Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003897.1 Hibiscus syriacus cultivar Beakdansim tig00008425_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: 53960
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:1802 original size:10 final size:10
Alignment explanation
Indices: 1787--1820 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
1777 TTGCTTGAAG
1787 AAAAAAATGAA
1 AAAAAAATG-A
1798 AAAAAAAT-A
1 AAAAAAATGA
1807 AAAAAAATGA
1 AAAAAAATGA
1817 AAAA
1 AAAA
1821 CACGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 5 0.23
11 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:2938 original size:55 final size:55
Alignment explanation
Indices: 2868--3218 Score: 591
Period size: 55 Copynumber: 6.4 Consensus size: 55
2858 TTGAAGCATC
2868 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
2923 AAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
2978 AAGATTGTTCGAGTCTTATACTCTATGAA-GAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
3032 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCATACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * *
3087 AAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTA
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
3142 AAGATTGTTCGAGTCTTATATTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
3197 AAGA-TGTTCGAGT-TCTATACTC
1 AAGATTGTTCGAGTCT-TATACTC
3219 CCTAAAGAAA
Statistics
Matches: 276, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
53 1 0.00
54 66 0.24
55 209 0.76
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:3063 original size:109 final size:110
Alignment explanation
Indices: 2868--3218 Score: 591
Period size: 109 Copynumber: 3.2 Consensus size: 110
2858 TTGAAGCATC
2868 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
* *
2933 AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTATTGTTG
66 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
2978 AAGATTGTTCGAGTCTTATACTCTATGAA-GAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
* *
3042 GAGTCTTATACTCTCTAAAGGAATAGGGAGCATACACGATTGTTG
66 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * *
3087 AAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTAAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
*
3152 GAGTCTTATATTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
66 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
3197 AAGA-TGTTCGAGT-TCTATACTC
1 AAGATTGTTCGAGTCT-TATACTC
3219 CCTAAAGAAA
Statistics
Matches: 226, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.00
109 118 0.52
110 107 0.47
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (110 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:3148 original size:164 final size:165
Alignment explanation
Indices: 2868--3225 Score: 623
Period size: 164 Copynumber: 2.2 Consensus size: 165
2858 TTGAAGCATC
*
2868 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
* *
2933 AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTATTGTTGAAGATTGTTCGAGTCTTATA
66 AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTAAAGATTGTTCGAGTCTTATA
2998 CTCTATGAA-GAATAGGGAGCAGACACGATTGTTG
131 CTCTATGAAGGAATAGGGAGCAGACACGATTGTTG
*
3032 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCATACACGATTGTTGAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
3097 AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTAAAGATTGTTCGAGTCTTATA
66 AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTAAAGATTGTTCGAGTCTTATA
* *
3162 TTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
131 CTCTATGAAGGAATAGGGAGCAGACACGATTGTTG
*
3197 AAGA-TGTTCGAGT-TCTATACTCCCTAAAG
1 AAGATTGTTCGAGTCT-TATACTCTCTAAAG
3226 AAAGAGGGGG
Statistics
Matches: 185, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
163 1 0.01
164 155 0.84
165 29 0.16
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (165 bp):
AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
AAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACAATTGTTAAAGATTGTTCGAGTCTTATA
CTCTATGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:3455 original size:111 final size:110
Alignment explanation
Indices: 3196--3626 Score: 460
Period size: 111 Copynumber: 3.9 Consensus size: 110
3186 CACGATTGTT
* * * * ** *
3196 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGGGCGAATCCGTGGGAAGAAGA-TGTTC
1 GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATTC
* * * * *
3260 GAGTTCCATACTCCCT-AAAGAAAGA-GGAGTGAACCTATAGGAA
66 GAGTTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCATAGGCA
* *
3303 GAAGATGTTT-GAGTTCTATACTCCCTGAAAGAAAGATGGAGCGAACCCGTTTGCAGAAGATTAT
1 GAAGAT-TTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTAT
* * * *
3367 TTGAGCTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCGTTGGCA
64 TCGAGTTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCATAGGCA
* * *
3414 GAAGATTTCTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGTAGAAGATTATT
1 GAAGATTT-TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATT
* ** *
3479 CGAGTTCTATACTCCTTGAAAGAAAGAGGAAAAGAACTCATAGGCA
65 CGAGTTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCATAGGCA
* ** * * *
3525 GAAGATTATTTGAGTTCTATACTCCCTGAAGTGATAGGGAGCAAACCCG-TTGAAAGAAGATTGT
1 GAAGATT-TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG-AAGAAGATTAT
* * * *
3589 TTGAGTTCTATACTCCATG-AAGTAATAGGGAGCGAACC
64 TCGAGTTCTATACTCCTTGAAAGAAAGAGGGAGCGAACC
3627 AGCTAGTCGA
Statistics
Matches: 271, Mismatches: 44, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
107 22 0.08
108 28 0.10
109 16 0.06
110 27 0.10
111 160 0.59
112 18 0.07
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (110 bp):
GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTATTC
GAGTTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCATAGGCA
Found at i:3472 original size:55 final size:55
Alignment explanation
Indices: 2868--3626 Score: 479
Period size: 55 Copynumber: 13.8 Consensus size: 55
2858 TTGAAGCATC
* * * *
2868 AAGATTGTTCGAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGATTGTTG
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGTTTGTAG
* * * *
2923 AAGATTGTTCAAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACAC-TATTGTTG
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGT-TTGTAG
** * * *
2978 AAGATTGTTCGAG-TCTTATACTCTATGAA-GAATAGGGAGC-AGACACGATTGTTG
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGTTTGTAG
* * * * *
3032 AAGATTGTTCGAG-TCTTATACTCTCTAAAGGAATAGGGAGC-ATACACGATTGTTG
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGTTTGTAG
* * * **
3087 AAGATTGTTCAAG-TCTTATACTCTCTGAAGGAATAGGGAGC-AGACACAATTGTTA-
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGTTTG-TAG
* * * * *
3142 AAGATTGTTCGAG-TCTTATATTCTCTGAAGGAATAGGGAGC-AGACACGATTGTTG
1 AAGATTGTTCGAGTTC-TATACTCCCTGAAGGAATAGGGAGCGA-ACCCGTTTGTAG
* * * * * ** *
3197 AAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGGGCGAATCCGTGGGAAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGAACCCGTTTGTAG
* * * ** ** *
3251 AAGA-TGTTCGAGTTCCATACTCCCT-AAAGAA-AGAGGAGTGAACCTATAGGAAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAG-GGAGCGAACCCGTTTGTAG
* * *
3304 AAGA-TGTTTGAGTTCTATACTCCCTGAAAGAA-AGATGGAGCGAACCCGTTTGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAG--GGAGCGAACCCGTTTGTAG
* * * * * * * *
3359 AAGATTATTTGAGCTCTATACTCCTTGAAAGAAAGAGGGAGCGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTG-AAGGAATAGGGAGCGAACCCGTTTGTAG
*
3415 AAGATT-TCTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGTAG
1 AAGATTGT-TCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGAACCCGTTTGTAG
* * * ** * * ** *
3470 AAGATTATTCGAGTTCTATACTCCTTGAAAGAA-AGAGGAAAAGAACTCATAGGCAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAG-GG-AGCGAACCCGTTTGTAG
* * * *
3526 AAGATTATTTGAGTTCTATACTCCCTGAAGTG-ATAGGGAGCAAACCCG-TTGAAAG
1 AAGATTGTTCGAGTTCTATACTCCCTGAAG-GAATAGGGAGCGAACCCGTTTG-TAG
* * *
3581 AAGATTGTTTGAGTTCTATACTCCATGAAGTAATAGGGAGCGAACC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGAACC
3627 AGCTAGTCGA
Statistics
Matches: 597, Mismatches: 86, Indels: 42
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.00
53 40 0.07
54 118 0.20
55 327 0.55
56 101 0.17
57 7 0.01
58 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (55 bp):
AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCGAACCCGTTTGTAG
Found at i:3817 original size:3 final size:3
Alignment explanation
Indices: 3804--3864 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
3794 GGGTTATAAA
* * *
3804 TAT TA- TAT TAT TAT TAT TAT AAC TAT TA- TAT TAT AAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
3848 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
3865 CATATTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3864 original size:33 final size:34
Alignment explanation
Indices: 3807--3873 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
3797 TTATAAATAT
3807 TATATTATTATTATTATAACTATT-ATATTATAA
1 TATATTATTATTATTATAACTATTAATATTATAA
* *
3840 TATATTATTATTATTATTATTATTACATATTATA
1 TATATTATTATTATTATAACTATTA-ATATTATA
3874 TTTTACAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 22 0.73
35 8 0.27
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTATTATTATTATAACTATTAATATTATAA
Found at i:10166 original size:17 final size:17
Alignment explanation
Indices: 10144--10191 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
10134 CATGTTCATA
10144 TTTAAAAAATA-TATATT
1 TTTAAAAAATATTATA-T
* *
10161 TTTAAATAATATTTTAT
1 TTTAAAAAATATTATAT
*
10178 TTTAAAAAAAATTA
1 TTTAAAAAATATTA
10192 AAAATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAAAAATATTATAT
Found at i:18175 original size:29 final size:30
Alignment explanation
Indices: 18130--18189 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
18120 TGTCTGATAA
*
18130 TTCCTTTTCATTCTGGATTTTCATATTTTT
1 TTCCTTTTCATTCTGGAGTTTCATATTTTT
*
18160 TTCC-TTTCATTTTGGAGTTTCATATTTTT
1 TTCCTTTTCATTCTGGAGTTTCATATTTTT
18189 T
1 T
18190 CTTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.63
Consensus pattern (30 bp):
TTCCTTTTCATTCTGGAGTTTCATATTTTT
Found at i:42750 original size:16 final size:17
Alignment explanation
Indices: 42718--42750 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42708 TCCAGCTACA
*
42718 CCATTTTGATCCGAAAC
1 CCATTTTGATCCAAAAC
42735 CCATTTT-ATCCAAAAC
1 CCATTTTGATCCAAAAC
42751 TTTAAAGAGA
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:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CCATTTTGATCCAAAAC
Found at i:46808 original size:16 final size:16
Alignment explanation
Indices: 46787--46817 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46777 GGGATCATGT
46787 TGCTGTTTGGAGCTGC
1 TGCTGTTTGGAGCTGC
46803 TGCTGTTTGGAGCTG
1 TGCTGTTTGGAGCTG
46818 TTTTTGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.39, T:0.39
Consensus pattern (16 bp):
TGCTGTTTGGAGCTGC
Done.