Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001456.1 Hibiscus syriacus cultivar Beakdansim tig00002811_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: 136018
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:94 original size:14 final size:15
Alignment explanation
Indices: 66--94 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56 AGAATCAGAG
66 ATTTAAAAAAGAAAT
1 ATTTAAAAAAGAAAT
81 ATTTAAAAAA-AAAT
1 ATTTAAAAAAGAAAT
95 TAGATAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
ATTTAAAAAAGAAAT
Found at i:3701 original size:2 final size:2
Alignment explanation
Indices: 3694--3729 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3684 TAAGATAAAA
3694 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
3730 TCACACACCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5848 original size:18 final size:18
Alignment explanation
Indices: 5806--5858 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 18
5796 TAAAAAATGG
5806 GTGATCTTTTTTTTAGTA
1 GTGATCTTTTTTTTAGTA
5824 -TG-T-TTTTTATTT-GTA
1 GTGATCTTTTT-TTTAGTA
5839 GTGATCTTTTCTTTTTAGTA
1 GTGATC-TTT-TTTTTAGTA
5859 TGGTTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 3 0.11
19 6 0.21
20 5 0.18
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (18 bp):
GTGATCTTTTTTTTAGTA
Found at i:5860 original size:35 final size:33
Alignment explanation
Indices: 5806--5870 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
5796 TAAAAAATGG
* *
5806 GTGATCTTTTTTTTAGTATGTTTTTTATTTGTA
1 GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
5839 GTGATCTTTTCTTTTTAGTATGGTTTTGATTT
1 GTGATC-TTT-TTTTTAGTATGGTTTTGATTT
5871 ATAGCTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.21
34 3 0.11
35 19 0.68
ACGTcount: A:0.14, C:0.05, G:0.17, T:0.65
Consensus pattern (33 bp):
GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
Found at i:13373 original size:158 final size:156
Alignment explanation
Indices: 13104--13393 Score: 440
Period size: 158 Copynumber: 1.8 Consensus size: 156
13094 CCTCATTTCA
*
13104 TTATTTCTTCAATTATTCCTTCACTTTAAGTCCATTTTTACCAAATTTAAACCACATGCTCATAA
1 TTATTTCTTCAATTATTCATTCACTTTAAGTCCATTTTTACCAAATTTAAACCACATGCTCATAA
* *
13169 ACCTTAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAATTTTTTATTTTTCAATT
66 ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTATTTTTCAATT
13234 TAGCCCTTCAATTTTTTAAAATCTCC
131 TAGCCCTTCAATTTTTTAAAATCTCC
* * * *
13260 TTATTTCTTCAATT-TATCATTTATTTTAAGTCTATTTTTTTACCAAATTTGAGA-CACATGCTC
1 TTATTTCTTCAATTAT-TCATTCACTTTAAGTCCA--TTTTTACCAAATTT-AAACCACATGCTC
* *
13323 CTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTTATAACAATTTTTTATTTTTC
62 ATAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTATTTTTC
*
13388 ACTTTA
127 AATTTA
13394 ATCCTTGAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
155 1 0.01
156 28 0.23
158 89 0.74
159 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (156 bp):
TTATTTCTTCAATTATTCATTCACTTTAAGTCCATTTTTACCAAATTTAAACCACATGCTCATAA
ACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTATTTTTCAATT
TAGCCCTTCAATTTTTTAAAATCTCC
Found at i:13448 original size:119 final size:121
Alignment explanation
Indices: 13301--13539 Score: 383
Period size: 120 Copynumber: 2.0 Consensus size: 121
13291 CTATTTTTTT
* *
13301 ACCAAATTTGAGACACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTT
1 ACCAAATTTGAGACACATACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTATTTT
* * *
13366 TTATAAC-AATTTTTTATTTTTCACTTTAATCCTTGAATTTGTCATAATCTCCTTC
66 TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
*
13421 ACCAAATTTGAGCCACA-ACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTATTTT
1 ACCAAATTTGAGACACATACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTATTTT
* * *
13485 TGATAACAAATTTTTTATTTTTCAATTTAGTCCTTTAATTTTTCATAAGCTCCTT
66 TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTT
13540 ATTCCTTCAA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
119 51 0.47
120 58 0.53
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (121 bp):
ACCAAATTTGAGACACATACTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTATTTT
TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
Found at i:23444 original size:17 final size:17
Alignment explanation
Indices: 23410--23457 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
23400 ATCAAGAAAA
* *
23410 ATTATTATTTTAGAGAG
1 ATTATTAATTTATAGAG
*
23427 ATTATTAATTTATCGAG
1 ATTATTAATTTATAGAG
*
23444 AATATTAATTTATA
1 ATTATTAATTTATA
23458 AAGGTTCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (17 bp):
ATTATTAATTTATAGAG
Found at i:25751 original size:21 final size:20
Alignment explanation
Indices: 25697--25740 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
25687 GGTATTTTAG
*
25697 TTTAAATAG-TTTTAAGTGT
1 TTTAATTAGTTTTTAAGTGT
*
25716 TTTAATTAGTATTTAAGATGT
1 TTTAATTAGTTTTTAAG-TGT
25737 TTTA
1 TTTA
25741 GCTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTAATTAGTTTTTAAGTGT
Found at i:26269 original size:20 final size:20
Alignment explanation
Indices: 26240--26277 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26230 TTTCAAAGGG
26240 ATGCACCGATGCACCAATCT
1 ATGCACCGATGCACCAATCT
*
26260 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
26278 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCT
Found at i:26365 original size:37 final size:36
Alignment explanation
Indices: 26324--26403 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
26314 TGCACTATCC
* *
26324 ATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGA
1 ATGCATCGATGCACTCAAGCTATTT-TG-AAACATCGA
*
26361 ATGCATTTGATGCACTCAAGCTATTTTGAAACATCGA
1 ATGCA-TCGATGCACTCAAGCTATTTTGAAACATCGA
26398 ATGCAT
1 ATGCAT
26404 TTTATGCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 1 0.03
37 19 0.50
38 15 0.39
39 3 0.08
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (36 bp):
ATGCATCGATGCACTCAAGCTATTTTGAAACATCGA
Found at i:26405 original size:19 final size:19
Alignment explanation
Indices: 26352--26406 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
26342 GGTTTTATGA
26352 AAACATCGAATGCA-TTTG
1 AAACATCGAATGCATTTTG
**
26370 ATGCACTC-AA-GCTATTTTG
1 AAACA-TCGAATGC-ATTTTG
26389 AAACATCGAATGCATTTT
1 AAACATCGAATGCATTTT
26407 ATGCATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
17 2 0.07
18 8 0.29
19 16 0.57
20 2 0.07
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (19 bp):
AAACATCGAATGCATTTTG
Found at i:26415 original size:18 final size:18
Alignment explanation
Indices: 26355--26419 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
26345 TTTATGAAAA
*
26355 CATCGAATGCATTTGATG
1 CATCGAATGCATTTTATG
**
26373 CACTC-AA-GCTATTTTGAAA
1 CA-TCGAATGC-ATTTT-ATG
26392 CATCGAATGCATTTTATG
1 CATCGAATGCATTTTATG
26410 CATCG-ATGCA
1 CATCGAATGCA
26420 CCCTTAGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
17 7 0.19
18 16 0.43
19 12 0.32
20 2 0.05
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (18 bp):
CATCGAATGCATTTTATG
Found at i:27495 original size:19 final size:18
Alignment explanation
Indices: 27444--27492 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
27434 AATCTCTTTA
27444 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
27463 TTTCTTTTATTTAATTATT
1 ATT-TTTTATTTAATTATT
27482 ATTTTTTATTT
1 ATTTTTTATTT
27493 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:27648 original size:23 final size:21
Alignment explanation
Indices: 27614--27656 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
27604 CTGGAATTTT
27614 ATGTTCTTTTAAAATCAAGAAAA
1 ATGTTCTTTT-AAATC-AGAAAA
27637 ATGTT-TTATTAAATCAGAAA
1 ATGTTCTT-TTAAATCAGAAA
27657 CACCACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
ATGTTCTTTTAAATCAGAAAA
Found at i:43465 original size:18 final size:19
Alignment explanation
Indices: 43439--43479 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
43429 GATATTAGGA
*
43439 GAGTAAACTTAAA-TTTAG
1 GAGTAAACTAAAATTTTAG
*
43457 GAGTGAACTAAAATTTTAG
1 GAGTAAACTAAAATTTTAG
43476 GAGT
1 GAGT
43480 TAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (19 bp):
GAGTAAACTAAAATTTTAG
Found at i:47216 original size:28 final size:28
Alignment explanation
Indices: 47140--47224 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
47130 AAATTGTCAT
* * *
47140 TTTTTCACAAACATTTTCAGAATGTCACCG
1 TTTTT-ACAAAAATTTCCAGAATGTCA-CA
** *
47170 TTTCCACAAAAATTCCCAGAATGTCACA
1 TTTTTACAAAAATTTCCAGAATGTCACA
47198 TTTTTACAAAAATTTCCAGAATGTCAC
1 TTTTTACAAAAATTTCCAGAATGTCAC
47225 TGGGTCAGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
28 25 0.54
29 18 0.39
30 3 0.07
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (28 bp):
TTTTTACAAAAATTTCCAGAATGTCACA
Found at i:49920 original size:24 final size:24
Alignment explanation
Indices: 49884--49929 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
49874 CCTATAACAC
49884 TAAACAGAGAGGAAAAAGATTTGA
1 TAAACAGAGAGGAAAAAGATTTGA
**
49908 TAAACAGTTAGGAAAAAGATTT
1 TAAACAGAGAGGAAAAAGATTT
49930 AATCTTCGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (24 bp):
TAAACAGAGAGGAAAAAGATTTGA
Found at i:54074 original size:59 final size:59
Alignment explanation
Indices: 53941--54074 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 59
53931 TTAAATTATG
* ** * *
53941 ACTCACATTCTAAATTAATATCTAATTTTTAAAATATTTTATATCAATCCTAAAACTATA
1 ACTCACATTCT-ATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTAAAACTATA
*
54001 ACTCACATTTTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCC-ATAAACTATCA
1 ACTCACATTCTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTA-AAACTAT-A
54061 A-T-ATCATTCTATTT
1 ACTCA-CATTCTATTT
54075 TTATTCTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
58 2 0.03
59 50 0.78
60 12 0.19
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (59 bp):
ACTCACATTCTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTAAAACTATA
Found at i:57155 original size:20 final size:20
Alignment explanation
Indices: 57127--57168 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
57117 GTCAGACCGG
* *
57127 TCAGGTCGGGTTGACTCGGT
1 TCAGCTCGGGTTGACTCAGT
57147 TCAGCTCGGGTTGACTCAGT
1 TCAGCTCGGGTTGACTCAGT
57167 TC
1 TC
57169 GGGTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (20 bp):
TCAGCTCGGGTTGACTCAGT
Found at i:58365 original size:7 final size:7
Alignment explanation
Indices: 58353--58381 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
58343 CTTTCTTATG
58353 AATTTTA
1 AATTTTA
58360 AATTTTA
1 AATTTTA
58367 AATTTTA
1 AATTTTA
58374 AATTTTA
1 AATTTTA
58381 A
1 A
58382 TTTCAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:62068 original size:6 final size:6
Alignment explanation
Indices: 62057--62081 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62047 TTTATTTTAA
62057 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
62082 TATTTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:62235 original size:31 final size:32
Alignment explanation
Indices: 62199--62270 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
62189 GTATTTTAAT
* * *
62199 TTTGTGACAG-AATATGTGGACCCATCTCAAA
1 TTTGTGACAGAAATATATGGACACATCACAAA
**
62230 TTTGTGAC-GAAATATATGGACATGTCACAAA
1 TTTGTGACAGAAATATATGGACACATCACAAA
62261 TTTGTGACAG
1 TTTGTGACAG
62271 GTCCATATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 32 0.94
32 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (32 bp):
TTTGTGACAGAAATATATGGACACATCACAAA
Found at i:62423 original size:92 final size:92
Alignment explanation
Indices: 62258--62438 Score: 231
Period size: 92 Copynumber: 2.0 Consensus size: 92
62248 GACATGTCAC
* * * * *
62258 AAATTTGTGACAGGTCCATATGTTCCATCACAAAATTTAAAGTTTTTTTATTTACCTGCTCATTT
1 AAATTTGTGACAGGTCCACATGTTCCATCACAAAATTTAAAGTTTTTTTACTTACCCGCCCATTA
*
62323 TCTCCAATTTCCCTCAATTGAAACATA
66 CCTCCAATTTCCCTCAATTGAAACATA
* * *
62350 AAATTTGTGAC-GGATTCACATGTTCCGTCACAAAATTTAGA-TATTTTTTACTTACCCGCCCAT
1 AAATTTGTGACAGG-TCCACATGTTCCATCACAAAATTTAAAGT-TTTTTTACTTACCCGCCCAT
* *
62413 TACCTTCAATTTCTCTCAATTGAAAC
64 TACCTCCAATTTCCCTCAATTGAAAC
62439 TGTTAGGAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
91 3 0.04
92 73 0.96
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (92 bp):
AAATTTGTGACAGGTCCACATGTTCCATCACAAAATTTAAAGTTTTTTTACTTACCCGCCCATTA
CCTCCAATTTCCCTCAATTGAAACATA
Found at i:70317 original size:108 final size:108
Alignment explanation
Indices: 70142--70347 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 108
70132 TGGCGGTGGC
*
70142 GACGACACTAGTGGAAAAGGCGATAACGGCGGTGACGATGGTGGTGATGACGACAACGGTGATGA
1 GACGACACTAGTGGAAAAGGCGATAACGGCGGTGACGATGGTGGTGATGACGACAACGGTGACGA
*
70207 TGGTGACAATGGTGACAACGGCGACGGCGGTGGTGGCAGCGGT
66 TGGTGACAATAGTGACAACGGCGACGGCGGTGGTGGCAGCGGT
* ** * * *
70250 GACGACACTGGTGGCGAAGGCGATAACGGTGGTGACGTTGGTGGTGGTGACGACAACGGTGACGA
1 GACGACACTAGTGGAAAAGGCGATAACGGCGGTGACGATGGTGGTGATGACGACAACGGTGACGA
** * *
70315 TGGTGATGATAGTGGCAACGGCGATGGCGGTGG
66 TGGTGACAATAGTGACAACGGCGACGGCGGTGG
70348 CGACAATGGT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.24, C:0.16, G:0.43, T:0.17
Consensus pattern (108 bp):
GACGACACTAGTGGAAAAGGCGATAACGGCGGTGACGATGGTGGTGATGACGACAACGGTGACGA
TGGTGACAATAGTGACAACGGCGACGGCGGTGGTGGCAGCGGT
Found at i:74265 original size:84 final size:84
Alignment explanation
Indices: 74090--74337 Score: 264
Period size: 84 Copynumber: 2.9 Consensus size: 84
74080 AATTTATTGA
* * * * * ** *
74090 CAGATAGCCCTTCTTGCCTTGAA-CTATGTTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATC
1 CAGATAGCCCTTCTAGCCTT-AAGCTATGCTGTAAA--TGATGTGCCTTTGAGCTGAGCGTAGTC
* *
74154 GAACTCGAGGGTCTTTGGTTGG
63 GAACTCAAAGGTCTTTGGTTGG
* *
74176 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGTAAAAGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
74241 CTCTAAGGTCTTTGGTTGG
66 CTCAAAGGTCTTTGGTTGG
* * * * * * * * *
74260 TAGATAACCCTTCTATCCTTGAGTTATGCTGCAACTGATGTGCCTTGGAGCTAAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
74325 CTCAAAGGTCTTT
66 CTCAAAGGTCTTT
74338 TGTTTCAAGA
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
84 106 0.77
85 2 0.01
86 30 0.22
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGG
Found at i:74388 original size:36 final size:35
Alignment explanation
Indices: 74336--74441 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 35
74326 TCAAAGGTCT
* **
74336 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGATGAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
74372 TTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
74408 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAA
74442 TGGTGAGCAC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 64 0.98
37 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (35 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA
Found at i:74751 original size:106 final size:106
Alignment explanation
Indices: 74565--75550 Score: 1426
Period size: 106 Copynumber: 9.4 Consensus size: 106
74555 GCATTGTTCC
* * ** *
74565 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * * * *
74629 ACCAACCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
74671 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
74736 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
74777 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
74842 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
74883 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACA
74947 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
74989 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
75054 CCA-CGGTCCCTTCGTCGTGAAGTTGAACATGC---GTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
75091 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACA
75155 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
75197 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
75262 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
75303 GAGTCCAATATCCTTCGCTGTG-AGTTGAAATTGGCTCTGAAATT--GAAAGTTG-TT-TTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACA
* *
75363 ACCA-C-ATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
75403 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCT-AACAGTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-ATTGGGAAATTGTTTATTGACA
*
75467 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
75509 GAGTCCAATTTTCTTCACTGCGAAGTTGAAATAGACTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
75551 TGAAATTGAA
Statistics
Matches: 801, Mismatches: 60, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
100 56 0.07
101 20 0.02
102 78 0.10
103 38 0.05
104 13 0.02
105 55 0.07
106 534 0.67
107 7 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:79105 original size:13 final size:13
Alignment explanation
Indices: 79087--79112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
79077 TCAAATGGAA
79087 AAAAATTAAAATT
1 AAAAATTAAAATT
79100 AAAAATTAAAATT
1 AAAAATTAAAATT
79113 TTAAAAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:80411 original size:30 final size:28
Alignment explanation
Indices: 80375--80433 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 28
80365 TTATTTAAAC
*
80375 ATAATTTATTAAGATATTATTTAAAAT-ATG
1 ATAATTT-TTAA-ATA-TATGTAAAATGATG
80405 ATAATTTTTAAATATATGTAAAATGATG
1 ATAATTTTTAAATATATGTAAAATGATG
80433 A
1 A
80434 CTAAGATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 4 0.15
30 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATAATTTTTAAATATATGTAAAATGATG
Found at i:84171 original size:18 final size:18
Alignment explanation
Indices: 84148--84182 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
84138 TACGTTTGTT
84148 CTTTATTTATTTTAAAAG
1 CTTTATTTATTTTAAAAG
84166 CTTTATTTATTTTAAAA
1 CTTTATTTATTTTAAAA
84183 ATGCTAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
CTTTATTTATTTTAAAAG
Found at i:86483 original size:22 final size:22
Alignment explanation
Indices: 86455--86499 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
86445 AGTTATTGGT
*
86455 CTTAATTAG-GTCTGGATTAGGG
1 CTTAATT-GCGTCTAGATTAGGG
86477 CTTAATTGCGTCTAGATTAGGG
1 CTTAATTGCGTCTAGATTAGGG
86499 C
1 C
86500 CCAATTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (22 bp):
CTTAATTGCGTCTAGATTAGGG
Found at i:86505 original size:22 final size:22
Alignment explanation
Indices: 86464--86505 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
86454 TCTTAATTAG
* **
86464 GTCTGGATTAGGGCTTAATTGC
1 GTCTAGATTAGGGCCCAATTGC
86486 GTCTAGATTAGGGCCCAATT
1 GTCTAGATTAGGGCCCAATT
86506 AATCACAAAA
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:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (22 bp):
GTCTAGATTAGGGCCCAATTGC
Found at i:92672 original size:20 final size:22
Alignment explanation
Indices: 92626--92673 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
92616 AATTAAATCC
92626 TTATTTTTATTGAATAAAAATA
1 TTATTTTTATTGAATAAAAATA
* * *
92648 ATATTTTT-TT-ATTAAATATA
1 TTATTTTTATTGAATAAAAATA
92668 TTATTT
1 TTATTT
92674 CGAGTTGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTTTTATTGAATAAAAATA
Found at i:103440 original size:159 final size:159
Alignment explanation
Indices: 103208--103604 Score: 507
Period size: 159 Copynumber: 2.5 Consensus size: 159
103198 TCTGATTCCA
* * * * *
103208 TTATTTTTTCAATTCCTCCTTCATTTTAAGTCCATT-TTTTTTACCAAATTTGAACCACTTGTTC
1 TTATTTCTTCAATTCATCATTTATTTTAAGT-C-TTGTTTTTTACCAAATTTGAACCACTTGCTC
* * *
103272 CTAAACCATAGTAGAATATATGTGTACTTTCAATT-ATTTTTTTCGATAACAATTTTTTTATTTT
64 CTAAACCATAGTAGAATACATGTGTACTTTCAATTCATATTTTT-GATAACAAATTTTTTATTTT
*
103336 TCAATTTAGTCCTTCAATTTTTCATAATCTTT
128 TCAATTTAGTCCTTCAATTTTTCATAATCTTC
* **
103368 TTATTTCTTCAATTCATCATTTATTTCAAGTCTTGTTTTTTACCAAATTTGAGTCA-TATGCTCC
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCTTGTTTTTTACCAAATTTGAACCACT-TGCTCC
* *
103432 TAAGCCATAGTAGAATACATGTGTACTTTCAATTCCTATTTTTGATAACAAATTTTTTATTTTTC
65 TAAACCATAGTAGAATACATGTGTACTTTCAATTCATATTTTTGATAACAAATTTTTTATTTTTC
*
103497 AATTTAGTCTTTCAATTTTTCATAATCTTC
130 AATTTAGTCCTTCAATTTTTCATAATCTTC
* * * * * **
103527 TTATTCCTTCAATTTATCATTTATTTTAAGT-TCG-TTTTTACCAAATTTAAACCACATGCTAAT
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCTTGTTTTTTACCAAATTTGAACCACTTGCTCCT
* *
103590 ATACCATAATAGAAT
66 AAACCATAGTAGAAT
103605 GCCTATGTAA
Statistics
Matches: 205, Mismatches: 28, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
157 34 0.17
158 5 0.02
159 134 0.65
160 32 0.16
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (159 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTCTTGTTTTTTACCAAATTTGAACCACTTGCTCCT
AAACCATAGTAGAATACATGTGTACTTTCAATTCATATTTTTGATAACAAATTTTTTATTTTTCA
ATTTAGTCCTTCAATTTTTCATAATCTTC
Found at i:103856 original size:3 final size:3
Alignment explanation
Indices: 103850--103879 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
103840 ATTTATTTAT
103850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
103880 AATTACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:105330 original size:26 final size:26
Alignment explanation
Indices: 105299--105351 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
105289 CCTGCACCAG
*
105299 CGCCTGACATGTCGGTCGCCTGCCAC
1 CGCCTGACACGTCGGTCGCCTGCCAC
*
105325 CGCCTGACACGTCGGTCGCCTGTCAC
1 CGCCTGACACGTCGGTCGCCTGCCAC
105351 C
1 C
105352 TCCATCTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.11, C:0.43, G:0.26, T:0.19
Consensus pattern (26 bp):
CGCCTGACACGTCGGTCGCCTGCCAC
Found at i:110752 original size:2 final size:2
Alignment explanation
Indices: 110745--110838 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
110735 CTTTGATTCA
110745 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
110787 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
110829 AT AT AT AT AT
1 AT AT AT AT AT
110839 TATTCCAGTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114636 original size:28 final size:28
Alignment explanation
Indices: 114587--114648 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
114577 CCAAAGAAAC
* *
114587 CAACCTGAAACACATTATCTCCCCAAAT
1 CAACCTGAAACACATTACCTCCACAAAT
*
114615 CAACCTGAAACAC-TCTACCTCCACAAGT
1 CAACCTGAAACACAT-TACCTCCACAAAT
114643 CAACCT
1 CAACCT
114649 AAGCCTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.19
Consensus pattern (28 bp):
CAACCTGAAACACATTACCTCCACAAAT
Found at i:123324 original size:21 final size:21
Alignment explanation
Indices: 123297--123345 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
123287 TGATTACGGT
*
123297 CGTCGCGGGCGCTATTGCGGC
1 CGTCGCGGACGCTATTGCGGC
*
123318 TGTCGCGGACGCTATTGCGGC
1 CGTCGCGGACGCTATTGCGGC
123339 CGTCGCG
1 CGTCGCG
123346 AGTAACTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.33, G:0.41, T:0.20
Consensus pattern (21 bp):
CGTCGCGGACGCTATTGCGGC
Found at i:123534 original size:14 final size:14
Alignment explanation
Indices: 123517--123550 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
123507 AGAGCTTAAT
123517 ATAAATATAAATTA
1 ATAAATATAAATTA
123531 ATAAATATAAATTA
1 ATAAATATAAATTA
123545 ATAAAT
1 ATAAAT
123551 TTAACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAATATAAATTA
Found at i:123800 original size:19 final size:19
Alignment explanation
Indices: 123776--123820 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
123766 AAATGACCAA
*
123776 CAAATTTGCAACACGATCT
1 CAAATTTGCAACACGAACT
* *
123795 CAAATTCGCAACGCGAACT
1 CAAATTTGCAACACGAACT
*
123814 CCAATTT
1 CAAATTT
123821 CACAACCCAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (19 bp):
CAAATTTGCAACACGAACT
Found at i:123883 original size:20 final size:20
Alignment explanation
Indices: 123860--124087 Score: 209
Period size: 20 Copynumber: 11.4 Consensus size: 20
123850 AATTTGTAAA
123860 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
123880 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
123900 TCACAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
123920 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
123940 TCGCAACGC-GAA-TCTGTAAA-
1 TCGCAACACAGAAGTC---AAAT
123960 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
123980 TCGCAATGCA-ATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
124000 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
124020 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
124040 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
* * *
124061 TCGCAACAC-GAATTTAATT
1 TCGCAACACAGAAGTCAAAT
124080 TCGCAACA
1 TCGCAACA
124088 GGTTTTAGTT
Statistics
Matches: 181, Mismatches: 17, Indels: 21
0.83 0.08 0.10
Matches are distributed among these distances:
18 2 0.01
19 19 0.10
20 137 0.76
21 21 0.12
22 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:123948 original size:100 final size:100
Alignment explanation
Indices: 123839--124087 Score: 331
Period size: 100 Copynumber: 2.5 Consensus size: 100
123829 AGTTTCCAAT
123839 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCAC
1 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCAC
* * * * * *
123904 AACGCGATAGTCAAATTCGCAACGCGATAGTCAAA
66 AACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
* ** * *
123939 TTCGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCAATAGTCAAATTCGC
1 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCAC
124004 AACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
66 AACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
* * * *
124039 TTCGCAACGCGGAATTT-CAAATTCGCAACAC-GAATTTAATTTCGCAACA
1 TTCGCAACGC-GAATTTGTAAA-TCGCAACACAGAAGTCAAATTCGCAACA
124088 GGTTTTAGTT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
100 115 0.89
101 14 0.11
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (100 bp):
TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCAC
AACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:123976 original size:60 final size:62
Alignment explanation
Indices: 123872--124073 Score: 238
Period size: 60 Copynumber: 3.3 Consensus size: 62
123862 GCAACACAGA
* * * *
123872 AGTCAAATTCGCAACAC-AA-AAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACGAATAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* ** * * *
123932 AGTCAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAATGCAAT
1 AGTCAAATTCGCAACACGAATAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
123992 AGTCAAATTCGCAACAC-AA-AAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGGA-
1 AGTCAAATTCGCAACACGAATAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGC-GAT
*
124052 ATTTCAAATTCGCAACACGAAT
1 A-GTCAAATTCGCAACACGAAT
124074 TTAATTTCGC
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
58 2 0.02
59 5 0.04
60 85 0.73
61 21 0.18
62 4 0.03
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (62 bp):
AGTCAAATTCGCAACACGAATAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:124084 original size:19 final size:19
Alignment explanation
Indices: 124039--124106 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
124029 AAAAGTCAAA
* *
124039 TTCGCAACGCGGAATTTCAAA
1 TTCGCAACAC-GAATTT-AAT
124060 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
124079 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
124097 TTCGCAACAC
1 TTCGCAACAC
124107 AAATGTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.37
19 11 0.27
20 6 0.15
21 9 0.22
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:124268 original size:16 final size:15
Alignment explanation
Indices: 124233--124271 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
124223 TCCCCATCTC
*
124233 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
124248 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
124264 TAATTTTT
1 TAATTTTT
124272 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:124888 original size:12 final size:12
Alignment explanation
Indices: 124867--124900 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
124857 ACCACATTTC
*
124867 CAATACCAAACA
1 CAATATCAAACA
124879 CAATATCAAACA
1 CAATATCAAACA
*
124891 CAATCTCAAA
1 CAATATCAAA
124901 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:125053 original size:24 final size:24
Alignment explanation
Indices: 125026--125079 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
125016 GTATTCAAAA
125026 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
125050 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
125074 TTTGAT
1 TTTGAT
125080 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:127365 original size:18 final size:18
Alignment explanation
Indices: 127342--127377 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
127332 AAGCAAAAGG
*
127342 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
127360 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
127378 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:127725 original size:20 final size:20
Alignment explanation
Indices: 127702--127747 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
127692 AATAAGCGTT
*
127702 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
127722 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
127742 GTGAAA
1 GCGAAA
127748 TCGCAAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:127987 original size:66 final size:65
Alignment explanation
Indices: 127905--128080 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
127895 AATTTAAAAC
127905 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
127970 A
65 A
* *
127971 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
128035 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
128081 GTGTACCCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:129454 original size:21 final size:21
Alignment explanation
Indices: 129430--129528 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
129420 GCATGCGGGA
*
129430 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
129451 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
*
129472 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
* * *
129493 TCTCTTGAACAAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
129514 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
129529 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:129476 original size:42 final size:42
Alignment explanation
Indices: 129430--129532 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
129420 GCATGCGGGA
* ** * *
129430 CCTCTTGAACGATGATAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGATAGGGGCCTCTTGAACAATAGGAGGCG
* *
129472 CCTCTTCG-ATGATGAGAGGGGTCTCTTGAACAATAGGAGGCG
1 CCTCTT-GAATGATGATAGGGGCCTCTTGAACAATAGGAGGCG
129514 CCTCTTGAATGATGATAGG
1 CCTCTTGAATGATGATAGG
129533 TGCATCGGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 49 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGATAGGGGCCTCTTGAACAATAGGAGGCG
Found at i:129704 original size:4 final size:4
Alignment explanation
Indices: 129672--129717 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
129662 GGACCGCTGA
* * * *
129672 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
129718 TGTCGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:129947 original size:21 final size:21
Alignment explanation
Indices: 129919--129968 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
129909 ACCATTATCT
* *
129919 TCACGTAAAGTATCAACCTCA
1 TCACGTAAAGCACCAACCTCA
* *
129940 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCAACCTCA
129961 TCACGTAA
1 TCACGTAA
129969 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCAACCTCA
Found at i:131690 original size:20 final size:20
Alignment explanation
Indices: 131660--131727 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
131650 TTTTAAAACT
*
131660 AAAATTCGCAACACGAAAATG
1 AAAA-TCGCAACGCGAAAATG
131681 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*
131701 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
131720 AAAATCGC
1 AAAATCGC
131728 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.18
20 33 0.73
21 4 0.09
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:131779 original size:20 final size:20
Alignment explanation
Indices: 131740--131779 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
131730 TGCGATTTTG
* * *
131740 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
131760 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
131780 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:132300 original size:20 final size:20
Alignment explanation
Indices: 132275--132457 Score: 186
Period size: 20 Copynumber: 9.1 Consensus size: 20
132265 TAATATTGTG
132275 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
132295 TTTCGCGTTTCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
132315 TATCACGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
132335 TATCGCGTTGCGGATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
132355 TTTTGTGTTGCGAATTTGAA
1 TTTCGCGTTGCGAATTTGAC
* * *
132375 ATTCAGTGTTGTGAATTTGAC
1 TTTC-GCGTTGCGAATTTGAC
***
132396 TTTTATGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
132416 TATCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
132436 TTTTGTGTTGCGGATTTGAC
1 TTTCGCGTTGCGAATTTGAC
132456 TT
1 TT
132458 CTGTGTTGCG
Statistics
Matches: 133, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
20 117 0.88
21 16 0.12
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:132385 original size:21 final size:21
Alignment explanation
Indices: 132359--132414 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
132349 TTTGACTTTT
132359 GTGTTGCGAATTTGAAATTCA
1 GTGTTGCGAATTTGAAATTCA
* ** *
132380 GTGTTGTGAATTTGACTTTTA
1 GTGTTGCGAATTTGAAATTCA
132401 -TGTTGCGAATTTGA
1 GTGTTGCGAATTTGA
132415 CTATCGCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.45
Consensus pattern (21 bp):
GTGTTGCGAATTTGAAATTCA
Found at i:132406 original size:81 final size:80
Alignment explanation
Indices: 132281--132454 Score: 242
Period size: 81 Copynumber: 2.2 Consensus size: 80
132271 TGTGTTTCGC
** *
132281 GTTGCGAATTTGACTTTCGCGTTTCGAATTTGACTATCACGTTGCGAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGAAATTCGCGTTTCGAATTTGACTATCACGTTGCGAATTTGACTATCGCATTGC
*
132346 GGATTTGACTTTTGT
66 GAATTTGACTTTTGT
* * * *
132361 GTTGCGAATTTGAAATTCAGTGTTGT-GAATTTGACTTTTATGTTGCGAATTTGACTATCGCATT
1 GTTGCGAATTTGAAATTC-GCGTT-TCGAATTTGACTATCACGTTGCGAATTTGACTATCGCATT
132425 GCGAATTTGACTTTTGT
64 GCGAATTTGACTTTTGT
*
132442 GTTGCGGATTTGA
1 GTTGCGAATTTGA
132455 CTTCTGTGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
80 16 0.19
81 66 0.80
82 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (80 bp):
GTTGCGAATTTGAAATTCGCGTTTCGAATTTGACTATCACGTTGCGAATTTGACTATCGCATTGC
GAATTTGACTTTTGT
Found at i:132467 original size:40 final size:39
Alignment explanation
Indices: 132281--132468 Score: 205
Period size: 40 Copynumber: 4.7 Consensus size: 39
132271 TGTGTTTCGC
* * * *
132281 GTTGCGAATTTGACTTTCGCGTTTCGAATTTGACTATCAC
1 GTTGCGAATTTGAC-TTCGCGTTGCGAATTTGACTTTTAT
* *
132321 GTTGCGAATTTGACTATCGCGTTGCGGATTTGACTTTTGT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTAT
* * *
132361 GTTGCGAATTTGAAATTCAGTGTTGTGAATTTGACTTTTAT
1 GTTGCGAATTTG-ACTTC-GCGTTGCGAATTTGACTTTTAT
* *
132402 GTTGCGAATTTGACTATCGCATTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTAT
* *
132442 GTTGCGGATTTGACTTCTGTGTTGCGA
1 GTTGCGAATTTGACTTC-GCGTTGCGA
132469 TTTACAGATT
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.02
40 87 0.70
41 34 0.27
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (39 bp):
GTTGCGAATTTGACTTCGCGTTGCGAATTTGACTTTTAT
Found at i:132480 original size:101 final size:101
Alignment explanation
Indices: 132281--132468 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 101
132271 TGTGTTTCGC
* * *
132281 GTTGCGAATTTGACTTTCGCGTTTCGAATTTGACTATCACGTTGCGAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGACTTTCACGTTGCGAATTTGACTATCACATTGCGAATTTGACTATCGCGTTGC
*
132346 GGATTTGACTTTTGTGTTGCGAATTTGAAATTCAGT
66 GGATTTGACTTCTGTGTTGCGAATTTGAAATTCAGT
* * * * * * *
132382 GTTGTGAATTTGACTTTTATGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTTTGTGTTGC
1 GTTGCGAATTTGACTTTCACGTTGCGAATTTGACTATCACATTGCGAATTTGACTATCGCGTTGC
132447 GGATTTGACTTCTGTGTTGCGA
66 GGATTTGACTTCTGTGTTGCGA
132469 TTTACAGATT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 76 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (101 bp):
GTTGCGAATTTGACTTTCACGTTGCGAATTTGACTATCACATTGCGAATTTGACTATCGCGTTGC
GGATTTGACTTCTGTGTTGCGAATTTGAAATTCAGT
Found at i:132485 original size:20 final size:20
Alignment explanation
Indices: 132462--132509 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
132452 TGACTTCTGT
132462 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCAC
* *
132482 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCAC
132502 GTTGCGAT
1 GTTGCGAT
132510 ATTGGAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCAC
Found at i:134553 original size:36 final size:36
Alignment explanation
Indices: 134513--134593 Score: 162
Period size: 36 Copynumber: 2.2 Consensus size: 36
134503 CTCCTCCCCC
134513 ACCCCCTTTTTTTCCACCATGTTTATCACCTCCTTT
1 ACCCCCTTTTTTTCCACCATGTTTATCACCTCCTTT
134549 ACCCCCTTTTTTTCCACCATGTTTATCACCTCCTTT
1 ACCCCCTTTTTTTCCACCATGTTTATCACCTCCTTT
134585 ACCCCCTTT
1 ACCCCCTTT
134594 GTACTTTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.14, C:0.41, G:0.02, T:0.43
Consensus pattern (36 bp):
ACCCCCTTTTTTTCCACCATGTTTATCACCTCCTTT
Found at i:134845 original size:12 final size:12
Alignment explanation
Indices: 134828--134918 Score: 91
Period size: 12 Copynumber: 7.8 Consensus size: 12
134818 GACCAAATTC
134828 CTCATCATCAAA
1 CTCATCATCAAA
134840 CTCATCATC--A
1 CTCATCATCAAA
134850 -TCATCATCAAA
1 CTCATCATCAAA
*
134861 CTCATCATCGAA
1 CTCATCATCAAA
* * *
134873 TTCATCGTCGAA
1 CTCATCATCAAA
* *
134885 CTCGTCATCGAA
1 CTCATCATCAAA
134897 CTCATCATCATAA
1 CTCATCATCA-AA
134910 -TCATCATCA
1 CTCATCATCA
134919 CTCCCATCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
9 8 0.12
10 1 0.01
11 1 0.01
12 55 0.82
13 2 0.03
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (12 bp):
CTCATCATCAAA
Done.