Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007319.1 Hibiscus syriacus cultivar Beakdansim tig00019534_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: 133019
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8351 original size:90 final size:90
Alignment explanation
Indices: 8198--8373 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 90
8188 TAACACATCA
*
8198 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAAATAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
* *
8263 TTCATTAATTGAAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
* *
8288 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
8353 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
8374 TTCGTGATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:9371 original size:33 final size:33
Alignment explanation
Indices: 9331--9399 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
9321 TATTACAATC
9331 ATCATATGATTGGTCTTTGGGCATACTCTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
*
9364 ATCATATGATTGGTCTTTGGGCATACTTTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
9397 ATC
1 ATC
9400 TCCCACTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (33 bp):
ATCATATGATTGGTCTTTGGGCATACTCTAACA
Found at i:15275 original size:24 final size:24
Alignment explanation
Indices: 15246--15314 Score: 120
Period size: 24 Copynumber: 2.8 Consensus size: 24
15236 AAAGAAATTG
15246 AAGCACTCAAAAGAAGAAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
*
15270 AAGCACTCAAAAAAAGAAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
15294 AAGCACTCAAAAAGAAGAAAA
1 AAGCACTC-AAAAGAAGAAAA
15315 AGAAAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 31 0.74
25 11 0.26
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (24 bp):
AAGCACTCAAAAGAAGAAAATTTC
Found at i:15322 original size:14 final size:14
Alignment explanation
Indices: 15303--15335 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15293 CAAGCACTCA
15303 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
15317 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
15331 AAAAG
1 AAAAG
15336 TTGAAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:17064 original size:11 final size:11
Alignment explanation
Indices: 17050--17074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17040 TCTGATTTCT
17050 TTCACTTGCAC
1 TTCACTTGCAC
17061 TTCACTTGCAC
1 TTCACTTGCAC
17072 TTC
1 TTC
17075 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:22159 original size:19 final size:19
Alignment explanation
Indices: 22132--22168 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22122 CATGATTTTT
*
22132 TTTTGATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
22151 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
22169 CTCTTGGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:33938 original size:19 final size:20
Alignment explanation
Indices: 33900--33950 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
33890 GAAACCCCTT
33900 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
33920 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
33939 TTAAGATACATG
1 TGAAAATACATG
33951 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:36212 original size:26 final size:26
Alignment explanation
Indices: 36178--36230 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
36168 AGTTGAAAAT
36178 GAGAAAGATGAATTTGGAGAAAAAGA
1 GAGAAAGATGAATTTGGAGAAAAAGA
36204 GAGAAAGATGAATTTGGAGAAAAAGA
1 GAGAAAGATGAATTTGGAGAAAAAGA
36230 G
1 G
36231 GAGAGTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.15
Consensus pattern (26 bp):
GAGAAAGATGAATTTGGAGAAAAAGA
Found at i:36443 original size:24 final size:24
Alignment explanation
Indices: 36432--36478 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
36422 TTTCAAAGAT
36432 AATGTCGTTTGAAGTTCCAAGAGA
1 AATGTCGTTTGAAGTTCCAAGAGA
** *
36456 AATGTCACTTGAAGTGCCAAGAG
1 AATGTCGTTTGAAGTTCCAAGAG
36479 TTGTGTCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (24 bp):
AATGTCGTTTGAAGTTCCAAGAGA
Found at i:46842 original size:11 final size:13
Alignment explanation
Indices: 46810--46839 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
46800 TGGCCAAAGA
46810 TGAAAAGGTATGT
1 TGAAAAGGTATGT
46823 TGAAAAGGTATG-
1 TGAAAAGGTATGT
46835 TGAAA
1 TGAAA
46840 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:50220 original size:24 final size:21
Alignment explanation
Indices: 50185--50227 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
50175 GGCTCATTCT
*
50185 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
50208 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
50228 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:51448 original size:5 final size:5
Alignment explanation
Indices: 51438--51463 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
51428 CTTCAACTTC
51438 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
51464 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:51509 original size:27 final size:27
Alignment explanation
Indices: 51452--51516 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
51442 TTTTCTTTTC
* **
51452 TTTTCTTTTCTTCTTTTTGAGTGCTGGA
1 TTTT-TTTTCTTCTTTTAGAGTGCTCAA
51480 TTTTTTTT-TTCTTTTAGAGTGCTTCAA
1 TTTTTTTTCTTCTTTTAGAGTGC-TCAA
*
51507 TTTCTTTTCT
1 TTTTTTTTCT
51517 GATTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 13 0.42
27 13 0.42
28 5 0.16
ACGTcount: A:0.09, C:0.14, G:0.12, T:0.65
Consensus pattern (27 bp):
TTTTTTTTCTTCTTTTAGAGTGCTCAA
Found at i:52890 original size:36 final size:36
Alignment explanation
Indices: 52817--52921 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
52807 ATTTATAAGT
* *
52817 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
52852 TGGTGATGATATAGGCGTGATAATGGCGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
52888 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
52922 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:64292 original size:13 final size:12
Alignment explanation
Indices: 64273--64358 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
64263 ATATAGGCGT
64273 GATATGGTGATG
1 GATATGGTGATG
64285 GAATATGGTGAT-
1 G-ATATGGTGATG
*
64297 GATATAGGCG-T-
1 GATAT-GGTGATG
64308 GATAATGGTGATG
1 GAT-ATGGTGATG
64321 GACTATGGTGAT-
1 GA-TATGGTGATG
*
64333 GATATAGGCG-T-
1 GATAT-GGTGATG
64344 GATAATGGTGATG
1 GAT-ATGGTGATG
64357 GA
1 GA
64359 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:64328 original size:36 final size:36
Alignment explanation
Indices: 64255--64359 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
64245 ATTTATAAGT
* *
64255 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
64290 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
64326 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
64360 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:71789 original size:145 final size:145
Alignment explanation
Indices: 71507--71798 Score: 536
Period size: 145 Copynumber: 2.0 Consensus size: 145
71497 CGATCTAGGA
71507 AATCAACAATGATCCGCACAAACAAGAAAGCTAAAAAATAGTTAAATGGAAAGATAAATATGGCA
1 AATCAACAATGATCCGCACAAACAAGAAAGCTAAAAAATAGTTAAATGGAAAGATAAATATGGCA
71572 GCGGAAAATATAAGTTGGTGATATGTTTAAAGGAAATGATGAAGTATGGTATTGGAAGTAGAATG
66 GCGGAAAATATAAGTTGGTGATATGTTTAAAGGAAATGATGAAGTATGGTATTGGAAGTAGAATG
71637 AAGGTGATGAAGATG
131 AAGGTGATGAAGATG
71652 AATCAACAATGATCCTGCACAAACAAGAAAGCT-AAAAATAGTTAAATGGAAAGATAAATATGGC
1 AATCAACAATGATCC-GCACAAACAAGAAAGCTAAAAAATAGTTAAATGGAAAGATAAATATGGC
71716 AGCGGAAAATATATAAGTTGGTGATATGTTT-AAGGAAATGATGAAGTATGGTATTGGAAGTAGA
65 AGCGG-AAA-ATATAAGTTGGTGATATGTTTAAAGGAAATGATGAAGTATGGTATTGGAAGTAGA
71780 ATGAA-GTGATGAAGATG
128 ATGAAGGTGATGAAGATG
71797 AA
1 AA
71799 AATGAAAAGT
Statistics
Matches: 144, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
145 65 0.45
146 58 0.40
147 21 0.15
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (145 bp):
AATCAACAATGATCCGCACAAACAAGAAAGCTAAAAAATAGTTAAATGGAAAGATAAATATGGCA
GCGGAAAATATAAGTTGGTGATATGTTTAAAGGAAATGATGAAGTATGGTATTGGAAGTAGAATG
AAGGTGATGAAGATG
Found at i:74275 original size:60 final size:58
Alignment explanation
Indices: 74184--74301 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 58
74174 GGGCATATAT
74184 TGAGCTCCATATTGGATTGATACTATTCAAAGTGCGTTGGAAATATAAGAGATAGGGG
1 TGAGCTCCATATTGGATTGATACTATTCAAAGTGCGTTGGAAATATAAGAGATAGGGG
74242 TGAGCTCCCAATATTGGATTGATACTATTCAAAGTGCGTTGGAAATATAAGAGATAGGGG
1 TGAGCT-CC-ATATTGGATTGATACTATTCAAAGTGCGTTGGAAATATAAGAGATAGGGG
74302 AGTAAATGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 6 0.10
59 2 0.03
60 50 0.86
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (58 bp):
TGAGCTCCATATTGGATTGATACTATTCAAAGTGCGTTGGAAATATAAGAGATAGGGG
Found at i:82039 original size:9 final size:9
Alignment explanation
Indices: 82018--82057 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
82008 TGCTTTCAAC
82018 TTTTC-TTT
1 TTTTCTTTT
*
82026 CTTTCTTTT
1 TTTTCTTTT
82035 TTTTCTTTT
1 TTTTCTTTT
82044 TTTTCTTTCT
1 TTTTCTTT-T
82054 TTTT
1 TTTT
82058 TCTGAGTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 4 0.14
9 19 0.68
10 5 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:82039 original size:13 final size:13
Alignment explanation
Indices: 82018--82058 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
82008 TGCTTTCAAC
82018 TTTTCTTTCTTTCT
1 TTTTCTTTCTTT-T
82032 TTTT-TTTCTTTT
1 TTTTCTTTCTTTT
82044 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
82057 TT
1 TT
82059 CTGAGTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.19
13 17 0.65
14 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:82042 original size:22 final size:22
Alignment explanation
Indices: 82017--82058 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
82007 GTGCTTTCAA
82017 CTTTTCTTTCTTTCTTTTTTTT
1 CTTTTCTTTCTTTCTTTTTTTT
*
82039 CTTTTTTTTCTTTCTTTTTT
1 CTTTTCTTTCTTTCTTTTTT
82059 CTGAGTGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
CTTTTCTTTCTTTCTTTTTTTT
Found at i:82091 original size:27 final size:28
Alignment explanation
Indices: 82043--82095 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
82033 TTTTTTCTTT
*
82043 TTTTTCTTTCTTTTTTCTGAGTGCTTGA
1 TTTTTCTTTCTTTTTTCGGAGTGCTTGA
82071 TTTTTC-TTCTTCTTTT-GGAGTGCTT
1 TTTTTCTTTCTT-TTTTCGGAGTGCTT
82096 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.64
Consensus pattern (28 bp):
TTTTTCTTTCTTTTTTCGGAGTGCTTGA
Found at i:82101 original size:28 final size:28
Alignment explanation
Indices: 82043--82101 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
82033 TTTTTTCTTT
* *
82043 TTTTTCTTTCTTTTTTCTGAGTGCTTGA
1 TTTTTCTTTCTTTTTTCGGAGTGCTTAA
82071 TTTTTC-TTCTTCTTTT-GGAGTGCTTCAA
1 TTTTTCTTTCTT-TTTTCGGAGTGCTT-AA
82099 TTT
1 TTT
82102 CTTTTGCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.08, C:0.15, G:0.14, T:0.63
Consensus pattern (28 bp):
TTTTTCTTTCTTTTTTCGGAGTGCTTAA
Found at i:82142 original size:11 final size:11
Alignment explanation
Indices: 82128--82152 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
82118 TTTATTTTTG
82128 TTCACTTGCAC
1 TTCACTTGCAC
82139 TTCACTTGCAC
1 TTCACTTGCAC
82150 TTC
1 TTC
82153 TTTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:87023 original size:2 final size:2
Alignment explanation
Indices: 87010--87048 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
87000 ATCACCAACT
*
87010 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87049 GATGGTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89741 original size:13 final size:13
Alignment explanation
Indices: 89723--89749 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
89713 AAACACCTTT
89723 AACATACCTTTTC
1 AACATACCTTTTC
89736 AACATACCTTTTC
1 AACATACCTTTTC
89749 A
1 A
89750 TCTTTGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (13 bp):
AACATACCTTTTC
Found at i:91274 original size:19 final size:19
Alignment explanation
Indices: 91250--91291 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
91240 TACATGATTT
91250 TTTTAATG-AAGATACATGA
1 TTTTAATGAAAG-TACATGA
*
91269 TTTTAATGAAAGTACATGC
1 TTTTAATGAAAGTACATGA
91288 TTTT
1 TTTT
91292 GGCCGAGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTTAATGAAAGTACATGA
Found at i:106802 original size:15 final size:17
Alignment explanation
Indices: 106766--106799 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
106756 TTTGATAACA
106766 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
106782 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
106798 TT
1 TT
106800 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:109267 original size:19 final size:20
Alignment explanation
Indices: 109233--109271 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
109223 TACATAAAAA
109233 ATACATGATTTTTTAATGAAG
1 ATACATGA-TTTTTAATGAAG
109254 ATACATGA-TTTTAATGAA
1 ATACATGATTTTTAATGAA
109272 AGTGCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
ATACATGATTTTTAATGAAG
Found at i:109571 original size:16 final size:16
Alignment explanation
Indices: 109550--109591 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
109540 TGCCTAGAGA
109550 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
109566 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
*
109582 TGAGCTAGGT
1 TGAACTAGGT
109592 GAGTGTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (16 bp):
TGAACTAGGTTCAAGG
Found at i:111289 original size:19 final size:21
Alignment explanation
Indices: 111239--111290 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
111229 GAAATCCCTT
111239 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
111260 AGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
111279 TGAAGATACATG
1 TGAAAATACATG
111291 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:114719 original size:18 final size:18
Alignment explanation
Indices: 114650--114719 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
114640 TTTCCTTGGC
114650 TTTCTTTCTCTTTTTGAAT
1 TTTCTTT-TCTTTTTGAAT
114669 TTTCTTTTTCTTTTAT-AAT
1 TTTC-TTTTCTTTT-TGAAT
**
114688 TTTC-TTTCTTTTTGTCT
1 TTTCTTTTCTTTTTGAAT
114705 TTTCTTTTCTTTTTG
1 TTTCTTTTCTTTTTG
114720 CACTCTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 13 0.29
18 10 0.22
19 17 0.38
20 4 0.09
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTCTTTTCTTTTTGAAT
Found at i:115016 original size:19 final size:20
Alignment explanation
Indices: 114988--115027 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
114978 GAATAATAAT
114988 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
115008 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
115027 A
1 A
115028 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:120256 original size:28 final size:27
Alignment explanation
Indices: 120225--120287 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
120215 GGTACAAAAG
*
120225 AAAGAAAATACAAAAAGAA-AAATTCAGA
1 AAAGAAAAAACAAAAAGAAGAAATTC--A
*
120253 AAAGAAGAAAAGAAAAAGAAGAAATTCA
1 AAAGAA-AAAACAAAAAGAAGAAATTCA
120281 AAAGAAA
1 AAAGAAA
120288 GCAAAGCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 1 0.03
28 13 0.42
29 11 0.35
30 6 0.19
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (27 bp):
AAAGAAAAAACAAAAAGAAGAAATTCA
Found at i:120256 original size:32 final size:29
Alignment explanation
Indices: 120219--120288 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 29
120209 AATTGGGGTA
120219 CAAAAGAAAGAAAATACAAAAAGAA-AAATT
1 CAAAAGAAAG-AAA-ACAAAAAGAAGAAATT
*
120249 CAGAAA-AGAAGAAAAGAAAAAGAAGAAATT
1 CA-AAAGA-AAGAAAACAAAAAGAAGAAATT
120279 CAAAAGAAAG
1 CAAAAGAAAG
120289 CAAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 15 0.43
30 14 0.40
31 6 0.17
ACGTcount: A:0.71, C:0.06, G:0.16, T:0.07
Consensus pattern (29 bp):
CAAAAGAAAGAAAACAAAAAGAAGAAATT
Found at i:120263 original size:17 final size:16
Alignment explanation
Indices: 120220--120276 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 16
120210 ATTGGGGTAC
120220 AAAAGAAAGAAAATACA
1 AAAAG-AAGAAAATACA
*
120237 AAAAG-A-AAAATTCA
1 AAAAGAAGAAAATACA
*
120251 GAAAAGAAG-AAA-AGA
1 -AAAAGAAGAAAATACA
120266 AAAAGAAGAAA
1 AAAAGAAGAAA
120277 TTCAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 15 0.45
15 9 0.27
16 4 0.12
17 5 0.15
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAGAAGAAAATACA
Found at i:121013 original size:24 final size:24
Alignment explanation
Indices: 120986--121038 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
120976 TCAAAACATC
*
120986 AAGAGATATGTCTTGT-GAATCACA
1 AAGAGACATGTCTTGTAG-ATCACA
*
121010 AAGAGACATGTCTTGTAGATCACG
1 AAGAGACATGTCTTGTAGATCACA
121034 AAGAG
1 AAGAG
121039 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTAGATCACA
Found at i:121831 original size:29 final size:30
Alignment explanation
Indices: 121799--121857 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
121789 CTTAGCTTTA
**
121799 TATTATGTTTACATATGTTTTAGAT-TCAT
1 TATTATGTTTACATATCATTTAGATATCAT
*
121828 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
121858 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTATGTTTACATATCATTTAGATATCAT
Found at i:122758 original size:19 final size:21
Alignment explanation
Indices: 122734--122785 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
122724 CGGCCAAGAG
*
122734 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
122753 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
122774 CATGTATTTTCA
1 CATGTATTTTCA
122786 AAGGGGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:123158 original size:13 final size:13
Alignment explanation
Indices: 123140--123184 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
123130 CATTGCCATT
*
123140 TCATCATCATCCA
1 TCATCAACATCCA
*
123153 TCATCAACATCCT
1 TCATCAACATCCA
*
123166 TCATCAAGA-CCA
1 TCATCAACATCCA
123178 TCATCAA
1 TCATCAA
123185 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:124557 original size:15 final size:14
Alignment explanation
Indices: 124513--124560 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
124503 TTGGAAATAA
124513 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
124527 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
124544 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
124559 GA
1 GA
124561 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:124557 original size:26 final size:24
Alignment explanation
Indices: 124509--124562 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
124499 TTAATTGGAA
124509 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
124535 ATAAGAAATGAAATGGAAA-GAAATG
1 ATAAGAAATGAAA--GAAAGGAAATG
124560 ATA
1 ATA
124563 TCAAGGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:129750 original size:24 final size:21
Alignment explanation
Indices: 129716--129758 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
129706 TCCACAAGAT
*
129716 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
129738 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
129759 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Done.