Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_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: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1544221 original size:52 final size:51
Alignment explanation
Indices: 1544128--1544243 Score: 187
Period size: 52 Copynumber: 2.3 Consensus size: 51
1544118 GCAACGAGAG
1544128 AATCGCAATGCGAAATGAAATCGCAACAAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCGCAACAAGAGAATCGCAATGCGAAATGAA
* * *
1544179 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATG-AAATCGCAACAAGAGAATCGCAATGCGAAATGAA
*
1544231 AATCGCATTGCGA
1 AATCGCAATGCGA
1544244 TTCTCCCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 17 0.28
52 43 0.72
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (51 bp):
AATCGCAATGCGAAATGAAATCGCAACAAGAGAATCGCAATGCGAAATGAA
Found at i:1544282 original size:19 final size:19
Alignment explanation
Indices: 1544250--1544328 Score: 100
Period size: 19 Copynumber: 4.5 Consensus size: 19
1544240 GCGATTCTCC
1544250 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
1544270 CATTGCG-TTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1544288 CATTGCGA--TTC--TTCG
1 CATTGCGATTTTCATTTCG
1544303 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1544320 CATTGCGAT
1 CATTGCGAT
1544329 AGTCAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.12
15 7 0.13
17 7 0.13
18 9 0.17
19 16 0.31
20 7 0.13
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1544452 original size:14 final size:14
Alignment explanation
Indices: 1544433--1544469 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1544423 CATCAATTAC
1544433 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1544447 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1544461 ACAAATCAA
1 ACAAATCAA
1544470 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:1546417 original size:19 final size:19
Alignment explanation
Indices: 1546377--1546492 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
1546367 TAGTTTACTT
* *
1546377 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
1546397 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1546416 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1546430 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1546449 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1546463 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1546482 TCGCAATGCGA
1 TCGCAACGCGA
1546493 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1546433 original size:14 final size:14
Alignment explanation
Indices: 1546414--1546470 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1546404 GCGAAATGAA
*
1546414 AATCGCAACGACAG
1 AATCGCAACGAAAG
1546428 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1546445 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1546461 AATCGCAACG
1 AATCGCAACG
1546471 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1546441 original size:33 final size:33
Alignment explanation
Indices: 1546395--1546487 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1546385 CGAAACTTAA
*
1546395 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1546428 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1546461 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1546488 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1546510 original size:19 final size:19
Alignment explanation
Indices: 1546488--1546616 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1546478 AAAATCGCAA
1546488 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1546507 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1546521 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1546540 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1546554 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1546573 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1546592 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1546612 TGCGA
1 TGCGA
1546617 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1546530 original size:33 final size:33
Alignment explanation
Indices: 1546488--1546579 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1546478 AAAATCGCAA
1546488 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1546521 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1546554 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1546580 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1546966 original size:93 final size:93
Alignment explanation
Indices: 1546660--1547125 Score: 858
Period size: 90 Copynumber: 5.1 Consensus size: 93
1546650 TTGAATGGAT
1546660 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--AC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546723 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1546751 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTATAG-ATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546814 AGTTTAGCAGAATTGGCAGCAACC-AAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1546841 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546906 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1546934 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT--A-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546996 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1547024 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1547089 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1547117 AAATTTACT
1 AAATTTACT
1547126 AAGCAATCTA
Statistics
Matches: 364, Mismatches: 3, Indels: 14
0.96 0.01 0.04
Matches are distributed among these distances:
89 2 0.01
90 148 0.41
91 83 0.23
92 31 0.09
93 100 0.27
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1546967 original size:183 final size:183
Alignment explanation
Indices: 1546660--1547125 Score: 877
Period size: 183 Copynumber: 2.6 Consensus size: 183
1546650 TTGAATGGAT
1546660 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--AC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546723 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1546787 TACTATTTCACAGTGTTATAGATACACAGTTTAGCAGAATTGGCAGCAACC-AAC
131 TACTATTTCACAGTGTTA-A-ATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1546841 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1546906 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1546971 TACTATTTCACAGTGTTAAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1547024 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1547089 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1547126 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
181 61 0.22
182 30 0.11
183 169 0.60
184 20 0.07
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (183 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1548854 original size:33 final size:33
Alignment explanation
Indices: 1548809--1548922 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
1548799 TCTTTTGGTT
1548809 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1548842 GAGATGACAATCGCAACGAGAG-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1548874 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1548907 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1548923 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.41
33 45 0.59
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1548855 original size:19 final size:18
Alignment explanation
Indices: 1548816--1548927 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
1548806 GTTGAAATGA
1548816 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1548831 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1548848 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1548864 --ATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1548880 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1548896 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1548913 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1548928 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 4, Indels: 28
0.71 0.04 0.26
Matches are distributed among these distances:
13 7 0.09
14 16 0.21
15 4 0.05
16 12 0.16
17 11 0.14
19 27 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1548958 original size:14 final size:14
Alignment explanation
Indices: 1548939--1548992 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1548929 TTTGGTTTCG
1548939 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1548953 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1548972 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1548986 CGTTGCG
1 CGTTGCG
1548993 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1548971 original size:33 final size:33
Alignment explanation
Indices: 1548923--1549039 Score: 144
Period size: 33 Copynumber: 3.4 Consensus size: 33
1548913 AAAATCGCAA
**
1548923 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1548956 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* * * *
1548989 TGCGCTTTTCATTTCTCTTTGCGACAGTCATTCTCGT
1 TGCGATTTTCATTTCGCGTTGCG--ATTC--TCTCGT
1549026 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1549040 ATCTCGTTGC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
33 51 0.70
35 3 0.04
37 19 0.26
ACGTcount: A:0.09, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1548977 original size:19 final size:19
Alignment explanation
Indices: 1548950--1549051 Score: 90
Period size: 19 Copynumber: 5.6 Consensus size: 19
1548940 GTTGCGATTC
1548950 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
1548969 TCGCGTTGCGA--TTC---
1 TCTCGTTGCGATTTTCATT
*
1548983 TCTCGTTGCGCTTTTCATT
1 TCTCGTTGCGATTTTCATT
* ***
1549002 TCTCTTTGCGACAGTCA-T
1 TCTCGTTGCGATTTTCATT
1549020 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCA-TT
1549040 ATCTCGTTGCGA
1 -TCTCGTTGCGA
1549052 CTCTTCTGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
14 9 0.14
16 3 0.05
17 3 0.05
18 14 0.22
19 22 0.35
20 1 0.02
21 11 0.17
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:1549006 original size:21 final size:21
Alignment explanation
Indices: 1548980--1549050 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1548970 CGCGTTGCGA
1548980 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGCTTTTCAT
**
1549001 TTCTCT--TTGCGAC-AGTCA-
1 TTCTCTCGTTGCG-CTTTTCAT
*
1549019 -T-TCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGCTTTTCAT
*
1549038 TTATCTCGTTGCG
1 TTCTCTCGTTGCG
1549051 ACTCTTCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
16 3 0.08
17 1 0.03
18 8 0.21
19 8 0.21
20 2 0.05
21 16 0.42
ACGTcount: A:0.10, C:0.25, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGCTTTTCAT
Found at i:1549178 original size:33 final size:33
Alignment explanation
Indices: 1549131--1549201 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1549121 AATACTAACT
* *
1549131 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1549164 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1549197 TGAAA
1 TGAAA
1549202 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1549435 original size:22 final size:22
Alignment explanation
Indices: 1549383--1549437 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1549373 TGGTTGTGAG
**
1549383 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1549405 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1549427 GGATTTCTTCG
1 GGATTTCTTCG
1549438 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1549603 original size:39 final size:40
Alignment explanation
Indices: 1549560--1549641 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
1549550 TACGCGTAGC
*
1549560 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
1549599 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
1549639 GAT
1 GAT
1549642 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:1549776 original size:20 final size:20
Alignment explanation
Indices: 1549583--1549775 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
1549573 CTTTAAATAT
1549583 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
1549604 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
1549623 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1549643 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1549663 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1549683 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1549703 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1549723 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1549743 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1549763 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1549776 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1549792 original size:21 final size:21
Alignment explanation
Indices: 1549762--1549844 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1549752 ATTTTCATAT
*
1549762 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1549783 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1549804 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1549825 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1549845 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1549835 original size:42 final size:43
Alignment explanation
Indices: 1549742--1549840 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1549732 ATTTATGTGT
* *
1549742 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1549783 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1549825 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1549841 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1559340 original size:60 final size:60
Alignment explanation
Indices: 1559247--1559371 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
1559237 AGCACACAAT
* * *
1559247 TGGTCCCTCGACTATAGGATATGGCTTTATTGAGTCCCTTGACTATTAGATGTTACAAAA
1 TGGTCCCCCGACTATAGGATATGGCTTTATTGAGTCCCTCGACTATTAAATGTTACAAAA
*
1559307 TGGTCCCCCGACTATAAGGAGT-T-GCTTTGTTGAGTCCCTCGACTATTAAATGTTACAAAA
1 TGGTCCCCCGACTAT-AGGA-TATGGCTTTATTGAGTCCCTCGACTATTAAATGTTACAAAA
1559367 TGGTC
1 TGGTC
1559372 ACTCGGCTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 53 0.90
61 5 0.08
62 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (60 bp):
TGGTCCCCCGACTATAGGATATGGCTTTATTGAGTCCCTCGACTATTAAATGTTACAAAA
Found at i:1560103 original size:16 final size:17
Alignment explanation
Indices: 1560053--1560104 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1560043 ATAAAAAATA
1560053 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1560070 TA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
1560085 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1560101 AATT
1 AATT
1560105 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1561657 original size:35 final size:34
Alignment explanation
Indices: 1561618--1561729 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
1561608 AAAATAGTCC
*
1561618 TCAATTTCATTCTAAACCTCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
1561653 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
** * *
1561688 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
1561723 TCAATTT
1 TCAATTT
1561730 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1563398 original size:35 final size:34
Alignment explanation
Indices: 1563352--1563460 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 34
1563342 AAGAAAGTAT
* **
1563352 TTGAAGTATTTTAGAATTTGGGGTTTAGAATTTAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
1563387 TTGAATTATTTTGGAATTTAGGGTTTAGAGTGAAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
1563422 TTGACATACTTTGGAATTTGAGGTTTAGAATGAAA
1 TTGA-ATATTTTGGAATTTGGGGTTTAGAATGAAA
1563457 TTGA
1 TTGA
1563461 GGACTGTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 62 0.98
36 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGAATATTTTGGAATTTGGGGTTTAGAATGAAA
Found at i:1563858 original size:126 final size:126
Alignment explanation
Indices: 1563633--1563886 Score: 508
Period size: 126 Copynumber: 2.0 Consensus size: 126
1563623 AAATTGGGGA
1563633 CCTAAATACAAACTTCAAAAATATTCAGTGACCATTACTATACTTTACCCTATTTTTTATTATTG
1 CCTAAATACAAACTTCAAAAATATTCAGTGACCATTACTATACTTTACCCTATTTTTTATTATTG
1563698 ATCGTTTACGATATTAATGTAACGGTTCATAGTGCTAATGTAATAATACTAACGTGACGAT
66 ATCGTTTACGATATTAATGTAACGGTTCATAGTGCTAATGTAATAATACTAACGTGACGAT
1563759 CCTAAATACAAACTTCAAAAATATTCAGTGACCATTACTATACTTTACCCTATTTTTTATTATTG
1 CCTAAATACAAACTTCAAAAATATTCAGTGACCATTACTATACTTTACCCTATTTTTTATTATTG
1563824 ATCGTTTACGATATTAATGTAACGGTTCATAGTGCTAATGTAATAATACTAACGTGACGAT
66 ATCGTTTACGATATTAATGTAACGGTTCATAGTGCTAATGTAATAATACTAACGTGACGAT
1563885 CC
1 CC
1563887 ACAATAATTG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 128 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (126 bp):
CCTAAATACAAACTTCAAAAATATTCAGTGACCATTACTATACTTTACCCTATTTTTTATTATTG
ATCGTTTACGATATTAATGTAACGGTTCATAGTGCTAATGTAATAATACTAACGTGACGAT
Found at i:1564458 original size:30 final size:30
Alignment explanation
Indices: 1564424--1564665 Score: 194
Period size: 30 Copynumber: 8.0 Consensus size: 30
1564414 ATTAAAAAAG
* *
1564424 TAAGATAACAATAACATATATTTTTTAAAT
1 TAAGATAAAAATAAAATATATTTTTTAAAT
** *
1564454 TAAGATAAAAAT---ATATATTTAATAATT
1 TAAGATAAAAATAAAATATATTTTTTAAAT
1564481 TAAGATAAAAATAAAATATA--TTTTAAATT
1 TAAGATAAAAATAAAATATATTTTTTAAA-T
* *
1564510 TGAGATCTATTAAAATAAAGA-ATTTTTTTTAAAAGT
1 TAAGA--TA--AAAATAAA-ATATATTTTTT-AAA-T
* *
1564546 TAAGATAAAAATAAAATATATTATTTAAGT
1 TAAGATAAAAATAAAATATATTTTTTAAAT
* *
1564576 TAAGATAAAACTAAAATATATTTTTTTAAGT
1 TAAGATAAAAATAAAATATA-TTTTTTAAAT
* * * *
1564607 TAAAATAAAAATAATATATA-TATTTAAGT
1 TAAGATAAAAATAAAATATATTTTTTAAAT
1564636 TAA-ATATAAATATAAAATATATTTTTTAAA
1 TAAGATA-AAA-ATAAAATATATTTTTTAAA
1564666 AATTAATAAG
Statistics
Matches: 172, Mismatches: 23, Indels: 33
0.75 0.10 0.14
Matches are distributed among these distances:
27 24 0.14
28 7 0.04
29 19 0.11
30 45 0.26
31 37 0.22
32 15 0.09
33 10 0.06
34 3 0.02
35 4 0.02
36 8 0.05
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAGATAAAAATAAAATATATTTTTTAAAT
Found at i:1564467 original size:25 final size:27
Alignment explanation
Indices: 1564439--1564493 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1564429 TAACAATAAC
**
1564439 ATATATTTTTTAAATTAAGATAAAAAT
1 ATATATTTAATAAATTAAGATAAAAAT
*
1564466 ATATATTTAATAATTTAAGATAAAAAT
1 ATATATTTAATAAATTAAGATAAAAAT
1564493 A
1 A
1564494 AAATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
ATATATTTAATAAATTAAGATAAAAAT
Found at i:1564555 original size:31 final size:29
Alignment explanation
Indices: 1564520--1564664 Score: 123
Period size: 31 Copynumber: 4.8 Consensus size: 29
1564510 TGAGATCTAT
1564520 TAAAATAAAGA-ATTTTTTTTAAAAGTTAAGA
1 TAAAATAAA-ATATTTTTTTT--AAGTTAAGA
* *
1564551 TAAAAATAAAATATATTATTTAAGTTAAGA
1 T-AAAATAAAATATTTTTTTTAAGTTAAGA
*
1564581 TAAAACTAAAATATATTTTTTTAAGTTAAAA
1 TAAAA-TAAAATAT-TTTTTTTAAGTTAAGA
* * * *
1564612 TAAAA-ATAATATATATATTTAAGTTAAATA
1 TAAAATAAAATAT-TTTTTTTAAGTT-AAGA
*
1564642 TAAATATAAAATATATTTTTTAA
1 TAAA-ATAAAATATTTTTTTTAA
1564665 AAATTAATAA
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
29 21 0.22
30 25 0.27
31 27 0.29
32 21 0.22
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAAATAAAATATTTTTTTTAAGTTAAGA
Found at i:1564674 original size:60 final size:61
Alignment explanation
Indices: 1564419--1564671 Score: 197
Period size: 61 Copynumber: 4.1 Consensus size: 61
1564409 TAAAAATTAA
* * * *
1564419 AAAAG-TAAGATAACAATAACATATATTTTTTAAATTAAGATAAAAAT---ATATA---TTT
1 AAAAGTTAA-ATAAAAATAAAATATATTATTTAAGTTAAGATAAAAATAAAATATATTTTTT
* * * * *
1564474 AATAATTTAAGATAAAAATAAAATATATT-TTAAATTTGAGATCTATTAAAATAAAGA-ATTTTT
1 AA-AAGTTAA-ATAAAAATAAAATATATTATTTAAGTTAAGA--TA--AAAATAAA-ATATATTT
1564537 TTT
59 TTT
*
1564540 AAAAGTTAAGATAAAAATAAAATATATTATTTAAGTTAAGATAAAACTAAAATATATTTTTT
1 AAAAGTTAA-ATAAAAATAAAATATATTATTTAAGTTAAGATAAAAATAAAATATATTTTTT
* *
1564602 -TAAGTTAAAATAAAAATAATATATA-TATTTAAGTTAA-ATATAAATATAAAATATATTTTTT
1 AAAAGTT-AAATAAAAATAAAATATATTATTTAAGTTAAGATA-AAA-ATAAAATATATTTTTT
*
1564663 AAAAATTAA
1 AAAAGTTAA
1564672 TAAGTGAAAT
Statistics
Matches: 161, Mismatches: 18, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
55 2 0.01
56 11 0.07
57 20 0.12
58 2 0.01
59 3 0.02
60 20 0.12
61 38 0.24
62 21 0.13
63 2 0.01
64 3 0.02
65 25 0.16
66 14 0.09
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (61 bp):
AAAAGTTAAATAAAAATAAAATATATTATTTAAGTTAAGATAAAAATAAAATATATTTTTT
Found at i:1565394 original size:22 final size:19
Alignment explanation
Indices: 1565354--1565409 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
1565344 AAAATTAAAT
*
1565354 TACTAAAAAATAAATATAC
1 TACTAAAAAATAAAAATAC
*
1565373 ATATTAAAAATATTAAAAATAC
1 -TACTAAAAA-A-TAAAAATAC
*
1565395 TACTAAAAACTAAAA
1 TACTAAAAAATAAAA
1565410 GAAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.17
20 8 0.27
21 9 0.30
22 8 0.27
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TACTAAAAAATAAAAATAC
Found at i:1569469 original size:18 final size:19
Alignment explanation
Indices: 1569438--1569477 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1569428 GTGTATCTTT
1569438 AAAAGATGGCTTAATATAA
1 AAAAGATGGCTTAATATAA
* *
1569457 AAAAG-TGGTTTAATGTAA
1 AAAAGATGGCTTAATATAA
1569475 AAA
1 AAA
1569478 CAGGTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (19 bp):
AAAAGATGGCTTAATATAA
Found at i:1571188 original size:19 final size:19
Alignment explanation
Indices: 1571164--1571201 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1571154 CTAGTCAACG
1571164 GGAAGTGTTGAGCATTACT
1 GGAAGTGTTGAGCATTACT
1571183 GGAAGTGTTGAGCATTACT
1 GGAAGTGTTGAGCATTACT
1571202 CAATTAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (19 bp):
GGAAGTGTTGAGCATTACT
Found at i:1577117 original size:3 final size:3
Alignment explanation
Indices: 1577109--1577134 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1577099 ACACTTGATT
1577109 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1577135 TTGTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1577910 original size:22 final size:22
Alignment explanation
Indices: 1577898--1577956 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
1577888 TTTTACTAAC
1577898 TTTTATTTATATTTGTTATCTA
1 TTTTATTTATATTTGTTATCTA
*
1577920 TTTTATTTAT-TTTATTAT-TA
1 TTTTATTTATATTTGTTATCTA
1577940 TTATTATATTAATATTT
1 TT-TTAT-TT-ATATTT
1577957 TTTCTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 11 0.34
22 12 0.38
23 2 0.06
24 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTTATATTTGTTATCTA
Found at i:1577988 original size:17 final size:17
Alignment explanation
Indices: 1577925--1577989 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
1577915 ATCTATTTTA
1577925 TTTATTTTAT-TATTATT
1 TTTATTTTATAT-TTATT
* *
1577942 ATTATATTAATATTT-TT
1 TTTAT-TTTATATTTATT
* *
1577959 TCTTGTTTCATATTTATT
1 T-TTATTTTATATTTATT
1577977 TTTATTTTATATT
1 TTTATTTTATATT
1577990 CTAACATCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 24 0.65
18 12 0.32
19 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTTATATTTATT
Found at i:1581708 original size:43 final size:43
Alignment explanation
Indices: 1581651--1581733 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
1581641 AACTCACTGC
* *
1581651 TTGTGCTAGTATTGCTCTTAAATTGC-GTAGGTGATATTGTGCT
1 TTGTGCCAGTATTGCTCTTAAATTGCAAT-GGTGATATTGTGCT
*
1581694 TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGT
1 TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGT
1581734 TGAAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (43 bp):
TTGTGCCAGTATTGCTCTTAAATTGCAATGGTGATATTGTGCT
Found at i:1583157 original size:12 final size:12
Alignment explanation
Indices: 1583124--1583157 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1583114 TCGTTTCAAG
1583124 TCCCCGTATCCA
1 TCCCCGTATCCA
*
1583136 TCCCCATATCCA
1 TCCCCGTATCCA
*
1583148 TCCCTGTATC
1 TCCCCGTATC
1583158 AGTATCAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.06, T:0.29
Consensus pattern (12 bp):
TCCCCGTATCCA
Found at i:1584209 original size:2 final size:2
Alignment explanation
Indices: 1584202--1584227 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1584192 AAATAACTGA
1584202 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
1584228 TATCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1584722 original size:32 final size:32
Alignment explanation
Indices: 1584686--1584749 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1584676 CTTTATCTCC
*
1584686 TCAACTATAAATCATTGTCCCGTTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
* *
1584718 TCAACTATAAATCATTGTTCTATTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
1584750 ATCGTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (32 bp):
TCAACTATAAATCATTGTCCCATTTATTCCAA
Found at i:1589313 original size:17 final size:18
Alignment explanation
Indices: 1589291--1589337 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1589281 TATGAAATTG
*
1589291 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1589308 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1589326 GATTCCAATTCC
1 GATTCCAATTCC
1589338 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1592862 original size:19 final size:19
Alignment explanation
Indices: 1592811--1592867 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
1592801 TATTTTAGCA
* *
1592811 TAAATAATTTATTAATAGT
1 TAAATATTTTATTTATAGT
*
1592830 CAAATATTTTATTTATAGT
1 TAAATATTTTATTTATAGT
*
1592849 TAAATATTTTATTTTTAGT
1 TAAATATTTTATTTATAGT
1592868 GTTTAGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (19 bp):
TAAATATTTTATTTATAGT
Found at i:1593480 original size:26 final size:26
Alignment explanation
Indices: 1593451--1593504 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
1593441 TATAAACAGT
* * *
1593451 TAATCGAATCAGTTTCTCAAATTAGC
1 TAATCAAATCAGTTGCTCAAACTAGC
* *
1593477 TAATTAAATCAGTTGGTCAAACTAGC
1 TAATCAAATCAGTTGCTCAAACTAGC
1593503 TA
1 TA
1593505 CTGTAATCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (26 bp):
TAATCAAATCAGTTGCTCAAACTAGC
Found at i:1594207 original size:35 final size:35
Alignment explanation
Indices: 1594161--1594272 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
1594151 AAAACATTCC
*
1594161 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1594196 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1594231 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1594266 TCAATTT
1 TCAATTT
1594273 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1595375 original size:35 final size:34
Alignment explanation
Indices: 1595326--1595438 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1595316 AAAAAAGGCA
*
1595326 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
*
1595361 GTAATTGAATTATTTTAGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* *
1595396 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
1595431 GAAATTGA
1 GAAATTGA
1595439 GGATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:1596207 original size:20 final size:21
Alignment explanation
Indices: 1596182--1596233 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1596172 TTTTCCCAAT
*
1596182 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1596202 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1596223 TCGCAATGCGA
1 TCGCAATGCGA
1596234 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1596247 original size:20 final size:20
Alignment explanation
Indices: 1596222--1596376 Score: 152
Period size: 20 Copynumber: 7.7 Consensus size: 20
1596212 AATTGGGAAA
1596222 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1596242 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1596262 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1596282 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
1596303 ATCGCAACGAGATATTGACT
1 ATCGCAATGCGATACTGACT
* * *
1596323 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1596343 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1596363 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1596377 TTTCAAAGCG
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.03
20 85 0.74
21 24 0.21
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1596307 original size:61 final size:61
Alignment explanation
Indices: 1596242--1596376 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
1596232 GATACTGACT
* * *
1596242 ATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
* * * * * * *
1596303 ATCGCAACGAGATATTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
1596364 ATCGCAATGCGAT
1 ATCGCAATGCGAT
1596377 TTTCAAAGCG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1596902 original size:20 final size:20
Alignment explanation
Indices: 1596849--1596906 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1596839 TGCGATTCTC
**
1596849 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCATTTTCGT
1596869 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1596889 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1596907 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1597097 original size:25 final size:24
Alignment explanation
Indices: 1597043--1597097 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1597033 TGTTTATTAT
* *
1597043 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1597067 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1597093 TGTTT
1 TGTTT
1597098 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1598247 original size:18 final size:18
Alignment explanation
Indices: 1598226--1598270 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1598216 TCCACTTCGG
*
1598226 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1598244 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1598262 GAGCCATCA
1 GAGCCATCA
1598271 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1598804 original size:14 final size:14
Alignment explanation
Indices: 1598785--1598881 Score: 95
Period size: 14 Copynumber: 6.4 Consensus size: 14
1598775 CAACGCGGAA
1598785 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
1598799 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
1598813 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
1598831 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
1598845 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
*
1598863 ATTTTGTCGTTACG
1 ATTTTGTCGTTGCG
1598877 ATTTT
1 ATTTT
1598882 CATTTCGCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
14 36 0.51
16 16 0.23
18 18 0.26
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:1598830 original size:32 final size:32
Alignment explanation
Indices: 1598794--1598897 Score: 190
Period size: 32 Copynumber: 3.2 Consensus size: 32
1598784 AATTTTGTCG
1598794 TTGCGATTTTGTCGTTGCGATTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTCATTTCGCA
1598826 TTGCGATTTTGTCGTTGCGATTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTCATTTCGCA
*
1598858 TTGCGATTTTGTCGTTACGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGA-TTTCATTTCGCA
1598891 TTGCGAT
1 TTGCGAT
1598898 ATCCATTTCC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 51 0.73
33 19 0.27
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTGTCGTTGCGATTTCATTTCGCA
Found at i:1598916 original size:20 final size:19
Alignment explanation
Indices: 1598881--1598937 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
1598871 GTTACGATTT
1598881 TCATTTCGCATTGCGATA-
1 TCATTTCGCATTGCGATAG
*
1598899 TCCATTTCCGCGTTGCGATAG
1 T-CATTT-CGCATTGCGATAG
1598920 TCATTTTCGCATTGCGAT
1 TCA-TTTCGCATTGCGAT
1598938 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 5 0.15
20 23 0.70
21 4 0.12
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1600826 original size:14 final size:14
Alignment explanation
Indices: 1600807--1600842 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1600797 ATTGTTTAAT
1600807 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1600821 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1600835 TGATTTGT
1 TGATTTGT
1600843 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1601003 original size:19 final size:19
Alignment explanation
Indices: 1600979--1601046 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1600969 ATCGCAACGA
1600979 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1600998 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1601017 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1601031 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1601047 TTTTCATTTC
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:1601110 original size:20 final size:20
Alignment explanation
Indices: 1601087--1601140 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1601077 CGATAGCCAT
*
1601087 TTTCGCGTTGCGATTTTTCA
1 TTTCGAGTTGCGATTTTTCA
*
1601107 TTTCGAATTGCGATTTTTCA
1 TTTCGAGTTGCGATTTTTCA
1601127 TTTCGAGTTGCGAT
1 TTTCGAGTTGCGAT
1601141 AGTCAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTCGAGTTGCGATTTTTCA
Found at i:1602218 original size:24 final size:24
Alignment explanation
Indices: 1602191--1602244 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1602181 GTATTCGAAA
*
1602191 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1602215 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1602239 TTTGAT
1 TTTGAT
1602245 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1602436 original size:12 final size:12
Alignment explanation
Indices: 1602419--1602455 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1602409 TTATAATCCT
1602419 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1602431 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1602443 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1602455 G
1 G
1602456 TCCCTGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1604769 original size:19 final size:19
Alignment explanation
Indices: 1604747--1604877 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1604737 GAAAATTACT
1604747 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1604766 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1604780 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1604799 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1604813 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1604832 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1604846 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1604865 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1604878 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1604789 original size:33 final size:33
Alignment explanation
Indices: 1604747--1604873 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1604737 GAAAATTACT
1604747 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1604780 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1604812 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1604846 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1604874 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1604854 original size:66 final size:66
Alignment explanation
Indices: 1604748--1604880 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1604738 AAAATTACTA
*
1604748 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1604813 T
66 T
*
1604814 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1604879 T
66 T
1604880 T
1 T
1604881 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1604895 original size:19 final size:19
Alignment explanation
Indices: 1604873--1604947 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
1604863 AAATCGCAAC
*
1604873 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1604892 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
1604906 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
1604925 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
1604944 GCGA
1 GCGA
1604948 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 2 0.04
18 1 0.02
19 31 0.67
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:1604948 original size:19 final size:19
Alignment explanation
Indices: 1604904--1604948 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1604894 GATTCTCTCG
*
1604904 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1604923 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1604942 TTGCGAT
1 TTGCGAT
1604949 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1605078 original size:14 final size:14
Alignment explanation
Indices: 1605059--1605095 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1605049 CATCAATTAA
1605059 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1605073 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1605087 ACAAATCAA
1 ACAAATCAA
1605096 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1606511 original size:42 final size:41
Alignment explanation
Indices: 1606452--1606657 Score: 146
Period size: 42 Copynumber: 4.9 Consensus size: 41
1606442 GTGAATCGGG
* *
1606452 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1606494 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * * *
1606536 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGGCAATGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
1606578 CTCTTGAATGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1606620 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1606658 GCGAGTCGGG
Statistics
Matches: 122, Mismatches: 34, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
41 9 0.07
42 102 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1606518 original size:21 final size:21
Alignment explanation
Indices: 1606452--1606518 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1606442 GTGAATCGGG
*
1606452 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1606472 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1606494 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1606515 CTCT
1 CTCT
1606519 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:1606595 original size:84 final size:84
Alignment explanation
Indices: 1606490--1606653 Score: 319
Period size: 84 Copynumber: 2.0 Consensus size: 84
1606480 ACGATGACAG
1606490 TGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
1 TGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
1606555 GACTCTTGAGGGATGGCAA
66 GACTCTTGAGGGATGGCAA
*
1606574 TGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
1 TGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
1606639 GACTCTTGAGGGATG
66 GACTCTTGAGGGATG
1606654 ACAGGCGAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (84 bp):
TGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGATAGGAGTG
GACTCTTGAGGGATGGCAA
Found at i:1607054 original size:91 final size:90
Alignment explanation
Indices: 1606874--1607058 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1606864 ATTTCAAACT
*
1606874 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAATTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAATTTAGC
*
1606939 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACAGAATAAATTTAC
*
1606967 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCA
*
1607031 GTATTGGCAGCAACAGAATAAATTTAC
64 GAATTGGCAGCAACAGAATAAATTTAC
1607058 T
1 T
1607059 AAACAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCAGA
ATTGGCAGCAACAGAATAAATTTAC
Found at i:1608776 original size:20 final size:19
Alignment explanation
Indices: 1608745--1608852 Score: 91
Period size: 20 Copynumber: 5.8 Consensus size: 19
1608735 TCTTTTGGTT
1608745 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1608764 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1608785 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1608804 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
** *
1608818 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGA
1608837 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1608853 TGCGATTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 26 0.37
20 29 0.41
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1608827 original size:33 final size:34
Alignment explanation
Indices: 1608770--1608835 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
1608760 ACGAGATAAT
1608770 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
*
1608804 GAGAATCGCAACG-TGAAATGACTATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACG
1608836 CGAAATGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.14
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACGA
Found at i:1608849 original size:19 final size:19
Alignment explanation
Indices: 1608745--1608857 Score: 92
Period size: 19 Copynumber: 6.1 Consensus size: 19
1608735 TCTTTTGGTT
*
1608745 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1608764 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1608784 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
1608802 G--A-GAGAATCGCAACGT
1 GAAATGAAAATCGCAACGC
**
1608818 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1608837 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1608856 GA
1 GA
1608858 TTTTGGTTTC
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 2 0.03
19 31 0.42
20 27 0.36
21 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1608879 original size:19 final size:19
Alignment explanation
Indices: 1608857--1608893 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1608847 TCGCAATGCG
*
1608857 ATTTTGGTTTCGCGTTGCT
1 ATTTTGATTTCGCGTTGCT
*
1608876 ATTTTTATTTCGCGTTGC
1 ATTTTGATTTCGCGTTGC
1608894 GATTCTCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.16, G:0.22, T:0.54
Consensus pattern (19 bp):
ATTTTGATTTCGCGTTGCT
Found at i:1609477 original size:20 final size:20
Alignment explanation
Indices: 1609452--1609504 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1609442 GCGTTATGTA
1609452 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1609472 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1609492 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1609505 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1609538 original size:20 final size:20
Alignment explanation
Indices: 1609513--1609566 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1609503 GATTTTGTAT
1609513 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1609533 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1609553 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1609567 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1609551 original size:61 final size:61
Alignment explanation
Indices: 1609453--1609569 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1609443 CGTTATGTAA
* * * * *
1609453 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1609514 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1609570 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1609585 original size:61 final size:61
Alignment explanation
Indices: 1609448--1609587 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
1609438 AATGGCGTTA
* * * * *
1609448 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
1609508 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
1609569 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
1609588 TTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:1609677 original size:21 final size:21
Alignment explanation
Indices: 1609637--1609677 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1609627 ACTGTAGACC
**
1609637 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1609658 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1609678 GCAAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1612000 original size:21 final size:21
Alignment explanation
Indices: 1611970--1612018 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1611960 CACCACAACA
1611970 CACATAATTTG-CACCGAAATG-C
1 CACAT-ATTTGTC-CCG-AATGAC
1611992 CACATATTTGTCCCGAATGAC
1 CACATATTTGTCCCGAATGAC
1612013 CACATA
1 CACATA
1612019 GAACCCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 15 0.60
22 6 0.24
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
CACATATTTGTCCCGAATGAC
Found at i:1612592 original size:21 final size:21
Alignment explanation
Indices: 1612540--1612603 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1612530 TCAAGCGCAC
*
1612540 TAGTATCGATACTT-CTCCTA
1 TAGTATCGATACTTCCTTCTA
* *
1612560 AAGTACCGATACTTCCTTCTA
1 TAGTATCGATACTTCCTTCTA
*
1612581 TGGTATCGATAC-TCACTTCTA
1 TAGTATCGATACTTC-CTTCTA
1612602 TA
1 TA
1612604 CCGATACCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (21 bp):
TAGTATCGATACTTCCTTCTA
Found at i:1613619 original size:6 final size:6
Alignment explanation
Indices: 1613610--1613673 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
1613600 CTCCCCTACC
* *
1613610 CTCCCT CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCTCA -TCCCA
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA
* *
1613657 CCCCCA -TCCCA CCCCCA
1 CTCCCA CTCCCA CTCCCA
1613674 AATCCTCCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 8 0.16
6 42 0.84
ACGTcount: A:0.16, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CTCCCA
Found at i:1614123 original size:22 final size:23
Alignment explanation
Indices: 1614086--1614132 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1614076 CAACGGTGAA
*
1614086 GGGAGAAGAGAAATGGGGTAAAT
1 GGGAGAAGAGAAATGGGATAAAT
*
1614109 GGGAGGAGA-AAATGGGATAAAT
1 GGGAGAAGAGAAATGGGATAAAT
1614131 GG
1 GG
1614133 TGTGATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.45, T:0.13
Consensus pattern (23 bp):
GGGAGAAGAGAAATGGGATAAAT
Found at i:1615258 original size:32 final size:33
Alignment explanation
Indices: 1615195--1615262 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 33
1615185 CATAACACAC
1615195 TCATTTCATCTCTTACACACACAAAACACTCCTT
1 TCATTTCATCTCTTACACACAC-AAACACTCCTT
1615229 TCATCTTCATTCTCTTACACA-AC-AA-ACTCCTT
1 TCAT-TTCA-TCTCTTACACACACAAACACTCCTT
1615261 TC
1 TC
1615263 TTTTAACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 9 0.28
33 2 0.06
34 4 0.12
35 6 0.19
36 11 0.34
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (33 bp):
TCATTTCATCTCTTACACACACAAACACTCCTT
Found at i:1617382 original size:10 final size:10
Alignment explanation
Indices: 1617367--1617432 Score: 105
Period size: 10 Copynumber: 6.6 Consensus size: 10
1617357 GAGCTTTACT
*
1617367 TATATAAATA
1 TATATATATA
1617377 TATATATATA
1 TATATATATA
1617387 TATATATATA
1 TATATATATA
1617397 TATATATATA
1 TATATATATA
1617407 TATATATATA
1 TATATATATA
*
1617417 TATATACATA
1 TATATATATA
*
1617427 CATATA
1 TATATA
1617433 ATAATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 53 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:1617383 original size:4 final size:4
Alignment explanation
Indices: 1617367--1617432 Score: 105
Period size: 4 Copynumber: 16.5 Consensus size: 4
1617357 GAGCTTTACT
*
1617367 TATA TAAA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1617415 TATA TATA CATA CATA TA
1 TATA TATA TATA TATA TA
1617433 ATAATTTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:1617383 original size:6 final size:6
Alignment explanation
Indices: 1617367--1617432 Score: 105
Period size: 6 Copynumber: 11.0 Consensus size: 6
1617357 GAGCTTTACT
*
1617367 TATATA AATATA TATATA TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
1617415 TATATA TACATA CATATA
1 TATATA TATATA TATATA
1617433 ATAATTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:1620081 original size:20 final size:21
Alignment explanation
Indices: 1620045--1620084 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1620035 ATTTAAAATA
*
1620045 ATAAAGGAAGTATCGATACTT
1 ATAAAGGAAGTACCGATACTT
1620066 ATAAAGG-AGTACCGATACT
1 ATAAAGGAAGTACCGATACT
1620085 CCCTATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
ATAAAGGAAGTACCGATACTT
Found at i:1623265 original size:49 final size:50
Alignment explanation
Indices: 1623154--1623265 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 50
1623144 TTCAAAAAAT
* * * *
1623154 TAAATTACTAAAAAATAAATTTATATTAAAAATGCTAAAATTATTATTGA
1 TAAATTATTAAAAAATAAATATATATTAAAAATGATAAAATAATTATTGA
* * * *
1623204 -AAGTT-TTAAAAAACTAAATATATATTATAACT-ATAAAATAATTATTTA
1 TAAATTATTAAAAAA-TAAATATATATTAAAAATGATAAAATAATTATTGA
1623252 TAAATTATTAAAAA
1 TAAATTATTAAAAA
1623266 TTTTAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
48 20 0.40
49 23 0.46
50 7 0.14
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (50 bp):
TAAATTATTAAAAAATAAATATATATTAAAAATGATAAAATAATTATTGA
Found at i:1623402 original size:22 final size:22
Alignment explanation
Indices: 1623377--1623421 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1623367 ATATGTTACT
1623377 TAAGATAATTATTGACCTGATA
1 TAAGATAATTATTGACCTGATA
1623399 TAAGATAATTATTGACCTGATA
1 TAAGATAATTATTGACCTGATA
1623421 T
1 T
1623422 TTTTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TAAGATAATTATTGACCTGATA
Found at i:1626557 original size:21 final size:21
Alignment explanation
Indices: 1626531--1626572 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1626521 AAGTGTTTGT
1626531 GGTGCTTTATTCTATAATTGC
1 GGTGCTTTATTCTATAATTGC
*
1626552 GGTGCTTTATTCTATGATTGC
1 GGTGCTTTATTCTATAATTGC
1626573 ATCATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (21 bp):
GGTGCTTTATTCTATAATTGC
Found at i:1635153 original size:23 final size:22
Alignment explanation
Indices: 1635107--1635171 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
1635097 TTGAATATAT
*
1635107 TATTATAATATTA-AAAAATATAA
1 TATTAT-ATATTATAAATAT-TAA
1635130 TATTATATTATTATAAATATTAA
1 TATTATA-TATTATAAATATTAA
1635153 TA--AGTATATTATAAATATT
1 TATTA-TATATTATAAATATT
1635172 TTAATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 14 0.37
22 3 0.08
23 16 0.42
24 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTATATATTATAAATATTAA
Found at i:1637544 original size:21 final size:22
Alignment explanation
Indices: 1637504--1637544 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1637494 TGCATGCTCC
**
1637504 TGAGAGAAAAAAGACTTGATGA
1 TGAGAGAAAAAAGAAATGATGA
1637526 TGAGAG-AAAAAGAAATGAT
1 TGAGAGAAAAAAGAAATGAT
1637545 AATTGAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.02, G:0.27, T:0.17
Consensus pattern (22 bp):
TGAGAGAAAAAAGAAATGATGA
Found at i:1642730 original size:36 final size:36
Alignment explanation
Indices: 1642679--1642771 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 36
1642669 CATTTAAAAA
* * *
1642679 ATTAAAAAATATATATATATATATATAA-TATA-AGTTT
1 ATTATAAACTATATATATAT-TATA-AACTATATA-ATT
*
1642716 ATATATAAACTATATTTATATTATAAACTATATAATT
1 AT-TATAAACTATATATATATTATAAACTATATAATT
*
1642753 ATTATAAGCTATATATATA
1 ATTATAAACTATATATATA
1642772 AATTATGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
36 17 0.36
37 14 0.30
38 16 0.34
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (36 bp):
ATTATAAACTATATATATATTATAAACTATATAATT
Found at i:1642742 original size:18 final size:18
Alignment explanation
Indices: 1642713--1642771 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1642703 ATAATATAAG
1642713 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
1642730 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
* *
1642748 -TAATTATTATAAGCTATA
1 TTTA-TATTATAAACTATA
*
1642766 TATATA
1 TTTATA
1642772 AATTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 26 0.74
19 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:1642805 original size:13 final size:13
Alignment explanation
Indices: 1642687--1642822 Score: 50
Period size: 13 Copynumber: 10.5 Consensus size: 13
1642677 AAATTAAAAA
*
1642687 ATATATATATA-T
1 ATATATATAAACT
*
1642699 ATATATAATATAAGT
1 ATATAT-ATA-AACT
*
1642714 TTATATATAAACT
1 ATATATATAAACT
* *
1642727 ATAT-T-TATATT
1 ATATATATAAACT
*
1642738 ATAAACTATATAA-T
1 ATATA-TATA-AACT
*
1642752 -TAT-TATAAGCT
1 ATATATATAAACT
*
1642763 ATATATATAAATT
1 ATATATATAAACT
* * *
1642776 ATGTTTATGTCAACT
1 A--TATATATAAACT
1642791 ATATATATAAACT
1 ATATATATAAACT
* * *
1642804 ATGTATATATATT
1 ATATATATAAACT
1642817 ATATAT
1 ATATAT
1642823 GTATAAATTA
Statistics
Matches: 89, Mismatches: 23, Indels: 23
0.66 0.17 0.17
Matches are distributed among these distances:
10 1 0.01
11 12 0.13
12 10 0.11
13 43 0.48
14 7 0.08
15 16 0.18
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:1642821 original size:9 final size:9
Alignment explanation
Indices: 1642807--1642901 Score: 58
Period size: 9 Copynumber: 11.0 Consensus size: 9
1642797 ATAAACTATG
1642807 TATATATAT
1 TATATATAT
*
1642816 TATATAT-G
1 TATATATAT
1642824 TATA-A-AT
1 TATATATAT
* * *
1642831 TATAAAAAG
1 TATATATAT
1642840 TATATAGT-T
1 TATATA-TAT
*
1642849 TATAAAATAT
1 TAT-ATATAT
* *
1642859 TGTTTATAT
1 TATATATAT
*
1642868 TA-ATATAG
1 TATATATAT
1642876 TATATATA-
1 TATATATAT
1642884 TATATATAT
1 TATATATAT
1642893 TATATATAT
1 TATATATAT
1642902 ACTATGCATA
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
7 5 0.08
8 19 0.29
9 36 0.55
10 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (9 bp):
TATATATAT
Found at i:1642900 original size:15 final size:15
Alignment explanation
Indices: 1642807--1642902 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 15
1642797 ATAAACTATG
1642807 TATATATATTATATA
1 TATATATATTATATA
* * *
1642822 TGTATAAATTATAAA
1 TATATATATTATATA
*
1642837 AAGTATATAGTT-TATA
1 TA-TATATA-TTATATA
* *
1642853 -A-A-ATATTGTTTA
1 TATATATATTATATA
1642865 TATTAATATAGTATATATA
1 TA-T-ATATA-T-TATATA
1642884 TATATATATTATATA
1 TATATATATTATATA
1642899 TATA
1 TATA
1642903 CTATGCATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
11 2 0.03
12 6 0.10
13 2 0.03
15 23 0.38
16 10 0.16
17 10 0.16
18 2 0.03
19 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
TATATATATTATATA
Found at i:1642902 original size:17 final size:17
Alignment explanation
Indices: 1642687--1642902 Score: 62
Period size: 17 Copynumber: 13.4 Consensus size: 17
1642677 AAATTAAAAA
1642687 ATATATATATATA-TAT
1 ATATATATATATATTAT
1642703 ATA-ATATA-AGT-TTAT
1 ATATATATATA-TATTAT
*
1642718 ATATAAACTATAT-TTAT
1 ATATATA-TATATATTAT
*
1642735 ATTATAAACTATATAATTAT
1 A-TATATA-TATAT-ATTAT
**
1642755 -TATA-AGCTATA-TAT
1 ATATATATATATATTAT
* *
1642769 ATAAAT-TATGT-TTAT
1 ATATATATATATATTAT
* *
1642784 GTCA-ACTATATATA-TAA
1 AT-ATA-TATATATATTAT
*
1642801 ACTATGTATATATATTAT
1 A-TATATATATATATTAT
*
1642819 ATATGTATA-A-ATTAT
1 ATATATATATATATTAT
*
1642834 A-A-AAAGTATATAGTT-T
1 ATATATA-TATATA-TTAT
* *
1642850 ATA-AAATAT-TGTT-T
1 ATATATATATATATTAT
*
1642864 ATAT-TA-ATATAGTAT
1 ATATATATATATATTAT
1642879 ATATATATATATATTAT
1 ATATATATATATATTAT
1642896 ATATATA
1 ATATATA
1642903 CTATGCATAA
Statistics
Matches: 152, Mismatches: 20, Indels: 55
0.67 0.09 0.24
Matches are distributed among these distances:
13 3 0.02
14 16 0.11
15 36 0.24
16 19 0.12
17 53 0.35
18 21 0.14
20 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
ATATATATATATATTAT
Found at i:1642920 original size:2 final size:2
Alignment explanation
Indices: 1642687--1642902 Score: 59
Period size: 2 Copynumber: 111.5 Consensus size: 2
1642677 AAATTAAAAA
* *
1642687 AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * *
1642729 AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T AT A- AG CT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1642767 AT AT AA AT -T AT GT TT AT GT CA- ACT AT AT AT AT AA ACT AT GT
1 AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT A-T AT AT
* * * * *
1642808 AT AT AT AT -T AT AT AT GT AT AA AT -T AT AA AA AGT AT AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
* * *
1642850 AT A- AA AT AT -T GT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1642889 AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT A
1642903 CTATGCATAA
Statistics
Matches: 156, Mismatches: 33, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
1 16 0.10
2 132 0.85
3 8 0.05
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1643479 original size:65 final size:64
Alignment explanation
Indices: 1643373--1643580 Score: 256
Period size: 65 Copynumber: 3.2 Consensus size: 64
1643363 TTTTTCAAAG
* * * * *
1643373 TAGTGTACCGATGCACCATTCAATGCATCGATGCACCCTTGAATTAATTGAAACTTCGAATGCAT
1 TAGTGTACCGATGCA-CA-ACCATGCATCGATGCACTCTTGAATTATTTGAAACATCGAATGCAT
1643438 T
64 T
*
1643439 TAGTGCACCGATGCACAAGCCATGCATCGATGCACTCTTGAA-TATTTTGAAACATCGAATGCAT
1 TAGTGTACCGATGCACAA-CCATGCATCGATGCACTCTTGAATTA-TTTGAAACATCGAATGCAT
1643503 T
64 T
* * ** * * *
1643504 TTGTGTACCGATGCACAACCATGCATCGATGCACTCCTGGCTTGTTTGAAACATCGAATGTAAT
1 TAGTGTACCGATGCACAACCATGCATCGATGCACTCTTGAATTATTTGAAACATCGAATGCATT
1643568 TAGTGTACCGATG
1 TAGTGTACCGATG
1643581 TTCCCCTAGT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
64 52 0.42
65 58 0.47
66 14 0.11
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (64 bp):
TAGTGTACCGATGCACAACCATGCATCGATGCACTCTTGAATTATTTGAAACATCGAATGCATT
Found at i:1649418 original size:44 final size:43
Alignment explanation
Indices: 1649334--1649431 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
1649324 TTTTGTACTT
* *
1649334 TGTGCATCGATACACTAGACAGTGTACCGATGCATCCCTTGAA
1 TGTGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAA
*
1649377 TGTGCATCGATACACCATGA-AGGTGCACCGATGTATCCCTTGAA
1 TGTGCATCGATACACCA-GACA-GTGCACCGATGCATCCCTTGAA
1649421 TGTGCATCGAT
1 TGTGCATCGAT
1649432 GCACTCTGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 17 0.34
44 33 0.66
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
TGTGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAA
Found at i:1649425 original size:23 final size:23
Alignment explanation
Indices: 1649359--1649432 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1649349 TAGACAGTGT
*
1649359 ACCGATGCATCCCTTGAATGTGC
1 ACCGATGTATCCCTTGAATGTGC
* * *
1649382 ATCGA--TA-CACCATGAAGGTGC
1 ACCGATGTATC-CCTTGAATGTGC
1649403 ACCGATGTATCCCTTGAATGTGC
1 ACCGATGTATCCCTTGAATGTGC
*
1649426 ATCGATG
1 ACCGATG
1649433 CACTCTGCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
23 22 0.56
24 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (23 bp):
ACCGATGTATCCCTTGAATGTGC
Found at i:1656230 original size:29 final size:29
Alignment explanation
Indices: 1656187--1656345 Score: 223
Period size: 29 Copynumber: 5.5 Consensus size: 29
1656177 GTTGACCATG
1656187 CTATTTTAGTAATTAATTCGAAATAGGTA
1 CTATTTTAGTAATTAATTCGAAATAGGTA
*
1656216 ATATTCTT-GTAATTAATTCGAAATAGGTA
1 CTATT-TTAGTAATTAATTCGAAATAGGTA
** *
1656245 CTATTTTAGTAATTAATTTAAAATAGGTG
1 CTATTTTAGTAATTAATTCGAAATAGGTA
*
1656274 CTATTTTAGTAATTAATTCGAAATAGGTG
1 CTATTTTAGTAATTAATTCGAAATAGGTA
** *
1656303 CTATTTTAGTAATTAATTTAAAAT-GGTG
1 CTATTTTAGTAATTAATTCGAAATAGGTA
1656331 CTATTTTAGTAATTA
1 CTATTTTAGTAATTA
1656346 TTTTAAAAAG
Statistics
Matches: 119, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.18
29 96 0.81
30 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (29 bp):
CTATTTTAGTAATTAATTCGAAATAGGTA
Found at i:1656286 original size:58 final size:58
Alignment explanation
Indices: 1656187--1656345 Score: 250
Period size: 58 Copynumber: 2.8 Consensus size: 58
1656177 GTTGACCATG
** **
1656187 CTATTTTAGTAATTAATTCGAAATAGGTAATATTCTT-GTAATTAATTCGAAATAGGTA
1 CTATTTTAGTAATTAATTTAAAATAGGTGCTATT-TTAGTAATTAATTCGAAATAGGTA
*
1656245 CTATTTTAGTAATTAATTTAAAATAGGTGCTATTTTAGTAATTAATTCGAAATAGGTG
1 CTATTTTAGTAATTAATTTAAAATAGGTGCTATTTTAGTAATTAATTCGAAATAGGTA
1656303 CTATTTTAGTAATTAATTTAAAAT-GGTGCTATTTTAGTAATTA
1 CTATTTTAGTAATTAATTTAAAATAGGTGCTATTTTAGTAATTA
1656346 TTTTAAAAAG
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
57 21 0.22
58 74 0.78
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (58 bp):
CTATTTTAGTAATTAATTTAAAATAGGTGCTATTTTAGTAATTAATTCGAAATAGGTA
Found at i:1656364 original size:29 final size:28
Alignment explanation
Indices: 1656185--1656365 Score: 193
Period size: 29 Copynumber: 6.3 Consensus size: 28
1656175 CCGTTGACCA
* *
1656185 TGCTATTTTAGTAATTAATTCGAAATAGG
1 TGCTATTTTAGTAATTAATT-TAAAAAGG
** * *
1656214 TAATATTCTT-GTAATTAATTCGAAATAGG
1 TGCTATT-TTAGTAATTAATT-TAAAAAGG
*
1656243 TACTATTTTAGTAATTAATTTAAAATAGG
1 TGCTATTTTAGTAATTAATTTAAAA-AGG
* *
1656272 TGCTATTTTAGTAATTAATTCGAAATAGG
1 TGCTATTTTAGTAATTAATT-TAAAAAGG
*
1656301 TGCTATTTTAGTAATTAATTTAAAATGG
1 TGCTATTTTAGTAATTAATTTAAAAAGG
*
1656329 TGCTATTTTAGTAATTATTTTAAAAAGGG
1 TGCTATTTTAGTAATTAATTTAAAAA-GG
*
1656358 TTCTATTT
1 TGCTATTT
1656366 CTGTAAAATG
Statistics
Matches: 133, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
28 34 0.26
29 94 0.71
30 5 0.04
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (28 bp):
TGCTATTTTAGTAATTAATTTAAAAAGG
Found at i:1657493 original size:116 final size:116
Alignment explanation
Indices: 1657288--1657578 Score: 467
Period size: 116 Copynumber: 2.5 Consensus size: 116
1657278 GTAAGTATTT
* *
1657288 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGATGTGT-ATCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1657353 GGAACCTACACATTATAGTGATGGAAGTGACTGGATGGAGAAGTTATTACTG
65 GGAACCTACACATTATAGTGATGGAAGTGACTGGATGGAGAAGTTATTACTG
*
1657405 CAGGCTCCTTTGATGTGTTTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGG
1 CAGGCTCCTTTGATGTGTATCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGG
*
1657470 GAACCTACACATTATAGTGATGGAAGTGACTGGATGGAGACGTTATTACTG
66 GAACCTACACATTATAGTGATGGAAGTGACTGGATGGAGAAGTTATTACTG
** * * *
1657521 CAGGCTCCTCGGTTTCGTGCAT-AGGGTAAGTCCTTACTGGTGTGCATGTGGGTGTATG
1 CAGGCTCCTTTG-AT-GTGTATCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1657579 TTTCGGGAAA
Statistics
Matches: 163, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
116 106 0.65
117 53 0.33
118 4 0.02
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (116 bp):
CAGGCTCCTTTGATGTGTATCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGG
GAACCTACACATTATAGTGATGGAAGTGACTGGATGGAGAAGTTATTACTG
Found at i:1659516 original size:65 final size:65
Alignment explanation
Indices: 1659410--1659617 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 65
1659400 TTTTTCAAAG
** * *
1659410 TAGTGTACCGATGCACCATTCAATGCATCGATGCACCCTTGAAT-TAATTGAAAC-TTGGAATGC
1 TAGTGTACCGATGCA-CAAGCCATGCATCGATGCACTCTTGAATAT-ATTGAAACATT-GAATGC
1659473 ATT
63 ATT
* *
1659476 TAGTGTACCGATGCACAAGCCATGCATTGATGCACTCTTGAATATTTTGAAACATTGAATGCATT
1 TAGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATATTGAAACATTGAATGCATT
* * * ** * * *
1659541 TTGTGTACTGATGCAC-AGACCATGCATCGATGCACTCCTGGCT-TGTTTGAAACATCGAATGTA
1 TAGTGTACCGATGCACAAG-CCATGCATCGATGCACTCTTGAATAT-ATTGAAACATTGAATGCA
*
1659604 AT
64 TT
1659606 TAGTGTACCGAT
1 TAGTGTACCGAT
1659618 CCACCCCTAG
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
64 3 0.02
65 100 0.83
66 18 0.15
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (65 bp):
TAGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATATTGAAACATTGAATGCATT
Found at i:1660617 original size:13 final size:13
Alignment explanation
Indices: 1660599--1660634 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1660589 ATTATGTATA
1660599 ATATATATAAACT
1 ATATATATAAACT
*
1660612 ATATATATAACCT
1 ATATATATAAACT
1660625 ATAGTATATA
1 ATA-TATATA
1660635 TATATACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:1660661 original size:55 final size:53
Alignment explanation
Indices: 1660551--1660689 Score: 145
Period size: 55 Copynumber: 2.5 Consensus size: 53
1660541 TGTATACATG
* * *
1660551 TAAACTATATATGTAACTTATAGTACATGTATGTATAAATTATGTATAATATATA
1 TAAACTATATATGTAACCTATAGT--ATATATATATAAATTATGTATAATATATA
* * *
1660606 TAAACTATATATATAACCTATAGTATATATATATACAATCTATTTAT-ATGTTATA
1 TAAACTATATATGTAACCTATAGTATATATATATA-AAT-TATGTATAAT-ATATA
* * *
1660661 TAAATTATATATGTATCCTATAGTTTATA
1 TAAACTATATATGTAACCTATAGTATATA
1660690 ATCAATAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
53 9 0.13
54 5 0.07
55 57 0.80
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (53 bp):
TAAACTATATATGTAACCTATAGTATATATATATAAATTATGTATAATATATA
Found at i:1660740 original size:21 final size:20
Alignment explanation
Indices: 1660714--1660791 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 20
1660704 TTAGTGTATT
1660714 ATATAGTTTATACTTTATAAC
1 ATATAGTTTATA-TTTATAAC
* *
1660735 ATATAGTATATAATTTATAAA
1 ATATAGTTTAT-ATTTATAAC
* *
1660756 ATATAGTTTATATTAATGTAC
1 ATATAGTTTATATTTAT-AAC
1660777 TATATAGTTTATATT
1 -ATATAGTTTATATT
1660792 AATGTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
20 5 0.10
21 28 0.58
22 15 0.31
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (20 bp):
ATATAGTTTATATTTATAAC
Found at i:1660793 original size:22 final size:22
Alignment explanation
Indices: 1660694--1660796 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
1660684 TTTATAATCA
* *
1660694 ATAGTTTATATTAGTGTATTAT
1 ATAGTTTATATTAATGTACTAT
* *
1660716 ATAGTTTATACTTTAT-AAC-AT
1 ATAGTTTATA-TTAATGTACTAT
* * **
1660737 ATAGTATATAATT--TATAAAAT
1 ATAGTTTAT-ATTAATGTACTAT
1660758 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTACTAT
1660780 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
1660797 TAATTATCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 4 0.06
21 22 0.34
22 34 0.53
23 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.50
Consensus pattern (22 bp):
ATAGTTTATATTAATGTACTAT
Found at i:1660824 original size:16 final size:16
Alignment explanation
Indices: 1660779--1660836 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1660769 TAATGTACTA
*
1660779 TATAGTTTATATTAA-
1 TATAATTTATATTAAC
* *
1660794 TGTTAA-TTATCTTAAC
1 T-ATAATTTATATTAAC
1660810 TATAATTTATATTAAC
1 TATAATTTATATTAAC
*
1660826 TATAGTTTATA
1 TATAATTTATA
1660837 AACTATACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (16 bp):
TATAATTTATATTAAC
Found at i:1660842 original size:14 final size:15
Alignment explanation
Indices: 1660806--1660843 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1660796 TTAATTATCT
1660806 TAACTATAATTTATA
1 TAACTATAATTTATA
*
1660821 TTAACTATAGTTTATA
1 -TAACTATAATTTATA
1660837 -AACTATA
1 TAACTATA
1660844 CTATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (15 bp):
TAACTATAATTTATA
Found at i:1660976 original size:27 final size:27
Alignment explanation
Indices: 1660929--1660981 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1660919 TTATAAACTA
1660929 TATTATATTAATATAAGTTAATATTAC
1 TATTATATTAATATAAGTTAATATTAC
1660956 TATTACTATTAAT-TATA-TTAATATTA
1 TATTA-TATTAATATA-AGTTAATATTA
1660982 ATTATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTATATTAATATAAGTTAATATTAC
Found at i:1660980 original size:15 final size:15
Alignment explanation
Indices: 1660951--1660987 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1660941 ATAAGTTAAT
*
1660951 ATTACTATTACTATTA
1 ATTA-TATTAATATTA
1660967 ATTATATTAATATTA
1 ATTATATTAATATTA
1660982 ATTATA
1 ATTATA
1660988 AATAGTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATATTAATATTA
Found at i:1661722 original size:6 final size:6
Alignment explanation
Indices: 1661713--1661863 Score: 74
Period size: 6 Copynumber: 24.8 Consensus size: 6
1661703 CTCTAACTTG
* * * * *
1661713 AACCCA AACCCTA AA-CTA GAACCCA ACCCCA AACCTA AGCCCA AACCTA
1 AACCCA AACCC-A AACCCA -AACCCA AACCCA AACCCA AACCCA AACCCA
* ** * * * * * *
1661762 AGCTTA AACCCA AA-CCG AACCAA AACCCG AACCCA AATCTA AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * *
1661809 AACCCA AATCCAA AACCCA AACTCA AA-CCA GAACCCAA AACTCG AACCCA
1 AACCCA AA-CCCA AACCCA AACCCA AACCCA -AACCC-A AACCCA AACCCA
1661859 AACCC
1 AACCC
1661864 TAACTTGAAT
Statistics
Matches: 103, Mismatches: 34, Indels: 16
0.67 0.22 0.10
Matches are distributed among these distances:
5 7 0.07
6 79 0.77
7 16 0.16
8 1 0.01
ACGTcount: A:0.46, C:0.41, G:0.05, T:0.07
Consensus pattern (6 bp):
AACCCA
Found at i:1661740 original size:18 final size:18
Alignment explanation
Indices: 1661696--1661746 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1661686 CATCTTTTGT
* *
1661696 AACCCAACTCT-AACTTG
1 AACCCAACCCTAAACTAG
1661713 AACCCAAACCCTAAACTAG
1 AACCC-AACCCTAAACTAG
*
1661732 AACCCAACCCCAAAC
1 AACCCAACCCTAAAC
1661747 CTAAGCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.17
18 14 0.48
19 10 0.34
ACGTcount: A:0.43, C:0.41, G:0.04, T:0.12
Consensus pattern (18 bp):
AACCCAACCCTAAACTAG
Found at i:1661857 original size:31 final size:29
Alignment explanation
Indices: 1661767--1661861 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 29
1661757 ACCTAAGCTT
*
1661767 AAACCCAAACCGAA-CCAAAACCCGAACCC
1 AAACTCAAACCGAACCCAAAA-CCGAACCC
* *
1661796 AAA-TCTAAACCCGAACCCAAATCCAAAACCC
1 AAACTC-AAA-CCGAACCCAAAACC-GAACCC
1661827 AAACTCAAACCAGAACCCAAAACTCGAACCC
1 AAACTCAAACC-GAACCCAAAAC-CGAACCC
1661858 AAAC
1 AAAC
1661862 CCTAACTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
28 1 0.02
29 6 0.11
30 9 0.17
31 35 0.65
32 3 0.06
ACGTcount: A:0.49, C:0.40, G:0.05, T:0.05
Consensus pattern (29 bp):
AAACTCAAACCGAACCCAAAACCGAACCC
Found at i:1662315 original size:119 final size:119
Alignment explanation
Indices: 1662104--1662482 Score: 625
Period size: 119 Copynumber: 3.2 Consensus size: 119
1662094 CTGAAAGAGG
* * *
1662104 TAAATAAATTGTTTAATTTGTAGCTACTGTTGATTTGTTTCATCTGTAGTCCTTGTTTTTGTTGT
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGT
*
1662169 TGGTTGTTCATTCGGATTACTTGTATAAGGTTGTTAGCTAG-CTTTATTTAGGTT
66 TGGTTGTTCATTCGGATTGCTTGTATAAGGTTGTTAGCT-GCCTTTATTTAGGTT
* * * *
1662223 TAAATAAACTGTTTAATTTATTGCTACTGTTGATTTGTTTCCTCTGCAGTCATTGTTTGTGTTGT
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGT
* *
1662288 TGGTTGTTCATTCGGATTGCTTGTATAAGGTTGTTAGTTGCCTTTATTAAGGTT
66 TGGTTGTTCATTCGGATTGCTTGTATAAGGTTGTTAGCTGCCTTTATTTAGGTT
*
1662342 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTCCTCTATAGTCCTTGTTTGTGTTGT
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGT
*
1662407 TGGTTGTTCATTCAGATTGCTTGTATAAGGTTGTTAGCTGCCTTTATTTAGGATT
66 TGGTTGTTCATTCGGATTGCTTGTATAAGGTTGTTAGCTGCCTTTATTTAGG-TT
1662462 TAAATAAACTGTTTAATTTGT
1 TAAATAAACTGTTTAATTTGT
1662483 TTCCTCTGTA
Statistics
Matches: 240, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
118 1 0.00
119 216 0.90
120 23 0.10
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (119 bp):
TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGT
TGGTTGTTCATTCGGATTGCTTGTATAAGGTTGTTAGCTGCCTTTATTTAGGTT
Done.