Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398056.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1364.0, 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: 4635
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.30
Warning! 851 characters in sequence are not A, C, G, or T
Found at i:560 original size:171 final size:171
Alignment explanation
Indices: 275--1096 Score: 678
Period size: 171 Copynumber: 4.8 Consensus size: 171
265 NNNNNNNNNN
* * * * * * * *
275 TAAATAGACTTTTCTTACTAATGAATGGTTTTTTATTCACGTTTCTCGAGGTAGATATTTAATTA
1 TAAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTA
* * * * **********
340 TAATCTATTTTAACCAAAAATGTTAAAAAATTCAACTTAAAATCAATTATGAGNNNNNNNNNNCA
66 TTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACCA
* *
405 TTTAAAGCGAGTAATAAGACTTTTGAAGGCATGGGTGACTA
131 TTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
* * *
446 TAAATAGGCTTTTCTTGCCGATGAATGCCTTTTTCTTCAAGTTGCTCAAGGTAGACATTTAATTA
1 TAAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTA
* * **********
511 TTGTCTCTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGANNNNNNNNNNA
66 TTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACCA
*
576 TTTAAAGCGAGTAATAAGGCTTTTGAAAGCATGAGTGACTA
131 TTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
* * * * * ** *
617 TAAATAGGCTTTTCTTACAAATGAATGGATCTTTCTTCATGTTTCTCAAGACAGACATTCAATTA
1 TAAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTA
********* * * * *
682 TTATCTNNNNNNNNNNAAAATA-TAAAAAAATTCAACTTAAAAACAATTGTGAGATCATAAAGCC
66 TTATCT-GTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACC
*
746 ATTAAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
130 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
* * ** *
788 TAAAT-GAGTTTTTCTTGCCAATGAATGGTTTTTTCTTCATA-TTTCTTGAGGTAGACAATTAAT
1 TAAATAG-GCTTTTCTTGCCAATGAATGGCTTTTTCTTCA-AGTTTCTCAAGGTAGACATTTAAT
* * * * * * ********** *
851 TATAATCTGTTTTAACTAGAAATGTAAAAAAAATCAACCTAAAANNNNNNNNNNGATTATAAAAC
64 TATTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAAC
* * * * *
916 CATTTAAAGTGAGTTATTAGGCTTTTGATGGTATGAGTGACTA
129 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
* * * * * * *
959 TAAATAGGCTTTTCTTGCTAATAAATGACTTTTTCTTCACGTTTTTCTAGGTAGACATTCAATTA
1 TAAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTA
* * * * *
1024 TTGTCTGTTTCAACCAAAAAGGTAAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAACCA
66 TTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACCA
*
1089 TTTCAAGC
131 TTTAAAGC
1097 ANNNNNNNNN
Statistics
Matches: 512, Mismatches: 133, Indels: 12
0.78 0.20 0.02
Matches are distributed among these distances:
170 4 0.01
171 502 0.98
172 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
TAAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAAGTTTCTCAAGGTAGACATTTAATTA
TTATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATCATAAAACCA
TTTAAAGCGAGTAATAAGGCTTTTGAAGGCATGAGTGACTA
Found at i:2867 original size:171 final size:170
Alignment explanation
Indices: 2479--3433 Score: 618
Period size: 171 Copynumber: 5.6 Consensus size: 170
2469 NNNNNNNNNN
* * * *
2479 TAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAGAACAGATAATAATTGAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAACAGTTGAA
* * * * ********* * **
2544 TGTTTACCT-AGAGAAACATAAAGAAAANNNNNNNNNNTGATAAGAAAAGTTTATTTATAGTCAC
66 TCTCTACCTAAG-GAAATATGAAGAAAA-ACCATTCATTGACAAGAAAAGCCTATTTATAGTCAC
* * * **
2608 CCATGCCTTTAAAAGCCTTATTACTCGCTTTAAACGGCTTTA
129 CCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
***********
2650 TAATCTCATAATTGATTTTANNNNNNNNNNATTTACATTTTTGGTTAAAACAGATAACAGTTGAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAACAGTTGAA
* * * * *
2715 TTTTTTCCTAAGGAAATATGAAGAAAAACACATTCATTGACAAGAAAATCCTATTCATAGTCACC
66 TCTCTACCTAAGGAAATATGAAGAAAAAC-CATTCATTGACAAGAAAAGCCTATTTATAGTCACC
* * ******
2780 CAAGCTTTCAAAAGCCTTATTACTTGCTTTAAATGNNNNNN
130 CAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
**** * * * * *
2821 NNNNCTCATAATTGATTTTAAGTTGAA-TGTTTTTAAATTGTTGGTTAAATCAGATAATAATT-A
1 TAATCTCATAATTGATTTTAAGTTGAAGT-TTTTTACATTTTTGGTTAAAACAGATAACAGTTGA
* * * *
2884 GATCTCTACGTCAA-GAAATGTGAACAAAAAGCCATTCATTGACAAGAAAAGCCTATTTATAATC
65 -ATCTCTACCT-AAGGAAATATGAAGAAAAA-CCATTCATTGACAAGAAAAGCCTATTTATAGTC
* **********
2948 ACCCATGCCTTCAAAAGCCTTATTANNNNNNNNNNATGATTTTA
127 ACCCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
* * * **
2992 TAATCTCATAATTGATTTTTAGTTGAAGTTTTTTCCTTTTTTGGTTAAAACAGATTGCAGTTGAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAACAGTTGAA
* *
3057 TGTCTACCTAAGGAAATATGAAGAAAAACCCATTCATTGGCAAGAAAAGCCTATTTATAGTCACC
66 TCTCTACCTAAGGAAATATGAAGAAAAA-CCATTCATTGACAAGAAAAGCCTATTTATAGTCACC
* * *
3122 CAAGCCTTCGAAAGCGTTATTACTCGCTTTAAATGGTTTTA
130 CAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
* * * * ** *** *
3163 TAATCTTC-TAATTGATTTGAAGTTTAATTTTTTTATATTTTTTATTAAAACAGATTGTAATTGA
1 TAATC-TCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAACAGTTGA
* * * * * * * * *
3227 TTTTCTATC-ATAGGAAACATGATGAAAAGA-TATTCATT-AGCAAGAAAAGTCTATTTATGGTT
65 ATCTCTACCTA-AGGAAATATGAAGAAAA-ACCATTCATTGA-CAAGAAAAGCCTATTTATAGTC
* ** * * * *
3289 ACCTATTCCTTCAAAAGTCTTATTGCTCGTTTTAAAT-TTTTTCA
127 ACCCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTT-A
* ** * * *
3333 TAATCTCATAATTGACTTTAAGTTGATTTTTTTTACATTTTTAGTTAGAACAGAT-ACTAATTGA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAAC-AGTTGA
* * * *
3397 ATGTTTACCT-AGAGAAACATAAAGAAAAAGCCATTCA
65 ATCTCTACCTAAG-GAAATATGAAGAAAAA-CCATTCA
3434 CTGATANNNN
Statistics
Matches: 593, Mismatches: 171, Indels: 40
0.74 0.21 0.05
Matches are distributed among these distances:
169 9 0.02
170 128 0.22
171 446 0.75
172 10 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.36
Consensus pattern (170 bp):
TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGGTTAAAACAGATAACAGTTGAA
TCTCTACCTAAGGAAATATGAAGAAAAACCATTCATTGACAAGAAAAGCCTATTTATAGTCACCC
AAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGATTTTA
Found at i:4131 original size:340 final size:323
Alignment explanation
Indices: 3486--4151 Score: 637
Period size: 340 Copynumber: 2.0 Consensus size: 323
3476 CTTTATAATC
*
3486 TCATAATTGATTTTAAGTTGAATTTATTTACATTTTTAGTTAAAACAGATAACAGTTGAATTTTT
1 TCATAATTGATTTTAAGTTGAATTTATTTACATTTTTAGTTAAAACAGATAACAGTTGAATGTTT
* * * * *
3551 TCCTGAGGAAATATGAAGAAAAACACATTCATTGGCAAGAAAAGCCTATTCATAGTCTCCTAAGC
66 ACCTAAGGAAATATGAAGAAAAACACATTCATTGGCAAGAAAAGCCAATTCATAGTCACCCAAGC
* * *** *
3616 TTTCAAAAGCCTTATTACTTGCNNNNNNNNNNTTTATAATCTCATAATTGATTAAGTTGAATGTT
131 CTTCAAAAGCATTATTACTTGC-------GGCTTTATAATCTCATAATTGATTAAGTTAAATGTT
* * * *
3681 TTTAAATTTTTGGTTAAATCAGATAATAATTAGATCTCTACGTTAAGAAACATGAACAAAAAGCC
189 TTTAAATTTTTGATTAAAACAGATAATAATTAGATCTCTACGCTAAGAAACATGAACAAAAAGAC
* *
3746 ATTCATTGGCAAGAAAAGACTATTTATAATCACTCATGCCTTCAAAAGCCTTATTACTCTCTTTA
254 ATTCATTGGCAAGAAAAGACCATTTATAATCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTA
3811 AATGA
319 AATGA
* * * **
3816 NNNNNNNNNNTCATAATTGATTTTCAGTTGAAGTTT-TTTACATTTTTGGTTATAACAGATTGCA
1 ----------TCATAATTGATTTTAAGTTGAA-TTTATTTACATTTTTAGTTAAAACAGATAACA
* *
3880 GTTGAATGTTTACCTAAGGAAATATGAAGAAAAACTCATTCATTGGCAAGAAAAGCCAATTTATA
55 GTTGAATGTTTACCTAAGGAAATATGAAGAAAAACACATTCATTGGCAAGAAAAGCCAATTCATA
* ***
3945 GTCACCCAAGCCTTCGAAAGCATTATTACTNNNNNNNNNNGGCTTTATAATCTCATAATTGATTT
120 GTCACCCAAGCCTTCAAAAGCATTATTACT-------TGCGGCTTTATAATCTCATAATTGA-TT
* * *
4010 CAAGTTAAAT-TTCTTTACATTTTTTATTAAAACAGATCATAATT-GAT-TGCCTAC-CTAAGGA
177 -AAGTTAAATGTT-TTTAAATTTTTGATTAAAACAGATAATAATTAGATCT--CTACGCTAA-GA
* * * * * *
4071 AACATGAA-AAAAAGATATTTATTGGCAAGAAAAGTCCGTTTCTAGTCAC-CTATG-CTTCAAAA
237 AACATGAACAAAAAGACATTCATTGGCAAGAAAAGACCATTTATAATCACTC-ATGCCTTCAAAA
*
4133 GGCTTATTACTCGCTTTAA
301 GCCTTATTACTCGCTTTAA
4152 NNNNNNNNNN
Statistics
Matches: 272, Mismatches: 39, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
340 175 0.64
341 49 0.18
342 48 0.18
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.34
Consensus pattern (323 bp):
TCATAATTGATTTTAAGTTGAATTTATTTACATTTTTAGTTAAAACAGATAACAGTTGAATGTTT
ACCTAAGGAAATATGAAGAAAAACACATTCATTGGCAAGAAAAGCCAATTCATAGTCACCCAAGC
CTTCAAAAGCATTATTACTTGCGGCTTTATAATCTCATAATTGATTAAGTTAAATGTTTTTAAAT
TTTTGATTAAAACAGATAATAATTAGATCTCTACGCTAAGAAACATGAACAAAAAGACATTCATT
GGCAAGAAAAGACCATTTATAATCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGA
Done.