Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004633.1 Hibiscus syriacus cultivar Beakdansim tig00010371_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: 61991
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2873 original size:20 final size:23
Alignment explanation
Indices: 2834--2892 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 23
2824 TTGGTGCAGA
*
2834 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
*
2854 GGG-ACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
2876 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
2893 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.12
20 12 0.38
21 1 0.03
22 3 0.09
23 12 0.38
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:3305 original size:18 final size:18
Alignment explanation
Indices: 3268--3305 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3258 AAAACACAAG
*
3268 AATTTTCTAAATTTTTAA
1 AATTTTCTAAATTTTAAA
*
3286 AATTTTTTAAATTTTAAA
1 AATTTTCTAAATTTTAAA
3304 AA
1 AA
3306 ATGTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTCTAAATTTTAAA
Found at i:11695 original size:56 final size:56
Alignment explanation
Indices: 11629--11741 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
11619 AACTTTGAGG
*
11629 TAACCTTAACTCTTAATCAGATATAATTGAGACATATACTTCACAAAATCAAACAA
1 TAACCTTAACTCTTAATCAGATATAATTGAGAAATATACTTCACAAAATCAAACAA
11685 TAACCTTAACTCTTAATCAGATATAATTGAGAAATATACTTCACAAAATCAAACAA
1 TAACCTTAACTCTTAATCAGATATAATTGAGAAATATACTTCACAAAATCAAACAA
11741 T
1 T
11742 CTTTTCATAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (56 bp):
TAACCTTAACTCTTAATCAGATATAATTGAGAAATATACTTCACAAAATCAAACAA
Found at i:19574 original size:22 final size:22
Alignment explanation
Indices: 19507--19588 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
19497 CCAGAACCCT
*
19507 AGGGGGTATCGATTCCCC-T-A
1 AGGGGGAATCGATTCCCCTTCA
* *
19527 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
19550 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
19572 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
19589 TCTGCCCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.28
21 1 0.02
22 16 0.30
23 21 0.40
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:22699 original size:18 final size:19
Alignment explanation
Indices: 22664--22700 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
22654 CACGGAATGT
22664 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
22684 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
22701 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:24268 original size:15 final size:15
Alignment explanation
Indices: 24248--24285 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
24238 TTCTTGTTCC
24248 TCTTCATCGAAATCT
1 TCTTCATCGAAATCT
24263 TCTTCATCGAAATCT
1 TCTTCATCGAAATCT
24278 TCTTCATC
1 TCTTCATC
24286 ACTCCATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.42
Consensus pattern (15 bp):
TCTTCATCGAAATCT
Found at i:27926 original size:6 final size:6
Alignment explanation
Indices: 27915--27997 Score: 166
Period size: 6 Copynumber: 13.8 Consensus size: 6
27905 TAGAGTAAAG
27915 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT
1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT
27963 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAG
1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAAG
27998 AACAATAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
AGAAGT
Found at i:30724 original size:20 final size:21
Alignment explanation
Indices: 30699--30752 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
30689 ATTTGGAGTA
*
30699 GTATCGGTACCCCTTGTAG-G
1 GTATCGGTACCCCTAGTAGTG
* *
30719 GTATCGATACTTCCCTAGTTGTG
1 GTATCGGTAC--CCCTAGTAGTG
30742 GTATCGGTACC
1 GTATCGGTACC
30753 ATGTCTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 9 0.33
21 1 0.04
22 7 0.26
23 10 0.37
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTACCCCTAGTAGTG
Found at i:31798 original size:36 final size:34
Alignment explanation
Indices: 31732--31799 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
31722 AACAAATATC
* * *
31732 AATATTTTCAAAAAAAAAAATATTAGTAATAACA
1 AATATATTCAAAAAAAAAAATAGTAATAATAACA
*
31766 AATATATTCATAATAAAAAAATAAGTAATAATAA
1 AATATATTCA-AAAAAAAAAAT-AGTAATAATAA
31800 GAAGAACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 9 0.32
35 10 0.36
36 9 0.32
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (34 bp):
AATATATTCAAAAAAAAAAATAGTAATAATAACA
Found at i:32011 original size:17 final size:17
Alignment explanation
Indices: 31979--32012 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31969 TTTATCAAGA
*
31979 TTTTTTTAATTATTTTC
1 TTTTTTTAAATATTTTC
*
31996 TTTTTTTAAATCTTTTC
1 TTTTTTTAAATATTTTC
32013 AAAATTACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTAAATATTTTC
Found at i:34861 original size:29 final size:29
Alignment explanation
Indices: 34819--34907 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
34809 TACCGGGGGT
*
34819 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
34848 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
34877 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
34906 AG
1 AG
34908 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:35175 original size:29 final size:29
Alignment explanation
Indices: 35114--35197 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
35104 ATGAATCCTT
** * **
35114 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
35143 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
35172 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
35198 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:36540 original size:33 final size:33
Alignment explanation
Indices: 36503--36574 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
36493 CGCTCGGCTT
* **
36503 CCCTCGCATAGCTCGTTCGGTTGCCCTCGGATG
1 CCCTCGCATAACTCGTTCGAATGCCCTCGGATG
* * *
36536 CCCTCACATAATTCGTTCGAATGGCCTCGGATG
1 CCCTCGCATAACTCGTTCGAATGCCCTCGGATG
*
36569 CTCTCG
1 CCCTCG
36575 GATGGCCTCG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.14, C:0.35, G:0.24, T:0.28
Consensus pattern (33 bp):
CCCTCGCATAACTCGTTCGAATGCCCTCGGATG
Found at i:36576 original size:10 final size:10
Alignment explanation
Indices: 36561--36598 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
36551 TTCGAATGGC
36561 CTCGGATGCT
1 CTCGGATGCT
36571 CTCGGATGGC-
1 CTCGGAT-GCT
36581 CTCGGATGCT
1 CTCGGATGCT
*
36591 CTGGGATG
1 CTCGGATG
36599 GCCTCGGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (10 bp):
CTCGGATGCT
Found at i:36581 original size:20 final size:20
Alignment explanation
Indices: 36556--36605 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
36546 ATTCGTTCGA
36556 ATGGCCTCGGATGCTCTCGG
1 ATGGCCTCGGATGCTCTCGG
*
36576 ATGGCCTCGGATGCTCTGGG
1 ATGGCCTCGGATGCTCTCGG
36596 ATGGCCTCGG
1 ATGGCCTCGG
36606 TCGGATGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.24
Consensus pattern (20 bp):
ATGGCCTCGGATGCTCTCGG
Found at i:36613 original size:14 final size:14
Alignment explanation
Indices: 36594--36631 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
36584 GGATGCTCTG
36594 GGATGGCCTCGGTC
1 GGATGGCCTCGGTC
36608 GGATGGCCTCGGTC
1 GGATGGCCTCGGTC
*
36622 GGATGACCTC
1 GGATGGCCTC
36632 AGATGCCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.21
Consensus pattern (14 bp):
GGATGGCCTCGGTC
Found at i:43216 original size:2 final size:2
Alignment explanation
Indices: 43209--43243 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43199 TTAAAAGAGA
43209 AT AT 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 AT AT A
43244 ATTTGAACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43516 original size:28 final size:27
Alignment explanation
Indices: 43485--43544 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
43475 TGAAATTAAA
*
43485 AAAAATTAAGAACTCAAATAATAAATAT
1 AAAAATGAAGAACT-AAATAATAAATAT
* * * *
43513 AAAAATGGAGATCTTAATTATAAATAT
1 AAAAATGAAGAACTAAATAATAAATAT
43540 AAAAA
1 AAAAA
43545 ATTAGGGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.27
Consensus pattern (27 bp):
AAAAATGAAGAACTAAATAATAAATAT
Found at i:43545 original size:28 final size:28
Alignment explanation
Indices: 43505--43572 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
43495 AACTCAAATA
*
43505 ATAAATAT-AAAAA-T-GGAGATCTTAATT
1 ATAAATATAAAAAATTAGG-GACCTT-ATT
43532 ATAAATATAAAAAATTAGGGACCTTATT
1 ATAAATATAAAAAATTAGGGACCTTATT
43560 ATAAATATAAAAA
1 ATAAATATAAAAA
43573 GTTGGGGCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 8 0.22
28 21 0.57
29 6 0.16
30 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (28 bp):
ATAAATATAAAAAATTAGGGACCTTATT
Found at i:45591 original size:2 final size:2
Alignment explanation
Indices: 45584--45631 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
45574 TACAAACTAC
45584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45626 TA TA TA
1 TA TA TA
45632 CAAGATTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56649 original size:19 final size:19
Alignment explanation
Indices: 56621--56657 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56611 AAGATGAAAG
*
56621 AAAGTTAAAGTAAAAAGAT
1 AAAGTAAAAGTAAAAAGAT
*
56640 AAAGTAAAAGTGAAAAGA
1 AAAGTAAAAGTAAAAAGA
56658 AAATACAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAGTAAAAGTAAAAAGAT
Done.