Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004176.1 Hibiscus syriacus cultivar Beakdansim tig00009131_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: 83147
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:5308 original size:201 final size:197
Alignment explanation
Indices: 5069--5649 Score: 513
Period size: 190 Copynumber: 2.9 Consensus size: 197
5059 ACTCTTCTTG
* * **
5069 AATTAAG-TGTGTCAAAAGTTGGGCTAAGAAGTAGTTCATCGTTACTAAATCACAACCGATTTAG
1 AATTAAGCTATGTCGAAAGTTGGGCTGGGAAGTAGTTCATCGTT-CTAAATCAC-A--GATTTAG
* * * * * *
5133 GT-ATTCTTCTTGACTTAAAGACCTTAGTTTGAATTTTA-TCGAAATGTACTTCCTCATTGCTAA
62 GTCA-TCTTCTCGACATAAAGACCTCAGTTTGAATTTGAGT-GAAAGGTAATTCCTCATTGCTAA
* *
5196 CATACAGTCAATGTGCTTACGAA-CTGAATGGAATCAAACTTGAAAGCCTTTAGTCGATAGATAG
125 CATACAGTCAATGTGCTTAC-AAGCTAAACGGAATCAAACTTGAAAGCCTTTAGTCGATAGATAG
*
5260 CTATTCCCA
189 CTATTACCA
* * * *
5269 AATTAAGCTATGTTGAAAGTTGGGTTGGTAAGTAGTTCATCG---T--A--GCAGATTTAGGTCA
1 AATTAAGCTATGTCGAAAGTTGGGCTGGGAAGTAGTTCATCGTTCTAAATCACAGATTTAGGTCA
* * * *
5327 TCTTCTCGACATAATGACCTCAGTTTTAATTTGAGTGAAAGGTAATTCCTCATTGCTAACATGCG
66 TCTTCTCGACATAAAGACCTCAGTTTGAATTTGAGTGAAAGGTAATTCCTCATTGCTAACATACA
* * *
5392 GTCAATGTGCTTTCAAGCTAAACGGAATCAAACTTGAAAGCCTTTAGTCGATAGATAGCTCTTAT
131 GTCAATGTGCTTACAAGCTAAACGGAATCAAACTTGAAAGCCTTTAGTCGATAGATAGCTATTAC
5457 CA
196 CA
* ** *
5459 ACTTAAGCTATGTCGAAAGTTGGGCTGGGAAGTAGTTTGTCGTTGCTAAATCGTAGCTGATTTAG
1 AATTAAGCTATGTCGAAAGTTGGGCTGGGAAGTAGTTCATCGTT-CTAAATC--A-CAGATTTAG
* * ** * *** * * *
5524 GTCTTTTTTCTCGATTTAATGACCTC-GATTTGAATTTTGACCAAAAGATAGTTCCTCGTTGCTA
62 GTC-ATCTTCTCGACATAAAGACCTCAG-TTTGAA-TTTGAGTGAAAGGTAATTCCTCATTGCTA
* ** * * * * *
5588 CCAT-GTGATCAATGTGCTTTCAAGCTAAATGGAATCGAACTAGAAAACCTTTAGTCGATAGA
124 ACATACAG-TCAATGTGCTTACAAGCTAAACGGAATCAAACTTGAAAGCCTTTAGTCGATAGA
5650 CAACTCTTGA
Statistics
Matches: 312, Mismatches: 50, Indels: 35
0.79 0.13 0.09
Matches are distributed among these distances:
189 2 0.01
190 156 0.50
191 2 0.01
192 1 0.00
193 1 0.00
194 1 0.00
195 1 0.00
196 1 0.00
197 1 0.00
200 7 0.02
201 39 0.12
202 24 0.08
203 76 0.24
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (197 bp):
AATTAAGCTATGTCGAAAGTTGGGCTGGGAAGTAGTTCATCGTTCTAAATCACAGATTTAGGTCA
TCTTCTCGACATAAAGACCTCAGTTTGAATTTGAGTGAAAGGTAATTCCTCATTGCTAACATACA
GTCAATGTGCTTACAAGCTAAACGGAATCAAACTTGAAAGCCTTTAGTCGATAGATAGCTATTAC
CA
Found at i:8423 original size:20 final size:19
Alignment explanation
Indices: 8398--8443 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
8388 AAGTTTGGTT
*
8398 TGAAAAATTCAATTTCTTAA
1 TGAAAAATT-AAATTCTTAA
8418 TGAAAAA-TAAATTCTTAA
1 TGAAAAATTAAATTCTTAA
8436 TGAAAAAT
1 TGAAAAAT
8444 GGGGAGCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 16 0.67
19 1 0.04
20 7 0.29
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (19 bp):
TGAAAAATTAAATTCTTAA
Found at i:8506 original size:19 final size:19
Alignment explanation
Indices: 8482--8540 Score: 100
Period size: 19 Copynumber: 3.0 Consensus size: 19
8472 CAACAATTGG
8482 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
8501 TAACAATTGATATCCTTTTGT
1 TAACAATTGATAT-CTTTT-T
8522 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
8541 CATTAAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.37
20 10 0.26
21 14 0.37
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:8791 original size:20 final size:20
Alignment explanation
Indices: 8766--8806 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
8756 ATTTACTATA
*
8766 TAAATAGTATCGACACTGTT
1 TAAATAGTAGCGACACTGTT
*
8786 TAAATAGTAGCGATACTGTT
1 TAAATAGTAGCGACACTGTT
8806 T
1 T
8807 GAACGGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (20 bp):
TAAATAGTAGCGACACTGTT
Found at i:8836 original size:30 final size:30
Alignment explanation
Indices: 8791--8851 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
8781 CTGTTTAAAT
* *
8791 AGTAGCGATACTGTTTGAACGGTAATGAAC
1 AGTAGCGATAATGTTTGAACAGTAATGAAC
* *
8821 AGTATCGATAATGTTTGAACAGTGATGAAC
1 AGTAGCGATAATGTTTGAACAGTAATGAAC
8851 A
1 A
8852 ATACCAAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (30 bp):
AGTAGCGATAATGTTTGAACAGTAATGAAC
Found at i:10698 original size:29 final size:31
Alignment explanation
Indices: 10621--10698 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
10611 CTTTTCAATA
* * *
10621 TTATATTTTTGGTCCCTAAACTTTTACAAAGT
1 TTATA-TTTTAGTCACTAAACTTTTACAAAGC
*
10653 TTATACTTTAG-CTACTAAACTTTTA-AAA-C
1 TTATATTTTAGTC-ACTAAACTTTTACAAAGC
10682 TTATATTTTAGTCACTA
1 TTATATTTTAGTCACTA
10699 GTAAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 14 0.36
30 5 0.13
31 15 0.38
32 5 0.13
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (31 bp):
TTATATTTTAGTCACTAAACTTTTACAAAGC
Found at i:14598 original size:10 final size:10
Alignment explanation
Indices: 14583--14607 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14573 ATAAATTTTT
14583 CATTTTCTTC
1 CATTTTCTTC
14593 CATTTTCTTC
1 CATTTTCTTC
14603 CATTT
1 CATTT
14608 CCAAGTCTTT
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:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (10 bp):
CATTTTCTTC
Found at i:26884 original size:62 final size:62
Alignment explanation
Indices: 26810--26944 Score: 243
Period size: 62 Copynumber: 2.2 Consensus size: 62
26800 AATCTTATAC
26810 TATCGATACTCTTGCTTCAGTATTGCTACCACCAATCTAAATTATCCTGAAAGGAAATGGAG
1 TATCGATACTCTTGCTTCAGTATTGCTACCACCAATCTAAATTATCCTGAAAGGAAATGGAG
* *
26872 TATCGATACTCTTGCTTCAGTATTGCTACCACCAATCTAAATTATCTTGAAAGGGAATGGAG
1 TATCGATACTCTTGCTTCAGTATTGCTACCACCAATCTAAATTATCCTGAAAGGAAATGGAG
*
26934 TATCGAAACTC
1 TATCGATACTC
26945 ACGTAGGAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (62 bp):
TATCGATACTCTTGCTTCAGTATTGCTACCACCAATCTAAATTATCCTGAAAGGAAATGGAG
Found at i:30707 original size:40 final size:41
Alignment explanation
Indices: 30642--30733 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
30632 TGTAAAGGGA
*
30642 GTATCGATACTGATGTGGTAATATCGATACTGGGACCTTAG
1 GTATCGATACTGATGTGGTAATATCGATACTGGAACCTTAG
* *
30683 GTATCG-TACTGATGTAGG-AGTATCGCTACTGGAACCTTAG
1 GTATCGATACTGATGT-GGTAATATCGATACTGGAACCTTAG
30723 GTATCGATACT
1 GTATCGATACT
30734 CCCTAGAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 34 0.74
41 12 0.26
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (41 bp):
GTATCGATACTGATGTGGTAATATCGATACTGGAACCTTAG
Found at i:35243 original size:13 final size:14
Alignment explanation
Indices: 35225--35253 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35215 ACTCTTGGGG
35225 AAGAAAAGAA-AGA
1 AAGAAAAGAAGAGA
35238 AAGAAAAGAAGAGA
1 AAGAAAAGAAGAGA
35252 AA
1 AA
35254 ATAAAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAGA
Found at i:39405 original size:49 final size:49
Alignment explanation
Indices: 39352--39475 Score: 203
Period size: 49 Copynumber: 2.5 Consensus size: 49
39342 CTTTATGCTG
39352 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATACCA
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATACCA
** *
39401 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGTCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATACCA
* *
39450 AAATGCACCATTACGCATTTAACTTT
1 AAATGCACCGTTATGCATTTAACTTT
39476 AGCACCCTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (49 bp):
AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATACCA
Found at i:51388 original size:27 final size:27
Alignment explanation
Indices: 51317--51377 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
51307 GATTGCGAGA
* **
51317 GGTCAAACTTCTCAAACTCGTTAAATT
1 GGTCAAACTTGTCAAACTTATTAAATT
51344 GGTCAAACTTGTCAAACTTATTAAATT
1 GGTCAAACTTGTCAAACTTATTAAATT
51371 GGTCAAA
1 GGTCAAA
51378 TTTTTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (27 bp):
GGTCAAACTTGTCAAACTTATTAAATT
Found at i:52725 original size:16 final size:17
Alignment explanation
Indices: 52695--52726 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52685 ATATTTATTT
52695 ATATAAAATATAATATA
1 ATATAAAATATAATATA
52712 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
52727 TATGGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:54868 original size:20 final size:20
Alignment explanation
Indices: 54843--54895 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
54833 TGTTGTACAA
54843 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
54863 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
54883 GGGGGGAATCGGT
1 GGGGGGAATCGGT
54896 TCCCTCCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:57060 original size:20 final size:21
Alignment explanation
Indices: 57012--57070 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
57002 CCCCTGTGGG
*
57012 GGGAATCGGTTCCCCTTCAAAGG
1 GGGAATCGGTT-CCC-TCAAAGA
*
57035 GGGAATCGGTTCCCTC-ATGA
1 GGGAATCGGTTCCCTCAAAGA
*
57055 GGGAATCGATTCCCTC
1 GGGAATCGGTTCCCTC
57071 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 3 0.09
23 11 0.33
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCAAAGA
Found at i:65202 original size:23 final size:23
Alignment explanation
Indices: 65168--65211 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
65158 GCATTTTCGT
65168 AAGAGTAATTTGTGTACTATGGC
1 AAGAGTAATTTGTGTACTATGGC
*
65191 AAGAGTACTTTGTGTACTATG
1 AAGAGTAATTTGTGTACTATG
65212 ACACTTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (23 bp):
AAGAGTAATTTGTGTACTATGGC
Found at i:66501 original size:23 final size:23
Alignment explanation
Indices: 66475--66518 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
66465 TATTTTATAA
*
66475 TTTTT-AAAAATTAATAATTATT
1 TTTTTAAAAAATTAAAAATTATT
66497 TTTTTAAAAAATTAAAAATTAT
1 TTTTTAAAAAATTAAAAATTAT
66519 AATTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTAAAAAATTAAAAATTATT
Found at i:67551 original size:36 final size:36
Alignment explanation
Indices: 67511--67649 Score: 242
Period size: 36 Copynumber: 3.9 Consensus size: 36
67501 ACAGTGCTGG
67511 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
67547 ACATTGATACACGAATGTATCAAAGCTAATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
67583 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
67619 ACATTGATACACGAATGTATCAAAGTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
67650 ATGGATAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:69615 original size:29 final size:29
Alignment explanation
Indices: 69583--69639 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
69573 TTGACCCTTT
69583 AATTTTCCAAAATTTA-ATTTTAGTCACTA
1 AATTTT-CAAAATTTACATTTTAGTCACTA
*
69612 AATTTTCAAATTTTACATTTTAGTCACT
1 AATTTTCAAAATTTACATTTTAGTCACT
69640 TAACAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (29 bp):
AATTTTCAAAATTTACATTTTAGTCACTA
Found at i:74448 original size:40 final size:40
Alignment explanation
Indices: 74388--74469 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
74378 ACTGTAGTCC
* *
74388 TACACATAAGTTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACATCGAAGTGTAT
74428 TACACATAAGGTCGTACCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACATCGAAGTGTAT
74468 TA
1 TA
74470 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (40 bp):
TACACATAAGGTCGTACCCACCATATACATCGAAGTGTAT
Found at i:74857 original size:28 final size:28
Alignment explanation
Indices: 74823--74877 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
74813 TTATGTCTTT
74823 CAAAATATATGAGCCTCACTATTGTCCA
1 CAAAATATATGAGCCTCACTATTGTCCA
*
74851 CAAAATATATGATCCTCACTATTGTCC
1 CAAAATATATGAGCCTCACTATTGTCC
74878 TCCATAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (28 bp):
CAAAATATATGAGCCTCACTATTGTCCA
Done.