Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401791.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4900.0, 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: 3100
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.26
Warning! 871 characters in sequence are not A, C, G, or T
Found at i:1625 original size:171 final size:169
Alignment explanation
Indices: 813--2440 Score: 1466
Period size: 171 Copynumber: 9.5 Consensus size: 169
803 NNNNNNAGAC
* * * * * *
813 ATTCAATTATAATCTGTTTTAGCCAAAAATATAAAAAAATTTAATTTAAAATCAAATCTGAGATT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATT
* ** * * * *
878 -TAAATCCATTTAAAGTGAGTAATAAGAATTTTGAAAGAGTGGGTGACTGTAAATGGTCTTTTCT
65 ATAAAACCATTT-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * * * * * * * *
942 TGCTAGTGAAT-ACTTTCTTTTTCACATCTCCCAAGGCAGAC
129 TGCCAATGAATGCCTTT-TTCTTCATATTTCTCAAGGTAGAT
* ** * *
983 ACTCAATTATAATCTGTTCTGGA-CAAAAATGTAAAAAAATTCACCATAAAATCAATTATGAGAT
1 ATTCAATTATAATCTGTT-TTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGAT
*
1047 TATAAAACCATTTAAAGTGAGTTAA-AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTT
64 TATAAAACCATTT-AAGTGAG-TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
* * * * * * ** *
1111 TTTGCCAATGAAAGACTTTGTCTTTACATTTCTTGAGGTAGAC
127 CTTGCCAATGAATGCCTTTTTCTTCATATTTCTCAAGGTAGAT
* * * * * *
1154 ATTCAATTATAATTTGTTTTAA-TAAGAAATGCATAAAGAATTCAAATTTAAATCAATTTTGAGA
1 ATTCAATTATAATCTGTTTTAACCAA-AAATG--TAAAAAATTCAACTTAAAATCAATTATGAGA
* **
1218 TTATAAAACCATTTAAAGTGAGTAATAAGGATTTTAGAA-GAATGGGTGACTATAAATGGTTTTT
63 TTATAAAACCATTT-AAGTGAGTAATAAGGCTTTT-GAAGGAATGGGTGACTATAAATGGACTTT
* * * ** *
1282 TCTT-ACAGATGAATGACTTTTTCTTTATATTTCAGAAGCTAGAT
126 TCTTGCCA-ATGAATGCCTTTTTCTTCATATTTCTCAAGGTAGAT
* * * * * * *
1326 ATTTAATTATAATCTGTTTTAACTAGATACGTAAATAAAGTTGAACTTAAAATCAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGTAAA-AAA-TTCAACTTAAAATCAATTATGAGAT
* ** * *
1391 TATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGCAATGAATGACTATAAATAGACTTTTG
64 TATAAAACCATTTAA-GTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
1456 TTGCCAATGAATGCCTTTTTC-TCGATATTTCTCAAGGTAGAT
128 TTGCCAATGAATGCCTTTTTCTTC-ATATTTCTCAAGGTAGAT
* * *
1498 ATGCAATTATAATCTGTTTTAACCAAAAATGTAGAAAAATTCAACTTAAAATTAATTATGAAATT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGTA-AAAAATTCAACTTAAAATCAATTATGAGATT
* * * *
1563 ATAAAACC-TTTTACTGCAGGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTC
65 ATAAAACCATTTAAGTG-A-GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
** * * * * *
1627 TTGCCAAAAAATAACC-TTTTCTTTATGTTTCTTGAA-GTAGAC
128 TTGCCAATGAAT-GCCTTTTTCTTCATATTTC-TCAAGGTAGAT
* * * *
1669 ATTCAATTATAATCTGTTTTAACTAAAATTGTAACAAAATTCAACTTAAAATCAATAATGACATT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGTAA-AAAATTCAACTTAAAATCAATTATGAGATT
* ** * *
1734 ATAAAATCATTTAAAGCAAGTAATAAGCCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCT
65 ATAAAACCATTT-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * ** *
1799 TACCAATGAATGCTTTTTTCTTCATATTTCTTGAGGTAGAA
129 TGCCAATGAATGCCTTTTTCTTCATATTTCTCAAGGTAGAT
* * * * * *
1840 ATTCAATTCTAGTCTTTTTTAACCAAAAATGTAAAAATATTCAACTTAAAAGCAGTTATTAG-TC
1 ATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAA-ATTCAACTTAAAATCAATTATGAGAT-
* * * * ** * *
1904 TATAAAACTATTTAAACTAAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATACATGGACTTTT-
64 TATAAAACCATTT-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
* * * * * * * *
1968 TGTGCCAATG-GTTCGTTTTTGCTTCATGTTCCCCAAGGCAGAC
128 T-TGCCAATGAATGCCTTTTT-CTTCATATTTCTCAAGGTAGAT
* * * * * * * *
2011 ATTTAATTATAGTCTTTTTTAACAAAAAATATAAAAAAATTCAACTTAGAATCAATTTTGAAATT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATT
* * * *
2076 ATAAAACCATTTAAAGCGAGTAATAAGCCTTCTGAAGGAATGAGTGACTATAAATGGACTTTTCT
65 ATAAAACCATTT-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * * * * *
2141 TGTCAATAAATACCTTTTTCTTCATGTTTCCCAAGATAGAT
129 TGCCAATGAATGCCTTTTTCTTCATATTTCTCAAGGTAGAT
* * ** *
2182 ATTCAATTATAATCTGTTCTAACTAAAACCGTCAAAAAATTCAACCTAAAATCAATTATGAGATT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATT
2247 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
65 ATAAAACCATTT-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* * * *
2312 TGCCAATGAAAGACTTTTTTCTTCATGTTTCTCTAGGTAGAT
129 TGCCAATGAATG-CCTTTTTCTTCATATTTCTCAAGGTAGAT
* * * * * * ** *
2354 ATTCAATTATAATATGTTTTATCCAAAAATATACAAAGACTTCAAATTTAAAGGAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAATGTA-AAA-AATTCAACTTAAAATCAATTATGAGAT
*
2419 TATAAAATCATTTAAAGTGAGT
64 TATAAAACCATTT-AAGTGAGT
2441 GAAAAAGCTT
Statistics
Matches: 1190, Mismatches: 229, Indels: 75
0.80 0.15 0.05
Matches are distributed among these distances:
169 2 0.00
170 81 0.07
171 707 0.59
172 348 0.29
173 52 0.04
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
ATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
CCAATGAATGCCTTTTTCTTCATATTTCTCAAGGTAGAT
Found at i:2101 original size:513 final size:511
Alignment explanation
Indices: 813--2434 Score: 1613
Period size: 513 Copynumber: 3.2 Consensus size: 511
803 NNNNNNAGAC
* ** * * * * * *
813 ATTCAATTATAATCTGTTTTAGCCAAAAATATAAA-AAAATTTAATTTAAAATCAAATCTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAACGTAAATAAAGTTCAACTTAAAAGCAATTTTGAGAT
* * * ** * * ** * * *
877 T-TAAATCCATTTAAAGTGAGTAATAAGAATTTTGAAAG-AGTGGGTGACTGTAAATGGTCTTTT
66 TATAAAACCATTTAAACTAAGTAATAAGGCTTTCG-AAGCAATGAATGACTATAAATAGACTTTT
* * * * * * * * *
940 CTTGCTAGTGAATACTTTCTTTTTC-ACA-TCTCCCAAGGCAGACACTCAATTATAATCTGTTCT
130 GTTGCCAATGAATGCCTT-TTTCTCGATATTC-CCCAAGGCAGACATTCAATTATAATCT-TTTT
** * * * *
1003 GGACAAAAATGTAAAAAAATTCACCATAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAG
192 TAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAG
* * * *
1068 TTAA-AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTTTTGCCAATGAAAGA-CTTTG
257 -TAATAAGGCTTTTGAAGGAAT-GGTGACTATAAATGGACTTTTCTTGCCAA-AAAATACCTTT-
** * * *
1131 TCTTTACATTTCTTGAGGTAGACATTCAATTATAATTTGTTTTAA-TAAGAAATGCATAAAGAAT
318 TCTTTATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAACTAA-AAATG--TAAAAAAT
* * * *
1195 TCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGATTTTAGAA-GA
380 TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT-GAAGGA
** * * *
1259 ATGGGTGACTATAAATGGTTTTTTCTTA-CAGATGAATGAC-TTTTTCTTTATATTTC-AGAAGC
444 ATGGGTGACTATAAATGGACTTTTCTTACCA-ATGAATGACTTTTTTCTTCATATTTCTTG-AGG
1321 TAGAT
507 TAGAT
* * * * * *
1326 ATTTAATTATAATCTGTTTTAACTAGATACGTAAATAAAGTTGAACTTAAAATCAATTTTGAGAT
1 ATTCAATTATAATCTGTTTTAACCAAAAACGTAAATAAAGTTCAACTTAAAAGCAATTTTGAGAT
** * *
1391 TATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGCAATGAATGACTATAAATAGACTTTTG
66 TATAAAACCATTTAAACTAAGTAATAAGGCTTTCGAAGCAATGAATGACTATAAATAGACTTTTG
* * * * * *
1456 TTGCCAATGAATGCCTTTTTCTCGATATTTCTCAAGGTAGATATGCAATTATAATCTGTTTTAAC
131 TTGCCAATGAATGCCTTTTTCTCGATATTCCCCAAGGCAGACATTCAATTATAATCTTTTTTAA-
* * * **
1521 CAAAAATGTAGAAAAATTCAACTTAAAATTAATTATGAAATTATAAAACCTTTTACTGC-AGGTA
195 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGA-GTA
*
1585 ATAAGGCTTTTGAAGAAATAGGTGACTATAAATGGACTTTTCTTGCCAAAAAATAACCTTTTCTT
259 ATAAGGCTTTTGAAGGAAT-GGTGACTATAAATGGACTTTTCTTGCCAAAAAAT-ACCTTTTCTT
*
1650 TATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAACTAAAATTGTAACAAAATTCAACT
322 TATGTTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTAA-AAAATTCAACT
* * * ** * *
1715 TAAAATCAATAATGACATTATAAAATCATTTAAAGCAAGTAATAAGCCTTTTGAAGGTATGGGTG
386 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
*
1780 ACTATAAATGGACTTTTCTTACCAATGAATG-CTTTTTTCTTCATATTTCTTGAGGTAGAA
451 ACTATAAATGGACTTTTCTTACCAATGAATGACTTTTTTCTTCATATTTCTTGAGGTAGAT
* * * * *
1840 ATTCAATTCTAGTCTTTTTTAACCAAAAATGTAAA-AATA-TTCAACTTAAAAGCAGTTATT-AG
1 ATTCAATTATAATCTGTTTTAACCAAAAACGTAAATAA-AGTTCAACTTAAAAGCAATT-TTGAG
* * * * *
1902 -TCTATAAAACTATTTAAACTAAGTAATAAGGCTTTCGAAGGC-TTGAGTGACTATACATGGACT
64 AT-TATAAAACCATTTAAACTAAGTAATAAGGCTTTCGAA-GCAATGAATGACTATAAATAGACT
* * * * * *
1965 TTT-TGTGCCAATG-GTTCGTTTTTGCTTC-ATGTTCCCCAAGGCAGACATTTAATTATAGTCTT
127 TTTGT-TGCCAATGAATGCCTTTTT-C-TCGATATTCCCCAAGGCAGACATTCAATTATAATCTT
* * *
2027 TTTTAACAAAAAATATAAAAAAATTCAACTTAGAATCAATTTTGAAATTATAAAACCATTTAAAG
189 TTTTAAC-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAG
* * * *
2092 CGAGTAATAAGCCTTCTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGTCAATAAATACCTT
253 CGAGTAATAAGGCTTTTGAAGGAATG-GTGACTATAAATGGACTTTTCTTGCCAAAAAATACC-T
* ** * * **
2157 TTTCTTCATGTTTC-CCAAGATAGATATTCAATTATAATCTGTTCTAACTAAAACCGTCAAAAAA
316 TTTCTTTATGTTTCTTGAAG-TAGACATTCAATTATAATCTGTTTTAACTAAAAATGT-AAAAAA
*
2221 TTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
379 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
* * *
2286 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGACTTTTTTCTTCATGTTTCTCT-AGGT
444 ATGGGTGACTATAAATGGACTTTTCTTACCAATGAATGACTTTTTTCTTCATATTTCT-TGAGGT
2350 AGAT
508 AGAT
* * * * * * *
2354 ATTCAATTATAATATGTTTTATCCAAAAA--TATACAAAGACTTCAAATTTAAAGGAATTTTGAG
1 ATTCAATTATAATCTGTTTTAACCAAAAACGTAAATAAAG--TTCAACTTAAAAGCAATTTTGAG
*
2417 ATTATAAAATCATTTAAA
64 ATTATAAAACCATTTAAA
2435 GTGAGTGAAA
Statistics
Matches: 919, Mismatches: 153, Indels: 72
0.80 0.13 0.06
Matches are distributed among these distances:
512 21 0.02
513 392 0.43
514 238 0.26
515 259 0.28
516 9 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (511 bp):
ATTCAATTATAATCTGTTTTAACCAAAAACGTAAATAAAGTTCAACTTAAAAGCAATTTTGAGAT
TATAAAACCATTTAAACTAAGTAATAAGGCTTTCGAAGCAATGAATGACTATAAATAGACTTTTG
TTGCCAATGAATGCCTTTTTCTCGATATTCCCCAAGGCAGACATTCAATTATAATCTTTTTTAAC
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTTGAAGGAATGGTGACTATAAATGGACTTTTCTTGCCAAAAAATACCTTTTCTTTATG
TTTCTTGAAGTAGACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAATTCAACTTAAAA
TCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
AAATGGACTTTTCTTACCAATGAATGACTTTTTTCTTCATATTTCTTGAGGTAGAT
Done.