Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001565.1 Hibiscus syriacus cultivar Beakdansim tig00003099_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: 79311
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1005 original size:11 final size:11
Alignment explanation
Indices: 989--1014 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
979 ATTTTCCACC
989 TATTATTTATT
1 TATTATTTATT
1000 TATTATTTATT
1 TATTATTTATT
1011 TATT
1 TATT
1015 TCGTAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTATT
Found at i:8929 original size:31 final size:32
Alignment explanation
Indices: 8852--8930 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
8842 AATAATGATG
* * * *
8852 AATTTTAAGAATAATTTTGTAGTAATTTAATA
1 AATTTTAATAATTATTTTGTACTAATTGAATA
* *
8884 AATTTTAATGATTATTTTGTACTAATTGGA-A
1 AATTTTAATAATTATTTTGTACTAATTGAATA
*
8915 ATTTTTAATAATTATT
1 AATTTTAATAATTATT
8931 CTATAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 15 0.38
32 24 0.62
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (32 bp):
AATTTTAATAATTATTTTGTACTAATTGAATA
Found at i:25208 original size:17 final size:17
Alignment explanation
Indices: 25163--25208 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
25153 AGTACGTGTT
25163 TATTAAT-TATA-TTTA
1 TATTAATATATATTTTA
* *
25178 TCTTATATAAATATTTTA
1 TATTA-ATATATATTTTA
25196 TATTAATATATAT
1 TATTAATATATAT
25209 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.17
16 2 0.08
17 10 0.42
18 8 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTAATATATATTTTA
Found at i:27556 original size:29 final size:29
Alignment explanation
Indices: 27511--27568 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
27501 GTGTTGGCCG
*
27511 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
27540 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
27569 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:27639 original size:10 final size:10
Alignment explanation
Indices: 27626--27658 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
27616 GCCATCCGAT
27626 CGAGGCCATC
1 CGAGGCCATC
27636 CGAGAG-CATC
1 CGAG-GCCATC
27646 CGAGGCCATC
1 CGAGGCCATC
27656 CGA
1 CGA
27659 ACGAGCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.24, C:0.36, G:0.30, T:0.09
Consensus pattern (10 bp):
CGAGGCCATC
Found at i:27646 original size:34 final size:33
Alignment explanation
Indices: 27607--27676 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
27597 AACACGCTGG
* *
27607 GCATCCAATGCCATCCGATCGAGGCCATCCGAGA
1 GCATCCAAGGCCATCCGAACGA-GCCATCCGAGA
* * *
27641 GCATCCGAGGCCATCCGAACGAGCTATGCGAGA
1 GCATCCAAGGCCATCCGAACGAGCCATCCGAGA
27674 GCA
1 GCA
27677 ACCGAGCGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (33 bp):
GCATCCAAGGCCATCCGAACGAGCCATCCGAGA
Found at i:27682 original size:33 final size:34
Alignment explanation
Indices: 27616--27682 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
27606 GGCATCCAAT
* *
27616 GCCATCCGATCGAGGCCATCCGAGAGCATCCGAG
1 GCCATCCGAACGAGGCCATCCGAGAGCAACCGAG
* *
27650 GCCATCCGAACGA-GCTATGCGAGAGCAACCGAG
1 GCCATCCGAACGAGGCCATCCGAGAGCAACCGAG
27683 CGAGCTATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.27, C:0.33, G:0.30, T:0.10
Consensus pattern (34 bp):
GCCATCCGAACGAGGCCATCCGAGAGCAACCGAG
Found at i:27704 original size:23 final size:24
Alignment explanation
Indices: 27653--27705 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
27643 ATCCGAGGCC
*
27653 ATCCGAACGAGCTATGCGAGAGCA
1 ATCCGAGCGAGCTATGCGAGAGCA
*
27677 A-CCGAGCGAGCTATGCGAG-GGA
1 ATCCGAGCGAGCTATGCGAGAGCA
27699 ATCCGAG
1 ATCCGAG
27706 GGAAGCCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 22 0.85
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.34, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCGAGAGCA
Found at i:27756 original size:29 final size:29
Alignment explanation
Indices: 27723--27778 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
27713 GAGCGAGGGT
*
27723 AGGTCG-CGCGGAGTGCATGGCGACCTACA
1 AGGTCGTC-CGGAGGGCATGGCGACCTACA
27752 AGGTCGTCCGGAGGGCATGGCGACCTA
1 AGGTCGTCCGGAGGGCATGGCGACCTA
27779 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGTCGTCCGGAGGGCATGGCGACCTACA
Found at i:27824 original size:12 final size:12
Alignment explanation
Indices: 27807--27831 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27797 TGCCATGCAA
27807 CACGTTCATTCT
1 CACGTTCATTCT
27819 CACGTTCATTCT
1 CACGTTCATTCT
27831 C
1 C
27832 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:27891 original size:29 final size:29
Alignment explanation
Indices: 27849--27905 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
27839 GAGCAAGGGT
27849 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
27878 AGGTCGCCCGGAGTGCCTGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
27906 GGCCAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.33, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:30693 original size:23 final size:24
Alignment explanation
Indices: 30649--30697 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
30639 ATACATTGAC
** *
30649 AAATTATATAAATGCAATAACATT
1 AAATTATATAAAAACAAAAACATT
30673 AAATTAT-TAAAAACAAAAACATT
1 AAATTATATAAAAACAAAAACATT
30696 AA
1 AA
30698 TTGAAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATTATATAAAAACAAAAACATT
Found at i:34101 original size:128 final size:128
Alignment explanation
Indices: 33687--34166 Score: 827
Period size: 128 Copynumber: 3.7 Consensus size: 128
33677 ACTATTCACA
* *
33687 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
33752 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
33815 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATTATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
33880 TTATGTCACTCATGTCCCCTCGGGGACACTAGAT-ATACCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGT-CCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
*
33944 TGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
34009 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * * *
34072 TGAAGGCGCGTTCCTGGGGGCGCGTCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
34137 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
34167 AATATATCAA
Statistics
Matches: 332, Mismatches: 17, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
127 1 0.00
128 209 0.63
129 121 0.36
130 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:34149 original size:257 final size:256
Alignment explanation
Indices: 33687--34172 Score: 864
Period size: 257 Copynumber: 1.9 Consensus size: 256
33677 ACTATTCACA
33687 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
33752 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
* * *
33817 AAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATTATTGCCCTATT
131 AAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATATT
*
33882 ATGTCACTCATGTCCCCTCGGGGACACTAGATATACCAGTACCTATTATTTCTCAGGGGACT
196 ATGTCACTCATGT-CCCTCGGGGACACTAAATATACCAGTACCTATTATTTCTCAGGGGACT
* * *
33944 TGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
34009 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
* **
34074 AAGGCGCGTTCCTGGGGGCGCGTCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATATT
131 AAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATATT
34139 ATGTCACTCATGTCCCTCGGGGACACTAAATATA
196 ATGTCACTCATGTCCCTCGGGGACACTAAATATA
34173 TCAATAAATC
Statistics
Matches: 218, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
256 20 0.09
257 198 0.91
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (256 bp):
TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
AAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATATT
ATGTCACTCATGTCCCTCGGGGACACTAAATATACCAGTACCTATTATTTCTCAGGGGACT
Found at i:34570 original size:34 final size:34
Alignment explanation
Indices: 34531--34637 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
34521 TAGGTTGAAA
* *
34531 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
34565 TTTAATTTTAAATTTTGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
34599 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
34633 TTTAA
1 TTTAA
34638 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:35224 original size:21 final size:21
Alignment explanation
Indices: 35157--35227 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
35147 TATGGTATAA
*
35157 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
35178 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
35199 AACCCTGCGGGCTTGGAATGT
1 AACCCTGCGGGCTAGGAATGT
35220 AACCCTGC
1 AACCCTGC
35228 AGAGATGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:35259 original size:21 final size:21
Alignment explanation
Indices: 35233--35280 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35223 CCTGCAGAGA
*
35233 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
35254 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
35275 GGGCAT
1 TGGCAT
35281 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:37068 original size:30 final size:32
Alignment explanation
Indices: 37004--37085 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
36994 TTAATAATTC
*
37004 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
37038 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
37068 TATAAAATATAATAATTA
1 TA-AAAA-ATAATAATTA
37086 TTTAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 6 0.14
31 4 0.09
32 11 0.26
33 18 0.42
34 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:50288 original size:16 final size:17
Alignment explanation
Indices: 50263--50294 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
50253 TCGTCGACCG
50263 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
50280 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
50295 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:50778 original size:36 final size:34
Alignment explanation
Indices: 50716--50817 Score: 98
Period size: 35 Copynumber: 2.9 Consensus size: 34
50706 CTACCAAAAT
*
50716 TTTACCAAACTTTGAAAAATA-TTTTTCAAAGAAACA
1 TTTACCAAACTTTGAAAAA-ACATTTTCAAAG--ACA
***
50752 TTTACCAAACTTTGAAAAAACATTTTCCAAAGTTG
1 TTTACCAAACTTTGAAAAAACATTTT-CAAAGACA
* * *
50787 GTTGCCAAACTTTGAAAAAACATTTCCAAAG
1 TTTACCAAACTTTGAAAAAACATTTTCAAAG
50818 TTGATTGCCA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 5 0.09
35 24 0.42
36 23 0.40
37 5 0.09
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (34 bp):
TTTACCAAACTTTGAAAAAACATTTTCAAAGACA
Found at i:50813 original size:34 final size:35
Alignment explanation
Indices: 50756--50837 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 35
50746 GAAACATTTA
*
50756 CCAAACTTTGAAAAAACATTTTCCAAAGTTGGTTG
1 CCAAACTTTGAAAAAACATTTTCCAAAGTTGATTG
50791 CCAAACTTTGAAAAAACA-TTTCCAAAGTTGATTG
1 CCAAACTTTGAAAAAACATTTTCCAAAGTTGATTG
50825 CCAAACTTTGAAA
1 CCAAACTTTGAAA
50838 CTTTTAACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 28 0.61
35 18 0.39
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (35 bp):
CCAAACTTTGAAAAAACATTTTCCAAAGTTGATTG
Found at i:51607 original size:7 final size:7
Alignment explanation
Indices: 51595--51693 Score: 198
Period size: 7 Copynumber: 14.1 Consensus size: 7
51585 TTTCTCATAC
51595 ACTATGT
1 ACTATGT
51602 ACTATGT
1 ACTATGT
51609 ACTATGT
1 ACTATGT
51616 ACTATGT
1 ACTATGT
51623 ACTATGT
1 ACTATGT
51630 ACTATGT
1 ACTATGT
51637 ACTATGT
1 ACTATGT
51644 ACTATGT
1 ACTATGT
51651 ACTATGT
1 ACTATGT
51658 ACTATGT
1 ACTATGT
51665 ACTATGT
1 ACTATGT
51672 ACTATGT
1 ACTATGT
51679 ACTATGT
1 ACTATGT
51686 ACTATGT
1 ACTATGT
51693 A
1 A
51694 TATATATATA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 92 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (7 bp):
ACTATGT
Found at i:55024 original size:35 final size:37
Alignment explanation
Indices: 54985--55056 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
54975 TCATTAAACC
* *
54985 TTTTTAT-ATTTTTAATTTTGTAAA-AAAATATATAA
1 TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
*
55020 TTTTTATGAATTTAAATTTTTTAAAGAAAATATATAA
1 TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
55057 ATATTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 7 0.22
36 14 0.44
37 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (37 bp):
TTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
Found at i:55242 original size:16 final size:16
Alignment explanation
Indices: 55192--55243 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
55182 ACATTCTCAA
*
55192 TAATTCTATTCCCTGA
1 TAATTCTATTCCCTGG
*
55208 TAATTCTATTCCCTAG
1 TAATTCTATTCCCTGG
*
55224 TAATTCTATTCACTGG
1 TAATTCTATTCCCTGG
55240 TAAT
1 TAAT
55244 CTTACATTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (16 bp):
TAATTCTATTCCCTGG
Found at i:60338 original size:20 final size:20
Alignment explanation
Indices: 60313--60350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60303 ATGTAGGATG
* *
60313 TTATTACATTATTTTTATAT
1 TTATTAAATGATTTTTATAT
60333 TTATTAAATGATTTTTAT
1 TTATTAAATGATTTTTAT
60351 TTAAAATACT
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:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTATTAAATGATTTTTATAT
Found at i:60913 original size:10 final size:11
Alignment explanation
Indices: 60888--60914 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60878 AACATAAATT
60888 TTTTTATTTAA
1 TTTTTATTTAA
60899 TTTTTATTTAA
1 TTTTTATTTAA
60910 TTTTT
1 TTTTT
60915 TAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:63840 original size:8 final size:9
Alignment explanation
Indices: 63822--63857 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
63812 TTTTTATTAA
63822 TAAATTATTT
1 TAAATT-TTT
63832 TAAATTTTT
1 TAAATTTTT
63841 TAAATTTTT
1 TAAATTTTT
63850 ATAAATTT
1 -TAAATTT
63858 ATACTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 12 0.48
10 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAAATTTTT
Found at i:63859 original size:41 final size:41
Alignment explanation
Indices: 63781--63859 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
63771 ATTAAAATTC
* **
63781 TAAATTATTATATATTTTAAATATTTTTATATTTTTATTAA
1 TAAATTATTATAAATTTTAAATATTTTTATAAATTTATTAA
* *
63822 TAAATTATTTTAAATTTTTTAA-ATTTTTATAAATTTAT
1 TAAATTATTATAAA-TTTTAAATATTTTTATAAATTTAT
63860 ACTAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 26 0.81
42 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
TAAATTATTATAAATTTTAAATATTTTTATAAATTTATTAA
Found at i:71350 original size:31 final size:31
Alignment explanation
Indices: 71311--71373 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 31
71301 CTTTACAAGG
*
71311 AAAAAATTATTTTAATTAAC-AATA-AATTAT
1 AAAAAATTA-TATAATTAACAAATATAATTAT
*
71341 AAAATAATTATATAATTTACAAATATAATTAT
1 AAAA-AATTATATAATTAACAAATATAATTAT
71373 A
1 A
71374 TTAGCTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.43
31 9 0.32
32 7 0.25
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATTATATAATTAACAAATATAATTAT
Found at i:73554 original size:24 final size:24
Alignment explanation
Indices: 73527--73575 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
73517 ACTGTTAATC
73527 AAACTAAATTATTAATCGAATTGA
1 AAACTAAATTATTAATCGAATTGA
73551 AAACTAAATTATTAATCGAATTGA
1 AAACTAAATTATTAATCGAATTGA
73575 A
1 A
73576 CAAAGTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AAACTAAATTATTAATCGAATTGA
Found at i:76860 original size:60 final size:60
Alignment explanation
Indices: 76718--76865 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
76708 ATTTTTAAGT
* * * * * * * *
76718 TTTTGTATATTTTAATTTTATCATCAAATTATGACTTTTATTTCAAATTAGTCTTTATAC
1 TTTTGAATATTTTAATTTCATCCTCAAACTATAACTTTCATTTCAAATTAGTCTCTAAAC
*
76778 TATTGAATATTTTAATTTCATCCTCAAACTATAACTTTCA-TTCTAAATTAGT-TCCTAAAC
1 TTTTGAATATTTTAATTTCATCCTCAAACTATAACTTTCATTTC-AAATTAGTCT-CTAAAC
* *
76838 TTTTGAATATTTCAATTTCATCCCCAAA
1 TTTTGAATATTTTAATTTCATCCTCAAA
76866 TTCATTCAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 4 0.05
60 70 0.95
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (60 bp):
TTTTGAATATTTTAATTTCATCCTCAAACTATAACTTTCATTTCAAATTAGTCTCTAAAC
Found at i:77908 original size:29 final size:29
Alignment explanation
Indices: 77874--77956 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
77864 TAGATTGAGA
77874 ATGAAAATGAAATATTCAAAAATTCGAGG
1 ATGAAAATGAAATATTCAAAAATTCGAGG
* *
77903 ATGAAAAT-AAAAATTC-AAAATT-TA--
1 ATGAAAATGAAATATTCAAAAATTCGAGG
*
77927 ATGAAAATGAAATATTCAAAAGTTCGAGG
1 ATGAAAATGAAATATTCAAAAATTCGAGG
77956 A
1 A
77957 CTGATTTAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
24 8 0.18
25 7 0.16
26 6 0.14
27 7 0.16
28 7 0.16
29 9 0.20
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.25
Consensus pattern (29 bp):
ATGAAAATGAAATATTCAAAAATTCGAGG
Done.