Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009200.1 Hibiscus syriacus cultivar Beakdansim tig00112784_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: 41467
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:6090 original size:93 final size:94
Alignment explanation
Indices: 5955--6140 Score: 288
Period size: 93 Copynumber: 2.0 Consensus size: 94
5945 TCGTGTATAG
*
5955 TTTTTCTCATGTCGCTCGAGACTCTGATTTACGATTTATCGGTGATCTTTTAATAGTTTCAT-CT
1 TTTTTCTCATGTCGCTC-AGACTCTGATTTACGATTTATCGGTGATCTTTCAATAG-TTCATCCT
6019 ATTTTGTAGTTTGTTTGCCGATGCAGTCAAA
64 ATTTTGTAGTTTGTTTGCCGATGCAGTCAAA
* * *
6050 TTTTTCTCATG-CTGCTC-GACTCTGATTTACGATTTATCGGTGGTCTTTCAGTAGTTCATCCTC
1 TTTTTCTCATGTC-GCTCAGACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTCATCCTA
6113 TTTTGTAGTTTGTTTGCCGATGCAGTCA
65 TTTTGTAGTTTGTTTGCCGATGCAGTCA
6141 TATTGTTCGT
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
92 5 0.06
93 64 0.75
94 1 0.01
95 15 0.18
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (94 bp):
TTTTTCTCATGTCGCTCAGACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTCATCCTAT
TTTGTAGTTTGTTTGCCGATGCAGTCAAA
Found at i:6846 original size:2 final size:2
Alignment explanation
Indices: 6841--6871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6831 TTTTTTTTAA
6841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6872 CTTTGAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12840 original size:16 final size:16
Alignment explanation
Indices: 12819--12852 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12809 TTACTATTCA
*
12819 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
12835 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
12851 CG
1 CG
12853 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:18860 original size:29 final size:29
Alignment explanation
Indices: 18825--18906 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
18815 AAACTAAATT
* *
18825 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
18854 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
18883 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
18907 GTTATGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:23588 original size:29 final size:29
Alignment explanation
Indices: 23553--23629 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
23543 AAACTAAATT
* *
23553 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
23582 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
23611 GATGTCATTGCTTACATCA
1 GATGTCATTGCTTACATCA
23630 ATTAGTTATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:28391 original size:51 final size:50
Alignment explanation
Indices: 28271--28578 Score: 190
Period size: 51 Copynumber: 6.1 Consensus size: 50
28261 ACGGGCGGGC
* * *
28271 GGAAGAAAGGGGGTTGG-GGAAG-GACGGGCGGCGGAAGAA-AGGGGGTTGGA
1 GGAAGAAA-GGGGTTGGAGGAAGAAAGGGGCGGCGGAAGAACA--GGGTCGGA
* * * * * * *
28321 GGAAG-GACGGG-CGGCGGAAGAAAGGGGGTTGGGGGAAGAAC-GGG-CGGC
1 GGAAGAAAGGGGTTGGAGGAAGAAA-GGGG-CGGCGGAAGAACAGGGTCGGA
* * * *
28369 GGAAGTAAAGGGGTTGGGGGAAG-AACGGGCGGCGGCAGAACGGGGTTCGGA
1 GGAAG-AAAGGGGTTGGAGGAAGAAAGGGGCGGCGGAAGAACAGGG-TCGGA
* *
28420 GGAAGAAAGGGGGTTGGAGGAAG-AATGGGCGGCGGCAGAACAGGGTTCGGA
1 GGAAGAAA-GGGGTTGGAGGAAGAAAGGGGCGGCGGAAGAACAGGG-TCGGA
* * * *
28471 GGAAGAAAGGGGTTGGGGGAAGAAAGGGGGTTGGAGGAAGAAC-GGG-CGGC
1 GGAAGAAAGGGGTTGGAGGAAGAAA-GGGG-CGGCGGAAGAACAGGGTCGGA
* * * * *
28521 GGCAGAACGGGGTTCGGAGGAAG-AATGGGCGGCGGCAGAACGGGGTTCGGA
1 GGAAGAAAGGGGTT-GGAGGAAGAAAGGGGCGGCGGAAGAACAGGG-TCGGA
28572 GGAAGAA
1 GGAAGAA
28579 TGGGCGGCGG
Statistics
Matches: 203, Mismatches: 36, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
47 2 0.01
48 33 0.16
49 17 0.08
50 47 0.23
51 89 0.44
52 6 0.03
53 9 0.04
ACGTcount: A:0.28, C:0.10, G:0.54, T:0.08
Consensus pattern (50 bp):
GGAAGAAAGGGGTTGGAGGAAGAAAGGGGCGGCGGAAGAACAGGGTCGGA
Found at i:28424 original size:33 final size:33
Alignment explanation
Indices: 28203--28426 Score: 268
Period size: 33 Copynumber: 6.9 Consensus size: 33
28193 TCTCCGGAGC
* *
28203 GGCGGCGGCAG-AAGTGGGTTTGGAGG--GAACG
1 GGCGGCGGAAGAAAG-GGGGTTGGAGGAAGAACG
*
28234 GGCGGC---AGAAAGGGGGTTGGAGGAAGGACG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACG
*
28264 GGCGGGCGGAAGAAAGGGGGTTGG-GGAAGGACG
1 GGC-GGCGGAAGAAAGGGGGTTGGAGGAAGAACG
*
28297 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACG
*
28330 GGCGGCGGAAGAAAGGGGGTTGGGGGAAGAACG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACG
*
28363 GGCGGCGGAAGTAAA-GGGGTTGGGGGAAGAACG
1 GGCGGCGGAAG-AAAGGGGGTTGGAGGAAGAACG
* *
28396 GGCGGCGGCAG-AACGGGGTTCGGAGGAAGAA
1 GGCGGCGGAAGAAAGGGGGTT-GGAGGAAGAA
28427 AGGGGGTTGG
Statistics
Matches: 176, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.07
29 3 0.02
30 7 0.04
31 11 0.06
32 26 0.15
33 100 0.57
34 17 0.10
ACGTcount: A:0.25, C:0.11, G:0.56, T:0.08
Consensus pattern (33 bp):
GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACG
Found at i:28472 original size:33 final size:33
Alignment explanation
Indices: 28429--28611 Score: 262
Period size: 33 Copynumber: 5.5 Consensus size: 33
28419 AGGAAGAAAG
28429 GGGGTT-GGAGGAAGAATGGGCGGCGGCAGAAC
1 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
* * * * * *
28461 AGGGTTCGGAGGAAGAAAGGGGTTGGGGGAAGAAAG
1 GGGGTTCGGAGGAAG-AATGGG-CGGCGGCAG-AAC
*
28497 GGGGTT-GGAGGAAGAACGGGCGGCGGCAGAAC
1 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
28529 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
1 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
28562 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
1 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
28595 GGGGTTCGGAGGAAGAA
1 GGGGTTCGGAGGAAGAA
28612 AAGGGGTTGG
Statistics
Matches: 133, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
32 13 0.10
33 89 0.67
34 10 0.08
35 14 0.11
36 7 0.05
ACGTcount: A:0.27, C:0.11, G:0.52, T:0.09
Consensus pattern (33 bp):
GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAAC
Found at i:28529 original size:15 final size:15
Alignment explanation
Indices: 28509--28597 Score: 70
Period size: 15 Copynumber: 5.5 Consensus size: 15
28499 GGTTGGAGGA
28509 AGAACGGGCGGCGGC
1 AGAACGGGCGGCGGC
* *
28524 AGAACGGGGTTCGGAGGA
1 AGAAC-GGG--CGGCGGC
*
28542 AGAATGGGCGGCGGC
1 AGAACGGGCGGCGGC
* *
28557 AGAACGGGGTTCGGAGGA
1 AGAAC-GGG--CGGCGGC
*
28575 AGAATGGGCGGCGGC
1 AGAACGGGCGGCGGC
28590 AGAACGGG
1 AGAACGGG
28598 GTTCGGAGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
15 26 0.46
16 6 0.11
17 6 0.11
18 18 0.32
ACGTcount: A:0.25, C:0.17, G:0.52, T:0.07
Consensus pattern (15 bp):
AGAACGGGCGGCGGC
Found at i:28598 original size:66 final size:67
Alignment explanation
Indices: 28405--28633 Score: 284
Period size: 68 Copynumber: 3.4 Consensus size: 67
28395 GGGCGGCGGC
* * *
28405 AGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGAAGAATGGGCGGCGGCAGAACAGGGTTCGG
1 AGAA-GGGG-TCGGCGGAAGAAACGGGGTTGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGG
28470 AGGA
64 AGGA
* * * *
28474 AGAAAGGGGTTGGGGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGA
1 AG-AAGGGGTCGGCGGAAGAAACGGGGTTGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGA
28539 GGA
65 GGA
* *
28542 AGAATGGG-CGGCGGCAG-AACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGA
1 AGAAGGGGTCGGCGGAAGAAACGGGGTT-GGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGA
28605 GGA
65 GGA
* *
28608 AGAAAAGGGGTTGGAGGAAG-AACGGG
1 AG--AAGGGGTCGGCGGAAGAAACGGG
28634 CGGCGGAAGA
Statistics
Matches: 141, Mismatches: 14, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
65 8 0.06
66 46 0.33
67 5 0.04
68 62 0.44
69 18 0.13
70 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.52, T:0.09
Consensus pattern (67 bp):
AGAAGGGGTCGGCGGAAGAAACGGGGTTGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAG
GA
Found at i:31639 original size:39 final size:34
Alignment explanation
Indices: 31607--31750 Score: 100
Period size: 38 Copynumber: 4.1 Consensus size: 34
31597 TAAAATGTTC
*
31607 TTGAAAGCTTATATACAATATATAAGTTTTAAAGCATT
1 TTGAAAG-TTATAT--AATATAT-AGTTTTAAAACATT
* *
31645 TTGAAAGTTATATAATATATAGTTTT-GATCATT
1 TTGAAAGTTATATAATATATAGTTTTAAAACATT
* *
31678 TTG-AA---ATATAATGTATAGTTTTAAAAAAATAT
1 TTGAAAGTTATATAATATATAGTTTT-AAAACAT-T
* *
31710 TTGGAAAATTTATATAATATATAGTTTAAAAAAACATT
1 TT-G-AAAGTTATATAATATATAGTTT--TAAAACATT
31748 TTG
1 TTG
31751 GAAAACTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
29 16 0.19
31 3 0.03
32 5 0.06
33 9 0.10
34 6 0.07
35 9 0.10
37 7 0.08
38 25 0.29
39 6 0.07
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.42
Consensus pattern (34 bp):
TTGAAAGTTATATAATATATAGTTTTAAAACATT
Found at i:31678 original size:33 final size:37
Alignment explanation
Indices: 31607--31683 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 37
31597 TAAAATGTTC
31607 TTGAAAGCTTATATACAATATATAAGTTTTAAAGCATT
1 TTGAAAGCTTATATA-AATATATAAGTTTTAAAGCATT
* *
31645 TTGAAAG-TTATAT-AATATAT-AGTTTT-GATCATT
1 TTGAAAGCTTATATAAATATATAAGTTTTAAAGCATT
31678 TTGAAA
1 TTGAAA
31684 TATAATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 11 0.30
34 6 0.16
35 7 0.19
37 6 0.16
38 7 0.19
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (37 bp):
TTGAAAGCTTATATAAATATATAAGTTTTAAAGCATT
Found at i:31734 original size:38 final size:38
Alignment explanation
Indices: 31683--31761 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
31673 TCATTTTGAA
* * *
31683 ATATAATGTATAGTTTTAAAAAA-ATATTTGGAAAATTT
1 ATATAATATATAGTTTAAAAAAACAT-TTTGGAAAACTT
31721 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
1 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
31759 ATA
1 ATA
31762 ATATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 35 0.95
39 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (38 bp):
ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
Found at i:31897 original size:24 final size:23
Alignment explanation
Indices: 31870--31923 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
31860 ATATATTATT
*
31870 ATTTTTTTATTATT-ATTTCATTTC
1 ATTTTTTCATT-TTAATTT-ATTTC
31894 ATTTTATTCATTTTAATTTATTTC
1 ATTTT-TTCATTTTAATTTATTTC
*
31918 GTTTTT
1 ATTTTT
31924 GTTTCAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.62
25 9 0.35
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTTTCATTTTAATTTATTTC
Found at i:33136 original size:15 final size:17
Alignment explanation
Indices: 33111--33149 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
33101 TTTTTATTCA
33111 ATTTGATCCTTT-TTTT-
1 ATTT-ATCCTTTGTTTTC
33127 ATTTATCCTTTGTTTTC
1 ATTTATCCTTTGTTTTC
33144 ATTTAT
1 ATTTAT
33150 TTTATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTATCCTTTGTTTTC
Found at i:33196 original size:21 final size:23
Alignment explanation
Indices: 33172--33218 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33162 CTTATATTTG
*
33172 TTTAA-CTCATTT-TTTGTTCTC
1 TTTAATCTCATTTATTTATTCTC
*
33193 TTTAATCTTATTTATTTATTCTC
1 TTTAATCTCATTTATTTATTCTC
33216 TTT
1 TTT
33219 CTTTGACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTAATCTCATTTATTTATTCTC
Found at i:33259 original size:15 final size:16
Alignment explanation
Indices: 33228--33264 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
33218 TCTTTGACTT
*
33228 TTTATTTATATATTTA
1 TTTATTTATACATTTA
33244 TTTATTTA-ACATTTA
1 TTTATTTATACATTTA
33259 TTTATT
1 TTTATT
33265 GTTATTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTATACATTTA
Found at i:33362 original size:6 final size:6
Alignment explanation
Indices: 33351--33378 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33341 TGAATCGAAT
33351 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
33379 TCAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Done.