Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1014
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: 54474
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:5381 original size:21 final size:20
Alignment explanation
Indices: 5331--5418 Score: 70
Period size: 23 Copynumber: 4.0 Consensus size: 20
5321 CGTCCTCCAC
5331 ACAAAAAAAAA-AAACCAAATAA
1 ACAAAAAAAAACAAA--AAA-AA
*
5353 ACAAAAAAAAGAAGGAAAAAAAA
1 AC-AAAAAAA-AA-CAAAAAAAA
5376 ACAAAACAAAAACAAAAAAAA
1 ACAAAA-AAAAACAAAAAAAA
5397 ACAAAAACAACAACAACAAAAA
1 ACAAAAA-AA-AACAA-AAAAA
5419 GGGTCCGGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
20 1 0.02
21 16 0.28
22 13 0.23
23 19 0.33
24 5 0.09
26 3 0.05
ACGTcount: A:0.82, C:0.14, G:0.03, T:0.01
Consensus pattern (20 bp):
ACAAAAAAAAACAAAAAAAA
Found at i:5387 original size:16 final size:15
Alignment explanation
Indices: 5333--5418 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 15
5323 TCCTCCACAC
*
5333 AAAAAAAAAAAACCA
1 AAAAAAAAAAAAACA
*
5348 AATAAACAAAAAAAAGAA
1 AA-AAA-AAAAAAAA-CA
5366 GGAAAAAAAAACAAAACA
1 --AAAAAAAAA-AAAACA
5384 AAAACAAAAAAAAACA
1 AAAA-AAAAAAAAACA
* * *
5400 AAAACAACAACAACA
1 AAAAAAAAAAAAACA
5415 AAAA
1 AAAA
5419 GGGTCCGGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
15 14 0.24
16 17 0.29
17 12 0.21
18 6 0.10
19 7 0.12
20 2 0.03
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:5393 original size:31 final size:28
Alignment explanation
Indices: 5333--5418 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 28
5323 TCCTCCACAC
* *
5333 AAAAAAAAAAAACCAAATAAACAAAAAAA
1 AAAAAAAAAAAACAAAACAAA-AAAAAAA
5362 AGAAGGAAAAAAAAACAAAACAAAAACAAAAA
1 A-AA--AAAAAAAAACAAAACAAAAA-AAAAA
*
5394 AAAACAAAAACAACAACAACAAAAA
1 AAAA-AAAAAAAACAA-AACAAAAA
5419 GGGTCCGGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 2 0.04
30 12 0.25
31 12 0.25
32 22 0.46
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (28 bp):
AAAAAAAAAAAACAAAACAAAAAAAAAA
Found at i:5404 original size:22 final size:21
Alignment explanation
Indices: 5335--5418 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
5325 CTCCACACAA
* *
5335 AAAAAAAAAAC-CAAATAAAC
1 AAAAAAAAAACAAAAAAAAAC
*
5355 AAAAAAAAGAAGGAAAAAAAAAC
1 AAAAAAAA-AA-CAAAAAAAAAC
*
5378 AAAACAAAAACAAAAAAAAAC
1 AAAAAAAAAACAAAAAAAAAC
* *
5399 AAAAACAACAACAACAAAAA
1 AAAAA-AAAAACAAAAAAAA
5419 GGGTCCGGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.15
21 16 0.31
22 14 0.27
23 14 0.27
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAAC
Found at i:5415 original size:6 final size:6
Alignment explanation
Indices: 5368--5412 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
5358 AAAAAGAAGG
*
5368 AAAA-A AAAAC- AAAACA AAAAC- AAAA-A AAAACA AAAACA ACAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
5412 A
1 A
5413 CAAAAAGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
5 17 0.49
6 18 0.51
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:6853 original size:29 final size:29
Alignment explanation
Indices: 6811--6923 Score: 163
Period size: 29 Copynumber: 3.9 Consensus size: 29
6801 TTCCTCACCC
6811 TTCCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCCAAAGCCCACAAGTCAGTGGCATCTT
*
6840 TTCCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCCAAAGCCCACAAGTCAGTGGCA-TCTT
* * *
6870 TTCCAAAGCCCACAAGTCAATGGTATCTC
1 TTCCAAAGCCCACAAGTCAGTGGCATCTT
* *
6899 TTCAAAAGCCCACAAGTTAGTGGCA
1 TTCCAAAGCCCACAAGTCAGTGGCA
6924 ACCTTCAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 48 0.65
30 26 0.35
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (29 bp):
TTCCAAAGCCCACAAGTCAGTGGCATCTT
Found at i:6873 original size:30 final size:29
Alignment explanation
Indices: 6815--6969 Score: 154
Period size: 29 Copynumber: 5.3 Consensus size: 29
6805 TCACCCTTCC
* *
6815 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
6844 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCA
* * * *
6874 AAAGCCCACAAGTCAATGGTATCTCTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTCA
*
6903 AAAGCCCACAAGTTAGTGGCAACC--TTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
* ** *
6931 AAAGCACACAAGTTGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTCA
6960 AAAGCCCACA
1 AAAGCCCACA
6970 CAAGTTGGTG
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.06
28 19 0.17
29 56 0.51
30 28 0.26
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTCA
Found at i:6881 original size:59 final size:59
Alignment explanation
Indices: 6811--6928 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
6801 TTCCTCACCC
* * * *
6811 TTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCCAAAGCCCACAAGTCAATGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
* *
6870 TTCCAAAGCCCACAAGTCAATGGTATCTCTTCAAAAGCCCACAAGTTAGTGGCAACCTT
1 TTCCAAAGCCCACAAGTCAATGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
6929 CAAAAGCACA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (59 bp):
TTCCAAAGCCCACAAGTCAATGGCATCTCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:6973 original size:31 final size:28
Alignment explanation
Indices: 6898--6979 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
6888 AATGGTATCT
*
6898 CTTCAAAAGCC-CACAAGTTAGTGGCAAC
1 CTTCAAAAGCCACACAAGTTGGT-GCAAC
6926 CTTCAAAAG-CACACAAGTTGGTGCAACC
1 CTTCAAAAGCCACACAAGTTGGTGCAA-C
6954 CTTTCAAAAGCCCACACAAGTTGGTG
1 C-TTCAAAAG-CCACACAAGTTGGTG
6980 GCATCTTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
27 5 0.10
28 21 0.44
29 8 0.17
31 14 0.29
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (28 bp):
CTTCAAAAGCCACACAAGTTGGTGCAAC
Found at i:6974 original size:88 final size:88
Alignment explanation
Indices: 6810--6969 Score: 209
Period size: 88 Copynumber: 1.8 Consensus size: 88
6800 ATTCCTCACC
* * * * * *
6810 CTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCA
1 CTTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGCACACAAGTCAGTGGCACCCTTTTCAA
6875 AAGCCCACAAGTCAATGGTATCT
66 AAGCCCACAAGTCAATGGTATCT
* **
6898 CTTCAAAAGCCCACAAGTTAGTGGCAAC-CTTCAAAAGCACACAAGTTGGT-GCAACCC-TTTCA
1 CTTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGCACACAAGTCAGTGGC-ACCCTTTTCA
6960 AAAGCCCACA
65 AAAGCCCACA
6970 CAAGTTGGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
86 16 0.26
87 21 0.34
88 25 0.40
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (88 bp):
CTTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGCACACAAGTCAGTGGCACCCTTTTCAA
AAGCCCACAAGTCAATGGTATCT
Found at i:7043 original size:43 final size:43
Alignment explanation
Indices: 6991--7635 Score: 552
Period size: 43 Copynumber: 14.0 Consensus size: 43
6981 CATCTTCTTC
* *
6991 TAAGTCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
7034 TAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* * *
7083 TAAGTCCAATGTAGCTGGCCTTGAATCAACACTTTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
7126 TAAGTCCAATATAGCAGGCCTAGAGTCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* *
7175 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
7218 CAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
7261 TAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----------C--CTT
* *
7316 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* *
7365 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
7408 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG---CA-C--CTT
* * *
7457 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
7500 CAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCCTCATCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--C-TT
* * *
7550 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
7593 TAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
7636 CATCATCTTT
Statistics
Matches: 496, Mismatches: 69, Indels: 74
0.78 0.11 0.12
Matches are distributed among these distances:
43 256 0.52
44 1 0.00
45 3 0.01
46 5 0.01
47 3 0.01
49 153 0.31
50 35 0.07
53 1 0.00
55 39 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:7152 original size:92 final size:92
Alignment explanation
Indices: 6986--7639 Score: 843
Period size: 92 Copynumber: 7.0 Consensus size: 92
6976 GGTGGCATCT
* * *
6986 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
1 TCTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
*
7051 GCCTTGAGTCAGCATATTGGCACCTTCA
65 GCCTTGAATCAGCATATTGGCACCTTCA
* * *
7079 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACTTTGGCACCTTTAAGTCCAATATAGCAGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
* *
7144 CCTAGAGTCAGCATATTGGCACCTTCA
66 CCTTGAATCAGCATATTGGCACCTTCA
** * *
7171 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCTAATGTAGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
*
7236 CCTTGAATCAGCACATTGGCA----C-
66 CCTTGAATCAGCATATTGGCACCTTCA
* * * *
7258 -CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGACATCCTTTTTCTCATCTTTAAGTC
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----------C--CTTTAAGTC
*
7322 CAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
54 CAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
** *
7361 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
*
7426 CCTTGAATCAGCATATTGGCACCATCA
66 CCTTGAATCAGCATATTGGCACCTTCA
* ** * *
7453 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGTTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
*
7518 CCTTGAATCAGCATATTGGCACCCTCA
66 CCTTGAATCAGCATATTGGCACCTTCA
* * * *
7545 TCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATTGTTG
1 TC-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
7610 GCCTTGAATCAGCATATTGGCACCTTCA
65 GCCTTGAATCAGCATATTGGCACCTTCA
7638 TC
1 TC
7640 ATCTTTAAAA
Statistics
Matches: 498, Mismatches: 44, Indels: 38
0.86 0.08 0.07
Matches are distributed among these distances:
86 38 0.08
88 1 0.00
92 293 0.59
93 89 0.18
94 1 0.00
96 1 0.00
98 36 0.07
102 1 0.00
104 38 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATTGGCACCTTCA
Found at i:7483 original size:282 final size:284
Alignment explanation
Indices: 7031--7593 Score: 871
Period size: 282 Copynumber: 2.0 Consensus size: 284
7021 ACATTGGCAC
*
7031 CTTTAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* ** *
7096 GCTGGCCTTGAATCAACACTTTGGCACCTTTAAGTCCAATATAGCAGGCCTAGAGTCAGCATATT
66 GCTGGCCTTGAATCAACACATTGGCACCTCCAAGTCCAATATAGCAGGCCTAGAATCAGCATATT
* * *
7161 GGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCTA
131 GGCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCA
* * *
7226 ATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-C-TTTAAGTCCAATATCGCTGGCCTTGAATT
196 ATATAGCTGGCCTTGAATCAGCACATTGGCACCACTTTTAAGCCCAATATCGCTGGCCTTGAATC
7288 AGCACATTGACATCCTTTTTCTCAT
261 AGCACATTGACA-CCTTTTTCTCAT
*
7313 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* * * *
7378 GCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
66 GCTGGCCTTGAATCAACACATTGGCACCTCCAAGTCCAATATAGCAGGCCTAGAATCAGCATATT
7443 GGCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCA
131 GGCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCA
* * * *
7508 ATATCGTTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTG
196 ATATAGCTGGCCTTGAATCAGCACATTGGCA--C-CA-CTTTTAAGCCCAATATCGCTGGCCTTG
*
7573 AATCAGCACATTGGCACCTTT
257 AATCAGCACATTGACACCTTT
7594 AAGTCCAATA
Statistics
Matches: 253, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
282 209 0.83
286 1 0.00
288 6 0.02
289 37 0.15
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (284 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAACACATTGGCACCTCCAAGTCCAATATAGCAGGCCTAGAATCAGCATATT
GGCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCA
ATATAGCTGGCCTTGAATCAGCACATTGGCACCACTTTTAAGCCCAATATCGCTGGCCTTGAATC
AGCACATTGACACCTTTTTCTCAT
Found at i:7727 original size:282 final size:267
Alignment explanation
Indices: 6986--7639 Score: 798
Period size: 282 Copynumber: 2.4 Consensus size: 267
6976 GGTGGCATCT
* *
6986 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
1 TCTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
* *
7051 GCCTTGAGTCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACT
66 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACA
* *
7116 TTGGCACCT-TT-AAGTCCAATATAGCAGGCCTAGAGTCAGCATATTGGCACCTTCATCTTTAAG
131 TTGGCACCTCTTCAAGTCCAATAT--C--G-CT--AGCCAGCATATTGGCACCATCATCTTTAAG
* * *
7179 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCTAATGTAGCTGGCCTTGAAT
189 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATAGCTGGCCTTGAAT
7244 CAGCACATTGGCAC
254 CAGCACATTGGCAC
* *
7258 -C-TTTAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGACATCCTTTTTCTCATCTTTAAGT
1 TCTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----------C--CTTTAAGT
*
7321 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
54 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
* *
7386 TGAATCAGCACATTGGCACCTC--CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
119 TGAATCAACACATTGGCACCTCTTCAAGTCCAATATCGCTAG-C------CAGCATATTGGCACC
*
7449 ATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCG
177 ATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATAG
* *
7514 TTGGCCTTGAATCAGCATATTGGCACCCTC
242 CTGGCCTTGAATCAGCACATTGGCA----C
* * * *
7544 ATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATTGTT
1 -TCTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCT
7609 GGCCTTGAATCAGCATATTGGCACCTTCATC
65 GGCCTTGAATCAGCATATTGGCACCTTCATC
7640 ATCTTTAAAA
Statistics
Matches: 331, Mismatches: 23, Indels: 51
0.82 0.06 0.13
Matches are distributed among these distances:
270 37 0.11
271 1 0.00
275 1 0.00
277 50 0.15
278 1 0.00
279 1 0.00
280 2 0.01
282 199 0.60
286 1 0.00
288 1 0.00
289 37 0.11
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (267 bp):
TCTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACA
TTGGCACCTCTTCAAGTCCAATATCGCTAGCCAGCATATTGGCACCATCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATAGCTGGCCTTGAATCAGCACA
TTGGCAC
Found at i:8362 original size:13 final size:13
Alignment explanation
Indices: 8344--8432 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
8334 CATAAAGTGT
8344 TGTATCGATACAA
1 TGTATCGATACAA
8357 TGTATCGATACATAA
1 TGTATCGATAC--AA
8372 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
8389 TGTATCGATACATAA
1 TGTATCGATAC--AA
8404 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
8421 TGTATCGATACA
1 TGTATCGATACA
8433 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8379 original size:32 final size:32
Alignment explanation
Indices: 8324--8456 Score: 248
Period size: 32 Copynumber: 4.1 Consensus size: 32
8314 TTCAACGATT
8324 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
8357 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
8389 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
8421 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
8453 TGTA
1 TGTA
8457 AGATACTGCC
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 86 0.87
33 13 0.13
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:8381 original size:19 final size:18
Alignment explanation
Indices: 8322--8451 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
8312 ATTTCAACGA
8322 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
8341 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
8357 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
8373 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
8389 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
8405 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
8421 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
8437 TTTTGTATCGATACA
1 -TTTGTATCGATACA
8452 ATGTAAGATA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:8512 original size:13 final size:13
Alignment explanation
Indices: 8494--8518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8484 ATTACTCAAA
8494 TGTATCGATACAT
1 TGTATCGATACAT
8507 TGTATCGATACA
1 TGTATCGATACA
8519 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8570 original size:52 final size:52
Alignment explanation
Indices: 8527--8707 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
8517 CACTGATCTT
* * * *
8527 TGTATTGATACATGCAAGTAAGTTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
8579 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
8631 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
8683 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
8708 TCATATTTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:16361 original size:20 final size:20
Alignment explanation
Indices: 16336--16410 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
16326 GCCAAGGAAA
16336 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTTTCTG
16356 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTTTCTG
*** *
16376 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTTTCTG
16396 TGTATCGATACATTT
1 TGTATCGATACATTT
16411 GGAAATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTG
Found at i:18821 original size:51 final size:51
Alignment explanation
Indices: 18754--19087 Score: 203
Period size: 51 Copynumber: 6.4 Consensus size: 51
18744 AATTCTCCAC
* * * * *
18754 AATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AT
** *
18805 AATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAATTT-TTCAT
* * * ** * * *
18859 AATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT-TT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA-----TT-TTTCAT
* * * * ***
18916 GA--GGGGATACTCCAACCCTGACTTTATTTCCAAAATATTGATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAT
* * * * *
18965 AATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-AT
* * *
19017 AATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCAT
*
19069 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
19088 TCGTTATTTC
Statistics
Matches: 210, Mismatches: 53, Indels: 39
0.70 0.18 0.13
Matches are distributed among these distances:
48 3 0.01
49 4 0.02
51 64 0.30
52 51 0.24
53 32 0.15
54 25 0.12
55 19 0.09
56 2 0.01
57 5 0.02
58 4 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCAT
Found at i:18930 original size:28 final size:27
Alignment explanation
Indices: 18863--18933 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
18853 CTTCACAATC
* *
18863 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
* **
18890 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTTAATCAT-A
18918 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
18934 TGACTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:19034 original size:52 final size:52
Alignment explanation
Indices: 18920--19087 Score: 178
Period size: 52 Copynumber: 3.2 Consensus size: 52
18910 ATTTTTGAGG
* * * *** *
18920 GGATACTCCAACCCTGACTTTATTTCC-AAAATATTGATTTTTCATAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCATAATCGA
* * * *
18971 GGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTTTAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCC-ATAATCGA
* * * *
19023 GGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCATAATCGA
19075 GGATACTCCAACC
1 GGATACTCCAACC
19088 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
51 34 0.36
52 47 0.49
53 14 0.15
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.33
Consensus pattern (52 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCATAATCGA
Found at i:19106 original size:28 final size:28
Alignment explanation
Indices: 19070--19151 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
19060 ATTTTTCACA
* *
19070 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
19098 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
19126 --CGAGGGAATACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
19152 ATCTCTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 43 0.90
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:19141 original size:211 final size:211
Alignment explanation
Indices: 18760--19144 Score: 594
Period size: 211 Copynumber: 1.8 Consensus size: 211
18750 CCACAATCAG
* * * **
18760 GGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTT
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACAC
*
18825 CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTAATCATC
66 CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTAATCATC
* ** *
18890 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGACTTTATTTCCAAAATATT
131 GGGGATACTCCAACCCCGTTACTTCCGAGGGAATACTCCAACCCTGACTTTATTTCCAAAATATT
18955 GATTTTTCATAATCGA
196 GATTTTTCATAATCGA
* *
18971 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACA
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACA
* * * *
19036 CCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGTTATTTCA
65 CCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA-ATCA
19099 TCGGGGATACTCCAACCCCGTTACTTCCGAGGGAATACTCCAACCC
129 TCGGGGATACTCCAACCCCGTTACTTCCGAGGGAATACTCCAACCC
19145 CGTTATTATC
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
210 27 0.17
211 95 0.61
212 34 0.22
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACAC
CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTAATCATC
GGGGATACTCCAACCCCGTTACTTCCGAGGGAATACTCCAACCCTGACTTTATTTCCAAAATATT
GATTTTTCATAATCGA
Found at i:31520 original size:12 final size:12
Alignment explanation
Indices: 31503--31570 Score: 84
Period size: 12 Copynumber: 5.6 Consensus size: 12
31493 TCTTCTCTTC
31503 AAAAAAAAAACA
1 AAAAAAAAAACA
*
31515 AAAAAAAAAGCA
1 AAAAAAAAAACA
31527 AAAAAAAAAA-A
1 AAAAAAAAAACA
*
31538 ACAAAACAAAACA
1 A-AAAAAAAAACA
*
31551 AAAAACAAAACA
1 AAAAAAAAAACA
31563 AAGAAAAA
1 AA-AAAAA
31571 GAGAGAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 2 0.04
12 41 0.84
13 6 0.12
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:31529 original size:17 final size:16
Alignment explanation
Indices: 31503--31570 Score: 88
Period size: 15 Copynumber: 4.2 Consensus size: 16
31493 TCTTCTCTTC
31503 AAAAAA-AAAACAAAA
1 AAAAAACAAAACAAAA
31518 AAAAAAGC-AAA-AAAA
1 AAAAAA-CAAAACAAAA
31533 AAAAAACAAAACAAAA
1 AAAAAACAAAACAAAA
31549 CAAAAAACAAAACAAAGA
1 -AAAAAACAAAACAAA-A
31567 AAAA
1 AAAA
31571 GAGAGAAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.02
15 19 0.40
16 7 0.15
17 19 0.40
18 1 0.02
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAACAAAA
Found at i:31585 original size:1 final size:1
Alignment explanation
Indices: 31503--31570 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
31493 TCTTCTCTTC
* ** * * * * * *
31503 AAAAAAAAAACAAAAAAAAAAGCAAAAAAAAAAAAACAAAACAAAACAAAAAACAAAACAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31568 AAA
1 AAA
31571 GAGAGAAAAG
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:32643 original size:60 final size:59
Alignment explanation
Indices: 32549--33216 Score: 889
Period size: 59 Copynumber: 11.4 Consensus size: 59
32539 TCTCCTTCCG
32549 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32609 TTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32669 CCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32728 CCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
32787 CCTTCAGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
32846 CCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA
* **
32906 CCTTTTAGTCCTCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32961 TTTTCCAGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
33016 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTT-TCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
33077 TTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCTACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
**
33137 CCTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
*
33192 TTTTCCAGTCCTCAAAGAGCAGGAC
1 CTTT-CAGTCCTCAAAGAGCAGGAC
33217 TGACAGAGTT
Statistics
Matches: 555, Mismatches: 38, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
54 6 0.01
55 134 0.24
56 6 0.01
57 1 0.00
59 205 0.37
60 128 0.23
61 75 0.14
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (59 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:35413 original size:16 final size:16
Alignment explanation
Indices: 35392--35475 Score: 100
Period size: 16 Copynumber: 5.2 Consensus size: 16
35382 AATCTTCACT
35392 TTTTTTTTTTGTTTTG
1 TTTTTTTTTTGTTTTG
*
35408 TTTTTTTTTTCTTTT-
1 TTTTTTTTTTGTTTTG
*
35423 TCCTTTTTTTTGTTTTG
1 T-TTTTTTTTTGTTTTG
*
35440 TTTTTTTTTTCTTTT-
1 TTTTTTTTTTGTTTTG
*
35455 TCCTTTTTTTTGTTTTG
1 T-TTTTTTTTTGTTTTG
35472 TTTT
1 TTTT
35476 CTTCTTTTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.04
16 52 0.93
17 2 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTGTTTTG
Found at i:35435 original size:32 final size:32
Alignment explanation
Indices: 35394--35475 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
35384 TCTTCACTTT
35394 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
35426 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
35458 TTTTTTTTGTTTTGTTTT
1 TTTTTTTTGTTTTGTTTT
35476 CTTCTTTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (32 bp):
TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCC
Found at i:35439 original size:37 final size:35
Alignment explanation
Indices: 35390--35484 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 35
35380 CAAATCTTCA
35390 CTTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1 CTTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
35425 C---TTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1 CTTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
* *
35457 CTTTTTTTTGTTTTGTTTTCTTCTTTTT
1 C-TTTTTTT-TTTTGTTTTGTTTTTTTT
35485 CCAATTGCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
32 32 0.60
35 1 0.02
36 4 0.08
37 16 0.30
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (35 bp):
CTTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
Found at i:35484 original size:1 final size:1
Alignment explanation
Indices: 35391--35475 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
35381 AAATCTTCAC
* * * ** * * *
35391 TTTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * *
35456 CCTTTTTTTTGTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTT
35476 CTTCTTTTTC
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:43480 original size:55 final size:54
Alignment explanation
Indices: 43331--43827 Score: 625
Period size: 55 Copynumber: 9.1 Consensus size: 54
43321 TAACCTATCA
* * *
43331 AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAGAGAGC
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTT-TCAGTCCTCAAAGAGC
*
43386 AGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
1 AGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGC
* * *
43447 AAGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGC
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGC
* * * *
43502 AGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGT
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGC
*
43557 AGGACACCTTTCAAAGCCCACACAAG-T--TGG---TTGCA-TCCTCAAAGAGC
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGC
*
43604 AGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGC
1 AGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGC
* *
43659 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGC
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGC
43714 AGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
1 AGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGC
* * *
43769 AGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGC
1 AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGC
43824 AGGA
1 AGGA
43828 TACACTTTAT
Statistics
Matches: 389, Mismatches: 29, Indels: 48
0.83 0.06 0.10
Matches are distributed among these distances:
47 34 0.09
48 5 0.01
49 2 0.01
50 3 0.01
52 3 0.01
54 16 0.04
55 269 0.69
56 8 0.02
61 49 0.13
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (54 bp):
AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGC
Found at i:43781 original size:212 final size:212
Alignment explanation
Indices: 43396--43799 Score: 611
Period size: 212 Copynumber: 1.9 Consensus size: 212
43386 AGGACGCCTT
* *
43396 CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACCTCTCAA
1 CACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCCCAAAGAGCAAGACACCTCTCAA
* *
43461 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACA
66 AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACA
* *
43526 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTTGC
131 AGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTTGC
43591 ATCCTCAAAGAGCAGGA
196 ATCCTCAAAGAGCAGGA
* *
43608 CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTTTC
1 CACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCCCAAAGAGCAAGACACCTCTC
* **
43671 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACACCTCTT-AAAGCCCA
64 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCA
* *
43734 CACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTG
127 CACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
43798 GT
191 GT
43800 GGCACTTTTT
Statistics
Matches: 174, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
211 3 0.02
212 161 0.93
213 10 0.06
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (212 bp):
CACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCCCAAAGAGCAAGACACCTCTCAA
AGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACA
AGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTTGC
ATCCTCAAAGAGCAGGA
Found at i:44605 original size:21 final size:21
Alignment explanation
Indices: 44558--44611 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44548 AAAAATTATC
*
44558 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
44579 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
44600 CAAATGTATCGA
1 CAAATGTATCGA
44612 CACAGGGTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:44758 original size:33 final size:33
Alignment explanation
Indices: 44716--44782 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
44706 ACCAAGGAAA
***
44716 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
44749 TGTATCGATATATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
44782 T
1 T
44783 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:47319 original size:31 final size:28
Alignment explanation
Indices: 47236--47307 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
47226 CTTCACAATC
* * ***
47236 GGGGACACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
47263 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
47291 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
47308 AACTTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:47352 original size:51 final size:51
Alignment explanation
Indices: 47293--47460 Score: 201
Period size: 52 Copynumber: 3.3 Consensus size: 51
47283 ATTTCCGAGG
* * *** *
47293 GGATACTCCAACCCCAACTTTATTTCCAAAATATTGATTTTTCATAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGA
* * * * *
47344 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-ATAATCGA
* *
47396 GGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATCGA
47448 GGATACTCCAACC
1 GGATACTCCAACC
47461 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 34 0.35
52 48 0.50
53 14 0.15
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGA
Found at i:47514 original size:211 final size:210
Alignment explanation
Indices: 47127--47518 Score: 581
Period size: 211 Copynumber: 1.9 Consensus size: 210
47117 AATTCTCCAC
* * * *
47127 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACTC
* *
47192 CAACTCCGATTTTATTTCCAAAAAACGCCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAAC-CCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * *
47257 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTTCCAA
130 ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCCCAACTTTATTTCCAA
47322 AATATTGATTTTTCAT
195 AATATTGATTTTTCAT
* *
47338 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGAGGATACT
* *
47403 CCAACACCGATTTTATTTCCAAAAATA-CCAATTT-TTCACAATCGAGGATACTCCAACCTCGTT
65 CCAACACCGATTTTATTTCCAAAAA-ACCCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
* * *
47466 ATTTCATCGGGGATACTCCAATCCTGTTACTTCCAAGGGAACACTCCAACCCC
129 A-ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCCC
47519 GTTATTATCT
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
210 27 0.17
211 94 0.58
212 39 0.24
213 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (210 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACTC
CAACACCGATTTTATTTCCAAAAAACCCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTAA
TCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGAACACTCCAACCCCAACTTTATTTCCAAA
ATATTGATTTTTCAT
Found at i:49203 original size:13 final size:13
Alignment explanation
Indices: 49182--49234 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
49172 CGATACATGG
*
49182 TACAATGTATCGA
1 TACATTGTATCGA
49195 TACATTGTATCGA
1 TACATTGTATCGA
49208 TACA-TG-AT-G-
1 TACATTGTATCGA
49217 -A-ATTGTATCGA
1 TACATTGTATCGA
49228 TACATTG
1 TACATTG
49235 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:49208 original size:33 final size:33
Alignment explanation
Indices: 49166--49234 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
49156 CTACCACTAT
*
49166 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
49199 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
49232 TTG
1 TTG
49235 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:49710 original size:20 final size:21
Alignment explanation
Indices: 49666--49716 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
49656 TTCTATAATT
49666 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAATAGTAAA
* *
49687 TGTATCGATACATA-AGTGAA
1 TGTATCGATACAAATAGTAAA
*
49707 TGTATTGATA
1 TGTATCGATA
49717 TATGCCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAAATAGTAAA
Found at i:53051 original size:19 final size:20
Alignment explanation
Indices: 53027--53077 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
53017 TACAAGCCAA
**
53027 TGTATCGATACAATTTTTG-
1 TGTATCGATACAATACTTGC
53046 TGTATCGATAC-ATACTTGC
1 TGTATCGATACAATACTTGC
53065 TGTATCGATACAA
1 TGTATCGATACAA
53078 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 22 0.79
20 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAATACTTGC
Found at i:53744 original size:37 final size:38
Alignment explanation
Indices: 53676--53759 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 38
53666 TTTCTTTTAT
**
53676 TTCT-CCCTTAATCAAAATAAATTAACAAATTTGTACA
1 TTCTCCCCTTAATCAAAATAAATTAACAAATTTACACA
* * *
53713 TTCTCCCCTTAAT-AAAATAATTGTAGC-AATTTACGCA
1 TTCTCCCCTTAATCAAAATAAAT-TAACAAATTTACACA
53750 TTCTCCCCTT
1 TTCTCCCCTT
53760 TATCTCCCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 29 0.73
38 11 0.28
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (38 bp):
TTCTCCCCTTAATCAAAATAAATTAACAAATTTACACA
Done.