Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009185.1 Hibiscus syriacus cultivar Beakdansim tig00112758_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: 682201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:633347 original size:41 final size:42
Alignment explanation
Indices: 633293--633384 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
633283 CCTCTTCAAC
* *
633293 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
633334 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
633376 GATGACAGG
1 GATGACAGG
633385 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:633349 original size:21 final size:21
Alignment explanation
Indices: 633320--633380 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
633310 GAACGGTGGG
*
633320 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
633341 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
633362 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
633381 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:633770 original size:20 final size:19
Alignment explanation
Indices: 633747--633814 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
633737 GAAACTTAAA
633747 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
633767 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
633787 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
633806 ATCGCAACG
1 ATCGCAACG
633815 ACAAAATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:633822 original size:39 final size:40
Alignment explanation
Indices: 633747--633822 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 40
633737 GAAACTTAAA
** *
633747 ATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGAAAATCGCAACGCGAAAATGGCT
*
633787 ATCGCAATGCG-AAATGAAAATCGCAACGAC-AAAATG
1 ATCGCAACGCGAAAATGAAAATCGCAACG-CGAAAATG
633823 CAATGCGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 20 0.65
40 11 0.35
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGAAAATCGCAACGCGAAAATGGCT
Found at i:633867 original size:20 final size:20
Alignment explanation
Indices: 633839--633995 Score: 72
Period size: 20 Copynumber: 8.6 Consensus size: 20
633829 GAAACACAAA
*
633839 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
633859 TCGCGTTGCGA--TT--TTG
1 TCGCGTTGCGATTTTCATTT
633875 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
* *
633892 TCGCATTGCGA--TT--TTG
1 TCGCGTTGCGATTTTCATTT
633908 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
* * ***
633925 TCGCATTACGATAGCCATTT
1 TCGCGTTGCGATTTTCATTT
* **
633945 CCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTT
* * *
633965 GCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCATTT
*
633985 TCGTGTTGCGA
1 TCGCGTTGCGA
633996 AAGTAAACTA
Statistics
Matches: 100, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
14 15 0.15
16 9 0.09
17 6 0.06
18 2 0.02
19 16 0.16
20 52 0.52
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:633879 original size:14 final size:14
Alignment explanation
Indices: 633862--633920 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
633852 TTCATTTTCG
633862 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
633876 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
633893 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
633909 CGTTGCGATTTT
1 CGTTGCGATTTT
633921 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:633901 original size:33 final size:33
Alignment explanation
Indices: 633844--633936 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
633834 ACAAATCGCA
*
633844 TTGCGATTTTCATTTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTTTGTCG
633878 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
633911 TTGCGATTTTCATTTCGCATTACGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
633937 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:635932 original size:20 final size:20
Alignment explanation
Indices: 635884--635942 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
635874 AATAGTTTCT
** *
635884 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
635904 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
635924 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
635943 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:636235 original size:22 final size:22
Alignment explanation
Indices: 636208--636262 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
636198 GGAGATAGAT
636208 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
636230 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
636252 GGATGTCGCCG
1 GGATTTCGCCG
636263 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.20
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:636541 original size:20 final size:20
Alignment explanation
Indices: 636448--636531 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
636438 GATTATGTAT
636448 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
636468 TATCGCGTTGAGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
636488 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
636508 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
636528 TATC
1 TATC
636532 ACATTGCGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:636623 original size:21 final size:22
Alignment explanation
Indices: 636571--636623 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
636561 ATTTACTTAT
636571 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
636592 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
636613 TCGCATTGCGA
1 TCGCATTGCGA
636624 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:640010 original size:46 final size:48
Alignment explanation
Indices: 639917--640010 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
639907 TTAGTGTAAT
* *
639917 TTTAATTTCCCGAATAAATGTATGCGAACTAGAGATCATGCGATTAGG
1 TTTAATTTCCCGAATAAATGCATGCGAACTAGAGATCATGAGATTAGG
* *
639965 TTTAATTTCTCGAAT-AA-GCATGCGAACTAGATGA-CATGAGGTTAGG
1 TTTAATTTCCCGAATAAATGCATGCGAACTAGA-GATCATGAGATTAGG
640011 ATGTTCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 23 0.56
47 4 0.10
48 14 0.34
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (48 bp):
TTTAATTTCCCGAATAAATGCATGCGAACTAGAGATCATGAGATTAGG
Found at i:645076 original size:233 final size:233
Alignment explanation
Indices: 644669--645241 Score: 878
Period size: 233 Copynumber: 2.5 Consensus size: 233
644659 AAAAAATGAA
* * * *
644669 ATGAGAAAGGTTTCTCATTCAAATCTGAAAATTAAAATTGTTGAAAAATAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * *** * * *
644734 CTAGTCAACTATTTCTAAAATTTATAAACCCTTCGGGTCATCAGTAAGTCTTTCGAGCGTGATGC
66 CTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
* * *
644799 TTAAATCCTTCAGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTACGGGCCATCCATAA
131 TTAAATCCTCCAGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATACAGGCCATCCATAA
*
644864 GACCTTT-GGGTAGGATGTTTTCACATGTCTATCAAAAT
196 G-CCTTTCGGGCAGGATGTTTTCACATGTCTATCAAAAT
*
644902 ATGAGAAAGGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
*
644967 TTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
66 CTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
* * * * * *
645032 TTAATTTCTCCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGGTCATCCATAA
131 TTAAATCCTCCAGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATACAGGCCATCCATAA
* * *
645097 GTCTTTCGTGCAGGATGTTTTCACATGTCTATCGAAAT
196 GCCTTTCGGGCAGGATGTTTTCACATGTCTATCAAAAT
645135 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
*
645200 CTAGTAAACTATTTCCAAAATTTGTAAGTTCTTCGGGCCATC
66 CTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATC
645242 TCTAAGTTTG
Statistics
Matches: 309, Mismatches: 30, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
232 4 0.01
233 305 0.99
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (233 bp):
ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
CTAGTAAACTATTTCCAAAATTTATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
TTAAATCCTCCAGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATACAGGCCATCCATAA
GCCTTTCGGGCAGGATGTTTTCACATGTCTATCAAAAT
Found at i:645782 original size:44 final size:44
Alignment explanation
Indices: 645727--645810 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
645717 ATTTTTAAAA
*
645727 AACCAGACCCG-ACCCTGACCCGAATATCACACTTAAAAAATCCC
1 AACCAGACCCGAACCC-GACCCGAATATCAAACTTAAAAAATCCC
*
645771 AACCTGACCCGAACCCGACCCGAATATCAAACTTAAAAAA
1 AACCAGACCCGAACCCGACCCGAATATCAAACTTAAAAAA
645811 CCCGACCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.42, C:0.36, G:0.10, T:0.13
Consensus pattern (44 bp):
AACCAGACCCGAACCCGACCCGAATATCAAACTTAAAAAATCCC
Found at i:647755 original size:31 final size:31
Alignment explanation
Indices: 647670--647789 Score: 118
Period size: 31 Copynumber: 3.8 Consensus size: 31
647660 AGGGTTTACA
*
647670 TATGTTCTACGGAACATATGGACAGAATTACC
1 TATGTTCTACGGAACATATGGACAGTA-TACC
* * *
647702 TATG-TCTTTCGGGACATTTGGACAGTATACC
1 TATGTTC-TACGGAACATATGGACAGTATACC
* *
647733 TATGTTCTAAGGAACATATGGACAGTTTACC
1 TATGTTCTACGGAACATATGGACAGTATACC
* * *
647764 TAGGTTCTTC-GAGACCTATGGACAGT
1 TATGTTCTACGGA-ACATATGGACAGT
647790 TGCCGAGGTT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
30 2 0.03
31 48 0.67
32 22 0.31
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (31 bp):
TATGTTCTACGGAACATATGGACAGTATACC
Found at i:649149 original size:113 final size:113
Alignment explanation
Indices: 648951--649576 Score: 866
Period size: 113 Copynumber: 5.5 Consensus size: 113
648941 CCTTCAAGTA
* *
648951 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGA
* *
649016 TCAACTCCCTCAGATCTGATTTTCCCTTGAGAGTAAGCGGAACAGGTC
66 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
* *
649064 TCTCTTTTCCAAGATTTGATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATGGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGA
*
649129 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGATCAGGTC
66 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
* * * * *
649177 TCTTTTTTCCAAGATTTGATATTCCCTTCAAAGTATGTGGAACAAGTCTACCCCGATTCAATGGG
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGA
* *
649242 T-GACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAATAGGTC
66 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
* * * *
649289 TCTCTTTTCCAAGATTTGATATT-CTTTCCAGAGTAAATGGAGCAAGTCTGCCCCGATTCAATGA
1 TCTCTTTTCCAAGATTTGATATTCCCTT-CAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGG
* * * * *
649353 ATCAACTCCCCTAGATCTAATATTCCCTTCAGAGTAAGCGAAACATGTC
65 ATCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
* * * *
649402 TCTCTTTTCTAAGATTTGGTATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGA
* * * **
649467 TCAAATCCCCCAATATCTGATATTCCCTTCAGAGTAAGCGGAACATATC
66 TCAACTCCCCC-AGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
* * *
649516 CCTCTTTTCCAAGATTTGATATTCCC-T--GAGTGACAGTGGAACAAGTCTACCCTGATTCAAT
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGT-A-AGTGGAACAAGTCTGCCCCGATTCAAT
649577 TTTCCCTGAG
Statistics
Matches: 455, Mismatches: 52, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
111 7 0.02
112 97 0.21
113 292 0.64
114 59 0.13
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (113 bp):
TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGA
TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTC
Found at i:649347 original size:225 final size:225
Alignment explanation
Indices: 648951--649540 Score: 849
Period size: 225 Copynumber: 2.6 Consensus size: 225
648941 CCTTCAAGTA
* *
648951 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
* *
649016 TCAACTCCCTCAGATCTGATTTTCCCTTGAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTT
66 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTT
* * *
649081 GATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATGGATCAACTCCCCCAGATCT
131 GAT-ATTCCTTCAGAGTAAATGGAACAAGTATGCCCCGATTCAATGAATCAACTCCCCCAGATCT
* * * *
649146 GATTTTCCCTTCAGAGTAAGCGGATCAGGTC
195 AATATTCCCTTCAGAGTAAGCGAAACAGGTC
* * * * * *
649177 TCTTTTTTCCAAGATTTGATATTCCCTTCAAAGTATGTGGAACAAGTCTACCCCGATTCAATGGG
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
* *
649242 T-GACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAATAGGTCTCTCTTTTCCAAGATTT
66 TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTT
* * * *
649306 GATATTCTTTCCAGAGTAAATGGAGCAAGTCTGCCCCGATTCAATGAATCAACTCCCCTAGATCT
131 GATATTCCTT-CAGAGTAAATGGAACAAGTATGCCCCGATTCAATGAATCAACTCCCCCAGATCT
*
649371 AATATTCCCTTCAGAGTAAGCGAAACATGTC
195 AATATTCCCTTCAGAGTAAGCGAAACAGGTC
* * *
649402 TCTCTTTTCTAAGATTTGGTATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
* * * ** *
649467 TCAAATCCCCCAATATCTGATATTCCCTTCAGAGTAAGCGGAACATATCCCTCTTTTCCAAGATT
66 TCAACTCCCCC-AGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATT
649532 TGATATTCC
130 TGATATTCC
649541 CTGAGTGACA
Statistics
Matches: 320, Mismatches: 41, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
224 5 0.02
225 194 0.61
226 66 0.21
227 55 0.17
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (225 bp):
TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGA
TCAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTT
GATATTCCTTCAGAGTAAATGGAACAAGTATGCCCCGATTCAATGAATCAACTCCCCCAGATCTA
ATATTCCCTTCAGAGTAAGCGAAACAGGTC
Found at i:649567 original size:338 final size:337
Alignment explanation
Indices: 648951--649576 Score: 938
Period size: 338 Copynumber: 1.9 Consensus size: 337
648941 CCTTCAAGTA
648951 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTGA
1 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTGA
* * * *
649016 TCAACTCCCTCAGATCTGATTTTCCCTTGAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTT
66 TCAACTCCCTCAGATCTAATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGATTT
* *
649081 GATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATGGATCAACTCCCCCAGATCT
131 GATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATAGATCAAATCCCCCAGATCT
* * * * *
649146 GATTTTCCCTTCAGAGTAAGCGGATCAGGTCTCTTTTTTCCAAGATTTGATATTCCCTTCAAAGT
196 GATATTCCCTTCAGAGTAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTT-AAAGT
*
649211 ATGTGGAACAAGTCTACCCCGATTCAATGGGTGACTCCCCCAGATCTGATTTTCCCTTCAGAGTA
260 AAGTGGAACAAGTCTACCCCGATTCAATGGGTGACTCCCCCAGATCTGATTTTCCCTTCAGAGTA
649276 AGCGGAATAGGTC
325 AGCGGAATAGGTC
* *
649289 TCTCTTTTCCAAGATTTGATATT-CTTTCCAGAGTAAATGGAGCAAGTCTGCCCCGATTCAA-TG
1 TCTCTTTTCCAAGATTTGATATTCCCTT-CAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTG
* *
649352 AATCAACTCCC-CTAGATCTAATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTTCTAAGA
65 -ATCAACTCCCTC-AGATCTAATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGA
* * * * *
649416 TTTGGTATTCCCTTTAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATAGATCAAATCCCCCAAT
128 TTTGATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATAGATCAAATCCCCC-AG
* *
649481 ATCTGATATTCCCTTCAGAGTAAGCGGAACATATCCCTCTTTTCCAAGATTTGATATTCCC-T-G
192 ATCTGATATTCCCTTCAGAGTAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTAA
*
649544 AGTGACAGTGGAACAAGTCTACCCTGATTCAAT
257 AGT-A-AGTGGAACAAGTCTACCCCGATTCAAT
649577 TTTCCCTGAG
Statistics
Matches: 258, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
336 3 0.01
337 7 0.03
338 192 0.74
339 56 0.22
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (337 bp):
TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAATGGAACAAGTCTGCCCCGATTCAATTGA
TCAACTCCCTCAGATCTAATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGATTT
GATAATCCCTTCAGAGTAAGTGGAACAAGTATGCCCCGATTCAATAGATCAAATCCCCCAGATCT
GATATTCCCTTCAGAGTAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCTTAAAGTA
AGTGGAACAAGTCTACCCCGATTCAATGGGTGACTCCCCCAGATCTGATTTTCCCTTCAGAGTAA
GCGGAATAGGTC
Found at i:649708 original size:135 final size:134
Alignment explanation
Indices: 649465--649763 Score: 390
Period size: 135 Copynumber: 2.2 Consensus size: 134
649455 CGATTCAATA
* *
649465 GATCAA-ATCCCCCAATATCTGATATTCCCTTCAGAGTAAGCGGAACATATCCCTCTTTTCCAAG
1 GATCAACAT-CCCCAA-ATCTGATATTCCCTTAAGAGTAAGCGGAACAGATCCCTCTTTTCCAAG
* * *
649529 ATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTGATTCAATTTTCCCTGAGTGACGA-
64 ATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATCTTCCCTGAGTGA-GAG
649593 CGGAATG
128 CGGAATG
* * * * * *
649600 TATCAACCTCCTCCAAATTTGATATTCCCTTAAGAAG-AAGCGGAATAGATCCTTCTTTTCTAAG
1 GATCAACATCC-CCAAATCTGATATTCCCTTAAG-AGTAAGCGGAACAGATCCCTCTTTTCCAAG
* *
649664 ATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTATCCC-GATTCAATCTTCCTTGAGTGATAG
64 ATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTA-CCCTGATTCAATCTTCCCTGAGTGAGAG
649728 CGGAATG
128 CGGAATG
*
649735 GATCAACATCCCCAGATCTGATATTCCCT
1 GATCAACATCCCCAAATCTGATATTCCCT
649764 GAGTGAAAAC
Statistics
Matches: 142, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
134 17 0.12
135 115 0.81
136 10 0.07
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (134 bp):
GATCAACATCCCCAAATCTGATATTCCCTTAAGAGTAAGCGGAACAGATCCCTCTTTTCCAAGAT
TTAATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATCTTCCCTGAGTGAGAGCGG
AATG
Found at i:649917 original size:3 final size:3
Alignment explanation
Indices: 649909--649953 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
649899 TTTTCCATCA
*
649909 TAT TAT TAT TA- TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
649954 TAAAAATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:651875 original size:2 final size:2
Alignment explanation
Indices: 651826--651858 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
651816 AATTCCATAG
651826 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 T
651859 GTTTATACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:658366 original size:19 final size:19
Alignment explanation
Indices: 658342--658379 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
658332 AGTGAAATTG
658342 AATATTAAAATGTTGATTT
1 AATATTAAAATGTTGATTT
*
658361 AATATTGAAATGTTGATTT
1 AATATTAAAATGTTGATTT
658380 TGGACTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
AATATTAAAATGTTGATTT
Found at i:658807 original size:14 final size:14
Alignment explanation
Indices: 658788--658814 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
658778 AATATATCAA
658788 TGTGATAATTTTTT
1 TGTGATAATTTTTT
658802 TGTGATAATTTTT
1 TGTGATAATTTTT
658815 ATATATGAAA
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:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (14 bp):
TGTGATAATTTTTT
Found at i:661134 original size:39 final size:39
Alignment explanation
Indices: 661091--661173 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
661081 CTCATGATTT
* *
661091 TATCAAAACCATGATAAACAATATCACACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCACACATAACAGACA
* *
661130 TATCAAAGCCATGATAAACAATATCATACATAACAGACA
1 TATCAAAACCATGATAAACAATATCACACATAACAGACA
661169 TATCA
1 TATCA
661174 TGTTCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCACACATAACAGACA
Found at i:664268 original size:30 final size:30
Alignment explanation
Indices: 664232--664307 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
664222 AAGACCTAGA
* *
664232 TTTTTAAAATTATACTTTTGGTCCCTAAAC
1 TTTTTAAATTTATACTTTTGGTACCTAAAC
* *
664262 TTTTTAAATTTACACTTTTGGTACTTAAAC
1 TTTTTAAATTTATACTTTTGGTACCTAAAC
*
664292 TTTCTAAATTTATACT
1 TTTTTAAATTTATACT
664308 CTATAGACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTTAAATTTATACTTTTGGTACCTAAAC
Found at i:664651 original size:29 final size:29
Alignment explanation
Indices: 664595--664673 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
664585 TGCATTTCTG
* * *
664595 TCATTCTACATGGGATTAAATCCCCATCC
1 TCATTCTGCATGGGATTATATACCCATCC
**
664624 TCATTCTGCATGGGATTATATATTCATCC
1 TCATTCTGCATGGGATTATATACCCATCC
*
664653 TGA-TCATGCATGGGATTATAT
1 TCATTC-TGCATGGGATTATAT
664674 CACTGTCCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 2 0.05
29 41 0.95
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (29 bp):
TCATTCTGCATGGGATTATATACCCATCC
Found at i:664693 original size:29 final size:30
Alignment explanation
Indices: 664661--664732 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
664651 CCTGATCATG
*
664661 CATGGGATTATATCACT-GTCCTGTTTTTA
1 CATGGGATCATATCACTCGTCCTGTTTTTA
* *
664690 CATGGGATCATAT-TCTCGTCCTGTTTTTG
1 CATGGGATCATATCACTCGTCCTGTTTTTA
*
664719 CGTGGGATCATATC
1 CATGGGATCATATC
664733 CCCAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (30 bp):
CATGGGATCATATCACTCGTCCTGTTTTTA
Found at i:665273 original size:16 final size:16
Alignment explanation
Indices: 665245--665275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
665235 AGTTCAATTT
665245 AGGTTAATTTCAGTTC
1 AGGTTAATTTCAGTTC
*
665261 AGGTTACTTTCAGTT
1 AGGTTAATTTCAGTT
665276 TGGCTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (16 bp):
AGGTTAATTTCAGTTC
Found at i:665348 original size:25 final size:24
Alignment explanation
Indices: 665320--665376 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
665310 TTTTTTGAGT
*
665320 TTCGAGTCAAATTT-GGGTCATCATG
1 TTCGAGTCAAATTTCGGGTC-TCA-A
*
665345 TTCGAGT-ATATTTCGGGTCTCAA
1 TTCGAGTCAAATTTCGGGTCTCAA
665368 TTCGAGTCA
1 TTCGAGTCA
665377 TCGGGTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.25
24 9 0.32
25 12 0.43
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (24 bp):
TTCGAGTCAAATTTCGGGTCTCAA
Found at i:665878 original size:24 final size:24
Alignment explanation
Indices: 665851--665900 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
665841 AATTATGAAC
*
665851 TCATATTC-TATTTACAGATTTAGA
1 TCATA-TCATATTTACAAATTTAGA
665875 TCATATCATATTTACAAATTTAGA
1 TCATATCATATTTACAAATTTAGA
665899 TC
1 TC
665901 GATTTCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (24 bp):
TCATATCATATTTACAAATTTAGA
Found at i:666446 original size:58 final size:58
Alignment explanation
Indices: 666339--666448 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
666329 ATAGTTGAGT
*
666339 GATCATTTGTAACTTTTAATAGTCGAAAGACTCAACAAAACAACATCCTATAATCGGG
1 GATCATTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATAATCGGG
* ** * * *
666397 GATCACTTTGTAACTTTTACTAGTCG-GGGAATCAACAAGATAATATCCTATA
1 GATCA-TTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATA
666449 GTCGATAGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 25 0.57
59 19 0.43
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (58 bp):
GATCATTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATAATCGGG
Found at i:666460 original size:59 final size:58
Alignment explanation
Indices: 666339--666464 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
666329 ATAGTTGAGT
* *
666339 GATCATTTGTAACTTTTAATAGTCGAAAGACTCAACAAAACAACATCCTATAATCGGG
1 GATCATTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATAATCGGA
* ** * * * * *
666397 GATCACTTTGTAACTTTTACTAGTCG-GGGAATCAACAAGATAATATCCTATAGTCGATA
1 GATCA-TTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATAATCG-GA
666456 GATCATTTG
1 GATCATTTG
666465 CCTACTTTAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 32 0.57
59 24 0.43
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (58 bp):
GATCATTTGTAACTTTTAATAGTCGAAAGAATCAACAAAACAACATCCTATAATCGGA
Found at i:679566 original size:15 final size:15
Alignment explanation
Indices: 679546--679580 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
679536 TGCTCACCAT
679546 TCGAACAAACTTCAC
1 TCGAACAAACTTCAC
*
679561 TCGAACAAGCTTCAC
1 TCGAACAAACTTCAC
679576 TCGAA
1 TCGAA
679581 GAGCCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (15 bp):
TCGAACAAACTTCAC
Found at i:680496 original size:117 final size:116
Alignment explanation
Indices: 680248--680496 Score: 390
Period size: 117 Copynumber: 2.1 Consensus size: 116
680238 CTTAGCTTTC
* * * * * *
680248 GCACCGAGCTTTACTTCGGTGGTGCAATCTCGCACCTTGTGTTGTCCACGCATTGGAAACACTTT
1 GCACCGAGCTTTGCTTCAGTGGTGCAATCTCGCACCTTGTGTTCTCCACACATCGGAAACACTTC
680313 AATGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
66 AATGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
* ** *
680364 TCACCGAGCCCTGCTTCATTGGTGCAATCTCGCACCTTGTGTTCTCCATCACATCGGAAACACTT
1 GCACCGAGCTTTGCTTCAGTGGTGCAATCTCGCACCTTGTGTTCTCCA-CACATCGGAAACACTT
*
680429 CAATGGCTCTCGCTTCTTTATCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
65 CAATGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
680481 GCACCGAGCTTTGCTT
1 GCACCGAGCTTTGCTT
680497 TGTTTGGGCA
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
116 41 0.35
117 77 0.65
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.33
Consensus pattern (116 bp):
GCACCGAGCTTTGCTTCAGTGGTGCAATCTCGCACCTTGTGTTCTCCACACATCGGAAACACTTC
AATGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
Done.