Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007542.1 Hibiscus syriacus cultivar Beakdansim tig00021128_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: 59783
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3602 original size:18 final size:17
Alignment explanation
Indices: 3568--3611 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3558 CTTGGCTTGC
3568 TTTCTCTTTTGAATTTCT
1 TTTCT-TTTTGAATTTCT
*
3586 TTTCTTTTCTGATTTTCT
1 TTTCTTTT-TGAATTTCT
*
3604 CTTCTTTT
1 TTTCTTTT
3612 GTCTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTCTTTTTGAATTTCT
Found at i:5991 original size:24 final size:21
Alignment explanation
Indices: 5957--5999 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
5947 TCCACAAGAT
*
5957 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
5979 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
6000 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:14259 original size:19 final size:20
Alignment explanation
Indices: 14212--14262 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
14202 GAAACCCCTT
**
14212 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
14232 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
14251 TGAAGATACATG
1 TGAAAATACATG
14263 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:17465 original size:14 final size:15
Alignment explanation
Indices: 17435--17480 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
17425 TTTTGCTTCA
17435 CTTTTTCTTTTC-TT
1 CTTTTTCTTTTCTTT
*
17449 -TTTTT-TATTC-TT
1 CTTTTTCTTTTCTTT
17461 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTT
17476 CTTTT
1 CTTTT
17481 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 4 0.15
15 7 0.26
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTTTCTTT
Found at i:18876 original size:35 final size:36
Alignment explanation
Indices: 18820--18887 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
18810 ATACAATCTG
18820 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
18856 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
18888 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:24560 original size:35 final size:36
Alignment explanation
Indices: 24504--24571 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
24494 ATACAATCTG
24504 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
24540 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
24572 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:25766 original size:19 final size:20
Alignment explanation
Indices: 25719--25769 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
25709 GAAACCCCTT
**
25719 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
25739 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
25758 TGAAGATACATG
1 TGAAAATACATG
25770 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:33071 original size:24 final size:25
Alignment explanation
Indices: 33032--33081 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
33022 TAGAAAAGGT
*
33032 TAAGAAAAGGATAAAG-TAATGAAA
1 TAAGAAAAGGATAAAGAAAATGAAA
33056 TAAGAAAA-GATAAAAGAAAATGAAA
1 TAAGAAAAGGAT-AAAGAAAATGAAA
33081 T
1 T
33082 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 12 0.52
25 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (25 bp):
TAAGAAAAGGATAAAGAAAATGAAA
Found at i:33342 original size:21 final size:21
Alignment explanation
Indices: 33303--33343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33293 TAGGAGTCTT
*
33303 TTCTTTCTCTTTTTGTTTTTC
1 TTCTTTCTCTTTTTCTTTTTC
33324 TTCTTTCT-TTTTCTCTTTTT
1 TTCTTTCTCTTTT-TCTTTTT
33344 GTTGCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TTCTTTCTCTTTTTCTTTTTC
Found at i:33752 original size:11 final size:11
Alignment explanation
Indices: 33730--33776 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
33720 TTTGAGAATT
33730 TGGTGATGATA
1 TGGTGATGATA
33741 TAGGTG-TGATA
1 T-GGTGATGATA
33752 TGGTGATGGACTA
1 TGGTGAT-GA-TA
33765 TGGTGATGATA
1 TGGTGATGATA
33776 T
1 T
33777 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:33758 original size:22 final size:24
Alignment explanation
Indices: 33730--33776 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
33720 TTTGAGAATT
33730 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
33752 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
33776 T
1 T
33777 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:33776 original size:35 final size:37
Alignment explanation
Indices: 33730--33809 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
33720 TTTGAGAATT
* *
33730 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
33765 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
33802 TGGTGATG
1 TGGTGATG
33810 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:41295 original size:28 final size:27
Alignment explanation
Indices: 41247--41306 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
41237 ACCAGAACTA
41247 TTTTTTTTTAATTTTCAGAATT-TTGT
1 TTTTTTTTTAATTTTCAGAATTCTTGT
**
41273 TTTTGTTTTTAAATTTTTGGAATTCTT-T
1 TTTT-TTTTT-AATTTTCAGAATTCTTGT
41301 TTTTTT
1 TTTTTT
41307 CAAGATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 7 0.24
28 16 0.55
29 2 0.07
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (27 bp):
TTTTTTTTTAATTTTCAGAATTCTTGT
Found at i:42249 original size:21 final size:21
Alignment explanation
Indices: 42210--42249 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42200 AAGGACGATT
*
42210 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
42231 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
42250 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:42298 original size:22 final size:20
Alignment explanation
Indices: 42272--42316 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
42262 GTTGCGGAAT
42272 TGATGGACTTGATGGATGAAGA
1 TGATGGACTTGAT-GATGAA-A
**
42294 TGATGGTGTTGATGATGAAA
1 TGATGGACTTGATGATGAAA
42314 TGA
1 TGA
42317 AGATGGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (20 bp):
TGATGGACTTGATGATGAAA
Found at i:46103 original size:13 final size:12
Alignment explanation
Indices: 46065--46148 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 12
46055 CCTTGGCTTG
*
46065 TTTTCTCTTTTTGA
1 TTTTCT-TTTTT-C
46079 TTTTC-TTTTTC
1 TTTTCTTTTTTC
46090 TTTTCTTTTATTC
1 TTTTCTTTT-TTC
46103 TTTTCTGAATTTTTC
1 TTTTCT---TTTTTC
46118 -TTT-TTTTTTC
1 TTTTCTTTTTTC
46128 TTTGTC-TTTTTC
1 TTT-TCTTTTTTC
46140 -TTTCTTTTT
1 TTTTCTTTTT
46149 GCACTCCAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
10 8 0.13
11 13 0.22
12 15 0.25
13 10 0.17
14 8 0.13
15 3 0.05
16 3 0.05
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:46135 original size:16 final size:16
Alignment explanation
Indices: 46116--46146 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46106 TCTGAATTTT
*
46116 TCTTTTTTTTTCTTTG
1 TCTTTTTCTTTCTTTG
46132 TCTTTTTCTTTCTTT
1 TCTTTTTCTTTCTTT
46147 TTGCACTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TCTTTTTCTTTCTTTG
Found at i:46402 original size:14 final size:14
Alignment explanation
Indices: 46383--46424 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
46373 AAATGAAAAT
46383 GATTAATAAAGGAA
1 GATTAATAAAGGAA
*
46397 GATTAATGAAATGAA
1 GATTAAT-AAAGGAA
*
46412 -ATAAATAAAGGAA
1 GATTAATAAAGGAA
46425 TGAGATGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 12 0.50
15 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (14 bp):
GATTAATAAAGGAA
Found at i:46468 original size:22 final size:21
Alignment explanation
Indices: 46442--46482 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
46432 GCTGTGGAAT
46442 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
46464 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
46483 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:47794 original size:19 final size:20
Alignment explanation
Indices: 47770--47815 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
47760 CGGCCAAGAG
**
47770 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
47789 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
47809 CATGTAT
1 CATGTAT
47816 TTTTAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:51124 original size:26 final size:26
Alignment explanation
Indices: 51089--51178 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
51079 ATCCATTTCT
*
51089 TAACCTTTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
* *
51115 TAAACATTTCTATCCTAACCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
51141 TAACCATTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
51167 TAACCATTTCTA
1 TAACCATTTCTA
51179 GACCCTAACC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (26 bp):
TAACCATTTCTATCCTACCCCTATCA
Found at i:59162 original size:19 final size:20
Alignment explanation
Indices: 59119--59159 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
59109 TATCCTTTCT
59119 TTATTTCATTTTCATTCTTA
1 TTATTTCATTTTCATTCTTA
59139 TTATTTC-TTTTCATTACTTA
1 TTATTTCATTTTCATT-CTTA
59159 T
1 T
59160 ATTATTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTCATTTTCATTCTTA
Found at i:59475 original size:17 final size:18
Alignment explanation
Indices: 59453--59487 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
59443 AAAAGAAGTG
*
59453 AAAAA-TCAGAAAAGAAA
1 AAAAATTCAAAAAAGAAA
59470 AAAAATTCAAAAAAGAAA
1 AAAAATTCAAAAAAGAAA
59488 GCAAGCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAAATTCAAAAAAGAAA
Done.