Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003721.1 Hibiscus syriacus cultivar Beakdansim tig00007959_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: 25434
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1081 original size:14 final size:14
Alignment explanation
Indices: 1062--1108 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
1052 TTCAAGTCGT
1062 AATCATTACTATCA
1 AATCATTACTATCA
1076 AATCATTAC--T-A
1 AATCATTACTATCA
*
1087 AATCATTAATATCA
1 AATCATTACTATCA
1101 AATCATTA
1 AATCATTA
1109 AATATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (14 bp):
AATCATTACTATCA
Found at i:1124 original size:21 final size:22
Alignment explanation
Indices: 1062--1118 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 22
1052 TTCAAGTCGT
*
1062 AATCATTACTATCAAATCATTACTA
1 AATCATTAATATCAAATCA-T--TA
1087 AATCATTAATATCAAATCATTA
1 AATCATTAATATCAAATCATTA
1109 AAT-ATTAATA
1 AATCATTAATA
1119 ATAAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 7 0.23
22 5 0.16
24 1 0.03
25 18 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
AATCATTAATATCAAATCATTA
Found at i:1129 original size:21 final size:22
Alignment explanation
Indices: 1062--1129 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 22
1052 TTCAAGTCGT
* *
1062 AATCATTACTATCAAATCATTACTA
1 AATCATTAATATC-AA--ATTATTA
*
1087 AATCATTAATATCAAATCATTA
1 AATCATTAATATCAAATTATTA
1109 AAT-ATTAATAAT-AAATTATTA
1 AATCATTAAT-ATCAAATTATTA
1130 TTACTAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 14 0.37
22 10 0.26
24 2 0.05
25 12 0.32
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
AATCATTAATATCAAATTATTA
Found at i:1151 original size:47 final size:49
Alignment explanation
Indices: 1080--1757 Score: 776
Period size: 47 Copynumber: 13.3 Consensus size: 49
1070 CTATCAAATC
* * *
1080 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1129 ATTACTAATCA-TACTATCAAATCATT-AAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1176 ATTACTAATCATTACTAAATCATAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCA-T--T--A-C----TATCAAATCATTAAAAATTAATAATAATTTCATT
*
1235 GTTACTAATCATTACTATCATTATCATCATTAAAAATTAATAATAATTTCA-T
1 ATTACTAATCATTACTATCA--A--ATCATTAAAAATTAATAATAATTTCATT
1287 -TTACTAATCATTACTATC-AATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1334 ATTACTAATCATTACTAAATCATTACAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAC----T-A-T-CAAATCATTAAAAATTAATAATAATTTCATT
* *
1390 A-TACTAATCA-TACTATCAAATTATTAAAAATTAAT-ATAATTCCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1436 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATAATATATTCATTATTACTAT
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-AT-A-ATA---A-T-TT-C-AT
*
1500 C
49 T
*
1501 ATTACTAAATCATTACTATCAAATCATT-AAAATTAAAAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1550 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1599 ATTACTAATCA-TACTATCAAATCATT-AAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1646 ATTACTAATCATTACTATCAAA-CATT-AAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1693 ATTACTAATTATTACTATC-AATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1741 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1758 AATCATTAAT
Statistics
Matches: 557, Mismatches: 19, Indels: 107
0.82 0.03 0.16
Matches are distributed among these distances:
46 54 0.10
47 135 0.24
48 108 0.19
49 51 0.09
50 6 0.01
51 27 0.05
52 9 0.02
53 29 0.05
54 7 0.01
55 12 0.02
56 34 0.06
57 1 0.00
58 17 0.03
59 31 0.06
61 4 0.01
62 6 0.01
63 3 0.01
64 5 0.01
65 8 0.01
66 10 0.02
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1240 original size:59 final size:55
Alignment explanation
Indices: 1129--1874 Score: 643
Period size: 47 Copynumber: 14.1 Consensus size: 55
1119 ATAAATTATT
1129 ATTACTAATCATACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATA-TATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
1186 ATTACTAAATCATAATATCAAATCATTAAATATTAATAATAATTTCATTGTTACTAATC
1 ATTACT-AATCAT-ATATCAAATCATTAAA-ATTAATAATAATTTCATT-TTACTAATC
1245 ATTACT-ATCAT-TATC--ATCATTAAAAATTAATAATAATTTCA-TTTACTAATC
1 ATTACTAATCATATATCAAATCATT-AAAATTAATAATAATTTCATTTTACTAATC
*
1296 ATTACT-ATC--A-ATC--AT--TAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATATATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
*
1344 ATTACTAAATCAT-TA-CAAATCATTAAAAATTAATAATAATTTCATTATACTAATC
1 ATTACT-AATCATATATCAAATCATT-AAAATTAATAATAATTTCATTTTACTAATC
*
1399 A-TACT-ATCA-A-AT----T-ATTAAAAATTAAT-ATAATTCCATTATTACTAATC
1 ATTACTAATCATATATCAAATCATT-AAAATTAATAATAATTTCATT-TTACTAATC
1446 ATTACTAAATCATTAATATCAAATCATT-AAA-T-ATAAT-ATATTCATTATTACT-ATC
1 ATTACT-AATCA-T-ATATCAAATCATTAAAATTAATAATAAT-TTCATT-TTACTAATC
*
1501 ATTACTAAATCATTACTATCAAATCATTAAAATTAAAAATAATTTCATTATTACTAATC
1 ATTACT-AATCA-TA-TATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
*
1560 ATTACT-ATCA-A-ATC--AT--TAAAAATTAATAATAATTTC-----A-T--T-
1 ATTACTAATCATATATCAAATCATTAAAATTAATAATAATTTCATTTTACTAATC
1599 ATTACTAATCATACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATA-TATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
*
1656 A-T--T-A-C---TATCAAA-CATTAAAATTAATAATAATTTCATTATTACTAATT
1 ATTACTAATCATATATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
*
1703 ATTACT-ATC--A-ATC--AT--TAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATATATCAAATCATTAAAATTAATAATAATTTCATT-TTACTAATC
1751 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCA-T-ATATCAAATCATTAAA-ATTAATAATAATTTCATT-TTACTAATC
* *
1811 ATTACTAAATCATTACTATCAAATCATT--AA-TATTAATAATTTCATCATTACTAATC
1 ATTACT-AATCA-TA-TATCAAATCATTAAAATTAATAATAATTTCAT-TTTACTAATC
1867 ATTACTAA
1 ATTACTAA
1875 ATCTTATAAA
Statistics
Matches: 594, Mismatches: 17, Indels: 158
0.77 0.02 0.21
Matches are distributed among these distances:
39 6 0.01
40 5 0.01
41 1 0.00
42 1 0.00
43 4 0.01
45 2 0.00
46 29 0.05
47 78 0.13
48 65 0.11
49 24 0.04
50 12 0.02
51 26 0.04
52 7 0.01
53 30 0.05
54 13 0.02
55 53 0.09
56 69 0.12
57 23 0.04
58 39 0.07
59 53 0.09
60 54 0.09
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (55 bp):
ATTACTAATCATATATCAAATCATTAAAATTAATAATAATTTCATTTTACTAATC
Found at i:1356 original size:11 final size:11
Alignment explanation
Indices: 1334--1368 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
1324 TAATTTCATT
1334 ATTACT-AATC
1 ATTACTAAATC
1344 ATTACTAAATC
1 ATTACTAAATC
1355 ATTAC-AAATC
1 ATTACTAAATC
1365 ATTA
1 ATTA
1369 AAAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1580 original size:48 final size:48
Alignment explanation
Indices: 1446--1757 Score: 452
Period size: 48 Copynumber: 6.4 Consensus size: 48
1436 ATTACTAATC
* * *
1446 ATTACTAAATCATTAATATCAAATCATT-AAATATAATATATTCATTATTACTATC
1 ATTACT-AATCATTACTATCAAATCATTAAAAT-TAATA-A-T-A--ATTTC-ATT
*
1501 ATTACTAAATCATTACTATCAAATCATTAAAATTAAAAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1550 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
1599 ATTACTAATCA-TACTATCAAATCATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1646 ATTACTAATCATTACTATCAAA-CATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
*
1693 ATTACTAATTATTACTATC-AATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
1741 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1758 AATCATTAAT
Statistics
Matches: 245, Mismatches: 7, Indels: 17
0.91 0.03 0.06
Matches are distributed among these distances:
46 2 0.01
47 79 0.32
48 83 0.34
49 39 0.16
50 4 0.02
52 1 0.00
53 1 0.00
54 1 0.00
55 31 0.13
56 4 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
Found at i:1654 original size:21 final size:21
Alignment explanation
Indices: 1583--1654 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1573 CATTAAAAAT
1583 TAATAATAATTTCATTATTAC
1 TAATAATAATTTCATTATTAC
** ** *
1604 TAATCATACTATCAAATCATTAAAAT
1 TAAT-A-A-TA--ATTTCATTATTAC
1630 TAATAATAATTTCATTATTAC
1 TAATAATAATTTCATTATTAC
1651 TAAT
1 TAAT
1655 CATTACTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 16 0.44
22 1 0.03
23 3 0.08
24 3 0.08
25 1 0.03
26 12 0.33
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATAATAATTTCATTATTAC
Found at i:1738 original size:95 final size:97
Alignment explanation
Indices: 1446--1817 Score: 466
Period size: 96 Copynumber: 3.7 Consensus size: 97
1436 ATTACTAATC
* * * *
1446 ATTACTAAATCATTAATATCAAATCATTAAATA-TAATATATTCATTATTACTATCATTACTAAA
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATA-A-T-A--ATTTC-ATTATTACT-AA
*
1510 TCATTACTATCAAATCATTAAAATTAAAAATAATTTCATT
58 TCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1550 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA-TACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1614 ATCAAATCATTAAAATTAATAATAATTTCATT
66 ATCAAATCATTAAAATTAATAATAATTTCATT
*
1646 ATTACTAATCATTACTATCAAA-CATT-AAAATTAATAATAATTTCATTATTACTAATTATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1709 ATC-AATCATTAAAAATTAATAATAATTTCATT
66 ATCAAATCATT-AAAATTAATAATAATTTCATT
*
1741 ATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATCA-T--T--A-C-----TATCAAATCATTAAAAATTAATAATAATTTCATTATTAC
1806 TAATCATTACTA
55 TAATCATTACTA
1818 AATCATTACT
Statistics
Matches: 244, Mismatches: 8, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
94 38 0.16
95 43 0.18
96 58 0.24
97 5 0.02
98 9 0.04
99 4 0.02
100 1 0.00
101 2 0.01
102 1 0.00
103 25 0.10
104 11 0.05
106 7 0.03
107 4 0.02
108 36 0.15
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (97 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
ATCAAATCATTAAAATTAATAATAATTTCATT
Found at i:1765 original size:21 final size:21
Alignment explanation
Indices: 1741--1828 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
1731 TAATTTCATT
1741 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
1762 ATTAAT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
1783 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
1801 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
1822 ATTACTA
1 ATTACTA
1829 TCAAATCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
17 2 0.04
18 12 0.24
20 6 0.12
21 20 0.40
22 10 0.20
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:4701 original size:25 final size:25
Alignment explanation
Indices: 4672--4724 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
4662 TATATAATCT
*
4672 ATATATAACTTAAACTAACAAATTA
1 ATATATAACTTAAACTAACAAACTA
4697 ATATATAACTTAAACTAACAAACTA
1 ATATATAACTTAAACTAACAAACTA
4722 ATA
1 ATA
4725 ATTTATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (25 bp):
ATATATAACTTAAACTAACAAACTA
Found at i:5513 original size:28 final size:28
Alignment explanation
Indices: 5413--5543 Score: 111
Period size: 28 Copynumber: 4.5 Consensus size: 28
5403 GACGCCGGGC
*
5413 ATGCATGGCGACCTATAAGGTCGCTGGG
1 ATGCATGGCGACCTACAAGGTCGCTGGG
* * * * *
5441 CGTGCAT-GCGACCTACTAGCTTGGTCCGGG
1 -ATGCATGGCGACCTACAAG-GTCG-CTGGG
*
5471 ATTGCTTGGCGACCTACAAGGTCGCTGGG
1 A-TGCATGGCGACCTACAAGGTCGCTGGG
***
5500 ATGCATGGCGACCTTGTAGGTCGCTGGG
1 ATGCATGGCGACCTACAAGGTCGCTGGG
*
5528 AGTGCTTGGCGACCTA
1 A-TGCATGGCGACCTA
5544 TGGTTGGGTT
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
28 34 0.43
29 24 0.30
30 10 0.13
31 11 0.14
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (28 bp):
ATGCATGGCGACCTACAAGGTCGCTGGG
Found at i:17878 original size:2 final size:2
Alignment explanation
Indices: 17871--17955 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
17861 TATTAATCAA
17871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17955 A
1 A
17956 CCCAACCCAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18325 original size:3 final size:3
Alignment explanation
Indices: 18317--18349 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
18307 TAATTAAAGG
*
18317 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18350 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:22891 original size:15 final size:15
Alignment explanation
Indices: 22872--22910 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
22862 TTTCCTCGAA
22872 TTTATTTTTATTT-T
1 TTTATTTTTATTTAT
22886 TATTATTTTTATTTAT
1 T-TTATTTTTATTTAT
22902 TTTATTTTT
1 TTTATTTTT
22911 TTGCAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.04
15 20 0.87
16 2 0.09
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:22900 original size:19 final size:17
Alignment explanation
Indices: 22878--22912 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
22868 CGAATTTATT
22878 TTTATTTTTATTATTTTTA
1 TTTA-TTTTATT-TTTTTA
22897 TTTATTTTATTTTTTT
1 TTTATTTTATTTTTTT
22913 GCAAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Done.