Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 62
Found at i:3975822 original size:19 final size:19
Alignment explanation
Indices: 3975753--3975909 Score: 190
Period size: 19 Copynumber: 8.7 Consensus size: 19
3975743 GCAACGAGAG
3975753 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3975772 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
3975786 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
3975806 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3975825 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3975844 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3975858 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
3975878 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3975897 AATCGCATTGCGA
1 AATCGCAATGCGA
3975910 TTCTCTCGTT
Statistics
Matches: 119, Mismatches: 7, Indels: 24
0.79 0.05 0.16
Matches are distributed among these distances:
14 20 0.17
15 3 0.03
16 2 0.02
17 3 0.03
19 64 0.54
20 27 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3975862 original size:72 final size:72
Alignment explanation
Indices: 3975753--3975909 Score: 269
Period size: 72 Copynumber: 2.2 Consensus size: 72
3975743 GCAACGAGAG
3975753 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
3975818 AAATGAA
66 AAATGAA
* * * *
3975825 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
3975890 AAATGAA
66 AAATGAA
*
3975897 AATCGCATTGCGA
1 AATCGCAATGCGA
3975910 TTCTCTCGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 79 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:3975886 original size:53 final size:51
Alignment explanation
Indices: 3975730--3975903 Score: 194
Period size: 53 Copynumber: 3.3 Consensus size: 51
3975720 ATCGCAACAC
* * *
3975730 GGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-
1 GGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAT
* *
3975780 --CAA-GAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAT
1 GGAAATGAAAATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAAT
3975834 GTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAAT
1 G-GAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAAT
3975887 GCGAAATGAAAATCGCA
1 G-GAAATGAAAATCGCA
3975904 TTGCGATTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
47 9 0.09
48 2 0.02
49 1 0.01
50 1 0.01
52 14 0.13
53 62 0.60
55 1 0.01
56 1 0.01
57 2 0.02
58 11 0.11
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (51 bp):
GGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAT
Found at i:3975943 original size:53 final size:52
Alignment explanation
Indices: 3975880--3975995 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
3975870 GAAATGAAAA
*
3975880 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
3975932 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3975985 TCGCATTGCGA
1 TCGCATTGCGA
3975996 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:3975958 original size:19 final size:19
Alignment explanation
Indices: 3975918--3976005 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
3975908 GATTCTCTCG
3975918 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3975938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3975957 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3975971 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3975990 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3976006 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3976115 original size:14 final size:14
Alignment explanation
Indices: 3976096--3976132 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3976086 CATCAATTAC
3976096 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3976110 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3976124 ACAAATCAA
1 ACAAATCAA
3976133 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3978093 original size:19 final size:19
Alignment explanation
Indices: 3978051--3978223 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
3978041 TAGTTTACTT
* *
3978051 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
3978071 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
3978090 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
3978109 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
3978128 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAATGAAAA
*
3978147 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3978161 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3978180 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
3978194 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3978213 TCGCAATGCGA
1 TCGCAACGCGA
3978224 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 6 0.05
17 7 0.06
18 1 0.01
19 82 0.65
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3978164 original size:14 final size:14
Alignment explanation
Indices: 3978145--3978201 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3978135 GCGAAATAAA
*
3978145 AATCGCAACGACAG
1 AATCGCAACGAAAG
3978159 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
3978176 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
3978192 AATCGCAACG
1 AATCGCAACG
3978202 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3978172 original size:33 final size:33
Alignment explanation
Indices: 3978126--3978218 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3978116 GCGAAACCAA
*
3978126 AATCGCAACGCGAAATAAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
3978159 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
3978192 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3978219 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:3978215 original size:52 final size:52
Alignment explanation
Indices: 3978085--3978223 Score: 140
Period size: 52 Copynumber: 2.7 Consensus size: 52
3978075 AACGCGAAAT
* * * *
3978085 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
*** **
3978137 GA-AATAAAAATCGC--AACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAA-CGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
3978189 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
3978224 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
52 48 0.71
53 6 0.09
54 4 0.06
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:3978254 original size:14 final size:14
Alignment explanation
Indices: 3978235--3978293 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3978225 TTTGGTTTCG
3978235 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3978249 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
3978266 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
3978282 CGTTGCGATTTT
1 CGTTGCGATTTT
3978294 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3978261 original size:33 final size:33
Alignment explanation
Indices: 3978219--3978342 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
3978209 AAAATCGCAA
*
3978219 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
3978252 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
3978285 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
3978318 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
3978343 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3978273 original size:19 final size:18
Alignment explanation
Indices: 3978219--3978310 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
3978209 AAAATCGCAA
3978219 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
3978238 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
3978252 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3978271 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
3978285 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
3978304 TGCGATT
1 TGCGATT
3978311 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:3978320 original size:14 final size:14
Alignment explanation
Indices: 3978268--3978324 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3978258 TTTGGTTTCG
*
3978268 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
3978282 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3978301 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3978315 CGTTGCGATT
1 CGTTGCGATT
3978325 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3978668 original size:92 final size:93
Alignment explanation
Indices: 3978440--3978754 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
3978430 TCAGGGTATT
3978440 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3978505 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
3978533 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3978598 TACTA-TTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
3978625 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3978690 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
3978718 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
3978755 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.42
93 128 0.58
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:3980470 original size:20 final size:20
Alignment explanation
Indices: 3980439--3980535 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
3980429 TTTTGGTTGA
3980439 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
3980459 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3980479 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
3980498 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
3980513 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3980533 AAT
1 AAT
3980536 CGCAACGTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3980491 original size:21 final size:21
Alignment explanation
Indices: 3980437--3980501 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3980427 TCTTTTGGTT
3980437 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
3980458 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3980478 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3980499 GAA
1 GAA
3980502 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:3980505 original size:14 final size:14
Alignment explanation
Indices: 3980486--3980542 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3980476 GAGAAATGAA
3980486 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3980500 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3980519 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3980533 AATCGCAACG
1 AATCGCAACG
3980543 TGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3980518 original size:33 final size:33
Alignment explanation
Indices: 3980437--3980559 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
3980427 TCTTTTGGTT
3980437 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GA
*
3980478 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
*
3980511 GAAATGAAAATCGCAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
3980544 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3980560 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGA
Found at i:3980595 original size:14 final size:14
Alignment explanation
Indices: 3980576--3980632 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3980566 TTTGGTTTCG
3980576 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3980590 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3980609 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3980623 CGTTGCGATT
1 CGTTGCGATT
3980633 TTCATTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3980608 original size:33 final size:33
Alignment explanation
Indices: 3980560--3980648 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
3980550 AAAATCGCAA
**
3980560 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3980593 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3980626 TGCGATTTTCATTTTCTCGTTGC
1 TGCGATTTTCA-TTTCGCGTTGC
3980649 AGATAGTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 42 0.81
34 10 0.19
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3980660 original size:21 final size:20
Alignment explanation
Indices: 3980587--3980692 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 20
3980577 GTTGCGATTC
3980587 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
3980606 TCGCGTTGCGA--TTC----
1 TCTCGTTGCGATTTTCATTT
3980620 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
**
3980640 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
3980661 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
3980681 ATCTCGTTGCGA
1 -TCTCGTTGCGA
3980693 CTCTTCTGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 10 0.14
20 18 0.25
21 27 0.38
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:3980814 original size:33 final size:33
Alignment explanation
Indices: 3980772--3980842 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3980762 AATACTAACT
3980772 TGAAAATCGCAACGAGAGAATAGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGTAACGCGAAA
* *
3980805 TGAAAATCGCAACGAGGGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGTAACGCGAAA
3980838 TGAAA
1 TGAAA
3980843 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGTAACGCGAAA
Found at i:3981225 original size:20 final size:20
Alignment explanation
Indices: 3981200--3981354 Score: 240
Period size: 20 Copynumber: 7.7 Consensus size: 20
3981190 CTTTAAAAAT
3981200 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3981220 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3981240 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3981261 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
3981281 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
3981301 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3981321 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
3981341 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
3981355 TGTGTTCACG
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
20 105 0.86
21 17 0.14
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3981366 original size:20 final size:20
Alignment explanation
Indices: 3981202--3981373 Score: 202
Period size: 20 Copynumber: 8.6 Consensus size: 20
3981192 TTAAAAATCG
*
3981202 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* ***
3981222 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACA
*
3981243 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* *
3981263 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACA
* *
3981283 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
3981303 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACA
*
3981323 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* *
3981343 CGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACG-GATACA
3981363 CGTTGCGATTT
1 CGTTGCGATTT
3981374 TCATATTCGC
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
20 116 0.87
21 17 0.13
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACA
Found at i:3981387 original size:60 final size:60
Alignment explanation
Indices: 3981200--3981392 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
3981190 CTTTAAAAAT
* **
3981200 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTGTTCACGTTGCGATTTACGGATA
* * * *
3981261 CGCGTTGCGATATACGGATACGCATTGCGATTTACG-GATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTG-TTCACGTTGCGATTTACGGATA
* * * ** *
3981321 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCACGTTGCGATTTACGGATA
3981381 CGCGTTGCGATT
1 CGCGTTGCGATT
3981393 CTGGAAAATC
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
60 84 0.74
61 29 0.26
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCACGTTGCGATTTACGGATA
Found at i:3982849 original size:19 final size:19
Alignment explanation
Indices: 3982822--3982861 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3982812 TTTTCTGATT
3982822 TTTACTTTAATAACTTTTTA
1 TTTACTTTAATAA-TTTTTA
*
3982842 TTTA-TTTAATCATTTTTA
1 TTTACTTTAATAATTTTTA
3982860 TT
1 TT
3982862 ACTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTACTTTAATAATTTTTA
Found at i:3987619 original size:12 final size:12
Alignment explanation
Indices: 3987602--3987634 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3987592 TTGCCTTGAA
3987602 TATTTAGCCATC
1 TATTTAGCCATC
3987614 TATTTAGCCATC
1 TATTTAGCCATC
3987626 TATTTAGCC
1 TATTTAGCC
3987635 TTTTTCCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (12 bp):
TATTTAGCCATC
Found at i:3989170 original size:18 final size:19
Alignment explanation
Indices: 3989142--3989180 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3989132 TTATCTTATT
3989142 TTTACTTTAATAGCTTTTA
1 TTTACTTTAATAGCTTTTA
* *
3989161 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATAGCTTTTA
3989179 TT
1 TT
3989181 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTACTTTAATAGCTTTTA
Found at i:3994956 original size:20 final size:19
Alignment explanation
Indices: 3994908--3995123 Score: 163
Period size: 20 Copynumber: 10.9 Consensus size: 19
3994898 AAATGACCAA
**
3994908 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAAGT
*
3994927 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAAGT
* *
3994946 CCAATTTCGCAAC-C-CAGTTT
1 -CAAATTCGCAACGCGAAG--T
*
3994966 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCG-A-A-GT
** **
3994989 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGA-AGT
3995007 CCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACGCGA-AGT
3995028 CAAATTCGC-ACGCGATAGT
1 CAAATTCGCAACGCGA-AGT
* *
3995047 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGC-GAAGT
3995067 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AAGT
3995087 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AAGT
3995107 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
3995124 TTTAATTTCG
Statistics
Matches: 164, Mismatches: 19, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.01
19 41 0.25
20 103 0.63
21 15 0.09
23 1 0.01
24 1 0.01
25 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACGCGAAGT
Found at i:3995081 original size:40 final size:40
Alignment explanation
Indices: 3995008--3995123 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 40
3994998 TGCGATTTTC
* *
3995008 CAAATTCGCAACGCGATAGTCAAATTCGC-ACGCGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAAGT
* *
3995047 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAAGT
3995087 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAA
3995124 TTTAATTTCG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 26 0.37
40 44 0.63
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAAGT
Found at i:3995096 original size:100 final size:99
Alignment explanation
Indices: 3994908--3995122 Score: 224
Period size: 100 Copynumber: 2.2 Consensus size: 99
3994898 AAATGACCAA
* * * *** *
3994908 CAAATTCGCAACGCGATCTCAAATTCGCAACGCGAATTCCAATTTCGCAACCCAGTTTCCAATTT
1 CAAATTCGCAACGCGATCTCAAATTCGCAACGCGAAGTCCAAATTCGCAACCAAAAGTCCAAATT
** ***
3994973 CGCAACGCGAATATGTAAATCGCATTGCGATTTT
66 CGCAACGCGAATATGTAAATCGCAACGCGAAAGT
*
3995007 CCAAATTCGCAACGCGATAGTCAAATTCGC-ACGCGATAGT-CAAATTCGCAACACAAAAGT-CA
1 -CAAATTCGCAACGCGAT-CTCAAATTCGCAACGCGA-AGTCCAAATTCGCAAC-CAAAAGTCCA
3995069 AATTCGCAACGCGAA-A-GTCAAATTCGCAACGCGAAAGT
62 AATTCGCAACGCGAATATGT-AAA-TCGCAACGCGAAAGT
3995107 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
3995123 ATTTAATTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
98 2 0.02
99 20 0.21
100 60 0.62
101 15 0.15
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (99 bp):
CAAATTCGCAACGCGATCTCAAATTCGCAACGCGAAGTCCAAATTCGCAACCAAAAGTCCAAATT
CGCAACGCGAATATGTAAATCGCAACGCGAAAGT
Found at i:3995904 original size:12 final size:12
Alignment explanation
Indices: 3995883--3995916 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3995873 ACCACATTTC
*
3995883 CAATACCAAACA
1 CAATATCAAACA
3995895 CAATATCAAACA
1 CAATATCAAACA
*
3995907 CAATCTCAAA
1 CAATATCAAA
3995917 ACCCACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:3996067 original size:24 final size:24
Alignment explanation
Indices: 3996040--3996095 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3996030 CAGTATTCGA
3996040 AATTTGATCTTGGTCAATACCCGG
1 AATTTGATCTTGGTCAATACCCGG
* *
3996064 AATTTGATCTTTGTCAATACTCGG
1 AATTTGATCTTGGTCAATACCCGG
*
3996088 ATTTTGAT
1 AATTTGAT
3996096 GATGTGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
AATTTGATCTTGGTCAATACCCGG
Found at i:3996278 original size:3 final size:3
Alignment explanation
Indices: 3996270--3996300 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3996260 ATATAACCCT
*
3996270 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3996301 TCCCCGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3996968 original size:66 final size:66
Alignment explanation
Indices: 3996885--3997027 Score: 241
Period size: 66 Copynumber: 2.2 Consensus size: 66
3996875 AATCAAAATC
*
3996885 GCAATCAAAATCATCTTTTGCTCTACCAAAAAATGGATCCTCATCAAAATCCAAAGCTCATATGG
1 GCAATCAAAATCATCTTTTCCTCTACCAAAAAATGGATCCTCATCAAAATCCAAAGCTCATATGG
3996950 T
66 T
* *
3996951 GCAATCACAATCATCTTTTCCTCTACCAAAAAATGGATCCTCATCAAAATCCAAAGTTCATATGG
1 GCAATCAAAATCATCTTTTCCTCTACCAAAAAATGGATCCTCATCAAAATCCAAAGCTCATATGG
3997016 T
66 T
*
3997017 GCCAAGCAAAA
1 G-CAATCAAAA
3997028 GGAAATCAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
66 64 0.90
67 7 0.10
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.26
Consensus pattern (66 bp):
GCAATCAAAATCATCTTTTCCTCTACCAAAAAATGGATCCTCATCAAAATCCAAAGCTCATATGG
T
Found at i:3997070 original size:12 final size:12
Alignment explanation
Indices: 3997029--3997070 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3997019 CAAGCAAAAG
3997029 GAAATCAAAATC
1 GAAATCAAAATC
*
3997041 GCAATCAAAATC
1 GAAATCAAAATC
*
3997053 GCAATCAAAATC
1 GAAATCAAAATC
*
3997065 AAAATC
1 GAAATC
3997071 CTAATCACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (12 bp):
GAAATCAAAATC
Found at i:3997077 original size:12 final size:12
Alignment explanation
Indices: 3997031--3997064 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3997021 AGCAAAAGGA
3997031 AATCAAAATCGC
1 AATCAAAATCGC
3997043 AATCAAAATCGC
1 AATCAAAATCGC
3997055 AATCAAAATC
1 AATCAAAATC
3997065 AAAATCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:3997410 original size:20 final size:20
Alignment explanation
Indices: 3997384--3997430 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3997374 AATCACAAAC
3997384 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
*
3997404 TGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
3997424 CGAATTT
1 CGAATTT
3997431 ACCTTCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:3997954 original size:18 final size:18
Alignment explanation
Indices: 3997933--3997969 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3997923 GTAATTGGAG
3997933 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3997951 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3997969 T
1 T
3997970 ATAAAATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3998367 original size:39 final size:39
Alignment explanation
Indices: 3998280--3998368 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
3998270 TCTGATGCTC
*
3998280 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
3998319 ATCAAAATCTAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
3998358 ATCAAAATCTA
1 ATCAAAATCTA
3998369 CAACTTGAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3999367 original size:2 final size:2
Alignment explanation
Indices: 3999360--3999390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3999350 AATTATAACT
3999360 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
3999391 TAATATGTAA
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:4001604 original size:55 final size:55
Alignment explanation
Indices: 4001544--4001902 Score: 465
Period size: 55 Copynumber: 6.6 Consensus size: 55
4001534 ACGAGTCCGT
* * * ***
4001544 TCCCTATTCTTTCAGGGAGCATAAGACTCGAACAATCTTTAACAATTATGTCTGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
* * *
4001599 TCCCTATTTATTCAGGGAGTATAAGACTCAAACAAGCTTCAACAAACGTGTCTGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
* * * *
4001654 TCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAATGTGTTTGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
*
4001709 TCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
* *
4001764 TCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACGGGTCTGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
* * * *
4001819 TCCCTATTCCTTCAGAGAGTATAAGACTCG----ATCTTCAATATAAACGTGTCCGC
1 TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTC-A-ACAAACGTGTCTGC
* * *
4001872 TCCCTATTCTTTCAGAGAGTATAGGACTCGA
1 TCCCTATTCATTCAGGGAGTATAAGACTCGA
4001903 TCTTCATAAA
Statistics
Matches: 270, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
51 6 0.02
52 1 0.00
53 39 0.14
55 224 0.83
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (55 bp):
TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGC
Found at i:4001969 original size:37 final size:37
Alignment explanation
Indices: 4001919--4001999 Score: 162
Period size: 37 Copynumber: 2.2 Consensus size: 37
4001909 TAAAATAAGT
4001919 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
4001956 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
4001993 TTGCTTC
1 TTGCTTC
4002000 GAAGGTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:4003318 original size:26 final size:27
Alignment explanation
Indices: 4003264--4003319 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
4003254 CTTGAACCCC
4003264 CTTTTATTTCTTTTTTCATCATTTTTT
1 CTTTTATTTCTTTTTTCATCATTTTTT
*
4003291 CTTTTCTTT-TTTCTTTC-TCATTTTTT
1 CTTTTATTTCTTT-TTTCATCATTTTTT
4003317 CTT
1 CTT
4003320 CCATTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (27 bp):
CTTTTATTTCTTTTTTCATCATTTTTT
Found at i:4003326 original size:26 final size:27
Alignment explanation
Indices: 4003269--4003327 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
4003259 ACCCCCTTTT
*
4003269 ATTTCTTTTTTCATCATTTTTTCTTTTC
1 ATTT-TTTTTTCATCATTTTTTCTTTCC
4003297 -TTTTTTCTTTC-TCATTTTTTC-TTCC
1 ATTTTTT-TTTCATCATTTTTTCTTTCC
4003322 ATTTTT
1 ATTTTT
4003328 CATTTTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 3 0.11
26 18 0.64
27 7 0.25
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (27 bp):
ATTTTTTTTTCATCATTTTTTCTTTCC
Found at i:4003327 original size:13 final size:14
Alignment explanation
Indices: 4003277--4003327 Score: 65
Period size: 12 Copynumber: 3.9 Consensus size: 14
4003267 TTATTTCTTT
4003277 TTTCATCATTTTTTC
1 TTTC-TCATTTTTTC
4003292 TTT-TC-TTTTTTC
1 TTTCTCATTTTTTC
4003304 TTTCTCATTTTTTC
1 TTTCTCATTTTTTC
4003318 -TTC-CATTTTT
1 TTTCTCATTTTT
4003328 CATTTTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 17 0.50
13 7 0.21
14 7 0.21
15 3 0.09
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTCTCATTTTTTC
Found at i:4012955 original size:45 final size:45
Alignment explanation
Indices: 4012888--4013038 Score: 230
Period size: 45 Copynumber: 3.3 Consensus size: 45
4012878 CCATGCTTTG
*
4012888 TTATTCACAAAAATAAATCCTAACTGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAA-CCTAACTGCATGATATCTAGTTCGCATGC
*
4012935 TTATTCAAAAAATAAACCTAACTGCATGATATCTAGTTCTCATGC
1 TTATTCAAAAAATAAACCTAACTGCATGATATCTAGTTCGCATGC
*
4012980 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACTGCATGATATCTAGTTCGCATGC
*
4013025 ATTTATTCGAAAAA
1 --TTATTCAAAAAA
4013039 CCAAAATAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
45 70 0.72
46 9 0.09
47 18 0.19
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACTGCATGATATCTAGTTCGCATGC
Found at i:4016622 original size:20 final size:20
Alignment explanation
Indices: 4016597--4016655 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
4016587 GCGATCAACG
*
4016597 CGAAAGTTAAATTCGCAAAA
1 CGAAAGTCAAATTCGCAAAA
**
4016617 CGAAAGTCAAATTCGCAACG
1 CGAAAGTCAAATTCGCAAAA
4016637 CGAAAGTCAAATTCGCAAA
1 CGAAAGTCAAATTCGCAAA
4016656 CCAAAAAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAAAA
Found at i:4016857 original size:14 final size:14
Alignment explanation
Indices: 4016821--4016874 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
4016811 ATAATTCTTA
*
4016821 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
4016835 TAAACAAATCAACT
1 TTTACAAATCAACT
* *
4016849 TTTATAAATCATCT
1 TTTACAAATCAACT
4016863 TTTACAAATCAA
1 TTTACAAATCAA
4016875 ATTAATCAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:4018944 original size:27 final size:27
Alignment explanation
Indices: 4018909--4018974 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
4018899 GTCACCTATT
*
4018909 ATGAGGTGATGGTGGAGAAGA-GACATG
1 ATGATGTGATGGTGGAGAAGATG-CATG
4018936 ATGATGTGATGGTGGAGAAGATGCATG
1 ATGATGTGATGGTGGAGAAGATGCATG
4018963 ATGATGTGATGG
1 ATGATGTGATGG
4018975 AATAGGTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.24
Consensus pattern (27 bp):
ATGATGTGATGGTGGAGAAGATGCATG
Found at i:4020612 original size:19 final size:20
Alignment explanation
Indices: 4020590--4020627 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4020580 AATCGCAACC
4020590 CGATTTT-AGTTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
*
4020609 CGATTTTCATTTTCGCGTT
1 CGATTTTCAGTTTCGCGTT
4020628 TCGAATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTG
Found at i:4020947 original size:22 final size:22
Alignment explanation
Indices: 4020887--4020948 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
4020877 GATGGAGATA
*
4020887 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAGATGGG
*
4020909 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
* *
4020931 GACGGATTTTGTGGGAGA
1 GACGGATTTCGTCGGAGA
4020949 GAGTGAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.42, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:4021090 original size:20 final size:20
Alignment explanation
Indices: 4021065--4021113 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
4021055 GCGTAAAAAC
4021065 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
4021085 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
4021105 ATTTGACTT
1 ATTTGACTT
4021114 CTGTATTGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:4021163 original size:40 final size:40
Alignment explanation
Indices: 4021094--4021188 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
4021084 AATTTGACTA
** *
4021094 TCGCGTTGCGAATTTGACTTCTGTATTGCG-ATTTACAAAT
1 TCGCGTTGCGAATTTGACAACTGTATTGCGAAATT-CAAAT
**
4021134 TCGCGTTGCGAATTTGGA-AACTG-AGTTGCGAAATTGGAAT
1 TCGCGTTGCGAATTT-GACAACTGTA-TTGCGAAATTCAAAT
4021174 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
4021189 TTTGGTCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.02
40 41 0.87
41 5 0.11
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACAACTGTATTGCGAAATTCAAAT
Found at i:4021181 original size:20 final size:20
Alignment explanation
Indices: 4021131--4021185 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
4021121 GCGATTTACA
*
4021131 AATTCGCGTTGCGAATTTGG
1 AATTCGCGTTGCGAAATTGG
* *
4021151 AA-ACTGAGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
4021171 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
4021186 TTTTTTGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:4022694 original size:21 final size:22
Alignment explanation
Indices: 4022660--4022724 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 22
4022650 TTTCATTAAA
* *
4022660 ATTTTGTAA-AAAAAATTAAGT
1 ATTTTATAATAAAAAAATAAGT
* *
4022681 -TTTTTTAATTAAAAAATAA-T
1 ATTTTATAATAAAAAAATAAGT
4022701 ATTTTATAATAAAAAAATAAGT
1 ATTTTATAATAAAAAAATAAGT
4022723 AT
1 AT
4022725 AGATACTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.22
21 25 0.69
22 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTTTATAATAAAAAAATAAGT
Found at i:4024242 original size:18 final size:20
Alignment explanation
Indices: 4024207--4024243 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
4024197 TATCAATATC
4024207 CAACAAGTAACAGTGTAAAA
1 CAACAAGTAACAGTGTAAAA
4024227 CAACAA-TAAC-GTGTAAA
1 CAACAAGTAACAGTGTAAA
4024244 GCATCCCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (20 bp):
CAACAAGTAACAGTGTAAAA
Found at i:4024397 original size:15 final size:15
Alignment explanation
Indices: 4024377--4024434 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
4024367 ATTTTAAAAA
4024377 ATATATTTAAAATTT
1 ATATATTTAAAATTT
*
4024392 ATATATTTTTAAA-TT
1 ATATA-TTTAAAATTT
*
4024407 A-A-ATTTAATATTT
1 ATATATTTAAAATTT
* *
4024420 TTATATTTATAATTT
1 ATATATTTAAAATTT
4024435 GAGGATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
12 5 0.15
13 3 0.09
14 2 0.06
15 17 0.52
16 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATATTTAAAATTT
Found at i:4025074 original size:7 final size:7
Alignment explanation
Indices: 4025062--4025104 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
4025052 CAGCAGTTCA
4025062 TCTCCTT
1 TCTCCTT
4025069 TCTCCTT
1 TCTCCTT
4025076 TCTCC-T
1 TCTCCTT
4025082 TCTCCTT
1 TCTCCTT
4025089 TCTCCTT
1 TCTCCTT
4025096 TCTCCTT
1 TCTCCTT
4025103 TC
1 TC
4025105 ACCTAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TCTCCTT
Found at i:4025087 original size:20 final size:20
Alignment explanation
Indices: 4025062--4025102 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4025052 CAGCAGTTCA
4025062 TCTCCTTTCTCCTTTCTCCT
1 TCTCCTTTCTCCTTTCTCCT
4025082 TCTCCTTTCTCCTTTCTCCT
1 TCTCCTTTCTCCTTTCTCCT
4025102 T
1 T
4025103 TCACCTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (20 bp):
TCTCCTTTCTCCTTTCTCCT
Found at i:4031435 original size:24 final size:24
Alignment explanation
Indices: 4031403--4031449 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4031393 TTGTTCTCCT
4031403 CGAAAGTTCTGAGTTTAAGGAGCG
1 CGAAAGTTCTGAGTTTAAGGAGCG
4031427 CGAAAGTTCTGAGTTTAAGGAGC
1 CGAAAGTTCTGAGTTTAAGGAGC
4031450 TGCTACAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.26
Consensus pattern (24 bp):
CGAAAGTTCTGAGTTTAAGGAGCG
Found at i:4036968 original size:134 final size:133
Alignment explanation
Indices: 4036589--4037050 Score: 801
Period size: 134 Copynumber: 3.5 Consensus size: 133
4036579 TTCTGTATCC
*
4036589 AAGAAATTCGTATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAA--
1 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAACT
*
4036652 -C-TCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACTAAACAAAAG
66 TCATCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACAAAACAAAAG
4036715 GAA
131 GAA
*
4036718 AAGAAATTCATATTATTTTCCGTGAAATTCC--TATCTCCAGCCAAACAATAAAATCCAGGAACT
1 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAACT
4036781 TCACTCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACAAAACAAAA
66 TCA-TCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACAAAACAAAA
4036846 GGAA
130 GGAA
* *
4036850 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTCTCTCCAGCCAAACAATCAAATCAAGGAACT
1 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAACT
*
4036915 TCAGTCGTTCAAACATAGCATCATGCTCAAAACATTATCCCTATTTCAATCAACACAAAACAAAA
66 TCA-TCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACAAAACAAAA
4036980 GGAA
130 GGAA
*
4036984 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTCTCTCCAGCCAAACAATCAAATCCAGGAACT
1 AAGAAATTCATATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAACT
4037049 TC
66 TC
4037051 CGAAATCGAT
Statistics
Matches: 317, Mismatches: 9, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
127 29 0.09
129 30 0.09
130 1 0.00
132 95 0.30
134 162 0.51
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (133 bp):
AAGAAATTCATATTATTTTCCGTGAAATTCCTTTATCTCCAGCCAAACAATCAAATCCAGGAACT
TCATCGTTCAAACATAGCATCATGCTCAAAACATAATCCCTATTTCAATCAACACAAAACAAAAG
GAA
Found at i:4042309 original size:64 final size:64
Alignment explanation
Indices: 4042189--4042308 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 64
4042179 ATTTTTTTTA
* * *
4042189 ATATTTGGAATCGGGTCGGATTTTTTTTAAAAAAATCAGGTTCATGTCGGGTTTTTTAAGTTTG
1 ATATTTGGAATCGGGTCGGATTTTTTTTAAAAAAATCAAGATCAAGTCGGGTTTTTTAAGTTTG
* * * ** *
4042253 ATATTTGG-GTCGGGTCGGGTTTTTTTTTAAAATTTCAAGATCAAGTCGGATTTTTT
1 ATATTTGGAATCGGGTCGGATTTTTTTTAAAAAAATCAAGATCAAGTCGGGTTTTTT
4042309 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
63 39 0.83
64 8 0.17
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (64 bp):
ATATTTGGAATCGGGTCGGATTTTTTTTAAAAAAATCAAGATCAAGTCGGGTTTTTTAAGTTTG
Found at i:4056082 original size:17 final size:19
Alignment explanation
Indices: 4056053--4056088 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4056043 TTATCTAACT
4056053 TTAAAATTTTC-AATTTCA
1 TTAAAATTTTCAAATTTCA
4056071 TTAAAA-TTTCAAATTTCA
1 TTAAAATTTTCAAATTTCA
4056089 AATTACTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATTTTCAAATTTCA
Found at i:4057157 original size:91 final size:91
Alignment explanation
Indices: 4056994--4057166 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
4056984 ACAGAAGTAT
4056994 TAATAGACTTCAACCCCACAATACATGCATGAACCTCAGGTAATGTGGAGAAAACATTGACTTGC
1 TAATAGACTTCAACCCCACAATACATGCATGAACCTCAGGTAATGTGGAGAAAACATTGACTTGC
*
4057059 AACCTTTGGGTCACATCCGTGTATAG
66 AACCTTTGAGTCACATCCGTGTATAG
* * * * * **
4057085 TAATAGACTTTAACCCCGCAATGCATGCATGAACCTCGGGTAATGTGGA-AAAATTATTGGTTTG
1 TAATAGACTTCAACCCCACAATACATGCATGAACCTCAGGTAATGTGGAGAAAA-CATTGACTTG
* *
4057149 TAATCTTTGAGTCACATC
65 CAACCTTTGAGTCACATC
4057167 TGTATATTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 4 0.06
91 67 0.94
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (91 bp):
TAATAGACTTCAACCCCACAATACATGCATGAACCTCAGGTAATGTGGAGAAAACATTGACTTGC
AACCTTTGAGTCACATCCGTGTATAG
Found at i:4067118 original size:28 final size:28
Alignment explanation
Indices: 4067065--4067121 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4067055 CCATCATTGC
* * *
4067065 TTTCAAGCACTGACTCGATGACATAATG
1 TTTCAAGCACTAACTCAACGACATAATG
*
4067093 TTTCAAGCACTAACTCAACGATATAATG
1 TTTCAAGCACTAACTCAACGACATAATG
4067121 T
1 T
4067122 AAATAGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTAACTCAACGACATAATG
Found at i:4067631 original size:15 final size:15
Alignment explanation
Indices: 4067607--4067644 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4067597 GCATCAATAG
4067607 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
*
4067622 AAATAGAAATAAAA-
1 AAATAAAAATAAAAT
*
4067636 AATTAAAAA
1 AAATAAAAA
4067645 AATATCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:4071593 original size:23 final size:23
Alignment explanation
Indices: 4071567--4071611 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4071557 CACCACAGCT
*
4071567 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
4071590 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
4071612 ATATAACAAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:4071829 original size:149 final size:149
Alignment explanation
Indices: 4071579--4071893 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
4071569 TATAATTGCA
4071579 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
4071643 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
4071708 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
4071728 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
4071793 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
4071858 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
4071877 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
4071894 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:4073382 original size:21 final size:21
Alignment explanation
Indices: 4073358--4073402 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4073348 TTTTGTTCGT
* *
4073358 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4073379 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4073400 TTG
1 TTG
4073403 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4076869 original size:150 final size:150
Alignment explanation
Indices: 4076567--4076883 Score: 521
Period size: 150 Copynumber: 2.1 Consensus size: 150
4076557 TATAATTGCA
4076567 CCGAAGTG-CCGCGTAGAATTGCACCGTAATGCCATATAACAATGTCCATAAAGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAATGCCATATAACAATGTCCATAAAGACCACATATTA
*
4076631 TTCCTTTAGAATCATATACATATACTAGGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGT
* * *
4076696 TCCACATAATATATATATATC
130 TCCAAAGAATATACATATATC
* * *
4076717 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAACAATGTCCATAAAGACCACATATTAT
*
4076782 TCCTTAAGAATCATATACATATACTA-GGGATCAAGTATGTGTCTTTCAAGATTTCACACATGTT
66 TCCTTAAGAATCATATACATATACTAGGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
*
4076846 CCAAAGAATATACATATTGTC
131 CCAAAGAATATACATA-TATC
4076867 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
4076884 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
149 51 0.33
150 105 0.67
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (150 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAACAATGTCCATAAAGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
CCAAAGAATATACATATATC
Found at i:4078370 original size:21 final size:21
Alignment explanation
Indices: 4078346--4078390 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4078336 TTTTGTTCGT
* *
4078346 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4078367 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4078388 TTG
1 TTG
4078391 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4083921 original size:17 final size:18
Alignment explanation
Indices: 4083883--4083921 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4083873 TTATTGGTCC
**
4083883 TAATCAAAATGAAAAAGT
1 TAATCAAAATGAAAAAAA
4083901 TAATCAAAAT-AAAAAAA
1 TAATCAAAATGAAAAAAA
4083918 TAAT
1 TAAT
4083922 AAATCAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
TAATCAAAATGAAAAAAA
Found at i:4090510 original size:13 final size:13
Alignment explanation
Indices: 4090483--4090520 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
4090473 TGGGGATTTA
4090483 AAATTAATGAAAAT
1 AAATTAAT-AAAAT
4090497 AAATTAATAAAAT
1 AAATTAATAAAAT
*
4090510 AAATAAATAAA
1 AAATTAATAAA
4090521 TCTTGAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAATTAATAAAAT
Found at i:4092025 original size:19 final size:18
Alignment explanation
Indices: 4091987--4092026 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4091977 CCTCTAATTT
**
4091987 TTTTTATTTTTTTTTCAA
1 TTTTTATTTTTTTTGAAA
4092005 TTTTTATTTTTTTATGAAA
1 TTTTTATTTTTTT-TGAAA
4092024 TTT
1 TTT
4092027 CTTCCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTATTTTTTTTGAAA
Found at i:4096225 original size:13 final size:13
Alignment explanation
Indices: 4096207--4096237 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4096197 AGCATTGTGA
*
4096207 AAAGAAAATAATG
1 AAAGAAAATAAAG
4096220 AAAGAAAATAAAG
1 AAAGAAAATAAAG
4096233 AAAGA
1 AAAGA
4096238 TGGAGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:4096681 original size:17 final size:17
Alignment explanation
Indices: 4096659--4096692 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4096649 GCTTCTATCC
4096659 AAAATAAACTCAA-AATA
1 AAAATAAA-TCAATAATA
4096676 AAAATAAATCAATAATA
1 AAAATAAATCAATAATA
4096693 TCCAAACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAATCAATAATA
Found at i:4101225 original size:29 final size:29
Alignment explanation
Indices: 4101181--4101257 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
4101171 TTGCATTGTG
* *
4101181 TTTTTCTGTACAGTTCAAACCATAACTG-A
1 TTTTTCTGCACTGTTCAAACCA-AACTGCA
* *
4101210 TTTTTCTGCACTGTTCGAACTAAACTGCACTA
1 TTTTTCTGCACTGTTCAAACCAAACTG--C-A
4101242 TTTTTCTGCACTGTTC
1 TTTTTCTGCACTGTTC
4101258 GAACAATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.12
29 18 0.45
32 17 0.43
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (29 bp):
TTTTTCTGCACTGTTCAAACCAAACTGCA
Found at i:4103754 original size:21 final size:21
Alignment explanation
Indices: 4103729--4103776 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
4103719 ATTTTTTTTC
*
4103729 TGGGAAGTAACTAATTTCTCT
1 TGGGAAGTAACCAATTTCTCT
4103750 TGGGAAGTAACCAATTTCTCT
1 TGGGAAGTAACCAATTTCTCT
4103771 TGGGAA
1 TGGGAA
4103777 ATTTCCAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
TGGGAAGTAACCAATTTCTCT
Found at i:4108479 original size:2 final size:2
Alignment explanation
Indices: 4108472--4108505 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4108462 TTTGATTCGA
4108472 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
4108506 TTAATTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4116049 original size:20 final size:19
Alignment explanation
Indices: 4116026--4116065 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4116016 TATTAAAACT
4116026 AATAATAAAAAATGAAAAAA
1 AATAATAAAAAA-GAAAAAA
**
4116046 AATAATTGAAAAGAAAAAA
1 AATAATAAAAAAGAAAAAA
4116065 A
1 A
4116066 CAACAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (19 bp):
AATAATAAAAAAGAAAAAA
Found at i:4119022 original size:44 final size:44
Alignment explanation
Indices: 4118950--4119178 Score: 280
Period size: 44 Copynumber: 5.2 Consensus size: 44
4118940 TTGAGATTTC
* * * *
4118950 GCGGCGTTTTTAGGATACAAACGTCGCTAAAGCTCTTGTATATA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGGTCTGGTATATA
* * * * *
4118994 GCGGCATTTTCAGTATATAAACGCCGCT-AAGTGTCAGGTATATA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAG-GTCTGGTATATA
*
4119038 GCGGCGTTTTTAGAATACAAACGCCGCTAAATGTCTGGTATATA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGGTCTGGTATATA
* * **
4119082 GCGGCTTTTTTAGAATACAAACGCCGTTAAATATCTGGTATATA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGGTCTGGTATATA
* * **
4119126 GCGTCGTTTTTAGGATGTAAACGCCGCTAAAGGTCTGGTATATA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGGTCTGGTATATA
4119170 GCGGCGTTT
1 GCGGCGTTT
4119179 GTATTCGAAA
Statistics
Matches: 157, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
43 3 0.02
44 152 0.97
45 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (44 bp):
GCGGCGTTTTTAGAATACAAACGCCGCTAAAGGTCTGGTATATA
Found at i:4119192 original size:44 final size:43
Alignment explanation
Indices: 4118968--4119221 Score: 182
Period size: 44 Copynumber: 5.8 Consensus size: 43
4118958 TTTAGGATAC
* * * * * * *
4118968 AAACGTCGCTAAAGCTCTTGTATATAGCGGCATTTTCAGTATAT
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTT-ATTAGAA
*
4119012 AAACGCCGCT-AAGTGTCAGGTATATAGCGGCG-TTT-TTAGAATA
1 AAACGCCGCTAAAG-GTCTGGTATATAGCGGCGTTTTATTAG-A-A
*
4119055 CAAACGCCGCTAAATGTCTGGTATATAGCGGC-TTTT-TTAGAATA
1 -AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTATTAG-A-A
* ** * *
4119099 CAAACGCCGTTAAATATCTGGTATATAGCGTCG-TTT-TTAGGATGT
1 -AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTATTA-GA--A
*
4119144 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTGTATTCGAA
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTT-TATTAGAA
* * *
4119188 AAACGCCACTAAAGGT-TGATATATAACGGCGTTT
1 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTT
4119222 GTTAAAAAAA
Statistics
Matches: 174, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 22 0.13
44 139 0.80
45 5 0.03
46 3 0.02
47 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTATTAGAA
Found at i:4119192 original size:132 final size:131
Alignment explanation
Indices: 4118950--4119221 Score: 312
Period size: 132 Copynumber: 2.1 Consensus size: 131
4118940 TTGAGATTTC
* * * * *
4118950 GCGGCGTTTTTAGGATACAAACGTCGCTAAAGCTCTTGTATATAGCGGCATTTTCAGTATATAAA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGATCTGGTATATAGCGGCATTTTCAGGATATAAA
* * * * * *
4119015 CGCCGCTAAGTGTCAGGTATATAGCGGCGTTTTTAGAATACAAACGCCGCTAAATGTCTGGTATA
66 CGCCGCTAAGTGTCAGGTATATAGCGGCGTTTGTAGAAGAAAAACGCCACTAAAGGT-TGATATA
4119080 TA
130 TA
* * * * * * *
4119082 GCGGCTTTTTTAGAATACAAACGCCGTTAAATATCTGGTATATAGCGTCGTTTTTAGGATGTAAA
1 GCGGCGTTTTTAGAATACAAACGCCGCTAAAGATCTGGTATATAGCGGCATTTTCAGGATATAAA
* ***
4119147 CGCCGCTAAAG-GTCTGGTATATAGCGGCGTTTGTATTCGAAAAACGCCACTAAAGGTTGATATA
66 CGCCGCT-AAGTGTCAGGTATATAGCGGCGTTTGTAGAAGAAAAACGCCACTAAAGGTTGATATA
4119211 TA
130 TA
*
4119213 ACGGCGTTT
1 GCGGCGTTT
4119222 GTTAAAAAAA
Statistics
Matches: 115, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
131 15 0.13
132 97 0.84
133 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (131 bp):
GCGGCGTTTTTAGAATACAAACGCCGCTAAAGATCTGGTATATAGCGGCATTTTCAGGATATAAA
CGCCGCTAAGTGTCAGGTATATAGCGGCGTTTGTAGAAGAAAAACGCCACTAAAGGTTGATATAT
A
Found at i:4119231 original size:41 final size:43
Alignment explanation
Indices: 4119144--4119231 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
4119134 TTTAGGATGT
* * * **
4119144 AAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTGTATTCGAA
1 AAACGCCACTAAAGGTCTGATATATAACGGCGTTTG-ATTAAAA
4119188 AAACGCCACTAAAGGT-TGATATATAACGGCGTTTG-TTAAAA
1 AAACGCCACTAAAGGTCTGATATATAACGGCGTTTGATTAAAA
4119229 AAA
1 AAA
4119232 TGCTTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 7 0.18
43 17 0.44
44 15 0.38
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (43 bp):
AAACGCCACTAAAGGTCTGATATATAACGGCGTTTGATTAAAA
Found at i:4124807 original size:21 final size:21
Alignment explanation
Indices: 4124770--4124814 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4124760 GATTTCTGGG
*
4124770 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
4124791 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
4124812 CAA
1 CAA
4124815 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:4125267 original size:22 final size:20
Alignment explanation
Indices: 4125242--4125282 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
4125232 TGAATGTGTG
*
4125242 ATATGTTATGATGATATAAACC
1 ATATGATATGAT-A-ATAAACC
4125264 ATATGATATGATAATAAAC
1 ATATGATATGATAATAAAC
4125283 TATGAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (20 bp):
ATATGATATGATAATAAACC
Found at i:4125864 original size:31 final size:31
Alignment explanation
Indices: 4125826--4125981 Score: 278
Period size: 31 Copynumber: 5.0 Consensus size: 31
4125816 AGGGTCGAGG
4125826 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4125857 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4125888 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4125919 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4125950 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4125981 G
1 G
4125982 GTCCTTCGGG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 121 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4129160 original size:21 final size:21
Alignment explanation
Indices: 4129134--4129178 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4129124 GATTTCTGGG
* *
4129134 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4129155 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4129176 CAA
1 CAA
4129179 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4129645 original size:20 final size:22
Alignment explanation
Indices: 4129605--4129661 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
4129595 TGAATGTGTG
*
4129605 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
4129627 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
4129647 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
4129662 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:4130227 original size:31 final size:31
Alignment explanation
Indices: 4130189--4130344 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
4130179 AGGGTCGAGG
4130189 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4130220 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4130251 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4130282 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4130313 ATTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4130344 G
1 G
4130345 GTCCTTCAGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4132641 original size:12 final size:12
Alignment explanation
Indices: 4132624--4132649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4132614 TATTTCAATG
4132624 AACCAGAACCAA
1 AACCAGAACCAA
4132636 AACCAGAACCAA
1 AACCAGAACCAA
4132648 AA
1 AA
4132650 ATGTTTGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.31, G:0.08, T:0.00
Consensus pattern (12 bp):
AACCAGAACCAA
Found at i:4134980 original size:13 final size:13
Alignment explanation
Indices: 4134959--4134990 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4134949 CATTACAATT
*
4134959 GAAGTACAGAAGA
1 GAAGAACAGAAGA
4134972 GAAGAACAGAAGA
1 GAAGAACAGAAGA
4134985 GAAGAA
1 GAAGAA
4134991 GTTGCTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.31, T:0.03
Consensus pattern (13 bp):
GAAGAACAGAAGA
Found at i:4135737 original size:23 final size:23
Alignment explanation
Indices: 4135707--4135756 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4135697 TTTAAAAAAC
4135707 TTAACAACAATCATACATTTTAA
1 TTAACAACAATCATACATTTTAA
4135730 TTAACAACAATCATACATTTTAA
1 TTAACAACAATCATACATTTTAA
4135753 TTAA
1 TTAA
4135757 GCCAGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAACAACAATCATACATTTTAA
Found at i:4137283 original size:82 final size:83
Alignment explanation
Indices: 4137191--4137511 Score: 330
Period size: 82 Copynumber: 3.9 Consensus size: 83
4137181 TTTATAAAAT
* * * * **
4137191 GCCACGATAAACAACA-TATTGCGGCGTTTATAGGATAAACGCCGCTAAATTATTACTCTATTAC
1 GCCACTATAAACAACACTATTGCGACGTTTGTAGAATAAACGCCGCTAAATTACCACTCTATTAC
* * *
4137255 GGTGTTT-TTTACACAAAT
66 GGCGTTTGTTGA-ACAAAC
* * ** * *
4137273 GCCACTATAAACAATACTATTGCGGCGTTTGTTTAATAAACGCCGCTAAATTACTAATCTA-TAC
1 GCCACTATAAACAACACTATTGCGACGTTTGTAGAATAAACGCCGCTAAATTACCACTCTATTA-
** *
4137337 CATCGTTTATTGAACAAAC
65 CGGCGTTTGTTGAACAAAC
* * * * *
4137356 GCCACTATAAATAACACTATCGCGACGTTTGTACAA-AAACGCCGCTACATTACCACTCTATTGC
1 GCCACTATAAACAACACTATTGCGACGTTTGTAGAATAAACGCCGCTAAATTACCACTCTATTAC
4137420 GGCGTTTGTTGAA-AAAC
66 GGCGTTTGTTGAACAAAC
* * * *
4137437 GCGACTATAAACAACTCTATTGCGACGTTTG-AGCTATAAACGCCGCTAAATTACCACTCTATTG
1 GCCACTATAAACAACACTATTGCGACGTTTGTAG-AATAAACGCCGCTAAATTACCACTCTATTA
4137501 CGGCGTTTGTT
65 CGGCGTTTGTT
4137512 TAAAAAACAC
Statistics
Matches: 200, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
80 1 0.00
81 32 0.16
82 85 0.43
83 79 0.40
84 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (83 bp):
GCCACTATAAACAACACTATTGCGACGTTTGTAGAATAAACGCCGCTAAATTACCACTCTATTAC
GGCGTTTGTTGAACAAAC
Found at i:4137398 original size:40 final size:40
Alignment explanation
Indices: 4137352--4137510 Score: 117
Period size: 41 Copynumber: 3.9 Consensus size: 40
4137342 TTTATTGAAC
* *
4137352 AAACGCCACTATAAATAACACTATCGCGACGTTTGTACAA
1 AAACGCCACTATAAATAACTCTATTGCGACGTTTGTACAA
* * * * **
4137392 AAACGCCGCTA-CATTACCACTCTATTGCGGCGTTTGTTGAA
1 AAACGCCACTATAAATA--ACTCTATTGCGACGTTTGTACAA
* * *
4137433 AAACGCGACTATAAACAACTCTATTGCGACGTTTG-AGCTAT
1 AAACGCCACTATAAATAACTCTATTGCGACGTTTGTA-C-AA
* * *
4137474 AAACGCCGCTA-AATTACCACTCTATTGCGGCGTTTGT
1 AAACGCCACTATAAATA--ACTCTATTGCGACGTTTGT
4137511 TTAAAAAACA
Statistics
Matches: 89, Mismatches: 22, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
39 3 0.03
40 30 0.34
41 37 0.42
42 19 0.21
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (40 bp):
AAACGCCACTATAAATAACTCTATTGCGACGTTTGTACAA
Found at i:4137428 original size:41 final size:41
Alignment explanation
Indices: 4137372--4137510 Score: 142
Period size: 41 Copynumber: 3.4 Consensus size: 41
4137362 ATAAATAACA
* *
4137372 CTATCGCGACGTTTGTACAAAAACGCCGCTACATTACCACT
1 CTATTGCGACGTTTGTACAAAAACGCCGCTAAATTACCACT
* ** *
4137413 CTATTGCGGCGTTTGTTGAAAAACG-CGACTATAA--ACAACT
1 CTATTGCGACGTTTGTACAAAAACGCCG-CTA-AATTACCACT
*
4137453 CTATTGCGACGTTTG-AGCTATAAACGCCGCTAAATTACCACT
1 CTATTGCGACGTTTGTA-C-AAAAACGCCGCTAAATTACCACT
*
4137495 CTATTGCGGCGTTTGT
1 CTATTGCGACGTTTGT
4137511 TTAAAAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
40 23 0.29
41 33 0.42
42 22 0.28
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (41 bp):
CTATTGCGACGTTTGTACAAAAACGCCGCTAAATTACCACT
Found at i:4137500 original size:42 final size:42
Alignment explanation
Indices: 4137390--4137509 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
4137380 ACGTTTGTAC
* *
4137390 AAAAACGCCGCTACATTACCACTCTATTGCGGCGTTT-GTTG
1 AAAAACGCCGCTAAATTACCACTCTATTGCGGCGTTTGGCTG
* *
4137431 AAAAACG-CGACTATAA--ACAACTCTATTGCGACGTTTGAGCT-
1 AAAAACGCCG-CTA-AATTACCACTCTATTGCGGCGTTTG-GCTG
*
4137472 ATAAACGCCGCTAAATTACCACTCTATTGCGGCGTTTG
1 AAAAACGCCGCTAAATTACCACTCTATTGCGGCGTTTG
4137510 TTTAAAAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
40 22 0.34
41 19 0.29
42 24 0.37
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
AAAAACGCCGCTAAATTACCACTCTATTGCGGCGTTTGGCTG
Found at i:4142167 original size:22 final size:22
Alignment explanation
Indices: 4142117--4142176 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
4142107 CAATTTTATT
* ** *
4142117 ATTTTATATTTATATAATTCAC
1 ATTTTAAATTTATATAATGAAA
*
4142139 ATGTTAAATTTATATAATGAAA
1 ATTTTAAATTTATATAATGAAA
*
4142161 ATTTTAATAGTTATAT
1 ATTTTAA-ATTTATAT
4142177 TTTAATTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTTAAATTTATATAATGAAA
Found at i:4142658 original size:18 final size:18
Alignment explanation
Indices: 4142623--4142666 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
4142613 TCAATATAAT
*
4142623 AAATAATATTATTTATTAA
1 AAATATTATTATTTATT-A
4142642 AAATATTATTA-TTATTA
1 AAATATTATTATTTATTA
4142659 AAATATTA
1 AAATATTA
4142667 GAATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 5 0.21
19 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATATTATTATTTATTA
Found at i:4142716 original size:25 final size:26
Alignment explanation
Indices: 4142688--4142741 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
4142678 TTAATATTAT
4142688 TTATGTCAATATTATT-AAT-AAAATA
1 TTATGTCAATATT-TTGAATAAAAATA
*
4142713 TTATGTCTATATTTTGAATAAAAATA
1 TTATGTCAATATTTTGAATAAAAATA
4142739 TTA
1 TTA
4142742 AGATTATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
TTATGTCAATATTTTGAATAAAAATA
Found at i:4147810 original size:23 final size:23
Alignment explanation
Indices: 4147782--4147868 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
4147772 CACATATTTG
*
4147782 TCCCGAAGGACAACATAGTTTTA
1 TCCCGAAGGACCACATAGTTTTA
** *
4147805 TCCCGAAGGACCACATAGGATTG
1 TCCCGAAGGACCACATAGTTTTA
* *
4147828 TCCCGAATGACCACATAAG-TTTG
1 TCCCGAAGGACCACAT-AGTTTTA
* *
4147851 TCCTGAAAGACCACATAG
1 TCCCGAAGGACCACATAG
4147869 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 2 0.04
23 51 0.93
24 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGTTTTA
Found at i:4147811 original size:44 final size:46
Alignment explanation
Indices: 4147763--4147869 Score: 114
Period size: 46 Copynumber: 2.4 Consensus size: 46
4147753 ATAATTTGCA
*
4147763 CCGAAGTG-CCACATA-TTTGTCCCGAAGGACAACAT-AGTTTTATC
1 CCGAAG-GACCACATAGATTGTCCCGAAGGACAACATAAGTTTTATC
* * *
4147807 CCGAAGGACCACATAGGATTGTCCCGAATGACCACATAAG-TTTGTC
1 CCGAAGGACCACATA-GATTGTCCCGAAGGACAACATAAGTTTTATC
* *
4147853 CTGAAAGACCACATAGA
1 CCGAAGGACCACATAGA
4147870 ACCCTCGACT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.02
44 13 0.25
45 2 0.04
46 35 0.66
47 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (46 bp):
CCGAAGGACCACATAGATTGTCCCGAAGGACAACATAAGTTTTATC
Found at i:4147844 original size:46 final size:46
Alignment explanation
Indices: 4147779--4147868 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
4147769 TGCCACATAT
*
4147779 TTGTCCCGAAGGACAACAT-AGTTTTATCCCGAAGGACCACATAGGA
1 TTGTCCCGAAGGACAACATAAG-TTTATCCCGAAAGACCACATAGGA
* * * *
4147825 TTGTCCCGAATGACCACATAAGTTTGTCCTGAAAGACCACATAG
1 TTGTCCCGAAGGACAACATAAGTTTATCCCGAAAGACCACATAG
4147869 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 36 0.95
47 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (46 bp):
TTGTCCCGAAGGACAACATAAGTTTATCCCGAAAGACCACATAGGA
Found at i:4154644 original size:21 final size:23
Alignment explanation
Indices: 4154619--4154701 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
4154609 ATAATTTGCA
4154619 CCGAAGTG-CCACAT-G-TTTGTC
1 CCGAAG-GACCACATAGTTTTGTC
*
4154640 TCGAAGGACCACATAGTTTTGTC
1 CCGAAGGACCACATAGTTTTGTC
* * *
4154663 CCGAATGACCATATAGGTTTGTC
1 CCGAAGGACCACATAGTTTTGTC
* *
4154686 CCGAATGACCATATAG
1 CCGAAGGACCACATAG
4154702 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 11 0.20
22 1 0.02
23 41 0.76
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
CCGAAGGACCACATAGTTTTGTC
Found at i:4154667 original size:23 final size:22
Alignment explanation
Indices: 4154606--4154701 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 22
4154596 CACCATAACT
*
4154606 CACATAATTTG-CACCGAAGTG-C
1 CACATAGTTTGTC-CCGAAG-GAC
*
4154628 CACAT-GTTTGTCTCGAAGGAC
1 CACATAGTTTGTCCCGAAGGAC
*
4154649 CACATAGTTTTGTCCCGAATGAC
1 CACATAG-TTTGTCCCGAAGGAC
* *
4154672 CATATAGGTTTGTCCCGAATGAC
1 CACATA-GTTTGTCCCGAAGGAC
*
4154695 CATATAG
1 CACATAG
4154702 AACCCTCGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.02
21 15 0.23
22 8 0.12
23 39 0.61
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
CACATAGTTTGTCCCGAAGGAC
Found at i:4157775 original size:9 final size:10
Alignment explanation
Indices: 4157754--4157783 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
4157744 GAGTCTAATT
4157754 AATTATAAAAA
1 AATT-TAAAAA
4157765 AATTTAAAAA
1 AATTTAAAAA
4157775 AATTTAAAA
1 AATTTAAAA
4157784 GTTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:4159527 original size:55 final size:55
Alignment explanation
Indices: 4159440--4159550 Score: 161
Period size: 55 Copynumber: 2.0 Consensus size: 55
4159430 TTTTACTACA
* *
4159440 ATTCGTGCTTTCTGTAAACTGTATGGCACTATTTGTGGCCTCTTCAAATGAATTT
1 ATTCGTGCTTTCTGTAAACTGTATGGCACTATTTGTGACCTCTTAAAATGAATTT
* * *
4159495 ATTCGTGCTTTCTG-AGAATTGTATGGCGCTATTTGTGACCTTTTAAAATGAATTT
1 ATTCGTGCTTTCTGTA-AACTGTATGGCACTATTTGTGACCTCTTAAAATGAATTT
4159550 A
1 A
4159551 GCTTATGATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 1 0.02
55 49 0.98
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (55 bp):
ATTCGTGCTTTCTGTAAACTGTATGGCACTATTTGTGACCTCTTAAAATGAATTT
Found at i:4168740 original size:23 final size:23
Alignment explanation
Indices: 4168709--4168792 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 23
4168699 AAAAAATAAT
4168709 TAAATAATTATTTATATATATTTA
1 TAAA-AATTATTTATATATATTTA
* * *
4168733 TAAAAATTAAATTAAAT-TA-TTC
1 TAAAAATT-ATTTATATATATTTA
4168755 TAAAAATTATATT-TATA-ATATTA
1 TAAAAATTAT-TTATATATAT-TTA
4168778 TAAAATATTTATTTA
1 TAAAA-A-TTATTTA
4168793 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
21 4 0.09
22 12 0.26
23 13 0.28
24 13 0.28
25 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATTATTTATATATATTTA
Found at i:4168841 original size:23 final size:23
Alignment explanation
Indices: 4168800--4168855 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
4168790 TTAATTTTTA
* *
4168800 AAATGATATT-ATTTTTTATTTG
1 AAATAATATTAATTTGTTATTTG
4168822 AAATAATATTAATTTGTTATTTG
1 AAATAATATTAATTTGTTATTTG
4168845 AAATAATATTA
1 AAATAATATTA
4168856 TTTTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
AAATAATATTAATTTGTTATTTG
Found at i:4170883 original size:2 final size:2
Alignment explanation
Indices: 4170876--4170907 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4170866 GCAACTTTTC
4170876 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
4170908 GCCAAGCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4174466 original size:9 final size:9
Alignment explanation
Indices: 4174452--4174477 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4174442 TTGTTTTTCC
4174452 TCATTATTA
1 TCATTATTA
4174461 TCATTATTA
1 TCATTATTA
4174470 TCATTATT
1 TCATTATT
4174478 TCTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (9 bp):
TCATTATTA
Found at i:4179391 original size:2 final size:2
Alignment explanation
Indices: 4179378--4179414 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4179368 TTCAAACAAT
*
4179378 TA TA TT 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 TA TA TA T
4179415 TATCAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4179950 original size:16 final size:17
Alignment explanation
Indices: 4179931--4179974 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
4179921 AAAATATACA
4179931 ATAAATCAGATATT-AG
1 ATAAATCAGATATTCAG
4179947 ATAAA-CA-ATATTCAG
1 ATAAATCAGATATTCAG
*
4179962 A-AAATCAGGTATT
1 ATAAATCAGATATT
4179975 GTGTCGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 8 0.33
15 7 0.29
16 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (17 bp):
ATAAATCAGATATTCAG
Found at i:4185699 original size:23 final size:24
Alignment explanation
Indices: 4185668--4185735 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
4185658 TCTTATATGA
*
4185668 CACTACGGTGC-ATTTCTACGTGG
1 CACTTCGGTGCAATTTCTACGTGG
*
4185691 CACTTCGGTGCAAATTCTACGTGG
1 CACTTCGGTGCAATTTCTACGTGG
* *
4185715 CACTTCGATGCAATTTATACG
1 CACTTCGGTGCAATTTCTACG
4185736 AGCTATGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 10 0.26
24 29 0.74
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
CACTTCGGTGCAATTTCTACGTGG
Found at i:4186556 original size:22 final size:22
Alignment explanation
Indices: 4186517--4186559 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4186507 ACAATGTATA
* *
4186517 ACTGTTCACGGTATTATTCATT
1 ACTGTTCACGATACTATTCATT
*
4186539 ACTGTTCATGATACTATTCAT
1 ACTGTTCACGATACTATTCAT
4186560 ACAATATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (22 bp):
ACTGTTCACGATACTATTCATT
Found at i:4192001 original size:20 final size:20
Alignment explanation
Indices: 4191954--4192006 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
4191944 TGTTTTTTGC
4191954 AGTATCGATACCACATGAATG
1 AGTATCGATACCACAT-AATG
* *
4191975 GGTATCGATACCATAT-ATG
1 AGTATCGATACCACATAATG
4191994 TAGTATCGATACC
1 -AGTATCGATACC
4192007 TTAGGCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 11 0.39
21 14 0.50
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCACATAATG
Found at i:4192988 original size:21 final size:21
Alignment explanation
Indices: 4192964--4193034 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
4192954 TTGCATTTCT
4192964 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* ** **
4192985 CGTTGCGAT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
4193005 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
4193026 CGTTGCGAT
1 CGTTGCGAT
4193035 TTTCCATTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:4193002 original size:41 final size:41
Alignment explanation
Indices: 4192957--4193054 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
4192947 ATTCGCGTTG
*
4192957 CATTTCTCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
4192998 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
4193039 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
4193055 TTTCTATTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Done.