Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002983.1 Hibiscus syriacus cultivar Beakdansim tig00006172_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: 138081
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:18348 original size:57 final size:57
Alignment explanation
Indices: 18260--18374 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
18250 ATGGAACCTT
18260 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
*
18317 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTGGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
18374 C
1 C
18375 TTTAGGTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (57 bp):
CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
Found at i:20953 original size:21 final size:21
Alignment explanation
Indices: 20911--20953 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20901 TTTCTGGGCC
* * *
20911 AGGGGAATCGGTACTCATTCA
1 AGGGGAATCGATACCCACTCA
*
20932 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
20953 A
1 A
20954 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:21418 original size:30 final size:31
Alignment explanation
Indices: 21364--21434 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
21354 GTTATATGAA
21364 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
*
21395 TTATGTGATAAAGGTAT-GAAAATGATATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
* *
21425 CTATGCGATA
1 TTATGTGATA
21435 TAAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (31 bp):
TTATGTGATAAAGGTATGGAAAATGAAATGT
Found at i:21652 original size:24 final size:25
Alignment explanation
Indices: 21625--21681 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
21615 TTATATGTGG
21625 TCCTTCGGGACAAA-TTCTACGCGA
1 TCCTTCGGGACAAAGTTCTACGCGA
21649 TCCTTCGGGACAAAGTTCTACGCGA
1 TCCTTCGGGACAAAGTTCTACGCGA
21674 -CACTTCGG
1 TC-CTTCGG
21682 TGCAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 15 0.48
25 16 0.52
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (25 bp):
TCCTTCGGGACAAAGTTCTACGCGA
Found at i:34680 original size:228 final size:229
Alignment explanation
Indices: 34282--34740 Score: 911
Period size: 228 Copynumber: 2.0 Consensus size: 229
34272 AATTGTATTT
34282 TGATAGAGAGGGTAATGATGAAGTAGAAGGTAATTGGGAAAGATATGTTTGGAAGGGGGTAGCTC
1 TGATAGAGAGGGTAATGATGAAGTAGAAGGTAATTGGGAAAGATATGTTTGGAAGGGGGTAGCTC
34347 CACCACGAGTGGAAACCTTTGTTTGGCAACTTGCTCATCACAGAGTAGTGGTGAAGGAGGAACTG
66 CACCACGAGTGGAAACCTTTGTTTGGCAACTTGCTCATCACAGAGTAGTGGTGAAGGAGGAACTG
34412 CTAAAGAGAGGAGTTACTGGGGTGGAAGACACTGTGTGCTCTTTGTGCAGGAAGTGTAATGAGTC
131 CTAAAGAGAGGAGTTACTGGGGTGGAAGACACTGTGTGCTCTTTGTGCAGGAAGTGTAATGAGTC
34477 GGTCTCACATTTGTTTCTGCACTGTGATGTGGTG
196 GGTCTCACATTTGTTTCTGCACTGTGATGTGGTG
34511 TGATAGAGAGGGTAATGATGAAGTAGAAGGTAATTGGGAAAGATATGTTTGGAAGGGGGTAGCTC
1 TGATAGAGAGGGTAATGATGAAGTAGAAGGTAATTGGGAAAGATATGTTTGGAAGGGGGTAGCTC
34576 CACCACGAGTGGAAACC-TTGTTTGGCAACTTGCTCATCACAGAGTAGTGGTGAAGGAGGAACTG
66 CACCACGAGTGGAAACCTTTGTTTGGCAACTTGCTCATCACAGAGTAGTGGTGAAGGAGGAACTG
34640 CTAAAGAGAGGAGTTACTGGGGTGGAAGACACTGTGTGCTCTTTGTGCAGGAAGTGTAATGAGTC
131 CTAAAGAGAGGAGTTACTGGGGTGGAAGACACTGTGTGCTCTTTGTGCAGGAAGTGTAATGAGTC
34705 GGTCTCACATTTGTTTCTGCACTGTGATGTGGTG
196 GGTCTCACATTTGTTTCTGCACTGTGATGTGGTG
34739 TG
1 TG
34741 GGACCTGTGG
Statistics
Matches: 230, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 148 0.64
229 82 0.36
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.27
Consensus pattern (229 bp):
TGATAGAGAGGGTAATGATGAAGTAGAAGGTAATTGGGAAAGATATGTTTGGAAGGGGGTAGCTC
CACCACGAGTGGAAACCTTTGTTTGGCAACTTGCTCATCACAGAGTAGTGGTGAAGGAGGAACTG
CTAAAGAGAGGAGTTACTGGGGTGGAAGACACTGTGTGCTCTTTGTGCAGGAAGTGTAATGAGTC
GGTCTCACATTTGTTTCTGCACTGTGATGTGGTG
Found at i:52776 original size:21 final size:21
Alignment explanation
Indices: 52750--52795 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52740 GATTTCTGGA
* *
52750 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
52771 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
52792 CAAG
1 CAAG
52796 CAAATATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:54447 original size:22 final size:22
Alignment explanation
Indices: 54419--54484 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
54409 TTATGGACAT
54419 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54441 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54463 -ATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54484 A
1 A
54485 TTTATACGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.49
22 22 0.51
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:54468 original size:21 final size:21
Alignment explanation
Indices: 54420--54486 Score: 125
Period size: 21 Copynumber: 3.1 Consensus size: 21
54410 TATGGACATA
54420 ATTCTACGGGCACTTCGGTGC
1 ATTCTACGGGCACTTCGGTGC
54441 AATTCTACGGGCACTTCGGTGC
1 -ATTCTACGGGCACTTCGGTGC
54463 ATTCTACGGGCACTTCGGTGC
1 ATTCTACGGGCACTTCGGTGC
54484 ATT
1 ATT
54487 TATACGAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 24 0.53
22 21 0.47
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
ATTCTACGGGCACTTCGGTGC
Found at i:57627 original size:22 final size:22
Alignment explanation
Indices: 57602--57648 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
57592 GATTTCTGGA
* *
57602 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
57624 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
57645 CAAG
1 CAAG
57649 CAAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:58255 original size:18 final size:18
Alignment explanation
Indices: 58232--58266 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58222 CTAGGAGATT
58232 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
58250 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
58267 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:59355 original size:22 final size:22
Alignment explanation
Indices: 59281--59347 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
59271 TTATGGACAT
59281 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
59303 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
59325 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
59347 A
1 A
59348 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:96737 original size:20 final size:20
Alignment explanation
Indices: 96712--96754 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
96702 TCTAAGACCT
* *
96712 CATTTAGGACCATGTAGATG
1 CATTTAGGAACATATAGATG
*
96732 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
96752 CAT
1 CAT
96755 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:100610 original size:22 final size:22
Alignment explanation
Indices: 100595--100659 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
100585 CGTATAAATA
100595 CACCGAAGTGCCCGTAGAATTG
1 CACCGAAGTGCCCGTAGAATTG
100617 CACCGAAGTGCCCGTAGAATTG
1 CACCGAAGTGCCCGTAGAATTG
100639 CACCGAAGTGCCCGTAGAATT
1 CACCGAAGTGCCCGTAGAATT
100660 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (22 bp):
CACCGAAGTGCCCGTAGAATTG
Found at i:101697 original size:17 final size:18
Alignment explanation
Indices: 101675--101708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
101665 TCCCCTCTAG
101675 CTTATC-TATATGTTCAT
1 CTTATCATATATGTTCAT
*
101692 CTTATCATTTATGTTCA
1 CTTATCATATATGTTCA
101709 AATCTCCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (18 bp):
CTTATCATATATGTTCAT
Found at i:102338 original size:22 final size:21
Alignment explanation
Indices: 102292--102334 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
102282 TTCATATTTG
* *
102292 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
102313 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
102334 C
1 C
102335 CTTGTCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:105474 original size:22 final size:22
Alignment explanation
Indices: 105457--105523 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
105447 CTCGTATAAA
105457 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
105479 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
105501 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
105523 T
1 T
105524 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:106095 original size:21 final size:20
Alignment explanation
Indices: 106058--106097 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
106048 ATTCTTATAC
* *
106058 CATAACATTCCTTTAACATA
1 CATAACATTCATGTAACATA
106078 CATAACATATCATGTAACAT
1 CATAACAT-TCATGTAACAT
106098 TATAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (20 bp):
CATAACATTCATGTAACATA
Found at i:106551 original size:18 final size:18
Alignment explanation
Indices: 106530--106564 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
106520 TCCCCTCTAG
106530 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
106548 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
106565 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:107192 original size:22 final size:21
Alignment explanation
Indices: 107146--107188 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
107136 TTCATATTTG
* *
107146 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
107167 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
107188 C
1 C
107189 CTTGTCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:112695 original size:90 final size:89
Alignment explanation
Indices: 112584--112756 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
112574 TATTCTCGAA
* *
112584 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAATCCCTAATATAAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAA-CCCTAATATAAT
112649 TAGAGTAACTTGGATATAAGAGGAT
65 TAGAGTAACTTGGATATAAGAGGAT
* *
112674 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAACCCTAATATAATT
* *
112739 AGGGTAACTTGGCTATAA
66 AGAGTAACTTGGATATAA
112757 AAGGGTATGT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 28 0.36
90 49 0.64
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAACCCTAATATAATT
AGAGTAACTTGGATATAAGAGGAT
Found at i:113197 original size:20 final size:20
Alignment explanation
Indices: 113172--113213 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
113162 CTAAGATCTT
* *
113172 ATTTAGGACCATGTAGATGC
1 ATTTAGGAACATATAGATGC
*
113192 ATTTAGGAACATATAGTTGC
1 ATTTAGGAACATATAGATGC
113212 AT
1 AT
113214 GTGGTGGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ATTTAGGAACATATAGATGC
Found at i:113590 original size:18 final size:18
Alignment explanation
Indices: 113567--113604 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
113557 TTTCCAGATG
*
113567 CCCATGCTGGACCACTGC
1 CCCATGCTGAACCACTGC
*
113585 CCCATGCTGAACCATTGC
1 CCCATGCTGAACCACTGC
113603 CC
1 CC
113605 AATCCTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (18 bp):
CCCATGCTGAACCACTGC
Found at i:114768 original size:22 final size:20
Alignment explanation
Indices: 114726--114769 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
114716 CACACTACCA
* *
114726 TCATTCTATTTTCACATCAT
1 TCATTCCATTTTCACAACAT
114746 TCATTCCATTTTGCCACAACAT
1 TCATTCCATTTT--CACAACAT
114768 TC
1 TC
114770 TCATTTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.43
Consensus pattern (20 bp):
TCATTCCATTTTCACAACAT
Found at i:115265 original size:20 final size:20
Alignment explanation
Indices: 115236--115289 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
115226 TTTCCTTTAG
115236 TTATCGAAAAAATTAC-ATTT
1 TTAT-GAAAAAATTACTATTT
*
115256 TTATGAAAAAATTACTTTTT
1 TTATGAAAAAATTACTATTT
115276 TTATGAAAAAATTA
1 TTATGAAAAAATTA
115290 AAATTACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
TTATGAAAAAATTACTATTT
Found at i:130771 original size:3 final size:3
Alignment explanation
Indices: 130736--130760 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
130726 ATGCACTCTT
130736 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
130761 GAGGACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Done.