Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002370.1 Hibiscus syriacus cultivar Beakdansim tig00004842_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: 88286
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3169 original size:63 final size:64
Alignment explanation
Indices: 3056--3187 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 64
3046 AAAATGGCCT
*
3056 CCCATAAAGAAGAAGCCAAGGGGCACTCTTAAGAACAAGAACAAGTGGTCCCTTGTCTCCAAAGC
1 CCCATAAAGAAGAAGCCAAGGGGAACTCTT----A-AAGAACAAGTGGTCCCTTGTCTCCAAAGC
3121 TTTG
61 TTTG
3125 CCCATAAAGAAGAAGCCAAGGGGAACTCTT-AAGAACAAGTGGTCCCTTGTCTCCAAAGCTTTG
1 CCCATAAAGAAGAAGCCAAGGGGAACTCTTAAAGAACAAGTGGTCCCTTGTCTCCAAAGCTTTG
3188 TTGCAGTTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
63 33 0.53
69 29 0.47
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (64 bp):
CCCATAAAGAAGAAGCCAAGGGGAACTCTTAAAGAACAAGTGGTCCCTTGTCTCCAAAGCTTTG
Found at i:7656 original size:9 final size:9
Alignment explanation
Indices: 7644--7677 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
7634 TAATATTTTG
7644 TATTTAATT
1 TATTTAATT
*
7653 TATTTAA-G
1 TATTTAATT
7661 TATTTAATT
1 TATTTAATT
7670 TATTTAAT
1 TATTTAAT
7678 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:7683 original size:17 final size:17
Alignment explanation
Indices: 7643--7681 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
7633 TTAATATTTT
7643 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
7660 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
7677 -TATTT
1 GTATTT
7682 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:29774 original size:43 final size:45
Alignment explanation
Indices: 29719--29806 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
29709 TATTAATCCA
* * *
29719 ACAAGTATTAGGTT-AA-GCTATGTCGTTAGTAAATCAATATTTT
1 ACAAGTAGTAGGTTAAAGGCTATGTCATGAGTAAATCAATATTTT
*
29762 ACAAGTAGTAGGTTAAAGGCTATGTCATGCGTAAATCAATATTTT
1 ACAAGTAGTAGGTTAAAGGCTATGTCATGAGTAAATCAATATTTT
29807 TACGTAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 13 0.33
44 2 0.05
45 24 0.62
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (45 bp):
ACAAGTAGTAGGTTAAAGGCTATGTCATGAGTAAATCAATATTTT
Found at i:34250 original size:6 final size:6
Alignment explanation
Indices: 34227--34264 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
34217 TTTAATTGCG
34227 AAAATT AAAAACTT -AAATT AAAATT AAAATT AAAATT A
1 AAAATT -AAAA-TT AAAATT AAAATT AAAATT AAAATT A
34265 TTCGATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.07
6 21 0.72
7 4 0.14
8 2 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:35785 original size:19 final size:19
Alignment explanation
Indices: 35758--35796 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35748 AAAAAATATG
* * *
35758 AAATTAAATTAAATTAATA
1 AAATAAAATAAAATAAATA
35777 AAATAAAATAAAATAAATA
1 AAATAAAATAAAATAAATA
35796 A
1 A
35797 TATGATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAAATAAAATAAATA
Found at i:35806 original size:19 final size:18
Alignment explanation
Indices: 35784--35823 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
35774 ATAAAATAAA
35784 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
35803 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
35821 ATA
1 ATA
35824 TTTCAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:35849 original size:39 final size:38
Alignment explanation
Indices: 35805--36120 Score: 188
Period size: 38 Copynumber: 8.6 Consensus size: 38
35795 AATATGATAT
* *
35805 AAACTATATAATATATATATTTCAACAATATGTTTTAGA
1 AAACTATATAATATATATATTTCAAAAAAATGTTTTA-A
* * ** *
35844 AAAC--TAT-ATAT-TATACTTAAAAAAAAAATTCT-A
1 AAACTATATAATATATATATTTCAAAAAAATGTTTTAA
* * *
35877 AAACTATATATTACATAGT-TTTC---AAAACGTTTTAA
1 AAACTATATAATATATA-TATTTCAAAAAAATGTTTTAA
*
35912 AAA-TAT-T-ATATA-AGT-TTTCAAAAAAATGTTTTTA
1 AAACTATATAATATATA-TATTTCAAAAAAATGTTTTAA
* *
35946 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTTTA
1 AAACTATATAATATATATATTTCA-AAAAAATG-TTTTAA
* *
35985 AAACTATATACTATATATGTTTTC---AAAATGTTTTAA
1 AAACTATATAATATATAT-ATTTCAAAAAAATGTTTTAA
* * *
36021 AAACTATATAATATATATAAACGGTT--ACAAAATGTTTTTA
1 AAACTATATAATATATAT--A--TTTCAAAAAAATGTTTTAA
* * *
36061 AAACTATATATTATATATATTTTAAAAATAAT-TTTCAA
1 AAACTATATAATATATATATTTCAAAAA-AATGTTTTAA
*
36099 AAACTATATAATATATAAATTT
1 AAACTATATAATATATATATTT
36121 TCGAAAATCA
Statistics
Matches: 217, Mismatches: 34, Indels: 53
0.71 0.11 0.17
Matches are distributed among these distances:
31 7 0.03
32 3 0.01
33 6 0.03
34 23 0.11
35 24 0.11
36 31 0.14
37 22 0.10
38 38 0.18
39 31 0.14
40 28 0.13
41 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (38 bp):
AAACTATATAATATATATATTTCAAAAAAATGTTTTAA
Found at i:36009 original size:78 final size:75
Alignment explanation
Indices: 35918--36116 Score: 212
Period size: 76 Copynumber: 2.6 Consensus size: 75
35908 TTAAAAATAT
* * *
35918 TATATAAGTTTTCAAAAAAATGTTTTTAAAACTATATATTATATAA-TTTCACAAAAAATGTTTT
1 TATATATGTTTTCAAAAAAATGTTTTAAAAACTATATATTATATAACGTT-AC--AAAATG-TTT
35982 TTAAAACTATATAC
62 TTAAAACTATATAC
35996 TATATATGTTTTC---AAAATGTTTTAAAAACTATATAATATATATAAACGGTTACAAAATGTTT
1 TATATATGTTTTCAAAAAAATGTTTTAAAAACTATAT-AT-TATAT-AAC-GTTACAAAATGTTT
*
36058 TTAAAACTATATAT
62 TTAAAACTATATAC
* * *
36072 TATATATATTTT-AAAAATAAT-TTTCAAAAACTATATAATATATAA
1 TATATATGTTTTCAAAAA-AATGTTTTAAAAACTATATATTATATAA
36117 ATTTTCGAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
75 22 0.21
76 34 0.32
77 12 0.11
78 30 0.29
79 5 0.05
80 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (75 bp):
TATATATGTTTTCAAAAAAATGTTTTAAAAACTATATATTATATAACGTTACAAAATGTTTTTAA
AACTATATAC
Found at i:36064 original size:40 final size:38
Alignment explanation
Indices: 35934--36115 Score: 171
Period size: 40 Copynumber: 4.8 Consensus size: 38
35924 AGTTTTCAAA
35934 AAAATGTTTTTAAAACTATAT-AT-TATATAA-TTTCAC
1 AAAATGTTTTTAAAACTATATAATATATATAAGTTT-AC
* *
35970 AAAAAATGTTTTTTAAAACTATATACTATATAT--GTTTTC
1 --AAAATG-TTTTTAAAACTATATAATATATATAAGTTTAC
* *
36009 AAAATGTTTTAAAAACTATATAATATATATAAACGGTTAC
1 AAAATGTTTTTAAAACTATATAATATATAT-AA-GTTTAC
* *
36049 AAAATGTTTTTAAAACTATATATTATATAT-ATTTTA-
1 AAAATGTTTTTAAAACTATATAATATATATAAGTTTAC
* *
36085 AAAATAATTTTCAAAAACTATATAATATATA
1 AAAAT-GTTTT-TAAAACTATATAATATATA
36116 AATTTTCGAA
Statistics
Matches: 121, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
36 27 0.22
37 13 0.11
38 24 0.20
39 16 0.13
40 36 0.30
41 5 0.04
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (38 bp):
AAAATGTTTTTAAAACTATATAATATATATAAGTTTAC
Found at i:36089 original size:76 final size:79
Alignment explanation
Indices: 35972--36115 Score: 231
Period size: 76 Copynumber: 1.9 Consensus size: 79
35962 AATTTCACAA
* * *
35972 AAAATGTTTTTTAAAACTATATACTATATATGTTTTCAAAAT-GTTTT-AAAAACTATATAATAT
1 AAAATGTTTTTTAAAACTATATACTATATATATTTTAAAAATAATTTTCAAAAACTATATAATAT
36035 ATATAAACGGTTAC
66 ATATAAACGGTTAC
*
36049 AAAATG-TTTTTAAAACTATATATTATATATATTTTAAAAATAATTTTCAAAAACTATATAATAT
1 AAAATGTTTTTTAAAACTATATACTATATATATTTTAAAAATAATTTTCAAAAACTATATAATAT
36113 ATA
66 ATA
36116 AATTTTCGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
76 32 0.52
77 10 0.16
78 19 0.31
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (79 bp):
AAAATGTTTTTTAAAACTATATACTATATATATTTTAAAAATAATTTTCAAAAACTATATAATAT
ATATAAACGGTTAC
Found at i:36154 original size:40 final size:38
Alignment explanation
Indices: 35914--36154 Score: 145
Period size: 39 Copynumber: 6.2 Consensus size: 38
35904 CGTTTTAAAA
* **
35914 ATATTATATAAGTTTTCAAAAA-AATGTTTTTAAAACTAT
1 ATATTATATAAATTTT-AAAAATAAT-TTTCAAAAACTAT
* **
35953 ATATTATAT-AATTTCACAAAA-AATGTTTTTTAAAACTAT
1 ATATTATATAAATTTTA-AAAATAA--TTTTCAAAAACTAT
* ** * *
35992 ATACTATATATGTTTTCAAAAT-GTTTT-AAAAACTAT
1 ATATTATATAAATTTTAAAAATAATTTTCAAAAACTAT
** * *
36028 ATAATATATATAAACGGTTACAAAAT-GTTTT-TAAAACTAT
1 AT-AT-TATATAAA-TTTTA-AAAATAATTTTCAAAAACTAT
*
36068 ATATTATATATATTTTAAAAATAATTTTCAAAAACTAT
1 ATATTATATAAATTTTAAAAATAATTTTCAAAAACTAT
* * * * *
36106 ATAATATATAAATTTTCGAAAATCATTTTCTGAAAATTAT
1 ATATTATATAAATTTT-AAAAATAATTTTC-AAAAACTAT
36146 ATATTATAT
1 ATATTATAT
36155 TTTGTCAAAA
Statistics
Matches: 161, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
36 15 0.09
37 13 0.08
38 45 0.28
39 49 0.30
40 39 0.24
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (38 bp):
ATATTATATAAATTTTAAAAATAATTTTCAAAAACTAT
Found at i:39504 original size:5 final size:5
Alignment explanation
Indices: 39494--39518 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39484 AGAGAACAAA
39494 GGAAT GGAAT GGAAT GGAAT GGAAT
1 GGAAT GGAAT GGAAT GGAAT GGAAT
39519 CAAAGTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GGAAT
Found at i:43648 original size:3 final size:3
Alignment explanation
Indices: 43642--43692 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
43632 TTTTTATTTG
* *
43642 TTA TTA TTA TTA TTTA TTA TTA TTA TT- TTGT TTA TTG TTA TTA TTAA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A
43689 TTA T
1 TTA T
43693 GTTACATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.05
3 31 0.76
4 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43651 original size:13 final size:13
Alignment explanation
Indices: 43642--43669 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43632 TTTTTATTTG
43642 TTATTATTATTAT
1 TTATTATTATTAT
43655 TTATTATTATTAT
1 TTATTATTATTAT
43668 TT
1 TT
43670 TGTTTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:51874 original size:28 final size:28
Alignment explanation
Indices: 51797--51897 Score: 150
Period size: 29 Copynumber: 3.6 Consensus size: 28
51787 TTCTCTTGAA
51797 AAAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTCCTTTTG
*
51825 AACAAAAATCTTGGAGTTTGTTCCTTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
*
51854 AATAAAAATCTTTGAG-TTGTTTCTTTTG
1 AA-AAAAATCTTTGAGTTTGTTCCTTTTG
*
51882 AAAAAAATATTTGAGT
1 AAAAAAATCTTTGAGT
51898 CTATTTATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
27 12 0.18
28 15 0.23
29 39 0.59
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (28 bp):
AAAAAAATCTTTGAGTTTGTTCCTTTTG
Found at i:51922 original size:28 final size:27
Alignment explanation
Indices: 51797--51912 Score: 83
Period size: 29 Copynumber: 4.1 Consensus size: 27
51787 TTCTCTTGAA
* *
51797 AAAAAAATCTTTGAGTT-TGTTCCTTTTG
1 AAAAAAATATTTGAGTTAT-TT-ATTTTG
* * *
51825 AACAAAAATCTTGGAGTT-TGTTCCTTTTG
1 AA-AAAAATATTTGAGTTAT-TT-ATTTTG
* * *
51854 AATAAAAATCTTTGAGTTGTTTCTTTTG
1 AA-AAAAATATTTGAGTTATTTATTTTG
51882 AAAAAAATATTTGAGTCTATTTATTTTG
1 AAAAAAATATTTGAGT-TATTTATTTTG
51910 AAA
1 AAA
51913 CAAAGTTTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
27 13 0.16
28 22 0.28
29 43 0.54
30 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (27 bp):
AAAAAAATATTTGAGTTATTTATTTTG
Found at i:51986 original size:52 final size:53
Alignment explanation
Indices: 51908--52010 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
51898 CTATTTATTT
*
51908 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGCGAAAAAATCTTTGAGTC
*
51960 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGCGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGCGAAAAAATCTTTGAG
52011 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.73
53 13 0.27
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGCGAAAAAATCTTTGAGTC
Found at i:52034 original size:30 final size:30
Alignment explanation
Indices: 51998--52128 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 30
51988 AATTTTGCGA
*
51998 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
52028 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
52058 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTGAGATTGTTTCTTTGGAAAC
52095 AAAAATCTTTGAG-TCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGAT-TGTTTCTTTGGAAAC
52125 AAAA
1 AAAA
52129 TTTTGTCTCT
Statistics
Matches: 80, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
29 1 0.01
30 53 0.66
31 2 0.03
36 2 0.03
37 22 0.28
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:52086 original size:37 final size:36
Alignment explanation
Indices: 52045--52165 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 36
52035 TTTGAGTTTG
52045 TTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTC-TTTAAGATAA
* **
52082 TTTCTTTTGAAACAAAAATCTTTGAGTC--T--G----
1 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTTTAAGATAA
52112 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCT-TTAAGATAA
*
52149 TTTCTTTTGAAACAAAA
1 TTTCTTTGGAAACAAAA
52166 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
28 6 0.09
29 5 0.08
30 12 0.18
31 1 0.02
33 1 0.02
34 1 0.02
36 1 0.02
37 28 0.42
38 5 0.08
39 6 0.09
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (36 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTTTAAGATAA
Found at i:52086 original size:67 final size:67
Alignment explanation
Indices: 52015--52183 Score: 311
Period size: 67 Copynumber: 2.5 Consensus size: 67
52005 TTTGAGATTG
* *
52015 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
52080 AA
66 AA
52082 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
52147 AA
66 AA
*
52149 TTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
52184 CTTAAAATGA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 99 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:52942 original size:36 final size:34
Alignment explanation
Indices: 52891--52986 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
52881 TTTGAGAAAA
* * * *
52891 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATCTACC
1 ATCTTTGAATCTGTTTCTTT-GAAACAAAAT-AAAC
*
52927 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTT-CTTTGAAACAAAATAAAC
52962 ATCTTTGAGATC-GTTTCTCTTGAAA
1 ATCTTTGA-ATCTGTTTCT-TTGAAA
52987 TGAATTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 20 0.39
36 27 0.53
37 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (34 bp):
ATCTTTGAATCTGTTTCTTTGAAACAAAATAAAC
Found at i:52978 original size:35 final size:36
Alignment explanation
Indices: 52912--52986 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
52902 TGTTTCTTTG
* *
52912 GAAACAAAATCTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATCAAACATCTTTGAATCTGTTTCCCTT
*
52948 GAAACAAAAT-AAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATCAAACATCTTTGA-ATCTGTTTCCCTT
52983 GAAA
1 GAAA
52987 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (36 bp):
GAAACAAAATCAAACATCTTTGAATCTGTTTCCCTT
Found at i:53590 original size:133 final size:134
Alignment explanation
Indices: 53319--53668 Score: 441
Period size: 133 Copynumber: 2.6 Consensus size: 134
53309 AACCATTATC
* * * * * * * *
53319 CCTAGAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCATATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACATATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
* * * *
53384 CATGTAGGATCCATGACAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
66 CATGTAGGAACCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC
53449 CCTA
131 CCTA
* * * *
53453 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGAACTCTTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACATATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
* * * * *
53518 CACGTAGGAGCCGTGTCATCC-TAGATAACCAGCCGTCCTCATCACGTAGGAATCGGGTTATCAC
66 CATGTAGGAACCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC
* *
53582 TCTT
131 CCTA
* * * *
53586 CCTAAAGATGACCAGAACTCTTCATCATATATGAGCAGTGTCATCCCTTGACCAGATTTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACATATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
*
53651 CATGTAGGAACCTTGTCA
66 CATGTAGGAACCATGTCA
53669 CCTTTAGACG
Statistics
Matches: 183, Mismatches: 33, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
133 114 0.62
134 69 0.38
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACATATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
CATGTAGGAACCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC
CCTA
Found at i:53874 original size:3 final size:3
Alignment explanation
Indices: 53868--53918 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
53858 CTTTTTTTTG
* *
53868 TTA TTA TTA TTA TTTA TTA TTA TTA TT- TTGT TTA TTG TTA TTA TTAA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A
53915 TTA T
1 TTA T
53919 GTTACATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 2 0.05
3 31 0.76
4 8 0.20
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:53886 original size:13 final size:13
Alignment explanation
Indices: 53868--53895 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53858 CTTTTTTTTG
53868 TTATTATTATTAT
1 TTATTATTATTAT
53881 TTATTATTATTAT
1 TTATTATTATTAT
53894 TT
1 TT
53896 TGTTTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:57946 original size:64 final size:63
Alignment explanation
Indices: 57841--57960 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
57831 CACATTCAAT
* * * *
57841 GTGTACCGATGCACAGGAAGTGCATCGATGCATACCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTACCGATGCACAAGAAGTGCATCGATACACACCCTT-AAATAAAAACATCGAATGCCATCA
* * * *
57905 GTGTATCGATGCACAAGTAGTGCATCGATACACCCCCTTAAATACAAACATCGAAT
1 GTGTACCGATGCACAAGAAGTGCATCGATACACACCCTTAAATAAAAACATCGAAT
57961 ATGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 16 0.33
64 32 0.67
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (63 bp):
GTGTACCGATGCACAAGAAGTGCATCGATACACACCCTTAAATAAAAACATCGAATGCCATCA
Found at i:58678 original size:23 final size:23
Alignment explanation
Indices: 58652--58704 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
58642 TATGGCAATA
58652 CGGTGTAATTCTACGCGGCACTT
1 CGGTGTAATTCTACGCGGCACTT
* * *
58675 CGGTGCAATTCTACGTGGTACTT
1 CGGTGTAATTCTACGCGGCACTT
58698 CGGTGTA
1 CGGTGTA
58705 TTTATATGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (23 bp):
CGGTGTAATTCTACGCGGCACTT
Found at i:65379 original size:46 final size:46
Alignment explanation
Indices: 65329--65465 Score: 145
Period size: 46 Copynumber: 3.0 Consensus size: 46
65319 TTAAGGAATT
*
65329 TTCTACGTGGTC-CTTAGG-GACAA-TCTTATATGGCACTACGGTGCAA
1 TTCTACGTGG-CACTTAGGTG-CAATTC-TACATGGCACTACGGTGCAA
* * * *
65375 TTCTACGCGGCACTTCGGTGCAATTCTACGTGGCACTTCGGTGCAA
1 TTCTACGTGGCACTTAGGTGCAATTCTACATGGCACTACGGTGCAA
* * * *
65421 TTCTACGTGGCACTTCGGTGCAATTCTACGTGACACTTCGGTGCA
1 TTCTACGTGGCACTTAGGTGCAATTCTACATGGCACTACGGTGCA
65466 TTTATACGAG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
45 1 0.01
46 77 0.95
47 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (46 bp):
TTCTACGTGGCACTTAGGTGCAATTCTACATGGCACTACGGTGCAA
Found at i:65473 original size:23 final size:23
Alignment explanation
Indices: 65359--65465 Score: 187
Period size: 23 Copynumber: 4.7 Consensus size: 23
65349 CAATCTTATA
*
65359 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
65382 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
65405 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
65428 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
65451 TGACACTTCGGTGCA
1 TGGCACTTCGGTGCA
65466 TTTATACGAG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:66194 original size:27 final size:27
Alignment explanation
Indices: 66164--66233 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
66154 GAATACGATT
*
66164 TTAGTGGCACTTACTCAATATATGACC
1 TTAGTGGCAATTACTCAATATATGACC
* * * *
66191 TTAGTGACAATTACGCGATATATGATC
1 TTAGTGGCAATTACTCAATATATGACC
* * *
66218 TTTGTAGCATTTACTC
1 TTAGTGGCAATTACTC
66234 GAAAAACAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (27 bp):
TTAGTGGCAATTACTCAATATATGACC
Found at i:70782 original size:12 final size:13
Alignment explanation
Indices: 70765--70793 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
70755 ATTTATCCAG
70765 AGAGAGAGAGC-C
1 AGAGAGAGAGCGC
70777 AGAGAGAGAGCGC
1 AGAGAGAGAGCGC
70790 AGAG
1 AGAG
70794 GCAAAGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.41, C:0.14, G:0.45, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGCGC
Found at i:71350 original size:84 final size:84
Alignment explanation
Indices: 71252--71416 Score: 312
Period size: 84 Copynumber: 2.0 Consensus size: 84
71242 AAATTTATGC
*
71252 GTTGTTTTTTCTTATTTCCAATTGAAGTTAAAATTATATATATTTATTTGTTCATTCAGTATGGT
1 GTTGTTTTTTCTTATTTCCAATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGT
71317 TTGGTGCATATTTCTGCTG
66 TTGGTGCATATTTCTGCTG
*
71336 GTTGTTTTTTCTTATTTCCAATTGAAGTGAAAATTATATATATTTATTTGTTCTTTCAGTATGGT
1 GTTGTTTTTTCTTATTTCCAATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGT
71401 TTGGTGCATATTTCTG
66 TTGGTGCATATTTCTG
71417 TTGGAGATTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (84 bp):
GTTGTTTTTTCTTATTTCCAATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGT
TTGGTGCATATTTCTGCTG
Found at i:71443 original size:84 final size:84
Alignment explanation
Indices: 71271--71436 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
71261 TCTTATTTCC
*
71271 AATTGAAGTTAAAATTATATATATTTATTTGTTCATTCAGTATGGTTTGGTGCATATTTCTGCTG
1 AATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGTTTGGTGCATATTTCTGCTG
* * * * *** *
71336 GTTGTTTTTTCTTATTTCC
66 GTAGATTTATCTGAGAGCA
* *
71355 AATTGAAGTGAAAATTATATATATTTATTTGTTCTTTCAGTATGGTTTGGTGCATATTTCTGTTG
1 AATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGTTTGGTGCATATTTCTGCTG
71420 G-AGATTTAT-TGAGAGCA
66 GTAGATTTATCTGAGAGCA
71437 GAAATTGCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 3 0.04
83 5 0.07
84 63 0.89
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (84 bp):
AATTGAAGTGAAAATTATATATATTTATTTGTTCATTCAGTATGGTTTGGTGCATATTTCTGCTG
GTAGATTTATCTGAGAGCA
Found at i:77910 original size:17 final size:16
Alignment explanation
Indices: 77887--77928 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
77877 CTCCACCATT
**
77887 TAATATAAATTTAAAA
1 TAATATAAATGAAAAA
77903 TCAATATAAATGAAAAA
1 T-AATATAAATGAAAAA
77920 TAATATAAA
1 TAATATAAA
77929 CATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
TAATATAAATGAAAAA
Done.