Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001449.1 Hibiscus syriacus cultivar Beakdansim tig00002800_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: 97313
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:13236 original size:3 final size:3
Alignment explanation
Indices: 13230--13285 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
13220 AATAATAATA
*
13230 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
13278 ATA ATG AT
1 ATG ATG AT
13286 AATTCCATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:13286 original size:6 final size:6
Alignment explanation
Indices: 13215--13288 Score: 58
Period size: 6 Copynumber: 11.8 Consensus size: 6
13205 TATATTTTAA
* * * * * * *
13215 ATAATA ATAATA ATAATG ATGATG ATGATG ATGATG ATGATG ATGATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
13263 ATAATG ATGATGATG ATAATG ATAAT
1 ATAATG AT-A--ATG ATAATG ATAAT
13289 TCCATATTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
6 55 0.89
7 1 0.02
8 1 0.02
9 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:14099 original size:69 final size:70
Alignment explanation
Indices: 14022--14153 Score: 239
Period size: 69 Copynumber: 1.9 Consensus size: 70
14012 TTTCTTTAAC
*
14022 ATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAA-TATTAACCAA
1 ATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATTAACCAA
14086 AACAA
66 AACAA
*
14091 ATTAATCGAACCGAAATTGTTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATTAACC
1 ATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATTAACC
14154 GAATTTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
69 52 0.87
70 8 0.13
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (70 bp):
ATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATTAACCAA
AACAA
Found at i:14422 original size:66 final size:68
Alignment explanation
Indices: 14336--14496 Score: 220
Period size: 66 Copynumber: 2.4 Consensus size: 68
14326 AAATTATTTG
* * * **
14336 ACCGTTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAATAAAAT-AAATTAT-TTTTTCC
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAAACGATATTTTTCC
14399 TTA
66 TTA
* * *
14402 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATATTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAAACGATATTTTTCC
14467 TTA
66 TTA
*
14470 ACCATTAATCGAACCGAAA-TTATTTGA
1 ACCGTTAATCGAACCGAAATTTATTTGA
14497 CCATTAATCA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
66 45 0.54
67 12 0.14
68 27 0.32
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (68 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAAACGATATTTTTCC
TTA
Found at i:14426 original size:93 final size:93
Alignment explanation
Indices: 14259--14429 Score: 245
Period size: 93 Copynumber: 1.8 Consensus size: 93
14249 AATTGAACTG
* * * * *
14259 AAATTTATTTGAAAATTATTAACCGAACCAAATCAATCGATTTTTTCTTTAACCATTAATTGAAT
1 AAATTTATTTGAAAATTATTAACCGAACAAAATAAATCGATTTTTTCCTTAACCATTAATCGAAC
*
14324 TGAAATTATTTGACCGTTAATCGAATCA
66 CGAAATTATTTGACCGTTAATCGAATCA
* * *
14352 AAATTTATTTGAAAATTATTAACCGAATAAAATAAAT-TATTTTTTCCTTAACCGTTAATCGAAC
1 AAATTTATTTGAAAATTATTAACCGAACAAAATAAATCGATTTTTTCCTTAACCATTAATCGAAC
14416 CGAAATTTATTTGA
66 CGAAA-TTATTTGA
14430 AAATTATTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 26 0.38
93 42 0.62
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (93 bp):
AAATTTATTTGAAAATTATTAACCGAACAAAATAAATCGATTTTTTCCTTAACCATTAATCGAAC
CGAAATTATTTGACCGTTAATCGAATCA
Found at i:14430 original size:159 final size:158
Alignment explanation
Indices: 14211--14522 Score: 500
Period size: 159 Copynumber: 2.0 Consensus size: 158
14201 TATTAACCGA
* * * *
14211 ATTAACCGAATAAGATAAATTATTTTTCTTTAACCGTTAATTGAACTGAAATTTATTTGAAAATT
1 ATTAACCGAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAATT
* * ** *
14276 ATTAACCGAACCAAATCAATCGAT-TTTTTCTTTAACCATTAATTGAATTGAAATTATTTGACCG
66 ATTAACCGAACCAAATCAACCGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCA
*
14340 TTAATCGAATCAAAATTTATTTGAAAATT
131 TTAATCAAATCAAAA-TTATTTGAAAATT
14369 ATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAAT
1 ATTAACCGAATAAAATAAATTA-TTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAAT
14434 TATTAACCGAACCAAATCAACCGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACC
65 TATTAACCGAACCAAATCAACCGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACC
*
14499 ATTAATCAAATCGAAATTATTTGA
130 ATTAATCAAATCAAAATTATTTGA
14523 CCGTTAATTG
Statistics
Matches: 141, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
158 21 0.15
159 71 0.50
160 49 0.35
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (158 bp):
ATTAACCGAATAAAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAATT
ATTAACCGAACCAAATCAACCGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCA
TTAATCAAATCAAAATTATTTGAAAATT
Found at i:14501 original size:26 final size:26
Alignment explanation
Indices: 14470--14549 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
14460 TTTTTCTTTA
*
14470 ACCATTAATCGAACCGAAATTATTTG
1 ACCATTAATCGAATCGAAATTATTTG
*
14496 ACCATTAATCAAATCGAAATTATTTG
1 ACCATTAATCGAATCGAAATTATTTG
* * *
14522 ACCGTTAATTGAATCAAAATTTATTTG
1 ACCATTAATCGAATCGAAA-TTATTTG
14549 A
1 A
14550 AAATTATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 39 0.83
27 8 0.17
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (26 bp):
ACCATTAATCGAATCGAAATTATTTG
Found at i:14663 original size:120 final size:122
Alignment explanation
Indices: 14390--14663 Score: 276
Period size: 120 Copynumber: 2.3 Consensus size: 122
14380 AAAATAAATT
* * * *
14390 ATTTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAAC
1 ATTTTTTCTTTAACCGTTAATTGAACCG-AATTTATTTGAAAATTATTAACCGAACAAAATCAAA
* *
14455 CGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCAAATCGA
65 CGATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACAATTAATCAAACCGA
* * * ** *
14513 A---ATTATTTGACCGTTAATTGAATCAAAATTTATTTGAAAATTATTAACCGAATAAAAT-AAA
1 ATTTTTTCTTTAACCGTTAATTGAA-CCGAATTTATTTGAAAATTATTAACCGAACAAAATCAAA
** * * **
14574 TTAT-TTTTTCTTTAACCGTTAATC-AATCCGAAATTTATTTGA-AATTTAT-TTACCGA
65 CGATATTTTTCTTTAACCATTAATCGAA-CCGAAA-TTATTTGACAATTAATCAAACCGA
*
14630 ATTTTTTTCTTTAACCATTAATTGAACCGAATTT
1 A-TTTTTTCTTTAACCGTTAATTGAACCGAATTT
14664 TTTCATTAAC
Statistics
Matches: 120, Mismatches: 24, Indels: 17
0.75 0.15 0.11
Matches are distributed among these distances:
117 7 0.06
118 30 0.25
119 12 0.10
120 52 0.43
121 18 0.15
123 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (122 bp):
ATTTTTTCTTTAACCGTTAATTGAACCGAATTTATTTGAAAATTATTAACCGAACAAAATCAAAC
GATATTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACAATTAATCAAACCGA
Found at i:15904 original size:12 final size:13
Alignment explanation
Indices: 15887--15915 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
15877 ACGTATATGT
15887 TTTTTAAA-AATA
1 TTTTTAAATAATA
15899 TTTTTAAATAATA
1 TTTTTAAATAATA
15912 TTTT
1 TTTT
15916 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAATAATA
Found at i:15935 original size:69 final size:70
Alignment explanation
Indices: 15854--15985 Score: 230
Period size: 69 Copynumber: 1.9 Consensus size: 70
15844 AACGTAAAAA
*
15854 AAACCTGTTAAGTGACACGTATCACGTATATGTTTTTTAAAAATATTTTTAAATAATATTTTATT
1 AAACCTGTTAAGTGACACGTATCACGTATATATTTTTTAAAAATATTTTTAAATAATATTTTATT
15919 TTTTT
66 TTTTT
* *
15924 AAACC-GTTAAGTGGCACGTATCACGTATATATTTTTTAAAAATATTTTTAAATAATTTTTTA
1 AAACCTGTTAAGTGACACGTATCACGTATATATTTTTTAAAAATATTTTTAAATAATATTTTA
15986 ACATTGATCA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
69 54 0.92
70 5 0.08
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (70 bp):
AAACCTGTTAAGTGACACGTATCACGTATATATTTTTTAAAAATATTTTTAAATAATATTTTATT
TTTTT
Found at i:15973 original size:12 final size:12
Alignment explanation
Indices: 15954--15986 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15944 TCACGTATAT
15954 ATTTTTTAAA-A
1 ATTTTTTAAATA
15965 ATATTTTTAAATA
1 AT-TTTTTAAATA
15978 ATTTTTTAA
1 ATTTTTTAA
15987 CATTGATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 15 0.75
13 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTTTAAATA
Found at i:20893 original size:16 final size:17
Alignment explanation
Indices: 20874--20909 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20864 TATTTTATTA
*
20874 TTTATTATA-TTTAAAT
1 TTTAATATATTTTAAAT
20890 TTTAATATATTTTAAAT
1 TTTAATATATTTTAAAT
20907 TTT
1 TTT
20910 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAATATATTTTAAAT
Found at i:20908 original size:23 final size:23
Alignment explanation
Indices: 20865--20908 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
20855 TAGTATAATT
* *
20865 ATTTTATTATTTATTATATTTAA
1 ATTTTAATATTTATTAAATTTAA
20888 ATTTTAATATATT-TTAAATTT
1 ATTTTAATAT-TTATTAAATTT
20909 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTAATATTTATTAAATTTAA
Found at i:21092 original size:15 final size:15
Alignment explanation
Indices: 21072--21128 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
21062 TTCTAAAAAA
*
21072 TGAATTACAGGAATT
1 TGAATTACTGGAATT
**
21087 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
21102 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
21117 TAAATT-CTGGAA
1 TGAATTACTGGAA
21129 AATAAATTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 6 0.17
15 30 0.83
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:21134 original size:14 final size:15
Alignment explanation
Indices: 21089--21138 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
21079 CAGGAATTTG
*
21089 AATTACTGGAAAATG
1 AATTACTGGAAAATA
**
21104 AATTACTGGAATTTA
1 AATTACTGGAAAATA
21119 AATT-CTGGAAAATA
1 AATTACTGGAAAATA
21133 AATTAC
1 AATTAC
21139 ATTTCTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (15 bp):
AATTACTGGAAAATA
Found at i:21136 original size:29 final size:30
Alignment explanation
Indices: 21068--21139 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
21058 GATTTTCTAA
*
21068 AAAATGAATTACAGGAATTTGAATTACTGG
1 AAAATGAATTACAGGAATTTAAATTACTGG
*
21098 AAAATGAATTACTGGAATTTAAATT-CTGG
1 AAAATGAATTACAGGAATTTAAATTACTGG
*
21127 AAAATAAATTACA
1 AAAATGAATTACA
21140 TTTCTGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (30 bp):
AAAATGAATTACAGGAATTTAAATTACTGG
Found at i:21144 original size:20 final size:20
Alignment explanation
Indices: 21121--21170 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
21111 GGAATTTAAA
21121 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
* *
21141 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
21161 TTCTGGAAAA
1 TTCTGGAAAA
21171 CATCTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:21546 original size:26 final size:27
Alignment explanation
Indices: 21494--21647 Score: 112
Period size: 28 Copynumber: 5.7 Consensus size: 27
21484 TTTACTAAAA
21494 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
21522 TCATTATTAAATATATAAAAAATTATTAT
1 T-ATTATTAAATATATAAATAA-TATTAT
* * *
21551 ATATTATTAAA-ATAAAAATATTATATCT
1 -TATTATTAAATATATAAATAATAT-TAT
*
21579 TATTATTATA-ATAT-AAT--TGATTA-
1 TATTATTAAATATATAAATAAT-ATTAT
21602 TATTATTAAACTA-A-AAATAATATTA-
1 TATTATTAAA-TATATAAATAATATTAT
21627 TATTA-TAAATATTAATAAATA
1 TATTATTAAATA-T-ATAAATA
21648 TTTTAAATTT
Statistics
Matches: 103, Mismatches: 9, Indels: 29
0.73 0.06 0.21
Matches are distributed among these distances:
23 11 0.11
24 10 0.10
25 12 0.12
26 5 0.05
27 20 0.19
28 25 0.24
29 19 0.18
30 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:21589 original size:50 final size:52
Alignment explanation
Indices: 21508--21645 Score: 135
Period size: 50 Copynumber: 2.7 Consensus size: 52
21498 ATTTAAATAT
21508 ATAAATAATATTATTCATTATTAAATATATAA-AAAATT-ATTATATATTATTAAA
1 ATAAA-AATATTATTCATTATT-AATATATAATAAAATTGA-T-TATATTATTAAA
*
21562 ATAAAAATATTATATC-TTATT-AT-TATAATATAATTGATTATATTATTAAA
1 ATAAAAATATTAT-TCATTATTAATATATAATAAAATTGATTATATTATTAAA
* * * *
21612 CTAAAAATAATATTATATTATAAATAT-TAATAAA
1 ATAAAAATATTATT-CATTATTAATATATAATAAA
21646 TATTTTAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
49 1 0.01
50 28 0.39
51 12 0.17
52 9 0.13
53 14 0.20
54 7 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (52 bp):
ATAAAAATATTATTCATTATTAATATATAATAAAATTGATTATATTATTAAA
Found at i:21888 original size:42 final size:42
Alignment explanation
Indices: 21841--21957 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 42
21831 ATGAATTGCG
*
21841 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
21883 TTCCGGAAAACGAATTACGTGAAACAAATACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* * * *
21925 TTCTGAAAAATGAATTACATGAAACAAACACGG
1 TTCCGGAAAACGAATTACGTGAAACAAACACGG
21958 ATTTCGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:30563 original size:41 final size:41
Alignment explanation
Indices: 30454--30565 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 41
30444 TAAATTCAAC
*
30454 TCTAAACTGGGATTGTACAACACATACAACATACACCAAAT
1 TCTAAACTGGGATTGTATAACACATACAACATACACCAAAT
* * *
30495 TCTAAACTGGGATTGCATGAA-ACATACAACATATATCAAAT
1 TCTAAACTGGGATTGTAT-AACACATACAACATACACCAAAT
* *
30536 TCTAAACTGGGATTATATAACATATACAAC
1 TCTAAACTGGGATTGTATAACACATACAAC
30566 CCAATATGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.03
41 58 0.94
42 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (41 bp):
TCTAAACTGGGATTGTATAACACATACAACATACACCAAAT
Found at i:34260 original size:9 final size:10
Alignment explanation
Indices: 34220--34271 Score: 58
Period size: 9 Copynumber: 5.6 Consensus size: 10
34210 TCCTCCCGAA
34220 ATTTTTA-A-
1 ATTTTTATAT
34228 ATTTTTATAT
1 ATTTTTATAT
* *
34238 AATTTAAT-T
1 ATTTTTATAT
34247 ATTTTTATAT
1 ATTTTTATAT
34257 -TTTTTATAT
1 ATTTTTATAT
34266 ATTTTT
1 ATTTTT
34272 TTTATTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 7 0.19
9 17 0.47
10 12 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:34262 original size:19 final size:19
Alignment explanation
Indices: 34228--34271 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
34218 AAATTTTTAA
34228 ATTTTTATATAATTTA-ATT
1 ATTTTTATATAATTTATA-T
**
34247 ATTTTTATATTTTTTATAT
1 ATTTTTATATAATTTATAT
34266 ATTTTT
1 ATTTTT
34272 TTTATTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTATATAATTTATAT
Found at i:43211 original size:2 final size:2
Alignment explanation
Indices: 43174--43198 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43164 TCAATCAAAT
43174 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43199 CACTCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45388 original size:20 final size:20
Alignment explanation
Indices: 45363--45455 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
45353 TTTTCCCAAT
45363 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
45383 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
45403 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
45424 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
45445 TCGCAATGCGA
1 TCGCAATGCGA
45456 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:45405 original size:41 final size:41
Alignment explanation
Indices: 45360--45455 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
45350 CGATTTTCCC
45360 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
45401 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
45442 AAATCGCAATGCGA
1 AATTCGCAATGCGA
45456 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:45409 original size:21 final size:20
Alignment explanation
Indices: 45363--45455 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
45353 TTTTCCCAAT
*
45363 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
45383 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
45403 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
45424 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
45445 TCGCAATGCGA
1 TCGCAATGCGA
45456 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:45469 original size:20 final size:20
Alignment explanation
Indices: 45444--45538 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
45434 AATTGGGAAA
*
45444 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
45464 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
45485 ATCGTAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
45505 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
45525 TTCGCAACGCGATA
1 ATCGCAACGCGATA
45539 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:45486 original size:41 final size:41
Alignment explanation
Indices: 45441--45518 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
45431 GCGAATTGGG
* * *
45441 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
45482 AAAATCGTAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
45519 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:45755 original size:23 final size:23
Alignment explanation
Indices: 45726--45770 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
45716 CACTCTCTCA
45726 CCCATCTCCGACGAAATCCGTCC
1 CCCATCTCCGACGAAATCCGTCC
*
45749 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
45771 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.18
Consensus pattern (23 bp):
CCCATCTCCGACGAAATCCGTCC
Found at i:46059 original size:20 final size:20
Alignment explanation
Indices: 46034--46071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46024 CGATTCTCTC
46034 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
46054 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
46072 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:47411 original size:18 final size:18
Alignment explanation
Indices: 47390--47434 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
47380 TCCACTTCGG
*
47390 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
47408 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
47426 GAGCCATCA
1 GAGCCATCA
47435 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:47960 original size:19 final size:20
Alignment explanation
Indices: 47906--47972 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
47896 TAGTTTACTT
* *
47906 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
47926 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
47946 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
47965 TCGCAACG
1 TCGCAACG
47973 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:47980 original size:14 final size:14
Alignment explanation
Indices: 47961--48018 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
47951 ATGCGAAATG
47961 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
47975 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
47991 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
48007 AAAATCGTAACG
1 AAAATCGCAACG
48019 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:48003 original size:32 final size:33
Alignment explanation
Indices: 47945--48035 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
47935 GGAAATGGCT
*
47945 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
47978 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
48010 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
48036 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:48040 original size:19 final size:18
Alignment explanation
Indices: 47945--48040 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
47935 GGAAATGGCT
47945 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
47964 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
47978 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
47996 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
*
48010 ATCGTAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
48029 ATCGCAATGCGA
1 ATCGCAA-GCGA
48041 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.19
19 20 0.34
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:48071 original size:14 final size:14
Alignment explanation
Indices: 48052--48109 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
48042 TTGTGTTTCG
48052 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
48066 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
48082 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
48098 CGTTGCGATTTT
1 CGTTGCGATTTT
48110 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48086 original size:32 final size:33
Alignment explanation
Indices: 48047--48117 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
48037 GCGATTTGTG
48047 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
48079 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
48112 TTTCGC
1 TTTCGC
48118 ATTGTGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:48152 original size:20 final size:19
Alignment explanation
Indices: 48098--48164 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
48088 GCGATTTTGT
**
48098 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
48117 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
48137 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
48156 CGTTGCGAT
1 CGTTGCGAT
48165 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:49844 original size:14 final size:14
Alignment explanation
Indices: 49825--49861 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49815 GATTGTTTAA
49825 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
49839 TTGATTTGTAAATG
1 TTGATTTGTAAAAG
49853 TTGATTTGT
1 TTGATTTGT
49862 TTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:51150 original size:24 final size:24
Alignment explanation
Indices: 51085--51152 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
51075 GTGAGTACTA
* * *
51085 GTCAGTATTCGAAATTTGATCTTG
1 GTCAATATCCGAAATTTGATATTG
* *
51109 GTCAATATCCGGACTTTGATATTG
1 GTCAATATCCGAAATTTGATATTG
*
51133 GTCAATA-CACGAATTTTGAT
1 GTCAATATC-CGAAATTTGAT
51153 GATGTTTCAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATATCCGAAATTTGATATTG
Found at i:51344 original size:12 final size:12
Alignment explanation
Indices: 51327--51351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51317 ATATAATCCT
51327 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51339 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51351 G
1 G
51352 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:53661 original size:19 final size:19
Alignment explanation
Indices: 53639--53736 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
53629 GGAAATTACT
53639 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
53658 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
53672 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
53691 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
53705 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
53724 ATCGCAACGCGAA
1 ATCGCAATGCGAA
53737 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:53681 original size:33 final size:33
Alignment explanation
Indices: 53639--53732 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
53629 GGAAATTACT
53639 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
53672 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
53705 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
53733 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:53914 original size:14 final size:14
Alignment explanation
Indices: 53895--53931 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53885 CATCAATTAA
53895 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
53909 ACAAATCACCTTTT
1 ACAAATCAACTTTT
53923 ACAAATCAA
1 ACAAATCAA
53932 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:55355 original size:21 final size:21
Alignment explanation
Indices: 55289--55355 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55279 GTGAATCGGG
*
55289 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
55309 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
55331 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
55352 CTCT
1 CTCT
55356 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:55374 original size:42 final size:41
Alignment explanation
Indices: 55289--55411 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
55279 GTGAATCGGG
* * * * *
55289 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
55331 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
55373 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
55412 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:57492 original size:33 final size:33
Alignment explanation
Indices: 57440--57535 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
57430 AGATAATGAA
* * *
57440 AATCGCAATGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACCAGAC
*
57474 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCGCAACCAGAC
**
57507 AATCGCAACGCGAAATGAAAATCGCAACC
1 AATCGCAACGCGAAATGACTATCGCAACC
57536 GCGAAATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 45 0.82
34 10 0.18
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACCAGAC
Found at i:57529 original size:19 final size:19
Alignment explanation
Indices: 57412--57577 Score: 145
Period size: 20 Copynumber: 9.1 Consensus size: 19
57402 TCTTTTGGTT
*
57412 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
57431 GATAATGAAAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
57451 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
57469 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
57485 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
57503 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
57518 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
57538 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
57557 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
57576 GA
1 GA
57578 TTTTAACGCG
Statistics
Matches: 120, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 44 0.37
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:57588 original size:30 final size:30
Alignment explanation
Indices: 57552--57611 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
57542 TTAAAATCGC
57552 AACGCGAAATGAAAATCGCAACGCGATTTT
1 AACGCGAAATGAAAATCGCAACGCGATTTT
*
57582 AACGCGAAATGAAAATCGCAATGCGATTTT
1 AACGCGAAATGAAAATCGCAACGCGATTTT
57612 TGGTTTCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (30 bp):
AACGCGAAATGAAAATCGCAACGCGATTTT
Found at i:57637 original size:19 final size:20
Alignment explanation
Indices: 57603--57648 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
57593 AAAATCGCAA
*
57603 TGCGATTTTTGGTTTCGCGT
1 TGCGATTTTTGATTTCGCGT
57623 TGCGATTTTT-ATTTCGCGT
1 TGCGATTTTTGATTTCGCGT
57642 TGCGATT
1 TGCGATT
57649 ATCTCGTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (20 bp):
TGCGATTTTTGATTTCGCGT
Found at i:58232 original size:20 final size:20
Alignment explanation
Indices: 58204--58255 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
58194 CGCTAAGTAA
* *
58204 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
58224 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
58244 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
58256 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:58331 original size:20 final size:20
Alignment explanation
Indices: 58287--58379 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
58277 ATAGTCAGTA
* **
58287 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
58308 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
58328 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
58349 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
58369 TCGCATTGCGA
1 TCGCATTGCGA
58380 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:58332 original size:41 final size:41
Alignment explanation
Indices: 58287--58382 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
58277 ATAGTCAGTA
*
58287 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
58328 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
58369 TCGCATTGCGAATT
1 TCGCATTGCGAATT
58383 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:59831 original size:23 final size:24
Alignment explanation
Indices: 59805--59849 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
59795 TGACATTTTA
59805 TAATTATC-AAGTT-TCATTAATGG
1 TAATT-TCGAAGTTCTCATTAATGG
*
59828 TAATTTCGAATTTCTCATTAAT
1 TAATTTCGAAGTTCTCATTAAT
59850 TGAATTCTAA
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:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (24 bp):
TAATTTCGAAGTTCTCATTAATGG
Found at i:61445 original size:2 final size:2
Alignment explanation
Indices: 61438--61512 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
61428 GATTTGTGAT
61438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61513 TCATTTGGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63958 original size:22 final size:22
Alignment explanation
Indices: 63933--63982 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
63923 AATAAAATAA
*
63933 AATA-AAATATAAGTATTTATTT
1 AATATAAATATAA-TATGTATTT
*
63955 AATATATATATAATATGTATTT
1 AATATAAATATAATATGTATTT
63977 AATATA
1 AATATA
63983 TTTAATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
AATATAAATATAATATGTATTT
Found at i:63983 original size:22 final size:23
Alignment explanation
Indices: 63939--63983 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
63929 ATAAAATAAA
*
63939 ATATAAGTATTTATTTAATATAT
1 ATATAAGTATGTATTTAATATAT
63962 ATATAA-TATGTATTTAATATAT
1 ATATAAGTATGTATTTAATATAT
63984 TTAATGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATAAGTATGTATTTAATATAT
Found at i:64071 original size:3 final size:3
Alignment explanation
Indices: 64058--64187 Score: 122
Period size: 3 Copynumber: 42.3 Consensus size: 3
64048 GCATAGTAAC
* * * *
64058 AAT AA- AAT AAT AAT AAT ACCAT AAT AAT GAT -AT AAT AGT AGT AGT
1 AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT
64103 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
64150 ACCAT AGT AAAT TAT AACT AAT AAT AAT ACT AAT AAT A
1 A--AT AAT -AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
64188 CTTACTAAAC
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
2 5 0.05
3 94 0.86
4 6 0.06
5 4 0.04
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:66955 original size:22 final size:22
Alignment explanation
Indices: 66927--66987 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
66917 GGCATGTGAA
66927 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
* *
66949 ATTTGTCCCGAATGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
* *
66971 ATATGTCCCAAAGGACC
1 ATTTGTCCCGAAGGACC
66988 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:67720 original size:42 final size:41
Alignment explanation
Indices: 67673--67751 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
67663 TGATTAAAGT
* *
67673 AGGTATCAGTATCCT-CTAAAGGGTATCGGTACACCCTAACTG
1 AGGTATCAGTACCCTGC-AAAGGGTATCGATAC-CCCTAACTG
* *
67715 AGGTATCGGTACCCTGCCAAGGGTATCGATACCCCTA
1 AGGTATCAGTACCCTGCAAAGGGTATCGATACCCCTA
67752 TTAAAATCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.16
42 26 0.81
43 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (41 bp):
AGGTATCAGTACCCTGCAAAGGGTATCGATACCCCTAACTG
Found at i:76181 original size:24 final size:24
Alignment explanation
Indices: 76154--76241 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
76144 TTCTATTAAA
*
76154 ATACATGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
76178 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
**
76202 ATACTTGACCTGGATTCTGATATG
1 ATACTTGACCTGGATTCTGATCGG
*
76226 ATACTTGACATGGATT
1 ATACTTGACCTGGATT
76242 ATGTTTTGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:76422 original size:2 final size:2
Alignment explanation
Indices: 76415--76447 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
76405 CGGATGGGAG
76415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76448 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76452 original size:2 final size:2
Alignment explanation
Indices: 76447--76535 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
76437 TATATATATA
76447 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
76489 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
76531 TG TG T
1 TG TG T
76536 TTTAAAAAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:84747 original size:2 final size:2
Alignment explanation
Indices: 84740--84797 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
84730 TGAGTACAAC
84740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84782 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
84798 GACTAAACTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84880 original size:3 final size:3
Alignment explanation
Indices: 84872--84902 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
84862 TCTAAAAAAT
84872 TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
84903 GTATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:84898 original size:22 final size:22
Alignment explanation
Indices: 84873--84920 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
84863 CTAAAAAATT
* *
84873 TATTATTATTAT-TATTATTATA
1 TATTATTAGTATATATT-TAATA
84895 TATTATTAGTATATATTTAATA
1 TATTATTAGTATATATTTAATA
84917 TATT
1 TATT
84921 TTAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTATTAGTATATATTTAATA
Found at i:84900 original size:13 final size:13
Alignment explanation
Indices: 84872--84911 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
84862 TCTAAAAAAT
84872 TTATTATTAT-TA
1 TTATTATTATATA
84884 TTATTATTATATA
1 TTATTATTATATA
*
84897 TTATTAGTATATA
1 TTATTATTATATA
84910 TT
1 TT
84912 TAATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTATTATTATATA
Done.