Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002452.1 Hibiscus syriacus cultivar Beakdansim tig00005025_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: 34528
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:484 original size:16 final size:17
Alignment explanation
Indices: 464--509 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
454 ACAAAAAAGG
464 AAATAATAAATAAAAAT
1 AAATAATAAATAAAAAT
*
481 -AATAATAAATAACAAT
1 AAATAATAAATAAAAAT
497 AAATAAT-AATAAA
1 AAATAATAAATAAA
510 TGATAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAAATAAAAAT
Found at i:490 original size:10 final size:10
Alignment explanation
Indices: 472--525 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
462 GGAAATAATA
472 AATAA-AAAT
1 AATAATAAAT
481 AATAATAAAT
1 AATAATAAAT
*
491 AACAATAAAT
1 AATAATAAAT
501 AATAATAAAT
1 AATAATAAAT
* * *
511 GATAGTAAAA
1 AATAATAAAT
521 AATAA
1 AATAA
526 ATAATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
9 5 0.14
10 32 0.86
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (10 bp):
AATAATAAAT
Found at i:534 original size:2 final size:2
Alignment explanation
Indices: 529--561 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
519 AAAATAAATA
529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
562 TCCTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:665 original size:39 final size:38
Alignment explanation
Indices: 568--893 Score: 352
Period size: 39 Copynumber: 8.6 Consensus size: 38
558 ATATTCCTTT
*
568 AAAAATGTTCCTTTAAAAACTATATATTATATATTAGTTTTT
1 AAAAATGTT--TTTAAAAACTATATATTATATA--AGTTTTC
*
610 AAAAATGTTTTCAAAAACTATATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
648 AAAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
* * *
687 AAAAAATGTTTTCAAAAAATATATATCATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
* *
726 AAAAAATGTTTTCAAAAATTATATATTATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
* *
765 -AAAATGATTTTT-AAAACCATATATTATACATA-TTTTC
1 AAAAATG-TTTTTAAAAACTATATATTATATA-AGTTTTC
*
802 TAAAATG-TTTTAAAAACTA-ATA-TATATATAGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATA-AGTTTTC
*
838 AAAAGTG-TTTTAAAAAC--TATATTATATACA-TTTT-
1 AAAAATGTTTTTAAAAACTATATATTATATA-AGTTTTC
* *
872 -TAAATGTTTTTAGAAACTATAT
1 AAAAATGTTTTTAAAAACTATAT
894 TATATACATA
Statistics
Matches: 253, Mismatches: 20, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
33 4 0.02
34 9 0.04
35 14 0.06
36 37 0.15
37 32 0.13
38 17 0.07
39 110 0.43
40 21 0.08
42 9 0.04
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (38 bp):
AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
Found at i:7610 original size:20 final size:20
Alignment explanation
Indices: 7585--7627 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7575 TTTCTTCGAT
7585 ATTAAAAAAATAAATAAATA
1 ATTAAAAAAATAAATAAATA
* * *
7605 ATTAAAACAATTAATATATA
1 ATTAAAAAAATAAATAAATA
7625 ATT
1 ATT
7628 TATAAAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAAAAATAAATAAATA
Found at i:8775 original size:3 final size:3
Alignment explanation
Indices: 8767--8838 Score: 62
Period size: 3 Copynumber: 25.0 Consensus size: 3
8757 GGCCTATTTT
*
8767 TAA TAA TAA T-T TAA TAA TAA T-A TAA T-A TAA TAA T-A TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
** **
8809 TTT TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8839 AAACAAAATG
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
2 7 0.13
3 44 0.81
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:8820 original size:12 final size:12
Alignment explanation
Indices: 8764--8833 Score: 76
Period size: 12 Copynumber: 6.1 Consensus size: 12
8754 TTTGGCCTAT
8764 TTTTAATAATAA
1 TTTTAATAATAA
8776 -TTTAATAATAA
1 TTTTAATAATAA
*
8787 -TATAAT-ATAA
1 TTTTAATAATAA
**
8797 TAAT-ATATATAA
1 TTTTAATA-ATAA
8809 TTTTAATAATAA
1 TTTTAATAATAA
8821 TTTTAATAATAA
1 TTTTAATAATAA
8833 T
1 T
8834 AATAAAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.12
11 18 0.36
12 23 0.46
13 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTTAATAATAA
Found at i:9314 original size:73 final size:73
Alignment explanation
Indices: 9194--9542 Score: 601
Period size: 73 Copynumber: 4.8 Consensus size: 73
9184 AACTCGAAAT
* * *
9194 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
9259 TTCAAGTGA
65 TTCGAGTGA
*
9268 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
9333 TCGAGTGA
66 TCGAGTGA
*
9341 AACTGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
9406 TCGAGTGA
66 TCGAGTGA
* *
9414 AACTGTATCAAGCGAGAC-AAATTTGTTTTAAGAAAATCAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
9478 TCGAGTGA
66 TCGAGTGA
*
9486 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
9543 TTGCTATTTG
Statistics
Matches: 262, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
72 69 0.26
73 172 0.66
74 21 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGA
Found at i:9494 original size:145 final size:146
Alignment explanation
Indices: 9194--9542 Score: 601
Period size: 145 Copynumber: 2.4 Consensus size: 146
9184 AACTCGAAAT
* * *
9194 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
9259 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
9324 AATTCTGTTTCGAGTGA
130 AATTCTGTTTCGAGTGA
*
9341 AACTGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
* *
9406 TCGAGTGAAACTGTATCAAGCGAGAC-AAATTTGTTTTAAGAAAATCAATCTCAAGTGAGATAAA
66 TCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
*
9470 GTTCTGTTTCGAGTGA
131 ATTCTGTTTCGAGTGA
*
9486 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
9543 TTGCTATTTG
Statistics
Matches: 192, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
145 107 0.56
146 64 0.33
147 21 0.11
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (146 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
ATTCTGTTTCGAGTGA
Found at i:10287 original size:22 final size:22
Alignment explanation
Indices: 10262--10316 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
10252 AATAAAGCTT
10262 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
10284 TCATCTTTTAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
10306 TCATCTTTGAA
1 TCATCTTTGAA
10317 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:11806 original size:76 final size:76
Alignment explanation
Indices: 11656--11830 Score: 217
Period size: 76 Copynumber: 2.3 Consensus size: 76
11646 AGGATGATAT
* * * *
11656 GGGCCTTCAGCATGCCCCAACA-TTAGCTAATACAAGTGTTCAAAATGCATCAACAGTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTAGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
11720 CTGATTGAAAG
66 CTGATTGAAAG
* * * * * * *
11731 GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAATATTCAGAATACTTCAATATTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTAGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
11796 CTGATTGAAAG
66 CTGATTGAAAG
* * *
11807 GGGTTTTCATCATGCCACAACATT
1 GGGCTTTCAGCATGCCCCAACATT
11831 CGATTCTTGT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 21 0.25
76 64 0.75
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (76 bp):
GGGCTTTCAGCATGCCCCAACATTTAGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
CTGATTGAAAG
Found at i:12810 original size:31 final size:31
Alignment explanation
Indices: 12767--12829 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
12757 AGAAGTGGTC
*
12767 TGAATTCATCAATTGCAGAGTTGACAGATTT
1 TGAAATCATCAATTGCAGAGTTGACAGATTT
12798 TGAAATCATCAATTGCAGAGTTGACAGATTT
1 TGAAATCATCAATTGCAGAGTTGACAGATTT
12829 T
1 T
12830 ATATGTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (31 bp):
TGAAATCATCAATTGCAGAGTTGACAGATTT
Found at i:13761 original size:11 final size:10
Alignment explanation
Indices: 13734--13760 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
13724 TCTTTCTCTC
13734 TTTTTTTCTT
1 TTTTTTTCTT
13744 TTTTTTTCTT
1 TTTTTTTCTT
13754 TTTTTTT
1 TTTTTTT
13761 TGAATCAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:19846 original size:121 final size:121
Alignment explanation
Indices: 19605--19837 Score: 278
Period size: 121 Copynumber: 1.9 Consensus size: 121
19595 TATATTAATT
* * * *
19605 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGGACATCCAGGTACCT
* * *
19670 TAAGACAGCTCTTTTCTTCGATATTAAAAAAATAAATAAATAATTAAAGCAATTAA
66 TAAGACAGCTCCTTTCTTCAATATTAAAAAAATAAATAAATAATTAAAACAATTAA
* * *
19726 TATATA-ATTTATAAAATAGAATATTTATTTATTTAAAAATATCAAAAAAATGGACATCCAGTTG
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATC-AAAAAA-GGACATCCAGGTA
** * *
19790 TTTTAAGACTG-TCCTTTCTT-AATATT-GAAAAATAAATAAAT-ATTAAAA
63 CCTTAAGACAGCTCCTTTCTTCAATATTAAAAAAATAAATAAATAATTAAAA
19838 TAGGATTAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
119 6 0.06
120 20 0.21
121 39 0.41
122 13 0.14
123 17 0.18
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (121 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGGACATCCAGGTACCT
TAAGACAGCTCCTTTCTTCAATATTAAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:21636 original size:31 final size:31
Alignment explanation
Indices: 21598--21784 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
21588 CCCGAAGGAC
* *
21598 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
21629 CAGTCCATATGTCCCGAAGGACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
21660 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21691 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21722 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21753 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
21784 C
1 C
21785 CCTCGACCCT
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:25075 original size:29 final size:31
Alignment explanation
Indices: 24934--25117 Score: 270
Period size: 31 Copynumber: 6.0 Consensus size: 31
24924 CCCGAAGGAC
* *
24934 CAGTCCATA-GATTCCGAAGAAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAG-AACATAGGTAAA
* *
24966 CAGTCCATATGTCCCGAAGGACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
24997 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25028 CAGTCCATATGTCCCGAAGAACAT-GGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25058 CAGT-CATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25087 CAGTCCATATGT-CCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25117 C
1 C
25118 CCTCGACCCT
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
29 40 0.28
30 23 0.16
31 62 0.44
32 16 0.11
33 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:28231 original size:31 final size:31
Alignment explanation
Indices: 28193--28375 Score: 277
Period size: 30 Copynumber: 6.0 Consensus size: 31
28183 CCCGAAGGAC
* *
28193 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
28224 CAGTCCATATGTCCCGAAGGACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
28255 CAGTCCATATGT-CCGAAGGACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28284 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28315 CAGTCCATATGT-CCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28344 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28375 C
1 C
28376 CCCGACCCTT
Statistics
Matches: 141, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
29 27 0.19
30 59 0.42
31 54 0.38
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:29758 original size:3 final size:3
Alignment explanation
Indices: 29750--29836 Score: 101
Period size: 3 Copynumber: 30.0 Consensus size: 3
29740 AGCCTGTTTG
*
29750 TAA TAA TAA T-T TAA TAA TAA T-A TAA T-A TAA TAA T-A TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* **
29792 TAT TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29837 CAAAATGGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
2 7 0.10
3 61 0.86
4 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Done.