Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004790.1 Hibiscus syriacus cultivar Beakdansim tig00010796_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: 51186
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1686 original size:2 final size:2
Alignment explanation
Indices: 1679--1705 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1669 CAATTAAATC
1679 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1706 CACTTACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3586 original size:14 final size:14
Alignment explanation
Indices: 3567--3620 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
3557 TAAATTTTGA
3567 ATAAATATTATATT
1 ATAAATATTATATT
*
3581 ATAAATATTTTA-T
1 ATAAATATTATATT
3594 AT-AATATTATTAATT
1 ATAAATATTA-T-ATT
3609 ATAAA-ATTATAT
1 ATAAATATTATAT
3621 AATATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 6 0.18
13 6 0.18
14 13 0.38
15 7 0.21
16 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAATATTATATT
Found at i:3611 original size:15 final size:14
Alignment explanation
Indices: 3566--3628 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
3556 TTAAATTTTG
3566 AATA-AATATTA-T
1 AATATAATATTATT
*
3578 ATTATAAATATT-TT
1 AATAT-AATATTATT
3592 -ATATAATATTATT
1 AATATAATATTATT
*
3605 AATTATAAAATTATAT
1 AA-TATAATATTAT-T
3621 AATATAAT
1 AATATAAT
3629 TATACCAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 9 0.22
13 5 0.12
14 8 0.20
15 15 0.38
16 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATAATATTATT
Found at i:4164 original size:2 final size:2
Alignment explanation
Indices: 4157--4185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4147 ATTAAAAATA
4157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4186 AGAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4711 original size:20 final size:20
Alignment explanation
Indices: 4675--4713 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4665 AATTTACATA
*
4675 TAGATGATTCATTTAATGTG
1 TAGATGATTCATATAATGTG
4695 TAGAT-ATTACATATAATGT
1 TAGATGATT-CATATAATGT
4714 AACTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGATGATTCATATAATGTG
Found at i:6148 original size:17 final size:17
Alignment explanation
Indices: 6126--6159 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6116 CACAATCGCA
6126 ATTTCGCGTTGCGATAG
1 ATTTCGCGTTGCGATAG
6143 ATTTCGCGTTGCGATAG
1 ATTTCGCGTTGCGATAG
6160 TTGAAAATCG
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:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
ATTTCGCGTTGCGATAG
Found at i:6175 original size:21 final size:21
Alignment explanation
Indices: 6146--6325 Score: 114
Period size: 21 Copynumber: 8.6 Consensus size: 21
6136 GCGATAGATT
6146 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
6167 TCGCATTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
6187 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
6208 TCGCGTTGCAAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
6228 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
6249 TCGCGTTGCAAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
*
6269 TCGCGTTGCGATAGTTAAAACA
1 TCGCGTTGCGATAGTTGAAA-A
*
6291 TTTCGCGTTACGATAGTTGAAAA
1 --TCGCGTTGCGATAGTTGAAAA
*
6314 TCGTGTTGCGAT
1 TCGCGTTGCGAT
6326 TTTCCATTTC
Statistics
Matches: 111, Mismatches: 42, Indels: 12
0.67 0.25 0.07
Matches are distributed among these distances:
20 41 0.37
21 51 0.46
23 1 0.01
24 18 0.16
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:6194 original size:41 final size:41
Alignment explanation
Indices: 6143--6288 Score: 249
Period size: 41 Copynumber: 3.6 Consensus size: 41
6133 GTTGCGATAG
* ** *
6143 ATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGCTTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
6184 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
6225 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
6266 ATTTCGCGTTGCGATAGTT-AAAA
1 ATTTCGCGTTGCGATAGTTGAAAA
6289 CATTTCGCGT
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 4 0.04
41 97 0.96
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (41 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTC
Found at i:6233 original size:20 final size:20
Alignment explanation
Indices: 6208--6277 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
6198 TAGTTGAAAA
6208 TCGCGTTGCAATTTTTCATT
1 TCGCGTTGCAATTTTTCATT
* * ** **
6228 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCAAT-TTTTCATT
6249 TCGCGTTGCAATTTTTCATT
1 TCGCGTTGCAATTTTTCATT
6269 TCGCGTTGC
1 TCGCGTTGC
6278 GATAGTTAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCAATTTTTCATT
Found at i:6297 original size:24 final size:25
Alignment explanation
Indices: 6265--6313 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
6255 TGCAATTTTT
*
6265 CATTTCGCGTTGCGATAGTT-AAAA
1 CATTTCGCGTTACGATAGTTGAAAA
6289 CATTTCGCGTTACGATAGTTGAAAA
1 CATTTCGCGTTACGATAGTTGAAAA
6314 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
CATTTCGCGTTACGATAGTTGAAAA
Found at i:6298 original size:65 final size:65
Alignment explanation
Indices: 6224--6348 Score: 214
Period size: 65 Copynumber: 1.9 Consensus size: 65
6214 TGCAATTTTT
* *
6224 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTTCATTTCGCGTTGCGATAGTTAAAA
1 CATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGTTAAAA
* *
6289 CATTTCGCGTTACGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 CATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGT
6349 CTACAGTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (65 bp):
CATTTCGCGTTACGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGTTAAAA
Found at i:6382 original size:19 final size:19
Alignment explanation
Indices: 6358--6405 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
6348 TCTACAGTTG
6358 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
6377 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
6396 TCGTTACGAT
1 TCGTTGCGAT
6406 AGTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:6508 original size:6 final size:6
Alignment explanation
Indices: 6477--6507 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6467 GTGTCGAAGA
*
6477 CACGAC CACGAC CACGAC CACGAC CCCGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
6508 CGAGACGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:7130 original size:22 final size:22
Alignment explanation
Indices: 7104--7174 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
7094 CAACGAATTT
7104 TCGCAACGACAACTGTAGACTA
1 TCGCAACGACAACTGTAGACTA
* * **
7126 TCGCAACG--AA-TTTGGAAAA
1 TCGCAACGACAACTGTAGACTA
7145 TCGCAACGACAACTGTAGACTA
1 TCGCAACGACAACTGTAGACTA
7167 TCGCAACG
1 TCGCAACG
7175 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (22 bp):
TCGCAACGACAACTGTAGACTA
Found at i:7185 original size:41 final size:44
Alignment explanation
Indices: 7104--7220 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 44
7094 CAACGAATTT
*
7104 TCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGG-AAAA
1 TCGCAACGACAACTGTAGACTATCGCAACGCGAATATGGAAAAA
7145 TCGCAACGACAACTGTAGACTATCGCAACGCGAA-AT-GAAAAA
1 TCGCAACGACAACTGTAGACTATCGCAACGCGAATATGGAAAAA
* * *
7187 TCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAT
1 TCGCAACGACAACTGT-AGACTATCGCAACGCGAAT
7221 TTGCGATAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
41 49 0.73
42 14 0.21
43 4 0.06
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (44 bp):
TCGCAACGACAACTGTAGACTATCGCAACGCGAATATGGAAAAA
Found at i:9547 original size:2 final size:2
Alignment explanation
Indices: 9540--9577 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9530 GATGCAAAGA
9540 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
9578 TGAAAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16494 original size:22 final size:22
Alignment explanation
Indices: 16461--16503 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16451 AAACCAAAAG
16461 CACAGCTCCTAA-CAATATCCTC
1 CACAGCTCCTAACCAAT-TCCTC
16483 CACAG-TCACTAACCAATTCCT
1 CACAGCTC-CTAACCAATTCCT
16504 GACTTAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.33, C:0.40, G:0.05, T:0.23
Consensus pattern (22 bp):
CACAGCTCCTAACCAATTCCTC
Found at i:21639 original size:31 final size:31
Alignment explanation
Indices: 21563--21639 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
21553 CAAAAATATT
* * * * *
21563 AAATTTTAATTTTACATCTAAACTTTATATA
1 AAATATTAATTTAATATCTAAACTTTAAACA
* *
21594 ACATATTAATTTAATATCTAAATTTTAAACA
1 AAATATTAATTTAATATCTAAACTTTAAACA
21625 AAATATTAATTTAAT
1 AAATATTAATTTAAT
21640 TCTTAAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (31 bp):
AAATATTAATTTAATATCTAAACTTTAAACA
Found at i:29328 original size:24 final size:24
Alignment explanation
Indices: 29301--29352 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
29291 TCAAATAATT
29301 AACAAGTAAATGTTCTCAATTTAG
1 AACAAGTAAATGTTCTCAATTTAG
29325 AACAAGTAAATGTTCTCAATTTAG
1 AACAAGTAAATGTTCTCAATTTAG
29349 AACA
1 AACA
29353 CTCATCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (24 bp):
AACAAGTAAATGTTCTCAATTTAG
Found at i:44686 original size:35 final size:36
Alignment explanation
Indices: 44640--44720 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
44630 AACACAGCCA
* * *
44640 TCAATTACATTCTAAACCCCAAATTTC-AAAATATT
1 TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
*
44675 TCAATTACATTCTAAACAGCAAATTCCAAAAATAAT
1 TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
44711 TCAATTACAT
1 TCAATTACAT
44721 GACCAACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 24 0.59
36 17 0.41
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACACCAAATTCCAAAAATAAT
Found at i:44734 original size:36 final size:35
Alignment explanation
Indices: 44640--44736 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 35
44630 AACACAGCCA
* * *
44640 TCAATTACATTCTAAACCCCAAATTTCAAAATATT
1 TCAATTACATACTAAACCCCAAATTCCAAAATAAT
* **
44675 TCAATTACATTCTAAACAGCAAATTCCAAAAATAAT
1 TCAATTACATACTAAACCCCAAATTCC-AAAATAAT
*
44711 TCAATTACATGAC-CAACCCCAAATTC
1 TCAATTACAT-ACTAAACCCCAAATTC
44737 ATAATCCATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
35 24 0.46
36 27 0.52
37 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATACTAAACCCCAAATTCCAAAATAAT
Found at i:45380 original size:148 final size:148
Alignment explanation
Indices: 45216--45502 Score: 475
Period size: 148 Copynumber: 1.9 Consensus size: 148
45206 AAACTATTTG
* *
45216 ATTAGAATCAAATAATATTATAGTATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
1 ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
* **** *
45281 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAATTCAAATCGAAATTTTTTTGAGTCAACTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACTA
45346 TTTTATAAACTAAACTGA
131 TTTTATAAACTAAACTGA
* * *
45364 ATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAA
1 ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
45429 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACTA
45494 TTTTATAAA
131 TTTTATAAA
45503 TTGAATTGAG
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
148 128 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (148 bp):
ATTAGAATAAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACTA
TTTTATAAACTAAACTGA
Found at i:45705 original size:35 final size:35
Alignment explanation
Indices: 45660--45760 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
45650 TTGAGATTTG
** * **
45660 ATTTT-GAATTTGGGGTTGGGCATGTAATTGAAGT
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
** *
45694 ATTTTGGAATTTGATGTTTAGAATGTAATTAAAAC
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
*
45729 ATTTTGGATTTTGGGGTTTAGAATGTAATTGA
1 ATTTTGGAATTTGGGGTTTAGAATGTAATTGA
45761 TGATTGTGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 5 0.09
35 49 0.91
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.44
Consensus pattern (35 bp):
ATTTTGGAATTTGGGGTTTAGAATGTAATTGAAAC
Done.