Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001364.1 Hibiscus syriacus cultivar Beakdansim tig00002657_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: 79971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:897 original size:54 final size:54
Alignment explanation
Indices: 814--1169 Score: 447
Period size: 54 Copynumber: 6.7 Consensus size: 54
804 TTACCAAATA
*
814 GGCACTAAGTGTGCAATTCATGGAATTCATCATAGGTTGATGAACAATCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * *
868 AGCACTAAGTGTGGAATTCATGGAATTCATCATAGGTTGATGAACAATCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * * *
922 AGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACACTCATTTT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * ** * *
976 GGCACAAAGTGTACAATTCACAGAATTCATC--ATG-TGATGAACAA-CTATTTT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATC-GTTTC
* *
1027 GGCACTAA--GTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCG-TTTC
* * * *
1080 GGCACTAAGTGTGCAATTCACGAAATTCATTATATG-TGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* *
1133 GGCACTAAGTGTGCAATTCATGAAATTCATCAAATGT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGT
1170 ATTTAGTTGG
Statistics
Matches: 270, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
49 19 0.07
50 1 0.00
51 24 0.09
52 13 0.05
53 49 0.18
54 140 0.52
55 24 0.09
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
Found at i:922 original size:26 final size:26
Alignment explanation
Indices: 839--922 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
829 ATTCATGGAA
839 TTCATCATAGGTTGATGAACAATCGT
1 TTCATCATAGGTTGATGAACAATCGT
* * * *
865 TTCAGCACTAAG-TG-TGGAATTC-ATGGAA
1 TTCATCA-TAGGTTGAT-GAA--CAATCG-T
893 TTCATCATAGGTTGATGAACAATCGT
1 TTCATCATAGGTTGATGAACAATCGT
919 TTCA
1 TTCA
923 GCACTAAGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 1 0.02
26 16 0.38
27 12 0.29
28 12 0.29
29 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (26 bp):
TTCATCATAGGTTGATGAACAATCGT
Found at i:2300 original size:24 final size:22
Alignment explanation
Indices: 2256--2304 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
2246 TTCAAACCCA
2256 AAATCATATAAAAACTATTTAGT
1 AAATCATATAAAAACTATTTA-T
2279 AAATCAGTATAAAAA-TATTTTAT
1 AAATCA-TATAAAAACTA-TTTAT
2302 AAA
1 AAA
2305 ATAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATCATATAAAAACTATTTAT
Found at i:2306 original size:24 final size:24
Alignment explanation
Indices: 2255--2306 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2245 ATTCAAACCC
2255 AAAATCATATAAAAACTATTTAGT
1 AAAATCATATAAAAACTATTTAGT
2279 -AAATCAGTATAAAAA-TATTTTA-T
1 AAAATCA-TATAAAAACTA-TTTAGT
2302 AAAAT
1 AAAAT
2307 AATTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAATCATATAAAAACTATTTAGT
Found at i:8163 original size:12 final size:12
Alignment explanation
Indices: 8146--8170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8136 AAAAAACTCT
8146 CTCTCTCTCTCC
1 CTCTCTCTCTCC
8158 CTCTCTCTCTCC
1 CTCTCTCTCTCC
8170 C
1 C
8171 CCTTCATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:8163 original size:14 final size:14
Alignment explanation
Indices: 8144--8173 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8134 AAAAAAAACT
*
8144 CTCTCTCTCTCTCC
1 CTCTCTCTCTCCCC
8158 CTCTCTCTCTCCCC
1 CTCTCTCTCTCCCC
8172 CT
1 CT
8174 TCATTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (14 bp):
CTCTCTCTCTCCCC
Found at i:10128 original size:16 final size:17
Alignment explanation
Indices: 10096--10130 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10086 TGATTAAGTG
10096 GCATTGACACTTTGTCTC
1 GCATTGACAC-TTGTCTC
10114 GCATTGACA-TTGTCTC
1 GCATTGACACTTGTCTC
10130 G
1 G
10131 AATCTTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (17 bp):
GCATTGACACTTGTCTC
Found at i:10762 original size:4 final size:4
Alignment explanation
Indices: 10755--10781 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10745 CACATGCATG
10755 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
10782 GCAATAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:15871 original size:30 final size:30
Alignment explanation
Indices: 15831--15900 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
15821 TTGTACTGGA
*
15831 ACTGATGGTGGACTAAGAGCTGCTGTTGGG
1 ACTGGTGGTGGACTAAGAGCTGCTGTTGGG
*
15861 ACTGGTGGTGGACTAGGAGCTGCTGTTGGG
1 ACTGGTGGTGGACTAAGAGCTGCTGTTGGG
*
15891 GCTGGTGGTG
1 ACTGGTGGTG
15901 TTGATCGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.14, C:0.13, G:0.46, T:0.27
Consensus pattern (30 bp):
ACTGGTGGTGGACTAAGAGCTGCTGTTGGG
Found at i:22901 original size:21 final size:19
Alignment explanation
Indices: 22863--22908 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
22853 ATTTAATCCT
22863 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
22883 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
22904 A-TAAT
1 ACTAAT
22909 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:23364 original size:11 final size:11
Alignment explanation
Indices: 23348--23373 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23338 CTATCTCTCG
23348 ATGCTCTTACA
1 ATGCTCTTACA
23359 ATGCTCTTACA
1 ATGCTCTTACA
23370 ATGC
1 ATGC
23374 CCATACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (11 bp):
ATGCTCTTACA
Found at i:25389 original size:42 final size:42
Alignment explanation
Indices: 25343--25427 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
25333 ACTATAACTA
* *
25343 ATGGTAAAGGCTCAAACCTTTAACCACTCCATGCTGAAAGTT
1 ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
*
25385 ATGGTAAAGGCTCCAACCTCTAACCACTCCATACTGAAAGTT
1 ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
25427 A
1 A
25428 GGTTCATCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (42 bp):
ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
Found at i:28312 original size:26 final size:25
Alignment explanation
Indices: 28283--28338 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 25
28273 ACCGTAGTGC
28283 TACACATAAGGTCGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCAT-A
28309 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
28334 TACAC
1 TACAC
28339 TTAGTGTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCACCATA
Found at i:32194 original size:41 final size:41
Alignment explanation
Indices: 32149--32294 Score: 156
Period size: 41 Copynumber: 3.6 Consensus size: 41
32139 TACATATATC
* *
32149 GTGGCGTTTTTAGATAAACGCTGCTAAAACCT-AGTACTTTA
1 GTGGCGTTTTTAGACAAACGCCGCTAAAA-CTAAGTACTTTA
* *
32190 GTGGCGTTTTAAG-CAAAACGCCGCTAAAACTCA-TACTTTA
1 GTGGCGTTTTTAGAC-AAACGCCGCTAAAACTAAGTACTTTA
* * *
32230 GAGGCGTTTATTGGACAAACACCGCTAAAGA-TAAGTACTTTA
1 GTGGCGTTT-TTAGACAAACGCCGCTAAA-ACTAAGTACTTTA
*
32272 GTGGCGTTTTTAAACAAACGCCG
1 GTGGCGTTTTTAGACAAACGCCG
32295 TAATAGGTAC
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
40 17 0.20
41 53 0.61
42 17 0.20
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
GTGGCGTTTTTAGACAAACGCCGCTAAAACTAAGTACTTTA
Found at i:32318 original size:82 final size:80
Alignment explanation
Indices: 32137--32323 Score: 193
Period size: 82 Copynumber: 2.3 Consensus size: 80
32127 ATCACAAAAG
* * *
32137 GGTACATATATCGTGGCGTTTTTAGATAAACGCTGCTAAAACCTAGTACTTTAGTGGCGTTTTAA
1 GGTACATATATCGTGGCGTTTTTAGACAAACACCGCTAAAA-CTAGTACTTTAGTGGCGTTTTAA
*
32202 GCAAAACGCCGCTAAA
65 ACAAAACGCCGCTAAA
** * * * *
32218 ACT-CATACTTTAGAGGCGTTTATTGGACAAACACCGCTAAAGA-TAAGTACTTTAGTGGCGTTT
1 GGTACATA-TATCGTGGCGTTT-TTAGACAAACACCGCTAAA-ACT-AGTACTTTAGTGGCG-TT
32281 TTAAAC-AAACGCCG-TAATA
61 TTAAACAAAACGCCGCTAA-A
32300 GGTACATATATCGTGGCGTTTTTA
1 GGTACATATATCGTGGCGTTTTTA
32324 AATAGAGCCT
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
80 4 0.05
81 17 0.20
82 50 0.60
83 12 0.14
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (80 bp):
GGTACATATATCGTGGCGTTTTTAGACAAACACCGCTAAAACTAGTACTTTAGTGGCGTTTTAAA
CAAAACGCCGCTAAA
Found at i:34357 original size:21 final size:21
Alignment explanation
Indices: 34331--34371 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
34321 CTTTGATTTA
34331 TTGTTATGGATTTCAAGTTTC
1 TTGTTATGGATTTCAAGTTTC
34352 TTGTTATGGATTTCAAGTTT
1 TTGTTATGGATTTCAAGTTT
34372 GTGTCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTATGGATTTCAAGTTTC
Found at i:34634 original size:43 final size:43
Alignment explanation
Indices: 34493--34914 Score: 498
Period size: 43 Copynumber: 9.9 Consensus size: 43
34483 TGAAAGGTAA
* *
34493 TTAGCGGCGTTTGTATCCAAAAAACGCCACTATAGGTCT-GACCT
1 TTAGCGGCGTTTGT-TCC-AAAAACGCCGCTATAGATCTCGACCT
* * ** * * *
34537 TTTGCGGCGTTTATTTAAAAAACGCTGCTATAGATCT-AACGT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
*** * *
34579 TTAGCTATGTTTGTTCCAAAAACGCCGCTATTGATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
** * *
34622 TTAGCGGCGTTTGTTCCAAAAGTGCCGCTATTGATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
34665 TTAGCGGCGTTTATTCCAAAAACGCCGCTATAGATCT-GACGT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
34707 TTAGCCGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
*
34750 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
34793 TTAGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* * *
34836 TTAGCGGCGTTTGTTTCAAAAACACCGTTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* * *
34879 TTA---G-ATTTGTTCCAAAAATGCCGCTATAAATCTCGA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGA
34915 TTTTTTGCAA
Statistics
Matches: 323, Mismatches: 53, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
39 26 0.08
40 1 0.00
42 85 0.26
43 199 0.62
44 12 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
Found at i:34721 original size:128 final size:128
Alignment explanation
Indices: 34492--34914 Score: 523
Period size: 128 Copynumber: 3.3 Consensus size: 128
34482 ATGAAAGGTA
* * * * **
34492 ATTAGCGGCGTTTGTATCCAAAAAACGCCACTATAGGTCT-GACCTTTTGCGGCGTTTATTTAAA
1 ATTAGCGGCGTTTGT-TCC-AAAAACGCCGCTATAGATCTCGACCATTAGCGGCGTTTATTCCAA
* * *** *
34556 AAACGCTGCTATAGATCTAACGTTTAGCTATGTTTGTTCCAAAAACGCCGCTATTGATCTCGACC
64 AAACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACC
** *
34621 ATTAGCGGCGTTTGTTCCAAAAGTGCCGCTATTGATCTCGACCATTAGCGGCGTTTATTCCAAAA
1 ATTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCATTAGCGGCGTTTATTCCAAAA
*
34686 ACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACC
66 ACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACC
* * * *
34749 TTTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCATTAGCGACTTTTGTTCCAAAA
1 ATTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCATTAGCGGCGTTTATTCCAAAA
* * * * *
34814 ACGCCGCTATAGATCTCGACCTTTAGCGGCGTTTGTTTCAAAAACACCGTTATAGATCTCGACC
66 ACGCCGCTATAGATCT-GACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACC
* * * *
34878 TTTA---G-ATTTGTTCCAAAAATGCCGCTATAAATCTCGA
1 ATTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGA
34915 TTTTTTGCAA
Statistics
Matches: 260, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
125 29 0.11
126 1 0.00
127 15 0.06
128 155 0.60
129 60 0.23
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (128 bp):
ATTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCATTAGCGGCGTTTATTCCAAAA
ACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACC
Found at i:43983 original size:3 final size:3
Alignment explanation
Indices: 43975--44003 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
43965 AGAAATATAT
43975 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44004 TAGTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:44071 original size:18 final size:17
Alignment explanation
Indices: 44048--44090 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
44038 ATATATACAT
44048 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
44066 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
44083 ATAA-AATA
1 ATAATAATA
44091 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:44848 original size:19 final size:19
Alignment explanation
Indices: 44824--44866 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
44814 TTGGATCGGA
*
44824 ATCGAACTCATAAATCTTC
1 ATCGAACTCAGAAATCTTC
44843 ATCGAACTCAGAAATCTTC
1 ATCGAACTCAGAAATCTTC
44862 ATCGA
1 ATCGA
44867 TATATAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (19 bp):
ATCGAACTCAGAAATCTTC
Found at i:45445 original size:105 final size:105
Alignment explanation
Indices: 45262--45878 Score: 974
Period size: 105 Copynumber: 5.9 Consensus size: 105
45252 GCATTGTTCA
* * ** *
45262 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
45322 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
45362 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGACATTGGGAAGTTTTTGTTGACAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
45427 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
45467 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
45532 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
45572 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
45637 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
45677 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
*
45742 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
45782 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-GTTGTTGACAA
* * *
45847 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
45879 TGTTTCCTCG
Statistics
Matches: 482, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
100 35 0.07
101 1 0.00
102 1 0.00
104 5 0.01
105 403 0.84
106 37 0.08
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:46626 original size:68 final size:65
Alignment explanation
Indices: 46490--46680 Score: 197
Period size: 67 Copynumber: 2.9 Consensus size: 65
46480 AAAGAGATAG
* * * * * *
46490 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATATGTTTCATGAGAAACGGTCTCAAGGGAAAC
1 AATTCGTTTTAAGGGAAATAAAT-TCAAAGGT-TTTGTTTCAAGAGAAACTGTCTCAAGGGAAAC
46554 AA
64 AA
** * *
46556 AATTACGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-CGTTTTAAGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGAGAAACTGTCTCAAGGGA-A
46621 A-AA
62 ACAA
* * *
46624 AATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGAAACTGTCTCAAG
1 AATTCGTTTTAAGGGAAATAAATTCAAAGGTTTTGTTTCAAGAGAAACTGTCTCAAG
46681 ATAGACGAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
65 22 0.21
66 7 0.07
67 40 0.38
68 33 0.32
69 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (65 bp):
AATTCGTTTTAAGGGAAATAAATTCAAAGGTTTTGTTTCAAGAGAAACTGTCTCAAGGGAAACAA
Found at i:46707 original size:36 final size:36
Alignment explanation
Indices: 46656--46779 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
46646 TTCAAAGGTT
*
46656 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* *
46692 TTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
46727 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
*
46765 TTATTTCAAGGGAAA
1 TTGTTTCAAGGGAAA
46780 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
Found at i:47771 original size:22 final size:22
Alignment explanation
Indices: 47746--47789 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47736 CATTTTTGTT
47746 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
47768 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
47790 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:48410 original size:9 final size:8
Alignment explanation
Indices: 48388--48425 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
48378 TTTTTGTCCC
48388 TTTTTC-T
1 TTTTTCTT
48395 TTTTTCTT
1 TTTTTCTT
48403 TTTGTTCTT
1 TTT-TTCTT
48412 TTTTTGCTT
1 TTTTT-CTT
48421 TTTTT
1 TTTTT
48426 TTTCTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 6 0.21
9 16 0.57
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:48414 original size:23 final size:24
Alignment explanation
Indices: 48377--48428 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
48367 TTTGCATGTG
48377 TTTTTTGTCC-CTTTTT-CTTTTT
1 TTTTTTGTCCTCTTTTTGCTTTTT
* *
48399 TCTTTTTGTTCTTTTTTTGCTTTTT
1 T-TTTTTGTCCTCTTTTTGCTTTTT
48424 TTTTT
1 TTTTT
48429 CTTTTTGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 8 0.32
24 9 0.36
25 7 0.28
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (24 bp):
TTTTTTGTCCTCTTTTTGCTTTTT
Found at i:49635 original size:8 final size:8
Alignment explanation
Indices: 49619--49657 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
49609 ATTTTAGATG
49619 AAAATGCA
1 AAAATGCA
*
49627 AAAAGGCA
1 AAAATGCA
49635 AAAATGC-
1 AAAATGCA
49642 AAAATGCA
1 AAAATGCA
*
49650 AGAATGCA
1 AAAATGCA
49658 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:49645 original size:15 final size:15
Alignment explanation
Indices: 49619--49657 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
49609 ATTTTAGATG
49619 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
49635 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
49650 AGAATGCA
1 AAAATGCA
49658 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:51052 original size:5 final size:5
Alignment explanation
Indices: 51042--51070 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
51032 GCAAGTGATG
51042 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
51071 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52793 original size:18 final size:17
Alignment explanation
Indices: 52770--52812 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
52760 ATATATACAT
52770 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
52788 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
52805 ATAA-AATA
1 ATAATAATA
52813 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:56923 original size:25 final size:25
Alignment explanation
Indices: 56890--56940 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
56880 TCCTTAGTTG
56890 TAAGATGATTACAAAGTAATATATC
1 TAAGATGATTACAAAGTAATATATC
* *
56915 TAAGGTGATTATAAAGTAATATATC
1 TAAGATGATTACAAAGTAATATATC
56940 T
1 T
56941 TCTAAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
TAAGATGATTACAAAGTAATATATC
Found at i:57689 original size:23 final size:23
Alignment explanation
Indices: 57663--57722 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
57653 TTTTTACCTT
*
57663 CTACTTCAACTG-TTCTGCCGCCA
1 CTACTCCAACTGCTT-TGCCGCCA
* *
57686 CTACTCCATCTGCTTTGCCGCCT
1 CTACTCCAACTGCTTTGCCGCCA
57709 CTACTCCAACTGCT
1 CTACTCCAACTGCT
57723 CCGTCGCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.15, C:0.42, G:0.12, T:0.32
Consensus pattern (23 bp):
CTACTCCAACTGCTTTGCCGCCA
Found at i:57730 original size:23 final size:23
Alignment explanation
Indices: 57662--57752 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
57652 ATTTTTACCT
* * *
57662 TCTACTTCAACTGTTCTGCCGCC
1 TCTACTCCAACTGCTCCGCCGCC
* * **
57685 ACTACTCCATCTGCTTTGCCGCC
1 TCTACTCCAACTGCTCCGCCGCC
*
57708 TCTACTCCAACTGCTCCGTCGCC
1 TCTACTCCAACTGCTCCGCCGCC
* * *
57731 ATGTTCCCCAACTGCTCCGCCG
1 -TCTACTCCAACTGCTCCGCCG
57753 TCAATTTCCC
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
23 36 0.68
24 17 0.32
ACGTcount: A:0.13, C:0.44, G:0.14, T:0.29
Consensus pattern (23 bp):
TCTACTCCAACTGCTCCGCCGCC
Found at i:57745 original size:24 final size:24
Alignment explanation
Indices: 57714--57767 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
57704 CGCCTCTACT
* *
57714 CCAACTGCTCCGTCG-CCATGTTCC
1 CCAACTGCTCCGCCGTCAAT-TTCC
57738 CCAACTGCTCCGCCGTCAATTTCC
1 CCAACTGCTCCGCCGTCAATTTCC
57762 CCAACT
1 CCAACT
57768 AGCTGCTGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.17, C:0.46, G:0.13, T:0.24
Consensus pattern (24 bp):
CCAACTGCTCCGCCGTCAATTTCC
Found at i:58790 original size:11 final size:11
Alignment explanation
Indices: 58770--58800 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
58760 TTTAATTTAG
*
58770 TATTTAATTAT
1 TATTTTATTAT
58781 TATTTTATTAT
1 TATTTTATTAT
58792 TATTTTATT
1 TATTTTATT
58801 TTAATCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:64781 original size:5 final size:5
Alignment explanation
Indices: 64771--64843 Score: 71
Period size: 5 Copynumber: 14.6 Consensus size: 5
64761 CATCAGGAAA
* * *
64771 AAAAG AAAAG AAAGAG AAAA- AAAAG AAAACA AAAAG AAAAG AGAA- AAGAG
1 AAAAG AAAAG AAA-AG AAAAG AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG
64821 AAAAG AAAAG AAGAA- AAAAG AAA
1 AAAAG AAAAG AA-AAG AAAAG AAA
64844 TTGAATCAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 8 0.14
5 37 0.66
6 11 0.20
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:64791 original size:19 final size:19
Alignment explanation
Indices: 64767--64837 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
64757 CATCCATCAG
*
64767 GAAAAAAAGAAAAGAAAGA
1 GAAAAAAAGAAAAGAAAAA
*
64786 GAAAAAAAAGAAAACAAAAA
1 G-AAAAAAAGAAAAGAAAAA
*
64806 G-AAAAGAGAAAAGAGAAAA
1 GAAAAAAAGAAAAGA-AAAA
*
64825 GAAAAGAAGAAAA
1 GAAAAAAAGAAAA
64838 AAGAAATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.26
19 6 0.14
20 26 0.60
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (19 bp):
GAAAAAAAGAAAAGAAAAA
Found at i:64793 original size:20 final size:21
Alignment explanation
Indices: 64769--64843 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
64759 TCCATCAGGA
64769 AAAAAAGAAAAGAAAGAGAA-
1 AAAAAAGAAAAGAAAGAGAAG
* *
64789 AAAAAAGAAAACAAAAAGAAAAG
1 AAAAAAG-AAA-AGAAAGAGAAG
64812 AGAAAAGAGAAAAGAAA-AGAAG
1 A-AAAA-AGAAAAGAAAGAGAAG
64834 AAAAAAGAAA
1 AAAAAAGAAA
64844 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
20 12 0.26
21 7 0.15
22 13 0.28
23 5 0.11
24 7 0.15
25 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAGAAAGAGAAG
Found at i:64804 original size:12 final size:12
Alignment explanation
Indices: 64769--64837 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
64759 TCCATCAGGA
64769 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
64781 AAAGAGAAAAAAAAG
1 -AA-A-AAAGAAAAG
*
64796 AAAACA-AAAAG
1 AAAAAAGAAAAG
*
64807 AAAAGAGAAAAG
1 AAAAAAGAAAAG
*
64819 AGAAAAGAAAAG
1 AAAAAAGAAAAG
64831 AAGAAAA
1 AA-AAAA
64838 AAGAAATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 10 0.22
12 18 0.39
13 7 0.15
14 3 0.07
15 8 0.17
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:66302 original size:50 final size:50
Alignment explanation
Indices: 66248--66492 Score: 348
Period size: 51 Copynumber: 4.8 Consensus size: 50
66238 GGTCCATATT
* *
66248 ATCCATGTGGGTATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTT
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* * *
66298 ATCCATATGGGTATCTTGAAGGCTCACATCAGCATGAAATGATAGAAGTA
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* *
66348 ATCTATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATATAAGTA
1 ATCCATGT-GGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* *
66399 ATCCATATGAGGCATCTTGAAGGCTCACATCAACATGAAAAAGATAGAAGTA
1 ATCCATGTG-GGCATCTTGAAGGCTCACATCAGCATG-AAAAGATAGAAGTA
*
66451 ATCCATGTGGGACATCTTGAAGGCTTACA-CTAGCATGAAAAG
1 ATCCATGTGGG-CATCTTGAAGGCTCACATC-AGCATGAAAAG
66493 GTTAGGATAT
Statistics
Matches: 175, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
50 54 0.31
51 79 0.45
52 42 0.24
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (50 bp):
ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
Found at i:66489 original size:103 final size:100
Alignment explanation
Indices: 66248--66492 Score: 366
Period size: 101 Copynumber: 2.4 Consensus size: 100
66238 GGTCCATATT
* * *
66248 ATCCATGTGGGTATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTTATCCATATGGGTATC
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATATGGGCATC
* *
66313 TTGAAGGCTCACATCAGCATGAAATGATAGAAGTA
66 TTGAAGGCTCACATCAACATGAAAAGATAGAAGTA
* *
66348 ATCTATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATATAAGTAATCCATATGAGGCA
1 ATCCATGT-GGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATATG-GGCA
66413 TCTTGAAGGCTCACATCAACATGAAAAAGATAGAAGTA
64 TCTTGAAGGCTCACATCAACATG-AAAAGATAGAAGTA
*
66451 ATCCATGTGGGACATCTTGAAGGCTTACA-CTAGCATGAAAAG
1 ATCCATGTGGG-CATCTTGAAGGCTCACATC-AGCATGAAAAG
66493 GTTAGGATAT
Statistics
Matches: 131, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
100 7 0.05
101 48 0.37
102 29 0.22
103 47 0.36
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (100 bp):
ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATATGGGCATC
TTGAAGGCTCACATCAACATGAAAAGATAGAAGTA
Found at i:66566 original size:40 final size:41
Alignment explanation
Indices: 66501--66593 Score: 97
Period size: 41 Copynumber: 2.3 Consensus size: 41
66491 AGGTTAGGAT
*
66501 ATTTTGAAAGTCCATTTCAACCAAAAAT-A--GAATGTTGGGGC
1 ATTTTGAAAG-CCATTTCAACCAAAAATGATCG-ATG-TGGGGA
66542 ATTTTGAAAGCCATTAT-AGA-CAAAAATGATCGATGTGGGGA
1 ATTTTGAAAGCCATT-TCA-ACCAAAAATGATCGATGTGGGGA
66583 ATTTTGAAAGC
1 ATTTTGAAAGC
66594 TCATGTTGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
40 13 0.28
41 29 0.63
42 3 0.07
43 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (41 bp):
ATTTTGAAAGCCATTTCAACCAAAAATGATCGATGTGGGGA
Found at i:67025 original size:14 final size:14
Alignment explanation
Indices: 67008--67035 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
66998 AACCAATGAT
67008 TATGGTGTTGAACC
1 TATGGTGTTGAACC
67022 TATGGTGTTGAACC
1 TATGGTGTTGAACC
67036 AATGTTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGGTGTTGAACC
Found at i:68394 original size:173 final size:176
Alignment explanation
Indices: 68044--68422 Score: 550
Period size: 173 Copynumber: 2.2 Consensus size: 176
68034 CTATATCCCA
* * *
68044 GATTTGTAAGTCCTACTGGTCATCCATAAGACCGTCAGTACATGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACAGGATGTTTTCAAATGAGATTTTA
* * * *
68109 GAAACCAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
66 AAAACCAAGCCTTCGGGGG-TTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAAC
* * *
68174 AAAAGGGTTTCTTGACAACTAAAAAACTAAGCCTTCAGCGTTTTCTT
130 AAAAGGGGTTCTTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
* *
68221 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACAGGATGTTTTCAAATGAGATTTTA
* *
68286 AAAATCAAGCCTTCGGGGG-TT-T-ACTATCTCAAAAGAGCTGTTAAAGGAAGCCGAGCCTAAC-
66 AAAACCAAGCCTTCGGGGGTTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAACA
* *
68347 AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGAGGTTTCTT
131 AAAGGGGTTC-TTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
* *
68394 GATTTGTAAGCCCTACGGGCCATCTATAA
1 GATTTGTAAGTCCTACGGGCCATCCATAA
68423 AAAAAATATA
Statistics
Matches: 183, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
172 9 0.05
173 94 0.51
174 1 0.01
175 2 0.01
177 77 0.42
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (176 bp):
GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACAGGATGTTTTCAAATGAGATTTTA
AAAACCAAGCCTTCGGGGGTTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAACA
AAAGGGGTTCTTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
Found at i:69654 original size:50 final size:52
Alignment explanation
Indices: 69599--69707 Score: 152
Period size: 50 Copynumber: 2.2 Consensus size: 52
69589 CTTATTCATC
*
69599 AATATATCCGTAACAATTATTTTGAACAGAATCA-AGAACATTC-TTTTGGT
1 AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
* ***
69649 AATATATCTGTAATGTTTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
1 AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
69701 AAT-TATC
1 AATATATC
69708 ACTATTGATG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 29 0.56
51 13 0.25
52 10 0.19
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (52 bp):
AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
Found at i:72025 original size:2 final size:2
Alignment explanation
Indices: 72018--72044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72008 TCTAATGATT
72018 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
72045 ATCACTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:76902 original size:15 final size:15
Alignment explanation
Indices: 76884--76939 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
76874 TAACCGGTTT
76884 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
76899 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
* *
76916 CGGTTATAAAAAAAT
1 CGGTTTTAAAAAAAC
*
76931 CGATTTTAA
1 CGGTTTTAA
76940 TATTATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 20 0.57
17 15 0.43
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:76909 original size:17 final size:17
Alignment explanation
Indices: 76887--76920 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
76877 CCGGTTTCGG
76887 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
76904 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
76921 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:76928 original size:17 final size:17
Alignment explanation
Indices: 76891--76929 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
76881 TTTCGGTTTT
* **
76891 AAAAAAACCGGTTTTTT
1 AAAAAAACCGGTTATAA
76908 AAAAAAACCGGTTATAA
1 AAAAAAACCGGTTATAA
76925 AAAAA
1 AAAAA
76930 TCGATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (17 bp):
AAAAAAACCGGTTATAA
Found at i:78139 original size:32 final size:33
Alignment explanation
Indices: 78043--78141 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
78033 AACTCAACAT
* * *
78043 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
78076 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
78109 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
78141 A
1 A
78142 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:78160 original size:21 final size:21
Alignment explanation
Indices: 78136--78176 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
78126 ACTTCAAGTT
78136 CGATAATTGAAACAAAGTTTG
1 CGATAATTGAAACAAAGTTTG
*
78157 CGATAATTGAAATAAAGTTT
1 CGATAATTGAAACAAAGTTT
78177 AAAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTG
Done.