Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397834.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1136.0, 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: 4446
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.23
Warning! 1645 characters in sequence are not A, C, G, or T
Found at i:1595 original size:172 final size:154
Alignment explanation
Indices: 1403--1712 Score: 289
Period size: 172 Copynumber: 1.9 Consensus size: 154
1393 CTTAAAATTG
* * * *
1403 ATTTTAAATTAAAGTTTTTTACATATTTCCTTAAAACAGATTATAATTGAATGTTTGCCTTAAGA
1 ATTTTAAATTAAAGTTTTTTACATATTTACTTAAAACAGACTATAATTGAATGTATACCTTAAGA
* * * *
1468 AACTTGTAGAATAA-GCCTTTCATTGAGAAGAAAAGTCTAATTTAGAGTCACCCATTCTTTCAAA
66 AACATGAAGAA-AAGGCCATTCA-T-A-AAGAAAAGTC-AATTTAGAGTCACCCATTCCTTCAAA
1532 AGCCTTATTACTCACTTTAAATTGTTTTA
126 AGCCTTATTACTCACTTTAAATTGTTTTA
* * * * * *
1561 NNNNNNNNNNNNNNATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAA
1 --------------ATTTTAAATTAAAGTTTTTTACATATTTACTTAAAACAGACTATAATTGAA
* * *
1626 TGTATACCTTAAGAAACATGAAGAAAAGGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCAT
52 TGTATACCTTAAGAAACATGAAGAAAAGGCCATTCATAAAGAAAAGTCAATTTAGAGTCACCCAT
1691 TCCTTCAAAAGCCTTATTACTC
117 TCCTTCAAAAGCCTTATTACTC
1713 GTTNNNNNNN
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
168 36 0.30
169 10 0.08
170 1 0.01
171 3 0.03
172 70 0.58
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (154 bp):
ATTTTAAATTAAAGTTTTTTACATATTTACTTAAAACAGACTATAATTGAATGTATACCTTAAGA
AACATGAAGAAAAGGCCATTCATAAAGAAAAGTCAATTTAGAGTCACCCATTCCTTCAAAAGCCT
TATTACTCACTTTAAATTGTTTTA
Found at i:1931 original size:171 final size:168
Alignment explanation
Indices: 1231--3285 Score: 775
Period size: 171 Copynumber: 12.1 Consensus size: 168
1221 NNNNNNNNNT
* * * *
1231 GATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAACAGACTATAATTAAATCTATACCTCAAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
** * * * * **********
1296 AAATGTGAGGCAAAAGGCATTCATTGGCATGAAAAGTCCATTTNNNNNNNNNNATTCCTTCAAAA
66 AAACATGAAGAAAAAGGCATTCA-T--AAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* * * *
1361 GCCTTATTAATCGCTT-TAAATTGTTTTATAATCTTAAAATT
128 GCCTTATTACTCG-TTATAAATTGTTTTATAAACTCAAAATA
* * * * ** * * * * * *
1402 GATTTTAAATTAAAGTTTTTTACATATTTCCTTAAAACAGATTATAATTGAATGTTTGCCTTAAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
* * * * * * * *
1467 AAACTTGTAGAATAAGCCTTTCATTGAGAAGAAAAGTCTAATTTAGAGTCACCCATTCTTTCAAA
66 AAACATGAAGAAAAAGGCATTCA-T-A-AAGAAAAGTC-CATTTATAGTCACCCATTCCTTCAAA
* *************
1532 AGCCTTATTACTCACTT-TAAATTGTTTTANNNNNNNNNNNNN
127 AGCCTTATTACTC-GTTATAAATTGTTTTATAAACTCAAAATA
* * *
1574 NATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATGTATACCTTAAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
*
1639 AAACATGAAGAAAAGGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
66 AAACATGAAGAAAAAGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
********** * *
1704 TTATTACTCGTTNNNNNNNNNNTTATAAACTCATAATT
131 TTATTACTCGTTATAAATTGTTTTATAAACTCAAAATA
* * **
1742 GATTTTAAGTTCAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATTTTTCTCAAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
* * * * ***
1807 AATCGTGAGGAAAAAGGCATTCATTGATAAGAAAAGTCCATTTATAGTCACCTATTCCTTCANNN
66 AAACATGAAGAAAAAGGCATTCA-T-A-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
******* *
1872 NNNNNNNTACTCGCTT-TAAATTGTTTTATAATCTCAAAATA
128 GCCTTATTACTCG-TTATAAATTGTTTTATAAACTCAAAATA
** * * *
1913 GATTTTAAGTTGAA-TTTTTTATGTTTTTCA-TTAAAATAGA--ATAATTGAATGCT-TGCCTCG
1 GATTTTAAGTTGAATTTTTTTACATTTTT-AGTTAAAATAGACTATAATTGAAT-ATATACCTCA
* * * * * * *
1973 AGAAACATGTAGAATAAGCCATTTATTAAGAAGAAAAGTCCATTTAGAGTCACCCATTGCTTTAA
64 AGAAACATGAAGAAAAAGGCATTCA-T-A-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
********** * * *
2038 AAGCCTTATTACTNNNNNNNNNNTGTTTTATAATCTCATAATT
126 AAGCCTTATTACTCGTTATAAATTGTTTTATAAACTCAAAATA
* * * * * * * * * *
2081 GATTTTAAATTAAATATTTTTACATTTTTGGTCAAAACAGACAATAATTGAATGTCT-CTCTGAA
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATAC-CTCAA
* * * * * * * *
2145 GAAACGTGAGGAAAAGGGCAATCATTGGCAAGAAAAGTCCATTTATTGTCACCTACTCCTTCAAA
65 GAAACATGAAGAAAAAGGCATTCA-T--AAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * ******
2210 AGCCTTATTACTCGTTTTAAATTGTTTTATAATCTCNNNNNN
127 AGCCTTATTACTCGTTATAAATTGTTTTATAAACTCAAAATA
**** * * * *
2252 NNNNTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGCT-TGCCTCAA
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAAT-ATATACCTCAA
** ** * *
2316 GAAACATGCGGAAAAAACCATTCAGTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAA
65 GAAACATGAAGAAAAAGGCATTCA-T-A-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
******************** *
2381 AGCCTTATTACTCGATT-TNNNNNNNNNNNNNNNNNNNTAATT
127 AGCCTTATTACTCG-TTATAAATTGTTTTATAAACTCAAAATA
* * * *** ***
2423 GATTTTAAGTTGAATTTTTTTACATTTTTCA-TTAAAACAGACTATAACTAAATGGGTGTTTCAA
1 GATTTTAAGTTGAATTTTTTTACATTTTT-AGTTAAAATAGACTATAATTGAATATATACCTCAA
* * * * * * *
2487 GAAACGT-ATAGAATAAA-TCATTTATTGAGAAGAAAAGTTCATTTAGAGTCACTCATTCTTTCA
65 GAAACATGA-AGAA-AAAGGCATTCA-T-A-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
* *********
2550 AAAGCCTTATTACTCACTT-TAAATTGTTTTATANNNNNNNNNNT-
125 AAAGCCTTATTACTC-GTTATAAATTGTTTTATA-AACTCAAAATA
* * * * * * *
2594 GATTTTAAGTTAAATTTTTTTACATTTTTAGTTAAAACA-AATATAATGGAATGTCTACCTTAAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
* * * * *
2658 AAACATAAAGAAAAGGGTATTCATAAAGAAAGGTCCATTTATAATCACCCATTCCTTCAAAAGCC
66 AAACATGAAGAAAAAGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
* * * *
2723 TTATTAGTCGCTT-TAAATAGTTTTATAACCTCATAATTA
131 TTATTACTCG-TTATAAATTGTTTTATAAACTCA-AAATA
* * * * * *
2762 -ATTTTAAATTGAATTATTATACATTTTTTA-ATAAAATAGACTATAATTGAATGCT-TGTCC-C
1 GATTTTAAGTTGAATTTTTTTACA-TTTTTAGTTAAAATAGACTATAATTGAAT-ATAT-ACCTC
* * * * * *
2823 AAGAAACGTGTAGAAAAAGCCATTTAACGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCA
63 AAGAAACATGAAGAAAAAGGCA-TTCA-TA-AAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
* * * *****
2888 AAAG-CTGTATCACTC-TCTTTAAATTGTTTTATAATCTCATNNNN
125 AAAGCCT-TATTACTCGT-TATAAATTGTTTTATAAACTCAAAATA
****** * * * * *
2932 NNNNNNAAGTTGAATTTTTTTATATTTTTTGTTAAAA-AGAACTATAATTGAATGTCTACCTCAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAG-ACTATAATTGAATATATACCTCAA
* * ********** *
2996 GAAACATGAAGAAAAAGGTATTCATTGGAAAGAAAAGTCTATNNNNNNNNNNCCATTTCTTCAAA
65 GAAACATGAAGAAAAAGGCATTCA-T--AAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* *
3061 AGCCTTATTACTCGATT-TAAATGGTTTTATAAACTCATAATTA
127 AGCCTTATTACTCG-TTATAAATTGTTTTATAAACTCA-AAATA
* * * **********
3104 -ATTTGAAGTTGAATTGTTTTTATATTTTTAGTTAAAACAGACTATAANNNNNNNNNNACCTCAA
1 GATTTTAAGTTGAATT-TTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAA
* * ** * *
3168 GAAACATGAAGAAAAAGACATTCATTGGCAAA-AGAAGTTTATTTATAGTCAGCTATTCCTTCAA
65 GAAACATGAAGAAAAAGGCATTCA-T---AAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
* * * * *
3232 AAGCCTTATTATTCGCTT-TAAATTGTTTTATTATCTCATAATT
126 AAGCCTTATTACTCG-TTATAAATTGTTTTATAAACTCAAAATA
3275 GATTTTAAGTT
1 GATTTTAAGTT
3286 NNNNNNNNNN
Statistics
Matches: 1382, Mismatches: 443, Indels: 117
0.71 0.23 0.06
Matches are distributed among these distances:
167 85 0.06
168 250 0.18
169 41 0.03
170 74 0.05
171 677 0.49
172 248 0.18
173 7 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.36
Consensus pattern (168 bp):
GATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATATATACCTCAAG
AAACATGAAGAAAAAGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCC
TTATTACTCGTTATAAATTGTTTTATAAACTCAAAATA
Found at i:2042 original size:339 final size:322
Alignment explanation
Indices: 1575--2394 Score: 671
Period size: 339 Copynumber: 2.4 Consensus size: 322
1565 NNNNNNNNNN
*
1575 ATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACTATAATTGAATGTATACCTTAAGA
1 ATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGAC-ATAATTGAATGTATACCTCAAGA
* *
1640 AACATGAAGAAAAGGGCATTCATAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCT
65 AACATGAAGAAAAGGCCATTCATAAAGAAAAGTCCATTTAGAGTCACCCATTCCTTCAAAAGCCT
**** * * *
1705 TATTACTCGTTNNNNNNNNNNTTATAAACTCATAATTGATTTTAAGTTCAATTTTTTTACATTTT
130 TATTACTCGTT------TGTTTTATAAACTCATAATTGATTTTAAATTAAATATTTTTACATTTT
* * * * * * * *
1770 TAGTTAAAATAGACTATAATTGAATATTTTTCTCAAGAATCGTGAGGAAAAAGGCATTCATTGAT
189 TAGTCAAAACAGACAATAATTGAATATCTCTCTCAAGAAACGTGAGGAAAAAGGCAATCATTGAC
*
1835 AAGAAAAGTCCATTTATAGTCACCTATTCCTTCANNNNNNNNNNTACTCGCTTTAAATTGTTTTA
254 AAGAAAAGTCCATTTATAGTCACCTACTCCTTCA----------TACTCGCTTTAAATTGTTTTA
1900 TAATCTCAAAATAG
309 TAATCTCAAAATAG
** * *
1914 ATTTTAAGTTGAA-TTTTTTATGTTTTTCA-TTAAAATAGA-ATAATTGAATGCT-TGCCTCGAG
1 ATTTTAAGTTGAATTTTTTTACATTTTT-AGTTAAAATAGACATAATTGAATG-TATACCTCAAG
* * * *
1975 AAACATGTAGAATAA-GCCATTTATTAAGAAGAAAAGTCCATTTAGAGTCACCCATTGCTTTAAA
64 AAACATGAAGAA-AAGGCCATTCA-T-A-AAGAAAAGTCCATTTAGAGTCACCCATTCCTTCAAA
**** *
2039 AGCCTTATTACTNNNNNNNNNNTGTTTTATAATCTCATAATTGATTTTAAATTAAATATTTTTAC
125 AGCCTTATTACT------CGTTTGTTTTATAAACTCATAATTGATTTTAAATTAAATATTTTTAC
* * * *
2104 ATTTTTGGTCAAAACAGACAATAATTGAATGTCTCTCTGAAGAAACGTGAGGAAAAGGGCAATCA
184 ATTTTTAGTCAAAACAGACAATAATTGAATATCTCTCTCAAGAAACGTGAGGAAAAAGGCAATCA
* * *
2169 TTGGCAAGAAAAGTCCATTTATTGTCACCTACTCCTTCAAAAGCCTTATTACTCGTTTTAAATTG
249 TTGACAAGAAAAGTCCATTTATAGTCACCTACTCCTT-------C--A-TACTCGCTTTAAATTG
*******
2234 TTTTATAATCTCNNNNNNN
304 TTTTATAATCTCAAAATAG
*** * * *
2253 NNNTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTGAATGCT-TGCCTCAAG
1 ATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGAC-ATAATTGAATG-TATACCTCAAG
** ** * * *
2317 AAACATGCGGAAAAAACCATTCAGTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAA
64 AAACATGAAGAAAAGGCCATTCA-T-A-AAGAAAAGTCCATTTAGAGTCACCCATTCCTTCAAAA
2382 GCCTTATTACTCG
126 GCCTTATTACTCG
2395 ATTTNNNNNN
Statistics
Matches: 387, Mismatches: 68, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
336 34 0.09
337 4 0.01
338 23 0.06
339 218 0.56
340 21 0.05
341 2 0.01
342 83 0.21
346 1 0.00
348 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (322 bp):
ATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGACATAATTGAATGTATACCTCAAGAA
ACATGAAGAAAAGGCCATTCATAAAGAAAAGTCCATTTAGAGTCACCCATTCCTTCAAAAGCCTT
ATTACTCGTTTGTTTTATAAACTCATAATTGATTTTAAATTAAATATTTTTACATTTTTAGTCAA
AACAGACAATAATTGAATATCTCTCTCAAGAAACGTGAGGAAAAAGGCAATCATTGACAAGAAAA
GTCCATTTATAGTCACCTACTCCTTCATACTCGCTTTAAATTGTTTTATAATCTCAAAATAG
Done.