Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008924.1 Hibiscus syriacus cultivar Beakdansim tig00112228_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: 27527
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4336 original size:29 final size:29
Alignment explanation
Indices: 4294--4352 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
4284 ATTTTCACCT
*
4294 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTAATGTAAGAAATGACATCAA
*
4323 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGAAATGACATCAA
4352 A
1 A
4353 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGAAATGACATCAA
Found at i:5529 original size:19 final size:19
Alignment explanation
Indices: 5471--5529 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
5461 AATACAAAAC
*
5471 TATATTATTTTGAATT-TTA
1 TATATTA-TTTAAATTATTA
*
5490 TGAATATTA-TGAAATTGATTA
1 T--ATATTATTTAAATT-ATTA
5511 TATATTATTTAAATTATTA
1 TATATTATTTAAATTATTA
5530 GAATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
19 16 0.50
20 6 0.19
21 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TATATTATTTAAATTATTA
Found at i:5547 original size:14 final size:14
Alignment explanation
Indices: 5524--5554 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5514 ATTATTTAAA
5524 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
5538 TTATTTGAATTTAT
1 TTATTAGAATTTAT
5552 TTA
1 TTA
5555 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:6494 original size:20 final size:20
Alignment explanation
Indices: 6469--6580 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
6459 TGGGAAAATT
* *
6469 GCAATGCGATACTGACTATC
1 GCAACGCGATAATGACTATC
* *
6489 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATAATGAC--TATC
* * *
6510 GCAACGAGATACTGACTTTC
1 GCAACGCGATAATGACTATC
** *
6530 GCAACGCGATTTTGACTTTC
1 GCAACGCGATAATGACTATC
6550 GCAACGCGATAAT-ACATAATC
1 GCAACGCGATAATGAC-T-ATC
*
6571 GCAATGCGAT
1 GCAACGCGAT
6581 TTTCAAAGCG
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.05
20 43 0.59
21 24 0.33
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAACGCGATAATGACTATC
Found at i:6772 original size:21 final size:21
Alignment explanation
Indices: 6746--6788 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6736 CACTCTCTCA
6746 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGGCGAAATCCGT
6767 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGGCGAAATCCGT
6788 C
1 C
6789 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGGCGAAATCCGT
Found at i:7102 original size:20 final size:20
Alignment explanation
Indices: 7048--7106 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
7038 GCGATTCTCT
**
7048 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
7068 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
7088 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
7107 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:7297 original size:25 final size:24
Alignment explanation
Indices: 7243--7297 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
7233 TGTTTATTAT
* *
7243 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
7267 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
7293 TGTTT
1 TGTTT
7298 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:8451 original size:18 final size:18
Alignment explanation
Indices: 8425--8469 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
8415 TCCACTTTGG
*
8425 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
8443 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
8461 GAGCCATCA
1 GAGCCATCA
8470 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:8998 original size:20 final size:20
Alignment explanation
Indices: 8948--9014 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
8938 ATAGTTACTT
*
8948 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
8968 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
8988 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
9007 TCGCAACG
1 TCGCAACG
9015 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:9021 original size:39 final size:34
Alignment explanation
Indices: 8986--9077 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 34
8976 CGAAAATGGC
8986 TATCGCAATGCGAAATGAAAATCGCAACGAC-AAA
1 TATCGCAATGCGAAATG-AAATCGCAACGACAAAA
9020 -ATCGCAATGCGAAATGAAATCGCAACGACAAAA
1 TATCGCAATGCGAAATGAAATCGCAACGACAAAA
*
9053 T-T-GCAACGCGAAATGAAAATCGCAA
1 TATCGCAATGCGAAATG-AAATCGCAA
9078 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
32 25 0.46
33 29 0.54
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (34 bp):
TATCGCAATGCGAAATGAAATCGCAACGACAAAA
Found at i:9022 original size:14 final size:14
Alignment explanation
Indices: 9003--9060 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
8993 ATGCGAAATG
9003 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
9017 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
9033 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
9049 AAAATTGCAACG
1 AAAATCGCAACG
9061 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:9045 original size:32 final size:33
Alignment explanation
Indices: 8987--9077 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
8977 GAAAATGGCT
8987 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
9020 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
9052 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
9078 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:9113 original size:14 final size:14
Alignment explanation
Indices: 9094--9133 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
9084 TTGTGTTTCG
9094 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
9108 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9122 CATTGCGATTTT
1 CGTTGCGATTTT
9134 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9168 original size:20 final size:19
Alignment explanation
Indices: 9134--9189 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
9124 TTGCGATTTT
*
9134 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
9153 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
9173 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
9190 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:11072 original size:14 final size:14
Alignment explanation
Indices: 11053--11088 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11043 ATTGTTTAAT
11053 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
11067 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
11081 TGATTTGT
1 TGATTTGT
11089 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11196 original size:20 final size:20
Alignment explanation
Indices: 11171--11209 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11161 ATGTTGAAGG
11171 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
11191 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
11210 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:11239 original size:19 final size:19
Alignment explanation
Indices: 11215--11279 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
11205 GCAACGAGAG
11215 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11234 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
11253 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
11267 AATCGCAATGCGA
1 AATCGCAATGCGA
11280 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:11332 original size:19 final size:20
Alignment explanation
Indices: 11305--11391 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
11295 GCGATTTTGT
*
11305 CGTTACGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
11324 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
11344 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
11364 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
11383 CATTGCGAT
1 CGTTGCGAT
11392 TTTGATGATG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.40
20 39 0.60
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:11353 original size:39 final size:39
Alignment explanation
Indices: 11305--11391 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
11295 GCGATTTTGT
*
11305 CGTTACGATAGCCA-TTTCGCGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCA-TTTCG
11344 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
1 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
*
11383 CATTGCGAT
1 CGTTGCGAT
11392 TTTGATGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 26 0.58
40 19 0.42
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (39 bp):
CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
Found at i:13928 original size:33 final size:33
Alignment explanation
Indices: 13886--14011 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
13876 GGAAATTACT
13886 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
13919 ATCGCAATGCGAAATG-AAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
13950 TTTCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
13984 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
14012 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
31 1 0.01
32 26 0.32
33 52 0.65
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:13992 original size:65 final size:66
Alignment explanation
Indices: 13887--14018 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
13877 GAAATTACTA
* * *
13887 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACGCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
13951 T
66 T
*
13952 TCGCAATGCGAAATAAAAATCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
14017 T
66 T
14018 T
1 T
14019 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 45 0.73
66 17 0.27
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:14064 original size:19 final size:19
Alignment explanation
Indices: 14040--14076 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
14030 GCGATTCTCT
14040 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
14059 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
14077 TAATTGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:14083 original size:19 final size:19
Alignment explanation
Indices: 14042--14086 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
14032 GATTCTCTCG
**
14042 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGAA
*
14061 TTGCGATTTTCATTTCTAA
1 TTGCGATTTTCATTTCGAA
14080 TTGCGAT
1 TTGCGAT
14087 AGTACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGAA
Found at i:14212 original size:14 final size:14
Alignment explanation
Indices: 14193--14229 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
14183 CATCAATTAA
14193 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
14207 ACAAATCACCTTTT
1 ACAAATCAACTTTT
14221 ACAAATCAA
1 ACAAATCAA
14230 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:15671 original size:42 final size:42
Alignment explanation
Indices: 15625--15787 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 42
15615 CGATGACAGT
* * *
15625 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * * * *
15667 GGCCTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* **
15709 GGCCTCTTGAACG-GGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
15750 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
15788 CAGGCGAGTC
Statistics
Matches: 96, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
41 33 0.34
42 63 0.66
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:15755 original size:83 final size:84
Alignment explanation
Indices: 15616--15790 Score: 334
Period size: 83 Copynumber: 2.1 Consensus size: 84
15606 CCTCTTCAAC
*
15616 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
15681 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
15700 GATGACAGTGGCCTCTTGAACGG-GGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
15764 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
15783 GATGACAG
1 GATGACAG
15791 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 67 0.74
84 23 0.26
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:16184 original size:91 final size:90
Alignment explanation
Indices: 16007--16193 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 90
15997 ATATTTCAAA
*
16007 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
16072 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
16100 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
16164 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
16191 ACT
1 ACT
16194 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.23
95 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:16396 original size:63 final size:63
Alignment explanation
Indices: 16337--16478 Score: 142
Period size: 63 Copynumber: 2.3 Consensus size: 63
16327 CTTAGAGCGG
* * *
16337 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** * *
16400 CGATCTCCTCACGCAAGGCATTGACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * *
16463 CGATCTCCTCATGCAA
1 CAACCTCCTCACGCAA
16479 GGCATTGACC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:16479 original size:63 final size:63
Alignment explanation
Indices: 16360--16490 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
16350 TAAAGTAGAC
16360 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
* *
16423 ACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCATGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
16486 ACCTC
1 ACCTC
16491 ATCACGTAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:18014 original size:33 final size:33
Alignment explanation
Indices: 17972--18034 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
17962 ACAAGATAAT
**
17972 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
18005 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
18035 TGCGAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:18091 original size:19 final size:19
Alignment explanation
Indices: 17947--18091 Score: 103
Period size: 19 Copynumber: 8.1 Consensus size: 19
17937 TCTTTTGGTT
***
17947 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAATGC
* *
17966 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAATGC
**
17986 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
18003 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGC
18019 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
18038 GAAATGAAAATCGCAAT--
1 GAAATGAAAATCGCAATGC
* *
18055 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGC
*
18071 GAAATGAAAATCGTAATGC
1 GAAATGAAAATCGCAATGC
18090 GA
1 GA
18092 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 56 0.55
20 16 0.16
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:18104 original size:52 final size:52
Alignment explanation
Indices: 17955--18091 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 52
17945 TTGAAATGAA
** * * **
17955 AATCGCAACAAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
18008 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
18060 AATCGCAACGCGAAATGAAAATCGTAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAATGCGA
18092 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
52 65 0.86
53 11 0.14
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:18109 original size:19 final size:19
Alignment explanation
Indices: 18087--18131 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
18077 AAAATCGTAA
*
18087 TGCGATTTTGGTTTCGCAT
1 TGCGATTTTGATTTCGCAT
* * *
18106 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCAT
18125 TGCGATT
1 TGCGATT
18132 CTCTCGTAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCAT
Found at i:18770 original size:20 final size:20
Alignment explanation
Indices: 18685--18814 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
18675 CGCTATGTAA
* * *
18685 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
18705 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
18725 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
18746 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
18766 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
18786 ATCGCATTGCAATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
18806 ATCGCATTG
1 ATCGCATTG
18815 TGATTTTCCC
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 79 0.82
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:23529 original size:6 final size:5
Alignment explanation
Indices: 23515--23554 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
23505 AAGTAATTAA
*
23515 TTATT TTATTT TTATT TTATT TTATT TTAGT TT-TT TTATT
1 TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT
23555 ATTTAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:23531 original size:11 final size:11
Alignment explanation
Indices: 23515--23558 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
23505 AAGTAATTAA
23515 TTATTTTATTT
1 TTATTTTATTT
23526 TTATTTTA-TT
1 TTATTTTATTT
23536 TTATTTTAGTTT
1 TTATTTTA-TTT
23548 TT-TTATTATTT
1 TTATT-TTATTT
23559 AATTGTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
11 13 0.43
12 7 0.23
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:23534 original size:16 final size:16
Alignment explanation
Indices: 23515--23559 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
23505 AAGTAATTAA
*
23515 TTATTTTATTTTTATT
1 TTATTTTATTTTTAGT
23531 TTATTTTA-TTTTAGT
1 TTATTTTATTTTTAGT
23546 TT-TTTTATTATTTA
1 TTATTTTATT-TTTA
23560 ATTGTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 5 0.19
15 9 0.35
16 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTTATTTTTAGT
Found at i:27070 original size:16 final size:15
Alignment explanation
Indices: 27049--27083 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
27039 ATAGAAAATA
*
27049 TAATTTTTTATTATTT
1 TAATTTATTATT-TTT
27065 TAATTTATTATTTTT
1 TAATTTATTATTTTT
27080 TAAT
1 TAAT
27084 AAAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTTATTATTTTT
Found at i:27204 original size:49 final size:49
Alignment explanation
Indices: 27131--27252 Score: 156
Period size: 49 Copynumber: 2.4 Consensus size: 49
27121 AGATGCACGT
* * *
27131 ATGTAAGTATATATTTATTGTTAGGTTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGT-TTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
27180 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGT-TTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
*
27230 ATATAAGTATGTTTTAATTGTTA
1 ATGTAAGTATGTTTT-ATTGTTA
27253 CACTTTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 46 0.73
50 17 0.27
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (49 bp):
ATGTAAGTATGTTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Done.