Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000615.1 Hibiscus syriacus cultivar Beakdansim tig00001193_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: 61110
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1310 original size:30 final size:30
Alignment explanation
Indices: 1276--1332 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1266 AAAAAAACAT
* *
1276 AAAAGATAAAATAAGATAAC-AAAGAAAAAG
1 AAAAGA-AAAAGAAAATAACAAAAGAAAAAG
1306 AAAAGAAAAAGAAAATAACAAAAGAAA
1 AAAAGAAAAAGAAAATAACAAAAGAAA
1333 TTAAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.07
Consensus pattern (30 bp):
AAAAGAAAAAGAAAATAACAAAAGAAAAAG
Found at i:1312 original size:11 final size:11
Alignment explanation
Indices: 1296--1320 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1286 ATAAGATAAC
1296 AAAGAAAAAGA
1 AAAGAAAAAGA
1307 AAAGAAAAAGA
1 AAAGAAAAAGA
1318 AAA
1 AAA
1321 TAACAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:1338 original size:29 final size:30
Alignment explanation
Indices: 1262--1332 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1252 TAGAAATTAC
* *
1262 AATAA-AAA-AAACATAAAAGATAAAATAA
1 AATAACAAAGAAAAATAAAAGATAAAAGAA
* *
1290 GATAACAAAGAAAAAGAAAAGA-AAAAGAA
1 AATAACAAAGAAAAATAAAAGATAAAAGAA
1319 AATAACAAAAGAAA
1 AATAAC-AAAGAAA
1333 TTAAAAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 14 0.40
30 17 0.49
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (30 bp):
AATAACAAAGAAAAATAAAAGATAAAAGAA
Found at i:3268 original size:104 final size:105
Alignment explanation
Indices: 2980--3325 Score: 473
Period size: 105 Copynumber: 3.3 Consensus size: 105
2970 AAGAGTGTTG
* * *
2980 TACGTGACAACATTAGGCTCAATGTCTTGCTTTCTCATTGTGTCGACAATATCTTCAGCTTCAGA
1 TACGTGACAACATTAGGCTCAATGACTTGCTTTCTCATTGTATCAACAATATCTTCAGCTTCAGA
* *
3045 AACCATTCCTTTCTTGCAATGTGCATCAACCAAAATACTA
66 AACCATTCCCTTCTTGCAATGTGCATCAACCAATATACTA
* *
3085 TACGTGACAACATTAGGCTCGATGATTTGCTTTCTCATTGTATCAACAATATCTTCAGCTTCAGA
1 TACGTGACAACATTAGGCTCAATGACTTGCTTTCTCATTGTATCAACAATATCTTCAGCTTCAGA
* *
3150 AACCA-TCCCTTTCTTGCAATGTGCATCAACCAATGTATTA
66 AACCATTCCC-TTCTTGCAATGTGCATCAACCAATATACTA
* ** * * *
3190 TACGTGACAACATCAGG-TCAATCCCTTGCTTTCTCATTTTATCAACAATATCTTTAGCTTCAAA
1 TACGTGACAACATTAGGCTCAATGACTTGCTTTCTCATTGTATCAACAATATCTTCAGCTTCAGA
* *
3254 AACCATTCCCTTCTTGCAATGAGCATCAACCAATATAGTA
66 AACCATTCCCTTCTTGCAATGTGCATCAACCAATATACTA
* * * *
3294 -ATGTGACAACATTAGGCTTAAGGCCTTGCTTT
1 TACGTGACAACATTAGGCTCAATGACTTGCTTT
3326 TCGTTAGGCT
Statistics
Matches: 213, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
103 14 0.07
104 87 0.41
105 112 0.53
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (105 bp):
TACGTGACAACATTAGGCTCAATGACTTGCTTTCTCATTGTATCAACAATATCTTCAGCTTCAGA
AACCATTCCCTTCTTGCAATGTGCATCAACCAATATACTA
Found at i:4478 original size:5 final size:5
Alignment explanation
Indices: 4470--4500 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4460 ATTTCATTTT
4470 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA A
4501 ATTTGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:9152 original size:18 final size:19
Alignment explanation
Indices: 9129--9169 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9119 GAATTTGTTA
*
9129 ATTTTTACTTTTAAAAAAT
1 ATTTTAACTTTTAAAAAAT
*
9148 ATTTTAGATTTTTAAAAAAT
1 ATTTTA-ACTTTTAAAAAAT
9168 AT
1 AT
9170 AAAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTAACTTTTAAAAAAT
Found at i:9864 original size:2 final size:2
Alignment explanation
Indices: 9859--9886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9849 TGTGTGTGTG
9859 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
9887 GATAGATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10450 original size:2 final size:2
Alignment explanation
Indices: 10445--10470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10435 TGTGTGTGTG
10445 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
10471 AATAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28173 original size:20 final size:20
Alignment explanation
Indices: 28148--28193 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28138 TTTGTCGCAT
28148 TAATTTTAATTTCTTT-TTTA
1 TAATTTTAATTT-TTTGTTTA
*
28168 TAATTTAAATTTTTTGTTTA
1 TAATTTTAATTTTTTGTTTA
28188 -AATTTT
1 TAATTTT
28194 TAGTGATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TAATTTTAATTTTTTGTTTA
Found at i:34837 original size:2 final size:2
Alignment explanation
Indices: 34794--34818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34784 AACTGTTGGT
34794 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 T
34819 GGTTAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43426 original size:54 final size:56
Alignment explanation
Indices: 43341--43448 Score: 157
Period size: 54 Copynumber: 1.9 Consensus size: 56
43331 CCTTCAACAC
* *
43341 CAGTTATAATGATCATCAATTTAGCATGATTCCTCCCCCAACCCACCTGGTATGGTG
1 CAGTTATAATGA-CATCAATTTAGAATGATTCCTCCCCCAACCCAACTGGTATGGTG
* *
43398 CAGTTATAAT-A-ATCAATTTCGAATGATTCCTCCCCCAGCCCAACTGGTATG
1 CAGTTATAATGACATCAATTTAGAATGATTCCTCCCCCAACCCAACTGGTATG
43449 ACTCCGCTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
54 36 0.77
56 1 0.02
57 10 0.21
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (56 bp):
CAGTTATAATGACATCAATTTAGAATGATTCCTCCCCCAACCCAACTGGTATGGTG
Found at i:48074 original size:37 final size:37
Alignment explanation
Indices: 48014--48098 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
48004 ATTATTATGT
* *
48014 TGATG-TGAGATTCAATAATATTGACATAACAACCTA
1 TGATGTTGACATTCAATAATATTGACATAACAACATA
* * * *
48050 TGATGTTGACATTTAATAGTATTGACATAACGATATA
1 TGATGTTGACATTCAATAATATTGACATAACAACATA
*
48087 TAATGTTGACAT
1 TGATGTTGACAT
48099 GATATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 5 0.12
37 36 0.88
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (37 bp):
TGATGTTGACATTCAATAATATTGACATAACAACATA
Found at i:48682 original size:11 final size:12
Alignment explanation
Indices: 48659--48687 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
48649 GAAAATGTTC
48659 ACGAACGGTTAA
1 ACGAACGGTTAA
48671 ACGAAC-GTTAA
1 ACGAACGGTTAA
48682 ACGAAC
1 ACGAAC
48688 ATAACATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (12 bp):
ACGAACGGTTAA
Found at i:51738 original size:18 final size:19
Alignment explanation
Indices: 51717--51755 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
51707 TTACAAAATT
51717 TTTAAAATTTTAAAT-TTA
1 TTTAAAATTTTAAATATTA
* *
51735 TTTATATTTTTAAATATTA
1 TTTAAAATTTTAAATATTA
51754 TT
1 TT
51756 ATACAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAAATTTTAAATATTA
Done.