Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001198.1 Hibiscus syriacus cultivar Beakdansim tig00002372_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: 73958
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:9988 original size:20 final size:20
Alignment explanation
Indices: 9944--10351 Score: 367
Period size: 20 Copynumber: 20.2 Consensus size: 20
9934 AATGACCAAC
*
9944 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
* *
9963 AAAATCGCAACACGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
9983 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
10003 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
10023 AAAATCGCAACGCGATATTCTA-
1 AAAATCGCAACGCG--ATTC-AG
* * *
10045 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
10065 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
10087 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
10107 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
10127 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
10147 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
10167 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
10187 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
10207 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
10227 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
10247 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
10267 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
10287 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
10307 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
10327 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
10347 AAAAT
1 AAAAT
10352 GAGTAAATTC
Statistics
Matches: 324, Mismatches: 37, Indels: 55
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.01
19 26 0.08
20 251 0.77
21 12 0.04
22 28 0.09
23 2 0.01
25 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:10137 original size:40 final size:40
Alignment explanation
Indices: 10020--10351 Score: 547
Period size: 40 Copynumber: 8.2 Consensus size: 40
10010 CAACGGTCAA
* *
10020 AAGAAAATCGCAACGCGATATTCTAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
* *
10062 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT
* *
10104 CAGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
*
10144 CAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
10184 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
10224 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
*
10264 CAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
10304 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
*
10344 CAGAAAAT
1 AAGAAAAT
10352 GAGTAAATTC
Statistics
Matches: 279, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
40 226 0.81
42 53 0.19
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
AAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
Found at i:10458 original size:6 final size:6
Alignment explanation
Indices: 10447--10521 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
10437 GACACGTATT
10447 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
10495 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
10522 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:11032 original size:6 final size:6
Alignment explanation
Indices: 11021--11149 Score: 258
Period size: 6 Copynumber: 21.5 Consensus size: 6
11011 TCTCGTCTCG
11021 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
11069 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
11117 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
11150 AATACGTGTC
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:11277 original size:20 final size:20
Alignment explanation
Indices: 11252--11451 Score: 253
Period size: 20 Copynumber: 9.8 Consensus size: 20
11242 CTCATTTTCT
11252 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
11272 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
11292 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
11312 GAATCGCGTTGCGATTCTCT-
1 GAATCGCGTTGCGATTCT-TG
* *
11332 TAATCGCGTTGCGATTCTTA
1 GAATCGCGTTGCGATTCTTG
*
11352 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
* *
11372 GAATCGCATCGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
11392 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
11414 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
11434 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
11452 TTCTTTTGAC
Statistics
Matches: 158, Mismatches: 12, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.03
20 120 0.76
21 6 0.04
22 27 0.17
23 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:11307 original size:40 final size:40
Alignment explanation
Indices: 11249--11451 Score: 291
Period size: 40 Copynumber: 5.0 Consensus size: 40
11239 TTACTCATTT
11249 TCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
1 TCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
11289 T-TGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
1 TCT-GAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
* * *
11329 TCTTAATCGCGTTGCGATTCTTAGAATCGCGTTGCGATTT
1 TCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
* *
11369 TCTGAATCGCATCGCGATTCTTGGAAGATCGCGTTGCGATTC
1 TCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTC
* *
11411 TCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCGATT
1 TCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATT
11452 TTCTTTTGAC
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 93 0.63
41 2 0.01
42 52 0.35
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (40 bp):
TCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTC
Found at i:11505 original size:20 final size:20
Alignment explanation
Indices: 11245--11532 Score: 178
Period size: 20 Copynumber: 14.2 Consensus size: 20
11235 GAATTTACTC
*
11245 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
11265 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
11285 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
11305 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
11325 ATTCTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
11345 ATTCT-TAGAATCGCGTTGCG
1 ATTTTCTA-AATCGCGTTGCG
* * *
11365 ATTTTCTGAATCGCATCGCG
1 ATTTTCTAAATCGCGTTGCG
**
11385 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
11407 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
11427 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
11449 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
11469 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
11489 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
11509 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
11528 ATTTT
1 ATTTT
11533 GTTGGTCATT
Statistics
Matches: 220, Mismatches: 35, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.01
19 19 0.09
20 158 0.72
21 16 0.07
22 25 0.11
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:19071 original size:111 final size:111
Alignment explanation
Indices: 18877--19098 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
18867 ATTAAAAAAA
* *
18877 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
18942 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
18988 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
19053 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
19099 ATGATTTTCA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:28874 original size:15 final size:15
Alignment explanation
Indices: 28854--28903 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
28844 CCGTAGGACC
*
28854 ACTACGTCCCGAAGA
1 ACTACGTCCCGAAGG
*
28869 ACTACGTCCCGATGG
1 ACTACGTCCCGAAGG
*
28884 ACTACGTCCTGAAGG
1 ACTACGTCCCGAAGG
28899 ACTAC
1 ACTAC
28904 AATACCCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:29147 original size:8 final size:7
Alignment explanation
Indices: 29127--29171 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
29117 TATCTCATAG
29127 CATATAT
1 CATATAT
29134 CATATAT
1 CATATAT
29141 GCATATAAT
1 -CATAT-AT
29150 CATATAT
1 CATATAT
29157 -ATCATAT
1 CAT-ATAT
29164 CATATAT
1 CATATAT
29171 C
1 C
29172 TTATGTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.06
7 18 0.53
8 12 0.35
9 2 0.06
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (7 bp):
CATATAT
Found at i:31044 original size:18 final size:19
Alignment explanation
Indices: 31021--31064 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
31011 TCAGTAATCC
31021 TATTCC-CTGGTAATCTTA
1 TATTCCACTGGTAATCTTA
31039 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
*
31059 CATTCC
1 TATTCC
31065 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:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:31052 original size:20 final size:20
Alignment explanation
Indices: 31027--31064 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31017 ATCCTATTCC
*
31027 CTGGTAATCTTATATTCCCA
1 CTGGTAATCTTACATTCCCA
31047 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
31065 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:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:37541 original size:16 final size:16
Alignment explanation
Indices: 37517--37553 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
37507 TATTTTATAT
*
37517 TTATATATATAATAGA
1 TTATTTATATAATAGA
*
37533 TTATTTATATAATGGA
1 TTATTTATATAATAGA
37549 TTATT
1 TTATT
37554 AGATTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TTATTTATATAATAGA
Found at i:72122 original size:14 final size:14
Alignment explanation
Indices: 72103--72132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
72093 CATTTTTGAA
72103 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
72117 AGGAGATCTATATG
1 AGGAGATCTAGATG
72131 AG
1 AG
72133 AACAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Done.