Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001683.1 Hibiscus syriacus cultivar Beakdansim tig00003361_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: 49930
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:525 original size:27 final size:26
Alignment explanation
Indices: 495--548 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
485 TTCACCCACT
*
495 CGACTCGGTCATCATTTCAGCATATGG
1 CGACTCGGTCATCA-TTAAGCATATGG
**
522 CGACTTTGTCATCATTAAGCATATGG
1 CGACTCGGTCATCATTAAGCATATGG
548 C
1 C
549 ACCACCGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (26 bp):
CGACTCGGTCATCATTAAGCATATGG
Found at i:803 original size:6 final size:6
Alignment explanation
Indices: 792--832 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
782 GAGGGTGTGA
* *
792 TGATGG TGATGG TGATGG TGGTGG TGATGA TGATGG TGATG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATG
833 ATCAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.00, G:0.49, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:833 original size:12 final size:12
Alignment explanation
Indices: 792--850 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
782 GAGGGTGTGA
*
792 TGATGGTGATGG
1 TGATGATGATGG
* *
804 TGATGGTGGTGG
1 TGATGATGATGG
816 TGATGATGATGG
1 TGATGATGATGG
*
828 TGATGATCA-GAG
1 TGATGATGATG-G
840 TGATGATGATG
1 TGATGATGATG
851 CCCGAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
11 1 0.03
12 38 0.95
13 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.32
Consensus pattern (12 bp):
TGATGATGATGG
Found at i:2377 original size:16 final size:16
Alignment explanation
Indices: 2356--2395 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2346 TCTCAAAAGA
*
2356 CATCCTCTTCTGGTGG
1 CATCCTCTTCCGGTGG
2372 CATCCTCTTCCGGTGG
1 CATCCTCTTCCGGTGG
2388 CATCCTCT
1 CATCCTCT
2396 ACTTAAGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.38, G:0.20, T:0.35
Consensus pattern (16 bp):
CATCCTCTTCCGGTGG
Found at i:4215 original size:23 final size:23
Alignment explanation
Indices: 4180--4242 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
4170 ACCACATAGA
* *
4180 TTTGCATCGAAGTGCCAAAAAGG
1 TTTGCACCAAAGTGCCAAAAAGG
* *
4203 TTTGCACCAAAGTGCCGAATAGG
1 TTTGCACCAAAGTGCCAAAAAGG
4226 TTTGCACCGAAA-TGCCA
1 TTTGCACC-AAAGTGCCA
4243 CATAATTGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
TTTGCACCAAAGTGCCAAAAAGG
Found at i:6159 original size:24 final size:25
Alignment explanation
Indices: 6117--6186 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 25
6107 TTTTTTAATT
* *
6117 TTATTAGTTTAATTTAATATATAAAA
1 TTATTA-TATAATTAAATATATAAAA
* *
6143 TTATTA-ATAATTAAATATGTAATA
1 TTATTATATAATTAAATATATAAAA
6167 TTATTATATATATATAAATA
1 TTATTATATA-AT-TAAATA
6187 AATGTAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 20 0.54
25 3 0.08
26 8 0.22
27 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTATATAATTAAATATATAAAA
Found at i:13342 original size:23 final size:21
Alignment explanation
Indices: 13287--13348 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
13277 ACAGAACCTC
13287 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGTATCGATTCCCCTA
* * *
13308 CAGGGGGAATCGGTTCCCCTT
1 CAGGGGGTATCGATTCCCCTA
13329 CAAGGGGGGTATCGATTCCC
1 C-A-GGGGGTATCGATTCCC
13349 TCTGCACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.56
22 1 0.03
23 14 0.41
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (21 bp):
CAGGGGGTATCGATTCCCCTA
Found at i:16890 original size:21 final size:20
Alignment explanation
Indices: 16859--16911 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
16849 TCAAAAGAAG
*
16859 TTTTAAGATCATCAATTTTC
1 TTTTGAGATCATCAATTTTC
*
16879 TTTT--GATTATCAATTTTC
1 TTTTGAGATCATCAATTTTC
16897 TTTTGATGATCATCA
1 TTTTGA-GATCATCA
16912 TTGACCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 17 0.61
20 4 0.14
21 7 0.25
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTGAGATCATCAATTTTC
Found at i:16892 original size:18 final size:18
Alignment explanation
Indices: 16869--16908 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16859 TTTTAAGATC
*
16869 ATCAATTTTCTTTTGATT
1 ATCAATTTTCTTTTGATG
16887 ATCAATTTTCTTTTGATG
1 ATCAATTTTCTTTTGATG
16905 ATCA
1 ATCA
16909 TCATTGACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (18 bp):
ATCAATTTTCTTTTGATG
Found at i:20098 original size:2 final size:2
Alignment explanation
Indices: 20091--20122 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20081 GTCATACTAT
20091 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
20123 ACTCAACATA
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):
TA
Found at i:22959 original size:52 final size:52
Alignment explanation
Indices: 22881--22988 Score: 200
Period size: 52 Copynumber: 2.1 Consensus size: 52
22871 AATCAAATTG
22881 AAAAAATCCTGCTTCATCAGTGGAATAAACAACTCACTGATATATTTCTTCT
1 AAAAAATCCTGCTTCATCAGTGGAATAAACAACTCACTGATATATTTCTTCT
22933 AAAAAATCCTGCTTCAT-ATGTGGAATAAACAACTCACTGATATATTTCTTCT
1 AAAAAATCCTGCTTCATCA-GTGGAATAAACAACTCACTGATATATTTCTTCT
22985 AAAA
1 AAAA
22989 TACTTCTAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 1 0.02
52 54 0.98
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (52 bp):
AAAAAATCCTGCTTCATCAGTGGAATAAACAACTCACTGATATATTTCTTCT
Found at i:22987 original size:26 final size:26
Alignment explanation
Indices: 22906--22987 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
22896 ATCAGTGGAA
22906 TAAACAACTCACTGATATATTTCTTC
1 TAAACAACTCACTGATATATTTCTTC
* * * ****
22932 TAAA-AAATC-CTGCTTCATATGTGGAA
1 TAAACAACTCACTG-AT-ATATTTCTTC
22958 TAAACAACTCACTGATATATTTCTTC
1 TAAACAACTCACTGATATATTTCTTC
22984 TAAA
1 TAAA
22988 ATACTTCTAG
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
24 3 0.08
25 5 0.13
26 22 0.58
27 5 0.13
28 3 0.08
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (26 bp):
TAAACAACTCACTGATATATTTCTTC
Found at i:24589 original size:36 final size:36
Alignment explanation
Indices: 24549--24647 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
24539 TGCTGGACAA
*
24549 TGATACATGAATGTACCAAAGCTGATATGATAACAT
1 TGATACACGAATGTACCAAAGCTGATATGATAACAT
24585 TGATACACGAATGTACCAAAGCTGATATGATAACAT
1 TGATACACGAATGTACCAAAGCTGATATGATAACAT
*
24621 TGATATACGAATGTACCAAAGCTGATA
1 TGATACACGAATGTACCAAAGCTGATA
24648 ATACTCAACT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
TGATACACGAATGTACCAAAGCTGATATGATAACAT
Found at i:26040 original size:2 final size:2
Alignment explanation
Indices: 26033--26065 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26023 AAAATAGGAA
26033 AT 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 AT A
26066 ATAACACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26523 original size:37 final size:37
Alignment explanation
Indices: 26471--26570 Score: 125
Period size: 34 Copynumber: 2.8 Consensus size: 37
26461 GCTTGTGAAC
* * * *
26471 CCTATATTTAAGAGTTTAAATCATAGTAGAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTAT
*
26508 CCTATTTTTAGGAGTTTGAATCCTA--A-AATTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTAT
*
26542 CATATTTTTAGGAGTTTGAATCCTAGTAG
1 CCTATTTTTAGGAGTTTGAATCCTAGTAG
26571 GACGAAAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 31 0.57
35 1 0.02
36 1 0.02
37 21 0.39
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCTAT
Found at i:29710 original size:57 final size:57
Alignment explanation
Indices: 29640--29811 Score: 236
Period size: 57 Copynumber: 3.0 Consensus size: 57
29630 TAGAGCCATA
* * * * * * *
29640 CAACCCCATCACGAATAGAAAGACCCTGAGCACAAAGTAGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGACCCTCAGCACAAAGTCGAAGAACCTACAAGTATT
*
29697 CAACCCCGTCACGAACAGTAAGACCCTCAACACAAAGTCGAAGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGACCCTCAGCACAAAGTCGAAGAACCTACAAGTATT
* * * *
29754 CAACCCCGTCACGAACAGTAAGGCACTCAGCACAAAGCCGATGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGACCCTCAGCACAAAGTCGAAGAACCTACAAGTATT
29811 C
1 C
29812 TTCCTCCAAC
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.39, C:0.30, G:0.17, T:0.14
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGACCCTCAGCACAAAGTCGAAGAACCTACAAGTATT
Found at i:29896 original size:24 final size:24
Alignment explanation
Indices: 29869--29976 Score: 65
Period size: 24 Copynumber: 4.5 Consensus size: 24
29859 TATATCAAAA
* *
29869 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * *
29893 ATCATATCAGAATCCAGGTCATGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * * *
29917 ATCAGATCAGAATCCATGTC-TGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * * * * *
29940 ATTAGATCATAATCCATGTCAGGT
1 ATCAAAACAGAATCCAGGTCAAGT
*
29964 ATCATAACAGAAT
1 ATCAAAACAGAAT
29977 TCAAATCGGA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
23 21 0.30
24 48 0.70
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAAGT
Found at i:29946 original size:23 final size:24
Alignment explanation
Indices: 29886--29976 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
29876 CATAATTCAG
* * *
29886 GTCAAGTATCATATCAGAATCCAG
1 GTCATGTATCAGATCAGAATCCAT
29910 GTCATGTATCAGATCAGAATCCAT
1 GTCATGTATCAGATCAGAATCCAT
* *
29934 GTC-TGTATTAGATCATAATCCAT
1 GTCATGTATCAGATCAGAATCCAT
* * *
29957 GTCAGGTATCATAACAGAAT
1 GTCATGTATCAGATCAGAAT
29977 TCAAATCGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 21 0.38
24 35 0.62
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (24 bp):
GTCATGTATCAGATCAGAATCCAT
Found at i:34334 original size:57 final size:57
Alignment explanation
Indices: 34264--34435 Score: 281
Period size: 57 Copynumber: 3.0 Consensus size: 57
34254 CAGAACCATA
* *
34264 CAACCCCATCACGAACAGTAAGGCCATGAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCCCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
34321 CAACCCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCGAGGTACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCCCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* * *
34378 CAACCCTATCACAAACAGTAAGGCCCTCAGCACAAAGCTGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCCCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
34435 C
1 C
34436 TTCCTCCAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 106 1.00
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (57 bp):
CAACCCCATCACGAACAGTAAGGCCCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:34520 original size:24 final size:24
Alignment explanation
Indices: 34493--34600 Score: 65
Period size: 24 Copynumber: 4.5 Consensus size: 24
34483 TATATCAAAA
* *
34493 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * *
34517 ATCATATCAGAATCCAGGTCATGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * * * *
34541 ATCAGATCAGAATCTATGTC-TGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * * * *
34564 ATTAGATCATAATCCAGGTCAGGT
1 ATCAAAACAGAATCCAGGTCAAGT
*
34588 ATCATAACAGAAT
1 ATCAAAACAGAAT
34601 TCAAATCAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
23 19 0.29
24 47 0.71
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAAGT
Found at i:34570 original size:23 final size:24
Alignment explanation
Indices: 34507--34600 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
34497 AAACATAATT
* *
34507 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCATGTATCAGATCAGAATC
34531 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCATGTATCAGATCAGAATC
* * * *
34555 TATGTC-TGTATTAGATCATAATC
1 CAGGTCATGTATCAGATCAGAATC
* * *
34578 CAGGTCAGGTATCATAACAGAAT
1 CAGGTCATGTATCAGATCAGAAT
34601 TCAAATCAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.34
24 37 0.66
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (24 bp):
CAGGTCATGTATCAGATCAGAATC
Found at i:40696 original size:21 final size:21
Alignment explanation
Indices: 40670--40717 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40660 ATCCTTTGGA
40670 TGTTCT-CTTCATACCGTTGAT
1 TGTTCTCCTT-ATACCGTTGAT
*
40691 TGTTCTCCTTATACCTTTGAT
1 TGTTCTCCTTATACCGTTGAT
*
40712 TCTTCT
1 TGTTCT
40718 TCTTTCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.25, G:0.10, T:0.52
Consensus pattern (21 bp):
TGTTCTCCTTATACCGTTGAT
Found at i:42549 original size:51 final size:51
Alignment explanation
Indices: 42481--42595 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
42471 GTAATTATTG
* * * *
42481 AATAAAATAATAATAAACTAAAAATAATGTTTTGATTTTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
* *
42532 AATAAAATAATAATAAACTACAAATAATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
*
42583 AATAAATTAATAA
1 AATAAAATAATAA
42596 ATCTAATCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
Found at i:43743 original size:23 final size:23
Alignment explanation
Indices: 43685--43743 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
43675 CTCAAAAAAA
43685 AAAATCTATTTTACTTCATCTTTT
1 AAAAT-TATTTTACTTCATCTTTT
* * *
43709 ACAATTACTTTTA-TTGATGTTTT
1 AAAATTA-TTTTACTTCATCTTTT
43732 CAAAATTATTTT
1 -AAAATTATTTT
43744 TAGTAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (23 bp):
AAAATTATTTTACTTCATCTTTT
Done.