Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008343.1 Hibiscus syriacus cultivar Beakdansim tig00111070_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: 738381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:188486 original size:33 final size:33
Alignment explanation
Indices: 188341--188488 Score: 233
Period size: 33 Copynumber: 4.3 Consensus size: 33
188331 TCTCGTTGCG
*
188341 CGCATTGCAATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
*
188374 CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT
188412 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
188445 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
188478 CGCATTGCGAT
1 CGCATTGCGAT
188489 AGTCATTTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
33 68 0.64
35 7 0.07
36 7 0.07
38 25 0.23
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:188496 original size:19 final size:19
Alignment explanation
Indices: 188359--188488 Score: 172
Period size: 19 Copynumber: 7.4 Consensus size: 19
188349 AATTCTCTCG
188359 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
188378 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
188397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
188416 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
188430 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
188449 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
188463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
188482 TTGCGAT
1 TTGCGAT
188489 AGTCATTTTT
Statistics
Matches: 97, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.12
16 14 0.14
17 14 0.14
19 57 0.59
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:188616 original size:14 final size:14
Alignment explanation
Indices: 188597--188633 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
188587 TCAATTAAAT
188597 AAATCAATTTTTAC
1 AAATCAATTTTTAC
188611 AAATC-ATCTTTTAC
1 AAATCAAT-TTTTAC
188625 AAATCAATT
1 AAATCAATT
188634 AAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATCAATTTTTAC
Found at i:188697 original size:84 final size:84
Alignment explanation
Indices: 188598--188773 Score: 289
Period size: 84 Copynumber: 2.1 Consensus size: 84
188588 CAATTAAATA
* ***
188598 AATCAATTTTTACAAATCATCTTTTACAAATCAATTAAACAATAAAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATAAAAAAATAAGCAATAAGAATT
*
188663 ATTTCCTCATTTACTATTG
66 ATTTCCTCATCTACTATTG
*
188682 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATAAAAAAATAAGCAATAAGAATT
*
188747 ATTTTCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
188766 AATCAACT
1 AATCAACT
188774 ATTGCAGCCA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATAAAAAAATAAGCAATAAGAATT
ATTTCCTCATCTACTATTG
Found at i:188705 original size:14 final size:14
Alignment explanation
Indices: 188682--188715 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
188672 TTTACTATTG
188682 AATCAACTTTTACA
1 AATCAACTTTTACA
*
188696 AATCATCTTTTACA
1 AATCAACTTTTACA
188710 AATCAA
1 AATCAA
188716 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:190624 original size:19 final size:19
Alignment explanation
Indices: 190584--190720 Score: 158
Period size: 19 Copynumber: 7.4 Consensus size: 19
190574 TAGTTTACTT
* *
190584 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
190604 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* **
190623 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
190642 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
190661 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
190680 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
190694 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
190713 TCGCAACG
1 TCGCAACG
190721 AGAGAATCGC
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 72 0.71
20 12 0.12
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:190701 original size:33 final size:33
Alignment explanation
Indices: 190659--190737 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
190649 GCGAAACCAA
190659 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
190692 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
190725 AATCGCAATGCGA
1 AATCGCAACGCGA
190738 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:190755 original size:19 final size:19
Alignment explanation
Indices: 190733--190845 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
190723 AGAATCGCAA
190733 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
190752 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
190766 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
190785 TGCGA--TT-CTAT--CGT
1 TGCGATTTTGGTTTCGCGT
**
190799 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
190818 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
190837 TGCGATTTT
1 TGCGATTTT
190846 AAGTTTCGTA
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 5 0.06
17 5 0.06
18 1 0.01
19 46 0.59
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:190768 original size:14 final size:14
Alignment explanation
Indices: 190749--190807 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
190739 TTTGGTTTCG
190749 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
190763 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
190780 CGCGTTGCGATTCTAT
1 --CGTTGCGATTTTGT
190796 CGTTGCGATTTT
1 CGTTGCGATTTT
190808 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 23 0.62
15 1 0.03
16 1 0.03
17 1 0.03
19 11 0.30
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:190775 original size:33 final size:33
Alignment explanation
Indices: 190733--190827 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
190723 AGAATCGCAA
190733 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
* *
190766 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
**
190799 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
190828 GTTTCGCGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:191025 original size:83 final size:86
Alignment explanation
Indices: 190909--191182 Score: 268
Period size: 94 Copynumber: 3.1 Consensus size: 86
190899 ATGGATTGCA
* * ** *
190909 TTACTTCAACCAATAGACAAAACAAAAACAAATACTAACTTCAG-G-G-TA-TTAGTTTAGCAGA
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAACAGA
*
190970 ATTGGCAGTAACCGAACAAAT
66 ATTGGCAGCAACCGAACAAAT
**
190991 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTTACAGTGTTAAAGAATACACAGTT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTT-CAGTG----AG-ATACACAGTT
* *
191056 TAACAGAATTGGCGGCAACCGAATAAAT
59 TAACAGAATTGGCAGCAACCGAACAAAT
*
191084 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT--CAGTG----AG-ATACACAGT
* *
191149 TTAGCAGAATTGGCAGCAACCGAATAAAT
58 TTAACAGAATTGGCAGCAACCGAACAAAT
191178 TTACT
1 TTACT
191183 AAGCAATCTA
Statistics
Matches: 164, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
82 4 0.02
83 33 0.20
84 3 0.02
85 1 0.01
90 1 0.01
92 21 0.13
93 48 0.29
94 53 0.32
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (86 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAACAGA
ATTGGCAGCAACCGAACAAAT
Found at i:191118 original size:93 final size:93
Alignment explanation
Indices: 190959--191182 Score: 360
Period size: 94 Copynumber: 2.4 Consensus size: 93
190949 TCAGGGTATT
* *
190959 AGTTTAGCAGAATTGGCAGTAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAA
* * *
191024 TACT-ATTTTACAGTGTTAAAGAATACAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
* *
191052 AGTTTAACAGAATTGGCGGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAAC-AAAGACAAA
191117 TACTAACTTCACAGTGTTAAAGAATAAAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
191146 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
191183 AAGCAATCTA
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
92 19 0.16
93 45 0.38
94 56 0.47
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAAT
ACTAACTTCACAGTGTTAAAGAATAAAC
Found at i:192921 original size:40 final size:37
Alignment explanation
Indices: 192877--192976 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 37
192867 TCTTTTGGTT
192877 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGA--ATCGCAACGC
*
192916 GGAAATAAAAATCGCAAC-A-AG-A-GAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
*
192950 GAAATGAAAATCGCAACGCGA-AATGAA
1 GAAATGAAAATCGCAACGAGAGAATGAA
192977 AATCGCAATG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
33 16 0.30
34 10 0.19
35 2 0.04
36 5 0.09
37 1 0.02
38 2 0.04
39 1 0.02
40 16 0.30
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
Found at i:192963 original size:19 final size:19
Alignment explanation
Indices: 192877--192989 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
192867 TCTTTTGGTT
*
192877 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
192896 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
192916 GGAAATAAAAATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
192934 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
192950 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
192969 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
192988 GA
1 GA
192990 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
15 2 0.03
16 1 0.01
18 3 0.04
19 35 0.45
20 25 0.32
21 2 0.03
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:193039 original size:19 final size:19
Alignment explanation
Indices: 193015--193092 Score: 93
Period size: 19 Copynumber: 3.9 Consensus size: 19
193005 GCGATTCTCT
193015 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
193034 CGTTGCGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
**
193053 CTTGTTGCGATAGTCATTTTCG
1 C--GTTGCGATTTTCA-TTTCG
*
193075 CGTTCCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
193093 TCTCGTTGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 23 0.47
20 10 0.20
21 11 0.22
22 5 0.10
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:193061 original size:21 final size:21
Alignment explanation
Indices: 193009--193105 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 21
192999 CGCGTTGCGA
193009 TTCTCTCGTTGCGATTTTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
193029 TT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
193049 TTCTCTTGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
193070 TT-TCGCGTTCCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
193090 TTCTCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
193106 CTTCTGCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
19 16 0.26
20 19 0.31
21 27 0.44
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:193070 original size:40 final size:41
Alignment explanation
Indices: 193009--193104 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
192999 CGCGTTGCGA
** *
193009 TTCTCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATAGTCATTTTCGCGTTCCGATTTTCAT
*
193049 TTCTCTTGTTGCGATAGTCATTTTCGCGTTCCGATTTTCAT
1 TTCTCTCGTTGCGATAGTCATTTTCGCGTTCCGATTTTCAT
193090 TTCTCTCGTTGCGAT
1 TTCTCTCGTTGCGAT
193105 TCTTCTGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 17 0.34
41 33 0.66
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.49
Consensus pattern (41 bp):
TTCTCTCGTTGCGATAGTCATTTTCGCGTTCCGATTTTCAT
Found at i:193649 original size:20 final size:20
Alignment explanation
Indices: 193624--193781 Score: 151
Period size: 20 Copynumber: 7.7 Consensus size: 20
193614 CTTTAAAAAT
193624 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
193644 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
193664 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
193685 TGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
193705 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
193726 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * *
193748 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
193768 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
193782 TATGTTCGCG
Statistics
Matches: 117, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.02
20 56 0.48
21 40 0.34
22 19 0.16
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:193683 original size:41 final size:41
Alignment explanation
Indices: 193626--193819 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 41
193616 TTAAAAATCG
193626 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
*
193667 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* **
193708 CGTTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTGT
* * * * *
193750 CGTTGCGATAGTAAGAAT-CGCGTTGCGATTTATATGT-TCG-
1 CGTTGCGAT-TTACGGATACGCGTTGCGATTT-TACGTATTGT
* ** *
193790 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
193820 CTGGAAAATC
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
39 3 0.02
40 21 0.16
41 71 0.54
42 32 0.24
43 5 0.04
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:193790 original size:20 final size:20
Alignment explanation
Indices: 193767--193819 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
193757 ATAGTAAGAA
*
193767 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
193787 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
193807 TCGCGTTGCGATT
1 TCGCGTTGCGATT
193820 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:197738 original size:23 final size:23
Alignment explanation
Indices: 197708--197791 Score: 161
Period size: 23 Copynumber: 3.7 Consensus size: 23
197698 CCCCCCCTGA
197708 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
197731 GGGAACCGA-TCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
197753 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
197776 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
197792 CACAGGGGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
22 22 0.37
23 38 0.63
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:197800 original size:21 final size:21
Alignment explanation
Indices: 197708--197812 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 21
197698 CCCCCCCTGA
*
197708 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
*
197731 GGGAACCGA-TCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
*
197753 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
197776 GGGAACCGATTCCCCC-CACAG
1 GGGAACCGATTCCCCCTCA-AG
* *
197797 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
197813 ATGGGGTTCT
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.01
21 16 0.21
22 22 0.29
23 38 0.49
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTCAAG
Found at i:197813 original size:20 final size:21
Alignment explanation
Indices: 197774--197813 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
197764 CCCCCTTTGA
*
197774 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
197795 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
197814 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:199807 original size:17 final size:17
Alignment explanation
Indices: 199774--199807 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
199764 TTGAATATTT
* *
199774 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
199791 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
199808 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:200539 original size:74 final size:74
Alignment explanation
Indices: 200399--200601 Score: 295
Period size: 74 Copynumber: 2.7 Consensus size: 74
200389 CAAAGCCAAA
* * * * * *
200399 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCAAAGGGGGTACCGATCCCCCCTTAATGGTT
1 AATTTCAGAATGCTCGGAGGGAACCGATTCCCCCC-AAGGGGGTACCGATTCCCCCTGAATAGTT
200464 TGGCTCCGAG
65 TGGCTCCGAG
200474 -ATTTCAAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGGGGTACCGATTCCCCCTGAATAGT
1 AATTTC-AGAATGCTCGGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCCCTGAATAGT
200537 TTGGCTCCGAG
64 TTGGCTCCGAG
*
200548 AATTTCAGTATGCTCGGAGGGAACCGATTCCCCCCAA-GGGGTACCGATTCCCCC
1 AATTTCAGAATGCTCGGAGGGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCC
200602 CTTATATAAC
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
73 18 0.15
74 67 0.57
75 32 0.27
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.22
Consensus pattern (74 bp):
AATTTCAGAATGCTCGGAGGGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCTGAATAGTTT
GGCTCCGAG
Found at i:203223 original size:19 final size:19
Alignment explanation
Indices: 203199--203242 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
203189 ATACTAATTT
203199 TTTTTTGTAATTTTTT-AGA
1 TTTTTTGT-ATTTTTTCAGA
*
203218 TTTTTTGTATTTTTTCTGA
1 TTTTTTGTATTTTTTCAGA
203237 TTTTTT
1 TTTTTT
203243 TATATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (19 bp):
TTTTTTGTATTTTTTCAGA
Found at i:203376 original size:16 final size:17
Alignment explanation
Indices: 203349--203380 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
203339 ATCTCTAGAG
203349 TAGAGATAGAGATGAGC
1 TAGAGATAGAGATGAGC
203366 TAGAG-TAGAGATGAG
1 TAGAGATAGAGATGAG
203381 GATTGGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.38, T:0.19
Consensus pattern (17 bp):
TAGAGATAGAGATGAGC
Found at i:205429 original size:22 final size:22
Alignment explanation
Indices: 205403--205447 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
205393 ATGTCGGTAG
205403 TATTGATACTACCTAGTGAGTA
1 TATTGATACTACCTAGTGAGTA
*
205425 TATTGGTACTACCTAGTGAGTA
1 TATTGATACTACCTAGTGAGTA
205447 T
1 T
205448 CGATACTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (22 bp):
TATTGATACTACCTAGTGAGTA
Found at i:205816 original size:54 final size:53
Alignment explanation
Indices: 205699--205817 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 53
205689 TTTCTTGCCT
* * *
205699 ACCTTAAAATTTGAGTTTTCTTTTATTAGCTACTTATTTTACTGACGGTACTC
1 ACCTTAAAATTTAAATTTTCTTTTATTAGCTACTTATTTTACTGACGGTACAC
*** *
205752 ACCCCGAAATTTAAATATTT-TTTTGATTAGTTACTTATTTTACTGACGGTACAC
1 ACCTTAAAATTTAAAT-TTTCTTTT-ATTAGCTACTTATTTTACTGACGGTACAC
205806 ACCTTAAAATTT
1 ACCTTAAAATTT
205818 TATTTGTACC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
53 15 0.28
54 39 0.72
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (53 bp):
ACCTTAAAATTTAAATTTTCTTTTATTAGCTACTTATTTTACTGACGGTACAC
Found at i:211581 original size:41 final size:41
Alignment explanation
Indices: 211527--211647 Score: 188
Period size: 41 Copynumber: 3.0 Consensus size: 41
211517 GCGACGAATT
*
211527 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
* * *
211568 TGGAAAATTGCAACGACACTGTACACTATCGCAATGCGAGA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
* *
211609 TGGCAAATCGCAATGACACTGTACACTATCGCAACGCGA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
211648 TTTTCAACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
Found at i:211641 original size:21 final size:21
Alignment explanation
Indices: 211577--211642 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
211567 ATGGAAAATT
*
211577 GCAACGACACTGTACACTATC
1 GCAATGACACTGTACACTATC
* * *
211598 GCAATG-CGAGATG-GCA-AATC
1 GCAATGAC-A-CTGTACACTATC
211618 GCAATGACACTGTACACTATC
1 GCAATGACACTGTACACTATC
211639 GCAA
1 GCAA
211643 CGCGATTTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
19 2 0.06
20 13 0.39
21 16 0.48
22 2 0.06
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (21 bp):
GCAATGACACTGTACACTATC
Found at i:211644 original size:62 final size:62
Alignment explanation
Indices: 211592--211780 Score: 234
Period size: 71 Copynumber: 2.9 Consensus size: 62
211582 GACACTGTAC
*
211592 ACTATCGCAATGCGAGATGGCAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAGATGGCAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
*
211654 ACTATCGCAACGCGAAATGGAAAATCGCAACGATCGCAATGACACTGTACACTATCGCAACGCGA
1 ACTATCGCAACGCG--A--G---ATGGCAA--ATCGCAATGACACTGTACACTATCGCAACGCGA
211719 TTTTCA
57 TTTTCA
* * * * *
211725 ACTATCGCAACGCGAAATGGAAAATCGTAACGACACTGTAGACTATCGCAACGCGA
1 ACTATCGCAACGCGAGATGGCAAATCGCAATGACACTGTACACTATCGCAACGCGA
211781 AATGGAAAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
62 43 0.39
64 6 0.05
66 1 0.01
69 7 0.06
71 53 0.48
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAGATGGCAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
Found at i:211731 original size:71 final size:71
Alignment explanation
Indices: 211615--211757 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
211605 GAGATGGCAA
211615 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
211680 GCAACG
66 GCAACG
211686 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
*
211751 GTAACG
66 GCAACG
211757 A
1 A
211758 CACTGTAGAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (71 bp):
ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
GCAACG
Found at i:211772 original size:21 final size:21
Alignment explanation
Indices: 211748--211839 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
211738 GAAATGGAAA
*
211748 ATCGTAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
211769 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
211789 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
211810 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
211831 ATCGCAACG
1 ATCGCAACG
211840 CGAAATGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 41 0.69
22 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:211772 original size:41 final size:41
Alignment explanation
Indices: 211725--211818 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
211715 GCGATTTTCA
*
211725 ACTATCGCAACGCGAAATGGAAAATCGTAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
211766 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
211807 ACTATCGCAACG
1 ACTATCGCAACG
211819 ACACTGTAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:211794 original size:20 final size:20
Alignment explanation
Indices: 211728--211797 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
211718 ATTTTCAACT
211728 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
211748 ATCGTAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
211769 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
211789 ATCGCAACG
1 ATCGCAACG
211798 ACACTGTAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 17 0.46
21 8 0.22
22 3 0.08
23 3 0.08
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:212776 original size:16 final size:17
Alignment explanation
Indices: 212755--212787 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
212745 AGAATTCATT
212755 TAAAAAT-TTTAAAAAA
1 TAAAAATATTTAAAAAA
212771 TAAAAATATTTAAAAAA
1 TAAAAATATTTAAAAAA
212788 ACAACAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:214040 original size:15 final size:15
Alignment explanation
Indices: 214017--214048 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
214007 TCGACGGCCT
214017 TTTAACTTCAATTTC
1 TTTAACTTCAATTTC
*
214032 TTTACCTTCAATTTC
1 TTTAACTTCAATTTC
214047 TT
1 TT
214049 GACCATCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAACTTCAATTTC
Found at i:214295 original size:63 final size:63
Alignment explanation
Indices: 214147--214296 Score: 162
Period size: 63 Copynumber: 2.4 Consensus size: 63
214137 TTTGGGTTGA
* * * *
214147 ATCGGGTCATTTCGGGTTTCAGTTTTATTCGGGTCTATAGTAGGTCGGGTCGGATCGGGTCGG
1 ATCGGGTCATATCGGGTATCAGTTTTATTCGGGTCTATAGTAAGTCGGGTCGGATCGGATCGG
* * * * *
214210 GTCGGGTTATTTCGGGTTTCAGTTTTATTCGGGTCTATAGTAAGTCGGG-CTGATGCAGGTATCG
1 ATCGGGTCATATCGGGTATCAGTTTTATTCGGGTCTATAGTAAGTCGGGTCGGAT-C-GG-ATCG
214274 G
63 G
*
214275 ATCTGGTCATATC-GG-ATCAGTT
1 ATCGGGTCATATCGGGTATCAGTT
214297 GATTTCGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
62 4 0.05
63 53 0.72
64 4 0.05
65 13 0.18
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.36
Consensus pattern (63 bp):
ATCGGGTCATATCGGGTATCAGTTTTATTCGGGTCTATAGTAAGTCGGGTCGGATCGGATCGG
Found at i:221744 original size:42 final size:42
Alignment explanation
Indices: 221685--221770 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
221675 GGAGGACTAC
* *
221685 CAGGTGTGGATGGAGGAGATAAAGTTTGCTCAGTGTTGGAAG
1 CAGGTGTGGATGGAGGAGATAAAGTTTGCGCAGTGTTAGAAG
*
221727 CAGGTGTTGATGGAGGAGATAAAGTTTGCGCAGTGTTAGAAG
1 CAGGTGTGGATGGAGGAGATAAAGTTTGCGCAGTGTTAGAAG
221769 CA
1 CA
221771 TTTGTGCGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.38, T:0.26
Consensus pattern (42 bp):
CAGGTGTGGATGGAGGAGATAAAGTTTGCGCAGTGTTAGAAG
Found at i:222166 original size:6 final size:6
Alignment explanation
Indices: 222155--222198 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
222145 TCGGCTCGGC
222155 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
222199 ATACGTGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:226610 original size:157 final size:157
Alignment explanation
Indices: 226324--226643 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 157
226314 AAGAATAAAG
226324 GAAGTAGTGTTTCCCAAACTGAATATGCTAAATTAATCGGAAGTTTAATGTTCTTAATGAACCAT
1 GAAGTAGTGTTTCCCAAACTGAATATGCTAAATTAATCGGAAGTTTAATGTTCTTAATGAACCAT
*
226389 ACTCGGCCTGATATTGCTTATGTTGTGAGTAGACTAAGTAGATATACTCATAATCCGAGTGGTGA
66 ACTCGGCCTGATATTGCTTATGCTGTGAGTAGACTAAGTAGATATACTCATAATCCGAGTGGTGA
*
226454 GCACTGGATTGCGCTTAAACGCTTACT
131 GCACTGGATTACGCTTAAACGCTTACT
*
226481 GAAGTAGTGTTTCCCAAACTGAATATGCTAAATTAATCGGAAGTTTAATGTTCTTAATGAACTAT
1 GAAGTAGTGTTTCCCAAACTGAATATGCTAAATTAATCGGAAGTTTAATGTTCTTAATGAACCAT
226546 ACTCGGCCTGATATTGCTTATGCTGTGAGTAGACTAAGTAGATATACTCATAATCCGAGTGGTGA
66 ACTCGGCCTGATATTGCTTATGCTGTGAGTAGACTAAGTAGATATACTCATAATCCGAGTGGTGA
226611 GCACTGGATTACGCTTAAACGCTTACT
131 GCACTGGATTACGCTTAAACGCTTACT
226638 GAAGTA
1 GAAGTA
226644 TCTTAAGGGT
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (157 bp):
GAAGTAGTGTTTCCCAAACTGAATATGCTAAATTAATCGGAAGTTTAATGTTCTTAATGAACCAT
ACTCGGCCTGATATTGCTTATGCTGTGAGTAGACTAAGTAGATATACTCATAATCCGAGTGGTGA
GCACTGGATTACGCTTAAACGCTTACT
Found at i:228209 original size:5 final size:5
Alignment explanation
Indices: 228195--228242 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
228185 GTCCGTCCGT
* * * *
228195 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTC
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTC
228243 ATGGTCGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.06, C:0.42, G:0.35, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:228255 original size:6 final size:6
Alignment explanation
Indices: 228244--228301 Score: 89
Period size: 6 Copynumber: 9.7 Consensus size: 6
228234 GCTCGGCTCA
* * *
228244 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG AGGTCG AGGTCG AGGTCG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG
228292 TGGTCG TGGT
1 TGGTCG TGGT
228302 AATACGTGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.05, C:0.16, G:0.50, T:0.29
Consensus pattern (6 bp):
TGGTCG
Found at i:230054 original size:22 final size:22
Alignment explanation
Indices: 230027--230068 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
230017 TTTGAAAAAA
230027 ATTGAATTTATATTC-TTTTTGT
1 ATTGAATTT-TATTCATTTTTGT
230049 ATTGAATTTTATTCATTTTT
1 ATTGAATTTTATTCATTTTT
230069 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (22 bp):
ATTGAATTTTATTCATTTTTGT
Found at i:230076 original size:30 final size:30
Alignment explanation
Indices: 230042--230100 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
230032 ATTTATATTC
*
230042 TTTTTGTATTG-AATTTTATTCATTTTTAA
1 TTTTTTTATTGCAATTTTATTCATTTTTAA
* *
230071 TTTTTTTATTGCATTTTTATTGATTTTTAA
1 TTTTTTTATTGCAATTTTATTCATTTTTAA
230101 AAAAATGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (30 bp):
TTTTTTTATTGCAATTTTATTCATTTTTAA
Found at i:230089 original size:11 final size:10
Alignment explanation
Indices: 230043--230099 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
230033 TTTATATTCT
230043 TTTTGTATTGA
1 TTTT-TATTGA
* *
230054 ATTTTATTCA
1 TTTTTATTGA
230064 TTTTTAATT--
1 TTTTT-ATTGA
230073 TTTTTATTGCA
1 TTTTTATTG-A
230084 TTTTTATTGA
1 TTTTTATTGA
230094 TTTTTA
1 TTTTTA
230100 AAAAAATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 3 0.08
9 5 0.13
10 16 0.41
11 15 0.38
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:230535 original size:30 final size:31
Alignment explanation
Indices: 230494--230557 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
230484 ATTTTTTAGC
230494 TTTATATTTTTTCTATTG-AATTTTATTCATT
1 TTTATATTTTTT-TATTGCAATTTTATTCATT
* *
230525 TTTA-ATTTTTTTATTGCATTTTTATTGATT
1 TTTATATTTTTTTATTGCAATTTTATTCATT
230555 TTT
1 TTT
230558 TAAAAAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 21 0.70
31 4 0.13
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (31 bp):
TTTATATTTTTTTATTGCAATTTTATTCATT
Found at i:230548 original size:11 final size:10
Alignment explanation
Indices: 230502--230557 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
230492 GCTTTATATT
230502 TTTTCTATTGA
1 TTTT-TATTGA
* *
230513 ATTTTATTCA
1 TTTTTATTGA
230523 TTTTTAATT--
1 TTTTT-ATTGA
230532 TTTTTATTGCA
1 TTTTTATTG-A
230543 TTTTTATTGA
1 TTTTTATTGA
230553 TTTTT
1 TTTTT
230558 TAAAAAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 3 0.08
9 5 0.13
10 15 0.39
11 15 0.39
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:230639 original size:32 final size:32
Alignment explanation
Indices: 230598--230669 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
230588 TATCAATTGT
230598 AATTAAAAGT--ATAAAAATGCAATAAAAAAAAG
1 AATTAAAAGTGAAT-AAAATGCAAT-AAAAAAAG
* *
230630 AATTAAAAGTGAATAAAATTCAATACAAAAAG
1 AATTAAAAGTGAATAAAATGCAATAAAAAAAG
230662 AATATAAA
1 AAT-TAAA
230670 GTCAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 20 0.57
33 13 0.37
34 2 0.06
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (32 bp):
AATTAAAAGTGAATAAAATGCAATAAAAAAAG
Found at i:231822 original size:22 final size:21
Alignment explanation
Indices: 231780--231822 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
231770 TTTTTTTAAT
*
231780 TTTTTAATAATAAAAATAATA
1 TTTTTAATAATAAAAAAAATA
231801 TTTTTAATTAA-AAAGAAAAATA
1 TTTTTAA-TAATAAA-AAAAATA
231823 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTTTAATAATAAAAAAAATA
Found at i:232368 original size:13 final size:13
Alignment explanation
Indices: 232346--232380 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
232336 CGACGTCTAT
*
232346 GGAAAAGGGAAGG
1 GGAAAGGGGAAGG
232359 GGAAAGGGGAAGG
1 GGAAAGGGGAAGG
*
232372 GAAAAGGGG
1 GGAAAGGGG
232381 GAGAGGGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (13 bp):
GGAAAGGGGAAGG
Found at i:232762 original size:26 final size:26
Alignment explanation
Indices: 232739--232791 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
232729 ATTAATTATA
*
232739 TCTTATATTTCATATAAAATATTAAT
1 TCTTAAATTTCATATAAAATATTAAT
*
232765 TCTTAAATTTTATATAAAATATTAAT
1 TCTTAAATTTCATATAAAATATTAAT
232791 T
1 T
232792 TCACCCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (26 bp):
TCTTAAATTTCATATAAAATATTAAT
Found at i:234156 original size:17 final size:17
Alignment explanation
Indices: 234134--234168 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
234124 CTTACAATGT
234134 TCCCACAATTCTACTTG
1 TCCCACAATTCTACTTG
234151 TCCCACAATTCTACTTG
1 TCCCACAATTCTACTTG
234168 T
1 T
234169 ATCAGTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (17 bp):
TCCCACAATTCTACTTG
Found at i:237103 original size:45 final size:45
Alignment explanation
Indices: 237054--237140 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
237044 GAACATCGAA
* *
237054 TGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
237099 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACT
237141 ATGGCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAACCATGCATCGATGCACTCAG
Found at i:247729 original size:18 final size:18
Alignment explanation
Indices: 247706--247745 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
247696 TGCTTATGTG
247706 CTAGATTTCAATCATGCC
1 CTAGATTTCAATCATGCC
247724 CTAGATTTCAATCATGCC
1 CTAGATTTCAATCATGCC
247742 CTAG
1 CTAG
247746 GAAATCACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (18 bp):
CTAGATTTCAATCATGCC
Found at i:258640 original size:21 final size:21
Alignment explanation
Indices: 258575--258669 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
258565 TTGTGCTTAA
*
258575 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
* *
258595 TGTATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
258617 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
258638 TGCACCGATGCACGACTTGAATG
1 TGCATCGATACAC--CTTGAATG
258661 TGCATCGAT
1 TGCATCGAT
258670 GCACAAGGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.17
21 20 0.34
22 12 0.21
23 16 0.28
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:258663 original size:23 final size:21
Alignment explanation
Indices: 258598--258673 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
258588 CTAACAGTGT
258598 ATCGATGCATCCTTGAATGTGC
1 ATCGATGCA-CCTTGAATGTGC
* * *
258620 ATCGATACACCATGAAGGTGC
1 ATCGATGCACCTTGAATGTGC
*
258641 ACCGATGCACGACTTGAATGTGC
1 ATCGATGCAC--CTTGAATGTGC
258664 ATCGATGCAC
1 ATCGATGCAC
258674 AAGGCCATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 18 0.41
22 8 0.18
23 18 0.41
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
ATCGATGCACCTTGAATGTGC
Found at i:261447 original size:45 final size:44
Alignment explanation
Indices: 261336--261459 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 44
261326 GATTAAATTG
*
261336 AACATCGAATGCATTTTATGCATCGATGCACTCAGTGCATTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACTCTGTGCATTTGA
** ****
261380 TGCATCG-ATGCACAAACCATGCATCGATGCACTCTG-GCTATTTTGA
1 AACATCGAATG--CATTTTATGCATCGATGCACTCTGTGC-A-TTTGA
*
261426 AACATCGAATGCATTTTATGCATCGATACACTCT
1 AACATCGAATGCATTTTATGCATCGATGCACTCT
261460 TAGTGCACCG
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
43 3 0.05
44 7 0.11
45 38 0.62
46 10 0.16
47 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCTGTGCATTTGA
Found at i:262252 original size:10 final size:10
Alignment explanation
Indices: 262234--262276 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
262224 ATAATTGAAC
262234 TTTAATAATA
1 TTTAATAATA
*
262244 TTTACTAATA
1 TTTAATAATA
262254 TTTAATAATA
1 TTTAATAATA
*
262264 TTTACTAATA
1 TTTAATAATA
262274 TTT
1 TTT
262277 TCAATATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAATAATA
Found at i:262259 original size:20 final size:20
Alignment explanation
Indices: 262234--262276 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
262224 ATAATTGAAC
262234 TTTAATAATATTTACTAATA
1 TTTAATAATATTTACTAATA
262254 TTTAATAATATTTACTAATA
1 TTTAATAATATTTACTAATA
262274 TTT
1 TTT
262277 TCAATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAATAATATTTACTAATA
Found at i:262364 original size:29 final size:24
Alignment explanation
Indices: 262306--262357 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
262296 GTTCGAAGTT
*
262306 TATTTAATAATATTTCCTCTAATC
1 TATTTAATAATATTTCCTCCAATC
262330 TATTTAATAATATTTCCTCCAATC
1 TATTTAATAATATTTCCTCCAATC
262354 TATT
1 TATT
262358 AAGTTTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTAATAATATTTCCTCCAATC
Found at i:264184 original size:24 final size:24
Alignment explanation
Indices: 264154--264217 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
264144 GTTCGAAGTT
*
264154 TATTTAATTATATTTACTCTAATC
1 TATTTAATTATATTTACTCCAATC
* *
264178 TATTTAATAATATTTCCTCCAATC
1 TATTTAATTATATTTACTCCAATC
264202 TA-TTAAGTT-TATTTAC
1 TATTTAA-TTATATTTAC
264218 CGTTGACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTAATTATATTTACTCCAATC
Found at i:267210 original size:50 final size:50
Alignment explanation
Indices: 267151--267250 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
267141 TGATTTCAAA
267151 ATCATATCTAAAATCTAGTTTTTGTTTCATTTTAGTATTCAAAATTTAAC
1 ATCATATCTAAAATCTAGTTTTTGTTTCATTTTAGTATTCAAAATTTAAC
267201 ATCATATCTAAAATCTAGTTTTTGTTTCATTTTAGTATTCAAAATTTAAC
1 ATCATATCTAAAATCTAGTTTTTGTTTCATTTTAGTATTCAAAATTTAAC
267251 GTTAAACTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (50 bp):
ATCATATCTAAAATCTAGTTTTTGTTTCATTTTAGTATTCAAAATTTAAC
Found at i:271823 original size:2 final size:2
Alignment explanation
Indices: 271810--271886 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
271800 TTACTTAGTC
*
271810 AT AT AG AT 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 AT AT AT AT
271852 AT AT AT AT 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 AT A
271887 ATAAATAATA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271918 original size:26 final size:25
Alignment explanation
Indices: 271889--271944 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
271879 TATATATAAT
** *
271889 AAATAATATTTATTTATTTATTATCA
1 AAATAATATTTATAAATTTAATAT-A
**
271915 AAATCCTATTTATAAATTTAATATA
1 AAATAATATTTATAAATTTAATATA
271940 AAATA
1 AAATA
271945 CTTTTAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATAATATTTATAAATTTAATATA
Found at i:275358 original size:15 final size:15
Alignment explanation
Indices: 275338--275371 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
275328 GGGATCAATA
275338 CATTTTGCATACATT
1 CATTTTGCATACATT
*
275353 CATTTTGTATACATT
1 CATTTTGCATACATT
275368 CATT
1 CATT
275372 ATTCATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (15 bp):
CATTTTGCATACATT
Found at i:276874 original size:13 final size:13
Alignment explanation
Indices: 276856--276885 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
276846 CATGGTATGA
276856 TGTGAAAGCACAC
1 TGTGAAAGCACAC
*
276869 TGTGAAAGCACAT
1 TGTGAAAGCACAC
276882 TGTG
1 TGTG
276886 TTTATCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (13 bp):
TGTGAAAGCACAC
Found at i:282735 original size:9 final size:10
Alignment explanation
Indices: 282712--282736 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
282702 GCTTGAAGAA
282712 AAAAATGATG
1 AAAAATGATG
282722 AAAAATGATG
1 AAAAATGATG
282732 AAAAA
1 AAAAA
282737 AAAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (10 bp):
AAAAATGATG
Found at i:282756 original size:33 final size:31
Alignment explanation
Indices: 282707--282770 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 31
282697 ATTATGCTTG
*
282707 AAGAAAAAAATGATGAAAAATGATGAAAAAA
1 AAGAAAAAAATAATGAAAAATGATGAAAAAA
282738 AAGAAAAAAATCAAATGAAAAATGATGAAAAAA
1 AAGAAAAAAAT--AATGAAAAATGATGAAAAAA
282771 TATATAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
33 19 0.63
ACGTcount: A:0.72, C:0.02, G:0.14, T:0.12
Consensus pattern (31 bp):
AAGAAAAAAATAATGAAAAATGATGAAAAAA
Found at i:283147 original size:21 final size:21
Alignment explanation
Indices: 283121--283161 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
283111 AGATTATCTT
*
283121 TTTGAAATTCAATTTCTTTTG
1 TTTGAAATTCAATTTATTTTG
283142 TTTGAAATTCAATTTATTTT
1 TTTGAAATTCAATTTATTTT
283162 TCACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTGAAATTCAATTTATTTTG
Found at i:286435 original size:12 final size:13
Alignment explanation
Indices: 286399--286440 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
286389 TTAATTAGTC
*
286399 TATATAGATATATA
1 TATATAAATA-ATA
*
286413 TATATATATAATA
1 TATATAAATAATA
286426 TA-ATAAATAATA
1 TATATAAATAATA
286438 TAT
1 TAT
286441 TATTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 5 0.20
14 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
TATATAAATAATA
Found at i:287368 original size:31 final size:31
Alignment explanation
Indices: 287296--287385 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
287286 AAAAACTACC
*
287296 AATT-TTAAA-TTTAGATAAAATATTAA-TT
1 AATTCTTAAATTTTATATAAAATATTAATTT
*
287324 -ATATCTTATATTTTATATAAAATATTAATTT
1 AAT-TCTTAAATTTTATATAAAATATTAATTT
287355 AATTCTTAAATTTTATATAAAATATTAATTT
1 AATTCTTAAATTTTATATAAAATATTAATTT
287386 GACCCTTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.04
28 1 0.02
29 4 0.07
30 16 0.30
31 29 0.54
32 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (31 bp):
AATTCTTAAATTTTATATAAAATATTAATTT
Found at i:291493 original size:5 final size:6
Alignment explanation
Indices: 291478--291502 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
291468 TTAAAATATA
291478 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
291503 GACAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:292196 original size:24 final size:24
Alignment explanation
Indices: 292164--292215 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
292154 GGTTCGACGT
292164 TATTTAATAATATTTACTCTAATC
1 TATTTAATAATATTTACTCTAATC
*
292188 TATTTAATAATATTTCCTCTAATC
1 TATTTAATAATATTTACTCTAATC
292212 TATT
1 TATT
292216 AAGTTTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTAATAATATTTACTCTAATC
Found at i:292303 original size:26 final size:24
Alignment explanation
Indices: 292272--292326 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
292262 TTATTATTAT
* *
292272 TTAAAATTTATTATTGATAAAAATA
1 TTAAAATATA-TATTGAAAAAAATA
*
292297 TGTAAAATATATATTTAAAAAAATA
1 T-TAAAATATATATTGAAAAAAATA
292322 TTAAA
1 TTAAA
292327 TCAAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 14 0.54
26 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TTAAAATATATATTGAAAAAAATA
Found at i:304244 original size:15 final size:16
Alignment explanation
Indices: 304213--304245 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
304203 TCGTTAGATT
304213 AAAAATATATATGAAA
1 AAAAATATATATGAAA
304229 AAAAATA-ATA-GAAA
1 AAAAATATATATGAAA
304243 AAA
1 AAA
304246 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAATATATATGAAA
Found at i:305667 original size:38 final size:37
Alignment explanation
Indices: 305614--305710 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
305604 GTAAATAAAT
*
305614 GTTTTAAAATC-ATATAATATATAATTTCAAAAAATTA-
1 GTTTTAAAAACTATATAATATATAATTTC-AAAAA-TAG
* * *
305651 TTTTTAAAAACTATATATTATATTATTTCAAAAATAGG
1 GTTTTAAAAACTATATAATATATAATTTCAAAAATA-G
*
305689 GTTTTAAAAACTATATTATATA
1 GTTTTAAAAACTATATAATATA
305711 GATATAGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
36 2 0.04
37 14 0.28
38 34 0.68
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (37 bp):
GTTTTAAAAACTATATAATATATAATTTCAAAAATAG
Found at i:306478 original size:84 final size:82
Alignment explanation
Indices: 306340--306850 Score: 522
Period size: 84 Copynumber: 6.2 Consensus size: 82
306330 TTGAATATAA
* * * *
306340 TCGAACTCGAAGGTC--TT-TAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTTTGTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATG
*
306402 CCGTTGAGCTGAGTGTAG
66 CC-TTGAGCTGAGCGTAG
* * * *
306420 TCGAACTCAAAGGTCTTTTGTTAGTAGACAACCCTTCTAGACTTAAGCTGTGCCGCAAATGATAT
1 TCGAACTCAAAGGTCTTTTG-TAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
306485 GCCTTGGAGCTGAGCGTAG
65 GCCTT-GAGCTGAGCGTAG
* * * * * *
306504 TCGAACTCGAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCAAAGGTCTTTTGTAG-CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATAT
* *
306568 GCCCTTGAAGCTGAGTGTAA
65 G-CCTTG-AGCTGAGCGTAG
* * * * *
306588 TCGAACTTAAGGGTC-TTTG--GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTTTGTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATG
306650 CCGTTGAGCTGAGCGTAG
66 CC-TTGAGCTGAGCGTAG
* * * * * *
306668 TCAAACTCAAAGGTCTTTTGGTCA-CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATA
1 TCGAACTCAAAGGTCTTTT-GT-AGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATA
* * *
306732 TGCCCTCGAAGCTGAGTGTAA
64 TG-CCTTG-AGCTGAGCGTAG
* * * *
306753 TCGAACTTAAGGGTC-TTTG--GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTTTGTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATG
306815 CCTTGGAGCTGAGCGTAG
66 CCTT-GAGCTGAGCGTAG
306833 TCGAACTCAAAGGTCTTT
1 TCGAACTCAAAGGTCTTT
306851 GGTTGGCAGA
Statistics
Matches: 349, Mismatches: 63, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
80 64 0.18
81 79 0.23
82 5 0.01
83 42 0.12
84 135 0.39
85 24 0.07
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (82 bp):
TCGAACTCAAAGGTCTTTTGTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATG
CCTTGAGCTGAGCGTAG
Found at i:306605 original size:248 final size:244
Alignment explanation
Indices: 306337--306850 Score: 674
Period size: 248 Copynumber: 2.1 Consensus size: 244
306327 AAGTTGAATA
306337 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTC-AAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
306402 CCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTT-GTTAGTAGACAACCCTTCTAGACTTAA
65 CCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCA-CAGACAACCCTTCTAGACTTAA
* * * *
306466 GCTGTGCCGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTGACA
129 GCTATGCCGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACT-GAAGGGTCTTT-G-G-CA
* * * * *
306529 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
190 GATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATG-CCTTGAAGCTGAGCG
* *
306585 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAA-GGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
306650 CCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
65 CCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAG
* ** * * *
306715 TTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAA
130 CTATGCCGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTGAAGGGTCTTTGGCAGATAA
* * *
306780 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
195 CCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCG
*
306830 TAGTCGAACTCAAAGGTCTTT
1 TAATCGAACTC-AAGGTCTTT
306851 GGTTGGCAGA
Statistics
Matches: 232, Mismatches: 29, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
245 29 0.12
246 38 0.16
247 3 0.01
248 131 0.56
249 31 0.13
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (244 bp):
TAATCGAACTCAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
CGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGC
TATGCCGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTGAAGGGTCTTTGGCAGATAAC
CCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCG
Found at i:306745 original size:165 final size:165
Alignment explanation
Indices: 306360--306850 Score: 700
Period size: 165 Copynumber: 3.0 Consensus size: 165
306350 AGGTCTTTAG
* * * * * * * * * *
306360 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGTGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
* * * * * * * *
306424 ACTCAAAGGTCTTTTGTTAGTAGACAACCCTTCTAGACTTAAGCTGTGCCGCAAATGATATGCCT
66 ACTTAAGGGTC-TTTG---GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
* *
306489 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGA
127 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
*
306527 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
*
306592 ACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-G
66 ACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGG
*
306656 AGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCA
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
*
306692 CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
306757 ACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
66 ACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
306822 GCTGAGCGTAGTCGAACTCAAAGGTCTTT
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTT
306851 GGTTGGCAGA
Statistics
Matches: 295, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
164 66 0.22
165 161 0.55
167 44 0.15
168 24 0.08
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGA
ACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
Found at i:307829 original size:422 final size:422
Alignment explanation
Indices: 307051--308371 Score: 2185
Period size: 422 Copynumber: 3.1 Consensus size: 422
307041 TATTGTTCTA
* * * * * * *
307051 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGACTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAA
* *
307115 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
65 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * *
307180 GTTGAAATTGACTCTGAAATCGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 GTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
307245 GAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGA
195 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGA
* * *
307310 AATGTTTGCTGACAACCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
260 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAAT
* * * *
307375 ATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAACCAGCGGTC
325 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTC
* *
307440 CCTTCGTCGTAAAGTTGAACTTGTATTGTCTGG
390 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
307473 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
307538 CAGCAGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
307603 TTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
307668 AACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
196 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
307733 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
261 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
307798 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
326 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
* *
307863 CTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
391 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
307895 AGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
307960 CAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
308025 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
308090 GAACTTGCGTTGCCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
195 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGA
*
308155 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAA
260 A-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAA
*
308220 TGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
324 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
* * *
308285 CCCTTAGTCGTGAAGTTGAACTTACGTTGTCTGG
389 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
308319 AGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
308372 AAATTTACTC
Statistics
Matches: 845, Mismatches: 51, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
422 539 0.64
423 100 0.12
424 206 0.24
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (422 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA
ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:308368 original size:106 final size:106
Alignment explanation
Indices: 307051--308371 Score: 2130
Period size: 106 Copynumber: 12.5 Consensus size: 106
307041 TATTGTTCTA
* ** * * * * *
307051 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGACTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAA
307115 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
307157 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
307221 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
307262 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATGTTTGCTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
307326 CAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
307367 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* **
307432 CAGCGGTCCCTTCGTCGTAAAGTTGAACTTGTATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
307473 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
307538 CAGCAGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
307579 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
307643 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
307684 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAA-ATGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
307748 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
307789 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
307854 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
307895 AGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
307960 CAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
308001 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
308066 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
308107 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
308172 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
308213 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
308278 CAGCGGTCCCTTAGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
308319 AGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
308372 AAATTTACTC
Statistics
Matches: 1141, Mismatches: 71, Indels: 6
0.94 0.06 0.00
Matches are distributed among these distances:
105 399 0.35
106 741 0.65
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:315793 original size:22 final size:23
Alignment explanation
Indices: 315737--315793 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
315727 GAAACTCCTA
*
315737 ATTTT-CTTCATCTTTCTTTGTCT
1 ATTTTCCTTC-TCTTTCTTTCTCT
315760 -TATTTCCATTCTCTTT-TTTCTCT
1 AT-TTTCC-TTCTCTTTCTTTCTCT
315783 ATTTTCCTTCT
1 ATTTTCCTTCT
315794 AGTAAATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 7 0.24
25 3 0.10
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTTCCTTCTCTTTCTTTCTCT
Found at i:322817 original size:21 final size:21
Alignment explanation
Indices: 322793--322857 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
322783 AATATCAATT
322793 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
322814 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
* *
322835 GTGCATCGATGTACTGCTACA
1 GTGTATCGATGCACTGCTACA
322856 GT
1 GT
322858 ACTTTCGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:323272 original size:23 final size:22
Alignment explanation
Indices: 323242--323285 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
323232 ACATATACCA
323242 TCATTAATACACATCATATAAT
1 TCATTAATACACATCATATAAT
**
323264 TCATGTAATACAGTTCATATAA
1 TCAT-TAATACACATCATATAA
323286 CTAAAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
TCATTAATACACATCATATAAT
Found at i:323627 original size:32 final size:33
Alignment explanation
Indices: 323523--323710 Score: 169
Period size: 31 Copynumber: 6.0 Consensus size: 33
323513 AACCTCGGCA
* *
323523 ACTGTCCATAGGTCCC-AAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
* * * **
323554 GCTGCCCATATGTTCC-TTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
323585 ACTGTCCATATGTCCCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
* * *
323617 TCTGTCCATATGTTCCG-TAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
* *
323648 ACTGTCCATATGTCCCGAAA-TACATATGTAAT
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
* * * *
323680 TCTGTCCATGTGTTCCG-TAGAACATAGGTAA
1 ACTGTCCATATGTCCCGAAAGAACATAGGTAA
323711 ACCCTCGACT
Statistics
Matches: 124, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
30 1 0.01
31 70 0.56
32 53 0.43
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (33 bp):
ACTGTCCATATGTCCCGAAAGAACATAGGTAAT
Found at i:323638 original size:63 final size:63
Alignment explanation
Indices: 323523--323709 Score: 279
Period size: 63 Copynumber: 3.0 Consensus size: 63
323513 AACCTCGGCA
* * * * *
323523 ACTGTCCATAGGTCCC-AAAGAACCTAGGTAA-GCTGCCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
323585 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
323648 ACTGTCCATATGTCCCGAAATACATATGTAATTCTGTCCATGTGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
323710 AACCCTCGAC
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
62 24 0.21
63 91 0.79
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (63 bp):
ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:325962 original size:31 final size:31
Alignment explanation
Indices: 325927--326026 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
325917 TTTAATTTCT
* *
325927 TAATTTAATTACTTTACTTTCAAATTACTCC
1 TAATTTAATTACTTAACTTTCAAATTACTTC
* * * ** *
325958 TAATTTAATCACTGAAGTTT--AATTTTTTT
1 TAATTTAATTACTTAACTTTCAAATTACTTC
*
325987 TAATTTAATTACTTAATTTTCAAATTACTTC
1 TAATTTAATTACTTAACTTTCAAATTACTTC
326018 TAATTTAAT
1 TAATTTAAT
326027 CATCGAGGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
29 22 0.42
31 31 0.58
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (31 bp):
TAATTTAATTACTTAACTTTCAAATTACTTC
Found at i:326008 original size:60 final size:59
Alignment explanation
Indices: 325908--326087 Score: 256
Period size: 60 Copynumber: 3.1 Consensus size: 59
325898 CTTATTTTGG
* *
325908 TCACTGAAGTTTAA-TTTCTTAATTTAATTACTTTACTTTCAAATTACTCCTAATTTAA
1 TCACTGAAGTTTAATTTTTTTAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAA
* *
325966 TCACTGAAGTTTAATTTTTTTTAATTTAATTACTTAATTTTCAAATTACTTCTAATTTAA
1 TCACTGAAGTTTAA-TTTTTTTAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAA
* * * *
326026 TCA-TCGAGGTTTAATTTTTTTAAATTAATTACTTAACTTTCAAATTACTCATATTTTAA
1 TCACT-GAAGTTTAATTTTTTTAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAA
326085 TCA
1 TCA
326088 TTCTAACTTT
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
58 14 0.13
59 44 0.40
60 51 0.47
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (59 bp):
TCACTGAAGTTTAATTTTTTTAATTTAATTACTTAACTTTCAAATTACTCCTAATTTAA
Found at i:326509 original size:13 final size:13
Alignment explanation
Indices: 326493--326520 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
326483 CTAAAAATAG
326493 TAATGAAAATTGA
1 TAATGAAAATTGA
326506 TAATGAAAATTGA
1 TAATGAAAATTGA
326519 TA
1 TA
326521 GTCTCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (13 bp):
TAATGAAAATTGA
Found at i:336361 original size:37 final size:36
Alignment explanation
Indices: 336297--336385 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 36
336287 GACTTAATAC
* * * * *
336297 TTCTATTGTATTGTTATGTAATGTAGGAGTTAATGCT
1 TTCTAATGTAATGTAATATAATATAGGAGTTAATG-T
* *
336334 TTTTAATGTGATGTAATATAATATAGGAGTTAATGT
1 TTCTAATGTAATGTAATATAATATAGGAGTTAATGT
336370 TTCTAATGTAATGTAA
1 TTCTAATGTAATGTAA
336386 GAGTTAATGT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46
Consensus pattern (36 bp):
TTCTAATGTAATGTAATATAATATAGGAGTTAATGT
Found at i:336381 original size:26 final size:26
Alignment explanation
Indices: 336360--336432 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
336350 TATAATATAG
336360 GAGTTAATGTTTCTAATGTAATGTAA
1 GAGTTAATGTTTCTAATGTAATGTAA
*
336386 GAGTTAATGTTTCTAATGTAATGTAT
1 GAGTTAATGTTTCTAATGTAATGTAA
* *
336412 GAGTTAATGCTTCTAACGTAA
1 GAGTTAATGTTTCTAATGTAA
336433 AACTTAGTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (26 bp):
GAGTTAATGTTTCTAATGTAATGTAA
Found at i:336381 original size:31 final size:28
Alignment explanation
Indices: 336344--336432 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 28
336334 TTTTAATGTG
336344 ATGTAATATAATATAGGAGTTAATGTTTCTA
1 ATGTAATAT-ATA-A-GAGTTAATGTTTCTA
*
336375 ATGT-A-ATGTAAGAGTTAATGTTTCTA
1 ATGTAATATATAAGAGTTAATGTTTCTA
* *
336401 ATGTAATGTAT--GAGTTAATGCTTCTA
1 ATGTAATATATAAGAGTTAATGTTTCTA
*
336427 ACGTAA
1 ATGTAA
336433 AACTTAGTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 38 0.75
27 2 0.04
28 4 0.08
29 2 0.04
30 1 0.02
31 4 0.08
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (28 bp):
ATGTAATATATAAGAGTTAATGTTTCTA
Found at i:342107 original size:19 final size:19
Alignment explanation
Indices: 342083--342135 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
342073 TGTTATAACC
342083 GTTTCTGGTTAGTTGAGTT
1 GTTTCTGGTTAGTTGAGTT
*
342102 GTTTCTAGTTAGTTGAGTT
1 GTTTCTGGTTAGTTGAGTT
*
342121 GTTTTTGGTTAGTTG
1 GTTTCTGGTTAGTTG
342136 GGCTAATCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.11, C:0.04, G:0.30, T:0.55
Consensus pattern (19 bp):
GTTTCTGGTTAGTTGAGTT
Found at i:343079 original size:35 final size:31
Alignment explanation
Indices: 343016--343108 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 31
343006 TGAATTTATA
343016 TTATATAAAAAAATTAGTTAATTAGTTTAAG
1 TTATATAAAAAAATTAGTTAATTAGTTTAAG
*
343047 TTATATAAAAGAATAATTATTTAAATTAGTTT-A-
1 TTATAT-AAA-AA-AATTAGTT-AATTAGTTTAAG
* **
343080 TTGT-TATAAATTATTAGTTAATTAGTTTA
1 TTATATA-AAAAAATTAGTTAATTAGTTTA
343109 TTATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 8 0.16
32 6 0.12
33 5 0.10
34 8 0.16
35 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATATAAAAAAATTAGTTAATTAGTTTAAG
Found at i:343091 original size:18 final size:18
Alignment explanation
Indices: 343068--343122 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
343058 AATAATTATT
343068 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
343086 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
343098 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
343115 TAAATTAG
1 TAAATTAG
343123 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:343437 original size:22 final size:22
Alignment explanation
Indices: 343412--343492 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
343402 AAACATTTAT
*
343412 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
343434 TAGTTTATTAGTTAACATTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
343464 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
343486 TAGTTTA
1 TAGTTTA
343493 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:343455 original size:30 final size:29
Alignment explanation
Indices: 343373--343468 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 29
343363 ATTAGTTAAT
*
343373 TAGTTTTTTAGTAATAAATTATAATTAAAAAA
1 TAGTTTATTAGT--TAAATTAT-ATTAAAAAA
* *
343405 CA-TTTATTAGTTTAAGTTATATTAAAAAA
1 TAGTTTATTAG-TTAAATTATATTAAAAAA
*
343434 TAGTTTATTAGTTAACATTATATTAAAGAA
1 TAGTTTATTAGTTAA-ATTATATTAAAAAA
343464 TAGTT
1 TAGTT
343469 AAAGTTATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
29 14 0.25
30 32 0.58
31 7 0.13
32 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (29 bp):
TAGTTTATTAGTTAAATTATATTAAAAAA
Found at i:344804 original size:23 final size:23
Alignment explanation
Indices: 344776--344820 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
344766 TTTAATTATT
*
344776 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
344799 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
344821 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:344820 original size:18 final size:20
Alignment explanation
Indices: 344770--344820 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
344760 GTTATTTTTA
344770 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
344791 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
344811 TTTATTATTT
1 ATTATTATTT
344821 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:345832 original size:14 final size:14
Alignment explanation
Indices: 345813--345860 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
345803 TTCAAGTCGT
345813 AAATCATTACTATC
1 AAATCATTACTATC
345827 AAATCATTAC--T-
1 AAATCATTACTATC
*
345838 AAATCATTAATATC
1 AAATCATTACTATC
345852 AAATCATTA
1 AAATCATTA
345861 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:345894 original size:48 final size:49
Alignment explanation
Indices: 345832--345943 Score: 190
Period size: 48 Copynumber: 2.3 Consensus size: 49
345822 CTATCAAATC
345832 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
* *
345881 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
345930 ATTACTAATCATTA
1 ATTACTAATCATTA
345944 CTAAATCATT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
48 37 0.62
49 23 0.38
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
Found at i:345960 original size:60 final size:60
Alignment explanation
Indices: 345881--346134 Score: 429
Period size: 60 Copynumber: 4.2 Consensus size: 60
345871 ATAAATTATT
*
345881 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
345940 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
346000 ATTACTAAATCATTACTATCAAATCATTAAATATTAATACTAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * * *
346060 ATTATTAAATCATTAATATTAAATTATTAAATATTAATAATAATTTGATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
346120 AATACTAAATCATTA
1 ATTACTAAATCATTA
346135 TTATAATTTC
Statistics
Matches: 183, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
59 6 0.03
60 177 0.97
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:346081 original size:14 final size:15
Alignment explanation
Indices: 346062--346096 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
346052 TACTAATCAT
346062 TATTAAATCATT-AA
1 TATTAAATCATTAAA
*
346076 TATTAAATTATTAAA
1 TATTAAATCATTAAA
346091 TATTAA
1 TATTAA
346097 TAATAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTAAATCATTAAA
Found at i:346235 original size:25 final size:25
Alignment explanation
Indices: 346207--346255 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
346197 GTTCAAGTCG
* **
346207 TAAATCATTACTATTTAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
346232 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
346256 AATATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:346291 original size:10 final size:10
Alignment explanation
Indices: 346276--346302 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
346266 ATAAATTATT
346276 ATTACTAATC
1 ATTACTAATC
346286 ATTACTAATC
1 ATTACTAATC
346296 ATTACTA
1 ATTACTA
346303 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:346379 original size:60 final size:59
Alignment explanation
Indices: 346222--346496 Score: 437
Period size: 60 Copynumber: 4.7 Consensus size: 59
346212 CATTACTATT
346222 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAC
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAC
* *
346281 TAATCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTAC
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-ATTATTATTAC
* * * *
346340 TAATTATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAT
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTAC
* *
346400 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTAT
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAC
*
346459 TAATCATTACT-AATCATTATTATCAAATCATTAAATAT
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATAT
346497 ACTAATCATT
Statistics
Matches: 202, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
58 61 0.30
59 52 0.26
60 89 0.44
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (59 bp):
TAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTAC
Found at i:346503 original size:40 final size:41
Alignment explanation
Indices: 346459--346537 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
346449 TTATTATTAT
*
346459 TAATCATTACT-AATCATTATTATCAAATCATTAAATATAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATAC
346499 TAATCATTACTAAATCATTACTATCAAATCATTAAATAT
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATAT
346538 TAATAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 11 0.30
41 26 0.70
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (41 bp):
TAATCATTACTAAATCATTACTATCAAATCATTAAATATAC
Found at i:346505 original size:16 final size:16
Alignment explanation
Indices: 346466--346507 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
346456 TATTAATCAT
*
346466 TACTAATCATT-ATTA
1 TACTAATCATTAAATA
*
346481 T-CAAATCATTAAATA
1 TACTAATCATTAAATA
346496 TACTAATCATTA
1 TACTAATCATTA
346508 CTAAATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (16 bp):
TACTAATCATTAAATA
Found at i:346658 original size:405 final size:398
Alignment explanation
Indices: 345776--346961 Score: 1134
Period size: 405 Copynumber: 3.0 Consensus size: 398
345766 CGAAAATATG
* * *
345776 GTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTATC-AAATCATTACTAA
1 GTTAATT--ACCAAACATAGTTCATTGTTCAAG-CGAAAATCATTACTAACTAAA-CATTACTAA
* * * * * * *
345840 ATCATTAATATCAAATCATTAAATAT-TAATAATAAAT-TATTATTACTAATCATTACTATCAAA
62 ATCATTAATATCAAATCATT-ACTATCAAATCATTACTAAATCATTACTAATCATTACTATCAAA
* * *
345903 TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
126 TCATTAAATATTAATAATAATTTTATTATTACTAATTATTATTAAATCATTAATATCAAATCATT
345968 AAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATA
191 AAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATA
* * * * * *
346033 TTAATACTAATTTCATTATTACTAATCATTATTAAATCATTAATATTAAATTATTAAATATTAAT
256 TTAATAATAAATT-ATTATTACTAATCATTACTAAATCATTAATATAAAATAATTAAATATTACT
* * * * * * * *
346098 AATAATT-T-GATTATTACTAATC-AAT-ACTAAATCATT-ATTATAATTTCATTACTAGTTAT-
320 AATCATTCTAAATCATTACT-ATCAAATCATTAAAT-ATTAATAATAATTTCATTATTACTAATC
* * *
346157 GTAACGAAA--A-TAT
383 ATTACTAAATCATTAT
* * ** *
346170 GGTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTATTTAATCATTACTAA
1 -GTTAATT--ACCAAACATAGTTCATTGTTCAAG-CGAAAATCATTACTAACTAAACATTACTAA
* * * *
346235 ATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTAATCATTA
62 ATCATTAATATCAAATCA-T---TACT-AT--CAAATCATTACTA--AATCATTACTAATCATTA
346300 CTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTATTAAATCATTAATATC
118 CTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTATTAAATCATTAATATC
*
346365 AAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTAAATCATTACTATCAAATC
183 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATC
* * * *
346430 ATTAAATATTAATAATAAATTATTATTATTAATCATTACT-AATCATTATTATCAAATCATTAAA
248 ATTAAATATTAATAATAAATTATTATTACTAATCATTACTAAATCATTAATATAAAATAATTAAA
346494 TA-TACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTA
313 TATTACTAATCATT-CTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTA
346558 CTAATCATTACTAAATCATTAT
377 CTAATCATTACTAAATCATTAT
* * * *
346580 -TATAATT-TCATTAC-TAGTT-A-TG-T-AA-CGAAAAT-ATGGTTAATTGAACTAAACATT-G
1 GT-TAATTACCA-AACATAGTTCATTGTTCAAGCGAAAATCA---TT-ACT-AACTAAACATTAC
** ** *
346635 TTCATTGTTCAA-GTCGTAAATCATTACTATCAAATCATTACTAAATCA-T--T-A--A-TA-T-
59 TAAATCATT-AATATC--AAATCATTACTATCAAATCATTACTAAATCATTACTAATCATTACTA
* *
346690 T-AAATCATTAAATATTAATAAT-A----A--A-T--T-ATTATTACT-AATCATTACTATCAAA
121 TCAAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTATTAAATCATTAATATCAAA
* *
346742 TCATTAAATATTAATAATAATTTCATTATTACTAACCATTACTAAATCATTAGTATCAAATCATT
186 TCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATT
*
346807 AAATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
251 AAATATTAATAATAAATTATTATTACTAATCATTAC--T-AAATCATT-AATA-TAA-AATAA-T
* * *
346872 TCATTATTACTAATCATTGCTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
309 TAAATATTACTAATCATT-CTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
346937 ATTACTAATCATTACTAAATCATTA
373 ATTACTAATCATTACTAAATCATTA
346962 CTATCAAATC
Statistics
Matches: 686, Mismatches: 64, Indels: 94
0.81 0.08 0.11
Matches are distributed among these distances:
374 112 0.16
375 8 0.01
376 2 0.00
378 8 0.01
379 3 0.00
380 2 0.00
381 5 0.01
382 5 0.01
383 81 0.12
385 1 0.00
386 21 0.03
387 1 0.00
388 1 0.00
389 2 0.00
390 1 0.00
392 1 0.00
393 1 0.00
395 78 0.11
396 8 0.01
398 12 0.02
399 4 0.01
400 8 0.01
401 3 0.00
402 20 0.03
403 33 0.05
404 34 0.05
405 182 0.27
406 31 0.05
407 8 0.01
408 1 0.00
409 6 0.01
410 3 0.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (398 bp):
GTTAATTACCAAACATAGTTCATTGTTCAAGCGAAAATCATTACTAACTAAACATTACTAAATCA
TTAATATCAAATCATTACTATCAAATCATTACTAAATCATTACTAATCATTACTATCAAATCATT
AAATATTAATAATAATTTTATTATTACTAATTATTATTAAATCATTAATATCAAATCATTAAATA
TTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT
AATAAATTATTATTACTAATCATTACTAAATCATTAATATAAAATAATTAAATATTACTAATCAT
TCTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAA
ATCATTAT
Found at i:346661 original size:444 final size:424
Alignment explanation
Indices: 345832--346920 Score: 1400
Period size: 444 Copynumber: 2.5 Consensus size: 424
345822 CTATCAAATC
* * *
345832 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACCATTAC
* * * * * * * * *
345896 TATCAAATCATTAAATAT-TAAT-AAT-AAT-TTCATTATTACTAATCATTACTAAATCATTAAT
65 --T-AAATCATT-AATATCAAATCATTAAATATTAATAATAAATTATTATTACT-AATCATTACT
* * *
345957 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAA
125 ATCAAATCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACTAAATCATTAATATCAA
* *
346022 ATCATTAAATATTAATACTAATTTCATTATTACTAATCATTATTAAATCATTAATATTAAATTAT
190 ATCATT-AA-A-T-ATACTAA--TC---A-T--T-A-C-----TAAATCATTAATATCAAATCAT
*
346087 TAAATATTAATAATAATTTGATTATTACTAATCAATACTAAATCATTATTATAATTTCATTACTA
236 TAAATATTAATAATAATTTCATTATTACTAATCAATACTAAATCATTATTATAATTTCATTACTA
346152 GTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTA
301 GTTATGTAACGAAAATATGGTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTA
**
346217 CTATTTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACT
366 CTATCAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAAT--A--A--ATTA-T
346282 AAT
424 --T
* ** *
346285 CATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATTATTAT
1 -ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACCATTAC
346350 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTAATCATTACTAAAT
65 TAAATCATTAATATCAAATCATTAAATATTAATAAT-A----A--ATTA-T--T-ATTACT-AAT
* *
346415 CATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTATTAATCATTACT-AATCATTA
118 CATTACTATCAAATCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACTAAATCATTA
* *
346478 TTATCAAATCATTAAATATACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATA
183 ATATCAAATCATTAAATATACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATA
*
346543 ATAATTTCATTATTACTAATCATTACTAAATCATTATTATAATTTCATTACTAGTTATGTAACGA
248 ATAATTTCATTATTACTAATCAATACTAAATCATTATTATAATTTCATTACTAGTTATGTAACGA
*
346608 AAATATGGTTAATTGAACTAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTATCAAATCAT
313 AAATATGGTTAATTGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTATCAAATCAT
*
346673 TACTAAATCATTAATATTAAATCATTAAATATTAATAATAAATTATT
378 TACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATT
346720 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACCATTACT
*
346785 AAATCATTAGTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAA
66 AAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAA
* *
346850 TCATTAAAAATTAATAATAATTTCATTATTACTAATCATTGCTAAATCATTAATATCAAATCATT
131 TCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
346915 AAATAT
196 AAATAT
346921 TAATAATAAT
Statistics
Matches: 582, Mismatches: 35, Indels: 66
0.85 0.05 0.10
Matches are distributed among these distances:
422 37 0.06
423 23 0.04
424 27 0.05
426 1 0.00
427 4 0.01
429 1 0.00
433 1 0.00
434 95 0.16
435 1 0.00
437 1 0.00
438 4 0.01
440 1 0.00
442 1 0.00
444 194 0.33
449 1 0.00
450 6 0.01
451 12 0.02
452 3 0.01
453 41 0.07
454 29 0.05
457 2 0.00
459 8 0.01
460 1 0.00
461 3 0.01
462 3 0.01
463 20 0.03
464 18 0.03
465 44 0.08
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (424 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACCATTACT
AAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAA
TCATTAAAAATTAATAATAAATTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATT
AAATATACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
TACTAATCAATACTAAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAAT
TGAACCAAACATTGTTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTA
ATATCAAATCATTAAATATTAATAATAAATTATT
Found at i:346700 original size:14 final size:14
Alignment explanation
Indices: 346651--346755 Score: 63
Period size: 14 Copynumber: 7.2 Consensus size: 14
346641 GTTCAAGTCG
*
346651 TAAATCATTACTAT
1 TAAATCATTAATAT
* *
346665 CAAATCA-T--TAC
1 TAAATCATTAATAT
346676 TAAATCATTAATAT
1 TAAATCATTAATAT
346690 TAAATCATTAAATAT
1 TAAATCATT-AATAT
* *
346705 TAATAATAAATTATTAT
1 T-A-AAT-CATTAATAT
*
346722 TACTAATCATTACTAT
1 TA--AATCATTAATAT
*
346738 CAAATCATTAAATAT
1 TAAATCATT-AATAT
346753 TAA
1 TAA
346756 TAATAATTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.11
12 1 0.01
13 1 0.01
14 24 0.34
15 12 0.17
16 10 0.14
17 12 0.17
18 3 0.04
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATCATTAATAT
Found at i:346707 original size:21 final size:22
Alignment explanation
Indices: 346651--346757 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 22
346641 GTTCAAGTCG
* *
346651 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATAAAATCA-T
*
346674 ACTAAATCATTAATATTAAATCAT
1 --TAAATCATTAATATAAAATCAT
*
346698 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTAAT-ATAAA--ATCAT
* *
346722 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATAAAATCAT
346746 TAAAT-ATTAATA
1 TAAATCATTAATA
346758 ATAATTTCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
21 12 0.18
22 12 0.18
24 13 0.19
25 19 0.28
26 7 0.10
27 5 0.07
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATATAAAATCAT
Found at i:346733 original size:48 final size:49
Alignment explanation
Indices: 346671--346889 Score: 253
Period size: 48 Copynumber: 4.3 Consensus size: 49
346661 CTATCAAATC
*
346671 ATTACTAAATCATTAATATTAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
* *
346720 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTC---A-T--T
*
346775 AACCATTACTAAATCATTAGTATCAAATCATTAAATATTAATAATAAATT-ATT
1 ----ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
* * *
346828 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
346877 ATTACTAATCATT
1 ATTACTAATCATT
346890 GCTAAATCAT
Statistics
Matches: 149, Mismatches: 8, Indels: 26
0.81 0.04 0.14
Matches are distributed among these distances:
48 72 0.48
49 28 0.19
52 1 0.01
53 2 0.01
55 2 0.01
56 1 0.01
59 6 0.04
60 37 0.25
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAAATTCATT
Found at i:346799 original size:60 final size:59
Alignment explanation
Indices: 346720--346844 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 59
346710 ATAAATTATT
*
346720 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAACC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAACC
* *
346779 ATTACTAAATCATTAGTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAACC
346838 ATTACTA
1 ATTACTA
346845 TCAAATCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 25 0.40
60 37 0.60
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (59 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAACC
Found at i:346828 original size:21 final size:22
Alignment explanation
Indices: 346779--346828 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 22
346769 ATTACTAACC
* *
346779 ATTACTAAATCATTAGT-ATCAA
1 ATTATTAAATCATTAATAAT-AA
*
346801 ATCATTAAAT-ATTAATAATAA
1 ATTATTAAATCATTAATAATAA
346822 ATTATTA
1 ATTATTA
346829 TTACTAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTATTAAATCATTAATAATAA
Found at i:346907 original size:60 final size:60
Alignment explanation
Indices: 346828--346975 Score: 262
Period size: 60 Copynumber: 2.5 Consensus size: 60
346818 ATAAATTATT
346828 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
346887 ATTGCTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
346947 ATTACTAAATCATTACTATCAAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA
346976 TTATTAAATC
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 5 0.06
60 78 0.94
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:347027 original size:26 final size:25
Alignment explanation
Indices: 346912--347251 Score: 137
Period size: 26 Copynumber: 13.6 Consensus size: 25
346902 ATATCAAATC
*
346912 ATTAAAT-ATTAATAATAAT-TTCATT
1 ATTAAATCATT-ATTATAATATT-ATT
* *
346937 ATTACTAATCATTACTA-AATCATTACT
1 ATTA--AATCATTATTATAAT-ATTATT
* *
346964 ATCAAATCATTATTATTAA-ATCATT
1 ATTAAATCATTATTA-TAATATTATT
*
346989 ATTATAATGATTATTATAATGATTATT
1 ATTA-AATCATTATTATAAT-ATTATT
347016 ATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTATTATAAT-ATTATT
* * * *
347042 ATCAAATCATTACTA-AATCATCAAATC
1 ATTAAATCATTATTATAAT-AT--TATT
347069 ATTAAAT-A-T-TTA-AATCATTATT
1 ATTAAATCATTATTATAAT-ATTATT
* *
347091 A-T-AATGATTATTACTAA-ATCATT
1 ATTAAATCATTATTA-TAATATTATT
* *
347114 ATTATAATGATTATTATCAA-ATCATT
1 ATTA-AATCATTATTAT-AATATTATT
* *
347140 ATTATAATGATTATTATCAA-ATCATT
1 ATTA-AATCATTATTAT-AATATTATT
* * * * * *
347166 ACTAAATCATCA-AATCAT-TAAAT
1 ATTAAATCATTATTATAATATTATT
347189 ATTAAATTCATTATTA-AAT-TTATT
1 ATTAAA-TCATTATTATAATATTATT
347213 ATTAAATC---ATTATAATGATTATT
1 ATTAAATCATTATTATAAT-ATTATT
* *
347236 ATCAAATCATTTTTAT
1 ATTAAATCATTATTAT
347252 GGTTAATTGA
Statistics
Matches: 249, Mismatches: 36, Indels: 59
0.72 0.10 0.17
Matches are distributed among these distances:
20 7 0.03
21 5 0.02
22 4 0.02
23 32 0.13
24 27 0.11
25 40 0.16
26 100 0.40
27 29 0.12
28 5 0.02
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTAAATCATTATTATAATATTATT
Found at i:347087 original size:61 final size:60
Alignment explanation
Indices: 347015--347224 Score: 273
Period size: 61 Copynumber: 3.6 Consensus size: 60
347005 TAATGATTAT
347015 TATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 TATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
* *
347075 TATTTAAATCATTATTATAATGATTATTA-CTAAATCATTA-T---T-AT--AATGATT-AT
1 TA-TTAAATCATTATTATAATGATTATTATC-AAATCATTACTAAATCATCAAATCATTAAA
*
347128 TATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 TATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
*
347188 TATTAAATTCATTATTA-AAT--TTATTATTAAATCATTA
1 TATTAAA-TCATTATTATAATGATTATTATCAAATCATTA
347225 TAATGATTAT
Statistics
Matches: 131, Mismatches: 7, Indels: 26
0.80 0.04 0.16
Matches are distributed among these distances:
52 34 0.26
53 5 0.04
54 6 0.05
56 3 0.02
57 3 0.02
58 16 0.12
59 6 0.05
60 14 0.11
61 44 0.34
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (60 bp):
TATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
Done.