Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397491.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1345.0, 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: 12671
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.29
Warning! 330 characters in sequence are not A, C, G, or T
Found at i:4746 original size:13 final size:13
Alignment explanation
Indices: 4728--4760 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4718 ATTATGAGTA
4728 ACTCCAAGCATAG
1 ACTCCAAGCATAG
4741 ACTCCAAGCATAG
1 ACTCCAAGCATAG
4754 ACTCCAA
1 ACTCCAA
4761 CAAAGTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.15
Consensus pattern (13 bp):
ACTCCAAGCATAG
Found at i:11860 original size:27 final size:27
Alignment explanation
Indices: 11829--11898 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
11819 GCCTAGGGTG
*
11829 TTCCAAATACAGAAGCACCCAGAAGCA
1 TTCCAAGTACAGAAGCACCCAGAAGCA
11856 TTCCAAGTACAGAAGCACCCAGAAGCA
1 TTCCAAGTACAGAAGCACCCAGAAGCA
11883 TTCCAAGTACAGAAGC
1 TTCCAAGTACAGAAGC
11899 GCTCAAGGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.41, C:0.29, G:0.17, T:0.13
Consensus pattern (27 bp):
TTCCAAGTACAGAAGCACCCAGAAGCA
Found at i:11870 original size:17 final size:17
Alignment explanation
Indices: 11848--11898 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
11838 CAGAAGCACC
11848 CAGAAGCATTCCAAGTA
1 CAGAAGCATTCCAAGTA
11865 CAGAAGCA--CC-----
1 CAGAAGCATTCCAAGTA
11875 CAGAAGCATTCCAAGTA
1 CAGAAGCATTCCAAGTA
11892 CAGAAGC
1 CAGAAGC
11899 GCTCAAGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
10 8 0.30
12 2 0.07
15 2 0.07
17 15 0.56
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.12
Consensus pattern (17 bp):
CAGAAGCATTCCAAGTA
Found at i:12019 original size:27 final size:27
Alignment explanation
Indices: 11989--12103 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
11979 ACTCAGGGGC
11989 GTTCCAAGCACAAAAACACCTAAGGAT
1 GTTCCAAGCACAAAAACACCTAAGGAT
*
12016 GTTCCAAGCACAAAAACACCCAGAGGCA-
1 GTTCCAAGCACAAAAACACCTA-AGG-AT
* * * *
12044 -TTCCAAACGCAAAAGCACCTAAGGGT
1 GTTCCAAGCACAAAAACACCTAAGGAT
* * *
12070 ATTCTAAGCACAAAAACGCCTAAGG-T
1 GTTCCAAGCACAAAAACACCTAAGGAT
12096 GTTCCAAG
1 GTTCCAAG
12104 TACAGAAGCG
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
26 10 0.14
27 57 0.80
28 3 0.04
29 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (27 bp):
GTTCCAAGCACAAAAACACCTAAGGAT
Found at i:12238 original size:107 final size:108
Alignment explanation
Indices: 12016--12330 Score: 296
Period size: 107 Copynumber: 2.9 Consensus size: 108
12006 ACCTAAGGAT
* * * * *** * * *
12016 GTTCCAAGCACAAAAACACCCAGAGGCATTCCAAACGCAAAAGCACCTAAGGGTATTCTAAGCAC
1 GTTCCAAGCGCAAAAGCACCCAGGGGCGTTCCAAGTACAAAAGCGCCTAAGGGCATTCCAAGCAC
* * *
12081 AAAAACGCCTAAGGTGTTCCAAGTACAGAAGCG-TTCAGGGAA
66 AGAAACACCTAAGGTGTTCCAAGTACAGAAGCGCCTCAGGGAA
* * ** * * * * * *
12123 GTTTCAAGCGTAGAAA-CGTCTAGGGGTGTTCCAAGTACAGAAGCTCTTAAGGGCATTCCAAGTA
1 GTTCCAAGCGCA-AAAGCACCCAGGGGCGTTCCAAGTACAAAAGCGCCTAAGGGCATTCCAAGCA
* * *
12187 CAGAAGCACCTAAGGTGTTCCAAGTATAGAAGCGCCT-AGAGG-C
65 CAGAAACACCTAAGGTGTTCCAAGTACAGAAGCGCCTCAG-GGAA
* **
12230 GTTCCAAGCGCAAAAGCACCCAGGGGCGTTCCAAGTACAAAAGCGCCTAGGGGTGTTCCAAGCAC
1 GTTCCAAGCGCAAAAGCACCCAGGGGCGTTCCAAGTACAAAAGCGCCTAAGGGCATTCCAAGCAC
* *
12295 AGAAACACCCAAGGGCGTTCCAAGTACAGAAGCGCC
66 AGAAACACCTAA-GGTGTTCCAAGTACAGAAGCGCC
12331 CAAGATAGTT
Statistics
Matches: 162, Mismatches: 41, Indels: 9
0.76 0.19 0.04
Matches are distributed among these distances:
106 3 0.02
107 132 0.81
108 27 0.17
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (108 bp):
GTTCCAAGCGCAAAAGCACCCAGGGGCGTTCCAAGTACAAAAGCGCCTAAGGGCATTCCAAGCAC
AGAAACACCTAAGGTGTTCCAAGTACAGAAGCGCCTCAGGGAA
Found at i:12274 original size:54 final size:54
Alignment explanation
Indices: 12150--12330 Score: 206
Period size: 54 Copynumber: 3.4 Consensus size: 54
12140 GTCTAGGGGT
* * * * * * *
12150 GTTCCAAGTACAGAAGCTCTTA-AGGGCATTCCAAGTACAGAAGCACCTAA-GGT
1 GTTCCAAGTACAGAAGCGCCTAGA-GGCGTTCCAAGCACAGAAACACCCAAGGGC
* * *
12203 GTTCCAAGTATAGAAGCGCCTAGAGGCGTTCCAAGCGCA-AAAGCACCCAGGGGC
1 GTTCCAAGTACAGAAGCGCCTAGAGGCGTTCCAAGCACAGAAA-CACCCAAGGGC
* * *
12257 GTTCCAAGTACAAAAGCGCCTAGGGGTGTTCCAAGCACAGAAACACCCAAGGGC
1 GTTCCAAGTACAGAAGCGCCTAGAGGCGTTCCAAGCACAGAAACACCCAAGGGC
12311 GTTCCAAGTACAGAAGCGCC
1 GTTCCAAGTACAGAAGCGCC
12331 CAAGATAGTT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
52 2 0.02
53 36 0.34
54 66 0.62
55 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.26, T:0.15
Consensus pattern (54 bp):
GTTCCAAGTACAGAAGCGCCTAGAGGCGTTCCAAGCACAGAAACACCCAAGGGC
Found at i:12342 original size:54 final size:54
Alignment explanation
Indices: 11823--12353 Score: 158
Period size: 54 Copynumber: 9.9 Consensus size: 54
11813 AAAAATGCCT
* * * * *
11823 AGGGTGTTCCAAATACAGAAGCACCC-AGA-AGCATTCCAAGTACAGAAGCACCC-
1 AGGGCGTTCCAAGTACAGAAGCGCCCAAGATAG--TTCCAAGCACAGAAACACCCA
* * * * * * **
11876 AGAAGCATTCCAAGTACAGAAGCGCTCAAGGT-GTTCCAAGCGCAGAAGCGTCC-
1 AG-GGCGTTCCAAGTACAGAAGCGCCCAAGATAGTTCCAAGCACAGAAACACCCA
* * * ** * * * * *
11929 AGGGACGTT-CTAGATATAGAAGCGCCCACGGGAATTCTAAGCGCAGAAGCACTCA
1 AGGG-CGTTCCAAG-TACAGAAGCGCCCAAGATAGTTCCAAGCACAGAAACACCCA
* * * * * * *
11984 GGGGCGTTCCAAGCACAAAAACACCTAAGGAT-GTTCCAAGCACAAAAACACCC-
1 AGGGCGTTCCAAGTACAGAAGCGCCCAA-GATAGTTCCAAGCACAGAAACACCCA
* *** * * * * * * * *
12037 AGAGGCATTCCAAACGCAAAAGCACCTAAGGGTA-TTCTAAGCACAAAAACGCCTA
1 AG-GGCGTTCCAAGTACAGAAGCGCCCAA-GATAGTTCCAAGCACAGAAACACCCA
* ** * * ** ** *
12092 A-GGTGTTCCAAGTACAGAAGCGTTCAGGGA-AGTTTCAAGCGTAGAAACGTCTA
1 AGGGCGTTCCAAGTACAGAAGCGCCCA-AGATAGTTCCAAGCACAGAAACACCCA
* * * ** ** * * *
12145 GGGGTGTTCCAAGTACAGAAGCTCTTAAGGGCA-TTCCAAGTACAGAAGCACCTA
1 AGGGCGTTCCAAGTACAGAAGCGCCCAA-GATAGTTCCAAGCACAGAAACACCCA
* * * ** *
12199 A-GGTGTTCCAAGTATAGAAGCG-CCTAGAGGCGTTCCAAGCGCA-AAAGCACCCA
1 AGGGCGTTCCAAGTACAGAAGCGCCCAAGA-TAGTTCCAAGCACAGAAA-CACCCA
* * * * *
12252 GGGGCGTTCCAAGTACAAAAGCGCCTAGGGGT-GTTCCAAGCACAGAAACACCCA
1 AGGGCGTTCCAAGTACAGAAGCGCCCA-AGATAGTTCCAAGCACAGAAACACCCA
* *
12306 AGGGCGTTCCAAGTACAGAAGCGCCCAAGATAGTTCCAACCGCAGAAA
1 AGGGCGTTCCAAGTACAGAAGCGCCCAAGATAGTTCCAAGCACAGAAA
12354 GTTCTGAAGT
Statistics
Matches: 343, Mismatches: 110, Indels: 49
0.68 0.22 0.10
Matches are distributed among these distances:
51 1 0.00
52 8 0.02
53 104 0.30
54 213 0.62
55 16 0.05
56 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.15
Consensus pattern (54 bp):
AGGGCGTTCCAAGTACAGAAGCGCCCAAGATAGTTCCAAGCACAGAAACACCCA
Found at i:12344 original size:27 final size:27
Alignment explanation
Indices: 12150--12334 Score: 158
Period size: 27 Copynumber: 6.9 Consensus size: 27
12140 GTCTAGGGGT
* **
12150 GTTCCAAGTACAGAAGCTCTTAAGGGC
1 GTTCCAAGTACAGAAGCACCCAAGGGC
* * *
12177 ATTCCAAGTACAGAAGCACCTAA-GGT
1 GTTCCAAGTACAGAAGCACCCAAGGGC
* * *
12203 GTTCCAAGTATAGAAGC-GCCTAGAGGC
1 GTTCCAAGTACAGAAGCACCCAAG-GGC
** * *
12230 GTTCCAAGCGCAAAAGCACCCAGGGGC
1 GTTCCAAGTACAGAAGCACCCAAGGGC
* * * * *
12257 GTTCCAAGTACAAAAGCGCCTAGGGGT
1 GTTCCAAGTACAGAAGCACCCAAGGGC
* *
12284 GTTCCAAGCACAGAAACACCCAAGGGC
1 GTTCCAAGTACAGAAGCACCCAAGGGC
*
12311 GTTCCAAGTACAGAAGCGCCCAAG
1 GTTCCAAGTACAGAAGCACCCAAG
12335 ATAGTTCCAA
Statistics
Matches: 123, Mismatches: 32, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
25 2 0.02
26 17 0.14
27 101 0.82
28 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (27 bp):
GTTCCAAGTACAGAAGCACCCAAGGGC
Done.