Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400049.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3269.0, 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: 5212
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.26
Warning! 1500 characters in sequence are not A, C, G, or T
Found at i:1768 original size:338 final size:334
Alignment explanation
Indices: 1131--1770 Score: 672
Period size: 338 Copynumber: 1.9 Consensus size: 334
1121 ATTGGCAAGA
* * * * ** * *
1131 AAAGTCCATTTATAGTCACTCATGCTTTCGAAAGCCTTATTTTTCTCTTTAAATGGTTTTATAAT
1 AAAGTCCATTTATAGTCACCCATGCCTTCAAAAGACTTATTACTCACTTTAAATAGTTTTATAAT
* * * *
1196 CTCATAATTGATTTTAAGGTAAATTGTTTTTTACATTTTTAGCTAAAACAGATAATAATTGAATG
66 ATCATAATTGATTTGAAGATAAATTGTTTTTTACATTTTTAGCTAAAACAGATAATAATTGAATA
* * * *
1261 CCTGCCATAGAAAACATGAAGAAAAAGATATCCATTGATAAGAAAAGTCCATTTGTAGCCACCCA
131 CATGCCATAGAAAACATGAAGAAAAAGATATCCATTGACAAGAAAACTCCATTTATAGCCACCCA
* ** * * * *
1326 TGTCTTCAAAAGTGTTATTACTAGCTTGAAATGCTTTTATAAACTCCTAATTGATTTTAGGTTGA
196 TCTCTTCAAAAGCCTTATTACTAGCTTGAAATGCTTTTAAAAACTCATAATTGATTTTAAGTTAA
*
1391 ATTCTTTTACGTTTTTGATTAAAATAGATAATAATTGAATGTTTGCCAAAGGAAATGTGAAGCAA
261 ATTCTTTTACATTTTTGATTAAAATAGATAATAATTGAATGTTTGCCAAAGGAAATGTGAAGCAA
1456 AAGATATCC
326 AAGATATCC
*
1465 ANNNNNNNNNNAAGTCCATTTATAGTCACCCATGCCTTCAAAAGACTTATTACTCAGTTTAAATA
1 A----------AAGTCCATTTATAGTCACCCATGCCTTCAAAAGACTTATTACTCACTTTAAATA
* * * *
1530 TTTTTATAATATCATAATTGATTTGAA-ATTAA-T-TTTTTTATATTTTTAGTTAAAACAGATAA
56 GTTTTATAATATCATAATTGATTTGAAGATAAATTGTTTTTTACATTTTTAGCTAAAACAGATAA
* * ** * *
1592 TAATTGAATATATATCTCA-AG-AAACATGAA-AAAAA-A-ATTTATTGGCAAGAAAACTCTATT
121 TAATTGAATACAT-GC-CATAGAAAACATGAAGAAAAAGATATCCATTGACAAGAAAACTCCATT
* * * * * *
1652 TATAGTCACCCATACT-TTTAAAAGCCTTATTACTCGCTTTATATG-TTTTAAAAATCTTATAAT
184 TATAGCCACCCAT-CTCTTCAAAAGCCTTATTACTAGCTTGAAATGCTTTTAAAAA-CTCATAAT
* * *
1715 TGATTTTAAGTTCAAATT-TTTTATATTTTTTATTAAAATAGATTATAATTGAATGT
247 TGATTTTAAGTT-AAATTCTTTTACATTTTTGATTAAAATAGATAATAATTGAATGT
1771 CTACCTCAAG
Statistics
Matches: 247, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
334 1 0.00
337 8 0.03
338 103 0.42
339 6 0.02
340 5 0.02
341 46 0.19
342 4 0.02
343 5 0.02
344 69 0.28
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.39
Consensus pattern (334 bp):
AAAGTCCATTTATAGTCACCCATGCCTTCAAAAGACTTATTACTCACTTTAAATAGTTTTATAAT
ATCATAATTGATTTGAAGATAAATTGTTTTTTACATTTTTAGCTAAAACAGATAATAATTGAATA
CATGCCATAGAAAACATGAAGAAAAAGATATCCATTGACAAGAAAACTCCATTTATAGCCACCCA
TCTCTTCAAAAGCCTTATTACTAGCTTGAAATGCTTTTAAAAACTCATAATTGATTTTAAGTTAA
ATTCTTTTACATTTTTGATTAAAATAGATAATAATTGAATGTTTGCCAAAGGAAATGTGAAGCAA
AAGATATCC
Found at i:2689 original size:170 final size:171
Alignment explanation
Indices: 2132--2832 Score: 756
Period size: 170 Copynumber: 4.1 Consensus size: 171
2122 NNNNNNNNNN
* **
2132 ATAGTCACCCATACCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAATACT-ATAATTG
1 ATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATATTTTTATAAT-CTCATAATTG
* * * * *
2196 A--TTAAGTTAATTTTTTTTTA-TATTTTGGGTTAAAATAGATAATAATTGAATGTCTACCAT-G
65 ATTTTAAATTAA-ATTTTTTTACGATTTT-GGTTAAAATAGATAATAATTGAATGTCTGCCTTAG
* * *
2257 AGAAACATGAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTT
128 -GAAACATGAAGAAAAAAATATCCATTGGCAAGAAAAATCCATTT
* * * ** *
2302 GTAGTCACCCATATCTTCAAAAGCCTTATTACTAGCTTTAAATGCTTTTATAAACTCATAATTGA
1 ATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATATTTTTATAATCTCATAATTGA
* * * * *
2367 TTTTAAATTGAATTTTTTTACG-TTTGTGGTTAAAACAGATAATAATTGTAGGTCTGCCTCAGGA
66 TTTTAAATTAAATTTTTTTACGATTT-TGGTTAAAATAGATAATAATTGAATGTCTGCCTTAGGA
* *
2431 AATATGAAGAAAAATATATCCATTGGCAAGAAAAATCCATTT
130 AACATGAAGAAAAAAATATCCATTGGCAAGAAAAATCCATTT
* * * *
2473 AAAGTCAACTATGCCTTCAAAAGCCTTATTACTCAG-TTTAAATATTTTTATAATCTCATAATTG
1 ATAGTCACCCATACCTTCAAAAGCCTTATTACTC-GCTTTAAATATTTTTATAATCTCATAATTG
* *
2537 ATTTTAAATTGAAACTTTTTTACGATTTTGGTTAAAATAGATAATAATTGAATATCTGCCTTAGG
65 ATTTTAAATT-AAATTTTTTTACGATTTTGGTTAAAATAGATAATAATTGAATGTCTGCCTTAGG
* ** * *
2602 AAACGT-AA-AAAAAAATATTTATTGGCAAGAAAATTCTATTT
129 AAACATGAAGAAAAAAATATCCATTGGCAAGAAAAATCCATTT
** * *
2643 ATAGTTGCCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATATTTTTAAAATCTTATAATTGA
1 ATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATATTTTTATAATCTCATAATTGA
* * * ** * * * * *
2708 GTTTAAGTTAAATTTTTTTA-TATTTTTTATTCAAAACAGATTATAATTGAATGTTTACCTTAAG
66 TTTTAAATTAAATTTTTTTACGA-TTTTGGTT-AAAATAGATAATAATTGAATGTCTGCCTTAGG
* * * * *
2772 AAATATGATGAAAAATATATCCATTGACAAGAAAAGTCCATTT
129 AAACATGAAGAAAAAAATATCCATTGGCAAGAAAAATCCATTT
*
2815 ATAGTCACCCATGCCTTC
1 ATAGTCACCCATACCTTC
2833 GANNNNNNNN
Statistics
Matches: 441, Mismatches: 76, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
168 1 0.00
169 19 0.04
170 176 0.40
171 143 0.32
172 99 0.22
173 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (171 bp):
ATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCTTTAAATATTTTTATAATCTCATAATTGA
TTTTAAATTAAATTTTTTTACGATTTTGGTTAAAATAGATAATAATTGAATGTCTGCCTTAGGAA
ACATGAAGAAAAAAATATCCATTGGCAAGAAAAATCCATTT
Found at i:3411 original size:171 final size:172
Alignment explanation
Indices: 3193--3574 Score: 445
Period size: 172 Copynumber: 2.2 Consensus size: 172
3183 TACGAGAGTT
* * * *
3193 TTATTACTCGCTTCAAATGGTTTGATAATCTCATAATTAATTTTAAGTTTA-ATTTTTTTACATT
1 TTATTACTCGCTTTAAATGGTTTGATAATCTCATAATTGAGTTTAAGTTGAGATTTTTTTACATT
* * * * *
3257 TTCT-ATTAAAACAGATTATAA-TTGAATTTCTACCTTAAGAAATGC-GA-AGAAAAAAATGTTC
66 TT-TGATGAAAACAGATAATAATTTG-ATGTCTACCTTAAGAAA--CAGACAGAAAAAAATATCC
* * *
3318 ATTGGTAAGAAAAGTCCATTTATAGTCACCAACACCTTTC-AAAGCC
127 ATTGGCAAGAAAAGTACATTTAGAGTCACCAACACC-TTCGAAAGCC
* * *
3364 TTCTTACTCGCTTTAAAT-GTCTTTATAATCTCATAATTGAGTTTAAGTTGAGTTTTTTTTACAT
1 TTATTACTCGCTTTAAATGGT-TTGATAATCTCATAATTGAGTTTAAGTTGAGATTTTTTTACAT
* * * *
3428 TTTTGGTGAAAACAGATAATAATTTGATGTCTACCTTAGGAAACATACAGAAAAAAGTATCCATT
65 TTTTGATGAAAACAGATAATAATTTGATGTCTACCTTAAGAAACAGACAGAAAAAAATATCCATT
* * **
3493 GGCAAGAAAAGTATATTTAGAGTCACCCATGCCTTCGAAAGCC
130 GGCAAGAAAAGTACATTTAGAGTCACCAACACCTTCGAAAGCC
*
3536 TTATTACTCACTTTAAATGGTTTGATAATCTCATAATTG
1 TTATTACTCGCTTTAAATGGTTTGATAATCTCATAATTG
3575 NNNNNNNNNN
Statistics
Matches: 177, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
170 3 0.02
171 47 0.27
172 122 0.69
173 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (172 bp):
TTATTACTCGCTTTAAATGGTTTGATAATCTCATAATTGAGTTTAAGTTGAGATTTTTTTACATT
TTTGATGAAAACAGATAATAATTTGATGTCTACCTTAAGAAACAGACAGAAAAAAATATCCATTG
GCAAGAAAAGTACATTTAGAGTCACCAACACCTTCGAAAGCC
Found at i:4571 original size:171 final size:170
Alignment explanation
Indices: 4239--4616 Score: 445
Period size: 171 Copynumber: 2.2 Consensus size: 170
4229 NNNNNNNNTT
* *
4239 TATAGTCACCCATACCTTCGAAAGCCTTATTACTCGCGTTAAACGGTTTTACAATCTCATAATTG
1 TATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAACAGTTTTACAATCTCATAATTG
* *
4304 AATTTGAGTTGAATTTTTTACATTATTTATTAAAACAGATTATAATTGAATGTCTACTTCAGGAC
66 AATTTAAGTTGAATTTTTTACATTATTTATTAAAACAGATTATAATTGAATGTCTACTTCAGGAA
* * **
4369 ACGTGAAGAAAAAGATATCTATTGGCAAGAAAAGTCCATG
131 ACATGAAGAAAAAGACATCTATTCACAAGAAAAGTCCATG
* * * * * * * *
4409 TCTAGTCACCCATGCTTTCAAAAGCCTTATTAGTTGCTTTGAATAGTTTTA-ACATCTCATAATT
1 TATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAACAGTTTTACA-ATCTCATAATT
* * * * *
4473 GATTTTAAGTTGAATTTTTTTACATTTTTTATTAAATCAGATTATAATTGAATGTCTTCTTCGGG
65 GAATTTAAGTTGAA-TTTTTTACATTATTTATTAAAACAGATTATAATTGAATGTCTACTTCAGG
* * *
4538 AAACATGAAGAAGAAGCCAGTC-ATTCACAAGAAAAGTCCATT
129 AAACATGAAGAAAAAGACA-TCTATTCACAAGAAAAGTCCATG
*** * * *
4580 TATAGTCACATGTGCCTTCCATAGCCTTATTACTCGC
1 TATAGTCACCCATACCTTCAAAAGCCTTATTACTCGC
4617 CTTATTATTG
Statistics
Matches: 172, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
169 1 0.01
170 64 0.37
171 105 0.61
172 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (170 bp):
TATAGTCACCCATACCTTCAAAAGCCTTATTACTCGCGTTAAACAGTTTTACAATCTCATAATTG
AATTTAAGTTGAATTTTTTACATTATTTATTAAAACAGATTATAATTGAATGTCTACTTCAGGAA
ACATGAAGAAAAAGACATCTATTCACAAGAAAAGTCCATG
Found at i:4910 original size:167 final size:165
Alignment explanation
Indices: 4652--5212 Score: 563
Period size: 167 Copynumber: 3.3 Consensus size: 165
4642 AAACGTGAAG
* * * * * *
4652 AAAAAAAATATCCATTGGCAAGAAAAATCTATTTATAGTAACTCATGCCTTCGAAAGCCTTATTA
1 AAAAAAAATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTTGAAAGCCTTATTA
* * * *
4717 CTCGCGTTAAATGGTTTTACAATCTCATAATTAAATTTGAGCTGAATTTTTTACATTGTTTATTA
66 CTCGCTTTAAATGGTTTTATAATCTCATAATT-AATTTTAGCTGAATTTTTTATATT-TTTATTA
* * * *
4782 AAACAGATAATAATTGAATGTTTGCCTCGAGAAACGT
129 AAACAGATTATAATTGAATGTCTACCTCGAGAAACAT
* * *
4819 AAAAACAAATATCCATTGGCAAG-AAAGTCCATTCATAGTCACCCACACCTTTGAAAGTCTTATT
1 AAAAA-AAATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTTGAAAGCCTTATT
* * * * * *
4883 ACTCGCTTTAAATGGTTTAATAATCTCACAGTTGATTTTAACTTTAAATTTTTTATATTTTTATT
65 ACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAGC--TGAATTTTTTATATTTTTATT
* * *
4948 GAAACAAATTATAATTGAATGTCTACCTCGAGAAACTT
128 AAAACAGATTATAATTGAATGTCTACCTCGAGAAACAT
** * * * ** *
4986 GAAGATAAAGGTATGCATTGGCAAGAAAAGTCCATTTA-CG--ACCCATGCAATTGAGAGCCTTA
1 -AA-A-AAAAATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTTGAAAGCCTTA
* * * *
5048 TTAGTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTTAGTTGAATTATTTTATATTTTTT
63 TTACTCGCTTTAAATGGTTTTATAATCTCATAATT-AATTTTAGCTGAATT-TTTTATA--TTTT
* ** *
5113 TATTCAAATGGATTATAATTGAATGTCTAACTCGAGAAACAT
124 TATTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACAT
* *
5155 AAAGAAAAAGATATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTTGAA
1 -AA-AAAAA-ATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTTGAA
Statistics
Matches: 316, Mismatches: 63, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
166 11 0.03
167 156 0.49
168 40 0.13
169 85 0.27
170 14 0.04
172 10 0.03
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (165 bp):
AAAAAAAATATCCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTTGAAAGCCTTATTA
CTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAGCTGAATTTTTTATATTTTTATTAAA
ACAGATTATAATTGAATGTCTACCTCGAGAAACAT
Done.