Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005614.1 Hibiscus syriacus cultivar Beakdansim tig00013059_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: 49316
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:5926 original size:22 final size:22
Alignment explanation
Indices: 5888--5947 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
5878 ATATGAGATT
5888 TGTCCCGAAT-ACCTATAAATA
1 TGTCCCGAATGACCTATAAATA
*
5909 TGTCCCGAATGACCTATAAGTA
1 TGTCCCGAATGACCTATAAATA
*
5931 TGTCCCGAAGGACCTAT
1 TGTCCCGAATGACCTAT
5948 GAACCCTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (22 bp):
TGTCCCGAATGACCTATAAATA
Found at i:8961 original size:39 final size:38
Alignment explanation
Indices: 8907--9022 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 38
8897 TTTTGCAACC
8907 AATTTCAACAAATGATGCACCGACAAGTTTGACCAACAA
1 AATTTCAACAAATGATGCACCG-CAAGTTTGACCAACAA
* *
8946 AATTTCAACAAATGATGAACCTGCAAGTTTGACCAACAG
1 AATTTCAACAAATGATGCACC-GCAAGTTTGACCAACAA
* *
8985 AATTTCAACAAATGATGCAACTGCAAGTTTGACGAACA
1 AATTTCAACAAATGATGC-ACCGCAAGTTTGACCAACA
9023 CATACTCTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
39 67 0.96
40 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (38 bp):
AATTTCAACAAATGATGCACCGCAAGTTTGACCAACAA
Found at i:9500 original size:15 final size:16
Alignment explanation
Indices: 9480--9514 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9470 TGTTACTACT
9480 TGCGAACC-TCAGCTA
1 TGCGAACCTTCAGCTA
*
9495 TGCGAACCTTCAGGTA
1 TGCGAACCTTCAGCTA
9511 TGCG
1 TGCG
9515 GACATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Consensus pattern (16 bp):
TGCGAACCTTCAGCTA
Found at i:17290 original size:21 final size:20
Alignment explanation
Indices: 17260--17300 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
17250 AGGTGTTGAA
* *
17260 ATTTAGGGATTTAGGGTTTAG
1 ATTTAAGGATTT-GAGTTTAG
17281 ATTTAAGGATTTGAGTTTAG
1 ATTTAAGGATTTGAGTTTAG
17301 GGATCTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (20 bp):
ATTTAAGGATTTGAGTTTAG
Found at i:17442 original size:17 final size:17
Alignment explanation
Indices: 17417--17449 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17407 ACGATTTTGG
17417 GATTCTTTTGAGAATTA
1 GATTCTTTTGAGAATTA
*
17434 GATTTTTTTGAGAATT
1 GATTCTTTTGAGAATT
17450 TTTGAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
GATTCTTTTGAGAATTA
Found at i:24037 original size:2 final size:2
Alignment explanation
Indices: 24030--24060 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24020 TGGGAGTACA
24030 AT 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 AT A
24061 CCATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30550 original size:2 final size:2
Alignment explanation
Indices: 30533--30616 Score: 136
Period size: 2 Copynumber: 43.0 Consensus size: 2
30523 TCACAATGTA
* *
30533 AT AT AC AT AC AT AT AT AT AT AT A- 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
30574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30615 AT
1 AT
30617 CTTCTTTCGT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 74 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30657 original size:9 final size:10
Alignment explanation
Indices: 30643--30731 Score: 51
Period size: 9 Copynumber: 8.6 Consensus size: 10
30633 TCATTTATCC
30643 TATTTTATTCT
1 TATTTTATT-T
30654 T-TTTTA-TT
1 TATTTTATTT
30662 TATTTTA-TT
1 TATTTTATTT
*
30671 TA-TATATTT
1 TATTTTATTT
30680 TATTTTTTATCTT
1 TA--TTTTAT-TT
*
30693 TATTTCTTTGTT
1 TATTT-TAT-TT
*
30705 TATTTTATTC
1 TATTTTATTT
*
30715 TATTTTGTCTT
1 TATTTTAT-TT
30726 TATTTT
1 TATTTT
30732 TATTCTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
8 5 0.08
9 14 0.23
10 13 0.21
11 13 0.21
12 13 0.21
13 4 0.06
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (10 bp):
TATTTTATTT
Found at i:30658 original size:10 final size:9
Alignment explanation
Indices: 30643--30720 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
30633 TCATTTATCC
30643 TATTTTATT
1 TATTTTATT
*
30652 CTTTTTTATT
1 -TATTTTATT
30662 TATTTTATT
1 TATTTTATT
*
30671 TA-TATATT
1 TATTTTATT
30679 T-TATTT-TT
1 TAT-TTTATT
30687 TATCTTTATT
1 TAT-TTTATT
* *
30697 T-CTTTGTT
1 TATTTTATT
30705 TATTTTATT
1 TATTTTATT
30714 CTATTTT
1 -TATTTT
30721 GTCTTTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
8 15 0.28
9 21 0.40
10 17 0.32
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (9 bp):
TATTTTATT
Found at i:30668 original size:5 final size:5
Alignment explanation
Indices: 30643--30731 Score: 51
Period size: 5 Copynumber: 17.2 Consensus size: 5
30633 TCATTTATCC
*
30643 TATTT TATTCT T-TTT TA-TT TATTT TA-TT TA-TA TATTT TATTTTT
1 TATTT TATT-T TATTT TATTT TATTT TATTT TATTT TATTT TA--TTT
* * *
30687 TATCTT TATTT CTTTGTT TATTT TATTC TATTT TGTCTT TATTT T
1 TAT-TT TATTT -TAT-TT TATTT TATTT TATTT TAT-TT TATTT T
30732 TATTCTTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
4 13 0.20
5 31 0.47
6 15 0.23
7 7 0.11
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:30678 original size:13 final size:13
Alignment explanation
Indices: 30646--30720 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
30636 TTTATCCTAT
*
30646 TTTATTCTTTTTTA
1 TTTATT-TTATTTA
30660 TTTATTTTATTTA
1 TTTATTTTATTTA
*
30673 TATATTTTATTT-
1 TTTATTTTATTTA
*
30685 TTTATCTTTATTTC
1 TTTAT-TTTATTTA
*
30699 TTT-GTTTATTTTA
1 TTTATTTTA-TTTA
30712 TTCTATTTT
1 TT-TATTTT
30721 GTCTTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
12 8 0.16
13 29 0.58
14 10 0.20
15 3 0.06
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:43320 original size:8 final size:8
Alignment explanation
Indices: 43303--43338 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
43293 TTTTTTGAAA
*
43303 TTTGGCTT
1 TTTGGTTT
43311 TTTGGTTT
1 TTTGGTTT
43319 TTTGGTTTT
1 TTTGG-TTT
43328 TTTGGTTT
1 TTTGGTTT
43336 TTT
1 TTT
43339 TTGAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.00, C:0.03, G:0.22, T:0.75
Consensus pattern (8 bp):
TTTGGTTT
Found at i:43341 original size:10 final size:9
Alignment explanation
Indices: 43309--43339 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
43299 GAAATTTGGC
43309 TTTTTGG-T
1 TTTTTGGTT
43317 TTTTTGGTT
1 TTTTTGGTT
43326 TTTTTGGTT
1 TTTTTGGTT
43335 TTTTT
1 TTTTT
43340 TGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (9 bp):
TTTTTGGTT
Done.