Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008833.1 Hibiscus syriacus cultivar Beakdansim tig00112027_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: 27241
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5060 original size:5 final size:5
Alignment explanation
Indices: 5041--5099 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
5031 GTCCGTCCGT
* * * * *
5041 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
5091 CTCGG CTCG
1 CTCGG CTCG
5100 TGGTCGTGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.07, C:0.41, G:0.37, T:0.15
Consensus pattern (5 bp):
CTCGG
Found at i:5108 original size:6 final size:6
Alignment explanation
Indices: 5097--5151 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
5087 TCGGCTCGGC
* *
5097 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
5145 TCGTGG T
1 TCGTGG T
5152 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:5451 original size:22 final size:22
Alignment explanation
Indices: 5426--5480 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5416 TCAGGAGTTA
* *
5426 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
5448 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
5470 CGGGAGTTATA
1 CAGGAGTTATA
5481 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:9613 original size:27 final size:27
Alignment explanation
Indices: 9575--9656 Score: 146
Period size: 27 Copynumber: 3.0 Consensus size: 27
9565 AAACTAAACT
* *
9575 TGCTCTATATCCTCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
9602 TGCTCTCTATCCCCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
9629 TGCTCTCTATCCCCTCTTCCATGACCC
1 TGCTCTCTATCCCCTCTTCCATGACCC
9656 T
1 T
9657 CTCAACTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.12, C:0.45, G:0.07, T:0.35
Consensus pattern (27 bp):
TGCTCTCTATCCCCTCTTCCATGACCC
Found at i:9658 original size:13 final size:13
Alignment explanation
Indices: 9588--9658 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
9578 TCTATATCCT
9588 CTCTTCCATGACC
1 CTCTTCCATGACC
* *
9601 CTGCTCTCTAT-CCC
1 CT-CT-TCCATGACC
9615 CTCTTCCATGACC
1 CTCTTCCATGACC
* *
9628 CTGCTCTCTAT-CCC
1 CT-CT-TCCATGACC
9642 CTCTTCCATGACC
1 CTCTTCCATGACC
9655 CTCT
1 CTCT
9659 CAACTTTCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
12 8 0.18
13 16 0.36
14 12 0.27
15 8 0.18
ACGTcount: A:0.11, C:0.48, G:0.07, T:0.34
Consensus pattern (13 bp):
CTCTTCCATGACC
Found at i:12618 original size:20 final size:20
Alignment explanation
Indices: 12588--12644 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
12578 TTTGGTTCAC
* *
12588 GGAATATAAGATTATTAGTG
1 GGAATAAAAGATTATCAGTG
*
12608 TGAATAAAAGATTATCAGTG
1 GGAATAAAAGATTATCAGTG
12628 GGAATAAAAGATTATCA
1 GGAATAAAAGATTATCA
12645 TAGAATAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (20 bp):
GGAATAAAAGATTATCAGTG
Found at i:12652 original size:18 final size:20
Alignment explanation
Indices: 12589--12652 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
12579 TTGGTTCACG
* * *
12589 GAATATAAGATTATTAGTGT
1 GAATAAAAGATTATCAGTGA
*
12609 GAATAAAAGATTATCAGTGG
1 GAATAAAAGATTATCAGTGA
12629 GAATAAAAGATTATCA-T-A
1 GAATAAAAGATTATCAGTGA
12647 GAATAA
1 GAATAA
12653 GATTATTGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.15
19 1 0.03
20 33 0.82
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (20 bp):
GAATAAAAGATTATCAGTGA
Found at i:14060 original size:23 final size:23
Alignment explanation
Indices: 14030--14092 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
14020 TGTACTTTAA
14030 TGCTGAATCATTCAACAGTGTTT
1 TGCTGAATCATTCAACAGTGTTT
*
14053 TGCTGAATCATTCAGCAGTGTTT
1 TGCTGAATCATTCAACAGTGTTT
14076 TGCTGAATCATTCAACA
1 TGCTGAATCATTCAACA
14093 CAGTCTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (23 bp):
TGCTGAATCATTCAACAGTGTTT
Found at i:15165 original size:31 final size:31
Alignment explanation
Indices: 15130--15196 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
15120 ATGTTATTTA
15130 TTTATAGTCAAAGA-AATA-ACTTTTCTATAAT
1 TTTATA-TCAAAGATAATATACTTTTCTAT-AT
* *
15161 TTTAT-TCAAAGATAATATAGTTTTCTATTT
1 TTTATATCAAAGATAATATACTTTTCTATAT
15191 TTTATA
1 TTTATA
15197 ATAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 7 0.23
30 10 0.32
31 14 0.45
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTATATCAAAGATAATATACTTTTCTATAT
Found at i:15192 original size:29 final size:27
Alignment explanation
Indices: 15128--15192 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
15118 AAATGTTATT
*
15128 TATTTATAGTCAAAGAAATAACTTTTC
1 TATTTTTAGTCAAAGAAATAACTTTTC
* *
15155 TATAATTTTATTCAAAGATAATATAGTTTTC
1 TAT--TTTTAGTCAAAGA-AATA-ACTTTTC
15186 TATTTTT
1 TATTTTT
15193 TATAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.10
29 15 0.48
30 4 0.13
31 9 0.29
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (27 bp):
TATTTTTAGTCAAAGAAATAACTTTTC
Found at i:15487 original size:143 final size:142
Alignment explanation
Indices: 15315--15600 Score: 563
Period size: 143 Copynumber: 2.0 Consensus size: 142
15305 CATTTAGTAT
15315 GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
1 GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
15380 TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
66 TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
15445 AAATTTGTTTGG
131 AAATTTGTTTGG
15457 GAATTTGAAATTAGATGAAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTA
1 GAATTTGAAATTAGATG-AGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTA
15522 GTTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTT
65 GTTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTT
15587 TAAATTTGTTTGG
130 TAAATTTGTTTGG
15600 G
1 G
15601 GTTTAACTAT
Statistics
Matches: 143, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 17 0.12
143 126 0.88
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (142 bp):
GAATTTGAAATTAGATGAGAATTTGAAATTTTCAATAACGATTGCCTCCCTCGATCCATCCTTAG
TTAAAAGTGATGATTGAATGATTTGTACATAATTATTTATAACTATATAGTTAATTATATTTTTT
AAATTTGTTTGG
Found at i:16152 original size:24 final size:24
Alignment explanation
Indices: 16120--16175 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
16110 GGATATGGTT
16120 TCTTCATCCGAGCTTACTCGGAAA
1 TCTTCATCCGAGCTTACTCGGAAA
16144 TCTTCATCCGAGCTTACTCGGAAA
1 TCTTCATCCGAGCTTACTCGGAAA
16168 TCTTCATC
1 TCTTCATC
16176 ATCTTTCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.32
Consensus pattern (24 bp):
TCTTCATCCGAGCTTACTCGGAAA
Done.