Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400625.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3814.0, 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: 1747
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.34
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:427 original size:172 final size:171
Alignment explanation
Indices: 249--603 Score: 369
Period size: 171 Copynumber: 2.1 Consensus size: 171
239 NNNNNNNNAT
* * *
249 GGTTTTATAATCTCAAAATTGATTTAAATTTGAA-TTCATTGTACATTTTTGGCTAAAACATATT
1 GGTTTTATAATCTCAAAATTGATTTAAAGTTGAACTT-ATTG-ACATTTTTAGCTAAAACAAATT
*
313 ATAATTGAATATCAACCTCAAG-AAACATGAAGAAAAAGGCATTCATT-AGCAAGAAATCG-CCA
64 ATAATTGAATATC-ACCTCAAGAAAACATGAAGAAAAAGGCATTCATTGA-CAAGAAA-AGTCCA
* * *
375 TTTATAGTTATCTA-TTCTTTCAAAAGCCTTATTACTCAGTTTAAAG
126 TTTATAGTCATCTATTTC-TTCAAAAGCCTCATTACTCACTTTAAAG
* * * * * * * *
421 GGTTTTATAATTTTATAATTGATTTTAAGTTGAACTTTTTGACCTTTTTAGTTAGAACAAATTAT
1 GGTTTTATAATCTCAAAATTGATTTAAAGTTGAACTTATTGACATTTTTAGCTAAAACAAATTAT
* * ** *** * * * *
486 CATTGAATTTCTGCTTTGGAAAACTTGTAGAAAAAGGTATTCATTGATAAGAAAAGTCCATTTAT
66 AATTGAATATCACCTCAAGAAAACATGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTAT
*
551 AGTCATCTATTTCTTCAAAAGCCTCATTACTCACTTTAAAT
131 AGTCATCTATTTCTTCAAAAGCCTCATTACTCACTTTAAAG
*
592 GGCTTTATAATC
1 GGTTTTATAATC
604 NNNNNNNNNN
Statistics
Matches: 149, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
170 4 0.03
171 107 0.72
172 36 0.24
173 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (171 bp):
GGTTTTATAATCTCAAAATTGATTTAAAGTTGAACTTATTGACATTTTTAGCTAAAACAAATTAT
AATTGAATATCACCTCAAGAAAACATGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTAT
AGTCATCTATTTCTTCAAAAGCCTCATTACTCACTTTAAAG
Found at i:1170 original size:170 final size:171
Alignment explanation
Indices: 882--1308 Score: 486
Period size: 170 Copynumber: 2.5 Consensus size: 171
872 NNNNNNNNNN
* * * * *
882 CATTCTTTCAAAAGCCTTATTACTCATTTTAAAGGGTTTTACAATCTCATAATTAATTTTAAGTT
1 CATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGATTTATAATCTCATAATTGATTTTAAGTT
* * * ** * * * *
947 GAACTTTTTGACATTTTTGGTTAGAACAGATTATAATTGAATGTCTGCCTTGGGAAACCTGTAGG
66 CAAATTTTTTACATTTTTGGCCAGAAAAGACTATAATTGAATGTCTGCCTTGGGAAACCTGAAGA
** * *
1012 AAAAGGTGTTCATTGGCAAGAAAAGTCCATTTAT-TGTCATC
131 AAAAGGCATTCATTGACAAGAAAAGTCCATTTATAT-TCACC
* * * * *
1053 CATTTTTTCAAAAGCCTTATTACTCACTATAAATGGCTTTATAATCTCAAAATTGATTTGAAGTT
1 CATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGATTTATAATCTCATAATTGATTTTAAGTT
* * **
1118 -AAATTTTTTACATTTTTGGCCCA-AAAAGGCTATAATTGAATGTCTGCCTTGGGGAATGTGAAG
66 CAAATTTTTTACATTTTTGG-CCAGAAAAGACTATAATTGAATGTCTGCCTTGGGAAACCTGAAG
* * *
1181 AAAAATGCATTTATTGATAAGAAAAGTCCATTTATATTCACC
130 AAAAAGGCATTCATTGACAAGAAAAGTCCATTTATATTCACC
* *
1223 CATTGC-TTCAAAAGCCTTACTACTTC-CTTTAAATGGATTTATAATCTCATAACTGATTTTAAG
1 CATT-CTTTCAAAAGCCTTATTAC-TCACTTTAAATGGATTTATAATCTCATAATTGATTTTAAG
1286 TTCAAACTTTTTTACATTTTTGG
64 TTCAAA-TTTTTTACATTTTTGG
1309 TTAATACATA
Statistics
Matches: 215, Mismatches: 35, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
170 136 0.63
171 63 0.29
172 16 0.07
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (171 bp):
CATTCTTTCAAAAGCCTTATTACTCACTTTAAATGGATTTATAATCTCATAATTGATTTTAAGTT
CAAATTTTTTACATTTTTGGCCAGAAAAGACTATAATTGAATGTCTGCCTTGGGAAACCTGAAGA
AAAAGGCATTCATTGACAAGAAAAGTCCATTTATATTCACC
Found at i:1484 original size:23 final size:22
Alignment explanation
Indices: 1433--1484 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1423 AATCTCATAA
1433 TTGATTTTAAGTGTAAATATTT
1 TTGATTTTAAGTGTAAATATTT
*
1455 TTAGATTTTTAGT-TAAAATATTT
1 TT-GATTTTAAGTGT-AAATATTT
1478 TGTGATT
1 T-TGATT
1485 GAATGTCTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.12
23 22 0.85
24 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TTGATTTTAAGTGTAAATATTT
Done.