Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008100.1 Hibiscus syriacus cultivar Beakdansim tig00110630_pilon, 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: 1372717
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 7 of 7
Found at i:1294084 original size:21 final size:21
Alignment explanation
Indices: 1294058--1294106 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1294048 AAATTGGTTT
1294058 GAGTATGTGTACTTGAGTTAA
1 GAGTATGTGTACTTGAGTTAA
1294079 GAGTATGTGTACTTGAGTTAA
1 GAGTATGTGTACTTGAGTTAA
1294100 GAGTATG
1 GAGTATG
1294107 AAAGGGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.37
Consensus pattern (21 bp):
GAGTATGTGTACTTGAGTTAA
Found at i:1296038 original size:16 final size:17
Alignment explanation
Indices: 1296011--1296044 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1296001 TTCTTCATTC
1296011 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1296028 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
1296044 T
1 T
1296045 GATACCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:1300967 original size:53 final size:53
Alignment explanation
Indices: 1300891--1301014 Score: 158
Period size: 53 Copynumber: 2.3 Consensus size: 53
1300881 TACCTTGACA
* * * *
1300891 TTGTAAGATATTTCAAGAGATGGCCTCATGCCTAGGCGAAACACTTCTAGACC
1 TTGTAAGAGATTTCGAGAAATGGCCTCATGCCTAGGCAAAACACTTCTAGACC
* * *
1300944 TTGTAAGAGATTTCGAGAAATGGCCTGATGCCTAGGTAAAACACTTCTATACC
1 TTGTAAGAGATTTCGAGAAATGGCCTCATGCCTAGGCAAAACACTTCTAGACC
* * *
1300997 TTATAAGAGCTTTTGAGA
1 TTGTAAGAGATTTCGAGA
1301015 GATTACCGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (53 bp):
TTGTAAGAGATTTCGAGAAATGGCCTCATGCCTAGGCAAAACACTTCTAGACC
Found at i:1303130 original size:21 final size:20
Alignment explanation
Indices: 1303102--1303140 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1303092 CATTGTAAGA
1303102 ATTTATGGCCTT-AACAAAAG
1 ATTTATGG-CTTCAACAAAAG
1303122 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
1303141 GACTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Found at i:1311149 original size:16 final size:15
Alignment explanation
Indices: 1311124--1311154 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1311114 ATATTCGAAT
1311124 CAAACAAGGGTTGTA
1 CAAACAAGGGTTGTA
1311139 CAAACCAAGGGTTGTA
1 CAAA-CAAGGGTTGTA
1311155 GTTAACGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (15 bp):
CAAACAAGGGTTGTA
Found at i:1311289 original size:209 final size:211
Alignment explanation
Indices: 1310929--1311338 Score: 797
Period size: 209 Copynumber: 1.9 Consensus size: 211
1310919 CAACAGTCTG
1310929 ACAAACCAAGGGTTGTAGTTAACGCTGAGTAGTTTTTCCATAGCAACCGTCTTAGAATACTCAGT
1 ACAAACCAAGGGTTGTAGTTAACGCTGAGTAGTTTTTCCATAGCAACCGTCTTAGAATACTCAGT
1310994 AATCCTGTCGGGCAATCTAAGCATATCATAACAAATCCTTCCAGACATAGAATAATTTCTCCCCA
66 AATCCTGTCGGGCAATCTAAGCATATCATAACAAATCCTTCCAGACATAGAATAATTTCTCCCCA
1311059 TAGCAAGACCAACTTAAGTGCTC-TGAAAAGTCTG-ATATGTGAGGTTATTCTAAATATATTCGA
131 TAGCAAGACCAACTTAAGTGCTCGTGAAAAGTCTGAATATGTGAGGTTATTCTAAATATATTCGA
1311122 ATCAAACAAGGGTTGT
196 ATCAAACAAGGGTTGT
1311138 ACAAACCAAGGGTTGTAGTTAACGCTGAGTAGTTTTTCCATAGCAACCGTCTTAGAATACTCAGT
1 ACAAACCAAGGGTTGTAGTTAACGCTGAGTAGTTTTTCCATAGCAACCGTCTTAGAATACTCAGT
1311203 AATCCTGTCGGGCAATCTAAGCATATCATAACAAATCCTTCCAGACATAGAATAATTTCTCCCCA
66 AATCCTGTCGGGCAATCTAAGCATATCATAACAAATCCTTCCAGACATAGAATAATTTCTCCCCA
1311268 TAGCAAGACCAACTTAAGTGCTCTGTGAAAAGTCTGAATATGTGAGGTTATTCTAAATATATTCG
131 TAGCAAGACCAACTTAAGTGCTC-GTGAAAAGTCTGAATATGTGAGGTTATTCTAAATATATTCG
1311333 AATCAA
195 AATCAA
1311339 CATTTTCTTT
Statistics
Matches: 198, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
209 153 0.77
211 11 0.06
212 34 0.17
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (211 bp):
ACAAACCAAGGGTTGTAGTTAACGCTGAGTAGTTTTTCCATAGCAACCGTCTTAGAATACTCAGT
AATCCTGTCGGGCAATCTAAGCATATCATAACAAATCCTTCCAGACATAGAATAATTTCTCCCCA
TAGCAAGACCAACTTAAGTGCTCGTGAAAAGTCTGAATATGTGAGGTTATTCTAAATATATTCGA
ATCAAACAAGGGTTGT
Found at i:1337485 original size:35 final size:35
Alignment explanation
Indices: 1337389--1337501 Score: 147
Period size: 34 Copynumber: 3.2 Consensus size: 35
1337379 TGGCCACGAC
*
1337389 CTTATGTGTCATAGCACTAGAGTGTATACTCAAGACA
1 CTTA-GTG-CATAGCACTAGAGTGTATACCCAAGACA
* * *
1337426 CTTAGTGCA-GGCGCTAGAGTGTATACCCAATACA
1 CTTAGTGCATAGCACTAGAGTGTATACCCAAGACA
* *
1337460 CTTAGTGCATAACACTAGAGTGTATACGCAAGACA
1 CTTAGTGCATAGCACTAGAGTGTATACCCAAGACA
1337495 CTTAGTG
1 CTTAGTG
1337502 TATATGGTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 30 0.45
35 29 0.44
36 3 0.05
37 4 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (35 bp):
CTTAGTGCATAGCACTAGAGTGTATACCCAAGACA
Found at i:1341974 original size:131 final size:132
Alignment explanation
Indices: 1341740--1342011 Score: 483
Period size: 131 Copynumber: 2.1 Consensus size: 132
1341730 TAAGATTTTA
*
1341740 ATTGATTTTTGGAGTAAATTAATGTACTGATTTCTTGAATTGGTTTTGAGGTTTTCTTAATGAAA
1 ATTGATTTTTGGAGTAAATTAATGTACTGATTTCTTGAATTGATTTTGAGGTTTTCTTAATGAAA
1341805 TTGATTTGTTATAGGAGTGATTATAATCATATTAAATCAG-TTTTTTTGATTTCAAATGATTTGG
66 TTGATTTGTTATAGGAGTGATTATAATCATATTAAATCAGTTTTTTTTGATTTCAAATGATTTGG
1341869 AT
131 AT
** *
1341871 ATTGATTTTTGGAGTAAATTAATGTGTTGATTTCTTGAATTGATTTTGATGTTTTCTTAATGAAA
1 ATTGATTTTTGGAGTAAATTAATGTACTGATTTCTTGAATTGATTTTGAGGTTTTCTTAATGAAA
*
1341936 TTGATTTGTTATAGGAGTGATTATAATCATATTAAATCAGTTTTTTTTTTATTTCAAATGATTTG
66 TTGATTTGTTATAGGAGTGATTATAATCATATTAAATCAG-TTTTTTTTGATTTCAAATGATTTG
1342001 GAT
130 GAT
1342004 ATTGATTT
1 ATTGATTT
1342012 CTTGAAAACA
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
131 101 0.75
133 33 0.25
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.50
Consensus pattern (132 bp):
ATTGATTTTTGGAGTAAATTAATGTACTGATTTCTTGAATTGATTTTGAGGTTTTCTTAATGAAA
TTGATTTGTTATAGGAGTGATTATAATCATATTAAATCAGTTTTTTTTGATTTCAAATGATTTGG
AT
Found at i:1347168 original size:34 final size:34
Alignment explanation
Indices: 1347125--1347257 Score: 169
Period size: 34 Copynumber: 3.9 Consensus size: 34
1347115 TATAATAGCA
*
1347125 CTAGAGTGTATACCCAAGACACTTGGTGTAGGTG
1 CTAGAGTGTATACCCAAGACACTTAGTGTAGGTG
* *
1347159 CTAGAGTGTATACTCAAGACACTTAGTGCAGGTG
1 CTAGAGTGTATACCCAAGACACTTAGTGTAGGTG
* * *
1347193 CTAGAGTGCATACCCAAGACACTTAGTGCATA-ATA
1 CTAGAGTGTATACCCAAGACACTTAGTG--TAGGTG
* *
1347228 CTAGAGTTTATACCCAATACACTTAGTGTA
1 CTAGAGTGTATACCCAAGACACTTAGTGTA
1347258 TACGGTGGGT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.02
34 57 0.66
35 26 0.30
36 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (34 bp):
CTAGAGTGTATACCCAAGACACTTAGTGTAGGTG
Done.