Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001211.1 Hibiscus syriacus cultivar Beakdansim tig00002393_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: 70988
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:96 original size:8 final size:8
Alignment explanation
Indices: 85--158 Score: 60
Period size: 8 Copynumber: 9.1 Consensus size: 8
75 AAAATATTTA
85 AATAAAAT
1 AATAAAAT
*
93 AATAAAAA
1 AATAAAAT
*
101 AATTAAAT
1 AATAAAAT
*
109 AATTAAAT
1 AATAAAAT
*
117 AATTAAAT
1 AATAAAAT
*
125 AA-AATACT
1 AATAA-AAT
*
133 AACAAAAT
1 AATAAAAT
*
141 ATTAAATAT
1 AATAAA-AT
150 AATAAAAT
1 AATAAAAT
158 A
1 A
159 TACCTTATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
7 1 0.02
8 44 0.81
9 9 0.17
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:96 original size:21 final size:21
Alignment explanation
Indices: 66--110 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56 TTTATAACTG
* *
66 TAAAAAAATAAAATATTTAAA
1 TAAAAAAATAAAAAAATTAAA
*
87 TAAAATAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
108 TAA
1 TAA
111 TTAAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATTAAA
Found at i:123 original size:37 final size:39
Alignment explanation
Indices: 76--148 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
66 TAAAAAAATA
*
76 AAATATTTAAATAAAATAATAA-AAAA-ATTAAATAATT
1 AAATAATTAAATAAAATAATAACAAAATATTAAATAATT
*
113 AAATAATTAAATAAAATACTAACAAAATATTAAATA
1 AAATAATTAAATAAAATAATAACAAAATATTAAATA
149 TAATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 20 0.62
38 4 0.12
39 8 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (39 bp):
AAATAATTAAATAAAATAATAACAAAATATTAAATAATT
Found at i:129 original size:13 final size:13
Alignment explanation
Indices: 71--130 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
61 AACTGTAAAA
*
71 AAATAAAATATTT
1 AAATAAAATAATT
84 AAATAAAATAA-T
1 AAATAAAATAATT
*
96 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
109 -AATTAAATAATT
1 AAATAAAATAATT
121 AAATAAAATA
1 AAATAAAATA
131 CTAACAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 4 0.10
12 13 0.33
13 22 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:9659 original size:20 final size:20
Alignment explanation
Indices: 9599--9661 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
9589 AACTTTGAAA
9599 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
9620 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
9634 AAATGTTTTCAAAGTTTGGT
1 AAATGTTTTCAAAGTTTGGT
9654 AAATGTTT
1 AAATGTTT
9662 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
19 7 0.21
20 10 0.29
21 4 0.12
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:9689 original size:37 final size:36
Alignment explanation
Indices: 9591--9708 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 36
9581 TGGTAACCAA
*
9591 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
9628 CTTTG-AAAAT-GTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* *
9662 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATATTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
9699 -GTTGAAAAAT
1 CTTTGAAAAAT
9709 GATAATGGGA
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
34 29 0.39
35 10 0.13
36 10 0.13
37 26 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:10104 original size:12 final size:12
Alignment explanation
Indices: 10087--10111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10077 ATTTTTTGTG
10087 AGGTTACTATTC
1 AGGTTACTATTC
10099 AGGTTACTATTC
1 AGGTTACTATTC
10111 A
1 A
10112 CGTGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:14302 original size:37 final size:36
Alignment explanation
Indices: 14203--14322 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 36
14193 TGGTAACCAA
14203 CTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTG-AAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
14240 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
14275 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
14312 -GTTGAAAAATG
1 CTTTGAAAAATG
14323 ATAATGGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
34 5 0.07
35 29 0.38
36 14 0.18
37 28 0.37
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:24444 original size:2 final size:2
Alignment explanation
Indices: 24437--24461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24427 AATTTCACTA
24437 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24462 ACGTAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26340 original size:21 final size:20
Alignment explanation
Indices: 26254--26411 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
26244 AAATGACCAA
**
26254 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
26273 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
26293 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
26313 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
26334 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
26355 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
26375 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
26396 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
26412 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:26402 original size:20 final size:20
Alignment explanation
Indices: 26378--26648 Score: 301
Period size: 20 Copynumber: 13.5 Consensus size: 20
26368 CGATTTTCCA
* ** *
26378 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
26398 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
26418 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
26438 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
26458 TAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
26478 AAATCGCAACGATAATACAT
1 AAATCGCAACGAGAATCCGT
* *
26498 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATCCGT
*
26519 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
26539 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
26559 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGAGAATCCGT
*
26579 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
26599 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
26619 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
26639 AAATCACAAC
1 AAATCGCAAC
26649 ACTGAAATTT
Statistics
Matches: 216, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
20 200 0.93
21 16 0.07
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:26509 original size:101 final size:101
Alignment explanation
Indices: 26397--26648 Score: 289
Period size: 101 Copynumber: 2.5 Consensus size: 101
26387 CGCGAATATG
* * * *
26397 AAAATCGCAACGCG-AACACATAAATCGCAACGCGT-ATCCGTAAATCGCAACGTGTATCCGTTA
1 AAAATCGCAACGCGTAAC-CATAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCCGTAA
* *
26460 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
64 ATCGCAACGAGAATCCGTAAATCGCAACGATAATACAT
* * *
26498 AAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAAT
1 AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
*
26563 CGCAACGAGAATCCGTAAATCGCAACGAGAAT-C-T
66 CGCAACGAGAATCCGTAAATCGCAACGATAATACAT
* * * * * *
26597 GTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATCACAAC
1 -AAAATCGCAACGCGTAA-CCATAAATCGCAACGATAATCCGTAAATCGCAAC
26649 ACTGAAATTT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
99 3 0.02
100 44 0.34
101 82 0.63
102 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (101 bp):
AAAATCGCAACGCGTAACCATAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTAAAT
CGCAACGAGAATCCGTAAATCGCAACGATAATACAT
Found at i:27369 original size:24 final size:24
Alignment explanation
Indices: 27330--27376 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27320 AAATTTGGTC
27330 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
27354 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
27377 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29929 original size:34 final size:33
Alignment explanation
Indices: 29846--29951 Score: 155
Period size: 33 Copynumber: 3.2 Consensus size: 33
29836 CGGAAATTAC
29846 AATCGCAACGAGAGAATCGC-ATGCGAAATG-A
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
29877 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
29911 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
29944 AATCGCAA
1 AATCGCAA
29952 TGCGAAATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
30 1 0.02
31 16 0.24
32 4 0.06
33 22 0.33
34 22 0.33
35 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:29949 original size:19 final size:19
Alignment explanation
Indices: 29886--30079 Score: 229
Period size: 19 Copynumber: 10.9 Consensus size: 19
29876 AAATCCCAAC
29886 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
29906 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
29921 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
29939 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
29958 ATGAAAATCGC-A-GCG--
1 ATGAAAATCGCAATGCGAA
*
29973 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
29991 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
30010 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
30029 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
30044 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
30062 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
30080 TTCTCCCGTT
Statistics
Matches: 151, Mismatches: 8, Indels: 31
0.79 0.04 0.16
Matches are distributed among these distances:
14 28 0.19
15 4 0.03
16 7 0.05
17 6 0.04
18 5 0.03
19 88 0.58
20 13 0.09
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:29975 original size:52 final size:52
Alignment explanation
Indices: 29886--30073 Score: 256
Period size: 52 Copynumber: 3.6 Consensus size: 52
29876 AAATCCCAAC
29886 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
29939 ATGAAAATCGCAATGCGAAATGAAAATCGCAGCGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
29991 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* *
30041 ACGAGAGAATCGCAATGCGAAATTAAAATCGCA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCA
30074 TTGCGATTCT
Statistics
Matches: 124, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 94 0.76
53 16 0.13
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:29981 original size:33 final size:33
Alignment explanation
Indices: 29944--30073 Score: 188
Period size: 33 Copynumber: 3.8 Consensus size: 33
29934 GCGAAATGAA
29944 AATCGCAATGCGAAATGAAAATCGCAGCGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAGCGAGAG
*
29977 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-GCG--A-GAG
*
30015 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAGCGAGAG
*
30048 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
30074 TTGCGATTCT
Statistics
Matches: 88, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
33 52 0.59
34 2 0.02
35 3 0.03
36 2 0.02
37 2 0.02
38 27 0.31
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAGCGAGAG
Found at i:30010 original size:71 final size:71
Alignment explanation
Indices: 29925--30079 Score: 283
Period size: 71 Copynumber: 2.2 Consensus size: 71
29915 GCAACGAGAG
*
29925 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAGCGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
29990 AATGAA
66 AATGAA
29996 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
30061 AATTAA
66 AATGAA
*
30067 AATCGCATTGCGA
1 AATCGCAATGCGA
30080 TTCTCCCGTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:30112 original size:19 final size:19
Alignment explanation
Indices: 30088--30183 Score: 132
Period size: 19 Copynumber: 5.4 Consensus size: 19
30078 GATTCTCCCG
*
30088 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
30107 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30126 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30140 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30159 TTGCGATTTT-ATTTCGCA
1 TTGCGATTTTCATTTCGCA
30177 TTGCGAT
1 TTGCGAT
30184 AGTCAATTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
18 15 0.22
19 34 0.49
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30112 original size:52 final size:52
Alignment explanation
Indices: 30051--30164 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 52
30041 ACGAGAGAAT
*
30051 CGCAATGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATTC
1 CGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATTC
** * ** * *
30103 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATTC
30155 CGCATTGCGA
1 CGCATTGCGA
30165 TTTTATTTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (52 bp):
CGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATTC
Found at i:30165 original size:52 final size:51
Alignment explanation
Indices: 30069--30183 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 51
30059 GAAATTAAAA
30069 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTT-ATT
* *
30121 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTATT
30172 TCGCATTGCGAT
1 TCGCATTGCGAT
30184 AGTCAATTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 15 0.25
52 46 0.75
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (51 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTCCGCATTGCGATTTTATT
Found at i:30305 original size:13 final size:14
Alignment explanation
Indices: 30289--30324 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30279 CATCAATTAC
30289 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
30302 ACAAATCATCTTTT
1 ACAAATCAACTTTT
30316 ACAAATCAA
1 ACAAATCAA
30325 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32269 original size:20 final size:20
Alignment explanation
Indices: 32244--32310 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
32234 TAGTTTACTT
* *
32244 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTAAAAA
*
32264 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTAAAAA
32283 TCGCAACGCGAAA-TGAAAAA
1 TCGCAACGCGAAACT-AAAAA
32303 TCGCAACG
1 TCGCAACG
32311 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.40
20 25 0.60
ACGTcount: A:0.46, C:0.27, G:0.16, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAACTAAAAA
Found at i:32320 original size:14 final size:14
Alignment explanation
Indices: 32297--32357 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
32287 AACGCGAAAT
32297 GAAA-AATCGCAAC
1 GAAAGAATCGCAAC
*
32310 GACAGAATCGCAATGC
1 GAAAGAATCGCAA--C
32326 GAAATGAAAATCGCAAC
1 GAAA-G--AATCGCAAC
32343 GAAAGAATCGCAAC
1 GAAAGAATCGCAAC
32357 G
1 G
32358 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.08
14 18 0.45
16 5 0.12
17 6 0.15
19 8 0.20
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (14 bp):
GAAAGAATCGCAAC
Found at i:32339 original size:19 final size:19
Alignment explanation
Indices: 32244--32379 Score: 121
Period size: 19 Copynumber: 7.6 Consensus size: 19
32234 TAGTTTACTT
* *
32244 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
32264 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
32283 TCGCAACGCGAAATGAAAAA
1 TCGCAACGCGAAATG-AAAA
*
32303 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
32317 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
32336 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
32350 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
32369 TCGCAATGCGA
1 TCGCAACGCGA
32380 TTATAATGGC
Statistics
Matches: 97, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 8 0.08
18 4 0.04
19 37 0.38
20 22 0.23
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:32341 original size:33 final size:33
Alignment explanation
Indices: 32281--32374 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
32271 GCGAAACCAA
*
32281 AATCGCAACGCGAAATGAAAAATCGCAACGACAG
1 AATCGCAACGCGAAATG-AAAATCGCAACGAAAG
*
32315 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
32348 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
32375 TGCGATTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 41 0.72
34 16 0.28
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:32445 original size:20 final size:20
Alignment explanation
Indices: 32420--32573 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
32410 CTTTAAATAT
32420 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32440 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
32462 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32481 CGCGTTGCGATTAACGGATA
1 CGCGTTGCGATTTACGGATA
*
32501 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32521 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
32541 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
32561 CGCGTTGCGATTT
1 CGCGTTGCGATTT
32574 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:32547 original size:40 final size:40
Alignment explanation
Indices: 32419--32573 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
32409 GCTTTAAATA
*
32419 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
32460 TATCGTTGCGATTTACGGATACGCGTTGCGATTAACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
32500 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
32540 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
32574 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:32590 original size:21 final size:21
Alignment explanation
Indices: 32560--32642 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
32550 ATTTTCATAT
*
32560 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
32581 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
32602 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
32623 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
32643 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:32633 original size:42 final size:43
Alignment explanation
Indices: 32540--32638 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
32530 ATTTATGTGT
* *
32540 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
32581 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
32623 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
32639 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:34334 original size:20 final size:21
Alignment explanation
Indices: 34292--34342 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
34282 TCTATATTTT
* *
34292 TATTATATTTTACTGTTTTTA
1 TATTATATTTTACTATTTATA
*
34313 TATTA-ATTTTATTATTTATA
1 TATTATATTTTACTATTTATA
34333 TAATT-TATTT
1 T-ATTATATTT
34343 GAAAAATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTATATTTTACTATTTATA
Found at i:35890 original size:16 final size:17
Alignment explanation
Indices: 35869--35903 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35859 CTCCCCCTTA
35869 CTTT-AACACTTCTCTC
1 CTTTAAACACTTCTCTC
35885 CTTTAAAACACTTCTCTC
1 CTTT-AAACACTTCTCTC
35903 C
1 C
35904 CTTTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (17 bp):
CTTTAAACACTTCTCTC
Found at i:37922 original size:22 final size:23
Alignment explanation
Indices: 37876--37937 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
37866 CGATTCCCCT
37876 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCATTCAA
*
37899 AGGGGGAATCGGTTCCCCTT-AA
1 AGGGGGAATCGGTTCCCATTCAA
* *
37921 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
37938 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCATTCAA
Found at i:44056 original size:27 final size:25
Alignment explanation
Indices: 44026--44164 Score: 94
Period size: 23 Copynumber: 5.6 Consensus size: 25
44016 TCAACATGAT
*
44026 AATATATAATATATAGTTTTGT-CAA
1 AATATATAATATATAGTTTT-TAAAA
*
44051 AA-A-ATAATATATAGTTTTT-GAA
1 AATATATAATATATAGTTTTTAAAA
*
44073 AATATAT-A-GTATAGTTTTTTAAAA
1 AATATATAATATATAG-TTTTTAAAA
* ** *
44097 AACATATTGTTATATAGTTTTGAAAA
1 AATATA-TAATATATAGTTTTTAAAA
*
44123 CATATA-ATATATATAGTTTTTGAAAA
1 AATATATA-ATATATAGTTTTT-AAAA
*
44149 ACATATGTAATATATA
1 A-ATATATAATATATA
44165 TACTTTTTGA
Statistics
Matches: 89, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
22 10 0.11
23 22 0.25
24 10 0.11
25 14 0.16
26 16 0.18
27 16 0.18
28 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (25 bp):
AATATATAATATATAGTTTTTAAAA
Found at i:44060 original size:23 final size:22
Alignment explanation
Indices: 44031--44098 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
44021 ATGATAATAT
44031 ATAATATATAGTTTTGTCAAAAA
1 ATAATATATAGTTTT-TCAAAAA
* *
44054 ATAATATATAGTTTTTGAAAAT
1 ATAATATATAGTTTTTCAAAAA
*
44076 AT-ATAGTATAGTTTTTTAAAAA
1 ATAATA-TATAGTTTTTCAAAAA
44098 A
1 A
44099 CATATTGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.08
22 22 0.55
23 15 0.38
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (22 bp):
ATAATATATAGTTTTTCAAAAA
Found at i:44117 original size:25 final size:25
Alignment explanation
Indices: 44058--44183 Score: 80
Period size: 24 Copynumber: 4.9 Consensus size: 25
44048 CAAAAAATAA
* * *
44058 TATATAGTTTTTGAAAATATATAG-
1 TATATAGTTTTTAAAAACATATTGT
44082 --TATAGTTTTTTAAAAAACATATTGT
1 TATATAG-TTTTT-AAAAACATATTGT
* **
44107 TATATAG-TTTTGAAAACATATAAT
1 TATATAGTTTTTAAAAACATATTGT
*
44131 ATATATAGTTTTTGAAAAACATATGTAAT
1 -TATATAGTTTTT-AAAAACATAT-T-GT
* *
44160 ATATATACTTTTTGAAAACATATT
1 -TATATAGTTTTTAAAAACATATT
44184 ATATGATTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
22 5 0.06
23 5 0.06
24 19 0.23
25 11 0.13
26 4 0.05
27 15 0.18
28 9 0.11
29 14 0.17
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (25 bp):
TATATAGTTTTTAAAAACATATTGT
Found at i:44160 original size:29 final size:27
Alignment explanation
Indices: 44057--44184 Score: 121
Period size: 27 Copynumber: 4.9 Consensus size: 27
44047 TCAAAAAATA
44057 ATATATAGTTTTTG-AAA-ATA-T-AT
1 ATATATAGTTTTTGAAAACATATTAAT
* * *
44080 A-GTATAGTTTTTTAAAAAACATATT-GT
1 ATATATAG-TTTTT-GAAAACATATTAAT
44107 -TATATAG-TTTTGAAAACATA-TAAT
1 ATATATAGTTTTTGAAAACATATTAAT
44131 ATATATAGTTTTTGAAAAACATATGTAAT
1 ATATATAGTTTTTG-AAAACATAT-TAAT
*
44160 ATATATACTTTTTGAAAACATATTA
1 ATATATAGTTTTTGAAAACATATTA
44185 TATGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
22 5 0.06
23 7 0.08
24 9 0.10
25 14 0.16
26 8 0.09
27 17 0.20
28 9 0.10
29 17 0.20
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (27 bp):
ATATATAGTTTTTGAAAACATATTAAT
Found at i:44210 original size:25 final size:24
Alignment explanation
Indices: 44179--44236 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
44169 TTTTGAAAAC
*
44179 ATATTATATGATTTTGAAATATA-AT
1 ATATTAT-TCATTTT-AAATATATAT
*
44204 ATATTATTCATTTTTAATATATAT
1 ATATTATTCATTTTAAATATATAT
44228 ATATGTATT
1 ATAT-TATT
44237 ATTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.21
24 12 0.41
25 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
ATATTATTCATTTTAAATATATAT
Found at i:45461 original size:15 final size:14
Alignment explanation
Indices: 45441--45481 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
45431 ATCCTTGGTT
45441 TTTAATTCTTTTCAA
1 TTTAATTCTTTT-AA
*
45456 TTTAATCCTTTTAA
1 TTTAATTCTTTTAA
45470 TTTAATT-TTTTA
1 TTTAATTCTTTTA
45482 TTCTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 11 0.46
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTCTTTTAA
Found at i:45473 original size:29 final size:27
Alignment explanation
Indices: 45423--45480 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 27
45413 TTAATTAATC
45423 TCAATTTAATCCTTGGTTTTTAATTCTTT
1 TCAATTTAATCCTT-GTTTTTAATT-TTT
45452 TCAATTTAATCCTT-TTAATTTAATTTTT
1 TCAATTTAATCCTTGTT--TTTAATTTTT
45480 T
1 T
45481 ATTCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.07
28 4 0.15
29 21 0.78
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.60
Consensus pattern (27 bp):
TCAATTTAATCCTTGTTTTTAATTTTT
Found at i:46233 original size:24 final size:27
Alignment explanation
Indices: 46200--46276 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
46190 ATTTGATTTT
*
46200 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
*
46225 AATTA-AATATTATTTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
46251 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
46277 TTTTTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 15 0.34
25 5 0.11
26 17 0.39
27 1 0.02
28 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:46290 original size:63 final size:63
Alignment explanation
Indices: 46183--46343 Score: 272
Period size: 63 Copynumber: 2.5 Consensus size: 63
46173 ATTTTATATT
*
46183 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTATTTTTTTA
1 ATATTATATTATAGATATTAATTTTAATATT-ATTTTTTAAATAAATTAAATATTATTTTTTTA
46245 ATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTATTTTTTTA
1 ATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTATTTTTTTA
46308 ATATTATATTATAGATATTTAATTTTATATATTATT
1 ATATTATATTATAGATA-TTAATTTTA-ATATTATT
46344 AAAATTTTAT
Statistics
Matches: 94, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
62 10 0.11
63 50 0.53
64 26 0.28
65 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (63 bp):
ATATTATATTATAGATATTAATTTTAATATTATTTTTTAAATAAATTAAATATTATTTTTTTA
Found at i:46314 original size:14 final size:13
Alignment explanation
Indices: 46164--46342 Score: 80
Period size: 14 Copynumber: 14.3 Consensus size: 13
46154 CAAAGAGGTT
46164 TTATA-TTTAAT-
1 TTATATTTTAATA
*
46175 TT-TATATT-ATA
1 TTATATTTTAATA
* *
46186 TTATA-TTTGATT
1 TTATATTTTAATA
46198 TTA-ATTTTAATA
1 TTATATTTTAATA
*
46210 TTAATTTTTTAA-A
1 TT-ATATTTTAATA
* *
46223 -TA-AATTAAATA
1 TTATATTTTAATA
*
46234 TTATTTTTTTAATA
1 TTA-TATTTTAATA
*
46248 TTATATTATAGATA
1 TTATATTTTA-ATA
46262 TTA-ATTTTAATA
1 TTATATTTTAATA
*
46274 TTATTTTTTAA-A
1 TTATATTTTAATA
* *
46286 -TA-AATTAAATA
1 TTATATTTTAATA
*
46297 TTATTTTTTTAATA
1 TTA-TATTTTAATA
*
46311 TTATATTATAGATA
1 TTATATTTTA-ATA
46325 TT-TAATTTTATATA
1 TTAT-ATTTTA-ATA
46339 TTAT
1 TTAT
46343 TAAAATTTTA
Statistics
Matches: 122, Mismatches: 26, Indels: 36
0.66 0.14 0.20
Matches are distributed among these distances:
10 12 0.10
11 14 0.11
12 26 0.21
13 24 0.20
14 45 0.37
15 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TTATATTTTAATA
Found at i:46366 original size:17 final size:18
Alignment explanation
Indices: 46325--46366 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
46315 ATTATAGATA
46325 TTTAATTTTATATATTAT
1 TTTAATTTTATATATTAT
** *
46343 TAAAATTTTAT-TTTTAT
1 TTTAATTTTATATATTAT
46360 TTTAATT
1 TTTAATT
46367 ATTTTGATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATTTTATATATTAT
Found at i:46870 original size:31 final size:31
Alignment explanation
Indices: 46833--46892 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
46823 TAGTTGTATG
* *
46833 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
46864 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
46893 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:46935 original size:16 final size:16
Alignment explanation
Indices: 46910--46952 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
46900 GTTTAAAAAA
46910 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
*
46926 TCATTTTATTTATATT
1 TCAGTTTATTTATATT
*
46942 TTAGTTTATTT
1 TCAGTTTATTT
46953 TAGCAGTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:48292 original size:29 final size:29
Alignment explanation
Indices: 48255--48342 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
48245 AATTTATCGA
48255 GAACTAAATTGAATTTTGATTAATTTTAG
1 GAACTAAATTGAATTTTGATTAATTTTAG
* *
48284 GAATTAAATTGAATTTTGATTAATTTTGG
1 GAACTAAATTGAATTTTGATTAATTTTAG
* * *
48313 GAACCAAAGTGAAATTTTGATTAAATTTAG
1 GAACTAAATTG-AATTTTGATTAATTTTAG
48343 ATCCAAATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 35 0.69
30 16 0.31
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (29 bp):
GAACTAAATTGAATTTTGATTAATTTTAG
Found at i:49727 original size:39 final size:39
Alignment explanation
Indices: 49661--49932 Score: 294
Period size: 39 Copynumber: 7.0 Consensus size: 39
49651 CGCTTTCCGT
* * *
49661 AGGCTTCTCGGCTTTGTGCTCAGGGTAAGTCGTTACTGC
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
* * * * * *
49700 ATGCTCCTTTGCTTTATGCTCAAGGTAAGTCCTAATTGC
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
* *
49739 AGGTTCCT-TGGCTTTGTGCTCAGAGTAAGTCCTTACTGC
1 AGGCTCCTCT-GCTTTGTGCTCAGGGTAAGTCCTTACTGC
* * * *
49778 ATGATCCACTACTTTGTGCTCAGGGTAAGTCCTTACTGC
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
* * *
49817 AGGCTCCTCAGCTTTATGCTCAGGGTAAGTCCTTACTGT
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
* * * * *
49856 AGGCTCCTCTGCTTTGTGCACAAGATAAGACCTTACTGA
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
* * *
49895 ATGCTCCTCTGCTTTGTGCACAGGGTAAGTTCTTACTG
1 AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTG
49933 GGTGTGCAGG
Statistics
Matches: 191, Mismatches: 40, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
38 1 0.01
39 189 0.99
40 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCCTTACTGC
Found at i:49890 original size:117 final size:117
Alignment explanation
Indices: 49672--49932 Score: 337
Period size: 117 Copynumber: 2.2 Consensus size: 117
49662 GGCTTCTCGG
* * ** *
49672 CTTTGTGCTCAGGGTAAGTCGTTACTGCATGCTCCTTTGCTTTATGCTCAAGGTAAGTCCTAATT
1 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCAGCTTTATGCTCAAGGTAAGTCCTAACT
* * * *
49737 GCAGGTTCCTTGGCTTTGTGCTCAGAGTAAGTCCTTACTGCATGATCCACTA
66 GCAGGCTCCTTGGCTTTGTGCACAGAGTAAGACCTTACTGAATGATCCACTA
* *
49789 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCAGCTTTATGCTCAGGGTAAGTCCTTACT
1 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCAGCTTTATGCTCAAGGTAAGTCCTAACT
* * * *
49854 GTAGGCTCCTCT-GCTTTGTGCACA-AGATAAGACCTTACTGAATGCTCCTCTG
66 GCAGGCTCCT-TGGCTTTGTGCACAGAG-TAAGACCTTACTGAATGATCCACTA
* *
49906 CTTTGTGCACAGGGTAAGTTCTTACTG
1 CTTTGTGCTCAGGGTAAGTCCTTACTG
49933 GGTGTGCAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
116 2 0.02
117 122 0.98
118 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (117 bp):
CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCAGCTTTATGCTCAAGGTAAGTCCTAACT
GCAGGCTCCTTGGCTTTGTGCACAGAGTAAGACCTTACTGAATGATCCACTA
Found at i:53579 original size:17 final size:17
Alignment explanation
Indices: 53554--53591 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53544 TATTTTTATT
*
53554 TTTTTAATAAGTTAAAG-
1 TTTTAAATAA-TTAAAGA
53571 TTTTAAATAATTAAAGA
1 TTTTAAATAATTAAAGA
53588 TTTT
1 TTTT
53592 TTTGAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
TTTTAAATAATTAAAGA
Found at i:64600 original size:3 final size:3
Alignment explanation
Indices: 64592--64638 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
64582 AAAATATATA
64592 TAT TAT TAT ATACT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
64638 T
1 T
64639 TTACAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 4 0.10
5 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:66424 original size:2 final size:2
Alignment explanation
Indices: 66417--66449 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
66407 CTTTACTGTT
66417 TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66450 TAATTTACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.