Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401544.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4669.0, 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: 2160
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.26
Warning! 617 characters in sequence are not A, C, G, or T
Found at i:1157 original size:171 final size:169
Alignment explanation
Indices: 869--1314 Score: 610
Period size: 171 Copynumber: 2.6 Consensus size: 169
859 NNNNNNNNNN
* *
869 TTTGAAGGAATGGGCGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTT-TTATGTTTCT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTATGTTTCT
** * * *
933 CAAGGTAAACATTCAATTATAGTCTGTTTTAATTAAAAATTTTAAAAAATTCAACTTGAAATCTA
66 CAAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAA-TGTAAAAAATTCAACTTAAAATCAA
* * *
998 TTTTGAGATTACAAAACCATTTAAAGTGAGTAAT-AGGGCT
130 TTATGAGATCACAAAACCATTTAAAGCGAGTAATGA-GGCT
* * *
1038 TTTTAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAAT-ACTTGTTTCTTCATGTTT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT-TTTCTT-ATGTTT
* * * * *
1102 CTCAAGCTAGACATTCAATTATAGTGTGTTTTAGCCAAAAATGTAAAAGAATTCAATTTAAAATC
64 CTCAAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA-AATTCAACTTAAAATC
* *
1167 AATTATGAGATCATAAAATCATTTAAAGCGAGTAATGAGGCT
128 AATTATGAGATCACAAAACCATTTAAAGCGAGTAATGAGGCT
1209 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATTATGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTC-TTATGTTTC
** *
1274 TTGAGGTAAACATTCAATTATAGTCTGTTTTAACCCAAAAT
65 TCAAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAAT
1315 ATAAGTTGAA
Statistics
Matches: 240, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
168 3 0.01
169 45 0.19
170 8 0.03
171 178 0.74
172 6 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (169 bp):
TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTATGTTTCT
CAAGGTAAACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAAT
TATGAGATCACAAAACCATTTAAAGCGAGTAATGAGGCT
Found at i:1679 original size:171 final size:171
Alignment explanation
Indices: 1316--2154 Score: 928
Period size: 171 Copynumber: 4.9 Consensus size: 171
1306 ACCCAAAATA
* * *
1316 TAAGTTGAA-TTTTTTATATTATTTG-TGAAAACAGACAATAATTGAATGTCTAGCTTGAGAAAC
1 TAAGTTGAATTTTTTTACATTATTGGCT-AAAACAGACAATAATTGAATGTCTACCTTGAGAAAC
* * *
1379 GTGAAGAAAAATA-CATCCATTGGCAAGAAAAGTCCA-TTATAGTCCCCCATTCCTTCAAAAGCC
65 ATGAAGAAAAA-AGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
* * ** * * *
1442 TTATTATTCACTTTTCATGGTTTTATCATCTGAAAATTGATTT
129 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * ** *
1485 TAAGTTGAATTTTTTTACATTTTTGGCCAAAACAAATTATTATTGAATGTCTACCTT-AGGAAAC
1 TAAGTTGAATTTTTTTACATTATTGGCTAAAACAGACAATAATTGAATGTCTACCTTGA-GAAAC
* * * **
1549 ATGAAGAAAAAAGCATTCATTGGCAAGAAAACTCTATTTATAGTCTCTTATTCCTTCAAAAGCCT
65 ATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCT
* *
1614 TATCACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTT
130 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * *** * * * * * *
1656 TAGGTAGAATTGTTTTGCATTTTTCATTAAAGCATACTATAATTGATTGCCTACCTCGAGAAACA
1 TAAGTTGAATTTTTTTACATTATTGGCTAAAACAGACAATAATTGAATGTCTACCTTGAGAAACA
* *
1721 TGTAG-AAAAAGCCATTCATTGAG-AAGAAAAGTCCATTTTTAGTCACCCATTCCTTCAAAAGCC
66 TGAAGAAAAAAG-CATTCATTG-GCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
* **
1784 TTATTACTTGCTTTAAATTATTTTATAATCTCATAATTGATTT
129 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * *
1827 TAAGTTGAA-TTTTTTACATTATTGGCTAAAATAGACAATAATTGAATGTCTAGCTTGAGAAACG
1 TAAGTTGAATTTTTTTACATTATTGGCTAAAACAGACAATAATTGAATGTCTACCTTGAGAAACA
* *
1891 TGAAGAAAAATA-CA-TCTAATGGCAAGAAAAGTCCATTCATAGTCACCCATTCCTTCAAAAGCC
66 TGAAGAAAAA-AGCATTC-ATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
* * * *
1954 TTATTACTCGCTTGAAATGGTTTTACAATCTAATAATTGACTT
129 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * *
1997 GAGGTTCAATTTTTTTACATTATTGGATAAAACAGACAATAATTGAATCTCTACCTTGAAAAACA
1 TAAGTTGAATTTTTTTACATTATTGGCTAAAACAGACAATAATTGAATGTCTACCTTGAGAAACA
* * *
2062 TGAAGAAAAATGCATCCATTGGCAAGAAAAG-CC-TATTATAGTCACCCATTCTTTCAAAAGCCT
66 TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCAT-TTATAGTCACCCATTCCTTCAAAAGCCT
* * *
2125 TATTATTCACTTTCAATGGTTTTATAATCT
130 TATTACTCGCTTTAAATGGTTTTATAATCT
2155 GAAAAT
Statistics
Matches: 555, Mismatches: 99, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
169 15 0.03
170 260 0.47
171 276 0.50
172 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (171 bp):
TAAGTTGAATTTTTTTACATTATTGGCTAAAACAGACAATAATTGAATGTCTACCTTGAGAAACA
TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
Found at i:1976 original size:341 final size:341
Alignment explanation
Indices: 1343--2160 Score: 965
Period size: 341 Copynumber: 2.4 Consensus size: 341
1333 ATTATTTGTG
* * * *
1343 AAAACAGACAATAATTGAATGTCTAGCTTGAGAAACGTGAAGAAAAATACATCCATTGGCAAGAA
1 AAAACAGACAATAATTGAATGCCTACCTTGAGAAACATGAAGAAAAA-GCATCCATTGGCAAGAA
* ** * *
1408 AAGTCCA-TTATAGTCCCCCATTCCTTCAAAAGCCTTATTATTCACTTTTCATGGTTTTATCATC
65 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTATTCACTTTAAATGATTTTATAATC
* * ** *
1472 TGAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGCCAAAACAAATTATTATTGAATGTCT
130 TCAAAATTGATTTTAAGTTGAATTTTTTTACATTATTGGCCAAAACAAACAATAATTGAATGTCT
* * * * **
1537 ACCTTAGGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAACTCTATTTATAGTCTCTTATTC
195 ACCTTAGGAAACATGAAGAAAAAAGCATTCAATGGCAAGAAAACTCCATTCATAGTCACCCATTC
* * * * * *
1602 CTTCAAAAGCCTTATCACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAGGTAGAATT
260 CTTCAAAAGCCTTATCACTCGCTTGAAATGGTTTTACAATCTAATAATTAACTTGAGGTACAATT
* *
1667 GTTTTGCATT-TTTCATT
325 GTTTTACATTATTGCA-T
* * * * * * *
1684 AAAGCATACTATAATTGATTGCCTACCTCGAGAAACATGTAGAAAAAGCCATTCATTGAG-AAGA
1 AAAACAGACAATAATTGAATGCCTACCTTGAGAAACATGAAGAAAAAG-CATCCATTG-GCAAGA
* * *
1748 AAAGTCCATTTTTAGTCACCCATTCCTTCAAAAGCCTTATTACTT-GCTTTAAATTATTTTATAA
64 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTA-TTCACTTTAAATGATTTTATAA
* * * *
1812 TCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTATTGGCTAAAATAGACAATAATTGAATGT
128 TCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTATTGGCCAAAACAAACAATAATTGAATGT
* * *
1876 CTAGCTT-GAGAAACGTGAAGAAAAATA-CA-TCTAATGGCAAGAAAAGTCCATTCATAGTCACC
193 CTACCTTAG-GAAACATGAAGAAAAA-AGCATTC-AATGGCAAGAAAACTCCATTCATAGTCACC
* * *
1938 CATTCCTTCAAAAGCCTTATTACTCGCTTGAAATGGTTTTACAATCTAATAATTGACTTGAGGTT
255 CATTCCTTCAAAAGCCTTATCACTCGCTTGAAATGGTTTTACAATCTAATAATTAACTTGAGGTA
* *
2003 CAATTTTTTTACATTATTGGAT
320 CAATTGTTTTACATTATTGCAT
*
2025 AAAACAGACAATAATTGAAT-CTCTACCTTGAAAAACATGAAGAAAAATGCATCCATTGGCAAGA
1 AAAACAGACAATAATTGAATGC-CTACCTTGAGAAACATGAAGAAAAA-GCATCCATTGGCAAGA
* * *
2089 AAAG-CC-TATTATAGTCACCCATTCTTTCAAAAGCCTTATTATTCACTTTCAATGGTTTTATAA
64 AAAGTCCAT-TTATAGTCACCCATTCCTTCAAAAGCCTTATTATTCACTTTAAATGATTTTATAA
*
2152 TCTGAAAAT
128 TCTCAAAAT
Statistics
Matches: 398, Mismatches: 66, Indels: 27
0.81 0.13 0.05
Matches are distributed among these distances:
339 3 0.01
340 60 0.15
341 261 0.66
342 72 0.18
343 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (341 bp):
AAAACAGACAATAATTGAATGCCTACCTTGAGAAACATGAAGAAAAAGCATCCATTGGCAAGAAA
AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTATTCACTTTAAATGATTTTATAATCT
CAAAATTGATTTTAAGTTGAATTTTTTTACATTATTGGCCAAAACAAACAATAATTGAATGTCTA
CCTTAGGAAACATGAAGAAAAAAGCATTCAATGGCAAGAAAACTCCATTCATAGTCACCCATTCC
TTCAAAAGCCTTATCACTCGCTTGAAATGGTTTTACAATCTAATAATTAACTTGAGGTACAATTG
TTTTACATTATTGCAT
Done.