Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002457.1 Hibiscus syriacus cultivar Beakdansim tig00005031_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: 61565
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:7364 original size:42 final size:40
Alignment explanation
Indices: 7318--7405 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
7308 GTCGAATTCA
*
7318 CAACTCGAATTTGACATTTTCGCAACAAGAATTTCT-TTTTCG
1 CAACTCGAATTTGA-A-ATTCGCAACAAGAATTT-TGTTTTCG
* * * *
7360 CAACTCGATTTTTAAATTCGCAACACGAGTTTTGTTTTCG
1 CAACTCGAATTTGAAATTCGCAACAAGAATTTTGTTTTCG
7400 CAACTC
1 CAACTC
7406 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 26 0.65
41 1 0.03
42 12 0.30
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (40 bp):
CAACTCGAATTTGAAATTCGCAACAAGAATTTTGTTTTCG
Found at i:7399 original size:20 final size:19
Alignment explanation
Indices: 7334--7403 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
7324 GAATTTGACA
*
7334 TTTTCGCAACAAGAATTTCT
1 TTTTCGCAACACGAATTT-T
*
7354 TTTTCGCAACTCG-ATTTT
1 TTTTCGCAACACGAATTTT
* *
7372 TAAATTCGCAACACGAGTTTT
1 T--TTTCGCAACACGAATTTT
7393 GTTTTCGCAAC
1 -TTTTCGCAAC
7404 TCAAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 29 0.73
21 4 0.10
22 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTTCGCAACACGAATTTT
Found at i:7472 original size:20 final size:20
Alignment explanation
Indices: 7425--7464 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7415 ATCCGCAACT
* *
7425 CGAATTTCATTTTTGAGTTG
1 CGAATTTCATTTTCGAATTG
7445 CGAATTTCATTTTCGAATTG
1 CGAATTTCATTTTCGAATTG
7465 TGATTTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (20 bp):
CGAATTTCATTTTCGAATTG
Found at i:7958 original size:12 final size:12
Alignment explanation
Indices: 7937--7970 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7927 ACCACATTTC
*
7937 CAATACCAAACA
1 CAATATCAAACA
7949 CAATATCAAACA
1 CAATATCAAACA
*
7961 CAATCTCAAA
1 CAATATCAAA
7971 ATCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:8107 original size:24 final size:24
Alignment explanation
Indices: 8089--8135 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
8079 AGTCAGTATT
8089 CGAAATTTGATCTTGGTCAATACA
1 CGAAATTTGATCTTGGTCAATACA
* *
8113 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
8136 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACA
Found at i:8140 original size:24 final size:24
Alignment explanation
Indices: 8094--8147 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
8084 GTATTCGAAA
8094 TTTGATCTTGGTCAATACACGGAC
1 TTTGATCTTGGTCAATACACGGAC
* *
8118 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACACGGAC
8142 TTTGAT
1 TTTGAT
8148 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACACGGAC
Found at i:10723 original size:14 final size:11
Alignment explanation
Indices: 10690--10722 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
10680 TCTGAAAACT
10690 CTTTCTTCTTC
1 CTTTCTTCTTC
10701 CTTTCTTCTTC
1 CTTTCTTCTTC
10712 CTTTCTTCTTC
1 CTTTCTTCTTC
10723 TCCCAACCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (11 bp):
CTTTCTTCTTC
Found at i:11730 original size:23 final size:22
Alignment explanation
Indices: 11703--11777 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
11693 TGAATATGCA
11703 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
11726 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
11748 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
11772 ATATGA
1 ATATGA
11778 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:11759 original size:46 final size:47
Alignment explanation
Indices: 11678--11789 Score: 167
Period size: 46 Copynumber: 2.4 Consensus size: 47
11668 CTATGTGACT
*
11678 ATATGAAATGATATATGA-ATATGCAATATGCAATACGTGATACATGTG
1 ATATGATATGA-A-ATGACATATGCAATATGCAATACGTGATACATGTG
*
11726 ATATGATATGAAATGACATATG-AATATGTAATACGTGATACATGTG
1 ATATGATATGAAATGACATATGCAATATGCAATACGTGATACATGTG
11772 ATATGATATGAAAT-ACAT
1 ATATGATATGAAATGACAT
11790 GGTTACACAT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
45 4 0.07
46 41 0.67
47 6 0.10
48 10 0.16
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (47 bp):
ATATGATATGAAATGACATATGCAATATGCAATACGTGATACATGTG
Found at i:11997 original size:38 final size:38
Alignment explanation
Indices: 11940--12035 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
11930 TATAAGACAT
* * *
11940 ATGATAGGTCCTACAGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
11978 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
12016 ATGATAGGTCATTCGGGACA
1 ATGATAGGTCCTTCGGGACA
12036 TTTATACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:13993 original size:53 final size:53
Alignment explanation
Indices: 13936--14045 Score: 148
Period size: 53 Copynumber: 2.1 Consensus size: 53
13926 TCGAAAATCG
* * * *
13936 AATTCGCAACTCGAAAATCGAATTCGCAATTCGAAACTCAAATTCGCAACTCA
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
* * * *
13989 AATTCGTAACTCGAAATTCAAATTCACAACTCGAAAATCGAATTCGCAACTCG
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
14042 AATT
1 AATT
14046 TCGAATTCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (53 bp):
AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCAAATTCGCAACTCA
Found at i:14000 original size:73 final size:73
Alignment explanation
Indices: 13916--14065 Score: 219
Period size: 73 Copynumber: 2.1 Consensus size: 73
13906 TCGAAAATCG
* * *
13916 AATTCGCAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATTCGCAATTCGAAACTCAAATTC
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATTC
13981 GCAACTCA
66 GCAACTCA
* * ** *
13989 AATTCGTAACTCGAAATTCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAATTTCGAATTC
1 AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATTC
*
14054 GCAACTCG
66 GCAACTCA
14062 AATT
1 AATT
14066 TCATTTTCGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (73 bp):
AATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAACTCAAATTC
GCAACTCA
Found at i:14054 original size:93 final size:93
Alignment explanation
Indices: 13895--14063 Score: 275
Period size: 93 Copynumber: 1.8 Consensus size: 93
13885 TACCTAGTGA
* *
13895 AAATTCGCAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATT
1 AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATT
*
13960 CGCAATTCGAAACTCAAATTCGCAACTC
66 CGCAACTCGAAACTCAAATTCGCAACTC
* * **
13988 AAATTCGTAACTCGAAATTCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAATTTCGAATT
1 AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATT
14053 CGCAACTCGAA
66 CGCAACTCGAA
14064 TTTCATTTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTCGCAACTCGAAAATCAAATTCACAACTCGAAAATCGAATTCGCAACTCGAAAATCGAATT
CGCAACTCGAAACTCAAATTCGCAACTC
Found at i:14065 original size:13 final size:13
Alignment explanation
Indices: 13926--14050 Score: 74
Period size: 13 Copynumber: 9.4 Consensus size: 13
13916 AATTCGCAAC
*
13926 TCGAAAATCGAAT
1 TCGAAACTCGAAT
* *
13939 TCGCAACTCGAAAA
1 TCGAAACTCG-AAT
*
13953 TCG-AATTCGCAAT
1 TCGAAACTCG-AAT
*
13966 TCGAAACTCAAAT
1 TCGAAACTCGAAT
* *
13979 TCGCAACTCAAAT
1 TCGAAACTCGAAT
*
13992 TCGTAACTCGAAAT
1 TCGAAACTCG-AAT
* * *
14006 TC-AAATTCACAAC
1 TCGAAACTC-GAAT
*
14019 TCGAAAATCGAAT
1 TCGAAACTCGAAT
*
14032 TCGCAACTCGAATT
1 TCGAAACTCGAA-T
14046 TCGAA
1 TCGAA
14051 TTCGCAACTC
Statistics
Matches: 85, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
13 61 0.72
14 24 0.28
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (13 bp):
TCGAAACTCGAAT
Found at i:14067 original size:20 final size:20
Alignment explanation
Indices: 13896--14063 Score: 206
Period size: 20 Copynumber: 8.8 Consensus size: 20
13886 ACCTAGTGAA
13896 AATTCGCAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
13916 AATTCGCAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
13936 AATTCGCAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
* * *
13956 AATTCGCAATTCGAAACTCA
1 AATTCGCAACTCGAAAATCG
13976 AATTCGCAACTC----A---
1 AATTCGCAACTCGAAAATCG
* * *
13989 AATTCGTAACTCGAAATTCA
1 AATTCGCAACTCGAAAATCG
*
14009 AATTCACAACTCGAAAATCG
1 AATTCGCAACTCGAAAATCG
**
14029 AATTCGCAACTCGAATTTCG
1 AATTCGCAACTCGAAAATCG
14049 AATTCGCAACTCGAA
1 AATTCGCAACTCGAA
14064 TTTCATTTTC
Statistics
Matches: 127, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.09
20 116 0.91
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.23
Consensus pattern (20 bp):
AATTCGCAACTCGAAAATCG
Found at i:14090 original size:19 final size:19
Alignment explanation
Indices: 14063--14124 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
14053 CGCAACTCGA
14063 ATTTCATTTTCGAGTTGCG
1 ATTTCATTTTCGAGTTGCG
* *
14082 ATTTTATTTTCAAGTTGCG
1 ATTTCATTTTCGAGTTGCG
14101 AATTTCATTTTCGAGTTGCG
1 -ATTTCATTTTCGAGTTGCG
14121 ATTT
1 ATTT
14125 TCGTGTTACG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.55
20 17 0.45
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.50
Consensus pattern (19 bp):
ATTTCATTTTCGAGTTGCG
Found at i:14110 original size:20 final size:20
Alignment explanation
Indices: 14060--14126 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
14050 ATTCGCAACT
14060 CGAATTTCATTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTG
* *
14080 CG-ATTTTATTTTCAAGTTG
1 CGAATTTCATTTTCGAGTTG
14099 CGAATTTCATTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTG
*
14119 CGATTTTC
1 CGAATTTC
14127 GTGTTACGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 17 0.41
20 24 0.59
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (20 bp):
CGAATTTCATTTTCGAGTTG
Found at i:14137 original size:34 final size:35
Alignment explanation
Indices: 14060--14153 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 35
14050 ATTCGCAACT
*
14060 CGAATTTCATTTTCGAGTTGCGATTTTATTTTCAAGTTG
1 CGAATTTCATTTTCGAGTTGCG----TATTTTCAAGTTA
**
14099 CGAATTTCATTTTCGAGTTGCG-ATTTTCGTGTTA
1 CGAATTTCATTTTCGAGTTGCGTATTTTCAAGTTA
14133 CGAA-TTCGATTTTCGAGTTGC
1 CGAATTTC-ATTTTCGAGTTGC
14154 AAAGAATTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
33 3 0.06
34 26 0.51
39 22 0.43
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (35 bp):
CGAATTTCATTTTCGAGTTGCGTATTTTCAAGTTA
Found at i:17552 original size:21 final size:21
Alignment explanation
Indices: 17508--17603 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
17498 AGTATGGAAT
*
17508 GTGAATTTTGAACGATGCGG-G
1 GTGAATCTTGAACGATG-GGAG
*
17529 GTGAATCTTGAATGATGGGAG
1 GTGAATCTTGAACGATGGGAG
* *
17550 GTGGATCCTGAACGATGGGAG
1 GTGAATCTTGAACGATGGGAG
* ** * * *
17571 GGGCCTCTTGAACAATGAGAA
1 GTGAATCTTGAACGATGGGAG
*
17592 GTGAATCCTGAA
1 GTGAATCTTGAA
17604 GAATAGGAGA
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 2 0.03
21 56 0.97
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGAATCTTGAACGATGGGAG
Found at i:17996 original size:21 final size:21
Alignment explanation
Indices: 17972--18057 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
17962 TGAAATAATC
*
17972 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* **
17993 TCACGTAAAGAACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
18014 TCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
*
18035 TCACGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
18056 TC
1 TC
18058 TCGTGGAGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.96
22 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:18251 original size:42 final size:42
Alignment explanation
Indices: 18157--18280 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
18147 GTGATGGAAT
* * *
18157 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCTACT--A-G
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
*
18196 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
* *
18238 AGGTGATGGATCTCAGTGTCGAAGTGAAGAATCGACTCGATG
1 AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
18280 A
1 A
18281 AAAAGTGGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 33 0.44
41 1 0.01
42 41 0.55
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGACTCGATG
Found at i:19465 original size:10 final size:9
Alignment explanation
Indices: 19450--19474 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19440 ATAATTATAT
19450 ATAAAAAAA
1 ATAAAAAAA
19459 ATAAAAAAA
1 ATAAAAAAA
19468 ATAAAAA
1 ATAAAAA
19475 CTAACCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:20748 original size:22 final size:22
Alignment explanation
Indices: 20668--20754 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
20658 GAGGGGGTAT
* *
20668 TCGGAGATGGGGA-TGAATGTCG
1 TCGGAGATGGGGACAG-GTGTCG
20690 TCGGAGATGGGGAC-GGATGTCG
1 TCGGAGATGGGGACAGG-TGTCG
20712 TCGGAGATGGGGACAGGTGTCG
1 TCGGAGATGGGGACAGGTGTCG
* *
20734 CCGAAGATGGGGACAGGTGTC
1 TCGGAGATGGGGACAGGTGTC
20755 ACCGGAGAGA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
22 57 0.97
23 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.47, T:0.18
Consensus pattern (22 bp):
TCGGAGATGGGGACAGGTGTCG
Found at i:20883 original size:20 final size:20
Alignment explanation
Indices: 20860--20989 Score: 100
Period size: 20 Copynumber: 6.5 Consensus size: 20
20850 ATTAAAAGCT
20860 GAGTTGCGAATTCGAAAATC
1 GAGTTGCGAATTCGAAAATC
* ** *
20880 GAGTTGTGAAAACGAAATTC
1 GAGTTGCGAATTCGAAAATC
* *
20900 GTGTTGCGAAATT-GAAACTC
1 GAGTTGCG-AATTCGAAAATC
* * *
20920 GCGTTGCGAATTAGAAAACC
1 GAGTTGCGAATTCGAAAATC
* ** *
20940 GAGTTGCAAAAACGAAATTC
1 GAGTTGCGAATTCGAAAATC
* **
20960 GTGTTGCGAATTTAAAAATC
1 GAGTTGCGAATTCGAAAATC
20980 GAGTTGCGAA
1 GAGTTGCGAA
20990 AAAGAAATTC
Statistics
Matches: 81, Mismatches: 27, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
19 4 0.05
20 75 0.93
21 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (20 bp):
GAGTTGCGAATTCGAAAATC
Found at i:20937 original size:60 final size:60
Alignment explanation
Indices: 20840--20989 Score: 212
Period size: 60 Copynumber: 2.5 Consensus size: 60
20830 GTTTATATAT
* * **
20840 GTGTTGCGAAATTAAAAGCT-GAGTTGCGAATTCGAAAATCGAGTTGTGAAAACGAAATTC
1 GTGTTGCGAAATTAAAA-CTCGAGTTGCGAATTAGAAAACCGAGTTGCAAAAACGAAATTC
* *
20900 GTGTTGCGAAATTGAAACTCGCGTTGCGAATTAGAAAACCGAGTTGCAAAAACGAAATTC
1 GTGTTGCGAAATTAAAACTCGAGTTGCGAATTAGAAAACCGAGTTGCAAAAACGAAATTC
* *
20960 GTGTTGCGAATTTAAAAATCGAGTTGCGAA
1 GTGTTGCGAAATTAAAACTCGAGTTGCGAA
20990 AAAGAAATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 2 0.03
60 77 0.97
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (60 bp):
GTGTTGCGAAATTAAAACTCGAGTTGCGAATTAGAAAACCGAGTTGCAAAAACGAAATTC
Found at i:20946 original size:40 final size:40
Alignment explanation
Indices: 20902--21009 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
20892 CGAAATTCGT
** * *
20902 GTTGCGAAATTGAAACTCGCGTTGCGAA-TTAGAAAACCGA
1 GTTGCGAAAAAGAAATTCGTGTTGCGAATTTA-AAAACCGA
*
20942 GTTGC-AAAAACGAAATTCGTGTTGCGAATTTAAAAATCGA
1 GTTGCGAAAAA-GAAATTCGTGTTGCGAATTTAAAAACCGA
20982 GTTGCGAAAAAGAAATTCGTGTTGCGAA
1 GTTGCGAAAAAGAAATTCGTGTTGCGAA
21010 ATTGTCAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
39 3 0.05
40 49 0.82
41 8 0.13
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (40 bp):
GTTGCGAAAAAGAAATTCGTGTTGCGAATTTAAAAACCGA
Found at i:21005 original size:20 final size:20
Alignment explanation
Indices: 20882--21010 Score: 93
Period size: 20 Copynumber: 6.5 Consensus size: 20
20872 CGAAAATCGA
* *
20882 GTTGTGAAAACGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
** * *
20902 GTTGCGAAATTGAAACTCGC
1 GTTGCGAAAAAGAAATTCGT
** ** *
20922 GTTGCGAATTAGAAAACCGA
1 GTTGCGAAAAAGAAATTCGT
20942 GTTGC-AAAAACGAAATTCGT
1 GTTGCGAAAAA-GAAATTCGT
* *
20962 GTTGCGAATTTAA-AAA-TCGA
1 GTTGCGAA--AAAGAAATTCGT
20982 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
21002 GTTGCGAAA
1 GTTGCGAAA
21011 TTGTCAAATT
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 69 0.82
21 5 0.06
23 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGT
Found at i:21022 original size:22 final size:21
Alignment explanation
Indices: 20860--21031 Score: 85
Period size: 20 Copynumber: 8.5 Consensus size: 21
20850 ATTAAAAGCT
*
20860 GAGTTGCG-AATTCG-AAAATC
1 GAGTTGCGAAATT-GTAAATTC
* **
20880 GAGTTGTGAAAACG-AAATTC
1 GAGTTGCGAAATTGTAAATTC
* *
20900 GTGTTGCGAAATTG-AAACTC
1 GAGTTGCGAAATTGTAAATTC
* **
20920 GCGTTGCG-AATTAG-AAAACC
1 GAGTTGCGAAATT-GTAAATTC
* **
20940 GAGTTGCAAAAACG-AAATTC
1 GAGTTGCGAAATTGTAAATTC
* *
20960 GTGTTGCG-AATT-TAAAAATC
1 GAGTTGCGAAATTGT-AAATTC
**
20980 GAGTTGCGAAAAAG-AAATTC
1 GAGTTGCGAAATTGTAAATTC
*
21000 GTGTTGCGAAATTGTCAAATTC
1 GAGTTGCGAAATTGT-AAATTC
21022 GAGTTGCGAA
1 GAGTTGCGAA
21032 TTTGACTTCT
Statistics
Matches: 112, Mismatches: 31, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
19 6 0.05
20 85 0.76
21 6 0.05
22 15 0.13
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.26
Consensus pattern (21 bp):
GAGTTGCGAAATTGTAAATTC
Found at i:21439 original size:23 final size:23
Alignment explanation
Indices: 21411--21475 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
21401 AATCAGTTGG
21411 AAATCTCGGCGTCTTTAGGGTGA
1 AAATCTCGGCGTCTTTAGGGTGA
21434 AAATCTCGGCGTCTTTAGGGTGA
1 AAATCTCGGCGTCTTTAGGGTGA
*
21457 AAATCTCAGCGTCTTTAGG
1 AAATCTCGGCGTCTTTAGG
21476 ATTTTAATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (23 bp):
AAATCTCGGCGTCTTTAGGGTGA
Found at i:24097 original size:21 final size:21
Alignment explanation
Indices: 24071--24114 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
24061 GACTGCATGA
24071 GATATCTCGACGCCTTCAAGG
1 GATATCTCGACGCCTTCAAGG
24092 GATATCTCGACGCCTTCAAGG
1 GATATCTCGACGCCTTCAAGG
24113 GA
1 GA
24115 ATATTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (21 bp):
GATATCTCGACGCCTTCAAGG
Found at i:26857 original size:35 final size:36
Alignment explanation
Indices: 26815--26896 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
26805 AAACTCTCAA
*
26815 AAAATAGGATAGAATTCTGCTA-GGATTCAACTCCT
1 AAAATAGGATAGAATTCTGCTATGGATTAAACTCCT
* **
26850 AAAATAGGATAGAATTTTGCTATGTTTTAAACTCCT
1 AAAATAGGATAGAATTCTGCTATGGATTAAACTCCT
26886 AAAGATAGGAT
1 AAA-ATAGGAT
26897 CCATAAGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.51
36 13 0.32
37 7 0.17
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (36 bp):
AAAATAGGATAGAATTCTGCTATGGATTAAACTCCT
Found at i:28005 original size:24 final size:24
Alignment explanation
Indices: 27978--28084 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
27968 AAACGGAGAT
*
27978 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
28002 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
28026 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
28050 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
28074 ATCAGAAATCA
1 ATCAGAAATCA
28085 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:28084 original size:48 final size:48
Alignment explanation
Indices: 27978--28086 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
27968 AAACGGAGAT
* * * *
27978 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
28026 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
28074 ATCAGAAATCAGA
1 ATCAGAAATCAGA
28087 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:30562 original size:7 final size:7
Alignment explanation
Indices: 30550--30581 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
30540 TGGTCAACTC
30550 CGGTCAA
1 CGGTCAA
30557 CGGTCAA
1 CGGTCAA
30564 CGGGTCAA
1 C-GGTCAA
30572 CGGTCAA
1 CGGTCAA
30579 CGG
1 CGG
30582 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:30571 original size:15 final size:15
Alignment explanation
Indices: 30551--30584 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
30541 GGTCAACTCC
30551 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
30566 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
30581 GGTC
1 GGTC
30585 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:30596 original size:18 final size:18
Alignment explanation
Indices: 30573--30637 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
30563 ACGGGTCAAC
30573 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
30591 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
30604 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
30622 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
30638 AAACCGGTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 13 0.31
18 29 0.69
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:30611 original size:31 final size:31
Alignment explanation
Indices: 30558--30646 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 31
30548 TCCGGTCAAC
*
30558 GGTCAACGGGTCAACGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTC--GGGTCAACGGGTCGGGTCG
30591 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
30622 GGTCAACGGGTCGGGTAAACCGGTC
1 GGTCAACGGGTCGGGTCAACGGGTC
30647 AAAACAGTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
31 41 0.77
33 12 0.23
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:30633 original size:8 final size:8
Alignment explanation
Indices: 30551--30615 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
30541 GGTCAACTCC
30551 GGTCAAC-
1 GGTCAACG
30558 GGTCAACG
1 GGTCAACG
30566 GGTCAAC-
1 GGTCAACG
30573 GGTCAACG
1 GGTCAACG
**
30581 GGTCGGGTCG
1 GGTC--AACG
30591 GGTCAACG
1 GGTCAACG
30599 GGT---CG
1 GGTCAACG
30604 GGTCAACG
1 GGTCAACG
30612 GGTC
1 GGTC
30616 GGGTCGGGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
5 5 0.11
7 14 0.30
8 22 0.47
10 6 0.13
ACGTcount: A:0.18, C:0.25, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:30637 original size:13 final size:13
Alignment explanation
Indices: 30584--30620 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
30574 GTCAACGGGT
30584 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
30597 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
30610 CGGGTCGGGTC
1 CGGGTCGGGTC
30621 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:32574 original size:2 final size:2
Alignment explanation
Indices: 32567--32603 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
32557 CTTTTAAAAC
32567 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
32604 CCCCCATCCG
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:32791 original size:24 final size:24
Alignment explanation
Indices: 32764--32870 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
32754 AAACGGAGAT
*
32764 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
32788 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
32812 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
32836 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
32860 ATCAGAAATCA
1 ATCAGAAATCA
32871 GATAAATATT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:32870 original size:48 final size:48
Alignment explanation
Indices: 32764--32872 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
32754 AAACGGAGAT
* * * *
32764 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
32812 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
32860 ATCAGAAATCAGA
1 ATCAGAAATCAGA
32873 TAAATATTCA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:35368 original size:18 final size:18
Alignment explanation
Indices: 35345--35421 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
35335 CAACGGTCAA
35345 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
35363 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
*
35381 CGGGT--AG---ACGGGT
1 CGGGTCGGGTCAACGGGT
35394 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
35412 CGGGTCGGGT
1 CGGGTCGGGT
35422 TGTGACCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 11 0.22
15 1 0.02
16 1 0.02
18 38 0.75
ACGTcount: A:0.12, C:0.19, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:35380 original size:31 final size:32
Alignment explanation
Indices: 35343--35417 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 32
35333 GTCAACGGTC
35343 AACGGGTCGGGTCA-ACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCAGACGGGTCGGGTCGGGTA
*
35374 AACGGGTCGGGT-AGACGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCAGACGGGTCGGGTCGGGTA
35405 AACGGGTCGGGTC
1 AACGGGTCGGGTC
35418 GGGTTGTGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (32 bp):
AACGGGTCGGGTCAGACGGGTCGGGTCGGGTA
Found at i:35417 original size:13 final size:13
Alignment explanation
Indices: 35339--35399 Score: 61
Period size: 13 Copynumber: 4.3 Consensus size: 13
35329 TCCGGTCAAC
35339 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35352 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35365 GGTCGGGTAAACGGGTCG
1 GGTC-----AACGGGTCG
35383 GGT-AGACGGGTCG
1 GGTCA-ACGGGTCG
35396 GGTC
1 GGTC
35400 GGGTCAACGG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.02
13 28 0.68
18 12 0.29
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:36534 original size:16 final size:16
Alignment explanation
Indices: 36513--36546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36503 CATGTATTTA
36513 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
36529 TATTATTTTACTTTAT
1 TATTATATTACATTAT
36545 TA
1 TA
36547 AATTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:36551 original size:24 final size:22
Alignment explanation
Indices: 36518--36578 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
36508 ATTTATATTA
* *
36518 TATTACATTATTATTATTTTACTT
1 TATTAAATTATTATT-TTTT-CGT
36542 TATTAAATTATTATTTTTTCGT
1 TATTAAATTATTATTTTTTCGT
*
36564 TATTATATTTATTAT
1 TATTA-AATTATTAT
36579 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 12 0.36
24 14 0.42
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTAAATTATTATTTTTTCGT
Found at i:41307 original size:20 final size:20
Alignment explanation
Indices: 41278--41335 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
41268 GGCAAAAGAA
*
41278 AAAGAA-AAGAAGCAAAAAGG
1 AAAGAACAAGAA-CAAAAAAG
41298 AAA-AACAAGAACAAAAAAG
1 AAAGAACAAGAACAAAAAAG
* *
41317 AAAGAACAAAAATAAAAAA
1 AAAGAACAAGAACAAAAAA
41336 AAGGGACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAGAACAAGAACAAAAAAG
Found at i:41345 original size:33 final size:35
Alignment explanation
Indices: 41276--41347 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
41266 AGGGCAAAAG
*
41276 AAAAAGAAAAGAAGCAAAAAGGAAAAACAAGAACA
1 AAAAAGAAAAGAAGCAAAAAGGAAAAAAAAGAACA
* *
41311 AAAAAG-AAAGAA-CAAAAA-TAAAAAAAAGGGACA
1 AAAAAGAAAAGAAGCAAAAAGGAAAAAAAA-GAACA
41344 AAAA
1 AAAA
41348 GCACATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 7 0.21
33 14 0.42
34 6 0.18
35 6 0.18
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.01
Consensus pattern (35 bp):
AAAAAGAAAAGAAGCAAAAAGGAAAAAAAAGAACA
Found at i:43187 original size:31 final size:31
Alignment explanation
Indices: 43149--43271 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
43139 GGGTCGAGGG
43149 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
43180 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
43211 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
43242 TTACCTAGGTTATTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
43272 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:47303 original size:31 final size:31
Alignment explanation
Indices: 47261--47414 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
47251 GGGTCGAGGG
47261 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
47292 TTATCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
47323 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
47354 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
47385 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
47415 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:48230 original size:22 final size:22
Alignment explanation
Indices: 48199--48247 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
48189 CCCCATCAAT
*
48199 CCTTTGAGCATCAAATACCAAA
1 CCTTTAAGCATCAAATACCAAA
*
48221 CCTTTAAGCATCAAATGCCAAA
1 CCTTTAAGCATCAAATACCAAA
48243 CCTTT
1 CCTTT
48248 GACCAAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (22 bp):
CCTTTAAGCATCAAATACCAAA
Found at i:49201 original size:37 final size:36
Alignment explanation
Indices: 49107--49211 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
49097 GTGCTCACCA
*
49107 TTGTCTCTCTTGTGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
49143 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * * *
49180 TTTTCTCCCTTGAGACAGTTTCTCTTGTAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
49212 TAAACATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 30 0.50
37 30 0.50
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:49301 original size:102 final size:102
Alignment explanation
Indices: 49125--49582 Score: 745
Period size: 102 Copynumber: 4.5 Consensus size: 102
49115 CTTGTGACAG
** * * * *
49125 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
49190 TGAGACAGTTTCTCTTGTAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * ** *
49227 TTTCCCTTGAAATGAGTTTTGTCTCTCTTAAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
49292 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
49329 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
49394 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
49431 TTTCCCTTGAAATGAATTTTGTCTCTCTTTAGATAGTTTCCCTCGAAACAAAATTTTATCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
49496 TGAGACAGTTTCTCTTGAAACGTAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
49533 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
49583 TAAACATTGA
Statistics
Matches: 329, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 329 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:49302 original size:37 final size:37
Alignment explanation
Indices: 49243--49516 Score: 130
Period size: 37 Copynumber: 7.9 Consensus size: 37
49233 TTGAAATGAG
* *
49243 TTTTGTCTCTC-TTAAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
** *
49280 TTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
49318 ---------CATTGGAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
*
49345 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
49382 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
49420 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* * *
49447 TTTTGTCTCTC-TTTAGATAGTTTCCCTCGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* * *
49484 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAAC
49517 GTAAACATTG
Statistics
Matches: 175, Mismatches: 31, Indels: 62
0.65 0.12 0.23
Matches are distributed among these distances:
27 4 0.02
29 30 0.17
30 9 0.05
35 7 0.04
36 30 0.17
37 89 0.51
38 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:49572 original size:65 final size:65
Alignment explanation
Indices: 49482--49647 Score: 287
Period size: 65 Copynumber: 2.6 Consensus size: 65
49472 CTCGAAACAA
* * *
49482 AATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACGTAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
* *
49547 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
49612 AATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACA
49648 AAATTTTGTC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 94 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (65 bp):
AATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:49583 original size:167 final size:169
Alignment explanation
Indices: 49365--49682 Score: 514
Period size: 167 Copynumber: 1.9 Consensus size: 169
49355 CTTGAGATAG
*
49365 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
** * *
49430 ATTTCCCTTGAAATGAATTTTGTCTCTCTTTAGATAGTTTCCCTCGAAACAAAATTTTATCTCCC
66 ATTTCCCTTGAAATGAATTTCATCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTATCTCCC
49495 TTGAGACAG-TTTCTCTTGAAACGTAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACGTAAACATTGAAAACA
** * *
49533 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * *
49597 ATTTCCCTTGAAATGAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCATCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTATCTCCC
49662 TTGAGACAGTTTTCTCTTGAA
131 TTGAGACAGTTTTCTCTTGAA
49683 GCATCATCTT
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
167 114 0.83
168 23 0.17
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCATCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTATCTCCC
TTGAGACAGTTTTCTCTTGAAACGTAAACATTGAAAACA
Found at i:49770 original size:104 final size:103
Alignment explanation
Indices: 49547--49788 Score: 265
Period size: 104 Copynumber: 2.4 Consensus size: 103
49537 CCTTGAAATG
* *
49547 AATTTCGTCTCTCTTGAGATAG-TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AATTTTGTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * *
49611 GAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAA
66 GAATTTCATCTCCCGTGAGACAATTTCTCTTGAAACAA
* * * * * * ** * *
49649 AATTTTGTCTCCCTTGAGACAGTTTTCTCTTGAAGCATCATCTTTGAATATGTTTTCCTTGGAAC
1 AATTTTGTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT-GAAA
* * *
49714 T-AATTTCATCTCCCCGTGAGACAATTTCTTTTGGAACTA
65 TGAATTTCATCT-CCCGTGAGACAATTTCTCTTGAAACAA
* *
49753 AGTTTTGTCTCTCTTGAGACAGTTTT-TCTTAAAACA
1 AATTTTGTCTCTCTTGAGACAGTTTTCTCTTGAAACA
49789 AAATTTTGTC
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
102 19 0.17
103 47 0.41
104 49 0.43
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (103 bp):
AATTTTGTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTCATCTCCCGTGAGACAATTTCTCTTGAAACAA
Found at i:49825 original size:37 final size:37
Alignment explanation
Indices: 49755--49826 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
49745 TGGAACTAAG
* * **
49755 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
49792 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
49827 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:50413 original size:55 final size:55
Alignment explanation
Indices: 50329--50455 Score: 218
Period size: 55 Copynumber: 2.3 Consensus size: 55
50319 ACAGCACAAG
* * *
50329 CTCAACTTCACAGCGAAGGGGCGGCTGACTTTCGACAAACAATTTCGGAGCCAAT
1 CTCAACTTCACAGCGAAAGGGCGACTGACTGTCGACAAACAATTTCGGAGCCAAT
*
50384 CTCAACTTCACAGCGAAAGGGCGACTGACTGTCGACAAGCAATTTCGGAGCCAAT
1 CTCAACTTCACAGCGAAAGGGCGACTGACTGTCGACAAACAATTTCGGAGCCAAT
50439 CTCAACTTCACAGCGAA
1 CTCAACTTCACAGCGAA
50456 GGATATTGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (55 bp):
CTCAACTTCACAGCGAAAGGGCGACTGACTGTCGACAAACAATTTCGGAGCCAAT
Found at i:50565 original size:106 final size:105
Alignment explanation
Indices: 50431--50999 Score: 559
Period size: 109 Copynumber: 5.4 Consensus size: 105
50421 AGCAATTTCG
* * * * *
50431 GAGCCAATCTCAACTTCAC-AGCGAAGGATATTGGATTCGAGACAACACAAGTTCAACTTCACAG
1 GAGCCAATTTCAACTCCACGA-CGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* *
50495 CGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCCAATTCCA
65 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTCCA
* *
50537 GAGCCGATTTCAACTCCACGACGGAGGATATCGTG-CTACCTGAGACAACACAAGTTCAACTTCA
1 GAGCCAATTTCAACTCCACGACGGAGGATATTG-GACT--C-GAGACAACACAAGTTCAACTTCA
* * * *
50601 CAACGAAGGGACGACTGGTTGTCAACGAACAACTTTTCAGTTTCA
62 CAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAGTTCCA
** * *
50646 -TCCGCGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCA
1 GAGC-CAATTTCAACTCCACGACGGAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCA
* * * *
50710 CAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCA
62 CAACGAAGGGACGGCTGGTTGTCAACAAACA-ATTTCCAGTTCCA
*
50755 GAGCCAATTTCAACTTCGCA-G-CGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
1 GAGCCAATTTCAAC-TC-CACGACGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
* *
50818 ACGAAGGGACGGCTGATTGTCAAC-AA-GATTT-C-GTT-CA
64 ACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTCCA
* * * * * * *
50855 GAGTCAATTTCAACTTCAC-AGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAG
1 GAGCCAATTTCAACTCCACGA-CGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
50919 CGAAGGGGCGACTGATTGTCAACAAACAATTTCCCGGTTCCA
65 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTCCA
* * *
50961 GAACCAATTTCAACTTCAC-AGCGGAGGATATTAGACTCG
1 GAGCCAATTTCAACTCCACGA-CGGAGGATATTGGACTCG
51000 GAACAATATT
Statistics
Matches: 394, Mismatches: 46, Indels: 46
0.81 0.09 0.09
Matches are distributed among these distances:
98 2 0.01
99 1 0.00
100 75 0.19
101 4 0.01
102 4 0.01
103 3 0.01
104 1 0.00
105 5 0.01
106 117 0.30
107 4 0.01
108 2 0.01
109 163 0.41
110 8 0.02
111 3 0.01
112 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (105 bp):
GAGCCAATTTCAACTCCACGACGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAAC
GAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTCCA
Found at i:51515 original size:37 final size:35
Alignment explanation
Indices: 51464--51534 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
51454 ATCCTACTAT
*
51464 GATTCAAACTCTAAAAAATATGATAGAATTCTGCTAG
1 GATTCAAACTCT--AAAATAGGATAGAATTCTGCTAG
*
51501 GATTC-AACTCCTAAAATAGGATAGAATTTTGCTA
1 GATTCAAACT-CTAAAATAGGATAGAATTCTGCTA
51535 TGTTTTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 20 0.65
36 4 0.13
37 7 0.23
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (35 bp):
GATTCAAACTCTAAAATAGGATAGAATTCTGCTAG
Found at i:52119 original size:14 final size:14
Alignment explanation
Indices: 52091--52132 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
52081 ACTATTATCA
*
52091 TTATATGTATATTTT
1 TTAT-TGTATTTTTT
52106 TTATTGTATTTTTT
1 TTATTGTATTTTTT
*
52120 TTATTTTATTTTT
1 TTATTGTATTTTT
52133 ACTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
TTATTGTATTTTTT
Found at i:52231 original size:16 final size:16
Alignment explanation
Indices: 52210--52248 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52200 CATGTATTTA
52210 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
52226 TATTATTTTACTTTAT
1 TATTATATTACATTAT
52242 TAATTAT
1 T-ATTAT
52249 TATTTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:52251 original size:23 final size:22
Alignment explanation
Indices: 52215--52274 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
52205 ATTTATATTA
*
52215 TATTACATTATTATTATTTTACTT
1 TATTACATTATTATT-TTTT-CGT
52239 TATTA-ATTATTATTTTTTCGT
1 TATTACATTATTATTTTTTCGT
*
52260 TATTATATTTATTAT
1 TATTACA-TTATTAT
52275 ATATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
23 16 0.48
24 5 0.15
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTACATTATTATTTTTTCGT
Found at i:52268 original size:26 final size:23
Alignment explanation
Indices: 52204--52256 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
52194 TTTTTTCATG
52204 TATTTATATTATATTACATTATTAT
1 TATTT-TATTATATTA-ATTATTAT
52229 TATTTTACTT-TATTAATTATTAT
1 TATTTTA-TTATATTAATTATTAT
52252 T-TTTT
1 TATTTT
52257 CGTTATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.15
23 9 0.33
24 7 0.26
25 7 0.26
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTATTATATTAATTATTAT
Found at i:53939 original size:24 final size:23
Alignment explanation
Indices: 53894--53942 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
53884 TAAGTATTTA
53894 GTAGTTAGCTGCTGGCTGTAGGT
1 GTAGTTAGCTGCTGGCTGTAGGT
53917 GTAGTTAG-TGCTGCTGCTGTAGGT
1 GTAGTTAGCTGCTG--GCTGTAGGT
53941 GT
1 GT
53943 TGTATGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 8 0.33
24 11 0.46
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.37
Consensus pattern (23 bp):
GTAGTTAGCTGCTGGCTGTAGGT
Done.