Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398675.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1960.0, 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: 10582
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.24
Warning! 3573 characters in sequence are not A, C, G, or T
Found at i:1365 original size:172 final size:170
Alignment explanation
Indices: 975--1377 Score: 398
Period size: 172 Copynumber: 2.3 Consensus size: 170
965 NNNNNNNNNN
* * * * **
975 TTTATAGTCACCCATACCTTGAACAACATTATTACTCAATTTAAATGATTTTGTAATGCCGTAAT
1 TTTATAGTCACCCATACCTTCAA-AACATTATTACTCACTTTAAATGGTTTTATAATGCCAAAAT
* * ** *** * *
1040 TAATTTTAAGTTGAATTGTTTTTTATTCTTTTGTTAAACAGACTAGAATTGAATATCTACCTCGA
65 TAATTTAAAGCTGAATACTTTCACATTCTTTGGTTAAAAAGACTAGAATTGAATATCTACCTCGA
* *
1105 AAAACATAAAGAAAAAGGCATTCATTGGTAACAGAAGTCCA
130 AAAACATAAAGAAAAAAGCATTCATTGGCAACAGAAGTCCA
* * * *********
1146 TTTATCGTCACCGATTCCTTCNNNNNNNNNNTTACTCACTTTAAATGGTTTTATAA-GCTCAAAA
1 TTTATAGTCACCCATACCTTC-AAAACATTATTACTCACTTTAAATGGTTTTATAATGC-CAAAA
* * *
1210 TTGATTTAAAGCTGAATACTTTGCACATT-TTTGGTTAAAAAAGACTAGAATTTAATGTCTACCA
64 TTAATTTAAAGCTGAATACTTT-CACATTCTTTGGTT-AAAAAGACTAGAATTGAATATCTACC-
* *
1274 T-GAGAAACATAAAGAAAAAAGCATTCATTGGCAAGAGAAGTCCA
126 TCGAAAAACATAAAGAAAAAAGCATTCATTGGCAACAGAAGTCCA
* *
1318 TTTATATTCACCCATACCTTCAAAAGCATTATTACTCACTTTAAATGGTTTTGTAATGCC
1 TTTATAGTCACCCATACCTTCAAAA-CATTATTACTCACTTTAAATGGTTTTATAATGCC
1378 GNNNNNNNNN
Statistics
Matches: 177, Mismatches: 48, Indels: 13
0.74 0.20 0.05
Matches are distributed among these distances:
170 2 0.01
171 65 0.37
172 107 0.60
173 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.34
Consensus pattern (170 bp):
TTTATAGTCACCCATACCTTCAAAACATTATTACTCACTTTAAATGGTTTTATAATGCCAAAATT
AATTTAAAGCTGAATACTTTCACATTCTTTGGTTAAAAAGACTAGAATTGAATATCTACCTCGAA
AAACATAAAGAAAAAAGCATTCATTGGCAACAGAAGTCCA
Found at i:4228 original size:172 final size:172
Alignment explanation
Indices: 3551--4252 Score: 609
Period size: 172 Copynumber: 4.1 Consensus size: 172
3541 NNNNNNNNNA
* * *
3551 ACATTCAATTCTAGTATGTTTTAACCAAAAATATACAAAGAATTCAAATTT-AATGAATTTTGAG
1 ACATTCAATTCTAGTATGCTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTCTGAG
* ********** *
3615 ATTATAAAACCATTTAAAGTGAGTAANNNNNNNNNNGA-AGGAATGGGTGGCTATAAATGGACTT
66 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGACA-GAATGGGTGACTATAAATGGACTT
* *
3679 TTCTTGCTAATGAATGCTCTCTTCTTTATGTTTCTCATGGTAG
130 TTCTTGCCAATGAATGCTCTTTTCTTTATGTTTCTCATGGTAG
* * *
3722 ACATTCAATTCTAGTATGTTTTAACCAAAAATATACAAAGAATTCACATTTAAATCAATTTTGAG
1 ACATTCAATTCTAGTATGCTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTCTGAG
********** * *
3787 ATTATNNNNNNNNNNAAAGTGAGTAATAAGTCTTTTGAC-GAAATGAGTGACTATAAATGGACTT
66 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGACAG-AATGGGTGACTATAAATGGACTT
** * *** **
3851 CTT-TCACCAATGAAGGC-CTTTTTCTTTACACTTCTCAAAGTAG
130 -TTCTTGCCAATGAATGCTC-TTTTCTTTATGTTTCTCATGGTAG
* * * * * * *
3894 GCATTCAATTTTAGTCT-CTTTAACAAAAAAAATTTA-AAAAAATT-AAACTTCAAATCAATTAC
1 ACATTCAATTCTAGTATGCTTTAAC--CAAAAATATACAAAGAATTCAAA-TTTAAATCAATT-C
* * * * *
3956 -G-GCATTACAAAATCATTTAAAGTGAGGAAT-AGAGCTTTTGAAAGTATGGGTGACTATAAATG
62 TGAG-ATTATAAAAACATTTAAAGTGAGTAATAAG-GCTTTTGACAGAATGGGTGACTATAAATG
********** *
4018 GACTTTTCTTNNNNNNNNNNGCT-TTTATCTTCATGTTTCTCATGGTAG
125 GACTTTTCTTGCCAATGAATGCTCTTT-TCTTTATGTTTCTCATGGTAG
* * *
4066 ACATTCAATTCTAGTTTGCTTTAACCAAAAATGTGCAAAGAATTCAAATTTAAATCAATTCTGAG
1 ACATTCAATTCTAGTATGCTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTCTGAG
*
4131 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGACAGAATGGGTGACTTTAAATGGACTTT
66 ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGACAGAATGGGTGACTATAAATGGACTTT
*
4196 TCTTGCCAATGAATGATCTTTTCTTTATGTTTCTCATGGTAG
131 TCTTGCCAATGAATGCTCTTTTCTTTATGTTTCTCATGGTAG
4238 ACATTCAATTCTAGT
1 ACATTCAATTCTAGT
4253 CNNNNNNNNN
Statistics
Matches: 406, Mismatches: 103, Indels: 43
0.74 0.19 0.08
Matches are distributed among these distances:
171 76 0.19
172 303 0.75
173 27 0.07
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.35
Consensus pattern (172 bp):
ACATTCAATTCTAGTATGCTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTCTGAG
ATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGACAGAATGGGTGACTATAAATGGACTTT
TCTTGCCAATGAATGCTCTTTTCTTTATGTTTCTCATGGTAG
Found at i:5270 original size:172 final size:172
Alignment explanation
Indices: 4958--5975 Score: 1032
Period size: 172 Copynumber: 5.9 Consensus size: 172
4948 NNNNNNNNNA
* * * * * * * * * *
4958 ATTCATTGGTAACAGAAGCCCATTTATAGTCATCGATTCCTTCAAAAGCCTTATTTCTTATTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
* * * *
5023 AATGGTTTTATAATCTAAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGA
66 AATGGTTTTATAATCTCAAAATTGATTTTAATTTGAATTTTTTGTACTTTTTTAGTTAAAACAGA
*
5088 CTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAAC
131 CTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAGC
* * * * *
5130 ATTCATTGGCAAGCAAAGTCCTTTTATGGTCACCCATACCTTCAAAAGCATTATCACTCACTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
* ** * * * * * *
5195 AATGGTTTTGTAATGC-CGTAATTGATTTTAAGTAGAATTGTTTTTTAGTTTTTTTGTT-AAAGA
66 AATGGTTTTATAAT-CTCAAAATTGATTTTAATTTGAATT-TTTTGTACTTTTTTAGTTAAAACA
* * **
5258 GACTATAATTGAATGTCTACC-TCTAGAAATGTAAA-AAAAAAGGC
129 GACTAGAATTGAATGTCTACCAT-GAGAAACATAAAGAAAAAA-GC
* * * * *
5302 CTTCATTGGTAAGAAAAGTCCATTTATAGTCACTCATTCCTTTAAAAGCCTTATTACTCACTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
* * * * *
5367 AATTGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTCAGTTAAAACAGA
66 AATGGTTTTATAATCTCAAAATTGATTTTAATTTGAATTTTTTGTACTTTTTTAGTTAAAACAGA
* * * *
5432 CTATAATTGAATGTCTACCATGAGAAACATGAAGAAGAGAGC
131 CTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAGC
** * *
5474 ATTCATTTCCAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAG-ACTTATTAGTCACTTT
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCA-TTATTACTCACTTT
* * * * * *
5538 ACATGTTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTGCATTTTTAGTTAAAACAG
65 AAATGGTTTTATAATCTCAAAATTGATTTTAATTTGAATTTTTTGTACTTTTTTAGTTAAAACAG
* * *
5603 ACTAGAATTTAATGT-TAACCTTGAGAAACATGAAGAAAAAAGC
130 ACTAGAATTGAATGTCT-ACCATGAGAAACATAAAGAAAAAAGC
* * * * **
5646 ATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTCGCCATA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
** * * * *
5711 AATGGTTTTATAATGC-CGTAATTGATTTTAAGTAGAATTTTTTTTA-TATTTTT-GTT-AAAGA
66 AATGGTTTTATAAT-CTCAAAATTGATTTTAATTTGAATTTTTTGTACT-TTTTTAGTTAAAACA
* * ** ** * * *
5772 GACTATAACTGAATGTCTACCACAAGAAATGTAATGAAAAAGGA
129 GACTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAGC
* ** * * * *
5816 ATTTATTCACAGGAGAAGTCCATTTATAGTCACCCATTCCTTCAAGAGCTTTATTACTCACTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
* * * * * *
5881 AATGATTTTATACTCTCAAAATTGA-TTTATATTTGAATGTTTTCTACTTTTTTGGTTAAAATAG
66 AATGGTTTTATAATCTCAAAATTGATTTTA-ATTTGAATTTTTTGTACTTTTTTAGTTAAAACAG
5945 ACTAGAATTGAATGTCTACCATGAGAAACAT
130 ACTAGAATTGAATGTCTACCATGAGAAACAT
5976 GAANNNNNNN
Statistics
Matches: 687, Mismatches: 140, Indels: 38
0.79 0.16 0.04
Matches are distributed among these distances:
169 5 0.01
170 124 0.18
171 29 0.04
172 509 0.74
173 20 0.03
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (172 bp):
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCATTATTACTCACTTTA
AATGGTTTTATAATCTCAAAATTGATTTTAATTTGAATTTTTTGTACTTTTTTAGTTAAAACAGA
CTAGAATTGAATGTCTACCATGAGAAACATAAAGAAAAAAGC
Found at i:6376 original size:170 final size:171
Alignment explanation
Indices: 6081--6561 Score: 463
Period size: 172 Copynumber: 2.8 Consensus size: 171
6071 NNNNNNNNAG
* * * * * * *
6081 ATCAATTTTAAGAGTATAAAACCATTTAAATTGAGTAATAAGGCTCTTG-AAGAAATGGGTGACT
1 ATCAATTATGAGATTATAAAAACATTTAAAATGAGTAATAAAGCTTTTGAAAG-AATGGGTGACT
* * * * * * **
6145 ATAAATGGACTTCTCTTGT-GAATGATTGCCTTTTTCTTTTTGTTTGTTTAGGTAGACATTCAAT
65 ATAAATGGACTTTTCTT-TCCAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAGACATTCAAT
* ********** *
6209 TATAGTCTGTTTAAC-AAAAATATANNNNNNNNNNAACTTAAA
129 TCTAGTCTGTTTAACTAAAAATATACAAAAAATTCAAATTAAA
* * *
6251 ATCAATTATG-GCATTA-CAAAACTATTTAAAACGAGTAATAAAGCTTTTGAAAGTATGGGTGAC
1 ATCAATTATGAG-ATTATAAAAAC-ATTTAAAATGAGTAATAAAGCTTTTGAAAGAATGGGTGAC
* *
6314 TATAAATGGACTTTTCTTTCCAATGAATGCTTTTTTCTTTATATTTCTCAAGGTAAACATTCAAT
64 TATAAATGGACTTTTCTTTCCAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAGACATTCAAT
* *
6379 TCTAGTCTGTTTTAACTAAAAATGTACAAAAAATTCAAATTTAA
129 TCTAGTCTG-TTTAACTAAAAATATACAAAAAATTCAAATTAAA
* * * * * *
6423 GTCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAAT-AAGTCTTTTGAAGGAATAGGCGACT
1 ATCAATTATGAGATTATAAAAACATTTAAAATGAGTAATAAAG-CTTTTGAAAGAATGGGTGACT
* * * *
6487 ATAAATGGACTTTTCTTGCCAATGAATGCTCTCTTCTTTATGTTTCTCATGGTAGACA-TCAATT
65 ATAAATGGACTTTTCTTTCCAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAGACATTCAATT
6551 CTAGTCTGTTT
130 CTAGTCTGTTT
6562 TTAGATTATA
Statistics
Matches: 253, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
169 6 0.02
170 106 0.42
171 26 0.10
172 109 0.43
173 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.38
Consensus pattern (171 bp):
ATCAATTATGAGATTATAAAAACATTTAAAATGAGTAATAAAGCTTTTGAAAGAATGGGTGACTA
TAAATGGACTTTTCTTTCCAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAGACATTCAATTC
TAGTCTGTTTAACTAAAAATATACAAAAAATTCAAATTAAA
Found at i:6672 original size:131 final size:132
Alignment explanation
Indices: 6428--6693 Score: 349
Period size: 131 Copynumber: 2.0 Consensus size: 132
6418 TTTAAGTCAA
* *
6428 TTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGTCTTTTGAAGGAATAGGCGACTATAAAT
1 TTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGCGACTATAAAT
* * * * * *
6493 GGACTTTTCTTGCCAATGAATGCTCTCTTCTTTATGTTTCTCATGGTAGACA-TCAATTCTAGTC
66 GGACTTCTCTTACCAATGAATCCTCTCTTCTTTACGCTTCTCATGGTAGACATTCAATTATAGTC
6557 TG
131 TG
* * * * * *
6559 TTTTTAGATTATAAAACCATTTAAAGTGAGTGATAAGGGTTTTAAAGGAATCGGTGACTATAAAT
1 TTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGCGACTATAAAT
* *
6624 GGACTTCTGTTACCAATGAATACCT-TTTTCTTTACGCTTCTCGA-GGTAGACATTCAATTATAG
66 GGACTTCTCTTACCAATGAAT-CCTCTCTTCTTTACGCTTCTC-ATGGTAGACATTCAATTATAG
6687 TCTG
129 TCTG
6691 TTT
1 TTT
6694 AACAAAAAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
131 97 0.84
132 19 0.16
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (132 bp):
TTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGGCGACTATAAAT
GGACTTCTCTTACCAATGAATCCTCTCTTCTTTACGCTTCTCATGGTAGACATTCAATTATAGTC
TG
Found at i:8195 original size:172 final size:171
Alignment explanation
Indices: 7990--8378 Score: 397
Period size: 172 Copynumber: 2.3 Consensus size: 171
7980 TGCTCGAGGC
* *
7990 AGACATTCAATTATAGTCTGTTTAACAAAAAAAT-TA-AAAGAAAATTCAACTTAAAATCAATTA
1 AGACATTCAATTCTAGTCTGTTTAAC-AAAAAATGTACAAAG--AATTCAAATTAAAATCAATTA
* *
8053 CGGCATTACAAAACCATTTAAAGTAAGTAATAATG-TTGTTGAACGTATGGGTGACTATAAATAG
63 CGGCATTACAAAACCATTTAAAGTAAGTAATAAGGCTT-CTGAACGTATGGGTGACTATAAATAG
* * * *
8117 ACTTTTGTTGCCAATGAATACTTTTTTCTTAAAGTTTCTCATGGT
127 AATTTTCTTGCCAATAAATACTTTTTTCTTAAAGATTCTCATGGT
* *********
8162 AGACATTCAATTCTAGTCTGTTTGAACAAAAAATGTACAAAGAATTCAAATTTAAANNNNNNNNN
1 AGACATTCAATTCTAGTCTGTTT-AACAAAAAATGTACAAAGAATTCAAATTAAAATCAATTACG
******* * * *
8227 NNNNNNNAAAACCATTTAAAGTGAGTAATAAGGCTTCTGAAGGTATGGGTGACTATAAATGGAAT
65 GCATTACAAAACCATTTAAAGTAAGTAATAAGGCTTCTGAACGTATGGGTGACTATAAATAGAAT
* * *
8292 TTTCTTGCCAATAAATGCTTTTTTCTTCATGATTCTCATGGT
130 TTTCTTGCCAATAAATACTTTTTTCTTAAAGATTCTCATGGT
* * *
8334 AGACATTCAATTCTAGTCTATTTTAACAAAAATTGTATAAAGAAT
1 AGACATTCAATTCTAGTCT-GTTTAACAAAAAATGTACAAAGAAT
8379 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 34, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
172 164 0.92
173 10 0.06
174 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.33
Consensus pattern (171 bp):
AGACATTCAATTCTAGTCTGTTTAACAAAAAATGTACAAAGAATTCAAATTAAAATCAATTACGG
CATTACAAAACCATTTAAAGTAAGTAATAAGGCTTCTGAACGTATGGGTGACTATAAATAGAATT
TTCTTGCCAATAAATACTTTTTTCTTAAAGATTCTCATGGT
Found at i:8801 original size:171 final size:169
Alignment explanation
Indices: 8506--8824 Score: 428
Period size: 171 Copynumber: 1.9 Consensus size: 169
8496 NTGTTTCTAG
*
8506 AGGTAAACATTCAATTATAGTCTGTTTAACAAAAAATATAACAAAAATTAAATTAAAATCAATTA
1 AGGTAAACATTCAATTATAGTCTGTTTAACAAAAAATATAACAAAAATCAAATTAAAATCAATTA
* * *
8571 CGGTATTACAAATCCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATTGGTGACTATAAATGGG
66 CGGCATTACAAATCCATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAATGGA
*
8636 CTTCTCTTACCGATGAATGCCTTTTCTTTACATTTCTCT
131 CTTCTCTTACCAATGAATGCCTTTTCTTTACATTTCTCT
* * * *
8675 AGGTAGACATTGAATTATAGTCTGTTTAACAAAAAGTATGAA-AACAAATCCAACTTAAAATCAA
1 AGGTAAACATTCAATTATAGTCTGTTTAACAAAAAATAT-AACAA-AAAT-CAAATTAAAATCAA
* * * * *
8739 TTACGGCATTACAAAAT-GATTTAAAGCGATTTATAAGGCTTTTAAAGGTA-TGAGTGACTATAA
63 TTACGGCATTAC-AAATCCATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATTG-GTGACTATAA
* *
8802 ATGGACTTTTCTTGCCAATGAAT
126 ATGGACTTCTCTTACCAATGAAT
8825 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
169 38 0.29
170 8 0.06
171 79 0.61
172 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (169 bp):
AGGTAAACATTCAATTATAGTCTGTTTAACAAAAAATATAACAAAAATCAAATTAAAATCAATTA
CGGCATTACAAATCCATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATTGGTGACTATAAATGGA
CTTCTCTTACCAATGAATGCCTTTTCTTTACATTTCTCT
Done.