Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002081.1 Hibiscus syriacus cultivar Beakdansim tig00004251_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: 60317
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2710 original size:28 final size:29
Alignment explanation
Indices: 2677--2732 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 29
2667 AAACATGATT
2677 TATTTTATTA-ATTTTTTATA-ATATATCA
1 TATTTTATTATA-TTTTTATACATATATCA
2705 TATTTTATTATCATTTTTATACATATAT
1 TATTTTATTAT-ATTTTTATACATATAT
2733 TATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 10 0.40
29 8 0.32
30 7 0.28
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTTATTATATTTTTATACATATATCA
Found at i:3092 original size:34 final size:33
Alignment explanation
Indices: 3028--3093 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
3018 ACAATTGTAA
3028 AATATTTATATTTTTCTTTAAAAAATTAAATTC
1 AATATTTATATTTTTCTTTAAAAAATTAAATTC
*
3061 AATATTTATATAATTTT-TTTACAAAATTAAATT
1 AATATTTATAT--TTTTCTTTAAAAAATTAAATT
3094 ATAAAAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 11 0.37
34 15 0.50
35 4 0.13
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (33 bp):
AATATTTATATTTTTCTTTAAAAAATTAAATTC
Found at i:4733 original size:23 final size:23
Alignment explanation
Indices: 4689--4763 Score: 114
Period size: 23 Copynumber: 3.2 Consensus size: 23
4679 GAGTAGAGGG
* *
4689 TTCTACGCGGTTCTTTTGGGACAA
1 TTCTACGTGG-TCCTTTGGGACAA
4713 TTCTACGTGGTCCTTTGGGACAA
1 TTCTACGTGGTCCTTTGGGACAA
*
4736 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTTGGGACAA
4759 TTCTA
1 TTCTA
4764 TGCTATCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 39 0.81
24 9 0.19
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (23 bp):
TTCTACGTGGTCCTTTGGGACAA
Found at i:4906 original size:23 final size:23
Alignment explanation
Indices: 4706--4906 Score: 188
Period size: 23 Copynumber: 8.7 Consensus size: 23
4696 CGGTTCTTTT
* * *
4706 GGGACAATTCTACGTGGTCCTTT
1 GGGACATTTCTATGTGGTCCTTC
* * *
4729 GGGACAATTCTACGTGGTCCTTT
1 GGGACATTTCTATGTGGTCCTTC
* *
4752 GGGACATTTCTATGCT-ATCATTC
1 GGGACATTTCTATG-TGGTCCTTC
* *
4775 GGGACATTTCTATGCGATCCTTC
1 GGGACATTTCTATGTGGTCCTTC
** * * *
4798 GAAACATATCTATGCGATCCTTC
1 GGGACATTTCTATGTGGTCCTTC
*
4821 GGGACATATCTATGTGGTCCTTC
1 GGGACATTTCTATGTGGTCCTTC
* *
4844 GGGACATATATATGTGGTCCTTC
1 GGGACATTTCTATGTGGTCCTTC
* * *
4867 GGGACATATCTATGTGGTCATTT
1 GGGACATTTCTATGTGGTCCTTC
*
4890 GGGACATTTCTACGTGG
1 GGGACATTTCTATGTGG
4907 CACTTCAGTG
Statistics
Matches: 156, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
23 155 0.99
24 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (23 bp):
GGGACATTTCTATGTGGTCCTTC
Found at i:7980 original size:40 final size:40
Alignment explanation
Indices: 7925--8003 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
7915 ATGTTACTAC
*
7925 TTGTATATATAGTGGATTTTGCTGTTTGATATAGAACTGT
1 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTGT
7965 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTG
1 TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTG
8004 AGCTTACAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (40 bp):
TTGTATATATAGTGGATTTTGCCGTTTGATATAGAACTGT
Found at i:13888 original size:20 final size:20
Alignment explanation
Indices: 13863--13907 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
13853 ATGGTTACCA
13863 AGGGATTTATGTTTTTTGAT
1 AGGGATTTATGTTTTTTGAT
13883 AGGGATTTATGTTTTTTGAT
1 AGGGATTTATGTTTTTTGAT
13903 AGGGA
1 AGGGA
13908 CGGATGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (20 bp):
AGGGATTTATGTTTTTTGAT
Found at i:13918 original size:21 final size:20
Alignment explanation
Indices: 13871--13918 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13861 CAAGGGATTT
***
13871 ATGTTTTTTGATAGGGATTT
1 ATGTTTTTTGATAGGGACGG
13891 ATGTTTTTTGATAGGGACGG
1 ATGTTTTTTGATAGGGACGG
*
13911 ATGATTTT
1 ATGTTTTT
13919 GGCTCACTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.50
Consensus pattern (20 bp):
ATGTTTTTTGATAGGGACGG
Found at i:16256 original size:2 final size:2
Alignment explanation
Indices: 16249--16276 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16239 AGCTTGCTTC
16249 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16277 AGATATTTCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20499 original size:23 final size:23
Alignment explanation
Indices: 20473--20520 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
20463 TCATGACAGT
20473 GGCATGTCTCGTTCCTGGTCCGG
1 GGCATGTCTCGTTCCTGGTCCGG
20496 GGCATGTCTCGTTCCTGGTCCGG
1 GGCATGTCTCGTTCCTGGTCCGG
20519 GG
1 GG
20521 ATCAAGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.29, G:0.38, T:0.29
Consensus pattern (23 bp):
GGCATGTCTCGTTCCTGGTCCGG
Found at i:28881 original size:7 final size:7
Alignment explanation
Indices: 28871--28908 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
28861 ACCCAAACTA
*
28871 TAAACCT
1 TAAACCC
*
28878 TAAATCC
1 TAAACCC
28885 TAAACCC
1 TAAACCC
28892 TAAACCC
1 TAAACCC
28899 TAAACCC
1 TAAACCC
28906 TAA
1 TAA
28909 CTCTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:28889 original size:21 final size:21
Alignment explanation
Indices: 28859--28908 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
28849 ACCCTACCTC
* *
28859 AAACCC-AAACTATAAACCTT
1 AAACCCTAAACCATAAACCCT
* *
28879 AAATCCTAAACCCTAAACCCT
1 AAACCCTAAACCATAAACCCT
28900 AAACCCTAA
1 AAACCCTAA
28909 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCATAAACCCT
Found at i:31680 original size:18 final size:18
Alignment explanation
Indices: 31657--31705 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
31647 CAACCCCTCC
*
31657 ACAAGTGTCACCCCTAAT
1 ACAAGTGCCACCCCTAAT
* *
31675 ACAAGTGCCACTCTTAAT
1 ACAAGTGCCACCCCTAAT
31693 ACAAGTGCCACCC
1 ACAAGTGCCACCC
31706 TGGGACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (18 bp):
ACAAGTGCCACCCCTAAT
Found at i:33079 original size:12 final size:12
Alignment explanation
Indices: 33064--33088 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33054 TTACATTAAA
33064 AAATAATATTTT
1 AAATAATATTTT
33076 AAATAATATTTT
1 AAATAATATTTT
33088 A
1 A
33089 CTAAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:33081 original size:44 final size:44
Alignment explanation
Indices: 32972--33081 Score: 143
Period size: 45 Copynumber: 2.5 Consensus size: 44
32962 TTTCTTGTAG
32972 AAAAAATAATATTTTAAATAACACCAAATATTAACATTTCAGGT
1 AAAAAATAATATTTTAAATAACACCAAATATTAACATTTCAGGT
* * * *
33016 ATAAAAATAACATTTTAAATAACGATC-AATATTAATATTTACA-TT
1 A-AAAAATAATATTTTAAATAAC-ACCAAATATTAACATTT-CAGGT
33061 AAAAAATAATATTTTAAATAA
1 AAAAAATAATATTTTAAATAA
33082 TATTTTACTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 20 0.34
45 34 0.59
46 4 0.07
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (44 bp):
AAAAAATAATATTTTAAATAACACCAAATATTAACATTTCAGGT
Found at i:34903 original size:95 final size:96
Alignment explanation
Indices: 34708--34904 Score: 360
Period size: 95 Copynumber: 2.1 Consensus size: 96
34698 TGGGCTGAGG
*
34708 GTATAAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
1 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
*
34773 TGTGAGAAGAGTATCGATACCCCTTCAAGGG
66 TGTGAGAAGAGTATCGATACCCCTTCAAGGA
34804 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGC-AAAATTCAAAAGGTT
1 GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
*
34868 TGTGAGGAGAGTATCGATACCCCTTCAAGGA
66 TGTGAGAAGAGTATCGATACCCCTTCAAGGA
34899 GTATCA
1 GTATCA
34905 ATACTACTCA
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 50 0.51
96 48 0.49
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (96 bp):
GTATCAGTATTGTTCATACAATACTGATACTGCTCGTCGAGAGTTGGGCAAAAATTCAAAAGGTT
TGTGAGAAGAGTATCGATACCCCTTCAAGGA
Found at i:34987 original size:18 final size:19
Alignment explanation
Indices: 34964--35013 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
34954 GGCAATTTTG
*
34964 GTATCGATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
*
34982 GTATCGATACTGAGGGTAGA
1 GTATCGATACTCAGGG-AGA
35002 GTATCGATACTC
1 GTATCGATACTC
35014 CCAGTAGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:35107 original size:20 final size:20
Alignment explanation
Indices: 35081--35137 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
35071 TGATACACAT
*
35081 GAGAGTATCGATACTGT-GG
1 GAGAGTATCGATACTGTCAG
* *
35100 GTAGAGTATCAATACTCTCAG
1 G-AGAGTATCGATACTGTCAG
35121 GAGAAGTATCGATACTG
1 GAG-AGTATCGATACTG
35138 AGGCTTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (20 bp):
GAGAGTATCGATACTGTCAG
Found at i:37071 original size:14 final size:14
Alignment explanation
Indices: 37033--37075 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
37023 TAGATTATAT
* * *
37033 GTTCGTTTATATTT
1 GTTCATTTATGTTC
37047 GTTCATTTATGTTC
1 GTTCATTTATGTTC
37061 GTTCATTTATGTTC
1 GTTCATTTATGTTC
37075 G
1 G
37076 AACAGAGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:37456 original size:16 final size:16
Alignment explanation
Indices: 37431--37462 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
37421 AAATTTTTTT
37431 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
37447 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
37463 CTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:37621 original size:31 final size:32
Alignment explanation
Indices: 37577--37647 Score: 126
Period size: 31 Copynumber: 2.2 Consensus size: 32
37567 GATAATAACT
*
37577 AATACTATCACCTTTCTTCTTATATGGCCAAC
1 AATACGATCACCTTTCTTCTTATATGGCCAAC
37609 AATACGAT-ACCTTTCTTCTTATATGGCCAAC
1 AATACGATCACCTTTCTTCTTATATGGCCAAC
37640 AATACGAT
1 AATACGAT
37648 TATTTGGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (32 bp):
AATACGATCACCTTTCTTCTTATATGGCCAAC
Found at i:39690 original size:49 final size:49
Alignment explanation
Indices: 39618--39717 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
39608 AAAGACACTT
39618 TTTTATGTGGTTAAAGAGAGTGTCAGACGGAGGAAGATACAACGAAATG
1 TTTTATGTGGTTAAAGAGAGTGTCAGACGGAGGAAGATACAACGAAATG
* *
39667 TTTTATGTGGTTAAAGAGAGTGTCATACGGATGAAGATACAACGAAATG
1 TTTTATGTGGTTAAAGAGAGTGTCAGACGGAGGAAGATACAACGAAATG
39716 TT
1 TT
39718 AAATTGCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (49 bp):
TTTTATGTGGTTAAAGAGAGTGTCAGACGGAGGAAGATACAACGAAATG
Found at i:46784 original size:19 final size:19
Alignment explanation
Indices: 46760--46796 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46750 ATGACCAACA
*
46760 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
46779 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
46797 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:46895 original size:21 final size:20
Alignment explanation
Indices: 46880--46917 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46870 TGCGATTTTA
46880 GAAAATCGCAACGCGATTAT
1 GAAAATCGCAACGCGATTAT
**
46900 GACTATCGCAACGCGATT
1 GAAAATCGCAACGCGATT
46918 CTGACTGTCG
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:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGCGATTAT
Found at i:46909 original size:20 final size:20
Alignment explanation
Indices: 46884--46932 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
46874 ATTTTAGAAA
46884 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
46904 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
46924 GTCGCAACG
1 ATCGCAACG
46933 TTGAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:47779 original size:24 final size:24
Alignment explanation
Indices: 47752--47804 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
47742 GTATTCGAAA
47752 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
47776 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
47800 TTTGA
1 TTTGA
47805 AGATGTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:50180 original size:21 final size:21
Alignment explanation
Indices: 50120--50189 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
50110 ATGAATCGGG
*
50120 CTCTTGAATGGTGGGATGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * * **
50141 CTCTTCAACGATGACAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
50162 CTCTTGAATGGTGGGAGGGGA-
1 CTCTTGAATGGTGGGA-GGGAC
50183 CTCTTGA
1 CTCTTGA
50190 GGGATGATAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:50748 original size:20 final size:20
Alignment explanation
Indices: 50723--50761 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
50713 GAATAGTTTC
50723 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
50743 TGAAACTTAAAATCGCAAC
1 TGAAACTTAAAATCGCAAC
50762 GCGAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (20 bp):
TGAAACTTAAAATCGCAACA
Found at i:50876 original size:19 final size:19
Alignment explanation
Indices: 50826--50897 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
50816 CGAAACTAAA
* *
50826 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTGA-T
* * *
50846 TTTGCGTTGCGATTTTGGT
1 TTCGCATTGCGATTTTGAT
*
50865 TTCGCATTGCGATTTTTAT
1 TTCGCATTGCGATTTTGAT
50884 TTCGCATTGCGATT
1 TTCGCATTGCGATT
50898 ATCCCGTTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (19 bp):
TTCGCATTGCGATTTTGAT
Found at i:50948 original size:19 final size:19
Alignment explanation
Indices: 50904--50969 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
50894 GATTATCCCG
*
50904 TTGCGATAGTCAAATTCGCG-
1 TTGCGATAGTC-ATTTC-CGT
50924 TTGCGATAGTCATTTCCGT
1 TTGCGATAGTCATTTCCGT
* *
50943 TTGCGATAGTTATTTTCGT
1 TTGCGATAGTCATTTCCGT
50962 GTTGCGAT
1 -TTGCGAT
50970 TTTTAAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
18 2 0.05
19 21 0.51
20 18 0.44
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (19 bp):
TTGCGATAGTCATTTCCGT
Found at i:50966 original size:20 final size:20
Alignment explanation
Indices: 50903--50969 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
50893 CGATTATCCC
** *
50903 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
*
50923 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTTTCGT
*
50943 -TTGCGATAGTTATTTTCGT
1 GTTGCGATAGTCATTTTCGT
50962 GTTGCGAT
1 GTTGCGAT
50970 TTTTAAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:52890 original size:20 final size:20
Alignment explanation
Indices: 52867--52966 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 20
52857 TCTGAAACTT
* *
52867 AAAATTGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
**
52887 AAAATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** **
52907 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
52927 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
52946 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
52966 A
1 A
52967 CTATCACAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
19 14 0.21
20 54 0.79
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:52968 original size:59 final size:60
Alignment explanation
Indices: 52873--52992 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 60
52863 ACTTAAAATT
* ** *
52873 GCAACACGAAAATGAAAATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATC
1 GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
* *
52933 GCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCACAATGCGAATTTGACTATC
1 GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
52992 G
1 G
52993 TTGTGATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
59 47 0.87
60 7 0.13
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (60 bp):
GCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCACAACGCGAATTTGACTATC
Found at i:53489 original size:20 final size:20
Alignment explanation
Indices: 53466--53570 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
53456 AAATCGAAAC
53466 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
53486 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
*
53507 GTGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* * * * *
53527 ACGAT-TTACATATTCGCATT
1 GCGATAGT-CAGAATCGCGTT
*
53547 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
53567 GCGA
1 GCGA
53571 ATCTAGAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.05
20 44 0.69
21 15 0.23
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:53564 original size:40 final size:41
Alignment explanation
Indices: 53466--53566 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 41
53456 AAATCGAAAC
* ** *
53466 GCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTT
1 GCGATAGTCAGAATCGCGTTACGATTACATATTATCGCATT
*
53507 GTGATAGTCAGAATCGCGTTACGATTTACATA-T-TCGCATT
1 GCGATAGTCAGAATCGCGTTACGA-TTACATATTATCGCATT
*
53547 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
53567 GCGAATCTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 24 0.46
41 23 0.44
42 5 0.10
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
GCGATAGTCAGAATCGCGTTACGATTACATATTATCGCATT
Found at i:53608 original size:20 final size:19
Alignment explanation
Indices: 53585--53630 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53575 AGAAACTGAT
* *
53585 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
53605 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
53624 TTGCGAT
1 TTGCGAT
53631 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:53620 original size:19 final size:19
Alignment explanation
Indices: 53596--53632 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53586 TGCGATACTG
*
53596 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
53615 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
53633 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:58942 original size:13 final size:13
Alignment explanation
Indices: 58924--58948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58914 ATATAAAATA
58924 TAATAAAATTTAG
1 TAATAAAATTTAG
58937 TAATAAAATTTA
1 TAATAAAATTTA
58949 TTATTTACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TAATAAAATTTAG
Done.