Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007452.1 Hibiscus syriacus cultivar Beakdansim tig00020406_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: 120950
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1829 original size:8 final size:8
Alignment explanation
Indices: 1816--1853 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
1806 AGACGAGAAC
1816 CAAGGAAA
1 CAAGGAAA
1824 CAAGGAAA
1 CAAGGAAA
1832 CAAGGAAA
1 CAAGGAAA
*
1840 CAAGGAAG
1 CAAGGAAA
1848 CAAGGA
1 CAAGGA
1854 TTGTGAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (8 bp):
CAAGGAAA
Found at i:18518 original size:29 final size:29
Alignment explanation
Indices: 18485--18544 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
18475 ATTCATTTAC
*
18485 ATCAAAGAAAGGCATCATTGGCGCAAATG
1 ATCAAAGAAAGGCATCATTGGCGAAAATG
* * *
18514 ATCAAAGTAAGGCATCGTTGGTGAAAATG
1 ATCAAAGAAAGGCATCATTGGCGAAAATG
18543 AT
1 AT
18545 ATGAATGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (29 bp):
ATCAAAGAAAGGCATCATTGGCGAAAATG
Found at i:18767 original size:27 final size:27
Alignment explanation
Indices: 18737--18793 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
18727 TTTAGTTAGA
* * * *
18737 TTTATTGTTTCAAATTATTTATGATGT
1 TTTAATGTTTCAAAGTAATTATGATAT
*
18764 TTTAATGTTTTAAAGTAATTATGATAT
1 TTTAATGTTTCAAAGTAATTATGATAT
18791 TTT
1 TTT
18794 GTGCTTTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.58
Consensus pattern (27 bp):
TTTAATGTTTCAAAGTAATTATGATAT
Found at i:22525 original size:19 final size:20
Alignment explanation
Indices: 22495--22545 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
22485 CGTCCAAGAG
* *
22495 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
*
22514 CGTGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
22534 CATGTATTTTCA
1 CATGTATTTTCA
22546 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:26234 original size:2 final size:2
Alignment explanation
Indices: 26227--26284 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
26217 TAAAAACATA
26227 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
26269 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
26285 TCATAAATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26799 original size:46 final size:46
Alignment explanation
Indices: 26743--26888 Score: 132
Period size: 47 Copynumber: 3.1 Consensus size: 46
26733 TAAAATAATC
* * *
26743 ATTTCATATATTTTTCCATTCAGACACATTTTAGAACTTTCACATTT
1 ATTTTATATATTTTTCCTTTCAGATAC-TTTTAGAACTTTCACATTT
* * * * * *
26790 ATTTT-TATATTCTTTTCTTTTAGATACTTTAAAAATTTTGACATTT
1 ATTTTATATATT-TTTCCTTTCAGATACTTTTAGAACTTTCACATTT
* * * *
26836 ATTTTCATATTTTTTTCTTTTCAGATACTTTTTAGAACATTCAAATTT
1 ATTTT-ATATATTTTTCCTTTCAGATAC-TTTTAGAACTTTCACATTT
26884 ATTTT
1 ATTTT
26889 CATAGCCCAA
Statistics
Matches: 76, Mismatches: 19, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
46 26 0.34
47 27 0.36
48 23 0.30
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (46 bp):
ATTTTATATATTTTTCCTTTCAGATACTTTTAGAACTTTCACATTT
Found at i:26892 original size:48 final size:47
Alignment explanation
Indices: 26744--26892 Score: 165
Period size: 48 Copynumber: 3.1 Consensus size: 47
26734 AAAATAATCA
* ** *
26744 TTTCATATATTTTTCCATTCAGACACATTTTAGAACTTTCACATTTAT
1 TTTCATATTTTTTTCTTTTCAGATAC-TTTTAGAACTTTCACATTTAT
* * * * * *
26792 TTTTATATTCTTTTCTTTT-AGATACTTTAAAAATTTTGACATTTAT
1 TTTCATATTTTTTTCTTTTCAGATACTTTTAGAACTTTCACATTTAT
* *
26838 TTTCATATTTTTTTCTTTTCAGATACTTTTTAGAACATTCAAATTTAT
1 TTTCATATTTTTTTCTTTTCAGATAC-TTTTAGAACTTTCACATTTAT
26886 TTTCATA
1 TTTCATA
26893 GCCCAAGGTA
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
46 34 0.42
47 11 0.14
48 36 0.44
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (47 bp):
TTTCATATTTTTTTCTTTTCAGATACTTTTAGAACTTTCACATTTAT
Found at i:28848 original size:15 final size:16
Alignment explanation
Indices: 28822--28852 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28812 AGTTACCGTT
28822 TTCCATTGAAAATATC
1 TTCCATTGAAAATATC
28838 TTCCA-TGAAAATATC
1 TTCCATTGAAAATATC
28853 CCATAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
TTCCATTGAAAATATC
Found at i:29873 original size:45 final size:44
Alignment explanation
Indices: 29820--29976 Score: 226
Period size: 45 Copynumber: 3.5 Consensus size: 44
29810 CCATTTATTA
* *
29820 ACCATAAGCTCGTAATCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-T
29865 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-T
* * *
29910 CCCATAAGCTCGTAAGCTTATTTTACCTATATACTTTCCATTATT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT-TT
*
29955 -CCATAAGCTTGTAAGCTTATTT
1 ACCATAAGCTCGTAAGCTTATTT
29977 GCATGCTTAC
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
44 21 0.20
45 82 0.79
46 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTT
Found at i:29974 original size:44 final size:44
Alignment explanation
Indices: 29799--29976 Score: 225
Period size: 45 Copynumber: 4.0 Consensus size: 44
29789 ATTTGCATCT
* *
29799 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAATCTTATTTTA
1 CCAATATACTTACCA-TTATT--CCATAAGCTCGTAAGCTTATTTTA
*
29845 CCAAAATACTTACCATT-TGTACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTAT-T-CCATAAGCTCGTAAGCTTATTTTA
*
29890 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
29935 CCTATATACTTTCCATTATTCCATAAGCTTGTAAGCTTATTT
1 CCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTT
29977 GCATGCTTAC
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
44 25 0.21
45 76 0.64
46 11 0.09
47 7 0.06
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (44 bp):
CCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:30107 original size:40 final size:40
Alignment explanation
Indices: 30058--30141 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
30048 ATAGGAGTCA
* * * *
30058 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
30098 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
30138 AATA
1 AATA
30142 CACCGTAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Found at i:36863 original size:24 final size:25
Alignment explanation
Indices: 36836--36883 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
36826 AAATCTTAAT
*
36836 TAAAACA-CTTAAAAATATTTAAAC
1 TAAAACACCTAAAAAATATTTAAAC
*
36860 TAAAATACCTAAAAAATATTTAAA
1 TAAAACACCTAAAAAATATTTAAA
36884 ATAATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAACACCTAAAAAATATTTAAAC
Found at i:36952 original size:68 final size:71
Alignment explanation
Indices: 36825--37010 Score: 204
Period size: 68 Copynumber: 2.6 Consensus size: 71
36815 TAAAACATTT
* * * *
36825 TAAATCTTAATTAAAACACTTAAAA-ATATTTAAACTAAAATACCTAAAAAATATTTAAA-AT-A
1 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAAGATTAAAATATAA
36887 ATATTA-
65 ATATTAC
*
36893 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAATCAAAGA-TAAAATATA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAA--AAAGATTAAAATAT-
36957 AAAATATTATCC
63 -AAATATTA--C
*
36969 TAAAACTTAATTAAAATACTAAAATCC-ATTTAAACTAAAATA
1 TAAATCTTAATTAAAATACTAAAA-CCTATTTAAACTAAAATA
37011 AAAAGATAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
67 5 0.05
68 39 0.39
69 4 0.04
70 6 0.06
73 7 0.07
76 37 0.37
77 2 0.02
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (71 bp):
TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAGATTAAAATATAAA
TATTAC
Found at i:43827 original size:71 final size:72
Alignment explanation
Indices: 43744--43969 Score: 267
Period size: 76 Copynumber: 3.1 Consensus size: 72
43734 TAAAACATCT
*
43744 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAT-TAATATTTAAAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAATATAATATTTAAAA
43807 TAATATTC
65 TAATATTC
* *
43815 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AA-AAATATAATAT-TTA
*
43880 AAATAATATTT
62 AAATAATATTC
* * * * *
43891 TAAAACTTAATTAAAATACTAAAATCTATTTAAACTAAAATACAAATATAAAATATAATGTTTAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC--CTA-AAAATATAATATTTAA
* *
43956 AATATTATCC
63 AATAATATTC
43966 TAAA
1 TAAA
43970 CTTGAGTTTA
Statistics
Matches: 132, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
70 5 0.04
71 38 0.29
73 2 0.02
74 4 0.03
75 19 0.14
76 62 0.47
77 1 0.01
78 1 0.01
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (72 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAATATAATATTTAAAAT
AATATTC
Found at i:43873 original size:25 final size:24
Alignment explanation
Indices: 43826--43873 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
43816 AAATCCTAAT
** *
43826 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
43850 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
43874 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:46481 original size:21 final size:21
Alignment explanation
Indices: 46442--46481 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46432 ATGTTCATGC
*
46442 TTAAATAAAATCAATAAATAA
1 TTAAATAAAATCAAGAAATAA
*
46463 TTAAATAAAATTAAGAAAT
1 TTAAATAAAATCAAGAAAT
46482 GATCATGTAA
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:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAAATAAAATCAAGAAATAA
Found at i:56842 original size:24 final size:23
Alignment explanation
Indices: 56815--56875 Score: 95
Period size: 24 Copynumber: 2.6 Consensus size: 23
56805 ATGTCAAATA
*
56815 ACACATCATTTGGAACTTCAAGT
1 ACACATCTTTTGGAACTTCAAGT
56838 GACACATCTTTTGGAACTTCAAGT
1 -ACACATCTTTTGGAACTTCAAGT
56862 ATCACATCTTTTGG
1 A-CACATCTTTTGG
56876 TCCTCCAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (23 bp):
ACACATCTTTTGGAACTTCAAGT
Found at i:59666 original size:21 final size:21
Alignment explanation
Indices: 59642--59683 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59632 ATGTTCATGC
*
59642 TTAAATAAAATCAATAAATAA
1 TTAAATAAAATCAAGAAATAA
*
59663 TTAAATAAAATTAAGAAATAA
1 TTAAATAAAATCAAGAAATAA
59684 ACATGTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TTAAATAAAATCAAGAAATAA
Found at i:59750 original size:18 final size:17
Alignment explanation
Indices: 59703--59778 Score: 71
Period size: 18 Copynumber: 4.4 Consensus size: 17
59693 TCAAGCTTTA
* *
59703 AATGAGCTAGTTTAATT
1 AATGAACTAGTTTAATG
* *
59720 AATAAAGTAGTTTAAATG
1 AATGAACTAGTTT-AATG
*
59738 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATG
* *
59755 AGTGAACTAGCTTTATTG
1 AATGAACTAG-TTTAATG
59773 AATGAA
1 AATGAA
59779 AAACATACTT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 22 0.48
18 24 0.52
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (17 bp):
AATGAACTAGTTTAATG
Found at i:59762 original size:17 final size:17
Alignment explanation
Indices: 59703--59778 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
59693 TCAAGCTTTA
*
59703 AATGAGCTAGTTTAATT
1 AATGAACTAGTTTAATT
* * *
59720 AATAAAGTAGTTTAAATG
1 AATGAACTAGTTT-AATT
59738 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATT
*
59755 AGTGAACTAGCTTT-ATT
1 AATGAACTAG-TTTAATT
59772 GAATGAA
1 -AATGAA
59779 AAACATACTT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 25 0.53
18 22 0.47
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Found at i:59775 original size:35 final size:35
Alignment explanation
Indices: 59703--59778 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
59693 TCAAGCTTTA
* *
59703 AATGAGCTAGTTTAATTAATAAAGTAGTTTAAATG
1 AATGAACTAGTTTAATTAATAAACTAGTTTAAATG
* * *
59738 AATGAACTAGTTTAATTAGTGAACTAGCTTT-ATTG
1 AATGAACTAGTTTAATTAATAAACTAG-TTTAAATG
59773 AATGAA
1 AATGAA
59779 AAACATACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 32 0.91
36 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (35 bp):
AATGAACTAGTTTAATTAATAAACTAGTTTAAATG
Found at i:63890 original size:55 final size:55
Alignment explanation
Indices: 63777--64355 Score: 765
Period size: 55 Copynumber: 10.6 Consensus size: 55
63767 ACGGGTTCGA
* * * * * *
63777 TCCCTCTTTCTTTAGGGAGTAT-AGCACTCGAAC-ATCTTTATCAATCGTGTTTGC
1 TCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGC
63831 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * * ** *
63886 TCCCTATTTTTTCAGAGAATATAAGACTCGAATAATCTTCTGCAATCGTGTCTGT
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * *
63941 TCCCTATTTTTTCAGAGAGTATAAGACTCGAGCAATCTTCAATAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
** * **
63996 TCCCTATTTCTTCAGAGAGTATAAGACTTAAATAATCTTCTGCAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
*
64051 TCCCTATTTCTTGAGAGAGTATAAGACTC-AAGCAATCTTCAACAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGTGTCTGC
*
64106 TCCCTATTTCTTGAGAGAGTATAAGACTC-AAGCAATCTTCAACAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGTGTCTGC
* * * *
64161 TCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCTACAATCGCGTCTAC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
64216 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* * * * ***
64271 TCTCTA-TTCGTTCAGAGAGTATAAGACTCAAACATTCTTCAA-TATCGCACCTGC
1 TCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
* *
64325 TCCCTATTTATTCAGAGAGTATAAGATTCGA
1 TCCCTATTTCTTCAGAGAGTATAAGACTCGA
64356 GCAAGTAAGA
Statistics
Matches: 467, Mismatches: 52, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
54 64 0.14
55 401 0.86
56 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (55 bp):
TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGC
Found at i:64475 original size:54 final size:54
Alignment explanation
Indices: 64365--64753 Score: 430
Period size: 54 Copynumber: 7.3 Consensus size: 54
64355 AGCAAGTAAG
* *
64365 ACTCAAACAATCTTCTAT-TAACGGGTTCGCTTCTTCTTT-TTTAAGGAGTATGGA
1 ACTCAAAC-ATCTTCT-TCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
*** * * * *
64419 ACTCAAACATCTTCTTCTTGCGGGTTCGCTCCCTCTTTCTTCAAAGAGTATAGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
* *
64473 ACTCAGACATTTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
* * ** * *
64527 ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCCAGGGAGTATAGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
* * * *
64581 ACTCGAACATC-TCTTCAAACAGG-TCGTTCCTTCTTTCTTTAGGGAGTATGGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
** * **
64633 ACTCGGACATCTTCTTCAAACGGGTTCACTCCTTCTTTCTTTAATCAGTATGGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
* ** *
64687 ACTCAAAAATCTTCTAAAAACGGGTTCGCTCCTT-TTT-TTTAAGGAGTGTGGA
1 ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
*
64739 ACTCGAACAATCTTC
1 ACTCAAAC-ATCTTC
64754 ACTTGCTTCA
Statistics
Matches: 282, Mismatches: 48, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
52 53 0.19
53 55 0.20
54 174 0.62
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (54 bp):
ACTCAAACATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
Found at i:64651 original size:106 final size:108
Alignment explanation
Indices: 64388--64753 Score: 422
Period size: 106 Copynumber: 3.4 Consensus size: 108
64378 TCTATTAACG
* * ***
64388 GGTTCGCTTCTTCTTT-TTTAAGGAGTATGGAACTCAAACATCTTCTTCTTGCGGGTTCGCTCCC
1 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCC
* * *
64452 TCTTTCTTCAAAGAGTATAGAACTCAGACATTTTCTTCAAACG
66 TCTTTCTCCAAAGAGTATAGAACTCAGACATTCTCTTCAAACA
64495 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCC
1 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCC
**
64560 TCTTTCTCCAGGGAGTATAGAACTC-GAACA-TCTCTTCAAACA
66 TCTTTCTCCAAAGAGTATAGAACTCAG-ACATTCTCTTCAAACA
* * * * *
64602 GG-TCGTTCCTTCTTTCTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCACTCCT
1 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCC
** ** * * * ** *
64666 TCTTTCTTTAATCAGTATGGAACTCA-AAAATCTTCTAAAAACG
66 TCTTTCTCCAAAGAGTATAGAACTCAGACATTC-TCTTCAAACA
*
64709 GGTTCGCTCCTT-TTT-TTTAAGGAGTGTGGAACTCGAACAATCTTC
1 GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAAC-ATCTTC
64754 ACTTGCTTCA
Statistics
Matches: 223, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
105 2 0.01
106 98 0.44
107 46 0.21
108 77 0.35
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (108 bp):
GGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCC
TCTTTCTCCAAAGAGTATAGAACTCAGACATTCTCTTCAAACA
Found at i:65188 original size:37 final size:36
Alignment explanation
Indices: 65121--65226 Score: 131
Period size: 37 Copynumber: 2.9 Consensus size: 36
65111 ACTCTTCTAA
* *
65121 GAAGGCTTAAAATGGATTGCTTCACTACTCTTTGGT
1 GAAGGCTTCAAATCGATTGCTTCACTACTCTTTGGT
* * *
65157 GAAGGCTTCAAATTGATTTGGTTCACTACTCTGTGGT
1 GAAGGCTTCAAATCGA-TTGCTTCACTACTCTTTGGT
* *
65194 GAAGGCTTCAGATCGAGTTGCTTCAATACTCTT
1 GAAGGCTTCAAATCGA-TTGCTTCACTACTCTT
65227 CGGTAAAGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
36 14 0.24
37 45 0.76
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTCAAATCGATTGCTTCACTACTCTTTGGT
Found at i:66439 original size:8 final size:8
Alignment explanation
Indices: 66426--66541 Score: 87
Period size: 8 Copynumber: 13.8 Consensus size: 8
66416 TTTTTTTCCA
66426 TTTCATTT
1 TTTCATTT
66434 TTTCATTCATT
1 TTTCA-T--TT
*
66445 TTTCTTTTTT
1 TTTC-ATT-T
66455 TTTC-TTT
1 TTTCATTT
**
66462 TTTCCCTT
1 TTTCATTT
66470 -TTCATTT
1 TTTCATTT
66477 TTTCATTT
1 TTTCATTT
66485 TTTCATTT
1 TTTCATTT
66493 TCCTTC-TTT
1 T--TTCATTT
66502 TTT-ATTCTT
1 TTTCA-T-TT
66511 TTTCATTTT
1 TTTCA-TTT
66520 TTTCATTT
1 TTTCATTT
66528 TTTCATTT
1 TTTCATTT
66536 TTTCAT
1 TTTCAT
66542 CTTCTTCGTT
Statistics
Matches: 91, Mismatches: 4, Indels: 26
0.75 0.03 0.21
Matches are distributed among these distances:
7 12 0.13
8 43 0.47
9 18 0.20
10 11 0.12
11 7 0.08
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTCATTT
Found at i:66491 original size:51 final size:50
Alignment explanation
Indices: 66426--66556 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 50
66416 TTTTTTTCCA
* *
66426 TTTCATTTTTTCATTCATT-TTTCTTTTTTTTTCTTTTTTC-CCTTTTCATTT
1 TTTCATTTTTTCATT--TTCCTTCTTTTTTATTC-TTTTTCACCTTTTCATTT
**
66477 TTTCATTTTTTCATTTTCCTTCTTTTTTATTCTTTTTCATTTTTTTCATTT
1 TTTCATTTTTTCATTTTCCTTCTTTTTTATTCTTTTTCA-CCTTTTCATTT
* *
66528 TTTCATTTTTTCATCTT-CTTCGTTTTTAT
1 TTTCATTTTTTCATTTTCCTTCTTTTTTAT
66557 CTTCAAGCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
49 8 0.11
50 23 0.32
51 40 0.56
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.73
Consensus pattern (50 bp):
TTTCATTTTTTCATTTTCCTTCTTTTTTATTCTTTTTCACCTTTTCATTT
Found at i:66503 original size:10 final size:10
Alignment explanation
Indices: 66490--66538 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
66480 CATTTTTTCA
*
66490 TTTTCCTTCT
1 TTTTCATTCT
*
66500 TTTTTATTCT
1 TTTTCATTCT
66510 TTTTCATT-T
1 TTTTCATTCT
66519 TTTTCA-T-T
1 TTTTCATTCT
66527 TTTTCATT-T
1 TTTTCATTCT
66536 TTT
1 TTT
66539 CATCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 8 0.23
9 12 0.34
10 15 0.43
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCATTCT
Found at i:68765 original size:8 final size:8
Alignment explanation
Indices: 68752--68797 Score: 56
Period size: 8 Copynumber: 5.4 Consensus size: 8
68742 TTTATTATTC
68752 TTTCTTTT
1 TTTCTTTT
68760 TTTCTTTT
1 TTTCTTTT
68768 TTCTCTTTTT
1 TT-TC-TTTT
*
68778 TCTTTTTTT
1 T-TTCTTTT
68787 TTTCTTTT
1 TTTCTTTT
68795 TTT
1 TTT
68798 TCGAGCGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 19 0.58
9 7 0.21
10 6 0.18
11 1 0.03
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTCTTTT
Found at i:68797 original size:9 final size:9
Alignment explanation
Indices: 68752--68799 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
68742 TTTATTATTC
68752 TTTC-TTTT
1 TTTCTTTTT
68760 TTTCTTTTT
1 TTTCTTTTT
*
68769 TCTCTTTTT
1 TTTCTTTTT
68778 TCTT-TTTTT
1 T-TTCTTTTT
68787 TTTCTTTTT
1 TTTCTTTTT
68796 TTTC
1 TTTC
68800 GAGCGTAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 6 0.17
9 28 0.80
10 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:72250 original size:55 final size:55
Alignment explanation
Indices: 72112--72253 Score: 178
Period size: 55 Copynumber: 2.6 Consensus size: 55
72102 CAACTTCAAA
* ** * * *
72112 CTTCATTCATCGGATGTCTTTCAGCATGGATCAGTCTTCAATCAGTTTCAGATTT
1 CTTCATTCATCGGATGTCCTTCTCCATGAATCAGTCTTCAATCAGGTTCAAATTT
* * *
72167 CTTCATTCATCGGATGTTCATCTTCATGAATC-GTTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTCCTTCTCCATGAATCAG-TCTTCAATCAGGTTCAAATTT
*
72222 CTTCGTTCATCGGATGTCCTTCTCCATGAATC
1 CTTCATTCATCGGATGTCCTTCTCCATGAATC
72254 CACTTGAATG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 1 0.01
55 73 0.99
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (55 bp):
CTTCATTCATCGGATGTCCTTCTCCATGAATCAGTCTTCAATCAGGTTCAAATTT
Found at i:72593 original size:47 final size:45
Alignment explanation
Indices: 72542--72675 Score: 130
Period size: 47 Copynumber: 2.9 Consensus size: 45
72532 ATCTACCCCC
*
72542 ATGCTTTGTTATTAAAAAATATCCTAACCGCATGATATCTAATTCGA
1 ATGCTTTGTTA-TAAAAAATA-CCTAACCGCATGATTTCTAATTCGA
* * * *
72589 ATGCTTAT-TCGAGAAAATAA-ACCTAACCGCATGATTTCTAGTTCGC
1 ATGCTT-TGT-TATAAAA-AATACCTAACCGCATGATTTCTAATTCGA
72635 ATGCTTTGTTCGATAAAATAA-ACCTAACCGCATGATTTCTA
1 ATGCTTTGTT--ATAAAA-AATACCTAACCGCATGATTTCTA
72676 GTTCACATAC
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
45 1 0.01
46 29 0.39
47 40 0.54
48 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (45 bp):
ATGCTTTGTTATAAAAAATACCTAACCGCATGATTTCTAATTCGA
Found at i:72676 original size:47 final size:46
Alignment explanation
Indices: 72564--72679 Score: 178
Period size: 47 Copynumber: 2.5 Consensus size: 46
72554 TAAAAAATAT
* *
72564 CCTAACCGCATGATATCTAATTCGAATGCTTATTCGAGAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGAATGCTTATTCGAGAAAATAAA
* * *
72610 CCTAACCGCATGATTTCTAGTTCGCATGCTTTGTTCGATAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGAATGC-TTATTCGAGAAAATAAA
72657 CCTAACCGCATGATTTCTAGTTC
1 CCTAACCGCATGATTTCTAGTTC
72680 ACATACATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
46 26 0.41
47 38 0.59
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (46 bp):
CCTAACCGCATGATTTCTAGTTCGAATGCTTATTCGAGAAAATAAA
Found at i:87817 original size:27 final size:27
Alignment explanation
Indices: 87756--87817 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
87746 TATAGCCTTA
87756 ACAGATAGAAACTTTGGTTTACTCATT
1 ACAGATAGAAACTTTGGTTTACTCATT
* *
87783 ACATATAGAAACTTTGGTTTAGTCATT
1 ACAGATAGAAACTTTGGTTTACTCATT
*
87810 ATAGATAG
1 ACAGATAG
87818 GGACTCAGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (27 bp):
ACAGATAGAAACTTTGGTTTACTCATT
Found at i:88731 original size:31 final size:32
Alignment explanation
Indices: 88670--88746 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
88660 AGGGGCCATG
*
88670 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACACATCTCAGGGCCGCA
* **
88702 GGGCCTACCTGAGAA-TGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACACATCTCAGGGCCGCA
* *
88733 GAGACTACCTAAGA
1 GGGCCTACCTAAGA
88747 GTCACGTTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (32 bp):
GGGCCTACCTAAGAACACATCTCAGGGCCGCA
Found at i:110835 original size:14 final size:14
Alignment explanation
Indices: 110812--110851 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
110802 TAAAAAAGTT
*
110812 TCTTTGTTTCTTCA
1 TCTTTCTTTCTTCA
110826 TCTTTCTTTCTTCA
1 TCTTTCTTTCTTCA
110840 T-TTCTCTTTCTT
1 TCTT-TCTTTCTT
110852 TCTTGTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 2 0.08
14 22 0.92
ACGTcount: A:0.05, C:0.25, G:0.03, T:0.68
Consensus pattern (14 bp):
TCTTTCTTTCTTCA
Found at i:119050 original size:23 final size:24
Alignment explanation
Indices: 119005--119064 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
118995 TCAACTTCCT
119005 GTATAAAATCAAAATGGAGTCCAA
1 GTATAAAATCAAAATGGAGTCCAA
* *
119029 GTATATAATCAATA-GGAGTCCAA
1 GTATAAAATCAAAATGGAGTCCAA
119052 GTATAAAATCAAA
1 GTATAAAATCAAA
119065 TTAACAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (24 bp):
GTATAAAATCAAAATGGAGTCCAA
Done.