Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399334.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2602.0, 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, 892
Length: 1487
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.28
Warning! 284 characters in sequence are not A, C, G, or T
Found at i:967 original size:171 final size:170
Alignment explanation
Indices: 479--1487 Score: 1093
Period size: 171 Copynumber: 5.9 Consensus size: 170
469 NNNNNNNNNN
* * * *
479 AGTAATAAGCTTTTTGAAAGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGCGTT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAAT-GGCTTT
* * * * * * *
544 TATGCATGTTTCTCAAGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACTTC
65 TTTGCATGTTTCTCCAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTC
* * **
609 AGCTTAAAATCAATTATGAGATTATAAAAGCATGAAAAGCG
130 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* *
650 AGTAATAAGCCTTTTGAAGGAATGGGTGAC-ATATAATAGGACTTTTCCTCTCAATCAATGGCTT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTATA-AAT-GGACTTTTCTTCTCAATGAATGGCTT
* * * * * * * *
714 TTTCTACACCT-TTTCT-GAGGTAGGCTTTCAATTATAGTCTGTTTTAA-AGGAAATTATAAAAA
64 TTT-TGCA--TGTTTCTCCAGGCAGACATTCAATTATAGTCTGTTTTAATA-AAAAATGTAAAAA
*
776 AATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAGC-
125 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * *
821 AGGTAATAAGACTTTTGAAGGAACGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGACTTT
1 A-GTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGC-TT
* * * * * *
886 TTTTGTACGTTTCTCCAGACAGACATTCAATTATAGTCTGTGTTAACAAAAAATGTAAAAGAATT
64 TTTTGCATGTTTCTCCAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATT
* *
951 CAAC-TAAAACTCAATTATGAGATTATAAAACTATTTAAAGCC
129 CAACTTAAAA-TCAATTATGAGATTATAAAACCATTTAAAGCG
* * * *
993 AATAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCCTGTCAATGAAT-GCTTGT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTT-T
* * * * * * *
1057 TTCTTCATGTTTCTCGAGGTAGAGATTCAATTATGGTATGTTTT-ATCCAAAAATGTAAAAAAAT
65 TT-TGCATGTTTCTCCAGGCAGACATTCAATTATAGTCTGTTTTAAT-AAAAAATGTAAAAAAAT
* *
1121 TCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAGGCG
128 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * *
1164 AGTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTGCTTCCCAATGAATGGGCTTT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAAT-GGCTTT
* * * * * *
1229 TATGCATGTTTCT-CAGGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACTT
65 TTTGCATGTTTCTCCA-GGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATT
* * * **
1293 CAGCTGAAAATCAATTATGAGATTATAAAAGCATGAAAAGCG
129 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * ** * * *
1335 AGTAATAAGCTTTTTGAAAGAATAAGCGACTATAAATGAACTTATCTTCTCAATGAATGGCTTTT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTT
* * * * * * *
1400 TTGCATATTT-TCCAAGGTAGACAATCGATTATATTCTATTTTAATAAAAAATATAAAAAAATTC
66 TTGCATGTTTCTCC-AGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTC
1464 AACTTAAAATCAATTATGAGATTA
130 AACTTAAAATCAATTATGAGATTA
Statistics
Matches: 693, Mismatches: 121, Indels: 49
0.80 0.14 0.06
Matches are distributed among these distances:
169 3 0.00
170 94 0.14
171 444 0.64
172 139 0.20
173 12 0.02
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (170 bp):
AGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTT
TTGCATGTTTCTCCAGGCAGACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
Found at i:1202 original size:342 final size:338
Alignment explanation
Indices: 479--1487 Score: 1257
Period size: 342 Copynumber: 3.0 Consensus size: 338
469 NNNNNNNNNN
* * *
479 AGTAATAAGCTTTTTGAAAGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGCGTT
1 AGTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGCTTT
*
544 TATGCATGTTTCTCAAGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACTTC
66 TATGCATGTTTCTCCAGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACTTC
609 AGCTTAAAATCAATTATGAGATTATAAAAGCATGAAAAGCGAGTAATAAGCCTTTTGAAGGAATG
131 AGC-TAAAATCAATTATGAGATTATAAAAGCATGAAAAGCGAGTAATAAGCCTTTTGAAGGAATG
*
674 GGTGAC-ATATAATAGGACTTTTCCTCTCAATCAATGGCTTTTTCTACACCTTTTCT-GAGGTAG
195 GGTGACTATA-AAT-GGACTTTTCCTCTCAATGAATGGCTTTTTCTACA--TTTTCTCGAGGTAG
* *
737 -GCTTTCAATTATAGTCTGTTTTA-AAGGAAATTATAAAAAAATTCAACTTAAAATCAATTATGA
256 AG-ATTCAATTATAGTCTGTTTTATAA--AAAATATAAAAAAATTCAACTTAAAATCAATTATGA
*
800 CATTATAAAACCATTTAAAGC
318 GATTATAAAACCATTTAAAGC
* * * * *
821 AGGTAATAAGACTTTTGAAGGAACGAGTGACTATAAATGGACTTTTCTTCTCAATGAAT-GACTT
1 A-GTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGC-T
* * * * * * * * * *
885 TTTTTGTACGTTTCTCCAGACAGACATTCAATTATAGTCTGTGTTAACAAAAAATGTAAAAGAA-
64 TTTATGCATGTTTCTCCAGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAA-AAC
* ** * *
949 TTCAACTAAAACTCAATTATGAGATTATAAAA-CTATTTAAAGCCAATAATAAGCCTTTTGAAGG
128 TTCAGCTAAAA-TCAATTATGAGATTATAAAAGC-ATGAAAAGCGAGTAATAAGCCTTTTGAAGG
* * *
1013 AATGGGTGACTCTAAATGGACTTTTCCTGTCAATGAAT-GCTTGTTTCTTCATGTTTCTCGAGGT
191 AATGGGTGACTATAAATGGACTTTTCCTCTCAATGAATGGCTT-TTTCTACAT-TTTCTCGAGGT
* * * * *
1077 AGAGATTCAATTATGGTATGTTTTATCCAAAAATGTAAAAAAATTCAACTTAAAATAAATTATGA
254 AGAGATTCAATTATAGTCTGTTTTAT-AAAAAATATAAAAAAATTCAACTTAAAATCAATTATGA
*
1142 GATTATAAAACCATTTAAGGC
318 GATTATAAAACCATTTAAAGC
* *
1163 GAGTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTGCTTCCCAATGAATGGGCTT
1 -AGTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGCTT
1228 TTATGCATGTTTCT-CAGGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACT
65 TTATGCATGTTTCTCCA-GGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACT
* *
1292 TCAGCTGAAAATCAATTATGAGATTATAAAAGCATGAAAAGCGAGTAATAAGCTTTTTGAAAGAA
129 TCAGCT-AAAATCAATTATGAGATTATAAAAGCATGAAAAGCGAGTAATAAGCCTTTTGAAGGAA
** * * * * * *
1357 TAAGCGACTATAAATGAACTTATCTTCTCAATGAATGGCTTTTT-TGCATATTT-TCCAAGGTAG
193 TGGGTGACTATAAATGGACTTTTCCTCTCAATGAATGGCTTTTTCTACAT-TTTCT-CGAGGTAG
* * * * *
1420 ACAATCGATTATATTCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
256 AGATTCAATTATAGTCTGTTTT-ATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
1485 TTA
320 TTA
Statistics
Matches: 564, Mismatches: 82, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
340 2 0.00
341 82 0.15
342 297 0.53
343 178 0.32
344 5 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (338 bp):
AGTAATAAGCCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTCTCAATGAATGGGCTTT
TATGCATGTTTCTCCAGGCAAAAATTTAATAATAGTCTGTTTTAATAAAAAATGTAAAAAACTTC
AGCTAAAATCAATTATGAGATTATAAAAGCATGAAAAGCGAGTAATAAGCCTTTTGAAGGAATGG
GTGACTATAAATGGACTTTTCCTCTCAATGAATGGCTTTTTCTACATTTTCTCGAGGTAGAGATT
CAATTATAGTCTGTTTTATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGC
Done.