Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002488.1 Hibiscus syriacus cultivar Beakdansim tig00005074_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: 92502
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10861 original size:100 final size:102
Alignment explanation
Indices: 10688--10925 Score: 354
Period size: 100 Copynumber: 2.3 Consensus size: 102
10678 CAAGCTCAAA
*
10688 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCTGACTTTCTTCACACA
1 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACACA
*
10753 AGAAGCCTCCCTACGAGTTTAAGTAAA-AT-ACAACT
66 AGAAGCCTCCCTACGAGTCTAAGTAAATATGACAACT
* * * *
10788 AAATCCTACACAAACAAATAGACAACTATTTCAATGAAAAGATCTTTTCAGTCTTTCTTCACGCG
1 AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACACA
* * * *
10853 AGAAGCCTCCCTATGAGTCTCATTAAATTATGACATCT
66 AGAAGCCTCCCTACGAGTCTAAGTAAA-TATGACAACT
*
10891 AAATCCTACACAAACAAATAGACAATTATTTCAAA
1 AAATCCTACACAAACAAATAGACAACTATTTCAAA
10926 CAATTATTTC
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
100 83 0.67
102 2 0.02
103 38 0.31
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (102 bp):
AAATCCTACACAAACAAATAGACAACTATTTCAAAGAAAAGATCTTTTCAGACTTTCTTCACACA
AGAAGCCTCCCTACGAGTCTAAGTAAATATGACAACT
Found at i:10930 original size:13 final size:13
Alignment explanation
Indices: 10912--10938 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10902 AAACAAATAG
10912 ACAATTATTTCAA
1 ACAATTATTTCAA
10925 ACAATTATTTCAA
1 ACAATTATTTCAA
10938 A
1 A
10939 GAAAACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ACAATTATTTCAA
Found at i:12699 original size:17 final size:17
Alignment explanation
Indices: 12661--12699 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
12651 TTAATGCCTT
12661 TTTTTAATTAATTAATA
1 TTTTTAATTAATTAATA
* *
12678 ATTTTATTTAATTAATA
1 TTTTTAATTAATTAATA
12695 TTTTT
1 TTTTT
12700 GTGTCGTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAATTAATTAATA
Found at i:13196 original size:13 final size:14
Alignment explanation
Indices: 13172--13204 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13162 GAAAATATAT
*
13172 ATATAGTTTTGAAA
1 ATATATTTTTGAAA
13186 A-ATATTTTTGAAA
1 ATATATTTTTGAAA
13199 ATATAT
1 ATATAT
13205 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
ATATATTTTTGAAA
Found at i:13238 original size:27 final size:27
Alignment explanation
Indices: 13205--13262 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
13195 GAAAATATAT
13205 ATATATATATATATTATAGTTTTGAAAAC
1 ATATATATAT-TA-TATAGTTTTGAAAAC
13234 ATATATATATTATATAGTTTTGAAAAC
1 ATATATATATTATATAGTTTTGAAAAC
13261 AT
1 AT
13263 TTCGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 17 0.59
28 2 0.07
29 10 0.34
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (27 bp):
ATATATATATTATATAGTTTTGAAAAC
Found at i:13274 original size:27 final size:27
Alignment explanation
Indices: 13219--13276 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
13209 ATATATATAT
* * *
13219 TATAGTTTTGAAAACATATATATATTA
1 TATAGTTTTGAAAACATATAGAAAATA
* *
13246 TATAGTTTTGAAAACATTTCGAAAATA
1 TATAGTTTTGAAAACATATAGAAAATA
13273 TATA
1 TATA
13277 TATTATAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (27 bp):
TATAGTTTTGAAAACATATAGAAAATA
Found at i:13274 original size:34 final size:34
Alignment explanation
Indices: 13236--13370 Score: 146
Period size: 34 Copynumber: 3.8 Consensus size: 34
13226 TTGAAAACAT
*
13236 ATATATATTATATAGTTTTGAAAACATTTCGAAA
1 ATATATATTATATAGTTTTGAAAACATTTTGAAA
*
13270 ATATATA-TATTATAGTTTTGAAAAGATTTTGAAAA
1 ATATATATTA-TATAGTTTTGAAAACATTTTG-AAA
* *
13305 CATATATATAATATAAAGTTTTTAAAAACATTTTTGAAA
1 -ATATATAT--TATATAG-TTTTGAAAACA-TTTTGAAA
* *
13344 ATGTATATTATATACTTTTGAAAACAT
1 ATATATATTATATAGTTTTGAAAACAT
13371 ATATAATATA
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
33 2 0.02
34 27 0.32
35 13 0.15
36 12 0.14
38 11 0.13
39 14 0.17
40 5 0.06
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (34 bp):
ATATATATTATATAGTTTTGAAAACATTTTGAAA
Found at i:13286 original size:61 final size:62
Alignment explanation
Indices: 13209--13478 Score: 227
Period size: 60 Copynumber: 4.2 Consensus size: 62
13199 ATATATATAT
*
13209 ATATATATATTATAGTTTTGAAAACATATATATATTATATAGTTTTGAAAACA-TTTCGAAA
1 ATATATATATTATAGTTTTGAAAACATATATATATTATATAGTTTTGAAAACATTTTTGAAA
* * *
13270 ATATATATATTATAGTTTTGAAAAGATTTTGAAAACATATATATAATATAAAGTTTTTAAAAACA
1 ATATATATA-T-TA----T----AG-TTTTGAAAACATATATATATTATATAG-TTTTGAAAACA
13335 TTTTTGAAA
54 TTTTTGAAA
* *
13344 ATGTATAT-TATATACTTTTGAAAACATATATA-A-TATATAGTTTTGAAAACATTTTTTGAAA
1 ATATATATAT-TATAGTTTTGAAAACATATATATATTATATAGTTTTGAAAACA-TTTTTGAAA
** *
13405 CAGT-T-T-TGAAAATA-TTTTGAAAA-ATATATATATATATATAGTTTT-AAAATATTTTTGAA
1 -A-TATATAT-ATTATAGTTTTGAAAACATATATATAT-TATATAGTTTTGAAAACATTTTTGAA
13464 A
62 A
13465 ATATATATATTATA
1 ATATATATATTATA
13479 TGGTTTTGGG
Statistics
Matches: 172, Mismatches: 13, Indels: 49
0.74 0.06 0.21
Matches are distributed among these distances:
58 1 0.01
59 9 0.05
60 35 0.20
61 34 0.20
62 15 0.09
63 20 0.12
64 1 0.01
67 1 0.01
68 1 0.01
71 2 0.01
72 29 0.17
73 10 0.06
74 14 0.08
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (62 bp):
ATATATATATTATAGTTTTGAAAACATATATATATTATATAGTTTTGAAAACATTTTTGAAA
Found at i:13313 original size:72 final size:71
Alignment explanation
Indices: 13166--13367 Score: 234
Period size: 72 Copynumber: 2.8 Consensus size: 71
13156 TTCTTTGAAA
* *
13166 ATATATATATAGTTTTGAAAAATATTTTTGAAAATATATATATATATATATATT--ATAGTTTTG
1 ATATATATATAGTTTTG-AAAACATTTTTGAAAATATATATATATATAT-T-TTGAAAAGTTTTG
13229 AAAACATAT
63 AAAACATAT
*
13238 ATATATTATATAGTTTTGAAAACA-TTTCGAAAATATATATAT-TATAGTTTTGAAAAGATTTTG
1 ATATA-TATATAGTTTTGAAAACATTTTTGAAAATATATATATATATA-TTTTGAAAAG-TTTTG
13301 AAAACATAT
63 AAAACATAT
* * *
13310 ATATAATATAAAGTTTTTAAAAACATTTTTGAAAATGTATAT-TATATACTTTTGAAAA
1 ATAT-ATATATAG-TTTTGAAAACATTTTTGAAAATATATATATATATA-TTTTGAAAA
13368 CATATATAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
69 2 0.02
70 5 0.04
71 21 0.19
72 34 0.30
73 24 0.21
74 27 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (71 bp):
ATATATATATAGTTTTGAAAACATTTTTGAAAATATATATATATATATTTTGAAAAGTTTTGAAA
ACATAT
Found at i:13366 original size:23 final size:23
Alignment explanation
Indices: 13336--13392 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
13326 TTAAAAACAT
* *
13336 TTTTGAAAATGTATATTATATAC
1 TTTTGAAAATATATAATATATAC
*
13359 TTTTGAAAACATATATAATATATAG
1 TTTTG-AAA-ATATATAATATATAC
13384 TTTTGAAAA
1 TTTTGAAAA
13393 CATTTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 17 0.59
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (23 bp):
TTTTGAAAATATATAATATATAC
Found at i:13381 original size:25 final size:25
Alignment explanation
Indices: 13347--13395 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13337 TTTGAAAATG
*
13347 TATATTATATACTTTTGAAAACATA
1 TATAATATATACTTTTGAAAACATA
*
13372 TATAATATATAGTTTTGAAAACAT
1 TATAATATATACTTTTGAAAACAT
13396 TTTTTGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (25 bp):
TATAATATATACTTTTGAAAACATA
Found at i:13461 original size:38 final size:38
Alignment explanation
Indices: 13406--13517 Score: 160
Period size: 38 Copynumber: 3.0 Consensus size: 38
13396 TTTTTGAAAC
13406 AGTTTTGAAAATA-TTTTGAAAAATATATATATATATAT
1 AGTTTTGAAAATATTTTTG-AAAATATATATATATATAT
13444 AGTTTT-AAAATATTTTTGAAAATATATATAT-TATAT
1 AGTTTTGAAAATATTTTTGAAAATATATATATATATAT
* *
13480 GGTTTTGGGAAATATTTTTGAAAATATATATA-ATATAT
1 AGTTTT-GAAAATATTTTTGAAAATATATATATATATAT
13518 TATTATTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
36 10 0.15
37 19 0.28
38 39 0.57
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (38 bp):
AGTTTTGAAAATATTTTTGAAAATATATATATATATAT
Found at i:22385 original size:31 final size:31
Alignment explanation
Indices: 22347--22502 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
22337 CCCGAAGGAC
* * *
22347 CAGTCCATA-GATTCCGAATAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
22378 CAGTCCATATGTCCCGAAGAACCTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
22409 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
22440 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
22471 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
22502 C
1 C
22503 CCTCGACCCT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:24282 original size:31 final size:31
Alignment explanation
Indices: 24259--24457 Score: 366
Period size: 31 Copynumber: 6.5 Consensus size: 31
24249 CATAGATTCT
*
24259 GAAGAACCTAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
24290 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
24321 GAAGAACATAGGT-AACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
24351 GAAGAACATAGGT-AACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
24381 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
24412 GAAGAACATAGGTAAACAGTCCATATGTCCT
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
24443 GAAGAACATAGGTAA
1 GAAGAACATAGGTAA
24458 CCCTCGACCC
Statistics
Matches: 165, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
30 60 0.36
31 105 0.64
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:24356 original size:61 final size:62
Alignment explanation
Indices: 24259--24457 Score: 366
Period size: 61 Copynumber: 3.2 Consensus size: 62
24249 CATAGATTCT
*
24259 GAAGAACCTAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
24321 GAAGAACATAGGT-AACAGTCCATATGTCCCGAAGAACATAGGT-AACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
*
24381 GAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCT
1 GAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
24443 GAAGAACATAGGTAA
1 GAAGAACATAGGTAA
24458 CCCTCGACCC
Statistics
Matches: 133, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
60 30 0.23
61 60 0.45
62 43 0.32
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (62 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:25620 original size:13 final size:15
Alignment explanation
Indices: 25589--25624 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
25579 TTCACACGTG
25589 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
25604 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
25616 GAGAAGAGA
1 GAGAAGAGA
25625 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:28762 original size:31 final size:31
Alignment explanation
Indices: 28727--28972 Score: 444
Period size: 31 Copynumber: 8.0 Consensus size: 31
28717 CCCGAAGGAC
*
28727 CAGTCCATA-GATTCCGAAGAACCA-AGGTAAA
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAA
28758 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28789 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28820 CAGTCCATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28850 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28881 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28912 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28943 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
28973 CCCTCGACCC
Statistics
Matches: 211, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.15
31 178 0.84
32 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:28946 original size:123 final size:123
Alignment explanation
Indices: 28727--28973 Score: 453
Period size: 123 Copynumber: 2.0 Consensus size: 123
28717 CCCGAAGGAC
*
28727 CAGTCCATAGATTCCGAAGAACCAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAG
1 CAGTCCATAGATCCCGAAGAACCAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAG
28792 TCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
66 TCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
28850 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CAGTCCATA-GATCCCGAAGAACCA-AGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAC
28913 AGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
64 AGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
28973 C
1 C
28974 CCTCGACCCT
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
122 2 0.02
123 118 0.98
124 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (123 bp):
CAGTCCATAGATCCCGAAGAACCAAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAG
TCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:30138 original size:13 final size:15
Alignment explanation
Indices: 30107--30142 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
30097 TTCACACGTG
30107 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
30122 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
30134 GAGAAGAGA
1 GAGAAGAGA
30143 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:30719 original size:3 final size:3
Alignment explanation
Indices: 30711--30742 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30701 TCTCGTACAT
*
30711 GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
30743 TGATGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:31125 original size:10 final size:10
Alignment explanation
Indices: 31110--31141 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
31100 AACTCAAGGC
31110 TCCAAATTGA
1 TCCAAATTGA
31120 TCCAAATTGA
1 TCCAAATTGA
31130 TCCAAATTGA
1 TCCAAATTGA
31140 TC
1 TC
31142 TCCAAGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (10 bp):
TCCAAATTGA
Found at i:36770 original size:3 final size:3
Alignment explanation
Indices: 36762--36795 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
36752 GAATTGGGTT
36762 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
36796 CTATTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:36969 original size:13 final size:15
Alignment explanation
Indices: 36939--36972 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
36929 AGGTTTAGAG
36939 TTTAAAATTTATAAT
1 TTTAAAATTTATAAT
36954 TTTAAAA-TTA-AAT
1 TTTAAAATTTATAAT
36967 TTTAAA
1 TTTAAA
36973 TTCTAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 3 0.16
15 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAATTTATAAT
Found at i:40551 original size:25 final size:26
Alignment explanation
Indices: 40523--40571 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
40513 TTCAATTCGG
* *
40523 TTAATATTTAAA-AAAATAAGTTTGA
1 TTAATAGTTAAAGAAAAGAAGTTTGA
40548 TTAATAGTTAAAGAAAAGAAGTTT
1 TTAATAGTTAAAGAAAAGAAGTTT
40572 AGTTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (26 bp):
TTAATAGTTAAAGAAAAGAAGTTTGA
Found at i:40577 original size:26 final size:24
Alignment explanation
Indices: 40522--40578 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
40512 GTTCAATTCG
* *
40522 GTTAATATTTAAAAAAATAAGTTT
1 GTTAATAGTTAAAAAAAGAAGTTT
40546 GATTAATAGTTAAAGAAAAGAAGTTT
1 G-TTAATAGTTAAA-AAAAGAAGTTT
40572 AGTTAAT
1 -GTTAAT
40579 TCAGTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 15 0.54
27 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (24 bp):
GTTAATAGTTAAAAAAAGAAGTTT
Found at i:47665 original size:50 final size:50
Alignment explanation
Indices: 47606--47705 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
47596 CAACTTTGAC
47606 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
1 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
47656 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
1 TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
47706 GATACCGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (50 bp):
TCTTTTGTATCACATATAACCCTTTGGTTTCTTTGCTGATATTTTCCAAT
Found at i:48660 original size:37 final size:37
Alignment explanation
Indices: 48581--48669 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
48571 GATCTACTAC
* * *
48581 GATTTAAACTCCTAAAAATATAATATAATTTTGTTAG
1 GATTTAAACTCCTAAAAATATAATAGAATTCTGCTAG
*
48618 GATTTAAACTCCTAAAAATA-AGATAGAATTCTGCTAT
1 GATTTAAACTCCTAAAAATATA-ATAGAATTCTGCTAG
* *
48655 TATTTAAATTCCTAA
1 GATTTAAACTCCTAA
48670 GGATAGGATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (37 bp):
GATTTAAACTCCTAAAAATATAATAGAATTCTGCTAG
Found at i:49124 original size:17 final size:17
Alignment explanation
Indices: 49069--49127 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
49059 ATTTAACCCT
* *
49069 TATTATTTATATGTATA
1 TATTATATATATATATA
*
49086 AATATATATATATATATA
1 TAT-TATATATATATATA
* * *
49104 TATTATATTTATTTATT
1 TATTATATATATATATA
49121 TATTATA
1 TATTATA
49128 AATTTTTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:49183 original size:2 final size:2
Alignment explanation
Indices: 49176--49211 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
49166 TTCCTATTAT
49176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49212 TATTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:49218 original size:6 final size:7
Alignment explanation
Indices: 49173--49217 Score: 54
Period size: 8 Copynumber: 5.9 Consensus size: 7
49163 ATTTTCCTAT
49173 TATTATA
1 TATTATA
49180 TATATATA
1 TAT-TATA
49188 TATATATA
1 TAT-TATA
49196 TATATATA
1 TAT-TATA
49204 TATTATA
1 TATTATA
49211 TTATTAT
1 -TATTAT
49218 TTTTTATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.19
8 29 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTATA
Found at i:49256 original size:13 final size:13
Alignment explanation
Indices: 49238--49262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49228 TGTTTACTTA
49238 TTTACTATATTTT
1 TTTACTATATTTT
49251 TTTACTATATTT
1 TTTACTATATTT
49263 CCTAACGTTA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:49437 original size:17 final size:17
Alignment explanation
Indices: 49407--49479 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
49397 TTATACATAC
*
49407 ATTTTTATATTTTTATAT
1 ATTTTTTTA-TTTTATAT
49425 ATTTTTTTATTTTAT-T
1 ATTTTTTTATTTTATAT
49441 A---TTTTA-TTTATACT
1 ATTTTTTTATTTTATA-T
*
49455 ATTTATTTATTTTCATTAT
1 ATTTTTTTATTTT-A-TAT
49474 ATTTTT
1 ATTTTT
49480 AGTTTCTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 2 0.05
16 2 0.05
17 10 0.23
18 11 0.25
19 7 0.16
20 2 0.05
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTATTTTATAT
Found at i:49442 original size:47 final size:49
Alignment explanation
Indices: 49385--49479 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 49
49375 TACTATTTAG
*
49385 TATTTTATTATATTATACATAC-ATTT-TTATATTTTTA-TATATTTTTT
1 TATTTTATTATATTATACATACTATTTATT-TATTTTCATTATATTTTTT
* **
49432 TATTTTATTATTTTATTTATACTATTTATTTATTTTCATTATATTTTT
1 TATTTTATTATATTATACATACTATTTATTTATTTTCATTATATTTTT
49480 AGTTTCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 19 0.46
48 11 0.27
49 11 0.27
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.68
Consensus pattern (49 bp):
TATTTTATTATATTATACATACTATTTATTTATTTTCATTATATTTTTT
Found at i:49599 original size:18 final size:16
Alignment explanation
Indices: 49555--49602 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
49545 TGTATATATA
*
49555 TATTTTTTTCTTCATT
1 TATTTTTTTATTCATT
49571 TATTTTATTTTATTCAATT
1 TA-TTT-TTTTATTC-ATT
49590 TCATTTTTTTATT
1 T-ATTTTTTTATT
49603 TGTTTCATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 3 0.11
18 14 0.52
19 7 0.26
20 1 0.04
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTTTATTCATT
Found at i:50787 original size:19 final size:19
Alignment explanation
Indices: 50763--50799 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
50753 ACCTTACACA
50763 CTCT-TTTTATTTT-TTTC
1 CTCTCTTTTATTTTATTTC
50780 CTCTCTTTTATTTTATTTC
1 CTCTCTTTTATTTTATTTC
50799 C
1 C
50800 ATCATCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (19 bp):
CTCTCTTTTATTTTATTTC
Found at i:54247 original size:21 final size:19
Alignment explanation
Indices: 54221--54273 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 19
54211 ACAAAAAGGG
54221 CAAAAACAAAAAAGAAAAGAAA
1 CAAAAA-AAAAAA-AAAAG-AA
54243 CAAAAAAAAGAAAAAAAAGAA
1 C-AAAAAAA-AAAAAAAAGAA
54264 CAAAAAAAAA
1 CAAAAAAAAA
54274 GGGACAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.07
20 7 0.24
21 3 0.10
22 8 0.28
23 9 0.31
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAGAA
Found at i:54251 original size:13 final size:12
Alignment explanation
Indices: 54222--54273 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
54212 CAAAAAGGGC
54222 AAAAACAAAAAA
1 AAAAACAAAAAA
* *
54234 GAAAAGAAACAAA
1 AAAAACAAA-AAA
*
54247 AAAAAGAAAAAA
1 AAAAACAAAAAA
*
54259 AAGAACAAAAAA
1 AAAAACAAAAAA
54271 AAA
1 AAA
54274 GGGACAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:54256 original size:9 final size:9
Alignment explanation
Indices: 54228--54270 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
54218 GGGCAAAAAC
54228 AAAAAAGAA
1 AAAAAAGAA
* *
54237 AAGAAACAA
1 AAAAAAGAA
54246 AAAAAAGAA
1 AAAAAAGAA
54255 AAAAAAGAA
1 AAAAAAGAA
54264 CAAAAAA
1 -AAAAAA
54271 AAAGGGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:54274 original size:22 final size:22
Alignment explanation
Indices: 54221--54274 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
54211 ACAAAAAGGG
* *
54221 CAAAAACAAA-AAAGAAAAGAA
1 CAAAAAAAAAGAAAAAAAAGAA
54242 -ACAAAAAAAAGAAAAAAAAGAA
1 CA-AAAAAAAAGAAAAAAAAGAA
54264 CAAAAAAAAAG
1 CAAAAAAAAAG
54275 GGACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 7 0.25
22 19 0.68
23 1 0.04
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAGAAAAAAAAGAA
Found at i:54282 original size:22 final size:22
Alignment explanation
Indices: 54221--54272 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
54211 ACAAAAAGGG
*
54221 CAAAAACAAA-AAAGAAAAGAAA
1 CAAAAA-AAAGAAAAAAAAGAAA
54243 CAAAAAAAAGAAAAAAAAG-AA
1 CAAAAAAAAGAAAAAAAAGAAA
54264 CAAAAAAAA
1 CAAAAAAAA
54273 AGGGACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAGAAAAAAAAGAAA
Found at i:54905 original size:22 final size:22
Alignment explanation
Indices: 54877--54931 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
54867 GCTACCCCAT
54877 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
54899 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
54921 CAAACCTTTGA
1 CAAACCTTTGA
54932 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:56022 original size:106 final size:106
Alignment explanation
Indices: 55893--57050 Score: 1813
Period size: 106 Copynumber: 11.0 Consensus size: 106
55883 ATATCGTGCC
* * * *
55893 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
55958 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
55999 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56064 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
56105 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
56170 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
56211 ACTCAAGACAACGCAAGTTCAACTTCATGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
56276 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
56317 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
56382 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
56423 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
56486 ----T------CAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
56517 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTTTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56582 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
56623 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56688 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
56729 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
56794 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
56835 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
56900 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
56941 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
57006 GATTCCAGAGCCAATTTTAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
57047 ACTC
1 ACTC
57051 GGAACAATGC
Statistics
Matches: 979, Mismatches: 59, Indels: 28
0.92 0.06 0.03
Matches are distributed among these distances:
94 86 0.09
96 1 0.00
100 2 0.00
104 1 0.00
105 1 0.00
106 888 0.91
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:56458 original size:43 final size:43
Alignment explanation
Indices: 56397--56552 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
56387 CAGAGCCAAT
*
56397 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
*** ** * * *
56440 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
*
56491 TTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAG
56534 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
56553 GACTGCTGGT
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
43 37 0.44
44 4 0.05
45 3 0.04
46 7 0.08
48 8 0.09
49 3 0.04
50 4 0.05
51 19 0.22
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:56887 original size:518 final size:521
Alignment explanation
Indices: 55893--57004 Score: 1861
Period size: 518 Copynumber: 2.1 Consensus size: 521
55883 ATATCGTGCC
55893 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTT-CC
*
55958 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACT
65 -A--T---A--CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACT
* *
56023 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTTAACTTC
122 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
56088 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
187 ACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
56153 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
252 TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
* *
56218 ACAACGCAAGTTCAACTTCATGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
317 ACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
56283 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
382 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
56348 AAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA
447 AAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAA
56413 AGGATATTGG
512 AGGATATTGG
* * * *
56423 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT-C-
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCA
56486 T-CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGA
66 TACAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGA
* * * * *
56550 AGGGACTGCTGGTTTTCAACAAATAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAA
131 AGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAA
56615 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
196 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * * *
56680 AATTTTCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGTATATTGGACTCCAGACAACGCAA
261 AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAA
*
56745 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
326 GTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
* *
56810 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
391 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACC
* *
56875 GCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTG
456 GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTG
56940 G
521 G
* *
56941 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCC
57005 CGATTCCAGA
Statistics
Matches: 548, Mismatches: 33, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
518 487 0.89
519 1 0.00
524 1 0.00
528 1 0.00
530 58 0.11
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (521 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCA
TACAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAA
GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAA
GTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACC
GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTG
G
Found at i:58320 original size:2 final size:2
Alignment explanation
Indices: 58302--58343 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
58292 CCTTATTATT
* *
58302 TA TA TG TA TA AA 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
58344 ATTATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:58479 original size:17 final size:18
Alignment explanation
Indices: 58440--58480 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
58430 TATATTATTA
58440 TTTT-TTTATCTATGTTT
1 TTTTATTTATCTATGTTT
**
58457 ACTTATTTA-CTATGTTT
1 TTTTATTTATCTATGTTT
58474 TTTTATT
1 TTTTATT
58481 ATATTTTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTATTTATCTATGTTT
Found at i:58657 original size:18 final size:18
Alignment explanation
Indices: 58634--58693 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
58624 TTATACATAC
58634 ATTTTTATATTTTTATAT
1 ATTTTTATATTTTTATAT
* *
58652 ATTTTTTTATTTTTTTAT
1 ATTTTTATATTTTTATAT
* * *
58670 TTTATTTATACTATTTATTT
1 ATT-TTTATA-TTTTTATAT
58690 ATTT
1 ATTT
58694 GCATTATGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 18 0.56
19 6 0.19
20 8 0.25
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTATATTTTTATAT
Found at i:58677 original size:9 final size:9
Alignment explanation
Indices: 58644--58693 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
58634 ATTTTTATAT
*
58644 TTTTATATA
1 TTTTATTTA
58653 TTTT-TTTA
1 TTTTATTTA
58661 TTTT-TTTA
1 TTTTATTTA
58669 TTTTATTTA
1 TTTTATTTA
**
58678 TACTATTTA
1 TTTTATTTA
58687 -TTTATTT
1 TTTTATTT
58694 GCATTATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 20 0.57
9 15 0.43
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:58806 original size:18 final size:19
Alignment explanation
Indices: 58782--58828 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
58772 TGTATATATA
*
58782 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
58799 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
58819 TTTTTTTATT
1 TTTTTTTATT
58829 TGTTTCATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.27
19 11 0.42
20 5 0.19
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:65203 original size:22 final size:22
Alignment explanation
Indices: 65153--65195 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
65143 AACTTATTGT
*
65153 CCAAACATTATATTTTGTTACCA
1 CCAAAC-TAATATTTTGTTACCA
*
65176 ACAAACTAATATTTTGTTAC
1 CCAAACTAATATTTTGTTAC
65196 TGCCAAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (22 bp):
CCAAACTAATATTTTGTTACCA
Found at i:83867 original size:24 final size:23
Alignment explanation
Indices: 83838--83892 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
83828 TTTTTAACTT
83838 TATTTTTTTCACTTTAGCCCTTA
1 TATTTTTTTCACTTTAGCCCTTA
83861 TATTTTTTTCACTTTAGCCCTTA
1 TATTTTTTTCACTTTAGCCCTTA
83884 TATTTTTTT
1 TATTTTTTT
83893 TCCTTGATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (23 bp):
TATTTTTTTCACTTTAGCCCTTA
Found at i:84474 original size:37 final size:39
Alignment explanation
Indices: 84395--84474 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
84385 ATCTAAAATA
* *
84395 ATATATATATATATATAATTTAAAAATATAATAACAATT
1 ATATATATATATATATAATTTAAAAATAGAATAACAAGT
* *
84434 ATATATATATATATATGGA-TTAAATATAGAA-AA-AAGT
1 ATATATATATATATAT-AATTTAAAAATAGAATAACAAGT
84471 ATAT
1 ATAT
84475 TAATTGTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 7 0.19
38 2 0.06
39 26 0.72
40 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (39 bp):
ATATATATATATATATAATTTAAAAATAGAATAACAAGT
Found at i:85752 original size:82 final size:83
Alignment explanation
Indices: 85635--85991 Score: 344
Period size: 82 Copynumber: 4.3 Consensus size: 83
85625 ATTTCTTCAA
* * * * * * **
85635 AAACGCCGCAATATGTTTCATCTATAGTGGCGTTTTGTCGACAAACGGCACAACCGAGTAGTATT
1 AAACGCCACAATATGGTTCATCTATAGTGTCGTTTTTTCAACAAACGCCACAAAGGAGTAGTATT
* *
85700 TTTGCGGTGTTTTTATAC
66 TTAGCGGAGTTTTTATAC
* * *
85718 AAACGCCACAATA-GGTACATCTATAGTGTCGTTTTTTCAACAAACGCCTCAAGGGAGTAGT-TT
1 AAACGCCACAATATGGTTCATCTATAGTGTCGTTTTTTCAACAAACGCCACAAAGGAGTAGTATT
*
85781 TTAGCAGAGTTTTTATAC
66 TTAGCGGAGTTTTTATAC
** * ** * * *
85799 AAACGCCACAATA-GGCCCATTTATAGTGTCGTTTTTTCAACAAACATCGCAAAGGAGTACTACT
1 AAACGCCACAATATGGTTCATCTATAGTGTCGTTTTTTCAACAAACGCCACAAAGGAGTAGTATT
* *
85863 TTAGCGGCGTATTTATAC
66 TTAGCGGAGTTTTTATAC
* * * * * ** * *
85881 AAACGCCGCGATATGGTTCACCTATAGTGACGTTTTTT-AATAAACGCTGCAAAGGAGTACTACT
1 AAACGCCACAATATGGTTCATCTATAGTGTCGTTTTTTCAACAAACGCCACAAAGGAGTAGTATT
*
85945 TTAGCGGCGTTTTTATAC
66 TTAGCGGAGTTTTTATAC
* * * *
85963 AAACGTCATAATATGGTTAACCTATAGTG
1 AAACGCCACAATATGGTTCATCTATAGTG
85992 GCATTTATGA
Statistics
Matches: 230, Mismatches: 42, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
81 70 0.30
82 129 0.56
83 31 0.13
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (83 bp):
AAACGCCACAATATGGTTCATCTATAGTGTCGTTTTTTCAACAAACGCCACAAAGGAGTAGTATT
TTAGCGGAGTTTTTATAC
Found at i:85754 original size:41 final size:41
Alignment explanation
Indices: 85716--85843 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 41
85706 GTGTTTTTAT
*
85716 ACAAACGCCACAATAGGTACATCTATAGTGTCGTTTTTTCA
1 ACAAACGCCACAATAGGTACATTTATAGTGTCGTTTTTTCA
* ** * * * *
85757 ACAAACGCCTCAAGGGAGTA-GTTTTTAGCAG-AG-TTTTT-A
1 ACAAACGCCACAATAG-GTACATTTATAG-TGTCGTTTTTTCA
**
85796 TACAAACGCCACAATAGGCCCATTTATAGTGTCGTTTTTTCA
1 -ACAAACGCCACAATAGGTACATTTATAGTGTCGTTTTTTCA
85838 ACAAAC
1 ACAAAC
85844 ATCGCAAAGG
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
39 3 0.05
40 25 0.40
41 30 0.48
42 5 0.08
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (41 bp):
ACAAACGCCACAATAGGTACATTTATAGTGTCGTTTTTTCA
Found at i:85833 original size:40 final size:40
Alignment explanation
Indices: 85708--85834 Score: 98
Period size: 40 Copynumber: 3.1 Consensus size: 40
85698 TTTTTGCGGT
* *
85708 GTTTTTATACAAACGCCACAATAGGTACATCTATAGTGTC
1 GTTTTTATACAAACGCCACAATAGGAACATTTATAGTGTC
* * ** * * *
85748 GTTTTT-TCAACAAACGCCTCAA-GGGAGTAGTTTTTAGCAG-A
1 GTTTTTAT--ACAAACGCCACAATAGGAACA-TTTATAG-TGTC
**
85789 GTTTTTATACAAACGCCACAATAGGCCCATTTATAGTGTC
1 GTTTTTATACAAACGCCACAATAGGAACATTTATAGTGTC
85829 GTTTTT
1 GTTTTT
85835 TCAACAAACA
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
39 2 0.03
40 33 0.52
41 26 0.41
42 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (40 bp):
GTTTTTATACAAACGCCACAATAGGAACATTTATAGTGTC
Found at i:85967 original size:41 final size:41
Alignment explanation
Indices: 85846--85967 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
85836 CAACAAACAT
*
85846 CGCAAAGGAGTACTACTTTAGCGGCGTATTTATACAAACGC
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
* * * * * * *
85887 CGCGATATG-GTTC-ACCTATAGTGACGTTTTT-TAATAAACGC
1 CGC-AAAGGAGTACTA-CTTTAGCGGCGTTTTTAT-ACAAACGC
*
85928 TGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
1 CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACG
85968 TCATAATATG
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
40 5 0.08
41 49 0.83
42 5 0.08
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (41 bp):
CGCAAAGGAGTACTACTTTAGCGGCGTTTTTATACAAACGC
Done.