Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004747.1 Hibiscus syriacus cultivar Beakdansim tig00010718_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: 57882
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:29868 original size:9 final size:9
Alignment explanation
Indices: 29856--29906 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
29846 ATATGAGTCG
29856 AATTAATTT
1 AATTAATTT
*
29865 AATTAAATATA
1 AATT-AAT-TT
*
29876 AATTATTTT
1 AATTAATTT
29885 AATTAATTT
1 AATTAATTT
*
29894 GATTAA-TT
1 AATTAATTT
29902 AATTA
1 AATTA
29907 TAAATTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 6 0.18
9 18 0.53
10 5 0.15
11 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:30673 original size:19 final size:18
Alignment explanation
Indices: 30649--30685 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
30639 TATGCAAATC
30649 AATTAAAGTATCATTATAT
1 AATTAAAGTATCA-TATAT
30668 AATTAAAGTATCATATAT
1 AATTAAAGTATCATATAT
30686 TGTGCAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTAAAGTATCATATAT
Found at i:32984 original size:31 final size:30
Alignment explanation
Indices: 32938--33039 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 30
32928 GGATTCAATA
* *
32938 TTAAATTGATATTTTATATAAAATTTAGAAG
1 TTAAATTAATTTTTTATATAAAATTTAG-AG
* * * *
32969 TTAAATTAATTTTTTATTTGAAGTTTAGGG
1 TTAAATTAATTTTTTATATAAAATTTAGAG
* * * *
32999 TCAAATTAGTATTTTTGTCTAAAATTTAGGAG
1 TTAAATTAAT-TTTTTATATAAAATTTA-GAG
*
33031 TTAAGTTAA
1 TTAAATTAA
33040 AATTTAACAA
Statistics
Matches: 53, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
30 9 0.17
31 36 0.68
32 8 0.15
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (30 bp):
TTAAATTAATTTTTTATATAAAATTTAGAG
Found at i:34394 original size:38 final size:39
Alignment explanation
Indices: 34284--34427 Score: 158
Period size: 39 Copynumber: 3.8 Consensus size: 39
34274 TTTTAATTTC
* * *
34284 ATAAAATTTAAATTTTAGTTAGATTATTAAAATATAAATT
1 ATAAAA-TTAATTTTTAATTAGATTATTAAAATATTAATT
* * *
34324 ATAAAAATAATTTTTATTTAGATTGTTAAAATATTAATT
1 ATAAAATTAATTTTTAATTAGATTATTAAAATATTAATT
*
34363 GTAAAATTAATTTTTAATTAGATTATT-AAATATT-A--
1 ATAAAATTAATTTTTAATTAGATTATTAAAATATTAATT
*
34398 AT--AA-TAATTTTTAATTATATTATTAAAATA
1 ATAAAATTAATTTTTAATTAGATTATTAAAATA
34428 CAATTGGACT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
32 19 0.21
33 7 0.08
35 1 0.01
37 1 0.01
38 7 0.08
39 51 0.55
40 6 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (39 bp):
ATAAAATTAATTTTTAATTAGATTATTAAAATATTAATT
Found at i:41291 original size:23 final size:24
Alignment explanation
Indices: 41265--41311 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
41255 CCATTTGGAT
41265 TACGAACCATAAGACATTG-TTTG
1 TACGAACCATAAGACATTGCTTTG
***
41288 TACGGTTCATAAGACATTGCTTTG
1 TACGAACCATAAGACATTGCTTTG
41312 ACGTAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (24 bp):
TACGAACCATAAGACATTGCTTTG
Found at i:41565 original size:20 final size:20
Alignment explanation
Indices: 41526--41580 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
41516 ATATTGTATG
* * *
41526 AATAGTACCGACAATGTGCA
1 AATAGTACCGATACTCTGCA
41546 AATAGTACCGATACTCTGCA
1 AATAGTACCGATACTCTGCA
* *
41566 AAAAGTATCGATACT
1 AATAGTACCGATACT
41581 ATGTGAACAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (20 bp):
AATAGTACCGATACTCTGCA
Found at i:41667 original size:21 final size:21
Alignment explanation
Indices: 41642--41698 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
41632 AGGAGTATCG
41642 ATACCCTGCTACAGTGTACCA
1 ATACCCTGCTACAGTGTACCA
41663 ATACCCTGCTACAGTGTACCA
1 ATACCCTGCTACAGTGTACCA
*
41684 ATACCCTACTACAGT
1 ATACCCTGCTACAGT
41699 AATTTCGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (21 bp):
ATACCCTGCTACAGTGTACCA
Found at i:42271 original size:31 final size:31
Alignment explanation
Indices: 42230--42387 Score: 198
Period size: 31 Copynumber: 5.2 Consensus size: 31
42220 TAGATCTATC
*
42230 AGAACCTAGGTAATCAGTCCATATATCCCGA
1 AGAACATAGGTAATCAGTCCATATATCCCGA
* *
42261 AGCACATAGGTAATCAGTCCATATGTCCCGA
1 AGAACATAGGTAATCAGTCCATATATCCCGA
*
42292 AGAACATAGGTAAAT-AGTCCATATGTCCCGA
1 AGAACATAGGT-AATCAGTCCATATATCCCGA
*
42323 AGAACATAGGTAAACA-TGCCATATATCCCGA
1 AGAACATAGGTAATCAGT-CCATATATCCCGA
* * *
42354 AGAACATAAGTAAACAGTCC--ATGTCCCGA
1 AGAACATAGGTAATCAGTCCATATATCCCGA
42383 AGAAC
1 AGAAC
42388 CATGTCCCGA
Statistics
Matches: 115, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
29 13 0.11
30 3 0.03
31 95 0.83
32 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
AGAACATAGGTAATCAGTCCATATATCCCGA
Found at i:42392 original size:15 final size:15
Alignment explanation
Indices: 42372--42402 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42362 AGTAAACAGT
42372 CCATGTCCCGAAGAA
1 CCATGTCCCGAAGAA
42387 CCATGTCCCGAAGAA
1 CCATGTCCCGAAGAA
42402 C
1 C
42403 GTAGGTAACC
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:0.32, C:0.35, G:0.19, T:0.13
Consensus pattern (15 bp):
CCATGTCCCGAAGAA
Done.