Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018562.1 Corchorus olitorius cultivar O-4 contig18595, 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: 79527
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5481 original size:30 final size:30
Alignment explanation
Indices: 5447--5509 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5437 ATATATTGGA
5447 TTTCTAGTTTTCTTT-GTTAAATAACTTATT
1 TTTCT-GTTTTCTTTAGTTAAATAACTTATT
* * *
5477 TTTCTTTTTTTTTTAGTTTAATAACTTATT
1 TTTCTGTTTTCTTTAGTTAAATAACTTATT
5507 TTT
1 TTT
5510 TCTCATGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (30 bp):
TTTCTGTTTTCTTTAGTTAAATAACTTATT
Found at i:6591 original size:19 final size:18
Alignment explanation
Indices: 6556--6607 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
6546 AACAAAATCA
*
6556 CTTTTCTTTTTCTT-TTTC
1 CTTTT-TTTTTCTTCTTTT
6574 CTTTTTTTTTCTTCTTTT
1 CTTTTTTTTTCTTCTTTT
*
6592 CTTTCTCTTTTCTTCT
1 CTTT-TTTTTTCTTCT
6608 CAAACCACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 12 0.40
19 10 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTTTTTTCTTCTTTT
Found at i:7436 original size:32 final size:32
Alignment explanation
Indices: 7400--7479 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
7390 CATAATTATT
7400 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
1 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
7432 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
1 AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
7464 AGTTCAGGGGGCAAAT
1 AGTTCAGGGGGCAAAT
7480 GGGCTATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (32 bp):
AGTTCAGGGGGCAAATTGGCCTAAATTTGCAA
Found at i:12265 original size:57 final size:57
Alignment explanation
Indices: 12204--12312 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
12194 TGATTACCCT
* * *
12204 TTTACTTCTTGATTAAATTGATTACCCTGAATTAAGCTCATTACTACTGATTGGTTC
1 TTTACTTCTTGATTAAATTAATTACCCTGAATTAAACTAATTACTACTGATTGGTTC
* * * *
12261 TTTACTTCTTGATTAACTTAATTGCTCTGAATTAAACTAATTACTATTGATT
1 TTTACTTCTTGATTAAATTAATTACCCTGAATTAAACTAATTACTACTGATT
12313 ACTTTTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (57 bp):
TTTACTTCTTGATTAAATTAATTACCCTGAATTAAACTAATTACTACTGATTGGTTC
Found at i:12428 original size:53 final size:52
Alignment explanation
Indices: 12350--12466 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 52
12340 CTTTTTTGCT
* * * *
12350 TCTTTTTAACTTAGTTATTCTGAATTAAATCC-ATTACTGATCACCATTTTTAC
1 TCTTTTTAACTTAATTACTCGGAATT-AAGCCAATTACTGATCACCA-TTTTAC
* *
12403 TCTTTTTAACTTAATTACTCGGAATTAAGCCAATTGCTGATTACCATTTTAC
1 TCTTTTTAACTTAATTACTCGGAATTAAGCCAATTACTGATCACCATTTTAC
*
12455 TCTTTTAAACTT
1 TCTTTTTAACTT
12467 GATTCCTGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
52 21 0.38
53 35 0.62
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (52 bp):
TCTTTTTAACTTAATTACTCGGAATTAAGCCAATTACTGATCACCATTTTAC
Found at i:12477 original size:33 final size:34
Alignment explanation
Indices: 12434--13361 Score: 527
Period size: 35 Copynumber: 27.2 Consensus size: 34
12424 GAATTAAGCC
*
12434 AATTGCTGATTACCA-TTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * **
12467 GATTCCTGATTACCATTTTTTACTCTTTTTGACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* * *
12502 AATTACTGATTATGATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTAC------TGATTAC-CATT----TTTA---CTCTTTTAAACTT
* * * *
12550 AATTACTTATTACAATTTTTACTCTTTTTAACAT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
** *
12584 AATTTTTTGATTACCATTTTTACTCTTTTTAACTT
1 AA-TTACTGATTACCATTTTTACTCTTTTAAACTT
* * *
12619 AATTTATTGATTACTATTTTTACTCTTTTTAACTT
1 AA-TTACTGATTACCATTTTTACTCTTTTAAACTT
* *
12654 AATTATTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
12689 GATTATTGATTA-C-TTTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* *
12721 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
12756 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
12791 GATTATTGATTA-C-TTTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* *
12823 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
12858 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
12893 AATTACTAATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
*
12928 AATTTATTGATTACCA--TTT-CTC-TTT--AC-T
1 AA-TTACTGATTACCATTTTTACTCTTTTAAACTT
* *
12956 GATTACT-ATCTTA-CACTTTTA---------ACTT
1 AATTACTGA--TTACCATTTTTACTCTTTTAAACTT
* *
12981 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
*
13016 GATTACTGATTACCATTTTTTACT-TTTTAAACTT
1 AATTACTGATTACCA-TTTTTACTCTTTTAAACTT
* *
13050 AATTACTGATTACCGTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * * * *
13084 AATTTATTGATTACCATTTCTCTTTACTGATTATCATCTT
1 AA-TTACTGATTACCA--T-T-TTTACT-CTTTTAAACTT
* * * *
13124 -ACT-CT-TTTA--ATTTAATTACTAATTACCTT-TACTT
1 AATTACTGATTACCATTT--TTACT-CTT---TTAAACTT
* * * *
13158 -TTTATTGATTAACA-TTTTACT-TTTTGAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * * *
13189 AATTATTGATTACCA-TTCTACTC-TTTGAATTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * *
13221 AATTACTGATTACCA-TCTTACTC-TGTGAACTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * *
13253 AATTACTGATTACCATTAATTTTTACTC-TCTGAATTT
1 AATTACTGATTACC----ATTTTTACTCTTTTAAACTT
* * *
13290 AATTACTGACTACCA-TTTTACTC-TTTGAATTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
* * *
13322 AATTACTGACTACCA-TTTTACTC-TTTGAATTT
1 AATTACTGATTACCATTTTTACTCTTTTAAACTT
13354 AATTACTG
1 AATTACTG
13362 TGAATTAAGC
Statistics
Matches: 756, Mismatches: 72, Indels: 135
0.79 0.07 0.14
Matches are distributed among these distances:
24 5 0.01
25 10 0.01
26 7 0.01
27 6 0.01
28 5 0.01
29 5 0.01
30 3 0.00
31 8 0.01
32 193 0.26
33 29 0.04
34 66 0.09
35 310 0.41
36 18 0.02
37 34 0.04
38 3 0.00
39 7 0.01
40 7 0.01
41 12 0.02
42 7 0.01
45 3 0.00
48 18 0.02
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (34 bp):
AATTACTGATTACCATTTTTACTCTTTTAAACTT
Found at i:12495 original size:35 final size:35
Alignment explanation
Indices: 12434--13102 Score: 653
Period size: 35 Copynumber: 18.5 Consensus size: 35
12424 GAATTAAGCC
* *
12434 AATTGCTGATTACCA--TTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
* * *
12467 GATTCCTGATTACCATTTTTTACTCTTTTTGACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12502 AATTACTGATTATGATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTAC------TGATTAC-CATT----TTTT--ACTCTTTTTAACTT
* * *
12550 AATTACTTATTA-CAATTTTTACTCTTTTTAACAT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
**
12584 AATTTTTTGATTACCA-TTTTTACTCTTTTTAACTT
1 AA-TTACTGATTACCATTTTTTACTCTTTTTAACTT
* *
12619 AATTTATTGATTACTA-TTTTTACTCTTTTTAACTT
1 AA-TTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12654 AATTATTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
* * *
12689 GATTATTGATTA-C--TTTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12721 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12756 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
* * *
12791 GATTATTGATTA-C--TTTTTACTCTTTTAAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12823 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12858 GATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
12893 AATTACTAATTACCATTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
* *
12928 AATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACACTTTT
1 AA-TTACTGATTACCA-TT-T-TTTAC----T-CT-TTTTA-AC--TT
*
12976 AACTTGATTACTGATTACCATTTTTTACTCTTTTTAACTT
1 AA-TT-A-C--TGATTACCATTTTTTACTCTTTTTAACTT
* *
13016 GATTACTGATTACCATTTTTTACT-TTTTAAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
13050 AATTACTGATTACC-GTTTTTACTCTTTTTAACTT
1 AATTACTGATTACCATTTTTTACTCTTTTTAACTT
*
13084 AATTTATTGATTACCATTT
1 AA-TTACTGATTACCATTT
13103 CTCTTTACTG
Statistics
Matches: 550, Mismatches: 42, Indels: 85
0.81 0.06 0.13
Matches are distributed among these distances:
32 58 0.11
33 23 0.04
34 62 0.11
35 291 0.53
36 19 0.03
37 2 0.00
38 2 0.00
39 7 0.01
40 5 0.01
41 7 0.01
42 10 0.02
43 5 0.01
44 4 0.01
45 5 0.01
46 6 0.01
48 25 0.05
49 6 0.01
50 2 0.00
51 2 0.00
52 9 0.02
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (35 bp):
AATTACTGATTACCATTTTTTACTCTTTTTAACTT
Found at i:12527 original size:48 final size:48
Alignment explanation
Indices: 12466--12561 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
12456 CTTTTAAACT
* *
12466 TGATTCCTGATTACCATTTTTTACTCTTTTTGACTTAATTACTGATTA
1 TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTA
*
12514 TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTTATTA
1 TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTA
12562 CAATTTTTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (48 bp):
TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTA
Found at i:12595 original size:83 final size:81
Alignment explanation
Indices: 12382--12665 Score: 236
Period size: 70 Copynumber: 3.6 Consensus size: 81
12372 AATTAAATCC
* * * *
12382 ATTACTGATCACC-ATTTTTACTCTTTTTAACTTAATTACTCGGAATTAAGCCAATTGCTGATTA
1 ATTACTGATTACCAATTTTTACTCTTTTTAACATAATTACT--G-ATTATG---ATTACTGATTA
*
12446 CCATTTTACTCTTTTAAACTTG
60 CCATTTTACTCTTTTAAACTTA
* * * *
12468 ATTCCTGATTACCATTTTTTACTCTTTTTGACTTAATTACTGATTATGATTACTGATTACCATTT
1 ATTACTGATTACCAATTTTTACTCTTTTTAACATAATTACTGATTATGATTACTGATTACCA--T
*
12533 TTTACTCTTTTTAACTTA
64 TTTACTCTTTTAAACTTA
* *
12551 ATTACTTATTA-CAATTTTTACTCTTTTTAACATAATT--T--TT-TGATTAC-CA-T----TTT
1 ATTACTGATTACCAATTTTTACTCTTTTTAACATAATTACTGATTATGATTACTGATTACCATTT
*
12604 TACTCTTTTTAACTTA
66 TACTCTTTTAAACTTA
* * * *
12620 ATTTATTGATTA-CTATTTTTACTCTTTTTAACTTAATTATTGATTA
1 A-TTACTGATTACCAATTTTTACTCTTTTTAACATAATTACTGATTA
12666 CCATTTTTTA
Statistics
Matches: 171, Mismatches: 18, Indels: 29
0.78 0.08 0.13
Matches are distributed among these distances:
69 20 0.12
70 32 0.19
72 1 0.01
74 2 0.01
75 1 0.01
76 1 0.01
77 7 0.04
78 2 0.01
80 1 0.01
81 13 0.08
82 23 0.13
83 26 0.15
84 5 0.03
85 1 0.01
86 11 0.06
87 25 0.15
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (81 bp):
ATTACTGATTACCAATTTTTACTCTTTTTAACATAATTACTGATTATGATTACTGATTACCATTT
TACTCTTTTAAACTTA
Found at i:12766 original size:102 final size:104
Alignment explanation
Indices: 12516--13102 Score: 713
Period size: 102 Copynumber: 5.5 Consensus size: 104
12506 ACTGATTATG
* *
12516 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTTATTA-CAATTTTTACTCTTTTTA
1 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTTTTTA
* * * *
12580 ACATAATTTTTTGATTACCATTTTTACTCTTTTTAACTTA
66 ACTTGA-TTATTGATTACCATTTTTACTCTTTTAAACTTA
* * *
12620 ATTTATTGATTACTA-TTTTTACTCTTTTTAACTTAATTATTGATTACCATTTTTTACTCTTTTT
1 A-TTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTTTTT
*
12684 AACTTGATTATTGATTA-C-TTTTTACTCTTTTAAACTTG
65 AACTTGATTATTGATTACCATTTTTACTCTTTTAAACTTA
*
12722 ATTACTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACTCTTTTTA
1 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTTTTTA
*
12787 ACTTGATTATTGATTA-C-TTTTTACTCTTTTAAACTTG
66 ACTTGATTATTGATTACCATTTTTACTCTTTTAAACTTA
*
12824 ATTACTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACTCTTTTTA
1 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTTTTTA
* * * *
12889 ACTTAATTACTAATTACCATTTTTTACTCTTTTTAACTTA
66 ACTTGATTATTGATTACCA-TTTTTACTCTTTTAAACTTA
* *
12929 ATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACACTTTTAACTTGATTACTGATTAC
1 A-TTACTGATTACCA------TTT--T--TTAC--TC-T----TTTTAACTTAATTACTGATTAC
*
12994 CATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACT-TTTTAAACTTA
48 CATTTTTTACTCTTTTTAACTTGATTATTGATTACCA-TTTTTACTCTTTTAAACTTA
* *
13051 ATTACTGATTACC-GTTTTTACTCTTTTTAACTTAATTTATTGATTACCATTT
1 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAA-TTACTGATTACCATTT
13103 CTCTTTACTG
Statistics
Matches: 431, Mismatches: 27, Indels: 50
0.85 0.05 0.10
Matches are distributed among these distances:
101 11 0.03
102 182 0.42
103 12 0.03
104 54 0.13
105 51 0.12
106 12 0.03
107 1 0.00
108 2 0.00
110 4 0.01
112 4 0.01
114 3 0.01
116 4 0.01
118 2 0.00
119 1 0.00
121 11 0.03
122 11 0.03
123 66 0.15
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (104 bp):
ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTTTTTA
ACTTGATTATTGATTACCATTTTTACTCTTTTAAACTTA
Found at i:12776 original size:137 final size:139
Alignment explanation
Indices: 12516--13102 Score: 742
Period size: 137 Copynumber: 4.1 Consensus size: 139
12506 ACTGATTATG
* * * *
12516 ATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTTATTACAATTTTTACTCTTTTTAA
1 ATTATTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTACTCTTTTTAA
* * ** * *
12581 CATAATTTTTTGATTACCA-TTTTTACTCTTTTTAACTTAATTTATTGATTACTA-TTTTTACTC
66 CTTGA-TTACTGATTACCATTTTTTACTCTTTTTAACTTAA-TTACTGATTACCATTTTTTACTC
12644 TTTTTAACTTA
129 TTTTTAACTTA
* *
12655 ATTATTGATTACCATTTTTTACTCTTTTTAACTTGATTATTGATTA-C-TTTTTACTCTTTTAAA
1 ATTATTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTACTCTTTTTAA
*
12718 CTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACTCTT
66 CTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTT
*
12783 TTTAACTTG
131 TTTAACTTA
*
12792 ATTATTGATTA-C--TTTTTACTCTTTTAAACTTGATTACTGATTACCATTTTTTACTCTTTTTA
1 ATTATTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCA-TTTTTACTCTTTTTA
*
12854 ACTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTAATTACCATTTTTTACTCT
65 ACTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCT
12919 TTTTAACTTA
130 TTTTAACTTA
12929 ATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACACTTTTAACTTGATTACTGATTAC
1 A-TTATTGATTACCA------TTT--T--TTAC--TC-T----TTTTAACTTGATTACTGATTAC
*
12994 CATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACT-TTTTAAACTTAATTACTG
48 CA-TTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTG
*
13058 ATTACC-GTTTTTACTCTTTTTAACTTA
112 ATTACCATTTTTTACTCTTTTTAACTTA
13085 ATTTATTGATTACCATTT
1 A-TTATTGATTACCATTT
13103 CTCTTTACTG
Statistics
Matches: 398, Mismatches: 24, Indels: 41
0.86 0.05 0.09
Matches are distributed among these distances:
134 29 0.07
135 1 0.00
136 23 0.06
137 155 0.39
138 10 0.03
139 43 0.11
147 2 0.01
149 1 0.00
150 3 0.01
151 4 0.01
153 2 0.01
154 1 0.00
156 35 0.09
157 22 0.06
158 67 0.17
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (139 bp):
ATTATTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTACTCTTTTTAA
CTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTTACTCTT
TTTAACTTA
Found at i:13095 original size:69 final size:68
Alignment explanation
Indices: 12972--13102 Score: 201
Period size: 69 Copynumber: 1.9 Consensus size: 68
12962 TATCTTACAC
* * *
12972 TTTTAACTTGATTACTGATTACCATTTTTTACTCTTTTTAACTTGATTACTGATTACCATTTTTT
1 TTTTAACTTAATTACTGATTACCAGTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTT
13037 ACT
66 ACT
*
13040 TTTTAAACTTAATTACTGATTACC-GTTTTTACTCTTTTTAACTTAATTTATTGATTACCATTT
1 TTTT-AACTTAATTACTGATTACCAGTTTTTACTCTTTTTAACTTAA-TTACTGATTACCATTT
13103 CTCTTTACTG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
68 24 0.42
69 33 0.58
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.54
Consensus pattern (68 bp):
TTTTAACTTAATTACTGATTACCAGTTTTTACTCTTTTTAACTTAATTACTGATTACCATTTTTT
ACT
Found at i:13114 original size:20 final size:22
Alignment explanation
Indices: 13086--13130 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
13076 TTTAACTTAA
*
13086 TTTATTGATTACCAT-TT-CTC
1 TTTACTGATTACCATCTTACTC
*
13106 TTTACTGATTATCATCTTACTC
1 TTTACTGATTACCATCTTACTC
13128 TTT
1 TTT
13131 TAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACCATCTTACTC
Found at i:13123 original size:156 final size:158
Alignment explanation
Indices: 12514--13150 Score: 723
Period size: 172 Copynumber: 3.9 Consensus size: 158
12504 TTACTGATTA
* * *
12514 TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTTATTA-CAATTTTTACTCTTTT
1 TGATTACTGATTACCATTTTTTACTCTTTTAAACTTAATTACTAATTACCAGTTTTTACTCTTTT
* * *
12578 TAACATAATTTTTTGATTACCATTTTTACTCTTTTTAACTTAATTTATTGATTACTATTTTTACT
66 TAACTTAATTTATTGATTACCA--TTT-CTC--TTT-AC---------TGATTACTA-TCTTACT
* *
12643 CTTTTTAACTTAATTATTGATTACCATTTTTTACTCTTTTTAACT
115 C-TTTTAACTTGATTACTGATTACCATTTTTTACTCTTTTTAACT
* * * *
12688 TGATTATTGATTA-C--TTTTTACTCTTTTAAACTTGATTACTGATTACCATTTTTTACTCTTTT
1 TGATTACTGATTACCATTTTTTACTCTTTTAAACTTAATTACTAATTACCAGTTTTTACTCTTTT
* * *
12750 TAACTTGA-TTACTGATTACCATTTTTTACTCTTTTTAACTTGATTATTGATTACTTTTTACTCT
66 TAACTTAATTTATTGATTACCA---TTT-CTC--TTT-AC-TGATTACT-A-T-C---TTACTCT
12814 TTTAAACTTGATTACTGATTACCATTTTTTACTCTTTTTAACT
117 TTT-AACTTGATTACTGATTACCATTTTTTACTCTTTTTAACT
* *
12857 TGATTACTGATTACCATTTTTTACTCTTTTTAACTTAATTACTAATTACCATTTTTTACTCTTTT
1 TGATTACTGATTACCATTTTTTACTCTTTTAAACTTAATTACTAATTACCAGTTTTTACTCTTTT
*
12922 TAACTTAATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACACTTTTAACTTGATTAC
66 TAACTTAATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACTCTTTTAACTTGATTAC
12987 TGATTACCATTTTTTACTCTTTTTAACT
131 TGATTACCATTTTTTACTCTTTTTAACT
*
13015 TGATTACTGATTACCATTTTTTACT-TTTTAAACTTAATTACTGATTACC-GTTTTTACTCTTTT
1 TGATTACTGATTACCATTTTTTACTCTTTTAAACTTAATTACTAATTACCAGTTTTTACTCTTTT
* *
13078 TAACTTAATTTATTGATTACCATTTCTCTTTACTGATTA-TCATCTTACTCTTTTAATTTAATTA
66 TAACTTAATTTATTGATTACCATTTCTCTTTACTGATTACT-ATCTTACTCTTTTAACTTGATTA
*
13142 CTAATTACC
130 CTGATTACC
13151 TTTACTTTTT
Statistics
Matches: 422, Mismatches: 28, Indels: 44
0.85 0.06 0.09
Matches are distributed among these distances:
155 1 0.00
156 80 0.19
157 22 0.05
158 64 0.15
159 9 0.02
162 1 0.00
163 1 0.00
164 9 0.02
165 10 0.02
166 2 0.00
167 3 0.01
168 4 0.01
169 58 0.14
170 4 0.01
171 39 0.09
172 90 0.21
173 13 0.03
174 12 0.03
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.54
Consensus pattern (158 bp):
TGATTACTGATTACCATTTTTTACTCTTTTAAACTTAATTACTAATTACCAGTTTTTACTCTTTT
TAACTTAATTTATTGATTACCATTTCTCTTTACTGATTACTATCTTACTCTTTTAACTTGATTAC
TGATTACCATTTTTTACTCTTTTTAACT
Found at i:13168 original size:52 final size:52
Alignment explanation
Indices: 13068--13214 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 52
13058 ATTACCGTTT
*
13068 TTACTCTTTTTAACTTAATTTATTGATTACCATTTCTCTTTACTGATTATCATC
1 TTACTC-TTTTAACTTAA-TTATTGATTACCATTTCTCTTTACTGATTAACATC
* * * * * *
13122 TTACTCTTTTAATTTAATTACTAATTACC-TTTACTTTTTATTGATTAACATT
1 TTACTCTTTTAACTTAATTATTGATTACCATTT-CTCTTTACTGATTAACATC
13174 TTACT-TTTTGAACTTAATTATTGATTACCATTCTACTCTTT
1 TTACTCTTTT-AACTTAATTATTGATTACCATT-T-CTCTTT
13215 GAATTTAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
51 7 0.09
52 46 0.59
53 12 0.15
54 13 0.17
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.54
Consensus pattern (52 bp):
TTACTCTTTTAACTTAATTATTGATTACCATTTCTCTTTACTGATTAACATC
Found at i:13195 original size:32 final size:32
Alignment explanation
Indices: 13163--13361 Score: 254
Period size: 32 Copynumber: 6.1 Consensus size: 32
13153 TACTTTTTAT
* * * *
13163 TGATTAACATTTTACTTTTTGAACTTAATTAT
1 TGATTACCATTTTACTCTTTGAATTTAATTAC
*
13195 TGATTACCATTCTACTCTTTGAATTTAATTAC
1 TGATTACCATTTTACTCTTTGAATTTAATTAC
* * *
13227 TGATTACCATCTTACTCTGTGAACTTAATTAC
1 TGATTACCATTTTACTCTTTGAATTTAATTAC
*
13259 TGATTACCATTAATTTTTACTCTCTGAATTTAATTAC
1 TGATTACC----A-TTTTACTCTTTGAATTTAATTAC
*
13296 TGACTACCATTTTACTCTTTGAATTTAATTAC
1 TGATTACCATTTTACTCTTTGAATTTAATTAC
*
13328 TGACTACCATTTTACTCTTTGAATTTAATTAC
1 TGATTACCATTTTACTCTTTGAATTTAATTAC
13360 TG
1 TG
13362 TGAATTAAGC
Statistics
Matches: 148, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
32 119 0.80
33 1 0.01
36 1 0.01
37 27 0.18
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (32 bp):
TGATTACCATTTTACTCTTTGAATTTAATTAC
Found at i:13292 original size:101 final size:101
Alignment explanation
Indices: 13172--13361 Score: 290
Period size: 101 Copynumber: 1.9 Consensus size: 101
13162 TTGATTAACA
* * * * *
13172 TTTTACTTTTTGAACTTAATTATTGATTACCATTCTACTCTTTGAATTTAATTACTGATTACCAT
1 TTTTACTCTCTGAACTTAATTACTGACTACCATTCTACTCTTTGAATTTAATTACTGACTACCAT
13237 CTTACTCTGTGAACTTAATTACTGATTACCATTAAT
66 CTTACTCTGTGAACTTAATTACTGATTACCATTAAT
* *
13273 TTTTACTCTCTGAATTTAATTACTGACTACCATTTTACTCTTTGAATTTAATTACTGACTACCAT
1 TTTTACTCTCTGAACTTAATTACTGACTACCATTCTACTCTTTGAATTTAATTACTGACTACCAT
* * *
13338 TTTACTCTTTGAATTTAATTACTG
66 CTTACTCTGTGAACTTAATTACTG
13362 TGAATTAAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (101 bp):
TTTTACTCTCTGAACTTAATTACTGACTACCATTCTACTCTTTGAATTTAATTACTGACTACCAT
CTTACTCTGTGAACTTAATTACTGATTACCATTAAT
Found at i:13305 original size:69 final size:64
Alignment explanation
Indices: 13182--13361 Score: 234
Period size: 69 Copynumber: 2.7 Consensus size: 64
13172 TTTTACTTTT
* * * *
13182 TGAACTTAATTATTGATTACCATTCTACTCTTTGAATTTAATTACTGATTACCATCTTACTCTG
1 TGAACTTAATTACTGACTACCATTTTACTCTTTGAATTTAATTACTGACTACCATCTTACTCTG
* * *
13246 TGAACTTAATTACTGATTACCATTAATTTTTACTCTCTGAATTTAATTACTGACTACCATTTTAC
1 TGAACTTAATTACTGACTACC----A-TTTTACTCTTTGAATTTAATTACTGACTACCATCTTAC
*
13311 TCTT
61 TCTG
*
13315 TGAATTTAATTACTGACTACCATTTTACTCTTTGAATTTAATTACTG
1 TGAACTTAATTACTGACTACCATTTTACTCTTTGAATTTAATTACTG
13362 TGAATTAAGC
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
64 44 0.43
65 1 0.01
68 1 0.01
69 56 0.55
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (64 bp):
TGAACTTAATTACTGACTACCATTTTACTCTTTGAATTTAATTACTGACTACCATCTTACTCTG
Found at i:13721 original size:21 final size:23
Alignment explanation
Indices: 13695--13742 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
13685 CTAAAAATCT
* *
13695 TTTTGAGAAAAA-C-ATTTTTTC
1 TTTTGAAAAAAATCAATTTCTTC
13716 TTTTGAAAAAAATCAATTTCTTC
1 TTTTGAAAAAAATCAATTTCTTC
13739 TTTT
1 TTTT
13743 TGGACAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTGAAAAAAATCAATTTCTTC
Found at i:16844 original size:1 final size:1
Alignment explanation
Indices: 16838--16863 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
16828 GCTAAAATAG
16838 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
16864 ATTATATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17028 original size:38 final size:33
Alignment explanation
Indices: 16955--17028 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 33
16945 TGTTATTAAT
* *
16955 TATATAGCTCTTTGATTTAGAAAAAAGATTATA
1 TATATAGCTCTTTGATTCAGAAAAAAAATTATA
16988 TATATAGCTCTTTGATTAACAGTAAAGAGAAAATTATA
1 TATATAGCTCTTTGATT--CAG-AAA-A-AAAATTATA
17026 TAT
1 TAT
17029 GGGATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 17 0.50
35 2 0.06
36 3 0.09
37 1 0.03
38 11 0.32
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (33 bp):
TATATAGCTCTTTGATTCAGAAAAAAAATTATA
Found at i:22074 original size:16 final size:16
Alignment explanation
Indices: 22053--22099 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
22043 CCTGCCACAG
22053 CAGAATGTTACCGCAA
1 CAGAATGTTACCGCAA
** *
22069 CAGAATGCCACCACAA
1 CAGAATGTTACCGCAA
22085 CAGAATGTTACCGCA
1 CAGAATGTTACCGCA
22100 GGATAGTAGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (16 bp):
CAGAATGTTACCGCAA
Found at i:25410 original size:11 final size:11
Alignment explanation
Indices: 25377--25410 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
25367 AAAATCTTCA
25377 AGTCTTCAAATT
1 AGTCTTCAAA-T
25389 A-TCTTCAAAT
1 AGTCTTCAAAT
25399 AGTCTTCAAAT
1 AGTCTTCAAAT
25410 A
1 A
25411 CGAACTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 18 0.86
12 1 0.05
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (11 bp):
AGTCTTCAAAT
Found at i:27342 original size:19 final size:20
Alignment explanation
Indices: 27297--27334 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27287 GAAAGAGACA
27297 AAAGACAACAACAACAACAAC
1 AAAGA-AACAACAACAACAAC
27318 AAAGAAACAAC-ACAACA
1 AAAGAAACAACAACAACA
27335 CATAAGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.68, C:0.26, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAGAAACAACAACAACAAC
Found at i:28581 original size:52 final size:52
Alignment explanation
Indices: 28521--28622 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
28511 GGGAACTTTC
*
28521 CCTAAATTGAACGCTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGA
* *
28573 CCTAAATTGAACACTTTGAAAACCTGCTGGGAACTTTCCCATTTTGAAAA
1 CCTAAATTGAACACTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAA
28623 CGAAAACCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (52 bp):
CCTAAATTGAACACTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGA
Found at i:28701 original size:129 final size:128
Alignment explanation
Indices: 28471--28751 Score: 436
Period size: 129 Copynumber: 2.2 Consensus size: 128
28461 AAACTTTTTG
* * * * *
28471 ATGGGAACTTTCCCTTTTTGAAAACGAAACGAAAACTGGCGGGAACTTTCCCTAAATTGAACGCT
1 ATGGGAACTTTCCCATTTTGAAAACGAAACCAAAACTGACGGGAACTTTCCCTAAATTGAACACC
* * *
28536 TTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAAACCTG
66 TTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACCTTGAAAACCTA
* *
28599 CTGGGAACTTTCCCATTTTGAAAACGAAAACCAAAATTGACGGGAACTTTCCCTAAATTGAACAC
1 ATGGGAACTTTCCCATTTTGAAAACG-AAACCAAAACTGACGGGAACTTTCCCTAAATTGAACAC
*
28664 CTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACGCCTTGAAAACCTA
65 CTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACCTTGAAAACCTA
* *
28728 ATGGGAACTTCCCCACTTTGAAAA
1 ATGGGAACTTTCCCATTTTGAAAA
28752 GACCTAAATT
Statistics
Matches: 138, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 24 0.17
129 114 0.83
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (128 bp):
ATGGGAACTTTCCCATTTTGAAAACGAAACCAAAACTGACGGGAACTTTCCCTAAATTGAACACC
TTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACCTTGAAAACCTA
Found at i:28709 original size:52 final size:52
Alignment explanation
Indices: 28650--28855 Score: 290
Period size: 52 Copynumber: 4.0 Consensus size: 52
28640 GGGAACTTTC
28650 CCTAAATTGAACACCTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATTGAACACCTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGA
* *
28702 CCTAAATTGAACGCCTTGAAAACCTAATGGGAACTTCCCCACTTTGAAAAGA
1 CCTAAATTGAACACCTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGA
* * *
28754 CCTAAATTGAACA-CTTCGAAAACTTGATGGGAACATTCCCA-TTTCGAAAAGA
1 CCTAAATTGAACACCTT-GAAAACCTAATGGGAACTTTCCCACTTT-GAAAAGA
* * * * *
28806 GCTAAATTGAACACTTTGAAAACTTGATGGGAAGTTTCCCACTTTGAAAA
1 CCTAAATTGAACACCTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAA
28856 CTTGATGGGA
Statistics
Matches: 139, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
51 6 0.04
52 128 0.92
53 5 0.04
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (52 bp):
CCTAAATTGAACACCTTGAAAACCTAATGGGAACTTTCCCACTTTGAAAAGA
Found at i:28857 original size:28 final size:28
Alignment explanation
Indices: 28817--28938 Score: 126
Period size: 28 Copynumber: 4.5 Consensus size: 28
28807 CTAAATTGAA
*
28817 CACTTTGAAAACTTGATGGGAAGTTTCC
1 CACTTTGAAAACTTGATGGGAACTTTCC
28845 CACTTTGAAAACTTGATGGGAACTTTCC
1 CACTTTGAAAACTTGATGGGAACTTTCC
*** * ***
28873 CACTTTGAAAA---GA-CCTAAATTGAA
1 CACTTTGAAAACTTGATGGGAACTTTCC
* *
28897 CACTTTGAAAACCTGATAGGAACTTTCC
1 CACTTTGAAAACTTGATGGGAACTTTCC
28925 CACTTTGAAAACTT
1 CACTTTGAAAACTT
28939 TGAAGGAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
24 15 0.20
25 2 0.03
27 2 0.03
28 55 0.74
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (28 bp):
CACTTTGAAAACTTGATGGGAACTTTCC
Found at i:28858 original size:80 final size:80
Alignment explanation
Indices: 28765--28938 Score: 278
Period size: 80 Copynumber: 2.2 Consensus size: 80
28755 CTAAATTGAA
* *
28765 CACTTCGAAAACTTGATGGGAACATTCCCA-TTTCGAAAAGAGCTAAATTGAACACTTTGAAAAC
1 CACTTTGAAAACTTGATGGGAACATTCCCACTTT-GAAAAGACCTAAATTGAACACTTTGAAAAC
* * *
28829 TTGATGGGAAGTTTCC
65 CTGATAGGAACTTTCC
*
28845 CACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAAACC
1 CACTTTGAAAACTTGATGGGAACATTCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAAACC
28910 TGATAGGAACTTTCC
66 TGATAGGAACTTTCC
28925 CACTTTGAAAACTT
1 CACTTTGAAAACTT
28939 TGAAGGAAAT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 84 0.97
81 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (80 bp):
CACTTTGAAAACTTGATGGGAACATTCCCACTTTGAAAAGACCTAAATTGAACACTTTGAAAACC
TGATAGGAACTTTCC
Found at i:29582 original size:16 final size:17
Alignment explanation
Indices: 29561--29593 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29551 TATTTACAAC
29561 GAGTACTT-AATCTAAT
1 GAGTACTTAAATCTAAT
29577 GAGTACTTAAATCTAAT
1 GAGTACTTAAATCTAAT
29594 TTGCTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
GAGTACTTAAATCTAAT
Found at i:29905 original size:16 final size:16
Alignment explanation
Indices: 29881--29917 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29871 GTTTCCCCTT
*
29881 TTCTATTTTCCTTTTA
1 TTCTTTTTTCCTTTTA
*
29897 TTCTTTTTTCCTTTTC
1 TTCTTTTTTCCTTTTA
29913 TTCTT
1 TTCTT
29918 CTATTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTTTTCCTTTTA
Found at i:33753 original size:24 final size:27
Alignment explanation
Indices: 33707--33759 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 27
33697 TCGGAGGCAC
*
33707 CTGCTGGTTAGCAGCTGGGTTTTCTTG
1 CTGCTGGTTAGCAGCTGGCTTTTCTTG
33734 CTGCTGGTTAG-A-C-GGCTTTTCTTG
1 CTGCTGGTTAGCAGCTGGCTTTTCTTG
33758 CT
1 CT
33760 CTTCTCGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 1 0.04
26 1 0.04
27 11 0.44
ACGTcount: A:0.08, C:0.21, G:0.30, T:0.42
Consensus pattern (27 bp):
CTGCTGGTTAGCAGCTGGCTTTTCTTG
Found at i:37789 original size:1 final size:1
Alignment explanation
Indices: 37783--37816 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
37773 TGTAAGAAGG
37783 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37817 CTGCTGCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38216 original size:24 final size:24
Alignment explanation
Indices: 38159--38231 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
38149 TCTCATAACA
* *
38159 TAAAA-ATAAGTAAACCATGAAGT
1 TAAAAGATAAGCAAACCATGAAAT
*
38182 GGAAAAGATAAGCAAACCATGAAAT
1 -TAAAAGATAAGCAAACCATGAAAT
38207 TAAAAGATAAGCAAACCATGAAAT
1 TAAAAGATAAGCAAACCATGAAAT
38231 T
1 T
38232 TCACCAGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 28 0.64
25 16 0.36
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (24 bp):
TAAAAGATAAGCAAACCATGAAAT
Found at i:42919 original size:1 final size:1
Alignment explanation
Indices: 42913--42987 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
42903 ACTTGTTCTT
* * * * * * * * * *
42913 AAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAACAAAAACAAAAACAAAAACAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
42978 AAAAGAAAAA
1 AAAAAAAAAA
42988 CTTTACCAAG
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:42928 original size:6 final size:6
Alignment explanation
Indices: 42913--42988 Score: 120
Period size: 6 Copynumber: 12.8 Consensus size: 6
42903 ACTTGTTCTT
42913 AAAA-A AAAACA AAAACA AAAACA AAAACA AAAAC- AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
*
42959 AAAACA AAAACAA AAAACA AAAAGA AAAAC
1 AAAACA AAAAC-A AAAACA AAAACA AAAAC
42989 TTTACCAAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
5 9 0.14
6 51 0.77
7 6 0.09
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:42954 original size:29 final size:30
Alignment explanation
Indices: 42913--42980 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
42903 ACTTGTTCTT
42913 AAAAA-AAAACAAAAACAAAAACAAAAAC-
1 AAAAACAAAACAAAAACAAAAACAAAAACA
42941 AAAAACAAAACAAAAACAAAAACAAAAACA
1 AAAAACAAAACAAAAACAAAAACAAAAACA
42971 AAAAACAAAA
1 AAAAACAAAA
42981 AGAAAAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 5 0.13
29 23 0.61
30 10 0.26
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAAACAAAACAAAAACAAAAACAAAAACA
Found at i:44184 original size:3 final size:3
Alignment explanation
Indices: 44176--44200 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44166 CAGGAGAGAA
44176 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
44201 CACATACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47910 original size:58 final size:58
Alignment explanation
Indices: 47843--47953 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 58
47833 ATAGGTTTCC
47843 ACAAGACCCTCAATAAACTCAGTCACCACATCTGCCACCACAATAACAAAAATTATTA
1 ACAAGACCCTCAATAAACTCAGTCACCACATCTGCCACCACAATAACAAAAATTATTA
* *
47901 ACAAGACCCTCAATAAACTCAGTCACCACATCTGCCACCACGATAAGAAAAAT
1 ACAAGACCCTCAATAAACTCAGTCACCACATCTGCCACCACAATAACAAAAAT
47954 AATAATAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.44, C:0.32, G:0.07, T:0.17
Consensus pattern (58 bp):
ACAAGACCCTCAATAAACTCAGTCACCACATCTGCCACCACAATAACAAAAATTATTA
Found at i:48092 original size:2 final size:2
Alignment explanation
Indices: 48085--48111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48075 TCTCAATAAA
48085 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
48112 AGCCTAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48775 original size:7 final size:7
Alignment explanation
Indices: 48763--48789 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48753 TTTCAGTCAG
48763 TTGAGAC
1 TTGAGAC
48770 TTGAGAC
1 TTGAGAC
48777 TTGAGAC
1 TTGAGAC
48784 TTGAGA
1 TTGAGA
48790 ATTGGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
TTGAGAC
Found at i:54087 original size:50 final size:53
Alignment explanation
Indices: 54028--54126 Score: 150
Period size: 50 Copynumber: 1.9 Consensus size: 53
54018 CAACACAAAC
54028 TCTTGACCAATTTTAATATCAACCAA-C-C-TCATCAACGTGATTATTTCTTT
1 TCTTGACCAATTTTAATATCAACCAATCTCTTCATCAACGTGATTATTTCTTT
* * *
54078 TCTTGACCAATTTTAATCTCAACCAATCTCTTGATCAATGTGATTATTT
1 TCTTGACCAATTTTAATATCAACCAATCTCTTCATCAACGTGATTATTT
54127 TTCTTTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 25 0.58
51 1 0.02
52 1 0.02
53 16 0.37
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (53 bp):
TCTTGACCAATTTTAATATCAACCAATCTCTTCATCAACGTGATTATTTCTTT
Found at i:68993 original size:6 final size:6
Alignment explanation
Indices: 68984--69019 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
68974 TCGTTCGAAC
*
68984 ATTTTT ATTTTT ATTCTT ATTTTT ATTTTT CATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT -ATTTT
69020 CATAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Done.