Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397933.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1238.0, 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: 3508
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.27
Warning! 1066 characters in sequence are not A, C, G, or T
Found at i:489 original size:171 final size:171
Alignment explanation
Indices: 189--541 Score: 499
Period size: 171 Copynumber: 2.1 Consensus size: 171
179 NNNNNNNNNN
* *
189 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAGCTTTTATAATGTCATAATTGACTTTAAGTTA
1 ATTCCTTCAAAAGCCTTATTAATCGCTTTAAAAGCTTTTATAATCTCATAATTGACTTTAAGTTA
* * * * * * * **
254 AATTTTTTTATATTTTTTGTTAAAACAAATTATAGTTGAATCCCTACGTTGGGAAACATGAAGAA
66 AAGTTTTTTACATCTCTTGTTAAAACAAATTATAATTGAATACCTACCTCAGGAAACATGAAGAA
*
319 AAAGGTATTCGTTAACAAGAAAAGTCCATTTATAGCCACCC
131 AAAGGTATTCATTAACAAGAAAAGTCCATTTATAGCCACCC
*
360 ATTCCTTCAAAAGCCTTATTAATCGCTTTAAAAGGTTTTATAATCTCATAATTGACTTTAAGTTA
1 ATTCCTTCAAAAGCCTTATTAATCGCTTTAAAAGCTTTTATAATCTCATAATTGACTTTAAGTTA
* * * **
425 AAGTTTTTTACATCTCTTGTTAAAACAGATTATAATTGAATATCTACCTCAGTAAATGTGAAGAA
66 AAGTTTTTTACATCTCTTGTTAAAACAAATTATAATTGAATACCTACCTCAGGAAACATGAAGAA
* * * **
490 AAAGGTTTTCATTGACAAGAAAAGTCCATTTATAGTCACTT
131 AAAGGTATTCATTAACAAGAAAAGTCCATTTATAGCCACCC
531 ATTCCTTCAAA
1 ATTCCTTCAAA
542 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
171 159 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (171 bp):
ATTCCTTCAAAAGCCTTATTAATCGCTTTAAAAGCTTTTATAATCTCATAATTGACTTTAAGTTA
AAGTTTTTTACATCTCTTGTTAAAACAAATTATAATTGAATACCTACCTCAGGAAACATGAAGAA
AAAGGTATTCATTAACAAGAAAAGTCCATTTATAGCCACCC
Found at i:1871 original size:172 final size:170
Alignment explanation
Indices: 1343--2423 Score: 617
Period size: 172 Copynumber: 6.3 Consensus size: 170
1333 NNNNNNNNNC
* * *
1343 ATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATATTCTCAAAATCGATTTTAAGTTC
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTT-
* * * * *
1408 AATTTTTTTTACATTTTCGTGTAAAACAGATTATAATTGACTGTCTACCATGAGAAACGTAAAGA
65 AA-ATTTTTTACATTTT-TTTTAAAACAGATTATAATTGAATGTCTACCATGAGAAACGTGAAGA
* * **
1473 AAAAGGCAATCATAGGTAAG-AAAAGTAC-ATTTATAGTCACCT
128 AAAAGGCATTCATTGACAAGAAAAAGT-CTATTTATAGTCACCT
* * * ** *
1515 ATTCCCTGAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTAAAATTAATTTTAATTTA
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTTA
********** * *
1580 AATTCTTTGTACATTTTTTGTTAAAACAGATTATAATTGAATGNNNNNNNNNNGAAACATGAAAA
66 AATT-TTT-TACATTTTTT-TTAAAACAGATTATAATTGAATGTCTACCATGAGAAACGTG-AAG
* * * *
1645 AAAAAGACATTCTTTGACAA-AAAAAGCCCT-TTTATAGTCACCC
127 AAAAAGGCATTCATTGACAAGAAAAAG-TCTATTTATAGTCACCT
* * * * *
1688 ATTCTTTCAAAAGCCTTATTACTCGCTTCACAAT-GTTTTGTAATCTCATAATTGATTTTAAGTT
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTA-AATGGTTTTATAATCTCAAAATCGATTTTAAGTT
* * * * * *
1752 GAGTTTTTTAACATTTTTTATTAAAACAAATTA-AGATTGAATGTCTGCCTTGAAAAACGTGAAG
65 AAATTTTTT-ACATTTTTT-TTAAAACAGATTATA-ATTGAATGTCTACCATGAGAAACGTGAAG
* * *
1816 AAAATGGTATTCATTGACAAGAAAAAGTCTATATATAGTCACCT
127 AAAAAGGCATTCATTGACAAGAAAAAGTCTATTTATAGTCACCT
* * * *
1860 ATTCCTTCAAAAACCTTATGACTCGCTTTAAATGGTTTTATATTCTCAAAATCGATTTTAAATTA
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTTA
* * ** * * *
1925 ACTTTTTTTTACATTTTCATTTAAAATTGATTATAATT-AACTGTTTACCTTGAGAAGCGTGAAG
66 A--ATTTTTTACATTTT-TTTTAAAACAGATTATAATTGAA-TGTCTACCATGAGAAACGTGAAG
* ** ********** * *
1989 AAAAAGACATTCATTGGTAAG-NNNNNNNNNNTTATTGTCACCC
127 AAAAAGGCATTCATTGACAAGAAAAAGTCTATTTATAGTCACCT
* * * * * **
2032 ATTCCTTCAAATGCCTTATTACTAGCTTTAAAAGTTTTTATAATCTCATAATTAATTTTAAGTTA
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTTA
* * * ** ********** * * * *
2097 ATTTTTTTTTACATTTTTAGTTAAAAAAGGCTATAATTNNNNNNNNNNCTTGGGGAACATGAAGA
66 A--ATTTTTTACATTTTT-TTTAAAACAGATTATAATTGAATGTCTACCATGAGAAACGTGAAGA
* * * *
2162 AAAAGGTATTTATTGGA-AA-AAAAAGTCCATTTATAGGCACCT
128 AAAAGGCATTCATT-GACAAGAAAAAGTCTATTTATAGTCACCT
* * * * * * *********** *
2204 ATTCTTTTAAAAGCCTTAATACTCGCTTTAAACGGTTTTATAATATCATAATTNNNNNNNNNNTG
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTTA
* * * * *
2269 ATTTTTTTACATTTTTTGTTAAAACGGATT-TTA-TGAATGTTTACTTCA--AGAAATGTGAAGA
66 AATTTTTTACATTTTTT-TTAAAACAGATTATAATTGAATGTCTAC--CATGAGAAACGTGAAGA
** * *
2330 AAAAGATATTCATTGACAAG-TAAAGTCCATTTATAGTCACCT
128 AAAAGGCATTCATTGACAAGAAAAAGTCTATTTATAGTCACCT
* * * * *
2372 ATTCTTTTAAAAGCGTTATTACTCGCTTTAAATTGTTTTATATTCTCAAAAT
1 ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAAT
2424 TGNNNNNNNN
Statistics
Matches: 679, Mismatches: 203, Indels: 58
0.72 0.22 0.06
Matches are distributed among these distances:
167 2 0.00
168 89 0.13
169 2 0.00
170 26 0.04
171 31 0.05
172 374 0.55
173 144 0.21
174 11 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAATCGATTTTAAGTTA
AATTTTTTACATTTTTTTTAAAACAGATTATAATTGAATGTCTACCATGAGAAACGTGAAGAAAA
AGGCATTCATTGACAAGAAAAAGTCTATTTATAGTCACCT
Done.