Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007199.1 Hibiscus syriacus cultivar Beakdansim tig00018993_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: 46562
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10802 original size:137 final size:138
Alignment explanation
Indices: 10555--10810 Score: 433
Period size: 137 Copynumber: 1.9 Consensus size: 138
10545 TACCGAAGTG
**
10555 TCGAAATGGAAATTCACAAACTCATTATGAATTTCATGGATGCACACATAGTGTCAAAAGTACAC
1 TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCAAAAGTACAC
* *
10620 ATAGTATTGATACGAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATACATA
66 ATAGTACTGATACGAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACTTTTATACATA
10685 ATTGTATA
131 ATTGTATA
* * *
10693 TCGAAATGGTAATTCACAAACTCATTATGAATACCATGGTTGCACAC-TAGTGTCGAAAGTACAC
1 TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCAAAAGTACAC
*
10757 ATAGTACTGATACGAAAATGCACCATTATGCATTAAACCAAATCGATCGATAAC
66 ATAGTACTGATACGAAAATGCACCATTATGCATTAAACAAAATCGATCGATAAC
10811 CATTACATAC
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
137 67 0.61
138 43 0.39
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (138 bp):
TCGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTCAAAAGTACAC
ATAGTACTGATACGAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACTTTTATACATA
ATTGTATA
Found at i:17468 original size:19 final size:19
Alignment explanation
Indices: 17444--17513 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
17434 GGAACACTTA
17444 GTGCATCGGTGCACCAAGT
1 GTGCATCGGTGCACCAAGT
17463 GTGCATCGGTGCACCAAGT
1 GTGCATCGGTGCACCAAGT
17482 GTGCATCGGTGCACCAAGT
1 GTGCATCGGTGCACCAAGT
*
17501 GTGCATCGATGCA
1 GTGCATCGGTGCA
17514 TAAAATACAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.21
Consensus pattern (19 bp):
GTGCATCGGTGCACCAAGT
Found at i:17556 original size:64 final size:63
Alignment explanation
Indices: 17482--17659 Score: 207
Period size: 64 Copynumber: 2.8 Consensus size: 63
17472 TGCACCAAGT
* * * * *
17482 GTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATACATTCGATGTTTGAA-AATAGCCTAA
1 GTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCAA
* *
17546 GTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
1 GTGCATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAA
* * *
17610 GTGCATCGATGCATAGAGAGTGCATCAATGCATGAAATGCATTCGATGTT
1 GTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
17660 CAATTTATTC
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
62 1 0.01
64 94 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
GTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAA
Found at i:20346 original size:23 final size:23
Alignment explanation
Indices: 20316--20375 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
20306 TGCATGACCC
*
20316 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGGTGCACATTCAAGG
20339 TGTGCATCGGTGCACATTCAAGG
1 TGTGCATCGGTGCACATTCAAGG
*
20362 TGTGTATCGGTGCA
1 TGTGCATCGGTGCA
20376 TCAACATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (23 bp):
TGTGCATCGGTGCACATTCAAGG
Found at i:26332 original size:93 final size:93
Alignment explanation
Indices: 26133--26324 Score: 357
Period size: 93 Copynumber: 2.1 Consensus size: 93
26123 GGGAGTGTCG
*
26133 GTGCATCGATGCATGACCATAGTGCATCGATGCATCAGTGTAAAATTCAAATATTTTGACTGTTG
1 GTGCATCGATGCATGACCATAGTGCATCGATGCATCAGTGTAAAATTCAAATATTTTGACCGTTG
26198 GAACACTTAGTGCATCGGTGCACCAAGT
66 GAACACTTAGTGCATCGGTGCACCAAGT
*
26226 GTGCATCGATGCATGACCATAGTGCATCGGTGCATCAGTGTAAAATTCAAATATTTTGACCGTTG
1 GTGCATCGATGCATGACCATAGTGCATCGATGCATCAGTGTAAAATTCAAATATTTTGACCGTTG
*
26291 GAACACTTAGTGCATTGGTGCACCAAGT
66 GAACACTTAGTGCATCGGTGCACCAAGT
26319 GTGCAT
1 GTGCAT
26325 TGTTGCATAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (93 bp):
GTGCATCGATGCATGACCATAGTGCATCGATGCATCAGTGTAAAATTCAAATATTTTGACCGTTG
GAACACTTAGTGCATCGGTGCACCAAGT
Found at i:26433 original size:64 final size:64
Alignment explanation
Indices: 26316--26477 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
26306 TGGTGCACCA
* * * * ** * *
26316 AGTGTGCATTGTTGCATAAAATGCATTCGATGTTTGAAAATAGCCTGACTGCATCGGTGCATTG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCAACTGCATCGATGCATAG
** * *
26380 TTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATGCATAG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AATAACCCAACTGCATCGATGCATAG
* *
26444 AGAGTGCATCGATGCATGAAATGCATTTGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
26478 CAATTTATTC
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 79 0.98
65 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCAACTGCATCGATGCATAG
Found at i:26916 original size:18 final size:18
Alignment explanation
Indices: 26885--26919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26875 TCATTCAGGA
*
26885 TGATGACGAGGACGATGT
1 TGATGACGACGACGATGT
*
26903 TGATGGCGACGACGATG
1 TGATGACGACGACGATG
26920 CACCATAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.40, T:0.20
Consensus pattern (18 bp):
TGATGACGACGACGATGT
Found at i:27229 original size:17 final size:17
Alignment explanation
Indices: 27207--27255 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
27197 AGAAACATCG
27207 AAGGTATCGGTACCACT
1 AAGGTATCGGTACCACT
*
27224 AAGGTATCAGTACCACT
1 AAGGTATCGGTACCACT
*
27241 AAGGTATTGGTACCA
1 AAGGTATCGGTACCA
27256 TGTAATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (17 bp):
AAGGTATCGGTACCACT
Found at i:29394 original size:19 final size:19
Alignment explanation
Indices: 29372--29417 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
29362 ATCGATAGAT
29372 TATCGAAATATAGGATCAC
1 TATCGAAATATAGGATCAC
29391 TATCGAAATATAGGATCAC
1 TATCGAAATATAGGATCAC
29410 TATCGAAA
1 TATCGAAA
29418 GAGTTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (19 bp):
TATCGAAATATAGGATCAC
Found at i:30241 original size:27 final size:27
Alignment explanation
Indices: 30188--30241 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
30178 ATACAAGGGC
* *
30188 ATTTTTGTAATTTTATCACAAGGTATT
1 ATTTTTGTAATTTCATCACAAGATATT
*
30215 ATTTTTGGTAATTTCATTACAA-ATATT
1 ATTTTT-GTAATTTCATCACAAGATATT
30242 TCCAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (27 bp):
ATTTTTGTAATTTCATCACAAGATATT
Found at i:41213 original size:2 final size:2
Alignment explanation
Indices: 41206--41233 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41196 TTCGAACCTT
41206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41234 AAGATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46025 original size:28 final size:28
Alignment explanation
Indices: 45993--46059 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
45983 TATCAATAAC
* *
45993 CACATATTTAACTAAACTCAAATGCATA
1 CACATATTTAACAAAAATCAAATGCATA
* * *
46021 CACATATGTAACAAAAATCGAATTCATA
1 CACATATTTAACAAAAATCAAATGCATA
*
46049 CAAATATTTAA
1 CACATATTTAA
46060 AACATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.28
Consensus pattern (28 bp):
CACATATTTAACAAAAATCAAATGCATA
Found at i:46164 original size:19 final size:19
Alignment explanation
Indices: 46142--46178 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46132 CTAAGTCTTC
*
46142 ATTCTTTTTCTTCTTATTT
1 ATTCATTTTCTTCTTATTT
46161 ATTCATTTTCTTCTTATT
1 ATTCATTTTCTTCTTATT
46179 CTTCTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTCATTTTCTTCTTATTT
Done.