Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003218.1 Hibiscus syriacus cultivar Beakdansim tig00006779_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: 184085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17732 original size:15 final size:15
Alignment explanation
Indices: 17712--17741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17702 CTAAAAGTAC
*
17712 CTTTTCAAATTATTT
1 CTTTTCAAATAATTT
17727 CTTTTCAAATAATTT
1 CTTTTCAAATAATTT
17742 TAAGAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTTTCAAATAATTT
Found at i:20187 original size:17 final size:16
Alignment explanation
Indices: 20143--20187 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
20133 TCATGCAAAC
20143 AAAAATAATAATAATA
1 AAAAATAATAATAATA
**
20159 AATGATAAATAATAATA
1 AAAAAT-AATAATAATA
20176 AAAAATATATAA
1 AAAAATA-ATAA
20188 AAATGGGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAATAATAATAATA
Found at i:21494 original size:31 final size:31
Alignment explanation
Indices: 21436--21496 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
21426 GTTAACTTTC
* *
21436 GGGTCGGGTTAATATCATATTAGTTGGTTTT
1 GGGTCGGGTCAATATCAAATTAGTTGGTTTT
*
21467 GGGTTGGGTCAATATCAAATT-GATTGGTTT
1 GGGTCGGGTCAATATCAAATTAG-TTGGTTT
21497 CAGTTTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.43
Consensus pattern (31 bp):
GGGTCGGGTCAATATCAAATTAGTTGGTTTT
Found at i:23065 original size:17 final size:17
Alignment explanation
Indices: 23043--23084 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
23033 CTCACATTAT
23043 AGAACATCTAATATGAA
1 AGAACATCTAATATGAA
23060 AGAACATCTAATATGAA
1 AGAACATCTAATATGAA
*
23077 AAAACATC
1 AGAACATC
23085 ATGCCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (17 bp):
AGAACATCTAATATGAA
Found at i:25411 original size:24 final size:24
Alignment explanation
Indices: 25379--25485 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
25369 ACGAAGATAT
* *
25379 CAGAAATCAAAATAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
25403 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
**
25427 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
*** *
25451 CATTTATCAGAACAGAATTCA-AGT
1 CAGAAATCAGAACAGAATTCAGA-A
25475 CAGAAATCAGA
1 CAGAAATCAGA
25486 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:25448 original size:12 final size:12
Alignment explanation
Indices: 25392--25448 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
25382 AAATCAAAAT
25392 AGAATTCAGAAC
1 AGAATTCAGAAC
25404 AG-ATATCAGAAC
1 AGAAT-TCAGAAC
* *
25416 AGAATCCAGATC
1 AGAATTCAGAAC
*
25428 AGAAATCAGAAC
1 AGAATTCAGAAC
25440 AGAATTCAG
1 AGAATTCAG
25449 GTCATTTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.16
Consensus pattern (12 bp):
AGAATTCAGAAC
Found at i:25448 original size:48 final size:47
Alignment explanation
Indices: 25377--25485 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
25367 AAACGAAGAT
* *
25377 ATCAGAAATCAAAATAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
25424 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
25472 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
25486 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:28022 original size:13 final size:13
Alignment explanation
Indices: 28003--28048 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
27993 CAACGGTCAA
28003 CGGGTCAACAGGT
1 CGGGTCAACAGGT
* *
28016 TGGGTCAACGGGT
1 CGGGTCAACAGGT
28029 CGGGTCAACAGGT
1 CGGGTCAACAGGT
28042 CGGGTCA
1 CGGGTCA
28049 GGTCAACGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.17
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:28047 original size:18 final size:18
Alignment explanation
Indices: 28024--28064 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28014 GTTGGGTCAA
*
28024 CGGGTCGGGTCAACAGGT
1 CGGGTCAGGTCAACAGGT
*
28042 CGGGTCAGGTCAACGGGT
1 CGGGTCAGGTCAACAGGT
28060 CGGGT
1 CGGGT
28065 AAACGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (18 bp):
CGGGTCAGGTCAACAGGT
Found at i:28058 original size:13 final size:13
Alignment explanation
Indices: 28042--28077 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28032 GTCAACAGGT
*
28042 CGGGTCAGGTCAA
1 CGGGTCAGGTAAA
*
28055 CGGGTCGGGTAAA
1 CGGGTCAGGTAAA
28068 CGGGTCAGGT
1 CGGGTCAGGT
28078 TATGACCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.44, T:0.17
Consensus pattern (13 bp):
CGGGTCAGGTAAA
Found at i:28058 original size:26 final size:28
Alignment explanation
Indices: 27970--28060 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 28
27960 TCAAAGTTTT
27970 GGTCAACAGTGGTCAAC--GTC-GGTCAAC
1 GGTCAAC-G-GGTCAACAGGTCGGGTCAAC
*
27997 GGTCAACGGGTCAACAGGTTGGGTCAAC
1 GGTCAACGGGTCAACAGGTCGGGTCAAC
28025 GGGT---CGGGTCAACAGGTCGGGTC-A-
1 -GGTCAACGGGTCAACAGGTCGGGTCAAC
28049 GGTCAACGGGTC
1 GGTCAACGGGTC
28061 GGGTAAACGG
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
23 3 0.05
25 8 0.15
26 25 0.45
27 9 0.16
28 7 0.13
29 3 0.05
ACGTcount: A:0.22, C:0.23, G:0.37, T:0.18
Consensus pattern (28 bp):
GGTCAACGGGTCAACAGGTCGGGTCAAC
Found at i:30164 original size:12 final size:12
Alignment explanation
Indices: 30139--30207 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
30129 ACGAAGATAT
* *
30139 CAGAAATCAAAA
1 CAGAATTCAGAA
30151 CAGAATTCAGAA
1 CAGAATTCAGAA
30163 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
30175 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
30187 TAGAAATCAGAA
1 CAGAATTCAGAA
30199 CAGAATTCA
1 CAGAATTCA
30208 TGTCATTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:30166 original size:24 final size:24
Alignment explanation
Indices: 30139--30207 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
30129 ACGAAGATAT
*
30139 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
30163 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
*
30187 TAGAAATCAGAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
30208 TGTCATTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.16
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:30243 original size:24 final size:24
Alignment explanation
Indices: 30138--30245 Score: 67
Period size: 24 Copynumber: 4.5 Consensus size: 24
30128 AACGAAGATA
* *
30138 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAAAATTCAAG
* * * *
30161 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAAAATTCAAG
* * *
30185 ATTAGAAATCAGAACAGAATTCATG
1 -TCAGAAATCAGAACAAAATTCAAG
***
30210 TCATTTATCAGAACAAAATTCAAG
1 TCAGAAATCAGAACAAAATTCAAG
*
30234 TCGGAAATCAGA
1 TCAGAAATCAGA
30246 TAAAATATTT
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.92
25 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAAG
Found at i:32781 original size:13 final size:13
Alignment explanation
Indices: 32762--32793 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
32752 CAACAGTCAA
32762 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
32775 TGGGTCAACGGGT
1 CGGGTCAACGGGT
32788 CGGGTC
1 CGGGTC
32794 GGGTTATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:33739 original size:19 final size:19
Alignment explanation
Indices: 33704--33748 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
33694 TTCTATATAT
*
33704 TTTTTTATTTTTCCTTTTA
1 TTTTTTATTTCTCCTTTTA
33723 TTTTTTATTATCT-CTTTTA
1 TTTTTTATT-TCTCCTTTTA
33742 TGTTTTT
1 T-TTTTT
33749 CTAGGACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTCTCCTTTTA
Found at i:35799 original size:24 final size:22
Alignment explanation
Indices: 35779--35844 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 22
35769 AGTATTTTCA
*
35779 TTAAGAATTATCTCTTTA--TT
1 TTAAGAATTATATCTTTATTTT
35799 TTAAGAATTATATCTTTA--TT
1 TTAAGAATTATATCTTTATTTT
*
35819 TTAGGAATTATAT-TTTACTTATT
1 TTAAGAATTATATCTTTA-TT-TT
35842 TTA
1 TTA
35845 GGACTTTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.10
20 31 0.77
23 5 0.12
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
TTAAGAATTATATCTTTATTTT
Found at i:35804 original size:20 final size:20
Alignment explanation
Indices: 35779--35835 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
35769 AGTATTTTCA
*
35779 TTAAGAATTATCTCTTTATT
1 TTAAGAATTATATCTTTATT
35799 TTAAGAATTATATCTTTATT
1 TTAAGAATTATATCTTTATT
*
35819 TTAGGAATTATAT-TTTA
1 TTAAGAATTATATCTTTA
35836 CTTATTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (20 bp):
TTAAGAATTATATCTTTATT
Found at i:36486 original size:33 final size:32
Alignment explanation
Indices: 36449--36559 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 32
36439 ACTAAATAAG
*
36449 TTTGTTACAATTTGTTATTGTGA-AAGAATATTA
1 TTTGTTACAATTTGTTATTATGAGAA-AATA-TA
* * * *
36482 TTTGTCACAATTTTTTATAATGAGAAATTAATA
1 TTTGTTACAATTTGTTATTATGAGAAAAT-ATA
* * ** *
36515 TTTGTTATAATTTGTTATTTTGATTAAATAAA
1 TTTGTTACAATTTGTTATTATGAGAAAATATA
36547 TTTGTTACAATTT
1 TTTGTTACAATTT
36560 TACATTTTGA
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
32 14 0.23
33 44 0.72
34 3 0.05
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (32 bp):
TTTGTTACAATTTGTTATTATGAGAAAATATA
Found at i:36551 original size:98 final size:98
Alignment explanation
Indices: 36413--36873 Score: 264
Period size: 98 Copynumber: 4.7 Consensus size: 98
36403 TTCGTCACTA
* * * * *
36413 AATATTTTTTATAACTTTTTACTGTGACTAAATAAGTTTGTTACAATTTGTTATTGTGAAAGAAT
1 AATATTTGTTATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAAT
36478 ATTATTTGTCACAATTTTTTATAATGAGAAATT
66 ATTATTTGTCACAATTTTTTATAATGAGAAATT
* * * * *
36511 AATATTTGTTATAATTTGTTATTTTGATTAAATAAATTTGTTACAATTT-TACATTTTGATAA-A
1 AATATTTGTTATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGT-TATTGTGA-AAGA
* *
36574 ATATTGGGACGAAATAAATT-TGACATATTTTTTACT-ATGATAAAACTT
64 ATATT--------AT---TTGTCACA-ATTTTTTA-TAATGA-GAAA-TT
* * **
36622 AACGTGTTATTGTGAATAAATCATT-TTGT---T--AT-AATTTGTT---A----T---TGTGAA
1 AA--T-AT-TTGT-TATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAA
* * * *
36670 AGAATATTACTTGACATAATTTTTTAAAATGAGAAATT
61 AGAATATTATTTGTCACAATTTTTTATAATGAGAAATT
* * *
36708 AATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAAT
1 AATATTTGTTATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAAT
* * ** *
36773 ATTATTTTTCATAATTTTTTATTTTGAGGAATT
66 ATTATTTGTCACAATTTTTTATAATGAGAAATT
* * * * *
36806 AATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAA-AA
1 AATATTTGTTATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTGTGA-AAGAA
36870 TATT
65 TATT
36874 GTGACGAAAT
Statistics
Matches: 278, Mismatches: 42, Indels: 86
0.68 0.10 0.21
Matches are distributed among these distances:
81 9 0.03
82 7 0.03
83 1 0.00
84 1 0.00
85 1 0.00
86 4 0.01
87 5 0.02
88 22 0.08
89 2 0.01
91 2 0.01
95 1 0.00
97 1 0.00
98 151 0.54
99 14 0.05
103 1 0.00
106 3 0.01
108 4 0.01
109 22 0.08
110 6 0.02
111 4 0.01
112 1 0.00
113 1 0.00
114 1 0.00
115 7 0.03
116 7 0.03
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (98 bp):
AATATTTGTTATAAATTGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAAT
ATTATTTGTCACAATTTTTTATAATGAGAAATT
Found at i:36552 original size:32 final size:32
Alignment explanation
Indices: 36514--36576 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
36504 AGAAATTAAT
* * *
36514 ATTTGTTATAATTTGT-TATTTTGATTAAATAA
1 ATTTGTTACAATTT-TACATTTTGATAAAATAA
36546 ATTTGTTACAATTTTACATTTTGATAAAATA
1 ATTTGTTACAATTTTACATTTTGATAAAATA
36577 TTGGGACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (32 bp):
ATTTGTTACAATTTTACATTTTGATAAAATAA
Found at i:36748 original size:32 final size:31
Alignment explanation
Indices: 36711--36864 Score: 114
Period size: 32 Copynumber: 4.8 Consensus size: 31
36701 AGAAATTAAT
*
36711 ATTTGTTATAAATTATTATTTTGATTAAATAA
1 ATTTGTTATAAATTGTTATTTTGA-TAAATAA
* * * * *
36743 ATTTGTTACAATTTGTTATTGTGAAAGAATATT
1 ATTTGTTATAAATTGTTATTTTGATA-AATA-A
* * * *
36776 ATTT-TTCATAATTTTTTATTTTGAGGAATTAA
1 ATTTGTT-ATAAATTGTTATTTTGA-TAAATAA
*
36808 TATTTGTTATAAATTGTTATTATGACTAAATAA
1 -ATTTGTTATAAATTGTTATTTTGA-TAAATAA
*
36841 ATTTGTCA-AAAGTTGTTATTTTGA
1 ATTTGTTATAAA-TTGTTATTTTGA
36865 GAAAATATTG
Statistics
Matches: 95, Mismatches: 20, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
31 4 0.04
32 44 0.46
33 44 0.46
34 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (31 bp):
ATTTGTTATAAATTGTTATTTTGATAAATAA
Found at i:36871 original size:32 final size:31
Alignment explanation
Indices: 36699--36871 Score: 107
Period size: 33 Copynumber: 5.3 Consensus size: 31
36689 TTTTTTAAAA
* *
36699 TGAGAAATTAATATTTGTTATAAATTATTATTT
1 TGAGAAAATAA-ATTTGTTA-AAATTGTTATTT
** * *
36732 TGATTAAATAAATTTGTTACAATTTGTTATTG
1 TGAGAAAATAAATTTGTTA-AAATTGTTATTT
* * *
36764 TGA-AAGAATATTATTT-TTCATAATTTTTTATTT
1 TGAGAA-AATA-AATTTGTT-A-AAATTGTTATTT
* * *
36797 TGAGGAATTAATATTTGTTATAAATTGTTATTA
1 TGAGAAAATAA-ATTTGTTA-AAATTGTTATTT
** *
36830 TGACTAAATAAATTTGTCAAAAGTTGTTATTT
1 TGAGAAAATAAATTTGTTAAAA-TTGTTATTT
36862 TGAGAAAATA
1 TGAGAAAATA
36872 TTGTGACGAA
Statistics
Matches: 108, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
31 4 0.04
32 49 0.45
33 52 0.48
34 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.49
Consensus pattern (31 bp):
TGAGAAAATAAATTTGTTAAAATTGTTATTT
Found at i:37852 original size:23 final size:22
Alignment explanation
Indices: 37816--37867 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
37806 TAAAACAAAG
37816 ATTT-AGTTAATTAGTTTGTTA
1 ATTTAAGTTAATTAGTTTGTTA
*
37837 GTTTAAGTTATATTAGTTTGTTA
1 ATTTAAGTTA-ATTAGTTTGTTA
37860 ATTTAAGT
1 ATTTAAGT
37868 GATGTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 19 0.70
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (22 bp):
ATTTAAGTTAATTAGTTTGTTA
Found at i:37916 original size:34 final size:34
Alignment explanation
Indices: 37871--37978 Score: 171
Period size: 34 Copynumber: 3.1 Consensus size: 34
37861 TTTAAGTGAT
* *
37871 GTTATAAATAAAAAAATATTTAATTTGTTTGTTA
1 GTTATATATAAAAAAATATTTAATTAGTTTGTTA
*
37905 GTTATATATAAAAAAAATTATTTAATTAGTTTGTTG
1 GTTATATAT-AAAAAAA-TATTTAATTAGTTTGTTA
37941 GTTATATATAAAAAAATATTTAATTAGTTTGTTA
1 GTTATATATAAAAAAATATTTAATTAGTTTGTTA
37975 GTTA
1 GTTA
37979 AATAGTTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
34 29 0.43
35 14 0.21
36 25 0.37
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
GTTATATATAAAAAAATATTTAATTAGTTTGTTA
Found at i:40065 original size:23 final size:23
Alignment explanation
Indices: 40039--40088 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
40029 GAACATAGTG
*
40039 GTTGGAATATATTAACAACACTA
1 GTTGGAATATATTAACAACACCA
40062 GTTGGAATATATTAACAACACCA
1 GTTGGAATATATTAACAACACCA
40085 GTTG
1 GTTG
40089 AAATGCCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (23 bp):
GTTGGAATATATTAACAACACCA
Found at i:41093 original size:36 final size:36
Alignment explanation
Indices: 41024--41134 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
41014 TAAAACTATT
41024 TAACTAACAAACTAATTAAAT--A-TTTTTTATATA
1 TAACTAACAAACTAATTAAATAAATTTTTTTATATA
*
41057 TAACCAACAAACTAATTAAATAAATTTTTTTATATA
1 TAACTAACAAACTAATTAAATAAATTTTTTTATATA
* * * *
41093 TAACTAATAAATTAATTAAAATAATTTTTTTTTATTTA
1 TAACTAACAAACTAATT-AAATAA-ATTTTTTTATATA
41131 TAAC
1 TAAC
41135 ATCACTTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
33 20 0.30
35 1 0.01
36 25 0.37
37 6 0.09
38 15 0.22
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (36 bp):
TAACTAACAAACTAATTAAATAAATTTTTTTATATA
Found at i:41296 original size:21 final size:22
Alignment explanation
Indices: 41270--41310 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41260 CACCCGGGTT
41270 CTTCCTTTC-TTCTTCTTCTTC
1 CTTCCTTTCTTTCTTCTTCTTC
*
41291 CTTCCTTTCTTTCTTTTTCT
1 CTTCCTTTCTTTCTTCTTCT
41311 GCTCAATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
CTTCCTTTCTTTCTTCTTCTTC
Found at i:47088 original size:21 final size:21
Alignment explanation
Indices: 47062--47120 Score: 91
Period size: 21 Copynumber: 2.7 Consensus size: 21
47052 CAGGGAATTG
47062 GAGGAATTAGAAAATGAAATC
1 GAGGAATTAGAAAATGAAATC
47083 GAGGAATTAGAAAATGAAATC
1 GAGGAATTAGAAAATGAAATC
*
47104 AAGGAATTCGAGAAAAT
1 GAGGAATT--AGAAAAT
47121 ATTTTCAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 28 0.80
23 7 0.20
ACGTcount: A:0.53, C:0.05, G:0.24, T:0.19
Consensus pattern (21 bp):
GAGGAATTAGAAAATGAAATC
Found at i:47466 original size:11 final size:11
Alignment explanation
Indices: 47450--47475 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47440 AGGCAACTCA
47450 TTTTGTTTTAT
1 TTTTGTTTTAT
47461 TTTTGTTTTAT
1 TTTTGTTTTAT
47472 TTTT
1 TTTT
47476 AGCACACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTAT
Found at i:50078 original size:20 final size:20
Alignment explanation
Indices: 50053--50093 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
50043 GATAGTGACC
*
50053 TTAGGTGGGTCAACGGAGGA
1 TTAGGTGGGTCAACGAAGGA
50073 TTAGGTGGGTCAACGAAGGA
1 TTAGGTGGGTCAACGAAGGA
50093 T
1 T
50094 ATGTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.41, T:0.22
Consensus pattern (20 bp):
TTAGGTGGGTCAACGAAGGA
Found at i:53307 original size:16 final size:17
Alignment explanation
Indices: 53273--53312 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
53263 TTATATTAAC
*
53273 TGATATGTGTTTATATG
1 TGATATGTGATTATATG
*
53290 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
53306 TGATATG
1 TGATATG
53313 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:53974 original size:24 final size:24
Alignment explanation
Indices: 53903--53976 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
53893 TACGGTGCAT
*
53903 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGATAAA
53927 TTCTACGTGGTCCTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGATAAA
53951 TTCTACGTGG-CACTTCGGTG-TAAA
1 TTCTACGTGGTC-CTTCGG-GATAAA
53975 TT
1 TT
53977 TATACGAGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
23 1 0.02
24 45 0.96
25 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGATAAA
Found at i:54762 original size:22 final size:21
Alignment explanation
Indices: 54723--54763 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54713 AACAGTACTT
*
54723 TAGCAGGGTATCGATTCCCTG
1 TAGCAGGGAATCGATTCCCTG
*
54744 TAGCAGGGGAATCGGTTCCC
1 TAGCA-GGGAATCGATTCCC
54764 CTCTTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (21 bp):
TAGCAGGGAATCGATTCCCTG
Found at i:59729 original size:16 final size:17
Alignment explanation
Indices: 59695--59734 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
59685 TTATATAAAC
*
59695 TGATATGTGTTTATATG
1 TGATATGTGATTATATG
*
59712 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
59728 TGATATG
1 TGATATG
59735 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:60366 original size:24 final size:24
Alignment explanation
Indices: 60334--60399 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
60324 TACGGTGCAT
60334 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
60358 TTCTACGTGGTCTTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
60382 TTCTACGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
60400 TGTAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:66765 original size:24 final size:24
Alignment explanation
Indices: 66725--66774 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
66715 TACGGCGCAT
66725 TTCTACGCGGTCATTCGG-GACAAA
1 TTCTACGCGGTCATTCGGTG-CAAA
*
66749 TTCTACGTGG-CACTTCGGTGCAAA
1 TTCTACGCGGTCA-TTCGGTGCAAA
66773 TT
1 TT
66775 TATACGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 2 0.09
24 20 0.87
25 1 0.04
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCATTCGGTGCAAA
Found at i:72061 original size:75 final size:76
Alignment explanation
Indices: 71964--72172 Score: 377
Period size: 75 Copynumber: 2.8 Consensus size: 76
71954 TCTTAAATCC
*
71964 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
72028 TATCCTA-AACT
65 TATCCTACAACT
*
72039 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAGTAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
72104 ATCCTACAACT
66 ATCCTACAACT
72115 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
72173 TATTTAAAAT
Statistics
Matches: 130, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
74 5 0.04
75 63 0.48
76 62 0.48
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.26
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTACAACT
Found at i:72070 original size:24 final size:24
Alignment explanation
Indices: 72043--72157 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 24
72033 TAAACTTAAT
72043 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** ** *
72067 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
72092 TATAAA-AGTAATATCCTACAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
72119 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
72143 TAAAATACCTAAAAC
1 TAAAATA-CTAAAAC
72158 AAAGATAAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 19 0.29
25 24 0.36
26 10 0.15
27 8 0.12
28 2 0.03
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:72963 original size:21 final size:21
Alignment explanation
Indices: 72937--72976 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
72927 GAAAAGAAAG
*
72937 GTTTAAAATATTGAAACAAAA
1 GTTTAAAATATCGAAACAAAA
72958 GTTTAAAATATCGAAACAA
1 GTTTAAAATATCGAAACAA
72977 GAGATCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (21 bp):
GTTTAAAATATCGAAACAAAA
Found at i:72986 original size:21 final size:21
Alignment explanation
Indices: 72941--72988 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
72931 AGAAAGGTTT
* * *
72941 AAAATATTGAAACAAAAGTTT
1 AAAATATCGAAACAAAAGATC
*
72962 AAAATATCGAAACAAGAGATC
1 AAAATATCGAAACAAAAGATC
72983 AAAATA
1 AAAATA
72989 ATTAAGAACA
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:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAATATCGAAACAAAAGATC
Found at i:73334 original size:5 final size:5
Alignment explanation
Indices: 73324--73414 Score: 78
Period size: 5 Copynumber: 17.8 Consensus size: 5
73314 TATTCGGAGA
* * *
73324 AAAAT AAAAT AAAAT TAAAT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGTTT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT
** *
73376 GCTAA- AAAAT AAAAT GAAAT AAAAT AAAAT AAAAT AAAA
1 -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
73415 ATAGAACGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
4 6 0.09
5 56 0.82
6 4 0.06
7 1 0.01
8 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:77074 original size:40 final size:40
Alignment explanation
Indices: 76995--77074 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
76985 ATAGGAGCCA
* * *
76995 AATATTGCACCGAAGTGCTGAGGTCGAGTTTTTCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGTTTTACCCACCT
* *
77035 AATAATGCACCGTAGTGCTGAGGTCGGGTTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGTTTTACCCACCT
77075 TGTACACCGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGTTTTACCCACCT
Found at i:80847 original size:12 final size:11
Alignment explanation
Indices: 80830--80916 Score: 63
Period size: 11 Copynumber: 7.5 Consensus size: 11
80820 TTAAATCTCA
*
80830 TTTTTTTCTTT
1 TTTTTTTATTT
80841 TTCTTTTTA-TT
1 TT-TTTTTATTT
80852 TTTTTTTATTT
1 TTTTTTTATTT
*
80863 TTTTTTAATTT
1 TTTTTTTATTT
80874 TTTATTTT-TTT
1 TTT-TTTTATTT
80885 ATTCGTTTTT-TTAT
1 -TT--TTTTTATT-T
*
80899 TTTTTTCTGTTT
1 TTTTTT-TATTT
80911 TTTTTT
1 TTTTTT
80917 CATATATCAT
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
10 6 0.09
11 28 0.44
12 18 0.28
13 10 0.16
14 2 0.03
ACGTcount: A:0.08, C:0.05, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:80853 original size:11 final size:10
Alignment explanation
Indices: 80829--80916 Score: 78
Period size: 10 Copynumber: 9.0 Consensus size: 10
80819 TTTAAATCTC
80829 ATTTTTTTCTT
1 ATTTTTTT-TT
*
80840 -TTTCTTTTT
1 ATTTTTTTTT
80849 ATTTTTTTTT
1 ATTTTTTTTT
80859 ATTTTTTTTT
1 ATTTTTTTTT
*
80869 A--ATTTTTT
1 ATTTTTTTTT
80877 A--TTTTTTT
1 ATTTTTTTTT
80885 ATTCGTTTTTTT
1 ATT--TTTTTTT
*
80897 ATTTTTTTCT
1 ATTTTTTTTT
*
80907 GTTTTTTTTT
1 ATTTTTTTTT
80917 CATATATCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
8 14 0.22
9 2 0.03
10 39 0.60
12 10 0.15
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:80868 original size:47 final size:47
Alignment explanation
Indices: 80814--80968 Score: 134
Period size: 48 Copynumber: 3.2 Consensus size: 47
80804 TCACAAGTGA
*
80814 TTTTTTTTAAATCTCATTTTTTTCTTTTTCTTTTTATTTTTTTTTAT
1 TTTTTTTTAAATATCATTTTTTTCTTTTTCTTTTTATTTTTTTTTAT
* * * * * * *
80861 TTTTTTTTAATTTTTTATTTTTTTATTCGTT-TTTTTATTTTTTTCTGT
1 TTTTTTTTAA-ATATCATTTTTTTCTT-TTTCTTTTTATTTTTTTTTAT
* *
80909 TTTTTTTTCATATATCATTTTTTCCTCTTTTTCTTTTT-TTCTTCGTTTTAT
1 TTTTTTTT-AAATATCATTTTTT--TCTTTTTCTTTTTATT-TT-TTTTTAT
80960 TTTTATTTT
1 TTTT-TTTT
80969 TATTTTTTAG
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
47 10 0.12
48 44 0.53
49 7 0.08
50 10 0.12
51 8 0.10
52 4 0.05
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (47 bp):
TTTTTTTTAAATATCATTTTTTTCTTTTTCTTTTTATTTTTTTTTAT
Found at i:80931 original size:1 final size:1
Alignment explanation
Indices: 80830--80916 Score: 57
Period size: 1 Copynumber: 87.0 Consensus size: 1
80820 TTAAATCTCA
* * * * ** * * **
80830 TTTTTTTCTTTTTCTTTTTATTTTTTTTTATTTTTTTTTAATTTTTTATTTTTTTATTCGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
80895 TTATTTTTTTCTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTT
80917 CATATATCAT
Statistics
Matches: 63, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.08, C:0.05, G:0.02, T:0.85
Consensus pattern (1 bp):
T
Found at i:85146 original size:6 final size:6
Alignment explanation
Indices: 85135--85272 Score: 58
Period size: 6 Copynumber: 22.8 Consensus size: 6
85125 AAATCTCATT
*
85135 TTTTTC TTTTTC -TTTTC TTTTAT- TTTTATA TTTTTC TATTTT- TTTCTT-
1 TTTTTC TTTTTC TTTTTC TTTT-TC TTTT-TC TTTTTC T-TTTTC TTT-TTC
* * * * * **
85183 TGTTTTC TTTTTA TTTTATT TTTTTC ATCTCTC ATTTT- TTCCTC TTTTTC
1 T-TTTTC TTTTTC TTTT-TC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
*
85233 -TTTTC TTTTTC TATTTT- TTCTTT- GTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC T-TTTTC TT-TTTC TTTTTC TTTTTC TTTTT
85273 TAAGCTCTTA
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
5 18 0.18
6 59 0.58
7 25 0.25
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:85169 original size:19 final size:18
Alignment explanation
Indices: 85133--85208 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 18
85123 TTAAATCTCA
85133 TTTTTTTCTT-TTTCTTTTC
1 TTTTTTT-TTATTT-TTTTC
*
85152 TTTTATTTTTATATTTTTC
1 TTTT-TTTTTATTTTTTTC
* *
85171 TATTTTTTTCTTTGTTTTC
1 TTTTTTTTTATTT-TTTTC
85190 TTTTTATTTTATTTTTTTC
1 TTTTT-TTTTATTTTTTTC
85209 ATCTCTCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.15
19 28 0.60
20 12 0.26
ACGTcount: A:0.08, C:0.09, G:0.01, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTTC
Found at i:85193 original size:24 final size:24
Alignment explanation
Indices: 85166--85273 Score: 68
Period size: 24 Copynumber: 4.5 Consensus size: 24
85156 ATTTTTATAT
85166 TTTTCTATTTTTTTCTTTGTTTTC
1 TTTTCTATTTTTTTCTTTGTTTTC
*
85190 TTTT-TA---TTTTATTT-TTTTC
1 TTTTCTATTTTTTTCTTTGTTTTC
* * *
85209 ATCTCTCATTTTTTCCTCTTTTTCTTTTC
1 TTTTCT-ATTTTTT--TC--TTTGTTTTC
85238 TTTTTCTA-TTTTTTCTTTGTTTTC
1 -TTTTCTATTTTTTTCTTTGTTTTC
*
85262 TTTT-TCTTTTTT
1 TTTTCTATTTTTT
85274 AAGCTCTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 25
0.66 0.08 0.26
Matches are distributed among these distances:
19 7 0.11
20 8 0.12
21 1 0.02
22 1 0.02
23 11 0.17
24 15 0.23
26 3 0.05
28 8 0.12
29 6 0.09
30 4 0.06
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTCTATTTTTTTCTTTGTTTTC
Found at i:85221 original size:43 final size:41
Alignment explanation
Indices: 85119--85251 Score: 117
Period size: 44 Copynumber: 3.1 Consensus size: 41
85109 CAAGTGAATA
** *
85119 TTTTTTAAATCTCATTTTTT-TCTTTTTC-TTTTCTTTTAT
1 TTTTTTATCTCTCATTTTTTCTCTTTTTCTTTTTATTTTAT
* * * *
85158 TTTTATATTTTTCTATTTTTTTCTTTGTTTTCTTTTTATTTTAT
1 TTTTTTATCTCTC-A-TTTTTTCTCT-TTTTCTTTTTATTTTAT
*
85202 TTTTTTCATCTCTCATTTTTTCCTCTTTTTCTTTTCTTTTTCTAT
1 TTTTTT-ATCTCTCATTTTTT-CTCTTTTTCTTTT-TATTT-TAT
85247 TTTTT
1 TTTTT
85252 CTTTGTTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
39 9 0.12
40 1 0.01
41 6 0.08
42 2 0.03
43 20 0.27
44 23 0.31
45 13 0.18
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.76
Consensus pattern (41 bp):
TTTTTTATCTCTCATTTTTTCTCTTTTTCTTTTTATTTTAT
Found at i:85248 original size:29 final size:30
Alignment explanation
Indices: 85216--85272 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
85206 TTCATCTCTC
85216 ATTTTTTCCTCT-TTTTC-TTTTCTTTTTCT
1 ATTTTTT-CTCTGTTTTCTTTTTCTTTTTCT
*
85245 ATTTTTTCTTTGTTTTCTTTTTCTTTTT
1 ATTTTTTCTCTGTTTTCTTTTTCTTTTT
85273 TAAGCTCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 12 0.48
30 10 0.40
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (30 bp):
ATTTTTTCTCTGTTTTCTTTTTCTTTTTCT
Found at i:85251 original size:15 final size:14
Alignment explanation
Indices: 85133--85273 Score: 56
Period size: 15 Copynumber: 9.4 Consensus size: 14
85123 TTAAATCTCA
85133 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
* *
85147 TTTTCTTTTATTTTTATA
1 -TTT-TTTT-CTTTT-TC
*
85165 TTTTTCTATTTTTTTC
1 TTTTT-T-TCTTTTTC
*
85181 TTTGTTTTCTTTTTA
1 TTT-TTTTCTTTTTC
85196 TTTTATTT-TTTTCATC
1 TTTT-TTTCTTTT--TC
* ** *
85212 TCTCATT-TTTTCC
1 TTTTTTTCTTTTTC
*
85225 TCTTTTTC-TTTTC
1 TTTTTTTCTTTTTC
85238 TTTTTCTAT-TTTTTC
1 TTTTT-T-TCTTTTTC
85253 TTTGTTTTCTTTTTC
1 TTT-TTTTCTTTTTC
85268 TTTTTT
1 TTTTTT
85274 AAGCTCTTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
13 14 0.14
14 10 0.10
15 40 0.41
16 16 0.16
17 15 0.15
18 2 0.02
ACGTcount: A:0.06, C:0.13, G:0.01, T:0.79
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:85252 original size:44 final size:41
Alignment explanation
Indices: 85128--85252 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 41
85118 ATTTTTTAAA
*
85128 TCTCATTTTTT-TCTTTTTCTTTTC-TTTTATTTTTAT-ATT
1 TCTCATTTTTTCTCTTTTTCTTTTCTTTTTATTTTT-TCATC
* *
85167 TTTCTATTTTTTTCTTTGTTTTCTTTT-TATTTTATTTTTTTCATC
1 TCTC-A-TTTTTTCTCT-TTTTCTTTTCT-TTTTA-TTTTTTCATC
85212 TCTCATTTTTTCCTCTTTTTCTTTTCTTTTTCTATTTTTTC
1 TCTCATTTTTT-CTCTTTTTCTTTTC-TTTT-TATTTTTTC
85253 TTTGTTTTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
39 3 0.04
40 1 0.01
41 6 0.09
42 2 0.03
43 24 0.35
44 20 0.29
45 13 0.19
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (41 bp):
TCTCATTTTTTCTCTTTTTCTTTTCTTTTTATTTTTTCATC
Found at i:88267 original size:40 final size:40
Alignment explanation
Indices: 88188--88267 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
88178 ATAGGAGTCA
* * *
88188 AATATTGCACCGAAGTGCTGAGGTTGAGCTTTTCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTTCCCACCT
*
88228 AATAATGCACC-ATAGTGCTGAGGTCG-GGTTTTACCCACCT
1 AATAATGCACCGA-AGTGCTGAGGTCGAGCTTTT-CCCACCT
88268 TGTACACCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCTTTTCCCACCT
Found at i:90490 original size:20 final size:19
Alignment explanation
Indices: 90465--90514 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
90455 TTAAAAGATT
*
90465 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGA-AA
*
90485 TAAT-AAATATAAAGGGAAA
1 TAATAAAATA-AAAGAGAAA
90504 TAATAAAATAA
1 TAATAAAATAA
90515 TAAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
TAATAAAATAAAAGAGAAA
Found at i:91992 original size:85 final size:85
Alignment explanation
Indices: 91892--92047 Score: 303
Period size: 85 Copynumber: 1.8 Consensus size: 85
91882 ATCCAAATTA
*
91892 AACAATTAATGATATCAAGATTCAAAACATTTTTGTTGTATAATATATAAAGTGTTAGAAATTAA
1 AACAATTAATGATATCAAGATTCAAAACATTTTTGTTGTATAATATATAAAATGTTAGAAATTAA
91957 AAACTTCTTATAAATAAGTT
66 AAACTTCTTATAAATAAGTT
91977 AACAATTAATGATATCAAGATTCAAAACATTTTTGTTGTATAATATATAAAATGTTAGAAATTAA
1 AACAATTAATGATATCAAGATTCAAAACATTTTTGTTGTATAATATATAAAATGTTAGAAATTAA
92042 AAACTT
66 AAACTT
92048 ATAAATTTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (85 bp):
AACAATTAATGATATCAAGATTCAAAACATTTTTGTTGTATAATATATAAAATGTTAGAAATTAA
AAACTTCTTATAAATAAGTT
Found at i:94699 original size:73 final size:74
Alignment explanation
Indices: 94572--95437 Score: 436
Period size: 74 Copynumber: 11.5 Consensus size: 74
94562 ATTTAATACC
* * * * *
94572 AAGATTTATCTC-CTTGAGATTATTTTTCTTAAAACAATATTTTATATCGCTTGAGATAGTTTCA
1 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTCA
94636 CTCGAAATAG
66 CTCGAAA-AG
** *
94646 AAGATTTAGGTCACTTGAGATTGTTTTT-TTAAAACAAGA-TTCATCTGGCTTGAGATAGTTTCA
1 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTCA
*
94709 CTCGAAACAT
66 CTCGAAA-AG
* ** * *
94719 AA-ATTTTATCTCACTTGAGATTGTTTTTCCTAAAACAA-ACTTTGTCTCGCTTGAGACGATTTT
1 AAGA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGA-TAGTTT
*
94782 TACTCGAAGCAAG
64 CACTCGAA--AAG
* * ** * * * *
94795 -ACATTTCATTTCACTCCATATTGTTTTTCTTAAAATAAGA-TTCATCTCGCCTGAGATAGTTTT
1 AAGATTT-ATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTC
*
94858 AATCGAAAGAG
65 ACTCGAAA-AG
* ** * * * * * * *
94869 AAGATTTTATATTGCTTGAGATAGTTTCATTC-GAAACAGAAGA-TTTAGCTCACTTGAGATTGT
1 AAGA-TTTATCTCACTTGAGATTGTTT--TTCTTAAA-ACAAGACTTCATCTCGCTTGAGATAGT
** * * *
94932 TTTTCT-TAAGAC
62 TTCACTCGAAAAG
* * * * * * * *
94944 AAGATTCATCTCGCTTGAGATAG--TTTCAATAGAAACATAATATTTTATCTCGCTTGAGATAAT
1 AAGATTTATCTCACTTGAGATTGTTTTTC-TTA-AAAC--AAGACTTCATCTCGCTTGAGATAGT
* *
95007 TTCACTAGAAACAT
62 TTCACTCGAAA-AG
* * * * * * ** * *
95021 AATATTTTATATCGCTTAATATAGTTTGACTCAAAACAAAAGA-TTCTATCTTGCTTGAGATAGT
1 AAGA-TTTATCTCACTTGAGATTGTTTTTCTTAAAAC--AAGACTTC-ATCTCGCTTGAGATAGT
* *
95085 TTCATTCAAAACAG
62 TTCACTCGAAA-AG
* * * * * * * *
95099 AAGATTTATCTCACTTGATATTGTTTTTCTTTAAACCATA-TTTATCTCACTCGAGATAGTTTCC
1 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTCA
95163 CTCGAAATAG
66 CTCGAAA-AG
* * ** * * * * *
95173 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCACGCTTGAGATAGTT
1 AAGA-TTTATCTCACTTGAGATTGTTTTTCT-TAAA-ACAAGACTTCATCTCGCTTGAGATAGTT
* * *
95238 CCACTTGAAACAA
63 TCACTCGAAA-AG
* * * * * *
95251 AAGATTTTATCTCACTTGAGATAGTTTCGTTC-GAAATAGAAGA-TTTATCTCACTTGAGATTGT
1 AAGA-TTTATCTCACTTGAGATTGTTT--TTCTTAAA-ACAAGACTTCATCTCGCTTGAGATAGT
* * *
95314 TTTACT-TAAAAC
62 TTCACTCGAAAAG
* * *
95326 AAGATTTATCTCACTTGAGATTGTTTTACTTAAAACAAGA-TTTATCTCTCTTGAGATAGTTTCA
1 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTCA
* *
95390 CTCAAAACAT
66 CTCGAAA-AG
* **
95400 AATAAATATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
95438 AATATGTCTC
Statistics
Matches: 611, Mismatches: 144, Indels: 74
0.74 0.17 0.09
Matches are distributed among these distances:
70 3 0.00
72 34 0.06
73 63 0.10
74 146 0.24
75 109 0.18
76 55 0.09
77 83 0.14
78 114 0.19
79 1 0.00
80 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (74 bp):
AAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGACTTCATCTCGCTTGAGATAGTTTCA
CTCGAAAAG
Found at i:94843 original size:76 final size:74
Alignment explanation
Indices: 94588--94865 Score: 213
Period size: 73 Copynumber: 3.7 Consensus size: 74
94578 TATCTCCTTG
* * * * * * *
94588 AGATTATTTTTCTTAAAACAATATTTTATATCGCTTGAGATAGTTTCACTCGAAATAGAAGATTT
1 AGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGAGAGTTTCACTCGAAACATAA-ATTT
** **
94653 -AGGTCACTTG
64 CATCTCACTCC
* * *
94663 AGATTGTTTTT-TTAAAACAAGATTCATCTGGCTTGAGATAGTTTCACTCGAAACATAAATTTTA
1 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGAGAGTTTCACTCGAAACATAAATTTCA
**
94727 TCTCACTTG
66 TCTCACTCC
* ** * * *
94736 AGATTGTTTTTCCTAAAACAA-ACTTTGTCTCGCTTGAGACGATTTTTACTCGAAGCA-AGACAT
1 AGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGA-GAGTTTCACTCGAAACATA-A-AT
*
94799 TTCATTTCACTCC
62 TTCATCTCACTCC
* * * * * *
94812 ATATTGTTTTTCTTAAAATAAGATTCATCTCGCCTGAGATAGTTTTAATCGAAA
1 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGAGAGTTTCACTCGAAA
94866 GAGAAGATTT
Statistics
Matches: 165, Mismatches: 31, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
72 4 0.02
73 51 0.31
74 32 0.19
75 35 0.21
76 42 0.25
77 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (74 bp):
AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGAGAGTTTCACTCGAAACATAAATTTCA
TCTCACTCC
Found at i:94889 original size:39 final size:39
Alignment explanation
Indices: 94838--95398 Score: 342
Period size: 39 Copynumber: 14.8 Consensus size: 39
94828 AATAAGATTC
* * *
94838 ATCTCGCCTGAGATAGTTTTAATCGAAAGAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * *
94877 ATATTGCTTGAGATAGTTTCATTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * ** * * *
94915 AGCTCACTTGAGATTGTTT--TTCTTAAGACAAGA-TTC
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * *
94951 ATCTCGCTTGAGATAGTTTCAATAGAAACATAATATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * *
94990 ATCTCGCTTGAGATAATTTCACTAGAAACATAATATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * * * * *
95029 ATATCGCTTAATATAGTTTGACTCAAAACAAAAGATTCT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * *
95068 ATCTTGCTTGAGATAGTTTCATTCAAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * *** ** * *
95106 ATCTCACTTGATATTGTTTTTCTTTAAAC--CATA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * ** *
95142 ATCTCACTCGAGATAGTTTCCCTCGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* *
95181 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * *
95220 ATCACGCTTGAGATAGTTCCACTTGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* ** *
95259 ATCTCACTTGAGATAGTTTCGTTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * * *
95297 ATCTCACTTGAGATTGTTTTACT-TAAA-ACAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * * * * *
95333 ATCTCACTTGAGATTGTTTTACT-TAAA-ACAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
* * *
95369 ATCTCTCTTGAGATAGTTTCACTCAAAACA
1 ATCTCGCTTGAGATAGTTTCAATCGAAACA
95399 TAATAAATAT
Statistics
Matches: 420, Mismatches: 94, Indels: 17
0.79 0.18 0.03
Matches are distributed among these distances:
36 118 0.28
37 6 0.01
38 71 0.17
39 225 0.54
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCAATCGAAACAGAAGATTTT
Found at i:94937 original size:113 final size:113
Alignment explanation
Indices: 94814--95277 Score: 299
Period size: 113 Copynumber: 4.1 Consensus size: 113
94804 TTCACTCCAT
* * * *
94814 ATTGTTTTTCTTAAAATAAGATTCATCTCGCCTGAGATAGTTTTAATCGAAAGAGAAGATTTTAT
1 ATTGTTTTTCTTAAAACAAGATTCATCTCGCCTGAGATAGTTTCAATAGAAACAGAAGATTTTAT
* * * *
94879 ATTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTAGCTCACTTGAG
66 ATCGCTTGAGATAATTTCACTAGAAACAGAAGATTTAGCTCACTTGAG
* * * *
94927 ATTGTTTTTCTTAAGACAAGATTCATCTCGCTTGAGATAGTTTCAATAGAAACATAATATTTTAT
1 ATTGTTTTTCTTAAAACAAGATTCATCTCGCCTGAGATAGTTTCAATAGAAACAGAAGATTTTAT
* * * ** * * *
94992 CTCGCTTGAGATAATTTCACTAGAAACATAATATTTTATATCGCTTAAT
66 ATCGCTTGAGATAATTTCACTAGAAACAGAAGA-TTTAGCTCACTTGAG
* ** * * * *
95041 ATAGTTTGACTCAAAACAAAAGATTCTATCTTGCTTGAGATAGTTTCATTCA-AAACAGAAGA-T
1 ATTGTTTTTCTTAAAAC--AAGATTC-ATCTCGCCTGAGATAGTTTCAAT-AGAAACAGAAGATT
* * * ** ** ** * * * *
95104 TTATCTCACTTGATATTGTTTTTCTTTAAAC--CATATTTATCTCACTCGAG
62 TTATATCGCTTGAGATAATTTCACTAGAAACAGAAGATTTAGCTCACTTGAG
* ** * * * * * * *
95154 ATAGTTTCCCTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTT
1 ATTGTTTTTCT-TAAA-ACAAGA-TTCATCTCGCCTGAGATAGTTTCAATAGAAACAGAAGATTT
* * * * *
95219 TATCA-CGCTTGAGATAGTTCCACTTGAAACAAAAGATTTTATCTCACTTGAG
63 TAT-ATCGCTTGAGATAATTTCACTAGAAACAGAAGA-TTTAGCTCACTTGAG
*
95271 ATAGTTT
1 ATTGTTT
95278 CGTTCGAAAT
Statistics
Matches: 274, Mismatches: 63, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
113 136 0.50
114 53 0.19
115 1 0.00
116 33 0.12
117 50 0.18
118 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (113 bp):
ATTGTTTTTCTTAAAACAAGATTCATCTCGCCTGAGATAGTTTCAATAGAAACAGAAGATTTTAT
ATCGCTTGAGATAATTTCACTAGAAACAGAAGATTTAGCTCACTTGAG
Found at i:95099 original size:191 final size:189
Alignment explanation
Indices: 94869--95403 Score: 648
Period size: 191 Copynumber: 2.8 Consensus size: 189
94859 ATCGAAAGAG
* *
94869 AAGATTTTATATTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTAGCTCACTTGAGATTGTTT
1 AAGATTTTATCTTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTATCTCACTTGAGATTGTTT
* * *
94934 TTCTTAAGACAAGATTCATCTCGCTTGAGATAGTTTCAATAGAAACATAATATTTTATCTCGCTT
66 TTCTTAA-ACAAGATTTATCTCACTTGAGATAGTTTCAATAGAAACA-AAGATTTTATCTCGCTT
* * **
94999 GAGATAATTTCACTAGAAACATAATATTTTAT-ATCGCTTAATATAGTTTGACTCAAAACAA
129 GAGATAGTTTCACTAGAAACATAATATTTTATCA-CGCTTAAGATAGTTCCACTCAAAACAA
* * *
95060 AAGATTCTATCTTGCTTGAGATAGTTTCATTCAAAACAGAAGATTTATCTCACTTGATATTGTTT
1 AAGATTTTATCTTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTATCTCACTTGAGATTGTTT
* * * ** * *
95125 TTCTTTAAACCATATTTATCTCACTCGAGATAGTTTCCCTCGAAATAGAAGATTTTATCTCGCTT
66 TTC-TTAAACAAGATTTATCTCACTTGAGATAGTTTCAATAGAAACA-AAGATTTTATCTCGCTT
* * * * * **
95190 GAGATAGTTTCACTCGAAATAGAAGATTTTATCACGCTTGAGATAGTTCCACTTGAAACAA
129 GAGATAGTTTCACTAGAAACATAATATTTTATCACGCTTAAGATAGTTCCACTCAAAACAA
** * *
95251 AAGATTTTATCTCACTTGAGATAGTTTCGTTCGAAATAGAAGATTTATCTCACTTGAGATTGTTT
1 AAGATTTTATCTTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTATCTCACTTGAGATTGTTT
* * * * *
95316 TACTTAAAACAAGATTTATCTCACTTGAGATTGTTTTACTTA-AAAC-AAGA-TTTATCTCTCTT
66 TTCTT-AAACAAGATTTATCTCACTTGAGATAGTTTCA-ATAGAAACAAAGATTTTATCTCGCTT
95378 GAGATAGTTTCACTCA-AAACATAATA
129 GAGATAGTTTCACT-AGAAACATAATA
95404 AATATCTCAC
Statistics
Matches: 290, Mismatches: 49, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
188 32 0.11
189 4 0.01
190 2 0.01
191 246 0.85
192 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (189 bp):
AAGATTTTATCTTGCTTGAGATAGTTTCATTCGAAACAGAAGATTTATCTCACTTGAGATTGTTT
TTCTTAAACAAGATTTATCTCACTTGAGATAGTTTCAATAGAAACAAAGATTTTATCTCGCTTGA
GATAGTTTCACTAGAAACATAATATTTTATCACGCTTAAGATAGTTCCACTCAAAACAA
Found at i:95143 original size:152 final size:153
Alignment explanation
Indices: 94987--95269 Score: 354
Period size: 152 Copynumber: 1.9 Consensus size: 153
94977 AACATAATAT
* * * * * *
94987 TTTATCTCGCTTGAGATAATTTCACTAGAAACATAATATTTTATATCGCTTAATATAGTTTGACT
1 TTTATCTCACTCGAGATAATTTCACTAGAAACAGAAGATTTTATATCGCTTAAGATAGTTTCACT
** * *
95052 CAAAACAAAAGATTCTATCTTGCTTGAGATAGTTTCA-TTCAAAACAGAAGA-TTTATCTCACTT
66 CAAAACAAAAGATTCTATCACGCTTGAGATAGTTCCACTT-AAAACAAAAGATTTTATCTCACTT
95115 GATATTGTTTTTCTTTAAACCATA
130 GATATTGTTTTTCTTTAAACCATA
* * * * * *
95139 TTTATCTCACTCGAGATAGTTTCCCTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
1 TTTATCTCACTCGAGATAATTTCACTAGAAACAGAAGATTTTATATCGCTTAAGATAGTTTCACT
* * * * *
95204 CGAAATAGAAGATTTTATCACGCTTGAGATAGTTCCACTTGAAACAAAAGATTTTATCTCACTTG
66 CAAAACAAAAGATTCTATCACGCTTGAGATAGTTCCACTTAAAACAAAAGATTTTATCTCACTTG
95269 A
131 A
95270 GATAGTTTCG
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
152 92 0.85
153 16 0.15
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (153 bp):
TTTATCTCACTCGAGATAATTTCACTAGAAACAGAAGATTTTATATCGCTTAAGATAGTTTCACT
CAAAACAAAAGATTCTATCACGCTTGAGATAGTTCCACTTAAAACAAAAGATTTTATCTCACTTG
ATATTGTTTTTCTTTAAACCATA
Found at i:95581 original size:59 final size:59
Alignment explanation
Indices: 95445--95585 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
95435 CAAAATATGT
* *
95445 CTCACTTGAGGGATTAACATTT--TTTTGCTCGATCCACAACAATTCGAATCATCAATGC
1 CTCACTTGAGGG-TTAACATTTCCTTTTGCTCGATCCACAACAATTCGAATCAACAACGC
* * * ** *
95503 CTTACTTAAGGGATAAACATTTCCTTTT-CTCGATTTACAACACTTCGAATCAACAACGC
1 CTCACTTGAGGG-TTAACATTTCCTTTTGCTCGATCCACAACAATTCGAATCAACAACGC
*
95562 CTCACTCGAGGGTTCAACATTTCC
1 CTCACTTGAGGGTT-AACATTTCC
95586 ACTGGAAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
58 20 0.29
59 44 0.65
60 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (59 bp):
CTCACTTGAGGGTTAACATTTCCTTTTGCTCGATCCACAACAATTCGAATCAACAACGC
Found at i:96443 original size:22 final size:22
Alignment explanation
Indices: 96412--96464 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
96402 AGTGTAGATC
*
96412 AGAGTTACCTTGGGTCGTCGGA
1 AGAGTCACCTTGGGTCGTCGGA
*
96434 GGAGTCACCTTGGGTCGTCGGA
1 AGAGTCACCTTGGGTCGTCGGA
96456 AGAGTCACC
1 AGAGTCACC
96465 AGAGCCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.23
Consensus pattern (22 bp):
AGAGTCACCTTGGGTCGTCGGA
Found at i:97203 original size:25 final size:22
Alignment explanation
Indices: 97171--97225 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
97161 TTATGTTTAC
*
97171 TTTATTTTTATTTTATGTTGTTTT
1 TTTATTTTTA--TTATGTTGTTAT
97195 TTTACTTTTTATTAT-TTGTTAT
1 TTTA-TTTTTATTATGTTGTTAT
97217 TTTATTTTT
1 TTTATTTTT
97226 TAAATTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 10 0.34
23 4 0.14
24 4 0.14
25 6 0.21
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATTATGTTGTTAT
Found at i:97219 original size:22 final size:23
Alignment explanation
Indices: 97183--97236 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
97173 TATTTTTATT
*
97183 TTATGTTGTTTTTTTACTTTTTA
1 TTATGTTGTTATTTTACTTTTTA
*
97206 TTAT-TTGTTATTTTATTTTTTAAA
1 TTATGTTGTTATTTTACTTTTT--A
97230 TTATGTT
1 TTATGTT
97237 TATTAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 15 0.58
23 4 0.15
24 5 0.19
25 2 0.08
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (23 bp):
TTATGTTGTTATTTTACTTTTTA
Found at i:100269 original size:72 final size:74
Alignment explanation
Indices: 100112--100765 Score: 269
Period size: 75 Copynumber: 8.7 Consensus size: 74
100102 TAATACGAAG
* * * * *
100112 ATTTATCTTACTTGAGATTGTTTTTCTTAAAATAAGATTTTATCTTGCTTGAGATAGTTTCACTG
1 ATTTATCTCACTTGAGATTG-TTTTCTTAAAACAAGATTTCATCTCGCTTGAGATAGTTTCACTC
* *
100177 GAAACATAAG
65 AAAACATAAA
* * *
100187 ATTTAGCTCACTTGAGATTGTTTT-TTAAAACAAGA-TTCATCTCGTTTTAGATAGTTTCACTCA
1 ATTTATCTCACTTGAGATTGTTTTCTTAAAACAAGATTTCATCTCGCTTGAGATAGTTTCACTCA
100250 AAACA-AAA
66 AAACATAAA
* * ** * * **
100258 ATTTTATCTCACTTGAGATTTTTTTTCTTAAAACAA-ACTT-ATTCTTTCCTGAGACAGTTTTTG
1 A-TTTATCTCACTTGAGA-TTGTTTTCTTAAAACAAGATTTCA-TCTCGCTTGAGATAG-TTTCA
*
100321 CT-AGAAGCA-AAA
62 CTCA-AAACATAAA
* ** * * *
100333 CATTTCATTTCACTCCAGATTTGTTTTCTTAAAACAAGA-TTCGTCTTGCCTGAGATAGTTTCAC
1 -ATTT-ATCTCACTTGAGA-TTGTTTTCTTAAAACAAGATTTCATCTCGCTTGAGATAGTTTCAC
* * *
100397 TCGAAAGAGAATA
63 TCAAAACATAA-A
* ** * ** * * * * ** * **
100410 TTTTATCTTGCTTGATATAATTTCACTCGAAACAAAAGATTT-AGCTCAATTGAGATTGTTTTTC
1 ATTTATCTCACTTGAGATTGTTT-TCT-TAAA-ACAAGATTTCATCTCGCTTGAGATAGTTTCAC
* *
100474 TTAAAAC--AAG
63 TCAAAACATAAA
* * * * * *
100484 ATTCATCTCGCTTGAGATAG-TTTCACTAGAAACAAAATATTTTATCTCGCTTGAGATAGTTTCA
1 ATTTATCTCACTTGAGATTGTTTTC-TTA-AAAC--AAGATTTCATCTCGCTTGAGATAGTTTCA
* *
100548 CTCGAAATA-AAA
62 CTCAAAACATAAA
* * * *
100560 AGTTTATCTTAGTTGAGATTGTTTTTCTTAAAACCAGATTT-ATCTCGCTTAAGATTA-TTTCAC
1 A-TTTATCTCACTTGAGATTG-TTTTCTTAAAACAAGATTTCATCTCGCTTGAGA-TAGTTTCAC
* *
100623 TCGAAACAAAAA
63 TCAAAACATAAA
* * * * * * * *
100635 ATTTTATTTCGCTTGAGATAGTTTCACTTGAAACATAAGATTTTATCTTGCTTGAGATAGTTCCA
1 A-TTTATCTCACTTGAGATTGTTT-TCTT-AAA-ACAAGATTTCATCTCGCTTGAGATAGTTTCA
* *
100700 CTCGAAACAGAAGA
62 CTCAAAACATAA-A
* ** * * *
100714 TTTTATCTTGCTTGAGATAGTTTCTCTTGAAACAAAAGATTT-ATCTCACTTG
1 ATTTATCTCACTTGAGATTGTTT-TCTT-AAA-ACAAGATTTCATCTCGCTTG
100766 CTATTATTTT
Statistics
Matches: 436, Mismatches: 108, Indels: 68
0.71 0.18 0.11
Matches are distributed among these distances:
71 3 0.01
72 45 0.10
73 22 0.05
74 78 0.18
75 100 0.23
76 57 0.13
77 59 0.14
78 67 0.15
79 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (74 bp):
ATTTATCTCACTTGAGATTGTTTTCTTAAAACAAGATTTCATCTCGCTTGAGATAGTTTCACTCA
AAACATAAA
Found at i:100478 original size:113 final size:113
Alignment explanation
Indices: 100356--100677 Score: 425
Period size: 113 Copynumber: 2.8 Consensus size: 113
100346 TCCAGATTTG
* * * * *
100356 TTTTCTTAAAACAAGATTCGTCTTGCCTGAGATAGTTTCACTCGAAAGAGAATATTTTATCTTGC
1 TTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAATATTTTATCTTGC
* *
100421 TTGATATAATTTCACTCGAAACAAAAGATTTAGCTCAATTGAGATTGT
66 TTGAGATAGTTTCACTCGAAACAAAAGATTTAGCTCAATTGAGATTGT
* *
100469 TTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTAGAAACAAAATATTTTATCTCGC
1 TTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAATATTTTATCTTGC
* * * *
100534 TTGAGATAGTTTCACTCGAAATAAAA-AGTTTATCTTAGTTGAGATTGT
66 TTGAGATAGTTTCACTCGAAACAAAAGA-TTTAGCTCAATTGAGATTGT
* * * *
100582 TTTTCTTAAAACCAGATTTATCTCGCTTAAGATTA-TTTCACTCGAAACAAAAAATTTTAT-TTC
1 TTTTCTTAAAACAAGATTCATCTCGCTTGAGA-TAGTTTCACTCGAAACAAAATATTTTATCTT-
* *
100645 GCTTGAGATAGTTTCACTTGAAACATAAGATTT
64 GCTTGAGATAGTTTCACTCGAAACAAAAGATTT
100678 TATCTTGCTT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
112 2 0.01
113 178 0.97
114 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (113 bp):
TTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAATATTTTATCTTGC
TTGAGATAGTTTCACTCGAAACAAAAGATTTAGCTCAATTGAGATTGT
Found at i:100537 original size:39 final size:38
Alignment explanation
Indices: 100383--100833 Score: 339
Period size: 39 Copynumber: 11.9 Consensus size: 38
100373 TCGTCTTGCC
* * * *
100383 TGAGATAGTTTCACTCGAAAGAGAATATTTTATCTTGCT
1 TGAGATAGTTTCACTCGAAACAAAAGA-TTTATCTCGCT
* * * **
100422 TGATATAATTTCACTCGAAACAAAAGATTTAGCTCAAT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCGCT
* ** * * *
100460 TGAGATTGTTTTTCT-TAAA-ACAAGATTCATCTCGCT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCGCT
* *
100496 TGAGATAGTTTCACTAGAAACAAAATATTTTATCTCGCT
1 TGAGATAGTTTCACTCGAAACAAAAGA-TTTATCTCGCT
* *
100535 TGAGATAGTTTCACTCGAAATAAAA-AGTTTATCTTAG-T
1 TGAGATAGTTTCACTCGAAACAAAAGA-TTTATC-TCGCT
* ** * **
100573 TGAGATTGTTTTTCT-TAAA-ACCAGATTTATCTCGCT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCGCT
* * *
100609 TAAGATTA-TTTCACTCGAAACAAAAAATTTTATTTCGCT
1 TGAGA-TAGTTTCACTCGAAACAAAAGA-TTTATCTCGCT
* * *
100648 TGAGATAGTTTCACTTGAAACATAAGATTTTATCTTGCT
1 TGAGATAGTTTCACTCGAAACAAAAGA-TTTATCTCGCT
* * *
100687 TGAGATAGTTCCACTCGAAACAGAAGATTTTATCTTGCT
1 TGAGATAGTTTCACTCGAAACAAAAGA-TTTATCTCGCT
* * *
100726 TGAGATAGTTTCTCTTGAAACAAAAGATTTATCTCACT
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCGCT
** ** *
100764 TGCTATTA-TTTTTCT-TAAAC--AAGATTTATCTCGCT
1 TGAGA-TAGTTTCACTCGAAACAAAAGATTTATCTCGCT
* * *
100799 TCAGATAGTTTCACTCGAAACAGAATATTTATCTC
1 TGAGATAGTTTCACTCGAAACAAAAGATTTATCTC
100834 ATCTGAGATT
Statistics
Matches: 322, Mismatches: 74, Indels: 33
0.75 0.17 0.08
Matches are distributed among these distances:
34 2 0.01
35 23 0.07
36 46 0.14
37 18 0.06
38 75 0.23
39 158 0.49
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (38 bp):
TGAGATAGTTTCACTCGAAACAAAAGATTTATCTCGCT
Found at i:100731 original size:191 final size:186
Alignment explanation
Indices: 100411--100856 Score: 484
Period size: 191 Copynumber: 2.4 Consensus size: 186
100401 AAGAGAATAT
* * * * * * **
100411 TTTATCTTGCTTGATATAATTTCACTCGAAACAAAAGATTTAGCTCAATTGAGATTGTTTTTCTT
1 TTTATCTCGCTTAAGATTATTTCACTCGAAACAAAAAATTTAGCTCAATTGAGATAGTTTCACTT
* *
100476 AAAACAAGATTCATCTCGCTTGAGATAGTTTCACTAGAAACAAAATATTTTATCTCGCTTGAGAT
66 AAAACAAGATTCATCTCGCTTGAGATAGTTCCACTAGAAACAAAAGATTTTATCTCGCTTGAGAT
* * * *
100541 AGTTTCACTCGAAATAAAAAG-TTTATCTTAGTTGAGATTGTTTTTCTTAAAACCAGA
131 AGTTTCACTCGAAA-AAAAAGATTTATCTCACTTGAGATTATTTTTCTT-AAACAAGA
** **
100598 TTTATCTCGCTTAAGATTATTTCACTCGAAACAAAAAATTTTATTTCGCTTGAGATAGTTTCACT
1 TTTATCTCGCTTAAGATTATTTCACTCGAAACAAAAAA-TTTAGCTCAATTGAGATAGTTTCACT
* * * * * *
100663 TGAAACATAAGATTTTATCTTGCTTGAGATAGTTCCACTCGAAACAGAAGATTTTATCTTGCTTG
65 T-AAA-ACAAGA-TTCATCTCGCTTGAGATAGTTCCACTAGAAACAAAAGATTTTATCTCGCTTG
* * * **
100728 AGATAGTTTCTCTTGAAACAAAAGATTTATCTCACTTGCTATTATTTTTCTTAAACAAGA
127 AGATAGTTTCACTCGAAAAAAAAGATTTATCTCACTTGAGATTATTTTTCTTAAACAAGA
* * * * * *
100788 TTTATCTCGCTTCAGA-TAGTTTCACTCGAAACAGAATATTTATCTC-ATCTGAGATTGTTTCTC
1 TTTATCTCGCTTAAGATTA-TTTCACTCGAAACAAAAAATTTAGCTCAAT-TGAGATAGTTTCAC
100851 TTAAAA
64 TTAAAA
100857 TAAAATACGG
Statistics
Matches: 216, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
187 34 0.16
188 24 0.11
189 26 0.12
190 49 0.23
191 83 0.38
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (186 bp):
TTTATCTCGCTTAAGATTATTTCACTCGAAACAAAAAATTTAGCTCAATTGAGATAGTTTCACTT
AAAACAAGATTCATCTCGCTTGAGATAGTTCCACTAGAAACAAAAGATTTTATCTCGCTTGAGAT
AGTTTCACTCGAAAAAAAAGATTTATCTCACTTGAGATTATTTTTCTTAAACAAGA
Found at i:101004 original size:59 final size:59
Alignment explanation
Indices: 100882--101007 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
100872 TTGAGTGATT
* **
100882 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCTCACTTGAGGGATA
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCTCACTCGAAAGATA
* ** ** * *
100941 AACATTTTCTTTGCTCGATTCACAACACTTCGAATCATTAACGTCTCGCTCGAAAGATC
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCTCACTCGAAAGATA
101000 AACATTTC
1 AACATTTC
101008 TGGTGGAAAG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (59 bp):
AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACACCTCACTCGAAAGATA
Found at i:103045 original size:29 final size:29
Alignment explanation
Indices: 103013--103257 Score: 318
Period size: 29 Copynumber: 8.5 Consensus size: 29
103003 CATAAATTAA
* * * *
103013 TTACAAAACTAACACCCTATTAAAAATAT
1 TTACGAAACTAACACCTTTTTAACAATAT
* *
103042 TTACGAAACTAGCA-CTCTTTTAAAAATAT
1 TTACGAAACTAACACCT-TTTTAACAATAT
103071 TTACGAAACTAACA-CTTTTTAACAA-AT
1 TTACGAAACTAACACCTTTTTAACAATAT
* * *
103098 TTATGAAACTAACACATTCTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATAT
*
103127 TTACGAAACTAACAACTTTTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATAT
* *
103156 TTACAAAACTAACACCTTCTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATAT
*
103185 TTACGAAACTAACACATTCTTT-ACAATAT
1 TTACGAAACTAACACCTT-TTTAACAATAT
*
103214 TTACGAAACTAACACCTTTTTAAAAATAT
1 TTACGAAACTAACACCTTTTTAACAATAT
103243 TTACGAAACTAACAC
1 TTACGAAACTAACAC
103258 ATTCAATAAT
Statistics
Matches: 190, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
27 15 0.08
28 21 0.11
29 152 0.80
30 2 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACGAAACTAACACCTTTTTAACAATAT
Found at i:103222 original size:87 final size:86
Alignment explanation
Indices: 103013--103257 Score: 350
Period size: 87 Copynumber: 2.8 Consensus size: 86
103003 CATAAATTAA
* ** * * *
103013 TTACAAAACTAACACCCTATTAAAAATATTTACGAAACTAGC-ACTCTTTTAAAAATATTTACGA
1 TTACGAAACTAACACATTCTTAACAATATTTACGAAACTAACAACT-TTTTAAAAATATTTACGA
*
103077 AACTAACA-CTTTTTAACAAAT
65 AACTAACACCTTCTTAACAAAT
* * *
103098 TTATGAAACTAACACATTCTTAACAATATTTACGAAACTAACAACTTTTTAACAATATTTACAAA
1 TTACGAAACTAACACATTCTTAACAATATTTACGAAACTAACAACTTTTTAAAAATATTTACGAA
103163 ACTAACACCTTCTTAACAATAT
66 ACTAACACCTTCTTAACAA-AT
* *
103185 TTACGAAACTAACACATTCTTTACAATATTTACGAAACTAACACCTTTTTAAAAATATTTACGAA
1 TTACGAAACTAACACATTCTTAACAATATTTACGAAACTAACAACTTTTTAAAAATATTTACGAA
103250 ACTAACAC
66 ACTAACAC
103258 ATTCAATAAT
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
85 59 0.42
86 13 0.09
87 70 0.49
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (86 bp):
TTACGAAACTAACACATTCTTAACAATATTTACGAAACTAACAACTTTTTAAAAATATTTACGAA
ACTAACACCTTCTTAACAAAT
Found at i:107552 original size:29 final size:28
Alignment explanation
Indices: 107257--107549 Score: 410
Period size: 28 Copynumber: 10.4 Consensus size: 28
107247 ATTAACTACA
* * *
107257 AAACTAACACCCTGTTAAAAATATTTACG
1 AAACTAACA-CTTTTTAACAATATTTACG
* *
107286 AAACTAGCACTCTTTTAAAAATATTTACG
1 AAACTAACACT-TTTTAACAATATTTACG
107315 AAACTAACACTTTTTAACAATATTTACG
1 AAACTAACACTTTTTAACAATATTTACG
107343 AAACTAACACTTTTTAACAATATTTACG
1 AAACTAACACTTTTTAACAATATTTACG
107371 AAACTAACACTTTTTAACAATATTTACG
1 AAACTAACACTTTTTAACAATATTTACG
*
107399 AAACTAACAGTTTTTAACAATATTTACG
1 AAACTAACACTTTTTAACAATATTTACG
*
107427 AAACTAACAC--CTTAACAATATTTACG
1 AAACTAACACTTTTTAACAATATTTACG
* *
107453 AAACTAACATCTTCTTGACAATATTTACG
1 AAACTAACA-CTTTTTAACAATATTTACG
* * *
107482 AATCTAACACCTTCTTAACGATATTTACG
1 AAACTAACA-CTTTTTAACAATATTTACG
*
107511 AAACTAACACCTTTTTAACAATATTTACA
1 AAACTAACA-CTTTTTAACAATATTTACG
107540 AAACTAACAC
1 AAACTAACAC
107550 CTTCTATAAC
Statistics
Matches: 243, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
26 24 0.10
27 1 0.00
28 110 0.45
29 108 0.44
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (28 bp):
AAACTAACACTTTTTAACAATATTTACG
Found at i:111706 original size:29 final size:29
Alignment explanation
Indices: 111673--112000 Score: 477
Period size: 29 Copynumber: 11.4 Consensus size: 29
111663 ATTAACTACA
* * * *
111673 AAACTAACACCCTGTTAAAAATATTTATG
1 AAACTAACACCTTTTTAACAATATTTACG
* *
111702 AAACTAGCA-CTCTTTTAAAAATATTTACG
1 AAACTAACACCT-TTTTAACAATATTTACG
*
111731 AAACTAA-AACTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
111759 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
111787 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
111815 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* *
111843 AAACTAAAACCTTCTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
*
111872 AAACTAACACCTTCTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* *
111901 AAACTAACATCTTCTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* * *
111930 AATCTAACACCTTCTTAACGATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
111959 AAACTAACACCTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
111988 AAACTAACACCTT
1 AAACTAACACCTT
112001 CTATAATATG
Statistics
Matches: 279, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
28 108 0.39
29 171 0.61
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTAACACCTTTTTAACAATATTTACG
Found at i:116194 original size:28 final size:29
Alignment explanation
Indices: 116121--116415 Score: 447
Period size: 29 Copynumber: 10.3 Consensus size: 29
116111 ATTAACTACA
* * *
116121 AAACTAACACCCTGTTAAAAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* *
116150 AAACTAGCA-CTCTTTTAAAAATATTTACG
1 AAACTAACACCT-TTTTAACAATATTTACG
116179 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
116207 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
116235 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
116263 AAACTAACA-CTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
*
116291 AAACTAACACCTTCTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* *
116320 AAACTAACATCTTCTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
* * *
116349 AATCTAACACCTTCTTAACGATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
116378 AAACTAACACCTTTTTAACAATATTTACG
1 AAACTAACACCTTTTTAACAATATTTACG
116407 AAACTAACA
1 AAACTAACA
116416 TCTTCTATAA
Statistics
Matches: 251, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
28 110 0.44
29 141 0.56
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTAACACCTTTTTAACAATATTTACG
Found at i:118442 original size:23 final size:23
Alignment explanation
Indices: 118416--118461 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
118406 AAATTAGGTT
118416 TATTAATTGTTTTGATTATCTCA
1 TATTAATTGTTTTGATTATCTCA
118439 TATTAATTGTTTTGATTATCTCA
1 TATTAATTGTTTTGATTATCTCA
118462 AAGTTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TATTAATTGTTTTGATTATCTCA
Found at i:120370 original size:26 final size:26
Alignment explanation
Indices: 120341--120392 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
120331 CGCCACTGTT
120341 GCAGATGGTGGCCGTTCAGTCCTAAA
1 GCAGATGGTGGCCGTTCAGTCCTAAA
120367 GCAGATGGTGGCCGTTCAGTCCTAAA
1 GCAGATGGTGGCCGTTCAGTCCTAAA
120393 TTTTATAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (26 bp):
GCAGATGGTGGCCGTTCAGTCCTAAA
Found at i:121041 original size:27 final size:28
Alignment explanation
Indices: 121011--121072 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 28
121001 TAAAGTAGGA
** *
121011 ATATTTATTTTAGTTCTTTATT-ATAAG
1 ATATTTATAATAGTTCTTTATTAACAAG
*
121038 ATA-TTATAATAGTTTTTTATTAACAAG
1 ATATTTATAATAGTTCTTTATTAACAAG
121065 ATATTTAT
1 ATATTTAT
121073 GTTAATCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.52
27 10 0.34
28 4 0.14
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (28 bp):
ATATTTATAATAGTTCTTTATTAACAAG
Found at i:121276 original size:43 final size:44
Alignment explanation
Indices: 121211--121301 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 44
121201 CAAGAATGTT
*
121211 TTTAATATGTTAGTTTGATGTATTTGTGGATTCTTACTTTGGA-
1 TTTAATATGTTAGTTTGATGTATTTGTGAATTCTTACTTTGGAG
* *
121254 TTTAATATGTTAGTTTGGTGTATTTGTGAATTGTTACTTTGGAG
1 TTTAATATGTTAGTTTGATGTATTTGTGAATTCTTACTTTGGAG
121298 TTTA
1 TTTA
121302 GATTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 40 0.91
44 4 0.09
ACGTcount: A:0.21, C:0.03, G:0.22, T:0.54
Consensus pattern (44 bp):
TTTAATATGTTAGTTTGATGTATTTGTGAATTCTTACTTTGGAG
Found at i:130188 original size:24 final size:24
Alignment explanation
Indices: 130152--130239 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
130142 TGAATTTCGT
*
130152 TATGATACCTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
130176 TTTGATACTTGACCTGGATACTGA
1 TATGATACTTGACCTGGATTCTGA
*
130200 TATGATACTTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
* *
130224 TCTAATACTTGACCTG
1 TATGATACTTGACCTG
130240 AATTATTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:132658 original size:13 final size:13
Alignment explanation
Indices: 132640--132668 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
132630 TCTTGACAAT
132640 AATAAAATTACTA
1 AATAAAATTACTA
132653 AATAAAATTACTA
1 AATAAAATTACTA
132666 AAT
1 AAT
132669 TATTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAAATTACTA
Found at i:146589 original size:18 final size:18
Alignment explanation
Indices: 146566--146608 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
146556 AATTATTTAA
146566 TTATTTTATCCGTATCTT
1 TTATTTTATCCGTATCTT
* *
146584 TTATTTTATTCTTATCTT
1 TTATTTTATCCGTATCTT
146602 TTATTTT
1 TTATTTT
146609 TAAAACAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTTATCCGTATCTT
Found at i:163006 original size:9 final size:9
Alignment explanation
Indices: 162989--163019 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
162979 AAATGGCAAT
*
162989 CATTCTTTA
1 CATTTTTTA
162998 CATTTTTTA
1 CATTTTTTA
163007 CATTTTTTA
1 CATTTTTTA
163016 CATT
1 CATT
163020 CATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (9 bp):
CATTTTTTA
Found at i:166578 original size:16 final size:15
Alignment explanation
Indices: 166551--166623 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 15
166541 ATGCTTGAAG
166551 AAAAAAATGAAATAAAT
1 AAAAAAA-GAAA-AAAT
*
166568 AGAAAAAGAAAAAA-
1 AAAAAAAGAAAAAAT
*
166582 AAAATAAAAATAAAAAT
1 AAAA-AAAGA-AAAAAT
166599 AAAAAAAGAAGAAAAT
1 AAAAAAAGAA-AAAAT
166615 AAAAAAAGA
1 AAAAAAAGA
166624 GGGTAAGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
14 3 0.06
15 8 0.17
16 27 0.56
17 10 0.21
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (15 bp):
AAAAAAAGAAAAAAT
Found at i:166586 original size:23 final size:24
Alignment explanation
Indices: 166548--166623 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 24
166538 ATTATGCTTG
*
166548 AAGAAAAAAATGAAATAAATAGAAA
1 AAGAAAAAAA-GAAATAAATAAAAA
166573 AAGAAAAAAA-AAATAAA-AATAAA
1 AAGAAAAAAAGAAATAAATAA-AAA
*
166596 AATAAAAAAAGAAGA-AAATAAAAA
1 AAGAAAAAAAGAA-ATAAATAAAAA
166620 AAGA
1 AAGA
166624 GGGTAAGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.02
23 19 0.43
24 11 0.25
25 13 0.30
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (24 bp):
AAGAAAAAAAGAAATAAATAAAAA
Found at i:166591 original size:12 final size:12
Alignment explanation
Indices: 166576--166605 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
166566 ATAGAAAAAG
166576 AAAAAAAAAATA
1 AAAAAAAAAATA
*
166588 AAAATAAAAATA
1 AAAAAAAAAATA
166600 AAAAAA
1 AAAAAA
166606 GAAGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAATA
Found at i:166994 original size:19 final size:19
Alignment explanation
Indices: 166946--167023 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 19
166936 ATTTATTAAT
166946 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-T-TG
166968 AAATTCAATTTATTTTTTG
1 AAATTCAATTTATTTTTTG
* *
166987 AGATTCAATTTA-TTTTCG
1 AAATTCAATTTATTTTTTG
167005 AAATTCAATTTATTCTTTT
1 AAATTCAATTTATT-TTTT
167024 ATTTTGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 17 0.35
19 13 0.27
20 11 0.22
21 2 0.04
22 6 0.12
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.55
Consensus pattern (19 bp):
AAATTCAATTTATTTTTTG
Found at i:168624 original size:113 final size:113
Alignment explanation
Indices: 168176--168611 Score: 685
Period size: 113 Copynumber: 3.9 Consensus size: 113
168166 ATCCATCACA
* * *
168176 ATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAATGCAGAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
168240 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCACTTG
*
168289 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
168354 TCATAATGAGAAGAGTTTGTTCAACCTTTTGCTCAAATTCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCACTTG
* *
168402 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * * ** *
168467 TCATAATGAGAAGAATTTATTCAACTTTTTGTTTGAATTCATCACTCG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCACTTG
* *
168515 ATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCACCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
168580 TCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGC
168612 ATGACCTTAT
Statistics
Matches: 298, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 296 0.99
114 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATCACTTG
Found at i:170411 original size:16 final size:16
Alignment explanation
Indices: 170377--170411 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
170367 TTTTTATTAA
* *
170377 AATTTTTATATGAATT
1 AATTTTTATATAAAAT
170393 AATTTTTATATAAAAT
1 AATTTTTATATAAAAT
170409 AAT
1 AAT
170412 AATAATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTTTTATATAAAAT
Done.