Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000363.1 Hibiscus syriacus cultivar Beakdansim tig00000662_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: 61588
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:14072 original size:60 final size:60
Alignment explanation
Indices: 13951--14105 Score: 179
Period size: 60 Copynumber: 2.6 Consensus size: 60
13941 GTATGTATGT
* * * *
13951 ATAGTTT-GGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAACTTAGAAAGAGGGTC
1 ATAGTTTAGGGATGAAATTGAAACGTTC-AAAAGTTTGAGGACCAACTTAGAAAGAGAGTC
* * * *
14011 ATAGTTTAGGGATGAAATTGAAACGTTCAAAAGTTTGAGGACTAA-TATTGAATGATAGTC
1 ATAGTTTAGGGATGAAATTGAAACGTTCAAAAGTTTGAGGACCAACT-TAGAAAGAGAGTC
* * *
14071 ATAGTTTAGGGATAAAATTGAAACATTTAAAAGTT
1 ATAGTTTAGGGATGAAATTGAAACGTTCAAAAGTT
14106 GAAAGACTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.01
60 63 0.77
61 18 0.22
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTGAAACGTTCAAAAGTTTGAGGACCAACTTAGAAAGAGAGTC
Found at i:14114 original size:60 final size:60
Alignment explanation
Indices: 13951--14133 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 60
13941 GTATGTATGT
* * ** ** * * *
13951 ATAGTTT-GGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAACTTAGAAA-GAGGGTC
1 ATAGTTTAGGGATAAAATTGAAACATTC-AAAAGTTTGAAGACTAATTTA-AAATGAGAGTC
* * * * *
14011 ATAGTTTAGGGATGAAATTGAAACGTTCAAAAGTTTGAGGACTAATATT-GAATGATAGTC
1 ATAGTTTAGGGATAAAATTGAAACATTCAAAAGTTTGAAGACTAAT-TTAAAATGAGAGTC
*
14071 ATAGTTTAGGGATAAAATTGAAACATTTAAAAG-TTGAAAGACTAATTTAAAATGAGAGTC
1 ATAGTTTAGGGATAAAATTGAAACATTCAAAAGTTTG-AAGACTAATTTAAAATGAGAGTC
14131 ATA
1 ATA
14134 CTTTGAGGAC
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 7 0.07
60 77 0.74
61 20 0.19
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (60 bp):
ATAGTTTAGGGATAAAATTGAAACATTCAAAAGTTTGAAGACTAATTTAAAATGAGAGTC
Found at i:16695 original size:22 final size:22
Alignment explanation
Indices: 16661--16710 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
16651 AAATACGGTA
* * *
16661 TGAACAGTAATGAACAGTAACG
1 TGAACAATAATGAAAAGTAACC
* *
16683 TGAACAATGATGAAAAGTACCC
1 TGAACAATAATGAAAAGTAACC
16705 TGAACA
1 TGAACA
16711 GTACCCGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (22 bp):
TGAACAATAATGAAAAGTAACC
Found at i:17648 original size:31 final size:31
Alignment explanation
Indices: 17561--17684 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 31
17551 AACCTCGGCA
* * *
17561 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* * **
17592 ACTGTCAATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
17623 ACTGTCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-A-T
* *
17656 A-TGTCCATATGTTCC-ATATAACATAGGTA
1 ACTGTCCATATGTCCCGA-AGAACATAGGTA
17685 AACTCTCGAC
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.01
31 49 0.64
32 23 0.30
33 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:19467 original size:65 final size:64
Alignment explanation
Indices: 19326--19488 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 64
19316 AATTGTTCAG
* * * * * *
19326 AGTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAGTT
1 AGTGTATCGATGCATATGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGAAATT
* * *
19390 AGTGCATCGATGCATTATG-AGTGCATCGATGCACCCCTCTTAAAATGAAAACATCGAAGGTAAA
1 AGTGTATCGATGCA-TATGAAGTGCATCGATGCACCCAT-TAAAAATGAAAACATCGAAGG-AAA
19454 TT
63 TT
* * *
19456 -GTGTATCGATGCATGTGTAGTGCATCCATGCAC
1 AGTGTATCGATGCATATGAAGTGCATCGATGCAC
19489 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 34 0.41
65 46 0.55
66 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (64 bp):
AGTGTATCGATGCATATGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGAAATT
Found at i:19521 original size:20 final size:20
Alignment explanation
Indices: 19496--19533 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19486 CACATGTTAA
19496 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
19516 AGAATGCATCGATTCACT
1 AGAATGCATCGATGCACT
19534 TCAAGGGAAA
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:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:20722 original size:30 final size:29
Alignment explanation
Indices: 20683--20741 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
20673 GAGAATTTAC
* *
20683 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
20712 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
20742 TATATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:21005 original size:23 final size:23
Alignment explanation
Indices: 20972--21085 Score: 129
Period size: 23 Copynumber: 5.0 Consensus size: 23
20962 CATTTTATAT
* * *
20972 GGCACTTCGGTACAATCCTACGT
1 GGCACTTCGGTGCAATTCTACGC
* *
20995 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
21018 GGCACTTCGGTGCAATTATATGA
1 GGCACTTCGGTGCAATTCTACGC
* *
21041 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
21064 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
21086 AACTGTGGTG
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:21045 original size:46 final size:46
Alignment explanation
Indices: 20972--21086 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
20962 CATTTTATAT
* ** *
20972 GGCACTTCGGTACAATCCTACGTGGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTATACGAGGCACTACGGTGCATTTCTACGC
*
21018 GGCACTTCGGTGCAATTATATGAGGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTATACGAGGCACTACGGTGCATTTCTACGC
21064 GGCACTTCGGTGCAATTATACGA
1 GGCACTTCGGTGCAATTATACGA
21087 ACTGTGGTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (46 bp):
GGCACTTCGGTGCAATTATACGAGGCACTACGGTGCATTTCTACGC
Found at i:23425 original size:54 final size:51
Alignment explanation
Indices: 23338--23489 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 51
23328 TTCGTATTCG
* *
23338 GTTT-TTTATTTTTAAAAGTGTTCATGTTCGTTTAAATCTTTAATATCGTGTTT
1 GTTTATTTATTTTTAAAAGTGTTCATATTCGTTTAAATTTTTAATATC-TG--T
* * * *
23391 GTTTATTTATTTTCAAAGGTGTTCATATTTGTTTAATTTTTTAATAT-TGT
1 GTTTATTTATTTTTAAAAGTGTTCATATTCGTTTAAATTTTTAATATCTGT
* *
23441 GTTTATTTATTTTTAAAAGTGCTCATATTCGTTTATATTTTTAATATCT
1 GTTTATTTATTTTTAAAAGTGTTCATATTCGTTTAAATTTTTAATATCT
23490 ATCCCTAAGC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
50 42 0.49
51 1 0.01
52 2 0.02
53 4 0.05
54 36 0.42
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.58
Consensus pattern (51 bp):
GTTTATTTATTTTTAAAAGTGTTCATATTCGTTTAAATTTTTAATATCTGT
Found at i:26076 original size:216 final size:216
Alignment explanation
Indices: 25693--26158 Score: 627
Period size: 216 Copynumber: 2.2 Consensus size: 216
25683 GGCACTTAGT
*
25693 TTTAAA-TTGGAATCATGTCTTACTTTTTCATATCAATGCTTAGCGTTGTTAATGGTCACATAGT
1 TTTAAATTTGGAATCATGTCTAACTTTTTCATATCAATGCTTAGCGTTGTTAATGGTCACATAGT
* * * * * *
25757 AGCTCCTTGATTTGTGGTTGATCCCTTGAGCTTTGATTTAGCTTTTTTTAATTGTTTCCTGCCTT
66 AGCTCCTTGATTTCTGGCTGAACCCTTGAACTTTGATTTAGCTGTTTTTAATTGTTTCCTGCCTA
* ** * * *
25822 GCTTCTAATGATTTCTGGACAACCGCTTAGTGGTTAGTTTTGAATTTCACCTAGTCTTCTGCATC
131 CCTTCTAATGATTTCCCGACAACCACTTAGTGGTTAGTTTTAAATTTCACCTAGTCTTCTGCACC
** * *
25887 ATTTTGGCAAGCTAGTTGAGG
196 ACCTTGGCAAGCTAATGGAGG
* *
25908 TTTAAATTTGGAATCATGTCTAACTTTTTCGTATCGATGCTTAG-GTTTGTTAATGGTCACATAG
1 TTTAAATTTGGAATCATGTCTAACTTTTTCATATCAATGCTTAGCG-TTGTTAATGGTCACATAG
* *
25972 TAGTTCCTTGATTTCTGGCTGAACCCTTGAACTTTGATTTTGCTGTTTTTAATTGTTTCCTGCCT
65 TAGCTCCTTGATTTCTGGCTGAACCCTTGAACTTTGATTTAGCTGTTTTTAATTGTTTCCTGCCT
* * *
26037 ACCTTCTAATGATTTCCCGACAAGCACTTAAGT-GTTAGTTTTAAATTTCTCCTAGTGTTCTGCA
130 ACCTTCTAATGATTTCCCGACAACCACTT-AGTGGTTAGTTTTAAATTTCACCTAGTCTTCTGCA
*
26101 CCACCTTGGCAAGTTAATGGAGG
194 CCACCTTGGCAAGCTAATGGAGG
* * *
26124 GTTAAATTTGAAATCATGTGT--CTTTTTCATATCAA
1 TTTAAATTTGGAATCATGTCTAACTTTTTCATATCAA
26159 GATAGTAGCT
Statistics
Matches: 218, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
214 12 0.06
215 7 0.03
216 196 0.90
217 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (216 bp):
TTTAAATTTGGAATCATGTCTAACTTTTTCATATCAATGCTTAGCGTTGTTAATGGTCACATAGT
AGCTCCTTGATTTCTGGCTGAACCCTTGAACTTTGATTTAGCTGTTTTTAATTGTTTCCTGCCTA
CCTTCTAATGATTTCCCGACAACCACTTAGTGGTTAGTTTTAAATTTCACCTAGTCTTCTGCACC
ACCTTGGCAAGCTAATGGAGG
Found at i:35435 original size:37 final size:36
Alignment explanation
Indices: 35394--35465 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
35384 TTAAAGTTTA
35394 GTTTTTATTTCATTTTAGT-CCCACTGTTAAAAATTTG
1 GTTTTTATTTCATTTTAGTACCC-C-GTTAAAAATTTG
* *
35431 GTTTTTGTTTCATTTTAGTACCCCGTTTAAAATTT
1 GTTTTTATTTCATTTTAGTACCCCGTTAAAAATTT
35466 ATGTTAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 10 0.31
37 19 0.59
38 3 0.09
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (36 bp):
GTTTTTATTTCATTTTAGTACCCCGTTAAAAATTTG
Found at i:36218 original size:20 final size:21
Alignment explanation
Indices: 36184--36222 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
36174 ACGGATACTA
*
36184 TTAACAGTTTTGAAACTTTTG
1 TTAACAGTTTCGAAACTTTTG
36205 TTAA-AGTTTCGAAACTTT
1 TTAACAGTTTCGAAACTTT
36223 GACCCACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (21 bp):
TTAACAGTTTCGAAACTTTTG
Found at i:41614 original size:18 final size:20
Alignment explanation
Indices: 41591--41638 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
41581 ATTTGAATTT
41591 AAAAAATTAGAAAAA-TAC-
1 AAAAAATTAGAAAAATTACA
*
41609 AAAAAATCAGAAAAATTACA
1 AAAAAATTAGAAAAATTACA
41629 AAAAAATTAG
1 AAAAAATTAG
41639 TATGCTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 3 0.12
20 9 0.35
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAAAATTAGAAAAATTACA
Found at i:42513 original size:23 final size:24
Alignment explanation
Indices: 42469--42516 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
42459 ATGTGTTATG
* **
42469 TTTTTTCTAAAATATTTTTAAATA
1 TTTTTTCTAAAAAATTAATAAATA
42493 TTTTTT-TAAAAAATTAATAAATA
1 TTTTTTCTAAAAAATTAATAAATA
42516 T
1 T
42517 AAACATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTTCTAAAAAATTAATAAATA
Found at i:54988 original size:3 final size:3
Alignment explanation
Indices: 54974--55067 Score: 152
Period size: 3 Copynumber: 31.3 Consensus size: 3
54964 TACCCATATC
* * *
54974 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55022 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55068 AATATATTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:55631 original size:14 final size:15
Alignment explanation
Indices: 55601--55634 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
55591 AATCAGTAGC
55601 AAAGAAACAGAAAAG
1 AAAGAAACAGAAAAG
*
55616 AAAGAAA-AGAAGAG
1 AAAGAAACAGAAAAG
55630 AAAGA
1 AAAGA
55635 CTTACCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAACAGAAAAG
Done.