Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007991.1 Hibiscus syriacus cultivar Beakdansim tig00110440_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: 76536
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:734 original size:22 final size:23
Alignment explanation
Indices: 703--753 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
693 TTAGAAGTTT
*
703 GTGATAATATAGGCGTGAT-ATG
1 GTGATGATATAGGCGTGATAATG
725 GTGATGATATAGGCGTGATAATG
1 GTGATGATATAGGCGTGATAATG
748 GTGATG
1 GTGATG
754 GACAGATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
GTGATGATATAGGCGTGATAATG
Found at i:9870 original size:26 final size:27
Alignment explanation
Indices: 9810--9870 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
9800 TTGGCTTGCT
9810 TTCTTTT-TGAATTTCTTTTTCTTTTC
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
* *
9836 TTCTATTCTG-ATTTTTTTTTCTTTT-
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
9861 TGTCTTTTCT
1 T-TCTTTTCT
9871 TTCTTTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 27 0.90
27 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.74
Consensus pattern (27 bp):
TTCTTTTCTGAATTTCTTTTTCTTTTC
Found at i:19975 original size:33 final size:33
Alignment explanation
Indices: 19933--20001 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19923 GTTGATGAAT
*
19933 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
19966 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
19999 GAA
1 GAA
20002 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:20042 original size:36 final size:36
Alignment explanation
Indices: 19972--20084 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
19962 AATGGAAGGA
* *
19972 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
20007 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
20043 TGATAATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
20079 TGATGA
1 TGATGA
20085 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:20044 original size:13 final size:11
Alignment explanation
Indices: 19986--20084 Score: 58
Period size: 13 Copynumber: 8.3 Consensus size: 11
19976 GTTATTGGCG
19986 TGATATGGTGA
1 TGATATGGTGA
19997 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
20010 TGATATAGGCG-
1 TGATAT-GGTGA
20021 TGATAATGGTGA
1 TGAT-ATGGTGA
20033 TGGACTATGGTGA
1 T-GA-TATGGTGA
* *
20046 TAATATAGGCG-
1 TGATAT-GGTGA
*
20057 TGATAATGGAGA
1 TGAT-ATGGTGA
20069 TGGATTATGGTGA
1 T-GA-TATGGTGA
20082 TGA
1 TGA
20085 AAATAGTATC
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
11 21 0.30
12 17 0.25
13 29 0.42
14 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:24392 original size:33 final size:33
Alignment explanation
Indices: 24350--24418 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
24340 GTTGATGAAT
*
24350 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
24383 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
24416 GAA
1 GAA
24419 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:24423 original size:13 final size:12
Alignment explanation
Indices: 24404--24500 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
24394 TTATTGGCGT
24404 GATATGGTGATG
1 GATATGGTGATG
24416 GAATATGGTGAT-
1 G-ATATGGTGATG
*
24428 GATATAGGCG-T-
1 GATAT-GGTGATG
24439 GATAATGGTGATG
1 GAT-ATGGTGATG
24452 GACTATGGTGAT-
1 GA-TATGGTGATG
*
24464 GATATAGGCG-T-
1 GATAT-GGTGATG
*
24475 GATAATGGAGATG
1 GAT-ATGGTGATG
24488 GATTATGGTGATG
1 GA-TATGGTGATG
24501 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:24459 original size:36 final size:36
Alignment explanation
Indices: 24389--24501 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
24379 AATGGAAGGA
* *
24389 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
24424 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
24460 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
24496 TGATGA
1 TGATGA
24502 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:29307 original size:24 final size:24
Alignment explanation
Indices: 29280--29331 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
29270 GACATGTCCT
* * *
29280 TTGACGTTCCAACAGCTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
29304 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
29328 TTGA
1 TTGA
29332 AGTGCCAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:37492 original size:13 final size:11
Alignment explanation
Indices: 37451--37535 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
37441 CCTTTCTGTC
37451 CATCACCATTAT
1 CATCACCA-TAT
*
37463 CA-CGCCTATAT
1 CATCACC-ATAT
37474 CATCACCATAGT
1 CATCACCATA-T
37486 CCATCACCATTAT
1 -CATCACCA-TAT
*
37499 CA-CGCCTATAT
1 CATCACC-ATAT
37510 CATCACCATATT
1 CATCACCATA-T
37522 CCATCACCATAT
1 -CATCACCATAT
37534 CA
1 CA
37536 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:37495 original size:36 final size:36
Alignment explanation
Indices: 37448--37552 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
37438 AGTCCTTTCT
37448 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
37484 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
37520 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
37553 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:50305 original size:17 final size:18
Alignment explanation
Indices: 50283--50334 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
50273 AATTGGAGTG
50283 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
50300 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
50318 CAGAAAAG-AAGAAAAGA
1 CA-AAAAGAAAGAAAAGA
50335 AGAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:50315 original size:11 final size:11
Alignment explanation
Indices: 50290--50361 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
50280 GTGCAAAAAG
50290 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
50303 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
50314 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
50325 GAAGAAAAGAA
1 AAAGAAAAGAA
*
50336 GAAGAAAAG-A
1 AAAGAAAAGAA
50346 AAAGAAAAGAA
1 AAAGAAAAGAA
50357 AAAGA
1 AAAGA
50362 GAAGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 12 0.25
11 26 0.54
12 2 0.04
13 8 0.17
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:50327 original size:5 final size:5
Alignment explanation
Indices: 50285--50358 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
50275 TTGGAGTGCA
* * **
50285 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
50329 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
50359 AGAGAAGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:50330 original size:8 final size:8
Alignment explanation
Indices: 50285--50351 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
50275 TTGGAGTGCA
50285 AAAAGAAAG
1 AAAAG-AAG
50294 AAAAGACA-
1 AAAAGA-AG
50302 AAAAGAAG
1 AAAAGAAG
*
50310 AGAAAAATCAG
1 A-AAAGA--AG
50321 AAAAGAAG
1 AAAAGAAG
50329 AAAAGAAG
1 AAAAGAAG
50337 AAGAA-AAG
1 AA-AAGAAG
50345 AAAAGAA
1 AAAAGAA
50352 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 27 0.55
9 12 0.24
10 4 0.08
11 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:50338 original size:16 final size:17
Alignment explanation
Indices: 50285--50350 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
50275 TTGGAGTGCA
50285 AAAAGAAAGAAAAGACA-
1 AAAAG-AAGAAAAGACAG
*
50302 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAGA-CAG
50321 AAAAGAAGAAAAGA-AG
1 AAAAGAAGAAAAGACAG
50337 AAGAA-AAGAAAAGA
1 AA-AAGAAGAAAAGA
50351 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 6 0.14
19 9 0.21
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGACAG
Found at i:50351 original size:16 final size:15
Alignment explanation
Indices: 50285--50358 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 15
50275 TTGGAGTGCA
50285 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
* *
50299 -ACA-AAAAGAAGAG
1 AAAAGAAAAGAAAAG
**
50312 AAAA-ATCAGAAAAG
1 AAAAGAAAAGAAAAG
50326 --AAGAAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
50340 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
50355 AAAA
1 AAAA
50359 AGAGAAGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 12 0.26
15 7 0.15
16 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:50361 original size:16 final size:16
Alignment explanation
Indices: 50326--50358 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
50316 ATCAGAAAAG
50326 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
50342 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
50357 AA
1 AA
50359 AGAGAAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:58573 original size:19 final size:20
Alignment explanation
Indices: 58551--58614 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
58541 TTTGAACTTC
58551 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
58570 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
* *
58589 TC-TTTTCTGATTTTTGTCT
1 TCTTTTTCTTATTTTTCTCT
58608 TCTTTTT
1 TCTTTTT
58615 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.25
19 26 0.65
20 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Done.