Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:3942740 original size:45 final size:45
Alignment explanation
Indices: 3942676--3942784 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
3942666 CTTTTTAATA
** *
3942676 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
*
3942721 TTTTCAAAACCTTTGGGTCATCCATAAGACCTACAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
3942766 TTTTCAAAAAGCCTTCGGG
1 TTTTC-AAAA-CCTTCGGG
3942785 AGCTTTTTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 46 0.81
46 4 0.07
47 7 0.12
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
Found at i:3942787 original size:121 final size:121
Alignment explanation
Indices: 3942554--3943038 Score: 555
Period size: 121 Copynumber: 3.9 Consensus size: 121
3942544 GTGCATGATG
* * *
3942554 TTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCGTGATGTTTTCAAAACCTTCGGGGTC
1 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGTC
* *
3942619 ATCCATAAGACCTACAGTGTAGGATGTTTTGAAAAAGCCTTCGGGAGCTTTTTAATA
65 ATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATA
* *
3942676 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTTGGGTCA
1 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
*
3942741 TCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
66 TCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATA
* *
3942797 CTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCA
1 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
** * * *
3942862 TCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTTATTTATAAGCCCTTTAGTG
66 TCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG---------AG--CTTT--T-
* *
3942925 CATGATG
117 --TAATA
* * * *
3942932 TTTTTAAAGCCTTCGGTTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
1 TTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
** * * *
3942997 TCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
66 TCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
3943039 CTATCTGTAA
Statistics
Matches: 323, Mismatches: 24, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
119 8 0.02
120 4 0.01
121 145 0.45
122 54 0.17
128 2 0.01
130 4 0.01
132 1 0.00
135 105 0.33
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (121 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
TCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATA
Found at i:3942849 original size:45 final size:45
Alignment explanation
Indices: 3942798--3943106 Score: 476
Period size: 45 Copynumber: 6.9 Consensus size: 45
3942788 TTTTTGATAC
*
3942798 TTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
*
3942843 TTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * * *
3942888 TTTCAAAACCTTCGGGTTATTTATAAGCCCTTTAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* * *
3942933 TTTTAAAGCCTTCGGTTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
3942978 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
3943023 TTTCAAAACCTTCGGG-CTATCTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTC-ATCTGTAAGCCCTTCAGTGCATGATGT
* * * * *
3943068 TTTTAAAGCCTTCGGGTCATTTGTAAGACCTACAGTGCA
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3943107 AGATAATAAG
Statistics
Matches: 240, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
44 1 0.00
45 238 0.99
46 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
Found at i:3943309 original size:10 final size:11
Alignment explanation
Indices: 3943284--3943323 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
3943274 TTTCATCATC
*
3943284 ATATTATTATT
1 ATATTATTAAT
3943295 ATATT-TTAAT
1 ATATTATTAAT
3943305 ATATTATT-AT
1 ATATTATTAAT
3943315 -TATTATTAA
1 ATATTATTAA
3943324 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 7 0.27
10 12 0.46
11 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTATTAAT
Found at i:3943326 original size:21 final size:21
Alignment explanation
Indices: 3943284--3943326 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3943274 TTTCATCATC
*
3943284 ATATTATTATTATATTTTAAT
1 ATATTATTATTATATTTAAAT
3943305 ATATTATTATTAT-TATTAAAT
1 ATATTATTATTATAT-TTAAAT
3943326 A
1 A
3943327 AAAAATACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTATTATTATATTTAAAT
Found at i:3944827 original size:22 final size:22
Alignment explanation
Indices: 3944782--3944823 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3944772 TAAAACCACG
3944782 TTTTAAAATATTTACTTTAATA
1 TTTTAAAATATTTACTTTAATA
3944804 TTTT-AAATATATTA-TTTAAT
1 TTTTAAAATAT-TTACTTTAAT
3944824 TATTGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATATTTACTTTAATA
Found at i:3946187 original size:23 final size:23
Alignment explanation
Indices: 3946161--3946263 Score: 100
Period size: 24 Copynumber: 4.4 Consensus size: 23
3946151 GTTCTACACT
*
3946161 GTCCTTCGGGACAAATCTATGTG
1 GTCCTTCGGGACAAATCTACGTG
* *
3946184 GTCCTTCAGGACAATTCTACGTG
1 GTCCTTCGGGACAAATCTACGTG
* * *
3946207 GTCATTCGGAACAAATTCTACGCG
1 GTCCTTCGGGACAAA-TCTACGTG
* *
3946231 GTCCTTCGGGAGAAATTATACGTG
1 GTCCTTCGGGACAAA-TCTACGTG
3946255 G-CACTTCGG
1 GTC-CTTCGG
3946264 TGCAAATTAT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
23 32 0.49
24 33 0.51
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (23 bp):
GTCCTTCGGGACAAATCTACGTG
Found at i:3947902 original size:31 final size:31
Alignment explanation
Indices: 3947862--3947935 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
3947852 TACAACGTCC
* * *
3947862 AAGTTACCAAAACCTAATAAAACGATAACGT
1 AAGTGACCAAAACCTAATAAAACAATAACAT
*
3947893 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACCTAATAAAACAATAACAT
*
3947924 AAGTGGCCAAAA
1 AAGTGACCAAAA
3947936 GTGTACAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (31 bp):
AAGTGACCAAAACCTAATAAAACAATAACAT
Found at i:3950763 original size:34 final size:34
Alignment explanation
Indices: 3950701--3950824 Score: 158
Period size: 34 Copynumber: 3.6 Consensus size: 34
3950691 TTGGAATAAT
* ** *
3950701 ATAATTTAATTTATTAAATTAATGTTAAATTTCGA
1 ATAATATAATTTA-TATTTTAATTTTAAATTTCGA
*
3950736 ATACTATAATTTATATTTTAATTTTAAATTTCGA
1 ATAATATAATTTATATTTTAATTTTAAATTTCGA
* * *
3950770 ATAATATTATTTTTATTTTTATTTTAAATTTCGA
1 ATAATATAATTTATATTTTAATTTTAAATTTCGA
*
3950804 ATAATATAATTTGTATTTTAA
1 ATAATATAATTTATATTTTAA
3950825 AAATATTTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
34 66 0.86
35 11 0.14
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
ATAATATAATTTATATTTTAATTTTAAATTTCGA
Found at i:3951374 original size:21 final size:20
Alignment explanation
Indices: 3951347--3951416 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
3951337 GGTATAAAAC
*
3951347 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
3951367 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
3951388 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
3951409 CCCTGCGG
1 -CCTGCGG
3951417 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:3951446 original size:21 final size:21
Alignment explanation
Indices: 3951420--3951488 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
3951410 CCTGCGGAGA
3951420 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGTGGGCT
3951441 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGTGGGCT
* *
3951462 TGGCATATGAAATGGAGGGCT
1 TGGCATATGAACTGGTGGGCT
*
3951483 GGGCAT
1 TGGCAT
3951489 GTACCCCTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.26
Consensus pattern (21 bp):
TGGCATATGAACTGGTGGGCT
Found at i:3952037 original size:6 final size:6
Alignment explanation
Indices: 3952028--3952073 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
3952018 ACTGAAACTG
*
3952028 AAATAT AAATAT AAATAT AAATAT ACAAT-T CAA-AT AAATA- AAATAT
1 AAATAT AAATAT AAATAT AAATAT A-AATAT AAATAT AAATAT AAATAT
3952074 TCTAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 10 0.29
6 21 0.62
7 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:3953285 original size:30 final size:32
Alignment explanation
Indices: 3953221--3953299 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
3953211 TTAATAATTC
*
3953221 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
3953255 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
3953285 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
3953300 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:3956888 original size:21 final size:21
Alignment explanation
Indices: 3956820--3956891 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
3956810 CCATATGGTA
* * *
3956820 TAACCCTACGGGATAGGCATG
1 TAACCCTGCGGGCTAGGAATG
3956841 TAA-CCTGGCGGGCTAGGAATG
1 TAACCCT-GCGGGCTAGGAATG
3956862 TAACCCTGCGGGCTAGGAATG
1 TAACCCTGCGGGCTAGGAATG
3956883 TAACCCTGC
1 TAACCCTGC
3956892 AGAGATGACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (21 bp):
TAACCCTGCGGGCTAGGAATG
Found at i:3958736 original size:31 final size:31
Alignment explanation
Indices: 3958669--3958769 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
3958659 ATAATAACAC
* * *
3958669 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
3958697 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
3958728 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
3958759 TAAAATATAAT
1 -AAAAAATAAT
3958770 AACTATTTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:3959114 original size:61 final size:60
Alignment explanation
Indices: 3958976--3959115 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 60
3958966 TTAATGAAAG
** *
3958976 GCGCGTCCCCGGGGATGCGCCTTTCACTTGTGGCAACTGAATCAGCAAAATAAAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCAAAATAAAGGTAAA
* * * * **
3959036 CCGCGTCCCCGGTGATGCGCCTTTCACACGTGGCATC-CAACTCAACGTAAAA-CCAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAA-TC-A-GCAAAATAAAGGTAAA
3959097 GCGCGTCCCCGGGGATGCG
1 GCGCGTCCCCGGGGATGCG
3959116 TATTTCGCCA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
59 2 0.03
60 34 0.52
61 25 0.38
62 5 0.08
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (60 bp):
GCGCGTCCCCGGGGATGCGCCTTTCACACGTGGCAACTCAATCAGCAAAATAAAGGTAAA
Found at i:3959739 original size:16 final size:16
Alignment explanation
Indices: 3959718--3959759 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3959708 CTTTTTATTT
3959718 GGGTTTAAAATTAATC
1 GGGTTTAAAATTAATC
3959734 GGGTTTAAAATTAATC
1 GGGTTTAAAATTAATC
*
3959750 GAGTTTAAAA
1 GGGTTTAAAA
3959760 ATATTAATGG
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:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (16 bp):
GGGTTTAAAATTAATC
Found at i:3966844 original size:14 final size:14
Alignment explanation
Indices: 3966811--3966845 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3966801 TGTTTCATTG
*
3966811 TCTTCTTTCTTTTT
1 TCTTCTTTCTTTCT
*
3966825 TTTTCTTTCTTTCT
1 TCTTCTTTCTTTCT
3966839 TCTTCTT
1 TCTTCTT
3966846 ACCATTGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTCTTTCTTTCT
Found at i:3968073 original size:2 final size:2
Alignment explanation
Indices: 3968066--3968090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3968056 GGTTTTAAGG
3968066 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3968091 AAAGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3968943 original size:22 final size:22
Alignment explanation
Indices: 3968915--3968978 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
3968905 ATAACTCCAC
*
3968915 CAATGCTAAGGCACTTTAGTAT
1 CAATGCTAAGGAACTTTAGTAT
* * *
3968937 CAATGCTAATGTACTTTTGTAT
1 CAATGCTAAGGAACTTTAGTAT
* *
3968959 CAGTGCTGAGGAACTTTAGT
1 CAATGCTAAGGAACTTTAGT
3968979 TATATGAATG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (22 bp):
CAATGCTAAGGAACTTTAGTAT
Found at i:3971362 original size:94 final size:94
Alignment explanation
Indices: 3971233--3971433 Score: 289
Period size: 94 Copynumber: 2.1 Consensus size: 94
3971223 GATACCGACG
* * * * * *
3971233 GGTAGTATCGATACCATGGTAAGGGTATCGTTACCAGGAAACATCGAATCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACCCAAAATGGGTATCAA
* *
3971298 TACCGAAA-AGGATATCGGTACCATAGTA
66 TACCAAAATAGGATATCGGTACCAGAGTA
3971326 TGGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACCCAAAATGGGTATCA
1 -GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACCCAAAATGGGTATCA
* *
3971391 ATACCAAAATAGGGTATCGGTACCAGGGTA
65 ATACCAAAATAGGATATCGGTACCAGAGTA
3971421 -GTAGTATCGATAC
1 GGTAGTATCGATAC
3971434 TATTGAGCTT
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 13 0.14
94 66 0.69
95 17 0.18
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACCCAAAATGGGTATCAA
TACCAAAATAGGATATCGGTACCAGAGTA
Found at i:3971988 original size:87 final size:83
Alignment explanation
Indices: 3971840--3972075 Score: 356
Period size: 87 Copynumber: 2.8 Consensus size: 83
3971830 CGAATGAATA
* * *
3971840 AAAGAATAATGCATATGGGTGCATTATTGTCATGAAAGGATGCCATAGCTGAAATGCATATGGGT
1 AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGT
3971905 GTATTCTCGGCATAAAAGAGTT
66 GTATTCTCGGCAT-AAA-A--T
3971927 AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGT
1 AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGT
*
3971992 GCATTCTCGGCATAAAAT
66 GTATTCTCGGCATAAAAT
3972010 ----AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGT-CATAGCTGAAATGTATATGGG
1 AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCCATAGCTGAAATGTATATGGG
3972070 TGTATT
65 TGTATT
3972076 ATTGGCGTGA
Statistics
Matches: 143, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
79 63 0.44
80 1 0.01
83 1 0.01
85 1 0.01
86 3 0.02
87 74 0.52
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (83 bp):
AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGT
GTATTCTCGGCATAAAAT
Found at i:3971990 original size:45 final size:44
Alignment explanation
Indices: 3971847--3972087 Score: 213
Period size: 45 Copynumber: 5.7 Consensus size: 44
3971837 ATAAAAGAAT
* *
3971847 AATGCATATGGGTGCATTATTGTCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCATAGCTGA
* * * * * *
3971892 AATGCATATGGGTGTATTCTCGGCAT-AAAAGAGTT-AAAG--AA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGA-TTCATAGCTGA
3971933 TAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGA
1 -AATGCATATGGGTGCATTATTGGCATGAAAGGATT-CATAGCTGA
* * *
3971979 AATGTATATGGGTGCATTCTCGGCAT-AAA--A-T-A-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCATAGCTGA
3972013 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCATAGCTGA
* * *
3972058 AATGTATATGGGTGTATTATTGGCGTGAAA
1 AATGCATATGGGTGCATTATTGGCATGAAA
3972088 AGATGCCATG
Statistics
Matches: 155, Mismatches: 23, Indels: 36
0.72 0.11 0.17
Matches are distributed among these distances:
34 23 0.15
35 3 0.02
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.01
40 1 0.01
41 3 0.02
42 26 0.17
43 9 0.06
44 11 0.07
45 73 0.47
46 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATTCATAGCTGA
Found at i:3972129 original size:48 final size:48
Alignment explanation
Indices: 3972073--3972172 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
3972063 ATATGGGTGT
* *
3972073 ATTATTGGCGTGAAAAGATGCCATGACAAAAAAAGCATGAACAGATGC
1 ATTATTGGCATGAAAAGATGCCATAACAAAAAAAGCATGAACAGATGC
** * * *
3972121 ATTATTGGCATGAATGGATGCCATAACTAAAAATGCATGAACGGATGC
1 ATTATTGGCATGAAAAGATGCCATAACAAAAAAAGCATGAACAGATGC
3972169 ATTA
1 ATTA
3972173 AGACATGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (48 bp):
ATTATTGGCATGAAAAGATGCCATAACAAAAAAAGCATGAACAGATGC
Found at i:3972201 original size:47 final size:48
Alignment explanation
Indices: 3972083--3972193 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
3972073 ATTATTGGCG
* * * * * *
3972083 TGAAAAGATGCCATGACAAAAAAAGCATGAACAGATGCATTATTGGCA
1 TGAAAGGATGCCATAACTAAAAATGCATGAACAGATGCATTATAGACA
* *
3972131 TGAATGGATGCCATAACTAAAAATGCATGAACGGATGCATTA-AGACA
1 TGAAAGGATGCCATAACTAAAAATGCATGAACAGATGCATTATAGACA
*
3972178 TGAAAGGATGTCATAA
1 TGAAAGGATGCCATAA
3972194 GTGAAAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
47 17 0.32
48 36 0.68
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.21
Consensus pattern (48 bp):
TGAAAGGATGCCATAACTAAAAATGCATGAACAGATGCATTATAGACA
Found at i:3972655 original size:68 final size:68
Alignment explanation
Indices: 3972543--3972714 Score: 272
Period size: 68 Copynumber: 2.5 Consensus size: 68
3972533 GATTAAAAGT
* * *
3972543 CTAACTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGTATTTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGA
3972608 GGC
66 GGC
*
3972611 CTTACTGTGTATTTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGTATTTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGA
3972676 GGC
66 GGC
* * * *
3972679 CTAACTGAGTAATTGGCAGAAAGGTGTCAATTATGC
1 CTAACTGTGTATTTGACAGAAAGGTGTCATTTATGC
3972715 TAGTAAGATA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 95 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (68 bp):
CTAACTGTGTATTTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:3972760 original size:29 final size:29
Alignment explanation
Indices: 3972719--3972806 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 29
3972709 TTATGCTAGT
3972719 AAGAT-AAACGGTTAAACACTGTTGAGTAA
1 AAGATGAAA-GGTTAAACACTGTTGAGTAA
*
3972748 AAGATGAAAGGTTAAACACTGTTAAGTAA
1 AAGATGAAAGGTTAAACACTGTTGAGTAA
* *
3972777 AAGATGAACGGTTAAACACTGTCGAGTAA
1 AAGATGAAAGGTTAAACACTGTTGAGTAA
3972806 A
1 A
3972807 TGGATAATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 51 0.94
30 3 0.06
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (29 bp):
AAGATGAAAGGTTAAACACTGTTGAGTAA
Found at i:3972945 original size:2 final size:2
Alignment explanation
Indices: 3972938--3972970 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3972928 TCAAGGGATG
3972938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3972971 ATCTACCACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3974649 original size:20 final size:20
Alignment explanation
Indices: 3974624--3974667 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3974614 ACATTATTGG
* *
3974624 TATTGTTCATGTAGTATCGA
1 TATTGTTCATGCAATATCGA
*
3974644 TATTGTTGATGCAATATCGA
1 TATTGTTCATGCAATATCGA
3974664 TATT
1 TATT
3974668 ATAAGAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (20 bp):
TATTGTTCATGCAATATCGA
Found at i:3975051 original size:19 final size:21
Alignment explanation
Indices: 3975027--3975066 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3975017 ACCAAAGCAA
*
3975027 AAGAAATATGT-T-ATAAAGG
1 AAGAAAAATGTATCATAAAGG
3975046 AAGAAAAATGTATCATAAAGG
1 AAGAAAAATGTATCATAAAGG
3975067 TAGAGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (21 bp):
AAGAAAAATGTATCATAAAGG
Found at i:3982374 original size:19 final size:20
Alignment explanation
Indices: 3982333--3982383 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3982323 GAAACCCCTT
*
3982333 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3982353 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3982372 TGAAGATACATG
1 TGAAAATACATG
3982384 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:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3986552 original size:19 final size:20
Alignment explanation
Indices: 3986511--3986561 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3986501 GAAACCCCTT
*
3986511 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3986531 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3986550 TGAAGATACATG
1 TGAAAATACATG
3986562 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:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3991607 original size:26 final size:26
Alignment explanation
Indices: 3991455--3991594 Score: 174
Period size: 26 Copynumber: 5.4 Consensus size: 26
3991445 TCATTTTTAC
*
3991455 TCGCACTCGAAAGTGTTATTTATCAT
1 TCGCACTCGAAAGTGCTATTTATCAT
* *
3991481 TCGCACTCGAAAGTTCTATTTATCAA
1 TCGCACTCGAAAGTGCTATTTATCAT
* * * *
3991507 TCACACTTGAAAGTGCTATTTTTCAC
1 TCGCACTCGAAAGTGCTATTTATCAT
*
3991533 TCGCACTCGAAAGTGCCATTTATCACT
1 TCGCACTCGAAAGTGCTATTTATCA-T
* *
3991560 T-GCACTCTAAAGTGCGATTTATCAT
1 TCGCACTCGAAAGTGCTATTTATCAT
3991585 TCGCACTCGA
1 TCGCACTCGA
3991595 TATTGCTTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
25 2 0.02
26 93 0.97
27 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.34
Consensus pattern (26 bp):
TCGCACTCGAAAGTGCTATTTATCAT
Found at i:3994557 original size:17 final size:18
Alignment explanation
Indices: 3994535--3994568 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3994525 TGCTATTTAT
3994535 ATCG-AAGATTGGTATCC
1 ATCGAAAGATTGGTATCC
*
3994552 ATCGAAAGCTTGGTATC
1 ATCGAAAGATTGGTATC
3994569 AATACCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (18 bp):
ATCGAAAGATTGGTATCC
Done.