Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002179.1 Hibiscus syriacus cultivar Beakdansim tig00004439_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: 76057
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:10655 original size:23 final size:23
Alignment explanation
Indices: 10584--10665 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
10574 ACACTTAATA
*
10584 GTGCATCGATGCATCTCTTTGAAT
1 GTGCATCGATGCA-CTCCTTGAAT
* * *
10608 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACTCCTTGAAT
10629 GTGCA-CTGATGCACTCCTTGAAT
1 GTGCATC-GATGCACTCCTTGAAT
10652 GTGCATCGATGCAC
1 GTGCATCGATGCAC
10666 AAGGCCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 1 0.02
23 20 0.43
24 11 0.23
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:12254 original size:21 final size:21
Alignment explanation
Indices: 12230--12276 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
12220 GCACCTCCTG
12230 CTCCTAGCTCTTCTCGTGCTT
1 CTCCTAGCTCTTCTCGTGCTT
12251 CTCCTAGCTCTTCTCGTGCTT
1 CTCCTAGCTCTTCTCGTGCTT
12272 CTCCT
1 CTCCT
12277 CCTCCTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.40, G:0.13, T:0.43
Consensus pattern (21 bp):
CTCCTAGCTCTTCTCGTGCTT
Found at i:16019 original size:20 final size:20
Alignment explanation
Indices: 15991--16038 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
15981 CAATAGTTTC
15991 GAAACTTTCATAAAAATTTT
1 GAAACTTTCATAAAAATTTT
* * * *
16011 GAAATTTTCCTTAAAGTTTT
1 GAAACTTTCATAAAAATTTT
16031 GAAACTTT
1 GAAACTTT
16039 GAGTTCCAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (20 bp):
GAAACTTTCATAAAAATTTT
Found at i:18945 original size:434 final size:434
Alignment explanation
Indices: 18089--18954 Score: 1369
Period size: 434 Copynumber: 2.0 Consensus size: 434
18079 TTTATCTATA
* * * *
18089 GTTATCTGTGTCATGAGTATTATAGATTTCAATAGTTGGTTCTAGAATTCTATAATTAGTTAGCT
1 GTTATCTATATCATGAGTATTATAGATTTCAATAGTTGGTTCTAGAATACTATAATTAGTTAGCC
* * *
18154 CATTCAGGTGTTTTATTATCATGAGCAATTAGTTTGTTGTTGGGCTGAACTATAATTATTGGTCT
66 CATTCAGGTATTTTATTATCACGAGCAATTAGTTTGTTGTTGGGCTGAACTATAATTATTGGTAT
* *
18219 TGGAATCTAGATAGGTTAGACCAATTGTATTGTAAATCTGTGGTTAATGAAATACATTCATTCTC
131 CGGAATCTAGATAGGTTAGACCAATTGTATTGTAAATCTGTGGTTAATGAAATACAATCATTCTC
*
18284 TTTGACTTTGTCAAAATCCCGAACTCTCCCTTCTCATTCTCAATTCTTTTCTGTTCTGTTTCATC
196 TTTGACTTTGTCAAAATCCCGAACTCTCCCATCTCATTCTCAATTCTTTTCTGTTCTGTTTCATC
* * * *
18349 TTCTTCCTTCTTTTGATTCGTTTGTTCTAAGGATTTCCATATAGTATCATAGCTATAATCTTCGT
261 TTCTTCCTTCTTCTAATTCGTTTGTTCTAAGAATTTCCATATAGTATCAGAGCTATAATCTTCGT
* * ** * * * *
18414 CGTTGTTATGTTGGTTCCTCTTTTTTGTTGTTTAATTGTTGCTGTTTGCATTTCACATTCGTCTT
326 CGCTATTATACTGATTCCTCTTTTCTCTTGTTTAATTGTTGCTGTTCGCATTTCACATTCGTCTT
* * *
18479 GTTCGCTGATCCCGTTCTTCGCTCAGCTTCTTCTTCTGGTTCTT
391 GTTCGCAGATCCCATTCTTCGCTAAGCTTCTTCTTCTGGTTCTT
* *
18523 GTTATCTATATCATGAGTATTATAGATTTCAATAGTTGGTTCTTGAATACTATAATTGGTTAGCC
1 GTTATCTATATCATGAGTATTATAGATTTCAATAGTTGGTTCTAGAATACTATAATTAGTTAGCC
* * *
18588 CATTCTGGTATTTTATTATCACGTGCAGTTAGTTTGTTGTTGGGCTGAACTATAATTATTGGTAT
66 CATTCAGGTATTTTATTATCACGAGCAATTAGTTTGTTGTTGGGCTGAACTATAATTATTGGTAT
* *
18653 CGGAATCTAGATGGGTTAGACCAATTGTATTGTAAATCTTTGGTTAATGAAATACAATCATTCTC
131 CGGAATCTAGATAGGTTAGACCAATTGTATTGTAAATCTGTGGTTAATGAAATACAATCATTCTC
*
18718 TTTGACTTTGTCAAAATTCCGAACTCTCCCATCTCATTCTCAATTCTTTTCTGTTCTGTTTCATC
196 TTTGACTTTGTCAAAATCCCGAACTCTCCCATCTCATTCTCAATTCTTTTCTGTTCTGTTTCATC
* *
18783 TTCTTCCTTCTTCTAATTCGTTTGTTCTAAGAATTTCCATATAGTGTCAGAGCTATAATCTTCTT
261 TTCTTCCTTCTTCTAATTCGTTTGTTCTAAGAATTTCCATATAGTATCAGAGCTATAATCTTCGT
* *
18848 CGCTATTATACTGATTCCTCTTTTCTCTTG-TTCA-T-TTGTTGTTCGCATTTCACATTCGTCTT
326 CGCTATTATACTGATTCCTCTTTTCTCTTGTTTAATTGTTGCTGTTCGCATTTCACATTCGTCTT
*
18910 GTTCGCAGATCTCATTCTTCGCTAAGCTTCTTCTTCTGGTTCTT
391 GTTCGCAGATCCCATTCTTCGCTAAGCTTCTTCTTCTGGTTCTT
18954 G
1 G
18955 ATTTCGTTTC
Statistics
Matches: 394, Mismatches: 38, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
431 66 0.17
432 1 0.00
433 3 0.01
434 324 0.82
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (434 bp):
GTTATCTATATCATGAGTATTATAGATTTCAATAGTTGGTTCTAGAATACTATAATTAGTTAGCC
CATTCAGGTATTTTATTATCACGAGCAATTAGTTTGTTGTTGGGCTGAACTATAATTATTGGTAT
CGGAATCTAGATAGGTTAGACCAATTGTATTGTAAATCTGTGGTTAATGAAATACAATCATTCTC
TTTGACTTTGTCAAAATCCCGAACTCTCCCATCTCATTCTCAATTCTTTTCTGTTCTGTTTCATC
TTCTTCCTTCTTCTAATTCGTTTGTTCTAAGAATTTCCATATAGTATCAGAGCTATAATCTTCGT
CGCTATTATACTGATTCCTCTTTTCTCTTGTTTAATTGTTGCTGTTCGCATTTCACATTCGTCTT
GTTCGCAGATCCCATTCTTCGCTAAGCTTCTTCTTCTGGTTCTT
Found at i:24444 original size:23 final size:23
Alignment explanation
Indices: 24414--24459 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
24404 TGAGTGTGTT
24414 TGCTTGTATGGGGTGGGAAGAGC
1 TGCTTGTATGGGGTGGGAAGAGC
24437 TGCTTGTATGGGGTGGGAAGAGC
1 TGCTTGTATGGGGTGGGAAGAGC
24460 ATGTGGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.48, T:0.26
Consensus pattern (23 bp):
TGCTTGTATGGGGTGGGAAGAGC
Found at i:43664 original size:20 final size:18
Alignment explanation
Indices: 43638--43694 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 18
43628 ACCCCTTCAA
43638 GTGGTATCGATACTAGGG
1 GTGGTATCGATACTAGGG
43656 GTCTGGTATC-AGTACTAAGGG
1 G--TGGTATCGA-TACT-AGGG
43677 G-GAGTATCGATACTAGGG
1 GTG-GTATCGATACTAGGG
43695 ACATGTTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
18 6 0.18
19 10 0.30
20 12 0.36
21 5 0.15
ACGTcount: A:0.25, C:0.12, G:0.37, T:0.26
Consensus pattern (18 bp):
GTGGTATCGATACTAGGG
Found at i:61829 original size:15 final size:15
Alignment explanation
Indices: 61800--61841 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61790 ATAAAATAAC
61800 ATTAAAAATATTATA
1 ATTAAAAATATTATA
61815 ATTAACAAATA-TATA
1 ATTAA-AAATATTATA
*
61830 AATAAAAA-ATTA
1 ATTAAAAATATTA
61842 AAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 5 0.21
15 13 0.54
16 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAAAATATTATA
Found at i:63552 original size:21 final size:21
Alignment explanation
Indices: 63528--63571 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
63518 CTTATGGATG
63528 GCCCGAAGAACTTAACATCTT
1 GCCCGAAGAACTTAACATCTT
*
63549 GCCCGAAGGACTTAACATCTT
1 GCCCGAAGAACTTAACATCTT
63570 GC
1 GC
63572 TCAAAAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (21 bp):
GCCCGAAGAACTTAACATCTT
Found at i:63581 original size:21 final size:21
Alignment explanation
Indices: 63537--63585 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63527 GGCCCGAAGA
* *
63537 ACTTAACATCTTGCCCGAAGG
1 ACTTAACATCTTGCCCAAAAG
*
63558 ACTTAACATCTTGCTCAAAAG
1 ACTTAACATCTTGCCCAAAAG
63579 AC-TAACA
1 ACTTAACA
63586 GATGACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
ACTTAACATCTTGCCCAAAAG
Found at i:63644 original size:42 final size:41
Alignment explanation
Indices: 63550--63645 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
63540 TAACATCTTG
* *
63550 CCCGAAGGACTTAACATCTTGCTCAAAAGACTAACAGATGA
1 CCCGAAGGATTTAACATCATGCTCAAAAGACTAACAGATGA
* * * * *
63591 CTCAAAGGATTTAAGCATCATGCTCGAAGGACTTACAGATGA
1 CCCGAAGGATTTAA-CATCATGCTCAAAAGACTAACAGATGA
*
63633 CCCGAATGATTTA
1 CCCGAAGGATTTA
63646 CAAATTTGGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 11 0.25
42 33 0.75
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (41 bp):
CCCGAAGGATTTAACATCATGCTCAAAAGACTAACAGATGA
Found at i:64086 original size:244 final size:235
Alignment explanation
Indices: 63640--64098 Score: 537
Period size: 244 Copynumber: 1.9 Consensus size: 235
63630 TGACCCGAAT
* * * * * *
63640 GATTTACAAATTTGGGAAATAGTTTAATGGGTAAGAAAGTTTGGAAATTGTTTTCTTACTTTTCA
1 GATTTACAAATTTGGGAAATAATTTAATGGGAAAAAAACTTTGGAAAATGCTTTCTTACTTTTCA
* *
63705 AAAAAATTCATTTTCTCAAAACATTAAACGATAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
66 AAAAAATTCATTTTCT-AAAACATTAAACGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTG
* * * * *
63770 AGAACATCCTACCTGATGGTTTTACGGATGGCCCGAAGGACTTATCATATTGCTTGAAAGACTTA
130 AGAACATCCTACCTGAAGGTCTTACGGATGGCCCAAAGGACTTAACATATTGCTCGAAAGACTTA
* *
63835 CAGATGACCTGAAGGATTTAAGAATCATCGATGACGCAAAG
195 CAGATGACCCGAAAGATTTAAGAATCATCGATGACGCAAAG
* * *
63876 GATTTGCACATTTGGGAAATAATTTACTGGGAAAAAAACTTTGGAAAATGCTTTCTTACTTTTC-
1 GATTTACAAATTTGGGAAATAATTTAATGGGAAAAAAACTTTGGAAAATGCTTTCTTACTTTTCA
* * * * *
63940 AAGAATTTTATTTTCT-GAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTGA
66 AAAAAATTCATTTTCTAAAACATTAAACGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTG-
* * *
64004 AAATCATGTGTAAACATCCTGCCTGAAGGTCTTATGGATGGCCCAAAGGACTTAACATCTTGCTC
130 -----A---G--AACATCCTACCTGAAGGTCTTACGGATGGCCCAAAGGACTTAACATATTGCTC
*
64069 GAAAG-TTTGACAGATGACCCGAAAGATTTA
185 GAAAGACTT-ACAGATGACCCGAAAGATTTA
64099 TACATCATGC
Statistics
Matches: 184, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
233 43 0.23
235 13 0.07
236 55 0.30
239 1 0.01
242 1 0.01
243 2 0.01
244 69 0.38
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (235 bp):
GATTTACAAATTTGGGAAATAATTTAATGGGAAAAAAACTTTGGAAAATGCTTTCTTACTTTTCA
AAAAAATTCATTTTCTAAAACATTAAACGAGAAACTTTGGTAATCACTTTCTCATTTTCATGTGA
GAACATCCTACCTGAAGGTCTTACGGATGGCCCAAAGGACTTAACATATTGCTCGAAAGACTTAC
AGATGACCCGAAAGATTTAAGAATCATCGATGACGCAAAG
Found at i:64127 original size:42 final size:42
Alignment explanation
Indices: 64058--64140 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
64048 AAAGGACTTA
*
64058 ACATCTTGCTCGAAAGTTTGACAGATGACCCGAAAGATTTAT
1 ACATCATGCTCGAAAGTTTGACAGATGACCCGAAAGATTTAT
*
64100 ACATCATGCTCGAAAGATTT-ACTGATGACCCGAAAGATTTA
1 ACATCATGCTCGAAAG-TTTGACAGATGACCCGAAAGATTTA
64141 AAAATTTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (42 bp):
ACATCATGCTCGAAAGTTTGACAGATGACCCGAAAGATTTAT
Found at i:64135 original size:20 final size:20
Alignment explanation
Indices: 64068--64140 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
64058 ACATCTTGCT
*
64068 CGAAAG-TTTGACAGATGACC
1 CGAAAGATTT-ACTGATGACC
* *
64088 CGAAAGATTTATACATCATG-CT
1 CGAAAGA-TT-TAC-TGATGACC
64110 CGAAAGATTTACTGATGACC
1 CGAAAGATTTACTGATGACC
64130 CGAAAGATTTA
1 CGAAAGATTTA
64141 AAAATTTGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.09
20 21 0.49
21 2 0.05
22 12 0.28
23 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (20 bp):
CGAAAGATTTACTGATGACC
Found at i:65665 original size:39 final size:39
Alignment explanation
Indices: 65558--65676 Score: 168
Period size: 39 Copynumber: 3.1 Consensus size: 39
65548 TCCATTCAAA
* * *
65558 ATTATTTATTGCTGATATGAGCCTTCAAAATGCCCCAAT
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATGTCCCAAC
* * *
65597 ATT-TTTCATGTTGATGTGAGCCTTCAAAATGTCCCAAC
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATGTCCCAAC
*
65635 ATTATTTCTTGCTGATATGAGCCTTTAAAATGTCCCAAC
1 ATTATTTCTTGCTGATATGAGCCTTCAAAATGTCCCAAC
65674 ATT
1 ATT
65677 CCAAGTTGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
38 32 0.46
39 37 0.54
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (39 bp):
ATTATTTCTTGCTGATATGAGCCTTCAAAATGTCCCAAC
Found at i:71172 original size:16 final size:16
Alignment explanation
Indices: 71153--71184 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
71143 CATGTATCAC
71153 TAACAACACGTGTCAT
1 TAACAACACGTGTCAT
71169 TAACAACACGTGTCAT
1 TAACAACACGTGTCAT
71185 GCTCTTATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
TAACAACACGTGTCAT
Found at i:72307 original size:14 final size:14
Alignment explanation
Indices: 72290--72318 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
72280 TTATAACATT
72290 TTAATTTATTTTTA
1 TTAATTTATTTTTA
72304 TTAATTTATTTTTA
1 TTAATTTATTTTTA
72318 T
1 T
72319 AAAATTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTAATTTATTTTTA
Done.