Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3568288 original size:60 final size:58
Alignment explanation
Indices: 3568165--3568344 Score: 161
Period size: 60 Copynumber: 3.0 Consensus size: 58
3568155 ATTCATCATA
* * *
3568165 CATCCTT-AATCTATGACTTTATTTTAAATTAGTCCCTAAA-TTTTAAAAAAATTCAATAT-
1 CATCCTTAAAT-TATGA-TTTATTTTAAATTAG-CCCTAAACTTTT-AAATATTTCAATTTC
3568224 CATCCTTAAATTATGATTATCATTTTAAATTAGCCCTCAAACTTTTAAATATTTC-ATTTC
1 CATCCTTAAATTATGATT-T-ATTTTAAATTAGCCCT-AAACTTTTAAATATTTCAATTTC
* ** * * *
3568284 CATCCCTAAATTATGAATCTTATACTAAATTAGTCCTTAAACTTTTAGATCTTTCAATTTC
1 CATCCTTAAATTATG-AT-TTATTTTAAATTAG-CCCTAAACTTTTAAATATTTCAATTTC
3568345 ATTCCCAGAT
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
58 2 0.02
59 20 0.20
60 64 0.63
61 15 0.15
62 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (58 bp):
CATCCTTAAATTATGATTTATTTTAAATTAGCCCTAAACTTTTAAATATTTCAATTTC
Found at i:3569239 original size:26 final size:26
Alignment explanation
Indices: 3569210--3569288 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
3569200 ATATTTACAC
3569210 TTATATATGAATCATATCAATTTAAA
1 TTATATATGAATCATATCAATTTAAA
**
3569236 TTATA-A--AAT-ATAAAAAATATT--A
1 TTATATATGAATCAT-ATCAAT-TTAAA
3569258 TTATATATGAA-CTATATCAATTTAAA
1 TTATATATGAATC-ATATCAATTTAAA
3569284 TTATA
1 TTATA
3569289 ACAAAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 8 0.20
23 8 0.20
24 4 0.10
25 7 0.17
26 13 0.32
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (26 bp):
TTATATATGAATCATATCAATTTAAA
Found at i:3569296 original size:43 final size:46
Alignment explanation
Indices: 3569210--3569305 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 46
3569200 ATATTTACAC
*
3569210 TTATATATGAATCATATCAATTTAAATTATAAAATATAAAAAATATTA
1 TTATATATGAATCATATCAATTTAAATTAT--AATATAAAAAATATAA
*
3569258 TTATATATGAA-CTATATCAATTTAAATTAT-A-A-CAAAAATATAA
1 TTATATATGAATC-ATATCAATTTAAATTATAATATAAAAAATATAA
3569301 TTATA
1 TTATA
3569306 ATAAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
43 14 0.31
44 1 0.02
45 1 0.02
47 1 0.02
48 28 0.62
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (46 bp):
TTATATATGAATCATATCAATTTAAATTATAATATAAAAAATATAA
Found at i:3569326 original size:17 final size:17
Alignment explanation
Indices: 3569282--3569316 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3569272 TATCAATTTA
*
3569282 AATTATAACAAAAATAT
1 AATTATAATAAAAATAT
3569299 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
3569316 A
1 A
3569317 TTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTATAATAAAAATAT
Found at i:3569411 original size:14 final size:14
Alignment explanation
Indices: 3569379--3569425 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
3569369 ATTTTTAAAT
*
3569379 AATTAAAATAAAT-
1 AATTAAAATTAATA
3569392 AATTAAAATTAATA
1 AATTAAAATTAATA
3569406 AATTAAAATTAATA
1 AATTAAAATTAATA
3569420 AATTAA
1 AATTAA
3569426 TTTTTAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 12 0.38
14 20 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAAATTAATA
Found at i:3571212 original size:16 final size:16
Alignment explanation
Indices: 3571187--3571229 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3571177 CATTTAATAA
3571187 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
3571203 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
*
3571219 ATAAACAAACA
1 ATAAACGAACA
3571230 TAAACGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:3571225 original size:22 final size:20
Alignment explanation
Indices: 3571183--3571235 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
3571173 CGTTCATTTA
*
3571183 ATAAATAAACGAACACGAAC
1 ATAAATAAACGAACACAAAC
*
3571203 ATAAATGAACACGAACATAAAC
1 ATAAAT-AA-ACGAACACAAAC
3571225 A-AACATAAACG
1 ATAA-ATAAACG
3571236 TTGGAGAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 9 0.32
21 6 0.21
22 13 0.46
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.11
Consensus pattern (20 bp):
ATAAATAAACGAACACAAAC
Found at i:3572318 original size:14 final size:14
Alignment explanation
Indices: 3572301--3572342 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
3572291 GATTGGGTTA
* *
3572301 AACATAAATGAATG
1 AACATAAACGAACG
3572315 AACATAAACGAACG
1 AACATAAACGAACG
*
3572329 AACATAACCGAACG
1 AACATAAACGAACG
3572343 TTCACGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:3575155 original size:31 final size:31
Alignment explanation
Indices: 3575117--3575199 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
3575107 ATTTTAAAAT
3575117 ATTAATAATTTAAGTACTAAAACATATTAAA
1 ATTAATAATTTAAGTACTAAAACATATTAAA
* *
3575148 ATTAATAATTTAAATAATAAAACATATTAAA
1 ATTAATAATTTAAGTACTAAAACATATTAAA
*
3575179 ATTAATAATTTTAGTACTAAA
1 ATTAATAATTTAAGTACTAAA
3575200 CACGTCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.37
Consensus pattern (31 bp):
ATTAATAATTTAAGTACTAAAACATATTAAA
Found at i:3575186 original size:19 final size:19
Alignment explanation
Indices: 3575134--3575186 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
3575124 ATTTAAGTAC
3575134 TAAAACATATTAAAATTAA
1 TAAAACATATTAAAATTAA
3575153 T---A-AT-TT-AAA-TAA
1 TAAAACATATTAAAATTAA
3575165 TAAAACATATTAAAATTAA
1 TAAAACATATTAAAATTAA
3575184 TAA
1 TAA
3575187 TTTTAGTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
12 4 0.15
13 3 0.11
14 2 0.07
15 3 0.11
16 3 0.11
17 2 0.07
18 3 0.11
19 7 0.26
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAACATATTAAAATTAA
Found at i:3576492 original size:2 final size:2
Alignment explanation
Indices: 3576485--3576510 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3576475 AGTAACTTTG
3576485 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
3576511 TAAATCAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3583628 original size:14 final size:14
Alignment explanation
Indices: 3583605--3583643 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
3583595 TTAGCTTCTG
3583605 CAAGTTCTTTGGAT
1 CAAGTTCTTTGGAT
*
3583619 CAATTTCTTTGGAT
1 CAAGTTCTTTGGAT
3583633 CAAGTTCTTTG
1 CAAGTTCTTTG
3583644 TTCCTCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (14 bp):
CAAGTTCTTTGGAT
Found at i:3590929 original size:21 final size:22
Alignment explanation
Indices: 3590896--3590943 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3590886 TTTATATCCG
*
3590896 ATTCTTTAAATTTTCTCT-AATT
1 ATTCTTTAAATTTT-TATGAATT
*
3590918 ATTCTTT-GATTTTTATGAATT
1 ATTCTTTAAATTTTTATGAATT
3590939 ATTCT
1 ATTCT
3590944 AATGTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTCTTTAAATTTTTATGAATT
Found at i:3600074 original size:31 final size:31
Alignment explanation
Indices: 3600039--3600099 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3600029 TTATGGTTAC
3600039 TTATGTTA-CTATTTTATTAAGTTTAGATCAT
1 TTATGTTATC-ATTTTATTAAGTTTAGATCAT
* *
3600070 TTATGTTATCGTTTTATTAAGTTTTGATCA
1 TTATGTTATCATTTTATTAAGTTTAGATCA
3600100 CTTAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (31 bp):
TTATGTTATCATTTTATTAAGTTTAGATCAT
Found at i:3604242 original size:65 final size:63
Alignment explanation
Indices: 3604172--3604292 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 63
3604162 GGGAAGACTT
*
3604172 AGTGCATCGGTACACTAGG-GGTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTG
1 AGTGCATCGATACA-T-GGCGGTGCATCGATGCATAAAATACATTCAATG-TTCAAATAAGCCTG
3604236 G
63 G
* * * *
3604237 AGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAAT
1 AGTGCATCGATACATGG-CGGTGCATCGATGCATAAAATACATTCAATGTTCAAAT
3604293 TATTTAGGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 2 0.04
64 8 0.16
65 39 0.80
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATACATGGCGGTGCATCGATGCATAAAATACATTCAATGTTCAAATAAGCCTGG
Found at i:3604324 original size:64 final size:65
Alignment explanation
Indices: 3604192--3604347 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 65
3604182 TACACTAGGG
* * *
3604192 GTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
* **
3604257 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATGC-C
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCT-GGAGTGCATCGATGCATGCTC
3604319 TT
65 -T
* * * *
3604321 GTGCAGCGGTACACAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
3604348 AATTCAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 50 0.63
65 27 0.34
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
Found at i:3604354 original size:64 final size:64
Alignment explanation
Indices: 3604235--3604360 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
3604225 AAATAAGCCT
* * * * **
3604235 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
* *
3604299 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATT
1 GGAGTGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT
3604361 CAAGGGCGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
Found at i:3604372 original size:64 final size:64
Alignment explanation
Indices: 3604235--3604379 Score: 150
Period size: 64 Copynumber: 2.3 Consensus size: 64
3604225 AAATAAGCCT
* * * * * ** *
3604235 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
* * *
3604299 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATTCA
1 GGAGCGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT-A
3604363 A
64 A
*
3604364 GG-GCGCATCAATGCAT
1 GGAGCGCATCGATGCAT
3604380 TATATAGTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 64 0.94
65 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
Found at i:3605914 original size:21 final size:21
Alignment explanation
Indices: 3605888--3605928 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3605878 ATTAGCGATG
*
3605888 GTTTCCGAATTGATGAAAATA
1 GTTTCCAAATTGATGAAAATA
3605909 GTTTCCAAATTGATGAAAAT
1 GTTTCCAAATTGATGAAAAT
3605929 GACTTCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
GTTTCCAAATTGATGAAAATA
Found at i:3606995 original size:20 final size:21
Alignment explanation
Indices: 3606966--3607023 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
3606956 AAAACCTGAT
*
3606966 GAGTGTATCGATGCACAGT-A
1 GAGTGCATCGATGCACAGTAA
*
3606986 GAGTGCATCGATGCACATTCAA
1 GAGTGCATCGATGCACAGT-AA
*
3607008 GAGTGCATCGGTGCAC
1 GAGTGCATCGATGCAC
3607024 CTTCAAGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (21 bp):
GAGTGCATCGATGCACAGTAA
Found at i:3607013 original size:22 final size:22
Alignment explanation
Indices: 3606966--3607067 Score: 104
Period size: 22 Copynumber: 4.7 Consensus size: 22
3606956 AAAACCTGAT
* *
3606966 GAGTGTATCGATGCACAGT--A
1 GAGTGCATCGATGCACATTCAA
3606986 GAGTGCATCGATGCACATTCAA
1 GAGTGCATCGATGCACATTCAA
* *
3607008 GAGTGCATCGGTGCACCTTCAA
1 GAGTGCATCGATGCACATTCAA
* *
3607030 G-GTGTATCGATGCATATTCAA
1 GAGTGCATCGATGCACATTCAA
3607051 -AGGATGCATCGATGCAC
1 GA-G-TGCATCGATGCAC
3607068 TGTCTAGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.25
21 16 0.24
22 23 0.34
23 11 0.16
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (22 bp):
GAGTGCATCGATGCACATTCAA
Found at i:3607049 original size:43 final size:43
Alignment explanation
Indices: 3606972--3607087 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
3606962 TGATGAGTGT
* * *
3606972 ATCGATGCACAGT-AGAGTGCATCGATGCACATTC-AA-GAGTGC
1 ATCGATGCACTGTCA-AGTGTATCGATGCATATTCAAAGGA-TGC
*
3607014 ATCGGTGCACCT-TCAAGGTGTATCGATGCATATTCAAAGGATGC
1 ATCGATGCA-CTGTCAA-GTGTATCGATGCATATTCAAAGGATGC
*
3607058 ATCGATGCACTGTCTAGTGTATCGATGCAT
1 ATCGATGCACTGTCAAGTGTATCGATGCAT
3607088 TATGCACTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 10 0.16
43 34 0.55
44 16 0.26
45 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
ATCGATGCACTGTCAAGTGTATCGATGCATATTCAAAGGATGC
Found at i:3612915 original size:45 final size:47
Alignment explanation
Indices: 3612815--3612925 Score: 156
Period size: 46 Copynumber: 2.4 Consensus size: 47
3612805 CATCGGTACA
*
3612815 CTAGGGGTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGC
1 CTAGGAGTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGC
* * *
3612862 CT-GGAGTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-T
1 CTAGGAGTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGC
*
3612906 TTAGGAGTGCATCGATGCAT
1 CTAGGAGTGCATCGATGCAT
3612926 GCCTTGTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.02
45 25 0.43
46 30 0.52
47 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (47 bp):
CTAGGAGTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGC
Found at i:3612938 original size:64 final size:64
Alignment explanation
Indices: 3612870--3612989 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
3612860 GCCTGGAGTG
* * ** *
3612870 CATCGATGCATAAAATGCATTCGATGTTCAAATTATT-TAGGAGTGCATCGATGCATGCCTTGTT
1 CATCGATACACAAAATGCATTCGAAATTCAAATTATTCAAGG-GTGCATCGATGCATGCCTTGTT
* *
3612934 CATCGGTACACAAAATGCATTCGAAATTCAATTTATTCAAGGGTGCATCGATGCAT
1 CATCGATACACAAAATGCATTCGAAATTCAAATTATTCAAGGGTGCATCGATGCAT
3612990 TATATAGTGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
64 45 0.94
65 3 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (64 bp):
CATCGATACACAAAATGCATTCGAAATTCAAATTATTCAAGGGTGCATCGATGCATGCCTTGTT
Found at i:3619394 original size:21 final size:21
Alignment explanation
Indices: 3619365--3619417 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3619355 ATTCTGACTA
3619365 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3619386 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3619407 TCGCAATGCGA
1 TCGCATTGCGA
3619418 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3619432 original size:20 final size:20
Alignment explanation
Indices: 3619407--3619517 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
3619397 TTTTCCTAAT
3619407 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
3619427 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
3619448 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
3619468 TCGCAATGC-AATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3619487 TCGCAATGCGAATAGGTAAA
1 TCGCAATGCGAATACGTAAA
3619507 TCGCAATGCGA
1 TCGCAATGCGA
3619518 TTTACATAGC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 18 0.23
20 45 0.58
21 15 0.19
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3619506 original size:39 final size:41
Alignment explanation
Indices: 3619407--3619522 Score: 155
Period size: 39 Copynumber: 2.9 Consensus size: 41
3619397 TTTTCCTAAT
* **
3619407 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGAAAA
* *
3619448 TCGCAATGCGATTACGTAAATCGCAATGC-AA-TACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGAAAA
* *
3619487 TCGCAATGCGAATAGGTAAATCGCAATGCGATTTAC
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAC
3619523 ATAGCGCCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
39 32 0.49
40 3 0.05
41 30 0.46
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGAAAA
Found at i:3619720 original size:22 final size:22
Alignment explanation
Indices: 3619695--3619756 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
3619685 GGCGACATCC
3619695 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
3619717 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3619735 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3619757 TTCATGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3620180 original size:20 final size:20
Alignment explanation
Indices: 3620093--3620181 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
3620083 CGATTCTGTC
*
3620093 GTTGTGATTTTCA-TTTCGT
1 GTTGCGATTTTCATTTTCGT
** ** *
3620112 GTTGCGATAGTCAAATTCGC
1 GTTGCGATTTTCATTTTCGT
**
3620132 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
3620152 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
3620172 GTTGCGATTT
1 GTTGCGATTT
3620182 AAAGTTTCAG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 10 0.17
20 49 0.83
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:3620189 original size:20 final size:20
Alignment explanation
Indices: 3620146--3620189 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3620136 CGATAGTCAT
** *
3620146 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
3620166 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
3620186 TTTC
1 TTTC
3620190 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:3622087 original size:20 final size:20
Alignment explanation
Indices: 3622058--3622161 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
3622048 AGAATAGTTT
*
3622058 ACTATTGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3622078 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3622098 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
3622114 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
3622132 ACTATCGCAATGCTAATTTG
1 ACTATCGCAATGCGAAAATG
3622152 ACTATCGCAA
1 ACTATCGCAA
3622162 CGAAAGAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 4 0.06
18 4 0.06
20 52 0.73
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:3622154 original size:54 final size:54
Alignment explanation
Indices: 3622064--3622182 Score: 193
Period size: 54 Copynumber: 2.2 Consensus size: 54
3622054 GTTTACTATT
*
3622064 GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATC
1 GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
* * **
3622118 GCAATGCGAAAATGACTATCGCAATGCTAATTTGACTATCGCAACGAAAGAATC
1 GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
3622172 GCAATGCGAAA
1 GCAATGCGAAA
3622183 TGAAAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (54 bp):
GCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATC
Found at i:3622254 original size:20 final size:20
Alignment explanation
Indices: 3622206--3622254 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3622196 GTGATTCTCT
*
3622206 CGTTGCGACAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
3622226 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3622246 CGTTGCGAT
1 CGTTGCGAT
3622255 TTTGTTGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3622308 original size:33 final size:33
Alignment explanation
Indices: 3622228--3622321 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 33
3622218 CAAATTCGCA
* * * *
3622228 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGCATTGCGATTCTCTCG
* ** *
3622262 TTACGATTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
*
3622295 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCA-TTTCGCATTGCGAT
3622322 AGTCATTTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
33 25 0.54
34 21 0.46
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
Found at i:3622318 original size:20 final size:20
Alignment explanation
Indices: 3622293--3622337 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3622283 GCGATTCTCT
3622293 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
3622313 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
3622333 CGTTG
1 CGTTG
3622338 TGATTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3622916 original size:21 final size:21
Alignment explanation
Indices: 3622825--3622923 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
3622815 GACTCACCTG
* *
3622825 TCATCATTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
3622847 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3622867 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3622888 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
3622909 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
3622924 TCCTTCCCAA
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3622932 original size:42 final size:42
Alignment explanation
Indices: 3622822--3622932 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
3622812 CCCGACTCAC
* * *
3622822 CTGTCATCATTCAAGAGG-CCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGGTCCTTCCC-ACCGTTCAAGAGGCCA
* ** *
3622864 CTATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGGT-CCTTCCCACCGTTCAAGAGGCCA
* *
3622906 CTGTCATCGTTGAAGAGGTCCTTCCCA
1 CTGTCATCATTCAAGAGGTCCTTCCCA
3622933 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.02
42 46 0.85
43 7 0.13
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGGTCCTTCCCACCGTTCAAGAGGCCA
Found at i:3624292 original size:14 final size:14
Alignment explanation
Indices: 3624273--3624322 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
3624263 ATTGTTTAAT
3624273 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
3624287 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* * *
3624301 TTATTTGTAAATGT
1 TGATTTGTAAAAGA
3624315 TGATTTGT
1 TGATTTGT
3624323 TTAATTGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3624462 original size:34 final size:34
Alignment explanation
Indices: 3624424--3624519 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
3624414 AAAACAGACT
* ** *
3624424 ATCGCAACGCGGAAATGACTATTGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
3624458 ATCGCAATGC-GAAATGAAAATCGTAACGAGTGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
3624491 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
3624520 CGAAACTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:3624593 original size:20 final size:20
Alignment explanation
Indices: 3624568--3624656 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
3624558 GCGATTCACT
*
3624568 CGTTGCGATTTTCATTTCCG
1 CGTTGCGATATTCATTTCCG
* * *
3624588 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATATTCATTTCCG
* *
3624608 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATATTCATTTCCG
* *
3624628 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATATTCAT-TTCCG
3624648 CGTTGCGAT
1 CGTTGCGAT
3624657 TTCCGTGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATATTCATTTCCG
Found at i:3624612 original size:40 final size:40
Alignment explanation
Indices: 3624568--3624658 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
3624558 GCGATTCACT
3624568 CGTTGCGATTTTCATTTCCGCGTTGCGATAGTCA-ATTCTG
1 CGTTGCGATTTTCATTTCCGCGTTGCGATAGTCATATTC-G
* ** *
3624608 CGTTGCAATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATTTTCATTTCCGCGTTGCGATAGTCATATTCG
3624648 CGTTGCGATTT
1 CGTTGCGATTT
3624659 CCGTGTTGCG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 39 0.91
41 4 0.09
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:3627111 original size:24 final size:24
Alignment explanation
Indices: 3627077--3627130 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3627067 CTGAAAAATC
3627077 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3627101 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3627125 ATCAAA
1 ATCAAA
3627131 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3627144 original size:24 final size:24
Alignment explanation
Indices: 3627077--3627144 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3627067 CTGAAAAATC
* * *
3627077 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3627101 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3627125 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3627145 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3628005 original size:20 final size:20
Alignment explanation
Indices: 3627993--3628118 Score: 125
Period size: 20 Copynumber: 6.2 Consensus size: 20
3627983 AGAATCTCGA
3627993 TGCGATTTACAGATTCGCAT
1 TGCGATTTACAGATTCGCAT
3628013 TGCGATTTAC-GTATTCGCAT
1 TGCGATTTACAG-ATTCGCAT
*
3628033 TGCGATTTA-TGTATTCGCAT
1 TGCGATTTACAG-ATTCGCAT
* *
3628053 TACGATTTAC-GTAATCGCAT
1 TGCGATTTACAG-ATTCGCAT
* * *
3628073 TGCGATTTTCCAAATTCGCGT
1 TGCGA-TTTACAGATTCGCAT
3628094 TGCGATTTAC-GTATTCGCAT
1 TGCGATTTACAG-ATTCGCAT
3628114 TGCGA
1 TGCGA
3628119 ATTAGGAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.01
20 74 0.82
21 15 0.17
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TGCGATTTACAGATTCGCAT
Found at i:3628037 original size:40 final size:40
Alignment explanation
Indices: 3627993--3628118 Score: 173
Period size: 40 Copynumber: 3.1 Consensus size: 40
3627983 AGAATCTCGA
3627993 TGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCAT
1 TGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCAT
* * *
3628033 TGCGATTTA-TGTATTCGCATTACGATTTACGTAATCGCAT
1 TGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCAT
* * *
3628073 TGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCAT
1 TGCGA-TTTACAGATTCGCATTGCGATTTACGTATTCGCAT
3628114 TGCGA
1 TGCGA
3628119 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 40 0.54
41 33 0.45
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCAT
Found at i:3628139 original size:21 final size:21
Alignment explanation
Indices: 3628115--3628160 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3628105 TATTCGCATT
3628115 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
3628136 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3628157 GCGA
1 GCGA
3628161 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3628442 original size:18 final size:21
Alignment explanation
Indices: 3628396--3628436 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3628386 GAAATTAATA
3628396 ATAAATAAATTATTTTCAATTT
1 ATAAATAAATTA-TTTCAATTT
3628418 ATAAATAAATTA-TTCAATT
1 ATAAATAAATTATTTCAATT
3628437 AAAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAATAAATTATTTCAATTT
Found at i:3629017 original size:37 final size:37
Alignment explanation
Indices: 3628919--3629017 Score: 162
Period size: 37 Copynumber: 2.7 Consensus size: 37
3628909 TTCGGGTTGA
* * * *
3628919 GTTTTTTATAGTAGAAGTTTGGGTCAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTTAGATCTAGTCAG
3628956 GTTTTTCAGAGTAGAAGTTCGGGTTAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTTAGATCTAGTCAG
3628993 GTTTTTCAGAGTAGAAGTTCGGGTT
1 GTTTTTCAGAGTAGAAGTTCGGGTT
3629018 GAGTTCGGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.23, C:0.09, G:0.29, T:0.38
Consensus pattern (37 bp):
GTTTTTCAGAGTAGAAGTTCGGGTTAGATCTAGTCAG
Found at i:3640968 original size:21 final size:21
Alignment explanation
Indices: 3640944--3640987 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3640934 ACTTATTCAG
3640944 ACTATAAACATTTCCTTTGCC
1 ACTATAAACATTTCCTTTGCC
3640965 ACTATAAACATTTCCTTTGCC
1 ACTATAAACATTTCCTTTGCC
3640986 AC
1 AC
3640988 GACATTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (21 bp):
ACTATAAACATTTCCTTTGCC
Found at i:3643424 original size:30 final size:29
Alignment explanation
Indices: 3643367--3643424 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3643357 GTATGGTTTG
*
3643367 AAAATAAATGAAAGTTTAGATACTAAAAT
1 AAAATAAATGAAAGTTTACATACTAAAAT
*
3643396 AAAATAAAATTAATAGTTTACA-ACTAAAA
1 AAAAT-AAATGAA-AGTTTACATACTAAAA
3643425 GTGTAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 13 0.52
31 7 0.28
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (29 bp):
AAAATAAATGAAAGTTTACATACTAAAAT
Found at i:3644385 original size:54 final size:55
Alignment explanation
Indices: 3644237--3644430 Score: 216
Period size: 55 Copynumber: 3.6 Consensus size: 55
3644227 CCTGTTTTTT
* * * * * * *
3644237 AGATGTATTCGATTCCCGGATCTCTATTTTTATGCTTCTTAATAGCAACAACTGA
1 AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
3644292 TAGATATACTCGATTTTGGG-CCCCTATTTTTATGCTTATTAATGGCAACAACTG-
1 -AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
** *
3644346 AGATATATTCGATTTCGGGACCCCTATTTTTATAATTATTAATGG-AACAATTGA
1 AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
* *
3644400 TACATATATTCGA-TTCGGGGCCCCTATTTTT
1 -AGATATATTCGATTTCGGGACCCCTATTTTT
3644431 TGGGGCCGTT
Statistics
Matches: 119, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
53 24 0.20
54 40 0.34
55 41 0.34
56 14 0.12
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (55 bp):
AGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
Found at i:3669584 original size:19 final size:21
Alignment explanation
Indices: 3669539--3669586 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3669529 TGTACTATAC
*
3669539 TTGAAATT-TATGTTAGAGTG
1 TTGAAATTGTATGTTAGAATG
3669559 TTGAAATTGT-TGTTAGAATG
1 TTGAAATTGTATGTTAGAATG
3669579 -TGAAATTG
1 TTGAAATTG
3669587 GGTTATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (21 bp):
TTGAAATTGTATGTTAGAATG
Found at i:3670580 original size:86 final size:88
Alignment explanation
Indices: 3670473--3670641 Score: 245
Period size: 91 Copynumber: 1.9 Consensus size: 88
3670463 CAGAGGTGGT
*
3670473 TGGCCGGAGGGGCGACAGGGATGGCTTGGTTT-GG-GG-TTTCACAAGGGGTTTAGTTATGGGTA
1 TGGCCAGAGGGGCGACAGGGATGGCTTGGTTTGGGTGGATTTCACAA-GGGTTTAGTTATGGGTA
3670535 TTTTCATACCTGAACCAAATTGGC
65 TTTTCATACCTGAACCAAATTGGC
* *
3670559 TGGCCAGAGGGGCGATAGGGATGGCTTGGTTTGGGGTTAGGATTTCATAAGGGTTTAGTTATGGG
1 TGGCCAGAGGGGCGACAGGGATGGCTTGGTTT-GGG-T-GGATTTCACAAGGGTTTAGTTATGGG
*
3670624 TATTTTCATACTTGAACC
63 TATTTTCATACCTGAACC
3670642 CAATATATAT
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
86 30 0.41
88 2 0.03
91 34 0.47
92 7 0.10
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (88 bp):
TGGCCAGAGGGGCGACAGGGATGGCTTGGTTTGGGTGGATTTCACAAGGGTTTAGTTATGGGTAT
TTTCATACCTGAACCAAATTGGC
Found at i:3670651 original size:2 final size:2
Alignment explanation
Indices: 3670644--3670691 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3670634 CTTGAACCCA
3670644 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
3670686 A- AT AT A
1 AT AT AT A
3670692 AATAAAGCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3678521 original size:11 final size:12
Alignment explanation
Indices: 3678492--3678526 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3678482 TTAGGTGCTG
3678492 GAAACAAGATAA
1 GAAACAAGATAA
*
3678504 GAAACAAGATTA
1 GAAACAAGATAA
3678516 -AAACAAGATAA
1 GAAACAAGATAA
3678527 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:3680758 original size:23 final size:21
Alignment explanation
Indices: 3680715--3680758 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
3680705 AGAAATTATC
**
3680715 GAAGAAAAGGGGATTTTAGAA
1 GAAGAAAAGGGGATTACAGAA
3680736 GAAGAAGAAGGGAGATTACAGAA
1 GAAGAA-AAGGG-GATTACAGAA
3680759 AAAGGATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.34, T:0.14
Consensus pattern (21 bp):
GAAGAAAAGGGGATTACAGAA
Found at i:3681120 original size:21 final size:21
Alignment explanation
Indices: 3681094--3681155 Score: 124
Period size: 21 Copynumber: 3.0 Consensus size: 21
3681084 ATCCTATTCA
3681094 TTCCTCCGTTCTTCATCTTCG
1 TTCCTCCGTTCTTCATCTTCG
3681115 TTCCTCCGTTCTTCATCTTCG
1 TTCCTCCGTTCTTCATCTTCG
3681136 TTCCTCCGTTCTTCATCTTC
1 TTCCTCCGTTCTTCATCTTC
3681156 TTCTCCAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.05, C:0.39, G:0.08, T:0.48
Consensus pattern (21 bp):
TTCCTCCGTTCTTCATCTTCG
Found at i:3686325 original size:21 final size:19
Alignment explanation
Indices: 3686298--3686363 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 19
3686288 CTGTTCGTTC
3686298 CTCCATTCTTCATCTTCATT
1 CTCCATTCTTCATCTTC-TT
3686318 CATCCATTCTTCATCTTCGTT
1 C-TCCATTCTTCATCTTC-TT
*
3686339 CCTCCGTTCTTCATCTTCTT
1 -CTCCATTCTTCATCTTCTT
3686359 CTCCA
1 CTCCA
3686364 ACTATAACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
21 33 0.80
22 1 0.02
ACGTcount: A:0.12, C:0.38, G:0.03, T:0.47
Consensus pattern (19 bp):
CTCCATTCTTCATCTTCTT
Found at i:3687944 original size:22 final size:23
Alignment explanation
Indices: 3687913--3687956 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3687903 TAGTACCTAA
3687913 CCTACAAATTTATACAAATAATC
1 CCTACAAATTTATACAAATAATC
*
3687936 CCTA-AAATTTATACAATTAAT
1 CCTACAAATTTATACAAATAAT
3687957 TATTTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (23 bp):
CCTACAAATTTATACAAATAATC
Found at i:3690325 original size:2 final size:2
Alignment explanation
Indices: 3690318--3690376 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
3690308 CCAATTGATG
3690318 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
3690360 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3690377 GCTTAAGCTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3692517 original size:23 final size:22
Alignment explanation
Indices: 3692463--3692546 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
3692453 TAGAACCTCC
* *
3692463 AGGGGGTATCGATTCCCCTACA
1 AGGGGGAATCGATTCCCCTTCA
3692485 AGGGGGAATCGATTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
* *
3692508 ATGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
3692530 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
3692547 TCTACACCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 34 0.63
23 20 0.37
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:3703659 original size:20 final size:20
Alignment explanation
Indices: 3703634--3703703 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
3703624 GGATTTAGGA
3703634 AATATCAATATTGTTCTTCC
1 AATATCAATATTGTTCTTCC
* * * *
3703654 AATATCGACATTGTTTTTTC
1 AATATCAATATTGTTCTTCC
* * *
3703674 AGTATCGATATTATTCTTCC
1 AATATCAATATTGTTCTTCC
3703694 AATATCAATA
1 AATATCAATA
3703704 GTCCTACCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.44
Consensus pattern (20 bp):
AATATCAATATTGTTCTTCC
Found at i:3708267 original size:121 final size:122
Alignment explanation
Indices: 3708044--3708279 Score: 393
Period size: 121 Copynumber: 1.9 Consensus size: 122
3708034 ACGTTAGGGG
*
3708044 TATTTTAGTTGCATTATGCCTAAAAAATCGGTATATCCCACCTCAAACCTTAAGAGTAAGAAAAA
1 TATTTTAGTTGCATTATGCCTAAAAAATCGGTATACCCCACCTCAAACCTTAAGAGTAAGAAAAA
* *
3708109 ACATAATGCCAAGATTCACTTCTAATGTTTTACAAAATATTTATTTTGATCCCTATT
66 ACATAATGCCAAGATTCACTTCTAATGTTTGACAAAATAGTTATTTTGATCCCTATT
* *
3708166 TATTTT-GTTGCATTATGCTTAAAAAATTGGTATACCCCACCTCAAACCTTAAGAGTAAGAAAAA
1 TATTTTAGTTGCATTATGCCTAAAAAATCGGTATACCCCACCTCAAACCTTAAGAGTAAGAAAAA
* * *
3708230 ACATAATGTCAAGGTTCACTTCTAATGTTTGATAAAATAGTTATTTTGAT
66 ACATAATGCCAAGATTCACTTCTAATGTTTGACAAAATAGTTATTTTGAT
3708280 ACATATTTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
121 100 0.94
122 6 0.06
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (122 bp):
TATTTTAGTTGCATTATGCCTAAAAAATCGGTATACCCCACCTCAAACCTTAAGAGTAAGAAAAA
ACATAATGCCAAGATTCACTTCTAATGTTTGACAAAATAGTTATTTTGATCCCTATT
Found at i:3709241 original size:13 final size:13
Alignment explanation
Indices: 3709223--3709247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3709213 ACAGACGCGT
3709223 ATATGAAGACTGC
1 ATATGAAGACTGC
3709236 ATATGAAGACTG
1 ATATGAAGACTG
3709248 TTCAACTATG
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:3709866 original size:2 final size:2
Alignment explanation
Indices: 3709859--3709888 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3709849 TTTCTAATTT
3709859 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
3709889 AATTTAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3714056 original size:18 final size:18
Alignment explanation
Indices: 3714035--3714075 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3714025 GGTGCAAAAG
3714035 ATCATGATCATGACCACA
1 ATCATGATCATGACCACA
* *
3714053 ATCATGATCATGGCCACG
1 ATCATGATCATGACCACA
3714071 ATCAT
1 ATCAT
3714076 CACCATCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (18 bp):
ATCATGATCATGACCACA
Found at i:3714101 original size:30 final size:30
Alignment explanation
Indices: 3714040--3714101 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3714030 AAAAGATCAT
* * **
3714040 GATCATGACCACAATCATGATCATGGCCAC
1 GATCATCACCACAATCATCATCATGAACAC
3714070 GATCATCACCATC-ATCATCATCATGAACAC
1 GATCATCACCA-CAATCATCATCATGAACAC
3714100 GA
1 GA
3714102 CCATAAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (30 bp):
GATCATCACCACAATCATCATCATGAACAC
Found at i:3719798 original size:15 final size:16
Alignment explanation
Indices: 3719770--3719801 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3719760 AAAATCTTTC
3719770 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
3719786 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
3719801 T
1 T
3719802 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:3720574 original size:16 final size:16
Alignment explanation
Indices: 3720550--3720583 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3720540 TATCGCCGAC
*
3720550 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3720566 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3720582 CG
1 CG
3720584 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:3724939 original size:12 final size:12
Alignment explanation
Indices: 3724922--3724948 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3724912 ACCGGCAATG
3724922 TCACCAACATTA
1 TCACCAACATTA
3724934 TCACCAACATTA
1 TCACCAACATTA
3724946 TCA
1 TCA
3724949 GCAATGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (12 bp):
TCACCAACATTA
Found at i:3729030 original size:3 final size:3
Alignment explanation
Indices: 3729022--3729048 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3729012 CTCCAACAAT
3729022 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3729049 AATTCCACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3735790 original size:9 final size:10
Alignment explanation
Indices: 3735774--3735805 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
3735764 GTTTGTCATA
3735774 ATTATATGTG
1 ATTATATGTG
3735784 A-TATATGTG
1 ATTATATGTG
3735793 ATTATATGT-
1 ATTATATGTG
3735802 ATTA
1 ATTA
3735806 CATTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (10 bp):
ATTATATGTG
Found at i:3735989 original size:2 final size:2
Alignment explanation
Indices: 3735984--3736097 Score: 228
Period size: 2 Copynumber: 57.0 Consensus size: 2
3735974 TGATATATTA
3735984 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3736026 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3736068 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3736098 AACATAAGAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 112 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3736874 original size:16 final size:15
Alignment explanation
Indices: 3736831--3736875 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
3736821 TAAGTGAACC
3736831 ATGTGTTTATATGTAT
1 ATGTGTTTATATG-AT
*
3736847 ATGT-TATATATGAT
1 ATGTGTTTATATGAT
3736861 ATGTGATTTATATGA
1 ATGTG-TTTATATGA
3736876 CAATAAGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (15 bp):
ATGTGTTTATATGAT
Found at i:3737169 original size:23 final size:23
Alignment explanation
Indices: 3737137--3737198 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3737127 ACCTTATATA
*
3737137 GCACTTCGGTGCATTTTTACACG
1 GCACTTCGGTGCATTTCTACACG
* * **
3737160 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACACG
3737183 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
3737199 ATATGAGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACACG
Found at i:3741323 original size:9 final size:10
Alignment explanation
Indices: 3741307--3741338 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
3741297 GTTTGTCATA
3741307 ATTATATGTG
1 ATTATATGTG
3741317 A-TATATGTG
1 ATTATATGTG
3741326 ATTATATGT-
1 ATTATATGTG
3741335 ATTA
1 ATTA
3741339 CATTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (10 bp):
ATTATATGTG
Found at i:3741516 original size:2 final size:2
Alignment explanation
Indices: 3741509--3741554 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3741499 TGAATCATTG
* *
3741509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3741551 AT AT
1 AT AT
3741555 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3741559 original size:2 final size:2
Alignment explanation
Indices: 3741554--3741583 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3741544 TGTATGTATA
3741554 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3741584 AACATAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3742634 original size:23 final size:23
Alignment explanation
Indices: 3742602--3742669 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3742592 GGGACAACCT
*
3742602 TATATAGCACTTCGGTGCATTTC
1 TATATGGCACTTCGGTGCATTTC
* *
3742625 TATATGGCACTACGGTGCAATTC
1 TATATGGCACTTCGGTGCATTTC
**
3742648 TACGTGGCACTTCGGTGCATTT
1 TATATGGCACTTCGGTGCATTT
3742670 ATACGAGCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TATATGGCACTTCGGTGCATTTC
Found at i:3742842 original size:39 final size:37
Alignment explanation
Indices: 3742782--3742862 Score: 85
Period size: 39 Copynumber: 2.1 Consensus size: 37
3742772 AATGTATGTA
*
3742782 ATATATGTATATGATGTGTGATATGAAT-TGTATGACATG
1 ATATATGTATATGATGGGTGAT-TGAATCTGT-T-ACATG
* *
3742821 ATATATGTGTGAT-ATGGGTGATTGCATCTGTTACATG
1 ATATATGTAT-ATGATGGGTGATTGAATCTGTTACATG
3742858 ATATA
1 ATATA
3742863 CATGAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 20 0.54
40 2 0.05
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (37 bp):
ATATATGTATATGATGGGTGATTGAATCTGTTACATG
Found at i:3752918 original size:2 final size:2
Alignment explanation
Indices: 3752913--3752956 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3752903 ACTTGAACTC
3752913 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
3752955 AT
1 AT
3752957 TATCATGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.