Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008462.1 Hibiscus syriacus cultivar Beakdansim tig00111275_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: 35585
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:10872 original size:20 final size:20
Alignment explanation
Indices: 10822--10872 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
10812 AAATTTTTAT
* *
10822 GTTCGAGTTACAAAATAGAA
1 GTTCGAGTTATAAAATAAAA
10842 GTTCGAGTTATAAAATAAAA
1 GTTCGAGTTATAAAATAAAA
*
10862 GTTCGCGTTAT
1 GTTCGAGTTAT
10873 GAATTTGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (20 bp):
GTTCGAGTTATAAAATAAAA
Found at i:11463 original size:19 final size:20
Alignment explanation
Indices: 11423--11461 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11413 ATTTATTAAA
11423 AAATAGTTATATTTAATTTT
1 AAATAGTTATATTTAATTTT
11443 AAATA-TTATTATTTAATTT
1 AAATAGTTA-TATTTAATTT
11462 AATTTACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AAATAGTTATATTTAATTTT
Found at i:12709 original size:15 final size:14
Alignment explanation
Indices: 12684--12717 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
12674 GTTTTAAATA
12684 TTTAATAATAATTT
1 TTTAATAATAATTT
12698 TTTAATTAATAATTT
1 TTTAA-TAATAATTT
12713 TTTAA
1 TTTAA
12718 AAAGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATAATAATTT
Found at i:22107 original size:24 final size:24
Alignment explanation
Indices: 22066--22112 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
22056 CTCAGATAAT
** * *
22066 TTTAAAATTTTCATTTTTTTAAAA
1 TTTAAAATTTAAAATTTTATAAAA
22090 TTTAAAATTTAAAATTTTATAAA
1 TTTAAAATTTAAAATTTTATAAA
22113 GGTCACACGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAATTTAAAATTTTATAAAA
Found at i:22241 original size:29 final size:29
Alignment explanation
Indices: 22189--22244 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
22179 ATTGAAAACG
* ***
22189 TTAGACACCTAAATTAGTCGAAATATAAT
1 TTAGACACCTAAATAAGAAAAAATATAAT
22218 TTAGACACCTAAATAAGAAAAAATATA
1 TTAGACACCTAAATAAGAAAAAATATA
22245 CAATTTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (29 bp):
TTAGACACCTAAATAAGAAAAAATATAAT
Found at i:23946 original size:19 final size:19
Alignment explanation
Indices: 23922--23958 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
23912 ATGACTAACA
*
23922 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
23941 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
23959 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:24040 original size:12 final size:12
Alignment explanation
Indices: 24023--24049 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24013 GATTTTAGAA
24023 AATCGCAATGCG
1 AATCGCAATGCG
24035 AATCGCAATGCG
1 AATCGCAATGCG
24047 AAT
1 AAT
24050 ATGTAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (12 bp):
AATCGCAATGCG
Found at i:24143 original size:21 final size:21
Alignment explanation
Indices: 24076--24212 Score: 140
Period size: 21 Copynumber: 6.6 Consensus size: 21
24066 GATTCTGACT
*
24076 ATCGCAACGTGATAATACATA
1 ATCGCAACGCGATAATACATA
**
24097 AT-GACAACGCGATTCTGAC-T-
1 ATCG-CAACGCGATAAT-ACATA
24117 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
24138 ATCGCAACACGATAATACATA
1 ATCGCAACGCGATAATACATA
**
24159 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
24179 ATCGCAATGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
24200 ATCGCAACTCGAT
1 ATCGCAACGCGAT
24213 TTTGACTATC
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.04
20 28 0.30
21 58 0.62
22 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:24152 original size:62 final size:62
Alignment explanation
Indices: 24076--24247 Score: 233
Period size: 62 Copynumber: 2.8 Consensus size: 62
24066 GATTCTGACT
**
24076 ATCGCAACGTGATAATACATAAT-GACAACGCGATTCTGACTATCGCAACGCGATAATACATA
1 ATCGCAACACGATAATACATAATCG-CAACGCGATTCTGACTATCGCAACGCGATAATACATA
*
24138 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACATA
1 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
* ** * *
24200 ATCGCAACTCGATTTTGAC-T-ATCGCAACGCGATTCTGATTGTCGCAAC
1 ATCGCAACACGATAAT-ACATAATCGCAACGCGATTCTGACTATCGCAAC
24248 AGGTTTTAGT
Statistics
Matches: 99, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
61 25 0.25
62 71 0.72
63 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (62 bp):
ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
Found at i:24193 original size:41 final size:41
Alignment explanation
Indices: 24138--24232 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
24128 ATAATACATA
*
24138 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* * *
24179 ATCGCAATGCGATAATACATAATCGCAACTCGATTTTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
24220 ATCGCAACGCGAT
1 ATCGCAACGCGAT
24233 TCTGATTGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
Found at i:24244 original size:20 final size:20
Alignment explanation
Indices: 24056--24247 Score: 124
Period size: 20 Copynumber: 9.4 Consensus size: 20
24046 GAATATGTAA
*
24056 ATCGCAAAGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
24076 ATCGCAACGTGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
24096 AAT-GACAACGCGATTCTGACT
1 -ATCG-CAACGCGATTCTGACT
**
24117 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* **
24137 AATCGCAACACGATAAT-ACAT
1 -ATCGCAACGCGATTCTGAC-T
24158 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* **
24179 ATCGCAATGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
24199 AATCGCAACTCGATTTTGACT
1 -ATCGCAACGCGATTCTGACT
*
24220 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
24240 GTCGCAAC
1 ATCGCAAC
24248 AGGTTTTAGT
Statistics
Matches: 137, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
19 6 0.04
20 65 0.47
21 60 0.44
22 6 0.04
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:32820 original size:24 final size:24
Alignment explanation
Indices: 32793--32846 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32783 GTATTCGAAA
32793 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
32817 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
32841 TTTGAT
1 TTTGAT
32847 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:35478 original size:21 final size:20
Alignment explanation
Indices: 35404--35561 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
35394 TTCATTTGAA
*
35404 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTAAC
35424 TATCGCAACGC-AA---AA-
1 TATCGCAACGCGAATTTAAC
35439 -ATCGCAACGCGAATTTAAC
1 TATCGCAACGCGAATTTAAC
35458 TATCGCAACGCGAATTTTAAC
1 TATCGCAACGCGAA-TTTAAC
* *
35479 TATCGCAACACGAA-TTGAC
1 TATCGCAACGCGAATTTAAC
* * *
35498 TATCGCAACGAGAATATGAC
1 TATCGCAACGCGAATTTAAC
*
35518 TATCACAACGC-AA---AA-
1 TATCGCAACGCGAATTTAAC
* *
35533 -ATCGCAACACGAATTTGAC
1 TATCGCAACGCGAATTTAAC
35552 TATCGCAACG
1 TATCGCAACG
35562 AGAAAATCGC
Statistics
Matches: 111, Mismatches: 13, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.16
15 4 0.04
16 2 0.02
18 3 0.03
19 20 0.18
20 45 0.41
21 19 0.17
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAATTTAAC
Found at i:35552 original size:34 final size:34
Alignment explanation
Indices: 35499--35581 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 34
35489 CGAATTGACT
*
35499 ATCGCAACGA-GAATATGACTATCACAACGCA-AAA
1 ATCGCAAC-ACGAATTTGACTATCACAACG-AGAAA
*
35533 ATCGCAACACGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACACGAATTTGACTATCACAACGAGAAA
35567 ATCGCAA-AGCGAATT
1 ATCGCAACA-CGAATT
35582 AGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
33 3 0.07
34 41 0.93
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (34 bp):
ATCGCAACACGAATTTGACTATCACAACGAGAAA
Done.