Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397786.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1086.0, 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: 9523
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.26
Warning! 2196 characters in sequence are not A, C, G, or T
Found at i:5165 original size:20 final size:19
Alignment explanation
Indices: 5131--5178 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
5121 TGTGAAATTG
5131 GAAAGAAA-TAGAGAGAAAA
1 GAAAGAAATTAGAGA-AAAA
5150 GGAACAGAAATTAGAGAAAAA
1 -GAA-AGAAATTAGAGAAAAA
5171 GAAAGAAA
1 GAAAGAAA
5179 AAGGAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 6 0.23
21 9 0.35
22 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.25, T:0.06
Consensus pattern (19 bp):
GAAAGAAATTAGAGAAAAA
Found at i:6904 original size:18 final size:18
Alignment explanation
Indices: 6877--6914 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6867 NNNNNNNNNN
*
6877 TTCTTTTCTT-TTGCTTCT
1 TTCTTGTCTTCTT-CTTCT
6895 TTCTTGTCTTCTTCTTCT
1 TTCTTGTCTTCTTCTTCT
6913 TT
1 TT
6915 TTCTTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (18 bp):
TTCTTGTCTTCTTCTTCT
Found at i:8530 original size:73 final size:73
Alignment explanation
Indices: 8413--8565 Score: 225
Period size: 73 Copynumber: 2.1 Consensus size: 73
8403 CTCTCAGTTA
* * *
8413 ACTAACAAAACTTCTTAGTCGATTAAGTTGTTTCTATCTCTGAACCCAATTTCTGGTAGTAAGCT
1 ACTAACAAAACTTCTTAGTCGATTAAGTCGTTTCTATCTATGAACCCAATTTCTGGAAGTAAGCT
8478 CTTAGTAG
66 CTTAGTAG
* * * * *
8486 GCTAACAAAACTTCTTAGTCGATTAAGTCGTTTTTGTCTATGAACCCAGTTTTTGGAAGTAAGCT
1 ACTAACAAAACTTCTTAGTCGATTAAGTCGTTTCTATCTATGAACCCAATTTCTGGAAGTAAGCT
*
8551 CTTAGTCG
66 CTTAGTAG
8559 ACTAACA
1 ACTAACA
8566 CTGTCTCTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (73 bp):
ACTAACAAAACTTCTTAGTCGATTAAGTCGTTTCTATCTATGAACCCAATTTCTGGAAGTAAGCT
CTTAGTAG
Found at i:9153 original size:172 final size:170
Alignment explanation
Indices: 8856--9523 Score: 594
Period size: 170 Copynumber: 3.9 Consensus size: 170
8846 TTTGCCAAGG
*
8856 GAAACATGAAGAAAAAGGCATTCATCGACAA-ACAAAGTCCATTTATAGTCACCCATTCCTTCAA
1 GAAACGTGAAGAAAAAGGCATTCATCGACAAGA-AAAGTCCATTTATAGTCACCCATTCCTTCAA
* * *
8920 AAGCTTTATTGCTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTCAGTTGAATTTTTTGT
65 AAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTAAGTTGAA-TTTTT-T
* * *
8985 ACATTTTTA-ATTAAAACAGAGTATAATTAAATTTTTACCTTGA
128 ACA-TTTTAGATTAAAACAGACTATAATTAAATGTCTACCTTGA
* * * *
9028 GAAACGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTACAATCACTCATTCCTTCAAA
1 GAAACGTGAAGAAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
********** * * *
9093 AGCCTTATTACTCNNNNNNNNNNGTTTTATAATCTTAAAATTGATTTTAAGTTTAATTTTTTACA
66 AGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTAAGTTGAATTTTTTACA
* *
9158 TTTTAGGTTAAAACAGACTATAATTGAATGTCTACCTTGA
131 TTTTAGATTAAAACAGACTATAATTAAATGTCTACCTTGA
*** ** * *
9198 GAAACGTGAAGAAAAAAAAATTCATCG-GTAGAAAAAGTCCATTTATAGTCACCCATTCTTTTAA
1 GAAACGTGAAGAAAAAGGCATTCATCGACAAG-AAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * * * * *
9262 AAGCCTTATCACTCGTTTTAAAT-GATTTCATAATGTCACAATTGATTTTAA-ATGAATTTGTTT
65 AAGCCTTATTACTCGCTTTAAATAG-TTTTATAATCTCAAAATTAATTTTAAGTTGAATTT-TTT
** * * * * * *
9325 ACATTTTTTATTAAAAAAGATTATAATTGAATGCCTGCC-TCA
128 ACATTTTAGATTAAAACAGACTATAATTAAATGTCTACCTTGA
* * * * ** * *
9367 GGAAATGTGAAGTAAAAA-GCTTTTATGGACAAGAAAAGTATACTTATGGTCACCCATTCCTTCA
1 -GAAACGTGAAG-AAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
* * * ** ** *
9431 AAAGCCTTATTACTCACTTTAAATGGTTTTAGAAGGTCGTAATTGATTTTAAGTTGAATTGTTTT
64 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTAAGTTGAA-T-TTTT
* *
9496 TACATTTTTGGTTAAAACAGACTATAAT
127 TACATTTTAGATTAAAACAGACTATAAT
Statistics
Matches: 396, Mismatches: 88, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
169 16 0.04
170 235 0.59
171 17 0.04
172 125 0.32
173 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (170 bp):
GAAACGTGAAGAAAAAGGCATTCATCGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
AGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTAAGTTGAATTTTTTACA
TTTTAGATTAAAACAGACTATAATTAAATGTCTACCTTGA
Done.