Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006229.1 Hibiscus syriacus cultivar Beakdansim tig00014844_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: 99934
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7236 original size:31 final size:31
Alignment explanation
Indices: 7198--7258 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
7188 TCACAATACG
7198 TCTAAAATATTATATTTATACATTTTACAGA
1 TCTAAAATATTATATTTATACATTTTACAGA
7229 TCTAAAATATTATATTTATACATTTTACAG
1 TCTAAAATATTATATTTATACATTTTACAG
7259 TTATCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (31 bp):
TCTAAAATATTATATTTATACATTTTACAGA
Found at i:11487 original size:16 final size:17
Alignment explanation
Indices: 11460--11495 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
11450 GATATAAGAA
11460 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
11477 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
11493 AAA
1 AAA
11496 ATATCGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:13865 original size:11 final size:11
Alignment explanation
Indices: 13849--13881 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13839 ATATAAACAA
13849 TTTTTCTCTAT
1 TTTTTCTCTAT
13860 TTTTTCTC-ATT
1 TTTTTCTCTA-T
13871 TTTTTCTCTAT
1 TTTTTCTCTAT
13882 GCCCTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTCTCTAT
Found at i:15320 original size:42 final size:41
Alignment explanation
Indices: 15274--15354 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
15264 TTTTAGCAGC
* *
15274 GTTTTTTAACAAATGCCGCTAAAGGTAATGATATTTAGTGGT
1 GTTTTTT-ACAAACGCCACTAAAGGTAATGATATTTAGTGGT
** * *
15316 GTTTTTTTGAAGCGCCACTAAAGGTTATGATATTTAGTG
1 GTTTTTTACAAACGCCACTAAAGGTAATGATATTTAGTG
15355 ACATTTTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 26 0.79
42 7 0.21
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (41 bp):
GTTTTTTACAAACGCCACTAAAGGTAATGATATTTAGTGGT
Found at i:15736 original size:19 final size:19
Alignment explanation
Indices: 15704--15760 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
15694 AGTATCAAAT
**
15704 AAACTTGACGTCCATAAAC
1 AAACTTGAAATCCATAAAC
*
15723 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCAT-A-AAC
15744 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
15761 TAATAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 17 0.52
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (19 bp):
AAACTTGAAATCCATAAAC
Found at i:19600 original size:40 final size:41
Alignment explanation
Indices: 19497--19659 Score: 220
Period size: 41 Copynumber: 4.0 Consensus size: 41
19487 TTGTAAACAC
*
19497 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
19538 AAACCCCACTAAAGTATGAGTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
19579 AAACG-CACTAAAGTACAAGTCTATAGTGGCGTTTGTATTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
19619 AAATGCCACTAAAGTAGGAGTCTTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
19660 TGTAATGATA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
40 34 0.33
41 70 0.67
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:19633 original size:81 final size:82
Alignment explanation
Indices: 19497--19659 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 82
19487 TTGTAAACAC
* * *
19497 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACCCCACTAAAGTATGAGTCTA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
*
19562 TAGCGACGTTTGTATAA
66 TAGCGACGTTTATATAA
* * ** *
19579 AAACG-CACTAAAGTACAAGTCTATAGTGGCGTTTGTATTAAAATGCCACTAAAGTAGGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
*
19643 TAGCGGCGTTTATATAA
66 TAGCGACGTTTATATAA
19660 TGTAATGATA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 66 0.93
82 5 0.07
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (82 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
TAGCGACGTTTATATAA
Found at i:19871 original size:41 final size:41
Alignment explanation
Indices: 19762--19872 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
19752 TTACGACGTC
* * *
19762 TGTATAAAAA-GCAACTAAAGTACAAGTCTTTAGCGGCGTT
1 TGTATAAAAATGCAACTAAAGTACGAGTCTATAGCGGCATT
* *
19802 TGTATAAAAATGCCACTAAAGTACGAGTCTATAGGGGCATT
1 TGTATAAAAATGCAACTAAAGTACGAGTCTATAGCGGCATT
* *
19843 TGTATAAAAATGCTACTAAAGTAGGAGTCT
1 TGTATAAAAATGCAACTAAAGTACGAGTCT
19873 TCAACAACAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 10 0.16
41 53 0.84
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (41 bp):
TGTATAAAAATGCAACTAAAGTACGAGTCTATAGCGGCATT
Found at i:19884 original size:41 final size:41
Alignment explanation
Indices: 19762--19906 Score: 116
Period size: 41 Copynumber: 3.6 Consensus size: 41
19752 TTACGACGTC
* * * * ** *
19762 TGTATAAAAA-GCAACTAAAGTACAAGTCTTTAGCGGCGTT
1 TGTATAAAAATGCCACTAAAGTACGAGTCTATAACAACATT
****
19802 TGTATAAAAATGCCACTAAAGTACGAGTCTATAGGGGCATT
1 TGTATAAAAATGCCACTAAAGTACGAGTCTATAACAACATT
* *
19843 TGTATAAAAATGCTACTAAAGTAGGAGTCT-TCAACAACATT
1 TGTATAAAAATGCCACTAAAGTACGAGTCTAT-AACAACATT
* *
19884 TGTATACAAACGCCA-TGAAAGTA
1 TGTATAAAAATGCCACT-AAAGTA
19907 TGATTCTTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
40 12 0.14
41 76 0.86
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (41 bp):
TGTATAAAAATGCCACTAAAGTACGAGTCTATAACAACATT
Found at i:20823 original size:43 final size:43
Alignment explanation
Indices: 20713--21165 Score: 288
Period size: 43 Copynumber: 10.3 Consensus size: 43
20703 CAACACCCTA
* * * *
20713 TGTGATGGAAGCGAGCGAAATGTTGATGTT-TGACCAA-TTCCTTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTAT--TCAACTT-ATTC
* * * *
20757 TATGATGGAATTGAATGAGATGTTGATGTTATTCAACTTATTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
*
20800 TGTCATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
* * ** * *
20843 TGTCATGGAATCGAACGAAATGTTAATGTTTAACCTACTCT-TTT
1 TGTGATGGAATCGAACGAAATGTTGATG-TTATTCAACT-TATTC
* * * * ** *
20887 TGTGATGGAATTGATCAAAATGTTAATGTTTGACCCAACTTCTTC
1 TGTGATGGAATCGAACGAAATGTTGATG-TT-ATTCAACTTATTC
* * ** **
20932 TGTGATGGAATC-AATAGAAATATTGATGTTTGACCCAACTCCTTC
1 TGTGATGGAATCGAA-CGAAATGTTGATG-TT-ATTCAACTTATTC
* * * * **
20977 TGTGATAGAATCGAGCGAAATATTGATGTTGTTCAACTCCTTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
* * * ** * *
21020 TATGATGGAATCTAATGAAATGTTGATGAAAAATCAACTCATTC
1 TGTGATGGAATCGAACGAAATGTTGATG-TTATTCAACTTATTC
* ** * * *
21064 TGTGATGGAATTGAACGAAATGTT-AGTGAAATTCATCTCATTT
1 TGTGATGGAATCGAACGAAATGTTGA-TGTTATTCAACTTATTC
* *
21107 TGTGATGGAATTGAACGAAATGTTGATGTTGATCCAACTCT-TTC
1 TGTGATGGAATCGAACGAAATGTTGATGTT-ATTCAACT-TATTC
*
21151 TGTGATGGAAGCGAA
1 TGTGATGGAATCGAA
21166 ACTTGAATTC
Statistics
Matches: 332, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
43 142 0.43
44 120 0.36
45 69 0.21
46 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (43 bp):
TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
Found at i:20895 original size:87 final size:87
Alignment explanation
Indices: 20713--21165 Score: 342
Period size: 87 Copynumber: 5.2 Consensus size: 87
20703 CAACACCCTA
* * * * * * * * *
20713 TGTGATGGAAGCGAGCGAAATGTTGATGTT-TGACCAATTCCTTCTATGATGGAATTGAATGAGA
1 TGTGATGGAATCGAACGAAATGTTGATGTTAT--TCAACTCATTCTGTGATGGAATCGAACGAAA
**
20777 TGTTGATG-TTATTCAACT-TATTC
64 TGTTGATGTTTAACCAACTCT-TTC
* * *
20800 TGTCATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTCTGTCATGGAATCGAACGAAATG
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTCATTCTGTGATGGAATCGAACGAAATG
* * *
20865 TTAATGTTTAACCTACTCTTTT
66 TTGATGTTTAACCAACTCTTTC
* * * * ** *
20887 TGTGATGGAATTGATCAAAATGTTAATGTTTGACCCAACTTC-TTCTGTGATGGAATC-AATAGA
1 TGTGATGGAATCGAACGAAATGTTGATG-TT-ATTCAAC-TCATTCTGTGATGGAATCGAA-CGA
* * *
20950 AATATTGATGTTTGACCCAACTCCTTC
62 AATGTTGATGTTT-AACCAACTCTTTC
* * * * * * * *
20977 TGTGATAGAATCGAGCGAAATATTGATGTTGTTCAACTCCTTCTATGATGGAATCTAATGAAATG
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTCATTCTGTGATGGAATCGAACGAAATG
*** * *
21042 TTGATGAAAAATCAACTCATTC
66 TTGATGTTTAACCAACTCTTTC
* ** * * *
21064 TGTGATGGAATTGAACGAAATGTT-AGTGAAATTCATCTCATTTTGTGATGGAATTGAACGAAAT
1 TGTGATGGAATCGAACGAAATGTTGA-TGTTATTCAACTCATTCTGTGATGGAATCGAACGAAAT
* *
21128 GTTGATGTTGATCCAACTCTTTC
65 GTTGATGTTTAACCAACTCTTTC
*
21151 TGTGATGGAAGCGAA
1 TGTGATGGAATCGAA
21166 ACTTGAATTC
Statistics
Matches: 282, Mismatches: 73, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
86 30 0.11
87 149 0.53
88 35 0.12
89 36 0.13
90 32 0.11
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (87 bp):
TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTCATTCTGTGATGGAATCGAACGAAATG
TTGATGTTTAACCAACTCTTTC
Found at i:21030 original size:177 final size:174
Alignment explanation
Indices: 20730--21088 Score: 389
Period size: 177 Copynumber: 2.0 Consensus size: 174
20720 GAAGCGAGCG
* * * * **
20730 AAATGTTGATGTTTGACCAATTCCTTCTATGATGGAATTGAATGAGATGTTGATGTTATTCAACT
1 AAATGTTAATGTTTGACCAATTCCTTCTATGATGGAATTCAATGAAATATTGATGTTACCCAACT
* * * * *
20795 TATTCTGTCATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTCTGTCATGGAATCGAACG
66 CATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATCGAACG
*** * * * *
20860 AAATGTTAATGTTTAACCTACTCTTTTTGTGATGGAATTGATCA
131 AAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
*
20904 AAATGTTAATGTTTGACCCAACTT-CTTCTGTGATGGAA-TCAATAGAAATATTGATGTTTGACC
1 AAATGTTAATGTTTGA-CCAA-TTCCTTCTATGATGGAATTCAAT-GAAATATTGATG-TT-ACC
* * * * * *
20967 CAACTCCTTCTGTGATAGAATCGAGCGAAATATTGATGTTGTTCAACTCCTTCTATGATGGAATC
61 CAACTCATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATC
* * * * *
21032 TAATGAAATGTTGATGAAAAATCAACTCATTCTGTGATGGAATTGAACG
126 GAACGAAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
21081 AAATGTTA
1 AAATGTTA
21089 GTGAAATTCA
Statistics
Matches: 150, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
174 19 0.13
175 27 0.18
176 4 0.03
177 100 0.67
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (174 bp):
AAATGTTAATGTTTGACCAATTCCTTCTATGATGGAATTCAATGAAATATTGATGTTACCCAACT
CATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATCGAACG
AAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
Found at i:24909 original size:23 final size:23
Alignment explanation
Indices: 24820--24949 Score: 90
Period size: 23 Copynumber: 5.8 Consensus size: 23
24810 GAGTCAAGGG
*
24820 TTCTACGCGGTCCTTCGGGACA-
1 TTCTACGTGGTCCTTCGGGACAT
* * *
24842 -TCTATGTGGTCCTTCTGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
*
24864 TTCTATC-TGGTCCTTTGGGACAT
1 TTCTA-CGTGGTCCTTCGGGACAT
* *
24887 TTCTACGTGATCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * * * *
24910 ATCTAAGTGCTCCATCGTGACA-
1 TTCTACGTGGTCCTTCGGGACAT
*
24932 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
24950 TGCAATTTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
21 19 0.23
22 12 0.15
23 51 0.62
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:27096 original size:3 final size:3
Alignment explanation
Indices: 27088--27120 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
27078 GAAATCTCTA
27088 TCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC
27121 ATCCTCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:28626 original size:23 final size:23
Alignment explanation
Indices: 28537--28650 Score: 106
Period size: 23 Copynumber: 5.0 Consensus size: 23
28527 GAGTCAAGGG
*
28537 TTCTACGCGGTCCTTCGGGACA-
1 TTCTACGTGGTCCTTCGGGACAT
* *
28559 -TCTATGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
* *
28581 TTCTACCTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
28604 TTCTACGTGATCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * * * *
28627 ATCTAAGTGCTCCATCGTGACAT
1 TTCTACGTGGTCCTTCGGGACAT
28650 T
1 T
28651 CTATATGGCA
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
21 19 0.26
23 54 0.74
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:30816 original size:3 final size:3
Alignment explanation
Indices: 30808--30837 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
30798 GAAATCTCTA
30808 TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC
30838 ATCCTCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:32306 original size:23 final size:22
Alignment explanation
Indices: 32253--32374 Score: 68
Period size: 23 Copynumber: 5.5 Consensus size: 22
32243 GAGTCGAGGG
* *
32253 TTCTACGCGGTCCTTTGGGACA
1 TTCTACGTGGTCCTTTAGGACA
*
32275 -TCTATGTGGTCCTTTAGGACAA
1 TTCTACGTGGTCCTTTAGGAC-A
* ** *
32297 TTCTACGTGGTTCTTCGGGATA
1 TTCTACGTGGTCCTTTAGGACA
**
32319 TTTCTACGCT-GTCCTACAGGACA
1 -TTCTACG-TGGTCCTTTAGGACA
* * * *
32342 TATCTATGTAGTCCTTTGGGAAA
1 T-TCTACGTGGTCCTTTAGGACA
*
32365 TTCTATGTGG
1 TTCTACGTGG
32375 CATTTTGGTG
Statistics
Matches: 76, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 17 0.22
22 12 0.16
23 46 0.61
24 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (22 bp):
TTCTACGTGGTCCTTTAGGACA
Found at i:32493 original size:15 final size:15
Alignment explanation
Indices: 32473--32501 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32463 AATGGGCTAT
32473 TAAAACGAGATAATA
1 TAAAACGAGATAATA
32488 TAAAACGAGATAAT
1 TAAAACGAGATAAT
32502 GGGCTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (15 bp):
TAAAACGAGATAATA
Found at i:49795 original size:19 final size:19
Alignment explanation
Indices: 49771--49808 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
49761 GTTTAAGAAC
49771 ATAATCTCTGCTTGTATCA
1 ATAATCTCTGCTTGTATCA
*
49790 ATAATCTCTTCTTGTATCA
1 ATAATCTCTGCTTGTATCA
49809 TCTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (19 bp):
ATAATCTCTGCTTGTATCA
Found at i:52283 original size:38 final size:38
Alignment explanation
Indices: 52228--52320 Score: 141
Period size: 38 Copynumber: 2.4 Consensus size: 38
52218 CTACAAAGGA
* * *
52228 GGGGGTTCGGGCAAAAAGGATAGATAAAAGAAAAAAGT
1 GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
*
52266 GGGGGTTCGGGCGAAAAGGAGAGAAAAAATAAAAAAGT
1 GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
*
52304 GGGGGTTCGAGCGAAAA
1 GGGGGTTCGGGCGAAAA
52321 AAGAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.44, C:0.06, G:0.38, T:0.12
Consensus pattern (38 bp):
GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
Found at i:52339 original size:38 final size:38
Alignment explanation
Indices: 52228--52331 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 38
52218 CTACAAAGGA
* * * * *
52228 GGGGGTTCGGGCAAAAAGGATAGATAAAAGAAAAAAGT
1 GGGGGTTCGAGCGAAAAGAAGAGAAAAAAGAAAAAAGT
* * *
52266 GGGGGTTCGGGCGAAAAGGAGAGAAAAAATAAAAAAGT
1 GGGGGTTCGAGCGAAAAGAAGAGAAAAAAGAAAAAAGT
52304 GGGGGTTCGAGCGAAAA-AAGA-AAAAAAG
1 GGGGGTTCGAGCGAAAAGAAGAGAAAAAAG
52332 GAGAAAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 6 0.10
37 3 0.05
38 50 0.85
ACGTcount: A:0.48, C:0.06, G:0.36, T:0.11
Consensus pattern (38 bp):
GGGGGTTCGAGCGAAAAGAAGAGAAAAAAGAAAAAAGT
Found at i:54626 original size:12 final size:12
Alignment explanation
Indices: 54601--54645 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
54591 AAAAAATGTA
54601 AATA-AATATAT
1 AATATAATATAT
*
54612 AATATAATTTAT
1 AATATAATATAT
54624 AATATAAATATAT
1 AATAT-AATATAT
54637 ATATATAAT
1 A-ATATAAT
54646 GACGAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 4 0.14
12 11 0.38
13 10 0.34
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAATATAT
Found at i:54630 original size:17 final size:19
Alignment explanation
Indices: 54605--54645 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54595 AATGTAAATA
*
54605 AATATATAATATA-ATTTAT
1 AATATA-AATATATATATAT
54624 AATATAAATATATATATAT
1 AATATAAATATATATATAT
54643 AAT
1 AAT
54646 GACGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATAAATATATATATAT
Found at i:55154 original size:105 final size:105
Alignment explanation
Indices: 54955--55695 Score: 1374
Period size: 105 Copynumber: 7.0 Consensus size: 105
54945 CGTTGTGAAG
* * * * *
54955 CTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTG
1 CTGAATTTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
55020 TCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
55061 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
55126 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
55166 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
55231 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
55271 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
55336 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
55376 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTG
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTG
55441 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
55482 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
55547 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
55587 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTG
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTG
*
55652 TCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
55693 CTG
1 CTG
55696 GGTAAAACCT
Statistics
Matches: 623, Mismatches: 10, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
105 456 0.73
106 167 0.27
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (105 bp):
CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:55338 original size:210 final size:211
Alignment explanation
Indices: 54955--55695 Score: 1378
Period size: 211 Copynumber: 3.5 Consensus size: 211
54945 CGTTGTGAAG
* * * * *
54955 CTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAAC-TTGCATT
1 CTGAATTTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTT
*
55019 GTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTG
65 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTG
55084 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
130 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
55149 TGAAGTTGAAATTGGCT
195 TGAAGTTGAAATTGGCT
55166 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTG
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTTG
55230 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
55295 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
55360 GAAGTTGAAATTGGCT
196 GAAGTTGAAATTGGCT
*
55376 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTG
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTTG
55441 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
55506 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
55571 GAAGTTGAAATTGGCT
196 GAAGTTGAAATTGGCT
*
55587 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTTGCGTTG
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTTG
*
55652 TCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
55696 GGTAAAACCT
Statistics
Matches: 521, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
210 247 0.47
211 274 0.53
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (211 bp):
CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTTG
TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
GAAGTTGAAATTGGCT
Found at i:56486 original size:14 final size:14
Alignment explanation
Indices: 56467--56493 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56457 CCCTAAGCGT
56467 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
56481 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
56494 CATTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:56499 original size:14 final size:14
Alignment explanation
Indices: 56468--56505 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
56458 CCTAAGCGTT
**
56468 TTTTGTTTTTTTGT
1 TTTTGTTTTTTTCA
56482 TTTTGTTTTTTTCA
1 TTTTGTTTTTTTCA
56496 TTTT-TTTTTT
1 TTTTGTTTTTT
56506 CAACTTAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTGTTTTTTTCA
Found at i:65960 original size:13 final size:13
Alignment explanation
Indices: 65944--65968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65934 TAAAAATAAC
65944 AAGAAAAAAACAT
1 AAGAAAAAAACAT
65957 AAGAAAAAAACA
1 AAGAAAAAAACA
65969 AATGATTAGG
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:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAGAAAAAAACAT
Found at i:67229 original size:2 final size:2
Alignment explanation
Indices: 67222--67261 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
67212 ACATACATAC
67222 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
67262 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68407 original size:2 final size:2
Alignment explanation
Indices: 68402--68451 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
68392 ATGTAAATAA
* *
68402 AT AT AT A- AT AT A- AT TT AT A- AT AT AA 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
68441 AT AT AT AT AT A
1 AT AT AT AT AT A
68452 ATGACGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:73418 original size:18 final size:19
Alignment explanation
Indices: 73375--73418 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
73365 AACACCTTGT
*
73375 GCAT-TTGTGTTTGCATTT
1 GCATATTGTGTTTGCATTG
73393 GCATTATTGT-TTTGCATTG
1 GCA-TATTGTGTTTGCATTG
73412 GCATATT
1 GCATATT
73419 AATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (19 bp):
GCATATTGTGTTTGCATTG
Found at i:74397 original size:2 final size:2
Alignment explanation
Indices: 74392--74444 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
74382 TATATCCAAC
74392 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
74434 AT AT AT AT AT A
1 AT AT AT AT AT A
74445 CATTAATATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82964 original size:41 final size:42
Alignment explanation
Indices: 82907--82988 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
82897 AAGGGTTTCT
*
82907 TGATTGGTAAGTCCTTC-GGCCAT-TAGTAAGCCTGTCGAGCA
1 TGATTGGTAAATCCTTCGGGCCATCTA-TAAGCCTGTCGAGCA
* * *
82948 TGATTGTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGC
1 TGATTGGTAAATCCTTCGGGCCATCTATAAGCCTGTCGAGC
82989 TAGAGGATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 15 0.43
42 18 0.51
43 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (42 bp):
TGATTGGTAAATCCTTCGGGCCATCTATAAGCCTGTCGAGCA
Found at i:83450 original size:260 final size:256
Alignment explanation
Indices: 82909--83735 Score: 927
Period size: 260 Copynumber: 3.2 Consensus size: 256
82899 GGGTTTCTTG
* * * * * *
82909 ATTGGTAAGTCCTT-CGGCCATTAGTAAGCCTGTCGAGCATGATTG-TTAAATCCTTCGGGTCAT
1 ATTGGTAAGTCCTTAGGGCCATCAATAAGTCTTTCGAGCAT-AATGATTAAATCCTTC-GGTCAT
* * * * * * * * * * * * **
82972 CTATAAGCCTTTCGAGCTAGAGGATAAGTCCTTCAGGTCATCCAGAAGGCCTTCGGACAGGATAT
64 CTGTCAGTCTTTCGAGCAAGAAGATAAGTCTTTCAGGCCATCTATAAGACCTTCGGGCAAGATGC
* * **
83037 TTTCACATGAAT--TTTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTTTTCTC
129 TTTCATAT-AATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTAAA--TTTTCAA
* *
83100 AAAATGAAAATTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAA
191 AAAATG-AATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAA
83165 AA
255 AA
* * *
83167 ATTGATAAGTCCTTCA-GGTCATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGAGTCAT
1 ATTGGTAAGTCCTT-AGGGCCATCAATAAGTCTTTCGAGCATAATGATTAAATCCTTCG-GTCAT
* * *
83231 TTGTCAGTCTTTCGAGCAAGATGATAAGTCATTTGA-GCCATCTATAAGACCTTCGGGCAAGATG
64 CTGTCAGTCTTTCGAGCAAGAAGATAAGTC-TTTCAGGCCATCTATAAGACCTTCGGGCAAGATG
* *
83295 CTTTCATATAATAATTTGAAAAATGAGAAAGCAATTTTCAAAGTTTC-CTATTTAGAATTTTCAA
128 CTTTCATATAATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTC-ATTTA-AATTTTC--
* * *
83359 AAAAAATGAATTTTTTGAAAATTAAGAAAACGATTTCCAAAGTTTCTTACCTAGT-AATTATTTC
189 AAAAAATGAA-TTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTC
*
83423 TAAA
253 AAAA
* ** * * *
83427 ATTGGTAAGTCCTTAGGGTCATCAATAAGTCTTTCGAGCATGTTGTTTAAATCCTTTGGGCTATC
1 ATTGGTAAGTCCTTAGGGCCATCAATAAGTCTTTCGAGCATAATGATTAAATCCTTCGGTC-ATC
* * *
83492 TGTCAGTCTTTCGATCAAGAAGATAAGT-TGTACAGGCCATCTATAAGACCTTTGGGCAAGATGC
65 TGTCAGTCTTTCGAGCAAGAAGATAAGTCT-TTCAGGCCATCTATAAGACCTTCGGGCAAGATGC
* *
83556 TTTCATATGATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTAATATTTTCAGAA
129 TTTCATATAATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTAA-ATTTTCAAAA
* * * *
83621 AATG-ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGCTTCTTATCTAGTAAACTATTTCCAAA
193 AATGAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAA
* * *
83684 ATTGGTAAGTCCTTTGGGCCATCAATAAGTCTTTCAAGCATGATGATTAAAT
1 ATTGGTAAGTCCTTAGGGCCATCAATAAGTCTTTCGAGCATAATGATTAAAT
83736 ATTTCGGGTA
Statistics
Matches: 487, Mismatches: 63, Indels: 39
0.83 0.11 0.07
Matches are distributed among these distances:
256 39 0.08
257 59 0.12
258 28 0.06
259 101 0.21
260 211 0.43
261 49 0.10
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (256 bp):
ATTGGTAAGTCCTTAGGGCCATCAATAAGTCTTTCGAGCATAATGATTAAATCCTTCGGTCATCT
GTCAGTCTTTCGAGCAAGAAGATAAGTCTTTCAGGCCATCTATAAGACCTTCGGGCAAGATGCTT
TCATATAATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTAAATTTTCAAAAAAT
GAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAA
Found at i:85807 original size:13 final size:15
Alignment explanation
Indices: 85781--85816 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
85771 ATATTTTGAT
85781 TATATTTGTATATAA
1 TATATTTGTATATAA
85796 TATATTT-T-TATAA
1 TATATTTGTATATAA
85809 TATATTTG
1 TATATTTG
85817 AAAATAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.60
14 1 0.05
15 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TATATTTGTATATAA
Found at i:87398 original size:17 final size:18
Alignment explanation
Indices: 87376--87409 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
87366 TATTGAGTCC
87376 TTTAATTTT-TTTTTTAT
1 TTTAATTTTGTTTTTTAT
87393 TTTAATTTTGTTTTTTA
1 TTTAATTTTGTTTTTTA
87410 ATAAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTAATTTTGTTTTTTAT
Found at i:92783 original size:39 final size:39
Alignment explanation
Indices: 92671--92785 Score: 115
Period size: 39 Copynumber: 2.9 Consensus size: 39
92661 TACTTTCTGG
* * * *
92671 AGGCTCCTCGGCTTTGTTCTCAGGGTAAGTCCTTACTGC
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTAC
** * *
92710 AGGCTCCTCTGCTTTGTGCACATAAG-AAGACCTTACTAT
1 AGGCTCCTCTGCTTTGTGCACA-GGGTAAGTCCTTACTAC
* * *
92749 GGGCTCCTTTGCTTTGTGCACAGGGTAATTCCTTACT
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACT
92786 GGGTGTACAG
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
38 1 0.02
39 58 0.97
40 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTAC
Found at i:93016 original size:18 final size:18
Alignment explanation
Indices: 92993--93032 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
92983 TCCCGCTCAT
92993 ACTCATAGTACAGTTCAG
1 ACTCATAGTACAGTTCAG
93011 ACTCATAGTACAGTTCAG
1 ACTCATAGTACAGTTCAG
93029 ACTC
1 ACTC
93033 CTGCAGGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (18 bp):
ACTCATAGTACAGTTCAG
Found at i:97014 original size:39 final size:39
Alignment explanation
Indices: 96971--97089 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 39
96961 TTATCGCTTT
* *
96971 CTGCAGGCTCCT-TGGCTTTGTGCTCAGGGTAAGTCCTTA
1 CTGCAGACTCCTCT-GCTTTGTGCACAGGGTAAGTCCTTA
* * * *
97010 CTGCAGACTCCTCTACTTTGTACACAGGATAAGACCTTA
1 CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
* *
97049 CTGCAGACT-CTCTGCTTTGTGCACATGGTAAGTTCTTA
1 CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
97087 CTG
1 CTG
97090 GATGTACATG
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
38 26 0.39
39 40 0.60
40 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (39 bp):
CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
Found at i:97455 original size:36 final size:37
Alignment explanation
Indices: 97415--97487 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
97405 ATGTATTATC
* *
97415 GGTATTTTGTTCCGTAAATGTTTTAT-AGTTTTCTGT
1 GGTATTTTGATACGTAAATGTTTTATAAGTTTTCTGT
* *
97451 GGTATTTTGATATGTATATGTTTTATACAGTTTTCTG
1 GGTATTTTGATACGTAAATGTTTTATA-AGTTTTCTG
97488 ACATATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 22 0.71
38 9 0.29
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (37 bp):
GGTATTTTGATACGTAAATGTTTTATAAGTTTTCTGT
Found at i:98165 original size:17 final size:17
Alignment explanation
Indices: 98143--98175 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
98133 AATAAACGAA
*
98143 CTAGTTTGATTAATGAT
1 CTAGTTTAATTAATGAT
98160 CTAGTTTAATTAATGA
1 CTAGTTTAATTAATGA
98176 ACTACTTCTC
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:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (17 bp):
CTAGTTTAATTAATGAT
Done.