Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005701.1 Hibiscus syriacus cultivar Beakdansim tig00013331_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: 57138
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3269 original size:25 final size:23
Alignment explanation
Indices: 3213--3270 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 23
3203 GTGAACACTC
3213 AAAATATTTTATATATTTAATAT
1 AAAATATTTTATATATTTAATAT
3236 AAATTATATTTTAATATCATTTTAATA-
1 AAA--ATATTTT-ATAT-A-TTTAATAT
3263 AAAATATT
1 AAAATATT
3271 AATTATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.10
25 12 0.40
26 4 0.13
27 4 0.13
28 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATTTTATATATTTAATAT
Found at i:3321 original size:21 final size:21
Alignment explanation
Indices: 3265--3323 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 21
3255 TTTTAATAAA
*
3265 AATATTAATTATTAAAATATTT
1 AATATTAATTA-TATAATATTT
3287 AATA-TACATATATATAAT-TTT
1 AATATTA-AT-TATATAATATTT
3308 AATATTATATTATATA
1 AATATTA-ATTATATA
3324 CACTCAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 15 0.47
22 15 0.47
23 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTAATTATATAATATTT
Found at i:3586 original size:27 final size:27
Alignment explanation
Indices: 3556--3620 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 27
3546 TTAAACAAAT
3556 AAACCAAACTTTTTTT-AATAGTTAATC
1 AAACCAAACTTTTTTTAAATA-TTAATC
*
3583 AAA-C-AATTTTTTTTAAAATATTAATC
1 AAACCAAACTTTTTTT-AAATATTAATC
*
3609 GAACCAAACTTT
1 AAACCAAACTTT
3621 ATTCATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 9 0.29
26 9 0.29
27 8 0.26
28 5 0.16
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (27 bp):
AAACCAAACTTTTTTTAAATATTAATC
Found at i:3788 original size:29 final size:30
Alignment explanation
Indices: 3742--3847 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 30
3732 CCGAAAAATA
* *
3742 TAATTCATTTGACATAAAACAATATT-AGG
1 TAATTCATTTTACATAAAACAATTTTCAGG
* **
3771 TAATTCATTTTACGT-AAACAATTTTCTTG
1 TAATTCATTTTACATAAAACAATTTTCAGG
** *
3800 TAATTCA-TTTATGTAAAACATTTTTTCAGG
1 TAATTCATTTTACATAAAACA-ATTTTCAGG
*
3830 TAATCCATTTTACATAAA
1 TAATTCATTTTACATAAA
3848 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 15 0.25
29 26 0.43
30 12 0.20
31 8 0.13
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTACATAAAACAATTTTCAGG
Found at i:11290 original size:4 final size:4
Alignment explanation
Indices: 11283--11362 Score: 106
Period size: 4 Copynumber: 20.0 Consensus size: 4
11273 ATATAGGTAC
* * * * *
11283 GTAT GTAT GTAT GTAT GTAC GTAC GTAT GTAT GTAC GTAT GTAC GTAC
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
11331 GTAT GTAT GTAT GTAT ATAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
11363 ATATATGTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (4 bp):
GTAT
Found at i:12752 original size:132 final size:131
Alignment explanation
Indices: 12515--12764 Score: 374
Period size: 132 Copynumber: 1.9 Consensus size: 131
12505 CAGTTCATTT
* * *
12515 TTCATGACCTCATCGCCCGGGGTCAAATCCAATGTCAGAACCAAATTATAATTTTTTAGATAAAT
1 TTCATGACCTCATCACCCAGGGTCAAATCCAATGTCAAAACCAAATTATAATTTTTTAGATAAAT
* *
12580 TACAAGTTTAATACTTAAACTATTACTTTTGATCTATTTTAATACTTAAACTTGTTTCACAGTCA
66 TACAAGTTTAATACTTAAACTATTACTTTTAATCTATTTTAATACCTAAACTTGTTTCACAGTCA
12645 G
131 G
* * *
12646 TTCATGACCTCATCACCCAGGGTCAAATCCAATGGTCAAAACCAGATTATAATTTTTTGGGTAAA
1 TTCATGACCTCATCACCCAGGGTCAAATCCAAT-GTCAAAACCAAATTATAATTTTTTAGATAAA
* * * * *
12711 TTACACGTTTAGTACTTAAATTATTAGTTTTAATCTGTTTTAATACCTAAACTT
65 TTACAAGTTTAATACTTAAACTATTACTTTTAATCTATTTTAATACCTAAACTT
12765 TTAATTTTTC
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 31 0.30
132 74 0.70
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (131 bp):
TTCATGACCTCATCACCCAGGGTCAAATCCAATGTCAAAACCAAATTATAATTTTTTAGATAAAT
TACAAGTTTAATACTTAAACTATTACTTTTAATCTATTTTAATACCTAAACTTGTTTCACAGTCA
G
Found at i:13190 original size:23 final size:25
Alignment explanation
Indices: 13159--13205 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
13149 TATTTTCAAA
*
13159 ATTTCATTTATTTTT-TAGAATTTT
1 ATTTCATTTATTTTTATAAAATTTT
13183 ATTT-ATTTATTTTTATAAAATTT
1 ATTTCATTTATTTTTATAAAATTT
13206 ATAAATTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
ATTTCATTTATTTTTATAAAATTTT
Found at i:13206 original size:23 final size:24
Alignment explanation
Indices: 13159--13207 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
13149 TATTTTCAAA
*
13159 ATTTCATTTATTTTTTAGAATTTT
1 ATTTCATTTATTTTTTAGAAATTT
13183 ATTT-ATTTATTTTTATA-AAATTT
1 ATTTCATTTATTTTT-TAGAAATTT
13206 AT
1 AT
13208 AAATTCCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATTTCATTTATTTTTTAGAAATTT
Found at i:26778 original size:22 final size:22
Alignment explanation
Indices: 26753--26795 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
26743 TTATCATTTC
*
26753 AGACAAGATATTGGTTGGAACA
1 AGACAAGATATTGGTAGGAACA
* *
26775 AGACCAGGTATTGGTAGGAAC
1 AGACAAGATATTGGTAGGAAC
26796 TGAACATCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (22 bp):
AGACAAGATATTGGTAGGAACA
Found at i:28267 original size:14 final size:14
Alignment explanation
Indices: 28248--28274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28238 AAATGATAAA
28248 CGAACATAAACGAG
1 CGAACATAAACGAG
28262 CGAACATAAACGA
1 CGAACATAAACGA
28275 ACATAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.19, T:0.07
Consensus pattern (14 bp):
CGAACATAAACGAG
Found at i:32166 original size:59 final size:60
Alignment explanation
Indices: 32020--32166 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 60
32010 AATTGTTATT
* *
32020 TAAACTTTTGAAAATTTTAATTTCATCCTTAAATCATGACTCTTATTTCAAATTAATCCT
1 TAAACTTTTGAAAATTTTAATTTCATCCTTAAATCATGACTCCTATTTCAAATTAATCCA
* * * * * *
32080 TAAACTTTTGAACATTTTGATTCCATCCTTAAA-CTATGAC-CCTCTTT-ATATTTAGTCCA
1 TAAACTTTTGAAAATTTTAATTTCATCCTTAAATC-ATGACTCCTATTTCA-AATTAATCCA
* *
32139 TAAACTTTTGAATATTCTAATTTCATCC
1 TAAACTTTTGAAAATTTTAATTTCATCC
32167 AAATATATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 37 0.51
60 35 0.48
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAACTTTTGAAAATTTTAATTTCATCCTTAAATCATGACTCCTATTTCAAATTAATCCA
Found at i:37469 original size:11 final size:11
Alignment explanation
Indices: 37432--37473 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
37422 TCAAATTTAT
37432 AAAATTATAACTA
1 AAAATTA-AA-TA
*
37445 AAAATT-AATT
1 AAAATTAAATA
37455 AAAATTAAATA
1 AAAATTAAATA
37466 AAAATTAA
1 AAAATTAA
37474 TTTTTAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 7 0.27
11 13 0.50
13 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAAATA
Found at i:37469 original size:21 final size:23
Alignment explanation
Indices: 37431--37475 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
37421 ATCAAATTTA
37431 TAAAATTATAACTAAAAATTAAT
1 TAAAATTATAACTAAAAATTAAT
37454 TAAAATTA-AA-TAAAAATTAAT
1 TAAAATTATAACTAAAAATTAAT
37475 T
1 T
37476 TTTAAGTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATTATAACTAAAAATTAAT
Found at i:39000 original size:32 final size:32
Alignment explanation
Indices: 38964--39029 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
38954 TGACTACTAT
38964 TTACAAT-AACTCTATCCAGACAAGCATTTTAA
1 TTACAATCAA-TCTATCCAGACAAGCATTTTAA
*
38996 TTACAATCAATCTATCCAGAGAAGCATTTTAA
1 TTACAATCAATCTATCCAGACAAGCATTTTAA
39028 TT
1 TT
39030 TTAATTACCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (32 bp):
TTACAATCAATCTATCCAGACAAGCATTTTAA
Found at i:44005 original size:20 final size:20
Alignment explanation
Indices: 43969--44007 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43959 ATACAATCAT
*
43969 ATGACTAATGTTTTAATTCG
1 ATGACTAATGTTGTAATTCG
43989 ATGA-TAATGATTGTAATTC
1 ATGACTAATG-TTGTAATTC
44008 ATGTTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGACTAATGTTGTAATTCG
Found at i:44561 original size:21 final size:21
Alignment explanation
Indices: 44535--44579 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
44525 ATGAAGCACT
*
44535 ATCACACTCCACTAAAAAAAG
1 ATCACACTCCACCAAAAAAAG
* *
44556 ATCACATTCCACCAAAGAAAG
1 ATCACACTCCACCAAAAAAAG
44577 ATC
1 ATC
44580 CAAACTAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.29, G:0.07, T:0.16
Consensus pattern (21 bp):
ATCACACTCCACCAAAAAAAG
Found at i:54116 original size:30 final size:30
Alignment explanation
Indices: 54082--54140 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
54072 ACACTTTCGG
* *
54082 TCACTTACATTATTGTTTATTAGGTTTTGA
1 TCACTTACATTATCGTTTATTAAGTTTTGA
** *
54112 TCACTTGTATTATCGTTTCTTAAGTTTTG
1 TCACTTACATTATCGTTTATTAAGTTTTG
54141 GTCAGTTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (30 bp):
TCACTTACATTATCGTTTATTAAGTTTTGA
Found at i:54962 original size:31 final size:31
Alignment explanation
Indices: 54889--54952 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
54879 TTCAATGTCA
*
54889 AAATAACCAAAATTTAATAAAACGATAACAT
1 AAATAACCAAAATTTAATAAAACGACAACAT
*
54920 AAATAACCAAAACTTT-ATAAAACGACAATAT
1 AAATAACCAAAA-TTTAATAAAACGACAACAT
54951 AA
1 AA
54953 GTGAGCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.61, C:0.14, G:0.03, T:0.22
Consensus pattern (31 bp):
AAATAACCAAAATTTAATAAAACGACAACAT
Found at i:56142 original size:18 final size:18
Alignment explanation
Indices: 56121--56157 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56111 CGAGTTATAA
* *
56121 TTATTATATTAATTATTT
1 TTATCATATAAATTATTT
56139 TTATCATATAAATTATTT
1 TTATCATATAAATTATTT
56157 T
1 T
56158 CATATACTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATCATATAAATTATTT
Done.