Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399045.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2320.0, 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: 6465
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.27
Warning! 2094 characters in sequence are not A, C, G, or T
Found at i:498 original size:171 final size:171
Alignment explanation
Indices: 1--733 Score: 479
Period size: 171 Copynumber: 4.3 Consensus size: 171
* * * *
1 TATAACCTCATAATTTGTTTTAATTTGAATTTTTTTATATTTTTTAATAAAACATATTATAATTA
1 TATAACCTCATAATTAGTTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAAATTATAATTG
* * * ***
66 AATGTTTTTCTCGAGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGNNN
66 AATGTTTTTCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGCCA
******************
131 NNNNNNNNNNNNNNNNNTTTATTACTCGCTTTAAATGATTT
131 CTCATACCGTCAAAAGACTTATTACTCGCTTTAAATGATTT
* * *
172 TATAACCCCATAATTAATTTTAATTTGAATATTTTTTATATTTTTTTATTAAAACAAATTCTAAT
1 TATAACCTCATAATTAGTTTTAATTTGAAT-TTTTTTATA-TTTTTTATTAAAACAAATTATAAT
* ** * * * *
237 TGAATGTCTGCCTCCAGAAACATAAAGAAAAAGATATCCATTAGTAAGAAAAG-TCTATTTATAG
64 TGAATGTTTTTCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTC-ATTTATAG
***********
301 TNNNNNNNNNNGTCAAAAGACTTATTACTCGCTTTAAATGATTT
128 CCACTCATACCGTCAAAAGACTTATTACTCGCTTTAAATGATTT
* * * * *
345 TATAACCTAATAATTTGTTTTAATTTGAATTTTTTTATATTTTTTATTGAAATAGATTATAATTG
1 TATAACCTCATAATTAGTTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAAATTATAATTG
* *
410 AATGTTTTTCTCAAGAAACGTGTAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGCCA
66 AATGTTTTTCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGCCA
* * * *
475 CTCATACCTTCGAAAGCCTTATTACTC-CATTTAAATGCTTT
131 CTCATACCGTCAAAAGACTTATTACTCGC-TTTAAATGATTT
* * * * * *****************
516 TTTAATCTCATAATTAGTTTTAAGTTAAACTTTTTTATATTTNNNNNNNNNNNNNNNNNTAATTG
1 TATAACCTCATAATTAGTTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAAATTATAATTG
* ** * * * * *
581 AATGTCTGCCTTAAGAAACGT-AATGAAAAAGATATCCATTGGTAAGAAGAG-TCTATTTATAGT
66 AATGTTTTTCTCAAGAAACATGAA-GAAAAAGATATCCATTGGCAAGAAAAGTTC-ATTTATAGC
* * * *
644 CAC-CTATGCCTTCAAAAGCCTTATTACTTGCTTTAAATGATTT
129 CACTC-ATACCGTCAAAAGACTTATTACTCGCTTTAAATGATTT
* * *
687 TATAACCTCGTAATTCA-TTTTAATTTAAATTTTTTTATATCTTTTAT
1 TATAACCTCATAATT-AGTTTTAATTTGAATTTTTTTATATTTTTTAT
734 NNNNNNNNNN
Statistics
Matches: 446, Mismatches: 106, Indels: 20
0.78 0.19 0.03
Matches are distributed among these distances:
170 5 0.01
171 286 0.64
172 23 0.05
173 132 0.30
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.40
Consensus pattern (171 bp):
TATAACCTCATAATTAGTTTTAATTTGAATTTTTTTATATTTTTTATTAAAACAAATTATAATTG
AATGTTTTTCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAGTTCATTTATAGCCA
CTCATACCGTCAAAAGACTTATTACTCGCTTTAAATGATTT
Found at i:1524 original size:171 final size:169
Alignment explanation
Indices: 1117--1768 Score: 553
Period size: 171 Copynumber: 3.8 Consensus size: 169
1107 NNNNNNNNNN
* * * * * * *
1117 TGAATTTTTTTATA-TTTTTATTAAAACATATTATAATTGAATGTCTACCTTGAGGAACATGAAG
1 TGAATTTTTTTACATTTTTTATCAAAACAGATTATAATTGAATGTCTATCTTAAGAAACATAAAG
* * * * * *
1181 AAAAAGATATCCATTGGCAA-AAAACGTCCATTTGTAGTCACCCATGTCTTCGAAAGCCTTATTA
66 AAATAGATATGCATTGGTAAGAAAA-GTCCATTTATAATCACCCATGCCTTCGAAAGCCTTATTA
*
1245 CTCACTTTAAGTAGTTTTTTAATCTCATAATTCGTTTTAAGT
130 CTCACTTTAAATA-TTTTTTAATCTCATAATT-GTTTTAAGT
* * * * * * **
1287 TGAACTTTTTTACATTTTTTA-CTAATACAGATTATAATTAAATGTCTACCCTAAAAAATGTAAA
1 TGAATTTTTTTACATTTTTTATC-AAAACAGATTATAATTGAATGTCTATCTTAAGAAACATAAA
********* * * *
1351 GAAA-ATGATAT-CNNNNNNNNNNATAAGTCCATTTCTAATCACCCATGCCTTCGAAAGCTTTAT
65 GAAATA-GATATGC-ATTGGTAAGAAAAGTCCATTTATAATCACCCATGCCTTCGAAAGCCTTAT
* * * *
1414 TACTCGCCTTAAATATTTTTTTAACCTTATAATTGTTTTTAAGT
128 TACTCACTTTAAATA-TTTTTTAATCTCATAATTG-TTTTAAGT
* * * *
1458 TGAATTTTTTTATATTTTTTATCAAAACAGATTATCATTGACTGTCTATCTTTAGAAACATAAAG
1 TGAATTTTTTTACATTTTTTATCAAAACAGATTATAATTGAATGTCTATCTTAAGAAACATAAAG
* *
1523 AAATAGATATGCATTGGTAAGAAAAGTCCATTTATAATCATCCATGCCTTTGAAAGCCTTATTAC
66 AAATAGATATGCATTGGTAAGAAAAGTCCATTTATAATCACCCATGCCTTCGAAAGCCTTATTAC
* * *
1588 TCACTTTAAATGATTTTTTAATCTCGTTATTGATTTTAATT
131 TCACTTTAAAT-ATTTTTTAATCTCATAATTG-TTTTAAGT
* * * *
1629 TGAATTTTTTTAGATTTTTTAGT--AAACCGCATTATAATTGAATGTCTATCTTGAGAAACATGA
1 TGAATTTTTTTACATTTTTTA-TCAAAACAG-ATTATAATTGAATGTCTATCTTAAGAAACATAA
********** ** * * *
1692 ANNNNNNNNNNTGCATTGACAAGAAAAGTCCATTTATAGTAACCCATGCTTTCGAAAGCCTTATT
64 AGAAATAGATATGCATTGGTAAGAAAAGTCCATTTATAATCACCCATGCCTTCGAAAGCCTTATT
1757 ACTCACTTTAAA
129 ACTCACTTTAAA
1769 NNNNNNNNNN
Statistics
Matches: 381, Mismatches: 89, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
170 20 0.05
171 353 0.93
172 8 0.02
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.39
Consensus pattern (169 bp):
TGAATTTTTTTACATTTTTTATCAAAACAGATTATAATTGAATGTCTATCTTAAGAAACATAAAG
AAATAGATATGCATTGGTAAGAAAAGTCCATTTATAATCACCCATGCCTTCGAAAGCCTTATTAC
TCACTTTAAATATTTTTTAATCTCATAATTGTTTTAAGT
Found at i:2060 original size:17 final size:17
Alignment explanation
Indices: 2038--2071 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2028 TGGAACATGA
* *
2038 AGAAAAAGATATCCATT
1 AGAAAAAAAGATCCATT
2055 AGAAAAAAAGATCCATT
1 AGAAAAAAAGATCCATT
2072 TGTAGTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (17 bp):
AGAAAAAAAGATCCATT
Found at i:6391 original size:170 final size:171
Alignment explanation
Indices: 6055--6368 Score: 425
Period size: 170 Copynumber: 1.8 Consensus size: 171
6045 NNNNNNNNNN
* * * *** *
6055 ATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAATCATCAAGAAA
1 ATTTTTTAATAATTTTTATTAAAAAAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAA
*
6120 AAGATATCCATTGGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCG
66 AAGATATCCATTAGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCG
6185 CTTTAAATCATTTTATAACCTCATAATTGTTTTTAATATAA
131 CTTTAAATCATTTTATAACCTCATAATTGTTTTTAATATAA
* **
6226 ATTTTTTAATAATTTTTGTTAAAAAAGATTATAATTGAATACCTACCTCGAGAAACAT-GGGAAA
1 ATTTTTTAATAATTTTTATTAAAAAAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAA
* * * * * * * *
6290 ACGATATTCATTAGTAAGAAAAGTCCATTTATAGTCAACC-ATGCCTTTGAAAGCTTTATTACTT
66 AAGATATCCATTAGTAAGAAAACTCCATTTATAGTC-ACCTAAGACTTCGAAAGCCTTATTACTC
*
6354 GCTTTAAATGATTTT
130 GCTTTAAATCATTTT
6369 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
170 69 0.57
171 53 0.43
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (171 bp):
ATTTTTTAATAATTTTTATTAAAAAAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAA
AAGATATCCATTAGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCG
CTTTAAATCATTTTATAACCTCATAATTGTTTTTAATATAA
Found at i:6401 original size:170 final size:169
Alignment explanation
Indices: 6057--6434 Score: 418
Period size: 170 Copynumber: 2.2 Consensus size: 169
6047 NNNNNNNNAT
* *** *
6057 TTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTTTACCTCGAGAATCATCAAGAAAAA
1 TTTTTTATAATTTTT-TTAAAACAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAAAA
*
6122 GATATCCATTGGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCGCT
65 GATATCCATTAGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCGCT
*
6187 TTAAATCATTTTATAACCTCATAATTGTTTTTAATATAAA
130 TTAAATCATTTTATAACCTCATAATTGATTTTAATATAAA
* **
6227 TTTTTTAATAATTTTTGTTAAAAAAGATTATAATTGAATACCTACCTCGAGAAACAT-GGGAAAA
1 TTTTTT-ATAATTTTT-TTAAAACAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAAA
* * * * * * * *
6291 CGATATTCATTAGTAAGAAAAGTCCATTTATAGTCAACC-ATGCCTTTGAAAGCTTTATTACTTG
64 AGATATCCATTAGTAAGAAAACTCCATTTATAGTC-ACCTAAGACTTCGAAAGCCTTATTACTCG
* ********** * *
6355 CTTTAAATGATTTTNNNNNNNNNNAATTGATTTTAATTTGAA
128 CTTTAAATCATTTTATAACCTCATAATTGATTTTAATATAAA
6397 TTTTTTATAATTTTCTTTAAAACAGATTATAATTGAAT
1 TTTTTTATAATTTT-TTTAAAACAGATTATAATTGAAT
6435 GTTTGCCTTA
Statistics
Matches: 172, Mismatches: 33, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
169 29 0.17
170 97 0.56
171 46 0.27
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.39
Consensus pattern (169 bp):
TTTTTTATAATTTTTTTAAAACAGATTATAATTGAATACCTACCTCGAGAAACATCAAGAAAAAG
ATATCCATTAGTAAGAAAACTCCATTTATAGTCACCTAAGACTTCGAAAGCCTTATTACTCGCTT
TAAATCATTTTATAACCTCATAATTGATTTTAATATAAA
Done.