Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398397.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1695.0, 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: 8725
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.26
Warning! 2450 characters in sequence are not A, C, G, or T
Found at i:310 original size:171 final size:171
Alignment explanation
Indices: 130--495 Score: 410
Period size: 171 Copynumber: 2.1 Consensus size: 171
120 NNNNNNNNNN
** * **
130 AACTTAAAATCAATTATGAGATTGTAAAA-CTATTTAAAGTGAGTAATGAGGCTTTTGAAAGAAT
1 AACTTAAAATCAATTATGAGATTAAAAAACCT-TTTAAAGCGAGTAACAAGGCTTTTGAAAGAAT
** * ** **********
194 GGGTGACTATAAATAAACTTTTGTTGTCAATGAATACCTTGTTCTTCNNNNNNNNNNAGGTAGAC
65 AAGTGACTATAAATAAACTTTTCTTACCAATGAATACCTTGTTCTTCAAGTTTCTCGAGGTAGAC
* * *
259 ATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTA
130 ATTCAATTATAGCCTGTTTGAACCAAAAATATAAAAAAATTA
* * * **
301 AATTTAAAATGAATTATGAGGTTAAAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGATGGAATA
1 AACTTAAAATCAATTATGAGATTAAAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGAAAGAATA
* * * *
366 AGTGACTATAAATAAACTTTTCTTACCAATGATTGCCTTTTTCTTTAAGTTTCTCGAGGTAGACA
66 AGTGACTATAAATAAACTTTTCTTACCAATGAATACCTTGTTCTTCAAGTTTCTCGAGGTAGACA
* *
431 TTCACTTATAGCCTGTTTGAACCAAAAATATAAAAAAATTC
131 TTCAATTATAGCCTGTTTGAACCAAAAATATAAAAAAATTA
472 AACTTAAAATCAATTATGAGATTA
1 AACTTAAAATCAATTATGAGATTA
496 TNNNNNNNNN
Statistics
Matches: 157, Mismatches: 37, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
171 155 0.99
172 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.34
Consensus pattern (171 bp):
AACTTAAAATCAATTATGAGATTAAAAAACCTTTTAAAGCGAGTAACAAGGCTTTTGAAAGAATA
AGTGACTATAAATAAACTTTTCTTACCAATGAATACCTTGTTCTTCAAGTTTCTCGAGGTAGACA
TTCAATTATAGCCTGTTTGAACCAAAAATATAAAAAAATTA
Found at i:1742 original size:171 final size:169
Alignment explanation
Indices: 1196--2200 Score: 612
Period size: 171 Copynumber: 5.9 Consensus size: 169
1186 NNNNNNATTT
* * * * **
1196 AACTTAAAATCAATTATAAGATTATAAAACAATTTTAAGTGAGAAATATGGCTTTTGAATCAAT-
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * * *
1260 GCGTTACTATAAATGGACTTTTCTTG-CTAGTGAATGCCTTTTTGTTCATGGTTCTCAAGGTACA
66 G-GTGACTATAAA-GGACTTTTCTTGTC-AATGAATGCCTTTTTCTTCA-GGTTCTCAAGGTAGA
* ** *
1324 CATTCAATTATAGTCTGTTTTTGCTAAAAATATAAAAAAATTC
127 CATTCAATTATAGTTTGTTTTAACTAAAAATATAAAACAATTC
********** * * * * * *
1367 AACTNNNNNNNNNNTATGAAATTATAAAACAATTTAAAATGAGCAATAAGACTTTTGAAGGTATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * * * **
1432 GGTGA--A-AAA-GACTTTTCTTCTCAATGAGTGCCTTTTTCTTCATGTTAGTTGAGGTAGACAT
66 GGTGACTATAAAGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAGGTT-CTCAAGGTAGACAT
*
1493 TCAATTATAGTTTGTTTTAACTAAAAATGTAAAACAATTC
130 TCAATTATAGTTTGTTTTAACTAAAAATATAAAACAATTC
***************** ** *
1533 AACTTANNNNNNNNNNNNNNNNNATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATA
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * * ** *
1598 GGTAACTATAAACGGACTTTTCTTGTCAATAAATGCCTTTTTCTTTAGGTTCCTTGAGATAGACA
66 GGTGACTATAAA-GGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAGGTT-CTCAAGGTAGACA
*
1663 TTCAATTATAGTTTGTTTTAACTAAAAATATAAAACATTTC
129 TTCAATTATAGTTTGTTTTAACTAAAAATATAAAACAATTC
* * * * *
1704 AACTTAAAATCAATTATGAGATTATACAACAATTTAAAGGGACTAATAAAGATTTTGAAGGAATA
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * *
1769 GGTGACTATAAAGGGACTTTTCTTGCCAATGAATGCC-TTTTCTTTCAAGTTTCTCAAGGTAGGC
66 GGTGACTATAAA-GGACTTTTCTTGTCAATGAATGCCTTTTTC-TTC-AGGTTCTCAAGGTAGAC
** *
1833 ATTCAATTATA-TTCTGTTTTAAAGAAAAATATAAAAAAATTC
128 ATTCAATTATAGTT-TGTTTTAACTAAAAATATAAAACAATTC
********** * * * * *
1875 ANNNNNNNNNNAATTATGAGATTATAAAATAATTTAATGTGAGCAATAAGGCTTTTGATGGAATG
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * * *********
1940 GGTGACTATAAATTGAAC-TTTCTTGCCAATGAATGCATTTTNNNNNNNNNNTCTCAAGGTAGAC
66 GGTGACTATAAA--GGACTTTTCTTGTCAATGAATGCCTTTT-TCTTCAGGTTCTCAAGGTAGAC
* * * *
2004 ATTCAATTATAGTCTGTTTGAACTAAAAATGT-TAACAAATTC
128 ATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAC-AATTC
* ********** *
2046 AACTTAAAATCAATTATGAGATTATAAAATAATTTNNNNNNNNNNATAAGCCTTTTGAAGGAA-A
1 AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
* * *** * **
2110 GGGTGACTATAATGGACTTTTCTTG-CAAAAGAATTTATTTTTCTTCATGTTTCTTGAGGTAGAC
66 -GGTGACTATAAAGGACTTTTCTTGTC-AATGAATGCCTTTTTCTTCA-GGTTCTCAAGGTAGAC
* *
2174 ATTCAATTATAGTCTGTTTTAATTAAA
128 ATTCAATTATAGTTTGTTTTAACTAAA
2201 NNNNNNNNNN
Statistics
Matches: 630, Mismatches: 184, Indels: 41
0.74 0.22 0.05
Matches are distributed among these distances:
165 3 0.00
166 122 0.19
167 1 0.00
168 4 0.01
169 8 0.01
170 63 0.10
171 417 0.66
172 12 0.02
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
AACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATA
GGTGACTATAAAGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAGGTTCTCAAGGTAGACATT
CAATTATAGTTTGTTTTAACTAAAAATATAAAACAATTC
Found at i:2922 original size:170 final size:160
Alignment explanation
Indices: 2687--3013 Score: 317
Period size: 170 Copynumber: 2.0 Consensus size: 160
2677 TTGAACGCGA
* * *
2687 ATAATAAGGCTTTGGTAAGAATGGGTGACTATAAATGGACTTTTTTTCTTAACAAATGACTTTTT
1 ATAATAAGGCTTTGGTAAGAATGGGTGACTACAAATAGACTTTTTTTCTCAACAAATGACTTTTT
2752 CAACACGTTTCT-TGAGGTAAGA-ATTCAATTATTA-TCTG-TTTAA-TAAAAAATATAAAAATA
66 CAACACGTTTCTAT-A-GT-AGACATTCAATTA-TAGTCTGTTTTAACTAAAAAATATAAAAA-A
2812 TTTAACTTAAAATCAATTATAAGATTATNNNNNNNNNNAAAGCCT
126 TTTAACTTAAAATCAATTATAAGATTAT----------AAAGCCT
* * * ** *
2857 ATAATAAGGCTTTTG-AAGGAATGTGTGACTCCAAATAGACTTTTCTTTC-CAATGAATGTCTTT
1 ATAATAAGGCTTTGGTAA-GAATGGGTGACTACAAATAGACTTTT-TTTCTCAACAAATGACTTT
** * * *
2920 TTCTTCATGTTTCTCATAGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATTTTAAAAAATT
64 TTCAACACGTTTCT-ATAGTAGACATTCAATTATAGTCTGTTTTAACTAAAAAATATAAAAAATT
2985 TAACTTAAAATCAATTATAAGATTATAAA
128 TAACTTAAAATCAATTATAAGATTATAAA
3014 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 14, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
161 3 0.02
169 7 0.05
170 72 0.53
171 39 0.29
172 14 0.10
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.38
Consensus pattern (160 bp):
ATAATAAGGCTTTGGTAAGAATGGGTGACTACAAATAGACTTTTTTTCTCAACAAATGACTTTTT
CAACACGTTTCTATAGTAGACATTCAATTATAGTCTGTTTTAACTAAAAAATATAAAAAATTTAA
CTTAAAATCAATTATAAGATTATAAAGCCT
Found at i:3579 original size:171 final size:166
Alignment explanation
Indices: 3221--3807 Score: 433
Period size: 171 Copynumber: 3.5 Consensus size: 166
3211 NNNNNNNNNN
* *
3221 ATATAAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAACAATTTAAAGCGAGCAATAAGA
1 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGCAATAAGA
* ** * * ** * *
3286 CTTTTGAAGGTATGGGTGAAAAAGACTTTTCTTGTTAATCAGTGCCTTTTTCTTCACATTACTCG
66 CTTTTGAAGGAATAAGTAAAAAAAACTTTTCTTGCCAATAAATGCCTTTTTCTTCACATTACTCG
3351 AGGAAGACATTCAATTATAGTCTGTTTTAACTAAAA
131 AGGAAGACATTCAATTATAGTCTGTTTTAACTAAAA
********** * ** * *
3387 ATATANNNNNNNNNNACTTAAAATCAATTACGAGATTATAAAACCTTTTAAAACGAGTAATAAGG
1 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGCAATAAGA
* * **
3452 CTTTTGAGGGAATAAGTAACTATAAACTAACTTTTCTTGCCAATAAATGCCTTTTTCTTTAGGTT
66 CTTTTGAAGGAATAAGTAA--A-AAA--AACTTTTCTTGCCAATAAATGCCTTTTTCTTCACATT
* * * *
3517 TCTTGAGGTAGACTTTCAATTATAGTCTGTTTTAACTAAAA
126 ACTCGAGGAAGACATTCAATTATAGTCTGTTTTAACTAAAA
* * **
3558 ATATAAAACATTTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGGGA-CTAATAAA
1 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGC-AAT-AA
* * ** ********** *
3622 GA-TTTTGAAAGAATAGGTGACTATAAATGGACTTNNNNNNNNNNTGAATGCCTTTTTCTTCA-A
64 GACTTTTGAAGGAATAAGT-A--A-AAA-AAACTTTTCTTGCCAATAAATGCCTTTTTCTTCACA
* * * * * **
3685 GTTTCTCAAGGTAGGCATTCAATTATATTCTGTTTTAAAGAAAA
124 -TTACTCGAGGAAGACATTCAATTATAGTCTGTTTTAACTAAAA
* * ***
3729 ATAAAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAATGTGAGCAATAAG
1 AT-ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGCAATAAG
*
3794 ACTTTTGATGGAAT
65 ACTTTTGAAGGAAT
3808 GGGTGACTAT
Statistics
Matches: 322, Mismatches: 84, Indels: 24
0.75 0.20 0.06
Matches are distributed among these distances:
166 62 0.19
168 1 0.00
169 3 0.01
171 185 0.57
172 67 0.21
173 3 0.01
174 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.34
Consensus pattern (166 bp):
ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACGAGCAATAAGA
CTTTTGAAGGAATAAGTAAAAAAAACTTTTCTTGCCAATAAATGCCTTTTTCTTCACATTACTCG
AGGAAGACATTCAATTATAGTCTGTTTTAACTAAAA
Found at i:6712 original size:172 final size:169
Alignment explanation
Indices: 6221--6713 Score: 503
Period size: 171 Copynumber: 2.9 Consensus size: 169
6211 TTACTCCCTC
* * * * * *
6221 TAAATTGTTTTATAATCTCATAATTGATTTTAAAGTGAATTTTTTTATATTTTTCTTTAAAATAG
1 TAAATTGTTTTATAATCTCATAATTGATTTT-AAGTTAAATATTTTACATTTTTTTTTAAAACAG
* * * * * *
6286 AAT-TAATTGAATACCTACCTCAAGAAACTTGAAAAAAAAGGCATTCATTGGCAAGAAAAGTCCA
65 ACTATAATTGAATGCTTA-CTCTAGAAACATGAAAAAAAAGGCATTCATTAGCAAGAAAAGTCCA
* * * *
6350 TTTACAGTCACGTCTTCCTTCAAAATCCCTATTAGTCCTTT
129 TTTATAGTCACCTATTCCTTCAAAAACCCTATTAGTCCTTT
* * * * ** *
6391 TAAATTGTTTTATAATCTTATAATTGATTTTATGTTGAATTATTTTACATATTTGGTTAAAACAA
1 TAAATTGTTTTATAATCTCATAATTGATTTTAAGTT-AAATATTTTACATTTTTTTTTAAAACAG
* * * *
6456 ACTATAATTGAATG-TCTACCCTGAGAAACCT-AAAGAAAAAGGCATTTATTAGTAAGAAAAGTC
65 ACTATAATTGAATGCT-TACTCT-AGAAACATGAAA-AAAAAGGCATTCATTAGCAAGAAAAGTC
* ** *
6519 TATTTATAGTCATCC-ATTCCTTCAAAAACTTTATTA-TTCTCTT
127 CATTTATAGTCA-CCTATTCCTTCAAAAACCCTATTAGTCCT-TT
*
6562 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATATTGTTACATTTTTTTATTAAAACA
1 TAAATTGTTTTATAATCTCATAATTGATTTTAAGTTAAATATT-TTACATTTTTTT-TTAAAACA
* * * * *
6627 GACTACAATTGAATGCTTGCTTCTAGAAACATGCAAAAAAAGCCATTCATCAAG-AAGAAAAGTC
64 GACTATAATTGAATGCTTAC-TCTAGAAACATGAAAAAAAAGGCATTCAT-TAGCAAGAAAAGTC
6691 CATTTATAGTCACCTATTCCTTC
127 CATTTATAGTCACCTATTCCTTC
6714 GAAAGCCTTN
Statistics
Matches: 265, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
169 3 0.01
170 67 0.25
171 116 0.44
172 72 0.27
173 7 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (169 bp):
TAAATTGTTTTATAATCTCATAATTGATTTTAAGTTAAATATTTTACATTTTTTTTTAAAACAGA
CTATAATTGAATGCTTACTCTAGAAACATGAAAAAAAAGGCATTCATTAGCAAGAAAAGTCCATT
TATAGTCACCTATTCCTTCAAAAACCCTATTAGTCCTTT
Done.