Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006298.1 Hibiscus syriacus cultivar Beakdansim tig00015056_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: 58508
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:8419 original size:18 final size:18
Alignment explanation
Indices: 8396--8446 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
8386 TATAAATTTG
8396 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
* *
8414 TCCCGAAAGACCACTATG
1 TCCCGAAGGACCACTATA
8432 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
8447 CCTTAAGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:14976 original size:36 final size:36
Alignment explanation
Indices: 14936--15083 Score: 233
Period size: 36 Copynumber: 4.1 Consensus size: 36
14926 ACAGTGCTGG
*
14936 ACATTGATACACAAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATATACCAAAGCTGATATGATA
* *
14972 ACATTGATACACGAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATATACCAAAGCTGATATGATA
15008 ACATTGATACACGAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATATACCAAAGCTGATATGATA
* *
15044 ACATTGATACACGAATGTATCAAAGCTGATAATGGATA
1 ACATTGATACACGAATATACCAAAGCTGAT-AT-GATA
15082 AC
1 AC
15084 TACTCAATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 95 0.92
37 2 0.02
38 6 0.06
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATATACCAAAGCTGATATGATA
Found at i:15053 original size:72 final size:74
Alignment explanation
Indices: 14936--15083 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 74
14926 ACAGTGCTGG
14936 ACATTGATACACAAATATACCAAAGCTGATATGATAACATTGATACACGAATGTATCAAAGCTGA
1 ACATTGATACACAAATATACCAAAGCTGATATGATAACATTGATACACGAATGTATCAAAGCTGA
15001 T-AT-GATA
66 TAATGGATA
*
15008 ACATTGATACACGAATATACCAAAGCTGATATGATAACATTGATACACGAATGTATCAAAGCTGA
1 ACATTGATACACAAATATACCAAAGCTGATATGATAACATTGATACACGAATGTATCAAAGCTGA
15073 TAATGGATA
66 TAATGGATA
15082 AC
1 AC
15084 TACTCAATTA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 65 0.89
73 2 0.03
74 6 0.08
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (74 bp):
ACATTGATACACAAATATACCAAAGCTGATATGATAACATTGATACACGAATGTATCAAAGCTGA
TAATGGATA
Found at i:18892 original size:76 final size:78
Alignment explanation
Indices: 18796--18948 Score: 220
Period size: 77 Copynumber: 2.0 Consensus size: 78
18786 AATATTTTAA
* * *
18796 AAATAAAAGAATTTCTATATTTACACAATAAAA-AACTCTTAAGAATAATAAAAAATATGTACAA
1 AAATAAAAGAAGTTCAATATTTACACAATAAAAGAACTCTTAAGAATAATAAAAAATATGGACAA
18860 TATTAA-AAAATT
66 TATTAAGAAAATT
* * * **
18872 AAATAAAAGAAGTTCAATATTTGCACAATAAAAGAATTCTTAAGAATAATAGAACTTATGGACAA
1 AAATAAAAGAAGTTCAATATTTACACAATAAAAGAACTCTTAAGAATAATAAAAAATATGGACAA
18937 TATTAAGAAAAT
66 TATTAAGAAAAT
18949 AAAAGAATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 30 0.45
77 32 0.48
78 5 0.07
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (78 bp):
AAATAAAAGAAGTTCAATATTTACACAATAAAAGAACTCTTAAGAATAATAAAAAATATGGACAA
TATTAAGAAAATT
Found at i:20627 original size:23 final size:24
Alignment explanation
Indices: 20557--20628 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
20547 TAAATTCTAT
*
20557 TTTA-ATTTTAA-TTATTATTAATA
1 TTTATATTTTAATTTAGTA-TAATA
*
20580 TTTTTA-TTT-ATTTAGTAT--TA
1 TTTATATTTTAATTTAGTATAATA
20600 GTTTATATTTTAATTTA-TATAATA
1 -TTTATATTTTAATTTAGTATAATA
20624 TTTAT
1 TTTAT
20629 TAAATTAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
20 2 0.05
21 5 0.13
22 8 0.21
23 21 0.54
24 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTATATTTTAATTTAGTATAATA
Found at i:22181 original size:21 final size:21
Alignment explanation
Indices: 22148--22188 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22138 CACAGCCGTT
** *
22148 TCAGATGGTACCGCAGCCATA
1 TCAGATGACACCGCAACCATA
22169 TCAGATGACACCGCAACCAT
1 TCAGATGACACCGCAACCAT
22189 TTAATATGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (21 bp):
TCAGATGACACCGCAACCATA
Found at i:22595 original size:6 final size:6
Alignment explanation
Indices: 22521--22591 Score: 124
Period size: 6 Copynumber: 11.8 Consensus size: 6
22511 TTGCTCCTGA
*
22521 TGATGA TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
*
22569 TGATGG TGATGG TGATGA TGATG
1 TGATGG TGATGG TGATGG TGATG
22592 ATGAGAGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:27359 original size:228 final size:227
Alignment explanation
Indices: 26957--27441 Score: 855
Period size: 228 Copynumber: 2.1 Consensus size: 227
26947 GTAAATTATC
* * * *
26957 TATCCTTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
27022 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
* *
27087 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATAG
27152 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
27185 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
27249 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
*
27314 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATA
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATA
27379 GAAACATAAATTACATAACTTTAAAAAAGTATA
195 GAAACATAAATTACATAACTTTAAAAAAGTATA
27412 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
27442 AAAAGTAGGT
Statistics
Matches: 246, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 41 0.17
228 196 0.80
229 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATAG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:27743 original size:20 final size:19
Alignment explanation
Indices: 27720--27766 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
27710 CGATATACCA
27720 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
27740 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
27760 GGTAAAA
1 GGTAAAA
27767 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:27854 original size:181 final size:182
Alignment explanation
Indices: 27508--27980 Score: 707
Period size: 181 Copynumber: 2.6 Consensus size: 182
27498 GATCCAAATT
* * * *
27508 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
27572 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
27637 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
27690 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
27755 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
27819 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
27871 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
27936 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
27981 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 168 0.63
182 97 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:27924 original size:20 final size:19
Alignment explanation
Indices: 27901--27947 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
27891 CGATATAACA
27901 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
27921 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
27941 GGTAAAA
1 GGTAAAA
27948 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:27949 original size:17 final size:19
Alignment explanation
Indices: 27910--27952 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
27900 AGGTAAAAAT
27910 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
27930 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
27947 ATGATA
1 ATGATA
27953 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:29259 original size:3 final size:3
Alignment explanation
Indices: 29238--29282 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
29228 TGAAGCTGGC
* * *
29238 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
29283 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:31058 original size:183 final size:182
Alignment explanation
Indices: 30784--31275 Score: 867
Period size: 183 Copynumber: 2.7 Consensus size: 182
30774 CAATGCTATA
* *
30784 GGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTG
1 GGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
*
30849 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACAT
66 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACAT
* *
30914 TTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACC
130 TTACACATCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATATAACC
*
30967 GGTATAAATATACCAGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
1 GGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
31032 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACAT
66 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACAT
*
31097 TTACACATCGGAACCCAGATTTATAATATAATAGATAATTTTGTAATATAACC
130 TTACACATCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATATAACC
* * *
31150 GGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACATATATCTACACTTTATAATATTG
1 GGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
31215 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
31276 GTAATTTTAA
Statistics
Matches: 296, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 292 0.99
184 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
GGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTG
TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACATT
TACACATCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATATAACC
Found at i:33771 original size:25 final size:25
Alignment explanation
Indices: 33743--33807 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
33733 TTATCATTAA
33743 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
33768 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
33793 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
33808 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:34185 original size:23 final size:23
Alignment explanation
Indices: 34154--34203 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
34144 ATAGGTAAAC
*
34154 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
34177 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
34200 ATAT
1 ATAT
34204 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:34649 original size:23 final size:23
Alignment explanation
Indices: 34620--34667 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
34610 AAATAGGTAA
* *
34620 ATATAAGCGCTACCTATTACATT
1 ATATAAGCACTACCTAGTACATT
*
34643 ATATAAGCACTACCTAGTATATT
1 ATATAAGCACTACCTAGTACATT
34666 AT
1 AT
34668 TGTACTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTAGTACATT
Found at i:37215 original size:17 final size:17
Alignment explanation
Indices: 37181--37213 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
37171 TTTAATTATA
37181 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
37198 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
37214 TACCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:41142 original size:48 final size:49
Alignment explanation
Indices: 41082--41178 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
41072 ATCAACATGT
41082 CCCAAACAATATCAA-TTTAGCCATATAATTATATTGACGAAACTATCA
1 CCCAAACAATATCAATTTTAGCCATATAATTATATTGACGAAACTATCA
* * * *
41130 CCCAAACGATATCAATTTTAGTCATGTCATTATATTGACGAAACTATCA
1 CCCAAACAATATCAATTTTAGCCATATAATTATATTGACGAAACTATCA
41179 ACTGTATCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 14 0.32
49 30 0.68
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (49 bp):
CCCAAACAATATCAATTTTAGCCATATAATTATATTGACGAAACTATCA
Done.