Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003255.1 Hibiscus syriacus cultivar Beakdansim tig00006841_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: 81782
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:12820 original size:262 final size:241
Alignment explanation
Indices: 12231--12834 Score: 756
Period size: 247 Copynumber: 2.4 Consensus size: 241
12221 ATTATTCATA
*
12231 TATTGAATAAAAATATTTTTTTTTATTTC---GGGTCGGGTTTCTAATTCATATATTCGGGTCGG
1 TATTGAATAAAAATATTTTTTATTATTTCGGTGGGTC-GGTTTCTAATTCATATATTCGGGTCGG
*
12293 GTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCGGGTTGAGT
65 GTCGAGTGAAACTTTATTTTGGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCGGGTTGA--
* *
12358 TCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATAATTTTACTTATATATTTAGGAATAA
128 TCAGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATAATTTTACTTATATATTTAGAAATAA
* *
12423 TTACAATAATACCCCTCTATATAATTTTTTTCAATTAAGTCATTGTTTT
193 TTACAATAATACCCCTATATATAATTTTTTTCAATTAAGTCACTGTTTT
12472 TATTGAATAAAAATATTTTTTTATTATTTCGGATTGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATA-TTTTTTATTATTTCGG--TGGGTCGG-TTTCTAATTCATATATTCGGGT
*
12537 CGGGTC-AGGTGAAACTTTATTTTGGTCGGGTCATGTCGGTTTTTTTTAAGTGTGATATTCGGGT
62 CGGGTCGA-GTGAAACTTTATTTTGGTCGGGTC--G--GG--TTTTTTAAGTGTAATATTCGGGT
*
12601 C-GG-T-A-CAGGTTTAGGGTGAAAAATACACAATCCGACCCGACCCAAATAATATATTTTTACC
120 CGGGTTGATCAGGTTTAGGGTGAAAAAT--AC---CCGACCCGA---AAAT-ATATAATTTTA-C
*
12662 TTATATATTTATAAATAATTACAATAATACCACTCTATATATATATATATTTTTCCAATTAAGTC
175 TTATATATTTAGAAATAATTACAATAATACC-C-CTATATATA-AT-T-TTTTT-CAATTAAGTC
12727 ACTGTTTT
234 ACTGTTTT
12735 TATTGAATAAAAATATTTTTTATTATTTCGGGTAGGGTCGAGTTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATATTTTTTATTATTTC-GGT-GGGTCG-GTTTCTAATTCATATATTCGGGTC
* *
12800 GGATCGAGTGAAACTTTATTTTGGTTGGGTCGGGT
63 GGGTCGAGTGAAACTTTATTTTGGTCGGGTCGGGT
12835 CTCGGATGGA
Statistics
Matches: 318, Mismatches: 11, Indels: 53
0.83 0.03 0.14
Matches are distributed among these distances:
241 15 0.05
242 13 0.04
246 2 0.01
247 75 0.24
249 3 0.01
250 1 0.00
251 3 0.01
252 11 0.03
253 23 0.07
255 4 0.01
256 11 0.03
257 30 0.09
258 3 0.01
259 8 0.03
260 3 0.01
261 2 0.01
262 75 0.24
263 36 0.11
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (241 bp):
TATTGAATAAAAATATTTTTTATTATTTCGGTGGGTCGGTTTCTAATTCATATATTCGGGTCGGG
TCGAGTGAAACTTTATTTTGGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCGGGTTGATCA
GGTTTAGGGTGAAAAATACCCGACCCGAAAATATATAATTTTACTTATATATTTAGAAATAATTA
CAATAATACCCCTATATATAATTTTTTTCAATTAAGTCACTGTTTT
Found at i:15990 original size:10 final size:10
Alignment explanation
Indices: 15975--16000 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15965 TTAGTGTATC
15975 AAAACTTATG
1 AAAACTTATG
15985 AAAACTTATG
1 AAAACTTATG
15995 AAAACT
1 AAAACT
16001 ACTGATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.27
Consensus pattern (10 bp):
AAAACTTATG
Found at i:19215 original size:36 final size:36
Alignment explanation
Indices: 19169--19239 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
19159 GTCATTGTTG
19169 ATAAACATTGAATTGTATTACCATTTCCTTTTATTT
1 ATAAACATTGAATTGTATTACCATTTCCTTTTATTT
*
19205 ATAAACATTGAATTGTATTACCATTTCTTTTTATT
1 ATAAACATTGAATTGTATTACCATTTCCTTTTATT
19240 CCTTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.51
Consensus pattern (36 bp):
ATAAACATTGAATTGTATTACCATTTCCTTTTATTT
Found at i:22748 original size:25 final size:23
Alignment explanation
Indices: 22714--22767 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
22704 AAATATAATA
22714 AATAATATTATTTATTATAAAAATT
1 AATAATATTATTT-TTA-AAAAATT
* *
22739 AATATTATTATTTTTAAAATATT
1 AATAATATTATTTTTAAAAAATT
22762 AA-AATA
1 AATAATA
22768 ATTTATTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 3 0.12
25 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAATATTATTTTTAAAAAATT
Found at i:22756 original size:22 final size:23
Alignment explanation
Indices: 22716--22774 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
22706 ATATAATAAA
22716 TAATATTATTTATTATAAAA-AT
1 TAATATTATTTATTATAAAATAT
*
22738 TAATATTA-TTATTTTTAAAATAT
1 TAATATTATTTA-TTATAAAATAT
* *
22761 TAAAATAATTTATT
1 TAATATTATTTATT
22775 CATTATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 15 0.48
23 10 0.32
24 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATATTATTTATTATAAAATAT
Found at i:22856 original size:19 final size:19
Alignment explanation
Indices: 22834--22898 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
22824 TAAGAATATT
22834 ATATTATATTAAAATAAAA
1 ATATTATATTAAAATAAAA
*
22853 ATATTATA--AATAATAGTAA
1 ATATTATATTAA-AATA-AAA
* * *
22872 TTATT-TATTAAAGTAAGA
1 ATATTATATTAAAATAAAA
22890 ATATTATAT
1 ATATTATAT
22899 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 2 0.06
18 11 0.31
19 20 0.57
20 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATATTATATTAAAATAAAA
Found at i:25320 original size:23 final size:22
Alignment explanation
Indices: 25294--25351 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 22
25284 TAAGCTACCA
25294 AAAGACAGAGAAAAGCGTGCCAC
1 AAAGACAGAGAAAA-CGTGCCAC
*
25317 AAAGACAGAGATAAACGTGCCAT
1 AAAGACAGAGA-AAACGTGCCAC
25340 AAAGACAGAGAA
1 AAAGACAGAGAA
25352 CATGTCACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 1 0.03
23 29 0.88
24 3 0.09
ACGTcount: A:0.52, C:0.17, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAGACAGAGAAAACGTGCCAC
Found at i:38375 original size:148 final size:150
Alignment explanation
Indices: 37946--38390 Score: 509
Period size: 153 Copynumber: 2.9 Consensus size: 150
37936 CTCATTCTCT
* * * * * *
37946 TAATACATTACACTATTTTTGTATACTTTTTT-AAAAATAATGGGATGCACATATTCTCTCATGG
1 TAAT-CATTAAACTAATTTT-TATATTTTTTTCTAAAATAATGGGATGTACATATTCT-T-AGGG
* * * * *
38010 GCTTAGTGCGTCCACCCTTGCTGTATGCATCAATCACAATTCTATAATAAACTTGCTAAATCTCC
62 GCTTAGTGCATCCACCCTTGTTGCATGCATCACTCACAATTCTATAGTAAACTTGCTAAATCTCC
* *
38075 CTATCAACAACCCCTCTCGGCCGC
127 CTACCAACAACCCCTCTCGACCGC
* * *
38099 TAATCATTAAACTAATTTTTATATGTTTTTTTCTAAAATAATGGAATGTAAATATTCTTTAGAGG
1 TAATCATTAAACTAATTTTTATA--TTTTTTTCTAAAATAATGGGATGTACATATTC-TTAGGGG
* * * * *
38164 CTCAGTGCATCCACCCTTGTTGCATGCATCACCCAGAGTTCTATAGTGAACTTGCTAAATCTCCC
63 CTTAGTGCATCCACCCTTGTTGCATGCATCACTCACAATTCTATAGTAAACTTGCTAAATCTCCC
*
38229 TACCAACAACCCCTCTCGACCGT
128 TACCAACAACCCCTCTCGACCGC
* * * *
38252 TAGTTATTAAACTGA-TTTTATA-TTTTTTCTAAAATAATGGGATGTGCATATTCTTAGGGGCTT
1 TAATCATTAAACTAATTTTTATATTTTTTTCTAAAATAATGGGATGTACATATTCTTAGGGGCTT
* * * * * *
38315 AGTGCATCCACCCTCGTTGCATACATCACTCACAATTCGATCGTAAACTTGTTAAATCTCCCAAC
66 AGTGCATCCACCCTTGTTGCATGCATCACTCACAATTCTATAGTAAACTTGCTAAATCTCCCTAC
*
38380 AAACAACCCCT
131 CAACAACCCCT
38391 TTCAGCCACT
Statistics
Matches: 247, Mismatches: 41, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
148 73 0.30
149 28 0.11
151 4 0.02
152 20 0.08
153 100 0.40
154 21 0.09
155 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (150 bp):
TAATCATTAAACTAATTTTTATATTTTTTTCTAAAATAATGGGATGTACATATTCTTAGGGGCTT
AGTGCATCCACCCTTGTTGCATGCATCACTCACAATTCTATAGTAAACTTGCTAAATCTCCCTAC
CAACAACCCCTCTCGACCGC
Found at i:48654 original size:21 final size:22
Alignment explanation
Indices: 48625--48667 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
48615 ATTTAATGGT
*
48625 CAAATTGAT-ATTTATCTAAAA
1 CAAAATGATAATTTATCTAAAA
*
48646 CAAAATGATAATTTATTTAAAA
1 CAAAATGATAATTTATCTAAAA
48668 TTTAAGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
CAAAATGATAATTTATCTAAAA
Found at i:53567 original size:17 final size:17
Alignment explanation
Indices: 53545--53579 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53535 GCAATTGATA
53545 TGAAAAAA-ATACTAAAT
1 TGAAAAAATATA-TAAAT
53562 TGAAAAAATATATAAAT
1 TGAAAAAATATATAAAT
53579 T
1 T
53580 AAGGTGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
TGAAAAAATATATAAAT
Found at i:55733 original size:61 final size:61
Alignment explanation
Indices: 55638--55760 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
55628 AAGAGTAAAC
* * * *
55638 TCTTTAATTTGTAATTAAAATTATTTGTATTGTTCTTTTATATATTTTTCATCGTATTTTT
1 TCTTTAATTTGTAATTAAAATGATTCGTATTGTTCTTTTATATACTTCTCATCGTATTTTT
* *
55699 TCTTTCATTTGTAATTAAAATGATTCGTATTGTTCTTTTATATACTTCTCATTGTATTTTT
1 TCTTTAATTTGTAATTAAAATGATTCGTATTGTTCTTTTATATACTTCTCATCGTATTTTT
55760 T
1 T
55761 TTCTTCTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (61 bp):
TCTTTAATTTGTAATTAAAATGATTCGTATTGTTCTTTTATATACTTCTCATCGTATTTTT
Found at i:60218 original size:14 final size:15
Alignment explanation
Indices: 60198--60240 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
60188 TTATGGTCAC
60198 ATTAAAATTATATAT
1 ATTAAAATTATATAT
60213 -TTAAAATCATATATAT
1 ATTAAAAT--TATATAT
60229 ATTAAAA-TATAT
1 ATTAAAATTATAT
60241 TGTTAGCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.48
16 7 0.28
17 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAAATTATATAT
Found at i:60227 original size:16 final size:16
Alignment explanation
Indices: 60198--60240 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
60188 TTATGGTCAC
60198 ATTAAAAT-TATATAT
1 ATTAAAATATATATAT
60213 -TTAAAATCATATATAT
1 ATTAAAAT-ATATATAT
60229 ATTAAAATATAT
1 ATTAAAATATAT
60241 TGTTAGCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.28
16 11 0.44
17 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAAATATATATAT
Found at i:61657 original size:17 final size:17
Alignment explanation
Indices: 61626--61659 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61616 TTAGTATAAA
**
61626 GTTTTTTTTTTTTTCTT
1 GTTTTTTTTCGTTTCTT
61643 GTTTTTTTTCGTTTCTT
1 GTTTTTTTTCGTTTCTT
61660 TAGAGTATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
GTTTTTTTTCGTTTCTT
Found at i:66816 original size:24 final size:24
Alignment explanation
Indices: 66751--66823 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
66741 CGTTCGGTAA
*
66751 TATGTTCGTTCATTTATATTAGTT
1 TATGTTCGTTCATTTATGTTAGTT
*
66775 TATGTTCATTCATTTATGTTCA-TT
1 TATGTTCGTTCATTTATGTT-AGTT
*
66799 TATGTTCGTTCGTTTATGTTTAGTT
1 TATGTTCGTTCATTTATG-TTAGTT
66824 CAATCTCTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 37 0.88
25 5 0.12
ACGTcount: A:0.18, C:0.10, G:0.14, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTTAGTT
Found at i:67044 original size:24 final size:24
Alignment explanation
Indices: 67012--67069 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
67002 TCATTTATTA
* * *
67012 TGTTCGTTTACTTTCGTTCGTTTG
1 TGTTTGTTTACGTTCATTCGTTTG
67036 TGTTTGTTTACGTTCATTCGTTTG
1 TGTTTGTTTACGTTCATTCGTTTG
67060 TGTTTGTTTA
1 TGTTTGTTTA
67070 TCATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.07, C:0.12, G:0.21, T:0.60
Consensus pattern (24 bp):
TGTTTGTTTACGTTCATTCGTTTG
Found at i:68554 original size:35 final size:34
Alignment explanation
Indices: 68477--68591 Score: 198
Period size: 35 Copynumber: 3.4 Consensus size: 34
68467 TTTGAAATTG
68477 TATTTATTTAATAGTTTAAGTTGATT-AAA-ATA
1 TATTTATTTAATAGTTTAAGTTGATTAAAAGATA
68509 TATTTATTTAATAGTTTAAGTTGATTAAAAGATAA
1 TATTTATTTAATAGTTTAAGTTGATTAAAAGAT-A
68544 TATTTATTTAATAGTTTAAGTTGATTAAAAGATTA
1 TATTTATTTAATAGTTTAAGTTGATTAAAAGA-TA
68579 TATTTATTTAATA
1 TATTTATTTAATA
68592 TTTTTTAATC
Statistics
Matches: 79, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
32 26 0.33
33 3 0.04
34 2 0.03
35 47 0.59
36 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.50
Consensus pattern (34 bp):
TATTTATTTAATAGTTTAAGTTGATTAAAAGATA
Found at i:68610 original size:67 final size:66
Alignment explanation
Indices: 68477--68613 Score: 179
Period size: 67 Copynumber: 2.0 Consensus size: 66
68467 TTTGAAATTG
* *
68477 TATTTATTTAATAGTTTAAGTTGATTAAAATATATTTATTTAATAGTTTAAGTTGATTAAAAGAT
1 TATTTATTTAATAGTTTAAGTTGATTAAAATATATTTATTTAATAGTTT-AGTTAATCAAAAGAT
68542 AA
65 AA
* **
68544 TATTTATTTAATAGTTTAAGTTGATTAAAAGATTATATTTATTTAATA-TTT-TTTAATCAATTG
1 TATTTATTTAATAGTTTAAGTTGATT-AAA-A-TATATTTATTTAATAGTTTAGTTAATCAAAAG
68607 ATAA
63 ATAA
68611 TAT
1 TAT
68614 GTATATATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
67 40 0.65
68 3 0.05
69 4 0.06
70 15 0.24
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (66 bp):
TATTTATTTAATAGTTTAAGTTGATTAAAATATATTTATTTAATAGTTTAGTTAATCAAAAGATA
A
Found at i:72058 original size:30 final size:31
Alignment explanation
Indices: 72014--72098 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
72004 TTAAGAGGAT
* * *
72014 GAATTTTAATTTATAAAATTTTTGG-G-GAAC
1 GAATTTAAACTTATAAAATTTTAGGAGTG-AC
*
72044 GAATTTAAACTTATATAATTTTAGGAGTGAC
1 GAATTTAAACTTATAAAATTTTAGGAGTGAC
* *
72075 CAACTTAAACTTATAAAATTTTAG
1 GAATTTAAACTTATAAAATTTTAG
72099 AAGGATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 21 0.46
31 24 0.52
32 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (31 bp):
GAATTTAAACTTATAAAATTTTAGGAGTGAC
Found at i:74866 original size:31 final size:32
Alignment explanation
Indices: 74785--74874 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 32
74775 TTTTAGTTTG
*
74785 ACCCCTGAACTTTAGA-AAAAATATTAATTTA
1 ACCCCTAAACTTTAGATAAAAATATTAATTTA
* * *
74816 A--CCTAAATTTTAAAT-AAAATATTATTTTA
1 ACCCCTAAACTTTAGATAAAAATATTAATTTA
*
74845 ACCCCT-AACTTTAGATAAAAATATCAATTT
1 ACCCCTAAACTTTAGATAAAAATATTAATTT
74875 GATCTTTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
29 24 0.51
30 8 0.17
31 15 0.32
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (32 bp):
ACCCCTAAACTTTAGATAAAAATATTAATTTA
Done.