Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009182.1 Hibiscus syriacus cultivar Beakdansim tig00112753_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: 18290
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Found at i:3677 original size:32 final size:32
Alignment explanation
Indices: 3641--3705 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3631 ATCACACTGG
3641 GAAGTTGGAATTCAATACACCATCCGCATCAA
1 GAAGTTGGAATTCAATACACCATCCGCATCAA
3673 GAAGTTGGAATTCAATACACCATCCGCATCAA
1 GAAGTTGGAATTCAATACACCATCCGCATCAA
3705 G
1 G
3706 TCATCCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (32 bp):
GAAGTTGGAATTCAATACACCATCCGCATCAA
Found at i:9328 original size:1 final size:1
Alignment explanation
Indices: 9322--9365 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
9312 ATTATGCTTG
* * *
9322 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9366 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:10473 original size:51 final size:52
Alignment explanation
Indices: 10300--10957 Score: 1218
Period size: 52 Copynumber: 12.7 Consensus size: 52
10290 TATGTGCTCA
*
10300 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
10352 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10404 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10455 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10507 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
10560 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10611 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10663 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
10714 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGAACAG-AC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10765 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10817 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
10869 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
10920 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
10958 CGAAGAAGTG
Statistics
Matches: 592, Mismatches: 9, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
51 248 0.42
52 292 0.49
53 52 0.09
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:10486 original size:103 final size:104
Alignment explanation
Indices: 10300--10957 Score: 1218
Period size: 103 Copynumber: 6.4 Consensus size: 104
10290 TATGTGCTCA
*
10300 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
10365 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10404 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
10468 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10507 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGATTGGACAGAACATAGCATCTTCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACATAGCATCTTCT
10572 GGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GACAGAAC
65 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10611 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
10676 GAAGTGTTCTTTGAGTTATCTGATCT-GTTGGACAGAAC
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
10714 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGAACAG-ACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
10778 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
10817 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
10882 GAAGTGTTCTTTGAGTTATCTGATCT-GATGGACAGAAC
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
10920 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
10958 CGAAGAAGTG
Statistics
Matches: 541, Mismatches: 8, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
102 44 0.08
103 312 0.58
104 134 0.25
105 51 0.09
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (104 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:11807 original size:112 final size:112
Alignment explanation
Indices: 11516--12282 Score: 1216
Period size: 112 Copynumber: 6.9 Consensus size: 112
11506 GATTCAAATT
* * *
11516 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
11581 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TGAATC
11629 CATCATTTGGTGGATCATC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
11693 AGAAG-AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAA-C
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTGAATC
11738 CATCATTT-GTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
11802 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TGAATC
11850 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
11915 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAA-C
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTA-CTGAATC
11962 CATCATTTGGTGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
12025 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTGAATC
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTGAATC
* *
12072 CATCATTTGGTGGATCATATTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** * *
12137 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTGAATC
* * * ** *
12184 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAG-ACTCATCT---GAA-G
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
12244 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
12283 GTTTGATATC
Statistics
Matches: 619, Mismatches: 25, Indels: 25
0.93 0.04 0.04
Matches are distributed among these distances:
108 48 0.08
109 67 0.11
110 106 0.17
111 103 0.17
112 169 0.27
113 125 0.20
114 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (112 bp):
CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTGAATC
Found at i:12080 original size:222 final size:224
Alignment explanation
Indices: 11516--12282 Score: 1259
Period size: 222 Copynumber: 3.5 Consensus size: 224
11506 GATTCAAATT
*
11516 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
11581 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
11646 TC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
11709 AGAAGAATTTGTTCAACCTTTTACTGAAC
196 AGAAGAATTTGTTCAACCTTTTACTGAAC
*
11738 CATCATTTG-TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
11802 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
11867 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
11932 AGAAGAATTTGTTCAACCTTTTACCTGAAC
196 AGAAGAATTTGTTCAACCTTTTA-CTGAAC
* *
11962 CATCATTTGGTGGATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
12025 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-TGAATCCATCATTTGGTGGATCA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
* *
12089 TATTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * ** * *
12154 AGAAGAACTTGTTCAACTTTTTGTTTAATT
196 AGAAGAATTTGTTCAACCTTTTACTGAA-C
* ** *
12184 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAG-ACTCATCT---GAA-G
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
12244 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
12283 GTTTGATATC
Statistics
Matches: 518, Mismatches: 20, Indels: 16
0.94 0.04 0.03
Matches are distributed among these distances:
220 41 0.08
221 123 0.24
222 187 0.36
223 92 0.18
224 57 0.11
225 18 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (224 bp):
CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGGATCA
TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACCTTTTACTGAAC
Found at i:12190 original size:334 final size:334
Alignment explanation
Indices: 11512--12282 Score: 1290
Period size: 334 Copynumber: 2.3 Consensus size: 334
11502 AAAAGATTCA
11512 AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
11577 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
11642 ATCATCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGTTCATAA
131 ATCATCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGTTCATAA
* *
11707 TGAGAAGAATTTGTTCAACCTTTTACTGAACCATCATTTGTGGATCATCTTTTCCAGAGAAAGTT
196 TGAGAAGAATTTGTTCAACCTTTTACTGAACCATCATTTGTGGATCATATTTCCCAGAGAAAGTT
11772 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
261 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
11837 TTTTGCTTG
326 TTTTGCTTG
* * * *
11846 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
11911 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAA-CCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
11975 ATCATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
131 ATCATC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AGTTCAT
12038 AATGAGAAGAATTTGTTCAACCTTTTACTGAATCCATCATTTGGTGGATCATATTTCCCAGAGAA
194 AATGAGAAGAATTTGTTCAACCTTTTACTGAA-CCATCATTT-GTGGATCATATTTCCCAGAGAA
12103 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
257 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
12168 AACTTTTTG-TTT
322 AACCTTTTGCTTG
* ** *
12180 AATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAG-ACTCATCT---G
1 AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
*
12241 AA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
12283 GTTTGATATC
Statistics
Matches: 412, Mismatches: 20, Indels: 14
0.92 0.04 0.03
Matches are distributed among these distances:
330 38 0.09
331 3 0.01
332 7 0.02
333 92 0.22
334 170 0.41
335 102 0.25
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (334 bp):
AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
ATCATCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTACTGAACCATCATTTGTGGATCATATTTCCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGCTTG
Found at i:12578 original size:3 final size:3
Alignment explanation
Indices: 12570--12642 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
12560 ATTTTTATCC
*
12570 ATT ATT ATT ATT ATT A-T ATT ATT ATT A-T ATT ATTT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
12614 ATT ATAT ATT ATT ATT ATT TTT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT A
12643 AATATATAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 52 0.84
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12650 original size:29 final size:28
Alignment explanation
Indices: 12570--12649 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 28
12560 ATTTTTATCC
12570 ATTATTATTATTATTATAT-TATTATTAT
1 ATTATT-TTATTATTATATATATTATTAT
*
12598 ATTA-TTTATTAATAT-TATTATATATTATT
1 ATTATTTTATTATTATATA-TAT-TATTA-T
*
12627 ATTATTTTTATTATTAAATATAT
1 ATTA-TTTTATTATTATATATAT
12650 AAATACAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.02
26 9 0.21
27 4 0.10
28 9 0.21
29 5 0.12
31 12 0.29
32 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTATTTTATTATTATATATATTATTAT
Found at i:13947 original size:18 final size:19
Alignment explanation
Indices: 13912--13949 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13902 CAATTTAGTC
13912 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
13931 ATTTATTTTAT-TGTTTTA
1 ATTTATTTTATATGTTTTA
13949 A
1 A
13950 ATATATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:13956 original size:19 final size:19
Alignment explanation
Indices: 13915--13956 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
13905 TTTAGTCATT
*
13915 TATTTTATATGTTTTAATT
1 TATTTTATATGTTTTAATA
13934 TATTTTAT-TGTTTTAAATA
1 TATTTTATATGTTTT-AATA
13953 TATT
1 TATT
13957 GTTTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTTATATGTTTTAATA
Found at i:14598 original size:20 final size:20
Alignment explanation
Indices: 14573--14610 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
14563 AAAAAATCAT
14573 AAGCATGTCATAGACCTATA
1 AAGCATGTCATAGACCTATA
14593 AAGCATGTCATAGACCTA
1 AAGCATGTCATAGACCTA
14611 AAAAATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
AAGCATGTCATAGACCTATA
Found at i:17085 original size:12 final size:12
Alignment explanation
Indices: 17005--17088 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 12
16995 GGAAAAGGAA
**
17005 AAAATAAAAATA
1 AAAATAAAAAGG
*
17017 AAAATTAAAAGG
1 AAAATAAAAAGG
*
17029 -AAATTAAAA-G
1 AAAATAAAAAGG
*
17039 ATAAATCAAAAGG
1 A-AAATAAAAAGG
* *
17052 AAAACAAATGAAGA
1 AAAATAAA--AAGG
17066 ATAAATAAAAAGG
1 A-AAATAAAAAGG
17079 AAAATAAAAA
1 AAAATAAAAA
17089 ATGAATAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 1 0.02
11 9 0.16
12 31 0.54
13 6 0.11
14 4 0.07
15 6 0.11
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAGG
Found at i:17095 original size:23 final size:23
Alignment explanation
Indices: 16981--17098 Score: 85
Period size: 23 Copynumber: 4.9 Consensus size: 23
16971 TGTAAAAGTA
**
16981 AAAATAAAAAA-AAAGGAAAAGG
1 AAAATAAAAAATAAATAAAAAGG
* *
17003 AAAAAATAAAAATAAAAATTAAAAGG
1 AAAATA-AAAAAT-AA-ATAAAAAGG
* * *
17029 AAATTAAAAGATAAATCAAAAGG
1 AAAATAAAAAATAAATAAAAAGG
*
17052 AAAACAAATGAAGAATAAATAAAAAGG
1 AAAA-TAA--AA-AATAAATAAAAAGG
*
17079 AAAATAAAAAATGAATAAAA
1 AAAATAAAAAATAAATAAAA
17099 CAAAAATATA
Statistics
Matches: 75, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
22 5 0.07
23 26 0.35
24 6 0.08
25 7 0.09
26 15 0.20
27 16 0.21
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.13
Consensus pattern (23 bp):
AAAATAAAAAATAAATAAAAAGG
Found at i:17103 original size:27 final size:27
Alignment explanation
Indices: 17035--17103 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
17025 AAGGAAATTA
*
17035 AAAG-ATAAATCAAAAGGAAAACAAAT
1 AAAGAATAAAACAAAAGGAAAACAAAT
* *
17061 GAAGAATAAATA-AAAAGGAAAATAAA-
1 AAAGAATAAA-ACAAAAGGAAAACAAAT
17087 AAATGAATAAAACAAAA
1 AAA-GAATAAAACAAAA
17104 ATATACATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (27 bp):
AAAGAATAAAACAAAAGGAAAACAAAT
Done.