Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008289.1 Hibiscus syriacus cultivar Beakdansim tig00110952_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: 518235
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:9898 original size:18 final size:18
Alignment explanation
Indices: 9877--9918 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
9867 ACTTCTCTTT
*
9877 TTCTTTTCT-TTTCTTTTC
1 TTCTTTTCTGATT-TTTTC
9895 TTCTTTTCTGATTTTTTC
1 TTCTTTTCTGATTTTTTC
9913 TTCTTT
1 TTCTTT
9919 CTGCACCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (18 bp):
TTCTTTTCTGATTTTTTC
Found at i:12198 original size:11 final size:11
Alignment explanation
Indices: 12182--12206 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12172 TATCAAAAAT
12182 AAGTGCAAGTG
1 AAGTGCAAGTG
12193 AAGTGCAAGTG
1 AAGTGCAAGTG
12204 AAG
1 AAG
12207 AAATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
AAGTGCAAGTG
Found at i:12280 original size:24 final size:23
Alignment explanation
Indices: 12231--12280 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
12221 CAAATAAATC
**
12231 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
12254 AAAGCACTCAAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
12278 AAA
1 AAA
12281 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:12298 original size:4 final size:5
Alignment explanation
Indices: 12264--12301 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
12254 AAAGCACTCA
*
12264 AAAAG AAGA- AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
12302 TTGAAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:18734 original size:28 final size:28
Alignment explanation
Indices: 18702--18757 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
18692 CGTGAATTAA
18702 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
18730 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
18758 TGAATGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGCTGTTATG
Found at i:22435 original size:24 final size:21
Alignment explanation
Indices: 22401--22443 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
22391 TCCACAAGAC
*
22401 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
22423 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
22444 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:24830 original size:16 final size:16
Alignment explanation
Indices: 24809--24841 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24799 TTCTGCCACC
24809 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
24825 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
24841 T
1 T
24842 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:32451 original size:19 final size:18
Alignment explanation
Indices: 32429--32475 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
32419 AGTGAATAAT
32429 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
32448 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
32467 AATA-AAGAA
1 AATATAAGAA
32476 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:39391 original size:18 final size:18
Alignment explanation
Indices: 39370--39412 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39360 ACTTCTCTTT
*
39370 TTCTTTTCT-TTTCTTTTC
1 TTCTTTTCTGATT-TTTTC
39388 TTCTTTTCTGATTTTTTC
1 TTCTTTTCTGATTTTTTC
39406 TTCTTTT
1 TTCTTTT
39413 TGCACCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
TTCTTTTCTGATTTTTTC
Found at i:42972 original size:16 final size:16
Alignment explanation
Indices: 42953--42985 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42943 TCTTTTTCTT
*
42953 TTCTTTTCTTATTTTC
1 TTCTTTTCTGATTTTC
42969 TTCTTTTCTGATTTTC
1 TTCTTTTCTGATTTTC
42985 T
1 T
42986 AACTTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (16 bp):
TTCTTTTCTGATTTTC
Found at i:42993 original size:17 final size:16
Alignment explanation
Indices: 42955--42994 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
42945 TTTTTCTTTT
* *
42955 CTTTTCTTATTTTCTT
1 CTTTTCTGATTTTCTA
42971 CTTTTCTGATTTTCTAA
1 CTTTTCTGATTTTCT-A
42988 CTTTTCT
1 CTTTTCT
42995 CTTCTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (16 bp):
CTTTTCTGATTTTCTA
Found at i:43308 original size:19 final size:20
Alignment explanation
Indices: 43269--43308 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43259 TAATAATAAT
*
43269 ATAAGTAATGAAAAGAGATA
1 ATAAGTAATGAAAAGAAATA
*
43289 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
43308 A
1 A
43309 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:52933 original size:24 final size:21
Alignment explanation
Indices: 52899--52941 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
52889 TGTACAAGAT
*
52899 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
52921 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
52942 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:55759 original size:22 final size:24
Alignment explanation
Indices: 55731--55777 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
55721 AAATGGAATT
55731 TGGTGAT-GA-TATAGGCG-TGATA
1 TGGTGATGGACTAT-GGCGATGATA
55753 TGGTGATGGACTATGGCGATGATA
1 TGGTGATGGACTATGGCGATGATA
55777 T
1 T
55778 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.06, G:0.36, T:0.32
Consensus pattern (24 bp):
TGGTGATGGACTATGGCGATGATA
Found at i:55810 original size:36 final size:35
Alignment explanation
Indices: 55731--55810 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
55721 AAATGGAATT
**
55731 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAAGA
*
55766 TGGCGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAAGA
55802 TGGTGATGA
1 TGGTGATGA
55811 ACAGATTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.28, C:0.05, G:0.39, T:0.29
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAAGA
Found at i:59479 original size:17 final size:17
Alignment explanation
Indices: 59457--59489 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59447 CGGCTTAAAA
59457 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
59474 AAATGGTTATGGTATA
1 AAATGGTTAGGGTATA
59490 AGGGTAGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:60233 original size:35 final size:36
Alignment explanation
Indices: 60189--60268 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
60179 AAATGGAATT
* **
60189 TGGTAATGATATAGGCGTGAT-ATGGGGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGGGATGGAAGA
*
60224 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGGGATGGAAGA
60260 TGGTGATGA
1 TGGTGATGA
60269 ACAGATTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.29, C:0.04, G:0.39, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGGGATGGAAGA
Found at i:61714 original size:12 final size:12
Alignment explanation
Indices: 61697--61723 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61687 ACAAACAAAG
61697 AAAGGAGATATA
1 AAAGGAGATATA
61709 AAAGGAGATATA
1 AAAGGAGATATA
61721 AAA
1 AAA
61724 AGAAATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (12 bp):
AAAGGAGATATA
Found at i:62756 original size:29 final size:30
Alignment explanation
Indices: 62704--62765 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
62694 TCTTGTGAGC
* *
62704 TGTTTGTGTCTCCCAAATGCTCCACCAAGT
1 TGTTTGTCTCTCCAAAATGCTCCACCAAGT
*
62734 TGTTTGTCT-TCCAAAATGCTCCACTAAGT
1 TGTTTGTCTCTCCAAAATGCTCCACCAAGT
62763 TGT
1 TGT
62766 AAGTTTCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (30 bp):
TGTTTGTCTCTCCAAAATGCTCCACCAAGT
Found at i:62778 original size:29 final size:30
Alignment explanation
Indices: 62718--62783 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
62708 TGTGTCTCCC
**
62718 AAATGCTCCACCAAGTTGTTTGTCTTCC-A
1 AAATGCTCCACCAAGTTGTAAGTCTTCCAA
*
62747 AAATGCTCCACTAAGTTGTAAGT-TTCCTAA
1 AAATGCTCCACCAAGTTGTAAGTCTTCC-AA
62777 AAATGCT
1 AAATGCT
62784 TCATCAAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.12
29 20 0.62
30 8 0.25
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (30 bp):
AAATGCTCCACCAAGTTGTAAGTCTTCCAA
Found at i:64423 original size:19 final size:19
Alignment explanation
Indices: 64380--64417 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
64370 GCTATTTTTT
*
64380 TAAAAAAACAAAAAAAAGG
1 TAAAAAAACAAAAAAAAAG
64399 TAAAAAAACAAAAAAAAAG
1 TAAAAAAACAAAAAAAAAG
64418 ACAAAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (19 bp):
TAAAAAAACAAAAAAAAAG
Found at i:64423 original size:20 final size:19
Alignment explanation
Indices: 64381--64423 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
64371 CTATTTTTTT
**
64381 AAAAAAACAAAAAAAAGGT
1 AAAAAAACAAAAAAAAGAC
64400 AAAAAAACAAAAAAAAAGAC
1 AAAAAAAC-AAAAAAAAGAC
64420 AAAA
1 AAAA
64424 TTTCAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGAC
Found at i:68596 original size:19 final size:20
Alignment explanation
Indices: 68555--68605 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
68545 GAAACCCCTT
*
68555 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
68575 TGAAAATGCATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
68594 TGAAGATACATG
1 TGAAAATACATG
68606 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:72035 original size:11 final size:10
Alignment explanation
Indices: 71984--72035 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
71974 TTTTGAATTC
*
71984 TTTTCTTTTC
1 TTTTCTTTTT
71994 TTTTCTTCTTT
1 TTTTCTT-TTT
*
72005 TCTTCTTCTTT
1 TTTTCTT-TTT
*
72016 TTGTCTTTTT
1 TTTTCTTTTT
*
72026 CTTTCTTTTT
1 TTTTCTTTTT
72036 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:72036 original size:18 final size:18
Alignment explanation
Indices: 71982--72036 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
71972 CTTTTTGAAT
71982 TCTTTTCTTTTCTTTTCT-
1 TCTTTTCTTTTCTTTT-TG
72000 TCTTTTCTTCTTCTTTTTG
1 TCTTTTCTT-TTCTTTTTG
72019 TCTTTT-TCTTTCTTTTTG
1 TCTTTTCT-TTTCTTTTTG
72037 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTTG
Found at i:72783 original size:19 final size:20
Alignment explanation
Indices: 72742--72792 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
72732 GAAACCCCTT
*
72742 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
72762 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
72781 TGAAGATACATG
1 TGAAAATACATG
72793 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:80672 original size:19 final size:20
Alignment explanation
Indices: 80623--80673 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
80613 GCTTGCTTTC
80623 TCTTTTTCTTTTCTGAATTT
1 TCTTTTTCTTTTCTGAATTT
*
80643 T-TTTCTTCTTTT-TGTATTT
1 TCTTT-TTCTTTTCTGAATTT
*
80662 TCTTTTCCTTTT
1 TCTTTTTCTTTT
80674 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.75
Consensus pattern (20 bp):
TCTTTTTCTTTTCTGAATTT
Found at i:90682 original size:9 final size:9
Alignment explanation
Indices: 90670--90698 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
90660 TGATGAAGGG
90670 TGTTGATGA
1 TGTTGATGA
90679 TGTTGATGA
1 TGTTGATGA
90688 TGTTGATGA
1 TGTTGATGA
90697 TG
1 TG
90699 GAATGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (9 bp):
TGTTGATGA
Found at i:94089 original size:18 final size:17
Alignment explanation
Indices: 94066--94100 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
94056 TAGGTTAGGG
94066 TAGAAAGAATAGAAGAAA
1 TAGAAAG-ATAGAAGAAA
*
94084 TAGAAAGGTAGAAGAAA
1 TAGAAAGATAGAAGAAA
94101 GGATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAGAAGAAA
Found at i:98097 original size:18 final size:17
Alignment explanation
Indices: 98074--98108 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
98064 TAGGTTAGGG
98074 TAGAAAGAATAGAAGAAA
1 TAGAAAG-ATAGAAGAAA
*
98092 TAGAAAGGTAGAAGAAA
1 TAGAAAGATAGAAGAAA
98109 GGATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAGAAGAAA
Found at i:98706 original size:20 final size:21
Alignment explanation
Indices: 98669--98707 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
98659 GATGGTCTTG
*
98669 ATGAAGGATGTTGATGATGGA
1 ATGAAGGATGGTGATGATGGA
*
98690 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
98708 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGGA
Found at i:104794 original size:30 final size:31
Alignment explanation
Indices: 104758--104817 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
104748 CTTAGCTTTA
**
104758 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
104788 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
104818 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:105739 original size:19 final size:20
Alignment explanation
Indices: 105715--105765 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
105705 CGGCCAAGAG
* *
105715 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
105734 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
105754 AATGTATTTTCA
1 CATGTATTTTCA
105766 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:106204 original size:19 final size:20
Alignment explanation
Indices: 106180--106219 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
106170 TATCCTTTCT
106180 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
106199 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
106219 T
1 T
106220 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:106517 original size:23 final size:23
Alignment explanation
Indices: 106470--106528 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
106460 ATTGGGGTGC
106470 AAAAAGAAAGAAAAGACAAAAAG-
1 AAAAAGAAA-AAAAGACAAAAAGA
*
106493 AAAAAGAAAAAAA-ATCAGAATAGA
1 AAAAAGAAAAAAAGA-CA-AAAAGA
106517 AGAAAAGAAAAA
1 A-AAAAGAAAAA
106529 TGACAATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 13 0.42
24 1 0.03
25 10 0.32
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAAAAAGACAAAAAGA
Found at i:108992 original size:30 final size:31
Alignment explanation
Indices: 108947--109006 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
108937 CTTAGCTTTA
**
108947 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
108977 TATTGTGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
109007 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:109928 original size:19 final size:20
Alignment explanation
Indices: 109904--109954 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
109894 CGGCCAAGAG
* *
109904 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
109923 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
109943 CATGTATTTTCA
1 CATGTATTTTCA
109955 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:110411 original size:19 final size:19
Alignment explanation
Indices: 110369--110408 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
110359 TATCCTTTCT
*
110369 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATACTTA
*
110388 TTATTTCTTTTCACTACTTA
1 TTATTTCATTTCA-TACTTA
110408 T
1 T
110409 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTCATTTCATACTTA
Found at i:111380 original size:13 final size:12
Alignment explanation
Indices: 111361--111425 Score: 66
Period size: 13 Copynumber: 5.4 Consensus size: 12
111351 ATATAGGCGT
111361 GATATGGTGATG
1 GATATGGTGATG
111373 GAATATGGTGAT-
1 G-ATATGGTGATG
111385 GATATAGGTG-T-
1 GATAT-GGTGATG
111396 GATAATGGTGATG
1 GAT-ATGGTGATG
111409 GATTATGGTGAT-
1 GA-TATGGTGATG
111421 GATAT
1 GATAT
111426 AGGCGTGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
11 15 0.32
12 11 0.23
13 20 0.43
14 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:111398 original size:11 final size:12
Alignment explanation
Indices: 111344--111428 Score: 65
Period size: 13 Copynumber: 7.2 Consensus size: 12
111334 TTTATAAGTT
*
111344 GGTGATAATATA
1 GGTGATGATATA
*
111356 GGCG-TGATAT-
1 GGTGATGATATA
111366 GGTGATGGA-ATA
1 GGTGAT-GATATA
111378 TGGTGATGATATA
1 -GGTGATGATATA
111391 GGTG-TGATA-A
1 GGTGATGATATA
111401 TGGTGATGGAT-TA
1 -GGTGAT-GATATA
111414 TGGTGATGATATA
1 -GGTGATGATATA
111427 GG
1 GG
111429 CGTGAAAATG
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
10 4 0.07
11 17 0.28
12 17 0.28
13 22 0.37
ACGTcount: A:0.29, C:0.01, G:0.36, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:111416 original size:36 final size:36
Alignment explanation
Indices: 111343--111446 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
111333 ATTTATAAGT
*
111343 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
111378 TGGTGATGATATAGGTGTGATAATGGTGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
111414 TGGTGATGATATAGGCGTGAAAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
111447 CAGATTGTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:112330 original size:32 final size:32
Alignment explanation
Indices: 112292--112353 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
112282 ACAAAATTAA
112292 AAGAAA-GAAATGATTAA-AATGGAATATGGAAG
1 AAGAAAGGAAATG-TTAAGAATGGAA-ATGGAAG
*
112324 AAGAAAGGAAATGTTAAGAATTGAAATGGA
1 AAGAAAGGAAATGTTAAGAATGGAAATGGA
112354 TAAAAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (32 bp):
AAGAAAGGAAATGTTAAGAATGGAAATGGAAG
Found at i:117728 original size:11 final size:13
Alignment explanation
Indices: 117696--117725 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
117686 TGGCCAAAGA
117696 TGAAAAGGTATGT
1 TGAAAAGGTATGT
117709 TGAAAAGGTATG-
1 TGAAAAGGTATGT
117721 TGAAA
1 TGAAA
117726 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:121355 original size:25 final size:28
Alignment explanation
Indices: 121291--121356 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
121281 CAAAAGGAAA
121291 AGAAAAGACA-AAAAGAAGAAAAAAATTC
1 AGAAAAGA-AGAAAAGAAGAAAAAAATTC
* *
121319 AGAAAAGAAGAAAAGAA-AAATAAATTT
1 AGAAAAGAAGAAAAGAAGAAAAAAATTC
121346 A-AAAAG-AGAAA
1 AGAAAAGAAGAAA
121357 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 10 0.29
28 15 0.43
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.09
Consensus pattern (28 bp):
AGAAAAGAAGAAAAGAAGAAAAAAATTC
Found at i:129267 original size:11 final size:11
Alignment explanation
Indices: 129253--129313 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 11
129243 TCTTTTTGAA
129253 TTCTTTTTCTT
1 TTCTTTTTCTT
129264 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
129277 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
129290 TGTCTTTTTC-T
1 T-TCTTTTTCTT
129301 TTCTTTTTGCTT
1 TTCTTTTT-CTT
129313 T
1 T
129314 GTACGCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 7 0.17
11 6 0.15
12 9 0.22
13 15 0.37
14 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:129277 original size:19 final size:18
Alignment explanation
Indices: 129253--129313 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
129243 TCTTTTTGAA
129253 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
129271 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
129290 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
*
129308 TGCTTT
1 TTCTTT
129314 GTACGCCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.11
18 16 0.42
19 13 0.34
20 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:130979 original size:21 final size:21
Alignment explanation
Indices: 130953--130992 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
130943 CTCCCAAAGC
130953 GTGTAGATTCGCCTTACATCA
1 GTGTAGATTCGCCTTACATCA
130974 GTGTAGATTCGCCTTACAT
1 GTGTAGATTCGCCTTACAT
130993 TAATTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (21 bp):
GTGTAGATTCGCCTTACATCA
Found at i:133437 original size:11 final size:10
Alignment explanation
Indices: 133411--133444 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
133401 TCCGAAAATT
*
133411 AAAAAAATAA
1 AAAAAAAGAA
133421 AAAAAAAGAA
1 AAAAAAAGAA
133431 AAGAAAAAGAA
1 AA-AAAAAGAA
133442 AAA
1 AAA
133445 GAATTCTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:147661 original size:23 final size:23
Alignment explanation
Indices: 147635--147708 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
147625 AAGGACTTGG
147635 ACCCGTTAGATAATAATCTAAGA
1 ACCCGTTAGATAATAATCTAAGA
* * *
147658 ACCCG-AAGTATCAA-AGGA-CT-TGG
1 ACCCGTTAG-AT-AATA--ATCTAAGA
147681 ACCCGTTAGATAATAATCTAAGA
1 ACCCGTTAGATAATAATCTAAGA
147704 ACCCG
1 ACCCG
147709 AAGTATCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
21 1 0.03
22 6 0.16
23 23 0.62
24 6 0.16
25 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (23 bp):
ACCCGTTAGATAATAATCTAAGA
Found at i:147689 original size:46 final size:46
Alignment explanation
Indices: 147622--147720 Score: 198
Period size: 46 Copynumber: 2.2 Consensus size: 46
147612 CGTTCAATGT
147622 TCAAAGGACTTGGACCCGTTAGATAATAATCTAAGAACCCGAAGTA
1 TCAAAGGACTTGGACCCGTTAGATAATAATCTAAGAACCCGAAGTA
147668 TCAAAGGACTTGGACCCGTTAGATAATAATCTAAGAACCCGAAGTA
1 TCAAAGGACTTGGACCCGTTAGATAATAATCTAAGAACCCGAAGTA
147714 TCAAAGG
1 TCAAAGG
147721 TTTAACACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (46 bp):
TCAAAGGACTTGGACCCGTTAGATAATAATCTAAGAACCCGAAGTA
Found at i:148639 original size:10 final size:10
Alignment explanation
Indices: 148624--148652 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
148614 AAATTCATCC
148624 ATTCATGCAT
1 ATTCATGCAT
148634 ATTCATGCAT
1 ATTCATGCAT
148644 ATTCATGCA
1 ATTCATGCA
148653 AGAAGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (10 bp):
ATTCATGCAT
Found at i:148719 original size:24 final size:24
Alignment explanation
Indices: 148687--148737 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
148677 CAAGGGGGAA
148687 GAATTTCAGCCAAGATACATTCAT
1 GAATTTCAGCCAAGATACATTCAT
148711 GAATTTCAGCCAAGATACATTCAT
1 GAATTTCAGCCAAGATACATTCAT
148735 GAA
1 GAA
148738 CATTCATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
GAATTTCAGCCAAGATACATTCAT
Found at i:152038 original size:15 final size:15
Alignment explanation
Indices: 152018--152050 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
152008 AAAGAAAAGA
152018 AATTGAAATGGAAAT
1 AATTGAAATGGAAAT
*
152033 AATTGAAATGGATAT
1 AATTGAAATGGAAAT
152048 AAT
1 AAT
152051 AGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
AATTGAAATGGAAAT
Found at i:152239 original size:35 final size:37
Alignment explanation
Indices: 152193--152268 Score: 120
Period size: 35 Copynumber: 2.1 Consensus size: 37
152183 TTTGAGAATT
*
152193 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
152228 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
152265 TGGT
1 TGGT
152269 TATGGAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 21 0.57
36 4 0.11
37 12 0.32
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:156726 original size:35 final size:37
Alignment explanation
Indices: 156675--156759 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 37
156665 GGAAATTTGA
* *
156675 GAATTTGGTGATGATATAGGCGTGAT-ATGG-TGATG
1 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
156710 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
1 GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
*
156747 GATTATGGTGATG
1 GAATATGGTGATG
156760 GAAATAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 25 0.56
36 4 0.09
37 16 0.36
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (37 bp):
GAATATGGTGATGATATAGGCGTGATAATGGAAGATG
Found at i:159382 original size:29 final size:29
Alignment explanation
Indices: 159301--159383 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
159291 GTTTGTGACC
* *
159301 TGTTTGTGTCTCCCAAATACTCCACCAAGT
1 TGTTTGTCT-TCCAAAATACTCCACCAAGT
159331 TGTTTGTCTTCCAAAATGA-TCCACCAAGT
1 TGTTTGTCTTCCAAAAT-ACTCCACCAAGT
159360 TGTTTGTCTTCCAAAATACTCCAC
1 TGTTTGTCTTCCAAAATACTCCAC
159384 TAAGCTGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 39 0.80
30 9 0.18
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (29 bp):
TGTTTGTCTTCCAAAATACTCCACCAAGT
Found at i:175200 original size:24 final size:24
Alignment explanation
Indices: 175172--175240 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
175162 GATTCAAGAA
175172 ACATGTCTTTTGAAGAACCAAAAG
1 ACATGTCTTTTGAAGAACCAAAAG
* * * ** * *
175196 CCATGACCTTTGGTGATCCACAAG
1 ACATGTCTTTTGAAGAACCAAAAG
175220 ACATGTCTTTTGAAGAACCAA
1 ACATGTCTTTTGAAGAACCAA
175241 CAATTATGTC
Statistics
Matches: 31, Mismatches: 14, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
ACATGTCTTTTGAAGAACCAAAAG
Found at i:178047 original size:27 final size:28
Alignment explanation
Indices: 177993--178050 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
177983 AAAAATCAGA
177993 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCCAAAAGAAAG
*
178021 AAAGAAATT-CAGCACT-CAAAAGCAAAG
1 AAAGAAATTGAAGCACTCCAAAAG-AAAG
178048 AAA
1 AAA
178051 AAAAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 13 0.46
28 9 0.32
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.10
Consensus pattern (28 bp):
AAAGAAATTGAAGCACTCCAAAAGAAAG
Found at i:179250 original size:24 final size:24
Alignment explanation
Indices: 179222--179290 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
179212 GATTCAAGAA
179222 ACATGTCTTTTGAAGAACCAAAAG
1 ACATGTCTTTTGAAGAACCAAAAG
* * * ** * *
179246 TCATGACCTTTGGTGATCCACAAG
1 ACATGTCTTTTGAAGAACCAAAAG
179270 ACATGTCTTTTGAAGAACCAA
1 ACATGTCTTTTGAAGAACCAA
179291 CAATTATGTC
Statistics
Matches: 31, Mismatches: 14, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (24 bp):
ACATGTCTTTTGAAGAACCAAAAG
Found at i:181793 original size:10 final size:9
Alignment explanation
Indices: 181774--181817 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
181764 ATTTTTTTTC
181774 AAAAAAACA
1 AAAAAAACA
181783 AAAAAACACA
1 AAAAAA-ACA
*
181793 AAAAAAGGCAA
1 AAAAAA-AC-A
181804 AAAAAAACA
1 AAAAAAACA
181813 AAAAA
1 AAAAA
181818 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 12 0.40
10 11 0.37
11 7 0.23
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:181804 original size:20 final size:18
Alignment explanation
Indices: 181773--181817 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
181763 TATTTTTTTT
*
181773 CAAAAAAACAAAAAAACA
1 CAAAAAAACAAAAAAAAA
181791 CAAAAAAAGGCAAAAAAAAA
1 CAAAAAAA--CAAAAAAAAA
181811 CAAAAAA
1 CAAAAAA
181818 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAAA
Found at i:187891 original size:27 final size:28
Alignment explanation
Indices: 187837--187894 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
187827 AAAAATCAGA
187837 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCCAAAAGAAAG
*
187865 AAAGAAATT-CAGCACT-CAAAAGCAAAG
1 AAAGAAATTGAAGCACTCCAAAAG-AAAG
187892 AAA
1 AAA
187895 AAAAAGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 13 0.46
28 9 0.32
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.10
Consensus pattern (28 bp):
AAAGAAATTGAAGCACTCCAAAAGAAAG
Found at i:189054 original size:24 final size:24
Alignment explanation
Indices: 189026--189094 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
189016 GATTCAAGAA
189026 ACATGTCTTTTGAAGAACCAAAAG
1 ACATGTCTTTTGAAGAACCAAAAG
* * * ** * *
189050 TCATGACCTTTGGTGATCCACAAG
1 ACATGTCTTTTGAAGAACCAAAAG
189074 ACATGTCTTTTGAAGAACCAA
1 ACATGTCTTTTGAAGAACCAA
189095 CAATTATGTC
Statistics
Matches: 31, Mismatches: 14, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (24 bp):
ACATGTCTTTTGAAGAACCAAAAG
Found at i:191578 original size:10 final size:10
Alignment explanation
Indices: 191563--191611 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
191553 CTATTTTTTC
191563 AAAAAAAACA
1 AAAAAAAACA
*
191573 AAAAAACACA
1 AAAAAAAACA
**
191583 AAAAAAGGCA
1 AAAAAAAACA
191593 AAAAAAAACA
1 AAAAAAAACA
191603 AACAAAAAA
1 AA-AAAAAA
191612 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 27 0.82
11 6 0.18
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:191597 original size:22 final size:23
Alignment explanation
Indices: 191572--191618 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
191562 CAAAAAAAAC
* *
191572 AAAAAAACACA-AAAAAAGGCAA
1 AAAAAAACAAACAAAAAAGCCAA
191594 AAAAAAACAAACAAAAAAGCCAA
1 AAAAAAACAAACAAAAAAGCCAA
191617 AA
1 AA
191619 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAACAAAAAAGCCAA
Found at i:197057 original size:19 final size:20
Alignment explanation
Indices: 197016--197066 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
197006 GAAACCCCTT
*
197016 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
197036 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
197055 TGAAGATACATG
1 TGAAAATACATG
197067 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:205671 original size:13 final size:12
Alignment explanation
Indices: 205652--205737 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
205642 ATATAGGCGT
205652 GATATGGTGATG
1 GATATGGTGATG
205664 GAATATGGTGAT-
1 G-ATATGGTGATG
*
205676 GATATAGGCG-T-
1 GATAT-GGTGATG
205687 GATAATGGTGATG
1 GAT-ATGGTGATG
205700 GACTATGGTGAT-
1 GA-TATGGTGATG
*
205712 GATATAGG-CAT-
1 GATAT-GGTGATG
205723 GATAATGGTGATG
1 GAT-ATGGTGATG
205736 GA
1 GA
205738 AATAGTAATG
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:205707 original size:36 final size:36
Alignment explanation
Indices: 205634--205738 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
205624 ATTTAGAAGT
*
205634 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
205669 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
205705 TGGTGATGATATAGGCATGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
205739 ATAGTAATGG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:213124 original size:35 final size:37
Alignment explanation
Indices: 213078--213157 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
213068 TTTGAGAATT
*
213078 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
213113 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
213150 TGGTGATG
1 TGGTGATG
213158 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:216731 original size:13 final size:14
Alignment explanation
Indices: 216713--216745 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
216703 GATGTAGGAG
216713 TCTTTTTCTTTTC-
1 TCTTTTTCTTTTCT
216726 TC-TTTTCTTTTCT
1 TCTTTTTCTTTTCT
216739 TCTTTTT
1 TCTTTTT
216746 GTTGCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.56
13 4 0.22
14 4 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTCTTTTCT
Found at i:217181 original size:35 final size:37
Alignment explanation
Indices: 217135--217214 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
217125 TTTGAGAATT
*
217135 TGGTGATGATATAGGCATGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
* *
217170 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
217207 TGGTGATG
1 TGGTGATG
217215 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
Found at i:221194 original size:13 final size:12
Alignment explanation
Indices: 221175--221283 Score: 61
Period size: 11 Copynumber: 9.2 Consensus size: 12
221165 ACATAGGCGT
221175 GATATGGTGATG
1 GATATGGTGATG
221187 GAATATGGTGAT-
1 G-ATATGGTGATG
*
221199 GATATAGGCG-T-
1 GATAT-GGTGATG
221210 GATAATGGTGATG
1 GAT-ATGGTGATG
221223 GACTATGGTGAT-
1 GA-TATGGTGATG
*
221235 GATATAGG-CAT-
1 GATAT-GGTGATG
221246 GATAATGGTGATG
1 GAT-ATGGTGATG
* * *
221259 GAAATAGTAATG
1 GATATGGTGATG
*
221271 GA-ATGTTGATG
1 GATATGGTGATG
221282 GA
1 GA
221284 GTTGGCGTGA
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
11 29 0.38
12 25 0.32
13 22 0.29
14 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:221230 original size:36 final size:36
Alignment explanation
Indices: 221157--221261 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
221147 ATTTAGAAGT
* *
221157 TGGTGATAACATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
221192 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
221228 TGGTGATGATATAGGCATGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
221262 ATAGTAATGG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:230377 original size:35 final size:37
Alignment explanation
Indices: 230326--230405 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
230316 TTTGAGAATT
*
230326 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
230361 TGGTTATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
230398 TGGTGATG
1 TGGTGATG
230406 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:266310 original size:25 final size:23
Alignment explanation
Indices: 266275--266326 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
266265 TTCTTCTACC
*
266275 AAGGCTCTGATTACCGCTTGATGT
1 AAGGCTCTGA-TACCACTTGATGT
*
266299 AAGGCTTCTGATGCCACTTGATGT
1 AAGGC-TCTGATACCACTTGATGT
266323 AAGG
1 AAGG
266327 AACTTGTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (23 bp):
AAGGCTCTGATACCACTTGATGT
Found at i:269338 original size:23 final size:24
Alignment explanation
Indices: 269285--269335 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
269275 ATTTATTTTC
* * *
269285 TTTTCATCTTTTTGAGTGCTTGAA
1 TTTTCTTCTTTTGGAGTGCTTCAA
269309 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTTCTTTTGGAGTGCTTCAA
269333 TTT
1 TTT
269336 CTTTACTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTCAA
Found at i:271663 original size:19 final size:20
Alignment explanation
Indices: 271625--271671 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
271615 GAAATCCCTT
271625 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
271645 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
271664 TGAAAATA
1 TGAAAATA
271672 AATGCTCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:276512 original size:14 final size:14
Alignment explanation
Indices: 276493--276523 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
276483 ATAAGATACT
*
276493 ATCTATTCATCACC
1 ATCTATCCATCACC
276507 ATCTATCCATCACC
1 ATCTATCCATCACC
276521 ATC
1 ATC
276524 CTCAATCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:279988 original size:16 final size:16
Alignment explanation
Indices: 279969--280008 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
279959 CTTTATTATC
279969 TTATTTTATCTTTCAT
1 TTATTTTATCTTTCAT
**
279985 TTA-TTTATCTTTTGT
1 TTATTTTATCTTTCAT
280000 TTATTTTAT
1 TTATTTTAT
280009 TCTTATCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (16 bp):
TTATTTTATCTTTCAT
Found at i:280363 original size:11 final size:11
Alignment explanation
Indices: 280347--280371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
280337 TTTTTTTTTC
280347 AAAAAAACAAA
1 AAAAAAACAAA
280358 AAAAAAACAAA
1 AAAAAAACAAA
280369 AAA
1 AAA
280372 GGCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:280379 original size:21 final size:20
Alignment explanation
Indices: 280346--280403 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
280336 ATTTTTTTTT
*
280346 CAAAAAAAC-AAAAAAAAAA
1 CAAAAAAGCAAAAAAAAAAA
280365 CAAAAAAGGCAAAAAAAAAAA
1 CAAAAAA-GCAAAAAAAAAAA
280386 GCCAAAAAA-CAAAAAAAA
1 --CAAAAAAGCAAAAAAAA
280404 GAGCCAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 7 0.21
20 1 0.03
21 19 0.56
23 7 0.21
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (20 bp):
CAAAAAAGCAAAAAAAAAAA
Found at i:280385 original size:23 final size:21
Alignment explanation
Indices: 280347--280403 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
280337 TTTTTTTTTC
*
280347 AAAAA-AACAAAAAAAAAACA
1 AAAAACAAAAAAAAAAAAACA
**
280367 AAAAAGGCAAAAAAAAAAAGCCA
1 AAAAA--CAAAAAAAAAAAAACA
280390 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
280404 GAGCCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.16
21 9 0.29
23 17 0.55
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAAAAAAAAACA
Found at i:280392 original size:34 final size:32
Alignment explanation
Indices: 280347--280414 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
280337 TTTTTTTTTC
*
280347 AAAAAAACAAAAAA-AAAACAAAAAAGGCAAAA
1 AAAAAAACAAAAAACAAAA-AAAAAAGCCAAAA
*
280379 AAAAAAAGCCAAAAAACAAAAAAAAGAGCCAAAA
1 AAAAAAA--CAAAAAACAAAAAAAAAAGCCAAAA
280413 AA
1 AA
280415 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.23
34 20 0.65
35 4 0.13
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAAAACAAAAAAAAAAGCCAAAA
Found at i:280393 original size:14 final size:14
Alignment explanation
Indices: 280360--280400 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
280350 AAAACAAAAA
*
280360 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGCC
280375 AAAAAAAAAAAGCC
1 AAAAAAAAAAAGCC
280389 AAAAAACAAAAA
1 AAAAAA-AAAAA
280401 AAAGAGCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGCC
Found at i:280421 original size:20 final size:20
Alignment explanation
Indices: 280348--280414 Score: 84
Period size: 20 Copynumber: 3.3 Consensus size: 20
280338 TTTTTTTTCA
280348 AAAAAACAAAAAAAAAA--C
1 AAAAAACAAAAAAAAAAGCC
280366 AAAAAAGGCAAAAAAAAAAAGCC
1 AAAAAA--C-AAAAAAAAAAGCC
*
280389 AAAAAACAAAAAAAAGAGCC
1 AAAAAACAAAAAAAAAAGCC
280409 AAAAAA
1 AAAAAA
280415 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.14
20 19 0.44
21 11 0.26
23 7 0.16
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAAAAAAGCC
Found at i:285790 original size:11 final size:11
Alignment explanation
Indices: 285769--285810 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
285759 GTGCTGGAAT
285769 CAAGATAAAAA
1 CAAGATAAAAA
* *
285780 TAAGATTAAAA
1 CAAGATAAAAA
285791 CAAGATAAAGAA
1 CAAGATAAA-AA
285803 -AAGATAAA
1 CAAGATAAA
285811 TGAATTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (11 bp):
CAAGATAAAAA
Found at i:297556 original size:18 final size:18
Alignment explanation
Indices: 297535--297576 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
297525 ACTTCTCTTT
*
297535 TTCTTTTCT-TTTCTTTTC
1 TTCTTTTCTGATT-TTTTC
297553 TTCTTTTCTGATTTTTTC
1 TTCTTTTCTGATTTTTTC
297571 TTCTTT
1 TTCTTT
297577 CTGCACCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (18 bp):
TTCTTTTCTGATTTTTTC
Found at i:299861 original size:11 final size:11
Alignment explanation
Indices: 299845--299869 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
299835 TATCAAAAAT
299845 AAGTGCAAGTG
1 AAGTGCAAGTG
299856 AAGTGCAAGTG
1 AAGTGCAAGTG
299867 AAG
1 AAG
299870 AAATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
AAGTGCAAGTG
Found at i:299943 original size:24 final size:23
Alignment explanation
Indices: 299894--299943 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
299884 CAAATAAATC
**
299894 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
299917 AAAGCACTCAAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
299941 AAA
1 AAA
299944 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:299961 original size:4 final size:5
Alignment explanation
Indices: 299927--299964 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
299917 AAAGCACTCA
*
299927 AAAAG AAGA- AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
299965 TTGAAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:306400 original size:28 final size:28
Alignment explanation
Indices: 306368--306423 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
306358 CGTGAATTAA
306368 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
306396 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
306424 TGAATGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGCTGTTATG
Found at i:310107 original size:24 final size:21
Alignment explanation
Indices: 310073--310115 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
310063 TCCACAAGAC
*
310073 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
310095 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
310116 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:312500 original size:16 final size:16
Alignment explanation
Indices: 312479--312511 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
312469 TTCTGCCACC
312479 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
312495 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
312511 T
1 T
312512 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:320258 original size:18 final size:18
Alignment explanation
Indices: 320235--320271 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
320225 TTAAGAAACT
320235 TCATCAGCAAGTTTGAGA
1 TCATCAGCAAGTTTGAGA
320253 TCATCAGCAAGTTTGAGA
1 TCATCAGCAAGTTTGAGA
320271 T
1 T
320272 AATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (18 bp):
TCATCAGCAAGTTTGAGA
Found at i:323551 original size:193 final size:193
Alignment explanation
Indices: 323202--323551 Score: 462
Period size: 193 Copynumber: 1.8 Consensus size: 193
323192 GTAATAGATC
* * *
323202 TGATGCAAGCACGTTTTCACCTACAAAGGGAGTACTCTTGAACATTTTTATGTTATATTTACTTT
1 TGATGCAAGCACGTTTTCAACTACAAAGGGAGTACTCTTGAACATCTTTATGTAATATTTACTTT
* * * * * *
323267 AAACTAGTTTAATGATATATGCTATTATGATACATCTCATGTTAAGGTTACTAGTTATGTAATTA
66 AAACTAGCTTAATAATATATACTATTATGATACATATCATGCTAAGGATACTAGTTATGTAATTA
*
323332 ATAAATAACCTAGCATGAACACATCTTCATAATAGATGCACATTGTTATTTAGATATGTTAAG
131 ATAAATAACATAGCATGAACACATCTTCATAATAGATGCACATTGTTATTTAGATATGTTAAG
*
323395 TGATGCAAGCACGTTTTCAACTATAAAGGGAGTACTCTTGAACATCTTT-T-TAATGCATTTACT
1 TGATGCAAGCACGTTTTCAACTACAAAGGGAGTACTCTTGAACATCTTTATGTAAT--ATTTACT
*
323458 TTATAA-TAGCCTT-ATAATATATACTATTAT-ATTACATATCATGCTAAGGATATTAGTTATG-
64 TTA-AACTAG-CTTAATAATATATACTATTATGA-TACATATCATGCTAAGGATACTAGTTATGT
* *
323519 AAGTTAA-AGAATAACATAGTATGAATACATCTT
126 AA-TTAATA-AATAACATAGCATGAACACATCTT
323552 ACACATTGTT
Statistics
Matches: 136, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
191 3 0.02
192 5 0.04
193 124 0.91
194 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (193 bp):
TGATGCAAGCACGTTTTCAACTACAAAGGGAGTACTCTTGAACATCTTTATGTAATATTTACTTT
AAACTAGCTTAATAATATATACTATTATGATACATATCATGCTAAGGATACTAGTTATGTAATTA
ATAAATAACATAGCATGAACACATCTTCATAATAGATGCACATTGTTATTTAGATATGTTAAG
Found at i:324272 original size:27 final size:27
Alignment explanation
Indices: 324234--324297 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
324224 ATCCTAGAGA
324234 AGCCATGTGCACGCCTTGTGACCAGCC
1 AGCCATGTGCACGCCTTGTGACCAGCC
324261 AGCCATGTGCACGCCTTGTGACCAGCC
1 AGCCATGTGCACGCCTTGTGACCAGCC
*
324288 AACCATGTGC
1 AGCCATGTGC
324298 TAGGCGTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.19
Consensus pattern (27 bp):
AGCCATGTGCACGCCTTGTGACCAGCC
Found at i:332553 original size:10 final size:9
Alignment explanation
Indices: 332548--332582 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
332538 AATTTTGGCT
332548 TTTTTTTTG
1 TTTTTTTTG
332557 CTTTTTTTTG
1 -TTTTTTTTG
332567 TTTTTTTTG
1 TTTTTTTTG
332576 TTTTTTT
1 TTTTTTT
332583 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:340994 original size:10 final size:10
Alignment explanation
Indices: 340963--340995 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
340953 TGACATCAAG
340963 TGTAGCTGAA
1 TGTAGCTGAA
*
340973 TATAGCTGAA
1 TGTAGCTGAA
340983 TGTAGCTGAA
1 TGTAGCTGAA
340993 TGT
1 TGT
340996 GTTGATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (10 bp):
TGTAGCTGAA
Found at i:342025 original size:11 final size:11
Alignment explanation
Indices: 342009--342034 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
341999 ATATCAAAAA
342009 GAAGTGCAAGT
1 GAAGTGCAAGT
342020 GAAGTGCAAGT
1 GAAGTGCAAGT
342031 GAAG
1 GAAG
342035 AAATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:342108 original size:24 final size:23
Alignment explanation
Indices: 342059--342108 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
342049 CAAATAAATC
**
342059 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAAAAG
342082 AAAGCACTCAAAAAGAAGAAAAAG
1 AAAGCACTC-AAAAGAAGAAAAAG
342106 AAA
1 AAA
342109 AGTTGAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAAAAG
Found at i:344155 original size:22 final size:20
Alignment explanation
Indices: 344130--344169 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
344120 ATGTTTATTT
344130 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
344152 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
344170 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:348419 original size:22 final size:20
Alignment explanation
Indices: 348394--348433 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
348384 ATGTTTATTT
348394 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
348416 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
348434 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:350929 original size:28 final size:28
Alignment explanation
Indices: 350897--350952 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
350887 CGTGAATTAA
350897 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
350925 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
350953 TGAATGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGCTGTTATG
Found at i:354650 original size:24 final size:21
Alignment explanation
Indices: 354616--354658 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
354606 TCCACAAGAC
*
354616 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
354638 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
354659 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:357037 original size:30 final size:31
Alignment explanation
Indices: 357001--357060 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
356991 CTTAGCTTTA
**
357001 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATAATTTAGATATCATT
*
357031 TATTATGTTTGCATATAATTTAGATATCAT
1 TATTATGTTTACATATAATTTAGATATCAT
357061 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATAATTTAGATATCATT
Found at i:359126 original size:6 final size:6
Alignment explanation
Indices: 359101--359138 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
359091 GTGCTGCAAC
*
359101 AAAAAG CAAAAG AAAGAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG A
359139 CTCATACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:384943 original size:23 final size:23
Alignment explanation
Indices: 384916--384972 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
384906 AAGAAAAATT
*
384916 AGAAAAAAAGTGAAGCACTCAAA
1 AGAAAAAAAGTCAAGCACTCAAA
* *
384939 AGAAAGAAAA-TCCAGCAGTCAAA
1 AGAAA-AAAAGTCAAGCACTCAAA
384962 AGAAGAAAAAG
1 AGAA-AAAAAG
384973 CAAAGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.61, C:0.12, G:0.19, T:0.07
Consensus pattern (23 bp):
AGAAAAAAAGTCAAGCACTCAAA
Found at i:387509 original size:16 final size:18
Alignment explanation
Indices: 387488--387524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
387478 TGAACACCGT
387488 TATATT-GATAT-TACTA
1 TATATTAGATATATACTA
*
387504 TATATTAGTTATATACTA
1 TATATTAGATATATACTA
387522 TAT
1 TAT
387525 GCTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATTAGATATATACTA
Found at i:388801 original size:30 final size:31
Alignment explanation
Indices: 388767--388826 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
388757 CTTAGCTTTA
**
388767 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
388797 TATTATGTTTTCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
388827 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:389421 original size:21 final size:19
Alignment explanation
Indices: 389381--389431 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 19
389371 CGGACAAGAG
*
389381 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
389400 CATGTATTTTCACTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
389421 CATGTATTTTC
1 CATGTATTTTC
389432 TATACTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:389984 original size:50 final size:50
Alignment explanation
Indices: 389916--390032 Score: 200
Period size: 50 Copynumber: 2.3 Consensus size: 50
389906 GTCATTGGCA
*
389916 TGCAAAACAGAAGAAAAATAGAAGAAAAGACTCCTACATCAAAATTGGAG
1 TGCAAAACAGAAGAAAAATAGAAGAAAAGACTCCTACATCAAAATTAGAG
*
389966 TGCAAAACAGAAGAAAAATATAAGAAAAGACTCCTACATCAAAATTAGAG
1 TGCAAAACAGAAGAAAAATAGAAGAAAAGACTCCTACATCAAAATTAGAG
390016 TGCAAAA-AGAAAGAAAA
1 TGCAAAACAG-AAGAAAA
390033 GACAAGACAC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 2 0.03
50 62 0.97
ACGTcount: A:0.57, C:0.13, G:0.16, T:0.14
Consensus pattern (50 bp):
TGCAAAACAGAAGAAAAATAGAAGAAAAGACTCCTACATCAAAATTAGAG
Found at i:399501 original size:19 final size:19
Alignment explanation
Indices: 399477--399526 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
399467 CGGCCAAGAG
* *
399477 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
399496 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
399515 CATGTATTTTCA
1 CATGTATTTTCA
399527 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:400491 original size:24 final size:24
Alignment explanation
Indices: 400464--400523 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
400454 GTTGGTTCTT
400464 CAAAAGACATGTCTTGTGGATCCC
1 CAAAAGACATGTCTTGTGGATCCC
* * * * * **
400488 CAAAGGTCATGACTTTTGGTTCTT
1 CAAAAGACATGTCTTGTGGATCCC
400512 CAAAAGACATGT
1 CAAAAGACATGT
400524 TTCTTGAATC
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (24 bp):
CAAAAGACATGTCTTGTGGATCCC
Found at i:401741 original size:27 final size:28
Alignment explanation
Indices: 401697--401753 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
401687 CTTTCTTTTT
* *
401697 TTTCTTTGCTTTTTAGTGC-TGAATTTC
1 TTTCTTTGCTTTTGAGTGCTTCAATTTC
401724 TTTCTTT-CTTTTGGAGTGCTTCAATTTC
1 TTTCTTTGCTTTT-GAGTGCTTCAATTTC
401752 TT
1 TT
401754 ACCTTCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 12 0.46
28 9 0.35
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.60
Consensus pattern (28 bp):
TTTCTTTGCTTTTGAGTGCTTCAATTTC
Found at i:404290 original size:24 final size:24
Alignment explanation
Indices: 404230--404296 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
404220 GACATAATTG
*
404230 TTGGTTCTTCAAAAGACATGTCTT
1 TTGGTTCTTCAAAAGACATGACTT
* * ** * *
404254 GTGGATCACCAAAGGTCATGACTT
1 TTGGTTCTTCAAAAGACATGACTT
404278 TTGGTTCTTCAAAAGACAT
1 TTGGTTCTTCAAAAGACAT
404297 ATTTCTTGAA
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (24 bp):
TTGGTTCTTCAAAAGACATGACTT
Found at i:405515 original size:27 final size:28
Alignment explanation
Indices: 405472--405529 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
405462 TTTCTTTTTT
*
405472 TTTCTTTGCTTTTGAGTGC-TGAATTTC
1 TTTCTTTGCTTTTGAGTGCTTCAATTTC
405499 TTTCTTT-CTTTTGGAGTGCTTCAATTTC
1 TTTCTTTGCTTTT-GAGTGCTTCAATTTC
405527 TTT
1 TTT
405530 TCTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 13 0.46
28 10 0.36
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.59
Consensus pattern (28 bp):
TTTCTTTGCTTTTGAGTGCTTCAATTTC
Found at i:408478 original size:35 final size:37
Alignment explanation
Indices: 408409--408488 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
408399 ATACTATTTC
*
408409 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
408446 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
408481 CATCACCA
1 CATCACCA
408489 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:411882 original size:27 final size:27
Alignment explanation
Indices: 411844--411912 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
411834 TGCTGCCCCA
411844 TTGATGCCATGTCACCTAGACACATGT
1 TTGATGCCATGTCACCTAGACACATGT
411871 TTGATGCCATGTCACCTAGACACATGT
1 TTGATGCCATGTCACCTAGACACATGT
*
411898 TTGATGCCAAGTCAC
1 TTGATGCCATGTCAC
411913 GCCTAAGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (27 bp):
TTGATGCCATGTCACCTAGACACATGT
Found at i:412568 original size:35 final size:37
Alignment explanation
Indices: 412499--412578 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
412489 ATACTATTTC
*
412499 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
412536 CATCACCATAGTCCATC-ACTA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
412571 CATCACCA
1 CATCACCA
412579 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 2 0.05
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:415116 original size:22 final size:23
Alignment explanation
Indices: 415091--415133 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
415081 TTAATATAAG
415091 ATATTAATTATCTT-TTAGGATC
1 ATATTAATTATCTTATTAGGATC
* *
415113 ATATTTATTATTTTATTAGGA
1 ATATTAATTATCTTATTAGGA
415134 ATTAAGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (23 bp):
ATATTAATTATCTTATTAGGATC
Done.