Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402600.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5671.0, 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: 1831
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.25
Warning! 607 characters in sequence are not A, C, G, or T
Found at i:296 original size:171 final size:170
Alignment explanation
Indices: 1--365 Score: 439
Period size: 171 Copynumber: 2.1 Consensus size: 170
* * *
1 ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTGCATTTTCAGTTAAAACAGACAATAATTGA
1 ATAATCTCATAATTGATTTTAAGTTCAATTTTTTTGCATTTGCA-TTAAAACAGACAATAATTAA
* * * * * * *
66 ATGTCTACCTCGAGGAACATGAAGACAAATGCATTCATTAGCAAGAAAAGTCTATTTATAGTTAT
65 ATGTCTACCTCAAGAAACATGAAGACAAAAGCATTCATTAACAAAAAAAGTCCATTTATAG-TAG
* ** *
131 CC-ATTTCTTCAAAACCCTTATTACTCACTTTAAGTGGTTTT
129 CCTATTCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
* * * ** *
172 ATAATCTCAAAATTGGTTTTAAGTTCAATTTTTTTGCTTATTTGC-TTAAAATAGATTATAGTTA
1 ATAATCTCATAATTGATTTTAAGTTCAATTTTTTTGC--ATTTGCATTAAAACAGACAATAATTA
* * *
236 AATGTCTACTTCAAGAAACGTGAAGA-AAAAGACATTTATTAACAAAAAAAGTCCATTTATAGTA
64 AATGTCTACCTCAAGAAACATGAAGACAAAAG-CATTCATTAACAAAAAAAGTCCATTTATAGTA
* *
300 GCCTATTCCTTCAAAAGCCTTATTACTCATTTTAAACGGATTT
128 GCCTATTCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
343 ATAATCTCATAATTGATTTTAAG
1 ATAATCTCATAATTGATTTTAAG
366 NNNNNNNNNN
Statistics
Matches: 163, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
170 8 0.05
171 150 0.92
173 5 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (170 bp):
ATAATCTCATAATTGATTTTAAGTTCAATTTTTTTGCATTTGCATTAAAACAGACAATAATTAAA
TGTCTACCTCAAGAAACATGAAGACAAAAGCATTCATTAACAAAAAAAGTCCATTTATAGTAGCC
TATTCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
Found at i:459 original size:171 final size:167
Alignment explanation
Indices: 1--545 Score: 423
Period size: 171 Copynumber: 3.2 Consensus size: 167
* * * * * *
1 ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTGCATT-TTCAGTTAAAACAGACAATAATTG
1 ATAATCTCAAAATTGATTTTAAGTTCAATTTTTATG-ATTATT-TGTTAAAATAGACTAT-ATTG
* * * * *
65 AATGTCTACCTCGAGGAACATGAAGACAAATGCATTCATTAGCAAGAAAAGTCTATTTATAGTTA
63 AATGTCTACCTCGAGAAACGTGAA-AAAAAGGCATTCATTA-CAAGAAAAGTCCATTTATAGTTA
* * ** *
130 TCCATTTCTTCAAAACCCTTATTACTCACTTTAAGTGGTTTT
126 GCCATTCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
* * * * *
172 ATAATCTCAAAATTGGTTTTAAGTTCAATTTTTTTGCTTATTTGCTTAAAATAGATTATAGTTAA
1 ATAATCTCAAAATTGATTTTAAGTTCAATTTTTATGATTATTTG-TTAAAATAGACTATA-TTGA
* * * * *
237 ATGTCTACTTCAAGAAACGTGAAGAAAAAGACATTTATTAACAAAAAAAGTCCATTTATAG-TAG
64 ATGTCTACCTCGAGAAACGTGAA-AAAAAGGCATTCATT-ACAAGAAAAGTCCATTTATAGTTAG
* *
301 CCTATTCCTTCAAAAGCCTTATTACTCATTTTAAACGGATTT
127 CC-ATTCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
* ******* *
343 ATAATCTCATAATTGATTTTAAGNNNNNNNNNNTTTAT-ATTTTTTGTTAAAATAGACTATGATT
1 ATAATCTCAAAATTGATTTTAAG---TTCAATTTTTATGATTATTTGTTAAAATAGACTAT-ATT
* * * ***
407 GAATGCCTACCTCGAGAAATGTGAACAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGNNN
62 GAATGTCTACCTCGAGAAACGTGAAAAAAAGGCATTCATT-ACAAGAAAAGTCCATTTATAGTTA
******* ** * *
472 NNNNNNNCTTCAAAAGTCATATTACTCACTTTAAA-TGATTTT
126 GCCATTCCTTCAAAACCCTTATTACTCACTTTAAACGGA-TTT
*
514 ATACTCTCAAAATTGATTTTAAGTTCAATTTT
1 ATAATCTCAAAATTGATTTTAAGTTCAATTTT
546 GTTTTTACTT
Statistics
Matches: 292, Mismatches: 71, Indels: 25
0.75 0.18 0.06
Matches are distributed among these distances:
168 2 0.01
170 10 0.03
171 233 0.80
172 36 0.12
173 7 0.02
174 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (167 bp):
ATAATCTCAAAATTGATTTTAAGTTCAATTTTTATGATTATTTGTTAAAATAGACTATATTGAAT
GTCTACCTCGAGAAACGTGAAAAAAAGGCATTCATTACAAGAAAAGTCCATTTATAGTTAGCCAT
TCCTTCAAAACCCTTATTACTCACTTTAAACGGATTT
Found at i:802 original size:171 final size:163
Alignment explanation
Indices: 479--803 Score: 327
Period size: 171 Copynumber: 1.9 Consensus size: 163
469 NNNNNNNNNN
* * * * *
479 CTTCAAAAGTCATATTACTCACTTTAAATGATTTTATACTCTCAAAATTGATTTTAAGTTCAATT
1 CTTCAAAAGCCATATCACCCACTTTAAATGATTTTATACACTCAAAATTGATTTTAAGCTCAATT
* * *** *
544 TTGTTTTTACTTTTTTAGTTAAAACAGATTATAATTGAATGTTTGTGTTAAGAAACATAAAGAAG
66 TTGTTTTTAC-TTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAG
*
609 AAGGCATTCATTGGTAAGAAAAGTNNNNNNNNNNTCACCCATTC
130 AAGGCATTCATTGGCAAGAAAAGT----------TCACCCATTC
* *
653 CTTCAAAAGCCTTATCACCCACTTTAAATGATTTTATTA-ACTCAAAATTGATTTTATGCTC-AT
1 CTTCAAAAGCCATATCACCCACTTTAAATGATTTTA-TACACTCAAAATTGATTTTAAGCTCAAT
* * *
716 TTT-TTTTATA-TTTTTAGTTAAAACATACTATAATTGAATGTCTACCTCAGGAAACATGAAGAA
65 TTTGTTTT-TACTTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAA
*
779 -AATGGTATTCATTGGCAAGAAAAGT
129 GAA-GGCATTCATTGGCAAGAAAAGT
804 CCATTTATAG
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
170 2 0.02
171 64 0.49
172 4 0.03
173 7 0.05
174 51 0.39
175 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38
Consensus pattern (163 bp):
CTTCAAAAGCCATATCACCCACTTTAAATGATTTTATACACTCAAAATTGATTTTAAGCTCAATT
TTGTTTTTACTTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAACATAAAGAAGA
AGGCATTCATTGGCAAGAAAAGTTCACCCATTC
Found at i:1823 original size:170 final size:171
Alignment explanation
Indices: 1392--1831 Score: 469
Period size: 170 Copynumber: 2.6 Consensus size: 171
1382 NNNGAGAAAT
* * * *
1392 ATGAAGAAAAAA-GCATTCATTGGCAAGAAATGTCCATTTATAGTCTCTCA-TCCTTCAAAAGCC
1 ATGAAAAAAAAAGGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCC
* * * *
1455 TTATTACTCATTTTAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTCAATTTTTTTTTACTT
66 TTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTGTAAGTTCAA-TATTTTTTACTT
*
1520 TTTTGGTGAAAACAAATTATAATTGAATGTCTACATCAAGAA
130 TTTTGGTGAAAACAAACTATAATTGAATGTCTACATCAAGAA
* ******** * * *
1562 A-CANNNNNNNNNNGGCATTCATT-AGCAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAA
1 ATGA--AAAAAAAAGGCATTCATTGA-CAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAA
* * * ** *
1625 GCGTTATTAATCGCTTTAAAAAGTTTTATAATCTCATAATTGATTGTAAGTTTAA-ATTTTTTA-
63 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTGTAAGTTCAATATTTTTTAC
* * * **
1688 TGTTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAA
128 T-TTTTTGGTGAAAACAAACTATAATTGAATGTCTACATCAAGAA
* *
1733 ATGAAAAAAAAAGGCATACATTGACACGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCC
1 ATGAAAAAAAAAGGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCC
* *
1798 TTATTACTCCCCTTAAATGGTTTTATAATCTCAT
66 TTATTACTCACTTTAAATGGTTTTATAATCTCAT
Statistics
Matches: 211, Mismatches: 51, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
169 1 0.00
170 76 0.36
171 46 0.22
172 32 0.15
173 56 0.27
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.37
Consensus pattern (171 bp):
ATGAAAAAAAAAGGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCTCATTCCTTCAAAAGCC
TTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTGTAAGTTCAATATTTTTTACTTT
TTTGGTGAAAACAAACTATAATTGAATGTCTACATCAAGAA
Done.