Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006372.1 Hibiscus syriacus cultivar Beakdansim tig00015325_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: 97255
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1755 original size:20 final size:20
Alignment explanation
Indices: 1727--1765 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1717 AATATAACAG
1727 GTTTAAATTTAACAAAATCA
1 GTTTAAATTTAACAAAATCA
*
1747 GTTTCAATTTAACAAAATC
1 GTTTAAATTTAACAAAATC
1766 GATAAAGAGC
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:0.13, G:0.05, T:0.36
Consensus pattern (20 bp):
GTTTAAATTTAACAAAATCA
Found at i:1991 original size:194 final size:194
Alignment explanation
Indices: 1636--2058 Score: 586
Period size: 194 Copynumber: 2.2 Consensus size: 194
1626 GTGATAAAAG
* * * *
1636 TCGGTACTTTA-TAATTAAAAAGAATTACAATAATAATGGCTATAAGTAGCGATACCTTATACAT
1 TCGGTACTTTAGGAATTTAAAAGAATTACAATAATAATGGCTATAAGTAGCGATACCTTAGACAC
*
1700 ATGTATCGATACATGACAATATAACAGGTTTAAATTTAACAAAATCAGTTTCAATTTAACAAAAT
66 ATGTATCGATACATGACAATATAACAGGTTTAAATTTAACAAAATCAGTTTCAATTTAACAAAAC
1765 CGATAAAGAGCTACCAAATGGTTGAAATTTGTATCGATACTTGTATAAGTATA-TACCAAAGTA
131 CGATAAAGAGCTACCAAATGGTTGAAATTTGTATCGATACTTGTATAAGTATAGTACCAAAGTA
** *
1828 TCGGTACTTTAGGAATTTAAAAGAATTACAATAATAATGGCTATAAAGTATTGATAGCTTAGACA
1 TCGGTACTTTAGGAATTTAAAAGAATTACAATAATAATGGCTAT-AAGTAGCGATACCTTAGACA
* * * ** *
1893 CATGTATCGATACATGACAATATAACATGTTTTAGA-TTGACAAAATTGGTTTCAATTTGACAAA
65 CATGTATCGATACATGACAATATAACA-GGTTTAAATTTAACAAAATCAGTTTCAATTTAACAAA
* * * * *
1957 ACCGCTAAAGAGCTACCGAAA-GGTTGACATTTGTATCGATGCTTTTATAAGTATATGTACCAAT
129 ACCGATAAAGAGCTACC-AAATGGTTGAAATTTGTATCGATACTTGTATAAGTATA-GTACCAAA
2021 GTA
192 GTA
* *
2024 TCAGTACTTTAGGAATTT-AAAGAATTGCAATAATA
1 TCGGTACTTTAGGAATTTAAAAGAATTACAATAATA
2059 GTGCCTATTT
Statistics
Matches: 204, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
192 11 0.05
193 30 0.15
194 112 0.55
195 25 0.12
196 26 0.13
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (194 bp):
TCGGTACTTTAGGAATTTAAAAGAATTACAATAATAATGGCTATAAGTAGCGATACCTTAGACAC
ATGTATCGATACATGACAATATAACAGGTTTAAATTTAACAAAATCAGTTTCAATTTAACAAAAC
CGATAAAGAGCTACCAAATGGTTGAAATTTGTATCGATACTTGTATAAGTATAGTACCAAAGTA
Found at i:8477 original size:92 final size:94
Alignment explanation
Indices: 8356--8539 Score: 270
Period size: 92 Copynumber: 2.0 Consensus size: 94
8346 ATACCAATGA
* *
8356 TAGTATCGATACCATGGTAAGGGTATCGATACCTA-GTAACATCGAA-TCTAAATTTGGTATCGA
1 TAGTATCGATACCATGGTAAGGGTATCGATACC-AGGAAACATCAAACT-TAAATTTGGTATCGA
8419 TA-CTGGAA-GGGGTATCGTACCATAGTATTG
64 TATC-GGAAGGGGGTATCGTACCATAGTATTG
* *
8449 TAGTATCGATACTA-GGTAAGGGTATCGATACCAGGAAATATCAAACTTAAATTTGGTATCGATA
1 TAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACTTAAATTTGGTATCGATA
8513 TCGGAAGGGGGTATCGTACCATAGTAT
66 TCGGAAGGGGGTATCGTACCATAGTAT
8540 AGAATTATCG
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
91 1 0.01
92 47 0.57
93 35 0.42
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (94 bp):
TAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCAAACTTAAATTTGGTATCGATA
TCGGAAGGGGGTATCGTACCATAGTATTG
Found at i:8549 original size:93 final size:92
Alignment explanation
Indices: 8357--8572 Score: 269
Period size: 93 Copynumber: 2.3 Consensus size: 92
8347 TACCAATGAT
* *
8357 AGTATCGATACCATGGTAAGGGTATCGATACCTAGTAACATCGAATCTAAATTTGGTATCGATAC
1 AGTATCGATACCA-GGTAAGGGTATCGATACCTAGAAACATCAAATCTAAATTTGGTATCGATAC
* *
8422 TGGAAGGGGTATCGTACCATAGTATTGT
65 TGGAAGGGGTATCGTACCATAGTATAGA
* *
8450 AGTATCGATACTAGGTAAGGGTATCGATACC-AGGAAATATCAAA-CTTAAATTTGGTATCGATA
1 AGTATCGATACCAGGTAAGGGTATCGATACCTA-GAAACATCAAATC-TAAATTTGGTATCGATA
8513 -TCGGAAGGGGGTATCGTACCATAGTATAGA
64 CT-GGAA-GGGGTATCGTACCATAGTATAGA
* * *
8543 ATTATCGGTACCAGGT-AGCAGTATCGATAC
1 AGTATCGATACCAGGTAAG-GGTATCGATAC
8573 TATGGAGCTA
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
91 3 0.03
92 49 0.45
93 56 0.52
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (92 bp):
AGTATCGATACCAGGTAAGGGTATCGATACCTAGAAACATCAAATCTAAATTTGGTATCGATACT
GGAAGGGGTATCGTACCATAGTATAGA
Found at i:8955 original size:59 final size:59
Alignment explanation
Indices: 8887--9186 Score: 428
Period size: 59 Copynumber: 5.1 Consensus size: 59
8877 ATGGCACTAA
* *
8887 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTTCGTATAGGGTACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* *
8946 ATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* * * *
9005 GTGTGCTAAAATTTTAATAAATTAATACTAAGTGTATGAATTTTCGTATAGGGTACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* * *
9064 TTGTGCTAAAATGTTAAGAAATTCATATTAAGTTTATGAA-TTTCTGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTC-GTATAGGGCACTTC
* *
9123 GTGTGCTAAAATG-TAAGAAATCCATACTAAGTGTATGAA-TTTCTGTATTGGGCACTAT-
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTC-GTATAGGGCACT-TC
9181 GTGTGC
1 GTGTGC
9187 ATAACACGGA
Statistics
Matches: 217, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
58 49 0.23
59 168 0.77
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
Found at i:9652 original size:45 final size:45
Alignment explanation
Indices: 9588--9678 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
9578 GTATAACGAC
**
9588 GTATAATAATGTATAAAAGGCTTGAAAGGATGCCATAAAT-GAAAT
1 GTATAATAATGTATAAAAGGAATGAAAGGATGCCA-AAATGGAAAT
* *
9633 GTATAATAGTGTATAAAAGGAATGAAATGATGCCAAAATGGAAAT
1 GTATAATAATGTATAAAAGGAATGAAAGGATGCCAAAATGGAAAT
9678 G
1 G
9679 GCATAATGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.25
Consensus pattern (45 bp):
GTATAATAATGTATAAAAGGAATGAAAGGATGCCAAAATGGAAAT
Found at i:11123 original size:20 final size:22
Alignment explanation
Indices: 11071--11124 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
11061 AAGTATGAAA
*
11071 ATGTCCAAGTATTGATACTTCTT
1 ATGTCC-AGTATGGATACTTCTT
11094 ATGTCC-GTATGGATACTT-TT
1 ATGTCCAGTATGGATACTTCTT
11114 AT-TCCAGTATG
1 ATGTCCAGTATG
11125 CTTGTCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 9 0.31
21 11 0.38
23 6 0.21
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (22 bp):
ATGTCCAGTATGGATACTTCTT
Found at i:11342 original size:146 final size:146
Alignment explanation
Indices: 10959--11326 Score: 551
Period size: 146 Copynumber: 2.5 Consensus size: 146
10949 GCTGATATCA
*
10959 ATACTTTTATTCCATTATGCTTGTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAA
1 ATACTTTTATTCCAGTATGCTTGTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAA
* * *
11024 AGTATCGATATTTTTAATTTCGATCAA-AATATATGCAAAGTATGAAAATGTCCAAGTATTGATA
66 AGTATCGATAATTATAATTTCGA--AACAATATATGCAAAGTATGAAAATGTCCAAGTATCGATA
*
11088 CTTCTTATGTCCGTATGG
129 CTTCTTACGTCCGTATGG
*
11106 ATACTTTTATTCCAGTATGCTTGTCAAACAATTTGCATGCCAAATGTATCGATACACATTATTAA
1 ATACTTTTATTCCAGTATGCTTGTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAA
* *
11171 AGTATCGATAATTATAATTTCGAAACAATGTATGCAAAGTATGAAAATGTCCATGTATCGATACT
66 AGTATCGATAATTATAATTTCGAAACAATATATGCAAAGTATGAAAATGTCCAAGTATCGATACT
*
11236 TCTTACGTCGGTATGG
131 TCTTACGTCCGTATGG
* * * ** **
11252 ATACTTTTATTCCAGTATGATTCTCAAATAATTTGCACGTAAAACATATCGATACACA-TATATA
1 ATACTTTTATTCCAGTATGCTTGTCAAACAATTTGCACGCCAAATGTATCGATACACATTAT-TA
11316 AAGTATCGATA
65 AAGTATCGATA
11327 CTTGGAATTT
Statistics
Matches: 202, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
145 5 0.02
146 113 0.56
147 84 0.42
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (146 bp):
ATACTTTTATTCCAGTATGCTTGTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAA
AGTATCGATAATTATAATTTCGAAACAATATATGCAAAGTATGAAAATGTCCAAGTATCGATACT
TCTTACGTCCGTATGG
Found at i:11802 original size:200 final size:199
Alignment explanation
Indices: 11245--12055 Score: 1187
Period size: 200 Copynumber: 4.1 Consensus size: 199
11235 TTCTTACGTC
* * * *
11245 GGTATGGATACTTTTATTCCAGTATGATTCTCAAATAATTTGCACGTAAAACATATCGATACACA
1 GGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACACA
*
11310 TATATAAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
66 TATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
* * * **
11375 TGTAAACGGTAAAAGTCTACCGTTATAATGAAAATAGGTGTAAATACCAAGTATCAATACTCTTT
131 TGTAAACGGTAAAAGTCTACTGATATAATGATAATAGGCATAAATACCAAGTATCAATACT-TTT
11440 ATATA
195 ATATA
* * * *
11445 GGTATGGATACTTATATTACAGTATGTTTCTCAAACAATTTGCACGCAAAATATATC-A-ATACA
1 GGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACACA
* * * * *
11508 TGTATAAAGTATCGATACTTGAAATTTCGAAACCTATTACTTTAAAGTAATAAGTAAATTAATAG
66 TATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
* * * *
11573 TGTAAATGGTAAAAGTCTATTGCTATAATGATAATAGGCGTAAATACCAAGTATCAATACTCTTT
131 TGTAAACGGTAAAAGTCTACTGATATAATGATAATAGGCATAAATACCAAGTATCAATACT-TTT
11638 ATATA
195 ATATA
* * *
11643 GGTATAGATACTTTTATTCCGGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCGATACACA
1 GGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACACA
* *
11708 TATATAAAGTATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTAATATGTAAATTAACAA
66 TATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
* * *
11773 TGTAAACAGTAAAAGTCTACTGGTATAATGATAATAGGCATAAATACCAAGTATCGATACTTTTA
131 TGTAAACGGTAAAAGTCTACTGATATAATGATAATAGGCATAAATACCAAGTATCAATACTTTTA
11838 TATA
196 TATA
* * * *
11842 GGTATGGATA-TTTGTATTCCAGTATACTTCTCAAACAATTTGCATGCAAAATGTATCAATACAC
1 GGTATGGATACTTT-TATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACAC
* **
11906 GTATATAAAGTATCGATACTTGGAATTTCGAAACAAATTACTTTAAAGTAATAGGTAAATTAACA
65 ATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACA
* * *
11971 ATGTAAATGGTACAAAGTCTACTGATATATTGATAATAGGCATAAATACCAAGTATCGATACTTT
130 ATGTAAACGGTA-AAAGTCTACTGATATAATGATAATAGGCATAAATACCAAGTATCAATACTTT
12036 TATATA
194 TATATA
*
12042 GGTATCGATACTTT
1 GGTATGGATACTTT
12056 CGATCTAAAC
Statistics
Matches: 553, Mismatches: 53, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
198 181 0.33
199 135 0.24
200 234 0.42
201 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (199 bp):
GGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACACA
TATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAA
TGTAAACGGTAAAAGTCTACTGATATAATGATAATAGGCATAAATACCAAGTATCAATACTTTTA
TATA
Found at i:12617 original size:18 final size:18
Alignment explanation
Indices: 12573--12631 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
12563 AAACCAAAAC
*
12573 CTTCTTCTAAACCAAGGT
1 CTTCTTCTCAACCAAGGT
*
12591 CATCTTCTCAACCAAGGT
1 CTTCTTCTCAACCAAGGT
**
12609 CTTCTTCTCAAGTAAGGT
1 CTTCTTCTCAACCAAGGT
12627 CTTCT
1 CTTCT
12632 GATCAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (18 bp):
CTTCTTCTCAACCAAGGT
Found at i:15280 original size:178 final size:179
Alignment explanation
Indices: 14954--15281 Score: 498
Period size: 179 Copynumber: 1.8 Consensus size: 179
14944 AGATTGAATA
* *
14954 TAATAGGTAAATTAACAATGTAAACGGTAAAAGTCAACCGGTATAATGATAATAGACGTAAATAA
1 TAATAGGTAAAATAACAATGTAAACGGTAAAAGTCAACCGATATAATGATAATAGACGTAAATAA
* *
15019 CAAGTATCGATGCTCTTTAAATAGGTATGGATATTTTTATTCCAATATGATTCTCAAACAATTTG
66 CAAGTATCAATACTCTTTAAATAGGTATGGATATTTTTATTCCAATATGATTCTCAAACAATTTG
* *
15084 CATGCAAAATGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAG
131 CACGCAAAATATATCGATACTTGGAATTTTGAAACCTATTACTTTAAAG
* * * *
15133 TAATAGGTAAAATAATAATGTAAACGGTAAAAGTCTATCGATATAATGATAATAGGCGTAAATAA
1 TAATAGGTAAAATAACAATGTAAACGGTAAAAGTCAACCGATATAATGATAATAGACGTAAATAA
* * * * *
15198 TAAGTA-CTAATACT-TTTATATAGGTATGGATATTTTTATTTCATTATGCTTCTCAAACAATTT
66 CAAGTATC-AATACTCTTTAAATAGGTATGGATATTTTTATTCCAATATGATTCTCAAACAATTT
15261 GCACGCAAAATATATCGATAC
130 GCACGCAAAATATATCGATAC
15282 ATATATATAA
Statistics
Matches: 133, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
178 65 0.49
179 68 0.51
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (179 bp):
TAATAGGTAAAATAACAATGTAAACGGTAAAAGTCAACCGATATAATGATAATAGACGTAAATAA
CAAGTATCAATACTCTTTAAATAGGTATGGATATTTTTATTCCAATATGATTCTCAAACAATTTG
CACGCAAAATATATCGATACTTGGAATTTTGAAACCTATTACTTTAAAG
Found at i:15452 original size:199 final size:200
Alignment explanation
Indices: 15094--15566 Score: 650
Period size: 199 Copynumber: 2.4 Consensus size: 200
15084 CATGCAAAAT
* * *
15094 GTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAAATAATAATGTAAACG
1 GTATTGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACG
* *
15159 GTAAAAGTCTATCGATATAATGATAATAGGCGTAAATAATAAGTACTAATACTTTTATATAGGTA
66 GTAAAAGTTTATCGATATAATGATAATAGGCGTAAATAACAAGTACTAATACTTTTATATAGGTA
* * * *
15224 TGGATATTTTTATTTCATTATGCTTCTCAAACAATTTGCACGCAAAATATATCGATACATATATA
131 TGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTACACGCAAAATATATCGATACATATATA
15289 TAA-A
196 TAACA
* * *
15293 GTATTGATACTTGGAATTTCGAAACCTATTGCTTTAAAGTAATAGGTTAATTAACAATGTAAACG
1 GTATTGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACG
* * * * *
15358 GTAAAGGTTTA-CTGCTATATTGATAATAGGCGTAAATACCAAGTA-TCGATACTTTTATATAGG
66 GTAAAAGTTTATC-GATATAATGATAATAGGCGTAAATAACAAGTACT-AATACTTTTATATAGG
* *
15421 TATGGATACTTTTATTCCAGTATGTTTCTCAAACAATTTACACGCAAAATGTATCGATACATATA
129 TATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTACACGCAAAATATATCGATACATATA
15486 TATAACA
194 TATAACA
** * * *
15493 -TATTGATACTTATAATTTTGAAATCC-ATCACTTTAAAGTAATAGGTAAATTAACAACGTATAC
1 GTATTGATACTTGGAATTTTGAAA-CCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* *
15556 AGTAAATGTTT
65 GGTAAAAGTTT
15567 CTACCAGTAT
Statistics
Matches: 241, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
198 2 0.01
199 236 0.98
200 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (200 bp):
GTATTGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACG
GTAAAAGTTTATCGATATAATGATAATAGGCGTAAATAACAAGTACTAATACTTTTATATAGGTA
TGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTACACGCAAAATATATCGATACATATATA
TAACA
Found at i:15710 original size:131 final size:130
Alignment explanation
Indices: 15497--15947 Score: 579
Period size: 131 Copynumber: 3.5 Consensus size: 130
15487 ATAACATATT
* * * *
15497 GATACTTATAATTTTGAAATCC-ATCACTTTAAAGTAATAGGTAAATTAACAACGTATACAGTAA
1 GATACTTATAATTTCGAAA-CCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAA
* * *
15561 ATGTTTCTACC-AGTATAATGAAAATATGCATAAATGTCCAAGTATTGATACTCATATACAAAGT
65 ACGTTTCTACCGA-TATAATGAAAATAAGCGTAAATGTCCAAGTATTGATACTCATATA-AAAGT
*
15625 ATC
128 ATA
* *
15628 GATACATATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACA-AGGTAA
1 GATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACA-GTAA
* * * * *
15692 ACGTTTGTACCGATATAATAAAAATAAGCGTAAATATCCAGGTATCGATACTCATATATAAAGTA
65 ACGTTTCTACCGATATAATGAAAATAAGCGTAAATGTCCAAGTATTGATACTCATATA-AAAGTA
*
15757 TT
129 TA
*
15759 GATACTTATAATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAA
1 GATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAA
* * * * * *
15824 CGTTTCTATCGGTATAATGAAAATAGGCGTAAATGTACAAGTATTGATAATGTCATAT--AATTA
66 CGTTTCTACCGATATAATGAAAATAAGCGTAAATGTCCAAGTATTGAT-A-CTCATATAAAAGTA
15887 TA
129 TA
* *
15889 GATACTTTTAGTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACAC
1 GATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACAC
15948 GGTATTATGT
Statistics
Matches: 280, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
130 64 0.23
131 207 0.74
132 3 0.01
133 6 0.02
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (130 bp):
GATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAA
CGTTTCTACCGATATAATGAAAATAAGCGTAAATGTCCAAGTATTGATACTCATATAAAAGTATA
Found at i:16517 original size:225 final size:226
Alignment explanation
Indices: 15953--16559 Score: 783
Period size: 225 Copynumber: 2.7 Consensus size: 226
15943 TACACGGTAT
*
15953 TATGTTGATAATATTGAAAAAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTATG
1 TATGTTGATAATATTG-AAAAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAG
* * * * * * *
16018 GTCTCATC-GACTTTAAACAGACGTTACATATTACATTAAATAAACGCTAC-TTTTATGTTATTA
65 GCCCCATCAG-CTTTAAACAGACGCTACCTATTACATTAAATAAGCACTACATGTTATGTTATTA
* * * * * *
16081 TTGTTGATAATATTTCTAGTAATTAACATATTTTATTATCGTCAGATTTCTTAGGCTCCATGAGC
129 TGGTTGATAATGTTTCTAGTAATTAACCTATTTTATTATCGTCAGATTTCTGAGACTCCATCAGC
* * * *
16146 ATAAACTTTGTTAACGTTTTAGGCGCTGCCCAA
194 ATAAACTTTGGTAACATTTTAGACGCTACCCAA
* * *
16179 TATGTTCATAATATTGAGAGAAAAAA-TGAGTAATTAACTTATTTTGTTATCGTCGGATTTCTAA
1 TATGTTGATAATATTGA-A-AAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAA
* * * * *
16243 GACTCCATCAACTTTAAACAGATGCTACCTATTACATT-AATAAGCACTACATGTTATTTTATTA
64 GGCCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATAAGCACTACATGTTATGTTATTA
*
16307 TGGTTGATAATGTTTCTAGTAATTAACCTATTTT-TTATCGTCATATTTCTGAGACTCCATCAGC
129 TGGTTGATAATGTTTCTAGTAATTAACCTATTTTATTATCGTCAGATTTCTGAGACTCCATCAGC
* * *
16371 TTAAACTTTGGTAACATTTTAGACGTTACCTAA
194 ATAAACTTTGGTAACATTTTAGACGCTACCCAA
* * * *
16404 TATGTTGATAATATTGATAACAAATTAAGTAATTAACCTAGTTTGTTATCGTCGAATTTCTAAGG
1 TATGTTGATAATATTGAAAAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGG
* * * *
16469 CCCCATCAGCTTTAAAAAGACACAACCTATTACGTTAAATAAGCACTACATGTTATGTTATTATG
66 CCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATAAGCACTACATGTTATGTTATTATG
* *
16534 GTTAATAATGTTTCCAGTAATTAACC
131 GTTGATAATGTTTCTAGTAATTAACC
16560 GGTTATGTTA
Statistics
Matches: 327, Mismatches: 48, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
223 5 0.02
224 64 0.20
225 130 0.40
226 122 0.37
227 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (226 bp):
TATGTTGATAATATTGAAAAAAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGG
CCCCATCAGCTTTAAACAGACGCTACCTATTACATTAAATAAGCACTACATGTTATGTTATTATG
GTTGATAATGTTTCTAGTAATTAACCTATTTTATTATCGTCAGATTTCTGAGACTCCATCAGCAT
AAACTTTGGTAACATTTTAGACGCTACCCAA
Found at i:18844 original size:17 final size:17
Alignment explanation
Indices: 18822--18857 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18812 ACTCACACTT
*
18822 AATAAAATTTAAATCAA
1 AATAAAATATAAATCAA
*
18839 AATAAAATATAAATTAA
1 AATAAAATATAAATCAA
18856 AA
1 AA
18858 ATCATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAATATAAATCAA
Found at i:25605 original size:47 final size:47
Alignment explanation
Indices: 25536--25630 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
25526 TTAACAGCCC
25536 ATAACAAGGTACCAAAATATAGTTATCTACTATCCCCTAAAGGAAAT
1 ATAACAAGGTACCAAAATATAGTTATCTACTATCCCCTAAAGGAAAT
25583 ATAACAAGGTACCAAAATATAGTTATCTACTATCCCCTAAAGGAAAT
1 ATAACAAGGTACCAAAATATAGTTATCTACTATCCCCTAAAGGAAAT
25630 A
1 A
25631 CAAGATAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (47 bp):
ATAACAAGGTACCAAAATATAGTTATCTACTATCCCCTAAAGGAAAT
Found at i:30683 original size:21 final size:19
Alignment explanation
Indices: 30650--30715 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
30640 TAGGGTTTAG
*
30650 AATAAAAAAAATAAAGTAA
1 AATAAAAAAAATAAAATAA
*
30669 AGATAAAAATGAATAAAATAA
1 A-ATAAAAA-AAATAAAATAA
30690 AATAAAGAAAAA-AAGAATAA
1 AATAAA-AAAAATAA-AATAA
30710 TAATAA
1 -AATAA
30716 TAATATATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 19 0.49
21 17 0.44
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.17
Consensus pattern (19 bp):
AATAAAAAAAATAAAATAA
Found at i:30686 original size:26 final size:25
Alignment explanation
Indices: 30657--30720 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 25
30647 TAGAATAAAA
* *
30657 AAAATAAAGTAAAGATAAAAATGAAT
1 AAAATAAAATAAAGA-AAAAAAGAAT
30683 AAAATAAAATAAAGAAAAAAAGAAT
1 AAAATAAAATAAAGAAAAAAAGAAT
30708 AATAATAATAATA
1 AA-AATAA-AATA
30721 TATACATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 11 0.32
26 19 0.56
27 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (25 bp):
AAAATAAAATAAAGAAAAAAAGAAT
Found at i:30765 original size:17 final size:18
Alignment explanation
Indices: 30717--30767 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
30707 TAATAATAAT
*
30717 AATATATACATAATAAGAA
1 AATAAATACA-AATAAGAA
*
30736 AATAAATAAAAATAAGAA
1 AATAAATACAAATAAGAA
*
30754 GA-AAATACAAATAA
1 AATAAATACAAATAA
30768 ATTAATGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.39
18 9 0.32
19 8 0.29
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (18 bp):
AATAAATACAAATAAGAA
Found at i:30784 original size:46 final size:49
Alignment explanation
Indices: 30676--30792 Score: 117
Period size: 49 Copynumber: 2.5 Consensus size: 49
30666 TAAAGATAAA
*
30676 AATGAATAAAATA-AAATAAAGAAAAAAAGAATAATAATAATAATATAT
1 AATGAATAAAAAATAAATAAAGAAAAAAAGAATAATAATAATAATATAT
*
30724 ACAT-AATAAGAAAATAAATAAA-AATAAGAAGAA-AATACA-AATAA-AT-T
1 A-ATGAATAA-AAAATAAATAAAGAA-AAAAAGAATAATA-ATAATAATATAT
30771 AATGAATAAAAAAT--ATAAAGAA
1 AATGAATAAAAAATAAATAAAGAA
30793 GATAAAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
44 5 0.08
45 2 0.03
46 7 0.12
47 7 0.12
48 8 0.13
49 16 0.27
50 15 0.25
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.21
Consensus pattern (49 bp):
AATGAATAAAAAATAAATAAAGAAAAAAAGAATAATAATAATAATATAT
Found at i:30893 original size:3 final size:3
Alignment explanation
Indices: 30885--30941 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
30875 TAAAATAGAG
30885 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30933 TAA TAA TAA
1 TAA TAA TAA
30942 CAGTAAATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32188 original size:19 final size:21
Alignment explanation
Indices: 32161--32213 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
32151 ATGAAACAAG
*
32161 TAATAAATATATATAT-T-TA
1 TAATTAATATATATATGTATA
32180 TAATTAATATAATATATGTATA
1 TAATTAATAT-ATATATGTATA
*
32202 TAAATAATATAT
1 TAATTAATATAT
32214 GTGGCACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 6 0.21
21 3 0.10
22 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATTAATATATATATGTATA
Found at i:32915 original size:84 final size:84
Alignment explanation
Indices: 32757--33360 Score: 715
Period size: 84 Copynumber: 7.2 Consensus size: 84
32747 AACTCGAACA
* * * * * * ** *
32757 TTTTGTTGACATATAGCCCTTCTTGCCTTGAGCCATGCTGTAAAATGACATGCCTTTGAGCTGAG
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTG-CAAATGATGTGCCTTGGAGCTGAG
* * *
32822 TGTAATCGAACTCGAAGTTC
65 CGTAGTCGAACTCGAAGGTC
* * * * * * *
32842 TTTTATTGGAAAATAGCCCTTCTTGCCTTGAACTATGTTACAAATGATGTGCCTTTGAGTTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
*
32907 GTAGTCGAACTAGAAGGTC
66 GTAGTCGAACTCGAAGGTC
** * * * **
32926 TTTTGTTGATAGATAACCCTT-TTACCCTTGAGTTATCCTGCAAATGATGTGCCTTGGAGCTGAG
1 TTTTGTTGGCAAATAACCCTTCTT-GCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAG
** *
32990 CGTAGTAAAACTCAAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * * *
33010 TTTTGTTGGTAAATAACCCTTCTTGCCTTAAGCTATGTTGCAAATGATATGCCTTGGAGTTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
33075 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * *
33094 TTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGT
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
33159 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
*
33178 TTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
*
33243 GTAGTAGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * ** *
33262 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTTTGCTATAAATGATGTGCCTTGGAACTGAGC
1 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
33327 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
33346 TTTTGTTGGCAAATA
1 TTTTGTTGGCAAATA
33361 GATGATCTAT
Statistics
Matches: 442, Mismatches: 75, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
83 2 0.00
84 406 0.92
85 34 0.08
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:33033 original size:168 final size:168
Alignment explanation
Indices: 32757--33361 Score: 798
Period size: 168 Copynumber: 3.6 Consensus size: 168
32747 AACTCGAACA
* * * * * ** * ** *
32757 TTTTGTTGACATATAGCCCTTCTTGCCTTGAGCCATGCTGTAAAATGACATGCCTTTGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTG-CAAATGATGTGCCTTGGAGCTGAG
* * * * * *
32822 TGTAATCGAACTCGAAGTTCTTTTATTGGAAAATAGCCCTTCTTGCCTTGAACTATGTTACAAAT
65 CGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAACTATGTTGCAAAT
* *
32887 GATGTGCCTTTGAGTTGAGCGTAGTCGAACTAGAAGGTC
130 GATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTC
** * * *
32926 TTTTGTTGATAGATAACCCTTTTACCCTTGAGTTATCCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
** * * *
32991 GTAGTAAAACTCAAAGGTCTTTTGTTGGTAAATAACCCTTCTTGCCTT-AAGCTATGTTGCAAAT
66 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAA-CTATGTTGCAAAT
*
33055 GATATGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTC
130 GATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTC
* * * * * *
33094 TTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
33159 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATG
66 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAACTATGTTGCAAATG
* *
33224 ATGTGCCTTGGAGCTGAGCGTAGTAGAACTCGAAGGTC
131 ATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTC
* ** *
33262 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTTTGCTATAAATGATGTGCCTTGGAACTGAGC
1 TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
33327 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAG
66 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAG
33362 ATGATCTATG
Statistics
Matches: 379, Mismatches: 55, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
167 2 0.01
168 345 0.91
169 32 0.08
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (168 bp):
TTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAACTATGTTGCAAATG
ATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTC
Found at i:33880 original size:248 final size:248
Alignment explanation
Indices: 33436--33923 Score: 714
Period size: 248 Copynumber: 2.0 Consensus size: 248
33426 CTTCTTGTGG
* *
33436 GCACGATATCCTTCACCGTCAAGTTGAAACCGTGGAGAGCCCCTTCGTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCACCGTCAAGTTAAAACCGTGGAGAGCCCATTCGTTGTGAAGTTGAGCCTTG
* * *
33501 AATTGGATATCCTTCTTCGTGAAGTTGAAATCCAATCAGAAGATAAATGTTGCTGGCGGGCACGA
66 AATTGGATATCCTTCTTCATGAAGTTGAAATCCAATCAGAAGATAAATGTTGCTGGCGAGAACGA
* * *
33566 TTCCATTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTGTGAAGTTGAGCCTTGAATTGG
131 TTCCATTCGTCATGAAGTTGAAACCATGGATGACCTCTTCGTTGTGAAGTTGAGCCTTGAATTGG
* * * *
33631 ATATCCTTCATCGTGAAATTAAAATCCAATCTAAATATTAATGTTACTGGTGA
196 ATATCCTTCACCGTGAAATTAAAATCCAATATAAAGATGAATGTTACTGGTGA
* *
33684 GCACGAT-TCCCTTCATCGTGAAGTTAAAACCGTGGATGA-CCCATTCGTTGTGAAGTTGAGCCT
1 GCACGATAT-CCTTCACCGTCAAGTTAAAACCGTGGA-GAGCCCATTCGTTGTGAAGTTGAGCCT
* *
33747 TGAATTGGATATCCTTCTTCATGAAGTTGAAATCCAAT-ATGAAGATGAATGTTGCTGGTGAGAA
64 TGAATTGGATATCCTTCTTCATGAAGTTGAAATCCAATCA-GAAGATAAATGTTGCTGGCGAGAA
* * *
33811 CGATTCCCTTCGTCATGAAGTTGAAACCATGGAT-AGCTCATTCGTTGTGAAGTTGAGCCTTGGA
128 CGATTCCATTCGTCATGAAGTTGAAACCATGGATGACCTC-TTCGTTGTGAAGTTGAGCCTTGAA
* * *
33875 TTGGATATCCTTCGCCGTGAAGTTGAAATCCAATATAAAGATGAATGTT
192 TTGGATATCCTTCACCGTGAAATTAAAATCCAATATAAAGATGAATGTT
33924 GTTTCGAGTC
Statistics
Matches: 214, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
247 6 0.03
248 206 0.96
249 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (248 bp):
GCACGATATCCTTCACCGTCAAGTTAAAACCGTGGAGAGCCCATTCGTTGTGAAGTTGAGCCTTG
AATTGGATATCCTTCTTCATGAAGTTGAAATCCAATCAGAAGATAAATGTTGCTGGCGAGAACGA
TTCCATTCGTCATGAAGTTGAAACCATGGATGACCTCTTCGTTGTGAAGTTGAGCCTTGAATTGG
ATATCCTTCACCGTGAAATTAAAATCCAATATAAAGATGAATGTTACTGGTGA
Found at i:33909 original size:124 final size:124
Alignment explanation
Indices: 33456--33924 Score: 640
Period size: 124 Copynumber: 3.8 Consensus size: 124
33446 CTTCACCGTC
* *
33456 AAGTTGAAACCGTGGAGAGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCGT
1 AAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCGT
* * * * *
33521 GAAGTTGAAATCCAATCA-GAAGATAAATGTTGCTGGCGGGCACGATTCCATTCGTCGTG
66 GAAGTTGAAATCCAAT-ATAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTG
* *
33580 AAGTTGAAATCGTGGAT-GACCTC-TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
1 AAGTTGAAACCGTGGATAG-CC-CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTC
* * * * * * *
33643 GTGAAATTAAAATCCAATCTAAATATTAATGTTACTGGTGAGCACGATTCCCTTCATCGTG
64 GTGAAGTTGAAATCCAATATAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTG
* *
33704 AAGTTAAAACCGTGGAT-GACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCA
1 AAGTTGAAACCGTGGATAG-CCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCG
* * *
33768 TGAAGTTGAAATCCAATATGAAGATGAATGTTGCTGGTGAGAACGATTCCCTTCGTCATG
65 TGAAGTTGAAATCCAATATAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTG
* * * **
33828 AAGTTGAAACCATGGATAGCTCATTCGTTGTGAAGTTGAGCCTTGGATTGGATATCCTTCGCCGT
1 AAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCGT
33893 GAAGTTGAAATCCAATATAAAGATGAATGTTG
66 GAAGTTGAAATCCAATATAAAGATGAATGTTG
33925 TTTCGAGTCC
Statistics
Matches: 304, Mismatches: 36, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
123 2 0.01
124 300 0.99
125 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (124 bp):
AAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCTTCGT
GAAGTTGAAATCCAATATAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTG
Found at i:35218 original size:97 final size:97
Alignment explanation
Indices: 35073--35336 Score: 290
Period size: 95 Copynumber: 2.7 Consensus size: 97
35063 GGCTAGATGA
* * *
35073 ATCCATAAAGCTGAGGCGTTTAACCAATTTCTCTAGAGGGATAGCTCAATATCATTGTATATATA
1 ATCCATAAAGC-GAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATATATA
*
35138 TTAT-ATTACCTTTATCAGGCTACCTGAATATT
65 TTATAATCACCTTTATCAGGCTACCTGAATATT
* * *
35170 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTC-A-ATC-TT-TATTTAAT
1 ATCCATAAAG-CGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATAT-AT
* *
35231 ATTATAATCACCTTTATCAGGCTAGCTGAATCTT
64 ATTATAATCACCTTTATCAGGCTACCTGAATATT
* * * * * *
35265 TTCCATAATGGCGAGACGTTTAACCAATTGCTTTATAGGGACAACTCAAGCT-TTATTGTATATA
1 ATCCATAA-AGCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA--TATCATTGTATATA
35329 TA-TATAAT
63 TATTATAAT
35337 ATTTATAATC
Statistics
Matches: 139, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
93 4 0.03
94 9 0.06
95 66 0.47
96 3 0.02
97 40 0.29
98 8 0.06
99 5 0.04
100 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (97 bp):
ATCCATAAAGCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATATATAT
TATAATCACCTTTATCAGGCTACCTGAATATT
Found at i:37675 original size:147 final size:149
Alignment explanation
Indices: 37479--37774 Score: 560
Period size: 147 Copynumber: 2.0 Consensus size: 149
37469 CAGAGATAGA
37479 AACTTTTCAAAAATTTGAAATCATTGAAAAAAATGTCAGTACAACTATTTATTTGAAAAATAAGC
1 AACTTTTCAAAAATTTGAAATCATTGAAAAAAATGTCAGTACAACTATTTATTTGAAAAATAAGC
*
37544 AAAGGTAAATAATTGGAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTTATATAAAAAG
66 AAAGGTAAATAATTGGAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTCATATAAAAAG
37609 ACAACCGAAAATTAATTCT
131 ACAACCGAAAATTAATTCT
*
37628 AACTTTTC-AAAATTTGAAATCATTG-AAAAAATGTCAGTACAACTATTTATTTGAAAAATAATC
1 AACTTTTCAAAAATTTGAAATCATTGAAAAAAATGTCAGTACAACTATTTATTTGAAAAATAAGC
37691 AAAGGTAAATAATTGGAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTCATATAAAAAG
66 AAAGGTAAATAATTGGAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTCATATAAAAAG
37756 ACAACCGAAAATTAATTCT
131 ACAACCGAAAATTAATTCT
37775 GGCCTGACTC
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 120 0.83
148 17 0.12
149 8 0.06
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.32
Consensus pattern (149 bp):
AACTTTTCAAAAATTTGAAATCATTGAAAAAAATGTCAGTACAACTATTTATTTGAAAAATAAGC
AAAGGTAAATAATTGGAATCGAATAAATAAATTAAAATTAAAATTTACTATTTTCATATAAAAAG
ACAACCGAAAATTAATTCT
Found at i:38221 original size:18 final size:19
Alignment explanation
Indices: 38198--38244 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
38188 GAAGTAAAGG
* *
38198 AAATAAAAAAGATACAG-A
1 AAATAAAAAAAATAAAGTA
38216 AAATAAAAAAAATAAAGTA
1 AAATAAAAAAAATAAAGTA
38235 AAGATAAAAA
1 AA-ATAAAAA
38245 TGAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
19 3 0.12
20 7 0.28
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (19 bp):
AAATAAAAAAAATAAAGTA
Found at i:38260 original size:14 final size:14
Alignment explanation
Indices: 38241--38267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38231 AGTAAAGATA
38241 AAAATGAAGAAAAT
1 AAAATGAAGAAAAT
38255 AAAATGAAGAAAA
1 AAAATGAAGAAAA
38268 AAGAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATGAAGAAAAT
Found at i:38264 original size:26 final size:25
Alignment explanation
Indices: 38215--38287 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
38205 AAAGATACAG
*
38215 AAAATAAAAAAAATAAAGTAAAGATA
1 AAAATAAAAAAAATAAAATAAAGA-A
* * *
38241 AAAATGAAGAAAATAAAATGAAGAA
1 AAAATAAAAAAAATAAAATAAAGAA
* * *
38266 AAAAGAATAATAATAAGAATAA
1 AAAATAAAAAAAATAA-AATAA
38288 TAATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
25 12 0.33
26 24 0.67
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (25 bp):
AAAATAAAAAAAATAAAATAAAGAA
Found at i:38279 original size:3 final size:3
Alignment explanation
Indices: 38271--38313 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
38261 AAGAAAAAAG
*
38271 AAT AAT AAT AAG AAT AAT AAT AAT AAT AAT ATAT ACAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AA
38314 GCAAATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38383 original size:21 final size:19
Alignment explanation
Indices: 38330--38383 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
38320 AAATAAAAAT
*
38330 AAGAAGAAAATACAAATAA
1 AAGAAGAAAAAACAAATAA
*
38349 ATGAATGAATAAAACAAATATA
1 AAGAA-GAA-AAAACAAATA-A
38371 AAGAAGATAAAAA
1 AAGAAGA-AAAAA
38384 AAGATAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 15 0.54
22 6 0.21
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (19 bp):
AAGAAGAAAAAACAAATAA
Found at i:38416 original size:26 final size:26
Alignment explanation
Indices: 38381--38430 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
38371 AAGAAGATAA
38381 AAAAAGATAAAGATAA-GGAATAAAAAT
1 AAAAAGATAAA-ATAATGGAA-AAAAAT
38408 AAAAA-ATAAAATAATGGAAAAAA
1 AAAAAGATAAAATAATGGAAAAAA
38431 TAGAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (26 bp):
AAAAAGATAAAATAATGGAAAAAAAT
Found at i:39689 original size:19 final size:21
Alignment explanation
Indices: 39662--39714 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
39652 ATGAAACAGG
*
39662 TAATAAATATATATAT-T-TA
1 TAATTAATATATATATGTATA
39681 TAATTAATATAATATATGTATA
1 TAATTAATAT-ATATATGTATA
*
39703 TAAATAATATAT
1 TAATTAATATAT
39715 GTGACACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 6 0.21
21 3 0.10
22 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATTAATATATATATGTATA
Found at i:44164 original size:20 final size:20
Alignment explanation
Indices: 44139--44189 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44129 GAACTGAGGT
* **
44139 AGTATCGATACTGACTTATC
1 AGTATCGATACTGACTCAAA
*
44159 AGTATCGATATTGACTCAAA
1 AGTATCGATACTGACTCAAA
44179 AGTATCGATAC
1 AGTATCGATAC
44190 CTCCATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTGACTCAAA
Found at i:49930 original size:24 final size:25
Alignment explanation
Indices: 49902--49953 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
49892 GAATGTAACT
*
49902 TTACCAAACCCAGCG-TACCAAAAC
1 TTACCAAACCCAACGCTACCAAAAC
* *
49926 TTACCGACCCCAACGTCTACCAAAAC
1 TTACCAAACCCAACG-CTACCAAAAC
49952 TT
1 TT
49954 CAGACTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.37, C:0.38, G:0.08, T:0.17
Consensus pattern (25 bp):
TTACCAAACCCAACGCTACCAAAAC
Found at i:56930 original size:20 final size:20
Alignment explanation
Indices: 56909--57014 Score: 106
Period size: 20 Copynumber: 5.2 Consensus size: 20
56899 AAATCACAAT
*
56909 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
56929 GCGATACTTACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
56949 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
56970 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
56990 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
57010 GCGAT
1 GCGAT
57015 TTACATAGCG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:56963 original size:61 final size:61
Alignment explanation
Indices: 56898--57014 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
56888 GCGAATTGGG
* * * * *
56898 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
56959 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
57015 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCACAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:57651 original size:20 final size:19
Alignment explanation
Indices: 57605--57770 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
57595 GAAACCAAAA
*
57605 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
57624 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
57643 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
57663 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
57679 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
57696 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATT
**
57712 TC-C-TTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
57729 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
57749 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
57769 TC
1 TC
57771 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 16 0.13
15 2 0.02
16 6 0.05
17 5 0.04
18 2 0.02
19 41 0.34
20 46 0.39
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:57686 original size:39 final size:39
Alignment explanation
Indices: 57610--57686 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
57600 CAAAATCGCA
* **
57610 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
57649 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
57687 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:57695 original size:33 final size:33
Alignment explanation
Indices: 57658--57745 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
57648 GTTGCGATTT
* **
57658 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCCTCGCGATAG
*
57691 TCATTTCGCGTTGCGATTCTCTCCTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCCTCGCGATAG
57724 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
57746 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCCTCGCGATAG
Found at i:60342 original size:12 final size:12
Alignment explanation
Indices: 60325--60349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60315 TCTTCGGGGA
60325 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60337 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60349 C
1 C
60350 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:60561 original size:23 final size:23
Alignment explanation
Indices: 60524--60576 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
60514 CTGAAACATC
*
60524 ATCAAATCCGTGTATTAACCAAT
1 ATCAAATCCGTGTATTAACCAAG
*
60547 ATCAAAGTCCG-GTATTGACCAAG
1 ATCAAA-TCCGTGTATTAACCAAG
60570 ATCAAAT
1 ATCAAAT
60577 TTCGAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.81
24 4 0.15
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTAACCAAG
Found at i:61651 original size:20 final size:20
Alignment explanation
Indices: 61626--61683 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
61616 ATTCATTTGA
61626 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
61646 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
61666 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
61684 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:61726 original size:14 final size:14
Alignment explanation
Indices: 61707--61760 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
61697 GAAAATCGCA
61707 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
61721 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
61738 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
61754 TTGCGAT
1 TTGCGAT
61761 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:61726 original size:33 final size:33
Alignment explanation
Indices: 61689--61759 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
61679 AAAATCGCAA
61689 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
61722 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
61755 TGCGA
1 TGCGA
61760 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:61760 original size:33 final size:33
Alignment explanation
Indices: 61702--61779 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
61692 GAAATGAAAA
***
61702 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
61735 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
61768 TCGCATTGCGAT
1 TCGCATTGCGAT
61780 AGTCTGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:61884 original size:14 final size:13
Alignment explanation
Indices: 61865--61900 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
61855 CATCAATTAA
61865 ACAAATCAACATTT
1 ACAAATCAAC-TTT
*
61879 ACAAATCATCTTT
1 ACAAATCAACTTT
61892 ACAAATCAA
1 ACAAATCAA
61901 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:62541 original size:190 final size:189
Alignment explanation
Indices: 62198--62577 Score: 751
Period size: 190 Copynumber: 2.0 Consensus size: 189
62188 TAGGCAGCGT
62198 CTCGAATATATTGCTCTAGCCATATAATGCCGAAACCACAAGCCTACTGCAGCTCTATCTCTATC
1 CTCGAATATATTGCTCTAGCCATATAATGCCGAAACCACAAGCCTACTGCAGCTCTATCTCTATC
62263 GGTGGGAGGTAAAACTCTGTGCTTCCCGTCGTCAAACGCGCCAAGCAAAGGCATACGAGAGGACC
66 GGTGGGAGGTAAAACTCTGTGCTTCCCGTCGTCAAACGCGCCAAGCAAAGGCATACGAGAGGACC
62328 ACAATCCCCTCTGGCTCCCGGCGATTGCTGTGGCGCGATCTCGTCTCTGACAACTGTGA
131 ACAATCCCCTCTGGCTCCCGGCGATTGCTGTGGCGCGATCTCGTCTCTGACAACTGTGA
62387 CTCGAATATATTGCTCTAGCCATATAATGCCGAAACCACAAGCCTACTGCAGCTCTATCTCTATC
1 CTCGAATATATTGCTCTAGCCATATAATGCCGAAACCACAAGCCTACTGCAGCTCTATCTCTATC
62452 GGTGGGAGGTAAAAACTCTGTGCTTCCCGTCGTCAAACGCGCCAAGCAAAGGCATACGAGAGGAC
66 GGTGGGAGGT-AAAACTCTGTGCTTCCCGTCGTCAAACGCGCCAAGCAAAGGCATACGAGAGGAC
62517 CACAATCCCCTCTGGCTCCCGGCGATTGCTGTGGCGCGATCTCGTCTCTGACAACTGTGA
130 CACAATCCCCTCTGGCTCCCGGCGATTGCTGTGGCGCGATCTCGTCTCTGACAACTGTGA
62577 C
1 C
62578 ATTGAACTTC
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 75 0.39
190 115 0.61
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (189 bp):
CTCGAATATATTGCTCTAGCCATATAATGCCGAAACCACAAGCCTACTGCAGCTCTATCTCTATC
GGTGGGAGGTAAAACTCTGTGCTTCCCGTCGTCAAACGCGCCAAGCAAAGGCATACGAGAGGACC
ACAATCCCCTCTGGCTCCCGGCGATTGCTGTGGCGCGATCTCGTCTCTGACAACTGTGA
Found at i:63959 original size:20 final size:19
Alignment explanation
Indices: 63924--64006 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 19
63914 GAAACATAAA
63924 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
63943 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
63963 ATCGCAATGCGAAATGA--
1 ATCGCAACGCGAAATGACT
* * *
63980 AACGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
63998 ATCGCAACG
1 ATCGCAACG
64007 ACAAAATCGC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
17 16 0.29
18 7 0.12
19 16 0.29
20 17 0.30
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:64015 original size:14 final size:14
Alignment explanation
Indices: 63996--64051 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
63986 ATGCGAAATG
63996 AAATCGCAACGACA
1 AAATCGCAACGACA
64010 AAATCGCAACG-CGAA
1 AAATCGCAACGAC--A
64025 ATGAATCGCAACGACA
1 A--AATCGCAACGACA
64041 AAATCGCAACG
1 AAATCGCAACG
64052 CGAAACACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 21 0.57
15 2 0.05
16 2 0.05
17 10 0.27
18 1 0.03
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:64035 original size:31 final size:32
Alignment explanation
Indices: 63982--64056 Score: 134
Period size: 31 Copynumber: 2.4 Consensus size: 32
63972 CGAAATGAAA
*
63982 CGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAACGCGAAATGAAATCGCAACGACAAAAT
64014 CGCAACGCGAAATG-AATCGCAACGACAAAAT
1 CGCAACGCGAAATGAAATCGCAACGACAAAAT
64045 CGCAACGCGAAA
1 CGCAACGCGAAA
64057 CACAAATCGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.09
Consensus pattern (32 bp):
CGCAACGCGAAATGAAATCGCAACGACAAAAT
Found at i:64036 original size:17 final size:17
Alignment explanation
Indices: 63923--64056 Score: 104
Period size: 17 Copynumber: 7.9 Consensus size: 17
63913 CGAAACATAA
63923 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
63940 ACTATCGCAACGCGGAAATGG
1 A--ATCGCAACGC-GAAAT-G
* *
63961 CTATCGCAATGCGAAATG
1 -AATCGCAACGCGAAATG
* *
63979 AAACGCAATGCGAAATG
1 AATCGCAACGCGAAATG
63996 AAATCGCAA--CGACAA--
1 -AATCGCAACGCGA-AATG
64011 AATCGCAACGCGAAATG
1 AATCGCAACGCGAAATG
64028 AATCGCAA--CGACAA--
1 AATCGCAACGCGA-AATG
64042 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
64057 CACAAATCGC
Statistics
Matches: 98, Mismatches: 5, Indels: 30
0.74 0.04 0.23
Matches are distributed among these distances:
14 16 0.16
15 7 0.07
16 11 0.11
17 26 0.27
18 8 0.08
19 15 0.15
20 14 0.14
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.12
Consensus pattern (17 bp):
AATCGCAACGCGAAATG
Found at i:64106 original size:14 final size:14
Alignment explanation
Indices: 64087--64142 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
64077 TCATTTCGCG
64087 TTGCGATTTTGTCA
1 TTGCGATTTTGTCA
*
64101 TTGCGATTTCATTTCGCA
1 TTGCGATTT--TGT--CA
*
64119 TTGCGATTTTGTCG
1 TTGCGATTTTGTCA
64133 TTGCGATTTT
1 TTGCGATTTT
64143 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.57
16 4 0.11
18 11 0.31
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCA
Found at i:64116 original size:32 final size:33
Alignment explanation
Indices: 64066--64158 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
64056 ACACAAATCG
*
64066 CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
64099 CATTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
64131 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
64159 AGCCATTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.53
33 27 0.47
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:64685 original size:18 final size:18
Alignment explanation
Indices: 64659--64703 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
64649 GTCGATCAGA
*
64659 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
64677 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
64695 TGATGGCTC
1 TGATGGCTC
64704 CCGAAGTTAA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:66349 original size:20 final size:20
Alignment explanation
Indices: 66324--66376 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
66314 GATTATGTAT
*
66324 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
66344 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
66364 TATCTCGTTGCGA
1 TATCGCGTTGCGA
66377 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:66420 original size:41 final size:41
Alignment explanation
Indices: 66344--66421 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
66334 CGAAAGTCAG
* * *
66344 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
* * *
66385 TATCGCATTGCGATAGTCAGTATCACATTGTGATTTT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTT
66422 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
Found at i:66437 original size:41 final size:41
Alignment explanation
Indices: 66407--66499 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
66397 ATAGTCAGTA
* * *
66407 TCACATTGTGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
66448 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
*
66489 TCGCATTGCGA
1 TCACATTGCGA
66500 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:66451 original size:20 final size:20
Alignment explanation
Indices: 66426--66499 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
66416 GATTTTCCCA
*
66426 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
66446 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
66467 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
66487 ATTCGCATTGCGA
1 ATTCGCATTGCGA
66500 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:69819 original size:58 final size:58
Alignment explanation
Indices: 69750--70099 Score: 542
Period size: 58 Copynumber: 6.0 Consensus size: 58
69740 CATAAGTTCA
* * * *
69750 AATACGGAAATTCATAAATAAATTATGAATTTCTTAACTTTTTCCACACAAAGTGCCT
1 AATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
69808 AATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTTGCACACAAAGTGCCC
1 AATACGAAAATTCATAAACAAATTATGAATTTCTTAAC-TTTTTGCACACAAAGTGCCC
69867 AATAC-AGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
1 AATACGA-AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * * *
69925 AATCCGGAAATTCATAAACAAATTATGAATCTCTTAACTTTTTGCACTCAAAGTGCCC
1 AATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
69983 AATAC-AGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAATGTCC
1 AATACGA-AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
70041 AATACGGAAATTCATAAACAAATTATGAATTTCTTAACATTTTGCACAAAAAGTGCCC
1 AATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
70099 A
1 A
70100 TTTGGTAATC
Statistics
Matches: 268, Mismatches: 19, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
58 214 0.80
59 54 0.20
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (58 bp):
AATACGAAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:71261 original size:13 final size:13
Alignment explanation
Indices: 71243--71308 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
71233 GTCATAAATC
*
71243 TATGACACGCATT
1 TATGACGCGCATT
*
71256 TATGACACGCATT
1 TATGACGCGCATT
* *
71269 TATGATGCTCATT
1 TATGACGCGCATT
* *
71282 TATGATGCACATT
1 TATGACGCGCATT
71295 TATGACGCGCATT
1 TATGACGCGCATT
71308 T
1 T
71309 CGCGTCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:71471 original size:2 final size:2
Alignment explanation
Indices: 71464--71530 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
71454 TTTCGTAAAT
71464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71506 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
71531 TGTAGATTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82970 original size:52 final size:54
Alignment explanation
Indices: 82892--82998 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 54
82882 TTATAATATT
* * *
82892 CTTGTGATTAGTTGTAATTCCCTAACTCTAGGCTAGTCTCTTA-TT-TATGTGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGC
*
82944 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATGTGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGC
82998 C
1 C
82999 ACATCTTGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 39 0.80
53 2 0.04
54 8 0.16
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (54 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGTGC
Found at i:83187 original size:58 final size:58
Alignment explanation
Indices: 83106--83528 Score: 631
Period size: 58 Copynumber: 7.4 Consensus size: 58
83096 AATTTCCTAG
* * *
83106 TTTTTCCACATAAAGTG-CCAATACGAAAATTCATAAACAAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* * *
83163 TTCTTGCACACAAAGTGCCTAATACAGAAATTCATAAACAAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* *
83221 TTTTTGCACACAAAGTGCCCAATACAGAAATTCATAAATAAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* *
83279 TTTTTGCACACAAAGTGCCCAATCCGGAAATTCATAAACAAATTATGAA-TTCTTTAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* *
83336 TTTTTGCACTCAAAGTGCCCAATATGGAAATTCATAAACAAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* *
83394 -ATTTGCACACAAAGTG-CCAATACGGAAATACATAAACAAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
* * * *
83450 TTTTAGCACACAAAAATGCCCAA-ATGGAAATTCATAAACAAATTACGAATTTCTTAAC
1 TTTTTGCACAC-AAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
*
83508 TTTTTCCACACAAAGTGCCCA
1 TTTTTGCACACAAAGTGCCCA
83529 TTTGGTAATC
Statistics
Matches: 331, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
56 38 0.11
57 98 0.30
58 191 0.58
59 4 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (58 bp):
TTTTTGCACACAAAGTGCCCAATACGGAAATTCATAAACAAATTATGAATTTCTTAAC
Done.