Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004668.1 Hibiscus syriacus cultivar Beakdansim tig00010470_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: 81290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6703 original size:30 final size:29
Alignment explanation
Indices: 6669--6731 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
6659 GTCAAGTCTT
*
6669 ACGTGTCCAAA-TATTGATGTTGATATTGTC
1 ACGTGTCCAAAGTA-TGATG-TAATATTGTC
**
6699 ACGTGTGTAAAGTATGATGTAATATTGTC
1 ACGTGTCCAAAGTATGATGTAATATTGTC
6728 ACGT
1 ACGT
6732 CATCATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 13 0.45
30 14 0.48
31 2 0.07
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (29 bp):
ACGTGTCCAAAGTATGATGTAATATTGTC
Found at i:12118 original size:59 final size:61
Alignment explanation
Indices: 12053--12214 Score: 154
Period size: 59 Copynumber: 2.7 Consensus size: 61
12043 AAATGTGTCT
*
12053 AAAAGTTTGGGGATCAATTTATAACGAAGATCATAGTTTGAG-GAAGAAAATG-AATATTC
1 AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGAGAAGAAAATGAAATATTC
** * * * * *
12112 AAAAGTTTGAAGATTAATTTAGAATGATAG-TCATAGTTT-AGAGATGAAATTGAAATATTT
1 AAAAGTTTGGGGATCAATTTATAATGA-AGATCATAGTTTGAGAGAAGAAAATGAAATATTC
* * * * *
12172 AAAACTTTAGGGA-CTAATTTATAATAAAAATCATAATTTGAGA
1 AAAAGTTTGGGGATC-AATTTATAATGAAGATCATAGTTTGAGA
12215 ATATATGATA
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
58 2 0.03
59 40 0.50
60 35 0.44
61 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (61 bp):
AAAAGTTTGGGGATCAATTTATAATGAAGATCATAGTTTGAGAGAAGAAAATGAAATATTC
Found at i:17329 original size:34 final size:34
Alignment explanation
Indices: 17281--17367 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 34
17271 AGGTGCAAAA
*
17281 TTGGCCACCTACCAAAGATGAATTTTCCAATAAG
1 TTGGCCACCAACCAAAGATGAATTTTCCAATAAG
* * *
17315 TTGGCCACAAACC-AAGATTATTTTTCCAATAAG
1 TTGGCCACCAACCAAAGATGAATTTTCCAATAAG
17348 TTGGCCACCAACCAAAGATG
1 TTGGCCACCAACCAAAGATG
17368 TCAACTTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 30 0.65
34 16 0.35
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (34 bp):
TTGGCCACCAACCAAAGATGAATTTTCCAATAAG
Found at i:19666 original size:37 final size:37
Alignment explanation
Indices: 19611--19715 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
19601 CCTTTTTGTC
*
19611 CTACCAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
19648 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
19685 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
19716 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:20129 original size:2 final size:2
Alignment explanation
Indices: 20124--20166 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20114 TTAGTGTTAT
20124 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
20166 T
1 T
20167 TTCCTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24624 original size:14 final size:14
Alignment explanation
Indices: 24605--24637 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
24595 AAATAAGAAG
*
24605 AATTCATCTGAAAT
1 AATTCATCCGAAAT
24619 AATTCATCCGAAAT
1 AATTCATCCGAAAT
24633 AATTC
1 AATTC
24638 TATCATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (14 bp):
AATTCATCCGAAAT
Found at i:24961 original size:8 final size:8
Alignment explanation
Indices: 24948--25014 Score: 80
Period size: 8 Copynumber: 7.8 Consensus size: 8
24938 AGATCCAATC
24948 AAGAAAAA
1 AAGAAAAA
*
24956 AAGAAAAT
1 AAGAAAAA
24964 AAGCAAAAA
1 AAG-AAAAA
24973 AAGAAAAAAA
1 AAG--AAAAA
24983 AAGAAAAA
1 AAGAAAAA
24991 AGAGAAACAA
1 A-AGAAA-AA
25001 AAGAAAAA
1 AAGAAAAA
25009 AAGAAA
1 AAGAAA
25015 GAACAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
8 24 0.46
9 17 0.33
10 11 0.21
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.01
Consensus pattern (8 bp):
AAGAAAAA
Found at i:24973 original size:17 final size:16
Alignment explanation
Indices: 24948--25014 Score: 80
Period size: 18 Copynumber: 3.9 Consensus size: 16
24938 AGATCCAATC
*
24948 AAGAAAAAAAGAAAAT
1 AAGAAAAAAAGAAAAA
24964 AAGCAAAAAAAGAAAAAAA
1 AAG-AAAAAAAG--AAAAA
24983 AAGAAAAAAGAGAAACAA
1 AAGAAAAAA-AGAAA-AA
25001 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
25015 GAACAAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
16 3 0.07
17 16 0.36
18 17 0.38
19 9 0.20
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.01
Consensus pattern (16 bp):
AAGAAAAAAAGAAAAA
Found at i:25030 original size:28 final size:27
Alignment explanation
Indices: 24948--25036 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 27
24938 AGATCCAATC
*
24948 AAGAAAAAAAGAAAATAAGCAAAAA-AAG
1 AAGAAAAAAAGAAAA-AA-CAAAAACAAA
* *
24976 AA-AAAAAAAGAAAAAAGAGAAAC-AA
1 AAGAAAAAAAGAAAAAACAAAAACAAA
*
25001 AAGAAAAAAAGAAAGAACAAAAATCAAA
1 AAGAAAAAAAGAAAAAACAAAAA-CAAA
25029 AAGAAAAA
1 AAGAAAAA
25037 GGGACAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 7 0.14
26 19 0.37
27 13 0.25
28 12 0.24
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (27 bp):
AAGAAAAAAAGAAAAAACAAAAACAAA
Found at i:25674 original size:22 final size:22
Alignment explanation
Indices: 25642--25696 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
25632 GCTACCCCAT
*
25642 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
25664 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
25686 CAAACCTTTGA
1 CAAACCTTTGA
25697 CCAAACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:26732 original size:106 final size:106
Alignment explanation
Indices: 26521--27364 Score: 1181
Period size: 106 Copynumber: 8.0 Consensus size: 106
26511 ATATCGTGCC
* * * * * *
26521 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
26585 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
26626 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
26691 AATTTCAGATCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
26732 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
26796 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
26838 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
26903 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
26944 ACTCCAGACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTG-CAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
27008 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
27049 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * * *
27114 AATTTCAGAGCCAATTTCAATTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
27155 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAA-CAA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* * *
27215 C-A-TTCAGAGTCAATTTCAACTTCACAGTGAAGAATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
27255 ACTCGAGAGAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** *
27320 GGTTCCAGAGCCAATTTCAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
27361 ACTC
1 ACTC
27365 AGAACAATGC
Statistics
Matches: 658, Mismatches: 67, Indels: 27
0.88 0.09 0.04
Matches are distributed among these distances:
100 73 0.11
101 4 0.01
102 6 0.01
104 5 0.01
105 151 0.23
106 416 0.63
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:27101 original size:317 final size:314
Alignment explanation
Indices: 26521--27365 Score: 1252
Period size: 317 Copynumber: 2.7 Consensus size: 314
26511 ATATCGTGCC
* *
26521 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTTCCA
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAA-AA-TTT-CA
*
26586 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
63 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
26651 CACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGATCCAATTTCAACTTCA
128 CACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
26716 CAGTGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGT
193 CAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGT
* *
26781 CAATAAACAACTTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
258 CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* *
26838 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAAC-AA-AA-TT-TC
* * *
26903 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTTAACT
62 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
26968 TCACGACGAAGGGACCGCTGGTTG-CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
127 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
27032 ACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTG
192 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTG
* * *
27097 TCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAATTTCTCAGCGAAGGATCTTGA
257 TCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* * * *
27155 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAACAAAATTTC-A-
1 ACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAAATTTCAAT
* * * * *
27217 TTCAGAGTCAATTTCAACTTCACAGTGAAGAATATTGGACTCGAGAGAACGCAAGTTCAACTTCA
65 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* ** *
27282 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-
130 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
27346 GAC-AGAGGATATTGGACTCA
195 G-CGA-AGGATATTGGACTCA
27366 GAACAATGCT
Statistics
Matches: 480, Mismatches: 42, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
311 80 0.17
312 54 0.11
313 2 0.00
314 2 0.00
315 2 0.00
316 4 0.01
317 244 0.51
318 91 0.19
319 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (314 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAAATTTCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
CGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAA
TAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
Found at i:28090 original size:37 final size:37
Alignment explanation
Indices: 28037--28141 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
28027 CCTTTTTGTC
28037 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
28074 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
28111 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
28142 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:28681 original size:35 final size:34
Alignment explanation
Indices: 28603--28681 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
28593 TTACTTTTGA
* *
28603 TTTTTTTTTTTATTATTTACTTATATATATATGC
1 TTTTTCTTTTTATTATTTACTCATATATATATGC
* * *
28637 TTTTACTTTTTATATATTTACTCATTTATTTAT-C
1 TTTTTCTTTTTAT-TATTTACTCATATATATATGC
28671 TATTTTCTTTT
1 T-TTTTCTTTT
28682 ATCTTTATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
34 13 0.35
35 24 0.65
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (34 bp):
TTTTTCTTTTTATTATTTACTCATATATATATGC
Found at i:31721 original size:33 final size:34
Alignment explanation
Indices: 31662--31751 Score: 130
Period size: 33 Copynumber: 2.7 Consensus size: 34
31652 GCCATGTGCA
* *
31662 AAGTT-GTCCACCTACCAAAGATGAATTTTCTAAT
1 AAGTTGGT-CACCAACCAAAGATGAATTTTCCAAT
31696 AAGTTGGTCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGTCACCAACCAAAGATGAATTTTCCAAT
*
31729 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGTCACCAACCAAAGATG
31752 TCAACTTTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 31 0.61
34 18 0.35
35 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (34 bp):
AAGTTGGTCACCAACCAAAGATGAATTTTCCAAT
Found at i:37362 original size:18 final size:18
Alignment explanation
Indices: 37327--37370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
37317 AAGAGATATG
**
37327 AATGATAACAATGTTAAT
1 AATGATAACAATAATAAT
*
37345 AATGATAAGAATAATAAT
1 AATGATAACAATAATAAT
*
37363 AAGGATAA
1 AATGATAA
37371 TGATGTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (18 bp):
AATGATAACAATAATAAT
Found at i:41781 original size:40 final size:42
Alignment explanation
Indices: 41732--41821 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 42
41722 GAGTTTTTTC
* *
41732 AAAAAATATATAACATATAG-TTTTTAGAAAA-CGGTTATTG
1 AAAAAATATATAACATATAGTTTTTTAAAAAATCAGTTATTG
* * *
41772 --AAAACATATAATATATAGTTTTTTAAAAAATCAGTTTTTG
1 AAAAAATATATAACATATAGTTTTTTAAAAAATCAGTTATTG
*
41812 AAAATATATA
1 AAAAAATATA
41822 ATATGGTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
38 16 0.41
39 10 0.26
40 7 0.18
42 6 0.15
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (42 bp):
AAAAAATATATAACATATAGTTTTTTAAAAAATCAGTTATTG
Found at i:41824 original size:40 final size:38
Alignment explanation
Indices: 41734--41825 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 38
41724 GTTTTTTCAA
* * *
41734 AAAATATATAACATATAGTTTTTAGAAAACGGTTATTG
1 AAAATATATAATATATAGTTTTTAAAAAACAGTTATTG
* *
41772 AAAACATATAATATATAGTTTTTTAAAAAATCAGTTTTTG
1 AAAATATATAATATATAG-TTTTTAAAAAA-CAGTTATTG
41812 AAAATATATAATAT
1 AAAATATATAATAT
41826 GGTTTTGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 16 0.35
39 10 0.22
40 20 0.43
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (38 bp):
AAAATATATAATATATAGTTTTTAAAAAACAGTTATTG
Found at i:41889 original size:2 final size:2
Alignment explanation
Indices: 41882--41918 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41872 ACAATTTTTA
41882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41919 GTTTTGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42046 original size:14 final size:15
Alignment explanation
Indices: 42007--42056 Score: 66
Period size: 14 Copynumber: 3.2 Consensus size: 15
41997 TAGTTTTTAA
42007 ATATTTTGAAAACATAT
1 ATATTTTGAAAAC--AT
42024 ATATATTTGAAAACAT
1 ATAT-TTTGAAAACAT
42040 AT-TTTTGAAAACAT
1 ATATTTTGAAAACAT
42054 ATA
1 ATA
42057 ATATATAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 13 0.42
15 1 0.03
16 4 0.13
17 4 0.13
18 9 0.29
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (15 bp):
ATATTTTGAAAACAT
Found at i:42102 original size:17 final size:17
Alignment explanation
Indices: 42056--42102 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
42046 GAAAACATAT
42056 AATATATAGTTTTTTAA
1 AATATATAGTTTTTTAA
* *
42073 AAAATGAT-TTTTTTTAA
1 AATAT-ATAGTTTTTTAA
42090 AATATATAGTTTT
1 AATATATAGTTTT
42103 GGAAATGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AATATATAGTTTTTTAA
Found at i:43668 original size:30 final size:30
Alignment explanation
Indices: 43634--43886 Score: 452
Period size: 30 Copynumber: 8.4 Consensus size: 30
43624 TCCGAAGGAC
*
43634 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
43664 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
43694 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
43724 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
43754 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
43784 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
43814 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
43844 CTATCCACAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
43874 CTGTCCAGAGGTC
1 CTATCCAGAGGTC
43887 CCGAAGAACC
Statistics
Matches: 213, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 213 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:44095 original size:4 final size:4
Alignment explanation
Indices: 44086--45677 Score: 3121
Period size: 4 Copynumber: 400.2 Consensus size: 4
44076 ATATAACCAT
44086 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44134 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44182 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44230 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44278 TACA TACA TACA TACA TACA TACA TACA TACA T-CA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44325 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44373 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44421 TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44468 TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44515 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44563 TACA TACA TA-A TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44610 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44658 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44706 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44754 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44800 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44848 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44896 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44944 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
44992 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45040 TACA TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45087 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45135 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45183 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45231 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45278 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45326 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45374 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45422 TACA TACA TACA -ACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45469 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45517 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45565 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45613 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
45661 TACA TACA TACA TACA T
1 TACA TACA TACA TACA T
45678 GTCATCATTT
Statistics
Matches: 1579, Mismatches: 0, Indels: 18
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
3 21 0.01
4 1556 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:46558 original size:24 final size:20
Alignment explanation
Indices: 46505--46581 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
46495 TTTCTCTTGA
46505 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
*
46525 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC---AAC
* *
46548 ATGTGCATCGATGCAGT-ACC
1 A-GTGCATCGATGCATTCAAC
*
46568 TGTGCATCGATGCA
1 AGTGCATCGATGCA
46582 CAAATCACCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.27
20 19 0.39
23 3 0.06
24 14 0.29
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:46664 original size:64 final size:62
Alignment explanation
Indices: 46550--46710 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 62
46540 TCTTTAGCAT
* * * * *
46550 GTGCATCGATGCAGTACCTGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTGTGCATCGATGCACAAATCACATTCGATGTTTCCAATTTAAGAG
* * *** * *
46613 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTCGTTGTTTCCAATTTAATAG
1 G-TGCATCGATGCACTCC-TGTGCATCGATGCACAAATCACATTCGATGTTTCCAATTTAAGAG
*
46677 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTGTGCATCGATGCACA
46711 TTGAACAATT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 29 0.36
64 51 0.64
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTGTGCATCGATGCACAAATCACATTCGATGTTTCCAATTTAAGAG
Found at i:52415 original size:16 final size:16
Alignment explanation
Indices: 52394--52427 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
52384 AAGACTCCCA
52394 TAATAAACTACAC-ATT
1 TAATAAA-TACACTATT
52410 TAATAAATACACTATT
1 TAATAAATACACTATT
52426 TA
1 TA
52428 TTTTAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAAATACACTATT
Found at i:53663 original size:30 final size:30
Alignment explanation
Indices: 53628--53692 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
53618 TTTTAATTTT
*
53628 TTTTATTTTCATCTCAACTTATTAAATATA
1 TTTTATTTTCATCTCAACCTATTAAATATA
** *
53658 TTTTATTTTTGTCTTAACCTATTAAATATA
1 TTTTATTTTCATCTCAACCTATTAAATATA
53688 TTTTA
1 TTTTA
53693 CTGTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTATTTTCATCTCAACCTATTAAATATA
Found at i:53721 original size:31 final size:29
Alignment explanation
Indices: 53683--53786 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 29
53673 AACCTATTAA
53683 ATATATTTTACTGTTATTTTAATGTAAAAAT
1 ATATATTTTACT-TTATTTTAAT-TAAAAAT
* *
53714 ATATATTTTATCTTTATCTTCACTTAAAAAT
1 ATATATTTTA-CTTTAT-TTTAATTAAAAAT
* *
53745 ATAT-TTTTATTTGTATCTTAATTTTTAAAAAT
1 ATATATTTTACTT-TATTTTAA---TTAAAAAT
53777 ATATATTTTA
1 ATATATTTTA
53787 AAAATATATT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
29 4 0.07
30 8 0.13
31 25 0.42
32 18 0.30
33 5 0.08
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (29 bp):
ATATATTTTACTTTATTTTAATTAAAAAT
Found at i:53753 original size:61 final size:62
Alignment explanation
Indices: 53653--53786 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 62
53643 AACTTATTAA
* * * *
53653 ATATATTTTATTTTTGTCTTAACCTATTAAATATATTTTACTGT-TATTTTAA-TGTAAAAAT
1 ATATATTTTATCTTTATCTTAACCTATAAAATATATTTTA-TGTGTATCTTAATTGTAAAAAT
* * * *
53714 ATATATTTTATCTTTATCTTCACTTA-AAAATATATTTTTATTTGTATCTTAATTTTTAAAAAT
1 ATATATTTTATCTTTATCTTAACCTATAAAATATA-TTTTATGTGTATCTTAA-TTGTAAAAAT
53777 ATATATTTTA
1 ATATATTTTA
53787 AAAATATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
60 9 0.15
61 34 0.56
63 18 0.30
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (62 bp):
ATATATTTTATCTTTATCTTAACCTATAAAATATATTTTATGTGTATCTTAATTGTAAAAAT
Found at i:53762 original size:30 final size:32
Alignment explanation
Indices: 53653--53786 Score: 111
Period size: 30 Copynumber: 4.3 Consensus size: 32
53643 AACTTATTAA
* * * **
53653 ATATATTTTATTTTTGTCTTAA-CCTATTAA-
1 ATATATTTTATCTTTATCTTAATCTTAAAAAT
* *
53683 ATATATTTTA-CTGTTATTTTAAT-GTAAAAAT
1 ATATATTTTATCT-TTATCTTAATCTTAAAAAT
*
53714 ATATATTTTATCTTTATCTTCA-CTTAAAAAT
1 ATATATTTTATCTTTATCTTAATCTTAAAAAT
*
53745 ATAT-TTTTAT-TTGTATCTTAATTTTTAAAAAT
1 ATATATTTTATCTT-TATCTTAA-TCTTAAAAAT
53777 ATATATTTTA
1 ATATATTTTA
53787 AAAATATATT
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
29 3 0.04
30 34 0.40
31 28 0.33
32 14 0.17
33 5 0.06
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (32 bp):
ATATATTTTATCTTTATCTTAATCTTAAAAAT
Found at i:53796 original size:13 final size:15
Alignment explanation
Indices: 53767--53795 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53757 GTATCTTAAT
53767 TTTTAAAAATATATA
1 TTTTAAAAATATATA
53782 TTTTAAAAATATAT
1 TTTTAAAAATATAT
53796 TAACTTAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAAAATATATA
Found at i:57153 original size:16 final size:16
Alignment explanation
Indices: 57122--57152 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
57112 ATTCACCGGT
57122 TCAATTACTAAAAAAA
1 TCAATTACTAAAAAAA
57138 TCAATTA-TAAAAAAA
1 TCAATTACTAAAAAAA
57153 AGTACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
TCAATTACTAAAAAAA
Found at i:61579 original size:3 final size:3
Alignment explanation
Indices: 61562--61611 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
61552 TGAGTTTACA
61562 TAT TGAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61607 TAT TA
1 TAT TA
61612 CTACTACTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:67375 original size:12 final size:12
Alignment explanation
Indices: 67338--67400 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
67328 ATCTGATACT
67338 TGACATGGATTC
1 TGACATGGATTC
*
67350 TGATAT-GATATC
1 TGACATGGAT-TC
67362 TGACATGGATTC
1 TGACATGGATTC
* *
67374 TGATAT-GATAC
1 TGACATGGATTC
*
67385 TTGACTTGGATTC
1 -TGACATGGATTC
67398 TGA
1 TGA
67401 TCTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:67454 original size:24 final size:24
Alignment explanation
Indices: 67323--67437 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
67313 TCGATTTGAT
*
67323 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
67347 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
67371 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
67395 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
67419 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
67438 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:67659 original size:2 final size:2
Alignment explanation
Indices: 67652--67676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67642 ACGATGGGGG
67652 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
67677 GTTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69562 original size:21 final size:21
Alignment explanation
Indices: 69536--69589 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
69526 AAATGATCAG
69536 TTTGACCGGTTTTGTAACCCA
1 TTTGACCGGTTTTGTAACCCA
*
69557 TTTGACCGGTTTTGTAACCTA
1 TTTGACCGGTTTTGTAACCCA
*
69578 TTTGACAGGTTT
1 TTTGACCGGTTT
69590 GACCGGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (21 bp):
TTTGACCGGTTTTGTAACCCA
Found at i:69650 original size:19 final size:19
Alignment explanation
Indices: 69613--69653 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
69603 CCGACCCGAC
**
69613 CCGTTGACCCGAACGTTGA
1 CCGTTGACCAAAACGTTGA
*
69632 CCGTTGACCAAAACTTTGA
1 CCGTTGACCAAAACGTTGA
69651 CCG
1 CCG
69654 GACATTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (19 bp):
CCGTTGACCAAAACGTTGA
Found at i:72057 original size:12 final size:12
Alignment explanation
Indices: 72020--72058 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
72010 ATCTGATACT
72020 TGACATGGATTC
1 TGACATGGATTC
*
72032 TGATAT-GATATC
1 TGACATGGAT-TC
72044 TGACATGGATTC
1 TGACATGGATTC
72056 TGA
1 TGA
72059 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:72136 original size:24 final size:24
Alignment explanation
Indices: 72005--72119 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
71995 TCGATTTGAT
*
72005 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
72029 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
72053 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
72077 TTCTAATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
72101 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
72120 GTGAATTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:76683 original size:42 final size:41
Alignment explanation
Indices: 76598--76704 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
76588 CCTGAAGGTC
* * * *
76598 TTATGGATGGCTCGAAGGACTTA-TCATCTTTCTCGAAAGAT
1 TTAT-GATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
*
76639 TTATAGATGGCCCGAAGGATTTACCCATCATGCTCGAAAGAT
1 TTAT-GATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
76681 TTAGTGATGGCCCGAAGGACTTAC
1 TTA-TGATGGCCCGAAGGACTTAC
76705 ATGTCAAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 20 0.35
42 36 0.63
43 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
TTATGATGGCCCGAAGGACTTACCCATCATGCTCGAAAGAT
Found at i:76966 original size:42 final size:42
Alignment explanation
Indices: 76886--76985 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
76876 TGGATGACTT
* *
76886 GAAGGACTTA-TCATCTTGCTCGAAAGACTTATAGATGGCCC
1 GAAGGACTTACGCATCATGCTCGAAAGACTTATAGATGGCCC
* *
76927 GAAGGACTTACGCATCATGCTCGAAAGATTTACTA-ATGGCTC
1 GAAGGACTTACGCATCATGCTCGAAAGACTTA-TAGATGGCCC
76969 GAAGGACTTACGCATCA
1 GAAGGACTTACGCATCA
76986 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 10 0.19
42 41 0.77
43 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
GAAGGACTTACGCATCATGCTCGAAAGACTTATAGATGGCCC
Found at i:76979 original size:20 final size:20
Alignment explanation
Indices: 76903--76979 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
76893 TTATCATCTT
76903 GCTCGAAAGACTTA-TAGATG
1 GCTCGAAAGACTTACTA-ATG
* * *
76923 GCCCGAAGGACTTACGCATCAT-
1 GCTCGAAAGACTTA--C-TAATG
*
76945 GCTCGAAAGATTTACTAATG
1 GCTCGAAAGACTTACTAATG
*
76965 GCTCGAAGGACTTAC
1 GCTCGAAAGACTTAC
76980 GCATCAAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
19 3 0.07
20 26 0.60
22 11 0.26
23 2 0.05
24 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (20 bp):
GCTCGAAAGACTTACTAATG
Found at i:77082 original size:275 final size:272
Alignment explanation
Indices: 76577--77409 Score: 1114
Period size: 275 Copynumber: 3.0 Consensus size: 272
76567 GGAAATGTTA
* * * *
76577 AAAACACCCTGCCTGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTTCTCGAAAGATTTA
1 AAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
* * *
76642 TAGATGGCCCGAAGGATTTACCCATCATGCTCGAAAGATTTAGTGATGGCCCGAAGGACTTACAT
66 TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGG-CCGAAGGACTTACAC
* ** *
76707 GTCAAGAAAAACTTGAAAATCAAGCTTAGTTTCTCAGTTGTCAAGGAACCCCTAAAAATTAGGCT
130 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCT-AAAATTAGGCT
* *
76772 TAGATTCCTTTCAAAAACTCTTTGGAGATAATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
194 TAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAA-CCCTAAAAATCAGGCTTAGTTT
*
76837 CTAAAAACTCATTTG
258 CTAAAAAATCATTTG
* * *
76852 AAAACATCCTACCCGAAGGTCTTATGGATGACTTGAAGGACTTATCATCTTGCTCGAAAGACTTA
1 AAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
* * *
76917 TAGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGATTTACTAATGGCTCGAAGGACTTACGC
66 TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGC-CGAAGGACTTACAC
*
76982 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTTAAGCT
130 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAA-TTAGGCT
*
77047 TAGCTTCCTTTTAAAAACTCTTT-GATGATAATCATCAAGAAACCCTGAAAATCAGGCTTAGTTT
194 TAGCTTCCTTTTAAAAACTCTTTGGA-GATAATCATCAAGAAACCCTAAAAATCAGGCTTAGTTT
* *
77111 TTAAAAAATCATTTA
258 CTAAAAAATCATTTG
** * * * * *
77126 AAAACAT-CTGGGTCGAAGTTCTTATGGTTGGCCCGAATGACTTATCATCTTGCTCAAAAGACTT
1 AAAACATCCT-GCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTT
** * * * * *
77190 ATAGATTACCCGAAGGATTTAAGTACCATGCT-GAAAGACTTACTGATGGCCTGAAGGACTTACT
65 ATAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGCC-GAAGGACTTACA
* * *
77254 CATCAAGAAACCCTTGAAAATTAAGCTTGGTTTCTTAGTTGTCATCAAGAAACCCCTAAAATTAG
129 CATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTG---TCAAGGAACCCCTAAAATTAG
* * * * * *
77319 GATTAACTTCTTTTTAAAAACTCTTTGGAGATAATCATCAAGAAATCCCTAAAAATTAGACTTAT
191 GCTTAGCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAA-CCCTAAAAATCAGGCTTAG
77384 TTTCTAAAAAATCATTTG
255 TTTCTAAAAAATCATTTG
77402 AAAACATC
1 AAAACATC
77410 AAGAAACCCC
Statistics
Matches: 491, Mismatches: 56, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
272 1 0.00
273 68 0.14
274 117 0.24
275 249 0.51
276 56 0.11
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (272 bp):
AAAACATCCTGCCCGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTA
TAGATGGCCCGAAGGATTTACGCATCATGCTCGAAAGATTTACTGATGGCCGAAGGACTTACACA
TCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTAAAATTAGGCTTA
GCTTCCTTTTAAAAACTCTTTGGAGATAATCATCAAGAAACCCTAAAAATCAGGCTTAGTTTCTA
AAAAATCATTTG
Found at i:77414 original size:52 final size:54
Alignment explanation
Indices: 77295--77465 Score: 172
Period size: 55 Copynumber: 3.1 Consensus size: 54
77285 TTCTTAGTTG
* * *
77295 TCATCAAGAAACCCCT-AAAATTAGGA-TTAACTTCTTTTTAAAAACTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTA-GACTT-ACTTC-TTCTAAAAAATCATT-GA-A-AA
*
77353 TCATCAAGAAATCCCTAAAAATTAGACTTA-TT-TTCTAAAAAATCATTTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGACTTACTTCTTCTAAAAAATCA-TTGAAAA
* * *
77406 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGACTTA-CTTCTTCTAAAAAATCATTGAAAA
77460 TCATCA
1 TCATCA
77466 TCAATAAACC
Statistics
Matches: 98, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
52 27 0.28
53 2 0.02
54 10 0.10
55 28 0.29
56 2 0.02
57 2 0.02
58 18 0.18
59 9 0.09
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (54 bp):
TCATCAAGAAACCCCTAAAAATTAGACTTACTTCTTCTAAAAAATCATTGAAAA
Found at i:77484 original size:58 final size:56
Alignment explanation
Indices: 77295--77508 Score: 181
Period size: 58 Copynumber: 3.8 Consensus size: 56
77285 TTCTTAGTTG
* * * * *
77295 TCATCAAGAAACCCCT-AAAATTAGGATTAACTTCTTTTTAAAAACTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTTTAAAAATTCATT-GAAAT-A
* * * *
77353 TCATCAAGAAATCCCTAAAAATTAGACTTA--TT-TTCTAAAAAATCATTTGAAA-A
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCA-TTGAAATA
77406 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTG-AAAT-A
* * * * * * *
77463 TCATCAATAAACCCTTGAAAATCAAGCTTAGTTTC-TTTAACAATTC
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTC
77509 TTTTTGAAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
52 27 0.21
53 1 0.01
54 5 0.04
55 27 0.21
56 2 0.02
57 13 0.10
58 43 0.33
59 11 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (56 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGAAATA
Found at i:77498 original size:110 final size:110
Alignment explanation
Indices: 77296--77498 Score: 259
Period size: 110 Copynumber: 1.8 Consensus size: 110
77286 TCTTAGTTGT
* * *
77296 CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTTAAAAACTCTTTGGAGATAATCATCAAG
1 CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTTAAAAACTCATTGAAAATAATCATCAAG
* *
77361 AAATCCCTAAAAATTAGACTTATTTTCTAAAAAATCATTTGAAAA
66 AAATCCCTAAAAATAAGACTTAGTTTCTAAAAAATCATTTGAAAA
* * * *
77406 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC-TTTTAAAAATTCATTGAAAATCATCATCAA
1 CATCAAGAAACCCCT-AAAATTAGGATTAACTTCTTTTTAAAAACTCATTGAAAATAATCATCAA
* *
77470 TAAA-CCCTTGAAAATCAAG-CTTAGTTTCT
65 GAAATCCC-TAAAAAT-AAGACTTAGTTTCT
77499 TTAACAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
109 3 0.04
110 58 0.73
111 18 0.23
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (110 bp):
CATCAAGAAACCCCTAAAATTAGGATTAACTTCTTTTTAAAAACTCATTGAAAATAATCATCAAG
AAATCCCTAAAAATAAGACTTAGTTTCTAAAAAATCATTTGAAAA
Found at i:79452 original size:4 final size:4
Alignment explanation
Indices: 79443--79522 Score: 69
Period size: 4 Copynumber: 20.2 Consensus size: 4
79433 TTTTATTGGT
*
79443 TTTC TTTC TTTC TTT- TTTC TTTC TTTC TTTTC CTT- TTTC -TT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC
* * *
79488 TTTTT TTTC TTTT TTTC TTTC TCTTT TTTC TTTC T
1 -TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC T
79523 CTTTTTTATG
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 9 0.15
4 42 0.69
5 10 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:79462 original size:15 final size:15
Alignment explanation
Indices: 79442--79522 Score: 84
Period size: 13 Copynumber: 5.7 Consensus size: 15
79432 TTTTTATTGG
79442 TTTTCTTTCTTTCTT
1 TTTTCTTTCTTTCTT
79457 TTTTCTTTCTTTC--
1 TTTTCTTTCTTTCTT
*
79470 TTTTCCTT-TTTC-T
1 TTTTCTTTCTTTCTT
*
79483 TTTTCTTTTTTTTCTTT
1 TTTTC-TTTCTTTC-TT
79500 TTTTCTTTC--TCTT
1 TTTTCTTTCTTTCTT
79513 TTTTCTTTCT
1 TTTTCTTTCT
79523 CTTTTTTATG
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
12 4 0.07
13 23 0.40
14 4 0.07
15 17 0.30
16 3 0.05
17 6 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTCTTTCTT
Found at i:79494 original size:35 final size:36
Alignment explanation
Indices: 79442--79529 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 36
79432 TTTTTATTGG
*
79442 TTTTCTTTCTT-TCTTTTTTCTTTCTTTCTTT-TCCT
1 TTTTCTTT-TTCTTTTTTTTCTTTCTTTCTTTCTCCT
* *
79477 TTTTCTTTTTCTTTTTTTTCTTTTTTTCTTTCTCTT
1 TTTTCTTTTTCTTTTTTTTCTTTCTTTCTTTCTCCT
*
79513 TTTTCTTTCTCTTTTTT
1 TTTTCTTTTTCTTTTTT
79530 ATGTATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
34 2 0.04
35 26 0.55
36 19 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTTCTTTTTCTTTTTTTTCTTTCTTTCTTTCTCCT
Found at i:79525 original size:27 final size:27
Alignment explanation
Indices: 79442--79529 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 27
79432 TTTTTATTGG
79442 TTTTCTTTCTTTCTTTTTTCTTTCT-TTCT
1 TTTTCTTTC--TCTTTTTTCTTTCTCTT-T
* * * *
79471 TTTCCTTTTTCTTTTTCTTTTTTTTCTTT
1 TTTTCTTTCTC-TTTT-TTCTTTCTCTTT
79500 TTTTCTTTCTCTTTTTTCTTTCTCTTT
1 TTTTCTTTCTCTTTTTTCTTTCTCTTT
79527 TTT
1 TTT
79530 ATGTATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
27 15 0.31
28 8 0.17
29 23 0.48
30 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTCTTTCTCTTTTTTCTTTCTCTTT
Found at i:79529 original size:15 final size:15
Alignment explanation
Indices: 79442--79529 Score: 80
Period size: 15 Copynumber: 6.1 Consensus size: 15
79432 TTTTTATTGG
79442 TTTTCTTTCT-TTCTT
1 TTTTCTTTCTCTT-TT
*
79457 TTTTCTTTCT-TTCT
1 TTTTCTTTCTCTTTT
* *
79471 TTTCCTTTTTCTTTT
1 TTTTCTTTCTCTTTT
*
79486 TCTTT-TTTTTC-TTT
1 T-TTTCTTTCTCTTTT
79500 TTTTCTTTCTC--TT
1 TTTTCTTTCTCTTTT
79513 TTTTCTTTCTCTTTT
1 TTTTCTTTCTCTTTT
79528 TT
1 TT
79530 ATGTATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
13 16 0.26
14 18 0.29
15 26 0.42
16 2 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTCTCTTTT
Found at i:79539 original size:36 final size:35
Alignment explanation
Indices: 79442--79539 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 35
79432 TTTTTATTGG
*
79442 TTTTCTTTCT-TTCTTTTTTCT-TTCTTTCTTTTCCT
1 TTTTCTTTCTCTT-TTTTATCTATT-TTTCTTTTCCT
* * * *
79477 TTTTCTTTTTCTTTTTTTTCTTTTTTTCTTTCTCTT
1 TTTTCTTTCTCTTTTTTATCTATTTTTCTTT-TCCT
*
79513 TTTTCTTTCTCTTTTTTATGTATTTTT
1 TTTTCTTTCTCTTTTTTATCTATTTTT
79540 TTGCTATATC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 24 0.44
36 30 0.56
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (35 bp):
TTTTCTTTCTCTTTTTTATCTATTTTTCTTTTCCT
Done.