Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401553.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4677.0, 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: 2701
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.28
Warning! 705 characters in sequence are not A, C, G, or T
Found at i:844 original size:171 final size:170
Alignment explanation
Indices: 559--956 Score: 508
Period size: 171 Copynumber: 2.3 Consensus size: 170
549 NNNNNNNNNN
* * * **
559 AATTGATTTTAGGTTAAATGTTTTTACATCCTTTGTTATGACAGACTATAATTGAATGTCTACCT
1 AATTGATTTTAAGTTAAATG-TTTTACATCTTTTGTTAAGACAGACTATAATTGAATACCTACCT
** * * *
624 CGAGAAACATGTAGAAAATGCCATTTATTTGAAAGAAAAGTCTATTTATAGTCTCCCATTCCTTC
65 CGAGAAACATGTAGAAAACACCATTCATTTGAAAGAAAAATCCATTTATAGTCTCCCATTCCTTC
* *
689 AAAAGCTTTATCACTCGCTTCAAATGGTTTTATAATCTCAT
130 AAAAGCTTTATCACTCGCTTCAAAAGGTTTTAAAATCTCAT
**
730 AATTGATTTTAAGTTAAATAGTTTTACATCTTTTGTTAAGACAGACTATAATTGAATACCTGTCT
1 AATTGATTTTAAGTTAAAT-GTTTTACATCTTTTGTTAAGACAGACTATAATTGAATACCTACCT
* * ***
795 TGGGAAACATGTAGAAAACACCATTCATTTGAAAGAAAAATCCATTTATAGTCTTTTATTCCTTC
65 CGAGAAACATGTAGAAAACACCATTCATTTGAAAGAAAAATCCATTTATAGTCTCCCATTCCTTC
* *
860 AAAAGCTTTATCACTTGCTTTAAAAGGTTTTAAAATCTCAT
130 AAAAGCTTTATCACTCGCTTCAAAAGGTTTTAAAATCTCAT
* * * * * * * *
901 AATTGATTTTAACTTTAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAA
1 AATTGATTTTAA-GTTAAATGTTTTACATCTTTTGTTAAGACAGACTATAATTGAA
957 GGTTTACCTC
Statistics
Matches: 196, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
171 190 0.97
172 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (170 bp):
AATTGATTTTAAGTTAAATGTTTTACATCTTTTGTTAAGACAGACTATAATTGAATACCTACCTC
GAGAAACATGTAGAAAACACCATTCATTTGAAAGAAAAATCCATTTATAGTCTCCCATTCCTTCA
AAAGCTTTATCACTCGCTTCAAAAGGTTTTAAAATCTCAT
Found at i:1294 original size:343 final size:331
Alignment explanation
Indices: 656--1299 Score: 672
Period size: 343 Copynumber: 1.9 Consensus size: 331
646 ATTTATTTGA
* * * * *
656 AAGAAAAGTCTATTTATAGTCTCCCATTCCTTCAAAAGCTTTATCACTCGCTTCAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTCATCACTCACTTCAAATGGTTTTA
* * ** * *
721 TAATCTCATAATTGATTTTAAGTTAAATAGTTTTACATCTTTTGTTAAGACAGACTATAATTGAA
66 TAATCTCATAATTGATGTTAAGTTAAATACTTTTACATCTTTTGACAAAACAGACTATAATTAAA
* * * * * *
786 TACCTGTCTTGGGAAACATGTAGAAAACACCATTCATTTGAAAGAAAAATCCATTTATAGTCTTT
131 TACCTATCATAGCAAACATGTAGAAAACACCATTCATTGGAAAGAAAAATCCATTTATAGTCTCT
* ** *
851 TATTCCTTCAAAAGCTTTATCACTTGCTTTAAAAGGTTTTAAAATCTCATAATTGATTTTAACTT
196 CATTCCTTCAAAAGCTTTATCACTCACTTTAAAAGGTTTTAAAATCTCATAATTGATTTTAAATT
916 TAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAAGGTTTACCTCGAGAAAGGTGAAGA
261 TAATTTTTTTATA-TTTTTATTAAAACAGATTATAATTGAAGGTTTACCTCGAGAAAGGTGAAGA
981 AAAAGNNNNNNNNNNGC
325 AAAAG----------GC
* *
998 AAGAAAAGTCCATTTATAGTCACCCATTCC-TCTAAAAGCCTCATTACTCACTTTAAATGGTTTT
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTCATCACTCACTTCAAATGGTTTT
* * * * *
1062 ATAATCTCCA-AATTGATGTTAATTTGAATTCCTTTTATAT-TTTTAGACAAAACAGATTATAAT
65 ATAATCT-CATAATTGATGTTAAGTT-AAATACTTTTACATCTTTT-GACAAAACAGACTATAAT
* * * * * * * *
1125 TAAATGCTTATCATAGCACACATGTAGAAAA-AGTCATTCATTGGGAATAAAAGTCCATTTATGG
127 TAAATACCTATCATAGCAAACATGTAGAAAACA-CCATTCATTGGAAAGAAAAATCCATTTATAG
** * * * **
1189 TCTCTCATTGTTTCAAAAGTTTTATTACTCACTTTAAATGGTTTTTCAATCTCCA-AATTGA-TT
191 TCTCTCATTCCTTCAAAAGCTTTATCACTCACTTTAAAAGGTTTTAAAATCT-CATAATTGATTT
1252 TAAATTTGAATTTATTTTATA-TTTTAGTTAAAACAGATTATAATTGAA
255 TAAATTT-AATTT-TTTTATATTTTTA-TTAAAACAGATTATAATTGAA
1300 TGCTTGTCTT
Statistics
Matches: 250, Mismatches: 43, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
341 2 0.01
342 92 0.37
343 147 0.59
344 9 0.04
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (331 bp):
AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTCATCACTCACTTCAAATGGTTTTA
TAATCTCATAATTGATGTTAAGTTAAATACTTTTACATCTTTTGACAAAACAGACTATAATTAAA
TACCTATCATAGCAAACATGTAGAAAACACCATTCATTGGAAAGAAAAATCCATTTATAGTCTCT
CATTCCTTCAAAAGCTTTATCACTCACTTTAAAAGGTTTTAAAATCTCATAATTGATTTTAAATT
TAATTTTTTTATATTTTTATTAAAACAGATTATAATTGAAGGTTTACCTCGAGAAAGGTGAAGAA
AAAGGC
Found at i:1387 original size:171 final size:171
Alignment explanation
Indices: 599--1396 Score: 665
Period size: 171 Copynumber: 4.7 Consensus size: 171
589 CTTTGTTATG
* * * * * *
599 ACAGACTATAATTGAATG-TCTACCTCGAGAAACATGTAGAAAATGCCATTTATTTGAAAGAAAA
1 ACAGATTATAATTGAATGCT-TATCTTGAGAAACATATAGAAAAAGCCATTCATTTGAAAGAAAA
* * * *
663 GTCTATTTATAGTCTCCCATTCCTTCAAAAGCTTTATCACTCGCTTCAAATGGTTTTATAATCTC
65 GTCCATTTATAGTCTCCCATTCCTTCAAAAGCTTTATTACTCACTTTAAATGGTTTTATAATCTC
* * * * *
728 ATAATTGATTTTAAGTTAA-ATAGTTTTACATCTTTT-GTTAAG
130 ATAATTGATTTAAATTTAATTTA-TTTTATAT-TTTTAGTTAAA
* * * * * *
770 ACAGACTATAATTGAATACCTGTCTTGGGAAACATGTAGAAAACA-CCATTCATTTGAAAGAAAA
1 ACAGATTATAATTGAATGCTTATCTTGAGAAACATATAGAAAA-AGCCATTCATTTGAAAGAAAA
* *** * ** * *
834 ATCCATTTATAGTCTTTTATTCCTTCAAAAGCTTTATCACTTGCTTTAAAAGGTTTTAAAATCTC
65 GTCCATTTATAGTCTCCCATTCCTTCAAAAGCTTTATTACTCACTTTAAATGGTTTTATAATCTC
*
899 ATAATTGATTTTAACTTTAATTT-TTTTATATTTTTTA-TTAAA
130 ATAATTGA-TTTAAATTTAATTTATTTTATA-TTTTTAGTTAAA
* * * * ** ********** *
941 ACAGATTATAATTGAAGGTTTACCTCGAGAAAGGTGA-AGAAAAAGNNNNNNNNNNGCAAGAAAA
1 ACAGATTATAATTGAATGCTTATCTTGAGAAACAT-ATAGAAAAAGCCATTCATTTGAAAGAAAA
* * *
1005 GTCCATTTATAGTCACCCATTCC-TCTAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATCT
65 GTCCATTTATAGTCTCCCATTCCTTC-AAAAGCTTTATTACTCACTTTAAATGGTTTTATAATCT
** **
1069 CCA-AATTGATGTT-AATTTGAATTCCTTTTATATTTTTAGACAAA
129 -CATAATTGAT-TTAAATTT-AATTTATTTTATATTTTTAGTTAAA
* * * * * * * *
1113 ACAGATTATAATTAAATGCTTATCAT-AGCACACATGTAGAAAAAGTCATTCATTGGGAATAAAA
1 ACAGATTATAATTGAATGCTTATCTTGAG-AAACATATAGAAAAAGCCATTCATTTGAAAGAAAA
* * ** *
1177 GTCCATTTATGGTCTCTCATTGTTTCAAAAGTTTTATTACTCACTTTAAATGGTTTT-TCAATCT
65 GTCCATTTATAGTCTCCCATTCCTTCAAAAGCTTTATTACTCACTTTAAATGGTTTTAT-AATCT
1241 CCA-AATTGATTTAAATTTGAATTTATTTTATA-TTTTAGTTAAA
129 -CATAATTGATTTAAATTT-AATTTATTTTATATTTTTAGTTAAA
* * * *
1284 ACAGATTATAATTGAATGCTTGTCTTAAGAAACATACA-AAAACAGCCATTCATTT-AGATGAAA
1 ACAGATTATAATTGAATGCTTATCTTGAGAAACATATAGAAAA-AGCCATTCATTTGA-AAGAAA
* *
1347 AGTCCATTTATAGTATCCCATTCCTTCAAAAGCCTTATTACTCACTTTAA
64 AGTCCATTTATAGTCTCCCATTCCTTCAAAAGCTTTATTACTCACTTTAA
1397 NNNNNNNNNN
Statistics
Matches: 491, Mismatches: 114, Indels: 44
0.76 0.18 0.07
Matches are distributed among these distances:
170 12 0.02
171 337 0.69
172 139 0.28
173 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
ACAGATTATAATTGAATGCTTATCTTGAGAAACATATAGAAAAAGCCATTCATTTGAAAGAAAAG
TCCATTTATAGTCTCCCATTCCTTCAAAAGCTTTATTACTCACTTTAAATGGTTTTATAATCTCA
TAATTGATTTAAATTTAATTTATTTTATATTTTTAGTTAAA
Done.