Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397555.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1417.0, 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: 7669
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.24
Warning! 2788 characters in sequence are not A, C, G, or T
Found at i:1987 original size:171 final size:171
Alignment explanation
Indices: 1711--2027 Score: 451
Period size: 171 Copynumber: 1.9 Consensus size: 171
1701 ATGAATACTT
* * *
1711 TTTTCTTCATGTTTCTCGAGATAGACAATCAATTGTTATCTGTTTTAATCAAAAATATAAAAAAA
1 TTTTATTCATGTTTCTCGAGATAGACAATCAATTATTATCTATTTTAATCAAAAATATAAAAAAA
* * * *
1776 TTTAACTAAAAATTAATTCTTAGATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTTGAAA-G
66 TTTAACTAAAAATTAATTATAAGATTAAAAAATCATTTAAAGCGAGTAATAAGGCTTTT-AAAGG
*
1840 ACTGGGAGACTATAAATAGACTTTTTTTACCAATGAAGGTTC
130 AATGGGAGACTATAAATAGACTTTTTTTACCAATGAAGGTTC
* ** * * *
1882 TTTTATTCATGTTTCTTGCTATAGACATTCAATTA-TATTCTATTTTAATGAAAAATGTAAAAAA
1 TTTTATTCATGTTTCTCGAGATAGACAATCAATTATTA-TCTATTTTAATCAAAAATATAAAAAA
1946 ATTTAACTAAAAATTAATTATAAGATTAAAAAA-CTATTTAAAGCGAGTAATAAGGCTTTTAAAG
65 ATTTAACTAAAAATTAATTATAAGATTAAAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTAAAG
*
2010 GAATGGGTGACTATAAAT
129 GAATGGGAGACTATAAAT
2028 GNNNNNNNNN
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
170 6 0.05
171 122 0.95
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (171 bp):
TTTTATTCATGTTTCTCGAGATAGACAATCAATTATTATCTATTTTAATCAAAAATATAAAAAAA
TTTAACTAAAAATTAATTATAAGATTAAAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAAGGA
ATGGGAGACTATAAATAGACTTTTTTTACCAATGAAGGTTC
Found at i:2864 original size:15 final size:15
Alignment explanation
Indices: 2844--2873 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2834 TTTATATTTT
2844 TCATTAATAGAAATA
1 TCATTAATAGAAATA
2859 TCATTAATAGAAATA
1 TCATTAATAGAAATA
2874 ATAGTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
TCATTAATAGAAATA
Found at i:4006 original size:343 final size:343
Alignment explanation
Indices: 3277--4140 Score: 996
Period size: 343 Copynumber: 2.5 Consensus size: 343
3267 TTTTATAATC
* ** *
3277 TCAT-ATTAATTTTAAGTTTAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCT
1 TCATAATTGATTTTAAGTAGAAGTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCT
* * * * ** * *
3341 GCCTTAA-AAAGCAT-AGAGAAAAAAGCATTCATTGGCAA-AAAAAGTGTATTTACAGACTCTTA
66 ACCATAAGAAAG--TGA-AGAAAAGAGCATTCATTGGTAAGAAAAA-TCAATTTATAGTCTCTTA
* * * *
3403 TTCCTTCAAAAGCCTTATTACTCA-CTTTGAATGGTTTTATAATCTAATAATTGATTTTAAGTTG
127 ATCCTTCAAAAGCCTTATTACT-AGCTTTAAATGGTTTTATAATCTAATAATTAATTTTAAGTTA
** * * *
3467 AATTTTTTTACATTTTTGATTAAAATGGACTATAATTGAATATCTATCTAGGGAAACGTGAAGAA
191 AATTTTTTTACATTTTTGATTAAAACAGACAATAATTGAATATCTATCTAGAGAAACATGAAGAA
* * ** *
3532 AAGATCATTCATTGACATGAAAAGTCCATTTGAGTCACCCATCTCTTCAAAACCTTTTTACTTTG
256 AAAAGCATTCATTGACAACAAAAGTCCATTTGAGTCACCCATCTCTTCAAAACCTTTTTACTTCG
* *
3597 CCTTTAGAATGGGTTTTCTAATC
321 CCTTTAGAATGGGTTTTCAAATA
* ** *
3620 TCATAATTGATTTTAAGTAGAATTTTTTTACATTTTT-ATTAAAATTGACAATAATTGAATGTCT
1 TCATAATTGATTTTAAGTAGAAGTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCT
* ** * * * *
3684 ACCGTAAGAAATGTGAAGAAAAGAGCATTTGTTGGTAAGAAAAATCCATTTGTAGTCTCCTAGTC
66 ACCATAAGAAA-GTGAAGAAAAGAGCATTCATTGGTAAGAAAAATCAATTTATAGTCTCTTAATC
*
3749 CTTCAAAAGCCTTATTACTAGCTTTAAATGATTTTATAATCTAATAATTAATTTTAAGTTAAATT
130 CTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAATCTAATAATTAATTTTAAGTTAAATT
* * * *
3814 TTTTTATTATTTTTGATTAAAACAGACAATAATTGATTGTCTATCTCGAGAAACATGAAGAAAAA
195 TTTTTA-CATTTTTGATTAAAACAGACAATAATTGAATATCTATCTAGAGAAACATGAAGAAAAA
* * *
3879 AGCATTCATTGGCAACAAAAGTCCATTTATAGTCACCCAT-TCCTTCAAAGCCTTTATTAC-TCG
259 AGCATTCATTGACAACAAAAGTCCATTT-GAGTCACCCATCT-CTTCAAAACCTTT-TTACTTCG
*
3942 -CTTTA-AAT-TGTTTTCAAATA
321 CCTTTAGAATGGGTTTTCAAATA
* * *
3962 TCATAATTGATTTTGAA-TTGAAGTTTTTTACATTTTTCATTAAAACAAACTATAATTGAATATC
1 TCATAATTGATTTT-AAGTAGAAGTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTC
* * * * *
4026 TACCACAAGAAACGTGAACAAAAGAGCATTCATGGGTAGGAAAAGTCAATTTATAGTCTCTTAAT
65 TACCATAAGAAA-GTGAAGAAAAGAGCATTCATTGGTAAGAAAAATCAATTTATAGTCTCTTAAT
* * * *
4091 CCTTCAAAAGCCTTGTTGCTCGCTTTAAATGGTTTTATAATCTCATAATT
129 CCTTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAATCTAATAATT
4141 GATNNNNNNN
Statistics
Matches: 441, Mismatches: 68, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
342 42 0.10
343 254 0.58
344 116 0.26
345 25 0.06
346 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (343 bp):
TCATAATTGATTTTAAGTAGAAGTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCT
ACCATAAGAAAGTGAAGAAAAGAGCATTCATTGGTAAGAAAAATCAATTTATAGTCTCTTAATCC
TTCAAAAGCCTTATTACTAGCTTTAAATGGTTTTATAATCTAATAATTAATTTTAAGTTAAATTT
TTTTACATTTTTGATTAAAACAGACAATAATTGAATATCTATCTAGAGAAACATGAAGAAAAAAG
CATTCATTGACAACAAAAGTCCATTTGAGTCACCCATCTCTTCAAAACCTTTTTACTTCGCCTTT
AGAATGGGTTTTCAAATA
Found at i:4072 original size:171 final size:171
Alignment explanation
Indices: 3207--4143 Score: 910
Period size: 171 Copynumber: 5.5 Consensus size: 171
3197 TTTCACTGAT
* * * * * * *
3207 AAGAAATGTCCATTTATAGCCTTCTCATTCCTTTAACAGCCTTTTTACTCG-TTCT-AATGATTT
1 AAGAAAAGTCCATTTATAGTCTCCT-ATTCCTTCAAAAGCCTTATTACTCGCTT-TAAATGGTTT
* *
3270 TATAATCTCAT-ATTAATTTTAAGTTTAATTTTTTTACATTTTTCATTAAAACAGACTATAATTG
64 TATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTG
* ** * *
3334 AATGTCTGCCTTAA-AAAGCAT-AGAGAAAAAAGCATTCATTGGC
129 AATGTCTACCACAAGAAA-CGTGA-AGAAAAGAGCATTCATTGGC
* ** * * * * *
3377 AAAAAAAGTGTATTTACAGACTCTTATTCCTTCAAAAGCCTTATTACTCACTTTGAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
* * **
3442 TAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATGGACTATAATTGAA
66 TAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAA
* * ** * *
3507 TATCTATCTA-GGGAAACGTGAAGAAAAGATCATTCATTGAC
131 TGTCTA-CCACAAGAAACGTGAAGAAAAGAGCATTCATTGGC
* * * * * *
3548 ATGAAAAGTCCATTT-GAGTCACCCA-TCTCTTCAAAA-CCTTTTTACTTTGCCTTTAGAATGGG
1 AAGAAAAGTCCATTTATAGTCTCCTATTC-CTTCAAAAGCCTTATTAC-TCG-CTTTA-AAT-GG
* * ** *
3610 TTTTCTAATCTCATAATTGATTTTAAGTAGAATTTTTTTACATTTTT-ATTAAAATTGACAATAA
61 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAA
** * ** *
3674 TTGAATGTCTACCGTAAGAAATGTGAAGAAAAGAGCATTTGTTGGT
126 TTGAATGTCTACCACAAGAAACGTGAAGAAAAGAGCATTCATTGGC
* * * * *
3720 AAGAAAAATCCATTTGTAGTCTCCTAGTCCTTCAAAAGCCTTATTACTAGCTTTAAATGATTTTA
1 AAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
* * * * * *
3785 TAATCTAATAATTAATTTTAAGTTAAATTTTTTTATTATTTTTGATTAAAACAGACAATAATTGA
66 TAATCTCATAATTGATTTTAAGTTGAATTTTTTTA-CATTTTTCATTAAAACAGACTATAATTGA
* * * * * *
3850 TTGTCTATCTCGAGAAACATGAAGAAAAAAGCATTCATTGGC
130 ATGTCTACCACAAGAAACGTGAAGAAAAGAGCATTCATTGGC
* * * *
3892 AACAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAGCCTTTATTACTCGCTTTAAATTGTTTT
1 AAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAGCC-TTATTACTCGCTTTAAATGGTTTT
* * *
3956 CA-AATATCATAATTGATTTTGAA-TTGAAGTTTTTTACATTTTTCATTAAAACAAACTATAATT
65 -ATAATCTCATAATTGATTTT-AAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATT
* * * *
4019 GAATATCTACCACAAGAAACGTGAACAAAAGAGCATTCATGGGT
128 GAATGTCTACCACAAGAAACGTGAAGAAAAGAGCATTCATTGGC
* * * * * *
4063 AGGAAAAGTCAATTTATAGTCTCTTAATCCTTCAAAAGCCTTGTTGCTCGCTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
4128 TAATCTCATAATTGAT
66 TAATCTCATAATTGAT
4144 NNNNNNNNNN
Statistics
Matches: 621, Mismatches: 124, Indels: 43
0.79 0.16 0.05
Matches are distributed among these distances:
169 32 0.05
170 87 0.14
171 222 0.36
172 204 0.33
173 66 0.11
174 10 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
AAGAAAAGTCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTA
TAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAA
TGTCTACCACAAGAAACGTGAAGAAAAGAGCATTCATTGGC
Done.