Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008696.1 Hibiscus syriacus cultivar Beakdansim tig00111726_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: 52163
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7519 original size:31 final size:32
Alignment explanation
Indices: 7449--7523 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 32
7439 GATACAATCT
*
7449 ATCCATCACCATTATCACGCCTATATCATCACC
1 ATCCATCACCATTATCAC-CCTATATCACCACC
* *
7482 AGCCATCACCATTATCA-CCTATATCACCA-T
1 ATCCATCACCATTATCACCCTATATCACCACC
7512 ATTCCATCACCA
1 A-TCCATCACCA
7524 CGCTATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 20 0.54
33 16 0.43
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.27
Consensus pattern (32 bp):
ATCCATCACCATTATCACCCTATATCACCACC
Found at i:11950 original size:13 final size:11
Alignment explanation
Indices: 11909--11993 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
11899 ACAATCTATC
11909 CATCACCATTAT
1 CATCACCA-TAT
*
11921 CA-CGCCTATAT
1 CATCACC-ATAT
11932 CATCACCATAGT
1 CATCACCATA-T
11944 CCATCACCATTAT
1 -CATCACCA-TAT
*
11957 CA-CGCCTATAT
1 CATCACC-ATAT
11968 CATCACCATATT
1 CATCACCATA-T
11980 CCATCACCATAT
1 -CATCACCATAT
11992 CA
1 CA
11994 CCTATATTAT
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:11954 original size:36 final size:36
Alignment explanation
Indices: 11907--12008 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
11897 ATACAATCTA
11907 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
11943 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
11979 TCCATCACCA-TATCA--CCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
12009 ACTTATAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
33 14 0.22
35 5 0.08
36 45 0.70
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:12007 original size:20 final size:20
Alignment explanation
Indices: 11969--12008 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
11959 CGCCTATATC
11969 ATCACCATATTCCATCACCAT
1 ATCACCATATT-CATCACCAT
11990 ATCACCTATATT-ATCACCA
1 ATCACC-ATATTCATCACCA
12009 ACTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (20 bp):
ATCACCATATTCATCACCAT
Found at i:17730 original size:27 final size:28
Alignment explanation
Indices: 17700--17761 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
17690 CTTTTCTTTG
* **
17700 CTTTTCTTCTTTTTGAGTGC-TGGATTT
1 CTTTTCTTCTTTTGGAGTGCTTCAATTT
17727 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAGTGCTTCAATTT
17755 CTTTTCT
1 CTTTTCT
17762 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 14 0.48
28 7 0.24
29 4 0.14
ACGTcount: A:0.08, C:0.18, G:0.15, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAGTGCTTCAATTT
Found at i:23421 original size:18 final size:17
Alignment explanation
Indices: 23417--23468 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
23407 TGAATAAAGT
23417 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
23434 TAGTTCATT-ATCAAAC
1 TAGTTCATTAATTAAAC
* *
23450 TAGATCATTTATTAAAC
1 TAGTTCATTAATTAAAC
23467 TA
1 TA
23469 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:25047 original size:33 final size:33
Alignment explanation
Indices: 25010--25078 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
25000 CATCACCATA
*
25010 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
25043 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
25076 TTC
1 TTC
25079 ATTCATCAAC
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:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:29489 original size:36 final size:36
Alignment explanation
Indices: 29437--29549 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
29427 GATACTATTT
*
29437 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
29473 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
29509 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
29544 ACATCA
1 TCATCA
29550 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:29492 original size:13 final size:11
Alignment explanation
Indices: 29437--29535 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
29427 GATACTATTT
29437 TCATCACCATAA
1 TCATCACCAT-A
*
29449 TCCATCTCCATTA
1 T-CATCACCA-TA
*
29462 TCA-CGCCTATA
1 TCATCACC-ATA
29473 TCATCACCATA
1 TCATCACCATA
29484 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
29498 TCA-CGCCTATA
1 TCATCACC-ATA
29509 TCATCACCATA
1 TCATCACCATA
29520 TTCCATCACCATA
1 -T-CATCACCATA
29533 TCA
1 TCA
29536 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:29564 original size:33 final size:33
Alignment explanation
Indices: 29449--29588 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
29439 ATCACCATAA
* * *
29449 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
29483 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
29521 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
29554 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
29587 TC
1 TC
29589 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:32737 original size:22 final size:21
Alignment explanation
Indices: 32707--32751 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
32697 AATCTCCATT
32707 TCATCATCAACACCA-ACAACA
1 TCATCATCAACACCATA-AACA
*
32728 TCATCCATCAAGACCATAAACA
1 TCAT-CATCAACACCATAAACA
32750 TC
1 TC
32752 TTCTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.18
Consensus pattern (21 bp):
TCATCATCAACACCATAAACA
Found at i:33103 original size:19 final size:17
Alignment explanation
Indices: 33073--33115 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
33063 TTCAAAGATA
*
33073 AAAAGAA-AAAAAATCAG
1 AAAAGAAGAAAAAA-AAG
33090 AAAAGAAG-AAAAAAAG
1 AAAAGAAGAAAAAAAAG
33106 AAAAGAAGAA
1 AAAAGAAGAA
33116 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAAAAG
Found at i:33107 original size:16 final size:17
Alignment explanation
Indices: 33073--33115 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
33063 TTCAAAGATA
33073 AAAAGAA-AAAAAATCAG
1 AAAAGAAGAAAAAA-CAG
33090 AAAAGAAGAAAAAA-AG
1 AAAAGAAGAAAAAACAG
33106 AAAAGAAGAA
1 AAAAGAAGAA
33116 TTTCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.48
17 7 0.28
18 6 0.24
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAACAG
Found at i:43512 original size:33 final size:33
Alignment explanation
Indices: 43470--43538 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
43460 GTTGATGAAT
*
43470 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
43503 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
43536 GAA
1 GAA
43539 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:43543 original size:13 final size:12
Alignment explanation
Indices: 43524--43620 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
43514 TTATTGGCGT
43524 GATATGGTGATG
1 GATATGGTGATG
43536 GAATATGGTGAT-
1 G-ATATGGTGATG
*
43548 GATATAGGCG-T-
1 GATAT-GGTGATG
43559 GATAATGGTGATG
1 GAT-ATGGTGATG
43572 GACTATGGTGAT-
1 GA-TATGGTGATG
*
43584 GATATAGGCG-T-
1 GATAT-GGTGATG
*
43595 GATAATGGAGATG
1 GAT-ATGGTGATG
43608 GATTATGGTGATG
1 GA-TATGGTGATG
43621 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:43579 original size:36 final size:36
Alignment explanation
Indices: 43509--43621 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
43499 AATGGAAGGA
* *
43509 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
43544 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
43580 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
43616 TGATGA
1 TGATGA
43622 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:45336 original size:33 final size:33
Alignment explanation
Indices: 45294--45362 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
45284 GTTGATGAAT
*
45294 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
45327 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
45360 GAA
1 GAA
45363 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:45367 original size:13 final size:12
Alignment explanation
Indices: 45348--45441 Score: 67
Period size: 13 Copynumber: 8.0 Consensus size: 12
45338 TTATTGGCGT
45348 GATATGGTGATG
1 GATATGGTGATG
45360 GAATATGGTGAT-
1 G-ATATGGTGATG
*
45372 GATA-GGCG-T-
1 GATATGGTGATG
45381 GATATGGTGATG
1 GATATGGTGATG
45393 GACTATGGTGAT-
1 GA-TATGGTGATG
*
45405 GATATAGGCG-T-
1 GATAT-GGTGATG
*
45416 GATAATGGAGATG
1 GAT-ATGGTGATG
45429 GATTATGGTGATG
1 GA-TATGGTGATG
45442 AAAATAGTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
9 5 0.07
10 6 0.09
11 14 0.21
12 12 0.18
13 29 0.43
14 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:45436 original size:36 final size:35
Alignment explanation
Indices: 45333--45442 Score: 152
Period size: 33 Copynumber: 3.2 Consensus size: 35
45323 AATGGAAGGA
* *
45333 TGATGTTATTGGCGTGATATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATATGGTGATGGAATATGG
*
45368 TGATG--ATAGGCGTGATATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATATGGTGATGGAATATGG
* *
45401 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGAT-ATGGTGATGGAATATGG
45437 TGATGA
1 TGATGA
45443 AAATAGTATC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
33 31 0.46
35 16 0.24
36 21 0.31
ACGTcount: A:0.26, C:0.04, G:0.37, T:0.33
Consensus pattern (35 bp):
TGATGATATAGGCGTGATATGGTGATGGAATATGG
Done.