Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009158.1 Hibiscus syriacus cultivar Beakdansim tig00112685_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: 61532
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:10416 original size:20 final size:20
Alignment explanation
Indices: 10391--10428 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10381 CCCCCTTTGA
*
10391 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
10411 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
10429 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:23544 original size:19 final size:19
Alignment explanation
Indices: 23497--23545 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
23487 TGAGAGAGAG
23497 AAGTAAAAAT-AAAGAAATA
1 AAGT-AAAATGAAAGAAATA
* *
23516 AAAT-AAATGAAAGGAATA
1 AAGTAAAATGAAAGAAATA
23534 AAGTAAAATGAA
1 AAGTAAAATGAA
23546 TATTTTCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (19 bp):
AAGTAAAATGAAAGAAATA
Found at i:25640 original size:22 final size:22
Alignment explanation
Indices: 25612--25654 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
25602 CTCTATTTCA
25612 CCATCAACACCATCAACATCTT
1 CCATCAACACCATCAACATCTT
*
25634 CCATCAAGACCATCAACATCT
1 CCATCAACACCATCAACATCT
25655 ACATAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (22 bp):
CCATCAACACCATCAACATCTT
Found at i:27124 original size:15 final size:15
Alignment explanation
Indices: 27104--27134 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27094 GACATTAGGA
27104 AACATTTGTTATCCT
1 AACATTTGTTATCCT
27119 AACATTTGTTATCCT
1 AACATTTGTTATCCT
27134 A
1 A
27135 CAAAACTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
AACATTTGTTATCCT
Found at i:31576 original size:35 final size:35
Alignment explanation
Indices: 31531--31610 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
31521 TTATGAGCAT
*
31531 ACATTTGCATATTATACTATACTTGAATTATCATA
1 ACATGTGCATATTATACTATACTTGAATTATCATA
31566 ACATGTGCATATTATACTATACTTGAATTATCATA
1 ACATGTGCATATTATACTATACTTGAATTATCATA
31601 ACATGTGCAT
1 ACATGTGCAT
31611 TCATTCTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (35 bp):
ACATGTGCATATTATACTATACTTGAATTATCATA
Found at i:37353 original size:14 final size:14
Alignment explanation
Indices: 37330--37367 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
37320 AGTGCTTCAA
*
37330 CTTTTTTTTTCTTT
1 CTTTTCTTTTCTTT
37344 CTTTTCTTTTCTTT
1 CTTTTCTTTTCTTT
37358 -TTCTTCTTTT
1 CTT-TTCTTTT
37368 GAGTGCTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTCTTTTCTTT
Found at i:37358 original size:19 final size:19
Alignment explanation
Indices: 37330--37367 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
37320 AGTGCTTCAA
37330 CTTTT-TTTTTCTTTCTTTT
1 CTTTTCTTTTTC-TTCTTTT
37349 CTTTTCTTTTTCTTCTTTT
1 CTTTTCTTTTTCTTCTTTT
37368 GAGTGCTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
CTTTTCTTTTTCTTCTTTT
Found at i:37391 original size:27 final size:27
Alignment explanation
Indices: 37355--37442 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
37345 TTTTCTTTTC
37355 TTTTTC-TTCTTTTGAGTGCTGGATTT
1 TTTTTCTTTCTTTTGAGTGCTGGATTT
*
37381 TTTTTCTTTCTTTTGAGTGATGGATTT
1 TTTTTCTTTCTTTTGAGTGCTGGATTT
* **
37408 TCTTTCTTTCTTTTGAGTGCTTCATTT
1 TTTTTCTTTCTTTTGAGTGCTGGATTT
37435 TCTTTTCT
1 T-TTTTCT
37443 GATTTTTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.11
27 43 0.80
28 5 0.09
ACGTcount: A:0.08, C:0.14, G:0.15, T:0.64
Consensus pattern (27 bp):
TTTTTCTTTCTTTTGAGTGCTGGATTT
Found at i:37478 original size:12 final size:12
Alignment explanation
Indices: 37463--37492 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
37453 TTTTTCTTTG
37463 ACTTTGCACTTC
1 ACTTTGCACTTC
37475 ACTTTGCACTTC
1 ACTTTGCACTTC
*
37487 ATTTTG
1 ACTTTG
37493 TATTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (12 bp):
ACTTTGCACTTC
Found at i:41795 original size:20 final size:20
Alignment explanation
Indices: 41766--41804 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41756 TTTCCACCAC
*
41766 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
41786 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
41805 TATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:44382 original size:18 final size:18
Alignment explanation
Indices: 44359--44403 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
44349 TGTGCCAGAA
*
44359 ATGCTTCATCATTTCAAT
1 ATGCTTCAGCATTTCAAT
44377 ATGCTTCAGCATTTCAAT
1 ATGCTTCAGCATTTCAAT
44395 ATGCTTCAG
1 ATGCTTCAG
44404 TAACATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (18 bp):
ATGCTTCAGCATTTCAAT
Found at i:50032 original size:30 final size:31
Alignment explanation
Indices: 49980--50039 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
49970 CTTAGCTTTA
**
49980 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
50010 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
50040 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:50966 original size:19 final size:20
Alignment explanation
Indices: 50942--50992 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
50932 CGGCCAAGAG
* *
50942 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
50961 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
50981 CATGTATTTTCA
1 CATGTATTTTCA
50993 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:51435 original size:18 final size:18
Alignment explanation
Indices: 51412--51448 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
51402 CTTTATTTCA
51412 TTTCATT-CTTATTATTAT
1 TTTCATTACTTA-TATTAT
51430 TTTCATTACTTATATTAT
1 TTTCATTACTTATATTAT
51448 T
1 T
51449 ATTCCCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCATTACTTATATTAT
Found at i:54034 original size:15 final size:15
Alignment explanation
Indices: 54014--54048 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
54004 TAAACTCCCT
54014 ATGCCGCCTATGTGA
1 ATGCCGCCTATGTGA
54029 ATGCCGCCTATGTGA
1 ATGCCGCCTATGTGA
54044 ATGCC
1 ATGCC
54049 TCATGACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGCCGCCTATGTGA
Done.