Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003089.1 Hibiscus syriacus cultivar Beakdansim tig00006448_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: 59251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1037 original size:47 final size:47
Alignment explanation
Indices: 968--1062 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
958 ACGTGCTAAT
968 ATTTTGCCACAATATCCTTTTATTAATATTTTATTAATGACGGTGAA
1 ATTTTGCCACAATATCCTTTTATTAATATTTTATTAATGACGGTGAA
* *
1015 ATTTTGCCATAGTATCCTTTTATTAATATTTTATTAATGACGGTGAA
1 ATTTTGCCACAATATCCTTTTATTAATATTTTATTAATGACGGTGAA
1062 A
1 A
1063 AATATGCCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (47 bp):
ATTTTGCCACAATATCCTTTTATTAATATTTTATTAATGACGGTGAA
Found at i:1118 original size:11 final size:11
Alignment explanation
Indices: 1098--1131 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1088 AATGCGAAAA
1098 GTAAATGCAAT
1 GTAAATGCAAT
* *
1109 GTAGATGCAAC
1 GTAAATGCAAT
1120 GTAAATGCAAT
1 GTAAATGCAAT
1131 G
1 G
1132 CATGGTGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (11 bp):
GTAAATGCAAT
Found at i:1524 original size:2 final size:2
Alignment explanation
Indices: 1517--1554 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1507 AACTATATTC
* *
1517 AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1555 GCTATAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4672 original size:15 final size:15
Alignment explanation
Indices: 4654--4686 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4644 CAAAGTAGTG
*
4654 TAAAAAAAAGAAAGA
1 TAAAAAAAAGAAAAA
4669 TAAAAAAAAGAAAAA
1 TAAAAAAAAGAAAAA
4684 TAA
1 TAA
4687 TTTCTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
TAAAAAAAAGAAAAA
Found at i:22043 original size:17 final size:18
Alignment explanation
Indices: 22021--22056 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
22011 ACCTTTAAAA
*
22021 TGCTTTTGTTT-TTGTTT
1 TGCTTTTATTTGTTGTTT
22038 TGCTTTTATTTGTTGTTT
1 TGCTTTTATTTGTTGTTT
22056 T
1 T
22057 CAAAACTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.03, C:0.06, G:0.17, T:0.75
Consensus pattern (18 bp):
TGCTTTTATTTGTTGTTT
Found at i:22585 original size:3 final size:3
Alignment explanation
Indices: 22579--22614 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
22569 AAGTATTAAT
22579 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22615 GGGATGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23265 original size:18 final size:18
Alignment explanation
Indices: 23242--23286 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
23232 AATTATTTTT
*
23242 TATTTATATTATATAAAA
1 TATTTATATTACATAAAA
23260 TATTTATA-T-CATAAAA
1 TATTTATATTACATAAAA
*
23276 TATTAATATTA
1 TATTTATATTA
23287 ATATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.57
17 2 0.09
18 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTATATTACATAAAA
Found at i:29717 original size:21 final size:21
Alignment explanation
Indices: 29693--29732 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29683 AAGTATATTA
*
29693 AGGGGAAGAGTATCTATACCC
1 AGGGGAAGAGTATCGATACCC
* *
29714 AGGGTAGGAGTATCGATAC
1 AGGGGAAGAGTATCGATAC
29733 TCGTGTAATT
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:0.33, C:0.15, G:0.33, T:0.20
Consensus pattern (21 bp):
AGGGGAAGAGTATCGATACCC
Found at i:30462 original size:14 final size:14
Alignment explanation
Indices: 30443--30470 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30433 GATGTGTTCC
30443 AATGTTCATAACCA
1 AATGTTCATAACCA
30457 AATGTTCATAACCA
1 AATGTTCATAACCA
30471 TACTTGCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AATGTTCATAACCA
Found at i:35169 original size:2 final size:2
Alignment explanation
Indices: 35162--35195 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35152 TGTTAATGCA
35162 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
35196 TATGGCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40593 original size:29 final size:29
Alignment explanation
Indices: 40527--40686 Score: 196
Period size: 29 Copynumber: 5.5 Consensus size: 29
40517 CCCGACCCGG
*
40527 TGATATTTTGGTAATTATTTTTAAAAA-A
1 TGATATTTTGGTAATTATTTTGAAAAAGA
* *
40555 TGATAGTTTGGTAACTATTTTGAAAAAGA
1 TGATATTTTGGTAATTATTTTGAAAAAGA
*
40584 TGATATTTTGGTAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAAAGA
* * *
40613 TGATATTTTGATATTTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTGAAAAAGA
* * *
40642 TGATATTTTGGTAATTTTTTTTAAAAATA
1 TGATATTTTGGTAATTATTTTGAAAAAGA
* *
40671 GTGCTATTTTCGTAAT
1 -TGATATTTTGGTAAT
40687 AATTGTTGTG
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 24 0.21
29 77 0.68
30 13 0.11
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.47
Consensus pattern (29 bp):
TGATATTTTGGTAATTATTTTGAAAAAGA
Found at i:40621 original size:17 final size:17
Alignment explanation
Indices: 40599--40651 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
40589 TTTTGGTAAT
40599 TATTTTGAAAAAGGTGA
1 TATTTTGAAAAAGGTGA
* *
40616 TATTTTG--ATA--T-T
1 TATTTTGAAAAAGGTGA
40628 TATTTTGAAAAAGGTGA
1 TATTTTGAAAAAGGTGA
40645 TATTTTG
1 TATTTTG
40652 GTAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.26
13 1 0.04
14 2 0.07
15 2 0.07
16 1 0.04
17 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (17 bp):
TATTTTGAAAAAGGTGA
Found at i:41649 original size:32 final size:31
Alignment explanation
Indices: 41576--41651 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
41566 TAATGTGACA
* *
41576 CTTAGGTAGGCTCTACGGCCCTGAGATCATT
1 CTTAGGTAGGCCCTACGGCCCTAAGATCATT
** * **
41607 CTCGGGTAGGCCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCCTACGGCCCTAAGAT-CATT
41639 CTTAGGTAGGCCC
1 CTTAGGTAGGCCC
41652 CATAGCCCCG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (31 bp):
CTTAGGTAGGCCCTACGGCCCTAAGATCATT
Found at i:41767 original size:25 final size:25
Alignment explanation
Indices: 41715--41767 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
41705 AGGGTAACTC
* *
41715 TTTTATGAGATTTATTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
41740 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
41765 TTT
1 TTT
41768 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:45905 original size:5 final size:5
Alignment explanation
Indices: 45854--45918 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
45844 TTTGGGTCTG
* * *
45854 TAATGA TAATT TAATA AAAT- TAATAA TAATA TGAATAA TATTA TAATA
1 TAAT-A TAATA TAATA TAATA TAAT-A TAATA T-AAT-A TAATA TAATA
45902 TAATA TAATA TAA-A TAA
1 TAATA TAATA TAATA TAA
45919 AGACTCAGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 7 0.14
5 27 0.55
6 13 0.27
7 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:51163 original size:55 final size:55
Alignment explanation
Indices: 51098--51215 Score: 218
Period size: 55 Copynumber: 2.1 Consensus size: 55
51088 ATATACTTGT
51098 TATTCTCTATTACCTTATTTAACTAACGATAATCCATGCATAATTGCATATACCCA
1 TATT-TCTATTACCTTATTTAACTAACGATAATCCATGCATAATTGCATATACCCA
*
51154 TATTTCTATTACCTTATTTAACTGACGATAATCCATGCATAATTGCATATACCCA
1 TATTTCTATTACCTTATTTAACTAACGATAATCCATGCATAATTGCATATACCCA
51209 TATTTCT
1 TATTTCT
51216 TTTTCACAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 57 0.93
56 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (55 bp):
TATTTCTATTACCTTATTTAACTAACGATAATCCATGCATAATTGCATATACCCA
Found at i:53869 original size:16 final size:16
Alignment explanation
Indices: 53848--53878 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53838 TATGTATGTG
53848 TATGTGTATAAATATA
1 TATGTGTATAAATATA
*
53864 TATGTGTATATATAT
1 TATGTGTATAAATAT
53879 CAACATGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (16 bp):
TATGTGTATAAATATA
Found at i:58264 original size:22 final size:22
Alignment explanation
Indices: 58211--58271 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
58201 GAATTTTTTA
**
58211 GTCAAAGTCAATGGTCAGACCT
1 GTCAAAGTCAATGGTTTGACCT
*
58233 GTC-AAGTCAACGGTTTGACCT
1 GTCAAAGTCAATGGTTTGACCT
58254 GTCAAAGTCAATGGTTTG
1 GTCAAAGTCAATGGTTTG
58272 GTTCGGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (22 bp):
GTCAAAGTCAATGGTTTGACCT
Done.