Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010678.1 Corchorus capsularis cultivar CVL-1 contig10699, 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: 72812
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6717 original size:15 final size:17
Alignment explanation
Indices: 6681--6726 Score: 78
Period size: 16 Copynumber: 2.8 Consensus size: 17
6671 GCGGTTTAGG
6681 GTTTTTTCGGGTTCTGA
1 GTTTTTTCGGGTTCTGA
6698 -TTTTTTCGGGTT-TGA
1 GTTTTTTCGGGTTCTGA
6713 GTTTTTTCGGGTTC
1 GTTTTTTCGGGTTC
6727 GGGTTCGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.04, C:0.11, G:0.28, T:0.57
Consensus pattern (17 bp):
GTTTTTTCGGGTTCTGA
Found at i:14836 original size:27 final size:25
Alignment explanation
Indices: 14806--14856 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
14796 TTTTTTAACT
14806 CTATCTTCATTCTACTTTTCTTTTTTA
1 CTATC-TCATTCT-CTTTTCTTTTTTA
* *
14833 CTATCTCTTTCTCTTTTTTTTTTT
1 CTATCTCATTCTCTTTTCTTTTTT
14857 TTTTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69
Consensus pattern (25 bp):
CTATCTCATTCTCTTTTCTTTTTTA
Found at i:16680 original size:14 final size:14
Alignment explanation
Indices: 16656--16689 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16646 TAGTTTTGTG
*
16656 AATTGTCATTAACA
1 AATTCTCATTAACA
*
16670 GATTCTCATTAACA
1 AATTCTCATTAACA
16684 AATTCT
1 AATTCT
16690 AAAAGGATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (14 bp):
AATTCTCATTAACA
Found at i:20311 original size:22 final size:24
Alignment explanation
Indices: 20260--20311 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
20250 GTTTTCTTAC
20260 CTTTTTAATCAATTTTCTAAAGAAA
1 CTTTTTAA-CAATTTTCTAAAGAAA
*
20285 C-TTTTAA-AATTTTCTTAA-AAA
1 CTTTTTAACAATTTTCTAAAGAAA
20306 CTTTTT
1 CTTTTT
20312 TCACTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
24 6 0.24
25 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (24 bp):
CTTTTTAACAATTTTCTAAAGAAA
Found at i:20495 original size:10 final size:9
Alignment explanation
Indices: 20483--20514 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
20473 TTTCTTTTCA
20483 TTTTTTTAT
1 TTTTTTTAT
20492 ATTTTTTTAT
1 -TTTTTTTAT
20502 TTTTTTTAT
1 TTTTTTTAT
20511 TTTT
1 TTTT
20515 AGAAAAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:20945 original size:21 final size:21
Alignment explanation
Indices: 20919--20960 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20909 GTACAAGTGA
*
20919 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
20940 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
20961 GCCCGCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:20982 original size:33 final size:33
Alignment explanation
Indices: 20940--21035 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
20930 ACTTGGAGAT
* *
20940 CCGGCCACGCGACTTGGAGATGCCC-GCGCAACA
1 CCGGCCACGCGACATGGACATGCCCGGC-CAACA
* *
20973 CCGGCCACGCGACATGGCCATGCCCGGCCATCA
1 CCGGCCACGCGACATGGACATGCCCGGCCAACA
*
21006 CCGGCCACGCGACATGGCCATGCCCGGCCA
1 CCGGCCACGCGACATGGACATGCCCGGCCA
21036 CATGACTCGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 56 0.97
34 2 0.03
ACGTcount: A:0.19, C:0.44, G:0.29, T:0.08
Consensus pattern (33 bp):
CCGGCCACGCGACATGGACATGCCCGGCCAACA
Found at i:23981 original size:6 final size:6
Alignment explanation
Indices: 23970--24010 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
23960 TTGATCGAGT
23970 AGCTCG AGCTCG A-CTCG AGCTCG ATG-TCG AGC-CG AGCTCG A
1 AGCTCG AGCTCG AGCTCG AGCTCG A-GCTCG AGCTCG AGCTCG A
24011 ACAGCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 11 0.35
6 19 0.61
7 1 0.03
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (6 bp):
AGCTCG
Found at i:24010 original size:11 final size:12
Alignment explanation
Indices: 23970--24010 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
23960 TTGATCGAGT
23970 AGCTCGAGCTCG
1 AGCTCGAGCTCG
23982 A-CTCGAGCTCG
1 AGCTCGAGCTCG
23993 ATG-TCGAGC-CG
1 A-GCTCGAGCTCG
24004 AGCTCGA
1 AGCTCGA
24011 ACAGCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 18 0.69
12 7 0.27
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (12 bp):
AGCTCGAGCTCG
Found at i:29000 original size:37 final size:38
Alignment explanation
Indices: 28950--29021 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
28940 TAAACTTTGG
28950 GTTTTCTTTCATTTCTT-ATTAGGG-CTCCTTACCATGT
1 GTTTTCTTTCATTTCTTAATT-GGGCCTCCTTACCATGT
*
28987 GTTTTCTTTCATTTTTTAATTGGGCCTCCTTACCA
1 GTTTTCTTTCATTTCTTAATTGGGCCTCCTTACCA
29022 AGATCTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.14, C:0.22, G:0.12, T:0.51
Consensus pattern (38 bp):
GTTTTCTTTCATTTCTTAATTGGGCCTCCTTACCATGT
Found at i:30590 original size:18 final size:19
Alignment explanation
Indices: 30567--30604 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30557 GTGCATGGGC
*
30567 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
30585 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
30604 T
1 T
30605 AACGATAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:32619 original size:52 final size:52
Alignment explanation
Indices: 32562--32716 Score: 238
Period size: 52 Copynumber: 3.0 Consensus size: 52
32552 TCCTTCAAGG
*
32562 TTTTCAAAGTGGGAAAGTTCCCATTAGGTTTTCAAAGCGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCGTTCAATTTAGGTC
* * * *
32614 TTTTCAAAGTGGGAAGGTTCCCATCAGGTATTCAAAGTGTTCAATTTAGATC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCGTTCAATTTAGGTC
* *
32666 TTTTCAAAGTGGGAAAATTCCCATCAGGTTTTTCAAAACGTTCAATTTAGG
1 TTTTCAAAGTGGGAAAGTTCCCATCAGG-TTTTCAAAGCGTTCAATTTAGG
32717 GAAAGTTCCC
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 73 0.80
53 18 0.20
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCGTTCAATTTAGGTC
Found at i:36274 original size:7 final size:7
Alignment explanation
Indices: 36262--36290 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
36252 TAATCTAGAA
36262 AATGGTT
1 AATGGTT
36269 AATGGTT
1 AATGGTT
36276 AATGGTT
1 AATGGTT
36283 AATGGTT
1 AATGGTT
36290 A
1 A
36291 CAAGCTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
AATGGTT
Found at i:38852 original size:13 final size:13
Alignment explanation
Indices: 38834--38879 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
38824 TTTACATAAA
38834 AAAACAAAAAAAT
1 AAAACAAAAAAAT
*
38847 AAAACAAAAAAAG
1 AAAACAAAAAAAT
38860 ACATAACCAAAAAAAT
1 A-A-AA-CAAAAAAAT
38876 AAAA
1 AAAA
38880 TTGTTCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 13 0.46
14 3 0.11
15 3 0.11
16 9 0.32
ACGTcount: A:0.80, C:0.11, G:0.02, T:0.07
Consensus pattern (13 bp):
AAAACAAAAAAAT
Found at i:45599 original size:11 final size:11
Alignment explanation
Indices: 45577--45613 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
45567 GAATTTGCAT
45577 AAAAA-AAGAA
1 AAAAAGAAGAA
45587 AAAAAGGAA-AA
1 AAAAA-GAAGAA
45598 AAAAAGAAGAA
1 AAAAAGAAGAA
45609 AAAAA
1 AAAAA
45614 TGTTTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 14 0.58
12 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:46238 original size:19 final size:18
Alignment explanation
Indices: 46197--46239 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
46187 TTCCCCAAAG
*
46197 AAAAAGAAGAAAAATGAT
1 AAAAAGAAGAAAAATGAA
*
46215 GAAAAGAAGGAAAAATGAA
1 AAAAAGAA-GAAAAATGAA
46234 AAAAAG
1 AAAAAG
46240 CACTTGGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (18 bp):
AAAAAGAAGAAAAATGAA
Found at i:48685 original size:105 final size:105
Alignment explanation
Indices: 48500--48786 Score: 400
Period size: 105 Copynumber: 2.7 Consensus size: 105
48490 AAGTCAAACC
* *
48500 CGTTTCCATACGAGTCGGTTTAAGCATTGGTTCCATCCAAGCATTTCGGGTTTTTCCACAAGCCA
1 CGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAGCATTTCGGGCTTTTCCACAAGCCA
* *
48565 AGTTCATTTCCATATGAATTCAGTCTTCCAAGACTAGTCT
66 AGTTCATTTCAATATGAATTCAGTCTTCCAAGACTAATCT
* * * *
48605 CGTTTCCATATGAGTCAGTTTAAGCCTTGGTCCCATTCAAGCATTTCGGGCTTTTCCACAAGCCG
1 CGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAGCATTTCGGGCTTTTCCACAAGCC-
48670 AA-TTCA-TTCGAATATGAATTCAGTCTTCCAAGACTAATCT
65 AAGTTCATTTC-AATATGAATTCAGTCTTCCAAGACTAATCT
* * * *
48710 TGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAACAGTTTC-GGCTTTTCCAAAAGTC
1 CGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAGCA-TTTCGGGCTTTTCCACAAGCC
*
48774 AAGCTCACTTTCA
65 AAGTTCA-TTTCA
48787 TGCGAAGCTA
Statistics
Matches: 159, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
104 5 0.03
105 144 0.91
106 7 0.04
107 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (105 bp):
CGTTTCCATACGAGTCGGTTTAAGCCTTGGTTCCATCCAAGCATTTCGGGCTTTTCCACAAGCCA
AGTTCATTTCAATATGAATTCAGTCTTCCAAGACTAATCT
Found at i:48925 original size:41 final size:42
Alignment explanation
Indices: 48876--49301 Score: 208
Period size: 41 Copynumber: 10.8 Consensus size: 42
48866 TAAAATGTTT
* *
48876 CAGAGTTGGTATCTGTTGGCCTTCTCTAAAAATCGAGCTTTT-
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAG-TTTTA
48918 CA-AGTTGGCATCGGTTGGCC-T-TCTAAAAAT---GTTTTA
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
* * * *
48954 AAGAGTTGGTATCGATTGGCCTTCTCTAAAAATCGAGCTTTTC
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAG-TTTTA
*
48997 CA-AGTTGGCATCGGTTGG-CTT-TCT-TAAAT---GTTTT-
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
* ** * **
49031 CAGAGTTGGTATTTGTTGGCCTTCTCTTAAAATAAAGTTTTA
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
* * * *
49073 TAAAAGTTGGCATCGGTTGGCCTTCT-TTAAAATCGAGTTTTTTTCTT
1 -CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAG----TTT-TA
* *
49120 CAAAAGTTGGCATCGGTTGG-CAT-TCT-AAAA---AGTTTT-
1 C-AGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
* ** *
49156 CAAAGTTGGCATCGGTTGGCCTTCT-TAAAGTTTTGA-TTTT-
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAA-AATCGAGTTTTA
* * *
49196 CAAAGTTGGCATCGGTTAGCC-T-TCT-AAAA---A-TTCT-
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
* ** *
49230 CAAAGTTGGCATCGGTTGGCCTTCT-TAAAGTTTTGAGTTTTTA
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAA-AATCGAG-TTTTA
49273 -A-AGTTGGCATCGGTTGGCCTTCT-TAAAAA
1 CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAA
49302 AAATAAAAAA
Statistics
Matches: 305, Mismatches: 37, Indels: 86
0.71 0.09 0.20
Matches are distributed among these distances:
34 26 0.09
35 41 0.13
36 13 0.04
37 23 0.08
38 11 0.04
39 24 0.08
40 29 0.10
41 51 0.17
42 32 0.10
43 25 0.08
45 5 0.02
46 6 0.02
47 19 0.06
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (42 bp):
CAGAGTTGGCATCGGTTGGCCTTCTCTAAAAATCGAGTTTTA
Found at i:48973 original size:37 final size:35
Alignment explanation
Indices: 48839--49055 Score: 140
Period size: 35 Copynumber: 5.8 Consensus size: 35
48829 AGCAAAAAGC
* *
48839 TTTTCA-AGTTGGCATTGGTTGGCCTTCT-AAAATG
1 TTTTCAGAGTTGGTA-TCGTTGGCCTTCTAAAAATG
48873 -TTTCAGAGTTGGTATCTGTTGGCCTTCTCTAAAAATCGAG
1 TTTTCAGAGTTGGTATC-GTTGGCC-T-TCTAAAAAT---G
*
48913 CTTTTCA-AGTTGGCATCGGTTGGCCTTCTAAAAATG
1 -TTTTCAGAGTTGGTATC-GTTGGCCTTCTAAAAATG
*
48949 TTTTAAAGAGTTGGTATCGATTGGCCTTCTCTAAAAATCGAG
1 TTTT-CAGAGTTGGTATCG-TTGGCC-T-TCTAAAAAT---G
* * *
48991 CTTTTCCA-AGTTGGCATCGGTTGGCTTTCT-TAAATG
1 -TTTT-CAGAGTTGGTATC-GTTGGCCTTCTAAAAATG
*
49027 TTTTCAGAGTTGGTATTTGTTGGCCTTCT
1 TTTTCAGAGTTGGTA-TCGTTGGCCTTCT
49056 CTTAAAATAA
Statistics
Matches: 147, Mismatches: 14, Indels: 43
0.72 0.07 0.21
Matches are distributed among these distances:
33 6 0.04
34 16 0.11
35 26 0.18
36 8 0.05
37 20 0.14
38 1 0.01
39 22 0.15
40 5 0.03
41 17 0.12
42 20 0.14
43 6 0.04
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (35 bp):
TTTTCAGAGTTGGTATCGTTGGCCTTCTAAAAATG
Found at i:49031 original size:35 final size:35
Alignment explanation
Indices: 48992--49299 Score: 195
Period size: 35 Copynumber: 7.9 Consensus size: 35
48982 AAAATCGAGC
* *
48992 TTTTCCAAGTTGGCATCGGTTGGCTTTCTTAAATG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAATG
* * **
49027 TTTTCAGAGTTGGTATTTGTTGGCCTTCTCTTAAAATAAAG
1 TTTTCAAAGTTGGCATCGGTTGGCC-T-TCTT-AAAT---G
*
49068 TTTTATAAAAGTTGGCATCGGTTGGCCTTCTTTAAAATCGAG
1 -TTT-TCAAAGTTGGCATCGGTTGGCCTTC-TT-AAAT---G
* * *
49110 TTTTTTTCTTCAAAAGTTGGCATCGGTTGGCATTCTAAAAAG
1 -----TT-TTC-AAAGTTGGCATCGGTTGGCCTTCTTAAATG
49152 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAA----TG
* **
49191 ATTTTCAAAGTTGGCATCGGTTAGCCTTC-TAAAAA
1 -TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAATG
*
49226 TTCTCAAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGAG
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAA----T--G
*
49267 TTTTTAAAGTTGGCATCGGTTGGCCTTCTTAAA
1 TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAA
49300 AAAAATAAAA
Statistics
Matches: 217, Mismatches: 29, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
34 26 0.12
35 49 0.23
36 4 0.02
37 6 0.03
38 4 0.02
39 5 0.02
40 27 0.12
41 34 0.16
42 14 0.06
43 17 0.08
45 3 0.01
46 5 0.02
47 23 0.11
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTTCAAAGTTGGCATCGGTTGGCCTTCTTAAATG
Found at i:49099 original size:78 final size:76
Alignment explanation
Indices: 48836--49098 Score: 359
Period size: 78 Copynumber: 3.4 Consensus size: 76
48826 TTAAGCAAAA
* *
48836 AGCTTTTCAAGTTGGCATTGGTTGGCCTTCTAAAATG-TTTCAGAGTTGGTATCTGTTGGCCTTC
1 AGCTTTTCAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAGAGTTGGTATTTGTTGGCCTTC
48900 TCTAAAAATCG
66 TCTAAAAATCG
* *
48911 AGCTTTTCAAGTTGGCATCGGTTGGCCTTCTAAAAATGTTTTAAAGAGTTGGTA-TCGATTGGCC
1 AGCTTTTCAAGTTGGCATCGGTTGGCCTTCT-AAAATGTTTT-CAGAGTTGGTATTTG-TTGGCC
48975 TTCTCTAAAAATCG
63 TTCTCTAAAAATCG
* *
48989 AGCTTTTCCAAGTTGGCATCGGTTGGCTTTCTTAAATGTTTTCAGAGTTGGTATTTGTTGGCCTT
1 AGCTTTT-CAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAGAGTTGGTATTTGTTGGCCTT
* **
49054 CTCTTAAAATAA
65 CTCTAAAAATCG
* *
49066 AGTTTTATAAAAGTTGGCATCGGTTGGCCTTCT
1 AGCTTT-T-CAAGTTGGCATCGGTTGGCCTTCT
49099 TTAAAATCGA
Statistics
Matches: 166, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
75 30 0.18
76 6 0.04
77 36 0.22
78 71 0.43
79 23 0.14
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (76 bp):
AGCTTTTCAAGTTGGCATCGGTTGGCCTTCTAAAATGTTTTCAGAGTTGGTATTTGTTGGCCTTC
TCTAAAAATCG
Found at i:49253 original size:74 final size:75
Alignment explanation
Indices: 49075--49301 Score: 305
Period size: 75 Copynumber: 2.9 Consensus size: 75
49065 AAGTTTTATA
*
49075 AAAGTTGGCATCGGTTGGCCTTCTTTAAAATCGAGTTTT-TTTCTTCAAAAGTTGGCATCGGTTG
1 AAAGTTGGCATCGGTTGGCCTTC-TT--AA---AGTTTTGATT-TTC-AAAGTTGGCATCGGTTG
* *
49139 GCATTCTAAAAAGTTTTC
58 GCCTTCTAAAAAGTTCTC
*
49157 AAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGATTTTCAAAGTTGGCATCGGTTAGCCTTCTA
1 AAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGATTTTCAAAGTTGGCATCGGTTGGCCTTCTA
49222 AAAA-TTCTC
66 AAAAGTTCTC
*
49231 AAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGAGTTTTTAAAGTTGGCATCGGTTGGCCTTCT
1 AAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGA-TTTTCAAAGTTGGCATCGGTTGGCCTTC-
49296 TAAAAA
64 TAAAAA
49302 AAATAAAAAA
Statistics
Matches: 136, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
74 39 0.29
75 53 0.39
76 15 0.11
77 2 0.01
79 2 0.01
81 2 0.01
82 23 0.17
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (75 bp):
AAAGTTGGCATCGGTTGGCCTTCTTAAAGTTTTGATTTTCAAAGTTGGCATCGGTTGGCCTTCTA
AAAAGTTCTC
Found at i:49787 original size:13 final size:13
Alignment explanation
Indices: 49769--49793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49759 TTTACATAAA
49769 AAAACAAAAAAAT
1 AAAACAAAAAAAT
49782 AAAACAAAAAAA
1 AAAACAAAAAAA
49794 AAGACATAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAACAAAAAAAT
Found at i:49982 original size:20 final size:20
Alignment explanation
Indices: 49954--49991 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49944 GAAGCAACAA
*
49954 CTGCTGCAGCACACTCTACT
1 CTGCAGCAGCACACTCTACT
*
49974 CTGCAGCAGCATACTCTA
1 CTGCAGCAGCACACTCTA
49992 GCAATAGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (20 bp):
CTGCAGCAGCACACTCTACT
Found at i:50310 original size:16 final size:17
Alignment explanation
Indices: 50289--50320 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
50279 ATTTCACTTT
50289 CAAAAA-CAAAAAAAAC
1 CAAAAACCAAAAAAAAC
50305 CAAAAACCAAAAAAAA
1 CAAAAACCAAAAAAAA
50321 TGTTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAACCAAAAAAAAC
Done.