Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400053.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3272.0, 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: 5608
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.21
Warning! 2332 characters in sequence are not A, C, G, or T
Found at i:3027 original size:340 final size:334
Alignment explanation
Indices: 2120--3359 Score: 1116
Period size: 340 Copynumber: 3.6 Consensus size: 334
2110 CTCGAGGTAG
** * * * * *
2120 ACATTCAATTATAATCTGTTTTAATAAAAAAAAGTAAAAGAATCCAACTTAAAATCAATTATGAG
1 ACATTCAATTATAATCT-TTTTAA-CCAAAAATGT-AAATAAT-TAACCTAAAATCAATGATGAG
* * * * ** * * *
2185 ATTATAAAACCATTTAAATCGAGTAATAAGGCTTTCGAAAGCTTGAGTGACCATAAATGGAC-TT
62 ATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGAACTTT
* * * *
2249 TCTTCACCAATGAATAGTTTTTGCTTT-ACGTTTCTTAAGGCATACATTCAATTATAATCTGTTT
127 TCTT-ATCAATGAAT-GTTTTT-CTTTCACGTTTCTCAAGGCAGACATTCAATTATAATCTATTT
* * * * * *
2313 TAACCAAAAATGTAAAAAACTTCAACCTAAAAACAATAACGATATTATAAAA-CTATTTAAAATG
189 TAACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATC-ATTTAAAGTG
* * * * *
2377 AGTAATAAAGCTTTTGAAAGCTTGGATGACTATAAATGGGCTTTCCTTAACAATGAATCACTTTT
253 AGTAATAAGGCTTTTGAAGGCTTGG-TGAATATAAATGGGCTTTCCTTACCAATGAATGAC-TTT
* *
2442 TCTTCATGTTTCTTAAGGTAA
316 TCTTCATGTTTC-CAAAG-AA
* * *
2463 ACATTCAATTATAATCTGTTTTATCCAAAAATATAAATAAATTTAACTTAAAATCAATGATGAGA
1 ACATTCAATTATAATCT-TTTTAACCAAAAATGTAAAT-AA-TTAACCTAAAATCAATGATGAGA
* * ** * * *
2528 TTATAAAACTATTTACAGTC-AACAAT-AAGACTTTTGAAGGAATAGGTCACTATAAATAAACTT
63 TTATAAAACCATTTAAAG-CGAGTAATAAAG-CTTTTGAAGGAATGGGTGACTATAAATGAACTT
* * ** * * * *
2591 TTCTTATTAATAAATACCTTTTCTTTCACGTTTCTCGATGTAGACATTCAATTATAATCTGTTTT
126 TTCTTATCAATGAAT-GTTTTTCTTTCACGTTTCTCAAGGCAGACATTCAATTATAATCTATTTT
* * * * *
2656 AACAAAAAAAGTAAAAAAATTTAACCTAAAATCAATTATGAGATTATAAAATCAATTAAAGTGAG
190 AACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATTTAAAGTGAG
* * * * *
2721 TAATAAGGCTTTTGAAGGCCTAGGTGATTATAAATGGGCTTTCCTTACCAATAAATGGCTTTTCC
255 TAATAAGGCTTTTGAAGG-CTTGGTGAATATAAATGGGCTTTCCTTACCAATGAATGACTTTTCT
*
2786 TCATGTTTCCCAAGACA
319 TCATGTTTCCAAAGA-A
* * * *
2803 GCCATTTAATTATAATCTATTTTAACTAAAAATGTCAAATAATAAACCTAAAATCAATGATGAGA
1 -ACATTCAATTATAATCT-TTTTAACCAAAAATGT-AAATAATTAACCTAAAATCAATGATGAGA
*
2868 TTATGAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTT
63 TTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTT
* * * * *
2933 ATTGTCAATGAATGTCTTTT-TTTACACGTTTTTTAAGGTAGACATTCAATTATAATCTATTTTA
128 CTTATCAATGAATGT-TTTTCTTT-CACGTTTCTCAAGGCAGACATTCAATTATAATCTATTTTA
* * * * * *
2997 ACTAAAATTGTAAAAGAATTCAAACTAAAATCAATTATCAAATTATAAAATCATTTAAAGTTAGT
191 ACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATTTAAAGTGAGT
* * *** * * * * *
3062 AATAAGGC-TTTGAAGGAATTGGTGAATATAAGTCAACTTTTCTCACCAATGCATGCCTTTTTTT
256 AATAAGGCTTTTGAAGG-CTTGGTGAATATAAATGGGCTTTCCTTACCAATGAATGACTTTTCTT
* *
3126 ACACGTTTTTCAAAGTAA
320 -CATG-TTTCCAAAG-AA
* * * * * *
3144 ACATTCAATTATAATATTATTTAACCAAAAAAGTAAAAAAAATTGA-CTCAAAATCAATTATGAC
1 ACATTCAATTATAATCTT-TTTAACCAAAAATGT--AAATAATTAACCT-AAAATCAATGATGAG
* * ** *
3208 ATTATAAAACCATTGAAA-CTGAGTAATAAGGCTTTTGAACAAATGGGTGGCTATAAAT-AGACT
62 ATTATAAAACCATTTAAAGC-GAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGA-ACT
* * **
3271 TTTCTT-GCAAGTGAATGTTTTTTTCTTCACGTTTCTCAAGGCAGGGATTCAATTATAATCTATT
125 TTTCTTATCAA-TGAATGTTTTTCT-TTCACGTTTCTCAAGGCAGACATTCAATTATAATCTATT
*
3335 TTTACCAAAAATGTAAAAAAATTCA
188 TTAACCAAAAATGTAAAAAAATTCA
3360 GCNNNNNNNN
Statistics
Matches: 732, Mismatches: 139, Indels: 54
0.79 0.15 0.06
Matches are distributed among these distances:
339 47 0.06
340 227 0.31
341 203 0.28
342 219 0.30
343 36 0.05
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (334 bp):
ACATTCAATTATAATCTTTTTAACCAAAAATGTAAATAATTAACCTAAAATCAATGATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT
ATCAATGAATGTTTTTCTTTCACGTTTCTCAAGGCAGACATTCAATTATAATCTATTTTAACCAA
AAATGTAAAAAAATTCAACCTAAAATCAATTATGAAATTATAAAATCATTTAAAGTGAGTAATAA
GGCTTTTGAAGGCTTGGTGAATATAAATGGGCTTTCCTTACCAATGAATGACTTTTCTTCATGTT
TCCAAAGAA
Found at i:3102 original size:170 final size:170
Alignment explanation
Indices: 1983--3359 Score: 1136
Period size: 171 Copynumber: 8.1 Consensus size: 170
1973 NNNNNNNNNN
* * * ** *
1983 AAAAAAATT-TAACTTAAAATCAATTGTAAGATTATAAAACCATTTAAAGCAAGTTATAAGGCTT
1 AAAAAAATTCAAAC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
** *** * * *
2047 TTGAAGGAA-TGAGCCACTATAAAT-AGACTTTTCTTGTTAATGGATATCTTTTTCTTCACATTT
65 TTGAAGGAATTG-GTGACTATAAATGA-ACTTTTCTTACCAATGAATGTCTTTTT-TTCACGTTT
* ** *
2110 CTCGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAAAAGT
127 CTCAAGGTAGACATTCAATTATAATCTGTTTTAA-CCAAAAATGT
* *
2155 AAAAGAA-TCCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA-TCGAGTAATAAGGCT
1 AAAAAAATTCAAAC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGT-GAGTAATAAGGCT
* * * * *
2218 TTCGAAAG-CTTGAGTGACCATAAATGGAC-TTTCTTCACCAATGAATAGT-TTTTGCTTT-ACG
64 TTTGAAGGAATTG-GTGACTATAAATGAACTTTTCTT-ACCAATGAAT-GTCTTTT--TTTCACG
* * *
2279 TTTCTTAAGGCATACATTCAATTATAATCTGTTTTAACCAAAAATGT
124 TTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * * * * * * *
2326 AAAAAACTTCAACCTAAAAACAATAACGATATTATAAAACTATTTAAAATGAGTAATAAAGCTTT
1 AAAAAAATTCAAACTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * ** * * ** *
2391 TGAAAG-CTTGGATGACTATAAATGGGCTTTCCTTAACAATGAATCACTTTTTCTTCATGTTTCT
66 TGAAGGAATTGG-TGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTTT-TTCACGTTTCT
* * * *
2455 TAAGGTAAACATTCAATTATAATCTGTTTTATCCAAAAATAT
129 CAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * * * * ** *
2497 AAATAAATT-TAACTTAAAATCAATGATGAGATTATAAAACTATTTACAGTCAACAATAAGACTT
1 AAAAAAATTCAAAC-TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * * ** * **
2561 TTGAAGGAATAGGTCACTATAAATAAACTTTTCTTATTAATAAATACCTTTTCTTTCACGTTTCT
65 TTGAAGGAATTGGTGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTT-TTTCACGTTTCT
* * * *
2626 CGATGTAGACATTCAATTATAATCTGTTTTAACAAAAAAAGT
129 CAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * *
2668 AAAAAAATTTAACCTAAAATCAATTATGAGATTATAAAATCAATTAAAGTGAGTAATAAGGCTTT
1 AAAAAAATTCAAACTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
** * * ** * * * ** * *
2733 TGAAGGCCTAGGTGATTATAAATGGGCTTTCCTTACCAATAAATGGCTTTTCCTCATGTTTCCCA
66 TGAAGGAATTGGTGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTTTTTCACGTTTCTCA
** * * * *
2798 AGACAGCCATTTAATTATAATCTATTTTAACTAAAAATGT
131 AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * * * *
2838 CAAATAA-T-AAACCTAAAATCAATGATGAGATTATGAAACCATTTAAAGCGAGTAATAAAGCTT
1 AAAAAAATTCAAA-CTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * ** *
2901 TTGAAGGAATGGGTGACTATAAATGAACTTTTATTGTCAATGAATGTCTTTTTTTACACGTTTTT
65 TTGAAGGAATTGGTGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTTTTT-CACGTTTCT
* * * *
2966 TAAGGTAGACATTCAATTATAATCTATTTTAACTAAAATTGT
129 CAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
* * * * *
3008 AAAAGAATTCAAACTAAAATCAATTATCAAATTATAAAATCATTTAAAGTTAGTAATAAGGC-TT
1 AAAAAAATTCAAACTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * * * * *
3072 TGAAGGAATTGGTGAATATAAGTCAACTTTTCTCACCAATGCATGCCTTTTTTTACACGTTTTTC
66 TGAAGGAATTGGTGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTTTTT-CACGTTTCTC
* * * *
3137 AAAGTAAACATTCAATTATAATAT-TATTTAACCAAAAAAGT
130 AAGGTAGACATTCAATTATAATCTGT-TTTAACCAAAAATGT
* * * *
3178 AAAAAAAATT--GACTCAAAATCAATTATGACATTATAAAACCATTGAAACTGAGTAATAAGGCT
1 -AAAAAAATTCAAACT-AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCT
** * * * *
3241 TTTGAACAAATGGGTGGCTATAAAT-AGACTTTTCTT-GCAAGTGAATGTTTTTTTCTTCACGTT
64 TTTGAAGGAATTGGTGACTATAAATGA-ACTTTTCTTACCAA-TGAATGTCTTTTT-TTCACGTT
* ** * *
3304 TCTCAAGGCAGGGATTCAATTATAATCTATTTTTACCAAAAATGT
126 TCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
3349 AAAAAAATTCA
1 AAAAAAATTCA
3360 GCNNNNNNNN
Statistics
Matches: 962, Mismatches: 210, Indels: 66
0.78 0.17 0.05
Matches are distributed among these distances:
168 2 0.00
169 92 0.10
170 241 0.25
171 483 0.50
172 140 0.15
173 3 0.00
174 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
AAAAAAATTCAAACTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
TGAAGGAATTGGTGACTATAAATGAACTTTTCTTACCAATGAATGTCTTTTTTTCACGTTTCTCA
AGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
Done.