Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001973.1 Hibiscus syriacus cultivar Beakdansim tig00003995_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: 63695
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2209 original size:17 final size:18
Alignment explanation
Indices: 2189--2229 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2179 TGTGTTTGAC
*
2189 TCAAACTCGAACT-AAAT
1 TCAAACTCAAACTCAAAT
*
2206 TCAAACTCAAACTCGAAT
1 TCAAACTCAAACTCAAAT
2224 TCAAAC
1 TCAAAC
2230 CTGAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
TCAAACTCAAACTCAAAT
Found at i:3400 original size:3 final size:3
Alignment explanation
Indices: 3382--3420 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
3372 TGGTCTTTTT
*
3382 TTA TTA CTA TTAA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
3421 CATCTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5317 original size:2 final size:2
Alignment explanation
Indices: 5310--5338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5300 ATTTTTACCC
5310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5339 TACCAATGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6032 original size:22 final size:22
Alignment explanation
Indices: 6007--6083 Score: 54
Period size: 22 Copynumber: 3.6 Consensus size: 22
5997 ACATCAAACA
6007 ATATCTTTCACAAGCAAAGCAC
1 ATATCTTTCACAAGCAAAGCAC
* * **
6029 ATATC-ATAAC-CTCAAA-CA-
1 ATATCTTTCACAAGCAAAGCAC
* *
6047 ATACCTTTCACAAACAAAGCAC
1 ATATCTTTCACAAGCAAAGCAC
*
6069 ATATCATTACACAAG
1 ATATC-TTTCACAAG
6084 GTTTCTTTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 9
0.64 0.20 0.15
Matches are distributed among these distances:
18 4 0.11
19 5 0.13
20 8 0.21
21 5 0.13
22 9 0.24
23 7 0.18
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.22
Consensus pattern (22 bp):
ATATCTTTCACAAGCAAAGCAC
Found at i:6055 original size:40 final size:40
Alignment explanation
Indices: 6000--6075 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
5990 TTATAAAACA
* *
6000 TCAAACAATATCTTTCACAAGCAAAGCACATATCATAACC
1 TCAAACAATACCTTTCACAAACAAAGCACATATCATAACC
6040 TCAAACAATACCTTTCACAAACAAAGCACATATCAT
1 TCAAACAATACCTTTCACAAACAAAGCACATATCAT
6076 TACACAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (40 bp):
TCAAACAATACCTTTCACAAACAAAGCACATATCATAACC
Found at i:10521 original size:23 final size:24
Alignment explanation
Indices: 10495--10548 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
10485 AAATGGAGAT
* *
10495 ATCATAAATCAAAATA-AATTCAG
1 ATCAGAAATCAAAATAGAATCCAG
* *
10518 ATCAGATATCATAATAGAATCCAG
1 ATCAGAAATCAAAATAGAATCCAG
10542 ATCAGAA
1 ATCAGAA
10549 TTCAGATCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (24 bp):
ATCAGAAATCAAAATAGAATCCAG
Found at i:10546 original size:24 final size:23
Alignment explanation
Indices: 10502--10547 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
10492 GATATCATAA
*
10502 ATCAAAATAAATTCAGATCAGAT
1 ATCAAAATAAATCCAGATCAGAT
*
10525 ATCATAATAGAATCCAGATCAGA
1 ATCAAAATA-AATCCAGATCAGA
10548 ATTCAGATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (23 bp):
ATCAAAATAAATCCAGATCAGAT
Found at i:10612 original size:24 final size:24
Alignment explanation
Indices: 10544--10621 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
10534 GAATCCAGAT
*
10544 CAGAATTCAGATCAGATATCATAA
1 CAGAATCCAGATCAGATATCATAA
* * *
10568 CAGAATCCAGCTCATAAATCATAA
1 CAGAATCCAGATCAGATATCATAA
* * * *
10592 TAGAATCCAGGTCAGGTATCAGAA
1 CAGAATCCAGATCAGATATCATAA
10616 CAGAAT
1 CAGAAT
10622 TCAATTCAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (24 bp):
CAGAATCCAGATCAGATATCATAA
Found at i:10635 original size:48 final size:48
Alignment explanation
Indices: 10545--10636 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
10535 AATCCAGATC
* * * *
10545 AGAATTCAGATCAGATATCATAACAGAATCCAGCTCATAAATCATAAT
1 AGAATCCAGATCAGATATCAGAACAGAATCCAACTCAAAAATCATAAT
* * * *
10593 AGAATCCAGGTCAGGTATCAGAACAGAATTCAATTCAAAAATCA
1 AGAATCCAGATCAGATATCAGAACAGAATCCAACTCAAAAATCA
10637 GATAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (48 bp):
AGAATCCAGATCAGATATCAGAACAGAATCCAACTCAAAAATCATAAT
Found at i:14259 original size:54 final size:54
Alignment explanation
Indices: 14174--14284 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
14164 GATTCTTTTA
** * *
14174 ACCTGAAAAGGTGAGTAATAGAGTGTTCTTTGGAAAGCTCAGTAATACAGAACT
1 ACCTGAAAAGGTGAGTAATAGAGTGAGCTTTGGAAAGCTCAGAAATACAAAACT
*
14228 ACCTGAAAATGTGAGTAATAGAGTGAGCTTTGGAAAGCTCAGAAATACAAAACT
1 ACCTGAAAAGGTGAGTAATAGAGTGAGCTTTGGAAAGCTCAGAAATACAAAACT
14282 ACC
1 ACC
14285 ATTTGATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (54 bp):
ACCTGAAAAGGTGAGTAATAGAGTGAGCTTTGGAAAGCTCAGAAATACAAAACT
Found at i:14825 original size:24 final size:24
Alignment explanation
Indices: 14750--14825 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
14740 CAGATAAGAT
* * *
14750 ATCATAACATAATTCAAATAAAAA
1 ATCATAACAGAATTCAAATCATAA
* * * ** **
14774 ATTAGAACAGAATCCAGGTCATGT
1 ATCATAACAGAATTCAAATCATAA
14798 ATCATAACAGAATTCAAATCATAA
1 ATCATAACAGAATTCAAATCATAA
14822 ATCA
1 ATCA
14826 GATAAAATAT
Statistics
Matches: 35, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (24 bp):
ATCATAACAGAATTCAAATCATAA
Found at i:16748 original size:17 final size:17
Alignment explanation
Indices: 16726--16758 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16716 TTTTATCAAA
16726 GTCAACAGTCAACAATG
1 GTCAACAGTCAACAATG
*
16743 GTCAACGGTCAACAAT
1 GTCAACAGTCAACAAT
16759 CAACGGCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (17 bp):
GTCAACAGTCAACAATG
Found at i:16802 original size:19 final size:20
Alignment explanation
Indices: 16780--16817 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
16770 TCCAGGCGGT
16780 TCGGCTCAGCTCGG-TTGGG
1 TCGGCTCAGCTCGGCTTGGG
16799 TCGGCTCAGCTCGGCTTGG
1 TCGGCTCAGCTCGGCTTGG
16818 TTTGGCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.05, C:0.29, G:0.39, T:0.26
Consensus pattern (20 bp):
TCGGCTCAGCTCGGCTTGGG
Found at i:18643 original size:24 final size:24
Alignment explanation
Indices: 18598--18643 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18588 CTAATCAGAG
**
18598 CATGTCCAACTAAATCTTTATTTA
1 CATGTCCAACTAAATCAGTATTTA
18622 CATG-CCAACTAGAATCAGTATT
1 CATGTCCAACTA-AATCAGTATT
18644 ATAAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (24 bp):
CATGTCCAACTAAATCAGTATTTA
Found at i:19096 original size:40 final size:40
Alignment explanation
Indices: 19026--19101 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
19016 TTATAAAACA
* * *
19026 TCAAGCAATACCTTTCACAAGCAGAGCACATATCATAACC
1 TCAAACAATACCTTTCACAAACAAAGCACATATCATAACC
*
19066 TCAAACAATACCTTTCACAAACAAATCACATATCAT
1 TCAAACAATACCTTTCACAAACAAAGCACATATCAT
19102 TGCACAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.43, C:0.29, G:0.05, T:0.22
Consensus pattern (40 bp):
TCAAACAATACCTTTCACAAACAAAGCACATATCATAACC
Found at i:19263 original size:21 final size:21
Alignment explanation
Indices: 19231--19452 Score: 99
Period size: 21 Copynumber: 10.3 Consensus size: 21
19221 CCAAAGTGCC
19231 ACATAGAATGTCCCGAAGGACA
1 ACATAG-ATGTCCCGAAGGACA
* * *
19253 ATATAGATGTCCCGAATGACC
1 ACATAGATGTCCCGAAGGACA
* *
19274 ACATAGATGTCCCAAAGGACC
1 ACATAGATGTCCCGAAGGACA
* * * *
19295 GCGTAGAAATGTCCCGAATGACC
1 ACATAG--ATGTCCCGAAGGACA
* *
19318 ACATATATGTCCCGAATGAGC-
1 ACATAGATGTCCCGAAGGA-CA
* ** *
19339 ACATAGAAATCTCCTTAAGGACC
1 ACATAG--ATGTCCCGAAGGACA
* * * *
19362 ACATATATATTCCAAAGGACCA
1 ACATAGATGTCCCGAAGGA-CA
* *
19384 A-ATATG-TGTCCCGAAGAACT
1 ACATA-GATGTCCCGAAGGACA
* * * **
19404 ACATATATGTTCCAAAGGATT
1 ACATAGATGTCCCGAAGGACA
* *
19425 ACATATATGTCCCGAAGGACC
1 ACATAGATGTCCCGAAGGACA
19446 ACATAGA
1 ACATAGA
19453 ACCCTCGACT
Statistics
Matches: 150, Mismatches: 40, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.01
21 109 0.73
22 9 0.06
23 30 0.20
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ACATAGATGTCCCGAAGGACA
Found at i:19317 original size:23 final size:21
Alignment explanation
Indices: 19229--19345 Score: 126
Period size: 21 Copynumber: 5.4 Consensus size: 21
19219 CACCAAAGTG
*
19229 CCACATAGAATGTCCCGAAGGA
1 CCACATAG-ATGTCCCGAATGA
* *
19251 CAATATAGATGTCCCGAATGA
1 CCACATAGATGTCCCGAATGA
* *
19272 CCACATAGATGTCCCAAAGGA
1 CCACATAGATGTCCCGAATGA
* *
19293 CCGCGTAGAAATGTCCCGAATGA
1 CCACATAG--ATGTCCCGAATGA
*
19316 CCACATATATGTCCCGAATGA
1 CCACATAGATGTCCCGAATGA
*
19337 GCACATAGA
1 CCACATAGA
19346 AATCTCCTTA
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
21 55 0.71
22 6 0.08
23 16 0.21
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (21 bp):
CCACATAGATGTCCCGAATGA
Found at i:19346 original size:44 final size:43
Alignment explanation
Indices: 19229--19369 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 43
19219 CACCAAAGTG
* * *
19229 CCACATAGAATGTCCCGAAGGACA-ATATAGATGTCCCGAATGA
1 CCACATA-TATGTCCCGAAGGACACATAGAAATGTCCCGAATGA
* * * *
19272 CCACATAGATGTCCCAAAGGACCGCGTAGAAATGTCCCGAATGA
1 CCACATATATGTCCCGAAGGA-CACATAGAAATGTCCCGAATGA
* * ** *
19316 CCACATATATGTCCCGAATGAGCACATAGAAATCTCCTTAAGGA
1 CCACATATATGTCCCGAAGGA-CACATAGAAATGTCCCGAATGA
19360 CCACATATAT
1 CCACATATAT
19370 ATTCCAAAGG
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 12 0.15
43 8 0.10
44 60 0.75
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (43 bp):
CCACATATATGTCCCGAAGGACACATAGAAATGTCCCGAATGA
Found at i:33747 original size:15 final size:15
Alignment explanation
Indices: 33729--33758 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33719 CCACGGTGCT
33729 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33744 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
33759 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:35429 original size:3 final size:3
Alignment explanation
Indices: 35412--35454 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
35402 TTCCTCCTCC
* *
35412 TCT TCT GCT TTT TCT TCT TCT TCTT TCTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC-T TC-T TCT TCT TCT TCT TC
35455 AAAGCAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:35445 original size:14 final size:15
Alignment explanation
Indices: 35412--35450 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
35402 TTCCTCCTCC
* *
35412 TCTTCTGCTTTTTCT
1 TCTTCTTCTTTCTCT
35427 TCTTCTTCTTTCT-T
1 TCTTCTTCTTTCTCT
35441 TCTTCTTCTT
1 TCTTCTTCTT
35451 CTTCAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:45322 original size:16 final size:17
Alignment explanation
Indices: 45291--45323 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45281 ATTGCCGACA
*
45291 AAATTTCACTATTCACG
1 AAATTTCACTAATCACG
45308 AAATTT-ACTAATCACG
1 AAATTTCACTAATCACG
45324 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (17 bp):
AAATTTCACTAATCACG
Found at i:49122 original size:17 final size:16
Alignment explanation
Indices: 49100--49139 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
49090 TTGATAAAAA
49100 ATAAAAATAAAAATATT
1 ATAAAAAT-AAAATATT
**
49117 ATAAAAATATGATATT
1 ATAAAAATAAAATATT
49133 ATAAAAA
1 ATAAAAA
49140 GACAATGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAAAATAAAATATT
Found at i:49281 original size:16 final size:18
Alignment explanation
Indices: 49243--49278 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
49233 ATCAATAGGA
49243 TTATCATCGTCATTGTTT
1 TTATCATCGTCATTGTTT
49261 TTATCATCGTCATT-TTT
1 TTATCATCGTCATTGTTT
49278 T
1 T
49279 ATCTTCATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (18 bp):
TTATCATCGTCATTGTTT
Done.