Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400401.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_36.0, 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: 31084
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.21
Warning! 12588 characters in sequence are not A, C, G, or T
Found at i:1748 original size:170 final size:170
Alignment explanation
Indices: 1409--1754 Score: 392
Period size: 170 Copynumber: 2.0 Consensus size: 170
1399 NNNNNNNNNT
* *
1409 TTATTATACGCCTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTATATTTC
1 TTATTAGACGCCTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTACATTTC
* * *
1474 TCATTAAAACAGACTATAATTGAATGCTTGCCTTGAGAAACCTAAAGAAAAACTCATTTATTTGG
66 TCATTAAAACAGACTATAATTGAATGCCTACCTAGAGAAACCTAAAGAAAAACTCATTTATTTGG
********** * * *
1539 AAGAAAAGTCCANNNNNNNNNNCTCATTTCTTCAAAAGCC
131 AAGAAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCC
* * * * * *
1579 TTATTAGACGCTTTAAATGGTTTTATAATCTTATAATTGATTTTAATTTCAATTTTTTACATTTT
1 TTATTAGACGCCTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTACATTTC
* * *
1644 TCATTACAACAGACTATAATTGAATGCCTACCTCAG-GAAACGTGTAA-AAAAAC-CTATTTATT
66 TCATTAAAACAGACTATAATTGAATGCCTACCT-AGAGAAACCT-AAAGAAAAACTC-ATTTATT
*
1706 TGGAAGAAAAGTCCATTTATAGTCACCCAATCCTTTAAAAGCC
128 TGGAAGAAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCC
1749 TTATTA
1 TTATTA
1755 CTCACTTTNN
Statistics
Matches: 145, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
169 1 0.01
170 141 0.97
171 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.38
Consensus pattern (170 bp):
TTATTAGACGCCTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTACATTTC
TCATTAAAACAGACTATAATTGAATGCCTACCTAGAGAAACCTAAAGAAAAACTCATTTATTTGG
AAGAAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGCC
Found at i:9190 original size:173 final size:162
Alignment explanation
Indices: 8868--9191 Score: 337
Period size: 173 Copynumber: 1.9 Consensus size: 162
8858 NNNNNNNNNN
* * * * *
8868 TTATTACTCGCTTTAAATGGTTTTATAATCTCACAATTGATTTTAAGTTCAATTATTTTTATTTT
1 TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATCGATTTGAAGTTCAATTATTTTTATTTT
* *
8933 TTTAGTTAAAACAAAATATAATTGAATATCTGCCTTGAGAAATATGAAGAAAAAAGTATTCATTG
66 TTTAGTTAAAACAAAATATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAAGTATTCATTG
** *
8998 GTAAGAAAAGTCCATTTATAGNNNNNNNNNNCTTCAAAAGCT
131 ACAAAAAAAGTCCATTTATAG----------CTTCAAAAGCT
* *
9040 TTATTACTTACTTTAAATAGTTTTATAATCTCAAAATCGATTTGAAGTTCAATTTTTTTTAAATT
1 TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATCGATTTGAAGTTCAATTATTTTT--ATT
* * * * * * *
9105 TTTTT-GTTGAAATAGATTATAATTGAATGTCTACCTT-ATGAAACGTGAAGAAAAAGGTATTCA
64 TTTTTAGTTAAAACAAAATATAATTGAATATCTACCTTGA-GAAACATGAAGAAAAAAGTATTCA
*
9168 TTGACAAAAAAAGTCTATTTATAG
128 TTGACAAAAAAAGTCCATTTATAG
9192 TCTCTCATTC
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
172 54 0.42
173 67 0.52
174 8 0.06
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.40
Consensus pattern (162 bp):
TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATCGATTTGAAGTTCAATTATTTTTATTTT
TTTAGTTAAAACAAAATATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAAGTATTCATTG
ACAAAAAAAGTCCATTTATAGCTTCAAAAGCT
Found at i:9209 original size:173 final size:171
Alignment explanation
Indices: 8868--9382 Score: 471
Period size: 172 Copynumber: 3.0 Consensus size: 171
8858 NNNNNNNNNN
* * * *
8868 TTATTACTCGCTTTAAATGGTTTTATAATCTCACAATTGATTTTAAGTTCAATTATTTTT-ATTT
1 TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTAATTT
* * * * * *
8932 TTTTAGTTAAAACAAAATATAATTGAATATCTGCCTTGA-GAAATATGAAGAAAAAAGTATTCAT
66 TTTT-GTTAAAACAGATTATAATTGAATGTCTACCTT-ATGAAACATGAAGAAAAAGGTATTCAT
** * ********* *
8996 TGGTAAGAAAAGTCCATTTATAGNNNNNNNNNNCTTCAAAAGCT
129 TGACAAGAAAAGTCTATTTATAG-TCACCCATTCTTCAAAAGCC
* * *
9040 TTATTACTTACTTTAAATAGTTTTATAATCTCAAAATCGATTTGAAGTTCAATTTTTTTTAAATT
1 TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTT-AATT
* * *
9105 TTTTTGTTGAAATAGATTATAATTGAATGTCTACCTTATGAAACGTGAAGAAAAAGGTATTCATT
65 TTTTTGTTAAAACAGATTATAATTGAATGTCTACCTTATGAAACATGAAGAAAAAGGTATTCATT
* * *
9170 GACAAAAAAAGTCTATTTATAGTCTCTCATTCTTTCAAAAGCC
130 GACAAGAAAAGTCTATTTATAGTCACCCATTC-TTCAAAAGCC
* ********** * * **
9213 TTACTACTCACTTTAAATAGNNNNNNNNNNTCAAAATTAATTTTAAGTTCAATGTTTTTTACCTT
1 TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTAATTT
* * * *
9278 TTTTGTTAAAACAGTTTATAATTGAATGTCTACCTCATGAAACATGAACAGAAAGGTATTCATT-
66 TTTTGTTAAAACAGATTATAATTGAATGTCTACCTTATGAAACATGAAGAAAAAGGTATTCATTG
9342 AGCAAGAAAAGT-TCATTTATAGTCACCCATTCCTTCAAAAG
131 A-CAAGAAAAGTCT-ATTTATAGTCACCCATT-CTTCAAAAG
9383 NNNNNNNNNN
Statistics
Matches: 278, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
171 2 0.01
172 147 0.53
173 121 0.44
174 8 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.38
Consensus pattern (171 bp):
TTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTAATTT
TTTTGTTAAAACAGATTATAATTGAATGTCTACCTTATGAAACATGAAGAAAAAGGTATTCATTG
ACAAGAAAAGTCTATTTATAGTCACCCATTCTTCAAAAGCC
Found at i:13781 original size:22 final size:22
Alignment explanation
Indices: 13753--13809 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
13743 ACAGAATGCT
13753 CTTAGTCGACTAACCATTATCA
1 CTTAGTCGACTAACCATTATCA
13775 CTTAGTCGACTAACCATTATCA
1 CTTAGTCGACTAACCATTATCA
13797 CTTAGTCGACTAA
1 CTTAGTCGACTAA
13810 GTGGTCTCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAGTCGACTAACCATTATCA
Found at i:13867 original size:32 final size:32
Alignment explanation
Indices: 13815--13901 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
13805 ACTAAGTGGT
* * *
13815 CTCTGTCTCTTAACCTAGTTTCTGGCAGTAGG
1 CTCTATCTCTGAACCTAGTTTCTGGCAGCAGG
*
13847 CTCTATCTCTGAACCCAGTTTCTGGCAGCAGG
1 CTCTATCTCTGAACCTAGTTTCTGGCAGCAGG
13879 CTCTATCTCTGAACCTAGTTTCT
1 CTCTATCTCTGAACCTAGTTTCT
13902 ACCAGTAACC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.36
Consensus pattern (32 bp):
CTCTATCTCTGAACCTAGTTTCTGGCAGCAGG
Found at i:16972 original size:32 final size:32
Alignment explanation
Indices: 16926--16993 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
16916 TAGTCGACCT
* *
16926 AGAGGCTACTGCCAGAAATTGGGTTCAGAGAC
1 AGAGCCTACTGCCAGAAACTGGGTTCAGAGAC
16958 AGAGCCTACTGCCAGAAACTGGGTTCAGAGAC
1 AGAGCCTACTGCCAGAAACTGGGTTCAGAGAC
16990 AGAG
1 AGAG
16994 ATGACTTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.31, T:0.16
Consensus pattern (32 bp):
AGAGCCTACTGCCAGAAACTGGGTTCAGAGAC
Done.