Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003850.1 Hibiscus syriacus cultivar Beakdansim tig00008262_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: 524162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:307861 original size:52 final size:52
Alignment explanation
Indices: 307526--307845 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
307516 AAATCCCAAC
307526 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
307579 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
307631 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
307683 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
307740 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
307792 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
307844 AT
1 AT
307846 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:307960 original size:19 final size:19
Alignment explanation
Indices: 307852--307952 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
307842 AAATTATAAA
307852 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
307871 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
307891 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
307907 CG--TTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
307923 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
307942 CGCATTGCGAT
1 CGCATTGCGAT
307953 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.08
19 29 0.39
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:308078 original size:14 final size:14
Alignment explanation
Indices: 308059--308095 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
308049 CATCAATTAC
308059 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
308073 ACAAATCATCTTTT
1 ACAAATCAACTTTT
308087 ACAAATCAA
1 ACAAATCAA
308096 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:308107 original size:12 final size:12
Alignment explanation
Indices: 308090--308162 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
308080 ATCTTTTACA
308090 AATCAATTAAAC
1 AATCAATTAAAC
*
308102 AATCAA--AAATTG
1 AATCAATTAAA--C
**
308114 AATCAACTTTTAC
1 AATCAA-TTAAAC
308127 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
308140 AATCAA-AAAAC
1 AATCAATTAAAC
308151 AATCAATTAAAC
1 AATCAATTAAAC
308163 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:308124 original size:38 final size:38
Alignment explanation
Indices: 308076--308148 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
308066 AACTTTTACA
*
308076 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
308114 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
308149 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:309990 original size:20 final size:19
Alignment explanation
Indices: 309965--310010 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
309955 TAGTTTACTT
*
309965 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAC-CAAAA
*
309985 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
310004 TCGCAAC
1 TCGCAAC
310011 GACAGAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.11
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:310005 original size:19 final size:18
Alignment explanation
Indices: 309965--310080 Score: 77
Period size: 19 Copynumber: 6.6 Consensus size: 18
309955 TAGTTTACTT
*
309965 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
309985 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
310004 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
*
310018 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
310037 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
*
310051 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
310070 TCGCAATGCGA
1 TCGCAACGCGA
310081 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
14 19 0.24
15 1 0.01
16 6 0.08
17 6 0.08
18 1 0.01
19 32 0.41
20 12 0.15
21 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:310021 original size:14 final size:14
Alignment explanation
Indices: 310002--310058 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
309992 GCGAAACCAA
*
310002 AATCGCAACGACAG
1 AATCGCAACGAAAG
310016 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
310033 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
310049 AATCGCAACG
1 AATCGCAACG
310059 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:310025 original size:33 final size:33
Alignment explanation
Indices: 309983--310075 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
309973 CGAAACTTAA
** *
309983 AATCGCAACGCGAAACCAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
310016 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
310049 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
310076 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:310098 original size:19 final size:19
Alignment explanation
Indices: 310076--310204 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
310066 AAAATCGCAA
310076 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
310095 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
310109 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
310128 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
310142 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
310161 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
310180 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
310200 TGCGA
1 TGCGA
310205 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:310118 original size:33 final size:33
Alignment explanation
Indices: 310076--310167 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
310066 AAAATCGCAA
310076 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
310109 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
310142 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
310168 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:310567 original size:92 final size:93
Alignment explanation
Indices: 310248--310624 Score: 717
Period size: 91 Copynumber: 4.1 Consensus size: 93
310238 TTGAATGGAT
310248 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
310313 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
310341 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--AC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
310404 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
310432 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
310496 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
310524 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
310588 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
310616 AAATTTACT
1 AAATTTACT
310625 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
90 21 0.08
91 104 0.37
92 88 0.32
93 66 0.24
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:312347 original size:14 final size:14
Alignment explanation
Indices: 312328--312417 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
312318 TTGAAATGAA
312328 AATCGCAACGAGAG
1 AATCGCAACGAGAG
312342 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
312359 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
312375 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
312394 AATCGCAACGAGAG
1 AATCGCAACGAGAG
312408 AATCGCAACG
1 AATCGCAACG
312418 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:312365 original size:33 final size:33
Alignment explanation
Indices: 312320--312434 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
312310 TCTTTTGGTT
312320 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
312353 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
312386 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
312419 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
312435 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:312366 original size:19 final size:18
Alignment explanation
Indices: 312327--312439 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
312317 GTTGAAATGA
312327 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
312342 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
312359 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
312375 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
312392 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
312408 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
312425 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
312440 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:312470 original size:14 final size:14
Alignment explanation
Indices: 312451--312505 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
312441 TTTGGTTTCG
312451 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
312465 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
312484 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
312498 CGTTGCGA
1 CGTTGCGA
312506 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:312667 original size:33 final size:33
Alignment explanation
Indices: 312625--312695 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
312615 AATACTAACT
*
312625 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
312658 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
312691 TGAAA
1 TGAAA
312696 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:312929 original size:22 final size:22
Alignment explanation
Indices: 312877--312931 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
312867 TGGTTGTGAG
**
312877 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
312899 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
312921 GGATTTCTTCG
1 GGATTTCTTCG
312932 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:313102 original size:20 final size:20
Alignment explanation
Indices: 313077--313270 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
313067 CTTTAAATAT
313077 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
313097 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
313119 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
313138 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
313158 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
313178 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
313198 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
313218 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
313238 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
313258 CGCGTTGCGATTT
1 CGCGTTGCGATTT
313271 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:313264 original size:60 final size:60
Alignment explanation
Indices: 313077--313270 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
313067 CTTTAAATAT
**
313077 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
313138 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
313198 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
313258 CGCGTTGCGATTT
1 CGCGTTGCGATTT
313271 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:313287 original size:21 final size:20
Alignment explanation
Indices: 313263--313339 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
313253 ATATTCGCGT
313263 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
313284 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
313304 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
313326 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
313340 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:313350 original size:20 final size:20
Alignment explanation
Indices: 313325--313376 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
313315 AAGAATCGCG
*
313325 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
313345 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
313365 TTGCGATTCTGG
1 TTGCGATTCTGG
313377 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:313552 original size:3 final size:3
Alignment explanation
Indices: 313544--313626 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
313534 TATCACCCAA
313544 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
313592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
313627 CAGCTTGTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:314540 original size:3 final size:3
Alignment explanation
Indices: 314532--314566 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
314522 TGGGACGATG
314532 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
314567 TCATTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:315639 original size:18 final size:18
Alignment explanation
Indices: 315618--315710 Score: 75
Period size: 18 Copynumber: 5.2 Consensus size: 18
315608 GTGATGGTGA
315618 TGGTGTCGGGGTAGCTGC
1 TGGTGTCGGGGTAGCTGC
* * *
315636 TGGTGGT-GGCGTTGGTGC
1 TGGT-GTCGGGGTAGCTGC
*
315654 CGGTGTCGGGGTAGCTGC
1 TGGTGTCGGGGTAGCTGC
* * *
315672 TGGTGGT-GGCGTTGGTG-
1 TGGT-GTCGGGGTAGCTGC
315689 TCGGTGTCGGGGTAGCTGC
1 T-GGTGTCGGGGTAGCTGC
315708 TGG
1 TGG
315711 AGGTGGCGGA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
17 5 0.09
18 45 0.82
19 5 0.09
ACGTcount: A:0.03, C:0.15, G:0.53, T:0.29
Consensus pattern (18 bp):
TGGTGTCGGGGTAGCTGC
Found at i:315640 original size:36 final size:35
Alignment explanation
Indices: 315612--315718 Score: 169
Period size: 36 Copynumber: 3.0 Consensus size: 35
315602 GTGATGGTGA
315612 TGGTGATGGTGTCGGGGTAGCTGCTGGTGGTGGCGT
1 TGGTG-TGGTGTCGGGGTAGCTGCTGGTGGTGGCGT
*
315648 TGGTGCCGGTGTCGGGGTAGCTGCTGGTGGTGGCGT
1 TGGTG-TGGTGTCGGGGTAGCTGCTGGTGGTGGCGT
*
315684 TGGTGTCGGTGTCGGGGTAGCTGCTGGAGGTGGCG
1 TGGTGT-GGTGTCGGGGTAGCTGCTGGTGGTGGCG
315719 GAGATGTTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.05, C:0.14, G:0.53, T:0.28
Consensus pattern (35 bp):
TGGTGTGGTGTCGGGGTAGCTGCTGGTGGTGGCGT
Found at i:317832 original size:23 final size:23
Alignment explanation
Indices: 317785--317834 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
317775 AATAACATAT
* **
317785 TAGGTAGCGCTTGTATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
317808 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
317831 TAGG
1 TAGG
317835 CATTTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:317896 original size:87 final size:87
Alignment explanation
Indices: 317748--317910 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
317738 TATATTATAT
* * *
317748 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTGTATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACAAATTAGGCAGCGCTTATATAATGTAATAGGT
*
317813 AGCGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
*
317835 CATTTAACCGAAAATATTATCAAGTACAATAACAAATTAGGCAGCGCTTATATAATTTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACAAATTAGGCAGCGCTTATATAATGTAATAGGT
317900 AACGCTTATAT
66 AACGCTTATAT
317911 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACAAATTAGGCAGCGCTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGG
Found at i:319628 original size:21 final size:21
Alignment explanation
Indices: 319604--319659 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
319594 GATTTTTAGG
319604 ATCGACACTTTTTCTAAATGT
1 ATCGACACTTTTTCTAAATGT
319625 ATCGACACTTTTTCTAAATGT
1 ATCGACACTTTTTCTAAATGT
*
319646 ATCGACATTTTTTC
1 ATCGACACTTTTTC
319660 GTGAACTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (21 bp):
ATCGACACTTTTTCTAAATGT
Found at i:320028 original size:199 final size:200
Alignment explanation
Indices: 319625--320315 Score: 782
Period size: 204 Copynumber: 3.5 Consensus size: 200
319615 TTCTAAATGT
* * * **
319625 ATCGACACTTTTTCTAAATGTATCGACA-TTTTTTCGTGAACTT-GTTTCGAAAATTTATTATGG
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTTGAAAATACATTATGG
* * * * *
319688 ACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACATTTT-T--TAATAAC
66 ACACAAAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTATACCTTTTCTCATAA-AAC
* * * *
319750 CGGTATATTTAGACTGGTTATATTGTTATGTTACCTATTACATTATAATTATGTGTTTCAATGTT
130 CGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTT
319815 TTTGGG
195 TTTGGG
* *
319821 ATCGACACTTGTTATAAATGTATCGACATTTTTTTCGTGCAA-TTGGTTTTG-AAATACATTCTG
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTG-AACTTGGTTTTGAAAATACATTATG
*
319884 GA-A-AACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTTTTCTCATAA
65 GACACAA-A-GTATCGACACAAATGAATAAAGTGTCGATACATTA-TGTATACCTTTTCTCATAA
* * * * * * * *
319946 AACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACAATATAGTTACGGGTTTCGAT
127 AACCGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGAT
320011 GTTTTTGGG
192 GTTTTTGGG
* * *
320020 ATCGACACTTGATATAAATGTATCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAAATACATT
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTG-GTT--TT-GAAAATACATT
* *
320084 ATGGACACAAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATACCTCTTTTCTCAT
62 ATGGACACAAAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTATA-C-CTTTTCTCAT
* *
320149 -AAACCGGTATATTTAGACCGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCG
125 AAAACCGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCG
*
320213 ATGTTTTTTGG
190 ATGTTTTTGGG
* * * * *
320224 ATCGATACTTTTTATAAATGTATCAACACTTTGTTCGT-ACACTTGG-TTTGGAAATACATTATG
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGA-ACTTGGTTTTGAAAATACATTATG
* * * *
320287 GATTAC-ATGTAACGACACGAATGAATAAA
65 GA-CACAAAGTATCGACACAAATGAATAAA
320316 TCAAATTCAT
Statistics
Matches: 417, Mismatches: 55, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
195 2 0.00
196 30 0.07
197 64 0.15
198 14 0.03
199 96 0.23
200 37 0.09
201 6 0.01
202 1 0.00
203 49 0.12
204 99 0.24
205 19 0.05
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (200 bp):
ATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTTGAAAATACATTATGG
ACACAAAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTATACCTTTTCTCATAAAACC
GGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGG
Found at i:321933 original size:3 final size:3
Alignment explanation
Indices: 321925--321968 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
321915 ACTTTTTTGG
* * * *
321925 ATC ATC ATC ATC ATC ATC ATC TTC ATC TTC ATC GTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
321969 TGACCGCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (3 bp):
ATC
Found at i:323134 original size:14 final size:15
Alignment explanation
Indices: 323102--323152 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
323092 TGATTTCCTC
*
323102 AGAAGAGTTGGGTTG
1 AGAAGAGATGGGTTG
*
323117 AGAAGAGGTGGG-TG
1 AGAAGAGATGGGTTG
323131 AGAAGAGATGGGTTG
1 AGAAGAGATGGGTTG
323146 AGAAGAG
1 AGAAGAG
323153 CCCCGATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.18
Consensus pattern (15 bp):
AGAAGAGATGGGTTG
Found at i:323869 original size:198 final size:198
Alignment explanation
Indices: 323618--324782 Score: 1931
Period size: 198 Copynumber: 5.9 Consensus size: 198
323608 TGACCATTTA
* * * * * *
323618 CATTCTGGACA-AAACGTATCGACGCAAAGTCAAA-GAGTGTAGATACTTTATGTATACATGTTT
1 CATTCTGGACACAAA-GTATCGACACAAA-TTAAACAAGTGTCGATACTTTATGTACACCTGTTT
* * * *
323681 TCTTATAAACTGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATATTTATGGA
64 TCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGG
* *
323746 TCTCGATGTTTTTAGGATCGATACTTATTATAAATGTATCGACACATTTCCATGCACTTGGTAAG
129 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAG
323811 GAAAT
194 GAAAT
* * * *
323816 CATTATGGACACAAAGTATCGACACAAATTCAACAAGTGTTGATACTTTATGTATACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* *
323881 TCATAAACCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTATATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
323946 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
324011 AAT
196 AAT
*
324014 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCAATACTTTATGTACACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
*
324079 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATAGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* *
324144 TCGATATTTTTGGGATCGATACTTTTTATAAATGTATTGACACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
324209 AAT
196 AAT
*
324212 CATTCTGGACACAAAGTATCGACACAAATTAAATAAGTGTCGATACTTTATGTACACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* *
324277 TCATAAACCGGTGTATTTAGACTGGTTAGATTCATAATTTACCTATTATATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
324342 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
324407 AAT
196 AAT
* * *
324410 CATTCCGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* *
324475 TCATAAACCGATGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGTGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* *
324540 TCAATGTTTTTGGGATCGATACTTTTTATAAATGTATCGATACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
324605 AAT
196 AAT
* * *
324608 CATTCTGGACACAAAGTATCGACACAAATTAAATAAGTGTCGATACTTTA-GTACACCTTTTTTT
1 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* *
324672 TCTATAAACCAGTGTATTTAGACCAGTTAGATTCATAATTTACCTATTACATTATAATTATGGGT
66 TC-ATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGT
* *
324737 CTCGATGTTTTTAGGATCGATACTTTTTATAAATTTATCGACACAT
130 CTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAT
324783 ATGTTTACCA
Statistics
Matches: 908, Mismatches: 56, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
197 16 0.02
198 889 0.98
199 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (198 bp):
CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTTTTC
TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
AAT
Found at i:325131 original size:17 final size:17
Alignment explanation
Indices: 325106--325150 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
325096 ATTACATTCA
*
325106 CATAC-AAATTATAAAT
1 CATACAAAATTAAAAAT
325122 CATACAAAATTAAAAAT
1 CATACAAAATTAAAAAT
325139 -ATACAAAATTAA
1 CATACAAAATTAA
325151 CCATACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (17 bp):
CATACAAAATTAAAAAT
Found at i:329210 original size:20 final size:20
Alignment explanation
Indices: 329164--329210 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
329154 ACCGGTAGCG
329164 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
329184 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
329205 -TTTACC
1 CTTTACC
329211 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:329448 original size:182 final size:182
Alignment explanation
Indices: 329140--329785 Score: 785
Period size: 182 Copynumber: 3.6 Consensus size: 182
329130 TAAAATACCA
* * * * * *
329140 ACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA-T
1 ACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCAGTTTTGTCATATT
* * * *
329204 TTTTACCTATTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCTA
66 TTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTA
* *
329269 TAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTATCG
131 TAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATTAATTTATCG
* * **
329322 ACACTTTCAATATATCTGGTAGCTTTTTACCGGTTTTATCATTT-GAGACTTGTTTTGTCATA-T
1 ACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCAGTTTTGTCATATT
*
329385 TCTTACCTGTTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTACCTG-TTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
**
329450 ATAACTTCTTCTC-TTT-AATTCAAAAGTGTCGATACTTATATTAACGTA-CG
130 ATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTATCG
* * *
329500 ACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGTGACC-GGTTTGTCATA-C
1 ACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCAGTTTTGTCATATT
* * * * *
329563 TTATACCTGTTATATTGTTATGGATCGATACGTTTTTTTATAAAGTATCAACACTTTATAGGTGC
66 TTTTACCTGTTATATTGCTATGGATCGATAC--ATTTTTATAAAGTATCGACACTTTATAGGCGC
* *
329628 TATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTT-TATTAAATCTAATCG
129 TATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTATATT-AAT-TTATCG
* * * * * * *
329684 ATACTTTCGATATAT-CAGTAG-TGGTTTACCGGTTTTATCATAAT-GAAACCAGTTTTATCATA
1 ACACTTTCAATATATCCGGTAGCT-CTTTACCGGTTTTATCAT-TTCGAGACCAGTTTTGTCATA
*
329746 TTTTTTTACCTGTTATATTGCTATGGAGCGATACATTTTT
64 -TTTTTTACCTGTTATATTGCTATGGATCGATACATTTTT
329786 CATTTGTATC
Statistics
Matches: 401, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
177 21 0.05
178 61 0.15
179 71 0.18
180 7 0.02
181 34 0.08
182 122 0.30
183 27 0.07
184 30 0.07
186 28 0.07
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
ACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCAGTTTTGTCATATT
TTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTA
TAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTATATTAATTTATCG
Found at i:330589 original size:16 final size:16
Alignment explanation
Indices: 330568--330600 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
330558 AATGTATGAA
330568 TCCTAAAACGCAATGT
1 TCCTAAAACGCAATGT
330584 TCCTAAAACGCAATGT
1 TCCTAAAACGCAATGT
330600 T
1 T
330601 TAATGCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (16 bp):
TCCTAAAACGCAATGT
Found at i:331212 original size:101 final size:101
Alignment explanation
Indices: 331066--331269 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 101
331056 CTTTGTAAAC
331066 AGATCGGATACCAGTGATTAAGTAAAAAAATTAATGGAAAAACTTAAGGATTAAATTGAGTATTA
1 AGATCGGATACCAGTGATTAAGTAAAAAAATTAATGGAAAAACTTAAGGATTAAATTGAGTATTA
*
331131 TGTCGATTAATGATTTGTTTAGAAGGATTAGATGAA
66 TGTCGATTAATGATTTGTTTAGAAGCATTAGATGAA
331167 AGATCGGATACCAGTGATTAAGTAAAAAAATTAATGGAAAAACTTAAGGATTAAATTGAGTATTA
1 AGATCGGATACCAGTGATTAAGTAAAAAAATTAATGGAAAAACTTAAGGATTAAATTGAGTATTA
331232 TGTCGATTAATGATTTGTTTAGAAGCATTAGATGAA
66 TGTCGATTAATGATTTGTTTAGAAGCATTAGATGAA
331268 AG
1 AG
331270 GTCGCGTTTT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (101 bp):
AGATCGGATACCAGTGATTAAGTAAAAAAATTAATGGAAAAACTTAAGGATTAAATTGAGTATTA
TGTCGATTAATGATTTGTTTAGAAGCATTAGATGAA
Found at i:331853 original size:25 final size:25
Alignment explanation
Indices: 331767--331834 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
331757 CCACATGTGT
331767 AATTACACAAGTAC-TTTTAAAAAA
1 AATTACACAAGTACTTTTTAAAAAA
331791 AATTACACAAGTACTTTTTAAAAAA
1 AATTACACAAGTACTTTTTAAAAAA
331816 AATTACACAAGTACTTTTT
1 AATTACACAAGTACTTTTT
331835 TTTTTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 14 0.33
25 29 0.67
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (25 bp):
AATTACACAAGTACTTTTTAAAAAA
Found at i:333452 original size:3 final size:3
Alignment explanation
Indices: 333444--333515 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
333434 TCATTTTCAT
* * * * *
333444 TTA TTA TTA TTA TAA TTA TATA ATA ATA ATA TTA TTA TTA TTA TAAA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA
333491 TGT- TTA TTA -TA TTA TTA -TA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA
333516 ATAAAATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.09
3 48 0.84
4 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:334309 original size:17 final size:18
Alignment explanation
Indices: 334276--334309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
334266 CGGCAGGCGG
334276 CGGTGATCGGCCCGGAAA
1 CGGTGATCGGCCCGGAAA
*
334294 CGGTGGTCGG-CCGGAA
1 CGGTGATCGGCCCGGAA
334310 CTCAGTGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.44, T:0.12
Consensus pattern (18 bp):
CGGTGATCGGCCCGGAAA
Found at i:337199 original size:43 final size:42
Alignment explanation
Indices: 337133--337214 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
337123 TGGCTTTAGA
*
337133 GAAGTTAGGAGGAAAGTTATCCCATATATGTAAAGTTTTGTT
1 GAAGTTAGGACGAAAGTTATCCCATATATGTAAAGTTTTGTT
* *
337175 GAAGTTAGGACCGAAAGTTGTCCCATTTATGTAAAGTTTT
1 GAAGTTAGGA-CGAAAGTTATCCCATATATGTAAAGTTTT
337215 TTTTGATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 10 0.28
43 26 0.72
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (42 bp):
GAAGTTAGGACGAAAGTTATCCCATATATGTAAAGTTTTGTT
Found at i:340673 original size:31 final size:32
Alignment explanation
Indices: 340635--340695 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
340625 CCTGGAAATA
* *
340635 AGAAGTATCTCTA-CGGATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATAAGCATAACAACG
340666 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
340696 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACG
Found at i:345313 original size:45 final size:45
Alignment explanation
Indices: 345259--345452 Score: 298
Period size: 45 Copynumber: 4.3 Consensus size: 45
345249 GGGAGCTTTT
* * *
345259 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
*
345304 TGATGTTTTCAAAACCTTCGGGTAATATGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
345349 TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
* ** * *
345394 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
*
345439 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
345453 AGCCTTTGGG
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
Found at i:345541 original size:45 final size:45
Alignment explanation
Indices: 345470--345898 Score: 614
Period size: 45 Copynumber: 9.5 Consensus size: 45
345460 GGGAGCTTTT
*
345470 TGATATTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
*
345515 TGAAT-TTTTCAAAACCTTCGGATCATCTGTAAGT-CCTTCAGTGCA
1 TG-ATGTTTTCAAAACCTTCGGGTCATCTGTAA-TCCCTTCAGTGCA
*
345560 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
* *
345605 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
*
345650 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGT-CCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAA-TCCCTTCAGTGCA
*
345695 GGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
* *
345740 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTACA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
* *
345785 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGT-CCTTCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAA-TCCCTTCAGTGCA
* ** ** *
345830 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
*
345875 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
345899 AGTTTTTTGA
Statistics
Matches: 349, Mismatches: 25, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
44 3 0.01
45 331 0.95
46 7 0.02
47 8 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCA
Found at i:345717 original size:135 final size:135
Alignment explanation
Indices: 345470--346270 Score: 1120
Period size: 135 Copynumber: 6.0 Consensus size: 135
345460 GGGAGCTTTT
* *
345470 TGATATTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGAAT-TTTTCAAAACCTTC
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG-ATGTTTTCAAAACCTTC
* *
345534 -GGATCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTT
65 AGG-TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTT
345598 CAGTGCA
129 CAGTGCA
* *
345605 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
* * *
345670 GGTCATCTATAAGTCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCTGTAA-TCCCTTC
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGT-CCTTC
345734 AGTGCA
130 AGTGCA
*
345740 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
* * * ** * *
345805 GGTCATCTGTAAGTCCTTCAATGCATGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCA
345870 GTGCA
131 GTGCA
*
345875 GGATGTTTTCAAAAAGCCTTCGGG--AGT-T-T------TT---TG-AT-A--TTTTCAAAACCT
1 TGATGTTTTC-AAAA-CCTTCGGGTCA-TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* *
345923 TCGGGTCATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCT
63 TCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCT
345988 TCAGTGCA
128 TCAGTGCA
* *
345996 TAATGTTTTCAAAACCTTCGGGTCATCTTTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
* *
346061 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCA
*
346126 GTGTA
131 GTGCA
* * *
346131 GGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCAGGATGTTTTCAAAACCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
* * *
346196 GGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAATCTTCGGGTCATCTGTAAGTCCTACA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCA
346261 GTGCA
131 GTGCA
*
346266 AGATG
1 TGATG
346271 ATAAAACCTC
Statistics
Matches: 595, Mismatches: 47, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
119 8 0.01
120 5 0.01
121 86 0.14
122 1 0.00
123 1 0.00
124 2 0.00
125 1 0.00
128 4 0.01
131 2 0.00
132 2 0.00
133 1 0.00
134 3 0.01
135 464 0.78
136 7 0.01
137 8 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (135 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCA
GTGCA
Found at i:345957 original size:76 final size:74
Alignment explanation
Indices: 345830--345972 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
345820 CTTCAATGCA
345830 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTC-AAAA-CCTT
345895 CGGGAGTTTTT
64 CGGGAGTTTTT
** * * **
345906 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAACCTTCG
345971 GG
66 GG
345973 TCATCTGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 49 0.80
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAACCTTCG
GGAGTTTTT
Found at i:345960 original size:45 final size:45
Alignment explanation
Indices: 345906--346270 Score: 559
Period size: 45 Copynumber: 8.1 Consensus size: 45
345896 GGGAGTTTTT
*
345906 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
345951 TTATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
345996 TAATGTTTTCAAAACCTTCGGGTCATCTTTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
346041 TGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
346086 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
346131 GGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
346176 GGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
346221 TGATGTTTTCAAAATCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
346266 AGATG
1 TGATG
346271 ATAAAACCTC
Statistics
Matches: 295, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 295 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:346076 original size:436 final size:436
Alignment explanation
Indices: 345264--346257 Score: 1740
Period size: 436 Copynumber: 2.3 Consensus size: 436
345254 CTTTTTGATA
* *
345264 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAA
1 TTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* * * *
345329 TATGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATCTGTAAGTCCTTCAGTGCA
66 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAATGCA
*
345394 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
131 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
* *
345459 TGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGAATTTTT
196 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAATTTTT
*
345524 CAAAACCTTCGGATCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTG
261 CAAAACCTTCGGATCATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCTG
** *
345589 TAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGAT
326 TAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCATGAT
345654 GTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCAGGATG
391 GTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCAGGATG
345700 TTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
1 TTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
* *
345765 TCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGTCCTTCAATGCA
66 TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAATGCA
345830 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
131 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
* *
345895 CGGGAGTTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT-TATGTTT
196 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAAT-TTT
*
345959 TCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCT
260 TCAAAACCTTCGGATCATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCT
*
346024 TTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCATGA
325 GTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCATGA
*
346089 TGTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGTAGGATG
390 TGTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCAGGATG
* *
346136 TTTTCAAAACCTTCGGGTCATCTGTAAGT-CCTTCAGTGCAGGATGTTTTCAAAACCTTCAGGTC
1 TTTTCAAAACCTTCGGGTCATCTGTAA-TCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
* *
346200 ATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAATCTTCGGGTCATCTGTAAGTCCT
65 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCT
346258 ACAGTGCAAG
Statistics
Matches: 530, Mismatches: 26, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
435 2 0.00
436 527 0.99
437 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (436 bp):
TTTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
TCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAATGCA
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAATTTTT
CAAAACCTTCGGATCATCTGTAAGTCCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCTG
TAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAGTGCATGAT
GTTTTCAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCAGGATG
Found at i:346462 original size:3 final size:3
Alignment explanation
Indices: 346454--346501 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
346444 TAATTATTTA
* *
346454 ATT ATT ATT ATT ATT ATA AAT ATTT ATT A-T ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
346498 ATT A
1 ATT A
346502 ATAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:346482 original size:16 final size:17
Alignment explanation
Indices: 346446--346512 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
346436 TTTTATTTTA
*
346446 ATTATT-TAATTATTATT
1 ATTATTATAAATA-TATT
346463 ATTATTATAAATAT-TT
1 ATTATTATAAATATATT
* *
346479 ATTA-TATTATTATATT
1 ATTATTATAAATATATT
346495 ATTATTAATAAATA-ATT
1 ATTATT-ATAAATATATT
346512 A
1 A
346513 CAAATACATT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 7 0.17
16 12 0.29
17 12 0.29
18 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTATAAATATATT
Found at i:346931 original size:22 final size:22
Alignment explanation
Indices: 346896--346938 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
346886 TTGGTCACTA
346896 AATTCAATTTATAA-TTATTTC
1 AATTCAATTTATAATTTATTTC
*
346917 AATTCGATCTTATAATTTATTT
1 AATTCAAT-TTATAATTTATTT
346939 TATTTTAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTCAATTTATAATTTATTTC
Found at i:350453 original size:16 final size:16
Alignment explanation
Indices: 350432--350466 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
350422 CTGCACTTGG
350432 TCTGGACCTCAGTTGC
1 TCTGGACCTCAGTTGC
*
350448 TCTGGACCTCGGTTGC
1 TCTGGACCTCAGTTGC
350464 TCT
1 TCT
350467 AAGGCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.31, G:0.26, T:0.34
Consensus pattern (16 bp):
TCTGGACCTCAGTTGC
Found at i:362790 original size:81 final size:81
Alignment explanation
Indices: 362689--362856 Score: 300
Period size: 81 Copynumber: 2.1 Consensus size: 81
362679 TTCAATCCCA
* *
362689 AAAGAAAGTATAGCCCTTTGAGTTAGCTGGCTTTGTCTTTTTGATGAGTTTATTCACGCTGAAGA
1 AAAGAAAGTATAGCCCTTTGAGTTAGCTGGCTTTGCCTTTCTGATGAGTTTATTCACGCTGAAGA
362754 CGACGGTCCTCTAGAC
66 CGACGGTCCTCTAGAC
*
362770 AAAGAAAGTATAGCCCTTTGAGTTAGGTGGCTTTGCCTTTCTGATGAGTTTATTCACGCTGAAGA
1 AAAGAAAGTATAGCCCTTTGAGTTAGCTGGCTTTGCCTTTCTGATGAGTTTATTCACGCTGAAGA
*
362835 CGACGGTCCTTTAGAC
66 CGACGGTCCTCTAGAC
362851 AAAGAA
1 AAAGAA
362857 GAAGGTAGAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (81 bp):
AAAGAAAGTATAGCCCTTTGAGTTAGCTGGCTTTGCCTTTCTGATGAGTTTATTCACGCTGAAGA
CGACGGTCCTCTAGAC
Found at i:363952 original size:53 final size:53
Alignment explanation
Indices: 363872--363978 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
363862 TATCAGAATA
363872 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
1 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
* **
363925 TGATAAGGATATACAATCAAGTTGAGAAAGTCAAAGGTGAAAATCAAGGGATT
1 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
363978 T
1 T
363979 TCACGTTTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (53 bp):
TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
Found at i:368107 original size:53 final size:53
Alignment explanation
Indices: 368027--368133 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
368017 CGCGGGGGCA
368027 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
1 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
* *
368080 TGATAAGGATATACAATCAAGTTGAGAAAGTCAAAGGAGAAAATCAAGGGATT
1 TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
368133 T
1 T
368134 TCACGTTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.21
Consensus pattern (53 bp):
TGATAAGGATATACAATCAAATTGAGAAAGTCAAAGAAGAAAATCAAGGGATT
Found at i:369080 original size:15 final size:14
Alignment explanation
Indices: 369060--369102 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
369050 ACTAAGAGAG
369060 AACAAAAACAAAGAA
1 AACAAAAACAAA-AA
*
369075 AACAAAGAACAAAAT
1 AACAAA-AACAAAAA
*
369090 AACAAAAAGAAAA
1 AACAAAAACAAAA
369103 TAGAATGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 6 0.24
ACGTcount: A:0.79, C:0.12, G:0.07, T:0.02
Consensus pattern (14 bp):
AACAAAAACAAAAA
Found at i:369507 original size:2 final size:2
Alignment explanation
Indices: 369502--369531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
369492 TATTTTTTAA
369502 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
369532 TTCTATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:373092 original size:26 final size:24
Alignment explanation
Indices: 373055--373104 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
373045 GACCTAGTAG
373055 TTTTAATATATATTTTTTAATTTTAA
1 TTTTAATATATA-TTTTT-ATTTTAA
373081 TTTTAAGT-TATATTTTTATTTTAA
1 TTTTAA-TATATATTTTTATTTTAA
373105 GTTCCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 5 0.22
26 10 0.43
27 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTAATATATATTTTTATTTTAA
Found at i:373120 original size:24 final size:22
Alignment explanation
Indices: 373064--373120 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
373054 GTTTTAATAT
373064 ATATTTTTTAATTTTAATTTTA
1 ATATTTTTTAATTTTAATTTTA
373086 AGTTATATTTTT-ATTTTAAGTTCCTTA
1 A--TAT-TTTTTAATTTTAA-TT--TTA
373113 ATATTTTT
1 ATATTTTT
373121 ACCTTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
22 1 0.03
24 14 0.48
25 10 0.34
27 4 0.14
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
ATATTTTTTAATTTTAATTTTA
Found at i:374398 original size:23 final size:23
Alignment explanation
Indices: 374372--374415 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
374362 TCCGAGAAAA
*
374372 AAAGA-AAAGCATACCATAAATGT
1 AAAGATAAA-CATACCACAAATGT
374395 AAAGATAAACATACCACAAAT
1 AAAGATAAACATACCACAAAT
374416 ACAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAGATAAACATACCACAAATGT
Found at i:380281 original size:12 final size:12
Alignment explanation
Indices: 380264--380289 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
380254 CGAGATAATG
380264 TTCTCTCTCTCT
1 TTCTCTCTCTCT
380276 TTCTCTCTCTCT
1 TTCTCTCTCTCT
380288 TT
1 TT
380290 GTGGTCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTCTCTCTCT
Found at i:382060 original size:26 final size:27
Alignment explanation
Indices: 382000--382074 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
381990 TGCAAGATAG
*
382000 TTTTTTTAACTTT-ATTTTTTTTTGAA
1 TTTTTTTAACTTTAATTTTTTTATGAA
**
382026 TTTGATTAA-TTTAATTTTTTTAT-AA
1 TTTTTTTAACTTTAATTTTTTTATGAA
* *
382051 TATTTTTTAATTTTAATTATTTTA
1 T-TTTTTTAACTTTAATTTTTTTA
382075 GATATAGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 6 0.15
26 22 0.55
27 12 0.30
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTTTAACTTTAATTTTTTTATGAA
Found at i:390701 original size:10 final size:10
Alignment explanation
Indices: 390671--390704 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
390661 TATTTGGGTG
390671 TTATGTAAGC
1 TTATGTAAGC
*
390681 TTAAGTAAAGC
1 TTATGT-AAGC
390692 TTATGTAAGC
1 TTATGTAAGC
390702 TTA
1 TTA
390705 AAACACCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (10 bp):
TTATGTAAGC
Found at i:391231 original size:24 final size:24
Alignment explanation
Indices: 391204--391264 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
391194 GCATGGATAG
391204 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCACATGTTAAGGAA
391228 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCACATGTTAAGGAA
*
391252 TACATCGATGCAC
1 TGCATCGATGCAC
391265 TGTAGAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGAA
Found at i:391994 original size:16 final size:16
Alignment explanation
Indices: 391973--392021 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
391963 TAAAAGGTAA
391973 TGCCCATGTCATGTGT
1 TGCCCATGTCATGTGT
391989 TGCCCATGTCATGTGT
1 TGCCCATGTCATGTGT
*
392005 TGCCCATGACATGTGT
1 TGCCCATGTCATGTGT
392021 T
1 T
392022 ATGAGAGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.37
Consensus pattern (16 bp):
TGCCCATGTCATGTGT
Found at i:392090 original size:18 final size:18
Alignment explanation
Indices: 392067--392127 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
392057 ATGGATTAAC
*
392067 AGTGGTACTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
392085 AGTGGTCCTTCAGGACAC
1 AGTGGTCCTTCGGGACAT
392103 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
392121 AGTGGTC
1 AGTGGTC
392128 TTATGGGACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:392135 original size:18 final size:18
Alignment explanation
Indices: 392067--392137 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
392057 ATGGATTAAC
* *
392067 AGTGGTACTTCGGGACAT
1 AGTGGTCCTTAGGGACAT
*
392085 AGTGGTCCTTCA-GGACAC
1 AGTGGTCCTT-AGGGACAT
*
392103 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTAGGGACAT
392121 AGTGGT-CTTATGGGACA
1 AGTGGTCCTTA-GGGACA
392138 AATTCTACGC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.07
18 41 0.93
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTAGGGACAT
Found at i:413916 original size:23 final size:22
Alignment explanation
Indices: 413871--413917 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
413861 TATGTTCAGA
*
413871 ATTTTTTTAAAAATTAAACAAT
1 ATTTTTTTAAAAAATAAACAAT
413893 ATTTTATTTAAAAAAATAAA-AAT
1 ATTTT-TTT-AAAAAATAAACAAT
413916 AT
1 AT
413918 AAATGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTTTAAAAAATAAACAAT
Found at i:414673 original size:22 final size:22
Alignment explanation
Indices: 414645--414687 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
414635 TATACATAGA
414645 TAGTTTATCAAGTAAGATTGAG
1 TAGTTTATCAAGTAAGATTGAG
414667 TAGTTTATCAAGTAAGATTGA
1 TAGTTTATCAAGTAAGATTGA
414688 AGGGTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (22 bp):
TAGTTTATCAAGTAAGATTGAG
Found at i:417260 original size:20 final size:20
Alignment explanation
Indices: 417237--417325 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
417227 GAACTCTAAT
417237 TTCGCAACACAATTTCCAAA
1 TTCGCAACACAATTTCCAAA
* *
417257 TTCGCAACTCAGTTTCTGC-AA
1 TTCGCAACACAATTTC--CAAA
* *
417278 -TCGCAACGCGATTTCCAAA
1 TTCGCAACACAATTTCCAAA
417297 TTCGCAACACGGAATTT-CAAA
1 TTCGCAACAC--AATTTCCAAA
417318 TTCGCAAC
1 TTCGCAAC
417326 GTGAATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 34 0.61
21 14 0.25
22 5 0.09
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (20 bp):
TTCGCAACACAATTTCCAAA
Found at i:417361 original size:20 final size:21
Alignment explanation
Indices: 417318--417386 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 21
417308 GAATTTCAAA
* * *
417318 TTCGCAACGTGAATTTTTTTT
1 TTCGCAACGCGAAGTTTCTTT
417339 TTCGCAACGCGAA-TTTCTTT
1 TTCGCAACGCGAAGTTTCTTT
* *
417359 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACGCGAAGTTTCTTT
417379 TTCGCAAC
1 TTCGCAAC
417387 AAGATTTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.05
20 29 0.67
21 12 0.28
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.41
Consensus pattern (21 bp):
TTCGCAACGCGAAGTTTCTTT
Found at i:417395 original size:20 final size:20
Alignment explanation
Indices: 417337--417395 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
417327 TGAATTTTTT
** *
417337 TTTTCGCAACGCGAATTTCT
1 TTTTCGCAACAAGAATTTCC
*
417357 TTTTCGCAACACA-AGTTTCC
1 TTTTCGCAACA-AGAATTTCC
*
417377 TTTTCGCAACAAGATTTTC
1 TTTTCGCAACAAGAATTTC
417396 TAAATCGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (20 bp):
TTTTCGCAACAAGAATTTCC
Found at i:418409 original size:24 final size:24
Alignment explanation
Indices: 418382--418428 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
418372 GTATTCGAAA
418382 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
418406 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
418429 TTTTTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:420715 original size:18 final size:18
Alignment explanation
Indices: 420692--420727 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
420682 AAGCAAAAGG
420692 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
420710 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
420728 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:421036 original size:20 final size:20
Alignment explanation
Indices: 420979--421029 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
420969 CTTAAATCGC
*
420979 GTTGCGATTTTCATTTTCGT
1 GTTGCGAATTTCATTTTCGT
420999 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTCATTTTCGT
421019 GTTGCGAATTT
1 GTTGCGAATTT
421030 AAGTTTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGAATTTCATTTTCGT
Found at i:421383 original size:22 final size:22
Alignment explanation
Indices: 421358--421412 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
421348 ATAGAGGGGG
*
421358 GTCGCCGGATATG-GGAACGGAT
1 GTCGCCGGAGATGAGG-ACGGAT
421380 GTCGCCGGAGATGAGGACGGAT
1 GTCGCCGGAGATGAGGACGGAT
*
421402 GTCGCTGGAGA
1 GTCGCCGGAGA
421413 GAGTGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.22, C:0.18, G:0.44, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGAGGACGGAT
Found at i:421626 original size:20 final size:20
Alignment explanation
Indices: 421603--421653 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
421593 GCGTTGCAAT
421603 TTACATATTCGTGTTACGAA
1 TTACATATTCGTGTTACGAA
*
421623 TTACATATTTGTGTTACGAA
1 TTACATATTCGTGTTACGAA
421643 TTACATATTCG
1 TTACATATTCG
421654 CGTTGCGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (20 bp):
TTACATATTCGTGTTACGAA
Found at i:422280 original size:42 final size:42
Alignment explanation
Indices: 422207--422420 Score: 143
Period size: 42 Copynumber: 5.2 Consensus size: 42
422197 CTCTTACAAG
* *
422207 GCGGCGTTTTTGTAATAAACGCTGCAGTAGTCATGCACCTTA
1 GCGGCGTTTTTGTAACAAACGCTGCAATAGTCATGCACCTTA
* * * *
422249 GCGGTGTTTTTGTAACAAATGTTGCAATAGTCATGCACTTTA
1 GCGGCGTTTTTGTAACAAACGCTGCAATAGTCATGCACCTTA
** * ** * * ** *
422291 GCAACG-TTTT-T-ATAAACGCCACAATAATCTTGTGCTTTA
1 GCGGCGTTTTTGTAACAAACGCTGCAATAGTCATGCACCTTA
* * * * *
422330 GTGGCGTTTTT-TTATAAACGTTGCAATAGTCATGCA-CTTT
1 GCGGCGTTTTTGTAACAAACGCTGCAATAGTCATGCACCTTA
* * * *
422370 GTGGCGTTTTTGGAATAAACG-TCGCAATAGTCATGCACTTTA
1 GCGGCGTTTTTGTAACAAACGCT-GCAATAGTCATGCACCTTA
*
422412 GTGGCGTTT
1 GCGGCGTTT
422421 AGTCATACAC
Statistics
Matches: 133, Mismatches: 34, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
39 22 0.17
40 20 0.15
41 41 0.31
42 50 0.38
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (42 bp):
GCGGCGTTTTTGTAACAAACGCTGCAATAGTCATGCACCTTA
Found at i:422357 original size:41 final size:41
Alignment explanation
Indices: 422209--422420 Score: 171
Period size: 41 Copynumber: 5.2 Consensus size: 41
422199 CTTACAAGGC
* * * *
422209 GGCGTTTTTGTAATAAACG-CTGCAGTAGTCATGCACCTTAGC
1 GGCGTTTTT-TTATAAACGTC-GCAATAGTCATGCACTTTAGT
* * * * * *
422251 GGTGTTTTTGTAACAAATGTTGCAATAGTCATGCACTTTAGC
1 GGCGTTTTT-TTATAAACGTCGCAATAGTCATGCACTTTAGT
** * * * * **
422293 AACG--TTTTTATAAACGCCACAATAATCTTGTGCTTTAGT
1 GGCGTTTTTTTATAAACGTCGCAATAGTCATGCACTTTAGT
*
422332 GGCGTTTTTTTATAAACGTTGCAATAGTCATGCACTTT-GT
1 GGCGTTTTTTTATAAACGTCGCAATAGTCATGCACTTTAGT
**
422372 GGCGTTTTTGGAATAAACGTCGCAATAGTCATGCACTTTAGT
1 GGCGTTTTT-TTATAAACGTCGCAATAGTCATGCACTTTAGT
422414 GGCGTTT
1 GGCGTTT
422421 AGTCATACAC
Statistics
Matches: 133, Mismatches: 32, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
39 23 0.17
40 14 0.11
41 51 0.38
42 45 0.34
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (41 bp):
GGCGTTTTTTTATAAACGTCGCAATAGTCATGCACTTTAGT
Found at i:422676 original size:14 final size:14
Alignment explanation
Indices: 422641--422690 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
422631 TAACACCCAA
* *
422641 CCATCACAGTGAAG
1 CCATCACCGTGCAG
*
422655 CCACCACCGTGCAG
1 CCATCACCGTGCAG
422669 CCATCACCGTGCAG
1 CCATCACCGTGCAG
422683 CCATCACC
1 CCATCACC
422691 ACAATCGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.26, C:0.44, G:0.18, T:0.12
Consensus pattern (14 bp):
CCATCACCGTGCAG
Found at i:424700 original size:96 final size:97
Alignment explanation
Indices: 424536--424768 Score: 432
Period size: 96 Copynumber: 2.4 Consensus size: 97
424526 AGATAACATA
*
424536 ATTACTTAACATTTGGTTAGAACATGCCTTAGAGGCGTTTTGTGAATAAAAATGCCACGACAAGT
1 ATTACTTAACATTTGGTTATAACATGCCTTAGAGGCGTTTTGTGAATAAAAATGCCACGACAAGT
424601 CATGACTATTAACGACGTTTGGGTG-AAAATG
66 CATGACTATTAACGACGTTTGGGTGAAAAATG
424632 ATTACTTAACATTTGGTTATAACATGCCTTAGAGGCGTTTTGTGAATAAAAATGCCACGACAAGT
1 ATTACTTAACATTTGGTTATAACATGCCTTAGAGGCGTTTTGTGAATAAAAATGCCACGACAAGT
*
424697 CATGACTATTAACGATGTTTGGGTGAAAAATG
66 CATGACTATTAACGACGTTTGGGTGAAAAATG
*
424729 ATTACTTAACATTTGGTTATAACATGCCTTAGAGACGTTT
1 ATTACTTAACATTTGGTTATAACATGCCTTAGAGGCGTTT
424769 GGGTGAAATT
Statistics
Matches: 133, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 88 0.66
97 45 0.34
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (97 bp):
ATTACTTAACATTTGGTTATAACATGCCTTAGAGGCGTTTTGTGAATAAAAATGCCACGACAAGT
CATGACTATTAACGACGTTTGGGTGAAAAATG
Found at i:428390 original size:15 final size:15
Alignment explanation
Indices: 428370--428398 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
428360 CGAATTAGCC
428370 ATTATGATTTTAATA
1 ATTATGATTTTAATA
428385 ATTATGATTTTAAT
1 ATTATGATTTTAAT
428399 CAAACAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTATGATTTTAATA
Found at i:429027 original size:123 final size:124
Alignment explanation
Indices: 428794--429019 Score: 321
Period size: 123 Copynumber: 1.8 Consensus size: 124
428784 AATAATTACA
* * * * *
428794 TTTTAATATATATTTATTTTTCAATATTAAGAAATGACAGTCTTAAAGCAATTGGATGTTCATTT
1 TTTTAATATATATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATTT
* *
428859 TCTGATATTTTTAAATAAATAAATATCTTAATTTTATAAATTATATCTATAGATAAATG
66 TCTGATATTTCTAAATAAATAAATATCTTAATCTTATAAATTATATCTATAGATAAATG
* * * *
428918 TTTTAATATTTATTTATTTTT-AATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAG-CCCTT
1 TTTTAATATATATTTATTTTTCAATATTAAGAAAAGA-CAGTCTTAAAGCAACTAGAAGTCCATT
428981 TTCTGATATTTCTAAATAAATAAATATCTTATATCTTAT
65 TTCTGATATTTCTAAATAAATAAATATCTTA-ATCTTAT
429020 TTATATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
123 47 0.53
124 42 0.47
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (124 bp):
TTTTAATATATATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATTT
TCTGATATTTCTAAATAAATAAATATCTTAATCTTATAAATTATATCTATAGATAAATG
Found at i:429544 original size:27 final size:27
Alignment explanation
Indices: 429514--429580 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
429504 AAATTCAAGT
* *
429514 TATACTTCTTTTTTTAAAATTTTTATA
1 TATACTTATTTTTTTAAAATATTTATA
* * *
429541 TATACTTATTATTTTCATATATTTATA
1 TATACTTATTTTTTTAAAATATTTATA
429568 TATA-TTATTTTTT
1 TATACTTATTTTTT
429581 ATTAATGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (27 bp):
TATACTTATTTTTTTAAAATATTTATA
Found at i:442032 original size:113 final size:113
Alignment explanation
Indices: 441834--442513 Score: 994
Period size: 113 Copynumber: 6.0 Consensus size: 113
441824 TATCAAAGAT
* *
441834 TTGAATTCATCACTTGATGGATCAACTTTTCCATAAGGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* **
441899 AGAAGGAAAAAGAAGTTCATAATGAGAAGAAAATGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
441947 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* *
442012 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTATGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* *
442060 TTGAATTCATCACTTGATGGATCACCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCTTCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
*
442125 AGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
442173 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
*
442238 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* *
442286 TTGAATTCATCACTCGATGGATCAACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* * *
442350 AG-AGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
** * *
442396 TTG-ATTCTATCACAGAAGGAGATAGATCAACATCAATATTTCCAGAAG-TGTTCATAATGAGAA
1 TTGAATTC-ATCAC-----TTGATGGATC-A-A-C--T-TTTCCAGAAGAAGTTCATAATGAGAA
* * * *
442459 GAACTCATCTGAAGAATG-AGAAGAAGTTCATAATAAGAATAACTTGTTCAACCTT
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTT
442514 AATTTGATTC
Statistics
Matches: 525, Mismatches: 28, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
109 4 0.01
110 13 0.02
111 37 0.07
112 29 0.06
113 359 0.68
115 7 0.01
116 1 0.00
117 1 0.00
118 1 0.00
121 70 0.13
122 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
TTGAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
Found at i:442437 original size:121 final size:120
Alignment explanation
Indices: 442306--442527 Score: 347
Period size: 121 Copynumber: 1.8 Consensus size: 120
442296 CACTCGATGG
*
442306 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAATAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATA
* **
442370 ATGAGAAGAACTTGTTCAACCTTTGTTTGATTCTATCACAGAAGGAGATAGATCAAC
65 ATAAGAAGAACTTGTTCAACCTTAATTTGATTC-ATCACAGAAGGAGATAGATCAAC
* * *
442427 ATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAATGAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*
442492 TAAGAATAACTTGTTCAACCTTAATTTGATTCATCA
66 TAAGAAGAACTTGTTCAACCTTAATTTGATTCATCA
442528 TCTATTGAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
120 4 0.04
121 86 0.93
122 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (120 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
TAAGAAGAACTTGTTCAACCTTAATTTGATTCATCACAGAAGGAGATAGATCAAC
Found at i:444335 original size:3 final size:3
Alignment explanation
Indices: 444327--444352 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
444317 AATATATTTA
444327 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
444353 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:450062 original size:18 final size:18
Alignment explanation
Indices: 450041--450077 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
450031 GTCTTCTGGA
450041 TCTTCAGCG-TCAGCAGGC
1 TCTTCAG-GTTCAGCAGGC
450059 TCTTCAGGTTCAGCAGGC
1 TCTTCAGGTTCAGCAGGC
450077 T
1 T
450078 GGGGACTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (18 bp):
TCTTCAGGTTCAGCAGGC
Found at i:468809 original size:139 final size:138
Alignment explanation
Indices: 468545--468809 Score: 512
Period size: 139 Copynumber: 1.9 Consensus size: 138
468535 CTTGCAACAG
468545 AACCATCCGGCAACAATAACAAAATGGACAATAACAAAAGGTACAAGTACAACCTTAAGTCATCA
1 AACCATCCGGCAACAATAACAAAATGGACAATAACAAAAGGTACAAGTACAACCTTAAGTCATCA
468610 TTTCAAACCCACCTGAAAAGCTGACAGCAAAGTAACAACAATATGGATACAGACTTGATCCGGCA
66 TTTCAAACCCACCTGAAAAGCTGACAGCAAAGTAACAACAATATGGATACAGACTTGATCCGGCA
468675 AAGTACAA
131 AAGTACAA
468683 AACCATCCGGCAACAATAACAAAATGGACAATAACAAAAGGTACAAGTACAACCTTAAGTCATTC
1 AACCATCCGGCAACAATAACAAAATGGACAATAACAAAAGGTACAAGTACAACCTTAAGTCA-TC
*
468748 ATTTCAAACCCACCTGAAGAGCTGACAGCAAAGTAACAACAATATGGATACAGACTTGATCC
65 ATTTCAAACCCACCTGAAAAGCTGACAGCAAAGTAACAACAATATGGATACAGACTTGATCC
468810 TTCTAACATT
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
138 62 0.50
139 63 0.50
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.17
Consensus pattern (138 bp):
AACCATCCGGCAACAATAACAAAATGGACAATAACAAAAGGTACAAGTACAACCTTAAGTCATCA
TTTCAAACCCACCTGAAAAGCTGACAGCAAAGTAACAACAATATGGATACAGACTTGATCCGGCA
AAGTACAA
Found at i:473403 original size:22 final size:22
Alignment explanation
Indices: 473372--473426 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
473362 CTTAGCATTA
*
473372 ATACTAAAGTGC-CTCAACACTG
1 ATACAAAAGTGCACTC-ACACTG
* *
473394 ATATAAAAGTGCATTCACACTG
1 ATACAAAAGTGCACTCACACTG
473416 ATACAAAAGTG
1 ATACAAAAGTG
473427 TTATAGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
ATACAAAAGTGCACTCACACTG
Found at i:476823 original size:22 final size:22
Alignment explanation
Indices: 476794--476847 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
476784 ATTAATTAAT
*
476794 CAGATCAATTAAGAAAATGTTA
1 CAGATCAATTAAGAAAATGCTA
*
476816 CATATCAATTAAGAAAATGCTA
1 CAGATCAATTAAGAAAATGCTA
476838 CAGATCAATT
1 CAGATCAATT
476848 TTATCACCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (22 bp):
CAGATCAATTAAGAAAATGCTA
Found at i:480009 original size:19 final size:19
Alignment explanation
Indices: 479974--480011 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
479964 ATACACATCG
*
479974 TGTTTATATATTTTAAAAA
1 TGTTTATATATTATAAAAA
479993 TGTTTATAT-TTAATAAAAA
1 TGTTTATATATT-ATAAAAA
480012 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TGTTTATATATTATAAAAA
Found at i:480193 original size:28 final size:28
Alignment explanation
Indices: 480156--480220 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
480146 TGATAGAGAT
480156 GACGCTAGACATGGATAATGAGTCGGAC
1 GACGCTAGACATGGATAATGAGTCGGAC
480184 GACGCTAGACATGGATAATGAGTCGGAC
1 GACGCTAGACATGGATAATGAGTCGGAC
480212 GACGCTAGA
1 GACGCTAGA
480221 GAGGGACAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.17
Consensus pattern (28 bp):
GACGCTAGACATGGATAATGAGTCGGAC
Found at i:491452 original size:60 final size:60
Alignment explanation
Indices: 491379--491529 Score: 232
Period size: 60 Copynumber: 2.5 Consensus size: 60
491369 GTTGCTTTAG
*
491379 TAAGTC-CTCCGACTATTAAAAGTTACAAAATAATATTTTGACTATAGAGAATTACTTTGT
1 TAAGTCTCT-CGACTATTAAAAGTTACAAAATAATATTTCGACTATAGAGAATTACTTTGT
* *
491439 TAAGTCTCTCGACTATTAAAAGTTACAAAATAATCTTTCGACTATAGGGAATTACTTTGT
1 TAAGTCTCTCGACTATTAAAAGTTACAAAATAATATTTCGACTATAGAGAATTACTTTGT
* * *
491499 TATGTCTATCGACTATTTAAAGTTACAAAAT
1 TAAGTCTCTCGACTATTAAAAGTTACAAAAT
491530 GATCACTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 82 0.98
61 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (60 bp):
TAAGTCTCTCGACTATTAAAAGTTACAAAATAATATTTCGACTATAGAGAATTACTTTGT
Found at i:491453 original size:31 final size:31
Alignment explanation
Indices: 491418--491514 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
491408 ATAATATTTT
*
491418 GACTATAGAGAATTACTTTGTTAAGTCTCTC
1 GACTATAGAGAATTACTTTGTTAAGTCTATC
**** *
491449 GACTATTA-A-AAGTTAC-AAAATAA-TCTTTC
1 GACTA-TAGAGAA-TTACTTTGTTAAGTCTATC
* *
491478 GACTATAGGGAATTACTTTGTTATGTCTATC
1 GACTATAGAGAATTACTTTGTTAAGTCTATC
491509 GACTAT
1 GACTAT
491515 TTAAAGTTAC
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
28 2 0.04
29 14 0.29
30 9 0.19
31 21 0.44
32 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (31 bp):
GACTATAGAGAATTACTTTGTTAAGTCTATC
Found at i:491481 original size:29 final size:29
Alignment explanation
Indices: 491388--491483 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
491378 GTAAGTCCTC
*
491388 CGACTATTAAAAGTTACAAAATAATATTT
1 CGACTATTAAAAGTTACAAAATAATCTTT
* **** *
491417 TGACTA-TAGAGAA-TTACTTTGTTAAGTCTCT
1 CGACTATTA-A-AAGTTAC-AAAATAA-TCTTT
491448 CGACTATTAAAAGTTACAAAATAATCTTT
1 CGACTATTAAAAGTTACAAAATAATCTTT
491477 CGACTAT
1 CGACTAT
491484 AGGGAATTAC
Statistics
Matches: 48, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 10 0.21
31 13 0.27
32 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (29 bp):
CGACTATTAAAAGTTACAAAATAATCTTT
Found at i:493712 original size:20 final size:20
Alignment explanation
Indices: 493687--493740 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
493677 AATATCAGTA
493687 GGGTATCGATACCCTATAGG
1 GGGTATCGATACCCTATAGG
493707 GGGTATCGATACCCTATAGG
1 GGGTATCGATACCCTATAGG
493727 GGGTATCGATACCC
1 GGGTATCGATACCC
493741 CCCTGAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCCTATAGG
Found at i:495177 original size:18 final size:18
Alignment explanation
Indices: 495144--495178 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
495134 CGAGGGTTAC
*
495144 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACAGGACAT
*
495162 AGTGGTCCTTCAGGACA
1 AGTGGTCCTACAGGACA
495179 ATACAATAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACAGGACAT
Found at i:495191 original size:21 final size:21
Alignment explanation
Indices: 495167--495246 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 21
495157 GACATAGTGG
495167 TCCTTCAGGACAATACAATAG-
1 TCCTTCAGGACAATACAAT-GT
495188 TCCTTC-GGAACAATACAATGT
1 TCCTTCAGG-ACAATACAATGT
* *
495209 TCATTCGGGACAATACAATGT
1 TCCTTCAGGACAATACAATGT
495230 TCCTT-AGGGACAATACA
1 TCCTTCA-GGACAATACA
495247 GTGGTCCTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 3 0.06
21 47 0.90
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (21 bp):
TCCTTCAGGACAATACAATGT
Found at i:495254 original size:21 final size:21
Alignment explanation
Indices: 495141--495281 Score: 93
Period size: 21 Copynumber: 7.0 Consensus size: 21
495131 AGTCGAGGGT
495141 TACAGTGGTCC-TACGGGAC-A
1 TACAGTGGTCCTTA-GGGACAA
495161 T--AGTGGTCCTTCA-GGACAA
1 TACAGTGGTCCTT-AGGGACAA
* * * *
495180 TACAATAGTCCTTCGGAACAA
1 TACAGTGGTCCTTAGGGACAA
* * * *
495201 TACAATGTTCATTCGGGACAA
1 TACAGTGGTCCTTAGGGACAA
* *
495222 TACAATGTTCCTTAGGGACAA
1 TACAGTGGTCCTTAGGGACAA
495243 TACAGTGGTCC-TACGGGAC-A
1 TACAGTGGTCCTTA-GGGACAA
*
495263 T--AGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTAGGGACAA
495282 ATTTTAGTGC
Statistics
Matches: 99, Mismatches: 13, Indels: 19
0.76 0.10 0.15
Matches are distributed among these distances:
18 25 0.25
19 5 0.05
20 6 0.06
21 63 0.64
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (21 bp):
TACAGTGGTCCTTAGGGACAA
Found at i:495260 original size:42 final size:42
Alignment explanation
Indices: 495162--495262 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
495152 TACGGGACAT
* *
495162 AGTGGTCCTTCAGGACAATACAATAGTCCTTCGGAACAATAC
1 AGTGGTCCTTCGGGACAATACAATAGTCCTTAGGAACAATAC
* * * *
495204 AATGTTCATTCGGGACAATACAAT-GTTCCTTAGGGACAATAC
1 AGTGGTCCTTCGGGACAATACAATAG-TCCTTAGGAACAATAC
*
495246 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
495263 TAGTGGTCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
AGTGGTCCTTCGGGACAATACAATAGTCCTTAGGAACAATAC
Found at i:495269 original size:18 final size:18
Alignment explanation
Indices: 495246--495280 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
495236 GGGACAATAC
495246 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
*
495264 AGTGGTCCTTCGGGACA
1 AGTGGTCCTACGGGACA
495281 AATTTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:502771 original size:24 final size:24
Alignment explanation
Indices: 502727--502776 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
502717 ATAAAGAACC
*
502727 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
502751 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
502775 AA
1 AA
502777 TTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:503616 original size:7 final size:7
Alignment explanation
Indices: 503606--503632 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
503596 TATGTTATTC
503606 TATGTGT
1 TATGTGT
503613 TATGTGT
1 TATGTGT
503620 TATGTGT
1 TATGTGT
503627 TATGTG
1 TATGTG
503633 ATATATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
TATGTGT
Found at i:503959 original size:21 final size:21
Alignment explanation
Indices: 503934--504027 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
503924 ATAGTGGTCC
503934 TTCGGGACAATACAATAGTCT
1 TTCGGGACAATACAATAGTCT
* *
503955 TTCGGGATAATACAATATTCAT
1 TTCGGGACAATACAATAGTC-T
* * *
503977 TT-GGGATAATACAGT-GTTCC
1 TTCGGGACAATACAATAG-TCT
* *
503997 TTCGGGACAATACAGTGGTCT
1 TTCGGGACAATACAATAGTCT
*
504018 TACGGGACAA
1 TTCGGGACAA
504028 ATTTCAGTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.03
21 55 0.90
22 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (21 bp):
TTCGGGACAATACAATAGTCT
Found at i:504741 original size:21 final size:22
Alignment explanation
Indices: 504708--504748 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
504698 ACGAAATTTA
504708 TGTAGCAAGGGTATCGATACAC
1 TGTAGCAAGGGTATCGATACAC
504730 TGTAGC-AGGGTATCGATAC
1 TGTAGCAAGGGTATCGATAC
504749 CCTTGCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (22 bp):
TGTAGCAAGGGTATCGATACAC
Found at i:507988 original size:55 final size:55
Alignment explanation
Indices: 507916--508033 Score: 202
Period size: 55 Copynumber: 2.2 Consensus size: 55
507906 ATCATCATAT
* * *
507916 ATTTTAT-ATATTTTATTTATATTTTTTATTGAAAATTTATTTTTATTCCTTAAA
1 ATTTTATAATATTTTATTTATATTTTTTATTAAAAAATTATATTTATTCCTTAAA
507970 ATTTTATAATATTTTATTTATATTTTTTATTAAAAAATTATATTTATTCCTTAAA
1 ATTTTATAATATTTTATTTATATTTTTTATTAAAAAATTATATTTATTCCTTAAA
508025 ATTTTATAA
1 ATTTTATAA
508034 ATTCACTCTT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
54 7 0.12
55 53 0.88
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (55 bp):
ATTTTATAATATTTTATTTATATTTTTTATTAAAAAATTATATTTATTCCTTAAA
Found at i:508047 original size:22 final size:22
Alignment explanation
Indices: 508019--508061 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
508009 ATATTTATTC
*
508019 CTTAAAATTTTATAAATTCACT
1 CTTAAAATTTTACAAATTCACT
508041 CTTAAAATTTTACAAATTCAC
1 CTTAAAATTTTACAAATTCAC
508062 GTCCCACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
CTTAAAATTTTACAAATTCACT
Found at i:511154 original size:3 final size:3
Alignment explanation
Indices: 511146--511204 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
511136 CGGGTCTTTT
*
511146 TTA TTA TTA TTTA TATA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
511193 TT- TATA TTA TTA
1 TTA T-TA TTA TTA
511205 CATATTTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 1 0.02
3 43 0.86
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:515785 original size:12 final size:12
Alignment explanation
Indices: 515770--515812 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
515760 GATCAACATT
515770 TTTGCATCTGCA
1 TTTGCATCTGCA
515782 TTTGCATCTTTGCA
1 TTTGCATC--TGCA
*
515796 TTTTGCATCTACA
1 -TTTGCATCTGCA
515809 TTTG
1 TTTG
515813 ATTTAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 12 0.44
13 3 0.11
14 4 0.15
15 8 0.30
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (12 bp):
TTTGCATCTGCA
Found at i:515802 original size:15 final size:14
Alignment explanation
Indices: 515769--515805 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
515759 GGATCAACAT
515769 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
515782 -TTTGCATCTTTGCA
1 TTTTGCATC-TTGCA
515796 TTTTGCATCT
1 TTTTGCATCT
515806 ACATTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTTGCATCTTGCA
Found at i:517124 original size:29 final size:29
Alignment explanation
Indices: 517068--517124 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
517058 TCAATCAAAA
* **
517068 CAAAGAGAAAGGAAGAAAAGGAAAAAGAG
1 CAAAGAGAAAAGAAGAAAAAAAAAAAGAG
517097 CAAAGAGAAAAG-AGAAAAAAAAACAAGA
1 CAAAGAGAAAAGAAGAAAAAAAAA-AAGA
517125 AAGAAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (29 bp):
CAAAGAGAAAAGAAGAAAAAAAAAAAGAG
Found at i:518819 original size:35 final size:35
Alignment explanation
Indices: 518729--518869 Score: 124
Period size: 36 Copynumber: 3.9 Consensus size: 35
518719 TGAGAATTTT
* * *
518729 AAAACAATTTTTTGTCTCGCTTGAGATAATTTTTCTC
1 AAAACAA-ATTTTATCTCGCTTGAGA-CATTTTTCTC
* * * *
518766 AAAACATACTTTGA-CTCGCTTGAGACAGTTTTCTA
1 AAAACA-AATTTTATCTCGCTTGAGACATTTTTCTC
*
518801 AAAACAAATTTTATCTCGCTTAAGACAATTTCTT-TC
1 AAAACAAATTTTATCTCGCTTGAGAC-ATTT-TTCTC
** *
518837 AAAACAAATTTCGTCTCACTTGAGACATTTTTC
1 AAAACAAATTTTATCTCGCTTGAGACATTTTTC
518870 CTTTGAGATA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
34 7 0.08
35 28 0.33
36 37 0.44
37 11 0.13
38 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (35 bp):
AAAACAAATTTTATCTCGCTTGAGACATTTTTCTC
Found at i:518820 original size:71 final size:72
Alignment explanation
Indices: 518729--518869 Score: 171
Period size: 71 Copynumber: 2.0 Consensus size: 72
518719 TGAGAATTTT
* * * * * *
518729 AAAACAATTTTTTGTCTCGCTTGAGATAATTT-TTCTCAAAACATACTTT-GACTCGCTTGAGAC
1 AAAACAATATTTTATCTCGCTTAAGACAATTTCTT-TCAAAACA-AATTTCGACTCACTTGAGAC
518792 AGTTTTCTA
64 AGTTTTCTA
* *
518801 AAAACAA-ATTTTATCTCGCTTAAGACAATTTCTTTCAAAACAAATTTCGTCTCACTTGAGACAT
1 AAAACAATATTTTATCTCGCTTAAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGACAG
518865 TTTTC
66 TTTTC
518870 CTTTGAGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
70 4 0.07
71 46 0.78
72 9 0.15
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (72 bp):
AAAACAATATTTTATCTCGCTTAAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGACAG
TTTTCTA
Found at i:519292 original size:66 final size:63
Alignment explanation
Indices: 519133--519314 Score: 242
Period size: 63 Copynumber: 2.8 Consensus size: 63
519123 AACAAAATGA
* * *
519133 AAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTTTG
1 AAAAATCTTTGAGTATGTTTCTTTGAAAACAAAAGTTTGTCTCTTTTGAGACAGTTTCTTTTG
*
519196 AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAAGTTTGTCTCTTTTGAGACAG-TTCATTTTGA
1 AAAAATCTTTGAGTATGTTTCTTTGAAAACAAAAGTTTGTCTCTTTTGAGACAGTTTC-TTTT--
519260 AG
63 -G
* * *
519262 AAAAATCTTTAAATATGTTT-TTATGAAAACAAAAGTTTGTCTCTTTTAAGACA
1 AAAAATCTTTGAGTATGTTTCTT-TGAAAACAAAAGTTTGTCTCTTTTGAGACA
519315 ATATGTATTA
Statistics
Matches: 106, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
62 3 0.03
63 54 0.51
65 2 0.02
66 47 0.44
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (63 bp):
AAAAATCTTTGAGTATGTTTCTTTGAAAACAAAAGTTTGTCTCTTTTGAGACAGTTTCTTTTG
Found at i:519409 original size:29 final size:29
Alignment explanation
Indices: 519325--519510 Score: 187
Period size: 29 Copynumber: 6.2 Consensus size: 29
519315 ATATGTATTA
* * *
519325 AAACAAACATCCTTGAGATTGTTTCCCTTG
1 AAACAAAAATCTTTGAG-TTGTTTCTCTTG
519355 AAACAAAACCTATCTTTGAGTTTGTTTCTCTTG
1 AAACAAAA---ATCTTTGAG-TTGTTTCTCTTG
*
519388 AAACAAAAATCTGTGAGTTGTTTCTCTTG
1 AAACAAAAATCTTTGAGTTGTTTCTCTTG
* * * *
519417 AAACAATAGTCTGTGAGTTGTTTCTTTTG
1 AAACAAAAATCTTTGAGTTGTTTCTCTTG
*
519446 AAATC-AAAATCTTTGAGTTGTTTCTTTTG
1 AAA-CAAAAATCTTTGAGTTGTTTCTCTTG
* *
519475 AAA-AAAATTCTTTGAGTCTGTTTCTTTTG
1 AAACAAAAATCTTTGAGT-TGTTTCTCTTG
*
519504 AACCAAA
1 AAACAAA
519511 GTTTTGTTTC
Statistics
Matches: 136, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
28 12 0.09
29 78 0.57
30 19 0.14
33 27 0.20
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (29 bp):
AAACAAAAATCTTTGAGTTGTTTCTCTTG
Found at i:519599 original size:29 final size:28
Alignment explanation
Indices: 519325--519599 Score: 180
Period size: 29 Copynumber: 9.2 Consensus size: 28
519315 ATATGTATTA
* **
519325 AAACAAACATCCTTGAGATTGTTTCCCTTG
1 AAACAAA-ATCTTTGAG-TTGTTTCTTTTG
*
519355 AAACAAAACCTATCTTTGAGTTTGTTTCTCTTG
1 AAAC-AAA---ATCTTTGAG-TTGTTTCTTTTG
* *
519388 AAACAAAAATCTGTGAGTTGTTTCTCTTG
1 AAAC-AAAATCTTTGAGTTGTTTCTTTTG
* *
519417 AAACAATAGTCTGTGAGTTGTTTCTTTTG
1 AAACAA-AATCTTTGAGTTGTTTCTTTTG
519446 AAATCAAAATCTTTGAGTTGTTTCTTTTG
1 AAA-CAAAATCTTTGAGTTGTTTCTTTTG
519475 AAA-AAAATTCTTTGAGTCTGTTTCTTTTG
1 AAACAAAA-TCTTTGAGT-TGTTTCTTTTG
* * * * *
519504 AACCAAAGT-TTTG-TTTCTTTAAGACAATTTCG
1 AAACAAAATCTTTGAGTTGTTT----C--TTTTG
** **
519536 TGA-AAAATCTTTGAGTCATTTCTTTTG
1 AAACAAAATCTTTGAGTTGTTTCTTTTG
*
519563 AAACCAAAATCTTTGAGTTTTTTTCTTTTG
1 AAA-CAAAATCTTTGAG-TTGTTTCTTTTG
519593 AAACAAA
1 AAACAAA
519600 GTTTTGTCTC
Statistics
Matches: 200, Mismatches: 26, Indels: 39
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.02
27 10 0.05
28 15 0.08
29 93 0.47
30 32 0.16
31 7 0.04
32 8 0.04
33 31 0.16
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (28 bp):
AAACAAAATCTTTGAGTTGTTTCTTTTG
Found at i:519861 original size:29 final size:30
Alignment explanation
Indices: 519818--519877 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
519808 GAAACAAAAT
*
519818 TATCAATCTTTGAGTCTGTTTCTTTTGAAA
1 TATCAATCTTTGAGTCGGTTTCTTTTGAAA
519848 TATC-ATCTTTGAGTCGGTTTCTTTTGAAA
1 TATCAATCTTTGAGTCGGTTTCTTTTGAAA
519877 T
1 T
519878 CATTATCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (30 bp):
TATCAATCTTTGAGTCGGTTTCTTTTGAAA
Found at i:520235 original size:40 final size:39
Alignment explanation
Indices: 520164--520239 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
520154 CAAAAGATGG
* *
520164 CCAGAACTCTTCATCGCGTATGAGCCTTGTCATCCCCCGA
1 CCAGAACTCCTCATCGCGTATGAGCCGTGTCA-CCCCCGA
* *
520204 CCAGATCTCCTCATCGCGTA-GAAGTCGTGTCACCCC
1 CCAGAACTCCTCATCGCGTATG-AGCCGTGTCACCCC
520240 TAGATAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 5 0.16
40 26 0.84
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (39 bp):
CCAGAACTCCTCATCGCGTATGAGCCGTGTCACCCCCGA
Done.