Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002906.1 Hibiscus syriacus cultivar Beakdansim tig00006005_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: 35611
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3826 original size:23 final size:23
Alignment explanation
Indices: 3781--3827 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3771 ATTTAAGGTA
** *
3781 AAAATTATAAAATTTTAAGAAAT
1 AAAATTATAAAATCATAAAAAAT
*
3804 AAAATTATATAATCATAAAAAAT
1 AAAATTATAAAATCATAAAAAAT
3827 A
1 A
3828 TAAAGAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATTATAAAATCATAAAAAAT
Found at i:4185 original size:41 final size:42
Alignment explanation
Indices: 4081--4295 Score: 226
Period size: 41 Copynumber: 5.2 Consensus size: 42
4071 AAAAAAAAAT
* * *
4081 GCCGTTAAA-ACTCATATTTTAGTGGCGTTTTAAGCATAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
* * *
4122 GCCACTAAAGACTCATACTTTAGTGGCGTTTT-TGTACAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
* * *
4163 GCCGCTAAAAACT-AGTAATTTAGTGGCGTTTTAAGCA-AAAA
1 GCCGCTAAAGACTCA-TACTTTAGTGGCGTTTTAAGCACAAAC
* * *
4204 GCCGCTAAATACTCATACTTTAGAGGCGTTTT--TCTACAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGC-ACAAAC
* * *
4245 GCCGCTAAAGACTCGTACTTTAGTGGTGTTTTAAGCACAAAT
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
*
4287 GCCACTAAA
1 GCCGCTAAA
4296 ATACTACTAT
Statistics
Matches: 142, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 2 0.01
41 101 0.71
42 37 0.26
43 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
Found at i:4232 original size:82 final size:83
Alignment explanation
Indices: 4098--4300 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 83
4088 AAACTCATAT
* * * * *
4098 TTTAGTGGCGTTTTAAGCATAAACGCCACTAAAGACTCATACTTTAGTGGCGTTTTTGTACAAAC
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
4163 GCCGCTAAAAACTAGTAA
66 GCCGCTAAAAACTAGTAA
*
4181 TTTAGTGGCGTTTTAAGCA-AAAAGCCGCTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
* * *
4245 GCCGCTAAAGACTCGTAC
66 GCCGCTAAAAACTAGTAA
* *
4263 TTTAGTGGTGTTTTAAGCACAAATGCCACTAAAATACT
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACT-AAATACT
4301 ACTATTGCGG
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
82 73 0.68
83 27 0.25
84 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (83 bp):
TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
GCCGCTAAAAACTAGTAA
Found at i:5916 original size:34 final size:34
Alignment explanation
Indices: 5851--5920 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
5841 AATCGATACC
**
5851 TTTTACATTTGTATATGTATTTGCATCTTTGCAT
1 TTTTACATTTGTATATACATTTGCATCTTTGCAT
* * * *
5885 TTTTACGTTTGTATTTACATTTTCATTTTTGCAT
1 TTTTACATTTGTATATACATTTGCATCTTTGCAT
5919 TT
1 TT
5921 ACATCTTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (34 bp):
TTTTACATTTGTATATACATTTGCATCTTTGCAT
Found at i:11116 original size:22 final size:21
Alignment explanation
Indices: 11091--11161 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
11081 CATTTGACTA
11091 AAGATTGTTTTCCTTGAAACAG
1 AAGATT-TTTTCCTTGAAACAG
* *
11113 AAGATTTTATTTCATT--CA-AG
1 AAGA-TTT-TTTCCTTGAAACAG
**
11133 ATTATTTTTTCCTTGAAACAG
1 AAGATTTTTTCCTTGAAACAG
11154 AAGATTTT
1 AAGATTTT
11162 ATCTCATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
18 6 0.17
19 3 0.08
20 5 0.14
21 9 0.25
22 5 0.14
23 8 0.22
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (21 bp):
AAGATTTTTTCCTTGAAACAG
Found at i:11358 original size:23 final size:23
Alignment explanation
Indices: 11332--11400 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
11322 TATCTCACTC
11332 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
11355 AAGA-T-TTTAT-C-T--CACTC
1 AAGATTGTTTTTCCTTGAAACAG
11372 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
11395 AAGATT
1 AAGATT
11401 CTATCTCACT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 5 0.16
20 2 0.06
21 5 0.16
22 1 0.03
23 12 0.38
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:11518 original size:23 final size:23
Alignment explanation
Indices: 11492--11560 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
11482 TATCTCACTC
11492 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* *
11515 AAGATT-TTATCTCATT----C--
1 AAGATTGTT-TTTCCTTGAAACAG
11532 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
11555 AAGATT
1 AAGATT
11561 TTATCTCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 17 0.50
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:11673 original size:40 final size:40
Alignment explanation
Indices: 11091--11647 Score: 911
Period size: 40 Copynumber: 13.9 Consensus size: 40
11081 CATTTGACTA
* *
11091 AAGATTG-TTTTCCTTGAAACAGAAGATTTTATTTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
11130 AAGATTATTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATT-GTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
11171 AAGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
11211 AAGATTATTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATT-GTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
11252 AATATTGTTTTTCCTTGAAACAGAAGATTCTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
11292 AAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
11332 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
11372 AAGATTGTTTTTCCTTGAAACAGAAGATTCTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
11412 AAGATTGTTTTTCCTTGAAACAGAAGATTCTATCTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
11452 AAGATTGTTTTTTCTTGATACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
11492 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
11532 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
11572 AATATTGTTTTTCCTTGAAACCA-AAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAA-CAGAAGATTTTATCTCACTC
*
11612 AATATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
11648 GCTTGAGATA
Statistics
Matches: 486, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
39 8 0.02
40 403 0.83
41 75 0.15
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (40 bp):
AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
Found at i:11771 original size:28 final size:28
Alignment explanation
Indices: 11685--11770 Score: 136
Period size: 28 Copynumber: 3.0 Consensus size: 28
11675 ATTGTCTCCC
*
11685 TTGAGATAGTTTCTCTTGAAACAAGTTT
1 TTGATATAGTTTCTCTTGAAACAAGTTT
*
11713 TTGATACAGTTTCTCTTGAAACAAGTTT
1 TTGATATAGTTTCTCTTGAAACAAGTTT
*
11741 TTGATATAGTTTCTCTTGAAAAAAAGTTT
1 TTGATATAGTTTCTCTTG-AAACAAGTTT
11770 T
1 T
11771 GTCTCCCTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 43 0.81
29 10 0.19
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (28 bp):
TTGATATAGTTTCTCTTGAAACAAGTTT
Found at i:11811 original size:36 final size:37
Alignment explanation
Indices: 11771--11946 Score: 110
Period size: 36 Copynumber: 4.8 Consensus size: 37
11761 AAAAAGTTTT
* ** *
11771 GTCTCCCTTGAGATGGTTTTTCTTAAAACCAAGCT-C
1 GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
** * *
11807 GTCTCACTTGAGACAGTTTTCCCTTGAAA-CAAAATAA
1 GTCTCACTTGAGATGGTTTT-TCTTAAAACCAAAATAA
* * * **
11844 ATCTCACTTGAGATGGTTTTTCTTAAAACC-TACTTC
1 GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
** ** * * *
11880 GTCTGGCTTGAGACAGTTTTCCTTTTAAA-CAAAATGTA
1 GTCTCACTTGAGATGGTTTTTC-TTAAAACCAAAAT-AA
11918 -TCTCACTTGAGATGGTTTTTCTTAAAACC
1 GTCTCACTTGAGATGGTTTTTCTTAAAACC
11947 TACTTCGTCT
Statistics
Matches: 100, Mismatches: 33, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
36 51 0.51
37 48 0.48
38 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
Found at i:11854 original size:73 final size:73
Alignment explanation
Indices: 11772--12018 Score: 311
Period size: 73 Copynumber: 3.4 Consensus size: 73
11762 AAAAGTTTTG
* * *
11772 TCTCCCTTGAGATGGTTTTTCTTAAAACCAAGC-TCGTCTCACTTGAGACAGTTTTCCCTTGAAA
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTA-CTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAA
*
11836 CAAAATAAA
65 CAAAATATA
* * *
11845 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTGGCTTGAGACAGTTTTCCTTTTAAAC
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAAC
*
11910 AAAATGTA
66 AAAATATA
* * * *
11918 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTTGCTTAAGACAATTTT-CCTTCGGAA
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTT-GAAA
* *
11982 TAAAATTTA
65 CAAAATATA
*
11991 TCTCACTTGAGA-GTGCTTTTCTTAAAAC
1 TCTCACTTGAGATG-GTTTTTCTTAAAAC
12019 AATTTTCTTA
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
72 5 0.03
73 149 0.97
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (73 bp):
TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAAC
AAAATATA
Found at i:11928 original size:37 final size:35
Alignment explanation
Indices: 11808--11945 Score: 96
Period size: 37 Copynumber: 3.8 Consensus size: 35
11798 ACCAAGCTCG
* *
11808 TCTCACTTGAGACAGTTTTCCCTTGAAACAAAATAAA
1 TCTCACTTGAGACAGTTTT-CCTTAAAACAAAAT-TA
** * ** * *
11845 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
1 TCTCACTTGAGACAGTTTTCCTTAAAACAAAATT-A
** *
11881 TCTGGCTTGAGACAGTTTTCCTTTTAAACAAAATGTA
1 TCTCACTTGAGACAGTTTTCC-TTAAAACAAAAT-TA
** *
11918 TCTCACTTGAGATGGTTTTTCTTAAAAC
1 TCTCACTTGAGACAGTTTTCCTTAAAAC
11946 CTACTTCGTC
Statistics
Matches: 73, Mismatches: 25, Indels: 7
0.70 0.24 0.07
Matches are distributed among these distances:
36 31 0.42
37 41 0.56
38 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (35 bp):
TCTCACTTGAGACAGTTTTCCTTAAAACAAAATTA
Found at i:12571 original size:105 final size:105
Alignment explanation
Indices: 12401--12680 Score: 357
Period size: 105 Copynumber: 2.6 Consensus size: 105
12391 AGGGATCGAA
12401 ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGA
1 ATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGA
* * * *
12466 AATTGTTCCTTTCAAATTCACCACATAATGAGGTGAACCAAC
64 AATTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
* * *
12508 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAATGA-AAAAGTTTATAATGAGAAGAA
1 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAA-TTCATAATAAGAAGAA
* * * *
12572 CTTGCTCTTTTCAAGTCCACCGCAGAAGGAGGTGAACCAAC
65 ATTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
* *
12613 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAA--AGG-AGAA-AA-TTCATAATAAGA
12677 AGAA
61 AGAA
12681 CTTGTTCAAC
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
104 6 0.04
105 117 0.76
106 3 0.02
107 7 0.05
108 2 0.01
109 18 0.12
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (105 bp):
ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGAAA
TTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
Found at i:12771 original size:117 final size:118
Alignment explanation
Indices: 12514--12928 Score: 468
Period size: 117 Copynumber: 3.6 Consensus size: 118
12504 CAACATTTCC
* * *
12514 AGAAGAGTTCATAATGAGAAGAACTCGTCC--T-A--AATGAAAAAGTTTATAATGAGAAGAACT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAA-GAAGAAGTTCATAATGAGAAGAACT
* * * ** * * *
12574 TG--C-TC-TT--TTCAAGTCCACCGCAGAAGGAGGTGAACCAACATTTCC---
65 TGTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
12619 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
** *
12684 GTTCAACATTGGTTTGATTCCATCAAAGAA-AGAGGTGGATCAACATTTTCAGT
66 GTTCAACATTGGTTCAATTCCATCAAAGAAGA-AGGTGGATCAACATTTCCAGT
* *
12737 AGAA-AGTTCATAATGAGAAAAACTCATCCAATGAGTAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * *
12801 GTTCAACCTTGGTTCAATTCCATCACAGAAGAAGGTGGATTAATATTTCCAGT
66 GTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
* * * * *
12854 -GAAGAGTTCATAATGAGAAGAACTCATCTAACGAGGAATAAGAAGTTCATAATGAGAAAAACTC
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
12918 GTTCAACATTG
66 GTTCAACATTG
12929 CATTAACATT
Statistics
Matches: 262, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
105 29 0.11
107 1 0.00
108 1 0.00
109 25 0.10
110 2 0.01
111 1 0.00
112 1 0.00
113 2 0.01
115 27 0.10
116 3 0.01
117 165 0.63
118 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (118 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
Found at i:12951 original size:91 final size:87
Alignment explanation
Indices: 12839--13010 Score: 245
Period size: 91 Copynumber: 1.9 Consensus size: 87
12829 AAGAAGGTGG
* *
12839 ATTAATATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTAACGAGGAATAAGAAGTTCAT
1 ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATC-AAC-AAG-A-AAGAAGTTCAT
12904 AATGAGAAAAACTCGTTCAACATTGC
62 AATGAGAAAAACTCGTTCAACATTGC
* * *
12930 ATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCACAAGAGAGAAGTTCATAATG
1 ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCAACAAGAAAGAAGTTCATAATG
* *
12995 AGAAGAACTTGTTCAA
66 AGAAAAACTCGTTCAA
13011 TTCAACACTT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 28 0.38
88 1 0.01
89 2 0.03
90 2 0.03
91 41 0.55
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (87 bp):
ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCAACAAGAAAGAAGTTCATAATG
AGAAAAACTCGTTCAACATTGC
Found at i:16753 original size:37 final size:37
Alignment explanation
Indices: 16712--16788 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
16702 ATTGGTCACT
16712 TAATTTATGTAATATTTTATGATAACGATATACATTA
1 TAATTTATGTAATATTTTATGATAACGATATACATTA
16749 TAATTTATGTAATATTTTATGATAACGATATACATTA
1 TAATTTATGTAATATTTTATGATAACGATATACATTA
16786 TAA
1 TAA
16789 GTATGTGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (37 bp):
TAATTTATGTAATATTTTATGATAACGATATACATTA
Found at i:31692 original size:24 final size:24
Alignment explanation
Indices: 31651--31709 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
31641 ACATTGCTGG
*
31651 ATGATTTGTGCAGTTTCAATGGTGGC
1 ATGA-TTG-GCAGCTTCAATGGTGGC
31677 ATGATTGGCAGCTTCAATGGTGGC
1 ATGATTGGCAGCTTCAATGGTGGC
31701 ATGATTGGC
1 ATGATTGGC
31710 GGCATCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 25 0.78
25 3 0.09
26 4 0.12
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (24 bp):
ATGATTGGCAGCTTCAATGGTGGC
Found at i:32662 original size:42 final size:41
Alignment explanation
Indices: 32569--32670 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
32559 AAGGTTTTAT
* * * * *
32569 AGATGGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTTAC
1 AGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAC
* *
32610 AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTAC
*
32652 TGATGGCCCGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
32671 TAAATTATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAC
Found at i:32802 original size:20 final size:20
Alignment explanation
Indices: 32769--32884 Score: 56
Period size: 20 Copynumber: 5.7 Consensus size: 20
32759 AAACATCATA
**
32769 CCCGAAGGTTTTACAGATGG
1 CCCGAAGGACTTACAGATGG
** *
32789 CCCGAAGGACTTACCATCTTG
1 CCCGAAGGACTTA-CAGATGG
** *
32810 CTCTAAAGG-CTTACAGATGA
1 C-CCGAAGGACTTACAGATGG
* *
32830 CCCGAAGGAATTA-AGCATCATG
1 CCCGAAGGACTTACAG-AT--GG
* * *
32852 CTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTACAGATGG
32872 CCCGAAGGACTTA
1 CCCGAAGGACTTA
32885 TAAATTGTGA
Statistics
Matches: 66, Mismatches: 23, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
19 7 0.11
20 32 0.48
21 9 0.14
22 17 0.26
23 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (20 bp):
CCCGAAGGACTTACAGATGG
Found at i:32836 original size:41 final size:41
Alignment explanation
Indices: 32779--32884 Score: 140
Period size: 42 Copynumber: 2.6 Consensus size: 41
32769 CCCGAAGGTT
* * *
32779 TTACAGATGGCCCGAAGGACTTACCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTACCATCATGCTCGAAAGAC
* * *
32820 TTACAGATGACCCGAAGGAATTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ACCATCATGCTCGAAAGAC
*
32862 TTACTGATGGCCCGAAGGACTTA
1 TTACAGATGGCCCGAAGGACTTA
32885 TAAATTGTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 21 0.38
42 34 0.62
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTACCATCATGCTCGAAAGAC
Found at i:32853 original size:214 final size:214
Alignment explanation
Indices: 32396--33257 Score: 1422
Period size: 214 Copynumber: 4.0 Consensus size: 214
32386 AGACTCATAA
* *
32396 ATGACCCGAAGGATTTAAGCATCATGATCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
1 ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
* * ** *
32461 GTAAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTT
66 GTGAAATTTTGAAAATTGCATTCTTATTTTTAAAAAATTCCATCTTCTTAAAACATCA--TTTTT
* * * * *
32526 CATTTTCAAATTCATGTGAAAACATCCTACCTGAAGGTTTTATAGATGGCCCGAAAGACTTATCA
129 CATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTACCA
32591 TCTTGCTCTAAAGGCTTACAG
194 TCTTGCTCTAAAGGCTTACAG
*
32612 ATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
1 ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
* * * * *
32677 ATTAAATTTTGAAAATTACATTTTTCA-TTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTC
66 GTGAAATTTTGAAAATTGCATTCTT-ATTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTC
* *
32741 ATTTTCAAATTCATGTGAAAACATCATACCCGAAGGTTTTACAGATGGCCCGAAGGACTTACCAT
130 ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTACCAT
32806 CTTGCTCTAAAGGCTTACAG
195 CTTGCTCTAAAGGCTTACAG
32826 ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
1 ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
* *
32891 GTGAAATTTTGAAAATTGCATTCTTATTTTTAAAAAATTTCATCTTCTTAAAACATCATTTTTTA
66 GTGAAATTTTGAAAATTGCATTCTTATTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTCA
*
32956 TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCTCGAAGGACTTACCATC
131 TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTACCATC
33021 TTGCTCTAAAGGCTTACAG
196 TTGCTCTAAAGGCTTACAG
*
33040 ATGACCCGAAGGAATCAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
1 ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
33105 GTGAAATTTTGAAAATTGCATTCTTATTTTTAAAAAAATT-CATCTTCTTAAAACATCATTTTTC
66 GTGAAATTTTGAAAATTGCATTCTTATTTTT-AAAAAATTCCATCTTCTTAAAACATCATTTTTC
** *
33169 ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
130 ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTACCAT
*
33234 CTTGCCCTAAAGGCTTACAG
195 CTTGCTCTAAAGGCTTACAG
33254 ATGA
1 ATGA
33258 GTTTGCTTCA
Statistics
Matches: 613, Mismatches: 30, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
213 1 0.00
214 489 0.80
215 8 0.01
216 115 0.19
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (214 bp):
ATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT
GTGAAATTTTGAAAATTGCATTCTTATTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTCA
TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTACCATC
TTGCTCTAAAGGCTTACAG
Found at i:33050 original size:41 final size:41
Alignment explanation
Indices: 32987--33098 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
32977 ATCCTACCCG
* * *
32987 AAGGTCTTACAGATGGCTCGAAGGACTTACCATCTTGCTCTA
1 AAGG-CTTACAGATGGCCCGAAGGACTTACCATCATGCTCGA
* * * *
33029 AAGGCTTACAGATGACCCGAAGGAATCAAGCATCATGCTCGA
1 AAGGCTTACAGATGGCCCGAAGGACT-TACCATCATGCTCGA
* *
33071 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACAGATGGCCCGAAGGACTTA
33099 TAAATTGTGA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 20 0.35
42 37 0.65
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (41 bp):
AAGGCTTACAGATGGCCCGAAGGACTTACCATCATGCTCGA
Found at i:33300 original size:35 final size:37
Alignment explanation
Indices: 33243--33327 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 37
33233 TCTTGCCCTA
33243 AAGGCTTACAGATGAGTTTGCTTCACTAC-CTCTAGTG
1 AAGGCTTA-AGATGAGTTTGCTTCACTACTCTCTAGTG
* * *
33280 AAGGCTTAAGTTG-GTTTGCTTCACTACTCTTTGGTG
1 AAGGCTTAAGATGAGTTTGCTTCACTACTCTCTAGTG
33316 AAGGCTTAAGAT
1 AAGGCTTAAGAT
33328 TGACTTGCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 14 0.33
36 21 0.49
37 8 0.19
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (37 bp):
AAGGCTTAAGATGAGTTTGCTTCACTACTCTCTAGTG
Found at i:34283 original size:126 final size:125
Alignment explanation
Indices: 34063--34366 Score: 423
Period size: 126 Copynumber: 2.4 Consensus size: 125
34053 AATAATTTCT
* * *
34063 TGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTATACTG
1 TGGTCTGAATCTTCTCATCTCAACATGATGTGGGTTCAATCATGCCCCAACATTATCTTATACTA
*
34128 GTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTC-ATGCCTCCA
66 GTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTC-TCAATGCCTACA
* * * * *
34188 TGGTCTGAATCTTTTCATCTCAACATGATGTGTGTTTAATCGTGCCCCCAACATTATTTTATA-T
1 TGGTCTGAATCTTCTCATCTCAACATGATGTGGGTTCAATCATG-CCCCAACATTATCTTATACT
* * *
34252 CAGTACGGGCCTTCAAAATGCCCCATTACCTCAAATTGTAAGGCTCGTTCTCAATGCCTACT
65 -AGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTCAATGCCTACA
* * * *
34314 TGTTCTGAATCTGCTCATCTCAACATGATGTGGCTTCAACCATGCCCCAACAT
1 TGGTCTGAATCTTCTCATCTCAACATGATGTGGGTTCAATCATGCCCCAACAT
34367 ATCCTAACTT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
125 51 0.32
126 106 0.68
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (125 bp):
TGGTCTGAATCTTCTCATCTCAACATGATGTGGGTTCAATCATGCCCCAACATTATCTTATACTA
GTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTCAATGCCTACA
Done.