAATATGACAAAACCGGTATCGAAATGACAAAACCG
22052 ATAGTAAAAA
Statistics
Matches: 163, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
181 4 0.02
182 159 0.98
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
CAGATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAG
AAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
GTAAAAATATGACAAAACCGGTATCGAAATGACAAAACCGGTAAAGAGCTAC
Found at i:22691 original size:23 final size:23
Alignment explanation
Indices: 22645--22692 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
22635 AAATAGGTCA
* *
22645 ATATAAGCGCTACTTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
22668 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
22691 AT
1 AT
22693 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:23836 original size:24 final size:24
Alignment explanation
Indices: 23800--23848 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
23790 TGTTCATGAA
* *
23800 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAATGTTCGTTTATGTT
23824 CGTTCGGTAATGTTCGTTTATGTT
1 CGTTCGGTAATGTTCGTTTATGTT
23848 C
1 C
23849 ATTCATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTAATGTTCGTTTATGTT
Found at i:23860 original size:24 final size:24
Alignment explanation
Indices: 23806--23861 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
23796 TGAACGTTTG
* *
23806 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
*
23830 GTAATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
23854 TTTATGTT
1 GTTATGTT
23862 TAACCCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:24281 original size:10 final size:10
Alignment explanation
Indices: 24266--24340 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
24256 GGGTCTCCAA
24266 CGTTTATGTT
1 CGTTTATGTT
24276 CGTTTATGTT
1 CGTTTATGTT
24286 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
24297 ATGTTCGTGTT
1 -CGTTTATGTT
24308 CGTTTATGTT
1 CGTTTATGTT
24318 CG----TGTT
1 CGTTTATGTT
24324 CGTTTATGTT
1 CGTTTATGTT
24334 CGTTTAT
1 CGTTTAT
24341 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:24297 original size:16 final size:16
Alignment explanation
Indices: 24272--24336 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
24262 CCAACGTTTA
24272 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
24288 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
24304 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24320 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24336 T
1 T
24337 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:24427 original size:16 final size:16
Alignment explanation
Indices: 24406--24438 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24396 AAAAAAAATT
24406 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24422 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24438 T
1 T
24439 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:26518 original size:2 final size:2
Alignment explanation
Indices: 26511--26576 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
26501 TGATTTTAAC
26511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
26553 AC AT AT AT GT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
26577 GACATAATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27783 original size:13 final size:13
Alignment explanation
Indices: 27765--27797 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
27755 TAATTTAAAC
27765 TAATAAATTTATA-
1 TAATAAA-TTATAG
27778 TAATAAATTATAG
1 TAATAAATTATAG
27791 TAATAAA
1 TAATAAA
27798 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
TAATAAATTATAG
Found at i:31711 original size:11 final size:10
Alignment explanation
Indices: 31697--31733 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 10
31687 TTTTGGTACG
31697 TTTTTTTAGTT
1 TTTTTTTA-TT
31708 TTTTTTTATTT
1 TTTTTTTA-TT
31719 TTTTTTTATT
1 TTTTTTTATT
31729 TTTTT
1 TTTTT
31734 AAGGTTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:33009 original size:20 final size:20
Alignment explanation
Indices: 32984--33064 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
32974 AATAACCAAC
32984 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
* * *
33004 GAATTCGCAACACAGAA-GTA
1 GAATTCGCAACTC-GAATTTG
**
33024 GAATTCGCAACTCGAACATG
1 GAATTCGCAACTCGAATTTG
33044 GAAATGTTCGCAACTCGAATT
1 G-AA--TTCGCAACTCGAATT
33065 CACCAAGTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.06
20 27 0.56
21 5 0.10
23 13 0.27
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
GAATTCGCAACTCGAATTTG
Found at i:33077 original size:22 final size:22
Alignment explanation
Indices: 33049--33102 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
33039 ACATGGAAAT
33049 GTTCGCAACTCGAATTCACCAA
1 GTTCGCAACTCGAATTCACCAA
33071 GTTCGCAACTCGAATTCACCAA
1 GTTCGCAACTCGAATTCACCAA
*
33093 TTTCGCAACT
1 GTTCGCAACT
33103 AAATTACCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (22 bp):
GTTCGCAACTCGAATTCACCAA
Found at i:43493 original size:31 final size:30
Alignment explanation
Indices: 43421--43539 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 30
43411 TTTTGAAAAA
* *
43421 TAAAAAATATATTTTATTCTTATTTTAACCAAAG
1 TAAAAAATATATTTTATTCTTATCTTAA-C---T
*
43455 TAAAAAATATATTTTAGTCTTATCTTAACTT
1 TAAAAAATATATTTTATTCTTATCTTAAC-T
* * *
43486 TAAAAAATACATTTTATTTTTACCTTAACT
1 TAAAAAATATATTTTATTCTTATCTTAACT
**
43516 TAAATATTTATATTTTATTCTTAT
1 TAAA-AAATATATTTTATTCTTAT
43540 AATATTCTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
30 5 0.07
31 39 0.55
33 1 0.01
34 26 0.37
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (30 bp):
TAAAAAATATATTTTATTCTTATCTTAACT
Found at i:43621 original size:24 final size:25
Alignment explanation
Indices: 43588--43638 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
43578 TGTTGTTAGG
43588 TTAAAATAAAAGT-AAAATATATAT
1 TTAAAATAAAAGTAAAAATATATAT
* *
43612 TTAAATTAAAAGTAAAAATGTATAT
1 TTAAAATAAAAGTAAAAATATATAT
43637 TT
1 TT
43639 TTAAGTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
TTAAAATAAAAGTAAAAATATATAT
Found at i:43668 original size:30 final size:29
Alignment explanation
Indices: 43632--43948 Score: 227
Period size: 30 Copynumber: 10.7 Consensus size: 29
43622 AGTAAAAATG
43632 TATATTTTTAAGTTAAGATAAGAATAAAA
1 TATATTTTTAAGTTAAGATAAGAATAAAA
* *
43661 -ATATATTTTAAGTTAAAATAAAAAT-AAA
1 TATAT-TTTTAAGTTAAGATAAGAATAAAA
* * *
43689 TAATATTTAATAATTTAAGGTGAA-AATAAAA
1 T-ATATTT-TTAAGTTAAGAT-AAGAATAAAA
* * * *
43720 TATATTTAATAATTTAAGTTAAGAATATAA
1 TATATTT-TTAAGTTAAGATAAGAATAAAA
** * *
43750 TATATGTAATATGTTAATATAA-AAT-AAA
1 TATAT-TTTTAAGTTAAGATAAGAATAAAA
* *
43778 T-TATTTTTAAAAGTTAAGATAAGAACAATA
1 TATATTTTT--AAGTTAAGATAAGAATAAAA
*
43808 TATATTTTTTAAGTTAAGGTGAA-AATAAAA
1 TATA-TTTTTAAGTTAAGAT-AAGAATAAAA
* *
43838 TAAATTTTTTAAGTTAAGATAAGATTTAAATA
1 TATA-TTTTTAAGTTAAGATAAGA-ATAAA-A
*
43870 TATATTTTT-AGTTAAAATAAGAATAAAA
1 TATATTTTTAAGTTAAGATAAGAATAAAA
* * *
43898 TATATTTAATAAGTTAAGATAAAAACAAAA
1 TATATTT-TTAAGTTAAGATAAGAATAAAA
*
43928 TATAATTTTTAAATTTAAGAT
1 TAT-ATTTTT-AAGTTAAGAT
43949 GTGAATTTAA
Statistics
Matches: 231, Mismatches: 35, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.01
27 3 0.01
28 28 0.12
29 34 0.15
30 122 0.53
31 33 0.14
32 9 0.04
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (29 bp):
TATATTTTTAAGTTAAGATAAGAATAAAA
Found at i:43813 original size:118 final size:120
Alignment explanation
Indices: 43642--43931 Score: 315
Period size: 118 Copynumber: 2.4 Consensus size: 120
43632 TATATTTTTA
* * * *
43642 AGTTAAGATAAGAATAAAAATATATTT--TAAGTTAAAATAAAAATAA-ATAATATTTAATAATT
1 AGTTAAAATAAGAAT-AAAATATATTTAATAAGTTAAGATAAAAACAATAT-ATATTTAATAAGT
* * * *
43704 TAAGGTGAAAATAAAATATATTTAATAATTTAAGTTAAGA-ATATAATATATGTA-AT
64 TAAGGTGAAAATAAAATAAATTTAATAAGTTAAGATAAGATATA-AATATATATATAT
* * * * **
43760 ATGTTAATATAA-AATAAATTATTTTTAA-AAGTTAAGATAAGAACAATATATATTTTTTAAGTT
1 A-GTTAAAATAAGAATAAAATATATTTAATAAGTTAAGATAAAAACAATATATATTTAATAAGTT
** * * *
43823 AAGGTGAAAATAAAATAAATTTTTTAAGTTAAGATAAGATTTAAATATATATTTTT
65 AAGGTGAAAATAAAATAAATTTAATAAGTTAAGATAAGATATAAATATATATATAT
*
43879 AGTTAAAATAAGAATAAAATATATTTAATAAGTTAAGATAAAAACAAAATATA
1 AGTTAAAATAAGAATAAAATATATTTAATAAGTTAAGATAAAAACAATATATA
43932 ATTTTTAAAT
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
117 9 0.06
118 81 0.57
119 29 0.21
120 22 0.16
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (120 bp):
AGTTAAAATAAGAATAAAATATATTTAATAAGTTAAGATAAAAACAATATATATTTAATAAGTTA
AGGTGAAAATAAAATAAATTTAATAAGTTAAGATAAGATATAAATATATATATAT
Found at i:43860 original size:60 final size:58
Alignment explanation
Indices: 43587--43948 Score: 222
Period size: 60 Copynumber: 6.1 Consensus size: 58
43577 TTGTTGTTAG
* * * * *
43587 GTTAAAATAAAAGTAAAATATA-TATTTAAATTAAAAGT-A-AAAATGTATA-TTTTTAA
1 GTTAAGATAAAA-TAAAATATATTTTTTAAGTTAAGA-TAAGAAAATATATATTTTTTAA
* * * **
43643 GTTAAGATAAGAATAAAA-ATATATTTTAAGTTAAAATAA-AAATAAATAATATTTAATAA
1 GTTAAGATAA-AATAAAATATATTTTTTAAGTTAAGATAAGAAA-ATAT-ATATTTTTTAA
* * ** * * * * ** *
43702 TTTAAGGTGAAAATAAAATATATTTAATAATTTAAGTTAAGAATATAATATATGTAATAT
1 GTTAAGAT-AAAATAAAATATATTTTTTAAGTTAAGATAAGAAAAT-ATATATTTTTTAA
* *
43762 GTTAATATAAAAT-AAAT-TATTTTTAAAAGTTAAGATAAGAACAATATATATTTTTTAA
1 GTTAAGATAAAATAAAATATATTTTT-TAAGTTAAGATAAGAA-AATATATATTTTTTAA
* *
43820 GTTAAGGTGAAAATAAAATAAATTTTTTAAGTTAAGATAAGATTTAAATATATA-TTTTT-A
1 GTTAAGAT-AAAATAAAATATATTTTTTAAGTTAAGATAAGA---AAATATATATTTTTTAA
* ** * * *
43880 GTTAAAATAAGAATAAAATATATTTAATAAGTTAAGATAAAAACAAAATATAATTTTTAAA
1 GTTAAGATAA-AATAAAATATATTTTTTAAGTTAAGATAAGAA-AATATAT-ATTTTTTAA
*
43941 TTTAAGAT
1 GTTAAGAT
43949 GTGAATTTAA
Statistics
Matches: 236, Mismatches: 47, Indels: 41
0.73 0.15 0.13
Matches are distributed among these distances:
55 4 0.02
56 29 0.12
57 10 0.04
58 41 0.17
59 33 0.14
60 88 0.37
61 22 0.09
62 8 0.03
63 1 0.00
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (58 bp):
GTTAAGATAAAATAAAATATATTTTTTAAGTTAAGATAAGAAAATATATATTTTTTAA
Found at i:43962 original size:18 final size:18
Alignment explanation
Indices: 43939--43984 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
43929 ATAATTTTTA
43939 AATTTAAGATGTGAATTT
1 AATTTAAGATGTGAATTT
*
43957 AATTTAATATGTGAATTT
1 AATTTAAGATGTGAATTT
*
43975 AAGTTAAGAT
1 AATTTAAGAT
43985 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.43
Consensus pattern (18 bp):
AATTTAAGATGTGAATTT
Found at i:44581 original size:21 final size:21
Alignment explanation
Indices: 44557--44596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44547 TGGTAAAAAT
44557 TACCGGAAATATTATTATTTC
1 TACCGGAAATATTATTATTTC
**
44578 TACCGGTTATATTATTATT
1 TACCGGAAATATTATTATT
44597 AGGCGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (21 bp):
TACCGGAAATATTATTATTTC
Found at i:46890 original size:11 final size:11
Alignment explanation
Indices: 46876--46905 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
46866 ATTTGATACA
46876 TATAATTTTAT
1 TATAATTTTAT
46887 TATAATTTTAT
1 TATAATTTTAT
46898 TAT-ATTTT
1 TATAATTTT
46906 CATTTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATAATTTTAT
Found at i:47681 original size:2 final size:2
Alignment explanation
Indices: 47674--47707 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
47664 TCTATCATTA
47674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47708 GAGATAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49340 original size:28 final size:28
Alignment explanation
Indices: 49309--49393 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 28
49299 ATTTTGTTTA
49309 TTTTGTTGCATGTTAATTAAATTATTTT
1 TTTTGTTGCATGTTAATTAAATTATTTT
* * * * *
49337 TTTTATTAACCT-TTAACTATATTGATATTT
1 TTTTGTT-GCATGTTAATTAAATT-AT-TTT
* *
49367 TTATG-TGCATGTTGATTAAATTATTTT
1 TTTTGTTGCATGTTAATTAAATTATTTT
49394 GTTAATTAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
27 3 0.07
28 19 0.46
29 13 0.32
30 6 0.15
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTTGTTGCATGTTAATTAAATTATTTT
Found at i:49377 original size:57 final size:57
Alignment explanation
Indices: 49315--49486 Score: 274
Period size: 57 Copynumber: 3.0 Consensus size: 57
49305 TTTATTTTGT
* * *
49315 TGCATGTTAATTAAATTATTTTTTTTATTAACCT-TTAACTATATTGATATTTTTATG
1 TGCATGTTGATTAAATTATTTTGTTTATTAA-CTATTAACTATATTGATATTTTTAGG
*
49372 TGCATGTTGATTAAATTATTTTGTTAATTAACTATTAACTATATTGATATTTTTAGG
1 TGCATGTTGATTAAATTATTTTGTTTATTAACTATTAACTATATTGATATTTTTAGG
* *
49429 TGCATGTTGATTAAATTATTTTGTTTATTAACTATTAAATATATTGATATTTTCAGG
1 TGCATGTTGATTAAATTATTTTGTTTATTAACTATTAACTATATTGATATTTTTAGG
49486 T
1 T
49487 TATACAAATT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
56 2 0.02
57 105 0.98
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (57 bp):
TGCATGTTGATTAAATTATTTTGTTTATTAACTATTAACTATATTGATATTTTTAGG
Found at i:52976 original size:21 final size:22
Alignment explanation
Indices: 52946--53026 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
52936 AGAACCCTAG
* *
52946 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
* *
52967 GGGGGAATCGGTTCTCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
52989 AGGGGAATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
53011 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
53027 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:59957 original size:21 final size:21
Alignment explanation
Indices: 59912--59957 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
59902 CAACATTGAT
*
59912 CCAAAGCTTCCCATCAACAGG
1 CCAAAGCTTCCCATCAACAGA
59933 CCAAAGCTTCCCATCATA-AGA
1 CCAAAGCTTCCCATCA-ACAGA
59954 CCAA
1 CCAA
59958 CAATTTGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (21 bp):
CCAAAGCTTCCCATCAACAGA
Found at i:69506 original size:15 final size:16
Alignment explanation
Indices: 69488--69520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
69478 AAACCCAACA
69488 AATTT-AAACTCGATT
1 AATTTAAAACTCGATT
*
69503 AATTTAAAACTTGATT
1 AATTTAAAACTCGATT
69519 AA
1 AA
69521 AATTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (16 bp):
AATTTAAAACTCGATT
Found at i:69868 original size:2 final size:2
Alignment explanation
Indices: 69861--69899 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
69851 CCAGGCCATC
69861 AT AT AT AT AT 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 AT AT AT AT AT A
69900 ATTGAAGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75933 original size:16 final size:16
Alignment explanation
Indices: 75909--75942 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
75899 TATCGCCGAT
*
75909 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
75925 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
75941 CG
1 CG
75943 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:78987 original size:74 final size:73
Alignment explanation
Indices: 78909--79147 Score: 213
Period size: 74 Copynumber: 3.2 Consensus size: 73
78899 TTTGACAAAG
*
78909 TATAATATATAATTTTCAGAAAAAGGTTTTTGAAAA-TATATATGGTATA-ATTTTAAAAACATT
1 TATAATATATAATTTTCAGAAAAA---TTTTGAAAATTATATATAGTATAGATTTTAAAAACATT
*
78972 TTTAAAATATA
63 TTAAAAATATA
* * *
78983 TATAATATAT-AGTTTC-GAAAACATTTTGAAAACATTTATATATTA-TATAGTTTTTAAAAGTC
1 TATAATATATAATTTTCAGAAAA-ATTTTG-AAA-A-TTATATA-TAGTATAGATTTTAAAA-AC
79045 ATTTTGAAAAATATA
60 ATTTT-AAAAATATA
* * * * *
79060 TATAATATATAGTTTTTA-AAACATTTTGAAAATTATATATAGTATATAGTTTTGAAAACATTTT
1 TATAATATATAATTTTCAGAAAAATTTTGAAAATTATATATAGTATAGA-TTTTAAAAACATTTT
*
79124 GAAAAT-TA
65 AAAAATATA
* *
79132 TATAGTATATAGTTTT
1 TATAATATATAATTTT
79148 GAAGATATTT
Statistics
Matches: 137, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
70 5 0.04
71 3 0.02
72 23 0.17
73 13 0.09
74 37 0.27
75 17 0.12
76 9 0.07
77 24 0.18
78 6 0.04
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (73 bp):
TATAATATATAATTTTCAGAAAAATTTTGAAAATTATATATAGTATAGATTTTAAAAACATTTTA
AAAATATA
Found at i:79085 original size:37 final size:37
Alignment explanation
Indices: 78936--79196 Score: 268
Period size: 37 Copynumber: 7.1 Consensus size: 37
78926 AGAAAAAGGT
* *
78936 TTTTG-AAAATATATATGGTATA-A-TTTTAAAAACA
1 TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
* * *
78970 TTTT-TAAAATATATATAATATATAGTTTCGAAAACA
1 TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
* * *
79006 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAGTCA
1 TTTTGAAAA-ATATATATAGTATATAGTTTTGAAAA--CA
* *
79046 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
*
79083 TTTTGAAAATTATATATAGTATATAGTTTTGAAAACA
1 TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
* *
79120 TTTTG-AAAAT-TATATAGTATATAGTTTTGAAGATA
1 TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
* * *
79155 TTTTTGAAAACATTTATATATTTATATA-TGTTG-AAACA
1 -TTTTGAAAA-ATATATATA-GTATATAGTTTTGAAAACA
79193 TTTT
1 TTTT
79197 AATATTTCGA
Statistics
Matches: 194, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.10
35 24 0.12
36 22 0.11
37 51 0.26
38 27 0.14
39 34 0.18
40 17 0.09
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATATATATAGTATATAGTTTTGAAAACA
Found at i:79173 original size:74 final size:71
Alignment explanation
Indices: 78936--79196 Score: 276
Period size: 77 Copynumber: 3.5 Consensus size: 71
78926 AGAAAAAGGT
* * * * *
78936 TTTTGAAAATATATATGGTATA-ATTTTAAAAACATTTTTAAAATATATATAATATATAGTTTCG
1 TTTTGAAAATTTATATAGTATATATTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTG
79000 AAAACA
66 AAAACA
* *
79006 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAGTCATTTTGAAAAATATATATAATATATA
1 TTTTG-AAA-ATTTATATAGTATATA-TTTTGAAAA--CATTTTG-AAAATATATATAATATATA
*
79071 GTTTTTAAAACA
60 GTTTTGAAAACA
*
79083 TTTTGAAAATTATATATAGTATATAGTTTTGAAAACATTTTGAAAAT-TATATAGTATATAGTTT
1 TTTTGAAAATT-TATATAGTATATA-TTTTGAAAACATTTTGAAAATATATATAATATATAGTTT
* *
79147 TGAAGATA
64 TGAAAACA
* *
79155 TTTTTGAAAACATTTATATATTTATATATGTTG-AAACATTTT
1 -TTTTG-AAA-ATTTATATA-GTATATATTTTGAAAACATTTT
79197 AATATTTCGA
Statistics
Matches: 164, Mismatches: 15, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
70 5 0.03
71 3 0.02
72 32 0.20
73 20 0.12
74 28 0.17
75 12 0.07
76 30 0.18
77 34 0.21
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (71 bp):
TTTTGAAAATTTATATAGTATATATTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTG
AAAACA
Found at i:85308 original size:20 final size:20
Alignment explanation
Indices: 85283--85344 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
85273 TTTTGGTGCA
85283 GAGGGAATCGATTCCCCCCT
1 GAGGGAATCGATTCCCCCCT
* *
85303 GAGGGAACCGATTCCCCCCA
1 GAGGGAATCGATTCCCCCCT
* *
85323 CAGGGGAATCGATACCCCCCT
1 GA-GGGAATCGATTCCCCCCT
85344 G
1 G
85345 GGGTTCTGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCCT
Found at i:87591 original size:27 final size:24
Alignment explanation
Indices: 87560--87617 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 24
87550 ATTTAACAAA
87560 AAGGGGGAGAAGAATAAGTGTTAAAGT
1 AAGGGGGAG-AG--TAAGTGTTAAAGT
87587 AA-GGGG-GAGTAAGTGTTAAAGT
1 AAGGGGGAGAGTAAGTGTTAAAGT
87609 AAGGGGGAG
1 AAGGGGGAG
87618 TAATTTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 15 0.52
23 4 0.14
24 3 0.10
25 1 0.03
26 4 0.14
27 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (24 bp):
AAGGGGGAGAGTAAGTGTTAAAGT
Found at i:87599 original size:22 final size:22
Alignment explanation
Indices: 87574--87620 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
87564 GGGAGAAGAA
87574 TAAGTGTTAAAGTAAGGGGGAG
1 TAAGTGTTAAAGTAAGGGGGAG
87596 TAAGTGTTAAAGTAAGGGGGAG
1 TAAGTGTTAAAGTAAGGGGGAG
87618 TAA
1 TAA
87621 TTTCTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (22 bp):
TAAGTGTTAAAGTAAGGGGGAG
Found at i:87644 original size:21 final size:20
Alignment explanation
Indices: 87618--87672 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
87608 TAAGGGGGAG
87618 TAATTTCTAATTTTAATTTT
1 TAATTTCTAATTTTAATTTT
* ** *
87638 CTAATTTCAAAACTTGATTTT
1 -TAATTTCTAATTTTAATTTT
87659 TAATTTTCTAATTT
1 TAA-TTTCTAATTT
87673 CAAAACTTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (20 bp):
TAATTTCTAATTTTAATTTT
Found at i:87659 original size:28 final size:28
Alignment explanation
Indices: 87628--87685 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
87618 TAATTTCTAA
87628 TTTTAATTTTCTAATTTCAAAACTTGAT
1 TTTTAATTTTCTAATTTCAAAACTTGAT
87656 TTTTAATTTTCTAATTTCAAAACTTGAT
1 TTTTAATTTTCTAATTTCAAAACTTGAT
87684 TT
1 TT
87686 CAAAAATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTTAATTTTCTAATTTCAAAACTTGAT
Found at i:88857 original size:39 final size:38
Alignment explanation
Indices: 88801--88958 Score: 150
Period size: 38 Copynumber: 4.3 Consensus size: 38
88791 CAATATAGTT
*
88801 TTTTTAAAAGACATTTTGAAAATATATATAATATATAG
1 TTTTTAAAAAACATTTTGAAAATATATATAATATATAG
88839 TTTTTAAAAAACATTTTTG-AAAT-TATAT-ATATA-A-
1 TTTTTAAAAAACA-TTTTGAAAATATATATAATATATAG
* * **
88873 TTTTT-TAAAACGTTTTTGAAAATACGTATAATATATAG
1 TTTTTAAAAAAC-ATTTTGAAAATATATATAATATATAG
* * * *
88911 TTTTCACAAAAGCATTTTGAAAATTTATATATTATAT-G
1 TTTTTA-AAAAACATTTTGAAAATATATATAATATATAG
*
88949 TTTTTGAAAA
1 TTTTTAAAAA
88959 CTTTTTATAT
Statistics
Matches: 96, Mismatches: 15, Indels: 19
0.74 0.12 0.15
Matches are distributed among these distances:
33 10 0.10
34 9 0.09
35 4 0.04
36 10 0.10
37 10 0.10
38 25 0.26
39 24 0.25
40 4 0.04
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (38 bp):
TTTTTAAAAAACATTTTGAAAATATATATAATATATAG
Found at i:88890 original size:72 final size:75
Alignment explanation
Indices: 88814--88964 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 75
88804 TTAAAAGACA
* *
88814 TTTTGAAAATATATATAATATATAGTTTTTA-AAAAACATTTTTG-AAA-TTATATA-TATAAT-
1 TTTTGAAAATACATATAATATATAGTTTTCACAAAAACA-TTTTGAAAATTTATATATTAT-ATG
88874 TTTTT-AAAACGT
64 TTTTTGAAAAC-T
* *
88886 TTTTGAAAATACGTATAATATATAGTTTTCACAAAAGCATTTTGAAAATTTATATATTATATGTT
1 TTTTGAAAATACATATAATATATAGTTTTCACAAAAACATTTTGAAAATTTATATATTATATGTT
88951 TTTGAAAACT
66 TTTGAAAACT
88961 TTTT
1 TTTT
88965 ATATATTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
72 33 0.48
73 9 0.13
74 9 0.13
75 13 0.19
76 5 0.07
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (75 bp):
TTTTGAAAATACATATAATATATAGTTTTCACAAAAACATTTTGAAAATTTATATATTATATGTT
TTTGAAAACT
Found at i:89009 original size:22 final size:22
Alignment explanation
Indices: 88968--89009 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
88958 ACTTTTTATA
* *
88968 TATTATTATTGTTTATTATTGT
1 TATTATTATTATTTACTATTGT
*
88990 TATTATTATTATTTCCTATT
1 TATTATTATTATTTACTATT
89010 TATTTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (22 bp):
TATTATTATTATTTACTATTGT
Found at i:90222 original size:13 final size:13
Alignment explanation
Indices: 90204--90232 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
90194 TTTCTCTTAA
90204 TTTATTTAATTTT
1 TTTATTTAATTTT
90217 TTTATTTAATTTT
1 TTTATTTAATTTT
90230 TTT
1 TTT
90233 TCTTTGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTAATTTT
Found at i:90386 original size:13 final size:13
Alignment explanation
Indices: 90370--90399 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
90360 CAAATCGGAT
*
90370 TTTTAAATTTAAG
1 TTTTAAATTTAAA
90383 TTTTAAATTTAAA
1 TTTTAAATTTAAA
90396 TTTT
1 TTTT
90400 CATAACTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTAAATTTAAA
Found at i:98643 original size:23 final size:22
Alignment explanation
Indices: 98584--98644 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
98574 TATAAAAGAT
*
98584 AAAAAATTTGTCA-AAAGATAT
1 AAAAAATTTGTCATAAAGATAG
* * * *
98605 AAAAAATGTATTATAAAGATGG
1 AAAAAATTTGTCATAAAGATAG
98627 AGAAAAATTTGTCATAAA
1 A-AAAAATTTGTCATAAA
98645 AAACATAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 10 0.33
22 7 0.23
23 13 0.43
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (22 bp):
AAAAAATTTGTCATAAAGATAG
Found at i:99374 original size:37 final size:37
Alignment explanation
Indices: 99298--99374 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
99288 TTTTTATATT
*
99298 TTTAATTTTGTAAACAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
* *
99335 TTTAATTTAT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTT-TGTAAACAAAATTATATAAATATTAT-CAA
99372 TTT
1 TTT
99375 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
Done.