Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006463.1 Hibiscus syriacus cultivar Beakdansim tig00015662_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: 91064
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6213 original size:21 final size:21
Alignment explanation
Indices: 6189--6228 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6179 ACAGTACTAG
*
6189 AGCAAGGTATCGGTACCCTGT
1 AGCAAGGTATCGATACCCTGT
*
6210 AGCAGGGTATCGATACCCT
1 AGCAAGGTATCGATACCCT
6229 ATTTGTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (21 bp):
AGCAAGGTATCGATACCCTGT
Found at i:14095 original size:28 final size:28
Alignment explanation
Indices: 14024--14121 Score: 133
Period size: 28 Copynumber: 3.4 Consensus size: 28
14014 TAAACCCGAC
*
14024 CCCGACCCGAATATCACAATTAAAAAACCCGA
1 CCCGACCCGAATATCACACTTAAAAAA----A
14056 CCCGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
* *
14084 CCTGACCTGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
14112 CCCGACCCGA
1 CCCGACCCGA
14122 CCCGAATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
28 35 0.57
32 26 0.43
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.14
Consensus pattern (28 bp):
CCCGACCCGAATATCACACTTAAAAAAA
Found at i:14222 original size:33 final size:33
Alignment explanation
Indices: 14015--14223 Score: 175
Period size: 32 Copynumber: 6.4 Consensus size: 33
14005 TTTTCACCCT
*
14015 AAACCCGACCCCGACCCGAATATCACA-ATTAAA
1 AAACCCGA-CCCGACCCGAATATCACACTTTAAA
14048 AAACCCGACCCGACCCGAATATCACAC-TTAAA
1 AAACCCGACCCGACCCGAATATCACACTTTAAA
* * *
14080 AAA----ACCTGACCTGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTTAAA
*
14109 AAACCCGACCCGACCCGAATATCAAAC-TTAAA
1 AAACCCGACCCGACCCGAATATCACACTTTAAA
* * ***
14141 AAACCCGACCTGA-CCTAA-ACTCGATTTTTTAAAAAA
1 AAACCCGACCCGACCCGAATA-TC-ACACTTT---AAA
* *
14177 AAATCCGAACCCGACCTGAATATCACACTTTAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTTAAA
*
14211 AAACCTGACCCGA
1 AAACCCGACCCGA
14224 ATGTCAAACT
Statistics
Matches: 140, Mismatches: 21, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
28 18 0.13
29 7 0.05
30 1 0.01
31 6 0.04
32 43 0.31
33 33 0.24
34 8 0.06
36 9 0.06
37 9 0.06
38 5 0.04
39 1 0.01
ACGTcount: A:0.43, C:0.32, G:0.09, T:0.17
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTTAAA
Found at i:14225 original size:28 final size:28
Alignment explanation
Indices: 14184--14252 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
14174 AAAAAATCCG
* * *
14184 AACCCGACCTGAATATCACACTTTAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
* *
14212 AACCTGACCCGAATGTCAAACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
14240 AACCCGACCCGAA
1 AACCCGACCCGAA
14253 CCCGGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.43, C:0.30, G:0.10, T:0.16
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTAAAAA
Found at i:14292 original size:31 final size:32
Alignment explanation
Indices: 14233--14315 Score: 123
Period size: 31 Copynumber: 2.6 Consensus size: 32
14223 AATGTCAAAC
*
14233 TTAAAAAAACCCGACCCGAACCCGGAATTTTT
1 TTAAAAAAATCCGACCCGAACCCGGAATTTTT
* *
14265 TTAAAAAAATCCGACTCGATCCC-GAATTTTT
1 TTAAAAAAATCCGACCCGAACCCGGAATTTTT
*
14296 TTAAAAAAATTCGACCCGAA
1 TTAAAAAAATCCGACCCGAA
14316 TACCAAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 25 0.56
32 20 0.44
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (32 bp):
TTAAAAAAATCCGACCCGAACCCGGAATTTTT
Found at i:31861 original size:24 final size:24
Alignment explanation
Indices: 31834--31887 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31824 CGAACGACGT
**
31834 ATGTTCGCGAACATTTAAATGAAC
1 ATGTTCGCGAACATTTAAACAAAC
*
31858 ATGTTCGTGAACATTTAAACAAAC
1 ATGTTCGCGAACATTTAAACAAAC
31882 ATGTTC
1 ATGTTC
31888 ACGATCGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (24 bp):
ATGTTCGCGAACATTTAAACAAAC
Found at i:38247 original size:35 final size:36
Alignment explanation
Indices: 38201--38322 Score: 131
Period size: 35 Copynumber: 3.4 Consensus size: 36
38191 TGGCAACCAA
38201 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATATTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATATTT
** * *
38238 -TTTTTAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATATTT
* * * *
38273 CTTTGAAAAATAATTTTTCAACGTTTGGTAGATGTTT
1 CTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATATTT
*
38310 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
38323 AATGGGATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 29 0.41
36 21 0.30
37 21 0.30
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATATTT
Found at i:42222 original size:33 final size:35
Alignment explanation
Indices: 42177--42290 Score: 133
Period size: 33 Copynumber: 3.3 Consensus size: 35
42167 CCAACTTTGA
42177 AAAAATGATTTTCAAAGTTTGGTAAATGTTT-TTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
* *
42211 -TAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
* * * * *
42245 GAAAAATAGTTTTTCAACGTTTGGTATATGTTTGTTG
1 -AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTT
42282 AAAAATGAT
1 AAAAATGAT
42291 AATGGGATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 28 0.42
34 3 0.04
35 2 0.03
36 10 0.15
37 24 0.36
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (35 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
Found at i:44226 original size:16 final size:16
Alignment explanation
Indices: 44205--44242 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
44195 TATTCACATA
*
44205 AATAGTGAATTTTGTG
1 AATAGTGAATTTCGTG
44221 AATAGTGAATTTCGTG
1 AATAGTGAATTTCGTG
44237 AATAGT
1 AATAGT
44243 AAAAACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (16 bp):
AATAGTGAATTTCGTG
Found at i:60859 original size:96 final size:96
Alignment explanation
Indices: 60688--60878 Score: 222
Period size: 96 Copynumber: 2.0 Consensus size: 96
60678 CAAGTAGTAA
* ** *
60688 CCAGTAGATTTCACGATCCATAAATCAGGAACGATCATATTTTTTAGTGAAAACAGGAAACCATA
1 CCAGTAGATTCCACGATCCATAAATCAGGAACGATCATATTTTACAATGAAAACAGGAAACCATA
* * * *
60753 TAACACATTTCAGGTAATCATAGTTCATAAT
66 GAACACATTTCAAGTAACCATAGTCCATAAT
** * * *
60784 CCAGTAGATTCCATTATCCATAAATCAGGAATGATCATATTTTACAATTAAAATA-GATAACCAT
1 CCAGTAGATTCCACGATCCATAAATCAGGAACGATCATATTTTACAATGAAAACAGGA-AACCAT
** *
60848 AGAGTATATTTCAAGTAACCATAGTCCATAA
65 AGAACACATTTCAAGTAACCATAGTCCATAA
60879 ACCAATAAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
95 2 0.03
96 76 0.97
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (96 bp):
CCAGTAGATTCCACGATCCATAAATCAGGAACGATCATATTTTACAATGAAAACAGGAAACCATA
GAACACATTTCAAGTAACCATAGTCCATAAT
Found at i:64622 original size:16 final size:17
Alignment explanation
Indices: 64593--64625 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
64583 GTACACGTGG
*
64593 TTTATAATTTAATTTAA
1 TTTATAATTGAATTTAA
64610 TTTA-AATTGAATTTAA
1 TTTATAATTGAATTTAA
64626 ATTTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTATAATTGAATTTAA
Found at i:64634 original size:11 final size:11
Alignment explanation
Indices: 64597--64634 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64587 ACGTGGTTTA
64597 TAATTT-AATT
1 TAATTTAAATT
64607 TAATTTAAATT
1 TAATTTAAATT
*
64618 GAATTTAAATT
1 TAATTTAAATT
*
64629 TTATTT
1 TAATTT
64635 TAATCCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:65756 original size:10 final size:10
Alignment explanation
Indices: 65741--65775 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
65731 TTTATCACAC
65741 CAAATTCTCT
1 CAAATTCTCT
65751 CAAATTCTCT
1 CAAATTCTCT
65761 -AAATTTCTCT
1 CAAA-TTCTCT
65771 CAAAT
1 CAAAT
65776 ACCCAACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:68985 original size:51 final size:50
Alignment explanation
Indices: 68882--69008 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 50
68872 CCCCTACGCG
*
68882 GCGTATAGCGCGG-AGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTA-CAGGGGGCGCGCTATACCCCACG-GTAACCCAATCA
* * *
68933 GCGTATAGCACGGTACAGGGGGCGCGCTATACTCCAC-GTAGCGCCAAATCA
1 GCGTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGGTAAC-CC-AATCA
* *
68984 GCATATAGCGCGGTTCAGGGGGCGC
1 GCGTATAGCGCGGTACAGGGGGCGC
69009 ACTTTACTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
49 4 0.06
50 2 0.03
51 59 0.89
52 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.34, T:0.15
Consensus pattern (50 bp):
GCGTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGGTAACCCAATCA
Found at i:80708 original size:6 final size:6
Alignment explanation
Indices: 80700--80870 Score: 299
Period size: 6 Copynumber: 28.7 Consensus size: 6
80690 ACCCCTGTAT
* *
80700 CCATAT CCATAC CCATAC TCATAC CCATAC CCATAC CCATAC CCATAC
1 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC
* *
80748 CCATAC CCATAC CCATAC CCATAC CTATAC CCATAC TCATAC CCATAC
1 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC
80796 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATA- CCATAC
1 CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC CCATAC
80843 CCATAC CCATAC CCATAC CCATAC CCAT
1 CCATAC CCATAC CCATAC CCATAC CCAT
80871 CTATTTGAAA
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
5 5 0.03
6 152 0.97
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.19
Consensus pattern (6 bp):
CCATAC
Found at i:83436 original size:2 final size:2
Alignment explanation
Indices: 83429--83466 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
83419 TCTGTATGTA
*
83429 TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
83467 GCTTTGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:86129 original size:50 final size:53
Alignment explanation
Indices: 86061--86196 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 53
86051 CTTAAGAGAT
* *
86061 AATAACAAATTTTTTAACTATTGAGATTGTTTGAACCCGAAAT-TTTAAA-AG
1 AATAATAAATTTTTTAACTATTGAGATTGTTTGAACCCGAAATCTTAAAACAG
* * * ** *
86112 -ATAATAATTTTTTTAACTACTGAGATTGCTTGAACTTGAGATCTTAAAACAG
1 AATAATAAATTTTTTAACTATTGAGATTGTTTGAACCCGAAATCTTAAAACAG
*
86164 AATAATAAATTTTGTAACTACTT-AGATTGTTTG
1 AATAATAAATTTTTTAACTA-TTGAGATTGTTTG
86197 GTTCATGCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
50 35 0.51
51 5 0.07
52 2 0.03
53 26 0.38
54 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (53 bp):
AATAATAAATTTTTTAACTATTGAGATTGTTTGAACCCGAAATCTTAAAACAG
Found at i:86191 original size:53 final size:51
Alignment explanation
Indices: 86037--86192 Score: 149
Period size: 50 Copynumber: 3.0 Consensus size: 51
86027 TGACATGCAC
* * *
86037 TGCTTGAA-TGAGATCTTAAGAGATAATAACAAATTTTTTAACTA-TTGAGAT
1 TGCTTGAACTGAGATCTTAA-AAAGAATAATAAATTTTTTAACTACTT-AGAT
* * * * * *
86088 TGTTTGAACCCGAAAT-TTTAAAAG-ATAATAATTTTTTTAACTACTGAGAT
1 TGCTTGAA-CTGAGATCTTAAAAAGAATAATAAATTTTTTAACTACTTAGAT
*
86138 TGCTTGAACTTGAGATCTTAAAACAGAATAATAAATTTTGTAACTACTTAGAT
1 TGCTTGAAC-TGAGATCTTAAAA-AGAATAATAAATTTTTTAACTACTTAGAT
86191 TG
1 TG
86193 TTTGGTTCAT
Statistics
Matches: 82, Mismatches: 16, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
49 1 0.01
50 32 0.39
51 15 0.18
52 5 0.06
53 29 0.35
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (51 bp):
TGCTTGAACTGAGATCTTAAAAAGAATAATAAATTTTTTAACTACTTAGAT
Done.