Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004959.1 Hibiscus syriacus cultivar Beakdansim tig00011147_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: 138213
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2942 original size:17 final size:17
Alignment explanation
Indices: 2920--2954 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2910 TAGAAAATAC
2920 ATATAAAAAAATTTAAA
1 ATATAAAAAAATTTAAA
*
2937 ATATAAAATAATTTAAA
1 ATATAAAAAAATTTAAA
2954 A
1 A
2955 AAATTAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAAAAAAATTTAAA
Found at i:3348 original size:52 final size:52
Alignment explanation
Indices: 3247--3363 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 52
3237 ATAATCTGAA
*
3247 TATTAATATTTAAAATAATTAAAATAATATATTTGTAACAATATATTATAAT
1 TATTAATATTTAAAATAATTAAAATAATATATTTATAACAATATATTATAAT
* * ** * *
3299 TATTTATATTTTAAATGGTTAATATAATATATTTTATAACAAT-TTTTAT-AT
1 TATTAATATTTAAAATAATTAAAATAATATA-TTTATAACAATATATTATAAT
* *
3350 TTTTAATAATTAAA
1 TATTAATATTTAAA
3364 GAATATATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
51 12 0.23
52 31 0.58
53 10 0.19
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (52 bp):
TATTAATATTTAAAATAATTAAAATAATATATTTATAACAATATATTATAAT
Found at i:3350 original size:42 final size:42
Alignment explanation
Indices: 3296--3375 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
3286 AATATATTAT
** *
3296 AATTATTTATATTTTAAATGGTTAATATAATATATTTTATAAC
1 AATTATTTATATTTTAAATAATTAA-AGAATATATTTTATAAC
*
3339 AATT-TTTATATTTTTAATAATTAAAGAATATATTTTA
1 AATTATTTATATTTTAAATAATTAAAGAATATATTTTA
3376 ATAATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 12 0.36
42 17 0.52
43 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (42 bp):
AATTATTTATATTTTAAATAATTAAAGAATATATTTTATAAC
Found at i:12683 original size:2 final size:2
Alignment explanation
Indices: 12676--12700 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12666 ATAAATCATT
12676 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12701 TTGATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13267 original size:2 final size:2
Alignment explanation
Indices: 13260--13287 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13250 TTTTAGATTA
13260 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
13288 TGTTTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24117 original size:20 final size:20
Alignment explanation
Indices: 24092--24158 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
24082 TTAGATCAAG
24092 TATTAAAATATAACTTTATA
1 TATTAAAATATAACTTTATA
* *
24112 TATTAAAATAT-ACGTCGATAATG
1 TATTAAAATATAAC-T---TTATA
24135 TATTAAAATATAACTTTATA
1 TATTAAAATATAACTTTATA
24155 TATT
1 TATT
24159 TATTTAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
23 15 0.39
24 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
TATTAAAATATAACTTTATA
Found at i:26018 original size:29 final size:27
Alignment explanation
Indices: 25986--26058 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 27
25976 TATCAATAAG
25986 TTTACTTTTTTACAATTTAA-TCTATTGAC
1 TTTA-TTTTTTACAATTTAACT-TATT-AC
*
26015 TTTATATTTTATTCAATTTAACTTATTAC
1 TTTAT-TTTT-TACAATTTAACTTATTAC
*
26044 TGTAATTTTTTACAA
1 T-TTATTTTTTACAA
26059 ATTCTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 5 0.14
29 15 0.41
30 16 0.43
31 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTATTTTTTACAATTTAACTTATTAC
Found at i:27151 original size:23 final size:23
Alignment explanation
Indices: 27085--27145 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
27075 AATACATAAA
* *
27085 AAAACGTGTCATAAAAACAGAAG
1 AAAACGTGTTATAAAAACAAAAG
*
27108 AAAGCGTGTTATAAAAACAAAAG
1 AAAACGTGTTATAAAAACAAAAG
27131 AAAACGTGTTATAAA
1 AAAACGTGTTATAAA
27146 TGCAAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAACGTGTTATAAAAACAAAAG
Found at i:30428 original size:20 final size:20
Alignment explanation
Indices: 30391--30428 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30381 TTAGTTTAAT
*
30391 TTGATTTGAAAATTTTAAAA
1 TTGATTTGAAAATCTTAAAA
30411 TTGAGTTTGAAAA-CTTAA
1 TTGA-TTTGAAAATCTTAA
30429 GATCATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (20 bp):
TTGATTTGAAAATCTTAAAA
Found at i:38616 original size:29 final size:29
Alignment explanation
Indices: 38574--38637 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
38564 TTGGATCTCT
*
38574 CTTTAATGAGCTATAAGGTTTCAGTATCC
1 CTTTAATGAGCTATAAGGTTTCAATATCC
*
38603 CTTTAATGAGCTATAAGGTTTCAATCTCC
1 CTTTAATGAGCTATAAGGTTTCAATATCC
38632 CTTTAA
1 CTTTAA
38638 ACTGACTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (29 bp):
CTTTAATGAGCTATAAGGTTTCAATATCC
Found at i:71740 original size:7 final size:7
Alignment explanation
Indices: 71728--71770 Score: 77
Period size: 7 Copynumber: 6.0 Consensus size: 7
71718 TCAATGACGT
71728 AAAAGAA
1 AAAAGAA
71735 AAAAGAA
1 AAAAGAA
71742 AAAATGAA
1 AAAA-GAA
71750 AAAAGAA
1 AAAAGAA
71757 AAAAGAA
1 AAAAGAA
71764 AAAAGAA
1 AAAAGAA
71771 GAGAGAGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:72148 original size:31 final size:32
Alignment explanation
Indices: 72105--72173 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
72095 CGAATCTGGA
* *
72105 CCGACCCGAATA-TCCCCTTAAAAAATCC-GAT
1 CCGAACCGAATATTACCCTTAAAAAA-CCTGAT
*
72136 CCGAACCGAATATTACCTTTAAAAAACCTGAT
1 CCGAACCGAATATTACCCTTAAAAAACCTGAT
72168 CC-AACC
1 CCGAACC
72174 CAACCCAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.20
Consensus pattern (32 bp):
CCGAACCGAATATTACCCTTAAAAAACCTGAT
Found at i:78171 original size:145 final size:145
Alignment explanation
Indices: 78014--78301 Score: 470
Period size: 145 Copynumber: 2.0 Consensus size: 145
78004 GTATAAAATA
*
78014 TAAATGTTAGGTATGATTTTAAAACAAATGAATAAATACTAAAACGAAACA-AACCAGATAATTT
1 TAAATGTTAGGTATGATTTTAAAACAAACGAATAAATACTAAAACGAAACATAA-CAGATAATTT
* * *
78078 AAATATTAAATATGTAACTTACTTTATAATTTGTTATGTCTTAATATTTTAAACGAATTTAGAAA
65 AAATATTAAATATATAACTTACCTTATAATTTATTATGTCTTAATATTTTAAACGAATTTAGAAA
78143 TTAAGTTGAATATATG
130 TTAAGTTGAATATATG
* * * *
78159 TAAATGTTAGGTATGATTTTAAAATAAACGAATAAATATTAAAACGAAACATAACATATATTTTA
1 TAAATGTTAGGTATGATTTTAAAACAAACGAATAAATACTAAAACGAAACATAACAGATAATTTA
*
78224 AATATTAAATATATAATTTACCTTATAATTTATTATGTCTTAATATTTTAAACGAATTTAGAAAT
66 AATATTAAATATATAACTTACCTTATAATTTATTATGTCTTAATATTTTAAACGAATTTAGAAAT
*
78289 TGAGTTGAATATA
131 TAAGTTGAATATA
78302 AATGAACGAA
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
145 130 0.98
146 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (145 bp):
TAAATGTTAGGTATGATTTTAAAACAAACGAATAAATACTAAAACGAAACATAACAGATAATTTA
AATATTAAATATATAACTTACCTTATAATTTATTATGTCTTAATATTTTAAACGAATTTAGAAAT
TAAGTTGAATATATG
Found at i:78501 original size:23 final size:23
Alignment explanation
Indices: 78473--78519 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
78463 TTCATGTTAA
*
78473 TTACCAAGCAATTCATTAAATGT
1 TTACCAAACAATTCATTAAATGT
78496 TTACCAAACAATTCATTAAATGT
1 TTACCAAACAATTCATTAAATGT
78519 T
1 T
78520 GGATTCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (23 bp):
TTACCAAACAATTCATTAAATGT
Found at i:90894 original size:22 final size:22
Alignment explanation
Indices: 90866--90914 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
90856 ATAAATTTAT
90866 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
90888 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
90910 AAATA
1 TAATA
90915 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:91050 original size:19 final size:18
Alignment explanation
Indices: 91026--91094 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
91016 ATATTATTAA
91026 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
91045 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
91063 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
91085 ATT-TTAATAA
1 ATTATTAATAA
91095 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:91069 original size:27 final size:27
Alignment explanation
Indices: 90989--91074 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
90979 AATAAAATTT
* *
90989 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
91016 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
91043 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
91072 ATA
1 ATA
91075 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:91437 original size:14 final size:14
Alignment explanation
Indices: 91418--91447 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
91408 CAGAAAATAT
*
91418 AATTCATTTTCCAG
1 AATTCAATTTCCAG
91432 AATTCAATTTCCAG
1 AATTCAATTTCCAG
91446 AA
1 AA
91448 AACCAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:91937 original size:38 final size:36
Alignment explanation
Indices: 91861--91938 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
91851 TTTTTATATT
* *
91861 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
* *
91897 TTTAATTTTTTAAAGAAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAAATATATAAATATTAT-CAA
91935 TTTA
1 TTTA
91939 TAATATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 13 0.36
37 17 0.47
38 6 0.17
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
Found at i:91958 original size:18 final size:18
Alignment explanation
Indices: 91914--91961 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
91904 TTTTAAAGAA
*
91914 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
91933 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
91950 AAATATATAATA
1 AAATATATAATA
91962 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:92119 original size:20 final size:20
Alignment explanation
Indices: 92083--92120 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92073 ATCCTATTCC
**
92083 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
92103 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
92121 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:94838 original size:18 final size:21
Alignment explanation
Indices: 94815--94854 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
94805 AAATTTCAGT
94815 TAAGT-AC-AATCAAA-AAAA
1 TAAGTAACTAATCAAATAAAA
94833 TAAGTAACTAATCAAATAAAA
1 TAAGTAACTAATCAAATAAAA
94854 T
1 T
94855 TCGAATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 2 0.11
20 7 0.37
21 5 0.26
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAGTAACTAATCAAATAAAA
Found at i:97798 original size:2 final size:2
Alignment explanation
Indices: 97793--97817 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97783 GTGTGGAATC
97793 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
97818 ATGAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:100673 original size:27 final size:27
Alignment explanation
Indices: 100643--100736 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
100633 TTAAAAGTTG
100643 ATTTTAATCTCTTTATTATAAAAAAAT
1 ATTTTAATCTCTTTATTATAAAAAAAT
* * **
100670 ATTTTAAT-TAGTTTATTTTACTTAAAAT
1 ATTTTAATCT-CTTTATTATA-AAAAAAT
* * *
100698 TTGTTGTAATTTCTGTATTATAAAAAAGAT
1 AT-TT-TAATCTCTTTATTATAAAAAA-AT
100728 ATTTTAATC
1 ATTTTAATC
100737 CTTGTATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
26 1 0.02
27 16 0.33
28 10 0.20
29 7 0.14
30 14 0.29
31 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (27 bp):
ATTTTAATCTCTTTATTATAAAAAAAT
Found at i:100721 original size:57 final size:59
Alignment explanation
Indices: 100625--100735 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 59
100615 AAAATCCATA
* *
100625 TATTATACTTAAAAGTTGATTTTAATCTCTTTATTATAAAAAA-ATATTTTAATTAGTT
1 TATTATACTTAAAAGTTGATTGTAATCTCTGTATTATAAAAAAGATATTTTAATTAGTT
* * *
100683 TATTTTACTTAAAATTTG-TTGTAATTTCTGTATTATAAAAAAGATATTTTAAT
1 TATTATACTTAAAAGTTGATTGTAATCTCTGTATTATAAAAAAGATATTTTAAT
100736 CCTTGTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (59 bp):
TATTATACTTAAAAGTTGATTGTAATCTCTGTATTATAAAAAAGATATTTTAATTAGTT
Found at i:101050 original size:17 final size:18
Alignment explanation
Indices: 101028--101069 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
101018 TATTTTTTAC
101028 AATTTTAAAAAATA-ATA
1 AATTTTAAAAAATATATA
101045 AATTTTAAAAAATATATA
1 AATTTTAAAAAATATATA
*
101063 ATTTTTA
1 AATTTTA
101070 TACTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTTAAAAAATATATA
Found at i:105232 original size:29 final size:28
Alignment explanation
Indices: 105185--105252 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
105175 ATTAATATAT
* *
105185 ATTTACTTTTGTTCTGTTTTAGCACACAAA
1 ATTTA-TTTTATTCCGTTTTAGCACAC-AA
* *
105215 ATTTATTTTATTCCGTTTTAGTACTCAA
1 ATTTATTTTATTCCGTTTTAGCACACAA
105243 ATCTTATTTT
1 AT-TTATTTT
105253 GTTTCAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTTATTTTATTCCGTTTTAGCACACAA
Found at i:110475 original size:16 final size:16
Alignment explanation
Indices: 110456--110512 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
110446 TTTCGGTCCC
110456 GGTTATTTTCGAATTG
1 GGTTATTTTCGAATTG
** *
110472 GGTTAAATTCGATTTG
1 GGTTATTTTCGAATTG
* **
110488 GATTGCTTTCGAATTG
1 GGTTATTTTCGAATTG
*
110504 AGTTATTTT
1 GGTTATTTT
110513 TCGGTTCGGA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (16 bp):
GGTTATTTTCGAATTG
Found at i:110503 original size:32 final size:32
Alignment explanation
Indices: 110462--110555 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
110452 TCCCGGTTAT
*
110462 TTTCGAATTGGGTTAAATTCGATTTGGATTGC
1 TTTCGAATTGGGTTAATTTCGATTTGGATTGC
* * * *
110494 TTTCGAATTGAGTTATTTTTCGGTTCGGATTGC
1 TTTCGAATTGGGTTA-ATTTCGATTTGGATTGC
* *
110527 TTTC-AGTTCAGGTTAATTTCGATTTGGAT
1 TTTCGAATT-GGGTTAATTTCGATTTGGAT
110556 ATTTCCGATT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
32 28 0.57
33 21 0.43
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (32 bp):
TTTCGAATTGGGTTAATTTCGATTTGGATTGC
Found at i:111227 original size:22 final size:22
Alignment explanation
Indices: 111155--111227 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
111145 CTAATTTCCA
*
111155 GTAGAAAAAAATAACATTTTAG
1 GTAGAAAAAAATAATATTTTAG
** * *
111177 GTATAGTCTAATATTAATATTTTTA-
1 G--TAG-AAAAAAATAATA-TTTTAG
111202 GTAGAAAAAAATAATATTTTAG
1 GTAGAAAAAAATAATATTTTAG
111224 GTAG
1 GTAG
111228 TGCTTTACCG
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
21 5 0.14
22 13 0.35
23 3 0.08
24 3 0.08
25 8 0.22
26 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.37
Consensus pattern (22 bp):
GTAGAAAAAAATAATATTTTAG
Found at i:111228 original size:25 final size:25
Alignment explanation
Indices: 111154--111228 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
111144 ACTAATTTCC
*
111154 AGTAGAAAAAAATAACATTTTAGGT
1 AGTAGAAAAAAATAATATTTTAGGT
** * *
111179 A-TAGTCTAATATTAATATTTT---T
1 AGTAG-AAAAAAATAATATTTTAGGT
111201 AGTAGAAAAAAATAATATTTTAGGT
1 AGTAGAAAAAAATAATATTTTAGGT
111226 AGT
1 AGT
111229 GCTTTACCGG
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
22 14 0.39
23 3 0.08
24 3 0.08
25 16 0.44
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (25 bp):
AGTAGAAAAAAATAATATTTTAGGT
Found at i:111389 original size:51 final size:52
Alignment explanation
Indices: 111332--111441 Score: 159
Period size: 57 Copynumber: 2.0 Consensus size: 52
111322 GTATATATAC
111332 ACACAAGTATTG-TTTTTTTCTTTTTTGCTTTATAAAAGAATTAATATAAAT
1 ACACAAGTATTGTTTTTTTTCTTTTTTGCTTTATAAAAGAATTAATATAAAT
*
111383 ACACAAGTATTGTTTTTCTTTTTTTCTTTTTTGCTTTATAAAAGAATTAATGTAAAT
1 ACACAAGTATTG----T-TTTTTTTCTTTTTTGCTTTATAAAAGAATTAATATAAAT
111440 AC
1 AC
111442 TATAACTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
51 12 0.23
57 40 0.77
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (52 bp):
ACACAAGTATTGTTTTTTTTCTTTTTTGCTTTATAAAAGAATTAATATAAAT
Found at i:112934 original size:25 final size:25
Alignment explanation
Indices: 112906--112957 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
112896 ATCTATTTTC
112906 ATCTCCTAAAATTATATAAACTCAT
1 ATCTCCTAAAATTATATAAACTCAT
112931 ATCTCCTAAAATTATATAAACTCAT
1 ATCTCCTAAAATTATATAAACTCAT
112956 AT
1 AT
112958 ATTTTAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (25 bp):
ATCTCCTAAAATTATATAAACTCAT
Found at i:115722 original size:31 final size:31
Alignment explanation
Indices: 115684--115756 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
115674 TTAATAAAAC
115684 GGCTAAATATTAATAATAAGTTGGTCTAATG
1 GGCTAAATATTAATAATAAGTTGGTCTAATG
** *
115715 GGCTAAATATTGTTTATAAGTTGGTCTAATG
1 GGCTAAATATTAATAATAAGTTGGTCTAATG
115746 GGCTAAATATT
1 GGCTAAATATT
115757 TTTTTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (31 bp):
GGCTAAATATTAATAATAAGTTGGTCTAATG
Found at i:121054 original size:36 final size:36
Alignment explanation
Indices: 120980--121054 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 36
120970 TTTTTATATT
*
120980 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
121016 TTTAATTTTTTTAAGAAAA-TATAT-AATATTTTACAA
1 TTTAA-TTTTGTAAAAAAATTATATAAATATTAT-CAA
121052 TTT
1 TTT
121055 GTAATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
35 7 0.21
36 15 0.45
37 11 0.33
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:126124 original size:18 final size:18
Alignment explanation
Indices: 126067--126130 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
126057 CGAAACCGGT
126067 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTC-GG
* *
126086 TTTTT---TAACGGTTTGG
1 TTTTTCGGT-TCGGTTCGG
126102 ATTTTTCGGTTCGGTTCGG
1 -TTTTTCGGTTCGGTTCGG
126121 TTTTTCGGTT
1 TTTTTCGGTT
126131 TTTCAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 3 0.08
17 10 0.28
18 10 0.28
19 12 0.33
20 1 0.03
ACGTcount: A:0.05, C:0.12, G:0.30, T:0.53
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:126271 original size:27 final size:29
Alignment explanation
Indices: 126241--126296 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
126231 AACCGAATTA
126241 AAAAAAT-GAAGCC-TTTAAA-CCGAACCG
1 AAAAAATCGAA-CCGTTTAAAGCCGAACCG
126268 --AAAATCGAACCGTTTAAAGCCGAACCG
1 AAAAAATCGAACCGTTTAAAGCCGAACCG
126295 AA
1 AA
126297 CCGAACTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.14
Consensus pattern (29 bp):
AAAAAATCGAACCGTTTAAAGCCGAACCG
Found at i:129954 original size:31 final size:31
Alignment explanation
Indices: 129915--129985 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
129905 ATAATAATTA
* * *
129915 TATTTTATAGT-ATTTAGATAAATTTATTAA-
1 TATTTTATAATCATTT-AATAAATTTAATAAG
*
129945 TAATTTTATAATCTTTTAATAAATTTAATAAG
1 T-ATTTTATAATCATTTAATAAATTTAATAAG
129977 TATTTTATA
1 TATTTTATA
129986 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
30 1 0.03
31 29 0.85
32 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (31 bp):
TATTTTATAATCATTTAATAAATTTAATAAG
Found at i:129995 original size:28 final size:31
Alignment explanation
Indices: 129927--129994 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
129917 TTTTATAGTA
*
129927 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTAATAATAATTTTATAATCT
* *
129959 TTTAATAAATTTAATAAGT-ATTTTATATTTT
1 TTTAATAAATTTAATAA-TAATTTTATAATCT
129990 TTTAA
1 TTTAA
129995 ACTTTATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTAATAAATTTAATAATAATTTTATAATCT
Found at i:130741 original size:11 final size:10
Alignment explanation
Indices: 130710--130803 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 10
130700 ATTTTCGTCA
130710 ATAAAAT-TT
1 ATAAAATATT
* *
130719 AAAAAAAATT
1 ATAAAATATT
130729 ATAAAATACTT
1 ATAAAATA-TT
*
130740 ATTAAAT-TT
1 ATAAAATATT
*
130749 ATTAAAAGATT
1 A-TAAAATATT
130760 ATAAAATTATT
1 ATAAAA-TATT
130771 A-ATAAAT-TT
1 ATA-AAATATT
* *
130780 ATCTAAATACT
1 AT-AAAATATT
130791 ATAAAATAATT
1 ATAAAAT-ATT
130802 AT
1 AT
130804 TTTATTATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
9 11 0.17
10 27 0.43
11 25 0.40
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (10 bp):
ATAAAATATT
Found at i:130763 original size:31 final size:30
Alignment explanation
Indices: 130713--130804 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
130703 TTCGTCAATA
*
130713 AAATTTA-AAAAAAATTATAAAATACTTATT
1 AAATTTATTAAAAAATTATAAAATA-TTATT
* *
130743 AAATTTATTAAAAGATTATAAAATTATTAAT
1 AAATTTATTAAAAAATTATAAAA-TATTATT
* *
130774 AAATTTATCT-AAATACTATAAAATAATTATT
1 AAATTTAT-TAAAAAATTATAAAAT-ATTATT
130805 TTATTATCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
30 8 0.15
31 41 0.79
32 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
AAATTTATTAAAAAATTATAAAATATTATT
Found at i:130770 original size:19 final size:21
Alignment explanation
Indices: 130723--130772 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
130713 AAATTTAAAA
*
130723 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAAGACTTATT
*
130743 AAATTTATTAAAAGA-TTA-T
1 AAAATTATTAAAAGACTTATT
130762 AAAATTATTAA
1 AAAATTATTAA
130773 TAAATTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 9 0.35
21 6 0.23
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATTATTAAAAGACTTATT
Found at i:131586 original size:21 final size:21
Alignment explanation
Indices: 131557--131600 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
131547 ATATATTAAT
131557 AATAATATAATATTTAAGTTA
1 AATAATATAATATTTAAGTTA
* * * *
131578 AATATTATACTTTTTAGGTTA
1 AATAATATAATATTTAAGTTA
131599 AA
1 AA
131601 ATCGAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
AATAATATAATATTTAAGTTA
Done.