Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003798.1 Hibiscus syriacus cultivar Beakdansim tig00008124_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: 61225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:408 original size:35 final size:35
Alignment explanation
Indices: 367--442 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
357 AATTGAATTT
* *
367 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* *
402 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
437 AATTGA
1 AATTGA
443 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:1718 original size:24 final size:25
Alignment explanation
Indices: 1670--1721 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
1660 GAGGACATAT
*
1670 GAAATTTGTCCCGAATGACCGCGTA
1 GAAATTTGTCCCGAATGACCACGTA
1695 GAAATTTG-CCCGAA-GTACCACGTA
1 GAAATTTGTCCCGAATG-ACCACGTA
1719 GAA
1 GAA
1722 TTGCACTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 16 0.64
25 8 0.32
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (25 bp):
GAAATTTGTCCCGAATGACCACGTA
Found at i:1881 original size:24 final size:24
Alignment explanation
Indices: 1845--1890 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1835 AAGAATACAT
* *
1845 ATATGTCCTGAAGGACCGCGTATG
1 ATATGTCCCGAAGAACCGCGTATG
1869 ATATGTCCCGAAGAACCGCGTA
1 ATATGTCCCGAAGAACCGCGTA
1891 GACCCTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (24 bp):
ATATGTCCCGAAGAACCGCGTATG
Found at i:2883 original size:215 final size:215
Alignment explanation
Indices: 2495--2915 Score: 697
Period size: 215 Copynumber: 2.0 Consensus size: 215
2485 CAAGAGTCAC
* *
2495 TTCTTACCGTAGTAACTCCTTCATTAACTCATTGCAAGCCAATGTTTGATCAATAATATAAGTAC
1 TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
**
2560 AATTAAATTGCACTCGTCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAACTT
66 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAACTT
2625 GTTTAGGCTCAATATCTACATAAACATAATTTCCGAGATGAATATCAGAAGCCTAAACCTTATAA
131 GTTTAGGCTCAATATCTACATAAACATAATTTCCGAGATGAATATCAGAAGCCTAAACCTTATAA
2690 CTTGATGTTAATAACTTCAT
196 CTTGATGTTAATAACTTCAT
* * *
2710 TTCTTACCGTAGTAACTCTTTCACTGACTCATCGCAAGTCAA-G-TTGATCAATAATATAAGTAC
1 TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
* *
2773 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCCTAACTT-TTTGATTGTTCTGGAAA
66 AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAA-TTCTTTGATTGTTC-CG-AA
2837 CTTGTTTAGGCTCAATATCTACATAAACATAACTTT-CGAGATGAATATCAGAAGCCTAAACCTT
128 CTTGTTTAGGCTCAATATCTACATAAACATAA-TTTCCGAGATGAATATCAGAAGCCTAAACCTT
2901 ATAACTTGATGTTAA
192 ATAACTTGATGTTAA
2916 AAATTAAGCT
Statistics
Matches: 193, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
213 72 0.37
214 4 0.02
215 114 0.59
216 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (215 bp):
TTCTTACCGTAGTAACTCCTTCACTAACTCATCGCAAGCCAATGTTTGATCAATAATATAAGTAC
AATTAAATTGCACTCACCTTAGCCTTGCTTTGATTTGATCATAATTCTTTGATTGTTCCGAACTT
GTTTAGGCTCAATATCTACATAAACATAATTTCCGAGATGAATATCAGAAGCCTAAACCTTATAA
CTTGATGTTAATAACTTCAT
Found at i:4061 original size:3 final size:3
Alignment explanation
Indices: 4055--4111 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
4045 ATCCATTTTT
* *
4055 TTA TTA TTA TTTA ATA TTA TTA ATA TTA -TA TTA TTTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
4101 -TA TTT TTA TTA
1 TTA TTA TTA TTA
4112 ATAAATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4086 original size:24 final size:25
Alignment explanation
Indices: 4054--4124 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
4044 TATCCATTTT
4054 TTTATTATTATTTAATATTATTAATA
1 TTTA-TATTATTTAATATTATTAATA
*
4080 -TTATATTATTTATTATTATT-ATA
1 TTTATATTATTTAATATTATTAATA
* * *
4103 TTTTTATTAATAAATATTATTA
1 TTTATATTATTTAATATTATTA
4125 CAAACATGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 3 0.08
24 32 0.84
25 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATATTATTTAATATTATTAATA
Found at i:4092 original size:34 final size:34
Alignment explanation
Indices: 4054--4123 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
4044 TATCCATTTT
*
4054 TTTATTATTATT-TAATATTATTAATATTATATTA
1 TTTATTATTATTATAATATTATTAATA-AATATTA
* *
4088 TTTATTATTATTATATTTTTATTAATAAATATTA
1 TTTATTATTATTATAATATTATTAATAAATATTA
4122 TT
1 TT
4124 ACAAACATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 20 0.62
35 12 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTATTATTATTATAATATTATTAATAAATATTA
Found at i:4093 original size:21 final size:20
Alignment explanation
Indices: 4069--4122 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
4059 TATTATTTAA
4069 TATTATTAATATTATATTATT
1 TATTATTAATATTATATT-TT
4090 TATTA-T--TATTATATTTT
1 TATTATTAATATTATATTTT
*
4107 TATTAATAAATATTAT
1 TATT-ATTAATATTAT
4123 TACAAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
20 1 0.04
21 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATTAATATTATATTTT
Found at i:5490 original size:18 final size:18
Alignment explanation
Indices: 5469--5511 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5459 TTATTATTAT
*
5469 TATTTA-ATTATAAATATA
1 TATTTATATGATAAATA-A
5487 TATTTATATGATAAATAA
1 TATTTATATGATAAATAA
5505 TATTTAT
1 TATTTAT
5512 TTTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTTATATGATAAATAA
Found at i:5493 original size:22 final size:20
Alignment explanation
Indices: 5468--5513 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
5458 ATTATTATTA
*
5468 TTATTTAATTATAAATATATAT
1 TTATTT-ATGATAAATA-ATAT
5490 TTA--TATGATAAATAATAT
1 TTATTTATGATAAATAATAT
5508 TTATTT
1 TTATTT
5514 TATTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 2 0.10
22 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTTATGATAAATAATAT
Found at i:5678 original size:107 final size:108
Alignment explanation
Indices: 5567--5768 Score: 255
Period size: 108 Copynumber: 1.9 Consensus size: 108
5557 CATGTTTTAA
* * * * * * *
5567 TATTTATTTATTTTTCAATAT-TAA-GAAAGGGCAGTCTTAAAATAACTGGATGTCCATTTTTTG
1 TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TTTTCTG
*
5630 ATATTTTTAAATAAATAAATATTCTATTTATAAATTATATAAAT
65 ATATTTCTAAATAAATAAATATTCTATTTATAAATTATATAAAT
* * ** *
5674 TATTTATTTATTTTTTAATATAAAATAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGA
1 TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGA
*
5739 TATTTCTAAATAAATAAATATTTTATTTAT
66 TATTTCTAAATAAATAAATATTCTATTTAT
5769 TTATATATAT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
107 20 0.25
108 37 0.47
109 22 0.28
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (108 bp):
TATTTATTTATTTTTCAATATAAAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGA
TATTTCTAAATAAATAAATATTCTATTTATAAATTATATAAAT
Found at i:5681 original size:24 final size:23
Alignment explanation
Indices: 5631--5684 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5621 CATTTTTTGA
*
5631 TATTTTTAAATAAATAAATATTC
1 TATTTATAAATAAATAAATATTC
*
5654 TATTTATAAATTATATAAATTATT-
1 TATTTATAAA-TAAATAAA-TATTC
5678 TATTTAT
1 TATTTAT
5685 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 14 0.52
25 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATTC
Found at i:6474 original size:17 final size:17
Alignment explanation
Indices: 6452--6485 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6442 ATGTTATTAA
6452 AATGACAAAACGTTTTG
1 AATGACAAAACGTTTTG
6469 AATGACAAAACGTTTTG
1 AATGACAAAACGTTTTG
6486 GGTTCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
AATGACAAAACGTTTTG
Found at i:7514 original size:23 final size:22
Alignment explanation
Indices: 7461--7505 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
7451 TTTTAATAAC
7461 TTTATC-C-TTATGACATATTT
1 TTTATCTCTTTATGACATATTT
*
7481 TTTATGTCTTTATGACATATTT
1 TTTATCTCTTTATGACATATTT
7503 TTT
1 TTT
7506 TCTACCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 1 0.05
22 16 0.73
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTATCTCTTTATGACATATTT
Found at i:8501 original size:19 final size:19
Alignment explanation
Indices: 8477--8517 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
8467 ACAAAATCGA
8477 ATTTACATAGTATAAATAG
1 ATTTACATAGTATAAATAG
* *
8496 ATTTACATTGTATAGATAG
1 ATTTACATAGTATAAATAG
8515 ATT
1 ATT
8518 GTAACTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTTACATAGTATAAATAG
Found at i:9267 original size:2 final size:2
Alignment explanation
Indices: 9260--9379 Score: 240
Period size: 2 Copynumber: 60.0 Consensus size: 2
9250 TTTGATTCCG
9260 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9302 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9344 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9380 TCCTAATAAA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 118 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9748 original size:2 final size:2
Alignment explanation
Indices: 9741--9777 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
9731 ACAGTGATAC
* *
9741 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9778 AATTTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:10516 original size:18 final size:17
Alignment explanation
Indices: 10478--10531 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
10468 ATTTATAAAA
* *
10478 ATATTATTTAAATTTTT
1 ATATTTTTTAAATTATT
10495 ATATTTTTTAAATTCATT
1 ATATTTTTTAAATT-ATT
*
10513 ATATTTTATTAAAATATT
1 ATATTTT-TTAAATTATT
10531 A
1 A
10532 ACGATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.41
18 13 0.41
19 6 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTTAAATTATT
Found at i:18737 original size:43 final size:45
Alignment explanation
Indices: 18665--18778 Score: 115
Period size: 49 Copynumber: 2.4 Consensus size: 45
18655 TTTTCTTTTG
* **
18665 ATTTTTGGTTTTTTTTTCTGATTTGAATGTT-GA-TTTCTTCTTCTA
1 ATTTTTGG--TTTTTTTCTTATTAAAATGTTGGATTTTCTTCTTCTA
*
18710 ATTTTTGGTTTTTTTCTTATTAAAATGTTGAGGATTTTTTCTTCTTCTG
1 ATTTTTGGTTTTTTTCTTATTAAAATGTT--GGA--TTTTCTTCTTCTA
*
18759 ATTTTTGGTTTTTTTATTAT
1 ATTTTTGGTTTTTTTCTTAT
18779 ATGTAGAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
43 18 0.31
45 8 0.14
46 2 0.03
49 30 0.52
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (45 bp):
ATTTTTGGTTTTTTTCTTATTAAAATGTTGGATTTTCTTCTTCTA
Found at i:18771 original size:24 final size:24
Alignment explanation
Indices: 18698--18773 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
18688 TGAATGTTGA
18698 TTTCTTCTTCTAATTTTTGGTTTT
1 TTTCTTCTTCTAATTTTTGGTTTT
* ** ** *
18722 TTTCTTATTAAAATGTTGAGGATTT
1 TTTCTTCTTCTAAT-TTTTGGTTTT
*
18747 TTTCTTCTTCTGATTTTTGGTTTT
1 TTTCTTCTTCTAATTTTTGGTTTT
18771 TTT
1 TTT
18774 ATTATATGTA
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
24 21 0.55
25 17 0.45
ACGTcount: A:0.13, C:0.09, G:0.12, T:0.66
Consensus pattern (24 bp):
TTTCTTCTTCTAATTTTTGGTTTT
Found at i:40239 original size:21 final size:22
Alignment explanation
Indices: 40204--40270 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
40194 ACAAGTGTTT
*
40204 ATATTATATTTTTTTATTTTA-A
1 ATATT-TAATTTTTTATTTTACA
*
40226 ATATTTAATTTTTT-TGTTACA
1 ATATTTAATTTTTTATTTTACA
* *
40247 ATGTTTAATATTTTATTTTACA
1 ATATTTAATTTTTTATTTTACA
40269 AT
1 AT
40271 CGTTTTAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 4 0.11
21 21 0.55
22 13 0.34
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (22 bp):
ATATTTAATTTTTTATTTTACA
Found at i:40260 original size:22 final size:22
Alignment explanation
Indices: 40214--40275 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
40204 ATATTATATT
*
40214 TTTTTATTTTA-AAT-ATTTAA
1 TTTTTATTTTACAATCGTTTAA
40234 TTTTT-TTGTTACAAT-GTTTAA
1 TTTTTATT-TTACAATCGTTTAA
40255 TATTTTATTTTACAATCGTTT
1 T-TTTTATTTTACAATCGTTT
40276 TAAGATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 9 0.25
22 11 0.31
23 6 0.17
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTTATTTTACAATCGTTTAA
Found at i:44178 original size:14 final size:14
Alignment explanation
Indices: 44159--44186 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44149 AGATACGTTC
44159 AGCCGACATAATTA
1 AGCCGACATAATTA
44173 AGCCGACATAATTA
1 AGCCGACATAATTA
44187 GGCTGGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AGCCGACATAATTA
Found at i:48361 original size:14 final size:14
Alignment explanation
Indices: 48335--48375 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
48325 ATTTATATTA
48335 ATATTAT-TTAAAT
1 ATATTATATTAAAT
48348 ATATTATATTAAAT
1 ATATTATATTAAAT
*
48362 -TAATTAAATTAAAT
1 AT-ATTATATTAAAT
48376 CTCCATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTATATTAAAT
Done.