Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002382.1 Hibiscus syriacus cultivar Beakdansim tig00004870_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: 47987
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8840 original size:17 final size:17
Alignment explanation
Indices: 8818--8851 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8808 TTAGAATTAC
*
8818 GAGAGAAAATTATTTTA
1 GAGAGAAAATAATTTTA
*
8835 GAGAGATAATAATTTTA
1 GAGAGAAAATAATTTTA
8852 AAATATATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
GAGAGAAAATAATTTTA
Found at i:14442 original size:17 final size:17
Alignment explanation
Indices: 14413--14451 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
14403 TTTAAGGTTT
* *
14413 TTAA-AATATATTTTTA
1 TTAATAATAAATTTTAA
14429 TTAATAATAAATTTTAA
1 TTAATAATAAATTTTAA
14446 TTAATA
1 TTAATA
14452 CTAAGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATAATAAATTTTAA
Found at i:19317 original size:3 final size:3
Alignment explanation
Indices: 19309--19356 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
19299 TGTAATAGAC
* *
19309 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19357 ATATGAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:22306 original size:27 final size:28
Alignment explanation
Indices: 22258--22311 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
22248 TTAGAAATAT
* *
22258 TAAATTAATAATATGATCAAAT-TTATA
1 TAAATTAATAATATCATAAAATATTATA
22285 TAAATATAA-AATATCATAAAATATTAT
1 TAAAT-TAATAATATCATAAAATATTAT
22312 TTATACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAATTAATAATATCATAAAATATTATA
Found at i:23442 original size:16 final size:16
Alignment explanation
Indices: 23423--23454 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23413 AATTATTCTA
23423 ATTATAAGCATATCAT
1 ATTATAAGCATATCAT
23439 ATTATAAGCATATCAT
1 ATTATAAGCATATCAT
23455 TGAATCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTATAAGCATATCAT
Found at i:24039 original size:28 final size:28
Alignment explanation
Indices: 23942--24038 Score: 140
Period size: 28 Copynumber: 3.5 Consensus size: 28
23932 TAATTGAATG
* *
23942 GTGATACGTAACACGACATATATCAACA
1 GTGACACGTGACACGACATATATCAACA
* * *
23970 GTGACACGTGATACGATATATGTCAACA
1 GTGACACGTGACACGACATATATCAACA
*
23998 GTGACACGTGACATGACATATATCAACA
1 GTGACACGTGACACGACATATATCAACA
24026 GTGACACGTGACA
1 GTGACACGTGACA
24039 TCATTCGATT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (28 bp):
GTGACACGTGACACGACATATATCAACA
Found at i:26511 original size:6 final size:6
Alignment explanation
Indices: 26500--26524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26490 TTTCCCCGAA
26500 GACTGC GACTGC GACTGC GACTGC G
1 GACTGC GACTGC GACTGC GACTGC G
26525 GCGGCGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GACTGC
Found at i:27463 original size:13 final size:13
Alignment explanation
Indices: 27445--27478 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
27435 AAATTTAGGC
27445 ACTAAAATCAGGT
1 ACTAAAATCAGGT
27458 ACTAAAATCAGGT
1 ACTAAAATCAGGT
27471 ACTAAAAT
1 ACTAAAAT
27479 GAACCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (13 bp):
ACTAAAATCAGGT
Found at i:30047 original size:26 final size:28
Alignment explanation
Indices: 29986--30047 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
29976 GAGTATTGCT
*
29986 GAGCTCGACTCGACTCGAAAACTCTGAAATT
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
*
30017 AAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
30043 GAGCT
1 GAGCT
30048 TAAAATTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
30 1 0.04
31 23 0.82
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:43522 original size:19 final size:19
Alignment explanation
Indices: 43498--43571 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 19
43488 TTCATTGAAA
43498 AACCGAAAAAACCGACCCG
1 AACCGAAAAAACCGACCCG
*
43517 AACCGAACCGAAAA---ACTCG
1 AACCGAA---AAAACCGACCCG
*
43536 AACCGTTAAAAAACCCGAACCG
1 AACCG--AAAAAA-CCGACCCG
43558 AACCGAAAAAACCG
1 AACCGAAAAAACCG
43572 GTTTCGATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 18
0.67 0.05 0.28
Matches are distributed among these distances:
18 4 0.09
19 19 0.44
20 6 0.14
21 2 0.05
22 12 0.28
ACGTcount: A:0.49, C:0.32, G:0.15, T:0.04
Consensus pattern (19 bp):
AACCGAAAAAACCGACCCG
Found at i:46745 original size:2 final size:2
Alignment explanation
Indices: 46730--46792 Score: 96
Period size: 2 Copynumber: 33.0 Consensus size: 2
46720 GGGCAGCCAA
46730 AT AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
46770 AT A- AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
46793 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Done.