Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003487.1 Hibiscus syriacus cultivar Beakdansim tig00007371_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: 42769
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1529 original size:3 final size:3
Alignment explanation
Indices: 1521--1559 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1511 AATTTGCAGA
1521 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1560 AATGATAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6855 original size:31 final size:33
Alignment explanation
Indices: 6797--6858 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
6787 AGATAAAAAA
*
6797 AATAAGTTTGAAAGTTAGAGTGATTAAATTAGG
1 AATAAGTTTGAAAGTTAGAGTAATTAAATTAGG
*
6830 AATAA-TTTGGAAGTTA-AGTAATTAAATTA
1 AATAAGTTTGAAAGTTAGAGTAATTAAATTA
6859 AAAAATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.44
32 10 0.37
33 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (33 bp):
AATAAGTTTGAAAGTTAGAGTAATTAAATTAGG
Found at i:6866 original size:32 final size:34
Alignment explanation
Indices: 6793--6866 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 34
6783 TTCGAGATAA
*
6793 AAAAAATAAGTTTGAAAGTTAGAGTGATTAAATT
1 AAAAAATAAGTTTGAAAGTTAGAGTAATTAAATT
** *
6827 -AGGAATAA-TTTGGAAGTTA-AGTAATTAAATT
1 AAAAAATAAGTTTGAAAGTTAGAGTAATTAAATT
6858 AAAAAATAA
1 AAAAAATAA
6867 ACTTTAGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 11 0.33
32 16 0.48
33 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (34 bp):
AAAAAATAAGTTTGAAAGTTAGAGTAATTAAATT
Found at i:13378 original size:21 final size:21
Alignment explanation
Indices: 13328--13422 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
13318 GATTTACATA
* *
13328 TTCGCATTGCGATAGGCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
13349 TT--TGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
13368 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
13391 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
13410 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
13423 TTATTCCAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 24 0.41
21 26 0.45
23 8 0.14
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:13405 original size:42 final size:42
Alignment explanation
Indices: 13352--13436 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
13342 GGCCAAGTTT
*
13352 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
13394 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
13436 G
1 G
13437 CAACGACTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:13413 original size:19 final size:19
Alignment explanation
Indices: 13334--13413 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 19
13324 CATATTCGCA
* *
13334 TTGCGATAGGCCAAGTTTG
1 TTGCGATAGTCCAAGTTCG
*
13353 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
13374 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
13395 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
13414 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
19 26 0.53
21 15 0.31
23 8 0.16
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:13436 original size:23 final size:23
Alignment explanation
Indices: 13368--13437 Score: 94
Period size: 21 Copynumber: 3.2 Consensus size: 23
13358 ATAGTCGAAG
13368 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGATTTATTCCAAA
* *
13391 TT--CGTTGCGA--TAGTCCAAG
1 TTCGCGTTGCGATTTATTCCAAA
13410 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGATTTATTCCAAA
13433 TTCGC
1 TTCGC
13438 AACGACTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 9 0.23
21 16 0.41
23 14 0.36
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (23 bp):
TTCGCGTTGCGATTTATTCCAAA
Found at i:14186 original size:21 final size:21
Alignment explanation
Indices: 14134--14376 Score: 148
Period size: 21 Copynumber: 12.0 Consensus size: 21
14124 TGTTGCGATT
*
14134 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
14153 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
**
14176 TTGGACTATCGCAACGAAAAC
1 TTGGACTATCGCAACGCGAAC
* * *
14197 TTCGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
* **
14216 TTAGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
14237 TTTGACTA-CTGCAA--CGAAT
1 TTGGACTATC-GCAACGCGAAC
**
14256 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
14277 TTTGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
14296 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
14317 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* **
14336 TTAGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* * *
14357 TTCGACTATCGTAATGCGAA
1 TTGGACTATCGCAACGCGAA
14377 TATGTAAATC
Statistics
Matches: 168, Mismatches: 42, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
19 63 0.38
20 2 0.01
21 93 0.55
23 10 0.06
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:14238 original size:40 final size:40
Alignment explanation
Indices: 14183--14367 Score: 291
Period size: 40 Copynumber: 4.6 Consensus size: 40
14173 AACTTGGACT
** *
14183 ATCGCAACGAAAACTTCGACTATCGCAACAAATTTAGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
* *
14223 ATCGCAACGCGAACTTTGACTA-CTGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATC-GCAACGAATTTAGAAA
* *
14263 ATCGCAACGCGAACTTTGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
14303 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
14343 ATCGCAACGCGAACTTCGACTATCG
1 ATCGCAACGCGAACTTCGACTATCG
14368 TAATGCGAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
39 1 0.01
40 134 0.99
41 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAAA
Found at i:14418 original size:21 final size:21
Alignment explanation
Indices: 14385--14435 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
14375 AATATGTAAA
* *
14385 TCACATTGCGATAGTCCAAGT
1 TCACGTTGTGATAGTCCAAGT
*
14406 TCACGTTGTGATAGTCGAAGT
1 TCACGTTGTGATAGTCCAAGT
*
14427 TCGCGTTGT
1 TCACGTTGT
14436 AAATCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
TCACGTTGTGATAGTCCAAGT
Found at i:16675 original size:20 final size:20
Alignment explanation
Indices: 16650--16687 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16640 TTTGGTTCAC
16650 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
16670 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
16688 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:16788 original size:62 final size:62
Alignment explanation
Indices: 16712--16835 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 62
16702 GGGAATGTTG
* * *
16712 TATTTTGTGTTTGGTTGGTTTAGCAGGAACGTAAGATTACCGTATTTGGTTAAAGGAATAAA
1 TATTTTGTGATTGGTTGGTTTAGCAGGAACATAAGATTACCGTATTTGATTAAAGGAATAAA
* * * **
16774 TATTTTGTGATTGGTTGGTTTAGTATGAATATAAGATTGTCGTATTTGATTAAAGGAATAAA
1 TATTTTGTGATTGGTTGGTTTAGCAGGAACATAAGATTACCGTATTTGATTAAAGGAATAAA
16836 AGATTATTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (62 bp):
TATTTTGTGATTGGTTGGTTTAGCAGGAACATAAGATTACCGTATTTGATTAAAGGAATAAA
Found at i:20006 original size:17 final size:17
Alignment explanation
Indices: 19984--20018 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19974 ATAATAGAGG
* *
19984 TTTTTAGTGTTAATAAC
1 TTTTTAATGGTAATAAC
20001 TTTTTAATGGTAATAAC
1 TTTTTAATGGTAATAAC
20018 T
1 T
20019 CTGAGTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTTTAATGGTAATAAC
Found at i:26053 original size:28 final size:28
Alignment explanation
Indices: 26012--26084 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
26002 ATATTAATAT
* *
26012 TTAAAGTTTTATTTTTAAAATATATTAC
1 TTAACGTTTAATTTTTAAAATATATTAC
26040 TTAACGTTTAATTTTTAAAATATATTAC
1 TTAACGTTTAATTTTTAAAATATATTAC
*
26068 TTAACGCTTAATTTTTA
1 TTAACGTTTAATTTTTA
26085 TTTTATATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (28 bp):
TTAACGTTTAATTTTTAAAATATATTAC
Found at i:38647 original size:15 final size:16
Alignment explanation
Indices: 38627--38658 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38617 TATTAAAGGC
38627 AAATATTTAACC-TTG
1 AAATATTTAACCATTG
38642 AAATATTTAACCATTG
1 AAATATTTAACCATTG
38658 A
1 A
38659 GCTAGACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATATTTAACCATTG
Found at i:38753 original size:17 final size:17
Alignment explanation
Indices: 38731--38798 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 17
38721 TTAATCGAAT
38731 AAAATTAATTAAAAATA
1 AAAATTAATTAAAAATA
* *
38748 AAAATT-ACTAATAATA
1 AAAATTAATTAAAAATA
* * *
38764 AAAAATGATATAAAAATT
1 AAAATTAAT-TAAAAATA
*
38782 AAAA-TAA-TAATAATA
1 AAAATTAATTAAAAATA
38797 AA
1 AA
38799 TACCACATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
15 8 0.20
16 13 0.32
17 9 0.22
18 10 0.25
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (17 bp):
AAAATTAATTAAAAATA
Found at i:41269 original size:27 final size:29
Alignment explanation
Indices: 41206--41271 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 29
41196 TCACGAAAAG
*
41206 AAAAT-AAAGACAAATAATTATTTGTACA
1 AAAATCAAGGACAAATAATTATTTGTACA
41234 AAAATCAAGGACAAATAA-TA-TTGTACA
1 AAAATCAAGGACAAATAATTATTTGTACA
41261 AAAATCAAGGA
1 AAAATCAAGGA
41272 TAATTTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 18 0.50
28 7 0.19
29 11 0.31
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.23
Consensus pattern (29 bp):
AAAATCAAGGACAAATAATTATTTGTACA
Found at i:41274 original size:23 final size:24
Alignment explanation
Indices: 41218--41280 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 24
41208 AATAAAGACA
41218 AATAATTATTTGTACAAAAATCAAGG
1 AATAA-TA-TTGTACAAAAATCAAGG
41244 ACAAATAATATTGTACAAAAATCAAGG
1 ---AATAATATTGTACAAAAATCAAGG
*
41271 -ATAATTTTGT
1 AATAATATTGT
41281 TATTATACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 9 0.27
27 17 0.52
28 2 0.06
29 5 0.15
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (24 bp):
AATAATATTGTACAAAAATCAAGG
Done.