Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004632.1 Hibiscus syriacus cultivar Beakdansim tig00010365_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: 54676
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4844 original size:16 final size:16
Alignment explanation
Indices: 4802--4869 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
4792 TGTATATGTT
4802 TATGTGTTACATGCA-C
1 TATGTGTTACATG-ATC
*
4818 TAT-T-CTACATGATC
1 TATGTGTTACATGATC
4832 TATGTGTTACATGATC
1 TATGTGTTACATGATC
*
4848 TATGTGATTATATG-TC
1 TATGTG-TTACATGATC
4864 TATGTG
1 TATGTG
4870 ATATAAGCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
13 1 0.02
14 10 0.22
15 2 0.04
16 26 0.58
17 6 0.13
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (16 bp):
TATGTGTTACATGATC
Found at i:4870 original size:16 final size:16
Alignment explanation
Indices: 4830--4884 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
4820 TTCTACATGA
*
4830 TCTATGTG-TTACATG
1 TCTATGTGATTATATG
4845 ATCTATGTGATTATATG
1 -TCTATGTGATTATATG
*
4862 TCTATGTGA-TATAAG
1 TCTATGTGATTATATG
4877 -CTATGTGA
1 TCTATGTGA
4885 AATGAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
14 8 0.22
15 5 0.14
16 17 0.47
17 6 0.17
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (16 bp):
TCTATGTGATTATATG
Found at i:5912 original size:21 final size:22
Alignment explanation
Indices: 5888--5928 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5878 AGAGCAGAGC
*
5888 AAACAACTAGAAGA-GAAATGG
1 AAACAACTAAAAGAGGAAATGG
5909 AAACAACTAAAAGAGGAAAT
1 AAACAACTAAAAGAGGAAAT
5929 TAGGGCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.61, C:0.10, G:0.20, T:0.10
Consensus pattern (22 bp):
AAACAACTAAAAGAGGAAATGG
Found at i:12550 original size:22 final size:22
Alignment explanation
Indices: 12492--12550 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
12482 CGCTATCAAG
12492 AAAGA-AGAAAA-AAAATGAAA
1 AAAGAGAGAAAATAAAATGAAA
* *
12512 AAAGGGGGAAAATAAAATGAAA
1 AAAGAGAGAAAATAAAATGAAA
12534 AAA-AGAGAAAATGAAAA
1 AAAGAGAGAAAAT-AAAA
12551 ATATCAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
22 16 0.50
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (22 bp):
AAAGAGAGAAAATAAAATGAAA
Found at i:14665 original size:14 final size:15
Alignment explanation
Indices: 14633--14665 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
14623 TATATGATTG
14633 TTTT-TATTTTACTT
1 TTTTATATTTTACTT
14647 TTTTATATTTTA-TT
1 TTTTATATTTTACTT
14661 TTTTA
1 TTTTA
14666 ATTAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTACTT
Found at i:18222 original size:36 final size:35
Alignment explanation
Indices: 18182--18303 Score: 102
Period size: 36 Copynumber: 3.3 Consensus size: 35
18172 AAGAAGACAT
18182 TTCATTGCACTACAGATTGTTTTTCTTAAAACAAGA
1 TTCATT-CACTACAGATTGTTTTTCTTAAAACAAGA
* ** * * *
18218 TTCATCTCGCTTGAGATAGTTTTTACTCGAAAGA-ATACA
1 TTCAT-TCACTACAGATTGTTTTT-CT-TAAA-ACA-AGA
*
18257 TTTCATTCACTACAAATTGTTTTTCTTAAAACAAGA
1 -TTCATTCACTACAGATTGTTTTTCTTAAAACAAGA
18293 TTCATCTCACT
1 TTCAT-TCACT
18304 TGAGATAGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
35 5 0.08
36 26 0.40
37 7 0.11
38 6 0.09
39 16 0.25
40 5 0.08
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (35 bp):
TTCATTCACTACAGATTGTTTTTCTTAAAACAAGA
Found at i:18289 original size:75 final size:75
Alignment explanation
Indices: 18161--18387 Score: 318
Period size: 75 Copynumber: 3.0 Consensus size: 75
18151 CTTCAAACAA
* *
18161 TTTTTACTAGAAAGAAGACATTTCATTGCACTACAGATTGTTTTTCTTAAAACAAGATTCATCTC
1 TTTTTACTCGAAAGAAGACATTTCATT-CACTACAAATTGTTTTTCTTAAAACAAGATTCATCTC
18226 GCTTGAGATAG
65 GCTTGAGATAG
* *
18237 TTTTTACTCGAAAGAATACATTTCATTCACTACAAATTGTTTTTCTTAAAACAAGATTCATCTCA
1 TTTTTACTCGAAAGAAGACATTTCATTCACTACAAATTGTTTTTCTTAAAACAAGATTCATCTCG
18302 CTTGAGATAG
66 CTTGAGATAG
* *
18312 TTTTTACTCGAAAAAAGACATTTCATTTCACT-CAAGATTG--TTT-TTAAAACAAGATTTATCT
1 TTTTTACTCGAAAGAAGACATTTCA-TTCACTACAA-ATTGTTTTTCTTAAAACAAGATTCATCT
* * *
18373 TGCTGGAGATTG
64 CGCTTGAGATAG
18385 TTT
1 TTT
18388 CACTTGAAAC
Statistics
Matches: 138, Mismatches: 11, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
73 28 0.20
74 3 0.02
75 72 0.52
76 35 0.25
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (75 bp):
TTTTTACTCGAAAGAAGACATTTCATTCACTACAAATTGTTTTTCTTAAAACAAGATTCATCTCG
CTTGAGATAG
Found at i:18315 original size:36 final size:36
Alignment explanation
Indices: 18195--18316 Score: 113
Period size: 36 Copynumber: 3.3 Consensus size: 36
18185 ATTGCACTAC
* *
18195 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTG
1 AGATAGTTTTTCTTAAAACAAGATTCATCTCACTTG
* * **
18231 AGATAGTTTTTACTCGAAAGA-ATACATTTCAT-TCACTAC
1 AGATAGTTTTT-CT-TAAA-ACA-AGA-TTCATCTCACTTG
* *
18270 AAATTGTTTTTCTTAAAACAAGATTCATCTCACTTG
1 AGATAGTTTTTCTTAAAACAAGATTCATCTCACTTG
18306 AGATAGTTTTT
1 AGATAGTTTTT
18317 ACTCGAAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
35 5 0.08
36 27 0.42
37 6 0.09
38 6 0.09
39 16 0.25
40 5 0.08
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (36 bp):
AGATAGTTTTTCTTAAAACAAGATTCATCTCACTTG
Found at i:18411 original size:39 final size:39
Alignment explanation
Indices: 18362--18612 Score: 353
Period size: 39 Copynumber: 6.5 Consensus size: 39
18352 TTTTTAAAAC
* * * *
18362 AAGA-TTTATCTTGCTGGAGATTGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
18400 AAGATTTTATCTCGCTTGAGATAGTTTCAATCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
18439 AAGATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
18478 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
18517 AAGATTTTATCTGGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * * *
18556 AAGAATTTATCTGGCTTGAGATAATTTTACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
18595 AAGA-TTTATCTCACTTGA
1 AAGATTTTATCTCGCTTGA
18613 TATTGTTTTT
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
38 16 0.08
39 177 0.92
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:18887 original size:137 final size:138
Alignment explanation
Indices: 18634--18892 Score: 412
Period size: 137 Copynumber: 1.9 Consensus size: 138
18624 TTAAAACCAA
* * *
18634 CTACGCCTCATTTGAGGGATTAACATTTTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCA
1 CTACGCCTCACTTGAGGGATCAACAATTTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCA
* *
18699 AGAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCGACCTATAGCTCGATTCACGGTATTT
66 ACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATAGCTCGATTCACGGTATTT
18764 TGAATCAG
131 TGAATCAG
* * *
18772 CTACGCCTCGCTTGAGGGATCAA-AATTTTCAAATGGAGAGTTTATAATGGGAAGAACTCATCCA
1 CTACGCCTCACTTGAGGGATCAACAATTTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCA
* * *
18836 ACATAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACTTATCGCTCGATTCA
66 ACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATAGCTCGATTCA
18893 TGGCTGTAAC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
137 90 0.82
138 20 0.18
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (138 bp):
CTACGCCTCACTTGAGGGATCAACAATTTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCA
ACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATAGCTCGATTCACGGTATTT
TGAATCAG
Found at i:21864 original size:13 final size:13
Alignment explanation
Indices: 21846--21882 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
21836 AAATAGTTTA
21846 AAATATGTTAGTT-
1 AAATAT-TTAGTTG
21859 AAATATTTA-TTG
1 AAATATTTAGTTG
21871 AAATATTTAGTT
1 AAATATTTAGTT
21883 TTAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 12 0.55
13 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (13 bp):
AAATATTTAGTTG
Found at i:21995 original size:15 final size:15
Alignment explanation
Indices: 21955--21988 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
21945 ATCCATAGGA
21955 AAGAAACATATTTTT
1 AAGAAACATATTTTT
21970 AAGAAACATATTTTT
1 AAGAAACATATTTTT
21985 AAGA
1 AAGA
21989 GCAATATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (15 bp):
AAGAAACATATTTTT
Found at i:22664 original size:2 final size:2
Alignment explanation
Indices: 22657--22688 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22647 AATTTTTGAA
22657 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22689 ATTAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35722 original size:13 final size:13
Alignment explanation
Indices: 35704--35745 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
35694 GAATTATAAA
35704 ATTTTAAAATTTT
1 ATTTTAAAATTTT
*
35717 ATTTTAAAAAATTT
1 ATTTT-AAAATTTT
*
35731 ATTTAAAAATTTT
1 ATTTTAAAATTTT
35744 AT
1 AT
35746 ATGCTTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTTAAAATTTT
Found at i:36152 original size:65 final size:65
Alignment explanation
Indices: 36010--36214 Score: 331
Period size: 65 Copynumber: 3.2 Consensus size: 65
36000 ATTTCAAATG
* *
36010 AAGTTTGAGTTATAAAATAAGATTCGAATAACTTTAAA-TTTTAGTAATTAGTGGATTGGTTTTT
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
36074 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
* * ** * *
36139 AAGCTTGAATTATAAAATAAGACTCGAATAACTCAAAATTTTTAGTAATTAGTGAATTGATTTTC
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
36204 AAGTTTGAGTT
1 AAGTTTGAGTT
36215 GAGTCTCTCA
Statistics
Matches: 130, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 37 0.28
65 93 0.72
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (65 bp):
AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
Found at i:45078 original size:19 final size:19
Alignment explanation
Indices: 45044--45082 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45034 TATTAACAAC
*
45044 AAATAACTTAATTGATATTT
1 AAATAACTTAAGTGAT-TTT
45064 AAATAA-TTAAGTGATTTT
1 AAATAACTTAAGTGATTTT
45082 A
1 A
45083 TTGACAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (19 bp):
AAATAACTTAAGTGATTTT
Found at i:49447 original size:31 final size:31
Alignment explanation
Indices: 49399--49469 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
49389 AAAATAAGTT
*
49399 CCTAAAGTATATCACATTTTTCATCTAGGTA
1 CCTAAAGTATATCACATTTTTCATCTAGATA
*
49430 CCTAGAGTATA-CGACATTTTTCATCTAGATA
1 CCTAAAGTATATC-ACATTTTTCATCTAGATA
49461 CCTAAAGTA
1 CCTAAAGTA
49470 ATTTTTAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (31 bp):
CCTAAAGTATATCACATTTTTCATCTAGATA
Found at i:52637 original size:22 final size:22
Alignment explanation
Indices: 52599--52641 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
52589 TTAATATCTC
52599 ATTTAAAAGCTTGAAAATAAATA
1 ATTTAAAAGCTTGAAAA-AAATA
52622 ATTTAAAAG-TTGAAAAAAAT
1 ATTTAAAAGCTTGAAAAAAAT
52642 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTTAAAAGCTTGAAAAAAATA
Found at i:53394 original size:72 final size:69
Alignment explanation
Indices: 53325--53466 Score: 162
Period size: 72 Copynumber: 2.0 Consensus size: 69
53315 GATATGGACC
*
53325 ATATAGGGAGTCTCGC-CCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCC
1 ATATACGGAG-CTCGCACCCAA-ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCC
53389 CATGG-
64 CATGGA
* * * *
53394 ATGTACGGTGCTTGCAAATTCCCCAATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTT
1 ATATACGGAGCTCGC--A--CCCAAATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTT
*
53459 CCCGTGGA
62 CCCATGGA
53467 TGCTACAGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
68 4 0.07
69 7 0.11
72 46 0.75
73 4 0.07
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (69 bp):
ATATACGGAGCTCGCACCCAAATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCA
TGGA
Found at i:53467 original size:72 final size:73
Alignment explanation
Indices: 53347--53490 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 73
53337 TCGCCCCAAT
*
53347 ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATG-TACGGTGCTTGCAA
1 ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTGCTTGCAA
53411 ATTCCCCA
66 ATTCCCCA
*
53419 ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCGTGGATGCTACAGTGCTTGCAA
1 ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTGCTTGCAA
53484 ATTCCCC
66 ATTCCCC
53491 GGTTCTTAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 49 0.71
73 20 0.29
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (73 bp):
ATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTGCTTGCAA
ATTCCCCA
Done.