Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400871.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4039.0, 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: 3649
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.31
Warning! 705 characters in sequence are not A, C, G, or T
Found at i:1079 original size:171 final size:161
Alignment explanation
Indices: 785--1279 Score: 301
Period size: 171 Copynumber: 3.0 Consensus size: 161
775 TAAGTTGAAG
* **
785 TTTTTTATATTTTTCGCTAAAACAGATTATAATTGAATGTCGACCTTAGGAAAGGTGAAGAAAAA
1 TTTTTTATATTTTTCGCTAAAACAAATTATAATTGAATGTCGACCTTAGGAAACATGAAGAAAAA
* * * * * * *
850 GTCATTCATTAACTAGAAAAGTCTATTTATAGTTACTCATGCCTTTGAAAGCCTTATTACTTACT
66 GCCATTCATTAACTAGAAAAGTCTACTTATAGTAACCCATGCCTTTCAAAACCTTATTACTGACT
*
915 TTAAACAGTTTTATAATCTCATAATTNNNNNNNNNNTAAAT
131 TTAAACAGCTTTATAATCTCATAATT----------TAAAT
* * *
956 TTTTTTATATTTTT-GGTCAAAACAAATTATAATTGATTGTCTG-CCTTAGTAAACATGAAGAAA
1 TTTTTTATATTTTTCGCT-AAAACAAATTATAATTGAATGTC-GACCTTAGGAAACATGAAGAAA
* ** *
1019 AAGCCGTTCATT-TGTAAGAAAAGTCTACTTATAGTAACCCA--CTTCTTCAAAACTCTTATTAC
64 AAGCCATTCATTAACT-AGAAAAGTCTACTTATAGTAACCCATGCCT-TTCAAAAC-CTTATTAC
* ** * *
1081 TGGCTTTAAATGGCTTTGTAATCTCATAATTGATTTTAAGT
126 TGACTTTAAACAGCTTTATAATCTCAT-A---A-TTTAAAT
* * * * **
1122 TGAATTGTTTATATTTTTGGTTAAAACATATTTTAATTGAATGTTTACCTT-GAGAAACATGAA-
1 T---TT-TTTATATTTTTCGCTAAAACAAATTATAATTGAATGTCGACCTTAG-GAAACATGAAG
** ** * * * *
1185 AAAAA-AAATTCATTGGCAAGAAAAGT-TCATTTATAGTCACCCATG-CTTTCAAATGCCTTATT
61 AAAAAGCCATTCATTAACTAGAAAAGTCT-ACTTATAGTAACCCATGCCTTTCAAA-ACCTTATT
** *
1247 ACTCG-CTTTAAATGGTTTTATAATCTCATAATT
124 ACT-GACTTTAAACAGCTTTATAATCTCATAATT
1280 CATTTTTTAA
Statistics
Matches: 259, Mismatches: 42, Indels: 54
0.73 0.12 0.15
Matches are distributed among these distances:
163 2 0.01
164 1 0.00
166 5 0.02
167 2 0.01
168 64 0.25
169 13 0.05
170 52 0.20
171 115 0.44
172 2 0.01
175 1 0.00
176 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.39
Consensus pattern (161 bp):
TTTTTTATATTTTTCGCTAAAACAAATTATAATTGAATGTCGACCTTAGGAAACATGAAGAAAAA
GCCATTCATTAACTAGAAAAGTCTACTTATAGTAACCCATGCCTTTCAAAACCTTATTACTGACT
TTAAACAGCTTTATAATCTCATAATTTAAAT
Found at i:1394 original size:341 final size:342
Alignment explanation
Indices: 694--1418 Score: 734
Period size: 341 Copynumber: 2.1 Consensus size: 342
684 TCTTTGGCAT
** * *
694 GAAAAGTCCATTTATAGCCACCTATTTCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTAATA
1 GAAAAGTCCATTTATAGTAACCCACTTCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTAATA
* *
759 ATCCCATAATTTATTTTAAGTTGAAGTTTTTTATATTTTTCGCTAAAACAGATTATAATTGAATG
66 ATCCCATAATTGATTTTAAGTTGAAGTTGTTTATATTTTTCGCTAAAACAGATTATAATTGAATG
** ** * * *
824 TCGACCTTAGGAAAGGTGAAGAAAAAGTCATTCATTAACTAGAAAAGTCTATTTATAGTTACTCA
131 TCGACCTTAGGAAACATGAAGAAAAAGAAATTCATTAACAAGAAAAGTCTATTTATAGTCACCCA
* * **********
889 TGCCTTTGAAAGCCTTATTACTTACTTTAAACAGTTTTATAATCTCATAATTNNNNNNNNNNTAA
196 TGCCTTTCAAAGCCTTATTACTCACTTTAAACAGTTTTATAATCTCATAATTTTTTTTAAGTTAA
* * * * * * **
954 ATTTTTTTATATTTTTGGTCAAAACAAATTATAATTGATTGTCTGCCTTAGTAAACATGAAGAAA
261 ATTGTTTTACATTTTTAGTCAAAACAAATTATAATTGAATATCTGCCTTAGGAAACAAAAAGAAA
*
1019 AAGCCGTTCATTTGTAA
326 AAGCCATTCATTTGTAA
* * ** * *
1036 GAAAAGTCTACTTATAGTAACCCACTTCTTCAAAA-CTCTTATTACTGGCTTTAAATGGCTTT-G
1 GAAAAGTCCATTTATAGTAACCCACTTCTTCAAAAGC-CTTATTACTCACTTTAAATAG-TTTAA
* * * * *
1099 TAATCTCATAATTGATTTTAAGTTGAA-TTGTTTATATTTTTGGTTAAAACATATTTTAATTGAA
64 TAATCCCATAATTGATTTTAAGTTGAAGTTGTTTATATTTTTCGCTAAAACAGATTATAATTGAA
** **
1163 TGTTTACCTT-GAGAAACATGAA-AAAAA-AAATTCATTGGCAAGAAAAGT-TCATTTATAGTCA
129 TGTCGACCTTAG-GAAACATGAAGAAAAAGAAATTCATTAACAAGAAAAGTCT-ATTTATAGTCA
* **
1224 CCCATG-CTTTCAAATGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTTT
192 CCCATGCCTTTCAAA-GCCTTATTACTCACTTTAAACAGTTTTATAATCTCATAATT--TTTTTT
** * *
1288 AAGTTAAATTGTTTTACATTTTTAGTTTAAACAGATTATAATTGAATATCTGCCTTGGGAAACAA
254 AAGTTAAATTGTTTTACATTTTTAGTCAAAACAAATTATAATTGAATATCTGCCTTAGGAAACAA
*
1353 AAAGAAAAAGCTATTCA-TTG-ACTA
319 AAAGAAAAAGCCATTCATTTGTA--A
* * * *
1377 GAAAAGCCCATTTATAGTCACTCA-TACCTTCAAAAGCCTTAT
1 GAAAAGTCCATTTATAGTAACCCACT-TCTTCAAAAGCCTTAT
1419 NNNNNNNNNN
Statistics
Matches: 309, Mismatches: 63, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
338 8 0.03
339 69 0.22
340 10 0.03
341 146 0.47
342 73 0.24
343 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.38
Consensus pattern (342 bp):
GAAAAGTCCATTTATAGTAACCCACTTCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTAATA
ATCCCATAATTGATTTTAAGTTGAAGTTGTTTATATTTTTCGCTAAAACAGATTATAATTGAATG
TCGACCTTAGGAAACATGAAGAAAAAGAAATTCATTAACAAGAAAAGTCTATTTATAGTCACCCA
TGCCTTTCAAAGCCTTATTACTCACTTTAAACAGTTTTATAATCTCATAATTTTTTTTAAGTTAA
ATTGTTTTACATTTTTAGTCAAAACAAATTATAATTGAATATCTGCCTTAGGAAACAAAAAGAAA
AAGCCATTCATTTGTAA
Done.