Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008986.1 Hibiscus syriacus cultivar Beakdansim tig00112350_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: 401385
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:3291 original size:31 final size:31
Alignment explanation
Indices: 3256--3321 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3246 TTCAATGACC
*
3256 ATTTTACAACAATTGGATAAATTTAATGATA
1 ATTTTACAACAATTCGATAAATTTAATGATA
* * *
3287 ATTTTATAATAATTCGATAAATTTAATGATT
1 ATTTTACAACAATTCGATAAATTTAATGATA
3318 ATTT
1 ATTT
3322 GTAACATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
ATTTTACAACAATTCGATAAATTTAATGATA
Found at i:8190 original size:19 final size:19
Alignment explanation
Indices: 8162--8210 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
8152 ATACGTTTTC
8162 ATGAACAGTACTATATAGT
1 ATGAACAGTACTATATAGT
* * *
8181 ATGAATAGTATTATATTGT
1 ATGAACAGTACTATATAGT
*
8200 ATTAACAGTAC
1 ATGAACAGTAC
8211 CGTGAACAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGAACAGTACTATATAGT
Found at i:14182 original size:3 final size:3
Alignment explanation
Indices: 14174--14239 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
14164 TTTTATCCAT
* *
14174 TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
14220 TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
14240 ATAAATAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
4 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:16286 original size:7 final size:7
Alignment explanation
Indices: 16274--16325 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
16264 TTTCAAATTT
16274 TTTATTA
1 TTTATTA
16281 TTTATTA
1 TTTATTA
*
16288 TTTTTATA
1 TTTAT-TA
16296 TATTATTA
1 T-TTATTA
16304 TTTATTA
1 TTTATTA
16311 TTTTATTTA
1 -TTTA-TTA
16320 TTTATT
1 TTTATT
16326 TTATTCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 19 0.49
8 14 0.36
9 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:16293 original size:16 final size:16
Alignment explanation
Indices: 16272--16327 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
16262 TCTTTCAAAT
16272 TTTTTATTATTTATTA
1 TTTTTATTATTTATTA
16288 TTTTTA-TATATTATTA
1 TTTTTATTAT-TTATTA
16304 TTTATTATTTTATTTATTTA
1 TTT-TTA--TTATTTA-TTA
16324 TTTT
1 TTTT
16328 ATTCAAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.09
16 15 0.44
17 3 0.09
19 4 0.12
20 9 0.26
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATTATTTATTA
Found at i:16294 original size:13 final size:14
Alignment explanation
Indices: 16278--16330 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 14
16268 AAATTTTTTA
16278 TTATTTATTATT-T
1 TTATTTATTATTAT
*
16291 TTATATATTATTAT
1 TTATTTATTATTAT
16305 TTA-TTATT-TTAT
1 TTATTTATTATTAT
16317 TTATTTATT-TTAT
1 TTATTTATTATTAT
16330 T
1 T
16331 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 7 0.19
13 25 0.69
14 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:16301 original size:20 final size:20
Alignment explanation
Indices: 16270--16330 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
16260 TTTCTTTCAA
*
16270 ATTTTTTATTATTTATTATT
1 ATTTTATATTATTTATTATT
16290 -TTTATATATTA-TTATTTATT
1 ATTT-TATATTATTTA-TTATT
16310 ATTTTAT-TTATTTATT-TT
1 ATTTTATATTATTTATTATT
16328 ATT
1 ATT
16331 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 17 0.47
21 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTATATTATTTATTATT
Found at i:16324 original size:23 final size:23
Alignment explanation
Indices: 16270--16325 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
16260 TTTCTTTCAA
16270 ATTT-TTTATTATTTATTATTTT
1 ATTTATTTATTATTTATTATTTT
*
16292 -TATATATTATTATTTATTATTTT
1 ATTTAT-TTATTATTTATTATTTT
16315 ATTTATTTATT
1 ATTTATTTATT
16326 TTATTCAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 1 0.03
23 22 0.76
24 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTATTTATTATTTATTATTTT
Found at i:17948 original size:14 final size:13
Alignment explanation
Indices: 17916--17966 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
17906 TTTTAAATAA
*
17916 TTTACATTTACAT
1 TTTACATTTGCAT
17929 TTTACATTTGCAT
1 TTTACATTTGCAT
17942 ATTTACATTTGGCAT
1 -TTTACATTT-GCAT
*
17957 TTTGCATTTG
1 TTTACATTTG
17967 TATTGCACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 13 0.38
14 17 0.50
15 4 0.12
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTACATTTGCAT
Found at i:17957 original size:21 final size:22
Alignment explanation
Indices: 17921--17963 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
17911 AATAATTTAC
*
17921 ATTTACATTTTACA-TTTGCAT
1 ATTTACATTTGACATTTTGCAT
*
17942 ATTTACATTTGGCATTTTGCAT
1 ATTTACATTTGACATTTTGCAT
17964 TTGTATTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTACATTTGACATTTTGCAT
Found at i:21245 original size:14 final size:13
Alignment explanation
Indices: 21226--21264 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
21216 TCCTGCAAAG
21226 AAAGAAGAAAAAAA
1 AAAGAA-AAAAAAA
21240 AAAGAAAAAAAAAA
1 AAAG-AAAAAAAAA
21254 AAAGAAAAAAA
1 AAAGAAAAAAA
21265 TTGAATCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.29
14 15 0.62
15 2 0.08
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:21246 original size:11 final size:11
Alignment explanation
Indices: 21230--21264 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
21220 GCAAAGAAAG
21230 AAGAAAAAAAA
1 AAGAAAAAAAA
21241 AAGAAAAAAAA
1 AAGAAAAAAAA
21252 AA-AAAGAAAAA
1 AAGAAA-AAAAA
21263 AA
1 AA
21265 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.13
11 20 0.87
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:23648 original size:83 final size:83
Alignment explanation
Indices: 23500--23681 Score: 303
Period size: 83 Copynumber: 2.2 Consensus size: 83
23490 AATGGAACAA
*
23500 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAAAACC
23565 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * *
23583 ATGAATTTGTTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGG-CAAAAC
*
23647 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTAGAAG
23666 ATGAATTTGCTCATAG
1 ATGAATTTGCTCATAG
23682 TAGAAATAAG
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 4 0.04
83 88 0.96
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAAAACC
AATCATTGAATTTAGAAG
Found at i:25974 original size:40 final size:40
Alignment explanation
Indices: 25919--25998 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
25909 TGAGCAGAGT
25919 CCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACATC
*
25959 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACATC
25999 TAAGCTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACATC
Found at i:26365 original size:22 final size:22
Alignment explanation
Indices: 26336--26390 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
26326 ATCTACACTC
*
26336 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
* *
26358 TTTAAAGATAACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
26380 TTCAAAGATGA
1 TTCAAAGATGA
26391 AAACTTTATG
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:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:26997 original size:113 final size:113
Alignment explanation
Indices: 26799--27922 Score: 2005
Period size: 113 Copynumber: 9.9 Consensus size: 113
26789 GATTCAAATT
* * *
26799 CATCATTTGGTGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
26864 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
26912 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
26977 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
27025 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27090 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
27138 CATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27203 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
27251 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27316 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
27364 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27429 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * *
27477 CATCATTTGGTGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27542 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
27590 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
27655 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
27703 CATCATTTGGTGGATCATTTTTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CATCATTTGGTGGATCA---TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* * *** * *
27768 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * * ** *
27819 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
**
27884 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
27923 GTTTGATATC
Statistics
Matches: 979, Mismatches: 28, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
113 812 0.83
114 63 0.06
116 104 0.11
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
Found at i:28227 original size:3 final size:3
Alignment explanation
Indices: 28219--28291 Score: 110
Period size: 3 Copynumber: 23.7 Consensus size: 3
28209 TTTATCCATT
* *
28219 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
28265 TTA TATA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT
28292 TAATAAATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28250 original size:22 final size:22
Alignment explanation
Indices: 28219--28293 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
28209 TTTATCCATT
28219 TTATTA-TTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
*
28240 TTAGTATTTATTATTATTATTA
1 TTATTATTTATTATTATTATTA
* *
28262 ATATTATATATTATTATTATTA
1 TTATTATTTATTATTATTATTA
28284 TTATTATTTA
1 TTATTATTTA
28294 ATAAATAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 5 0.11
22 42 0.89
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (22 bp):
TTATTATTTATTATTATTATTA
Found at i:28250 original size:25 final size:25
Alignment explanation
Indices: 28220--28291 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
28210 TTATCCATTT
28220 TATTATTATTATTATTATTATTAGTA
1 TATTATTATTATTATTATTATTA-TA
*
28246 T-TTATTATTATTATTAATATTATA
1 TATTATTATTATTATTATTATTATA
28270 TATTATTATTATTATTATTATT
1 TATTATTATTATTATTATTATT
28292 TAATAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
24 3 0.07
25 39 0.91
26 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (25 bp):
TATTATTATTATTATTATTATTATA
Found at i:34472 original size:96 final size:98
Alignment explanation
Indices: 34251--34476 Score: 280
Period size: 101 Copynumber: 2.3 Consensus size: 98
34241 ACACAATTTT
* * * * * *
34251 AATATTAGGTGCAACCTAATATGTTGATAATCTTTAAGTAATTATTTACCTATTTTTTTATTGTC
1 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCA--TACATATTTTGTTATCGTC
* * *
34316 GGATTTCTAAGGCTCCATATGCTTAAACTTTGGTAA
64 GGATTTCCAAGACTCCATATGCTTAAAC-GTGGTAA
34352 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCA-ACATATTTTGTTATCGTCGG
1 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCATACATATTTTGTTATCGTCGG
34416 ATTTCCAAGAC-CC-TATCAGCTTAAA-GTGGTAA
66 ATTTCCAAGACTCCATAT--GCTTAAACGTGGTAA
* *
34448 CATATTAGGCGTTACCTAATATGTTGATA
1 AATATTAGGCGCTACCTAATATGTTGATA
34477 TTATTAATAA
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
96 36 0.32
97 2 0.02
98 33 0.29
101 41 0.37
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (98 bp):
AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCATACATATTTTGTTATCGTCGG
ATTTCCAAGACTCCATATGCTTAAACGTGGTAA
Found at i:34812 original size:108 final size:108
Alignment explanation
Indices: 34501--34813 Score: 403
Period size: 108 Copynumber: 2.9 Consensus size: 108
34491 CAAGGCCTCG
* ** *
34501 TCAACTTAAACTTTGGTAACATATTAAACCCTACCTAATATGTTGATAATATTATCAAAAAAATA
1 TCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAATA
* * * *
34566 AATAATTTCCCTATTTTTTTATCGTCAGATTTCTAAAACTCAA
66 AGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAAACTCAA
* * * * * *
34609 TCAGCTTAAACTTTAGTAACACTTTAGGCGCTACTTAATATGTTGATAGTATTATCAACAAAATA
1 TCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAATA
* * * *
34674 AGTAATTTACCTATTTTGTAATTGTCGGATTTCTAAGACTCCA
66 AGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAAACTCAA
* * * *
34717 TCAACTTAAACTTTGGTAACATTTTAGGCTCTACCTAGTATGTTGATATTATTAAT-AACATAAT
1 TCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATT-ATCAACAAAAT
*
34781 AAGTAATTTACCTATTTTGTTATCGTTGGATTT
65 AAGTAATTTACCTATTTTGTTATCGTCGGATTT
34814 TCTGATTGCA
Statistics
Matches: 175, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
108 173 0.99
109 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (108 bp):
TCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAATA
AGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAAACTCAA
Found at i:37846 original size:2 final size:2
Alignment explanation
Indices: 37839--37872 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37829 TTATATCACC
37839 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
37873 GGAGAAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38428 original size:59 final size:59
Alignment explanation
Indices: 38331--38450 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
38321 CAAAAGGTTT
* *
38331 TGATAATGGTTACAGCAAACATAGAAAGAAATTATTCATCCAAGAGGGTAAACTATAGA
1 TGATAATGATTACAGCAAACATAGAAAGAAAGTATTCATCCAAGAGGGTAAACTATAGA
* *
38390 TGATAATGATTATAGCAAACATAGAAAGAAAGTGTTCATCCAAGAGGGTAAACTATAGA
1 TGATAATGATTACAGCAAACATAGAAAGAAAGTATTCATCCAAGAGGGTAAACTATAGA
38449 TG
1 TG
38451 CACCCGACCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (59 bp):
TGATAATGATTACAGCAAACATAGAAAGAAAGTATTCATCCAAGAGGGTAAACTATAGA
Found at i:50450 original size:9 final size:8
Alignment explanation
Indices: 50428--50515 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 8
50418 CGAACCCGAA
*
50428 AATATTAT
1 AATATAAT
50436 ATATATAATT
1 A-ATATAA-T
*
50446 AATATAAA
1 AATATAAT
50454 AATATAA-
1 AATATAAT
*
50461 AATATTAT
1 AATATAAT
50469 ATATATAATT
1 A-ATATAA-T
50479 AATATAA-
1 AATATAAT
*
50486 AATATATAA
1 AATATA-AT
*
50495 AATATTAT
1 AATATAAT
50503 ATATATATAT
1 A-ATATA-AT
50513 AAT
1 AAT
50516 CGGGGCGGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
7 12 0.19
8 12 0.19
9 33 0.52
10 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATAAT
Found at i:50468 original size:33 final size:34
Alignment explanation
Indices: 50426--50509 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
50416 CCCGAACCCG
50426 AAAATATTATATATATAATTAATATAAAA-ATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
50459 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
50493 AAAATATTATATATATA
1 AAAATATTATATATATA
50510 TATAATCGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 29 0.58
34 21 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAATATAT
Found at i:56076 original size:31 final size:31
Alignment explanation
Indices: 56037--56162 Score: 200
Period size: 31 Copynumber: 4.1 Consensus size: 31
56027 GTCCCGAAGG
* *
56037 ACAGTCCATA-GATTCCGAAGAACCTAGGTAA
1 ACAGTCCATATG-TCCCGAAGAACATAGGTAA
* *
56068 TCAGTCCATATGTCCCGAAGGACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
56099 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
56130 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
56161 AC
1 AC
56163 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
ACAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:59540 original size:31 final size:31
Alignment explanation
Indices: 59502--59626 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
59492 CCCGAAGGAC
* * *
59502 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
59533 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59564 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59595 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
59626 C
1 C
59627 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:61668 original size:15 final size:15
Alignment explanation
Indices: 61648--61680 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
61638 TGAGACATTA
*
61648 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
61663 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
61678 CCC
1 CCC
61681 ACCTAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:63643 original size:18 final size:18
Alignment explanation
Indices: 63620--63654 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
63610 TAATCTCAGC
63620 TATTAGCTTAGACTTTCA
1 TATTAGCTTAGACTTTCA
63638 TATTAGCTTAGACTTTC
1 TATTAGCTTAGACTTTC
63655 TTTTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TATTAGCTTAGACTTTCA
Found at i:65838 original size:30 final size:30
Alignment explanation
Indices: 65798--65860 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
65788 ACTTAAGGAG
* **
65798 GGGGTAAAGTATAATTAATTATAAAAATGA
1 GGGGCAAAGTATAATTAACCATAAAAATGA
*
65828 GGGGCAAAGTATAATTAACCATAGAAATGA
1 GGGGCAAAGTATAATTAACCATAAAAATGA
65858 GGG
1 GGG
65861 ACACAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.24
Consensus pattern (30 bp):
GGGGCAAAGTATAATTAACCATAAAAATGA
Found at i:71453 original size:13 final size:13
Alignment explanation
Indices: 71437--71461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71427 TGAGTGATTA
71437 TTATTTTTCTTAT
1 TTATTTTTCTTAT
71450 TTATTTTTCTTA
1 TTATTTTTCTTA
71462 CTAAGTTCTT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTCTTAT
Found at i:72153 original size:25 final size:25
Alignment explanation
Indices: 72124--72180 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
72114 CTAGACCAAC
72124 TAATTG-TCTAT-ATAAAAAAATAAA
1 TAATTGATCTATGA-AAAAAAATAAA
* *
72148 GTAATTGATCTTTGAAAAAAAATATA
1 -TAATTGATCTATGAAAAAAAATAAA
72174 TAATTGA
1 TAATTGA
72181 CCCTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.46
26 14 0.50
27 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (25 bp):
TAATTGATCTATGAAAAAAAATAAA
Found at i:72345 original size:2 final size:2
Alignment explanation
Indices: 72338--72403 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
72328 ATTTCCATTC
72338 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
72380 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
72404 GTTTATATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86862 original size:19 final size:20
Alignment explanation
Indices: 86824--86862 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
86814 TTTGAAGATT
* *
86824 TTATTTTTTCAAATAAATTA
1 TTATATTTTCAAAAAAATTA
86844 TTATATTTT-AAAAAAATTA
1 TTATATTTTCAAAAAAATTA
86863 AAAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATATTTTCAAAAAAATTA
Found at i:87845 original size:37 final size:36
Alignment explanation
Indices: 87770--87845 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
87760 TTTTTATATT
*
87770 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
87806 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
87843 TTT
1 TTT
87846 GTATTATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:88027 original size:20 final size:20
Alignment explanation
Indices: 87991--88028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
87981 ATCTTATTCC
**
87991 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
88011 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
88029 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:89232 original size:20 final size:21
Alignment explanation
Indices: 89205--89320 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 21
89195 ACGCGAAATA
89205 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGAGTCCCC
* ** **
89225 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGAGTCCCC
* ***
89245 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAGTCCCC
89266 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGAGTCCCC
* ** **
89286 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGAGTCCCC
89306 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
89321 ATATGAAAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 2 0.03
20 48 0.70
21 19 0.28
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.17
Consensus pattern (21 bp):
AAAATCGCAACGCGAGTCCCC
Found at i:89281 original size:61 final size:60
Alignment explanation
Indices: 89185--89340 Score: 269
Period size: 61 Copynumber: 2.6 Consensus size: 60
89175 AAATGACCAA
*
89185 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
* *
89244 CAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
89305 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
89341 ACATATAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 16 0.18
60 17 0.19
61 57 0.63
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (60 bp):
CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
Found at i:89329 original size:20 final size:19
Alignment explanation
Indices: 89306--89359 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
89296 ATCAGTTTCC
*
89306 AAAATCGCAACGCGAATAT
1 AAAATCGCAACGCGAACAT
89325 GAAAATCGCAACGCGAACAT
1 -AAAATCGCAACGCGAACAT
89345 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
89360 TATCCGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAACAT
Found at i:89369 original size:20 final size:20
Alignment explanation
Indices: 89346--89500 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
89336 CGCGAACATA
89346 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
89366 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
89386 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
89406 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
89426 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
89446 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
89466 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
89487 TAAATCGCAACGCG
1 TAAATCGCAACGCG
89501 ATATTTAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.85
21 15 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:89371 original size:60 final size:60
Alignment explanation
Indices: 89307--89501 Score: 230
Period size: 60 Copynumber: 3.2 Consensus size: 60
89297 TCAGTTTCCA
** *
89307 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT
* * * **** *
89367 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT
* * **
89427 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATA-AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGT
89488 AAATCGCAACGCGA
1 AAATCGCAACGCGA
89502 TATTTAAAGC
Statistics
Matches: 110, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
60 78 0.71
61 31 0.28
62 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT
Found at i:89921 original size:33 final size:33
Alignment explanation
Indices: 89882--89952 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
89872 TTCACTTAGA
* *
89882 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
89915 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
89948 TTTCA
1 TTTCA
89953 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:90076 original size:20 final size:20
Alignment explanation
Indices: 90032--90127 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 20
90022 TGCAGAAGAG
*
90032 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
90053 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
90073 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
90094 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
90113 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
90128 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.28
20 20 0.31
21 26 0.41
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:90089 original size:41 final size:40
Alignment explanation
Indices: 90030--90126 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 40
90020 TTTGCAGAAG
* *
90030 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGAA
* *
90071 TGTCGCAACGAGAGAAATGAAAATCGCAACGCGAAATGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
*
90111 AATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAA
90127 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (40 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
Found at i:90168 original size:19 final size:19
Alignment explanation
Indices: 90146--90243 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
90136 GAAACCAAAA
*
90146 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
90165 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
90179 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
90198 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
90212 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
90231 TCGCGTTGCGATT
1 TCGCGTTGCGATT
90244 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:90187 original size:14 final size:14
Alignment explanation
Indices: 90168--90257 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
90158 TTTCATTTCG
90168 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
90182 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
90201 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
90215 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
90232 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
90248 CGTTGCGATT
1 CGTTGCGATT
90258 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:90193 original size:33 final size:33
Alignment explanation
Indices: 90151--90265 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
90141 CAAAATCGCA
90151 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
90184 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
90217 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
90250 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
90266 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:92121 original size:93 final size:93
Alignment explanation
Indices: 91962--92342 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
91952 TAGATTGCTT
*
91962 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
92027 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
92055 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
92120 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
92148 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
92213 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
92241 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
92306 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
92334 AGTAAATTT
1 AGTAAATTT
92343 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:92426 original size:19 final size:19
Alignment explanation
Indices: 92386--92514 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
92376 TAGTTTACTT
* *
92386 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
92406 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
92425 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
92444 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
92458 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
92477 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
92491 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
92510 TCGCA
1 TCGCA
92515 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:92465 original size:33 final size:32
Alignment explanation
Indices: 92422--92514 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
92412 CGCGAAACCA
**
92422 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
92454 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
92487 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
92515 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:92512 original size:52 final size:52
Alignment explanation
Indices: 92386--92514 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
92376 TAGTTTACTT
**
92386 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
92438 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
92491 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
92515 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:92532 original size:19 final size:19
Alignment explanation
Indices: 92510--92644 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
92500 GAAACCAAAA
*
92510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
92529 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
92545 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
92562 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
92578 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
92595 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
92614 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
92634 TCGTGTTGCGA
1 TCGCGTTGCGA
92645 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:92551 original size:14 final size:14
Alignment explanation
Indices: 92532--92588 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
92522 TTTCATTTCG
92532 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
92546 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
92563 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
92579 CGTTGCGATT
1 CGTTGCGATT
92589 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:92557 original size:33 final size:33
Alignment explanation
Indices: 92515--92607 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
92505 CAAAATCGCA
*
92515 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
92548 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
92581 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
92608 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:94587 original size:14 final size:14
Alignment explanation
Indices: 94568--94603 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
94558 ATTGTTTAAT
94568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
94582 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
94596 TGATTTGT
1 TGATTTGT
94604 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:94734 original size:19 final size:19
Alignment explanation
Indices: 94710--94807 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
94700 AAAATTGACT
94710 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
94729 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
94748 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
94762 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
94781 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
94801 ATCGCAA
1 ATCGCAA
94808 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:94839 original size:53 final size:53
Alignment explanation
Indices: 94710--94826 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
94700 AAAATTGACT
94710 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
94762 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
94815 ATCGCAATGCGA
1 ATCGCAATGCGA
94827 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:96952 original size:24 final size:24
Alignment explanation
Indices: 96918--96964 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
96908 CTGAAACATC
96918 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
96942 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
96965 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:97675 original size:20 final size:20
Alignment explanation
Indices: 97647--97896 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
97637 AAATTTCAGT
* *
97647 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
97667 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
97687 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
97707 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
97727 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
97747 GTTGCGATTTACGGACTATC
1 GTTGCGATTTACGGATTCTC
* *
97767 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
97787 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
97807 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
97827 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
97847 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
97867 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
97887 GTTGCGATTT
1 GTTGCGATTT
97897 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:97913 original size:21 final size:21
Alignment explanation
Indices: 97883--97965 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
97873 ATTTTCATAT
*
97883 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
97904 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
97925 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
97946 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
97966 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:97956 original size:42 final size:43
Alignment explanation
Indices: 97863--97961 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
97853 ATTTATGTGT
* *
97863 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
97904 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
97946 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
97962 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:99781 original size:10 final size:10
Alignment explanation
Indices: 99766--99790 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
99756 ATCCTGGCAA
99766 CACTGCAGCT
1 CACTGCAGCT
99776 CACTGCAGCT
1 CACTGCAGCT
99786 CACTG
1 CACTG
99791 GAGCGTCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (10 bp):
CACTGCAGCT
Found at i:102418 original size:2 final size:2
Alignment explanation
Indices: 102413--102440 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
102403 CAATACATAC
102413 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
102441 TTCATTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102520 original size:33 final size:33
Alignment explanation
Indices: 102480--102545 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
102470 AAATCACAAA
102480 TTTTAGATGA-ACATAAGTTAAAAAAGGAAGGTT
1 TTTTAGAT-ATACATAAGTTAAAAAAGGAAGGTT
102513 TTTTAGATATACATAAGTTAAAAAAGGAAGGTT
1 TTTTAGATATACATAAGTTAAAAAAGGAAGGTT
102546 GAAGACGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (33 bp):
TTTTAGATATACATAAGTTAAAAAAGGAAGGTT
Found at i:105588 original size:4 final size:4
Alignment explanation
Indices: 105579--105608 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
105569 ATTCTACAAC
105579 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
105609 TTCCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:118731 original size:21 final size:21
Alignment explanation
Indices: 118705--118744 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
118695 CAGAACCCCA
*
118705 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
118726 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
118745 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:125596 original size:4 final size:4
Alignment explanation
Indices: 125587--126697 Score: 1942
Period size: 4 Copynumber: 284.8 Consensus size: 4
125577 TCTAGTAAAC
125587 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125633 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125680 CATA CACTA CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125727 CATA CATA CATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125774 CATA CATA CATA C-TA CATA CATA CATA CATA CATA CATA CATA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125820 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125866 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125912 CATA CATA C-TA CATA CATA -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
125958 CA-A CAT- -ATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126002 CATA CATA CATA CATA CATA CATA CATA CATA CATAA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA
*
126051 CATA CATA CATA CATA CATA CAGA CATA C-TA CATA CATA CATA CCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA
*
126099 CATA C-TA CATA CATA CATA C-TA CATA -ATA CATA CATA CAGA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126144 CAT- CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126191 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
126239 CATA CATA CATA CATA CATA CATA CAT- CATA TA-A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126285 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126333 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126381 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126428 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126476 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126524 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126570 CATA CATA CATA CATA CATA CATA CA-A CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
126615 CATA CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
126663 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
126698 GCAGCCTGAT
Statistics
Matches: 1065, Mismatches: 8, Indels: 68
0.93 0.01 0.06
Matches are distributed among these distances:
2 14 0.01
3 50 0.05
4 989 0.93
5 12 0.01
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:127778 original size:31 final size:31
Alignment explanation
Indices: 127740--127895 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
127730 CCCGAAGGAC
* * *
127740 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
127771 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
127802 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
**
127833 CAGTCCATATGTCCCGAAGAACATATATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
127864 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
127895 C
1 C
127896 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:129944 original size:30 final size:30
Alignment explanation
Indices: 129910--129970 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
129900 ACATAGTCAA
129910 TACATTAATATCAAGTATTATATCTATTCC
1 TACATTAATATCAAGTATTATATCTATTCC
*
129940 TACATTAATATCAAGTATTATATCTCTTCC
1 TACATTAATATCAAGTATTATATCTATTCC
129970 T
1 T
129971 TGTTTAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.44
Consensus pattern (30 bp):
TACATTAATATCAAGTATTATATCTATTCC
Found at i:133022 original size:29 final size:30
Alignment explanation
Indices: 132975--133031 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
132965 ATTTGAATAT
* *
132975 AAATTTAATCAAAATTTCACTTTGATCCCC
1 AAATTTAATCAAAATTTCAATTTAATCCCC
133005 AAATTTAATCAAAA-TTCAATTTAATCC
1 AAATTTAATCAAAATTTCAATTTAATCC
133032 TCTAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATTTAATCAAAATTTCAATTTAATCCCC
Found at i:134450 original size:44 final size:44
Alignment explanation
Indices: 134357--134450 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 44
134347 TTCCTTGGAA
* * *
134357 ATTGATACGGTCATTTAATACTATAACCATTTCGATCCATAAAT
1 ATTGATACGGTCATTTAATACTATAACAATTTCGATCAAGAAAT
* ** * * **
134401 TTTGATATTGTCATTTAATATTATAATAATTTCGATCAAGCTAT
1 ATTGATACGGTCATTTAATACTATAACAATTTCGATCAAGAAAT
134445 ATTGAT
1 ATTGAT
134451 TAATATTTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (44 bp):
ATTGATACGGTCATTTAATACTATAACAATTTCGATCAAGAAAT
Found at i:136521 original size:33 final size:33
Alignment explanation
Indices: 136484--136581 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
136474 GTTGCAAGAA
**
136484 AGGAGGAGAGGCAACGGTTGGGAGCAAGAGAGG
1 AGGAGGAGAGGCGGCGGTTGGGAGCAAGAGAGG
136517 AGGAGGAGAGGCGGCGGTTGGGAGCAAGAGAGG
1 AGGAGGAGAGGCGGCGGTTGGGAGCAAGAGAGG
*
136550 AGGAGGAGAGGCGGCGGTAGGGAGCAAGAGAG
1 AGGAGGAGAGGCGGCGGTTGGGAGCAAGAGAG
136582 TTTATACGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.31, C:0.09, G:0.55, T:0.05
Consensus pattern (33 bp):
AGGAGGAGAGGCGGCGGTTGGGAGCAAGAGAGG
Found at i:141822 original size:80 final size:80
Alignment explanation
Indices: 141689--141846 Score: 271
Period size: 80 Copynumber: 2.0 Consensus size: 80
141679 GACCTTTCGC
* *
141689 GTTCCTCTGGTTTTTGCTGCATATCTGTTTCAGATTTTCATCATTTACTGGCTGGGGGTAGCACT
1 GTTCCTCTGGTTTTTGCTGCACAGCTGTTTCAGATTTTCATCATTTACTGGCTGGGGGTAGCACT
141754 TATGCTCTTCCTCTG
66 TATGCTCTTCCTCTG
* *
141769 GTTCCTCTGGTTTTTGCTTCACAGCTGTTTCAGATTTTCATCATTTTCTGGCTGGGGGTAGCACT
1 GTTCCTCTGGTTTTTGCTGCACAGCTGTTTCAGATTTTCATCATTTACTGGCTGGGGGTAGCACT
*
141834 TCTGCTCTTCCTC
66 TATGCTCTTCCTC
141847 GCTGAAACTG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (80 bp):
GTTCCTCTGGTTTTTGCTGCACAGCTGTTTCAGATTTTCATCATTTACTGGCTGGGGGTAGCACT
TATGCTCTTCCTCTG
Found at i:152392 original size:2 final size:2
Alignment explanation
Indices: 152385--152418 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
152375 AGATTGTACA
152385 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
152419 TGAGTATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:156469 original size:5 final size:5
Alignment explanation
Indices: 156459--156485 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
156449 TAGGGGTGTA
156459 TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TT
156486 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:156932 original size:14 final size:14
Alignment explanation
Indices: 156909--156975 Score: 116
Period size: 14 Copynumber: 4.8 Consensus size: 14
156899 TTCGCCCATC
156909 ATACACTTACTCTT
1 ATACACTTACTCTT
*
156923 ATATACTTACTCTT
1 ATACACTTACTCTT
156937 ATACACTTACTCTT
1 ATACACTTACTCTT
156951 ATACACTTACTCTT
1 ATACACTTACTCTT
*
156965 ATACATTTACT
1 ATACACTTACT
156976 GTTGTTTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (14 bp):
ATACACTTACTCTT
Found at i:157270 original size:15 final size:15
Alignment explanation
Indices: 157250--157412 Score: 202
Period size: 15 Copynumber: 10.5 Consensus size: 15
157240 TAATAAGATT
157250 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
157265 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
157280 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
157295 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
157310 ATTTATTATACAATA
1 ATTTATTTTAAAATA
*
157325 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
157340 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
157355 AATTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
157374 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
157392 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
157406 ATTTATT
1 ATTTATT
157413 AGTATGAATT
Statistics
Matches: 131, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
14 12 0.09
15 99 0.76
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:157304 original size:45 final size:45
Alignment explanation
Indices: 157227--157412 Score: 218
Period size: 45 Copynumber: 4.1 Consensus size: 45
157217 TATTAAAATA
* *
157227 ATTTT-AAATAATTTA--ATAAGATTATTTATTTTAAAATAATTT
1 ATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
157269 ATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
1 ATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
* * *
157314 ATTATACAATAATTTATTATAAAATAATTTATTTTAAAATAAATT
1 ATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
* *
157359 ATTATAAAATATGAATTGATTTATTTTAAAATAATTTATTTT-AAATAATTT
1 ATT-TTAAA-AT--A---ATTTATTATAAAATAATTTATTTTAAAATAATTT
157410 ATT
1 ATT
157413 AGTATGAATT
Statistics
Matches: 124, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
42 5 0.04
43 10 0.08
45 70 0.56
46 2 0.02
47 2 0.02
49 1 0.01
51 11 0.09
52 23 0.19
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (45 bp):
ATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
Found at i:157503 original size:32 final size:32
Alignment explanation
Indices: 157462--157929 Score: 303
Period size: 32 Copynumber: 15.7 Consensus size: 32
157452 TATTGTAGTT
157462 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
157494 GTATGGATTGATTTA-CTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157517 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
157548 GTATGTATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157574 G-A---ATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
157602 GTATGGATTGATTTATTTTAAA-ATATTGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * *
157633 G-ATTTATT-ATTGTAGTTGTATAGATTGATTTATT-
1 GTATGGATTGATT-TA-TT-T-TA-AATAATTTATTA
* * * * * *
157667 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
157704 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157736 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157759 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
157790 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
157822 GTATGGATCGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157845 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
157876 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
157908 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
157930 ATATGGATTG
Statistics
Matches: 349, Mismatches: 28, Indels: 118
0.71 0.06 0.24
Matches are distributed among these distances:
22 54 0.15
23 12 0.03
24 2 0.01
25 4 0.01
26 12 0.03
27 2 0.01
28 12 0.03
29 7 0.02
30 9 0.03
31 19 0.05
32 179 0.51
33 6 0.02
34 11 0.03
36 7 0.02
37 1 0.00
38 2 0.01
39 1 0.00
40 9 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:157520 original size:22 final size:22
Alignment explanation
Indices: 157495--157537 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
157485 AATTTATTAG
157495 TATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTACTTTAAAA
*
157517 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTACTTTAAA
157538 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTACTTTAAAA
Found at i:157527 original size:54 final size:54
Alignment explanation
Indices: 157463--158041 Score: 412
Period size: 54 Copynumber: 10.6 Consensus size: 54
157453 ATTGTAGTTG
*
157463 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
* *
157517 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
* *
157571 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
* * * * * * *
157625 TATTGATTGATTTATTATT--GTAGTTGTA-TAG-ATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATT-TTAAATAATT-TATTAGTATGGATTGA--TT---TAATTTA-AAA
** ** * ** * *
157683 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTAATTTA-AAA
** ** * ** * *
157737 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTAATTTA-AAA
* * * *
157791 TATAGATTGATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
* *
157845 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTT-ATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
* * * ** * * * ***
157898 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA--ATT-TA-AAA
** *
157957 TATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
158011 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
158042 TTTTAGTTGT
Statistics
Matches: 431, Mismatches: 66, Indels: 56
0.78 0.12 0.10
Matches are distributed among these distances:
50 16 0.04
52 9 0.02
53 15 0.03
54 296 0.69
55 14 0.03
56 5 0.01
57 11 0.03
58 39 0.09
59 8 0.02
60 2 0.00
62 16 0.04
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAATTTAAAA
Found at i:157565 original size:22 final size:22
Alignment explanation
Indices: 157549--157591 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
157539 AATTTATTAG
*
157549 TATGTATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
157571 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
157592 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:157605 original size:188 final size:188
Alignment explanation
Indices: 157392--158026 Score: 815
Period size: 188 Copynumber: 3.3 Consensus size: 188
157382 TTTTAAAATA
*
157392 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATACGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
157457 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATGG
66 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
157522 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGAATTG
131 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGAATTG
* *
157580 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
157645 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
66 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
* *
157710 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
131 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGAATTG
* * **
157768 ATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAATAATTTATTTGTATGGATCG
1 ATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTT-AA-AA--TA--TGGATTGATTT
* *** *
157832 ATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTA
59 A-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-
** * *
157896 AATAATTTATTTGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAGTTG
122 -A-AA---A----TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGTATTGATT-TA-TTT
157957 T---ATA--AATTG
175 TAAAATATGAATTG
*
157966 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
158027 TTAAATAATT
Statistics
Matches: 395, Mismatches: 30, Indels: 41
0.85 0.06 0.09
Matches are distributed among these distances:
188 220 0.56
189 2 0.01
190 2 0.01
191 2 0.01
192 10 0.03
194 57 0.14
195 7 0.02
196 3 0.01
197 4 0.01
198 43 0.11
200 4 0.01
201 3 0.01
202 7 0.02
203 5 0.01
204 26 0.07
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGAATTG
Found at i:157607 original size:86 final size:84
Alignment explanation
Indices: 157515--157899 Score: 285
Period size: 86 Copynumber: 4.7 Consensus size: 84
157505 TTTACTTTAA
157515 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGAATTG
1 AATATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTT-AAATATGAATTG
157580 ATTTATTTTAAATAATTTATT
64 ATTTATTTTAAATAATTTATT
* * * *
157601 AGTATGGATTGATTTATTTTAAA-ATATTGATT-G-ATTTATT-ATTGTAGTTGT--ATA-G-AT
1 AATATGGATTGATTTATTTTAAATA-ATTTATTAGTA-TGATTGATT-TA-TTTTAAATATGAAT
157658 TGATTTATTTTAAATAATTTATT
62 TGATTTATTTTAAATAATTTATT
* **
157681 AGTATGGATTGATTTATTTT-AA-AA--TA-T-G---GATTGATTTATTTTAAATAATTTATTAG
1 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAT-ATGAATT-G
** * ** * *
157737 TATGGA-TTGATTTATTTTA-A
64 -ATTTATTTTAAATAATTTATT
*
157757 AATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AA-AT-AATTTA
1 AATATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAATATGAATTGA
* * ** *
157819 TTT-GTATGGATCGATTTATTTT
65 TTTATTTTAAAT-AATTTA--TT
157841 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA
1 --AATATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAATA
157900 ATTTATTTGT
Statistics
Matches: 240, Mismatches: 28, Indels: 60
0.73 0.09 0.18
Matches are distributed among these distances:
71 3 0.01
72 5 0.02
73 5 0.02
74 1 0.00
75 2 0.01
76 23 0.10
77 12 0.05
78 6 0.03
79 3 0.01
80 51 0.21
81 6 0.03
82 7 0.03
83 5 0.02
84 6 0.03
85 8 0.03
86 94 0.39
87 2 0.01
88 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (84 bp):
AATATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAATATGAATTGAT
TTATTTTAAATAATTTATT
Found at i:157708 original size:22 final size:22
Alignment explanation
Indices: 157683--157725 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
157673 AATTTATTAG
157683 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
157705 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
157726 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:157762 original size:22 final size:22
Alignment explanation
Indices: 157737--157779 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
157727 AATTTATTAG
157737 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
157759 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
157780 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:157787 original size:14 final size:14
Alignment explanation
Indices: 157768--157821 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
157758 ATATGGATTG
157768 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
157782 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
157800 ATTTATTTTAAATA
1 ATTTATTTTAAATA
157814 ATTTATTT
1 ATTTATTT
157822 GTATGGATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:157848 original size:22 final size:22
Alignment explanation
Indices: 157823--157865 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
157813 AATTTATTTG
157823 TATGGATCGATTTATTTTAAAA
1 TATGGATCGATTTATTTTAAAA
*
157845 TATGGATTGATTTATTTTAAA
1 TATGGATCGATTTATTTTAAA
157866 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATCGATTTATTTTAAAA
Found at i:157873 original size:14 final size:14
Alignment explanation
Indices: 157854--157907 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
157844 ATATGGATTG
157854 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
157868 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
157886 ATTTATTTTAAATA
1 ATTTATTTTAAATA
157900 ATTTATTT
1 ATTTATTT
157908 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:157900 original size:86 final size:86
Alignment explanation
Indices: 157709--158041 Score: 563
Period size: 86 Copynumber: 3.9 Consensus size: 86
157699 TTAAAATATG
157709 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
157774 TTTAAATAATTTATTAGTATA
66 TTTAAATAATTTATTAGTATA
* *
157795 GATTGATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
157860 TTTAAATAATTTATTAGTATA
66 TTTAAATAATTTATTAGTATA
*
157881 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
*
157945 -TT--AT--TGTAGTT-GTATA
66 TTTAAATAATTTA-TTAGTATA
*
157961 AATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
158026 TTTAAATAATTTATTA
66 TTTAAATAATTTATTA
158042 TTTTAGTTGT
Statistics
Matches: 232, Mismatches: 7, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
80 70 0.30
81 2 0.01
82 4 0.02
84 4 0.02
85 2 0.01
86 150 0.65
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (86 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAGTATA
Found at i:158044 original size:21 final size:22
Alignment explanation
Indices: 157989--158031 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
157979 AATTTATTAG
157989 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
158011 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
158032 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:158091 original size:31 final size:31
Alignment explanation
Indices: 158056--158114 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
158046 AGTTGTATGG
* *
158056 ATTATTTAAATTTCAGTAATGTAAAACTAAA
1 ATTATTTAAATATCAGTAATGCAAAACTAAA
*
158087 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAGTAATGCAAAACT
158115 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTATTTAAATATCAGTAATGCAAAACTAAA
Found at i:161215 original size:22 final size:22
Alignment explanation
Indices: 161190--161240 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
161180 TGGTTCGAGG
161190 AAATGTATAATTTGAATAAT-TA-
1 AAATGTATAATTT-AA-AATATAT
161212 AAAT-TGATAATTTAAAATATAT
1 AAATGT-ATAATTTAAAATATAT
161234 AAATGTA
1 AAATGTA
161241 AGATTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 16 0.64
23 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATGTATAATTTAAAATATAT
Found at i:165684 original size:18 final size:20
Alignment explanation
Indices: 165663--165709 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
165653 ATTTAAGATT
165663 TTATTTTA-A-ATATTTTAA
1 TTATTTTATATATATTTTAA
* *
165681 TTATTTTATATATCTTTTAG
1 TTATTTTATATATATTTTAA
165701 TTATTTTAT
1 TTATTTTAT
165710 CTTTTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
20 16 0.64
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTATATATATTTTAA
Found at i:170957 original size:81 final size:81
Alignment explanation
Indices: 170822--170978 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 81
170812 ACAATGAGCA
* * * * *
170822 GACTCTTTTCCTCAACGTCGTCTCCTATTAGTCTTCCCGGCTTCTCTCCCTCATCATCCGA-TGA
1 GACTCTCTTCCTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCCCTCATCATCAGATTG-
170886 TTTTTCACCAGCAATTG
65 TTTTTCACCAGCAATTG
* *
170903 GACTCTCTTCTTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTC-CCTTTCATCATCAGATTG
1 GACTCTCTTCCTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCC-CTCATCATCAGATTG
170967 TTTTTCACCAGC
65 TTTTTCACCAGC
170979 GAAATAACTC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 2 0.03
81 63 0.94
82 2 0.03
ACGTcount: A:0.17, C:0.35, G:0.11, T:0.37
Consensus pattern (81 bp):
GACTCTCTTCCTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCCCTCATCATCAGATTGT
TTTTCACCAGCAATTG
Found at i:170989 original size:81 final size:81
Alignment explanation
Indices: 170823--170996 Score: 210
Period size: 81 Copynumber: 2.1 Consensus size: 81
170813 CAATGAGCAG
* * * * * *
170823 ACTCTTTTCCTCAACGTCGTCTCCTATTAGTCTTCCCGGCTTCTCTCCCTCATCATCCGATGATT
1 ACTCTCTTCTTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCCCTCATCATCAGATGATT
* *
170888 TTTCACCAGCAATTGG
66 TTTCACCAGCAAATGA
*
170904 ACTCTCTTCTTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTC-CCTTTCATCATCAGATTG-
1 ACTCTCTTCTTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCC-CTCATCATCAGA-TGA
170967 TTTTTCACCAGCGAAAT-A
64 TTTTTCACCAGC-AAATGA
*
170985 ACTCTCTACTTC
1 ACTCTCTTCTTC
170997 GACTTCCCCT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
80 2 0.03
81 73 0.91
82 5 0.06
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.37
Consensus pattern (81 bp):
ACTCTCTTCTTCAACGTCGTCTCCCAATAATCTTCCCGGCTTCTCTCCCTCATCATCAGATGATT
TTTCACCAGCAAATGA
Found at i:173113 original size:84 final size:84
Alignment explanation
Indices: 172934--173116 Score: 188
Period size: 84 Copynumber: 2.2 Consensus size: 84
172924 TCAACATCAT
* * **
172934 CATCAGATGGTTTTTCAC-AGGCAGATTAACTTTCTAATTCAACATCATCTTATAATAATATTCT
1 CATCAGATGGTTTTTGACTA-GCGGACAAACTTTCTAATTCAACATCATCTTATAATAATATTCT
** * * *
172998 TTTAGGCTTCTCTCCCTTAT
65 AATAGGCTTCTCACCCTCAA
* * * * * *
173018 CATCATATGGTTTTTGACTAGCGGACAAACTTTCTGATTCAACATCGTCTTCTAGTAATCTTCTA
1 CATCAGATGGTTTTTGACTAGCGGACAAACTTTCTAATTCAACATCATCTTATAATAATATTCTA
*
173083 ATCGGCTTCTCACCCTCAA
66 ATAGGCTTCTCACCCTCAA
* *
173102 CATTAGGTGGTTTTT
1 CATCAGATGGTTTTT
173117 CACCAACAAA
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
84 78 0.99
85 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (84 bp):
CATCAGATGGTTTTTGACTAGCGGACAAACTTTCTAATTCAACATCATCTTATAATAATATTCTA
ATAGGCTTCTCACCCTCAA
Found at i:173487 original size:119 final size:118
Alignment explanation
Indices: 173251--173488 Score: 252
Period size: 119 Copynumber: 2.0 Consensus size: 118
173241 GGATTCAACA
* * *
173251 TTATCTTCTAGCAATCTTTTTTTCGGTTTATCTCCCTCATCATCAGATGTTTTTCATTGGCAGAC
1 TTATCTTCTAGCAATCTTCTTTTCGCTTTATCTCCCTCATCATCAGATGTTTTTCACTGGCAGAC
* ** *
173316 AAACTTTCTAATTCAACATCGTCTTCTAGTAATCTTTTTTTTTTGCTTCTCCCC
66 AAACTTTCTAATTCAACATCGTCTTCTAGTAATC-TTTCTTTACGCTGCTCCCC
* * *
173370 TTATCTTCTAGTAATCTTCTTTTCAGCTTT-TCTCCCTCATCATCATATGGTTTTTCACTGGCCG
1 TTATCTTCTAGCAATCTTCTTTTC-GCTTTATCTCCCTCATCATCAGAT-GTTTTTCACTGGCAG
* ** *
173434 ACAGACGTTT-TGGTTTAACA-CAGTCTTCTCA-TAATC-TTCTTTACGACTGCTCCCC
64 ACAAAC-TTTCTAATTCAACATC-GTCTTCT-AGTAATCTTTCTTTACG-CTGCTCCCC
173489 CTCATCATCA
Statistics
Matches: 99, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
118 6 0.06
119 48 0.48
120 41 0.41
121 4 0.04
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.45
Consensus pattern (118 bp):
TTATCTTCTAGCAATCTTCTTTTCGCTTTATCTCCCTCATCATCAGATGTTTTTCACTGGCAGAC
AAACTTTCTAATTCAACATCGTCTTCTAGTAATCTTTCTTTACGCTGCTCCCC
Found at i:173529 original size:84 final size:83
Alignment explanation
Indices: 173373--173895 Score: 363
Period size: 84 Copynumber: 6.2 Consensus size: 83
173363 TCTCCCCTTA
* * *
173373 TCTTCTAGTAATCTTCTTTTC-AGCTTTTCTCCCTCATCATCATATGGTTTTTCACTGGCCGACA
1 TCTTCTAGTAATCTTCTTTTCGA-CTTCTCCCCCTCATCATCATATGGTTTTTCACTGGCC-AAA
* *
173437 GACGTTTTGGTTTAACACAG
64 GACTTTTTGATTTAACACAG
* * * * * *
173457 TCTTCTCA-TAATCTTCTTTACGACTGCTCCCCCTCATCATCATATGGTTTTTTACCGACCAATG
1 TCTTCT-AGTAATCTTCTTTTCGACTTCTCCCCCTCATCATCATATGGTTTTTCACTGGCCAA-A
* *
173521 GAATTTTTGATTAAACATC-G
64 GACTTTTTGATTTAACA-CAG
* * * *
173541 TCCTCTAGTAATCTTCTTTTC-AGCTTCTCTCTCC-CATCATTAGATGGTTTTTCACTGGCCTAA
1 TCTTCTAGTAATCTTCTTTTCGA-CTTCTC-CCCCTCATCATCATATGGTTTTTCACTGGCC-AA
* *
173604 AGACTTTCTGATTTAACACAT
63 AGACTTTTTGATTTAACACAG
* * * *
173625 TCTTCTAGTAAACTTCTTTTCG-CTTCTCTCCCTCATCATCATATGGTTTTTCAAC-CGCGGACA
1 TCTTCTAGTAATCTTCTTTTCGACTTCTCCCCCTCATCATCATATGGTTTTTC-ACTGGC-CA-A
* *
173688 A-ACTTTCTGATCTAACACTA-
63 AGACTTTTTGATTTAACAC-AG
* * * * * * * *
173708 CCTTCTAGTAATTTTCTTTTCGACTTATCTCTCTCAT-ATTCAGATGGTTTTTCACTGGTCGACA
1 TCTTCTAGTAATCTTCTTTTCGACTTCTCCCCCTCATCA-TCATATGGTTTTTCACTGG-CCAAA
* * **
173772 GACTTTCTGATTCAACATTG
64 GACTTTTTGATTTAACACAG
* * * * ** *
173792 TCTTCTAGTAATCTTCTTTTC-AGCTT-TGCTCTCTTATCATCAGATGGTTTTTCACCT-ATCGA
1 TCTTCTAGTAATCTTCTTTTCGA-CTTCT-CCCCCTCATCATCATATGGTTTTTCA-CTGGCCAA
* *
173854 AGAACTTTTTGATTCAACACCG
63 AG-ACTTTTTGATTTAACACAG
173876 TCATT-TAGTAATCTTCTTTT
1 TC-TTCTAGTAATCTTCTTTT
173896 TGGCTTCCCC
Statistics
Matches: 353, Mismatches: 59, Indels: 54
0.76 0.13 0.12
Matches are distributed among these distances:
82 2 0.01
83 73 0.21
84 264 0.75
85 14 0.04
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.42
Consensus pattern (83 bp):
TCTTCTAGTAATCTTCTTTTCGACTTCTCCCCCTCATCATCATATGGTTTTTCACTGGCCAAAGA
CTTTTTGATTTAACACAG
Found at i:173755 original size:167 final size:170
Alignment explanation
Indices: 173374--173845 Score: 515
Period size: 167 Copynumber: 2.8 Consensus size: 170
173364 CTCCCCTTAT
* * *
173374 CTTCTAGTAATCTTCTTTTCAGCTTTTCTCCCTCATCA-TCATATGGTTTTTCACTGGCCGACAG
1 CTTCTAGTAATCTTCTTTTCAGCTTATCTCTCTCATCATTCAGATGGTTTTTCACTGGCCGACAG
* * * * *
173438 ACGTTT-TGGTTTAACACAGTCTTCTCA-TAATCTTCTTTACGACTGCTCCCCCTCATCATCATA
66 AC-TTTCTGATTTAACACATTCTTCT-AGTAATCTTCTTTTCG-CTTCTCTCCCTCATCATCATA
* ** *
173501 TGGTTTTT-TACCGACCAATGGAATTTTTGATTAAACATCGTC
128 TGGTTTTTCAACCGACCAATCAAATTTCTGATTAAACATCGTC
* * * *
173543 C-TCTAGTAATCTTCTTTTCAGCTTCTCTCTCCCATCATT-AGATGGTTTTTCACTGGCCTAAAG
1 CTTCTAGTAATCTTCTTTTCAGCTTATCTCTCTCATCATTCAGATGGTTTTTCACTGGCCGACAG
*
173606 ACTTTCTGATTTAACACATTCTTCTAGTAAACTTCTTTTCGCTTCTCTCCCTCATCATCATATGG
66 ACTTTCTGATTTAACACATTCTTCTAGTAATCTTCTTTTCGCTTCTCTCCCTCATCATCATATGG
**
173671 TTTTTCAACCG-CGGA-CAAACTTTCTGATCT-AACA-C-TAC
131 TTTTTCAACCGACCAATCAAA-TTTCTGAT-TAAACATCGT-C
* *
173709 CTTCTAGTAATTTTCTTTTC-GACTTATCTCTCTCAT-ATTCAGATGGTTTTTCACTGGTCGACA
1 CTTCTAGTAATCTTCTTTTCAG-CTTATCTCTCTCATCATTCAGATGGTTTTTCACTGGCCGACA
* * * * *
173772 GACTTTCTGATTCAACA-TTGTCTTCTAGTAATCTTCTTTTCAGCTT-TGCTCTCTTATCATCAG
65 GACTTTCTGATTTAACACAT-TCTTCTAGTAATCTTCTTTTC-GCTTCT-CTCCCTCATCATCAT
173835 ATGGTTTTTCA
127 ATGGTTTTTCA
173846 CCTATCGAAG
Statistics
Matches: 260, Mismatches: 30, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
165 1 0.00
166 10 0.04
167 130 0.50
168 117 0.45
169 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (170 bp):
CTTCTAGTAATCTTCTTTTCAGCTTATCTCTCTCATCATTCAGATGGTTTTTCACTGGCCGACAG
ACTTTCTGATTTAACACATTCTTCTAGTAATCTTCTTTTCGCTTCTCTCCCTCATCATCATATGG
TTTTTCAACCGACCAATCAAATTTCTGATTAAACATCGTC
Found at i:173817 original size:251 final size:252
Alignment explanation
Indices: 173373--173846 Score: 575
Period size: 251 Copynumber: 1.9 Consensus size: 252
173363 TCTCCCCTTA
* * * *
173373 TCTTCTAGTAATCTTCTTTTCAGCTTTTCTCCCTCATCATCATATGGTTTTTCACTGGCCGACAG
1 TCTTCTAGTAAACTTCTTTTCAGCTTCTCTCCCTCATCATCATATGGTTTTTCACTCGCCGACAA
* * * * *
173438 ACGTTTTGGTTTAACACAGTCTTCTCATAATCTTCTTTACGACTGCTCCCCCTCATCATCATATG
66 ACGTTTTGATCTAACACAGCCTTCTCATAATCTTCTTTACGACTGATCCCCCTCATCATCAGATG
* ** *
173503 GTTTTTTACCGACCAATGGAATTTTTGATTAAACATCGTCCTCTAGTAATCTTCTTTTCAGCTTC
131 GTTTTTCACCGACCAACAGAATTTCTGATTAAACATCGTCCTCTAGTAATCTTCTTTTCAGCTT-
*
173568 T-CTCTCCCATCATTAGATGGTTTTTCACTGGCCTAAAGACTTTCTGATTTAACACAT
195 TGCTCTCCCATCATCAGATGGTTTTTCACTGGCCTAAAGACTTTCTGATTTAACACAT
*
173625 TCTTCTAGTAAACTTCTTTTC-GCTTCTCTCCCTCATCATCATATGGTTTTTCAAC-CGCGGACA
1 TCTTCTAGTAAACTTCTTTTCAGCTTCTCTCCCTCATCATCATATGGTTTTTC-ACTCGCCGACA
* * * * *
173688 AAC-TTTCTGATCTAACACTA-CCTTCT-AGTAATTTTCTTTTCGACTTATCTCTCTCAT-ATTC
65 AACGTTT-TGATCTAACAC-AGCCTTCTCA-TAATCTTCTTTACGACTGATCCCCCTCATCA-TC
* ** * * * * *
173749 AGATGGTTTTTCACTGGTCGACAGACTTTCTGATTCAACATTGTCTTCTAGTAATCTTCTTTTCA
126 AGATGGTTTTTCACCGACCAACAGAATTTCTGATTAAACATCGTCCTCTAGTAATCTTCTTTTCA
**
173814 GCTTTGCTCTCTTATCATCAGATGGTTTTTCAC
191 GCTTTGCTCTCCCATCATCAGATGGTTTTTCAC
173847 CTATCGAAGA
Statistics
Matches: 186, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
250 6 0.03
251 157 0.84
252 23 0.12
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.42
Consensus pattern (252 bp):
TCTTCTAGTAAACTTCTTTTCAGCTTCTCTCCCTCATCATCATATGGTTTTTCACTCGCCGACAA
ACGTTTTGATCTAACACAGCCTTCTCATAATCTTCTTTACGACTGATCCCCCTCATCATCAGATG
GTTTTTCACCGACCAACAGAATTTCTGATTAAACATCGTCCTCTAGTAATCTTCTTTTCAGCTTT
GCTCTCCCATCATCAGATGGTTTTTCACTGGCCTAAAGACTTTCTGATTTAACACAT
Found at i:181279 original size:223 final size:228
Alignment explanation
Indices: 181020--181441 Score: 665
Period size: 223 Copynumber: 1.9 Consensus size: 228
181010 TTTCTCTCCC
* *
181020 TCATCATCATCATTAAGTGGTTTTTCACCGGCGAACGGACTCTCTTCCTCGACATCTAGACTATT
1 TCATCATCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTAGACTATT
181085 CGCTTCAACATCGTCTCCTAGTAAACTTATTTTCGGCTTCTCT-C-C-TCATCATCATCATCAAG
66 CGCTTCAACATCGTCTCCTAGTAAACTTATTTTCGGCTTCTCTCCTCATCATCATCATCATCAAG
181147 TGG-TTTTCACCAACAAAAGGA-CTCTTCCTCAACATCTGGACTTTTAGCTTCAACGTCGTCTCC
131 TGGTTTTTCACCAACAAAAGGACCTCTTCCTCAACATCTGGACTTTTAGCTTCAACGTCGTCTCC
181210 TAGTAATATTCTTTTCTTCTCTCCCTCTCATCA
196 TAGTAATATTCTTTTCTTCTCTCCCTCTCATCA
* *
181243 TCATCATCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTT
1 TCATCATCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTAGACTATT
** * * *
181308 CGCTTCAATGTCTTCTCCTAGTAATCTTCTTTTCGGCTTCTCTCCCTCATCATCATCATCATCAA
66 CGCTTCAACATCGTCTCCTAGTAAACTTATTTTCGGCTTCTCT-CCTCATCATCATCATCATCAA
* * * * *
181373 GTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTCAACGTCGTCT
130 GTGGTTTTTCACCAACAAAAGGAC-CTCTTCCTCAACATCTGGACTTTTAGCTTCAACGTCGTCT
181438 CCTA
194 CCTA
181442 TCGGCTTCTC
Statistics
Matches: 178, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
223 99 0.56
225 1 0.01
226 1 0.01
227 20 0.11
228 15 0.08
230 42 0.24
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (228 bp):
TCATCATCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTAGACTATT
CGCTTCAACATCGTCTCCTAGTAAACTTATTTTCGGCTTCTCTCCTCATCATCATCATCATCAAG
TGGTTTTTCACCAACAAAAGGACCTCTTCCTCAACATCTGGACTTTTAGCTTCAACGTCGTCTCC
TAGTAATATTCTTTTCTTCTCTCCCTCTCATCA
Found at i:181467 original size:93 final size:93
Alignment explanation
Indices: 181363--181737 Score: 536
Period size: 93 Copynumber: 3.8 Consensus size: 93
181353 CTCATCATCA
181363 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181428 AACGTCGTCTCCTATCGGCTTCTCTCCC
66 AACGTCGTCTCCTATCGGCTTCTCTCCC
* *
181456 TCATCATCAAGTGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181521 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCCTC
66 AACGTCGTCT-C-------C-TA---TCGGCTTCTCT-CC-C
*
181563 ATCATCATCATCAAGTGGTTTTTCACCAGCGAACGGGCTCTCTTCCTCGACATCTGGACTTTT-G
1 ----TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCG
181627 CTTCAACGTCGTCTCCTATCGGCTTCTCTCCC
62 CTTCAACGTCGTCTCCTATCGGCTTCTCTCCC
* *
181659 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACTTCTGGACTTTTCGCTTG
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181724 AACGTCGTCTCCTA
66 AACGTCGTCTCCTA
181738 GTAATCTTCT
Statistics
Matches: 255, Mismatches: 8, Indels: 38
0.85 0.03 0.13
Matches are distributed among these distances:
92 57 0.22
93 91 0.36
94 1 0.00
96 1 0.00
97 2 0.01
98 11 0.04
101 3 0.01
102 3 0.01
105 11 0.04
106 2 0.01
107 1 0.00
109 1 0.00
110 15 0.06
111 56 0.22
ACGTcount: A:0.17, C:0.33, G:0.16, T:0.34
Consensus pattern (93 bp):
TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
AACGTCGTCTCCTATCGGCTTCTCTCCC
Found at i:181591 original size:111 final size:111
Alignment explanation
Indices: 181456--181763 Score: 420
Period size: 111 Copynumber: 2.9 Consensus size: 111
181446 CTTCTCTCCC
* *
181456 TCATCATCAAGTGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181521 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCCTCATCA
66 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCCTCATCA
*
181567 TCATCATCAAGTGGTTTTTCACCAGCGAACGGGCTCTCTTCCTCGACATCTGGACTTTT-GCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181631 AACGTCGTCT-C-------C-TA---TCGGCTTCTCTCCCTCATCA
66 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCCTCATCA
* *
181665 T------CAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACTTCTGGACTTTTCGCTTG
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
* *
181724 AACGTCGTCTCCTAGTAATCTTCTTTTCGCCTTCTCTCCC
66 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCC
181764 CCTTGTAGAA
Statistics
Matches: 176, Mismatches: 8, Indels: 32
0.81 0.04 0.15
Matches are distributed among these distances:
92 50 0.28
93 14 0.08
94 1 0.01
98 21 0.12
101 3 0.02
102 2 0.01
105 13 0.07
109 1 0.01
110 15 0.09
111 56 0.32
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (111 bp):
TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCCTCATCA
Found at i:181711 original size:92 final size:93
Alignment explanation
Indices: 181567--181737 Score: 308
Period size: 92 Copynumber: 1.8 Consensus size: 93
181557 TCCCTCATCA
*
181567 TCATCATCAAGTGGTTTTTCACCAGCGAACGGGCTCTCTTCCTCGACATCTGGACTTTT-GCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181631 AACGTCGTCTCCTATCGGCTTCTCTCCC
66 AACGTCGTCTCCTATCGGCTTCTCTCCC
* *
181659 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACTTCTGGACTTTTCGCTTG
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
181724 AACGTCGTCTCCTA
66 AACGTCGTCTCCTA
181738 GTAATCTTCT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 57 0.76
93 18 0.24
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (93 bp):
TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
AACGTCGTCTCCTATCGGCTTCTCTCCC
Found at i:181715 original size:203 final size:205
Alignment explanation
Indices: 181249--181763 Score: 917
Period size: 203 Copynumber: 2.5 Consensus size: 205
181239 ATCATCATCA
181249 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
* *
181314 AATGTCTTCTCCTAGTAATCTTCTTTTCGGCTTCTCTCCCTCATCATCATCATCATCAAGTGGTT
66 AACGTCGTCTCCTAGTAATCTTCTTTTCGGCTTCTCT-CC-CATCATCATCATCATCAAGTGGTT
181379 TTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTCAACGTCGTCTCCTATC
129 TTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTCAACGTCGTCTCCTATC
181444 GGCTTCTCTCCC
194 GGCTTCTCTCCC
* *
181456 TCATCATCAAGTGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
*
181521 AACGTCGTCTCCTAGTAATCTTATTTTCGGCTTCTCTCCC-TCATCATCATCATCAAGTGGTTTT
66 AACGTCGTCTCCTAGTAATCTTCTTTTCGGCTTCTCTCCCATCATCATCATCATCAAGTGGTTTT
*
181585 TCACCAGCGAACGGGCTCTCTTCCTCGACATCTGGACTTTT-GCTTCAACGTCGTCTCCTATCGG
131 TCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTCAACGTCGTCTCCTATCGG
181649 CTTCTCTCCC
196 CTTCTCTCCC
* *
181659 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACTTCTGGACTTTTCGCTTG
1 TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
*
181724 AACGTCGTCTCCTAGTAATCTTCTTTTCGCCTTCTCTCCC
66 AACGTCGTCTCCTAGTAATCTTCTTTTCGGCTTCTCTCCC
181764 CCTTGTAGAA
Statistics
Matches: 296, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
203 132 0.45
204 64 0.22
205 1 0.00
206 2 0.01
207 97 0.33
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.36
Consensus pattern (205 bp):
TCATCATCAAGTGGTTTTTCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTC
AACGTCGTCTCCTAGTAATCTTCTTTTCGGCTTCTCTCCCATCATCATCATCATCAAGTGGTTTT
TCACCAGCGAACGGACTCTCTTCCTCGACATCTGGACTTTTCGCTTCAACGTCGTCTCCTATCGG
CTTCTCTCCC
Found at i:191951 original size:12 final size:12
Alignment explanation
Indices: 191936--191982 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
191926 CCGGTTTTTT
*
191936 AACCGGATAAAA
1 AACCGGTTAAAA
191948 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
191963 AACCGGTTAAAA
1 AACCGGTTAAAA
191975 AACCGGTT
1 AACCGGTT
191983 TTTATCCGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:194287 original size:21 final size:21
Alignment explanation
Indices: 194263--194302 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
194253 TTTATTTTAT
194263 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
194284 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
194303 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:194350 original size:33 final size:33
Alignment explanation
Indices: 194297--194396 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
194287 TTTGTTTCAA
194297 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
194329 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
194362 TTATCAAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATC-GAACTTGGAAGTTTTTAAGTATTTGAAT
194396 T
1 T
194397 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 11 0.17
33 26 0.41
34 26 0.41
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:194425 original size:13 final size:13
Alignment explanation
Indices: 194382--194436 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
194372 TTGGAAGTAT
194382 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
194395 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
194409 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
194422 TTAAGTATTTGAA
1 TTAAGTATTTCAA
194435 TT
1 TT
194437 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:195003 original size:15 final size:17
Alignment explanation
Indices: 194977--195008 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
194967 TTCTATGGGA
194977 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
194993 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
195009 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:196929 original size:4 final size:4
Alignment explanation
Indices: 196907--196949 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
196897 TCTCACCAAA
* * *
196907 ATAC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
196950 AAAACCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:199448 original size:23 final size:23
Alignment explanation
Indices: 199416--199496 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
199406 CCAACACGCT
199416 GGGCATCCGAGCGAGCTATGCGA
1 GGGCATCCGAGCGAGCTATGCGA
* * * *
199439 GAGCATCCGAGGCCATCCGAT-CGA
1 GGGCATCCGA-GCGA-GCTATGCGA
199463 GGGCATCCGAGCGAGCTATGCGA
1 GGGCATCCGAGCGAGCTATGCGA
199486 GGGCATCCGAG
1 GGGCATCCGAG
199497 GGCAAGAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.06
23 26 0.55
24 15 0.32
25 3 0.06
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.12
Consensus pattern (23 bp):
GGGCATCCGAGCGAGCTATGCGA
Found at i:199568 original size:29 final size:29
Alignment explanation
Indices: 199526--199601 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
199516 GGAGCAGGAG
199526 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCC
199555 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCC
*
199584 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCGACCTA
199602 TGTTTGGGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.21, C:0.29, G:0.37, T:0.13
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCC
Found at i:208745 original size:21 final size:21
Alignment explanation
Indices: 208719--208876 Score: 148
Period size: 21 Copynumber: 7.7 Consensus size: 21
208709 CGAATATGTA
208719 AATCGCAACGCGATAATACGT
1 AATCGCAACGCGATAATACGT
* **
208740 AATCGCAACGTGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACGT
*
208761 -ATCGCAACGTGATAATACGT
1 AATCGCAACGCGATAATACGT
* * **
208781 AATCGCAATGTGATTCTGAC--
1 AATCGCAACGCGATAAT-ACGT
*
208801 AATCGCAACGCGATAATAAGT
1 AATCGCAACGCGATAATACGT
**
208822 AATCGCAACGCGATTCTAAC-T
1 AATCGCAACGCGATAAT-ACGT
208843 -ATCGCAACGCGATAATACGT
1 AATCGCAACGCGATAATACGT
208863 AATCGCAACGCGAT
1 AATCGCAACGCGAT
208877 TCTGACTATC
Statistics
Matches: 110, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.05
20 43 0.39
21 57 0.52
22 5 0.05
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
AATCGCAACGCGATAATACGT
Found at i:208765 original size:41 final size:41
Alignment explanation
Indices: 208720--208891 Score: 281
Period size: 41 Copynumber: 4.2 Consensus size: 41
208710 GAATATGTAA
*
208720 ATCGCAACGCGATAATACGTAATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
* * * *
208761 ATCGCAACGTGATAATACGTAATCGCAATGTGATTCTGACA
1 ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
* *
208802 ATCGCAACGCGATAATAAGTAATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
208843 ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
208884 ATCGCAAC
1 ATCGCAAC
208892 ACTGAATTTC
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 120 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGATAATACGTAATCGCAACGCGATTCTGACT
Found at i:212032 original size:18 final size:18
Alignment explanation
Indices: 212006--212040 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
211996 AGCAAAAGGC
* *
212006 AATCGAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
212024 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
212041 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:212369 original size:140 final size:140
Alignment explanation
Indices: 212098--212516 Score: 756
Period size: 140 Copynumber: 3.0 Consensus size: 140
212088 GCAAACGTTG
212098 TATTATGTGTA-TTT-TATGT--ACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
212159 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
212224 CGAATTTGAC
131 CGAATTTGAC
212234 TATTATGTGTATTTTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
212299 TTGAACATTGCTATGATATGTTCAGTTGTTATCATTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
212364 CGAATTTGAC
131 CGAATTTGAC
* *
212374 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
212439 TTGAACATTGTTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
212504 CGAATTTGAC
131 CGAATTTGAC
212514 TAT
1 TAT
212517 CACAATGCGA
Statistics
Matches: 272, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
136 11 0.04
137 3 0.01
138 5 0.02
140 253 0.93
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:212616 original size:74 final size:74
Alignment explanation
Indices: 212495--212635 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 74
212485 TCATTTGAAT
* * * ** *
212495 ATCGCAACGCGAATTTGACTATCACAATGCGAATTTGACTATCGCAACGTGAATTTGACTATTGC
1 ATCGCAACGCGAATTTGACTATCACAACGCAAATTTGACAATCGCAACACGAATTTGACTATCGC
212560 AATGCAAAA
66 AATGCAAAA
* *
212569 ATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACAATTGCAACACGAATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCACAACGCAAATTTGACAATCGCAACACGAATTTGACTATCGC
212634 AA
66 AA
212636 CGTGCATTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCACAACGCAAATTTGACAATCGCAACACGAATTTGACTATCGC
AATGCAAAA
Found at i:212646 original size:20 final size:20
Alignment explanation
Indices: 212487--212637 Score: 161
Period size: 20 Copynumber: 7.8 Consensus size: 20
212477 TTACACATTC
*
212487 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
212507 ATTTGACTATCACAATGCGA
1 ATTTGACTATCGCAACGCGA
*
212527 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
212547 ATTTGACTATTGCAATGC-A
1 ATTTGACTATCGCAACGCGA
*
212566 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
212581 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* * *
212601 ATTTGACAATTGCAACACGA
1 ATTTGACTATCGCAACGCGA
212621 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
212638 TGCATTTGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
14 8 0.08
15 3 0.03
19 3 0.03
20 90 0.87
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Done.