Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399995.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_322.0, 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: 25898
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.22
Warning! 10409 characters in sequence are not A, C, G, or T
Found at i:287 original size:171 final size:170
Alignment explanation
Indices: 1--964 Score: 860
Period size: 171 Copynumber: 5.6 Consensus size: 170
* * * * *
1 CTATAAATAGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGACAAACATTGAA
1 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* ********** *
66 TTTTAATCTGTTTTAA-AGAAAATTATAAAAAAATNNNNNNNNNNATCAATTATAAGGTTATAAA
66 TTATAATCTGTTTTAATA-AAAA-TATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAA
* * * * *
130 ATTATTTAAATCGAGTAATAAGGCTTTCTAAGGGATGGGTGA
129 ATCATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
* * * * *
172 CTATAAATCGAC-TTTCTTTGCTAATGGATATCTTTTTCATCATGTTTCTCATGGTAAACATTCA
1 CTATAAATGGACTTTTC-TTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCA
* * **********
236 ATTATAATCTTTTTTAATAAAAATTATTAAAAAATTCAAATTAAAATCAATTATGNNNNNNNNNN
65 ATTATAATCTGTTTTAATAAAAA-TATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAA
* * **
301 ATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTATATGA
129 ATCATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
** * * * * ** * *
343 CTATAAATGGACTTTTCTCACCAATGGATATCTTTTTTTTGACGTTTATTGATGCAGACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* * *
408 TTATAATCTATTTTAATAAAAAAATATAAAAAAAATTTAAATTAAAATC-ATTGATGAGATTATA
66 TTATAATCTGTTTTAAT--AAAAATAT-AAAAAAATTCAAATTAAAATCAATT-ATGAGGTTATA
* * *
472 AAATCATTTAAAGCGAGTAATAATGCTTTCGAAAGCATGGATGA
127 AAATCATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
* * * * * *
516 CTATGAATGGACTTTTCTTGCCAATGAATATCTTTTTGTTTATGTTTCTCAAGGTAAACATTTAA
1 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* * * *
581 TTATAATCTTTTTTAATAAAAA-ATAAATAAAATTTAACTTAAAATCAATTATGAGGTGATAAAA
66 TTATAATCTGTTTTAATAAAAATATAAA-AAAATTCAAATTAAAATCAATTATGAGGTTATAAAA
* * **
645 ACATTTAAGCCGAGTAATAAGGCTTTCGAAGGCATATATGA
130 TCATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
* * * * * *
686 CTATAAATGGATTTTTCTTGCCAATAGATATCATTTTCTTCACGTTTCTTAAGGAAAACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* * ******
751 TTATAATCTGTTTTAATAAAAATTATAAAAGAATTCAAATTAAAATAAATTATGAGGTTNNNNNN
66 TTATAATCTGTTTTAATAAAAA-TATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAA
**** * * *
816 NNNNTTAAACCGAGTAATAAGGCTTTTGAAAGCATGGGTGA
130 TCATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
* * * ** * *
857 TTATAAATGGACTTCTCTTGCCAATGGATATCGTTTTCTTTACAT-TTT-TTGAGACAGACATTC
1 CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTC-TT-CATGTTTCTCAAGGCAAACATTC
*
920 AATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAACTTAAA
64 AATTATAATCTGTTTTAATAAAAATATAAAAAAATTCAAATTAAA
965 NNNNNNNNNN
Statistics
Matches: 636, Mismatches: 144, Indels: 27
0.79 0.18 0.03
Matches are distributed among these distances:
169 3 0.00
170 163 0.26
171 316 0.50
172 21 0.03
173 133 0.21
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.37
Consensus pattern (170 bp):
CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
TTATAATCTGTTTTAATAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAAT
CATTTAAACCGAGTAATAAGGCTTTCGAAGGCATGGATGA
Found at i:1968 original size:171 final size:170
Alignment explanation
Indices: 1405--2715 Score: 691
Period size: 171 Copynumber: 7.7 Consensus size: 170
1395 NNNNNNATGT
* * * * * * *
1405 ACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCGAGGTAGACACTCAATTATAATCTG
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
*
1470 TTTTAATGAAAAATATAACAAAA-TTCTAA-TTAAAA-TCAATTATGAGGTTATAAAAT-CATTT
66 TTTTAAT-AAAAATATAA-AAAATTTC-AACTTAAAACT-AATTATGAGATTA-AAAATGCATTT
*********** * ** *
1531 NNNNNNNNNNGTAAGGCTTTTGAAGGCATCAGTGACTATAAATAG
126 AAAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * * * * * *
1576 ACTTTTTTTGCTAATGTATATCTTTTTCTTCATGTTTTTTGAAGTAAACATAT-AATTATAATCT
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACAT-TCAATTATAATCT
* ********** *
1640 GTTTTAATAATAAATNNNNNNNNNNTCAACTTAAAAGTAATTATGAGATTAAGAAA--CTATTTA
65 ATTTTAATAA-AAATATAAAAAATTTCAACTTAAAACTAATTATGAGATTAA-AAATGC-ATTTA
* * * *
1703 AAGCGAGTAATGAGGCTTTCGAAGGCATGGGTGACAATAAATGA
127 AAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * * **********
1747 ACTGTTCTTACCAATGGATATCTTTTTCTTTACGNNNNNNNNNNCAGACATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
* *
1812 TTTTAATAAGAACTATAAAAAAGTTCAACTTAAAACTAATTATGAGATTAAAAATGCATTTAAAG
66 TTTTAATAA-AAATATAAAAAATTTCAACTTAAAACTAATTATGAGATTAAAAATGCATTTAAAG
* **********
1877 CAAGTAATAAGGCTTCCGAAGGCATGGGTGANNNNNNNNNN
130 CAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
*
1918 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGACAGACATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
* * ********** *
1983 TTTCAATAAAAATATAAAAAAATTTCAAATTNNNNNNNNNNATGAGGTTATAAAAT-CATTTAAA
66 TTTTAATAAAAATAT-AAAAAATTTCAACTTAAAACTAATTATGAGATTA-AAAATGCATTTAAA
* * * * *
2047 -CTGAGTAATAAAGCTTTTGAAGGCATGAGTGATTATAAATGG
129 GC-AAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * *
2089 AGTTCTCTTGCTAATGGATATC-ATTCTCTTCACAT-TTT-TTGAGGCAGACATTCAATTATAAT
1 ACTTTTCTTGCCAATGGATATCTATT-TCTT-A-ATGTTTCTTGAGGCAGACATTCAATTATAAT
* * *********
2151 CTGTTTTAGTAAAAATATAAAAAATTTCAACTTAAAACTAATTANNNNNNNNNNAAA-GCATTTA
63 CTATTTTAATAAAAATATAAAAAATTTCAACTTAAAACTAATTA-TGAGATTAAAAATGCATTTA
* *
2215 AAGCAAGTAATAAGGCTTTCGAAAGCATGGGTAACTATAAATGG
127 AAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* *
2259 ACTTTTCTTGCCAATGGATATCTTTTTCTTAATGTTTCTCGAGGCAGACATTCAATTATAATCTA
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
********** * * * *
2324 TTTTAATAAAAATATAAAATAATNNNNNNNNNNATC-AATTATGAGGTTATAAAAT-TATTAAAA
66 TTTTAATAAAAATATAAAA-AATTTCAACTTAAAACTAATTATGAGATTA-AAAATGCATTTAAA
* * * * * * * *
2387 GCGAGTGATGAGACTTTTGAAGGCGTGAGTGACTATAAGTGG
129 GCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * * *********
2429 ACTTTTCTTGCCAATGAATATCTTTTTATT-TTGGTTTCTTGAGGCAGACGTTCAANNNNNNNNN
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAAT-GTTTCTTGAGGCAGACATTCAATTATAATCT
* * * * * * * *
2493 NTTTTTATAAAAATTGTAAAAAA-TT-AACTTAACACAAATTATGAGGTTATACAAT-CTTTTAA
65 ATTTTAATAAAAA-TATAAAAAATTTCAACTTAAAACTAATTATGAGATTA-AAAATGCATTTAA
* * * ** *
2555 AGCGACTAATAAGGCTTTTGAAGGCACAGGTGACAATAAATGG
128 AGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
* * * * *** ** * * *
2598 ACTTTTTTTACCAATGGATATCTTTTTCTTCACACTTCCCGAAGCAGACATTTAATTGTAATCT-
1 ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
*
2662 TTTTAATAAAAAATATAAAAAATTTCAACTTAAAACTAATTATGGGATTAAAAA
66 TTTTAAT-AAAAATATAAAAAATTTCAACTTAAAACTAATTATGAGATTAAAAA
2716 NNNNNNNNNN
Statistics
Matches: 836, Mismatches: 272, Indels: 66
0.71 0.23 0.06
Matches are distributed among these distances:
168 17 0.02
169 111 0.13
170 271 0.32
171 423 0.51
172 12 0.01
173 2 0.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
ACTTTTCTTGCCAATGGATATCTATTTCTTAATGTTTCTTGAGGCAGACATTCAATTATAATCTA
TTTTAATAAAAATATAAAAAATTTCAACTTAAAACTAATTATGAGATTAAAAATGCATTTAAAGC
AAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG
Found at i:9095 original size:171 final size:162
Alignment explanation
Indices: 8903--9223 Score: 329
Period size: 171 Copynumber: 1.9 Consensus size: 162
8893 GTTTATTTAT
* * * ******
8903 AGTCACCGATGCCTTCAAAAGCGTTATTACTCGCTTTAAATGATTTTATAACCTCATAANNNNNN
1 AGTCACCCATGCCTTCAAAAGCGTTATTACTCGCTTGAAATGATTTTACAACCTCATAATTGATT
**** * *
8968 NNNNTTTGAATTTTTTTATA-TTTTTTATTAAAACAGATTAAAATTAAATGTTTGACTCGAAAAA
66 TTAATTTGAATTTCTTTATATTTTTTTATTAAAACAGATTAAAATTAAATGTCTGACTCGAAAAA
*
9032 CATGAAGAAAAAGATATCCATTGACAAGAAAA
131 CATAAAGAAAAAGATATCCATTGACAAGAAAA
* * *
9064 NNNNNNNNNNAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCTTGATATGATTTTCCAACCTC
1 ----------AGTCACCCATGCCTTCAAAAGCGTTATTACTCGCTTGAAATGATTTTACAACCTC
* * *
9129 ATAATTGATTTTAATTTGAATTTCTTTATATTTTTTTATTAAAATAGATTACAATTGAATGTCTG
56 ATAATTGATTTTAATTTGAATTTCTTTATATTTTTTTATTAAAACAGATTAAAATTAAATGTCTG
* *
9194 CCTCGAGAAACATAAAGAAAAAGATATCCA
121 ACTCGAAAAACATAAAGAAAAAGATATCCA
9224 NNNNNNNNNN
Statistics
Matches: 125, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
171 68 0.54
172 57 0.46
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.34
Consensus pattern (162 bp):
AGTCACCCATGCCTTCAAAAGCGTTATTACTCGCTTGAAATGATTTTACAACCTCATAATTGATT
TTAATTTGAATTTCTTTATATTTTTTTATTAAAACAGATTAAAATTAAATGTCTGACTCGAAAAA
CATAAAGAAAAAGATATCCATTGACAAGAAAA
Found at i:20359 original size:171 final size:170
Alignment explanation
Indices: 20182--20574 Score: 421
Period size: 171 Copynumber: 2.3 Consensus size: 170
20172 NNNNNNNNNN
20182 GACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTTAAAGCAAACATTC
1 GACTATAAATGGACTTTT-TTGCCAATGGATATCTTTTTCTTCACGTTTCTTAAAGCAAACATTC
* * ** *
20247 AATTATAATCTGTTTTAATAAAACA-TATAAAAAAATTTAACTTAAAATTAATTATGATG-TTAT
65 AATTATAATCTGTTTTAAGAAAA-ATTATAAAAAAATTCAACTTAAAACAAATTATGA-GATTAA
* * *
20310 AAAAACATTTAAAGCAAGTCATAAGGCTTTTGAAGGCATAGGT
128 AAAAACATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGC
* * * ** * * * * *
20353 GACTATAAATAGACTTCTGTTGCTAATGGATATCAATTTCTTAATGTTTTTTGAGGCAAACATTC
1 GACTATAAATGGACTT-TTTTGCCAATGGATATCTTTTTCTTCACGTTTCTTAAAGCAAACATTC
* * **
20418 AATTATAATCTGTTTTAAGAAAAATTGTAAAAAAGTTCAACTTAAAACAAATTATGAGATTAANN
65 AATTATAATCTGTTTTAAGAAAAATTATAAAAAAATTCAACTTAAAACAAATTATGAGATTAAAA
******** *
20483 NNNNNNNNAAAGCGAGTAATAAGGCTTTCGAAGGCATAGGC
130 AAACATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGC
* * *
20524 GACTACAAATGGACCTGTTTTGTCAATGGATATCTTTTTCTTCACGTTTCT
1 GACTATAAATGGA-CTTTTTTGCCAATGGATATCTTTTTCTTCACGTTTCT
20575 CGAGGTAGAC
Statistics
Matches: 176, Mismatches: 42, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
170 2 0.01
171 171 0.97
172 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
GACTATAAATGGACTTTTTTGCCAATGGATATCTTTTTCTTCACGTTTCTTAAAGCAAACATTCA
ATTATAATCTGTTTTAAGAAAAATTATAAAAAAATTCAACTTAAAACAAATTATGAGATTAAAAA
AACATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATAGGC
Done.