Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009005.1 Hibiscus syriacus cultivar Beakdansim tig00112389_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: 39416
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:779 original size:19 final size:18
Alignment explanation
Indices: 755--808 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
745 ATTGGAGTGC
755 AAAAAGAAAGAAAAAGACA
1 AAAAAGAAAGAAAAAGA-A
774 AAAAAG-AA-AAAAAGAA
1 AAAAAGAAAGAAAAAGAA
*
790 GAAAAGAAAAGAAAAAGAA
1 AAAAAG-AAAGAAAAAGAA
809 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 6 0.19
17 7 0.23
18 4 0.13
19 14 0.45
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAA
Found at i:781 original size:15 final size:16
Alignment explanation
Indices: 761--808 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
751 GTGCAAAAAG
*
761 AAAGAAAAAGACAA-A
1 AAAGAAAAAAACAAGA
*
776 AAAGAAAAAAAGAAGA
1 AAAGAAAAAAACAAGA
792 AAAGAAAAGAAA-AAGA
1 AAAGAAAA-AAACAAGA
808 A
1 A
809 TTCAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAACAAGA
Found at i:784 original size:8 final size:8
Alignment explanation
Indices: 755--799 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
745 ATTGGAGTGC
755 AAAAAGAAA
1 AAAAAG-AA
764 GAAAAAGACA
1 -AAAAAGA-A
774 AAAAAGAA
1 AAAAAGAA
782 AAAAAGAA
1 AAAAAGAA
*
790 GAAAAGAA
1 AAAAAGAA
798 AA
1 AA
800 GAAAAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 17 0.53
9 8 0.25
10 7 0.22
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:794 original size:16 final size:15
Alignment explanation
Indices: 755--808 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
745 ATTGGAGTGC
755 AAAAAG-AAAGAAAA
1 AAAAAGAAAAGAAAA
*
769 AGACAA-AAAAGAAAA
1 A-AAAAGAAAAGAAAA
784 AAAGAAGAAAAGAAAA
1 AAA-AAGAAAAGAAAA
800 GAAAAAGAA
1 -AAAAAGAA
809 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 2 0.06
15 14 0.42
16 14 0.42
17 3 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:20604 original size:8 final size:8
Alignment explanation
Indices: 20589--20628 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
20579 TTTGAACTTC
20589 TCTTTTTT
1 TCTTTTTT
*
20597 CTTTTTTTT
1 -TCTTTTTT
20606 TCTTTTTT
1 TCTTTTTT
*
20614 TCTTTTCT
1 TCTTTTTT
20622 TCTTTTT
1 TCTTTTT
20629 CTGATTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TCTTTTTT
Found at i:20619 original size:23 final size:24
Alignment explanation
Indices: 20593--20648 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
20583 AACTTCTCTT
*
20593 TTTTCTTTTTTTTTCT-TTTTTTC
1 TTTTCTTTTTTTTTCTGATTTTTC
*
20616 TTTTC-TTCTTTTTCTGATTTTTC
1 TTTTCTTTTTTTTTCTGATTTTTC
*
20639 TCTTCTTTTT
1 TTTTCTTTTT
20649 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.33
23 15 0.56
24 3 0.11
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTCTTTTTTTTTCTGATTTTTC
Found at i:20629 original size:9 final size:9
Alignment explanation
Indices: 20592--20648 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 9
20582 GAACTTCTCT
20592 TTTTTCTT-
1 TTTTTCTTC
20600 TTTTT-TTC
1 TTTTTCTTC
20608 TTTTT-TTC
1 TTTTTCTTC
20616 -TTTTCTTC
1 TTTTTCTTC
20624 TTTTTCTGAT-
1 TTTTTCT--TC
20634 TTTTCTCTTC
1 TTTT-TCTTC
20644 TTTTT
1 TTTTT
20649 GCACTCCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.14
8 16 0.38
9 8 0.19
10 8 0.19
11 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:28501 original size:8 final size:8
Alignment explanation
Indices: 28499--28526 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28489 TTTTTCCTTT
28499 TTTTTTTC
1 TTTTTTTC
28507 TTTTTTTC
1 TTTTTTTC
28515 TTTTTTTC
1 TTTTTTTC
28523 TTTT
1 TTTT
28527 CTGATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:28501 original size:12 final size:11
Alignment explanation
Indices: 28481--28528 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
28471 CTTTTTGAAC
28481 TTCTCTTTTTTT
1 TTCT-TTTTTTT
*
28493 TCCTTTTTTTT
1 TTCTTTTTTTT
*
28504 TTCTTTTTTTC
1 TTCTTTTTTTT
*
28515 TT-TTTTTCTT
1 TTCTTTTTTTT
28525 TTCT
1 TTCT
28529 GATTTTTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.27
11 19 0.63
12 3 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:28505 original size:16 final size:17
Alignment explanation
Indices: 28481--28528 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
28471 CTTTTTGAAC
* *
28481 TTCTCTTTTT-TTTCCT
1 TTCTTTTTTTCTTTTCT
28497 TT-TTTTTTTCTTTT-T
1 TTCTTTTTTTCTTTTCT
28512 TTCTTTTTTTCTTTTCT
1 TTCTTTTTTTCTTTTCT
28529 GATTTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTCTTTTTTTCTTTTCT
Found at i:28510 original size:21 final size:21
Alignment explanation
Indices: 28484--28546 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
28474 TTTGAACTTC
28484 TCTTTTTTTTCCTTTTTTTTT
1 TCTTTTTTTTCCTTTTTTTTT
*
28505 TC-TTTTTTTCTTTTTTTCTTT
1 TCTTTTTTTTCCTTTTTT-TTT
** *
28526 TCTGATTTTTCTCTTCTTTTT
1 TCTTTTTTTTC-CTTTTTTTT
28547 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 14 0.41
21 7 0.21
22 8 0.24
23 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (21 bp):
TCTTTTTTTTCCTTTTTTTTT
Found at i:28512 original size:20 final size:21
Alignment explanation
Indices: 28487--28528 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
28477 GAACTTCTCT
28487 TTTTTTTCCTTTTTT-TTTTC
1 TTTTTTTCCTTTTTTCTTTTC
*
28507 TTTTTTTCTTTTTTTCTTTTC
1 TTTTTTTCCTTTTTTCTTTTC
28528 T
1 T
28529 GATTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTCCTTTTTTCTTTTC
Found at i:30818 original size:19 final size:20
Alignment explanation
Indices: 30794--30839 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
30784 GAACTGTATC
*
30794 ATTTTCATT-AAAGTCATGT
1 ATTTTCATTAAAAATCATGT
30813 ATTTTCATTAAAAATCATGT
1 ATTTTCATTAAAAATCATGT
30833 ATTTTCA
1 ATTTTCA
30840 AAGGGATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (20 bp):
ATTTTCATTAAAAATCATGT
Found at i:35479 original size:2 final size:2
Alignment explanation
Indices: 35472--35500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35462 TGGCAGTGGA
35472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35501 ATTTGGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38129 original size:41 final size:41
Alignment explanation
Indices: 38080--38165 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
38070 TTCCAAATCC
38080 TTTGAAGATGGCGTTGGTGTGCTCACATCAT-CCCCCTTCT
1 TTTGAAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCT
38120 TTTGCAAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCT
1 TTTG-AAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCT
38162 TTTG
1 TTTG
38166 TGATTTGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 4 0.09
41 27 0.61
42 13 0.30
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.36
Consensus pattern (41 bp):
TTTGAAGATGGCGTTGGTGTGCTCACATCATCCCCCCTTCT
Done.