Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002543.1 Hibiscus syriacus cultivar Beakdansim tig00005162_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: 95722
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7397 original size:25 final size:25
Alignment explanation
Indices: 7369--7416 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
7359 CCCTAAATCC
*
7369 TAAACTCT-AATCTTTAAATCATACT
1 TAAACCCTAAATC-TTAAATCATACT
*
7394 TAAACCCTAAATCTTATATCATA
1 TAAACCCTAAATCTTAAATCATA
7417 TATTTAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAACCCTAAATCTTAAATCATACT
Found at i:9670 original size:35 final size:35
Alignment explanation
Indices: 9630--9705 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
9620 AGTAAGATTT
9630 TTCATTCA-ATAAAGCT-AGTTCAGTAATTAAACTAG
1 TTCATTCATATAAA-CTGA-TTCAGTAATTAAACTAG
* *
9665 TTCATTCATTTAAACTGATTCATTAATTAAACTAG
1 TTCATTCATATAAACTGATTCAGTAATTAAACTAG
*
9700 CTCATT
1 TTCATT
9706 TAAGCTTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 31 0.86
36 5 0.14
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (35 bp):
TTCATTCATATAAACTGATTCAGTAATTAAACTAG
Found at i:9677 original size:18 final size:17
Alignment explanation
Indices: 9630--9705 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
9620 AGTAAGATTT
9630 TTCATTCAA-TAAAGCTAG
1 TTCATT-AATTAAA-CTAG
*
9648 TTCAGTAATTAAACTAG
1 TTCATTAATTAAACTAG
*
9665 TTCATTCATTTAAACT-G
1 TTCATT-AATTAAACTAG
9682 ATTCATTAATTAAACTAG
1 -TTCATTAATTAAACTAG
*
9700 CTCATT
1 TTCATT
9706 TAAGCTTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
17 25 0.51
18 24 0.49
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:11846 original size:27 final size:24
Alignment explanation
Indices: 11821--11868 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
11811 ATATAACATT
*
11821 ATATTACTGTGTAATATATATTAC
1 ATATCACTGTGTAATATATATTAC
11845 --ATCACTGTGTAATATATATTAC
1 ATATCACTGTGTAATATATATTAC
11867 AT
1 AT
11869 CAAAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (24 bp):
ATATCACTGTGTAATATATATTAC
Found at i:11851 original size:22 final size:22
Alignment explanation
Indices: 11826--11870 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11816 ACATTATATT
11826 ACTGTGTAATATATATTACATC
1 ACTGTGTAATATATATTACATC
11848 ACTGTGTAATATATATTACATC
1 ACTGTGTAATATATATTACATC
11870 A
1 A
11871 AAGATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
ACTGTGTAATATATATTACATC
Found at i:22310 original size:18 final size:17
Alignment explanation
Indices: 22282--22318 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
22272 AGTGGTTTAG
22282 TTTGTTTGTTGTCTTAT
1 TTTGTTTGTTGTCTTAT
22299 TTTGTATTGTTGTCTTAT
1 TTTGT-TTGTTGTCTTAT
22317 TT
1 TT
22319 CATTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTGTCTTAT
Found at i:28218 original size:21 final size:21
Alignment explanation
Indices: 28191--28268 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
28181 CAAGGGAAGC
*
28191 AGAGAGAGCAGCAGCAAAAGA
1 AGAGAGAGAAGCAGCAAAAGA
* * * * *
28212 AGCGAGAGTAGCAACAGAAGT
1 AGAGAGAGAAGCAGCAAAAGA
* *
28233 AGAGAGAGAAGCAGCTAAAGT
1 AGAGAGAGAAGCAGCAAAAGA
*
28254 ACAGAGAGAAGCAGC
1 AGAGAGAGAAGCAGC
28269 GACAACACAG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.47, C:0.14, G:0.33, T:0.05
Consensus pattern (21 bp):
AGAGAGAGAAGCAGCAAAAGA
Found at i:28261 original size:42 final size:42
Alignment explanation
Indices: 28177--28266 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
28167 AGATGAAAAT
** *
28177 GAAGCAAGGGAAGCAGAGAGAGCAGCAGCAAAAGAAGCGAGA
1 GAAGCAACAGAAGCAGAGAGAGAAGCAGCAAAAGAAGCGAGA
* * * *
28219 GTAGCAACAGAAGTAGAGAGAGAAGCAGCTAAAGTA-CAGAGA
1 GAAGCAACAGAAGCAGAGAGAGAAGCAGCAAAAGAAGC-GAGA
28261 GAAGCA
1 GAAGCA
28267 GCGACAACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.48, C:0.13, G:0.34, T:0.04
Consensus pattern (42 bp):
GAAGCAACAGAAGCAGAGAGAGAAGCAGCAAAAGAAGCGAGA
Found at i:28278 original size:21 final size:21
Alignment explanation
Indices: 28235--28287 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
28225 ACAGAAGTAG
* *
28235 AGAGAGAAGCAGCTAAAGTAC
1 AGAGAGAAGCAGCGAAAGCAC
28256 AGAGAGAAGCAGCGACAA-CAC
1 AGAGAGAAGCAGCGA-AAGCAC
28277 AGAGAGAAGCA
1 AGAGAGAAGCA
28288 ACATATCAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.49, C:0.17, G:0.30, T:0.04
Consensus pattern (21 bp):
AGAGAGAAGCAGCGAAAGCAC
Found at i:28852 original size:43 final size:43
Alignment explanation
Indices: 28795--29045 Score: 213
Period size: 43 Copynumber: 5.9 Consensus size: 43
28785 TGTTTATGGG
* * **
28795 AAAACGTCACTAAATCTCAACACCTATTGCGGCGTTTGTTTAA
1 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
* * * *
28838 AAAGCGTCGCTAAATCTCAACACCTATTGTGACGTTTGT-GAGA
1 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGA-A
* * ** * *
28881 AAAACGCCCCTAAATCTCAAAACCTATTGCGTAGTCTGTGAAA
1 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
* * * *
28924 AAAATGCCGCTAAATCTCAACACCTATTACAGCGTTTGTGGGA
1 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
* * * *
28967 AAAA-GCCGCTAAACCTCAACACCTATTACGACATTTGT--AA
1 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
* ***
29007 GACAAACGCCGCTAAATATCGTTACCTATTGCGGCGTTT
1 -A-AAACGCCGCTAAATCTCAACACCTATTGCGGCGTTT
29046 TTTGTTACCA
Statistics
Matches: 166, Mismatches: 37, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 34 0.20
43 129 0.78
44 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGAA
Found at i:30348 original size:24 final size:23
Alignment explanation
Indices: 30307--30393 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
30297 GAAGTGCCAT
* * *
30307 GTAGATTTGTCCCAAAGGACCGC
1 GTAGAATTGTCCCGAAGGACCAC
* * *
30330 GTAAAATTTGTCTCGAAGGACAAC
1 GTAGAA-TTGTCCCGAAGGACCAC
**
30354 GTAGAATTGTCTTGAAGGACCAC
1 GTAGAATTGTCCCGAAGGACCAC
30377 GTAGAATTGTCCCGAAG
1 GTAGAATTGTCCCGAAG
30394 CACATTAACG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 34 0.65
24 18 0.35
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (23 bp):
GTAGAATTGTCCCGAAGGACCAC
Found at i:32742 original size:18 final size:17
Alignment explanation
Indices: 32710--32743 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
32700 GCTTGGAGGT
*
32710 ACTTTGGGTTATTTTAC
1 ACTTTGGGATATTTTAC
32727 ACTTTAGGGATATTTTA
1 ACTTT-GGGATATTTTA
32744 GTCATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (17 bp):
ACTTTGGGATATTTTAC
Found at i:33686 original size:15 final size:15
Alignment explanation
Indices: 33666--33744 Score: 85
Period size: 15 Copynumber: 5.5 Consensus size: 15
33656 AAGTCAACGG
*
33666 GTTGACTCTGTCTAA
1 GTTGACTCTGTCTGA
**
33681 GTTGACTC-AAC-GA
1 GTTGACTCTGTCTGA
33694 GTTGACTCTGTCTGA
1 GTTGACTCTGTCTGA
**
33709 GTTGACTC-AAC-GA
1 GTTGACTCTGTCTGA
33722 GTTGACTCTGTCTGA
1 GTTGACTCTGTCTGA
33737 GTTGACTC
1 GTTGACTC
33745 AACGAGTTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 19 0.37
14 4 0.08
15 28 0.55
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (15 bp):
GTTGACTCTGTCTGA
Found at i:33698 original size:13 final size:13
Alignment explanation
Indices: 33680--33758 Score: 86
Period size: 13 Copynumber: 5.8 Consensus size: 13
33670 ACTCTGTCTA
33680 AGTTGACTCAACG
1 AGTTGACTCAACG
**
33693 AGTTGACTCTGTCTG
1 AGTTGACTC-AAC-G
33708 AGTTGACTCAACG
1 AGTTGACTCAACG
**
33721 AGTTGACTCTGTCTG
1 AGTTGACTC-AAC-G
33736 AGTTGACTCAACG
1 AGTTGACTCAACG
33749 AGTTGACTCA
1 AGTTGACTCA
33759 GCTTGACTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
13 30 0.56
14 4 0.07
15 20 0.37
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (13 bp):
AGTTGACTCAACG
Found at i:33699 original size:28 final size:28
Alignment explanation
Indices: 33659--33757 Score: 180
Period size: 28 Copynumber: 3.5 Consensus size: 28
33649 TCAGTCAAAG
* *
33659 TCAACGGGTTGACTCTGTCTAAGTTGAC
1 TCAACGAGTTGACTCTGTCTGAGTTGAC
33687 TCAACGAGTTGACTCTGTCTGAGTTGAC
1 TCAACGAGTTGACTCTGTCTGAGTTGAC
33715 TCAACGAGTTGACTCTGTCTGAGTTGAC
1 TCAACGAGTTGACTCTGTCTGAGTTGAC
33743 TCAACGAGTTGACTC
1 TCAACGAGTTGACTC
33758 AGCTTGACTC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (28 bp):
TCAACGAGTTGACTCTGTCTGAGTTGAC
Found at i:38673 original size:3 final size:3
Alignment explanation
Indices: 38667--38714 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
38657 ATTATTTTTT
38667 TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
38712 TAA
1 TAA
38715 ATAAATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39417 original size:113 final size:113
Alignment explanation
Indices: 39075--39895 Score: 831
Period size: 116 Copynumber: 7.2 Consensus size: 113
39065 ATAAAATTAT
** * *
39075 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTC-TTCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
39136 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT-TA
66 ATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
*
39183 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGAT---GAGTTCTT
* ** *
39248 CTCATTATGAACTCTACCTGGCAATTTTGATCCATCAAATGATGGATTCAA
63 CTCATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
* *
39299 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
39364 ATTATGAACTCGAACTGGTAATGTTGATCCATTGAATCATGAATTCAA
66 ATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
** *
39412 GCAAAAATTTGAACAAGTTCTTCTCATTATGAA---CTTC-TTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
39473 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT-TA
66 ATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
*
39520 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGAT---GAGTTCTT
* * * *
39585 CTCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGGATTCAA
63 CTCATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
* * *
39636 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * * * *** * *
39701 ATTATGAACTCGAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAGTCAA
66 ATTATGAACTCTATCT-G----G-CAATGCTGATC---C--ATTAAATGATGGATTCAA
* ** *
39760 GCAAAAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATAAGTTCTTC
1 GC--AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTC
* * * **
39824 TCATTATGAAC-CT-TCTGGCAACGCTGATCCATTGAATGATGAATTTGA
64 TCATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
39872 GCAAAAGGTTGAACAAATTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCT
39896 TTCTTCGGAT
Statistics
Matches: 594, Mismatches: 90, Indels: 56
0.80 0.12 0.08
Matches are distributed among these distances:
108 61 0.10
109 56 0.09
110 23 0.04
111 8 0.01
112 36 0.06
113 102 0.17
114 2 0.00
115 100 0.17
116 104 0.18
117 9 0.02
118 2 0.00
119 9 0.02
122 2 0.00
123 2 0.00
124 13 0.02
125 27 0.05
126 38 0.06
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTATCTGGCAATGCTGATCCATTAAATGATGGATTCAA
Found at i:39595 original size:337 final size:346
Alignment explanation
Indices: 38969--39895 Score: 1272
Period size: 337 Copynumber: 2.7 Consensus size: 346
38959 TTGAATAAGC
* * ****
38969 TCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * ** *** * * * * * *
39034 AAAGGTTGATGCTAATATATCTCCTTCTGTGATAAAATTATGC--AAAAGGTTGAACAAGCTCTT
66 --A-GTTAATGCTGATCCATCTGAATCTATGA-AGAGTCAAGCAAAAAAGATTGAACAAGCTCTT
* *
39097 CTCATTGTGAACTTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTG
127 CTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTG
39162 ATCCATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTC
192 ATCCATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTC
*
39227 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATTTTGATCCATCAAATGAT
257 TTCTTCAGATGACGAGTTCTTCTCATTATGAACT-TACTCTGGCAATGTTGATCCATCAAATGAT
39291 GGATTCAAACAAAAGGTTGAACAAAT
321 GGATTCAAACAAAAGGTTGAACAAAT
39317 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT-G
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * *
39381 -G-TAATGTTGATCCAT-TGAATC-ATG-A-ATTCAAGC-AAAAA-TTTGAACAAGTTCTTCTCA
66 AGTTAATGCTGATCCATCTGAATCTATGAAGAGTCAAGCAAAAAAGATTGAACAAGCTCTTCTCA
39438 TTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCC
131 TTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCC
39503 ATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCT
196 ATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCT
*
39568 TCAGATGACGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGGATT
261 TCAGATGACGAGTTCTTCTCATTATGAACTTACTCTGGCAATGTTGATCCATCAAATGATGGATT
39633 CAAACAAAAGGTTGAACAAAT
326 CAAACAAAAGGTTGAACAAAT
*
39654 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* *** *
39719 AAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAGTCAAGCAAAAAAGATTGAACAAGCTCTT
66 --A-GTTAATGCTGATCCATCTGAATCTATGA-AGAGTCAAGCAAAAAAGATTGAACAAGCTCTT
* * * *
39784 CTCATTATGAACTTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAAC-CT-TCTGGCAACG
127 CTCATTATGAACTTCTTC--T-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
* *
39847 CTGATCCATTGAA-TGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCT
189 CTGATCCA-TCAAGTGATGGATTT-AGCAAAAGGTTGAACAAATTCTTCT
39896 TTCTTCGGAT
Statistics
Matches: 519, Mismatches: 40, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
336 2 0.00
337 293 0.56
338 6 0.01
340 2 0.00
341 3 0.01
342 10 0.02
343 13 0.03
344 3 0.01
345 2 0.00
347 2 0.00
348 64 0.12
349 5 0.01
350 31 0.06
351 25 0.05
352 30 0.06
353 28 0.05
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (346 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AGTTAATGCTGATCCATCTGAATCTATGAAGAGTCAAGCAAAAAAGATTGAACAAGCTCTTCTCA
TTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCC
ATCAAGTGATGGATTTAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCT
TCAGATGACGAGTTCTTCTCATTATGAACTTACTCTGGCAATGTTGATCCATCAAATGATGGATT
CAAACAAAAGGTTGAACAAAT
Found at i:39663 original size:224 final size:223
Alignment explanation
Indices: 39075--39895 Score: 831
Period size: 224 Copynumber: 3.6 Consensus size: 223
39065 ATAAAATTAT
** * *
39075 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTC-TTCTTCTTCAAAT-GAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATAGAGTTCTTCTC
* * * *
39136 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT-TAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
39200 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
131 TTCTTCTCATTATGAA--TCTTC-TTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* ***
39265 CTGGCAATTTTGATCCATCAAATGATGGATTCAA
190 CTGGAAAAGCTGATCCATCAAATGATGGATTCAA
* *
39299 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATAGAGTTCTTCT
**** * ** * * **
39363 CATTATGAACTCGAACTGGTAATGTTGATCCATTGAATCATGAATTCAAGCAAAAATTTGAACAA
65 CATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAA
* *
39428 GTTCTTCTCATTATGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGG
130 ATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG
* *
39491 AAAAGCTGATCCATCAAGTGATGGATT-TA
194 AAAAGCTGATCCATCAAATGATGGATTCAA
39520 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGAT-A-GAGTTCTT
* *
39585 CTCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGGATTCAAACAAAAGGTTGAAC
63 CTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAAC
* * *
39650 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCGAA
128 AAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* *** * *
39715 CTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAGTCAA
190 CTGG-AA----AA-GCTGATC---CATC--AAATGATGGATTCAA
* **
39760 GCAAAAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATA-AGTTCTT
1 GC--AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATAGAGTTCTT
* * * * ** * **
39823 CTCATTATGAAC-CT-TCTGGCAACGCTGATCCATTGAATGATGAATTTGAGCAAAAGGTTGAAC
63 CTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAAC
39886 AAATTCTTCT
128 AAATTCTTCT
39896 TTCTTCGGAT
Statistics
Matches: 501, Mismatches: 68, Indels: 44
0.82 0.11 0.07
Matches are distributed among these distances:
221 54 0.11
222 47 0.09
224 108 0.22
225 13 0.03
226 4 0.01
227 10 0.02
228 90 0.18
229 33 0.07
233 2 0.00
234 7 0.01
236 51 0.10
237 4 0.01
238 19 0.04
239 8 0.02
240 4 0.01
241 9 0.02
242 38 0.08
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (223 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATAGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
TTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAA
AAGCTGATCCATCAAATGATGGATTCAA
Found at i:40974 original size:115 final size:114
Alignment explanation
Indices: 40653--40990 Score: 577
Period size: 114 Copynumber: 3.0 Consensus size: 114
40643 AATCATGCGG
* * * * * *
40653 TTCATCTTTCAATTCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
40718 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
40767 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
40832 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
40881 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
40946 AACACTTCCAGAAGATGCTATCGAGTCTTCTTATTTCTACTATGA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGA
40991 TAACGTGGTA
Statistics
Matches: 212, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 131 0.62
115 81 0.38
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:41308 original size:19 final size:17
Alignment explanation
Indices: 41284--41332 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
41274 AAAATAAAAG
41284 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
41303 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
41319 AATAAATTGAATTT
1 AATAAATTGAATTT
41333 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:49039 original size:15 final size:15
Alignment explanation
Indices: 49016--49047 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49006 TGCAATGAAT
49016 AATGAATGTATGTAA
1 AATGAATGTATGTAA
*
49031 AATGCATGTATGTAA
1 AATGAATGTATGTAA
49046 AA
1 AA
49048 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (15 bp):
AATGAATGTATGTAA
Found at i:52348 original size:20 final size:21
Alignment explanation
Indices: 52309--52359 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
52299 ATTTAATACT
*
52309 TGAAAA-AAAATAAATCATTAA
1 TGAAAATAATATAAATCATT-A
52330 T-AAAATAATATAAAT-ATTA
1 TGAAAATAATATAAATCATTA
52349 TGAAAATAATA
1 TGAAAATAATA
52360 AATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
TGAAAATAATATAAATCATTA
Found at i:52366 original size:20 final size:21
Alignment explanation
Indices: 52331--52376 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
52321 AATCATTAAT
*
52331 AAAATAATATAAATAT-TATG
1 AAAATAATATAAATATATATA
52351 AAAATAATA-AATATATATATA
1 AAAATAATATAA-ATATATATA
52372 AAAAT
1 AAAAT
52377 TTTGAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 13 0.57
21 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATAATATAAATATATATA
Found at i:52373 original size:30 final size:28
Alignment explanation
Indices: 52327--52384 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
52317 AATAAATCAT
*
52327 TAATAAAATAATATAAATATTATGAAAA
1 TAATAAAATAATATAAAAATTATGAAAA
*
52355 TAATAAATATATATATAAAAATTTTGAAAA
1 TAATAAA-ATA-ATATAAAAATTATGAAAA
52385 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 3 0.12
30 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TAATAAAATAATATAAAAATTATGAAAA
Found at i:53181 original size:9 final size:9
Alignment explanation
Indices: 53158--53198 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
53148 AATTATTATT
53158 TATATATATA
1 TATATATA-A
53168 TATATATAA
1 TATATATAA
53177 TATATATAA
1 TATATATAA
53186 TA-ATAATAA
1 TATAT-ATAA
53195 TATA
1 TATA
53199 AACAAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.07
9 18 0.62
10 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATATAA
Found at i:54093 original size:31 final size:30
Alignment explanation
Indices: 54049--54124 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
54039 TTTCTCTCGC
54049 TCTTCTCTTTTTGTT-T-TGTTGTTTGCTTTCT
1 TCTTCT-TTTTTGTTCTCTGTT-TTTGC-TTCT
*
54080 GTCTTTTTTTTTGTTCTCTGTTTTTGCTTCT
1 -TCTTCTTTTTTGTTCTCTGTTTTTGCTTCT
*
54111 TCTTCTTTTCTGTT
1 TCTTCTTTTTTGTT
54125 GGTTGTCGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
30 12 0.31
31 12 0.31
32 11 0.28
33 4 0.10
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.71
Consensus pattern (30 bp):
TCTTCTTTTTTGTTCTCTGTTTTTGCTTCT
Found at i:54516 original size:3 final size:3
Alignment explanation
Indices: 54510--54572 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
54500 ATTATTTTTT
* *
54510 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
54555 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
54573 ATAAATAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:54583 original size:15 final size:15
Alignment explanation
Indices: 54514--54589 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
54504 TTTTTTTAAT
54514 AATAAT-AATAATATA
1 AATAATAAATAA-ATA
* *
54529 TATAATAATTATAAT-
1 AATAATAAATA-AATA
*
54544 AATAATAATTATAAT-
1 AATAATAAATA-AATA
54559 AATAAT-AAT-AATA
1 AATAATAAATAAATA
54572 AATAAATAAATAAATA
1 AAT-AATAAATAAATA
54588 AA
1 AA
54590 AATGGGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 5 0.10
15 28 0.55
16 11 0.22
17 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:57031 original size:37 final size:37
Alignment explanation
Indices: 56990--57075 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
56980 TGAAGAGCAG
56990 GCCTGAAGTTGCGTTCTTGATCTGGTTTCACAAAGAA
1 GCCTGAAGTTGCGTTCTTGATCTGGTTTCACAAAGAA
57027 GCCTGAAGTTGCGTTCTTGATCTGGTTTCACAAAGAA
1 GCCTGAAGTTGCGTTCTTGATCTGGTTTCACAAAGAA
57064 GCCTGAAGTTGC
1 GCCTGAAGTTGC
57076 AGGCCTATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (37 bp):
GCCTGAAGTTGCGTTCTTGATCTGGTTTCACAAAGAA
Found at i:75428 original size:30 final size:30
Alignment explanation
Indices: 75375--75476 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
75365 TGTGTAATGT
* * *
75375 GGTACCCAACTTTTTTT-GT-GTGCAATTA
1 GGTACCTAACTTTTTTTAATGGTGCAAATA
*
75403 GGCACCTAACTTTTTTTAATGGTGCAAATA
1 GGTACCTAACTTTTTTTAATGGTGCAAATA
* *
75433 GGTACATAACCTTTTTTAATGGTGCAAATA
1 GGTACCTAACTTTTTTTAATGGTGCAAATA
*
75463 GGTACCCAACTTTT
1 GGTACCTAACTTTT
75477 ATTTTTGGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.24
29 1 0.02
30 46 0.74
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (30 bp):
GGTACCTAACTTTTTTTAATGGTGCAAATA
Found at i:78105 original size:22 final size:22
Alignment explanation
Indices: 78075--78118 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
78065 TAGATAATTG
*
78075 CTATGTTTGAAGGTCGTCATGT
1 CTATATTTGAAGGTCGTCATGT
78097 CTATATTTGAAGGTCGTCATGT
1 CTATATTTGAAGGTCGTCATGT
78119 TGAAATGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (22 bp):
CTATATTTGAAGGTCGTCATGT
Found at i:86723 original size:24 final size:24
Alignment explanation
Indices: 86649--86757 Score: 73
Period size: 24 Copynumber: 4.5 Consensus size: 24
86639 AAATATTTTA
*
86649 TCTGATTTCCGAAT-TGAATTCTGT
1 TCTGATTTCTG-ATCTGAATTCTGT
* * * *
86673 TCTGA-TACATTACCTGAA-TCTTAT
1 TCTGATTTC-TGATCTGAATTC-TGT
*
86697 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
86721 TCTGATATCT-ATTTTGAATTCTGT
1 TCTGATTTCTGA-TCTGAATTCTGT
*
86745 TTTGATTTCTGAT
1 TCTGATTTCTGAT
86758 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
23 6 0.10
24 52 0.83
25 5 0.08
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:86739 original size:48 final size:47
Alignment explanation
Indices: 86649--86757 Score: 109
Period size: 48 Copynumber: 2.3 Consensus size: 47
86639 AAATATTTTA
*
86649 TCTGATTTCCGAATTGAATTCTGTTCTGATACATTACCTGAA-TCT-TAT
1 TCTGATTTCTG-ATTGAATTCTGTTCTGATACATTA-CTGAATTCTGT-T
* *
86697 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTATT-TTGAATTCTGTT
1 TCTGATTTCTGAT-TGAATTCTGTTCTGATA-C-ATTACTGAATTCTGTT
86746 T-TGATTTCTGAT
1 TCTGATTTCTGAT
86758 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
47 2 0.04
48 41 0.77
49 6 0.11
50 4 0.08
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.50
Consensus pattern (47 bp):
TCTGATTTCTGATTGAATTCTGTTCTGATACATTACTGAATTCTGTT
Found at i:91305 original size:24 final size:24
Alignment explanation
Indices: 91277--91384 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
91267 AAATATTTTA
*
91277 TCTGATTTCCGACTTGAATTTTGT
1 TCTGATTTCTGACTTGAATTTTGT
* * * *
91301 TCTGA-TACATGACCTGAATTCTAT
1 TCTGATTTC-TGACTTGAATTTTGT
* *
91325 TCTGATTTCTGATTTGGATTTTGT
1 TCTGATTTCTGACTTGAATTTTGT
* * *
91349 TCTGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGACT-TGAATTTTGT
*
91373 TTTGATTTCTGA
1 TCTGATTTCTGA
91385 TATCTCTGTT
Statistics
Matches: 64, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
23 4 0.06
24 58 0.91
25 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTTTGT
Found at i:91371 original size:12 final size:12
Alignment explanation
Indices: 91314--91383 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
91304 GATACATGAC
*
91314 CTGAATTCTATT
1 CTGAATTCTGTT
*
91326 CTGATTTCTGATT
1 CTGAATTCTG-TT
* *
91339 -TGGATTTTGTT
1 CTGAATTCTGTT
91350 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
91362 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
91374 TTGATTTCTG
1 CTGAATTCTG
91384 ATATCTCTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 4 0.09
12 38 0.83
13 4 0.09
ACGTcount: A:0.16, C:0.13, G:0.17, T:0.54
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:91382 original size:48 final size:48
Alignment explanation
Indices: 91277--91385 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
91267 AAATATTTTA
* *
91277 TCTGATTTCCGACTTGAATTTTGTTCTGATACATGACCTGAATTCTAT
1 TCTGATTTCTGATTTGAATTTTGTTCTGATACATGACCTGAATTCTAT
* ** *
91325 TCTGATTTCTGATTTGGATTTTGTTCTGATATC-TGTTCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTTTGTTCTGATA-CATGACCTGAATTCTAT
*
91373 TTTGATTTCTGAT
1 TCTGATTTCTGAT
91386 ATCTCTGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATTTGAATTTTGTTCTGATACATGACCTGAATTCTAT
Found at i:94092 original size:19 final size:20
Alignment explanation
Indices: 94049--94096 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
94039 TCTAAATCAT
*
94049 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
94069 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
94088 TTTTCAAAA
1 TTTTCAAAA
94097 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:95018 original size:35 final size:33
Alignment explanation
Indices: 94955--95027 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 33
94945 ACCTTACAAC
* * *
94955 TCCCTAGTTTTTCCGGGCTAAACTAGAACTTTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
*
94988 TCCCTAGATTTTACACGGGATAAGCTAGAACCTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTTT
*
95023 CCCCT
1 TCCCT
95028 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 7 0.21
34 5 0.15
35 21 0.64
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.34
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
Found at i:95398 original size:21 final size:21
Alignment explanation
Indices: 95372--95452 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
95362 CGTTAGACAT
95372 GGGGGAATCAGTACCCCCTGG
1 GGGGGAATCAGTACCCCCTGG
* *
95393 GGGGGAATCAGTTCCCCCT-A
1 GGGGGAATCAGTACCCCCTGG
* *
95413 GGGGGAATCTGTACCCCTTGG
1 GGGGGAATCAGTACCCCCTGG
*
95434 GGGGGAATCTGTACCCCCT
1 GGGGGAATCAGTACCCCCT
95453 AGGCAATCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
20 16 0.31
21 36 0.69
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGGAATCAGTACCCCCTGG
Found at i:95429 original size:41 final size:41
Alignment explanation
Indices: 95372--95455 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
95362 CGTTAGACAT
*
95372 GGGGGAATCAGTACCCCCTGGGGGGGAATCAGTTCCCCCTA
1 GGGGGAATCAGTACCCCCTGGGGGGGAATCAGTACCCCCTA
* * *
95413 GGGGGAATCTGTACCCCTTGGGGGGGAATCTGTACCCCCTA
1 GGGGGAATCAGTACCCCCTGGGGGGGAATCAGTACCCCCTA
95454 GG
1 GG
95456 CAATCTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.19
Consensus pattern (41 bp):
GGGGGAATCAGTACCCCCTGGGGGGGAATCAGTACCCCCTA
Done.