Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401532.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4658.0, 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: 8978
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 716 characters in sequence are not A, C, G, or T
Found at i:488 original size:157 final size:157
Alignment explanation
Indices: 202--513 Score: 507
Period size: 157 Copynumber: 2.0 Consensus size: 157
192 GGATTGACCC
* *
202 TTGAGCAAGGGAGGGTTGATCCTAGCTTGATGAGCCCATCAACAAGCTTCTGGAATGTCCTAAGA
1 TTGAGCAAGGGAGGGTTGATCCTAGCCTGATGAGCCCATCAACAAGCTTCTGGAATGGCCTAAGA
* * * *
267 TCGACCACTCCAAGAAAAGGGTTGATCCTAATAAAAGAAAACACTTAGGAATGTTCTGGGAAACC
66 TCAACCACACCAAGAAAAGGGTTGATCCTAACAAAAGAAAACACTTAAGAATGTTCTGGGAAACC
* *
332 TTAGGATCAACCCTCAATGGAAAAAGG
131 TTAGAATCAACCCCCAATGGAAAAAGG
* *
359 TTGAGCAAGGGAGGGTTGATCCTAGCCTGATGAGCCCATCAACAAGCTTTTGGAATGGCCTAGGA
1 TTGAGCAAGGGAGGGTTGATCCTAGCCTGATGAGCCCATCAACAAGCTTCTGGAATGGCCTAAGA
* * *
424 TCAACCACACCAAGATAAGGGTTGATCCTAACAAAAGGAAACACTTAAGACTGTTCTGGGAAACC
66 TCAACCACACCAAGAAAAGGGTTGATCCTAACAAAAGAAAACACTTAAGAATGTTCTGGGAAACC
489 TTAGAATCAACCCCCAATGGAAAAA
131 TTAGAATCAACCCCCAATGGAAAAA
514 TAAAACCACC
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
157 142 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (157 bp):
TTGAGCAAGGGAGGGTTGATCCTAGCCTGATGAGCCCATCAACAAGCTTCTGGAATGGCCTAAGA
TCAACCACACCAAGAAAAGGGTTGATCCTAACAAAAGAAAACACTTAAGAATGTTCTGGGAAACC
TTAGAATCAACCCCCAATGGAAAAAGG
Found at i:1340 original size:14 final size:14
Alignment explanation
Indices: 1321--1348 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1311 TTAATAAGCA
1321 GGAGTGCTTATTTT
1 GGAGTGCTTATTTT
1335 GGAGTGCTTATTTT
1 GGAGTGCTTATTTT
1349 CTCTAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
GGAGTGCTTATTTT
Found at i:1455 original size:63 final size:63
Alignment explanation
Indices: 1379--1507 Score: 197
Period size: 63 Copynumber: 2.0 Consensus size: 63
1369 AGTAAAAGAT
* *
1379 TTTAGTATCTTTGGTTTGG-CTAACCAAAGTGAGATTTTGGCTATTTGAGTATCTATAGTGGGG
1 TTTAGTATCTTTGGTTTGGTC-AACCAAAGTGAGATTTGGGCTATTTGAATATCTATAGTGGGG
* * *
1442 TTTAGTATCTTTGGTTTGGTCAACCAAAGTTAGATTTGGGCTATTTTAATATCTTTAGTGGGG
1 TTTAGTATCTTTGGTTTGGTCAACCAAAGTGAGATTTGGGCTATTTGAATATCTATAGTGGGG
1505 TTT
1 TTT
1508 CCAAGCTTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 59 0.98
64 1 0.02
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (63 bp):
TTTAGTATCTTTGGTTTGGTCAACCAAAGTGAGATTTGGGCTATTTGAATATCTATAGTGGGG
Found at i:8477 original size:171 final size:170
Alignment explanation
Indices: 7999--8978 Score: 778
Period size: 171 Copynumber: 5.7 Consensus size: 170
7989 NNNNNNNNNN
* * * * *
7999 TTTTTGGTTAAAATAGACTATAATTGAATGTCTACATTGAGAAACGTGAAGAAAAATGCATTTAT
1 TTTTTGGTTAAAACAGACTATAATTAAATGTCTAC-TTGAGAAACATGAAGAAAAAGGCATTCAT
* * * ** * **
8064 TGATAAGAAAAGTCTATTTATAATCACCTATTCCTTCAAAAGCCTTATTA-TATACTTTAGATCA
65 TG-CAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACT-CGCTTTAAATGG
* * * *
8128 TTGTT-TTATCCCAAAATTGATTTTATGTTCAATTTTTATTAACA
128 TT-TTATAATCTCAAAATTGATTTTAAGTTCAATTTTT-TTTACA
* * * ** * *
8172 TTTTTGATTAAAATAGACTATAATTGAATGTCTAGCTCAAGAAACATGAAGAAAAAAGCTTTCAT
1 TTTTTGGTTAAAACAGACTATAATTAAATGTCTA-CTTGAGAAACATGAAGAAAAAGGCATTCAT
* * * * **********
8237 TGGCAAAAAAAATCTATTTATAGTCATCC-GTTCCTTCAAAAGCCTTATTACTCNNNNNNNNNNG
65 T-GCAAGAAAAGTCCATTTATAGTCA-CCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
*
8301 TTTTATAATCTCAAAATTGATTTTAAGTT-AATTTTTTTTACT
128 TTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACA
* * * *
8343 TTTTTAGTTAAAACAGATTATAATTAAATGTTTACATTGAGAAACATGAGGAAAAAGGCATTCAT
1 TTTTTGGTTAAAACAGACTATAATTAAATGTCTAC-TTGAGAAACATGAAGAAAAAGGCATTCAT
* * * * *
8408 TAGCAAGAAAAGTACATTTACAGTCTCCAATTCCTTCAAAATCCTTATTACTCGCTTTAAATGGT
65 T-GCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
********** * *
8473 TTTATAATCTCANNNNNNNNNNTAAGTT-GA-TATTTTTACA
129 TTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACA
* * * * * * * ** *
8513 TTTTTCGTTAAAATATACTATAATTAAATG-CTTGCCTCGAGAAACGTGTAGAAAAATACATTTA
1 TTTTTGGTTAAAACAGACTATAATTAAATGTC-T-ACTTGAGAAACATGAAGAAAAAGGCATTCA
* * * * * * * *
8577 TT-TAGAGAAAAAGTCCATTTATAGTCTCTTATTCTTTCAAAAGTCATATTGCTTGCTTTAAATG
64 TTGCA-AG-AAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATG
* * * * *
8641 GCTTTATAATCTCATAATTAATTTTAAGTTCAATTTTGTTCACA
127 GTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACA
* * **
8685 TTTTTGGTTAAAACAGA-TAATAATTGAATGTCTACTTTGAAAAACATGAAGAAAAACACATTCA
1 TTTTTGGTTAAAACAGACT-ATAATTAAATGTCTAC-TTGAGAAACATGAAGAAAAAGGCATTCA
* * ** * * *
8749 TTGGCAAGGAAAGTCCATTTATAGTCACCAATTTTTTCAAAAGCCATATTACTCACTTTAAACGG
64 TT-GCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
*
8814 TTTTATAATCTC-AAATCGATTTTAAGTTCAATTTTTTTTACA
128 TTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACA
* * * *
8856 CTTTTGGTTAAAACAGATTAGAATTAAATGTTTACTTGAAGAAA-AGTGAAGAAAAAGGCATTCA
1 TTTTTGGTTAAAACAGACTATAATTAAATGTCTACTTG-AGAAACA-TGAAGAAAAAGGCATTCA
* * *
8920 TTGACAAGAAAAGTCCATTTATAGTAACCTATTCTTTC-AAATCCTTATTACTCGCTTTA
64 TTG-CAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCTTTA
Statistics
Matches: 632, Mismatches: 153, Indels: 47
0.76 0.18 0.06
Matches are distributed among these distances:
168 1 0.00
169 2 0.00
170 149 0.24
171 228 0.36
172 124 0.20
173 122 0.19
174 6 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.38
Consensus pattern (170 bp):
TTTTTGGTTAAAACAGACTATAATTAAATGTCTACTTGAGAAACATGAAGAAAAAGGCATTCATT
GCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
TATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTACA
Done.