Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006906.1 Hibiscus syriacus cultivar Beakdansim tig00017644_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: 100728
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4309 original size:24 final size:22
Alignment explanation
Indices: 4282--4349 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 22
4272 ATACTTTTTA
4282 TTTTTTATACTTGAGGTCTTTAA-
1 TTTTTTATA-TT-AGGTCTTTAAT
4305 TTTTTT-T-TTA-GT-TTT-AT
1 TTTTTTATATTAGGTCTTTAAT
4322 TTTTTTATAATTAAGGTCTTTAAT
1 TTTTTTAT-ATT-AGGTCTTTAAT
4346 TTTT
1 TTTT
4350 GTAATCTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
16 1 0.03
17 9 0.24
18 3 0.08
19 1 0.03
20 4 0.11
21 1 0.03
22 3 0.08
23 9 0.24
24 6 0.16
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (22 bp):
TTTTTTATATTAGGTCTTTAAT
Found at i:4679 original size:43 final size:42
Alignment explanation
Indices: 4406--4695 Score: 206
Period size: 42 Copynumber: 6.9 Consensus size: 42
4396 ATATTTTACA
* * * *
4406 TTATAATTAAGGTCCTTAATGTTTTCAATCTCACTTTTTACCT
1 TTATAATTGA-GTCCCTAATTTTTTCAATATCACTTTTTACCT
* * *
4449 TTATAATTGAGTCCCTATTTTTTTCAATATCGCTTTCTACCT
1 TTATAATTGAGTCCCTAATTTTTTCAATATCACTTTTTACCT
* *
4491 TTATAATCGAAG-CCCGTAA-TTTTT-AATCTCACTTTTTACC-
1 TTATAATTG-AGTCCC-TAATTTTTTCAATATCACTTTTTACCT
* * *
4531 TTATAATT-AGACTCCT-AGTTTTT--ATCTCA-TCTTTTACCT
1 TTATAATTGAGTC-CCTAATTTTTTCAATATCACT-TTTTACCT
* * *
4570 TTATAATTGAAGCCCCCTAATTTTTT-AATCA-AACTTTTTACAT
1 TTATAATTG-AG-TCCCTAATTTTTTCAAT-ATCACTTTTTACCT
* * * *
4613 TTATATCTTTGAGGCACTTAATTTTTTCAATATCATTTTTTACCT
1 TTATA--ATTGAGTC-CCTAATTTTTTCAATATCACTTTTTACCT
*
4658 TTATTATTGATGTCCCTAATTTTTTTCAATATCACTTT
1 TTATAATTGA-GTCCCTAA-TTTTTTCAATATCACTTT
4696 CTAAATTTGT
Statistics
Matches: 197, Mismatches: 29, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
37 1 0.01
38 16 0.08
39 15 0.08
40 9 0.05
41 18 0.09
42 49 0.25
43 37 0.19
44 33 0.17
45 19 0.10
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (42 bp):
TTATAATTGAGTCCCTAATTTTTTCAATATCACTTTTTACCT
Found at i:4711 original size:44 final size:44
Alignment explanation
Indices: 4364--4726 Score: 115
Period size: 44 Copynumber: 8.6 Consensus size: 44
4354 TCTCCTTTTT
* *** *
4364 ATTTATAATTGAAGCCCCTAATTTTTTACCCCAT-A-TTT-TAC
1 ATTTATAATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
* * * * * *
4405 A-TTATAATT-AAGGTCCTTAA-TGTTTTCAATCTCACTTTTTAC
1 ATTTATAATTGAA-GCCCCTAATTTTTTTCAATATCACTTTCTAA
* * * *
4447 CTTTATAATTG-AGTCCCT-ATTTTTTTCAATATCGCTTTCTAC
1 ATTTATAATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
* * * * *
4489 CTTTATAATCGAAGCCCGTAA--TTTTT-AATCTCACTTT-TTA
1 ATTTATAATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
** * * * *
4529 CCTTATAATT--AGACTCCT-A-GTTTTT--ATCTCATCTTT-TAC
1 ATTTATAATTGAAG-CCCCTAATTTTTTTCAATATCA-CTTTCTAA
* * * *
4568 CTTTATAATTGAAGCCCCCTAA-TTTTTT-AATCA-AACTTTTTAC
1 ATTTATAATTGAAG-CCCCTAATTTTTTTCAAT-ATCACTTTCTAA
* * * * * * *
4611 ATTTATATCTTTGAGGCACTTAA-TTTTTTCAATATCATTTTTTAC
1 ATTTATA--ATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
* * * *
4656 CTTTATTATTGATGTCCCTAATTTTTTTCAATATCACTTTCTAA
1 ATTTATAATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
* *
4700 ATTTGTAATTGAAGCCCCTAATCTTTT
1 ATTTATAATTGAAGCCCCTAATTTTTT
4727 AATCTATTGA
Statistics
Matches: 243, Mismatches: 56, Indels: 43
0.71 0.16 0.13
Matches are distributed among these distances:
38 9 0.04
39 30 0.12
40 24 0.10
41 20 0.08
42 51 0.21
43 35 0.14
44 53 0.22
45 21 0.09
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (44 bp):
ATTTATAATTGAAGCCCCTAATTTTTTTCAATATCACTTTCTAA
Found at i:7896 original size:27 final size:28
Alignment explanation
Indices: 7866--7918 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
7856 TATTTTTGTT
*
7866 TTAACTTATTAAATAT-TTTTATTTTTC
1 TTAACTTATTAAATATATTTGATTTTTC
* *
7893 TTAATTTATTAAGTATATTTGATTTT
1 TTAACTTATTAAATATATTTGATTTT
7919 ATTTAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (28 bp):
TTAACTTATTAAATATATTTGATTTTTC
Found at i:8084 original size:33 final size:33
Alignment explanation
Indices: 7988--8085 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 33
7978 ATATAACTTG
* * *
7988 AAATATATTTAAACATTTTAATATTAATTTAATATA
1 AAATATATAT-AATATTTTAATATT--TTTTATATA
* *
8024 AAA-ATATAT-ATATTTTAATCTTATTTTTATTTA
1 AAATATATATAATATTTTAAT-AT-TTTTTATATA
8057 AAATATATATAATATTTTAATATTTTTTA
1 AAATATATATAATATTTTAATATTTTTTA
8086 AAAGTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
33 25 0.48
34 8 0.15
35 16 0.31
36 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (33 bp):
AAATATATATAATATTTTAATATTTTTTATATA
Found at i:8121 original size:26 final size:26
Alignment explanation
Indices: 8092--8223 Score: 79
Period size: 26 Copynumber: 4.7 Consensus size: 26
8082 TTTAAAAGTT
8092 AATAATAAAATATATTTTTAAATTAA
1 AATAATAAAATATATTTTTAAATTAA
* * *
8118 AATAAGAAAAAATAATTTTTAAGTAAGATAA
1 AATAATAAAATAT-ATTTTT-A--AA-TTAA
*
8149 GAATAA-AATATATATATTTTTTAATTTAA
1 -AATAATAA-A-ATATA-TTTTTAAATTAA
*
8178 AATAAGAGTAAAATATATTTTTATATTAA
1 AAT-A-A-TAAAATATATTTTTAAATTAA
*
8207 ATTAATAATAA-ATATTT
1 AATAATAA-AATATATTT
8224 AAATATATTT
Statistics
Matches: 83, Mismatches: 9, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
26 20 0.24
27 9 0.11
28 5 0.06
29 16 0.19
30 9 0.11
31 6 0.07
32 10 0.12
33 8 0.10
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATAAAATATATTTTTAAATTAA
Found at i:8218 original size:29 final size:29
Alignment explanation
Indices: 8095--8218 Score: 119
Period size: 29 Copynumber: 4.2 Consensus size: 29
8085 AAAAGTTAAT
*
8095 AATAAAATATATTTTTAAATTAAAATAAG
1 AATAAAATATATTTTTATATTAAAATAAG
* *
8124 AA-AAAATA-ATTTTTA-AGTAAGATAAG
1 AATAAAATATATTTTTATATTAAAATAAG
*
8150 AATAAAATATATATATTTTTTAATTTAAAATAAG
1 AAT-AAA-ATATAT-TTTTAT-A-TTAAAATAAG
* * *
8184 AGTAAAATATATTTTTATATTAAATTAAT
1 AATAAAATATATTTTTATATTAAAATAAG
8213 AATAAA
1 AATAAA
8219 TATTTAAATA
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
26 11 0.14
27 7 0.09
28 9 0.12
29 18 0.23
30 3 0.04
31 9 0.12
32 6 0.08
33 4 0.05
34 10 0.13
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
AATAAAATATATTTTTATATTAAAATAAG
Found at i:8348 original size:29 final size:29
Alignment explanation
Indices: 8304--8365 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
8294 ATATTAAAAT
*
8304 AAAAAACAAAATATATTTAATAATTTAAGA
1 AAAAAACAAAATATATTTAATAAATTAA-A
*
8334 AAAAAATAAAA-ATATTTAATAAATTAAA
1 AAAAAACAAAATATATTTAATAAATTAAA
8362 AAAA
1 AAAA
8366 TGAAGAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.17
29 15 0.50
30 10 0.33
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAAAACAAAATATATTTAATAAATTAAA
Found at i:10818 original size:15 final size:15
Alignment explanation
Indices: 10796--10838 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10786 AGAAAATATA
10796 CGAATAACACATACT
1 CGAATAACACATACT
* *
10811 CGATTAACATATACT
1 CGAATAACACATACT
*
10826 CGAATACCACATA
1 CGAATAACACATA
10839 TCCGAATTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (15 bp):
CGAATAACACATACT
Found at i:11315 original size:236 final size:236
Alignment explanation
Indices: 10902--11341 Score: 871
Period size: 236 Copynumber: 1.9 Consensus size: 236
10892 GAACATAAAG
*
10902 CATAATATGAATCCGATAAATATCACATGTTACATAACGTAATTTTATGAATTCCAACTGATACA
1 CATAATATGAATCCGATAAATATCACATGTCACATAACGTAATTTTATGAATTCCAACTGATACA
10967 ACAATATCATAGAATAATCATGCTTGAAACCAATTTCCAAACAACATGCTTAACCGAATTATATT
66 ACAATATCATAGAATAATCATGCTTGAAACCAATTTCCAAACAACATGCTTAACCGAATTATATT
11032 TAAAGCAACATAACACATAACAGTTAAGCTCACAATCAATTCCAAACAATCAAACAATTTAACAC
131 TAAAGCAACATAACACATAACAGTTAAGCTCACAATCAATTCCAAACAATCAAACAATTTAACAC
11097 AGAACAAATTTCCAACTGATACAACAATATCATAGAATAAT
196 AGAACAAATTTCCAACTGATACAACAATATCATAGAATAAT
11138 CATAATATGAATCCGATAAATATCACATGTCACATAACGTAATTTTATGAATTCCAACTGATACA
1 CATAATATGAATCCGATAAATATCACATGTCACATAACGTAATTTTATGAATTCCAACTGATACA
11203 ACAATATCATAGAATAATCATGCTTGAAACCAATTTCCAAACAACATGCTTAACCGAATTATATT
66 ACAATATCATAGAATAATCATGCTTGAAACCAATTTCCAAACAACATGCTTAACCGAATTATATT
11268 TAAAGCAACATAACACATAACAGTTAAGCTCACAATCAATTCCAAACAATCAAACAATTTAACAC
131 TAAAGCAACATAACACATAACAGTTAAGCTCACAATCAATTCCAAACAATCAAACAATTTAACAC
11333 AGAACAAAT
196 AGAACAAAT
11342 ATAGCACCGG
Statistics
Matches: 203, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
236 203 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (236 bp):
CATAATATGAATCCGATAAATATCACATGTCACATAACGTAATTTTATGAATTCCAACTGATACA
ACAATATCATAGAATAATCATGCTTGAAACCAATTTCCAAACAACATGCTTAACCGAATTATATT
TAAAGCAACATAACACATAACAGTTAAGCTCACAATCAATTCCAAACAATCAAACAATTTAACAC
AGAACAAATTTCCAACTGATACAACAATATCATAGAATAAT
Found at i:11716 original size:22 final size:22
Alignment explanation
Indices: 11691--11749 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
11681 CAGGTTTGGT
11691 TCGAATATAGCATTCTGCCAGA
1 TCGAATATAGCATTCTGCCAGA
11713 TCGAATATAGCATTCTGCCAGA
1 TCGAATATAGCATTCTGCCAGA
*
11735 TCGAATATAACATTC
1 TCGAATATAGCATTC
11750 GTAAAACTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (22 bp):
TCGAATATAGCATTCTGCCAGA
Found at i:11801 original size:20 final size:20
Alignment explanation
Indices: 11772--11809 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11762 AACTGATTAG
11772 TATAAAGTAATAGGTAAATT
1 TATAAAGTAATAGGTAAATT
* *
11792 TATAATGTAATCGGTAAA
1 TATAAAGTAATAGGTAAA
11810 AGTATACCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (20 bp):
TATAAAGTAATAGGTAAATT
Found at i:11815 original size:20 final size:20
Alignment explanation
Indices: 11770--11815 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11760 GAAACTGATT
11770 AGTATAAAGTAATAGGTAAA
1 AGTATAAAGTAATAGGTAAA
** * *
11790 TTTATAATGTAATCGGTAAA
1 AGTATAAAGTAATAGGTAAA
11810 AGTATA
1 AGTATA
11816 CCGATTTAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTATAAAGTAATAGGTAAA
Found at i:15083 original size:6 final size:6
Alignment explanation
Indices: 15072--15171 Score: 58
Period size: 6 Copynumber: 16.7 Consensus size: 6
15062 TTTATGTAAT
* * * *
15072 TTTCAA TTTCAA TTTC-A TACTGAA TTTCAT TTTCAA TTTCAA TTTTAA
1 TTTCAA TTTCAA TTTCAA T-TTCAA TTTCAA TTTCAA TTTCAA TTTCAA
** * * * * * * * *
15120 TTGGAG TTTGAA TTTGAA TTTGAA TTTGAG TTTGAA TTTCAA TTTAAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
15168 TTTC
1 TTTC
15172 GCCTCCACTA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
5 2 0.03
6 71 0.95
7 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (6 bp):
TTTCAA
Found at i:15121 original size:24 final size:24
Alignment explanation
Indices: 15072--15171 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
15062 TTTATGTAAT
* *
15072 TTTCAATTTCAATTTC-ATACTGAA
1 TTTCAGTTTCAATTTCAAT-TTGAA
* *
15096 TTTCATTTTCAATTTCAATTTTAA
1 TTTCAGTTTCAATTTCAATTTGAA
** * *
15120 TTGGAGTTTGAATTTGAATTTGAA
1 TTTCAGTTTCAATTTCAATTTGAA
* * *
15144 TTTGAGTTTGAATTTCAATTTAAA
1 TTTCAGTTTCAATTTCAATTTGAA
15168 TTTC
1 TTTC
15172 GCCTCCACTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
24 60 0.97
25 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTTCAATTTCAATTTGAA
Found at i:15169 original size:12 final size:12
Alignment explanation
Indices: 15072--15171 Score: 76
Period size: 12 Copynumber: 8.3 Consensus size: 12
15062 TTTATGTAAT
*
15072 TTTCAATTTCAA
1 TTTCAATTTGAA
*
15084 TTTC-ATACTGAA
1 TTTCAAT-TTGAA
* *
15096 TTTCATTTTCAA
1 TTTCAATTTGAA
*
15108 TTTCAATTTTAA
1 TTTCAATTTGAA
** *
15120 TTGGAGTTTGAA
1 TTTCAATTTGAA
*
15132 TTTGAATTTGAA
1 TTTCAATTTGAA
* *
15144 TTTGAGTTTGAA
1 TTTCAATTTGAA
*
15156 TTTCAATTTAAA
1 TTTCAATTTGAA
15168 TTTC
1 TTTC
15172 GCCTCCACTA
Statistics
Matches: 69, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
11 2 0.03
12 66 0.96
13 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (12 bp):
TTTCAATTTGAA
Found at i:16448 original size:27 final size:28
Alignment explanation
Indices: 16406--16483 Score: 131
Period size: 27 Copynumber: 2.8 Consensus size: 28
16396 TATTGTACAC
16406 AAACTAGTTAAAATTTGACAAAATTT-T
1 AAACTAGTTAAAATTTGACAAAATTTCT
* *
16433 AAATTAGTTGAAATTTGACAAAATTTCT
1 AAACTAGTTAAAATTTGACAAAATTTCT
16461 AAACTAGTTAAAATTTGACAAAA
1 AAACTAGTTAAAATTTGACAAAA
16484 CGGTTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.35
Consensus pattern (28 bp):
AAACTAGTTAAAATTTGACAAAATTTCT
Found at i:16531 original size:19 final size:19
Alignment explanation
Indices: 16467--16521 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
16457 TTCTAAACTA
16467 GTTAAAATTTGACAAAACG
1 GTTAAAATTTGACAAAACG
16486 GTTAAAATTTGACAAAACG
1 GTTAAAATTTGACAAAACG
16505 GTTAAAATTTGACAAAA
1 GTTAAAATTTGACAAAA
16522 TCGATTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (19 bp):
GTTAAAATTTGACAAAACG
Found at i:20239 original size:226 final size:225
Alignment explanation
Indices: 19860--20344 Score: 756
Period size: 226 Copynumber: 2.1 Consensus size: 225
19850 TAACAAATCA
* * * *
19860 AGTAATTAACTGGTTATGTTATCGTCAGATTCCTAAGGCTACATCAACTTAAATTTTGTTAACAT
1 AGTAATTAAC-GGTTATGCTATCGTCAGATTTCTAAGGCTACATCAACTTAAACTTTGGTAACAT
* *
19925 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
65 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTCGTTAT
19990 CGTCGAATTTCTAAGGCCCCATCAGCTTTAATAATGA-GCTACCTATTACGTTACATAAGCGCTA
130 CGTCGAATTTCTAAGGCCCCATCAGCTTTAATAAT-ACGCTACCTATTACGTTACATAAGCGCTA
20054 CCTAATATGTTATTATGCTTGATAATGTTTCC
194 CCTAATATGTTATTATGCTTGATAATGTTTCC
* * * * *
20086 AGTAATTAATCGGTTATGCTATCGTCGGATTTCTAAGGCTTCATTAGCTTAAACTTTGGTAATAT
1 AGTAATTAA-CGGTTATGCTATCGTCAGATTTCTAAGGCTACATCAACTTAAACTTTGGTAACAT
20151 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTCGTTAT
65 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTCGTTAT
* * * * *
20216 CGTTGGATTTCTAGGGCCCCATCAGCTTTAATAATACGCTACCTATTACGTTACATAAGTGCTAT
130 CGTCGAATTTCTAAGGCCCCATCAGCTTTAATAATACGCTACCTATTACGTTACATAAGCGCTAC
20281 CTAATATGTTATTATGCTTGATAATGTTTCC
195 CTAATATGTTATTATGCTTGATAATGTTTCC
* * *
20312 AATAATTAACCGGTTATACTATAGTCAGATTTC
1 AGTAATTAA-CGGTTATGCTATCGTCAGATTTC
20345 CAAAGCCCCA
Statistics
Matches: 236, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
225 1 0.00
226 234 0.99
227 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (225 bp):
AGTAATTAACGGTTATGCTATCGTCAGATTTCTAAGGCTACATCAACTTAAACTTTGGTAACATT
TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTCGTTATC
GTCGAATTTCTAAGGCCCCATCAGCTTTAATAATACGCTACCTATTACGTTACATAAGCGCTACC
TAATATGTTATTATGCTTGATAATGTTTCC
Found at i:20374 original size:118 final size:118
Alignment explanation
Indices: 20231--20446 Score: 324
Period size: 118 Copynumber: 1.8 Consensus size: 118
20221 GATTTCTAGG
* * * * * * *
20231 GCCCCATCAGCTTTAATAATACGCTACCTATTACGTTACATAAGTGCTATCTAATATGTTATTAT
1 GCCCCATCAGCTTTAAAAAGACGCTACCTATCACATTACATAAGCGCTACCTAATATATTATTAT
* *
20296 GCTTGATAATGTTTCCAATAATTAACCGGTTATACTATAGTCAGATTTCCAAA
66 GCTTGATAATGTTTCCAACAATTAACCGATTATACTATAGTCAGATTTCCAAA
* * *
20349 GCCCCATCAGTTTTAAAAAGGCGCTACCTATCACATTATATAAGCGCTACCTAATATATTATTAT
1 GCCCCATCAGCTTTAAAAAGACGCTACCTATCACATTACATAAGCGCTACCTAATATATTATTAT
20414 GCTTGATAATGTTTCCAACAATTAACCGATTAT
66 GCTTGATAATGTTTCCAACAATTAACCGATTAT
20447 GTTATCGTCT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 86 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (118 bp):
GCCCCATCAGCTTTAAAAAGACGCTACCTATCACATTACATAAGCGCTACCTAATATATTATTAT
GCTTGATAATGTTTCCAACAATTAACCGATTATACTATAGTCAGATTTCCAAA
Found at i:23609 original size:65 final size:65
Alignment explanation
Indices: 23505--23635 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 65
23495 TGCTACTTTC
* *
23505 TCCTAAAGCTAACATTGCCTCATCATGCACTTTTGAGTATTGCTTGTTGAGTCCGTTGGATTCTA
1 TCCTAAAGCTAACATTACCTCATCATGCACTTTTGAGTATTGCTCGTTGAGTCCGTTGGATTCTA
23570 TCCTAGAA-CTAACATTACCTCATCATGCACTTTTGAGTATTGCTCGTTGAGTCCGTTGGATTCT
1 TCCTA-AAGCTAACATTACCTCATCATGCACTTTTGAGTATTGCTCGTTGAGTCCGTTGGATTCT
23634 A
65 A
23635 T
1 T
23636 GTTTCTCCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 61 0.97
66 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (65 bp):
TCCTAAAGCTAACATTACCTCATCATGCACTTTTGAGTATTGCTCGTTGAGTCCGTTGGATTCTA
Found at i:26476 original size:104 final size:103
Alignment explanation
Indices: 26297--26484 Score: 288
Period size: 104 Copynumber: 1.8 Consensus size: 103
26287 TTTGAAAAGA
* * *
26297 ACTTTTGCTATTTGCCAAAAGGGAAAAATGTGACTTTTTCTTTAACATGTCTATGTTGCTTTACC
1 ACTTTTGATATTTGCCAAAAGGGAAAAATGTGACTTTTGCTTCAACATGTCTATGTTGCTTTACC
*
26362 GATTTCATGTTCAAACAACTTGTAGTAAGTAATTTGCT
66 AATTTCATGTTCAAACAACTTGTAGTAAGTAATTTGCT
*
26400 ACTTTTGATATTTTCCAAAAGGGAAAAAATGTGACTTTTGCTTCAACATGTCTATGTTGCTTTAC
1 ACTTTTGATATTTGCCAAAAGGG-AAAAATGTGACTTTTGCTTCAACATGTCTATGTTGCTTTAC
* *
26465 TAAGTTT-ATGTTCAAGCAAC
65 CAA-TTTCATGTTCAAACAAC
26485 CTGCAGTAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
103 21 0.28
104 52 0.68
105 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (103 bp):
ACTTTTGATATTTGCCAAAAGGGAAAAATGTGACTTTTGCTTCAACATGTCTATGTTGCTTTACC
AATTTCATGTTCAAACAACTTGTAGTAAGTAATTTGCT
Found at i:31751 original size:22 final size:22
Alignment explanation
Indices: 31726--31768 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31716 TAGCTAAGTC
31726 AGGA-ATTGGTTAGTGA-CTGTGG
1 AGGATATT-GTTAG-GAGCTGTGG
31748 AGGATATTGTTAGGAGCTGTG
1 AGGATATTGTTAGGAGCTGTG
31769 CTTTTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 14 0.74
23 3 0.16
ACGTcount: A:0.23, C:0.05, G:0.40, T:0.33
Consensus pattern (22 bp):
AGGATATTGTTAGGAGCTGTGG
Found at i:45145 original size:23 final size:23
Alignment explanation
Indices: 45119--45163 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
45109 CACCACAGCT
*
45119 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
45142 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
45164 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:45430 original size:149 final size:147
Alignment explanation
Indices: 45142--45443 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 147
45132 CGAAGTGCCC
*
45142 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
45207 CATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 CATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
45272 TATGTCCCGAAGAACCG
131 TATGTCCCGAAGAACCG
45289 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
45354 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 C--ATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
45419 CATATGTCCCGAAGAACCG
129 CATATGTCCCGAAGAACCG
45438 CGTAGA
1 CGTAGA
45444 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 65 0.43
149 87 0.57
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCG
Found at i:46332 original size:18 final size:18
Alignment explanation
Indices: 46311--46345 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46301 TCCCATCTAG
46311 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
46329 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
46346 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:46952 original size:21 final size:21
Alignment explanation
Indices: 46928--46972 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46918 TCTTGTTCGT
* * *
46928 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGATACCGATTCCCC
*
46949 TTGAATGGATACCGATTCCCC
1 TTGAAGGGATACCGATTCCCC
46970 TTG
1 TTG
46973 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGATACCGATTCCCC
Found at i:50351 original size:149 final size:149
Alignment explanation
Indices: 50170--50473 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
50160 GAGTCGAGGG
*
50170 TCTACGTGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
50235 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
50300 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
50319 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
50384 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
50449 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
50468 TCTACG
1 TCTACG
50474 GGGCACTACG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:50474 original size:13 final size:13
Alignment explanation
Indices: 50456--50497 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
50446 TTATATGGCA
50456 CTACGGTGCAATT
1 CTACGGTGCAATT
*
50469 CTACGGGGC-A--
1 CTACGGTGCAATT
50479 CTACGGTGCAATT
1 CTACGGTGCAATT
50492 CTACGG
1 CTACGG
50498 GGTACTTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.33
11 1 0.04
12 1 0.04
13 14 0.58
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:50519 original size:23 final size:23
Alignment explanation
Indices: 50452--50511 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
50442 ATCATTATAT
50452 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTCTACGG
50475 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTCTACGG
* *
50498 GGTACTTCGGTGCA
1 GGCACTACGGTGCA
50512 TTTATACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGG
Found at i:54350 original size:27 final size:27
Alignment explanation
Indices: 54312--54371 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
54302 CGTTATTAGT
* *
54312 GAACCGGCCAGAACCGTTGAACTGTTC
1 GAACCGGCCAGAACAGTTGAACCGTTC
*
54339 GAACCGGTCAGAACAGTTGAACCGTTC
1 GAACCGGCCAGAACAGTTGAACCGTTC
54366 GAACCG
1 GAACCG
54372 AACCGACTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (27 bp):
GAACCGGCCAGAACAGTTGAACCGTTC
Found at i:54371 original size:9 final size:9
Alignment explanation
Indices: 54322--54371 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
54312 GAACCGGCCA
54322 GAACCGTT-
1 GAACCGTTC
*
54330 GAACTGTTC
1 GAACCGTTC
*
54339 GAACCGGTC
1 GAACCGTTC
*
54348 AGAACAGTT-
1 -GAACCGTTC
54357 GAACCGTTC
1 GAACCGTTC
54366 GAACCG
1 GAACCG
54372 AACCGACTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 14 0.42
9 13 0.39
10 6 0.18
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (9 bp):
GAACCGTTC
Found at i:55470 original size:30 final size:30
Alignment explanation
Indices: 55418--55494 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
55408 CTTTTAAAAC
** *
55418 TTGCAATACAATCCCTCAACATTTAGTCTGT
1 TTGCAATATGATCCC-CAACATTTAGTCCGT
55449 TTGCAATATGATCCCCAACATTTAGTCCGT
1 TTGCAATATGATCCCCAACATTTAGTCCGT
*
55479 TTACAATATGATCCCC
1 TTGCAATATGATCCCC
55495 GACGTAACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (30 bp):
TTGCAATATGATCCCCAACATTTAGTCCGT
Found at i:59720 original size:17 final size:18
Alignment explanation
Indices: 59695--59728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59685 TCAATATCAT
59695 TATTCTAAA-AAAATAAG
1 TATTCTAAACAAAATAAG
*
59712 TATTTTAAACAAAATAA
1 TATTCTAAACAAAATAA
59729 TAAAGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
TATTCTAAACAAAATAAG
Found at i:59861 original size:20 final size:21
Alignment explanation
Indices: 59838--59894 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
59828 GAACTCCAAT
*
59838 TTCGTAACACAGTTT-CCAGA
1 TTCGCAACACAGTTTCCCAGA
* *
59858 TTCGCAACGCGAATTTCCCAGA
1 TTCGCAACAC-AGTTTCCCAGA
*
59880 TTCGCAACTCAGTTT
1 TTCGCAACACAGTTT
59895 TGAAATTCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.27
21 8 0.27
22 14 0.47
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (21 bp):
TTCGCAACACAGTTTCCCAGA
Found at i:59906 original size:42 final size:42
Alignment explanation
Indices: 59814--59916 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
59804 AAATAACCAA
* *
59814 CAAATTCGCAACGCGAA-CT-CCAATTTCGTAACACAGTTTC
1 CAAATTCGCAACGCGAATTTCCCAATTTCGCAACACAGTTTC
* * *
59854 CAGATTCGCAACGCGAATTTCCCAGA-TTCGCAACTCAGTTTT
1 CAAATTCGCAACGCGAATTTCCCA-ATTTCGCAACACAGTTTC
* * *
59896 GAAATTCGCAACTCAAATTTC
1 CAAATTCGCAACGCGAATTTC
59917 TTTTCCGCAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 16 0.31
41 1 0.02
42 33 0.65
43 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATTTCCCAATTTCGCAACACAGTTTC
Found at i:59965 original size:20 final size:20
Alignment explanation
Indices: 59937--59987 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
59927 CGCGATTTTC
*
59937 TAAATTCGCAACTCAGAAGT
1 TAAATTCGCAACACAGAAGT
*
59957 TAAAATCGCAACACAGAAGT
1 TAAATTCGCAACACAGAAGT
*
59977 CAAATTCGCAA
1 TAAATTCGCAA
59988 AGCGTGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.20
Consensus pattern (20 bp):
TAAATTCGCAACACAGAAGT
Found at i:60181 original size:22 final size:22
Alignment explanation
Indices: 60154--60221 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
60144 TCACTCTCTA
*
60154 CGGTGACATTCGTCCCCATCTC
1 CGGTGACATCCGTCCCCATCTC
* *
60176 TGGTGACATCCATCCCCATCTC
1 CGGTGACATCCGTCCCCATCTC
** *
60198 CGACGACATCCGTCCCCATATC
1 CGGTGACATCCGTCCCCATCTC
60220 CG
1 CG
60222 ACGACCCCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.18, C:0.43, G:0.16, T:0.24
Consensus pattern (22 bp):
CGGTGACATCCGTCCCCATCTC
Found at i:60222 original size:22 final size:22
Alignment explanation
Indices: 60180--60226 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
60170 CATCTCTGGT
*
60180 GACATCCATCCCCATCTCCGAC
1 GACATCCATCCCCATATCCGAC
*
60202 GACATCCGTCCCCATATCCGAC
1 GACATCCATCCCCATATCCGAC
60224 GAC
1 GAC
60227 CCCCCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.47, G:0.13, T:0.17
Consensus pattern (22 bp):
GACATCCATCCCCATATCCGAC
Found at i:60580 original size:20 final size:20
Alignment explanation
Indices: 60568--60606 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
60558 AATTCTTAAT
60568 ACGAAAATGAAATTCGCAAC
1 ACGAAAATGAAATTCGCAAC
60588 ACGAAAATGAAATTCGCAA
1 ACGAAAATGAAATTCGCAA
60607 TGCGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
ACGAAAATGAAATTCGCAAC
Found at i:62217 original size:42 final size:42
Alignment explanation
Indices: 62142--62229 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
62132 GAGTGTCATA
* * * * *
62142 ACCTGATCGAGCTGATTCTACAGCTCGACACCGAGAGCCATT
1 ACCTGATCGAGCCGATTATACACCTCCACACCGAGAGCCATC
*
62184 ACCTGATCGAGCCGATTATACACCTCCATACCGAGAGCCATC
1 ACCTGATCGAGCCGATTATACACCTCCACACCGAGAGCCATC
62226 ACCT
1 ACCT
62230 ATTCCATCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (42 bp):
ACCTGATCGAGCCGATTATACACCTCCACACCGAGAGCCATC
Found at i:62634 original size:12 final size:12
Alignment explanation
Indices: 62617--62658 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
62607 TTTTTCGGCA
*
62617 TTATTTATTTAT
1 TTATTTATTAAT
*
62629 TTATTTAGTAAT
1 TTATTTATTAAT
*
62641 TTATGTATTAAT
1 TTATTTATTAAT
62653 TTATTT
1 TTATTT
62659 TTAGCGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:62789 original size:21 final size:21
Alignment explanation
Indices: 62761--62858 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
62751 CTTTCACCTG
62761 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
**
62782 -CTATCGTTCAAGATACCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
*
62803 TCATTGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
62824 TCATTGTTTAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
62845 TCACCGTTCAAGAG
1 TCATCGTTCAAGAG
62859 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:64461 original size:20 final size:20
Alignment explanation
Indices: 64436--64481 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
64426 ACGTTGCGAT
*
64436 TTTCGCGTTGCGAATTTGAA
1 TTTCGCGTTACGAATTTGAA
*
64456 TTTCGCGTTACGAATTTGAC
1 TTTCGCGTTACGAATTTGAA
64476 TTTCGC
1 TTTCGC
64482 AACAATCGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTACGAATTTGAA
Found at i:64741 original size:18 final size:18
Alignment explanation
Indices: 64718--64753 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
64708 AAGCCGGTTG
*
64718 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
64736 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
64754 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:66835 original size:3 final size:3
Alignment explanation
Indices: 66827--66854 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66817 TCTTCGGGGA
66827 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
66855 AGGGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:67063 original size:24 final size:24
Alignment explanation
Indices: 67029--67082 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
67019 CTGAAACATC
67029 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
67053 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
67077 ATCAAA
1 ATCAAA
67083 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:67096 original size:24 final size:24
Alignment explanation
Indices: 67029--67096 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
67019 CTGAAACATC
* * *
67029 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
67053 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
67077 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
67097 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:67842 original size:16 final size:16
Alignment explanation
Indices: 67821--67854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
67811 AAATCATTGA
*
67821 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
67837 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
67853 AA
1 AA
67855 TTAGAGATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:68116 original size:20 final size:20
Alignment explanation
Indices: 68092--68149 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
68082 GTTGCGATTT
68092 AGAAAATCT-TGTTGCGAAAA
1 AGAAAAT-TGTGTTGCGAAAA
* *
68112 GGAAACTTGTGTTGCGAAAA
1 AGAAAATTGTGTTGCGAAAA
*
68132 AG-AAATTCGCGTTGCGAA
1 AGAAAATT-GTGTTGCGAA
68150 TTTAGAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (20 bp):
AGAAAATTGTGTTGCGAAAA
Found at i:68125 original size:40 final size:40
Alignment explanation
Indices: 68037--68149 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
68027 AAATTCGTGT
*
68037 TTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAA
1 TTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAA
* * ** * *
68077 TTCATGTTGCGATTTAGAAAATCTTGTTGCGAAAAGGAAAC
1 TTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAA-CAAAA
** * *
68118 TT-GTGTTGCGAAAAAGAAATTCGCGTTGCGAA
1 TTCGTGTTGCGAATTAGAAAATCGAGTTGCGAA
68150 TTTAGAAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 53 0.91
41 5 0.09
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (40 bp):
TTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAACAAAA
Found at i:68158 original size:21 final size:20
Alignment explanation
Indices: 68132--68211 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
68122 GTTGCGAAAA
68132 AGAAATTCGCGTTGCGAATTT
1 AGAAA-TCGCGTTGCGAATTT
*
68153 AGAAATCGAGTTGCGAATTT
1 AGAAATCGCGTTGCGAATTT
* *
68173 -GAAATTTCGTGTTACGAATTT
1 AGAAA--TCGCGTTGCGAATTT
* *
68194 GGAAATCGCATT-CGAATT
1 AGAAATCGCGTTGCGAATT
68212 GGAAAATCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.20
20 19 0.37
21 18 0.35
22 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (20 bp):
AGAAATCGCGTTGCGAATTT
Found at i:68165 original size:20 final size:21
Alignment explanation
Indices: 68132--68199 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
68122 GTTGCGAAAA
*
68132 AGAAATTCGCGTTGCGAATTT
1 AGAAATTCGAGTTGCGAATTT
68153 AGAAA-TCGAGTTGCGAATTT
1 AGAAATTCGAGTTGCGAATTT
* *
68173 -GAAATTTCGTGTTACGAATTT
1 AGAAA-TTCGAGTTGCGAATTT
*
68194 GGAAAT
1 AGAAAT
68200 CGCATTCGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.10
20 14 0.34
21 19 0.46
22 4 0.10
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (21 bp):
AGAAATTCGAGTTGCGAATTT
Found at i:68257 original size:20 final size:20
Alignment explanation
Indices: 68234--68275 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
68224 TGTGATTTCA
*
68234 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
68254 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
68274 GA
1 GA
68276 GTTTGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:68810 original size:23 final size:23
Alignment explanation
Indices: 68783--68838 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
68773 TTCGTGTTCG
68783 ATTCATTTAATATTCACAAACAT
1 ATTCATTTAATATTCACAAACAT
* *
68806 ATTCATTTAATATTCACGAATAT
1 ATTCATTTAATATTCACAAACAT
*
68829 GTTCATTTAA
1 ATTCATTTAA
68839 CATTTGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTCATTTAATATTCACAAACAT
Found at i:69155 original size:32 final size:29
Alignment explanation
Indices: 69100--69201 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 29
69090 TATAGGGTCC
* **
69100 AATTATTTTTAATACTTGCTATTAGAGG-TT
1 AATT-TTTTTAATATTTATTATTAG-GGCTT
69130 CAATTTTTTCCTAATATTTATTATTATGGGCTT
1 -AATTTTTT--TAATATTTATTATTA-GGGCTT
*
69163 AATTTTTTTAATATTTATTATTAGGAGCCT
1 AATTTTTTTAATATTTATTATTAGG-GCTT
*
69193 ACTTTTTTT
1 AATTTTTTT
69202 TTCTAATATT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
29 2 0.03
30 30 0.49
31 4 0.07
32 22 0.36
33 3 0.05
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.55
Consensus pattern (29 bp):
AATTTTTTTAATATTTATTATTAGGGCTT
Found at i:69199 original size:30 final size:30
Alignment explanation
Indices: 69131--69201 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
69121 TTAGAGGTTC
*
69131 AATTTTTTCCTAATATTTATTATTATGGGCTT
1 AATTTTTT--TAATATTTATTATTATGGGCCT
69163 AATTTTTTTAATATTTATTATTA-GGAGCCT
1 AATTTTTTTAATATTTATTATTATGG-GCCT
*
69193 ACTTTTTTT
1 AATTTTTTT
69202 TTCTAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 26 0.72
32 8 0.22
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (30 bp):
AATTTTTTTAATATTTATTATTATGGGCCT
Found at i:69402 original size:30 final size:29
Alignment explanation
Indices: 69242--69415 Score: 88
Period size: 29 Copynumber: 5.7 Consensus size: 29
69232 TGCCAATATT
* * *
69242 TTTTTCTAACATTTGTTATT-GAAGGCCTAG
1 TTTTT-TAATATTTGTTATTAG-AGGTCTAA
* * *
69272 TTTTTCAATACTTGTTATTAG-GGTTCCAA
1 TTTTTTAATATTTGTTATTAGAGG-TCTAA
* * *
69301 TTTTTCAATATTTATTATTA-ATGGTTTAA
1 TTTTTTAATATTTGTTATTAGA-GGTCTAA
*
69330 TTTTTTTCTAATATTTATTTGTTGTTATGA-GTCTAA
1 --TTTTT-T-A-A--TATTTGTTATTA-GAGGTCTAA
*
69366 TTTTTTAGTACTTT-TTATTAGAGGTCTAA
1 TTTTTTAATA-TTTGTTATTAGAGGTCTAA
69395 TTTTTTTAATATTTGTTATTA
1 -TTTTTTAATATTTGTTATTA
69416 TGAGCATACT
Statistics
Matches: 110, Mismatches: 17, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
28 4 0.04
29 50 0.45
30 26 0.24
31 5 0.05
32 1 0.01
33 2 0.02
34 6 0.05
36 15 0.14
38 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTTTTAATATTTGTTATTAGAGGTCTAA
Found at i:72626 original size:30 final size:30
Alignment explanation
Indices: 72582--72655 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
72572 CCTCCAGTGG
72582 CGCCAGAACCACCACCACCTGAAGCCAGAC
1 CGCCAGAACCACCACCACCTGAAGCCAGAC
*
72612 CGCC-GAATCCACCACCACCTGAAGCCAAAC
1 CGCCAGAA-CCACCACCACCTGAAGCCAGAC
*
72642 CACCA-AAGCCACCA
1 CGCCAGAA-CCACCA
72656 GTAGTAGAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.35, C:0.47, G:0.14, T:0.04
Consensus pattern (30 bp):
CGCCAGAACCACCACCACCTGAAGCCAGAC
Found at i:72645 original size:15 final size:15
Alignment explanation
Indices: 72595--72645 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
72585 CAGAACCACC
*
72595 ACCACCTGAAGCCAG
1 ACCACCTGAAGCCAA
* * *
72610 ACCGCC-GAATCCACC
1 ACCACCTGAAGCCA-A
72625 ACCACCTGAAGCCAA
1 ACCACCTGAAGCCAA
72640 ACCACC
1 ACCACC
72646 AAAGCCACCA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.33, C:0.47, G:0.14, T:0.06
Consensus pattern (15 bp):
ACCACCTGAAGCCAA
Done.