Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005240.1 Hibiscus syriacus cultivar Beakdansim tig00011862_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: 54021
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5257 original size:61 final size:60
Alignment explanation
Indices: 5131--5266 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 60
5121 TGCTAGAGTC
* *** * *
5131 TTTACGACCACTTTCCGCTTGAGATGCTTTTCAATACCAGAGTTTTCTGCGTTCGAAAAA
1 TTTATGACCACTTTCCGCTTGAGATGCTTTTCAATACCAGAACCTTCCGCATTCGAAAAA
** *
5191 TTTATGACCACTTTCCGCTTGAGATGGCTTTTCAATGTC-GAAACCTTCCGCATTCGGAAAA
1 TTTATGACCACTTTCCGCTTGAGAT-GCTTTTCAATACCAG-AACCTTCCGCATTCGAAAAA
*
5252 TTTATGGCCACTTTC
1 TTTATGACCACTTTC
5267 ATGTCACACC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 25 0.39
61 39 0.61
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (60 bp):
TTTATGACCACTTTCCGCTTGAGATGCTTTTCAATACCAGAACCTTCCGCATTCGAAAAA
Found at i:6301 original size:19 final size:20
Alignment explanation
Indices: 6261--6325 Score: 100
Period size: 19 Copynumber: 3.4 Consensus size: 20
6251 ACCCGACCCA
*
6261 TTGACTTTGA-CA-TGACCG
1 TTGACTTTAACCATTGACCG
6279 TTGACTTTAACCATTGA-CG
1 TTGACTTTAACCATTGACCG
6298 TTGACTTTAACCATTGACCG
1 TTGACTTTAACCATTGACCG
6318 TTGACTTT
1 TTGACTTT
6326 GGCCCAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
18 9 0.21
19 21 0.49
20 13 0.30
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGACTTTAACCATTGACCG
Found at i:6924 original size:28 final size:28
Alignment explanation
Indices: 6871--6926 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6861 CTTGATTACA
* * *
6871 TATGATTTATTAGATTTAAAGTCTGATT
1 TATGATTTACTAAATTTAAAGCCTGATT
6899 TATGATTTACTAAAGTTT-AAGCCTGATT
1 TATGATTTACTAAA-TTTAAAGCCTGATT
6927 GTTTGATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (28 bp):
TATGATTTACTAAATTTAAAGCCTGATT
Found at i:7110 original size:35 final size:35
Alignment explanation
Indices: 7062--7129 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
7052 AAGTCTCTGC
** *
7062 AGGTTCAGCTCGATAAAATTGGTAATTCCTTATAT
1 AGGTTCAAATCGATAAAACTGGTAATTCCTTATAT
** *
7097 AGGTTCAAATCGATCGAGCTGGTAATTCCTTAT
1 AGGTTCAAATCGATAAAACTGGTAATTCCTTAT
7130 GGACCTAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (35 bp):
AGGTTCAAATCGATAAAACTGGTAATTCCTTATAT
Found at i:8072 original size:61 final size:62
Alignment explanation
Indices: 7960--8156 Score: 167
Period size: 61 Copynumber: 3.2 Consensus size: 62
7950 GGGGGTTACA
* *
7960 CTTCCGTTTGTGATGGATTTTCAATGTCGAAGCCTTTCGCGTTCGGGAAATTT-GTGGCCAC
1 CTTCCGTTTGTGATGGATTTTCAATGCCGAAGCCTTTCGCGTTCGGAAAATTTAGTGGCCAC
* ** *
8021 CTTCCGTTTGTTG-TGGCTTTTCAATGCC-AGAGCC-TTCTGCGTTTTGAAAATTTATTGGCCAC
1 CTTCCGTTTG-TGATGGATTTTCAATGCCGA-AGCCTTTC-GCGTTCGGAAAATTTAGTGGCCAC
** * * * *
8083 CTTTTGCTTGTGAT-GACTTTCAATGCCAAAGTCTTAT-GCGTTC-GAAATATTTA-TGGCCAC
1 CTTCCGTTTGTGATGGATTTTCAATGCCGAAGCCTT-TCGCGTTCGGAAA-ATTTAGTGGCCAC
* *
8143 TTTCCGCTTGTGAT
1 CTTCCGTTTGTGAT
8157 TAGGCCTGTA
Statistics
Matches: 111, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
60 26 0.23
61 65 0.59
62 19 0.17
63 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (62 bp):
CTTCCGTTTGTGATGGATTTTCAATGCCGAAGCCTTTCGCGTTCGGAAAATTTAGTGGCCAC
Found at i:8343 original size:10 final size:10
Alignment explanation
Indices: 8330--8363 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
8320 GTTCGTGAAC
*
8330 GTTCGGTTAT
1 GTTCGTTTAT
8340 GTTCGTTTAT
1 GTTCGTTTAT
*
8350 GTCCGTTTAT
1 GTTCGTTTAT
8360 GTTC
1 GTTC
8364 ATTCATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.53
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:9475 original size:16 final size:16
Alignment explanation
Indices: 9455--9514 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
9445 TCCAACGTTT
*
9455 ATGTTCGTTTATGTTT
1 ATGTTCGTTTATGTTC
* *
9471 GTGTTCATTTATGTTC
1 ATGTTCGTTTATGTTC
*
9487 GTGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
9503 ATGTTCGTTTAT
1 ATGTTCGTTTAT
9515 TTATTAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.58
Consensus pattern (16 bp):
ATGTTCGTTTATGTTC
Found at i:9496 original size:26 final size:26
Alignment explanation
Indices: 9452--9504 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
9442 GTCTCCAACG
* *
9452 TTTATGTTCGTTTATGTTTGTGTTCA
1 TTTATGTTCGTTTACGTTTATGTTCA
9478 TTTATGTTCGTGTT-CGTTTATGTTCA
1 TTTATGTTCGT-TTACGTTTATGTTCA
9504 T
1 T
9505 GTTCGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.60
Consensus pattern (26 bp):
TTTATGTTCGTTTACGTTTATGTTCA
Found at i:14093 original size:20 final size:20
Alignment explanation
Indices: 14070--14158 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
14060 GCTTCCAGAT
*
14070 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
14090 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
14110 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
*
14130 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
14150 TCGCAACGC
1 TCGCAACGC
14159 TGAATTTCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 56 0.97
21 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:15026 original size:24 final size:24
Alignment explanation
Indices: 14975--15028 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
14965 GTATTCGAAA
*
14975 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
14999 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
15023 TTTGAT
1 TTTGAT
15029 GTTGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:15247 original size:14 final size:14
Alignment explanation
Indices: 15218--15254 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15208 AGAAAAATAA
15218 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
15233 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
15247 GAAGAAAA
1 GAAGAAAA
15255 TGCCACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:17633 original size:140 final size:140
Alignment explanation
Indices: 17381--17663 Score: 557
Period size: 140 Copynumber: 2.0 Consensus size: 140
17371 GCAAACGTTG
17381 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
17446 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
17511 CGAATTTGAC
131 CGAATTTGAC
*
17521 TATTATGTGTATTTTATGTGTAAACTTTTAGCATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
17586 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
17651 CGAATTTGAC
131 CGAATTTGAC
17661 TAT
1 TAT
17664 CGAAACGTGA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:17659 original size:20 final size:20
Alignment explanation
Indices: 17634--17764 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
17624 TTACACATTC
*
17634 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
17654 ATTTGACTATCGAAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
17674 ATTTGACTAACGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
17693 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
17708 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
17728 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
17748 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
17765 AGAAAATCGC
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.09
15 3 0.03
19 3 0.03
20 76 0.84
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:17755 original size:74 final size:74
Alignment explanation
Indices: 17634--17808 Score: 237
Period size: 74 Copynumber: 2.4 Consensus size: 74
17624 TTACACATTC
* * *
17634 ATTTGAATATCGCAACGCGAATTTGACTATCGAAACGTGAATTTGACTAACGCAACTCA-AAAAT
1 ATTTGACTATCGCAACGTGAATTTGACTATCGAAACGGGAATTTGACTAACGCAAC-CAGAAAAT
*
17698 CGCAACGCGA
65 CGCAAAGCGA
* * * *
17708 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGTGAATTTGACTATCGAAACGGGAATTTGACTAACGCAACCAGAAAATC
*
17773 GCAAAGCGT
66 GCAAAGCGA
*
17782 ATTAGACTATCGCAACGTGAA-TTGACT
1 ATTTGACTATCGCAACGTGAATTTGACT
17809 TTCGCGTTGC
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
73 6 0.07
74 83 0.93
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (74 bp):
ATTTGACTATCGCAACGTGAATTTGACTATCGAAACGGGAATTTGACTAACGCAACCAGAAAATC
GCAAAGCGA
Found at i:17838 original size:20 final size:20
Alignment explanation
Indices: 17803--17866 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
17793 GCAACGTGAA
* * *
17803 TTGACTTTCGCGTTGCAATT
1 TTGACTTTCACATTGCGATT
*
17823 TTGGCTTTCACATTGCGATT
1 TTGACTTTCACATTGCGATT
*
17843 TTGACTTTCGCATTGCGATT
1 TTGACTTTCACATTGCGATT
17863 TTGA
1 TTGA
17867 GTTTAGCGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (20 bp):
TTGACTTTCACATTGCGATT
Found at i:18019 original size:14 final size:14
Alignment explanation
Indices: 18000--18036 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
17990 CATCAATTAA
18000 ACAAATCAACTTTT
1 ACAAATCAACTTTT
18014 ACAAATCAACTTTT
1 ACAAATCAACTTTT
18028 ACAAATCAA
1 ACAAATCAA
18037 TTAAACAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:19477 original size:42 final size:42
Alignment explanation
Indices: 19418--19540 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
19408 ATGAATCGGT
* * *
19418 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAAAGATGACAGGGGC
** *
19460 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAAAGATGACAGGGGC
* *
19502 CTCTTGAACGATAGGAGAGG-CCTCTTGAAAGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAAAGATGACAGG
19541 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 63 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAAAGATGACAGGGGC
Found at i:19478 original size:21 final size:21
Alignment explanation
Indices: 19418--19530 Score: 93
Period size: 21 Copynumber: 5.4 Consensus size: 21
19408 ATGAATCGGT
* *
19418 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
19439 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
19460 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
19481 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
19502 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
19523 CTCTTGAA
1 CTCTTGAA
19531 AGATGACAGG
Statistics
Matches: 69, Mismatches: 21, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
20 3 0.04
21 64 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:20046 original size:19 final size:20
Alignment explanation
Indices: 20015--20056 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
20005 ATAGTTTCTA
20015 AAACTTAAAATCGCAACACG
1 AAACTTAAAATCGCAACACG
*
20035 AAACTT-AAATCGCAACGCG
1 AAACTTAAAATCGCAACACG
20054 AAA
1 AAA
20057 ATGACTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACG
Found at i:20068 original size:20 final size:20
Alignment explanation
Indices: 20043--20091 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
20033 CGAAACTTAA
20043 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
20063 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
20083 ATCGCAACG
1 ATCGCAACG
20092 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:20133 original size:33 final size:34
Alignment explanation
Indices: 20083--20158 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
20073 GAATTTGACT
*
20083 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
20116 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
20150 ATCGCAACG
1 ATCGCAACG
20159 CGAATTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:20148 original size:20 final size:20
Alignment explanation
Indices: 20125--20162 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20115 AATCGCAACG
*
20125 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
20145 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
20163 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:20180 original size:19 final size:19
Alignment explanation
Indices: 20158--20197 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20148 AAATCGCAAC
20158 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
20177 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
20196 GC
1 GC
20198 CATTTTCTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.30, T:0.42
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:20202 original size:19 final size:19
Alignment explanation
Indices: 20167--20203 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20157 CGCGAATTTA
*
20167 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCCATTTTG
20186 GTTTCGCGTTGCCATTTT
1 GTTTCGCGTTGCCATTTT
20204 CTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.19, G:0.27, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCCATTTTG
Found at i:20243 original size:33 final size:33
Alignment explanation
Indices: 20173--20247 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
20163 TTTAGTTTCG
* * * * *
20173 CGTTGCGATTTTGGTTTCGCGTTGCCATTTTCT
1 CGTTGCGATTTTGATGTCGCATTGCCATTATCC
* *
20206 CGTTGCGATTTTTATGTCGCATTGCGATTATCC
1 CGTTGCGATTTTGATGTCGCATTGCCATTATCC
20239 CGTTGCGAT
1 CGTTGCGAT
20248 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTGATGTCGCATTGCCATTATCC
Found at i:22201 original size:20 final size:20
Alignment explanation
Indices: 22178--22233 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
22168 TCTGAAACTT
22178 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
22198 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
22218 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
22234 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:22239 original size:20 final size:19
Alignment explanation
Indices: 22181--22297 Score: 82
Period size: 20 Copynumber: 6.2 Consensus size: 19
22171 GAAACTTAAA
* **
22181 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCG-AAATGACT
*
22201 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
22221 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
*
22241 ATCGCAA--CGAGAT-A--
1 ATCGCAACGCGAAATGACT
**
22255 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
22274 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
22294 ATCG
1 ATCG
22298 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.09
16 6 0.08
17 2 0.03
18 3 0.04
19 15 0.19
20 47 0.59
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:22913 original size:20 final size:20
Alignment explanation
Indices: 22888--22936 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
22878 ATTTTGTATT
*
22888 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
22908 ATCGCGTTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
22928 ATCGCGTTG
1 ATCGCGTTG
22937 TGAATCTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:22989 original size:19 final size:19
Alignment explanation
Indices: 22965--23001 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22955 TGCGATACTG
* *
22965 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGCGATTTA
22984 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
23002 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:24910 original size:29 final size:29
Alignment explanation
Indices: 24862--24929 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
24852 ATTCTACAAT
*
24862 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
* *
24891 GACCAAGGAGGTCTCTATGCACGCCCAAC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
24920 GACCAAGGAG
1 GACCAAGGAG
24930 AGGGACTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.31, C:0.34, G:0.26, T:0.09
Consensus pattern (29 bp):
GACCAAGGAGGTCGCCATGCACGCCCAAC
Found at i:25748 original size:21 final size:22
Alignment explanation
Indices: 25723--25774 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
25713 AATTAGTTTG
* *
25723 TTAGTATAAATTATTTGTTAT-
1 TTAGTATAAATTATATATTATA
* *
25744 TTAGTTTAAGTTATATATTATA
1 TTAGTATAAATTATATATTATA
25766 TTA-TATAAA
1 TTAGTATAAA
25775 AAATTAGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (22 bp):
TTAGTATAAATTATATATTATA
Found at i:26257 original size:17 final size:17
Alignment explanation
Indices: 26235--26296 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
26225 AGATAATTTC
26235 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
26252 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
26271 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
26290 TGTTTAA
1 TGTTTAA
26297 TTTATATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 3 0.08
19 7 0.19
20 3 0.08
21 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:26300 original size:22 final size:23
Alignment explanation
Indices: 26257--26300 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
26247 TATTGTGTTT
**
26257 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
26280 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
26301 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:26468 original size:22 final size:23
Alignment explanation
Indices: 26425--26468 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
26415 TATTGTGTTT
**
26425 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
26448 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
26469 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:26521 original size:168 final size:169
Alignment explanation
Indices: 26242--26587 Score: 676
Period size: 168 Copynumber: 2.1 Consensus size: 169
26232 TTCTGTTTAA
26242 AAAAATATTGTGTTTAAAAATATTTAGTGTTGTTTTAAAAAAATATTTTGTTTAATTTATATTGT
1 AAAAATATTGTGTTTAAAAATATTTAGTGTTGTTTTAAAAAAATATTTTGTTTAATTTATATTGT
26307 ATGTGTAAATTAGTAAGGAGTAAAAATTAATTGAATGAAATAATCCGGCCAACGCATTATCACGA
66 ATGTGTAAATTAGTAAGGAGTAAAAATTAATTGAATGAAATAATCCGGCCAACGCATTATCACGA
*
26372 TATTTTGCCTAACAAATTTGTTTGATATTTTAAAAATAT
131 TATTTTGCCTAACAAATTTGTTTGATATTTTAAAAAAAT
26411 -AAAATATTGTGTTTAAAAATATTTAGTGTTGTTTTAAAAAAATATTTTGTTTAATTTATATTGT
1 AAAAATATTGTGTTTAAAAATATTTAGTGTTGTTTTAAAAAAATATTTTGTTTAATTTATATTGT
26475 ATGTGTAAATTAGTAAGGAGTAAAAATTAATTGAATGAAATAATCCGGCCAACGCATTATCACGA
66 ATGTGTAAATTAGTAAGGAGTAAAAATTAATTGAATGAAATAATCCGGCCAACGCATTATCACGA
26540 TATTTTGCCTAACAAATTTGTTTGATATTTTAAAAAAAT
131 TATTTTGCCTAACAAATTTGTTTGATATTTTAAAAAAAT
26579 AAAAATATT
1 AAAAATATT
26588 ATCAAACTAA
Statistics
Matches: 175, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
168 167 0.95
169 8 0.05
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (169 bp):
AAAAATATTGTGTTTAAAAATATTTAGTGTTGTTTTAAAAAAATATTTTGTTTAATTTATATTGT
ATGTGTAAATTAGTAAGGAGTAAAAATTAATTGAATGAAATAATCCGGCCAACGCATTATCACGA
TATTTTGCCTAACAAATTTGTTTGATATTTTAAAAAAAT
Found at i:32466 original size:15 final size:16
Alignment explanation
Indices: 32441--32473 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
32431 TATCGCCGAC
32441 CGAATTTCACTATTCA
1 CGAATTTCACTATTCA
32457 CGAA-TTCACTATTCA
1 CGAATTTCACTATTCA
32472 CG
1 CG
32474 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.33
Consensus pattern (16 bp):
CGAATTTCACTATTCA
Found at i:34250 original size:27 final size:26
Alignment explanation
Indices: 34220--34278 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
34210 ATTTTATATA
* * *
34220 TTTTAATTTAAATACATTTTTAATTT
1 TTTTAATTTAAATAAATTTTCAAGTT
34246 CTTTTAA-TTAAATAAATTTTCAAGTT
1 -TTTTAATTTAAATAAATTTTCAAGTT
34272 TTTTAAT
1 TTTTAAT
34279 AATTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 16 0.57
27 6 0.21
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTAATTTAAATAAATTTTCAAGTT
Found at i:35444 original size:85 final size:83
Alignment explanation
Indices: 35294--35495 Score: 260
Period size: 85 Copynumber: 2.4 Consensus size: 83
35284 TCTCAGCCTA
* * * * *
35294 TTACAGCATAGCTCAAGGCGATAAGGGCTATCTGTTAACAAACCTTCGAGTTTGATTACACTCAG
1 TTACAGCATAACTCAAGGCGAAAAGGGTTATCTATTAAAAAACCTTCGAGTTTGATTACACTCAG
35359 CTCAAGGGCACATCAAAT
66 CTCAAGGGCACATCAAAT
* * *
35377 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTATTAATAAAAACCTTCGAGTTTGATTACATTC
1 TTACAGCATAACTCAAGGCGAAAAGGGTTATCTATT-A-AAAAACCTTCGAGTTTGATTACACTC
* * *
35442 AGCTTAATGGCATATCAAAT
64 AGCTCAAGGGCACATCAAAT
* *
35462 TTTCAGCATAACTCAAGGGCGAAAAGAGTTATCT
1 TTACAGCATAACTCAA-GGCGAAAAGGGTTATCT
35496 GTCAACAAGA
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
83 31 0.30
84 1 0.01
85 55 0.54
86 15 0.15
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (83 bp):
TTACAGCATAACTCAAGGCGAAAAGGGTTATCTATTAAAAAACCTTCGAGTTTGATTACACTCAG
CTCAAGGGCACATCAAAT
Found at i:35530 original size:86 final size:85
Alignment explanation
Indices: 35294--35532 Score: 212
Period size: 85 Copynumber: 2.8 Consensus size: 85
35284 TCTCAGCCTA
* * * * * * * * * *
35294 TTACAGCATAGCTCAAGGCGATAAGGGCTATCTGTTAAC--AAACCTTCGAGTTTGATTACACTC
1 TTACAGCATAACTCAAGGCGAAAAGAGTTATCTATCAACAAAAACCTTCGAGATCGATCACATTC
35357 AGCTCAAGGGCACATCAAAT
66 AGCTCAAGGGCACATCAAAT
* * * * * * * *
35377 TTACAGTATAACTCAAGGCGAGAAGGGTTATCTATTAATAAAAACCTTCGAGTTTGATTACATTC
1 TTACAGCATAACTCAAGGCGAAAAGAGTTATCTATCAACAAAAACCTTCGAGATCGATCACATTC
* * *
35442 AGCTTAATGGCATATCAAAT
66 AGCTCAAGGGCACATCAAAT
* * * * **
35462 TTTCAGCATAACTCAAGGGCGAAAAGAGTTATCTGTCAACAAGAACTTTCGAGATCGATCATGTT
1 TTACAGCATAACTCAA-GGCGAAAAGAGTTATCTATCAACAAAAACCTTCGAGATCGATCACATT
35527 CAGCTC
65 CAGCTC
35533 GAGAGCGTAC
Statistics
Matches: 128, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
83 33 0.26
85 54 0.42
86 41 0.32
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (85 bp):
TTACAGCATAACTCAAGGCGAAAAGAGTTATCTATCAACAAAAACCTTCGAGATCGATCACATTC
AGCTCAAGGGCACATCAAAT
Found at i:36224 original size:10 final size:12
Alignment explanation
Indices: 36190--36225 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
36180 TATATAACCC
36190 ATACTACTACAT
1 ATACTACTACAT
36202 ATACTACTACAT
1 ATACTACTACAT
36214 ATAC-A-TACAT
1 ATACTACTACAT
36224 AT
1 AT
36226 TAACTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.29
11 1 0.04
12 16 0.67
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (12 bp):
ATACTACTACAT
Found at i:37747 original size:26 final size:26
Alignment explanation
Indices: 37718--37772 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
37708 ATTGTTTATA
37718 TTTTTA-TAT-TTTTAATTTAAATAAT
1 TTTTTAGTATCTTTTAA-TTAAATAAT
* *
37743 TTTTTAGTTTCTTTTAATTAAATAAA
1 TTTTTAGTATCTTTTAATTAAATAAT
37769 TTTT
1 TTTT
37773 CAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.23
26 14 0.54
27 6 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTTAGTATCTTTTAATTAAATAAT
Found at i:37758 original size:27 final size:26
Alignment explanation
Indices: 37726--37785 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
37716 TATTTTTATA
* * *
37726 TTTTTAATTTAAATAATTTTTTAGTT
1 TTTTTAATTTAAATAAATTTTCAATT
37752 TCTTTTAA-TTAAATAAATTTTCAATT
1 T-TTTTAATTTAAATAAATTTTCAATT
37778 TTTTTAAT
1 TTTTTAAT
37786 AATTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.21
26 17 0.59
27 6 0.21
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTTAATTTAAATAAATTTTCAATT
Found at i:41008 original size:21 final size:21
Alignment explanation
Indices: 40969--41009 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40959 CAGTAAAAAT
* **
40969 TACCTAAAATATTTTTATTTA
1 TACCTAAAACATTAATATTTA
40990 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
41010 TTTAACAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTA
Found at i:42134 original size:2 final size:2
Alignment explanation
Indices: 42117--42186 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
42107 AAAACTAAAA
* *
42117 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42187 GAATATAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46897 original size:21 final size:21
Alignment explanation
Indices: 46871--46924 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
46861 TTATAAGGGT
* *
46871 AGTATCGATACTCAATGAATG
1 AGTATCGATACTCAAGGAAGG
* *
46892 AGTATCGATAC-CAGGGCAGG
1 AGTATCGATACTCAAGGAAGG
46912 AGTATCGATACTC
1 AGTATCGATACTC
46925 CCCATAGGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (21 bp):
AGTATCGATACTCAAGGAAGG
Found at i:50148 original size:266 final size:269
Alignment explanation
Indices: 49771--50278 Score: 681
Period size: 266 Copynumber: 1.9 Consensus size: 269
49761 ATCACCAAAT
*
49771 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATTG--AGATGAGTTCTTCTCATTATGAAC
* * *
49836 TCCCTGCTGGAAATATTGATGCAGGTTGAACAAGTTCTACTCATTATAAACTTATTCTCCCTCGT
64 TCCCTACTAGAAATATTGAGGCAGGTTGAACAAGTTCTACTCATTATAAACTTATTCTCCCTCGT
* *
49901 TGGATGAGTTCTTCTCATTATGAACTCT-TCACTGGAAATGCTGAGCCAAGGTTGAACAAG-TC-
129 TGGATGAGTTCTTCTCATTATGAACTCTCT-ACTGGAAATACTGAGCCAAGATTGAACAAGTTCT
* * *
49963 T-TCGTTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATCAACCCTCAATTAGAAA
193 TCTCATTATAAACTTCTTCTCCCTCGTTGAATGAGTTCTTCACATTATCAACCCTCAATTAGAAA
50027 TATGATGCAAGA
258 TATGATGCAAGA
* *
50039 TTGAACAAG-TCTTCTCATTATGAACTATCTTCTTCATTG-GATGAGTTTTTCTCATTATGAACT
1 TTGAACAAGTTCTTCTCATTATGAACT-TCTTCTCCATTGAGATGAGTTCTTCTCATTATGAACT
* * * * * *
50102 CTCC-ACTAGAAATGTTG-GGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTC
65 C-CCTACTAGAAATATTGAGG-C-AGGTTGAACAAGTTCTACTCATTATAAACTTATTCTCCCTC
* * * * *
50165 GTTGGATGGGTTCTTCTCATTATGAACTCTCTACTGGAAATATTGGGCCAATATTGAGCAAGTTC
127 GTTGGATGAGTTCTTCTCATTATGAACTCTCTACTGGAAATACTGAGCCAAGATTGAACAAGTTC
* *
50230 TTCTCATTATAAACTTCTTCTCCCTTGTTGGATGAGTTCTTCACATTAT
192 TTCTCATTATAAACTTCTTCTCCCTCGTTGAATGAGTTCTTCACATTAT
50279 GAACTCTTCA
Statistics
Matches: 208, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
264 1 0.00
265 35 0.17
266 91 0.44
267 20 0.10
268 20 0.10
269 41 0.20
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (269 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCATTGAGATGAGTTCTTCTCATTATGAACTC
CCTACTAGAAATATTGAGGCAGGTTGAACAAGTTCTACTCATTATAAACTTATTCTCCCTCGTTG
GATGAGTTCTTCTCATTATGAACTCTCTACTGGAAATACTGAGCCAAGATTGAACAAGTTCTTCT
CATTATAAACTTCTTCTCCCTCGTTGAATGAGTTCTTCACATTATCAACCCTCAATTAGAAATAT
GATGCAAGA
Found at i:50151 original size:178 final size:180
Alignment explanation
Indices: 49771--50285 Score: 627
Period size: 178 Copynumber: 2.9 Consensus size: 180
49761 ATCACCAAAT
* *
49771 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTG-TCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGA-ATGAGTTCTTCTCATTATGAA
* * * * *
49835 CTCC-CTGCTGGAAATATTGATGC-AGGTTGAACAAGTTCTACTCATTATAAACTTATTCTCCCT
65 C-CCTCTACTGGAAATATTGATGCAAGATTGAACAAGTTCTTCTCATTATAAAC-TA-TCTTCTT
* *
49898 CGTTGGATGAGTTCTTCTCATTATGAACTCTTCACTGGAAATGCTGAGCCAAGG
127 CGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGCTGAGCCAAGG
* *
49952 TTGAACAAG-TC-T-TCGTTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATCAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATGAAC
* * * * *
50014 CCTCAATTAGAAATA-TGATGCAAGATTGAACAAG-TCTTCTCATTATGAACTATCTTCTTCATT
66 CCTCTACTGGAAATATTGATGCAAGATTGAACAAGTTCTTCTCATTATAAACTATCTTCTTCGTT
* * *
50077 GGATGAGTTTTTCTCATTATGAACTCTCCACTAGAAATGTTGGGCCAAGG
131 GGATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGCTGAGCCAAGG
* * * *
50127 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGGGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATGAAC
* * * *
50192 TCTCTACTGGAAATATTG-GGCCAATATTGAGCAAGTTCTTCTCATTATAAACT-TCTTCTCCCT
66 CCTCTACTGGAAATATTGATG-CAAGATTGAACAAGTTCTTCTCATTATAAACTATCTTCT---T
* *
50255 TGTTGGATGAGTTCTTCACATTATGAACTCT
127 CGTTGGATGAGTTCTTCTCATTATGAACTCT
50286 TCATGTTAAT
Statistics
Matches: 285, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
175 62 0.22
176 4 0.01
177 23 0.08
178 118 0.41
179 23 0.08
180 18 0.06
181 9 0.03
182 28 0.10
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (180 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATGAAC
CCTCTACTGGAAATATTGATGCAAGATTGAACAAGTTCTTCTCATTATAAACTATCTTCTTCGTT
GGATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGCTGAGCCAAGG
Found at i:50187 original size:91 final size:91
Alignment explanation
Indices: 49771--50285 Score: 545
Period size: 91 Copynumber: 5.7 Consensus size: 91
49761 ATCACCAAAT
* **
49771 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTT-GTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCGTTGGATGAGTTCTTCTCATTATGAA
* *
49835 CTC-CCTGCTGGAAATATTGATG-C-AGG
65 CTCTCC-ACTGGAAATATTG-GGCCAAGG
* * * * *
49861 TTGAACAAGTTCTACTCATTATAAACTTATTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGAGTTCTTCTCATTATGAAC
* ** *
49926 TCTTCACTGGAAATGCTGAGCCAAGG
66 TCTCCACTGGAAATATTGGGCCAAGG
* * * * *
49952 TTGAACAAG-TC-T-TCGTTATGAACTTCTTCTCCCTCGTTGAATGAGTTCTTCTCATTATCAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGAGTTCTTCTCATTATGAAC
* * * * * *
50014 CCTCAATTAGAAATA-TGATG-CAAGA
66 TCTCCACTGGAAATATTG-GGCCAAGG
* *
50039 TTGAACAAG-TCTTCTCATTATGAACTATC--TT-CTTCATTGGATGAGTTTTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACT-TCTTTTCCTTCGTTGGATGAGTTCTTCTCATTATGAA
* *
50100 CTCTCCACTAGAAATGTTGGGCCAAGG
65 CTCTCCACTGGAAATATTGGGCCAAGG
*
50127 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGGGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGAGTTCTTCTCATTATGAAC
* **
50192 TCTCTACTGGAAATATTGGGCCAATA
66 TCTCCACTGGAAATATTGGGCCAAGG
* * * *
50218 TTGAGCAAGTTCTTCTCATTATAAACTTCTTCTCCCTT-GTTGGATGAGTTCTTCACATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCGTTGGATGAGTTCTTCTCATTATGAA
50282 CTCT
65 CTCT
50286 TCATGTTAAT
Statistics
Matches: 357, Mismatches: 53, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
87 55 0.15
88 74 0.21
89 32 0.09
90 72 0.20
91 119 0.33
92 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTCCACTGGAAATATTGGGCCAAGG
Found at i:52506 original size:28 final size:28
Alignment explanation
Indices: 52474--52534 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
52464 GATAAAATGA
*
52474 TCAGGCTGACTTGGGAAGGTAATGTGTT
1 TCAGGCTAACTTGGGAAGGTAATGTGTT
* * *
52502 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGCTAACTTGGGAAGGTAATGTGTT
52530 TCAGG
1 TCAGG
52535 TGGTTTCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.08, G:0.36, T:0.34
Consensus pattern (28 bp):
TCAGGCTAACTTGGGAAGGTAATGTGTT
Done.