Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003847.1 Hibiscus syriacus cultivar Beakdansim tig00008253_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: 96936
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:272 original size:15 final size:14
Alignment explanation
Indices: 238--273 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
228 TATCAATGAT
238 TAATATTTTTAAAA
1 TAATATTTTTAAAA
252 TAATATTTTTAAAA
1 TAATATTTTTAAAA
266 TATATATT
1 TA-ATATT
274 ATCATTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTTTAAAA
Found at i:7415 original size:22 final size:21
Alignment explanation
Indices: 7387--7434 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
7377 TTTTTCTTTT
*
7387 TTTTTGTTAGAAACAGTGAACA
1 TTTTTGTTAGAAACAATGAA-A
**
7409 TTTTTGTTCTAAACAATGAAA
1 TTTTTGTTAGAAACAATGAAA
7430 TTTTT
1 TTTTT
7435 TTCTTCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (21 bp):
TTTTTGTTAGAAACAATGAAA
Found at i:16099 original size:29 final size:29
Alignment explanation
Indices: 16067--16122 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
16057 GAAGATAAGG
16067 ATAAAATAAT-A-AAATAATAAATAATAATT
1 ATAAAATAATGATAAA-AATAAA-AATAATT
*
16096 ATAAGATAATGATAAAAATAAAAATAA
1 ATAAAATAATGATAAAAATAAAAATAA
16123 AAGGGGGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 14 0.58
30 7 0.29
31 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (29 bp):
ATAAAATAATGATAAAAATAAAAATAATT
Found at i:16833 original size:33 final size:33
Alignment explanation
Indices: 16796--16859 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16786 AAAATTGCAA
*
16796 AAAACTTGAAAGAA-ATAGAAGAGAAAATTTTAT
1 AAAACTAGAAAGAAGA-AGAAGAGAAAATTTTAT
* *
16829 AAAACTAGAGAGAAGAAGAAGAGTAAATTTT
1 AAAACTAGAAAGAAGAAGAAGAGAAAATTTT
16860 TAGTTGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (33 bp):
AAAACTAGAAAGAAGAAGAAGAGAAAATTTTAT
Found at i:18323 original size:20 final size:20
Alignment explanation
Indices: 18300--18340 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18290 GGTGGTATCG
*
18300 ATACCTAGGGTACCGATACC
1 ATACCGAGGGTACCGATACC
* *
18320 ATACGGAGGGTATCGATACC
1 ATACCGAGGGTACCGATACC
18340 A
1 A
18341 AATAATTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
ATACCGAGGGTACCGATACC
Found at i:18920 original size:22 final size:22
Alignment explanation
Indices: 18890--18931 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18880 AGTCGAGGGT
* *
18890 TACATAGGTTCTTCGGGACATA
1 TACAGAGGTCCTTCGGGACATA
18912 TACAGAGGTCCTTCGGGACA
1 TACAGAGGTCCTTCGGGACA
18932 AATTTATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
TACAGAGGTCCTTCGGGACATA
Found at i:28545 original size:5 final size:5
Alignment explanation
Indices: 28535--28573 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
28525 GAATCAAATG
28535 GACTC GACTC GAGCTC GACTC GACTC GAGCTC GACTC GA
1 GACTC GACTC GA-CTC GACTC GACTC GA-CTC GACTC GA
28574 GCCTAAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 22 0.69
6 10 0.31
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (5 bp):
GACTC
Found at i:28556 original size:16 final size:16
Alignment explanation
Indices: 28535--28573 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
28525 GAATCAAATG
28535 GACTCGACTCGAGCTC
1 GACTCGACTCGAGCTC
28551 GACTCGACTCGAGCTC
1 GACTCGACTCGAGCTC
28567 GACTCGA
1 GACTCGA
28574 GCCTAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (16 bp):
GACTCGACTCGAGCTC
Found at i:28575 original size:11 final size:10
Alignment explanation
Indices: 28535--28573 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
28525 GAATCAAATG
28535 GACTCGACTC
1 GACTCGACTC
28545 GAGCTCGACTC
1 GA-CTCGACTC
28556 GACTCGAGCTC
1 GACTCGA-CTC
28567 GACTCGA
1 GACTCGA
28574 GCCTAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 7 0.26
11 20 0.74
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (10 bp):
GACTCGACTC
Found at i:28799 original size:14 final size:14
Alignment explanation
Indices: 28782--28815 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28772 CCCTAAATCA
28782 TAAATTATAAACCC
1 TAAATTATAAACCC
* *
28796 TAAACTATAAGCCC
1 TAAATTATAAACCC
28810 TAAATT
1 TAAATT
28816 GTACTTACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAATTATAAACCC
Found at i:28878 original size:7 final size:7
Alignment explanation
Indices: 28866--28911 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
28856 GTCTTTGCAA
28866 TAAACCC
1 TAAACCC
28873 TAAACCC
1 TAAACCC
**
28880 TAAACTA
1 TAAACCC
28887 TAAACCC
1 TAAACCC
28894 TAAACCC
1 TAAACCC
*
28901 TAAAACC
1 TAAACCC
28908 TAAA
1 TAAA
28912 TCCAATTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:28911 original size:21 final size:21
Alignment explanation
Indices: 28865--28904 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28855 TGTCTTTGCA
28865 ATAAACCCTAAACCCTAAACT
1 ATAAACCCTAAACCCTAAACT
28886 ATAAACCCTAAACCCTAAA
1 ATAAACCCTAAACCCTAAA
28905 ACCTAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAAACCCTAAACCCTAAACT
Found at i:32398 original size:2 final size:2
Alignment explanation
Indices: 32391--32434 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
32381 GTCGTTTTGA
32391 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
32433 AT
1 AT
32435 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32778 original size:20 final size:21
Alignment explanation
Indices: 32753--32795 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32743 TCTTTGGTGG
32753 TTCCACGG-TGAG-TTTAAGAC
1 TTCCACGGTTG-GCTTTAAGAC
32773 TTCCACGGTTGGCTTTAAGAC
1 TTCCACGGTTGGCTTTAAGAC
32794 TT
1 TT
32796 TCCGATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCCACGGTTGGCTTTAAGAC
Found at i:33348 original size:3 final size:3
Alignment explanation
Indices: 33340--33394 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
33330 AAAATAACAT
33340 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33387 TAA TAA TA
1 TAA TAA TA
33395 CATATAATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:33680 original size:91 final size:91
Alignment explanation
Indices: 33567--33826 Score: 443
Period size: 91 Copynumber: 2.9 Consensus size: 91
33557 AAGCGTTGGA
**
33567 TTGAA-AAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTAAATGAGTTCTTCTCATTATGAA
1 TTGAACAAA-TTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAA
*
33631 CTCTTCACTAGAAATACTGATGCAAGG
65 CTCTCCACTAGAAATACTGATGCAAGG
*
33658 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
*
33723 TCTCCACTGGAAATACTGATGCAAGG
66 TCTCCACTAGAAATACTGATGCAAGG
*
33749 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
33814 TCTCCACTA-AAAT
66 TCTCCACTAGAAAT
33827 GTCAATCCCT
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
90 4 0.03
91 153 0.96
92 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (91 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
TCTCCACTAGAAATACTGATGCAAGG
Found at i:33993 original size:136 final size:135
Alignment explanation
Indices: 33759--34370 Score: 883
Period size: 136 Copynumber: 4.5 Consensus size: 135
33749 TTGAACAAAT
** *
33759 TCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTTCTTCTCATTATGAACTCTCCACT-A
1 TCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGA
* *
33823 AAATGTCAATCCCTCAAGCGAGGCT-TCACTGATTCGAAATACCGGGAATTGAGTGATAGGTCGA
66 AAATGTCAATCCCTCAAGCGAGG-TGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGA
*
33887 ACAAGA
130 ACAAGC
* *
33893 TCTTCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATAAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * *
33958 GAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATTGAGTGATAGGTCGA
65 AAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGA
34023 ACAAGC
130 ACAAGC
* * *
34029 TCTTCTCATTATGAACTTATTCTCCCACTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * * *
34094 AAAATGTCAATCCCTCAAGCGAGGCGTTACTGACTCGAAA-AGACATGAATCGAGTGATAGGTCG
65 AAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATA-CCGTGAATCGAGTGATAGGTCG
34158 AACAAGC
129 AACAAGC
* ** *
34165 TTTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCTATT-
1 TCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* * * *
34229 AAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGCAGTGAATCAAGTGATAGGTCGA
65 AAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGA
34294 ACAAGC
130 ACAAGC
*
34300 TCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATAAGTTCTTCTCATT-TGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACTCTCCATTG
34364 AAAATGT
65 AAAATGT
34371 TGATCTGTTT
Statistics
Matches: 428, Mismatches: 43, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
134 40 0.09
135 144 0.34
136 244 0.57
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (135 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGA
AAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGATAGGTCGAA
CAAGC
Found at i:34294 original size:271 final size:271
Alignment explanation
Indices: 33759--34370 Score: 955
Period size: 271 Copynumber: 2.3 Consensus size: 271
33749 TTGAACAAAT
** * *
33759 TCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTTCTTCTCATTATGAACTCTCCACT-A
1 TCTTCTCATTATGAACTTCTTCTCCCTCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGA
* * * *
33823 AAATGTCAATCCCTCAAGCGAGGCTTCACTGATTCGAAATACCGGGAATTGAGTGATAGGTCGAA
66 AAATGTCAATCCCTCAAGCGAGGCTTCACTGACTCGAAATAACAGGAATCGAGTGATAGGTCGAA
*
33888 CAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTATAAACTCTC
131 CAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATAAACTCTC
* * **
33953 CATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATTGAGTGATAG
196 CATTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCAGTGAATCAAGTGATAG
34018 GTCGAACAAGC
261 GTCGAACAAGC
* *
34029 TCTTCTCATTATGAACTTATTCTCCCACTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCT-TCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
*
34094 AAAATGTCAATCCCTCAAGCGAGGCGTT-ACTGACTCGAAA-AGACATGAATCGAGTGATAGGTC
65 AAAATGTCAATCCCTCAAGCGAGGC-TTCACTGACTCGAAATA-ACAGGAATCGAGTGATAGGTC
* * *
34157 GAACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACT
128 GAACAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATAAACT
* *
34222 CTCTATT-AAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGCAGTGAATCAAGTGA
193 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCAGTGAATCAAGTGA
34286 TAGGTCGAACAAGC
258 TAGGTCGAACAAGC
*
34300 TCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATAAGTTCTTCTCATT-TGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTC-TTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
34364 AAAATGT
65 AAAATGT
34371 TGATCTGTTT
Statistics
Matches: 313, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
270 46 0.15
271 144 0.46
272 121 0.39
273 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (271 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGA
AAATGTCAATCCCTCAAGCGAGGCTTCACTGACTCGAAATAACAGGAATCGAGTGATAGGTCGAA
CAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATAAACTCTC
CATTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCAGTGAATCAAGTGATAG
GTCGAACAAGC
Found at i:34864 original size:65 final size:68
Alignment explanation
Indices: 34780--34943 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 68
34770 AGTGAGATTC
* * *
34780 AATTTCTTGTTTCAAGGGAAACTATCTCAAA-AACT-TGTTTCAAGGGAAAACTGTCTTAAGAGA
1 AATTT-TTGTTTCAAGGGAAACTATCTCAAAGAACTGTGTTTCAAGAG-AAACTATCTCAAGAGA
34843 AAC-A
64 AACAA
* ** * *
34847 AA-TTTTGTTTCAAGGGAAACGT-TTTCAAAGTTCTGTGTTTCAAGAGAAACTATCTCAAGGGAG
1 AATTTTTGTTTCAAGGGAAAC-TATCTCAAAGAACTGTGTTTCAAGAGAAACTATCTCAAGAGAA
34910 ACAA
65 ACAA
*
34914 AATTTTTCGTTTCAAGGAAAACTATCTCAA
1 AATTTTT-GTTTCAAGGGAAACTATCTCAA
34944 GCGAGATAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
65 22 0.28
66 20 0.25
67 15 0.19
68 5 0.06
69 18 0.22
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (68 bp):
AATTTTTGTTTCAAGGGAAACTATCTCAAAGAACTGTGTTTCAAGAGAAACTATCTCAAGAGAAA
CAA
Found at i:34937 original size:39 final size:39
Alignment explanation
Indices: 34883--34973 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
34873 AAAGTTCTGT
*
34883 GTTTCAA-GAGAAACTATCTCAAGGGAGACAAAATTTTTC
1 GTTTCAAGGA-AAACTATCTCAAGCGAGACAAAATTTTTC
* *
34922 GTTTCAAGGAAAACTATCTCAAGCGAGATAAAATTTTTT
1 GTTTCAAGGAAAACTATCTCAAGCGAGACAAAATTTTTC
34961 GTTTCAAGGAAAA
1 GTTTCAAGGAAAA
34974 ACAATCTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (39 bp):
GTTTCAAGGAAAACTATCTCAAGCGAGACAAAATTTTTC
Found at i:34975 original size:40 final size:40
Alignment explanation
Indices: 34882--35256 Score: 428
Period size: 40 Copynumber: 9.4 Consensus size: 40
34872 CAAAGTTCTG
* * * * * *
34882 TGTTTCAA-GAGAAACTATCTCAAGGGAGACAAAAT-TTT
1 TGTTTCAAGGAAAAACAATCTGAAGTGAGATAAAATCTTC
* * * * *
34920 TCGTTTCAAGG-AAAACTATCTCAAGCGAGATAAAATTTTT
1 T-GTTTCAAGGAAAAACAATCTGAAGTGAGATAAAATCTTC
* *
34960 TGTTTCAAGGAAAAACAATCTTGAA-CGAGATAAAAACTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
35000 TGTTTCAAGGAAAAACAATCTTG-AGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
*
35040 TGTTTCAAGGAAAAATAATCTTGAA-TGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
* *
35080 TGTTTCAAGGAGAAACAATCTTGAA-TGAGATTAAATCTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
*
35120 TATTTCAAGGAAAAACAATCTTG-AGTGAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
* *
35160 TGTTTCAAGGAAAAACAATCTTG-AGTGAGATAAAATATTT
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
*
35200 TGTTTCAAGGAAAAACAATCTTGAA-TAAGATAAAATCTTC
1 TGTTTCAAGGAAAAACAATC-TGAAGTGAGATAAAATCTTC
35240 TGTTTCAAGGAAAAACA
1 TGTTTCAAGGAAAAACA
35257 GTCCTGAGTC
Statistics
Matches: 305, Mismatches: 23, Indels: 16
0.89 0.07 0.05
Matches are distributed among these distances:
38 1 0.00
39 40 0.13
40 259 0.85
41 5 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (40 bp):
TGTTTCAAGGAAAAACAATCTGAAGTGAGATAAAATCTTC
Found at i:35033 original size:80 final size:80
Alignment explanation
Indices: 34922--35265 Score: 510
Period size: 80 Copynumber: 4.3 Consensus size: 80
34912 AAAATTTTTC
* ** * * * *
34922 GTTTCAAGG-AAAACTATCTCAAGCGAGATAAAATTTTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
34986 GAGATAAAAACTTCT
66 GAGATAAAATCTTCT
*
35001 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAAT
1 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
35066 GAGATAAAATCTTCT
66 GAGATAAAATCTTCT
* * * * *
35081 GTTTCAAGGAGAAACAATCTTGAATGAGATTAAATCTTCTATTTCAAGGAAAAACAATCTTGAGT
1 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
35146 GAGATAAAATCTTCT
66 GAGATAAAATCTTCT
* *
35161 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
35226 AAGATAAAATCTTCT
66 GAGATAAAATCTTCT
* *
35241 GTTTCAAGGAAAAACAGTCCTGAGT
1 GTTTCAAGGAAAAACAATCTTGAGT
35266 CAAATGAAAT
Statistics
Matches: 239, Mismatches: 25, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
79 9 0.04
80 230 0.96
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (80 bp):
GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
GAGATAAAATCTTCT
Found at i:35090 original size:120 final size:120
Alignment explanation
Indices: 34946--35265 Score: 523
Period size: 120 Copynumber: 2.7 Consensus size: 120
34936 TATCTCAAGC
* * *
34946 GAGATAAAATTTTTTGTTTCAAGGAAAAACAATCTTGAACGAGATAAAAACTTCTGTTTCAAGGA
1 GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
*
35011 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAAT
66 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* * * * *
35066 GAGATAAAATCTTCTGTTTCAAGGAGAAACAATCTTGAATGAGATTAAATCTTCTATTTCAAGGA
1 GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
*
35131 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
35186 GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAATAAGATAAAATCTTCTGTTTCAAGGA
1 GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
* *
35251 AAAACAGTCCTGAGT
66 AAAACAATCTTGAGT
35266 CAAATGAAAT
Statistics
Matches: 183, Mismatches: 17, Indels: 0
0.92 0.09 0.00
Matches are distributed among these distances:
120 183 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (120 bp):
GAGATAAAATATTTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
Found at i:36611 original size:41 final size:41
Alignment explanation
Indices: 36554--36860 Score: 161
Period size: 41 Copynumber: 7.7 Consensus size: 41
36544 ATTTTTTGTC
* *
36554 TGAAATGGGCCTTCAAAATGCCCCAACATTCTATTTCTAGT
1 TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
* *
36595 TGAAATAGACCTTCAAAATATCCCAACA---T-TTTC-A--
1 TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
* * * **
36629 TGCTAATGTGAGCCTTCAAGATGCCTCCATGGA-TC-ATTTCT-GT
1 TG-AAATG-GA-CCTTCAAAATACC-CCA-ACATTCTATTTCTAGT
* * *
36672 CTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGT
1 -TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
*
36714 TGAAATGGACCTTCAAAATATCCCAACA---T-TTTC-A--
1 TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
* * * **
36748 TGCTAATGTGAGCCTTCAAGATGCCTCC--CA-TGGATTTCT-GT
1 TG-AAATG-GA-CCTTCAAAATACC-CCAACATTCTATTTCTAGT
* * *
36789 CTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGT
1 -TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
* *
36831 TGAAATGGACATTCAAAATATCCCAACATT
1 TGAAATGGACCTTCAAAATACCCCAACATT
36861 TTCATGTTGA
Statistics
Matches: 198, Mismatches: 38, Indels: 60
0.67 0.13 0.20
Matches are distributed among these distances:
34 4 0.02
35 7 0.04
36 7 0.04
37 28 0.14
38 9 0.05
39 17 0.09
40 8 0.04
41 107 0.54
42 6 0.03
43 4 0.02
44 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (41 bp):
TGAAATGGACCTTCAAAATACCCCAACATTCTATTTCTAGT
Found at i:36685 original size:119 final size:120
Alignment explanation
Indices: 36515--36884 Score: 579
Period size: 119 Copynumber: 3.1 Consensus size: 120
36505 CTTGCTGATA
* ** * * *
36515 TGAGCCTTCAAAATGCC-CCCAAATAAATCATTTTTTGTCTGAAATGGGCCTTCAAAATGCCCCA
1 TGAGCCTTCAAGATGCCTCCC--ATGGATCA-TTTCTGTCTAAAATGGGCCTTCAAAATACCCCA
* *
36579 ACATTCTATTTCTAGTTGAAATAGACCTTCAAAATATCCCAACATTTTCATGCTAATG
63 ACATTCTATTTCTGGTTGAAATGGACCTTCAAAATATCCCAACATTTTCATGCTAATG
36637 TGAGCCTTCAAGATGCCT-CCATGGATCATTTCTGTCTAAAATGGGCCTTCAAAATACCCCAACA
1 TGAGCCTTCAAGATGCCTCCCATGGATCATTTCTGTCTAAAATGGGCCTTCAAAATACCCCAACA
36701 TTCTATTTCTGGTTGAAATGGACCTTCAAAATATCCCAACATTTTCATGCTAATG
66 TTCTATTTCTGGTTGAAATGGACCTTCAAAATATCCCAACATTTTCATGCTAATG
36756 TGAGCCTTCAAGATGCCTCCCATGG---ATTTCTGTCTAAAATGGGCCTTCAAAATACCCCAACA
1 TGAGCCTTCAAGATGCCTCCCATGGATCATTTCTGTCTAAAATGGGCCTTCAAAATACCCCAACA
* * *
36818 TTCTATTTCTGGTTGAAATGGACATTCAAAATATCCCAACATTTTCATGTTGATG
66 TTCTATTTCTGGTTGAAATGGACCTTCAAAATATCCCAACATTTTCATGCTAATG
36873 TGAGCCTTCAAG
1 TGAGCCTTCAAG
36885 GTACCAACAT
Statistics
Matches: 235, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
117 101 0.43
119 104 0.44
120 12 0.05
122 18 0.08
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (120 bp):
TGAGCCTTCAAGATGCCTCCCATGGATCATTTCTGTCTAAAATGGGCCTTCAAAATACCCCAACA
TTCTATTTCTGGTTGAAATGGACCTTCAAAATATCCCAACATTTTCATGCTAATG
Found at i:36838 original size:117 final size:117
Alignment explanation
Indices: 36550--36884 Score: 573
Period size: 117 Copynumber: 2.8 Consensus size: 117
36540 AATCATTTTT
* * * *
36550 TGTCTGAAATGGGCCTTCAAAATGCCCCAACATTCTATTTCTAGTTGAAATAGACCTTCAAAATA
1 TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACCTTCAAAATA
36615 TCCCAACATTTTCATGCTAATGTGAGCCTTCAAGATGCCTCCATGGATCATTTC
66 TCCCAACATTTTCATGCTAATGTGAGCCTTCAAGATGCCTCCATGGA--ATTTC
36669 TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACCTTCAAAATA
1 TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACCTTCAAAATA
36734 TCCCAACATTTTCATGCTAATGTGAGCCTTCAAGATGCCTCCCATGG-ATTTC
66 TCCCAACATTTTCATGCTAATGTGAGCCTTCAAGATGCCT-CCATGGAATTTC
*
36786 TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACATTCAAAATA
1 TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACCTTCAAAATA
* *
36851 TCCCAACATTTTCATGTTGATGTGAGCCTTCAAG
66 TCCCAACATTTTCATGCTAATGTGAGCCTTCAAG
36885 GTACCAACAT
Statistics
Matches: 208, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
117 101 0.49
119 101 0.49
120 6 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (117 bp):
TGTCTAAAATGGGCCTTCAAAATACCCCAACATTCTATTTCTGGTTGAAATGGACCTTCAAAATA
TCCCAACATTTTCATGCTAATGTGAGCCTTCAAGATGCCTCCATGGAATTTC
Found at i:44471 original size:2 final size:2
Alignment explanation
Indices: 44459--44519 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
44449 GTCGTTTTGA
44459 AT AT A- 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
44500 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
44520 GAAATTATAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44851 original size:20 final size:21
Alignment explanation
Indices: 44828--44866 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
44818 TCTTTGGTGG
44828 TTCCACGGT-GACTTTAAGCC
1 TTCCACGGTCGACTTTAAGCC
*
44848 TTCCACGGTCGGCTTTAAG
1 TTCCACGGTCGACTTTAAG
44867 ACTTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (21 bp):
TTCCACGGTCGACTTTAAGCC
Found at i:45423 original size:3 final size:3
Alignment explanation
Indices: 45415--45482 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
45405 AAAATAACAT
45415 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45463 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
45483 CATATAATGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:45867 original size:11 final size:11
Alignment explanation
Indices: 45851--45901 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
45841 AATCCGTCTT
45851 CGAGCTTCAAA
1 CGAGCTTCAAA
* *
45862 CGAGCTTGAAT
1 CGAGCTTCAAA
*
45873 CGAGCTTAAAA
1 CGAGCTTCAAA
*
45884 TCGAGCTTCAAT
1 -CGAGCTTCAAA
45896 CGAGCT
1 CGAGCT
45902 CGAGTCTCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (11 bp):
CGAGCTTCAAA
Found at i:45896 original size:23 final size:22
Alignment explanation
Indices: 45850--45901 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
45840 TAATCCGTCT
* *
45850 TCGAGCTTCAAACGAGCTTGAA
1 TCGAGCTTAAAACGAGCTTCAA
45872 TCGAGCTTAAAATCGAGCTTCAA
1 TCGAGCTTAAAA-CGAGCTTCAA
45895 TCGAGCT
1 TCGAGCT
45902 CGAGTCTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (22 bp):
TCGAGCTTAAAACGAGCTTCAA
Found at i:45913 original size:13 final size:13
Alignment explanation
Indices: 45895--45938 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
45885 CGAGCTTCAA
45895 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
45908 TCGAGCTTCG-G--
1 TCGAGC-TCGAGTC
45919 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
45932 TCGAGCT
1 TCGAGCT
45939 TCGGTCGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
13 14 0.52
14 3 0.11
ACGTcount: A:0.14, C:0.30, G:0.32, T:0.25
Consensus pattern (13 bp):
TCGAGCTCGAGTC
Found at i:45916 original size:24 final size:24
Alignment explanation
Indices: 45884--45950 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
45874 GAGCTTAAAA
**
45884 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCGGTCGAGCTCGAGTC
45908 TCGAGCTTCGGTCGAGCTCGAGTC
1 TCGAGCTTCGGTCGAGCTCGAGTC
45932 TCGAGCTTCGGTCGAGCTC
1 TCGAGCTTCGGTCGAGCTC
45951 TTGAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (24 bp):
TCGAGCTTCGGTCGAGCTCGAGTC
Found at i:45924 original size:11 final size:11
Alignment explanation
Indices: 45908--45949 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
45898 AGCTCGAGTC
45908 TCGAGCTTCGG
1 TCGAGCTTCGG
45919 TCGAGC-TCGAG
1 TCGAGCTTCG-G
45930 TCTCGAGCTTCGG
1 --TCGAGCTTCGG
45943 TCGAGCT
1 TCGAGCT
45950 CTTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.11
11 14 0.52
13 7 0.26
14 3 0.11
ACGTcount: A:0.12, C:0.29, G:0.33, T:0.26
Consensus pattern (11 bp):
TCGAGCTTCGG
Found at i:55806 original size:28 final size:28
Alignment explanation
Indices: 55774--55834 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
55764 TCCTTATTAT
55774 ATTAAAATATTTAGCCTGATTATAAGTG
1 ATTAAAATATTTAGCCTGATTATAAGTG
55802 ATTAAAATATTTAGCCTGATTATAAGTG
1 ATTAAAATATTTAGCCTGATTATAAGTG
55830 ATTAA
1 ATTAA
55835 GTTCTATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (28 bp):
ATTAAAATATTTAGCCTGATTATAAGTG
Found at i:61684 original size:17 final size:16
Alignment explanation
Indices: 61631--61690 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
61621 AGTAGTATTG
* *
61631 CGAGGAGAGCAGCGCT
1 CGAGGAGAGCGGCACT
* *
61647 CGACGAAAGCGGCACT
1 CGAGGAGAGCGGCACT
61663 GCGAGGAGAGCGGCACCT
1 -CGAGGAGAGCGGCA-CT
*
61681 CGAGAAGAGC
1 CGAGGAGAGC
61691 AACGCTGCGA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 12 0.34
17 21 0.60
18 2 0.06
ACGTcount: A:0.28, C:0.27, G:0.40, T:0.05
Consensus pattern (16 bp):
CGAGGAGAGCGGCACT
Found at i:62207 original size:152 final size:154
Alignment explanation
Indices: 61931--62239 Score: 595
Period size: 152 Copynumber: 2.0 Consensus size: 154
61921 AAAGAAAAAA
61931 ATTCCATCTTACACAAGAGGATACATAAGATTTTTATACACATGAATTAGAGGCCTAGATAAGAT
1 ATTCCATCTTACACAAGAGGATACATAAGATTTTTATACACATGAATTAGAGGCCTAGATAAGAT
61996 AGAAATCATATTTTCTAGAAATTAAGAGATAGTTTTAGAGATAAGTTAAGACTCAGAGTTTGACT
66 AGAAATCATATTTTCTAGAAATTAAGAGATAGTTTTAGAGATAAGTTAAGACTCAGAGTTTGACT
62061 C-AGTTTGACTCAGAA-TTTAGAG
131 CAAGTTTGACTCAGAATTTTAGAG
62083 ATTCCATCTTACACAAGAGGATACATAAGATTTTTATACACATGAATTAGAGGCCTAGATAAGAT
1 ATTCCATCTTACACAAGAGGATACATAAGATTTTTATACACATGAATTAGAGGCCTAGATAAGAT
62148 AGAAATCATATTTTCTAGAAATTAAGAGATAGTTTTAGAGATAAGTTAAGACTCAGAGTTTGACT
66 AGAAATCATATTTTCTAGAAATTAAGAGATAGTTTTAGAGATAAGTTAAGACTCAGAGTTTGACT
62213 CAGAGTTTGACTCAGAATTTTAGAG
131 CA-AGTTTGACTCAGAATTTTAGAG
62238 AT
1 AT
62240 AAGGATGGGG
Statistics
Matches: 154, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 131 0.85
154 14 0.09
155 9 0.06
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (154 bp):
ATTCCATCTTACACAAGAGGATACATAAGATTTTTATACACATGAATTAGAGGCCTAGATAAGAT
AGAAATCATATTTTCTAGAAATTAAGAGATAGTTTTAGAGATAAGTTAAGACTCAGAGTTTGACT
CAAGTTTGACTCAGAATTTTAGAG
Found at i:62214 original size:12 final size:12
Alignment explanation
Indices: 62197--62228 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
62187 GATAAGTTAA
62197 GACTCAGAGTTT
1 GACTCAGAGTTT
62209 GACTCAGAGTTT
1 GACTCAGAGTTT
62221 GACTCAGA
1 GACTCAGA
62229 ATTTTAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (12 bp):
GACTCAGAGTTT
Found at i:76601 original size:3 final size:3
Alignment explanation
Indices: 76593--76622 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
76583 TTTCTCCCTT
76593 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
76623 AATTCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:83298 original size:20 final size:20
Alignment explanation
Indices: 83273--83310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
83263 ATTGAAGAAT
83273 AAATAATTAAAAAATTAAGC
1 AAATAATTAAAAAATTAAGC
* *
83293 AAATAATTTAAAATTTAA
1 AAATAATTAAAAAATTAA
83311 TACATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATAATTAAAAAATTAAGC
Found at i:94663 original size:24 final size:24
Alignment explanation
Indices: 94636--94694 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
94626 ATCTGATTTC
94636 TGACTTGAATTCTATTATGATACA
1 TGACTTGAATTCTATTATGATACA
* * * * *
94660 TGACCTGGATTCTGTTCTGATATA
1 TGACTTGAATTCTATTATGATACA
*
94684 TGATTTGAATT
1 TGACTTGAATT
94695 ATGTTTGATT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (24 bp):
TGACTTGAATTCTATTATGATACA
Done.