Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401398.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4527.0, 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: 5406
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.31
Warning! 1014 characters in sequence are not A, C, G, or T
Found at i:1690 original size:173 final size:171
Alignment explanation
Indices: 1306--1746 Score: 462
Period size: 172 Copynumber: 2.6 Consensus size: 171
1296 NNNNNNNNNT
* * * * *
1306 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTTATAATTGA-TTAAAGTTGAATT
1 CTTCAAAAGCCTTATTACTCGCTTGAAATGGTTTTATAATCTCATAATTGATTTTATGTCGAATT
* * *
1370 TTTTTATATTTTTAGTTAAAACAAACTATAATTGAATCTCTACATTGAGAATCATGAAGAAAAGA
66 TTTTTATATTTTTAGTTAAAACAGACTATAATTGAATCTCTACATTGAAAATCATGAAGAAAAAA
* * * * *
1435 GCATTCATAGGTAAAAAAAGTCTATTTATAGTCACTCATAC
131 ACATTCATAAGTAAAAAAAGTCCATTTACAGTCACTCAAAC
* ********** * *
1476 CTTCAAAAGCCTTGTTACTCGCNNNNNNNNNNTTTATAATCTCATAATTAATTTTTTGTCGAATT
1 CTTCAAAAGCCTTATTACTCGCTTGAAATGGTTTTATAATCTCATAATTGATTTTATGTCGAATT
* *
1541 GTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGCT-TACCTTGGAAAAT-ATGCAA-AA
66 -TTTTTATATTTTTAGTTAAAACAGACTATAATTGAAT-CTCTACATT-GAAAATCATG-AAGAA
*
1603 AAAAACTATTCATTAAG-AAGAAAAGTCCATTTACAGTCA-TCAAATC
127 AAAAAC-ATTCA-TAAGTAAAAAAAGTCCATTTACAGTCACTCAAA-C
* * * * *
1649 GTTCAAAAGCCTTATTACTCTCTTGAAATGGTTTTATAATCTCATCATTGGTTTTATGTCAAATT
1 CTTCAAAAGCCTTATTACTCGCTTGAAATGGTTTTATAATCTCATAATTGATTTTATGTCGAATT
*
1714 TTTTTATATTTTTGGTTAAAACAGACTATAATT
66 TTTTTATATTTTTAGTTAAAACAGACTATAATT
1747 NNNNNNNNNN
Statistics
Matches: 215, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
170 38 0.18
171 9 0.04
172 84 0.39
173 81 0.38
174 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.39
Consensus pattern (171 bp):
CTTCAAAAGCCTTATTACTCGCTTGAAATGGTTTTATAATCTCATAATTGATTTTATGTCGAATT
TTTTTATATTTTTAGTTAAAACAGACTATAATTGAATCTCTACATTGAAAATCATGAAGAAAAAA
ACATTCATAAGTAAAAAAAGTCCATTTACAGTCACTCAAAC
Found at i:3277 original size:171 final size:168
Alignment explanation
Indices: 2213--3970 Score: 629
Period size: 171 Copynumber: 10.3 Consensus size: 168
2203 NNNNNNNNNN
* * * * * ** *
2213 AAGTCTATTTATAGTCACCTATTCTTTCAAAAACCTTATTACTCACTTTAAATACTTTTATTATC
1 AAGTCCATTTATAGTCACCCATCCTATCAAAAGCCTTATTACTCACTTT-AATGGTTTTATAATC
* * * * * * *
2278 TCAAAATTGATTTTATGTTCAATTGTTTTTATATTTTTGGTTAAAATAGATTATAATTGAATGTC
65 TCATAATTGATTTTAAGTTGAATT-TTTTTACATTCTTGATTAAAACAGATTATAATTGAATGTC
** ********** *
2343 TACCTTGAGAAACATGAAGAANNNNNNNNNNATTGGCAAGAA
129 TA-CTCAAG-AACATGAAGAAAAAGATATTCATTGACAAGAA
** * *
2385 AAGTCCATTTATAGTCACTTATTCCT-TCAAAAGCCTTATTACAT-GCTTTAAATGGTTTTACAA
1 AAGTCCATTTATAGTCACCCA-TCCTATCAAAAGCCTTATTAC-TCACTTT-AATGGTTTTATAA
* * ******** * *
2448 TCTCATAATTGATTTTAGGTTAAATTNNNNNNNNNNTT-TTG-TTAAAATAGACTATAATTGAAT
63 TCTCATAATTGATTTTAAGTTGAATT--TTTTTACATTCTTGATTAAAACAGATTATAATTGAAT
* * * * *
2511 GTTTGTCGCAGGAA-ACGTATAGAAAAA-ACTATTCATGTGA-AAGAA
126 GTCT-ACTCAAGAACATG-A-AGAAAAAGA-TATTCAT-TGACAAGAA
* * * * * *
2556 AAGTCCATTTATACTCTCTCATTCCT-TTAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAAT
1 AAGTCCATTTATAGTCACCCA-TCCTATCAAAAGCCTTATTACTCACTTT-AATGGTTTTATAAT
* * * *
2620 GTTATAATTGATTTTTAGTTGAATTTTTTTTACATT-TTTAGTTAAAACAGATTATAATTGAATG
64 CTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTCTTGA-TTAAAACAGATTATAATTGAATG
* ** **********
2684 TCAACCTTGAGAA-AGGTGAAGAAAAANNNNNNNNNNGACAAGAA
127 TCTA-CTCAAGAACA--TGAAGAAAAAGATATTCATTGACAAGAA
* ** * * *
2728 AAGTCCATTTATAGCCACTTATTCT-TACAAAAGCCTTATTAGTCGTA-TTAAATGGTTTTATAA
1 AAGTCCATTTATAGTCACCCATCCTAT-CAAAAGCCTTATTACTC--ACTTTAATGGTTTTATAA
* * * * * * *
2791 TCTCTTAACTGATTTTAAGTTGAATTTGTTTATC-TTTTTGGCTT-AAATAGATTAGAATTGAAT
63 TCTCATAATTGATTTTAAGTTGAATTTTTTTA-CATTCTT-GATTAAAACAGATTATAATTGAAT
* * * * *
2854 G-CTTACCTTAAGAAACAT-ATAGAAAAAG-TCATTCATTAAGATGGA
126 GTC-TA-CTCAAG-AACATGA-AGAAAAAGAT-ATTCATTGACAAGAA
* * * *********
2899 AAGTCCATTTATTGTCTCCCATTCCT-TCAAAAGCCTTATTACTCGCTTTAANNNNNNNNNNAAT
1 AAGTCCATTTATAGTCACCCA-TCCTATCAAAAGCCTTATTACTCACTTTAA-TGGTTTTATAAT
* * * * ** *
2963 CTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAAAAGGGTATAATTGAATATC
64 CTCATAATTGATTTTAAGTTGAATTTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGTC
* * * ** ** * *
3028 TGCCTTAGGGAACATGAAGCCAAAGCCATCCATTGACACGAA
129 T-ACTCA-AGAACATGAAGAAAAAGATATTCATTGACAAGAA
************ ** *
3070 AAGTCCATTTATAGTCACTNNNNNNNNNNGAAGCCTTATTACTTGCTTTAAATGGTTTTATAAAC
1 AAGTCCATTTATAGTCACCCATCCTATCAAAAGCCTTATTACTCACTTT-AATGGTTTTATAATC
* * * * * *
3135 TCTTAATTAATTTTTAGTTGAAGTTTTTTACATTCTTGATTAAAACAGATTATAATTAAATATCT
65 TCATAATTGATTTTAAGTTGAATTTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGTCT
3200 ATCTCAAGATACATGAAGAAAAAGATATTCATTGACAAGAA
130 A-CTCAAGA-ACATGAAGAAAAAGATATTCATTGACAAGAA
* *
3241 AAG-CACATTTATAGTCACCCATACCT-TCAAAAGCCTTATTACTCACTTTCAATGGTATTAGAA
1 AAGTC-CATTTATAGTCACCCAT-CCTATCAAAAGCCTTATTACTCACTTT-AATGGTTTTATAA
* ********** *
3304 TGTCATAATTGATTTTAAGTTGAATTTTTTTNNNNNNNNNNTTAAAACAGACTATAATTGAATGT
63 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGT
* * * * * **
3369 CTACCTCGACAAGCATAAACAAAAAGACATTCATTGGTAAGAA
128 CTA-CTCAAGAA-CATGAAGAAAAAGATATTCATTGACAAGAA
* * * *
3412 AAGTCTATTTATATTCACCCATTCTATCAAAAACCTT-TTACTCACTTTAATGGTTTTATAATCT
1 AAGTCCATTTATAGTCACCCATCCTATCAAAAGCCTTATTACTCACTTTAATGGTTTTATAATCT
* * * * *
3476 CAAAATTGATTTTAATTTGAATTCTTTTTACATTTTTTATTAAAATAGATTATAATTGAATGT-T
66 CATAATTGATTTTAAGTTGAATT-TTTTTACATTCTTGATTAAAACAGATTATAATTGAATGTCT
* **********
3540 CACATCAAGAAACATGAAGAAAAAGGTATTCNNNNNNNNNNA
130 -AC-TCAAG-AACATGAAGAAAAAGATATTCATTGACAAGAA
* * * * * *
3582 AAGTCCATTTATAGTCATCCAAT-CTTTCAAAAACCTTATTACTCGCTTGAAATAGTTTTATAAT
1 AAGTCCATTTATAGTCA-CCCATCCTATCAAAAGCCTTATTACTCACTT-TAATGGTTTTATAAT
* ** ** * * * * * *
3646 ATCATAATT-AGTTTTCTGTCAAATGTTTTTACATTTTTGGTTAAAACAGACTATAGTTGAATGC
64 CTCATAATTGA-TTTTAAGTTGAATTTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGT
* * * ** ****
3710 CTACCTTAGGAAACATGTAGAAAAAGCCATTCATTTGA-ANNNN
128 CTA-CTCAAG-AACATGAAGAAAAAGATATTCA-TTGACAAGAA
****** * * * * *
3753 NNNNNNATTTATAGTCTCCCATTCCT-TCAAATGTCTTATTACTCACTTTAAAAGGTTTTATACT
1 AAGTCCATTTATAGTCACCCA-TCCTATCAAAAGCCTTATTACTCACTTT-AATGGTTTTATAAT
* ********* * * *
3817 GTCATAATTGATTTTAAGTTGAATNNNNNNNNNNTT-TTGGTTAAAACCGACTATAATTGAATGT
64 CTCATAATTGATTTTAAGTTGAAT-TTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGT
* * * * * *
3881 CTACCTTAAGAAACATAAAGAAAGAGACATTCATCGGCAAGAA
128 CTA-CTCAAG-AACATGAAGAAAAAGATATTCATTGACAAGAA
* * * *
3924 AAGTTCATTTATAATTACCTATTCC-ATCAAAAGCCTTATTACTCACT
1 AAGTCCATTTATAGTCACCCA-TCCTATCAAAAGCCTTATTACTCACT
3971 CCAAATNNNN
Statistics
Matches: 1157, Mismatches: 364, Indels: 131
0.70 0.22 0.08
Matches are distributed among these distances:
169 38 0.03
170 115 0.10
171 761 0.66
172 232 0.20
173 10 0.01
174 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.36
Consensus pattern (168 bp):
AAGTCCATTTATAGTCACCCATCCTATCAAAAGCCTTATTACTCACTTTAATGGTTTTATAATCT
CATAATTGATTTTAAGTTGAATTTTTTTACATTCTTGATTAAAACAGATTATAATTGAATGTCTA
CTCAAGAACATGAAGAAAAAGATATTCATTGACAAGAA
Found at i:4533 original size:52 final size:52
Alignment explanation
Indices: 4471--4572 Score: 141
Period size: 52 Copynumber: 2.0 Consensus size: 52
4461 AGAAAATTAC
** * *
4471 ATTTATAGTCACCCATTCCATCAAAAGCCTTGTTGCTAACTTTAAATAGTCT
1 ATTTATAGTCACAAATTCCATCAAAAGCCTTATTACTAACTTTAAATAGTCT
* * *
4523 ATTTATAGTCACAAATTTCTTCAAAAGCCTTATTACTCACTTTAAATAGT
1 ATTTATAGTCACAAATTCCATCAAAAGCCTTATTACTAACTTTAAATAGT
4573 TTTAATATCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (52 bp):
ATTTATAGTCACAAATTCCATCAAAAGCCTTATTACTAACTTTAAATAGTCT
Found at i:5305 original size:171 final size:171
Alignment explanation
Indices: 5006--5398 Score: 511
Period size: 171 Copynumber: 2.3 Consensus size: 171
4996 NNNNNNNNNN
* * **
5006 TGATTTTAGGTTGAATTTTTTTACATTTTTAGTTACAACAGATTATAATTGAATATCTACCTTGG
1 TGATTTTAGGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTTAA
* * * * * *
5071 GTAAGGTAAAGAAAAAGGAATTCATTTGCAAGAAAAGTCCATTTATAGTAATCCATTCTTTCAAA
66 GAAACGTAAAGAAAAAAGAATTCATTGGCAAGAAAAGTACATTTATAGTAATCCATACTTTCAAA
*
5136 AGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATATT
131 AGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAAT
** * * *
5177 TGATTTTAGGTTGAACATTTTTGCATTTTTAGTTAAAACAGACTATAATTGAATCTCTTCCTTAA
1 TGATTTTAGGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTTAA
* * * * *
5242 GAAACGTGAAGAAAAAAGTATTCATTGGTAAGAAAAGTATATTTATAGTCA-CCTATACTTTCAA
66 GAAACGTAAAGAAAAAAGAATTCATTGGCAAGAAAAGTACATTTATAGTAATCC-ATACTTTCAA
* *
5306 AAGCCTTCTTACTCGCTTTAAATGGTTTTATAATGTCATAAT
130 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAAT
** * *
5348 TGATTTTTTGTTGAATTTTTTTATATTTTTCA-TTAAAACATACTATAATTG
1 TGATTTTAGGTTGAATTTTTTTACATTTTT-AGTTAAAACAGACTATAATTG
5399 TATGTCCA
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
170 2 0.01
171 187 0.98
172 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (171 bp):
TGATTTTAGGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTTAA
GAAACGTAAAGAAAAAAGAATTCATTGGCAAGAAAAGTACATTTATAGTAATCCATACTTTCAAA
AGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATAAT
Done.