Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:207 original size:12 final size:12
Alignment explanation
Indices: 190--214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
180 ATATAATCCT
190 GAAGAAGAAAAA
1 GAAGAAGAAAAA
202 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214 G
1 G
215 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2533 original size:19 final size:19
Alignment explanation
Indices: 2511--2788 Score: 363
Period size: 19 Copynumber: 15.4 Consensus size: 19
2501 CGGAAAATAC
*
2511 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2530 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2544 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2564 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2578 AATCGCAATGCGAAATGAG
1 AATCGCAATGCGAAATGAA
2597 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2616 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
2634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2672 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
2686 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2705 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
2724 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2743 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2762 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2781 AATCGCAA
1 AATCGCAA
2789 CGAGATAATC
Statistics
Matches: 231, Mismatches: 11, Indels: 34
0.84 0.04 0.12
Matches are distributed among these distances:
14 27 0.12
15 3 0.01
16 8 0.03
17 7 0.03
18 22 0.10
19 151 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2767 original size:109 final size:109
Alignment explanation
Indices: 2511--2820 Score: 474
Period size: 109 Copynumber: 2.9 Consensus size: 109
2501 CGGAAAATAC
* *
2511 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* * * *
2571 ACGAGAGAATCGCAATGCGAAATGAGAATCGCAATGCGAAATGAA
65 ACGAGATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
2616 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG-AA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
2679 CCGACATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
66 -CGAGATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
2724 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
2789 CGAGATAATCGCAATGCGAAATTATAAA-CGCA
66 CGAGATAATCGCAATGCGAAATTA-AAATCGCA
2821 TTGCGATTTT
Statistics
Matches: 188, Mismatches: 8, Indels: 14
0.90 0.04 0.07
Matches are distributed among these distances:
104 8 0.04
105 16 0.09
106 1 0.01
107 2 0.01
108 69 0.37
109 87 0.46
110 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (109 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
Found at i:2926 original size:19 final size:19
Alignment explanation
Indices: 2817--2918 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2807 AAATTATAAA
2817 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2836 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2856 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2872 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2889 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2908 CGCATTGCGAT
1 CGCATTGCGAT
2919 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3044 original size:14 final size:14
Alignment explanation
Indices: 3025--3061 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3015 CATCAATTAC
3025 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3039 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3053 ACAAATCAA
1 ACAAATCAA
3062 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:5035 original size:14 final size:14
Alignment explanation
Indices: 5016--5072 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5006 GCGAAATGAA
*
5016 AATCGCAACGACAG
1 AATCGCAACGAAAG
5030 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5047 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5063 AATCGCAACG
1 AATCGCAACG
5073 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:5043 original size:33 final size:33
Alignment explanation
Indices: 4997--5089 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
4987 GCGAAACCAA
*
4997 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5030 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5063 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5090 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:5054 original size:19 final size:19
Alignment explanation
Indices: 4960--5094 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
4950 TAGTTTACTT
* *
4960 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4980 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
4999 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5018 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5032 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5051 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5065 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5084 TCGCAATGCGA
1 TCGCAACGCGA
5095 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5112 original size:19 final size:19
Alignment explanation
Indices: 5090--5218 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5080 AAAATCGCAA
5090 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5109 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5123 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5142 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5156 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5175 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5194 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5214 TGCGA
1 TGCGA
5219 AAGTAACTAT
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:5132 original size:33 final size:33
Alignment explanation
Indices: 5090--5181 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5080 AAAATCGCAA
5090 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5123 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5156 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5182 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:5565 original size:92 final size:93
Alignment explanation
Indices: 5261--5731 Score: 921
Period size: 92 Copynumber: 5.1 Consensus size: 93
5251 TTGAATGGAT
5261 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5325 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5353 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5418 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5446 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5510 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5538 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5602 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5630 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5695 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5723 AAATTTACT
1 AAATTTACT
5732 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
91 14 0.04
92 188 0.50
93 174 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:7444 original size:14 final size:14
Alignment explanation
Indices: 7425--7514 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
7415 TTGAAATGAA
7425 AATCGCAACGAGAG
1 AATCGCAACGAGAG
7439 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
7456 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
7472 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
7491 AATCGCAACGAGAG
1 AATCGCAACGAGAG
7505 AATCGCAACG
1 AATCGCAACG
7515 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:7462 original size:33 final size:33
Alignment explanation
Indices: 7417--7531 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
7407 TCTTTTGGTT
7417 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
7450 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7483 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7516 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
7532 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:7463 original size:19 final size:18
Alignment explanation
Indices: 7424--7536 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
7414 GTTGAAATGA
7424 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
7439 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
7456 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
7472 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
7489 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
7505 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
7522 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
7537 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:7567 original size:14 final size:14
Alignment explanation
Indices: 7548--7602 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
7538 TTTGGTTTCG
7548 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7562 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
7581 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
7595 CGTTGCGA
1 CGTTGCGA
7603 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7765 original size:33 final size:33
Alignment explanation
Indices: 7723--7793 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
7713 AATACTAACT
*
7723 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
7756 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
7789 TGAAA
1 TGAAA
7794 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:8026 original size:22 final size:22
Alignment explanation
Indices: 7974--8028 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
7964 TGGTTGTGAG
**
7974 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
7996 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
8018 GGATTTCTTCG
1 GGATTTCTTCG
8029 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:8199 original size:20 final size:20
Alignment explanation
Indices: 8174--8367 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
8164 CTTTAAATAT
8174 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8194 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
8216 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8235 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
8255 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
8275 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8295 CACGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* *
8315 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
8335 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
8355 CGCGTTGCGATTT
1 CGCGTTGCGATTT
8368 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:8361 original size:60 final size:60
Alignment explanation
Indices: 8174--8367 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
8164 CTTTAAATAT
**
8174 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
8235 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
8295 CACGTTGCGATTTATGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
8355 CGCGTTGCGATTT
1 CGCGTTGCGATTT
8368 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:8384 original size:21 final size:20
Alignment explanation
Indices: 8360--8436 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
8350 ATATTCGCGT
8360 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
8381 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
8401 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
8423 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
8437 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:8447 original size:20 final size:20
Alignment explanation
Indices: 8422--8473 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
8412 AAGAATCGCG
*
8422 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8442 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8462 TTGCGATTCTGG
1 TTGCGATTCTGG
8474 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:8753 original size:11 final size:12
Alignment explanation
Indices: 8721--8757 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
8711 TACTTATAAA
8721 ATCTTTGAAAAT
1 ATCTTTGAAAAT
8733 ATCTTTGAAAAT
1 ATCTTTGAAAAT
8745 ATC-TTGAAAAT
1 ATCTTTGAAAAT
8756 AT
1 AT
8758 ATAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (12 bp):
ATCTTTGAAAAT
Found at i:10721 original size:22 final size:22
Alignment explanation
Indices: 10696--10741 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
10686 TAAATTACAT
*
10696 TTATATTTTTAACTA-TTTATAA
1 TTATATGTTTAA-TACTTTATAA
10718 TTATATGTTTAATACTTTATAA
1 TTATATGTTTAATACTTTATAA
10740 TT
1 TT
10742 TAACATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATATGTTTAATACTTTATAA
Found at i:11502 original size:2 final size:2
Alignment explanation
Indices: 11491--11523 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11481 TCCCCTTTAT
11491 TA TA TA -A TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11524 TGCTCTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11509 original size:13 final size:14
Alignment explanation
Indices: 11487--11522 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
11477 CAATTCCCCT
11487 TTAT-TATATAATA
1 TTATATATATAATA
11500 -TATATATAT-ATA
1 TTATATATATAATA
11512 TTATATATATA
1 TTATATATATA
11523 TTGCTCTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATATATATAATA
Found at i:11511 original size:15 final size:15
Alignment explanation
Indices: 11491--11523 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11481 TCCCCTTTAT
11491 TATATAATATATATA
1 TATATAATATATATA
*
11506 TATATATTATATATA
1 TATATAATATATATA
11521 TAT
1 TAT
11524 TGCTCTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATAATATATATA
Found at i:11524 original size:11 final size:11
Alignment explanation
Indices: 11488--11524 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
11478 AATTCCCCTT
11488 TATTATATA-A
1 TATTATATATA
11498 TATATATATATA
1 TAT-TATATATA
11510 TATTATATATA
1 TATTATATATA
11521 TATT
1 TATT
11525 GCTCTGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.72
12 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTATATATA
Found at i:18573 original size:29 final size:30
Alignment explanation
Indices: 18520--18594 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
18510 TATTAAAGTA
* * *
18520 TATTTTATTATATTTAATATTTTTAGTAATT
1 TATTTAATTAT-TTTAATATGTTTAATAATT
*
18551 TATTTAATTATTTTAAT-TGTTTAATATTT
1 TATTTAATTATTTTAATATGTTTAATAATT
*
18580 TATTCAATTAATTTT
1 TATTTAATT-ATTTT
18595 TTTTTGCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 17 0.45
30 11 0.29
31 10 0.26
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (30 bp):
TATTTAATTATTTTAATATGTTTAATAATT
Found at i:20782 original size:13 final size:13
Alignment explanation
Indices: 20764--20810 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
20754 TATTTAGTAC
*
20764 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
20777 TGTTTATTGGACT
1 TTTTTATTGTAAT
20790 TTTTTATTGTAAT
1 TTTTTATTGTAAT
20803 TTTTTATT
1 TTTTTATT
20811 ATTTATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:25061 original size:74 final size:74
Alignment explanation
Indices: 24982--25130 Score: 208
Period size: 74 Copynumber: 2.0 Consensus size: 74
24972 ATTTAATATT
* * *** *
24982 AGAGAAAATAACTTCAGTGACCGAAAATGCCTTATAATATACGATTTTAACCATCTTTTTTTGGA
1 AGAGAAAATAACCTCAGTGACCAAAAAAAACTTATAATATACGATTTTAACCAACTTTTTTTGGA
25047 TTTGCAAAA
66 TTTGCAAAA
** *
25056 AGAGAAAATCGCCTCAGTGACCAAAAAAAAGTTATAATATACGATTTTAACCAACTTTTTTTGGA
1 AGAGAAAATAACCTCAGTGACCAAAAAAAACTTATAATATACGATTTTAACCAACTTTTTTTGGA
*
25121 TTTGCCAAA
66 TTTGCAAAA
25130 A
1 A
25131 TGACCAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (74 bp):
AGAGAAAATAACCTCAGTGACCAAAAAAAACTTATAATATACGATTTTAACCAACTTTTTTTGGA
TTTGCAAAA
Found at i:25224 original size:21 final size:20
Alignment explanation
Indices: 25138--25294 Score: 84
Period size: 20 Copynumber: 7.8 Consensus size: 20
25128 AAATGACCAA
**
25138 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
25157 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
25177 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
25197 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
25218 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
25238 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
25258 CCAAAATCGCAACGCAAATAT
1 -CAAAATCGCAACGCGATTTT
*
25279 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
25295 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 9
0.72 0.22 0.06
Matches are distributed among these distances:
19 16 0.16
20 55 0.54
21 31 0.30
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:25304 original size:20 final size:20
Alignment explanation
Indices: 25281--25454 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
25271 GCAAATATGA
* *
25281 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
25301 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
25321 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
25341 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
25361 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
25381 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
25401 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
25421 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
25442 AAATCGCAACGCG
1 AAATCGCAACGCG
25455 ATATTTAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 109 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:25346 original size:60 final size:60
Alignment explanation
Indices: 25281--25454 Score: 240
Period size: 60 Copynumber: 2.9 Consensus size: 60
25271 GCAAATATGA
* *
25281 AAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
25341 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
** *
25401 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGTAAATCGCAACGCG
25455 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:25876 original size:33 final size:33
Alignment explanation
Indices: 25837--25907 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
25827 TTCACTTAGA
25837 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
25870 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
25903 TTTCA
1 TTTCA
25908 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:26031 original size:20 final size:19
Alignment explanation
Indices: 25987--26090 Score: 92
Period size: 19 Copynumber: 5.6 Consensus size: 19
25977 TGCAGAAGAG
*
25987 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AAATGACAA
**
26008 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGA-AATGACAA
*
26028 TCGCAACGCGAAATGACAA
1 TCGCAACGAGAAATGACAA
26047 TCGCAACGAG--AT---AA
1 TCGCAACGAGAAATGACAA
* *
26061 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGACAA
26080 TCGCAACGAGA
1 TCGCAACGAGA
26091 GAATCGCAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 28 0.41
20 15 0.22
21 10 0.15
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
TCGCAACGAGAAATGACAA
Found at i:26064 original size:14 final size:14
Alignment explanation
Indices: 26045--26106 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
26035 GCGAAATGAC
*
26045 AATCGCAACGAGAT
1 AATCGCAACGAGAA
26059 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAA
*
26078 AATCGCAACGAGAG
1 AATCGCAACGAGAA
*
26092 AATCGCAACGCGAA
1 AATCGCAACGAGAA
26106 A
1 A
26107 CCAAAATCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 23 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAA
Found at i:26070 original size:33 final size:33
Alignment explanation
Indices: 25999--26117 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
25989 GCAACGAGAT
25999 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
* *
26038 AAATGACAATCGCAACGAGATAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
26071 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
26104 AAACCAAAATCGCA
1 AAATGAAAATCGCA
26118 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 53 0.72
36 1 0.01
38 1 0.01
39 19 0.26
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:26154 original size:14 final size:14
Alignment explanation
Indices: 26135--26224 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
26125 TTTTATTTCG
26135 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26149 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
26168 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26182 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
26201 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26215 CGTTGCGATT
1 CGTTGCGATT
26225 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26160 original size:33 final size:33
Alignment explanation
Indices: 26118--26232 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
26108 CAAAATCGCA
*
26118 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
26151 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
26184 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
26217 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
26233 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:26173 original size:19 final size:19
Alignment explanation
Indices: 26113--26210 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
26103 GAAACCAAAA
* *
26113 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
26132 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
26146 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26165 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
26179 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
26198 TCGCGTTGCGATT
1 TCGCGTTGCGATT
26211 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28142 original size:93 final size:93
Alignment explanation
Indices: 27928--28394 Score: 886
Period size: 93 Copynumber: 5.1 Consensus size: 93
27918 TAGATTGCTT
*
27928 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27993 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28020 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28085 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
28113 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCAAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28178 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28205 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28270 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
28298 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28363 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28390 AGTAA
1 AGTAA
28395 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 161 0.44
93 208 0.56
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:28159 original size:185 final size:185
Alignment explanation
Indices: 27928--28394 Score: 891
Period size: 185 Copynumber: 2.5 Consensus size: 185
27918 TAGATTGCTT
*
27928 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27993 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
28058 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
28113 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCAAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28178 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
28243 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
28298 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28363 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
28395 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 252 0.91
186 25 0.09
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:28467 original size:20 final size:19
Alignment explanation
Indices: 28442--28570 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
28432 TAGTTTACTT
* *
28442 TCGCAACACGAAAGTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
28462 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
28481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
28500 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
28514 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
28533 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAATCAAAA
*
28547 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
28566 TCGCA
1 TCGCA
28571 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.52
20 12 0.13
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:28482 original size:19 final size:19
Alignment explanation
Indices: 28458--28570 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
28448 CACGAAAGTT
28458 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
28477 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
28496 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
28510 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
28529 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
28543 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
28562 AAAATCGCA
1 AAAATCGCA
28571 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:28521 original size:33 final size:32
Alignment explanation
Indices: 28478--28570 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
28468 CGCGAAACCA
**
28478 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
28510 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
28543 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
28571 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:28568 original size:52 final size:51
Alignment explanation
Indices: 28458--28570 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
28448 CACGAAAGTT
* *
28458 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
28510 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
28562 AAAATCGCA
1 AAAATCGCA
28571 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:28588 original size:19 final size:19
Alignment explanation
Indices: 28566--28700 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
28556 GAAACCAAAA
*
28566 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28585 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
28601 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
28618 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
28634 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
28651 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
28670 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
28690 TCGTGTTGCGA
1 TCGCGTTGCGA
28701 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28607 original size:14 final size:14
Alignment explanation
Indices: 28588--28644 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
28578 TTTCATTTCG
28588 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
28602 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
28619 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
28635 CGTTGCGATT
1 CGTTGCGATT
28645 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:28613 original size:33 final size:33
Alignment explanation
Indices: 28571--28663 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
28561 CAAAATCGCA
*
28571 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
28604 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
28637 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
28664 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:30642 original size:14 final size:14
Alignment explanation
Indices: 30623--30658 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
30613 ATTGTTTAAT
30623 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
30637 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
30651 TGATTTGT
1 TGATTTGT
30659 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30781 original size:19 final size:19
Alignment explanation
Indices: 30765--30866 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
30755 AAAAATGATT
30765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30784 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30803 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30817 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30836 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
30856 ATCGCAATGCG
1 ATCGCAATGCG
30867 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30919 original size:19 final size:19
Alignment explanation
Indices: 30895--31253 Score: 436
Period size: 19 Copynumber: 20.4 Consensus size: 19
30885 GATTCTCTCG
30895 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30914 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30933 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
30947 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30966 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30985 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31004 TTGCGAGTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31023 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
31037 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31056 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31075 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
31089 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31108 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31127 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31141 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31160 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31179 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31193 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31213 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
31227 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
31246 TTGCGATT
1 TTGCGATT
31254 GTAATTTCCG
Statistics
Matches: 298, Mismatches: 11, Indels: 62
0.80 0.03 0.17
Matches are distributed among these distances:
14 41 0.14
16 38 0.13
17 35 0.12
18 3 0.01
19 169 0.57
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30935 original size:52 final size:52
Alignment explanation
Indices: 30912--31253 Score: 186
Period size: 52 Copynumber: 6.6 Consensus size: 52
30902 TTTCATTTCG
* *
30912 CATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTT
1 CATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TGT
* *
30962 CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAGT-T-T
1 --CATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGT
* *
31014 CATTTCGCA-TTGCGA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT-T-T
1 CATTGCG-ATTTGC-ATTTC-G-CATTGCGATTTTCATTTCGCATTGCGATTCTGT
* *
31066 CATTTCGCA-TTGCGA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT-T-T
1 CATTGCG-ATTTGC-ATTTC-G-CATTGCGATTTTCATTTCGCATTGCGATTCTGT
* * *
31118 CATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-T
1 CATTGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTCTGT
* * *
31170 CATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATT-T-T
1 CATTGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTGT
* * *
31223 CATGTTGGGATTTTCATTTCGCGTTGCGATT
1 CA--TTGCGATTTGCATTTCGCATTGCGATT
31254 GTAATTTCCG
Statistics
Matches: 265, Mismatches: 10, Indels: 29
0.87 0.03 0.10
Matches are distributed among these distances:
50 12 0.05
51 3 0.01
52 193 0.73
53 30 0.11
54 9 0.03
55 12 0.05
57 6 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (52 bp):
CATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGT
Found at i:30970 original size:71 final size:71
Alignment explanation
Indices: 30895--31253 Score: 428
Period size: 71 Copynumber: 5.1 Consensus size: 71
30885 GATTCTCTCG
30895 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
30960 TTCGCA
66 TTCGCA
30966 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAGTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
*
31029 TTC-TGTCG--
61 TTCATTTCGCA
*
31037 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
31102 TTCGCA
66 TTCGCA
*
31108 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
31168 TTCATTTCGCA
61 TTCATTTCGCA
* *
31179 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTC--GTTGCGATTTT
*
31237 CATTTCGCG
63 CATTTCGCA
31246 TTGCGATT
1 TTGCGATT
31254 GTAATTTCCG
Statistics
Matches: 254, Mismatches: 9, Indels: 52
0.81 0.03 0.17
Matches are distributed among these distances:
66 18 0.07
67 27 0.11
68 21 0.08
69 21 0.08
70 2 0.01
71 138 0.54
72 6 0.02
73 7 0.03
74 8 0.03
76 6 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:31197 original size:33 final size:33
Alignment explanation
Indices: 30914--31253 Score: 262
Period size: 33 Copynumber: 9.8 Consensus size: 33
30904 TCATTTCGCA
*
30914 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
30947 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
30983 CATTGCGATTTTCATTTCGCATTGCGAGTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
31021 CATTGCGATTCTGTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
31056 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
31089 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
31125 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
31160 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
31193 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
31227 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
31254 GTAATTTCCG
Statistics
Matches: 255, Mismatches: 28, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
31 18 0.07
32 10 0.04
33 97 0.38
34 29 0.11
35 11 0.04
36 9 0.04
37 4 0.02
38 53 0.21
39 6 0.02
40 18 0.07
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:33551 original size:12 final size:12
Alignment explanation
Indices: 33534--33558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33524 TCTTCGGGGA
33534 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33546 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33558 C
1 C
33559 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:33767 original size:24 final size:24
Alignment explanation
Indices: 33733--33779 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33723 CTGAAACATC
33733 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
33757 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
33780 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:34489 original size:20 final size:20
Alignment explanation
Indices: 34461--34670 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
34451 AAATTTCAGT
* * *
34461 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34481 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
34501 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34521 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
34541 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
34561 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* * *
34581 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
34601 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34621 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
34641 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
34661 GTTGCGATTT
1 GTTGCGATTT
34671 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:34687 original size:21 final size:20
Alignment explanation
Indices: 34637--34734 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
34627 ATTTATGTGT
* * * *
34637 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
34657 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
34678 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
34698 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
34719 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
34735 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:34729 original size:41 final size:41
Alignment explanation
Indices: 34637--34793 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
34627 ATTTATGTGT
* * *
34637 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
34678 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
34719 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
34759 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
34794 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:34937 original size:20 final size:21
Alignment explanation
Indices: 34914--34958 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
34904 GAACTCCTAT
34914 TTCGCAATACAG-TTTCCAAA
1 TTCGCAATACAGTTTTCCAAA
* *
34934 TTCGCAATGCGGTTTTCCAAA
1 TTCGCAATACAGTTTTCCAAA
34955 TTCG
1 TTCG
34959 TAACACGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (21 bp):
TTCGCAATACAGTTTTCCAAA
Found at i:34990 original size:20 final size:20
Alignment explanation
Indices: 34967--35028 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
34957 CGTAACACGA
34967 ATCTGAAATTTGCAACGCGG
1 ATCTGAAATTTGCAACGCGG
* * *
34987 ATCTG-ATTTTCGCAATGCGA
1 ATCTGAAATTT-GCAACGCGG
*
35007 ATCTGAAATTCGCAACGCGG
1 ATCTGAAATTTGCAACGCGG
35027 AT
1 AT
35029 TTATAAATCG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (20 bp):
ATCTGAAATTTGCAACGCGG
Found at i:35040 original size:40 final size:40
Alignment explanation
Indices: 34964--35048 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
34954 ATTCGTAACA
* ** *
34964 CGAATCTGAAATTTGCAACGCGGATCTGATTTTCGCAATG
1 CGAATCTGAAATTCGCAACGCGGATCTGATAATCGCAACG
*
35004 CGAATCTGAAATTCGCAACGCGGAT-TTATAAATCGCAACG
1 CGAATCTGAAATTCGCAACGCGGATCTGAT-AATCGCAACG
35044 CGAAT
1 CGAAT
35049 TTGTGTAGCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.08
40 36 0.92
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
CGAATCTGAAATTCGCAACGCGGATCTGATAATCGCAACG
Found at i:37988 original size:17 final size:18
Alignment explanation
Indices: 37966--37999 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37956 AATTTAAATT
*
37966 TAAAAAAGTAAA-CAAAC
1 TAAAAAAATAAATCAAAC
37983 TAAAAAAATAAATCAAA
1 TAAAAAAATAAATCAAA
38000 GTATAAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (18 bp):
TAAAAAAATAAATCAAAC
Found at i:43120 original size:15 final size:15
Alignment explanation
Indices: 43102--43142 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
43092 TAACCGGTTT
43102 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
43117 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
*
43134 CGATTTTAA
1 CGGTTTTAA
43143 TATTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:43127 original size:17 final size:17
Alignment explanation
Indices: 43105--43140 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
43095 CCGGTTTCGG
*
43105 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGATT
43122 TTTTAAAAAAACCGATT
1 TTTTAAAAAAACCGATT
43139 TT
1 TT
43141 AATATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAACCGATT
Found at i:43595 original size:21 final size:21
Alignment explanation
Indices: 43564--43620 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
43554 TTTTACACTT
*
43564 AGGGAACCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
*
43585 AGGGTATCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
43606 AGGGTACCGATTCCC
1 AGGGTACCGATTCCC
43621 CTCACGCTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (21 bp):
AGGGTACCGATTCCCTATGAG
Found at i:44325 original size:32 final size:33
Alignment explanation
Indices: 44229--44327 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
44219 AACTCAACAT
* * *
44229 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44262 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44295 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44327 A
1 A
44328 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:44346 original size:21 final size:21
Alignment explanation
Indices: 44322--44363 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44312 ACTTCAAGTT
44322 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
44343 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
44364 AAAATAAACT
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:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:46681 original size:11 final size:12
Alignment explanation
Indices: 46660--46705 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
46650 TCCGGATAAA
46660 AACCGGTTTTTT
1 AACCGGTTTTTT
46672 AACCGGTTTTTTT
1 AACCGG-TTTTTT
46685 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
46699 ATCCGGT
1 AACCGGT
46706 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:46690 original size:15 final size:14
Alignment explanation
Indices: 46659--46698 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
46649 TTCCGGATAA
46659 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
46672 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
46685 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
46699 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:48976 original size:43 final size:43
Alignment explanation
Indices: 48929--49014 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
48919 ATATATTTTG
*
48929 TTTATCAAATAAATTATACAGTTAACTTTTCGAATCAAATCAA
1 TTTATCAAATAAATTATACAGTCAACTTTTCGAATCAAATCAA
*
48972 TTTATCAAATAAATTATACCGTCAACTTTTCGAATCAAATCAA
1 TTTATCAAATAAATTATACAGTCAACTTTTCGAATCAAATCAA
49015 AATACAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (43 bp):
TTTATCAAATAAATTATACAGTCAACTTTTCGAATCAAATCAA
Found at i:52133 original size:19 final size:21
Alignment explanation
Indices: 52046--52144 Score: 91
Period size: 20 Copynumber: 5.0 Consensus size: 21
52036 AAATGACCAA
52046 CAAATTCGCAACGCGAA-TTC
1 CAAATTCGCAACGCGAATTTC
* * *
52066 CAATTTCGCAACTC-AGTTTC
1 CAAATTCGCAACGCGAATTTC
* *
52086 CAATTTCGCAACGCGAATTTG
1 CAAATTCGCAACGCGAATTTC
* *
52107 TAAA-TCGCAAC-TGAATTT-
1 CAAATTCGCAACGCGAATTTC
*
52125 CAAATTCGCAAAGCGAATTT
1 CAAATTCGCAACGCGAATTT
52145 AATTTCGTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.05
19 13 0.21
20 41 0.65
21 6 0.10
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATTTC
Found at i:53076 original size:24 final size:24
Alignment explanation
Indices: 53049--53102 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
53039 GTATTCGAAA
* *
53049 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGATAAATACCCGGAC
* * *
53073 TTTGATCTTGATAAATACTCGGAT
1 TTTGATATTGATAAATACCCGGAC
53097 TTTGAT
1 TTTGAT
53103 GATGTGATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGATAAATACCCGGAC
Found at i:55749 original size:20 final size:20
Alignment explanation
Indices: 55724--55771 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
55714 AATAAGCATT
55724 GCGAATTTGACTATCGCGTA
1 GCGAATTTGACTATCGCGTA
* *
55744 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTATCGCGTA
55764 GCGAATTT
1 GCGAATTT
55772 ACCTTCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
GCGAATTTGACTATCGCGTA
Found at i:55877 original size:25 final size:25
Alignment explanation
Indices: 55837--55886 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
55827 AAATCAATTA
* *
55837 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
55862 AACATTGTTATAGGTACATTATTTG
1 AACATTGTTATAGGTACATTATTTG
55887 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTGTTATAGGTACATTATTTG
Found at i:56295 original size:18 final size:18
Alignment explanation
Indices: 56274--56310 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56264 GTAATTGGAG
56274 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
56292 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
56310 T
1 T
56311 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:56317 original size:24 final size:24
Alignment explanation
Indices: 56266--56318 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56256 TTTCATATGT
* * *
56266 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
56290 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
56314 AATTT
1 AATTT
56319 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:56643 original size:39 final size:39
Alignment explanation
Indices: 56586--56672 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
56576 TTCGATGCTC
*
56586 ATCAAAATTCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
56625 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
56664 ATCAAAATC
1 ATCAAAATC
56673 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:58246 original size:21 final size:21
Alignment explanation
Indices: 58222--58317 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
58212 GGCGGGACCA
*
58222 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
58243 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* *
58264 CTTCG-ATGATGAGAAGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
58285 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
58306 CTTGAATGATGA
1 CTTGAACGATGA
58318 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:58300 original size:42 final size:42
Alignment explanation
Indices: 58222--58317 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
58212 GGCGGGACCA
* * * * * * *
58222 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCGCCT
58264 CTTCG-ATGATGAGAAGGGCCTCTTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCGCCT
58306 CTTGAATGATGA
1 CTTGAATGATGA
58318 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGAGAAGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:60768 original size:22 final size:22
Alignment explanation
Indices: 60740--60787 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
60730 GATGGAGATA
*
60740 GACGGATTTCGTCGGAAATGAG
1 GACGGATTTCGTCAGAAATGAG
*
60762 GACGGATTTCGTCAGAGATGAG
1 GACGGATTTCGTCAGAAATGAG
60784 GACG
1 GACG
60788 ATGTTGCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGAG
Found at i:60913 original size:20 final size:20
Alignment explanation
Indices: 60888--60992 Score: 99
Period size: 20 Copynumber: 5.2 Consensus size: 20
60878 GCGTAAAAAC
60888 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
60908 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
60928 ATTTGACTATT-ACGTTGCGA
1 ATTTGACT-TTCGCGTTGCGA
* * *
60948 ATTTGACTTTTGTGTTG-GG
1 ATTTGACTTTCGCGTTGCGA
*
60967 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
60988 ATTTG
1 ATTTG
60993 GAAAATCGCA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
18 2 0.03
19 7 0.10
20 52 0.78
21 6 0.09
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:65022 original size:31 final size:30
Alignment explanation
Indices: 64977--65041 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
64967 TTTTATGATC
* * *
64977 ATAAAATTCGATAAATTTAATAATTATTTT
1 ATAAAATTCAATAAATTTAATAAATATCTT
65007 ATAATAATTCAATAAATTTAATAAATATCTT
1 ATAA-AATTCAATAAATTTAATAAATATCTT
65038 ATAA
1 ATAA
65042 CAGAATAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAAAATTCAATAAATTTAATAAATATCTT
Found at i:65509 original size:22 final size:22
Alignment explanation
Indices: 65481--65531 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
65471 TTTCTACCTC
65481 TCATCTACAATATTCACTCTCT
1 TCATCTACAATATTCACTCTCT
* *
65503 TTATCTACAATATTCCCTCTCT
1 TCATCTACAATATTCACTCTCT
65525 TCATCTA
1 TCATCTA
65532 TACTACATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATCTACAATATTCACTCTCT
Found at i:84610 original size:16 final size:15
Alignment explanation
Indices: 84589--84683 Score: 63
Period size: 16 Copynumber: 6.2 Consensus size: 15
84579 AAAGAAGAAA
84589 AAAATGAGAAAAAAGG
1 AAAATGA-AAAAAAGG
* *
84605 AAAATGATGGAAAACACG
1 AAAATGA---AAAAAAGG
84623 AAAA-GAAAAAAA--
1 AAAATGAAAAAAAGG
* *
84635 AGAA-GAAAAAATGG
1 AAAATGAAAAAAAGG
*
84649 AAAATGAAAAAAGAGA
1 AAAATGAAAAAA-AGG
84665 AAAATGAAAAAAAGAG
1 AAAATGAAAAAAAG-G
84681 AAA
1 AAA
84684 TAAAAGAGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
12 10 0.16
14 8 0.13
15 9 0.14
16 23 0.37
17 2 0.03
18 11 0.17
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAATGAAAAAAAGG
Found at i:84676 original size:44 final size:43
Alignment explanation
Indices: 84563--84682 Score: 108
Period size: 44 Copynumber: 2.8 Consensus size: 43
84553 AATAATAATA
*
84563 AAAATGAG-AAGA-AGAAAAAGAAGAAAAAAATG-AGAAAAAAGG
1 AAAATGAGAAAAACAGAAAAAGAA-AAAAAAA-GAAGAAAAAAGG
*
84605 AAAATGATGGAAAACACG-AAAAG-AAAAAAAAGAAGAAAAAATGG
1 AAAATGA-GAAAAACA-GAAAAAGAAAAAAAAAGAAGAAAAAA-GG
* *
84649 AAAATGA-AAAAAGAGAAAAATGAAAAAAAGAGAA
1 AAAATGAGAAAAACAGAAAAA-GAAAAAAAAAGAA
84683 ATAAAAGAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
41 1 0.02
42 17 0.26
43 17 0.26
44 23 0.35
45 6 0.09
46 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.06
Consensus pattern (43 bp):
AAAATGAGAAAAACAGAAAAAGAAAAAAAAAGAAGAAAAAAGG
Found at i:84678 original size:17 final size:16
Alignment explanation
Indices: 84649--84683 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
84639 GAAAAAATGG
84649 AAAATGAAAAAAGAGA
1 AAAATGAAAAAAGAGA
84665 AAAATGAAAAAAAGAGA
1 AAAATG-AAAAAAGAGA
84682 AA
1 AA
84684 TAAAAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAATGAAAAAAGAGA
Found at i:84684 original size:15 final size:15
Alignment explanation
Indices: 84622--84688 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
84612 TGGAAAACAC
*
84622 GAAAAGAAAAAAA-A
1 GAAATGAAAAAAAGA
*
84636 G-AA-GAAAAAATG-
1 GAAATGAAAAAAAGA
84648 GAAAATGAAAAAAGAGA
1 G-AAATGAAAAAA-AGA
*
84665 AAAATGAAAAAAAGA
1 GAAATGAAAAAAAGA
84680 GAAAT-AAAA
1 GAAATGAAAA
84689 GAGAGTTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 8 0.19
13 2 0.05
14 7 0.16
15 14 0.33
16 12 0.28
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
GAAATGAAAAAAAGA
Found at i:86024 original size:55 final size:55
Alignment explanation
Indices: 85964--86497 Score: 722
Period size: 55 Copynumber: 9.7 Consensus size: 55
85954 TTTATGAAGA
* *
85964 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACTCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* *
86019 TCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTATGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* *
86074 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACTCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* *
86129 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTATGAAGATTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
*
86184 TCGAGTTCTATACTCTCTGAAGGAAAAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * * * *
86239 TCGAGTTCTATACTCCCTGAATGAATAGGGAACAGACCCGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGT
86294 TCGAGTTCTATACTCT-TGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * * * *
86348 TCGAGTTCTATACTCCCTGGATGAATAGGGAGCGGACCCG-TTTATTGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGT
* * * * * *
86403 TCGAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACACATTTT-TCGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTAT-GAAGATTGT
* *
86458 TCGAG-TCTTATACTC-CTTGAAAGAATAGGGAGCGGACCCG
1 TCGAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGGACCCG
86498 CCATTTGAAG
Statistics
Matches: 431, Mismatches: 40, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.00
54 55 0.13
55 371 0.86
56 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
Found at i:94147 original size:79 final size:78
Alignment explanation
Indices: 94008--94152 Score: 193
Period size: 79 Copynumber: 1.8 Consensus size: 78
93998 TTTTAATATT
* * * *
94008 TCCGATAAAGTGTTAATATTAACATTTATGATAGAAAAATAATGTTTTAGGTAACGTTTTACCGA
1 TCCGATAAAGTATTAATAATAACATTTATGATAAAAAAATAATGTTTTAGATAACGTTTTACCGA
94073 ATACGTTAACAAA
66 ATACGTTAACAAA
* * **
94086 TCCGATAAAGTATTGAATAATAACATTTTTGGTAAAAATAAT-ATGTTTTAGATAATTTTTTACC
1 TCCGATAAAGTATT-AATAATAACATTTATGATAAAAA-AATAATGTTTTAGATAACGTTTTACC
94150 GAA
64 GAA
94153 AATATTAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
78 13 0.23
79 41 0.72
80 3 0.05
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (78 bp):
TCCGATAAAGTATTAATAATAACATTTATGATAAAAAAATAATGTTTTAGATAACGTTTTACCGA
ATACGTTAACAAA
Found at i:94186 original size:16 final size:15
Alignment explanation
Indices: 94165--94199 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
94155 TATTAGAAAA
94165 ATAATAATATTTTTG
1 ATAATAATATTTTTG
94180 TATAATAATATTTTTG
1 -ATAATAATATTTTTG
94196 ATAA
1 ATAA
94200 CGTCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
ATAATAATATTTTTG
Found at i:105616 original size:69 final size:69
Alignment explanation
Indices: 105525--105654 Score: 224
Period size: 69 Copynumber: 1.9 Consensus size: 69
105515 ATCAATGGTT
* * *
105525 TTCATTTTTGATTCATCTATTAATTAATTATAAAAGATGTGTATATATATAGATCAAATCTCAGT
1 TTCATATTTGATTCATCAATTAACTAATTATAAAAGATGTGTATATATATAGATCAAATCTCAGT
105590 GTTC
66 GTTC
*
105594 TTCATATTTGATTGATCAATTAACTAATTATAAAAGATGTGTATATATATAGATCAAATCT
1 TTCATATTTGATTCATCAATTAACTAATTATAAAAGATGTGTATATATATAGATCAAATCT
105655 TAGAAATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (69 bp):
TTCATATTTGATTCATCAATTAACTAATTATAAAAGATGTGTATATATATAGATCAAATCTCAGT
GTTC
Found at i:107295 original size:18 final size:17
Alignment explanation
Indices: 107272--107305 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
107262 ATCTATATCA
107272 AATCAAAATTTATAAAAT
1 AATC-AAATTTATAAAAT
*
107290 AATCAAGTTTATAAAA
1 AATCAAATTTATAAAA
107306 CTATTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (17 bp):
AATCAAATTTATAAAAT
Found at i:117470 original size:24 final size:24
Alignment explanation
Indices: 117434--117483 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
117424 CTATTGTTAA
*
117434 AAAAATAATAATCATATTGAAAAT
1 AAAAATAACAATCATATTGAAAAT
*
117458 AAAATTAACAATCATATTGAAAAT
1 AAAAATAACAATCATATTGAAAAT
117482 AA
1 AA
117484 TTATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAATAACAATCATATTGAAAAT
Found at i:117742 original size:22 final size:22
Alignment explanation
Indices: 117713--117757 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
117703 AGAATTTAAA
117713 ATTCAAGATTTAGGGTC-ATAT
1 ATTCAAGATTTAGGGTCTATAT
*
117734 ATTCTAAGATTTATGGTCTATAT
1 ATTC-AAGATTTAGGGTCTATAT
117757 A
1 A
117758 GAGTTTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (22 bp):
ATTCAAGATTTAGGGTCTATAT
Found at i:120755 original size:29 final size:29
Alignment explanation
Indices: 120713--120771 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
120703 ATTTTCACCT
120713 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
120742 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
120771 A
1 A
120772 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:125698 original size:29 final size:29
Alignment explanation
Indices: 125664--125722 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
125654 CCTAAATTAA
125664 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
125693 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
125722 T
1 T
125723 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:130240 original size:23 final size:23
Alignment explanation
Indices: 130203--130294 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
130193 CACCACAGCT
* *
130203 CGTATAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
130226 TGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
130249 CGTAGAATTGCACC-AGAGTGACA
1 CGTAGAATTGCACCGA-AGTGCCA
*
130272 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
130295 TATAATAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:130531 original size:103 final size:103
Alignment explanation
Indices: 130310--130624 Score: 569
Period size: 103 Copynumber: 3.1 Consensus size: 103
130300 TAATGTCCAT
* * * *
130310 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
130375 GACTT-ACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
130412 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
130477 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
130515 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
130580 GACTTCACACATGTTCCAAAGAATACATATATATTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
130618 AAGGACC
1 AAGGACC
130625 GCGTAGACCC
Statistics
Matches: 206, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
102 66 0.32
103 140 0.68
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:136074 original size:3 final size:3
Alignment explanation
Indices: 136066--136151 Score: 156
Period size: 3 Copynumber: 28.7 Consensus size: 3
136056 AGTGAGCCAA
136066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
136112 AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
136152 CAAGGAATTG
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.02
3 76 0.94
4 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:137066 original size:24 final size:24
Alignment explanation
Indices: 137034--137092 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
137024 TCTACAGGGT
137034 ATCGATGCACTCCTTAATGTGTGC
1 ATCGATGCACTCCTTAATGTGTGC
137058 ATCGATGCACTCCTTAATGTGTGC
1 ATCGATGCACTCCTTAATGTGTGC
137082 ATCGATGCACT
1 ATCGATGCACT
137093 ACCCATGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (24 bp):
ATCGATGCACTCCTTAATGTGTGC
Found at i:140168 original size:23 final size:23
Alignment explanation
Indices: 140137--140228 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
140127 CACCACAGCT
* *
140137 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
140160 CATAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
140183 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
*
140206 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
140229 TATAATAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:140417 original size:103 final size:103
Alignment explanation
Indices: 140251--140557 Score: 528
Period size: 103 Copynumber: 3.0 Consensus size: 103
140241 CATAAGGGCT
* * * * *
140251 ACATATCATTCCTTGAGAAT-A-ATATATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
140314 CACATGTTCCAAAGAATACATATATGTCCCGAATGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
140352 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
140417 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
140455 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
* *
140520 CATATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
140558 GCGTAGACCC
Statistics
Matches: 196, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
101 19 0.10
102 1 0.01
103 176 0.90
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
Found at i:142266 original size:21 final size:21
Alignment explanation
Indices: 142242--142286 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
142232 TTTTGTTCGT
* *
142242 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
142263 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
142284 TTG
1 TTG
142287 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:145324 original size:23 final size:23
Alignment explanation
Indices: 145298--145366 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
145288 CACCACAGCT
*
145298 CGTATAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
* *
145321 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCA
145344 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
145367 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:145553 original size:103 final size:103
Alignment explanation
Indices: 145389--145702 Score: 529
Period size: 103 Copynumber: 3.0 Consensus size: 103
145379 CATAAGGACT
* * * * * *
145389 ACATATCATTCCTTAAGAGTCATATATATATACTAGGGATTAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
145454 CACATGTTCCAAAGAATACATATATGTCTCGAAAGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
145492 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
145557 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
*
145595 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTTACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
*
145660 CACATGTTCCAAAGAATACATATATGTCCCGAATGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
*
145698 GCATA
1 ACATA
145703 GACCCTCAAT
Statistics
Matches: 200, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 200 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAAAGACC
Found at i:147409 original size:21 final size:21
Alignment explanation
Indices: 147385--147450 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
147375 TTTTGTTCGT
* * *
147385 TTGAAGGGGTATCGGTTCCCC
1 TTGAATGGGTACCGATTCCCC
147406 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
147427 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
147448 TTG
1 TTG
147451 CCCAGAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:150652 original size:3 final size:3
Alignment explanation
Indices: 150644--150675 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
150634 AGTGAGGCAA
*
150644 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
150676 GGAATTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:150953 original size:23 final size:23
Alignment explanation
Indices: 150894--150954 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
150884 CTCGTATAAA
*
150894 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
* *
150917 TGCACCAAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
150940 TGCACCGTAGTGCTA
1 TGCACCGAAGTGCTA
150955 TATAAGATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCTACGTAGAAT
Found at i:159108 original size:22 final size:20
Alignment explanation
Indices: 159059--159113 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
159049 TGATCACTTA
159059 ATTATTTAATTATATGAACG
1 ATTATTTAATTATATGAACG
* *
159079 ATCT-TTTAATTTTATTAATCAG
1 AT-TATTTAATTATATGAA-C-G
159101 ATTATTTAATTAT
1 ATTATTTAATTAT
159114 TTAAATGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 14 0.50
21 3 0.11
22 11 0.39
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTATTTAATTATATGAACG
Found at i:159624 original size:31 final size:31
Alignment explanation
Indices: 159583--159657 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
159573 TTAAATAATT
* * *
159583 ATTAAATTTATTGAACTGTTATAAAACTATC
1 ATTAATTTTATTGAAATGTTATAAAACGATC
159614 ATTAATTTTATTGAAATGTTATAAAACGATC
1 ATTAATTTTATTGAAATGTTATAAAACGATC
159645 ATTAAATTTTATT
1 ATT-AATTTTATT
159658 CATATGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 31 0.77
32 9 0.22
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (31 bp):
ATTAATTTTATTGAAATGTTATAAAACGATC
Found at i:161023 original size:70 final size:70
Alignment explanation
Indices: 160910--161050 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 70
160900 GTGAGAGGCA
* * *
160910 TGAGGTTCAGTTCCCCGCACCTCCAATCTCTCTTTTACTACATTTATGTGAGAATGTCTTAAATG
1 TGAGGTTCAATTCCCCACACCTCCAATCTCTCTTTTACTACATTTATGTGAGAATGTCATAAATG
160975 CAGGT
66 CAGGT
*
160980 TGAGGTTCAATTCCCCACACCTCCAATCTGTCTTTTACTACATTTATGTGAGAATGTCATAAATG
1 TGAGGTTCAATTCCCCACACCTCCAATCTCTCTTTTACTACATTTATGTGAGAATGTCATAAATG
161045 CAGGT
66 CAGGT
161050 T
1 T
161051 TTGTTTTAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (70 bp):
TGAGGTTCAATTCCCCACACCTCCAATCTCTCTTTTACTACATTTATGTGAGAATGTCATAAATG
CAGGT
Found at i:166105 original size:15 final size:14
Alignment explanation
Indices: 166080--166109 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
166070 ATGCGGGCTT
166080 TTTAACCCGCACCG
1 TTTAACCCGCACCG
166094 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
166109 T
1 T
166110 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:166875 original size:3 final size:3
Alignment explanation
Indices: 166867--166909 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
166857 CTCAATAAAC
166867 ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
166910 GGTATAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:167258 original size:21 final size:21
Alignment explanation
Indices: 167207--167259 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
167197 ATTATGACTA
167207 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
167228 TCTCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
167249 TCGCAATGCGA
1 TCGCAATGCGA
167260 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:167292 original size:21 final size:21
Alignment explanation
Indices: 167249--167321 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
167239 TTTTCCCAAT
* *
167249 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
167269 TCGCAATGCGAATTTTGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
167290 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
167311 TCGCAACGCGA
1 TCGCAATGCGA
167322 TATATACTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 12 0.26
21 35 0.74
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:167356 original size:21 final size:21
Alignment explanation
Indices: 167330--167373 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
167320 GATATATACT
167330 TAATACAAAATCGCAACGCGA
1 TAATACAAAATCGCAACGCGA
167351 TAATACAAAATCGCAACGCGA
1 TAATACAAAATCGCAACGCGA
167372 TA
1 TA
167374 CTGACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.16
Consensus pattern (21 bp):
TAATACAAAATCGCAACGCGA
Found at i:167392 original size:20 final size:20
Alignment explanation
Indices: 167361--167433 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
167351 TAATACAAAA
167361 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * * *
167381 TTGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
*
167401 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
167421 TCGCAACGAGATA
1 TCGCAACGCGATA
167434 ATACATAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:169290 original size:18 final size:18
Alignment explanation
Indices: 169269--169316 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
169259 TCCACTTCGG
*
169269 GAGCCATCACCTTACCCA
1 GAGCCATCACCTCACCCA
*
169287 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
169305 GAGCCATCACCT
1 GAGCCATCACCT
169317 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Done.