Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008948.1 Hibiscus syriacus cultivar Beakdansim tig00112271_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: 81999
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1470 original size:19 final size:20
Alignment explanation
Indices: 1434--1475 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1424 GAAACCCCTT
1434 TGAAAACACATGATTTTTAA
1 TGAAAACACATGATTTTTAA
*
1454 TGAAAATACAT-ATTTTTAA
1 TGAAAACACATGATTTTTAA
1473 TGA
1 TGA
1476 GATAAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
TGAAAACACATGATTTTTAA
Found at i:3360 original size:19 final size:20
Alignment explanation
Indices: 3322--3364 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3312 GAAACCCCTT
*
3322 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
3342 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
3361 TGAA
1 TGAA
3365 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:17903 original size:16 final size:16
Alignment explanation
Indices: 17882--17920 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
17872 CCTGTGGCAC
17882 TTCTTTGCATTTTGAT
1 TTCTTTGCATTTTGAT
*
17898 TTCTTTTCATTTTGAT
1 TTCTTTGCATTTTGAT
17914 TTCTTTG
1 TTCTTTG
17921 TTTCCATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.13, G:0.10, T:0.67
Consensus pattern (16 bp):
TTCTTTGCATTTTGAT
Found at i:23540 original size:19 final size:20
Alignment explanation
Indices: 23502--23544 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
23492 GAAACCCCTT
*
23502 TGAAAACACATTATTTTTAA
1 TGAAAACACATTAATTTTAA
*
23522 TGAAAATACA-TAATTTTAA
1 TGAAAACACATTAATTTTAA
23541 TGAA
1 TGAA
23545 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TGAAAACACATTAATTTTAA
Found at i:25512 original size:19 final size:20
Alignment explanation
Indices: 25474--25516 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
25464 GAAACCCCTT
*
25474 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
25494 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
25513 TGAA
1 TGAA
25517 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:30209 original size:35 final size:37
Alignment explanation
Indices: 30163--30242 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
30153 TTTGAGAATT
*
30163 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
30198 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
30235 TGGTGATG
1 TGGTGATG
30243 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:33565 original size:24 final size:25
Alignment explanation
Indices: 33538--33587 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
33528 TAGAAAAGGT
*
33538 TAAGAAAATGAT-AAAG-TAATGAAA
1 TAAGAAAAT-ATGAAAGAAAATGAAA
33562 TAAGAAAATATGAAAGAAAATGAAA
1 TAAGAAAATATGAAAGAAAATGAAA
33587 T
1 T
33588 GAAATAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 13 0.57
25 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (25 bp):
TAAGAAAATATGAAAGAAAATGAAA
Found at i:33841 original size:11 final size:10
Alignment explanation
Indices: 33806--33856 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
33796 GATGTAAGAG
33806 TCTTTTTCTTT
1 TCTTTTT-TTT
*
33817 TCTTTTTGTT
1 TCTTTTTTTT
*
33827 T-TTTTTTCT
1 TCTTTTTTTT
33836 TCTTTTTTGTT
1 TCTTTTTT-TT
*
33847 GCTTTTTTTT
1 TCTTTTTTTT
33857 GTAGCACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 7 0.21
10 11 0.33
11 15 0.45
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:33842 original size:20 final size:21
Alignment explanation
Indices: 33808--33855 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
33798 TGTAAGAGTC
*
33808 TTTTTCTTTTCTTTTTGTTTT
1 TTTTTCTTCTCTTTTTGTTTT
33829 TTTTTCTTCT-TTTTTGTTGCTT
1 TTTTTCTTCTCTTTTTGTT--TT
33851 TTTTT
1 TTTTT
33856 TGTAGCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 9 0.38
22 7 0.29
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.83
Consensus pattern (21 bp):
TTTTTCTTCTCTTTTTGTTTT
Found at i:34277 original size:35 final size:37
Alignment explanation
Indices: 34231--34310 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
34221 TTTAAGAATT
*
34231 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
34266 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
34303 TGGTGATG
1 TGGTGATG
34311 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:37342 original size:19 final size:20
Alignment explanation
Indices: 37304--37346 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
37294 GAAACCCCTT
*
37304 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
37324 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
37343 TGAA
1 TGAA
37347 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:42759 original size:14 final size:13
Alignment explanation
Indices: 42742--42776 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
42732 TCTTTTTTTG
42742 TTTTTTTGCCGTTT
1 TTTTTTTGCC-TTT
42756 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
42769 TTTGTTTT
1 TTT-TTTT
42777 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:42760 original size:23 final size:22
Alignment explanation
Indices: 42734--42793 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
42724 TTTTTGGCTC
42734 TTTTTTTGTTTTTTTGCCGTTT
1 TTTTTTTGTTTTTTTGCCGTTT
* ***
42756 TTTTTTTGCCTTTTTTGTTTTTT
1 TTTTTTTG-TTTTTTTGCCGTTT
*
42779 TTTTTTTTTTTTTTT
1 TTTTTTTGTTTTTTT
42794 TGAAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTGCCGTTT
Found at i:44867 original size:35 final size:37
Alignment explanation
Indices: 44820--44899 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
44810 TTTAAGAATT
* *
44820 TGGTGATAATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
44855 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
44892 TGGTGATG
1 TGGTGATG
44900 GAAATAATAT
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:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:48671 original size:19 final size:20
Alignment explanation
Indices: 48633--48675 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
48623 GAAACCCCTT
*
48633 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
48653 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
48672 TGAA
1 TGAA
48676 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:53538 original size:15 final size:17
Alignment explanation
Indices: 53513--53549 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
53503 TAAAGGTTAT
*
53513 AAATAACTAATGAA-TA
1 AAATAACTAATAAACTA
53529 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
53545 AAATA
1 AAATA
53550 TCTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:57446 original size:26 final size:26
Alignment explanation
Indices: 57417--57477 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
57407 TCGTTTATAA
*
57417 TTTTGTTTGAAATTTTGGC-TTTTTTG
1 TTTT-TTTGAAATTTTGCCTTTTTTTG
***
57443 TTTTTTTGTTTTTTTGCCTTTTTTTG
1 TTTTTTTGAAATTTTGCCTTTTTTTG
57469 TTTTTTTGA
1 TTTTTTTGA
57478 TTGTTTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.07, C:0.05, G:0.15, T:0.74
Consensus pattern (26 bp):
TTTTTTTGAAATTTTGCCTTTTTTTG
Found at i:57447 original size:8 final size:8
Alignment explanation
Indices: 57436--57476 Score: 64
Period size: 8 Copynumber: 4.9 Consensus size: 8
57426 AAATTTTGGC
57436 TTTTTTGT
1 TTTTTTGT
57444 TTTTTTGT
1 TTTTTTGT
57452 TTTTTTGCCT
1 TTTTTTG--T
57462 TTTTTTGT
1 TTTTTTGT
57470 TTTTTTG
1 TTTTTTG
57477 ATTGTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 23 0.74
10 8 0.26
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTTGT
Found at i:57484 original size:18 final size:16
Alignment explanation
Indices: 57436--57476 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
57426 AAATTTTGGC
57436 TTTTTTGTTTTTTTGT
1 TTTTTTGTTTTTTTGT
57452 TTTTTTGCCTTTTTTTGT
1 TTTTTTG--TTTTTTTGT
57470 TTTTTTG
1 TTTTTTG
57477 ATTGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
18 16 0.70
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTTTTGTTTTTTTGT
Found at i:58263 original size:15 final size:17
Alignment explanation
Indices: 58238--58274 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
58228 TAAAGGTCCT
*
58238 AAATAACTAATGAA-TA
1 AAATAACTAATAAACTA
58254 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
58270 AAATA
1 AAATA
58275 TCTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:58320 original size:45 final size:45
Alignment explanation
Indices: 58250--58354 Score: 110
Period size: 50 Copynumber: 2.3 Consensus size: 45
58240 ATAACTAATG
*
58250 AATAAAATAATAATAAACTAAAATATCTTAA-C-TC-TAATTCCT
1 AATAAAATAATAATAAACTAAAATATCTTAACCACCTTAATTCCT
*
58292 AATAAAATAATAAT-AACTAAAGATAATATTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAAACT--A-A-AATATCTTAA-CC-ACCTTAATTCCT
58342 AATAAAATAATAA
1 AATAAAATAATAA
58355 ATATAATCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
41 4 0.08
42 14 0.27
43 1 0.02
44 1 0.02
45 9 0.17
47 1 0.02
49 1 0.02
50 21 0.40
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (45 bp):
AATAAAATAATAATAAACTAAAATATCTTAACCACCTTAATTCCT
Found at i:61840 original size:10 final size:10
Alignment explanation
Indices: 61825--61850 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
61815 TCTTTGATAA
61825 CATTTCTATC
1 CATTTCTATC
61835 CATTTCTATC
1 CATTTCTATC
61845 CATTTC
1 CATTTC
61851 CTTTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (10 bp):
CATTTCTATC
Found at i:62087 original size:30 final size:30
Alignment explanation
Indices: 62051--62107 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
62041 CAAGTGCTGC
* *
62051 AACAAAAGCAACAAA-AAGAGAAAAAGAAAG
1 AACAAAAACAA-AAAGAAAAGAAAAAGAAAG
62081 AACAAAAACAAAAAGAAAAGAAAAAGA
1 AACAAAAACAAAAAGAAAAGAAAAAGA
62108 CTCCTACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (30 bp):
AACAAAAACAAAAAGAAAAGAAAAAGAAAG
Found at i:69008 original size:22 final size:25
Alignment explanation
Indices: 68956--69009 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
68946 TTCTTTTCTT
*
68956 TTTCTTCATTTTTTAGTGCTTACAAA
1 TTTCTTCA-TTTTGAGTGCTTACAAA
68982 TTTCTTC-TTTTGAGTGCTT-C-AA
1 TTTCTTCATTTTGAGTGCTTACAAA
69004 TTTCTT
1 TTTCTT
69010 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 8 0.30
23 1 0.04
24 11 0.41
26 7 0.26
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTCTTCATTTTGAGTGCTTACAAA
Found at i:69043 original size:11 final size:11
Alignment explanation
Indices: 69029--69053 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
69019 TTTTATTTTT
69029 TTCACTTGCAC
1 TTCACTTGCAC
69040 TTCACTTGCAC
1 TTCACTTGCAC
69051 TTC
1 TTC
69054 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:73747 original size:35 final size:37
Alignment explanation
Indices: 73678--73757 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
73668 ATACTATTTC
*
73678 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
73715 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
73750 CATCACCA
1 CATCACCA
73758 AATTATCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:79429 original size:35 final size:37
Alignment explanation
Indices: 79361--79437 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
79351 TACTATTTCT
*
79361 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
*
79398 ATCACCATAGTCCATC-ACCA-TATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
79433 ATCAC
1 ATCAC
79438 TAAATTCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 20 0.53
36 3 0.08
37 15 0.39
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACGCCTATATC
Done.