Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000848.1 Kokia drynarioides strain JFW-HI SEQ_111950, 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: 23896
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:275 original size:96 final size:96
Alignment explanation
Indices: 96--282 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 96
86 GCGAGAAGAA
* ** * *
96 TATTTGATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATC
1 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACC
161 GAAGATAAGAAAACATTGCCTCGATTAAAGG
66 GAAGATAAGAAAACATTGCCTCGATTAAAGG
* *
192 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGTGCAA-ATTTTCGAAAC
1 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA-
*
256 CCGAA-ATAA-AAGAATATTGCCTCGATT
64 CCGAAGATAAGAA-AACATTGCCTCGATT
283 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 3 0.04
96 73 0.91
97 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACC
GAAGATAAGAAAACATTGCCTCGATTAAAGG
Found at i:703 original size:59 final size:59
Alignment explanation
Indices: 640--848 Score: 228
Period size: 59 Copynumber: 3.5 Consensus size: 59
630 TTTGGGGGGT
* *
640 AAAATGGTAATTTTGGAAGTTTAGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCA
1 AAAATGGGAATTTTGGAAGTTTCGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCA
* * * *
699 AAAATGGGATTTTTTGAAG-TTCGAGGGTAAAATAGTAAATTTTGGAAGGTTCGGGGTCA
1 AAAATGGGAATTTTGGAAGTTTCG-GGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCA
* * ** * *
758 AAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGT-AATTTTCAAAAGTTCAAGGGT--
1 AAAATGGGAATTTTGGAAGTTTCGGGGTAAAATGGTAAATTTTGGAAGGTTCGA-GGTCA
* *
815 AAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAA
1 AAAATGG-GAATTTTGGAAGTTTCGGGGT-AAAA
849 ATGGGATTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 7 0.06
58 32 0.25
59 85 0.67
60 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (59 bp):
AAAATGGGAATTTTGGAAGTTTCGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCA
Found at i:770 original size:88 final size:88
Alignment explanation
Indices: 591--858 Score: 278
Period size: 88 Copynumber: 3.0 Consensus size: 88
581 AAAGGGTAAT
* * * * * *
591 TTTTGAAAGGTTC-AGGGTCAAAAATGAGATATTTGGAAGTTTGGGGGGTAAAATGGT-AATTTT
1 TTTTGGAAGGTTCGA-GGTCAAAAATGGGATTTTTAGAAG-TTCGAGGGTAAAATGGTAAATTTT
* * *
654 GGAAGTTTAGGGGT--AAAATGGTAAA
64 GGAAGGTTCGGGGTCAAAAATGG--GA
* *
679 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGAAGTTCGAGGGTAAAATAGTAAATTTTGG
1 TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGTAAATTTTGG
744 AAGGTTCGGGGTCAAAAATGGGA
66 AAGGTTCGGGGTCAAAAATGGGA
* * * * * * *
767 TTTTTGGAAGTTTGGGGGT--AAAATGGTAATTTTCAAAAGTTCAAGGGTAAAATGGTAAATTTT
1 -TTTTGGAAGGTTCGAGGTCAAAAATGG-GATTTTTAGAAGTTCGAGGGTAAAATGGTAAATTTT
830 GGAAGGTTCGGGGTCAAAAATGGGA
64 GGAAGGTTCGGGGTCAAAAATGGGA
855 TTTT
1 TTTT
859 TAGAAATTTG
Statistics
Matches: 155, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
87 25 0.16
88 107 0.69
89 16 0.10
90 7 0.05
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.32
Consensus pattern (88 bp):
TTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAATGGTAAATTTTGG
AAGGTTCGGGGTCAAAAATGGGA
Found at i:818 original size:147 final size:145
Alignment explanation
Indices: 570--946 Score: 547
Period size: 147 Copynumber: 2.6 Consensus size: 145
560 AATTTCAAAC
* * * * *
570 ATTCGGGGGTAAAAGGGTAATTTTTGAAAGGTTCAGGGTCAAAAATGAGATATTTGGAAGTTTGG
1 ATTC-GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT-G
** * *
635 GGGGTAAAATGGTAATTTTGGAAGTTTAGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCAA
64 GGGGTAAAATGGTAATTTTAAAAGTTCAAGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCAA
*
700 AAATGGGATTTTTTGAA
129 AAATGGGATTTTTAGAA
* * *
717 GTTCGAGGGTAAAATAGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGG
1 ATTCG-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGG
*
782 GGGTAAAATGGTAATTTTCAAAAGTTCAAGGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAA
65 GGGTAAAATGGTAATTTT-AAAAGTTCAAGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCAA
847 AAATGGGATTTTTAGAA
129 AAATGGGATTTTTAGAA
* * **
864 ATTTGGGGATAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTAAG
1 ATTCGGGG-TAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGG
929 GGGTAAAATGGTAATTTT
65 GGGTAAAATGGTAATTTT
947 TGGATAGTTT
Statistics
Matches: 206, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
146 24 0.12
147 182 0.88
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (145 bp):
ATTCGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGG
GGTAAAATGGTAATTTTAAAAGTTCAAGGGTAAAATGGTAAATTTTGGAAGGTTCGAGGTCAAAA
ATGGGATTTTTAGAA
Found at i:859 original size:88 final size:88
Alignment explanation
Indices: 636--887 Score: 305
Period size: 88 Copynumber: 2.9 Consensus size: 88
626 GAAGTTTGGG
* * * * * * *
636 GGGTAAAATGGT-AATTTTGGAAGTTTAGGGGT--AAAATGGTAAATTTTGGAAGGTTCGAGGTC
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGG-GATTTTTGGAAGTTTGGGGGT-
* *** *
698 AAAAATGG-GATTTTTTGAAGTTCGA
64 -AAAATGGTAATTTTCAAAAGTTCAA
*
723 GGGTAAAATAGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
788 AATGGTAATTTTCAAAAGTTCAA
66 AATGGTAATTTTCAAAAGTTCAA
* * *
811 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGAAATTTGGGGATAA
1 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
876 AATGGTAATTTT
66 AATGGTAATTTT
888 TGGAAGGTTC
Statistics
Matches: 144, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
87 18 0.12
88 103 0.72
89 16 0.11
90 7 0.05
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (88 bp):
GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
AATGGTAATTTTCAAAAGTTCAA
Found at i:877 original size:59 final size:59
Alignment explanation
Indices: 811--950 Score: 219
Period size: 59 Copynumber: 2.4 Consensus size: 59
801 AAAAGTTCAA
* * *
811 GGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGAAATT-TG
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAATTAAG
* *
869 GGGATAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTAAG
1 GGG-TAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAATTAAG
929 GGGTAAAATGGTAATTTTTGGA
1 GGGTAAAATGGTAATTTTTGGA
951 TAGTTTAGGG
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 3 0.04
59 68 0.91
60 4 0.05
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGAAATTAAG
Found at i:2833 original size:30 final size:30
Alignment explanation
Indices: 2770--2826 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2760 GCTACTTTGC
* *
2770 AATTGGGCTGTTTTTATTTGGGCCATTCAT
1 AATTGGGCTGTTTTAATTTGGACCATTCAT
2800 AATTGGGCTGTTTGTAATTT-GACCATT
1 AATTGGGCTGTTT-TAATTTGGACCATT
2827 TCTAATTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (30 bp):
AATTGGGCTGTTTTAATTTGGACCATTCAT
Found at i:2889 original size:17 final size:17
Alignment explanation
Indices: 2867--2939 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
2857 TTGGACTTTC
*
2867 TAAATTTAATTTTATAA
1 TAAATTTAAATTTATAA
*
2884 TAAATTTAAATTTCTAA
1 TAAATTTAAATTTATAA
*
2901 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAA
*
2918 TAAACTTAAATTTA-AA
1 TAAATTTAAATTTATAA
2934 TAAATT
1 TAAATT
2940 CAATTTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 7 0.14
17 43 0.86
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:2951 original size:16 final size:17
Alignment explanation
Indices: 2867--2954 Score: 92
Period size: 17 Copynumber: 5.3 Consensus size: 17
2857 TTGGACTTTC
*
2867 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
*
2884 TAAATTTAAATTTCTAA
1 TAAATTTAAATTTCAAA
*
2901 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTCAAA
*
2918 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
2934 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
2950 TAAAT
1 TAAAT
2955 CCAAACAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
15 7 0.11
16 13 0.21
17 36 0.59
18 5 0.08
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:4929 original size:30 final size:29
Alignment explanation
Indices: 4903--5083 Score: 213
Period size: 30 Copynumber: 6.1 Consensus size: 29
4893 TTTTTGACCT
*
4903 CCAAAGTTTTCAAAAATTCAAATTTGACCC
1 CCAAAGTTTTCAAAAATTCAAATTT-AACC
**
4933 CCAATTTTTTCAAAAATTCAAATTTAATCC
1 CCAAAGTTTTCAAAAATTCAAATTTAA-CC
*
4963 CCAAATTTTTCAAAAATTCAAATTTAATCC
1 CCAAAGTTTTCAAAAATTCAAATTTAA-CC
*
4993 CCAAAGTTTTC-AAAATTCAAATTTGACC
1 CCAAAGTTTTCAAAAATTCAAATTTAACC
*
5021 ACTTAAA-TTTTCTAAAAATTCAAATTTAACC
1 -C-CAAAGTTTTC-AAAAATTCAAATTTAACC
* *
5052 TCTAAAGTTTTCAAAAATTAAAATTTAACC
1 -CCAAAGTTTTCAAAAATTCAAATTTAACC
5082 CC
1 CC
5084 GTTTTAATGT
Statistics
Matches: 134, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
28 2 0.01
29 22 0.16
30 88 0.66
31 22 0.16
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (29 bp):
CCAAAGTTTTCAAAAATTCAAATTTAACC
Found at i:4966 original size:90 final size:90
Alignment explanation
Indices: 4903--5083 Score: 253
Period size: 90 Copynumber: 2.0 Consensus size: 90
4893 TTTTTGACCT
*
4903 CCAAAGTTTTCAAAAATTCAAATTTGACC-CCC-AATTTTTTCAAAAATTCAAATTTAATCCCCA
1 CCAAAGTTTTC-AAAATTCAAATTTGACCACCCAAATTTTCT-AAAAATTCAAATTTAATCCCCA
4966 AATTTTTCAAAAATTCAAATTTAATCC
64 AATTTTTCAAAAATTCAAATTTAATCC
** *
4993 CCAAAGTTTTCAAAATTCAAATTTGACCACTTAAATTTTCTAAAAATTCAAATTTAA-CCTCTAA
1 CCAAAGTTTTCAAAATTCAAATTTGACCACCCAAATTTTCTAAAAATTCAAATTTAATCC-CCAA
* *
5057 AGTTTTCAAAAATTAAAATTTAA-CC
65 ATTTTTCAAAAATTCAAATTTAATCC
5082 CC
1 CC
5084 GTTTTAATGT
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
89 23 0.28
90 52 0.63
91 7 0.09
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (90 bp):
CCAAAGTTTTCAAAATTCAAATTTGACCACCCAAATTTTCTAAAAATTCAAATTTAATCCCCAAA
TTTTTCAAAAATTCAAATTTAATCC
Found at i:12088 original size:29 final size:29
Alignment explanation
Indices: 12049--12176 Score: 175
Period size: 29 Copynumber: 4.4 Consensus size: 29
12039 GAAATAATAC
12049 AGATACAGTTACAGATACAATCATGTCAG
1 AGATACAGTTACAGATACAATCATGTCAG
*
12078 AGATACAGTTACAGATACAATCATGTTAG
1 AGATACAGTTACAGATACAATCATGTCAG
* * *
12107 AGATACAGTTACAGATACAGTCATGTTAA
1 AGATACAGTTACAGATACAATCATGTCAG
* * * *
12136 AGATACAGTTATAGATATAGTCATGTCAT
1 AGATACAGTTACAGATACAATCATGTCAG
*
12165 AGATATAGTTAC
1 AGATACAGTTAC
12177 GGATGCAGAC
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (29 bp):
AGATACAGTTACAGATACAATCATGTCAG
Found at i:12110 original size:17 final size:17
Alignment explanation
Indices: 12056--12142 Score: 59
Period size: 17 Copynumber: 5.7 Consensus size: 17
12046 TACAGATACA
12056 GTTACAGATACAATCAT
1 GTTACAGATACAATCAT
* *
12073 G-T-CAGAGA-TA-CA-
1 GTTACAGATACAATCAT
12085 GTTACAGATACAATCAT
1 GTTACAGATACAATCAT
*
12102 GTTAGAGAT---A-CA-
1 GTTACAGATACAATCAT
*
12114 GTTACAGATACAGTCAT
1 GTTACAGATACAATCAT
*
12131 GTTAAAGATACA
1 GTTACAGATACA
12143 GTTATAGATA
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
12 9 0.17
13 5 0.10
14 7 0.13
15 6 0.12
16 5 0.10
17 20 0.38
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (17 bp):
GTTACAGATACAATCAT
Found at i:12203 original size:58 final size:58
Alignment explanation
Indices: 12049--12206 Score: 167
Period size: 58 Copynumber: 2.7 Consensus size: 58
12039 GAAATAATAC
* *
12049 AGATACAGTTACAGATACA-ATCATG-TCAGAGATACAGTTACAGATACAATCATGTTAG
1 AGATACAGTTACAGATACAGA-CATGAT-AAAGATACAGTTACAGATACAATCATGTCAG
* * * * * *
12107 AGATACAGTTACAGATACAGTCATGTTAAAGATACAGTTATAGATATAGTCATGTCAT
1 AGATACAGTTACAGATACAGACATGATAAAGATACAGTTACAGATACAATCATGTCAG
* * * * *
12165 AGATATAGTTACGGATGCAGACATGATACAGATGCAGTTACA
1 AGATACAGTTACAGATACAGACATGATAAAGATACAGTTACA
12207 TAGACAGACG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 82 0.99
59 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (58 bp):
AGATACAGTTACAGATACAGACATGATAAAGATACAGTTACAGATACAATCATGTCAG
Found at i:12344 original size:40 final size:40
Alignment explanation
Indices: 12289--12387 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
12279 GACATGTTGT
*
12289 AGTGTTTACAGTGTCACTGTCAGTTCAGTGATAACCTTGC
1 AGTGTTTACAGTGTCACTGTCAGTTCAGTGATAACATTGC
* * * * * *
12329 AGTGTTTATAGTGTCACTGTCGGTTTAGTTATAATATTGT
1 AGTGTTTACAGTGTCACTGTCAGTTCAGTGATAACATTGC
12369 AGTGTTTACAGTGTCACTG
1 AGTGTTTACAGTGTCACTG
12388 CCAACTCAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.40
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTGTCAGTTCAGTGATAACATTGC
Found at i:12908 original size:53 final size:53
Alignment explanation
Indices: 12851--13067 Score: 139
Period size: 53 Copynumber: 4.1 Consensus size: 53
12841 TCATGTGTCA
* * *
12851 GCCCATGCGTCAGCCCATCTTCCCTAAAACAGTATACACAAACCCTGACACAC
1 GCCCATGCGTCAGCCCATCTGCCCCAAAACAGTATACACAAACCCTAACACAC
* * * * * *
12904 GCCCATGTGTCAGCCCGTGTGCCCCAGAATAGTATACACACACCCTAACACAC
1 GCCCATGCGTCAGCCCATCTGCCCCAAAACAGTATACACAAACCCTAACACAC
* ** * * * * * * * * * *
12957 GTCTGTGTGCCAGCCCGTGTGCCTCAAAAAAGTATACACACACCTTGACCCAC
1 GCCCATGCGTCAGCCCATCTGCCCCAAAACAGTATACACAAACCCTAACACAC
* * * * * * *
13010 GCCCGTGTGCCAGCCCGTATGCCTCC-AAACAATGTACACACACACCCTAACACAC
1 GCCCATGCGTCAGCCCATCTGCC-CCAAAAC-A-GTATACACAAACCCTAACACAC
13065 GCC
1 GCC
13068 TTGTGCAGCC
Statistics
Matches: 133, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
53 110 0.83
54 2 0.02
55 21 0.16
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.17
Consensus pattern (53 bp):
GCCCATGCGTCAGCCCATCTGCCCCAAAACAGTATACACAAACCCTAACACAC
Found at i:13024 original size:106 final size:106
Alignment explanation
Indices: 12876--13087 Score: 277
Period size: 106 Copynumber: 2.0 Consensus size: 106
12866 CATCTTCCCT
* * * *
12876 AAAACAGTATACACAAACCCTGACACACGCCCATGTGTCAGCCCGTGTGCC-CC--AGAATAGTA
1 AAAAAAGTATACACAAACCCTGACACACGCCCATGTGCCAGCCCGTATGCCTCCAAACAAT-GTA
* * *
12938 TACACACACCCTAACACACGTCTGTGTGCCAGCCCGTGTGCCTC
65 CACACACACCCTAACACACGCCT-TGTG-CAGCCCATGTGCCTC
* * * *
12982 AAAAAAGTATACACACACCTTGACCCACGCCCGTGTGCCAGCCCGTATGCCTCCAAACAATGTAC
1 AAAAAAGTATACACAAACCCTGACACACGCCCATGTGCCAGCCCGTATGCCTCCAAACAATGTAC
13047 ACACACACCCTAACACACGCCTTGTGCAGCCCATGTGCCTC
66 ACACACACCCTAACACACGCCTTGTGCAGCCCATGTGCCTC
13088 CTGTACCTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
106 58 0.63
107 6 0.07
108 24 0.26
109 4 0.04
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (106 bp):
AAAAAAGTATACACAAACCCTGACACACGCCCATGTGCCAGCCCGTATGCCTCCAAACAATGTAC
ACACACACCCTAACACACGCCTTGTGCAGCCCATGTGCCTC
Found at i:13077 original size:53 final size:54
Alignment explanation
Indices: 12882--13088 Score: 219
Period size: 53 Copynumber: 3.9 Consensus size: 54
12872 CCCTAAAACA
* * * * *
12882 GTATACACAAACCCTGACACACGCCCATGTGTCAGCCCGTGTGCC-CC-AGAAT
1 GTATACACACACCCTAACACACGCCCTTGTGCCAGCCCGTGTGCCTCCAAAAAT
* *
12934 AGTATACACACACCCTAACACACG-TCTGTGTGCCAGCCCGTGTGCCT-CAAAAAA
1 -GTATACACACACCCTAACACACGCCCT-TGTGCCAGCCCGTGTGCCTCCAAAAAT
* * * * *
12988 GTATACACACACCTTGACCCACGCCCGTGTGCCAGCCCGTATGCCTCCAAACAAT
1 GTATACACACACCCTAACACACGCCCTTGTGCCAGCCCGTGTGCCTCCAAA-AAT
* *
13043 GTACACACACACCCTAACACACG-CCTTGTG-CAGCCCATGTGCCTCC
1 GTATACACACACCCTAACACACGCCCTTGTGCCAGCCCGTGTGCCTCC
13089 TGTACCTTAT
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 91 0.72
54 14 0.11
55 21 0.17
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.18
Consensus pattern (54 bp):
GTATACACACACCCTAACACACGCCCTTGTGCCAGCCCGTGTGCCTCCAAAAAT
Found at i:17386 original size:19 final size:18
Alignment explanation
Indices: 17364--17402 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
17354 AAATTACCCT
*
17364 TTTTACTTAAAATAAATAA
1 TTTTACTCAAAATAAA-AA
*
17383 TTTTAGTCAAAATAAAAA
1 TTTTACTCAAAATAAAAA
17401 TT
1 TT
17403 AAGAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTTACTCAAAATAAAAA
Found at i:23717 original size:13 final size:14
Alignment explanation
Indices: 23686--23728 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
23676 CTTCTCCTCA
*
23686 AAAAAATTTTTTCT
1 AAAAAATATTTTCT
23700 AAAAAATATTTT-T
1 AAAAAATATTTTCT
*
23713 GAAAAATA-TTTCT
1 AAAAAATATTTTCT
23726 AAA
1 AAA
23729 CTAAGGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.12
13 11 0.44
14 11 0.44
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (14 bp):
AAAAAATATTTTCT
Done.