Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003945.1 Hibiscus syriacus cultivar Beakdansim tig00008527_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: 58402
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4494 original size:16 final size:16
Alignment explanation
Indices: 4473--4504 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4463 GTTTATCAAC
4473 GGTTGCATAGTACTAA
1 GGTTGCATAGTACTAA
4489 GGTTGCATAGTACTAA
1 GGTTGCATAGTACTAA
4505 TTATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
GGTTGCATAGTACTAA
Found at i:8620 original size:51 final size:51
Alignment explanation
Indices: 8544--8644 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
8534 TAAGGAAAGG
*
8544 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACTA
*
8595 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACT
8645 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTGAAATTCCTTGTAACTA
Found at i:10424 original size:14 final size:14
Alignment explanation
Indices: 10405--10432 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10395 CCTGATACCA
10405 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
10419 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
10433 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:17489 original size:60 final size:60
Alignment explanation
Indices: 17352--17490 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
17342 TAAATGTTCT
* * * *
17352 AATTTCATCCCTAAAATATCACTATCATTTTAAATTAGTCCTAAAACTATTGAACATTTC
1 AATTTCATCCCTAAACTATCACTATCATTTCAAATTAGTCCCAAAACTATTGAACATTCC
* * * * * * *
17412 AATTTCATCCCTAAACTATGATTTTCATTTCAAATTGGTACCCAAAATTTTTGAATATTCC
1 AATTTCATCCCTAAACTATCACTATCATTTCAAATTAGT-CCCAAAACTATTGAACATTCC
17473 AATTTCATCCC-AAACTAT
1 AATTTCATCCCTAAACTAT
17491 ACATATATAC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 40 0.60
61 27 0.40
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (60 bp):
AATTTCATCCCTAAACTATCACTATCATTTCAAATTAGTCCCAAAACTATTGAACATTCC
Found at i:17745 original size:29 final size:29
Alignment explanation
Indices: 17668--17748 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
17658 AATATAGTCA
* *
17668 TAGTATAGAGATGAAATTAGAATGTTCAAG
1 TAGTTTAGAGATTAAATTAGAATGTTC-AG
* *
17698 -AGTTTA-AGGACTAATTTAGAATGATTC-G
1 TAGTTTAGA-GATTAAATTAGAATG-TTCAG
17726 TAGTTTAGAGATTAAATTAGAAT
1 TAGTTTAGAGATTAAATTAGAAT
17749 ATTAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.05
29 35 0.85
30 4 0.10
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.35
Consensus pattern (29 bp):
TAGTTTAGAGATTAAATTAGAATGTTCAG
Found at i:19547 original size:17 final size:17
Alignment explanation
Indices: 19525--19557 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19515 TTTATAAAAA
*
19525 AAAAATATTTTATTAAG
1 AAAAATATGTTATTAAG
19542 AAAAATATGTTATTAA
1 AAAAATATGTTATTAA
19558 ACTCATACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAAATATGTTATTAAG
Found at i:35603 original size:4 final size:4
Alignment explanation
Indices: 35594--35622 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
35584 AGACAAGGTG
35594 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
35623 TTGACATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:36154 original size:24 final size:23
Alignment explanation
Indices: 36122--36168 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
36112 TCATGACCTA
*
36122 TAAAAAAACTCAAGATAAAATAAT
1 TAAAAAAACT-AAGAAAAAATAAT
* *
36146 TAAATAAACTAATAAAAAATAAT
1 TAAAAAAACTAAGAAAAAATAAT
36169 CTATTGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (23 bp):
TAAAAAAACTAAGAAAAAATAAT
Found at i:36964 original size:18 final size:18
Alignment explanation
Indices: 36938--36973 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36928 GAATTTTGGA
36938 TGGTCTCACTCATGTGGC
1 TGGTCTCACTCATGTGGC
*
36956 TGGTTTCACTCATGTGGC
1 TGGTCTCACTCATGTGGC
36974 ATTATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.25, G:0.28, T:0.36
Consensus pattern (18 bp):
TGGTCTCACTCATGTGGC
Found at i:41030 original size:24 final size:24
Alignment explanation
Indices: 40998--41048 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
40988 TCGACAATAT
*
40998 AAAATATATTAACATAAAATATAA
1 AAAAAATATTAACATAAAATATAA
*
41022 AAAAAATATTAACATAAATTATAA
1 AAAAAATATTAACATAAAATATAA
41046 AAA
1 AAA
41049 TAAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAAATATTAACATAAAATATAA
Found at i:43165 original size:195 final size:198
Alignment explanation
Indices: 42758--43443 Score: 499
Period size: 195 Copynumber: 3.5 Consensus size: 198
42748 GACTAGTCAC
* * * * * * * *
42758 GTTTCTCATATCCAATTCATCCCTCGCAAAATTCAAGGGTTCTGGAGATGAGGAAATGGAGTTCA
1 GTTTCTCATATCCAGTTCATCCCTCACAACATTTATGTGTTCTGGAGATGAAGAAATGCAGTTC-
* * * ** * **** * **
42823 CAATATCCATTTGTTGAATACCGGAGGGAACGGAGTTCCTGTTGTCCACTTCTTTGACACCAGAA
65 CAATATCCATTTCTTTAACACAAGAGGGAACGGAGTTCATAACATCCAATTCTTCAACACCAGAA
* * * * * * * * * ** * *
42888 TAAGCCGAAACATTTTG-TG---TTGAAGCTTCAGAGAAACTTGATATAACAGCCACTGGTCTAG
130 TAATCCAAAACATTTGGCTGAACTTAAAACTCCAGAGCAACTTGAAACAATGGCCACAGGACTAG
42949 TCAA-
195 -CAAT
* * * * *
42953 ATTTCTCATACCCAGTTCACCCCTCACAACATTTATGGGTTCTGGAGATGAAGAAATGGAGTTCA
1 GTTTCTCATATCCAGTTCATCCCTCACAACATTTATGTGTTCTGGAGATGAAGAAATGCAGTTC-
** * *
43018 CAATATCCATTTCTTTAACACAAGAGGGGGCGGTGTTCATAACATCC-ATT-TT-GACACCAGAA
65 CAATATCCATTTCTTTAACACAAGAGGGAACGGAGTTCATAACATCCAATTCTTCAACACCAGAA
* * * * ** * *
43080 TAATCCAAGACATTTGG-TGAACTTAAAACTCCAGGGGAATTTGATGCAATGGTCACAGGACTGG
130 TAATCCAAAACATTTGGCTGAACTTAAAACTCCAGAGCAACTTGAAACAATGGCCACAGGACTAG
**
43144 CCGT
195 CAAT
* * * ** * ***
43148 GTTTCTCTTATCCAGTTCATCCGTCGCAACATTTACATGTTTTGGAGATGAAGAAACATAGTTCC
1 GTTTCTCATATCCAGTTCATCCCTCACAACATTTATGTGTTCTGGAGATGAAGAAATGCAGTTCC
* * * * * * *
43213 TATCATCTATTTCTTTAACACCAGAGTGAATGGAGTTCCTAACATCCAATTCTTCAACACCGGAA
66 AAT-ATCCATTTCTTTAACACAAGAGGGAACGGAGTTCATAACATCCAATTCTTCAACACCAGAA
* * * * *
43278 TAATCCAAAACATTTGGCCTTGAGCTTAAAGCTTCAGAGCAACTTGAAATAATGGCCACTGGACT
130 TAATCCAAAACATTTGG-C-TGAACTTAAAACTCCAGAGCAACTTGAAACAATGGCCACAGGACT
*
43343 AGTAAT
193 AGCAAT
* * * * *
43349 GGTTCTCATATCCAGTTCATCCCTCACAACATTCATGTGTTCTGGAGACGAGGAAATGCAGTGCC
1 GTTTCTCATATCCAGTTCATCCCTCACAACATTTATGTGTTCTGGAGATGAAGAAATGCAGTTCC
* * *
43414 TAGTATCCATTTCTTTAACACCAGAAGGAA
66 -AATATCCATTTCTTTAACACAAGAGGGAA
43444 TAGAGTTCCT
Statistics
Matches: 377, Mismatches: 102, Indels: 18
0.76 0.21 0.04
Matches are distributed among these distances:
192 25 0.07
193 2 0.01
194 6 0.02
195 204 0.54
196 3 0.01
197 2 0.01
198 24 0.06
201 110 0.29
202 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (198 bp):
GTTTCTCATATCCAGTTCATCCCTCACAACATTTATGTGTTCTGGAGATGAAGAAATGCAGTTCC
AATATCCATTTCTTTAACACAAGAGGGAACGGAGTTCATAACATCCAATTCTTCAACACCAGAAT
AATCCAAAACATTTGGCTGAACTTAAAACTCCAGAGCAACTTGAAACAATGGCCACAGGACTAGC
AAT
Found at i:43430 original size:201 final size:199
Alignment explanation
Indices: 42504--43582 Score: 799
Period size: 201 Copynumber: 5.4 Consensus size: 199
42494 AAAGTCTGAT
* * * * *
42504 GTTGAACTTAAAGCTTCGGAGAAGCTTGTTGAAATGGTCACTGGACTAGTCATGGTTCTCATA-C
1 GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATATC
* * * * ** * * *
42568 TGAATTCATCTCTCACAACA-TCAATGGGTTTTAGAGACCAGGAAATGGTGTTCCTAGTATTCAT
66 -CAATTCATCCCTCACAACATTC-ATGGGTTCTGGAGATGAGGAAATGGAGTTCCTAATATCCAT
* * * * * * * * *
42632 TTGTTTAATAAC-GAAGGGCATTGAGTGCCTAACATCCATTTCTTTC-AGACCAGAATAATCTGA
129 TTCTTTAACACCAG-AGGGAATGGAGTTCCTAACATCCAATTC-TTCGACACCAGAATAATCCGA
*
42695 AACATCTGG
192 AACAT-TTG
* * * ** * * * *
42704 CGTTGAACTTGAAGCTTCGGAGCAGTTTGATGCAAGGGTCGCTGGACTAGTCACGTTTCTCATAT
1 -GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATAT
* * *
42769 CCAATTCATCCCTCGCAAAATTCAAGGGTTCTGGAGATGAGGAAATGGAGTTCAC-AATATCCAT
65 CCAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAATGGAGTTC-CTAATATCCAT
* * * * * **** * * *
42833 TTGTTGAATACCGGAGGGAACGGAGTTCCTGTTGTCCACTTCTTTGACACCAGAATAAGCCGAAA
129 TTCTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAAA
*
42898 CATTTT
194 CATTTG
* * ** * * ** *
42904 G-TG---TTGAAGCTTCAGAGAAACTTGATATAACAGCCACTGGTCTAGTCAAATTTCTCATACC
1 GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATATC
* * * *
42965 CAGTTCACCCCTCACAACATTTATGGGTTCTGGAGATGAAGAAATGGAGTTCAC-AATATCCATT
66 CAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAATGGAGTTC-CTAATATCCATT
* *** * *
43029 TCTTTAACACAAGAGGGGGCGGTGTTCATAACATCC-ATT-TT-GACACCAGAATAATCC-AAGA
130 TCTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAA-A
43090 CATTTG
194 CATTTG
* * * * * * * * * * *
43096 G-TGAACTTAAAACTCCAGGGGAATTTGATGCAATGGTCACAGGACTGGCCGTGTTTCTCTTATC
1 GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATATC
* * * * * *** *
43160 CAGTTCATCCGTCGCAACATTTACAT--GTTTTGGAGATGAAGAAACATAGTTCCT-ATCATCTA
66 CAATTCATCCCTCACAACA-TT-CATGGGTTCTGGAGATGAGGAAATGGAGTTCCTAAT-ATCCA
* * * *
43222 TTTCTTTAACACCAGAGTGAATGGAGTTCCTAACATCCAATTCTTCAACACCGGAATAATCCAAA
128 TTTCTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAA
43287 ACATTTG
193 ACATTTG
* * ** * * *
43294 GCCTTGAGCTTAAAGCTTCAGAGCAACTTGAAATAATGGCCACTGGACTAGTAATGGTTCTCATA
1 G--TTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATA
* * * * * *
43359 TCCAGTTCATCCCTCACAACATTCATGTGTTCTGGAGACGAGGAAATGCAGTGCCTAGTATCCAT
64 TCCAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAATGGAGTTCCTAATATCCAT
* * * * * * * * *
43424 TTCTTTAACACCAGAAGGAATAGAGTTCCTACCATCTACTCCTTTGTCACCTGAATAATCCGAAA
129 TTCTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAAA
43489 CATTTGG
194 CATTT-G
** ** *
43496 TGTTGAACTTATTGCTTCAGAGAAACTTGATGTAGGGGTCACTGGACTAGTCATGTTTCTTATAT
1 -GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATAT
* *
43561 CCAATTCACCCCTCGCAACATT
65 CCAATTCATCCCTCACAACATT
43583 TATGAGTTTC
Statistics
Matches: 685, Mismatches: 168, Indels: 50
0.76 0.19 0.06
Matches are distributed among these distances:
191 2 0.00
192 24 0.04
193 2 0.00
194 5 0.01
195 235 0.34
196 5 0.01
197 4 0.01
198 24 0.04
199 6 0.01
200 5 0.01
201 365 0.53
202 7 0.01
203 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (199 bp):
GTTGAACTTAAAGCTTCAGAGAAACTTGATGTAATGGTCACTGGACTAGTCATGTTTCTCATATC
CAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAATGGAGTTCCTAATATCCATTT
CTTTAACACCAGAGGGAATGGAGTTCCTAACATCCAATTCTTCGACACCAGAATAATCCGAAACA
TTTG
Found at i:44260 original size:165 final size:166
Alignment explanation
Indices: 44071--44403 Score: 560
Period size: 168 Copynumber: 2.0 Consensus size: 166
44061 TTGCTAGGGA
*
44071 GGGAATCTTCCCAAGCAGTTGGTCCACTTACAGGGGCCTTTTCCCCAATACTTGACCAGCTT-GG
1 GGGAATCTTCCCAAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTGACCAGCTTAGG
*
44135 GGCATCATCTCTAATACTTAACCTGCTTATAGGGGCATCATTACAGCTACTTGGCCTGCTTATTG
66 GGCATCATCTCTAATACTTAACCTGCTTATAGGAGCATCATTACAGCTACTTGGCCTGCTTATTG
*
44200 GAGAATCATCCCAAGTGCTTGAGCTGCTCATGGAGG
131 GAGAATCATCCCAAGTGCTTGAGCTGCTCATAGAGG
* * * *
44236 GGGAATCTTCCCCAGCAGTTGGTCCACTTATATGGGCATTTTCCCTAATACTTGACCAGCTTGCA
1 GGGAATCTTCCCAAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTGACCAGCTT--A
*
44301 GGGGCATCATCTCTAATACTTAACCTGCTTATAGGAGCATCATTACTGCTACTTGGCCTGCTTAT
64 GGGGCATCATCTCTAATACTTAACCTGCTTATAGGAGCATCATTACAGCTACTTGGCCTGCTTAT
*
44366 TGGAGCATCATCCCAAGTGCTTGAGCTGCTCATAGAGG
129 TGGAGAATCATCCCAAGTGCTTGAGCTGCTCATAGAGG
44404 CATCACCCCT
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
165 57 0.37
168 99 0.63
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (166 bp):
GGGAATCTTCCCAAGCAGTTGGTCCACTTACAGGGGCATTTTCCCCAATACTTGACCAGCTTAGG
GGCATCATCTCTAATACTTAACCTGCTTATAGGAGCATCATTACAGCTACTTGGCCTGCTTATTG
GAGAATCATCCCAAGTGCTTGAGCTGCTCATAGAGG
Found at i:44341 original size:33 final size:34
Alignment explanation
Indices: 44280--44377 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 34
44270 GGCATTTTCC
* ** *
44280 CTAATACTTGACCAGCTTGCAGGGGCATCATCT-
1 CTAATACTTGACCTGCTTATAGGAGCATCATCTA
*
44313 CTAATACTTAACCTGCTTATAGGAGCATCAT-TA
1 CTAATACTTGACCTGCTTATAGGAGCATCATCTA
** * *
44346 CTGCTACTTGGCCTGCTTATTGGAGCATCATC
1 CTAATACTTGACCTGCTTATAGGAGCATCATC
44378 CCAAGTGCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (34 bp):
CTAATACTTGACCTGCTTATAGGAGCATCATCTA
Done.