Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397748.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1045.0, 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: 2532
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.35
Warning! 215 characters in sequence are not A, C, G, or T
Found at i:998 original size:171 final size:170
Alignment explanation
Indices: 590--1047 Score: 499
Period size: 171 Copynumber: 2.7 Consensus size: 170
580 GTGGGAAACT
* * * *
590 TGAAGAAAAAGCCATTCATTGGTAAGTAAAGTCCATTTACAGTTAGCCATGCCTTCAAAAGCCTA
1 TGAAGAAAAAGCCATTCATTAGTAAGAAAAGTCCATTTATAGTTACCCATGCCTTC-AAAGCCTA
* * *
655 ATTACATGCTTTAAATAGTTTTATTATCTCATGATTGATTTTAGGTTGAATGTTTATACATTTTT
65 ATTACTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTGAATGTTTATACATTTTT
* *
720 TGTAAAAACAGATTAAAATCAAATGTCGACCTCAAGAAATG
130 GGTAAAAACAGATTAAAATCAAATGTCGACATCAAGAAATG
* * * ** * * *
761 TGAAGAAGAACCCATTCATTAGCAAGAAAAGTAAATTTCTAGTCACCCAAGCCTTCGAAAGCCTA
1 TGAAGAAAAAGCCATTCATTAGTAAGAAAAGTCCATTTATAGTTACCCATGCCTTC-AAAGCCTA
** * *
826 ATTACTTGCAGTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTGTA-GTTTTTTACATTTT
65 ATTACTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTGAATG-TTTATACATTTT
* * ** * * *
890 TGGTTAAAACCA-ATTATAATTGAATGTCTACATTAGGAAATG
129 TGG-TAAAAACAGATTAAAATCAAATGTCGACATCAAGAAATG
* * **
932 TGAAGAAAAAGCCATTCATTAGTAAGAAAAATCCATTTATAGTTATCCATGTATTCAAATGCCTA
1 TGAAGAAAAAGCCATTCATTAGTAAGAAAAGTCCATTTATAGTTACCCATGCCTTCAAA-GCCTA
* * * * * *
997 ATTGCTCGCTTTTAAT-GATTTTATAATGTCATAATTAATTTTAAGTTGAAT
65 ATTACTTGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAGGTTGAAT
1048 CCTACATTTT
Statistics
Matches: 232, Mismatches: 50, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
170 5 0.02
171 220 0.95
172 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (170 bp):
TGAAGAAAAAGCCATTCATTAGTAAGAAAAGTCCATTTATAGTTACCCATGCCTTCAAAGCCTAA
TTACTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTGAATGTTTATACATTTTTG
GTAAAAACAGATTAAAATCAAATGTCGACATCAAGAAATG
Found at i:1496 original size:168 final size:171
Alignment explanation
Indices: 1287--1656 Score: 455
Period size: 171 Copynumber: 2.2 Consensus size: 171
1277 ATAGAGCCAT
* * * * ** *
1287 TCATTGGCAAGAAAAGTTTATTTATAGTCACCCAAGCCTTTGAAGGCCTTATTGCTTGCTTTAAA
1 TCATTAGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAA
* * * *
1352 TGGTTTT-TAATCTCATAATTGATT-TTAAGTTAGA-TTTTTTACATTTTTGGT-GAAACAGATT
66 TGGTTTTATAATCTCATAATTGATTGCT-AGTTAAATTTTTTTACATTTTTAGTAAAAACAGATT
* * * *
1413 ATAATTAAATGTTTGCCTTA-AGAAACGTGAAGAAATAGGCTA
130 ATAATTAAATGTCTACC-TAGAGAAACATGAAGAAAAAGGCTA
* * *
1455 TTATTAGCAAGAAAAGTCTATTTATATTCACCCATGCCTTTGAAAGCCTTATTACCCGCTTCAAA
1 TCATTAGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAA
* * *
1520 TGGTTTTATAATCTGATAATTGATTGCTAGTTAAATTTTTTTACGTTTTTAGTAAAAACATATTA
66 TGGTTTTATAATCTCATAATTGATTGCTAGTTAAATTTTTTTACATTTTTAGTAAAAACAGATTA
*
1585 TAATTAAATGTCTACCTAGGGAAACATGAAGAAAAAGGCTA
131 TAATTAAATGTCTACCTAGAGAAACATGAAGAAAAAGGCTA
* *
1626 TCATTGGCAAG-AAAGATCCATTTATAGTCAC
1 TCATTAGCAAGAAAAG-TCTATTTATAGTCAC
1657 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
168 62 0.36
169 22 0.13
170 22 0.13
171 64 0.38
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (171 bp):
TCATTAGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAA
TGGTTTTATAATCTCATAATTGATTGCTAGTTAAATTTTTTTACATTTTTAGTAAAAACAGATTA
TAATTAAATGTCTACCTAGAGAAACATGAAGAAAAAGGCTA
Found at i:1651 original size:171 final size:168
Alignment explanation
Indices: 1225--1656 Score: 485
Period size: 168 Copynumber: 2.5 Consensus size: 168
1215 NNNNNNNNAT
* * ** * * * *
1225 ATTTTTTGTTAAAACATATTATATTTGGATGTCTGCCTTAGGAAACATAAAGATAGA-GCCATTC
1 ATTTTTAG-TAAAACATATTATAATTAAATGTCTGCCTTAGGAAACATGAAGAAAAAGGCTA-TC
* * * ** *
1289 ATTGGCAAGAAAAGTTTATTTATAGTCACCCAAGCCTTTGAAGGCCTTATTGCTTGCTTTAAATG
64 ATTGGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAATG
* *
1354 GTTTTTAATCTCATAATTGATTTTAAGTTAGATTTTTTAC
129 GTTTTTAATCTCATAATTGATTCTAAGTTAAATTTTTTAC
* * * * * * * *
1394 ATTTTTGGTGAAACAGATTATAATTAAATGTTTGCCTTAAGAAACGTGAAGAAATAGGCTATTAT
1 ATTTTTAGTAAAACATATTATAATTAAATGTCTGCCTTAGGAAACATGAAGAAAAAGGCTATCAT
* * *
1459 TAGCAAGAAAAGTCTATTTATATTCACCCATGCCTTTGAAAGCCTTATTACCCGCTTCAAATGGT
66 TGGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAATGGT
*
1524 TTTATAATCTGATAATTGATTGCT-AGTTAAATTTTTTTAC
131 TTT-TAATCTCATAATTGATT-CTAAGTTAAA-TTTTTTAC
* *
1564 GTTTTTAGTAAAAACATATTATAATTAAATGTCTACC-TAGGGAAACATGAAGAAAAAGGCTATC
1 ATTTTTAGT-AAAACATATTATAATTAAATGTCTGCCTTA-GGAAACATGAAGAAAAAGGCTATC
*
1628 ATTGGCAAG-AAAGATCCATTTATAGTCAC
64 ATTGGCAAGAAAAG-TCTATTTATAGTCAC
1657 NNNNNNNNNN
Statistics
Matches: 217, Mismatches: 39, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
168 99 0.46
169 32 0.15
170 22 0.10
171 64 0.29
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (168 bp):
ATTTTTAGTAAAACATATTATAATTAAATGTCTGCCTTAGGAAACATGAAGAAAAAGGCTATCAT
TGGCAAGAAAAGTCTATTTATAGTCACCCAAGCCTTTGAAAGCCTTATTACCCGCTTCAAATGGT
TTTTAATCTCATAATTGATTCTAAGTTAAATTTTTTAC
Found at i:2331 original size:171 final size:171
Alignment explanation
Indices: 1824--2526 Score: 629
Period size: 170 Copynumber: 4.1 Consensus size: 171
1814 NNNNNNNNAG
* * * * ** **
1824 GTTGAATT-TTCTTACATTTTTTGTGAAACCAGATTATAATTGAATGTCTACCTTGGGAAATGTG
1 GTTGAATTGTT-TTACATTTTTTGTTAAAACATATTATAATTAAATGTCTACCTTGAAAAACATG
* ********** * *
1888 AAGAAAAAGGCTA-TCATTAGCAAGAAAAGNNNNNNNNNNGTCACCCATGCCTTTGAAAGCCTTA
65 AAGAAAAA-GCAATTCATTAGCAAGAAAAGTCCATTTCTTGTCACTCATGCCTTTGAAAGCCTAA
* * * * **
1952 TTACTCGCTGTATATGATTTTATATTCTGTTAATTGATTTTAA
129 TTACACGCTTTAAATGATTTTATAATCTCATAATTGATTTTAA
* * * * *
1995 GTTCAATTGTTTTAC-TTTGTTTGTTAAAACATATTATAATTGAATCTCTACCTTGGAAAACCTG
1 GTTGAATTGTTTTACATTT-TTTGTTAAAACATATTATAATTAAATGTCTACCTTGAAAAACATG
* * * * * * *
2059 AA-AAAAAACTATTTATTAGCAAGAAAAGTCCATTTCTTGTTACCCATGGCTTCGAAAGCCTAAT
65 AAGAAAAAGCAATTCATTAGCAAGAAAAGTCCATTTCTTGTCACTCATGCCTTTGAAAGCCTAAT
* * *
2123 TACTCGCTTTAAATGATTTTATCATCTCATAATTGATTTTAG
130 TACACGCTTTAAATGATTTTATAATCTCATAATTGATTTTAA
* * * * *
2165 GTAGAATTGTTTTACATTTTTTGTTAAAACAAATTATAATCAAATGTATACCTCGAAAAACATGA
1 GTTGAATTGTTTTACATTTTTTGTTAAAACATATTATAATTAAATGTCTACCTTGAAAAACATGA
* * *
2230 AGAAAAAGCAATTCATTAGTAAGAAAAGTCCATTTCTTGTCACTCGA-GCCTTTGAAAGCATTAT
66 AGAAAAAGCAATTCATTAGCAAGAAAAGTCCATTTCTTGTCACTC-ATGCCTTTGAAAGCCTAAT
*
2294 TACACGCTTTAAATTG-TTTTATAACCTCATAATTGATTTTAA
130 TACACGCTTTAAA-TGATTTTATAATCTCATAATTGATTTTAA
* ** * * *
2336 GTTGAATTTTTTTTGTATTGTTTT-CTAAAACATATTATAATTAAATGTCCACCTTGCAAAACAT
1 GTTGAA-TTGTTTTACATT-TTTTGTTAAAACATATTATAATTAAATGTCTACCTTGAAAAACAT
* * * * * * * *
2400 G--GAGAAAGCCATTCAAT-GCCAAGAAAAGTCCATTTATAGTCAGTCATG-GTTGTGAAAGCGT
64 GAAGAAAAAGCAATTCATTAG-CAAGAAAAGTCCATTTCTTGTCACTCATGCCTT-TGAAAGCCT
*
2461 AATTACACGCTTTAAATTG-TTTTATAATCTCATAATTAATTTTAA
127 AATTACACGCTTTAAA-TGATTTTATAATCTCATAATTGATTTTAA
*
2506 GTTGAATTCTTTTACATTTTT
1 GTTGAATTGTTTTACATTTTT
2527 GGTGAA
Statistics
Matches: 439, Mismatches: 81, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
168 3 0.01
169 16 0.04
170 224 0.51
171 144 0.33
172 48 0.11
173 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.38
Consensus pattern (171 bp):
GTTGAATTGTTTTACATTTTTTGTTAAAACATATTATAATTAAATGTCTACCTTGAAAAACATGA
AGAAAAAGCAATTCATTAGCAAGAAAAGTCCATTTCTTGTCACTCATGCCTTTGAAAGCCTAATT
ACACGCTTTAAATGATTTTATAATCTCATAATTGATTTTAA
Done.