Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399603.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2857.0, 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: 4423
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.24
Warning! 1373 characters in sequence are not A, C, G, or T
Found at i:296 original size:171 final size:170
Alignment explanation
Indices: 5--1134 Score: 1128
Period size: 171 Copynumber: 6.7 Consensus size: 170
1 GGGT
* * *
5 GACTATAAATGGACTTTTCTTCCCAATGAATGCTTTTTTCTTCATGTTTCCCGAGGTAAACGTTC
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * * * *
70 ATTTATAGTTTCTTTTAACCGAAAAA-GTGAAAAAATTTAACTCAAAATCAATTATGAGATTATA
66 AATTATAGTCTGTTTTAACC-AAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * *
134 AAACAATTTAAAGCGAGTAATAAGGCCTTTGAAGGAATATGA
129 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA
* * *
176 GACTATAAATAGACTTTTCTTACCAATGAATGCTTTTTTCTTCAAGTTTCTCTAGGTAAACATTC
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * * *
241 AATTATAGTCTGTTGTAACCAAAAATGTGAAAAAATTAAACATAAAATTAATTATGAGATTA-AA
66 AATTATAGTCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * *
305 AACCATTTAAAGTGAATAATAAGGCTTTTTAAGGAATGGGTA
130 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-A
* * * *
347 -ACTATAAATGGACTTTTCTTACCAATGAATGCTTGTTTCTTCATGTTTCTCAAGTTAGACATTC
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * * *
411 AATTATACTGTGTTTTAACCAAAAATATAAAAACATTCTACTTAAAATCAATTATGAGATTATAA
66 AATTATAGTCTGTTTTAACCAAAAATGTAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * *
476 AACCATTTAAAACGAGTAATAAAGCTTTTAAAGGGATGGGT
130 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA
* * *** * * * * * *
517 GACTATAAATGGACTTTTTTTGCTTGTGAATGCCTTATTCTTCATGCTTCCCAAGGTAAAAATTC
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * *
582 AATTATAGTCTGTTTTAACCAAGAATACTAAAAAATTCAACTTAAAATCAATTACGAG-------
66 AATTATAGTCTGTTTTAACCAAAAAT-GTAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * *
640 ----A--TAAAGTGAGTAATATGGCTTTTGAAGGAA-ATGGT
130 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATA-GGA
* * ** * * *
675 GACTATAAATGGACTTTTCCTATCAATGAATATTTTTTTCTTCACGTTTCTAGAGATAAACATTC
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
* * * * * * *
740 AATTATAATATATTTTAACCAATAATGTAAAAATAATTGAACTAAAAATCAATTTTGAGATTATA
66 AATTATAGTCTGTTTTAACCAAAAATGT-AAAA-AATTCAACTTAAAATCAATTATGAGATTATA
* * * *
805 AAACCATTTAAAGTGAGTAATAGGGCTTTTGAAAGAATAGAA
129 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA
* ** * * * * * *
847 GACTATAAATGAACTTTTCTTGTCAATGAACGCTTGTTTCTTTACGTTTATC-ATGGTAGACATT
1 GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGA-GGTAAACATT
* * * * *
911 CAATTATAGTCAGTTTTAACAAAAAATGTAAAAAAAATTTAACTTAAAATCAATTATGAGGTTAC
65 CAATTATAGTCTGTTTTAACCAAAAATGT--AAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
976 AAAACAATTTAAAGCGAGTAACAAGGCTTTTAAAGGAATAGGA
128 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA
* * * * * *
1019 GACTATAAATGGACCTGTC-TAGCCAATAAATGCTTGTTTCTTCATATTTCTCGAGGTAAACTTT
1 GACTATAAATGGACTTTTCTTA-CCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATT
* * *
1083 TAATTATAGTTTGTTTTAACAAAAAATGTAAAACAATTCAACTTAAAATCAA
65 CAATTATAGTCTGTTTTAACCAAAAATGTAAAA-AATTCAACTTAAAATCAA
1135 NNNNNNNNNN
Statistics
Matches: 785, Mismatches: 146, Indels: 56
0.80 0.15 0.06
Matches are distributed among these distances:
157 1 0.00
158 99 0.13
159 21 0.03
160 1 0.00
169 5 0.01
170 151 0.19
171 259 0.33
172 241 0.31
173 7 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
GACTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCGAGGTAAACATTC
AATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA
Found at i:912 original size:172 final size:172
Alignment explanation
Indices: 641--1029 Score: 446
Period size: 172 Copynumber: 2.3 Consensus size: 172
631 AATTACGAGA
* * * *
641 TAAAGTGAGTAATATGGCTTTTGAAGGAA-ATGGTGACTATAAATGGACTTTTCCTATCAATGAA
1 TAAAGTGAGTAATAAGGCTTTTGAAAGAATA-GGAGACTATAAATGAACTTTTCCTATCAATGAA
* * * * * *
705 TATTTTTTTCTTCACGTTTCTAGAGATAAACATTCAATTATAAT-ATATTTTAACCAATAATGTA
65 CACTTGTTTCTTCACGTTTATAGAGATAAACATTCAATTATAATCA-ATTTTAACAAAAAATGTA
* * * *
769 AAAATAATTGAACTAAAAATCAATTTTGAGATTATAAAACCATT
129 AAAAAAATTGAACTAAAAATCAATTATGAGATTACAAAACAATT
* * * *
813 TAAAGTGAGTAATAGGGCTTTTGAAAGAATAGAAGACTATAAATGAACTTTTCTTGTCAATGAAC
1 TAAAGTGAGTAATAAGGCTTTTGAAAGAATAGGAGACTATAAATGAACTTTTCCTATCAATGAAC
* * * * *
878 GCTTGTTTCTTTACGTTTATCATG-G-TAGACATTCAATTATAGTCAGTTTTAACAAAAAATGTA
66 ACTTGTTTCTTCACGTTTAT-A-GAGATAAACATTCAATTATAATCAATTTTAACAAAAAATGTA
* * *
941 AAAAAAATTTAACTTAAAATCAATTATGAGGTTACAAAACAATT
129 AAAAAAATTGAACTAAAAATCAATTATGAGATTACAAAACAATT
* *
985 TAAAGCGAGTAACAAGGCTTTT-AAAGGAATAGGAGACTATAAATG
1 TAAAGTGAGTAATAAGGCTTTTGAAA-GAATAGGAGACTATAAATG
1030 GACCTGTCTA
Statistics
Matches: 183, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
171 3 0.02
172 175 0.96
173 4 0.02
174 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (172 bp):
TAAAGTGAGTAATAAGGCTTTTGAAAGAATAGGAGACTATAAATGAACTTTTCCTATCAATGAAC
ACTTGTTTCTTCACGTTTATAGAGATAAACATTCAATTATAATCAATTTTAACAAAAAATGTAAA
AAAAATTGAACTAAAAATCAATTATGAGATTACAAAACAATT
Found at i:1056 original size:172 final size:171
Alignment explanation
Indices: 711--1134 Score: 458
Period size: 172 Copynumber: 2.5 Consensus size: 171
701 TGAATATTTT
* * * * * * * * *
711 TTTCTTCACGTTTCTAGAGATAAACATTCAATTATAATATATTTTAACCAATAATGTAAAAATAA
1 TTTCTTCACATTTATCGAGGTAAACATTCAATTATAGTA-GTTTTAACAAAAAATGTAAAAAAAA
* * * * * * * *
776 TTGAACTAAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAGGGCTTTTGAAAGA
65 TTCAACTTAAAATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAACAAGGCTTTTGAAAGA
* * * * *
841 ATAGAAGACTATAAATGAACTTTTCTTGTCAATGAACGCTTG
130 ATAGAAGACTATAAATGAACCTGTCTAGCCAATAAACGCTTG
* * *
883 TTTCTTTACGTTTATC-ATGGTAGACATTCAATTATAGTCAGTTTTAACAAAAAATGTAAAAAAA
1 TTTCTTCACATTTATCGA-GGTAAACATTCAATTATAGT-AGTTTTAACAAAAAATGTAAAAAAA
* *
947 ATTTAACTTAAAATCAATTATGAGGTTACAAAACAATTTAAAGCGAGTAACAAGGCTTTT-AAAG
64 ATTCAACTTAAAATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAACAAGGCTTTTGAAA-
* * *
1011 GAATAGGAGACTATAAATGGACCTGTCTAGCCAATAAATGCTTG
128 GAATAGAAGACTATAAATGAACCTGTCTAGCCAATAAACGCTTG
* * * * * *
1055 TTTCTTCATATTTCTCGAGGTAAACTTTTAATTATAGTTTGTTTTAACAAAAAATGT-AAAACAA
1 TTTCTTCACATTTATCGAGGTAAACATTCAATTATAG-TAGTTTTAACAAAAAATGTAAAAAAAA
1119 TTCAACTTAAAATCAA
65 TTCAACTTAAAATCAA
1135 NNNNNNNNNN
Statistics
Matches: 210, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
171 25 0.12
172 182 0.87
173 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
TTTCTTCACATTTATCGAGGTAAACATTCAATTATAGTAGTTTTAACAAAAAATGTAAAAAAAAT
TCAACTTAAAATCAATTATGAGATTACAAAACAATTTAAAGCGAGTAACAAGGCTTTTGAAAGAA
TAGAAGACTATAAATGAACCTGTCTAGCCAATAAACGCTTG
Found at i:1132 original size:502 final size:499
Alignment explanation
Indices: 142--1134 Score: 1215
Period size: 502 Copynumber: 2.0 Consensus size: 499
132 TAAAACAATT
*
142 TAAAGCGAGTAATAAGGCCTTTGAAGGAATATGAGACTATAAATAGACTTTTCTTACCAATGAAT
1 TAAAGCGAGTAATAAGGCCTTTGAAGGAATATGAGACTATAAATAGACTTTTCCTACCAATGAAT
* ** * * * * *
207 GCTTTTTTCTTCAAGTTTCTCTAGGTAAACATTCAATTATAGTCTGTTGTAACCAAAAATGTGAA
66 ACTTTTTTCTTCAAGTTTCTAGAGATAAACATTCAATTATAATATATTGTAACCAAAAATGTAAA
* *
272 AAAATTAAACATAAAATTAATTATGAGATTAAAAACCATTTAAAGTGAATAATAAGGCTTTTTAA
131 AAAATTAAACATAAAATCAATTATGAGATTAAAAACCATTTAAAGTGAATAATAAGGCTTTTGAA
* * * * * * * *
337 GGAATGGGTAACTATAAATGGACTTTTCTTACCAATGAATGCTTGTTTCTTCATGTTTCTCAAGT
196 AGAATGAGAAACTATAAATGAACTTTTCTTACCAATGAACGCTTGTTTCTTCACGTTTATCAAGG
** * *
402 TAGACATTCAATTATACTGTGTTTTAACCAAAAATATAAAAACATTCTACTTAAAATCAATTATG
261 TAGACATTCAATTATACTCAGTTTTAACAAAAAATATAAAAAAATTCTACTTAAAATCAATTATG
* * * * * * *
467 AGATTATAAAACCATTTAAAACGAGTAATAAAGCTTTTAAAGGGATGGGTGACTATAAATGGACT
326 AGATTACAAAACAATTTAAAACGAGTAACAAAGCTTTTAAAGGAATAGGAGACTATAAATGGACC
* * * *** * *
532 TTTTTTGCTTGTGAATGCCTTATTCTTCATGCTTCCCAAGGTAAAAATTCAATTATAGTCTGTTT
391 TGTCTAGCCAATAAATGCCTTATTCTTCATACTTCCCAAGGTAAAAATTCAATTATAGTCTGTTT
* *
597 TAACCAAGAATACTAAAAAATTCAACTTAAAATCAATTACGAGA
456 TAACAAAAAATACTAAAAAATTCAACTTAAAATCAATTACGAGA
* * * * * *
641 TAAAGTGAGTAATATGGCTTTTGAAGGAA-ATGGTGACTATAAATGGACTTTTCCTATCAATGAA
1 TAAAGCGAGTAATAAGGCCTTTGAAGGAATAT-GAGACTATAAATAGACTTTTCCTACCAATGAA
* * * *
705 TATTTTTTTCTTCACGTTTCTAGAGATAAACATTCAATTATAATATATTTTAACCAATAATGTAA
65 TACTTTTTTCTTCAAGTTTCTAGAGATAAACATTCAATTATAATATATTGTAACCAAAAATGTAA
* * * *
770 AAATAATTGAAC-TAAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAGGGCTTT
130 AAA-AATTAAACAT-AAAATCAATTATGAGATTA-AAAACCATTTAAAGTGAATAATAAGGCTTT
** *
834 TGAAAGAAT-AGAAGACTATAAATGAACTTTTCTTGTCAATGAACGCTTGTTTCTTTACGTTTAT
192 TGAAAGAATGAGAA-ACTATAAATGAACTTTTCTTACCAATGAACGCTTGTTTCTTCACGTTTAT
* * *
898 CATGGTAGACATTCAATTATAGTCAGTTTTAACAAAAAATGTAAAAAAAATT-TAACTTAAAATC
256 CAAGGTAGACATTCAATTATACTCAGTTTTAACAAAAAATAT-AAAAAAATTCT-ACTTAAAATC
* * *
962 AATTATGAGGTTACAAAACAATTTAAAGCGAGTAACAAGGCTTTTAAAGGAATAGGAGACTATAA
319 AATTATGAGATTACAAAACAATTTAAAACGAGTAACAAAGCTTTTAAAGGAATAGGAGACTATAA
* * * * ** *
1027 ATGGACCTGTCTAGCCAATAAATG-CTTGTTTCTTCATATTTCTCGAGGTAAACTTTTAATTATA
384 ATGGACCTGTCTAGCCAATAAATGCCTT-ATTCTTCATACTTCCCAAGGTAAAAATTCAATTATA
* *
1091 GTTTGTTTTAACAAAAAAT-GTAAAACAATTCAACTTAAAATCAA
448 GTCTGTTTTAACAAAAAATACTAAAA-AATTCAACTTAAAATCAA
1135 NNNNNNNNNN
Statistics
Matches: 413, Mismatches: 72, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
498 2 0.00
499 111 0.27
500 26 0.06
501 122 0.30
502 152 0.37
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (499 bp):
TAAAGCGAGTAATAAGGCCTTTGAAGGAATATGAGACTATAAATAGACTTTTCCTACCAATGAAT
ACTTTTTTCTTCAAGTTTCTAGAGATAAACATTCAATTATAATATATTGTAACCAAAAATGTAAA
AAAATTAAACATAAAATCAATTATGAGATTAAAAACCATTTAAAGTGAATAATAAGGCTTTTGAA
AGAATGAGAAACTATAAATGAACTTTTCTTACCAATGAACGCTTGTTTCTTCACGTTTATCAAGG
TAGACATTCAATTATACTCAGTTTTAACAAAAAATATAAAAAAATTCTACTTAAAATCAATTATG
AGATTACAAAACAATTTAAAACGAGTAACAAAGCTTTTAAAGGAATAGGAGACTATAAATGGACC
TGTCTAGCCAATAAATGCCTTATTCTTCATACTTCCCAAGGTAAAAATTCAATTATAGTCTGTTT
TAACAAAAAATACTAAAAAATTCAACTTAAAATCAATTACGAGA
Found at i:3589 original size:172 final size:171
Alignment explanation
Indices: 3250--3665 Score: 512
Period size: 172 Copynumber: 2.4 Consensus size: 171
3240 NNNNNNNNNN
* * * * * *
3250 CTATAAATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATATTTCTCGAGGTAAACATTCAA
1 CTATAAATGGATTTTTCTTATCAATGAATGCTTGTTTCTTCATGTTTCTCAAGCTAAACATTCAA
* * * * *
3315 TTATCGTCTATTTTAACTAAAAATCTAAGAAAATTCTACTTAAAATCAATTATGAGATTACAAAA
66 TTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAA
* * *
3380 CTATTTAAAGTGAGTAATAAGGCTTTTTAAGGAATAGGTGA
131 CCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGA
* * *
3421 CTATAAATGGATTTTTCTTGTTAATGAATGCTTGTTTCTTCATGTTTCTCAAGCTAGACATTCAA
1 CTATAAATGGATTTTTCTTATCAATGAATGCTTGTTTCTTCATGTTTCTCAAGCTAAACATTCAA
* * * * *
3486 TTATAGTTTGTTTTAACCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTATAGA
66 TTATAGTCTATTTTAACCAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGAGATTACAAA
*
3551 ACCATTTAAAGTGCGTAATAAGGCTTTTGAAGGAATAGGAGA
130 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGA
* ** * * * * *
3593 CTATAGATGGACTCGTT-TTATCAATAAATGATTGTTTCTTCATGTTTCTTGAAG-TCAACATTT
1 CTATAAATGGA-TTTTTCTTATCAATGAATGCTTGTTTCTTCATGTTTC-TCAAGCTAAACATTC
3656 AATTATAGTC
64 AATTATAGTC
3666 NNNNNNNNNN
Statistics
Matches: 207, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
171 81 0.39
172 119 0.57
173 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (171 bp):
CTATAAATGGATTTTTCTTATCAATGAATGCTTGTTTCTTCATGTTTCTCAAGCTAAACATTCAA
TTATAGTCTATTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTACAAAA
CCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGAGA
Found at i:4290 original size:171 final size:171
Alignment explanation
Indices: 3976--4415 Score: 548
Period size: 171 Copynumber: 2.6 Consensus size: 171
3966 NNNNNNNNNN
* *
3976 AAACAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACAAGTAGTAAGGCTTTT
1 AAAC-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC-AGTAATAAGGCTTTT
* * * * * * * * * **
4041 GAAAGAATGGGTGATTATAACT-GAACTTTTCTCCTTAATTAATTGCTTTTTCTGCATATTTCTC
64 GAAAGAATGAGTGACTATAAATAG-ACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCAA
* * *
4105 GAGGCGGACATTCAATTATAGTCTGTTTTAAAGAAAAATGT-AA
128 GAGACAGACATTCAATTATAGTCTGTTTTAAAGAAAAAAGTGAA
**
4148 AAACATTCAACTTAAAATCAATTATGAGATTATAAAATTATTTAAAGCGAGTAATAAGGCTTTTG
1 AAACATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC-AGTAATAAGGCTTTTG
* *
4213 AAAGAATGAGTTACTATAAATAGACTTTTCTTCTCAATGAATGGTTTTTTCTACACATTTCAAGA
65 AAAGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCAAGA
**
4278 GACA-AGCATTCAATTATAGTCTGTTTTAACTAAAAAAGTGAA
130 GACAGA-CATTCAATTATAGTCTGTTTTAAAGAAAAAAGTGAA
* *
4320 AAA-ATTCAGCTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCACCTAATAAGGCTTTTG
1 AAACATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCA-GTAATAAGGCTTTTG
* *
4384 AAAGAATAAGAGACTATAAATTA-ACTTTTCTT
65 AAAGAATGAGTGACTATAAA-TAGACTTTTCTT
4416 GCAAATGA
Statistics
Matches: 233, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
170 2 0.01
171 219 0.94
172 12 0.05
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
AAACATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCAGTAATAAGGCTTTTGA
AAGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACACATTTCAAGAG
ACAGACATTCAATTATAGTCTGTTTTAAAGAAAAAAGTGAA
Done.