Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002597.1 Hibiscus syriacus cultivar Beakdansim tig00005254_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: 68156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4914 original size:39 final size:40
Alignment explanation
Indices: 4860--4944 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 40
4850 TACTACTGCA
* *
4860 AAACAGATACGTTAGCACTAAC-TGTTTGG-AAAATAAATC
1 AAACAGATACATTAGCACTAACAT-CTTGGAAAAATAAATC
*
4899 AAACAGATACATTAGCACTAACATCTTGGAAAAATAATTC
1 AAACAGATACATTAGCACTAACATCTTGGAAAAATAAATC
4939 AAACAG
1 AAACAG
4945 TAAACAAGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 25 0.61
40 16 0.39
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (40 bp):
AAACAGATACATTAGCACTAACATCTTGGAAAAATAAATC
Found at i:24258 original size:20 final size:20
Alignment explanation
Indices: 24233--24286 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
24223 GACCAACAAA
24233 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
24253 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
24273 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
24287 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:24323 original size:21 final size:21
Alignment explanation
Indices: 24294--24360 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
24284 AATATGTAAA
*
24294 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
24315 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
** *
24336 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
24356 TCGCA
1 TCGCA
24361 ACGCGAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 10 0.25
21 30 0.75
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:24356 original size:20 final size:20
Alignment explanation
Indices: 24331--24375 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
24321 TGCGATATTC
*
24331 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
24351 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
24371 CAAAT
1 CAAAT
24376 GTTTTTACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:24528 original size:22 final size:22
Alignment explanation
Indices: 24503--24553 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
24493 CTATGGCGAC
24503 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
24525 ATCCGCCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
24547 ATCCGTC
1 ATCCGTC
24554 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:24842 original size:19 final size:19
Alignment explanation
Indices: 24773--24834 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
24763 AACACCAAAT
* *
24773 TCGCAACGCGAAAATGAAAA
1 TCGCAATGCGAAACT-AAAA
24793 TCGCAATGCGAAACTAAAA
1 TCGCAATGCGAAACTAAAA
24812 TCGCAATGCGAAACTAAAA
1 TCGCAATGCGAAACTAAAA
24831 TCGC
1 TCGC
24835 GTTGCGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 27 0.68
20 13 0.32
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAACTAAAA
Found at i:27018 original size:21 final size:21
Alignment explanation
Indices: 26992--27047 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
26982 TATGCTCGAT
26992 GCACCTATCATCATTCAAGAG
1 GCACCTATCATCATTCAAGAG
* *
27013 GCACCT-CCTATCGTTCAAGAG
1 GCACCTATC-ATCATTCAAGAG
*
27034 GCCCCTATCATCAT
1 GCACCTATCATCAT
27048 CGAAGAAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (21 bp):
GCACCTATCATCATTCAAGAG
Found at i:27042 original size:42 final size:42
Alignment explanation
Indices: 26995--27077 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
26985 GCTCGATGCA
* *
26995 CCTATCATCATTC-AAG-AGGCACCTCCTATCGTTCAAGAGGCC
1 CCTATCATCA-TCGAAGAAGGC-CCTCCCACCGTTCAAGAGGCC
*
27037 CCTATCATCATCGAAGAAGTCCCTCCCACCGTTCAAGAGGC
1 CCTATCATCATCGAAGAAGGCCCTCCCACCGTTCAAGAGGC
27078 TACTGTCATC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 31 0.86
43 3 0.08
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.22
Consensus pattern (42 bp):
CCTATCATCATCGAAGAAGGCCCTCCCACCGTTCAAGAGGCC
Found at i:31929 original size:19 final size:20
Alignment explanation
Indices: 31905--32056 Score: 116
Period size: 20 Copynumber: 7.6 Consensus size: 20
31895 ACTAAAACCT
*
31905 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
31924 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
31944 GTTGCGAATTTGGAATATCGC
1 GTTGCGAATTTGAAAT-TCGC
*
31965 GTTGCGAATTTAGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
31986 AATGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
32006 GTTGCGAAATTGAAA-ACTGG
1 GTTGCGAATTTGAAATTC-GC
*
32026 GTTGCGAATTTGAGA-TCGC
1 GTTGCGAATTTGAAATTCGC
*
32045 GTTTCGAATTTG
1 GTTGCGAATTTG
32057 TTGGTCATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 30 0.29
20 42 0.40
21 27 0.26
22 4 0.04
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:40905 original size:2 final size:2
Alignment explanation
Indices: 40898--40924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40888 TGTTTAGGGT
40898 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40925 TAATTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41233 original size:18 final size:19
Alignment explanation
Indices: 41210--41245 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41200 TGACATTTTT
*
41210 ATTGAAA-AATATTAAAAG
1 ATTGAAATAATAATAAAAG
41228 ATTGAAATAATAATAAAA
1 ATTGAAATAATAATAAAA
41246 TGAAAGCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (19 bp):
ATTGAAATAATAATAAAAG
Found at i:41490 original size:20 final size:19
Alignment explanation
Indices: 41456--41499 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
41446 GGCTTGTATG
41456 AAAAATAAACCATTAATATAAA
1 AAAAATAAA-CATTAA-A-AAA
41478 AAAAATAAA-ATTAAAAAA
1 AAAAATAAACATTAAAAAA
41496 AAAA
1 AAAA
41500 TATGAACGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 5 0.23
22 9 0.41
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAATAAACATTAAAAAA
Found at i:50750 original size:19 final size:19
Alignment explanation
Indices: 50726--50771 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
50716 AAATAGCCAG
50726 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGGCT
50745 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGGCT
*
50764 GGTGCATC
1 AGTGCATC
50772 AAATGCATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.26
Consensus pattern (19 bp):
AGTGCATCGATGCATGGCT
Found at i:56523 original size:22 final size:21
Alignment explanation
Indices: 56481--56520 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56471 GAGTTTATTT
*
56481 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
56502 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
56521 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:58491 original size:18 final size:17
Alignment explanation
Indices: 58437--58485 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
58427 TTGGACCCTT
* *
58437 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
58455 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
58473 AGTGCATTCGATG
1 AGTGCA-TCGATG
58486 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:58590 original size:65 final size:65
Alignment explanation
Indices: 58457--58616 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
58447 TGCACTAAGA
* *
58457 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
58521 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
58584 AT
65 -G
*
58586 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
58617 CAATTTAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 29 0.34
65 54 0.63
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:58655 original size:65 final size:64
Alignment explanation
Indices: 58457--58666 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
58447 TGCACTAAGA
* * ** *
58457 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
58521 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
58584 AT-
63 -TG
* * *
58586 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATACATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
58650 G
64 G
* *
58651 GTGCATTGGTGCATCA
1 GTGCATCGATGCATCA
58667 CTTTGATAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 50 0.41
65 62 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:61856 original size:46 final size:47
Alignment explanation
Indices: 61767--61859 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
61757 CTTTTTTTAC
* * *
61767 TTTAAGTACCTAAATTATATTTTGGTCAAATTAAGTTTTTAAACTAT
1 TTTAAGTACCTAAATTATATTTTGGTCAAATGAAGTCTCTAAACTAT
61814 TTTAAGTACCTAAATTAT-TTTTGGTCAAAATGAA-TCTCTAAACTAT
1 TTTAAGTACCTAAATTATATTTTGGTC-AAATGAAGTCTCTAAACTAT
61860 GACTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 18 0.43
47 24 0.57
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (47 bp):
TTTAAGTACCTAAATTATATTTTGGTCAAATGAAGTCTCTAAACTAT
Found at i:66948 original size:6 final size:6
Alignment explanation
Indices: 66937--67035 Score: 104
Period size: 6 Copynumber: 17.2 Consensus size: 6
66927 AAATATTATT
66937 AATATA AATATA AATATA AATAT- AA-AT- AATATA AATATA AATA-A
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
* *
66981 ATAAATA AATATA AATA-A ATAAATA AATATA AATATA TAATATA AAT-T-
1 A-ATATA AATATA AATATA A-ATATA AATATA AATATA -AATATA AATATA
67029 AATATA A
1 AATATA A
67036 TTTAATATTA
Statistics
Matches: 80, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
4 7 0.09
5 10 0.12
6 53 0.66
7 10 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:66980 original size:4 final size:4
Alignment explanation
Indices: 66958--67032 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
66948 AAATATAAAT
66958 ATAA ATAA TATAA AT-- ATAA ATAA ATAA ATAA AT-- ATAA ATAA ATAA
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* *
67003 ATAA AT-- ATAA ATAT ATAA TATAA ATTA ATA
1 ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATA
67033 TAATTTAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
2 6 0.10
4 45 0.76
5 8 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAA
Found at i:66980 original size:10 final size:10
Alignment explanation
Indices: 66946--67035 Score: 91
Period size: 10 Copynumber: 9.0 Consensus size: 10
66936 TAATATAAAT
66946 ATAAATATAA
1 ATAAATATAA
66956 ATATAA-ATAA
1 ATA-AATATAA
66966 TATAAATATAA
1 -ATAAATATAA
66977 AT-AA-ATAA
1 ATAAATATAA
66985 ATAAATATAA
1 ATAAATATAA
66995 AT-AA-ATAA
1 ATAAATATAA
67003 ATAAATATAAA
1 ATAAATAT-AA
67014 TATATAATATAA
1 -ATA-AATATAA
*
67026 ATTAATATAA
1 ATAAATATAA
67036 TTTAATATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
8 12 0.17
9 8 0.12
10 26 0.38
11 13 0.19
12 5 0.07
13 5 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAAATATAA
Found at i:67040 original size:10 final size:10
Alignment explanation
Indices: 66934--67043 Score: 86
Period size: 10 Copynumber: 10.8 Consensus size: 10
66924 ATTAAATATT
66934 ATTAATATAA
1 ATTAATATAA
66944 ATATAAATATAA
1 AT-T-AATATAA
66956 ATATAA-ATAA
1 AT-TAATATAA
*
66966 TATAAATATAA
1 -ATTAATATAA
66977 A-TAA-ATAA
1 ATTAATATAA
*
66985 ATAAATATAA
1 ATTAATATAA
66995 A-TAA-ATAA
1 ATTAATATAA
*
67003 ATAAATATAAA
1 ATTAATAT-AA
67014 TATATAATATAA
1 -AT-TAATATAA
67026 ATTAATATAA
1 ATTAATATAA
*
67036 TTTAATAT
1 ATTAATAT
67044 TACTTATTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
8 10 0.12
9 8 0.10
10 31 0.38
11 13 0.16
12 15 0.18
13 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATTAATATAA
Done.