Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002076.1 Hibiscus syriacus cultivar Beakdansim tig00004240_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: 73235
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2341 original size:21 final size:21
Alignment explanation
Indices: 2317--2363 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2307 TCAAATTATA
2317 TTTATT-TAATTAATTTTATTT
1 TTTATTATAA-TAATTTTATTT
*
2338 TTTATTGATAATATTTTTATTT
1 TTTATT-ATAATAATTTTATTT
2360 TTTA
1 TTTA
2364 AAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 14 0.61
23 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTATTATAATAATTTTATTT
Found at i:6828 original size:8 final size:8
Alignment explanation
Indices: 6789--6855 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
6779 CATGCATACG
*
6789 TACGTACG
1 TACGTACA
*
6797 TACGTACG
1 TACGTACA
*
6805 TACATACA
1 TACGTACA
*
6813 TACATACA
1 TACGTACA
6821 TACGTACA
1 TACGTACA
* *
6829 TATGTATA
1 TACGTACA
*
6837 TACATACA
1 TACGTACA
6845 TA--TACA
1 TACGTACA
6851 TACGT
1 TACGT
6856 GTCTGTATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 6 0.12
8 43 0.88
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (8 bp):
TACGTACA
Found at i:6828 original size:12 final size:12
Alignment explanation
Indices: 6777--6830 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
6767 CACACATGCA
*
6777 TACATGCATACG
1 TACATACATACG
* *
6789 TACGTACGTACG
1 TACATACATACG
* *
6801 TACGTACATACA
1 TACATACATACG
6813 TACATACATACG
1 TACATACATACG
6825 TACATA
1 TACATA
6831 TGTATATACA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (12 bp):
TACATACATACG
Found at i:6853 original size:4 final size:4
Alignment explanation
Indices: 6770--6846 Score: 55
Period size: 4 Copynumber: 19.2 Consensus size: 4
6760 TTCAATGCAC
* * * * * * *
6770 ACAT GCAT ACAT GCAT ACGT ACGT ACGT ACGT ACGT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** *
6818 ACAT ACGT ACAT ATGT ATAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
6847 TACATACGTG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:14781 original size:13 final size:14
Alignment explanation
Indices: 14753--14788 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
14743 GAATAAATTG
14753 TATTTTTCTAAAAAA
1 TATTTTT-TAAAAAA
14768 TATTTTTT-AAAAA
1 TATTTTTTAAAAAA
14781 TATTTTTT
1 TATTTTTT
14789 GGAGTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 1 0.05
15 7 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTTTTAAAAAA
Found at i:15916 original size:21 final size:21
Alignment explanation
Indices: 15887--15929 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
15877 TTCTAATTTT
*
15887 TTAGTATTA-GTATGAACAAAA
1 TTAGAATTATGTAT-AACAAAA
*
15908 TTAGAATTATTTATAACAAAA
1 TTAGAATTATGTATAACAAAA
15929 T
1 T
15930 GAGGAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
TTAGAATTATGTATAACAAAA
Found at i:16086 original size:3 final size:3
Alignment explanation
Indices: 16078--16132 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
16068 ACTTAATAAA
* * *
16078 ATT ATT ATT GTT ATT ATT ATT -TT ATT AAT -TT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16124 ATT -TT ATT A
1 ATT ATT ATT A
16133 ATTTAAGACG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16110 original size:28 final size:28
Alignment explanation
Indices: 16079--16137 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
16069 CTTAATAAAA
16079 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
16107 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
16135 TTA
1 TTA
16138 AGACGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (28 bp):
TTATTATTGTTATTATTATTTTATTAAT
Found at i:29293 original size:19 final size:18
Alignment explanation
Indices: 29250--29294 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29240 AATATAGTCC
29250 AACCAAATTGGCAAATTT
1 AACCAAATTGGCAAATTT
* *
29268 ATTCCAATTTGGCAAATTCT
1 A-ACCAAATTGGCAAATT-T
29288 AACCAAA
1 AACCAAA
29295 ATCGAGACGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
AACCAAATTGGCAAATTT
Found at i:35170 original size:23 final size:23
Alignment explanation
Indices: 35140--35196 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
35130 ACGAACGGAT
* * *
35140 GTAAACGAACAGAATAAATTAAC
1 GTAAACGAAAACAATAAATGAAC
35163 GTAAACGAAAACAATAAATGAAC
1 GTAAACGAAAACAATAAATGAAC
* *
35186 ATAAATGAAAA
1 GTAAACGAAAA
35197 TAGATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.16
Consensus pattern (23 bp):
GTAAACGAAAACAATAAATGAAC
Found at i:35386 original size:14 final size:14
Alignment explanation
Indices: 35363--35469 Score: 124
Period size: 14 Copynumber: 7.6 Consensus size: 14
35353 TTGACTAAAT
*
35363 ATAAATGAACGAAC
1 ATAAACGAACGAAC
35377 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* * *
35391 ATAAATGAACAAAT
1 ATAAACGAACGAAC
35405 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* *
35419 ATAAATGAATGAAC
1 ATAAACGAACGAAC
*
35433 ATAAACGATCGAAC
1 ATAAACGAACGAAC
* *
35447 ATAAATGGACGAAC
1 ATAAACGAACGAAC
*
35461 ATATACGAA
1 ATAAACGAA
35470 TATATATATA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 75 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:35397 original size:28 final size:28
Alignment explanation
Indices: 35363--35469 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
35353 TTGACTAAAT
35363 ATAAATGAACGAACATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
35391 ATAAATGAACAAATATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
35419 ATAAATGAATGAACATAAACGATCGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
35447 ATAAATGGACGAACATATACGAA
1 ATAAATGAACGAACATAAACGAA
35470 TATATATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (28 bp):
ATAAATGAACGAACATAAACGAACGAAC
Found at i:35418 original size:42 final size:42
Alignment explanation
Indices: 35359--35469 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
35349 AAATTTGACT
*
35359 AAATATAAATGAACGAACATAAACGAACGAACATAAATGAAC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
35401 AAATATAAACGAACGAACATAAATGAATGAACATAAACGATC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
35443 GAACATAAATGGACGAACATATACGAA
1 AAATATAAATGAACGAACATAAACGAA
35470 TATATATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.15
Consensus pattern (42 bp):
AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
Found at i:38592 original size:10 final size:10
Alignment explanation
Indices: 38577--38601 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38567 TTTACCTTTC
38577 TGTCTTGAGA
1 TGTCTTGAGA
38587 TGTCTTGAGA
1 TGTCTTGAGA
38597 TGTCT
1 TGTCT
38602 GTGTTGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (10 bp):
TGTCTTGAGA
Found at i:39820 original size:13 final size:13
Alignment explanation
Indices: 39802--39827 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39792 ATTTTTTCTA
39802 AAAAATATTTTTT
1 AAAAATATTTTTT
39815 AAAAATATTTTTT
1 AAAAATATTTTTT
39828 GGAGTTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:40951 original size:21 final size:21
Alignment explanation
Indices: 40922--40964 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40912 TTCTAATTTT
*
40922 TTAGTATTA-GTATGAACAAAA
1 TTAGAATTATGTAT-AACAAAA
*
40943 TTAGAATTATTTATAACAAAA
1 TTAGAATTATGTATAACAAAA
40964 T
1 T
40965 GAGGAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
TTAGAATTATGTATAACAAAA
Found at i:41121 original size:3 final size:3
Alignment explanation
Indices: 41113--41167 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
41103 ACTTAATAAA
* * *
41113 ATT ATT ATT GTT ATT ATT ATT -TT ATT AAT -TT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41159 ATT -TT ATT A
1 ATT ATT ATT A
41168 ATTTAAGACG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41145 original size:28 final size:28
Alignment explanation
Indices: 41114--41172 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
41104 CTTAATAAAA
41114 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
41142 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
41170 TTA
1 TTA
41173 AGACGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (28 bp):
TTATTATTGTTATTATTATTTTATTAAT
Found at i:54272 original size:19 final size:18
Alignment explanation
Indices: 54229--54273 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
54219 AAAATAGTCC
54229 AACCAAATTGGCAAATTT
1 AACCAAATTGGCAAATTT
* *
54247 ATTCCAATTTGGCAAATTCT
1 A-ACCAAATTGGCAAATT-T
54267 AACCAAA
1 AACCAAA
54274 ATCGAGACGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
AACCAAATTGGCAAATTT
Found at i:56514 original size:19 final size:18
Alignment explanation
Indices: 56480--56516 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56470 AGAATCAAAC
56480 ATAAATTAATAAAATTTA
1 ATAAATTAATAAAATTTA
*
56498 ATAAATGTAATATAATTTA
1 ATAAAT-TAATAAAATTTA
56517 TTGTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAAATTAATAAAATTTA
Found at i:57156 original size:23 final size:21
Alignment explanation
Indices: 57130--57176 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
57120 TGAATTCAAA
* *
57130 TTAGGATTTATTTTATTTATATT
1 TTAGGAATTATCTT-TTTA-ATT
57153 TTAGGAATTATCTTTTTAATT
1 TTAGGAATTATCTTTTTAATT
57174 TTA
1 TTA
57177 AATGTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TTAGGAATTATCTTTTTAATT
Found at i:60107 original size:23 final size:23
Alignment explanation
Indices: 60077--60133 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
60067 ACGAACGGAT
* * *
60077 GTAAACGAACAGAATAAATTAAC
1 GTAAACGAAAACAATAAATGAAC
60100 GTAAACGAAAACAATAAATGAAC
1 GTAAACGAAAACAATAAATGAAC
* *
60123 ATAAATGAAAA
1 GTAAACGAAAA
60134 TAGATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.16
Consensus pattern (23 bp):
GTAAACGAAAACAATAAATGAAC
Found at i:60323 original size:14 final size:14
Alignment explanation
Indices: 60300--60406 Score: 124
Period size: 14 Copynumber: 7.6 Consensus size: 14
60290 TTGACTAAAT
*
60300 ATAAATGAACGAAC
1 ATAAACGAACGAAC
60314 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* * *
60328 ATAAATGAACAAAT
1 ATAAACGAACGAAC
60342 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* *
60356 ATAAATGAATGAAC
1 ATAAACGAACGAAC
*
60370 ATAAACGATCGAAC
1 ATAAACGAACGAAC
* *
60384 ATAAATGGACGAAC
1 ATAAACGAACGAAC
*
60398 ATATACGAA
1 ATAAACGAA
60407 TATATATATA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 75 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:60334 original size:28 final size:28
Alignment explanation
Indices: 60300--60406 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
60290 TTGACTAAAT
60300 ATAAATGAACGAACATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
60328 ATAAATGAACAAATATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
60356 ATAAATGAATGAACATAAACGATCGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
60384 ATAAATGGACGAACATATACGAA
1 ATAAATGAACGAACATAAACGAA
60407 TATATATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (28 bp):
ATAAATGAACGAACATAAACGAACGAAC
Found at i:60355 original size:42 final size:42
Alignment explanation
Indices: 60296--60406 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
60286 AAATTTGACT
*
60296 AAATATAAATGAACGAACATAAACGAACGAACATAAATGAAC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
60338 AAATATAAACGAACGAACATAAATGAATGAACATAAACGATC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
60380 GAACATAAATGGACGAACATATACGAA
1 AAATATAAATGAACGAACATAAACGAA
60407 TATATATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.15
Consensus pattern (42 bp):
AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
Found at i:63527 original size:10 final size:10
Alignment explanation
Indices: 63512--63536 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
63502 TTTACCTTTC
63512 TGTCTTGAGA
1 TGTCTTGAGA
63522 TGTCTTGAGA
1 TGTCTTGAGA
63532 TGTCT
1 TGTCT
63537 GTGTTGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (10 bp):
TGTCTTGAGA
Found at i:72846 original size:18 final size:18
Alignment explanation
Indices: 72823--72857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72813 GGAAAATAAC
*
72823 ACTTTAATCAAACATATA
1 ACTTTAATAAAACATATA
*
72841 ACTTTATTAAAACATAT
1 ACTTTAATAAAACATAT
72858 GTCCGAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (18 bp):
ACTTTAATAAAACATATA
Done.