Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000218.1 Hibiscus syriacus cultivar Beakdansim tig00000386_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: 82558
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:12255 original size:25 final size:25
Alignment explanation
Indices: 12219--12266 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12209 ACCGAAGTGT
* * *
12219 TAATACACATAAGTTTGTTCCCACC
1 TAATACAAATAAGGTTGTGCCCACC
12244 TAATACAAATAAGGTTGTGCCCA
1 TAATACAAATAAGGTTGTGCCCA
12267 TGATATGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (25 bp):
TAATACAAATAAGGTTGTGCCCACC
Found at i:30442 original size:2 final size:2
Alignment explanation
Indices: 30435--30469 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30425 TATTATTTAT
*
30435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30470 GACTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:30581 original size:6 final size:6
Alignment explanation
Indices: 30542--30574 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30532 CTTATATATT
*
30542 TAAAAA -AACAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
30575 TTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
TAAAAA
Found at i:31971 original size:3 final size:3
Alignment explanation
Indices: 31965--32029 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
31955 AAAATTTATT
* * * *
31965 TAA TAA TAA TAA TAA TAA -AA TTA TTA TAG TAA TAA TAA AAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
32010 TAA TAA -ATA TAA TAAA TAA T
1 TAA TAA TA-A TAA T-AA TAA T
32030 GAGTAATGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 3 0.06
3 41 0.80
4 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31978 original size:26 final size:26
Alignment explanation
Indices: 31949--32009 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
31939 TTGGATCTAA
31949 AATAATAAAATTTATT-TAATAATAAT
1 AATAATAAAA-TTATTATAATAATAAT
*
31975 AATAATAAAATTATTATAGTAATAAT
1 AATAATAAAATTATTATAATAATAAT
*
32001 AAAAATAAA
1 AATAATAAA
32010 TAATAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AATAATAAAATTATTATAATAATAAT
Found at i:32018 original size:20 final size:19
Alignment explanation
Indices: 31969--32028 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
31959 TTTATTTAAT
*
31969 AATAATAATAATAAAATTA
1 AATAATAATAATAAAAATA
* *
31988 TTATAGTAATAATAAAAATA
1 -AATAATAATAATAAAAATA
32008 AATAATAA-ATATAATAAATA
1 AATAATAATA-ATAA-AAATA
32028 A
1 A
32029 TGAGTAATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 1 0.03
19 10 0.30
20 22 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AATAATAATAATAAAAATA
Found at i:32510 original size:113 final size:112
Alignment explanation
Indices: 32372--32700 Score: 493
Period size: 113 Copynumber: 2.9 Consensus size: 112
32362 ATAGAATCAT
* *
32372 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCTTTCTTCAGATGAGTTCTTCTC
* * * * *
32437 ATTATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
65 ATTATGAACTCGAC-CTGGCAATGTTGATCCATCGAATGATGAATTCAA
* *
32485 GCAAAAAGTTGAACAAATTCTTCTCATTATGAAC--TTCTTCTTTCTTCAGATGAGTTGTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCTTTCTTCAGATGAGTTCTTCTCA
* *
32548 TTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTTAA
66 TTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAA
* *
32595 GCCAAAAGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCTTTCTTCAGATGAGTTCTTCTC
32660 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATG
65 ATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATG
32701 GATTTGAATC
Statistics
Matches: 196, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
110 96 0.49
111 1 0.01
113 99 0.51
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (112 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCTTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAA
Found at i:34613 original size:75 final size:75
Alignment explanation
Indices: 34437--34613 Score: 176
Period size: 75 Copynumber: 2.4 Consensus size: 75
34427 CCAAAATGAT
* * * * * * * *
34437 ATAGGCCTTCAACATGCCCTAACATTT-GTCGATACAAGCGTTCAAAATGCGTCAACATTCCTCT
1 ATAGGCTTTCAGCATGCCCCAACATTTACT-GATACAAACGTTCAAAATACATCAACATTCCTCA
* *
34501 TTCTGATTGAT
65 TTCTGATTAAA
* * * * *
34512 ATGGGCTTTCAGCTTTCCCCAGCATTTACTGATACAAACGTTCAAAATACATCAACATTCCTGAT
1 ATAGGCTTTCAGCATGCCCCAACATTTACTGATACAAACGTTCAAAATACATCAACATTCCTCAT
34577 TCTGATTAAA
66 TCTGATTAAA
** *
34587 ATATTCTTTCAGCATGCCTCAACATTT
1 ATAGGCTTTCAGCATGCCCCAACATTT
34614 GCTTATTGTT
Statistics
Matches: 79, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
75 78 0.99
76 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (75 bp):
ATAGGCTTTCAGCATGCCCCAACATTTACTGATACAAACGTTCAAAATACATCAACATTCCTCAT
TCTGATTAAA
Found at i:37818 original size:8 final size:8
Alignment explanation
Indices: 37805--37833 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
37795 ATGATTTAAT
37805 TTTTTTCC
1 TTTTTTCC
37813 TTTTTTCC
1 TTTTTTCC
37821 -TTTTTCC
1 TTTTTTCC
37828 TTTTTT
1 TTTTTT
37834 TTTTGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:39935 original size:19 final size:19
Alignment explanation
Indices: 39911--39948 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39901 TGCATCAATA
39911 CCATGCATCGATGCACTCT
1 CCATGCATCGATGCACTCT
39930 CCATGCATCGATGCACTCT
1 CCATGCATCGATGCACTCT
39949 GATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (19 bp):
CCATGCATCGATGCACTCT
Found at i:40035 original size:17 final size:19
Alignment explanation
Indices: 40007--40055 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
39997 ATTTTTCAAA
40007 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
40025 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
40044 CACCGATGCACT
1 CATCGATGCACT
40056 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:48150 original size:21 final size:21
Alignment explanation
Indices: 48126--48165 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48116 TTTTCAAAGG
48126 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
48147 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
48166 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:48262 original size:64 final size:66
Alignment explanation
Indices: 48127--48251 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 66
48117 TTTCAAAGGC
*
48127 ATGCACCGATGCA-TCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 ATGCACCGATGCACTC-ATACCATGCATCGATGCATC-ATGAATAAATTAAAACATCGAATGCAT
48191 TCT
64 TCT
* *
48194 ATGCACCGATGCACTC-T-CCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATG
1 ATGCACCGATGCACTCATACCATGCATCGATGCA-TCATGAATAAATTAAAACATCGAATG
48252 TATTTGATGC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
64 20 0.38
65 15 0.28
66 3 0.06
67 13 0.25
68 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (66 bp):
ATGCACCGATGCACTCATACCATGCATCGATGCATCATGAATAAATTAAAACATCGAATGCATTC
T
Found at i:48270 original size:64 final size:64
Alignment explanation
Indices: 48146--48271 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
48136 TGCATCAATA
* *
48146 CCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATTCTATGCACCGATGCACTCT
1 CCATGCATCGATGCATC-ATGAATAAATTAAAACATCGAATGCATTCTATGCACCAATGCACTCT
* * * *
48211 CCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGTATT-TGATGCATCAATGCAC
1 CCATGCATCGATGCA-TCATGAATAAATTAAAACATCGAATGCATTCT-ATGCACCAATGCAC
48272 CAAGCTATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.02
64 35 0.66
65 15 0.28
66 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (64 bp):
CCATGCATCGATGCATCATGAATAAATTAAAACATCGAATGCATTCTATGCACCAATGCACTCT
Found at i:54094 original size:24 final size:22
Alignment explanation
Indices: 54067--54146 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
54057 CACTTAACAA
54067 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
54091 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
54111 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
54135 TGCATCGATGCA
1 TGCATCGATGCA
54147 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:56712 original size:21 final size:21
Alignment explanation
Indices: 56688--56727 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56678 TTTTCAAAGG
56688 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
56709 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
56728 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:56777 original size:19 final size:19
Alignment explanation
Indices: 56753--56791 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
56743 TCGAATACAT
56753 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
56772 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
56791 T
1 T
56792 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:56824 original size:64 final size:65
Alignment explanation
Indices: 56688--56852 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 65
56678 TTTTCAAAGG
*
56688 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATAC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATAC
56751 ATTC
62 ATTC
* * * *
56755 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATACATTC
* **
56819 GATGCATCC-ATGCACAATCCATGCATCGATGCAC
1 CATGCA-CCGATGCACTCTCCATGCATCGATGCAC
56853 CAGGCTATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
64 51 0.59
65 17 0.20
66 3 0.03
67 14 0.16
68 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATACATTC
Found at i:56870 original size:64 final size:64
Alignment explanation
Indices: 56688--56890 Score: 182
Period size: 64 Copynumber: 3.1 Consensus size: 64
56678 TTTTCAAAGG
** ** * *
56688 CATGCA-CCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATACA
1 CATGCATCCGATGCA-CAAT-CCATGCATCGATGCA-CGCTG-ATTTATTAAAACATCGAATGCA
*
56752 TTC
62 TTT
** *
56755 CATGCA-CCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * *
56819 GATGCATCC-ATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATGCAC
1 CATGCATCCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCAT
56881 TT
63 TT
56883 CATGCATC
1 CATGCATC
56891 GTTGCACTCT
Statistics
Matches: 115, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 73 0.63
65 18 0.16
66 6 0.05
67 16 0.14
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (64 bp):
CATGCATCCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:58997 original size:28 final size:28
Alignment explanation
Indices: 58915--58998 Score: 69
Period size: 34 Copynumber: 2.8 Consensus size: 28
58905 ATATGTAACT
* * *
58915 ATGCAAATACAACGATGCAAAAATAAAA
1 ATGCAAATGCAAAGATGCAAACATAAAA
* *
58943 ATGCAAATTGTGCAATACAAAAGCAAACATAAAA
1 ATGCAAA---TGC-A-A-AGATGCAAACATAAAA
58977 ATGCAAATGCAAAGATGCAAAC
1 ATGCAAATGCAAAGATGCAAAC
58999 GCAAAAAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
28 15 0.35
29 1 0.02
30 1 0.02
31 5 0.12
32 1 0.02
33 1 0.02
34 19 0.44
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (28 bp):
ATGCAAATGCAAAGATGCAAACATAAAA
Found at i:59162 original size:43 final size:44
Alignment explanation
Indices: 59081--59163 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
59071 TTGTGCATCA
* * *
59081 AACAAAACTTTTATATGTAGGGGACAACTTTCAGTCCTAATTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAATTTC
* * *
59125 AACAAAAC-TTTACATATATGGGATAACTTTCCCTCCTAA
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAA
59164 CTTCTCTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 25 0.76
44 8 0.24
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAATTTC
Found at i:61433 original size:14 final size:15
Alignment explanation
Indices: 61414--61443 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
61404 AATAGTAATA
61414 ATAAAAAAA-TAAAC
1 ATAAAAAAATTAAAC
61428 ATAAAAAAATTAAAC
1 ATAAAAAAATTAAAC
61443 A
1 A
61444 ATGAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
ATAAAAAAATTAAAC
Found at i:62050 original size:13 final size:13
Alignment explanation
Indices: 62032--62058 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62022 CTTTTCTCTC
62032 TAACTGAGAGATT
1 TAACTGAGAGATT
62045 TAACTGAGAGATT
1 TAACTGAGAGATT
62058 T
1 T
62059 CCCCCCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (13 bp):
TAACTGAGAGATT
Found at i:62943 original size:3 final size:3
Alignment explanation
Indices: 62937--63008 Score: 62
Period size: 3 Copynumber: 24.3 Consensus size: 3
62927 AAAATTTATT
* * *
62937 TAA TAA TAA TAA TAA TAA TAA -AA TTA TTA TAG TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
62982 TAA TAAA TAA -AA TAAA TAA TAAA TAA T
1 TAA T-AA TAA TAA T-AA TAA T-AA TAA T
63009 GAGTAATGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
2 8 0.14
3 41 0.71
4 9 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62972 original size:29 final size:29
Alignment explanation
Indices: 62920--62988 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
62910 TTTGGATCTG
62920 AAATAATAAAATTTATTTAATAATAATAA
1 AAATAATAAAATTTATTTAATAATAATAA
* *
62949 TAATAATAAAA-TTATTATAGTAATAATAA
1 AAATAATAAAATTTATT-TAATAATAATAA
62978 AATATAATAAA
1 AA-ATAATAAA
62989 TAAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 22 0.63
30 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATAATAAAATTTATTTAATAATAATAA
Found at i:62987 original size:13 final size:13
Alignment explanation
Indices: 62969--63004 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
62959 ATTATTATAG
62969 TAATAATAAAATA
1 TAATAATAAAATA
62982 TAATAAATAAAATA
1 TAAT-AATAAAATA
62996 -AATAATAAA
1 TAATAATAAA
63005 TAATGAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAAAATA
Found at i:63000 original size:16 final size:14
Alignment explanation
Indices: 62969--63007 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
62959 ATTATTATAG
62969 TAAT-AATAAAATA
1 TAATAAATAAAATA
62982 TAATAAATAAAATAAA
1 TAATAAATAAAAT--A
62998 TAATAAATAA
1 TAATAAATAA
63008 TGAGTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
16 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAATAAAATA
Found at i:69375 original size:21 final size:21
Alignment explanation
Indices: 69343--69382 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
69333 GTCTGATACT
69343 GGGGGTTCGGTATCGAGACTG
1 GGGGGTTCGGTATCGAGACTG
69364 GGGGGCTT-GGTATCGAGAC
1 GGGGG-TTCGGTATCGAGAC
69383 AATATTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.15, C:0.15, G:0.47, T:0.23
Consensus pattern (21 bp):
GGGGGTTCGGTATCGAGACTG
Found at i:71820 original size:32 final size:32
Alignment explanation
Indices: 71775--71888 Score: 115
Period size: 32 Copynumber: 3.6 Consensus size: 32
71765 ACTTATTCAA
* * *
71775 TTAG-TGATGTGACACATGTCACATCATCATT
1 TTAGATGATATGACACATATCACATCATCACT
*
71806 TTAGATGATATGACACATATCACATCGTCACT
1 TTAGATGATATGACACATATCACATCATCACT
* * **
71838 TT-GACTAATATGACACATAACATGTCATCACT
1 TTAGA-TGATATGACACATATCACATCATCACT
* *
71870 GTAGATGATGTGACACATA
1 TTAGATGATATGACACATA
71889 ACATGTCATC
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 6 0.09
32 60 0.88
33 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (32 bp):
TTAGATGATATGACACATATCACATCATCACT
Done.