Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002320.1 Hibiscus syriacus cultivar Beakdansim tig00004723_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: 69022
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:866 original size:21 final size:21
Alignment explanation
Indices: 824--868 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
814 AATATGTAAA
**
824 TCGCATTGCGATTTTATGAAT
1 TCGCATTGCGATTTTACAAAT
* *
845 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
866 TCG
1 TCG
869 TAACGCGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:899 original size:20 final size:20
Alignment explanation
Indices: 874--934 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
864 ATTCGTAACG
874 CGAATCTGTAAATCGCAACA
1 CGAATCTGTAAATCGCAACA
*
894 CGAATCTGTAAATCGCAACG
1 CGAATCTGTAAATCGCAACA
914 CGAATCTGTAAATCGCAACA
1 CGAATCTGTAAATCGCAACA
934 C
1 C
935 AGAAGCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (20 bp):
CGAATCTGTAAATCGCAACA
Found at i:954 original size:40 final size:39
Alignment explanation
Indices: 860--956 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
850 TTGCGATTTT
* *
860 CCAAATTCGTAACGCGAATCTGTAAATCGCAACACGAAT
1 CCAAATTCGAAACGCGAATCTGTAAATCGCAACACGAAG
* *
899 CTGTAAA-TCGCAACGCGAATCTGTAAATCGCAACACAGAAG
1 C--CAAATTCGAAACGCGAATCTGTAAATCGCAACAC-GAAG
940 CCAAATTCGAAACGCGA
1 CCAAATTCGAAACGCGA
957 TTTTTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
39 4 0.08
40 38 0.78
41 7 0.14
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (39 bp):
CCAAATTCGAAACGCGAATCTGTAAATCGCAACACGAAG
Found at i:1062 original size:20 final size:20
Alignment explanation
Indices: 983--1066 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
973 GCGATTTACA
**
983 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC-GAATTTTG
*
1004 AATTCGCAACTCG-ATTTCTG
1 AATTCGCAACACGAATTT-TG
* * *
1024 AATTCACAACTCGATTTTTG
1 AATTCGCAACACGAATTTTG
1044 AATTCGCAACACGAATTTT-
1 AATTCGCAACACGAATTTTG
1063 AATT
1 AATT
1067 TTGCAACAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.15
20 31 0.58
21 14 0.26
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
AATTCGCAACACGAATTTTG
Found at i:1248 original size:14 final size:15
Alignment explanation
Indices: 1229--1266 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1219 TTCCCATCTC
1229 TAATTTTTTT-TATA
1 TAATTTTTTTCTATA
1243 TAATTTTATTTCTATA
1 TAATTTT-TTTCTATA
1259 TAATTTTT
1 TAATTTTT
1267 CAATGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTTTCTATA
Found at i:2032 original size:24 final size:24
Alignment explanation
Indices: 2005--2058 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1995 GTATTCGAAA
2005 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2029 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2053 TTTGAT
1 TTTGAT
2059 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2250 original size:12 final size:12
Alignment explanation
Indices: 2233--2260 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2223 ATATAACCCT
2233 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2245 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2257 GAAG
1 GAAG
2261 TCCCCGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4342 original size:12 final size:12
Alignment explanation
Indices: 4327--4356 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4317 AGAAAAAGGA
4327 AATCAAAATCGC
1 AATCAAAATCGC
*
4339 AATCAAAATCTC
1 AATCAAAATCGC
4351 AATCAA
1 AATCAA
4357 CCGGCTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.20
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:5135 original size:25 final size:25
Alignment explanation
Indices: 5099--5146 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5089 ATCAATTAAT
*
5099 CATTGTTGTGGGCACATTATTTGAA
1 CATTGTTATGGGCACATTATTTGAA
*
5124 CATTGTTATGGGTACATTATTTG
1 CATTGTTATGGGCACATTATTTG
5147 GAAAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (25 bp):
CATTGTTATGGGCACATTATTTGAA
Found at i:5553 original size:18 final size:18
Alignment explanation
Indices: 5532--5568 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5522 ATAATTGGAG
5532 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5550 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5568 T
1 T
5569 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5576 original size:24 final size:23
Alignment explanation
Indices: 5513--5572 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
5503 TTTCAAATTC
*
5513 ATTTCACATATAATTGGAGTTTGA
1 ATTTCA-ATATAATTTGAGTTTGA
* *
5537 ATTTAAATTTCAATTTGAGTTTGA
1 ATTTCAATAT-AATTTGAGTTTGA
5561 ATTTCAATATAA
1 ATTTCAATATAA
5573 ATTTCGACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (23 bp):
ATTTCAATATAATTTGAGTTTGA
Found at i:6866 original size:29 final size:29
Alignment explanation
Indices: 6785--6858 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
6775 AATTCGCAAC
*
6785 GCGAAAGTCAAATTCGCGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCGTTGCGATTCTT
*
6814 GCGAAAGTTAAATTCGCGTTGCGATTCTT
1 GCGAAAGTCAAATTCGCGTTGCGATTCTT
6843 GCGAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
6859 AAACGCGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (29 bp):
GCGAAAGTCAAATTCGCGTTGCGATTCTT
Found at i:6899 original size:20 final size:20
Alignment explanation
Indices: 6876--6980 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
6866 AAATCGCAAC
**
6876 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCGCATT
*
6896 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
6916 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCATT
* * * **
6936 GAGAATTTTACTATCGCAAC
1 GCGAATTTGACTTTCGCATT
*
6956 GCGAATTTGACTTTCGCTTT
1 GCGAATTTGACTTTCGCATT
6976 GCGAA
1 GCGAA
6981 AGTGTACCTT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:7139 original size:64 final size:66
Alignment explanation
Indices: 7035--7189 Score: 215
Period size: 64 Copynumber: 2.4 Consensus size: 66
7025 TGAAATTTAA
7035 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
1 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
7100 T
66 T
* * *** * *
7101 -A-AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAAT
1 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
7164 T
66 T
*
7165 AAACAACAAATCAACTTTTATAAAT
1 -AACAACAAATCAACTTTTACAAAT
7190 ACATCAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 56 0.72
65 1 0.01
66 1 0.01
67 20 0.26
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (66 bp):
AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
T
Found at i:8590 original size:21 final size:21
Alignment explanation
Indices: 8526--8596 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
8516 GTGAATCGGG
*
8526 CTCTCGAACGGTGGGAGTGA-C
1 CTCTTGAACGGTGGGAG-GAGC
* ** *
8547 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGAGC
8568 CTCTTGAACGGTGGGAGGAGC
1 CTCTTGAACGGTGGGAGGAGC
*
8589 CTTTTGAA
1 CTCTTGAA
8597 GGATGATAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGAGC
Found at i:8596 original size:42 final size:42
Alignment explanation
Indices: 8526--8648 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
8516 GTGAATCGGG
* *
8526 CTCTCGAACGGTGGGAGTGA-CCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAG-GAGCCTTTTGAACGATGACAGGGGC
* *
8568 CTCTTGAACGGTGGGAGGAGCCTTTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGAGCCTTTTGAACGATGACAGGGGC
* * *
8610 CTCTTGAATGATAGGA-GAGGCCTTTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGA-GCCTTTTGAACGATGACAGG
8649 TGCTTCGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.06
42 66 0.94
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGAGCCTTTTGAACGATGACAGGGGC
Found at i:8611 original size:21 final size:21
Alignment explanation
Indices: 8546--8644 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
8536 GTGGGAGTGA
*
8546 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
8567 CCTCTTGAACGGTGGGAGGAG
1 CCTCTTGAACGATGAGAGGGG
* * *
8588 CCTTTTGAAGGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
8609 CCTCTTGAATGAT-AGGAGAGG
1 CCTCTTGAACGATGA-GAGGGG
*
8630 CCTTTTGAACGATGA
1 CCTCTTGAACGATGA
8645 CAGGTGCTTC
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:8922 original size:21 final size:21
Alignment explanation
Indices: 8898--8948 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
8888 TGCAACAATC
*
8898 TCACGTAAAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
8919 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
8940 -CTACGTAAA
1 TC-ACGTAAA
8949 ACACTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:9048 original size:21 final size:21
Alignment explanation
Indices: 9024--9073 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
9014 ACCATTGTCT
* *
9024 TCACGTAAAGTATCGACCTCC
1 TCACGTAAAGCATCGACCTCA
* *
9045 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCATCGACCTCA
9066 TCACGTAA
1 TCACGTAA
9074 CTCCTCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCATCGACCTCA
Found at i:10832 original size:20 final size:20
Alignment explanation
Indices: 10795--10832 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10785 CTAAAATCAC
* *
10795 GTTGCGAATTTCATTTTCTT
1 GTTGCGAATTTAAGTTTCTT
10815 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
10833 AAATAGTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.50
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCTT
Found at i:11233 original size:22 final size:22
Alignment explanation
Indices: 11153--11233 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
11143 CTCTGAGACA
*
11153 TGGAGATA--GACGGATTTCGC
1 TGGAGATAGGGACGGATTTCGT
* *
11173 TGGAGATAGGGATGAATTTCGT
1 TGGAGATAGGGACGGATTTCGT
*
11195 TGGAGATAGGGATGGATTTCGT
1 TGGAGATAGGGACGGATTTCGT
*
11217 TGGAGATGGGGACGGAT
1 TGGAGATAGGGACGGAT
11234 GTCGCCGTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 8 0.15
22 45 0.85
ACGTcount: A:0.25, C:0.07, G:0.41, T:0.27
Consensus pattern (22 bp):
TGGAGATAGGGACGGATTTCGT
Found at i:11356 original size:25 final size:26
Alignment explanation
Indices: 11327--11375 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
11317 ATTTGTGTTG
* * *
11327 CGAAATTAATATT-GTGTTTCGAATT
1 CGAAAATAAAATTCGTGTTGCGAATT
11352 CGAAAATAAAATTCGTGTTGCGAA
1 CGAAAATAAAATTCGTGTTGCGAA
11376 AATAAACGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (26 bp):
CGAAAATAAAATTCGTGTTGCGAATT
Found at i:11366 original size:19 final size:20
Alignment explanation
Indices: 11344--11381 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11334 AATATTGTGT
11344 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
11363 TTCGTGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
11382 CGTGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:11430 original size:20 final size:20
Alignment explanation
Indices: 11407--11456 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
11397 TGACTTCTGT
11407 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
11427 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
11447 GTTGCGAATT
1 GTTGCGAATT
11457 TGGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:14601 original size:10 final size:10
Alignment explanation
Indices: 14588--14620 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
14578 CGTTCGATAA
14588 TATGTTTGTT
1 TATGTTTGTT
14598 TATGTTTGTT
1 TATGTTTGTT
*
14608 TATGTTCGTT
1 TATGTTTGTT
14618 TAT
1 TAT
14621 ATGCGTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (10 bp):
TATGTTTGTT
Found at i:14833 original size:23 final size:23
Alignment explanation
Indices: 14807--14866 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
14797 TCTATTTTCA
14807 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
* *
14830 TTTACGTTTATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
*
14853 TTTATGTTCGTTTA
1 TTTATGTTCATTTA
14867 CACCCGTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.13, C:0.08, G:0.17, T:0.62
Consensus pattern (23 bp):
TTTATGTTCATTTATTGTGTTCG
Found at i:15991 original size:16 final size:16
Alignment explanation
Indices: 15970--16094 Score: 76
Period size: 16 Copynumber: 7.9 Consensus size: 16
15960 AAACTTTAGT
*
15970 TGAACCGAACATAACC
1 TGAACCGAAAATAACC
15986 TGAACC-AAAATGAACC
1 TGAACCGAAAAT-AACC
* *
16002 TAAACCGAAAATAACG
1 TGAACCGAAAATAACC
* * *
16018 TTAACTGAAAACAACC
1 TGAACCGAAAATAACC
** * **
16034 CAAATCGAAAGCAACC
1 TGAACCGAAAATAACC
*
16050 AGAACC-AAAA-AACC
1 TGAACCGAAAATAACC
** *
16064 CAAACCGAAAGTAACC
1 TGAACCGAAAATAACC
*
16080 CGAACCGAAAATAAC
1 TGAACCGAAAATAAC
16095 TCAAATTTAG
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
14 8 0.10
15 10 0.12
16 61 0.73
17 5 0.06
ACGTcount: A:0.52, C:0.27, G:0.11, T:0.10
Consensus pattern (16 bp):
TGAACCGAAAATAACC
Found at i:16064 original size:30 final size:32
Alignment explanation
Indices: 16024--16100 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 32
16014 AACGTTAACT
16024 GAAAACAACCCAAATCGAAAGCAACCAGAACC
1 GAAAACAACCCAAATCGAAAGCAACCAGAACC
* * *
16056 -AAAA-AACCCAAACCGAAAGTAACCCGAACC
1 GAAAACAACCCAAATCGAAAGCAACCAGAACC
* *
16086 GAAAATAACTCAAAT
1 GAAAACAACCCAAAT
16101 TTAGTTTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 23 0.61
31 8 0.21
32 7 0.18
ACGTcount: A:0.55, C:0.29, G:0.10, T:0.06
Consensus pattern (32 bp):
GAAAACAACCCAAATCGAAAGCAACCAGAACC
Found at i:16090 original size:62 final size:63
Alignment explanation
Indices: 15982--16100 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 63
15972 AACCGAACAT
* * *** *
15982 AACCTGAACCAAAATGAACCTAAACCGAAAATAACGTTAACTGAAAACAACCCAAATCGAAAGC
1 AACCAGAACCAAAA-GAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAATCGAAAGC
* * *
16046 AACCAGAACCAAAA-AACCCAAACCGAAAGTAACCCGAACCGAAAATAACTCAAAT
1 AACCAGAACCAAAAGAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAAT
16101 TTAGTTTATC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
62 33 0.72
64 13 0.28
ACGTcount: A:0.53, C:0.27, G:0.10, T:0.10
Consensus pattern (63 bp):
AACCAGAACCAAAAGAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAATCGAAAGC
Found at i:26522 original size:18 final size:18
Alignment explanation
Indices: 26499--26542 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
26489 AAAAATATGG
*
26499 TGGATATTATATGTTTGT
1 TGGATATTATATGTTGGT
* *
26517 TGGATAATATGTGTTGGT
1 TGGATATTATATGTTGGT
*
26535 TAGATATT
1 TGGATATT
26543 GATGTATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (18 bp):
TGGATATTATATGTTGGT
Found at i:28998 original size:21 final size:22
Alignment explanation
Indices: 28959--28999 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28949 GATACTCAAG
28959 AAAGTATAGATACCTTAAACCA
1 AAAGTATAGATACCTTAAACCA
*
28981 AAAGTATCGATA-CTTAAAC
1 AAAGTATAGATACCTTAAAC
29000 TAGAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (22 bp):
AAAGTATAGATACCTTAAACCA
Found at i:29084 original size:19 final size:19
Alignment explanation
Indices: 29046--29118 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
29036 AATAAGTCAG
* *
29046 TAGTATCAATACCCAGAGGT
1 TAGTATCGATA-CTAGAGGT
29066 TAGTATCGATACTAGAGGT
1 TAGTATCGATACTAGAGGT
* * *
29085 CAGTACCGATACTGAGAGATT
1 TAGTATCGATACT-AGAG-GT
*
29106 TAGTATCGGTACT
1 TAGTATCGATACT
29119 CACAAATAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 18 0.42
20 14 0.33
21 11 0.26
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (19 bp):
TAGTATCGATACTAGAGGT
Found at i:35372 original size:33 final size:34
Alignment explanation
Indices: 35319--35384 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
35309 TGCAGAAAAT
*
35319 ACTGTAGCAGTTACTGTAGCGTATCGATGCATAC
1 ACTGTAGCAGTTACTGTAGCGTATCGAAGCATAC
35353 ACTGTAGCAG-TACTGTAGCGTATCGAAGCATA
1 ACTGTAGCAGTTACTGTAGCGTATCGAAGCATA
35385 ATATTAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (34 bp):
ACTGTAGCAGTTACTGTAGCGTATCGAAGCATAC
Found at i:50018 original size:82 final size:80
Alignment explanation
Indices: 49911--50069 Score: 248
Period size: 82 Copynumber: 2.0 Consensus size: 80
49901 GAATTTCAAG
* * *
49911 AGAGTTTTACTCTAACTAAAACTCTTTTAATATCTAAATTTAAATGGATAATGATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAAT-ATATCTTTT-AA
49976 TTTTAAATATTAAACCTA
64 -TTTAAATATTAAACCTA
*
49994 AGAG-TTTACTCAAACCAAAACTCTTTTAATATTTAAATTTAAATAGATAATATATCTTTTAATT
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATATATCTTTTAATT
50058 TAAATATTAAAC
66 TAAATATTAAAC
50070 AAATATTTCC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
79 14 0.19
80 2 0.03
81 9 0.12
82 43 0.60
83 4 0.06
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (80 bp):
AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATATATCTTTTAATT
TAAATATTAAACCTA
Found at i:51875 original size:21 final size:21
Alignment explanation
Indices: 51849--51905 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
51839 ACAGTGATAT
*
51849 AGTGTATCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
51870 AGTGTACCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
51891 AGTGTACCGATGCAT
1 AGTGTACCGATGCAT
51906 AAAAACATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
AGTGTACCGATGCATTGCTAC
Found at i:51951 original size:21 final size:21
Alignment explanation
Indices: 51926--51990 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
51916 AATATAAATT
* *
51926 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTTCTACA
51947 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
51968 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
51989 GT
1 GT
51991 AACTTCAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (21 bp):
GTGTACCGATGCACTTCTACA
Found at i:60008 original size:21 final size:21
Alignment explanation
Indices: 59984--60064 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
59974 TTGGTGCAGA
*
59984 GGGAATCGATACCCCCTGAAG
1 GGGAACCGATACCCCCTGAAG
*
60005 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC--TGAAG
* * *
60028 GGGAACCAATTCCCCCTGTAG
1 GGGAACCGATACCCCCTGAAG
* *
60049 GAGAATCGATACCCCC
1 GGGAACCGATACCCCC
60065 CTGGGGTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 30 0.60
23 20 0.40
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:60030 original size:23 final size:22
Alignment explanation
Indices: 59984--60044 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
59974 TTGGTGCAGA
* *
59984 GGGAATCGATACCCCC-TGAAG
1 GGGAACCGATTCCCCCTTGAAG
60005 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
60028 GGGAACCAATTCCCCCT
1 GGGAACCGATTCCCCCT
60045 GTAGGAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 20 0.57
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:62868 original size:11 final size:11
Alignment explanation
Indices: 62852--62877 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62842 ACAAGCAACT
62852 AGAATCAAGAG
1 AGAATCAAGAG
62863 AGAATCAAGAG
1 AGAATCAAGAG
62874 AGAA
1 AGAA
62878 GCATCAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:65320 original size:56 final size:55
Alignment explanation
Indices: 65234--65383 Score: 153
Period size: 56 Copynumber: 2.7 Consensus size: 55
65224 GATTCGAGAC
65234 TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAGA-AGAATCATACTTGAT
1 TTTCAAGAAATAAATTCAACAATTTATTTC-TTTTACAA-ATAGAATCATACTTGAT
* ** **
65290 TTTCAAGAGATAAATTC-ATGATTTAATTTCTTTTACAAATAGAATCATACAAGAT
1 TTTCAAGAAATAAATTCAACAATTT-ATTTCTTTTACAAATAGAATCATACTTGAT
* * * *
65345 TCT-ATGAATATAAATTTAACAATTTATTTTCTTCTACAA
1 TTTCAAGAA-ATAAATTCAACAATTTA-TTTCTTTTACAA
65384 GATGAATTCG
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
54 4 0.05
55 36 0.47
56 37 0.48
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (55 bp):
TTTCAAGAAATAAATTCAACAATTTATTTCTTTTACAAATAGAATCATACTTGAT
Found at i:65339 original size:55 final size:56
Alignment explanation
Indices: 65234--65390 Score: 153
Period size: 55 Copynumber: 2.8 Consensus size: 56
65224 GATTCGAGAC
65234 TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAGAAGAATCATACTTGAT
1 TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAGAAGAATCATACTTGAT
* ** **
65290 TTTCAAGAGATAAATTC-ATGATTTAATTTC-TTTTACAA-ATAGAATCATACAAGAT
1 TTTCAAGAAATAAATTCAACAATTT-ATTTCTTTTTACAAGA-AGAATCATACTTGAT
* * * * *
65345 TCT-ATGAATATAAATTTAACAATTTATTT-TCTTCTACAAGATGAAT
1 TTTCAAGAA-ATAAATTCAACAATTTATTTCT-TTTTACAAGAAGAAT
65391 TCGATCAAGA
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
54 4 0.05
55 39 0.48
56 37 0.46
57 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (56 bp):
TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAGAAGAATCATACTTGAT
Found at i:67104 original size:74 final size:77
Alignment explanation
Indices: 66927--67162 Score: 322
Period size: 73 Copynumber: 3.1 Consensus size: 77
66917 AGAAAGTTTG
*
66927 CTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTAAAATA
1 CTCCAACCAAAACTCTTTTAATATCTAAATTTAAA-AAATAATAATATCTTTTAAATTT-AAATA
*
66992 TTAAATCTGAGAATTTTA
64 TTAAA-C--A-TATTTTA
67010 CTCCAACCAAAACTC-TTTAATATCTAAATTTAAAAAAT-ATAATATCTTTTAAATTTAAATA-T
1 CTCCAACCAAAACTCTTTTAATATCTAAATTTAAAAAATAATAATATCTTTTAAATTTAAATATT
67072 AAACATATTTTA
66 AAACATATTTTA
* *
67084 CT-CAACCAAAACTCTTTTAATAACT-AATTT-AAACATAATAATATCTTTTAAATTTAAATATT
1 CTCCAACCAAAACTCTTTTAATATCTAAATTTAAAAAATAATAATATCTTTTAAATTTAAATATT
*
67146 AAACATATATTTC
66 AAACATAT-TTTA
67159 CTCC
1 CTCC
67163 TTGATTATTC
Statistics
Matches: 143, Mismatches: 5, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
72 5 0.03
73 40 0.28
74 26 0.18
75 6 0.04
76 1 0.01
77 1 0.01
78 4 0.03
79 5 0.03
80 18 0.13
81 4 0.03
82 19 0.13
83 14 0.10
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (77 bp):
CTCCAACCAAAACTCTTTTAATATCTAAATTTAAAAAATAATAATATCTTTTAAATTTAAATATT
AAACATATTTTA
Done.