Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399185.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2455.0, 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: 12747
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.28
Warning! 3014 characters in sequence are not A, C, G, or T
Found at i:2437 original size:171 final size:168
Alignment explanation
Indices: 1826--2681 Score: 575
Period size: 171 Copynumber: 5.0 Consensus size: 168
1816 NNNNNNNNNN
* * * *
1826 AAAGCGAGTAATGAGGTTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTG-TCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATG-GTGACTATAAATAGACTTTTCTTGCT-AATGAAT
** * ** * * * * *
1890 GTTTTTTTTTTCACATTTCTTAG-GGTAAACATTCAATTATAATATGTTTTAACAAAAAAAT-T-
64 ACTTTTTCTTT-ATGTTT-TTCGAGGTAGACATTCAATTATAATCTGTTCTAAC-CAAAAATGTA
* * * * * * *
1952 AAGAAATTGAACTTCAAATCAATT-TTAGGTTTATAAAACTATTT
126 AAAAAATTCAAC-TAAAATTAATTATGA-GATTATAAAACCATTT
* * * * * *
1996 AAAGCTAGTAATAAGGCTTTTGAAGGAATGTGTGACTGTAAAT-GAATTTTTTTTG-TCAATAAA
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATG-GTGACTATAAATAG-ACTTTTCTTGCT-AATGAA
* * * ** * * * *
2059 TATCTTTTTCTTCACGTTTCTCTCGGTAAACATTCAATTATAGTCTGTTTTAACC-TAAATGTAA
63 TA-CTTTTTCTTTATGTTTTTCGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTAA
* **********
2123 AAAAATT-AACTTAAAATCAATTATNNNNNNNNNNAACCATTT
127 AAAAATTCAAC-TAAAATTAATTATGAGATTATAAAACCATTT
* * * * * * *
2165 AAAAC-ATGTAATAAGGCTTTTGAATGAATGGATGACTATAAAT-GAAATTTTTTTACCAATGAA
1 AAAGCGA-GTAATAAGGCTTTTAAAGGAATGG-TGACTATAAATAG-ACTTTTCTTGCTAATGAA
* * *
2228 TGCTTTTTCTTTATGTTTTTCAAGGTAGACATTCAATTATAGTCTGTTCTAACCAAAAATGTAAA
63 TACTTTTTCTTTATGTTTTTCGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTAAA
********* *
2293 AAAATTCAACTNNNNNNNNNNTATGAGATTATAAAACTATTT
128 AAAATTCAACT-AAAATTAATTATGAGATTATAAAACCATTT
*
2335 AAAGCGAGTAATAAGGCTTTTAAAGGAATGTGTGACTCTAAATAGACTTTTCTTGCTAATGAATA
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATG-GTGACTATAAATAGACTTTTCTTGCTAATGAATA
* * * *
2400 TCTTTTTCTTTACGTTTTTCGAGGTAGCCATTCAATTATAATCTGTTCTAACCAAAAATGCAGAA
65 -CTTTTTCTTTATGTTTTTCGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTAAAA
2465 AAATTCAACCTAAAATTAATTATGAGATTATAAAACCATTT
129 AAATTCAA-CTAAAATTAATTATGAGATTATAAAACCATTT
* **********
2506 AAAGCGAGCAATAAGNNNNNNNNNNGAATGGGTGACTATAAATAGACTTTTCTTGCTAATGAATA
1 AAAGCGAGTAATAAGGCTTTTAAAGGAAT-GGTGACTATAAATAGACTTTTCTTGCTAATGAATA
* * * * *
2571 CTTTTTTCTTCATATTTGTT-GAGCTAGACATTCAATTATAAACTGTTTTAACCAAAAATGTAAA
65 C-TTTTTCTTTATGTTT-TTCGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTAAA
* * * * * *
2635 AAAATTTAACTAAAAATAAATCATAAGTTTATAAAACTATTT
128 AAAATTCAACT-AAAATTAATTATGAGATTATAAAACCATTT
2677 AAAGC
1 AAAGC
2682 AAGTTCTCCA
Statistics
Matches: 544, Mismatches: 121, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
168 51 0.09
169 92 0.17
170 161 0.30
171 235 0.43
172 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.36
Consensus pattern (168 bp):
AAAGCGAGTAATAAGGCTTTTAAAGGAATGGTGACTATAAATAGACTTTTCTTGCTAATGAATAC
TTTTTCTTTATGTTTTTCGAGGTAGACATTCAATTATAATCTGTTCTAACCAAAAATGTAAAAAA
ATTCAACTAAAATTAATTATGAGATTATAAAACCATTT
Found at i:2997 original size:170 final size:171
Alignment explanation
Indices: 2762--3181 Score: 428
Period size: 171 Copynumber: 2.5 Consensus size: 171
2752 NNNNNNNNNN
** * * * *
2762 ATTATAAAACCATTTAAAGTGAGTAATATGGCTTTTGAAA-GAATGAGA-CACTATAAATAGACT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGC-TTTGAAAGGCATG-GATGACTATAAATGGACT
* * * * **
2825 TTTCTTCCCAATGAAT-G-CTTT-CTCTACACGTTTCTCAAGGTAGGTATTCAATTATAG-TCTA
64 TTTCGTACCAATGAATGGCCTTTGCT-T-CACGTTCCCCAAGGTAGACATTCAATTATAGCT-TA
* * *
2886 TTTTAA-TGCAAAATGTAAAAACATTCAACTTAAAATCAATTATCAG
126 TTTTAACT-AAAAAAGTAAAAACATTCAACTTAAAATCAATAATCAG
* * * * *
2932 ATTATAAATCCATTTCAAGCAAGTAATAGGGCTTTCG-ATGGC-TTGAGTGACTATAAATGGACT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-GAAAGGCATGGA-TGACTATAAATGGACT
* * * *
2995 TTTCGTACCAATGGATGGCCTTTGCTTCATGTTCCCCAAGGTAGACATTCAATTGTAGCTTTTTT
64 TTTCGTACCAATGAATGGCCTTTGCTTCACGTTCCCCAAGGTAGACATTCAATTATAGCTTATTT
* *
3060 TAACTAAAAAAGTAAAAACTTTCAACTTAAAATCAATAATGAG
129 TAACTAAAAAAGTAAAAACATTCAACTTAAAATCAATAATCAG
* *
3103 ATTATAAAACCATTTAAAGCCAGTAATAAGGCTTTGAAAGGCATGGATGACTATAAATGGAGTTT
1 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTGAAAGGCATGGATGACTATAAATGGA-CTT
*
3168 TTC-TACTAATGAAT
65 TTCGTACCAATGAAT
3182 CACGTTTTCT
Statistics
Matches: 204, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
168 2 0.01
169 5 0.02
170 56 0.27
171 124 0.61
172 15 0.07
173 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (171 bp):
ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTGAAAGGCATGGATGACTATAAATGGACTTT
TCGTACCAATGAATGGCCTTTGCTTCACGTTCCCCAAGGTAGACATTCAATTATAGCTTATTTTA
ACTAAAAAAGTAAAAACATTCAACTTAAAATCAATAATCAG
Found at i:3248 original size:171 final size:172
Alignment explanation
Indices: 2895--3286 Score: 427
Period size: 171 Copynumber: 2.3 Consensus size: 172
2885 ATTTTAATGC
* * *
2895 AAAATGTAAAAACATTCAACTTAAAATCAATTATCAGATTATAAATCCATTTCAAGCAAGTAATA
1 AAAATGTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * * **
2960 GGGCTTTCGATGGCTTGAGTGACTATAAATGGACTTTTCGTACCAATGGATGGCCTTTGCTTCAT
66 AGGCTTTCGAAGGCTGGAGTGACTATAAATGGACTTTTCGTACCAATGAATCACCTTTGCTTCAT
* * * * * *
3025 GTTCCCCAAGGTAGACATTCAATTGTAGCTTTTTTTAACTAA
131 GTTCCCAAAGGTAAACACTCAATTATAACTTATTTTAACTAA
* * *
3067 AAAA-GTAAAAACTTTCAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCCAGTAATA
1 AAAATGTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
* * * *
3131 AGGCTTT-GAAAGGCATGGA-TGACTATAAATGGAGTTTTTC-TACTAATGAATCACGTTTTCTT
66 AGGCTTTCG-AAGGC-TGGAGTGACTATAAATGGA-CTTTTCGTACCAATGAATCACCTTTGCTT
* * **
3193 CATGTTTCTAAAGGTAAACACTCAATTATAAAC-TATTTT-GGTAA
128 CATGTTCCCAAAGGTAAACACTCAATTAT-AACTTATTTTAACTAA
* * * * *
3237 AAAATGTAAAAAAATTCAACTGAAAATTAATTATGAGATCATAAGACCAT
1 AAAATGTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
3287 NNNNNNNNNN
Statistics
Matches: 182, Mismatches: 33, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
170 8 0.04
171 160 0.88
172 14 0.08
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (172 bp):
AAAATGTAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATA
AGGCTTTCGAAGGCTGGAGTGACTATAAATGGACTTTTCGTACCAATGAATCACCTTTGCTTCAT
GTTCCCAAAGGTAAACACTCAATTATAACTTATTTTAACTAA
Found at i:3364 original size:21 final size:21
Alignment explanation
Indices: 3339--3380 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3329 AATAGACTTC
* *
3339 TCTTATTAATGGATGTGTTTT
1 TCTTACTAATGGATGGGTTTT
3360 TCTTACTAATGGATGGGTTTT
1 TCTTACTAATGGATGGGTTTT
3381 ACATCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.52
Consensus pattern (21 bp):
TCTTACTAATGGATGGGTTTT
Found at i:7493 original size:171 final size:170
Alignment explanation
Indices: 7056--7578 Score: 478
Period size: 171 Copynumber: 3.1 Consensus size: 170
7046 NNNNNNNNNN
* * ** * * *
7056 TAAATGGTTTTATAA-ACTCATAATTTATTTTTAGTTGAATTTTTTTTCATTTTTGGTTAAAACA
1 TAAATAGTTTTATAATA-TCATAATTGATTTAAAGTTGAATTGTTTTACATTTTTAGTTAAAACA
** * * * ** *
7120 GGTTATAATTGAATGTCTAC-CTCTAGAAATGTGTAGAAAAAGGCATTCATTGGCAAGAAAAGTC
65 GACTATAACTGAACGT-TACTCTCAAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTC
* * *
7184 TATTTATAATCACCCATTCCTTCGC-AAGCCTTATTACTTGCTT
128 CATTTATAGTCACCCATTCCTTC-CAAAGCCTTATTACTCGCTT
* ** * * * * *
7227 TAAATGGTTTTATAATATCATAATTGATTTTTAGTTGAATTTTTTTATATTTTTATTTAAAATAT
1 TAAATAGTTTTATAATATCATAATTGATTTAAAGTTGAATTGTTTTACATTTTTAGTTAAAACAG
* * * * *
7292 ATTATAACTGAACGTTTCTCTCAGGAAACATGATGAAAAAGTCATTCATTGGCTAGAAAAGTCCA
66 ACTATAACTGAACGTTACTCTCAAGAAACATGAAGAAAAAG-CATTCATTGGCAAGAAAAGTCCA
* ** *
7357 TTTATAGTCACCTACACCTTCCAAAGCCTTATTACTCGTTT
130 TTTATAGTCACCCATTCCTTCCAAAGCCTTATTACTCGCTT
* *
7398 TAAATAGTTTTATAATCTCATTATTGATTTAAAGTTGAATTGTTTTACATTTTTAGTTAAAACAG
1 TAAATAGTTTTATAATATCATAATTGATTTAAAGTTGAATTGTTTTACATTTTTAGTTAAAACAG
* ********* * *
7463 ACTGTAANNNNNNNNNNAC-CTCAAGAAACATGAAGAAAAAAGCATTCATTGGCAAAAAAAGACC
66 ACTATAA-CTGAACGTTACTCTCAAGAAACATGAAG-AAAAAGCATTCATTGGCAAGAAAAGTCC
* ** *
7527 ATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTCACTT
129 ATTTATAGTCACCCATTCCTTCCAAAGCCTTATTACTCGCTT
7569 TAAATAGTTT
1 TAAATAGTTT
7579 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 60, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
170 4 0.01
171 274 0.96
172 8 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.38
Consensus pattern (170 bp):
TAAATAGTTTTATAATATCATAATTGATTTAAAGTTGAATTGTTTTACATTTTTAGTTAAAACAG
ACTATAACTGAACGTTACTCTCAAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCAT
TTATAGTCACCCATTCCTTCCAAAGCCTTATTACTCGCTT
Found at i:9353 original size:173 final size:170
Alignment explanation
Indices: 8876--9409 Score: 551
Period size: 171 Copynumber: 3.1 Consensus size: 170
8866 NNNNNNNNNN
* * * * * *
8876 TTTTATAATTTCATAATTGATTTTAAGTTGAA-TTGTTTTATATTTTTCA-TTAAAATATACTAT
1 TTTTATAATCTCAAAATTGATTTTAAGTTCAACTT-TTTTACATTTTT-AGTAAAAATAGACTAT
* * ** * * *
8939 AATGGAATGCTTACCTAAAAAAACGTGCAGAAAAAGACATTGATTGAG-AAGAAAAGTCTATTTA
64 AATTGAAAGCTTACCTTGAGAAACGTGAAGAAAAAGACATTCATTG-GCAAGAAAAGTCTATTTA
** * * **
9003 TAGTCACCCATTTATTCAAAAGCCTTATTACTCGCTTGAAATAA
128 TAGTCACCCATTCCTTCAAAAGCCTTATTAC-CACTTTAAATGG
* * * * *
9047 TGTTATAATTTCACAATTGATTTTAAGTTGAACTTTTTTACATTTTTGGTAAAAATAGACTATAA
1 TTTTATAATCTCAAAATTGATTTTAAGTTCAACTTTTTTACATTTTTAGTAAAAATAGACTATAA
* * * *
9112 TTGAAAGCTTACCTTGAGAAACGTGAAGAAAAAAACATTCGTTGACAAAAAAAGTCTATTTATAG
66 TTGAAAGCTTACCTTGAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATTTATAG
*
9177 TCACCCATTCCTTGAAAAGCCTTATTACCACCTTTAAATGG
131 TCACCCATTCCTTCAAAAGCCTTATTACCA-CTTTAAATGG
* * * *
9218 TTTTATTATCTCAAAATTGATTTTAAGTTCAATTTATTTTTACATTTTTAGTCAAAACT-GATTA
1 TTTTATAATCTCAAAATTGATTTTAAGTTCAA-CT-TTTTTACATTTTTAGT-AAAAATAGACTA
* * *
9282 TAATT-AAATG-TCTACCTTGAGAAACGTGAAGAAAAAGGCGTTCATTGGCAAGAAAAGT-TCAG
63 TAATTGAAA-GCT-TACCTTGAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAAGTCT-AT
* * *
9344 TTATAGTCACCTATTCCTTCAAAAGACTTATTATTCACTTTAAATGG
125 TTATAGTCACCCATTCCTTCAAAAGCCTTATTA-CCACTTTAAATGG
*
9391 TTTTATAATCTCATAATTG
1 TTTTATAATCTCAAAATTG
9410 NNNNNNNNNN
Statistics
Matches: 306, Mismatches: 46, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
170 1 0.00
171 167 0.55
172 8 0.03
173 123 0.40
174 7 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (170 bp):
TTTTATAATCTCAAAATTGATTTTAAGTTCAACTTTTTTACATTTTTAGTAAAAATAGACTATAA
TTGAAAGCTTACCTTGAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAAGTCTATTTATAG
TCACCCATTCCTTCAAAAGCCTTATTACCACTTTAAATGG
Done.