Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401128.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4285.0, 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: 3129
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.27
Warning! 873 characters in sequence are not A, C, G, or T
Found at i:349 original size:172 final size:172
Alignment explanation
Indices: 1--1512 Score: 1453
Period size: 172 Copynumber: 8.8 Consensus size: 172
* * * * * * *
1 TTGAATGTTTACCTCAAGAAACATTAAGAAAAAGGCATTCATTGGCAATAAAAGTCAATTTATAG
1 TTGAATGTCTACCT-GAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* ** * * * * *
66 TAACATATTCATTCGAGAGCCTTATTAC-CTAGTTTAAATAGTTTTATAATCTCAAAATTGA-TT
65 TCACCCATTCCTTCAAAAGCCTTATTACTC-ACTTTAAATGGTTTTATAATCTCAAAATTGATTT
* * ** * *
129 TAAATTTGGATGT-TTTGTACATTTTTCTTTAAAATAGAATAGAA
129 TAAGTTTGAAT-TCTTTGTACATTTTTGGTTAAAACAGACTAGAA
* *
173 TTGAATTTCTACCATGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTTATAG
1 TTGAATGTCTACC-TGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* * *
238 TCACCCATTGCTTCAAAAGCCTCATTAATCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
65 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
** * * *
303 AAGTTCAAAATT-TTT-TAC-TTTTCTGGTTAAAACATATTATAA
130 AAGTT-TGAATTCTTTGTACATTTT-TGGTTAAAACAGACTAGAA
* * * * * *
345 TTGAATGTCTAGCCCGAGAAACATAAAGAAGAGAGTATTCATTGGCAAGAGAAGTACATTTATAG
1 TTGAATGTCTA-CCTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
*
410 TCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATGGTTTTATAATCTCAAAATTGA-TTT
65 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
* * * *
474 AAATTTGAATTCTTTGTACATTTTTAGTTAAAATAGACTAGGA
130 AAGTTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAA
* * * * * *
517 TTGAATGTCTACCTTGAGAATCATGAAGAAAAATGCATTTATTGGCAAGAAAAGTTCATTTA-CG
1 TTGAATGTCTACC-TGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
** * * * * * *
581 ATCACCCACACCTTCAAAAG-TTGTATTATTCACTTTTAATGGTTTTGTAATGC-CATAATTTAT
65 -TCACCCATTCCTTCAAAAGCCT-TATTACTCACTTTAAATGGTTTTATAAT-CTCAAAATTGAT
* * *
644 TTTAAG-TTGAATT-TTTCTACAATTTTTGTTTAAAA-AGACTATAA
127 TTTAAGTTTGAATTCTTTGTAC-ATTTTTGGTTAAAACAGACTAGAA
* * *
688 TTGAATGTCTACCTCGAGAAATAT-ATAG-AAAAAGTCATTCATTAGTAAGAAAAGTCCATTTAT
1 TTGAATGTCTACCT-GAGAAACATGA-AGAAAAAAGT-ATTCATTGGCAAGAAAAGTCCATTTAT
* * * * * *
751 ATTCACCTATTCCTTCAAAACCCTTATTACTCACTTTCAACT--TTTTATAATCTGAAATTTGA-
63 AGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT-AAATGGTTTTATAATCTCAAAATTGAT
* *
813 TTTAAATTTGAATTCTTTGTACATTTTTGTTTAAAACAGACTAGAA
127 TTTAAGTTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAA
* *
859 TTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGTCAAGAAAAGTCCATTTATAG
1 TTGAATGTCTACCT-GAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* * * * *
924 TCA--CATGTACCTTCAACAGCCTTATTACTCACTTGAAATGGTTTTGTAATGC-CATAATTAAT
65 TCACCCAT-T-CCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT-CTCAAAATTGAT
* * * * * * *
986 TTTAAG-TTCAATTATTT-TTCTATTTTTGGTT-AAACTGACAATAG
127 TTTAAGTTTGAATTCTTTGTAC-ATTTTTGGTTAAAACAGACTAGAA
* * * * * * ***
1030 TTAAATGTCTACCTCGAGAAACATAAACAGAAAAGTAATCATTGGCAAGAGAAGTTGTTTTATAG
1 TTGAATGTCTACCT-GAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* * * ** *
1095 TCACCCATTCCATCAAAAGCCTTATTACTCACTTTAAATAGCTTTATAATCTGTAAATTGATTTG
65 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
* * **
1160 AA-TTCGAATTCTTTGCACATTTTTTATTAAAACAGACTA-AGA
130 AAGTTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGA-A
* * * *
1202 TTGAATGTCTACCTTCAGAAACATGAAGAAAAAGGTATTCATTGGTAAAAAAAGTCCATTTATAG
1 TTGAATGTCTACC-TGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* * * *
1267 TCACCAATTCCTTCAAGAGCCTTATTACTTAGTTTAAATGGTTTTATAATCTCAAAATTGA-TTT
65 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTT
* * * *
1331 AAATTTGAATTCTTTGTATATTTTTGGCTAAAACAGAATAGAA
130 AAGTTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAA
* * *
1374 TTGAATGTCTACCATGAGAAACATGATGAAAAAAGTAATCGTTGGCAAGAAAAGTCCATTTATAG
1 TTGAATGTCTACC-TGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAG
* * * * * * * *
1439 TCAACTATACCTTCAAAAGCCTTATTAGTCGCTTTAAATAGTTTTGTAATGC-CATAATTGATTT
65 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAAT-CTCAAAATTGATTT
1503 TAAG-TTGAAT
129 TAAGTTTGAAT
1513 NNNNNNNNNN
Statistics
Matches: 1085, Mismatches: 209, Indels: 92
0.78 0.15 0.07
Matches are distributed among these distances:
169 8 0.01
170 50 0.05
171 326 0.30
172 657 0.61
173 42 0.04
174 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (172 bp):
TTGAATGTCTACCTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGT
CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTA
AGTTTGAATTCTTTGTACATTTTTGGTTAAAACAGACTAGAA
Found at i:3090 original size:172 final size:170
Alignment explanation
Indices: 2510--3128 Score: 606
Period size: 172 Copynumber: 3.6 Consensus size: 170
2500 NNNNNNNNNN
* * * * *
2510 TAGTCACCCATACCTTCAAAAGCCTTATTACCCGCTTTAAATGGTTTTGTAATGC-CATAATTAA
1 TAGTTACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAAT-CTCATAATTGA
* * * * * * * **
2574 TTTTAAGTTCAATTGTTTTTCTATTTTTGGTTAAATAGACAATAATTG-TATGTCTACCTAGAGA
65 TTTAAAGTTGAATTCTTTGTATATTTTTTGTTAAACAGACAGGAATTGAT-TGTCTACCT-GAGA
* * * * * *
2638 AACGTAAAGAGAAAGGCATTCATTGGCAAGAGAAGTCTATTTA
128 AACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTA
* * *
2681 TAGTTACCCATTCCATCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTGCA-AATTGA
1 TAGTTACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCT-CATAATTGA
* * * * * *
2745 TTTAAATTTGAATTCTTTGCACATTTTTTATTAAAACAGACTAGG-ATTGAATGTCTACCTTCAG
65 TTTAAAGTTGAATTCTTTGTATATTTTTTGTT-AAACAGAC-AGGAATTGATTGTCTACC-TGAG
* * **
2809 AAATATGAAGAAAAAGGTATGCATTGATAAGAAAAGTCCATTTA
127 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTA
* * *
2853 TAGTTACCCATTCCTTCAAGAA-CCTTATTACTTAG-TTTAAATAGTTTTATAATCTCAAAATTG
1 TAGTTACCCATACCTTCAA-AAGCCTTATTAC-TCGCTTTAAATAGTTTTATAATCTCATAATTG
* * * *
2916 ATTTAAATTTGAATTCTTAGTATATTTTTTGTTAAAACAGACCGGAATTGATTATCTACCATGAG
64 ATTTAAAGTTGAATTCTTTGTATATTTTTTGTT-AAACAGACAGGAATTGATTGTCTACC-TGAG
* * *
2981 AAACATGATGAAAAAAGTATTCTTTGGCAAGAAAAGTCCATTTA
127 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTA
* * * * *
3025 TAGTAACCTATACCTTCAGAAGCCTTATTACTCGCTTTAAATAGTTTTGTAATGC-CATTATTGA
1 TAGTTACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAAT-CTCATAATTGA
* * *
3089 TTTTAAGTTGAATT-TGTTTTATATTTTTAGTTAAACAGAC
65 TTTAAAGTTGAATTCT-TTGTATATTTTTTGTTAAACAGAC
3129 T
Statistics
Matches: 369, Mismatches: 65, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
170 1 0.00
171 90 0.24
172 272 0.74
173 6 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (170 bp):
TAGTTACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGAT
TTAAAGTTGAATTCTTTGTATATTTTTTGTTAAACAGACAGGAATTGATTGTCTACCTGAGAAAC
ATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCCATTTA
Done.