Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006456.1 Hibiscus syriacus cultivar Beakdansim tig00015645_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: 58623
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2581 original size:2 final size:2
Alignment explanation
Indices: 2568--2624 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
2558 CTAAACACTT
*
2568 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2610 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2625 GTTGTGGTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8151 original size:156 final size:156
Alignment explanation
Indices: 7930--8238 Score: 537
Period size: 156 Copynumber: 2.0 Consensus size: 156
7920 CAGAAAACTG
* * *
7930 ATCCCTCTCAAGCATAACTGATTGAAGGTCTGCCTCAAGACTAGATGCTCTCTTTTCTGATTCTT
1 ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTTCTGACTCTT
*
7995 CCAAATCAGTAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
66 CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
*
8060 CTTTCATGCTTAGCATCTGAAAGAGC
131 CTTTCATGATTAGCATCTGAAAGAGC
*
8086 ATCCCTCTCCAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTTCTGACTCTT
1 ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTTCTGACTCTT
*
8151 CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTT
66 CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
* *
8216 TTTTCATGATTAGCTTCTGAAAG
131 CTTTCATGATTAGCATCTGAAAG
8239 TGCCCCTCCT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
156 144 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (156 bp):
ATCCCTCTCAAGCATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTTCTGACTCTT
CCAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGACTATCAATCTTCTTCTGCAAAGAATTT
CTTTCATGATTAGCATCTGAAAGAGC
Found at i:14512 original size:13 final size:13
Alignment explanation
Indices: 14479--14516 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
14469 CTTTTTATCG
14479 ATTATTTATT-AT
1 ATTATTTATTAAT
**
14491 AAAATTTATTAAT
1 ATTATTTATTAAT
14504 ATTATTTATTAAT
1 ATTATTTATTAAT
14517 TATCAATTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATTTATTAAT
Found at i:17541 original size:25 final size:25
Alignment explanation
Indices: 17465--17547 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
17455 TCAAATAATT
17465 AAAT-AATAAAAACATTAAGAAACA
1 AAATAAATAAAAACATTAAGAAACA
*
17489 AAATAAATAAAAA-A-T-----CCA
1 AAATAAATAAAAACATTAAGAAACA
*
17507 TAATTAAATAAAAACATTAAGAAACA
1 -AAATAAATAAAAACATTAAGAAACA
17533 AAATAAATAAAAACA
1 AAATAAATAAAAACA
17548 ACACCACATG
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
18 2 0.04
19 12 0.26
20 1 0.02
21 1 0.02
23 1 0.02
24 5 0.11
25 22 0.48
26 2 0.04
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.18
Consensus pattern (25 bp):
AAATAAATAAAAACATTAAGAAACA
Found at i:19237 original size:18 final size:19
Alignment explanation
Indices: 19198--19234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19188 AATAAATAGT
19198 ATACGAAAAATATAAATTA
1 ATACGAAAAATATAAATTA
*
19217 ATACTAAAAA-AT-AATTA
1 ATACGAAAAATATAAATTA
19234 A
1 A
19235 ATAAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (19 bp):
ATACGAAAAATATAAATTA
Found at i:19871 original size:44 final size:44
Alignment explanation
Indices: 19808--19898 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
19798 CCACACTTTA
19808 TTAAAAAAATGTGTTAAATTAGTAATATTTAAAGAAAGAATGCC
1 TTAAAAAAATGTGTTAAATTAGTAATATTTAAAGAAAGAATGCC
19852 TTAAAAAAATGTGTTAAATTAGTAATATTTAAAGAAAGAATGCC
1 TTAAAAAAATGTGTTAAATTAGTAATATTTAAAGAAAGAATGCC
19896 TTA
1 TTA
19899 TAAATAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (44 bp):
TTAAAAAAATGTGTTAAATTAGTAATATTTAAAGAAAGAATGCC
Found at i:22740 original size:59 final size:59
Alignment explanation
Indices: 22669--22782 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
22659 CACACTATGA
* * * *
22669 CACATTATAAATTAACCCCTAAACGTTAAACTATTTTATATCAATCTTTAACTATTACC
1 CACATTATAAATTAACCCCTAAACGTTAAAATATTTTATACCAATCCTAAACTATTACC
* ** *
22728 CACATT-TCAAATTAATCTTTAAACTTTAAAATATTTTATACCAATCCTAAACTAT
1 CACATTAT-AAATTAACCCCTAAACGTTAAAATATTTTATACCAATCCTAAACTAT
22783 GAATAACATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.39
Consensus pattern (59 bp):
CACATTATAAATTAACCCCTAAACGTTAAAATATTTTATACCAATCCTAAACTATTACC
Found at i:25918 original size:15 final size:17
Alignment explanation
Indices: 25898--25933 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25888 CTGGAAGTCC
25898 CAAAAAAA-T-CAGAAA
1 CAAAAAAATTCCAGAAA
25913 CAAAAAAATTCCAGAAA
1 CAAAAAAATTCCAGAAA
25930 CAAA
1 CAAA
25934 TACGTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (17 bp):
CAAAAAAATTCCAGAAA
Found at i:26054 original size:65 final size:64
Alignment explanation
Indices: 25983--26115 Score: 230
Period size: 65 Copynumber: 2.1 Consensus size: 64
25973 TAAGATGTAC
* *
25983 AAAAACAAGGTGATAAGGCAATAAATTCTAGCCGAACAAACAAAATACAGCTATACAAGCTTAA
1 AAAAACAAGGTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACTATACAAGCTTAA
*
26047 GAAAAACAAGGTGATAAGGCAATAAATTCTATCCAAACAAACAAAATACAACTATACAAGCTTAA
1 -AAAAACAAGGTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACTATACAAGCTTAA
26112 AAAA
1 AAAA
26116 TGCATACATG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 4 0.06
65 61 0.94
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (64 bp):
AAAAACAAGGTGATAAGGCAATAAATTCTAGCCAAACAAACAAAATACAACTATACAAGCTTAA
Found at i:29892 original size:35 final size:35
Alignment explanation
Indices: 29833--29944 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
29823 AAAACATTCC
* *
29833 TCAATTTCATTATAAATCCC-AAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCTAAATTTCAAAATAAT
*
29868 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
* *
29903 TCAATTACATTCTAAACCCTAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTTC-AAAATAAT
29938 TCAATTT
1 TCAATTT
29945 AAGGAGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.07
35 63 0.93
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:31002 original size:35 final size:34
Alignment explanation
Indices: 30953--31065 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
30943 TAAAAAGACA
* *
30953 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
30988 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
31023 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
31058 GAAATTGA
1 GAAATTGA
31066 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:31495 original size:19 final size:19
Alignment explanation
Indices: 31428--31496 Score: 50
Period size: 22 Copynumber: 3.4 Consensus size: 19
31418 TAAAAGTTCG
* *
31428 ATAATATAATAATTATTTT
1 ATAATTTAATAAATATTTT
31447 ATAGTATTTAGATAAAT-TTATT
1 ATA--ATTTA-ATAAATATT-TT
*
31469 AATAAATTTAATAAGTATTTT
1 -AT-AATTTAATAAATATTTT
31490 ATAATTT
1 ATAATTT
31497 TTTAAACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
19 8 0.20
20 2 0.05
21 13 0.32
22 14 0.35
23 2 0.05
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATAATTTAATAAATATTTT
Found at i:32887 original size:76 final size:78
Alignment explanation
Indices: 32748--32902 Score: 206
Period size: 76 Copynumber: 2.0 Consensus size: 78
32738 AAAAAATAAT
* * **
32748 ATTTTAGGTAGCATTTAATATTAACATTTTCGATAGAAAAAAATAATGTTTTAGGTAGTGCTTTA
1 ATTTTAGGTAGCAGTCAATATTAACATTTTC-A-AGAAAAAAATAATGTTTTAGGTAACGCTTTA
*
32813 CCGAAAATGTTAAAC
64 CCAAAAATGTTAAAC
* * *
32828 ATTTTAGGTAGCGGTCAATATTAACA-TTTC-AGAAAAAAATAATGTTTTATGTAACGCTTTACT
1 ATTTTAGGTAGCAGTCAATATTAACATTTTCAAGAAAAAAATAATGTTTTAGGTAACGCTTTACC
32891 AAAAATGTTAAA
66 AAAAATGTTAAA
32903 AAATATTAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 40 0.60
79 4 0.06
80 23 0.34
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (78 bp):
ATTTTAGGTAGCAGTCAATATTAACATTTTCAAGAAAAAAATAATGTTTTAGGTAACGCTTTACC
AAAAATGTTAAAC
Found at i:36887 original size:14 final size:14
Alignment explanation
Indices: 36847--36943 Score: 84
Period size: 14 Copynumber: 7.4 Consensus size: 14
36837 TAATGTCTAA
*
36847 TAATAATGATGACT
1 TAATAATGATGATT
36861 TAATAATGATGATT
1 TAATAATGATGATT
*
36875 TAATAATAATGA--
1 TAATAATGATGATT
* * *
36887 TGAT-TTGATAATGT
1 TAATAATGATGAT-T
36901 TAATAATGATGATT
1 TAATAATGATGATT
36915 TAAT-A--ATG--T
1 TAATAATGATGATT
36924 TAATAATGATGATT
1 TAATAATGATGATT
36938 TAATAA
1 TAATAA
36944 AAAATTAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
9 5 0.08
10 1 0.02
11 7 0.11
12 6 0.09
13 1 0.02
14 39 0.60
15 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.41
Consensus pattern (14 bp):
TAATAATGATGATT
Found at i:36890 original size:17 final size:17
Alignment explanation
Indices: 36844--36921 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
36834 ATTTAATGTC
*
36844 TAATAATAATGATGA-C
1 TAATAATAATGATGATT
36860 T--TAATAATGATGATT
1 TAATAATAATGATGATT
36875 TAATAATAATGATGATTT
1 TAATAATAATGATGA-TT
36893 GATAATGTTAATAATGATGATT
1 --TAA---TAATAATGATGATT
36915 TAATAAT
1 TAATAAT
36922 GTTAATAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 17
0.74 0.01 0.24
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
16 1 0.02
17 16 0.31
18 2 0.04
20 6 0.12
22 2 0.04
23 12 0.23
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (17 bp):
TAATAATAATGATGATT
Found at i:36908 original size:23 final size:23
Alignment explanation
Indices: 36878--36943 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
36868 GATGATTTAA
*
36878 TAATAATGATGATTTGATAATGT
1 TAATAATGATGATTTAATAATGT
36901 TAATAATGATGATTTAATAATGT
1 TAATAATGATGATTTAATAATGT
36924 TAATAATGATGATTTAATAA
1 TAATAATGATGATTTAATAA
36944 AAAATTAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (23 bp):
TAATAATGATGATTTAATAATGT
Found at i:37058 original size:24 final size:23
Alignment explanation
Indices: 36995--37048 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
36985 ATGCTTCTCC
36995 ACAAGGCTGACGCATGCTGAAAA
1 ACAAGGCTGACGCATGCTGAAAA
37018 ACAAGGCTGACGCATGCTGAAAA
1 ACAAGGCTGACGCATGCTGAAAA
37041 ACAAGGCT
1 ACAAGGCT
37049 ACATGCATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (23 bp):
ACAAGGCTGACGCATGCTGAAAA
Found at i:38084 original size:20 final size:19
Alignment explanation
Indices: 38055--38095 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
38045 ATGGTAAGCC
*
38055 AAATTTATAAACACTTTATA
1 AAATTCATAAACACTTT-TA
38075 AAATTCATAAACACTTTTA
1 AAATTCATAAACACTTTTA
38094 AA
1 AA
38096 TTTGTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTCATAAACACTTTTA
Found at i:40300 original size:16 final size:16
Alignment explanation
Indices: 40279--40337 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
40269 TCCCCCTTAC
40279 TTTAACACTTCTCCCA
1 TTTAACACTTCTCCCA
* *
40295 TTTAACCCTTAT----
1 TTTAACACTTCTCCCA
40307 TTTAACACTTCTCCCA
1 TTTAACACTTCTCCCA
40323 TTTAACACTTCTCCC
1 TTTAACACTTCTCCC
40338 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 10 0.29
16 25 0.71
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAACACTTCTCCCA
Found at i:40312 original size:28 final size:28
Alignment explanation
Indices: 40272--40328 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40262 AAATTACTCC
40272 CCCTTACTTTAACACTTCTCCCATTTAA
1 CCCTTACTTTAACACTTCTCCCATTTAA
*
40300 CCCTTATTTTAACACTTCTCCCATTTAA
1 CCCTTACTTTAACACTTCTCCCATTTAA
40328 C
1 C
40329 ACTTCTCCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (28 bp):
CCCTTACTTTAACACTTCTCCCATTTAA
Found at i:42592 original size:20 final size:20
Alignment explanation
Indices: 42563--42612 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
42553 AATTCCAGAA
42563 CCCC-AGGGGGGTATAGATT
1 CCCCTAGGGGGGTATAGATT
42582 CCCCTAGGGGGGTATAGATT
1 CCCCTAGGGGGGTATAGATT
42602 CCCCTACGGGG
1 CCCCTA-GGGG
42613 AAATCGGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.20
Consensus pattern (20 bp):
CCCCTAGGGGGGTATAGATT
Found at i:48713 original size:13 final size:13
Alignment explanation
Indices: 48695--48719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48685 TCGAATATAC
48695 TTAGAAAATCTTT
1 TTAGAAAATCTTT
48708 TTAGAAAATCTT
1 TTAGAAAATCTT
48720 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:49302 original size:27 final size:28
Alignment explanation
Indices: 49264--49322 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
49254 TTATTCTAGT
49264 TGTTGAACTACATTACATTTCACTT-AA
1 TGTTGAACTACATTACATTTCACTTGAA
49291 TGTTGAACTACATTACATTTCACTTGAA
1 TGTTGAACTACATTACATTTCACTTGAA
49319 TGTT
1 TGTT
49323 TGTAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (28 bp):
TGTTGAACTACATTACATTTCACTTGAA
Found at i:57189 original size:12 final size:12
Alignment explanation
Indices: 57172--57196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57162 GCTTCATCTC
57172 TCGCTCGCTCGT
1 TCGCTCGCTCGT
57184 TCGCTCGCTCGT
1 TCGCTCGCTCGT
57196 T
1 T
57197 GTTTCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.24, T:0.36
Consensus pattern (12 bp):
TCGCTCGCTCGT
Done.