Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402827.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5881.0, 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, 789
Length: 1316
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:490 original size:171 final size:171
Alignment explanation
Indices: 1--985 Score: 1053
Period size: 171 Copynumber: 5.8 Consensus size: 171
* * *
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTCTCATTAACACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACAG
* * * * * *
66 ATTATAATTAAATGTTTACCTTGAGAAGCATGCAGAAAAACCCATTCATTGGCAAGAAAGGCACA
66 ATTATAATTGAATGTTTTCCTTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
** * * *
131 TTTATAGTCACTTAAGCCTTCAAAAGCCTTATCACTTTCTG
131 TTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
* * *
172 TAAATGGTTTAATAATCTCATAATTGATTTAAAGTTGAATTATTTGACA-TTTTGATTAACACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACAG
* * * * * * *
236 ATTATACTTCAATGTTTCCCTCGAGAACC-TGAAGAAAAATCCATTCATTGACAAGAAAAGCACA
66 ATTATAATTGAATGTTTTCCTTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
* * *
300 TTTATAGTCACCGAAGCCTTCAAAAACCTTATTACTCTTTT
131 TTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
* *
341 TAAATGATTTTATAATCTAATAATTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACAG
* * *
406 ATTGTAATTGAATATTTTCCTTGACAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
66 ATTATAATTGAATGTTTTCCTTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
* * *
471 TTTATAGTCACCCAAGCCTTCAAAAGTCTAATTTCTCTCTT
131 TTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
* * ***
512 TAAATGGTTTTATAATCTCATAATTGAATTT-AAGTTGAATTTTTATTATATTTTTGGCCAA-AC
1 TAAATGGTTTTATAATCTCATAATTG-ATTTGAAGTTGAATTATT-TTACATTTTTGATTAACAC
* * * *** *
575 AGATTATAATTGAATGTTTACCTTTG-GAAACATGAAG-AAAACACATTCATT-GCAA-TTTAGA
64 AGATTATAATTGAATGTTTTCC-TTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGC
* * * *
636 CTATTTATTA-TCACCCAAGCCTTTAAAACCCTTGTTACTCTCTT
128 CCATTTA-TAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
* * *
680 TAAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATGT-TTTTACATTTTT-AGTTAAAAC
1 TAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAAT-TATTTTACATTTTTGA-TTAACAC
* * * * * * * *
743 AGATTATAATTGAATATTTTTCATGGGAAACGTGAAGAAAAACCCATTCATCGGCAAGAAAAACC
64 AGATTATAATTGAATGTTTTCCTTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCC
* * * *
808 CATTTATAATCACCCAAGTCTTTAAAAGCCTTATTACTCTATT
129 CATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
* * * * * * * * * *
851 GAAATGGTTTCATAACCTCAAAATTTAATTTTAA-TTGAATTTTTTTATATTTTTGGTTAAAACA
1 TAAATGGTTTTATAATCTCATAA-TTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACA
* * * * *
915 GATTATAATTGAATGTTTTCCATGTGA-AACC-TAAAGAAAAGCTCATTTATTTGCAAGAAAAGC
65 GATTATAATTGAATGTTTTCC-T-TGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGC
*
978 TCATTTAT
128 CCATTTAT
986 TTGCAAGAAA
Statistics
Matches: 686, Mismatches: 108, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
167 17 0.02
168 103 0.15
169 128 0.19
170 94 0.14
171 311 0.45
172 31 0.05
173 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
TAAATGGTTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTGATTAACACAG
ATTATAATTGAATGTTTTCCTTGAGAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
TTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTT
Found at i:781 original size:339 final size:338
Alignment explanation
Indices: 1--1312 Score: 1208
Period size: 339 Copynumber: 3.8 Consensus size: 338
* *
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTCTCA-TTAACACA
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTT-TTAGTTAAAACA
* * * * * *
65 GATTATAATTAAATGTTTACCTTGAGAAGCATGCAGAAAAACCCATTCATTGGCAAGAAAGGCAC
65 GATTATAATTGAATATTTACCTTGAGAAACATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
** * * *
130 ATTTATAGTCACTTAAGCCTTCAAAAGCCTTATCACTTTCTGTAAATGGTTTAATAATCTCATAA
130 ATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTAATAATCTCATAA
* * * * * * * * *
195 TTG-ATTTAAAGTTGAATTATTTGACA-TTTTGATTAACACAGATTATACTTCAATGTTTCCCTC
195 TTGAATTT-AAGTTGAATTTTTTTATATTTTTG-GTAAAACAGATTATAATTGAATGTTTCCATG
*** * *
258 GAGAACCTGAAGAAAA-ATCCATTCATTGACAAGAAAAGCAC-ATTTATAGTCACCGAAGCCTTC
258 GA-AACCTGAAGAAAACA--CATTCATTGACAA-TTTAGAACTATTTATAGTCACCCAAGCCTTC
*
321 AAAAACCTTATTACTCTTTT
319 AAAAACCTTATTACTCTATT
* *
341 TAAATGATTTTATAATCTAATAATTGATTTGAAGTTGAATTATTTTACATTTTT-GATTAACACA
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTAG-TTAAAACA
* * * *
405 GATTGTAATTGAATATTTTCCTTGACAACCATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
65 GATTATAATTGAATATTTACCTTGAGAAACATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
* * * *
470 ATTTATAGTCACCCAAGCCTTCAAAAGTCTAATTTCTCTCTTTAAATGGTTTTATAATCTCATAA
130 ATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTAATAATCTCATAA
** *
535 TTGAATTTAAGTTGAATTTTTATTATATTTTTGGCCAAACAGATTATAATTGAATGTTTACCTTT
195 TTGAATTTAAGTTGAATTTTT-TTATATTTTTGGTAAAACAGATTATAATTGAATGTTT-CC-AT
* *
600 GGAAACATGAAGAAAACACATTCATTG-CAATTTAG-ACTATTTATTA-TCACCCAAGCCTTTAA
257 GGAAACCTGAAGAAAACACATTCATTGACAATTTAGAACTATTTA-TAGTCACCCAAGCCTTCAA
* * *
662 AACCCTTGTTACTCTCTT
321 AAACCTTATTACTCTATT
* * *
680 TAAATGGTTTTATAACCTCATAATTGATTTTAAGTTGAATGT-TTTTACATTTTTAGTTAAAACA
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAAT-TATTTTACATTTTTAGTTAAAACA
** * * * * *
744 GATTATAATTGAATATTTTTCATGGGAAACGTGAAGAAAAACCCATTCATCGGCAAGAAAAACCC
65 GATTATAATTGAATATTTACCTTGAGAAACATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
* * * * * * * *
809 ATTTATAATCACCCAAGTCTTTAAAAGCCTTATTACTCTATTGAAATGGTTTCATAACCTCAAAA
130 ATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTAATAATCTCATAA
*
874 TTTAATTTTAA-TTGAATTTTTTTATATTTTTGGTTAAAACAGATTATAATTGAATGTTTTCCAT
195 TTGAA-TTTAAGTTGAATTTTTTTATATTTTTGG-TAAAACAGATTATAATTGAATG-TTTCCAT
* * *
938 GTGAAACCTAAAGAAAAGCTCATTTATTTGCAAGAAAAGCTCATTTATTTGCAAGAAAAGCTCAT
257 G-GAAACCTGAAGAAAA-CACATTCA-TT----G---A---CA---ATTT---AG--AA-CT-AT
* *
1003 TTATAGTCACCTAAGCCTTCAAAAGCCTTATTACTCTATT
299 TTATAGTCACCCAAGCCTTCAAAAACCTTATTACTCTATT
* * * * * * * *
1043 TAAATGGTTTTACAATCTCATAATTGATTTTAGGTTAAAATGTTTTACATTTTTAGTTAAAATAG
1 TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTAGTTAAAACAG
* ** * *
1108 TTTATAATTGAATGGTTACCTT-AGGAAATATGAAGAAAAACCCATTCACTGGCAAGAAAAGCCC
66 ATTATAATTGAATATTTACCTTGA-GAAACATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
* ********** * * *
1172 ATTTATAGTCACCTAAGCNNNNNNNNNNCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAA
130 ATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTAATAATCTCATAA
* * * ** * * *
1237 TTGATTTTAAGTCGAAATTTTTTATATTTTTATTTAAAACAGACTATAACTGAATGATTTCCAAG
195 TTGAATTTAAGTTGAATTTTTTTATATTTTT-GGTAAAACAGATTATAATTGAATG-TTTCC-AT
1302 GGAAACCTGAA
257 GGAAACCTGAA
1313 TAAA
Statistics
Matches: 803, Mismatches: 123, Indels: 69
0.81 0.12 0.07
Matches are distributed among these distances:
338 16 0.02
339 251 0.31
340 207 0.26
341 38 0.05
342 19 0.02
343 4 0.00
345 1 0.00
352 2 0.00
355 4 0.00
358 2 0.00
361 1 0.00
362 10 0.01
363 246 0.31
364 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (338 bp):
TAAATGATTTTATAATCTCATAATTGATTTGAAGTTGAATTATTTTACATTTTTAGTTAAAACAG
ATTATAATTGAATATTTACCTTGAGAAACATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
TTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTAATAATCTCATAAT
TGAATTTAAGTTGAATTTTTTTATATTTTTGGTAAAACAGATTATAATTGAATGTTTCCATGGAA
ACCTGAAGAAAACACATTCATTGACAATTTAGAACTATTTATAGTCACCCAAGCCTTCAAAAACC
TTATTACTCTATT
Found at i:974 original size:21 final size:21
Alignment explanation
Indices: 948--1006 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
938 GTGAAACCTA
948 AAGAAAAGCTCATTTATTTGC
1 AAGAAAAGCTCATTTATTTGC
969 AAGAAAAGCTCATTTATTTGC
1 AAGAAAAGCTCATTTATTTGC
990 AAGAAAAGCTCATTTAT
1 AAGAAAAGCTCATTTAT
1007 AGTCACCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
AAGAAAAGCTCATTTATTTGC
Found at i:1146 original size:192 final size:192
Alignment explanation
Indices: 777--1177 Score: 446
Period size: 192 Copynumber: 2.1 Consensus size: 192
767 GGGAAACGTG
* * ** * *
777 AAGAAAAACCCATTCATCGGCAAGAAAAACCCATTTATAATCACCCAAGTCTTTAAAAGCCTTAT
1 AAGAAAAGCCCATTTATTTGCAAGAAAAACCCATTTATAATCACCCAAGCCTTCAAAAGCCTTAT
* * * * * *
842 TACTCTATTGAAATGGTTTCATAACCTCAAAATTTAATTTTAATTGAATTTTTTTATATTTTTGG
66 TACTCTATTGAAATGGTTTCACAACCTCAAAATTTAATTTTAATTAAAATGTTTTACATTTTTAG
* * * * * * * *
907 TTAAAACAGATTATAATTGAATGTTTTCCATGTGAAACCTAAAGAAAAGCTCATTTATTTGC
131 TTAAAACAGATTATAATTGAATGGTTACCATGTGAAACATAAAGAAAAACCCATTCACTGGC
* * * * *
969 AAGAAAAGCTCATTTATTTGCAAGAAAAGCTCATTTATAGTCACCTAAGCCTTCAAAAGCCTTAT
1 AAGAAAAGCCCATTTATTTGCAAGAAAAACCCATTTATAATCACCCAAGCCTTCAAAAGCCTTAT
* * * * * *
1034 TACTCTATTTAAATGGTTTTACAATCTCATAA-TTGATTTTAGGTTAAAATGTTTTACATTTTTA
66 TACTCTATTGAAATGGTTTCACAACCTCAAAATTTAATTTTA-ATTAAAATGTTTTACATTTTTA
* * * * *
1098 GTTAAAATAGTTTATAATTGAATGGTTACCTTAG-GAAATATGAAGAAAAACCCATTCACTGGC
130 GTTAAAACAGATTATAATTGAATGGTTACCAT-GTGAAACATAAAGAAAAACCCATTCACTGGC
1161 AAGAAAAGCCCATTTAT
1 AAGAAAAGCCCATTTAT
1178 AGTCACCTAA
Statistics
Matches: 170, Mismatches: 37, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
191 8 0.05
192 161 0.95
193 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (192 bp):
AAGAAAAGCCCATTTATTTGCAAGAAAAACCCATTTATAATCACCCAAGCCTTCAAAAGCCTTAT
TACTCTATTGAAATGGTTTCACAACCTCAAAATTTAATTTTAATTAAAATGTTTTACATTTTTAG
TTAAAACAGATTATAATTGAATGGTTACCATGTGAAACATAAAGAAAAACCCATTCACTGGC
Done.