Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009401.1 Hibiscus syriacus cultivar Beakdansim tig00113328_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: 61249
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:12798 original size:19 final size:18
Alignment explanation
Indices: 12766--12824 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
12756 TTGGAGTGCA
* *
12766 AAAAGAAGACAAAATCAG
1 AAAAGAAGAAAAAATAAG
12784 AAAAGAAGAGAAAAATAAG
1 AAAAGAAGA-AAAAATAAG
12803 AAAAGAAGAAAAGAA-AAG
1 AAAAGAAGAAAA-AATAAG
12821 AAAA
1 AAAA
12825 AGAGAGTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 19 0.51
19 18 0.49
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAAAAAATAAG
Found at i:20997 original size:5 final size:5
Alignment explanation
Indices: 20987--21060 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
20977 GAACTTCTCT
**
20987 TTTTC TTTTC TTTTC TTTTC TTCTTC TTTTC --TTC TTTTC TGAT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
* *
21035 TCTTC -TTT- TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
21061 GCACTCCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:21000 original size:11 final size:11
Alignment explanation
Indices: 20984--21055 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
20974 TTTGAACTTC
20984 TCTTTTTCTTT
1 TCTTTTTCTTT
20995 TC-TTTTCTTT
1 TCTTTTTCTTT
*
21005 TCTTCTTCTTT
1 TCTTTTTCTTT
*
21016 TCTTCTTT-TCT
1 TCTT-TTTCTTT
** *
21027 GATTTTTCTCT
1 TCTTTTTCTTT
21038 TCTTTTTGTCTTT
1 TC-TTTT-TCTTT
21051 TCTTT
1 TCTTT
21056 CTTTTGCACT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 13 0.27
11 20 0.42
12 9 0.19
13 6 0.12
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:21005 original size:16 final size:17
Alignment explanation
Indices: 20984--21019 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
20974 TTTGAACTTC
20984 TCTTTTTCTT-TTCTTT
1 TCTTTTTCTTCTTCTTT
21000 TC-TTTTCTTCTTCTTT
1 TCTTTTTCTTCTTCTTT
21016 TCTT
1 TCTT
21020 CTTTTCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 10 0.56
17 1 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTCTTCTTT
Found at i:21010 original size:8 final size:8
Alignment explanation
Indices: 20994--21060 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
20984 TCTTTTTCTT
20994 TTCTTTTC
1 TTCTTTTC
21002 TT-TTCTTC
1 TTCTT-TTC
21010 TTCTTTTC
1 TTCTTTTC
21018 TTCTTTTC
1 TTCTTTTC
*
21026 TGATTTTTCTC
1 T--TCTTT-TC
21037 TTCTTTT-
1 TTCTTTTC
21044 TGTCTTTTC
1 T-TCTTTTC
21053 TTTCTTTT
1 -TTCTTTT
21061 GCACTCCAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 26 0.53
9 12 0.24
10 5 0.10
11 3 0.06
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:21026 original size:16 final size:17
Alignment explanation
Indices: 20995--21060 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
20985 CTTTTTCTTT
20995 TCTTTTCTT-TTCTTCT-
1 TCTTTTCTTCTT-TTCTG
21011 TCTTTTCTTCTTTTCTG
1 TCTTTTCTTCTTTTCTG
*
21028 ATTTTTCTCTTCTTTT-TG
1 -TCTTT-TCTTCTTTTCTG
21046 TCTTTTCTTTCTTTT
1 TCTTTTC-TTCTTTT
21061 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 15 0.35
17 13 0.30
18 6 0.14
19 9 0.21
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTCTTCTTTTCTG
Found at i:21032 original size:27 final size:27
Alignment explanation
Indices: 20980--21053 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
20970 ATCTTTTGAA
**
20980 CTTCTCTTTT-TCTTTTCTTTTCTTTTCTT
1 CTTCT-TTTTGTCTTTTCTGAT-TTTTC-T
21009 CTTCTTTTCT-TCTTTTCTGATTTTTCT
1 CTTCTTTT-TGTCTTTTCTGATTTTTCT
21036 CTTCTTTTTGTCTTTTCT
1 CTTCTTTTTGTCTTTTCT
21054 TTCTTTTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 1 0.02
27 17 0.41
28 8 0.20
29 15 0.37
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (27 bp):
CTTCTTTTTGTCTTTTCTGATTTTTCT
Found at i:21061 original size:16 final size:17
Alignment explanation
Indices: 21011--21060 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
21001 CTTTTCTTCT
21011 TCTTTTC-TTCTTTTCTG
1 TCTTTTCTTTCTTTT-TG
21028 AT-TTTTCTCTTCTTTTTG
1 -TCTTTTCT-TTCTTTTTG
21046 TCTTTTCTTTCTTTT
1 TCTTTTCTTTCTTTT
21061 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 13 0.45
18 9 0.31
19 7 0.24
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.74
Consensus pattern (17 bp):
TCTTTTCTTTCTTTTTG
Found at i:27166 original size:32 final size:32
Alignment explanation
Indices: 27130--27221 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
27120 TGCTTATACA
27130 CTCTTTCGTATACGCAACTGATCTTGTTGCAC
1 CTCTTTCGTATACGCAACTGATCTTGTTGCAC
* *
27162 CTCTTT-G----CGTC-A-TG--CTT-ATACA-
1 CTCTTTCGTATACG-CAACTGATCTTGTTGCAC
27184 CTCTTTCGTATACGCAACTGATCTTGTTGCAC
1 CTCTTTCGTATACGCAACTGATCTTGTTGCAC
27216 CTCTTT
1 CTCTTT
27222 TGGTGTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 24
0.61 0.06 0.33
Matches are distributed among these distances:
22 6 0.14
23 4 0.09
24 3 0.07
26 3 0.07
27 6 0.14
28 3 0.07
30 3 0.07
31 4 0.09
32 12 0.27
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.40
Consensus pattern (32 bp):
CTCTTTCGTATACGCAACTGATCTTGTTGCAC
Found at i:27172 original size:54 final size:54
Alignment explanation
Indices: 27109--27221 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
27099 TGGGGTTTTA
27109 TCTTTGCGTCATGCTTATACACTCTTTCGTATACGCAACTGATCTTGTTGCACC
1 TCTTTGCGTCATGCTTATACACTCTTTCGTATACGCAACTGATCTTGTTGCACC
27163 TCTTTGCGTCATGCTTATACACTCTTTCGTATACGCAACTGATCTTGTTGCACC
1 TCTTTGCGTCATGCTTATACACTCTTTCGTATACGCAACTGATCTTGTTGCACC
27217 TCTTT
1 TCTTT
27222 TGGTGTCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (54 bp):
TCTTTGCGTCATGCTTATACACTCTTTCGTATACGCAACTGATCTTGTTGCACC
Found at i:28171 original size:13 final size:12
Alignment explanation
Indices: 28152--28237 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
28142 ATATAGGCGT
28152 GATATGGTGATG
1 GATATGGTGATG
28164 GAATATGGTGAT-
1 G-ATATGGTGATG
*
28176 GATATAGGCG-T-
1 GATAT-GGTGATG
28187 GATAATGGTGATG
1 GAT-ATGGTGATG
28200 GACTATGGTGAT-
1 GA-TATGGTGATG
*
28212 GATATAGGCG-T-
1 GATAT-GGTGATG
28223 GATAATGGTGATG
1 GAT-ATGGTGATG
28236 GA
1 GA
28238 CAGAAAGGAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:28207 original size:36 final size:36
Alignment explanation
Indices: 28134--28238 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
28124 ATTTATAAGT
* *
28134 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
28169 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
28205 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
28239 AGAAAGGACT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:36401 original size:24 final size:24
Alignment explanation
Indices: 36355--36406 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
36345 TCTTGGCACT
* * *
36355 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
* *
36379 TCAAGTGGCATAGCTGTTGGAACG
1 TCAAGTGGCACAGCTGTTGGAACA
36403 TCAA
1 TCAA
36407 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:41231 original size:36 final size:36
Alignment explanation
Indices: 41179--41291 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
41169 GATACTATTT
*
41179 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
41215 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
41251 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
41286 ACATCA
1 TCATCA
41292 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:41234 original size:13 final size:11
Alignment explanation
Indices: 41179--41277 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
41169 GATACTATTT
41179 TCATCACCATAA
1 TCATCACCAT-A
*
41191 TCCATCTCCATTA
1 T-CATCACCA-TA
*
41204 TCA-CGCCTATA
1 TCATCACC-ATA
41215 TCATCACCATA
1 TCATCACCATA
41226 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
41240 TCA-CGCCTATA
1 TCATCACC-ATA
41251 TCATCACCATA
1 TCATCACCATA
41262 TTCCATCACCATA
1 -T-CATCACCATA
41275 TCA
1 TCA
41278 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:41306 original size:33 final size:33
Alignment explanation
Indices: 41191--41330 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
41181 ATCACCATAA
* * *
41191 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
41225 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
41263 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
41296 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
41329 TC
1 TC
41331 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:45644 original size:36 final size:36
Alignment explanation
Indices: 45592--45704 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
45582 GATACTATTT
*
45592 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
45628 TTATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
45664 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
45699 ACATCA
1 TCATCA
45705 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:45648 original size:13 final size:11
Alignment explanation
Indices: 45592--45690 Score: 58
Period size: 13 Copynumber: 8.3 Consensus size: 11
45582 GATACTATTT
45592 TCATCACCATAA
1 TCATCACCAT-A
*
45604 TCCATCTCCATTA
1 T-CATCACCA-TA
*
45617 TCA-CGCCTATA
1 TCATCACC-ATA
*
45628 TTATCACCATA
1 TCATCACCATA
45639 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
45653 TCA-CGCCTATA
1 TCATCACC-ATA
45664 TCATCACCATA
1 TCATCACCATA
45675 TTCCATCACCATA
1 -T-CATCACCATA
45688 TCA
1 TCA
45691 CGCCAATAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.33
12 16 0.23
13 27 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:45719 original size:33 final size:33
Alignment explanation
Indices: 45640--45743 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
45630 ATCACCATAG
* *
45640 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
45676 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
45709 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
45742 TC
1 TC
45744 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:55830 original size:27 final size:27
Alignment explanation
Indices: 55800--55861 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
55790 GCAAAAAGAA
55800 AGAAAAGACA-AAAAGAAAAAAAAAATC
1 AGAAAAGA-AGAAAAGAAAAAAAAAATC
* * *
55827 AGAATAGAAGAAAAGAAAAAGAAATTC
1 AGAAAAGAAGAAAAGAAAAAAAAAATC
55854 A-AAAAGAA
1 AGAAAAGAA
55862 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAAAAAAATC
Done.