Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006572.1 Hibiscus syriacus cultivar Beakdansim tig00016100_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: 59760
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:355 original size:36 final size:37
Alignment explanation
Indices: 315--418 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
305 GTGCTTGTGG
* * *
315 ATCCTATCTTTAGGA-TTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
351 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
388 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
419 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 14 0.23
37 46 0.77
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:10280 original size:30 final size:30
Alignment explanation
Indices: 10237--10330 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 30
10227 AATTTGGAAC
10237 AGTTTAGGG-ACCAAAGGGATAATTTTCAAA
1 AGTTT-GGGTACCAAAGGGATAATTTTCAAA
* * *
10267 TGTTTGGGTACCAAAAGTATAATTTTCAAA
1 AGTTTGGGTACCAAAGGGATAATTTTCAAA
* *
10297 AGTTTAGGTACCAAAAGTG-TAATTTTCAAA
1 AGTTTGGGTACC-AAAGGGATAATTTTCAAA
10327 AGTT
1 AGTT
10331 AAGTATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.06
30 48 0.89
31 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (30 bp):
AGTTTGGGTACCAAAGGGATAATTTTCAAA
Found at i:10296 original size:15 final size:15
Alignment explanation
Indices: 10278--10329 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
10268 GTTTGGGTAC
10278 CAAAAGTATAATTTT
1 CAAAAGTATAATTTT
* ** **
10293 CAAAAGTTTAGGTAC
1 CAAAAGTATAATTTT
*
10308 CAAAAGTGTAATTTT
1 CAAAAGTATAATTTT
10323 CAAAAGT
1 CAAAAGT
10330 TAAGTATTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
CAAAAGTATAATTTT
Found at i:16487 original size:90 final size:89
Alignment explanation
Indices: 16335--16507 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 89
16325 ACACACCCTT
16335 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
16400 ATTAATTGAAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
16424 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
16489 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
16508 TTCAGGATTA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 30 0.38
90 50 0.62
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:22710 original size:8 final size:8
Alignment explanation
Indices: 22697--22743 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
22687 AACCCGACCC
22697 GACCCGTT
1 GACCCGTT
22705 GACCC---
1 GACCCGTT
22710 GACCCGTT
1 GACCCGTT
22718 GA-CCGTT
1 GACCCGTT
22725 GACCCGTT
1 GACCCGTT
22733 GA-CCGTT
1 GACCCGTT
22740 GACC
1 GACC
22744 GACTTTGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:22710 original size:13 final size:13
Alignment explanation
Indices: 22692--22736 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
22682 GTCACAACCC
22692 GACCCGACCCGTT
1 GACCCGACCCGTT
22705 GACCCGACCCGTT
1 GACCCGACCCGTT
*
22718 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
22733 GACC
1 GACC
22737 GTTGACCGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:22725 original size:7 final size:7
Alignment explanation
Indices: 22713--22744 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
22703 TTGACCCGAC
22713 CCGTTGA
1 CCGTTGA
22720 CCGTTGA
1 CCGTTGA
22727 CCCGTTGA
1 -CCGTTGA
22735 CCGTTGA
1 CCGTTGA
22742 CCG
1 CCG
22745 ACTTTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:22730 original size:15 final size:15
Alignment explanation
Indices: 22697--22743 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
22687 AACCCGACCC
*
22697 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
22710 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
22725 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
22740 GACC
1 GACC
22744 GACTTTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:27487 original size:13 final size:13
Alignment explanation
Indices: 27483--27543 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
27473 CCGTTGACCC
27483 GACCCGACCCGTT
1 GACCCGACCCGTT
*
27496 TACCCGACCCGTT
1 GACCCGACCCGTT
27509 GACTCGACCTGACCCGTT
1 GA--C--CC-GACCCGTT
27527 GACCCGACCCGTT
1 GACCCGACCCGTT
27540 GACC
1 GACC
27544 GTTGACCGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 25 0.61
14 2 0.05
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.16, C:0.44, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:27506 original size:18 final size:18
Alignment explanation
Indices: 27461--27537 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
27451 ACCGGTCACA
*
27461 ACCCGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
27479 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
27496 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
27510 ACTCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
27528 ACCCGACCCG
1 ACCCGACCCG
27538 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
13 12 0.25
18 36 0.75
ACGTcount: A:0.18, C:0.48, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:27509 original size:31 final size:31
Alignment explanation
Indices: 27465--27543 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
27455 GTCACAACCC
*
27465 GACCCAACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
27496 TACCCGACCCGTTGACTCGACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
27527 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
27544 GTTGACCGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:30135 original size:24 final size:24
Alignment explanation
Indices: 30041--30140 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
30031 ATATTTTATC
* *
30041 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
30065 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
30089 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
30113 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
30137 TGAT
1 TGAT
30141 TTTTTATATC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:31908 original size:20 final size:21
Alignment explanation
Indices: 31853--31908 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
31843 TAATTAAATC
31853 TATATTTAATTAATTAAAATTAA
1 TATATTTAATT-ATTAAAA-TAA
*
31876 -ATATTCAGGATTATTAAAA-AA
1 TATATTTA--ATTATTAAAATAA
31897 TATATTTAATTA
1 TATATTTAATTA
31909 ACTCTAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 4 0.14
21 2 0.07
22 12 0.43
23 7 0.25
24 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATTTAATTATTAAAATAA
Found at i:42784 original size:37 final size:36
Alignment explanation
Indices: 42709--42784 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
42699 TTTTTATATT
*
42709 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
42745 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
42782 TTT
1 TTT
42785 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:42947 original size:18 final size:19
Alignment explanation
Indices: 42924--42967 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
42914 CCAGTAATCC
*
42924 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
42942 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
42962 TATTCC
1 TATTCC
42968 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:42955 original size:20 final size:20
Alignment explanation
Indices: 42930--42967 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42920 ATCCTATTCC
*
42930 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
42950 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
42968 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:44040 original size:8 final size:9
Alignment explanation
Indices: 44006--44039 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
43996 ATCCTTTTCC
44006 TTAAAATATT
1 TTAAAA-ATT
44016 TTAAAAATT
1 TTAAAAATT
44025 TTAAAAATT
1 TTAAAAATT
44034 TTAAAA
1 TTAAAA
44040 TAGATGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAAATT
Found at i:46317 original size:2 final size:2
Alignment explanation
Indices: 46312--46343 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46302 CATACGTGTG
46312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46344 AGGTTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47710 original size:191 final size:191
Alignment explanation
Indices: 47386--47766 Score: 744
Period size: 191 Copynumber: 2.0 Consensus size: 191
47376 TTTGATTAAT
*
47386 TACTAAATAATTGGGTTTTTTATTTTTTTAGATTCAATAATTTTAAGGGAATTGAGAACTCAGTT
1 TACTAAATAATTGGGTTTTTTATTTTTTTAGATTCAATAATTTTAAGGGAATTGAGAACTCAGCT
47451 TTGTGTTGCTTGATTGTGTTTTTCGCTTTTCCTCACACATTGTGCACTTGCATTATCATGAAATT
66 TTGTGTTGCTTGATTGTGTTTTTCGCTTTTCCTCACACATTGTGCACTTGCATTATCATGAAATT
47516 AGCTAAAACATCGCTCTTCTCATTTAAGTGAGAGTGAGAAGTTATACCTTCGTAATGGTTA
131 AGCTAAAACATCGCTCTTCTCATTTAAGTGAGAGTGAGAAGTTATACCTTCGTAATGGTTA
47577 TACTAAATAATTGGGTTTTTTATTTTTTTAGATTCAATAATTTTAAGGGAATTGAGAACTCAGCT
1 TACTAAATAATTGGGTTTTTTATTTTTTTAGATTCAATAATTTTAAGGGAATTGAGAACTCAGCT
*
47642 TTGTGTTGTTTGATTGTGTTTTTCGCTTTTCCTCACACATTGTGCACTTGCATTATCATGAAATT
66 TTGTGTTGCTTGATTGTGTTTTTCGCTTTTCCTCACACATTGTGCACTTGCATTATCATGAAATT
47707 AGCTAAAACATCGCTCTTCTCATTTAAGTGAGAGTGAGAAGTTATACCTTCGTAATGGTT
131 AGCTAAAACATCGCTCTTCTCATTTAAGTGAGAGTGAGAAGTTATACCTTCGTAATGGTT
47767 TTCACCATTG
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 188 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (191 bp):
TACTAAATAATTGGGTTTTTTATTTTTTTAGATTCAATAATTTTAAGGGAATTGAGAACTCAGCT
TTGTGTTGCTTGATTGTGTTTTTCGCTTTTCCTCACACATTGTGCACTTGCATTATCATGAAATT
AGCTAAAACATCGCTCTTCTCATTTAAGTGAGAGTGAGAAGTTATACCTTCGTAATGGTTA
Done.