Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005198.1 Hibiscus syriacus cultivar Beakdansim tig00011743_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: 95756
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2150 original size:14 final size:14
Alignment explanation
Indices: 2131--2158 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2121 GAGTATAGTT
2131 CCTTGCAATCTATC
1 CCTTGCAATCTATC
2145 CCTTGCAATCTATC
1 CCTTGCAATCTATC
2159 TCGTAGAACT
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:0.36, G:0.07, T:0.36
Consensus pattern (14 bp):
CCTTGCAATCTATC
Found at i:6976 original size:8 final size:8
Alignment explanation
Indices: 6963--6993 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6953 TCACCACAGA
6963 CATGCATC
1 CATGCATC
6971 CATGCATC
1 CATGCATC
*
6979 CATGCATA
1 CATGCATC
6987 CATGCAT
1 CATGCAT
6994 GCATAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (8 bp):
CATGCATC
Found at i:11669 original size:24 final size:21
Alignment explanation
Indices: 11615--11672 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
11605 ATTTACTGTG
11615 ATTGCGGTCGTCGCGGGCGCT
1 ATTGCGGTCGTCGCGGGCGCT
11636 ATTGCGGTCGTCGCGGGCGCT
1 ATTGCGGTCGTCGCGGGCGCT
*
11657 ATTGCGGCCGTCGCGG
1 ATTGCGGTCGTCGCGG
11673 AGTCGCAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.05, C:0.29, G:0.43, T:0.22
Consensus pattern (21 bp):
ATTGCGGTCGTCGCGGGCGCT
Found at i:13881 original size:10 final size:10
Alignment explanation
Indices: 13866--13916 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 10
13856 AGCTTTATAA
13866 ATAATAATAT
1 ATAATAATAT
13876 ATAATAATTTAT
1 ATAATAA--TAT
*
13888 ATATTAATAT
1 ATAATAATAT
13898 ATGTAATAATAT
1 A--TAATAATAT
13910 ATAATAA
1 ATAATAA
13917 CATAACACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 17 0.49
12 18 0.51
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATAATAATAT
Found at i:13899 original size:24 final size:24
Alignment explanation
Indices: 13859--13913 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
13849 GCCTTCGAGC
13859 TTTATAAATAATAATATATAATAA
1 TTTATAAATAATAATATATAATAA
* *
13883 TTTATATATTAAT-ATATGTAATAA
1 TTTATA-AATAATAATATATAATAA
*
13907 TATATAA
1 TTTATAA
13914 TAACATAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 21 0.78
25 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTATAAATAATAATATATAATAA
Found at i:14507 original size:20 final size:20
Alignment explanation
Indices: 14448--14515 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
14438 GATGACCCAA
* *
14448 AGGATTTACAAATTATCCGA
1 AGGATTTACAAATTACCCGG
*
14468 AGGTTTTACAAATTACCCGG
1 AGGATTTACAAATTACCCGG
*
14488 AGGATTTACAAATGACCCGG
1 AGGATTTACAAATTACCCGG
*
14508 AGGCTTTA
1 AGGATTTA
14516 ATTTTCTAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
AGGATTTACAAATTACCCGG
Found at i:14663 original size:20 final size:20
Alignment explanation
Indices: 14640--14681 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
14630 AGTCTAGCAG
14640 ATGACCCGAAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
*
14660 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGATTTACAA
14680 AT
1 AT
14682 TCGTGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ATGACCCGAAGGATTTACAA
Found at i:15321 original size:22 final size:22
Alignment explanation
Indices: 15296--15345 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
15286 AGCTTCCATT
15296 TTTGAAAAGAGAATCTATCATC
1 TTTGAAAAGAGAATCTATCATC
*
15318 TTTGAAAAGATAATCTATCATC
1 TTTGAAAAGAGAATCTATCATC
15340 TTTGAA
1 TTTGAA
15346 GCATGTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TTTGAAAAGAGAATCTATCATC
Found at i:22770 original size:26 final size:26
Alignment explanation
Indices: 22734--22791 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
22724 TTTATTTTGG
22734 GCAATTTATATATAGAGGACCAATGT
1 GCAATTTATATATAGAGGACCAATGT
22760 GCAATTTATATATAGAGGACCAATGT
1 GCAATTTATATATAGAGGACCAATGT
*
22786 TCAATT
1 GCAATT
22792 ACATGTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (26 bp):
GCAATTTATATATAGAGGACCAATGT
Found at i:26986 original size:34 final size:34
Alignment explanation
Indices: 26948--27026 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
26938 AGCCAGAGAA
* *
26948 ATAACTCTACTCGTAAACACATAAGGACAACGA-G
1 ATAACTCAACTCATAAACACATAAGGACAAC-ATG
** *
26982 ATAACTCAACTCATCCACATATAAGGACAACATG
1 ATAACTCAACTCATAAACACATAAGGACAACATG
27016 ATAACTCAACT
1 ATAACTCAACT
27027 TTTCCACACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.20
Consensus pattern (34 bp):
ATAACTCAACTCATAAACACATAAGGACAACATG
Found at i:30958 original size:85 final size:85
Alignment explanation
Indices: 30817--30986 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
30807 CCAACACCAA
30817 AGCTAGCGGCCCAACACCAAAGTTAGTGTCCCTTTCGGTTGCAAAGATGAAGAAAAAAGACTGAT
1 AGCTAGCGGCCCAACACCAAAGTTAGTGTCCCTTTCGGTTGCAAAGATGAAGAAAAAAGACTGAT
30882 GGTCTTGATTACTTTTTTAT
66 GGTCTTGATTACTTTTTTAT
30902 AGCTAGCGGCCCAACACCAAAGTTAGTGTCCCTTTCGGTTGCAAAGATGAAGAAAAAAGACTGAT
1 AGCTAGCGGCCCAACACCAAAGTTAGTGTCCCTTTCGGTTGCAAAGATGAAGAAAAAAGACTGAT
30967 GGTCTTGATTACTTTTTTAT
66 GGTCTTGATTACTTTTTTAT
30987 CCATGGGCTA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (85 bp):
AGCTAGCGGCCCAACACCAAAGTTAGTGTCCCTTTCGGTTGCAAAGATGAAGAAAAAAGACTGAT
GGTCTTGATTACTTTTTTAT
Found at i:34575 original size:22 final size:22
Alignment explanation
Indices: 34549--34590 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34539 AGTCGAGGGT
34549 TACATAGGTCATTCGAGACATA
1 TACATAGGTCATTCGAGACATA
* *
34571 TACATAGGTCCTTCGGGACA
1 TACATAGGTCATTCGAGACA
34591 AATTTCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TACATAGGTCATTCGAGACATA
Found at i:39251 original size:22 final size:22
Alignment explanation
Indices: 39223--39264 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39213 AGTCGAGTGT
*
39223 TACATAGGTCTTTCAGGACATA
1 TACATAGGTCCTTCAGGACATA
*
39245 TACATAGGTCCTTCGGGACA
1 TACATAGGTCCTTCAGGACA
39265 AATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (22 bp):
TACATAGGTCCTTCAGGACATA
Found at i:43382 original size:83 final size:83
Alignment explanation
Indices: 43241--43404 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 83
43231 AATTTCAAGG
* * * *
43241 AGTATACAAAAAGATATGAAGTTTTAATCAATGATAGGTCAGAAAATAGGGCAGTAGATTCTGCT
1 AGTATACAAAAAGATATGAAGTTTTAATCAAGGATAGGTCAGAAAACAGGGCAATAGATTATGCT
*
43306 CAATACAGCTTCTGTAGA
66 CAAAACAGCTTCTGTAGA
* *
43324 AGTATACAAAAAGATATGAAGTTTTAATCGAGGATAGGTCAGAAAACAGTGCAATAGATTATGCT
1 AGTATACAAAAAGATATGAAGTTTTAATCAAGGATAGGTCAGAAAACAGGGCAATAGATTATGCT
*
43389 CAAAACTGCTTCTGTA
66 CAAAACAGCTTCTGTA
43405 TGTCAACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (83 bp):
AGTATACAAAAAGATATGAAGTTTTAATCAAGGATAGGTCAGAAAACAGGGCAATAGATTATGCT
CAAAACAGCTTCTGTAGA
Found at i:44119 original size:19 final size:19
Alignment explanation
Indices: 44103--44149 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
44093 GTTATGAACT
44103 TGAAAATAAGCTATGAATA
1 TGAAAATAAGCTATGAATA
* * *
44122 TGAAATTAAGTTATGAATC
1 TGAAAATAAGCTATGAATA
44141 TG-AAATAAG
1 TGAAAATAAG
44150 TTGAGTCTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (19 bp):
TGAAAATAAGCTATGAATA
Found at i:44326 original size:18 final size:18
Alignment explanation
Indices: 44303--44367 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
44293 TGAAAAATAA
44303 TATGATATGACTATTATG
1 TATGATATGACTATTATG
** *
44321 TATGATATTGTTTATCATG
1 TATGATA-TGACTATTATG
* *
44340 ACTTTGATATGACTACTATG
1 --TATGATATGACTATTATG
44360 TATGATAT
1 TATGATAT
44368 TGTTTATCAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
18 14 0.40
19 8 0.23
20 7 0.20
21 6 0.17
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:44353 original size:39 final size:39
Alignment explanation
Indices: 44305--44387 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
44295 AAAAATAATA
*
44305 TGATATGACTATTATGTATGATATTGTTTATCATGACTT
1 TGATATGACTACTATGTATGATATTGTTTATCATGACTT
**
44344 TGATATGACTACTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTACTATGTATGATATTGTTTATCATGACTT
44383 TGATA
1 TGATA
44388 AAATTATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (39 bp):
TGATATGACTACTATGTATGATATTGTTTATCATGACTT
Found at i:47460 original size:57 final size:57
Alignment explanation
Indices: 47366--47490 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 57
47356 GATGACTTCT
* *
47366 CAGAATGGATAAGCCATATAAGAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
* * *
47423 CAGAATGCATAAGCCATATAAAAAGTTGGATATACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
*
47480 CATAATGCATA
1 CAGAATGCATA
47491 TATGTTCCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (57 bp):
CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
Found at i:49594 original size:15 final size:15
Alignment explanation
Indices: 49574--49604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49564 CAACAAATAG
49574 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
49589 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
49604 A
1 A
49605 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:52941 original size:113 final size:113
Alignment explanation
Indices: 52743--52969 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
52733 CACGTTTACT
52743 ACCTCAAGTTTTGGACAGTGCTCTCGATGCAAAGGTAAACCTTTGGTTTTTAAAAGGGAAAAAAA
1 ACCTCAAGTTTTGGACAGTGCTCTCGATGCAAAGGTAAACCTTTGGTTTTTAAAAGGGAAAAAAA
52808 GGTTGACAATGAAATTTGGATGTTATTTTTTTAATATAGGAAGTCAGG
66 GGTTGACAATGAAATTTGGATGTTATTTTTTTAATATAGGAAGTCAGG
52856 ACCTCAAGTTTTGGACAGTGCTCTCGATGCAAAGGTAAACCTTTGGTTTTTAAAAGGGAAAAAAA
1 ACCTCAAGTTTTGGACAGTGCTCTCGATGCAAAGGTAAACCTTTGGTTTTTAAAAGGGAAAAAAA
52921 GGTTGACAATGAAATTTGGATGTTATTTTTTTAATATAGGAAGTCAGG
66 GGTTGACAATGAAATTTGGATGTTATTTTTTTAATATAGGAAGTCAGG
52969 A
1 A
52970 AAAGAATTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (113 bp):
ACCTCAAGTTTTGGACAGTGCTCTCGATGCAAAGGTAAACCTTTGGTTTTTAAAAGGGAAAAAAA
GGTTGACAATGAAATTTGGATGTTATTTTTTTAATATAGGAAGTCAGG
Found at i:57276 original size:9 final size:9
Alignment explanation
Indices: 57262--57306 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
57252 TCACTGGTTC
57262 AACCGGTCG
1 AACCGGTCG
57271 AACCGGTCCG
1 AACCGGT-CG
57281 -ACCGGTCG
1 AACCGGTCG
57289 AACCGGTCCG
1 AACCGGT-CG
57299 -ACCGGTCG
1 AACCGGTCG
57307 GAAGAACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 4 0.12
9 25 0.76
10 4 0.12
ACGTcount: A:0.18, C:0.38, G:0.33, T:0.11
Consensus pattern (9 bp):
AACCGGTCG
Found at i:57316 original size:22 final size:18
Alignment explanation
Indices: 57263--57306 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
57253 CACTGGTTCA
57263 ACCGGTCGAACCGGTCCG
1 ACCGGTCGAACCGGTCCG
57281 ACCGGTCGAACCGGTCCG
1 ACCGGTCGAACCGGTCCG
57299 ACCGGTCG
1 ACCGGTCG
57307 GAAGAACCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.39, G:0.34, T:0.11
Consensus pattern (18 bp):
ACCGGTCGAACCGGTCCG
Found at i:58786 original size:14 final size:14
Alignment explanation
Indices: 58767--58798 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
58757 CCTATGTCAA
*
58767 CTAAACGATACCAG
1 CTAAACGATAACAG
58781 CTAAACGATAACAG
1 CTAAACGATAACAG
58795 CTAA
1 CTAA
58799 GCCCTATATT
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:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (14 bp):
CTAAACGATAACAG
Found at i:70381 original size:15 final size:15
Alignment explanation
Indices: 70361--70400 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
70351 TTCCCACTTC
70361 TCTTCTCTTCATTCT
1 TCTTCTCTTCATTCT
70376 TC-T-TCTTCATTTCT
1 TCTTCTCTTCA-TTCT
70390 TCTTC-CTTCAT
1 TCTTCTCTTCAT
70401 CTCCTTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTTCTCTTCATTCT
Found at i:70963 original size:21 final size:21
Alignment explanation
Indices: 70930--70988 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
70920 ATCCCTTTTC
* * *
70930 AAAAGGATTGATCCCTTAGAG
1 AAAATGATCGATCCCTTAGAA
*
70951 AAAATGATCGATCCC-TCGAA
1 AAAATGATCGATCCCTTAGAA
70971 AGAAATGATCGATCCCTT
1 A-AAATGATCGATCCCTT
70989 CTTTGTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.12
21 27 0.84
22 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (21 bp):
AAAATGATCGATCCCTTAGAA
Found at i:72072 original size:44 final size:45
Alignment explanation
Indices: 72019--72121 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 45
72009 GCCTAAGGTA
* *
72019 TTGGGAGGTGTTGATGCTATGTAACCT-GACCTCGCCTGAGATAC
1 TTGGGAGGTGTTGATGCGATGTAACCTAGACCTCACCTGAGATAC
* * * *
72063 TTGGAAGGTGTCG-TGCGATGTGACCTAGACCTCACTTGAGATAC
1 TTGGGAGGTGTTGATGCGATGTAACCTAGACCTCACCTGAGATAC
*
72107 TTGGGAGATGTTGAT
1 TTGGGAGGTGTTGAT
72122 ACTGTGTGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 11 0.23
44 36 0.75
45 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.30
Consensus pattern (45 bp):
TTGGGAGGTGTTGATGCGATGTAACCTAGACCTCACCTGAGATAC
Found at i:73281 original size:45 final size:45
Alignment explanation
Indices: 73230--73408 Score: 268
Period size: 45 Copynumber: 4.0 Consensus size: 45
73220 CATTTAAAGA
*
73230 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGC
* * *
73275 ATCCTTTCATGCCTTTCATGAACCATTATACATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGC
* *
73320 ATCCTTTCATGCCTTTCATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGC
* * * *
73365 ATCTTTTCATGCCTTTAATGTATCATTATGCGTTTCATTTATGG
1 ATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGG
73409 ATTCATTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 121 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (45 bp):
ATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGC
Found at i:73327 original size:90 final size:90
Alignment explanation
Indices: 73230--73408 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
73220 CATTTAAAGA
*
73230 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTCATG
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATG
73295 AACCATTATACATTTCATTTATGGC
66 AACCATTATACATTTCATTTATGGC
* *
73320 ATCCTTTCATGCCTTTCATGCACCGTTATGCATTTCATTTATGGCATCTTTTCATGCCTTTAATG
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATG
* * * *
73385 TATCATTATGCGTTTCATTTATGG
66 AACCATTATACATTTCATTTATGG
73409 ATTCATTTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (90 bp):
ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATG
AACCATTATACATTTCATTTATGGC
Found at i:73994 original size:95 final size:94
Alignment explanation
Indices: 73831--74013 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 94
73821 ACTACCATGA
* *
73831 TATCGATACTTCTATACTATGGTACCGATACCCTCTCTCAGTATCGATACCATTTATACATTCTG
1 TATCGATACTTCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTATACATTCTG
*
73896 TAATGCATGGCATCGATACCTTTCTCTCAG
66 TAATCCATGGCATCGATA-CTTTCTCTCAG
** *
73926 TATCGATACTAT-TATACTATAGTATTGATACCCCCTTTCAGTATCGATACCATTT-TGACATTC
1 TATCGATACT-TCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTAT-ACATTC
*
73989 TGTAATCCATGGTATCGATACTTTC
64 TGTAATCCATGGCATCGATACTTTC
74014 CCTTTTAGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
94 6 0.08
95 72 0.91
96 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (94 bp):
TATCGATACTTCTATACTATAGTACCGATACCCCCTCTCAGTATCGATACCATTTATACATTCTG
TAATCCATGGCATCGATACTTTCTCTCAG
Found at i:76605 original size:18 final size:18
Alignment explanation
Indices: 76582--76616 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76572 CTACCGGTTC
*
76582 ACTGGTTCAACCGGTCGA
1 ACTGGTCCAACCGGTCGA
*
76600 ACTGGTCCGACCGGTCG
1 ACTGGTCCAACCGGTCG
76617 GAAGAACCGG
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:0.31, G:0.31, T:0.20
Consensus pattern (18 bp):
ACTGGTCCAACCGGTCGA
Found at i:78607 original size:39 final size:39
Alignment explanation
Indices: 78498--78616 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
78488 TTAAATGTTT
* *
78498 ATTTATAATTT-TCAAATTATTTCAC-TCTAATATTCTAA
1 ATTTATAATTTCTTAAATTATTTCACAT-TAACATTCTAA
** *
78536 ATTCCTAATTTCTTAAATT-TTACTACCA-TAACATTCTAA
1 ATTTATAATTTCTTAAATTATTTC-A-CATTAACATTCTAA
* *
78575 ATTTTTAATTTCTTAAATTATTTCACATTAACATCCTAA
1 ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
78614 ATT
1 ATT
78617 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 14 0.21
39 48 0.73
40 4 0.06
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (39 bp):
ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
Found at i:84303 original size:21 final size:21
Alignment explanation
Indices: 84252--84304 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
84242 ATTATGACTA
84252 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
84273 TCGCGTTGCGATTTTTCCAA-T
1 TCGCAATGCGA-TTTTCCAATT
84294 TCGCAATGCGA
1 TCGCAATGCGA
84305 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:84337 original size:21 final size:21
Alignment explanation
Indices: 84294--84358 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
84284 TTTTTCCAAT
** *
84294 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
84314 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
84335 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
84356 TCG
1 TCG
84359 TAACGCAACG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 12 0.29
21 29 0.71
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:84405 original size:21 final size:19
Alignment explanation
Indices: 84362--84413 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
84352 AAAATCGTAA
* *
84362 CGCAACGCGATACTACTAT
1 CGCAACGCGATAATACAAT
84381 CGCAACGCGATAATACAAAAT
1 CGCAACGCGATAATAC--AAT
84402 CGCAACGCGATA
1 CGCAACGCGATA
84414 CTTACTTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.15
Consensus pattern (19 bp):
CGCAACGCGATAATACAAT
Found at i:84426 original size:20 final size:20
Alignment explanation
Indices: 84362--84468 Score: 110
Period size: 20 Copynumber: 5.3 Consensus size: 20
84352 AAAATCGTAA
*
84362 CGCAACGCGATAC-TACTAT
1 CGCAACGCGATACTTACTTT
* **
84381 CGCAACGCGATA-ATACAAAAT
1 CGCAACGCGATACTTAC--TTT
84402 CGCAACGCGATACTTACTTT
1 CGCAACGCGATACTTACTTT
* *
84422 CGCAACGTGATACTTAATTT
1 CGCAACGCGATACTTACTTT
* *
84442 CGCAACGCGATACTGAATTT
1 CGCAACGCGATACTTACTTT
84462 CGCAACG
1 CGCAACG
84469 AAATATATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
19 15 0.20
20 44 0.58
21 14 0.18
22 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
CGCAACGCGATACTTACTTT
Found at i:84445 original size:40 final size:41
Alignment explanation
Indices: 84362--84468 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 41
84352 AAAATCGTAA
*
84362 CGCAACGCGATAC-TACTATCGCAACGCGATAATACAAAAT
1 CGCAACGCGATACTTACTTTCGCAACGCGATAATACAAAAT
* * * **
84402 CGCAACGCGATACTTACTTTCGCAACGTGATACT-TAATTT
1 CGCAACGCGATACTTACTTTCGCAACGCGATAATACAAAAT
* *
84442 CGCAACGCGATACTGAATTTCGCAACG
1 CGCAACGCGATACTTACTTTCGCAACG
84469 AAATATATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 41 0.71
41 17 0.29
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (41 bp):
CGCAACGCGATACTTACTTTCGCAACGCGATAATACAAAAT
Found at i:84683 original size:22 final size:22
Alignment explanation
Indices: 84655--84698 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
84645 CACTCTCTCA
84655 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
84677 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
84699 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:84985 original size:20 final size:20
Alignment explanation
Indices: 84960--85008 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
84950 TTTATTCTCT
84960 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * **
84980 CGTTGCAATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
85000 TGTTGCGAT
1 CGTTGCGAT
85009 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:85014 original size:20 final size:20
Alignment explanation
Indices: 84976--85018 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
84966 GATAGTCAAA
84976 TTCGCGTTGCAATTGTCATT
1 TTCGCGTTGCAATTGTCATT
* * *
84996 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCAATTGTCATT
85016 TTC
1 TTC
85019 AGAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCAATTGTCATT
Found at i:86351 original size:18 final size:18
Alignment explanation
Indices: 86330--86377 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
86320 TCCACTTCGG
86330 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
86348 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
86366 GAGCCATCACCT
1 GAGCCATCACCT
86378 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:86945 original size:20 final size:19
Alignment explanation
Indices: 86922--86964 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
86912 CGCAACACGA
86922 AAATGACTATCGCAATGTGG
1 AAATGACTATCGCAATGT-G
*
86942 AAATGGCTATCGCAATGTG
1 AAATGACTATCGCAATGTG
86961 AAAT
1 AAAT
86965 AAAAATCGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (19 bp):
AAATGACTATCGCAATGTG
Found at i:86972 original size:19 final size:19
Alignment explanation
Indices: 86950--87032 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
86940 GGAAATGGCT
* *
86950 ATCGCAATGTGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
86969 ATCGCAA--CGACA--A-A
1 ATCGCAATGCGAAATGAAA
86983 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
87002 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87021 ATCGCAATGCGA
1 ATCGCAATGCGA
87033 TTTGTGTTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
14 8 0.15
15 1 0.02
16 4 0.07
17 3 0.06
18 1 0.02
19 37 0.69
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:87104 original size:20 final size:20
Alignment explanation
Indices: 87070--87124 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
87060 TTGCGATTTT
*
87070 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
87089 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
87109 CATTTCCGTGTTGCGA
1 CATTTCCGCGTTGCGA
87125 AAGTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:87524 original size:21 final size:20
Alignment explanation
Indices: 87498--87565 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
87488 CTGTCATCTC
87498 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
87519 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
87540 TCAAGAGTCCCC-CCACCGT
1 TCAAGAGTCCCCTCCATCGT
87559 TCAAGAG
1 TCAAGAG
87566 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:87577 original size:40 final size:42
Alignment explanation
Indices: 87488--87577 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 42
87478 CCTGACTCAC
* * *
87488 CTGTCATCTCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
87530 CTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
87570 CTGTCATC
1 CTGTCATC
87578 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 21 0.49
41 2 0.05
42 20 0.47
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:89010 original size:14 final size:14
Alignment explanation
Indices: 88976--89014 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
88966 TTGATTGTTT
88976 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
88990 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
89004 TGTTGATTTGT
1 AATTGATTTGT
89015 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:89237 original size:18 final size:20
Alignment explanation
Indices: 89198--89240 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
89188 GCGATTTTTC
89198 GCGATAGCCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
*
89218 GCGATAGTCA-TTTC-CGTT
1 GCGATAGCCATTTTCGCGTT
89236 GCGAT
1 GCGAT
89241 TGTTGCGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (20 bp):
GCGATAGCCATTTTCGCGTT
Found at i:89550 original size:21 final size:21
Alignment explanation
Indices: 89524--89578 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
89514 ATAGTCAGTA
* *
89524 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTTACAAAT
**
89545 TCGCATTGC-AATTTACTTAT
1 TCGCATTGCGAATTTACAAAT
89565 TCGCATTGCGAATT
1 TCGCATTGCGAATT
89579 GGGAAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGAATTTACAAAT
Found at i:89611 original size:20 final size:20
Alignment explanation
Indices: 89586--89693 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
89576 ATTGGGAAAA
89586 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTTACTT
*
89606 TCGCAACACGATACTTACTT
1 TCGCAACGCGATACTTACTT
89626 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTTACTT
* * *
89646 TCGCAACGTGATTCTGACTT
1 TCGCAACGCGATACTTACTT
* *
89666 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTTACTT
89686 TCGCAACG
1 TCGCAACG
89694 AGATTCTGAC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGATACTTACTT
Found at i:90465 original size:24 final size:24
Alignment explanation
Indices: 90438--90491 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
90428 GTATTCGAAA
*
90438 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
90462 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
90486 TTTGAT
1 TTTGAT
90492 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:90673 original size:3 final size:3
Alignment explanation
Indices: 90665--90706 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
90655 ATATAATCCT
* * *
90665 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
90707 AAAGTCTCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:90682 original size:12 final size:12
Alignment explanation
Indices: 90665--90706 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
90655 ATATAATCCT
90665 GAAGAAGAAAAA
1 GAAGAAGAAAAA
90677 GAAGAAGAAAAA
1 GAAGAAGAAAAA
90689 GAAGAAGAAAAA
1 GAAGAAGAAAAA
90701 GAAGAA
1 GAAGAA
90707 AAAGTCTCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:92998 original size:16 final size:16
Alignment explanation
Indices: 92977--93008 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
92967 ATCTTAATGT
92977 CTATCGCAACGCGAAA
1 CTATCGCAACGCGAAA
*
92993 CTATCGCAATGCGAAA
1 CTATCGCAACGCGAAA
93009 TGAAAGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (16 bp):
CTATCGCAACGCGAAA
Found at i:93049 original size:19 final size:19
Alignment explanation
Indices: 93025--93084 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
93015 CGAACGAGAG
93025 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
93044 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
93058 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
93077 AATCGCAA
1 AATCGCAA
93085 CGAGGGAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:93059 original size:33 final size:33
Alignment explanation
Indices: 92995--93119 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
92985 ACGCGAAACT
*
92995 ATCGCAATGCGAAATG-AAAGCG-AACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
93026 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
93059 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
93092 ATCGCAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
93120 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 16 0.19
32 5 0.06
33 65 0.76
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:93146 original size:18 final size:17
Alignment explanation
Indices: 93123--93209 Score: 94
Period size: 18 Copynumber: 5.2 Consensus size: 17
93113 CACAACGCGA
93123 ATTTAGTTTCGCGTTGCG
1 ATTTA-TTTCGCGTTGCG
93141 ATTTAGTTTCGCGTTGCG
1 ATTTA-TTTCGCGTTGCG
*
93159 A-TT-TTT--CATTGCG
1 ATTTATTTCGCGTTGCG
93172 ATTTTATTTCGCGTTGCG
1 A-TTTATTTCGCGTTGCG
93190 ATTTCATTTCGC-TTGCG
1 ATTT-ATTTCGCGTTGCG
93207 ATT
1 ATT
93210 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
13 7 0.11
15 5 0.08
16 3 0.05
17 13 0.21
18 33 0.54
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (17 bp):
ATTTATTTCGCGTTGCG
Found at i:93201 original size:49 final size:49
Alignment explanation
Indices: 93119--93241 Score: 160
Period size: 49 Copynumber: 2.5 Consensus size: 49
93109 AAATCACAAC
* *
93119 GCGAATTTAGTTTCGCGTTGCGATTTAGTTTCGCGTTGCGATT-TTTCATT
1 GCGATTTTA-TTTCGCGTTGCGATTTAGTTTCGC-TTGCGATTCTCTCATT
*
93169 GCGATTTTATTTCGCGTTGCGATTTCA-TTTCGCTTGCGATTCTCTCGTT
1 GCGATTTTATTTCGCGTTGCGATTT-AGTTTCGCTTGCGATTCTCTCATT
*
93218 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTT-ATTTCGCGTTGCGAT
93242 AGTCATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
48 8 0.12
49 35 0.53
50 23 0.35
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (49 bp):
GCGATTTTATTTCGCGTTGCGATTTAGTTTCGCTTGCGATTCTCTCATT
Found at i:93249 original size:19 final size:17
Alignment explanation
Indices: 93129--93241 Score: 89
Period size: 18 Copynumber: 6.8 Consensus size: 17
93119 GCGAATTTAG
93129 TTTCGCGTTGCGATTT-A
1 TTTCGC-TTGCGATTTCA
93146 GTTTCGCGTTGCGA-TT--
1 -TTTCGC-TTGCGATTTCA
* *
93162 TTTC-ATTGCGATTTTA
1 TTTCGCTTGCGATTTCA
93178 TTTCGCGTTGCGATTTCA
1 TTTCGC-TTGCGATTTCA
93196 TTTCGCTTGCGA-TTC-
1 TTTCGCTTGCGATTTCA
*
93211 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
93228 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
93242 AGTCATTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
13 6 0.08
14 8 0.10
15 8 0.10
16 10 0.12
17 12 0.15
18 30 0.38
19 6 0.08
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:93364 original size:13 final size:14
Alignment explanation
Indices: 93348--93383 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
93338 CATCAATTAA
93348 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
93361 ACAAATCACCTTTT
1 ACAAATCAACTTTT
93375 ACAAATCAA
1 ACAAATCAA
93384 TTAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:94761 original size:21 final size:21
Alignment explanation
Indices: 94695--94761 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
94685 ATGTGAATCG
*
94695 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
94715 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
94737 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
94758 CTCT
1 CTCT
94762 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:95144 original size:89 final size:84
Alignment explanation
Indices: 95028--95202 Score: 230
Period size: 84 Copynumber: 2.0 Consensus size: 84
95018 TATTTCAACT
* *
95028 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACTAGTTTAGCA
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAAC-TCACAGTGTT----AATA-AAGTTTAGCA
95093 -ATTGGCAGCAACCGAATAAATTTAC
60 GATTGGCAGCAA-CGAATAAATTTAC
95118 TTCAACCAAAA-A-AAATAAAAAGACAAATACTAACTCACAGTGTTAATAAAGTTTAGCAGTATT
1 TTCAACCAAAAGACAAA-AAAAAGACAAATACTAACTCACAGTGTTAATAAAGTTTAGCAG-ATT
95181 GGCAGCAACGAATAAATTTAC
64 GGCAGCAACGAATAAATTTAC
95202 T
1 T
95203 AAGCAATCTA
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
83 9 0.11
84 18 0.22
85 11 0.14
88 13 0.16
89 18 0.22
90 11 0.14
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (84 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTCACAGTGTTAATAAAGTTTAGCAGATTGG
CAGCAACGAATAAATTTAC
Found at i:95631 original size:20 final size:18
Alignment explanation
Indices: 95591--95631 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
95581 CGGGTCGATC
*
95591 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGAGTG
95609 AGGTGATGGCTCTCGAAGTG
1 AGGTGATGGCTCT-G-AGTG
95629 AGG
1 AGG
95632 AAGTGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 1 0.05
20 6 0.30
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.24
Consensus pattern (18 bp):
AGGTGATGGCTCTGAGTG
Done.