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 8 of 62
Found at i:1784209 original size:16 final size:16
Alignment explanation
Indices: 1784188--1784218 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1784178 CAACATTTGA
*
1784188 ATTGTTTGATTTTGGG
1 ATTGTTGGATTTTGGG
1784204 ATTGTTGGATTTTGG
1 ATTGTTGGATTTTGG
1784219 ATATATGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.32, T:0.55
Consensus pattern (16 bp):
ATTGTTGGATTTTGGG
Found at i:1786924 original size:20 final size:21
Alignment explanation
Indices: 1786899--1786991 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1786889 TTTTCCCAAT
*
1786899 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1786919 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1786940 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1786960 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1786981 TCGCAATGCGA
1 TCGCAATGCGA
1786992 TACTGACTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1786944 original size:41 final size:41
Alignment explanation
Indices: 1786899--1786991 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1786889 TTTTCCCAAT
1786899 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1786940 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1786981 TCGCAATGCGA
1 TCGCAATGCGA
1786992 TACTGACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1787043 original size:16 final size:16
Alignment explanation
Indices: 1787022--1787052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1787012 TAATAAAAAA
1787022 TCGCAACGAGATACTT
1 TCGCAACGAGATACTT
*
1787038 TCGCAACGCGATACT
1 TCGCAACGAGATACT
1787053 GACTTTCGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (16 bp):
TCGCAACGAGATACTT
Found at i:1787286 original size:22 final size:22
Alignment explanation
Indices: 1787258--1787301 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1787248 CTCTCTCTCA
1787258 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1787280 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1787302 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:1787590 original size:20 final size:20
Alignment explanation
Indices: 1787565--1787602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1787555 CGATTCTCTC
1787565 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1787585 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1787603 AAACTATTCT
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:1788910 original size:18 final size:18
Alignment explanation
Indices: 1788885--1788926 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1788875 ACTTCGGGAT
*
1788885 CCATCACCTCGCCCAGAG
1 CCATCACCTCACCCAGAG
*
1788903 CTATCACCTCACCCAGAG
1 CCATCACCTCACCCAGAG
1788921 CCATCA
1 CCATCA
1788927 TCTGATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.48, G:0.12, T:0.14
Consensus pattern (18 bp):
CCATCACCTCACCCAGAG
Found at i:1789424 original size:20 final size:20
Alignment explanation
Indices: 1789399--1789444 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1789389 TAGTTTACTT
1789399 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
1789419 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
1789439 TCGCAA
1 TCGCAA
1789445 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:1789453 original size:19 final size:20
Alignment explanation
Indices: 1789410--1789465 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1789400 CGCAACACGA
1789410 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
1789430 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
1789449 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1789466 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:1789473 original size:14 final size:14
Alignment explanation
Indices: 1789454--1789511 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1789444 ATGCGAAATG
1789454 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1789468 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1789484 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1789500 AAAATCACAACG
1 AAAATCGCAACG
1789512 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1789496 original size:32 final size:33
Alignment explanation
Indices: 1789438--1789528 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1789428 AGAAATGGCT
1789438 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1789471 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1789503 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1789529 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1789564 original size:14 final size:14
Alignment explanation
Indices: 1789545--1789602 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1789535 TTGTGTTTCG
1789545 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1789559 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1789575 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1789591 CGTTGCGATTTT
1 CGTTGCGATTTT
1789603 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1789579 original size:32 final size:33
Alignment explanation
Indices: 1789540--1789618 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1789530 GCGATTTGTG
1789540 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1789572 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1789605 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1789619 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1789617 original size:19 final size:19
Alignment explanation
Indices: 1789559--1789660 Score: 90
Period size: 19 Copynumber: 5.6 Consensus size: 19
1789549 GCGATTTTGT
1789559 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1789577 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1789591 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1789610 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1789630 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
1789649 CGTTGCGATTTT
1 CGTTGCGATTTT
1789661 AAGTCGTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
14 8 0.12
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.16
19 25 0.37
20 17 0.25
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1789637 original size:20 final size:19
Alignment explanation
Indices: 1789603--1789657 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1789593 TTGCGATTTT
*
1789603 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1789622 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1789642 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1789658 TTTAAGTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1791683 original size:19 final size:19
Alignment explanation
Indices: 1791661--1791728 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1791651 ATCGCAACGA
1791661 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1791680 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1791699 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1791713 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1791729 TTTTTATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1792886 original size:24 final size:24
Alignment explanation
Indices: 1792835--1792888 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1792825 GTATTCGAAA
* *
1792835 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
1792859 TTTGATATTGGTCAATACATGGAT
1 TTTGATATTGGTCAATACACGGAC
1792883 TTTGAT
1 TTTGAT
1792889 GAGTTTCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1795347 original size:33 final size:33
Alignment explanation
Indices: 1795305--1795431 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1795295 GGAAATTACT
1795305 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1795338 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1795370 TTTCGCAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1795404 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1795432 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1795412 original size:66 final size:66
Alignment explanation
Indices: 1795306--1795438 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1795296 GAAATTACTA
* *
1795306 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1795371 T
66 T
*
1795372 TCGCAATGCGAAATGAAAATCACAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1795437 T
66 T
1795438 T
1 T
1795439 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1795630 original size:13 final size:14
Alignment explanation
Indices: 1795614--1795648 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1795604 CATCAATTAA
1795614 ACAAATCA-CTTTT
1 ACAAATCACCTTTT
1795627 ACAAATCACCTTTT
1 ACAAATCACCTTTT
1795641 ACAAATCA
1 ACAAATCA
1795649 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCACCTTTT
Found at i:1797069 original size:21 final size:21
Alignment explanation
Indices: 1797003--1797069 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1796993 GTGAATCGGG
*
1797003 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1797023 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1797045 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1797066 CTCT
1 CTCT
1797070 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1797088 original size:42 final size:41
Alignment explanation
Indices: 1797003--1797125 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1796993 GTGAATCGGG
* * * *
1797003 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
1797045 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1797087 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
1797126 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1799137 original size:20 final size:19
Alignment explanation
Indices: 1799106--1799166 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1799096 TCTTTTGGTT
1799106 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1799125 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1799146 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1799165 GA
1 GA
1799167 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1799189 original size:32 final size:33
Alignment explanation
Indices: 1799131--1799228 Score: 135
Period size: 32 Copynumber: 3.0 Consensus size: 33
1799121 ACGAGATAAT
*
1799131 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1799165 GAGAATCGCAACGCG-AATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1799197 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1799229 GCGAAAAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 29 0.51
33 14 0.25
34 14 0.25
ACGTcount: A:0.39, C:0.27, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1799222 original size:19 final size:19
Alignment explanation
Indices: 1799200--1799261 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
1799190 GCGACCAGAC
1799200 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1799219 AATCGCAACCGCGAAA--AA
1 AATCGCAA-CGCGAAATGAA
*
1799237 ACTCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1799256 AATCGC
1 AATCGC
1799262 GTTGCGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 7 0.18
18 9 0.24
19 15 0.39
20 7 0.18
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1799888 original size:41 final size:41
Alignment explanation
Indices: 1799836--1799913 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1799826 CGAAAGTCAG
* * *
1799836 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1799877 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1799914 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1799910 original size:20 final size:20
Alignment explanation
Indices: 1799817--1799910 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1799807 CGCTATGTAA
*
1799817 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1799837 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1799857 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1799878 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1799898 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1799911 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1799929 original size:41 final size:41
Alignment explanation
Indices: 1799836--1799931 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1799826 CGAAAGTCAG
* * * ** *
1799836 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
1799877 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
1799919 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1799932 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:1801019 original size:15 final size:15
Alignment explanation
Indices: 1800983--1801022 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1800973 AATAAAATAG
*
1800983 TGATTAAAAGTTTAA
1 TGATTAAAATTTTAA
**
1800998 TTTTTAAAATTTTAA
1 TGATTAAAATTTTAA
1801013 TGATTAAAAT
1 TGATTAAAAT
1801023 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TGATTAAAATTTTAA
Found at i:1801688 original size:3 final size:3
Alignment explanation
Indices: 1801674--1801703 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1801664 TTAGGAATTC
*
1801674 CTT CTC CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1801704 TTACTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:1812306 original size:4 final size:4
Alignment explanation
Indices: 1812297--1812349 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
1812287 ATCTTCCTAC
*
1812297 AATT AATT AAAT AA-- AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
1812343 AATT AAT
1 AATT AAT
1812350 CATAAAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.04
4 44 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:1812723 original size:22 final size:22
Alignment explanation
Indices: 1812681--1812724 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1812671 ATAAATAAAA
1812681 CATTACCTTTTTTTTCTTCTTC
1 CATTACCTTTTTTTTCTTCTTC
1812703 CATT-CCTTTCTTTATTC-TCTTC
1 CATTACCTTT-TTT-TTCTTCTTC
1812725 GGTGATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 12 0.60
23 3 0.15
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (22 bp):
CATTACCTTTTTTTTCTTCTTC
Found at i:1815809 original size:45 final size:44
Alignment explanation
Indices: 1815737--1815927 Score: 202
Period size: 45 Copynumber: 4.2 Consensus size: 44
1815727 GAGATAAGGT
* * * * *
1815737 TGTTTCGGAAGGAAAGAAGATTAATATTGTATCAGAAAATGATAC
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCA-AAAATGATAC
*
1815782 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAAAAGATGATAT
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAAAA-ATGATAC
* * * *
1815827 TGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAACGATAC
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCAT-CAAAAATGATAC
* * * * **
1815872 AGTTTTGGATGAAAAGAGGATTGATCTTGCATCAAATGATGGCAC
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAAA-AATGATAC
1815917 TGTTTTGGAAG
1 TGTTTTGGAAG
1815928 GATATAGCAC
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
44 6 0.05
45 112 0.92
46 4 0.03
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (44 bp):
TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAAAAATGATAC
Found at i:1815842 original size:23 final size:23
Alignment explanation
Indices: 1815775--1815843 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1815765 GTATCAGAAA
*
1815775 ATGATACTGTTTTGGAAGAAAAG
1 ATGATATTGTTTTGGAAGAAAAG
* * * **
1815798 A-G-GATTGATATTGCATCAAAAG
1 ATGATATTG-TTTTGGAAGAAAAG
1815820 ATGATATTGTTTTGGAAGAAAAG
1 ATGATATTGTTTTGGAAGAAAAG
1815843 A
1 A
1815844 GAATTGATCT
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 13 0.41
24 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (23 bp):
ATGATATTGTTTTGGAAGAAAAG
Found at i:1815889 original size:90 final size:90
Alignment explanation
Indices: 1815736--1815927 Score: 242
Period size: 90 Copynumber: 2.1 Consensus size: 90
1815726 GGAGATAAGG
* * * * *
1815736 TTGTTTCGGAAGGAAAGAAGATTAATATTGTATCAGAAAATGATACTGTTTTGGAAGAAAAGAGG
1 TTGTTTTGGAAGAAAAGAAGATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAGG
*
1815801 ATTGATATTGCATCAAAAGATGATA
66 ATTGATATTGCATCAAAAGATGACA
* * * *
1815826 TTGTTTTGGAAGAAAAG-AGAATTGATCTTGCATCCGAAAACGATACAGTTTTGGATGAAAAGAG
1 TTGTTTTGGAAGAAAAGAAG-ATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAG
* * *
1815890 GATTGATCTTGCATCAAATGATGGCA
65 GATTGATATTGCATCAAAAGATGACA
*
1815916 CTGTTTTGGAAG
1 TTGTTTTGGAAG
1815928 GATATAGCAC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 2 0.02
90 85 0.98
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (90 bp):
TTGTTTTGGAAGAAAAGAAGATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAGG
ATTGATATTGCATCAAAAGATGACA
Found at i:1816426 original size:63 final size:63
Alignment explanation
Indices: 1816325--1816455 Score: 219
Period size: 63 Copynumber: 2.1 Consensus size: 63
1816315 TTATGATGTT
* *
1816325 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTTC-GAGACGATGATGATCCCATC
1 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATC-TTTCGGAGACGACGATGAACCCATC
*
1816388 ACTCCGGTTACTATCAATGATCAAAACAGCAGACAATCTTTCGGAGACGACGATGAACCCATC
1 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTCGGAGACGACGATGAACCCATC
1816451 ACTCC
1 ACTCC
1816456 TATTGGTGCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
62 4 0.06
63 60 0.94
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (63 bp):
ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTCGGAGACGACGATGAACCCATC
Found at i:1817400 original size:2 final size:2
Alignment explanation
Indices: 1817393--1817442 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1817383 AATTTTAAGA
1817393 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
1817435 AT AT AT AT
1 AT AT AT AT
1817443 TATTAAATAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1819028 original size:15 final size:15
Alignment explanation
Indices: 1819008--1819038 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1818998 TCGTGATGGC
1819008 GAGTAGAGATAGAGA
1 GAGTAGAGATAGAGA
*
1819023 GAGTAGAGATCGAGA
1 GAGTAGAGATAGAGA
1819038 G
1 G
1819039 CTTCTAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.42, T:0.13
Consensus pattern (15 bp):
GAGTAGAGATAGAGA
Found at i:1822558 original size:55 final size:55
Alignment explanation
Indices: 1822450--1822560 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
1822440 ATACTTCTTG
* *
1822450 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATATGAAAATTGATTGT
1 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
**
1822505 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAGGTAGATTGT
1 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
1822560 C
1 C
1822561 GATGATTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (55 bp):
CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
Found at i:1835592 original size:12 final size:12
Alignment explanation
Indices: 1835575--1835599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1835565 AGAGATCAAA
1835575 TATAATTTAAGT
1 TATAATTTAAGT
1835587 TATAATTTAAGT
1 TATAATTTAAGT
1835599 T
1 T
1835600 GGGGTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATAATTTAAGT
Found at i:1845550 original size:35 final size:35
Alignment explanation
Indices: 1845509--1845584 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1845499 AAAACAGTCC
* * *
1845509 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1845544 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1845579 TCAATT
1 TCAATT
1845585 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1846150 original size:127 final size:128
Alignment explanation
Indices: 1845968--1846210 Score: 389
Period size: 127 Copynumber: 1.9 Consensus size: 128
1845958 TATTTATATA
* **
1845968 ATCAATTTGGTTCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1846033 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATATTATATATGCT
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATATTATATATGCT
1846096 ATCAATTTGGTCCTAAATTAAATA-AATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
1846160 TTAACACATGATCATTATATATGTTATTAGTGACACATGTCACCACCTAAT
66 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAAT
1846211 TAGAAGAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
127 82 0.78
128 23 0.22
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (128 bp):
ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATATTATATATGCT
Found at i:1847803 original size:2 final size:2
Alignment explanation
Indices: 1847792--1847871 Score: 56
Period size: 2 Copynumber: 45.5 Consensus size: 2
1847782 GAACCCGAAA
* *
1847792 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1847828 AT A- AA AT AT AT A- AT -T A- AT AT A- 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
1847865 AT AT AT A
1 AT AT AT A
1847872 ATCGGGGTGG
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
1 11 0.17
2 53 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1847868 original size:16 final size:15
Alignment explanation
Indices: 1847791--1847873 Score: 78
Period size: 13 Copynumber: 6.2 Consensus size: 15
1847781 CGAACCCGAA
1847791 AATAT-TATATATAT
1 AATATATATATATAT
1847805 AAT-TA-ATATA-A-
1 AATATATATATATAT
*
1847816 AATATATA-AAATAT
1 AATATATATATATAT
*
1847830 AAAATATATA-AT-T
1 AATATATATATATAT
1847843 AATATA-ATATATAT
1 AATATATATATATAT
1847857 -ATATATATATATAT
1 AATATATATATATAT
1847871 AAT
1 AAT
1847874 CGGGGTGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
11 3 0.05
12 8 0.14
13 21 0.38
14 21 0.38
15 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:1849758 original size:22 final size:22
Alignment explanation
Indices: 1849733--1849783 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1849723 CTACGGTGAC
1849733 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
*
1849755 ATCCGTCCCCATCTCCTGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
1849777 ATCCGTC
1 ATCCGTC
1849784 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.45, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGGCGAA
Found at i:1850146 original size:20 final size:20
Alignment explanation
Indices: 1850123--1850161 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1850113 TTTGAAACTT
1850123 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
1850143 AAATTCGTAACACGAAAAT
1 AAATTCGCAACACGAAAAT
1850162 CGCAATGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:1850201 original size:20 final size:19
Alignment explanation
Indices: 1850167--1850221 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1850157 AAAATCGCAA
1850167 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
1850186 TGCGATTTTTATTTTCGCGT
1 TGCGA-TTTTAGTTTCGCGT
*
1850206 TGCGAATTTAAGTTTC
1 TGCG-ATTTTAGTTTC
1850222 AGAAACTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 25 0.81
21 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:1851602 original size:42 final size:42
Alignment explanation
Indices: 1851543--1851639 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
1851533 CCCCACTTCA
* * * *
1851543 AGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
*
1851585 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACT
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
1851627 AGAGCCATCACCT
1 AGAGCCATCACCT
1851640 ATTCCATCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.29, C:0.37, G:0.16, T:0.18
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACC
Found at i:1851796 original size:21 final size:22
Alignment explanation
Indices: 1851753--1851809 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
1851743 AGTTAGGGAG
1851753 TTACGTGATGAGGT-CGGTGCT
1 TTACGTGATGAGGTACGGTGCT
* *
1851774 TTGCGTGATGAGGTACTGT-CT
1 TTACGTGATGAGGTACGGTGCT
*
1851795 TTACGTGGTGAGGTA
1 TTACGTGATGAGGTA
1851810 GATGTTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.16, C:0.12, G:0.37, T:0.35
Consensus pattern (22 bp):
TTACGTGATGAGGTACGGTGCT
Found at i:1851818 original size:21 final size:21
Alignment explanation
Indices: 1851753--1851820 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1851743 AGTTAGGGAG
* * *
1851753 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTAGATGTT
* *
1851774 TTGCGTGATGAGGTA-CTGTCT
1 TTACGTGATGAGGTAGATGT-T
*
1851795 TTACGTGGTGAGGTAGATGTT
1 TTACGTGATGAGGTAGATGTT
1851816 TTACG
1 TTACG
1851821 CAATGACAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 33 0.87
22 3 0.08
ACGTcount: A:0.16, C:0.12, G:0.35, T:0.37
Consensus pattern (21 bp):
TTACGTGATGAGGTAGATGTT
Found at i:1852198 original size:21 final size:21
Alignment explanation
Indices: 1852168--1852266 Score: 128
Period size: 21 Copynumber: 4.7 Consensus size: 21
1852158 GATTCACTTG
1852168 TCATCGTTCAAGAGGTCCCTTC
1 TCATCGTTCAAGAGG-CCCTTC
* *
1852190 T-ATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCTTC
*
1852210 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCTTC
* * *
1852231 CCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCTTC
1852252 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
1852267 TCTATCCCAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.09
21 60 0.90
22 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCTTC
Found at i:1852215 original size:42 final size:42
Alignment explanation
Indices: 1852168--1852286 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
1852158 GATTCACTTG
* * *
1852168 TCATCGTTCAAGAGGTCCCTTCTATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTC
* * * *
1852210 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTC
** *
1852252 TCATCGTTCAAGAGGTCTATCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAG
1852287 CCCGATTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTC
Found at i:1852280 original size:21 final size:20
Alignment explanation
Indices: 1852195--1852286 Score: 76
Period size: 21 Copynumber: 4.4 Consensus size: 20
1852185 CCTTCTATCA
* * *
1852195 TTCAAGAGGCCCCTCTCATCG
1 TTCAAGAGG-CCTTCCCACCG
*
1852216 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGG-CCTTCCCACCG
** *
1852237 TTCAAGAGGCCCTTGTCATCG
1 TTCAAGAGG-CCTTCCCACCG
*
1852258 TTCAAGAGGTCTATCCCACCG
1 TTCAAGAGGCCT-TCCCACCG
1852279 TTCAAGAG
1 TTCAAGAG
1852287 CCCGATTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 2 0.03
21 58 0.97
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.23
Consensus pattern (20 bp):
TTCAAGAGGCCTTCCCACCG
Found at i:1852894 original size:37 final size:37
Alignment explanation
Indices: 1852844--1852917 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1852834 ACTAAGCTTT
1852844 ATCCTGTGTGGTGGGAGGTAGATAAGGTTAGTATTTA
1 ATCCTGTGTGGTGGGAGGTAGATAAGGTTAGTATTTA
*
1852881 ATCCTGTGTGGTGGGAGGTCGATAAGGTTAGTATTTA
1 ATCCTGTGTGGTGGGAGGTAGATAAGGTTAGTATTTA
1852918 TTTTTAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (37 bp):
ATCCTGTGTGGTGGGAGGTAGATAAGGTTAGTATTTA
Found at i:1853891 original size:29 final size:29
Alignment explanation
Indices: 1853841--1853897 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1853831 TTTTCGCAAC
* *
1853841 GCGAAAGTCAAATCCGCGTTGCGATTGTT
1 GCGAAAGTAAAATCCGCATTGCGATTGTT
*
1853870 GCGAAAGTAAAATTCGCATTGCGATTGT
1 GCGAAAGTAAAATCCGCATTGCGATTGT
1853898 AAAATTCGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (29 bp):
GCGAAAGTAAAATCCGCATTGCGATTGTT
Found at i:1853893 original size:20 final size:20
Alignment explanation
Indices: 1853868--1853913 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1853858 GTTGCGATTG
1853868 TTGCGAAAGTAAAATTCGCA
1 TTGCGAAAGTAAAATTCGCA
**
1853888 TTGCGATTGTAAAATTCGCA
1 TTGCGAAAGTAAAATTCGCA
1853908 TTGCGA
1 TTGCGA
1853914 TTTTCACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
TTGCGAAAGTAAAATTCGCA
Found at i:1853914 original size:20 final size:20
Alignment explanation
Indices: 1853876--1853915 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1853866 TGTTGCGAAA
1853876 GTAAAATTCGCATTGCGATT
1 GTAAAATTCGCATTGCGATT
1853896 GTAAAATTCGCATTGCGATT
1 GTAAAATTCGCATTGCGATT
1853916 TTCACGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
GTAAAATTCGCATTGCGATT
Found at i:1853937 original size:20 final size:20
Alignment explanation
Indices: 1853915--1853980 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1853905 GCATTGCGAT
* * *
1853915 TTTCACGTTGCGAATTTGAT
1 TTTCGCGTTACGAATTTGAC
* *
1853935 TTTTGCGTTACGAATTTTAC
1 TTTCGCGTTACGAATTTGAC
*
1853955 TTTCGCGTTTCGAATTTGAC
1 TTTCGCGTTACGAATTTGAC
1853975 TTTCGC
1 TTTCGC
1853981 AATAATCGCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (20 bp):
TTTCGCGTTACGAATTTGAC
Found at i:1856549 original size:471 final size:468
Alignment explanation
Indices: 1855899--1856839 Score: 1748
Period size: 471 Copynumber: 2.0 Consensus size: 468
1855889 CATTCATGTC
1855899 AGTCATAATTTCATGTCCCCGATATACCTTGCCATTCAAAAACATTAACTCATCCAGAAAACCAC
1 AGTCATAATTTCATGTCCCCGATATACCTTGCCATTCAAAAACATTAACTCATCCAGAAAACCAC
1855964 CCAACACCTTTTTGTTTGTCTGTCTATGGTAAGGAAAAACTTGGGTTCTTGAACATGTATGTTTA
66 CCAACACCTTTTTGTTTGTCTGTCTATGGTAAGGAAAAACTTGGGTTCTTGAACATGTATGTTTA
1856029 TCAATAAAAGTCCTAACTTGAAACATTTCGCAATCTTTTATCCTCTTTGCAATCATACGCCACAT
131 TCAATAAAAGTCCTAACTTGAAACATTTCGCAATCTTTTATCCTCTTTGCAATCATACGCCACAT
1856094 ACATTTTTTGTCAATCATACACTTTGTTTCGAAACGATATTTGCTTGATTTGTTAACTTTTAGTT
196 ACATTTTTTGTCAATCATACAC-TTGTTTCG-AACGATATTTGCTTGATTTGTTAACTTTTAGTT
1856159 GATAGCCATCTTCCACACATTTCATATACAAAGCTATCTTCAAGTCTTCATTTGTATCAAAACAA
259 GATAGCCATCTTCCA-ACATTTCATATACAAAGCTATCTTCAAGTCTTCATTTGTATCAAAACAA
1856224 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGATATCTTTACCAACTCTTCTTC
323 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGATATC-TTA-CAACTCTTCTTC
*
1856289 CGGGTATCTGAAGTAA-TGGCATATTCCAGTTATACTCCGTGACATTTTCTTC-TTTTCTTTTCT
386 CGGGTATCTGAAGTAATTGGCATATTCCAGTTAT-CCCCGTGACATTTTCTTCTTTTTCTTTTCT
1856352 TCGGGGACTTCTTCTTCTTCT
450 TC--GGACTTCTTCTTCTTCT
1856373 AGTCATAATTTCATGT-CCCGATATACCTTGCCATTCAAAAACATTAACTCATCCAGAAAACCAC
1 AGTCATAATTTCATGTCCCCGATATACCTTGCCATTCAAAAACATTAACTCATCCAGAAAACCAC
1856437 CC-AC-CCTTTTTGTTTGTCTGTCTATGGTAAGGAAAAACTTGGGTTCTTGAACATGTATGTTTA
66 CCAACACCTTTTTGTTTGTCTGTCTATGGTAAGGAAAAACTTGGGTTCTTGAACATGTATGTTTA
1856500 TCAATAAAAGTCCTAACTTGAAACATTTCGCAATCTTTTATCCTCTTTGCAATCATACGCCACAT
131 TCAATAAAAGTCCTAACTTGAAACATTTCGCAATCTTTTATCCTCTTTGCAATCATACGCCACAT
1856565 ACATTTTTTGTCAATCATACACTTGTTTCGAACGATATTTGCTTGATTTGTTAACTTTTAGTTGA
196 ACATTTTTTGTCAATCATACACTTGTTTCGAACGATATTTGCTTGATTTGTTAACTTTTAGTTGA
1856630 TAGCCATCTTCCAACATTTCATATACAAAGCTATCTTCAAGTCTTCATTTGTATCAAAACAATCA
261 TAGCCATCTTCCAACATTTCATATACAAAGCTATCTTCAAGTCTTCATTTGTATCAAAACAATCA
1856695 TCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGATATCTTACAACTCTTCTTCCGGGT
326 TCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGATATCTTACAACTCTTCTTCCGGGT
1856760 ATCTGAAGTAATTCTGGCATATTCCAGTTATCCCCGTGACATTTTCTTCTTTTTCTTTTCTTCGG
391 ATCTGAAGTAA-T-TGGCATATTCCAGTTATCCCCGTGACATTTTCTTCTTTTTCTTTTCTTCGG
1856825 ACTTCTTCTTCTTCT
454 ACTTCTTCTTCTTCT
1856840 TCTTCAGGGT
Statistics
Matches: 462, Mismatches: 1, Indels: 15
0.97 0.00 0.03
Matches are distributed among these distances:
466 28 0.06
467 20 0.04
468 114 0.25
469 78 0.17
470 8 0.02
471 146 0.32
472 2 0.00
473 50 0.11
474 16 0.03
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (468 bp):
AGTCATAATTTCATGTCCCCGATATACCTTGCCATTCAAAAACATTAACTCATCCAGAAAACCAC
CCAACACCTTTTTGTTTGTCTGTCTATGGTAAGGAAAAACTTGGGTTCTTGAACATGTATGTTTA
TCAATAAAAGTCCTAACTTGAAACATTTCGCAATCTTTTATCCTCTTTGCAATCATACGCCACAT
ACATTTTTTGTCAATCATACACTTGTTTCGAACGATATTTGCTTGATTTGTTAACTTTTAGTTGA
TAGCCATCTTCCAACATTTCATATACAAAGCTATCTTCAAGTCTTCATTTGTATCAAAACAATCA
TCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGATATCTTACAACTCTTCTTCCGGGT
ATCTGAAGTAATTGGCATATTCCAGTTATCCCCGTGACATTTTCTTCTTTTTCTTTTCTTCGGAC
TTCTTCTTCTTCT
Found at i:1857044 original size:24 final size:24
Alignment explanation
Indices: 1857012--1857065 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1857002 CTGAAACATC
1857012 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1857036 ATCAAAATCTGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1857060 ATCAAA
1 ATCAAA
1857066 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1857079 original size:24 final size:24
Alignment explanation
Indices: 1857012--1857079 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1857002 CTGAAACATC
* * *
1857012 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCTGAATACTGACCAAG
** *
1857036 ATCAAAATCTGGGTATTGACCAAG
1 ATCAAAATCTGAATACTGACCAAG
* *
1857060 ATCAAATTTTGAATACTGAC
1 ATCAAAATCTGAATACTGAC
1857080 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAATACTGACCAAG
Found at i:1857827 original size:16 final size:16
Alignment explanation
Indices: 1857806--1857844 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1857796 GAAATCATTG
* *
1857806 AAAATTATATAGAAAT
1 AAAATTATATAAAAAA
*
1857822 AAAATTATGTAAAAAA
1 AAAATTATATAAAAAA
1857838 AAAATTA
1 AAAATTA
1857845 GAGACGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAATTATATAAAAAA
Found at i:1858006 original size:20 final size:20
Alignment explanation
Indices: 1857981--1858114 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 20
1857971 CAAAACATTT
1857981 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
1858001 GTGTTGCG-AATTCGAAAATT-
1 GTGTTGCGAAATT--AAAATTC
* **
1858021 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
* * *
1858041 GCGTTGTG-ATTTCAGAAA-TC
1 GTGTTGCGAAATT-A-AAATTC
* * *
1858061 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
1858081 AGTGTTGCGAATTTAGAAACT-
1 -GTGTTGCGAAATTA-AAATTC
*
1858102 GTGTTACGAAATT
1 GTGTTGCGAAATT
1858115 GGAGTTCGCG
Statistics
Matches: 88, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
19 14 0.16
20 43 0.49
21 27 0.31
22 4 0.05
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:1858038 original size:40 final size:40
Alignment explanation
Indices: 1857983--1858150 Score: 135
Period size: 40 Copynumber: 4.2 Consensus size: 40
1857973 AAACATTTGT
*
1857983 GTTGCGAAATTAAAATTCGTGTTGCGAATTC-GAAAATTGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAG-AAATCGA
** * * *
1858023 GTTGCGAAAACAAAATTCGCGTTGTGATTTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGA
* * * *
1858063 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTAGAAA-CTGT
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCAGAAATC-GA
* ** * * * *
1858104 GTTACGAAATTGGAGTTCGCGTTGCGAATTC-GAGATCGT
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGA
1858143 GTTGCGAA
1 GTTGCGAA
1858151 TTTGTTGGTC
Statistics
Matches: 101, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
39 12 0.12
40 59 0.58
41 30 0.30
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGA
Found at i:1861670 original size:46 final size:46
Alignment explanation
Indices: 1861617--1861707 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
1861607 AAAATTAATT
* * *
1861617 AGCAATTTACGATATTTTTTATGGGAGCTTGTTATCCAGATGTGAG
1 AGCAATTTACGATATCTTTTATGAGAACTTGTTATCCAGATGTGAG
*
1861663 AGCAATTTACGATATCTTTTATTAGAACTTGTTATCCAGATGTGA
1 AGCAATTTACGATATCTTTTATGAGAACTTGTTATCCAGATGTGA
1861708 CATATCTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.40
Consensus pattern (46 bp):
AGCAATTTACGATATCTTTTATGAGAACTTGTTATCCAGATGTGAG
Found at i:1871790 original size:20 final size:19
Alignment explanation
Indices: 1871742--1871879 Score: 123
Period size: 20 Copynumber: 6.9 Consensus size: 19
1871732 AAATGACCAA
*
1871742 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAACT
1871761 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
* * *
1871780 CCAATTTCGCAATGCGAAAGT
1 -CAAATTCGCAACGCG-AACT
* *
1871801 CAAAATCGCAACGCGAAAGT
1 CAAATTCGCAACGCG-AACT
* *
1871821 CAAATTCGCAACGTGGAAGT
1 CAAATTCGCAACG-CGAACT
*
1871841 CAAATTCGCAACGTGAATTCT
1 CAAATTCGCAACGCGAA--CT
*
1871862 CTAAATTCGCAACTCGAA
1 C-AAATTCGCAACGCGAA
1871880 TTTCGCAACG
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
19 21 0.21
20 59 0.59
21 6 0.06
22 14 0.14
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:1871810 original size:40 final size:40
Alignment explanation
Indices: 1871742--1871879 Score: 136
Period size: 40 Copynumber: 3.4 Consensus size: 40
1871732 AAATGACCAA
**
1871742 CAAATTCGCAACGCG-ATCTCAAATTCGCAACGCG-AACT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAACT
* * * *
1871780 CCAATTTCGCAATGCGAAAGTCAAAATCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAACT
* * * *
1871821 CAAATTCGCAACGTGGAAGTCAAATTCGCAACGTGAATTCT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAA-ACT
*
1871862 CTAAATTCGCAACTCGAA
1 C-AAATTCGCAACGCGAA
1871880 TTTCGCAACG
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
39 13 0.17
40 47 0.60
41 5 0.06
42 13 0.17
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAACT
Found at i:1872057 original size:20 final size:20
Alignment explanation
Indices: 1872034--1872080 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1872024 TGGAACCTGT
*
1872034 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAAATTGGAGATCGC
*
1872054 GTTGC-AAATTTGAGATCGC
1 GTTGCGAAATTGGAGATCGC
1872073 GTTGCGAA
1 GTTGCGAA
1872081 TTTGTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTGGAGATCGC
Found at i:1872911 original size:38 final size:38
Alignment explanation
Indices: 1872860--1872955 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 38
1872850 CTCGTATAAA
* *
1872860 TGTCCCGAAGGACCTATCATCCCGAATGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
1872898 TGTCCCGAAGGACCTCTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
1872936 TGTCTCGTAA-GACCTATCAT
1 TGTCCCG-AAGGACCTATCAT
1872956 ATGTCTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
38 50 0.96
39 2 0.04
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:1873161 original size:46 final size:46
Alignment explanation
Indices: 1873104--1873208 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
1873094 ATGTGTAACC
1873104 ATGT-ATTTCATATCATATCACATGTATCACGTATTACAAATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACAAATTCAT
* *
1873149 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACAAATTCAT
*
1873195 ATATCATTTCATAT
1 ATGTCATTTCATAT
1873209 AGTCACATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACAAATTCAT
Found at i:1878647 original size:2 final size:2
Alignment explanation
Indices: 1878640--1878689 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1878630 GGTTTATGTC
1878640 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
*
1878682 AT GT AT AT
1 AT AT AT AT
1878690 GCTGATTTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1883137 original size:15 final size:14
Alignment explanation
Indices: 1883092--1883141 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1883082 TCCTCCGGAA
1883092 GAAGACGAAGAAGAG
1 GAAGA-GAAGAAGAG
*
1883107 GAAGAAAAGAAAGAG
1 GAAGAGAAG-AAGAG
*
1883122 GAAGAGGAAGAGGAG
1 GAAGA-GAAGAAGAG
1883137 GAAGA
1 GAAGA
1883142 TCCTGAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.80
16 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (14 bp):
GAAGAGAAGAAGAG
Found at i:1887511 original size:2 final size:2
Alignment explanation
Indices: 1887504--1887537 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1887494 AGTGCTATGT
1887504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1887538 GGTGTGTTGG
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):
TA
Found at i:1888632 original size:21 final size:23
Alignment explanation
Indices: 1888589--1888633 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1888579 TAAAATAATA
1888589 TTATTAAATAATAATATTTTATTAT
1 TTATTAAATAATAATA--TTATTAT
1888614 TTATTAAA-AATAATA-TATTA
1 TTATTAAATAATAATATTATTA
1888634 GTTAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTAAATAATAATATTATTAT
Found at i:1891297 original size:19 final size:19
Alignment explanation
Indices: 1891273--1891312 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1891263 ATGTAATCGT
1891273 TGCAAAAGAAGTGCAGTGC
1 TGCAAAAGAAGTGCAGTGC
1891292 TGCAAAAGAAGTGCAGTGC
1 TGCAAAAGAAGTGCAGTGC
1891311 TG
1 TG
1891313 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.33, T:0.17
Consensus pattern (19 bp):
TGCAAAAGAAGTGCAGTGC
Found at i:1891320 original size:2 final size:2
Alignment explanation
Indices: 1891313--1891339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1891303 TGCAGTGCTG
1891313 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 T
1891340 TATTTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1891539 original size:17 final size:19
Alignment explanation
Indices: 1891517--1891558 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1891507 ACAGACTTTG
1891517 ATTTATTATAT-TAT-TAT
1 ATTTATTATATATATGTAT
*
1891534 ATTTATTTTATATATGTAT
1 ATTTATTATATATATGTAT
1891553 -TTTATT
1 ATTTATT
1891559 TAGAAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 9 0.41
19 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTATATATATGTAT
Found at i:1891544 original size:22 final size:22
Alignment explanation
Indices: 1891518--1891560 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1891508 CAGACTTTGA
1891518 TTTATTATAT-TATTATATTTAT
1 TTTA-TATATGTATTATATTTAT
*
1891540 TTTATATATGTATTTTATTTA
1 TTTATATATGTATTATATTTA
1891561 GAAATTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATATATGTATTATATTTAT
Found at i:1891546 original size:19 final size:18
Alignment explanation
Indices: 1891518--1891559 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1891508 CAGACTTTGA
*
1891518 TTTATTATAT-TAT-TAT
1 TTTATTTTATATATGTAT
1891534 ATTTATTTTATATATGTAT
1 -TTTATTTTATATATGTAT
1891553 TTTATTT
1 TTTATTT
1891560 AGAAATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 10 0.45
19 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATTTTATATATGTAT
Found at i:1891871 original size:12 final size:12
Alignment explanation
Indices: 1891849--1891894 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
1891839 ATATCACTTT
1891849 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
1891862 TTATTTTTAAAA
1 TTATTTTTAAAA
1891874 TTA-TTTTAAAA
1 TTATTTTTAAAA
1891885 TGTATTTTTA
1 T-TATTTTTA
1891895 GGTATTCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.29
12 13 0.42
13 9 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:1898460 original size:2 final size:2
Alignment explanation
Indices: 1898455--1898491 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1898445 CCATATTCTT
1898455 TA TA TA 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
1898492 CACCATCAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1901308 original size:14 final size:16
Alignment explanation
Indices: 1901289--1901321 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1901279 GTGATAATTC
1901289 ACGGTCC-TGATG-TG
1 ACGGTCCATGATGTTG
1901303 ACGGTCCATGATGTTG
1 ACGGTCCATGATGTTG
1901319 ACG
1 ACG
1901322 TGACAGTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.27
Consensus pattern (16 bp):
ACGGTCCATGATGTTG
Found at i:1907911 original size:16 final size:16
Alignment explanation
Indices: 1907890--1907933 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1907880 TTAATAAATA
1907890 AACATAAACGAACACG
1 AACATAAACGAACACG
*
1907906 AACATAAATGAACACG
1 AACATAAACGAACACG
1907922 AACATAAACGAA
1 AACATAAACGAA
1907934 TATAAAACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:1909058 original size:23 final size:23
Alignment explanation
Indices: 1909026--1909090 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
1909016 CGACGAACAT
*
1909026 GAACGAACATAACGAACGTTCAC
1 GAACGTACATAACGAACGTTCAC
1909049 GAACGTACATAACCGAACGTTCAC
1 GAACGTACATAA-CGAACGTTCAC
*
1909073 GAA-GTAAATTAACGAACG
1 GAACGTACA-TAACGAACG
1909091 AGACCTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 21 0.55
24 17 0.45
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.15
Consensus pattern (23 bp):
GAACGTACATAACGAACGTTCAC
Found at i:1909070 original size:24 final size:23
Alignment explanation
Indices: 1909026--1909075 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
1909016 CGACGAACAT
1909026 GAACGAACATAACGAACGTTCAC
1 GAACGAACATAACGAACGTTCAC
*
1909049 GAACGTACATAACCGAACGTTCAC
1 GAACGAACATAA-CGAACGTTCAC
1909073 GAA
1 GAA
1909076 GTAAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (23 bp):
GAACGAACATAACGAACGTTCAC
Found at i:1910327 original size:3 final size:3
Alignment explanation
Indices: 1910313--1910381 Score: 66
Period size: 3 Copynumber: 21.7 Consensus size: 3
1910303 TATTTTTTCA
* * *
1910313 TAT TAT TTT TAT TAT TAT TAT TAA AAT TAT TAT ATAT ATAT ATAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT -TAT
*
1910362 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1910382 AAAAAATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 42 0.74
4 15 0.26
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1910756 original size:3 final size:3
Alignment explanation
Indices: 1910748--1910785 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1910738 GTTCGACGGC
1910748 TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1910786 AAAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1912318 original size:135 final size:133
Alignment explanation
Indices: 1912174--1912503 Score: 318
Period size: 135 Copynumber: 2.4 Consensus size: 133
1912164 TTATTTTATT
*
1912174 TTTTATATATATTAAAT-A-AAA-ATCCTA-TTTATAAATT-TA-AT-TTTATATAATTACTTTT
1 TTTTATAT-TATTAAATAATAAATATCATATTTTATAAATTATATATATTTATATAATTA-TTTT
* *
1912232 AAGAAAATAATCATATT-TTAATATTTATTTATTTATTTTTATATTAAGAAATGGGCTGTCTTAA
64 AAG-AAAT-AT--T-TTATTAATATTTA-TTA--T-TTTTAATATTAAGAAATGGGCTATCTTAA
1912296 AGCACCTAGAAGTCC
120 AGCACCTAGAAGT-C
* * *
1912311 TTTTATATTCTTAAATAAATAAATATCATATTTTATAAATTATATATATTTATTTAATTATTTTT
1 TTTTATATTATTAAAT-AATAAATATCATATTTTATAAATTATATATATTTATATAATTATTTTA
*
1912376 AGAAATGTTTTATTAATATTTATTATTTTTAATATTAAGAAATGGGCTATCTTAAAGCACCTAGA
65 AGAAATATTTTATTAATATTTATTATTTTTAATATTAAGAAATGGGCTATCTTAAAGCACCTAGA
1912441 AGTC
130 AGTC
* * * * *
1912445 TTTTCTGATATT-TCTAAGTAAATAAATATCTTATTTATAAAAATAATATATATATATAT
1 -TTT-T-ATATTAT-TAAAT-AATAAATATCATATTT-TATAAATTATATATATTTATAT
1912504 TATATATATA
Statistics
Matches: 166, Mismatches: 13, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
134 1 0.01
135 43 0.26
136 10 0.06
137 33 0.20
138 24 0.14
139 14 0.08
140 5 0.03
141 11 0.07
142 6 0.04
143 8 0.05
144 11 0.07
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (133 bp):
TTTTATATTATTAAATAATAAATATCATATTTTATAAATTATATATATTTATATAATTATTTTAA
GAAATATTTTATTAATATTTATTATTTTTAATATTAAGAAATGGGCTATCTTAAAGCACCTAGAA
GTC
Found at i:1912497 original size:2 final size:2
Alignment explanation
Indices: 1912490--1912518 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1912480 TATAAAAATA
1912490 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1912519 TTTCTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1912506 original size:135 final size:135
Alignment explanation
Indices: 1912257--1912506 Score: 357
Period size: 135 Copynumber: 1.9 Consensus size: 135
1912247 TTTTAATATT
*
1912257 TATTTATTTATTTTTATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTATATTCT
1 TATTTATTTATTTTTATATTAAGAAATGGGCTATCTTAAAGCACCTAGAAGTCCTTTTATATTCT
* * *
1912322 TAAATAAATAAATATCATATTTTATAAATTATATATATTTATTTAATTATTTTTAGAAATGTTTT
66 TAAATAAATAAATATCATATTTTATAAAATATATATATATATATAATTATTTTTAGAAATGTTTT
1912387 ATTAA
131 ATTAA
*
1912392 TATTTA-TTATTTTTAATATTAAGAAATGGGCTATCTTAAAGCACCTAGAAGTCTTTTCTGATAT
1 TATTTATTTATTTTT-ATATTAAGAAATGGGCTATCTTAAAGCACCTAGAAGTCCTTT-T-ATAT
* *
1912456 T-TCTAAGTAAATAAATATCTTA-TTTATAAAA-ATA-ATATATATATATATTAT
63 TCT-TAAATAAATAAATATCATATTTTATAAAATATATATATATATATA-ATTAT
1912507 ATATATATAT
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
134 17 0.17
135 54 0.52
136 10 0.10
137 22 0.21
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (135 bp):
TATTTATTTATTTTTATATTAAGAAATGGGCTATCTTAAAGCACCTAGAAGTCCTTTTATATTCT
TAAATAAATAAATATCATATTTTATAAAATATATATATATATATAATTATTTTTAGAAATGTTTT
ATTAA
Found at i:1912507 original size:13 final size:13
Alignment explanation
Indices: 1912491--1912516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1912481 ATAAAAATAA
1912491 TATATATATATAT
1 TATATATATATAT
1912504 TATATATATATAT
1 TATATATATATAT
1912517 ATTTTCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:1912514 original size:15 final size:15
Alignment explanation
Indices: 1912490--1912519 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1912480 TATAAAAATA
1912490 ATATATATATATATT
1 ATATATATATATATT
1912505 ATATATATATATATT
1 ATATATATATATATT
1912520 TTCTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:1914597 original size:21 final size:20
Alignment explanation
Indices: 1914569--1914612 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1914559 GAGTAACATC
*
1914569 TTTTCATACATGCATTTTCA
1 TTTTCATACATACATTTTCA
**
1914589 TTTTGCATATTTACATTTTCA
1 TTTT-CATACATACATTTTCA
1914610 TTT
1 TTT
1914613 ATACTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTCATACATACATTTTCA
Found at i:1915025 original size:40 final size:41
Alignment explanation
Indices: 1914959--1915039 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 41
1914949 AGATATGATT
* *
1914959 GATCAAGTAAAAAAGTTCCAGGTGATTCAAATGAACAAATG
1 GATCAAGTAAAAAAGTTCCAGATGATTCAAAAGAACAAATG
* *
1915000 GATCAAG-CAAAAA-TTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAGTAAAAAAGTTCC-AGATGATTCAAAAGAACAAATG
1915040 ACAAAACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 4 0.11
40 24 0.69
41 7 0.20
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.20
Consensus pattern (41 bp):
GATCAAGTAAAAAAGTTCCAGATGATTCAAAAGAACAAATG
Found at i:1921498 original size:53 final size:52
Alignment explanation
Indices: 1921405--1921534 Score: 145
Period size: 53 Copynumber: 2.4 Consensus size: 52
1921395 GAAATCTATG
* * * *
1921405 CAGAAATCACAGAAAAGGATGAACGTGTTGTCAAATGCTTTAC-AAACATCTGGC
1 CAGAAACCACAGAAAA-GATGAATGTGTTATCAAAAGCTTTACGAAA-AT-TGGC
* * *
1921459 CATAAGCCACAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATTGGG
1 CAGAAACCACAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATTGGC
*
1921511 CAGAAACCACGAGAAAGGATGAAT
1 CAGAAACCAC-AGAAAAGATGAAT
1921535 ATATTGTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
52 11 0.17
53 37 0.58
54 16 0.25
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (52 bp):
CAGAAACCACAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATTGGC
Found at i:1921946 original size:22 final size:22
Alignment explanation
Indices: 1921918--1921960 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1921908 CATTCTTCAA
1921918 AGATTCTCTCTTCAAAGATGAT
1 AGATTCTCTCTTCAAAGATGAT
*
1921940 AGATTCTCTTTTCAAAGATGA
1 AGATTCTCTCTTCAAAGATGA
1921961 AAGCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
AGATTCTCTCTTCAAAGATGAT
Found at i:1922687 original size:45 final size:45
Alignment explanation
Indices: 1922604--1922867 Score: 353
Period size: 45 Copynumber: 6.0 Consensus size: 45
1922594 CTATTTCCCA
1922604 CATCTGTAAGCCCTTCA-TGC---ATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1922645 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1922690 CATCTGTAAGCCCTTCAGTGC---ATGTTTTCAAAACTTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1922732 CATTTGTAAGCCCTTCAGTGCATGTTGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1922777 CATCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * *
1922822 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1922868 AGTTTTTTAT
Statistics
Matches: 196, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
41 17 0.09
42 42 0.21
45 126 0.64
46 4 0.02
47 7 0.04
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1922749 original size:87 final size:87
Alignment explanation
Indices: 1922604--1922857 Score: 366
Period size: 87 Copynumber: 2.9 Consensus size: 87
1922594 CTATTTCCCA
1922604 CATCTGTAAGCCCTTCA-TGCATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
1 CATCTGTAAGCCCTTCAGTGCATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
1922668 GATGTTTTCAAAACATTCGGGT
66 GATGTTTTCAAAACATTCGGGT
* * *
1922690 CATCTGTAAGCCCTTCAGTGCATGTTTTCAAAACTTTTGGGTCATTTGTAAGCCCTTCAGTGCAT
1 CATCTGTAAGCCCTTCAGTGCATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
* *
1922755 GTTGTTTTCAAAACCTTCGGGT
66 GATGTTTTCAAAACATTCGGGT
* * ** * *
1922777 CATCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGCCCTTCAGTGC---ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
1922842 CAAGATGTTTTCAAAA
63 CATGATGTTTTCAAAA
1922858 AGCCTTCGGG
Statistics
Matches: 148, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
86 17 0.11
87 84 0.57
90 47 0.32
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (87 bp):
CATCTGTAAGCCCTTCAGTGCATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
GATGTTTTCAAAACATTCGGGT
Found at i:1923224 original size:3 final size:3
Alignment explanation
Indices: 1923216--1923264 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1923206 TAATTTTTCA
* *
1923216 TAT TAT TAT TAT TAT TAT TAT TA- AAA TAT ATAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
1923260 TAT TA
1 TAT TA
1923265 AAAAAATACA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.08
3 34 0.85
4 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1923244 original size:26 final size:26
Alignment explanation
Indices: 1923215--1923267 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
1923205 TTAATTTTTC
1923215 ATAT-TATTATTATTATTATTATTAAA
1 ATATATATTA-TATTATTATTATTAAA
1923241 ATATATATTATATTATTATTATTAAA
1 ATATATATTATATTATTATTATTAAA
1923267 A
1 A
1923268 AAATACAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATATATTATATTATTATTATTAAA
Found at i:1924632 original size:8 final size:7
Alignment explanation
Indices: 1924556--1924638 Score: 50
Period size: 6 Copynumber: 11.6 Consensus size: 7
1924546 AAGTTTTTAC
1924556 TTTATAT
1 TTTATAT
1924563 TTTA-AT
1 TTTATAT
**
1924569 ACTATAGT
1 TTTATA-T
1924577 TTTA-AT
1 TTTATAT
1924583 TTTATTTAT
1 TTTA--TAT
1924592 TTTAGTCAT
1 TTTA-T-AT
1924601 TTT-TA-
1 TTTATAT
1924606 TTTATA-
1 TTTATAT
1924612 TTTATAT
1 TTTATAT
1924619 TTTATAT
1 TTTATAT
1924626 GTTTATAT
1 -TTTATAT
1924634 ATTTA
1 -TTTA
1924639 ATTATTATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
5 3 0.05
6 18 0.30
7 14 0.23
8 15 0.25
9 11 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (7 bp):
TTTATAT
Found at i:1924654 original size:23 final size:23
Alignment explanation
Indices: 1924608--1924651 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1924598 CATTTTTATT
1924608 TATATTTATATTTTATATGTTTA
1 TATATTTATATTTTATATGTTTA
1924631 TATATTTA-ATTATTAT-TGTTT
1 TATATTTATATT-TTATATGTTT
1924652 TATTATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
TATATTTATATTTTATATGTTTA
Found at i:1924886 original size:22 final size:22
Alignment explanation
Indices: 1924844--1924897 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
1924834 CTTTTTCTGA
1924844 TATTTTTAAATAAATAAATATCT
1 TATTTTT-AATAAATAAATATCT
* *
1924867 TATTTTT-ATAAAT-TATATAT
1 TATTTTTAATAAATAAATATCT
1924887 TATTATTTAAT
1 TATT-TTTAAT
1924898 TATTTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.33
21 9 0.33
22 2 0.07
23 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTTAATAAATAAATATCT
Found at i:1925023 original size:2 final size:2
Alignment explanation
Indices: 1925016--1925061 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1925006 TCTTATTTAA
1925016 AT AT AT AT AT AT AT AT A- 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
1925057 A- AT AT
1 AT AT AT
1925062 TTCTTAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1928623 original size:13 final size:13
Alignment explanation
Indices: 1928605--1928631 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1928595 TATGATTAAT
1928605 GTCTACTGGTAGC
1 GTCTACTGGTAGC
1928618 GTCTACTGGTAGC
1 GTCTACTGGTAGC
1928631 G
1 G
1928632 GTTTTAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (13 bp):
GTCTACTGGTAGC
Found at i:1936001 original size:19 final size:19
Alignment explanation
Indices: 1935977--1936085 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
1935967 TTATTTTGGA
1935977 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1935996 TTTTTCACTATCGCAACTACAC
1 TTTTTCACTATCGC-A--ACAC
*
1936018 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
1936040 ATTTTAACTCTCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
1936059 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1936078 ATTTTTCA
1 -TTTTTCA
1936086 AAATCGCGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 45 0.58
20 6 0.08
21 4 0.05
22 8 0.10
23 6 0.08
24 1 0.01
25 7 0.09
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1939171 original size:20 final size:21
Alignment explanation
Indices: 1939123--1939175 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1939113 TACTATTACG
*
1939123 GTGCTGATGTGGTAGTTCACT
1 GTGCTGACGTGGTAGTTCACT
* **
1939144 CTATTGACGTGG-AGTTCACT
1 GTGCTGACGTGGTAGTTCACT
1939164 GTGCTGACGTGG
1 GTGCTGACGTGG
1939176 CAGTCCGCGA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (21 bp):
GTGCTGACGTGGTAGTTCACT
Found at i:1940613 original size:84 final size:85
Alignment explanation
Indices: 1940387--1940659 Score: 467
Period size: 85 Copynumber: 3.2 Consensus size: 85
1940377 AATTACACCT
* *
1940387 AAAGAATCAAGAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
*
1940452 GAAAAAAGGTTAAATTCAAA
66 GAAAAAAGGTTAAATTTAAA
1940472 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1940537 GAAAAAAGGTTAAATTTAAA
66 GAAAAAAGGTTAAATTTAAA
* * *
1940557 AAAGATTAAAAAATGTTAGATCGTAAAATAAAGTAAAAATT-AATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1940621 GAAAAAAAGGTTAAATTTAAA
66 G-AAAAAAGGTTAAATTTAAA
*
1940642 AAAGGTTCAAAAATGTTA
1 AAAGATTCAAAAATGTTA
1940660 AAAGAGAAAA
Statistics
Matches: 179, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
84 24 0.13
85 155 0.87
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (85 bp):
AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
GAAAAAAGGTTAAATTTAAA
Found at i:1940742 original size:36 final size:34
Alignment explanation
Indices: 1940659--1940743 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 34
1940649 CAAAAATGTT
1940659 AAAAGAGAAAAA-AATAAAAAAGATATTAAATTTA
1 AAAAGA-AAAAATAATAAAAAAGATATTAAATTTA
*
1940693 AAAAGAAACAAAATAAGTAAAAAA-ATGTTAAATTTTGA
1 AAAAG-AA-AAAATAA-TAAAAAAGATATTAAA-TTT-A
1940731 AAAAGAAAAAATA
1 AAAAGAAAAAATA
1940744 TCAACCGAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
34 6 0.14
35 5 0.11
36 15 0.34
37 12 0.27
38 6 0.14
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.20
Consensus pattern (34 bp):
AAAAGAAAAAATAATAAAAAAGATATTAAATTTA
Found at i:1941708 original size:20 final size:20
Alignment explanation
Indices: 1941683--1941720 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1941673 ATCTTTCATA
1941683 GGGGTATCGGTACCCTCTAG
1 GGGGTATCGGTACCCTCTAG
1941703 GGGGTATCGGTACCCTCT
1 GGGGTATCGGTACCCTCT
1941721 GGGTAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCCTCTAG
Found at i:1942641 original size:21 final size:21
Alignment explanation
Indices: 1942611--1942650 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1942601 GGTTAGGTGG
* *
1942611 GAATCTATGGATGTAAACCAT
1 GAATCCATGGATGCAAACCAT
1942632 GAATCCATGGATGCAAACC
1 GAATCCATGGATGCAAACC
1942651 GTAAGTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
GAATCCATGGATGCAAACCAT
Found at i:1944407 original size:23 final size:23
Alignment explanation
Indices: 1944378--1944435 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
1944368 CCTCATGTGT
*
1944378 GGGTATCGATACCCATTCAAAGA
1 GGGTATCGATACCCATACAAAGA
*
1944401 GGGTATC-AGTACCCATACAAAGG
1 GGGTATCGA-TACCCATACAAAGA
1944424 GGGTATCGATAC
1 GGGTATCGATAC
1944436 ATAGCACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGTATCGATACCCATACAAAGA
Found at i:1945838 original size:20 final size:20
Alignment explanation
Indices: 1945813--1945850 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1945803 ATCTTTCATA
1945813 GGGGTATCGGTACCCTCTAG
1 GGGGTATCGGTACCCTCTAG
1945833 GGGGTATCGGTACCCTCT
1 GGGGTATCGGTACCCTCT
1945851 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCCTCTAG
Found at i:1947088 original size:2 final size:2
Alignment explanation
Indices: 1947083--1947407 Score: 232
Period size: 2 Copynumber: 169.5 Consensus size: 2
1947073 AAAATGATAA
* *
1947083 AT AT AT AT AT GT AT A- AT A- AA AT A- AT AT AT A- AT A- AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
1947121 A- AT AT AT A- AT AA AT A- AT AT AT AT AA AT AT AT A- AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * *
1947160 A- AT AT AT AT AT AT AT AT AT AT AC AT ACC AT AT -T AC ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
* * *
1947202 A- AT AT AT A- AT AT AT AA AT AT ACT AT AT CAT AT AT A- AC GT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT
*
1947243 AA AT AT AT A- AT AT AT AT AT AT AT AT AT AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
1947284 AT AT AT AT AT AT AT AC ACT AT AT A- AT AT A- AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
1947325 A- AT CAT AT A- AT AT GT AT AT AT -T AT AT A- AT AT AT AT AA AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1947364 AT ACT AT AG AT AT A- AT AT AT A- AT AT AT A- AT AT AT AT ACT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
1947405 AT A
1 AT A
1947408 AAAAAGGTTG
Statistics
Matches: 257, Mismatches: 30, Indels: 72
0.72 0.08 0.20
Matches are distributed among these distances:
1 25 0.10
2 213 0.83
3 19 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1947102 original size:30 final size:29
Alignment explanation
Indices: 1947068--1947181 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
1947058 GGACCTAAAC
1947068 ATAAAAAAATGATAAATATATATATGTATA
1 ATAAAAAAAT-ATAAATATATATATGTATA
* *
1947098 ATAAAATAATATATAATA-ATAGTAATATATA
1 ATAAAAAAATATA-AATATATA-T-ATGTATA
1947129 ATAAATAATATATATAAATATATA-ATGATATA
1 ATAAA-AA-A-ATATAAATATATATATG-TATA
* * * *
1947161 ATATATATATATATATATATA
1 ATAAAAAAATATAAATATATA
1947182 CATACCATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
29 18 0.26
30 14 0.21
31 14 0.21
32 9 0.13
33 5 0.07
34 8 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
ATAAAAAAATATAAATATATATATGTATA
Found at i:1947109 original size:23 final size:24
Alignment explanation
Indices: 1947082--1947412 Score: 126
Period size: 27 Copynumber: 13.0 Consensus size: 24
1947072 AAAAATGATA
*
1947082 AATATATAT-ATGTATAATAAAAT
1 AATATATATAATATATAATAAAAT
1947105 AATATATAATAATAGTAATATATAATAAAT
1 AATATAT-ATAATA-T-ATA-AT-A-AAAT
* *
1947135 AATATATATAAATATATAATGATAT
1 AATATATAT-AATATATAATAAAAT
*
1947160 AATATATAT-ATATATATATATACAT
1 AATATATATAATATATA-ATA-AAAT
* *
1947185 ACCATAT-TACACTATATAATATATAAT
1 A--ATATATATAATATATAATA-A-AAT
* * * *
1947212 ATATAAATATACTATATCAT-ATAT
1 A-ATATATATAATATATAATAAAAT
** *
1947236 AACGTATA-AATATATAAT-ATAT
1 AATATATATAATATATAATAAAAT
*
1947258 -ATATATAT-ATATATACTATATAAT
1 AATATATATAATATATA--ATAAAAT
*
1947282 -ATATATATATATATATACACT-ATAT
1 AATATATATA-ATATATA-A-TAAAAT
* *
1947307 AATATAATATAAATATATAATCATAT
1 AATAT-ATAT-AATATATAATAAAAT
* *
1947333 AATATGTATATATTATATAATATATAT
1 AATA--TATATAATATATAATA-AAAT
1947360 AAATATACTATAGATATAATATATAATATAT
1 -AATATA-TATA-ATAT-ATA-ATAA-A-AT
*
1947391 AATATATATACTATATAA-AAAA
1 AATATATATAATATATAATAAAA
1947413 GGTTGGACGA
Statistics
Matches: 242, Mismatches: 30, Indels: 72
0.70 0.09 0.21
Matches are distributed among these distances:
21 12 0.05
22 12 0.05
23 21 0.09
24 18 0.07
25 25 0.10
26 44 0.18
27 55 0.23
28 17 0.07
29 12 0.05
30 24 0.10
31 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATATATAATATATAATAAAAT
Found at i:1947201 original size:74 final size:71
Alignment explanation
Indices: 1947079--1947398 Score: 210
Period size: 65 Copynumber: 4.5 Consensus size: 71
1947069 TAAAAAAATG
* * * * *
1947079 ATAAATATATATATGTATAATAAAATAATATATAATAATAGTA-ATATATAATA-AATA-AT-AT
1 ATAAATATATA-ATATATAAT-ATAT-ATATATAAT-ATA-TACATACATATTATACTATATAAT
1947140 ATATAA-ATAT
61 ATATAATATAT
* *
1947150 AT-AATGATATAATATAT-ATATATATATAT-ATACATAC---CATATTACACTATATAATATAT
1 ATAAAT-ATATAATATATAATATATATATATAATATATACATACATATTATACTATATAATATAT
1947209 AATATAT
65 AATATAT
* * *
1947216 A-AATATACTATATCATATATAACGTATAAATATATAATATATATATATATATATATACTATATA
1 ATAA-ATA-TATA--ATATATAA--TATATATATATAATATATACATACATAT-TATACTATATA
1947280 ATATAT-ATATAT
59 ATATATAATATAT
* * * * *
1947292 AT--ATATACACTATATAATATA-ATATA-AATATATA-AT-CATATAATATGTATATATTATAT
1 ATAAATATATAATATATAATATATATATATAATATATACATACATATTATA-CTATATAATATAT
1947351 AATATAT
65 AATATAT
*
1947358 ATAAATATACTATAGATATAATATATAATATATAATATATA
1 ATAAATATA-TA-ATATATAATATAT-ATATATAATATATA
1947399 TACTATATAA
Statistics
Matches: 200, Mismatches: 20, Indels: 56
0.72 0.07 0.20
Matches are distributed among these distances:
62 5 0.03
63 3 0.01
64 7 0.04
65 25 0.12
66 19 0.09
67 20 0.10
68 13 0.06
69 13 0.06
70 19 0.09
71 14 0.07
72 15 0.08
73 17 0.09
74 3 0.01
76 11 0.05
77 16 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (71 bp):
ATAAATATATAATATATAATATATATATATAATATATACATACATATTATACTATATAATATATA
ATATAT
Found at i:1947360 original size:144 final size:140
Alignment explanation
Indices: 1947085--1947407 Score: 340
Period size: 144 Copynumber: 2.2 Consensus size: 140
1947075 AATGATAAAT
* *
1947085 ATATATATGTATAATAAAATAATATATA-ATAATAGTAATATATAATAAATAATATATATAAATA
1 ATATA-ATATATAAT-ATATAATATATATAT-ATA-T-ATATATAATAAATAATATATATAAATA
* *
1947149 TATAATGATATAATATATATATATATATATATACATACCATATTACACTATATAATATATAATAT
61 TATAATGATATAATATATATAAATATATATATACATACAATATTACACTATATAATATATAATAT
*
1947214 ATAAATATACTATATC
126 ATAAATATACTATA-G
* *
1947230 ATAT-ATAACGTATAAATATATAATATATATATATATATATATACTATATAATATATATATATAT
1 ATATAAT-A--TAT-AATATATAATATATATATATATATATATAATAAATAATATATATA-A-AT
* *
1947294 ATATACACT-ATATAATATAATATAAATATATA-AT-CATATAATATGT--A-TATATTATATA-
60 ATATA-A-TGATATAATAT-ATATAAATATATATATACATACAATAT-TACACTATATAATATAT
1947352 ATATATATAAATATACTATAG
121 A-ATATATAAATATACTATAG
1947373 ATATAATATATAATATATAATATATATACTATATA
1 ATATAATATATAATATATAATATATATA-TATATA
1947408 AAAAAGGTTG
Statistics
Matches: 155, Mismatches: 9, Indels: 32
0.79 0.05 0.16
Matches are distributed among these distances:
140 17 0.11
141 9 0.06
143 8 0.05
144 51 0.33
145 7 0.05
146 32 0.21
147 18 0.12
148 13 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (140 bp):
ATATAATATATAATATATAATATATATATATATATATATAATAAATAATATATATAAATATATAA
TGATATAATATATATAAATATATATATACATACAATATTACACTATATAATATATAATATATAAA
TATACTATAG
Found at i:1947407 original size:74 final size:71
Alignment explanation
Indices: 1947087--1947408 Score: 274
Period size: 72 Copynumber: 4.5 Consensus size: 71
1947077 TGATAAATAT
* *
1947087 ATATATGTATA-ATA-AAATA-ATATATA-ATAATAGTAATATATAATAAATAATATATATAAAT
1 ATATATATATACATATAAATATATATATATATAATA-T-ATATATAATATATAATATATATAAAT
1947148 ATATA-ATG
64 ATATATA-G
* * * * * *
1947156 ATATAATATATATATATATATATATACATACCATATTACACTATATAATATAT-A-ATATATAAA
1 ATAT-ATATATACATATAAATATATATATA-TATAATATA-TATATAATATATAATATATATAAA
1947219 TATACTAT--
63 TATA-TATAG
* * *
1947227 ATCATATATA-ACGTATAAATATATAATATATATATATATATATATACTATATAATATATATATA
1 AT-ATATATATACATATAAATATAT-ATATATATA-ATATATATATAATATATAATATATATAAA
*
1947291 TATATATAC
63 TATATATAG
* *
1947300 ACTATATAATATA-ATATAAATATATA-ATCATATAATATGTATATATTATATAATATATATAAA
1 A-TATAT-ATATACATATAAATATATATAT-ATATAATATATATATAATATATAATATATATAAA
1947363 TATACTATAG
63 TATA-TATAG
1947373 ATATAATATATA-ATATATAATATATATACTATATAA
1 ATAT-ATATATACATATA-AATATATATA-TATATAA
1947409 AAAAGGTTGG
Statistics
Matches: 208, Mismatches: 20, Indels: 45
0.76 0.07 0.16
Matches are distributed among these distances:
69 4 0.02
70 31 0.15
71 21 0.10
72 76 0.37
73 36 0.17
74 33 0.16
75 7 0.03
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (71 bp):
ATATATATATACATATAAATATATATATATATAATATATATATAATATATAATATATATAAATAT
ATATAG
Found at i:1956962 original size:21 final size:24
Alignment explanation
Indices: 1956936--1956980 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1956926 CCCCCCCCCC
1956936 TTTTC-TTT-TACTTTCTC-CTTT
1 TTTTCTTTTGTACTTTCTCTCTTT
1956957 TTTTCTTTTGTACTTTCTCTCTTT
1 TTTTCTTTTGTACTTTCTCTCTTT
1956981 CCAACATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 9 0.43
24 4 0.19
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTCTTTTGTACTTTCTCTCTTT
Done.