Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005239.1 Hibiscus syriacus cultivar Beakdansim tig00011861_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: 78322
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2526 original size:17 final size:17
Alignment explanation
Indices: 2494--2528 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2484 ATAAAAATAA
*
2494 AACTTGAAAATAAAAAG
1 AACTTGAAAAGAAAAAG
*
2511 AACTTGAAAAGGAAAAG
1 AACTTGAAAAGAAAAAG
2528 A
1 A
2529 GAAAACTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.17, T:0.14
Consensus pattern (17 bp):
AACTTGAAAAGAAAAAG
Found at i:3385 original size:21 final size:21
Alignment explanation
Indices: 3361--3400 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3351 CAATGGGATT
*
3361 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
3382 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
3401 GGATGACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:10312 original size:29 final size:29
Alignment explanation
Indices: 10278--10353 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
10268 GAATCAAATG
10278 ATAAAATAAATGAGAAAATGGTGGC-TAA
1 ATAAAATAAATGAGAAAATGGTGGCATAA
*
10306 ATTAAAATAAATGCA-AACAA-GGTGTCATAA
1 A-TAAAATAAATG-AGAA-AATGGTGGCATAA
10336 ATAAAATAAAT-AGAAAAT
1 ATAAAATAAATGAGAAAAT
10354 AGAAATGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 28 0.68
30 7 0.17
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.22
Consensus pattern (29 bp):
ATAAAATAAATGAGAAAATGGTGGCATAA
Found at i:14439 original size:20 final size:19
Alignment explanation
Indices: 14414--14458 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
14404 AATAAGTTTG
* *
14414 AAAAACAATATAATTATATC
1 AAAAACAA-ACAATTAAATC
14434 AAAAAC-AACAATTAAATC
1 AAAAACAAACAATTAAATC
14452 AAAAACA
1 AAAAACA
14459 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 15 0.68
19 1 0.05
20 6 0.27
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAACAAACAATTAAATC
Found at i:18691 original size:20 final size:21
Alignment explanation
Indices: 18653--18691 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18643 TTTCTTTTCA
* *
18653 AAATCTTTTATTTTGACTTGC
1 AAATCTTTAATCTTGACTTGC
18674 AAATCTTTAATCTT-ACTT
1 AAATCTTTAATCTTGACTT
18692 TCGAGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (21 bp):
AAATCTTTAATCTTGACTTGC
Found at i:20660 original size:44 final size:45
Alignment explanation
Indices: 20562--20661 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 45
20552 CAATTCAACG
* **
20562 GTATCGATACC-TCTCAAGGAGTATCGATACTACTATATGTAGTA
1 GTATCGATACCGTCTCAAGGAATATCGATACTACTATATAAAGTA
* * * *
20606 ATATCAATACCGTC-CAAGGAATATCGATACTACTATGTAAAGTC
1 GTATCGATACCGTCTCAAGGAATATCGATACTACTATATAAAGTA
20650 GTATCGATACCG
1 GTATCGATACCG
20662 ATCATGGTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (45 bp):
GTATCGATACCGTCTCAAGGAATATCGATACTACTATATAAAGTA
Found at i:21380 original size:139 final size:139
Alignment explanation
Indices: 21123--21629 Score: 683
Period size: 139 Copynumber: 3.6 Consensus size: 139
21113 CCAATCTGGA
* * * * * * *
21123 GATAATTTGGTGATAACACGATTCCTACGTGACGAGGAAGTCTAATTGTCTGAGGGTGACACTGC
1 GATAATTTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACAGC
* * * * *
21188 TCCTACGTGTTGACGAGATCTGGTCGGTGGACGACATTATTCCTACGTTATGAGGACATCTAGCC
66 TCCTACGCGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACATCTAGCC
21253 ATCTTTAGG
131 ATCTTTAGG
*
21262 GATAAATTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACAGC
1 GATAATTTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACAGC
*
21327 TCCTACGCGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACGTCTAGCC
66 TCCTACGCGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACATCTAGCC
* *
21392 GTATTTAGG
131 ATCTTTAGG
* * * *
21401 GATAATTTAGAGATAACACGATTCTTATGTGATGAGGAAGTCTGGTTATCTGAGGATGACACTGC
1 GATAATTTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACAGC
* * * * * *
21466 TCCTACGCGTTGAGGAGGTTTGGTCGATGGATAACATTGTTCCTATATGATGAGGACATCTAGCC
66 TCCTACGCGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACATCTAGCC
21531 ATCTTTAGG
131 ATCTTTAGG
* * * * * ** *
21540 GATAATTTAGAGACAACTCGGTTCCTACATGATGAGGAAGTCTGGTTATCTTCGGATGACA-ATA
1 GATAATTTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACA-G
*
21604 CTCCTACGTGTTGAGGAGATCTGGTC
65 CTCCTACGCGTTGAGGAGATCTGGTC
21630 AGTTGGCGAT
Statistics
Matches: 324, Mismatches: 43, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
139 324 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (139 bp):
GATAATTTAGAGATAACACGATTCCTACGTGATGAGGAAGTCTAGTTATCTGAGGATGACACAGC
TCCTACGCGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACATCTAGCC
ATCTTTAGG
Found at i:43052 original size:24 final size:24
Alignment explanation
Indices: 43025--43079 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
43015 AAGATTAACA
43025 TGTTATTAATTGATGACAACAAGT
1 TGTTATTAATTGATGACAACAAGT
* *
43049 TGTTATTTATTGATGACAACGAGT
1 TGTTATTAATTGATGACAACAAGT
43073 TGTTATT
1 TGTTATT
43080 GACATAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (24 bp):
TGTTATTAATTGATGACAACAAGT
Found at i:45471 original size:15 final size:15
Alignment explanation
Indices: 45451--45482 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
45441 CTAAAAGAAA
45451 AGCCAAAGCTGATTT
1 AGCCAAAGCTGATTT
45466 AGCCAAAGCTGATTT
1 AGCCAAAGCTGATTT
45481 AG
1 AG
45483 GAAATTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (15 bp):
AGCCAAAGCTGATTT
Found at i:47060 original size:17 final size:17
Alignment explanation
Indices: 47034--47070 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
47024 AACAATATGA
*
47034 TGTATGCGAATCTTACT
1 TGTATACGAATCTTACT
47051 TGTATACGAATCTTACT
1 TGTATACGAATCTTACT
47068 TGT
1 TGT
47071 TGGGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (17 bp):
TGTATACGAATCTTACT
Found at i:47729 original size:17 final size:17
Alignment explanation
Indices: 47707--47751 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
47697 AAAGTATTTG
*
47707 TTTCTCGAACA-AGAGTT
1 TTTCTCGAA-AGAGAATT
47724 TTTCTCGAAAGAGAATT
1 TTTCTCGAAAGAGAATT
47741 TTTCTC-AAAGA
1 TTTCTCGAAAGA
47752 AAGGGAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (17 bp):
TTTCTCGAAAGAGAATT
Found at i:61637 original size:12 final size:12
Alignment explanation
Indices: 61622--61647 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61612 TAACTCCAAT
61622 GAATTAGTATTG
1 GAATTAGTATTG
61634 GAATTAGTATTG
1 GAATTAGTATTG
61646 GA
1 GA
61648 GGAATAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (12 bp):
GAATTAGTATTG
Found at i:76238 original size:5 final size:5
Alignment explanation
Indices: 76228--76290 Score: 74
Period size: 5 Copynumber: 12.2 Consensus size: 5
76218 AAACACTATG
* *
76228 AAAAT AAAAT AATAAT AAAAAT AGAAT -AAAT AGAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AA-AAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
76279 AAAAT ATAAAT A
1 AAAAT A-AAAT A
76291 TAAAGATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
4 3 0.06
5 34 0.68
6 11 0.22
7 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:78002 original size:22 final size:22
Alignment explanation
Indices: 77974--78030 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
77964 GGTGGAGCTG
77974 GCAGGGTATGGTGACT-GGAGCA
1 GCAGGGTATGGTGACTGGGA-CA
77996 GCAGGGTATGGTGACTGGGACA
1 GCAGGGTATGGTGACTGGGACA
*
78018 GCAAGGTATGGTG
1 GCAGGGTATGGTG
78031 TTGCAATTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.23, C:0.12, G:0.46, T:0.19
Consensus pattern (22 bp):
GCAGGGTATGGTGACTGGGACA
Done.