Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008454.1 Hibiscus syriacus cultivar Beakdansim tig00111262_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: 49293
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:685 original size:25 final size:25
Alignment explanation
Indices: 634--707 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
624 GAACCAACCC
634 ATCAGATTAGGGTTTCAAAACCCTAA
1 ATCAGATTAGGGTTTC-AAACCCTAA
660 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
685 AACAAATTAGGGTTT--AACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
708 TCCCCTAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
23 8 0.17
25 22 0.48
26 16 0.35
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:15069 original size:88 final size:89
Alignment explanation
Indices: 14921--15164 Score: 314
Period size: 90 Copynumber: 2.7 Consensus size: 89
14911 CAGACCAGAT
* *
14921 CTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATCACGTAGGAACCGT
**
14986 GTTATCA-CCTTTAGATGGCCAAGAA
64 GTTATCACCCTAAAGATGGCCAAGAA
15011 CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
15076 TATCATCCCTAAAGATGGCCAAGAA
66 TATCA-CCCTAAAGATGGCCAAGAA
* * * * * ** * *
15101 TTCTTCATCATGTAGGAGCAGTGTCATCC-CCTGACCAGATC-TCCTCATCACGTAGGAGCCGTG
1 CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAG-TCGTCCTCATCACGTAGGAACCGTG
15164 T
65 T
15165 CACCCTTAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
88 39 0.28
89 29 0.21
90 70 0.51
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (89 bp):
CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
TATCACCCTAAAGATGGCCAAGAA
Found at i:15373 original size:3 final size:3
Alignment explanation
Indices: 15362--15409 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
15352 CGGGTTTTTT
** *
15362 TTA TATA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15407 TTA
1 TTA
15410 ATTTACAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:15532 original size:25 final size:25
Alignment explanation
Indices: 15503--15601 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
15493 GAACCAACCC
15503 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
15528 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
15553 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * *
15578 AACAAATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
15602 TCCCTTAATG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 8 0.11
25 63 0.89
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:23005 original size:10 final size:10
Alignment explanation
Indices: 22990--23064 Score: 66
Period size: 10 Copynumber: 7.6 Consensus size: 10
22980 TTTTAGCAAA
22990 ATATAAAAAT
1 ATATAAAAAT
23000 ATATAAAAAT
1 ATATAAAAAT
*
23010 ATA-AAAAGAA
1 ATATAAAA-AT
*
23020 ATAGAAAAA-
1 ATATAAAAAT
*
23029 ATTATAAAATT
1 A-TATAAAAAT
*
23040 ATAAAAAAAT
1 ATATAAAAAT
*
23050 ATTTAAAAAT
1 ATATAAAAAT
23060 -TATAA
1 ATATAA
23065 TTTGTTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.17
10 39 0.74
11 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:23048 original size:21 final size:21
Alignment explanation
Indices: 23024--23064 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23014 AAAGAAATAG
23024 AAAAAA-TTATAAAATTATAAA
1 AAAAAATTTA-AAAATTATAAA
*
23045 AAAATATTTAAAAATTATAA
1 AAAAAATTTAAAAATTATAA
23065 TTTGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATTTAAAAATTATAAA
Found at i:31932 original size:20 final size:21
Alignment explanation
Indices: 31907--31948 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31897 TTGCCCACCT
31907 TATACACT-AAGTGTCTTGTA
1 TATACACTCAAGTGTCTTGTA
*
31927 TATACACTCTAGTGTCTTGTA
1 TATACACTCAAGTGTCTTGTA
31948 T
1 T
31949 CGTGTGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (21 bp):
TATACACTCAAGTGTCTTGTA
Found at i:35223 original size:31 final size:31
Alignment explanation
Indices: 35163--35223 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
35153 GGTCAAAGTG
* *
35163 AACGGTCAAGGTCAAAGTCAATGTGTTGGTT
1 AACGGTCAAGGGCAAAGTCAATATGTTGGTT
35194 AACGGTCAACGGGC-AAGTCAACTAT-TTGGT
1 AACGGTCAA-GGGCAAAGTCAA-TATGTTGGT
35224 CAAAGTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (31 bp):
AACGGTCAAGGGCAAAGTCAATATGTTGGTT
Found at i:35239 original size:18 final size:19
Alignment explanation
Indices: 35208--35245 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
35198 GTCAACGGGC
*
35208 AAGTCAACTATTT-GGTCA
1 AAGTCAACGATTTGGGTCA
*
35226 AAGTCAACGGTTTGGGTCA
1 AAGTCAACGATTTGGGTCA
35245 A
1 A
35246 GGTTAACGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (19 bp):
AAGTCAACGATTTGGGTCA
Found at i:36926 original size:29 final size:30
Alignment explanation
Indices: 36875--36942 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
36865 TTACCACTTA
* ** *
36875 GGTCCCTAAACTTTTCCCAATTT-TATGTTT
1 GGTCACTAAACTTTTCAAAATTTACAT-TTT
36905 GGTCACTAAAC-TTTCAAAATTTACATTTT
1 GGTCACTAAACTTTTCAAAATTTACATTTT
36934 GGTCACTAA
1 GGTCACTAA
36943 TAAAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (30 bp):
GGTCACTAAACTTTTCAAAATTTACATTTT
Done.