Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010093.1 Kokia drynarioides strain JFW-HI SEQ_124874, 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: 27586
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Warning! 175 characters in sequence are not A, C, G, or T
Found at i:643 original size:30 final size:30
Alignment explanation
Indices: 602--728 Score: 145
Period size: 29 Copynumber: 4.4 Consensus size: 30
592 ACCCTTTCAC
602 CCTCG-AACTTCCAAAAATCCCATTTTTGA
1 CCTCGAAACTTCCAAAAATCCCATTTTTGA
* * *
631 CCTCGAAACTTCCAAAAATTCTATTCTT-A
1 CCTCGAAACTTCCAAAAATCCCATTTTTGA
* * *
660 CCCCAAAACTTCC-AAAATCCCAATTTTGA
1 CCTCGAAACTTCCAAAAATCCCATTTTTGA
*
689 CCTCGAAACTTCCAAAAATCCTA-TTTTGA
1 CCTCGAAACTTCCAAAAATCCCATTTTTGA
* *
718 CCCCAAAACTT
1 CCTCGAAACTT
729 TCGTTTTCAC
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 10 0.12
29 44 0.54
30 27 0.33
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (30 bp):
CCTCGAAACTTCCAAAAATCCCATTTTTGA
Found at i:687 original size:58 final size:59
Alignment explanation
Indices: 607--728 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 59
597 TTCACCCTCG
* *
607 AACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTCTT-ACCCCAA
1 AACTTCCAAAAATCCCAATTTTGACCTCGAAACTTCCAAAAATCCTATT-TTGACCCCAA
666 AACTTCC-AAAATCCCAATTTTGACCTCGAAACTTCCAAAAATCCTATTTTGACCCCAA
1 AACTTCCAAAAATCCCAATTTTGACCTCGAAACTTCCAAAAATCCTATTTTGACCCCAA
724 AACTT
1 AACTT
729 TCGTTTTCAC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
57 2 0.03
58 51 0.85
59 7 0.12
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (59 bp):
AACTTCCAAAAATCCCAATTTTGACCTCGAAACTTCCAAAAATCCTATTTTGACCCCAA
Found at i:755 original size:30 final size:30
Alignment explanation
Indices: 720--905 Score: 109
Period size: 30 Copynumber: 6.3 Consensus size: 30
710 TATTTTGACC
* *
720 CCAAAACTTTCGTTTTCACCCTTGAAACTT
1 CCAAAAATTTCGTTTTCACCCTCGAAACTT
* *
750 CCAAAAATCTCGTTTTTGA-CCTCGAAACTT
1 CCAAAAATTTCG-TTTTCACCCTCGAAACTT
** * * *
780 TTAAAAATTTCATTTTCACCCCCG-AACGT
1 CCAAAAATTTCGTTTTCACCCTCGAAACTT
* * * *
809 CCAAAAACTCCATTCTCGA-CCTCGAAAC-T
1 CCAAAAATTTCGTTTTC-ACCCTCGAAACTT
838 CTC-AAAATTACTC-TTTT-ACCCTC-AAACTT
1 C-CAAAAATT--TCGTTTTCACCCTCGAAACTT
* * * * *
867 CCAAAAATTCCATTTTAAACCTTGAAACTT
1 CCAAAAATTTCGTTTTCACCCTCGAAACTT
897 CCAAAAATT
1 CCAAAAATT
906 ACCATTTTAC
Statistics
Matches: 120, Mismatches: 23, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
27 1 0.01
28 10 0.08
29 48 0.40
30 55 0.46
31 6 0.05
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.32
Consensus pattern (30 bp):
CCAAAAATTTCGTTTTCACCCTCGAAACTT
Found at i:830 original size:59 final size:58
Alignment explanation
Indices: 767--989 Score: 186
Period size: 58 Copynumber: 3.8 Consensus size: 58
757 TCTCGTTTTT
*
767 GACCTCGAAACTTTTAAAAATT-TCATTTTCACCCCCGAACGTCCAAAAACTCCATTCTC
1 GACCTCGAAAC-TCTAAAAATTATCATTTT-ACCCCCGAACGTCCAAAAACTCCATTCTC
* * * * * * *
826 GACCTCGAAACTCTCAAAATTACTC-TTTTACCCTCAAACTTCCAAAAATTCCATTTTA
1 GACCTCGAAACTCTAAAAATTA-TCATTTTACCCCCGAACGTCCAAAAACTCCATTCTC
* * * * * * **
884 AACCTTGAAACTTCCAAAAATTACCATTTTACTCCC-AGATGTCCAAAAACTTTATTCTC
1 GACCTCGAAAC-TCTAAAAATTATCATTTTACCCCCGA-ACGTCCAAAAACTCCATTCTC
* * *
943 GACCTCGAAACTCTCAAAATTA-CATTTTTA-CCCCGAATGTCTAAAAA
1 GACCTCGAAACTCTAAAAATTATCA-TTTTACCCCCGAACGTCCAAAAA
990 TCTCATTTTT
Statistics
Matches: 129, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
57 15 0.12
58 57 0.44
59 55 0.43
60 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.30
Consensus pattern (58 bp):
GACCTCGAAACTCTAAAAATTATCATTTTACCCCCGAACGTCCAAAAACTCCATTCTC
Found at i:866 original size:138 final size:137
Alignment explanation
Indices: 596--863 Score: 321
Period size: 138 Copynumber: 1.9 Consensus size: 137
586 AAAATTACCC
596 TTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTCTTAC
1 TTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTCTTAC
* * * *
661 CCCAAAACTTCCAAAATCCCAATTTTGACCTCGAAACTTCCAAAAATCCTATTTTGACCCCAAAA
66 CCCAAAACGTCCAAAAACCCAATTTCGACCTCGAAACTTCCAAAAATACTATTTTGACCCCAAAA
726 CTTTCGT
131 CTTTCGT
* * * **
733 TTTCACCCTTGAAACTTCCAAAAATCTCGTTTTTGACCTCGAAACTTTTAAAAATT-TCATT-TT
1 TTTCACCCTCG-AACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCT-ATTCTT
** * *
796 CACCCCCGAACGTCCAAAAACTCC-ATTCTCGACCTCGAAAC-TCTCAAAATTACTCTTTT-ACC
64 -ACCCCAAAACGTCCAAAAAC-CCAATT-TCGACCTCGAAACTTC-CAAAAATACTATTTTGACC
858 CTCAAA
125 C-CAAA
864 CTTCCAAAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
137 13 0.12
138 68 0.61
139 30 0.27
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (137 bp):
TTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTCTTAC
CCCAAAACGTCCAAAAACCCAATTTCGACCTCGAAACTTCCAAAAATACTATTTTGACCCCAAAA
CTTTCGT
Found at i:874 original size:29 final size:29
Alignment explanation
Indices: 841--915 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
831 CGAAACTCTC
841 AAAATTACTC-TTTTACCCTCAAACTTCCA
1 AAAATTAC-CATTTTACCCTCAAACTTCCA
* *
870 AAAATT-CCATTTTAAACCTTGAAACTTCCA
1 AAAATTACCATTTT--ACCCTCAAACTTCCA
900 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
916 TCCCAGATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 1 0.03
28 5 0.12
29 8 0.20
30 19 0.47
31 7 0.17
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCAAACTTCCA
Found at i:1000 original size:117 final size:116
Alignment explanation
Indices: 807--1029 Score: 294
Period size: 117 Copynumber: 1.9 Consensus size: 116
797 ACCCCCGAAC
807 GTCCAAAAACTCCATTCTCGACCTCGAAACTCTCAAAATTACTCTTTTACCCTCAAACTTCCAAA
1 GTCCAAAAACTCCATTCTCGACCTCGAAACTCTCAAAATTACTCTTTTACCCTCAAACTTCCAAA
*
872 AATTCCATTTTAAACCTTGAAA-CTTCCAAAAATTACCATTTTACTCCCAGAT
66 AATTCCATTTT-AACCCT-AAATCTTCCAAAAATTACCATTTTACTCCCAGAT
** * *
924 GTCCAAAAACTTTATTCTCGACCTCGAAACTCTCAAAATTACAT-TTTTACCC-CGAA-TGTCTA
1 GTCCAAAAACTCCATTCTCGACCTCGAAACTCTCAAAATTAC-TCTTTTACCCTCAAACT-TCCA
* *
986 AAAA-TCTCATTTTTAACCCTAAATTTTCCCAAAATTACCATTTT
64 AAAATTC-CA-TTTTAACCCTAAATCTTCCAAAAATTACCATTTT
1030 GCCTCCGAGA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
115 6 0.06
116 35 0.37
117 52 0.55
118 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (116 bp):
GTCCAAAAACTCCATTCTCGACCTCGAAACTCTCAAAATTACTCTTTTACCCTCAAACTTCCAAA
AATTCCATTTTAACCCTAAATCTTCCAAAAATTACCATTTTACTCCCAGAT
Found at i:1047 original size:28 final size:28
Alignment explanation
Indices: 1014--1076 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1004 CTAAATTTTC
*
1014 CCAAAATTACCATTTTGCCTCCGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
*
1042 CCAAAATTACCATTTTGCCCCCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
*
1070 CCGAAAT
1 CCAAAAT
1077 GTCTCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:11541 original size:30 final size:30
Alignment explanation
Indices: 11514--11728 Score: 290
Period size: 30 Copynumber: 7.2 Consensus size: 30
11504 TCGAACTTTT
11514 AAAAATCCCATTTTTAACCCCAAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
*
11544 AAAAATCCCATTTTT-ACCCCTAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
*
11573 AAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
*
11603 AAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
* ** *
11633 AAAAATCCCATTTTTGACCCTTAAATTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
* * *
11663 AAAAATTCTA-TTTTCACCCCAAAAACTTCC
1 AAAAATCCCATTTTTAACCCC-AAAACTTCC
* * *
11693 AAAAATCCCATTTTTTACCTCGAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCC
11723 AAAAAT
1 AAAAAT
11729 TTCGTTTTCA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
29 36 0.22
30 119 0.73
31 8 0.05
ACGTcount: A:0.39, C:0.30, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAAATCCCATTTTTAACCCCAAAACTTCC
Found at i:11713 original size:90 final size:89
Alignment explanation
Indices: 11514--11728 Score: 324
Period size: 90 Copynumber: 2.4 Consensus size: 89
11504 TCGAACTTTT
*
11514 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAAT
1 AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAAT
*
11579 CCCATTTTTAACCTCAAAACTTCC
66 CCCATTTTTAACCCCAAAACTTCC
* *
11603 AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTTGACCCTTAAATTTCCAAAAA
1 AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTT-ACCCCTAAACTTCCAAAAA
* * *
11668 TTCTA-TTTTCACCCCAAAAACTTCC
65 TCCCATTTTTAACCCC-AAAACTTCC
* *
11693 AAAAATCCCATTTTTTACCTCGAAACTTCCAAAAAT
1 AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAAT
11729 TTCGTTTTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
89 52 0.45
90 63 0.55
ACGTcount: A:0.39, C:0.30, G:0.01, T:0.31
Consensus pattern (89 bp):
AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAAT
CCCATTTTTAACCCCAAAACTTCC
Found at i:11757 original size:60 final size:59
Alignment explanation
Indices: 11514--11853 Score: 305
Period size: 60 Copynumber: 5.7 Consensus size: 59
11504 TCGAACTTTT
* * * * *
11514 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCC
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTCACCCCAAAACTTCC
* * * *
11573 AAAAATCCCATTTTTAACCTCAAAACTTCCAAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCA-TTTTCACCCCAAAACTTCC
* * * *
11633 AAAAATCCCATTTTTGACC-CTTAAATTTCCAAAAATTCTATTTTCACCCCAAAAACTTCC
1 AAAAATCCCATTTTTAACCTC-GAAACTTCCAAAAATTCCATTTTCACCCC-AAAACTTCC
* * * ** *
11693 AAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTTCGTTTTCACCCCCGAACATCC
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTCACCCCAAAACTTCC
* ** * ** *
11752 AAAAAAT-CCATTCTCGACCTCGAAAC-TCTC-AAAATTACCCTTTT-ACGATC-GAACTTCC
1 -AAAAATCCCATTTTTAACCTCGAAACTTC-CAAAAATT-CCATTTTCAC-CCCAAAACTTCC
* * * *
11810 AAAAATTCCATTTTAAACCTTGAAACTTCCAAAAATTACATTTT
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTT
11854 GCCCCCGGAT
Statistics
Matches: 236, Mismatches: 34, Indels: 23
0.81 0.12 0.08
Matches are distributed among these distances:
57 6 0.03
58 38 0.16
59 85 0.36
60 106 0.45
61 1 0.00
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTCACCCCAAAACTTCC
Found at i:11839 original size:30 final size:30
Alignment explanation
Indices: 11514--11853 Score: 257
Period size: 30 Copynumber: 11.5 Consensus size: 30
11504 TCGAACTTTT
* * *
11514 AAAAATCCCATTTTTAACCCCAAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * *
11544 AAAAATCCCATTTTT-ACCCCTAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
11573 AAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
11603 AAAAATCCCATTTTTAACCTCAAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * * *
11633 AAAAATCCCATTTTTGACC-CTTAAATTTCC
1 AAAAATTCCATTTTTAACCTC-GAAACTTCC
* * * *
11663 AAAAATTCTA-TTTTCACCCCAAAAACTTCC
1 AAAAATTCCATTTTTAACCTC-GAAACTTCC
* *
11693 AAAAATCCCATTTTTTACCTCGAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * * * * *
11723 AAAAATTTCGTTTTCACCCCCG-AACATCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * **
11752 AAAAAATCCATTCTCGACCTCGAAAC-TCTC
1 AAAAATTCCATTTTTAACCTCGAAACTTC-C
* *
11782 -AAAATTACC-CTTTT-ACGATCG-AACTTCC
1 AAAAATT-CCATTTTTAAC-CTCGAAACTTCC
* *
11810 AAAAATTCCATTTTAAACCTTGAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
*
11840 AAAAATTACATTTT
1 AAAAATTCCATTTT
11854 GCCCCCGGAT
Statistics
Matches: 255, Mismatches: 42, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.03
29 82 0.32
30 157 0.62
31 8 0.03
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCC
Found at i:11896 original size:116 final size:117
Alignment explanation
Indices: 11686--11988 Score: 373
Period size: 116 Copynumber: 2.6 Consensus size: 117
11676 TCACCCCAAA
* * *
11686 AACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTTCGTTTTCACCCCCGAACATC
1 AACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTCACCCCCGAACATC
* *
11751 CAAAAAATCCATTCTCGACCTCGAAACTCTCAAAATTACCCTTTTACGATCG
66 CAAAAAATCCATTCTCGACCACGAAACTCTCAAAATTACCCTTTTACCATCG
* * * * * **
11803 AACTTCCAAAAATTCCATTTTAAACCTTGAAACTTCCAAAAATTACATTTT-GCCCCCGGATGTC
1 AACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTCACCCCCGAACATC
* *
11867 CAAAAACTCCATTCTCGACCACGAAACTCTCAAAATTACCCTTTTACCCTCG
66 CAAAAAATCCATTCTCGACCACGAAACTCTCAAAATTACCCTTTTACCATCG
* * * *
11919 AA-TGTCTAAAAATCCCATTTTTAACC-CCAAATTTTCCCAAAATTACCA-TTTCACCCCCGAGA
1 AACT-TCCAAAAATCCCATTTTTAACCTCGAAA-CTTCCAAAAATTA-CATTTTCACCCCCGA-A
11981 -ATCCAAAA
62 CATCCAAAA
11989 TTACCATTTT
Statistics
Matches: 157, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
115 4 0.03
116 92 0.59
117 60 0.38
118 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (117 bp):
AACTTCCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTCACCCCCGAACATC
CAAAAAATCCATTCTCGACCACGAAACTCTCAAAATTACCCTTTTACCATCG
Found at i:13877 original size:152 final size:154
Alignment explanation
Indices: 13647--14050 Score: 573
Period size: 155 Copynumber: 2.6 Consensus size: 154
13637 TCTTGTTACG
* ** *
13647 GATTCTCCACAGCTCGTGTGAGTAGCATTTTGTATCTAACATCCCGACCCACAGCTCGTGTGAGC
1 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCCACAGCTCGTGTGAGC
* * *
13712 AGACCAATTTCACAGCTCGTGTGAGCATTACATGATAC-GGT-TGGTCTTAGATGTTCTA-CTAT
66 AGACCCATTTCACAGCTCGTGTGAGCATTACATGATACGGGTCTGGTCTTAGATGTCCTACCGA-
**
13774 TGGTTGAGGTCCTGCATTTATTGCA
130 TGACTGAGGTCCTGCATTTATTGCA
*
13799 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCAACCCACAGCTCGTGTGAGC
1 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCCACAGCTCGTGTGAGC
* *
13864 AGGCCCATTTCACAGCTCGTGTGAGCATTACATGATACGGGTGCTGGTCTTGGATGTCCTACCGA
66 AGACCCATTTCACAGCTCGTGTGAGCATTACATGATACGGGT-CTGGTCTTAGATGTCCTACCGA
* * **
13929 TGACTGAGGTCCTGTATTTGTTGTG
130 TGACTGAGGTCCTGCATTTATTGCA
* * *
13954 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCCATAGCTCATGTGAGT
1 GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCCACAGCTCGTGTGAGC
* *
14019 ATACCCATTTCACAGCTCGTGTGGGCA-TACAT
66 AGACCCATTTCACAGCTCGTGTGAGCATTACAT
14051 AATTACAATC
Statistics
Matches: 225, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
152 96 0.43
153 3 0.01
154 5 0.02
155 119 0.53
156 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (154 bp):
GATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTAACATCCCGACCCACAGCTCGTGTGAGC
AGACCCATTTCACAGCTCGTGTGAGCATTACATGATACGGGTCTGGTCTTAGATGTCCTACCGAT
GACTGAGGTCCTGCATTTATTGCA
Found at i:17962 original size:24 final size:24
Alignment explanation
Indices: 17930--17977 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17920 TGATGTGGAA
*
17930 CCAGTAGAAAATGAAGATCCAACT
1 CCAGTAGAAAATAAAGATCCAACT
17954 CCAGTAGAAAATAAAGATCCAACT
1 CCAGTAGAAAATAAAGATCCAACT
17978 TCGTGTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.17
Consensus pattern (24 bp):
CCAGTAGAAAATAAAGATCCAACT
Found at i:19912 original size:75 final size:74
Alignment explanation
Indices: 19789--19937 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 74
19779 GTTATGGAGA
19789 CCATTAGGCGTCGACTTGGTATCCCACCTAGGTCATACGGGGTTGATCTCCAGAATAGTCATTGC
1 CCATTAGGCGTCGACTTGGTATCCCACCTAGGTCATACGGGGTTGATCTCCAGAATAGTCATTGC
19854 GATTGTAGG
66 GATTGTAGG
*
19863 NCCATTGGGCGTCGACTTGGTATCCCACCTAGGTCATACGGGGTTGATCTCCAGAATAGTCATTG
1 -CCATTAGGCGTCGACTTGGTATCCCACCTAGGTCATACGGGGTTGATCTCCAGAATAGTCATTG
19928 CGATTGTAGG
65 CGATTGTAGG
19938 AGGTTTGATA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (74 bp):
CCATTAGGCGTCGACTTGGTATCCCACCTAGGTCATACGGGGTTGATCTCCAGAATAGTCATTGC
GATTGTAGG
Found at i:26903 original size:97 final size:97
Alignment explanation
Indices: 26728--26904 Score: 250
Period size: 97 Copynumber: 1.8 Consensus size: 97
26718 AACCTTGGAA
* * *
26728 AAGGGAATTCGATTATCCCGATTTGAAGAAAAGTCGTGCTAAGTAAGTTAAGGCATAAATTTTCA
1 AAGGGAATTCGATTATCCCGATTTGAAGAAAAATCGTGCTAAGTAAGTTAAGGAACAAATTTTCA
*
26793 AAACCAGAGATAAAGAAACATTACCTCGATTT
66 AAACCAGAAATAAAGAAACATTACCTCGATTT
* ** *
26825 AAGGGTATTCGATTATTTCGGTTTGAAGAAAAATCGTGCCT-AGTAAGTTAAGGAACAAATTTTC
1 AAGGGAATTCGATTATCCCGATTTGAAGAAAAATCGTG-CTAAGTAAGTTAAGGAACAAATTTTC
26889 AAAACCCA-AAATAAAG
65 AAAA-CCAGAAATAAAG
26905 GAATATTGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
97 65 0.93
98 5 0.07
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (97 bp):
AAGGGAATTCGATTATCCCGATTTGAAGAAAAATCGTGCTAAGTAAGTTAAGGAACAAATTTTCA
AAACCAGAAATAAAGAAACATTACCTCGATTT
Done.