Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007356.1 Hibiscus syriacus cultivar Beakdansim tig00019716_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: 116197
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--149 Score: 298
Period size: 7 Copynumber: 21.3 Consensus size: 7
1 GAGAAGA
1 GAGAAGA
8 GAGAAGA
1 GAGAAGA
15 GAGAAGA
1 GAGAAGA
22 GAGAAGA
1 GAGAAGA
29 GAGAAGA
1 GAGAAGA
36 GAGAAGA
1 GAGAAGA
43 GAGAAGA
1 GAGAAGA
50 GAGAAGA
1 GAGAAGA
57 GAGAAGA
1 GAGAAGA
64 GAGAAGA
1 GAGAAGA
71 GAGAAGA
1 GAGAAGA
78 GAGAAGA
1 GAGAAGA
85 GAGAAGA
1 GAGAAGA
92 GAGAAGA
1 GAGAAGA
99 GAGAAGA
1 GAGAAGA
106 GAGAAGA
1 GAGAAGA
113 GAGAAGA
1 GAGAAGA
120 GAGAAGA
1 GAGAAGA
127 GAGAAGA
1 GAGAAGA
134 GAGAAGA
1 GAGAAGA
141 GAGAAGA
1 GAGAAGA
148 GA
1 GA
150 ATTGGACTGA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 142 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAGAAGA
Found at i:1497 original size:76 final size:77
Alignment explanation
Indices: 1370--1518 Score: 282
Period size: 76 Copynumber: 1.9 Consensus size: 77
1360 TGTCTGGTTT
*
1370 GTACTTAGTTTACTGGGTTAGTGTAAGAAGGATGGAATATGTTGTCATTAATATTGTTGTTTCTT
1 GTACTTAGTTTACTGGGTTAGTGTAAGAAGGATGAAATATGTTGTCATTAATATTGTTGTTTCTT
1435 TCTCTCTCTTGG
66 TCTCTCTCTTGG
1447 GTACTTAGTTTA-TGGGTTAGTGTAAGAAGGATGAAATATGTTGTCATTAATATTGTTGTTTCTT
1 GTACTTAGTTTACTGGGTTAGTGTAAGAAGGATGAAATATGTTGTCATTAATATTGTTGTTTCTT
1511 TCTCTCTC
66 TCTCTCTC
1519 AAACATTTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 59 0.83
77 12 0.17
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (77 bp):
GTACTTAGTTTACTGGGTTAGTGTAAGAAGGATGAAATATGTTGTCATTAATATTGTTGTTTCTT
TCTCTCTCTTGG
Found at i:2416 original size:20 final size:21
Alignment explanation
Indices: 2391--2434 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2381 ATATTATATA
2391 AATCTA-TTATGTATCATTT-T
1 AATCTACTT-TGTATCATTTAT
*
2411 AATCTACTTTGTTTCATTTAT
1 AATCTACTTTGTATCATTTAT
2432 AAT
1 AAT
2435 ATCGATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.55
Consensus pattern (21 bp):
AATCTACTTTGTATCATTTAT
Found at i:3368 original size:1 final size:1
Alignment explanation
Indices: 3362--3387 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3352 CAGAAACTGC
3362 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3388 GAGAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7094 original size:3 final size:3
Alignment explanation
Indices: 7086--7123 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
7076 TTTTTACCCA
7086 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
7124 AATATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:8611 original size:13 final size:13
Alignment explanation
Indices: 8595--8641 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
8585 ATATAATAAA
8595 TAAATATTTATTT
1 TAAATATTTATTT
*
8608 TAAATAAATTATTT
1 TAAAT-ATTTATTT
8622 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
8635 TCAATAT
1 TAAATAT
8642 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:9300 original size:17 final size:17
Alignment explanation
Indices: 9271--9314 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
9261 TTTAATTTTT
*
9271 AATTTTT-TCTTTTCAA
1 AATTTTTATATTTTCAA
*
9287 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
9304 AATATTTATAT
1 AATTTTTATAT
9315 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:19987 original size:11 final size:11
Alignment explanation
Indices: 19967--20001 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
19957 ATGCTTGAAG
19967 AAAAGAAAGAAA
1 AAAAG-AAGAAA
19979 AAAAGAAGAAA
1 AAAAGAAGAAA
19990 AAAAGAA-AAA
1 AAAAGAAGAAA
20000 AA
1 AA
20002 CCCGCAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:19988 original size:20 final size:19
Alignment explanation
Indices: 19963--20001 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
19953 TATTATGCTT
19963 GAAGAAAAGAAAGAAAAAAA
1 GAAGAAAA-AAAGAAAAAAA
19983 GAAGAAAAAAAGAAAAAAA
1 GAAGAAAAAAAGAAAAAAA
20002 CCCGCAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
GAAGAAAAAAAGAAAAAAA
Found at i:20331 original size:13 final size:13
Alignment explanation
Indices: 20313--20337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20303 CTATTTCAAG
20313 TTCAATTTATTTA
1 TTCAATTTATTTA
20326 TTCAATTTATTT
1 TTCAATTTATTT
20338 GTAGAAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCAATTTATTTA
Found at i:21361 original size:83 final size:83
Alignment explanation
Indices: 21125--22282 Score: 2171
Period size: 83 Copynumber: 14.0 Consensus size: 83
21115 GAAAGAGACT
21125 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
*
21190 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
21208 CAATAGCATCTTCTGGAAGTG-T-TTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21271 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21289 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21354 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21372 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21437 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
21455 CAATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21520 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21538 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21603 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
* *
21621 CAATAGCATCTTCTGGAAGCGTTCTTTAAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
*
21686 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
*
21704 CAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21769 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21787 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21852 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21870 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
21935 -TTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
21952 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
*
22017 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
22035 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
22100 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
22118 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
22183 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
* * * *
22201 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAGCTAATCTGGTTGGGCAG-ACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
*
22265 TTTGGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
22283 TCATAGTAAA
Statistics
Matches: 1056, Mismatches: 16, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
81 79 0.07
82 114 0.11
83 863 0.82
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
TTTAGAAGATGAATTTGC
Found at i:23471 original size:228 final size:223
Alignment explanation
Indices: 23074--23624 Score: 836
Period size: 228 Copynumber: 2.4 Consensus size: 223
23064 TAGCAAAGAT
* * *
23074 TCAAATCCATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCTATCACTTGATGGATC-ACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
23139 GAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTCATCATTTGAT
*
23204 GGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAA
130 GGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAA
23269 TTCATAATGAGAAGAATCTGTTCAACCTTTTG
192 TTCATAATGAGAAGAATCTGTTCAACCTTTTG
*
23301 CTCAAATCTATCACTTGATGGAGCAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGA
1 -TCAAATCTATCACTTGATGGATCA-CTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGA
23366 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTCATCATTTGA
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTCATCATTTGA
* *
23431 TGGATCAATATTGCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
129 TGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
*
23495 TCATAATGAGAAGAATTTGTTCAACCTTTTG
193 TCATAATGAGAAGAATCTGTTCAACCTTTTG
* * * * *
23526 TCCGAAT-TCATCACATGATGGATTATTTTTGCCCGAGAAGGTTCATAATGAGAAGAACTCATCT
1 T-CAAATCT-ATCACTTGATGGATCACTTTT-CCAGAGAA-GTTCATAATGAGAAGAACTCATCT
*
23590 GAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
23625 CATCTGAAGA
Statistics
Matches: 299, Mismatches: 18, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
224 6 0.02
225 77 0.26
226 59 0.20
227 1 0.00
228 153 0.51
229 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (223 bp):
TCAAATCTATCACTTGATGGATCACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTCATCATTTGATG
GATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCA
TAATGAGAAGAATCTGTTCAACCTTTTG
Found at i:23499 original size:113 final size:113
Alignment explanation
Indices: 23081--23624 Score: 785
Period size: 113 Copynumber: 4.8 Consensus size: 113
23071 GATTCAAATC
*
23081 CATCACTTGATGGATCAACATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
23145 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATT
* * *
23193 CATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCACTTGATGGATCAATATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * *
23257 AGGAAGAAGAAATTCATAATGAGAAGAA-TCTGTTCAACCTTTTG-CTCAAAT
62 AGGAAGAAGAAGTTCATAATGAGAAGAACT-TGTTCAACCTTTTGTCTGAATT
* * *
23308 CTATCACTTGATGGAGCAGCT-TTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAG
1 C-ATCACTTGATGGATCA-ATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAG
23371 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATT
64 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATT
*
23421 CATCATTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
23486 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATT
* * * * *
23534 CATCACATGATGGATTATTTTTGCCCGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
23599 AGAAAAAGTTCATAATGAGAAGAACT
66 AGAAGAAGTTCATAATGAGAAGAACT
23625 CATCTGAAGA
Statistics
Matches: 388, Mismatches: 31, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
111 3 0.01
112 102 0.26
113 187 0.48
115 24 0.06
116 70 0.18
117 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (113 bp):
CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATT
Found at i:23650 original size:40 final size:40
Alignment explanation
Indices: 23566--23642 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
23556 GCCCGAGAAG
23566 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAA
23606 GTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAA
23643 TTTGTTCAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 2 0.06
40 34 0.94
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.18
Consensus pattern (40 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAA
Found at i:23765 original size:65 final size:65
Alignment explanation
Indices: 23635--23865 Score: 437
Period size: 65 Copynumber: 3.6 Consensus size: 65
23625 CATCTGAAGA
23635 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-TCATATGAAGAAGGAAGAAGAAGTTCATAAT
1 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATATGAAGAAGGAAGAAGAAGTTCATAAT
23699 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATATGAAGAAGGAAGAAGAAGTTCATAAT
1 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATATGAAGAAGGAAGAAGAAGTTCATAAT
* *
23764 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATCTGAAGAATGAAGAAGAAGTTCATAAT
1 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATATGAAGAAGGAAGAAGAAGTTCATAAT
23829 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCA
1 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCA
23866 CTTGATGGAT
Statistics
Matches: 164, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
64 33 0.20
65 131 0.80
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (65 bp):
GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATATGAAGAAGGAAGAAGAAGTTCATAAT
Found at i:23941 original size:40 final size:40
Alignment explanation
Indices: 23890--23989 Score: 182
Period size: 40 Copynumber: 2.5 Consensus size: 40
23880 TTTGCCAGAG
23890 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
*
23930 AAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAA
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
*
23970 GAAGTTCATAATGAGAAGAA
1 AAAGTTCATAATGAGAAGAA
23990 TTTGTTCAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
Found at i:23967 original size:153 final size:154
Alignment explanation
Indices: 23798--24109 Score: 520
Period size: 154 Copynumber: 2.0 Consensus size: 154
23788 TTTGAATTCA
* **
23798 TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGTTTGAAT-T
1 TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCT
*
23861 CATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 -ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
23926 AGAAAAAGTTCATAATGAGAAGAAC
130 AGAAAAAGTTCATAATGAGAAGAAC
23951 TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCT
1 TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCT
* * **
24016 ATTACTTGATGGGTTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
66 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
*
24081 GAGAAAGTTCATAATGAGAAGAAC
131 GAAAAAGTTCATAATGAGAAGAAC
24105 TCATC
1 TCATC
24110 AAAAGCTTAT
Statistics
Matches: 148, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
153 50 0.34
154 97 0.66
155 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (154 bp):
TCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCT
ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAAAAGTTCATAATGAGAAGAAC
Found at i:24363 original size:3 final size:3
Alignment explanation
Indices: 24355--24416 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
24345 ATTTTACCCA
*
24355 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24403 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
24417 AATATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25896 original size:13 final size:13
Alignment explanation
Indices: 25880--25926 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
25870 ATATAATAAA
25880 TAAATATTTATTT
1 TAAATATTTATTT
*
25893 TAAATAAATTATTT
1 TAAAT-ATTTATTT
25907 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
25920 TCAATAT
1 TAAATAT
25927 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:35377 original size:76 final size:76
Alignment explanation
Indices: 35251--35402 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
35241 GATATAATTA
*
35251 TTAGTATCTACTTCATTGATTAATTAGTTTAAATAAAATACGATAGAGATTTATCAACAATCAGT
1 TTAGTATCTACTTCATTGATTAATTAGTTTAAATAAAATACGATAGAGATTTACCAACAATCAGT
35316 TGGTCTAGTGG
66 TGGTCTAGTGG
*
35327 TTAGTATCTACTTCATTGATTAATTAGTTTAAATAAAGTACGATAGAGATTTACCAACAATCAGT
1 TTAGTATCTACTTCATTGATTAATTAGTTTAAATAAAATACGATAGAGATTTACCAACAATCAGT
35392 TGGTCTAGTGG
66 TGGTCTAGTGG
35403 GATGAGGCAC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (76 bp):
TTAGTATCTACTTCATTGATTAATTAGTTTAAATAAAATACGATAGAGATTTACCAACAATCAGT
TGGTCTAGTGG
Found at i:36657 original size:93 final size:93
Alignment explanation
Indices: 36543--36728 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
36533 AGCTCAAAAT
36543 TAATAACATTAATTGTTGAAATATATTGTATTTTTTCTATTCGAATTCAATTAACACTTATAATG
1 TAATAACATTAATTGTTGAAATATATTGTATTTTTTCTATTCGAATTCAATTAACACTTATAATG
36608 ATTAATTTTAAAATCTACATCCTATAAG
66 ATTAATTTTAAAATCTACATCCTATAAG
36636 TAATAACATTAATTGTTGAAATATATTGTATTTTTTCTATTCGAATTCAATTAACACTTATAATG
1 TAATAACATTAATTGTTGAAATATATTGTATTTTTTCTATTCGAATTCAATTAACACTTATAATG
36701 ATTAATTTTAAAATCTACATCCTATAAG
66 ATTAATTTTAAAATCTACATCCTATAAG
36729 GCCTTTGTGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (93 bp):
TAATAACATTAATTGTTGAAATATATTGTATTTTTTCTATTCGAATTCAATTAACACTTATAATG
ATTAATTTTAAAATCTACATCCTATAAG
Found at i:37404 original size:31 final size:32
Alignment explanation
Indices: 37366--37433 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 32
37356 AATAAATCTG
*
37366 TCACTAATGTTATTGATTTGTAAC-AAAATGA
1 TCACTAATGTTATCGATTTGTAACAAAAATGA
37397 TCACTAATGTTATCGATTTGTAACAAAAATGA
1 TCACTAATGTTATCGATTTGTAACAAAAATGA
37429 TCACT
1 TCACT
37434 CTACCACCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (32 bp):
TCACTAATGTTATCGATTTGTAACAAAAATGA
Found at i:37959 original size:31 final size:31
Alignment explanation
Indices: 37924--38001 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
37914 ATGACGGTGG
*
37924 AGTGACCATTTTGTTACAAATCGATAACATT
1 AGTGACCATTTTGTTACAAATCAATAACATT
* *
37955 AGTGACTATTTTGTTATAAATCAATAACATT
1 AGTGACCATTTTGTTACAAATCAATAACATT
*
37986 AATGACCGA-TTTGTTA
1 AGTGACC-ATTTTGTTA
38002 TTTTTGAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCAATAACATT
Found at i:38307 original size:4 final size:4
Alignment explanation
Indices: 38300--38354 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
38290 TATATATATA
* * * * * *
38300 TATG TATG CATG CATG CATG CATG CATG TATG TATG TATG TTTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
38348 TATG TAT
1 TATG TAT
38355 TATAAATCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:39767 original size:14 final size:14
Alignment explanation
Indices: 39748--39809 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
39738 CTTAAGATCT
*
39748 TAAATTCTAAACCC
1 TAAACTCTAAACCC
39762 TAAA-T-TATAACCC
1 TAAACTCTA-AACCC
*
39775 TATAACCTCTAAACCA
1 TA-AA-CTCTAAACCC
*
39791 TAAGCTCTAAACCC
1 TAAACTCTAAACCC
39805 TAAAC
1 TAAAC
39810 CCTAGCCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 2 0.05
13 8 0.21
14 19 0.49
15 1 0.03
16 7 0.18
17 2 0.05
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.26
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:54017 original size:12 final size:12
Alignment explanation
Indices: 54002--54034 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
53992 CGATTCTCGG
54002 CCCAATACCTGA
1 CCCAATACCTGA
*
54014 CCCAATACCTGG
1 CCCAATACCTGA
54026 CCCAATACC
1 CCCAATACC
54035 CGTTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.45, G:0.09, T:0.15
Consensus pattern (12 bp):
CCCAATACCTGA
Found at i:54314 original size:17 final size:17
Alignment explanation
Indices: 54292--54327 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54282 AATCACACTA
54292 AATTTATTTTCTGAATT
1 AATTTATTTTCTGAATT
54309 AATTTATTTTCTGAATT
1 AATTTATTTTCTGAATT
54326 AA
1 AA
54328 AAATCACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
AATTTATTTTCTGAATT
Found at i:61937 original size:29 final size:29
Alignment explanation
Indices: 61873--61929 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
61863 CAAAGCATAG
*
61873 TAACTGTAAGAAATGCTTGCAGCCAATAT
1 TAACAGTAAGAAATGCTTGCAGCCAATAT
* *
61902 TAACAGTAAGACATGTTTGCAGCCAATA
1 TAACAGTAAGAAATGCTTGCAGCCAATA
61930 ATTTCAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (29 bp):
TAACAGTAAGAAATGCTTGCAGCCAATAT
Found at i:62070 original size:2 final size:2
Alignment explanation
Indices: 62063--62104 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
62053 ACAACTTGTT
62063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62105 GTACATCGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71552 original size:26 final size:25
Alignment explanation
Indices: 71523--71573 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
71513 TATTTCAAAA
**
71523 ATTTTGTATTTTTTAAATATAATTTT
1 ATTTTGTAAATTTTAAATA-AATTTT
*
71549 ATTTTTTAAATTTTAAATAAATTTT
1 ATTTTGTAAATTTTAAATAAATTTT
71574 TAAAATTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTTGTAAATTTTAAATAAATTTT
Found at i:72941 original size:14 final size:14
Alignment explanation
Indices: 72922--72948 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72912 TTTATCTTAA
72922 AAATTATAGAAATC
1 AAATTATAGAAATC
72936 AAATTATAGAAAT
1 AAATTATAGAAAT
72949 ATCGAAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AAATTATAGAAATC
Found at i:73023 original size:27 final size:27
Alignment explanation
Indices: 72973--73045 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
72963 AAAAAGGTTT
72973 TTAAGTGTCAAAGTGAAGCAAAAACAG
1 TTAAGTGTCAAAGTGAAGCAAAAACAG
*
73000 CTTAAGTGTTAAA-TGAAGCAAAAACAG
1 -TTAAGTGTCAAAGTGAAGCAAAAACAG
73027 TTCAAGTGTCAAAGTGAAG
1 TT-AAGTGTCAAAGTGAAG
73046 GCACAGATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 2 0.05
27 23 0.56
28 16 0.39
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (27 bp):
TTAAGTGTCAAAGTGAAGCAAAAACAG
Found at i:78214 original size:17 final size:17
Alignment explanation
Indices: 78180--78231 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
78170 ACCGGACAAA
* *
78180 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
78197 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
78214 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
78229 TTT
1 TTT
78232 CTACTGTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:91636 original size:39 final size:39
Alignment explanation
Indices: 91587--91725 Score: 174
Period size: 39 Copynumber: 3.6 Consensus size: 39
91577 TTCAACATAA
* *
91587 AAGA-AGAACTTCTCTAGGTATAGACAGTGGGAACCATT
1 AAGATAGAACTTCTCTAGGTATGGACAGTGGAAACCATT
* *
91625 AAGAAATAACTTCAT-TAGGTATGGACAGTGGAAACCATT
1 AAGATAGAACTTC-TCTAGGTATGGACAGTGGAAACCATT
* * * *
91664 AGGATAGAACATCTTTAGGTATGGACAATGGAAACCATT
1 AAGATAGAACTTCTCTAGGTATGGACAGTGGAAACCATT
*
91703 AAGATGGAACTTCTCTAGGTATG
1 AAGATAGAACTTCTCTAGGTATG
91726 AAAACTGGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 5 0.06
39 80 0.93
40 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (39 bp):
AAGATAGAACTTCTCTAGGTATGGACAGTGGAAACCATT
Found at i:94349 original size:81 final size:81
Alignment explanation
Indices: 94214--94376 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
94204 GAGACTGCTG
94214 ATGAGAGGTCTTTGGGCCATGGAAAAAGAGAATTCACATCACCATTGGGATTAACCACATAAGAA
1 ATGAGAGGTCTTTGGGCCATGGAAAAAGAGAATTCACATCACCATTGGGATTAACCACATAAGAA
94279 GAAGCTGGGCATGGAA
66 GAAGCTGGGCATGGAA
*
94295 ATGAGAGGTTTTTGGGCCATGGAAAAAGAGAATTCACATCACCATTGGGATTAACCACATAAGAA
1 ATGAGAGGTCTTTGGGCCATGGAAAAAGAGAATTCACATCACCATTGGGATTAACCACATAAGAA
*
94360 GAAGCTGGGCTTGGAA
66 GAAGCTGGGCATGGAA
94376 A
1 A
94377 GGATGATGAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (81 bp):
ATGAGAGGTCTTTGGGCCATGGAAAAAGAGAATTCACATCACCATTGGGATTAACCACATAAGAA
GAAGCTGGGCATGGAA
Found at i:99852 original size:23 final size:23
Alignment explanation
Indices: 99832--99898 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
99822 TTTATTTATT
99832 GTTCATGAACATGTTCATTTACC
1 GTTCATGAACATGTTCATTTACC
* ** *
99855 GTTCATGAATATGTTTGTTTAAC
1 GTTCATGAACATGTTCATTTACC
* * *
99878 GTTCGTGAACATATTCGTTTA
1 GTTCATGAACATGTTCATTTA
99899 TATATTCAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (23 bp):
GTTCATGAACATGTTCATTTACC
Found at i:102863 original size:10 final size:9
Alignment explanation
Indices: 102841--102880 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
102831 TAATTTACTC
*
102841 TTTTTATTA
1 TTTTTAATA
102850 TTTTTAATA
1 TTTTTAATA
102859 TTTTTAATA
1 TTTTTAATA
*
102868 TTTTTAAAA
1 TTTTTAATA
102877 TTTT
1 TTTT
102881 CAATTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTAATA
Found at i:103394 original size:15 final size:15
Alignment explanation
Indices: 103376--103441 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
103366 TTTCGGAAAA
103376 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
103391 TGAATTACTGAAATT
1 TGAATTACTGGAATT
* **
103406 TGAATTATTGGAAAA
1 TGAATTACTGGAATT
103421 TGAATTACTGGAATT
1 TGAATTACTGGAATT
103436 TGAATT
1 TGAATT
103442 CTGTAAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:103412 original size:30 final size:30
Alignment explanation
Indices: 103376--103457 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
103366 TTTCGGAAAA
**
103376 TGAATTACTGGAATTTGAATTACTGAAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
* *
103406 TGAATTATTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGAAATT
*
103436 TGAATT-CTGTAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
103458 ATTTTTGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 14 0.30
30 32 0.70
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGAAATT
Found at i:103455 original size:14 final size:15
Alignment explanation
Indices: 103370--103457 Score: 90
Period size: 15 Copynumber: 5.9 Consensus size: 15
103360 TTGGTTTTTC
103370 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
103385 GGAATTTGAATTACT
1 GGAAAATGAATTACT
* *
103400 -GAAATTTGAATTATT
1 GGAAA-ATGAATTACT
103415 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
103430 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
*
103444 GTAAAATGAATTAC
1 GGAAAATGAATTAC
103458 ATTTTTGGAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
14 14 0.24
15 41 0.69
16 4 0.07
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:103743 original size:33 final size:33
Alignment explanation
Indices: 103705--103783 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
103695 TAATTTTATT
103705 AATAAAAATATTAATTTTTGTATATTTTAGTGA
1 AATAAAAATATTAATTTTTGTATATTTTAGTGA
103738 AATAAAAATATTAATTTTTGTATATTTTAGTGA
1 AATAAAAATATTAATTTTTGTATATTTTAGTGA
103771 AATAAAAATATTA
1 AATAAAAATATTA
103784 TAAATTATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.46
Consensus pattern (33 bp):
AATAAAAATATTAATTTTTGTATATTTTAGTGA
Found at i:103829 original size:28 final size:30
Alignment explanation
Indices: 103789--103852 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 30
103779 TATTATAAAT
* *
103789 TATATTAATTATTTATTAAAATAATAGTTA-
1 TATATTAATTATTT-TAAAAATAATAATTAG
*
103819 TATATT-A-TATTTTAAAAATATTAATTAG
1 TATATTAATTATTTTAAAAATAATAATTAG
103847 TATATT
1 TATATT
103853 TTAAATATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 12 0.40
28 11 0.37
29 1 0.03
30 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
TATATTAATTATTTTAAAAATAATAATTAG
Found at i:103874 original size:23 final size:23
Alignment explanation
Indices: 103825--103887 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
103815 GTTATATATT
* **
103825 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
103848 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
103871 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
103888 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:103883 original size:11 final size:11
Alignment explanation
Indices: 103863--103908 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
103853 TTAAATATCT
103863 TTATTAAAATA
1 TTATTAAAATA
*
103874 TTATTTAAATA
1 TTATTAAAATA
*
103885 -TATAAATAATA
1 TTATTAA-AATA
103896 TTATT-AAATA
1 TTATTAAAATA
103906 TTA
1 TTA
103909 AATATTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 11 0.38
11 15 0.52
12 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:103898 original size:22 final size:20
Alignment explanation
Indices: 103870--103912 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 20
103860 TCTTTATTAA
103870 AATATTATTTAAATATATAAAT
1 AATATTA-TTAAATAT-TAAAT
103892 AATATTATTAAATATTAAAT
1 AATATTATTAAATATTAAAT
103912 A
1 A
103913 TTAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTATTAAATATTAAAT
Found at i:103909 original size:7 final size:7
Alignment explanation
Indices: 103878--103925 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
103868 AAAATATTAT
103878 TTAAATA
1 TTAAATA
103885 TATAAATA
1 T-TAAATA
* *
103893 AT-ATTA
1 TTAAATA
103899 TTAAATA
1 TTAAATA
103906 TTAAATA
1 TTAAATA
103913 TTAAATA
1 TTAAATA
103920 TATAAA
1 T-TAAA
103926 AAAAATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
6 4 0.12
7 20 0.59
8 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATA
Found at i:103963 original size:24 final size:24
Alignment explanation
Indices: 103879--103968 Score: 64
Period size: 24 Copynumber: 3.8 Consensus size: 24
103869 AAATATTATT
*
103879 TAAATATATAAATAATATTATT-AAA
1 TAAAAATAT-AAT-ATATTATTAAAA
*
103904 TATTAAATATTAA-ATA-TA-TAAAA
1 TA-AAAATA-TAATATATTATTAAAA
* *
103927 -AAAATTATTATATATTATTAAAA
1 TAAAAATATAATATATTATTAAAA
*
103950 TAAAAATATAATATCTTAT
1 TAAAAATATAATATATTAT
103969 ATTATTATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 4 0.08
23 10 0.20
24 18 0.36
25 2 0.04
26 6 0.12
27 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAAAATATAATATATTATTAAAA
Found at i:104213 original size:42 final size:42
Alignment explanation
Indices: 104151--104267 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
104141 AATTACGTTA
* * * * * *
104151 CGGAAAACCAATTACATGAAATAAATATTGGAAAATATTTTC
1 CGGAAAACAAATTACGTGAAACAAACATGGGAAAACATTTTC
104193 CGGAAAACAAATTACGTGAAACAAACATGGGAAAACATTTTC
1 CGGAAAACAAATTACGTGAAACAAACATGGGAAAACATTTTC
* * *
104235 CGAAAAACGAATTACGTGAAACAAACACGGGAA
1 CGGAAAACAAATTACGTGAAACAAACATGGGAA
104268 TTCGGGGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (42 bp):
CGGAAAACAAATTACGTGAAACAAACATGGGAAAACATTTTC
Found at i:105325 original size:18 final size:19
Alignment explanation
Indices: 105291--105327 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
105281 ACGGAATGTG
105291 AGATTACCAGTGGGAATAAA
1 AGATTACCAG-GGGAATAAA
105311 AGATTACCA-GGGAATAA
1 AGATTACCAGGGGAATAA
105328 GATTAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AGATTACCAGGGGAATAAA
Found at i:108747 original size:24 final size:22
Alignment explanation
Indices: 108704--108747 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
108694 ATTATCAAAT
**
108704 TTTATATATTTTATTCTTTTAA
1 TTTATATATTTTATAATTTTAA
108726 TTTATAATAATTTTATAATTTT
1 TTTAT-AT-ATTTTATAATTTT
108748 TCAGTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATATATTTTATAATTTTAA
Done.