Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402772.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5831.0, 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: 1678
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.29
Warning! 377 characters in sequence are not A, C, G, or T
Found at i:802 original size:171 final size:161
Alignment explanation
Indices: 546--869 Score: 334
Period size: 171 Copynumber: 2.0 Consensus size: 161
536 TTAAAATCAT
* *
546 TTATGAGATTACAAAACAATTTAAAGCAAGTAATAAGGCTTTTGAAGAAATTAGTGACTATAAAT
1 TTATTAGATTACAAAACAATTTAAAACAAGTAATAAGGCTTTTGAAGAAATTAGTGACTATAAAT
** * * *
611 AGACTTTTTCTAGCAATGAATGTTTTTTTCTTCATGTTTTTCGA-GGTAGACGTTCAATTGTAGT
66 AGACTTTTTCTAGCAATGAATGTGCTTTTCTTCATGTTTCTC-ATGGTAGACATTCAATTATAGT
* *
675 CTGTTTTAACTAAAAATGTAAAAAAATTCAAC
130 CTATTTTAACCAAAAATGTAAAAAAATTCAAC
* *
707 TNNNNNNNNNNTATTAGATTATAAAATAATTTAAAACAAGTAATAAGGCTTTTGAA-AGAA-TAG
1 T----------TATTAGATTACAAAACAATTTAAAACAAGTAATAAGGCTTTTGAAGA-AATTAG
* *
770 ATGACTATAAATAGACGTTTCTTGT-G-AATGAATGTGCTTTTCTTCATGTTTCTCATGGTAGAT
55 -TGACTATAAATAGAC-TTT-TTCTAGCAATGAATGTGCTTTTCTTCATGTTTCTCATGGTAGAC
* * *
833 ATTTAATTATAGTGTATTTTATCCAAAAATGTAAAAA
117 ATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAA
870 GGCTTTTGAG
Statistics
Matches: 132, Mismatches: 16, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
161 1 0.01
170 5 0.04
171 119 0.90
172 4 0.03
173 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.37
Consensus pattern (161 bp):
TTATTAGATTACAAAACAATTTAAAACAAGTAATAAGGCTTTTGAAGAAATTAGTGACTATAAAT
AGACTTTTTCTAGCAATGAATGTGCTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTC
TATTTTAACCAAAAATGTAAAAAAATTCAAC
Found at i:1170 original size:170 final size:168
Alignment explanation
Indices: 961--1668 Score: 590
Period size: 170 Copynumber: 4.2 Consensus size: 168
951 NNNNNNNNNN
* * *
961 GTCTGTTTTAAGCT-AAAATGTAAAAAAATTTAACTTAAAATTAATTCTGAGATTATAAAAAAAT
1 GTCTGTTTT-AGCTAAAAATGT-AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAAT
* * * * *
1025 TTAGAATGAGTAATAAGGCTGTTGAAGGAACGAGTGACTACAAATAGGCTTTTCTTGCCAATTAA
64 TTA-AACGAGTAATAAGGCTGTTGAAAGAACGAGTGACTATAAATAGACTTTTCTTGCCAATGAA
*
1090 TGTCTTTTTCTTCATGTTTCTCGAGTAGACATTCAATTACA
128 TGTCTTTTTCTTCATGTTTCTCGAGTAGACATTCAATTATA
* * *
1131 GTCTGTTTTAGCTAAAAATATATAAAAATTGAACTTAAAATCAATTATGAGATTATGAAACAATT
1 GTCTGTTTTAGCTAAAAATGTA-AAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATT
* * * *
1196 TAAAGCGTA-TAATAAGGTTTTTGAAAGAA-TAGGTGACTATAAATAGACTTTTTCTTTCCAAT-
65 TAAA-CG-AGTAATAAGGCTGTTGAAAGAACGA-GTGACTATAAATAGAC-TTTTCTTGCCAATG
* * * * *
1258 AAGTGTGTTTTTCTTCATGTTTCTTGTGGTAGATATTTAATTATA
126 AA-TGTCTTTTTCTTCATGTTTCTCG-AGTAGACATTCAATTATA
* * * * **********
1303 GTCTATTTTATCCAAAAATATAAAAAATTTAACTTAAAANNNNNNNNNNGATTATAAAACAATTT
1 GTCTGTTTTAGCTAAAAATGTAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTT
** * * *
1368 AGAACGAGTAATAAGGCT-TTTCAAGCAATGAGTGACTATAAATAGACTTTT-TTTCTATATGAA
66 A-AACGAGTAATAAGGCTGTTGAAAG-AACGAGTGACTATAAATAGACTTTTCTTGCCA-ATGAA
* * * * * *
1431 TAAT-TTTTTCTACACGTTTCTCAAGGT-GTGCATTCAATTGTA
128 T-GTCTTTTTCTTCATGTTTCTCGA-GTAG-ACATTCAATTATA
* * * * *********
1473 GTATGTTTTAAGCT-AAAATGTAAAAGAATTCAACTTAAAACCAATTATAAGATTANNNNNNNNN
1 GTCTGTTTT-AGCTAAAAATGTAAAA-AATTTAACTTAAAATCAATTATGAGATTATAAAACAAT
* * *
1537 NTAAAGCGAGTAATAAGGCTGTTGAAAGAACGAGTGTCTATAAATGGACTTTTCTTGCCAATGAA
64 TTAAA-CGAGTAATAAGGCTGTTGAAAGAACGAGTGACTATAAATAGACTTTTCTTGCCAATGAA
* *
1602 T-TCTTTTTTTTCATGTTTCTTGAGTAGACATTCAATTATA
128 TGTCTTTTTCTTCATGTTTCTCGAGTAGACATTCAATTATA
*
1642 GTCTGTTTTAACTAAAAATGTAAAAAA
1 GTCTGTTTTAGCTAAAAATGTAAAAAA
1669 ATTCAACCTA
Statistics
Matches: 421, Mismatches: 92, Indels: 52
0.75 0.16 0.09
Matches are distributed among these distances:
168 5 0.01
169 47 0.11
170 162 0.38
171 162 0.38
172 45 0.11
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.36
Consensus pattern (168 bp):
GTCTGTTTTAGCTAAAAATGTAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACAATTT
AAACGAGTAATAAGGCTGTTGAAAGAACGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGT
CTTTTTCTTCATGTTTCTCGAGTAGACATTCAATTATA
Found at i:1341 original size:171 final size:169
Alignment explanation
Indices: 983--1668 Score: 476
Period size: 171 Copynumber: 4.0 Consensus size: 169
973 CTAAAATGTA
* * *
983 AAAAAATTTAACTTAAAATTAATTCTGAGATTATAAAAAAATTTAGAATGAGTAATAAGGCTGTT
1 AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAAAATTTAGAACGAGTAATAAGGCTGTT
* * *
1048 GAAGGAACGAGTGACTACAAATAGGCTTTTCTTGCCAATTAATGTCTTTTTCTTCATGTTTCTCG
66 GAAAGAAAGAGTGACTACAAATAGACTTTTCTTGCCAATTAATGTCTTTTTCTTCATGTTTCTCG
* *
1113 AGTAGACATTCAATTACAGTCTGTTTTAGCTAAAAATAT
131 AGTAGACATTCAATTACAGTCTATTTTAGCCAAAAATAT
* * * *
1152 ATAAAAATTGAACTTAAAATCAATTATGAGATTATGAAACAATTTA-AAGCGTA-TAATAAGGTT
1 A-AAAAATTTAACTTAAAATCAATTATGAGATTATAAAAAAATTTAGAA-CG-AGTAATAAGGCT
* * * *
1215 TTTGAAAGAATAG-GTGACTATAAATAGACTTTTTCTTTCCAA-TAAGTGTGTTTTTCTTCATGT
63 GTTGAAAGAA-AGAGTGACTACAAATAGAC-TTTTCTTGCCAATTAA-TGTCTTTTTCTTCATGT
* * * * * *
1278 TTCTTGTGGTAGATATTTAATTATAGTCTATTTTATCCAAAAATAT
125 TTCTCG-AGTAGACATTCAATTACAGTCTATTTTAGCCAAAAATAT
********** *
1324 AAAAAATTTAACTTAAAANNNNNNNNNNGATTATAAAACAATTTAGAACGAGTAATAAGGCT-TT
1 AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAAAATTTAGAACGAGTAATAAGGCTGTT
** * * * * * * * *
1388 TCAAGCAATGAGTGACTATAAATAGACTTTT-TTTCTATATGAATAAT-TTTTTCTACACGTTTC
66 GAAAG-AAAGAGTGACTACAAATAGACTTTTCTTGCCA-ATTAAT-GTCTTTTTCTTCATGTTTC
* * ** * * * *
1451 TCAAGGT-GTGCATTCAATTGTAGTATGTTTTAAG-CTAAAATGT
128 TCGA-GTAG-ACATTCAATTACAGTCTATTTT-AGCCAAAAATAT
* * * **********
1494 AAAAGAATTCAACTTAAAACCAATTATAAGATTANNNNNNNNNNTA-AAGCGAGTAATAAGGCTG
1 AAAA-AATTTAACTTAAAATCAATTATGAGATTATAAAAAAATTTAGAA-CGAGTAATAAGGCTG
* * * * * *
1558 TTGAAAGAACGAGTGTCTATAAATGGACTTTTCTTGCCAATGAAT-TCTTTTTTTTCATGTTTCT
64 TTGAAAGAAAGAGTGACTACAAATAGACTTTTCTTGCCAATTAATGTCTTTTTCTTCATGTTTCT
* * * * * *
1622 TGAGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGT
129 CGAGTAGACATTCAATTACAGTCTATTTTAGCCAAAAATAT
1663 AAAAAA
1 AAAAAA
1669 ATTCAACCTA
Statistics
Matches: 399, Mismatches: 94, Indels: 49
0.74 0.17 0.09
Matches are distributed among these distances:
168 3 0.01
169 42 0.11
170 149 0.37
171 161 0.40
172 44 0.11
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.36
Consensus pattern (169 bp):
AAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAAAATTTAGAACGAGTAATAAGGCTGTT
GAAAGAAAGAGTGACTACAAATAGACTTTTCTTGCCAATTAATGTCTTTTTCTTCATGTTTCTCG
AGTAGACATTCAATTACAGTCTATTTTAGCCAAAAATAT
Done.