Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000187.1 Hibiscus syriacus cultivar Beakdansim tig00000336_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: 209407
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:223 original size:2 final size:2
Alignment explanation
Indices: 216--269 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
206 GTTGATCAAT
216 TA TA TA TA TA TA TA TA TA TA T- 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
257 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
270 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3911 original size:12 final size:13
Alignment explanation
Indices: 3888--3933 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
3878 TAATTTTTTT
3888 AATTATATTTAAA
1 AATTATATTTAAA
*
3901 AATTA-ATTTAAT
1 AATTATATTTAAA
*
3913 AATTATATGTAAA
1 AATTATATTTAAA
*
3926 AAATATAT
1 AATTATAT
3934 AAAAATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AATTATATTTAAA
Found at i:4387 original size:92 final size:92
Alignment explanation
Indices: 4227--4394 Score: 309
Period size: 92 Copynumber: 1.8 Consensus size: 92
4217 CACAAGTTAA
* *
4227 ATGATAGTAACACATGCTATCATTTAATTGGAGATTAAATTTATTAAATTAAATGAAAATTGTGA
1 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTAA
*
4292 CCAAAGTAATAAATTTTTTTTTCTAAT
66 CCAAACTAATAAATTTTTTTTTCTAAT
4319 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTAA
1 ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTAA
4384 CCAAACTAATA
66 CCAAACTAATA
4395 TAAATTATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (92 bp):
ATGATAGTAACACATGCTATCATTTAATTGGAGATAAAATTTATTAAATTAAATGAAAATTGTAA
CCAAACTAATAAATTTTTTTTTCTAAT
Found at i:6226 original size:17 final size:18
Alignment explanation
Indices: 6183--6226 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
6173 TTATATTTGC
6183 ATTT-TAATATTATGATT
1 ATTTATAATATTATGATT
6200 ATGATTATAATATTATG-TT
1 AT--TTATAATATTATGATT
6219 ATTTATAA
1 ATTTATAA
6227 GTAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 8 0.33
19 6 0.25
20 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
ATTTATAATATTATGATT
Found at i:10410 original size:14 final size:14
Alignment explanation
Indices: 10387--10424 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
10377 TCTGTCTATA
*
10387 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
10400 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
10415 TGCAGGGATT
1 TGCAGGGATT
10425 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:14398 original size:20 final size:20
Alignment explanation
Indices: 14373--14421 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
14363 AACGAACTAG
14373 CATTCAAGTGGTACCTATGC
1 CATTCAAGTGGTACCTATGC
14393 CATTCAAGTGGTACCTATGC
1 CATTCAAGTGGTACCTATGC
14413 CATTCAAGT
1 CATTCAAGT
14422 AATGATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (20 bp):
CATTCAAGTGGTACCTATGC
Found at i:17581 original size:26 final size:26
Alignment explanation
Indices: 17542--17594 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
17532 ATGTACTCTA
*
17542 GTTATCAAATTGTAAAGAAATCGTGG
1 GTTATCAAACTGTAAAGAAATCGTGG
17568 GTTATCAAACTGTAAAGAAATCGTGG
1 GTTATCAAACTGTAAAGAAATCGTGG
17594 G
1 G
17595 AGGCATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (26 bp):
GTTATCAAACTGTAAAGAAATCGTGG
Found at i:18701 original size:23 final size:23
Alignment explanation
Indices: 18637--18711 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
18627 TCAAAGCTGA
18637 GTTGACTGTTGATCGTTGATCGAC
1 GTTGACT-TTGATCGTTGATCGAC
* * ** *
18661 GTTTACTTTAATTATTGACCGAC
1 GTTGACTTTGATCGTTGATCGAC
*
18684 GTTGACTTTGACCGTTGATCGAC
1 GTTGACTTTGATCGTTGATCGAC
*
18707 ATTGA
1 GTTGA
18712 TTTTTTCGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 33 0.85
24 6 0.15
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (23 bp):
GTTGACTTTGATCGTTGATCGAC
Found at i:22039 original size:12 final size:11
Alignment explanation
Indices: 22022--22067 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
22012 TTTAAAAATA
22022 TTATTTATTTAT
1 TTATTTA-TTAT
22034 TTATTTATTA-
1 TTATTTATTAT
22044 TTA-TTATTAT
1 TTATTTATTAT
*
22054 TATATTTTTTAT
1 T-TATTTATTAT
22066 TT
1 TT
22068 TTATAAACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 6 0.20
10 4 0.13
11 6 0.20
12 14 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:22153 original size:8 final size:8
Alignment explanation
Indices: 22140--22168 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
22130 ACCTACCTAC
22140 TAAACTAT
1 TAAACTAT
22148 TAAACTAT
1 TAAACTAT
22156 TAAACTAT
1 TAAACTAT
22164 TAAAC
1 TAAAC
22169 ACCTAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (8 bp):
TAAACTAT
Found at i:24299 original size:2 final size:2
Alignment explanation
Indices: 24292--24329 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24282 TTTATTATTA
24292 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
24330 GTTACGGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31988 original size:13 final size:14
Alignment explanation
Indices: 31960--32185 Score: 55
Period size: 13 Copynumber: 15.8 Consensus size: 14
31950 CAAACTAAAT
31960 AATAAAAACAATTA
1 AATAAAAACAATTA
*
31974 AATATAAAC-ATTA
1 AATAAAAACAATTA
** *
31987 AATACTAAC-GTTA
1 AATAAAAACAATTA
* **
32000 CAGTTCAAACAATTA
1 -AATAAAAACAATTA
*
32015 AATAATAAAAAATTA
1 AATAA-AAACAATTA
* * *
32030 AGAAACAAAATAAATA
1 A-ATA-AAAACAATTA
* *
32046 AATAAATCCATAATTA
1 AATAAA--AACAATTA
32062 AATAAAAAC-ATT-
1 AATAAAAACAATTA
32074 AATAAACAA-AA-TA
1 AATAAA-AACAATTA
32087 AATAAAAAGTTCATAGTTA
1 AATAAAAA---CA-A-TTA
32106 AATAAAAAC-ATTA
1 AATAAAAACAATTA
* *
32119 AGTAACAA-AA-TA
1 AATAAAAACAATTA
32131 AATAAAAAGTACATAATTA
1 AAT-AAAA--AC--AATTA
32150 AATAAAAAC-ATTA
1 AATAAAAACAATTA
*
32163 AGA-AACAA-AA-TA
1 A-ATAAAAACAATTA
32175 AATAAAAACAA
1 AATAAAAACAA
32186 GTCTATTGAT
Statistics
Matches: 157, Mismatches: 26, Indels: 59
0.65 0.11 0.24
Matches are distributed among these distances:
11 1 0.01
12 20 0.13
13 51 0.32
14 21 0.13
15 15 0.10
16 26 0.17
17 2 0.01
18 6 0.04
19 15 0.10
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (14 bp):
AATAAAAACAATTA
Found at i:32107 original size:44 final size:44
Alignment explanation
Indices: 32018--32182 Score: 260
Period size: 44 Copynumber: 3.8 Consensus size: 44
32008 ACAATTAAAT
* *
32018 AATAAAAA-ATTAAGAAACAAAATAAATAAATAAATCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAA-AAGTACATAATTA
* * *
32062 AATAAAAACATTAATAAACAAAATAAATAAAAAGTTCATAGTTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTACATAATTA
*
32106 AATAAAAACATTAAGTAACAAAATAAATAAAAAGTACATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTACATAATTA
32150 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
32183 CAAGTCTATT
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 90 0.81
45 21 0.19
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.22
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTACATAATTA
Found at i:32132 original size:25 final size:25
Alignment explanation
Indices: 32104--32184 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 25
32094 AGTTCATAGT
32104 TAAATAAAAACATTAAGTAACAAAA
1 TAAATAAAAACATTAAGTAACAAAA
*
32129 TAAAT---AA-A--AAGT-ACATAAT
1 TAAATAAAAACATTAAGTAACA-AAA
*
32148 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGTAACAAAA
32173 TAAATAAAAACA
1 TAAATAAAAACA
32185 AGTCTATTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
18 3 0.07
19 11 0.24
21 1 0.02
22 4 0.09
23 1 0.02
25 22 0.49
26 3 0.07
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAATAAAAACATTAAGTAACAAAA
Found at i:32255 original size:47 final size:47
Alignment explanation
Indices: 32202--32295 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
32192 TGATGTCTGC
* *
32202 GTCTTGAATGTGTTCCACAGGGCGGTGGTTGTCTATTTCGATGATGA
1 GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
*
32249 GTCTTGAATTTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
1 GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
32296 TTTATTCGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (47 bp):
GTCTTGAATGTGTTCCACAGGGAGGTGGCTGTCTATTTCGATGATGA
Found at i:32591 original size:21 final size:21
Alignment explanation
Indices: 32567--32618 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
32557 ACTATGATAA
*
32567 CATCAGAAACGGTTGTGGTGT
1 CATCAGAAACGGTTGTGGTGG
*
32588 CATCTA-AAATGGTTGTGGTGG
1 CATC-AGAAACGGTTGTGGTGG
*
32609 CATCTGAAAC
1 CATCAGAAAC
32619 AGCTACAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
CATCAGAAACGGTTGTGGTGG
Found at i:36951 original size:43 final size:43
Alignment explanation
Indices: 36875--36996 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
36865 ACAGAACGGG
* * * * ** *
36875 GATGATGCCCTCCATAGAGGATCCTATATAGAATCATGATAAG-
1 GATGATGCCATTCGTAGAGGATCCCATGCAGAATCAGGA-AAGT
*
36918 GATGATG-CATTGCGTAGAGGATCCCATGCAGAATCAGGACAGT
1 GATGATGCCATT-CGTAGAGGATCCCATGCAGAATCAGGAAAGT
* * *
36961 GATGTTGCCCTTCGTAGAGGATCCCATGCAAAATCA
1 GATGATGCCATTCGTAGAGGATCCCATGCAGAATCA
36997 AGACGAGGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
42 4 0.06
43 58 0.89
44 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (43 bp):
GATGATGCCATTCGTAGAGGATCCCATGCAGAATCAGGAAAGT
Found at i:37021 original size:43 final size:43
Alignment explanation
Indices: 36930--37045 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
36920 TGATGCATTG
* * * *
36930 CGTAGAGGATCCCATGCAGAATCAGGACAGTGATGTTGCCCTT
1 CGTAGAGGATCCCATGCAAAATCAAGACAGTGATGATACCCTT
36973 CGTAGAGGATCCCATGCAAAATCAAGACGAG-GATGATACCCTAT
1 CGTAGAGGATCCCATGCAAAATCAAGAC-AGTGATGATACCCT-T
* *
37017 -GTAGAAGATCCCATGTAAAATCAAGACAG
1 CGTAGAGGATCCCATGCAAAATCAAGACAG
37046 AGATATAATC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
42 2 0.03
43 60 0.92
44 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (43 bp):
CGTAGAGGATCCCATGCAAAATCAAGACAGTGATGATACCCTT
Found at i:37680 original size:13 final size:14
Alignment explanation
Indices: 37656--37687 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
37646 CTTAAAAAAA
37656 TCAATGGGTCAAAG
1 TCAATGGGTCAAAG
37670 TCAAT-GGTCAAAG
1 TCAATGGGTCAAAG
37683 TCAAT
1 TCAAT
37688 TATCGATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (14 bp):
TCAATGGGTCAAAG
Found at i:37723 original size:23 final size:23
Alignment explanation
Indices: 37696--37757 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
37686 ATTATCGATG
* *
37696 GTCAACAGGTCGAGTCGATAAAA
1 GTCAACAGGTAGAGTCAATAAAA
* *
37719 GTCAACAGGTTGAGTCAATCAAA
1 GTCAACAGGTAGAGTCAATAAAA
*
37742 GTCAACGGGTAGAGTC
1 GTCAACAGGTAGAGTC
37758 TGATTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.19
Consensus pattern (23 bp):
GTCAACAGGTAGAGTCAATAAAA
Found at i:41259 original size:42 final size:42
Alignment explanation
Indices: 41212--41314 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
41202 GTTCTTATTT
* * *
41212 TGCATGTGATCCTCTATGAAGG-CATCATCCCCGTCCTGATTC
1 TGCATG-GATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
* *
41254 TGCATGGAATCCTCTATAAAGGCCAACATCTCCATCTTGATTC
1 TGCATGG-ATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
* *
41297 TACATGAGATCTTCTATA
1 TGCATG-GATCCTCTATA
41315 CATCCACGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 19 0.37
43 30 0.59
44 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (42 bp):
TGCATGGATCCTCTATAAAGGCCAACATCCCCATCCTGATTC
Found at i:44390 original size:14 final size:14
Alignment explanation
Indices: 44354--44407 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
44344 ACTATATAAT
*
44354 ATATGTTTT-CAAA
1 ATATGTTTTAAAAA
*
44367 AT-TATTTTAAAAA
1 ATATGTTTTAAAAA
44380 ATATGTTTTAAAAA
1 ATATGTTTTAAAAA
44394 ATATGTTTTCAAAA
1 ATATGTTTT-AAAA
44408 CTATATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 19 0.54
15 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (14 bp):
ATATGTTTTAAAAA
Found at i:44440 original size:95 final size:92
Alignment explanation
Indices: 44337--44513 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 92
44327 TCAAAAACCA
*
44337 TTTTAAAACTATATAATATATGTTTTC-AAAATTATTTTAAAAAATATGTTTTAAAAAATATGTT
1 TTTTAAAACTATATAATATATGTTTTCAAAAATTATATT-AAAAATATGTTTTAAAAAATA--TT
* *
44401 TTCAAAACTATATAATATATATTATATATG
63 TTAAAAACCATATAATATATATTATATATG
* * * *
44431 TTTTCAAAACTATATATTATATGTTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTTT
1 TTTT-AAAACTATATAATATATGTTTTCAAAAATTATATTAAAAATATGTTTTAAAAAATATTTT
*
44496 AAAAACCATATATTATAT
65 AAAAACCATATAATATAT
44514 GTTTTAAAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
93 19 0.26
94 4 0.05
95 40 0.55
96 10 0.14
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (92 bp):
TTTTAAAACTATATAATATATGTTTTCAAAAATTATATTAAAAATATGTTTTAAAAAATATTTTA
AAAACCATATAATATATATTATATATG
Found at i:44444 original size:25 final size:25
Alignment explanation
Indices: 44414--44492 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 25
44404 AAAACTATAT
44414 AATATATATTATATATGTTTTCAAA
1 AATATATATTATATATGTTTTCAAA
*
44439 ACTATATA-T-TATATGTTTTCAAA
1 AATATATATTATATATGTTTTCAAA
44462 AAT-TATATTATATATATGTTTTCAAA
1 AATATATA-T-TATATATGTTTTCAAA
44488 AATAT
1 AATAT
44493 TTTAAAAACC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.09
23 16 0.34
24 1 0.02
25 8 0.17
26 17 0.36
27 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (25 bp):
AATATATATTATATATGTTTTCAAA
Found at i:44622 original size:36 final size:35
Alignment explanation
Indices: 44581--44663 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 35
44571 AAAAATATAT
44581 ATATATTATATGTTTTCAAAAACCATTTTCTAAAAAC
1 ATATATTATATGTTTTCAAAAA-CATTTTC-AAAAAC
*
44618 TATATATTATATGTTTTCAAAAATATTTTCAAAAAC
1 -ATATATTATATGTTTTCAAAAACATTTTCAAAAAC
*
44654 -TATACTATAT
1 ATATATTATAT
44664 TATTATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 9 0.21
36 6 0.14
37 6 0.14
38 22 0.51
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (35 bp):
ATATATTATATGTTTTCAAAAACATTTTCAAAAAC
Found at i:44622 original size:38 final size:37
Alignment explanation
Indices: 44470--44657 Score: 149
Period size: 35 Copynumber: 5.1 Consensus size: 37
44460 AAAATTATAT
* *
44470 TATA-TATATGTTTTCAAAAATA-TTT-TAAAAACCA
1 TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
* * *
44504 TATATTATATGTTTT--AAAACGTGTTT-TTAAAACCA
1 TATATTATATGTTTTCAAAAACAT-TTTCTAAAAACTA
* * * *
44539 TAT-TATATATATTTTCGAAAATCAATTTTTATAAAAATATATA
1 TATAT-TATATGTTTTC-AAAAAC-A-TTTTCT-AAAA-A-CTA
44582 TATATTATATGTTTTCAAAAACCATTTTCTAAAAACTA
1 TATATTATATGTTTTCAAAAA-CATTTTCTAAAAACTA
*
44620 TATATTATATGTTTTCAAAAATATTTTC-AAAAACTA
1 TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
44656 TA
1 TA
44658 CTATATTATT
Statistics
Matches: 125, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
33 4 0.03
34 5 0.04
35 33 0.26
36 10 0.08
37 6 0.05
38 27 0.22
39 4 0.03
40 6 0.05
41 8 0.06
42 6 0.05
43 15 0.12
44 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATTATATGTTTTCAAAAACATTTTCTAAAAACTA
Found at i:45271 original size:200 final size:199
Alignment explanation
Indices: 45019--45386 Score: 443
Period size: 200 Copynumber: 1.8 Consensus size: 199
45009 TCAAAAGTTT
* *
45019 ATTTTGTTGACAGACAACTTTTCTCGACTTAAGCTATGCCATAAATTAGGCTGGGAGATAGTTCC
1 ATTTTGTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTCA
* ***
45084 TTGTTGCTAAATCAAATCCAAC-CTAGGTCTTCTTCTTGGTTTAAAGACC-TAGGTTTAAAATTC
66 TTGTTGCTAAATCAAAGCCAACAC-AGGTCTTCTTCTTAACTTAAAGACCTTA-GTTTAAAATTC
* * * * *
45147 ATCTGGAAAGTAGTTCCTCGATGTTTCCCTACAGTTGATATGCCCTCGAGATGAATATAATCGAA
129 AACCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATATGCCCTCGAGATGAATATAATCGAA
45212 CTAAAA
194 CTAAAA
* ** * *** * * *
45218 ATTTTCGTTGACAGATAGTTTTTCTTGACTTAAGATATGTTGTAACTTAGGCTGTGATATAGTTC
1 ATTTT-GTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
** * * *
45283 ATTGTTGCTAAATCGCAGCCAACACAGGTCTTTTTCTTAACTTAAAGACCTTAGTTTGAACTTCA
65 ATTGTTGCTAAATCAAAGCCAACACAGGTCTTCTTCTTAACTTAAAGACCTTAGTTTAAAATTCA
* *
45348 ACCGGAAAGTAGTTCATCGTTGATTCCATACGGTTGATA
130 ACCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATA
45387 CGTCATTGAG
Statistics
Matches: 138, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
199 5 0.04
200 130 0.94
201 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (199 bp):
ATTTTGTTGACAGACAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTCA
TTGTTGCTAAATCAAAGCCAACACAGGTCTTCTTCTTAACTTAAAGACCTTAGTTTAAAATTCAA
CCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATATGCCCTCGAGATGAATATAATCGAACT
AAAA
Found at i:45411 original size:200 final size:200
Alignment explanation
Indices: 45019--45436 Score: 430
Period size: 200 Copynumber: 2.1 Consensus size: 200
45009 TCAAAAGTTT
* *
45019 ATTTT-GTTGACAGACAACTTTTCTCGACTTAAGCTATGCCATAAATTAGGCTGGGAGATAGTTC
1 ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
* * ***
45083 CTTGTTGCTAAATCAAATCCAACCTAGGTCTTCTTCTTGGTTTAAAGACCTAGGTTTAAAATTCA
66 ATTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTAGGTTTAAAATTCA
* * * * * * * *
45148 TCTGGAAAGTAGTTCCTCGATGTTTCCCTACAGTTGATATGCCCTCGAGATGAATATAATCGAAC
131 ACCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATACGCCATCGAGATGAATAGAATCGAAC
45213 TA-AAA
196 -ACAAA
** * *** * * *
45218 ATTTTCGTTGACAGATAGTTTTTCTTGACTTAAGATATGTTGTAACTTAGGCTGTGATATAGTTC
1 ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
** * * *
45283 ATTGTTGCTAAATCGCAGCCAACAC-AGGTCTTTTTCTTAACTTAAAGACCTTA-GTTTGAACTT
66 ATTGTTGCTAAATCAAAGCCAAC-CTAGGTCTTCTTCTTAACTTAAAGACC-TAGGTTTAAAATT
* * * * * * *
45346 CAACCGGAAAGTAGTTCATCGTTGATTCCATACGGTTGATACGTCATTGAGCTGAGTGGAATCGA
129 CAACCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATACGCCATCGAGATGAATAGAATCGA
45411 ACACGAAA
194 ACAC-AAA
* *
45419 GTTTTCATTGACAGATAA
1 ATTTTCGTTGACAGATAA
45437 TCCTTCTCTC
Statistics
Matches: 175, Mismatches: 39, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
199 6 0.03
200 148 0.85
201 21 0.12
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (200 bp):
ATTTTCGTTGACAGATAACTTTTCTCGACTTAAGATATGCCATAAATTAGGCTGGGAGATAGTTC
ATTGTTGCTAAATCAAAGCCAACCTAGGTCTTCTTCTTAACTTAAAGACCTAGGTTTAAAATTCA
ACCGGAAAGTAGTTCATCGATGATTCCATACAGTTGATACGCCATCGAGATGAATAGAATCGAAC
ACAAA
Found at i:46806 original size:2 final size:2
Alignment explanation
Indices: 46799--46872 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
46789 AAGATCTTTG
46799 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
46841 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
46873 GAAATATTAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51365 original size:13 final size:13
Alignment explanation
Indices: 51347--51371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51337 TCATGAGGGT
51347 ATCGATACCCCCA
1 ATCGATACCCCCA
51360 ATCGATACCCCC
1 ATCGATACCCCC
51372 TAAAGGAAAA
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:0.28, C:0.48, G:0.08, T:0.16
Consensus pattern (13 bp):
ATCGATACCCCCA
Found at i:53082 original size:103 final size:103
Alignment explanation
Indices: 52857--53074 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
52847 GTCGAGGGTC
52857 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
52922 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
52960 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
53025 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
53063 TATGTGGTCCTT
1 TATGTGGTCCTT
53075 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:53118 original size:23 final size:23
Alignment explanation
Indices: 53091--53150 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
53081 ATTATTATAT
53091 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTCTACGC
* * *
53114 GGCACTACGGTGCAATTCTATGT
1 GGCACTATGGTGCAATTCTACGC
53137 GGCACT-TCGGTGCA
1 GGCACTAT-GGTGCA
53151 TTTATATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTATGGTGCAATTCTACGC
Found at i:53158 original size:23 final size:23
Alignment explanation
Indices: 53081--53158 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
53071 CCTTATGGAC
* *
53081 ATTATTATATGGCACTATGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
53105 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
53128 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
53151 TTTATATG
1 ATTATATG
53159 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:56743 original size:167 final size:167
Alignment explanation
Indices: 56467--56799 Score: 621
Period size: 167 Copynumber: 2.0 Consensus size: 167
56457 ATATGGATCT
*
56467 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTTATTTCCCAAAATG
1 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
*
56532 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTTAAAGAAATGTTA
66 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
*
56597 TTTTAAAAGAAATGTTCAAATATATAAAAGATAAATA
131 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAATA
*
56634 TTTTTTTATTAAAGGAATTTGATCTCGGCATATGTCAAAAGGCTATAACCTCATTTCCCAAAATG
1 TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
*
56699 TGCATTTCATTATACTTGATATTCATTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
66 TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
56764 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAAT
131 TTTTAAAAGAAATGTTCAAACATATAAAAGATAAAT
56800 TCAAATAAGA
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 161 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (167 bp):
TTTTTTTATTAAAGGAATTTGATCTCGGCATATATCAAAAGGCTATAACCTCATTTCCCAAAATG
TGCATTTCATTATACTTGATATTCACTGAATTTCAAACAATTCTTTATTACTCAAAGAAATGTTA
TTTTAAAAGAAATGTTCAAACATATAAAAGATAAATA
Found at i:60480 original size:14 final size:14
Alignment explanation
Indices: 60461--60488 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60451 TACTTGTCCC
60461 CAGTGGAGTTGCCA
1 CAGTGGAGTTGCCA
60475 CAGTGGAGTTGCCA
1 CAGTGGAGTTGCCA
60489 ATCTGTCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (14 bp):
CAGTGGAGTTGCCA
Found at i:60840 original size:3 final size:3
Alignment explanation
Indices: 60834--60882 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
60824 TTTTTTTAAA
60834 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
60880 AAT
1 AAT
60883 TTAAAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62032 original size:3 final size:3
Alignment explanation
Indices: 62024--62110 Score: 88
Period size: 3 Copynumber: 28.7 Consensus size: 3
62014 GGACCCCTAA
* *
62024 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
62072 AAC AA- CAT AAT -AT AAT ATT ATAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT -AAT AAT AA
62111 ACAATACATA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
2 3 0.04
3 61 0.84
4 9 0.12
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:62237 original size:37 final size:35
Alignment explanation
Indices: 62164--62477 Score: 179
Period size: 35 Copynumber: 8.7 Consensus size: 35
62154 ATACATTATA
* *
62164 TTTTCAAAAACCATTTTAAAAACTATATACTATATG
1 TTTTCAAAAA-TATTTTAAAAACTATATATTATATG
62200 TTTTCAAAAATATTTTAAAAACTATATATTATATATG
1 TTTTCAAAAATATTTTAAAAACTATATA-T-TATATG
* *
62237 TTTTCATAAATATGTTTTCAAAACTATATATTATATG
1 TTTTCA-AAA-ATATTTTAAAAACTATATATTATATG
*
62274 TTTTCAAAAACTA---T----A-T-TATA-TATACG
1 TTTTCAAAAA-TATTTTAAAAACTATATATTATATG
*
62300 TTTTCAAAAATATTTTAAAAACCATATATTATATG
1 TTTTCAAAAATATTTTAAAAACTATATATTATATG
* * * * *
62335 TTTT-AAAACGTGTTTTCAAAACCATAT-TATATATA
1 TTTTCAAAA-ATATTTTAAAAACTATATAT-TATATG
* *
62370 TTTTCAAAAACTAATTTTTTTTTATATATA-TATATATTATTTG
1 TTTTCAAAAA-T-A-----TTTTA-A-AAACTATATATTATATG
* * *
62413 TTTTCAAAAACCGT-TTTCTAAAAGCTATATAATATATT
1 TTTTCAAAAA---TATTT-TAAAAACTATATATTATATG
*
62451 TTTTCAAAAATAATTTCAAAAACTATA
1 TTTTCAAAAAT-ATTTTAAAAACTATA
62478 CTATATTATT
Statistics
Matches: 217, Mismatches: 27, Indels: 68
0.70 0.09 0.22
Matches are distributed among these distances:
25 2 0.01
26 15 0.07
27 4 0.02
28 2 0.01
29 1 0.00
32 1 0.00
33 1 0.00
34 9 0.04
35 52 0.24
36 28 0.13
37 28 0.13
38 28 0.13
39 19 0.09
42 4 0.02
43 19 0.09
44 3 0.01
45 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTCAAAAATATTTTAAAAACTATATATTATATG
Found at i:62288 original size:24 final size:26
Alignment explanation
Indices: 62246--62309 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
62236 GTTTTCATAA
62246 ATATGTTTTC-AAAACTATA-TAT-T
1 ATATGTTTTCAAAAACTATATTATAT
62269 ATATGTTTTCAAAAACTATATTATAT
1 ATATGTTTTCAAAAACTATATTATAT
*
62295 ATACGTTTTCAAAAA
1 ATATGTTTTCAAAAA
62310 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
23 10 0.27
24 9 0.24
25 3 0.08
26 15 0.41
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATGTTTTCAAAAACTATATTATAT
Found at i:62327 original size:61 final size:62
Alignment explanation
Indices: 62212--62342 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 62
62202 TTCAAAAATA
* * * *
62212 TTTTAAAAACTATATATTATATATGTTTTCATAAATATGTTTTCAAAACTATATATTATATG
1 TTTTAAAAACTATATATTATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
62274 TTTTCAAAAACTATAT-TATATATACGTTTTCA-AAA-ATATTTTAAAAACCATATATTATATG
1 TTTT-AAAAACTATATAT-TATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
62335 TTTTAAAA
1 TTTTAAAA
62343 CGTGTTTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
60 4 0.06
61 27 0.43
62 8 0.13
63 24 0.38
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (62 bp):
TTTTAAAAACTATATATTATATACGTTTTCATAAATATATTTTAAAAACCATATATTATATG
Found at i:62397 original size:100 final size:100
Alignment explanation
Indices: 62176--62382 Score: 288
Period size: 96 Copynumber: 2.1 Consensus size: 100
62166 TTCAAAAACC
*
62176 ATTTT-AAAAACTATA-TACTATAT--GTTTTCAAAAATATTTTAAAAACTATATATTATATATG
1 ATTTTCAAAAACTATATTA-TATATACGTTTTCAAAAATATTTTAAAAACCATATATTATATATG
* *
62237 TTTTCATAAATATGTTTTCAAAACTATATATTATAT
65 TTTTCATAAACATGTTTTCAAAACCATATATTATAT
*
62273 GTTTTCAAAAACTATATTATATATACGTTTTCAAAAATATTTTAAAAACCATATA-T-TATATGT
1 ATTTTCAAAAACTATATTATATATACGTTTTCAAAAATATTTTAAAAACCATATATTATATATGT
*
62336 TTT-A-AAACGTGTTTTCAAAACCATAT-TATATAT
66 TTTCATAAACATGTTTTCAAAACCATATAT-TATAT
62369 ATTTTCAAAAACTA
1 ATTTTCAAAAACTA
62383 ATTTTTTTTT
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
95 1 0.01
96 37 0.37
97 5 0.05
98 25 0.25
99 3 0.03
100 28 0.28
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (100 bp):
ATTTTCAAAAACTATATTATATATACGTTTTCAAAAATATTTTAAAAACCATATATTATATATGT
TTTCATAAACATGTTTTCAAAACCATATATTATAT
Found at i:62902 original size:7 final size:7
Alignment explanation
Indices: 62863--62887 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62853 ATATTTTTTA
62863 AATAAAT
1 AATAAAT
62870 AATAAAT
1 AATAAAT
62877 AATAAAT
1 AATAAAT
62884 AATA
1 AATA
62888 TTTCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:68546 original size:4 final size:4
Alignment explanation
Indices: 68537--68574 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
68527 AAATTAGTAT
* *
68537 TTTA TTTA TTTA TTTA TTCA TATA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
68575 TTATTCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:68574 original size:27 final size:27
Alignment explanation
Indices: 68538--68592 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
68528 AATTAGTATT
68538 TTATTTATTTATTTATTCA-T-ATATTTA
1 TTATTTA-TT-TTTATTCACTAATATTTA
68565 TTATTTATTTTTATTCACTAATATTTA
1 TTATTTATTTTTATTCACTAATATTTA
68592 T
1 T
68593 ATGAAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 8 0.31
26 3 0.12
27 15 0.58
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTTTTATTCACTAATATTTA
Found at i:69422 original size:22 final size:21
Alignment explanation
Indices: 69382--69445 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
69372 AATTTATAAT
69382 TTTTTATATATATACATATTA
1 TTTTTATATATATACATATTA
* *
69403 TTTTTATAGTATTTATATA-TA
1 TTTTTATA-TATATACATATTA
* *
69424 TTATTA-ATAT-TACATTTTA
1 TTTTTATATATATACATATTA
69443 TTT
1 TTT
69446 GCAAGTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.11
19 7 0.20
20 1 0.03
21 15 0.43
22 8 0.23
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTATATATATACATATTA
Found at i:69424 original size:24 final size:22
Alignment explanation
Indices: 69365--69428 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 22
69355 TAAAATTTCA
* *
69365 TATATTTA-ATTTATAATTTTT
1 TATATTTATATATATTATTTTT
* *
69386 TATATATATACATATTATTTTT
1 TATATTTATATATATTATTTTT
69408 ATAGTATTTATATATATTATT
1 -TA-TATTTATATATATTATT
69429 AATATTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.21
22 10 0.29
23 2 0.06
24 15 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TATATTTATATATATTATTTTT
Found at i:70876 original size:15 final size:14
Alignment explanation
Indices: 70851--70892 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
70841 TTTTCATGCA
70851 TACAT-TTGCATTT
1 TACATCTTGCATTT
70864 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
70879 TTCATTTTGCATTT
1 TACATCTTGCATTT
70893 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:76749 original size:114 final size:114
Alignment explanation
Indices: 76549--76861 Score: 509
Period size: 114 Copynumber: 2.7 Consensus size: 114
76539 CCATATGCTC
* * *
76549 ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTAAAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
* *
76614 CATTAGATTTGAAAGATGAATTTGCTTATAGTAGAAATAAGAAGACCCA
66 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
76663 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
*
76728 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
66 CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
* * * * * *
76777 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTCGGTAGGAACCCCAGAACTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
*
76842 CATTGGAATTGAAAGATGAA
66 CATTGGATTTGAAAGATGAA
76862 CTGCATGATC
Statistics
Matches: 186, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 186 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (114 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACTAAT
CATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGAAGACCCA
Found at i:79576 original size:22 final size:22
Alignment explanation
Indices: 79545--79599 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
79535 ATCTACACTC
**
79545 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
79567 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
79589 TTCAAAGATGA
1 TTCAAAGATGA
79600 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:80404 original size:76 final size:76
Alignment explanation
Indices: 80278--80455 Score: 293
Period size: 76 Copynumber: 2.3 Consensus size: 76
80268 TTCCCACATT
*
80278 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACC
*
80343 TTAGGGTCATC
66 TTAGGGTCAGC
*
80354 TGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACC
*
80419 TTCGGGTCAGC
66 TTAGGGTCAGC
* * *
80430 TATAAGCCCTACAGTGCATAATGTTT
1 TGTAAGTCCTACAGTGCATGATGTTT
80456 TTTCTTAAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 95 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (76 bp):
TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACC
TTAGGGTCAGC
Found at i:80799 original size:112 final size:112
Alignment explanation
Indices: 80466--80883 Score: 700
Period size: 111 Copynumber: 3.8 Consensus size: 112
80456 TTTCTTAAAA
*
80466 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAA
*
80531 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAA
65 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
*
80579 CATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATAAG
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAG
*
80643 AAGAACTTGTTCAACCTTTTTCTTGAATTCATCATTCGATGGATCAG
66 AAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
* *
80690 CATTTCCA-GAAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAA
80754 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
65 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
* ** *
80802 CATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAGG-AGAAG-AGTTCATAATGAG
1 CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAG
80865 AAGAACTTGTTCAACCTTT
66 AAGAACTTGTTCAACCTTT
80884 GCATGACTCT
Statistics
Matches: 291, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
110 32 0.11
111 112 0.38
112 109 0.37
113 38 0.13
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
CATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAG
AAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAG
Found at i:80962 original size:223 final size:222
Alignment explanation
Indices: 80479--80889 Score: 612
Period size: 223 Copynumber: 1.9 Consensus size: 222
80469 TTCCAGGTAG
* * * *
80479 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCAGAATGAGAAGAACACATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
80544 AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAA
66 AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAGAAGAGTTCATAATGAGAAGAA
* *
80609 CTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTTCTTGAATTCA
131 CTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGAATTCA
* ** * *
80674 TCATTCGATGGATCAGCATTTCCAGAAG
196 TCA-TCGAGGGATCAGCATCACCACAAC
* *
80702 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCAGAATGAGAAGAACACATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* **
80767 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGA
66 AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCA-GAAGAGTTCATAATGAGAAGA
* *
80832 ACTCATCTGAAGA-GGAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACC-TTTGCATGA
130 ACTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGA
80890 CTCTATCACA
Statistics
Matches: 177, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
221 7 0.04
222 28 0.16
223 110 0.62
224 32 0.18
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (222 bp):
AGTTCAGAATGAGAAGAACACATCTCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAGAAGAGTTCATAATGAGAAGAA
CTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCATGAATTCA
TCATCGAGGGATCAGCATCACCACAAC
Found at i:82216 original size:27 final size:29
Alignment explanation
Indices: 82175--82231 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
82165 AATTAGTATT
82175 TTATTTATTTATTTATTCA-T-ATATTTA
1 TTATTTATTTATTTATTCACTAATATTTA
82202 TTATTTATATT-TTTATTCACTAATATTTA
1 TTATTTAT-TTATTTATTCACTAATATTTA
82231 T
1 T
82232 ATGAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 3 0.11
29 8 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTTATTTATTTATTCACTAATATTTA
Found at i:92343 original size:10 final size:10
Alignment explanation
Indices: 92315--92367 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
92305 CTATTTTTTC
92315 AAAAAA-AAA
1 AAAAAACAAA
*
92324 TAAAAACAAA
1 AAAAAACAAA
**
92334 AAAAGGCAAA
1 AAAAAACAAA
92344 AAAAAACAAAA
1 AAAAAAC-AAA
92355 AAAAAACAAA
1 AAAAAACAAA
92365 AAA
1 AAA
92368 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 5 0.14
10 21 0.58
11 10 0.28
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:92368 original size:30 final size:30
Alignment explanation
Indices: 92315--92374 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
92305 CTATTTTTTC
* *
92315 AAAAAAAAATAAAAACAAAAAAAGGCAAAA
1 AAAAAAAAAAAAAAACAAAAAAAGCCAAAA
92345 AAAAACAAAAAAAAAAC-AAAAAAGCCAAAA
1 AAAAA-AAAAAAAAAACAAAAAAAGCCAAAA
92375 TTTCAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.83, C:0.10, G:0.05, T:0.02
Consensus pattern (30 bp):
AAAAAAAAAAAAAAACAAAAAAAGCCAAAA
Found at i:99365 original size:15 final size:15
Alignment explanation
Indices: 99345--99377 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
99335 CATTCATGGC
99345 ACAAAACATGATACA
1 ACAAAACATGATACA
99360 ACAAAACATGATACA
1 ACAAAACATGATACA
99375 ACA
1 ACA
99378 TATGTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (15 bp):
ACAAAACATGATACA
Found at i:101348 original size:2 final size:2
Alignment explanation
Indices: 101341--101386 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
101331 TGAAAACCTC
101341 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
101383 AT AT
1 AT AT
101387 TTAATTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101994 original size:14 final size:14
Alignment explanation
Indices: 101975--102008 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
101965 GGATATAATT
*
101975 TAAAAAAATATTAA
1 TAAAAAAATAATAA
*
101989 TAAAAAAATAATAT
1 TAAAAAAATAATAA
102003 TAAAAA
1 TAAAAA
102009 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAAAATAATAA
Found at i:102190 original size:18 final size:18
Alignment explanation
Indices: 102154--102190 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
102144 TCTGCCTTGA
*
102154 TCATCTTCGTTTTCATCT
1 TCATCTTCGTTTGCATCT
*
102172 TCATCTTCGTTTGCTTCT
1 TCATCTTCGTTTGCATCT
102190 T
1 T
102191 GAAGAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.57
Consensus pattern (18 bp):
TCATCTTCGTTTGCATCT
Found at i:103360 original size:16 final size:16
Alignment explanation
Indices: 103339--103399 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
103329 TAATAAATAA
103339 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
103355 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
103371 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
103387 ACGAACATAAACG
1 ACGAACATAAACG
103400 TTAGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:103851 original size:10 final size:10
Alignment explanation
Indices: 103836--103869 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
103826 ATAAATGAAT
103836 GAACATAAAC
1 GAACATAAAC
103846 GAACATAAAC
1 GAACATAAAC
*
103856 GAACATAACC
1 GAACATAAAC
103866 GAAC
1 GAAC
103870 GTTCACGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.09
Consensus pattern (10 bp):
GAACATAAAC
Found at i:105153 original size:2 final size:2
Alignment explanation
Indices: 105146--105188 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
105136 ATATTATTTG
105146 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
105188 T
1 T
105189 CGGGTACTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:112444 original size:16 final size:17
Alignment explanation
Indices: 112404--112447 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
112394 CCCGACTTGA
112404 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
112421 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
112437 TTAAATATTTA
1 TTAAATATTTA
112448 TTTTTACATA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:112469 original size:20 final size:20
Alignment explanation
Indices: 112423--112475 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
112413 TAATAAATTT
112423 TTATATTTTTAAATTTAAATA
1 TTATATTTTTAAA-TTAAATA
*
112444 TT-TATTTTTACA-TAAATCA
1 TTATATTTTTAAATTAAAT-A
*
112463 TTATATTATTAAA
1 TTATATTTTTAAA
112476 CAAAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 3 0.11
20 17 0.63
21 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATATTTTTAAATTAAATA
Found at i:116592 original size:19 final size:18
Alignment explanation
Indices: 116550--116593 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
116540 AAAAAAGAAG
*
116550 AAAATACAAATAAATAAA
1 AAAATACAAAGAAATAAA
*
116568 ACAAATATAAAGAAGATAAA
1 A-AAATACAAAGAA-ATAAA
116588 AAAATA
1 AAAATA
116594 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATACAAAGAAATAAA
Found at i:116643 original size:10 final size:9
Alignment explanation
Indices: 116617--116715 Score: 53
Period size: 9 Copynumber: 10.4 Consensus size: 9
116607 AATAGAGGGG
*
116617 AAAATAAAA
1 AAAATAAAT
116626 AAAGATAAAT
1 AAA-ATAAAT
116636 AGAAATAAAT
1 A-AAATAAAT
116646 AAAATAGAAT
1 AAAATA-AAT
116656 AATAAT-AAT
1 AA-AATAAAT
*
116665 AATACT-AAT
1 AA-AATAAAT
116674 AATAATAAA-
1 AA-AATAAAT
*
116683 AACAATAAGT
1 AA-AATAAAT
116693 AAAGAGT-AAT
1 AAA-A-TAAAT
*
116703 AAAAAAAAT
1 AAAATAAAT
116712 AAAA
1 AAAA
116716 ATAGAATGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
9 40 0.54
10 28 0.38
11 6 0.08
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:116892 original size:20 final size:20
Alignment explanation
Indices: 116851--116893 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
116841 TAATAGAGAG
* *
116851 AAAAAAATAATAATAAATTA
1 AAAAAAATAATAACAAAATA
116871 AAAAAAGATAA-AACAAAATA
1 AAAAAA-ATAATAACAAAATA
116891 AAA
1 AAA
116894 CATATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAATAATAACAAAATA
Found at i:118649 original size:110 final size:110
Alignment explanation
Indices: 118466--118865 Score: 669
Period size: 110 Copynumber: 3.7 Consensus size: 110
118456 TTGTGTCGCT
* *
118466 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
*
118531 TGACAGTCAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
* * *
118576 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
** *
118641 TGACAGTCAGTCGCCTATTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
* *
118686 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATTAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
*
118751 TGACAGTTAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
*
118796 TCGAGTCAAATATCCTTCGCTGTGAAGTTGAAA--GACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
118859 TGACAGT
66 TGACAGT
118866 AAGCTTTTCT
Statistics
Matches: 271, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
108 36 0.13
110 235 0.87
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
Found at i:119941 original size:20 final size:20
Alignment explanation
Indices: 119900--119942 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
119890 TAATAGAGAG
* *
119900 AAAAAAATAATAATAAATTA
1 AAAAAAATAATAACAAAATA
119920 AAAAAAGATAA-AACAAAATA
1 AAAAAA-ATAATAACAAAATA
119940 AAA
1 AAA
119943 TATATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAATAATAACAAAATA
Found at i:121707 original size:110 final size:110
Alignment explanation
Indices: 121524--121923 Score: 669
Period size: 110 Copynumber: 3.7 Consensus size: 110
121514 TTGTGTCGCT
* *
121524 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
* *
121589 TGACAGTCAGTCACCCCTTCATTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
* * *
121634 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
** *
121699 TGACAGTCAGTCGCCTATTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
* *
121744 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATTAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
*
121809 TGACAGTTAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
121854 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAA--GACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
121917 TGACAGT
66 TGACAGT
121924 AAGCTTTTCT
Statistics
Matches: 271, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
108 36 0.13
110 235 0.87
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
TGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
Found at i:123619 original size:14 final size:13
Alignment explanation
Indices: 123602--123657 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
123592 TTTTTCGTTA
*
123602 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
123615 TTTTTATTTTCTCT
1 TTTTT-TTTTCTCT
* *
123629 TTGTTTTTCCT-T
1 TTTTTTTTTCTCT
123641 TGTTTTTTTTC-CT
1 T-TTTTTTTTCTCT
123654 TTTT
1 TTTT
123658 GTTCTGATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 5 0.14
13 19 0.54
14 11 0.31
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:125728 original size:15 final size:15
Alignment explanation
Indices: 125708--125741 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
125698 TCTATCCCGT
125708 AAGTTGATTTTGAAC
1 AAGTTGATTTTGAAC
125723 AAGTTGATTTTGAAC
1 AAGTTGATTTTGAAC
125738 AAGT
1 AAGT
125742 CCTAACCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (15 bp):
AAGTTGATTTTGAAC
Found at i:126884 original size:10 final size:9
Alignment explanation
Indices: 126856--126939 Score: 50
Period size: 9 Copynumber: 8.8 Consensus size: 9
126846 ATAGAGGGGA
*
126856 AAAATAAAA
1 AAAATAAAT
126865 AAAAGGTAAAT
1 AAAA--TAAAT
126876 AGAAATAAAT
1 A-AAATAAAT
126886 AAAATAGAAT
1 AAAATA-AAT
126896 AATAAT-AAT
1 AA-AATAAAT
126905 AATAAT-AAT
1 AA-AATAAAT
126914 AATAAT-AAT
1 AA-AATAAAT
126923 AATAAT-AAT
1 AA-AATAAAT
126932 AATAATAA
1 AA-AATAA
126940 TAATAATACT
Statistics
Matches: 68, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
9 45 0.66
10 12 0.18
11 8 0.12
12 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (9 bp):
AAAATAAAT
Found at i:126901 original size:3 final size:3
Alignment explanation
Indices: 126893--126957 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
126883 AATAAAATAG
126893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
126941 AAT AAT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
126958 AAACAATAAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:126965 original size:12 final size:12
Alignment explanation
Indices: 126893--126995 Score: 89
Period size: 12 Copynumber: 8.3 Consensus size: 12
126883 AATAAAATAG
*
126893 AATAATAATAAT
1 AATAAAAATAAT
*
126905 AATAATAATAAT
1 AATAAAAATAAT
*
126917 AATAATAATAAT
1 AATAAAAATAAT
*
126929 AATAATAATAAT
1 AATAAAAATAAT
* *
126941 AATAATACTAAT
1 AATAAAAATAAT
*
126953 AATAAAAACAAT
1 AATAAAAATAAT
*
126965 AAGTAAAGAGTAAT
1 AA-TAAA-AATAAT
* *
126979 AAAAGAAAATAAA
1 AATA-AAAATAAT
126992 AATA
1 AATA
126996 GAAGGGTATA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
12 58 0.74
13 12 0.15
14 8 0.10
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:127040 original size:29 final size:29
Alignment explanation
Indices: 127008--127082 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
126998 AGGGTATAAG
127008 AATAATAAATAAAATATATTTATATATGT
1 AATAATAAATAAAATATATTTATATATGT
127037 AATAATAAATAAAATATATTTATATATGT
1 AATAATAAATAAAATATATTTATATATGT
*
127066 AATAATAAATATAATAT
1 AATAATAAATAAAATAT
127083 TTGCAACAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AATAATAAATAAAATATATTTATATATGT
Found at i:127186 original size:28 final size:28
Alignment explanation
Indices: 127162--127228 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
127152 AATAATAGAG
127162 AAAAATAATAATAA-AT-TAAAAAATATA
1 AAAAATAATAATAACATATAAAAAATA-A
*
127189 AAACAA-AATAA-AACATATAAAATATAA
1 AAA-AATAATAATAACATATAAAAAATAA
127216 TAAAAATAATAAT
1 -AAAAATAATAAT
127229 GAAGTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
26 2 0.06
27 13 0.39
28 18 0.55
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (28 bp):
AAAAATAATAATAACATATAAAAAATAA
Found at i:127224 original size:9 final size:9
Alignment explanation
Indices: 127162--127227 Score: 57
Period size: 9 Copynumber: 7.2 Consensus size: 9
127152 AATAATAGAG
127162 AAAAATAAT
1 AAAAATAAT
*
127171 AATAAATTA-
1 AA-AAATAAT
127180 AAAAAT-AT
1 AAAAATAAT
*
127188 AAAACAAAAT
1 AAAA-ATAAT
127198 AAAACAT-AT
1 AAAA-ATAAT
127207 AAAATATAAT
1 AAAA-ATAAT
127217 AAAAATAAT
1 AAAAATAAT
127226 AA
1 AA
127228 TGAAGTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
7 1 0.02
8 8 0.17
9 20 0.42
10 19 0.40
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAATAAT
Found at i:127665 original size:37 final size:37
Alignment explanation
Indices: 127615--127726 Score: 190
Period size: 37 Copynumber: 3.0 Consensus size: 37
127605 ATGCTTATGG
* *
127615 ATCATCTTTTTAGGAGTTTGAATCATAGTAAAAGTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
127652 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
127689 ATCATATTTTTAGGAGTTTGAATTC-TAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAA-TCATAGTAAAACTCT
127726 A
1 A
127727 ACGTTATGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
37 70 0.97
38 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:131032 original size:31 final size:30
Alignment explanation
Indices: 130972--131028 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
130962 ATAATTTCAA
* *
130972 AAAATATTAAGTTTTTTTAAAAATAAATTT
1 AAAATATTAAGTGTTTTCAAAAATAAATTT
131002 AAAAT-TTAAGTGTTTTCATAAAATAAA
1 AAAATATTAAGTGTTTTCA-AAAATAAA
131029 ATTTTATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
AAAATATTAAGTGTTTTCAAAAATAAATTT
Found at i:133226 original size:18 final size:18
Alignment explanation
Indices: 133185--133227 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
133175 AACTCTAAAC
*
133185 TCAAATCTTAATCAAATA
1 TCAAACCTTAATCAAATA
*
133203 TTAAACCTTATATCAAA-A
1 TCAAACCTTA-ATCAAATA
133221 TCAAACC
1 TCAAACC
133228 CTAAAATCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (18 bp):
TCAAACCTTAATCAAATA
Found at i:135841 original size:15 final size:15
Alignment explanation
Indices: 135821--135857 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
135811 ATATTTAGCT
*
135821 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
135836 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
135851 GGGCGGG
1 GGGCGGG
135858 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:139804 original size:54 final size:54
Alignment explanation
Indices: 139740--140276 Score: 678
Period size: 54 Copynumber: 9.9 Consensus size: 54
139730 TGACCAATTA
* * * * *
139740 GGCATTAAGTGTGCATTTCATGAAATTCATCCTATGTAGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
139794 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
139848 GGCACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * ** * ** * *
139902 GGCACTAAATGTGCATTTCATGGAATTTATAATTTGTTTACGAATAACCGTATC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
139956 GACAATAAGTATGCATTTCACGGAATTCAACCTAGGTGGATGAATAACCGTTTA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
140010 AGCACTAAGTGTGCATTTCACGGAATTCATCCTACGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
140064 GACACTAGGTGTGCATTTCACGGAATTCATCCTACGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** * *
140118 GGAACTAAGAGTGCATTTCATAGAATTTATCCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
140172 GGCACTAAGTGTGCATTTCACGGAATTCATCATACGTAGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
140226 GACAATAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACCGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGT
140277 ACAGGCATTA
Statistics
Matches: 409, Mismatches: 74, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 409 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:140323 original size:55 final size:55
Alignment explanation
Indices: 140264--140458 Score: 263
Period size: 55 Copynumber: 3.6 Consensus size: 55
140254 ATCTTATGTG
* *
140264 GATGAATAACCGTACAGGCATTATGTGTACAAATCCAC-GAAATTCATCATGAGTT
1 GATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAG-AATTCATCATGAGTT
* * *
140319 GATGAATAACCGTACATGCACTATGTGTGTAAATCCACAGAATTCATCATGAGAT
1 GATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
* *
140374 GATGAATAACCGTACAGGCA-TGATGTGTGC-AACCCACATAATTCATCATGAGTT
1 GATGAATAACCGTACAGGCACT-ATGTGTGCAAATCCACAGAATTCATCATGAGTT
*
140428 GATGAACT-ACCGTATAGGCACTATGTGTGCA
1 GATGAA-TAACCGTACAGGCACTATGTGTGCA
140459 TCTTAATAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
54 47 0.38
55 76 0.61
56 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (55 bp):
GATGAATAACCGTACAGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTT
Found at i:143824 original size:19 final size:19
Alignment explanation
Indices: 143719--143858 Score: 63
Period size: 19 Copynumber: 7.2 Consensus size: 19
143709 TGTATTTTAG
*
143719 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
143738 TTTAATTAAGTTTTAGGATAT
1 TTTAATTAGGTTTTA-G-TAT
* ** *
143759 TATT-TTTATATTTTTGTAT
1 T-TTAATTAGGTTTTAGTAT
* *
143778 TTGT-TTTAGGTATTT--TAG
1 TT-TAATTAGGT-TTTAGTAT
*
143796 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
143815 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
143834 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
143855 TTTA
1 TTTA
143859 GTTTAAATAG
Statistics
Matches: 90, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
17 4 0.04
18 10 0.11
19 44 0.49
20 13 0.14
21 17 0.19
22 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:150013 original size:14 final size:14
Alignment explanation
Indices: 149989--150024 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
149979 ACATTTTTGT
*
149989 TTTATTTTCATTCTA
1 TTTA-TTTCATTCCA
150004 TTTATTTCATTCCA
1 TTTATTTCATTCCA
150018 TTTATTT
1 TTTATTT
150025 TTATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTCATTCCA
Found at i:151747 original size:32 final size:32
Alignment explanation
Indices: 151704--151765 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
151694 TTTAAATAGG
151704 TTTTAGTATTTTA-ATTAGGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-GGTTTTAGG-TATTAT
*
151737 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTGGTTTTAGGTATT
151766 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTGGTTTTAGGTATTAT
Found at i:151811 original size:66 final size:65
Alignment explanation
Indices: 151741--151869 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 65
151731 TATTATTTTT
* *
151741 ATATTTTA-TATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTTAGTATTTTAATTAGGATTTA
1 ATATTATATTATTT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTA
151805 GA
64 GA
*
151807 ATATTATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATTATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
151870 CGATGTTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
65 24 0.41
66 30 0.51
67 5 0.08
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.57
Consensus pattern (65 bp):
ATATTATATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGA
Found at i:153365 original size:18 final size:18
Alignment explanation
Indices: 153342--153384 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
153332 GTTGGTTATT
153342 GAAGCTTTGAGTATGATA
1 GAAGCTTTGAGTATGATA
153360 GAAGCTTTGAGTATGATA
1 GAAGCTTTGAGTATGATA
153378 GAAGCTT
1 GAAGCTT
153385 AAAGTAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (18 bp):
GAAGCTTTGAGTATGATA
Found at i:153390 original size:18 final size:18
Alignment explanation
Indices: 153351--153390 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
153341 TGAAGCTTTG
**
153351 AGTATGATAGAAGCTTTG
1 AGTATGATAGAAGCTTAA
153369 AGTATGATAGAAGCTTAA
1 AGTATGATAGAAGCTTAA
153387 AGTA
1 AGTA
153391 GGATTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (18 bp):
AGTATGATAGAAGCTTAA
Found at i:153847 original size:54 final size:54
Alignment explanation
Indices: 153783--154150 Score: 445
Period size: 54 Copynumber: 6.9 Consensus size: 54
153773 ATCAATTAGG
* *
153783 CACTAAGTGTGCATTTCATGGATTTCATCCTATGTGGATGAATAACTATTTCGA
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
* *
153837 CACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAAC-AGTTTCAA
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTA-TTTCGA
* * * * * * * *
153891 CACTAAGTATTCATTTTACGAAATTCATCCTACGTCGATGAATAACTGTTTCGG
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
* * * * *
153945 CACTAAGTGTGCATTTCATGAAATTCATCCTACGTTGATGAATAAATGTTTCGG
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
* * * **
153999 CACTAAGTGTGCATTCCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
* * * *
154053 CACTAAGTATGCA--TCATGGAATTCATCCTATGTGGATAAATAACTATTTCGG
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
** *
154105 CACTAAGTGTGCATTTCACAGAATTTATCCTACGTGGATGAATAAC
1 CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAAC
154151 CGTACATGCA
Statistics
Matches: 270, Mismatches: 40, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
52 44 0.16
53 1 0.00
54 225 0.83
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCATGGAATTCATCCTACGTGGATGAATAACTATTTCGA
Found at i:154058 original size:162 final size:160
Alignment explanation
Indices: 153781--154149 Score: 506
Period size: 162 Copynumber: 2.3 Consensus size: 160
153771 TTATCAATTA
* * * *
153781 GGCACTAAGTGTGCATTTCATGGATTTCATCCTATGTGGATGAATAACTATTTCGACACTAAGTG
1 GGCACTAAGTGTGCATTTCATGAAATTCATCCTACGTGGATGAATAAATATTTCGACACTAAGTG
* * * * *
153846 TGCATTTCATGGAATTCATCCTATGTGGATGAATAACAGTTTCAACACTAAGTATTCATTTTACG
66 TGCATTCCACGGAATTCATCCTAGGTGGATGAATAACAGTTTCAACACTAAGTATGCA--TCACG
* *
153911 AAATTCATCCTACGTCGATGAATAACTGTTTC
129 AAATTCATCCTACGTCGATAAATAACTATTTC
* * *
153943 GGCACTAAGTGTGCATTTCATGAAATTCATCCTACGTTGATGAATAAATGTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCATGAAATTCATCCTACGTGGATGAATAAATATTTCGACACTAAGTG
* * * *
154008 TGCATTCCACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGACACTAAGTATGCATCATGGA
66 TGCATTCCACGGAATTCATCCTAGGTGGATGAATAACAGTTTCAACACTAAGTATGCATCACGAA
* *
154073 ATTCATCCTATGTGGATAAATAACTATTTC
131 ATTCATCCTACGTCGATAAATAACTATTTC
* *
154103 GGCACTAAGTGTGCATTTCA-CAGAATTTATCCTACGTGGATGAATAA
1 GGCACTAAGTGTGCATTTCATGA-AATTCATCCTACGTGGATGAATAA
154150 CCGTACATGC
Statistics
Matches: 183, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
159 1 0.01
160 72 0.39
162 110 0.60
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (160 bp):
GGCACTAAGTGTGCATTTCATGAAATTCATCCTACGTGGATGAATAAATATTTCGACACTAAGTG
TGCATTCCACGGAATTCATCCTAGGTGGATGAATAACAGTTTCAACACTAAGTATGCATCACGAA
ATTCATCCTACGTCGATAAATAACTATTTC
Found at i:154162 original size:54 final size:54
Alignment explanation
Indices: 153782--154281 Score: 287
Period size: 54 Copynumber: 9.3 Consensus size: 54
153772 TATCAATTAG
** * * **
153782 GCACTAAGTGTGCATTTCATGGATTTCATCCTATGTGGATGAATAA-C-TATTT
1 GCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTACAT
** * * *
153834 CGACACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACAGTTTCA-
1 -G-CACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCG-TACAT
* * * * * * * *
153890 ACACTAAGTATTCATTTTAC-GAAATTCATCCTACGTCGATGAATAACTGTTTC-G
1 GCACTAAGTGTGCATTTCACAG-AATTCATCCTACGTGGATGAATAACCG-TACAT
* * ** * *
153944 GCACTAAGTGTGCATTTCA-TGAAATTCATCCTACGTTGATGAATAAATGTTTC-G
1 GCACTAAGTGTGCATTTCACAG-AATTCATCCTACGTGGATGAATAACCG-TACAT
* * * *
153998 GCACTAAGTGTGCATTCCACGGAATTCATCCTAGGTGGATGAATAACCGT--TT
1 GCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTACAT
* ** * * **
154050 CGACACTAAGTATGCA--TCATGGAATTCATCCTATGTGGATAAATAA-C-TATTT
1 -G-CACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTACAT
*
154102 CGGCACTAAGTGTGCATTTCACAGAATTTATCCTACGTGGATGAATAACCGTACAT
1 --GCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTACAT
* ** * *
154158 GCACTATGTGTGCAAATC-CACGAAATTCATCATGA-GTTGATGAATAACCGTACAT
1 GCACTAAGTGTGCATTTCACA-G-AATTCATCCT-ACGTGGATGAATAACCGTACAT
* ** ** *
154213 GCACTATGTGTGCAAATC-CATGGAATTCATTATGA-GTTGATGAATAACCGTACAT
1 GCACTAAGTGTGCATTTCACA--GAATTCATCCT-ACGTGGATGAATAACCGTACAT
*
154268 GCACTATGTGTGCA
1 GCACTAAGTGTGCA
154282 AATCCACGTA
Statistics
Matches: 377, Mismatches: 48, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.00
51 1 0.00
52 40 0.11
53 7 0.02
54 228 0.60
55 94 0.25
56 5 0.01
57 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTACAT
Found at i:154208 original size:55 final size:55
Alignment explanation
Indices: 154141--154364 Score: 339
Period size: 55 Copynumber: 4.1 Consensus size: 55
154131 ATCCTACGTG
154141 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
* * *
154196 GATGAATAACCGTACATGCACTATGTGTGCAAATCCATGGAATTCATTATGAGTT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
* *
154251 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGTAATTCA-CATGAGAT
1 GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
* *
154305 GATGAATAACCGTACA-GACACGATGTGTGC-AACCCAC-AGAATTCATCATGAGTT
1 GATGAATAACCGTACATG-CACTATGTGTGCAAATCCACGA-AATTCATCATGAGTT
154359 GATGAA
1 GATGAA
154365 CTACCATATA
Statistics
Matches: 155, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
53 13 0.08
54 46 0.30
55 96 0.62
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (55 bp):
GATGAATAACCGTACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
Found at i:156782 original size:2 final size:2
Alignment explanation
Indices: 156770--156800 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
156760 AAGTTTACAA
*
156770 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
156801 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:157405 original size:22 final size:23
Alignment explanation
Indices: 157374--157418 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
157364 TATATTGGAT
*
157374 GAACATTATCGATACT-TAAGAA
1 GAACAATATCGATACTGTAAGAA
*
157396 GAACAATATCGGTACTGTAAGAA
1 GAACAATATCGATACTGTAAGAA
157419 TAATACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (23 bp):
GAACAATATCGATACTGTAAGAA
Found at i:162224 original size:61 final size:62
Alignment explanation
Indices: 162125--162247 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 62
162115 TTTCAGCTAA
* *
162125 TTCGAATAATTTGTTTGATTAATTCAATTAAAACTGAAGTTTAAACACTTTAATATATAAAT
1 TTCGAATAATTTGTTGGATTAATTCAATTAAAACTGAAGTTTAAACACTCTAATATATAAAT
* * *
162187 TTCGATTAATTTGTTGGA-TAATTCGATTAAAATTGAAGTTTAAACACTCTAATATATAAAT
1 TTCGAATAATTTGTTGGATTAATTCAATTAAAACTGAAGTTTAAACACTCTAATATATAAAT
162248 AATATACATA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 40 0.71
62 16 0.29
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (62 bp):
TTCGAATAATTTGTTGGATTAATTCAATTAAAACTGAAGTTTAAACACTCTAATATATAAAT
Found at i:162260 original size:17 final size:17
Alignment explanation
Indices: 162236--162281 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
162226 TTAAACACTC
162236 TAATATATAAATA-ATA
1 TAATATATAAATACATA
*
162252 TACATATATATATACATA
1 TA-ATATATAAATACATA
*
162270 TAATATTTAAAT
1 TAATATATAAAT
162282 TTTCAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 18 0.72
18 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATATAAATACATA
Found at i:165238 original size:42 final size:42
Alignment explanation
Indices: 165190--165355 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 42
165180 TATTAAGCTC
* *
165190 CTAATTTTTT-AATCTCCCTTTTAACTTTTATAATTGAGACCCT
1 CTAATTTTTTCAATC-CCCTTTTTACCTTTATAATTGAG-CCCT
*
165233 -TAATTTTTTTCAATCCTACTTTTTACCTTTATAATTGAGCCCT
1 CTAA-TTTTTTCAATCC-CCTTTTTACCTTTATAATTGAGCCCT
* * * *
165276 CCAATTTTTTCAATCCCCTTTTTACCTTTATAAGTGTTGGCC-
1 CTAATTTTTTCAATCCCCTTTTTACCTTTATAATTG-AGCCCT
* * * *
165318 CGATTTTTTTCAATCTCACTTTCTACCTTTATAATTGA
1 CTAATTTTTTCAATC-CCCTTTTTACCTTTATAATTGA
165356 AGCCTTTAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
42 34 0.33
43 44 0.43
44 25 0.24
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49
Consensus pattern (42 bp):
CTAATTTTTTCAATCCCCTTTTTACCTTTATAATTGAGCCCT
Found at i:165382 original size:85 final size:85
Alignment explanation
Indices: 165235--165393 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 85
165225 GAGACCCTTA
* * **
165235 ATTTTTTTCAATCCTACTTTTTACCTTTATAATTGAGCCCTCCAATTTTTTCAATCCCCTTTTTA
1 ATTTTTTTCAATCCTACTTTCTACCTTTATAATTGAGCCCTCCAATTTGTTCAATCAACTTTTTA
165300 CCTTTATAAGTGTTGGCCCG
66 CCTTTATAAGTGTTGGCCCG
** *
165320 ATTTTTTTCAAT-CTCACTTTCTACCTTTATAATTGAAG-CCTTTAA-TTGTTCCATCAAACTTT
1 ATTTTTTTCAATCCT-ACTTTCTACCTTTATAATTG-AGCCCTCCAATTTGTTCAATC-AACTTT
*
165382 TTACTTTTATAA
63 TTACCTTTATAA
165394 TTGAAGCCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
84 10 0.16
85 51 0.81
86 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.06, T:0.48
Consensus pattern (85 bp):
ATTTTTTTCAATCCTACTTTCTACCTTTATAATTGAGCCCTCCAATTTGTTCAATCAACTTTTTA
CCTTTATAAGTGTTGGCCCG
Found at i:170444 original size:70 final size:69
Alignment explanation
Indices: 170367--170960 Score: 352
Period size: 70 Copynumber: 8.5 Consensus size: 69
170357 AAGTTACCTG
** * *
170367 AAATTAATTATGATTAGGTGCTCTTGTACGAGCCACTCTAATATTTCGGAGCTTCCGTACGAGTC
1 AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCTTTCGG-GCTTCCGTACGAGTC
170432 ACTCA
65 ACTCA
** * *
170437 AAATTAATTATGATTAGGTTTTC-CTGTACGAGTCACTCTAATCCTTCGGGAC-TCCTGTACGAG
1 AAATTAATTATGATTAGGTGCTCTC-ATACGAGTCACTCTAATCTTTCGGG-CTTCC-GTACGAG
*
170500 TCACTCG
63 TCACTCA
* * * * *
170507 GAATTAATTATGATTAGGT-AT-TCAT-CAAGCCACTCTAATCCTTTGGGGATCTT--GTACGAG
1 AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAAT-CTTTCGGG--CTTCCGTACGAG
* *
170567 TCACCCG
63 TCACTCA
* * * *** * * * *
170574 AAATTAATTATGATTAAGTGCTCCCTTTTAAGTCACTTTAATCCTTCGGGGCTTCTGTATGAGTC
1 AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCTTTC-GGGCTTCCGTACGAGTC
170639 ACTCCA
65 ACT-CA
* * * * * *
170645 TAATTAATTATGATTTGGTGTTCCCATACGAGTCACTCTAATTTTTCGGGACTCCCGTACGAGTC
1 AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCTTTCGGG-CTTCCGTACGAGTC
*
170710 ACCCA
65 ACTCA
* * * *
170715 TAAA-TAATTATGATTAGGTGCTCTCATACGAGTCACTTTAAT-TCTTCAAGGC-TCCTGTAAGT
1 -AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCT-TTC-GGGCTTCC-GTACGA
* *
170777 GTCACCCT
62 GTCACTCA
** ** * * * **
170785 AAATTAATTATGATTAAATGCTCCTTTTTA--AGTCACGCTAATCCTTCGGGGTTTCTATACGAG
1 AAATTAATTATGATTAGGTGCT-C-TCATACGAGTCACTCTAATCTTTC-GGGCTTCCGTACGAG
* *
170848 TCACCCT
63 TCACTCA
* ** * * * * *
170855 TAATTAATTATGATTAGGTATTCCCGTACAAGTCACTCTAATCCTTT-GAGACTCCCGTACGAGT
1 AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAAT-CTTTCG-GGCTTCCGTACGAGT
*
170919 CACCCA
64 CACTCA
* * *
170925 TAAA-TAATTATAATTAGGTGCCCTCGTACGAGTCAC
1 -AAATTAATTATGATTAGGTGCTCTCATACGAGTCAC
170961 CCTTAATTAA
Statistics
Matches: 404, Mismatches: 91, Indels: 58
0.73 0.16 0.10
Matches are distributed among these distances:
67 42 0.10
68 13 0.03
69 20 0.05
70 264 0.65
71 62 0.15
72 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (69 bp):
AAATTAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCTTTCGGGCTTCCGTACGAGTCA
CTCA
Found at i:170931 original size:210 final size:210
Alignment explanation
Indices: 170424--170960 Score: 668
Period size: 210 Copynumber: 2.6 Consensus size: 210
170414 GGAGCTTCCG
* * * * *
170424 TACGAGTCACTCAAAATTAATTATGATTAGGTTTTCCTGTACGAGTCACTCTAATCCTTCGGGAC
1 TACGAGTCACCCATAATTAATTATGATTAGGTATTCCCGTACGAGTCACTCTAATCCTTTGGGAC
* * ** * * * * *
170489 TCCTGTACGAGTCACTCGGAATTAATTATGATTAGGT-AT-TCAT-CAAGCCACTCTAATCCTTT
66 TCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCCTTC
** * * * **
170551 GGGGATCTTGTACGAGTCACCCGAAATTAATTATGATTAAGTGCTCCCTTTTAAGTCACTTTAAT
131 AAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTCACGCTAAT
*
170616 CCTTCGGGGCTTCTG
196 CCTTCGGGGCTTCTA
* * * * *
170631 TATGAGTCACTCCATAATTAATTATGATTTGGTGTTCCCATACGAGTCACTCTAAT-TTTTCGGG
1 TACGAGTCAC-CCATAATTAATTATGATTAGGTATTCCCGTACGAGTCACTCTAATCCTTT-GGG
* *
170695 ACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTTTAATTCT
64 ACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCCT
* * * *
170760 TCAAGGCTCCTGTAAGTGTCACCCTAAATTAATTATGATTAAATGCTCCTTTTTAAGTCACGCTA
129 TCAAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTCACGCTA
*
170825 ATCCTTCGGGGTTTCTA
194 ATCCTTCGGGGCTTCTA
* * *
170842 TACGAGTCACCCTTAATTAATTATGATTAGGTATTCCCGTACAAGTCACTCTAATCCTTTGAGAC
1 TACGAGTCACCCATAATTAATTATGATTAGGTATTCCCGTACGAGTCACTCTAATCCTTTGGGAC
* * *
170907 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCGTACGAGTCAC
66 TCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCAC
170961 CCTTAATTAA
Statistics
Matches: 280, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
207 11 0.04
208 76 0.27
209 1 0.00
210 99 0.35
211 93 0.33
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (210 bp):
TACGAGTCACCCATAATTAATTATGATTAGGTATTCCCGTACGAGTCACTCTAATCCTTTGGGAC
TCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCTAATCCTTC
AAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTCACGCTAAT
CCTTCGGGGCTTCTA
Found at i:170959 original size:140 final size:140
Alignment explanation
Indices: 170371--170960 Score: 462
Period size: 140 Copynumber: 4.2 Consensus size: 140
170361 TACCTGAAAT
* ** * ** * *
170371 TAATTATGATTAGGTGCTCTTGTACGAGCCACTCTAATATTTCGGAGCTTCCGTACGAGTCACTC
1 TAATTATGATTAGGTGCCCTCATACGAGTCACTCTAATCCTTCGGGGCTTCCGTACGAGTCACCC
** * * *
170436 AAAATTAATTATGATTAGGTTTTCCTGTACGAGTCACTCTAATCCTTCGGGACTCCTGTACGAGT
66 AAAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCTGTACGAGT
* ** *
170501 CACTCGGAAT
131 CACCCATAAA
** * * *
170511 TAATTATGATTAGGT--ATTCAT-CAAGCCACTCTAATCCTTTGGGGATCTT--GTACGAGTCAC
1 TAATTATGATTAGGTGCCCTCATACGAGTCACTCTAATCCTTCGGGG--CTTCCGTACGAGTCAC
* * * ** * * * * *
170571 CCGAAATTAATTATGATTAAGTGCTCCCTTTTAAGTCACTTTAATCCTTCGGGGCTTCTGTATGA
64 CCAAAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCTGTACGA
*
170636 GTCACTCCATAAT
129 GTCAC-CCATAAA
* * ** * *
170649 TAATTATGATTTGGTGTTCC-CATACGAGTCACTCTAATTTTTCGGGACTCCCGTACGAGTCACC
1 TAATTATGATTAGGTG-CCCTCATACGAGTCACTCTAATCCTTCGGGGCTTCCGTACGAGTCACC
* * * * * * * * *
170713 CATAAA-TAATTATGATTAGGTGCTCTCATACGAGTCACTTTAATTCTTCAAGGCTCCTGTAAGT
65 CA-AAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCTGTACGA
170777 GTCACCC-TAAA
129 GTCACCCATAAA
** ** * * **
170788 TTAATTATGATTAAATGCTCCTTTTTA--AGTCACGCTAATCCTTCGGGGTTTCTATACGAGTCA
1 -TAATTATGATTAGGTGC-CC-TCATACGAGTCACTCTAATCCTTCGGGGCTTCCGTACGAGTCA
** ** * *
170851 CCCTTAATTAATTATGATTAGGTATTCCCGTACAAGTCACTCTAATCCTTTGAGACTCCCGTACG
63 CCCAAAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCTGTACG
170916 AGTCACCCATAAA
128 AGTCACCCATAAA
* *
170929 TAATTATAATTAGGTGCCCTCGTACGAGTCAC
1 TAATTATGATTAGGTGCCCTCATACGAGTCAC
170961 CCTTAATTAA
Statistics
Matches: 348, Mismatches: 84, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
137 85 0.24
138 23 0.07
139 12 0.03
140 138 0.40
141 85 0.24
142 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (140 bp):
TAATTATGATTAGGTGCCCTCATACGAGTCACTCTAATCCTTCGGGGCTTCCGTACGAGTCACCC
AAAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCTGTACGAGT
CACCCATAAA
Found at i:170972 original size:39 final size:38
Alignment explanation
Indices: 170908--171069 Score: 149
Period size: 39 Copynumber: 4.4 Consensus size: 38
170898 CTTTGAGACT
170908 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
1 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
* * *
170946 CCTCGTACGAGTCACCCTTAATTAATTATGATTAGGTGC
1 CC-CGTACGAGTCACCCATAAATAATTATAATTAGGTGC
* * ** ** * *
170985 TCCCGTACAAGTCACTC-T-AATCCTT-CGA-GA-CT--
1 -CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
171017 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
1 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
171055 CCTCGTACGAGTCAC
1 CC-CGTACGAGTCAC
171070 TTTAATTCTT
Statistics
Matches: 95, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
31 14 0.15
32 1 0.01
33 5 0.05
34 2 0.02
35 2 0.02
36 3 0.03
37 4 0.04
38 5 0.05
39 57 0.60
40 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (38 bp):
CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGC
Found at i:170981 original size:109 final size:109
Alignment explanation
Indices: 170842--171069 Score: 429
Period size: 109 Copynumber: 2.1 Consensus size: 109
170832 GGGGTTTCTA
* *
170842 TACGAGTCACCCTTAATTAATTATGATTAGGTATTCCCGTACAAGTCACTCTAATCCTTTGAGAC
1 TACGAGTCACCCTTAATTAATTATGATTAGGTACTCCCGTACAAGTCACTCTAATCCTTCGAGAC
170907 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
66 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
*
170951 TACGAGTCACCCTTAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAGAC
1 TACGAGTCACCCTTAATTAATTATGATTAGGTACTCCCGTACAAGTCACTCTAATCCTTCGAGAC
171016 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
66 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
171060 TACGAGTCAC
1 TACGAGTCAC
171070 TTTAATTCTT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 116 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (109 bp):
TACGAGTCACCCTTAATTAATTATGATTAGGTACTCCCGTACAAGTCACTCTAATCCTTCGAGAC
TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
Found at i:171092 original size:70 final size:70
Alignment explanation
Indices: 170949--171082 Score: 198
Period size: 70 Copynumber: 1.9 Consensus size: 70
170939 TAGGTGCCCT
* * *
170949 CGTACGAGTCACCCTTAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
1 CGTACGAGTCACCCATAAATAATTATAATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
171014 ACTCC
66 ACTCC
* * *
171019 CGTACGAGTCACCCATAAATAATTATAATTAGGTGC-CCTCGTACGAGTCACTTTAATTCTTCGA
1 CGTACGAGTCACCCATAAATAATTATAATTAGGTGCTCC-CGTACAAGTCACTCTAATCCTTCGA
171083 AGCTGCCGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 2 0.04
70 55 0.96
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (70 bp):
CGTACGAGTCACCCATAAATAATTATAATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
ACTCC
Found at i:171100 original size:70 final size:70
Alignment explanation
Indices: 170949--171101 Score: 184
Period size: 70 Copynumber: 2.2 Consensus size: 70
170939 TAGGTGCCCT
* * * *
170949 CGTACGAGTCACCCTTAATTAATTATGATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
1 CGTAAGAGTCACCCATAAATAATTATAATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
171014 ACTCC
66 ACTCC
* * * *
171019 CGTACGAGTCACCCATAAATAATTATAATTAGGTGC-CCTCGTACGAGTCACTTTAATTCTTCGA
1 CGTAAGAGTCACCCATAAATAATTATAATTAGGTGCTCC-CGTACAAGTCACTCTAATCCTTCGA
*
171083 -AGCTGC
65 GA-CTCC
*
171089 CGTAAGTGTCACC
1 CGTAAGAGTCACC
171102 TAGAATTAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
69 3 0.04
70 69 0.96
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (70 bp):
CGTAAGAGTCACCCATAAATAATTATAATTAGGTGCTCCCGTACAAGTCACTCTAATCCTTCGAG
ACTCC
Found at i:171319 original size:102 final size:102
Alignment explanation
Indices: 171176--171528 Score: 363
Period size: 102 Copynumber: 3.5 Consensus size: 102
171166 ATTCTACGAA
* * * * * * *
171176 TGAAACTTAATATAGACTTACA-CTGGT-AAATTAAACTCTTAATTCCAACAATGGAAGTTAACA
1 TGAAACTTAACATAGACTTATATC-GGTGAAATT-AACACTTAATTCCAATAATGAAACTTATCA
* *
171239 TAGACTTACACCGGTGAAATTAAGACTTAA-TTCTAGTAG
64 TAGACTTACACTGGTGAAATTAACACTTAATTTC-AGTAG
* ** * *
171278 TGAAACTTAACATAGACTTATATCAGTGAAATTAACACTTAATTATAATAGTGAAACTTATTATA
1 TGAAACTTAACATAGACTTATATCGGTGAAATTAACACTTAATTCCAATAATGAAACTTATCATA
** ** * *
171343 GGGTTACACTAATGAAATTAACATTTAATTTCAGCAG
66 GACTTACACTGGTGAAATTAACACTTAATTTCAGTAG
* * *
171380 TAAAACTTAACATAGACTTATATCGGTGAAATTAACACTAAATTCCAGTAATGAAACTTATCATA
1 TGAAACTTAACATAGACTTATATCGGTGAAATTAACACTTAATTCCAATAATGAAACTTATCATA
* * * * *
171445 GACTTAAAATGGTTAAATTAACACATAATTTCAGTTG
66 GACTTACACTGGTGAAATTAACACTTAATTTCAGTAG
* * *
171482 TGGAACTTAACATAAACTTA-ATCCGGTGAAATTAACACTTGATTCCA
1 TGAAACTTAACATAGACTTATAT-CGGTGAAATTAACACTTAATTCCA
171529 CTAGTAAAGC
Statistics
Matches: 203, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
101 2 0.01
102 192 0.95
103 9 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (102 bp):
TGAAACTTAACATAGACTTATATCGGTGAAATTAACACTTAATTCCAATAATGAAACTTATCATA
GACTTACACTGGTGAAATTAACACTTAATTTCAGTAG
Found at i:171323 original size:25 final size:24
Alignment explanation
Indices: 171252--171333 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 24
171242 ACTTACACCG
* *
171252 GTGAAATTAAGACTTAATTCTAGTA
1 GTGAAATTAACACTTAATTATA-TA
171277 GTGAAACTTAACA--TAGACTTATATCA
1 GTGAAA-TTAACACTTA-A-TTATAT-A
171303 GTGAAATTAACACTTAATTATAATA
1 GTGAAATTAACACTTAATTAT-ATA
171328 GTGAAA
1 GTGAAA
171334 CTTATTATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 2 0.04
25 25 0.52
26 19 0.40
27 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (24 bp):
GTGAAATTAACACTTAATTATATA
Found at i:171542 original size:51 final size:50
Alignment explanation
Indices: 171160--171542 Score: 258
Period size: 51 Copynumber: 7.5 Consensus size: 50
171150 TTTAATTTAC
* * * *
171160 CACTTAATTCTACGAATGAAACTTAATATAGACTTACA-CTGGT-AAATTAAA
1 CACTTAATTCCACTAGTGAAACTTAACATAGACTTA-ATC-GGTGAAATT-AA
* * * * *
171211 CTCTTAATTCCAAC-AATGGAAGTTAACATAGACTTACACCGGTGAAATTAA
1 CACTTAATTCC-ACTAGTGAAACTTAACATAGACTTA-ATCGGTGAAATTAA
* * * *
171262 GACTTAATTCTAGTAGTGAAACTTAACATAGACTTATATCAGTGAAATTAA
1 CACTTAATTCCACTAGTGAAACTTAACATAGACTTA-ATCGGTGAAATTAA
** * ** ** **
171313 CACTTAATTATAATAGTGAAACTTATTATAGGGTTACA-CTAATGAAATTAA
1 CACTTAATTCCACTAGTGAAACTTAACATAGACTTA-ATC-GGTGAAATTAA
* * *
171364 CATTTAATTTCAGC-AGTAAAACTTAACATAGACTTATATCGGTGAAATTAA
1 CACTTAATTCCA-CTAGTGAAACTTAACATAGACTTA-ATCGGTGAAATTAA
* * * * *
171415 CACTAAATTCCAGTAATGAAACTTATCATAGACTTAAAAT-GGTTAAATTAA
1 CACTTAATTCCACTAGTGAAACTTAACATAGACTT--AATCGGTGAAATTAA
* * * * * *
171466 CACATAATTTCAGTTGTGGAACTTAACATAAACTTAATCCGGTGAAATTAA
1 CACTTAATTCCACTAGTGAAACTTAACATAGACTTAAT-CGGTGAAATTAA
*
171517 CACTTGATTCCACTAGT-AAAGCTTAA
1 CACTTAATTCCACTAGTGAAA-CTTAA
171543 AATTTCGTCT
Statistics
Matches: 260, Mismatches: 59, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
49 3 0.01
50 4 0.02
51 241 0.93
52 11 0.04
53 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (50 bp):
CACTTAATTCCACTAGTGAAACTTAACATAGACTTAATCGGTGAAATTAA
Found at i:172937 original size:20 final size:21
Alignment explanation
Indices: 172912--173004 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
172902 TTTTCCCAAT
*
172912 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
172932 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
172953 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
172973 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
172994 TCGCAATGCGA
1 TCGCAATGCGA
173005 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:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:172969 original size:41 final size:41
Alignment explanation
Indices: 172912--173004 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
172902 TTTTCCCAAT
172912 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
172953 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
172994 TCGCAATGCGA
1 TCGCAATGCGA
173005 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:173017 original size:41 final size:41
Alignment explanation
Indices: 172931--173065 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
172921 GAATAAGTAA
* *
172931 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
172972 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
173013 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
173054 TTCGCAACGCGA
1 ATCGCAACGCGA
173066 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:173018 original size:20 final size:19
Alignment explanation
Indices: 172993--173107 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
172983 AATTGGGAAA
*
172993 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
173013 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
173034 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
173054 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
173074 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
173094 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
173108 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:173635 original size:20 final size:20
Alignment explanation
Indices: 173581--173639 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
173571 GCGATTCTCT
**
173581 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
173601 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
173621 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
173640 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:174980 original size:18 final size:18
Alignment explanation
Indices: 174959--175003 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
174949 TCCACTTCGG
*
174959 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
174977 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
174995 GAGCCATCA
1 GAGCCATCA
175004 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:175510 original size:20 final size:20
Alignment explanation
Indices: 175485--175559 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
175475 TAGTTTACTT
* * *
175485 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGGCTA
175505 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
175525 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
175545 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
175560 AAAATCACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 6 0.12
20 45 0.88
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:175603 original size:32 final size:33
Alignment explanation
Indices: 175544--175634 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
175534 GGAAATGGCT
*
175544 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
175577 ATCGCAATGAGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
175609 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
175635 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:175729 original size:20 final size:19
Alignment explanation
Indices: 175695--175750 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
175685 TTACGATTTT
*
175695 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
175714 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
175734 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
175751 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:176736 original size:19 final size:19
Alignment explanation
Indices: 176714--176772 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
176704 GGAAATTACT
176714 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
176733 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
*
176747 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
176766 ATCGCAA
1 ATCGCAA
176773 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 2 0.06
17 3 0.09
18 2 0.06
19 15 0.47
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Done.