Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401184.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4335.0, 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: 2006
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.37
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:460 original size:170 final size:172
Alignment explanation
Indices: 214--527 Score: 379
Period size: 170 Copynumber: 1.8 Consensus size: 172
204 NNNNAATCCC
* * **
214 AAAATTAATTTTAAGTTAAATTTTTTTTACATTTGTGGTTAAAACAGACAATAATTGGCCATCTA
1 AAAATTAATTTTAAGTTAAATTTTTTTTACATTTGTAGTCAAAACAGACAATAATTGAACATCTA
* * * * * * *
279 CTAAGAAAAATGTTAAGAAAAA-TACATTCATCGGTAAGAAAAGTCTA-TTATAGTCGC-CGATT
66 CTAAGAAAAATGTGAAGAAAAAGGA-ATTCATCAGCAAAAAAAGTCCATTTATAGTCACTC-ATT
*
341 CCTTCAAAAGCTTTATTACTCTCTTTAAAAGGTTTTGTAATCTA
129 CCTTCAAAAGCCTTATTACTCTCTTTAAAAGGTTTTGTAATCTA
* * **
385 AAAATTGATTTTAAGTTCAA-TTTTTTTACATTTGTAGTCAAAACAGA-ATATAATTGAATGTCT
1 AAAATTAATTTTAAGTTAAATTTTTTTTACATTTGTAGTCAAAACAGACA-ATAATTGAACATCT
** *
448 ACCT-TTAAAAATGTGAAGAAAAAGGAATTCATTAGCAAAAAAAGTCCATTTATAGTCACTCATT
65 A-CTAAGAAAAATGTGAAGAAAAAGGAATTCATCAGCAAAAAAAGTCCATTTATAGTCACTCATT
512 CCTTCAAAAGCCTTAT
129 CCTTCAAAAGCCTTAT
528 NNNNNNNNNN
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
169 1 0.01
170 69 0.58
171 48 0.40
172 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (172 bp):
AAAATTAATTTTAAGTTAAATTTTTTTTACATTTGTAGTCAAAACAGACAATAATTGAACATCTA
CTAAGAAAAATGTGAAGAAAAAGGAATTCATCAGCAAAAAAAGTCCATTTATAGTCACTCATTCC
TTCAAAAGCCTTATTACTCTCTTTAAAAGGTTTTGTAATCTA
Found at i:1446 original size:170 final size:171
Alignment explanation
Indices: 1180--1517 Score: 385
Period size: 170 Copynumber: 2.0 Consensus size: 171
1170 NNNNTAAATA
* * * *
1180 GTTTTATAATCTCATAATTAATTTTAAGTTAAATTTGTTTACATTTTTAGTTAAAATAGATAATA
1 GTTTTATAATCTCAAAATTAAATTTAAGTTAAATTTGTTTACATTTGTAGTCAAAATAGATAATA
* * * *
1245 ATTGACCATCTACTAAAACAAACGTAAAGAAAAATGCATTCATTGGTAAGAAAAGTCCA-TTATA
66 ATTGAACATCTACTAAAACAAACGCAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATA
*
1309 GTCACCCATCCCTTCAAAAGCCTTATTACTCACTTTAATTG
131 GTCACCCATCCCTTCAAAAGCATTATTACTCACTTTAATTG
* * *
1350 GTTTTATAATCTCAAAATTAAATTTAAGTTCAATTTTTTTACATTTGTGGTCAAAATAGA-ATAT
1 GTTTTATAATCTCAAAATTAAATTTAAGTTAAATTTGTTTACATTTGTAGTCAAAATAGATA-AT
* ** ** * * * * *
1414 AATTTAATGTCTATCT-CGAGAAATGCAAAGAAAAAGGGATTCCTTGGCAAGAAAAGTCTATTTA
65 AATTGAACATCTA-CTAAAACAAACGCAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTA
* ** * * *
1478 TCGTTGCCCATTCCTTCAAAAGTATTATTACTGACTTTAA
129 TAGTCACCCATCCCTTCAAAAGCATTATTACTCACTTTAA
1518 ATAGTTTTNN
Statistics
Matches: 137, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
169 1 0.01
170 98 0.72
171 38 0.28
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (171 bp):
GTTTTATAATCTCAAAATTAAATTTAAGTTAAATTTGTTTACATTTGTAGTCAAAATAGATAATA
ATTGAACATCTACTAAAACAAACGCAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATA
GTCACCCATCCCTTCAAAAGCATTATTACTCACTTTAATTG
Found at i:1655 original size:11 final size:11
Alignment explanation
Indices: 1639--1664 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1629 TGGTAAGAAA
1639 AGTCCATTTAT
1 AGTCCATTTAT
1650 AGTCCATTTAT
1 AGTCCATTTAT
1661 AGTC
1 AGTC
1665 ATTCATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (11 bp):
AGTCCATTTAT
Done.