Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000328.1 Hibiscus syriacus cultivar Beakdansim tig00000611_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: 82400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:820 original size:2 final size:2
Alignment explanation
Indices: 813--841 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
803 TGAGTATTAA
813 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
842 TTGTCAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:832 original size:13 final size:13
Alignment explanation
Indices: 814--839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
804 GAGTATTAAA
814 TATATATATATAT
1 TATATATATATAT
827 TATATATATATAT
1 TATATATATATAT
840 ATTTGTCAAC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:833 original size:15 final size:15
Alignment explanation
Indices: 813--842 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
803 TGAGTATTAA
813 ATATATATATATATT
1 ATATATATATATATT
828 ATATATATATATATT
1 ATATATATATATATT
843 TGTCAACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:833 original size:17 final size:17
Alignment explanation
Indices: 807--841 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
797 TAAGTGTGAG
807 TATTAAATATATATATA
1 TATTAAATATATATATA
*
824 TATTATATATATATATA
1 TATTAAATATATATATA
841 T
1 T
842 TTGTCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAATATATATATA
Found at i:9976 original size:36 final size:37
Alignment explanation
Indices: 9929--10001 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
9919 AATGTGTCAG
9929 TTTTGATCCAGAAAACACCCTAC-AAGTGACCTCCCA
1 TTTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
*
9965 TTTTGATCCAGAAAACACCCTACAAAGTGTCCTCCCA
1 TTTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
10002 AAATGGACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.23
Consensus pattern (37 bp):
TTTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
Found at i:18378 original size:30 final size:30
Alignment explanation
Indices: 18342--18400 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18332 TTATAATTAT
18342 ATATATT-TA-ATTAATTGATTAATTTAAATA
1 ATATATTGTATATTAATTGATT--TTTAAATA
*
18372 ATATATTGTATTTTAATTGATTTTTAAAT
1 ATATATTGTATATTAATTGATTTTTAAAT
18401 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 14 0.54
31 2 0.08
32 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
ATATATTGTATATTAATTGATTTTTAAATA
Found at i:28660 original size:18 final size:18
Alignment explanation
Indices: 28637--28684 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
28627 AAATTGTCTT
* *
28637 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
28655 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
28672 TATTTATATATTT
1 TA-TTATATATTT
28685 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:28742 original size:32 final size:31
Alignment explanation
Indices: 28657--28742 Score: 84
Period size: 37 Copynumber: 2.6 Consensus size: 31
28647 TTGTATAATA
28657 TTAT-AAATTATAAAATATTTATATATTTTCT
1 TTATAAAATTA-AAAATATTTATATATTTTCT
* *
28688 TTAAAAAATTAAATTCATAATATTTATATAATTTTTT
1 TTATAAAATT-AA---A-AATATTTATAT-ATTTTCT
28725 TTATAAAATTAAAAATAT
1 TTATAAAATTAAAAATAT
28743 AAAACAGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
31 3 0.07
32 11 0.24
33 2 0.04
35 1 0.02
36 13 0.29
37 15 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATAAAATTAAAAATATTTATATATTTTCT
Found at i:29229 original size:21 final size:21
Alignment explanation
Indices: 29191--29230 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29181 AAAAAAATAT
*
29191 TTAAAAAATTATTATTTTTAC
1 TTAAAAAATTAATATTTTTAC
* *
29212 TTAAAATATTAATGTTTTT
1 TTAAAAAATTAATATTTTT
29231 TTTTAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAAAAAATTAATATTTTTAC
Found at i:31246 original size:21 final size:21
Alignment explanation
Indices: 31221--31263 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31211 TTTTTATTGT
*
31221 AATTTATACAAAATAAAATAA
1 AATTTAAACAAAATAAAATAA
* *
31242 AATTTAAACATAATATAATAA
1 AATTTAAACAAAATAAAATAA
31263 A
1 A
31264 TTCAAGTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTTAAACAAAATAAAATAA
Found at i:31280 original size:15 final size:17
Alignment explanation
Indices: 31260--31291 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
31250 CATAATATAA
31260 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
31275 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
31292 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:31329 original size:21 final size:21
Alignment explanation
Indices: 31287--31329 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31277 AATTGCAAGA
**
31287 TAGATAAAAATACATTGAAAT
1 TAGATAAAAATACATACAAAT
* *
31308 TAGATAAATATACATACTAAT
1 TAGATAAAAATACATACAAAT
31329 T
1 T
31330 TTTTGAAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
TAGATAAAAATACATACAAAT
Found at i:31838 original size:3 final size:3
Alignment explanation
Indices: 31830--31872 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
31820 TGGCCACGCT
31830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31873 AATTTCTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:36131 original size:24 final size:26
Alignment explanation
Indices: 36104--36169 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 26
36094 ATATATATAT
*
36104 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
36128 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
36152 ATATATATATATATATAT
1 ATA-ATATAAATATATAT
36170 ATATACCCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 18 0.51
25 1 0.03
26 1 0.03
27 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:36146 original size:19 final size:19
Alignment explanation
Indices: 36122--36161 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
36112 AATAAATTTA
36122 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
36141 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
36160 AT
1 AT
36162 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:38112 original size:253 final size:253
Alignment explanation
Indices: 37664--38166 Score: 934
Period size: 253 Copynumber: 2.0 Consensus size: 253
37654 GCTCAACACA
*
37664 GTACTGCATATGTTCTTTTAGTTTTCGCCTGCAGTTAATAGCACGTTATATATGCCACAATAATA
1 GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
* *
37729 GGAAACAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAGATACCCAAATTCCT
66 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
*
37794 TGTTCATGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
131 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
* *
37859 TTGACACGCTCCAGAGATGCAATAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
196 TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
*
37917 GTACTGCATATGTTCTTTTAGTTTTGGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
1 GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
37982 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
66 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
38047 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
131 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
*
38112 TTGGCACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAA
196 TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAA
38167 CAACACAAAA
Statistics
Matches: 242, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
253 242 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (253 bp):
GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
Found at i:39163 original size:11 final size:11
Alignment explanation
Indices: 39130--39164 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
39120 TACTGTTGGC
39130 TTTTTGTTTTT
1 TTTTTGTTTTT
*
39141 CTTTTGTTTTT
1 TTTTTGTTTTT
39152 TTTTTGTTTTT
1 TTTTTGTTTTT
39163 TT
1 TT
39165 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:39928 original size:2 final size:2
Alignment explanation
Indices: 39921--39983 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
39911 GCAATTTTAC
39921 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
39963 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
39984 ACCACAAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46404 original size:2 final size:2
Alignment explanation
Indices: 46397--46427 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46387 TAATTATTAT
46397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46428 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56994 original size:18 final size:18
Alignment explanation
Indices: 56961--56995 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56951 AGATAACATA
56961 ATAATTAATAAAATTAAT
1 ATAATTAATAAAATTAAT
56979 ATAA-TAATAAATATTAA
1 ATAATTAATAAA-ATTAA
56996 AAAGAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATTAATAAAATTAAT
Found at i:57480 original size:15 final size:15
Alignment explanation
Indices: 57460--57493 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57450 GAATAAACTG
57460 TTTTCTTTC-TCTTTT
1 TTTTCTTTCAT-TTTT
57475 TTTTCTTTCATTTTT
1 TTTTCTTTCATTTTT
57490 TTTT
1 TTTT
57494 TTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTCATTTTT
Found at i:57500 original size:4 final size:4
Alignment explanation
Indices: 57493--57575 Score: 114
Period size: 4 Copynumber: 21.0 Consensus size: 4
57483 CATTTTTTTT
* *
57493 TTTA TTTA TTTA -TTA TTTA TTTA TTTA CTTA TTTA ATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
57540 TTTA CTTA CTTA TTTA TTTA TTTA CTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
57576 CATTGAATGG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
3 3 0.04
4 67 0.96
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:74847 original size:2 final size:2
Alignment explanation
Indices: 74840--74898 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
74830 TTAACATTCC
74840 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
74882 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
74899 CCCTTCCACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.