Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000348.1 Hibiscus syriacus cultivar Beakdansim tig00000641_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: 72403
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:9543 original size:21 final size:21
Alignment explanation
Indices: 9511--9561 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
9501 CATGATCCGA
9511 AAATATAT-ATAATTCAAGAAC
1 AAATA-ATCATAATTCAAGAAC
9532 AAATAATCATAATTCAAGAAC
1 AAATAATCATAATTCAAGAAC
9553 AAATAATCA
1 AAATAATCA
9562 AAACGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (21 bp):
AAATAATCATAATTCAAGAAC
Found at i:9571 original size:21 final size:21
Alignment explanation
Indices: 9526--9572 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
9516 TATATAATTC
* ***
9526 AAGAACAAATAATCATAATTC
1 AAGAACAAATAATCAAAACGA
9547 AAGAACAAATAATCAAAACGA
1 AAGAACAAATAATCAAAACGA
9568 AAGAA
1 AAGAA
9573 AAAAAAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.13, G:0.09, T:0.15
Consensus pattern (21 bp):
AAGAACAAATAATCAAAACGA
Found at i:11859 original size:60 final size:60
Alignment explanation
Indices: 11752--11866 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
11742 CATGTGATCA
* * *
11752 TTTTGTAACTTTTAATAGTCGATGGACTCAACAAATCAACTCTCTATAGTTGGGAGACTG
1 TTTTATAACTTTTAATAGTCGATGGACTCAACAAAACAACTCTCTATAGTCGGGAGACTG
* *
11812 TTTTATAACTTTTAATAGT-TATGAGACTCAATAAAACATTA-TC-CTATAGTCGGGA
1 TTTTATAACTTTTAATAGTCGATG-GACTCAACAAAACA--ACTCTCTATAGTCGGGA
11867 TCATTTATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
59 3 0.06
60 41 0.87
61 2 0.04
62 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGATGGACTCAACAAAACAACTCTCTATAGTCGGGAGACTG
Found at i:20668 original size:35 final size:37
Alignment explanation
Indices: 20597--20669 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
20587 ACTATAAGAT
* * *
20597 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTATTTAAAAAATTAAAAATCATAAA
*
20634 ATTTATATAATTT-TTTATAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTATTTAAAAAATTAAAAATCATAAA
20669 A
1 A
20670 AAGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 6 0.19
36 14 0.44
37 12 0.38
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATAATTTATTTAAAAAATTAAAAATCATAAA
Found at i:23109 original size:14 final size:14
Alignment explanation
Indices: 23092--23136 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
23082 TGTTTGTCCG
23092 TTTATGTGCGTTCA
1 TTTATGTGCGTTCA
*
23106 TTTA--T--GTTCG
1 TTTATGTGCGTTCA
23116 TTTATGTGCGTTCA
1 TTTATGTGCGTTCA
23130 TTTATGT
1 TTTATGT
23137 TTAGCCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 8 0.32
12 2 0.08
14 15 0.60
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (14 bp):
TTTATGTGCGTTCA
Found at i:23134 original size:38 final size:38
Alignment explanation
Indices: 23056--23136 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
23046 CATTCGGTAA
* ** *
23056 TATGTTCGTTCATTTATATTCGTTTATGTTTGTCCGTT
1 TATGTGCGTTCATTTATATTCGTTTATGTGCGTCCATT
* *
23094 TATGTGCGTTCATTTATGTTCGTTTATGTGCGTTCATT
1 TATGTGCGTTCATTTATATTCGTTTATGTGCGTCCATT
23132 TATGT
1 TATGT
23137 TTAGCCTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.56
Consensus pattern (38 bp):
TATGTGCGTTCATTTATATTCGTTTATGTGCGTCCATT
Found at i:23137 original size:24 final size:24
Alignment explanation
Indices: 23090--23137 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23080 TATGTTTGTC
23090 CGTTTATGTGCGTTCATTTATGTT
1 CGTTTATGTGCGTTCATTTATGTT
23114 CGTTTATGTGCGTTCATTTATGTT
1 CGTTTATGTGCGTTCATTTATGTT
23138 TAGCCTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.54
Consensus pattern (24 bp):
CGTTTATGTGCGTTCATTTATGTT
Found at i:29317 original size:14 final size:14
Alignment explanation
Indices: 29300--29326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29290 GAGAGAATGG
29300 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
29314 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
29327 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:29526 original size:17 final size:19
Alignment explanation
Indices: 29504--29538 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29494 GCTTTTGTTC
29504 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
29521 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
29539 GAGATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:36437 original size:10 final size:10
Alignment explanation
Indices: 36415--36453 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
36405 AAAATCTATT
36415 TTCATTTATG
1 TTCATTTATG
* *
36425 TTCGTTTACG
1 TTCATTTATG
36435 TTCATTTATG
1 TTCATTTATG
36445 TTCATTTAT
1 TTCATTTAT
36454 TGTGTTCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:36440 original size:20 final size:20
Alignment explanation
Indices: 36415--36452 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36405 AAAATCTATT
*
36415 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
36435 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
36453 TTGTGTTCGT
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:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:36485 original size:24 final size:23
Alignment explanation
Indices: 36452--36512 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
36442 ATGTTCATTT
*
36452 ATTGTGTTCGTTTCCATTCGTTC
1 ATTGTGTTCGTTTACATTCGTTC
* *
36475 ATTTGTGTTCGTTTACGTTCGTTT
1 A-TTGTGTTCGTTTACATTCGTTC
*
36499 ATTGTATTCGTTTA
1 ATTGTGTTCGTTTA
36513 TGTTCGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.11, C:0.15, G:0.18, T:0.56
Consensus pattern (23 bp):
ATTGTGTTCGTTTACATTCGTTC
Found at i:36508 original size:23 final size:23
Alignment explanation
Indices: 36434--36522 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
36424 GTTCGTTTAC
* * *
36434 GTTCATTTATGTTCATTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
* * *
36457 GTTCGTTTCCATTCGTTCATTTGT
1 GTTCGTTTACGTTCGTTTA-TTGT
36481 GTTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
* *
36504 ATTCGTTTATGTTCGTTTA
1 GTTCGTTTACGTTCGTTTA
36523 GATCCATTCG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 34 0.63
24 20 0.37
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.57
Consensus pattern (23 bp):
GTTCGTTTACGTTCGTTTATTGT
Found at i:36541 original size:57 final size:57
Alignment explanation
Indices: 36415--36544 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 57
36405 AAAATCTATT
* * * *
36415 TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTGTTCGTTTCCATTCG
1 TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTATGTTCGTTTACATCCA
* * *
36472 TTCATTTGTGTTCGTTTACGTTCGTTTAT-TGT-ATTCGT-TTATGTTCGTTTAGATCCA
1 TTCATTTATGTTCGTTTACGTTCATTTATGT-TCATT--TATTATGTTCGTTTACATCCA
*
36529 TTCGTTTATGTTCGTT
1 TTCATTTATGTTCGTT
36545 CATTTGTGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
56 4 0.07
57 56 0.92
58 1 0.02
ACGTcount: A:0.13, C:0.15, G:0.16, T:0.56
Consensus pattern (57 bp):
TTCATTTATGTTCGTTTACGTTCATTTATGTTCATTTATTATGTTCGTTTACATCCA
Found at i:36544 original size:10 final size:10
Alignment explanation
Indices: 36419--36522 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
36409 TCTATTTTCA
36419 TTTATGTTCG
1 TTTATGTTCG
* *
36429 TTTACGTTCA
1 TTTATGTTCG
*
36439 TTTATGTTCA
1 TTTATGTTCG
36449 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
36462 TTTCCATTCGTTCA
1 TTT--A-T-GTTCG
*
36476 TTTGTGTTCG
1 TTTATGTTCG
*
36486 TTTACGTTCG
1 TTTATGTTCG
36496 TTTATTGTATTCG
1 TTTA-TG--TTCG
36509 TTTATGTTCG
1 TTTATGTTCG
36519 TTTA
1 TTTA
36523 GATCCATTCG
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
10 45 0.61
11 2 0.03
12 2 0.03
13 17 0.23
14 7 0.09
15 1 0.01
ACGTcount: A:0.12, C:0.13, G:0.16, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:36559 original size:24 final size:24
Alignment explanation
Indices: 36468--36561 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
36458 TTCGTTTCCA
* *
36468 TTCGTTCATTTGTGTTCGTTTACG
1 TTCGTTCATTTGTATTCGTTTATG
*
36492 TTCGTTTA-TTGTATTCGTTTATG
1 TTCGTTCATTTGTATTCGTTTATG
* ** **
36515 TTCGTTTAGATCCATTCGTTTATG
1 TTCGTTCATTTGTATTCGTTTATG
* *
36539 TTCGTTCATTTGTGTTTGTTTAT
1 TTCGTTCATTTGTATTCGTTTAT
36562 CATTTAAATG
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 21 0.38
24 35 0.62
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (24 bp):
TTCGTTCATTTGTATTCGTTTATG
Found at i:37246 original size:30 final size:30
Alignment explanation
Indices: 37196--37270 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
37186 ACGGTGCTGC
* *
37196 TCAGACTCTCCATTTTATTGAAGTACCCATG
1 TCAGACACT-CATTCTATTGAAGTACCCATG
37227 TCAGACACTCATTCTATTGAAGTACCCATG
1 TCAGACACTCATTCTATTGAAGTACCCATG
37257 TCAGACACTCATTC
1 TCAGACACTCATTC
37271 CTCTCCAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 34 0.81
31 8 0.19
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (30 bp):
TCAGACACTCATTCTATTGAAGTACCCATG
Found at i:55536 original size:14 final size:14
Alignment explanation
Indices: 55517--55544 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55507 CGCTGGGCAT
55517 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
55531 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
55545 GGCCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:55546 original size:24 final size:22
Alignment explanation
Indices: 55514--55597 Score: 100
Period size: 24 Copynumber: 3.8 Consensus size: 22
55504 ACACGCTGGG
55514 CATCCGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCATCCGA-CGA-GC
55538 CATCCGAGGCCATCCGA-GAG-
1 CATCCGAGGCCATCCGACGAGC
55558 CATCCGAGGCCATCCGAACGAGC
1 CATCCGAGGCCATCCG-ACGAGC
* * *
55581 TATGCGAGGGCATCCGA
1 CATCCGAGGCCATCCGA
55598 GGGCAACCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
20 16 0.30
21 2 0.04
22 6 0.11
23 13 0.24
24 17 0.31
ACGTcount: A:0.24, C:0.36, G:0.30, T:0.11
Consensus pattern (22 bp):
CATCCGAGGCCATCCGACGAGC
Found at i:55563 original size:44 final size:43
Alignment explanation
Indices: 55513--55608 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
55503 AACACGCTGG
*
55513 GCATCCGAGGCCATCCGACCGAGGCCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAACGA-GCCATCCGAGGCCATCCGAGA
* * * *
55557 GCATCCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGG
1 GCATCCGAGGCCATCCGAACGAGCCATCCGAGGCCATCCGAGA
*
55600 GCAACCGAG
1 GCATCCGAG
55609 AGAGCTATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 25 0.54
44 21 0.46
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.09
Consensus pattern (43 bp):
GCATCCGAGGCCATCCGAACGAGCCATCCGAGGCCATCCGAGA
Found at i:55600 original size:10 final size:10
Alignment explanation
Indices: 55511--55633 Score: 75
Period size: 10 Copynumber: 11.3 Consensus size: 10
55501 CCAACACGCT
55511 GGGCATCCGA
1 GGGCATCCGA
*
55521 GGCCATCCGA
1 GGGCATCCGA
55531 CCGAGGCCATCCGA
1 --G-GG-CATCCGA
*
55545 GGCCATCCGA
1 GGGCATCCGA
*
55555 GAGCATCCGA
1 GGGCATCCGA
*
55565 GGCCATCCGAA
1 GGGCATCCG-A
* *
55576 CGAGCTATGCGA
1 -GGGC-ATCCGA
55588 GGGCATCCGA
1 GGGCATCCGA
*
55598 GGGCAACCGA
1 GGGCATCCGA
*
55608 GAGAGCTATGCGA
1 G-G-GC-ATCCGA
*
55621 GGGAATCCGA
1 GGGCATCCGA
55631 GGG
1 GGG
55634 AAGCCGAGCG
Statistics
Matches: 86, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
10 54 0.63
11 7 0.08
12 8 0.09
13 10 0.12
14 7 0.08
ACGTcount: A:0.24, C:0.30, G:0.36, T:0.10
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:55633 original size:33 final size:34
Alignment explanation
Indices: 55559--55645 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 34
55549 ATCCGAGAGC
* * *
55559 ATCCGAGGCCATCCGA-ACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGACGAGCTATGCGAGGGA
55592 ATCCGAGGGCAACCGAGA-GAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGACGAGCTATGCGAGGGA
55625 ATCCGAGGG-AAGCCGAG-CGAG
1 ATCCGAGGGCAA-CCGAGACGAG
55646 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 2 0.04
33 45 0.94
34 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.38, T:0.09
Consensus pattern (34 bp):
ATCCGAGGGCAACCGAGACGAGCTATGCGAGGGA
Found at i:55682 original size:29 final size:29
Alignment explanation
Indices: 55649--55704 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
55639 GAGCGAGGGT
* *
55649 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGACGACCTACA
55678 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGGGCATGACGACCTA
55705 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGACGACCTACA
Found at i:55750 original size:12 final size:12
Alignment explanation
Indices: 55733--55757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55723 TGCCATGCAA
55733 CACGTTCATTCT
1 CACGTTCATTCT
55745 CACGTTCATTCT
1 CACGTTCATTCT
55757 C
1 C
55758 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:55818 original size:29 final size:29
Alignment explanation
Indices: 55775--55831 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
55765 GAGCAAGGGT
*
55775 AGGTCGCCCGAAGTGCATGGCGGCCTACA
1 AGGTCGCCCGAAGTGCATGGCGACCTACA
* *
55804 AGGTCGCCTGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGAAGTGCATGGCGACCTAC
55832 TGCCAATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.35, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGAAGTGCATGGCGACCTACA
Found at i:67412 original size:22 final size:22
Alignment explanation
Indices: 67379--67420 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
67369 TAAACATTCA
*
67379 GAAAATTGCAAATACTTTTGAT
1 GAAAATTGCAAAAACTTTTGAT
67401 GAAAA-TGCCAAAAACTTTTG
1 GAAAATTG-CAAAAACTTTTG
67421 TCTGCCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (22 bp):
GAAAATTGCAAAAACTTTTGAT
Done.