Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008994.1 Hibiscus syriacus cultivar Beakdansim tig00112370_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: 399360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:896 original size:30 final size:30
Alignment explanation
Indices: 810--894 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
800 TGAAACATAC
810 CAAAACTGATAGTTTATTACTAAAATGGAT
1 CAAAACTGATAGTTTATTACTAAAATGGAT
* *
840 CAAAATTGATTGTTTATTACTAAAATGGAT
1 CAAAACTGATAGTTTATTACTAAAATGGAT
* *
870 CAAAACTGGTAGTTTAGGTACTAAA
1 CAAAACTGATAGTTTA-TTACTAAA
895 TGCATAGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 41 0.85
31 7 0.15
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (30 bp):
CAAAACTGATAGTTTATTACTAAAATGGAT
Found at i:2064 original size:21 final size:21
Alignment explanation
Indices: 2026--2065 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2016 ATAAAAAAAA
*
2026 ATAAAAGAAAACATAAATGTG
1 ATAAAAGAAAACAAAAATGTG
*
2047 ATAAAAGAAAAGAAAAATG
1 ATAAAAGAAAACAAAAATG
2066 CAATAAAGAA
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:0.68, C:0.03, G:0.15, T:0.15
Consensus pattern (21 bp):
ATAAAAGAAAACAAAAATGTG
Found at i:2071 original size:21 final size:21
Alignment explanation
Indices: 2025--2072 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2015 AATAAAAAAA
* *
2025 AATAAAAGAAAACATAAATGT
1 AATAAAAGAAAACAAAAATGC
* *
2046 GATAAAAGAAAAGAAAAATGC
1 AATAAAAGAAAACAAAAATGC
2067 AATAAA
1 AATAAA
2073 GAATACTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (21 bp):
AATAAAAGAAAACAAAAATGC
Found at i:4450 original size:8 final size:8
Alignment explanation
Indices: 4434--4467 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4424 TTTCCAAATT
4434 TGCATGTA
1 TGCATGTA
*
4442 TGTATGTA
1 TGCATGTA
*
4450 TGCATGCA
1 TGCATGTA
4458 TGCATGTA
1 TGCATGTA
4466 TG
1 TG
4468 TGTAACGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (8 bp):
TGCATGTA
Found at i:4594 original size:4 final size:4
Alignment explanation
Indices: 4585--4664 Score: 105
Period size: 4 Copynumber: 21.0 Consensus size: 4
4575 CCAAATTTGC
* *
4585 ATGT ATGT ATGT ATGC ATGC ATGT A--T ATGT ATGT ATGT ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
4630 -TGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
4665 GTAATGATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
4 64 0.94
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:4616 original size:22 final size:21
Alignment explanation
Indices: 4588--4663 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 21
4578 AATTTGCATG
4588 TATGTATGTATGCATGCATGTA
1 TATGTATGTATGCATG-ATGTA
4610 TATGTATGTATG--T-ATGTA
1 TATGTATGTATGCATGATGTA
*
4628 TGTGTATGTATGCATGTATGTA
1 TATGTATGTATGCATG-ATGTA
4650 TGTATGTATGTATG
1 --TATGTATGTATG
4664 TGTAATGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 16 0.35
20 2 0.04
22 17 0.37
24 11 0.24
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (21 bp):
TATGTATGTATGCATGATGTA
Found at i:4660 original size:30 final size:28
Alignment explanation
Indices: 4585--4667 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 28
4575 CCAAATTTGC
* *
4585 ATGTATGTATGTATGCATGCATGTATATGT
1 ATGTATGTATGTATGTATG--TGTACATGT
* *
4615 ATGTATGTATGTATGTGTATGTATGCATGT
1 ATGTATGTATGTA--TGTATGTGTACATGT
4645 ATGTATGTATGTATGTATGTGTA
1 ATGTATGTATGTATGTATGTGTA
4668 ATGATAATGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.18
30 32 0.71
32 5 0.11
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (28 bp):
ATGTATGTATGTATGTATGTGTACATGT
Found at i:4812 original size:196 final size:193
Alignment explanation
Indices: 4437--4813 Score: 517
Period size: 196 Copynumber: 1.9 Consensus size: 193
4427 CCAAATTTGC
*
4437 ATGTATGTATGTATGCATGCATGCATGTATGTGTAACGATAATGGTGCTGTGATTCAATAAAGAA
1 ATGTATGCATGTATGCATGCATGCATGTATGTGTAACGATAA--GTGCTGTGATTCAATAAAGAA
*
4502 CCTGCTGATTCTTAGTATGAGTCCGGCCTGAATGCACTGTGCCTGAAACCAAATTTAAGATCAAG
64 CATGCTGATTCTTAGTATGAGTCCGGCCTGAATGCACTGTGCCTGAAACCAAATTTAAGATCAAG
4567 GTGTGTTTCCAAATTTGCATGTATGTATGTATGCATGCATGTATATGTATGTATGTATGTATGTG
129 GTGTGTTTCCAAATTTGCATGTATGTATGTATGCATGCATG-ATATGTATGTATGTATGTATGTG
4632 T
193 T
* * * *
4633 ATGTATGCATGTATGTATGTATGTATGTATGTGTAATGATAA-TG-TGTGATTCAATAAAGAACA
1 ATGTATGCATGTATGCATGCATGCATGTATGTGTAACGATAAGTGCTGTGATTCAATAAAGAACA
* *
4696 TGCTGATTCTTAGTATGAGGTCTGGCCTGAATGCACTGATGCGCCTTAAACCAAATTTAAGATCA
66 TGCTGATTCTTAGTATGA-GTCCGGCCTGAATGCACTG-T--GCCTGAAACCAAATTTAAGATCA
* * * * * * *
4761 GGGTTTGTTTCTAAATTTGTATGTATTTGTGTGTATGTATGGATG-TATGTATG
127 AGGTGTGTTTCCAAATTTGCATGTA--TGTATGTATGCATGCATGATATGTATG
4814 ACAATAATGG
Statistics
Matches: 160, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
192 36 0.22
193 20 0.12
194 1 0.01
196 88 0.55
198 15 0.09
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (193 bp):
ATGTATGCATGTATGCATGCATGCATGTATGTGTAACGATAAGTGCTGTGATTCAATAAAGAACA
TGCTGATTCTTAGTATGAGTCCGGCCTGAATGCACTGTGCCTGAAACCAAATTTAAGATCAAGGT
GTGTTTCCAAATTTGCATGTATGTATGTATGCATGCATGATATGTATGTATGTATGTATGTGT
Found at i:24377 original size:23 final size:23
Alignment explanation
Indices: 24351--24400 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
24341 AAAGTAGAAG
* *
24351 AAAATGCACCGTAAAGGCAAATA
1 AAAATACACCGTAAAGACAAATA
* *
24374 AAAATATACCGTAAAGACAAGTA
1 AAAATACACCGTAAAGACAAATA
24397 AAAA
1 AAAA
24401 CGTGTCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (23 bp):
AAAATACACCGTAAAGACAAATA
Found at i:24727 original size:16 final size:15
Alignment explanation
Indices: 24702--24731 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24692 CTTCACTTAA
24702 TAAAAAATAATAATT
1 TAAAAAATAATAATT
24717 TAAAAATATAATAAT
1 TAAAAA-ATAATAAT
24732 GATCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAAAATAATAATT
Found at i:30037 original size:60 final size:59
Alignment explanation
Indices: 29939--30121 Score: 165
Period size: 60 Copynumber: 3.1 Consensus size: 59
29929 TCGTCACATG
* * * * * ** *
29939 TCCTTAAAGTATGATCTTTATTTTAAATTGGTCTTTAAACTTG-TAAATATTTTGATTTTA
1 TCCTTAAATTATGA-CTTTATTCTAAATTAGTCCTTAAA-TTGTTAAACATTTCAATTTCA
*
29999 TCCTTAAATTATGACTATTATTCTAAATTAGTCCTTAAATTGTTGAACATTTCAATTTCA
1 TCCTTAAATTATGACT-TTATTCTAAATTAGTCCTTAAATTGTTAAACATTTCAATTTCA
* * * * *
30059 TCCCTAAATTATGACCTTCATTATAAATT-GATCCTCAAAATT-TTGAACATTTCAATTTCA
1 TCCTTAAATTATGA-CTTTATTCTAAATTAG-TCCT-TAAATTGTTAAACATTTCAATTTCA
30119 TCC
1 TCC
30122 CCAACTACAC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
59 6 0.06
60 92 0.88
61 7 0.07
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (59 bp):
TCCTTAAATTATGACTTTATTCTAAATTAGTCCTTAAATTGTTAAACATTTCAATTTCA
Found at i:30121 original size:29 final size:28
Alignment explanation
Indices: 30035--30122 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
30025 ATTAGTCCTT
*
30035 AAATTGTTGAACATTTCAATTTCATCCCT
1 AAATT-TTGAACATTTCAATTTCATCCCA
* * * *
30064 AAATTATGACCTTCATTAT-AAATTGATCCTCA
1 AAATTTTGA---ACATT-TCAATTTCATCC-CA
30096 AAATTTTGAACATTTCAATTTCATCCC
1 AAATTTTGAACATTTCAATTTCATCCC
30123 CAACTACACG
Statistics
Matches: 44, Mismatches: 9, Indels: 13
0.67 0.14 0.20
Matches are distributed among these distances:
28 5 0.11
29 17 0.39
31 12 0.27
32 10 0.23
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (28 bp):
AAATTTTGAACATTTCAATTTCATCCCA
Found at i:30122 original size:60 final size:60
Alignment explanation
Indices: 29993--30122 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
29983 AAATATTTTG
* * * * *
29993 ATTTTATCCTTAAATTATGACTATTATTCTAAATTAGTCCTTAAATTGTTGAACATTTCA
1 ATTTCATCCCTAAATTATGACTATCATTATAAATTAGTCCTAAAATTGTTGAACATTTCA
30053 ATTTCATCCCTAAATTATGACCT-TCATTATAAATT-GATCCTCAAAATT-TTGAACATTTCA
1 ATTTCATCCCTAAATTATGA-CTATCATTATAAATTAG-TCCT-AAAATTGTTGAACATTTCA
30113 ATTTCATCCC
1 ATTTCATCCC
30123 CAACTACACG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
59 1 0.02
60 54 0.87
61 7 0.11
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTCATCCCTAAATTATGACTATCATTATAAATTAGTCCTAAAATTGTTGAACATTTCA
Found at i:32466 original size:20 final size:21
Alignment explanation
Indices: 32429--32467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32419 TTGAATATTT
32429 TAAATTAAAATAATATCTATG
1 TAAATTAAAATAATATCTATG
*
32450 TAAATTAAAA-GATATCTA
1 TAAATTAAAATAATATCTA
32468 AATCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAATTAAAATAATATCTATG
Found at i:36986 original size:43 final size:43
Alignment explanation
Indices: 36925--37044 Score: 231
Period size: 43 Copynumber: 2.8 Consensus size: 43
36915 CAGTTCTATC
36925 AAAGCAGTTTACATATCTAGTTTCGAAGAAACTTATCATCATA
1 AAAGCAGTTTACATATCTAGTTTCGAAGAAACTTATCATCATA
36968 AAAGCAGTTTACATATCTAGTTTCGAAGAAACTTATCATCATA
1 AAAGCAGTTTACATATCTAGTTTCGAAGAAACTTATCATCATA
*
37011 AAAGCAGTTTACATATCTAGTTTCAAAGAAACTT
1 AAAGCAGTTTACATATCTAGTTTCGAAGAAACTT
37045 TTGATGGTAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (43 bp):
AAAGCAGTTTACATATCTAGTTTCGAAGAAACTTATCATCATA
Found at i:38901 original size:50 final size:50
Alignment explanation
Indices: 38847--38943 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
38837 TTTTATTTTT
** *
38847 ATATTTTATATTTTTGTTATAATTTAAATTGATATAATTCATATATAATA
1 ATATTTTATAAATTTATTATAATTTAAATTGATATAATTCATATATAATA
* ** * *
38897 ATATTTTTTAAATTTATTATTGTTTAAATTGATATGATTTATATATA
1 ATATTTTATAAATTTATTATAATTTAAATTGATATAATTCATATATA
38944 TATATATAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (50 bp):
ATATTTTATAAATTTATTATAATTTAAATTGATATAATTCATATATAATA
Found at i:44085 original size:32 final size:33
Alignment explanation
Indices: 44049--44127 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 33
44039 CTAAACTTAA
*
44049 ATTTTAAGTATATTTGAGTTTGATTA-AAATTG
1 ATTTTAAGTATATTTGAATTTGATTATAAATTG
* * *
44081 ATTTT--TTATCATTTTAATTTGATTATAAATTT
1 ATTTTAAGTAT-ATTTGAATTTGATTATAAATTG
44113 ATATTTAAGT-TATTT
1 AT-TTTAAGTATATTT
44128 TTCTAAATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
30 3 0.08
31 13 0.35
32 12 0.32
33 7 0.19
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.57
Consensus pattern (33 bp):
ATTTTAAGTATATTTGAATTTGATTATAAATTG
Found at i:44873 original size:27 final size:25
Alignment explanation
Indices: 44816--44874 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
44806 TAAGCTATAC
*
44816 TTAAATTTTAAGTATATTTTTTTAT
1 TTAAATTTTAAGTATATTGTTTTAT
*
44841 TGAAATTTTAAGTATATTGAGTTTTAT
1 TTAAATTTTAAGTATATT--GTTTTAT
44868 TTAAATT
1 TTAAATT
44875 GATTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 17 0.59
27 12 0.41
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (25 bp):
TTAAATTTTAAGTATATTGTTTTAT
Found at i:46823 original size:23 final size:23
Alignment explanation
Indices: 46809--46853 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46799 ATATATTCGG
*
46809 TAACGCTTATATAATGTAATAGA
1 TAACGCTTATATAATATAATAGA
* *
46832 TAGCGCTTATATAATAAAATAG
1 TAACGCTTATATAATATAATAG
46854 GTATTTAACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
TAACGCTTATATAATATAATAGA
Found at i:46914 original size:87 final size:87
Alignment explanation
Indices: 46768--46930 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
46758 TATGTTTTAT
* *
46768 TATTTAACCGGAAATATTATCAAGTACAATAATATATTCGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
46833 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
46855 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
46920 AGCGCTTATAT
66 AGCGCTTATAT
46931 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:50577 original size:183 final size:183
Alignment explanation
Indices: 50265--50835 Score: 975
Period size: 183 Copynumber: 3.1 Consensus size: 183
50255 TTAAAATTAG
50265 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
50330 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAGATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGA
* *
50395 CACTTTTTGACAAGGTATCGACACATTTTTCTTCAATTCTGGGCATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
50448 TGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
50513 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGA
*
50578 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTAGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
* *
50631 CGACACAATATTAAAAAGTGTCGCTATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * *
50696 ATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATGTTTTTTCAA--T
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATG---TGTAAATGT
*
50759 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
50815 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
50836 GAAAACTTTG
Statistics
Matches: 368, Mismatches: 17, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
183 288 0.78
184 76 0.21
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCAATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:52053 original size:3 final size:3
Alignment explanation
Indices: 52045--52083 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
52035 ACTTGTTTGG
* *
52045 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
52084 GTCAGCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:52084 original size:12 final size:12
Alignment explanation
Indices: 52049--52087 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
52039 GTTTGGATCA
*
52049 TCATCATCATCA
1 TCATCATCATCG
52061 TCATCATCATCG
1 TCATCATCATCG
*
52073 TCATCTTCATCG
1 TCATCATCATCG
52085 TCA
1 TCA
52088 GCTTCATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:53922 original size:200 final size:200
Alignment explanation
Indices: 53598--54561 Score: 1705
Period size: 200 Copynumber: 4.8 Consensus size: 200
53588 AACATTAAAC
* * * * *
53598 AGTGTCGATACA-TATTATATACCAATTATCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
53662 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATTGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATAT
*
53727 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
53792 TACAAA
195 TACAAA
* *
53798 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTATCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * * *
53863 AAAATTACATATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATA
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
*
53928 GATCGACACTTTATTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
53993 ACAAA
196 ACAAA
*
53998 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
54063 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCAGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
54128 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
54193 ACAAA
196 ACAAA
*
54198 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
54263 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
*
54328 GATCGACACTTTATTGTTGTACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
54393 ACAAA
196 ACAAA
*
54398 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
54463 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
*
54528 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
54562 ATTGTAAATT
Statistics
Matches: 733, Mismatches: 30, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
200 729 0.99
201 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:54806 original size:18 final size:17
Alignment explanation
Indices: 54783--54841 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
54773 TCTCATTCAT
*
54783 AATTATATTCACATACAA
1 AATTATAATCACATAC-A
*
54801 AATTATAAATCATATACA
1 AATTAT-AATCACATACA
**
54819 AATTATAAATCTTATACA
1 AATTAT-AATCACATACA
54837 AATTA
1 AATTA
54842 ACCCTACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 29 0.78
19 8 0.22
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATAATCACATACA
Found at i:56688 original size:33 final size:32
Alignment explanation
Indices: 56634--56698 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
56624 CATCTTAATA
*
56634 TCACCCCTTACACCCCAACTTCTTTCACCACT
1 TCACCCCTAACACCCCAACTTCTTTCACCACT
* *
56666 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCT-AACACCCCAACTTCTTTCACCACT
56699 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (32 bp):
TCACCCCTAACACCCCAACTTCTTTCACCACT
Found at i:56757 original size:21 final size:20
Alignment explanation
Indices: 56732--56795 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
56722 CCCCTTATGC
*
56732 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGT-TCTCTTCGACT
56753 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAG-TTCTCTTCGACT
* *
56774 CTATCAAGTTCTTTTCGACT
1 CTCTCAAGTTCTCTTCGACT
56794 CT
1 CT
56796 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.33
21 25 0.64
22 1 0.03
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (20 bp):
CTCTCAAGTTCTCTTCGACT
Found at i:56899 original size:15 final size:15
Alignment explanation
Indices: 56879--56907 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56869 TATGTTTTCC
56879 CTCACCGTCATCCCA
1 CTCACCGTCATCCCA
56894 CTCACCGTCATCCC
1 CTCACCGTCATCCC
56908 CTAATACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.55, G:0.07, T:0.21
Consensus pattern (15 bp):
CTCACCGTCATCCCA
Found at i:60295 original size:21 final size:22
Alignment explanation
Indices: 60269--60321 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
60259 AGAGTCGAAG
*
60269 AACTTGATAGAGT-CGAAGAGA
1 AACTTGAGAGAGTCCGAAGAGA
*
60290 AACTTGAGAGAGTCCGAAGATA
1 AACTTGAGAGAGTCCGAAGAGA
*
60312 CACTTGAGAG
1 AACTTGAGAG
60322 GCATAGGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (22 bp):
AACTTGAGAGAGTCCGAAGAGA
Found at i:60407 original size:32 final size:32
Alignment explanation
Indices: 60353--60416 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
60343 AAATAGATGG
*
60353 AGTGGTGAAAGAAGTAGAGGTGTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTGAAGGGTGA
* * *
60385 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTGAAGGGTGA
60417 TATTAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTGAAGGGTGA
Found at i:62169 original size:19 final size:19
Alignment explanation
Indices: 62145--62193 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
62135 AATGTAGGGT
62145 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
62164 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
62183 TAATTTTGTAT
1 TAATTTTGTAT
62194 GTGAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:62773 original size:194 final size:195
Alignment explanation
Indices: 62422--62778 Score: 635
Period size: 194 Copynumber: 1.8 Consensus size: 195
62412 TTACAATATG
*
62422 GCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
1 GCAAACAGGGTGCAACCATAAAGTGGCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
*
62487 AACCCAAAAGTATAATGTAATTGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATG
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATG
*
62552 AGAGAATAGGTCTAAATAATGTATCGACACTTTGTAGTTTGTTGATATTTTGGTCCAGAATGAAT
131 AGAGAATAGGTCTAAATAATATATCGACACTTTGTAGTTTGTTGATATTTTGGTCCAGAATGAAT
*
62617 GCAAACAGGGTGCAA-CATAAAGTGGCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGA
1 GCAAACAGGGTGCAACCATAAAGTGGCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
*
62681 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACTGGTTTTATG
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATG
* **
62746 AGAGAATATGTCTAAATCCTATATCGACACTTT
131 AGAGAATAGGTCTAAATAATATATCGACACTTT
62779 TTAATATTGT
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
194 139 0.90
195 15 0.10
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (195 bp):
GCAAACAGGGTGCAACCATAAAGTGGCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATG
AGAGAATAGGTCTAAATAATATATCGACACTTTGTAGTTTGTTGATATTTTGGTCCAGAATGAAT
Found at i:66386 original size:82 final size:81
Alignment explanation
Indices: 66292--66441 Score: 239
Period size: 80 Copynumber: 1.8 Consensus size: 81
66282 AAAATAGGTC
* *
66292 AAGCGTTATCTATTACATTATAAGCGCTACCTAATATGTTATTGTAC-TGATAATATTTCCCGTT
1 AAGCGCTATCTATTACATTAT-A-CGCTACCTAATATGTTATTGTACTTGATAATATTTCCCGTG
66356 AAATACCTATTTTTTATA
64 AAATACCTATTTTTTATA
* *
66374 AAGCGCTATCTATTACATTATACGTTACCTAATATGTTATTGTACTTGATAATATTTCCGGTGAA
1 AAGCGCTATCTATTACATTATACGCTACCTAATATGTTATTGTACTTGATAATATTTCCCGTGAA
66439 ATA
66 ATA
66442 ATATAACATA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 22 0.35
81 21 0.33
82 20 0.32
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (81 bp):
AAGCGCTATCTATTACATTATACGCTACCTAATATGTTATTGTACTTGATAATATTTCCCGTGAA
ATACCTATTTTTTATA
Found at i:69460 original size:6 final size:6
Alignment explanation
Indices: 69449--69484 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
69439 TTATTAACAT
* *
69449 TTTTAA TTTTAA TTTTAA TTTTTA TTTTAA TATTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
69485 ATGATGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:70013 original size:21 final size:21
Alignment explanation
Indices: 69959--70019 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
69949 CATCGTACGT
* * *
69959 TATCATATCAACACCATAAAT
1 TATCATATCAATACAATAAAC
*
69980 TATCATATTAATACAATAAAC
1 TATCATATCAATACAATAAAC
* *
70001 TATCACATCAATACTATAA
1 TATCATATCAATACAATAA
70020 CGATCAACGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (21 bp):
TATCATATCAATACAATAAAC
Found at i:71062 original size:21 final size:20
Alignment explanation
Indices: 70976--71133 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
70966 AAATGACCAA
**
70976 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
70995 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
71015 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
71035 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
71056 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
71077 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
71097 CCAAAATCACAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
71118 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
71134 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:71143 original size:20 final size:20
Alignment explanation
Indices: 71120--71253 Score: 164
Period size: 20 Copynumber: 6.7 Consensus size: 20
71110 GCGAATATGA
* *
71120 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
71140 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
71160 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
71180 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
71200 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
71220 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
71241 AAATCGCAACGCG
1 AAATCGCAACGCG
71254 ATATTTAAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.01
20 79 0.81
21 17 0.17
22 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:71150 original size:40 final size:40
Alignment explanation
Indices: 71120--71254 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
71110 GCGAATATGA
71120 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
* * * *
71160 AAATCGCAACGTGTATC-CGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGT
** *
71200 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGT
71241 AAATCGCAACGCGA
1 AAATCGCAACGCGA
71255 TATTTAAAGC
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 46 0.57
41 33 0.41
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
Found at i:71675 original size:33 final size:33
Alignment explanation
Indices: 71636--71706 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
71626 TTCACTTAGA
*
71636 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
71669 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
71702 TTTCA
1 TTTCA
71707 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:71812 original size:21 final size:20
Alignment explanation
Indices: 71786--71893 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
71776 TGCAGAAGAG
71786 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
71807 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
71827 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
71848 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
71862 TCGCAACGTG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
71881 TCGCAACGCGAAA
1 TCGCAACGAGAAA
71894 CCAAAATCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 15
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 18 0.26
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:71830 original size:20 final size:20
Alignment explanation
Indices: 71786--71862 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
71776 TGCAGAAGAG
*
71786 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
71807 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
71827 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
71848 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
71863 CGCAACGTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:71843 original size:41 final size:41
Alignment explanation
Indices: 71785--71862 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
71775 TTGCAGAAGA
*
71785 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
71826 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
71863 CGCAACGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:71884 original size:19 final size:19
Alignment explanation
Indices: 71786--71904 Score: 95
Period size: 19 Copynumber: 6.3 Consensus size: 19
71776 TGCAGAAGAG
71786 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGAAAA
***
71807 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGA-AATGAAAA
71827 TCGCAACGAGAGAAATGAAAA
1 TCGCAAC--GAGAAATGAAAA
71848 TCGCAACGAG--A-G--AA
1 TCGCAACGAGAAATGAAAA
*
71862 TCGCAACGTGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
* **
71881 TCGCAACGCGAAACCAAAA
1 TCGCAACGAGAAATGAAAA
71900 TCGCA
1 TCGCA
71905 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
14 11 0.14
16 2 0.03
17 2 0.03
19 27 0.34
20 12 0.15
21 22 0.28
22 4 0.05
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:71922 original size:19 final size:19
Alignment explanation
Indices: 71900--71964 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
71890 GAAACCAAAA
*
71900 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
71919 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
71933 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
71952 TCGCGTTGCGATT
1 TCGCGTTGCGATT
71965 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:71941 original size:14 final size:14
Alignment explanation
Indices: 71922--71978 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
71912 TTTCATTTCG
71922 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
71936 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
71955 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
71969 CGTTGCGATT
1 CGTTGCGATT
71979 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:71947 original size:33 final size:33
Alignment explanation
Indices: 71905--71986 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
71895 CAAAATCGCA
71905 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
71938 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
71971 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
71987 AACCAAAGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:73843 original size:93 final size:93
Alignment explanation
Indices: 73684--74152 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
73674 TAGATTGCTT
*
73684 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
73749 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
73777 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
73842 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
73870 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
73935 TTTGTCTTTGTTTTGTCTTTTGATTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
73963 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
74028 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
74056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
74121 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
74148 AGTAA
1 AGTAA
74153 TGCAATCCAT
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 367 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:74240 original size:19 final size:19
Alignment explanation
Indices: 74200--74298 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
74190 TAGTTTACTT
* *
74200 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
74220 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
74239 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
74258 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
74272 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
74291 TCGCAACG
1 TCGCAACG
74299 ATTTTCATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.58
20 13 0.19
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:74279 original size:33 final size:33
Alignment explanation
Indices: 74237--74299 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
74227 GCGAAACCAA
**
74237 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAACCAAAATCGCAACGACAG
74270 AATCGCAACGCGAAACCAAAATCGCAACGA
1 AATCGCAACGCGAAACCAAAATCGCAACGA
74300 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (33 bp):
AATCGCAACGCGAAACCAAAATCGCAACGACAG
Found at i:74330 original size:14 final size:14
Alignment explanation
Indices: 74311--74367 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
74301 TTTCATTTCG
74311 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
74325 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
74342 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
74358 CGTTGCGATT
1 CGTTGCGATT
74368 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:74339 original size:33 final size:33
Alignment explanation
Indices: 74297--74386 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
74287 AAAATCGCAA
*
74297 CGATTTTCATTTCGCGTTGCGATTCTTTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTGTCGTTG
*
74330 CGATTTTCATTTCGCATTGCGATTCTGTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTGTCGTTG
74363 CGATTTTCATTTCGCGTTGCGATT
1 CGATTTTCATTTCGCGTTGCGATT
74387 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTGTCGTTG
Found at i:74351 original size:19 final size:19
Alignment explanation
Indices: 74297--74423 Score: 121
Period size: 19 Copynumber: 7.2 Consensus size: 19
74287 AAAATCGCAA
74297 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
74316 CGA--TTC-TTT--CGTTG
1 CGATTTTCATTTCGCGTTG
*
74330 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCGTTG
*
74349 CGA--TTC-TGT--CGTTG
1 CGATTTTCATTTCGCGTTG
74363 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
**
74382 CGATTTTGGTTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
74401 CGATTTTAAGTTTCGTGTTG
1 CGATTTTCA-TTTCGCGTTG
74421 CGA
1 CGA
74424 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 15 0.17
16 11 0.12
17 11 0.12
19 39 0.44
20 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:76362 original size:14 final size:14
Alignment explanation
Indices: 76343--76378 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
76333 ATTGTTTAAT
76343 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
76357 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
76371 TGATTTGT
1 TGATTTGT
76379 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:76509 original size:19 final size:19
Alignment explanation
Indices: 76485--76601 Score: 163
Period size: 19 Copynumber: 6.4 Consensus size: 19
76475 AAAATTGACT
76485 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
76504 ATCGCAATCCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
76523 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
76542 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
76556 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
76575 ATCGCAATGCGGAAATTAAA
1 ATCGCAATGC-GAAATGAAA
76595 ATCGCAA
1 ATCGCAA
76602 CGGGAGAATC
Statistics
Matches: 87, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 56 0.64
20 15 0.17
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:76561 original size:52 final size:53
Alignment explanation
Indices: 76503--76616 Score: 194
Period size: 52 Copynumber: 2.2 Consensus size: 53
76493 GCGAAATGAA
76503 AATCGCAATCCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATCCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
* * *
76555 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATTAAAATCGCAACGGGAG
1 AATCGCAATCCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
76608 AATCGCAAT
1 AATCGCAAT
76617 GCGATTTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.50
53 29 0.50
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (53 bp):
AATCGCAATCCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:76564 original size:33 final size:36
Alignment explanation
Indices: 76485--76581 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 36
76475 AAAATTGACT
76485 ATCGCAATGCGAAATGAAAATCGCAATCCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-CCG-AATGAAA
*
76523 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAACCGAATGAAA
76556 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
76582 TGCGGAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
33 29 0.50
34 1 0.02
36 2 0.03
38 26 0.45
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAACCGAATGAAA
Found at i:76633 original size:53 final size:53
Alignment explanation
Indices: 76503--76620 Score: 202
Period size: 53 Copynumber: 2.2 Consensus size: 53
76493 GCGAAATGAA
*
76503 AATCGCAATCCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
* *
76555 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATTAAAATCGCAACGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
76608 AATCGCAATGCGA
1 AATCGCAATGCGA
76621 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:76638 original size:19 final size:19
Alignment explanation
Indices: 76610--76870 Score: 265
Period size: 19 Copynumber: 14.7 Consensus size: 19
76600 AACGGGAGAA
* *
76610 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
76629 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
76645 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76662 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76681 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
76697 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76714 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76733 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76752 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
76770 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76786 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
76805 TCGCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
76824 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
76842 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
76858 TCGCATTGCGATT
1 TCGCATTGCGATT
76871 CTCTCGTTGC
Statistics
Matches: 203, Mismatches: 17, Indels: 44
0.77 0.06 0.17
Matches are distributed among these distances:
14 34 0.17
16 18 0.09
17 15 0.07
18 2 0.01
19 105 0.52
20 29 0.14
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:76673 original size:52 final size:52
Alignment explanation
Indices: 76610--76842 Score: 242
Period size: 52 Copynumber: 4.3 Consensus size: 52
76600 AACGGGAGAA
* *
76610 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
76662 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * *
76714 TCGCATTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
* * * *
76770 T-G--TTGGGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC---TCTCGTTGCGATTTTCATT
76824 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
76843 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
52 89 0.57
53 28 0.18
54 6 0.04
55 4 0.03
56 4 0.03
58 24 0.15
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:76800 original size:72 final size:72
Alignment explanation
Indices: 76648--76870 Score: 369
Period size: 72 Copynumber: 3.1 Consensus size: 72
76638 GATTCTCTCG
* * *
76648 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
76711 ATTTCGCA
65 ATTTCGCA
*
76719 TTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
*
76784 TTTCGCG
66 TTTCGCA
*
76791 TTGCGATTTTCATTTCGCGTTGCAATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
76856 TTTCGCA
66 TTTCGCA
76863 TTGCGATT
1 TTGCGATT
76871 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
71 32 0.23
72 109 0.77
73 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
TTTCGCA
Found at i:76892 original size:33 final size:33
Alignment explanation
Indices: 76667--76884 Score: 215
Period size: 33 Copynumber: 6.2 Consensus size: 33
76657 TCATTTCGCA
76667 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
76700 TTGCGATTTTCATTTCGCATTGCAATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCTCG
*
76738 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* * *
76772 TTGGGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCTCG
* *
76810 TTGCAATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
76844 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
76877 TTGCGATT
1 TTGCGATT
76885 GTAATTTCCG
Statistics
Matches: 151, Mismatches: 18, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
32 1 0.01
33 55 0.36
34 33 0.22
35 5 0.03
37 4 0.03
38 35 0.23
39 18 0.12
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:76899 original size:53 final size:51
Alignment explanation
Indices: 76730--76903 Score: 145
Period size: 53 Copynumber: 3.3 Consensus size: 51
76720 TGCAATTTTC
* * * *
76730 ATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTT-TCATGTTGGGATTTTC
1 ATTTCGTGTTGCGATTTTCATTT-CGCATTGCGATTTCTC--GTTGCGATTGTA
* * * * * *
76783 ATTTCGCGTTGCGATTTTCATTTCGCGTTGCAATTT-TCATTTCCGCATTGCGA
1 ATTTCGTGTTGCGATTTTCATTTCGCATTGCGATTTCTC-GTTGCG-ATTG-TA
* * *
76836 TTTTCATGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTA
1 ATTTCGTGTTGCGATTTTCATTTCGCATTGCGATT-TCTCGTTGCGATTGTA
76888 ATTTCCGTGTTGCGAT
1 ATTT-CGTGTTGCGAT
76904 AGTCAAATGC
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
51 3 0.03
52 20 0.21
53 65 0.68
54 5 0.05
55 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.46
Consensus pattern (51 bp):
ATTTCGTGTTGCGATTTTCATTTCGCATTGCGATTTCTCGTTGCGATTGTA
Found at i:79330 original size:24 final size:24
Alignment explanation
Indices: 79296--79342 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
79286 CTGAAACATC
79296 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
79320 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
79343 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:80053 original size:20 final size:20
Alignment explanation
Indices: 80025--80294 Score: 290
Period size: 20 Copynumber: 13.5 Consensus size: 20
80015 AAATTTCAGT
* * *
80025 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
80045 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
80065 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
80085 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
80105 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
80125 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
80145 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
80165 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
80185 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
80205 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
80225 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
80245 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
80265 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
80285 GTTGCGATTT
1 GTTGCGATTT
80295 TGGAAAATCG
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:80311 original size:21 final size:21
Alignment explanation
Indices: 80281--80363 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
80271 ATTTTCATAT
*
80281 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
80302 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
80323 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
80344 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
80364 CTGATTTGAG
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:80354 original size:42 final size:43
Alignment explanation
Indices: 80261--80359 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
80251 ATTTATGTGT
* *
80261 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
80302 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
80344 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
80360 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:80825 original size:31 final size:31
Alignment explanation
Indices: 80787--80915 Score: 222
Period size: 31 Copynumber: 4.2 Consensus size: 31
80777 GTGACGTGTC
*
80787 ACTTTAAGCGTTGATTCATTTATACCATCAA
1 ACTTTAAGCGTTGATTCGTTTATACCATCAA
80818 ACTTTAAGCGTTGATTCGTTTATACCATCAA
1 ACTTTAAGCGTTGATTCGTTTATACCATCAA
*
80849 ACTTTAAGCGTTGATTCGTTTATACCATTAA
1 ACTTTAAGCGTTGATTCGTTTATACCATCAA
* *
80880 ACTTTAAGCGTTGATTCGTTTATACTACCAA
1 ACTTTAAGCGTTGATTCGTTTATACCATCAA
80911 ACTTT
1 ACTTT
80916 TAATTTTAAC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 93 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (31 bp):
ACTTTAAGCGTTGATTCGTTTATACCATCAA
Found at i:81166 original size:118 final size:118
Alignment explanation
Indices: 80958--81194 Score: 456
Period size: 118 Copynumber: 2.0 Consensus size: 118
80948 AATTATGTCA
80958 CTTCGTCCTTATGAGTTCAACATGAATACGGAGAAAAATAAAGAGTCGGAACAGCATGGCATGGG
1 CTTCGTCCTTATGAGTTCAACATGAATACGGAGAAAAATAAAGAGTCGGAACAGCATGGCATGGG
81023 ATTCTGGTACCTTGTCAAGAAGATGGTTCCGATTGACTCGCTGCCTGCTTTGG
66 ATTCTGGTACCTTGTCAAGAAGATGGTTCCGATTGACTCGCTGCCTGCTTTGG
* *
81076 CTTCGTCCTTATGAGTTCAACATGAATACTGAGAAAAATATAGAGTCGGAACAGCATGGCATGGG
1 CTTCGTCCTTATGAGTTCAACATGAATACGGAGAAAAATAAAGAGTCGGAACAGCATGGCATGGG
81141 ATTCTGGTACCTTGTCAAGAAGATGGTTCCGATTGACTCGCTGCCTGCTTTGG
66 ATTCTGGTACCTTGTCAAGAAGATGGTTCCGATTGACTCGCTGCCTGCTTTGG
81194 C
1 C
81195 CTGAACTGTC
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (118 bp):
CTTCGTCCTTATGAGTTCAACATGAATACGGAGAAAAATAAAGAGTCGGAACAGCATGGCATGGG
ATTCTGGTACCTTGTCAAGAAGATGGTTCCGATTGACTCGCTGCCTGCTTTGG
Found at i:83667 original size:13 final size:13
Alignment explanation
Indices: 83649--83673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83639 TTCATGTAAT
83649 TTTAAAAAAAATA
1 TTTAAAAAAAATA
83662 TTTAAAAAAAAT
1 TTTAAAAAAAAT
83674 TAAAATTATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTAAAAAAAATA
Found at i:83745 original size:16 final size:17
Alignment explanation
Indices: 83724--83758 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
83714 AAATTAAAAA
83724 AAAAAT-TCAAATCCCT
1 AAAAATCTCAAATCCCT
83740 AAAAATCTCAAATCCCT
1 AAAAATCTCAAATCCCT
83757 AA
1 AA
83759 CCTTAATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATCTCAAATCCCT
Found at i:92410 original size:19 final size:18
Alignment explanation
Indices: 92369--92414 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
92359 AGAATTAATT
* *
92369 TTTATTAATTACATTTTA
1 TTTATTTATTACATTATA
*
92387 CTTATTTATTATCATTATA
1 TTTATTTATTA-CATTATA
92406 TTTATTTAT
1 TTTATTTAT
92415 AAAATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTATTACATTATA
Found at i:96256 original size:18 final size:18
Alignment explanation
Indices: 96233--96267 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96223 GAAAGATCTC
*
96233 CATGGCCTGTCATCATTG
1 CATGGCCTGTCAGCATTG
*
96251 CATGGCTTGTCAGCATT
1 CATGGCCTGTCAGCATT
96268 TTGAGCAAGC
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:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (18 bp):
CATGGCCTGTCAGCATTG
Found at i:97100 original size:19 final size:19
Alignment explanation
Indices: 97076--97113 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
97066 TGTTCTTCTA
97076 CCTTTATGCACCACTGGAC
1 CCTTTATGCACCACTGGAC
97095 CCTTTATGCACCACTGGAC
1 CCTTTATGCACCACTGGAC
97114 TGACTGGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (19 bp):
CCTTTATGCACCACTGGAC
Found at i:98914 original size:41 final size:43
Alignment explanation
Indices: 98849--98939 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
98839 GAAAAGATGA
* * *
98849 AATTTTTACTTTCTTTTAATGAAAAA-CTA-TCAATTTTTCCCC
1 AATTTTTACTTTCATTTAATGAAAAATC-AGTAAATTTTCCCCC
*
98891 AATTTTTAC-TTGATTTAATGAAAAATCAGTAAATTTTCCCCC
1 AATTTTTACTTTCATTTAATGAAAAATCAGTAAATTTTCCCCC
98933 AATTTTT
1 AATTTTT
98940 TTCCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 15 0.35
42 28 0.65
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.46
Consensus pattern (43 bp):
AATTTTTACTTTCATTTAATGAAAAATCAGTAAATTTTCCCCC
Found at i:99386 original size:21 final size:21
Alignment explanation
Indices: 99356--99395 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
99346 TTGTTGATTG
* *
99356 TTATGATTCTGATGTGACAAT
1 TTATGATTCTAACGTGACAAT
*
99377 TTATGGTTCTAACGTGACA
1 TTATGATTCTAACGTGACA
99396 GTCCATTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (21 bp):
TTATGATTCTAACGTGACAAT
Found at i:104036 original size:16 final size:17
Alignment explanation
Indices: 104015--104048 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
104005 TATTTTTATT
*
104015 ATTTAATATA-AAAATA
1 ATTTAAAATACAAAATA
104031 ATTTAAAATACAAAATA
1 ATTTAAAATACAAAATA
104048 A
1 A
104049 AAACATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTTAAAATACAAAATA
Found at i:104249 original size:40 final size:40
Alignment explanation
Indices: 104205--104284 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
104195 AAAACGGGAA
104205 CAATTCCCAAATTTGGTGAGTAAGTTAGAAAAACTAAAAG
1 CAATTCCCAAATTTGGTGAGTAAGTTAGAAAAACTAAAAG
104245 CAATTCCCAAATTTGGTGAGTAAGTTAGAAAAACTAAAAG
1 CAATTCCCAAATTTGGTGAGTAAGTTAGAAAAACTAAAAG
104285 TATAGTGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (40 bp):
CAATTCCCAAATTTGGTGAGTAAGTTAGAAAAACTAAAAG
Found at i:113826 original size:18 final size:18
Alignment explanation
Indices: 113793--113842 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
113783 TCAATTCATT
*
113793 TTAATAATTTAAATATATA
1 TTAAT-ATTAAAATATATA
113812 TTAATATTAAAATATATA
1 TTAATATTAAAATATATA
113830 TTAA-ATTAAAATA
1 TTAATATTAAAATA
113843 AGTACTCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 9 0.30
18 16 0.53
19 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATATTAAAATATATA
Found at i:116130 original size:31 final size:31
Alignment explanation
Indices: 116092--116214 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
116082 CCCGAAGGAC
* *
116092 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
116123 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
116154 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
116185 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
116215 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:118724 original size:20 final size:20
Alignment explanation
Indices: 118679--118720 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
118669 CAACGGTCAA
118679 CGGTCAACGGTCGGTCGGGT
1 CGGTCAACGGTCGGTCGGGT
118699 CGGTCAAC-GTCGGGTC-GGT
1 CGGTCAACGGTC-GGTCGGGT
118718 CGG
1 CGG
118721 GTCAGACCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.10, C:0.26, G:0.45, T:0.19
Consensus pattern (20 bp):
CGGTCAACGGTCGGTCGGGT
Found at i:119970 original size:228 final size:226
Alignment explanation
Indices: 119573--120026 Score: 874
Period size: 228 Copynumber: 2.0 Consensus size: 226
119563 TCTTCAAGAT
119573 ACGAAATGGTCCAATAAATCTTGGACTCAATTTACCCTTACGCCCAAATCTCAATACTTTCTTCA
1 ACGAAATGGTCCAATAAATCTTGGACTCAATTTACCCTTACGCCCAAATCTCAATACTTTCTTCA
119638 GGGTGAACTTTCAAAAAGATCCGATCTCCCACTTCAAACTGATATCCTTCCTTCTTTGATCTGCA
66 GGGTGAACTTTCAAAAAGATCCGATCTCCCACTTCAAACTGATATCCTTCCTTCTTTGATCTGCA
119703 TAAGATTTCTACCTATCAAATGCCTCTTTCAGACGGTCACGGATTAATCTGACTGTGTCCTCCGT
131 TAAGATTTCTACCTATCAAATGCCTCTTTCAGACGGTCACGGATTAATCTGACTGTGTCCTCCGT
119768 CTCTCGCACTAACTCAGGTCCAAA-GTTTTC
196 CTCTCGCACTAACTCAGGTCCAAACGTTTTC
119798 ACGAAATGGTCCAATAAATCTTGGACTCAATTTACCCTTACGCCCAAATCTCAATACTTTCTTCC
1 ACGAAATGGTCCAATAAATCTTGGACTCAATTTACCCTTACGCCCAAATCTCAATACTTTCTT-C
119863 AGGGTGAAACTTTCAAAAAGATCCGATCTCCCACTTCAAACTGTATATCCTTCCTTCTTTGATCT
65 AGGGTG-AACTTTCAAAAAGATCCGATCTCCCACTTCAAACTG-ATATCCTTCCTTCTTTGATCT
119928 GCATAAGATTTCTACCTATCAAATGCCTCTTTCAGACGGTCACGGATTAATCTGACTGTGTCCTC
128 GCATAAGATTTCTACCTATCAAATGCCTCTTTCAGACGGTCACGGATTAATCTGACTGTGTCCTC
119993 CGTCTCTCGCACTAACTCAGGTCCAAACGTTTTC
193 CGTCTCTCGCACTAACTCAGGTCCAAACGTTTTC
120027 CTATCACGCA
Statistics
Matches: 225, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
225 63 0.28
226 7 0.03
227 36 0.16
228 113 0.50
229 6 0.03
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (226 bp):
ACGAAATGGTCCAATAAATCTTGGACTCAATTTACCCTTACGCCCAAATCTCAATACTTTCTTCA
GGGTGAACTTTCAAAAAGATCCGATCTCCCACTTCAAACTGATATCCTTCCTTCTTTGATCTGCA
TAAGATTTCTACCTATCAAATGCCTCTTTCAGACGGTCACGGATTAATCTGACTGTGTCCTCCGT
CTCTCGCACTAACTCAGGTCCAAACGTTTTC
Found at i:125740 original size:7 final size:7
Alignment explanation
Indices: 125728--125758 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
125718 ACGTCGAAAA
125728 GTCAACG
1 GTCAACG
125735 GTCAACG
1 GTCAACG
125742 GTCAACG
1 GTCAACG
*
125749 ATCAACG
1 GTCAACG
125756 GTC
1 GTC
125759 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:131517 original size:30 final size:30
Alignment explanation
Indices: 131483--131554 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
131473 ACAAAACCTC
131483 CTCTGTTGCAGCAACTCTTCTCTCTTCCCT
1 CTCTGTTGCAGCAACTCTTCTCTCTTCCCT
131513 CTCTGTTGCAGCAACTCTTCTCTCTTCCCT
1 CTCTGTTGCAGCAACTCTTCTCTCTTCCCT
*
131543 CGCTGTTGCAGC
1 CTCTGTTGCAGC
131555 TCCATAGGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.10, C:0.39, G:0.14, T:0.38
Consensus pattern (30 bp):
CTCTGTTGCAGCAACTCTTCTCTCTTCCCT
Found at i:131595 original size:19 final size:19
Alignment explanation
Indices: 131553--131596 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
131543 CGCTGTTGCA
131553 GCTCCATAGGTCGCCAAGT
1 GCTCCATAGGTCGCCAAGT
* **
131572 ACTCCATAGGTCGCCTTGT
1 GCTCCATAGGTCGCCAAGT
131591 GCTCCA
1 GCTCCA
131597 GGACCTATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.34, G:0.23, T:0.25
Consensus pattern (19 bp):
GCTCCATAGGTCGCCAAGT
Found at i:132984 original size:114 final size:114
Alignment explanation
Indices: 132784--133012 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
132774 AAATTGGAAA
132784 TGGTTTCAATTTTTTGGATTGTAAAGTTAAAGTGAAGGAAATGAGAACTAGATCCTAACAATCTC
1 TGGTTTCAATTTTTTGGATTGTAAAGTTAAAGTGAAGGAAATGAGAACTAGATCCTAACAATCTC
132849 GCCTTTGGATCTGTCTGTCTGGTTTGGTGTTTTGTTAAATGGAATTCAG
66 GCCTTTGGATCTGTCTGTCTGGTTTGGTGTTTTGTTAAATGGAATTCAG
132898 TGGTTTCAATTTTTTGGATTGTAAAGTTAAAGTGAAGGAAATGAGAACTAGATCCTAACAATCTC
1 TGGTTTCAATTTTTTGGATTGTAAAGTTAAAGTGAAGGAAATGAGAACTAGATCCTAACAATCTC
132963 GCCTTTGGATCTGTCTGTCTGGTTTGGTGTTTTGTTAAATGGAATTCAG
66 GCCTTTGGATCTGTCTGTCTGGTTTGGTGTTTTGTTAAATGGAATTCAG
133012 T
1 T
133013 TAATGGTTGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (114 bp):
TGGTTTCAATTTTTTGGATTGTAAAGTTAAAGTGAAGGAAATGAGAACTAGATCCTAACAATCTC
GCCTTTGGATCTGTCTGTCTGGTTTGGTGTTTTGTTAAATGGAATTCAG
Found at i:136052 original size:110 final size:110
Alignment explanation
Indices: 135859--136074 Score: 360
Period size: 110 Copynumber: 2.0 Consensus size: 110
135849 TGTATTCGAC
* * *
135859 TGATCTGATGCTGCTAAACACATGATTATATTTCATGTTTGTGTTGATTGATCTCTTTAGCATAG
1 TGATCAGATGCTGCTAAACACATGATTACATTTCATGTTTGTGTTAATTGATCTCTTTAGCATAG
*
135924 GGTGCTCTTTCATGTTTGTGTTGATTCTGTCAAACGAGTGCTGGT
66 GGTGATCTTTCATGTTTGTGTTGATTCTGTCAAACGAGTGCTGGT
* * *
135969 TGATCAGATGCTGCTATACACATGATTGCATTTCATGTTTGTGTTAATTGATCTCTTTTGCATAG
1 TGATCAGATGCTGCTAAACACATGATTACATTTCATGTTTGTGTTAATTGATCTCTTTAGCATAG
*
136034 GGTGATCTTTCATGTTTGTGTTGATTCTGTCAAAGGAGTGC
66 GGTGATCTTTCATGTTTGTGTTGATTCTGTCAAACGAGTGC
136075 CTGTGTGATT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (110 bp):
TGATCAGATGCTGCTAAACACATGATTACATTTCATGTTTGTGTTAATTGATCTCTTTAGCATAG
GGTGATCTTTCATGTTTGTGTTGATTCTGTCAAACGAGTGCTGGT
Found at i:145826 original size:130 final size:130
Alignment explanation
Indices: 145681--145941 Score: 522
Period size: 130 Copynumber: 2.0 Consensus size: 130
145671 TGGAAAAATG
145681 TAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAATTTAAACTTCTAATTTTTTAAAGCTTTAA
1 TAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAATTTAAACTTCTAATTTTTTAAAGCTTTAA
145746 GTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACCGGGTAAATCTATTATATGAACAAATTAA
66 GTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACCGGGTAAATCTATTATATGAACAAATTAA
145811 TAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAATTTAAACTTCTAATTTTTTAAAGCTTTAA
1 TAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAATTTAAACTTCTAATTTTTTAAAGCTTTAA
145876 GTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACCGGGTAAATCTATTATATGAACAAATTAA
66 GTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACCGGGTAAATCTATTATATGAACAAATTAA
145941 T
1 T
145942 TAATTCCACA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (130 bp):
TAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAATTTAAACTTCTAATTTTTTAAAGCTTTAA
GTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACCGGGTAAATCTATTATATGAACAAATTAA
Found at i:145982 original size:130 final size:130
Alignment explanation
Indices: 145718--145982 Score: 370
Period size: 130 Copynumber: 2.0 Consensus size: 130
145708 AAGTTTTAAT
145718 TTAAACTTCTAATTTTTTAAAGCTTTAAGTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACC
1 TTAAACTTCTAATTTTTTAAAGCTTTAAGTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACC
* * * ***** *
145783 GGGTAAATCTATTATATGAACAAATTAATAAACTAAACTTTTTTAAAAAATTTAAAAGTTTTAAT
66 GGGTAAATCTATTATATGAACAAATTAATAAACTAAACTTATCTAAAAAATATAAAACAACCAAA
145848 TTAAACTTCTAATTTTTTAAAGCTTTAAGTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACC
1 TTAAACTTCTAATTTTTTAAAGCTTTAAGTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACC
* * ** ** *
145913 GGGTAAATCTATTATATGAACAAATTAATTAATTCCACATTATCT-ATGAATATAGAACAACCAA
66 GGGTAAATCTATTATATGAACAAATTAATAAACTAAAC-TTATCTAAAAAATATAAAACAACCAA
145977 A
130 A
145978 TTAAA
1 TTAAA
145983 TATACATTTA
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 114 0.97
131 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (130 bp):
TTAAACTTCTAATTTTTTAAAGCTTTAAGTTGACCCCCAAAACTTTATCATCAAGTTCCGTCACC
GGGTAAATCTATTATATGAACAAATTAATAAACTAAACTTATCTAAAAAATATAAAACAACCAAA
Found at i:147106 original size:2 final size:2
Alignment explanation
Indices: 147099--147140 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
147089 ATTAGCAAAT
147099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
147141 GGAGTCTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:149629 original size:146 final size:146
Alignment explanation
Indices: 149365--149657 Score: 586
Period size: 146 Copynumber: 2.0 Consensus size: 146
149355 AGAGTAGAAC
149365 TATGTCTAGTTTAAGACATCGAGTTCTTCCTCCACAATTGCTACTGAAATGGCCGAAGGAAGCTT
1 TATGTCTAGTTTAAGACATCGAGTTCTTCCTCCACAATTGCTACTGAAATGGCCGAAGGAAGCTT
149430 CGTTTTGTTTGTGGTTATTGCATCCCGAGCCAAGTAGTCGTCCAAAAATGGGGTAATCTCTCCTT
66 CGTTTTGTTTGTGGTTATTGCATCCCGAGCCAAGTAGTCGTCCAAAAATGGGGTAATCTCTCCTT
149495 GGTTTTTGCATATTCA
131 GGTTTTTGCATATTCA
149511 TATGTCTAGTTTAAGACATCGAGTTCTTCCTCCACAATTGCTACTGAAATGGCCGAAGGAAGCTT
1 TATGTCTAGTTTAAGACATCGAGTTCTTCCTCCACAATTGCTACTGAAATGGCCGAAGGAAGCTT
149576 CGTTTTGTTTGTGGTTATTGCATCCCGAGCCAAGTAGTCGTCCAAAAATGGGGTAATCTCTCCTT
66 CGTTTTGTTTGTGGTTATTGCATCCCGAGCCAAGTAGTCGTCCAAAAATGGGGTAATCTCTCCTT
149641 GGTTTTTGCATATTCA
131 GGTTTTTGCATATTCA
149657 T
1 T
149658 TCACCATTAT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 147 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (146 bp):
TATGTCTAGTTTAAGACATCGAGTTCTTCCTCCACAATTGCTACTGAAATGGCCGAAGGAAGCTT
CGTTTTGTTTGTGGTTATTGCATCCCGAGCCAAGTAGTCGTCCAAAAATGGGGTAATCTCTCCTT
GGTTTTTGCATATTCA
Found at i:158442 original size:31 final size:31
Alignment explanation
Indices: 158407--158474 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
158397 TCGAAAAATA
* * * *
158407 TAAGATTTGGTCAATTTTGTTTCGTTTT-GAT
1 TAAGATGTGATCAATTTCGTCTCGTTTTAG-T
*
158438 TAAGATGTGATCACTTTCGTCTCGTTTTAGT
1 TAAGATGTGATCAATTTCGTCTCGTTTTAGT
158469 TAAGAT
1 TAAGAT
158475 AAGGTCACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (31 bp):
TAAGATGTGATCAATTTCGTCTCGTTTTAGT
Found at i:164092 original size:37 final size:36
Alignment explanation
Indices: 164017--164092 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
164007 TTTTTATATT
*
164017 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
164053 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
164090 TTT
1 TTT
164093 GTAATATTAT
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:164274 original size:20 final size:20
Alignment explanation
Indices: 164238--164275 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
164228 ATCATATTCC
**
164238 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
164258 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
164276 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:170395 original size:15 final size:14
Alignment explanation
Indices: 170358--170404 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
170348 ATCGTTATTC
170358 TAAATCCTAAACCCT
1 TAAATCCTAAA-CCT
170373 TAAA-CCTAAACCT
1 TAAATCCTAAACCT
170386 TACAATCCTAAACCT
1 TA-AATCCTAAACCT
170401 TAAA
1 TAAA
170405 ATTTAAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.17
14 10 0.33
15 15 0.50
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATCCTAAACCT
Found at i:170418 original size:14 final size:14
Alignment explanation
Indices: 170401--170432 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
170391 TCCTAAACCT
170401 TAAAATTTAAACTC
1 TAAAATTTAAACTC
*
170415 TAAACTTTAAACTC
1 TAAAATTTAAACTC
170429 TAAA
1 TAAA
170433 TATCCGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAATTTAAACTC
Found at i:170432 original size:21 final size:21
Alignment explanation
Indices: 170393--170432 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
170383 CCTTACAATC
*
170393 CTAAACCTTAAAATTTAAACT
1 CTAAACCTTAAAATCTAAACT
* *
170414 CTAAACTTTAAACTCTAAA
1 CTAAACCTTAAAATCTAAA
170433 TATCCGTAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
CTAAACCTTAAAATCTAAACT
Found at i:170490 original size:14 final size:14
Alignment explanation
Indices: 170471--170500 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
170461 CAAATCTTAC
170471 AACCTTAAACTCTA
1 AACCTTAAACTCTA
170485 AACCTTAAACTCTA
1 AACCTTAAACTCTA
170499 AA
1 AA
170501 TATCCGATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AACCTTAAACTCTA
Found at i:173811 original size:60 final size:59
Alignment explanation
Indices: 173739--173960 Score: 176
Period size: 60 Copynumber: 3.5 Consensus size: 59
173729 TTGCGTCATT
* * *
173739 TGACAATTAAAAGTTATAAAATGATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCA
1 TGACTATTAAAAGTTA-CAAATGATCACTCGATTATATGATGTTGCTTTGTTAAGTCTCA
* * * ** * *
173799 CGACTATTAAAAGTTACAATTGATAACTCGACTATTCATATGTTCCAAACTCATCCTTTTGTTGA
1 TGACTATTAAAAGTTACAAATGATCACTCG---ATT-ATATG------A-TGTTGC-TTTGTTAA
*
173864 GTAC-CT
54 GT-CTCA
* * *
173870 TGACTATTAAAAGTTATGAAATAATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCA
1 TGACTATTAAAAGTTA-CAAATGATCACTCGATTATATGATGTTGCTTTGTTAAGTCTCA
173930 TGACTATTAAAAGTTACAAATGATCACTCGA
1 TGACTATTAAAAGTTACAAATGATCACTCGA
173961 CTATTCATAT
Statistics
Matches: 122, Mismatches: 25, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
59 23 0.19
60 40 0.33
61 3 0.02
62 4 0.03
63 5 0.04
68 5 0.04
69 4 0.03
70 3 0.02
71 25 0.20
72 10 0.08
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (59 bp):
TGACTATTAAAAGTTACAAATGATCACTCGATTATATGATGTTGCTTTGTTAAGTCTCA
Found at i:173959 original size:131 final size:131
Alignment explanation
Indices: 173738--173989 Score: 423
Period size: 131 Copynumber: 1.9 Consensus size: 131
173728 GTTGCGTCAT
*
173738 TTGACAATTAAAAGTTATAAAATGATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCACGAC
1 TTGACAATTAAAAGTTATAAAATAATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCACGAC
* *
173803 TATTAAAAGTTACAATTGATAACTCGACTATTCATATGTTCCAAACTCATCCTTTTGTTGAGTAC
66 TATTAAAAGTTACAAATGATAACTCGACTATTCATATATTCCAAACTCATCCTTTTGTTGAGTAC
173868 C
131 C
* * *
173869 TTGACTATTAAAAGTTATGAAATAATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCATGAC
1 TTGACAATTAAAAGTTATAAAATAATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCACGAC
* * *
173934 TATTAAAAGTTACAAATGATCACTCGACTATTCATATATTCCAAATTCATCGTTTT
66 TATTAAAAGTTACAAATGATAACTCGACTATTCATATATTCCAAACTCATCCTTTT
173990 TGGTTAATAA
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 112 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (131 bp):
TTGACAATTAAAAGTTATAAAATAATCATTCGATTATATGATGTTGCTTTGTTAAGTCTCACGAC
TATTAAAAGTTACAAATGATAACTCGACTATTCATATATTCCAAACTCATCCTTTTGTTGAGTAC
C
Found at i:177742 original size:19 final size:19
Alignment explanation
Indices: 177718--177774 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
177708 AAACCGAACT
*
177718 GAACCGAACCGAAAAACCC
1 GAACCGAACCGAAAAAACC
***
177737 GAACCG--TTTAAAAAACC
1 GAACCGAACCGAAAAAACC
177754 GAACCGAACCGAAAAAACC
1 GAACCGAACCGAAAAAACC
177773 GA
1 GA
177775 TTTCGATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 13 0.45
19 16 0.55
ACGTcount: A:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (19 bp):
GAACCGAACCGAAAAAACC
Found at i:190396 original size:21 final size:21
Alignment explanation
Indices: 190370--190412 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
190360 GTTATAGTGT
190370 TAACGTAACAATTCAAGATAC
1 TAACGTAACAATTCAAGATAC
* * *
190391 TAACGTGACGATTCACGATAC
1 TAACGTAACAATTCAAGATAC
190412 T
1 T
190413 GGTTTGACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (21 bp):
TAACGTAACAATTCAAGATAC
Found at i:194672 original size:17 final size:17
Alignment explanation
Indices: 194650--194691 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
194640 ATAATTAAAA
*
194650 AAATCCTTAATTCTTCG
1 AAATCCCTAATTCTTCG
194667 AAATCCCTAATTCTTCG
1 AAATCCCTAATTCTTCG
194684 AAATCCCT
1 AAATCCCT
194692 TGCCCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (17 bp):
AAATCCCTAATTCTTCG
Found at i:197213 original size:28 final size:28
Alignment explanation
Indices: 197178--197235 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
197168 CGTCAACTTA
* *
197178 ATTGTAAATTATTAATTTTTTTCAAATT
1 ATTGTAAATTATTAAATTTGTTCAAATT
197206 ATTGTAAATTATTAAATTTGTTCAAATT
1 ATTGTAAATTATTAAATTTGTTCAAATT
197234 AT
1 AT
197236 GAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTGTAAATTATTAAATTTGTTCAAATT
Found at i:197242 original size:28 final size:28
Alignment explanation
Indices: 197178--197246 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
197168 CGTCAACTTA
* * *
197178 ATTGTAAATTATTAATTTTTTTCAAATT
1 ATTGAAAATTATTAAATTTGTTCAAATT
*
197206 ATTGTAAATTATTAAATTTGTTCAAATT
1 ATTGAAAATTATTAAATTTGTTCAAATT
*
197234 A-TGAAAAATATTA
1 ATTGAAAATTATTA
197247 TCTTTGTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 10 0.27
28 27 0.73
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (28 bp):
ATTGAAAATTATTAAATTTGTTCAAATT
Found at i:206323 original size:52 final size:52
Alignment explanation
Indices: 206260--206365 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
206250 CGCAGTGTTT
*
206260 TCAACATTAATTCAACGCCTATCTGCGATAGTAGAAAGAAGAAGCATTCCGA
1 TCAACATTAATTCAACGCCTATCTGCAATAGTAGAAAGAAGAAGCATTCCGA
* *
206312 TCAACTTTAATTCAACGCCTATCTGCAATCGTAGAAAGAAGAAGCATTCCGA
1 TCAACATTAATTCAACGCCTATCTGCAATAGTAGAAAGAAGAAGCATTCCGA
206364 TC
1 TC
206366 GGATCTATTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.25
Consensus pattern (52 bp):
TCAACATTAATTCAACGCCTATCTGCAATAGTAGAAAGAAGAAGCATTCCGA
Found at i:214492 original size:32 final size:31
Alignment explanation
Indices: 214419--214495 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
214409 CTAATGTGAC
* * *
214419 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** **
214450 TCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
214482 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
214496 CACGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:214502 original size:63 final size:63
Alignment explanation
Indices: 214419--214542 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
214409 CTAATGTGAC
* ** * *
214419 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCT-GCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCTCG-GACCCTAAGATGTGT
* * *
214482 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCGGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCGGACCCTAAGATGT
214543 TCCCTTAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 49 0.96
64 2 0.04
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCGGACCCTAAGATGTGT
Found at i:214888 original size:29 final size:31
Alignment explanation
Indices: 214854--214913 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
214844 AAATTTTGAA
*
214854 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
214883 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
214914 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:217015 original size:31 final size:29
Alignment explanation
Indices: 216971--217040 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
216961 ATTTAAGTGT
216971 CTAAATTATTTTTTAATCAAAATAAATAC
1 CTAAATTATTTTTTAATCAAAATAAATAC
* *
217000 CTAAAGTTATCTTTTTTATCAAAATAAGTAC
1 CTAAA-TTAT-TTTTTAATCAAAATAAATAC
*
217031 CTAAACTATT
1 CTAAATTATT
217041 CAAACTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.17
30 7 0.19
31 23 0.64
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (29 bp):
CTAAATTATTTTTTAATCAAAATAAATAC
Found at i:219289 original size:2 final size:2
Alignment explanation
Indices: 219282--219306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219272 TAGTTTATCC
219282 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 A
219307 GGAAAAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219871 original size:27 final size:27
Alignment explanation
Indices: 219817--219871 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
219807 CAAATAAATT
* * * *
219817 TTTTTATTCAAACTTGTCATGTCAATA
1 TTTTTATTAAAACTCGACACGTCAATA
*
219844 TTTTTATTAAAACTCGACACGTCGATA
1 TTTTTATTAAAACTCGACACGTCAATA
219871 T
1 T
219872 GATGAGTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (27 bp):
TTTTTATTAAAACTCGACACGTCAATA
Found at i:220285 original size:19 final size:19
Alignment explanation
Indices: 220261--220315 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
220251 TTTCCTAAAA
*
220261 AGTTTCGATACTTTTCAAG
1 AGTTTCGAAACTTTTCAAG
*
220280 AGTTTCGAAACTATCTCAAG
1 AGTTTCGAAACT-TTTCAAG
220300 AGTTTCGAAACTTTTC
1 AGTTTCGAAACTTTTC
220316 TTAAGTTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (19 bp):
AGTTTCGAAACTTTTCAAG
Found at i:220324 original size:19 final size:20
Alignment explanation
Indices: 220261--220332 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 20
220251 TTTCCTAAAA
*
220261 AGTTTCGATACTTTTC-AAG
1 AGTTTCGAAACTTTTCTAAG
*
220280 AGTTTCGAAAC-TATCTCAAG
1 AGTTTCGAAACTTTTCT-AAG
*
220300 AGTTTCGAAACTTTTCTTA-
1 AGTTTCGAAACTTTTCTAAG
*
220319 AGTTTCGATACTTT
1 AGTTTCGAAACTTT
220333 GGCTCCAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.07
19 23 0.51
20 15 0.33
21 4 0.09
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (20 bp):
AGTTTCGAAACTTTTCTAAG
Found at i:228860 original size:19 final size:19
Alignment explanation
Indices: 228823--228879 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
228813 TTTTTATAAA
228823 TTAATTAAAAAAATTTATTT
1 TTAATTAAAAAAA-TTATTT
228843 TTAATTAAAAATAA-TATTT
1 TTAATTAAAAA-AATTATTT
228862 TTATTATTAAAAAAATTA
1 TTA--ATTAAAAAAATTA
228880 AAAATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 8 0.24
20 13 0.39
21 12 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTAAAAAAATTATTT
Found at i:231783 original size:22 final size:22
Alignment explanation
Indices: 231742--231784 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
231732 GCATCGATGC
* * *
231742 ACTGTTCATGGTATTGTTCATT
1 ACTGTTCACGGTACTATTCATT
231764 ACTGTTCACGGTACTATTCAT
1 ACTGTTCACGGTACTATTCAT
231785 ACCATATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (22 bp):
ACTGTTCACGGTACTATTCATT
Found at i:240603 original size:170 final size:170
Alignment explanation
Indices: 240246--240577 Score: 402
Period size: 170 Copynumber: 2.0 Consensus size: 170
240236 GTTTTAGTAC
* *
240246 CTAAACTTTAAAAAAAATCAAAATTTAACGTCAAATTTTGAATGGATACTAAAATGAAACAAAAA
1 CTAAACTCTAAAAAAAATCAAAATTTAACGTCAAATATTGAATGGATACTAAAATGAAACAAAAA
* * * *
240311 CTAAATTTTGTGTATGGTTTAAAAAAAATAAAAGTTTAGGAACTAAAGTAGACCAAAATTGATAG
66 CTAAACTTTATGTATGGTTTAAAAAAAATAAAAGTTTAGGAACTAAAATAGACCAAAACTGATAG
* * ** **** *
240376 TTTATGTACTAAAAAAATTAGTTTTGACCCGTTTTAGCAC
131 TTTATGTACTAAAAAAAGTAATTTACACAAAATTTAGCAA
*
240416 CTAAACTTTAAAAAAAATC-AAATTCTAACGTCAAATATTGAACAT-G-TACTAAAATGAAACAA
1 CTAAACTCTAAAAAAAATCAAAATT-TAACGTCAAATATTG-A-ATGGATACTAAAATGAAACAA
* * * *
240478 AAACTAAACTTTATGTATGGTTTTAAGAAAATTAAAAGTTTAGGTACTAAAATAGATCAAAACTG
63 AAACTAAACTTTATGTATGG-TTTAAAAAAAATAAAAGTTTAGGAACTAAAATAGACCAAAACTG
* *
240543 ATAGTTTATGTACT-AAAGACGTAATTTACACAAAA
127 ATAGTTTATGTACTAAAAAAAGTAATTTACACAAAA
240578 AAATTTATAA
Statistics
Matches: 139, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
169 5 0.04
170 78 0.56
171 54 0.39
172 2 0.01
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (170 bp):
CTAAACTCTAAAAAAAATCAAAATTTAACGTCAAATATTGAATGGATACTAAAATGAAACAAAAA
CTAAACTTTATGTATGGTTTAAAAAAAATAAAAGTTTAGGAACTAAAATAGACCAAAACTGATAG
TTTATGTACTAAAAAAAGTAATTTACACAAAATTTAGCAA
Found at i:243072 original size:17 final size:16
Alignment explanation
Indices: 243041--243076 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
243031 TTAGAAATAA
*
243041 TTAAAAAAAATAAAGT
1 TTAAAAAAAAAAAAGT
243057 TTAAATAAAAAAAAAGT
1 TTAAA-AAAAAAAAAGT
243074 TTA
1 TTA
243077 TATATTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
TTAAAAAAAAAAAAGT
Found at i:244427 original size:32 final size:33
Alignment explanation
Indices: 244365--244430 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
244355 ATCAGATTCA
*
244365 TTTTTAAAAGTTTAGGTTCAAGTCAGGTCGAGT
1 TTTTTAAAAGATTAGGTTCAAGTCAGGTCGAGT
* *
244398 TTTTTAAAA-ATTATGTTCGAGTC-GAGTCGAGT
1 TTTTTAAAAGATTAGGTTCAAGTCAG-GTCGAGT
244430 T
1 T
244431 CGATTTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 19 0.66
33 9 0.31
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (33 bp):
TTTTTAAAAGATTAGGTTCAAGTCAGGTCGAGT
Found at i:245188 original size:2 final size:2
Alignment explanation
Indices: 245183--245232 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
245173 TAAATAAAAA
* * * *
245183 AT AT AT AT AT TT AT AT AT TT A- AT TT AA 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
245224 AT AT AT AT A
1 AT AT AT AT A
245233 CTCGGCCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:245203 original size:29 final size:29
Alignment explanation
Indices: 245170--245229 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
245160 AATAAATTTA
*
245170 ATTTAAATAAAAAATATATATATTTATAT
1 ATTTAAATAAAAAATATATATATATATAT
* * *
245199 ATTTAATTTAAATATATATATATATATAT
1 ATTTAAATAAAAAATATATATATATATAT
245228 AT
1 AT
245230 ATACTCGGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTAAATAAAAAATATATATATATATAT
Done.