Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008410.1 Hibiscus syriacus cultivar Beakdansim tig00111181_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: 59205
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:399 original size:24 final size:24
Alignment explanation
Indices: 312--399 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
302 ATTTCCGACT
*
312 TGAATTCTGTTCTGATA-CATGACC
1 TGAATTCTGTTCTGATATC-TGATC
* * *
336 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATC
* * * *
360 TGGATTCTGCTATGATATCTAATC
1 TGAATTCTGTTCTGATATCTGATC
*
384 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
400 TTTTGATATC
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:17875 original size:54 final size:54
Alignment explanation
Indices: 17631--17853 Score: 340
Period size: 54 Copynumber: 4.1 Consensus size: 54
17621 GATTACCAAA
*
17631 TCGGCACTAATTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * *
17685 TTGTCACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * *
17739 TCGACACTAAGTGTGCATTTCACGAAATTCATCC-ATTGTGGATGAATAATCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTA-TGTGGATGAATAACCGTT
* * *
17793 TCAGCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
17847 TCGGCAC
1 TCGGCAC
17854 CATGAGTGCA
Statistics
Matches: 151, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 149 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
Found at i:17893 original size:108 final size:108
Alignment explanation
Indices: 17669--17875 Score: 263
Period size: 108 Copynumber: 1.9 Consensus size: 108
17659 TCATCCTATG
* ** *
17669 TGGATGAATAACCGTTTTGTCACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAA
1 TGGATGAATAACCGTTTAGTCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAA
* * *** * *
17734 CCGTTTCGACACTAAGTGTGCATTTCACGAAATTCATCCATTG
66 CCGTTTCGACACCAAGAGTGCAAAACACGAAATTCATCAATTA
*
17777 TGGATGAATAATCGTTTCAG-CACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATA
1 TGGATGAATAACCGTTT-AGTCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATA
* * *
17841 ACCGTTTCGGCACCATGAGTGCAAAACACGGAATT
65 ACCGTTTCGACACCAAGAGTGCAAAACACGAAATT
17876 TATAATATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
108 84 0.99
109 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (108 bp):
TGGATGAATAACCGTTTAGTCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAA
CCGTTTCGACACCAAGAGTGCAAAACACGAAATTCATCAATTA
Found at i:17909 original size:108 final size:108
Alignment explanation
Indices: 17689--17901 Score: 230
Period size: 108 Copynumber: 2.0 Consensus size: 108
17679 ACCGTTTTGT
** * * *
17689 CACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTG
1 CACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACCAAGAGTG
*** * * * * *
17754 CATTTCACGAAATTCATCCATTGTGGATGAATAATCGTTTCAG
66 CAAAACACGAAATTCATCAATTATGGATGAATAACCATATCAG
* *
17797 CACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACCATGAGTG
1 CACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACCAAGAGTG
* * ** *
17862 CAAAACACGGAATTTAT-AATATATTTATGAATGACCATAT
66 CAAAACACGAAATTCATCAAT-TATGGATGAATAACCATAT
17902 GGGCACTATA
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
107 2 0.02
108 82 0.98
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACCAAGAGTG
CAAAACACGAAATTCATCAATTATGGATGAATAACCATATCAG
Found at i:17982 original size:2 final size:2
Alignment explanation
Indices: 17975--18040 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
17965 AACAATAATG
17975 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
18017 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
18041 TGATTTCATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20938 original size:18 final size:18
Alignment explanation
Indices: 20917--20965 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
20907 ACCTAATTTT
*
20917 GGTATCGATACCGGAGGG
1 GGTATCGATACCAGAGGG
20935 GGTATCGATACCAGAGGG
1 GGTATCGATACCAGAGGG
20953 GGTATCGATACCA
1 GGTATCGATACCA
20966 TAGCGTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.37, T:0.18
Consensus pattern (18 bp):
GGTATCGATACCAGAGGG
Found at i:21000 original size:112 final size:114
Alignment explanation
Indices: 20859--21122 Score: 331
Period size: 112 Copynumber: 2.3 Consensus size: 114
20849 GGTACTAATG
* ** *
20859 AGGTAGTATCGATACTATGGTAAGGGTATCTATACCCGGTAACATCGAACCTAATTTTGGTATCG
1 AGGTAGTATCGATACTATGGT-AGGGTATCAATACCAAGCAACATCGAACCTAATTTTGGTATCG
*
20924 ATACCGG-AGGGGGTATCGATACC-AG-AGGG-GGTATCGATACCATAGCGT
65 ATACCGGAAGGGGGTATCGATACCAAGTAGGGTAGTATCGATACCATA--GT
* *
20972 A-GTAGTATCGATACTATGGTGAGGGTATCAATACCAAGCCACATCGAAGCTAATTTTGGTATCG
1 AGGTAGTATCGATACTATGGT-AGGGTATCAATACCAAGCAACATCGAACCTAATTTTGGTATCG
* *
21036 ATACTGGAAGGGGGTATCGATACCATAGTAGGGTAGTATTGATACCATAGT
65 ATACCGGAAGGGGGTATCGATACCA-AGTAGGGTAGTATCGATACCATAGT
* *
21087 AGGGTAGTATCGATACCATGGTAGGGGTATCGATAC
1 A-GGTAGTATCGATACTATGGTA-GGGTATCAATAC
21123 TGAATGGCCA
Statistics
Matches: 131, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
112 62 0.47
113 17 0.13
115 5 0.04
116 5 0.04
117 42 0.32
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (114 bp):
AGGTAGTATCGATACTATGGTAGGGTATCAATACCAAGCAACATCGAACCTAATTTTGGTATCGA
TACCGGAAGGGGGTATCGATACCAAGTAGGGTAGTATCGATACCATAGT
Found at i:21079 original size:22 final size:22
Alignment explanation
Indices: 21049--21122 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
21039 CTGGAAGGGG
21049 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
21071 GTATTGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
*
21093 GTATCGATACCATGGTAGGG--
1 GTATCGATACCATAGTAGGGTA
21113 GTATCGATAC
1 GTATCGATAC
21123 TGAATGGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 10 0.20
22 39 0.80
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:21750 original size:54 final size:54
Alignment explanation
Indices: 21412--21731 Score: 478
Period size: 54 Copynumber: 5.9 Consensus size: 54
21402 TTACCAAATA
* * * *
21412 GGCACTAATTGTGCATTTCACGAAATTCGTCCTTTGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
21466 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGCATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
21520 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ***
21574 GGCACTAAGTTTGTATTTCAAAAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
21628 GGCACTAAGTGTGCATTTCACGAAATTTATCCTATGTGGATGAATAATCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
21682 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCG
21732 GTTTGGTACC
Statistics
Matches: 238, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 238 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:21765 original size:162 final size:162
Alignment explanation
Indices: 21430--21765 Score: 465
Period size: 162 Copynumber: 2.1 Consensus size: 162
21420 TTGTGCATTT
* * *
21430 CACGAAATTCGTCCTTTGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCA
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCA
* * * *
21495 TCCTATGTGGATGCATAACCGTTTCGGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGA
66 TCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGA
* * * ** * ***
21560 TGAATAATCGTTTTGGCACTAAGTTTGTATTT
131 TGAATAACCGGTTTGGCACCAAGAGTGCAAAA
** *
21592 CAAAAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTTA
1 CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCA
*
21657 TCCTATGTGGATGAATAATCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGA
66 TCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGA
* *
21722 TGAATAACCGGTTTGGTACCATGAGTGCAAAA
131 TGAATAACCGGTTTGGCACCAAGAGTGCAAAA
*
21754 CACGGAATTCAT
1 CACGAAATTCAT
21766 AATATATTTA
Statistics
Matches: 149, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
162 149 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (162 bp):
CACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCA
TCCTATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGA
TGAATAACCGGTTTGGCACCAAGAGTGCAAAA
Found at i:21796 original size:162 final size:162
Alignment explanation
Indices: 21448--21804 Score: 401
Period size: 162 Copynumber: 2.2 Consensus size: 162
21438 TCGTCCTTTG
* * * * *
21448 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGCATAA
1 TGGATGAATAACCATATAGGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAA
* * * * *
21513 CCGTTTCGGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTTGGCA
66 CCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGGTTTGGCA
* ** * *** ** *
21578 CTAAGTTTGTATTTCAAAAAATTCATCCTATG
131 CCAAGAGTGCAAAACAAAAAATTCATAATATA
* * * *
21610 TGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTTATCCTATGTGGATGAATAA
1 TGGATGAATAACCATATAGGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAA
* *
21675 TCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGGTTTGGTA
66 CCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGGTTTGGCA
* ***
21740 CCATGAGTGCAAAACACGGAATTCATAATATA
131 CCAAGAGTGCAAAACAAAAAATTCATAATATA
** *
21772 TTTATGAATGACCATATAGGCACTATAG-GTGCA
1 TGGATGAATAACCATATAGGCACTA-AGTGTGCA
21805 CTATAAAGAA
Statistics
Matches: 164, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
162 162 0.99
163 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (162 bp):
TGGATGAATAACCATATAGGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAA
CCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGGTTTGGCA
CCAAGAGTGCAAAACAAAAAATTCATAATATA
Found at i:30660 original size:21 final size:21
Alignment explanation
Indices: 30634--30673 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30624 CCCCATTTGA
*
30634 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
30655 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
30674 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:36643 original size:22 final size:23
Alignment explanation
Indices: 36617--36663 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
36607 ATATAATAAA
*
36617 TAATATTTTTATTATAAAAA-CT
1 TAATATTATTATTATAAAAATCT
*
36639 TAATATTATTATTTTAAAAATCT
1 TAATATTATTATTATAAAAATCT
36662 TA
1 TA
36664 GAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTATTATTATAAAAATCT
Found at i:37026 original size:13 final size:13
Alignment explanation
Indices: 36994--37056 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
36984 TATTAAAACA
36994 ATAATATAATAAT
1 ATAATATAATAAT
* * *
37007 ATCATATATTATT
1 ATAATATAATAAT
37020 ATAATATAACTAACT
1 ATAATATAA-TAA-T
37035 AT-ATAATAATAAT
1 ATAAT-ATAATAAT
37048 AATAATATA
1 -ATAATATA
37057 TATTATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
13 18 0.46
14 12 0.31
15 9 0.23
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:37040 original size:12 final size:10
Alignment explanation
Indices: 36997--37058 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 10
36987 TAAAACAATA
36997 ATATAATAAT
1 ATATAATAAT
37007 ATCAT-AT-AT
1 AT-ATAATAAT
*
37016 -TATTATAAT
1 ATATAATAAT
*
37025 ATA-ACTAACT
1 ATATAATAA-T
37035 ATATAATAAT
1 ATATAATAAT
37045 A-ATAATAAT
1 ATATAATAAT
37054 ATATA
1 ATATA
37059 TTATTAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.07
9 16 0.38
10 15 0.36
11 6 0.14
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAATAAT
Found at i:37474 original size:31 final size:31
Alignment explanation
Indices: 37431--37492 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
37421 AAAGCATAAA
*
37431 AATAATGATGATTTTAATGTCATAGAAAATT
1 AATAATGATGATTTTAATGTCACAGAAAATT
*
37462 AATAATGGTGATTTTAATGTCACAGAAAATT
1 AATAATGATGATTTTAATGTCACAGAAAATT
37493 CATACAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
AATAATGATGATTTTAATGTCACAGAAAATT
Found at i:39783 original size:128 final size:127
Alignment explanation
Indices: 39528--39843 Score: 348
Period size: 128 Copynumber: 2.5 Consensus size: 127
39518 AAGTTGAACA
* * * * ** * *
39528 AATGCTTCTACTTTCATTGGAATATGTAGTTTTAATATGCGCCAATATTGATAAATTGAACGGTA
1 AATGCTTCTACTTTCATTGGAATATGTAGTTTTGATACGCACCAATATTGATTAATAAAATGGCA
* * * * ** * * *
39593 TCGTTTTTTCTTTAGAATTTTCATTAAGACATCGTCGTTTTGAAGTGTGTTTTTACCGGTTC
66 TCGTTTATTCTATAGAATTTTCATTAAAACATCATCGTTTTGAAGAATGATTCTACCAGTTC
* *
39655 AATGCTTCTATTTTTCATTGGAATATGTAGTTTTGATACGCACCGATATTGATTAATAAAATGGC
1 AATGCTTCTA-CTTTCATTGGAATATGTAGTTTTGATACGCACCAATATTGATTAATAAAATGGC
* * * * *
39720 GTTGTTATATT-TATAGAATTTTGATTAAAACGTCATCGTTTTGAAGAATGATTCTATCAGTTC
65 ATCGTT-TATTCTATAGAATTTTCATTAAAACATCATCGTTTTGAAGAATGATTCTACCAGTTC
* ** *
39783 AATGCTTCTAGTTTCATTGGAATATGTAGTTTTGATACATACCAATAATGA-TAATAAAATG
1 AATGCTTCTACTTTCATTGGAATATGTAGTTTTGATACGCACCAATATTGATTAATAAAATG
39844 TTGTGTTTAG
Statistics
Matches: 158, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
126 10 0.06
127 46 0.29
128 99 0.63
129 3 0.02
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (127 bp):
AATGCTTCTACTTTCATTGGAATATGTAGTTTTGATACGCACCAATATTGATTAATAAAATGGCA
TCGTTTATTCTATAGAATTTTCATTAAAACATCATCGTTTTGAAGAATGATTCTACCAGTTC
Found at i:47943 original size:4 final size:4
Alignment explanation
Indices: 47934--47965 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
47924 TAGCCTGTGA
*
47934 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
47966 TAGAACGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:50657 original size:48 final size:46
Alignment explanation
Indices: 50586--50678 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 46
50576 TGATTCATCA
50586 TTCTCTAACAAGCAAAATGAAAATGGTAAAGAAACTATTAAATTATAT
1 TTCTCTAACAAGCAAAATGAAAATGGT-AA-AAACTATTAAATTATAT
* *
50634 TTCTCTGACAAGCAAAATGAAAATGGTAAAAATTATTAAATTATA
1 TTCTCTAACAAGCAAAATGAAAATGGTAAAAACTATTAAATTATA
50679 ATTCAATTCG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 15 0.35
47 2 0.05
48 26 0.60
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (46 bp):
TTCTCTAACAAGCAAAATGAAAATGGTAAAAACTATTAAATTATAT
Found at i:54316 original size:19 final size:20
Alignment explanation
Indices: 54294--54335 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54284 ATACTTTTGG
*
54294 AATTATTTA-TTTTTTTAAT
1 AATTATTTAGATTTTTTAAT
*
54313 AATTCTTTAGATTTTTTAAT
1 AATTATTTAGATTTTTTAAT
54333 AAT
1 AAT
54336 CTATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
AATTATTTAGATTTTTTAAT
Found at i:54345 original size:17 final size:20
Alignment explanation
Indices: 54304--54345 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
54294 AATTATTTAT
*
54304 TTTTTTAATAATTCTTTAGA
1 TTTTTTAATAATTCTATAGA
54324 TTTTTTAATAA-TCTATA-A
1 TTTTTTAATAATTCTATAGA
54342 TTTT
1 TTTT
54346 CATGTGACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTAATAATTCTATAGA
Found at i:56686 original size:56 final size:55
Alignment explanation
Indices: 56607--56757 Score: 155
Period size: 57 Copynumber: 2.7 Consensus size: 55
56597 TATGACAAAT
* * * *
56607 ATTTTGAATTAGTCCCCAAACTTTTGAACATACCAATTCAT-CTCTAAACTATGACTC
1 ATTTTAAATTGGT-CCCAAACTTTTGAACATTCCAATTCATCCTCAAAAC-ATGAC-C
56664 ATTTTAAATTGGTCCCAAAC-TTTGAACATTCCAAATTCATCCTCAAAACATGACC
1 ATTTTAAATTGGTCCCAAACTTTTGAACATTCC-AATTCATCCTCAAAACATGACC
* *
56719 CTTATTCTAATTAGG-CCTCAAACTTTTGAACATTCCAAT
1 ATT-TT-AAATT-GGTCC-CAAACTTTTGAACATTCCAAT
56758 AACATCCCCC
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
55 14 0.17
56 21 0.26
57 24 0.30
58 10 0.12
59 12 0.15
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (55 bp):
ATTTTAAATTGGTCCCAAACTTTTGAACATTCCAATTCATCCTCAAAACATGACC
Found at i:56710 original size:28 final size:28
Alignment explanation
Indices: 56623--56710 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
56613 AATTAGTCCC
*
56623 CAAACTTTTGAACATACC-AATTCAT-CT
1 CAAAC-TTTGAACATTCCAAATTCATCCT
* * ** **
56650 CTAAACTATGACTCATTTTAAATTGGTCC-
1 C-AAACTTTGA-ACATTCCAAATTCATCCT
56679 CAAACTTTGAACATTCCAAATTCATCCT
1 CAAACTTTGAACATTCCAAATTCATCCT
56707 CAAA
1 CAAA
56711 ACATGACCCT
Statistics
Matches: 43, Mismatches: 13, Indels: 9
0.66 0.20 0.14
Matches are distributed among these distances:
27 17 0.40
28 19 0.44
29 6 0.14
30 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (28 bp):
CAAACTTTGAACATTCCAAATTCATCCT
Found at i:56958 original size:26 final size:27
Alignment explanation
Indices: 56922--56986 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
56912 CCCATACCCA
56922 TTAGGTGCCTAAA-CCTTTTGATCAAT
1 TTAGGTGCCTAAATCCTTTTGATCAAT
56948 TTAGGTGCCTAAATCCTTTTGATCAAT
1 TTAGGTGCCTAAATCCTTTTGATCAAT
56975 TTAGGTGCCTAA
1 TTAGGTGCCTAA
56987 TGTTTCAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 13 0.34
27 25 0.66
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
TTAGGTGCCTAAATCCTTTTGATCAAT
Found at i:58408 original size:18 final size:18
Alignment explanation
Indices: 58385--58443 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
58375 TATATATAAT
58385 TTTAAAAGTAAAATATTA
1 TTTAAAAGTAAAATATTA
* * *
58403 TTTAAAAATAATATATAA
1 TTTAAAAGTAAAATATTA
58421 TTTATAAAAGTAAAATA-TA
1 -TT-TAAAAGTAAAATATTA
58440 TTTA
1 TTTA
58444 TTAAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 2 0.06
18 17 0.52
19 3 0.09
20 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTAAAAGTAAAATATTA
Found at i:58409 original size:40 final size:39
Alignment explanation
Indices: 58364--58452 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 39
58354 TAATAAAACA
58364 TTAAAAAATAATATATATAATTT-TAAAAGTAAAATATTAT
1 TTAAAAAATAA-ATATATAATTTATAAAAGTAAAATA-TAT
58404 TT-AAAAAT-AATATATAATTTATAAAAGTAAAATATAT
1 TTAAAAAATAAATATATAATTTATAAAAGTAAAATATAT
58441 TTATTAAAAATA
1 TTA--AAAAATA
58453 TCAGAAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
37 16 0.36
38 14 0.32
39 6 0.14
40 8 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (39 bp):
TTAAAAAATAAATATATAATTTATAAAAGTAAAATATAT
Found at i:58425 original size:22 final size:20
Alignment explanation
Indices: 58367--58452 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
58357 TAAAACATTA
*
58367 AAAAATAATATATATAATT-TT
1 AAAAATAA-A-ATATATTTATT
* *
58388 AAAAGTAAAATAT-TAT-TT
1 AAAAATAAAATATATTTATT
*
58406 AAAAATAATATATAATTTA-T
1 AAAAATAAAATAT-ATTTATT
*
58426 AAAAGTAAAATATATTTATT
1 AAAAATAAAATATATTTATT
58446 AAAAATA
1 AAAAATA
58453 TCAGAAAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 14 0.27
19 9 0.17
20 22 0.42
21 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATAAAATATATTTATT
Found at i:58438 original size:20 final size:20
Alignment explanation
Indices: 58378--58449 Score: 89
Period size: 19 Copynumber: 3.8 Consensus size: 20
58368 AAAATAATAT
58378 ATATAATTT-TAAAAGTAAA
1 ATATAATTTATAAAAGTAAA
* *
58397 ATATTATTTA-AAAA-TAAT
1 ATATAATTTATAAAAGTAAA
58415 ATATAATTTATAAAAGTAAA
1 ATATAATTTATAAAAGTAAA
58435 ATAT-ATTTATTAAAA
1 ATATAATTTA-TAAAA
58450 ATATCAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
18 12 0.27
19 21 0.47
20 12 0.27
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
ATATAATTTATAAAAGTAAA
Found at i:58442 original size:37 final size:39
Alignment explanation
Indices: 58367--58443 Score: 124
Period size: 37 Copynumber: 2.0 Consensus size: 39
58357 TAAAACATTA
58367 AAAAATAATATATATAATTTTAAAAGTAAAATATTATTT
1 AAAAATAATATATATAATTTTAAAAGTAAAATATTATTT
58406 AAAAAT-A-ATATATAATTTATAAAAGTAAAATA-TATTT
1 AAAAATAATATATATAATTT-TAAAAGTAAAATATTATTT
58443 A
1 A
58444 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
37 17 0.46
38 14 0.38
39 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (39 bp):
AAAAATAATATATATAATTTTAAAAGTAAAATATTATTT
Done.