Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002596.1 Hibiscus syriacus cultivar Beakdansim tig00005252_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: 49108
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2905 original size:29 final size:27
Alignment explanation
Indices: 2830--2906 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
2820 TTACTAGTGA
* *
2830 CTAAAATGTAAATTTTAAAAGTTTATGG
1 CTAAAATGT-AATTTTGAAAGTTTAGGG
* * *
2858 CTAAAGTATAACTTGTGAAAGTTTAGGGG
1 CTAAAATGTAA-TTTTGAAAGTTTA-GGG
2887 CTAAAAATGTAATTTTGAAA
1 CT-AAAATGTAATTTTGAAA
2907 AGTTATATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
27 2 0.05
28 18 0.47
29 11 0.29
30 7 0.18
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (27 bp):
CTAAAATGTAATTTTGAAAGTTTAGGG
Found at i:16968 original size:30 final size:31
Alignment explanation
Indices: 16927--17006 Score: 128
Period size: 30 Copynumber: 2.6 Consensus size: 31
16917 GATTCAGGTA
*
16927 TCGGGTCGGATCAAATCGGATGGGTTGA-TT
1 TCGGGTTGGATCAAATCGGATGGGTTGATTT
16957 TCGGGTTGGATCAAATCGGATGGGTTGATTT
1 TCGGGTTGGATCAAATCGGATGGGTTGATTT
*
16988 TC-AGTTGGATCAAATCGGA
1 TCGGGTTGGATCAAATCGGA
17007 ACGATTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 43 0.91
31 4 0.09
ACGTcount: A:0.23, C:0.12, G:0.34, T:0.31
Consensus pattern (31 bp):
TCGGGTTGGATCAAATCGGATGGGTTGATTT
Found at i:17018 original size:30 final size:30
Alignment explanation
Indices: 16961--17018 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16951 TTGATTTCGG
** * *
16961 GTTGGATCAAATCGGATGGGTTGATTTTCA
1 GTTGGATCAAATCGGAACGATTAATTTTCA
16991 GTTGGATCAAATCGGAACGATTAATTTT
1 GTTGGATCAAATCGGAACGATTAATTTT
17019 TGGGTCAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (30 bp):
GTTGGATCAAATCGGAACGATTAATTTTCA
Found at i:17785 original size:16 final size:16
Alignment explanation
Indices: 17748--17791 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
17738 AATTAAATTA
17748 GGGTTACTTTTGATTC
1 GGGTTACTTTTGATTC
**
17764 AAGTTA-TTTTCGATTC
1 GGGTTACTTTT-GATTC
17780 GGGTTACTTTTG
1 GGGTTACTTTTG
17792 GTTTGACTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (16 bp):
GGGTTACTTTTGATTC
Found at i:23903 original size:21 final size:21
Alignment explanation
Indices: 23879--23952 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
23869 TATCGCAAAT
23879 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
23900 TCGCGTTGCGCT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
*
23920 TCGAGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
23941 CCGCGTTGCGAT
1 TCGCGTTGCGAT
23953 TTTCCATTTC
Statistics
Matches: 37, Mismatches: 15, Indels: 2
0.69 0.28 0.04
Matches are distributed among these distances:
20 13 0.35
21 24 0.65
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:23940 original size:41 final size:41
Alignment explanation
Indices: 23878--23975 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
23868 CTATCGCAAA
* * *
23878 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCTAT
1 TTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCAT
*
23919 TTCGAGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCAT
23960 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
23976 CTACAGTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCAT
Found at i:24115 original size:6 final size:6
Alignment explanation
Indices: 24106--24193 Score: 158
Period size: 6 Copynumber: 14.7 Consensus size: 6
24096 AGACACGTAT
* *
24106 GACCAT GACCAT GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
24154 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
24194 CAAGACGAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.48, G:0.17, T:0.02
Consensus pattern (6 bp):
GACCAC
Found at i:24717 original size:6 final size:6
Alignment explanation
Indices: 24702--24762 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
24692 TCTCGTCTCG
*
24702 GGTCGT GGTCGG GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24748 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
24763 AATACGTGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
5 10 0.19
6 43 0.81
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:24882 original size:13 final size:13
Alignment explanation
Indices: 24845--24884 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
24835 TTTAACTATT
*
24845 ACAACGAATTTTCG
1 ACAACGAA-TTTGG
24859 -CAACGAATTTGG
1 ACAACGAATTTGG
24871 ACAACGAATTTGG
1 ACAACGAATTTGG
24884 A
1 A
24885 AAATCGCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (13 bp):
ACAACGAATTTGG
Found at i:25262 original size:21 final size:21
Alignment explanation
Indices: 25219--25311 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
25209 TTTTCCCAAT
** *
25219 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
25239 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
25260 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
25280 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
25301 TCGCAATGCGA
1 TCGCAATGCGA
25312 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:25325 original size:20 final size:20
Alignment explanation
Indices: 25300--25434 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
25290 AATTGGGAAA
25300 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
25320 ATCGCAATACGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
25341 ATCGCAACT-AGATACTTACT
1 ATCGCAA-TGCGATACTGACT
* *
25361 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
25381 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
25401 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
25421 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
25435 TTTCAAAGCG
Statistics
Matches: 93, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.04
20 63 0.68
21 23 0.25
22 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:25327 original size:41 final size:41
Alignment explanation
Indices: 25219--25311 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
25209 TTTTCCCAAT
*
25219 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
25260 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
25301 TCGCAATGCGA
1 TCGCAATGCGA
25312 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
Found at i:25342 original size:41 final size:41
Alignment explanation
Indices: 25297--25434 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
25287 GCGAATTGGG
* **
25297 AAAATCGCAATGCGATACTGACTATCGCAATACGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
* * *
25338 AAAATCGCAACT-AGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAA-TGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
25380 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
25419 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
25435 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
39 2 0.03
40 29 0.38
41 42 0.55
42 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:25630 original size:22 final size:22
Alignment explanation
Indices: 25602--25645 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25592 CACTCTCTCA
25602 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
25624 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
25646 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:27287 original size:18 final size:18
Alignment explanation
Indices: 27266--27310 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
27256 TCCACTTCGG
*
27266 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
27284 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
27302 GAGCCATCA
1 GAGCCATCA
27311 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:27846 original size:19 final size:20
Alignment explanation
Indices: 27792--27858 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
27782 TAGTTTACTT
* *
27792 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
27812 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
27832 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
27851 TCGCAACG
1 TCGCAACG
27859 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:27866 original size:14 final size:14
Alignment explanation
Indices: 27847--27903 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
27837 ATGCGAAATG
27847 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
27861 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
27877 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
27893 AAAATCGCAAC
1 AAAATCGCAAC
27904 ACGAAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.54
16 7 0.20
18 9 0.26
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:27894 original size:32 final size:33
Alignment explanation
Indices: 27831--27919 Score: 144
Period size: 32 Copynumber: 2.7 Consensus size: 33
27821 GGAAATGGCT
27831 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
27864 ATCGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
**
27896 ATCGCAACACGAAATGAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGC
27920 GTAATGTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 29 0.56
33 23 0.44
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:29960 original size:33 final size:33
Alignment explanation
Indices: 29918--30044 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
29908 GGAAATTACT
29918 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
29951 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
29983 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
30017 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
30045 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:30025 original size:66 final size:66
Alignment explanation
Indices: 29919--30051 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
29909 GAAATTACTA
*
29919 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
29984 T
66 T
* *
29985 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGTGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
30050 T
66 T
30051 T
1 T
30052 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:30097 original size:33 final size:33
Alignment explanation
Indices: 30044--30125 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
30034 AAATCGCAAC
* * *
30044 GCGAATTTAATTTCGCGTTGCGTTTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
30077 GCGATTTTCATTTCGTGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
30110 GCGATTTTCATTTCGC
1 GCGATTTTCATTTCGC
30126 ATTACGATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:30098 original size:19 final size:18
Alignment explanation
Indices: 30074--30124 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
30064 CGTTTCTCTC
30074 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
*
30092 TGTTGCGA--TTC-TCTC-
1 -GTTGCGATTTTCATTTCG
30107 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
30125 CATTACGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 7 0.27
16 6 0.23
17 6 0.23
19 7 0.27
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.49
Consensus pattern (18 bp):
GTTGCGATTTTCATTTCG
Found at i:30113 original size:14 final size:14
Alignment explanation
Indices: 30059--30115 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
30049 TTTAATTTCG
*
30059 CGTTGCGTTTCTCT
1 CGTTGCGATTCTCT
*
30073 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
30090 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
30106 CGTTGCGATT
1 CGTTGCGATT
30116 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.07, C:0.23, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:30259 original size:14 final size:14
Alignment explanation
Indices: 30240--30276 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
30230 CATCAATTAA
30240 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
30254 ACAAATCACCTTTT
1 ACAAATCAACTTTT
30268 ACAAATCAA
1 ACAAATCAA
30277 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:31692 original size:21 final size:21
Alignment explanation
Indices: 31626--31692 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31616 GTGAATCGGG
*
31626 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
31646 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
31668 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
31689 CTCT
1 CTCT
31693 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:31711 original size:42 final size:41
Alignment explanation
Indices: 31626--31748 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
31616 GTGAATCGGG
* * * *
31626 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
31668 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
31710 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
31749 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:32142 original size:91 final size:90
Alignment explanation
Indices: 31964--32150 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 90
31954 ATATTTCAAA
* *
31964 ACTTCATCCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
32029 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
32057 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
32121 CAGTATTGGAAGCAACCGAATAAATTT
64 CAGAATTGGAAGCAACCGAATAAATTT
32148 ACT
1 ACT
32151 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.47
93 20 0.23
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGAAGCAACCGAATAAATTT
Found at i:32353 original size:63 final size:63
Alignment explanation
Indices: 32294--32435 Score: 160
Period size: 63 Copynumber: 2.3 Consensus size: 63
32284 CTTAGAGCGG
* * * *
32294 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCATAGAGCAC
* * * *** *
32357 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCATAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCATAGAGCAC
*
32420 CAATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
32436 GGCATTGACC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.19
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCATAGAGCAC
Found at i:32436 original size:63 final size:63
Alignment explanation
Indices: 32317--32447 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
32307 TAAAGTAGAC
* *
32317 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCATAGAGTACCAATCTCCTCACGCAAGGCATTG
32380 ACCTCCACACGCCATGCACCATCGTTATCGCATAGAGTACCAATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCATAGAGTACCAATCTCCTCACGCAAGGCATTG
32443 ACCTC
1 ACCTC
32448 ATCACGTAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCATAGAGTACCAATCTCCTCACGCAAGGCATTG
Found at i:33933 original size:20 final size:19
Alignment explanation
Indices: 33902--34022 Score: 109
Period size: 19 Copynumber: 6.8 Consensus size: 19
33892 TCTTTTGGTT
33902 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
33921 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
**
33941 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
33960 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
33974 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
33993 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
34007 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
34023 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
14 21 0.26
16 4 0.05
17 4 0.05
19 36 0.44
20 17 0.21
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:33969 original size:14 final size:14
Alignment explanation
Indices: 33950--34005 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
33940 CGAAATGACT
33950 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
33964 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
33983 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
33997 ATCGCAACG
1 ATCGCAACG
34006 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:33969 original size:33 final size:33
Alignment explanation
Indices: 33927--34022 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
33917 ACGAGATAAT
**
33927 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
33960 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
33993 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
34023 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:34045 original size:19 final size:19
Alignment explanation
Indices: 34023--34067 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
34013 AAAATCGCAA
*
34023 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
34042 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
34061 TGCGATT
1 TGCGATT
34068 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:34699 original size:20 final size:20
Alignment explanation
Indices: 34614--34727 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
34604 CGCTATGTAA
* * *
34614 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
34634 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
34654 ATCTCGTTGCGATTTTATATT
1 ATCGCATTGCGATAGT-CAGT
*
34675 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
34695 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
34715 ATCGCATTGCGAT
1 ATCGCATTGCGAT
34728 TTTTCCAATT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:34712 original size:61 final size:61
Alignment explanation
Indices: 34614--34730 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
34604 CGCTATGTAA
* * * * *
34614 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTATATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
* * *
34675 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
34731 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
Found at i:34746 original size:61 final size:61
Alignment explanation
Indices: 34614--34748 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
34604 CGCTATGTAA
* * * * * *
34614 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTATATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATAAT
* * *
34675 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-TCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTAT--AAT
34737 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
34749 TTACTTATTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 1 0.02
61 59 0.95
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATAAT
Found at i:34838 original size:21 final size:21
Alignment explanation
Indices: 34798--34838 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34788 ACTGTAGACC
**
34798 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
34819 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
34839 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:36521 original size:112 final size:112
Alignment explanation
Indices: 36301--36648 Score: 536
Period size: 112 Copynumber: 3.1 Consensus size: 112
36291 ACATTTCAAC
* * * **
36301 AAAGCATCGATACATTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGAT-CCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
36366 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
*
36414 AAAGTATCGAT-CTTTTGTATAAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGATCCTTTT-TATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
36478 TTTGTTATAATGAAACTGGTTTTTTCATATTTTTACCTATTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
* * * *
36526 AAAGTATTGATCCTTTTTATAAATAGGATCGATACTTTCAACATATTAGGTAAATCTTACCGGTT
1 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
*
36591 TTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTATTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
*
36638 AAAATATCGAT
1 AAAGTATCGAT
36649 ACATATATAT
Statistics
Matches: 214, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
111 4 0.02
112 195 0.91
113 15 0.07
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (112 bp):
AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
Found at i:37254 original size:112 final size:112
Alignment explanation
Indices: 37057--37322 Score: 433
Period size: 112 Copynumber: 2.4 Consensus size: 112
37047 AAATTTTACC
* *
37057 GGTTTTGTTATATTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCGATA
1 GGTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCAATA
* *
37122 CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTTATAATAAAATT
66 CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACT
*
37169 GGTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAATGATCAATA
1 GGTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCAATA
* *
37234 CTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACT
66 CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACT
* * * *
37281 AGTTTTGTCATATTTTTATCTATTATATTATAAAGTATCGAT
1 GGTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGAT
37323 AATTATATAT
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 143 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (112 bp):
GGTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCAATA
CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACT
Found at i:37706 original size:674 final size:676
Alignment explanation
Indices: 35956--37738 Score: 2855
Period size: 674 Copynumber: 2.6 Consensus size: 676
35946 CGATACATAT
* * *
35956 ATATATATAAGTGCTC-ATACCTATTTCAATGTGGAAAACATTAATTTAAAGTTATCTTTTGAGT
1 ATATATATAAGTG-TCGATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
* * *
36020 GAGTTTTAAGATATTAATTTAGTAATTATACGCTTCTAATGATTTATTTTTTATGTTACGGTATA
65 GAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTA-TTTTTATGTTACGATATA
36085 TATTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAA
129 TATTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAA
*
36150 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
194 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGT
*
36215 AAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAGCACTATTAAAAAATTTTGAAAC
259 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAGCACTATTAAAAAATTTTGAAAC
** *
36280 ATAAATTACAT-ACATTTCAACAAAGCATCGATACATTTTTATAAAAAGTATTTATACTTTCAAC
324 ATAAATTACATAAC-TTTCAACAAAATATCGATACATTTTTATAAAAAGTATATATACTTTCAAC
36344 ATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTAT
388 ATATCAGGTAAATTTTACC-G----GT--T--T-----T-G---TGTCATATTTTTACCTGTTAT
*
36409 ATTGTAAAGTATCGATCTTTTGTATAAAAATGATCGATACTTTCAACATATCAGGTAAATTTTAC
435 ATTGTAAAGTATCGATCTTTTGTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTAC
* *
36474 CGGTTTTGTTATAATGAAACTGGTTTTTTCATATTTTTACCTATTATATTGTAAAGTATTGATCC
500 CGGTTTTGTTATAATAAAACTGGTTTTTTCATATTTTTACCTATTATATTGTAAAGTATCGATCC
* *
36539 TTTTTATAAATAGGATCGATACTTTCAACATATTAGGTAAATCTTACCGGTTTTGTCATAATGAA
565 TTTTTATAAAAAGGATCAATACTTTCAACATATTAGGTAAATCTTACCGGTTTTGTCATAATGAA
* * *
36604 ATTGGTTTTGTCATATTTTTACCTATTATATTGTAAAATATCGATAC
630 ACTAGTTTTGTCATATTTTTACCTATTATATTATAAAATATCGATAC
* * *
36651 ATATATATAAGTGTCGATAATTATTTCACTGTGAAAAACATTAATTTAAGATTATCTTTTGAGTG
1 ATATATATAAGTGTCGATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
* *
36716 AGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGGTTTATTTTTATGTTAC-AGTATTT
66 AGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTATTTTTATGTTACGA-TATAT
* *
36780 ATTATAATTAAATTAATAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAAT
130 ATTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAAT
36845 TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
195 TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
* *
36910 AATGAAATTATTAAATTAATATTGTAGGTGG-AAACATGAATCACTATTAAAAAAATTTGAAACA
260 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAGCACTATTAAAAAATTTTGAAACA
* *
36974 TAAATTACATAACTTTCAACAAAATATCGATATATTTTTATAAAAAAATATATATACTTTCAACA
325 TAAATTACATAACTTTCAACAAAATATCGATACATTTTTAT-AAAAAGTATATATACTTTCAACA
37039 TATCAGGTAAATTTTACCGGTTTTGT-T-ATATTTTTACCTGTTATATTGTAAAGTATCGATCCT
389 TATCAGGTAAATTTTACCGGTTTTGTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CT
37102 TTT-TATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTTATAATAAA
453 TTTGTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTTATAATAAA
* *
37166 ATTGGTTTTGTT-ATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAATGATC
518 ACTGGTTTT-TTCATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATC
*
37230 AATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACTAGTTTTGTCATATT
582 AATACTTTCAACATATTAGGTAAATCTTACCGGTTTTGTCATAATGAAACTAGTTTTGTCATATT
* *
37295 TTTATCTATTATATTATAAAGTATCGATA-
647 TTTACCTATTATATTATAAAATATCGATAC
* * *
37324 ATTATATATAAGTGTCGACACTTATTTCACTGTGGAAAATATTAATTTAAGGTTATATTTTGAGT
1 A-TATATATAAGTGTCGATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGT
* *
37389 GAGTTTTAAGATATTAATTTCGTAATTATATGCGTCTAATGATTTATTTTTATCTTACGATATAT
65 GAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTATTTTTATGTTACGATATAT
*
37454 ATTATTATTAAATTAAAAATAATAAACATATATATTACATATTTATTATTATCTTTGGTTAAAAT
130 ATTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAAT
*
37519 TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTATGTA
195 TGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
*
37584 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAGCACTATTAAAAAATTTTGAAACA
260 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAGCACTATTAAAAAATTTTGAAACA
* *
37649 TAAATTATATAACTTTCAACAAAATATCGATACATTTTTATAAAAAGTATCTATACTTTCAACAT
325 TAAATTACATAACTTTCAACAAAATATCGATACATTTTTATAAAAAGTATATATACTTTCAACAT
*
37714 ATCAGGTAAATTTTACCAGTTTTGT
390 ATCAGGTAAATTTTACCGGTTTTGT
37739 CATAATGAAA
Statistics
Matches: 1022, Mismatches: 57, Indels: 39
0.91 0.05 0.03
Matches are distributed among these distances:
673 1 0.00
674 555 0.54
675 78 0.08
676 1 0.00
679 1 0.00
680 1 0.00
685 1 0.00
687 1 0.00
689 2 0.00
693 67 0.07
694 216 0.21
695 98 0.10
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (676 bp):
ATATATATAAGTGTCGATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
AGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTATTTTTATGTTACGATATATA
TTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATT
GTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAGCACTATTAAAAAATTTTGAAACAT
AAATTACATAACTTTCAACAAAATATCGATACATTTTTATAAAAAGTATATATACTTTCAACATA
TCAGGTAAATTTTACCGGTTTTGTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTT
GTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTTATAATAAAACT
GGTTTTTTCATATTTTTACCTATTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCAATA
CTTTCAACATATTAGGTAAATCTTACCGGTTTTGTCATAATGAAACTAGTTTTGTCATATTTTTA
CCTATTATATTATAAAATATCGATAC
Found at i:38058 original size:28 final size:31
Alignment explanation
Indices: 38026--38098 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
38016 ATAAAATATC
*
38026 AAAATAATTAAATAAT-TT-T-TGTGTAAAT
1 AAAATTATTAAATAATGTTGTATGTGTAAAT
38054 AAAATTATTAAATTAATGTTGTATGTGTAAAT
1 AAAATTATTAAA-TAATGTTGTATGTGTAAAT
*
38086 GAAATTATTAAAT
1 AAAATTATTAAAT
38099 TATATAGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 11 0.28
29 4 0.10
30 2 0.05
31 2 0.05
32 20 0.51
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (31 bp):
AAAATTATTAAATAATGTTGTATGTGTAAAT
Found at i:45519 original size:15 final size:14
Alignment explanation
Indices: 45495--45536 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
45485 TGAGTGTTTG
45495 TTTGTTTATTTTTA
1 TTTGTTTATTTTTA
45509 TTTGTTTTATTTTT-
1 TTTG-TTTATTTTTA
* *
45523 TATCTTTATTTTTA
1 TTTGTTTATTTTTA
45537 ATATTAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 9 0.38
14 6 0.25
15 9 0.38
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTGTTTATTTTTA
Found at i:46689 original size:12 final size:12
Alignment explanation
Indices: 46674--46718 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
46664 GTGAAAAAGT
46674 GAAGAAAAAAAA
1 GAAGAAAAAAAA
*
46686 GAAGAAAAAAAG
1 GAAGAAAAAAAA
*
46698 GAA-AAAAAGAA
1 GAAGAAAAAAAA
46709 -AAGAAAAAAA
1 GAAGAAAAAAA
46719 TGTGTACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 2 0.07
11 12 0.43
12 14 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:46710 original size:25 final size:24
Alignment explanation
Indices: 46667--46718 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
46657 TAAAAAAGTG
*
46667 AAAAAGTGAAGAAAAAAAAGAAGAA
1 AAAAAGTGAAAAAAAAAAAGAA-AA
46692 AAAAAG-GAAAAAAAGAAAAGAAAA
1 AAAAAGTGAAAAAAA-AAAAGAAAA
46716 AAA
1 AAA
46719 TGTGTACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAAAGTGAAAAAAAAAAAGAAAA
Done.