Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 15
Found at i:1673 original size:15 final size:15
Alignment explanation
Indices: 1649--1678 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1639 TTATGGGTGC
1649 AATGCAACATATGTT
1 AATGCAACATATGTT
*
1664 AATGCCACATATGTT
1 AATGCAACATATGTT
1679 CATGGAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (15 bp):
AATGCAACATATGTT
Found at i:6188 original size:18 final size:19
Alignment explanation
Indices: 6154--6189 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6144 AAATTCGAAC
6154 TTCAAATCAGAATTAAAAA
1 TTCAAATCAGAATTAAAAA
6173 TTCAAATCAG-ATTAAAA
1 TTCAAATCAGAATTAAAA
6190 TTAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (19 bp):
TTCAAATCAGAATTAAAAA
Found at i:9238 original size:37 final size:38
Alignment explanation
Indices: 9188--9264 Score: 129
Period size: 37 Copynumber: 2.0 Consensus size: 38
9178 AGTACACGAA
*
9188 AAAGATCATAGAGAAAACCCATTAGAGAG-ATGAACAT
1 AAAGATCATAGAGAAAAACCATTAGAGAGAATGAACAT
9225 AAAGATCATAGAGAAAAACCATTAGAGAGAAATGAACAT
1 AAAGATCATAGAGAAAAACCATTAGAGAG-AATGAACAT
9264 A
1 A
9265 CTTACATCCG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 28 0.76
39 9 0.24
ACGTcount: A:0.55, C:0.12, G:0.18, T:0.16
Consensus pattern (38 bp):
AAAGATCATAGAGAAAAACCATTAGAGAGAATGAACAT
Found at i:10297 original size:20 final size:20
Alignment explanation
Indices: 10272--10312 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10262 TTCAAGGTAG
10272 AAGGAGCTGATGCCAAGAAC
1 AAGGAGCTGATGCCAAGAAC
10292 AAGGAGCTGATGCCAAGAAC
1 AAGGAGCTGATGCCAAGAAC
10312 A
1 A
10313 TCTTCTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.29, T:0.10
Consensus pattern (20 bp):
AAGGAGCTGATGCCAAGAAC
Found at i:18232 original size:11 final size:11
Alignment explanation
Indices: 18216--18240 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18206 CAGTAAATGT
18216 TTTCATGTAAA
1 TTTCATGTAAA
18227 TTTCATGTAAA
1 TTTCATGTAAA
18238 TTT
1 TTT
18241 TAATACACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTCATGTAAA
Found at i:18592 original size:22 final size:23
Alignment explanation
Indices: 18562--18605 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
18552 CATACATTAT
*
18562 TATGTATTATTAT-AATAAAACG
1 TATGCATTATTATCAATAAAACG
18584 TATGCATTATTATGCAATAAAA
1 TATGCATTATTAT-CAATAAAA
18606 ACCCCACGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
TATGCATTATTATCAATAAAACG
Found at i:19275 original size:36 final size:34
Alignment explanation
Indices: 19228--19314 Score: 111
Period size: 36 Copynumber: 2.5 Consensus size: 34
19218 CAAAATGGTC
* * *
19228 ATTTCCAATACTATTGGAATAACCTAATTTGAGTAT
1 ATTTCAAATACTAGTGGAATAACCTAA-TT-AGCAT
*
19264 ATTTCAAATACTAGTGGGATAACCTAATTAGCAT
1 ATTTCAAATACTAGTGGAATAACCTAATTAGCAT
*
19298 ATTTCTAATACTAGTGG
1 ATTTCAAATACTAGTGG
19315 TATGGCCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 20 0.43
35 2 0.04
36 24 0.52
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (34 bp):
ATTTCAAATACTAGTGGAATAACCTAATTAGCAT
Found at i:19308 original size:34 final size:36
Alignment explanation
Indices: 19228--19334 Score: 119
Period size: 34 Copynumber: 3.0 Consensus size: 36
19218 CAAAATGGTC
* * *
19228 ATTTCCAATACTATTGGAATAACCTAATTTGAGTAT
1 ATTTCAAATACTAGTGGAATAACCTAATTTGAGCAT
*
19264 ATTTCAAATACTAGTGGGATAACCTAA-TT-AGCAT
1 ATTTCAAATACTAGTGGAATAACCTAATTTGAGCAT
* * **
19298 ATTTCTAATACTAGTGGTATGGCCTAATTATGAGCAT
1 ATTTCAAATACTAGTGGAATAACCTAATT-TGAGCAT
19335 TATCAACAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
34 27 0.45
35 3 0.05
36 25 0.42
37 5 0.08
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (36 bp):
ATTTCAAATACTAGTGGAATAACCTAATTTGAGCAT
Found at i:20836 original size:24 final size:23
Alignment explanation
Indices: 20792--20836 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
20782 TTTATATTTC
*
20792 TTTTCTATAGTTTTATCTTTTAT
1 TTTTCTATAGTTTTAGCTTTTAT
* *
20815 TTTTCTTATATTTTTAGGTTTT
1 TTTTC-TATAGTTTTAGCTTTT
20837 TCTCAGTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTCTATAGTTTTAGCTTTTAT
Found at i:26884 original size:11 final size:11
Alignment explanation
Indices: 26868--26894 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
26858 ACCACACTCT
26868 AAAAAAAAGAA
1 AAAAAAAAGAA
26879 AAAAAAAAGAA
1 AAAAAAAAGAA
26890 AAAAA
1 AAAAA
26895 TGAGATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:29327 original size:24 final size:23
Alignment explanation
Indices: 29283--29327 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
29273 TTTATATTTC
*
29283 TTTTCTATAGTTTTATCTTTTAT
1 TTTTCTATAGTTTTAGCTTTTAT
* *
29306 TTTTCTTATATTTTTAGGTTTT
1 TTTTC-TATAGTTTTAGCTTTT
29328 TCTCAGTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTCTATAGTTTTAGCTTTTAT
Found at i:41225 original size:33 final size:33
Alignment explanation
Indices: 41183--41253 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
41173 TATACAAAGT
*
41183 AGAAGTCATGGAAATTACTACAAAGGCATTAAA
1 AGAAGTCATGGAAATTACTACAAAGACATTAAA
41216 AGAAGTCATGGAAATTACTACAAAGACATTAAA
1 AGAAGTCATGGAAATTACTACAAAGACATTAAA
41249 AGAAG
1 AGAAG
41254 ATAGAAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (33 bp):
AGAAGTCATGGAAATTACTACAAAGACATTAAA
Found at i:45411 original size:21 final size:20
Alignment explanation
Indices: 45383--45426 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
45373 TAAAAATTAA
* *
45383 ATTTATAATTATATTAATTT
1 ATTTATAATCATATCAATTT
*
45403 ATTTAATAATCATGTCAATTT
1 ATTT-ATAATCATATCAATTT
45424 ATT
1 ATT
45427 CGCCAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTTATAATCATATCAATTT
Found at i:46013 original size:21 final size:21
Alignment explanation
Indices: 45987--46037 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
45977 CTTGGCGTTA
45987 ATGGGTCTGAGCCAGA-TTTTG
1 ATGGGTCTGAGCCA-ATTTTTG
*
46008 ATGGGT-TCAAGCCAATTTTTG
1 ATGGGTCT-GAGCCAATTTTTG
46029 ATGGGTCTG
1 ATGGGTCTG
46038 CGCCGGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
ATGGGTCTGAGCCAATTTTTG
Found at i:46513 original size:3 final size:3
Alignment explanation
Indices: 46505--46542 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
46495 AACCACCGAT
46505 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
46543 AACAGACGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:52121 original size:19 final size:19
Alignment explanation
Indices: 52093--52138 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
52083 GATGAAGGAT
52093 TGATTATGTGATGTTTATAG
1 TGATT-TGTGATGTTTATAG
52113 TGATTTGTGATGTTTATAG
1 TGATTTGTGATGTTTATAG
52132 TGATTTG
1 TGATTTG
52139 GAAATAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (19 bp):
TGATTTGTGATGTTTATAG
Found at i:54774 original size:31 final size:31
Alignment explanation
Indices: 54711--54798 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
54701 GAAGGACCTA
* *
54711 TCCATATATTCTGAAGAACATAGGT-AACTG
1 TCCATATATCCTGAAGGACATAGGTAAACTG
*
54741 TCCATATATCCCGAAGGACATAGGTAAACTG
1 TCCATATATCCTGAAGGACATAGGTAAACTG
*
54772 TCCATATGTCCTGAAGGACATAGGTAA
1 TCCATATATCCTGAAGGACATAGGTAA
54799 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
30 22 0.42
31 30 0.58
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCATATATCCTGAAGGACATAGGTAAACTG
Found at i:57459 original size:14 final size:14
Alignment explanation
Indices: 57440--57467 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57430 ACCATTAAAA
57440 ATTTGTCAGAGCAT
1 ATTTGTCAGAGCAT
57454 ATTTGTCAGAGCAT
1 ATTTGTCAGAGCAT
57468 GTGTACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
ATTTGTCAGAGCAT
Found at i:57990 original size:30 final size:31
Alignment explanation
Indices: 57956--58015 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
57946 TCCGAAGAAC
57956 ATAGGT-AACTGTCCATATGTCCCAAATGAT
1 ATAGGTAAACTGTCCATATGTCCCAAATGAT
** *
57986 ATAGGTAAACTGTTTATATGTCCCGAATGA
1 ATAGGTAAACTGTCCATATGTCCCAAATGA
58016 CATATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (31 bp):
ATAGGTAAACTGTCCATATGTCCCAAATGAT
Found at i:63254 original size:18 final size:17
Alignment explanation
Indices: 63233--63291 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
63223 AACCAACATA
*
63233 CTTAAATAAACTAGCATG
1 CTTAAATGAACT-GCATG
*
63251 CTTAATTGAACTGCATG
1 CTTAAATGAACTGCATG
* *
63268 CTTTAATGAACTGTATG
1 CTTAAATGAACTGCATG
63285 CTTAAAT
1 CTTAAAT
63292 CAAGTACATG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
17 25 0.71
18 10 0.29
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (17 bp):
CTTAAATGAACTGCATG
Found at i:64962 original size:32 final size:32
Alignment explanation
Indices: 64921--64984 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
64911 ATTTTGGTCA
64921 CTAATCATGGGTCTTTTATAAATCCAAAATAG
1 CTAATCATGGGTCTTTTATAAATCCAAAATAG
64953 CTAATCATGGGTCTTTTATAAATCCAAAATAG
1 CTAATCATGGGTCTTTTATAAATCCAAAATAG
64985 TTCAGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (32 bp):
CTAATCATGGGTCTTTTATAAATCCAAAATAG
Found at i:71644 original size:3 final size:3
Alignment explanation
Indices: 71623--71712 Score: 67
Period size: 3 Copynumber: 30.0 Consensus size: 3
71613 TTTGTCCGTT
* * * *
71623 TTA TTT TTA TTA TTT TTA TTA TTA -TA TTTG TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * * *
71668 TAA TTA TTA CTA TTA TTA -TA TTT TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
71713 CATATTACAT
Statistics
Matches: 65, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 4 0.06
3 58 0.89
4 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:71656 original size:21 final size:21
Alignment explanation
Indices: 71623--71710 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
71613 TTTGTCCGTT
* **
71623 TTATTTTTATTATTTTTATTA
1 TTATATTTATTATAATTATTA
*
71644 TTATATTTGTTATAATTATTA
1 TTATATTTATTATAATTATTA
*
71665 TTATAATTATTACT-ATTATTA
1 TTATATTTATTA-TAATTATTA
* *
71686 -TATTTTTATTAATAAATATTA
1 TTATATTTATT-ATAATTATTA
71707 TTAT
1 TTAT
71711 TACATATTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 9 0.17
21 41 0.76
22 4 0.07
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATATTTATTATAATTATTA
Found at i:75671 original size:2 final size:2
Alignment explanation
Indices: 75664--75746 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
75654 CCCATAATAC
75664 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
75706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75747 CAGGACCACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76169 original size:55 final size:56
Alignment explanation
Indices: 76078--76554 Score: 604
Period size: 55 Copynumber: 8.7 Consensus size: 56
76068 GGGTTCACTT
* * * *
76078 CCTATTTCTTTCAG-GCAGTAT-AGAACTCGAATAATCTTTAATAATCGTGTTTGCTC
1 CCTATTTCTTTCAGAG-AGTATGAG-ACTCGAACAATCTTCAACAATCGTGTCTGCTC
* *
76134 TCTATTTCTTT-AGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTATGCTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
76189 CCTATTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
* * * *
76244 CTTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTGTGTTTGCTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
* * * * *
76299 CCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAATAATTGTGCCTACTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
* * *
76354 CCTA-TTCTTTCAGGGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGCTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
* *
76409 CCTA-TTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGCTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
* *
76464 CCTA-TTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT-TCGTTC
1 CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT-GCTC
* *
76519 CCTA-TTC-TTCAGGGAGTAT-AGAACTC-AAAAATCTTC
1 CCTATTTCTTTCAGAGAGTATGAG-ACTCGAACAATCTTC
76555 TTCTTACGGG
Statistics
Matches: 388, Mismatches: 27, Indels: 15
0.90 0.06 0.03
Matches are distributed among these distances:
53 11 0.03
54 21 0.05
55 343 0.88
56 13 0.03
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (56 bp):
CCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
Found at i:76581 original size:54 final size:54
Alignment explanation
Indices: 76523--77368 Score: 1103
Period size: 54 Copynumber: 15.6 Consensus size: 54
76513 TCGTTCCCTA
*
76523 TTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
76577 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTC-AAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
** *
76632 TTCTTCAGGAAGTATAGAACTCAAGTATCTTCTTCTTACGGGTTCACTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
76686 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTAT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
76740 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTATGGGGTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTC-AAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
76795 TTCTTCAGGAAGTATAGAACTCAAGAATCTTCTTCTTACGGGTTCGCTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTAC-GG---G-TTCGCTCCCTCT
* * * * ** * *
76854 TTCTTTAGGAAGTATAGAACTCGAACATTTTCTTCAAACGGATTCGTTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
76908 TTCTTCAGGAAGTATAAAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * * *
76962 TTCTTCTGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTCGCTACCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
77016 TTCTTCAGGAACTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * * *
77070 TTCTTTAGGAAGTATAGAACTCGAAAATATTCTTCTTACAGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * **
77124 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * **
77178 TTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* **** * *
77229 TTCTTCA-GAGAGTATAGAACTCGAACAATCTTCTGAAAATGAGTTCGCTCCCTCT
1 TTCTTCAGGA-AGTATAGAACTC-AAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* ** *
77284 TTCTTCAGGGAGTATAGAACTCAAAAA---TCTTCAAACGGGTTCGGTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
77335 TTCTTCAGGGAGTATAGAACTCGAAAATATTCTT
1 TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTT
77369 TTGCTTCACT
Statistics
Matches: 706, Mismatches: 70, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.00
51 88 0.12
52 3 0.00
54 422 0.60
55 145 0.21
56 1 0.00
58 3 0.00
59 43 0.06
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (54 bp):
TTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
Found at i:83267 original size:21 final size:21
Alignment explanation
Indices: 83243--83297 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
83233 CAATGAGAAG
83243 TGGTCTTCAT-GTCTTTATGAA
1 TGGTCTTC-TCGTCTTTATGAA
* *
83264 TGGTATTCTCGTCTTTATGAC
1 TGGTCTTCTCGTCTTTATGAA
*
83285 TGATCTTCTCGTC
1 TGGTCTTCTCGTC
83298 CTTGGTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTTATGAA
Found at i:85683 original size:2 final size:2
Alignment explanation
Indices: 85676--85727 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
85666 TAATACATAC
85676 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
85718 AT AT AT AT AT
1 AT AT AT AT AT
85728 TTACAGGACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86232 original size:17 final size:17
Alignment explanation
Indices: 86212--86275 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
86202 TTTTTAATAA
*
86212 ATAAATATTTTACTTTT
1 ATAAATATTTTATTTTT
86229 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTATTTTT
86251 AAATAAATATTTTATTTTT
1 --ATAAATATTTTATTTTT
86270 ATAAAT
1 ATAAAT
86276 TATATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 8 0.21
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAAATATTTTATTTTT
Found at i:86241 original size:22 final size:20
Alignment explanation
Indices: 86203--86275 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
86193 TTTCTGATAT
86203 TTTTAATAAATAAATATTTTA
1 TTTT-ATAAATAAATATTTTA
* *
86224 CTTTTATAAATTATATATATTA
1 -TTTTATAAA-TAAATATTTTA
86246 TTTT-TAAATAAATATTTTA
1 TTTTATAAATAAATATTTTA
86265 TTTTTATAAAT
1 -TTTTATAAAT
86276 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.20
20 8 0.18
21 14 0.32
22 13 0.30
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAAATAAATATTTTA
Found at i:86265 original size:19 final size:19
Alignment explanation
Indices: 86209--86270 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
86199 ATATTTTTAA
86209 TAAATAAATATTTTACTTTT
1 TAAATAAATATTTTA-TTTT
* *
86229 ATAAATTATATATATTATTTT
1 -TAAA-TAAATATTTTATTTT
86250 TAAATAAATATTTTATTTT
1 TAAATAAATATTTTATTTT
86269 TA
1 TA
86271 TAAATTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.42
20 4 0.11
21 8 0.22
22 9 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAATAAATATTTTATTTT
Found at i:86282 original size:22 final size:21
Alignment explanation
Indices: 86200--86275 Score: 93
Period size: 22 Copynumber: 3.6 Consensus size: 21
86190 TATTTTCTGA
86200 TATTTTTAATAAATAAATATTT
1 TATTTTT-ATAAATAAATATTT
* * *
86222 TACTTTTATAAATTATATATAT
1 TATTTTTATAAA-TAAATATTT
86244 TA-TTTT-TAAATAAATATTT
1 TATTTTTATAAATAAATATTT
86263 TATTTTTATAAAT
1 TATTTTTATAAAT
86276 TATATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.20
20 8 0.17
21 14 0.30
22 15 0.33
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTATAAATAAATATTT
Found at i:92918 original size:2 final size:2
Alignment explanation
Indices: 92911--92954 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
92901 AAAAAGGAAC
92911 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
92953 AT
1 AT
92955 TAAAATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96984 original size:19 final size:19
Alignment explanation
Indices: 96929--96985 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
96919 GGTTCAGGAA
96929 AATATTATTTAAAATTAAAT
1 AATATTATTT-AAATTAAAT
96949 AGATA--ATTT-AA--AAAT
1 A-ATATTATTTAAATTAAAT
96964 AATATTATTTAAATTAAAT
1 AATATTATTTAAATTAAAT
96983 AAT
1 AAT
96986 TAGTATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
14 3 0.10
15 5 0.16
16 4 0.13
17 4 0.13
19 11 0.35
20 1 0.03
21 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATTATTTAAATTAAAT
Found at i:97019 original size:23 final size:23
Alignment explanation
Indices: 96960--97039 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
96950 GATAATTTAA
*
96960 AAATAATATTATTTAAATTAAAT
1 AAATAATATAATTTAAATTAAAT
* *
96983 AATTAGTATAATTTCAAA-TAAAT
1 AAATAATATAATTT-AAATTAAAT
*
97006 AAATAATATGATTTAAAAATTAAAT
1 AAATAATATAATTT--AAATTAAAT
97031 AAATAATAT
1 AAATAATAT
97040 TAAAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 27 0.57
24 6 0.13
25 14 0.30
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (23 bp):
AAATAATATAATTTAAATTAAAT
Found at i:97042 original size:21 final size:20
Alignment explanation
Indices: 96929--97050 Score: 81
Period size: 21 Copynumber: 6.0 Consensus size: 20
96919 GGTTCAGGAA
* *
96929 AATATTATTTAAAATTAAAT
1 AATATAATTTAAAAATAAAT
*
96949 -AGATAATTTAAAAATAATAT
1 AATATAATTTAAAAATAA-AT
* * * *
96969 TATTTAAATT--AAATAATT
1 AATATAATTTAAAAATAAAT
*
96987 AGTATAATTTCAAATAAATAAAT
1 AATATAATTT--AA-AAATAAAT
*
97010 AATATGATTTAAAAATTAAAT
1 AATATAATTTAAAAA-TAAAT
97031 AA-ATAATATTAAAAATAAAT
1 AATATAAT-TTAAAAATAAAT
97051 TTTTATAATA
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
18 7 0.09
19 20 0.26
20 14 0.18
21 22 0.28
23 15 0.19
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (20 bp):
AATATAATTTAAAAATAAAT
Found at i:98531 original size:45 final size:45
Alignment explanation
Indices: 98467--98553 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
98457 TCGAAACAAC
*
98467 GTAGGGAAGTGAACCCGAATAAATTATAAGAATGACTTAGAAAAT
1 GTAGGGAAGTGAACCCGAATAAATTATAAGAACGACTTAGAAAAT
98512 GTAGGGAAGTGAACCCGAATAAATTATAAGAACGACTTAGAA
1 GTAGGGAAGTGAACCCGAATAAATTATAAGAACGACTTAGAA
98554 GAGTTGGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (45 bp):
GTAGGGAAGTGAACCCGAATAAATTATAAGAACGACTTAGAAAAT
Found at i:100641 original size:3 final size:3
Alignment explanation
Indices: 100633--100747 Score: 157
Period size: 3 Copynumber: 39.0 Consensus size: 3
100623 CCGGGTCTTT
*
100633 TTA TTA TTA TT- TTA -TA TTA -AA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
100678 TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA TTA TTA TTA TTA TGT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
100726 TTA TTAA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA
100748 CAAGGATACA
Statistics
Matches: 100, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
2 6 0.06
3 90 0.90
4 4 0.04
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:102347 original size:30 final size:30
Alignment explanation
Indices: 102259--102349 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
102249 TATTGTTTAG
* * *
102259 CCTTATAAGTTTCTGTTTTTGCCATTTTAGT
1 CCTT-TAAGTTTATGTTTTTGCTATTTTGGT
* * * *
102290 CCTTTAAATTCATGTTTGTACTATTTTGGT
1 CCTTTAAGTTTATGTTTTTGCTATTTTGGT
*
102320 CCTTTGAGTTTATGTTTTTGCTATTTTGGT
1 CCTTTAAGTTTATGTTTTTGCTATTTTGGT
102350 TCTTGTAATT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
30 44 0.92
31 4 0.08
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (30 bp):
CCTTTAAGTTTATGTTTTTGCTATTTTGGT
Found at i:103123 original size:17 final size:17
Alignment explanation
Indices: 103097--103135 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
103087 ACACATACCA
103097 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
103114 TTTTTTTCTTAAAATTG
1 TTTTTGTCTTAAAAATG
103131 TTTTT
1 TTTTT
103136 AAAAGACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:103433 original size:18 final size:18
Alignment explanation
Indices: 103410--103446 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
103400 TATATAGACG
103410 ATATCTTTCTACTTGTTA
1 ATATCTTTCTACTTGTTA
103428 ATATCTTTCTACTTGTTA
1 ATATCTTTCTACTTGTTA
103446 A
1 A
103447 AGAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATCTTTCTACTTGTTA
Found at i:103859 original size:42 final size:42
Alignment explanation
Indices: 103800--103885 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
103790 GCCTGGGGTA
*
103800 TCCCAGGCAACCCCTCAAAATTTTAACTTAGTGTTAATTTTT
1 TCCCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
103842 TCCCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
1 TCCCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
103884 TC
1 TC
103886 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (42 bp):
TCCCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
Found at i:103981 original size:82 final size:82
Alignment explanation
Indices: 103844--104005 Score: 306
Period size: 82 Copynumber: 2.0 Consensus size: 82
103834 TAATTTTTTC
* *
103844 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTTTCTATTTTTTTAATTAATATAATTG
1 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
103909 CTACCCCTAATATTACT
66 CTACCCCTAATATTACT
103926 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
1 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
103991 CTACCCCTAATATTA
66 CTACCCCTAATATTA
104006 TGTGTAAATG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (82 bp):
CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
CTACCCCTAATATTACT
Found at i:106951 original size:21 final size:21
Alignment explanation
Indices: 106925--106978 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
106915 CTCGGAGGGA
*
106925 ACCGATTCCCCCATGGGGGGT
1 ACCGATTCCCCCATAGGGGGT
*
106946 ACCGATTCCCCCATAGTGGGT
1 ACCGATTCCCCCATAGGGGGT
106967 ACCGATTCCCCC
1 ACCGATTCCCCC
106979 TGTTTAACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.20
Consensus pattern (21 bp):
ACCGATTCCCCCATAGGGGGT
Found at i:112756 original size:21 final size:23
Alignment explanation
Indices: 112730--112781 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
112720 AGGGAATCGA
112730 TCCCCCCATG-A-GGGAACCAAT
1 TCCCCCCATGAAGGGGAACCAAT
** *
112751 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCAAT
112774 TCCCCCCA
1 TCCCCCCA
112782 CAGGGGAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCAAT
Found at i:119689 original size:26 final size:25
Alignment explanation
Indices: 119639--119690 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
119629 GAATTTCAGG
*
119639 TTTTCTTGTTTGAAGAATATTTTGTT
1 TTTTCTTG-TTGAAGAATATGTTGTT
119665 TTTTCTTG-TGAAGAATTCATGTTGTT
1 TTTTCTTGTTGAAGAA-T-ATGTTGTT
119691 AGTTTGCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 7 0.30
25 1 0.04
26 15 0.65
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (25 bp):
TTTTCTTGTTGAAGAATATGTTGTT
Found at i:122013 original size:31 final size:31
Alignment explanation
Indices: 121978--122039 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
121968 AAAACATAAT
121978 ATTTGGTCACTTTTATTTTTATTTAATTAAG
1 ATTTGGTCACTTTTATTTTTATTTAATTAAG
* *
122009 ATTTGGTTACTTTTGTTTTTATTTAATTAAG
1 ATTTGGTCACTTTTATTTTTATTTAATTAAG
122040 GTGTAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.60
Consensus pattern (31 bp):
ATTTGGTCACTTTTATTTTTATTTAATTAAG
Found at i:129772 original size:94 final size:94
Alignment explanation
Indices: 129655--129842 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
129645 CAAAAGAGGT
129655 AACAATCACACCCGAAGCAACTCAACAAACTGCTATTGTTGGTGATTCCAAAGACATCCAGGAGT
1 AACAATCACACCCGAAGCAACTCAACAAACTGCTATTGTTGGTGATTCCAAAGACATCCAGGAGT
129720 TGCAGAGTACTACTTCGATCGTAACACCG
66 TGCAGAGTACTACTTCGATCGTAACACCG
129749 AACAATCACACCCGAAGCAACTCAACAAACTGCTATTGTTGGTGATTCCAAAGACATCCAGGAGT
1 AACAATCACACCCGAAGCAACTCAACAAACTGCTATTGTTGGTGATTCCAAAGACATCCAGGAGT
129814 TGCAGAGTACTACTTCGATCGTAACACCG
66 TGCAGAGTACTACTTCGATCGTAACACCG
129843 GAAGAAAATG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (94 bp):
AACAATCACACCCGAAGCAACTCAACAAACTGCTATTGTTGGTGATTCCAAAGACATCCAGGAGT
TGCAGAGTACTACTTCGATCGTAACACCG
Found at i:135216 original size:17 final size:18
Alignment explanation
Indices: 135173--135213 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
135163 GAATTATATT
135173 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
135190 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
135208 ATTAAA
1 AGTAAA
135214 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:136431 original size:30 final size:30
Alignment explanation
Indices: 136397--136473 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
136387 ATAGTCCAAA
136397 TGATCGGTTTGACCGGTTTTAGTAAATAGT
1 TGATCGGTTTGACCGGTTTTAGTAAATAGT
136427 TGATCGGTTTGACCGGTTTTAGTAAATAGT
1 TGATCGGTTTGACCGGTTTTAGTAAATAGT
136457 TGATCGGTTTGACCGGT
1 TGATCGGTTTGACCGGT
136474 CACAACCCGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.39
Consensus pattern (30 bp):
TGATCGGTTTGACCGGTTTTAGTAAATAGT
Found at i:136505 original size:18 final size:18
Alignment explanation
Indices: 136482--136521 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
136472 GTCACAACCC
136482 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
136500 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
136518 GACC
1 GACC
136522 GTTGACCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.23, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:138982 original size:47 final size:48
Alignment explanation
Indices: 138929--139043 Score: 162
Period size: 47 Copynumber: 2.4 Consensus size: 48
138919 TTCGATTTGA
138929 ATTCTGATCTGATACTTGACATGGATTCTGAT-TGATA-TCTGACATAG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTGATACT-TGACATAG
* * *
138976 ATTCTGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACATAG
* *
139024 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
139044 CTGATTTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 31 0.51
48 29 0.48
49 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACATAG
Found at i:139046 original size:24 final size:24
Alignment explanation
Indices: 138929--139043 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
138919 TTCGATTTGA
138929 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
138953 ATTCTGAT-TGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
138976 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
139000 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
139024 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
139044 CTGATTTATG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.01
23 20 0.24
24 60 0.73
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:141421 original size:18 final size:18
Alignment explanation
Indices: 141398--141432 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
141388 GTCACAACCC
141398 GACCCGACCCGTTGACCT
1 GACCCGACCCGTTGACCT
141416 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
141433 GTTGACCGTC
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:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCT
Found at i:143989 original size:24 final size:24
Alignment explanation
Indices: 143896--143991 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
143886 TCTGATGATA
* * *
143896 GATTCTGATTTGATA-TCTGACATA
1 GATTCTGATCTGATACT-TGACCTG
*
143920 GATTCTGATCTGATACTTGACTTG
1 GATTCTGATCTGATACTTGACCTG
143944 GATTCTGATCTGATACTTGACCTG
1 GATTCTGATCTGATACTTGACCTG
* *
143968 GATTTTGATATGATACTTGACCTG
1 GATTCTGATCTGATACTTGACCTG
143992 ATTTATGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (24 bp):
GATTCTGATCTGATACTTGACCTG
Found at i:151234 original size:2 final size:2
Alignment explanation
Indices: 151227--151251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
151217 AAAAGAGTGT
151227 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
151252 TAATATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152806 original size:16 final size:18
Alignment explanation
Indices: 152774--152808 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
152764 CCTTAAACCT
152774 ATTAATATTTAAAACCCA
1 ATTAATATTTAAAACCCA
152792 ATTAAT-TTT-AAACCCA
1 ATTAATATTTAAAACCCA
152808 A
1 A
152809 ATAAAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAATATTTAAAACCCA
Found at i:154100 original size:54 final size:54
Alignment explanation
Indices: 154037--154146 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
154027 TCTCAGTGTC
*
154037 TATCATTGATTTTAATGATTGTTTACCACA-TATCTCACTACCTAGTGAAAATGA
1 TATCATTGATTTTAATGATTGTTTACCACAGT-TCCCACTACCTAGTGAAAATGA
**
154091 TATCATTGATTTTAATGATTGTTTACCACAGTTCCCGGTACCTAGTGAAAATGA
1 TATCATTGATTTTAATGATTGTTTACCACAGTTCCCACTACCTAGTGAAAATGA
154145 TA
1 TA
154147 ACAACTTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (54 bp):
TATCATTGATTTTAATGATTGTTTACCACAGTTCCCACTACCTAGTGAAAATGA
Found at i:159489 original size:146 final size:146
Alignment explanation
Indices: 159225--159509 Score: 527
Period size: 146 Copynumber: 2.0 Consensus size: 146
159215 AGACAAATTG
159225 AGAATATGACAACACTTAAATCGTTAAAATAAACACAATAGTTTATTTGCAATTGATTTAAGATT
1 AGAATATGACAACACTTAAATCGTTAAAATAAACACAATAGTTTATTTGCAATTGATTTAAGATT
*
159290 TTAATGTTTTTAAACTAAATTTATTATTTCCATATTTATTTTTTAATAATTATATATATGAAATT
66 TTAATATTTTTAAACTAAATTTATTATTTCCATATTTATTTTTTAATAATTATATATATGAAATT
159355 ATTAAAAATCAAACTA
131 ATTAAAAATCAAACTA
*
159371 AGAATATGACAACACTTAAATCGTTAAAATAAAC-CTAATAGTTTATTTGTAATTGATTTAAGAT
1 AGAATATGACAACACTTAAATCGTTAAAATAAACAC-AATAGTTTATTTGCAATTGATTTAAGAT
*
159435 TTTAATATTTTTAAACTAAATTTATTATTTCCATATTTATTTTTTAATGATTATATATATGAAAT
65 TTTAATATTTTTAAACTAAATTTATTATTTCCATATTTATTTTTTAATAATTATATATATGAAAT
159500 TATTAAAAAT
130 TATTAAAAAT
159510 AATTTAATAT
Statistics
Matches: 135, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
145 1 0.01
146 134 0.99
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (146 bp):
AGAATATGACAACACTTAAATCGTTAAAATAAACACAATAGTTTATTTGCAATTGATTTAAGATT
TTAATATTTTTAAACTAAATTTATTATTTCCATATTTATTTTTTAATAATTATATATATGAAATT
ATTAAAAATCAAACTA
Found at i:161217 original size:30 final size:30
Alignment explanation
Indices: 161183--161254 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
161173 ATGATCAAGT
161183 GAGCAAAATGATTTGATAATAAAGTTCAGC
1 GAGCAAAATGATTTGATAATAAAGTTCAGC
**
161213 GAGCAAAATGATTTGATTGTAAAGTTCAGC
1 GAGCAAAATGATTTGATAATAAAGTTCAGC
* *
161243 GAACAAATTGAT
1 GAGCAAAATGAT
161255 CAAATTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (30 bp):
GAGCAAAATGATTTGATAATAAAGTTCAGC
Found at i:168281 original size:30 final size:30
Alignment explanation
Indices: 168245--168301 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
168235 CCGAATATAG
168245 AACCGTATACAAACGGGACTGCATTGACCA
1 AACCGTATACAAACGGGACTGCATTGACCA
168275 AACCGTATACAAACGGGACTGCATTGA
1 AACCGTATACAAACGGGACTGCATTGA
168302 GCAATCGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (30 bp):
AACCGTATACAAACGGGACTGCATTGACCA
Found at i:174232 original size:24 final size:24
Alignment explanation
Indices: 174200--174256 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
174190 TTATCTACAA
174200 CTGAAGCTGAATACATGGCAGCGG
1 CTGAAGCTGAATACATGGCAGCGG
174224 CTGAAGCTGAATACATGGCAGCGG
1 CTGAAGCTGAATACATGGCAGCGG
174248 CTGAAGCTG
1 CTGAAGCTG
174257 CAAAAGAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.33, T:0.18
Consensus pattern (24 bp):
CTGAAGCTGAATACATGGCAGCGG
Found at i:176016 original size:5 final size:5
Alignment explanation
Indices: 176006--176038 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
175996 CGTATTACCA
176006 CGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGA
176039 GTCGAGCCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.58, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:179153 original size:30 final size:31
Alignment explanation
Indices: 179113--179185 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
179103 AATTGATTTA
* * *
179113 TTTA-GTGACCAAATTATATATTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAATTTGGAAAAG
*
179143 TTT-GGTGACCAAAGTATAAATTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAATTTGGAAAAG
179173 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
179186 ATGTAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.34
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAATTTGGAAAAG
Found at i:188602 original size:17 final size:17
Alignment explanation
Indices: 188582--188617 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
188572 ATAATTTCAT
*
188582 AAATTTTATTCAATTTG
1 AAATTTTATTAAATTTG
*
188599 AAATTTTTTTAAATTTG
1 AAATTTTATTAAATTTG
188616 AA
1 AA
188618 TTGGTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATTTTATTAAATTTG
Found at i:190557 original size:18 final size:18
Alignment explanation
Indices: 190524--190564 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
190514 TCATCTTTAG
*
190524 CATCAAACTCCTCATCGT
1 CATCAAACTCCACATCGT
* *
190542 CATCAAACTCGACATCTT
1 CATCAAACTCCACATCGT
190560 CATCA
1 CATCA
190565 TCAACAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.27
Consensus pattern (18 bp):
CATCAAACTCCACATCGT
Found at i:204077 original size:6 final size:6
Alignment explanation
Indices: 204066--204116 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
204056 GAGAACGTCT
204066 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC
204114 CTT
1 CTT
204117 CTAGTTTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CTTTCC
Found at i:209910 original size:130 final size:132
Alignment explanation
Indices: 209607--209910 Score: 380
Period size: 135 Copynumber: 2.3 Consensus size: 132
209597 AGTTTGGGTC
* ** *
209607 ATCTAAGGGTGACATGGTTCCTACGTGATGAGGATATCTAAACAGGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
* * * *
209672 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAAGTGATAACTTGGTTCCTACGCGATGAGGACAGC
66 TGATGAAGAGTTCTTGGCCATCTTT---AAAAGCGATAACATAGTTCCTACGCAATGAGGACAGC
209737 TGGTT
128 TGGTT
* *
209742 ATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACTGCTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
* * **
209807 TGATGAAGAGTTCTTGGCCAT-TTT-ATAGCGATAACATAGTTCCTACGTAATGAGGATGGCTGG
66 TGATGAAGAGTTCTTGGCCATCTTTAAAAGCGATAACATAGTTCCTACGCAATGAGGACAGCTGG
209870 TT
131 TT
* * ** *
209872 ATCTAATGTTGACGTTG-CTCCTACATGATGAGGAGATCT
1 ATCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAGATCT
209911 GGTCAGCTGA
Statistics
Matches: 148, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
130 64 0.43
131 1 0.01
134 3 0.02
135 80 0.54
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (132 bp):
ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAAACAGGGGATGACACTGCTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAAAAGCGATAACATAGTTCCTACGCAATGAGGACAGCTGG
TT
Found at i:218037 original size:30 final size:30
Alignment explanation
Indices: 218002--218064 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
217992 TTAAATTCGA
**
218002 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
218032 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
218062 ATG
1 ATG
218065 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:221684 original size:13 final size:12
Alignment explanation
Indices: 221652--221683 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
221642 TCATAACCTC
221652 TTTTTTTTAACT
1 TTTTTTTTAACT
221664 TTTTTTTTAACT
1 TTTTTTTTAACT
221676 TTTTTTTT
1 TTTTTTTT
221684 TCATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTAACT
Found at i:222593 original size:15 final size:15
Alignment explanation
Indices: 222553--222585 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
222543 CATCAAATAA
222553 AATAACAATAAAAAT
1 AATAACAATAAAAAT
222568 AATAACAATAAAAAT
1 AATAACAATAAAAAT
222583 AAT
1 AAT
222586 TTCTATAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAACAATAAAAAT
Found at i:224409 original size:50 final size:50
Alignment explanation
Indices: 224334--224435 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
224324 CTCTTTGTTC
*
224334 TCGATCTAACCGACTTTGGTCATTAATTTTTTAATTAATTGCGCTTGGTT
1 TCGATCTAACCAACTTTGGTCATTAATTTTTTAATTAATTGCGCTTGGTT
224384 TCGATCTAACCAACTTTGGTCATTAATTTTTTAATTAATTGCGCTTGGTT
1 TCGATCTAACCAACTTTGGTCATTAATTTTTTAATTAATTGCGCTTGGTT
224434 TC
1 TC
224436 TTATGTTACC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (50 bp):
TCGATCTAACCAACTTTGGTCATTAATTTTTTAATTAATTGCGCTTGGTT
Found at i:225310 original size:21 final size:21
Alignment explanation
Indices: 225286--225361 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
225276 ATTCTGACTA
*
225286 TCGCGTTGCGAATTTCCAAAT
1 TCGCGTTGCGAATTTCCTAAT
*
225307 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGAATTTCCTAAT
*
225328 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGAATTTCCTAAT
**
225349 TCGCAATGCGAAT
1 TCGCGTTGCGAAT
225362 ACGTAAACCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGAATTTCCTAAT
Found at i:225375 original size:20 final size:20
Alignment explanation
Indices: 225349--225421 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
225339 TTTTCCTAAT
225349 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
225369 CCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
225389 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
225409 TCGCAATGCGAAT
1 TCGCAATGCGAAT
225422 CTGACTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:225431 original size:20 final size:20
Alignment explanation
Indices: 225408--225459 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
225398 GAATACGTAA
225408 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
225428 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
225448 ATCGCAATGCGA
1 ATCGCAATGCGA
225460 TTTACATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:225662 original size:22 final size:22
Alignment explanation
Indices: 225637--225702 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
225627 GGTGACATCC
*
225637 GTCCCCATCTCCGATGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
225659 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
225681 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
225703 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:226095 original size:20 final size:20
Alignment explanation
Indices: 226070--226119 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
226060 TGCGATTCTT
226070 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
226090 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
226110 GTGTTGCGAT
1 GCGTTGCGAT
226120 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:226127 original size:20 final size:20
Alignment explanation
Indices: 226104--226142 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
226094 TGCGATAGTC
*
226104 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTACGATTTTT
226124 ATTTTCGTGTTACGATTTT
1 ATTTTCGTGTTACGATTTT
226143 AAGTTTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
ATTTTCGTGTTACGATTTTT
Found at i:226149 original size:20 final size:20
Alignment explanation
Indices: 226106--226149 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
226096 CGATAGTCAT
* * *
226106 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTACGATTTTAAG
226126 TTTCGTGTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
226146 TTTC
1 TTTC
226150 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:228038 original size:20 final size:20
Alignment explanation
Indices: 228013--228137 Score: 133
Period size: 20 Copynumber: 5.8 Consensus size: 20
228003 AGAATAGTTT
*
228013 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
228033 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
228053 ACTATCGCAACGAGAAAATCG
1 ACTATCGCAACGCGAAAAT-G
*
228074 CAACAACAAAATCGCAACGCGAAAATG
1 -----AC--TATCGCAACGCGAAAATG
*
228101 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
228121 ACTATCGCAATGCGAAA
1 ACTATCGCAACGCGAAA
228138 TGAAAATCGT
Statistics
Matches: 91, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
20 70 0.77
21 1 0.01
22 2 0.02
26 2 0.02
27 1 0.01
28 15 0.16
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:228075 original size:14 final size:14
Alignment explanation
Indices: 228056--228099 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
228046 GAAAATGACT
228056 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
* *
228070 ATCGCAACAACAAA
1 ATCGCAACGAGAAA
*
228084 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
228098 AT
1 AT
228100 GACTATCGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:228188 original size:20 final size:20
Alignment explanation
Indices: 228163--228345 Score: 191
Period size: 20 Copynumber: 9.3 Consensus size: 20
228153 GATTCTCTCG
**
228163 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
228183 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
228203 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
228223 TTGCGATAATCATTTTCGCGCA
1 TTGCGATAGTCATTTT--CGCA
*
228245 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
228259 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
**
228279 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
228299 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
228319 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
228339 TTGCGAT
1 TTGCGAT
228346 TTTAAGTTTC
Statistics
Matches: 140, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.05
16 4 0.03
18 3 0.02
19 6 0.04
20 110 0.79
22 10 0.07
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:228263 original size:96 final size:95
Alignment explanation
Indices: 228148--228346 Score: 337
Period size: 96 Copynumber: 2.1 Consensus size: 95
228138 TGAAAATCGT
**
228148 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAGT
228213 CATTTTCGCGTTGCGATAATCATTTTCGCG
66 CATTTTCGCGTTGCGATAATCATTTTCGCG
*
228243 CATTGCGATTCTCTCGTTGCGATAGTCAAATTTGCATTGCGATAGTCAAATTCGCATTGCGATAG
1 -ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAG
* *
228308 TCATTTTCGCGTTGTGATAGTCATTTTCGCG
65 TCATTTTCGCGTTGCGATAATCATTTTCGCG
228339 -TTGCGATT
1 ATTGCGATT
228347 TTAAGTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 8 0.08
96 90 0.92
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (95 bp):
ATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATAGT
CATTTTCGCGTTGCGATAATCATTTTCGCG
Found at i:228920 original size:21 final size:21
Alignment explanation
Indices: 228825--228927 Score: 75
Period size: 21 Copynumber: 4.9 Consensus size: 21
228815 GCCCGACTCA
*
228825 CCTGTCATCATTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
**
228846 TCCCCT-ATCGTTCAAGAGGCC
1 -CCTGTCATCGTTCAAGAGGCC
* ** *
228867 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
* *
228888 CCT-CCTACCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* *
228909 ACTGTCATCGTTGAAGAGG
1 CCTGTCATCGTTCAAGAGG
228928 TCTCTCCCAA
Statistics
Matches: 61, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
20 4 0.07
21 53 0.87
22 4 0.07
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:228926 original size:42 final size:42
Alignment explanation
Indices: 228826--228927 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
228816 CCCGACTCAC
* *
228826 CTGTCATCATTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCATTCAAGAGGCCTCCCCTACCGTTCAAGAGGCCA
* ** *
228868 CTATCATCCCTCAAGAGTCC-CCTCCTACCGTTCAAGAGGCCA
1 CTGTCATCATTCAAGAGGCCTCC-CCTACCGTTCAAGAGGCCA
* *
228910 CTGTCATCGTTGAAGAGG
1 CTGTCATCATTCAAGAGG
228928 TCTCTCCCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.24
Consensus pattern (42 bp):
CTGTCATCATTCAAGAGGCCTCCCCTACCGTTCAAGAGGCCA
Found at i:230485 original size:14 final size:14
Alignment explanation
Indices: 230466--230500 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
230456 GGAAATGACT
230466 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
230480 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
230494 ATCGCAA
1 ATCGCAA
230501 TGCGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:230619 original size:33 final size:33
Alignment explanation
Indices: 230552--230632 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
230542 CGATTTTCAT
* * * * **
230552 TTTCGTATTGCGATTCTCTCGTTTCGTTTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCA
230585 TTTCGCATTGCGATTCTCTCATTGCGATAGTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATAGTCA
*
230618 TTTCTGCGTTGCGAT
1 TTTC-GCATTGCGAT
230633 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCATTGCGATAGTCA
Found at i:230631 original size:20 final size:20
Alignment explanation
Indices: 230606--230717 Score: 179
Period size: 20 Copynumber: 5.6 Consensus size: 20
230596 GATTCTCTCA
*
230606 TTGCGATAGTCATTTCTGCG
1 TTGCGATAGTCATTTCCGCG
*
230626 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCATTTCCGCG
230646 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
230666 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
* *
230686 TTGCGATAGTCATATGCGCG
1 TTGCGATAGTCATTTCCGCG
230706 TTGCGATAGTCA
1 TTGCGATAGTCA
230718 AATGAATGTC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:233141 original size:24 final size:24
Alignment explanation
Indices: 233107--233160 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
233097 CTGAAAAATC
233107 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
233131 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
233155 ATCAAA
1 ATCAAA
233161 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:234024 original size:20 final size:20
Alignment explanation
Indices: 233999--234085 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
233989 AAATTCAGTA
233999 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
234019 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
234039 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
234059 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
234079 TTGCGAT
1 TTGCGAT
234086 TTACGTATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:234095 original size:20 final size:20
Alignment explanation
Indices: 234072--234207 Score: 236
Period size: 20 Copynumber: 6.8 Consensus size: 20
234062 CGATAGTCAG
*
234072 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
234092 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
234112 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
234132 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
234152 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
234172 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
234192 ATTCGCGTTGCGATTT
1 ATTCGCATTGCGATTT
234208 CGCATTGCGA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 110 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:234259 original size:21 final size:21
Alignment explanation
Indices: 234207--234259 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
234197 CGTTGCGATT
*
234207 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
234228 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
234249 TCGTAATGCGA
1 TCGCAATGCGA
234260 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:235405 original size:31 final size:31
Alignment explanation
Indices: 235370--235451 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
235360 CTACTTATAA
* * *
235370 TATCAACTTATAACATTTTGATCACTCATAT
1 TATCAATTTGTAATATTTTGATCACTCATAT
235401 TATCAATTTGTAATATTTTGATCACTCATAT
1 TATCAATTTGTAATATTTTGATCACTCATAT
235432 TATCAATTTGTAATATTTTG
1 TATCAATTTGTAATATTTTG
235452 GTCATTGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (31 bp):
TATCAATTTGTAATATTTTGATCACTCATAT
Found at i:235959 original size:16 final size:17
Alignment explanation
Indices: 235922--235956 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
235912 ACATGGTATA
235922 TTATATTTTAATAAATT
1 TTATATTTTAATAAATT
235939 TTATATTTTAATAAATT
1 TTATATTTTAATAAATT
235956 T
1 T
235957 ATAACAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATTTTAATAAATT
Found at i:236379 original size:29 final size:29
Alignment explanation
Indices: 236347--236429 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 29
236337 TAAATAATTG
236347 AATAATCATTTTATAACTTTTAATAATCA
1 AATAATCATTTTATAACTTTTAATAATCA
* * **** * *
236376 AATATTAAAAAAATAACATCTT-ATAATTA
1 AATAATCATTTTATAAC-TTTTAATAATCA
*
236405 AATTATCATTTTATAACTTTTAATA
1 AATAATCATTTTATAACTTTTAATA
236430 GTTAGAATTT
Statistics
Matches: 36, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
28 3 0.08
29 30 0.83
30 3 0.08
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (29 bp):
AATAATCATTTTATAACTTTTAATAATCA
Found at i:237959 original size:195 final size:195
Alignment explanation
Indices: 237627--237985 Score: 630
Period size: 195 Copynumber: 1.8 Consensus size: 195
237617 GATGAATATA
*
237627 GAAACATTAAATCCTCGAATGCATATATCCAGTTGTTGGAAACAAAAGTCCTTGAGCAGGAAATG
1 GAAACATTAAATCCTCGAATGCATAAATCCAGTTGTTGGAAACAAAAGTCCTTGAGCAGGAAATG
* * *
237692 AATAATTGGATATACGGTATTGTTTTCTTACACGTGGTTCGGAATAGTATTTGGTATAATGGTTC
66 AATAATTGGATATACAGTACTGTTTTCTTACACGTGGTTCAGAATAGTATTTGGTATAATGGTTC
237757 ATCATTGGTGTATTTGCCTCAAGTTGAGCCAAATACACGTTGTGTATTTGATATAACGGTTGTTC
131 ATCATTGGTGTATTTGCCTCAAGTTGAGCCAAATACACGTTGTGTATTTGATATAACGGTTGTTC
*
237822 GAAACATTAAATCCTCGAATGCATAAATCCGGTTGTTGGAAACAAAAGTCCTTGAGCAGGAAATG
1 GAAACATTAAATCCTCGAATGCATAAATCCAGTTGTTGGAAACAAAAGTCCTTGAGCAGGAAATG
*
237887 AATAATTGGATATATAGTACTGTTTTCTTACACGTGGTTCAGAATAGTATTTGGTATAATGGTTT
66 AATAATTGGATATACAGTACTGTTTTCTTACACGTGGTTCAGAATAGTATTTGGTATAATGG-TT
* *
237952 C-TCATTGGTGTATTTGCCTCAAGTTTAGCGAAAT
130 CATCATTGGTGTATTTGCCTCAAGTTGAGCCAAAT
237986 TGCAAAATAG
Statistics
Matches: 155, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
195 152 0.98
196 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (195 bp):
GAAACATTAAATCCTCGAATGCATAAATCCAGTTGTTGGAAACAAAAGTCCTTGAGCAGGAAATG
AATAATTGGATATACAGTACTGTTTTCTTACACGTGGTTCAGAATAGTATTTGGTATAATGGTTC
ATCATTGGTGTATTTGCCTCAAGTTGAGCCAAATACACGTTGTGTATTTGATATAACGGTTGTTC
Found at i:245262 original size:42 final size:42
Alignment explanation
Indices: 245198--245289 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
245188 AAAATGTTAA
245198 AACAAAATGCTTTGAGGCTTAATAATCAAATATCCAGAATCC
1 AACAAAATGCTTTGAGGCTTAATAATCAAATATCCAGAATCC
*
245240 AACAAAATGCTTTGA-GCTTTAATTATCAAATATCCAGAATCC
1 AACAAAATGCTTTGAGGC-TTAATAATCAAATATCCAGAATCC
*
245282 AAAAAAAT
1 AACAAAAT
245290 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 2 0.04
42 45 0.96
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (42 bp):
AACAAAATGCTTTGAGGCTTAATAATCAAATATCCAGAATCC
Found at i:246053 original size:13 final size:13
Alignment explanation
Indices: 246035--246081 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
246025 TAAATACTAC
246035 TTTGTAATCACAT
1 TTTGTAATCACAT
246048 TTTGTAATCACAT
1 TTTGTAATCACAT
*
246061 TTTGTAATAACAT
1 TTTGTAATCACAT
246074 TTTGTAAT
1 TTTGTAAT
246082 TAAATGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (13 bp):
TTTGTAATCACAT
Found at i:255970 original size:15 final size:17
Alignment explanation
Indices: 255952--255983 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
255942 CATCTTCTCT
255952 AAATAA-AATAA-ATAG
1 AAATAAGAATAATATAG
255967 AAATAAGAATAATATAG
1 AAATAAGAATAATATAG
255984 TGAAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (17 bp):
AAATAAGAATAATATAG
Found at i:260862 original size:2 final size:2
Alignment explanation
Indices: 260855--260893 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
260845 ACCATATAAC
260855 AT AT AT AT -T 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
260894 CATGTTAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:261263 original size:30 final size:30
Alignment explanation
Indices: 261195--261288 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
261185 GAAGGACCTA
* * *
261195 TCCAGAGGTCACAAAG-ACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* *
261224 TCCAGAGGTCATAAAGAACCTCGGCAACTG
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* * *
261254 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGAACCTCGG-AAACTG
261285 TCCA
1 TCCA
261289 TATGTTCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.28
30 30 0.56
31 9 0.17
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGAAACTG
Found at i:261287 original size:31 final size:31
Alignment explanation
Indices: 261249--261343 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
261239 GAACCTCGGC
* *
261249 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
261280 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
261311 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
261342 AA
1 AA
261344 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:262414 original size:18 final size:19
Alignment explanation
Indices: 262367--262414 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
262357 TTTTAAAGGG
* *
262367 ATGCAGCGATGCACTCCTT
1 ATGCATCGATGCACTCATT
262386 ATGCATCGATGCAC-CATT
1 ATGCATCGATGCACTCATT
262404 -TGCATTCGATG
1 ATGCA-TCGATG
262415 TTTCTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 13 0.50
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCATT
Found at i:265038 original size:22 final size:24
Alignment explanation
Indices: 265012--265056 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
265002 CAATTATACT
265012 CATTCACATATACC-T-TAACATG
1 CATTCACATATACCATATAACATG
*
265034 CATTCACGTATACCATATAACAT
1 CATTCACATATACCATATAACAT
265057 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (24 bp):
CATTCACATATACCATATAACATG
Found at i:265438 original size:30 final size:30
Alignment explanation
Indices: 265370--265463 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
265360 GAAGGACCTA
* * *
265370 TCCAGAGGTCACAAAG-ACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* *
265399 TCCAGAGGTCATAAAGAACCTCGGCAACTG
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* * *
265429 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGAACCTCGG-AAACTG
265460 TCCA
1 TCCA
265464 TATGTTCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.28
30 30 0.56
31 9 0.17
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGAAACTG
Found at i:265462 original size:31 final size:31
Alignment explanation
Indices: 265424--265518 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
265414 GAACCTCGGC
* *
265424 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
265455 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * *
265486 TATTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
265517 AA
1 AA
265519 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
31 48 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:265973 original size:25 final size:25
Alignment explanation
Indices: 265945--266000 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
265935 CCATACTTTG
265945 TTTATCTCACTTTTCATATCATTCA
1 TTTATCTCACTTTTCATATCATTCA
265970 TTTATCTCACTTTTCATATCATTCA
1 TTTATCTCACTTTTCATATCATTCA
265995 TTTATC
1 TTTATC
266001 ACACATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATCTCACTTTTCATATCATTCA
Found at i:266503 original size:20 final size:22
Alignment explanation
Indices: 266478--266535 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
266468 TTCCCCTTGA
266478 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
266498 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
266521 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
266536 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:266601 original size:64 final size:63
Alignment explanation
Indices: 266523--266663 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
266513 TCTTTAACAT
* *
266523 GTGCATCGATGCACTACC-CATGCATCGATAAACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATAAACAAATTACATTCGATG-TTTCATCTTTAAAGA
* ** * * * *
266586 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATAAACAAATTACATTCGATGTTTCATCTTTAAAGA
266650 GTGCATCGATGCAC
1 GTGCATCGATGCAC
266664 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATAAACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:274135 original size:13 final size:13
Alignment explanation
Indices: 274117--274148 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
274107 GTAATTTAGT
274117 ATATATCTAACAC
1 ATATATCTAACAC
274130 ATATATCTAACAC
1 ATATATCTAACAC
*
274143 TTATAT
1 ATATAT
274149 ATGATCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATCTAACAC
Found at i:275544 original size:18 final size:19
Alignment explanation
Indices: 275509--275545 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
275499 CACGTAATGT
275509 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
275529 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
275546 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:277364 original size:7 final size:7
Alignment explanation
Indices: 277341--277374 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
277331 TATACATAGA
277341 TTTTAAT
1 TTTTAAT
*
277348 TCTATAAT
1 T-TTTAAT
277356 TTTTAAT
1 TTTTAAT
277363 TTTTAAT
1 TTTTAAT
277370 TTTTA
1 TTTTA
277375 TAAGACTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAT
Found at i:278598 original size:21 final size:21
Alignment explanation
Indices: 278554--278606 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
278544 ATTCTGACTA
278554 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
278575 TCGCGTTGCGATTTTCCTATT
1 TCGCATTGCGATTTCCCAAAT
*
278596 TCGCAATGCGA
1 TCGCATTGCGA
278607 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:278621 original size:20 final size:21
Alignment explanation
Indices: 278596--278647 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
278586 TTTTCCTATT
*
278596 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
278616 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
278637 TCACAATGCGA
1 TCGCAATGCGA
278648 TTTAGTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:279539 original size:24 final size:24
Alignment explanation
Indices: 279512--279565 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
279502 AGTATTCGAA
279512 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
279536 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
279560 TTTGAT
1 TTTGAT
279566 GATTTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:282065 original size:19 final size:19
Alignment explanation
Indices: 282023--282085 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
282013 CAATCATCTT
* *
282023 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAATGC-GA
282043 AATGACTATCGCAATGCGA
1 AATGACTATCGCAATGCGA
** *
282062 AATGAAAATCACAATGCGA
1 AATGACTATCGCAATGCGA
282081 AATGA
1 AATGA
282086 AAATCGCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
AATGACTATCGCAATGCGA
Found at i:282115 original size:33 final size:33
Alignment explanation
Indices: 282068--282162 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
282058 GCGAAATGAA
*
282068 AATCACAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
282101 AATTGCAATGCGAAATGAAAATCGCAACGAGGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
282134 AATCGCAAAGCGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
282163 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:282158 original size:19 final size:19
Alignment explanation
Indices: 282030--282166 Score: 87
Period size: 19 Copynumber: 7.7 Consensus size: 19
282020 CTTAATGTCT
* **
282030 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
282050 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
* *
282069 ATCACAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
282088 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
* *
282102 ATTGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
282121 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
282135 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
282154 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
282167 TTTAGTTTCG
Statistics
Matches: 90, Mismatches: 17, Indels: 21
0.70 0.13 0.16
Matches are distributed among these distances:
14 14 0.16
15 5 0.06
16 4 0.04
17 4 0.04
18 4 0.04
19 50 0.56
20 9 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:282214 original size:33 final size:33
Alignment explanation
Indices: 282172--282289 Score: 164
Period size: 33 Copynumber: 3.4 Consensus size: 33
282162 GCGAATTTAG
*
282172 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
282205 TTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTC---T--CGTTGCGATTTTCA
*
282243 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
*
282276 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
282290 AGTCATTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.57
35 1 0.01
36 1 0.01
38 31 0.40
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
Found at i:282297 original size:19 final size:19
Alignment explanation
Indices: 282191--282289 Score: 145
Period size: 19 Copynumber: 5.5 Consensus size: 19
282181 GCGATTTTGT
282191 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
282210 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
282229 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
282248 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
282262 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
282281 CATTGCGAT
1 CGTTGCGAT
282290 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 56 0.78
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Done.