Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006993.1 Hibiscus syriacus cultivar Beakdansim tig00018031_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: 53135
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:295 original size:16 final size:15
Alignment explanation
Indices: 272--313 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
262 ATAGGTCCAT
272 TATAATATATACAAA
1 TATAATATATACAAA
287 TATATATATATA-AAA
1 TATA-ATATATACAAA
*
302 TAAAATATATAC
1 TATAATATATAC
314 CCATTACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 7 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAATATATACAAA
Found at i:309 original size:14 final size:16
Alignment explanation
Indices: 275--313 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
265 GGTCCATTAT
275 AATATATACAAATATA
1 AATATATACAAATATA
*
291 TATATATA-AAATA-A
1 AATATATACAAATATA
305 AATATATAC
1 AATATATAC
314 CCATTACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.40
15 5 0.25
16 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATATACAAATATA
Found at i:596 original size:16 final size:16
Alignment explanation
Indices: 553--602 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
543 TTTTTTAAAT
*
553 TAATTTGATTAAATTA
1 TAATTTGATTAGATTA
569 TAATTTGATTAGATTA
1 TAATTTGATTAGATTA
585 TAATTTGATTAGTATTA
1 TAATTTGATTAG-ATTA
602 T
1 T
603 GTATCATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TAATTTGATTAGATTA
Found at i:12210 original size:39 final size:39
Alignment explanation
Indices: 12164--12280 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
12154 TTACTTGAGT
* * *
12164 TTGGTTCTAGTTTCCACCATCTAAATGTGTGACTAGTTC
1 TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
12203 TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
1 TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
12242 TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
1 TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
12281 CCAAAAAGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (39 bp):
TTGGTTCTTGTTTCTACCGTCTAAATGTGTGACTAGTTC
Found at i:19310 original size:2 final size:2
Alignment explanation
Indices: 19305--19336 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19295 AAAAAATACA
19305 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
19337 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19813 original size:2 final size:2
Alignment explanation
Indices: 19808--19858 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19798 TATATGAATC
19808 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
19850 AT AT AT AT A
1 AT AT AT AT A
19859 GGGTAGGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23909 original size:23 final size:23
Alignment explanation
Indices: 23883--23946 Score: 128
Period size: 23 Copynumber: 2.8 Consensus size: 23
23873 CTTTTATTTG
23883 CATAAAAATTGTTAGGTATGGCT
1 CATAAAAATTGTTAGGTATGGCT
23906 CATAAAAATTGTTAGGTATGGCT
1 CATAAAAATTGTTAGGTATGGCT
23929 CATAAAAATTGTTAGGTA
1 CATAAAAATTGTTAGGTA
23947 CATGGTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (23 bp):
CATAAAAATTGTTAGGTATGGCT
Found at i:30605 original size:23 final size:23
Alignment explanation
Indices: 30573--30640 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
30563 TAAACCAACG
* *
30573 TTAAACAAATATTTTCGTGAATA
1 TTAAACAAATATGTTCGTGAACA
* **
30596 TTAAATAAATATGTTCACGAACA
1 TTAAACAAATATGTTCGTGAACA
*
30619 TTAAACAAACATGTTCGTGAAC
1 TTAAACAAATATGTTCGTGAAC
30641 GCTAAAAGAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.32
Consensus pattern (23 bp):
TTAAACAAATATGTTCGTGAACA
Found at i:33026 original size:20 final size:20
Alignment explanation
Indices: 33001--33062 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
32991 TTCGACCATC
33001 GTGAATAGTGACCGATGGTG
1 GTGAATAGTGACCGATGGTG
* * *
33021 GTGAATAATGATCGGTGGTG
1 GTGAATAGTGACCGATGGTG
* *
33041 GTGAATAGTGACTGAAGGTG
1 GTGAATAGTGACCGATGGTG
33061 GT
1 GT
33063 CGGAATAGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.27
Consensus pattern (20 bp):
GTGAATAGTGACCGATGGTG
Found at i:33070 original size:22 final size:23
Alignment explanation
Indices: 33034--33077 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
33024 AATAATGATC
*
33034 GGTGGTGGTGAATAGTGACTGAA
1 GGTGGTCGTGAATAGTGACTGAA
*
33057 GGTGGTCG-GAATAGTTACTGA
1 GGTGGTCGTGAATAGTGACTGA
33078 CGATGACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.25, C:0.07, G:0.41, T:0.27
Consensus pattern (23 bp):
GGTGGTCGTGAATAGTGACTGAA
Found at i:33662 original size:30 final size:29
Alignment explanation
Indices: 33634--33689 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
33624 TTTCTTTTAG
33634 AAATTAATA-TTTTCTTATTTTTATTTTT
1 AAATTAATATTTTTCTTATTTTTATTTTT
**
33662 ATTTTAATATTTTTCTTAATTTTTATTT
1 AAATTAATATTTTTCTT-ATTTTTATTT
33690 ATTTCTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 7 0.29
30 10 0.42
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (29 bp):
AAATTAATATTTTTCTTATTTTTATTTTT
Found at i:33665 original size:12 final size:12
Alignment explanation
Indices: 33648--33689 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
33638 TAATATTTTC
*
33648 TTATTTTTATTT
1 TTATTTTAATTT
33660 TTATTTTAATATT
1 TTATTTTAAT-TT
*
33673 TT-TCTTAATTT
1 TTATTTTAATTT
33684 TTATTT
1 TTATTT
33690 ATTTCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 4 0.16
12 17 0.68
13 4 0.16
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTTAATTT
Found at i:33690 original size:28 final size:27
Alignment explanation
Indices: 33637--33693 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 27
33627 CTTTTAGAAA
33637 TTAATATTTTCTTATTTTTATTTTTATT
1 TTAATATTTTCTTATTTTTA-TTTTATT
33665 TTAATATTTTTCTTAATTTTTA-TTTATT
1 TTAATA-TTTTCTT-ATTTTTATTTTATT
33693 T
1 T
33694 CTCTTGTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 13 0.48
29 7 0.26
30 7 0.26
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (27 bp):
TTAATATTTTCTTATTTTTATTTTATT
Found at i:33748 original size:11 final size:11
Alignment explanation
Indices: 33722--33758 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
33712 CACATTATTA
33722 TTATTTTTTAT
1 TTATTTTTTAT
33733 CTTATTTTTTAT
1 -TTATTTTTTAT
*
33745 TTATTTTTAAT
1 TTATTTTTTAT
33756 TTA
1 TTA
33759 ATCTTCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:33873 original size:12 final size:12
Alignment explanation
Indices: 33856--33882 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33846 GAATTGAATT
33856 TTTAAATTTCAA
1 TTTAAATTTCAA
33868 TTTAAATTTCAA
1 TTTAAATTTCAA
33880 TTT
1 TTT
33883 TCGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:34043 original size:15 final size:16
Alignment explanation
Indices: 34004--34045 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
33994 AACGCATACC
*
34004 AATTTTTTTGTCTTAAA
1 AATTATTTT-TCTTAAA
*
34021 AATGATTTTTCTT-AA
1 AATTATTTTTCTTAAA
34036 AATTATTTTT
1 AATTATTTTT
34046 AAAAAGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (16 bp):
AATTATTTTTCTTAAA
Found at i:38303 original size:130 final size:129
Alignment explanation
Indices: 38002--38589 Score: 610
Period size: 130 Copynumber: 4.5 Consensus size: 129
37992 ACTCCATTGT
* * * *
38002 TCTTCAGGGTAGATCATATCTGAAAATGTTGATTCATTCCACTACTCTTCAGAGAAGATTGAATC
1 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACTA-TTTTCAGGGAAGATTGAATC
* * * * ** * * * **
38067 GAAGTAAATTTGTTCCACTGCTCCTCA-AGGAAAATCAAATATGGAAAAAGGGGATCTACTCCGT
65 GAGGCAGACTTGTTCCA-TTATCCTCAGA-GAAGATCAAATATGGAAAAA-GGGATATGCTCCAC
*
38131 TGC
127 TAC
* * *
38134 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTTATTCCACTATTATTCATGGAAGATTGAATA
1 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACTATT-TTCAGGGAAGATTGAATC
* *
38199 GAGGCATACTTGTTCCAGTTATTCTCAGAGAAGATCAAATAT-GAAAAAGGGATATGCTCCACTA
65 GAGGCAGACTTGTTCCA-TTATCCTCAGAGAAGATCAAATATGGAAAAAGGGATATGCTCCACTA
38263 C
129 C
* * *
38264 TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAGGAATATTGAATC
1 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACTA-TTTTCAGGGAAGATTGAATC
* * *
38329 GAGGCAGATTTGTTCC-TCTATTCCTCATG-GAAGATCAAATAT-GAAAAAGGGATCTGCTCCGC
65 GAGGCAGACTTGTTCCAT-TA-TCCTCA-GAGAAGATCAAATATGGAAAAAGGGATATGCTCCAC
38391 TAC
127 TAC
* * ** * * * *
38394 TCTTTAGGGTATATCATATCTGGAAATATTGATTCATTCTATTGGTTTTCAGGGAATATTGAATC
1 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACT-ATTTTCAGGGAAGATTGAATC
* * *
38459 GAGGCAGACTTGTTCCACTACTCCTCAGGGAAGATCAAATCTGGAAAAAGGAGATATGCTCCACT
65 GAGGCAGACTTGTTCCATTA-TCCTCAGAGAAGATCAAATATGGAAAAAGG-GATATGCTCCACT
**
38524 GT
128 AC
* * * * *
38526 TTTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTCCACTATTTTTTAGGGAAGATTGAAT
1 TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACTA-TTTTCAGGGAAGATTGAAT
38590 TAAATTCAAT
Statistics
Matches: 385, Mismatches: 59, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
128 1 0.00
129 3 0.01
130 212 0.55
131 18 0.05
132 150 0.39
133 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (129 bp):
TCTTCAGGGTAGATCATATCTGGAAACGTTGATTCATTCCACTATTTTCAGGGAAGATTGAATCG
AGGCAGACTTGTTCCATTATCCTCAGAGAAGATCAAATATGGAAAAAGGGATATGCTCCACTAC
Found at i:38517 original size:262 final size:262
Alignment explanation
Indices: 38002--38589 Score: 727
Period size: 262 Copynumber: 2.2 Consensus size: 262
37992 ACTCCATTGT
* * * *
38002 TCTTCAGGGTAGATCATATCTGAAAATGTTGATTCATTCCACTACTCTTC-AGAGAAGATTGAAT
1 TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAG-GAAGATTGAAT
* * *
38066 CGAAGTAAATTTGTTCCACTGCTCCTCAAGGAAAATCAAATATGGAAAAAGGGGATCTACTCCGT
65 CGAAGCAAATTTGTTCCACTACTCCTCAAGGAAAATCAAATATGGAAAAAGGGGATCTACTCCGC
* * * *
38131 TGCTCTTCAGGGTAGATCATATCTGGAAACGTTGATTTATTCCACTATTATTCATGGAAGATTGA
130 TACTCTTCAGGGTAGATCATATCTGGAAACATTGATTCATTCCACTATTATTCAGGGAAGATTGA
* * *
38196 ATAGAGGCATACTTGTTCCAGTTATTCTCAGAGAAGATCAAATATGAAAAAGGGATATGCTCCAC
195 ATAGAGGCAGACTTGTTCCAGCTATCCTCAGAGAAGATCAAATATGAAAAAGGGATATGCTCCAC
38261 TAC
260 TAC
*
38264 TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAGGAATATTGAATC
1 TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAGGAAGATTGAATC
* * * * * * *
38329 GAGGCAGATTTGTTCCTCTATTCCTCATGGAAGATCAAATAT-GAAAAA-GGGATCTGCTCCGCT
66 GAAGCAAATTTGTTCCACTACTCCTCAAGGAAAATCAAATATGGAAAAAGGGGATCTACTCCGCT
* * * * * * *
38392 ACTCTTTAGGGTATATCATATCTGGAAATATTGATTCATTCTATTGGTT-TTCAGGGAATATTGA
131 ACTCTTCAGGGTAGATCATATCTGGAAACATTGATTCATTCCACT-ATTATTCAGGGAAGATTGA
* * *
38456 ATCGAGGCAGACTTGTTCCA-CTACTCCTCAGGGAAGATCAAATCTGGAAAAAGGAGATATGCTC
195 ATAGAGGCAGACTTGTTCCAGCTA-TCCTCAGAGAAGATCAAATAT-GAAAAAGG-GATATGCTC
**
38520 CACTGT
257 CACTAC
* * * * * * *
38526 TTTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTCCACTATTTTTTAGGGAAGATTGAAT
1 TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAGGAAGATTGAAT
38590 TAAATTCAAT
Statistics
Matches: 279, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
259 2 0.01
260 99 0.35
261 16 0.06
262 160 0.57
263 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (262 bp):
TCTTCAGGGTAGATCAAATCTGGAAACGTTGATTCATTCCACTACTTTTCAAGGAAGATTGAATC
GAAGCAAATTTGTTCCACTACTCCTCAAGGAAAATCAAATATGGAAAAAGGGGATCTACTCCGCT
ACTCTTCAGGGTAGATCATATCTGGAAACATTGATTCATTCCACTATTATTCAGGGAAGATTGAA
TAGAGGCAGACTTGTTCCAGCTATCCTCAGAGAAGATCAAATATGAAAAAGGGATATGCTCCACT
AC
Found at i:52158 original size:23 final size:23
Alignment explanation
Indices: 52118--52180 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
52108 GACATTTTAT
* *
52118 GGCACTACAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * * *
52141 GGTACTTCGGTGCCATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
52164 GGCACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
52181 TATACGAGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:53009 original size:13 final size:13
Alignment explanation
Indices: 52991--53016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52981 GCTATGGTGA
52991 CTACTTACAATTG
1 CTACTTACAATTG
53004 CTACTTACAATTG
1 CTACTTACAATTG
53017 ATATCAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CTACTTACAATTG
Done.