Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1579
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: 80561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3533 original size:16 final size:17
Alignment explanation
Indices: 3512--3544 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3502 AGAAAAGTGT
*
3512 GAAAGAGAGAG-GAAAA
1 GAAAGAAAGAGAGAAAA
3528 GAAAGAAAGAGAGAAAA
1 GAAAGAAAGAGAGAAAA
3545 AGGAGCAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAGAGAAAA
Found at i:6731 original size:28 final size:27
Alignment explanation
Indices: 6689--6748 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
6679 AATCTCATGA
*
6689 TATTTAAGTAAATTATCAAAATAATAT
1 TATTTAAATAAATTATCAAAATAATAT
** *
6716 TATTTAAAATAAATTATTGAAATATTAT
1 TATTT-AAATAAATTATCAAAATAATAT
6744 TATTT
1 TATTT
6749 TGATATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TATTTAAATAAATTATCAAAATAATAT
Found at i:7118 original size:14 final size:13
Alignment explanation
Indices: 7101--7146 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
7091 ATATAATTAT
7101 TTTAAAATATTTAA
1 TTTAAAAT-TTTAA
**
7115 TTTAATTTGTTTAA
1 TTTAAAAT-TTTAA
7129 TTTAAAATTTTAA
1 TTTAAAATTTTAA
7142 TTTAA
1 TTTAA
7147 GTTGTAACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TTTAAAATTTTAA
Found at i:7254 original size:38 final size:40
Alignment explanation
Indices: 7188--7268 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 40
7178 TCATCTACTT
*
7188 ATTTTAAATTAAGAGTTGTAATCATTTAATTA-TTTTAAA
1 ATTTTAAATTAAGAGTTATAATCATTTAATTATTTTTAAA
* *
7227 ATTTTAATTTAA-AGTTATAATCTTTTAATTATTTTTAAA
1 ATTTTAAATTAAGAGTTATAATCATTTAATTATTTTTAAA
7266 ATT
1 ATT
7269 ATGATTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 17 0.45
39 21 0.55
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (40 bp):
ATTTTAAATTAAGAGTTATAATCATTTAATTATTTTTAAA
Found at i:7560 original size:20 final size:20
Alignment explanation
Indices: 7503--7560 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
7493 TAATAAAAAC
7503 TATTATTATATT-TATAACAA
1 TATTATTAT-TTATATAACAA
* * * **
7523 TATTAATAATAACCTAACAA
1 TATTATTATTTATATAACAA
7543 TATTATTATTTATATAAC
1 TATTATTATTTATATAAC
7561 GCTAACCACT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTATTATTTATATAACAA
Found at i:13363 original size:24 final size:25
Alignment explanation
Indices: 13330--13379 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
13320 TTTTTAAATA
13330 ACTTTAAA-TTTCATAAAAATTATT
1 ACTTTAAATTTTCATAAAAATTATT
*
13354 ACTTTGAATTTTCATAAAAATTATT
1 ACTTTAAATTTTCATAAAAATTATT
13379 A
1 A
13380 TATAATAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (25 bp):
ACTTTAAATTTTCATAAAAATTATT
Found at i:16093 original size:15 final size:15
Alignment explanation
Indices: 16073--16101 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16063 TCAATTAAGT
16073 CATTTATTTAATTAC
1 CATTTATTTAATTAC
16088 CATTTATTTAATTA
1 CATTTATTTAATTA
16102 AATGGAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
CATTTATTTAATTAC
Found at i:20188 original size:26 final size:26
Alignment explanation
Indices: 20142--20191 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20132 GAATAGTAGT
* *
20142 TTTTGTTTCAAATATGTCACTAGTGA
1 TTTTGTTTCAAACATGCCACTAGTGA
20168 TTTT-TTTCAAACCATGCCACTAGT
1 TTTTGTTTCAAA-CATGCCACTAGT
20192 TTAAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (26 bp):
TTTTGTTTCAAACATGCCACTAGTGA
Found at i:20269 original size:39 final size:37
Alignment explanation
Indices: 20192--20284 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 37
20182 TGCCACTAGT
* *
20192 TTAAAATAGTGATTTTTCTTTTGAACTGTGTTACCAG
1 TTAAAATAGTGTTTTTTCTTTTGAACTGTGCTACCAG
* ** *
20229 TTAAGAATAGTAGTTTTTTGTTTTGATTTGTGCTATCAG
1 TTAA-AATAGT-GTTTTTTCTTTTGAACTGTGCTACCAG
*
20268 TTGAAAATAGTGGTTTT
1 TT-AAAATAGTGTTTTT
20285 CATTCAAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
37 4 0.09
38 11 0.24
39 29 0.63
40 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (37 bp):
TTAAAATAGTGTTTTTTCTTTTGAACTGTGCTACCAG
Found at i:21046 original size:13 final size:13
Alignment explanation
Indices: 21028--21061 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21018 ATTTTTCACT
21028 ATGTATCGATACA
1 ATGTATCGATACA
*
21041 ATGTATCAATACA
1 ATGTATCGATACA
*
21054 ATATATCG
1 ATGTATCG
21062 TGTATCGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21607 original size:16 final size:17
Alignment explanation
Indices: 21569--21607 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
21559 CTGATAAATC
21569 TGATTTTGAAAATAATA
1 TGATTTTGAAAATAATA
*
21586 TGATTTTGAAATTAATA
1 TGATTTTGAAAATAATA
21603 T-ATTT
1 TGATTT
21608 AGTGAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (17 bp):
TGATTTTGAAAATAATA
Found at i:26135 original size:13 final size:13
Alignment explanation
Indices: 26117--26144 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26107 AATTATTTAA
26117 TGTATCGATACAT
1 TGTATCGATACAT
26130 TGTATCGATACAT
1 TGTATCGATACAT
26143 TG
1 TG
26145 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26139 original size:33 final size:33
Alignment explanation
Indices: 26097--26162 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
26087 GCCAATGAAA
26097 TGTATCGATAAATT-AT-TTAATGTATCGATACAT
1 TGTATCGATAAATTGATCTT--TGTATCGATACAT
*
26130 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATAAATTGATCTTTGTATCGATACAT
26163 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 26 0.87
34 2 0.07
35 2 0.07
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATAAATTGATCTTTGTATCGATACAT
Found at i:41109 original size:12 final size:12
Alignment explanation
Indices: 41089--41152 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
41079 CGTCCTCCGT
*
41089 AAAAAAAAAAGA
1 AAAAAAAAAACA
*
41101 GACAAAAAAAA-A
1 -AAAAAAAAAACA
*
41113 AACAAAAAAACA
1 AAAAAAAAAACA
*
41125 AAAAAGAAAAA-G
1 AAAAA-AAAAACA
*
41137 AAAAAAACAACA
1 AAAAAAAAAACA
41149 AAAA
1 AAAA
41153 GGGTCCGGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
11 12 0.29
12 15 0.37
13 14 0.34
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:41114 original size:20 final size:20
Alignment explanation
Indices: 41089--41152 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
41079 CGTCCTCCGT
* *
41089 AAAAAAA-AAAGAGACAAAA
1 AAAAAAACAAAAAAACAAAA
41108 AAAAAAACAAAAAAACAAAA
1 AAAAAAACAAAAAAACAAAA
*
41128 AAGAAAAAGAAAAAAACAACAA
1 AA-AAAAACAAAAAAACAA-AA
41150 AAA
1 AAA
41153 GGGTCCGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 7 0.18
20 12 0.31
21 16 0.41
22 4 0.10
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAACAAAA
Found at i:41122 original size:29 final size:28
Alignment explanation
Indices: 41089--41152 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
41079 CGTCCTCCGT
*
41089 AAAAAAAAAAGAGACAAAA-AAAAAAACA
1 AAAAAAAAAAAAGA-AAAAGAAAAAAACA
41117 AAAAAACAAAAAAGAAAAAGAAAAAAACA
1 AAAAAA-AAAAAAGAAAAAGAAAAAAACA
*
41146 ACAAAAA
1 AAAAAAA
41153 GGGTCCGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAAAAGAAAAAGAAAAAAACA
Found at i:41134 original size:24 final size:24
Alignment explanation
Indices: 41089--41152 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
41079 CGTCCTCCGT
*
41089 AAAAAAAAAAGAGACAAAA-AAAAA-
1 AAAAAAAAAACA-A-AAAAGAAAAAG
*
41113 AACAAAAAAACAAAAAAGAAAAAG
1 AAAAAAAAAACAAAAAAGAAAAAG
*
41137 AAAAAAACAACAAAAA
1 AAAAAAAAAACAAAAA
41153 GGGTCCGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 24 0.71
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAACAAAAAAGAAAAAG
Found at i:42217 original size:37 final size:37
Alignment explanation
Indices: 42176--42257 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
42166 TGCCACAATC
42176 ATGCATTTGTGACATTCATAACATTTCATTTTGCATA
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATA
*
42213 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATA
42250 ATGCATTT
1 ATGCATTT
42258 ATGCTTCAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATA
Found at i:42674 original size:29 final size:28
Alignment explanation
Indices: 42627--43368 Score: 737
Period size: 29 Copynumber: 25.9 Consensus size: 28
42617 CCTCACCTTC
** * *
42627 CAAAGCCCACACTTTAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
42655 CAAAAGCCCACAAGTCAGTGGCAACCTTTT
1 C-AAAGCCCACAAGTCAGTGGC-ACCTTTT
*
42685 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
* *
42713 CAAAAGCCCACAAGTCGGTGGCACCCCTTT
1 C-AAAGCCCACAAGTCAGTGGCA-CCTTTT
*
42743 CAAAGCCTACAAGTCAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* * *
42770 CAGAAGCCCATAGGTCGGTGGCACCATTTT
1 CA-AAGCCCACAAGTCAGTGGCACC-TTTT
* * *
42800 CAAAGCCTACAAGTCAGTGGTATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
42828 CAAAAGCCCACAAGTTAGTGGCACCCTTTT
1 C-AAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * * *
42858 CAAAGCCCATAAATTAGTGGTATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
** *
42886 CAAAAGTTCACAAGTTAGTGGCACCCTTTT
1 C-AAAGCCCACAAGTCAGTGGCA-CCTTTT
* *
42916 CAAAGCCCACAAGTCAGTGGTATCTTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* *
42945 CAAAGCCTATAAGTCAGTGGCACCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
42973 CAAAGCCCACAAGTTAGTGGCACCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
43001 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
43029 CAAAAGCCCACAAGTCAGTGGCACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
* * * *
43058 TAAAGCCCACAAGTTAATGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
43086 CAAAAGCCCACAAGTTAGTGGCACCCTTTT
1 C-AAAGCCCACAAGTCAGTGGCA-CCTTTT
43116 CAAAGCCCACAAGTCAGTGGCATCC-TTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * *
43144 CAAAAGTCGATAAGTCAGTGGCACTTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
* *
43173 CAAAGCTCATAAGTCAGTGGCAACC-TTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* * * * *
43201 AAAAGCCCATAAGTCGGTGGTACCCCTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
*
43230 CAAAGCCCACAAGTTAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
*
43257 CGAAAGCCCACAAGTTAGTGGCACC-TTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
*
43285 CGAAAGCCCACAAGTTAGTGGGCACCTTTT
1 C-AAAGCCCACAAGTCAGT-GGCACCTTTT
*
43315 CAAAGCCCAAAAGTCAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* *
43342 CAAAGCCCATAAGGCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTT
43369 CGAAAGCACA
Statistics
Matches: 605, Mismatches: 80, Indels: 57
0.82 0.11 0.08
Matches are distributed among these distances:
27 39 0.06
28 203 0.34
29 323 0.53
30 40 0.07
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCACCTTTT
Found at i:43056 original size:57 final size:56
Alignment explanation
Indices: 42627--43368 Score: 737
Period size: 57 Copynumber: 13.0 Consensus size: 56
42617 CCTCACCTTC
** * *
42627 CAAAGCCCACACTTTAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGC-ACCTTTT
* * *
42685 CAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCGGTGGCACCCCTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * *
42743 CAAAGCCTACAAGTCAGTGGCAACC--TTCAGAAGCCCATAGGTCGGTGGCACCATTTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTTCA-AAGCCCACAAGTCAGTGGCACC-TTTT
* * * *
42800 CAAAGCCTACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * * * ** *
42858 CAAAGCCCATAAATTAGTGGTATCTTTTCAAAAGTTCACAAGTTAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * *
42916 CAAAGCCCACAAGTCAGTGGTATCTTTTTCAAAGCCTATAAGTCAGTGGCACCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTT
* *
42973 CAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTT
* * * *
43029 CAAAAGCCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTTAATGGCATCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTT
*
43086 CAAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTT
1 C-AAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTT
* * * * * *
43144 CAAAAGTCGATAAGTCAGTGGCACTTTTTCAAAGCTCATAAGTCAGTGGCAACC-TTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTT
* * * * * *
43201 AAAAGCCCATAAGTCGGTGGTACCCCTTTCAAAGCCCACAAGTTAGTGGCAACC--TT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTT
* *
43257 CGAAAGCCCACAAGTTAGTGGCACC-TTTCGAAAGCCCACAAGTTAGTGGGCACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGT-GGCACCTTTT
* * *
43315 CAAAGCCCAAAAGTCAGTGGCAACC--TTCAAAGCCCATAAGGCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGC-ACCTT
43369 CGAAAGCACA
Statistics
Matches: 589, Mismatches: 74, Indels: 44
0.83 0.10 0.06
Matches are distributed among these distances:
55 7 0.01
56 96 0.16
57 240 0.41
58 235 0.40
59 11 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (56 bp):
CAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTT
Found at i:43493 original size:43 final size:43
Alignment explanation
Indices: 43431--43516 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
43421 CATCTTCTTC
* * * * *
43431 TAAGTGCAATATTGCTGGCCTTGAATTAGCATATTGGTACCTT
1 TAAGTCCAATATTACTGGCCTTGAATCAGCACATTGGAACCTT
*
43474 TAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGAACCTT
1 TAAGTCCAATATTACTGGCCTTGAATCAGCACATTGGAACCTT
43517 CATCTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (43 bp):
TAAGTCCAATATTACTGGCCTTGAATCAGCACATTGGAACCTT
Found at i:43543 original size:49 final size:49
Alignment explanation
Indices: 43471--43920 Score: 429
Period size: 49 Copynumber: 8.9 Consensus size: 49
43461 ATATTGGTAC
** *
43471 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGAACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
43520 CTTTAAATCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCAT
* * *
43572 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTTTTA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
43620 CTTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * **
43670 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGTGCATTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-G-GCACCT-TCAT
* * **
43722 CTTTAAGTCCAGTGTCGCTGGCCTTGAACCAGCACATTAACACCTTCA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
** * * *
43770 CTTTTAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTTTT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTC--AT
* * * *
43823 CTTTAAGTCTAATGTCGCTGACCATGAATCAGCACATTGGCATTCTTTACAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--CCTT-CAT
* * ** * *
43875 CTTTAAGCCCAATATCATTGGTCC-TGAATTAGCATATTGGCACCTT
1 CTTTAAGTCCAATGTCGCTGG-CCTTGAATCAGCACATTGGCACCTT
43921 TATCACTCTT
Statistics
Matches: 325, Mismatches: 60, Indels: 31
0.78 0.14 0.07
Matches are distributed among these distances:
48 2 0.01
49 152 0.47
50 13 0.04
51 5 0.02
52 146 0.45
53 6 0.02
54 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:43646 original size:101 final size:98
Alignment explanation
Indices: 43471--43917 Score: 436
Period size: 101 Copynumber: 4.4 Consensus size: 98
43461 ATATTGGTAC
* * * * *
43471 CTTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGAAC-CTTCATCTTTAAATCCAATAT
1 CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTC-TCTTTAAGTCCAATGT
* *
43535 CGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
65 CGCTGGCCTTGAATCAGCACATTGGCACC--T-TCAT
* *
43572 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTTTTACT-TTTAAGTCCAATGT
1 CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTT-CTCTTTAAGTCCAATGT
*
43636 TGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
65 CGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
43670 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGTGCA-TTTGTCATCTTTAAGTCCAG
1 CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATT-G-GCACTTT-TC-TCTTTAAGTCCAA
* **
43734 TGTCGCTGGCCTTGAACCAGCACATTAACACCTTCA-
62 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
** ** * *
43770 CTTTTAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTTTTCTTTAAGTCTAA
1 C-TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCA--CTT-TTCTCTTTAAGTCCAA
* * *
43835 TGTCGCTGACCATGAATCAGCACATTGGCATTCTTTACAT
62 TGTCGCTGGCCTTGAATCAGCACATTGGCA--CCTT-CAT
* * * * *
43875 CTTTAAGCCCAATATCATTGGTCC-TGAATTAGCATATTGGCAC
1 CTTTAAGTCCAATGTCACTGG-CCTTGAATCAGCACATTGGCAC
43918 CTTTATCACT
Statistics
Matches: 290, Mismatches: 39, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
98 39 0.13
99 8 0.03
100 7 0.02
101 186 0.64
102 7 0.02
103 5 0.02
104 35 0.12
105 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (98 bp):
CTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTCTCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:43648 original size:150 final size:150
Alignment explanation
Indices: 43472--43810 Score: 525
Period size: 150 Copynumber: 2.3 Consensus size: 150
43462 TATTGGTACC
* *
43472 TTTAAGTCCAATGTTACTGGCCTTGAATCAGCACATTGGAACCTTCATCTTTAAATCCAATATCG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGAACCTTCATCTTTAAATCCAATATCA
* * *
43537 TTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACC
* * *
43602 AGCACATTAGCACTTTTACT
131 AGCACATTAACACCTTCACT
* *
43622 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGAACCTTCATCTTTAAATCCAATATCA
** *
43687 CTGGCCTTGAATCAGCATATTGGTGCATTTGTCATCTTTAAGTCCAGTGTCGCTGGCCTTGAACC
66 CTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACC
43752 AGCACATTAACACCTTCACT
131 AGCACATTAACACCTTCACT
** * *
43772 TTTAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGG
43811 CATTCTTCTT
Statistics
Matches: 172, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
150 172 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (150 bp):
TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGAACCTTCATCTTTAAATCCAATATCA
CTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACC
AGCACATTAACACCTTCACT
Found at i:43811 original size:150 final size:150
Alignment explanation
Indices: 43479--43864 Score: 520
Period size: 150 Copynumber: 2.6 Consensus size: 150
43469 ACCTTTAAGT
** * * *
43479 CCAATGTTACTGGCCTTGAATCAGCACATTGGAACCTTCATCTTTAAATCCAATATCGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
* *
43544 TGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
66 TGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACCAGCACAT
* * * **
43609 TAGCACTTTTACTTTTAAGT
131 TAACACCTTCACTTTTAAAC
* *
43629 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
** *
43694 TGAATCAGCATATTGGTGCATTTGTCATCTTTAAGTCCAGTGTCGCTGGCCTTGAACCAGCACAT
66 TGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACCAGCACAT
43759 TAACACCTTCACTTTTAAAC
131 TAACACCTTCACTTTTAAAC
* * * * * *
43779 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTTTTCTTTAAGTCTAATGTCGCTGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTC--ATCTTTAAGTCCAATATCGCTGG
* *
43844 CCATGAATCAGCACATTGGCA
63 CCTTGAATCAGCATATTGGCA
43865 TTCTTTACAT
Statistics
Matches: 206, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
150 167 0.81
151 4 0.02
153 35 0.17
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (150 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
TGAATCAGCATATTGGCACATTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAACCAGCACAT
TAACACCTTCACTTTTAAAC
Found at i:53294 original size:52 final size:51
Alignment explanation
Indices: 53215--53333 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 51
53205 TCAAATTTAA
* *
53215 CTAG-ATGTATCAATACATTGAAGAATGTATCAATACATTTGGATCAAGAAC
1 CTAGAATGTATCGATACAATGAAGAATGTATCAATACATTTGGATCAA-AAC
* *
53266 CTAGAATGTATCGATACAATGAATAATGTATCGATACATTTGGATCAAAAC
1 CTAGAATGTATCGATACAATGAAGAATGTATCAATACATTTGGATCAAAAC
*
53317 CCAGAATGTATCGATAC
1 CTAGAATGTATCGATAC
53334 GATACAAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 23 0.37
52 39 0.63
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (51 bp):
CTAGAATGTATCGATACAATGAAGAATGTATCAATACATTTGGATCAAAAC
Found at i:53983 original size:164 final size:166
Alignment explanation
Indices: 53662--53984 Score: 490
Period size: 167 Copynumber: 2.0 Consensus size: 166
53652 GAGATGTTTA
* *
53662 CATTTGTAAATACTAAAAATTTGGTTTCAAGGCCAAAGTTACTTGGCTAAATCTTTCTTATGACT
1 CATTTGTAAATACTAAAAATTTGGTTCCAAGGCCAAAGTTACTTGGCCAAATCTTTCTTATGAC-
* *
53727 TTTTTTTTTATGATTTTAGGTATGGATTTTGATATGTTTGATATTTAGTTTTGTGTTTGATTATA
65 TTTTTTTTGATGATTTTAGGTATGGATTTTGATATGTTTGATATTTAATTTTGTGTTTGATTATA
* *
53792 TAAGGATTAATTTGTAATTTTAGAAAGTTTAGGGGTT
130 TAAGGATCAATTTGTAATTTCAGAAAGTTTAGGGGTT
* * *
53829 CATTTGTAAATAC-AAGCAATTTTGTTCCAAGGCCAAAGTTACTTGGCCAAATCTTTTTTATGAC
1 CATTTGTAAATACTAA-AAATTTGGTTCCAAGGCCAAAGTTACTTGGCCAAATCTTTCTTATGAC
* * * *
53893 -TTTTTTTGGTGATTTTAGGTGTTGATTTTGATAT-TTTGATATTTAATTTTTTGTTTGATTATA
65 TTTTTTTTGATGATTTTAGGTATGGATTTTGATATGTTTGATATTTAATTTTGTGTTTGATTATA
53956 TAAGGATCAATTTGTAATTTCAGAAAGTT
130 TAAGGATCAATTTGTAATTTCAGAAAGTT
53985 CAAGGGTTAA
Statistics
Matches: 142, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 54 0.38
165 30 0.21
166 2 0.01
167 56 0.39
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (166 bp):
CATTTGTAAATACTAAAAATTTGGTTCCAAGGCCAAAGTTACTTGGCCAAATCTTTCTTATGACT
TTTTTTTGATGATTTTAGGTATGGATTTTGATATGTTTGATATTTAATTTTGTGTTTGATTATAT
AAGGATCAATTTGTAATTTCAGAAAGTTTAGGGGTT
Found at i:55944 original size:77 final size:77
Alignment explanation
Indices: 55817--55968 Score: 250
Period size: 77 Copynumber: 2.0 Consensus size: 77
55807 TCTTTCAATG
* *
55817 CTCACACTAAATTAACGTGATTCGATTGTCTCTTTCAACGTAGATATTGGAATCTCTAGTCAACT
1 CTCACACTAAATTAACGTGATTCGATTGTCCCTTTCAACGTAAATATTGGAATCTCTAGTCAACT
55882 AGATTGGGTTAC
66 AGATTGGGTTAC
* * *
55894 CTCACACTAAATTAACGTGGTTCGATTGTCCCTTTTAACGTAAATATTGGAATCTCTTGTCAACT
1 CTCACACTAAATTAACGTGATTCGATTGTCCCTTTCAACGTAAATATTGGAATCTCTAGTCAACT
*
55959 AGGTTGGGTT
66 AGATTGGGTT
55969 GCCATTATGT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (77 bp):
CTCACACTAAATTAACGTGATTCGATTGTCCCTTTCAACGTAAATATTGGAATCTCTAGTCAACT
AGATTGGGTTAC
Found at i:56858 original size:69 final size:69
Alignment explanation
Indices: 56734--56870 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
56724 ACATTCTCTA
*
56734 TGCCCATATCTTTCATATCAAACTTACTGGTCAACCATACTTTGATAACTCTAATGATCTTATAA
1 TGCCCATATCTTTCATATCAAACTTACTAGTCAACCATACTTTGATAACTCTAATGATCTTATAA
56799 TTAT
66 TTAT
* * * * *
56803 TGCCTATATCTTTCATATCGAACTTACTAGTCAACCATACTTTGGTAGC-CTTAATGATCTTATC
1 TGCCCATATCTTTCATATCAAACTTACTAGTCAACCATACTTTGATAACTC-TAATGATCTTATA
56867 ATTA
65 ATTA
56871 CTGCATAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 1 0.02
69 60 0.98
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (69 bp):
TGCCCATATCTTTCATATCAAACTTACTAGTCAACCATACTTTGATAACTCTAATGATCTTATAA
TTAT
Found at i:56889 original size:69 final size:69
Alignment explanation
Indices: 56747--56891 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 69
56737 CCATATCTTT
* * * *
56747 CATATCAAACTTACTGGTCAACCATACTTTGATAACTCTAATGATCTTATAATTATTGCCTATAT
1 CATATCAAACTTACTAGTCAACCATACTTTGATAACTCTAATGATCTTATAATTACTGCATAAAT
**
56812 CTTT
66 CTAA
* * * *
56816 CATATCGAACTTACTAGTCAACCATACTTTGGTAGC-CTTAATGATCTTATCATTACTGCATAAA
1 CATATCAAACTTACTAGTCAACCATACTTTGATAACTC-TAATGATCTTATAATTACTGCAT-AA
56880 ATC-AA
64 ATCTAA
56885 CATATCA
1 CATATCA
56892 TTTACATAGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 1 0.02
69 58 0.92
70 4 0.06
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (69 bp):
CATATCAAACTTACTAGTCAACCATACTTTGATAACTCTAATGATCTTATAATTACTGCATAAAT
CTAA
Found at i:59439 original size:96 final size:95
Alignment explanation
Indices: 59271--59501 Score: 234
Period size: 96 Copynumber: 2.4 Consensus size: 95
59261 AACGAGGCTA
* * * * * * * *
59271 GAGTATCCCTTCAGAGAAATGGGGTTGAAGTGTCCCCGACGATTACAATTTAACGAAAATAAAAT
1 GAGTATCCCCTCAGA-AGATGAGGTTGAAGTATCCCCGATGATGACAATTTAACAAAAACAAAAT
* * *
59336 TTAAATCTT-GACAAGTTTAAAAATGGGGTT-
65 TTAAATCTTGGA-AAATTTAAAAATAGAGTTC
* *
59366 GAAGTATCCCCTCAGAAGATGAGGTTGGAA-TATCCCCGATGATGGCAATTTAAGCAAAAACAAG
1 G-AGTATCCCCTCAGAAGATGAGGTT-GAAGTATCCCCGATGATGACAATTTAA-CAAAAACAAA
*
59430 ATTTGAATCTTGGAAAATTTAAAAATAGAGTTC
63 ATTTAAATCTTGGAAAATTTAAAAATAGAGTTC
* * * *
59463 GAGTATCCCCTTAAAAGATGAGATTAAAGTATCCCCGAT
1 GAGTATCCCCTCAGAAGATGAGGTTGAAGTATCCCCGAT
59502 AAATAAAATT
Statistics
Matches: 112, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
95 30 0.27
96 79 0.71
97 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (95 bp):
GAGTATCCCCTCAGAAGATGAGGTTGAAGTATCCCCGATGATGACAATTTAACAAAAACAAAATT
TAAATCTTGGAAAATTTAAAAATAGAGTTC
Found at i:63354 original size:22 final size:22
Alignment explanation
Indices: 63326--63377 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
63316 ATTTTCATCA
*
63326 AAGAAAATAGCAA-GAAAAAGTT
1 AAGAAAA-AGCAACGAAAAAGGT
63348 AAG-AAAAGCAACGAAAAAGGT
1 AAGAAAAAGCAACGAAAAAGGT
63369 AAGAAAAAG
1 AAGAAAAAG
63378 AAAAAAGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 14 0.52
22 8 0.30
ACGTcount: A:0.65, C:0.06, G:0.21, T:0.08
Consensus pattern (22 bp):
AAGAAAAAGCAACGAAAAAGGT
Found at i:69508 original size:21 final size:21
Alignment explanation
Indices: 69482--69538 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
69472 AAAAAAATTA
69482 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
69503 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
69524 AATGTATCGATACAT
1 AATGTATCGATACAT
69539 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:69618 original size:19 final size:19
Alignment explanation
Indices: 69594--69661 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
69584 AATTCAACAA
69594 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
69613 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
69628 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
69645 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
69662 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:69633 original size:13 final size:13
Alignment explanation
Indices: 69615--69639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69605 ACATAAGTTT
69615 TGTATCGATACAA
1 TGTATCGATACAA
69628 TGTATCGATACA
1 TGTATCGATACA
69640 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:69637 original size:32 final size:32
Alignment explanation
Indices: 69596--69658 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
69586 TTCAACAATT
*
69596 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
69628 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
69659 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:69719 original size:13 final size:13
Alignment explanation
Indices: 69701--69726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69691 CATTTTTCTG
69701 TGTATCGATACAT
1 TGTATCGATACAT
69714 TGTATCGATACAT
1 TGTATCGATACAT
69727 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:69723 original size:33 final size:33
Alignment explanation
Indices: 69681--69747 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
69671 GCCAAGGAAA
***
69681 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
69714 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
69747 T
1 T
69748 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:72298 original size:51 final size:51
Alignment explanation
Indices: 72222--72392 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
72212 TTATTTCTGA
* ***
72222 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
72273 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
72326 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
72378 GAGGATACTCCAACC
1 GGGGATACTCCAACC
72393 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 35 0.36
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:72411 original size:28 final size:28
Alignment explanation
Indices: 72375--72456 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
72365 ATTTTTCACA
*
72375 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
72403 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
72431 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
72457 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.