Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008253.1 Hibiscus syriacus cultivar Beakdansim tig00110905_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: 59911
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:188 original size:15 final size:15
Alignment explanation
Indices: 164--197 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
154 AATTTGATAA
164 TTAAGATTTAAATT-
1 TTAAGATTTAAATTG
178 TTAACGATTTAAATTG
1 TTAA-GATTTAAATTG
194 TTAA
1 TTAA
198 TCGCATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 10 0.56
16 4 0.22
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (15 bp):
TTAAGATTTAAATTG
Found at i:1279 original size:4 final size:4
Alignment explanation
Indices: 1265--1338 Score: 89
Period size: 4 Copynumber: 18.8 Consensus size: 4
1255 TCACTTGATT
*
1265 TATG ATATG TATG TATG TATG TA-G -ATG TATG TATA TATG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
1312 TATG TATG TATA TGTA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1339 ATGTATATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
2 1 0.02
3 2 0.03
4 54 0.89
5 4 0.07
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1310 original size:16 final size:16
Alignment explanation
Indices: 1269--1375 Score: 97
Period size: 16 Copynumber: 7.2 Consensus size: 16
1259 TTGATTTATG
1269 ATATGTATGTATGTAT
1 ATATGTATGTATGTAT
*
1285 GTA-G-ATGTATGTAT
1 ATATGTATGTATGTAT
1299 ATATGTATGTATGTAT
1 ATATGTATGTATGTAT
*
1315 GTATGTA--TATG--T
1 ATATGTATGTATGTAT
* *
1327 ATATGTATGTATATGT
1 ATATGTATGTATGTAT
*
1343 ATATGTATATAT-TAT
1 ATATGTATGTATGTAT
*
1358 ATA--TATGTATATAT
1 ATATGTATGTATGTAT
1372 ATAT
1 ATAT
1376 ATGATATCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
12 7 0.09
13 6 0.08
14 25 0.33
15 7 0.09
16 30 0.40
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
ATATGTATGTATGTAT
Found at i:1347 original size:12 final size:12
Alignment explanation
Indices: 1282--1375 Score: 77
Period size: 12 Copynumber: 7.8 Consensus size: 12
1272 TGTATGTATG
*
1282 TATGTAGATGTA
1 TATGTATATGTA
* *
1294 TGTATATATGTA
1 TATGTATATGTA
1306 TGTATGTATGTATGTA
1 --TATGTA--TATGTA
1322 TATGTATATG--
1 TATGTATATGTA
1332 TATGTATATGTA
1 TATGTATATGTA
*
1344 TATGTATATAT-
1 TATGTATATGTA
*
1355 TATATATATGTA
1 TATGTATATGTA
*
1367 TATATATAT
1 TATGTATAT
1376 ATGATATCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
10 10 0.15
11 9 0.13
12 32 0.48
14 10 0.15
16 6 0.09
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (12 bp):
TATGTATATGTA
Found at i:1372 original size:4 final size:4
Alignment explanation
Indices: 1296--1388 Score: 62
Period size: 4 Copynumber: 23.0 Consensus size: 4
1286 TAGATGTATG
* * * * * * * * *
1296 TATA TATG TATG TATG TATG TATG TATA TGTA TATG TATG TATA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1344 TATG TATA TAT- TATA TATA TGTA TATA TATA TATGA TATCA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TAT-A TAT-A TATA
1389 AATTCAAATT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
3 3 0.04
4 63 0.85
5 8 0.11
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:1613 original size:33 final size:33
Alignment explanation
Indices: 1567--1643 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
1557 TCAGCAACCT
*
1567 CCGCCGCCGCCTCCACCTCCACAACCTCCGCCG
1 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
1600 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
1 CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
* *
1633 CCTCCTCCACC
1 CCGCCGCCACC
1644 CACCGCCACC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.65, G:0.12, T:0.10
Consensus pattern (33 bp):
CCGCCGCCACCTCCACCTCCACAACCTCCGCCG
Found at i:2739 original size:86 final size:85
Alignment explanation
Indices: 2594--2757 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 85
2584 GATATCAAAG
*
2594 AACTTGTAAGGCTGACATTTACTTGGTCCATGTGGCCACAATGTTTTTATTTATTTTAATTTTTA
1 AACTTGTAAGGCTGACATTTACTTGGTCCATCTGGCCACAATGTTTTTATTTATTTTAA-TTTTA
2659 TTTTAGACTTTTCATAAATAA
65 TTTTAGACTTTTCATAAATAA
* *
2680 AACTTGTAAGGTTGACATTTACTTTGTCCATCTGGGCCACAATGTTTTTATTTA-TTTAATTTTA
1 AACTTGTAAGGCTGACATTTACTTGGTCCATCT-GGCCACAATGTTTTTATTTATTTTAATTTTA
2744 TTTTAGACTTTTCA
65 TTTTAGACTTTTCA
2758 AATTTTTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
85 19 0.26
86 35 0.47
87 20 0.27
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (85 bp):
AACTTGTAAGGCTGACATTTACTTGGTCCATCTGGCCACAATGTTTTTATTTATTTTAATTTTAT
TTTAGACTTTTCATAAATAA
Found at i:5894 original size:12 final size:13
Alignment explanation
Indices: 5871--5908 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
5861 TCATTTGGAT
*
5871 TAGGATTAGGAGG
1 TAGGATTTGGAGG
5884 T-GGATTTGGAGG
1 TAGGATTTGGAGG
5896 TAGG-TTTGGAGG
1 TAGGATTTGGAGG
5908 T
1 T
5909 CGGTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
TAGGATTTGGAGG
Found at i:6175 original size:20 final size:20
Alignment explanation
Indices: 6134--6176 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6124 ATTTTTCATT
*
6134 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
*
6154 AAAACAACA-ATTTAAAAACA
1 AAAACAACATAATT-AAAACA
6174 AAA
1 AAA
6177 CATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:8708 original size:12 final size:12
Alignment explanation
Indices: 8691--8715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8681 ATGATGGTTC
8691 TCCAACGTCATG
1 TCCAACGTCATG
8703 TCCAACGTCATG
1 TCCAACGTCATG
8715 T
1 T
8716 GCTTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:11102 original size:18 final size:17
Alignment explanation
Indices: 11075--11112 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11065 TACCTCTTTG
11075 CCTAGGGGTA-TCGGTAC
1 CCTAGGGGTATTC-GTAC
11092 CCTATGGGGTATTCGTAC
1 CCTA-GGGGTATTCGTAC
11110 CCT
1 CCT
11113 TATTGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 13 0.68
19 2 0.11
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (17 bp):
CCTAGGGGTATTCGTAC
Found at i:25881 original size:22 final size:22
Alignment explanation
Indices: 25853--25902 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
25843 GTCTGTTTAT
*
25853 TATATATGATGTTTATCATGAA
1 TATATATGATATTTATCATGAA
25875 TATATATGATATTTATCATGAA
1 TATATATGATATTTATCATGAA
25897 TGATAT
1 T-ATAT
25903 TGCAGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (22 bp):
TATATATGATATTTATCATGAA
Found at i:26211 original size:86 final size:86
Alignment explanation
Indices: 26050--26214 Score: 231
Period size: 86 Copynumber: 1.9 Consensus size: 86
26040 CTTATCAGAT
* ** ** **
26050 CATACTAAAGGATACCTAGTGCGAGTCAGTACTAACTGATACCTAGTGCTGATGGTGGGGATGAC
1 CATACTAAAGGATACCTAATGCGAGTCAGTACTAAAGGATACCTAGTGCTGATGGCAGACATGAC
* *
26115 CTTATGTGTCATATTTAAGGC
66 CTCATATGTCATATTTAAGGC
*
26136 CATACTAAAGGATACCTAATGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGCAGACATGAC
1 CATACTAAAGGATACCTAATGCGAGTCAGTACTAAAGGATACCTAGTGCTGATGGCAGACATGAC
*
26201 CTCCTATGTCATAT
66 CTCATATGTCATAT
26215 CAGTTTAGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (86 bp):
CATACTAAAGGATACCTAATGCGAGTCAGTACTAAAGGATACCTAGTGCTGATGGCAGACATGAC
CTCATATGTCATATTTAAGGC
Found at i:38589 original size:21 final size:21
Alignment explanation
Indices: 38565--38640 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
38555 AAAGGTTAAG
38565 ACCTTTTGATGAAAGGACTTA
1 ACCTTTTGATGAAAGGACTTA
* * *
38586 ACCTTTTGATTAAAAGACTTC
1 ACCTTTTGATGAAAGGACTTA
* *
38607 TCCTTTTGATGAAAGGGCTTA
1 ACCTTTTGATGAAAGGACTTA
*
38628 ACCTTTTCATGAA
1 ACCTTTTGATGAA
38641 GAGAATTGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (21 bp):
ACCTTTTGATGAAAGGACTTA
Found at i:44305 original size:21 final size:23
Alignment explanation
Indices: 44257--44305 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
44247 CCCCCTGTGG
44257 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
44280 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
44301 GGGGG
1 GGGGG
44306 ATCAATTCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.18, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:51449 original size:2 final size:2
Alignment explanation
Indices: 51442--51489 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
51432 TAACAAAGTG
51442 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51482 TA TGA TA T
1 TA T-A TA T
51490 GTTTGTTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54681 original size:17 final size:17
Alignment explanation
Indices: 54659--54695 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
54649 AGGAGCATTC
54659 AACAGATTTAGAAACAT
1 AACAGATTTAGAAACAT
54676 AACAGATTTAGAAACAT
1 AACAGATTTAGAAACAT
54693 AAC
1 AAC
54696 CACTGCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (17 bp):
AACAGATTTAGAAACAT
Done.