Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008509.1 Hibiscus syriacus cultivar Beakdansim tig00111362_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: 231169
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3357 original size:36 final size:35
Alignment explanation
Indices: 3306--3416 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
3296 TAAGATACTA
3306 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * * *
3341 CCTATAACATCACCATCCTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
3376 CC-ATTATCATTACCATCTTCTATCACCATTTCACG
1 CCTA-TAACATCACCATCTTCCATCACCATTTCACG
*
3411 CTTATA
1 CCTATA
3417 TAACCACCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
34 1 0.02
35 38 0.62
36 22 0.36
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:5331 original size:40 final size:40
Alignment explanation
Indices: 5276--5357 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
5266 ACCAAAACAC
5276 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
1 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
5316 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
1 CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
5356 CA
1 CA
5358 TTTTGGTACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (40 bp):
CAAGGGATGCTTCCTATTCACCCAAAGACTCATTCTTCTT
Found at i:11356 original size:11 final size:11
Alignment explanation
Indices: 11303--11356 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
11293 CTCTTTTGAA
*
11303 TTTCTTTTTGT
1 TTTCTTTTTCT
*
11314 TTTCTTTTTTT
1 TTTCTTTTTCT
**
11325 TTTCTGATTCT
1 TTTCTTTTTCT
11336 TTGGTCTTTTTCT
1 TT--TCTTTTTCT
11349 TTTCTTTT
1 TTTCTTTT
11357 ACACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 26 0.74
13 9 0.26
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:13835 original size:1 final size:1
Alignment explanation
Indices: 13831--13873 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
13821 CTTTTTTGGC
* * *
13831 TTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13874 GAAAAAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:13845 original size:20 final size:20
Alignment explanation
Indices: 13822--13867 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13812 AAATTTTGGC
13822 TTTTTTGGCTT-TTTTTTTTG
1 TTTTTT-GCTTGTTTTTTTTG
**
13842 TTTTTTTTTTGTTTTTTTTG
1 TTTTTTGCTTGTTTTTTTTG
13862 TTTTTT
1 TTTTTT
13868 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (20 bp):
TTTTTTGCTTGTTTTTTTTG
Found at i:13868 original size:20 final size:20
Alignment explanation
Indices: 13833--13871 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13823 TTTTTGGCTT
13833 TTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTGTTTTTTTTTTG
13853 TTTTTTTTGTTTTTTTTTT
1 TTTTTTTTGTTTTTTTTTT
13872 TTGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (20 bp):
TTTTTTTTGTTTTTTTTTTG
Found at i:13871 original size:11 final size:11
Alignment explanation
Indices: 13831--13874 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
13821 CTTTTTTGGC
13831 TTTTTTTTTTG
1 TTTTTTTTTTG
13842 TTTTTTTTTTG
1 TTTTTTTTTTG
13853 TTTTTTTTGTT-
1 TTTTTTTT-TTG
13864 TTTTTTTTTTG
1 TTTTTTTTTTG
13875 AAAAAAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 27 0.87
12 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:21284 original size:47 final size:47
Alignment explanation
Indices: 21208--21298 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
21198 TCATTACTGA
* * *
21208 TGTAAGGTACTTGTACCTTATCGATTGATTGTGGATCTAGGAAGTGG
1 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAGTGG
21255 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAG
1 TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAG
21299 GAAGAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (47 bp):
TGTAAGGCACTTGTACCTTATCAACTGATTGTGGATCTAGGAAGTGG
Found at i:24564 original size:27 final size:27
Alignment explanation
Indices: 24515--24571 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
24505 GAAAATCATA
*
24515 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
* *
24543 AAAGAAATT-CAGCATTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
24569 AAA
1 AAA
24572 AGCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 11 0.42
28 9 0.35
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Found at i:33711 original size:19 final size:21
Alignment explanation
Indices: 33674--33716 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
33664 TAACTTTTTC
33674 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
33694 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
33714 TTT
1 TTT
33717 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:33722 original size:19 final size:20
Alignment explanation
Indices: 33673--33722 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
33663 TTAACTTTTT
*
33673 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
33693 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
33712 CTTTTACCTTT
1 CTTTTACCTTT
33723 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:41131 original size:36 final size:36
Alignment explanation
Indices: 41091--41162 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
41081 GATACAATCT
* *
41091 GTCCATCACCATCATCACGCCTTTATCATCGCCATA
1 GTCCATCACCATCATCACGCCTATATCATCACCATA
*
41127 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATCATCACGCCTATATCATCACCATA
41163 TCACGCCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATCATCACGCCTATATCATCACCATA
Found at i:41167 original size:22 final size:23
Alignment explanation
Indices: 41113--41182 Score: 90
Period size: 22 Copynumber: 3.0 Consensus size: 23
41103 CATCACGCCT
41113 TTATCATCGCC-ATAGTCCATCACCA
1 TTATCA-CGCCTATA-T-CATCACCA
41138 TTATCACGCCTATATCATCACCA
1 TTATCACGCCTATATCATCACCA
*
41161 -TATCACGCCTATATTATCACCA
1 TTATCACGCCTATATCATCACCA
41183 ACTTATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
22 21 0.49
23 8 0.19
24 5 0.12
25 9 0.21
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.30
Consensus pattern (23 bp):
TTATCACGCCTATATCATCACCA
Found at i:66498 original size:35 final size:37
Alignment explanation
Indices: 66452--66531 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
66442 TTTGAGAATT
*
66452 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
66487 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
66524 TGGTGATG
1 TGGTGATG
66532 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:72180 original size:35 final size:37
Alignment explanation
Indices: 72134--72212 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
72124 TTTGAGAATT
*
72134 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
72169 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
72206 TGGTGAT
1 TGGTGAT
72213 AGAAATAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:74060 original size:24 final size:24
Alignment explanation
Indices: 74033--74078 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
74023 GGGGTGATTT
74033 ATAAAGGCTTAAAGGACGTGACTC
1 ATAAAGGCTTAAAGGACGTGACTC
*
74057 ATAAAGGCTTAACGGACGTGAC
1 ATAAAGGCTTAAAGGACGTGAC
74079 CCTTGAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (24 bp):
ATAAAGGCTTAAAGGACGTGACTC
Found at i:75226 original size:30 final size:30
Alignment explanation
Indices: 75192--75279 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
75182 GGACAACTTC
*
75192 GTGGAGCACTTGGAAGACATATACAGCTTA
1 GTGGAGCATTTGGAAGACATATACAGCTTA
* *
75222 GTGGAGCATTTGGAAGATATATAGAGCTTA
1 GTGGAGCATTTGGAAGACATATACAGCTTA
* *
75252 GTGGAACATTTGGGAGACAT-TGACAGCT
1 GTGGAGCATTTGGAAGACATAT-ACAGCT
75280 CACAAACAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (30 bp):
GTGGAGCATTTGGAAGACATATACAGCTTA
Found at i:83828 original size:13 final size:13
Alignment explanation
Indices: 83810--83834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83800 TTCCATGCAT
83810 GTTCATGTTATGG
1 GTTCATGTTATGG
83823 GTTCATGTTATG
1 GTTCATGTTATG
83835 AGCTACAAAT
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:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
GTTCATGTTATGG
Found at i:90292 original size:8 final size:8
Alignment explanation
Indices: 90281--90305 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
90271 TCTTTTTCTT
90281 TTCTTTTC
1 TTCTTTTC
90289 TTCTTTTC
1 TTCTTTTC
90297 TTCTTTTC
1 TTCTTTTC
90305 T
1 T
90306 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:94729 original size:35 final size:37
Alignment explanation
Indices: 94683--94762 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
94673 TTTAAGAATT
*
94683 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
94718 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
94755 TGGTGATG
1 TGGTGATG
94763 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:96731 original size:11 final size:11
Alignment explanation
Indices: 96715--96752 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
96705 ATTTTTTTTC
96715 AAAAAAACAAA
1 AAAAAAACAAA
96726 AAAAAAACAAA
1 AAAAAAACAAA
*
96737 AAAAAAGCCAAA
1 AAAAAA-ACAAA
96749 AAAA
1 AAAA
96753 TTCCAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:96732 original size:12 final size:12
Alignment explanation
Indices: 96715--96752 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
96705 ATTTTTTTTC
96715 AAAAAAAC-AAA
1 AAAAAAACAAAA
96726 AAAAAAACAAAA
1 AAAAAAACAAAA
**
96738 AAAAAGCCAAAA
1 AAAAAAACAAAA
96750 AAA
1 AAA
96753 TTCCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:105161 original size:35 final size:37
Alignment explanation
Indices: 105107--105186 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
105097 TTTGAGAATT
* * *
105107 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGACATAGACGTGATAATGGAAGATGGACTA
*
105142 TGGTGATGACATAGACGTGATAATGGAAGATGGATTA
1 TGGTGATGACATAGACGTGATAATGGAAGATGGACTA
105179 TGGTGATG
1 TGGTGATG
105187 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (37 bp):
TGGTGATGACATAGACGTGATAATGGAAGATGGACTA
Found at i:107738 original size:14 final size:13
Alignment explanation
Indices: 107719--107777 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
107709 CCTTGCTTGC
107719 TTTCTTTTTTGACT
1 TTTCTTTTTT-ACT
*
107733 TTTCTTCTTTTTCT
1 TTTCTT-TTTTACT
107747 TTTCTTTTTT-C-
1 TTTCTTTTTTACT
107758 -TTC-TTTTTATCT
1 TTTCTTTTTTA-CT
107770 TTTCTTTT
1 TTTCTTTT
107778 CTTTTGTACT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
9 5 0.13
10 3 0.08
11 1 0.03
12 1 0.03
13 7 0.18
14 17 0.45
15 4 0.11
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTCTTTTTTACT
Found at i:107749 original size:21 final size:21
Alignment explanation
Indices: 107725--107765 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
107715 TTGCTTTCTT
*
107725 TTTTGACTTTTCTTCTTTTTC
1 TTTTCACTTTTCTTCTTTTTC
**
107746 TTTTCTTTTTTCTTCTTTTT
1 TTTTCACTTTTCTTCTTTTT
107766 ATCTTTTCTT
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:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCACTTTTCTTCTTTTTC
Found at i:107758 original size:18 final size:19
Alignment explanation
Indices: 107731--107782 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
107721 TCTTTTTTGA
*
107731 CTTTTCTTCTT-TTTCTTTT
1 CTTTTCTTCTTCTTT-TTAT
107750 CTTTT-TTCTTCTTTTTAT
1 CTTTTCTTCTTCTTTTTAT
107768 CTTTTCTT-TTCTTTT
1 CTTTTCTTCTTCTTTT
107783 GTACTCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.67
19 10 0.33
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTTCTTCTTCTTTTTAT
Found at i:107770 original size:23 final size:21
Alignment explanation
Indices: 107732--107777 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 21
107722 CTTTTTTGAC
107732 TTTTCTTCTTTTTCTTTTCTT
1 TTTTCTTCTTTTTCTTTTCTT
107753 TTTTCTTCTTTTTATCTTTTCTT
1 TTTTCTTC-TTTT-TCTTTTCTT
107776 TT
1 TT
107778 CTTTTGTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTTCTTTTTCTTTTCTT
Found at i:107777 original size:21 final size:19
Alignment explanation
Indices: 107731--107780 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 19
107721 TCTTTTTTGA
107731 CTTTTCTTCTTTTTCTTTT
1 CTTTTCTTCTTTTTCTTTT
107750 CTTTTTTCTTCTTTTTATCTTTT
1 C--TTTTCTTC-TTTT-TCTTTT
107773 CTTTTCTT
1 CTTTTCTT
107781 TTGTACTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
21 15 0.56
22 4 0.15
23 7 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTTCTTCTTTTTCTTTT
Found at i:111478 original size:13 final size:13
Alignment explanation
Indices: 111460--111484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111450 TGCCGTGCAT
111460 GTTCATGTTATGG
1 GTTCATGTTATGG
111473 GTTCATGTTATG
1 GTTCATGTTATG
111485 AGTTACAAAT
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:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
GTTCATGTTATGG
Found at i:115826 original size:20 final size:21
Alignment explanation
Indices: 115793--115850 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
115783 TTAGAGTGCA
*
115793 AAAAGAA-AAGAAAAAGACA-
1 AAAAGAAGAAAAAAAAGACAG
* *
115812 AAAATAAGAAAAAAAA-TCAG
1 AAAAGAAGAAAAAAAAGACAG
115832 AAAAGAAGAAAAGAAAAGA
1 AAAAGAAGAAAA-AAAAGA
115851 AATTCAAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (21 bp):
AAAAGAAGAAAAAAAAGACAG
Found at i:117894 original size:30 final size:31
Alignment explanation
Indices: 117842--117901 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
117832 CTTAGCTTTA
**
117842 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
117872 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
117902 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:118831 original size:19 final size:20
Alignment explanation
Indices: 118807--118857 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
118797 CGGCCAAGAG
* *
118807 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCCAAAAT
118826 CATGTATTTTCATCCAAAAT
1 CATGTATTTTCATCCAAAAT
118846 CATGTATTTTCA
1 CATGTATTTTCA
118858 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCCAAAAT
Found at i:119610 original size:13 final size:13
Alignment explanation
Indices: 119592--119627 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
119582 ATCAGGAAAT
119592 AAGAAAAGAAGAA
1 AAGAAAAGAAGAA
119605 AAGAAAA-AGAGAA
1 AAGAAAAGA-AGAA
119618 AAGAAAAGAA
1 AAGAAAAGAA
119628 AAAGAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAGAA
Found at i:119623 original size:18 final size:18
Alignment explanation
Indices: 119600--119635 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
119590 ATAAGAAAAG
119600 AAGAAAAGAAAAAGAGAA
1 AAGAAAAGAAAAAGAGAA
119618 AAGAAAAGAAAAAGAGAA
1 AAGAAAAGAAAAAGAGAA
119636 GTTCAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAAAGAAAAAGAGAA
Found at i:119635 original size:13 final size:13
Alignment explanation
Indices: 119595--119632 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
119585 AGGAAATAAG
119595 AAAAGAAGAAAAGA
1 AAAAG-AGAAAAGA
119609 AAAAGAGAAAAG-
1 AAAAGAGAAAAGA
119621 AAAAGA-AAAAGA
1 AAAAGAGAAAAGA
119633 GAAGTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 6 0.26
13 7 0.30
14 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAGA
Found at i:119878 original size:12 final size:12
Alignment explanation
Indices: 119861--119900 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
119851 ATGCGGAATT
119861 ATGGTCTTGATG
1 ATGGTCTTGATG
119873 ATGGTCTTGATG
1 ATGGTCTTGATG
* *
119885 AAGGATGTTGATG
1 ATGG-TCTTGATG
119898 ATG
1 ATG
119901 TTGATGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38
Consensus pattern (12 bp):
ATGGTCTTGATG
Found at i:128096 original size:17 final size:17
Alignment explanation
Indices: 128074--128106 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
128064 TGGCATAAAA
128074 GAAATGGATATGGTAAT
1 GAAATGGATATGGTAAT
128091 GAAATGGATATGGTAA
1 GAAATGGATATGGTAA
128107 AGGTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
GAAATGGATATGGTAAT
Found at i:129857 original size:19 final size:20
Alignment explanation
Indices: 129833--129872 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
129823 TATCCTTTTT
129833 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
129852 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
129872 T
1 T
129873 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:135767 original size:5 final size:5
Alignment explanation
Indices: 135757--135782 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
135747 TGACTTAGAA
135757 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
135783 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:138626 original size:16 final size:16
Alignment explanation
Indices: 138592--138625 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
138582 TTCAACTTTC
*
138592 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
138608 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
138623 TTT
1 TTT
138626 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:142675 original size:20 final size:20
Alignment explanation
Indices: 142650--142688 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
142640 CCATGATATG
142650 TAAATG-ATATGAAAACATAA
1 TAAATGAATAT-AAAACATAA
142670 TAAATGAATATAAAACATA
1 TAAATGAATATAAAACATA
142689 TGTAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:144606 original size:35 final size:37
Alignment explanation
Indices: 144560--144639 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
144550 TTTGAGAATT
*
144560 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
144595 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
144632 TGGTGATG
1 TGGTGATG
144640 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:151571 original size:19 final size:18
Alignment explanation
Indices: 151521--151571 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
151511 TTCTTTTTGA
*
151521 CTTTT-TTTTTTAATTTT
1 CTTTTCTTTTTTACTTTT
151538 -TTCTTCTTTTTTACTTTT
1 CTT-TTCTTTTTTACTTTT
151556 CTTTTCTTTTTGTACT
1 CTTTTCTTTTT-TACT
151572 CCAATTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 19 0.66
19 6 0.21
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.76
Consensus pattern (18 bp):
CTTTTCTTTTTTACTTTT
Found at i:151890 original size:16 final size:15
Alignment explanation
Indices: 151869--151902 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
151859 GCTGCGGAAT
151869 TGATGGTCTTGATGGA
1 TGATGGTCTTGAT-GA
*
151885 TGATGGTGTTGATGA
1 TGATGGTCTTGATGA
151900 TGA
1 TGA
151903 AATGAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.21, C:0.03, G:0.38, T:0.38
Consensus pattern (15 bp):
TGATGGTCTTGATGA
Found at i:157895 original size:6 final size:6
Alignment explanation
Indices: 157881--157915 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
157871 TGTAGGAGTC
*
157881 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
157916 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:157910 original size:13 final size:12
Alignment explanation
Indices: 157881--157915 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
157871 TGTAGGAGTC
*
157881 TTTTCTTTTTGT
1 TTTTCTTTTTCT
157893 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
157906 TTTTCTTTTT
1 TTTTCTTTTT
157916 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:158181 original size:15 final size:15
Alignment explanation
Indices: 158139--158174 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
158129 AAGAAGAAAG
*
158139 GAAATGATAAGCATT
1 GAAATGATAAGAATT
158154 GAAATGATAAGAATT
1 GAAATGATAAGAATT
158169 GAAATG
1 GAAATG
158175 GATAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (15 bp):
GAAATGATAAGAATT
Found at i:162573 original size:11 final size:11
Alignment explanation
Indices: 162557--162595 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
162547 CTATTTTTTT
162557 CAAAAAAAAAA
1 CAAAAAAAAAA
**
162568 C-AAAAAAAGG
1 CAAAAAAAAAA
162578 CAAAAAAAAAA
1 CAAAAAAAAAA
162589 CAAAAAA
1 CAAAAAA
162596 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:162596 original size:20 final size:21
Alignment explanation
Indices: 162557--162602 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
162547 CTATTTTTTT
*
162557 CAAAAAAAAAACAAAAAAAGG
1 CAAAAAAAAAACAAAAAAAGC
162578 CAAAAAAAAAAC-AAAAAAGC
1 CAAAAAAAAAACAAAAAAAGC
162598 CAAAA
1 CAAAA
162603 TTTCAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.80, C:0.13, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAACAAAAAAAGC
Found at i:170976 original size:19 final size:20
Alignment explanation
Indices: 170938--170980 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
170928 GAAACCCCTT
*
170938 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
170958 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
170977 TGAA
1 TGAA
170981 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:173813 original size:35 final size:36
Alignment explanation
Indices: 173764--173844 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
173754 CACATCAAGA
173764 ATGGTGATGATATAGGCATG-AAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATGAAAATGGTGATGGAAG
* * *
173799 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAT
1 ATGGTGATGATATAGGCATGAAAATGGTGATGGAAG
173835 ATGGTGATGA
1 ATGGTGATGA
173845 ACAGATAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 18 0.44
36 23 0.56
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.28
Consensus pattern (36 bp):
ATGGTGATGATATAGGCATGAAAATGGTGATGGAAG
Found at i:173840 original size:13 final size:13
Alignment explanation
Indices: 173786--173843 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
173776 TAGGCATGAA
*
173786 ATGGTGATGGAAG
1 ATGGTGATGGAAT
**
173799 ATGGTGATGTTAT
1 ATGGTGATGGAAT
* *
173812 A-GGCG-T-GAAA
1 ATGGTGATGGAAT
173822 ATGGTGATGGAAT
1 ATGGTGATGGAAT
173835 ATGGTGATG
1 ATGGTGATG
173844 AACAGATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:179749 original size:54 final size:54
Alignment explanation
Indices: 179618--180220 Score: 820
Period size: 54 Copynumber: 11.2 Consensus size: 54
179608 ATTATATGGT
** ** * * ***
179618 TTGCACACGTAGTGCCAATACGGTAATTCATAAACTCATTATGAATTACGTGGGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTC-TTAAG
* * * *
179673 TTGCACACATAGTGACAATACGAAAATTCATAAACTTATTATAAATTTATTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
179727 TTGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGGATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * *
179781 TTGCACACACTGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAT
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * *
179835 TTGTACACACAGTGCCAATACGAAGATTCATAAACTTATTATGAATTACTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
179889 TTGCACACACAGTGCCAATACGGAAATTTATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * * *
179943 TTGCACAGACAGTGTCATTACGAAAATTCATAAACTTATTATGAATTTCTT-CG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * * *
179996 TTGCACACATATTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAT
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* * *
180050 TTGCACACGCAGTGCCAATACAAAAATTTATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
* *
180104 TTGCGCACACAGTGCCAATACAAAAATTCAT-AA---ATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
*
180154 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
*
180208 TTGCATACACAGT
1 TTGCACACACAGT
180221 ACCATTTGGT
Statistics
Matches: 482, Mismatches: 61, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
50 45 0.09
51 2 0.00
53 48 0.10
54 346 0.72
55 41 0.09
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
Found at i:182654 original size:18 final size:19
Alignment explanation
Indices: 182631--182668 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
182621 GCAATTCATC
*
182631 TTGAAAGGTAAAAA-AAAA
1 TTGAAAAGTAAAAATAAAA
*
182649 TTGAAAATTAAAAATAAAA
1 TTGAAAAGTAAAAATAAAA
182668 T
1 T
182669 AAAAAAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
TTGAAAAGTAAAAATAAAA
Found at i:192418 original size:12 final size:11
Alignment explanation
Indices: 192385--192433 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
192375 CAAAAGCAAC
*
192385 AAAAAGAGAAA
1 AAAAAAAGAAA
192396 AATAAAGAAGAAA
1 AA-AAA-AAGAAA
192409 AACAAAAAGAAA
1 AA-AAAAAGAAA
*
192421 AAGAAAAGAAA
1 AAAAAAAGAAA
192432 AA
1 AA
192434 GACTCCTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 12 0.36
12 11 0.33
13 10 0.30
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:192421 original size:6 final size:6
Alignment explanation
Indices: 192386--192435 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
192376 AAAAGCAACA
* *
192386 AAAAGAG AAAAAT AAAGAAG AAAAAC AAAAAG AAAAAG -AAAAG AAAAAG
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
192435 A
1 A
192436 CTCCTACATC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 23 0.62
7 9 0.24
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:196890 original size:6 final size:6
Alignment explanation
Indices: 196849--196892 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
196839 AAAAGTAACA
*
196849 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
196893 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:197734 original size:14 final size:14
Alignment explanation
Indices: 197715--197742 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
197705 AAGTTTGAAA
197715 AAGAGTTGCATCGG
1 AAGAGTTGCATCGG
197729 AAGAGTTGCATCGG
1 AAGAGTTGCATCGG
197743 TTTGACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (14 bp):
AAGAGTTGCATCGG
Found at i:207500 original size:15 final size:15
Alignment explanation
Indices: 207482--207567 Score: 68
Period size: 15 Copynumber: 5.5 Consensus size: 15
207472 TATCTTCATT
207482 TTTCTTATTATTTCA
1 TTTCTTATTATTTCA
* *
207497 TTTCGTATTTCTTTCA
1 TTTCTTA-TTATTTCA
207513 TATT-TTATTATTTCA
1 T-TTCTTATTATTTCA
* *
207528 TTTCGTATTTCTTTCA
1 TTTCTTA-TTATTTCA
*
207544 TATT-TTCTTATTTCA
1 T-TTCTTATTATTTCA
207559 TTTCCTTAT
1 TTT-CTTAT
207568 CCTTTTCTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
14 4 0.07
15 24 0.44
16 22 0.41
17 4 0.07
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTCTTATTATTTCA
Found at i:207513 original size:16 final size:16
Alignment explanation
Indices: 207492--207544 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
207482 TTTCTTATTA
207492 TTTCATTTCGTATTTC
1 TTTCATTTCGTATTTC
* *
207508 TTTCATATT-TTA-TTA
1 TTTCAT-TTCGTATTTC
207523 TTTCATTTCGTATTTC
1 TTTCATTTCGTATTTC
207539 TTTCAT
1 TTTCAT
207545 ATTTTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
16 16 0.53
17 2 0.07
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTCATTTCGTATTTC
Found at i:207516 original size:11 final size:11
Alignment explanation
Indices: 207490--207548 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
207480 TTTTTCTTAT
*
207490 TATTTCATTTCG
1 TATTTC-TTTCA
207502 TATTTCTTTCA
1 TATTTCTTTCA
*
207513 TATTT-TAT--
1 TATTTCTTTCA
*
207521 TATTTCATTTCG
1 TATTTC-TTTCA
207533 TATTTCTTTCA
1 TATTTCTTTCA
207544 TATTT
1 TATTT
207549 TCTTATTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 5 0.13
10 4 0.10
11 18 0.46
12 12 0.31
ACGTcount: A:0.19, C:0.14, G:0.03, T:0.64
Consensus pattern (11 bp):
TATTTCTTTCA
Found at i:207521 original size:31 final size:31
Alignment explanation
Indices: 207486--207562 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
207476 TTCATTTTTC
207486 TTATTATTTCATTTCGTATTTCTTTCATATT
1 TTATTATTTCATTTCGTATTTCTTTCATATT
207517 TTATTATTTCATTTCGTATTTCTTTCATATT
1 TTATTATTTCATTTCGTATTTCTTTCATATT
*
207548 TTCTTATTTCATTTC
1 TTATTATTTCATTTC
207563 CTTATCCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.03, T:0.65
Consensus pattern (31 bp):
TTATTATTTCATTTCGTATTTCTTTCATATT
Found at i:213210 original size:11 final size:11
Alignment explanation
Indices: 213196--213251 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
213186 TCTTTTTGAA
213196 TTCTTTTTCTT
1 TTCTTTTTCTT
213207 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
213220 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
213233 TGTCTTTTTC-T
1 T-TCTTTTTCTT
213244 TTCTTTTT
1 TTCTTTTT
213252 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:213220 original size:19 final size:18
Alignment explanation
Indices: 213196--213251 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
213186 TCTTTTTGAA
213196 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
213214 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
213233 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
213251 T
1 T
213252 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:217123 original size:14 final size:14
Alignment explanation
Indices: 217104--217131 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
217094 ATACTATATA
217104 TTTCCATCACCATC
1 TTTCCATCACCATC
217118 TTTCCATCACCATC
1 TTTCCATCACCATC
217132 CTCCATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:217330 original size:15 final size:15
Alignment explanation
Indices: 217312--217354 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
217302 TTTCCATTTC
217312 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
217327 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
217342 CATTTCCTTTCTT
1 CATTTCCTTTCTT
217355 CTTCCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (15 bp):
CATTTCCTTTCTTAT
Found at i:225363 original size:14 final size:13
Alignment explanation
Indices: 225346--225395 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
225336 GTGCAAAAAG
225346 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
225360 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
225373 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
225384 AAAGAAAAAGAA
1 AAAGAAAAAGAA
225396 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:225392 original size:19 final size:18
Alignment explanation
Indices: 225340--225395 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
225330 ATTGGAGTGC
225340 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
225357 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
225376 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
225395 A
1 A
225396 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:225393 original size:11 final size:11
Alignment explanation
Indices: 225340--225395 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
225330 ATTGGAGTGC
225340 AAAAAG-AAAG
1 AAAAAGAAAAG
225350 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
225364 AAGAAGAAAAG
1 AAAAAGAAAAG
225375 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
225388 AAAAAGAA
1 AAAAAGAA
225396 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Done.