Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009369.1 Hibiscus syriacus cultivar Beakdansim tig00113235_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: 88322
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3580 original size:2 final size:2
Alignment explanation
Indices: 3573--3640 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
3563 TATATTCTAT
*
3573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3615 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3641 GAAGAGAGAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7347 original size:2 final size:2
Alignment explanation
Indices: 7340--7412 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
7330 TACATACCTT
7340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7413 CGAAAGGGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11192 original size:2 final size:2
Alignment explanation
Indices: 11185--11217 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11175 AATTCTATTA
11185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11218 GAAAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11565 original size:26 final size:26
Alignment explanation
Indices: 11515--11566 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11505 TCGCTCGATG
* * *
11515 AGGTGACCGACCCGTTGTACCCGAGA
1 AGGTGACAGACCCATTATACCCGAGA
*
11541 AGGTGACAGACCCATTATACTCGAGA
1 AGGTGACAGACCCATTATACCCGAGA
11567 GGTAGTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (26 bp):
AGGTGACAGACCCATTATACCCGAGA
Found at i:20096 original size:66 final size:66
Alignment explanation
Indices: 19982--20122 Score: 187
Period size: 66 Copynumber: 2.1 Consensus size: 66
19972 ATCAGCATGC
* * *
19982 TCTACATCTCTGTTACTCTCAACAGCAGAGACAGATAATGCGTCGGAATTCTTTTCACCGATATG
1 TCTACATCTCTGTTACTCTCAACAGCAGAGACAGATAACGAGTCGGAATTCTTTTCACCAATATG
20047 A
66 A
* *
20048 TCTACATCTCTGTTAGTCTCAACAGCAGAGGA-AGATAACGAG-CTGGAATTCTTTTCATCAATA
1 TCTACATCTCTGTTACTCTCAACAGCAGA-GACAGATAACGAGTC-GGAATTCTTTTCACCAATA
*
20111 TGT
64 TGA
*
20114 TCCACATCT
1 TCTACATCT
20123 GCCCTAGTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.02
66 63 0.95
67 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (66 bp):
TCTACATCTCTGTTACTCTCAACAGCAGAGACAGATAACGAGTCGGAATTCTTTTCACCAATATG
A
Found at i:20136 original size:66 final size:66
Alignment explanation
Indices: 19998--20137 Score: 151
Period size: 66 Copynumber: 2.1 Consensus size: 66
19988 TCTCTGTTAC
* * * * **
19998 TCTCAACAGCAGAGACAGATAATGCGTCGGAATTCTTTTCACCGATATGATCTACATCTCTGTTA
1 TCTCAACAGCAGAGACAGATAACGAGTCGGAATTCTTTTCACCAATATGATCCACATCTCTCCTA
20063 G
66 G
* *
20064 TCTCAACAGCAGAGGA-AGATAACGAG-CTGGAATTCTTTTCATCAATATGTTCCACATCTGC-C
1 TCTCAACAGCAGA-GACAGATAACGAGTC-GGAATTCTTTTCACCAATATGATCCACATCT-CTC
20126 CTAG
63 CTAG
*
20130 TGTCAACA
1 TCTCAACA
20138 TCGTCTTCGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
65 1 0.02
66 58 0.94
67 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (66 bp):
TCTCAACAGCAGAGACAGATAACGAGTCGGAATTCTTTTCACCAATATGATCCACATCTCTCCTA
G
Found at i:27748 original size:20 final size:20
Alignment explanation
Indices: 27691--27790 Score: 107
Period size: 20 Copynumber: 5.0 Consensus size: 20
27681 AATGACCAAC
*
27691 AAATTCGCAACGCGATCTC-
1 AAATTCGCAACGCGATTTCT
*
27710 AAATTCGCAACAC-AGTTTCT
1 AAATTCGCAACGCGA-TTTCT
*
27730 AAATTCGCAACTCGATTTCT
1 AAATTCGCAACGCGATTTCT
*
27750 GCAA-TCGCAACGCGATTTCT
1 -AAATTCGCAACGCGATTTCT
*
27770 GAATTCGCAACGCGACTTTCT
1 AAATTCGCAACGCGA-TTTCT
27791 TTTTCGCAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
18 1 0.01
19 17 0.25
20 43 0.62
21 8 0.12
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTCT
Found at i:27796 original size:20 final size:19
Alignment explanation
Indices: 27754--27820 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
27744 ATTTCTGCAA
**
27754 TCGCAACGCGATTTCTGAAT
1 TCGCAACGCGATTTCT-TTT
27774 TCGCAACGCGACTTTCTTTT
1 TCGCAACGCGA-TTTCTTTT
* * *
27794 TCGCAACACAAGTTTCCTTT
1 TCGCAACGCGA-TTTCTTTT
27814 TCGCAAC
1 TCGCAAC
27821 AAGATTTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 35 0.88
21 5 0.12
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (19 bp):
TCGCAACGCGATTTCTTTT
Found at i:27857 original size:20 final size:20
Alignment explanation
Indices: 27773--27902 Score: 88
Period size: 20 Copynumber: 6.5 Consensus size: 20
27763 GATTTCTGAA
* *
27773 TTCGCAACGCG-ACTTTCTTT
1 TTCGCAACACGAATTTTC-TT
*
27793 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTTCTT
* *
27813 TTCGCAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTTCT-T
* *
27833 ATCGCAACACGAATTTTGTT
1 TTCGCAACACGAATTTTCTT
* **
27853 TTCGCAACTCG-ATTTTCGAA
1 TTCGCAACACGAATTTTC-TT
**
27873 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTCTT
27893 TTCGCAACAC
1 TTCGCAACAC
27903 AAATGTTTTG
Statistics
Matches: 85, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
19 10 0.12
20 61 0.72
21 14 0.16
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTTCTT
Found at i:27889 original size:40 final size:40
Alignment explanation
Indices: 27694--27900 Score: 129
Period size: 40 Copynumber: 5.2 Consensus size: 40
27684 GACCAACAAA
* * * * * *
27694 TTCGCAACGCGA-TCTCAAATTCGCAACAC-AGTTTCTAAA
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTT-TGAT
* *
27733 TTCGCAACTCGA-TTTCTGCAA-TCGCAACGCG-ATTTCTGAA
1 TTCGCAACTCGATTTTC-G-AATTCGCAACACGAATTT-TGAT
* * *** ***
27773 TTCGCAACGCGACTTTCTTTTTCGCAACAC-AAGTTTCCTT
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAA-TTTTGAT
** * * *
27813 TTCGCAACAAGATTTTCTAAATCGCAACACGAATTTTGTT
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTGAT
*
27853 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAAT
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTGAT
27893 TTCGCAAC
1 TTCGCAAC
27901 ACAAATGTTT
Statistics
Matches: 131, Mismatches: 29, Indels: 15
0.75 0.17 0.09
Matches are distributed among these distances:
39 14 0.11
40 106 0.81
41 11 0.08
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTGAT
Found at i:28690 original size:24 final size:24
Alignment explanation
Indices: 28656--28709 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
28646 GTATTCGAAA
* *
28656 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
28680 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
28704 TTTGAT
1 TTTGAT
28710 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:31499 original size:21 final size:21
Alignment explanation
Indices: 31475--31572 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
31465 GTGAATCGGG
* *
31475 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
31496 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
31517 CTCTTGAACGATGAGAGAGGC
1 CTCTTGAACGATGAGAGGGGC
31538 CTCTTGAACGAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
31559 CTCTTGAACGATGA
1 CTCTTGAACGATGA
31573 AAGGTGAATC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.01
21 69 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:31870 original size:21 final size:21
Alignment explanation
Indices: 31846--31898 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31836 TAAAACAATC
* *
31846 TCACGTAGAGCGGCTACCTCA
1 TCACGTAAAGCGGATACCTCA
*
31867 TCACGTAAAGTGGATACCTCA
1 TCACGTAAAGCGGATACCTCA
*
31888 CCACGTAAAGC
1 TCACGTAAAGC
31899 ACCATTGTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCGGATACCTCA
Found at i:32002 original size:21 final size:21
Alignment explanation
Indices: 31978--32017 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31968 GTTGTCACGT
*
31978 AAAGTACCGACCTCATCACAC
1 AAAGCACCGACCTCATCACAC
*
31999 AAAGCACTGACCTCATCAC
1 AAAGCACCGACCTCATCAC
32018 GTAACTCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACAC
Found at i:32920 original size:23 final size:25
Alignment explanation
Indices: 32884--32930 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
32874 TCTTTTCTTT
*
32884 TTTTCATGTAATTTTTTTTTTTACA
1 TTTTCATGTAATTTTCTTTTTTACA
32909 TTTT-ATGT-ATTTTCTTTTTTAC
1 TTTTCATGTAATTTTCTTTTTTAC
32931 TTTAGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTCATGTAATTTTCTTTTTTACA
Found at i:33045 original size:18 final size:18
Alignment explanation
Indices: 33005--33047 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
32995 TCATTATCTG
33005 TTTTATTAATTTATATAT
1 TTTTATTAATTTATATAT
* * * *
33023 ATTTATTATTTTTTATGT
1 TTTTATTAATTTATATAT
33041 TTTTATT
1 TTTTATT
33048 TGTTTTATAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTATTAATTTATATAT
Found at i:33045 original size:36 final size:40
Alignment explanation
Indices: 32976--33064 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 40
32966 CACATATATA
32976 TATATATATATATTAATTTTCATTATCTGTTTTA-TTAATT
1 TATATATATATATTAATTTT-ATTATCTGTTTTATTTAATT
* * **
33016 TATATATATTTATT-ATTTT-TTATGT-TTTTATTTGTTT
1 TATATATATATATTAATTTTATTATCTGTTTTATTTAATT
33053 TATATATATATA
1 TATATATATATA
33065 CCTATTATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
36 5 0.12
37 20 0.47
39 5 0.12
40 13 0.30
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (40 bp):
TATATATATATATTAATTTTATTATCTGTTTTATTTAATT
Found at i:33227 original size:9 final size:9
Alignment explanation
Indices: 33186--33257 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
33176 TATTTTCTAG
33186 TATTTTATT
1 TATTTTATT
*
33195 TATTTCATT
1 TATTTTATT
* *
33204 TGCTTTTATG
1 T-ATTTTATT
*
33214 GATTTTATT
1 TATTTTATT
*
33223 TATTTTTTATG
1 TA--TTTTATT
33234 TATTTTATT
1 TATTTTATT
33243 T-TATTTATT
1 TAT-TTTATT
33252 TATTTT
1 TATTTT
33258 TCTTTTCGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
8 1 0.02
9 33 0.69
10 6 0.12
11 8 0.17
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (9 bp):
TATTTTATT
Found at i:33232 original size:20 final size:21
Alignment explanation
Indices: 33207--33254 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
33197 TTTCATTTGC
33207 TTTTATGGATTTTA-TTTATT
1 TTTTATGGATTTTATTTTATT
*
33227 TTTTATGTATTTTATTTTATT
1 TTTTATGGATTTTATTTTATT
33248 TATTTAT
1 T-TTTAT
33255 TTTTCTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 7 0.28
22 5 0.20
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTATGGATTTTATTTTATT
Found at i:36451 original size:21 final size:21
Alignment explanation
Indices: 36401--36452 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
36391 TCAGAACAAA
36401 AAGAGAAAAAAAAGGAAATAG
1 AAGAGAAAAAAAAGGAAATAG
* * * *
36422 AAAATAAAAAAAATGAAAGTTG
1 AAGAGAAAAAAAAGGAAA-TAG
36444 AAGA-AAAAA
1 AAGAGAAAAA
36453 GAAGACAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (21 bp):
AAGAGAAAAAAAAGGAAATAG
Found at i:36631 original size:69 final size:69
Alignment explanation
Indices: 36513--36650 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
36503 GATTCAAACT
* * *
36513 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTAATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCGAAGATCATAGAGCA
36578 TCAA
66 TCAA
* *
36582 ATGAGATTAATCAAGCACAATCATTTTTGAATCACTAAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTAATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCGAAGATCATAGAGCA
36647 TCAA
66 TCAA
36651 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (69 bp):
ATGAGATTAATCAAGCACAATCATTTCTGAATCACTAAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:38028 original size:20 final size:20
Alignment explanation
Indices: 38003--38042 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
37993 AAATGACCAA
38003 CAAATTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
*
38023 CAAATTCGCAACTCAGTTTC
1 CAAATTCGCAACACAGTTTC
38043 TGCAATCGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:38051 original size:20 final size:20
Alignment explanation
Indices: 38025--38084 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
38015 ACAGTTTCCA
38025 AATTCGCAACTC-AGTTTCTG
1 AATTCGCAACTCGA-TTTCTG
38045 CAA-TCGCAACTCGATTTCTG
1 -AATTCGCAACTCGATTTCTG
*
38065 AATTCGCAACGCGAATTTCT
1 AATTCGCAACTCG-ATTTCT
38085 TTTTCGCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 2 0.06
20 24 0.69
21 9 0.26
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (20 bp):
AATTCGCAACTCGATTTCTG
Found at i:38090 original size:20 final size:20
Alignment explanation
Indices: 38067--38195 Score: 84
Period size: 20 Copynumber: 6.5 Consensus size: 20
38057 GATTTCTGAA
*
38067 TTCGCAACGCGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
*
38087 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTCTTT
* * **
38107 TTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAATTTCTTT
*
38127 ATCGCAACACGAATTT-TATT
1 TTCGCAACACGAATTTCT-TT
* * ***
38147 TTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAATTTCTTT
* *
38167 TTCGCAACACAAATTT-TAAT
1 TTCGCAACACGAATTTCT-TT
38187 TTCGCAACA
1 TTCGCAACA
38196 GCTTTTATTT
Statistics
Matches: 81, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
19 3 0.04
20 77 0.95
21 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTCTTT
Found at i:38124 original size:40 final size:38
Alignment explanation
Indices: 38087--38201 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 38
38077 GAATTTCTTT
**
38087 TTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACAA-TTTTATTTTCGCAAC-AGATTTTCTAA
* * *
38127 ATCGCAACACGAATTTTATTTTCGCAACTCGATTTTCGAA
1 TTCGCAACAC-AATTTTATTTTCGCAAC-AGATTTTCTAA
* *
38167 TTCGCAACACAAATTTTAATTTCGCAACAGCTTTT
1 TTCGCAACAC-AATTTTATTTTCGCAACAGATTTT
38202 ATTTTCGCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 5 0.08
40 56 0.89
41 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (38 bp):
TTCGCAACACAATTTTATTTTCGCAACAGATTTTCTAA
Found at i:38992 original size:12 final size:12
Alignment explanation
Indices: 38971--39004 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38961 ACCACATTTC
*
38971 CAATACCAAACA
1 CAATATCAAACA
38983 CAATATCAAACA
1 CAATATCAAACA
*
38995 CAATCTCAAA
1 CAATATCAAA
39005 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:39181 original size:24 final size:24
Alignment explanation
Indices: 39124--39183 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
39114 TAGTTAGTAT
*
39124 TCGAAATTTGATCTTGGTTAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
39148 -CCAGACTTTGATCTTGGTCAATAC
1 TCGA-AATTTGATCTTGGTCAATAC
*
39172 TCGAATTTTGAT
1 TCGAAATTTGAT
39184 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.07
24 25 0.86
25 2 0.07
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:41820 original size:20 final size:20
Alignment explanation
Indices: 41771--41823 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
41761 GAAAGTAAAA
*
41771 TTCGTGTTGCAAATTTGACT
1 TTCGTGTTGCGAATTTGACT
** *
41791 TTCGCATTGCGAATTTGATT
1 TTCGTGTTGCGAATTTGACT
41811 TTCGTGTTGCGAA
1 TTCGTGTTGCGAA
41824 AGTGTACCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCGTGTTGCGAATTTGACT
Found at i:43700 original size:63 final size:63
Alignment explanation
Indices: 43633--43754 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
43623 GTAGAGCGGC
* * * * *
43633 TACCTCACCACGTAAAGCACCATCGTCATCATGTAAAATAGCTACCTCACCACGTAAAGACCG
1 TACCTCACCACGCAAAGCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAGACCG
* * * * * *
43696 TACCTCATCACGCCATGCACCATTGTCGTCACGTAAAATACCGACCTCATCACGCAAAG
1 TACCTCACCACGCAAAGCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAG
43755 CACTAACCTC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.20
Consensus pattern (63 bp):
TACCTCACCACGCAAAGCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAGACCG
Found at i:43748 original size:21 final size:21
Alignment explanation
Indices: 43724--43773 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
43714 ACCATTGTCG
* *
43724 TCACGTAAAATACCGACCTCA
1 TCACGTAAAACACCAACCTCA
* * *
43745 TCACGCAAAGCACTAACCTCA
1 TCACGTAAAACACCAACCTCA
43766 TCACGTAA
1 TCACGTAA
43774 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (21 bp):
TCACGTAAAACACCAACCTCA
Found at i:43764 original size:63 final size:63
Alignment explanation
Indices: 43649--43770 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
43639 ACCACGTAAA
* * * *
43649 GCACCATCGTCATCATGTAAAATAGCTACCTCACCACGTAAAGACCGTACCTCATCACGCCAT
1 GCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAGACCGTACCTCATCACGCCAT
* * *
43712 GCACCATTGTCGTCACGTAAAATACCGACCTCATCACGCAAAG-CAC-TAACCTCATCACG
1 GCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAGAC-CGT-ACCTCATCACG
43771 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.20
Consensus pattern (63 bp):
GCACCATCGTCATCACGTAAAATACCGACCTCACCACGCAAAGACCGTACCTCATCACGCCAT
Found at i:45455 original size:20 final size:20
Alignment explanation
Indices: 45432--45495 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
45422 TTTGAAACTT
* * *
45432 AAATTCGCAACATGAAAATG
1 AAATTTGCAACACGAAAATA
*
45452 AAATTTGCAACGCGAAAATA
1 AAATTTGCAACACGAAAATA
* *
45472 AAATTTGCAACGCGAAACTA
1 AAATTTGCAACACGAAAATA
45492 AAAT
1 AAAT
45496 CGCGTTGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (20 bp):
AAATTTGCAACACGAAAATA
Found at i:45530 original size:20 final size:20
Alignment explanation
Indices: 45507--45549 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
45497 GCGTTGCTAT
*
45507 TTTCATTTTCGTGTTGCGAA
1 TTTCATTTTCGTGTTGCAAA
45527 TTTCATTTTCGTGTTGCAAA
1 TTTCATTTTCGTGTTGCAAA
45547 TTT
1 TTT
45550 AAGTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTCATTTTCGTGTTGCAAA
Found at i:45556 original size:20 final size:20
Alignment explanation
Indices: 45513--45556 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
45503 CTATTTTCAT
* * *
45513 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCAAATTTAAG
45533 TTTCGTGTTGCAAATTTAAG
1 TTTCGTGTTGCAAATTTAAG
45553 TTTC
1 TTTC
45557 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCAAATTTAAG
Found at i:46033 original size:19 final size:20
Alignment explanation
Indices: 46011--46048 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46001 AATATTGTGT
46011 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
46030 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
46049 CGCGCTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:46083 original size:20 final size:20
Alignment explanation
Indices: 46058--46103 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
46048 ACGCGCTTTT
46058 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
46078 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
*
46098 TGAATT
1 CGAATT
46104 ACATGTTCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
CGAATTTGACTTCTGTGTTG
Found at i:46211 original size:19 final size:20
Alignment explanation
Indices: 46189--46226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46179 AACATTGTGT
46189 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
46208 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
46227 CGCGCTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:46242 original size:178 final size:178
Alignment explanation
Indices: 45943--46302 Score: 675
Period size: 178 Copynumber: 2.0 Consensus size: 178
45933 CTAAGTTGTG
* * * *
45943 ATTTAGAGTTTTAGGTTATGAGTTGCAATTATATTGTTTATATTTGTGTTGCGAAATTAATATTG
1 ATTTAGAGCTTTAGGTTATGAGTTGCAATTATATTGTTTACATTTATGTTGCGAAATTAACATTG
46008 TGTTTCGAATTCGAAAATAAAATTCGCGTTGCGAAAATAAACGCGCTTTTCGAATTTGACTTCTG
66 TGTTTCGAATTCGAAAATAAAATTCGCGTTGCGAAAATAAACGCGCTTTTCGAATTTGACTTCTG
*
46073 TGTTGCGAATTTGACTTCTGTGTTGTGAATTACATGTTCGCGTTGCGA
131 TGTTGCGAATTTGACTTCTGTGTTGTGAATTACATATTCGCGTTGCGA
46121 ATTTAGAGCTTTAGGTTATGAGTTGCAATTATATTGTTTACATTTATGTTGCGAAATTAACATTG
1 ATTTAGAGCTTTAGGTTATGAGTTGCAATTATATTGTTTACATTTATGTTGCGAAATTAACATTG
46186 TGTTTCGAATTCGAAAATAAAATTCGCGTTGCGAAAATAAACGCGCTTTTCGAATTTGACTTCTG
66 TGTTTCGAATTCGAAAATAAAATTCGCGTTGCGAAAATAAACGCGCTTTTCGAATTTGACTTCTG
46251 TGTTGCGAATTTGACTTCTGTGTTGTGAATTACATATTCGCGTTGCGA
131 TGTTGCGAATTTGACTTCTGTGTTGTGAATTACATATTCGCGTTGCGA
46299 ATTT
1 ATTT
46303 GAAAAATCGC
Statistics
Matches: 177, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (178 bp):
ATTTAGAGCTTTAGGTTATGAGTTGCAATTATATTGTTTACATTTATGTTGCGAAATTAACATTG
TGTTTCGAATTCGAAAATAAAATTCGCGTTGCGAAAATAAACGCGCTTTTCGAATTTGACTTCTG
TGTTGCGAATTTGACTTCTGTGTTGTGAATTACATATTCGCGTTGCGA
Found at i:46261 original size:20 final size:20
Alignment explanation
Indices: 46236--46281 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
46226 ACGCGCTTTT
46236 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
46256 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
*
46276 TGAATT
1 CGAATT
46282 ACATATTCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
CGAATTTGACTTCTGTGTTG
Found at i:46395 original size:20 final size:21
Alignment explanation
Indices: 46369--46422 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
46359 AATCTAGGAA
46369 ATTCGCGTTGCGAAATTGGAG
1 ATTCGCGTTGCGAAATTGGAG
*
46390 -TTCGCGTTGCAAAATTGGAG
1 ATTCGCGTTGCGAAATTGGAG
46410 ATT-GCGTTGCGAA
1 ATTCGCGTTGCGAA
46423 TTTGTTGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAG
Found at i:46512 original size:2 final size:2
Alignment explanation
Indices: 46505--46533 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46495 AGTTATTTTC
46505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46534 TCTAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48944 original size:200 final size:193
Alignment explanation
Indices: 48533--48952 Score: 549
Period size: 200 Copynumber: 2.1 Consensus size: 193
48523 ATGCCTTGGG
*
48533 GAAGATCATACTGTGGAGAGCAGATGCCGAAACCATCAATGTATCTCAAAGGCCCTCATTTATAA
1 GAAGATCATACTATGGAGAGCAGATGCCGAAACCATCAATGTATCTCAAAGGCCCTCATTTATAA
* **
48598 GATAAAAACACAGTTTAGTAATATGTTCTAGGCCTCAGAAAGGTACCATTCTGGACATCTTTGTA
66 GATAAAAACACAGTTTAGAAATATGTTCTAGGCCTCAG-AAGGTACCATTCCAGACATCTTTGTA
* *
48663 CTGTGTTAGAACATATCAAGGAAAGGGTAGTCAAAAATGAAGATGGTTATCGTAATTCGATCAA
130 CTGAGTTAGAACATATCAAGGAAAGGGTAATCAAAAATGAAGATGGTTATCGTAATTCGATCAA
** * *
48727 GAAGATTGTATTATGGAGAGAAGATGCCGAAACCATATCAATGTATCTCAAAGGCCCTCATTTAT
1 GAAGATCATACTATGGAGAGCAGATGCCGAAACC--ATCAATGTATCTCAAAGGCCCTCATTTAT
* * *
48792 AAGATAAAAACACAGTTTCGAAATCTGTTCTAATTCTAGGCCTCAG-AGGTACTATTCCAGACAT
64 AAGATAAAAACACAGTTTAGAAATATG------TTCTAGGCCTCAGAAGGTACCATTCCAGACAT
** **
48856 -TATTGTACTGAGATT-GAACATATCAAGGAAAGGGTAATCAAAGTTGAAGATGGTTATCGTTTT
123 CT-TTGTACTGAG-TTAGAACATATCAAGGAAAGGGTAATCAAAAATGAAGATGGTTATCGTAAT
* *
48919 TTGATCGA
186 TCGATCAA
48927 GAAGATCATACTATGGAGAGCAGATG
1 GAAGATCATACTATGGAGAGCAGATG
48953 TCGGAACAGT
Statistics
Matches: 193, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
194 29 0.15
196 53 0.27
199 1 0.01
200 95 0.49
201 2 0.01
202 13 0.07
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (193 bp):
GAAGATCATACTATGGAGAGCAGATGCCGAAACCATCAATGTATCTCAAAGGCCCTCATTTATAA
GATAAAAACACAGTTTAGAAATATGTTCTAGGCCTCAGAAGGTACCATTCCAGACATCTTTGTAC
TGAGTTAGAACATATCAAGGAAAGGGTAATCAAAAATGAAGATGGTTATCGTAATTCGATCAA
Found at i:50610 original size:2 final size:2
Alignment explanation
Indices: 50603--50633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50593 ATTGAGGGGT
50603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50634 TAAAGTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50783 original size:2 final size:2
Alignment explanation
Indices: 50776--50801 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50766 TATGAAAATA
50776 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
50802 TATGGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51547 original size:61 final size:60
Alignment explanation
Indices: 51400--51568 Score: 182
Period size: 61 Copynumber: 2.8 Consensus size: 60
51390 TTTGGATGAA
* * *
51400 TTTGGGGATGATATTGGAATATTCAAAAGTTT-GGGATTAATTTAGAAA-GAGGTTCATAG
1 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGGTTCATAG
* ** * * * *
51459 TTTAGGGATGAAATTATAACACTCAAAATTTTAAGGACTAATTTAAAATGTGAG-TCATAG
1 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAG-GTTCATAG
* *
51519 TTTGGGGGATAAAATTGGAATATTCAAAAGTTTAAAGACTAATTTAAAAT
1 TTT-GGGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAAT
51569 AAGGGTTAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 28 0.32
60 21 0.24
61 39 0.44
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGTTCATAG
Found at i:51733 original size:30 final size:30
Alignment explanation
Indices: 51699--51757 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
51689 AATATATGGC
*
51699 CACTTTCGTTTTTATTTAATTAAGTTGTGG
1 CACTTTCGTTTTTATTTAATTAAGATGTGG
51729 CACTTTCGTTTTTATTTAATTAAGATGTG
1 CACTTTCGTTTTTATTTAATTAAGATGTG
51758 ATCACCACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (30 bp):
CACTTTCGTTTTTATTTAATTAAGATGTGG
Found at i:53702 original size:20 final size:20
Alignment explanation
Indices: 53677--53724 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
53667 ATTAAATATG
53677 ATTTTTTCCCGAAAAAGTTA
1 ATTTTTTCCCGAAAAAGTTA
*
53697 ATTTTTTTCCGAAAAAGTTA
1 ATTTTTTCCCGAAAAAGTTA
53717 ATTTTTTC
1 ATTTTTTC
53725 GTCAAAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (20 bp):
ATTTTTTCCCGAAAAAGTTA
Found at i:53823 original size:24 final size:24
Alignment explanation
Indices: 53791--53851 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
53781 AAAGGTCAGC
* *
53791 TCTGAGTTGACTTGACTGACTCGT
1 TCTGAGTTGACTCGACTGACTCGA
*
53815 TCTGAGTTGACTCGATTGACTCGA
1 TCTGAGTTGACTCGACTGACTCGA
*
53839 TCTGAGTCGACTC
1 TCTGAGTTGACTC
53852 AATTTCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (24 bp):
TCTGAGTTGACTCGACTGACTCGA
Found at i:55834 original size:31 final size:31
Alignment explanation
Indices: 55799--55876 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
55789 TTAAAAAGCA
*
55799 TAAGTTTTGGTCACTTATGCTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGCTATCGTTTTAT
*
55830 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGCTATCGTTTTAT
55861 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
55877 TGACATTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGCTATCGTTTTAT
Found at i:56146 original size:16 final size:16
Alignment explanation
Indices: 56125--56163 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
56115 TTCAAAGACT
*
56125 AATAATGCATTTCAAG
1 AATAATGCATTACAAG
56141 AATAATGCATTACAAG
1 AATAATGCATTACAAG
56157 AATAATG
1 AATAATG
56164 AAAGATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (16 bp):
AATAATGCATTACAAG
Found at i:57512 original size:31 final size:31
Alignment explanation
Indices: 57477--57539 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
57467 AGTGATTACG
* * *
57477 TCTTAATTAAAGTGAAATGAAAGTGACTAAA
1 TCTTAATTAAAATGAAACGAAAGTGACCAAA
57508 TCTTAATTAAAATGAAACGAAAGTGACCAAA
1 TCTTAATTAAAATGAAACGAAAGTGACCAAA
57539 T
1 T
57540 ATTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (31 bp):
TCTTAATTAAAATGAAACGAAAGTGACCAAA
Found at i:64645 original size:22 final size:22
Alignment explanation
Indices: 64603--64645 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
64593 AATTGATAGT
*
64603 TCAAATTAATTTTGAGTTAGAA
1 TCAAATTAATTTTGAGATAGAA
*
64625 TCAATTTACATTTTGA-ATAGA
1 TCAAATTA-ATTTTGAGATAGA
64646 TAAGTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
TCAAATTAATTTTGAGATAGAA
Found at i:69732 original size:12 final size:11
Alignment explanation
Indices: 69698--69744 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
69688 TAAAGTTAAC
69698 TAATTATTAT-
1 TAATTATTATA
* *
69708 TATTTAGTATA
1 TAATTATTATA
69719 TAATTATCTATA
1 TAATTAT-TATA
69731 TAA-TATTATA
1 TAATTATTATA
69741 TAAT
1 TAAT
69745 ATAATATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 15 0.50
11 8 0.27
12 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TAATTATTATA
Found at i:72494 original size:22 final size:23
Alignment explanation
Indices: 72469--72511 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
72459 TATTCTAATA
72469 TTTTTAAAAT-AATAATATTAAG
1 TTTTTAAAATAAATAATATTAAG
*
72491 TTTTTATAATAAATAATATTA
1 TTTTTAAAATAAATAATATTA
72512 TTTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTAAAATAAATAATATTAAG
Found at i:72519 original size:22 final size:20
Alignment explanation
Indices: 72467--72520 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
72457 ATTATTCTAA
*
72467 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
72487 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
72510 TATTTATTATA
1 TATTT-TTATA
72521 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:73345 original size:15 final size:15
Alignment explanation
Indices: 73325--73353 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73315 AATATCCAAA
73325 AATATTAAAAATAAG
1 AATATTAAAAATAAG
73340 AATATTAAAAATAA
1 AATATTAAAAATAA
73354 AAAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AATATTAAAAATAAG
Found at i:73349 original size:24 final size:24
Alignment explanation
Indices: 73282--73352 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
73272 AGTTTTTTTA
* *
73282 AAAAATAAAAATCATTATAAATTTT
1 AAAAATAAAAAT-ATTAAAAATATT
* * *
73307 AAATAT-ACAATATCCAAAAATATT
1 AAAAATAAAAATAT-TAAAAATATT
*
73331 AAAAATAAGAATATTAAAAATA
1 AAAAATAAAAATATTAAAAATA
73353 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
23 2 0.06
24 23 0.64
25 11 0.31
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAAATAAAAATATTAAAAATATT
Found at i:73450 original size:42 final size:43
Alignment explanation
Indices: 73357--73451 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 43
73347 AAAATAAAAA
* *
73357 AAATTATTAAAAAATATTAAATATATAAGTTAAAAATACTATT
1 AAATTATTAAAAAATATGAAATATATAAGTCAAAAATACTATT
* * *
73400 AAA-AATTAAAAGAA-ATGAAATATAT-A-TCATAAATAACTTTT
1 AAATTATTAAAA-AATATGAAATATATAAGTCAAAAAT-ACTATT
73441 AAATTATTAAA
1 AAATTATTAAA
73452 GTACTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
40 6 0.14
41 9 0.21
42 23 0.53
43 5 0.12
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (43 bp):
AAATTATTAAAAAATATGAAATATATAAGTCAAAAATACTATT
Found at i:75058 original size:24 final size:23
Alignment explanation
Indices: 75026--75071 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
75016 GAGAGTGTGA
75026 GAAG-AAAAAGAAGGAAGAAGGAAG
1 GAAGAAAAAAGAA-GAAG-AGGAAG
75050 GAAGAAAAAAGAAGAAGAGGAA
1 GAAGAAAAAAGAAGAAGAGGAA
75072 ACAGAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAAGAAGAAGAGGAAG
Found at i:75503 original size:15 final size:13
Alignment explanation
Indices: 75486--75553 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 13
75476 ATATTTTTAA
75486 TATTTTTATTATAT
1 TATTTTTATTAT-T
*
75500 ATATGTTTA--ATT
1 -TATTTTTATTATT
75512 TATTTTTATT-TT
1 TATTTTTATTATT
75524 TATTTTTAATATATT
1 TATTTTT-AT-TATT
*
75539 TATTTTTATTTTT
1 TATTTTTATTATT
75552 TA
1 TA
75554 AATATTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 7 0.16
12 10 0.22
13 9 0.20
14 3 0.07
15 16 0.36
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.72
Consensus pattern (13 bp):
TATTTTTATTATT
Found at i:75523 original size:5 final size:6
Alignment explanation
Indices: 75510--75551 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
75500 ATATGTTTAA
75510 TTTATT TTTATT TTTATT TTTAATAT ATTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTT-AT-T -TTTATT TTTATT TTT
75552 TAAATATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 24 0.73
7 3 0.09
8 3 0.09
9 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:75542 original size:21 final size:21
Alignment explanation
Indices: 75516--75559 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
75506 TTAATTTATT
75516 TTTATTTTTA-TTTTTAATATA
1 TTTATTTTTATTTTTTAA-ATA
75537 TTTATTTTTATTTTTTAAATA
1 TTTATTTTTATTTTTTAAATA
75558 TT
1 TT
75560 CAAATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATTTTTATTTTTTAAATA
Found at i:82238 original size:2 final size:2
Alignment explanation
Indices: 82226--82262 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
82216 TTTTGACTCG
82226 AT AT GAT 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
82263 CATTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84584 original size:49 final size:50
Alignment explanation
Indices: 84528--84651 Score: 146
Period size: 49 Copynumber: 2.5 Consensus size: 50
84518 TTAGCAGGAA
*
84528 AGCGCGCCCCCTGCACCGCGCTATATGCTGATTTGGCGCCACGT-GGTAC
1 AGCGCGCCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGGGTAC
* * * * * * *
84577 AGCGCGCCCCTTGC-CCCCGATATACGGTGATCTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGGGTAC
84626 AGCGCGCCCCCTG-ATCCGCGCTATAT
1 AGCGCGCCCCCTGCA-CCGCGCTATAT
84652 CTGGATATCT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
48 23 0.38
49 29 0.48
50 8 0.13
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGGGTAC
Found at i:86379 original size:49 final size:50
Alignment explanation
Indices: 86319--86424 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 50
86309 CGCGGATCAG
* * * *
86319 GGGGCGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCAGGGCA-
1 GGGGCGCGCTATACCCACGTGACGCCAAATCACCATATAGCGCAGGGCAC
* *
86368 GGGGCGCGCTATACCCACGTGACGCCAAATCAGCATATAGCGCAGTGCAC
1 GGGGCGCGCTATACCCACGTGACGCCAAATCACCATATAGCGCAGGGCAC
86418 GGGGCGC
1 GGGGCGC
86425 TTTCCTGCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 43 0.86
50 7 0.14
ACGTcount: A:0.22, C:0.32, G:0.33, T:0.13
Consensus pattern (50 bp):
GGGGCGCGCTATACCCACGTGACGCCAAATCACCATATAGCGCAGGGCAC
Done.