Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398815.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_21.0, 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: 42425
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.21
Warning! 18971 characters in sequence are not A, C, G, or T
Found at i:15344 original size:171 final size:169
Alignment explanation
Indices: 14731--15642 Score: 720
Period size: 171 Copynumber: 5.3 Consensus size: 169
14721 NNNNNNNNNG
* * **
14731 TAGAAAAAGTCATTCATTGAG-AAGAAATA-TCCATTTATAGTCAACCATTCCTTCAAAAGTCTT
1 TAGAAAAAG-CATTCATTG-GCAAGAAA-AGTCCATTTATAGTCACCCATTTCTTCAAAAACCTT
* * *
14794 ATTACTCGCTTTAAATTATTTTATTATCTCATAATTGCTTTTAAGTT-AATTTTTTTATATTTTT
63 ATTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA-ATTTTT
*
14858 AGTTAAAACAGTCTATAATTGAATGTCTACCTTAAGAAACATGA
127 AGTTAAAACAGACTATAATTGAATGTCTACCTT-AGAAACATGA
* * * * * **
14902 -ACAAAAAAGCATTCATTGGTAAGAAAAGTCTATTTATAGCCACCTA-TTCTTTCAAAAGGCTTA
1 TA-GAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTC-TTCAAAAACCTTA
* * ********** *
14965 TTGCTCACTTTAAATNNNNNNNNNNTCTCATAATTGATTTTAAGTTGAATTTGTTTTTGCATTTT
64 TTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TT-TTTTT-AATTTT
* ** * * *
15030 TAATTAAAGTAGACTATAATTGAGTGTCTACCTCAAGAAATATGA
126 TAGTTAAAACAGACTATAATTGAATGTCTACCT-TAGAAACATGA
* * * *
15075 -ACAAAAAGGCATTCATTGGCAA-AAAAGTCCATTTCTAGTCTCCC-TTTCCTTCAAAACCCTTA
1 TAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTT-CTTCAAAAACCTTA
* * **********
15137 TTACTCTCTTTAAATGGTTTNNNNNNNNNNTAATTGATTTTAAGTTGAATTTTTTTAATTTTTTA
64 TTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAA-TTTTTA
* *
15202 GTTAAAACAGACTATAATTGAATGCCTACCTTGGAAA-ATGTA
128 GTTAAAACAGACTATAATTGAATGTCTACCTTAGAAACATG-A
* * * * *
15244 TAGAAAAAGCCATTTATTGACAATAAAAGTCTATTTATAGTCACCCATTTCTCCAAAAACCTTAT
1 TAGAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAACCTTAT
* * * *
15309 TACTCGCTTTAAATTGTTTTGTAATCTCATAATTGATTTTAAG-TCAATTTTTTTTACATTATTG
65 TACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTA-ATTTTTA
* * *
15373 GTTAAAACAGATTATAATTGTATGTCTACCCTGAGAAACATG-
128 GTTAAAACAGACTATAATTGAATGTCTA-CCTTAGAAACATGA
* * * *
15415 TAGATAAAAGTATTCATTGGCAAGAAAAGTGCATTTATAGTCACCCATTCCTTCAAAAATCTTAT
1 TAGA-AAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAACCTTAT
* * ******** *
15480 TACTCGCTTTAAA-AGATTTTATAATCTCATAATTGATTTTAAGTTGAGTTTTNNNNNNNNNNTC
65 TACTCGCTTTAAATTG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTT--TTTAATTTTT
* *
15544 A-TTAAAACAGACTATAATTGAATGCCTACCTTGGGAAACATG-
127 AGTTAAAACAGACTATAATTGAATGTCTACCTT-AGAAACATGA
* * * *
15586 TACAAAAAGTTATTCATTGAG-AAGAAAAGTCCATTTATAGTCAACCATTCCTTCAAA
1 TAGAAAAAG-CATTCATTG-GCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAA
15643 NNNNNNNNNN
Statistics
Matches: 595, Mismatches: 116, Indels: 60
0.77 0.15 0.08
Matches are distributed among these distances:
168 3 0.01
169 11 0.02
170 141 0.24
171 281 0.47
172 94 0.16
173 65 0.11
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
TAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAACCTTATT
ACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAATTTTTAGTT
AAAACAGACTATAATTGAATGTCTACCTTAGAAACATGA
Found at i:26680 original size:21 final size:18
Alignment explanation
Indices: 26649--26688 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
26639 AAGGAATGAG
26649 TGACTATAAATGGACTTTTT
1 TGACTATAAAT-G-CTTTTT
26669 TGACTAATAAATGCTTTTT
1 TGACT-ATAAATGCTTTTT
26688 T
1 T
26689 ATTCACGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (18 bp):
TGACTATAAATGCTTTTT
Found at i:26820 original size:171 final size:169
Alignment explanation
Indices: 26469--26858 Score: 484
Period size: 171 Copynumber: 2.3 Consensus size: 169
26459 NNNNNNNNNN
* ** *
26469 GAAGGAATAAGTGACTATAAATGGACTTTTCTTCTCAATGGATGGCTTTTTCTATATGTTTCTTG
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATAAATGGCTTTTTCTATACGTTTCTTG
* * * *
26534 ACGCAGACATTTAATTATAGGCTGTTTTAACCACAAATGAAAAAATTCAACTTAAAATCAATTAT
66 ACGCAGACATTTAACTATAGGCTGTCTTAACCAAAAATGAAAAAAATCAACTTAAAATCAATTAT
*
26599 GAGGTCATAAAACCAATTAAAGCGAGTAAAAAACCTTTT
131 GAGATCATAAAACCAATTAAAGCGAGTAAAAAACCTTTT
26638 GAAGGAATGAGTGACTATAAATGGACTTTT-TTGACT-AATAAAT-GCTTTTT-TATTCACGTTT
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTT--CTCAATAAATGGCTTTTTCTA-T-ACGTTT
* * * *
26699 CTTGAGGTAGATATTTAACTATAGTCTGTCTTAACCAAAAATGTAAAAAAAATCAA-TTGAAAAT
62 CTTGACGCAGACATTTAACTATAGGCTGTCTTAACCAAAAATG--AAAAAAATCAACTT-AAAAT
* * * * **
26763 CAATTATGAGATTATAGAACCATTTAAAGCGAGTAATAAATGTTTT
124 CAATTATGAGATCATAAAACCAATTAAAGCGAGTAAAAAACCTTTT
* * *
26809 GAAGAAATGAGTGGCTATAAATGGACTTTTCTTCTCAATGAATGGCTTTT
1 GAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATAAATGGCTTTT
26859 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 22, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
167 2 0.01
168 10 0.05
169 75 0.40
170 6 0.03
171 88 0.47
172 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (169 bp):
GAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATAAATGGCTTTTTCTATACGTTTCTTG
ACGCAGACATTTAACTATAGGCTGTCTTAACCAAAAATGAAAAAAATCAACTTAAAATCAATTAT
GAGATCATAAAACCAATTAAAGCGAGTAAAAAACCTTTT
Found at i:36033 original size:27 final size:27
Alignment explanation
Indices: 36001--36055 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
35991 GAGAAACAAG
36001 AACAAAAAATCATTCATTGGCAAGAAA
1 AACAAAAAATCATTCATTGGCAAGAAA
36028 AACAAAAAATCATTCATTGGCAAGAAA
1 AACAAAAAATCATTCATTGGCAAGAAA
36055 A
1 A
36056 GTCCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (27 bp):
AACAAAAAATCATTCATTGGCAAGAAA
Done.