Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006969.1 Hibiscus syriacus cultivar Beakdansim tig00017947_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: 47616
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:4775 original size:60 final size:59
Alignment explanation
Indices: 4696--4838 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 59
4686 TGAATGATCA
* * * *
4696 AAAAGTTTGGGGACCAATTTAGAA-TAGGGATCATACTTTGGGGATGAAATTAAAAT-TTT
1 AAAAGTTTGAGGACCAATTTA-AATTAGAG-TCATACTTTAGGGATAAAATTAAAATATTT
** * *
4755 CAAAAGTTTGAGGATTAATTTAAATTTATAGTCATAGTTTAGGGATAAAATTAAAATATTT
1 -AAAAGTTTGAGGACCAATTTAAA-TTAGAGTCATACTTTAGGGATAAAATTAAAATATTT
4816 AAAAGTTT-AGGGACCAATTTAAA
1 AAAAGTTTGA-GGACCAATTTAAA
4839 ATCCATCTCG
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
59 3 0.04
60 60 0.87
61 6 0.09
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (59 bp):
AAAAGTTTGAGGACCAATTTAAATTAGAGTCATACTTTAGGGATAAAATTAAAATATTT
Found at i:13060 original size:35 final size:35
Alignment explanation
Indices: 13013--13083 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
13003 CGTTCAAATA
13013 TGGTATCAATACT-TTCCTTAAGGTATCAATACCCT
1 TGGTATCAATACTGTTCCTTAA-GTATCAATACCCT
* * *
13048 TGGTATCGATACTGTTCTTTAAGTATCTATACCCT
1 TGGTATCAATACTGTTCCTTAAGTATCAATACCCT
13083 T
1 T
13084 TGAATTCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (35 bp):
TGGTATCAATACTGTTCCTTAAGTATCAATACCCT
Found at i:22559 original size:19 final size:19
Alignment explanation
Indices: 22535--22603 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
22525 TTGGACCCTT
*
22535 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
* *
22554 AGTGCATCGATACA-TCA-
1 AGTGCATCGATGCACTAAG
*
22571 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
22590 AGTGCATCGATGCA
1 AGTGCATCGATGCA
22604 TCAAGTGCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 12 0.29
18 4 0.10
19 25 0.61
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:22576 original size:17 final size:17
Alignment explanation
Indices: 22535--22613 Score: 77
Period size: 19 Copynumber: 4.4 Consensus size: 17
22525 TTGGACCCTT
* *
22535 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
*
22553 GAGTGCATCGATACATCA
1 -AGTGCATCGATGCATCA
* *
22571 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
22589 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
22607 AGTGCAT
1 AGTGCAT
22614 TCGACGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
17 19 0.38
18 6 0.12
19 25 0.50
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:22582 original size:36 final size:36
Alignment explanation
Indices: 22535--22613 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
22525 TTGGACCCTT
22535 AGTGCATCGGTGCACTAAGAGTGCATCGATACATCA
1 AGTGCATCGGTGCACTAAGAGTGCATCGATACATCA
*
22571 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATCA
1 AGTGCATCGGTGCACTAAGAGTGCATCGATACATCA
22607 AGTGCAT
1 AGTGCAT
22614 TCGACGTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (36 bp):
AGTGCATCGGTGCACTAAGAGTGCATCGATACATCA
Found at i:22659 original size:64 final size:64
Alignment explanation
Indices: 22590--22745 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
22580 GTGCACTAAG
*
22590 AGTGCATCGATGCATCAAGTGCATTCGACG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATCAA-TGCATTCGACGTTTTCATAAA-AGCCACAGTGCATCGATGCATGG-
22653 T-
63 TA
* * * * * ** *
22654 GGTGCATCGATACATCAATGCATTTGATGTTTTCATAAAATCTTCAGTGCATCGGTGCATGGTA
1 AGTGCATCGATGCATCAATGCATTCGACGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTA
*
22718 AGTGCATCGATGCATGAAATGCATTCGA
1 AGTGCATCGATGCAT-CAATGCATTCGA
22746 TGTTCAATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
63 10 0.13
64 52 0.69
65 13 0.17
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATCAATGCATTCGACGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTA
Found at i:28977 original size:60 final size:60
Alignment explanation
Indices: 28909--29021 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
28899 CAATAATCCT
* * *
28909 TCGACTATAGGGTGTTGCTTTGTTTAGTACCTTATCTATTAAAAGTTAAAAAAATGTCTC
1 TCGACTATAGGGTGTTGCTTTGTTGAGTACCTCAACTATTAAAAGTTAAAAAAATGTCTC
* *
28969 TCGACTATAGGGTGTTGCTTTGTTGAGTCCCTCAACTATTAAAAGTTAGAAAA
1 TCGACTATAGGGTGTTGCTTTGTTGAGTACCTCAACTATTAAAAGTTAAAAAA
29022 TGGTCACTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (60 bp):
TCGACTATAGGGTGTTGCTTTGTTGAGTACCTCAACTATTAAAAGTTAAAAAAATGTCTC
Found at i:39083 original size:20 final size:20
Alignment explanation
Indices: 39060--39115 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39050 CACATGCAAC
* *
39060 TATATGCTCATAAATGCATA
1 TATATGGTCCTAAATGCATA
* *
39080 TATATGGTCCTAAATTCATC
1 TATATGGTCCTAAATGCATA
39100 TATATGGTCCTAAATG
1 TATATGGTCCTAAATG
39116 GACTCTTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
TATATGGTCCTAAATGCATA
Found at i:45544 original size:19 final size:19
Alignment explanation
Indices: 45520--45559 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
45510 AGATACCATA
45520 CTGACAGGCTATGTAGATG
1 CTGACAGGCTATGTAGATG
45539 CTGACAGGCTATGTAGATG
1 CTGACAGGCTATGTAGATG
45558 CT
1 CT
45560 AACTTAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (19 bp):
CTGACAGGCTATGTAGATG
Done.