Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007830.1 Hibiscus syriacus cultivar Beakdansim tig00110169_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: 39232
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:690 original size:1 final size:1
Alignment explanation
Indices: 686--737 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
676 AAATTTTGGC
** *** *
686 TTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTGCCTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
738 GAAAAAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (1 bp):
T
Found at i:697 original size:15 final size:15
Alignment explanation
Indices: 692--734 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
682 TGGCTTTTTT
*
692 TTTTTTTTTTTTTCC
1 TTTTTTTTTTTTGCC
707 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
722 TTTTTTTTGTTTT
1 TTTTTTTT-TTTT
735 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:703 original size:21 final size:21
Alignment explanation
Indices: 679--718 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
669 TTTTTTGAAA
*
679 TTTTGGCTTTTTTTTTTTTTT
1 TTTTGCCTTTTTTTTTTTTTT
*
700 TTTTTCCTTTTTTTTTTTT
1 TTTTGCCTTTTTTTTTTTT
719 GCCTTTTTTT
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:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (21 bp):
TTTTGCCTTTTTTTTTTTTTT
Found at i:9830 original size:28 final size:28
Alignment explanation
Indices: 9797--9930 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
9787 TCGTGGGGTT
9797 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
9825 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * ** **
9853 --TAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
9877 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
9905 CATAACAACATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
9931 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.20
27 4 0.05
28 53 0.67
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:9897 original size:80 final size:80
Alignment explanation
Indices: 9797--9957 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
9787 TCGTGGGGTT
* * *
9797 CATAACAGCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTAAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
*
9862 GTGCACTCACATTCA
66 GTGCACCCACATTCA
* *
9877 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
9942 GTGCACCCACATTCA
66 GTGCACCCACATTCA
9957 C
1 C
9958 TTTACAACAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (80 bp):
CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
GTGCACCCACATTCA
Found at i:11684 original size:19 final size:20
Alignment explanation
Indices: 11660--11711 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
11650 CGGCCAAGAG
*
11660 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
11679 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
11700 CATGTATTTTCA
1 CATGTATTTTCA
11712 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:12275 original size:11 final size:11
Alignment explanation
Indices: 12251--12295 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
12241 TTGGTGCTGG
12251 AAACAAGATAA
1 AAACAAGATAA
* *
12262 AAATAAGATTA
1 AAACAAGATAA
12273 AAACAAGATAA
1 AAACAAGATAA
12284 AGAA-AAGATAA
1 A-AACAAGATAA
12295 A
1 A
12296 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:12279 original size:22 final size:22
Alignment explanation
Indices: 12251--12292 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
12241 TTGGTGCTGG
12251 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
12273 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
12293 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:15916 original size:11 final size:10
Alignment explanation
Indices: 15858--15915 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
15848 AAATTTTGGC
15858 TTTTTTGTTT
1 TTTTTTGTTT
15868 TTTTTTGTTTT
1 TTTTTTG-TTT
*
15879 TTTTTTGCCTT
1 TTTTTTG-TTT
****
15890 TTTTTCCCCT
1 TTTTTTGTTT
15900 TTTTTTGTTT
1 TTTTTTGTTT
15910 TTTTTT
1 TTTTTT
15916 TTGAAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 21 0.55
11 17 0.45
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:16259 original size:11 final size:11
Alignment explanation
Indices: 16235--16279 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
16225 TTGATGTTGG
16235 AAACAAGATAA
1 AAACAAGATAA
* *
16246 AAATAAGATTA
1 AAACAAGATAA
16257 AAACAAGATAA
1 AAACAAGATAA
16268 AGAA-AAGATAA
1 A-AACAAGATAA
16279 A
1 A
16280 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:16263 original size:22 final size:22
Alignment explanation
Indices: 16235--16276 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
16225 TTGATGTTGG
16235 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
16257 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
16277 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:16804 original size:22 final size:23
Alignment explanation
Indices: 16763--16805 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
16753 CAACCTTAAT
16763 TCCTAATAAAATAATAAATCAGA
1 TCCTAATAAAATAATAAATCAGA
* *
16786 TCCTAA-AAGATAATTAATCA
1 TCCTAATAAAATAATAAATCA
16806 TCCTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (23 bp):
TCCTAATAAAATAATAAATCAGA
Found at i:19485 original size:33 final size:33
Alignment explanation
Indices: 19443--19511 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19433 GTTGATGAAT
*
19443 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
19476 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
19509 GAA
1 GAA
19512 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:19539 original size:9 final size:11
Alignment explanation
Indices: 19496--19592 Score: 74
Period size: 13 Copynumber: 8.3 Consensus size: 11
19486 GTTATTGGCG
19496 TGATATGGTGA
1 TGATATGGTGA
19507 TGGAATATGGTGA
1 T-G-ATATGGTGA
19520 TGATATAGGTGA
1 TGATAT-GGTGA
19532 T-A-ATGGTGA
1 TGATATGGTGA
19541 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
19554 TGATATAGGCG-
1 TGATAT-GGTGA
*
19565 TGATAATGGAGA
1 TGAT-ATGGTGA
19577 TGGATTATGGTGA
1 T-GA-TATGGTGA
19590 TGA
1 TGA
19593 AAATAGTATC
Statistics
Matches: 71, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
11 17 0.24
12 18 0.25
13 27 0.38
14 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:19579 original size:36 final size:36
Alignment explanation
Indices: 19482--19592 Score: 156
Period size: 34 Copynumber: 3.2 Consensus size: 36
19472 AATGGAAGGA
* *
19482 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
19517 TGATGATATA-G-GTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
19551 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
19587 TGATGA
1 TGATGA
19593 AAATAGTATC
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
33 5 0.07
34 27 0.40
35 9 0.13
36 27 0.40
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:23982 original size:33 final size:33
Alignment explanation
Indices: 23940--24008 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
23930 GTTGATGAAT
*
23940 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
23973 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
24006 GAA
1 GAA
24009 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:24028 original size:35 final size:36
Alignment explanation
Indices: 23979--24090 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 36
23969 AATGGAAGGA
* *
23979 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
24014 TGATGATATAGGCGTGATAATGGTGATGGACTAT-G
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
24049 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
24085 TGATGA
1 TGATGA
24091 AAATAGTATC
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 49 0.70
36 21 0.30
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:29176 original size:1 final size:1
Alignment explanation
Indices: 29172--29237 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
29162 TTTTTGGCTC
*** *** *
29172 TTTTTTTTTTTTGCCTTTTTTTTTTTTGCCTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29237 T
1 T
29238 GAAAAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.06, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:29180 original size:16 final size:15
Alignment explanation
Indices: 29161--29238 Score: 87
Period size: 15 Copynumber: 5.5 Consensus size: 15
29151 AAATTTTGGC
*
29161 TTTTTTGGCTCTTTTT
1 TTTTTTTGC-CTTTTT
29177 TTTTTTTGCCTTTTT
1 TTTTTTTGCCTTTTT
29192 TTTTTTTGCCTTTTT
1 TTTTTTTGCCTTTTT
*
29207 TTGTTTT---TTTTT
1 TTTTTTTGCCTTTTT
29219 TTTTTTT---TTTTT
1 TTTTTTTGCCTTTTT
29231 TTTTTTTG
1 TTTTTTTG
29239 AAAAAAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
12 23 0.40
15 27 0.47
16 8 0.14
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (15 bp):
TTTTTTTGCCTTTTT
Found at i:29207 original size:41 final size:39
Alignment explanation
Indices: 29154--29238 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
29144 TTTTTTGAAA
*
29154 TTTTGGCTTTTTTGGCTCTTTTTTTTTTTTGCCTTTTTTTT
1 TTTTGCCTTTTTTGG-T-TTTTTTTTTTTTGCCTTTTTTTT
* ***
29195 TTTTGCCTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTGCCTTTTTTGGTTTTTTTTTTTTTGCCTTTTTTTT
29234 TTTTG
1 TTTTG
29239 AAAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 25 0.64
40 1 0.03
41 13 0.33
ACGTcount: A:0.00, C:0.08, G:0.09, T:0.82
Consensus pattern (39 bp):
TTTTGCCTTTTTTGGTTTTTTTTTTTTTGCCTTTTTTTT
Found at i:33847 original size:1 final size:1
Alignment explanation
Indices: 33843--33904 Score: 79
Period size: 1 Copynumber: 62.0 Consensus size: 1
33833 TTTTTGGCTC
*** * *
33843 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCTTTTTTTGTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33905 GAAAAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.92
Consensus pattern (1 bp):
T
Found at i:33871 original size:34 final size:34
Alignment explanation
Indices: 33833--33905 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
33823 AAATTTTGGC
33833 TTTTTGGCTCTTTTTTT-TTTTTTTT-TTTTTTTT
1 TTTTTGGC-CTTTTTTTGTTTTTTTTGTTTTTTTT
*
33866 TTTTTTGCCTTTTTTTGTTTTTTTTGTTTTTTTT
1 TTTTTGGCCTTTTTTTGTTTTTTTTGTTTTTTTT
33900 TTTTTG
1 TTTTTG
33906 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 8 0.22
33 15 0.42
34 13 0.36
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (34 bp):
TTTTTGGCCTTTTTTTGTTTTTTTTGTTTTTTTT
Found at i:36918 original size:1 final size:1
Alignment explanation
Indices: 36914--36967 Score: 81
Period size: 1 Copynumber: 54.0 Consensus size: 1
36904 AAATTTTGGC
* * *
36914 TTTTTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36968 AAAAAATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:36936 original size:26 final size:23
Alignment explanation
Indices: 36914--36967 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
36904 AAATTTTGGC
36914 TTTTTTTTTGTTTTTTTTTTTTTG
1 TTTTTTTTT-TTTTTTTTTTTTTG
36938 -TTTTTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTG
36960 TTTTTTTT
1 TTTTTTTT
36968 AAAAAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (23 bp):
TTTTTTTTTTTTTTTTTTTTTTG
Found at i:37301 original size:11 final size:11
Alignment explanation
Indices: 37277--37320 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
37267 TTGGTGCTGG
37277 AAACAAGATAA
1 AAACAAGATAA
* *
37288 AAATAAGATTA
1 AAACAAGATAA
37299 AAACAAGATAA
1 AAACAAGATAA
37310 AGAA-AAGATAA
1 A-AACAAGATAA
37321 TGAATTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 26 0.93
12 2 0.07
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:37305 original size:22 final size:22
Alignment explanation
Indices: 37277--37318 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
37267 TTGGTGCTGG
37277 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
37299 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
37319 AATGAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Done.