Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006829.1 Hibiscus syriacus cultivar Beakdansim tig00017364_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: 52356
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Found at i:390 original size:3 final size:3
Alignment explanation
Indices: 382--430 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
372 TTTGTAGATG
382 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
430 T
1 T
431 GAAGGTCGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1297 original size:15 final size:14
Alignment explanation
Indices: 1277--1325 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 14
1267 GATATTTTTA
1277 TTTTTTTT-CTCTTCT
1 TTTTTTTTGC-CTT-T
1292 TTTTTTTTGCC--T
1 TTTTTTTTGCCTTT
1304 TTTTTTTTGCCTTT
1 TTTTTTTTGCCTTT
1318 TTTTTTTT
1 TTTTTTTT
1326 TTAAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.39
14 9 0.29
15 9 0.29
16 1 0.03
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (14 bp):
TTTTTTTTGCCTTT
Found at i:1324 original size:13 final size:12
Alignment explanation
Indices: 1290--1323 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1280 TTTTTCTCTT
1290 CTTTTTTTTTGC
1 CTTTTTTTTTGC
1302 CTTTTTTTTTGC
1 CTTTTTTTTTGC
1314 CTTTTTTTTT
1 CTTTTTTTTT
1324 TTTTAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
CTTTTTTTTTGC
Found at i:3315 original size:24 final size:24
Alignment explanation
Indices: 3260--3322 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3250 CATTCACTCG
* * *
3260 TTTGTGTTCGTGTACGTTCGTTTA
1 TTTGTGTTCGTTTATGTTCGTTCA
** *
3284 CATCTGTTCGTTTATGTTCGTTCA
1 TTTGTGTTCGTTTATGTTCGTTCA
3308 TTTGTGTTCGTTTAT
1 TTTGTGTTCGTTTAT
3323 CATTTAAATG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.56
Consensus pattern (24 bp):
TTTGTGTTCGTTTATGTTCGTTCA
Found at i:3559 original size:2 final size:2
Alignment explanation
Indices: 3552--3600 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3542 ACCTATTACA
3552 AT AT 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 AT AT
3594 AT AT AT A
1 AT AT AT A
3601 AAACTTACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3805 original size:29 final size:29
Alignment explanation
Indices: 3725--3794 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
3715 TTAAATATTT
*
3725 TTAATATGTATTTAATTATTAATTAATTA
1 TTAACATGTATTTAATTATTAATTAATTA
3754 TTAACATGTATTTAATTATTAATTAATTA
1 TTAACATGTATTTAATTATTAATTAATTA
3783 TTAACATGTATT
1 TTAACATGTATT
3795 AGTTAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (29 bp):
TTAACATGTATTTAATTATTAATTAATTA
Found at i:13522 original size:18 final size:18
Alignment explanation
Indices: 13488--13560 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
13478 ACTGAATATT
* *
13488 TGTCCCGAATGATCACTA
1 TGTCCCGAAGGACCACTA
*
13506 TATCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * **
13525 TTGTTCTGAATAACCACTA
1 -TGTCCCGAAGGACCACTA
13544 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
13561 GATTATCCCT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
18 27 0.66
19 2 0.05
20 12 0.29
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:16612 original size:63 final size:64
Alignment explanation
Indices: 16558--16720 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
16548 CGGTGCACCA
*
16558 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
16621 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
16686 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
16721 CAATTAATTC
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 29 0.34
64 15 0.18
65 41 0.48
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:16702 original size:65 final size:63
Alignment explanation
Indices: 16562--16769 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
16552 GCACCAAGTG
* ** * *
16562 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTG-GTGCATCGATGCATGGCTTG-
1 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGG--AGA
16625 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTGAAAATATTCAGAGTGCATCGATGCATGGAG-A
* ** * * * * *
16690 TGCATCGGTGCATGGAATGCATTCGATGTTT-CAATTAATTCACTAATGCATCGATGCATGGTTG
1 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAAT-ATTCA-GAGTGCATCGATGCATGG-AG
16754 A
63 A
*
16755 TGCATCGGTGCATCA
1 TGCATCGATGCATCA
16770 CCTCAAATAA
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
63 31 0.25
64 20 0.16
65 71 0.58
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
Found at i:16709 original size:17 final size:19
Alignment explanation
Indices: 16671--16717 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
16661 ATATTCAGAG
16671 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
16690 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
16707 TGCATTCGATG
1 TGCA-TCGATG
16718 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:24185 original size:64 final size:64
Alignment explanation
Indices: 24132--24295 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
24122 CGGTGCACCA
*
24132 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
24196 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
24261 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
24296 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:24284 original size:17 final size:19
Alignment explanation
Indices: 24246--24292 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
24236 ATATTCAGAG
24246 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
24265 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
24282 TGCATTCGATG
1 TGCA-TCGATG
24293 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:24315 original size:65 final size:62
Alignment explanation
Indices: 24136--24342 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
24126 GCACCAAGTG
* *
24136 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
24200 -
62 A
* *
24200 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
24264 A
62 A
* * * * *
24265 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
24330 TGCATCGGTGCAT
1 TGCATCGATGCAT
24343 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:29081 original size:18 final size:20
Alignment explanation
Indices: 29033--29097 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
29023 CACTGAATAT
29033 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
29053 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
29072 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
*
29091 TTATCCC
1 TTGTCCC
29098 TCGAATCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 15 0.39
19 2 0.05
20 21 0.55
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:31073 original size:31 final size:31
Alignment explanation
Indices: 30789--31067 Score: 445
Period size: 31 Copynumber: 9.0 Consensus size: 31
30779 AGCTCATATA
*
30789 GTAATTTGTCCATATGTCCCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
30820 GTAATCTGTCCATATGTCCCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
30851 GTAATCTGTCCATATGTCCCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
* *
30882 GTAATCTGTTCATATGTCTCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
* *
30913 GTAATATGTCCATATGTCCCAAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
*
30944 GTAATCTATCCATATGTCCCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
30975 GTAATCTGTCCATATGTCCCGAAGAACATAG
1 GTAATCTGTCCATATGTCCCGAAGAACATAG
* *
31006 GTAAAT-TGTCCTTATGTCCCGAAAAACATAG
1 GT-AATCTGTCCATATGTCCCGAAGAACATAG
*
31037 GTAAACTGTCCATATGTCCCGAATGAA-ATAG
1 GTAATCTGTCCATATGTCCCGAA-GAACATAG
31068 ATAAACCTCA
Statistics
Matches: 229, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
30 2 0.01
31 222 0.97
32 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
GTAATCTGTCCATATGTCCCGAAGAACATAG
Found at i:33670 original size:46 final size:46
Alignment explanation
Indices: 33618--33706 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
33608 TTGCTTTAAT
* * * *
33618 TACCTAAACTATTTTTTTGTCAAACTAAATC-CTTAAACTATTATAG
1 TACCTAAACAATTTTTTGGTAAAAATAAATCTC-TAAACTATTATAG
*
33664 TACCTAAACAATTTTTTGGTAAAAATAAGTCTCTAAACTATTA
1 TACCTAAACAATTTTTTGGTAAAAATAAATCTCTAAACTATTA
33707 CTCTTTTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (46 bp):
TACCTAAACAATTTTTTGGTAAAAATAAATCTCTAAACTATTATAG
Found at i:36844 original size:12 final size:12
Alignment explanation
Indices: 36827--36851 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36817 AATAGCTTCC
36827 TTGATCTCTGCA
1 TTGATCTCTGCA
36839 TTGATCTCTGCA
1 TTGATCTCTGCA
36851 T
1 T
36852 CAGAGAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGATCTCTGCA
Found at i:45388 original size:21 final size:21
Alignment explanation
Indices: 45362--45412 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
45352 AAGCATAATG
* *
45362 TCATTCAAATCAACACAATTA
1 TCATTCAAATCAACAAAATCA
*
45383 TCATTCAAATTAACAAAATCA
1 TCATTCAAATCAACAAAATCA
45404 TCATTCAAA
1 TCATTCAAA
45413 ATAATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (21 bp):
TCATTCAAATCAACAAAATCA
Found at i:47130 original size:26 final size:26
Alignment explanation
Indices: 47099--47159 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
47089 CGAGCACCGT
*
47099 TGAGCATCACTAACGCTGAGAACTGA
1 TGAGCACCACTAACGCTGAGAACTGA
47125 TGAGCACCACTAACGCTGAGAACTGA
1 TGAGCACCACTAACGCTGAGAACTGA
47151 TGAGCACCA
1 TGAGCACCA
47160 TTAATATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (26 bp):
TGAGCACCACTAACGCTGAGAACTGA
Found at i:47438 original size:16 final size:16
Alignment explanation
Indices: 47417--47449 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47407 GATACTCATT
47417 GTTAATTATTCTTACC
1 GTTAATTATTCTTACC
47433 GTTAATTATTCTTACC
1 GTTAATTATTCTTACC
47449 G
1 G
47450 ATGCTCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (16 bp):
GTTAATTATTCTTACC
Found at i:48365 original size:2 final size:2
Alignment explanation
Indices: 48358--48447 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
48348 CACATTTCAA
48358 AT AT 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 AT AT
48400 AT AT AT AT AT AT AT AT -T 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 AT AT
48441 AT AT AT A
1 AT AT AT A
48448 ATTTAACTGT
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.