Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 41 of 42
Found at i:9462890 original size:2 final size:2
Alignment explanation
Indices: 9462879--9462910 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9462869 CCATTCAACC
9462879 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9462911 GACAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9463592 original size:21 final size:20
Alignment explanation
Indices: 9463548--9463613 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
9463538 GATTCGCAAC
9463548 GCGATTTTAACAATCGCATT
1 GCGATTTTAACAATCGCATT
*
9463568 GCGATTTTCAA-AATCCGCGTT
1 GCGATTTT-AACAAT-CGCATT
* *
9463589 GCGATTTTAGATAATCGCAAT
1 GCGATTTTA-ACAATCGCATT
9463610 GCGA
1 GCGA
9463614 ATATGTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 12 0.31
21 24 0.62
22 3 0.08
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
GCGATTTTAACAATCGCATT
Found at i:9463648 original size:21 final size:19
Alignment explanation
Indices: 9463622--9463737 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 19
9463612 GAATATGTAA
9463622 ATCGCAACGCGATAAC-ACGT
1 ATCGCAACGCGAT-ACGAC-T
*
9463642 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATAC-GACT
* *
9463663 ATCGCAACGTGATTCGGACT
1 ATCGCAACGCGATAC-GACT
**
9463683 ATCGCAACGCGATAATACGT
1 ATCGCAACGCGATACGAC-T
* * *
9463703 GATCGCAACGGGATTCTTACT
1 -ATCGCAACGCGATAC-GACT
9463724 ATCGCAACGCGATA
1 ATCGCAACGCGATA
9463738 ATATAAAATC
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.03
20 44 0.56
21 27 0.35
22 5 0.06
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
ATCGCAACGCGATACGACT
Found at i:9463668 original size:20 final size:20
Alignment explanation
Indices: 9463643--9463736 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
9463633 ATAACACGTG
9463643 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
9463663 ATCGCAACGTGATTCGGACT
1 ATCGCAACGCGATTCTGACT
**
9463683 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
* *
9463703 GATCGCAACGGGATTCTTACT
1 -ATCGCAACGCGATTCTGACT
9463724 ATCGCAACGCGAT
1 ATCGCAACGCGAT
9463737 AATATAAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:9463708 original size:41 final size:41
Alignment explanation
Indices: 9463663--9463740 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
9463653 GATTCTGACT
*
9463663 ATCGCAACGTGATTCGGACTATCGCAACGCGATAATACGTG
1 ATCGCAACGGGATTCGGACTATCGCAACGCGATAATACGTG
**
9463704 ATCGCAACGGGATTCTTACTATCGCAACGCGATAATA
1 ATCGCAACGGGATTCGGACTATCGCAACGCGATAATA
9463741 TAAAATCGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
ATCGCAACGGGATTCGGACTATCGCAACGCGATAATACGTG
Found at i:9463749 original size:41 final size:41
Alignment explanation
Indices: 9463663--9463751 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
9463653 GATTCTGACT
* ***
9463663 ATCGCAACGTGATTCGGACTATCGCAACGCGATAATACGTG
1 ATCGCAACGGGATTCGGACTATCGCAACGCGATAATACAAA
** *
9463704 ATCGCAACGGGATTCTTACTATCGCAACGCGATAATATAAA
1 ATCGCAACGGGATTCGGACTATCGCAACGCGATAATACAAA
9463745 ATCGCAA
1 ATCGCAA
9463752 TGCGATTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
ATCGCAACGGGATTCGGACTATCGCAACGCGATAATACAAA
Found at i:9464283 original size:20 final size:20
Alignment explanation
Indices: 9464258--9464313 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
9464248 CGCAACGACA
*
9464258 AAATTCGCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAATC
9464278 AAATTCGCGTTGCGATAATC
1 AAATTCGCGTTGCGATAATC
** *
9464298 ATTTTCGTGTTGCGAT
1 AAATTCGCGTTGCGAT
9464314 TTTCATTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
AAATTCGCGTTGCGATAATC
Found at i:9464319 original size:20 final size:20
Alignment explanation
Indices: 9464281--9464336 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
9464271 GATAGTCAAA
* **
9464281 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
9464301 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
9464321 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
9464337 AAGTTTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:9466098 original size:32 final size:32
Alignment explanation
Indices: 9466056--9466118 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
9466046 TTTGTCTTTG
*
9466056 TTTTGTCTTTTGG-TTGAAGTTAGTAAATTCATA
1 TTTTGTCTTTTGGATTG--CTTAGTAAATTCATA
9466089 TTTT-TCTTTTGGATTGCTTAGTAAATTCAT
1 TTTTGTCTTTTGGATTGCTTAGTAAATTCAT
9466119 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 13 0.46
32 8 0.29
33 7 0.25
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (32 bp):
TTTTGTCTTTTGGATTGCTTAGTAAATTCATA
Found at i:9466302 original size:34 final size:34
Alignment explanation
Indices: 9466256--9466392 Score: 139
Period size: 34 Copynumber: 3.9 Consensus size: 34
9466246 GAAAATGATT
**
9466256 ATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGGGATA
* * **
9466290 ATCGCAATGCGAAAACGACTATCGCAACGCATAAATGA
1 ATCGCAACGCGAAAATGACTATCGCAACG---GGAT-A
**
9466328 CTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 --ATCGCAACGCGAAAATGACTATCGCAACGGGATA
*
9466364 ATCGCAATGCGAAAATGACTATCGCAACG
1 ATCGCAACGCGAAAATGACTATCGCAACG
9466393 CGAATTTAGT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 51 0.62
36 1 0.01
37 4 0.05
38 1 0.01
40 25 0.30
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGGGATA
Found at i:9466358 original size:20 final size:20
Alignment explanation
Indices: 9466237--9466396 Score: 121
Period size: 20 Copynumber: 8.6 Consensus size: 20
9466227 AGAAGAATAG
* *
9466237 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
**
9466257 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
9466277 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
* *
9466291 TCGCAATGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
9466311 TCGCAACGC-ATAAATGACTA
1 TCGCAACGCGA-AAATGACTA
**
9466331 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
9466351 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
*
9466365 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
9466385 TCGCAACGCGAA
1 TCGCAACGCGAA
9466397 TTTAGTTTCG
Statistics
Matches: 108, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
14 16 0.15
15 2 0.02
16 2 0.02
17 5 0.05
18 2 0.02
19 3 0.03
20 77 0.71
21 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:9466358 original size:74 final size:74
Alignment explanation
Indices: 9466248--9466393 Score: 274
Period size: 74 Copynumber: 2.0 Consensus size: 74
9466238 CGCAACACGA
*
9466248 AAATGATTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
9466313 GCAACGCAT
66 GCAACGCAT
*
9466322 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAATGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
9466387 GCAACGC
66 GCAACGC
9466394 GAATTTAGTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (74 bp):
AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAACGACTATC
GCAACGCAT
Found at i:9466470 original size:20 final size:20
Alignment explanation
Indices: 9466447--9466486 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9466437 ATAATTTTTG
9466447 TGTTACGATTTTAAGTTTCA
1 TGTTACGATTTTAAGTTTCA
*
9466467 TGTTGCGATTTTAAGTTTCA
1 TGTTACGATTTTAAGTTTCA
9466487 AAAACTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (20 bp):
TGTTACGATTTTAAGTTTCA
Found at i:9467039 original size:21 final size:21
Alignment explanation
Indices: 9466970--9467073 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
9466960 CACATGTCAT
* * *
9466970 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
**
9466991 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* *
9467013 C-CTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* ** *
9467033 CGTTCAAGAGGCCCTTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
9467054 CGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCCCTCCCA
9467074 ACATTCTAGA
Statistics
Matches: 61, Mismatches: 20, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
20 2 0.03
21 58 0.95
22 1 0.02
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:9467054 original size:42 final size:42
Alignment explanation
Indices: 9466964--9467073 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
9466954 CTGACTCACA
** * * *
9466964 TGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCC
1 TGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCC
* * *
9467006 TATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCT
1 TGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCC
** * *
9467048 TGTCATCGTTGAAGAGGTCCCTCCCA
1 TGTCATCCCTCAAGAGGCCCCTCCCA
9467074 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (42 bp):
TGTCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCC
Found at i:9468526 original size:36 final size:30
Alignment explanation
Indices: 9468446--9468511 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
9468436 ATAAGAGTTG
*
9468446 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
9468476 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
9468506 ATTTGT
1 ATTTGT
9468512 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:9468692 original size:20 final size:19
Alignment explanation
Indices: 9468667--9468916 Score: 163
Period size: 20 Copynumber: 13.5 Consensus size: 19
9468657 TTCTCATTGT
9468667 GATAGTCAAATTTC-CGTTGC
1 GATAGTC-AA-TTCGCGTTGC
*
9468687 GATAGTCAATATCCCGTTGC
1 GATAGTCAAT-TCGCGTTGC
* *
9468707 GATAATCAAATTCGTGTTGC
1 GATAGTC-AATTCGCGTTGC
*
9468727 GATAGTCATTTCGCGTTGC
1 GATAGTCAATTCGCGTTGC
*
9468746 GAT--T--A-TCTCGTTGC
1 GATAGTCAATTCGCGTTGC
*
9468760 GATAGTCAAATTCGCATTGC
1 GATAGTC-AATTCGCGTTGC
* *
9468780 GATAGTCATTTTCGCATTGC
1 GATAGTCA-ATTCGCGTTGC
*
9468800 GAT--T--A-TCCCGTTGC
1 GATAGTCAATTCGCGTTGC
*
9468814 GATAGTCAAATTCGAGTTGC
1 GATAGTC-AATTCGCGTTGC
* *
9468834 GATAGTCATTTTCGCATTGC
1 GATAGTCA-ATTCGCGTTGC
*
9468854 GAT--T--A-TCCCGTTGC
1 GATAGTCAATTCGCGTTGC
* *
9468868 GATATTCAAATTCACGTTGC
1 GATAGTC-AATTCGCGTTGC
9468888 GATAGTCATATTCGCGTTGC
1 GATAGTCA-ATTCGCGTTGC
9468908 GATAGTCAA
1 GATAGTCAA
9468917 ATGAATGTGT
Statistics
Matches: 181, Mismatches: 25, Indels: 49
0.71 0.10 0.19
Matches are distributed among these distances:
14 31 0.17
16 3 0.02
17 1 0.01
18 3 0.02
19 24 0.13
20 116 0.64
21 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (19 bp):
GATAGTCAATTCGCGTTGC
Found at i:9468782 original size:93 final size:94
Alignment explanation
Indices: 9468617--9468787 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 94
9468607 TTCAATATGC
* * * *
9468617 ATCATATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCATTGTGATAGTCAAATTTCC
1 ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCATTGCGATAGTCAAATTTCC
*
9468682 GTTGCGATAGTCAATATCCCGTTGCGATA
66 ATTGCGATAGTCAATATCCCGTTGCGATA
* * * * *
9468711 ATCAAATTCGTGTTGCGATAGTC-ATTTCGCGTTGCGATTATCTCGTTGCGATAGTCAAA-TTCG
1 ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCATTGCGATAGTCAAATTTC-
9468774 CATTGCGATAGTCA
65 CATTGCGATAGTCA
9468788 TTTTCGCATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
92 3 0.05
93 42 0.64
94 21 0.32
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (94 bp):
ATCAAATTCGCGTTGCGATAGTCTAATACACGTTGCGATTATCTCATTGCGATAGTCAAATTTCC
ATTGCGATAGTCAATATCCCGTTGCGATA
Found at i:9468816 original size:54 final size:54
Alignment explanation
Indices: 9468696--9468910 Score: 317
Period size: 54 Copynumber: 4.0 Consensus size: 54
9468686 CGATAGTCAA
* ** *
9468696 TATCCCGTTGCGATAATCAAATTCGTGTTGCGATAGTCA-TTTCGCGTTGCGAT
1 TATCCCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
*
9468749 TATCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
1 TATCCCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
9468803 TATCCCGTTGCGATAGTCAAATTCG-AGTTGCGATAGTCATTTTCGCATTGCGAT
1 TATCCCGTTGCGATAGTCAAATTCGCA-TTGCGATAGTCATTTTCGCATTGCGAT
* * * * *
9468857 TATCCCGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 TATCCCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
9468911 AGTCAAATGA
Statistics
Matches: 148, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
53 36 0.24
54 112 0.76
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (54 bp):
TATCCCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
Found at i:9469116 original size:18 final size:18
Alignment explanation
Indices: 9469093--9469127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9469083 AAGCCGTTTG
*
9469093 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
9469111 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
9469128 GCCTTTTGCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:9472264 original size:20 final size:20
Alignment explanation
Indices: 9472236--9472362 Score: 166
Period size: 20 Copynumber: 6.3 Consensus size: 20
9472226 AATTCAATGA
*
9472236 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
9472256 TGCGATAGTCAGAATCACGT
1 TGCGATAGTCAGAATCGCGT
** *
9472276 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCGT
9472297 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
9472317 TGCGATAGTCCGAATAGCGT
1 TGCGATAGTCAGAATCGCGT
9472337 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
9472357 TGCGAT
1 TGCGAT
9472363 CACGTGTTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 74 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:9472402 original size:20 final size:20
Alignment explanation
Indices: 9472377--9472424 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
9472367 TGTTATCGTG
9472377 TTGCGATTTACATATTCACA
1 TTGCGATTTACATATTCACA
*
9472397 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCACA
*
9472417 TTGAGATT
1 TTGCGATT
9472425 ATCTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACATATTCACA
Found at i:9472534 original size:19 final size:19
Alignment explanation
Indices: 9472510--9472546 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9472500 TGCGATAATG
*
9472510 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
9472529 GAGATCGTATTACGATTT
1 GAGATCGCATTACGATTT
9472547 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:9475109 original size:16 final size:18
Alignment explanation
Indices: 9475077--9475110 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
9475067 TATTAATGTA
9475077 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
9475095 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
9475111 AATAAGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:9475789 original size:128 final size:124
Alignment explanation
Indices: 9475577--9475832 Score: 404
Period size: 128 Copynumber: 2.0 Consensus size: 124
9475567 AATTTTCTTC
*
9475577 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTTAACACATGTCAGATCC
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTTAACACATGTCAGATCC
** *
9475642 TGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATAAA
66 TAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT--CATATAAA
* * *
9475703 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGT--TAACACATGTCAGAT
*
9475768 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATTATATAAA
64 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
9475829 TAAT
1 TAAT
9475833 AAAAACTGAA
Statistics
Matches: 120, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
126 55 0.46
128 65 0.54
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (124 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
Found at i:9476279 original size:35 final size:35
Alignment explanation
Indices: 9476218--9476293 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
9476208 AATTGAATTT
* * *
9476218 AATTGAATTATTTTGGAATTTAGGGTTTAGAATAA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATAA
* *
9476253 AATTGAATTACTTTAGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATAA
9476288 AATTGA
1 AATTGA
9476294 GGACTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTAGAAATTAGGGTTTAGAATAA
Found at i:9479710 original size:30 final size:30
Alignment explanation
Indices: 9479676--9479732 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
9479666 AAAAAAGGTA
*
9479676 TAGACA-TCTAAATAATCACGTTTGTAATGT
1 TAGACACT-TAAATAATCACATTTGTAATGT
9479706 TAGACACTTAAATAATCACATTTGTAA
1 TAGACACTTAAATAATCACATTTGTAA
9479733 CATTGGTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (30 bp):
TAGACACTTAAATAATCACATTTGTAATGT
Found at i:9482529 original size:57 final size:59
Alignment explanation
Indices: 9482420--9482574 Score: 164
Period size: 57 Copynumber: 2.7 Consensus size: 59
9482410 AATTCTATAC
* *
9482420 GAGATTATATC-CTGTCCTGATTCTGCATAGGATT-TGAT-CACTGGCATGATTTTGTAT
1 GAGATTATATCACTGTCCTGATTCTGCTTAGGATTAT-ATCCACTGGCATAATTTTGTAT
* * *
9482477 GGGATT-TGATCA-TGTCCTGATTCTGCTTAGGATTATATCCAC-GTCCTAATTTTGTAT
1 GAGATTAT-ATCACTGTCCTGATTCTGCTTAGGATTATATCCACTGGCATAATTTTGTAT
*
9482534 GAGATTATATCACTGTCCT-ATTTCTGTGTTA-GATTATATCC
1 GAGATTATATCACTGTCCTGA-TTCTG-CTTAGGATTATATCC
9482575 TCATACCGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
56 1 0.01
57 53 0.64
58 26 0.31
59 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (59 bp):
GAGATTATATCACTGTCCTGATTCTGCTTAGGATTATATCCACTGGCATAATTTTGTAT
Found at i:9482539 original size:29 final size:30
Alignment explanation
Indices: 9482507--9482574 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
9482497 TTCTGCTTAG
9482507 GATTATATCCAC-GTCCTAATTT-TGTATGA
1 GATTATATCCACTGTCCT-ATTTCTGTATGA
* *
9482536 GATTATAT-CACTGTCCTATTTCTGTGTTA
1 GATTATATCCACTGTCCTATTTCTGTATGA
9482565 GATTATATCC
1 GATTATATCC
9482575 TCATACCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 26 0.76
30 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (30 bp):
GATTATATCCACTGTCCTATTTCTGTATGA
Found at i:9483552 original size:28 final size:29
Alignment explanation
Indices: 9483489--9483552 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
9483479 GCAGGAATGT
9483489 AAGATTACCGTGTTTGGTTAAAGGAATAA
1 AAGATTACCGTGTTTGGTTAAAGGAATAA
9483518 AAGATTACCGTGTTTGGTTAAA-GAATAA
1 AAGATTACCGTGTTTGGTTAAAGGAATAA
9483546 AAGATTA
1 AAGATTA
9483553 TTGGAATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (29 bp):
AAGATTACCGTGTTTGGTTAAAGGAATAA
Found at i:9486556 original size:100 final size:100
Alignment explanation
Indices: 9486244--9486579 Score: 280
Period size: 100 Copynumber: 3.4 Consensus size: 100
9486234 TTATTTATTG
* * ** * * * * *
9486244 TGCTCGTGATAAAGTAGTAGGTAACACCATTTTTAATGTCAACTGTTTAAGTTAAAAGTATGAAA
1 TGCTCATGATAATGTACCAGGTAACACCTTTTTTAATGTCATCCGTTTAAATTATAAGTATGAAA
** * * *
9486309 TTGTTTATATAACGCAAAAGTA-AGACAAAACATTT
66 CCGTTTATATTATGCAAAAGTAGA-ACAAAACATGT
** ** ** * ** * * * * * ** * **
9486344 TTTTCATGATAACATAATAGGTAGCGTCTTTTTTTATTTCAACTGATTATGTTGTAAGTATTTAA
1 TGCTCATGATAATGTACCAGGTAACACCTTTTTTAATGTCATCCGTTTAAATTATAAGTATGAAA
9486409 CCGTTTATATTATGCAAAAGTAGAACAAAACATGT
66 CCGTTTATATTATGCAAAAGTAGAACAAAACATGT
* *
9486444 TGCTCATGATAATGTACCAGGTGACACTTTTTTTAATGTCATCCGTTTAAATTATAAGTATGAAA
1 TGCTCATGATAATGTACCAGGTAACACCTTTTTTAATGTCATCCGTTTAAATTATAAGTATGAAA
*
9486509 CCTTTTATATTATGCAAAAGTA-AGACAAAACATGT
66 CCGTTTATATTATGCAAAAGTAGA-ACAAAACATGT
* * * *
9486544 TGCTTATTATAATGTATCAGGTAACGCCTTTTTTAA
1 TGCTCATGATAATGTACCAGGTAACACCTTTTTTAA
9486580 AATGTTAATC
Statistics
Matches: 183, Mismatches: 51, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
99 1 0.01
100 181 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (100 bp):
TGCTCATGATAATGTACCAGGTAACACCTTTTTTAATGTCATCCGTTTAAATTATAAGTATGAAA
CCGTTTATATTATGCAAAAGTAGAACAAAACATGT
Found at i:9487044 original size:71 final size:74
Alignment explanation
Indices: 9486952--9487109 Score: 200
Period size: 71 Copynumber: 2.2 Consensus size: 74
9486942 CGACTTGTTC
* * *
9486952 AATATATAAAAGTATCGATCATCA-TCGCATAAGTATCAATATTTTAAATTTTGAT-TT-T-TAT
1 AATATTTAAAAGTATCAATCATCACT-GCATAAGTATCAATATTTGAAATTTTGATCTTATCT-T
9487013 CAAC-TTTTTT
64 CAACTTTTTTT
* * * *
9487023 AATTTTTAAAAGTATCAATCATTACTGCATAAGTATTAATATTTGATATTTTGATCTTATCTTCA
1 AATATTTAAAAGTATCAATCATCACTGCATAAGTATCAATATTTGAAATTTTGATCTTATCTTCA
9487088 ACTTTTTTT
66 ACTTTTTTT
9487097 AATATTTAAAAGT
1 AATATTTAAAAGT
9487110 GTTGATAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
71 46 0.62
72 3 0.04
73 6 0.08
74 19 0.26
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (74 bp):
AATATTTAAAAGTATCAATCATCACTGCATAAGTATCAATATTTGAAATTTTGATCTTATCTTCA
ACTTTTTTT
Found at i:9487327 original size:82 final size:82
Alignment explanation
Indices: 9487203--9487354 Score: 191
Period size: 82 Copynumber: 1.9 Consensus size: 82
9487193 TATTAATATA
* * * * * ** *
9487203 ACATATCACAACCTATTTCATAGTGAACTATGATATTCTTGGGCGTAACCTATTTTATTAA-AAC
1 ACATACCACAACCTATTTCATAGTGAACTATAACAATATTGGGCACAACCTATTTTATTAATAAA
9487267 AATATCAACATTACATT
66 AATATCAACATTACATT
*
9487284 ACATACCACAACCTACTTT-ATTAGTGAACTATAACAATATTGGGCACAACCTATTTTGTTAATA
1 ACATACCACAACCTA-TTTCA-TAGTGAACTATAACAATATTGGGCACAACCTATTTTATTAATA
9487348 AAAATAT
64 AAAATAT
9487355 TAATATTGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.25
82 37 0.63
83 7 0.12
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (82 bp):
ACATACCACAACCTATTTCATAGTGAACTATAACAATATTGGGCACAACCTATTTTATTAATAAA
AATATCAACATTACATT
Found at i:9494961 original size:32 final size:33
Alignment explanation
Indices: 9494914--9494983 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 33
9494904 AGGAAACGTG
9494914 TTATTGAAAATATTATTATTTTTTAATAAAAA-A
1 TTATTGAAAATATTATT-TTTTTTAATAAAAATA
* *
9494947 TTATTTAAAA-ATTATTTTTTTTATTAAAAATA
1 TTATTGAAAATATTATTTTTTTTAATAAAAATA
9494979 TTATT
1 TTATT
9494984 ATTGGGTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 13 0.38
32 12 0.35
33 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (33 bp):
TTATTGAAAATATTATTTTTTTTAATAAAAATA
Found at i:9495119 original size:19 final size:20
Alignment explanation
Indices: 9495090--9495130 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
9495080 AGAAATCTTA
9495090 AAAAAATTAATGTTTTAGGT
1 AAAAAATTAATGTTTTAGGT
9495110 AAAAAA-TAATGTTTTAGGT
1 AAAAAATTAATGTTTTAGGT
9495129 AA
1 AA
9495131 TATTTACGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (20 bp):
AAAAAATTAATGTTTTAGGT
Found at i:9495787 original size:10 final size:10
Alignment explanation
Indices: 9495772--9495797 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9495762 TTAATAAATA
9495772 AACGAATACG
1 AACGAATACG
9495782 AACGAATACG
1 AACGAATACG
9495792 AACGAA
1 AACGAA
9495798 CGAACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.08
Consensus pattern (10 bp):
AACGAATACG
Found at i:9496103 original size:14 final size:16
Alignment explanation
Indices: 9496084--9496115 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
9496074 GTCATCTATT
9496084 CGAACATA-AA-TGAA
1 CGAACATATAATTGAA
9496098 CGAACATATAATTGAA
1 CGAACATATAATTGAA
9496114 CG
1 CG
9496116 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (16 bp):
CGAACATATAATTGAA
Found at i:9502008 original size:41 final size:41
Alignment explanation
Indices: 9501948--9502029 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
9501938 TCAATGCAAA
*
9501948 TATTTACTTCCCATTAAAGAAATTAGGTAATAACAGATAAT
1 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
9501989 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
1 TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
9502030 CATCTATCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (41 bp):
TATTTACTTCCCATAAAAGAAATTAGGTAATAACAGATAAT
Found at i:9515245 original size:21 final size:19
Alignment explanation
Indices: 9515209--9515248 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
9515199 ATGTTGATCC
*
9515209 CTTGGTCCTTCTTACTACA
1 CTTGGTCCTTCCTACTACA
9515228 CTTGGTCCTCTTCCTACTACA
1 CTTGGT-C-CTTCCTACTACA
9515249 TGTGTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (19 bp):
CTTGGTCCTTCCTACTACA
Found at i:9516095 original size:44 final size:44
Alignment explanation
Indices: 9516042--9516195 Score: 229
Period size: 44 Copynumber: 3.5 Consensus size: 44
9516032 CGAGGTCTGA
* * ** * *
9516042 GTCACATAGCATCGACACCTTATAAACTCTTTAGCTAGGTCAGG
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
*
9516086 GTCATATAGCATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
*
9516130 GTCATATAACACCGACACCTTGCAGACTCTTTGGCTAGGTCA-G
1 GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
9516173 GTCATATAACATCGACACCTTGC
1 GTCATATAACATCGACACCTTGC
9516196 CATGCCAGTC
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
43 23 0.23
44 79 0.77
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
GTCATATAACATCGACACCTTGCAGACTCTTTGGCTAGGTCAGG
Found at i:9522739 original size:11 final size:11
Alignment explanation
Indices: 9522711--9522751 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
9522701 TAATTTTTAA
9522711 ATAAAATAA-T
1 ATAAAATAATT
9522721 AT-AAATAATT
1 ATAAAATAATT
* *
9522731 TTGAAATAATT
1 ATAAAATAATT
9522742 ATAAAATAAT
1 ATAAAATAAT
9522752 ATGAAACAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
9 6 0.23
10 4 0.15
11 16 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAAAATAATT
Found at i:9522752 original size:25 final size:25
Alignment explanation
Indices: 9522700--9522750 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9522690 GAAAGGAAGC
* *
9522700 ATAATTTTTAAATAAAATAATATAA
1 ATAATTTTGAAATAAAATAAAATAA
*
9522725 ATAATTTTGAAATAATTATAAAATAA
1 ATAATTTTGAAATAA-AATAAAATAA
9522751 TATGAAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATTTTGAAATAAAATAAAATAA
Found at i:9522756 original size:21 final size:20
Alignment explanation
Indices: 9522714--9522757 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
9522704 TTTTTAAATA
*
9522714 AAATAATATAAATAATTTTG
1 AAATAATATAAATAATTATG
9522734 AAATAATTATAAAATAA-TATG
1 AAATAA-TAT-AAATAATTATG
9522755 AAA
1 AAA
9522758 CAGAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATAATATAAATAATTATG
Found at i:9537241 original size:128 final size:127
Alignment explanation
Indices: 9537089--9537345 Score: 455
Period size: 128 Copynumber: 2.0 Consensus size: 127
9537079 TTAGAAAAGA
9537089 TTAAAAGTTTAGGGACTTAAATGAAAAGTGTTGATGTTGGATTTAATAACAAAGTTTGAAAGTAA
1 TTAAAAGTTTAGGGACTTAAATGAAAAGTGTTGATGTTGGATTTAATAACAAAGTTTGAAAGTAA
*
9537154 TAAGGGTAAAATAGTAATAGAGAGAAATGAAAGAAAATTCGGGAGTTTGTTTTATCTTCTT-CTC
66 TAA-GGTAAAATAGTAATAGAGAGAAATAAAAGAAAATT--GGAGTTTGTTTTATCTTCTTCCTC
9537218 TTAAAAGTTTA-GGACTTAAATGAAAAGTGTTGATGTTGGATTTAATAACAAAGTTTGAAAGTAA
1 TTAAAAGTTTAGGGACTTAAATGAAAAGTGTTGATGTTGGATTTAATAACAAAGTTTGAAAGTAA
*
9537282 TAAGGTAAAATGGTAATAGAGAGAAATAAAAGAAAATTGGAGTTTGTTTTATCTTCTTCCTC
66 TAAGGTAAAATAGTAATAGAGAGAAATAAAAGAAAATTGGAGTTTGTTTTATCTTCTTCCTC
9537344 TT
1 TT
9537346 CTCTTCTCGT
Statistics
Matches: 125, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
125 20 0.16
126 5 0.04
127 33 0.26
128 56 0.45
129 11 0.09
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (127 bp):
TTAAAAGTTTAGGGACTTAAATGAAAAGTGTTGATGTTGGATTTAATAACAAAGTTTGAAAGTAA
TAAGGTAAAATAGTAATAGAGAGAAATAAAAGAAAATTGGAGTTTGTTTTATCTTCTTCCTC
Found at i:9538342 original size:2 final size:2
Alignment explanation
Indices: 9538337--9538379 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
9538327 TGATGTGTGA
9538337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
9538380 GTAATCATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9538731 original size:23 final size:23
Alignment explanation
Indices: 9538692--9538775 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
9538682 ACATCTTATA
9538692 TGGCACTAT-GGTGCAATTCTACG
1 TGGCACT-TCGGTGCAATTCTACG
* *
9538715 CGGAACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
9538738 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
9538761 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
9538776 TTTATATGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
22 1 0.02
23 55 0.98
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:9539560 original size:13 final size:13
Alignment explanation
Indices: 9539519--9539553 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
9539509 TACGTCATAA
*
9539519 ATTTATGACGCAC
1 ATTTATGACACAC
9539532 ATTTATGACACAC
1 ATTTATGACACAC
9539545 ATTTATGAC
1 ATTTATGAC
9539554 TTACATTGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:9539675 original size:85 final size:85
Alignment explanation
Indices: 9539532--9539697 Score: 260
Period size: 85 Copynumber: 2.0 Consensus size: 85
9539522 TATGACGCAC
* * *
9539532 ATTTATGACACACATTTATGACTTACATTGCGCGTCATTGAAGCCCCTGTCATAAATGAAGATGA
1 ATTTATGACACACATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
9539597 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
* * * *
9539617 ATTTATGGCACGCATTTATAACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGG
1 ATTTATGACACACATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
9539682 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
9539698 GTGATTGTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACACATTTATAACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:9539734 original size:11 final size:11
Alignment explanation
Indices: 9539718--9539744 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9539708 TTCGTGAATA
9539718 TATATATATTT
1 TATATATATTT
9539729 TATATATATTT
1 TATATATATTT
9539740 TATAT
1 TATAT
9539745 TGACAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATATATTT
Found at i:9545916 original size:15 final size:15
Alignment explanation
Indices: 9545896--9545928 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9545886 TACACGGCGG
9545896 CAGCAGCAGCAATAC
1 CAGCAGCAGCAATAC
9545911 CAGCAGCAGCAATAC
1 CAGCAGCAGCAATAC
9545926 CAG
1 CAG
9545929 AACCAGGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.21, T:0.06
Consensus pattern (15 bp):
CAGCAGCAGCAATAC
Found at i:9545946 original size:24 final size:24
Alignment explanation
Indices: 9545914--9546011 Score: 162
Period size: 24 Copynumber: 4.1 Consensus size: 24
9545904 GCAATACCAG
9545914 CAGCAGCAATACCAGAACCAGGCA
1 CAGCAGCAATACCAGAACCAGGCA
9545938 CAGCAGCAATACCAGAACCAGGCA
1 CAGCAGCAATACCAGAACCAGGCA
*
9545962 CAGCAGCAATACCAGAACCAGGCG
1 CAGCAGCAATACCAGAACCAGGCA
*
9545986 CAGCCA-CAATACCAGAATCAGGCA
1 CAG-CAGCAATACCAGAACCAGGCA
9546010 CA
1 CA
9546012 TGAATACGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
24 68 0.97
25 2 0.03
ACGTcount: A:0.41, C:0.34, G:0.20, T:0.05
Consensus pattern (24 bp):
CAGCAGCAATACCAGAACCAGGCA
Found at i:9549816 original size:18 final size:19
Alignment explanation
Indices: 9549793--9549831 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9549783 AGTGATTCCC
9549793 CCCAT-GGTAAAGCAGTGT
1 CCCATGGGTAAAGCAGTGT
9549811 CCCATGGGTAAAGCAGTGT
1 CCCATGGGTAAAGCAGTGT
9549830 CC
1 CC
9549832 TTGGATCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (19 bp):
CCCATGGGTAAAGCAGTGT
Found at i:9553589 original size:2 final size:2
Alignment explanation
Indices: 9553582--9553625 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
9553572 TTCTTCCATT
9553582 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9553623 TA T
1 TA T
9553626 CGAACATCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9558793 original size:28 final size:26
Alignment explanation
Indices: 9558754--9558812 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
9558744 GAAAATGATT
*
9558754 AAATT-TAATCTAATGTTTTAAGAAAA
1 AAATTATAATCTAATATTTTAA-AAAA
* *
9558780 AAATTATATATCTATTATTTTAAAATA
1 AAATTATA-ATCTAATATTTTAAAAAA
9558807 AAATTA
1 AAATTA
9558813 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.18
27 11 0.39
28 12 0.43
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (26 bp):
AAATTATAATCTAATATTTTAAAAAA
Found at i:9558891 original size:17 final size:17
Alignment explanation
Indices: 9558869--9558902 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9558859 CTTAATGAAT
9558869 CCTCAACTTTCTTCAAC
1 CCTCAACTTTCTTCAAC
9558886 CCTCAACTTTCTTCAAC
1 CCTCAACTTTCTTCAAC
9558903 GAAGACGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (17 bp):
CCTCAACTTTCTTCAAC
Found at i:9564294 original size:2 final size:2
Alignment explanation
Indices: 9564287--9564320 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9564277 GATTTCATCA
9564287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9564321 TACTTGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9567211 original size:11 final size:11
Alignment explanation
Indices: 9567195--9567220 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9567185 GCCCCACTAA
9567195 TTCTAAGGAGG
1 TTCTAAGGAGG
9567206 TTCTAAGGAGG
1 TTCTAAGGAGG
9567217 TTCT
1 TTCT
9567221 GTGTGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (11 bp):
TTCTAAGGAGG
Found at i:9574760 original size:17 final size:15
Alignment explanation
Indices: 9574738--9574780 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
9574728 TTATTATGCT
9574738 AAAATAATATTTACATA
1 AAAAT-ATATTTA-ATA
* *
9574755 AAAATATTTTTATTA
1 AAAATATATTTAATA
9574770 AAAATATATTT
1 AAAATATATTT
9574781 TATGATCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 6 0.26
17 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATATATTTAATA
Found at i:9574773 original size:15 final size:16
Alignment explanation
Indices: 9574753--9574783 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9574743 AATATTTACA
9574753 TAAAAATAT-TTTTAT
1 TAAAAATATATTTTAT
9574768 TAAAAATATATTTTAT
1 TAAAAATATATTTTAT
9574784 GATCCTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAAATATATTTTAT
Found at i:9575099 original size:20 final size:19
Alignment explanation
Indices: 9575069--9575116 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
9575059 TTTTTATTAA
9575069 TTTTTTAATTAATTAAT-AT
1 TTTTTTAATT-ATTAATAAT
*
9575088 TTTTTTATATTATTTATAAT
1 TTTTTTA-ATTATTAATAAT
9575108 TTTTTTAAT
1 TTTTTTAAT
9575117 ATCCCCAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTAATTATTAATAAT
Found at i:9575840 original size:31 final size:31
Alignment explanation
Indices: 9575798--9575860 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
9575788 TTTACGTCGA
9575798 ATGGTGAAGAGATTAGAAGGGAAAAGAGAAG
1 ATGGTGAAGAGATTAGAAGGGAAAAGAGAAG
* *
9575829 ATGGTGGAGAGATTAGAAGGGAGAAGAGAAG
1 ATGGTGAAGAGATTAGAAGGGAAAAGAGAAG
9575860 A
1 A
9575861 CGACGGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (31 bp):
ATGGTGAAGAGATTAGAAGGGAAAAGAGAAG
Found at i:9575869 original size:31 final size:31
Alignment explanation
Indices: 9575805--9575871 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
9575795 CGAATGGTGA
* **
9575805 AGAGATTAGAAGGGAAAAGAGAAGATGGTGG
1 AGAGATTAGAAGGGAAAAGAGAAGACGACGG
*
9575836 AGAGATTAGAAGGGAGAAGAGAAGACGACGG
1 AGAGATTAGAAGGGAAAAGAGAAGACGACGG
9575867 AGAGA
1 AGAGA
9575872 AATTTGAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.03, G:0.42, T:0.09
Consensus pattern (31 bp):
AGAGATTAGAAGGGAAAAGAGAAGACGACGG
Found at i:9586946 original size:27 final size:27
Alignment explanation
Indices: 9586916--9587006 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
9586906 ACATACCTTA
*
9586916 ATTTATAAAAAAAATATAACGCTAACT
1 ATTTATAAAAAAAATATAACACTAACT
9586943 ATTT-TAAAAAAAA-ACTAA-ACTAAACT
1 ATTTATAAAAAAAATA-TAACACT-AACT
* * * *
9586969 ACTCATAAAAAAACTATAACACTAACC
1 ATTTATAAAAAAAATATAACACTAACT
*
9586996 ATTTTTAAAAA
1 ATTTATAAAAA
9587007 CCCTAAAGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
25 3 0.06
26 18 0.35
27 26 0.51
28 4 0.08
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.27
Consensus pattern (27 bp):
ATTTATAAAAAAAATATAACACTAACT
Found at i:9587219 original size:21 final size:21
Alignment explanation
Indices: 9587205--9587249 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9587195 AAATCACACA
9587205 TTTAATATTTAAAATATCAAT
1 TTTAATATTTAAAATATCAAT
* *
9587226 TTTAATATTTAAATTTTCAAT
1 TTTAATATTTAAAATATCAAT
9587247 TTT
1 TTT
9587250 GTACAACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATATTTAAAATATCAAT
Found at i:9589032 original size:23 final size:23
Alignment explanation
Indices: 9589006--9589053 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
9588996 ATAAAGTACA
*
9589006 ATAACATACTAGGTAGCCCTTAT
1 ATAACATAATAGGTAGCCCTTAT
* *
9589029 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCCCTTAT
9589052 AT
1 AT
9589054 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCCCTTAT
Found at i:9589300 original size:30 final size:29
Alignment explanation
Indices: 9589259--9589325 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
9589249 CATTTGCACA
* * *
9589259 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
9589289 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
9589318 AATAATAT
1 AA-AATAT
9589326 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:9589511 original size:23 final size:23
Alignment explanation
Indices: 9589485--9589543 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
9589475 AACCACTACC
9589485 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
9589508 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
9589531 TATTACATCATAT
1 TATTACATTATAT
9589544 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:9590003 original size:34 final size:34
Alignment explanation
Indices: 9589963--9590028 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
9589953 AAGTTGTAGA
*
9589963 TTTTGATTTCCTTTTGCTTGGCATCATATGAGAT
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
9589997 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
1 TTTTGATTTCCTTTTGCTTGGCACCATATGAG
9590029 CTTTGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (34 bp):
TTTTGATTTCCTTTTGCTTGGCACCATATGAGAT
Found at i:9590325 original size:18 final size:18
Alignment explanation
Indices: 9590302--9590338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9590292 CGAAATATAT
9590302 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
9590320 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
9590338 A
1 A
9590339 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:9590750 original size:25 final size:25
Alignment explanation
Indices: 9590693--9590758 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
9590683 CACTCAAAAG
*
9590693 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
9590718 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
9590743 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
9590759 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:9593537 original size:183 final size:183
Alignment explanation
Indices: 9593225--9593894 Score: 1152
Period size: 183 Copynumber: 3.7 Consensus size: 183
9593215 TTAAAATTAC
*
9593225 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* * * * *
9593289 TATTATAAAGTGTCGATATAGGTTGGAGACCTATTCGCTCATAAAACCGTTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
* *
9593354 TATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* * *
9593408 CGATACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
9593472 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
9593537 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
9593591 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGCACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
*
9593656 ATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
9593721 ATATTAC-AAATTATCTATTACATTAT--TTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
9593771 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
*
9593836 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATA
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
9593895 ATATGTTGAA
Statistics
Matches: 468, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
180 145 0.31
182 19 0.04
183 301 0.64
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:9593893 original size:363 final size:365
Alignment explanation
Indices: 9593225--9593894 Score: 1150
Period size: 363 Copynumber: 1.8 Consensus size: 365
9593215 TTAAAATTAC
* * *
9593225 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTAAAATGGTATCGACACATTTTTCTTCCAATCTGCACATAAAGTACCGACACAAG
* * * *
9593290 ATTATAAAGTGTCGATATAGGTTGGAGACCTATTCGCTCATAAAACCGTTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGGAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
9593355 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
131 ATATTACAAAATTATCTATTACATTAT-AATATGGGTTCCGATGTGTAAATGTCGACACTTTTTA
*
9593420 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
195 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAAAGTGT
*
9593485 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
260 CGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATACCGGTTATATTACAAAAT
9593550 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
325 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
9593591 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGCACATAAAGTACCGACACAA
1 CGACACTTTTTAA-AATGGTATCGACACATTTTTCTTCCAATCTGCACATAAAGTACCGACACAA
*
9593655 GATTAAAAAGTGTCGATATAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGGAGACATATTCGCGCATAAAACCGGTATATTTATACCGGT
*
9593720 TATATTAC-AAATTATCTATTACATTAT-TTATGGGTTCCGATGTGTAAATGTCGACACTTTTTA
130 TATATTACAAAATTATCTATTACATTATAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTA
*
9593783 ACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAGATTAAAAAGTG
195 A-AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAAAGTG
9593847 TCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATA
259 TCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATA
9593895 ATATGTTGAA
Statistics
Matches: 287, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
363 137 0.48
364 3 0.01
365 19 0.07
366 125 0.44
367 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (365 bp):
CGACACTTTTTAAAATGGTATCGACACATTTTTCTTCCAATCTGCACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGGAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTAA
AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAGATTAAAAAGTGTC
GATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATACCGGTTATATTACAAAATT
ATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:9594278 original size:23 final size:23
Alignment explanation
Indices: 9594252--9594314 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
9594242 ATATAACCAC
9594252 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
9594275 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
9594298 TACCTATTACATCATAT
1 TACCTATTACATTATAT
9594315 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:9595792 original size:3 final size:3
Alignment explanation
Indices: 9595784--9595864 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
9595774 ACTTGTTTGG
* * * * **
9595784 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTT ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
9595832 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
9595865 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:9595807 original size:18 final size:18
Alignment explanation
Indices: 9595788--9595879 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
9595778 GTTTGGATCA
* *
9595788 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
9595806 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
* ** * * *
9595824 TTATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
9595842 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
9595860 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
9595878 TC
1 TC
9595880 TGCGACCGCT
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:9595847 original size:36 final size:36
Alignment explanation
Indices: 9595800--9595876 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
9595790 ATCTTCATCA
* *
9595800 TCATCATCATCATCGTCATCATCTTTATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
9595836 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
9595872 TCATC
1 TCATC
9595877 TTCTGCGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:9595879 original size:6 final size:6
Alignment explanation
Indices: 9595788--9595879 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
9595778 GTTTGGATCA
* * * * * * * * *
9595788 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TTATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
9595836 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
9595880 TGCGACCGCT
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:9597666 original size:197 final size:199
Alignment explanation
Indices: 9597331--9598281 Score: 1604
Period size: 197 Copynumber: 4.9 Consensus size: 199
9597321 TTTAAATTAG
9597331 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
9597396 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
9597461 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
9597525 -AAA
196 GAAA
*
9597528 TATCGACACAAACTATATTAGTGTCGACACATTATTTATATATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
9597593 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
9597658 CGACACTTTTTATATATGGAT------TTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
9597717 GAAA
196 GAAA
* *
9597721 TATCGACACAAACTATATTAGTGTCGATACA-TATTTATACATATTATCTC--AAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
9597783 A-TGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
9597846 CGACACTTTTTATATATGGATCGAAACTTTATGGGTGCACCCTGTTTTCCATTCA-TCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
9597910 AAAA
196 GAAA
*
9597914 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
*
9597978 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACCTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
9598043 CGACAC-TTTTATATATGGATCGAC-CTTTATGGGTGCACCCTGTTTTCCATTCATTCTAGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
9598106 GAAA
196 GAAA
* * *
9598110 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATT-T-T-TTAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
* * *
9598172 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
9598237 TTGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
9598282 GGCCATATTG
Statistics
Matches: 718, Mismatches: 19, Indels: 36
0.93 0.02 0.05
Matches are distributed among these distances:
188 67 0.09
189 16 0.02
190 12 0.02
191 34 0.05
192 21 0.03
193 90 0.13
194 100 0.14
195 87 0.12
196 79 0.11
197 212 0.30
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
GAAA
Found at i:9598446 original size:19 final size:19
Alignment explanation
Indices: 9598399--9598446 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
9598389 TTATATTCAC
*
9598399 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
9598418 ATAC-AAATTATAAATCTT
1 ATACAAAATTATAAATCGT
9598436 ATACAAAATTA
1 ATACAAAATTA
9598447 ACCCTACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:9600370 original size:21 final size:21
Alignment explanation
Indices: 9600309--9600370 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
9600299 CCTTATGCTC
* * **
9600309 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCGA
* *
9600330 TCGAGTTTCTCTAACGACTCGA
1 TCAAGTTTCTCT-TCGACTCGA
9600352 TCAAGTTTCTCTTCGACTC
1 TCAAGTTTCTCTTCGACTC
9600371 TTGATTGTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCGA
Found at i:9602573 original size:17 final size:18
Alignment explanation
Indices: 9602551--9602592 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
9602541 CATATATCCG
9602551 TATCATTT-TACCGGTTT
1 TATCATTTGTACCGGTTT
*
9602568 TATCATTTTGTATCGGTTT
1 TATCA-TTTGTACCGGTTT
9602587 TATCAT
1 TATCAT
9602593 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 13 0.59
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.55
Consensus pattern (18 bp):
TATCATTTGTACCGGTTT
Found at i:9602761 original size:19 final size:19
Alignment explanation
Indices: 9602737--9602794 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
9602727 CCGGTAACGT
9602737 TTACCGGTTTATCATTTTG
1 TTACCGGTTTATCATTTTG
*
9602756 TTACCGGTTTTATCATATT-
1 TTACCGG-TTTATCATTTTG
* *
9602775 TTACCTGGTATATCGTTTTG
1 TTACC-GGTTTATCATTTTG
9602795 GATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (19 bp):
TTACCGGTTTATCATTTTG
Found at i:9602907 original size:177 final size:179
Alignment explanation
Indices: 9602525--9602990 Score: 604
Period size: 179 Copynumber: 2.6 Consensus size: 179
9602515 CGTACTTACG
* * * ** *
9602525 AAAGTATCGACACTTT-CATATATCC-GTATCATTTTACCGGTTTTATCATTTTGTATCGGTTTT
1 AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTGTACCGGTTTT
* * * *
9602588 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTATA
66 ATCATAGTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTATA
* * *
9602653 GGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTTGATCCTTATAT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
9602703 AAAGTATCGACACTTTTAATATATCCGGTAACG-TTTACCGG-TTTATCATTTTGTTACCGGTTT
1 AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTG-TACCGGTTT
* *
9602766 TATCATA-TTTTACCTGGTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACTTTATA
65 TATCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
** *
9602830 GGATTTAAAACTGCTTCTC-TTTAAATTCACGAAGTGTCGATCCTTATATT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
9602880 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCTATACAGGTTT
1 AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTT-TGTACCGGTTT
* *
9602945 TGTCATAGTTTTACCTGTTATAT-GTTTTGGATCGACACATTTTTAA
65 TATCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
9602991 TTTGGATCGA
Statistics
Matches: 255, Mismatches: 25, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
176 27 0.11
177 68 0.27
178 64 0.25
179 77 0.30
180 19 0.07
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (179 bp):
AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTGTACCGGTTTT
ATCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:9603537 original size:227 final size:225
Alignment explanation
Indices: 9603054--9603751 Score: 1170
Period size: 222 Copynumber: 3.1 Consensus size: 225
9603044 ACCTACTTTT
*
9603054 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTAAAGTTATGTAATTTATGTTTC-A
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTGAAAGTTATGTAATTTATGTTTCAA
* *
9603118 TTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA-TAATTAATAATTTAATTTACACAAAAT
66 TTT-TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTAATAATTTCATTTACACAAAAA
9603182 ATTATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGAATTTAAATTTAACAATATTAACC-
130 ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCA
9603245 AAATAATAATAAATATGTTTTCAACAGTGAA
195 AAATAATAATAAATATGTTTTCAACAGTGAA
9603276 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTGAAAGTTATGTAATTTATGTTTCAA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTGAAAGTTATGTAATTTATGTTTCAA
9603341 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
66 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA-TTAATAATTTCATTTACACAAAAA
*
9603406 ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAAAATTTAAATTTAACAATATTAACCA
130 ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCA
9603471 AATATAATAATAAATATGTTTTCAACAGTGAA
195 AA-ATAATAATAAATATGTTTTCAACAGTGAA
9603503 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTG-AAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATAC-TTTTTGAAAGTTATGTAATTTATGTTTCA
9603567 ATTTTTTTAATA--GTTTCATGTTTTCCACCTACAATATTAATTAATAATTTCATTTACAC--AA
65 A-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTAATAATTTCATTTACACAAAA
* *
9603628 AATTATTTGATTG--TTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAACT
129 AATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACC
*
9603691 AAAGATAATAATAAATATATTTTC-ACAGTGAA
194 AAA-ATAATAATAAATATGTTTTCAACAGTGAA
* *
9603723 ATAAGTAT-GAAACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
9603752 GATAATTTAC
Statistics
Matches: 457, Mismatches: 11, Indels: 19
0.94 0.02 0.04
Matches are distributed among these distances:
219 19 0.04
220 16 0.04
221 69 0.15
222 95 0.21
223 22 0.05
224 48 0.11
225 55 0.12
226 30 0.07
227 87 0.19
228 16 0.04
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (225 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTGAAAGTTATGTAATTTATGTTTCAA
TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTAATAATTTCATTTACACAAAAAA
TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
AATAATAATAAATATGTTTTCAACAGTGAA
Found at i:9607525 original size:148 final size:150
Alignment explanation
Indices: 9607251--9608003 Score: 1347
Period size: 148 Copynumber: 5.1 Consensus size: 150
9607241 CCAGAAACTA
*
9607251 TAGCC-TTACAATGTTATTTTTAATAGTTTAGGGTGATTAC-AAATAGTATCTATCCAAAATCTA
1 TAGCCATTACAATGTTA-TTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTA
9607314 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTT-CACCC
65 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCC
*
9607378 CTAAAGCCGTTCAATGAGTTA
130 CTAAAGCCGTTCAATGAGTTG
9607399 TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTAC-AAATAGTATCTATCCAAAATCTAT
1 TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
9607463 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAA-AAACAACACTCCCTTCCACCCC
66 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCCC
9607527 TAAAGCCGTTCAATGAGTTG
131 TAAAGCCGTTCAATGAGTTG
9607547 TAGCCATTACAATGTTATTTTAATAG-TTAGGATGATTACAAAATAGTATCTATCC-AAATCTAT
1 TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
9607610 CTTAA-CCCTG-AGACAATGTTCAAACCCGAAA-CTCTAAAACAAACAACACTCCCTTCCACCCC
66 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCCC
9607672 TAAAGCCGTTCAATGAGTTG
131 TAAAGCCGTTCAATGAGTTG
9607692 TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAATA-TATCTATCCAAAATCTAT
1 TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
9607756 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTT-CA-CCC
66 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCCC
9607819 TAAAGCCGTTCAATGAGTTG
131 TAAAGCCGTTCAATGAGTTG
*
9607839 TAGCCATTACAATG-TATTTTTAATAGTTTAGGATAATTACAAAATAGTATCTATCCAAAATCTA
1 TAGCCATTACAATGTTA-TTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTA
9607903 TCTTAACCCCTGAAGAC-ATGTTCAAACCCGAAACCTCTAAAACAACACAACACTCCCTTCCACC
65 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAA-ACAACACTCCCTTCCACC
9607967 CCTAAAGCCGTTCAATGAGTTG
129 CCTAAAGCCGTTCAATGAGTTG
9607989 TAGCCATTACAATGT
1 TAGCCATTACAATGT
9608004 CGAATTAATT
Statistics
Matches: 587, Mismatches: 3, Indels: 27
0.95 0.00 0.04
Matches are distributed among these distances:
144 8 0.01
145 98 0.17
146 39 0.07
147 139 0.24
148 229 0.39
149 37 0.06
150 37 0.06
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (150 bp):
TAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCCC
TAAAGCCGTTCAATGAGTTG
Found at i:9607872 original size:293 final size:298
Alignment explanation
Indices: 9607251--9608003 Score: 1343
Period size: 293 Copynumber: 2.6 Consensus size: 298
9607241 CCAGAAACTA
*
9607251 TAGCC-TTACAATGTTATTTTTAATAGTTTAGGGTGATTAC-AAATAGTATCTATCCAAAATCTA
1 TAGCCATTACAATG-TATTTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTA
9607314 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTT-CACCC
65 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCC
*
9607378 CTAAAGCCGTTCAATGAGTTATAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAT
130 CTAAAGCCGTTCAATGAGTTGTAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAT
9607443 AGTATCTATCCAAAATCTATCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAAAAA
195 AGTATCTATCCAAAATCTATCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAAAAA
9607508 CAACACTCCCTTCCACCCCTAAAGCCGTTCAATGAGTTG
260 CAACACTCCCTTCCACCCCTAAAGCCGTTCAATGAGTTG
9607547 TAGCCATTACAATGT-TATTTTAATAG-TTAGGATGATTACAAAATAGTATCTATCC-AAATCTA
1 TAGCCATTACAATGTAT-TTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTA
9607609 TCTTAA-CCCTG-AGACAATGTTCAAACCCGAAA-CTCTAAAACAAACAACACTCCCTTCCACCC
65 TCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCC
9607671 CTAAAGCCGTTCAATGAGTTGTAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAAA
130 CTAAAGCCGTTCAATGAGTTGTAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTAC-AAA
9607736 TA-TATCTATCCAAAATCTATCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACA
194 TAGTATCTATCCAAAATCTATCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAA-A
9607800 AACAACACTCCCTT-CA-CCCTAAAGCCGTTCAATGAGTTG
258 AACAACACTCCCTTCCACCCCTAAAGCCGTTCAATGAGTTG
*
9607839 TAGCCATTACAATGTATTTTTAATAGTTTAGGATAATTACAAAATAGTATCTATCCAAAATCTAT
1 TAGCCATTACAATGTATTTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
9607904 CTTAACCCCTGAAGAC-ATGTTCAAACCCGAAACCTCTAAAACAACACAACACTCCCTTCCACCC
66 CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAA-ACAACACTCCCTTCCACCC
9607968 CTAAAGCCGTTCAATGAGTTGTAGCCATTACAATGT
130 CTAAAGCCGTTCAATGAGTTGTAGCCATTACAATGT
9608004 CGAATTAATT
Statistics
Matches: 441, Mismatches: 3, Indels: 25
0.94 0.01 0.05
Matches are distributed among these distances:
292 71 0.16
293 177 0.40
294 38 0.09
295 47 0.11
296 45 0.10
297 63 0.14
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (298 bp):
TAGCCATTACAATGTATTTTTAATAGTTTAGGATGATTACAAAATAGTATCTATCCAAAATCTAT
CTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAACAAACAACACTCCCTTCCACCCC
TAAAGCCGTTCAATGAGTTGTAGCCATTACAATGTTATTTTAATAGTTTAGGATGATTACAAATA
GTATCTATCCAAAATCTATCTTAACCCCTGAAGACAATGTTCAAACCCGAAACCTCTAAAAAAAC
AACACTCCCTTCCACCCCTAAAGCCGTTCAATGAGTTG
Found at i:9609221 original size:29 final size:29
Alignment explanation
Indices: 9609189--9609262 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
9609179 GAAAAATAAA
**
9609189 AAAATAAAAAATTTTAA-AAGTAATAAAAT
1 AAAATAAAAAATAATAAGAAGTAA-AAAAT
9609218 AAAAT-AAAAATAATAAGAAGTAAAAAAT
1 AAAATAAAAAATAATAAGAAGTAAAAAAT
*
9609246 AAAATAAATAATAATAA
1 AAAATAAAAAATAATAA
9609263 AAAATGCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (29 bp):
AAAATAAAAAATAATAAGAAGTAAAAAAT
Found at i:9609225 original size:19 final size:19
Alignment explanation
Indices: 9609203--9609264 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 19
9609193 TAAAAAATTT
9609203 TAAAAGTAATAA-AATAAAA
1 TAAAA-TAATAAGAATAAAA
9609222 TAAAAATAATAAGAAGTAAAAAA
1 T-AAAATAATAAGAA-T--AAAA
*
9609245 TAAAATAAATAATAATAAAA
1 TAAAAT-AATAAGAATAAAA
9609265 AATGCTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 7 0.19
20 10 0.28
21 1 0.03
22 6 0.17
23 12 0.33
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (19 bp):
TAAAATAATAAGAATAAAA
Found at i:9609227 original size:28 final size:28
Alignment explanation
Indices: 9609189--9609262 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
9609179 GAAAAATAAA
**
9609189 AAAATAAAAAATTTTAA-AAGTAATAAAAT
1 AAAAT-AAAAATAATAAGAAGTAA-AAAAT
9609218 AAAATAAAAATAATAAGAAGTAAAAAAT
1 AAAATAAAAATAATAAGAAGTAAAAAAT
9609246 AAAATAAATAATAATAA
1 AAAATAAA-AATAATAA
9609263 AAAATGCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 22 0.54
29 19 0.46
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (28 bp):
AAAATAAAAATAATAAGAAGTAAAAAAT
Found at i:9609245 original size:23 final size:22
Alignment explanation
Indices: 9609181--9609267 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
9609171 ATCAAAGGGA
9609181 AAAATAAA-AA-AATAAAAAATTTT
1 AAAATAAATAAGAATAAAAAA---T
*
9609204 AAAAGT-AATAA-AATAAAATA-
1 AAAA-TAAATAAGAATAAAAAAT
9609224 AAAAT-AATAAGAAGTAAAAAAT
1 AAAATAAATAAGAA-TAAAAAAT
*
9609246 AAAATAAATAATAATAAAAAAT
1 AAAATAAATAAGAATAAAAAAT
9609268 GCTAAAAATT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
19 6 0.11
20 6 0.11
21 6 0.11
22 13 0.24
23 13 0.24
24 11 0.20
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAATAAATAAGAATAAAAAAT
Found at i:9609943 original size:3 final size:3
Alignment explanation
Indices: 9609935--9609981 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
9609925 AAAATAATGA
9609935 AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAAT AAT -AT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT AAT AAT AAT AAT
9609981 A
1 A
9609982 TTTTTGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 26 0.63
4 11 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9609955 original size:23 final size:23
Alignment explanation
Indices: 9609927--9609977 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
9609917 GGCTTGAAAA
9609927 AATAATGAAAT-AAT-AATAATAAT
1 AATAAT-AAATAAATAAATAAT-AT
9609950 AATAATAAATAAATAAATAATAT
1 AATAATAAATAAATAAATAATAT
9609973 AATAA
1 AATAA
9609978 AATATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.15
23 16 0.62
24 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAATAAATAAATAAATAATAT
Found at i:9616863 original size:29 final size:28
Alignment explanation
Indices: 9616822--9616881 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
9616812 TATTAGAAAG
* *
9616822 TTATTAAATTAGTAATTTA-TCATTTTT
1 TTATTAAATTAGTAAATTAGTAATTTTT
9616849 TTATTATATATTAGTAAATTAGTAATTTTT
1 TTATTA-A-ATTAGTAAATTAGTAATTTTT
9616879 TTA
1 TTA
9616882 ATACAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 1 0.04
29 11 0.39
30 10 0.36
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
TTATTAAATTAGTAAATTAGTAATTTTT
Found at i:9629545 original size:29 final size:30
Alignment explanation
Indices: 9629468--9629545 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
9629458 ATAACTTCTG
* * ** *
9629468 AAAATTTACATTTCTAGTCCTTAAACTTTT
1 AAAATTTACACTTCCAGTCCCCAAACTTTC
*
9629498 ACAACTTTACACTT-CAGTCCCCAAACTTTC
1 A-AAATTTACACTTCCAGTCCCCAAACTTTC
9629528 AAAATTTACA-TTCCAGTC
1 AAAATTTACACTTCCAGTC
9629546 AATATTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.05
29 13 0.33
30 14 0.36
31 10 0.26
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTTACACTTCCAGTCCCCAAACTTTC
Found at i:9633774 original size:28 final size:24
Alignment explanation
Indices: 9633718--9633767 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
9633708 CAGAAAGTAA
9633718 ATAAATGAATACTTACCAATGACG
1 ATAAATGAATACTTACCAATGACG
9633742 ATAAATGAATACTTACCAATGACG
1 ATAAATGAATACTTACCAATGACG
9633766 AT
1 AT
9633768 TACTAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (24 bp):
ATAAATGAATACTTACCAATGACG
Found at i:9639252 original size:18 final size:20
Alignment explanation
Indices: 9639217--9639253 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
9639207 TAAAGGTAAT
9639217 TATACTATTTTAAAATTTAA
1 TATACTATTTTAAAATTTAA
9639237 TATA-TATTTT-AAATTTA
1 TATACTATTTTAAAATTTA
9639254 CGAAATTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TATACTATTTTAAAATTTAA
Found at i:9648670 original size:17 final size:17
Alignment explanation
Indices: 9648648--9648687 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
9648638 ACCAAACTCA
9648648 AATGCAATATAATCTAT
1 AATGCAATATAATCTAT
9648665 AATGCAATATAATCTAT
1 AATGCAATATAATCTAT
9648682 AATGCA
1 AATGCA
9648688 TTTACCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (17 bp):
AATGCAATATAATCTAT
Found at i:9650685 original size:15 final size:16
Alignment explanation
Indices: 9650658--9650688 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9650648 GTAGATGTGG
9650658 ATTTTAGATTCATATT
1 ATTTTAGATTCATATT
9650674 ATTTTA-ATTCATATT
1 ATTTTAGATTCATATT
9650689 CGAATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTAGATTCATATT
Found at i:9651948 original size:29 final size:29
Alignment explanation
Indices: 9651913--9651994 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
9651903 AAACTAAATT
*
9651913 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
9651942 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
9651971 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
9651995 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:9656709 original size:29 final size:29
Alignment explanation
Indices: 9656674--9656755 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
9656664 AAACTAAATT
*
9656674 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
9656703 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
9656732 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
9656756 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:9661859 original size:25 final size:25
Alignment explanation
Indices: 9661815--9661863 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9661805 TAAAAATATT
9661815 TTATTATATATATATTTATTTTTTA
1 TTATTATATATATATTTATTTTTTA
9661840 TTATTAT-TAT-TATTAATATTTTTT
1 TTATTATATATATATT--TATTTTTT
9661864 TAATTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 3 0.14
25 15 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTATATATATATTTATTTTTTA
Found at i:9662373 original size:29 final size:33
Alignment explanation
Indices: 9662305--9662382 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 33
9662295 TTTCCAAATT
*
9662305 TTAATATTTTTTATTTCTTTTTACATTGTTTTA
1 TTAATATTATTTATTTCTTTTTACATTGTTTTA
9662338 -T-ATATATATTTATTT-TTTTT-CATT-TTTTA
1 TTAATAT-TATTTATTTCTTTTTACATTGTTTTA
9662367 TTAATATTATTATATT
1 TTAATATTATT-TATT
9662383 AATATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 5 0.12
30 9 0.22
31 17 0.43
32 9 0.22
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (33 bp):
TTAATATTATTTATTTCTTTTTACATTGTTTTA
Found at i:9667306 original size:21 final size:21
Alignment explanation
Indices: 9667262--9667306 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9667252 AAATCGCGGC
* *
9667262 ATTACGGTCATAACGGGCGCT
1 ATTACGATCATAACGGACGCT
* *
9667283 ATTACGATCGTAACGGACGTT
1 ATTACGATCATAACGGACGCT
9667304 ATT
1 ATT
9667307 GGATGTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
ATTACGATCATAACGGACGCT
Found at i:9668018 original size:15 final size:15
Alignment explanation
Indices: 9667994--9668032 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
9667984 TTTTTATCTT
*
9667994 AAAATTAAATG-TTA
1 AAAATAAAATGCTTA
9668008 ATAAATAAAATGCTTA
1 A-AAATAAAATGCTTA
9668024 AAAATAAAA
1 AAAATAAAA
9668033 ATTAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.77
16 4 0.18
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAATAAAATGCTTA
Found at i:9670489 original size:177 final size:175
Alignment explanation
Indices: 9670188--9670543 Score: 559
Period size: 177 Copynumber: 2.0 Consensus size: 175
9670178 TGAAGCGATT
* * * * *
9670188 AAAATGTTAAAAGATTTTCTGTTATCTCTTGATGTCACTAGTTCGAGCATCATATATGTAGGACT
1 AAAAGGTTAAAAGATTTTCTGTTATCTATTGATGTCACTAGTTCAAGCACCACATATGTAGGACT
* * *
9670253 ATGAACGTTTATTGCCGAATGGTTGAGAATCTTTGAACAAATAATATCTTATATTCACCACAGAT
66 AGGAACGTTTATTACCGAATAGTTGAGAATCTTTGAACAAATAATATCTTATATTCACCACAGAT
*
9670318 TTATCAAAAAAAAAAAAGATTAGAGAAAATTGGAGAGATTAAATATA
131 TTATC--AAAAAAAAAAGATTAGAGAAAATTGGAGAGACTAAATATA
* *
9670365 AAAAGGTTAAAAGATTTTTTGTTATCTATTGATGTCTCTAGTTCAAGCACCACATATGTAGGACT
1 AAAAGGTTAAAAGATTTTCTGTTATCTATTGATGTCACTAGTTCAAGCACCACATATGTAGGACT
** *
9670430 AGGAACGTTTATTATTGAATAGTTGAGAATCTTTGAACAAATAATATCTTATATTCACCACATAT
66 AGGAACGTTTATTACCGAATAGTTGAGAATCTTTGAACAAATAATATCTTATATTCACCACAGAT
*
9670495 TTATCAAAAATAAAAGATTAGAGAAAATTGGAGAGACTAAATATA
131 TTATCAAAAAAAAAAGATTAGAGAAAATTGGAGAGACTAAATATA
9670540 AAAA
1 AAAA
9670544 TTAATAGATA
Statistics
Matches: 164, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
175 42 0.26
177 122 0.74
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (175 bp):
AAAAGGTTAAAAGATTTTCTGTTATCTATTGATGTCACTAGTTCAAGCACCACATATGTAGGACT
AGGAACGTTTATTACCGAATAGTTGAGAATCTTTGAACAAATAATATCTTATATTCACCACAGAT
TTATCAAAAAAAAAAGATTAGAGAAAATTGGAGAGACTAAATATA
Found at i:9671253 original size:7 final size:7
Alignment explanation
Indices: 9671241--9671266 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9671231 AATAATTAAA
9671241 TGATTTG
1 TGATTTG
9671248 TGATTTG
1 TGATTTG
9671255 TGATTTG
1 TGATTTG
9671262 TGATT
1 TGATT
9671267 GCTGCATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
TGATTTG
Found at i:9688718 original size:20 final size:21
Alignment explanation
Indices: 9688693--9688733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9688683 GTCATGATGG
*
9688693 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
9688713 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
9688734 TCGATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:9692192 original size:20 final size:21
Alignment explanation
Indices: 9692167--9692207 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9692157 GTCATGATGG
*
9692167 AAGA-GGAATTAGGGTTGAAA
1 AAGAGGGAATTAGGGATGAAA
*
9692187 AAGAGGGAATTGGGGATGAAA
1 AAGAGGGAATTAGGGATGAAA
9692208 TTGATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (21 bp):
AAGAGGGAATTAGGGATGAAA
Found at i:9693041 original size:22 final size:21
Alignment explanation
Indices: 9693000--9693042 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
9692990 TTTTTAATTC
*
9693000 TAAAAAATATTTGAATATTTT
1 TAAAAAATATTTGAAAATTTT
9693021 TAAAAAATCTATTT-AAAATTTT
1 TAAAAAA--TATTTGAAAATTTT
9693043 ATTATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAAAAATATTTGAAAATTTT
Found at i:9703734 original size:20 final size:19
Alignment explanation
Indices: 9703709--9703839 Score: 91
Period size: 20 Copynumber: 6.5 Consensus size: 19
9703699 TTTTCCTAAT
9703709 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATG-AAA
* *
9703729 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATAT-G-AAA
** * *
9703750 TTACAATGCGATTACGTAAA
1 TCGCAATGCGAATATG-AAA
* *
9703770 TCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATATGA-AA
* *
9703790 TCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATATGA-AA
* *
9703810 TCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATATGA-AA
9703830 TCGCAATGCG
1 TCGCAATGCG
9703840 TTTTACATAG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.85
21 13 0.14
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGAATATGAAA
Found at i:9704046 original size:22 final size:22
Alignment explanation
Indices: 9704021--9704079 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 22
9704011 GACATCCGTT
*
9704021 CCCATCTCCGACGAAATCAGTC
1 CCCATCTCCGACGAAATCAATC
*
9704043 CCCA----CGACGATATCAATC
1 CCCATCTCCGACGAAATCAATC
* *
9704061 TCCATCTCCGGCGAAATCA
1 CCCATCTCCGACGAAATCA
9704080 TTCACGGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
18 15 0.54
22 13 0.46
ACGTcount: A:0.29, C:0.39, G:0.14, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCAATC
Found at i:9704488 original size:20 final size:20
Alignment explanation
Indices: 9704415--9704504 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
9704405 GCGATTCTGT
*
9704415 CGTTGTGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
9704434 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
9704454 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
9704474 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
9704494 TGTTGCGATTT
1 CGTTGCGATTT
9704505 AAAGTTTCAG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:9704512 original size:20 final size:20
Alignment explanation
Indices: 9704469--9704512 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
9704459 CGATAGTCAT
** *
9704469 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
9704489 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
9704509 TTTC
1 TTTC
9704513 AGAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:9706408 original size:20 final size:20
Alignment explanation
Indices: 9706383--9706520 Score: 165
Period size: 20 Copynumber: 7.5 Consensus size: 20
9706373 AGAATAGTTT
9706383 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
9706403 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
9706419 A--ATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
9706437 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
9706457 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
9706473 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
9706491 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
9706511 ACTATCGCAA
1 ACTATCGCAA
9706521 CTAAAGAATC
Statistics
Matches: 100, Mismatches: 6, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
14 14 0.14
16 7 0.07
17 8 0.08
18 8 0.08
20 63 0.63
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:9706538 original size:54 final size:54
Alignment explanation
Indices: 9706383--9706558 Score: 282
Period size: 54 Copynumber: 3.3 Consensus size: 54
9706373 AGAATAGTTT
*
9706383 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
9706437 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
* * *
9706491 ACTATCGCAATGCGAAAATGACTATCGCAACTAAAGAATCACAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
** *
9706544 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
9706559 TTCTCTCGTT
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 17 0.15
54 98 0.85
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (54 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
Found at i:9706592 original size:20 final size:20
Alignment explanation
Indices: 9706567--9706706 Score: 150
Period size: 20 Copynumber: 7.3 Consensus size: 20
9706557 GATTCTCTCG
**
9706567 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
9706587 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
* *
9706607 TTGCAATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
**
9706627 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
9706646 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
9706660 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
9706680 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
9706700 TTGCGAT
1 TTGCGAT
9706707 TTTAAGTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 2 0.02
18 4 0.04
19 13 0.13
20 69 0.68
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:9707283 original size:21 final size:21
Alignment explanation
Indices: 9707192--9707289 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
9707182 GACTCACCTG
*
9707192 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
9707214 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
9707234 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
9707255 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
9707276 TCATCGTTGAAGAG
1 TCATCGTTCAAGAG
9707290 ATCTCTCCCA
Statistics
Matches: 59, Mismatches: 16, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:9707289 original size:42 final size:42
Alignment explanation
Indices: 9707189--9707289 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
9707179 ACCGACTCAC
* * *
9707189 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
* ** *
9707231 CTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGCCA
*
9707273 CTGTCATCGTTGAAGAG
1 CTGTCATCGTTCAAGAG
9707290 ATCTCTCCCA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
41 2 0.04
42 45 0.96
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:9708675 original size:14 final size:14
Alignment explanation
Indices: 9708656--9708691 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
9708646 ATTGTTTAAT
9708656 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
9708670 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
9708684 TGATTTGT
1 TGATTTGT
9708692 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:9708881 original size:34 final size:33
Alignment explanation
Indices: 9708793--9708888 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
9708783 AAAACAGACT
* **
9708793 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
9708827 ATCGCAATGTGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
9708860 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
9708889 CGAAGCTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Done.