Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004761.1 Hibiscus syriacus cultivar Beakdansim tig00010740_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: 96856
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2815 original size:20 final size:20
Alignment explanation
Indices: 2790--2848 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
2780 TCATATTGTT
*
2790 CAGGGGGTACAGCTTCCCCC
1 CAGGGGGTACAGATTCCCCC
*
2810 CAGGGGGAACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
2830 CAGGGGGTATC-GATTCCCC
1 CAGGGGGTA-CAGATTCCCC
2849 GGGAACAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.15
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:2860 original size:35 final size:35
Alignment explanation
Indices: 2814--2899 Score: 138
Period size: 34 Copynumber: 2.5 Consensus size: 35
2804 TCCCCCCAGG
*
2814 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAAGGGGTATCGATTCCCC
*
2849 GGGAACAGATT-CTCCCAAGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAAGGGGTATCGATTCCCC
*
2883 GGGTACAGATTCCCCCC
1 GGGAACAGATTCCCCCC
2900 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 31 0.67
35 15 0.33
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAAGGGGTATCGATTCCCC
Found at i:2893 original size:15 final size:15
Alignment explanation
Indices: 2841--2897 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
2831 AGGGGGTATC
*
2841 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
2856 GATTCTCCCAAGGGGTATC-
1 GATTC-CCC---GGGTA-CA
2875 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
2890 GATTCCCC
1 GATTCCCC
2898 CCTGCATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:3035 original size:21 final size:21
Alignment explanation
Indices: 3011--3052 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3001 ATTTTAATAT
**
3011 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
3032 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3053 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3114 original size:21 final size:21
Alignment explanation
Indices: 3081--3120 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3071 TTTTTGTAGA
*
3081 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3103 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3121 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3374 original size:34 final size:32
Alignment explanation
Indices: 3335--3404 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3325 TTTTGTAAAG
* *
3335 GGGAAAGGTTCTAGCTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGC-C-TGGAAAAACTA
*
3369 GGGAAAGGTTCTAGTTTAGCCTGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCTGGAAAAACTA
3401 GGGA
1 GGGA
3405 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 13 0.39
33 1 0.03
34 19 0.58
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCTGGAAAAACTA
Found at i:6298 original size:72 final size:72
Alignment explanation
Indices: 6164--6297 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
6154 AGTTGAGTCC
* *
6164 GACTCGACTTGAAAGCTTGCGAGCTTAAAATTATCAAGCTCAACTAGAACTTTAAATCAAAAACT
1 GACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATCAAAAACT
6229 GAAGTTT
66 GAAGTTT
* * * * *
6236 GACTCGACTTGAAAGCTTACGAGCTTAAAATTGTCTAGTTC-GCTTGAACTTGAAATCAAAAA
1 GACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATCAAAAA
6298 ATTGAAACTC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
71 18 0.33
72 37 0.67
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (72 bp):
GACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATCAAAAACT
GAAGTTT
Found at i:6312 original size:72 final size:72
Alignment explanation
Indices: 6163--6314 Score: 189
Period size: 72 Copynumber: 2.1 Consensus size: 72
6153 CAGTTGAGTC
* *
6163 CGACTCGACTTGAAAGCTTGCGAGCTTAAAATTATCAAGCTCAACTAGAACTTTAAATCAAAAAC
1 CGACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATCAAAAAC
**
6228 TGAAGTT
66 TGAAACT
* * * * * *
6235 TGACTCGACTTGAAAGCTTACGAGCTTAAAATTGTCTAGTTC-GCTTGAACTTGAAATCAAAAAA
1 CGACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATC-AAAAA
*
6299 TTGAAACT
65 CTGAAACT
6307 CGACTCGA
1 CGACTCGA
6315 GATCAAAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
71 13 0.19
72 54 0.81
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (72 bp):
CGACTCGACTTGAAAGCTTACGAGCTTAAAATTATCAAGCTCAACTAGAACTTGAAATCAAAAAC
TGAAACT
Found at i:9807 original size:31 final size:31
Alignment explanation
Indices: 9772--9834 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
9762 CCTCTTCTTT
9772 TGTCCTCCCTTG-CTTTCTCATTTTAGCATTG
1 TGTCCTCCCTTGCCTTT-TCATTTTAGCATTG
*
9803 TGTCCTTCCTTGCCTTTTCATTTTAGCATTG
1 TGTCCTCCCTTGCCTTTTCATTTTAGCATTG
9834 T
1 T
9835 TTTTTATGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.10, C:0.27, G:0.13, T:0.51
Consensus pattern (31 bp):
TGTCCTCCCTTGCCTTTTCATTTTAGCATTG
Found at i:19562 original size:165 final size:165
Alignment explanation
Indices: 19289--19693 Score: 648
Period size: 165 Copynumber: 2.5 Consensus size: 165
19279 GATTTGGATT
* *
19289 ATGATAAGAATGAGGGGTCAAAGGAAGATAATTGTTTGGGGATTAATGGAGTTGATTCGGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
* * * *
19354 AGGATACGAGAAGATCATATTGGTGTCGTAGTGGCCGGATCAGATGAGAGGTTGGAAGAAAGAGT
66 AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
* **
19419 GGATAGTGGAAGTGAGGACAATGCGGTTGTAAAAC
131 GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
19454 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
* * * * *
19519 AGGAAACAAGAGGAACATATTGGTGTTGAAGTGGCCAGATCAGATGAGAGGTTGGAAGTAAGATT
66 AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
*
19584 GGATAGTGGAAGTGAAGACAATGAAGTTGTAGAAC
131 GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
* *
19619 ATGCTAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCTGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
*
19684 AAGATACAAG
66 AGGATACAAG
19694 TTTCCGGAGA
Statistics
Matches: 221, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
165 221 1.00
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (165 bp):
ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
Found at i:28987 original size:8 final size:8
Alignment explanation
Indices: 28974--29014 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
28964 CTCATTTTCA
28974 GAGAATTT
1 GAGAATTT
28982 GAGAATTT
1 GAGAATTT
*
28990 -AGAGTTT
1 GAGAATTT
*
28997 GGGAATTT
1 GAGAATTT
29005 GAGAATTT
1 GAGAATTT
29013 GA
1 GA
29015 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:29307 original size:126 final size:126
Alignment explanation
Indices: 29082--29683 Score: 1120
Period size: 126 Copynumber: 4.8 Consensus size: 126
29072 CTATAATCGG
* *
29082 TTCACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
29147 TCATTGGCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
29208 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
29273 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
29332 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
29397 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
29458 TTCACTATTCACGTGAAGGCACGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
29523 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
29584 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
29648 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
29684 ATAACTTAAA
Statistics
Matches: 464, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
124 123 0.27
125 70 0.15
126 271 0.58
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:29523 original size:250 final size:251
Alignment explanation
Indices: 29082--29683 Score: 1118
Period size: 250 Copynumber: 2.4 Consensus size: 251
29072 CTATAATCGG
* *
29082 TTCACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
29147 TCATTGGCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
*
29212 CTATTCACGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACGTGAAGGCACGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATTATCAT
29277 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAG-ATATCAGTACCTATTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTAT
29332 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
29397 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
**
29462 CTATTCACGTGAAGGCACGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACGTGAAGGCACGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATTATCAT
29527 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTAT
29584 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
29648 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
29684 ATAACTTAAA
Statistics
Matches: 343, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
250 227 0.66
251 71 0.21
252 45 0.13
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (251 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CTATTCACGTGAAGGCACGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATTATCAT
TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTAT
Found at i:30149 original size:34 final size:34
Alignment explanation
Indices: 30070--30168 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
30060 AAATTTAATG
*
30070 TTAAATTTCGAATACTATAATTTATA-TTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
30103 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
30136 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
30169 AACATTTATC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
32 14 0.25
33 21 0.38
34 20 0.36
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:30716 original size:21 final size:21
Alignment explanation
Indices: 30692--30752 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
30682 ATAAAACCCT
30692 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
30713 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
*
30734 GCGGGCTAGGAATGTAACC
1 GCGGGCTAGGCATGTAACC
30753 CTGCGAACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.18
Consensus pattern (21 bp):
GCGGGCTAGGCATGTAACCTG
Found at i:30770 original size:42 final size:42
Alignment explanation
Indices: 30692--30773 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
30682 ATAAAACCCT
* ** *
30692 GCGGGCTAGGCATGTAACCTGGCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTGGCGAACTAGGAATGTAACCTG
*
30734 GCGGGCTAGGAATGTAACCCT-GCGAACTCGGAATGTAACC
1 GCGGGCTAGGAATGTAA-CCTGGCGAACTAGGAATGTAACC
30774 CTGCGAAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.23, C:0.24, G:0.34, T:0.18
Consensus pattern (42 bp):
GCGGGCTAGGAATGTAACCTGGCGAACTAGGAATGTAACCTG
Found at i:30809 original size:21 final size:21
Alignment explanation
Indices: 30783--30830 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
30773 CCTGCGAAGA
*
30783 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
30804 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
30825 GGGCAT
1 TGGCAT
30831 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:32592 original size:34 final size:31
Alignment explanation
Indices: 32549--32625 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 31
32539 TTAATAATTC
* *
32549 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATA-TA--TTAA
*
32583 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
32614 TATAAAAAATAA
1 TA-AAAAAATAA
32626 CTATTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 6 0.15
32 9 0.23
33 2 0.05
34 22 0.56
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:36665 original size:34 final size:35
Alignment explanation
Indices: 36627--36718 Score: 91
Period size: 34 Copynumber: 2.7 Consensus size: 35
36617 GATTAAGTTA
* * *
36627 AACATAAAT-GAATGAACATAAACAAACATAAACG
1 AACATAAATCAAACGAACATAAACAAAAATAAACG
**
36661 AACAT-AATCAAACGAACATAAACAAAAATAATTG
1 AACATAAATCAAACGAACATAAACAAAAATAAACG
* * *
36695 AACAT-AACCGAACGAATATAAACA
1 AACATAAATCAAACGAACATAAACA
36719 TTCACAAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 3 0.06
34 46 0.94
ACGTcount: A:0.61, C:0.16, G:0.08, T:0.15
Consensus pattern (35 bp):
AACATAAATCAAACGAACATAAACAAAAATAAACG
Found at i:36673 original size:24 final size:24
Alignment explanation
Indices: 36646--36692 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
36636 GAATGAACAT
* *
36646 AAACAAACATAAACGAACATAATC
1 AAACAAACATAAACAAAAATAATC
*
36670 AAACGAACATAAACAAAAATAAT
1 AAACAAACATAAACAAAAATAAT
36693 TGAACATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.66, C:0.17, G:0.04, T:0.13
Consensus pattern (24 bp):
AAACAAACATAAACAAAAATAATC
Found at i:36679 original size:14 final size:14
Alignment explanation
Indices: 36656--36686 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
36646 AAACAAACAT
*
36656 AAACGAACATAATC
1 AAACGAACATAAAC
36670 AAACGAACATAAAC
1 AAACGAACATAAAC
36684 AAA
1 AAA
36687 AATAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:40111 original size:28 final size:26
Alignment explanation
Indices: 40078--40313 Score: 136
Period size: 28 Copynumber: 8.3 Consensus size: 26
40068 AAAATATTTT
*
40078 TTTTATTTTTGTTTAACTTATAAATCTA
1 TTTTATTTTT-TTTAACTTA-AAATATA
* *
40106 TTTTATTCTAATTTTAA-TATAAAAAATA
1 TTTTATT-T-TTTTTAACT-TAAAATATA
* * *
40134 TTTTATTACTATCTTCACTTAAAACTATA
1 TTTTATT--TTTTTTAACTTAAAA-TATA
40163 TTTTATTCTTATTTTGAA-TTAAAATATA
1 TTTTATT-TT-TTTT-AACTTAAAATATA
*
40191 TTTTATTTTTGTCTTAACTTAGAAATCTA
1 TTTTATTTTT-T-TTAACTTA-AAATATA
*
40220 TTTTATTCTTATTTTAA-TATAAAAGATA
1 TTTTATT-TT-TTTTAACT-TAAAATATA
* *
40248 TTTTATTATTATCTTCACTTAAAATATATA
1 TTTTATT-TT-TTTTAACTT-AAA-ATATA
*
40278 TTTTATTCTTATTTTAAATTAAAAATATA
1 TTTTATT-TT-TTTTAACTT-AAAATATA
40307 TTTTATT
1 TTTTATT
40314 ATTATCTTAA
Statistics
Matches: 170, Mismatches: 20, Indels: 35
0.76 0.09 0.16
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 69 0.41
29 65 0.38
30 29 0.17
31 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTATTTTTTTTAACTTAAAATATA
Found at i:40122 original size:29 final size:29
Alignment explanation
Indices: 40089--40336 Score: 197
Period size: 29 Copynumber: 8.6 Consensus size: 29
40079 TTTATTTTTG
* *
40089 TTTAACTTATAAATCTATTTTATTCTAAT
1 TTTAACTTATAAATATATTTTATTCTTAT
*
40118 TTTAA--TATAAAAAATATTTTATTAC-TAT
1 TTTAACTTAT-AAATATATTTTATT-CTTAT
* *
40146 CTTCACTTA-AAACTATATTTTATTCTTAT
1 TTTAACTTATAAA-TATATTTTATTCTTAT
* *
40175 TTTGAA-TTA-AAATATATTTTATTTTTGT
1 TTT-AACTTATAAATATATTTTATTCTTAT
* * *
40203 CTTAACTTAGAAATCTATTTTATTCTTAT
1 TTTAACTTATAAATATATTTTATTCTTAT
* *
40232 TTTAA--TATAAAAGATATTTTATTATTAT
1 TTTAACTTAT-AAATATATTTTATTCTTAT
* * *
40260 CTTCACTTAAAATATATATTTTATTCTTAT
1 TTTAACTTATAA-ATATATTTTATTCTTAT
* * *
40290 TTTAAATTAAAAATATATTTTATTATTAT
1 TTTAACTTATAAATATATTTTATTCTTAT
* * *
40319 CTTAACTTTTAAAAATAT
1 TTTAACTTATAAATATAT
40337 AATTTTTAAA
Statistics
Matches: 173, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
27 7 0.04
28 59 0.34
29 78 0.45
30 29 0.17
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTAACTTATAAATATATTTTATTCTTAT
Found at i:40169 original size:57 final size:56
Alignment explanation
Indices: 40090--40326 Score: 298
Period size: 57 Copynumber: 4.1 Consensus size: 56
40080 TTATTTTTGT
* * *
40090 TTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAAATATTTTATTACTATC
1 TTAACTTA-AAATATATTTTATTCTTATTTTAATATAAAAAATATTTTATTATTATC
* * * *
40147 TTCACTTAAAACTATATTTTATTCTTATTTTGAAT-TAAAATATATTTTATTTTTGTC
1 TTAACTTAAAA-TATATTTTATTCTTATTTT-AATATAAAAAATATTTTATTATTATC
* *
40204 TTAACTTAGAAATCTATTTTATTCTTATTTTAATATAAAAGATATTTTATTATTATC
1 TTAACTTA-AAATATATTTTATTCTTATTTTAATATAAAAAATATTTTATTATTATC
*
40261 TTCACTTAAAATATATATTTTATTCTTATTTTAA-ATTAAAAATATATTTTATTATTATC
1 TTAACTT-AAA-ATATATTTTATTCTTATTTTAATA-TAAAAA-ATATTTTATTATTATC
40320 TTAACTT
1 TTAACTT
40327 TTAAAAATAT
Statistics
Matches: 156, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
56 6 0.04
57 95 0.61
58 33 0.21
59 22 0.14
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (56 bp):
TTAACTTAAAATATATTTTATTCTTATTTTAATATAAAAAATATTTTATTATTATC
Found at i:40219 original size:114 final size:116
Alignment explanation
Indices: 40078--40326 Score: 405
Period size: 114 Copynumber: 2.2 Consensus size: 116
40068 AAAATATTTT
*
40078 TTTTATTTTTGT-TTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAAATATTTTATTA
1 TTTTATTTTTGTCTTAACTTAGAAATCTATTTTATTCTAATTTTAATATAAAAAATATTTTATTA
* *
40142 CTATCTTCACTTAAAA-CTATATTTTATTCTTATTTTGAATT-AAAATATA
66 CTATCTTCACTTAAAATATATATTTTATTCTTATTTTAAATTAAAAATATA
* *
40191 TTTTATTTTTGTCTTAACTTAGAAATCTATTTTATTCTTATTTTAATATAAAAGATATTTTATTA
1 TTTTATTTTTGTCTTAACTTAGAAATCTATTTTATTCTAATTTTAATATAAAAAATATTTTATTA
*
40256 TTATCTTCACTTAAAATATATATTTTATTCTTATTTTAAATTAAAAATATA
66 CTATCTTCACTTAAAATATATATTTTATTCTTATTTTAAATTAAAAATATA
* *
40307 TTTTATTATTATCTTAACTT
1 TTTTATTTTTGTCTTAACTT
40327 TTAAAAATAT
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
113 12 0.10
114 64 0.51
115 23 0.18
116 26 0.21
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (116 bp):
TTTTATTTTTGTCTTAACTTAGAAATCTATTTTATTCTAATTTTAATATAAAAAATATTTTATTA
CTATCTTCACTTAAAATATATATTTTATTCTTATTTTAAATTAAAAATATA
Found at i:40345 original size:15 final size:17
Alignment explanation
Indices: 40320--40358 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
40310 TATTATTATC
*
40320 TTAACTTTTAAAA-ATA
1 TTAATTTTTAAAACATA
40336 -TAATTTTTAAAACATA
1 TTAATTTTTAAAACATA
40352 TTAATTT
1 TTAATTT
40359 CAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATTTTTAAAACATA
Found at i:50291 original size:36 final size:36
Alignment explanation
Indices: 50244--50398 Score: 231
Period size: 36 Copynumber: 4.3 Consensus size: 36
50234 AGTCAATCCT
50244 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
50280 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
50316 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
50352 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
50388 AAGTCTTCACC
1 AAGCCTTCACC
50399 AAAAAGTAGT
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
35 1 0.01
36 108 0.98
37 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:50399 original size:36 final size:36
Alignment explanation
Indices: 50243--50432 Score: 229
Period size: 36 Copynumber: 5.2 Consensus size: 36
50233 AAGTCAATCC
*
50243 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* * * *
50279 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* * *
50315 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* *
50351 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
* * * *
50387 TAAGTCTTCACCA-AAAAGTAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCAGAGAA-TAGTGAAGCA-AACCATCT
50424 TAAGCCTTC
1 TAAGCCTTC
50433 TCAGAAGAGT
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 2 0.01
36 120 0.88
37 14 0.10
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (36 bp):
TAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCT
Found at i:50936 original size:53 final size:51
Alignment explanation
Indices: 50813--51119 Score: 321
Period size: 53 Copynumber: 5.8 Consensus size: 51
50803 GAAGATATAC
* *
50813 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTT-AA-AGATGTT
1 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAGAT-TT
* *
50863 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 -GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAGAT-T-T
* *
50917 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATTATTT
1 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGA-GATTT
* * * *
50969 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGCTTTTAAAAGATTTT
1 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTTGAAGAGA-TTT
* * * * *
51022 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATTC
1 -GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTT--GAAGA-GATTT
* * *
51078 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTT
1 GAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
51120 CCAAAAGATT
Statistics
Matches: 219, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
51 39 0.18
52 39 0.18
53 59 0.27
54 39 0.18
55 18 0.08
56 24 0.11
57 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAGATTT
Found at i:51119 original size:56 final size:53
Alignment explanation
Indices: 50803--51156 Score: 362
Period size: 51 Copynumber: 6.6 Consensus size: 53
50793 TGAAGCAAAT
* *
50803 GAAGATATACGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCG-TTTA
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTA
* * * *
50855 -AAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCG-TTT-
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTA
* * *
50905 GAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCC-ATTT-
1 GAAGATAT-TC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTA
* * * *
50958 GAAGATTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGCTTTTA
1 GAAGA-TATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTTTA
* * * *
51013 AAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCA
1 GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTT-A
* * *
51067 GAAGATCATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCA
1 GAAGAT-ATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT-TA
* *
51123 AAAGATTATTCGAG-TCTCATACTCTCTGAAAGAA
1 GAAGA-TATTCGAGTTCT-ATACTCCCT-AAAGAA
51157 TAGGGAGTAG
Statistics
Matches: 257, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
51 51 0.20
52 37 0.14
53 48 0.19
54 47 0.18
55 25 0.10
56 48 0.19
57 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (53 bp):
GAAGATATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTTA
Found at i:51190 original size:55 final size:55
Alignment explanation
Indices: 51124--51650 Score: 667
Period size: 55 Copynumber: 9.7 Consensus size: 55
51114 CCGTTTCCAA
* * * * * *
51124 AAGATTATTCGAGTCTCATACTCTCTGAA-AGAATAGGGAGTAGACACGATTGTTA
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGGGCAGACACAATTGTTG
* * *
51179 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGGGCATACACAATCGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
* * *
51234 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
* * *
51289 AAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
*
51342 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGATG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
* *
51397 AAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
* * * ** * *
51450 AAGATTGTTCGAGTCTTATACTCTTTAAAGAAATAGGGGGCATATGCGATTGATG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
* * * **
51505 AAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
*
51558 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA-AGTTTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACA-ATTGTTG
* *
51613 AAGA-TGATTCAAGTCTTATACCCTCTGAAGAAATAGGG
1 AAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
51651 AGCGAACCCA
Statistics
Matches: 412, Mismatches: 51, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
53 139 0.34
54 9 0.02
55 263 0.64
56 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTG
Found at i:51349 original size:108 final size:108
Alignment explanation
Indices: 51124--51650 Score: 752
Period size: 108 Copynumber: 4.8 Consensus size: 108
51114 CCGTTTCCAA
* * * * * *
51124 AAGATTATTCGAGTCTCATACTCTCTGAA-AGAATAGGGAGTAGACACGATTGTTAAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGGGCAGACACGATTGATGAAGATTG-T
* * *
51188 CGAGTCTCATACTCTCTGAAGAAATAGGGGGCATACACAATCGTTG
64 -GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
*
51234 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
*
51299 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTG
66 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
*
51342 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGATGAAGATTGTGG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
51407 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
66 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
* * * ** *
51450 AAGATTGTTCGAGTCTTATACTCTTTAAAGAAATAGGGGGCATATGCGATTGATGAAGATTATGG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
* *
51515 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCATTG
66 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
* * *
51558 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGA-TGATT
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTG--T
** *
51622 CAAGTCTTATACCCTCTGAAGAAATAGGG
64 -GGGTCTTATACTCTCTGAAGAAATAGGG
51651 AGCGAACCCA
Statistics
Matches: 378, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
107 1 0.00
108 296 0.78
109 2 0.01
110 78 0.21
111 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (108 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
Found at i:57023 original size:16 final size:15
Alignment explanation
Indices: 56976--57024 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
56966 CTGAACCTAG
56976 AATAACTCAAACTAAA
1 AATAACTCAAA-TAAA
56992 AATAAC-CAAATAAAA
1 AATAACTCAAAT-AAA
* *
57007 AATAACTCGAATGAA
1 AATAACTCAAATAAA
57022 AAT
1 AAT
57025 GAACCCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 1 0.03
15 18 0.62
16 10 0.34
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.18
Consensus pattern (15 bp):
AATAACTCAAATAAA
Found at i:60572 original size:95 final size:95
Alignment explanation
Indices: 60409--60586 Score: 338
Period size: 95 Copynumber: 1.9 Consensus size: 95
60399 TACAACGTGT
60409 AGTTTAAACTATAATTTAATAATGAGAAGGATAAGTAATAACTTTTTGAGTAAAGTACACAAATG
1 AGTTTAAACTATAATTTAATAATGAGAAGGATAAGTAATAACTTTTTGAGTAAAGTACACAAATG
*
60474 ATCCCTCGATTATAGGATATTACTTTGTTG
66 ATCCCTCGAGTATAGGATATTACTTTGTTG
*
60504 AGTTTAAACTATAATTTAATAATGAGAAGGATAAGTAATAACTTTTTGGGTAAAGTACACAAATG
1 AGTTTAAACTATAATTTAATAATGAGAAGGATAAGTAATAACTTTTTGAGTAAAGTACACAAATG
60569 ATCCCTCGAGTATAGGAT
66 ATCCCTCGAGTATAGGAT
60587 CAATTTGTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (95 bp):
AGTTTAAACTATAATTTAATAATGAGAAGGATAAGTAATAACTTTTTGAGTAAAGTACACAAATG
ATCCCTCGAGTATAGGATATTACTTTGTTG
Found at i:63062 original size:2 final size:2
Alignment explanation
Indices: 63009--63049 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
62999 TTATAAGTAT
*
63009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63049 T
1 T
63050 GTGTGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:63253 original size:28 final size:25
Alignment explanation
Indices: 63217--63270 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
63207 GCGACAATAA
*
63217 TTTTAAAATTGTATTTTTGTAATTATTT
1 TTTTAAAATT-TA-ATTT-TAATTATTT
*
63245 TTTTCAAATTTAATTTTAATTATTT
1 TTTTAAAATTTAATTTTAATTATTT
63270 T
1 T
63271 AATTACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 2 0.08
28 9 0.38
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTAAAATTTAATTTTAATTATTT
Found at i:63525 original size:18 final size:18
Alignment explanation
Indices: 63504--63565 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
63494 AAGTTTTAGA
63504 AAAATATCATTAAAAGTT
1 AAAATATCATTAAAAGTT
** **
63522 AAAA-AAAATGTAAACTTT
1 AAAATATCAT-TAAAAGTT
63540 ACAAATTATCATTAAAAGTT
1 A-AAA-TATCATTAAAAGTT
63560 AAAATA
1 AAAATA
63566 CGATAAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 6 0.19
20 7 0.22
21 3 0.09
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (18 bp):
AAAATATCATTAAAAGTT
Found at i:63750 original size:25 final size:24
Alignment explanation
Indices: 63722--63780 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 24
63712 AATTTCCTCA
63722 CAATAGGTTTCGTAAAATTCGATCT
1 CAATA-GTTTCGTAAAATTCGATCT
63747 CAATTAGTTTCGTAAAATTCGATCT
1 CAA-TAGTTTCGTAAAATTCGATCT
63772 CAATTAGTT
1 CAA-TAGTT
63781 AATCAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (24 bp):
CAATAGTTTCGTAAAATTCGATCT
Found at i:65398 original size:22 final size:23
Alignment explanation
Indices: 65358--65400 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
65348 ACAAACTCAA
* *
65358 ATATAGATTCAAAATAATTGTAT
1 ATATACATTCAAAAAAATTGTAT
65381 ATATACATT-AAAAAAATTGT
1 ATATACATTCAAAAAAATTGT
65401 CAGATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (23 bp):
ATATACATTCAAAAAAATTGTAT
Found at i:67991 original size:23 final size:23
Alignment explanation
Indices: 67958--68005 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
67948 CCTTTCGGGC
67958 AAAGAGAAGACCCCACCGACCTG
1 AAAGAGAAGACCCCACCGACCTG
*
67981 AAAGAGCAGACCCCACCGACCTG
1 AAAGAGAAGACCCCACCGACCTG
68004 AA
1 AA
68006 GATTACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.35, G:0.21, T:0.04
Consensus pattern (23 bp):
AAAGAGAAGACCCCACCGACCTG
Found at i:73785 original size:29 final size:30
Alignment explanation
Indices: 73753--73816 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
73743 CAATTCTTCC
73753 CTTTTATTTTTATATA-AAAAATCAT-TATT
1 CTTTTATTTTTATATATAAAAAT-ATCTATT
*
73782 CTTTTATTTTTATATATGAAAATATCTATT
1 CTTTTATTTTTATATATAAAAATATCTATT
73812 CTTTT
1 CTTTT
73817 TGTATACCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (30 bp):
CTTTTATTTTTATATATAAAAATATCTATT
Found at i:74031 original size:28 final size:29
Alignment explanation
Indices: 73956--74032 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 29
73946 ACAAAACGAC
*
73956 GTTTAATTAT-TAAATAAAATTAATGACAT
1 GTTTAATTATATATAT-AAATTAATGACAT
* * *
73985 GTTTTTTAAATAAAAATATAAA-TAATGACAT
1 G---TTTAATTATATATATAAATTAATGACAT
74016 GTTTAATTATATATATA
1 GTTTAATTATATATATA
74033 TATATTATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
28 13 0.35
29 1 0.03
31 10 0.27
32 10 0.27
33 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
GTTTAATTATATATATAAATTAATGACAT
Found at i:77252 original size:2 final size:2
Alignment explanation
Indices: 77245--77298 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
77235 TTCCTGAAAT
77245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
77287 TA TA TA CA TA TA
1 TA TA TA TA TA TA
77299 AATTTATACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:78651 original size:21 final size:23
Alignment explanation
Indices: 78617--78658 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
78607 ATAGTCTTTT
78617 TTTTTACCACTTTTT-ATAATTC
1 TTTTTACCACTTTTTAATAATTC
*
78639 TTTTTA-CATTTTTTAATAAT
1 TTTTTACCACTTTTTAATAAT
78659 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTACCACTTTTTAATAATTC
Found at i:95586 original size:203 final size:193
Alignment explanation
Indices: 95362--95750 Score: 534
Period size: 203 Copynumber: 2.0 Consensus size: 193
95352 AAATAGTAAT
*
95362 AATATAATATAAAGAAGTAAAGAAATAGGGT-AAATACAAAATGTGTACATATATACATATATAT
1 AATATAATATAAAGAAGTAAAG-AATAGGGTAAAATACAAAATGTGTACATATATACACATATAT
* * * *
95426 ATATACATGTAATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATG-TAG
65 ATATAAATAT-ATAACATATAAATGAAATAATAC--TA-TAATAAT--ATATATACGAATGATAA
*
95490 AAAAACTAATAATAGTATAAA-ATATATAAAATATTATAATGTAATATAAAAAGATAATT-AAAC
124 AAAAACTAATAATAATA-AAACATATAT-AAATATTAT-ATGT-A-AT-AAAAGATAATTAAAAC
95553 TAATGTAAATA
183 TAATGTAAATA
*
95564 AATATAATAATAAAGAAGTAAAGAATAGGGTAAAATACAAAATGTGTACATATATATACATATAT
1 AATATAAT-ATAAAGAAGTAAAGAATAGGGTAAAATACAAAATGTGTACATATATACACATATAT
* *
95629 ATATAAATATATAACATATAAGTGAAATAATACTATAATACTATATATACGAATGTATAAAAAAA
65 ATATAAATATATAACATATAAATGAAATAATACTATAATAATATATATACGAATG-ATAAAAAAA
95694 CTAATAATAATAAAACATATATAAATATTATATGTAATAAAAGATAATTAAAACTAA
129 CTAATAATAATAAAACATATATAAATATTATATGTAATAAAAGATAATTAAAACTAA
95751 AATCCAGAGA
Statistics
Matches: 172, Mismatches: 9, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
194 11 0.06
195 9 0.05
196 1 0.01
197 16 0.09
198 12 0.07
199 30 0.17
200 2 0.01
202 38 0.22
203 53 0.31
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (193 bp):
AATATAATATAAAGAAGTAAAGAATAGGGTAAAATACAAAATGTGTACATATATACACATATATA
TATAAATATATAACATATAAATGAAATAATACTATAATAATATATATACGAATGATAAAAAAACT
AATAATAATAAAACATATATAAATATTATATGTAATAAAAGATAATTAAAACTAATGTAAATA
Found at i:95625 original size:10 final size:10
Alignment explanation
Indices: 95610--95648 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
95600 ACAAAATGTG
95610 TACATATATA
1 TACATATATA
95620 TACATATATA
1 TACATATATA
* *
95630 TATAAATATA
1 TACATATATA
95640 TAACATATA
1 T-ACATATA
95649 AGTGAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
TACATATATA
Found at i:95630 original size:12 final size:12
Alignment explanation
Indices: 95613--95648 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
95603 AAATGTGTAC
95613 ATATATATACAT
1 ATATATATACAT
95625 ATATATATA-A-
1 ATATATATACAT
95635 ATATATA-ACAT
1 ATATATATACAT
95646 ATA
1 ATA
95649 AGTGAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.05
10 8 0.36
11 4 0.18
12 9 0.41
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATACAT
Done.