Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007388.1 Hibiscus syriacus cultivar Beakdansim tig00019891_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: 60230
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1909 original size:20 final size:19
Alignment explanation
Indices: 1866--1910 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1856 AAGTGGCTCA
1866 AATTTCACAGTCTAACATC
1 AATTTCACAGTCTAACATC
* * *
1885 GATTTCAACATTCTAACATT
1 AATTTC-ACAGTCTAACATC
1905 AATTTC
1 AATTTC
1911 CAGCATAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTTCACAGTCTAACATC
Found at i:11628 original size:3 final size:3
Alignment explanation
Indices: 11622--11686 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
11612 CTTCTTCTTC
* *
11622 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
11670 TTA TTA TATA TTT TTA T
1 TTA TTA T-TA TTA TTA T
11687 CATTTTCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25081 original size:16 final size:16
Alignment explanation
Indices: 25060--25091 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25050 TCCCCCTTTT
25060 ATATTTATTACTATTA
1 ATATTTATTACTATTA
*
25076 ATATTTATTATTATTA
1 ATATTTATTACTATTA
25092 TTTTTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTATTACTATTA
Found at i:35959 original size:17 final size:18
Alignment explanation
Indices: 35937--35983 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
35927 TCAAATGGCA
35937 ATCATTTTTTCTT-TCAT
1 ATCATTTTTTCTTATCAT
*
35954 ATCATTATTTTTTTATCAT
1 ATCATT-TTTTCTTATCAT
* *
35973 TTCTTTTTTTC
1 ATCATTTTTTC
35984 GTTTTGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (18 bp):
ATCATTTTTTCTTATCAT
Found at i:38713 original size:19 final size:20
Alignment explanation
Indices: 38678--38715 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38668 CATATCATTA
38678 TTTGTTTATCATTTCTTTTT
1 TTTGTTTATCATTTCTTTTT
*
38698 TTTGTTT-TCCTTTCTTTT
1 TTTGTTTATCATTTCTTTT
38716 CTCCAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTGTTTATCATTTCTTTTT
Found at i:45495 original size:232 final size:231
Alignment explanation
Indices: 45081--45498 Score: 538
Period size: 232 Copynumber: 1.8 Consensus size: 231
45071 AGAGAAGAAC
* *
45081 AAAAATAAAATCAGAATATATTTGCTAAGAGTCCAACTCAAAAGACACAATAATATGTTACAAAG
1 AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACAAAG
* * * * *
45146 GGTAATTTTCTTTGTAATAAATTAGGATATATGATGAGAAATTGAGTTATGAAATAATAAGAAAT
66 GGT-ATTTTCTTTATAATAAATTAGGATATATAAGGAGAAATTGAATTATAAAATAATAAGAAAT
* * *** * *
45211 TACTTTGGTTATTTTGTGTGATTTAGGGGTTGCAAGTTTTATAATCTCATAATTAGGAAAATTTT
130 TACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAGGAAAATTTT
45276 AAAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
195 AAAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
* * * * * *
45313 AAAAATAAAATCATAATGTAATTGTTAAGGGTCCAACTCAAAAAAGATAATAATATGTTACATAA
1 AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACA-AA
* *
45378 TGTGGT-TCTTT-TTTATATTAAGTTATGGA-ATATAAGGAGAAATTGAATTA-AAAATAATAAG
65 -G-GGTAT-TTTCTTTATAATAAATTA-GGATATATAAGGAGAAATTGAATTATAAAATAATAAG
* *
45439 CAATTACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATGATATCATAATTAG
126 AAATTACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAG
45499 TAATACTTTT
Statistics
Matches: 157, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
232 115 0.73
233 32 0.20
234 7 0.04
235 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (231 bp):
AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACAAAG
GGTATTTTCTTTATAATAAATTAGGATATATAAGGAGAAATTGAATTATAAAATAATAAGAAATT
ACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAGGAAAATTTTA
AAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
Found at i:51772 original size:3 final size:3
Alignment explanation
Indices: 51736--51821 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
51726 TCAAATTCCA
* * * *
51736 TTC TTC TTT TTC TTT TTC TTA TTC TTC TTA TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
51784 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
51822 ATTATTATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:51826 original size:3 final size:3
Alignment explanation
Indices: 51820--51900 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
51810 CTTCTTCTTC
51820 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51868 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51901 CTACTATTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56367 original size:54 final size:54
Alignment explanation
Indices: 56277--56543 Score: 376
Period size: 54 Copynumber: 4.9 Consensus size: 54
56267 CGTAGTACTT
* * **
56277 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTTA
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
* * * *
56331 ATACAGTAGTTCATCAACATATGATAAATTTTGTGGGTTGCACACTTAGTATCG
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
* * * * *
56385 ATACGGTCGTTCATCAACACATGTTGAGTTTCGTGGGTTGCACACTTAGTGTTG
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
56439 ATACAGTCGTTCATCAACATATGATGAATTAT-GTGGGTTGCACACTTAGTGTCG
1 ATACAGTCGTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTGTCG
*
56493 ATACGGTCGTTCATCAACATATGATGAA-TTCGATGGGTTGCACACTTAGTG
1 ATACAGTCGTTCATCAACATATGATGAATTTCG-TGGGTTGCACACTTAGTG
56544 CTGATAGTAC
Statistics
Matches: 187, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
52 1 0.01
53 2 0.01
54 183 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
Found at i:56549 original size:108 final size:107
Alignment explanation
Indices: 56277--56549 Score: 438
Period size: 108 Copynumber: 2.5 Consensus size: 107
56267 CGTAGTACTT
*
56277 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTTAATACAGTAGTT
1 ATACGGTCGTTCATCAACATATGATGAATT-CGTGGGTTGCACACTTAGTGTTGATACAGTAGTT
*
56342 CATCAACATATGATAAATTTTGTGGGTTGCACACTTAGTATCG
65 CATCAACATATGATAAATTATGTGGGTTGCACACTTAGTATCG
* * * *
56385 ATACGGTCGTTCATCAACACATGTTGAGTTTCGTGGGTTGCACACTTAGTGTTGATACAGTCGTT
1 ATACGGTCGTTCATCAACATATGATGA-ATTCGTGGGTTGCACACTTAGTGTTGATACAGTAGTT
* *
56450 CATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGTCG
65 CATCAACATATGATAAATTATGTGGGTTGCACACTTAGTATCG
*
56493 ATACGGTCGTTCATCAACATATGATGAATTCGATGGGTTGCACACTTAGTGCTGATA
1 ATACGGTCGTTCATCAACATATGATGAATTCG-TGGGTTGCACACTTAGTGTTGATA
56550 GTACACATAG
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
107 4 0.03
108 145 0.96
109 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (107 bp):
ATACGGTCGTTCATCAACATATGATGAATTCGTGGGTTGCACACTTAGTGTTGATACAGTAGTTC
ATCAACATATGATAAATTATGTGGGTTGCACACTTAGTATCG
Done.