Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 55 of 55
Found at i:11067462 original size:20 final size:19
Alignment explanation
Indices: 11067416--11067462 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
11067406 TCCGGTATCA
*
11067416 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
11067435 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
11067456 TTTTACC
1 TTTTACC
11067463 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:11067610 original size:20 final size:20
Alignment explanation
Indices: 11067584--11067629 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
11067574 CACTTTTAAA
11067584 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
11067603 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
11067624 TTTACC
1 TTTACC
11067630 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:11068119 original size:228 final size:224
Alignment explanation
Indices: 11067697--11068136 Score: 733
Period size: 228 Copynumber: 1.9 Consensus size: 224
11067687 AAACTGCTTT
11067697 AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
1 AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
*
11067762 TTAATAATTTAATTTACACAAAATTTTTTGATTGTTTTGATATTTTATAAATATTATTTAGCATT
66 TTAATAATTTAATTTACACAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGCATT
* * *
11067827 TAAATTTAACAATATTAACCAAATATAATAATAATATGTTTTCAATAGTGAAATAAGTATGGACA
131 TAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTGAAATAAGTATGGACA
*
11067892 CTTTTATAAAAATGATATATACTTTTTTG
196 CTTTTATAAAAAGGATATATACTTTTTTG
11067921 AAAGTTATGTAATTTATGTTTCAAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAATATTA
1 AAAGTTATGTAATTTATGTTTC-AATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTA
*
11067985 ATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA
65 A-TTAATAATTTAATTTACAC--AAAATTATTTGATTGTTTTGATATTTTAT-AAATATTATTTA
*
11068050 G-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAGT
126 GCA-TTTAAATTTAACAATATTAACCAAAGATAATAAT-AATATATTTTCAACAGTGAAATAAGT
11068113 ATGGACACTTTTATAAAAAGGATA
189 ATGGACACTTTTATAAAAAGGATA
11068137 GATAATTTAC
Statistics
Matches: 202, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
224 59 0.29
225 23 0.11
227 29 0.14
228 81 0.40
229 10 0.05
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (224 bp):
AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
TTAATAATTTAATTTACACAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGCATT
TAAATTTAACAATATTAACCAAAGATAATAATAATATATTTTCAACAGTGAAATAAGTATGGACA
CTTTTATAAAAAGGATATATACTTTTTTG
Found at i:11070686 original size:32 final size:32
Alignment explanation
Indices: 11070639--11070714 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
11070629 ATCTATTTAC
* *
11070639 TTGCATTCACTCTTTCAAATAGTTATTATTTT
1 TTGCATTCACACTTTCAAATAGTTACTATTTT
* *
11070671 TTTCATTTACACTTTCAAATAGTTACTATTTT
1 TTGCATTCACACTTTCAAATAGTTACTATTTT
11070703 TTGCATTCACAC
1 TTGCATTCACAC
11070715 CCTGGGATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (32 bp):
TTGCATTCACACTTTCAAATAGTTACTATTTT
Found at i:11075103 original size:19 final size:19
Alignment explanation
Indices: 11075079--11075118 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11075069 GTGTTCAAAA
*
11075079 ATCAAATTTTACAAACTTT
1 ATCAAATATTACAAACTTT
*
11075098 ATCAAATATTATAAACTTT
1 ATCAAATATTACAAACTTT
11075117 AT
1 AT
11075119 TTATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (19 bp):
ATCAAATATTACAAACTTT
Found at i:11079702 original size:15 final size:15
Alignment explanation
Indices: 11079682--11079712 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11079672 ATTTGGCATA
11079682 CTGGTTTTCCTTTCT
1 CTGGTTTTCCTTTCT
11079697 CTGGTTTTCCTTTCT
1 CTGGTTTTCCTTTCT
11079712 C
1 C
11079713 CCACCGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.13, T:0.58
Consensus pattern (15 bp):
CTGGTTTTCCTTTCT
Found at i:11081348 original size:21 final size:18
Alignment explanation
Indices: 11081315--11081363 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
11081305 TATTCATTAT
11081315 TTAATAATTAAATACCAAA
1 TTAATAATTAAATA-CAAA
11081334 TTAATAAATTTAAATACAAA
1 TTAAT-AA-TTAAATACAAA
*
11081354 TTAATTATTA
1 TTAATAATTA
11081364 TCATATCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 6 0.22
20 11 0.41
21 7 0.26
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAATTAAATACAAA
Found at i:11090762 original size:15 final size:15
Alignment explanation
Indices: 11090683--11090767 Score: 62
Period size: 15 Copynumber: 5.3 Consensus size: 15
11090673 AATATATCAA
* *
11090683 TATTTTAAAATAATA
1 TATTTTATAATAATT
11090698 TATTTTATAATAATATAT
1 TATTTTATAAT-A-AT-T
* * *
11090716 TATAATTATTATTATT
1 TAT-TTTATAATAATT
*
11090732 TAATTATTAAAATAATT
1 T-ATT-TTATAATAATT
11090749 TATTTTATAATAATT
1 TATTTTATAATAATT
11090764 TATT
1 TATT
11090768 ATAATTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 24 0.44
16 6 0.11
17 15 0.28
18 3 0.06
19 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTATAATAATT
Found at i:11090786 original size:41 final size:41
Alignment explanation
Indices: 11090717--11090796 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
11090707 ATAATATATT
* * * *
11090717 ATAATTATTATTATTTAATTATTAAAATAATTTATTTTATA
1 ATAATTATTATAATTAAATAATTAAAATAATATATTTTATA
11090758 ATAATTTATTATAATTAAATAATT-AAATAATATATTTTA
1 ATAA-TTATTATAATTAAATAATTAAAATAATATATTTTA
11090797 ATATTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
ATAATTATTATAATTAAATAATTAAAATAATATATTTTATA
Found at i:11090799 original size:21 final size:21
Alignment explanation
Indices: 11090730--11090799 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
11090720 ATTATTATTA
* *
11090730 TTTAATTATTAAAATAATTTAT
1 TTTAATAATT-AAATAATATAT
* * *
11090752 TTT-ATAA-TAATTTATTATAA
1 TTTAATAATTAA-ATAATATAT
*
11090772 TTAAATAATTAAATAATATAT
1 TTTAATAATTAAATAATATAT
11090793 TTTAATA
1 TTTAATA
11090800 TTATAAAAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 7
0.67 0.19 0.13
Matches are distributed among these distances:
19 2 0.06
20 8 0.23
21 19 0.54
22 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATAATTAAATAATATAT
Found at i:11092983 original size:17 final size:17
Alignment explanation
Indices: 11092961--11092997 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11092951 CGGTCAACGA
*
11092961 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCAGG
11092978 TCAACGGTCGGGTCAGG
1 TCAACGGTCGGGTCAGG
11092995 TCA
1 TCA
11092998 GACCGGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.41, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCAGG
Found at i:11093044 original size:29 final size:29
Alignment explanation
Indices: 11092993--11093062 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
11092983 GGTCGGGTCA
* *
11092993 GGTCAG-ACCGG-TCAAACCTGTCAAACC
1 GGTCAGAACCGGTTGAAACCGGTCAAACC
11093020 GGTTC-GAACCGGTTGAAACCGGTCAAACC
1 GG-TCAGAACCGGTTGAAACCGGTCAAACC
11093049 GGTCAGAACCGGTT
1 GGTCAGAACCGGTT
11093063 TCCAGCAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 9 0.24
29 25 0.68
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (29 bp):
GGTCAGAACCGGTTGAAACCGGTCAAACC
Found at i:11093049 original size:9 final size:9
Alignment explanation
Indices: 11092993--11093061 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
11092983 GGTCGGGTCA
*
11092993 GGTCAGACC
1 GGTCAAACC
11093002 GGTCAAACC
1 GGTCAAACC
*
11093011 TGTCAAACC
1 GGTCAAACC
*
11093020 GGTTCGAACC
1 GG-TCAAACC
*
11093030 GGTTGAAACC
1 GG-TCAAACC
11093040 GGTCAAACC
1 GGTCAAACC
11093049 GGTCAGAACC
1 GGTCA-AACC
11093059 GGT
1 GGT
11093062 TTCCAGCAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
9 28 0.55
10 23 0.45
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:11100258 original size:17 final size:17
Alignment explanation
Indices: 11100236--11100294 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 17
11100226 CGGTCAACGA
11100236 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
11100253 TCAACGGTCGGGTCAGGTCGGG
1 TCAACGGTC--G---GGTCGGG
11100275 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
11100292 TCA
1 TCA
11100295 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 19 0.51
19 1 0.03
20 1 0.03
22 16 0.43
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:11100263 original size:12 final size:12
Alignment explanation
Indices: 11100246--11100288 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
11100236 TCAACGGTCG
11100246 GGTCGGGTCAAC
1 GGTCGGGTCAAC
11100258 GGTCGGGTC-A-
1 GGTCGGGTCAAC
11100268 GGTCGGGTCAAC
1 GGTCGGGTCAAC
11100280 GGTCGGGTC
1 GGTCGGGTC
11100289 GGGTCAGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.31
11 2 0.07
12 18 0.62
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:11100271 original size:22 final size:22
Alignment explanation
Indices: 11100241--11100293 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
11100231 AACGATCAAC
11100241 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
*
11100263 GGTCAGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
11100285 GGTCGGGTC
1 GGTCGGGTC
11100294 AGACCGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:11100308 original size:9 final size:9
Alignment explanation
Indices: 11100290--11100369 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
11100280 GGTCGGGTCG
*
11100290 GGTCAGACC
1 GGTCAAACC
11100299 GGTCAAACC
1 GGTCAAACC
*
11100308 GGTTCGAACC
1 GG-TCAAACC
*
11100318 GGTTGAAACC
1 GG-TCAAACC
11100328 GGTCAAACC
1 GGTCAAACC
11100337 GGTCAGAACC
1 GGTCA-AACC
*
11100347 GGTTGAAAACC
1 GG-T-CAAACC
*
11100358 GGTTAAACC
1 GGTCAAACC
11100367 GGT
1 GGT
11100370 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 29 0.48
10 23 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:11100330 original size:29 final size:31
Alignment explanation
Indices: 11100296--11100370 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
11100286 GTCGGGTCAG
11100296 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
11100325 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
11100355 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
11100371 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:11101547 original size:16 final size:16
Alignment explanation
Indices: 11101526--11101556 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11101516 TAATATTGAA
11101526 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
11101542 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
11101557 AAAAAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:11104898 original size:3 final size:3
Alignment explanation
Indices: 11104890--11104932 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
11104880 TTACAATTCA
* *
11104890 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11104933 TCAACAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11105107 original size:14 final size:15
Alignment explanation
Indices: 11105081--11105127 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
11105071 TTAATCGATC
*
11105081 AATAAATTAAATATA
1 AATAAATTAAATAAA
11105096 AATAAA-TAAATAAA
1 AATAAATTAAATAAA
11105110 AAT-AATTACAA-AAA
1 AATAAATTA-AATAAA
11105124 AATA
1 AATA
11105128 GTAACTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 2 0.07
14 18 0.64
15 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAATTAAATAAA
Found at i:11107070 original size:34 final size:34
Alignment explanation
Indices: 11106991--11107103 Score: 145
Period size: 34 Copynumber: 3.2 Consensus size: 34
11106981 CCGAATCCGG
11106991 CCCGAATATCACACTTAAAAAAACCCGACCCAAA
1 CCCGAATATCACACTTAAAAAAACCCGACCCAAA
11107025 CTTGATCCGAATATCACACTTAAAAAAACCCGACCCAAA
1 C-----CCGAATATCACACTTAAAAAAACCCGACCCAAA
* * * *
11107064 CCCGAATATCAAACTTTAAAAAACCCAACCCGAA
1 CCCGAATATCACACTTAAAAAAACCCGACCCAAA
11107098 CCCGAA
1 CCCGAA
11107104 ATTTAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
34 36 0.51
39 34 0.49
ACGTcount: A:0.45, C:0.34, G:0.07, T:0.14
Consensus pattern (34 bp):
CCCGAATATCACACTTAAAAAAACCCGACCCAAA
Found at i:11117143 original size:13 final size:13
Alignment explanation
Indices: 11117122--11117155 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
11117112 ATCACTCCTA
*
11117122 AACACAGCTACTT
1 AACAAAGCTACTT
11117135 AACAAAGCTACTT
1 AACAAAGCTACTT
11117148 AACAAAGC
1 AACAAAGC
11117156 ATTGAAAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.18
Consensus pattern (13 bp):
AACAAAGCTACTT
Found at i:11118348 original size:2 final size:2
Alignment explanation
Indices: 11118341--11118386 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11118331 AAGTATTAAG
11118341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11118383 AT AT
1 AT AT
11118387 GATTCATCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11119746 original size:13 final size:14
Alignment explanation
Indices: 11119730--11119759 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
11119720 TTCTCGAGGT
11119730 TTCAGCTTC-CAGC
1 TTCAGCTTCTCAGC
11119743 TTCAGCTTCTCAGC
1 TTCAGCTTCTCAGC
11119757 TTC
1 TTC
11119760 CTTTTTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.13, C:0.37, G:0.13, T:0.37
Consensus pattern (14 bp):
TTCAGCTTCTCAGC
Found at i:11127903 original size:3 final size:3
Alignment explanation
Indices: 11127889--11127937 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
11127879 GCTTGCTAAC
*
11127889 TCT TCAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
11127935 TCT
1 TCT
11127938 CATCCTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:11129165 original size:18 final size:18
Alignment explanation
Indices: 11129110--11129173 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
11129100 CGAAACCGAT
11129110 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
11129128 TTTTT---TTAACGGTTTGGG
1 TTTTTCGGTT--CGG-TTCGG
11129146 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
11129164 TTTATCGGTT
1 TTTTTCGGTT
11129174 TTTCAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
15 2 0.05
17 3 0.08
18 27 0.73
19 3 0.08
21 2 0.05
ACGTcount: A:0.05, C:0.12, G:0.30, T:0.53
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:11129325 original size:26 final size:26
Alignment explanation
Indices: 11129274--11129327 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
11129264 ACTCGAACCG
* *
11129274 AACCGAATCAAAAAATGAAGCCTTTA
1 AACCGAACCAAAAAACGAAGCCTTTA
*
11129300 AACCGAACCAAAAACCGAA-CCGTTTA
1 AACCGAACCAAAAAACGAAGCC-TTTA
11129326 AA
1 AA
11129328 ACCAAATCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.50, C:0.24, G:0.11, T:0.15
Consensus pattern (26 bp):
AACCGAACCAAAAAACGAAGCCTTTA
Found at i:11145016 original size:25 final size:24
Alignment explanation
Indices: 11144972--11145023 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
11144962 CAAGTTACTG
**
11144972 TAAAATATATTAATTTTTAT-AAT
1 TAAAATATATTAATAATTATAAAT
11144995 TAAAATAATATATAATAATTATAAAT
1 TAAAAT-ATAT-TAATAATTATAAAT
11145021 TAA
1 TAA
11145024 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 4 0.17
25 8 0.33
26 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATATATTAATAATTATAAAT
Found at i:11146425 original size:158 final size:158
Alignment explanation
Indices: 11146120--11146425 Score: 506
Period size: 158 Copynumber: 1.9 Consensus size: 158
11146110 CTTTATTTCT
*
11146120 TTTAAAATGCTAAGTATGATTTCTATCATACTTAGCTAAGTTTTCCGTAGCCAAAGACTGAAGCG
1 TTTAAAATGCTAAGTATGATTTCTATCATACTTAGCTAAGTTTTCCATAGCCAAAGACTGAAGCG
*
11146185 ATGACTCAATTCCGATCGTGAGAATTGAAAAGCACTCAATACCCTTCGAGTTACATTCTCAATTT
66 ATGACTCAATTCCGATCGTGAGAATTGAAAAGCACTCAATACCATTCGAGTTACATTCTCAATTT
* *
11146250 TATGGAATTAATGATCGGCAATCGACCA
131 TATGGAATCAATAATCGGCAATCGACCA
* *
11146278 TTTAAAATGCTAAGTATGATTTCTATCATACTTAGCTAAGTTTTTCATAGCCAAAGGCTGAAGCG
1 TTTAAAATGCTAAGTATGATTTCTATCATACTTAGCTAAGTTTTCCATAGCCAAAGACTGAAGCG
* * *
11146343 ATGACTCAATTCTGATTGTGAGAATTGAAAAGCACTCAATACCATTCGAGTTACATTCTCAGTTT
66 ATGACTCAATTCCGATCGTGAGAATTGAAAAGCACTCAATACCATTCGAGTTACATTCTCAATTT
*
11146408 TTTGTG-ATCAATAATCGG
131 TATG-GAATCAATAATCGG
11146426 TAATTGACTA
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
158 136 0.99
159 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (158 bp):
TTTAAAATGCTAAGTATGATTTCTATCATACTTAGCTAAGTTTTCCATAGCCAAAGACTGAAGCG
ATGACTCAATTCCGATCGTGAGAATTGAAAAGCACTCAATACCATTCGAGTTACATTCTCAATTT
TATGGAATCAATAATCGGCAATCGACCA
Found at i:11146884 original size:16 final size:17
Alignment explanation
Indices: 11146863--11146898 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11146853 TAGATTTTTA
11146863 TTTCAA-CTTTACTTTC
1 TTTCAATCTTTACTTTC
*
11146879 TTTCAATTTTTACTTTC
1 TTTCAATCTTTACTTTC
11146896 TTT
1 TTT
11146899 AATTCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCAATCTTTACTTTC
Found at i:11146902 original size:16 final size:17
Alignment explanation
Indices: 11146870--11146902 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11146860 TTATTTCAAC
11146870 TTTACTTTCTTTCAATT
1 TTTACTTTCTTTCAATT
11146887 TTTACTTTCTTT-AATT
1 TTTACTTTCTTTCAATT
11146903 CTTCAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTACTTTCTTTCAATT
Found at i:11148482 original size:77 final size:77
Alignment explanation
Indices: 11148355--11148641 Score: 506
Period size: 77 Copynumber: 3.8 Consensus size: 77
11148345 AAGTCAAAAA
* * *
11148355 TTCCAGATTACTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
1 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
11148420 TGGCTCCGAGAT
66 TGGCTCCGAGAT
*
11148432 TTCCAGAATGCTCGGAGGGAACCGATTTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
1 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
11148497 TGGCTCCGAGAT
66 TGGCTCCGAGAT
11148509 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
1 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
11148574 TGGCTCCGAGAT
66 TGGCTCCGAGAT
* *
11148586 TTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCA-AGGGGGTACCGATTCCCCCCTG
1 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTG
11148642 TTCAACGGTC
Statistics
Matches: 203, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 20 0.10
76 7 0.03
77 176 0.87
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (77 bp):
TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTT
TGGCTCCGAGAT
Found at i:11153070 original size:22 final size:21
Alignment explanation
Indices: 11153045--11153088 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
11153035 TCTCAATCTC
11153045 TTTAAATTATTTAATTAATTAT
1 TTTAAATTATTTAATT-ATTAT
**
11153067 TTTATTTTATTTAATTATTAT
1 TTTAAATTATTTAATTATTAT
11153088 T
1 T
11153089 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTAAATTATTTAATTATTAT
Found at i:11153080 original size:18 final size:19
Alignment explanation
Indices: 11153050--11153091 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
11153040 ATCTCTTTAA
11153050 ATTA-TTTAATTAATTATT
1 ATTATTTTAATTAATTATT
*
11153068 -TTATTTTATTTAATTATT
1 ATTATTTTAATTAATTATT
11153086 ATTATT
1 ATTATT
11153092 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATTTTAATTAATTATT
Found at i:11153093 original size:22 final size:22
Alignment explanation
Indices: 11153051--11153095 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
11153041 TCTCTTTAAA
11153051 TTATTTAATTAATTATTTTATT
1 TTATTTAATTAATTATTTTATT
11153073 TTATTTAATT-ATTATTATTATT
1 TTATTTAATTAATTATT-TTATT
11153095 T
1 T
11153096 AAAAAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTTAATTAATTATTTTATT
Found at i:11154422 original size:30 final size:29
Alignment explanation
Indices: 11154388--11154472 Score: 69
Period size: 30 Copynumber: 3.1 Consensus size: 29
11154378 AGTAAATGAT
11154388 ATGAACATGAATAAATTTTAAATGATGAAC
1 ATGAA-ATGAATAAATTTTAAATGATGAAC
** *
11154418 ATG-AAT---T-TTTTTTAAA--ATG-AT
1 ATGAAATGAATAAATTTTAAATGATGAAC
11154439 ATGAAGATGAATAAATTTTAAATGATGAAC
1 ATGAA-ATGAATAAATTTTAAATGATGAAC
11154469 ATGA
1 ATGA
11154473 TTTTTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 2 0.05
24 7 0.17
25 1 0.03
26 1 0.03
27 7 0.17
28 2 0.05
29 4 0.10
30 8 0.20
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (29 bp):
ATGAAATGAATAAATTTTAAATGATGAAC
Found at i:11154451 original size:51 final size:53
Alignment explanation
Indices: 11154381--11154504 Score: 198
Period size: 51 Copynumber: 2.3 Consensus size: 53
11154371 CTTGACGAGT
11154381 AAATGATATGAACATGAATAAATTTTAAATGATGAACATGA-ATTTTTTTT-A
1 AAATGATATGAACATGAATAAATTTTAAATGATGAACATGATATTTTTTTTAA
* *
11154432 AAATGATATGAAGATGAATAAATTTTAAATGATGAACATGATTTTTTTTTTTAAA
1 AAATGATATGAACATGAATAAATTTTAAATGATGAACATGA-TATTTTTTTT-AA
11154487 AAATGATATGAACATGAA
1 AAATGATATGAACATGAA
11154505 AACATTTACA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
51 40 0.61
53 8 0.12
55 18 0.27
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (53 bp):
AAATGATATGAACATGAATAAATTTTAAATGATGAACATGATATTTTTTTTAA
Found at i:11154457 original size:27 final size:26
Alignment explanation
Indices: 11154380--11154472 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 26
11154370 TCTTGACGAG
11154380 TAAATGATATGAACATGAATAAATTT
1 TAAATGATATGAACATGAATAAATTT
***
11154406 TAAATG--ATGAACATGAATTTTTTT
1 TAAATGATATGAACATGAATAAATTT
*
11154430 TAAAATGATATGAAGATGAATAAATTT
1 T-AAATGATATGAACATGAATAAATTT
11154457 TAAATG--ATGAACATGA
1 TAAATGATATGAACATGA
11154473 TTTTTTTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
24 25 0.45
25 5 0.09
26 11 0.20
27 15 0.27
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.35
Consensus pattern (26 bp):
TAAATGATATGAACATGAATAAATTT
Found at i:11159086 original size:20 final size:19
Alignment explanation
Indices: 11159061--11159099 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11159051 TGCTGTTCAA
11159061 ATTGATGATTGCTTTTGCTG
1 ATTGAT-ATTGCTTTTGCTG
* *
11159081 ATTGATCTTGTTTTTGCTG
1 ATTGATATTGCTTTTGCTG
11159100 CATTTCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (19 bp):
ATTGATATTGCTTTTGCTG
Done.