Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003974.1 Hibiscus syriacus cultivar Beakdansim tig00008628_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: 52789
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5592 original size:20 final size:19
Alignment explanation
Indices: 5550--5592 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5540 AAATGGGTAT
* *
5550 TGATACCAAGGGTCGGTAT
1 TGATACCAAGGGTCAGTAC
*
5569 TGATACTCAGGGGTCAGTAC
1 TGATAC-CAAGGGTCAGTAC
5589 TGAT
1 TGAT
5593 GAAGGCTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (19 bp):
TGATACCAAGGGTCAGTAC
Found at i:7516 original size:15 final size:16
Alignment explanation
Indices: 7496--7532 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
7486 GTGTTATATT
7496 ATTTGGTTATTTTT-G
1 ATTTGGTTATTTTTGG
7511 ATTTGGTTATTTTTGG
1 ATTTGGTTATTTTTGG
7527 ATTTGG
1 ATTTGG
7533 GTTTATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (16 bp):
ATTTGGTTATTTTTGG
Found at i:9935 original size:31 final size:31
Alignment explanation
Indices: 9860--9938 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
9850 ATAATGACAG
*
9860 AGTGACCATTTTGTTACAAATCGATAATGTT
1 AGTGACCATTTTGTTACAAATCGATAACGTT
* **
9891 -GATGGCCATTTTGTTACAAATTTATAACGTT
1 AG-TGACCATTTTGTTACAAATCGATAACGTT
*
9922 AGTGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
9939 TTTGAAACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAACGTT
Found at i:10679 original size:17 final size:18
Alignment explanation
Indices: 10657--10691 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
10647 ATGATCTAAG
10657 TAAAAAAAATTAA-AAAT
1 TAAAAAAAATTAACAAAT
10674 TAAAAAAAATTAACAAAT
1 TAAAAAAAATTAACAAAT
10692 GATCATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAAAAATTAACAAAT
Found at i:12819 original size:19 final size:19
Alignment explanation
Indices: 12804--12845 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12794 TCAAGTTATT
12804 TTTTAATTTTTTAGTTTAG
1 TTTTAATTTTTTAGTTTAG
*
12823 TTTTAATTTTTTATTGTTAG
1 TTTTAATTTTTTAGT-TTAG
12843 TTT
1 TTT
12846 CATATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTTTAGTTTAG
Found at i:12826 original size:20 final size:21
Alignment explanation
Indices: 12798--12845 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
12788 TCGTTTTCAA
*
12798 GTTATTTTTTAATTTTTTAGT
1 GTTAGTTTTTAATTTTTTAGT
*
12819 -TTAG-TTTTAATTTTTTATT
1 GTTAGTTTTTAATTTTTTAGT
12838 GTTAGTTT
1 GTTAGTTT
12846 CATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.61
20 7 0.30
21 2 0.09
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (21 bp):
GTTAGTTTTTAATTTTTTAGT
Found at i:12852 original size:21 final size:19
Alignment explanation
Indices: 12808--12857 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
12798 GTTATTTTTT
* *
12808 AATTTTTTAGTTTAGTTTT
1 AATTTTTTATTTTAGTTTC
12827 AATTTTTTATTGTTAGTTTC
1 AATTTTTTATT-TTAGTTTC
*
12847 ATATTTATTAT
1 A-ATTTTTTAT
12858 CAAAAAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 8 0.31
21 8 0.31
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (19 bp):
AATTTTTTATTTTAGTTTC
Found at i:12893 original size:19 final size:19
Alignment explanation
Indices: 12856--12893 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
12846 CATATTTATT
*
12856 ATCAAAAAGAGAATAAAAA
1 ATCAAAAAGAGAAAAAAAA
*
12875 ATCAAAAA-AGAAAAGAAA
1 ATCAAAAAGAGAAAAAAAA
12893 A
1 A
12894 GAAAAAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (19 bp):
ATCAAAAAGAGAAAAAAAA
Found at i:17316 original size:21 final size:21
Alignment explanation
Indices: 17292--17340 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
17282 CTATGTACAT
17292 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
*
17313 CGATGCACATTCAATTTGTAC
1 CGATGCACATTCAATGTGTAC
17334 CGATGCA
1 CGATGCA
17341 TCAAGGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
CGATGCACATTCAATGTGTAC
Found at i:17442 original size:64 final size:63
Alignment explanation
Indices: 17369--17490 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 63
17359 AATGGTTCAA
* *
17369 GGTGTATCGATGCACATGAAGTGCATCGATGCACTCCT-TTAAAATAAAAACATCGAATGTCATC
1 GGTGTATCGATGCACAAGAAGTGCATCAATGCAC-CCTCTT-AAATAAAAACATCGAATGTCATC
* * *
17433 GGTGTATCGATGCACAAGTAGTGCATCAATGCACCCTCTTAAATACAAGCATCGAATG
1 GGTGTATCGATGCACAAGAAGTGCATCAATGCACCCTCTTAAATAAAAACATCGAATG
17491 GGATTTATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 19 0.37
64 33 0.63
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (63 bp):
GGTGTATCGATGCACAAGAAGTGCATCAATGCACCCTCTTAAATAAAAACATCGAATGTCATC
Found at i:25485 original size:19 final size:18
Alignment explanation
Indices: 25452--25488 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
25442 TCATTAGAAT
25452 TCTATTTTATTGTCTTAA
1 TCTATTTTATTGTCTTAA
*
25470 TCTATTCTTCTTGTCTTAA
1 TCTATT-TTATTGTCTTAA
25489 CTTCAGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.59
Consensus pattern (18 bp):
TCTATTTTATTGTCTTAA
Found at i:26908 original size:10 final size:10
Alignment explanation
Indices: 26893--26922 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
26883 AAAACAAAAA
26893 TCCCGATTTT
1 TCCCGATTTT
26903 TCCCGATTTT
1 TCCCGATTTT
*
26913 TTCCGATTTT
1 TCCCGATTTT
26923 CAACCGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.53
Consensus pattern (10 bp):
TCCCGATTTT
Found at i:29894 original size:34 final size:34
Alignment explanation
Indices: 29855--29921 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
29845 TTTAAACTCC
29855 CATTTTTGAATTCCTGAGTTTGTCACTGTGTATT
1 CATTTTTGAATTCCTGAGTTTGTCACTGTGTATT
* *
29889 CATTTTTGAATTCCTGAGTTTGTTATTGTGTAT
1 CATTTTTGAATTCCTGAGTTTGTCACTGTGTAT
29922 GACAACCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (34 bp):
CATTTTTGAATTCCTGAGTTTGTCACTGTGTATT
Found at i:30350 original size:111 final size:111
Alignment explanation
Indices: 30154--30375 Score: 365
Period size: 111 Copynumber: 2.0 Consensus size: 111
30144 ATATTTTCTG
* *
30154 TCGTAATCTTTTCCAATCCTAAATTAGACTAAATTTCTTAGACTCTCCCGTAGGACTTGTCAGCA
1 TCGTAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCA
*
30219 GAAAGACGTCGCAAAGGGAAGGCGCCTGGAGGCAGCCCCACAGGTC
66 GAAAGACGTCGCAAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTC
* * **
30265 TCGTAATTTTTTCCAATCCTAAGTTAGACGACCTTTCTTAGACTCTCCCCTAGGACTTGTCAGCA
1 TCGTAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCA
30330 GAAAGACGTCGCGAAA-GGAAGGCGCCTGGAGCCAGCCCCACAGGTC
66 GAAAGACGTCGC-AAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTC
30376 CTAAACACGA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 100 0.97
112 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (111 bp):
TCGTAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCA
GAAAGACGTCGCAAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTC
Found at i:38244 original size:3 final size:3
Alignment explanation
Indices: 38233--38283 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
38223 CGGGTTTTTT
** *
38233 TTA TATA TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38278 TTA TTA
1 TTA TTA
38284 ATTTACAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:38406 original size:25 final size:25
Alignment explanation
Indices: 38377--38450 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
38367 GAACCAACCC
38377 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
38402 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * * *
38427 AACAAATTAGGATTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
38451 TCCCCTAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:52612 original size:43 final size:42
Alignment explanation
Indices: 52561--52700 Score: 115
Period size: 47 Copynumber: 3.2 Consensus size: 42
52551 ACCAATCTCT
* *
52561 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACC-TAGATAACCAGACGTCC
* * * ** *
52604 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAAC-TCT
1 TCATCACGTAAGAGCCGTGTCA--ACC--TAGATAACC-AG-ACGTCC
*
52651 TCATCACGTAAGAGCCGTGTCAACCT-GATAACCA-TCGTCC
1 TCATCACGTAAGAGCCGTGTCAACCTAGATAACCAGACGTCC
52691 TCATCACGTA
1 TCATCACGTA
52701 GGAATCGTGT
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.01
40 12 0.16
41 1 0.01
42 5 0.07
43 20 0.26
45 6 0.08
46 7 0.09
47 23 0.30
48 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCACGTAAGAGCCGTGTCAACCTAGATAACCAGACGTCC
Found at i:52714 original size:87 final size:91
Alignment explanation
Indices: 52557--52761 Score: 292
Period size: 89 Copynumber: 2.3 Consensus size: 91
52547 CCAGACCAAT
*
52557 CTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
**
52622 GTTATCA-CCTTTAGATGGCCAAGAA
66 GTTATCACCCTAAAGATGGCCAAGAA
* *
52647 CTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCA-TCGTCCTCATCACGTAGGAATCGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
52709 GTTATCATCCCTAAAGATGGCCAAGAA
66 GTTATCA-CCCTAAAGATGGCCAAGAA
* * * *
52736 TTCTTCATCATGTAGGAGCAGTGTCA
1 CTCTTCATCACGTAAGAGCCGTGTCA
52762 TCCCCTGACC
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
87 29 0.28
88 8 0.08
89 39 0.38
90 28 0.27
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (91 bp):
CTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
GTTATCACCCTAAAGATGGCCAAGAA
Done.