Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004421.1 Hibiscus syriacus cultivar Beakdansim tig00009694_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: 79229
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:677 original size:23 final size:19
Alignment explanation
Indices: 651--702 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 19
641 AACATGATAA
651 ATCGATGCATATTCAAAGGATGT
1 ATCGATGCATATT--AA-G-TGT
*
674 ATCGATGCATGTTAAGTGT
1 ATCGATGCATATTAAGTGT
693 ATCGATGCAT
1 ATCGATGCAT
703 GAAACACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 2 0.07
23 12 0.43
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (19 bp):
ATCGATGCATATTAAGTGT
Found at i:6537 original size:64 final size:63
Alignment explanation
Indices: 6469--6643 Score: 185
Period size: 64 Copynumber: 2.7 Consensus size: 63
6459 ACACTTAGTA
* * * *
6469 CATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATA-GCATGAGT
1 CATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA--AGT
6532 G
63 G
* * * *
6533 CATCGGTGCAT-TGCTTGTGCATCGATGCTTGAAATGCATTTGATGTTTTAATAAAACCCAAGTG
1 CATCGGTGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTG
* *
6597 CATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 CATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
6644 CAATTTATTC
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
64 85 0.92
65 3 0.03
66 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (63 bp):
CATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTG
Found at i:6662 original size:64 final size:64
Alignment explanation
Indices: 6485--6667 Score: 167
Period size: 64 Copynumber: 2.9 Consensus size: 64
6475 TGCACCAAGT
* * * * * * ***
6485 GTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGC-ATGAGTGCATCGGTGCATTGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACCAATG-GTGCATCGATGCATAGAGA
* * * *
6549 GTGCATCGATGCTTGAAATGCATTTGATGTTTTAATAAAACCCAA--GTGCATCGATGCATAGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAT-ATA-CCAATGGTGCATCGATGCATAGAG
6612 A
64 A
* *
6613 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCAATGGTGCATCGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-CCAATGGTGCATCGAT
6668 ACATCGGTGC
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
62 4 0.04
63 5 0.05
64 82 0.86
65 2 0.02
66 1 0.01
67 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATACCAATGGTGCATCGATGCATAGAGA
Found at i:9588 original size:16 final size:17
Alignment explanation
Indices: 9557--9590 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9547 CGTATCGTCG
9557 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
9574 ACAAAATTT-ACTATTC
1 ACAAAATTTCACTATTC
9590 A
1 A
9591 TGTGAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:10037 original size:21 final size:21
Alignment explanation
Indices: 10013--10073 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
10003 AAACATCTAC
10013 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
10034 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
10049 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
10070 CAAA
1 CAAA
10074 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:10050 original size:36 final size:36
Alignment explanation
Indices: 9995--10074 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
9985 CTCATTCCTA
*
9995 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
*
10030 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
10066 TTTTCAAAG
1 TTTTCAAAG
10075 TTGGTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 5 0.12
36 37 0.88
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:32528 original size:21 final size:21
Alignment explanation
Indices: 32495--32539 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
32485 AAAGTATGTG
*
32495 TTTATCACCTAAACTATCAGT
1 TTTATCACCTAAACTATCAAT
* * *
32516 TTTATTACTTAAACTTTCAAT
1 TTTATCACCTAAACTATCAAT
32537 TTT
1 TTT
32540 TTTCAAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATCACCTAAACTATCAAT
Found at i:43771 original size:37 final size:38
Alignment explanation
Indices: 43692--43778 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
43682 TTCACCCTAA
43692 ACCCGAACCCGACCAGAATATCACACTTAAAAAAATCCG
1 ACCCG-ACCCGACCAGAATATCACACTTAAAAAAATCCG
* *
43731 ACCCGACTCGACCCGAATATCACACTT-AAAAAA-CCTG
1 ACCCGACCCGACCAGAATATCACACTTAAAAAAATCC-G
43768 ACCCGACCCGA
1 ACCCGACCCGA
43779 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 2 0.05
37 17 0.39
38 20 0.45
39 5 0.11
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.13
Consensus pattern (38 bp):
ACCCGACCCGACCAGAATATCACACTTAAAAAAATCCG
Found at i:43991 original size:37 final size:37
Alignment explanation
Indices: 43941--44011 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
43931 CCTAAACCCG
43941 AACCCGACCCGACCCGAATATCACACTTAAAAAAAAC
1 AACCCGACCCGACCCGAATATCACACTTAAAAAAAAC
* *
43978 AACCCGACTCGACCCGAATTTCACACTTAAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAA
44012 CCCGACCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (37 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAAAAC
Found at i:44009 original size:248 final size:239
Alignment explanation
Indices: 43649--44211 Score: 766
Period size: 248 Copynumber: 2.3 Consensus size: 239
43639 ATATAAGGTA
43649 AAATTATATAT-TTTTTCGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGACCAGAATAT
1 AAATTATATATATTTTT-GGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGACCAGAATAT
* *
43713 CACACTTAAAAAAATCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCTGACCCGACCCG
65 CACACTTAAAAAAATACAACCCGACTCGACCCGAATATCACACTT-AAAAA----ACCCGACCCG
* *
43778 AACAAAATAAAGTTTCAT-CCGACCCGAATATATAAATTAAAAATCCGACCCGACCCGAAATAAT
125 AACAAAATAAAGTTTCATCCCGACCCGAATATATAAACTAAAAATCCAACCCGACCCGAAATAAT
43842 AAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCC
190 AAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCC
43892 AAATTATATATATTTTTGGGTCGGTCCGGGTTTTTTCACCCTAAACCCGAACCCGACCCGACCCG
1 AAATTATATATATTTTTGGGTCGGTCC-GGTTTTTTCACCCTAAACCCGAACCCGA-CC-A---G
* *
43957 AATATCACACTTAAAAAAA-ACAACCCGACTCGACCCGAATTTCACACTTAAAAAACCCGACCTG
60 AATATCACACTTAAAAAAATACAACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCG
* * *
44021 AACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAACTAGAAATCCAACTCGACCCGAAA
125 AACAAAATAAAGTTTCAT----CCCGACCCGAATATATAAACTAAAAATCCAACCCGACCCGAAA
* * *
44086 TAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCT
186 TAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCC
* ** * *
44140 GAATTATATATATTTTCAGGTCAGTCCCGTTTTTTCACCCTAAACCCG-A--C--CC-GAATATC
1 AAATTATATATATTTTTGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGACCAGAATATC
44199 ACACTTAAAAAAA
66 ACACTTAAAAAAA
44212 CCCGATCCGA
Statistics
Matches: 291, Mismatches: 17, Indels: 31
0.86 0.05 0.09
Matches are distributed among these distances:
236 20 0.07
241 2 0.01
243 48 0.16
244 34 0.12
245 2 0.01
246 2 0.01
247 25 0.09
248 138 0.47
249 20 0.07
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (239 bp):
AAATTATATATATTTTTGGGTCGGTCCGGTTTTTTCACCCTAAACCCGAACCCGACCAGAATATC
ACACTTAAAAAAATACAACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAA
ATAAAGTTTCATCCCGACCCGAATATATAAACTAAAAATCCAACCCGACCCGAAATAATAAAAAA
ATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCC
Found at i:51326 original size:29 final size:29
Alignment explanation
Indices: 51294--51370 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
51284 AATTCGACCT
51294 TTGAATTTTAGATAAAATACAATTTAACC
1 TTGAATTTTAGATAAAATACAATTTAACC
51323 TTGAATTTTAGATAAAATACAATTTAACC
1 TTGAATTTTAGATAAAATACAATTTAACC
*
51352 TTGAATTTTAGATAGAATA
1 TTGAATTTTAGATAAAATA
51371 TCATACTAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (29 bp):
TTGAATTTTAGATAAAATACAATTTAACC
Found at i:61741 original size:16 final size:16
Alignment explanation
Indices: 61720--61753 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
61710 CGACTCAGGG
61720 CAGCATGTAGGAGCAT
1 CAGCATGTAGGAGCAT
*
61736 CAGCATGTAGGGGCAT
1 CAGCATGTAGGAGCAT
61752 CA
1 CA
61754 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.18
Consensus pattern (16 bp):
CAGCATGTAGGAGCAT
Found at i:69477 original size:14 final size:14
Alignment explanation
Indices: 69455--69498 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 14
69445 TAACAGACTT
*
69455 GTCTATTTTCTACA
1 GTCTGTTTTCTACA
69469 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
69485 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
69499 TGGTATCAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:69487 original size:16 final size:16
Alignment explanation
Indices: 69466--69498 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
69456 TCTATTTTCT
69466 ACAGTCTGTTTTCTAC
1 ACAGTCTGTTTTCTAC
69482 ACAGTCTGTTTTCTAC
1 ACAGTCTGTTTTCTAC
69498 A
1 A
69499 TGGTATCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (16 bp):
ACAGTCTGTTTTCTAC
Found at i:69660 original size:14 final size:15
Alignment explanation
Indices: 69635--69672 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
69625 TCTCAATCTG
* *
69635 ATTTTCAGATTTCAG
1 ATTTTCAAATTTCAA
69650 A-TTTCAAATTTCAA
1 ATTTTCAAATTTCAA
69664 ATTTTCAAA
1 ATTTTCAAA
69673 GCAACAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (15 bp):
ATTTTCAAATTTCAA
Found at i:75668 original size:20 final size:20
Alignment explanation
Indices: 75630--75669 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
75620 CTTTTTATTA
* *
75630 ATAAGTGATAGTATCTGTTT
1 ATAAGTGATAGCATATGTTT
*
75650 ATAAGTGGTAGCATATGTTT
1 ATAAGTGATAGCATATGTTT
75670 CCCATGACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (20 bp):
ATAAGTGATAGCATATGTTT
Done.