Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000569.1 Hibiscus syriacus cultivar Beakdansim tig00001115_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: 37054
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6427 original size:50 final size:50
Alignment explanation
Indices: 6352--6457 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
6342 GTGTATCCAA
*
6352 TCAATACTTAGCTAATTTAGAAAAGTTTGATCCTACTCAATTAATGATTT
1 TCAATACTTAGCTAATTTAGAAAAGTTTGATCATACTCAATTAATGATTT
*
6402 TCAATACTTAGCTAATTTAGAAAAGTTTGATCATACTCAATTAATTATTT
1 TCAATACTTAGCTAATTTAGAAAAGTTTGATCATACTCAATTAATGATTT
6452 TCAATA
1 TCAATA
6458 TTGTAGTAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (50 bp):
TCAATACTTAGCTAATTTAGAAAAGTTTGATCATACTCAATTAATGATTT
Found at i:9929 original size:65 final size:65
Alignment explanation
Indices: 9794--9953 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
9784 TGCACTAAGA
* * *
9794 GTGCATCGTTGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * * *
9858 GTGCATCGATACATCAAATGCATTCGATGTTTTTATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
9921 AT
65 -G
* *
9923 GTGCATCGATGCATGAAATACATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
9954 CAATTTAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 27 0.33
65 51 0.63
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:16675 original size:22 final size:21
Alignment explanation
Indices: 16633--16672 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16623 TGAGTTTATT
*
16633 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
16654 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
16673 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:18656 original size:64 final size:63
Alignment explanation
Indices: 18586--18764 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 63
18576 TTGGACCCTT
* *
18586 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATGTTTTA-AAATAGCCA
1 AGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTATAAA-AGCCA
*
18649 G
63 C
* * *
18650 AGTGCATCGATGCATGGCTAGTGCATC-ATGCATCAAATGCATTCGATGTTTTTATAAAATCCTC
1 AGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATG-TTTTATAAAAGCCAC
*
18714 AGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
18765 CAATTTAATT
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 23 0.23
64 54 0.53
65 23 0.23
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTATAAAAGCCAC
Found at i:18783 original size:64 final size:64
Alignment explanation
Indices: 18605--18794 Score: 187
Period size: 64 Copynumber: 3.0 Consensus size: 64
18595 GTGCACTAAG
* * *
18605 AGTGCATCGATGCATCAAGTGCATTCGATGTT-TTA-AAATAGCCA-GAGTGCATCGATGCATGG
1 AGTGCATC-ATGCATCAAATGCATTCGATGTTATTATAAA-A-TCATCAGTGCATCGATGCATGG
18667 CT
63 CT
* * *
18669 AGTGCATCATGCATCAAATGCATTCGATGTTTTTATAAAATCCTCAGTGCATCGGTGCATGG-T
1 AGTGCATCATGCATCAAATGCATTCGATGTTATTATAAAATCATCAGTGCATCGATGCATGGCT
* * *
18732 ATGTGCATCGATGCATGAAATGCATTCGATGTTCAATT-T-AATTCAT-GGTGCATCGATGCATG
1 A-GTGCATC-ATGCATCAAATGCATTCGATGTT--ATTATAAAATCATCAGTGCATCGATGCATG
18794 G
62 G
18795 ATTGGTACAT
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
63 25 0.23
64 50 0.46
65 30 0.28
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
AGTGCATCATGCATCAAATGCATTCGATGTTATTATAAAATCATCAGTGCATCGATGCATGGCT
Found at i:21363 original size:18 final size:19
Alignment explanation
Indices: 21340--21378 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
21330 TTTAAATAGT
21340 AATAAAAA-TGATTAAA-TA
1 AATAAAAACT-ATTAAAGTA
21358 AATAAAAACTATTAAAGTA
1 AATAAAAACTATTAAAGTA
21377 AA
1 AA
21379 AATAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (19 bp):
AATAAAAACTATTAAAGTA
Found at i:22199 original size:17 final size:17
Alignment explanation
Indices: 22179--22215 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
22169 TTAAACTAGT
22179 CTCCTAATGCAACTCTG
1 CTCCTAATGCAACTCTG
22196 CTCCTAATGCAACTCTG
1 CTCCTAATGCAACTCTG
22213 CTC
1 CTC
22216 GTCAATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.38, G:0.11, T:0.30
Consensus pattern (17 bp):
CTCCTAATGCAACTCTG
Found at i:27205 original size:15 final size:15
Alignment explanation
Indices: 27182--27232 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
27172 CACCCCACAT
*
27182 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
27197 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCAC
* * *
27212 CCTCCCCACATCCGC
1 CCGCCCCGCATCCAC
27227 CCGCCC
1 CCGCCC
27233 AACTAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.14, C:0.67, G:0.12, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:33083 original size:18 final size:19
Alignment explanation
Indices: 33060--33098 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33050 TTTAAATAGT
33060 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
33078 AATAAAAGCTATTAAAGTA
1 AATAAAAACGATTAAAGTA
33097 AA
1 AA
33099 AATAACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Done.