Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008505.1 Hibiscus syriacus cultivar Beakdansim tig00111357_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: 57617
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2937 original size:25 final size:25
Alignment explanation
Indices: 2909--2956 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2899 TTGTGGACTT
*
2909 TTTGGCTGCTAT-TTTTTTGTTGCTC
1 TTTGGCT-CTATCTTTTTTCTTGCTC
*
2934 TTTGTCTCTATCTTTTTTCTTGC
1 TTTGGCTCTATCTTTTTTCTTGC
2957 AGGTGATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.04, C:0.19, G:0.15, T:0.62
Consensus pattern (25 bp):
TTTGGCTCTATCTTTTTTCTTGCTC
Found at i:3480 original size:3 final size:3
Alignment explanation
Indices: 3474--3518 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
3464 TTTATTATTA
*
3474 AAT AAT AAT AAT AAT AAT AAT ATT AACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA
3519 AACATGACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3487 original size:25 final size:26
Alignment explanation
Indices: 3469--3518 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
3459 ATAAATTTAT
3469 TATTAAATAATAATAAT-AATAATAA
1 TATTAAATAATAATAATAAATAATAA
*
3494 TATTAACTAATAATAAT-AATAATAA
1 TATTAAATAATAATAATAAATAATAA
3519 AACATGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TATTAAATAATAATAATAAATAATAA
Found at i:8863 original size:13 final size:13
Alignment explanation
Indices: 8847--8879 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
8837 ATTACCTTTT
8847 AAAATAATTTTAA
1 AAAATAATTTTAA
8860 AAAATAATTTTAA
1 AAAATAATTTTAA
*
8873 AAGATAA
1 AAAATAA
8880 AAAATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:12230 original size:2 final size:2
Alignment explanation
Indices: 12223--12260 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12213 TCTTGCTTTC
12223 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
12261 CATGCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21249 original size:31 final size:31
Alignment explanation
Indices: 21191--21250 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21181 TGGTATACAA
* **
21191 AGGAAGGAAGCAGAGCTAGCCGCATATTATG
1 AGGAAGGAAGCAAAGCTAGCCAAATATTATG
*
21222 AGGAAGTAAGCAAAGCTAGCCAAATATTA
1 AGGAAGGAAGCAAAGCTAGCCAAATATTA
21251 AGGGAAGCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.17
Consensus pattern (31 bp):
AGGAAGGAAGCAAAGCTAGCCAAATATTATG
Found at i:21390 original size:22 final size:22
Alignment explanation
Indices: 21362--21403 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21352 TAATCTTCAA
* *
21362 ACTCTGGGAATGTTGTTTTGAT
1 ACTCTGGGAATATTATTTTGAT
21384 ACTCTGGGAATATTATTTTG
1 ACTCTGGGAATATTATTTTG
21404 GTGTGATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (22 bp):
ACTCTGGGAATATTATTTTGAT
Found at i:34882 original size:41 final size:41
Alignment explanation
Indices: 34786--35019 Score: 378
Period size: 41 Copynumber: 5.7 Consensus size: 41
34776 AGATTCGCAA
* *
34786 TGCGATAGTCGAAGTTCACGTTGCGATTCATTCCAAATTCGT
1 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGT
*
34828 TGCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
1 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
*
34869 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGT
1 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
* *
34910 TGCGATAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGT
1 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
*
34951 TGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGT
1 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGT
*
34993 TGCGATAGGCGAAGTTTGCGTTGCGAT
1 TGCGATAGGCGAAGTTCGCGTTGCGAT
35020 AGTCCAAATA
Statistics
Matches: 182, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 117 0.64
42 65 0.36
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (41 bp):
TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
Found at i:35110 original size:6 final size:6
Alignment explanation
Indices: 35099--35134 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
35089 GACCCGTATT
35099 ACCACG ACCACG ACCACG ACCA-G ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
35135 CGAGACGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 13 0.45
6 16 0.55
ACGTcount: A:0.31, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35904 original size:19 final size:19
Alignment explanation
Indices: 35880--35947 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
35870 CAAATGCAAT
35880 ATTTGGACTATTGCAACGA
1 ATTTGGACTATTGCAACGA
*
35899 ATTTGGAATGAATTGCAACGCGA
1 ATTTGGACT--ATTGCAA--CGA
* * * *
35922 ACTTCGCCTATCGCAACGA
1 ATTTGGACTATTGCAACGA
35941 ATTTGGA
1 ATTTGGA
35948 ATAAATCGCA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 15 0.42
21 13 0.36
23 8 0.22
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (19 bp):
ATTTGGACTATTGCAACGA
Found at i:35939 original size:42 final size:42
Alignment explanation
Indices: 35885--35977 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
35875 GCAATATTTG
* * *
35885 GACTATTGCAACGAATTTGGAATGAATTGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
35927 GCCTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
35969 GACTATCGC
1 GACTATCGC
35978 GTTGCGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:35976 original size:21 final size:20
Alignment explanation
Indices: 35913--35977 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
35903 GGAATGAATT
*
35913 GCAACGCGAACTTCGCCTATC
1 GCAA-GCGAACTTCGACTATC
* * *
35934 GCAA-CGAATTTGGAATAAATC
1 GCAAGCGAACTTCGACT--ATC
35955 GCAATGCGAACTTCGACTATC
1 GCAA-GCGAACTTCGACTATC
35976 GC
1 GC
35978 GTTGCGAATC
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 8 0.24
21 16 0.48
23 9 0.27
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAAGCGAACTTCGACTATC
Found at i:36724 original size:24 final size:25
Alignment explanation
Indices: 36676--36724 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36666 TTGAGAGGAC
36676 TTATTTAATTTAAAAAAATAGAAAT
1 TTATTTAATTTAAAAAAATAGAAAT
*
36701 TTATTTAGA-TTAAAAATATA-AAAT
1 TTATTTA-ATTTAAAAAAATAGAAAT
36725 ATAAACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 17 0.77
26 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
TTATTTAATTTAAAAAAATAGAAAT
Found at i:40497 original size:17 final size:17
Alignment explanation
Indices: 40477--40514 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40467 TTAATAATTA
* *
40477 TATTTCCTTATAATTTT
1 TATTTACTTATAATCTT
40494 TATTTACTTATAATCTT
1 TATTTACTTATAATCTT
40511 TATT
1 TATT
40515 CATATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTACTTATAATCTT
Found at i:45463 original size:3 final size:3
Alignment explanation
Indices: 45455--45483 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45445 ATTTTACGTT
45455 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
45484 TTTTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.