Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398698.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1984.0, 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: 1956
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:561 original size:171 final size:171
Alignment explanation
Indices: 1--1081 Score: 897
Period size: 171 Copynumber: 6.3 Consensus size: 171
* * * * *
1 AAAACCAATTATGAAATTATAAAACCAATTAAAGCGAGTAATAAGGCTTTTGAAAGAAT-GGTTG
1 AAAATCAATTATGAGATTATAAAACTATTTAAA-CGAGTAATAAGGCTTTTGAAGGAATAGG-TG
* * * * * * * *
65 ACTATATATAAACTTTTTTTCCCAATGAATGG-TATTTTGTACACGTTTCTCGAGAC-ATACATT
64 ACTATAAATAGACTTTTCTTGCCAATGAATGGCT-TTTTCTACACGTTTCTCAAGGCAAGACATT
* * * *
128 CAATTATAGCCTGTTCTAACCCAAA-ATCTAATAAAATTCAACTT
128 CAATTATAGTCTGTTTTAA-CCAAATATATAAAAAAATTCAACTT
* * * * *
172 AAAATCAATTATGAGACTATAAAA-TAATTTAACGCGAGTACTAAGGCTTTTAAAGAAAT-GAGT
1 AAAATCAATTATGAGATTATAAAACT-ATTTAA-ACGAGTAATAAGGCTTTTGAAGGAATAG-GT
* * * * * **
235 GACTATAAATGGATTTTTCTT-CTCAATGAATGGCTTTTT-TACATGTTTCTCAATG-TAGGTAT
63 GACTATAAATAGACTTTTCTTGC-CAATGAATGGCTTTTTCTACACGTTTCTCAAGGCAAGACAT
* * *
297 TCAATTATAGTCTGTTTTAACTAAAAATA-AAAAAAATTCAACGT
127 TCAATTATAGTCTGTTTTAACCAAATATATAAAAAAATTCAACTT
* * *
341 AAAATCAATTATGAGATTATAAAACAATATAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGTGA
1 AAAATCAATTATGAGATTATAAAACTATTTAAA-CGAGTAATAAGGCTTTTGAAGGAATAGGTGA
* * * *
406 CTACAAATAGACTTTTCTT-CTCAATGAATGGCTTGTTCCACACGTTTTTCAAGGCAAG-CATTC
65 CTATAAATAGACTTTTCTTGC-CAATGAATGGCTTTTTCTACACGTTTCTCAAGGCAAGACATTC
*
469 AATTATAGTCTGTTTTAACCAAATGTATAAAAAAATTCAACTT
129 AATTATAGTCTGTTTTAACCAAATATATAAAAAAATTCAACTT
* * * * *
512 AAAATCTATTATGAGATTATAAAACTCTTTAGAACGAGTAATGAGGCTTTT-AAGGGAATATGAG
1 AAAATCAATTATGAGATTATAAAACTATTTA-AACGAGTAATAAGGCTTTTGAA-GGAATAGGTG
** * * * * * *
576 AGAATAAGTGGACTTTTCTTGCCAATGAGT-GCTTGTTTCTTCACGTTTCTCAAGG-TAGACATC
64 ACTATAAATAGACTTTTCTTGCCAATGAATGGCTT-TTTCTACACGTTTCTCAAGGCAAGACATT
* * * * *
639 CAATTATAGTCTATTTTAACTAAAAATGTAAATAAATTCAACTT
128 CAATTATAGTCTGTTTTAACCAAATATATAAAAAAATTCAACTT
* * * * *
683 AGAATCAATTATGAGATTATATAACCATTTAAAGCGACTAATAAGGCTTTTGAAGGAATATGTGA
1 AAAATCAATTATGAGATTATAAAACTATTTAAA-CGAGTAATAAGGCTTTTGAAGGAATAGGTGA
* * * * * *
748 CTATAAAT-G-CTCTTCTCTTGCCAATGAATGTCTTTTTATTCATGTTTCTCGAGG-TAGACATT
65 CTATAAATAGACT-TT-TCTTGCCAATGAATGGCTTTTTCTACACGTTTCTCAAGGCAAGACATT
* * * *
810 CAATTATAATCTATTTTAACC-AATAAAATAAAACAAATT-GACTT
128 CAATTATAGTCTGTTTTAACCAAAT-ATATAAAA-AAATTCAACTT
* * * * * * *
854 AAAATCAATTATTAGATTACAAAACAATTTATAGCGATTAATAAGGTTTTTGAAAGAATTA-GTG
1 AAAATCAATTATGAGATTATAAAACTATTTA-AACGAGTAATAAGGCTTTTGAAGGAA-TAGGTG
* * * * * *
918 ACTATAAA-AGGACTTTTCTTACCAAGGAATGCCTTTTTCTTCATGTTTCTCAA-GCTAGACATT
64 ACTATAAATA-GACTTTTCTTGCCAATGAATGGCTTTTTCTACACGTTTCTCAAGGCAAGACATT
* *
981 CAATTATAATCTGTTTTAA--ATAATA-ATGAAAAAAA--AAACTT
128 CAATTATAGTCTGTTTTAACCA-AATATAT-AAAAAAATTCAACTT
* * * * *
1022 AAAATCAATTTTAAGATTATAAAACTATTTAGA-GCAGGTAATGAGGCTTTTGAGGGAATA
1 AAAATCAATTATGAGATTATAAAACTATTTAAACG-A-GTAATAAGGCTTTTGAAGGAATA
1082 AAAGACTATA
Statistics
Matches: 746, Mismatches: 127, Indels: 78
0.78 0.13 0.08
Matches are distributed among these distances:
166 1 0.00
167 3 0.00
168 47 0.06
169 110 0.15
170 98 0.13
171 464 0.62
172 21 0.03
173 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAACTATTTAAACGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
TATAAATAGACTTTTCTTGCCAATGAATGGCTTTTTCTACACGTTTCTCAAGGCAAGACATTCAA
TTATAGTCTGTTTTAACCAAATATATAAAAAAATTCAACTT
Found at i:1223 original size:150 final size:147
Alignment explanation
Indices: 957--1224 Score: 349
Period size: 150 Copynumber: 1.8 Consensus size: 147
947 TGCCTTTTTC
* * *
957 TTCATGTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAAATAATAATGAAAAAAAAAACTT
1 TTCACGTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAAACAAAAATGAAAAAAAAAACTT
* * * * * *
1022 AAAATCAATTTTAAGATTATAAAACTATTTAGAGCAGGTAATGAGGCTTTTGAGGGAATAAAAGA
66 AAAATCAATTATAAGATTATAAAACTATTTAAAGCAAGTAATAAAGATTTTGAGGGAATAAAAGA
1087 CTATAAATGCTTGTTTG
131 CTATAAATGCTTGTTTG
* * * *
1104 TTCACGTTTCTCAAGGC-AGGCATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTTA
1 TTCACGTTTCTCAA-GCTAGACATTCAATTATAATCTGTTTTAAACAAAAATG-AAAAAAA--AA
* * *
1168 ACTTAGAATCAATTATAAGATTATAAAACTTTTTAAAGTAAGTAATAAAGATTTTGA
62 ACTTAAAATCAATTATAAGATTATAAAACTATTTAAAGCAAGTAATAAAGATTTTGA
1225 ATGAATGGGT
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
147 43 0.43
148 9 0.09
150 49 0.49
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (147 bp):
TTCACGTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAAACAAAAATGAAAAAAAAAACTT
AAAATCAATTATAAGATTATAAAACTATTTAAAGCAAGTAATAAAGATTTTGAGGGAATAAAAGA
CTATAAATGCTTGTTTG
Found at i:1843 original size:170 final size:170
Alignment explanation
Indices: 1092--1956 Score: 772
Period size: 171 Copynumber: 5.1 Consensus size: 170
1082 AAAGACTATA
* * *
1092 AATGCTTGTTTGTTCACGTTTCTCAAGGC-AGGCATTCAATTATAGTCTGTTTTAACCAAAAATG
1 AATGCTT-TTTCTTCACGTTTCTCAAGGCTA-ACATTCAATTATAGTCTGTTTTAACCAAAAATA
* * * * * *
1156 TAAAAAAATTTAACTTAGAATCAATTATAAGATTATAAAACTTTTTAAAGTAAGTAATAAAGATT
64 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTT
* * *
1221 TTGAATGAATGGGTGACTATAAATAGACTTTTTTTG-TCAATG
129 TTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCT-AATG
* * * *
1263 AATGCCTTTT-TTCACGTTTCTCGAGG-TAAACATTCAATTATTA-TCTATTTTAACCAATAATA
1 AATGCTTTTTCTTCACGTTTCTCAAGGCT-AACATTCAATTA-TAGTCTGTTTTAACCAAAAATA
* * * * * *
1325 TAAAACAAA-TTGACTTAAAATCAATTATTAGATTACAAAACAATTTTAAGCGAGTAATAAGGCT
64 TAAAA-AAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCT
* * * *
1389 TTTGAAAGTATGGGTGACTATAAA-AGGAATTTTCTTGCTAATG
128 TTTGAAGGAATGAGTGACTATAAATA-GACTTTTCTTGCTAATG
* * * * * *
1432 AATACTTGTTTCTTTACGTTTCTCAAGGCTGACATTCAATTACAATCTGTTTTAACCAAAAATAC
1 AATGCTT-TTTCTTCACGTTTCTCAAGGCTAACATTCAATTATAGTCTGTTTTAACCAAAAATAT
* *
1497 AAAAACATTTAACTTAAAATCAATTATGAGAATAT-AAACTTATTTAAAGCAAGTAATAAGGCTT
65 AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAC-TATTTAAAGCAAGTAATAAGGCTT
* *
1561 TTAAAGGAAT-AGGTGACTATAAATAGACTTTTCTT-CTTAGTG
129 TTGAAGGAATGA-GTGACTATAAATAGACTTTTCTTGC-TAATG
* * * * * *
1603 AATGACTTTTTCTACATGTTTC-CTAAGGC-AGACAATCAAGTATAGTATATTTTAA--AAAAAT
1 AATG-CTTTTTCTTCACGTTTCTC-AAGGCTA-ACATTCAATTATAGTCTGTTTTAACCAAAAAT
* * * *
1664 ATATAAAAATATTCAACTT-AAATCATTTATGAGATTATAAAACCATTTAAAGCAAGTAATGAGG
63 ATA-AAAAA-ATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGG
* * *
1728 CTTTCGAAGGAATGAGTGGCTATAAATAGACTTTTCTTGCAAATG
126 CTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCTAATG
* * * * * * * *
1773 AATGTTTGTTTCTTTACGTTTTTTAAGACTAACATTCAATTATAGTCTGTTTTATCTAAAAATGT
1 AATGCTT-TTTCTTCACGTTTCTCAAGGCTAACATTCAATTATAGTCTGTTTTAACCAAAAATAT
*********** * * * ** *
1838 AAAAATNNNNNNNNNNAAATCAATTATGAGATTATAAAACTATTTAAAACGAGTAGTAAACCTTA
65 AAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTT
*
1903 TGAAGGAAT-AGGTGACTATAAATAGACTTTTCTTGCCAATG
130 TGAAGGAATGA-GTGACTATAAATAGACTTTTCTTGCTAATG
1944 AATGCCTTTTTCT
1 AATG-CTTTTTCT
Statistics
Matches: 560, Mismatches: 103, Indels: 62
0.77 0.14 0.09
Matches are distributed among these distances:
168 1 0.00
169 140 0.25
170 136 0.24
171 268 0.48
172 15 0.03
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (170 bp):
AATGCTTTTTCTTCACGTTTCTCAAGGCTAACATTCAATTATAGTCTGTTTTAACCAAAAATATA
AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTT
GAAGGAATGAGTGACTATAAATAGACTTTTCTTGCTAATG
Found at i:1860 original size:341 final size:340
Alignment explanation
Indices: 1096--1954 Score: 867
Period size: 341 Copynumber: 2.5 Consensus size: 340
1086 ACTATAAATG
* * * * * * **
1096 CTTGTTTGTTCACGTTTCTCAAGGC-AGGCATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
1 CTTGTTTCTTTACGTTTCTCAAGACTA-ACATTCAATTACAATCTGTTTTAACCAAAAATACAAA
* * * * *
1160 AAAATTTAACTTAGAATCAATTATAAGATTATAAAACTT-TTTAAAGTAAGTAATAAAGATTTTG
65 AACATTTAACTTAAAATCAATTATGAGATTATAAAACTTATTTAAAGCAAGTAATAAAGCTTTTG
* * * * * *
1224 AATGAATGGGTGACTATAAATAGACTTTTTTTGTCAATGAATGCCTTTTTTCACGTTTCTCGAGG
130 AAGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTTCACGTTTCTCAAGG
* * * * * * *
1289 TAAACATTCAATTATTATCTATTTTAACCAATAATATAAAACAAATTGACTTAAAATCAATTATT
195 CAAACAATCAAGTATTATATATTTTAA-CAAAAATATAAAACAAATTAACTTAAAATCAATTATG
* * * * *
1354 AGATTACAAAACAATTTTAAGCGAGTAATAAGGCTTTTGAAAGTATGGGTGACTATAAAAGGAAT
259 AGATTACAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATGAGTGACTATAAAAGGAAT
*
1419 TTTCTTGCTAATGAATA
324 TTTCTTGCAAATGAATA
* *
1436 CTTGTTTCTTTACGTTTCTCAAGGCTGACATTCAATTACAATCTGTTTTAACCAAAAATACAAAA
1 CTTGTTTCTTTACGTTTCTCAAGACTAACATTCAATTACAATCTGTTTTAACCAAAAATACAAAA
* * *
1501 ACATTTAACTTAAAATCAATTATGAGAATAT-AAACTTATTTAAAGCAAGTAATAAGGCTTTTAA
66 ACATTTAACTTAAAATCAATTATGAGATTATAAAACTTATTTAAAGCAAGTAATAAAGCTTTTGA
* * *
1565 AGGAATAGGTGACTATAAATAGACTTTTCTTCTTAGTGAATGACTTTTTCTACATGTTTC-CTAA
131 AGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTT-T-CACGTTTCTC-AA
* *
1629 GGCAGACAATCAAGTA-TAGTATATTTTAA-AAAAATATATAAA-AATATTCAACTT-AAATCAT
193 GGCAAACAATCAAGTATTA-TATATTTTAACAAAAATATA-AAACAA-ATT-AACTTAAAATCAA
* * * * *
1690 TTATGAGATTATAAAACCATTTAAAGCAAGTAATGAGGCTTTCGAAGGAATGAGTGGCTATAAAT
254 TTATGAGATTACAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATGAGTGACTATAAA-
* *
1755 A-GACTTTTCTTGCAAATGAATG
318 AGGAATTTTCTTGCAAATGAATA
* * * * * * * **
1777 TTTGTTTCTTTACGTTTTTTAAGACTAACATTCAATTATAGTCTGTTTTATCTAAAAATGTAAAA
1 CTTGTTTCTTTACGTTTCTCAAGACTAACATTCAATTACAATCTGTTTTAACCAAAAATACAAAA
*********** * * * * *
1842 ATNNNNNNNNNNAAATCAATTATGAGATTATAAAAC-TATTTAAAACGAGTAGTAAACCTTATGA
66 ACATTTAACTTAAAATCAATTATGAGATTATAAAACTTATTTAAAGCAAGTAATAAAGCTTTTGA
*
1906 AGGAATAGGTGACTATAAATAGACTTTTCTTGC-CAATGAATGCCTTTTT
131 AGGAATAGGTGACTATAAATAGACTTTTCTT-CTCAATGAATGACTTTTT
1955 CT
Statistics
Matches: 427, Mismatches: 80, Indels: 23
0.81 0.15 0.04
Matches are distributed among these distances:
339 6 0.01
340 157 0.37
341 225 0.53
342 39 0.09
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (340 bp):
CTTGTTTCTTTACGTTTCTCAAGACTAACATTCAATTACAATCTGTTTTAACCAAAAATACAAAA
ACATTTAACTTAAAATCAATTATGAGATTATAAAACTTATTTAAAGCAAGTAATAAAGCTTTTGA
AGGAATAGGTGACTATAAATAGACTTTTCTTCTCAATGAATGACTTTTTTCACGTTTCTCAAGGC
AAACAATCAAGTATTATATATTTTAACAAAAATATAAAACAAATTAACTTAAAATCAATTATGAG
ATTACAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATGAGTGACTATAAAAGGAATTT
TCTTGCAAATGAATA
Done.