Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008556.1 Hibiscus syriacus cultivar Beakdansim tig00111461_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: 73429
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2802 original size:14 final size:14
Alignment explanation
Indices: 2783--2819 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2773 TAAGATACTA
2783 TTTCCATCACCATC
1 TTTCCATCACCATC
2797 TTTCCATCACCATC
1 TTTCCATCACCATC
*
2811 -ATCCATCAC
1 TTTCCATCAC
2820 TTTCACGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.32
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:3274 original size:11 final size:12
Alignment explanation
Indices: 3222--3277 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 12
3212 AGTAAGTGCT
*
3222 ACAACAAAAAGTA
1 ACAAGAAAAAG-A
3235 ACAAG--AAAGA
1 ACAAGAAAAAGA
*
3245 AGAAGAAAAA-A
1 ACAAGAAAAAGA
3256 ACAA-AAAAAGA
1 ACAAGAAAAAGA
3267 A-AAGAAAAAGA
1 ACAAGAAAAAGA
3278 CTCCTACATC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 12 0.33
11 17 0.47
12 3 0.08
13 4 0.11
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (12 bp):
ACAAGAAAAAGA
Found at i:5584 original size:14 final size:15
Alignment explanation
Indices: 5565--5602 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5555 CACGATAAGA
5565 ATAAATAAA-CAAAG
1 ATAAATAAATCAAAG
*
5579 ATAAATAAATGAAAG
1 ATAAATAAATCAAAG
5594 ATGAAATAA
1 AT-AAATAA
5603 GATAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.18
Consensus pattern (15 bp):
ATAAATAAATCAAAG
Found at i:9145 original size:12 final size:12
Alignment explanation
Indices: 9128--9190 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
9118 AAATTTTGGC
*
9128 TTTTTTTGGCTT
1 TTTTTTTGCCTT
**
9140 TTTTTTT-TTTT
1 TTTTTTTGCCTT
*
9151 TTTTTTTGCCGT
1 TTTTTTTGCCTT
9163 TTTTTTTGCCTT
1 TTTTTTTGCCTT
9175 TTTTTTTG--TT
1 TTTTTTTGCCTT
9185 TTTTTT
1 TTTTTT
9191 GAAAAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
10 8 0.18
11 9 0.20
12 27 0.61
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.83
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:9993 original size:43 final size:47
Alignment explanation
Indices: 9940--10041 Score: 115
Period size: 50 Copynumber: 2.2 Consensus size: 47
9930 ACTAAAGAAT
*
9940 AAATATTAATAAACT-AAACA-TGTTTTAA-C-CC-TAATTCCTAATA
1 AAATAATAAT-AACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
*
9983 AAATAATAATAACTAAAAATATTGTTTTAACCCAACCTTAATTCCTAATA
1 AAATAATAATAACT-AAAACATTGTTTTAA-CC-ACCTTAATTCCTAATA
10033 AAATAATAA
1 AAATAATAA
10042 ATATGATCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
42 4 0.08
43 9 0.18
44 4 0.08
45 8 0.16
47 1 0.02
49 2 0.04
50 21 0.43
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (47 bp):
AAATAATAATAACTAAAACATTGTTTTAACCACCTTAATTCCTAATA
Found at i:22316 original size:22 final size:21
Alignment explanation
Indices: 22269--22317 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
22259 AAAAATTCAG
22269 CAAAGAAAAATCAAAGCACTC
1 CAAAGAAAAATCAAAGCACTC
* *
22290 AAAAGAAGAAATTGAAAGCAC-C
1 CAAAGAA-AAA-TCAAAGCACTC
22312 CAAAGA
1 CAAAGA
22318 GGAAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 9 0.39
23 8 0.35
ACGTcount: A:0.59, C:0.18, G:0.14, T:0.08
Consensus pattern (21 bp):
CAAAGAAAAATCAAAGCACTC
Found at i:25100 original size:23 final size:25
Alignment explanation
Indices: 25072--25126 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
25062 AAATTCAGCA
*
25072 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACCCAAAGAGG
* *
25095 AAGAAATTGAAAGCACCCAAAGAGG
1 AAGAAAATCAAAGCACCCAAAGAGG
25120 AAGAAAA
1 AAGAAAA
25127 AAAGAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.60, C:0.15, G:0.18, T:0.07
Consensus pattern (25 bp):
AAGAAAATCAAAGCACCCAAAGAGG
Found at i:27897 original size:23 final size:25
Alignment explanation
Indices: 27869--27923 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
27859 AAATTCAGCA
*
27869 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACCCAAAGAGG
* *
27892 AAGAAATTGAAAGCACCCAAAGAGG
1 AAGAAAATCAAAGCACCCAAAGAGG
27917 AAGAAAA
1 AAGAAAA
27924 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.60, C:0.15, G:0.18, T:0.07
Consensus pattern (25 bp):
AAGAAAATCAAAGCACCCAAAGAGG
Found at i:40122 original size:13 final size:13
Alignment explanation
Indices: 40104--40198 Score: 56
Period size: 13 Copynumber: 7.7 Consensus size: 13
40094 TAGGCGTGCA
40104 ATGGTGATGGAAT
1 ATGGTGATGGAAT
**
40117 ATGGTGATGTTAT
1 ATGGTGATGGAAT
* *
40130 A-GGCG-T-GAAA
1 ATGGTGATGGAAT
*
40140 ATGGTGATGGAAG
1 ATGGTGATGGAAT
**
40153 ATGGTGATGTTAT
1 ATGGTGATGGAAT
* * *
40166 A-GG-AATGAAAA
1 ATGGTGATGGAAT
*
40177 ATGGTGATGGAAG
1 ATGGTGATGGAAT
40190 ATGGTGATG
1 ATGGTGATG
40199 TTATAGGTAG
Statistics
Matches: 59, Mismatches: 18, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
10 2 0.03
11 9 0.15
12 8 0.14
13 40 0.68
ACGTcount: A:0.33, C:0.01, G:0.38, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:40187 original size:37 final size:36
Alignment explanation
Indices: 40057--40205 Score: 203
Period size: 35 Copynumber: 4.2 Consensus size: 36
40047 TTACTGGTTA
* * * *
40057 TATAGGCGT-TAAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
* *
40092 TATAGGCGTG-CAATGGTGATGGAATATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
40127 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
**
40163 TATAGGAATGAAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAAATGGTGATGGAAGATGGTGATGT
40200 TATAGG
1 TATAGG
40206 TAGTATCTTA
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
35 39 0.38
36 31 0.30
37 32 0.31
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.30
Consensus pattern (36 bp):
TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
Found at i:44209 original size:11 final size:10
Alignment explanation
Indices: 44193--44243 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
44183 GATGTAATAC
44193 TCTTTTTATTT
1 TCTTTTT-TTT
44204 TCTTTTTTTT
1 TCTTTTTTTT
44214 T-TTGTTTTTCT
1 TCTT-TTTTT-T
*
44225 TCTTTCTTTT
1 TCTTTTTTTT
44235 TCTATTTTT
1 TCT-TTTTT
44244 GTTGCTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 2 0.06
10 13 0.38
11 17 0.50
12 2 0.06
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:44242 original size:21 final size:18
Alignment explanation
Indices: 44195--44243 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
44185 TGTAATACTC
44195 TTTTTA-TTTTCTTTTTT
1 TTTTTATTTTTCTTTTTT
*
44212 TTTTTGTTTTTCTTCTTTCT
1 TTTTTATTTTTCTT-TTT-T
44232 TTTTCTATTTTT
1 TTTT-TATTTTT
44244 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 3 0.12
20 5 0.19
21 6 0.23
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.84
Consensus pattern (18 bp):
TTTTTATTTTTCTTTTTT
Found at i:44471 original size:26 final size:26
Alignment explanation
Indices: 44426--44477 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
44416 AAGTTGTTAA
44426 ATAAATGGATAATTAAGAAA-GGAAAT
1 ATAAATGGATAATT-AGAAATGGAAAT
44452 ATAAATGGAAATAATT-GAAATGGAAA
1 ATAAATGG--ATAATTAGAAATGGAAA
44478 GAAATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 12 0.52
27 5 0.22
28 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (26 bp):
ATAAATGGATAATTAGAAATGGAAAT
Found at i:44728 original size:36 final size:35
Alignment explanation
Indices: 44630--44748 Score: 148
Period size: 35 Copynumber: 3.4 Consensus size: 35
44620 TTGTTGGTTA
* * * * *
44630 TATAGGCATAAAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
44665 TATAGGCGTGCAATGATGATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
*
44700 TATAGACGTGAATATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAA-ATGGTGATGGAAGATGGTGATGT
*
44736 TGTAGGCGTGAAA
1 TATAGGCGTGAAA
44749 AAATGGTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 39 0.55
36 32 0.45
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:47901 original size:11 final size:13
Alignment explanation
Indices: 47869--47898 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47859 TGGCCAAAGA
47869 TGAAAAGGTATGT
1 TGAAAAGGTATGT
47882 TGAAAAGGTATG-
1 TGAAAAGGTATGT
47894 TGAAA
1 TGAAA
47899 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:52139 original size:20 final size:19
Alignment explanation
Indices: 52104--52145 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
52094 AGCATTTATC
*
52104 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
52123 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
52143 TTC
1 TTC
52146 GAAGGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:57273 original size:14 final size:14
Alignment explanation
Indices: 57256--57289 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
57246 CAGTACTCAA
57256 AAAGAAAA-AAAAG
1 AAAGAAAAGAAAAG
57269 CAAAGAAAAGAAAAG
1 -AAAGAAAAGAAAAG
57284 AAAGAA
1 AAAGAA
57290 GTTGAAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:66674 original size:17 final size:17
Alignment explanation
Indices: 66649--66688 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
66639 GTATGTTGTT
*
66649 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
66666 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
66683 CATTTA
1 CATTTA
66689 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:66715 original size:17 final size:17
Alignment explanation
Indices: 66695--66753 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
66685 TTTAGGGAAG
66695 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
66712 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
66728 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
66745 TAGTTCATT
1 TAGTTCATT
66754 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Done.