Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008266.1 Hibiscus syriacus cultivar Beakdansim tig00110921_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: 58340
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2169 original size:19 final size:20
Alignment explanation
Indices: 2145--2195 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2135 CGGCCAAGAG
* *
2145 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2164 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2184 CATGTATTTTCA
1 CATGTATTTTCA
2196 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3126 original size:13 final size:13
Alignment explanation
Indices: 3108--3174 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
3098 TTGAAGTGAA
**
3108 GGTGATGGACTAT
1 GGTGATGGAAGAT
3121 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
3134 GGTGATGTTATA-
1 GGTGATGGAAGAT
*
3146 GGTG-T-GAAAAT
1 GGTGATGGAAGAT
3157 GGTGATGGAAGAT
1 GGTGATGGAAGAT
3170 GGTGA
1 GGTGA
3175 AGTTTAGGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 5 0.12
13 30 0.71
ACGTcount: A:0.28, C:0.01, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:3541 original size:19 final size:19
Alignment explanation
Indices: 3517--3566 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3507 GAAACCCCTT
3517 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
3536 TGAAAATTCATGATTTTAA
1 TGAAAATACATGATTTTAA
*
3555 TGAAGATACATG
1 TGAAAATACATG
3567 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:16301 original size:22 final size:22
Alignment explanation
Indices: 16263--16306 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
16253 AAAGTGCTAC
16263 AACAAAAAGTAACAAGAAGAAGA
1 AACAAAAAGTAACAAGAA-AAGA
16286 AACAAAAGAG-AA-AAGAAAAGA
1 AACAAAA-AGTAACAAGAAAAGA
16307 CTCATACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 9 0.45
24 2 0.10
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.02
Consensus pattern (22 bp):
AACAAAAAGTAACAAGAAAAGA
Found at i:21769 original size:15 final size:16
Alignment explanation
Indices: 21746--21777 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
21736 CTTGATGAAC
21746 TCAAGCTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
21762 TCAA-CTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
21777 T
1 T
21778 GGTCTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (16 bp):
TCAAGCTAGTTAGCTT
Found at i:22328 original size:37 final size:37
Alignment explanation
Indices: 22278--22353 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
22268 AAACATAGCA
22278 TGAACATGACATGGGCTAATAAATGAATGATACATGC
1 TGAACATGACATGGGCTAATAAATGAATGATACATGC
22315 TGAACATGACATGGGCTAATAAATGAATGATACATGC
1 TGAACATGACATGGGCTAATAAATGAATGATACATGC
22352 TG
1 TG
22354 CCATGATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (37 bp):
TGAACATGACATGGGCTAATAAATGAATGATACATGC
Found at i:24706 original size:13 final size:12
Alignment explanation
Indices: 24682--24715 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
24672 TTTCTTTGAA
*
24682 TTTTTGTTTTTC
1 TTTTTCTTTTTC
24694 TTTATTCTTTTTC
1 TTT-TTCTTTTTC
24707 TTTTTCTTT
1 TTTTTCTTT
24716 CTTTTGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:24707 original size:6 final size:6
Alignment explanation
Indices: 24682--24715 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
24672 TTTCTTTGAA
*
24682 TTTTTG TTTTTC TTTATTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTT
24716 CTTTTGCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:24781 original size:12 final size:11
Alignment explanation
Indices: 24746--24793 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
24736 TGTAGGAGTC
24746 TTTTCTTTCTGTT
1 TTTTCTTT-T-TT
*
24759 TTTTATTTTTT
1 TTTTCTTTTTT
24770 TTTTCTTGTTTT
1 TTTTCTT-TTTT
*
24782 TTTTCTCTTTT
1 TTTTCTTTTTT
24793 T
1 T
24794 GTTACTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 13 0.42
12 11 0.35
13 7 0.23
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:25655 original size:19 final size:20
Alignment explanation
Indices: 25605--25647 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
25595 GAAACCCCTT
25605 TGAAAATACATGATATTTAA
1 TGAAAATACATGATATTTAA
25625 TGAAAATACATGAT-TTTAA
1 TGAAAATACATGATATTTAA
25644 TGAA
1 TGAA
25648 GTTACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATATTTAA
Found at i:28734 original size:17 final size:17
Alignment explanation
Indices: 28714--28755 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28704 AAGATATGGT
*
28714 AATGAAATAATTAAAAA
1 AATGAAATAACTAAAAA
* *
28731 AATGAAA-GACTAAAGA
1 AATGAAATAACTAAAAA
28747 AATGAAATA
1 AATGAAATA
28756 GTAAGAAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (17 bp):
AATGAAATAACTAAAAA
Found at i:29024 original size:20 final size:19
Alignment explanation
Indices: 28972--29024 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
28962 TGTAGGAGTC
*
28972 TTTTCTTTCTATTTTTTTAT
1 TTTTCTTACT-TTTTTTTAT
**
28992 TTTTCTTGTTTTTTTTCTAT
1 TTTTCTTACTTTTTTT-TAT
*
29012 TTTTGTTACTTTT
1 TTTTCTTACTTTT
29025 GTTGCAGTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.08, C:0.09, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTCTTACTTTTTTTTAT
Found at i:32468 original size:17 final size:17
Alignment explanation
Indices: 32446--32481 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
32436 ACCTATAGTT
*
32446 CACATCTTTATAATATG
1 CACATCATTATAATATG
*
32463 CACATCATTATATTATG
1 CACATCATTATAATATG
32480 CA
1 CA
32482 TTATAGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:33309 original size:19 final size:21
Alignment explanation
Indices: 33285--33336 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
33275 CGGCCAAGAG
* *
33285 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
33304 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
33325 CATGTATTTTCA
1 CATGTATTTTCA
33337 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:37406 original size:19 final size:21
Alignment explanation
Indices: 37382--37433 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
37372 CGGCCAAGAG
* *
37382 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
37401 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
37422 CATGTATTTTCA
1 CATGTATTTTCA
37434 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:38500 original size:13 final size:13
Alignment explanation
Indices: 38435--38503 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
38425 CTGGCGTGAA
*
38435 GGTGATGGACTAT
1 GGTGATGGAATAT
*
38448 GGTGATGGAAGAT
1 GGTGATGGAATAT
**
38461 GGTGATGTTATA-
1 GGTGATGGAATAT
* *
38473 GG-CAT-GAAAAT
1 GGTGATGGAATAT
38484 GGTGATGGAATAT
1 GGTGATGGAATAT
38497 GGTGATG
1 GGTGATG
38504 TTTAGTATCT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.29, C:0.03, G:0.39, T:0.29
Consensus pattern (13 bp):
GGTGATGGAATAT
Found at i:41651 original size:13 final size:13
Alignment explanation
Indices: 41633--41701 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
41623 CTGGCGTGAA
**
41633 GGTGATGGACTAT
1 GGTGATGGAAGAT
41646 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
41659 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
41671 GGCG-T-GAAAAT
1 GGTGATGGAAGAT
41682 GGTGATGGAAGAT
1 GGTGATGGAAGAT
41695 GGTGATG
1 GGTGATG
41702 TTTAGTATCT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:52336 original size:43 final size:46
Alignment explanation
Indices: 52236--52340 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 46
52226 AGGATCAGAT
* *
52236 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACAATAGTTTAGTTA
52285 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-AT-GTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTAG-TTA
52328 TTATTATTTTATT
1 TTATTATTTTATT
52341 CTTTAATATT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 5 0.09
43 18 0.34
44 9 0.17
48 1 0.02
49 20 0.38
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACAATAGTTTAGTTA
Found at i:53104 original size:10 final size:10
Alignment explanation
Indices: 53089--53168 Score: 54
Period size: 10 Copynumber: 7.5 Consensus size: 10
53079 ATTTTTTCAA
53089 AAAAAAAAAC
1 AAAAAAAAAC
*
53099 AAAAAAAGGA-
1 AAAAAAA-AAC
**
53109 AAAAAAAAGG
1 AAAAAAAAAC
*
53119 AAAAAAAAGGC
1 AAAAAAAA-AC
*
53130 AAAAAAAGGCAAA
1 AAAAAAA---AAC
53143 ACAAAAAAAAC
1 A-AAAAAAAAC
53154 AAAAAAAAAC
1 AAAAAAAAAC
53164 AAAAA
1 AAAAA
53169 TACCAAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 36 0.64
11 12 0.21
13 1 0.02
14 7 0.12
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:53176 original size:19 final size:19
Alignment explanation
Indices: 53089--53168 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 19
53079 ATTTTTTCAA
**
53089 AAAAAAAAACAAAAAAAGG
1 AAAAAAAAACAAAAAAAAC
*
53108 AAAAAAAAAGGAAAAAAAAGGC
1 AAAAAAAAA-CAAAAAAAA--C
53130 AAAAAAAGGCAAAACAAAAAAAAC
1 --AAAAA---AAAACAAAAAAAAC
53154 AAAAAAAAACAAAAA
1 AAAAAAAAACAAAAA
53169 TACCAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
19 19 0.39
20 7 0.14
22 5 0.10
24 6 0.12
26 8 0.16
27 4 0.08
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAC
Found at i:57315 original size:22 final size:23
Alignment explanation
Indices: 57280--57322 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
57270 GCAATTCATT
*
57280 ATCTTTTTCTTTATCTTGTTTTA
1 ATCTTATTCTTTATCTTGTTTTA
57303 ATCTTATT-TTTATCTTGTTT
1 ATCTTATTCTTTATCTTGTTT
57323 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTATTCTTTATCTTGTTTTA
Found at i:57655 original size:11 final size:11
Alignment explanation
Indices: 57639--57690 Score: 97
Period size: 11 Copynumber: 4.8 Consensus size: 11
57629 GCTATTTTTT
57639 AAAAAAAAAAC
1 AAAAAAAAAAC
57650 AAAAAAAAAAC
1 AAAAAAAAAAC
57661 -AAAAAAAAAC
1 AAAAAAAAAAC
57671 AAAAAAAAAAC
1 AAAAAAAAAAC
57682 AAAAAAAAA
1 AAAAAAAAA
57691 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.25
11 30 0.75
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:57697 original size:11 final size:11
Alignment explanation
Indices: 57639--57697 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
57629 GCTATTTTTT
*
57639 AAAAAAAAAAC
1 AAAAAAAAACC
*
57650 AAAAAAAAAAC
1 AAAAAAAAACC
57661 AAAAAAAAA-C
1 AAAAAAAAACC
*
57671 AAAAAAAAAAC
1 AAAAAAAAACC
57682 AAAAAAAAAGCC
1 AAAAAAAAA-CC
57694 AAAA
1 AAAA
57698 TTTCAAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
10 10 0.22
11 30 0.67
12 5 0.11
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:57697 original size:21 final size:21
Alignment explanation
Indices: 57640--57690 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
57630 CTATTTTTTA
57640 AAAAAAAAACAAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAAC
57661 AAAAAAAAACAAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAAC
57682 AAAAAAAAA
1 AAAAAAAAA
57691 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAAAC
Found at i:57709 original size:1 final size:1
Alignment explanation
Indices: 57639--57690 Score: 68
Period size: 1 Copynumber: 52.0 Consensus size: 1
57629 GCTATTTTTT
* * * *
57639 AAAAAAAAAACAAAAAAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
57691 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.