Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000462.1 Hibiscus syriacus cultivar Beakdansim tig00000857_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: 66109
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1810 original size:16 final size:16
Alignment explanation
Indices: 1789--1820 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1779 AGGGGGAGTA
1789 ATTTCAAACTTAATTT
1 ATTTCAAACTTAATTT
*
1805 ATTTCAAACTTGATTT
1 ATTTCAAACTTAATTT
1821 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTCAAACTTAATTT
Found at i:1938 original size:13 final size:13
Alignment explanation
Indices: 1922--1946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1912 AATGAATTTT
1922 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1935 AAGATTTTCTAA
1 AAGATTTTCTAA
1947 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:7283 original size:31 final size:30
Alignment explanation
Indices: 7227--7285 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
7217 TTAGGTCCAT
*
7227 AAGGAATTACCAGTCGGTGCTGAACCTATAC
1 AAGGAATTACCAGTCGATGC-GAACCTATAC
7258 AAGGAATTACCAGTAGCGATG-GAACCTA
1 AAGGAATTACCAGT--CGATGCGAACCTA
7286 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 21 0.84
33 4 0.16
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (30 bp):
AAGGAATTACCAGTCGATGCGAACCTATAC
Found at i:13511 original size:19 final size:18
Alignment explanation
Indices: 13473--13507 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13463 ATTTTACATC
13473 AAAAACTGAACTTAATCG
1 AAAAACTGAACTTAATCG
13491 AAAAACT-AACTTGAATC
1 AAAAACTGAACTT-AATC
13508 CGAAGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (18 bp):
AAAAACTGAACTTAATCG
Found at i:14614 original size:3 final size:3
Alignment explanation
Indices: 14606--14659 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
14596 TAAATAATTG
14606 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14654 AAT AAT
1 AAT AAT
14660 TGTATGTCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:15112 original size:19 final size:19
Alignment explanation
Indices: 15055--15115 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
15045 TACACACTAT
15055 ATTTAATTTATTATTTCTTA
1 ATTTAATTTATTATTT-TTA
*
15075 ATCTTGAA-ATATT-TGTTTTA
1 AT-TT-AATTTATTAT-TTTTA
15095 ATTTAATTTATTATTTTTA
1 ATTTAATTTATTATTTTTA
15114 AT
1 AT
15116 AATTTTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 2 0.06
19 13 0.38
20 9 0.26
21 8 0.24
22 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTAATTTATTATTTTTA
Found at i:15826 original size:17 final size:19
Alignment explanation
Indices: 15799--15840 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
15789 TTATCGAAAT
15799 ATTTT-ATATTAT-ATA-A
1 ATTTTGATATTATGATATA
15815 ATTTTGATATTATGATATA
1 ATTTTGATATTATGATATA
15834 ATTTTGA
1 ATTTTGA
15841 ATATATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 3 0.13
19 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTTTGATATTATGATATA
Found at i:15847 original size:19 final size:19
Alignment explanation
Indices: 15803--15847 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
15793 CGAAATATTT
*
15803 TATATTATATAAATTTTGA
1 TATATGATATAAATTTTGA
15822 TATTATGATAT-AATTTTGAA
1 TA-TATGATATAAATTTTG-A
15842 TATATG
1 TATATG
15848 TTGTCTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (19 bp):
TATATGATATAAATTTTGA
Found at i:16736 original size:9 final size:9
Alignment explanation
Indices: 16722--16763 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
16712 AGTGCACATC
16722 ATTAAAGGA
1 ATTAAAGGA
*
16731 ATTAAAGAA
1 ATTAAAGGA
16740 ATTAAAGG-
1 ATTAAAGGA
*
16748 ATTAATATGA
1 ATTAA-AGGA
16758 ATTAAA
1 ATTAAA
16764 AAATTAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 5 0.18
9 18 0.64
10 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (9 bp):
ATTAAAGGA
Found at i:16829 original size:18 final size:19
Alignment explanation
Indices: 16806--16851 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
16796 CAAATATTAA
* *
16806 AATTTTATTTTATT-TTTT
1 AATTTTAATTGATTATTTT
16824 AATTTTAATTGATTATTTT
1 AATTTTAATTGATTATTTT
16843 AATTATTAA
1 AATT-TTAA
16852 AATAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 8 0.33
20 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
AATTTTAATTGATTATTTT
Found at i:16984 original size:19 final size:19
Alignment explanation
Indices: 16957--17015 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
16947 GTAAAATTTT
16957 ATATTAAAAAAATTATAAA
1 ATATTAAAAAAATTATAAA
* **
16976 ATCTTAAAAATAAAAATAAA
1 ATATTAAAAA-AATTATAAA
* *
16996 TTATTAATAAAATTATAAA
1 ATATTAAAAAAATTATAAA
17015 A
1 A
17016 AAAATATCTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATTAAAAAAATTATAAA
Found at i:21170 original size:2 final size:2
Alignment explanation
Indices: 21163--21188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21153 AGCCCCTACC
21163 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
21189 GTTAAGAATT
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):
TA
Found at i:26825 original size:38 final size:39
Alignment explanation
Indices: 26757--26837 Score: 137
Period size: 38 Copynumber: 2.1 Consensus size: 39
26747 TGAATTCTGT
26757 TTTAACTCTATTTTTAAAAAAAAAATCATGATACAACTCG
1 TTTAACTCTATTTTT-AAAAAAAAATCATGATACAACTCG
*
26797 TTTAACTCTATTTTT-AAAAAAATTCATGATACAACTCG
1 TTTAACTCTATTTTTAAAAAAAAATCATGATACAACTCG
26835 TTT
1 TTT
26838 GATGAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 25 0.62
40 15 0.38
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.40
Consensus pattern (39 bp):
TTTAACTCTATTTTTAAAAAAAAATCATGATACAACTCG
Found at i:31135 original size:15 final size:15
Alignment explanation
Indices: 31115--31163 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
31105 TAATATGAAT
31115 CCTAAACAAATTAAA
1 CCTAAACAAATTAAA
31130 CCTAAACTAAATTAAA
1 CCTAAAC-AAATTAAA
* * *
31146 CATGAATAAATTAAA
1 CCTAAACAAATTAAA
31161 CCT
1 CCT
31164 CATGCGTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.24
Consensus pattern (15 bp):
CCTAAACAAATTAAA
Found at i:32574 original size:55 final size:54
Alignment explanation
Indices: 32533--33215 Score: 958
Period size: 55 Copynumber: 12.4 Consensus size: 54
32523 TGACAGGTTT
* *
32533 GCTCCCTATTCTTTCA-AGTAGTATA-AGACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCAA-AAACGGGTCC
*
32588 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAATGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* * * *
32643 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTGCAACAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
*
32698 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* * * * *
32753 GCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCATAAAACGGGCCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
* * * *
32808 GCTCTCTATTCCTTTAAAGAGTATAGAATTCGAACAATCTTCAACAAACAGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* *
32863 GCTCTCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
* *
32918 ACTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* *
32973 ACTCCCTATT-CTATCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCTCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
33028 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
*
33083 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
* **
33138 GCTCTCTATTCCTTTAGAGAGTATAGAACTCGAACAATCTTCAACAAACATGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
*
33193 GCTCTCTATTTCTTCAGAGAGTA
1 GCTCTCTATTCCTTCAGAGAGTA
33216 CAGGACTCAA
Statistics
Matches: 567, Mismatches: 51, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
54 5 0.01
55 554 0.98
56 8 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (54 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACGGGTCC
Found at i:33772 original size:29 final size:29
Alignment explanation
Indices: 33718--33935 Score: 206
Period size: 29 Copynumber: 7.6 Consensus size: 29
33708 AAAAATAATA
* * * *
33718 TTTTGATATATTACAATAAAGACCAAAAC
1 TTTTTATAAATTACAAAAAATACCAAAAC
*
33747 -TTTTATAAATTACAAACAAATGCC-AAAC
1 TTTTTATAAATTACAAA-AAATACCAAAAC
33775 TTTTTATAAATTACAAAAAATACCAAAAC
1 TTTTTATAAATTACAAAAAATACCAAAAC
33804 TTTTTATAAATTACAAAAAATACCAAAAC
1 TTTTTATAAATTACAAAAAATACCAAAAC
* * *
33833 TTTTTATAAATTACAACAAATGCCAAAAA
1 TTTTTATAAATTACAAAAAATACCAAAAC
*** * ** * ***
33862 AAATTAAAAATTACAACTAATTCCAATTG
1 TTTTTATAAATTACAAAAAATACCAAAAC
* * ***
33891 TTTTTATAAATTACAACAAATTCCAATTG
1 TTTTTATAAATTACAAAAAATACCAAAAC
33920 TTTTTATAAATTACAA
1 TTTTTATAAATTACAA
33936 TCAAAGAAAA
Statistics
Matches: 163, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.14
29 140 0.86
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTTATAAATTACAAAAAATACCAAAAC
Found at i:33898 original size:87 final size:86
Alignment explanation
Indices: 33718--33940 Score: 232
Period size: 87 Copynumber: 2.6 Consensus size: 86
33708 AAAAATAATA
* * * * **** *
33718 TTTTGATATATTACAATAAAGACCAAAAC-TTTTATAAATTACAAACAAATGCCAAACTTTTTAT
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTAC-AACAAATGCCAAAAAAATTAA
33782 AAATTACAAAAAATACCAAAAC
65 AAATTACAAAAAATACCAAAAC
33804 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAAATTAA
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATGCC-AAAAAAATTAA
** * ***
33869 AAATTACAACTAATTCCAATTG
65 AAATTACAAAAAATACCAAAAC
* * ***
33891 TTTTTATAAATTACAACAAATTCCAATTGTTTTTATAAATTACAATCAAA
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAA-CAAA
33941 GAAAAAACTT
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
86 35 0.31
87 75 0.66
88 4 0.04
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (86 bp):
TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAATTAAA
AATTACAAAAAATACCAAAAC
Found at i:33960 original size:87 final size:85
Alignment explanation
Indices: 33718--33968 Score: 220
Period size: 87 Copynumber: 2.9 Consensus size: 85
33708 AAAAATAATA
* * * * * **** *
33718 TTTTGATATATTACAATAAAGACCAAAAC-TTTTATAAATTACAAACAAATGCCAAACTTTTTAT
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTAC-AACAAATGCAAAAAAAATTAA
* * ***
33782 AAATTACAAAAAATACCAAAAC
65 AAATTAC-AATAATTCCAATTG
33804 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAAATTAA
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATG-CAAAAAAAATTAA
33869 AAATTACAACTAATTCCAATTG
65 AAATTACAA-TAATTCCAATTG
* * *** **
33891 TTTTTATAAATTACAACAAATTCCAATTGTTTTTATAAATTACAATCAAA-G-AAAAAACTTCTA
1 TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAA-CAAATGCAAAAAAAAT-TA
33954 ATAAATTACAATAAT
64 A-AAATTACAATAAT
33969 GACTTGAGAG
Statistics
Matches: 137, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
85 7 0.05
86 42 0.31
87 84 0.61
88 4 0.03
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.33
Consensus pattern (85 bp):
TTTTTATAAATTACAAAAAATACCAAAACTTTTTATAAATTACAACAAATGCAAAAAAAATTAAA
AATTACAATAATTCCAATTG
Found at i:35447 original size:36 final size:36
Alignment explanation
Indices: 35406--35481 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
35396 ATTTTCGGGA
*
35406 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
35442 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
35478 TTTT
1 TTTT
35482 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:35923 original size:15 final size:15
Alignment explanation
Indices: 35903--35932 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35893 TATCACAATC
35903 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
35918 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
35933 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:40443 original size:36 final size:36
Alignment explanation
Indices: 40402--40477 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
40392 ATTTTCGGGA
*
40402 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
40438 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
40474 TTTT
1 TTTT
40478 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:42900 original size:17 final size:17
Alignment explanation
Indices: 42868--42902 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42858 TATCTTCATC
42868 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
42885 TCAAT-CTTCAACTATCT
1 TCAATGCTTCAA-TATCT
42902 T
1 T
42903 TGGGAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.43
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:43949 original size:6 final size:7
Alignment explanation
Indices: 43932--44083 Score: 52
Period size: 7 Copynumber: 21.7 Consensus size: 7
43922 TTTTCTTTAT
43932 TTTTTCA
1 TTTTTCA
43939 TTTTTCA
1 TTTTTCA
*
43946 TTTTTCTC
1 TTTTTC-A
43954 TTTCTTC-
1 TTT-TTCA
43961 TTTCTTC-
1 TTT-TTCA
*
43968 TTCTTTGA
1 TT-TTTCA
43976 TTTTTTCA
1 -TTTTTCA
*
43984 TTTTTTA
1 TTTTTCA
43991 TTTTT--
1 TTTTTCA
*
43996 TCTTTTCT
1 T-TTTTCA
*
44004 TTTTTCTTC
1 TTTTTC--A
44013 TTTTTC-
1 TTTTTCA
**
44019 TTTCACCA
1 TTT-TTCA
44027 TTTTTCA
1 TTTTTCA
44034 -TTTT--
1 TTTTTCA
*
44038 TTTCTCA
1 TTTTTCA
*
44045 TTTTACA
1 TTTTTCA
44052 TTTTTCA
1 TTTTTCA
44059 -TTTTCA
1 TTTTTCA
* *
44065 TTTTCCT
1 TTTTTCA
*
44072 TTTTTTA
1 TTTTTCA
44079 TTTTT
1 TTTTT
44084 TCCTTTTTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
5 4 0.04
6 17 0.15
7 67 0.60
8 12 0.11
9 11 0.10
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:43986 original size:45 final size:44
Alignment explanation
Indices: 43924--44039 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 44
43914 CCCTTTTATT
43924 TTCTTTATTTTTTCATTTTTCA-TTTTTCTCTTTCTTCTTTCTTC
1 TTCTTTATTTTTTCATTTTTCATTTTTTCT-TTTCTTCTTTCTTC
* *
43968 TTCTTTGATTTTTTCATTTTTTATTTTTTCTTTTCTTTTTTCTTC
1 TTCTTT-ATTTTTTCATTTTTCATTTTTTCTTTTCTTCTTTCTTC
* ***
44013 TT-TTTCTTTCACCATTTTTCATTTTTT
1 TTCTTTATTTTTTCATTTTTCATTTTTT
44040 TCTCATTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
43 17 0.27
44 9 0.14
45 30 0.48
46 7 0.11
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (44 bp):
TTCTTTATTTTTTCATTTTTCATTTTTTCTTTTCTTCTTTCTTC
Found at i:43999 original size:30 final size:29
Alignment explanation
Indices: 43927--44109 Score: 105
Period size: 30 Copynumber: 6.4 Consensus size: 29
43917 TTTTATTTTC
43927 TTTATTTTTTCATTTTTCATTTTTCTCTTT
1 TTTATTTTTTC-TTTTTCATTTTTCTCTTT
* * * *
43957 CTTCTTTCTTCTTCTTTGATTTTT-TCATTT
1 TTTATTTTTTCTT-TTTCATTTTTCTC-TTT
*
43987 TTTATTTTTTC-TTTTCTTTTTTCT-TCTT
1 TTTATTTTTTCTTTTTCATTTTTCTCT-TT
* *** * *
44015 TTTCTTTCACCATTTTTCATTTTTTTCTCAT
1 TTTATTTTTTC-TTTTTCATTTTTCTCT-TT
* * *
44046 TTTACATTTTTCATTTTCATTTTCCT-TTT
1 TTTA-TTTTTTCTTTTTCATTTTTCTCTTT
*
44075 TTTATTTTTTC-CTTT--TTTTT-TC-TT
1 TTTATTTTTTCTTTTTCATTTTTCTCTTT
44099 TTTATTTTTTC
1 TTTATTTTTTC
44110 ATCAAGCGAA
Statistics
Matches: 116, Mismatches: 28, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
24 14 0.12
25 4 0.03
27 4 0.03
28 23 0.20
29 11 0.09
30 40 0.34
31 17 0.15
32 3 0.03
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTATTTTTTCTTTTTCATTTTTCTCTTT
Found at i:44037 original size:58 final size:59
Alignment explanation
Indices: 43927--44068 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 59
43917 TTTTATTTTC
** *
43927 TTTATTTTTTCATTTTTCATTTTTCTCTTTCTTCTTTCTTCTTCTTTGATTTTTTCATTT
1 TTTATTTTTTCA-TTTTCATTTTTCTCTTTCTTCTTTCACCTTCTTTCATTTTTTCATTT
* *
43987 TTTATTTTTTC-TTTTCTTTTTTCTTCTTT-TTCTTTCACCATT-TTTCATTTTTTTC-TCAT
1 TTTATTTTTTCATTTTCATTTTTC-TCTTTCTTCTTTCACC-TTCTTTCA-TTTTTTCAT-TT
*
44046 TTTACATTTTTCATTTTCATTTT
1 TTTA-TTTTTTCATTTTCATTTT
44069 CCTTTTTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
58 24 0.35
59 19 0.28
60 17 0.25
61 9 0.13
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.73
Consensus pattern (59 bp):
TTTATTTTTTCATTTTCATTTTTCTCTTTCTTCTTTCACCTTCTTTCATTTTTTCATTT
Found at i:44067 original size:20 final size:19
Alignment explanation
Indices: 44025--44082 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
44015 TTTCTTTCAC
* *
44025 CATTTTTCATTTTT-TTCT
1 CATTTTACATTTTTATTTT
44043 CATTTTACATTTTTCATTTT
1 CATTTTACATTTTT-ATTTT
* *
44063 CATTTTCCTTTTTTTATTTT
1 CATTTTAC-ATTTTTATTTT
44083 TTCCTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.39
20 15 0.45
21 5 0.15
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
CATTTTACATTTTTATTTT
Found at i:44100 original size:16 final size:16
Alignment explanation
Indices: 44059--44100 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
44049 ACATTTTTCA
44059 TTTTCATTTTCCTTTTT
1 TTTTC-TTTTCCTTTTT
44076 TTATT-TTTTCCTTTTT
1 TT-TTCTTTTCCTTTTT
44092 TTTTCTTTT
1 TTTTCTTTT
44101 TATTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 2 0.09
18 2 0.09
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTCCTTTTT
Found at i:53583 original size:45 final size:47
Alignment explanation
Indices: 53517--53619 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 47
53507 TGTTATTCAC
* *
53517 AAAAAGAAATCCTAACTGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
53563 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
53610 AAAAACGAAA
1 AAAAA-GAAA
53620 ATAAATGACT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 27 0.55
46 8 0.16
47 11 0.22
48 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:55069 original size:15 final size:15
Alignment explanation
Indices: 55049--55097 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
55039 TAATATGAAT
55049 CCTAAACAAATTAAA
1 CCTAAACAAATTAAA
55064 CCTAAACTAAATTAAA
1 CCTAAAC-AAATTAAA
* * *
55080 CATGAATAAATTAAA
1 CCTAAACAAATTAAA
55095 CCT
1 CCT
55098 CACGCGTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.24
Consensus pattern (15 bp):
CCTAAACAAATTAAA
Found at i:56427 original size:5 final size:5
Alignment explanation
Indices: 56418--56481 Score: 75
Period size: 5 Copynumber: 13.8 Consensus size: 5
56408 TCTCAACTCC
* *
56418 CCCTC CCCTC CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT -CCTT -CCTT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT
56466 -CCTT -CCTT -CCTT CCCT
1 CCCTT CCCTT CCCTT CCCT
56482 CCTCCCCCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
4 20 0.35
5 37 0.65
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CCCTT
Found at i:56463 original size:4 final size:4
Alignment explanation
Indices: 56429--56484 Score: 58
Period size: 4 Copynumber: 12.8 Consensus size: 4
56419 CCTCCCCTCC
56429 CCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCTT CCTT CCTT CCTT CCTT
1 CCTT -CCTT -CCTT -CCTT -CCTT -CCTT CCTT CCTT CCTT CCTT CCTT
*
56478 CCCT CCT
1 CCTT CCT
56485 CCCCCAACCT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 25 0.51
5 24 0.49
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (4 bp):
CCTT
Found at i:63455 original size:14 final size:13
Alignment explanation
Indices: 63433--63467 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
63423 AATCAAAAAG
63433 AAAAAAAAAAGCA
1 AAAAAAAAAAGCA
63446 AAAAAGAAAAAGCA
1 AAAAA-AAAAAGCA
63460 AAGAAAAA
1 AA-AAAAA
63468 GGGATGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGCA
Found at i:63462 original size:19 final size:18
Alignment explanation
Indices: 63427--63467 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
63417 AACAAGAATC
63427 AAAAAGAAAAAAAAAAGCA
1 AAAAAGAAAAAAAAAAG-A
**
63446 AAAAAGAAAAAGCAAAGA
1 AAAAAGAAAAAAAAAAGA
63464 AAAA
1 AAAA
63468 GGGATGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:64510 original size:32 final size:32
Alignment explanation
Indices: 64474--64547 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
64464 GCATCTTTAA
*
64474 AGATTCAACAGCAAATGTTAGGGCATATTTGG
1 AGATTCAACAGCAAATATTAGGGCATATTTGG
* * *** *
64506 AGATTTACCATTGAATATTGGGGCATATTTGG
1 AGATTCAACAGCAAATATTAGGGCATATTTGG
*
64538 GGATTCAACA
1 AGATTCAACA
64548 TCCTGATGTA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.31
Consensus pattern (32 bp):
AGATTCAACAGCAAATATTAGGGCATATTTGG
Found at i:64899 original size:64 final size:64
Alignment explanation
Indices: 64805--64935 Score: 219
Period size: 64 Copynumber: 2.0 Consensus size: 64
64795 GGAGCGTCTG
*
64805 TCAACAAACAACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
1 TCAACAAACAACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
* *
64869 TCAACAAACAA-TTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGTATATTGAAC
1 TCAACAAACAACTTTT-CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
64933 TCA
1 TCA
64936 TAATTTGCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 4 0.06
64 59 0.94
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (64 bp):
TCAACAAACAACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
Found at i:65263 original size:43 final size:43
Alignment explanation
Indices: 65099--65252 Score: 191
Period size: 43 Copynumber: 3.6 Consensus size: 43
65089 TGAAGGAGGC
* *
65099 CATCCACGATTTCAACTTCACGACGGAGAATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
* * * * *
65142 CATTCACTATTTCAACTCCACGACGGAGTATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
* * *
65185 GATCAACGATTTCAACTCCACGATGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
* * *
65228 CAACCACGGTTTCAACTTCACGACG
1 CATCCACGATTTCAACTCCACGACG
65253 AAGGGAATCG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
Found at i:65263 original size:86 final size:86
Alignment explanation
Indices: 65104--65265 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 86
65094 GAGGCCATCC
* ** * *
65104 ACGATTTCAACTTCACGACGGAGAATATCGTGCCCACACATTCACTATTTCAACTCCACGACGGA
1 ACGATTTCAACTCCACGACGGAGAATATCGTGCCCACACAACCACGATTTCAACTCCACGACGAA
*
65169 GTATATCGTACCAACAGATCA
66 GGATATCGTACCAACAGATCA
* * * *
65190 ACGATTTCAACTCCACGATGGAGGATATCGTGCCCACACAACCACGGTTTCAACTTCACGACGAA
1 ACGATTTCAACTCCACGACGGAGAATATCGTGCCCACACAACCACGATTTCAACTCCACGACGAA
65255 GGGA-ATCGTAC
66 -GGATATCGTAC
65266 ACACAAGCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
86 63 0.97
87 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (86 bp):
ACGATTTCAACTCCACGACGGAGAATATCGTGCCCACACAACCACGATTTCAACTCCACGACGAA
GGATATCGTACCAACAGATCA
Found at i:65567 original size:83 final size:83
Alignment explanation
Indices: 65343--65889 Score: 608
Period size: 83 Copynumber: 6.5 Consensus size: 83
65333 GAGTATCTAC
* * * * * * * *
65343 CAAAGACCTTCGAGTTCGATTACACTCATCTCAAAGGCATATAATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
*
65408 AGAAGGATTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * * *
65426 CTAAAGACCTTCGAGTTTGATTATACTTAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
1 C-AAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGG
65491 CTAGAAGGGTTATCTGTCAA
64 CTAGAAGGGTTATCTGTCAA
* * *
65511 CAAAGACCTTTGAGTTCAATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
65576 AGAAGGGTTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * * * * ** * *
65594 AAAACACCTTCGAGTTTGATTTCACTAAACTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
* *
65659 AGAAGGGTTATCTGCCGA
66 AGAAGGGTTATCTGTCAA
* * * * * * * *
65677 CAAAAGACCTTCGAGTGCAACTACACTCAGCTCAATGGCATATCAATTGCAGCATAACTCAAAGC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
65742 TAGAAGGGTTATGTGTCAA
65 TAGAAGGGTTATCTGTCAA
* * *
65761 TAATGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTCAAGG
* * *
65826 CGAGAAGGGCTATCTGTCAT
64 CTAGAAGGGTTATCTGTCAA
* * * * *
65846 CAAAGACCTTCGAGTTTGATTTCATTCAGCTCAAGGGCATATCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
65890 ACCGCATGGT
Statistics
Matches: 383, Mismatches: 76, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
83 158 0.41
84 113 0.30
85 112 0.29
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCAA
Found at i:65706 original size:167 final size:165
Alignment explanation
Indices: 65343--65889 Score: 646
Period size: 167 Copynumber: 3.3 Consensus size: 165
65333 GAGTATCTAC
* * * * * * *
65343 CAAAGACCTTCGAGTTCGATTACACTCATCTCAAAGGCATATAATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGCT
* * * *
65408 AGAAGGATTATCTGTCAACTAAAGACCTTCGAGTTTGATTAT-ACTTAGCTTCGAGGGCACATCA
66 AGAAGGGTTATCTGTCAA-TAAAGACCTTCGAGTTTGATT-TCACTAAGC-TCAAAGGCACATCA
* *
65472 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA
128 TTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTC-A
* * **
65511 CAAAGACCTTTGAGTTCAATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGCT
* * *
65576 AGAAGGGTTATCTGTCAAAAAACACCTTCGAGTTTGATTTCACTAAACTCAAAGGCACATCATTT
66 AGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTTGATTTCACTAAGCTCAAAGGCACATCATTT
** *
65641 GTAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCGA
131 ACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTC-A
* * * * *
65677 CAAAAGACCTTCGAGTGCAACTACACTCAGCTCAATGGCATATCAATTGCAGCATAACTCAAAGC
1 C-AAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGC
* * * * *
65742 TAGAAGGGTTATGTGTCAATAATGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAA
65 TAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTTGATTTCACTAAGCTCAAAGGCACATC--A
* *
65807 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCA
128 TTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCA
** * * *
65845 TCAAAGACCTTCGAGTTTGATTTCATTCAGCTCAAGGGCATATCA
1 -CAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCATATCA
65890 ACCGCATGGT
Statistics
Matches: 321, Mismatches: 53, Indels: 10
0.84 0.14 0.03
Matches are distributed among these distances:
166 47 0.15
167 132 0.41
168 108 0.34
169 34 0.11
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (165 bp):
CAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTTGATTTCACTAAGCTCAAAGGCACATCATTT
ACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCA
Done.