Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003563.1 Hibiscus syriacus cultivar Beakdansim tig00007521_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: 55590
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Found at i:21 original size:7 final size:7
Alignment explanation
Indices: 6--147 Score: 80
Period size: 7 Copynumber: 20.1 Consensus size: 7
1 AGAAC
6 AAAAAAT
1 AAAAAAT
*
13 AAAATAT
1 AAAAAAT
20 AAAAAAT
1 AAAAAAT
27 AAAAAAT
1 AAAAAAT
34 AAATAAAT
1 AAA-AAAT
*
42 AATAACCA-
1 AA-AA-AAT
50 AAAAAAT
1 AAAAAAT
57 -AAAAAT
1 AAAAAAT
*
63 AAATAAT
1 AAAAAAT
70 AAATAAAT
1 AAA-AAAT
*
78 -AAAAAG
1 AAAAAAT
**
84 AAAAAGG
1 AAAAAAT
91 AAAAAA-
1 AAAAAAT
***
97 ATTTAAT
1 AAAAAAT
*
104 ACAAAATT
1 A-AAAAAT
112 AAAGAAA-
1 AAA-AAAT
*
119 AAATAAT
1 AAAAAAT
126 AAAAAAT
1 AAAAAAT
133 -AAAAAT
1 AAAAAAT
139 AAAATAAT
1 AAAA-AAT
147 A
1 A
148 TTAATAAAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
6 21 0.20
7 59 0.57
8 21 0.20
9 2 0.02
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:30 original size:6 final size:6
Alignment explanation
Indices: 7--247 Score: 70
Period size: 6 Copynumber: 38.0 Consensus size: 6
1 AGAACA
* *
7 AAAAAT AAAATAT AAAAAAT AAAAA- ATAAAT AAATAAT AACCAA- AAAAAT
1 AAAAAT AAAA-AT -AAAAAT AAAAAT AAAAAT AAA-AAT AA-AAAT AAAAAT
* * *
57 AAAAAT AAATAAT AAATAAAT AAAAAG AAAAAGG AAAAA- AATTTAAT
1 AAAAAT AAA-AAT -AA-AAAT AAAAAT AAAAA-T AAAAAT AA--AAAT
*
104 ACAAAATT AAAGAAA AAATAAT AAAAAAT AAAAAT -AAAAT AATATTAAT
1 A-AAAA-T AAA-AAT AAA-AAT -AAAAAT AAAAAT AAAAAT AA-A--AAT
* * * * *
153 -AAAAT AGATAAAT AGAGAT --AAAT AAAATTT AGTAAAAT AATAAT AATAAT
1 AAAAAT A-A-AAAT AAAAAT AAAAAT AAAA-AT A--AAAAT AAAAAT AAAAAT
* * * *
203 AATAAT GAAAAT AAAAAT -AAAAT -AAACT AAATA- AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
248 GGTTAAATAT
Statistics
Matches: 181, Mismatches: 23, Indels: 62
0.68 0.09 0.23
Matches are distributed among these distances:
4 3 0.02
5 29 0.16
6 75 0.41
7 41 0.23
8 25 0.14
9 8 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:31 original size:15 final size:15
Alignment explanation
Indices: 6--63 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1 AGAAC
6 AAAAAAT-AAAATAT
1 AAAAAATAAAAATAT
20 AAAAAATAAAAA-AT
1 AAAAAATAAAAATAT
**
34 AAATAAATAATAACCA-
1 AAA-AAATAA-AAATAT
50 AAAAAATAAAAATA
1 AAAAAATAAAAATA
64 AATAATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.41
15 16 0.43
16 5 0.14
17 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATAAAAATAT
Found at i:38 original size:25 final size:24
Alignment explanation
Indices: 6--87 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 24
1 AGAAC
6 AAAAAATAAA-ATATAAAAAATAAA
1 AAAAAATAAATA-ATAAAAAATAAA
30 AAATAAATAAATAATAACCAAAA-AAA
1 AAA-AAATAAATAATAA--AAAATAAA
*
56 TAAAAATAAATAATAAATAAATAAA
1 AAAAAATAAATAATAAA-AAATAAA
81 AAGAAAA
1 AA-AAAA
88 AGGAAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
23 1 0.02
24 6 0.12
25 28 0.57
26 10 0.20
27 4 0.08
ACGTcount: A:0.79, C:0.02, G:0.01, T:0.17
Consensus pattern (24 bp):
AAAAAATAAATAATAAAAAATAAA
Found at i:39 original size:11 final size:11
Alignment explanation
Indices: 9--244 Score: 80
Period size: 11 Copynumber: 20.3 Consensus size: 11
1 AGAACAAA
*
9 AAATAAAATAT
1 AAATAAAAAAT
20 AAA-AAATAAA-
1 AAATAAA-AAAT
30 AAATAAATAAAT
1 AAATAAA-AAAT
42 -AATAACCAAAA-
1 AAATAA--AAAAT
53 AAAT-AAAAAT
1 AAATAAAAAAT
*
63 AAATAATAAAT
1 AAATAAAAAAT
*
74 AAATAAAAAGAA
1 AAATAAAAA-AT
*
86 AAAGGAAAAAAATT
1 AAA--TAAAAAA-T
* *
100 TAATACAAAATT
1 AAATA-AAAAAT
*
112 AAAGAAAAAAT
1 AAATAAAAAAT
123 -AATAAAAAAT
1 AAATAAAAAAT
133 AAA-AATAAAAT
1 AAATAA-AAAAT
144 AATATTAATAAAAT
1 AA-A-TAA-AAAAT
*
158 AGATAAATAGAGAT
1 AAATAAA-A-A-AT
*
172 AAAT-AAAATT
1 AAATAAAAAAT
* *
182 TAGTAAAATAAT
1 AAATAAAA-AAT
194 -AATAATAATAAT
1 AAATAA-AA-AAT
206 -AATGAAAATAA-
1 AAAT-AAAA-AAT
217 AAATAAAATAAACT
1 AAAT-AAA-AAA-T
231 AAATAAAAAAT
1 AAATAAAAAAT
242 AAA
1 AAA
245 AATGGTTAAA
Statistics
Matches: 175, Mismatches: 21, Indels: 58
0.69 0.08 0.23
Matches are distributed among these distances:
9 4 0.02
10 24 0.14
11 58 0.33
12 48 0.27
13 16 0.09
14 25 0.14
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:97 original size:36 final size:35
Alignment explanation
Indices: 20--98 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
10 AATAAAATAT
*
20 AAAAAATAAAAAATAAATAAATAATAACCAAAAAA
1 AAAAAATAAAAAATAAATAAATAATAAACAAAAAA
* *
55 ATAAAAATAAATAATAAATAAATAA-AAAGAAAAAGGA
1 A-AAAAATAAAAAATAAATAAATAATAAACAAAAA--A
92 AAAAAAT
1 AAAAAAT
99 TTAATACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
35 8 0.21
36 28 0.74
37 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (35 bp):
AAAAAATAAAAAATAAATAAATAATAAACAAAAAA
Found at i:2222 original size:85 final size:84
Alignment explanation
Indices: 2035--2354 Score: 385
Period size: 85 Copynumber: 3.8 Consensus size: 84
2025 TGTCGTCGAC
* * ** * * *
2035 CTGAATGGAATCGAACTCGATA-GTGTTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATGCTA
1 CTGAATGTAATCGAACTCGA-AGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTG
*
2099 TAAA-TTGACATGTCC-TTGAG
64 TAAATTTGATATG-CCTTTGAG
* * * *
2119 CTGAATGTAATCGAACTCGTAGGTATTTATTGACATATAACCCTTCTCGCCTTGAGTTATGCTGT
1 CTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
2184 AAATTTGATATGCCTTTGAG
65 AAATTTGATATGCCTTTGAG
* * * *
2204 CTGAATGTAATCGAACTCGAAGGTCTTGGTTGATAGATAACCCTTCTTGCCTTGAGCTATGTTGT
1 CTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
*
2269 AAATTTGATATGCCTTTGAA
65 AAATTTGATATGCCTTTGAG
* * *
2289 CTGAATGTAATCGAACTCAAAGGTTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGT
1 CTGAATGTAATCGAACTCGAAGGTTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
2354 A
65 A
2355 CTTGGTTGGG
Statistics
Matches: 204, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
83 1 0.00
84 58 0.28
85 145 0.71
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (84 bp):
CTGAATGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTA
AATTTGATATGCCTTTGAG
Found at i:2670 original size:64 final size:65
Alignment explanation
Indices: 2483--2725 Score: 327
Period size: 64 Copynumber: 3.8 Consensus size: 65
2473 GTGAAGTTGA
* * * *
2483 GCTTTGAGTTGGATATCCTTCGCTGTGAAGTTGAAATCCAA---GGA-T-TGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* * * * *
2543 GTTTTGAGTTGGATATCCTTCATCGTGAAGTTAAAATCCAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* *
2608 GCTTTGAGTTGGATATCATTCGTTGTG-ATTTGAAATCCGATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
* *
2672 GCTTTGAGTTAGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGTGTAAGTT
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTT
2726 GCGTTATTTT
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
60 36 0.23
63 2 0.01
64 61 0.38
65 60 0.38
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (65 bp):
GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
Found at i:2834 original size:124 final size:125
Alignment explanation
Indices: 2698--2930 Score: 393
Period size: 124 Copynumber: 1.9 Consensus size: 125
2688 CATTCGTTGT
* *
2698 GAAGTTGAAATCCAATCTTGTGTAAGTTGCGTTATTTT-GAGTCCAATATCCTTTGCTGTGAAGT
1 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATT-TTTTCGAGTCCAATATCCTTCGCTGTGAAGT
2762 TGAA-ATTGACTCTGAATG-AACTGGAA-AGTTGTTTGTTGACAGACGCTCATCGTTGTGAAG
65 T-AATATTGACTCTGAATGAAACTGGAACA-TTGTTTGTTGACAGACGCTCATCGTTGTGAAG
2822 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
1 GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
2887 AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGAC
66 AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGAC
2931 AGTTTTTCTC
Statistics
Matches: 103, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
123 6 0.06
124 72 0.70
125 24 0.23
126 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (125 bp):
GAAGTTGAAATCCAATCTTGTGTAAGTTGCATTTTTTCGAGTCCAATATCCTTCGCTGTGAAGTT
AATATTGACTCTGAATGAAACTGGAACATTGTTTGTTGACAGACGCTCATCGTTGTGAAG
Found at i:4619 original size:19 final size:16
Alignment explanation
Indices: 4588--4671 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 16
4578 TTTTCTTCGC
* *
4588 TTTTTCCTTTATTTTT
1 TTTTTTCTTTTTTTTT
* *
4604 GTTTATCTTTTTTATTT
1 TTTTTTCTTTTTT-TTT
4621 TCTCTTTTCTTTTTCTTTGTT
1 T-T-TTTTC-TTTT-TTT-TT
4642 TTTTTTCTTTTTTTCTT
1 TTTTTTCTTTTTTT-TT
4659 TTTTTCTCTTTTT
1 TTTTT-TCTTTTT
4672 GTTCTGATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.17
17 13 0.24
18 12 0.22
19 9 0.17
20 6 0.11
21 5 0.09
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:4628 original size:7 final size:6
Alignment explanation
Indices: 4599--4671 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
4589 TTTTCCTTTA
* * *
4599 TTTTTG TTTATC TTTTT- TATTTTC TCTTTTC TTTTTC TTTGTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC T-TTTTC TTTTTC TTT-TTC TTTTTC
4649 TTTTT- TTCTTT- TTTTCTC TTTTT
1 TTTTTC TT-TTTC TTTT-TC TTTTT
4672 GTTCTGATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
5 5 0.09
6 34 0.62
7 16 0.29
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:4628 original size:13 final size:11
Alignment explanation
Indices: 4599--4663 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 11
4589 TTTTCCTTTA
*
4599 TTTTTGTTTATC
1 TTTTT-TTTTTC
4611 TTTTTTATTTTC
1 TTTTTT-TTTTC
4623 TCTTTTCTTTTTC
1 T-TTTT-TTTTTC
*
4636 TTTGTTTTTT-
1 TTTTTTTTTTC
*
4646 TTCTTTTTTTC
1 TTTTTTTTTTC
4657 TTTTTTT
1 TTTTTTT
4664 CTCTTTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
10 8 0.18
11 12 0.27
12 13 0.30
13 10 0.23
14 1 0.02
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4628 original size:25 final size:26
Alignment explanation
Indices: 4600--4659 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
4590 TTTCCTTTAT
*
4600 TTTTGTTTATCTTT-TTTATTTTCTC
1 TTTTCTTTATCTTTGTTTATTTTCTC
* * *
4625 TTTTCTTTTTCTTTGTTTTTTTTCTTT
1 TTTTCTTTATCTTTGTTTATTTTC-TC
4652 TTTTCTTT
1 TTTTCTTT
4660 TTTTCTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.41
26 8 0.28
27 9 0.31
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (26 bp):
TTTTCTTTATCTTTGTTTATTTTCTC
Found at i:4635 original size:42 final size:42
Alignment explanation
Indices: 4587--4670 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
4577 TTTTTCTTCG
4587 CTTTTTCCTTTATTTTTGTTT-ATCTTTT-TTATTTTCTCTTTT
1 CTTTTT-CTTTATTTTT-TTTCATCTTTTCTTATTTTCTCTTTT
* * * *
4629 CTTTTTCTTTGTTTTTTTTCTTTTTTTCTTTTTTTCTCTTTT
1 CTTTTTCTTTATTTTTTTTCATCTTTTCTTATTTTCTCTTTT
4671 TGTTCTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.08
41 14 0.39
42 19 0.53
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (42 bp):
CTTTTTCTTTATTTTTTTTCATCTTTTCTTATTTTCTCTTTT
Found at i:4654 original size:8 final size:8
Alignment explanation
Indices: 4641--4671 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
4631 TTTTCTTTGT
4641 TTTTTTTC
1 TTTTTTTC
4649 TTTTTTTC
1 TTTTTTTC
4657 TTTTTTTC
1 TTTTTTTC
*
4665 TCTTTTT
1 TTTTTTT
4672 GTTCTGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4670 original size:27 final size:27
Alignment explanation
Indices: 4625--4676 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4615 TTATTTTCTC
* *
4625 TTTTCTTTTTCTTTGTTTTTTTTCTTT
1 TTTTCTTTTTCTTTCTTTTTGTTCTTT
4652 TTTTCTTTTT-TTCTCTTTTTGTTCT
1 TTTTCTTTTTCTT-TCTTTTTGTTCT
4677 GATTGGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (27 bp):
TTTTCTTTTTCTTTCTTTTTGTTCTTT
Found at i:4671 original size:11 final size:10
Alignment explanation
Indices: 4613--4671 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
4603 TGTTTATCTT
4613 TTTTATTTTCTC
1 TTTT-TTTT-TC
4625 TTTTCTTTTTC
1 TTTT-TTTTTC
4636 TTTGTTTTTT-
1 TTT-TTTTTTC
4646 TTCTTTTTTTC
1 TT-TTTTTTTC
*
4657 TTTTTTTCTC
1 TTTTTTTTTC
4667 TTTTT
1 TTTTT
4672 GTTCTGATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 20 0.48
11 13 0.31
12 9 0.21
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:7633 original size:13 final size:13
Alignment explanation
Indices: 7617--7646 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7607 TTTAATTACG
7617 AAAATTAAAAATT
1 AAAATTAAAAATT
*
7630 AAAATTAAAATTT
1 AAAATTAAAAATT
7643 AAAA
1 AAAA
7647 ACCCGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:7766 original size:4 final size:4
Alignment explanation
Indices: 7736--7822 Score: 53
Period size: 4 Copynumber: 22.8 Consensus size: 4
7726 TCTAAGAACA
* * *
7736 AAAT AAA- AAAT AAA- AAAT AACT AAAT AAAT AAA- ATAAT AAACC AAAGG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAA-T AAA-T
* *
7784 AAA- AAAG AGA- AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
7823 AAAGTCAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
3 16 0.24
4 44 0.66
5 7 0.10
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (4 bp):
AAAT
Found at i:7876 original size:11 final size:12
Alignment explanation
Indices: 7862--7995 Score: 56
Period size: 12 Copynumber: 9.8 Consensus size: 12
7852 AATTAAAGAC
*
7862 AAATAACAAA-A
1 AAATAAAAAATA
7873 AAATAAAAAATA
1 AAATAAAAAATA
*
7885 AAATAATAATATTA
1 AAATAA-AA-AATA
7899 AAATAAATAAAATAGA
1 AAAT-AA-AAAAT--A
7915 TAAATAGAGATAAATA
1 -AAATA-A-A-AAATA
*
7931 AAATTTAGTAAAATA
1 AAA--TA-AAAAATA
7946 ATAATAATAATAATGA
1 A-AATAA-AA-AAT-A
7962 AAATAAAAAATA
1 AAATAAAAAATA
7974 AAATAAAATAA-A
1 AAATAAAA-AATA
7986 AAATGAAAAA
1 AAAT-AAAAA
7996 GGGTTAAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 33
0.72 0.04 0.24
Matches are distributed among these distances:
11 9 0.09
12 22 0.22
13 11 0.11
14 15 0.15
15 22 0.22
16 8 0.08
17 9 0.09
18 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:7906 original size:23 final size:23
Alignment explanation
Indices: 7880--7934 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
7870 AAAAAATAAA
7880 AAATAAAATA-ATAATATTA-AAAT
1 AAATAAAATAGATAA-A-TAGAAAT
*
7903 AAATAAAATAGATAAATAGAGAT
1 AAATAAAATAGATAAATAGAAAT
7926 AAATAAAAT
1 AAATAAAAT
7935 TTAGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.79
24 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (23 bp):
AAATAAAATAGATAAATAGAAAT
Found at i:7973 original size:53 final size:55
Alignment explanation
Indices: 7883--7986 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 55
7873 AAATAAAAAA
* *
7883 TAAAATAATAATATTAAAATAAATAAAATAGATAAATAGAGAT-AAATAAAATTTAG
1 TAAAATAATAATA-TAAAATAAATAAAATAGAAAAATA-AAATAAAATAAAATTTAG
*
7939 TAAAATAATAATA-ATAAT-AATGAAAATA-AAAAATAAAATAAAATAAAA
1 TAAAATAATAATATAAAATAAAT-AAAATAGAAAAATAAAATAAAATAAAA
7987 AATGAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
52 3 0.07
53 17 0.40
54 10 0.23
56 13 0.30
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (55 bp):
TAAAATAATAATATAAAATAAATAAAATAGAAAAATAAAATAAAATAAAATTTAG
Found at i:8045 original size:4 final size:4
Alignment explanation
Indices: 8036--8062 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8026 AATGTTACGA
8036 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
8063 AGGGATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:11104 original size:37 final size:37
Alignment explanation
Indices: 11054--11125 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
11044 GGTGGCATGG
11054 ATAACAGTTACTGATGTGGTTTGTCACTCCAAAACAA
1 ATAACAGTTACTGATGTGGTTTGTCACTCCAAAACAA
*
11091 ATAACGGTTACTGATGTGGTTTGTCACTCCAAAAC
1 ATAACAGTTACTGATGTGGTTTGTCACTCCAAAAC
11126 GATTTTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (37 bp):
ATAACAGTTACTGATGTGGTTTGTCACTCCAAAACAA
Found at i:13964 original size:29 final size:29
Alignment explanation
Indices: 13900--13955 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
13890 TTTGGACTCA
*
13900 AATTTAATTAAAATTCATTTTAATCGTCT
1 AATTTAATTAAAATTCATTTTAATCATCT
*
13929 AATTTAATTGAAATTCATTTTAATCAT
1 AATTTAATTAAAATTCATTTTAATCAT
13956 TGAGATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (29 bp):
AATTTAATTAAAATTCATTTTAATCATCT
Found at i:17820 original size:14 final size:13
Alignment explanation
Indices: 17795--17828 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17785 GAAAAAGGAG
17795 GAAAAATGAGAGA
1 GAAAAATGAGAGA
17808 GAAAAATGTAGAGA
1 GAAAAATG-AGAGA
17822 GAGAAAA
1 GA-AAAA
17829 GCTGAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 7 0.37
15 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.09
Consensus pattern (13 bp):
GAAAAATGAGAGA
Found at i:21445 original size:128 final size:128
Alignment explanation
Indices: 21217--21479 Score: 508
Period size: 128 Copynumber: 2.0 Consensus size: 128
21207 CCGTCTGTAA
*
21217 TTAAGGCTACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
1 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
21282 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
66 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
21345 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
1 TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
21410 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
66 GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
21473 TCTAAGG
1 T-TAAGG
21480 AAATATGGGA
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
128 128 0.96
129 5 0.04
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (128 bp):
TTAAGGCCACTGTCAGGGATCATTTCTTTAAAACTTTTAATGATCGGTCTACATTGGAAGTTGAT
GACATAAGGTTGAATTTTTCCAGAATTTCTTTGGAGCAGAGTCTGTTTTTAGAAAAAGAATTT
Found at i:28647 original size:12 final size:12
Alignment explanation
Indices: 28630--28654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28620 TCAGTTTGGC
28630 ATTGTTTTTTAA
1 ATTGTTTTTTAA
28642 ATTGTTTTTTAA
1 ATTGTTTTTTAA
28654 A
1 A
28655 AGTTCGATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATTGTTTTTTAA
Found at i:29001 original size:27 final size:27
Alignment explanation
Indices: 28949--29001 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28939 AATTATTAAA
* *
28949 AGTAATAAATTATTTTTTAAAGATGTT
1 AGTAATAAATTATTATATAAAGATGTT
*
28976 AGTATTAAATTATTAATATAAA-ATGT
1 AGTAATAAATTATT-ATATAAAGATGT
29002 ATTATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (27 bp):
AGTAATAAATTATTATATAAAGATGTT
Found at i:30998 original size:21 final size:21
Alignment explanation
Indices: 30954--30998 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30944 GATTTCTGGG
* * *
30954 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
30975 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
30996 CAA
1 CAA
30999 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:31376 original size:24 final size:24
Alignment explanation
Indices: 31332--31379 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31322 CCTATGTTTA
*
31332 ATGCATGAATATGATTATATGTAT
1 ATGCATGAATATAATTATATGTAT
*
31356 ATGCATGACATA-AATTGTATGTAT
1 ATGCATGA-ATATAATTATATGTAT
31380 GCATGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGCATGAATATAATTATATGTAT
Found at i:31948 original size:31 final size:31
Alignment explanation
Indices: 31890--31967 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
31880 AGAGTCAAGG
*
31890 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
31921 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
*
31952 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
31968 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:31974 original size:30 final size:30
Alignment explanation
Indices: 31940--32218 Score: 506
Period size: 30 Copynumber: 9.3 Consensus size: 30
31930 GGTTCTTCGG
*
31940 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
31970 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
32000 GACCTCTTGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32030 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32060 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32090 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32120 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32150 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
32180 GACCTCTGGATAGTTACC-AGGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
32209 GACCTCTGGA
1 GACCTCTGGA
32219 TAGGTCCTTC
Statistics
Matches: 243, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
29 19 0.08
30 224 0.92
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:32501 original size:2 final size:2
Alignment explanation
Indices: 32491--32546 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
32481 GTATGTGTGG
*
32491 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
32533 AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT
32547 GAAAGGTGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35389 original size:21 final size:21
Alignment explanation
Indices: 35345--35389 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35335 GATTTCTGGG
* * *
35345 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
35366 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
35387 CAA
1 CAA
35390 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:36341 original size:31 final size:31
Alignment explanation
Indices: 36283--36360 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
36273 AGAGTCGAGG
*
36283 GTTTACCTATGTCTTTCGAGACATATGGAAA
1 GTTTACCTAGGTCTTTCGAGACATATGGAAA
* * *
36314 GTTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTAGGTCT-TTCGAGACATATGGAAA
*
36345 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
36361 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGAAA
Found at i:36367 original size:30 final size:30
Alignment explanation
Indices: 36333--36641 Score: 566
Period size: 30 Copynumber: 10.3 Consensus size: 30
36323 GGTTCTTCGG
*
36333 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36363 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36393 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36423 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
36453 GACCTCTGGACAGTTACCAAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36483 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36513 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36543 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36573 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
36603 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
36632 GACCTCTGGA
1 GACCTCTGGA
36642 TAGGTCCTTC
Statistics
Matches: 273, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
29 18 0.07
30 255 0.93
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:36924 original size:2 final size:2
Alignment explanation
Indices: 36914--36955 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
36904 GTATGTGTGG
* *
36914 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36956 GAAAGGTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38354 original size:22 final size:20
Alignment explanation
Indices: 38304--38375 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
38294 GTAAAAATGA
38304 TATCGATACCAT-G-ATAGGG
1 TATCGATACCATAGTA-AGGG
*
38323 TATC-AGTACCATAGTATGGTAG
1 TATCGA-TACCATAGTAAGG--G
*
38345 TATCGATACCATGGTAAGGG
1 TATCGATACCATAGTAAGGG
38365 TATCGATACCA
1 TATCGATACCA
38376 GGAAACATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.02
19 10 0.23
20 15 0.34
21 1 0.02
22 16 0.36
23 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
TATCGATACCATAGTAAGGG
Found at i:38971 original size:47 final size:47
Alignment explanation
Indices: 38920--39194 Score: 392
Period size: 47 Copynumber: 5.9 Consensus size: 47
38910 AATTGAAAAT
* *
38920 GCATGAAAGGATGCCATAATTGAAAATCCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * *
38967 GCATGAAAAGATGCCATAATTGAAAATGCATGAAAGGATACATAAAG
1 GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * * *
39014 GCATGAAAGGATGTCATAATTTAAAATGCATGAAAGGGTGCATTACG
1 GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
* * *
39061 ACATGAAATGATGCCATAATTGAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
*
39108 GCATGAAAGGATGTCATAATTGAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
*
39155 GCATGAAAGGATGTCATAAGTT-AAAATGCAT-AAATGGATG
1 GCATGAAAGGATGCCATAA-TTGAAAATGCATGAAA-GGATG
39195 TGTTAATACG
Statistics
Matches: 203, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
46 3 0.01
47 198 0.98
48 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (47 bp):
GCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAG
Found at i:39045 original size:27 final size:26
Alignment explanation
Indices: 38893--39195 Score: 173
Period size: 27 Copynumber: 12.5 Consensus size: 26
38883 ATGCATTAAG
38893 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATGTCATAATT-AAAAT
*
38920 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGTCATAATT-AAAAT
* * *
38947 CCATGAAATGATG-C---ATT--AAG
1 GCATGAAAGGATGTCATAATTAAAAT
* *
38967 GCATGAAAAGATGCCATAATTGAAAAT
1 GCATGAAAGGATGTCATAATT-AAAAT
* *
38994 GCATGAAAGGA--T-A-CA-T-AAAG
1 GCATGAAAGGATGTCATAATTAAAAT
39014 GCATGAAAGGATGTCATAATTTAAAAT
1 GCATGAAAGGATGTCATAA-TTAAAAT
* **
39041 GCATGAAAGGGTG-C---ATTACGA-
1 GCATGAAAGGATGTCATAATTAAAAT
* *
39062 -CATGAAATGATGCCATAATTGAAAAT
1 GCATGAAAGGATGTCATAATT-AAAAT
* *
39088 GCATGAAATGATG-C---ATT--AAG
1 GCATGAAAGGATGTCATAATTAAAAT
39108 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATGTCATAATT-AAAAT
*
39135 GCATGAAAGGATG-C---ATT--AAG
1 GCATGAAAGGATGTCATAATTAAAAT
39155 GCATGAAAGGATGTCATAAGTTAAAAT
1 GCATGAAAGGATGTCATAA-TTAAAAT
39182 GCAT-AAATGGATGT
1 GCATGAAA-GGATGT
39196 GTTAATACGT
Statistics
Matches: 215, Mismatches: 25, Indels: 72
0.69 0.08 0.23
Matches are distributed among these distances:
20 66 0.31
21 4 0.02
22 6 0.03
23 12 0.06
24 12 0.06
25 4 0.02
26 8 0.04
27 103 0.48
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (26 bp):
GCATGAAAGGATGTCATAATTAAAAT
Found at i:39127 original size:141 final size:141
Alignment explanation
Indices: 38921--39185 Score: 467
Period size: 141 Copynumber: 1.9 Consensus size: 141
38911 ATTGAAAATG
38921 CATGAAAGGATGCCATAATTGAAAATCCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAA
1 CATGAAAGGATGCCATAATTGAAAATCCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAA
*
38986 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAATTTAAAATGCATGAAAGG
66 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCATGAAAGG
39051 GTGCATTACGA
131 GTGCATTACGA
* * * *
39062 CATGAAATGATGCCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAA
1 CATGAAAGGATGCCATAATTGAAAATCCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAA
* *
39127 TTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAGTTAAAATGCAT
66 TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCAT
39186 AAATGGATGT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 117 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (141 bp):
CATGAAAGGATGCCATAATTGAAAATCCATGAAATGATGCATTAAGGCATGAAAAGATGCCATAA
TTGAAAATGCATGAAAGGATACATAAAGGCATGAAAGGATGTCATAAGTTAAAATGCATGAAAGG
GTGCATTACGA
Found at i:39174 original size:20 final size:20
Alignment explanation
Indices: 39088--39167 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 20
39078 AATTGAAAAT
*
39088 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
39108 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
39135 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
39155 GCATGAAAGGATG
1 GCATGAAAGGATG
39168 TCATAAGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
20 27 0.54
21 1 0.02
23 3 0.06
24 3 0.06
26 1 0.02
27 15 0.30
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:45215 original size:28 final size:28
Alignment explanation
Indices: 45175--45235 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
45165 GTTTTTCCCT
45175 ATTATTGTTCTTTTGCATTATCTAACAC
1 ATTATTGTTCTTTTGCATTATCTAACAC
*
45203 ATTATTGTTCTTTTTCATTATCTAACAC
1 ATTATTGTTCTTTTGCATTATCTAACAC
45231 ATTAT
1 ATTAT
45236 CTAACTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTATTGTTCTTTTGCATTATCTAACAC
Found at i:50713 original size:20 final size:20
Alignment explanation
Indices: 50665--50718 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
50655 ATGTAAAAAT
*
50665 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTAAG
50685 GTAGTATCGATACCAT-GATAAG
1 G--GTATCGATACCATAG-TAAG
50707 GGTATCGATACC
1 GGTATCGATACC
50719 TGGCAACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 17 0.57
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:51277 original size:47 final size:47
Alignment explanation
Indices: 51203--51508 Score: 447
Period size: 47 Copynumber: 6.5 Consensus size: 47
51193 TAAATCGAAT
* *
51203 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
51250 -CTATAATTGAAATTGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 TC-ATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
51297 TCATAATTGAAAACGCATGAAATGATGCATTTAGGCATGAAAGGATG
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * * *
51344 CCATAATTTAAAATGCATGAAAGGATGCTTTAAGGCATGAAAAGATG
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
51391 TCATAATTAAAAATACATGAAATGATGCATTAAGGCATGAAAGGATG
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
51438 TCATAATTGAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATG
1 TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
51485 TCATAAATT-AAAATGCAT-AAATGA
1 TCAT-AATTGAAAATGCATGAAATGA
51509 ATATGTTAAT
Statistics
Matches: 232, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
46 6 0.03
47 221 0.95
48 5 0.02
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (47 bp):
TCATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:51315 original size:27 final size:25
Alignment explanation
Indices: 51204--51463 Score: 102
Period size: 20 Copynumber: 11.0 Consensus size: 25
51194 AAATCGAATT
*
51204 CATAATTAAAAATGCATGAAAGGATG
1 CATAATT-AAAACGCATGAAAGGATG
*
51230 C---ATT--AAGGCATGAAAGGATG
1 CATAATTAAAACGCATGAAAGGATG
** *
51250 CTATAATTGAAATTGCATGAAATGATG
1 C-ATAATT-AAAACGCATGAAAGGATG
*
51277 C---ATT--AAGGCATGAAAGGATG
1 CATAATTAAAACGCATGAAAGGATG
*
51297 TCATAATTGAAAACGCATGAAATGATG
1 -CATAATT-AAAACGCATGAAAGGATG
*
51324 CAT--TT---AGGCATGAAAGGATG
1 CATAATTAAAACGCATGAAAGGATG
*
51344 CCATAATTTAAAATGCATGAAAGGATG
1 -CATAA-TTAAAACGCATGAAAGGATG
* *
51371 C-T--TT--AAGGCATGAAAAGATG
1 CATAATTAAAACGCATGAAAGGATG
** *
51391 TCATAATTAAAAATACATGAAATGATG
1 -CATAATT-AAAACGCATGAAAGGATG
*
51418 C---ATT--AAGGCATGAAAGGATG
1 CATAATTAAAACGCATGAAAGGATG
*
51438 TCATAATTGAAAATGCATGAAAGGAT
1 -CATAATT-AAAACGCATGAAAGGAT
51464 ACATTAAGGC
Statistics
Matches: 178, Mismatches: 21, Indels: 69
0.66 0.08 0.26
Matches are distributed among these distances:
20 69 0.39
21 6 0.03
22 3 0.02
23 9 0.05
24 15 0.08
25 1 0.01
26 6 0.03
27 69 0.39
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (25 bp):
CATAATTAAAACGCATGAAAGGATG
Done.