Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007082.1 Corchorus capsularis cultivar CVL-1 contig07103, 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: 18275
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Found at i:299 original size:27 final size:28
Alignment explanation
Indices: 234--300 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
224 TGCTTCTTAC
*
234 TGATTCTGCTTTGTTTTCATGCTTGACACT
1 TGATT-TGC-TTGTTTTCATGCTGGACACT
264 TGATTTGCTTGTTTTCATGCTGGA-ACT
1 TGATTTGCTTGTTTTCATGCTGGACACT
291 TGATTTGCTT
1 TGATTTGCTT
301 CGATTCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 13 0.36
28 15 0.42
29 3 0.08
30 5 0.14
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.51
Consensus pattern (28 bp):
TGATTTGCTTGTTTTCATGCTGGACACT
Found at i:310 original size:28 final size:28
Alignment explanation
Indices: 251--313 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
241 GCTTTGTTTT
* * *
251 CATGCTTGACACTTGATTTGCTTGTTTT
1 CATGCTGGACACTTGATTTGCTTGATTC
279 CATGCTGGA-ACTTGATTTGCTTCGATTC
1 CATGCTGGACACTTGATTTGCTT-GATTC
307 CATGCTG
1 CATGCTG
314 AATTGACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (28 bp):
CATGCTGGACACTTGATTTGCTTGATTC
Found at i:1493 original size:88 final size:87
Alignment explanation
Indices: 1241--1528 Score: 260
Period size: 88 Copynumber: 3.2 Consensus size: 87
1231 AATATTTGGT
* * * * *
1241 TCACCGAGTCAAATTCTGAAGAAATATTGCACCGCATTAACTTGATCCACCGAATCAAACTTTGA
1 TCACCGAATCCAATTTTGAAG-AA-A-TGCACCGCATTAACTTGATTCACCGAATC-AAC-CTGA
* * *
1306 ACTGTTTGAAAATGTGTTGTACCGAGC
61 ACTGTCTGAAAATGTGCTGCACCGAGC
* * * * ** * *
1333 TTACTGAATCCAATCTTGAAGAAATAAGGCACCGCCTCGACTTGATTCACCGAATCATCCTGAAA
1 TCACCGAATCCAATTTTGAAGAAAT---GCACCGCATTAACTTGATTCACCGAATCAACCTGAAC
*
1398 TGCCTGAAAATGTGCTGCACCGAGC
63 TGTCTGAAAATGTGCTGCACCGAGC
* *
1423 TCACCGAATCCAATATTTGAATAAATGCACCGCATTAACTTGATTCACCGAATC-GCCATGAACT
1 TCACCGAATCCAAT-TTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATCAACC-TGAACT
*
1487 GTCTGAAAATGTGCTGGCA---AGA
64 GTCTGAAAATGTGCT-GCACCGAGC
1509 TCACCGAATCCAATCTTTGA
1 TCACCGAATCCAAT-TTTGA
1529 TATTCCTGCA
Statistics
Matches: 161, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
86 21 0.13
87 2 0.01
88 44 0.27
89 4 0.02
90 38 0.24
91 13 0.08
92 39 0.24
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (87 bp):
TCACCGAATCCAATTTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATCAACCTGAACTGT
CTGAAAATGTGCTGCACCGAGC
Found at i:1576 original size:35 final size:35
Alignment explanation
Indices: 1537--1835 Score: 377
Period size: 35 Copynumber: 8.5 Consensus size: 35
1527 GATATTCCTG
* *
1537 CACCGAGTCATCTGAATCCGATTTTGAAGATGCTA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
* * * *
1572 CACCGAGTCATTTGAAACCAACTTTGAAAATGCTA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
*
1607 CACCGAGTCATCTGAACCCAATTTTTTTTAAGATGCTA
1 CACCGAGTCATCTGAACCCAA---TTTTGAAGATGCTA
*
1645 CACCGAGTTATCTGAACCCAATTTTGAAGATG-TAA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCT-A
* *** *
1680 CACCAAGTCATCTGAAAATAATTTTAAAGATGCTA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
*
1715 CACCGAGTCATCTGAACCCAATTTTGAAGATTCTA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
* *
1750 CACCGAGTCATCTGAACCTAATGTT-AAGGATGCTA
1 CACCGAGTCATCTGAACCCAATTTTGAA-GATGCTA
* *
1785 CACCGAGTCATCTGAACCCAACTTCGAAGATGCTA
1 CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
1820 CACCGAGTCATCTGAA
1 CACCGAGTCATCTGAA
1836 TCCACCGAAT
Statistics
Matches: 226, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
34 3 0.01
35 189 0.84
36 3 0.01
38 31 0.14
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (35 bp):
CACCGAGTCATCTGAACCCAATTTTGAAGATGCTA
Found at i:1943 original size:43 final size:44
Alignment explanation
Indices: 1802--1989 Score: 308
Period size: 44 Copynumber: 4.3 Consensus size: 44
1792 TCATCTGAAC
* *
1802 CCAACTTCGAAGATGCTACACCGAGTCATCTGAATCCACCGAAT
1 CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
1846 CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
1 CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
* * *
1890 TCAACTTTGAAGATGCTTCACCGAGTCATCTG-ATTCACCGAGT
1 CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
*
1933 CCAACTTTGAAGATGCTTCACCGAGTCATCTG-ATTCACCGAAT
1 CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
1976 CCAACTTTGAAGAT
1 CCAACTTTGAAGAT
1990 AAACCCTAAA
Statistics
Matches: 137, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
43 64 0.47
44 73 0.53
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (44 bp):
CCAACTTTGAAGATGCTTCACCGAGTCATCTGAATCCACCGAAT
Found at i:1955 original size:87 final size:87
Alignment explanation
Indices: 1802--1989 Score: 306
Period size: 87 Copynumber: 2.2 Consensus size: 87
1792 TCATCTGAAC
*
1802 CCAACTTCGAAGATGCTACACCGAGTCATCTGAATCCACCGAATCCAACTTTGAAGATGCTTCAC
1 CCAACTTTGAAGATGCTACACCGAGTCATCTGAATCCACCGAATCCAACTTTGAAGATGCTTCAC
1867 CGAGTCATCTGAATCCACCGAAT
66 CGAGTCATCTG-ATCCACCGAAT
* * * *
1890 TCAACTTTGAAGATGCTTCACCGAGTCATCTG-ATTCACCGAGTCCAACTTTGAAGATGCTTCAC
1 CCAACTTTGAAGATGCTACACCGAGTCATCTGAATCCACCGAATCCAACTTTGAAGATGCTTCAC
*
1954 CGAGTCATCTGATTCACCGAAT
66 CGAGTCATCTGATCCACCGAAT
1976 CCAACTTTGAAGAT
1 CCAACTTTGAAGAT
1990 AAACCCTAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 23 0.25
87 41 0.44
88 29 0.31
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (87 bp):
CCAACTTTGAAGATGCTACACCGAGTCATCTGAATCCACCGAATCCAACTTTGAAGATGCTTCAC
CGAGTCATCTGATCCACCGAAT
Found at i:2086 original size:55 final size:54
Alignment explanation
Indices: 2027--2142 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 54
2017 GACCGATCAT
* * * *
2027 ACTGGTTCACTTAAAGATAAAATTAATACCAT-TGGAGACTTTCTTGATTGACCGC
1 ACTGGATCACTTAAAGATAAAATTAA-ACC-TCTAGAAACTCTCTTGATTGACCGC
* * *
2082 ACTGGATCACTTGATGATAAACTTAAACCTCTAGAAACTCTCTTGATTGACCGC
1 ACTGGATCACTTAAAGATAAAATTAAACCTCTAGAAACTCTCTTGATTGACCGC
*
2136 AGTGGAT
1 ACTGGAT
2143 GTCTTCTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
53 1 0.02
54 29 0.56
55 22 0.42
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (54 bp):
ACTGGATCACTTAAAGATAAAATTAAACCTCTAGAAACTCTCTTGATTGACCGC
Found at i:2333 original size:54 final size:55
Alignment explanation
Indices: 2222--2346 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 55
2212 CAATCTGGTT
*
2222 ACCGCACTGGATCACTTGAAGATAAACGTAATACCACCGGAAACTATCTTGATTG
1 ACCGCACTGGATCACTAGAAGATAAACGTAATACCACCGGAAACTATCTTGATTG
* * ** *
2277 ACCGCACTGGATCACTAGAGGATAAACTTAA-ACCACTTGAAACTTTCTTGATTG
1 ACCGCACTGGATCACTAGAAGATAAACGTAATACCACCGGAAACTATCTTGATTG
*
2331 ACCGCACTTGATCACT
1 ACCGCACTGGATCACT
2347 CACTGGAAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 35 0.56
55 28 0.44
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (55 bp):
ACCGCACTGGATCACTAGAAGATAAACGTAATACCACCGGAAACTATCTTGATTG
Found at i:2372 original size:37 final size:37
Alignment explanation
Indices: 2310--2383 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
2300 AAACTTAAAC
*
2310 CACTTGAAACTTTCTTGATTGACCGCACTTGATCACT
1 CACTGGAAACTTTCTTGATTGACCGCACTTGATCACT
* *
2347 CACTGGAAGCTTTCTTGATTTACCGCACTTGATCACT
1 CACTGGAAACTTTCTTGATTGACCGCACTTGATCACT
2384 TGATGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (37 bp):
CACTGGAAACTTTCTTGATTGACCGCACTTGATCACT
Found at i:3650 original size:15 final size:14
Alignment explanation
Indices: 3629--3671 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
3619 GTTTTATCTT
3629 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
3643 TCTTTCTT-TTTTTC
1 T-TTTCTTCTTTTTC
*
3657 TTTCTTTTCTTTTTC
1 TTT-TCTTCTTTTTC
3672 GATTGCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 12 0.48
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:3651 original size:12 final size:11
Alignment explanation
Indices: 3625--3664 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
3615 TAGAGTTTTA
3625 TCTTTTTTC-T
1 TCTTTTTTCTT
3635 TCTTTTTCTCTT
1 TCTTTTT-TCTT
3647 TCTTTTTTTCTT
1 TC-TTTTTTCTT
3659 TCTTTT
1 TCTTTT
3665 CTTTTTCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.26
11 6 0.22
12 9 0.33
13 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:3759 original size:21 final size:23
Alignment explanation
Indices: 3734--3781 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
3724 CTAAAAACCT
*
3734 TTTTGAGAAAAA-C-ATTTTTTC
1 TTTTGAGAAAAATCAATTTCTTC
*
3755 TTTTGTGAAAAATCAATTTCTTC
1 TTTTGAGAAAAATCAATTTCTTC
3778 TTTT
1 TTTT
3782 TTTTTGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTTGAGAAAAATCAATTTCTTC
Found at i:3766 original size:22 final size:23
Alignment explanation
Indices: 3732--3782 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3722 CTCTAAAAAC
*
3732 CTTTTTGAGAAAAAC-ATTTTTT
1 CTTTTTGAGAAAAACAATTTCTT
*
3754 CTTTTGTGA-AAAATCAATTTCTT
1 CTTTT-TGAGAAAAACAATTTCTT
3777 CTTTTT
1 CTTTTT
3783 TTTTGGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (23 bp):
CTTTTTGAGAAAAACAATTTCTT
Found at i:4418 original size:12 final size:14
Alignment explanation
Indices: 4391--4437 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
4381 CAAAAAAAAA
4391 TTTGAAAACTCATT
1 TTTGAAAACTCATT
4405 TTTGAAAAC-C-TT
1 TTTGAAAACTCATT
* *
4417 TTCGAAAA-TGATT
1 TTTGAAAACTCATT
4430 TTTGAAAA
1 TTTGAAAA
4438 ATACTTCTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.32
13 10 0.36
14 9 0.32
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (14 bp):
TTTGAAAACTCATT
Found at i:7670 original size:35 final size:34
Alignment explanation
Indices: 7624--8174 Score: 514
Period size: 35 Copynumber: 16.3 Consensus size: 34
7614 TGCTTACTAA
*
7624 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTG-ACT
* * * *
7659 ACTTAATTACCCTGAATTAAGTTTCTCATTAACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
*
7693 CACTTAATTACCCTGAATTAAAGTTGA-TTACTGATT
1 -ACTTAATTACCCTGAATT-AAGTT-ACTTACTGACT
*
7729 CACTTAATTACCCTGAATTAAGCTACTTACTG---
1 -ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* * *
7761 ACTTAATCACCCTTAATTAAGTCA-TTAACTGACT
1 ACTTAATTACCCTGAATTAAGTTACTT-ACTGACT
* *
7795 CACTTAATTACCATGAATTAAGTTATTTACTG---
1 -ACTTAATTACCCTGAATTAAGTTACTTACTGACT
*
7827 ACTTAATTACCCTGAATTAAGTTA-TTCACTGGCTT
1 ACTTAATTACCCTGAATTAAGTTACTT-ACTGAC-T
**
7862 ACTTAATTACCCTGAATTAAGTTACTGCCT---T
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* * *
7893 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAC--T
*
7929 ACTTAATTACCCTGAATTAAGCTACTTACTG---
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* *
7960 ACTTAATTACCCTGAATTAAGTTACCTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAC-T
* * *
7994 ACTTATTTACCCTGAATTAAGTTGCTGACT---T
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
* *
8025 ACTTAATTACCCTTAATTAAGCTA-TTCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTACTT-ACTGAC-T
* *
8060 ACTTAATTGCCCTGAATTAAGTTACTTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTACTTACTG-ACT
* *
8095 ACTTAATTACCCTGGATTAAGTTAATTACTGACT
1 ACTTAATTACCCTGAATTAAGTTACTTACTGACT
*
8129 CACTTAATTACCCTGAATTAAGTTGA-GTACTGACT
1 -ACTTAATTACCCTGAATTAAGTT-ACTTACTGACT
8164 CACTTAATTAC
1 -ACTTAATTAC
8175 TAAATTACTT
Statistics
Matches: 431, Mismatches: 50, Indels: 70
0.78 0.09 0.13
Matches are distributed among these distances:
30 6 0.01
31 128 0.30
34 30 0.07
35 203 0.47
36 64 0.15
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGACT
Found at i:7812 original size:66 final size:65
Alignment explanation
Indices: 7624--8152 Score: 596
Period size: 66 Copynumber: 7.9 Consensus size: 65
7614 TGCTTACTAA
* *
7624 ACTTAATTACCCTGAATTAAGTTACTTATTGAAC-TACTTAATTACCCTGAATTAAGTTTCTCAT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACTTACTTAATTACCCTGAATTAAG-TT-AC-T
*
7688 TAACTC
61 T-ACTG
*
7694 ACTTAATTACCCTGAATTAAAGTTGATTACTGA-TTCACTTAATTACCCTGAATTAAGCTACTTA
1 ACTTAATTACCCTGAATT-AAGTT-ATTACTGACTT-ACTTAATTACCCTGAATTAAGTTACTTA
7758 CTG
63 CTG
* * * * * *
7761 ACTTAATCACCCTTAATTAAGTCATTAACTGACTCACTTAATTACCATGAATTAAGTTATTTACT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
7826 G
65 G
* **
7827 ACTTAATTACCCTGAATTAAGTTATTCACTGGCTTACTTAATTACCCTGAATTAAGTTACTGCCT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
*
7892 T
65 G
* * * *
7893 ACTTAATTTCCCTGAACTAAGTTACTAACTGACTTTACTTAATTACCCTGAATTAAGCTACTTAC
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGAC-TTACTTAATTACCCTGAATTAAGTTACTTAC
7958 TG
64 TG
* * * * *
7960 ACTTAATTACCCTGAATTAAGTTACCTA-TTACTTACTTATTTACCCTGAATTAAGTTGCTGACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
*
8024 T
65 G
* * *
8025 ACTTAATTACCCTTAATTAAGCTATTCACTGACTTACTTAATTGCCCTGAATTAAGTTACTTACT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGACTTACTTAATTACCCTGAATTAAGTTACTTACT
8090 G
65 G
* *
8091 AATTACTTAATTACCCTGGATTAAGTTAATTACTGACTCACTTAATTACCCTGAATTAAGTT
1 ----ACTTAATTACCCTGAATTAAGTT-ATTACTGACTTACTTAATTACCCTGAATTAAGTT
8153 GAGTACTGAC
Statistics
Matches: 390, Mismatches: 54, Indels: 30
0.82 0.11 0.06
Matches are distributed among these distances:
64 1 0.00
65 54 0.14
66 153 0.39
67 74 0.19
68 2 0.01
69 1 0.00
70 70 0.18
71 34 0.09
72 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (65 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTTACTTAATTACCCTGAATTAAGTTACTTACTG
Found at i:7979 original size:14 final size:15
Alignment explanation
Indices: 7931--7985 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
7921 CTGACTTTAC
7931 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
* * *
7945 TTAAGCTACTTACTGAC
1 TTAAGTTAC--CCTGAA
7962 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
7976 TTAAGTTACC
1 TTAAGTTACC
7986 TATTACTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
14 12 0.39
15 8 0.26
16 3 0.10
17 8 0.26
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (15 bp):
TTAAGTTACCCTGAA
Found at i:8093 original size:17 final size:17
Alignment explanation
Indices: 8071--8270 Score: 99
Period size: 16 Copynumber: 11.5 Consensus size: 17
8061 CTTAATTGCC
*
8071 CTGAATTAAGTTACTTA
1 CTGAATTAAGTTAATTA
*
8088 CTGAATT-ACTTAATTA
1 CTGAATTAAGTTAATTA
*
8104 CCCTGGATTAAGTTAATTA
1 --CTGAATTAAGTTAATTA
* * *
8123 CTG-ACTCACTTAATTA
1 CTGAATTAAGTTAATTA
* *
8139 CCCTGAATTAAGTTGAGTA
1 --CTGAATTAAGTTAATTA
* * *
8158 CTG-ACTCACTTAATTA
1 CTGAATTAAGTTAATTA
* *
8174 CTAAATT-ACTTAATTA
1 CTGAATTAAGTTAATTA
*
8190 CCCTGAATTAAGTTGAA-AA
1 --CTGAATTAAGTT-AATTA
*
8209 CTGAATT-ACTTAATTA
1 CTGAATTAAGTTAATTA
*
8225 CCCTGAATTAAGTTGATTA
1 --CTGAATTAAGTTAATTA
*
8244 CTGAATT-ACTTAATTA
1 CTGAATTAAGTTAATTA
8260 TCCTGAATTAA
1 --CTGAATTAA
8271 TTTTATTATT
Statistics
Matches: 137, Mismatches: 28, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.01
16 47 0.34
17 29 0.21
18 29 0.21
19 28 0.20
20 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (17 bp):
CTGAATTAAGTTAATTA
Found at i:8174 original size:51 final size:51
Alignment explanation
Indices: 8116--8225 Score: 157
Period size: 51 Copynumber: 2.2 Consensus size: 51
8106 CTGGATTAAG
* * ** *
8116 TTAATTACTGACTCACTTAATTACCCTGAATTAAGTTGAGTACTGACTCAC
1 TTAATTACTAAATCACTTAATTACCCTGAATTAAGTTGAAAACTGAATCAC
* *
8167 TTAATTACTAAATTACTTAATTACCCTGAATTAAGTTGAAAACTGAATTAC
1 TTAATTACTAAATCACTTAATTACCCTGAATTAAGTTGAAAACTGAATCAC
8218 TTAATTAC
1 TTAATTAC
8226 CCTGAATTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (51 bp):
TTAATTACTAAATCACTTAATTACCCTGAATTAAGTTGAAAACTGAATCAC
Found at i:8185 original size:86 final size:86
Alignment explanation
Indices: 8085--8259 Score: 262
Period size: 86 Copynumber: 2.0 Consensus size: 86
8075 ATTAAGTTAC
* * * *
8085 TTACTGAATTACTTAATTACCCTGGATTAAGTT-AATTACTGACTCACTTAATTACCCTGAATTA
1 TTACTAAATTACTTAATTACCCTGAATTAAGTTGAA-AACTGAATCACTTAATTACCCTGAATTA
*
8149 AGTTGAGTACTGACTCACTTAA
65 AGTTGAGTACTGAATCACTTAA
*
8171 TTACTAAATTACTTAATTACCCTGAATTAAGTTGAAAACTGAATTACTTAATTACCCTGAATTAA
1 TTACTAAATTACTTAATTACCCTGAATTAAGTTGAAAACTGAATCACTTAATTACCCTGAATTAA
* *
8236 GTTGATTACTGAATTACTTAA
66 GTTGAGTACTGAATCACTTAA
8257 TTA
1 TTA
8260 TCCTGAATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 78 0.98
87 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (86 bp):
TTACTAAATTACTTAATTACCCTGAATTAAGTTGAAAACTGAATCACTTAATTACCCTGAATTAA
GTTGAGTACTGAATCACTTAA
Found at i:8223 original size:35 final size:35
Alignment explanation
Indices: 8170--8306 Score: 188
Period size: 35 Copynumber: 4.0 Consensus size: 35
8160 GACTCACTTA
*
8170 ATTACTAAATTACTTAATTACCCTGAATTAAGTTG
1 ATTACTGAATTACTTAATTACCCTGAATTAAGTTG
**
8205 AAAACTGAATTACTTAATTACCCTGAATTAAGTTG
1 ATTACTGAATTACTTAATTACCCTGAATTAAGTTG
* * *
8240 ATTACTGAATTACTTAATTATCCTGAATTAATTTT
1 ATTACTGAATTACTTAATTACCCTGAATTAAGTTG
* *
8275 ATTA-TTACTTAC-TAATTACCCTGAATTAAGTT
1 ATTACTGAATTACTTAATTACCCTGAATTAAGTT
8307 ACTTATTACT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
33 18 0.20
34 6 0.07
35 66 0.73
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTACTGAATTACTTAATTACCCTGAATTAAGTTG
Found at i:8302 original size:121 final size:121
Alignment explanation
Indices: 8052--8270 Score: 332
Period size: 121 Copynumber: 1.8 Consensus size: 121
8042 TAAGCTATTC
* * ** *
8052 ACTGACTTACTTAATTGCCCTGAATTAAGTTACTTACTGAATTACTTAATTACCCTGGATTAAGT
1 ACTGAATTACTTAATTACCCTGAATTAAGTTACAAACTGAATTACTTAATTACCCTGAATTAAGT
*
8117 TAATTACTGACTCACTTAATTACCCTGAATTAAGTTGAGTACTGACTCACTTAATT
66 TAATTACTGAATCACTTAATTACCCTGAATTAAGTTGAGTACTGACTCACTTAATT
*
8173 ACTAAATTACTTAATTACCCTGAATTAAGTTGA-AAACTGAATTACTTAATTACCCTGAATTAAG
1 ACTGAATTACTTAATTACCCTGAATTAAGTT-ACAAACTGAATTACTTAATTACCCTGAATTAAG
* * *
8237 TTGATTACTGAATTACTTAATTATCCTGAATTAA
65 TTAATTACTGAATCACTTAATTACCCTGAATTAA
8271 TTTTATTATT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 86 0.99
122 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (121 bp):
ACTGAATTACTTAATTACCCTGAATTAAGTTACAAACTGAATTACTTAATTACCCTGAATTAAGT
TAATTACTGAATCACTTAATTACCCTGAATTAAGTTGAGTACTGACTCACTTAATT
Found at i:9646 original size:18 final size:19
Alignment explanation
Indices: 9625--9666 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
9615 CTTTTTTCTT
9625 CCCCTCAA-TTTTTTCGCC
1 CCCCTCAATTTTTTTCGCC
*
9643 CCCCTCAATTTTTTTTGCC
1 CCCCTCAATTTTTTTCGCC
9662 CCCCT
1 CCCCT
9667 TTCAACTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.10, C:0.45, G:0.05, T:0.40
Consensus pattern (19 bp):
CCCCTCAATTTTTTTCGCC
Found at i:11258 original size:19 final size:19
Alignment explanation
Indices: 11231--11273 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
11221 ATTATGACCC
11231 AAAGCAAAGTCC-AACAAG
1 AAAGCAAAGTCCAAACAAG
*
11249 TAAAGGAAAGTCCAAACAAG
1 -AAAGCAAAGTCCAAACAAG
11269 AAAGC
1 AAAGC
11274 CCAAAGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.56, C:0.19, G:0.19, T:0.07
Consensus pattern (19 bp):
AAAGCAAAGTCCAAACAAG
Found at i:11951 original size:13 final size:12
Alignment explanation
Indices: 11935--11982 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
11925 TTAGGCTGAG
11935 TTTTTTTC-TTC
1 TTTTTTTCTTTC
*
11946 TCTTTTTCTTTTC
1 TTTTTTTC-TTTC
11959 TTTTTTTCTTTC
1 TTTTTTTCTTTC
11971 TTTTCTTTCTTT
1 TTTT-TTTCTTT
11983 TGTCTTTGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 7 0.22
12 8 0.25
13 17 0.53
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:11988 original size:28 final size:24
Alignment explanation
Indices: 11935--11983 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11925 TTAGGCTGAG
11935 TTTTTTTCTTCTCTTTTTCTTTTC
1 TTTTTTTCTTCTCTTTTTCTTTTC
11959 TTTTTTTCTT-TC-TTTTC-TTTC
1 TTTTTTTCTTCTCTTTTTCTTTTC
11980 TTTT
1 TTTT
11984 GTCTTTGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 8 0.32
22 5 0.20
23 2 0.08
24 10 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTTCTTCTCTTTTTCTTTTC
Found at i:11989 original size:11 final size:10
Alignment explanation
Indices: 11937--11989 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
11927 AGGCTGAGTT
11937 TTTTTCTTCTC
1 TTTTTCTT-TC
11948 TTTTTCTTTTC
1 TTTTTC-TTTC
11959 TTTTTTTCTTTC
1 --TTTTTCTTTC
11971 -TTTTCTTTC
1 TTTTTCTTTC
11980 TTTTGTCTTT
1 TTTT-TCTTT
11990 GCGCTGAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.24
10 3 0.08
11 13 0.35
12 6 0.16
13 6 0.16
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:12591 original size:14 final size:13
Alignment explanation
Indices: 12567--12619 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
12557 TAAAAACTCA
*
12567 AAAACCTTTTTTG
1 AAAACCATTTTTG
12580 AAAACTCATTTTTG
1 AAAAC-CATTTTTG
* *
12594 CAAACCTTTTCTTG
1 AAAACCATTT-TTG
*
12608 AAAACAATTTTT
1 AAAACCATTTTT
12620 TTTGAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:12617 original size:27 final size:27
Alignment explanation
Indices: 12568--12619 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12558 AAAAACTCAA
*
12568 AAACCTTTTTTGAAAACTCATTTTTGC
1 AAACCTTTTTTGAAAACTAATTTTTGC
12595 AAACCTTTTCTTGAAAAC-AATTTTT
1 AAACCTTTT-TTGAAAACTAATTTTT
12620 TTTGAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (27 bp):
AAACCTTTTTTGAAAACTAATTTTTGC
Found at i:15413 original size:65 final size:68
Alignment explanation
Indices: 15333--15466 Score: 166
Period size: 69 Copynumber: 2.0 Consensus size: 68
15323 TTACACTGAG
* * * * *
15333 TTAAGTTAATTACCAAGTTACTTGA-TT-TGA-TAGTTTACTTAATTGCACCGAATTGAGTTAAT
1 TTAAGTTAATTACCAAATTACTTAACTTATGACCAATTTACTTAATTGCACCGAATTAAGTTAAT
15395 TAC
66 TAC
* * *
15398 TTAATTTAATTACCAAATTACTTAACTTAATTACCAATTTTCTTAATTGCACCGAATTAAGTTAA
1 TTAAGTTAATTACCAAATTACTTAACTT-ATGACCAATTTACTTAATTGCACCGAATTAAGTTAA
15463 TTAC
65 TTAC
15467 CAAGTTACTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
65 22 0.39
66 2 0.04
68 2 0.04
69 31 0.54
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (68 bp):
TTAAGTTAATTACCAAATTACTTAACTTATGACCAATTTACTTAATTGCACCGAATTAAGTTAAT
TAC
Found at i:15416 original size:21 final size:21
Alignment explanation
Indices: 15392--15445 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15382 GAATTGAGTT
15392 AATTACTTAATTTAATTACCA
1 AATTACTTAATTTAATTACCA
*
15413 AATTACTTAACTTAATTACCA
1 AATTACTTAATTTAATTACCA
* *
15434 ATTTTCTTAATT
1 AATTACTTAATT
15446 GCACCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTACTTAATTTAATTACCA
Found at i:15467 original size:56 final size:56
Alignment explanation
Indices: 15398--15530 Score: 178
Period size: 56 Copynumber: 2.4 Consensus size: 56
15388 AGTTAATTAC
* * * *
15398 TTAATTTAATTACCAAATTACTTAA-CTTAATTACCAATTTTCTTAATTGCACCGAA
1 TTAAGTTAATTACCAAATTACTTAATC-TAATTACCAAATTGCTTAATTACACCGAA
* * *
15454 TTAAGTTAATTACCAAGTTACTTAATCTAATTATCAAATTGCTTAATTACACTGAA
1 TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
*
15510 TTAAGTTGATTACCAAATTAC
1 TTAAGTTAATTACCAAATTAC
15531 CAATTTACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
56 66 0.99
57 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (56 bp):
TTAAGTTAATTACCAAATTACTTAATCTAATTACCAAATTGCTTAATTACACCGAA
Found at i:15484 original size:21 final size:21
Alignment explanation
Indices: 15460--15500 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15450 CGAATTAAGT
*
15460 TAATTACCAAGTTACTTAATC
1 TAATTACCAAATTACTTAATC
* *
15481 TAATTATCAAATTGCTTAAT
1 TAATTACCAAATTACTTAAT
15501 TACACTGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
TAATTACCAAATTACTTAATC
Found at i:15529 original size:43 final size:43
Alignment explanation
Indices: 15482--15573 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
15472 TACTTAATCT
* * *
15482 AATTATCAAATTGCTTAATTACACTGAATTAAGTTGATTACCA
1 AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
* * *
15525 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCC
1 AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
15568 AATTAC
1 AATTAC
15574 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (43 bp):
AATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:15634 original size:43 final size:43
Alignment explanation
Indices: 15586--15826 Score: 313
Period size: 43 Copynumber: 5.3 Consensus size: 43
15576 AAATTTAATC
15586 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
15629 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
15672 ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAAT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACC-----A---AA--T--T
15727 CACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 -ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
* *
15771 ACCACTTTACTTAATTACACCGAATTAAGTTGTTTACCAGATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
*
15814 ACC-ATTTTCTTAA
1 ACCAATTTACTTAA
15827 ATCTTGTCCT
Statistics
Matches: 177, Mismatches: 8, Indels: 27
0.83 0.04 0.13
Matches are distributed among these distances:
42 8 0.05
43 123 0.69
44 1 0.01
46 1 0.01
48 3 0.02
51 2 0.01
53 1 0.01
55 1 0.01
56 37 0.21
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (43 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
Found at i:15673 original size:100 final size:98
Alignment explanation
Indices: 15426--15673 Score: 361
Period size: 100 Copynumber: 2.5 Consensus size: 98
15416 TACTTAACTT
* * ** * *
15426 AATTACCAATTTTCTTAATTGCACCGAATTAAGTTAATTACCAAGTTACTTAATCTAATTATCAA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAA-TTACTTAATCTAATCACCAA
* *
15491 ATTGCTTAATTACACTGAATTAAGTTGATTACCA
65 ATTACTTAATTACACCGAATTAAGTTGATTACCA
*
15525 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCCAATTACTTAAATTTAATCACCA
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTA-CCAATTACTT-AATCTAATCACCA
* *
15590 ATTTACTTAATTACACCGAATTAAGTTGTTTACCA
64 AATTACTTAATTACACCGAATTAAGTTGATTACCA
15625 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATTAC
1 AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA-ATTAC
15674 CAATTTACTT
Statistics
Matches: 135, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
99 45 0.33
100 90 0.67
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (98 bp):
AATTACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAATTACTTAATCTAATCACCAAA
TTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:15791 original size:142 final size:143
Alignment explanation
Indices: 15495--15826 Score: 587
Period size: 142 Copynumber: 2.3 Consensus size: 143
15485 TATCAAATTG
* * * *
15495 CTTAATTACACTGAATTAAGTTGATTACCAAATTACCAATTTACTTAATTACACCGAATTAAGTT
1 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATCACACCGAATTAAGTT
*
15560 GTTTACCCAATTACTTAAATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
66 GTTTACCAAATTACTTAAATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
15625 AATTACCAATTTA
131 AATTACCAATTTA
15638 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATCACACCGAATTAAGTT
1 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATCACACCGAATTAAGTT
15703 GTTTACCAAATTACTT-AATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
66 GTTTACCAAATTACTTAAATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
*
15767 AATTACCACTTTA
131 AATTACCAATTTA
*
15780 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACC-ATTTTCTTAA
1 CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAA
15827 ATCTTGTCCT
Statistics
Matches: 182, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 9 0.05
142 97 0.53
143 76 0.42
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (143 bp):
CTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATCACACCGAATTAAGTT
GTTTACCAAATTACTTAAATTTAATCACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCA
AATTACCAATTTA
Found at i:15800 original size:99 final size:99
Alignment explanation
Indices: 15629--15815 Score: 338
Period size: 99 Copynumber: 1.9 Consensus size: 99
15619 TTACCAAATT
*
15629 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAGATTACCAATTTACTTAATCACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATCACACCG
15694 AATTAAGTTGTTTACCAAATTACTTAATTTAATC
66 AATTAAGTTGTTTACCAAATTACTTAATTTAATC
* *
15728 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCACTTTACTTAATTACACCG
1 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATCACACCG
*
15793 AATTAAGTTGTTTACCAGATTAC
66 AATTAAGTTGTTTACCAAATTAC
15816 CATTTTCTTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 84 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (99 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACCAATTTACTTAATCACACCG
AATTAAGTTGTTTACCAAATTACTTAATTTAATC
Found at i:18205 original size:27 final size:27
Alignment explanation
Indices: 18140--18233 Score: 152
Period size: 27 Copynumber: 3.4 Consensus size: 27
18130 TGCTTCTTAC
18140 TGATTCTGCTTTGTTTTCATGCTGGACACT
1 TGATT-TGC-TTGTTTTCATGCTGGA-ACT
*
18170 TGATTTGCTTGTTTTCGTGCTGGAACT
1 TGATTTGCTTGTTTTCATGCTGGAACT
18197 TGATTTGCTTGTTTTCATGCTGGAACT
1 TGATTTGCTTGTTTTCATGCTGGAACT
18224 TGATTTGCTT
1 TGATTTGCTT
18234 CGATTCCATG
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
27 39 0.63
28 15 0.24
29 3 0.05
30 5 0.08
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (27 bp):
TGATTTGCTTGTTTTCATGCTGGAACT
Found at i:18246 original size:55 final size:57
Alignment explanation
Indices: 18140--18246 Score: 157
Period size: 55 Copynumber: 1.9 Consensus size: 57
18130 TGCTTCTTAC
* * *
18140 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGTTTTCGTGCTGGAACT
1 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGATTCCATGCTGGAACT
18197 TGATT-TGC-TTGTTTTCATGCTGGA-ACTTGATTTGCTTCGATTCCATGCTG
1 TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTT-GATTCCATGCTG
18247 AATTGACCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 13 0.28
55 25 0.54
56 3 0.07
57 5 0.11
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (57 bp):
TGATTCTGCTTTGTTTTCATGCTGGACACTTGATTTGCTTGATTCCATGCTGGAACT
Done.