Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005715.1 Hibiscus syriacus cultivar Beakdansim tig00013365_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: 47840
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:271 original size:54 final size:55
Alignment explanation
Indices: 107--415 Score: 380
Period size: 55 Copynumber: 5.7 Consensus size: 55
97 AAGTGTGCAA
* * *
107 AAACATAAGAAATTCACACTAATTGGATGAATTTCTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * * *
162 AAACTTAAGAAATTCATACCAAGCGGATGAATTTCTATATGGGCACTTTACGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * * * *
217 AAACTTGATAAATGCATACTAA-TGGATGAATTTCCGCATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
271 AAACTT-A-AAATT-ATACTAAGTGGATGAATTTCTGTAT-GGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * * *
322 AAACTTAAGGAATTCTTACTAAGTGGATGAATTTATGTATGGGCACTTTATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTG-T
* * * *
378 AAAC-TAGGAAATTCTTACTAAGTGTAT-AATTTCCGTAT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTAT
416 TGGTAGTGGG
Statistics
Matches: 220, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
51 27 0.12
52 20 0.09
53 5 0.02
54 65 0.30
55 99 0.45
56 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
Found at i:411 original size:160 final size:161
Alignment explanation
Indices: 124--412 Score: 413
Period size: 160 Copynumber: 1.8 Consensus size: 161
114 AGAAATTCAC
*
124 ACTAATTGGATGAATTTCTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACCAAGCGGA
1 ACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACCAAGCGGA
* * * *
189 TGAATTTCTATATGGGCACTTTACGTGTAAACTTGATAAATGCATACTAATGGATGAATTTCCGC
66 TGAATTTATATATGGGCACTTTACGTGAAAACTAGAGAAATGCATACTAATGGATGAATTTCCGC
254 ATGGGCACTTTATGTGTAAACTTAAAATTAT
131 ATGGGCACTTTATGTGTAAACTTAAAATTAT
* * * *
285 ACTAAGTGGATGAATTTCTGTAT-GGCACTTTATGTGTAAACTTAAGGAATTCTTACTAAGTGGA
1 ACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACCAAGCGGA
* * * * *
349 TGAATTTATGTATGGGCACTTTATGTGCAAAACTAG-GAAATTCTTACTAAGTGTAT-AATTTCC
66 TGAATTTATATATGGGCACTTTACGTG-AAAACTAGAGAAATGCATACTAA-TGGATGAATTTCC
412 G
129 G
413 TATTGGTAGT
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
160 80 0.71
161 32 0.29
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (161 bp):
ACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACCAAGCGGA
TGAATTTATATATGGGCACTTTACGTGAAAACTAGAGAAATGCATACTAATGGATGAATTTCCGC
ATGGGCACTTTATGTGTAAACTTAAAATTAT
Found at i:6227 original size:27 final size:27
Alignment explanation
Indices: 6197--6257 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
6187 AAATGTGGTG
6197 TGATTCTTAGAATCAAATTATCTTGAT
1 TGATTCTTAGAATCAAATTATCTTGAT
6224 TGATTCTTAGAATCAAATTATCTTGAT
1 TGATTCTTAGAATCAAATTATCTTGAT
*
6251 GGATTCT
1 TGATTCT
6258 AGATGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (27 bp):
TGATTCTTAGAATCAAATTATCTTGAT
Found at i:6579 original size:19 final size:22
Alignment explanation
Indices: 6555--6605 Score: 81
Period size: 19 Copynumber: 2.5 Consensus size: 22
6545 TGCAAAAATG
6555 GTATCGATACCAT-A-ATAG-A
1 GTATCGATACCATAATATAGTA
6574 GTATCGATACCATAATATAGTA
1 GTATCGATACCATAATATAGTA
6596 GTATCGATAC
1 GTATCGATAC
6606 AATGGTAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.45
20 1 0.03
21 4 0.14
22 11 0.38
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAATATAGTA
Found at i:7047 original size:55 final size:55
Alignment explanation
Indices: 6963--7276 Score: 472
Period size: 55 Copynumber: 5.7 Consensus size: 55
6953 AAGTGTGCAA
* * * *
6963 AAACTTAAGAGATTCACACTAAATGGATGAATTTACGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
*
7018 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTACGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
*
7073 AAACTTAAGAAATTCATACTAAGTGGATGAATTTACGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* *
7128 AAACTTAATAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATTTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* * *
7183 AAACTTAAGGAATTCATACTAAGTGGATGAATTTTTGTATGGGCAC-TTATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTG-T
* *
7238 AAAC-T-AGAAAATTCATACTAAGTGTATAAATTTTCGTAT
1 AAACTTAAG-AAATTCATACTAAGTGGATGAATTTTCGTAT
7277 TGGTAGTGGG
Statistics
Matches: 238, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.01
54 34 0.14
55 202 0.85
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
Found at i:7728 original size:25 final size:27
Alignment explanation
Indices: 7678--7728 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
7668 TTTTGTTTAC
7678 TTACGTAAATTTAATGAATGATTTATTA
1 TTACGTAAATTTAA-GAATGATTTATTA
*
7706 TTAC-TAAATTTAA-AATGTTTTAT
1 TTACGTAAATTTAAGAATGATTTAT
7729 AAAAAGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
27 9 0.41
28 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (27 bp):
TTACGTAAATTTAAGAATGATTTATTA
Found at i:8159 original size:8 final size:8
Alignment explanation
Indices: 8148--8178 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
8138 TATTTTCTTC
8148 TTTTTCCT
1 TTTTTCCT
8156 TTTTTCCTT
1 TTTTTCC-T
8165 TTTTTCCT
1 TTTTTCCT
8173 TTTTTC
1 TTTTTC
8179 ATCTCTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCCT
Found at i:8160 original size:9 final size:9
Alignment explanation
Indices: 8134--8177 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
8124 TCTTGAGCCC
8134 CCTTTATTTT
1 CCTTT-TTTT
8144 -CTTCTTTTT
1 CCTT-TTTTT
8153 CC-TTTTTT
1 CCTTTTTTT
8161 CCTTTTTTT
1 CCTTTTTTT
8170 CCTTTTTT
1 CCTTTTTT
8178 CATCTCTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.23
9 22 0.71
10 2 0.06
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
CCTTTTTTT
Found at i:8168 original size:17 final size:18
Alignment explanation
Indices: 8134--8178 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
8124 TCTTGAGCCC
*
8134 CCTTTATTTTCTTCTTTTT
1 CCTTT-TTTCCTTCTTTTT
8153 CCTTTTTTCCTT-TTTTT
1 CCTTTTTTCCTTCTTTTT
8170 CCTTTTTTC
1 CCTTTTTTC
8179 ATCTCTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.56
18 6 0.24
19 5 0.20
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (18 bp):
CCTTTTTTCCTTCTTTTT
Found at i:17999 original size:25 final size:25
Alignment explanation
Indices: 17906--18004 Score: 157
Period size: 25 Copynumber: 4.0 Consensus size: 25
17896 AGTTAGGGGA
*
17906 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
*
17930 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
17955 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
17980 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
18005 GGGTTGTTGG
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.11
25 62 0.89
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:18363 original size:43 final size:43
Alignment explanation
Indices: 18315--18545 Score: 151
Period size: 43 Copynumber: 5.2 Consensus size: 43
18305 AATGAAGAGG
* *
18315 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAAA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * *
18358 TCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACG
1 TCTGGTCATC--T---AAGGGTG---ACACGGCTCCTACGTGATGAGGACA
* * * * * *
18409 GCTGGTTATC--AGGTTGACACGGCTCTTACGTGATGAAGAGA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * * *
18450 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
1 TCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGATGAGGACA
* * * * * * *
18496 GCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
18539 TCTGGTC
1 TCTGGTC
18546 CGGGGGATGA
Statistics
Matches: 138, Mismatches: 37, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
41 26 0.19
43 35 0.25
44 8 0.06
45 4 0.03
46 29 0.21
48 7 0.05
51 29 0.21
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (43 bp):
TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
Found at i:18496 original size:87 final size:92
Alignment explanation
Indices: 18331--18543 Score: 319
Period size: 87 Copynumber: 2.3 Consensus size: 92
18321 CGTCTAAGGG
* * * * *
18331 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTA
18396 CGTGATGAGGACGGCTGGTTATC-A-GGT
64 CGTGATGAGGACGGCTGGTTATCTATGGT
*
18423 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
18485 TGATGAGGACGGCTGGTTATCTATGGT
66 TGATGAGGACGGCTGGTTATCTATGGT
18512 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
18544 TCCGGGGGAT
Statistics
Matches: 113, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
87 41 0.36
88 3 0.03
89 34 0.30
90 2 0.02
92 33 0.29
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (92 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGGCTGGTTATCTATGGT
Found at i:18507 original size:46 final size:45
Alignment explanation
Indices: 18377--18533 Score: 139
Period size: 46 Copynumber: 3.6 Consensus size: 45
18367 CTTTAGGAAG
*
18377 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATC--A
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
* * * * * **
18420 GGT--TGACACGGCTCTTACGTGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-AA
*
18464 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
* * *
18509 GGT--TGACACGGCTCATACGTGATGA
1 GGTGATAACACGGTTCCTACGTGATGA
18534 AGAGATCTGG
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 27 0.31
43 22 0.25
44 4 0.05
45 4 0.05
46 29 0.33
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (45 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAA
Found at i:18573 original size:130 final size:134
Alignment explanation
Indices: 18423--18669 Score: 353
Period size: 135 Copynumber: 1.9 Consensus size: 134
18413 GTTATCAGGT
* * *
18423 TGACACGGCTCTTACGTGATGAAGAGA-TCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTAC
1 TGACACGGCTCATACATGATGAA-AAACTCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTAC
*
18484 GTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCC
65 GTGATGAGGACGACTGGTTATCCTAAT-GTTGACACGGCTCATACGTGATGAAGAGATCTGGTCC
18547 GGGGGA
129 GGGGGA
* *
18553 TGACACGGTTCATACATGATGAAAAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACATGATGAAAAACTCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTA
*
18618 CGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCCTACGTGATGA
64 CGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGA
18670 GGAAGTCCGG
Statistics
Matches: 102, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
129 2 0.02
130 30 0.29
132 2 0.02
134 2 0.02
135 39 0.38
136 25 0.25
137 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (134 bp):
TGACACGGCTCATACATGATGAAAAACTCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCGG
GGGA
Found at i:29753 original size:14 final size:14
Alignment explanation
Indices: 29734--29760 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29724 TACACACTCA
29734 AAAATAAAATAAAT
1 AAAATAAAATAAAT
29748 AAAATAAAATAAA
1 AAAATAAAATAAA
29761 AAGGTTAGAG
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:33270 original size:25 final size:25
Alignment explanation
Indices: 33232--33330 Score: 173
Period size: 25 Copynumber: 4.0 Consensus size: 25
33222 AGTTAGGGGA
33232 TTAGGG-TTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
33256 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
33281 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
33306 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
33331 GGGTTGTTGG
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
24 6 0.08
25 67 0.92
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:41792 original size:47 final size:47
Alignment explanation
Indices: 41732--41858 Score: 141
Period size: 46 Copynumber: 2.7 Consensus size: 47
41722 ATTTTTTTCC
* *
41732 TTTGAAAAGTATTTTCAGATATCTTCTAAAATTAATAG-TTCTCTACT
1 TTTGAAAAATATTTTGAGATATCTTCTAAAATTAA-AGTTTCTCTACT
* * * * *
41779 TTTGAAAAATATTTTGAGAGATTTTCTGAAATT-AAGTTTCTTTCCT
1 TTTGAAAAATATTTTGAGATATCTTCTAAAATTAAAGTTTCTCTACT
* * *
41825 TTTGAAAATTGTTTTGAGATATCTTCTACAATTA
1 TTTGAAAAATATTTTGAGATATCTTCTAAAATTA
41859 GTCCCTAATT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
45 2 0.03
46 35 0.54
47 28 0.43
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (47 bp):
TTTGAAAAATATTTTGAGATATCTTCTAAAATTAAAGTTTCTCTACT
Found at i:41840 original size:46 final size:46
Alignment explanation
Indices: 41777--41913 Score: 129
Period size: 46 Copynumber: 3.0 Consensus size: 46
41767 TAGTTCTCTA
* **
41777 CTTTTGAAAAATATTTTGAGAGATTTTCTGAAATTAAGTTTCT-TTC
1 CTTTTG-AAAATATTTTGAGAGATATTCTGAAATTAAGTCCCTATTC
* * *
41823 CTTTTGAAAATTGTTTTGAGATATCTTCT-ACAATT-AGTCCCTAATTC
1 CTTTTGAAAA-TATTTTGAGAGATATTCTGA-AATTAAGTCCCT-ATTC
* * *
41870 CTTTTGAAAATATTTTAAGAGATATTATGAAATTAA-TCTCTATT
1 CTTTTGAAAATATTTTGAGAGATATTCTGAAATTAAGTCCCTATT
41914 TTATTTTGAA
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
45 13 0.18
46 46 0.62
47 15 0.20
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (46 bp):
CTTTTGAAAATATTTTGAGAGATATTCTGAAATTAAGTCCCTATTC
Found at i:45673 original size:16 final size:17
Alignment explanation
Indices: 45641--45701 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
45631 TGAGTACAAT
45641 AAATAAAAAATAAAGAA
1 AAATAAAAAATAAAGAA
*
45658 AAATAAAGAAAAAGAAGAAA
1 AAATAAA-AAATA-AAG-AA
* *
45678 AAATATATAAATAAA-AC
1 AAATA-AAAAATAAAGAA
45695 AAATAAA
1 AAATAAA
45702 TACAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
16 1 0.03
17 13 0.37
18 4 0.11
19 5 0.14
20 11 0.31
21 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.13
Consensus pattern (17 bp):
AAATAAAAAATAAAGAA
Found at i:45679 original size:9 final size:10
Alignment explanation
Indices: 45646--45679 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
45636 ACAATAAATA
45646 AAAAATAAAG
1 AAAAATAAAG
45656 AAAAATAAAG
1 AAAAATAAAG
*
45666 AAAAA-GAAG
1 AAAAATAAAG
45675 AAAAA
1 AAAAA
45680 ATATATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:45748 original size:48 final size:49
Alignment explanation
Indices: 45673--45807 Score: 138
Period size: 46 Copynumber: 2.8 Consensus size: 49
45663 AAGAAAAAGA
* * **
45673 AGAAAAAATATATAAATA-AAACAAATAAATACAATAATAATAAAAAAGT
1 AGAAAATATATATATATATAAATTAATAAATACAATAATAATAAAAAA-T
* * *
45722 A-AAAATATATATATATATATA-TAATAAATA-AA-AACATTAAAAAAT
1 AGAAAATATATATATATATAAATTAATAAATACAATAATAATAAAAAAT
*
45767 AGTAAATATATATATATATAAATTAATAAA-ACAAGTAATAA
1 AGAAAATATATATATATATAAATTAATAAATACAA-TAATAA
45808 AAATTAACAT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
45 2 0.03
46 29 0.41
47 11 0.16
48 22 0.31
49 6 0.09
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (49 bp):
AGAAAATATATATATATATAAATTAATAAATACAATAATAATAAAAAAT
Found at i:45798 original size:42 final size:46
Alignment explanation
Indices: 45728--45827 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 46
45718 AAGTAAAAAT
*
45728 ATATATATATATATATAATAAATAAAAAC-ATTAA-AAAATAGTAA-
1 ATATATATATATATATAATAAATAAAAACAAGTAATAAAA-AGTAAC
* *
45772 ATATATATATATATA-AATTAAT-AAAACAAGTAATAAAAATTAAC
1 ATATATATATATATATAATAAATAAAAACAAGTAATAAAAAGTAAC
45816 ATATATATATAT
1 ATATATATATAT
45828 GTAATCTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
42 5 0.10
43 14 0.28
44 31 0.62
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (46 bp):
ATATATATATATATATAATAAATAAAAACAAGTAATAAAAAGTAAC
Found at i:45809 original size:46 final size:47
Alignment explanation
Indices: 45680--45827 Score: 141
Period size: 48 Copynumber: 3.2 Consensus size: 47
45670 AGAAGAAAAA
* * * *
45680 ATATATAAATA-AAACA-AATAAATACAATAATAATAAAAAAGTAAAA
1 ATATATATATATAAATATAATAAATACAATAATAA-AAAATAGTAAAT
* *
45726 ATATATATATATATATATAATAAATA-AAAACATTAAAAAATAGTAAAT
1 ATATATATATATAAATATAATAAATACAATA-A-TAAAAAATAGTAAAT
45774 ATATATATATATAAAT-TAATAAA-ACAAGTAAT-AAAAAT--TAACAT
1 ATATATATATATAAATATAATAAATACAA-TAATAAAAAATAGTAA-AT
45818 ATATATATAT
1 ATATATATAT
45828 GTAATCTAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 16
0.78 0.07 0.14
Matches are distributed among these distances:
43 3 0.03
44 12 0.14
45 6 0.07
46 12 0.14
47 16 0.18
48 35 0.40
49 3 0.03
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.30
Consensus pattern (47 bp):
ATATATATATATAAATATAATAAATACAATAATAAAAAATAGTAAAT
Found at i:46426 original size:36 final size:37
Alignment explanation
Indices: 46374--46447 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
46364 ATGCTTGTGG
46374 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
46411 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
46447 A
1 A
46448 ACGTTATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:47124 original size:84 final size:83
Alignment explanation
Indices: 47016--47840 Score: 706
Period size: 84 Copynumber: 10.1 Consensus size: 83
47006 ATTTGGTTTT
* * * * *
47016 CCTTTGAGCTGAGTGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAG
*
47081 ATATGCTGCAAATGATGTG
65 TTATGCTGCAAATGATGTG
* * * * *
47100 CCTTGGAGCTGAGCGTAGTTGAACTTGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGT
* *
47165 TATGCTACAAATTATGTG
66 TATGCTGCAAATGATGTG
* * * * * ** * *
47183 CCCTCGAAGCTCAGTGTAATCGAACTCG-AGG-GATT-TTAGCAGATAGCCCTTCTCGACTTAAG
1 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG
*
47245 TTATGTTGCAAATGATGTG
65 TTATGCTGCAAATGATGTG
** *
47264 CCTTGGAGCTGAGCGT-GTTAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGT
* * *
47328 TATGCTGCAAATTATATA
66 TATGCTGCAAATGATGTG
* * * ** *
47346 CCTTGGAGCT-ACGCATAGTCGAACTCGAAGGTCTTT-TCGTGACAGGTAACCCTTCGAGCCTTG
1 CCTTGGAGCTGA-GCGTAGTCGAACTCGAAGGTCTTTGT--TGGCAGATAACCCTTCTCGACTT-
*
47409 AA-TTATGCTGTAAATGATGTG
62 AAGTTATGCTGCAAATGATGTG
* * * * * * * *
47430 CCCTCGAAGCTG-GTGTAATCGAACTCGAGGGTC--T-TTGGCAGATAGCCTTTCTCTACTTAAG
1 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
47491 CTATGTTAC-AATGA--TG
65 TTATGCTGCAAATGATGTG
* * *
47507 CCTTGGAGCTGAGCTTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAG
* *
47572 TTATGTTGCAAATGATATG
65 TTATGCTGCAAATGATGTG
* * ** * * * *
47591 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
47656 TTATACTGTAAATGA-G-C
65 TTATGCTGCAAATGATGTG
* * * * * * * * *
47673 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-CT-TTAGCAGATAGCCCTTCTAGACTTAAGT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGT
*
47736 TATGCTGCAAATAATGTG
66 TATGCTGCAAATGATGTG
* * *
47754 TCTT--A---GAGCATAGTCGAACTCGAAGGTCTTTGTTGGAAGATAACCCTTCTCGACTTAAGT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGT
* *
47814 TATGCTGCAAACGATATG
66 TATGCTGCAAATGATGTG
47832 CCTTGGAGC
1 CCTTGGAGC
Statistics
Matches: 577, Mismatches: 135, Indels: 60
0.75 0.17 0.08
Matches are distributed among these distances:
76 28 0.05
77 18 0.03
78 42 0.07
79 48 0.08
80 38 0.07
81 74 0.13
82 89 0.15
83 60 0.10
84 167 0.29
85 13 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGT
TATGCTGCAAATGATGTG
Found at i:47473 original size:246 final size:246
Alignment explanation
Indices: 47037--47840 Score: 1032
Period size: 245 Copynumber: 3.3 Consensus size: 246
47027 AGTGTAATCG
* * * * *
47037 AACTCGAAAGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
* * *
47102 TTGGAGCTGAGCGTAGTTGAACTTGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG-TGACAGATAACCCTTCTAGCCTTGAGTT
** * *
47166 ATGCTACAAATTATGTGCCCTCGAAGCTCAGTGTAATCGAACTCGAGGGAT-TTTAGCAGATAGC
130 ATGCTGTAAATGATGTGCCCTCGAAGCT-GGTGTAATCGAACTCGAGGG-TCTTTAGCAGATAGC
47230 CCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGT-GTTA
193 CCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAG-TA
* *
47284 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATATACC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
* * * *
47348 TTGGAGCT-ACGCATAGTCGAACTCGAAGGTCTTTTCGTGACAGGTAACCCTTCGAGCCTTGAAT
66 TTGGAGCTGA-GCGTAGTCGAACTCGAAGGTCTTTT-GTGACAGATAACCCTTCTAGCCTTGAGT
*
47412 TATGCTGTAAATGATGTGCCCTCGAAGCTGGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCC
129 TATGCTGTAAATGATGTGCCCTCGAAGCTGGTGTAATCGAACTCGAGGGTCTTTAGCAGATAGCC
* * * * *
47477 TTTCTCTACTTAAGCTATGTTAC-AATGA--TGCCTTGGAGCTGAGCTTAGTCA
194 CTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT-A
* * *
47528 AACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCC
1 AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
* * *
47593 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAGTT
66 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-GTGACAGATAACCCTTCTAGCCTTGAGTT
*
47658 ATACTGTAAATGA---GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCCTTTAGCAGATAGC
130 ATGCTGTAAATGATGTGCCCTCGAAGCTG-GTGTAATCGAACTCGAGGGT-CTTTAGCAGATAGC
* * * * * *
47720 CCTTCTAGACTTAAGTTATGCTGCAAATAATGTGTCTT--A---GAGCATAGTCG
193 CCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT-A
*
47770 AACTCGAAGGTCTTT-GTTGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAACGATATGC
1 AACTCGAAGGTCTTTGGTT-GACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
47833 CTTGGAGC
65 CTTGGAGC
Statistics
Matches: 490, Mismatches: 53, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
241 51 0.10
242 37 0.08
243 38 0.08
244 47 0.10
245 124 0.25
246 121 0.25
247 71 0.14
248 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (246 bp):
AACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTGACAGATAACCCTTCTAGCCTTGAGTTA
TGCTGTAAATGATGTGCCCTCGAAGCTGGTGTAATCGAACTCGAGGGTCTTTAGCAGATAGCCCT
TCTCGACTTAAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTA
Found at i:47587 original size:161 final size:166
Alignment explanation
Indices: 47055--47644 Score: 424
Period size: 164 Copynumber: 3.6 Consensus size: 166
47045 AGTCTTTGGT
* * * * *
47055 TGGCAGATAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGCGTA-T
** * * * * * *
47119 TGAACTTGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATTATG-TG
65 CAAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTCGACTTAAGCTATGCTACAAATTA-GAT-
* * * ** * * * **
47183 CCCTCGAAGCT-CAGTGTAATCGAACTC-GAGG-GATTT--
127 ACCTTGGAGCTAC-GCATAGTCAAACTCAAAGGTCTTTTCG
* * * * * *
47219 TAGCAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATGATGTG-CCTTGGAGCTGAGCGTGTT
1 TGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGCGTATC
* * *
47283 AAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATATACC
66 AAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTCGACTTAAGCTATGCTACAAATTAGATACC
* *
47348 TTGGAGCTACGCATAGTCGAACTCGAAGGTCTTTTCG
130 TTGGAGCTACGCATAGTCAAACTCAAAGGTCTTTTCG
* * ** * * * *
47385 TGACAGGTAACCCTTCGAGCCTTGAA-TTATGCTGTAAATGATGTGCCCTCGAAGCTG-GTGTAA
1 TGGCAGATAACCCTTCTCGACTT-AAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGCGT-A
* * * * * * *
47448 TCGAACTCGAGGGTCTTTG-G-CAGATAGCCTTTCTCTACTTAAGCTATGTTAC-AA-T-GATGC
64 TCAAACTCGAAGGTCTTTGTGACAGATAACCCTTCTCGACTTAAGCTATGCTACAAATTAGATAC
* *
47508 CTTGGAGCTGA-GCTTAGTCAAACTCAAAGGTC-TTTGG
129 CTTGGAGCT-ACGCATAGTCAAACTCAAAGGTCTTTTCG
* * *
47545 TTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGCGTA-
* * *
47609 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTT
64 TCAAACTCGAAGGTC-TTT-GTGACAGATAACCCTT
47645 TTAGCCTTGA
Statistics
Matches: 343, Mismatches: 65, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
160 16 0.05
161 80 0.23
162 24 0.07
163 62 0.18
164 87 0.25
165 11 0.03
166 36 0.10
167 27 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (166 bp):
TGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGCGTATC
AAACTCGAAGGTCTTTGTGACAGATAACCCTTCTCGACTTAAGCTATGCTACAAATTAGATACCT
TGGAGCTACGCATAGTCAAACTCAAAGGTCTTTTCG
Done.