Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 33
Found at i:4475328 original size:33 final size:33
Alignment explanation
Indices: 4475286--4475378 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
4475276 GCGAAACCAA
*
4475286 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4475319 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4475352 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4475379 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:4475375 original size:52 final size:54
Alignment explanation
Indices: 4475249--4475383 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
4475239 TAGTTTACTT
*
4475249 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
4475307 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
4475354 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
4475384 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:4475401 original size:19 final size:19
Alignment explanation
Indices: 4475379--4475507 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4475369 AAAATCGCAA
4475379 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4475398 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
4475412 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4475431 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4475445 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4475464 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4475483 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4475503 TGCGA
1 TGCGA
4475508 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4475421 original size:33 final size:33
Alignment explanation
Indices: 4475379--4475470 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4475369 AAAATCGCAA
4475379 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
4475412 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
4475445 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
4475471 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:4475710 original size:93 final size:93
Alignment explanation
Indices: 4475551--4475930 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
4475541 TTGAATGGAT
4475551 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4475616 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4475644 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4475709 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4475737 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4475801 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4475829 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
4475894 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4475922 AAATTTACT
1 AAATTTACT
4475931 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:4475864 original size:185 final size:186
Alignment explanation
Indices: 4475551--4475930 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
4475541 TTGAATGGAT
4475551 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4475616 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
4475681 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
4475737 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4475801 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
4475866 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
4475922 AAATTTACT
1 AAATTTACT
4475931 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:4477656 original size:14 final size:14
Alignment explanation
Indices: 4477637--4477726 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
4477627 TTGAAATGAA
4477637 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4477651 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
4477668 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
4477684 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4477703 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4477717 AATCGCAACG
1 AATCGCAACG
4477727 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4477674 original size:33 final size:33
Alignment explanation
Indices: 4477629--4477743 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
4477619 TCTTTTGGTT
4477629 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
4477662 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4477695 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4477728 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4477744 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4477675 original size:19 final size:18
Alignment explanation
Indices: 4477636--4477748 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
4477626 GTTGAAATGA
4477636 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
4477651 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
4477668 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
4477684 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
4477701 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
4477717 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
4477734 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
4477749 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:4477841 original size:20 final size:20
Alignment explanation
Indices: 4477767--4477855 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
4477757 TCGCGTTGCG
*
4477767 ATTCTCTCGTTGCGATTTCC
1 ATTCTCTCGTTGCGATTTTC
*
4477787 ATT-TCGCGTTGCGA--TTC
1 ATTCTCTCGTTGCGATTTTC
***
4477804 --TCT-T-GTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
4477820 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
4477840 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
4477856 CTCTTCTGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 3 0.06
17 2 0.04
18 3 0.06
19 11 0.21
20 13 0.25
21 13 0.25
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:4477977 original size:33 final size:33
Alignment explanation
Indices: 4477935--4478005 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4477925 AATACTAACT
*
4477935 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
4477968 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
4478001 TGAAA
1 TGAAA
4478006 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:4478239 original size:22 final size:22
Alignment explanation
Indices: 4478187--4478241 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4478177 TGGTTGTGAG
**
4478187 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4478209 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
4478231 GGATTTCTTCG
1 GGATTTCTTCG
4478242 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:4478412 original size:20 final size:20
Alignment explanation
Indices: 4478387--4478580 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4478377 CTTTAAATAT
4478387 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4478407 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4478429 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4478448 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4478468 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4478488 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4478508 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4478528 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4478548 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4478568 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4478581 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4478574 original size:60 final size:60
Alignment explanation
Indices: 4478387--4478580 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4478377 CTTTAAATAT
**
4478387 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
4478448 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
4478508 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
4478568 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4478581 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:4478597 original size:21 final size:20
Alignment explanation
Indices: 4478573--4478649 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
4478563 ATATTCGCGT
4478573 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
4478594 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
4478614 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
4478636 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
4478650 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:4478660 original size:20 final size:20
Alignment explanation
Indices: 4478635--4478686 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4478625 AAGAATCGCG
*
4478635 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
4478655 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
4478675 TTGCGATTCTGG
1 TTGCGATTCTGG
4478687 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:4483430 original size:2 final size:2
Alignment explanation
Indices: 4483425--4483452 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4483415 ACACACACAC
4483425 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
4483453 TAAATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4483600 original size:17 final size:16
Alignment explanation
Indices: 4483578--4483612 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4483568 TAATAATATA
4483578 TAAATTATATTAGAAAT
1 TAAATTATATTA-AAAT
*
4483595 TAAATTTTATTAAAAT
1 TAAATTATATTAAAAT
4483611 TA
1 TA
4483613 TTTAGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAATTATATTAAAAT
Found at i:4483674 original size:121 final size:121
Alignment explanation
Indices: 4483545--4483767 Score: 365
Period size: 121 Copynumber: 1.8 Consensus size: 121
4483535 ATGAATTTAA
* * * * * *
4483545 TATTTTTTACAATTATTTTTAAGTAATAATATATAAATTATATTAGAAATTAAATTTTATTAAAA
1 TATTTTTTACAATTATTTTTAAATAACAATATATAAATTATATTAAAAATAAAATTATACTAAAA
* * *
4483610 TTATTTAGAGAATTCAAGTCACAAAGTAAAAATAAATTTAATATTTTTATTTAAAT
66 TTATTTAGAGAATCCAAATCACAAAATAAAAATAAATTTAATATTTTTATTTAAAT
4483666 TATTTTTTACAATTATTTTTAAATAACAATATATAAATTATATTAAAAATAAAATTATACTAAAA
1 TATTTTTTACAATTATTTTTAAATAACAATATATAAATTATATTAAAAATAAAATTATACTAAAA
4483731 TTATTTAGAGAATCCAAATCACAAAATAAAAATAAAT
66 TTATTTAGAGAATCCAAATCACAAAATAAAAATAAAT
4483768 AAAAATATTA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 93 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (121 bp):
TATTTTTTACAATTATTTTTAAATAACAATATATAAATTATATTAAAAATAAAATTATACTAAAA
TTATTTAGAGAATCCAAATCACAAAATAAAAATAAATTTAATATTTTTATTTAAAT
Found at i:4484339 original size:15 final size:16
Alignment explanation
Indices: 4484309--4484339 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4484299 AAAAAATTAA
4484309 AAATATTTTATATTTT
1 AAATATTTTATATTTT
4484325 AAATATTTT-TATTTT
1 AAATATTTTATATTTT
4484340 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AAATATTTTATATTTT
Found at i:4484340 original size:16 final size:16
Alignment explanation
Indices: 4484309--4484358 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4484299 AAAAAATTAA
4484309 AAATA-TTTTATATTTT
1 AAATATTTTTAT-TTTT
4484325 AAATATTTTTATTTTT
1 AAATATTTTTATTTTT
*
4484341 --TTATTTTTAATTTTT
1 AAATATTTTT-ATTTTT
4484356 AAA
1 AAA
4484359 AATATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 9 0.32
17 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AAATATTTTTATTTTT
Found at i:4485109 original size:14 final size:14
Alignment explanation
Indices: 4485076--4485109 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4485066 TGAATTATAT
*
4485076 TTTTAAGAAAATCA
1 TTTTATGAAAATCA
4485090 -TTTATGAAAATCA
1 TTTTATGAAAATCA
4485103 TTTTATG
1 TTTTATG
4485110 TGTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (14 bp):
TTTTATGAAAATCA
Found at i:4485218 original size:17 final size:17
Alignment explanation
Indices: 4485198--4485293 Score: 77
Period size: 17 Copynumber: 5.5 Consensus size: 17
4485188 CAATAAATAG
4485198 TATTATTTATTAAAAAA
1 TATTATTTATTAAAAAA
*
4485215 TATTATTT-TTTAAAAA
1 TATTATTTATTAAAAAA
* ***
4485231 TATTATAATAATTTATTTAA
1 TATTAT--TTA-TTAAAAAA
*
4485251 TACTATTTATTAAAAAA
1 TATTATTTATTAAAAAA
* *
4485268 TATTATTTTTTAAAAAT
1 TATTATTTATTAAAAAA
*
4485285 TATTTTTTA
1 TATTATTTA
4485294 ATTATCAAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
16 13 0.22
17 34 0.58
18 3 0.05
20 9 0.15
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTTATTAAAAAA
Found at i:4485286 original size:14 final size:15
Alignment explanation
Indices: 4485264--4485294 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4485254 TATTTATTAA
4485264 AAAATATTATTTTTT
1 AAAATATTATTTTTT
4485279 AAAA-ATTATTTTTT
1 AAAATATTATTTTTT
4485293 AA
1 AA
4485295 TTATCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAATATTATTTTTT
Found at i:4485324 original size:29 final size:29
Alignment explanation
Indices: 4485289--4485352 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
4485279 AAAAATTATT
4485289 TTTTAATTATCAAAATAAAAATATTAAAA
1 TTTTAATTATCAAAATAAAAATATTAAAA
* * *
4485318 TTTTAATTATTAAAATAAGAATATTATAA
1 TTTTAATTATCAAAATAAAAATATTAAAA
*
4485347 TATTAA
1 TTTTAA
4485353 AAATTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
TTTTAATTATCAAAATAAAAATATTAAAA
Found at i:4485358 original size:29 final size:29
Alignment explanation
Indices: 4485300--4485358 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4485290 TTTAATTATC
* **
4485300 AAAATAAAAATATTAAAATTTTAATTATT
1 AAAATAAAAATATTAAAATATTAAAAATT
* *
4485329 AAAATAAGAATATTATAATATTAAAAATT
1 AAAATAAAAATATTAAAATATTAAAAATT
4485358 A
1 A
4485359 TATTACTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATAAAAATATTAAAATATTAAAAATT
Found at i:4485427 original size:26 final size:25
Alignment explanation
Indices: 4485348--4485427 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
4485338 ATATTATAAT
* *
4485348 ATTAAAAATTATATTACTATAA-TATA
1 ATTAAATATTATATTA-TAAAATTA-A
*
4485374 ATTAAATA-TATTATTATAACAATAAA
1 ATTAAATATTA-TATTATAA-AATTAA
*
4485400 ATTTAATATTATATTATTAAAATTAA
1 ATTAAATATTATATTA-TAAAATTAA
4485426 AT
1 AT
4485428 ATTTTAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 4 0.09
26 34 0.77
27 6 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAATATTATATTATAAAATTAA
Found at i:4485433 original size:29 final size:28
Alignment explanation
Indices: 4485380--4485455 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 28
4485370 TATAATTAAA
*
4485380 TATATTATTATAACAATAAAATTTAAT-AT
1 TATATTATTA-AA-ATTAAAATTTAATAAT
4485409 TATATTATTAAAATTAAATATTTTAATAAT
1 TATATTATTAAAATTAAA-A-TTTAATAAT
4485439 TAATATCTTATTAAAAT
1 T-ATA--TTATTAAAAT
4485456 AGTACTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 5 0.12
28 3 0.08
29 16 0.40
30 3 0.08
31 3 0.08
33 10 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATTATTAAAATTAAAATTTAATAAT
Found at i:4485439 original size:16 final size:16
Alignment explanation
Indices: 4485410--4485455 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
4485400 ATTTAATATT
4485410 ATATTATTAAAATTAA
1 ATATTATTAAAATTAA
4485426 ATATT-TTAATAATTAA
1 ATATTATTAA-AATTAA
*
4485442 TATCTTATTAAAAT
1 -ATATTATTAAAAT
4485456 AGTACTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 7 0.27
18 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTATTAAAATTAA
Found at i:4486002 original size:14 final size:14
Alignment explanation
Indices: 4485955--4486006 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4485945 GAGACTGAGC
* *
4485955 TGAATATAAACAAA
1 TGAACATAAACGAA
* *
4485969 TGGACATAAGCGAA
1 TGAACATAAACGAA
**
4485983 CAAACATAAACGAA
1 TGAACATAAACGAA
4485997 TGAACATAAA
1 TGAACATAAA
4486007 TATAAACGAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.15
Consensus pattern (14 bp):
TGAACATAAACGAA
Found at i:4486280 original size:2 final size:2
Alignment explanation
Indices: 4486273--4486303 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4486263 ATTTTTAATC
4486273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4486304 TCAATTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4486818 original size:24 final size:23
Alignment explanation
Indices: 4486768--4486829 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
4486758 ATAGCTGTTA
*
4486768 TTGTGACACATTTTTCTCTACTC
1 TTGTGACACATTTTTCTATACTC
* * *
4486791 TTGTGACATATGTTTTCTATGCTT
1 TTGTGACACAT-TTTTCTATACTC
4486815 TTGTGACACGATTTT
1 TTGTGACAC-ATTTT
4486830 AATAACTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 10 0.31
24 20 0.62
25 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (23 bp):
TTGTGACACATTTTTCTATACTC
Found at i:4487139 original size:14 final size:14
Alignment explanation
Indices: 4487120--4487153 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4487110 AACATTTGTG
*
4487120 GCCAAAAAATTGCC
1 GCCAAAAAATTACC
4487134 GCCAAAAAATTACC
1 GCCAAAAAATTACC
4487148 GCCAAA
1 GCCAAA
4487154 TGCACTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.29, G:0.12, T:0.12
Consensus pattern (14 bp):
GCCAAAAAATTACC
Found at i:4487627 original size:105 final size:106
Alignment explanation
Indices: 4487457--4487654 Score: 344
Period size: 105 Copynumber: 1.9 Consensus size: 106
4487447 TATAGTGACG
* **
4487457 TTTTTGTATAAACGCCGCAAATGATCTAAAACTTTAGTGGCATTTTATTCTAAAACGTCGGTATT
1 TTTTTGTATAAACGCCACAAATGATCTAAAACTTTAGTGGCATTTTATTCTAAAACACCGGTATT
4487522 GATTATGTATTTAGTGGCGTTTGTTATATCTATAGTGGCTT
66 GATTATGTATTTAGTGGCGTTTGTTATATCTATAGTGGCTT
* *
4487563 TTTTTGTATAAACGCCACAAATGATCT-AAATTTTAGTGGCGTTTTATTCTAAAACACCGGTATT
1 TTTTTGTATAAACGCCACAAATGATCTAAAACTTTAGTGGCATTTTATTCTAAAACACCGGTATT
4487627 GATTATGTATTTAGTGGCGTTTGTTATA
66 GATTATGTATTTAGTGGCGTTTGTTATA
4487655 CAAACGCCGC
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 61 0.70
106 26 0.30
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (106 bp):
TTTTTGTATAAACGCCACAAATGATCTAAAACTTTAGTGGCATTTTATTCTAAAACACCGGTATT
GATTATGTATTTAGTGGCGTTTGTTATATCTATAGTGGCTT
Found at i:4487786 original size:21 final size:21
Alignment explanation
Indices: 4487760--4487803 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4487750 CATGACATCT
*
4487760 ATAACAACAAACTTTAATTCC
1 ATAACAACAAACTTTAAATCC
*
4487781 ATAACAACCAACTTTAAATCC
1 ATAACAACAAACTTTAAATCC
4487802 AT
1 AT
4487804 TATAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAACAACAAACTTTAAATCC
Found at i:4489583 original size:20 final size:18
Alignment explanation
Indices: 4489549--4489586 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
4489539 GGTATCGGTA
4489549 CCTTTGGTACGATACTTC
1 CCTTTGGTACGATACTTC
4489567 CCTTTAGGTATCGATACTTC
1 CCTTT-GGTA-CGATACTTC
4489587 TTGAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.39
Consensus pattern (18 bp):
CCTTTGGTACGATACTTC
Found at i:4490518 original size:64 final size:63
Alignment explanation
Indices: 4490432--4490592 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 63
4490422 ATTGTTTAAG
* * *
4490432 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCAAATGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
4490495 T
63 T
*
4490496 ATGCATCGATGCATAATG-AGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCA-AATGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
4490560 ATGCACCGATGCACAA-GTAGTGCATCGATGCAT
1 ATGCATCGATGCA-AATGCAGTGCATCGATGCAT
4490593 ACATTCATTG
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
63 3 0.03
64 72 0.84
65 10 0.12
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCAAATGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:4494757 original size:64 final size:63
Alignment explanation
Indices: 4494671--4494827 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 63
4494661 AATGTTTAAG
* * *
4494671 ATGCATCGATGCACATGCAGTGCATCGATACAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCAAATGCAGTGCATCGATACATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
4494734 T
63 T
* *
4494735 ATGCATCGATGCATAATG-AGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCA-AATGCAGTGCATCGATACAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
4494799 ATGCACCGATGCACAA-GTAGTGCATCGAT
1 ATGCATCGATGCA-AATGCAGTGCATCGAT
4494828 GCATACATTC
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.83
65 10 0.12
66 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCAAATGCAGTGCATCGATACATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:4494828 original size:64 final size:65
Alignment explanation
Indices: 4494708--4494831 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
4494698 ATACATGAAT
* * *
4494708 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAATGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGCATTTATGCACCGATGCACAATGAGTGCATCGATGCATCCCCA
4494773 TTAAATA-AAAACATCGAAT-GCATTTTATGCACCGATGCACAA-GTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGCA-TTTATGCACCGATGCACAATG-AGTGCATCGATGCAT
4494832 ACATTCATTG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 3 0.06
64 44 0.81
65 7 0.13
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGCATTTATGCACCGATGCACAATGAGTGCATCGATGCATCCCCA
Found at i:4495546 original size:30 final size:30
Alignment explanation
Indices: 4495510--4495573 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
4495500 AAGGAACATA
* *
4495510 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
4495540 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
4495570 TGGA
1 TGGA
4495574 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:4497911 original size:83 final size:83
Alignment explanation
Indices: 4497816--4498166 Score: 280
Period size: 83 Copynumber: 4.2 Consensus size: 83
4497806 TTTTTATAAC
* *
4497816 AAACGCCACTATAGATGAACCCTATTGCAGTGTTTGTATAAAAACGCCGCTAATGTACTACTATG
1 AAACGCCACTATAGATGAACCCTATTGCAGCGTTTGTATAAAAACGCCGCTAATGTACTACTCTG
4497881 TTGCGGCGTTTGTTGAAA
66 TTGCGGCGTTTGTTGAAA
* * * * * * * *
4497899 AAATGCCACTATAGATGAACTCTATTGCGGCGTTTGT-TCAAAAACGCCGCTGACGTATTAATTT
1 AAACGCCACTATAGATGAACCCTATTGCAGCGTTTGTAT-AAAAACGCCGCTAATGTACTACTCT
* * *
4497963 GTTGCGACATTTTTTGAAAAAA
65 GTTGCGGCGTTTGTTG---AAA
* * * * * * *
4497985 AAATGCCACTATAGATTAACCCTATTG-AGGCGTTTTTGTAAAAATGCTGCT-ATAGTACTTCTC
1 AAACGCCACTATAGATGAACCCTATTGCA-GCGTTTGTATAAAAACGCCGCTAAT-GTACTACTC
* * * * * **
4498048 CGGTGCAGTGTTTGTTTAGG
64 TGTTGCGGCGTTTGTTGAAA
* * * * * *
4498068 AAACGCCATTAAAGATGAA-CCTATTGCGGCGTTTGTATAAAAACGCC-ATGAAAGTACTACCCT
1 AAACGCCACTATAGATGAACCCTATTGCAGCGTTTGTATAAAAACGCCGCT-AATGTACTACTCT
*
4498131 GTTGCGGTGTTTGTTGAAA
65 GTTGCGGCGTTTGTTGAAA
* *
4498150 AAGCACCACTATAGATG
1 AAACGCCACTATAGATG
4498167 CCGCTAAAGT
Statistics
Matches: 202, Mismatches: 56, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
81 1 0.00
82 57 0.28
83 83 0.41
85 1 0.00
86 59 0.29
87 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (83 bp):
AAACGCCACTATAGATGAACCCTATTGCAGCGTTTGTATAAAAACGCCGCTAATGTACTACTCTG
TTGCGGCGTTTGTTGAAA
Found at i:4503808 original size:24 final size:24
Alignment explanation
Indices: 4503774--4503867 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
4503764 CGTAGAATTT
4503774 TGCACCGAAGTGCCACATAGAATA
1 TGCACCGAAGTGCCACATAGAATA
*
4503798 TGCACCAAAGTGCCACATAGAATA
1 TGCACCGAAGTGCCACATAGAATA
* *
4503822 TGCACCGAAGTGCGACATAG-ATT
1 TGCACCGAAGTGCCACATAGAATA
*
4503845 TGTC-CCGAAGAGCCACATAGAAT
1 TG-CACCGAAGTGCCACATAGAAT
4503868 TGTCCCGAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 18 0.29
24 44 0.71
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (24 bp):
TGCACCGAAGTGCCACATAGAATA
Found at i:4503840 original size:48 final size:47
Alignment explanation
Indices: 4503774--4503867 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
4503764 CGTAGAATTT
*
4503774 TGCACCGAAGTGCCACATAGAATATG-CACCAAAGTGCCACATAGAATA
1 TGCACCGAAGTGCCACATAG-ATATGTC-CCAAAGAGCCACATAGAATA
* * *
4503822 TGCACCGAAGTGCGACATAGATTTGTCCCGAAGAGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGATATGTCCCAAAGAGCCACATAGAAT
4503868 TGTCCCGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 21 0.51
48 20 0.49
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (47 bp):
TGCACCGAAGTGCCACATAGATATGTCCCAAAGAGCCACATAGAATA
Found at i:4503862 original size:23 final size:23
Alignment explanation
Indices: 4503778--4503900 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
4503768 GAATTTTGCA
*
4503778 CCGAAGTGCCACATAGAATATG-C
1 CCGAAGTGCCACATAG-ATTTGTC
* *
4503801 ACCAAAGTGCCACATAGAATATG-C
1 -CCGAAGTGCCACATAG-ATTTGTC
*
4503825 ACCGAAGTGCGACATAGATTTGTC
1 -CCGAAGTGCCACATAGATTTGTC
* *
4503849 CCGAAGAGCCACATAGAATTGTC
1 CCGAAGTGCCACATAGATTTGTC
* *
4503872 CCGAAG-GACCACGTAGAATTGTC
1 CCGAAGTG-CCACATAGATTTGTC
4503895 CCGAAG
1 CCGAAG
4503901 GGCCGCGCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.01
23 50 0.56
24 38 0.43
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CCGAAGTGCCACATAGATTTGTC
Found at i:4503895 original size:46 final size:47
Alignment explanation
Indices: 4503774--4503900 Score: 145
Period size: 46 Copynumber: 2.7 Consensus size: 47
4503764 CGTAGAATTT
* *
4503774 TGCACCGAAGTGCCACATAGAATATG-CACCAAAGTGCCACATAGAATA
1 TGCACCGAAGTGCCACATAGAAT-TGTC-CCGAAGAGCCACATAGAATA
* *
4503822 TGCACCGAAGTGCGACATAGATTTGTCCCGAAGAGCCACATAGAAT-
1 TGCACCGAAGTGCCACATAGAATTGTCCCGAAGAGCCACATAGAATA
*
4503868 TGTC-CCGAAG-GACCACGTAGAATTGTCCCGAAG
1 TG-CACCGAAGTG-CCACATAGAATTGTCCCGAAG
4503901 GGCCGCGCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 1 0.01
46 26 0.38
47 20 0.29
48 22 0.32
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (47 bp):
TGCACCGAAGTGCCACATAGAATTGTCCCGAAGAGCCACATAGAATA
Found at i:4506406 original size:32 final size:33
Alignment explanation
Indices: 4506370--4506432 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
4506360 GTCAATATCA
*
4506370 GGTCGGGTCAATACCGGATCAGTT-GATTTCTG
1 GGTCGGGTCAATACCAGATCAGTTAGATTTCTG
* *
4506402 GGTCGGGTTAATACTAGATCAGTTAGATTTC
1 GGTCGGGTCAATACCAGATCAGTTAGATTTC
4506433 AAGTGGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (33 bp):
GGTCGGGTCAATACCAGATCAGTTAGATTTCTG
Found at i:4507063 original size:19 final size:18
Alignment explanation
Indices: 4507041--4507095 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
4507031 AACTTTCTAT
4507041 TATTTTATTATAAATCTAA
1 TATTTTATTATAAAT-TAA
*
4507060 TATTTT-TTATAAATTATC
1 TATTTTATTATAAATTA-A
4507078 TATTTTATT-TAAATTAA
1 TATTTTATTATAAATTAA
4507095 T
1 T
4507096 TTATTATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 21 0.66
19 8 0.25
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTATTATAAATTAA
Found at i:4507214 original size:16 final size:16
Alignment explanation
Indices: 4507181--4507236 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
4507171 TTAAATTCGG
*
4507181 TTCGAGTTAATTTCGGT
1 TTCG-GTTAATTTTGGT
* **
4507198 TTGGGTTGCTTTTGGT
1 TTCGGTTAATTTTGGT
4507214 TTCGGTTAATTTTGGT
1 TTCGGTTAATTTTGGT
4507230 TTCGGTT
1 TTCGGTT
4507237 CGGATTAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 29 0.91
17 3 0.09
ACGTcount: A:0.09, C:0.09, G:0.29, T:0.54
Consensus pattern (16 bp):
TTCGGTTAATTTTGGT
Found at i:4507245 original size:54 final size:54
Alignment explanation
Indices: 4507176--4507282 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
4507166 TCAGGTTAAA
* * * * *
4507176 TTCGGTTCGAGTTAATTTCGGTTTGGGTTGCTTTTGGTTTCGGTTAATTTTGGT
1 TTCGGTTCGAGTTAATTTCAGTTTGGGTTGATTTCGGTTTCGCTAAATTTTGGT
*
4507230 TTCGGTTCG-GATTAATTTCAGTTTTGGTTGATTTCGGTTTCGCTAAATTTTGG
1 TTCGGTTCGAG-TTAATTTCAGTTTGGGTTGATTTCGGTTTCGCTAAATTTTGG
4507283 ATCGGGTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.02
54 45 0.98
ACGTcount: A:0.12, C:0.10, G:0.27, T:0.50
Consensus pattern (54 bp):
TTCGGTTCGAGTTAATTTCAGTTTGGGTTGATTTCGGTTTCGCTAAATTTTGGT
Found at i:4507253 original size:22 final size:21
Alignment explanation
Indices: 4507214--4507258 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
4507204 TGCTTTTGGT
**
4507214 TTCGGTTAATTTTGGTTTCGG
1 TTCGGTTAATTTCAGTTTCGG
*
4507235 TTCGGATTAATTTCAGTTTTGG
1 TTCGG-TTAATTTCAGTTTCGG
4507257 TT
1 TT
4507259 GATTTCGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.13, C:0.09, G:0.24, T:0.53
Consensus pattern (21 bp):
TTCGGTTAATTTCAGTTTCGG
Found at i:4508789 original size:12 final size:12
Alignment explanation
Indices: 4508772--4508809 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4508762 ATTACTCGAT
* *
4508772 TACCCGGCCTGA
1 TACCCGACCCGA
4508784 TACCCGACCCGA
1 TACCCGACCCGA
4508796 TACCCGACCCGA
1 TACCCGACCCGA
4508808 TA
1 TA
4508810 AATATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (12 bp):
TACCCGACCCGA
Found at i:4508894 original size:17 final size:17
Alignment explanation
Indices: 4508872--4508912 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4508862 AAATTAAAAA
*
4508872 ATATATATAATATATAT
1 ATATATATAATATAAAT
* *
4508889 ATATATTTAATTTAAAT
1 ATATATATAATATAAAT
4508906 ATATATA
1 ATATATA
4508913 CCCGGCCTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATAATATAAAT
Found at i:4509561 original size:11 final size:11
Alignment explanation
Indices: 4509545--4509583 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
4509535 TTTTCAGATT
4509545 GAATTAAATTA
1 GAATTAAATTA
4509556 GAATTAAATTA
1 GAATTAAATTA
*
4509567 AAATTAAATTA
1 GAATTAAATTA
4509578 -AATTAA
1 GAATTAA
4509584 TAAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (11 bp):
GAATTAAATTA
Found at i:4509565 original size:5 final size:5
Alignment explanation
Indices: 4509546--4509583 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
4509536 TTTCAGATTG
4509546 AATTA AATTA GAATTA AATTAA AATTA AATTA AATTA A
1 AATTA AATTA -AATTA AATT-A AATTA AATTA AATTA A
4509584 TAAAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:4509567 original size:16 final size:15
Alignment explanation
Indices: 4509546--4509583 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
4509536 TTTCAGATTG
4509546 AATTAAATTAGAATTA
1 AATTAAATTA-AATTA
4509562 AATTAAAATTAAATTA
1 AATT-AAATTAAATTA
4509578 AATTAA
1 AATTAA
4509584 TAAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AATTAAATTAAATTA
Found at i:4510367 original size:21 final size:22
Alignment explanation
Indices: 4510327--4510368 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4510317 TTAATAAGAC
4510327 ATTTTAAATAAAATAATTTAAA
1 ATTTTAAATAAAATAATTTAAA
4510349 ATTTT-AA-AAAATAAATTTAA
1 ATTTTAAATAAAAT-AATTTAA
4510369 TGATATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTTAAATAAAATAATTTAAA
Found at i:4510459 original size:14 final size:14
Alignment explanation
Indices: 4510437--4510488 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
4510427 GTAATTAGTT
*
4510437 TTCTAGAAATTGAA
1 TTCTGGAAATTGAA
*
4510451 TTCTGGAAAATGAA
1 TTCTGGAAATTGAA
* *
4510465 TTATTGGAATTTGAA
1 TT-CTGGAAATTGAA
4510480 TTCTGGAAA
1 TTCTGGAAA
4510489 ACGTTTTCTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:4510461 original size:15 final size:15
Alignment explanation
Indices: 4510443--4510489 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4510433 AGTTTTCTAG
4510443 AAATTGAATTCTGGA
1 AAATTGAATTCTGGA
*
4510458 AAA-TGAATTATTGG-
1 AAATTGAATT-CTGGA
*
4510472 AATTTGAATTCTGGA
1 AAATTGAATTCTGGA
4510487 AAA
1 AAA
4510490 CGTTTTCTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (15 bp):
AAATTGAATTCTGGA
Found at i:4510839 original size:23 final size:23
Alignment explanation
Indices: 4510810--4510854 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4510800 AGTGTTATAT
4510810 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
4510833 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
4510855 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:4510860 original size:23 final size:23
Alignment explanation
Indices: 4510811--4510897 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
4510801 GTGTTATATT
* * **
4510811 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
4510834 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
4510857 ATATTATTAGAT-TATTATATTAATA
1 ATATT-TTAAATATATT-TATTAA-A
* *
4510882 TTAATATTAAATATAT
1 AT-ATTTTAAATATAT
4510898 AAATAATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
23 28 0.55
24 11 0.22
25 7 0.14
26 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:4511107 original size:23 final size:23
Alignment explanation
Indices: 4511054--4511120 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
4511044 ATAATGTTAA
4511054 AAATA-TAAT-AATATATTATTAG
1 AAATATTAATAAATATATT-TTAG
4511076 AAATATTAATAAATATATTTTA-
1 AAATATTAATAAATATATTTTAG
* *
4511098 AATATTTTAATAATTAATATTTT
1 AA-ATATTAATAAAT-ATATTTT
4511121 GATTAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.18
23 17 0.44
24 15 0.38
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
AAATATTAATAAATATATTTTAG
Found at i:4514604 original size:20 final size:20
Alignment explanation
Indices: 4514579--4514671 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
4514569 TTTTCCCAAT
*
4514579 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
4514599 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
4514619 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
4514640 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
4514661 TCGCAATGCGA
1 TCGCAATGCGA
4514672 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:4514624 original size:21 final size:20
Alignment explanation
Indices: 4514596--4514671 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
4514586 GCAAATAAGT
4514596 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
4514616 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
4514637 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
*
4514657 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
4514672 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:4514634 original size:41 final size:41
Alignment explanation
Indices: 4514576--4514671 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
4514566 CGATTTTCCC
*
4514576 AATTCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
4514617 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
4514658 AAATCGCAATGCGA
1 AATTCGCAATGCGA
4514672 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:4514684 original size:41 final size:41
Alignment explanation
Indices: 4514598--4514732 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
4514588 AAATAAGTAA
* * *
4514598 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
4514639 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
4514680 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
4514721 TTCGCAACGCGA
1 ATCGCAACGCGA
4514733 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:4514685 original size:20 final size:20
Alignment explanation
Indices: 4514660--4514754 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
4514650 AATTGGGAAA
*
4514660 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
4514680 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
4514701 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
4514721 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
4514741 TTCGCAACGCGATA
1 ATCGCAACGCGATA
4514755 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4514970 original size:22 final size:22
Alignment explanation
Indices: 4514942--4514985 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4514932 CACTCTCTCA
4514942 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
4514964 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
4514986 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4515274 original size:20 final size:20
Alignment explanation
Indices: 4515249--4515286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4515239 CGATTCTCTC
4515249 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
4515269 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
4515287 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:4516627 original size:18 final size:18
Alignment explanation
Indices: 4516606--4516650 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4516596 TCCACTTCGG
*
4516606 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* **
4516624 GAGCTATCACCTCACTTA
1 GAGCCATCACCTCACCCA
4516642 GAGCCATCA
1 GAGCCATCA
4516651 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:4517145 original size:20 final size:20
Alignment explanation
Indices: 4517120--4517165 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4517110 TAGTTTACTT
4517120 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
4517140 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
4517160 TCGCAA
1 TCGCAA
4517166 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:4517217 original size:32 final size:33
Alignment explanation
Indices: 4517159--4517249 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
4517149 GGAAATGGCT
*
4517159 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
*
4517192 ATCGCAACGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGACAAA
* *
4517224 ATCGCAACGCGAAACACAAATCGCAA
1 ATCGCAACGCGAAATAAAAATCGCAA
4517250 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCGCAACGACAAA
Found at i:4517244 original size:19 final size:18
Alignment explanation
Indices: 4517159--4517254 Score: 73
Period size: 14 Copynumber: 5.7 Consensus size: 18
4517149 GGAAATGGCT
* *
4517159 ATCGCAATGCGAAATAAAA
1 ATCGCAACGCGAAA-CAAA
4517178 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
**
4517192 ATCGCAACGCGAAATGAA
1 ATCGCAACGCGAAACAAA
4517210 ATCGCAA--CG--ACAAA
1 ATCGCAACGCGAAACAAA
4517224 ATCGCAACGCGAAACACAA
1 ATCGCAACGCGAAACA-AA
*
4517243 ATCGCAATGCGA
1 ATCGCAACGCGA
4517255 TTTGTGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 20 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 13 0.21
19 20 0.32
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (18 bp):
ATCGCAACGCGAAACAAA
Found at i:4517304 original size:19 final size:19
Alignment explanation
Indices: 4517280--4517346 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
4517270 GCGATGTTGT
**
4517280 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
4517299 CGTTGCGATAGCCATTTACG
1 CGTTGCGATAGTCATTT-CG
4517319 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
4517338 CGTTGCGAT
1 CGTTGCGAT
4517347 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:4517322 original size:20 final size:19
Alignment explanation
Indices: 4517292--4517346 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
4517282 TTGCGATTTT
4517292 CATTTCGCGTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4517311 CATTTACGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
4517331 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
4517347 TTTAAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4519362 original size:14 final size:14
Alignment explanation
Indices: 4519343--4519396 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
4519333 CGAAATGGCT
4519343 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
4519357 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
4519376 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
4519390 ATCGCAA
1 ATCGCAA
4519397 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:4519414 original size:33 final size:33
Alignment explanation
Indices: 4519324--4519401 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
4519314 AAAACAGACT
* ***
4519324 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
4519357 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
4519390 ATCGCAATGCGA
1 ATCGCAATGCGA
4519402 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:4519445 original size:20 final size:20
Alignment explanation
Indices: 4519420--4519457 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4519410 TCGCATTGCG
*
4519420 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4519440 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4519458 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:4520682 original size:166 final size:167
Alignment explanation
Indices: 4520408--4520740 Score: 659
Period size: 166 Copynumber: 2.0 Consensus size: 167
4520398 TAATCCAAAT
4520408 CCAAATCAACTTTCAGCACCAAATTCCGGTTTTCGTATTGACCAATTAGACGATGATAAGCCAAG
1 CCAAATCAACTTTCAGCACCAAATTCCGGTTTTCGTATTGACCAATTAGACGATGATAAGCCAAG
4520473 AGAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTC-ATACCTGGACTTTGATAT
66 AGAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCTGGACTTTGATAT
4520537 TGGTCAATACACGGATTTTGATGATGTTTCAGAAGAA
131 TGGTCAATACACGGATTTTGATGATGTTTCAGAAGAA
4520574 CCAAATCAACTTTCAGCACCAAATTCCGGTTTTCGTATTGACCAATTAGACGATGATAAGCCAAG
1 CCAAATCAACTTTCAGCACCAAATTCCGGTTTTCGTATTGACCAATTAGACGATGATAAGCCAAG
4520639 AGAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCTGGACTTTGATAT
66 AGAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCTGGACTTTGATAT
4520704 TGGTCAATACACGGATTTTGATGATGTTTCAGAAGAA
131 TGGTCAATACACGGATTTTGATGATGTTTCAGAAGAA
4520741 GAAACAGACC
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 111 0.67
167 55 0.33
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (167 bp):
CCAAATCAACTTTCAGCACCAAATTCCGGTTTTCGTATTGACCAATTAGACGATGATAAGCCAAG
AGAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCTGGACTTTGATAT
TGGTCAATACACGGATTTTGATGATGTTTCAGAAGAA
Found at i:4523243 original size:33 final size:33
Alignment explanation
Indices: 4523200--4523292 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
4523190 CGGAAATTAC
4523200 TATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
* **
4523234 -ATCGCAATGCGAAAAGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
4523266 TTTCGCAATGCGAAATGAAAATCGCAA
1 TATCGCAATGCGAAATGAAAATCGCAA
4523293 TGCGAAATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.16
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:4523289 original size:52 final size:52
Alignment explanation
Indices: 4523233--4523344 Score: 206
Period size: 52 Copynumber: 2.2 Consensus size: 52
4523223 GCAACGAGAG
*
4523233 AATCGCAATGCGAAAAGAAAATCGCAACGCTAATTTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAAAGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAA
*
4523285 AATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAA
1 AATCGCAATGCGAAAAGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAA
4523337 AATCGCAA
1 AATCGCAA
4523345 CGATGGAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.17
Consensus pattern (52 bp):
AATCGCAATGCGAAAAGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAA
Found at i:4523324 original size:33 final size:33
Alignment explanation
Indices: 4523287--4523386 Score: 159
Period size: 33 Copynumber: 3.0 Consensus size: 33
4523277 GAAATGAAAA
4523287 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
4523320 TCGCAATGCGAAATGAAAATCGCAACGATGGAA--
1 TCGCAATGCGAAATGAAAATCGCAACG--CGAATT
4523353 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
4523386 T
1 T
4523387 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
31 3 0.05
33 55 0.90
35 3 0.05
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:4523326 original size:85 final size:84
Alignment explanation
Indices: 4523201--4523383 Score: 271
Period size: 85 Copynumber: 2.2 Consensus size: 84
4523191 GGAAATTACT
*
4523201 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAAGAAAATCGCAACGCT-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAAGAAAATCGCAACGATGA
4523265 ATTTCGCAATGCGAAATGAAA
66 A--TCGCAATGCGAAATGAAA
* * *
4523286 ATCGCAATGCGAAATGAAAATCGCAACGCGA-ATTTCGCAATGCGAAATGAAAATCGCAACGATG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA-ATCGCAATGCGAAAAGAAAATCGCAACGAT-
4523350 GAATCGCAATGCGAAATGAAA
64 GAATCGCAATGCGAAATGAAA
*
4523371 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4523384 TTTAATTTCG
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
84 1 0.01
85 87 0.97
87 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (84 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAAGAAAATCGCAACGATGA
ATCGCAATGCGAAATGAAA
Found at i:4523401 original size:19 final size:20
Alignment explanation
Indices: 4523379--4523421 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4523369 AAATCGCAAC
4523379 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
4523398 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
4523418 GCGA
1 GCGA
4523422 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:4523406 original size:14 final size:14
Alignment explanation
Indices: 4523407--4523440 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4523397 TGCGATTTTC
4523407 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
4523421 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
4523435 ATTTTC
1 ATTTTC
4523441 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:4523581 original size:14 final size:14
Alignment explanation
Indices: 4523562--4523598 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4523552 CATTAATTAA
4523562 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4523576 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4523590 ACAAATCAA
1 ACAAATCAA
4523599 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4525026 original size:41 final size:42
Alignment explanation
Indices: 4524981--4525063 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4524971 CGATGACAGT
* * *
4524981 GGCCTCTTGAACG-TGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
* * *
4525022 GGCCTCTTCAACGATAGGAGTGGAATCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
4525064 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGAATCTCGAGGAATGATAGG
Found at i:4527045 original size:33 final size:33
Alignment explanation
Indices: 4526990--4527086 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
4526980 GAGATAATGG
*
4526990 GAATCGCAACGCGGAAATGACTATCGCAACGAGA
1 GAATCGCAACGC-GAAATGACTATCGCAACCAGA
*
4527024 GAATCGCAACGCGAAATGACTATCGCGACCAGA
1 GAATCGCAACGCGAAATGACTATCGCAACCAGA
* * **
4527057 CAATGGCAACGCGAAATGAAAATCGCAACC
1 GAATCGCAACGCGAAATGACTATCGCAACC
4527087 GCGAAATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.79
34 12 0.21
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (33 bp):
GAATCGCAACGCGAAATGACTATCGCAACCAGA
Found at i:4527105 original size:39 final size:38
Alignment explanation
Indices: 4527062--4527139 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 38
4527052 CCAGACAATG
*
4527062 GCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATC
1 GCAACACGAAATGAAAATCGCAA-CGCGAAATAAAAATC
*
4527101 GCAACACGAAATGAAAATCGCAACGCGAAATGAAAATC
1 GCAACACGAAATGAAAATCGCAACGCGAAATAAAAATC
4527139 G
1 G
4527140 TAATGCGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 15 0.41
39 22 0.59
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (38 bp):
GCAACACGAAATGAAAATCGCAACGCGAAATAAAAATC
Found at i:4527147 original size:19 final size:19
Alignment explanation
Indices: 4526963--4527139 Score: 140
Period size: 19 Copynumber: 9.7 Consensus size: 19
4526953 TCTTTTGGTT
*
4526963 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
4526982 GATAATGGGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4527002 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
4527020 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
4527036 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
* *
4527054 ---A-GACAATGGCAACGC
1 GAAATGAAAATCGCAACGC
4527069 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
4527089 GAAATAAAAATCGCAACAC
1 GAAATGAAAATCGCAACGC
4527108 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4527127 GAAATGAAAATCG
1 GAAATGAAAATCG
4527140 TAATGCGATT
Statistics
Matches: 125, Mismatches: 20, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
14 18 0.14
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 52 0.42
20 43 0.34
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4527165 original size:19 final size:19
Alignment explanation
Indices: 4527143--4527187 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4527133 AAAATCGTAA
*
4527143 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
4527162 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
4527181 TGCGATT
1 TGCGATT
4527188 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:4527755 original size:20 final size:20
Alignment explanation
Indices: 4527730--4527781 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4527720 CGCTATGTAA
4527730 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
4527750 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
4527770 ATCTCGTTGCGA
1 ATCGCGTTGCGA
4527782 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:4528277 original size:21 final size:21
Alignment explanation
Indices: 4528248--4528321 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
4528238 GATTACACCC
*
4528248 TAAATCCTAAACTATAAACTA
1 TAAACCCTAAACTATAAACTA
*
4528269 TAAACCCTAAACTATAGATCT-
1 TAAACCCTAAACTATA-AACTA
* * *
4528290 TAAACTCTAAA-TCTAAACCA
1 TAAACCCTAAACTATAAACTA
*
4528310 TGAACCCTAAAC
1 TAAACCCTAAAC
4528322 CCTAAACTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 25 0.60
22 3 0.07
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACTA
Found at i:4528293 original size:14 final size:14
Alignment explanation
Indices: 4528262--4528321 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
4528252 TCCTAAACTA
4528262 TAAACTATAAACCC
1 TAAACTATAAACCC
* * *
4528276 TAAACTATAGATCT
1 TAAACTATAAACCC
* *
4528290 TAAACTCTAAA-TC
1 TAAACTATAAACCC
* *
4528303 TAAACCATGAACCC
1 TAAACTATAAACCC
4528317 TAAAC
1 TAAAC
4528322 CCTAAACTCT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
13 8 0.24
14 26 0.76
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAACTATAAACCC
Found at i:4528452 original size:7 final size:7
Alignment explanation
Indices: 4528402--4528469 Score: 75
Period size: 7 Copynumber: 9.7 Consensus size: 7
4528392 GCTAAAATAT
4528402 ACCCTAA
1 ACCCTAA
*
4528409 ATCCTAA
1 ACCCTAA
*
4528416 ATCCTAA
1 ACCCTAA
4528423 ACCCTAA
1 ACCCTAA
4528430 ACCCTAA
1 ACCCTAA
*
4528437 A-TCTCAA
1 ACCCT-AA
4528444 ACCCTAA
1 ACCCTAA
* *
4528451 ACCATAC
1 ACCCTAA
4528458 ACCCTAA
1 ACCCTAA
4528465 ACCCT
1 ACCCT
4528470 TAATCTAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
6 2 0.04
7 47 0.92
8 2 0.04
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:4529935 original size:11 final size:11
Alignment explanation
Indices: 4529919--4530006 Score: 86
Period size: 11 Copynumber: 8.0 Consensus size: 11
4529909 TTAACCCTTG
4529919 GAGTTTGAATC
1 GAGTTTGAATC
*
4529930 GAGTTTTAATC
1 GAGTTTGAATC
* **
4529941 AAACTTGAATC
1 GAGTTTGAATC
*
4529952 GAGCTTGAATC
1 GAGTTTGAATC
* *
4529963 GAGTTTTAATT
1 GAGTTTGAATC
*
4529974 GAGATTGAATC
1 GAGTTTGAATC
*
4529985 GAGTTTTAATC
1 GAGTTTGAATC
*
4529996 GAGCTTGAATC
1 GAGTTTGAATC
4530007 AAGGTCGAGT
Statistics
Matches: 60, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 60 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (11 bp):
GAGTTTGAATC
Found at i:4529960 original size:33 final size:32
Alignment explanation
Indices: 4529923--4530008 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
4529913 CCCTTGGAGT
4529923 TTGAATCGAGTTTTAATCAAACTTGAATCGAGC
1 TTGAATCGAGTTTTAATCAAA-TTGAATCGAGC
* * *
4529956 TTGAATCGAGTTTTAATTGAGATTGAATCGAGT
1 TTGAATCGAGTTTTAA-TCAAATTGAATCGAGC
* * *
4529989 TTTAATCGAGCTTGAATCAA
1 TTGAATCGAGTTTTAATCAA
4530009 GGTCGAGTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.05
33 39 0.89
34 3 0.07
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
TTGAATCGAGTTTTAATCAAATTGAATCGAGC
Found at i:4544586 original size:21 final size:21
Alignment explanation
Indices: 4544560--4544612 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
4544550 GTTTCCAGAT
4544560 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
4544581 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
4544602 TCGCAATGCGA
1 TCGCAACGCGA
4544613 TAGTCCAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:4544677 original size:42 final size:42
Alignment explanation
Indices: 4544616--4545097 Score: 606
Period size: 42 Copynumber: 11.7 Consensus size: 42
4544606 AATGCGATAG
* * * *
4544616 TCCAAGTTTGTTGTGATAGTCGAAGTTCTCGTTGTGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * ** *
4544658 TCCAAATTCGTTGCGATAGTCCAAGTTCGCAATGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* ** *
4544698 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCAATGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
4544738 TCGAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * * *
4544780 TCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
4544820 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
4544862 TCCAAATTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
4544904 TCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
4544946 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
4544986 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * ** *
4545028 TCCAAATTCGTTGCGATAGTCCAAGTTCGCAATGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
4545068 ACTAAGTTCGTTGCGATAGTCCAAGTTCGC
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGC
4545098 AATGCGATAG
Statistics
Matches: 390, Mismatches: 44, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
40 176 0.45
42 214 0.55
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:4544784 original size:82 final size:82
Alignment explanation
Indices: 4544658--4545187 Score: 698
Period size: 82 Copynumber: 6.5 Consensus size: 82
4544648 TGTGATTTAT
* * ** * *
4544658 TCCAAATTCGTTGCGATAGTCCAAGTTCGCAATGCGA--TAGTCCAAGTTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
4544721 AGTTCGCAATGCGATAG
66 AGTTCGCATTGCGATAG
* *
4544738 TCGAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
4544803 AGTTCGCATTGCGATAG
66 AGTTCGCATTGCGATAG
*
4544820 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
4544885 AGTTCGCATTGCGATTTAT
66 AGTTCGCATTGCGA--TAG
* *
4544904 TCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
4544969 AGTTCGCGTTGCGATAG
66 AGTTCGCATTGCGATAG
4544986 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
4545051 AGTTCGCAATGCGATAG
66 AGTTCGCATTGCGATAG
* * * ** * * *
4545068 ACTAAGTTCGTTGCGATAGTCCAAGTTCGCAATGCGA--TAGTCCAAGTTCATGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC--GTTGCGA--TAG
*
4545131 TCCAAATTCG--TTGCGATAG
62 TCCAAGTTCGCATTGCGATAG
* *
4545150 TCCAACTTCGTAATGCGATAGTCCAAGTT--CGTTGCGAT
1 TCCAAGTTCGT--TGCGATAGTCGAAGTTCGCGTTGCGAT
4545188 AGTCGAATTT
Statistics
Matches: 404, Mismatches: 35, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
80 41 0.10
82 257 0.64
84 106 0.26
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (82 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCGCATTGCGATAG
Found at i:4545020 original size:21 final size:20
Alignment explanation
Indices: 4544608--4545278 Score: 494
Period size: 21 Copynumber: 32.6 Consensus size: 20
4544598 ACTATCGCAA
*
4544608 TGCGATAGTCCAAGTT-TGT
1 TGCGATAGTCCAAGTTCCGT
* *
4544627 TGTGATAGTCGAAGTTCTCGT
1 TGCGATAGTCCAAGTTC-CGT
* * *
4544648 TGTGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
**
4544669 TGCGATAGTCCAAGTTCGCAA
1 TGCGATAGTCCAAGTTC-CGT
4544690 TGCGATAGTCCAAGTT-CGT
1 TGCGATAGTCCAAGTTCCGT
**
4544709 TGCGATAGTCCAAGTTCGCAA
1 TGCGATAGTCCAAGTTC-CGT
*
4544730 TGCGATAGTCGAAGTT-CGT
1 TGCGATAGTCCAAGTTCCGT
*
4544749 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
* * *
4544770 TGCAATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
*
4544791 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTC-CGT
4544812 TGCGATAGTCCAAGTT-CGT
1 TGCGATAGTCCAAGTTCCGT
*
4544831 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4544852 TGCGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
* *
4544873 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCCAAGTTC-CGT
*
4544894 TGCGATTTATTCCAAGTT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
*
4544915 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4544936 TGCGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
*
4544957 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
4544978 TGCGATAGTCCAAGTT-CGT
1 TGCGATAGTCCAAGTTCCGT
*
4544997 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4545018 TGCGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
**
4545039 TGCGATAGTCCAAGTTCGCAA
1 TGCGATAGTCCAAGTTC-CGT
* *
4545060 TGCGATAGACTAAGTT-CGT
1 TGCGATAGTCCAAGTTCCGT
**
4545079 TGCGATAGTCCAAGTTCGCAA
1 TGCGATAGTCCAAGTTC-CGT
*
4545100 TGCGATAGTCCAAGTTCATGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4545121 TGCGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
*
4545142 TGCGATAGTCCAACTT-CGT
1 TGCGATAGTCCAAGTTCCGT
4545161 AATGCGATAGTCCAAGTT-CGT
1 --TGCGATAGTCCAAGTTCCGT
* *
4545182 TGCGATAGTCGAATTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4545203 TGCGATTTATTCCAAATT-CGT
1 TGCGA--TAGTCCAAGTTCCGT
*
4545224 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTC-CGT
* *
4545245 TGCGATTTATTCCAAGTT-CAT
1 TGCGA--TAGTCCAAGTTCCGT
4545266 TGCGATAGTCCAA
1 TGCGATAGTCCAA
4545279 AATCGCAACG
Statistics
Matches: 519, Mismatches: 85, Indels: 96
0.74 0.12 0.14
Matches are distributed among these distances:
19 191 0.37
21 253 0.49
23 75 0.14
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (20 bp):
TGCGATAGTCCAAGTTCCGT
Found at i:4545188 original size:82 final size:78
Alignment explanation
Indices: 4544658--4545279 Score: 454
Period size: 82 Copynumber: 7.6 Consensus size: 78
4544648 TGTGATTTAT
* * * *
4544658 TCCAAATTCGTTGCGATAGTCCAAGTTCGCAATGCGATAGTCCAAGTTCGTTGCGA--TAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCG--TTGCGATAGTCCAAATTCGTTGCGATTTATTCCA
* *
4544721 AGTTCGCAATGCGATAG
64 AATTCG--TTGCGATAG
* * * * *
4544738 TCGAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGA--TAGTC
1 TCCAAGTTCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGTTGCGATTTATTC
*
4544801 CAAGTTCGCATTGCGATAG
62 CAAATTCG--TTGCGATAG
* * *
4544820 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTC
1 TCCAAGTTCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGTTGCGATTTATTC
* * *
4544883 GAAGTTCGCATTGCGATTTAT
62 CAAATTCG--TTGCGA--TAG
* * *
4544904 TCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTC
1 TCCAAGTTCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGTTGCGATTTATTC
* *
4544967 GAAGTTCGCGTTGCGATAG
62 CAAATT--CGTTGCGATAG
* * *
4544986 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTC
1 TCCAAGTTCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGTTGCGATTTATTC
* *
4545049 CAAGTTCGCAATGCGATAG
62 CAAATTCG--TTGCGATAG
* * * *
4545068 ACTAAGTTCGTTGCGATAGTCCAAGTTCGCAATGCGATAGTCCAAGTTCATGTTGCGATTTATTC
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCG--TTGCGATAGTCCAAATTC--GTTGCGATTTATTC
4545133 CAAATTCGTTGCGATAG
62 CAAATTCGTTGCGATAG
* * *
4545150 TCCAACTTCGTAATGCGATAGTCCAAGTTCGTTGCGATAGTCGAATTTCGCGTTGCGATTTATTC
1 TCCAAGTTCGT--TGCGATAGTCCAAGTTCGTTGCGATAGTCCAAATT--CGTTGCGATTTATTC
4545215 CAAATTCGTTGCGATAG
62 CAAATTCGTTGCGATAG
* * *
4545232 TCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCCAAA
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAA
4545280 ATCGCAACGA
Statistics
Matches: 480, Mismatches: 38, Indels: 44
0.85 0.07 0.08
Matches are distributed among these distances:
80 42 0.09
82 303 0.63
84 133 0.28
86 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (78 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAATTCGTTGCGATTTATTCCAAA
TTCGTTGCGATAG
Found at i:4545379 original size:6 final size:6
Alignment explanation
Indices: 4545368--4545401 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4545358 GACACGTATT
4545368 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
4545402 TGGCCACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4546189 original size:21 final size:21
Alignment explanation
Indices: 4546165--4546236 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
4546155 ATTTTGGACT
4546165 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGTAATAA
* * *
4546186 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGTAATAA
*
4546207 GTCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGTAATAA
*
4546228 ATCGTAACG
1 ATCGCAACG
4546237 CGAACTTGGA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
19 9 0.24
21 20 0.53
23 9 0.24
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCGCAACGAATTTGTAATAA
Found at i:4546217 original size:42 final size:42
Alignment explanation
Indices: 4546158--4546381 Score: 303
Period size: 42 Copynumber: 5.4 Consensus size: 42
4546148 CGTTGTGATT
*
4546158 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
4546200 TTGGACTGTCGCAACGAATTTGTAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
4546242 TTGGACTATCGCAACAAATTTGGAAGAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
4546284 TTGGACTATCGCAACGAATTTGG-A-AAATCGCAACGGGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
4546324 TTCGACTATCGCAACGCGAACTTGGACT--ATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
*
4546366 TTAGACTATCGCAACG
1 TTGGACTATCGCAACG
4546382 CGAACTTGGA
Statistics
Matches: 164, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
40 30 0.18
41 1 0.01
42 133 0.81
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:4546252 original size:21 final size:21
Alignment explanation
Indices: 4546186--4546406 Score: 220
Period size: 21 Copynumber: 10.6 Consensus size: 21
4546176 TTTGTAATAA
4546186 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * * *
4546207 GTCGCAA--CGAATTTGTAAT
1 ATCGCAACGCGAACTTGGACT
*
4546226 AAATCGTAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* * **
4546249 ATCGCAA--CAAATTTGGAAGAA
1 ATCGCAACGCGAACTTGG-A-CT
4546270 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
4546291 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* *
4546310 ATCGCAACGGGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
4546331 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
4546352 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTGGACT
4546373 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
4546394 ATCGCAATGCGAA
1 ATCGCAACGCGAA
4546407 TATGTAAATC
Statistics
Matches: 159, Mismatches: 31, Indels: 20
0.76 0.15 0.10
Matches are distributed among these distances:
19 32 0.20
20 1 0.01
21 109 0.69
22 1 0.01
23 16 0.10
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:4546382 original size:42 final size:40
Alignment explanation
Indices: 4546158--4546406 Score: 273
Period size: 42 Copynumber: 6.0 Consensus size: 40
4546148 CGTTGTGATT
*
4546158 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAAT--ATCGCAACGCGAAC
* * *
4546200 TTGGACTGTCGCAACGAATTTGTAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAAT--ATCGCAACGCGAAC
* *
4546242 TTGGACTATCGCAACAAATTTGGAAGAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGG-A-ATATCGCAACGCGAAC
* *
4546284 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGGGAAC
1 TTGGACTATCGCAACGAATTTGGAATATCGCAACGCGAAC
* * *
4546324 TTCGACTATCGCAACGCGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAATTTGGAATATCGCAACGCGAAC
* * * *
4546366 TTAGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA--CGAATTTGGAATATCGCAACGCGAA
4546407 TATGTAAATC
Statistics
Matches: 187, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
40 28 0.15
41 1 0.01
42 156 0.83
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGAATTTGGAATATCGCAACGCGAAC
Found at i:4547858 original size:25 final size:25
Alignment explanation
Indices: 4547830--4547912 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
4547820 AGTTTATATC
4547830 TAAAATAATGTATATATTAACCCAT
1 TAAAATAATGTATATATTAACCCAT
* *
4547855 TAAAATAATTTATATATTAGCCCAT
1 TAAAATAATGTATATATTAACCCAT
*
4547880 TAAAATAATGTATATATTATCCCAT
1 TAAAATAATGTATATATTAACCCAT
4547905 TAAAATAA
1 TAAAATAA
4547913 GGTACATCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (25 bp):
TAAAATAATGTATATATTAACCCAT
Found at i:4549091 original size:2 final size:2
Alignment explanation
Indices: 4549084--4549120 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4549074 CAATAATTTA
4549084 AT 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 AT A
4549121 CTAAACCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4550506 original size:3 final size:3
Alignment explanation
Indices: 4550498--4550584 Score: 140
Period size: 3 Copynumber: 29.0 Consensus size: 3
4550488 ATGATATTAG
4550498 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4550546 TAA TAA TAA TAA TAA TAA TAC T-A TAG TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
4550585 ATAAAATATA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
2 1 0.01
3 75 0.96
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4550596 original size:21 final size:20
Alignment explanation
Indices: 4550482--4550597 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 20
4550472 ATAAAATATA
*
4550482 AATAAAATGATAT-TAGTAAT
1 AATAAAAT-ATATATAATAAT
*
4550502 AATAATA-ATA-ATAATAAT
1 AATAAAATATATATAATAAT
4550520 AATAATAATA-ATAATAATAAT
1 AATAA-AATATAT-ATAATAAT
4550541 AATAATAATA-ATAATAATAAT
1 AATAA-AATATAT-ATAATAAT
**
4550562 AATACTATAGTATATAATAAT
1 AATAAAATA-TATATAATAAT
4550583 AAATAAAATATATAT
1 -AATAAAATATATAT
4550598 TTTAATCCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 15
0.79 0.07 0.15
Matches are distributed among these distances:
18 14 0.17
19 2 0.02
20 10 0.12
21 46 0.57
22 9 0.11
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (20 bp):
AATAAAATATATATAATAAT
Found at i:4550603 original size:24 final size:27
Alignment explanation
Indices: 4550495--4550596 Score: 114
Period size: 24 Copynumber: 4.1 Consensus size: 27
4550485 AAAATGATAT
4550495 TAGTA-ATAATAATAATAATAATA--A
1 TAGTATATAATAATAATAATAATACTA
*
4550519 TAATA-ATAATAATAATAATAATA--A
1 TAGTATATAATAATAATAATAATACTA
*
4550543 TAATA-ATAATAATAATAATAATACTA
1 TAGTATATAATAATAATAATAATACTA
4550569 TAGTATATAATAATAAATAA-AATA-TA
1 TAGTATATAATAAT-AATAATAATACTA
4550595 TA
1 TA
4550597 TTTTAATCCC
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
24 46 0.64
26 9 0.12
27 12 0.17
28 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (27 bp):
TAGTATATAATAATAATAATAATACTA
Found at i:4551124 original size:91 final size:92
Alignment explanation
Indices: 4550962--4551136 Score: 280
Period size: 91 Copynumber: 1.9 Consensus size: 92
4550952 GAGATAGGTC
* *
4550962 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCATCGTTCGGATGAGTTCTTCTCATTATGAACT
4551027 CTCCATTGAAAATGTTGATGCGAAGTT
66 CTCCATTGAAAATGTTGATGCGAAGTT
* * * *
4551054 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCGTT-GGATGATTTCTTTTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCATCGTTCGGATGAGTTCTTCTCATTATGAACT
*
4551118 CTCCATTGGAAATGTTGAT
66 CTCCATTGAAAATGTTGAT
4551137 CCATATCTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
91 41 0.54
92 35 0.46
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCATCGTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTTGATGCGAAGTT
Found at i:4551229 original size:16 final size:16
Alignment explanation
Indices: 4551173--4551229 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
4551163 AGGAACAAGT
4551173 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
4551189 T-TTCTCCTTTATGACGAGT
1 TCTTCT-CATTATGA--A-C
4551208 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
4551224 TCTTCT
1 TCTTCT
4551230 GAAAATGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
17 1 0.03
18 1 0.03
19 8 0.25
20 4 0.12
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:4551366 original size:332 final size:331
Alignment explanation
Indices: 4550721--4551692 Score: 1542
Period size: 332 Copynumber: 2.9 Consensus size: 331
4550711 CGTCGTTGGA
* *
4550721 TTGAACAAGTTCTTCTCATTATGAACTTTTTC-TCTCTTGTGGATGAATTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCAT-TGGATGAATTCTTCTCATTATGAAC
* * * *
4550785 TCTTCACTGAAAATGTTGAGTCACCTAT-TTCTATG-G-TGGACTTGAAAGGAACAAGTTCTTCT
65 TCTCCATTGGAAATGTTGA-TC-CATATCTT-TATGTGATGGACTTGAAAGGAACAAGTTCTTCT
* * *
4550847 CATTATGAACTTTCTCCTTTAAGATGAGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCC
127 CATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCC
* * *
4550912 CTTTAACGAGGCGTCACTGATTCGAAATTTCGTGAATCGAGAGATAGGTCGAACAAGCTCTTCTC
192 CTCTAACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTC
4550977 ATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGT
257 ATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGT
4551042 TGATGCGAAG
322 TGATGCGAAG
* * *
4551052 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCGTTGGATGATTTCTTTTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TCATTGGATGAATTCTTCTCATTATGAAC
4551117 TCTCCATTGGAAATGTTGATCCATATCTTTATGTGATGGACTTGAAAGGAACAAGTTCTTCTCAT
65 TCTCCATTGGAAATGTTGATCCATATCTTTATGTGATGGACTTGAAAGGAACAAGTTCTTCTCAT
*
4551182 TATGAACTTTCTCCTTTATGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTC
130 TATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTC
* * * * *
4551247 TAATGAGGCGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCAAACAAGCTCTTCTTATT
195 TAACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATT
*
4551312 ATGAACTTCTTCTCCCTCTTTCGGATGATTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGA
260 ATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGA
4551377 TGCGAAG
325 TGCGAAG
*
4551384 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCGTCATTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TCATTGGATGAATTCTTCTCATTATGAAC
* *
4551449 TCTCCATTGGAAATGTTGAT-CATTCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
65 TCTCCATTGGAAATGTTGATCCA-TATCTTTATGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
* *
4551513 TTATGAACTTTCTCCTTTACGACGAGTTCTTCTCATTATGAACTCTTCTAAAAATGTCAATCCCT
129 TTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCT
* * * *
4551578 C-AAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATTGGTTGAACAAGCTCTTCTCA
194 CTAA-CGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCA
*
4551642 TTATGAACTTTTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCT
258 TTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCT
4551693 TCTGGAAAGG
Statistics
Matches: 594, Mismatches: 40, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
330 8 0.01
331 40 0.07
332 543 0.91
333 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (331 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCATTGGATGAATTCTTCTCATTATGAACT
CTCCATTGGAAATGTTGATCCATATCTTTATGTGATGGACTTGAAAGGAACAAGTTCTTCTCATT
ATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCCCTCT
AACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTA
TGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGAT
GCGAAG
Found at i:4551453 original size:91 final size:92
Alignment explanation
Indices: 4551295--4551468 Score: 278
Period size: 91 Copynumber: 1.9 Consensus size: 92
4551285 TGATAGGTCA
* * *
4551295 AACAAGCTCTTCTTATTATGAACTTCTTCTCCCTCTTTCGGATGATTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTCGGATGAGTTCTTCTCATTATGAACTC
4551360 TCCATTGAAAATGTTGATGCGAAGTTG
66 TCCATTGAAAATGTTGATGCGAAGTTG
* * *
4551387 AACAAGTTCTTCTCATTATGAACTTCTTCTTCGTCATT-GGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTCGGATGAGTTCTTCTCATTATGAACTC
*
4551451 TCCATTGGAAATGTTGAT
66 TCCATTGAAAATGTTGAT
4551469 CATTCTCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
91 42 0.56
92 33 0.44
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (92 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTCGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATGCGAAGTTG
Found at i:4552607 original size:8 final size:8
Alignment explanation
Indices: 4552589--4552633 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
4552579 TTGTTTTTCA
4552589 TTTTCATTT
1 TTTTCA-TT
4552598 TTTTCATT
1 TTTTCATT
*
4552606 TTTTCATC
1 TTTTCATT
4552614 TTTTCATT
1 TTTTCATT
* *
4552622 TGTTCCTT
1 TTTTCATT
4552630 TTTT
1 TTTT
4552634 TCTTCAAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
8 25 0.81
9 6 0.19
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTCATT
Found at i:4552608 original size:16 final size:16
Alignment explanation
Indices: 4552582--4552635 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
4552572 TTTCATTTTG
4552582 TTTTTCA-TTTTCATT
1 TTTTTCATTTTTCATT
4552597 TTTTTCATTTTTTCA-T
1 TTTTTCA-TTTTTCATT
* *
4552613 CTTTTCATTTGTTCCTT
1 TTTTTCATTT-TTCATT
4552630 TTTTTC
1 TTTTTC
4552636 TTCAAGCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 10 0.31
16 10 0.31
17 12 0.38
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTCATTTTTCATT
Found at i:4552617 original size:25 final size:27
Alignment explanation
Indices: 4552570--4552622 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4552560 TCTCTTTTAA
**
4552570 TTTTTCATTTTGTTTTTCATTTTCATT
1 TTTTTCATTTTGTTCATCATTTTCATT
4552597 TTTTTCATTTT-TTCATC-TTTTCATT
1 TTTTTCATTTTGTTCATCATTTTCATT
4552622 T
1 T
4552623 GTTCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 4 0.17
27 11 0.46
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTCATTTTGTTCATCATTTTCATT
Found at i:4560033 original size:6 final size:6
Alignment explanation
Indices: 4560022--4560046 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4560012 TTATGCAAAT
4560022 ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA A
4560047 AGGTATCGAT
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:4567423 original size:2 final size:2
Alignment explanation
Indices: 4567416--4567463 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4567406 AATAATTTAA
4567416 AT AT AT 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
4567458 AT AT AT
1 AT AT AT
4567464 CCAAGTAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.