Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001429.1 Hibiscus syriacus cultivar Beakdansim tig00002775_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: 48721
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13742 original size:21 final size:21
Alignment explanation
Indices: 13701--13745 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13691 TACATTTACC
* *
13701 AATAAATCGGATTATTCGATT
1 AATAAATCGAATTAGTCGATT
13722 AATAAATCGAATATAGT-GATT
1 AATAAATCGAAT-TAGTCGATT
13743 AAT
1 AAT
13746 TCAAAACGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (21 bp):
AATAAATCGAATTAGTCGATT
Found at i:16285 original size:26 final size:25
Alignment explanation
Indices: 16236--16294 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
16226 TATTTAAGGG
*
16236 GGTTTTGTGAGAAATTAGCGATTTT
1 GGTTTTCTGAGAAATTAGCGATTTT
16261 AGGTTTTCTGAGAAATTAG-GAATTTT
1 -GGTTTTCTGAGAAATTAGCG-ATTTT
16287 GGATTTTC
1 GG-TTTTC
16295 AAATAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.44
Consensus pattern (25 bp):
GGTTTTCTGAGAAATTAGCGATTTT
Found at i:22245 original size:14 final size:14
Alignment explanation
Indices: 22226--22258 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22216 CGCTGGGCAT
22226 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
22240 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
22254 ACGAG
1 CCGAG
22259 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:22273 original size:23 final size:23
Alignment explanation
Indices: 22241--22299 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
22231 GCCATCCGAC
*
22241 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
22264 CGAGGGCATCCGAGCGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
22287 CGAGGGAATCCGA
1 CGAGGGCATCCGA
22300 GGGAAGTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.36, T:0.12
Consensus pattern (23 bp):
CGAGGGCATCCGAACGAGCTATG
Found at i:22351 original size:29 final size:29
Alignment explanation
Indices: 22318--22402 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
22308 GAGCGAGGGT
*
22318 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
22347 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
* *
22376 AGATCGCCCGGAGGGCATGGCAACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
22403 TGTGTTGGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.22, C:0.31, G:0.35, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:22448 original size:12 final size:12
Alignment explanation
Indices: 22431--22455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22421 TGCCATGCAA
22431 CACGTTCATTCT
1 CACGTTCATTCT
22443 CACGTTCATTCT
1 CACGTTCATTCT
22455 C
1 C
22456 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:31225 original size:41 final size:41
Alignment explanation
Indices: 31126--31226 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 41
31116 ATTCGCGTTG
* * *
31126 CATTTCGCGTTGCGATAATTGAAAATCGCTTTGCTATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
** *
31167 CATTTCATGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
31208 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
31227 CTACAGTTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:31260 original size:19 final size:19
Alignment explanation
Indices: 31236--31323 Score: 113
Period size: 19 Copynumber: 4.5 Consensus size: 19
31226 TCTACAGTTG
31236 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
31255 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
31274 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
31295 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
31315 TCGTTGCGA
1 TCGTTGCGA
31324 AAATTCGTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 38 0.66
20 5 0.09
21 5 0.09
22 10 0.17
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:32108 original size:20 final size:20
Alignment explanation
Indices: 32083--32196 Score: 111
Period size: 20 Copynumber: 5.6 Consensus size: 20
32073 ACTGTAGACT
32083 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
32103 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
32123 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
** ** *
32144 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
32165 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
32185 ATCGCAACGCGA
1 ATCGCAACGCGA
32197 TTTTCAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 46 0.57
21 35 0.43
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:32151 original size:21 final size:21
Alignment explanation
Indices: 32125--32215 Score: 130
Period size: 21 Copynumber: 4.4 Consensus size: 21
32115 AATGGAAAAG
32125 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
32146 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** ** *
32167 CGCAACGCGAAATGGAA-AAT
1 CGCAACGCGATTTTCAACTAT
32187 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
32208 CGCAACGC
1 CGCAACGC
32216 AAAATGCAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:32189 original size:41 final size:41
Alignment explanation
Indices: 32080--32221 Score: 160
Period size: 41 Copynumber: 3.5 Consensus size: 41
32070 ACAACTGTAG
** **
32080 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * ** ** *
32121 A-AAGCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCA
32162 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
32203 ACTATCGCAACGCAAAATG
1 ACTATCGCAACGCGAAATG
32222 CAACGCGAAT
Statistics
Matches: 80, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
40 14 0.17
41 52 0.65
42 14 0.17
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:32225 original size:21 final size:21
Alignment explanation
Indices: 32080--32225 Score: 118
Period size: 21 Copynumber: 7.1 Consensus size: 21
32070 ACAACTGTAG
*
32080 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* *
32101 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
32121 A-AAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
** *
32141 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
32162 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
32183 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
32203 ACTATCGCAACGCAAAATGCA
1 ACTATCGCAACGCGAAATGCA
32224 AC
1 AC
32226 GCGAATTTGC
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 49 0.49
21 52 0.51
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:32635 original size:2 final size:2
Alignment explanation
Indices: 32628--32667 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32618 TTACTTTGAA
32628 AT AT AT AT AT 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
32668 TAGTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42158 original size:15 final size:15
Alignment explanation
Indices: 42138--42167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42128 GTTTGGGAAT
42138 AATTAAAATAAATTA
1 AATTAAAATAAATTA
*
42153 AATTAAAATAGATTA
1 AATTAAAATAAATTA
42168 TATATTCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATTAAAATAAATTA
Found at i:48125 original size:25 final size:25
Alignment explanation
Indices: 48096--48145 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
48086 TTTTTCGTCC
*
48096 CCTAAAATTTACTAGTTGAACCCCT
1 CCTAAAATTTACAAGTTGAACCCCT
*
48121 CCTAAATTTTACAAGTTGAACCCCT
1 CCTAAAATTTACAAGTTGAACCCCT
48146 AACATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (25 bp):
CCTAAAATTTACAAGTTGAACCCCT
Done.