Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400469.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3666.0, 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: 11352
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 3726 characters in sequence are not A, C, G, or T
Found at i:3920 original size:168 final size:159
Alignment explanation
Indices: 3665--4131 Score: 377
Period size: 168 Copynumber: 2.8 Consensus size: 159
3655 ATGTTTTTAT
* * * *
3665 AATCTCATAATTGATTTTAA-ATTAATTTTTTTTAGGTTTTTCATTAAAACAGATAATAATTAAA
1 AATCTCATAATTGATTTTAAGTTTAATTTTTTATA--TTTTT-ATTAAAACAGATTATAATTGAA
* * * * * *
3729 TGTCTTCCTTTG-GAAATGTGAAGAAAAAGGTATCTATTGGTAAGAAAAGTCCAATTATAGTCA-
63 TGTCTACC-TTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCAC
*
3792 AATGA-CTTCAAAAGCCTTATTACTCACTTTAANNNNNNNNNN
127 AAT-ATCTTCAAAAGCCTTATTACTCACTTTAA---------A
* * *
3834 AATCTTATAATTGATTTTAAGTTTAATTTTTTATATTAGTTATTAAAACAGATTACAATTGAATG
1 AATCTCATAATTGATTTTAAGTTTAATTTTTTATATT-TTTATTAAAACAGATTATAATTGAATG
* * *
3899 TCTACCTTGAGAAACGTGAAGAAAAAGATACCCATTGACAAGAAAAGTCCATTTATAGTCACTCA
65 TCTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCAC-AA
* **
3964 TATCTTCGAAAGCCTTATTACTTGCTTTAAA
129 TATCTTCAAAAGCCTTATTACTCACTTTAAA
* * *
3995 NNNNNNNNNNATCTCATAATTTG-TTTCAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATT
1 ---------AATCTCATAA-TTGATTTTAAGTTTAA-TTTTTTATA-TTTTTATTAAAACAGATT
* * ** * *
4059 TTAATTGAATGTTTACCTCAAGAAACATGAAGAAAAAGTTATCCATTTGGCAAGAAAAGTCCATT
54 ATAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAGATATCCA-TTGGCAAGAAAAGTCCATT
4124 TATAGTCA
118 TATAGTCA
4132 TCCATGCTTT
Statistics
Matches: 245, Mismatches: 34, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
167 3 0.01
168 72 0.29
169 22 0.09
170 57 0.23
171 63 0.26
172 28 0.11
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.37
Consensus pattern (159 bp):
AATCTCATAATTGATTTTAAGTTTAATTTTTTATATTTTTATTAAAACAGATTATAATTGAATGT
CTACCTTGAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACAATA
TCTTCAAAAGCCTTATTACTCACTTTAAA
Found at i:4092 original size:171 final size:169
Alignment explanation
Indices: 3433--4405 Score: 681
Period size: 171 Copynumber: 5.7 Consensus size: 169
3423 NNNNNNNNNN
* * * * *
3433 AAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATTA-TTCGCTTTAAATGTTTCTCTAAT
1 AAGTCCATTTATAGTCA-TCAT-CCTTCGAAAGCCTTATTACTT-GCTTTAAATATTTTTATAAT
* * ** * *
3497 CTCATAATTGATTTTAAATTGAATTATTTTT---TGTTTTTAGTTAAAATGGATAATAATTAAAT
63 CTCATAATTGATTTTAAGTTTAATT-TTTTTACAT-TTTTTA-TTAAAACAGATTATAATTGAAT
* ** * *
3559 GTCTGTCTCAGGAAACATGAAGAAAAAGATATCCATTGGCAAGAA
125 GTTTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAA
********** * * * *
3604 AAGTCCATTTATAGNNNNNNNNNNNNTCAAAAGCCTTATTTCTCGCTTTAAATGTTTTTATAATC
1 AAGTCCATTTATAG--TCATCATCCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATC
* ** * * *
3669 TCATAATTGATTTTAA-ATTAATTTTTTTTAGGTTTTTCATTAAAACAGATAATAATTAAATGTC
64 TCATAATTGATTTTAAGTTTAA-TTTTTTTACATTTTTTATTAAAACAGATTATAATTGAATGT-
*** * * * *
3733 TT-CCTTTGGAAATGTGAAGAAAAAGGTATCTATTGGTAAGAA
127 TTACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAA
* * * * ** **********
3775 AAGTCCAATTATAGTCA-AATGACTTCAAAAGCCTTATTACTCACTTTAANNNNNNNNNNAATCT
1 AAGTCCATTTATAGTCATCAT-CCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATCT
* * ** * *
3839 TATAATTGATTTTAAGTTTAA-TTTTTTATATTAGTTATTAAAACAGATTACAATTGAATGTCTA
65 CATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTATAATTGAATGTTTA
** * *
3903 CCTTGAGAAACGTGAAGAAAAAGATACCCATTGACAAGAA
130 CCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAA
* **********
3943 AAGTCCATTTATAGTCACTCATATCTTCGAAAGCCTTATTACTTGCTTTAAANNNNNNNNNNATC
1 AAGTCCATTTATAGTCA-TCAT-CCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATC
* *
4008 TCATAATTTG-TTTCAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTTTAATTGAATGTT
64 TCATAA-TTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTATAATTGAATGTT
* *
4072 TACCTCAAGAAACATGAAGAAAAAGTTATCCATTTGGCAAGAA
128 TACCTCAAGAAACGTGAAGAAAAAGATATCCA-TTGGCAAGAA
* * * * *
4115 AAGTCCATTTATAGTCATCCATGCTTTCGAAAGCCTTGTTATTTGCCTTAAATATTTTTATAATA
1 AAGTCCATTTATAGTCAT-CAT-CCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATC
** * * * * * *
4180 TCATAATTGATTTTAAGTAGAATATTTTTACCTTTTTTATTAAAAAAAATTATAATTGAGTGCTT
64 TCATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTATAATTGAATGTTT
* * * *
4245 ACCTCAGGAAATGTGAA-AAAAAGATATTCATTGGCAAAAA
129 ACCTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAA
* * * * *
4285 AAGTCTACTTATAGTCAGTCATGCCTTCAAAAGCCTTATTACCTGCTTTAAATGTTTTTATAATC
1 AAGTCCATTTATAGTCA-TCAT-CCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATC
* * ** * * *
4350 TAATAATTGACTTTAAGTAGAA-TTTTTTATATTTTTTATTAAAATAGATTGTAATT
64 TCATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTATAATT
4406 NNNNNNNNNN
Statistics
Matches: 640, Mismatches: 143, Indels: 40
0.78 0.17 0.05
Matches are distributed among these distances:
167 1 0.00
168 80 0.12
169 70 0.11
170 148 0.23
171 213 0.33
172 127 0.20
173 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.38
Consensus pattern (169 bp):
AAGTCCATTTATAGTCATCATCCTTCGAAAGCCTTATTACTTGCTTTAAATATTTTTATAATCTC
ATAATTGATTTTAAGTTTAATTTTTTTACATTTTTTATTAAAACAGATTATAATTGAATGTTTAC
CTCAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAA
Found at i:4358 original size:170 final size:171
Alignment explanation
Indices: 4031--4393 Score: 462
Period size: 170 Copynumber: 2.1 Consensus size: 171
4021 CAAGTTTAAT
* * * *
4031 TTTTTTACATTTTTTATTAAAACAGATTTTAATTGAATGTTTACCTCAAGAAACATGAAGAAAAA
1 TTTTTTACATTTTTTATTAAAAAAAATTATAATTGAATGCTTACCTCAAGAAACATGAAGAAAAA
* * * * * * **
4096 GTTATCCATTTGGCAAGAAAAGTCCATTTATAGTCATCCATGCTTTCGAAAGCCTTGTTATTTGC
66 GATATCCATTTGGCAAAAAAAGTCCACTTATAGTCATCCATGCCTTCAAAAGCCTTATTACCTGC
* *
4161 CTTAAATATTTTTATAATATCATAATTGATTTTAAGTAGAA
131 CTTAAATATTTTTATAATATAATAATTGACTTTAAGTAGAA
* * * **
4202 TATTTTTACCTTTTTTATTAAAAAAAATTATAATTGAGTGCTTACCTCAGGAAATGTGAA-AAAA
1 T-TTTTTACATTTTTTATTAAAAAAAATTATAATTGAATGCTTACCTCAAGAAACATGAAGAAAA
* *
4266 AGATATTCA-TTGGCAAAAAAAGTCTACTTATAGTCAGT-CATGCCTTCAAAAGCCTTATTACCT
65 AGATATCCATTTGGCAAAAAAAGTCCACTTATAGTCA-TCCATGCCTTCAAAAGCCTTATTACCT
* * *
4329 GCTTTAAATGTTTTTATAATCTAATAATTGACTTTAAGTAGAA
129 GCCTTAAATATTTTTATAATATAATAATTGACTTTAAGTAGAA
*
4372 TTTTTTATATTTTTTATTAAAA
1 TTTTTTACATTTTTTATTAAAA
4394 TAGATTGTAA
Statistics
Matches: 164, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
169 19 0.12
170 83 0.51
171 13 0.08
172 49 0.30
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (171 bp):
TTTTTTACATTTTTTATTAAAAAAAATTATAATTGAATGCTTACCTCAAGAAACATGAAGAAAAA
GATATCCATTTGGCAAAAAAAGTCCACTTATAGTCATCCATGCCTTCAAAAGCCTTATTACCTGC
CTTAAATATTTTTATAATATAATAATTGACTTTAAGTAGAA
Found at i:4912 original size:171 final size:170
Alignment explanation
Indices: 4576--4951 Score: 400
Period size: 171 Copynumber: 2.2 Consensus size: 170
4566 NNTCATTACT
* * *
4576 TGCTTTAAATGTTTTTATTATCTCATAATTGATTGTAAGTTGAATTCTTTTACCTTTTGCGCTAA
1 TGCTTTAAATATTTTTATAATCTCATAATTGATTGTAAGTTGAATTCTTTTAACTTTTGCGCTAA
* *
4641 AACAGATAATAATTGAATATCTACCTCAATAAGCATGAAGAAAAAGATATCCACTGGCAAGAAAA
66 AACAGATAATAATTGAATATCTACCTCAAGAAACATGAAGAAAAAGATATCCACTGGCAAGAAAA
* * **********
4706 GTCCATTTATAGTTACCCANNNNNNNNNNAGCCTTAGTAC
131 CTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAGTAC
* * *
4746 TCGCTTTAAATATTTTTATAATCTCATAATTGATTTTAA-TTGAATTTTTTTTATATTTTTG-GC
1 T-GCTTTAAATATTTTTATAATCTCATAATTGATTGTAAGTTGAA-TTCTTTTA-ACTTTTGCGC
* * * *** * * *
4809 TAAAATAGTTAATAATTGAATGTCTACCTTGGGAAATATGAAGAAAAAGATATCCATTGGTAAGA
63 TAAAACAGATAATAATTGAATATCTACCTCAAGAAACATGAAGAAAAAGATATCCACTGGCAAGA
*
4874 AAACTCCATTTATAGTCACCCATACCTTCGAAAGCCTTATTAC
128 AAACTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAGTAC
4917 ATGCTTTAAATGATTTTGTA-AA-CTCATAATTGATT
1 -TGCTTTAAAT-ATTTT-TATAATCTCATAATTGATT
4952 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
170 6 0.04
171 149 0.88
172 13 0.08
173 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (170 bp):
TGCTTTAAATATTTTTATAATCTCATAATTGATTGTAAGTTGAATTCTTTTAACTTTTGCGCTAA
AACAGATAATAATTGAATATCTACCTCAAGAAACATGAAGAAAAAGATATCCACTGGCAAGAAAA
CTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAGTAC
Found at i:7331 original size:171 final size:170
Alignment explanation
Indices: 6955--7552 Score: 671
Period size: 171 Copynumber: 3.5 Consensus size: 170
6945 NNNNNNNNNC
* * * *
6955 TTAAAATCAATTATAAGATTATAAAAATATTTAAAGCAAGTAATAAGGCTTTT-AATGTCCTAGA
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAA-GTCATAGG
* * * * ** *
7019 TGACTATAATTGGACTTTTCATACCAATAGATACCAATTTTTCATATTTCCTGAGGAAGACATTC
65 TGACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTTCATGTTTCCTGAGGAAGACATTC
* *
7084 AATTATTATCTGTTTTAACGAAAAACATAAAAAAATTCAAT
130 AATTATTATCTGTTTTAACCAAAAATATAAAAAAATTCAAT
* * * * *
7125 TTAACATCAATTAAGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTTGAAGTTATGGGT
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGTCATAGGT
* *
7190 GACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTTCCATGTTTCCTGAGGTAGATATTC
66 GACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTT-CATGTTTCCTGAGGAAGACATTC
* ** * *
7255 AATTCTTATCCATTTTCACCAAAAATATAAAATAATTCAAT
130 AATTATTATCTGTTTTAACCAAAAATATAAAAAAATTCAAT
********** * *
7296 TTAAAATCAATTATGAGNNNNNNNNNNTATTTAAAGCGAGTAATAAGGCTTTAGAAGGCATAGGT
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGTCATAGGT
* * * * * * * *
7361 GACTATAAATGGATTTTTCTTGCTAATGGATTTTTTTTTTTCATGTTTCTTGAGGCAGACATTTA
66 GACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTTCATGTTTCCTGAGGAAGACATTCA
7426 ATTATTATCTGTTTTAACCAAAAACGTA-AAAAAAATTCAAT
131 ATTATTATCTGTTTTAACCAAAAA--TATAAAAAAATTCAAT
* * * *
7467 TTAAAATCAATTATGAGATTATAAAAACATTTAAAG-TATGGAATAAGGCTTTTGAAGTCATGGG
1 TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGA-GTAATAAGGCTTTTGAAGTCATAGG
* *
7531 TGACTAAAAATTGACTTTTCTT
65 TGACTATAAATGGACTTTTCTT
7553 GTCAANNNNN
Statistics
Matches: 348, Mismatches: 75, Indels: 9
0.81 0.17 0.02
Matches are distributed among these distances:
170 129 0.37
171 217 0.62
172 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.36
Consensus pattern (170 bp):
TTAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGAAGTCATAGGT
GACTATAAATGGACTTTTCTTACCAATGGATATCTTTTTTTCATGTTTCCTGAGGAAGACATTCA
ATTATTATCTGTTTTAACCAAAAATATAAAAAAATTCAAT
Found at i:8551 original size:171 final size:169
Alignment explanation
Indices: 8374--8856 Score: 434
Period size: 172 Copynumber: 2.8 Consensus size: 169
8364 NNNNNNNNNN
* *
8374 GTGACTATAAATGGACCTTTCTTGTCAATGGATATTTTTTTCTTCACATTTCTCAAGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTC-CAAGGTAGACAT
* * *
8439 TCAATCATAATCTATTTTAATAACAAATAGAAAAAAATTTAATTTAAAATCAATTATGAGATTAT
65 TCAATCATAATCTGTTTTAA-AAAAAATAGAAAAAAATTTAACTTAAAATCAATTATGAGATTAT
* * *
8504 AAAAACATTTAAAGC-ATGGAATAAGGCTTTGGAAGTCATGG
129 AAAAACATTTAAAGCGA-GGAATAAGGCTTTCGAAGGCATGA
* * * ** * * *
8545 GTGACTAAAAATGAACTTTTCTTGTCAATTGATATCTTTTTCTTCATGTTTCCTGAGGTAGATAA
1 GTGACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCC-AAGGTAGACAT
* * * * * *
8610 TAAATTATAATCTGCTTTAAAAAATATATATAAAAAAATTCAACATAAAATCAATTATGAGATTA
65 TCAATCATAATCTGTTTTAAAAAA-A-ATAGAAAAAAATTTAACTTAAAATCAATTATGAGATTA
********** *
8675 TNNNNNNNNNNAAAGCGAGTAATAAGGCTTTCGAAGGCATGA
128 TAAAAACATTTAAAGCGAGGAATAAGGCTTTCGAAGGCATGA
* * * * * *
8717 GTGACTATACA-GAGACTTTTTTTGTCAATGGATATCTTTTCCTTCGCATTTCCCAAGGCAAACA
1 GTGACTATAAATG-GACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTT-CCAAGGTAGACA
* * * *
8781 TTCAA-CTATTACCTGTTTTAACAAAAAAT-GTACAAAAATTTAAGTTAAAATCAATTATGAGAT
64 TTCAATC-ATAATCTGTTTTAA-AAAAAATAG-AAAAAAATTTAACTTAAAATCAATTATGAGAT
* *
8844 TCTAAAAATATTT
126 TATAAAAACATTT
8857 TTGCCACAAA
Statistics
Matches: 235, Mismatches: 68, Indels: 18
0.73 0.21 0.06
Matches are distributed among these distances:
170 4 0.02
171 103 0.44
172 121 0.51
173 7 0.03
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (169 bp):
GTGACTATAAATGGACTTTTCTTGTCAATGGATATCTTTTTCTTCACATTTCCAAGGTAGACATT
CAATCATAATCTGTTTTAAAAAAAATAGAAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
AAACATTTAAAGCGAGGAATAAGGCTTTCGAAGGCATGA
Found at i:10931 original size:170 final size:171
Alignment explanation
Indices: 10755--11115 Score: 442
Period size: 171 Copynumber: 2.1 Consensus size: 171
10745 NNNNNNNCTT
*
10755 AAAATCAATTATAAGATTATAAAAATATTTAAAG-GAGTAATAAGGCTTTTGATGTCATGGGTGA
1 AAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGATGTCATGGGTGA
* *
10819 CTATAATTGAACTTTTCATACCAATAGATACCTTTCTCTTCATATTTCCT-GAGG-AATAGATTC
66 CTATAAATGAACTTTTCATACCAATAGATACCTTTCTCTTCATATTTCCTAG-GGCAA-ACATTC
* * *
10882 AATTATTCTCTGTTTTAACGAAAAACGTAAAA-AGATTCAATTC
129 AATTATTATCCGTTTTAACGAAAAACATAAAACA-ATTCAATTC
**********
10925 AAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTNNNNNNNNNNGTGA
1 AAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGATGTCATGGGTGA
* * * * * * *
10990 CTATAAATGGACTTTTCTTGCCAATGGATAGCTTTTTCTTCATGTTTCCTAGGGCAAACATTCAA
66 CTATAAATGAACTTTTCATACCAATAGATACCTTTCTCTTCATATTTCCTAGGGCAAACATTCAA
* *
11055 TTATTATCCGTTTTAACTAAAAACATAAAACAATTCAATTT
131 TTATTATCCGTTTTAACGAAAAACATAAAACAATTCAATTC
11096 AAAATCAATTATGAGATTAT
1 AAAATCAATTATGAGATTAT
11116 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
170 33 0.20
171 125 0.77
172 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.35
Consensus pattern (171 bp):
AAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTTGATGTCATGGGTGA
CTATAAATGAACTTTTCATACCAATAGATACCTTTCTCTTCATATTTCCTAGGGCAAACATTCAA
TTATTATCCGTTTTAACGAAAAACATAAAACAATTCAATTC
Done.