Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001779.1 Hibiscus syriacus cultivar Beakdansim tig00003596_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: 66287
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4954 original size:26 final size:26
Alignment explanation
Indices: 4920--4975 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
4910 TCTATTCTAA
*
4920 AGGTCTCATAATTAGTAACATATACT
1 AGGTATCATAATTAGTAACATATACT
4946 AGGTATCATAATTAGTAACATATACT
1 AGGTATCATAATTAGTAACATATACT
4972 AGGT
1 AGGT
4976 CTCTAACCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (26 bp):
AGGTATCATAATTAGTAACATATACT
Found at i:11107 original size:23 final size:22
Alignment explanation
Indices: 11067--11112 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
11057 AACATCAAAT
**
11067 ACAAAAAATAATGTTAATATTA
1 ACAAAAAATAATAATAATATTA
*
11089 ACAAAATAATAATAATAATTTTA
1 ACAAAA-AATAATAATAATATTA
11112 A
1 A
11113 AATATTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ACAAAAAATAATAATAATATTA
Found at i:11221 original size:24 final size:24
Alignment explanation
Indices: 11149--11226 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 24
11139 ATTTATGTCA
** *
11149 ATATTATTATTAAAATATTATATATA
1 ATATT-TTATTAAAATAAAAT-TATT
* *
11175 AAATTTTATAAAATATTAAAATTATT
1 ATATTTTATTAAA-A-TAAAATTATT
11201 ATATTTTATTAAAATAAAATTATT
1 ATATTTTATTAAAATAAAATTATT
11225 AT
1 AT
11227 TATACTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
24 12 0.28
25 8 0.19
26 19 0.44
27 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTTATTAAAATAAAATTATT
Found at i:11488 original size:23 final size:21
Alignment explanation
Indices: 11420--11489 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 21
11410 TTTTTAAAAT
*
11420 AAAAATATAATATTATATATTGT
1 AAAAATATAATATTA-ATATT-A
* *
11443 AATAATATAAT-TATAATAATA
1 AAAAATATAATAT-TAATATTA
11464 AAAAATATAATATTACATTATTA
1 AAAAATATAATATTA-A-TATTA
11487 AAA
1 AAA
11490 TTATTAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 12 0.32
22 7 0.18
23 19 0.50
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
AAAAATATAATATTAATATTA
Found at i:11551 original size:13 final size:13
Alignment explanation
Indices: 11524--11573 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
11514 TGAATATTTT
11524 TATTAAAAT--TA
1 TATTAAAATAATA
11535 TATTAAAATAATA
1 TATTAAAATAATA
*
11548 TATTAAATTAA-A
1 TATTAAAATAATA
11560 TATATAAAATAATA
1 TAT-TAAAATAATA
11574 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 9 0.27
12 4 0.12
13 19 0.58
14 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTAAAATAATA
Found at i:11559 original size:29 final size:26
Alignment explanation
Indices: 11525--11584 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
11515 GAATATTTTT
11525 ATTAAAATTATATTAAAATAATATATTAA
1 ATTAAAATTATA-TAAAATAATA-A-TAA
11554 ATT-AAA-TATATAAAATAATAATAA
1 ATTAAAATTATATAAAATAATAATAA
11578 A-TAAAAT
1 ATTAAAAT
11585 GTTTGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 1 0.03
24 7 0.24
25 1 0.03
26 10 0.34
27 4 0.14
28 3 0.10
29 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTAAAATTATATAAAATAATAATAA
Found at i:14487 original size:24 final size:24
Alignment explanation
Indices: 14436--14488 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
14426 CATAATTCAA
* *
14436 GTCAAGTAGCAGATCAGAATCCAT
1 GTCAAGTAGCAGATCAAAATCCAG
* * *
14460 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTAGCAGATCAAAATCCAG
14484 GTCAA
1 GTCAA
14489 AAATCAGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTAGCAGATCAAAATCCAG
Found at i:15238 original size:30 final size:29
Alignment explanation
Indices: 15204--15380 Score: 148
Period size: 29 Copynumber: 6.2 Consensus size: 29
15194 ACACAATTAT
*
15204 CACCCTTTTAAGAAATATTTACGAAAATAA
1 CACCCTTTTAA-AAATAATTACGAAAATAA
* * *
15234 CACCCTTTTAAAAATAATTATGAATATAT
1 CACCCTTTTAAAAATAATTACGAAAATAA
*
15263 CACCATTTTAAAAATAATTACGAAAATAA
1 CACCCTTTTAAAAATAATTACGAAAATAA
*** * *
15292 CAAATTTTTTTAAAAA-ATTTACGAAAATAG
1 C--ACCCTTTTAAAAATAATTACGAAAATAA
* *
15322 CA--CTCTT-AAAA-AATTACAAAAATAA
1 CACCCTTTTAAAAATAATTACGAAAATAA
* * * *
15347 CACCATTTTCAAAATAATTATGAAAATAT
1 CACCCTTTTAAAAATAATTACGAAAATAA
15376 CACCC
1 CACCC
15381 GATCAACGTT
Statistics
Matches: 117, Mismatches: 24, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
25 17 0.15
26 3 0.03
27 3 0.03
28 5 0.04
29 55 0.47
30 24 0.21
31 10 0.09
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (29 bp):
CACCCTTTTAAAAATAATTACGAAAATAA
Found at i:21730 original size:24 final size:24
Alignment explanation
Indices: 21621--21724 Score: 145
Period size: 24 Copynumber: 4.3 Consensus size: 24
21611 AAACATAATT
* * * *
21621 CAGGTCAAGTAGCAGATCAGAATC
1 CAGGTCAAGTATCATATAAAAATC
* *
21645 CATGTCATGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
21669 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
*
21693 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATAAAAATC
21717 CAGGTCAA
1 CAGGTCAA
21725 AAATCAGATA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAAAATC
Found at i:21736 original size:48 final size:48
Alignment explanation
Indices: 21641--21736 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
21631 AGCAGATCAG
* * ** *
21641 AATCCATGTCATGTATCATATAAAAATCCAGGTCAAGTATCATATAAA
1 AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
*
21689 AATCCAGGTCAAGTATCATATCAAAATCCAGGTCAAAAATCAGATAAA
1 AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
21737 CTATTCATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (48 bp):
AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
Found at i:22397 original size:29 final size:29
Alignment explanation
Indices: 22332--22510 Score: 145
Period size: 29 Copynumber: 6.3 Consensus size: 29
22322 TTTACACAAT
*
22332 TATCACCCTTTTAAAAAATATTTACGAAAA
1 TATCACCCTTTT-AAAAATAATTACGAAAA
* * *
22362 TAACACCCTTTTAAAAATAATTATGAATA
1 TATCACCCTTTTAAAAATAATTACGAAAA
*
22391 TATCACCATTTTAAAAATAATTACGAAAA
1 TATCACCCTTTTAAAAATAATTACGAAAA
* *** *
22420 TAACATTTTTTTTAAAAAAAATTACGAAAA
1 TATCA-CCCTTTTAAAAATAATTACGAAAA
* * * *
22450 TA-GA-ACTTTTTAAAA-AATTGC-AAAA
1 TATCACCCTTTTAAAAATAATTACGAAAA
* *
22475 -AT-AGCCATTTTCAAAATAATTACGAAAA
1 TATCA-CCCTTTTAAAAATAATTACGAAAA
22503 TATCACCC
1 TATCACCC
22511 GATCAACGGG
Statistics
Matches: 118, Mismatches: 23, Indels: 17
0.75 0.15 0.11
Matches are distributed among these distances:
24 2 0.02
25 4 0.03
26 13 0.11
27 13 0.11
28 4 0.03
29 48 0.41
30 34 0.29
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (29 bp):
TATCACCCTTTTAAAAATAATTACGAAAA
Found at i:22433 original size:59 final size:59
Alignment explanation
Indices: 22332--22443 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
22322 TTTACACAAT
* * *
22332 TATCACCCTTTTAAAAAATATTTACGAAAATAACACCCTTTTAAAAATAATTATGAATA
1 TATCACCATTTTAAAAAATAATTACGAAAATAACACCCTTTTAAAAAAAATTATGAATA
***
22391 TATCACCATTTT-AAAAATAATTACGAAAATAACATTTTTTTTAAAAAAAATTA
1 TATCACCATTTTAAAAAATAATTACGAAAATAACA-CCCTTTTAAAAAAAATTA
22444 CGAAAATAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 21 0.46
59 25 0.54
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (59 bp):
TATCACCATTTTAAAAAATAATTACGAAAATAACACCCTTTTAAAAAAAATTATGAATA
Found at i:22466 original size:59 final size:59
Alignment explanation
Indices: 22340--22467 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 59
22330 ATTATCACCC
* * * * *
22340 TTTTAAAAAATATTTACGAAAATAACACCCTTTTAAAAATAATTATGAATATATCACCA
1 TTTTAAAAAATAATTACGAAAATAACACCCTTTTAAAAAAAATTACGAAAATATCAACA
*** * *
22399 TTTT-AAAAATAATTACGAAAATAACATTTTTTTTAAAAAAAATTACGAAAATA-GAACT
1 TTTTAAAAAATAATTACGAAAATAACA-CCCTTTTAAAAAAAATTACGAAAATATCAACA
22457 TTTTAAAAAAT
1 TTTTAAAAAAT
22468 TGCAAAAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 27 0.47
59 30 0.53
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTTAAAAAATAATTACGAAAATAACACCCTTTTAAAAAAAATTACGAAAATATCAACA
Found at i:26238 original size:8 final size:8
Alignment explanation
Indices: 26225--26257 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
26215 AAATGTATAT
26225 ATATATGA
1 ATATATGA
26233 ATATATGA
1 ATATATGA
26241 ATATATGTA
1 ATATATG-A
26250 ATATATGA
1 ATATATGA
26258 TATGAGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (8 bp):
ATATATGA
Found at i:26260 original size:16 final size:15
Alignment explanation
Indices: 26220--26260 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
26210 AGATAAAATG
26220 TATAT-ATATATGAA
1 TATATGATATATGAA
26234 TATATGAATATATGTAA
1 TATATG-ATATATG-AA
26251 TATATGATAT
1 TATATGATAT
26261 GAGTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (15 bp):
TATATGATATATGAA
Found at i:31160 original size:21 final size:21
Alignment explanation
Indices: 31134--31173 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31124 AAAACTTTTG
*
31134 AAAAGTTTCGAAACTCTTAAT
1 AAAAGTTTCCAAACTCTTAAT
31155 AAAAGTTTCCAAACTCTTA
1 AAAAGTTTCCAAACTCTTA
31174 CAATGTTTTC
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:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAAGTTTCCAAACTCTTAAT
Found at i:31969 original size:19 final size:20
Alignment explanation
Indices: 31942--31994 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
31932 ATACATTGGG
*
31942 CTATAAATATGAAAATGA-T
1 CTATGAATATGAAAATGAGT
*
31961 CTATGAATATAAAAATGAGT
1 CTATGAATATGAAAATGAGT
*
31981 -TATGAATCTGAAAA
1 CTATGAATATGAAAA
31995 GAAAGAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (20 bp):
CTATGAATATGAAAATGAGT
Found at i:33648 original size:2 final size:2
Alignment explanation
Indices: 33641--33678 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
33631 GAAGTGTAAG
33641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33679 CCATCTTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41509 original size:21 final size:20
Alignment explanation
Indices: 41476--41514 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41466 TATCAAGATC
*
41476 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
41497 TTTGTCGATGCCATAAAT
1 TTTGTCGAAGCCATAAAT
41515 TCATGTAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:59771 original size:32 final size:32
Alignment explanation
Indices: 59735--59797 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
59725 AATGATTGTA
* *
59735 TCTGTTGCGCATTGTCTAAATGCAACACTAAC
1 TCTGTTACGCATTATCTAAATGCAACACTAAC
*
59767 TCTGTTATGCATTATCTAAATGCAACACTAA
1 TCTGTTACGCATTATCTAAATGCAACACTAA
59798 TACTACGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (32 bp):
TCTGTTACGCATTATCTAAATGCAACACTAAC
Found at i:62150 original size:3 final size:3
Alignment explanation
Indices: 62144--62280 Score: 256
Period size: 3 Copynumber: 45.0 Consensus size: 3
62134 CAACTCCTCC
62144 TCT TCTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
62190 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
62238 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
62281 CCTCCTCTTA
Statistics
Matches: 132, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
3 126 0.95
4 6 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:64451 original size:21 final size:21
Alignment explanation
Indices: 64425--64466 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64415 GAGATTGATA
64425 CTTTTCATCGAGGGATCGATC
1 CTTTTCATCGAGGGATCGATC
*
64446 CTTTTCATTGAGGGATCGATC
1 CTTTTCATCGAGGGATCGATC
64467 ATTTGGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
CTTTTCATCGAGGGATCGATC
Found at i:64600 original size:11 final size:11
Alignment explanation
Indices: 64578--64607 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
64568 TGATTTAATT
64578 ATCATCATCATC
1 ATCAT-ATCATC
64590 ATCATATCATC
1 ATCATATCATC
64601 ATCATAT
1 ATCATAT
64608 TATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (11 bp):
ATCATATCATC
Found at i:65738 original size:106 final size:106
Alignment explanation
Indices: 65550--65751 Score: 263
Period size: 106 Copynumber: 1.9 Consensus size: 106
65540 AAACTCACTT
*
65550 TTTAGTCCCCTAAGTTAGTCGTGCTTTTGCATGTTAGTCATCTGTGAGGACCAAAGTTGTTATTT
1 TTTAGTCCCCTAAGTTAGTCGTGCTTTTGCATGTTAGTCAACTGTGAGGACCAAAGTTGTTATTT
*
65615 ACCCTTTTTTTTGCATG-TATATATTTTTTGTGATATTTTTA
66 A-CCTTTTTATTGCATGTTATATATTTTTTGTGATATTTTTA
*
65656 TTTAGTCCCC-ATAGTTTAG-CGTGTTTTTGCATGTTAGTCAACT-TGTATGGACCAAAGTTGTT
1 TTTAGTCCCCTA-AG-TTAGTCGTGCTTTTGCATGTTAGTCAACTGTG-A-GGACCAAAGTTGTT
*
65718 ATTTA-CTTGTTTCATT-CATGTTATGTATTTTTTG
62 ATTTACCTT-TTT-ATTGCATGTTATATATTTTTTG
65752 GAATATTGTT
Statistics
Matches: 85, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
105 6 0.07
106 42 0.49
107 37 0.44
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (106 bp):
TTTAGTCCCCTAAGTTAGTCGTGCTTTTGCATGTTAGTCAACTGTGAGGACCAAAGTTGTTATTT
ACCTTTTTATTGCATGTTATATATTTTTTGTGATATTTTTA
Done.