Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001733.1 Hibiscus syriacus cultivar Beakdansim tig00003498_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: 49543
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:779 original size:21 final size:21
Alignment explanation
Indices: 753--801 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
743 TAGGTCCTTA
753 TATTTTGTGTTTAT-TTTAATT
1 TATTTTGTG-TTATCTTTAATT
*
774 TATTTTGTGTTATCTTTATTT
1 TATTTTGTGTTATCTTTAATT
795 TACTTTT
1 TA-TTTT
802 TATTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.71
Consensus pattern (21 bp):
TATTTTGTGTTATCTTTAATT
Found at i:1940 original size:61 final size:62
Alignment explanation
Indices: 1863--1983 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 62
1853 TGCACTATGA
* *
1863 GTGCATCGATGCATCAAGTGCATTCGA-GTTTCA-AAATAGCCAGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCACAGTGCATCGATGCATGGT
* *
1924 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAGTGCATCGATGCATG
1984 AAATGCATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
61 26 0.48
62 25 0.46
63 3 0.06
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAGTGCATCGATGCATGGT
Found at i:1991 original size:62 final size:61
Alignment explanation
Indices: 1864--1997 Score: 171
Period size: 62 Copynumber: 2.2 Consensus size: 61
1854 GCACTATGAG
* * ***
1864 TGCATCGATGCATCAAGTGCATTCGAGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTG
1 TGCATCGATGCATCAAATGCATTCGAGTTTCAAAATAGCCACAGTGCATCGATGCATGAAA
* *
1925 TGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGAAA
1 TGCATCGATGCATCAAATGCATTCGA-GTTTCA-AAATAGCCACAGTGCATCGATGCATGAAA
1987 TGCATTCGATG
1 TGCA-TCGATG
1998 TTCAATTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
61 25 0.40
62 29 0.46
63 9 0.14
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (61 bp):
TGCATCGATGCATCAAATGCATTCGAGTTTCAAAATAGCCACAGTGCATCGATGCATGAAA
Found at i:11128 original size:22 final size:21
Alignment explanation
Indices: 11086--11125 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11076 GAGTTTATTT
*
11086 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
11107 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
11126 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:21009 original size:15 final size:15
Alignment explanation
Indices: 20974--21049 Score: 55
Period size: 17 Copynumber: 4.8 Consensus size: 15
20964 GTGTTATGTG
*
20974 ATTTATATCATTACAC
1 ATTTATAT-ATTACAT
20990 A-TTATATATTACAT
1 ATTTATATATTACAT
*
21004 ATTTATAATATATATAT
1 ATTTAT-ATAT-TACAT
* *
21021 ATATATATATATATTAT
1 ATTTATATAT-TA-CAT
*
21038 AGTTATATATTA
1 ATTTATATATTA
21050 TATGGAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.14
15 10 0.20
16 14 0.27
17 20 0.39
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.50
Consensus pattern (15 bp):
ATTTATATATTACAT
Found at i:21063 original size:2 final size:2
Alignment explanation
Indices: 20992--21052 Score: 60
Period size: 2 Copynumber: 32.5 Consensus size: 2
20982 CATTACACAT
* *
20992 TA TA TA T- TA CA TA TT TA TA -A 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 TA TA TA TA TA
21032 TA T- TA TA GT- TA TA TA T- TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA T
21053 GGAGAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
1 5 0.10
2 43 0.88
3 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21234 original size:22 final size:22
Alignment explanation
Indices: 21187--21234 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
21177 ATCTTGGAGC
* * *
21187 AACCTGAACTGACCCAAGTTGC
1 AACCCGAACCGACCCAAGTTGA
21209 AACCCGAACCGACCCAA-TCTGA
1 AACCCGAACCGACCCAAGT-TGA
21231 AACC
1 AACC
21235 TTAAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.35, C:0.38, G:0.15, T:0.12
Consensus pattern (22 bp):
AACCCGAACCGACCCAAGTTGA
Found at i:22299 original size:55 final size:55
Alignment explanation
Indices: 22234--22363 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 55
22224 TAGTTTCTGT
* *
22234 TTATTGTTATTATTATTATTTTCT-CCTAACGTTA-TATATATATATATATTATC-
1 TTATTATTATTATTATTATTTTCTACCTAACATTATTATATATATATAT-TTATCA
* * * * *
22287 TTATTTATTTATTTTTATTATTTTTTACCTAACATTCTTATGTATATATATTTTTCA
1 TTA-TTA-TTATTATTATTATTTTCTACCTAACATTATTATATATATATATTTATCA
22344 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
22364 ATTATTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
53 3 0.05
54 2 0.03
55 29 0.45
56 15 0.23
57 15 0.23
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (55 bp):
TTATTATTATTATTATTATTTTCTACCTAACATTATTATATATATATATTTATCA
Found at i:22351 original size:3 final size:3
Alignment explanation
Indices: 22343--22369 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22333 TATATTTTTC
22343 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
22370 TAATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:22426 original size:13 final size:12
Alignment explanation
Indices: 22389--22532 Score: 66
Period size: 12 Copynumber: 11.7 Consensus size: 12
22379 TAATACTACA
22389 TTTTATTTTATAT
1 TTTTATTTTAT-T
* *
22402 ATTTATTGTATT
1 TTTTATTTTATT
22414 TTTTATTCTTATT
1 TTTTATT-TTATT
* *
22427 TTTT-TGTTTGTG
1 TTTTAT-TTTATT
*
22439 TTTT-TTTAATT
1 TTTTATTTTATT
**
22450 TATTTAATTCCATT
1 T-TTT-ATTTTATT
*
22464 TTTTCTTCCTTA-T
1 TTTTATT--TTATT
*
22477 TTTTATTTTTACT
1 TTTTA-TTTTATT
22490 TTTTA-TTTATT
1 TTTTATTTTATT
22501 TATTTA-TTTATT
1 T-TTTATTTTATT
*
22513 TATTATTTT-TAT
1 TTTTATTTTAT-T
22525 TTTTATTT
1 TTTTATTT
22533 AAATTTCACT
Statistics
Matches: 101, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
11 14 0.14
12 46 0.46
13 32 0.32
14 9 0.09
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:22492 original size:12 final size:12
Alignment explanation
Indices: 22473--22532 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 12
22463 TTTTTCTTCC
22473 TTATTTTTATTT
1 TTATTTTTATTT
22485 TTACTTTTTATTTAT
1 TTA-TTTTTA-TT-T
22500 TTATTTATTTATTT
1 TTA-TT-TTTATTT
22514 ATTATTTTTATTT
1 -TTATTTTTATTT
22527 TTATTT
1 TTATTT
22533 AAATTTCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
12 9 0.21
13 13 0.31
14 5 0.12
15 11 0.26
16 4 0.10
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:22533 original size:4 final size:4
Alignment explanation
Indices: 22491--22526 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
22481 ATTTTTACTT
*
22491 TTTA TTTA TTTA TTTA TTTA TTTA TTATT TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTT
22527 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:22551 original size:36 final size:34
Alignment explanation
Indices: 22473--22564 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 34
22463 TTTTTCTTCC
*
22473 TTATTT-TTATTTTTACTTTTTATTTATTTATTTAT
1 TTATTTATTATTTTTA-TTTTTATTTA-TAATTTAT
22508 TTATTTATTATTTTTATTTTTATTTA-AATTTCACT
1 TTATTTATTATTTTTATTTTTATTTATAATTT-A-T
* *
22543 TTACTTTATTTTTTTTCTTTTT
1 TTA-TTTATTATTTTTATTTTT
22565 TTGGAGATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.08
34 1 0.02
35 20 0.40
36 25 0.50
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (34 bp):
TTATTTATTATTTTTATTTTTATTTATAATTTAT
Found at i:36786 original size:8 final size:8
Alignment explanation
Indices: 36775--36809 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
36765 ATATATATTC
36775 ATATTTTA
1 ATATTTTA
*
36783 ATATTATA
1 ATATTTTA
*
36791 ATTTTTTA
1 ATATTTTA
36799 ATATTTTA
1 ATATTTTA
36807 ATA
1 ATA
36810 AAAATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATTTTA
Found at i:36844 original size:35 final size:36
Alignment explanation
Indices: 36796--36909 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 36
36786 TTATAATTTT
** *
36796 TTAATATTTTAATAAAAATATTATTTTAAT-AATTA
1 TTAATATAATAATAATAATATTATTTTAATAAATTA
* * * *
36831 TTAATATAATAATAATATTCTTAATTTAATAAATAA
1 TTAATATAATAATAATAATATTATTTTAATAAATTA
* * * *
36867 TAAATATAGGTTATAATAATTTTATTTTAATAAATTA
1 TTAATATA-ATAATAATAATATTATTTTAATAAATTA
36904 -TAATAT
1 TTAATAT
36910 TCATAAATTA
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
35 24 0.39
36 16 0.26
37 22 0.35
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (36 bp):
TTAATATAATAATAATAATATTATTTTAATAAATTA
Found at i:38980 original size:60 final size:60
Alignment explanation
Indices: 38899--39019 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
38889 GTAGTAATTA
* * * *
38899 ACATACTTACACCAATATAAGTATGTACATCTCTCATTATCTTGGTACCTAAACATAAAC
1 ACATACTTACACCAATATAAGTATGTACATCTCTCAATATCTTAGTACATAAAAATAAAC
* * *
38959 ACATACTTACGCCGATGTAAGTATGTACATCTCTCAATATCTTAGTACATAAAAATAAAC
1 ACATACTTACACCAATATAAGTATGTACATCTCTCAATATCTTAGTACATAAAAATAAAC
39019 A
1 A
39020 TATAATTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (60 bp):
ACATACTTACACCAATATAAGTATGTACATCTCTCAATATCTTAGTACATAAAAATAAAC
Found at i:39367 original size:16 final size:17
Alignment explanation
Indices: 39335--39367 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39325 TAATATCCCA
39335 ATAATATGTTAAGTAAT
1 ATAATATGTTAAGTAAT
*
39352 ATAATAT-TTCAGTAAT
1 ATAATATGTTAAGTAAT
39368 CTTATTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (17 bp):
ATAATATGTTAAGTAAT
Found at i:39534 original size:28 final size:27
Alignment explanation
Indices: 39492--39576 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 27
39482 GGAAGAAATG
*
39492 TTTTTTGGGTCGTTAAACGAACGATATA
1 TTTTTTAGGTCGTT-AACGAACGATATA
*
39520 TTTTTTAGGTGGTT-ACGAACGATATA
1 TTTTTTAGGTCGTTAACGAACGATATA
*
39546 TTTTTTAGGTCGTTATACGAACGATAAA
1 TTTTTTAGGTCGTTA-ACGAACGATATA
39574 TTT
1 TTT
39577 GTGATTTCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 25 0.49
28 26 0.51
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (27 bp):
TTTTTTAGGTCGTTAACGAACGATATA
Found at i:41916 original size:7 final size:7
Alignment explanation
Indices: 41901--41938 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
41891 TGTCCGTACT
*
41901 TCGTGTC
1 TCGTTTC
41908 TCGTTTC
1 TCGTTTC
41915 TCGTTTC
1 TCGTTTC
41922 TCGTTTC
1 TCGTTTC
41929 TCGTTTC
1 TCGTTTC
41936 TCG
1 TCG
41939 GTCACCTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.18, T:0.53
Consensus pattern (7 bp):
TCGTTTC
Done.