Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005655.1 Hibiscus syriacus cultivar Beakdansim tig00013225_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: 194601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:184674 original size:37 final size:37
Alignment explanation
Indices: 184624--184700 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
184614 ATTGACTATG
184624 ATATTAATTATAGATTTATAGTACAGTATGAGTTCAA
1 ATATTAATTATAGATTTATAGTACAGTATGAGTTCAA
184661 ATATTAATTATAGATTTATAGTACAGTATGAGTTCAA
1 ATATTAATTATAGATTTATAGTACAGTATGAGTTCAA
184698 ATA
1 ATA
184701 GCATATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (37 bp):
ATATTAATTATAGATTTATAGTACAGTATGAGTTCAA
Found at i:187282 original size:2 final size:2
Alignment explanation
Indices: 187275--187303 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
187265 ACCGTGATTA
187275 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 A
187304 ATACTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:187508 original size:15 final size:15
Alignment explanation
Indices: 187488--187519 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
187478 ATTGATTTTA
*
187488 TGAAAAATGAATTAC
1 TGAAAAATGAAATAC
187503 TGAAAAATGAAATAC
1 TGAAAAATGAAATAC
187518 TG
1 TG
187520 GAATTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
TGAAAAATGAAATAC
Found at i:187852 original size:31 final size:29
Alignment explanation
Indices: 187784--187853 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
187774 AATATTATTT
*
187784 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
187814 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
187847 TTATATT
1 TTATATT
187854 AATTACTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:187933 original size:23 final size:23
Alignment explanation
Indices: 187884--187934 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
187874 GTGTTATATT
**
187884 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
187907 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
187930 ATATT
1 ATATT
187935 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:187946 original size:19 final size:19
Alignment explanation
Indices: 187922--187992 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
187912 TTAAATATCT
*
187922 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
187941 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
187960 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
187980 TTATTAAATATAT
1 TTATTAAA-ATAT
187993 AAAAAATATT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:187991 original size:28 final size:29
Alignment explanation
Indices: 187953--188116 Score: 111
Period size: 30 Copynumber: 5.4 Consensus size: 29
187943 ATTATATTAA
187953 TATTAAATATATAAATAATATTAT-TCA-T
1 TATTAAATATATAAATAATATTATAT-ATT
*
187981 TATTAAATATATAAAAAATATTATATATT
1 TATTAAATATATAAATAATATTATATATT
*
188010 TATTAAA-ATAAAAATATAATATCTTATATTATAT
1 TATTAAATAT-ATAA-ATAATA--TTATA-TAT-T
* * *
188044 TATTATAATATAATTAATAATTTTAT-TATAA
1 TATTA-AATAT-ATAAATAATATTATATAT-T
* * * *
188075 TATTAAAAATATAATATTATATTATAAATA
1 TATTAAATATATAA-ATAATATTATATATT
*
188105 TAATAAATATAT
1 TATTAAATATAT
188117 TTTAAATATT
Statistics
Matches: 110, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
28 26 0.24
29 15 0.14
30 28 0.25
31 11 0.10
32 5 0.05
33 7 0.06
34 6 0.05
35 7 0.06
36 5 0.05
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTAAATATATAAATAATATTATATATT
Found at i:188050 original size:23 final size:23
Alignment explanation
Indices: 188040--188134 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 23
188030 ATCTTATATT
188040 ATATTATTATAATATAATTAATA
1 ATATTATTATAATATAATTAATA
* **
188063 ATTTTATTATAATATTAAAAATATA
1 ATATTATTATAATA-TAATTA-ATA
*
188088 ATATTATATTATAAATATAATAAAT-
1 ATA-T-TATTAT-AATATAATTAATA
*
188113 ATATT-TTA-AATAT-TTTAATA
1 ATATTATTATAATATAATTAATA
188133 AT
1 AT
188135 TAATATTTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
19 4 0.07
20 7 0.12
22 3 0.05
23 14 0.24
24 5 0.08
25 8 0.14
26 3 0.05
27 11 0.19
28 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTATTATAATATAATTAATA
Found at i:188394 original size:42 final size:42
Alignment explanation
Indices: 188338--188429 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
188328 TTCCTCCAAC
* * *
188338 CAAACACCGGAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
*
188380 CAAACACGGGAAAACATTTTCCGAAAAACGGATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
188422 CAAACACG
1 CAAACACG
188430 AGATTTCGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
Found at i:190475 original size:21 final size:20
Alignment explanation
Indices: 190446--190485 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
190436 GTAGGAGTAC
*
190446 TGTAGCAGGGTATCGGTACCT
1 TGTAACAGGGTATC-GTACCT
190467 TGTAACAGGGTATCGTACC
1 TGTAACAGGGTATCGTACC
190486 CCTGAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (20 bp):
TGTAACAGGGTATCGTACCT
Found at i:191462 original size:59 final size:57
Alignment explanation
Indices: 191370--191503 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 57
191360 GAATATATGA
** *
191370 ATAGTCGAGGAATCATTTTGTAACTTTCAATAGTAAAGG-GACTTAACAAAGTAGTA-ACT
1 ATAGTCGA-G-ATCATTTTAAAACTTTCAATAGT--AGGAGACTTAACAAAGTAGCACACT
* * *
191429 ATAGTCAAGAGATCATTTTAAAACTTTTAATAGTCGGAGACTTAACAAAGTAGCACCCT
1 ATAGTC--GAGATCATTTTAAAACTTTCAATAGTAGGAGACTTAACAAAGTAGCACACT
191488 ATAGTCGAGATCATTT
1 ATAGTCGAGATCATTT
191504 GTGTACCTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
57 12 0.18
58 16 0.25
59 34 0.52
60 1 0.02
61 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (57 bp):
ATAGTCGAGATCATTTTAAAACTTTCAATAGTAGGAGACTTAACAAAGTAGCACACT
Found at i:191811 original size:5 final size:5
Alignment explanation
Indices: 191791--191897 Score: 165
Period size: 5 Copynumber: 22.8 Consensus size: 5
191781 AAGTATTGAC
191791 ATAAT AT-AT A-AAT ATAAT ATAAT ATAAT A-AAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
191837 ATAAT ATAAT AT-AT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
191884 ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAA
191898 AATATAGTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 14
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.02
4 20 0.21
5 73 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:191859 original size:47 final size:47
Alignment explanation
Indices: 191791--191903 Score: 180
Period size: 47 Copynumber: 2.5 Consensus size: 47
191781 AAGTATTGAC
*
191791 ATAATAT-ATAAATATAATATAATATAATAA-ATATATATAATATAAT
1 ATAATATAATATATATAATATAATATAATAATATA-ATATAATATAAT
191837 ATAATATAATATATATAATATAATATAATAATATAATATAATATAAT
1 ATAATATAATATATATAATATAATATAATAATATAATATAATATAAT
191884 ATAATATAATATA-A-AATATA
1 ATAATATAATATATATAATATA
191904 GTATTTTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
45 6 0.09
46 8 0.12
47 47 0.73
48 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (47 bp):
ATAATATAATATATATAATATAATATAATAATATAATATAATATAAT
Done.