Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399444.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2708.0, 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: 2715
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.30
Warning! 604 characters in sequence are not A, C, G, or T
Found at i:1216 original size:170 final size:161
Alignment explanation
Indices: 1027--1530 Score: 447
Period size: 171 Copynumber: 3.0 Consensus size: 161
1017 NNNNNAAAGC
* *
1027 CTTATTACTAGCTTTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAATTGTTTTACATT
1 CTTATTACTCGCATTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAATTGTTTTACATT
* *
1092 TTTTGCTAAGACAGACTATAATCGAATGTCTACATCAAGAAACGTGAAAAAAAATTATTCATTGG
66 TTTTGCTAAAACAGACTATAATCGAATGTCTAC-TCAAGAAACGTGAAAAAAAATCATTCATTGG
1157 AAAGAAAAGTCCATTTATAGTCACCCATTCATT
130 AAA-AAAAGTCCATTTATAGTCACCCATTCATT
*** * * *
1190 CNNNNNNNNNNTTACTCGCATTAAATTGTTTTATAATCTCATAATTGATTTTAGGTTGAATTTGT
1 C-------TTATTACTCGCATTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAA-TTGT
* * * * * *
1255 TTTACATTTTTAGCTAAAACAGACTATAATTGAATTTCTACTTAGAGAAACTTGAAGAAAAATAC
58 TTTACATTTTTTGCTAAAACAGACTATAATCGAATGTCTACTCA-AGAAACGTGAAAAAAAAT-C
** ***
1320 ATTCATTTACAAAAAAAAGTCCATTTATAGTCACCCATTCCNNNNNNNNN
121 ATTCA-TT-GGAAAAAAAGTCCATTTATAGTCACCCATT-C------ATT
* * **
1370 NTTATTACTCG-ATTTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTG-ATTTTTTTTTAT
1 CTTATTACTCGCA-TTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAATTGTTTTACAT
* * * * * * * *
1433 TTATTGTTAAAACAGACTAGAATGGAATGCCTGCTTCTAGAAATGTGTAAAAAAAAATCATTCAT
65 TTTTTGCTAAAACAGACTATAATCGAATGTCTAC-TCAAGAAACGTG--AAAAAAAATCATTCAT
1498 TGAGAAAACAAA-TCCATTTATAGTCACCCATTC
127 TG-GAAAA-AAAGTCCATTTATAGTCACCCATTC
1531 CTTCAAAAGC
Statistics
Matches: 270, Mismatches: 46, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
163 1 0.00
170 47 0.17
171 124 0.46
172 17 0.06
173 77 0.29
174 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (161 bp):
CTTATTACTCGCATTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAATTGTTTTACATT
TTTTGCTAAAACAGACTATAATCGAATGTCTACTCAAGAAACGTGAAAAAAAATCATTCATTGGA
AAAAAAGTCCATTTATAGTCACCCATTCATT
Found at i:1618 original size:343 final size:335
Alignment explanation
Indices: 880--1870 Score: 777
Period size: 342 Copynumber: 2.9 Consensus size: 335
870 NNNNNNNNNN
880 ATAATCTCATAATTGATTTTAAGTTGAATATTTTTTAAATTTTTAGTTAAAACAGACTATAATTG
1 ATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTT-AATTTTTAGTTAAAACAGACTATAATTG
* * * *
945 AATTTCTAGTTAGAGAAACGTGAAGAAAAATGCATTCGTTTACAAGAAAAGTCCATTTATAGTCA
64 AATTTCTACTTAGAGAAACGTGAAGAAAAATACATTCATTTACAAAAAAAGTCCATTTATAGTCA
****** *
1010 CCNNNNNNNNNNAAAGCCTTATTACTAGCTTTAAATTGTTTTATAATCGCATAATTAATTTTAAG
129 CC----CATTCCAAAGCCTTATTACTAGATTTAAATTGTTTTATAATCGCATAATTAATTTTAAG
* * * *
1075 TTGAATTGTTTTACATTTTTTGCTAAGACAGACTATAATCGAATGTCTACATCAAGAAACGTGAA
190 TTGAATTGTTTTACATTTATTGCTAAAACAGACTAGAATCGAATGCCTACATCAAGAAACGTGAA
* *********
1140 AAAAAATTATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCATTCATTCNNNNNNNNNNTTAC
255 AAAAAATCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCATTCATTC-AAAAGCCTTTTAC
*
1205 TCGCATTAAATTGTTTT
319 TCGCATTAAATTATTTT
* *
1222 ATAATCTCATAATTGATTTTAGGTTGAATTTGTTTTACATTTTTAGCTAAAACAGACTATAATTG
1 ATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTA-ATTTTTAGTTAAAACAGACTATAATTG
*
1287 AATTTCTACTTAGAGAAACTTGAAGAAAAATACATTCATTTACAAAAAAAAGTCCATTTATAGTC
64 AATTTCTACTTAGAGAAACGTGAAGAAAAATACATTCATTTAC-AAAAAAAGTCCATTTATAGTC
****** *
1352 ACCCATTCCNNNNNNNNNNTTATTACTCGATTTAAATTGTTTTATAATCGCATAATTAATTTTAA
128 ACCCATTCC----AAAGCCTTATTACTAGATTTAAATTGTTTTATAATCGCATAATTAATTTTAA
* ** * * * * * *
1417 GTTG-ATTTTTTTTTATTTATTGTTAAAACAGACTAGAATGGAATGCCTGCTTCTAGAAATGTGT
189 GTTGAATTGTTTTACATTTATTGCTAAAACAGACTAGAATCGAATGCCTACATCAAGAAACGTG-
*
1481 AAAAAAAAATCATTCATTGAGAAA-ACAAA-TCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
253 -AAAAAAAATCATTCATTG-GAAAGA-AAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTT
*********
1544 NNNNNNNNNNTTAAATTATTTT
315 -TTACTCGCATTAAATTATTTT
** *
1566 ATAATCTCATAATTGATTTTAAAATGAATTTTTTTATATTTTTTA-TTAAAACAGGCTATAATTG
1 ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA-A-TTTTTAGTTAAAACAGACTATAATTG
* * * * * * * * * * *
1630 -ATTACATGCCTT-GAGAAACGTTCAA-AAAAA-GCTATTTACTGAGAAGAAAAGTCTATTTTTA
64 AATTTC-T-ACTTAGAGAAACG-TGAAGAAAAATAC-ATTCATTTACAAAAAAAGTCCATTTATA
* * * * * * *
1691 GCCACCCATTCCTTCAAAAGCCTTATTACTTA-TTTTAAATTATTTTTTAATCTCATAATTGATA
125 GTCACCCATT-C--C-AAAGCCTTATTAC-TAGATTTAAATTGTTTTATAATCGCATAATTAATT
* * * * * * **
1755 TTAAGATGAATT-TTTTACATTT-TTGGTTAAATCAGACAATAATTGAATGTTTAGC-TC-AGCA
185 TTAAGTTGAATTGTTTTACATTTATT-GCTAAAACAGACTAGAATCGAATGCCTA-CATCAAG-A
* ** * *
1816 AACATGAAAAAAAGCCATTCATT-GACAAGAGAAGTCCATTTATAGTCACCTATTC
247 AACGTGAAAAAAAATCATTCATTGGA-AAGAAAAGTCCATTTATAGTCACCCATTC
1871 NNNNNNNNNN
Statistics
Matches: 517, Mismatches: 104, Indels: 58
0.76 0.15 0.09
Matches are distributed among these distances:
338 2 0.00
339 4 0.01
340 36 0.07
341 7 0.01
342 248 0.48
343 119 0.23
344 93 0.18
345 8 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (335 bp):
ATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAATTTTTAGTTAAAACAGACTATAATTGAA
TTTCTACTTAGAGAAACGTGAAGAAAAATACATTCATTTACAAAAAAAGTCCATTTATAGTCACC
CATTCCAAAGCCTTATTACTAGATTTAAATTGTTTTATAATCGCATAATTAATTTTAAGTTGAAT
TGTTTTACATTTATTGCTAAAACAGACTAGAATCGAATGCCTACATCAAGAAACGTGAAAAAAAA
TCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCCATTCATTCAAAAGCCTTTTACTCGCATT
AAATTATTTT
Done.