Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400216.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3427.0, 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: 2442
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Found at i:1640 original size:55 final size:54
Alignment explanation
Indices: 1458--1840 Score: 306
Period size: 55 Copynumber: 7.0 Consensus size: 54
1448 ATTTTCCCCC
* * * *
1458 AATCCCACATCACTTAGGAAATCG-GAATCTGGCTAATATATATGAGGGCTTCCGA
1 AATCCCACATCGCTTAGGAAA--GAGAATCTGGGTAATATATAGGAGTGCTTCCGA
* * * * * * * * * *
1513 AAT-CCACCGTCACTTAGAAAAGCGGA-GTGATGGTCATACATATGAGTCCTTCCGA
1 AATCCCA-CATCGCTTAGGAAAGAGAATCTG--GGTAATATATAGGAGTGCTTCCGA
** * * * * * *
1568 AATCCCACATCTTTTAGGAGATAG-GAATCCGTGTGATATACATGAGGGCTTCCGA
1 AATCCCACATCGCTTAGGA-A-AGAGAATCTGGGTAATATATAGGAGTGCTTCCGA
*
1623 AATCCCACATCGCTTAGGAAAGCAGATTCTGGGTAATATATAGGAGTGCTTCCGA
1 AATCCCACATCGCTTAGGAAAG-AGAATCTGGGTAATATATAGGAGTGCTTCCGA
* *
1678 AATCCCACATCGCTTAGGAAAGTGTAAGCTGGGTAATATATAGGAGTGCTTCCGA
1 AATCCCACATCGCTTAGGAAAGAG-AATCTGGGTAATATATAGGAGTGCTTCCGA
* * * ** *
1733 AATCCCACATCACTTAGGAAAGTGGAGTCTGGGTAATATATATTAGTTCTTCCGA
1 AATCCCACATCGCTTAGGAAAG-AGAATCTGGGTAATATATAGGAGTGCTTCCGA
* * * * **
1788 AATCCCACATCCCTTAGGAAAGTGGAGTCTGGGTAGTATATATTAGTGCTTCC
1 AATCCCACATCGCTTAGGAAAG-AGAATCTGGGTAATATATAGGAGTGCTTCC
1841 AAAACAAAAA
Statistics
Matches: 272, Mismatches: 44, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
53 5 0.02
54 7 0.03
55 250 0.92
56 7 0.03
57 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (54 bp):
AATCCCACATCGCTTAGGAAAGAGAATCTGGGTAATATATAGGAGTGCTTCCGA
Found at i:1732 original size:165 final size:164
Alignment explanation
Indices: 1458--1840 Score: 412
Period size: 165 Copynumber: 2.3 Consensus size: 164
1448 ATTTTCCCCC
* * * *
1458 AATCCCACATCACTTAGGAAATCGGAATCTGGCTAATATATATGAGGGCTTCCGAAATCCACCGT
1 AATCCCACATCACTTAGGAAAGCGGAATCTGGGTAATATATATGAGTGCTTCCGAAATCCACCAT
* * * ** *
1523 CACTTAGAAAAGCGGAGTGATGGTCATACATATGAGTCCTTCCGAAATCCCACATCTTTTAGGAG
66 CACTTAGAAAAGCGAAGTGA-GGTAATACATAGGAGTCCTTCCGAAATCCCACATCACTTAGGAA
* *
1588 A-TAGGAATCCGTGTGATATACATGAGGGCTTCCGA
130 AGT-GGAATCCGGGTAATATACATGAGGGCTTCCGA
* * * *
1623 AATCCCACATCGCTTAGGAAAGCAGATTCTGGGTAATATATAGGAGTGCTTCCGAAATCC-CACA
1 AATCCCACATCACTTAGGAAAGCGGAATCTGGGTAATATATATGAGTGCTTCCGAAATCCAC-CA
* * * * *
1687 TCGCTTAGGAAAGTGTAAGCTG-GGTAATATATAGGAGTGCTTCCGAAATCCCACATCACTTAGG
65 TCACTTAGAAAAGCG-AAG-TGAGGTAATACATAGGAGTCCTTCCGAAATCCCACATCACTTAGG
* * * * **
1751 AAAGTGGAGTCTGGGTAATATATATTAGTTCTTCCGA
128 AAAGTGGAATCCGGGTAATATACATGAGGGCTTCCGA
* * * * *
1788 AATCCCACATCCCTTAGGAAAGTGGAGTCTGGGTAGTATATATTAGTGCTTCC
1 AATCCCACATCACTTAGGAAAGCGGAATCTGGGTAATATATATGAGTGCTTCC
1841 AAAACAAAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
164 1 0.01
165 174 0.97
166 3 0.02
167 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (164 bp):
AATCCCACATCACTTAGGAAAGCGGAATCTGGGTAATATATATGAGTGCTTCCGAAATCCACCAT
CACTTAGAAAAGCGAAGTGAGGTAATACATAGGAGTCCTTCCGAAATCCCACATCACTTAGGAAA
GTGGAATCCGGGTAATATACATGAGGGCTTCCGA
Found at i:1808 original size:110 final size:109
Alignment explanation
Indices: 1458--1840 Score: 396
Period size: 110 Copynumber: 3.5 Consensus size: 109
1448 ATTTTCCCCC
* *
1458 AATCCCACATCACTTAGGAAA-TCGGAATCTGGCTAATATATATGAGGGCTTCCGAAAT-CCACC
1 AATCCCACATCACTTAGGAAAGT--GAAGCTGGGTAATATATATGAGGGCTTCCGAAATCCCA-C
* * * * *
1521 GTCACTTAGAAAAGCGGAGTGAT-GGTCATACATATGAGTCCTTCCGA
63 ATCACTTAGGAAAGCGGAGT-CTGGGTAATATATATGAGTCCTTCCGA
** * * * * *
1568 AATCCCACATCTTTTAGGAGATAG-GAATCCGTGTGATATACATGAGGGCTTCCGAAATCCCACA
1 AATCCCACATCACTTAGGA-A-AGTGAAGCTGGGTAATATATATGAGGGCTTCCGAAATCCCACA
* * * * *
1632 TCGCTTAGGAAAGCAGATTCTGGGTAATATATAGGAGTGCTTCCGA
64 TCACTTAGGAAAGCGGAGTCTGGGTAATATATATGAGTCCTTCCGA
* * *
1678 AATCCCACATCGCTTAGGAAAGTGTAAGCTGGGTAATATATAGGAGTGCTTCCGAAATCCCACAT
1 AATCCCACATCACTTAGGAAAGTG-AAGCTGGGTAATATATATGAGGGCTTCCGAAATCCCACAT
* * *
1743 CACTTAGGAAAGTGGAGTCTGGGTAATATATATTAGTTCTTCCGA
65 CACTTAGGAAAGCGGAGTCTGGGTAATATATATGAGTCCTTCCGA
* * * * *
1788 AATCCCACATCCCTTAGGAAAGTGGAGTCTGGGTAGTATATATTAGTGCTTCC
1 AATCCCACATCACTTAGGAAAGTGAAG-CTGGGTAATATATATGAGGGCTTCC
1841 AAAACAAAAA
Statistics
Matches: 227, Mismatches: 38, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
108 2 0.01
109 5 0.02
110 215 0.95
111 4 0.02
112 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (109 bp):
AATCCCACATCACTTAGGAAAGTGAAGCTGGGTAATATATATGAGGGCTTCCGAAATCCCACATC
ACTTAGGAAAGCGGAGTCTGGGTAATATATATGAGTCCTTCCGA
Found at i:2185 original size:225 final size:225
Alignment explanation
Indices: 1781--2227 Score: 633
Period size: 225 Copynumber: 2.0 Consensus size: 225
1771 TATATTAGTT
* * *
1781 CTTCCGAAATCCCACATCCCTTAGGAAAGTGGAGTCTGGGTAGTATATATTAGTGCTTCCAAAAC
1 CTTCCGAAATCCCACATCCCTCAGGAAAGTGGAGTCTGGGTAATATATATGAGTGCTTCCAAAAC
* *
1846 AAAAAGCCTGTGTTCGGAGAAAGGAGAGATGGTTGGCATCTCTCCTGACTGCGTCGAGAACAGCC
66 AAAAAGCCTGTGTTCGGAGAAAGGAGAGATGGTTGGCATCTCCCCTGACAGCGTCGAGAACAGCC
* * * * *
1911 CTTGGGCTGATCTGTGAGCAACACATTCGGTTAAGACTCTCCCCCTTCAAGGTGGATCCCTAGAC
131 CTCGGGCTGACCTGTGACCAACACATTCGGTTAAGACTCTCCACCTTCAAGGTGGATCCCTAAAC
*
1976 CCATTTTTTCTTTTTGTCTTGTAAATCGTG
196 ACATTTTTTCTTTTTGTCTTGTAAATCGTG
* * *
2006 CTTCCGAAATCCCACATCGCTCAGGAAAGTGGAGTCTGGGTAATATATATGAGTGCTTCCTATAC
1 CTTCCGAAATCCCACATCCCTCAGGAAAGTGGAGTCTGGGTAATATATATGAGTGCTTCCAAAAC
** * * * *
2071 AATGAGCCTGTGTTCGTAGATAGGAGAGATGGTTGGCATCTCCCCTGACAGGGTCGGGAACAGCC
66 AAAAAGCCTGTGTTCGGAGAAAGGAGAGATGGTTGGCATCTCCCCTGACAGCGTCGAGAACAGCC
* * * * * **
2136 CTCGGGCTTACCTGTTACCAACACATTCTGTTAAGGCTTTCCACCTTCAAGGTGGATTTCTAAAC
131 CTCGGGCTGACCTGTGACCAACACATTCGGTTAAGACTCTCCACCTTCAAGGTGGATCCCTAAAC
**
2201 ATTTTTTTTCTTTTTGTCTTGTAAATC
196 ACATTTTTTCTTTTTGTCTTGTAAATC
2228 CAAGATAATT
Statistics
Matches: 193, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
225 193 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (225 bp):
CTTCCGAAATCCCACATCCCTCAGGAAAGTGGAGTCTGGGTAATATATATGAGTGCTTCCAAAAC
AAAAAGCCTGTGTTCGGAGAAAGGAGAGATGGTTGGCATCTCCCCTGACAGCGTCGAGAACAGCC
CTCGGGCTGACCTGTGACCAACACATTCGGTTAAGACTCTCCACCTTCAAGGTGGATCCCTAAAC
ACATTTTTTCTTTTTGTCTTGTAAATCGTG
Done.