Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006925.1 Hibiscus syriacus cultivar Beakdansim tig00017764_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: 97326
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3656 original size:17 final size:17
Alignment explanation
Indices: 3609--3681 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
3599 ATTCTAAATG
*
3609 TTTATAGTTATCAGACA
1 TTTATAGTTATCAGATA
*
3626 TTTCATCGTTATCAGATA
1 TTT-ATAGTTATCAGATA
*
3644 TTTATAATTATCAGATGA
1 TTTATAGTTATCAGAT-A
* * *
3662 -TTACAGTTATAAGATG
1 TTTATAGTTATCAGATA
3678 TTTA
1 TTTA
3682 CAGAAATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 29 0.64
18 16 0.36
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTATAGTTATCAGATA
Found at i:3682 original size:17 final size:17
Alignment explanation
Indices: 3651--3697 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3641 ATATTTATAA
* *
3651 TTATCAGATGATTACAG
1 TTATAAGATGTTTACAG
3668 TTATAAGATGTTTACAG
1 TTATAAGATGTTTACAG
**
3685 AAATAAGATGTTT
1 TTATAAGATGTTT
3698 TATAGTTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (17 bp):
TTATAAGATGTTTACAG
Found at i:8142 original size:20 final size:21
Alignment explanation
Indices: 8090--8150 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
8080 TCCCCTGTGG
8090 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
8113 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
8133 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
8151 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:14893 original size:81 final size:81
Alignment explanation
Indices: 14752--14912 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 81
14742 TTATAATTCC
* * * * *
14752 TTTAGTCTTTTACCCAAAGGCCTTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCA
1 TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACC-
14817 AATGCACAGTTAGGCCA
65 AATGCACAGTTAGGCCA
* * * *
14834 TTTA-TCTTTTACTCAATGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTATCA
1 TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACCA
14898 ATGCACAGTTAGGCC
66 ATGCACAGTTAGGCC
14913 TCAAAGGCAC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
80 16 0.23
81 50 0.71
82 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTAGTCTTTTACCCAAAGGCCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTACCA
ATGCACAGTTAGGCCA
Found at i:14960 original size:67 final size:67
Alignment explanation
Indices: 14863--15191 Score: 284
Period size: 67 Copynumber: 4.7 Consensus size: 67
14853 TCTTTAACCG
*
14863 TTCATCTAACT-AGCATAATTGACACATTTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGA-CATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAG
14927 CCT
65 CCT
* * *
14930 TTCATCTAACTGACATAATTGATACCTTTCTGTCAATGCACAGTTAGACCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
14995 CT
66 CT
* * * * * * *****
14997 TTCATCTAAATGGCATACTTGACACATTTCTGTCAATGTACAGTTAGGCTATTTATCTTTTACTC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGC--CTCA-AAGGCACT-
* *
15062 AATGGTCT
62 --TAGCCT
* * * *
15070 TTAATCATTCATA-TAACTGACATAATTGACACATTTCTATCAATGCACAGTTAGGCCTCAAAGG
1 TTCATC--T-A-ACTGAC--A-T-AATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGG
15134 CACTTAGCCT
58 CACTTAGCCT
* * * *
15144 TTCATCTAACTGGCATAATTAACACCTTTCTGTCAATACACAGTTAGG
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGG
15192 TTATTTATCT
Statistics
Matches: 202, Mismatches: 44, Indels: 32
0.73 0.16 0.12
Matches are distributed among these distances:
67 131 0.65
68 1 0.00
69 3 0.01
70 4 0.02
71 3 0.01
72 1 0.00
73 9 0.04
74 9 0.04
75 1 0.00
76 3 0.01
77 4 0.02
78 3 0.01
80 30 0.15
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:15136 original size:214 final size:215
Alignment explanation
Indices: 14766--15190 Score: 669
Period size: 214 Copynumber: 2.0 Consensus size: 215
14756 GTCTTTTACC
* * *
14766 CAAAGGCCTTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCAAATGCACAGTTAGG
1 CAAAGGCCTTTAACCTTTCATCTAAATGGCATGATTGACACATTTCTGCCAAATGCACAGTTAGG
* *
14831 CCATTTATCTTTTACTCAATGGTCTTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTAT
66 CCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAGCATAATTGACACATTTCTAT
* *
14896 CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGATACCTTTCT
131 CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTTTCT
*
14961 GTCAATGCACAGTTAGACCT
196 GTCAATACACAGTTAGACCT
* * *
14981 CAAAGGCAC-TTAGCCTTTCATCTAAATGGCAT-ACTTGACACATTTCTGTC-AATGTACAGTTA
1 CAAAGGC-CTTTAACCTTTCATCTAAATGGCATGA-TTGACACATTTCTGCCAAATGCACAGTTA
* *
15043 GGCTATTTATCTTTTACTCAATGGTCTTTAATCATTCATATAACT-GACATAATTGACACATTTC
64 GGCCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAG-CATAATTGACACATTTC
*
15107 TATCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTAACACCTT
128 TATCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTT
15172 TCTGTCAATACACAGTTAG
193 TCTGTCAATACACAGTTAG
15191 GTTATTTATC
Statistics
Matches: 193, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
213 1 0.01
214 150 0.78
215 41 0.21
216 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (215 bp):
CAAAGGCCTTTAACCTTTCATCTAAATGGCATGATTGACACATTTCTGCCAAATGCACAGTTAGG
CCATTTATCTTTTACTCAATGGTCTTTAACCATTCATATAACTAGCATAATTGACACATTTCTAT
CAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTAACACCTTTCT
GTCAATACACAGTTAGACCT
Found at i:15179 original size:147 final size:147
Alignment explanation
Indices: 14930--15352 Score: 630
Period size: 147 Copynumber: 2.9 Consensus size: 147
14920 CACTTAGCCT
* * *
14930 TTCATCTAACTGACATAATTGATACCTTTCTGTCAATGCACAGTTAGACCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * * *
14995 CTTTCATCTAAATGGCATACTTGACACATTTCTGTCAATGTACAGTTAGGCTATTTATCTTTTAC
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
* *
15060 TCAATGGTCTTTAATCA
131 TCAATGCTCTTTAACCA
* *
15077 TTCATATAACTGACATAATTGACACATTTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * *
15142 CTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAATACACAGTTAGGTTATTTATCTTTTAC
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
*
15207 TCAATGCTCTTTAACCG
131 TCAATGCTCTTTAACCA
* * *
15224 TTCATCTAACTAACATAATTGACACATTTTTGTCAATGCACTGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * * * * *
15289 CTTTCATCTAATTAGCATAATTTACACCTTTCTGTCAATGCACAATTATGCCATTTATCTTTTA
66 CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTA
15353 TTTTGGAATA
Statistics
Matches: 248, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 248 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (147 bp):
TTCATCTAACTGACATAATTGACACATTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CTTTCATCTAAATGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCTATTTATCTTTTAC
TCAATGCTCTTTAACCA
Found at i:15579 original size:57 final size:57
Alignment explanation
Indices: 15513--15682 Score: 286
Period size: 57 Copynumber: 3.0 Consensus size: 57
15503 TAAAGTTCTT
*
15513 ATACGGAAATTCATAAACAAATTATTAATTTCTTAACTTTTTGCACACTCAGTGTCC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
* *
15570 ATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGCCC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
* * *
15627 ATACGGAAATTCATAAACATATTATGAATTTCTTAATTTTTTGCACACTCACTGTC
1 ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTC
15683 ATTATGTAAT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 105 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (57 bp):
ATACGGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTCAGTGTCC
Found at i:16056 original size:19 final size:19
Alignment explanation
Indices: 16029--16069 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
16019 GTATCGATGC
16029 TACTATACTATGGTACCGA
1 TACTATACTATGGTACCGA
*
16048 TACTCTACTATGGTACCGA
1 TACTATACTATGGTACCGA
16067 TAC
1 TAC
16070 CATTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (19 bp):
TACTATACTATGGTACCGA
Found at i:16118 original size:20 final size:19
Alignment explanation
Indices: 16093--16161 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
16083 TGTTTCGGAT
16093 GGTATCGATACCTTCCATTC
1 GGTATCGATACCTTCC-TTC
* *
16113 GGTATCGATA-CTCCCTCC
1 GGTATCGATACCTTCCTTC
*
16131 GGTATC-AAACTCTCTCCTTC
1 GGTATCGATAC-CT-TCCTTC
16151 GGTATCGATAC
1 GGTATCGATAC
16162 TGATTCATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 6 0.15
20 20 0.51
21 3 0.08
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (19 bp):
GGTATCGATACCTTCCTTC
Found at i:16135 original size:18 final size:20
Alignment explanation
Indices: 16093--16136 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
16083 TGTTTCGGAT
*
16093 GGTATCGATACCTTCCATTC
1 GGTATCGATACCTTCCATCC
*
16113 GGTATCGATA-C-TCCCTCC
1 GGTATCGATACCTTCCATCC
16131 GGTATC
1 GGTATC
16137 AAACTCTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCTTCCATCC
Found at i:18834 original size:25 final size:25
Alignment explanation
Indices: 18806--18866 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
18796 CTCAAATTCA
*
18806 TTTTTATTTTATTCTGATTTAC-TAT
1 TTTTTATTTTATT-TAATTTACATAT
* *
18831 TTTTAATTTTATTTAATTTACATGT
1 TTTTTATTTTATTTAATTTACATAT
18856 TTTTTATTTTA
1 TTTTTATTTTA
18867 CCTCATCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (25 bp):
TTTTTATTTTATTTAATTTACATAT
Found at i:26841 original size:25 final size:25
Alignment explanation
Indices: 26807--26857 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
26797 AAAAGAAAGC
* *
26807 TTTGATTGTTATTGTGCTTTTGGAT
1 TTTGACTGTTATTGTGCCTTTGGAT
26832 TTTGACTGTTATTGTGCCTTTGGAT
1 TTTGACTGTTATTGTGCCTTTGGAT
26857 T
1 T
26858 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.57
Consensus pattern (25 bp):
TTTGACTGTTATTGTGCCTTTGGAT
Found at i:26875 original size:6 final size:6
Alignment explanation
Indices: 26859--26890 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
26849 CTTTGGATTA
26859 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
26891 ATGTTTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:27280 original size:208 final size:208
Alignment explanation
Indices: 26922--27335 Score: 792
Period size: 208 Copynumber: 2.0 Consensus size: 208
26912 CATAATCCCT
* *
26922 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTTTTTATTTTAATGAAATTTAA
1 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
*
26987 TATCATTTCAAGATAAAAAAATTATAAAAAAACTCAAGCCAATCAATGATTGACACGTGTCAATT
66 TATCATTTCAAGATAAAAAAATTATAAAAAAACTCAAGCCAATCAATGATTGACACGTGACAATT
27052 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
131 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
27117 TAATTTTGCCTAA
196 TAATTTTGCCTAA
27130 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
1 AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
*
27195 TATCATTTCAAGATAAAAAAATTATAAAAAAACTCAAGCCAATCAATGATTGACATGTGACAATT
66 TATCATTTCAAGATAAAAAAATTATAAAAAAACTCAAGCCAATCAATGATTGACACGTGACAATT
27260 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
131 CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
27325 TAATTTTGCCT
196 TAATTTTGCCT
27336 TCAATTTTTT
Statistics
Matches: 202, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
208 202 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (208 bp):
AAAAAATTCTCTTTAATTGGTTACATTGTTAAAATTATATCTTTCTTTATTTCAATGAAATTTAA
TATCATTTCAAGATAAAAAAATTATAAAAAAACTCAAGCCAATCAATGATTGACACGTGACAATT
CCCCCTAAAAACACCTTTTACTTAGATATAATAGTAAGATTAATAATCAAAAGTTTACTATTTTC
TAATTTTGCCTAA
Found at i:31180 original size:207 final size:200
Alignment explanation
Indices: 30832--31224 Score: 554
Period size: 207 Copynumber: 1.9 Consensus size: 200
30822 TCCCAACTGT
* *
30832 GTATGTGTGACTTGTGTGTTTTAATATATCAAAAATTAATAAATATTAAAATAATAGTCAATATG
1 GTATGTGTGACTTGTATGTTTTAATATATCAAAAATTAATAAATAATAAAATAATAGTCAATATG
* * *
30897 TTGGGTATGTATTAGGGATGGCAAACAAGTATAATTTTACGAATTTCTCAATGTATCCGTTTCAA
66 TTGGGTATGTATTAGGGATGGCAAACAAGTATAATTTTACGAATTTCGCAACGTACCCGTTTCAA
*
30962 TTGGAATGAGGATGAGTATAAGTTTAATGGGTAGTAGGCAAGTGTGAATGTAAAAAAAATCATAT
131 TTGGAATGAGGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAAAAATCATAT
31027 CCGCC
196 CCGCC
* *
31032 GTATGTGTGACTTGTATGTTTTGATGTATCAAAAAGTAATACATCTTAAAGTAATAAAATAATAG
1 GTATGTGTGACTTGTATGTTTTAATATATCAAAAA-T--TA-A---TAAA-TAATAAAATAATAG
* * * *
31097 TTAATATGTTGGGTATGTATTA-GGATGGCAGACGAGTATAATTTTACGAATTTCGCACCGTACC
58 TCAATATGTTGGGTATGTATTAGGGATGGCAAACAAGTATAATTTTACGAATTTCGCAACGTACC
* * * * *
31161 CGTTTCAATTGGGATGAGGATGAGTATACGTTTAATGGATAGTGGGCGAGTGTGGATGTAAAAA
123 CGTTTCAATTGGAATGAGGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAA
31225 TATCATACCC
Statistics
Matches: 168, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
200 32 0.19
201 1 0.01
203 2 0.01
204 1 0.01
207 98 0.58
208 34 0.20
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.34
Consensus pattern (200 bp):
GTATGTGTGACTTGTATGTTTTAATATATCAAAAATTAATAAATAATAAAATAATAGTCAATATG
TTGGGTATGTATTAGGGATGGCAAACAAGTATAATTTTACGAATTTCGCAACGTACCCGTTTCAA
TTGGAATGAGGATGAGTATAAGTTTAATGGATAGTAGGCAAGTGTGAATGTAAAAAAAATCATAT
CCGCC
Found at i:31791 original size:2 final size:2
Alignment explanation
Indices: 31784--31837 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
31774 ATGTGCACTA
31784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31826 AT AT AT AT AT AT
1 AT AT AT AT AT AT
31838 CAGTCCTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32206 original size:20 final size:20
Alignment explanation
Indices: 32181--32233 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
32171 TAATACAAAA
*
32181 TCGCAACGAGATACTGATTT
1 TCGCAACGAGATACTGACTT
* *
32201 TCGCAACGTGATTCTGACTT
1 TCGCAACGAGATACTGACTT
*
32221 TCGCAACGCGATA
1 TCGCAACGAGATA
32234 ATACATAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:34124 original size:18 final size:18
Alignment explanation
Indices: 34103--34147 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
34093 TCCACTTCGG
*
34103 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
34121 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
34139 GAGCCATCA
1 GAGCCATCA
34148 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:34677 original size:19 final size:20
Alignment explanation
Indices: 34623--34668 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
34613 TAGTTTACTT
* *
34623 TCGCAACATGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
34643 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
34663 TCGCAA
1 TCGCAA
34669 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:34684 original size:19 final size:19
Alignment explanation
Indices: 34662--34758 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
34652 GGAAATGGCT
34662 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34681 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
34695 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34714 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
34728 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34747 GTCGCAATGCGA
1 ATCGCAATGCGA
34759 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34697 original size:14 final size:14
Alignment explanation
Indices: 34678--34734 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34668 ATGCGAAATG
34678 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
34692 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
34711 AAAATCGCAACGAC
1 AAAATCGCAACGAC
34725 AAAATCGCAA
1 AAAATCGCAA
34735 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:34704 original size:33 final size:33
Alignment explanation
Indices: 34662--34753 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
34652 GGAAATGGCT
34662 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
34695 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
34728 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
34754 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:34789 original size:14 final size:15
Alignment explanation
Indices: 34770--34845 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 15
34760 TTGTGTTTCG
34770 CGTTGCGATTT-TGT
1 CGTTGCGATTTATGT
*
34784 CGTTGCGATTTCATTT
1 CGTTGCGATTT-ATGT
*
34800 CGCGTTGCGATTTTCATTT
1 --CGTTGCGA-TTT-ATGT
34819 CGCATTGCGATTT-TGT
1 CG--TTGCGATTTATGT
34835 CGTTGCGATTT
1 CGTTGCGATTT
34846 GCATTTCGCA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
14 20 0.38
16 6 0.11
17 2 0.04
18 11 0.21
19 14 0.26
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (15 bp):
CGTTGCGATTTATGT
Found at i:34799 original size:19 final size:18
Alignment explanation
Indices: 34765--34904 Score: 107
Period size: 19 Copynumber: 7.9 Consensus size: 18
34755 GCGATTTGTG
34765 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
34781 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
34797 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
34816 TTTCGCATTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
34832 TGT--CGTTGCGATTTGCA
1 TTTCGCGTTGCGATTT-CA
* **
34849 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
34868 TTTCTGCGTTGCGATAGTCA
1 TTTC-GCGTTGCGAT-TTCA
34888 TTTTCGCGTTGCGATTT
1 -TTTCGCGTTGCGATTT
34905 TAAGTTTCGT
Statistics
Matches: 99, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
14 21 0.21
16 6 0.06
17 2 0.02
18 11 0.11
19 32 0.32
20 23 0.23
21 4 0.04
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:34820 original size:51 final size:52
Alignment explanation
Indices: 34765--34882 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 52
34755 GCGATTTGTG
* ***
34765 TTTCGCGTTGCGATTTTGTCGTTGCGATTT-CATTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTGCATTTCGCATTGCGATAGCCA
*
34816 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCATTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTGCATTTCGCATTGCGATAGCCA
34868 TTTCTGCGTTGCGAT
1 TTTC-GCGTTGCGAT
34883 AGTCATTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 29 0.49
52 21 0.36
53 9 0.15
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (52 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTGCATTTCGCATTGCGATAGCCA
Found at i:34881 original size:20 final size:20
Alignment explanation
Indices: 34847--34902 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
34837 TTGCGATTTG
*
34847 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
34866 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
34886 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
34903 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:35364 original size:41 final size:42
Alignment explanation
Indices: 35268--35355 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
35258 GACTCACCTG
* *
35268 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
35310 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
35351 TCATC
1 TCATC
35356 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:36799 original size:14 final size:14
Alignment explanation
Indices: 36765--36803 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
36755 TTGATTGTTT
36765 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
36779 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
36793 TGTTGATTTGT
1 AATTGATTTGT
36804 TTAATTTGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:36924 original size:20 final size:20
Alignment explanation
Indices: 36899--36937 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36889 ATGTTGAAGG
36899 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
36919 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
36938 GAGAAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:36964 original size:19 final size:19
Alignment explanation
Indices: 36940--37007 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
36930 ATCGCAACGA
36940 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36959 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
36978 GAAAATTGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
36992 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
37008 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:37051 original size:20 final size:20
Alignment explanation
Indices: 37026--37121 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
37016 TCGCATTGCG
*
37026 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
***
37046 ATTTTCGCA-TTGCGATTTTTC
1 ATTTTCG-AGTTGCGA-TAGCC
* *
37067 A-TTTCGAATTGCCATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
37086 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
37106 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
37122 TTCCCCATTG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.07
20 53 0.87
21 4 0.07
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:37112 original size:40 final size:41
Alignment explanation
Indices: 37026--37112 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 41
37016 TCGCATTGCG
* * * ***
37026 ATTTTCTAGTTGCGATAGCCATTTTCGCATTGCGATTTTTC
1 ATTTTCGAATTGCCATAGCCATTTTCGCATTGCGATTAGCC
*
37067 A-TTTCGAATTGCCATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCGAATTGCCATAGCCATTTTCGCATTGCGATTAGCC
37106 ATTTTCG
1 ATTTTCG
37113 CGTTGCGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.08
40 34 0.89
41 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (41 bp):
ATTTTCGAATTGCCATAGCCATTTTCGCATTGCGATTAGCC
Found at i:37442 original size:21 final size:21
Alignment explanation
Indices: 37412--37486 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
37402 AGTCAGTATT
37412 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
*
37433 GCATTACGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
37454 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
37475 GCATTGCGATTT
1 GCATTGCGATTT
37487 ACTTATTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (21 bp):
GCATTGCGATTTTCCAAATTC
Found at i:37721 original size:12 final size:12
Alignment explanation
Indices: 37702--37731 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
37692 CTCTCCGGCG
37702 ACATCCGTTCCT
1 ACATCCGTTCCT
*
37714 ATATCCGTTCCT
1 ACATCCGTTCCT
37726 ACATCC
1 ACATCC
37732 TTCTCCATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.40, G:0.07, T:0.33
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:38509 original size:12 final size:12
Alignment explanation
Indices: 38492--38516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38482 ATATAATCCT
38492 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38504 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38516 G
1 G
38517 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:40502 original size:19 final size:19
Alignment explanation
Indices: 40480--40537 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
40470 GGAAATTACT
40480 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40499 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
40513 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40532 ATCGCA
1 ATCGCA
40538 TCGCGTTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 15 0.50
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40567 original size:19 final size:18
Alignment explanation
Indices: 40543--40601 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
40533 TCGCATCGCG
40543 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCG-A
**
40562 TTGCGA--TTC-CCTCG-
1 TTGCGATTTTCATTTCGA
40576 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
40595 TTGCGAT
1 TTGCGAT
40602 AGTACTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:40727 original size:14 final size:14
Alignment explanation
Indices: 40708--40744 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40698 CATCAATTAA
40708 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
40722 ACAAATCACCTTTT
1 ACAAATCAACTTTT
40736 ACAAATCAA
1 ACAAATCAA
40745 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:42164 original size:21 final size:21
Alignment explanation
Indices: 42098--42164 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
42088 GTGAATCGGG
*
42098 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
42118 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
42140 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
42161 CTCT
1 CTCT
42165 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:42183 original size:42 final size:41
Alignment explanation
Indices: 42098--42220 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
42088 GTGAATCGGG
* * * *
42098 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
42140 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
42182 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
42221 CGAGTCAGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:42612 original size:90 final size:90
Alignment explanation
Indices: 42438--42621 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 90
42428 ATTTCAAACT
* *
42438 TTCAACCAAAAGACAAAACAAGGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
*
42503 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAACAACCGAATAAATTTAC
42531 TTCAACCAAAAGACAAAAAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGCA
1 TTCAACCAAAAGAC-AAAAAAAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGCA
*
42594 GTATTGGCAACAACCGAATAAATTTAC
64 GAATTGGCAACAACCGAATAAATTTAC
42621 T
1 T
42622 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
90 35 0.41
93 14 0.16
94 35 0.41
95 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTGGCAACAACCGAATAAATTTAC
Found at i:44339 original size:20 final size:19
Alignment explanation
Indices: 44308--44429 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
44298 TCTTTTGGTT
44308 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
44327 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
44348 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
44367 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
44381 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
44400 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
44414 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
44430 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 29 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:44376 original size:14 final size:14
Alignment explanation
Indices: 44357--44412 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
44347 GGAAATGACT
44357 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
44371 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
44388 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
44404 ATCGCAACG
1 ATCGCAACG
44413 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:44390 original size:33 final size:33
Alignment explanation
Indices: 44333--44429 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
44323 ACGAGATAAT
44333 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
44367 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
44400 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
44430 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:44463 original size:19 final size:19
Alignment explanation
Indices: 44430--44474 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44420 AAAATCGCAA
*
44430 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
44449 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
44468 TGCGATT
1 TGCGATT
44475 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:45070 original size:20 final size:19
Alignment explanation
Indices: 45029--45082 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
45019 GCTATGTAAA
*
45029 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGAT-TTAAGAT
*
45049 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTAAG-AT
* *
45069 TCACGTTGCGATTT
1 TCGCATTGCGATTT
45083 TCCTAATTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTAAGAT
Found at i:45160 original size:21 final size:21
Alignment explanation
Indices: 45090--45161 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
45080 TTTTCCTAAT
45090 TCGC-ATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * * *
45110 TCGCAACGTGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAA
45130 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
45151 TTGCATTGCGA
1 TCGCAATGCGA
45162 TAGTCAGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
20 20 0.50
21 20 0.50
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:45215 original size:20 final size:21
Alignment explanation
Indices: 45171--45222 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
45161 ATAGTCAGTA
*
45171 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
45192 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
45212 TCGCATTGCGA
1 TCGCATTGCGA
45223 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:45237 original size:41 final size:41
Alignment explanation
Indices: 45090--45237 Score: 99
Period size: 41 Copynumber: 3.6 Consensus size: 41
45080 TTTTCCTAAT
** * *
45090 TCGCA-TGCGAATTAGGAAAATCGCAACGTGAATACGT-A-AA
1 TCGCATTGCGAATTAGGAAAATCGCATTGCG-ATAC-TCAGTA
* * *
45130 TCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGTA
1 TCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGTA
* *** * *
45171 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTA-T-
1 TCGCATTGCGAATTAGGAAAATCGCATTGCGA--TACTCAGTA
*
45212 TCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCGAATTAGGAAAATCGCA
45238 ACGCGAAATT
Statistics
Matches: 83, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.01
40 9 0.11
41 68 0.82
42 1 0.01
43 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (41 bp):
TCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGTA
Found at i:45264 original size:21 final size:22
Alignment explanation
Indices: 45212--45264 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
45202 ATTTACTTAT
45212 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
45233 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
45254 TCGCATTGCGA
1 TCGCATTGCGA
45265 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:51028 original size:20 final size:20
Alignment explanation
Indices: 51003--51041 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
50993 CTATTATTAG
51003 TTGCATGACAACTAATAATT
1 TTGCATGACAACTAATAATT
51023 TTGCATGACAACTAATAAT
1 TTGCATGACAACTAATAAT
51042 CTCCCACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (20 bp):
TTGCATGACAACTAATAATT
Found at i:55680 original size:21 final size:20
Alignment explanation
Indices: 55640--55681 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
55630 CCAACTTACA
*
55640 ATGCATTATAAACCATTATT
1 ATGCATCATAAACCATTATT
*
55660 ATGCATCATACAACTATTATT
1 ATGCATCATA-AACCATTATT
55681 A
1 A
55682 GTTGCATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (20 bp):
ATGCATCATAAACCATTATT
Found at i:56165 original size:20 final size:20
Alignment explanation
Indices: 56140--56197 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
56130 AACACGATGG
56140 GCATCTGAGGCCATCCGAGA
1 GCATCTGAGGCCATCCGAGA
*
56160 GCATCTGAGGCCATCCAAGA
1 GCATCTGAGGCCATCCGAGA
56180 GCATCTGAGGCCATCCGA
1 GCATCTGAGGCCATCCGA
56198 ATGAGCTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.16
Consensus pattern (20 bp):
GCATCTGAGGCCATCCGAGA
Found at i:56223 original size:10 final size:10
Alignment explanation
Indices: 56138--56256 Score: 58
Period size: 10 Copynumber: 11.3 Consensus size: 10
56128 CCAACACGAT
*
56138 GGGCATCTGA
1 GGGCATCCGA
*
56148 GGCCATCCGA
1 GGGCATCCGA
* *
56158 GAGCATCTGA
1 GGGCATCCGA
* *
56168 GGCCATCCAA
1 GGGCATCCGA
* *
56178 GAGCATCTGA
1 GGGCATCCGA
*
56188 GGCCATCCGAA
1 GGGCATCCG-A
* *
56199 TGAGCTATGCGA
1 -GGGC-ATCCGA
56211 GGGCATCCGA
1 GGGCATCCGA
*
56221 GGGCAACCGA
1 GGGCATCCGA
*
56231 GCGAGCTATGCGA
1 G-G-GC-ATCCGA
*
56244 GGGAATCCGA
1 GGGCATCCGA
56254 GGG
1 GGG
56257 AACCCGAGCG
Statistics
Matches: 77, Mismatches: 26, Indels: 12
0.67 0.23 0.10
Matches are distributed among these distances:
10 56 0.73
11 6 0.08
12 6 0.08
13 9 0.12
ACGTcount: A:0.25, C:0.26, G:0.35, T:0.13
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:56237 original size:33 final size:33
Alignment explanation
Indices: 56200--56268 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
56190 CCATCCGAAT
*
56200 GAGCTATGCGAGGGCATCCGAGGGCAA-CCGAGC
1 GAGCTATGCGAGGGAATCCGAGGG-AACCCGAGC
56233 GAGCTATGCGAGGGAATCCGAGGGAACCCGAGC
1 GAGCTATGCGAGGGAATCCGAGGGAACCCGAGC
56266 GAG
1 GAG
56269 GGTAGGTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.26, C:0.25, G:0.41, T:0.09
Consensus pattern (33 bp):
GAGCTATGCGAGGGAATCCGAGGGAACCCGAGC
Found at i:56440 original size:29 final size:29
Alignment explanation
Indices: 56398--56454 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
56388 GAGTAAGGGT
56398 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
56427 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
56455 GGCCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:59080 original size:2 final size:2
Alignment explanation
Indices: 59059--59106 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
59049 CCACAGATAA
* * *
59059 AT AT AA AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59101 AT AT AT
1 AT AT AT
59107 CCACTAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:59421 original size:28 final size:28
Alignment explanation
Indices: 59388--59453 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
59378 TGTGTCTTTG
*
59388 TTTCTATTTTGATCAATCAA-TTTTAAAA
1 TTTCTATTTTAATCAATCAACTTTT-AAA
* *
59416 TTTCTAATTTAATCACTCAACTTTTAAA
1 TTTCTATTTTAATCAATCAACTTTTAAA
59444 TTTCTATTTT
1 TTTCTATTTT
59454 TTTTCTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTCTATTTTAATCAATCAACTTTTAAA
Found at i:60028 original size:29 final size:28
Alignment explanation
Indices: 59964--60028 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
59954 TTAAGTTAGT
* *
59964 GTGTAAATTTGAACTTATAAAATTTCAG
1 GTGTGAATTTAAACTTATAAAATTTCAG
* *
59992 GGGATGAATTTAAACTTATAAAATTTTGAG
1 GTG-TGAATTTAAACTTATAAAA-TTTCAG
60022 GTGTGAA
1 GTGTGAA
60029 AATAGATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (28 bp):
GTGTGAATTTAAACTTATAAAATTTCAG
Found at i:67047 original size:13 final size:13
Alignment explanation
Indices: 67022--67062 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
67012 TGAAAACTAC
67022 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
67036 ACATTGTTTTCAA
1 ACATTGTTTTCAA
*
67049 ACATAGTTTTCAA
1 ACATTGTTTTCAA
67062 A
1 A
67063 ATTTTCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:69182 original size:22 final size:22
Alignment explanation
Indices: 69141--69201 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
69131 AGATTGCCCG
69141 GATGGTACCGATA-CCCCCTCA
1 GATGGTACCGATACCCCCCTCA
* *
69162 GATTGTACCGGTACCCCCCTCA
1 GATGGTACCGATACCCCCCTCA
*
69184 GATGGTACTGATACCCCC
1 GATGGTACCGATACCCCC
69202 ATGCCAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 11 0.32
22 23 0.68
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.21
Consensus pattern (22 bp):
GATGGTACCGATACCCCCCTCA
Found at i:70388 original size:124 final size:124
Alignment explanation
Indices: 70201--70448 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 124
70191 TTTGGTTGTT
70201 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
1 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
*
70266 TTAAAAATATCATGTCAGCAATTTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
66 TTAAAAATATCATGTCAGCAAATTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
70325 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
1 GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
*
70390 TTAAAAATATCATGTTAGCAAATTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
66 TTAAAAATATCATGTCAGCAAATTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
70449 ATCACAACGT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (124 bp):
GCTAAAAAATTAAGGATGATACTGACATGTCATCATAAGGTAATATTATATGATACTTAAAAAAA
TTAAAAATATCATGTCAGCAAATTTGCTAATTTTTTTAACAGTGAGTGATTAAAATGAA
Found at i:71869 original size:33 final size:32
Alignment explanation
Indices: 71814--71887 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
71804 ATTTATATAT
*
71814 TTTTTAAATTATTTTACCTTAATATTTAAATTA
1 TTTTTAAATTATTTTACCTTAATA-TGAAATTA
**
71847 CTTTTTAAATTA-TTTATTTTAATATGAAATTA
1 -TTTTTAAATTATTTTACCTTAATATGAAATTA
71879 -TTTTAAATT
1 TTTTTAAATT
71888 TAGTTGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.24
32 7 0.19
33 10 0.27
34 11 0.30
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (32 bp):
TTTTTAAATTATTTTACCTTAATATGAAATTA
Found at i:72050 original size:17 final size:18
Alignment explanation
Indices: 72018--72052 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
72008 TGAATTTTAC
*
72018 TAAAAAATTAATATAAAT
1 TAAAAAATTAAAATAAAT
72036 TAAAAAA-TAAAATAAAT
1 TAAAAAATTAAAATAAAT
72053 ATTAATCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATTAAAATAAAT
Found at i:73752 original size:20 final size:20
Alignment explanation
Indices: 73724--73765 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
73714 AAGATTTGCT
*
73724 AAAATATATAATTATA-TTTA
1 AAAAAATATAATT-TAGTTTA
73744 AAAAAATATAATTTAGTTTA
1 AAAAAATATAATTTAGTTTA
73764 AA
1 AA
73766 CTATGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAAATATAATTTAGTTTA
Found at i:74002 original size:3 final size:3
Alignment explanation
Indices: 73994--74050 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
73984 AATTAATTTT
*
73994 ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
74041 ATA ATA ATA A
1 ATA ATA ATA A
74051 AAAGAAGGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:74190 original size:15 final size:15
Alignment explanation
Indices: 74149--74194 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
74139 TTTAAATATA
74149 ATTTTTAACTATTTGAT
1 ATTTTTAA-TATTT-AT
*
74166 A--TTAAATATTTAT
1 ATTTTTAATATTTAT
74179 ATTTTTAATATTTAT
1 ATTTTTAATATTTAT
74194 A
1 A
74195 ATATTCGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 5 0.20
15 16 0.64
17 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTTAATATTTAT
Found at i:75413 original size:26 final size:26
Alignment explanation
Indices: 75362--75414 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
75352 CCTTTTTTAT
**
75362 ATTAGTGATGCATTTCAATGTGTGTC
1 ATTAGTGATGCATTTCAATGAATGTC
*
75388 ATTAGTGGTGCATTTCAATGAATGTC
1 ATTAGTGATGCATTTCAATGAATGTC
75414 A
1 A
75415 CTCATTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTAGTGATGCATTTCAATGAATGTC
Found at i:75715 original size:34 final size:34
Alignment explanation
Indices: 75672--75743 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
75662 CCCATCATTT
*
75672 CAAAGCCTACAAAAAAATGAAAAACAATTAAAAG
1 CAAAGCCTACAAAAAAATGAAAAACAATGAAAAG
75706 CAAAGCCTACAAAAAAATGAAAAACAATGAAAAG
1 CAAAGCCTACAAAAAAATGAAAAACAATGAAAAG
75740 CAAA
1 CAAA
75744 AAGCGCTGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.65, C:0.15, G:0.10, T:0.10
Consensus pattern (34 bp):
CAAAGCCTACAAAAAAATGAAAAACAATGAAAAG
Found at i:76926 original size:17 final size:17
Alignment explanation
Indices: 76904--76940 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
76894 TCCAAGTAAC
76904 TTAGCATAACAGTGTAT
1 TTAGCATAACAGTGTAT
76921 TTAGCATAACAGTGTAT
1 TTAGCATAACAGTGTAT
76938 TTA
1 TTA
76941 TGCGTCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (17 bp):
TTAGCATAACAGTGTAT
Found at i:79693 original size:18 final size:17
Alignment explanation
Indices: 79663--79696 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
79653 ATATTTATTT
*
79663 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
79680 ATATGAAAAAATAATAT
1 ATAT-AAAAAATAATAT
79697 TGTGATCTCA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:79810 original size:17 final size:17
Alignment explanation
Indices: 79766--79815 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
79756 TTCAAAATTA
*
79766 AATATTATTTTTA-AAT
1 AATAATATTTTTACAAT
79782 AATTACAT-TTTTTACAAT
1 AA-TA-ATATTTTTACAAT
*
79800 AATAATATTTTCACAA
1 AATAATATTTTTACAA
79816 CATAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 6 0.21
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAATATTTTTACAAT
Found at i:79925 original size:38 final size:37
Alignment explanation
Indices: 79882--79964 Score: 125
Period size: 35 Copynumber: 2.3 Consensus size: 37
79872 CTACTCAAAT
79882 TTATTAATATTTTATTAAATTAAACTATTTGTATATTA
1 TTATTAATATTTTA-TAAATTAAACTATTTGTATATTA
* *
79920 TTATT-AT-GTTTATAAATTAAACTCTTTGTATATTA
1 TTATTAATATTTTATAAATTAAACTATTTGTATATTA
79955 TTATTAATAT
1 TTATTAATAT
79965 GAAAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
35 27 0.68
36 6 0.15
37 2 0.05
38 5 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (37 bp):
TTATTAATATTTTATAAATTAAACTATTTGTATATTA
Found at i:82171 original size:6 final size:6
Alignment explanation
Indices: 82163--82196 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
82153 ATGAGAAGAT
*
82163 GAAGGT GAAGGC GAAGGC GAAGGC GAAGGC GAAG
1 GAAGGC GAAGGC GAAGGC GAAGGC GAAGGC GAAG
82197 ATTGAGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.50, T:0.03
Consensus pattern (6 bp):
GAAGGC
Found at i:84434 original size:45 final size:45
Alignment explanation
Indices: 84379--84474 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
84369 CTTAATAATT
*
84379 AGTTTATGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
1 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
*
84424 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCATGA
1 AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
84469 AGTTTC
1 AGTTTC
84475 GTCCCCTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (45 bp):
AGTTTCTGACTCTCGTTTTATTACTATTTATAATTATTTTCACGA
Found at i:85074 original size:52 final size:52
Alignment explanation
Indices: 85012--85117 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
85002 GATTGAATCA
85012 ACAATTGATTTAACCTGTGTAACAAACTTATAGAAAGAAAAAGTTTTAGGGT
1 ACAATTGATTTAACCTGTGTAACAAACTTATAGAAAGAAAAAGTTTTAGGGT
85064 ACAATTGATTTAACCTGTGTAACAAACTTATAGAAAGAAAAAGTTTTAGGGT
1 ACAATTGATTTAACCTGTGTAACAAACTTATAGAAAGAAAAAGTTTTAGGGT
85116 AC
1 AC
85118 GCAAACTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (52 bp):
ACAATTGATTTAACCTGTGTAACAAACTTATAGAAAGAAAAAGTTTTAGGGT
Found at i:86611 original size:194 final size:192
Alignment explanation
Indices: 86273--86643 Score: 573
Period size: 194 Copynumber: 1.9 Consensus size: 192
86263 ATAATTGACT
* * * * * *
86273 GATATGGCGGAGGTTGACATATCTTTTGGTTACTACATTTCCTGTTACTGAAGCTTCTTTTCTTT
1 GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
86338 TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
66 TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
* * * *
86403 CTGACTTTTATGCCTTGTATATTGTAATCTTTAGCTTTTTCCCTTGATTCCTTGAGATGAGACC
131 CCGACTTTTATGCCTTG--TATTGTAATCTTGAGCATCTTCCCTTGATTCCTTGAGATGAGACC
* *
86467 GATATCGCAGAGGTTGACATCTCCTTTGGTCACTACATTTCCGGTTAGTCAAGCTTCTTTTCTTT
1 GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
* *
86532 TTTGTTCATATCCATAGTAGATCTTATGTTTCCAG-TTAGTGAAACTCGGTATGTTGATCTTTTG
66 TTTGTTCATATCCATAGTAGATCTTATATTTCC-GTTTAGTGAAACTCGGTATGTCGATCTTTTG
*
86596 ACCGACTTTTATGCCTTGTATTGTTATCTTGAGCATCTTCCCTTGATT
130 ACCGACTTTTATGCCTTGTATTGTAATCTTGAGCATCTTCCCTTGATT
86644 GCACCAGTGT
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
192 26 0.16
194 134 0.83
195 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.44
Consensus pattern (192 bp):
GATATCGCAGAGGTTGACATATCCTTTGGTCACTACATTTCCGGTTACTCAAGCTTCTTTTCTTT
TTTGTTCATATCCATAGTAGATCTTATATTTCCGTTTAGTGAAACTCGGTATGTCGATCTTTTGA
CCGACTTTTATGCCTTGTATTGTAATCTTGAGCATCTTCCCTTGATTCCTTGAGATGAGACC
Done.