Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400337.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_354.0, 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: 18177
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.20
Warning! 8460 characters in sequence are not A, C, G, or T
Found at i:10212 original size:342 final size:331
Alignment explanation
Indices: 9635--10282 Score: 640
Period size: 342 Copynumber: 1.9 Consensus size: 331
9625 NNNNNNNNNN
* * * *
9635 TATAATGTCATAATTGATTTTAAGTTGAATTGTTTTACATTTTTAGTTAAAACTATCTATAATTG
1 TATAATATCATAATTGATTTTAAGTTGAATTGGTTTACATATTTAGTTAAAACTAACTATAATTG
*
9700 AATATCTACCTCAAGAAACATAAAGAAAAAGGCATTCATTAGCAAAAAAAATCCATTTATAGTCA
66 AATATCTACCTCAAGAAACATAAAGAAAAAAGCATTCATTAGCAAAAAAAATCCATTTATAGTCA
* *
9765 CTCATTCCTTCAAAAACATTATTACTAACTTTAAATAGTTTTCTAACATCAAAATTAATTTTACT
131 CTCATTCCTTCAAAAACATTATTACTAACTTTAAATAGTTTTATAACATCAAAATTAATTTTACA
********** * * *
9830 TTGAATTCTTTGTANNNNNNNNNNTGAAACAAATTATAATTGAATGTTTACCGT-GAGAAACATG
196 TTGAATTCTTTGTAACATTTTTTATGAAACAAACTATAATTGAATGTGTACC-TCAAGAAACAT-
* * * * *
9894 AAAAAAAGGTATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTTCGTNNNNNNNNNNATT
259 AAAAAAAAGCAATCATTGGCAAGAAAAGTCCATTTATAGTCACACATTTCGT----------ATT
9959 ACTTGCTTTAAATGATTT
314 ACTTGCTTTAAATGATTT
* *
9977 TATAATATCATAATTGATTTTAAGTTGAATTGGTTTATATATTTGGTTAAAAC-AGACTATAATT
1 TATAATATCATAATTGATTTTAAGTTGAATTGGTTTACATATTTAGTTAAAACTA-ACTATAATT
* ** * * * * *
10041 GAATGTCTACCTCAAGAAATGTAAATAAAAAAGCATTCATTGGTAAGAAAAGT-CATTTTATAGT
65 GAATATCTACCTCAAGAAACATAAAGAAAAAAGCATTCATTAGCAAAAAAAATCCA-TTTATAGT
* * * * ********** *
10105 CAC-CTATTTCTTCAAAAGCATTATTACTCACTTTAAATGGTTTTATANNNNNNNNNNTGATTTT
129 CACTC-ATTCCTTCAAAAACATTATTACTAACTTTAAATAGTTTTATAACATCAAAATTAATTTT
*
10169 ACATTGAATTCTTTGT-ACATTTTTTATTAAAGCAAACTATAATTGAATGTGTACCTCAAGAAAC
193 ACATTGAATTCTTTGTAACATTTTTTATGAAA-CAAACTATAATTGAATGTGTACCTCAAGAAAC
* *
10233 ATAAAAAAAAGCAATCATTGGCAAGAAGAGTCTATTTATAGTCACACATT
257 ATAAAAAAAAGCAATCATTGGCAAGAAAAGTCCATTTATAGTCACACATT
10283 CCTTCAAAAG
Statistics
Matches: 248, Mismatches: 53, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
341 50 0.20
342 198 0.80
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.36
Consensus pattern (331 bp):
TATAATATCATAATTGATTTTAAGTTGAATTGGTTTACATATTTAGTTAAAACTAACTATAATTG
AATATCTACCTCAAGAAACATAAAGAAAAAAGCATTCATTAGCAAAAAAAATCCATTTATAGTCA
CTCATTCCTTCAAAAACATTATTACTAACTTTAAATAGTTTTATAACATCAAAATTAATTTTACA
TTGAATTCTTTGTAACATTTTTTATGAAACAAACTATAATTGAATGTGTACCTCAAGAAACATAA
AAAAAAGCAATCATTGGCAAGAAAAGTCCATTTATAGTCACACATTTCGTATTACTTGCTTTAAA
TGATTT
Found at i:10338 original size:170 final size:169
Alignment explanation
Indices: 9499--10386 Score: 572
Period size: 171 Copynumber: 5.2 Consensus size: 169
9489 NNNNNNNNNN
* * ** * **
9499 TACATTTTTCATTAAAATAGGCTATAATTAAATG-CTTACCTCAAGAAACATGTAAAAAAAGCCA
1 TACATTTTTGATTAAAACAAACTATAATTGAATGTC-TACCTCAAGAAACATAAAAAAAAAG-CA
* * * * * **
9563 TTCATGTAG-AAGAAAAGTCTATTTATAGTCTCCCATTTCTTCAAAAGCCTTATTACTCACTTNN
64 TTCAT-TGGCAAGAAAAGTCCATTTATAGTC-ACCATTCCTTCAAAAGCATTATTACTCACTTTA
******** * * *
9627 NNNNNNNNTATAATGTCATAATTGATTTTAAGTTGAATTGTTT
127 AATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTT
* * * *
9670 TACATTTTT-AGTTAAAACTATCTATAATTGAATATCTACCTCAAGAAACATAAAGAAAAAGGCA
1 TACATTTTTGA-TTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATAAA-AAAAAAGCA
* * * * *
9734 TTCATTAGCAAAAAAAATCCATTTATAGTCACTCATTCCTTCAAAAACATTATTACTAACTTTAA
64 TTCATTGGCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCATTATTACTCACTTTAA
* * **
9799 ATAGTTTTCTAA-CATCAAAATTAATTTTACTTTGAATTCTTT
128 ATAGTTTTATAATC-TCAAAATTGATTTTAAGTTGAATTCTTT
********** * * * * * * *
9841 GTANNNNNNNNNNTGAAACAAATTATAATTGAATGTTTACCGT-GAGAAACATGAAAAAAAGGTA
1 -TACATTTTTGATTAAAACAAACTATAATTGAATGTCTACC-TCAAGAAACATAAAAAAAAAGCA
* * * ********** **
9905 TTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTTCGTNNNNNNNNNNATTACTTGCTTTAA
64 TTCATTGGCAAGAAAAGTCCATTTATAGTCA-CCATTCCTTCAAAAGCATTATTACTCACTTTAA
* * **
9970 AT-GATTTTATAATATCATAATTGATTTTAAGTTGAATTGGTT
128 ATAG-TTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTT
* * * * **
10012 TATATATTTGGTTAAAACAGACTATAATTGAATGTCTACCTCAAGAAATGTAAATAAAAAAGCAT
1 TACATTTTTGATTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATAAA-AAAAAAGCAT
* *
10077 TCATTGGTAAGAAAAGT-CATTTTATAGTCACCTATTTCTTCAAAAGCATTATTACTCACTTTAA
65 TCATTGGCAAGAAAAGTCCA-TTTATAGTCACC-ATTCCTTCAAAAGCATTATTACTCACTTTAA
* **********
10141 ATGGTTTTATANNNNNNNNNNTGATTTTACA-TTGAATTCTTT
128 ATAGTTTTATAATCTCAAAATTGATTTTA-AGTTGAATTCTTT
* * * *
10183 GTACATTTTTTATTAAAGCAAACTATAATTGAATGTGTACCTCAAGAAACAT-AAAAAAAAGCAA
1 -TACATTTTTGATTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATAAAAAAAAAGCAT
* * * * *
10247 TCATTGGCAAGAAGAGTCTATTTATAGTCACACATTCCTTCAAAAGCCTTATTGCTCGCTTTAAA
65 TCATTGGCAAGAAAAGTCCATTTATAGTCAC-CATTCCTTCAAAAGCATTATTACTCACTTTAAA
* * *
10312 TAGTTTTATAATCTTAGAATTGATTTTAAGTTAAATT-TTT
129 TAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTT
* *
10352 TAACATTGTTGATTAAAACAGACTATAATTGAATG
1 T-ACATTTTTGATTAAAACAAACTATAATTGAATG
10387 CTTGACTTAG
Statistics
Matches: 538, Mismatches: 156, Indels: 48
0.73 0.21 0.06
Matches are distributed among these distances:
168 1 0.00
169 34 0.06
170 130 0.24
171 286 0.53
172 86 0.16
173 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.36
Consensus pattern (169 bp):
TACATTTTTGATTAAAACAAACTATAATTGAATGTCTACCTCAAGAAACATAAAAAAAAAGCATT
CATTGGCAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGCATTATTACTCACTTTAAATA
GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTT
Found at i:13467 original size:21 final size:21
Alignment explanation
Indices: 13425--13467 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13415 GGGAAACATG
* *
13425 AAGAAAAATGTATTCATTGGC
1 AAGAAAAATGCATTCATAGGC
* *
13446 AAGAAAAGTGCATTTATAGGC
1 AAGAAAAATGCATTCATAGGC
13467 A
1 A
13468 CCCATTTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (21 bp):
AAGAAAAATGCATTCATAGGC
Done.