Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000165.1 Hibiscus syriacus cultivar Beakdansim tig00000291_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 89583
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1555 original size:32 final size:32
Alignment explanation
Indices: 1514--1575 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
1504 GAAGAAATGA
1514 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1546 TTGTTATGCTCATCTTGTAGAGATACTTCT
1 TTGTTATGCTCATCTTGTAGAGATACTTCT
1576 TATTTCCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (32 bp):
TTGTTATGCTCATCTTGTAGAGATACTTCTCG
Found at i:5080 original size:43 final size:42
Alignment explanation
Indices: 4988--5071 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
4978 CGTGCATCAA
* * *
4988 ACAAAACTTTACATATAGGGGACATCTTTCAGTCTTATCTTT
1 ACAAAACTTTACATATAGGGGACAACTTTCACTCTTAACTTT
* * *
5030 AACAAAACTTTACATATAGGGTATAACTTTCCCTCTTAACTT
1 -ACAAAACTTTACATATAGGGGACAACTTTCACTCTTAACTT
5072 CTCTAAAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (42 bp):
ACAAAACTTTACATATAGGGGACAACTTTCACTCTTAACTTT
Found at i:5853 original size:24 final size:24
Alignment explanation
Indices: 5826--5901 Score: 152
Period size: 24 Copynumber: 3.2 Consensus size: 24
5816 TGAGAAAGGA
5826 AAAATAAATTGGTTAGTACCAATT
1 AAAATAAATTGGTTAGTACCAATT
5850 AAAATAAATTGGTTAGTACCAATT
1 AAAATAAATTGGTTAGTACCAATT
5874 AAAATAAATTGGTTAGTACCAATT
1 AAAATAAATTGGTTAGTACCAATT
5898 AAAA
1 AAAA
5902 GAAAAAAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.32
Consensus pattern (24 bp):
AAAATAAATTGGTTAGTACCAATT
Found at i:6546 original size:12 final size:12
Alignment explanation
Indices: 6532--6572 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
6522 GACTAAGATA
6532 AAAATAATAA-T
1 AAAATAATAATT
6543 AAAATAATAATT
1 AAAATAATAATT
6555 AAAATAATAATT
1 AAAATAATAATT
6567 AAAATA
1 AAAATA
6573 TAAAAGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:6587 original size:12 final size:11
Alignment explanation
Indices: 6532--6590 Score: 70
Period size: 12 Copynumber: 5.5 Consensus size: 11
6522 GACTAAGATA
6532 AAAATAATAAT
1 AAAATAATAAT
6543 AAAATAATAATT
1 AAAATAATAA-T
6555 AAAATAATAATT
1 AAAATAATAA-T
6567 AAAAT-AT-A-
1 AAAATAATAAT
*
6575 AAAGTAATAAT
1 AAAATAATAAT
6586 AAAAT
1 AAAAT
6591 TATATTGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 16 0.38
12 18 0.43
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:6594 original size:20 final size:19
Alignment explanation
Indices: 6532--6594 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 19
6522 GACTAAGATA
6532 AAAATAATAATAAAATAATAATT
1 AAAATAATAATAAAAT--T-A-T
6555 AAAATAATAATTAAAA-TAT
1 AAAATAATAA-TAAAATTAT
6574 AAAAGTAATAATAAAATTAT
1 AAAA-TAATAATAAAATTAT
6594 A
1 A
6595 TTGTAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 10 0.27
20 11 0.30
21 1 0.03
23 10 0.27
24 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAATAATAAAATTAT
Found at i:6603 original size:31 final size:31
Alignment explanation
Indices: 6532--6590 Score: 54
Period size: 31 Copynumber: 1.9 Consensus size: 31
6522 GACTAAGATA
6532 AAAATAATAA-TAAAATAATAATTAAAATA-
1 AAAATAATAATTAAAATAATAATTAAAATAT
*
6561 ATAATTAA-AATATAAAAGTAATAA-TAAAAT
1 A-AAATAATAAT-TAAAA-TAATAATTAAAAT
6591 TATATTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
29 3 0.12
30 5 0.20
31 11 0.44
32 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAATAATAATTAAAATAATAATTAAAATAT
Found at i:7893 original size:3 final size:3
Alignment explanation
Indices: 7885--7925 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
7875 AATATTTATT
*
7885 TAA TAA TAA TAAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
7926 AAGCAAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7901 original size:13 final size:13
Alignment explanation
Indices: 7885--7926 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
7875 AATATTTATT
7885 TAATAATAATAAA
1 TAATAATAATAAA
7898 TAATAATAATAATGTA
1 TAATAATAATAA---A
7914 TAATAATAATAAA
1 TAATAATAATAAA
7927 AGCAAACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 13 0.50
16 13 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:7906 original size:16 final size:16
Alignment explanation
Indices: 7885--7925 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
7875 AATATTTATT
7885 TAATAATAATAAATAA
1 TAATAATAATAAATAA
**
7901 TAATAATAATGTATAA
1 TAATAATAATAAATAA
7917 TAATAATAA
1 TAATAATAA
7926 AAGCAAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:9320 original size:14 final size:14
Alignment explanation
Indices: 9298--9331 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9288 TTGATTGATA
* *
9298 TATACATTATAATT
1 TATATATTAAAATT
9312 TATATATTAAAATT
1 TATATATTAAAATT
9326 TATATA
1 TATATA
9332 CTAATTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATTAAAATT
Found at i:10155 original size:22 final size:22
Alignment explanation
Indices: 10127--10179 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
10117 TGTTCGGGTT
10127 TTCAAAAGCTATTACTTTCCTA
1 TTCAAAAGCTATTACTTTCCTA
* *
10149 TTCAAAAGCTATTATTTTTCTA
1 TTCAAAAGCTATTACTTTCCTA
*
10171 TTCGAAAGC
1 TTCAAAAGC
10180 AGAAAAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (22 bp):
TTCAAAAGCTATTACTTTCCTA
Found at i:10792 original size:83 final size:82
Alignment explanation
Indices: 10604--10875 Score: 244
Period size: 83 Copynumber: 3.3 Consensus size: 82
10594 ATTTTTATAA
* * * * *
10604 AAACGCCACTATAAACAAACATATTACGGCTTTCGTACGACAAACACCGCTAAATTA-TTACTCT
1 AAACGCCACTATAAACAACCCTATTACGGCTTT-GTATGAAAAACGCCGCTAAATTACTT-CTCT
* * * *
10668 ATTGCGGCATTTTTTGCAC
64 ATAGCGGCGTTTGTTGGAC
* * * * *
10687 AAATGCCACTATAAGCATCCCTATTACGGCGTTTGTTTGATAAACGCCGCTAAATTACTTCTCTA
1 AAACGCCACTATAAACAACCCTATTACGGC-TTTGTATGAAAAACGCCGCTAAATTACTTCTCTA
*
10752 TAGCGTCGTTTGTTGGAC
65 TAGCGGCGTTTGTTGGAC
* ** * * *
10770 AAACGCCACCATAAACAACCCTATTGTGGCATTTGTAT-AAAAACGTCACTAAATTACTACTCTA
1 AAACGCCACTATAAACAACCCTATTACGGC-TTTGTATGAAAAACGCCGCTAAATTACTTCTCTA
*
10834 TTA-CGGCGTTTGTTGGAA
65 -TAGCGGCGTTTGTTGGAC
** **
10852 AAACTTCGTTATAAACAACCCTAT
1 AAACGCCACTATAAACAACCCTAT
10876 CCCGACGTTT
Statistics
Matches: 153, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
82 54 0.35
83 94 0.61
84 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (82 bp):
AAACGCCACTATAAACAACCCTATTACGGCTTTGTATGAAAAACGCCGCTAAATTACTTCTCTAT
AGCGGCGTTTGTTGGAC
Found at i:11522 original size:16 final size:16
Alignment explanation
Indices: 11501--11534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11491 CCGGGTATCG
11501 GGTACCCGCAAAATCC
1 GGTACCCGCAAAATCC
* *
11517 GGTACCCGTAACATCC
1 GGTACCCGCAAAATCC
11533 GG
1 GG
11535 GTCGGGACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (16 bp):
GGTACCCGCAAAATCC
Found at i:11614 original size:16 final size:16
Alignment explanation
Indices: 11572--11614 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
11562 ACCCAGAAGT
*
11572 TCCGGGTACCCGGAAA
1 TCCGGGTACCCGAAAA
*
11588 T-CGGATACCCGAAAA
1 TCCGGGTACCCGAAAA
11603 TCCGGGTACCCG
1 TCCGGGTACCCG
11615 GATTTGCCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.14
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:17067 original size:19 final size:19
Alignment explanation
Indices: 17026--17072 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
17016 GTAATGAGAT
* *
17026 ATTTAAAT-AATAAAAGCG
1 ATTTAAATAAATAAAAACA
17044 A-TTAAATAAATAAAAACA
1 ATTTAAATAAATAAAAACA
17062 ATTTAAATAAA
1 ATTTAAATAAA
17073 AATAAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAACA
Found at i:20268 original size:1 final size:1
Alignment explanation
Indices: 20264--20314 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
20254 AATGAAAATG
* * * * *
20264 AAAAAAATAAAAATAAAAAATAAAAAAAAAAAAAAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20315 TATAACGGAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (1 bp):
A
Found at i:20275 original size:6 final size:6
Alignment explanation
Indices: 20266--20316 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
20256 TGAAAATGAA
* *
20266 AAAAAT AAAAAT AAAAAAT AAAAAAA AAAAAA AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
20316 A
1 A
20317 TAACGGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 30 0.71
7 12 0.29
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:20281 original size:20 final size:20
Alignment explanation
Indices: 20244--20316 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
20234 CGCTTGATCG
*
20244 AAAAAAAT-AAAATGAAAAT
1 AAAAAAATAAAAATAAAAAT
20263 GAAAAAAATAAAAATAAAAAAT
1 -AAAAAAATAAAAAT-AAAAAT
20285 AAAAAAA-AAAAA-AAAAA-
1 AAAAAAATAAAAATAAAAAT
*
20302 ATAAAAATAAAAATA
1 AAAAAAATAAAAATA
20317 TAACGGAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.13
18 10 0.21
19 1 0.02
20 13 0.28
21 12 0.26
22 5 0.11
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (20 bp):
AAAAAAATAAAAATAAAAAT
Found at i:20300 original size:32 final size:33
Alignment explanation
Indices: 20245--20319 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
20235 GCTTGATCGA
* **
20245 AAAAAATAAAATGAAAATGAAAAAAATAAAAAT
1 AAAAAATAAAATAAAAAAAAAAAAAATAAAAAT
20278 AAAAAATAAAA-AAAAAAAAAAAAAATAAAAAT
1 AAAAAATAAAATAAAAAAAAAAAAAATAAAAAT
20310 AAAAATATAA
1 AAAAA-ATAA
20320 CGGAATTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (33 bp):
AAAAAATAAAATAAAAAAAAAAAAAATAAAAAT
Found at i:23080 original size:18 final size:19
Alignment explanation
Indices: 23057--23095 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
23047 ATATTTAAGT
*
23057 AATAAAAGTGA-TTAAATA
1 AATAAAAGTAATTTAAATA
23075 AATAAAAGTAATTTAAATA
1 AATAAAAGTAATTTAAATA
23094 AA
1 AA
23096 AATAAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (19 bp):
AATAAAAGTAATTTAAATA
Found at i:34562 original size:7 final size:7
Alignment explanation
Indices: 34550--34626 Score: 63
Period size: 7 Copynumber: 10.9 Consensus size: 7
34540 TTTTATATTT
34550 AATTTTA
1 AATTTTA
34557 AATTTTA
1 AATTTTA
34564 AACTTTT-
1 AA-TTTTA
*
34571 TATATTT-
1 AAT-TTTA
34578 AATTTTA
1 AATTTTA
34585 AATTTTA
1 AATTTTA
34592 AACTTTT-
1 AA-TTTTA
*
34599 TATATTT-
1 AAT-TTTA
34606 AATTTTA
1 AATTTTA
34613 AATTTTA
1 AATTTTA
34620 AACTTTT
1 AA-TTTT
34627 TATAAATAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
6 8 0.14
7 39 0.66
8 12 0.20
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (7 bp):
AATTTTA
Found at i:34637 original size:28 final size:28
Alignment explanation
Indices: 34536--34630 Score: 190
Period size: 28 Copynumber: 3.4 Consensus size: 28
34526 ATCAATTCTC
34536 AACTTTTTATATTTAATTTTAAATTTTA
1 AACTTTTTATATTTAATTTTAAATTTTA
34564 AACTTTTTATATTTAATTTTAAATTTTA
1 AACTTTTTATATTTAATTTTAAATTTTA
34592 AACTTTTTATATTTAATTTTAAATTTTA
1 AACTTTTTATATTTAATTTTAAATTTTA
34620 AACTTTTTATA
1 AACTTTTTATA
34631 AATAATTCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
AACTTTTTATATTTAATTTTAAATTTTA
Found at i:35162 original size:17 final size:15
Alignment explanation
Indices: 35140--35182 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
35130 TATTTAATAT
35140 AATATTTTTATATAAAA
1 AATA-TTTTAT-TAAAA
35157 AATATTTTATTAAAA
1 AATATTTTATTAAAA
*
35172 AA-ATTATATTA
1 AATATTTTATTA
35183 TCAATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 6 0.24
17 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTATTAAAA
Found at i:35175 original size:16 final size:17
Alignment explanation
Indices: 35140--35173 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
35130 TATTTAATAT
35140 AATATTTTTATATAAAA
1 AATATTTTTATATAAAA
35157 AATA-TTTTAT-TAAAA
1 AATATTTTTATATAAAA
35172 AA
1 AA
35174 ATTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTTTTATATAAAA
Found at i:39348 original size:29 final size:28
Alignment explanation
Indices: 39298--39356 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
39288 ATAATTAAAC
* *
39298 ATTTTTTATTATTTTAATTTTGTTAATA
1 ATTTTTTATTATTATAATTTTGGTAATA
39326 ATTTTTTATTATTCATACA-TTTGGTAATA
1 ATTTTTTATTATT-ATA-ATTTTGGTAATA
39355 AT
1 AT
39357 AATATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 13 0.48
30 1 0.04
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTTTTATTATTATAATTTTGGTAATA
Found at i:39839 original size:31 final size:32
Alignment explanation
Indices: 39782--39841 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
39772 GTTCAATGGT
*
39782 TTATGATTGTTTTGGGTTAAAATGGTTTAAGG
1 TTATGATTGTTTTAGGTTAAAATGGTTTAAGG
* *
39814 TTATGATT-TTTTATGTTGAAATGGTTTA
1 TTATGATTGTTTTAGGTTAAAATGGTTTA
39842 GAGTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (32 bp):
TTATGATTGTTTTAGGTTAAAATGGTTTAAGG
Found at i:39848 original size:24 final size:24
Alignment explanation
Indices: 39821--39870 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
39811 AGGTTATGAT
*
39821 TTTTTATGTTGAAATGGTTTAGAG
1 TTTTTATGTTCAAATGGTTTAGAG
*
39845 TTTTTTTGTTCAAATGGTTTAGAG
1 TTTTTATGTTCAAATGGTTTAGAG
39869 TT
1 TT
39871 AGATTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (24 bp):
TTTTTATGTTCAAATGGTTTAGAG
Found at i:39956 original size:2 final size:2
Alignment explanation
Indices: 39949--40003 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
39939 TAAATTGCAA
39949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39991 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
40004 AATAAGGAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40100 original size:30 final size:31
Alignment explanation
Indices: 40032--40112 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
40022 TGTAAAATAA
* *
40032 AAGAAAATAAAATCACGTTAATTGAAAGTAC
1 AAGAAAATAAAATCACATAAATTGAAAGTAC
*
40063 AAGAAAATAAAATCACATAAATTGAAA-TAT
1 AAGAAAATAAAATCACATAAATTGAAAGTAC
* * *
40093 TAGAAAATACAATTACATAA
1 AAGAAAATAAAATCACATAA
40113 GTGATGGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.43
31 25 0.57
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (31 bp):
AAGAAAATAAAATCACATAAATTGAAAGTAC
Found at i:40974 original size:22 final size:22
Alignment explanation
Indices: 40920--40981 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
40910 ATTGATTCAT
40920 GGGGTATCGATACCTATAT-GAA
1 GGGGTATCGATACC-ATATGGAA
***
40942 CAAG-ATCGATACCATATGGAA
1 GGGGTATCGATACCATATGGAA
40963 GGGGTATCGATACC-TATGG
1 GGGGTATCGATACCATATGG
40982 GGAGGATATC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.12
21 18 0.56
22 10 0.31
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (22 bp):
GGGGTATCGATACCATATGGAA
Found at i:40991 original size:21 final size:21
Alignment explanation
Indices: 40920--40996 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
40910 ATTGATTCAT
*
40920 GGGGTATCGATACCTATATGAA
1 GGGGTATCGATACC-ATATGGA
***
40942 CAAG-ATCGATACCATATGGAA
1 GGGGTATCGATACCATATGG-A
40963 GGGGTATCGATACC-TATGG-
1 GGGGTATCGATACCATATGGA
40982 GGAGGATATCGATAC
1 GG-GG-TATCGATAC
40997 TCGGGGAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.05
20 7 0.16
21 25 0.57
22 10 0.23
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (21 bp):
GGGGTATCGATACCATATGGA
Found at i:41072 original size:22 final size:21
Alignment explanation
Indices: 41036--41076 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
41026 CGGTACTTGG
*
41036 ATAGGGTATCGGTACCCTAGC
1 ATAGGGTATCAGTACCCTAGC
41057 ATAGAGGTATCAGTACCCTA
1 ATAG-GGTATCAGTACCCTA
41077 AGGGTAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
ATAGGGTATCAGTACCCTAGC
Found at i:43760 original size:159 final size:160
Alignment explanation
Indices: 43446--43762 Score: 600
Period size: 159 Copynumber: 2.0 Consensus size: 160
43436 AACTAAACCG
43446 GTTGAACCGCTATTAGTGAACTGACCGGAACCGTTGAACCGTTCGAACCGGACCGGCTGAAAACC
1 GTTGAACCGCTATTAGTGAACTGACCGGAACCGTTGAACCGTTCGAACCGGACCGGCTGAAAACC
* *
43511 GGAAAAAACCAAAAAAAACCGCCAATTTTGTTTTTTTTTAAAAAAATTAAACCAAACGACGTCGT
66 GGAAAAAAACAAAAAAAACCGCCAATTTTGTATTTTTTTAAAAAAATTAAACCAAACGACGTCGT
43576 TTGTTAAACGAACCAAGTCGAACTCGAGCA
131 TTGTTAAACGAACCAAGTCGAACTCGAGCA
43606 GTTGAACCGCTATTAGTGAACTGACCGGAACCGTTGAACCGTTCGAACCGGACCGGCTGAAAACC
1 GTTGAACCGCTATTAGTGAACTGACCGGAACCGTTGAACCGTTCGAACCGGACCGGCTGAAAACC
43671 -GAAAAAAACAAAAAAAACCGCCAATTTTGTATTTTTTTAAAAAAATTAAACCAAACGACGTCGT
66 GGAAAAAAACAAAAAAAACCGCCAATTTTGTATTTTTTTAAAAAAATTAAACCAAACGACGTCGT
*
43735 TTGTTAAACGAGCCAAGTCGAACTCGAG
131 TTGTTAAACGAACCAAGTCGAACTCGAG
43763 TATTGCTGAG
Statistics
Matches: 154, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
159 89 0.58
160 65 0.42
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (160 bp):
GTTGAACCGCTATTAGTGAACTGACCGGAACCGTTGAACCGTTCGAACCGGACCGGCTGAAAACC
GGAAAAAAACAAAAAAAACCGCCAATTTTGTATTTTTTTAAAAAAATTAAACCAAACGACGTCGT
TTGTTAAACGAACCAAGTCGAACTCGAGCA
Found at i:47206 original size:36 final size:34
Alignment explanation
Indices: 47113--47238 Score: 164
Period size: 35 Copynumber: 3.6 Consensus size: 34
47103 CATTATATCC
47113 ATAAGGAATTACCAGTTTGATCGGTCTGAACCTAT
1 ATAAGGAATTACCAGTTTGATCGGT-TGAACCTAT
* *
47148 ATAAGGAATTACTAGTTTGATCGAGTTGAACCTGT
1 ATAAGGAATTACCAGTTTGATCG-GTTGAACCTAT
* *
47183 CGTAAGGAATTACCAGTTCGATCGGTTTGAACCTAT
1 -ATAAGGAATTACCAGTTTGATCGG-TTGAACCTAT
*
47219 ATAAGGAATTATCA-TTTGAT
1 ATAAGGAATTACCAGTTTGAT
47239 TAAGCTAAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
34 5 0.06
35 43 0.54
36 31 0.39
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (34 bp):
ATAAGGAATTACCAGTTTGATCGGTTGAACCTAT
Found at i:48944 original size:17 final size:17
Alignment explanation
Indices: 48922--48954 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48912 GTCGAAAAAT
48922 ATAAAATATGACTTTTC
1 ATAAAATATGACTTTTC
*
48939 ATAAAATTTGACTTTT
1 ATAAAATATGACTTTT
48955 TGGTCAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
ATAAAATATGACTTTTC
Found at i:48974 original size:13 final size:14
Alignment explanation
Indices: 48956--48995 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
48946 TTGACTTTTT
*
48956 GGTCAAAATCAAC-
1 GGTCAAAGTCAACA
48969 GGTCAAAGTCAACA
1 GGTCAAAGTCAACA
*
48983 TGTCAAAGTCAAC
1 GGTCAAAGTCAAC
48996 TAGTTGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (14 bp):
GGTCAAAGTCAACA
Found at i:49919 original size:24 final size:24
Alignment explanation
Indices: 49876--49963 Score: 88
Period size: 24 Copynumber: 3.6 Consensus size: 24
49866 TTAATCTAAT
* *
49876 CCTAAACCA-TTTAAACAAAAAAC
1 CCTAAACCACTTTACATAAAAAAC
*
49899 CCTAAACCACTTTACTTAAAAAAC
1 CCTAAACCACTTTACATAAAAAAC
* *
49923 CCTAAATCATTTTAACATAAAATCAAC
1 CCTAAACCACTTT-ACATAAAA--AAC
*
49950 TCTAAACCACTTTA
1 CCTAAACCACTTTA
49964 ACCTAAACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
23 9 0.17
24 22 0.42
25 7 0.13
26 1 0.02
27 13 0.25
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (24 bp):
CCTAAACCACTTTACATAAAAAAC
Found at i:51679 original size:15 final size:15
Alignment explanation
Indices: 51643--51681 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
51633 TTATGAATAC
51643 ATAAAAATATAAACA
1 ATAAAAATATAAACA
*
51658 AGTAAAACTA-AAACA
1 A-TAAAAATATAAACA
51673 ATAAAAATA
1 ATAAAAATA
51682 CAACTAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 7 0.33
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (15 bp):
ATAAAAATATAAACA
Found at i:52562 original size:19 final size:17
Alignment explanation
Indices: 52527--52565 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52517 ATTTGATTTC
52527 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
52544 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
52563 TCT
1 TCT
52566 TTGTCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:52807 original size:15 final size:16
Alignment explanation
Indices: 52756--52795 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
52746 GGACGTGGCA
52756 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
52771 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
52787 GCGGCTGGA
1 GCGGCTGGA
52796 TTAGAGGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.17, C:0.17, G:0.57, T:0.07
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:52816 original size:17 final size:15
Alignment explanation
Indices: 52767--52807 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
52757 CGGTGGAGGC
**
52767 AGAGGCGGCTGGAGGC
1 AGAGGCGGCTGGA-TT
52783 AGAGGCGGCTGGATT
1 AGAGGCGGCTGGATT
52798 AGAGGCGGCT
1 AGAGGCGGCT
52808 AGGGATTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.20, C:0.17, G:0.51, T:0.12
Consensus pattern (15 bp):
AGAGGCGGCTGGATT
Found at i:52923 original size:3 final size:3
Alignment explanation
Indices: 52915--53004 Score: 126
Period size: 3 Copynumber: 30.0 Consensus size: 3
52905 ATGTATTTAT
* * *
52915 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
52963 TAA TAA TAA TAA TAA TTA TAA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53005 ATTAATATGG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:53303 original size:42 final size:40
Alignment explanation
Indices: 53256--53364 Score: 191
Period size: 42 Copynumber: 2.7 Consensus size: 40
53246 GAATAAGCTC
53256 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCGCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTT--CTT
53298 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
*
53338 TCGATGAGTTCTTCTCATTATGAACTT
1 TTGATGAGTTCTTCTCATTATGAACTT
53365 TCTCTAGAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 29 0.44
42 37 0.56
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (40 bp):
TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
Found at i:53626 original size:113 final size:113
Alignment explanation
Indices: 53415--53787 Score: 486
Period size: 113 Copynumber: 3.3 Consensus size: 113
53405 TAGAATTATG
* ** * *
53415 CAAAAAGTTGAACAAGCTCTTCTTATTATGAAC---TTCTT-ATTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTC
* * *
53476 TCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAA
63 TCATTATGAACT-TACTCTGGAAAAGATAATCCATCAAATGATGAATTTAAA
*
53527 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCCGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
53592 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
66 TTATGAACTTACTCTGGAAAAGATAATCCATCAAATGATGAATTTAAA
* *
53640 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
53705 TTATGAACTTCCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAG
66 TTATGAACTTACTCTGGAAAAGATAATCCATCAAATGATGAATTTAAA
* *
53753 TAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
53788 TCTCTAGAAA
Statistics
Matches: 232, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
112 31 0.13
113 187 0.81
115 5 0.02
116 9 0.04
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTACTCTGGAAAAGATAATCCATCAAATGATGAATTTAAA
Found at i:53801 original size:186 final size:186
Alignment explanation
Indices: 53581--53929 Score: 583
Period size: 186 Copynumber: 1.9 Consensus size: 186
53571 TCTTCCGATG
* * * *
53581 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTAATCCATCAAATGATGAATTCAAACAAAAG
*
53646 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
53711 ACTTCCTCTGGAAAAGAT-AATCCATCAATTGATGAATTCAAGTAAAAGGTTGAACA
131 ACTTCCTCTGGAAAAG-TCAATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACA
* **
53767 AGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTAATCCATCAAGTGATGAATTCAGGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTAATCCATCAAATGATGAATTCAAACAAAAG
53832 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
53897 ACTTTCTCTGGAAATGTCAATCCATCAAATGAT
131 ACTTCCTCTGGAAAAGTCAATCCATCAAATGAT
53930 AGATTTGAAT
Statistics
Matches: 151, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
185 1 0.01
186 150 0.99
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (186 bp):
AGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTAATCCATCAAATGATGAATTCAAACAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTCCTCTGGAAAAGTCAATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACA
Found at i:53817 original size:73 final size:73
Alignment explanation
Indices: 53694--53861 Score: 264
Period size: 73 Copynumber: 2.3 Consensus size: 73
53684 TCTTCAGATG
* * * *
53694 AGTTCTTCTTATTATGAACTTCCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAGTAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAG
53759 GTTGAACA
66 GTTGAACA
* * *
53767 AGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTAATCCATCAAGTGATGAATTCAGGCAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAG
53832 GTTGAACA
66 GTTGAACA
*
53840 AATTCTTCTCATTATGAACTTC
1 AGTTCTTCTCATTATGAACTTC
53862 TTCTTCCTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTTCCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAG
GTTGAACA
Found at i:54790 original size:83 final size:84
Alignment explanation
Indices: 54651--54872 Score: 412
Period size: 83 Copynumber: 2.7 Consensus size: 84
54641 GTAGTTCCTA
54651 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
54716 ATTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
54734 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
54799 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
54818 CC-AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
54873 ACATTTGTTC
Statistics
Matches: 136, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
83 124 0.91
84 12 0.09
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
ATTCAATGATTGGTTCTGT
Found at i:67478 original size:15 final size:15
Alignment explanation
Indices: 67442--67480 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
67432 TTATGAATAC
67442 ATAAAAATATAAACA
1 ATAAAAATATAAACA
*
67457 AGTAAAACTA-AAACA
1 A-TAAAAATATAAACA
67472 ATAAAAATA
1 ATAAAAATA
67481 CAACTAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 7 0.33
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (15 bp):
ATAAAAATATAAACA
Found at i:68363 original size:19 final size:17
Alignment explanation
Indices: 68328--68366 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
68318 ATTTGATTTC
68328 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
68345 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
68364 TCT
1 TCT
68367 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:68608 original size:15 final size:16
Alignment explanation
Indices: 68561--68596 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
68551 GTGGCAGCGA
68561 TGGAGGCAGAGGCGGC
1 TGGAGGCAGAGGCGGC
68577 TGGAGGCAGAGGCGGC
1 TGGAGGCAGAGGCGGC
68593 TGGA
1 TGGA
68597 TTAGAGGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.56, T:0.08
Consensus pattern (16 bp):
TGGAGGCAGAGGCGGC
Found at i:68617 original size:17 final size:15
Alignment explanation
Indices: 68568--68608 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
68558 CGATGGAGGC
**
68568 AGAGGCGGCTGGAGGC
1 AGAGGCGGCTGGA-TT
68584 AGAGGCGGCTGGATT
1 AGAGGCGGCTGGATT
68599 AGAGGCGGCT
1 AGAGGCGGCT
68609 AGGGATTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.20, C:0.17, G:0.51, T:0.12
Consensus pattern (15 bp):
AGAGGCGGCTGGATT
Found at i:68724 original size:3 final size:3
Alignment explanation
Indices: 68716--68826 Score: 177
Period size: 3 Copynumber: 37.0 Consensus size: 3
68706 ATGTATTTAT
* *
68716 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
68764 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
68812 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
68827 ATTAATATGG
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:68987 original size:22 final size:21
Alignment explanation
Indices: 68947--68997 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
68937 AATATAAAAT
*
68947 TTAA-ATTATATTTATACTTA
1 TTAATATTATATATATACTTA
68967 TTAATATTATGATATATACTTA
1 TTAATATTAT-ATATATACTTA
68989 TTAATATTA
1 TTAATATTA
68998 ATAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 19 0.68
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAATATTATATATATACTTA
Found at i:69322 original size:22 final size:24
Alignment explanation
Indices: 69297--69349 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
69287 AACTATTCAA
*
69297 AAATAAAATATA-TATTATAAAT-
1 AAATAAAAGATATTATTATAAATG
69319 AAATTTAAAAGATATTATTATAAATG
1 AAA--TAAAAGATATTATTATAAATG
69345 AAATA
1 AAATA
69350 TATCAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
24 10 0.38
25 10 0.38
26 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATAAAAGATATTATTATAAATG
Found at i:69327 original size:24 final size:26
Alignment explanation
Indices: 69300--69348 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
69290 TATTCAAAAA
*
69300 TAAAATATA-TATTATAAAT-AAATT
1 TAAAAGATATTATTATAAATGAAATT
69324 TAAAAGATATTATTATAAATGAAAT
1 TAAAAGATATTATTATAAATGAAAT
69349 ATATCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
TAAAAGATATTATTATAAATGAAATT
Found at i:69487 original size:20 final size:21
Alignment explanation
Indices: 69459--69501 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
69449 TCTATTTATT
*
69459 TTAAGTAATGAAAA-AAATTA
1 TTAAATAATGAAAATAAATTA
*
69479 TTAAATAATTAAAATAAATTA
1 TTAAATAATGAAAATAAATTA
69500 TT
1 TT
69502 TAGAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TTAAATAATGAAAATAAATTA
Found at i:75976 original size:19 final size:19
Alignment explanation
Indices: 75948--75986 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
75938 AAAATTTCAT
*
75948 TTTGATTTTCAAAATCAAA
1 TTTGACTTTCAAAATCAAA
75967 TTTGACTTTCAAAATCAAA
1 TTTGACTTTCAAAATCAAA
75986 T
1 T
75987 CATTTTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTGACTTTCAAAATCAAA
Found at i:81903 original size:59 final size:59
Alignment explanation
Indices: 81811--81924 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
81801 TGAGGATGGA
* *
81811 TAAGTGTCCTATCGAACCTTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACAC
1 TAAGTGTCCTATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACAC
* *
81870 TAAGTGTCCTATCGAACCCTCTTAGTCGCAATGAAAAGGAAAACTCGATAATATG
1 TAAGTGTCCTATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATG
81925 GCTTAAACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACAC
Found at i:86564 original size:17 final size:17
Alignment explanation
Indices: 86538--86580 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
86528 ACAAACCATT
* *
86538 AAAGTTTACAGTGCATG
1 AAAGTATACAATGCATG
86555 AAAGTATACAATGCATG
1 AAAGTATACAATGCATG
*
86572 AAAATATAC
1 AAAGTATAC
86581 TTTTTTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (17 bp):
AAAGTATACAATGCATG
Found at i:89251 original size:251 final size:252
Alignment explanation
Indices: 88835--89537 Score: 762
Period size: 251 Copynumber: 2.8 Consensus size: 252
88825 AAGTCATTCA
** *
88835 GGCATGAT-TTTTCACGTGATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAAAT
1 GGCATGATGTTTTCACACGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAAT
* * * *
88899 CTTTATGAAAAATTG-AAATTTT--AA-TAAGGAAGCAATTTCCAAAGTTTC-TACATAGTAAAT
66 ATTTATG-AAAATTGAAAATTTTAAAAGTAAGAAAGC-GTTTCCAAAGTTTCTTACATAG-AAAA
* *
88959 TATTTCTTC-AA-TGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCC
128 AATTTC--CAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG-ATAAATCC
*
89022 TTCGGGTCA-CTATAAGCCTTTGAGTAAGATGATAAGTCATTCGGGTCATC-ATAAGA-CTTTCG
190 TTCGGGTCATCTATAAGCCTTTGAGTAAGATGATAAGTCATTCGGGTCATCTAT-AGACCATT-G
*
89084 GGCATGATGTTTTCACACGATTTTCAAAAAATGAGAAAACGA-TTCCAAAGTTTCTCATTTAAAT
1 GGCATGATGTTTTCACACGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAAT
* *
89148 ATTTTTGAAAATTGAAAATTTTAAAAGTAAGAAAGCGTTTCCAAAGTTTCTTACGTAGAAAAAAT
66 ATTTATGAAAATTGAAAATTTTAAAAGTAAGAAAGCGTTTCCAAAGTTTCTTACATAGAAAAAAT
* * * * * *
89213 TTCCAAATTGGTAAATCCTTCAGGCAATCAGTAAGTCTTTTGAGCATGATGATTAATCCTTCAGG
131 TTCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGG
* * * *
89278 TCATCTATCATCTTTTGAGTAAGATGATAAGTCTTTCGGGTCATCTATAGACCATTG
196 TCATCTATAAGCCTTTGAGTAAGATGATAAGTCATTCGGGTCATCTATAGACCATTG
* * * * * *
89335 GGCAAGATGCTTTCATAGGATAACTT-GAAAAATGAGGAAAACGATTTTCAAAGTTTCT--TTT-
1 GGCATGATGTTTTCACACGAT--TTTCGAAAAATGA-GAAAACGATTTCCAAAGTTTCTCATTTA
* ** * *
89396 AGTATGTTCA-GAAAA-TGAATTTTTTGAAAAGCAAGGGAAA-CGATTTCCAAAGTTTCTTACCT
63 AATAT-TT-ATGAAAATTGAAAATTTT-AAAAGTAA--GAAAGCG-TTTCCAAAGTTTCTTACAT
* *
89458 AG-TAAACTATTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGT
122 AGAAAAAAT-TTCC-AAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA-T
89522 AAATCCTTCGGGTCAT
184 AAATCCTTCGGGTCAT
89538 TTAGTAGTCT
Statistics
Matches: 386, Mismatches: 44, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
248 7 0.02
249 43 0.11
250 45 0.12
251 132 0.34
252 44 0.11
253 16 0.04
254 40 0.10
255 44 0.11
256 15 0.04
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (252 bp):
GGCATGATGTTTTCACACGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAAT
ATTTATGAAAATTGAAAATTTTAAAAGTAAGAAAGCGTTTCCAAAGTTTCTTACATAGAAAAAAT
TTCCAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGG
TCATCTATAAGCCTTTGAGTAAGATGATAAGTCATTCGGGTCATCTATAGACCATTG
Found at i:89304 original size:40 final size:40
Alignment explanation
Indices: 89248--89325 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
89238 AATCAGTAAG
*
89248 TCTTTTGAGCATGATGATTAA-TCCTTCAGGTCATCTATCA
1 TCTTTTGAGCAAGATGA-TAAGTCCTTCAGGTCATCTATCA
* * *
89288 TCTTTTGAGTAAGATGATAAGTCTTTCGGGTCATCTAT
1 TCTTTTGAGCAAGATGATAAGTCCTTCAGGTCATCTAT
89326 AGACCATTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.09
40 30 0.91
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (40 bp):
TCTTTTGAGCAAGATGATAAGTCCTTCAGGTCATCTATCA
Done.