Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009305.1 Hibiscus syriacus cultivar Beakdansim tig00113041_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: 62901
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:560 original size:11 final size:11
Alignment explanation
Indices: 544--568 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
534 CCAACCCAAA
544 AAATAATAAAT
1 AAATAATAAAT
555 AAATAATAAAT
1 AAATAATAAAT
566 AAA
1 AAA
569 AACATTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:11262 original size:14 final size:14
Alignment explanation
Indices: 11243--11269 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11233 AAAAAAAAGC
11243 ATGTTACTTATATA
1 ATGTTACTTATATA
11257 ATGTTACTTATAT
1 ATGTTACTTATAT
11270 TTGAGATCAA
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:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
ATGTTACTTATATA
Found at i:16487 original size:44 final size:44
Alignment explanation
Indices: 16437--16621 Score: 176
Period size: 44 Copynumber: 4.2 Consensus size: 44
16427 TTTTTTATGA
* * *
16437 AAACGCCGCAATAGGTCTGGTATTTAGC-AGCGTTTTTAGGGTAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGA-CGTTTTTAGGATAC
* ** * ** * *
16481 ATACGCCGCTTTAGGACTGGTATATAATGGCGTTTTT-GCTATAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGACGTTTTTAG-GATAC
* * * *
16525 AAACGCCGCGATAGGTGTGGTATATAGCGTCATTTTTAGGACAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGACGTTTTTAGGATAC
* *
16569 AAACGCTGCGATAGCTCTGGTATATAGCGACGTTTTTAGGATAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGACGTTTTTAGGATAC
*
16613 AAACACCGC
1 AAACGCCGC
16622 TAAAAGTTGG
Statistics
Matches: 109, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.01
44 107 0.98
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
AAACGCCGCGATAGGTCTGGTATATAGCGACGTTTTTAGGATAC
Found at i:25519 original size:40 final size:41
Alignment explanation
Indices: 25408--25519 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
25398 ACTGCCCTAG
* * * *
25408 TTTATAGCGGCGTTTATATAAAAACACCGCAAAATATTATA
1 TTTATTGCGGCGTTTGTATAAAAACGCCACAAAATATTATA
* * * *
25449 TCTATTGTGGCGTTTGT-TGCAAAAAAGCCACAAAATATTATC
1 TTTATTGCGGCGTTTGTAT--AAAAACGCCACAAAATATTATA
*
25491 TTTATTGCGACGTTTGTAT-AAAACGCCAC
1 TTTATTGCGGCGTTTGTATAAAAACGCCAC
25520 TAATGGAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
40 10 0.18
41 13 0.23
42 32 0.57
43 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (41 bp):
TTTATTGCGGCGTTTGTATAAAAACGCCACAAAATATTATA
Found at i:33568 original size:2 final size:2
Alignment explanation
Indices: 33563--33595 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33553 GCCATTAATT
33563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33596 TATGTCGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34872 original size:31 final size:31
Alignment explanation
Indices: 34805--34864 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
34795 CAATTTAAGG
*
34805 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
34836 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
34865 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:34952 original size:19 final size:19
Alignment explanation
Indices: 34928--34993 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
34918 AATGTTTTTA
* *
34928 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
34947 TGAATAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
*
34966 TGAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
34985 TGAACAGTA
1 TGAACAGTA
34994 CCCCGAGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:35126 original size:21 final size:21
Alignment explanation
Indices: 35100--35139 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35090 ATTTGAATAT
*
35100 TATGAAGGGGTATCGATTCGC
1 TATGAAGGGGTACCGATTCGC
35121 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
35140 CCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCGC
Found at i:35204 original size:21 final size:21
Alignment explanation
Indices: 35170--35209 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
35160 TTTTTGCAGA
*
35170 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
35192 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
35210 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:36377 original size:19 final size:20
Alignment explanation
Indices: 36353--36400 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
36343 AACGATTTTC
*
36353 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
36372 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
36392 TTTTGAAAA
1 TTTTGAAAA
36401 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:37718 original size:31 final size:31
Alignment explanation
Indices: 37651--37710 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
37641 CAATTTAAGG
*
37651 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
37682 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
37711 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:37798 original size:19 final size:19
Alignment explanation
Indices: 37774--37839 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
37764 AATGTTTTTA
* *
37774 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
37793 TGAATAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
37812 TTAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
37831 TGAACAGTA
1 TGAACAGTA
37840 CCCCGAGGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:37972 original size:21 final size:21
Alignment explanation
Indices: 37946--37985 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37936 ATTTGAATAT
*
37946 TATGAAGGGGTATCGATTCGC
1 TATGAAGGGGTACCGATTCGC
37967 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
37986 CCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCGC
Found at i:38050 original size:21 final size:21
Alignment explanation
Indices: 38016--38055 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
38006 TTTTTGCAGA
*
38016 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
38038 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
38056 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:38729 original size:15 final size:15
Alignment explanation
Indices: 38709--38744 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38699 TAATTATTCG
38709 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
38724 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
38739 ATTAAT
1 TTTAAT
38745 TTAATGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:38811 original size:2 final size:2
Alignment explanation
Indices: 38804--38844 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
38794 TCGCATCATC
38804 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
38845 AACAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49434 original size:23 final size:23
Alignment explanation
Indices: 49401--49468 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
49391 ATTATTATAT
*
49401 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * *
49424 GGTACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
* *
49447 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
49469 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:55263 original size:4 final size:4
Alignment explanation
Indices: 55254--55295 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
55244 TTCATCACCG
55254 TACA TACA TACA TTAACA T--A TACA TACA TACA TACA TACA TA
1 TACA TACA TACA -T-ACA TACA TACA TACA TACA TACA TACA TA
55296 TGTGTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
4 27 0.79
5 2 0.06
6 3 0.09
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:57076 original size:36 final size:36
Alignment explanation
Indices: 57026--57099 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
57016 TAAATATTGG
*
57026 TGCAAGTCTGAGTTAGCAATGAGTTGCTTCTGCAAA
1 TGCAAGTCTGAGTTAGCAATGAGTTACTTCTGCAAA
* *
57062 TGCAAGTCTTAGTTAGCTATGAGTTACTTCTGCAAA
1 TGCAAGTCTGAGTTAGCAATGAGTTACTTCTGCAAA
57098 TG
1 TG
57100 AAGGTTTCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (36 bp):
TGCAAGTCTGAGTTAGCAATGAGTTACTTCTGCAAA
Found at i:62054 original size:29 final size:29
Alignment explanation
Indices: 62011--62093 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
62001 CTCACCTAAC
62011 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
62041 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
62070 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
62094 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Done.