Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:2077 original size:19 final size:19
Alignment explanation
Indices: 2055--2358 Score: 365
Period size: 19 Copynumber: 17.4 Consensus size: 19
2045 CGGAAAATAC
*
2055 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2074 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2088 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2107 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2121 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2140 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
2158 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2172 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
2190 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2209 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
2223 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
2242 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2261 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2280 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2299 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2313 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2332 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2351 AATCGCAA
1 AATCGCAA
2359 CGAGATAATC
Statistics
Matches: 249, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.00
14 47 0.19
15 1 0.00
16 18 0.07
17 14 0.06
18 24 0.10
19 144 0.58
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2101 original size:33 final size:34
Alignment explanation
Indices: 2055--2380 Score: 277
Period size: 33 Copynumber: 9.5 Consensus size: 34
2045 CGGAAAATAC
* *
2055 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
* *
2088 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
2121 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
*
2158 AATCGCAA--CG--A-GAGAATCGCAATGCGAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-AATGAA
* * *
2190 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
*
2223 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
2261 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
2299 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* *
2332 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
2365 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2381 TATAAACGCA
Statistics
Matches: 253, Mismatches: 18, Indels: 44
0.80 0.06 0.14
Matches are distributed among these distances:
31 4 0.02
32 22 0.09
33 128 0.51
34 5 0.02
35 11 0.04
36 8 0.03
37 20 0.08
38 55 0.22
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:2287 original size:90 final size:88
Alignment explanation
Indices: 2083--2380 Score: 368
Period size: 90 Copynumber: 3.4 Consensus size: 88
2073 AAATCCCAAC
* * * * *
2083 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGAA-AATCGC
1 ATGAAAATCGCAATGCG-AATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAAGAATCGC
*
2146 AATGCGAAA-TGAAATCGCAA--CG--
62 AATGCGAAATTAAAATCGCAATGCGAA
*
2168 A-GAGAATCGCAATGCGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAAT
1 ATGAAAATCGCAATGCGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-AGAATCGCAAT
2232 GCGAAATTAAAATCGCAATGCGAA
65 GCGAAATTAAAATCGCAATGCGAA
2256 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
1 ATGAAAATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAAAATCGCAACG-AAGAATCGCAA
*
2321 TGCGAAATGAAAATCGCAATGCGAA
64 TGCGAAATTAAAATCGCAATGCGAA
*
2346 ATGAAAATCGCAA--CG-A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAATGAAAATCGCAATGCGAAAT
2381 TATAAACGCA
Statistics
Matches: 192, Mismatches: 10, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
81 7 0.04
82 7 0.04
83 32 0.17
84 24 0.12
85 19 0.10
86 3 0.02
88 3 0.02
89 14 0.07
90 82 0.43
91 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (88 bp):
ATGAAAATCGCAATGCGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATG
CGAAATTAAAATCGCAATGCGAA
Found at i:2338 original size:52 final size:55
Alignment explanation
Indices: 2055--2380 Score: 337
Period size: 52 Copynumber: 6.3 Consensus size: 55
2045 CGGAAAATAC
* *
2055 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
2107 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATGA
*
2158 AATCGCAA--CG--A-GAGAATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
2209 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
2261 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
2313 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
2365 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2381 TATAAACGCA
Statistics
Matches: 253, Mismatches: 6, Indels: 30
0.88 0.02 0.10
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 1 0.00
50 25 0.10
51 50 0.20
52 128 0.51
53 2 0.01
54 5 0.02
55 6 0.02
57 26 0.10
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:2496 original size:19 final size:19
Alignment explanation
Indices: 2387--2488 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2377 AAATTATAAA
2387 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2406 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2426 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2442 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2459 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2478 CGCATTGCGAT
1 CGCATTGCGAT
2489 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:2614 original size:14 final size:14
Alignment explanation
Indices: 2595--2631 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2585 CATCAATTAC
2595 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2609 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2623 ACAAATCAA
1 ACAAATCAA
2632 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:4537 original size:20 final size:18
Alignment explanation
Indices: 4512--4621 Score: 56
Period size: 19 Copynumber: 6.3 Consensus size: 18
4502 TAGTTTACTT
4512 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA--TAAAA
* *
4532 TCGCAACGCGAAATGAAA
1 TCGCAACACGAAATAAAA
* *
4550 TCGC-A-ACG--ACAGAA
1 TCGCAACACGAAATAAAA
**
4564 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAAT-AAAA
*
4583 TCGC-A-ACG-AA-AGAA
1 TCGCAACACGAAATAAAA
*
4597 TCGCAACGCGAAATGAAAA
1 TCGCAACACGAAAT-AAAA
4616 TCGCAA
1 TCGCAA
4622 TGCGATTTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 21
0.66 0.13 0.21
Matches are distributed among these distances:
14 14 0.21
15 2 0.03
16 8 0.12
17 5 0.07
18 10 0.15
19 16 0.24
20 12 0.18
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (18 bp):
TCGCAACACGAAATAAAA
Found at i:4567 original size:14 final size:14
Alignment explanation
Indices: 4548--4604 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4538 CGCGAAATGA
*
4548 AATCGCAACGACAG
1 AATCGCAACGAAAG
4562 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
4579 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4595 AATCGCAACG
1 AATCGCAACG
4605 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:4586 original size:19 final size:17
Alignment explanation
Indices: 4529--4626 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 17
4519 ACGAAACTTA
4529 AAATCGCAACGCGAAATG
1 AAATCGCAA-GCGAAATG
*
4547 AAATCGCAA-CGACA-G
1 AAATCGCAAGCGAAATG
4562 -AATCGCAATGCGAAATG
1 AAATCGCAA-GCGAAATG
4579 AAAATCGCAA-CGAAA-G
1 -AAATCGCAAGCGAAATG
4595 -AATCGCAACGCGAAATG
1 AAATCGCAA-GCGAAATG
4612 AAAATCGCAATGCGA
1 -AAATCGCAA-GCGA
4627 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
14 16 0.24
15 1 0.01
16 14 0.21
17 7 0.10
18 9 0.13
19 20 0.30
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (17 bp):
AAATCGCAAGCGAAATG
Found at i:4589 original size:33 final size:33
Alignment explanation
Indices: 4530--4621 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
4520 CGAAACTTAA
*
4530 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
4562 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4595 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4622 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 16 0.29
33 40 0.71
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:4644 original size:19 final size:19
Alignment explanation
Indices: 4622--4750 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4612 AAAATCGCAA
4622 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4641 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
4655 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4674 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4688 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4707 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4726 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4746 TGCGA
1 TGCGA
4751 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:4664 original size:33 final size:33
Alignment explanation
Indices: 4622--4713 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
4612 AAAATCGCAA
4622 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
4655 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
4688 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
4714 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:4952 original size:92 final size:93
Alignment explanation
Indices: 4794--5171 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
4784 TTGAATGGAT
4794 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4859 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4887 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4951 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4979 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5042 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5070 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5135 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5163 AAATTTACT
1 AAATTTACT
5172 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 89 0.32
92 96 0.34
93 96 0.34
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:6907 original size:19 final size:18
Alignment explanation
Indices: 6883--6980 Score: 86
Period size: 19 Copynumber: 5.7 Consensus size: 18
6873 TCGCAACGAG
6883 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
6901 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
6916 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
6935 AATCGCAA--CGAGA-G-
1 AATCGCAACGCGAGATGA
*
6949 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
*
6968 AATCGCAATGCGA
1 AATCGCAACGCGA
6981 TTTGGTTTCG
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 16 0.25
16 10 0.15
17 11 0.17
19 28 0.43
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:6921 original size:14 final size:14
Alignment explanation
Indices: 6871--6958 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
6861 TTGAAATGAA
6871 AATCGCAAC--GAG
1 AATCGCAACGAGAG
6883 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
6900 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
6916 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6935 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6949 AATCGCAACG
1 AATCGCAACG
6959 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
12 8 0.13
14 21 0.34
15 1 0.02
16 5 0.08
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6922 original size:33 final size:33
Alignment explanation
Indices: 6863--6975 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
6853 TCTTTTGGTT
6863 GAAATGAAAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
6894 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6927 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6960 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6976 TGCGATTTGG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 15 0.20
33 61 0.80
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:7010 original size:14 final size:14
Alignment explanation
Indices: 6991--7045 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6981 TTTGGTTTCG
6991 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7005 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
7024 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
7038 CGTTGCGA
1 CGTTGCGA
7046 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7053 original size:33 final size:33
Alignment explanation
Indices: 6986--7067 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
6976 TGCGATTTGG
***
6986 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
7019 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
7052 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
7068 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:7072 original size:20 final size:20
Alignment explanation
Indices: 6998--7086 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
6988 TCGCGTTGCG
6998 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
7018 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
7031 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
7051 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
7071 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
7087 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:7208 original size:33 final size:33
Alignment explanation
Indices: 7166--7236 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
7156 AATACTAACT
*
7166 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
7199 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
7232 TGAAA
1 TGAAA
7237 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:7469 original size:22 final size:22
Alignment explanation
Indices: 7417--7471 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
7407 TGGTTGTGAG
**
7417 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
7439 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
7461 GGATTTCTTCG
1 GGATTTCTTCG
7472 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:7641 original size:20 final size:20
Alignment explanation
Indices: 7616--7808 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
7606 CTTTAAATAT
7616 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
7636 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
7658 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
7677 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
7697 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
7717 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
7737 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
7757 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
7777 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
7797 CGCGTTGCGATT
1 CGCGTTGCGATT
7809 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:7803 original size:60 final size:60
Alignment explanation
Indices: 7616--7808 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
7606 CTTTAAATAT
**
7616 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
7677 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
7737 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
7797 CGCGTTGCGATT
1 CGCGTTGCGATT
7809 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, 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:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:7889 original size:20 final size:20
Alignment explanation
Indices: 7864--7915 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
7854 AAGAATCGCG
*
7864 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
7884 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
7904 TTGCGATTCTGG
1 TTGCGATTCTGG
7916 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:12481 original size:31 final size:31
Alignment explanation
Indices: 12438--12515 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
12428 GATAACATCT
12438 TAGTTTAGGTACTAAAATAGACCAAAATTGA
1 TAGTTTAGGTACTAAAATAGACCAAAATTGA
* *
12469 TAGTTTAAGTACTAAAATAGATCAAAATTGA
1 TAGTTTAGGTACTAAAATAGACCAAAATTGA
*
12500 TAGTTTAGGCACTAAA
1 TAGTTTAGGTACTAAA
12516 TGTATAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (31 bp):
TAGTTTAGGTACTAAAATAGACCAAAATTGA
Found at i:12908 original size:15 final size:15
Alignment explanation
Indices: 12863--12909 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12853 GTCATCGGTT
12863 CGTTCGATTTTAGTC
1 CGTTCGATTTTAGTC
* *
12878 CCTAACG-TTATTAGTC
1 CGT-TCGATT-TTAGTC
12894 CGTTCGATTTTAGTC
1 CGTTCGATTTTAGTC
12909 C
1 C
12910 TTCAACCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (15 bp):
CGTTCGATTTTAGTC
Found at i:13103 original size:15 final size:15
Alignment explanation
Indices: 13080--13116 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
13070 GGACGGATGA
13080 CAACCTCTAAGATTT
1 CAACCTCTAAGATTT
*
13095 CAACTTCTAAGATTT
1 CAACCTCTAAGATTT
13110 CAACCTC
1 CAACCTC
13117 GGACCAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (15 bp):
CAACCTCTAAGATTT
Found at i:15844 original size:26 final size:27
Alignment explanation
Indices: 15801--15851 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
15791 TCAAATATCG
*
15801 TTTTTCACGAATAGGTGTCTAAAATAT
1 TTTTTCACGAATAGGTGTCAAAAATAT
* *
15828 TTTTTGACTAATA-GTGTCAAAAAT
1 TTTTTCACGAATAGGTGTCAAAAAT
15852 TACATACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (27 bp):
TTTTTCACGAATAGGTGTCAAAAATAT
Found at i:20307 original size:51 final size:50
Alignment explanation
Indices: 20218--20387 Score: 232
Period size: 51 Copynumber: 3.3 Consensus size: 50
20208 CTTCCAATGA
*
20218 CTGATCTATATTATATTGAACATTTTTTTCCCACGTTTGCTTTATTAGTTGG
1 CTGATTTATATTATA-TGAAC-TTTTTTTCCCACGTTTGCTTTATTAGTTGG
* ** *
20270 CTGATTTATATTATATAGAGCTTTTTCCCCCACGTTTGCTTTCTTAGTTGG
1 CTGATTTATATTATAT-GAACTTTTTTTCCCACGTTTGCTTTATTAGTTGG
* * *
20321 CTGATTTATATTATACTGACCTTTTTTTTCCACGTTTGCTTTATTGGTTGG
1 CTGATTTATATTATA-TGAACTTTTTTTCCCACGTTTGCTTTATTAGTTGG
20372 CTGATTTATATTATAT
1 CTGATTTATATTATAT
20388 TACTTTATTG
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 86 0.82
52 18 0.17
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (50 bp):
CTGATTTATATTATATGAACTTTTTTTCCCACGTTTGCTTTATTAGTTGG
Found at i:21864 original size:26 final size:28
Alignment explanation
Indices: 21802--21864 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
21792 CGAGTATTGT
*
21802 TGAGCTCGACTCGACTCGAAAACTCTGAAA
1 TGAGCTCAACTCGACTCGAAAACTCTG--A
21832 TGAAGCTCAACTCGACTCGAAAACTC-G-
1 TG-AGCTCAACTCGACTCGAAAACTCTGA
21859 TGAGCT
1 TGAGCT
21865 TAAAGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 2 0.06
30 3 0.10
31 22 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (28 bp):
TGAGCTCAACTCGACTCGAAAACTCTGA
Found at i:22634 original size:18 final size:20
Alignment explanation
Indices: 22590--22633 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
22580 CTAAAAAGAT
22590 AGTTTTAATTCAATAAGAGA
1 AGTTTTAATTCAATAAGAGA
*
22610 AGTTTTAATTCAATGAGAG-
1 AGTTTTAATTCAATAAGAGA
22629 AGTTT
1 AGTTT
22634 ATGTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (20 bp):
AGTTTTAATTCAATAAGAGA
Found at i:23074 original size:22 final size:21
Alignment explanation
Indices: 23011--23068 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
23001 CACCGAAAAA
*
23011 CTAAGAAGAAAAAAGAATATTTT
1 CTAAGAAG-AAGAA-AATATTTT
*
23034 CTAAGAAGGAGAAAATATTTT
1 CTAAGAAGAAGAAAATATTTT
*
23055 TTAAG-AGAAGAAAA
1 CTAAGAAGAAGAAAA
23069 GTTATTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 3 0.10
23 8 0.26
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.24
Consensus pattern (21 bp):
CTAAGAAGAAGAAAATATTTT
Found at i:23262 original size:44 final size:44
Alignment explanation
Indices: 23174--23283 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
23164 TTCAAACTCT
23174 AAAAGAT-A-ATATA-TTTTAATTATCTTTTAATTTTAAATATTA
1 AAAAGATAATATATATTTTTAA-TATCTTTTAATTTTAAATATTA
*
23216 AAAAGATAATGATATATTTTTAATATC-TTTAATATTT-AATTTTA
1 AAAAGATAAT-ATATATTTTTAATATCTTTTAAT-TTTAAATATTA
* *
23260 AAAATATAATAAATATCTTTTAAT
1 AAAAGATAATATATAT-TTTTAAT
23284 TTAAAATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
42 7 0.12
43 6 0.10
44 28 0.47
45 12 0.20
46 6 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (44 bp):
AAAAGATAATATATATTTTTAATATCTTTTAATTTTAAATATTA
Found at i:23354 original size:63 final size:63
Alignment explanation
Indices: 23279--23397 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
23269 TAAATATCTT
*
23279 TTAATTTAAAATATTCAAAA-TATATAAACT-TCTTTTACTATTCAAACTTAAATAGACATTATG
1 TTAATTTAAAATATTCAAAAGTATAT-AACTATCTTTTAATA-TCAAACTTAAATAGACATTATG
* * *
23342 TTAATTTGAAATATTCAAAAGTATATAATTATCTTTTAATATCAAAGTTAAATAGA
1 TTAATTTAAAATATTCAAAAGTATATAACTATCTTTTAATATCAAACTTAAATAGA
23398 TAATAAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 36 0.72
64 14 0.28
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (63 bp):
TTAATTTAAAATATTCAAAAGTATATAACTATCTTTTAATATCAAACTTAAATAGACATTATG
Found at i:29624 original size:21 final size:21
Alignment explanation
Indices: 29598--29637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29588 ACAAACCCCA
*
29598 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
29619 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
29638 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:33528 original size:22 final size:21
Alignment explanation
Indices: 33486--33525 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33476 GAGTTTGTTT
*
33486 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
33507 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
33526 ACAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:55174 original size:217 final size:217
Alignment explanation
Indices: 54799--55229 Score: 862
Period size: 217 Copynumber: 2.0 Consensus size: 217
54789 AGCAAGTTCG
54799 GGGCCACAAAGTCAAGTTCACAGGTGTACTGAATGAAGCGGTTGTTGAATCTTGAACAGCTTGCC
1 GGGCCACAAAGTCAAGTTCACAGGTGTACTGAATGAAGCGGTTGTTGAATCTTGAACAGCTTGCC
54864 TTCTCAAGTCACCCAACCTTGAAGAAAAGAAGTCCCTACTTTGCAGTGAAGAAGAGGGATAATCC
66 TTCTCAAGTCACCCAACCTTGAAGAAAAGAAGTCCCTACTTTGCAGTGAAGAAGAGGGATAATCC
54929 TGTAACCTCTCCTCAAACATGATTTGGATTGAGCTCCCACATCTTGTGTCCTTGCTTGTTGAACT
131 TGTAACCTCTCCTCAAACATGATTTGGATTGAGCTCCCACATCTTGTGTCCTTGCTTGTTGAACT
54994 GTAGATTCCCTACTCAGTTTTC
196 GTAGATTCCCTACTCAGTTTTC
55016 GGGCCACAAAGTCAAGTTCACAGGTGTACTGAATGAAGCGGTTGTTGAATCTTGAACAGCTTGCC
1 GGGCCACAAAGTCAAGTTCACAGGTGTACTGAATGAAGCGGTTGTTGAATCTTGAACAGCTTGCC
55081 TTCTCAAGTCACCCAACCTTGAAGAAAAGAAGTCCCTACTTTGCAGTGAAGAAGAGGGATAATCC
66 TTCTCAAGTCACCCAACCTTGAAGAAAAGAAGTCCCTACTTTGCAGTGAAGAAGAGGGATAATCC
55146 TGTAACCTCTCCTCAAACATGATTTGGATTGAGCTCCCACATCTTGTGTCCTTGCTTGTTGAACT
131 TGTAACCTCTCCTCAAACATGATTTGGATTGAGCTCCCACATCTTGTGTCCTTGCTTGTTGAACT
55211 GTAGATTCCCTACTCAGTT
196 GTAGATTCCCTACTCAGTT
55230 CAATGTGAGA
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 214 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
GGGCCACAAAGTCAAGTTCACAGGTGTACTGAATGAAGCGGTTGTTGAATCTTGAACAGCTTGCC
TTCTCAAGTCACCCAACCTTGAAGAAAAGAAGTCCCTACTTTGCAGTGAAGAAGAGGGATAATCC
TGTAACCTCTCCTCAAACATGATTTGGATTGAGCTCCCACATCTTGTGTCCTTGCTTGTTGAACT
GTAGATTCCCTACTCAGTTTTC
Found at i:55326 original size:42 final size:42
Alignment explanation
Indices: 55267--55349 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
55257 CCGTCTTAGC
*
55267 AGATGATATTCCATCAGCCCTACCAGACATAAGATTCGTCCA
1 AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCCA
*
55309 AGATGATATTCCATCAGCCCTACAAGCCATAAGATTCGTCC
1 AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCC
55350 TATTGATCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (42 bp):
AGATGATATTCCATCAGCCCTACAAGACATAAGATTCGTCCA
Found at i:58561 original size:16 final size:16
Alignment explanation
Indices: 58542--58572 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58532 AAAGGGTTGC
58542 AACCTAAAATGTGGTA
1 AACCTAAAATGTGGTA
*
58558 AACCTAAATTGTGGT
1 AACCTAAAATGTGGT
58573 GCAAATATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
AACCTAAAATGTGGTA
Found at i:63767 original size:103 final size:103
Alignment explanation
Indices: 63583--63800 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
63573 GTCGAGGGTC
*
63583 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
63648 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
* *
63686 TATGTGGTCCTTCGGGACATATATGTATTCTTTGTAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
63751 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
63789 TATGTGGTCCTT
1 TATGTGGTCCTT
63801 ATGGATATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:65357 original size:36 final size:36
Alignment explanation
Indices: 65278--65357 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
65268 TGAAATAGCT
**
65278 GGATCATCAGACAATGAAGTCATACCCGAAGAAGTT
1 GGATCATCAGACAATGAAGTCATACCCGAAGAAGCC
* * * *
65314 GGGTCATCAGGCAATGAAGTTAT-CACCGAAGGAGCC
1 GGATCATCAGACAATGAAGTCATAC-CCGAAGAAGCC
65350 GGATCATC
1 GGATCATC
65358 GAACGATGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (36 bp):
GGATCATCAGACAATGAAGTCATACCCGAAGAAGCC
Found at i:65996 original size:54 final size:55
Alignment explanation
Indices: 65892--66009 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
65882 TTTTAAAAAT
*
65892 TATAATAAATTAAAAAATATAAAATAAAATAACAAAGCCTATGAGTTTATTAAAG
1 TATAATAAATTAAAAAATATAAAATAAAATAACAAAGCCCATGAGTTTATTAAAG
* * * *
65947 -ATAATAAATTTTAAAAATATAAAATAAAATAA-TAGGTCCCATTA-TTTATTAAAG
1 TATAATAAA-TTAAAAAATATAAAATAAAATAACAAAG-CCCATGAGTTTATTAAAG
*
66001 TAAAATAAA
1 TATAATAAA
66010 AATTAAGCGT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 20 0.37
55 34 0.63
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (55 bp):
TATAATAAATTAAAAAATATAAAATAAAATAACAAAGCCCATGAGTTTATTAAAG
Found at i:68634 original size:53 final size:53
Alignment explanation
Indices: 68571--68677 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
68561 TGTGGAAAGG
68571 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
1 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
68624 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
1 TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
68677 T
1 T
68678 TTCATATCCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (53 bp):
TGGGATAAATGTTTCCAAGTATCTTTTGGTTCATACAATTACCAATAGAATAC
Found at i:71674 original size:24 final size:24
Alignment explanation
Indices: 71638--71788 Score: 137
Period size: 24 Copynumber: 6.4 Consensus size: 24
71628 GATGATTCAG
71638 GAGTCTTCAACCCCATCACCGACC
1 GAGTCTTCAACCCCATCACCGACC
* *
71662 GAGGCTTCAACCCCATCACCGACT
1 GAGTCTTCAACCCCATCACCGACC
* * * * *
71686 GAGGCTTCAAGCCAATCTCCGATC
1 GAGTCTTCAACCCCATCACCGACC
* *
71710 GAGTCTTCAACCACATCTCC-A--
1 GAGTCTTCAACCCCATCACCGACC
* * **
71731 GAGTCTTCAACCCCATCCCCAATT
1 GAGTCTTCAACCCCATCACCGACC
* * *
71755 GAGTCTTCAACCCCATCTCTGACT
1 GAGTCTTCAACCCCATCACCGACC
71779 GAGTCTTCAA
1 GAGTCTTCAA
71789 ACTCATATCG
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.17
22 1 0.01
23 1 0.01
24 87 0.81
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (24 bp):
GAGTCTTCAACCCCATCACCGACC
Found at i:71763 original size:69 final size:71
Alignment explanation
Indices: 71638--71788 Score: 173
Period size: 69 Copynumber: 2.1 Consensus size: 71
71628 GATGATTCAG
* * *
71638 GAGTCTTCAACCCCATCACCGACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAGCCAATC
1 GAGTCTTCAACCACATCACCGA-CGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATC
71703 TCCGA-T
65 TCCGACT
* * * * * *
71709 CGAGTCTTCAACCACATCTCC-A-GAGTCTTCAACCCCATCCCCAATTGAGTCTTCAACCCCATC
1 -GAGTCTTCAACCACATCACCGACGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATC
*
71772 TCTGACT
65 TCCGACT
71779 GAGTCTTCAA
1 GAGTCTTCAA
71789 ACTCATATCG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
69 48 0.71
70 1 0.01
71 1 0.01
72 18 0.26
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (71 bp):
GAGTCTTCAACCACATCACCGACGAGGCTTCAACCCCATCACCAACTGAGGCTTCAACCCAATCT
CCGACT
Found at i:71805 original size:24 final size:24
Alignment explanation
Indices: 71638--71844 Score: 136
Period size: 24 Copynumber: 8.8 Consensus size: 24
71628 GATGATTCAG
* * **
71638 GAGTCTTCAACCCCATCACCGACC
1 GAGTCTTCAACCCCATCTCGGAAT
* * * *
71662 GAGGCTTCAACCCCATCACCGACT
1 GAGTCTTCAACCCCATCTCGGAAT
* * * *
71686 GAGGCTTCAAGCCAATCTCCG-AT
1 GAGTCTTCAACCCCATCTCGGAAT
* *
71709 CGAGTCTTCAACCACATCTC--CA-
1 -GAGTCTTCAACCCCATCTCGGAAT
**
71731 GAGTCTTCAACCCCATC-CCCAATT
1 GAGTCTTCAACCCCATCTCGGAA-T
* *
71755 GAGTCTTCAACCCCATCTCTGACT
1 GAGTCTTCAACCCCATCTCGGAAT
* * *
71779 GAGTCTTCAAACTCATATCGGAAT
1 GAGTCTTCAACCCCATCTCGGAAT
**
71803 GAGAATTCAACCCCATCTCGGAAT
1 GAGTCTTCAACCCCATCTCGGAAT
* *
71827 GAGTCTCCAACCTCATCT
1 GAGTCTTCAACCCCATCT
71845 AATAAAAGTT
Statistics
Matches: 147, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
20 1 0.01
21 16 0.11
22 1 0.01
23 2 0.01
24 125 0.85
25 2 0.01
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (24 bp):
GAGTCTTCAACCCCATCTCGGAAT
Found at i:71812 original size:93 final size:93
Alignment explanation
Indices: 71638--71821 Score: 210
Period size: 93 Copynumber: 2.0 Consensus size: 93
71628 GATGATTCAG
* * *
71638 GAGTCTTCAACCCCATCACCGACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAGCCAATC
1 GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAACCAATA
**
71703 TCCGATCGAGTCTTCAACCACATCTCCA
66 TCCGATCGAGAATTCAACCACATCTCCA
* ** * * * *
71731 GAGTCTTCAACCCCATCCCCAATTGAGTCTTCAACCCCATCTCTGACTGAGTCTTCAAACTC-AT
1 GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAAC-CAAT
* *
71795 ATCGGAAT-GAGAATTCAACCCCATCTC
65 ATCCG-ATCGAGAATTCAACCACATCTC
71822 GGAATGAGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
93 72 0.96
94 3 0.04
ACGTcount: A:0.27, C:0.37, G:0.14, T:0.23
Consensus pattern (93 bp):
GAGTCTTCAACCCCATCACCAACCGAGGCTTCAACCCCATCACCGACTGAGGCTTCAAACCAATA
TCCGATCGAGAATTCAACCACATCTCCA
Found at i:74831 original size:2 final size:2
Alignment explanation
Indices: 74824--74850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
74814 ACAAAAACTA
74824 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
74851 CACACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79060 original size:24 final size:24
Alignment explanation
Indices: 79028--79074 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
79018 AGCCTTGAGG
79028 CGCGAAGCGCATGAAAGGCGCGGA
1 CGCGAAGCGCATGAAAGGCGCGGA
79052 CGCGAAGCGCATGAAAGGCGCGG
1 CGCGAAGCGCATGAAAGGCGCGG
79075 GATTCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.43, T:0.04
Consensus pattern (24 bp):
CGCGAAGCGCATGAAAGGCGCGGA
Found at i:82486 original size:21 final size:21
Alignment explanation
Indices: 82462--82531 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
82452 GACTATCACA
82462 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
82483 TTGCGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
82504 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
82525 TTGCGAT
1 TTGCGAT
82532 TTATTCCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 9 0.21
21 23 0.55
23 10 0.24
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:82509 original size:42 final size:42
Alignment explanation
Indices: 82460--82573 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
82450 TCGACTATCA
*
82460 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
82502 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
82544 CATTGCGATTTATTCCAAGTT--CGTTGCGAT
1 CATTGCGA--TAGTCCAAGTTCGCGTTGCGAT
82574 AGTCCAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
42 55 0.86
44 9 0.14
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (42 bp):
CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:82549 original size:21 final size:21
Alignment explanation
Indices: 82525--82573 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
82515 GAAGTTCGCG
82525 TTGCGATTTATTCCAAATTCA
1 TTGCGATTTATTCCAAATTCA
* *
82546 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAATTCA
82567 TTGCGAT
1 TTGCGAT
82574 AGTCCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCA
Found at i:83385 original size:21 final size:21
Alignment explanation
Indices: 83294--83386 Score: 109
Period size: 21 Copynumber: 4.4 Consensus size: 21
83284 ATTTTGGACT
*
83294 ATCGCAAAGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
83315 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
83336 ATCGCAAAGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
83357 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
83378 ATCGCAACG
1 ATCGCAACG
83387 CGAACTTGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
19 8 0.14
21 43 0.73
23 8 0.14
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:83402 original size:21 final size:20
Alignment explanation
Indices: 83287--83426 Score: 88
Period size: 21 Copynumber: 6.7 Consensus size: 20
83277 CGTTGCAATT
* *
83287 TTGGACTATCGCAA-AGAAT
1 TTGGACTATCGCAAGCGAAC
*
83306 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
83329 TTCGACTATCGCAA-AGAAT
1 TTGGACTATCGCAAGCGAAC
* *
83348 TTGGAATAAATCGCAA-CGAAT
1 TTGGACT--ATCGCAAGCGAAC
*
83369 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
83392 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAA-GCGAAC
*
83413 TTCGACTATCGCAA
1 TTGGACTATCGCAA
83427 TACCGGAGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.14
21 67 0.68
23 18 0.18
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:83424 original size:63 final size:61
Alignment explanation
Indices: 83290--83426 Score: 184
Period size: 63 Copynumber: 2.2 Consensus size: 61
83280 TGCAATTTTG
* *
83290 GACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAATTTG
1 GACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTC
* * * *
83351 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAATGCGAACTTC
1 GACT--ATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--AGAACTTC
83416 GACTATCGCAA
1 GACTATCGCAA
83427 TACCGGAGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 3 0.05
63 54 0.83
65 8 0.12
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (61 bp):
GACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAAGAACTTC
Found at i:84920 original size:27 final size:28
Alignment explanation
Indices: 84871--84928 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
84861 AGGGGTGCAC
84871 AAAAAATCCGAATATTCGATTTTGCGAA
1 AAAAAATCCGAATATTCGATTTTGCGAA
* *
84899 AAAAATATCCGAA-A-TCGGTTTTGGGAA
1 AAAAA-ATCCGAATATTCGATTTTGCGAA
84926 AAA
1 AAA
84929 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (28 bp):
AAAAAATCCGAATATTCGATTTTGCGAA
Found at i:87380 original size:21 final size:21
Alignment explanation
Indices: 87356--87395 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
87346 TTTATTTTAT
87356 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
87377 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
87396 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:87456 original size:33 final size:33
Alignment explanation
Indices: 87390--87486 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
87380 TTTGTTTCAA
87390 TTATCGAACTT-GAAG-TTTTAAGTA-TTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
87420 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
87453 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
87486 T
1 T
87487 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
30 11 0.18
31 4 0.07
32 9 0.15
33 37 0.61
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:87515 original size:13 final size:13
Alignment explanation
Indices: 87472--87526 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
87462 TTGGAAGTAT
87472 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
87485 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
87499 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
87512 TTAAGTATTTGAA
1 TTAAGTATTTCAA
87525 TT
1 TT
87527 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:87948 original size:15 final size:15
Alignment explanation
Indices: 87923--87978 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
87913 ATCTGGAATA
*
87923 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
87938 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
87953 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
87970 TTAAAACCG
1 TTAAAACCG
87979 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:87987 original size:21 final size:18
Alignment explanation
Indices: 87942--87975 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
87932 GTTTTTTTAT
87942 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
87959 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
87976 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:88096 original size:15 final size:17
Alignment explanation
Indices: 88070--88101 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
88060 TTCTATGGGA
88070 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
88086 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
88102 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:96418 original size:24 final size:24
Alignment explanation
Indices: 96391--96446 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
96381 AAGTAACTCT
*
96391 GCTTATCCCGATAAGTGCATGACC
1 GCTTATCCCGATAAGTGAATGACC
*
96415 GCTTATCCCGATAAGTGAATGACT
1 GCTTATCCCGATAAGTGAATGACC
96439 GCTTATCC
1 GCTTATCC
96447 GCTTATCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (24 bp):
GCTTATCCCGATAAGTGAATGACC
Found at i:96943 original size:21 final size:21
Alignment explanation
Indices: 96896--96945 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
96886 ACGTATAATT
*
96896 ATAAATTAGTTAAAATAAAAG
1 ATAAATTATTTAAAATAAAAG
*
96917 -TAAATTATTTAAAATAAATG
1 ATAAATTATTTAAAATAAAAG
96937 ATAAATTAT
1 ATAAATTAT
96946 GCTAGTGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
ATAAATTATTTAAAATAAAAG
Found at i:105396 original size:11 final size:11
Alignment explanation
Indices: 105376--105450 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
105366 TTTATGTATT
105376 TAAT-ATATAA
1 TAATAATATAA
105386 TAATAATATAA
1 TAATAATATAA
* *
105397 TAATATTTTAA
1 TAATAATATAA
**
105408 -AATAATACTTTT
1 TAATAATA--TAA
*
105420 TAA-AATATATT
1 TAATAATATA-A
105431 TAA-AATATAA
1 TAATAATATAA
105441 TAATAATATA
1 TAATAATATA
105451 TTTAAAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
10 13 0.25
11 31 0.61
12 5 0.10
13 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAATATAA
Found at i:105411 original size:13 final size:13
Alignment explanation
Indices: 105395--105437 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 13
105385 ATAATAATAT
105395 AATAATATTTTAA
1 AATAATATTTTAA
105408 AATAATACTTTTTAA
1 AATAATA--TTTTAA
105423 AAT-ATA-TTTAA
1 AATAATATTTTAA
105434 AATA
1 AATA
105438 TAATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.30
13 7 0.26
14 3 0.11
15 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATATTTTAA
Found at i:105438 original size:57 final size:57
Alignment explanation
Indices: 105372--105484 Score: 169
Period size: 55 Copynumber: 2.0 Consensus size: 57
105362 ATAATTTATG
* *
105372 TATTTAATATATAATAATAATATA-AT--AATATTTTAAAATAATACTTTTTAAAATA
1 TATTTAAAATATAATAATAATATATATAAAATATATT-AAATAATACTTTTTAAAATA
*
105427 TATTTAAAATATAATAATAATATATTTAAAATATATTAAATAATACTTTTTAAAATA
1 TATTTAAAATATAATAATAATATATATAAAATATATTAAATAATACTTTTTAAAATA
105484 T
1 T
105485 GATATAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 23 0.44
56 1 0.02
57 21 0.40
58 7 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (57 bp):
TATTTAAAATATAATAATAATATATATAAAATATATTAAATAATACTTTTTAAAATA
Found at i:105449 original size:22 final size:22
Alignment explanation
Indices: 105423--105494 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
105413 TACTTTTTAA
105423 AATATATTTAAAATATAATAAT
1 AATATATTTAAAATATAATAAT
*
105445 AATATATTTAAAATATATTAAAT
1 AATATATTTAAAATATAAT-AAT
* *
105468 AATACTTTTTAAAATATGAT-AT
1 AATA-TATTTAAAATATAATAAT
105490 AATAT
1 AATAT
105495 TATTATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 1 0.02
22 24 0.55
23 7 0.16
24 12 0.27
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
AATATATTTAAAATATAATAAT
Found at i:105467 original size:9 final size:11
Alignment explanation
Indices: 105418--105484 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
105408 AATAATACTT
105418 TTTAAAATATA
1 TTTAAAATATA
105429 TTTAAAATATA
1 TTTAAAATATA
*
105440 -ATAATAATATA
1 TTTAA-AATATA
105451 TTTAAAATATA
1 TTTAAAATATA
* *
105462 TTAAATAATACTT
1 TTTAA-AATA-TA
105475 TTTAAAATAT
1 TTTAAAATAT
105485 GATATAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
10 3 0.06
11 28 0.60
12 11 0.23
13 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:107459 original size:19 final size:19
Alignment explanation
Indices: 107435--107471 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
107425 AGCACCGTCG
*
107435 TTCTCAACTCAGCTTCCGT
1 TTCTCAACTCAGATTCCGT
107454 TTCTCAACTCAGATTCCG
1 TTCTCAACTCAGATTCCG
107472 CTTCAAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.11, T:0.35
Consensus pattern (19 bp):
TTCTCAACTCAGATTCCGT
Found at i:110657 original size:11 final size:11
Alignment explanation
Indices: 110641--110670 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
110631 CACAATCTTC
110641 TTCTTCTTTAT
1 TTCTTCTTTAT
110652 TTCTTCTTTAT
1 TTCTTCTTTAT
110663 TT-TTCTTT
1 TTCTTCTTT
110671 TCATGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTCTTTAT
Found at i:111187 original size:17 final size:17
Alignment explanation
Indices: 111165--111199 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
111155 AATTATTTTC
111165 AGTTGCCACGACAATCG
1 AGTTGCCACGACAATCG
*
111182 AGTTGCCTCGACAATCG
1 AGTTGCCACGACAATCG
111199 A
1 A
111200 CTACTCAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (17 bp):
AGTTGCCACGACAATCG
Found at i:115261 original size:18 final size:18
Alignment explanation
Indices: 115210--115261 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 18
115200 CGACAATCAA
115210 GCAACTTATTTTATGGTT
1 GCAACTTATTTTATGGTT
* *
115228 G----TCATTTTA-AGTT
1 GCAACTTATTTTATGGTT
115241 GCAACTTATTTTATGGTT
1 GCAACTTATTTTATGGTT
115259 GCA
1 GCA
115262 TCACATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 10
0.64 0.10 0.26
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
17 7 0.28
18 7 0.28
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (18 bp):
GCAACTTATTTTATGGTT
Found at i:115414 original size:13 final size:13
Alignment explanation
Indices: 115392--115492 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 13
115382 TATTTTTTTA
*
115392 ATATAATAAAAAT
1 ATATATTAAAAAT
*
115405 ATATATT-AAATT
1 ATATATTAAAAAT
*
115417 ATTTATGTAAAAA-
1 ATATAT-TAAAAAT
*
115430 ATTTATTAAAAA-
1 ATATATTAAAAAT
*
115442 ATATA-AAAATAAT
1 ATATATTAAA-AAT
*
115455 -TTTATTAAAAATT
1 ATATATTAAAAA-T
* *
115468 AAATTTAATAAAAAT
1 --ATATATTAAAAAT
115483 ATATATTAAA
1 ATATATTAAA
115493 GTATTTGTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.04
12 26 0.38
13 25 0.37
14 3 0.04
15 1 0.01
16 10 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (13 bp):
ATATATTAAAAAT
Found at i:115441 original size:12 final size:12
Alignment explanation
Indices: 115398--115465 Score: 50
Period size: 13 Copynumber: 5.5 Consensus size: 12
115388 TTTAATATAA
*
115398 TAAAAATATATAT
1 TAAAAA-ATTTAT
**
115411 TAAATTATTTAT
1 TAAAAAATTTAT
115423 GTAAAAAATTTAT
1 -TAAAAAATTTAT
115436 TAAAAAA--TAT
1 TAAAAAATTTAT
*
115446 AAAAATAATTTTAT
1 TAAAA-AA-TTTAT
115460 TAAAAA
1 TAAAAA
115466 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
10 7 0.16
11 2 0.05
12 12 0.28
13 15 0.35
14 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (12 bp):
TAAAAAATTTAT
Found at i:115474 original size:16 final size:16
Alignment explanation
Indices: 115444--115482 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
115434 ATTAAAAAAT
*
115444 ATAAAAA-TAATTTTA
1 ATAAAAATTAAATTTA
*
115459 TTAAAAATTAAATTTA
1 ATAAAAATTAAATTTA
115475 ATAAAAAT
1 ATAAAAAT
115483 ATATATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATTAAATTTA
Found at i:115542 original size:78 final size:78
Alignment explanation
Indices: 115395--115543 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 78
115385 TTTTTTAATA
* * ** *
115395 TAATAAAAATATATATTAAATTATTTATGTAAAAAATTTATTAAAAAATATAAAAATAATTTTAT
1 TAATAAAAATATATATTAAAGTATTTATATAAAAAATTTATTAAAAAATATAAAAATAATAATAA
115460 TAAAAATTAAATT
66 TAAAAATTAAATT
* * * *
115473 TAATAAAAATATATATTAAAGTATTTGTATATAAATTTTATT-AAAAATATATAAATTAGA-AAT
1 TAATAAAAATATATATTAAAGTATTTATATAAAAAATTTATTAAAAAATATA-AAAATA-ATAAT
115536 AATAAAAA
64 AATAAAAA
115544 GTATATTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 9 0.15
78 50 0.83
79 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (78 bp):
TAATAAAAATATATATTAAAGTATTTATATAAAAAATTTATTAAAAAATATAAAAATAATAATAA
TAAAAATTAAATT
Found at i:115753 original size:40 final size:41
Alignment explanation
Indices: 115709--115815 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 41
115699 TTTCAAACTT
115709 TTATTTGAATTT-AATTATAAAT-A-TTTATAATATTATAATA
1 TTATTTG-ATTTCAATT-TAAATGATTTTATAATATTATAATA
115749 TTATTTGATTTCAATTTAAATGA---T-T--T-TTATAATA
1 TTATTTGATTTCAATTTAAATGATTTTATAATATTATAATA
115783 TTATTTGATTTCAATTTAAATGATTTTTATAAT
1 TTATTTGATTTCAATTTAAATGA-TTTTATAAT
115816 CATATACAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
34 31 0.53
35 1 0.02
37 1 0.02
38 2 0.03
39 10 0.17
40 12 0.21
41 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (41 bp):
TTATTTGATTTCAATTTAAATGATTTTATAATATTATAATA
Found at i:115779 original size:34 final size:34
Alignment explanation
Indices: 115741--115815 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
115731 ATTTATAATA
115741 TTATAATATTATTTGATTTCAATTTAAATGATTT
1 TTATAATATTATTTGATTTCAATTTAAATGATTT
115775 TTATAATATTATTTGATTTCAATTTAAATGATTT
1 TTATAATATTATTTGATTTCAATTTAAATGATTT
115809 TTATAAT
1 TTATAAT
115816 CATATACAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTATAATATTATTTGATTTCAATTTAAATGATTT
Found at i:116328 original size:2 final size:2
Alignment explanation
Indices: 116321--116350 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
116311 TTCATTTGTC
116321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116351 AATAGACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128056 original size:38 final size:38
Alignment explanation
Indices: 128014--128114 Score: 121
Period size: 47 Copynumber: 2.4 Consensus size: 38
128004 ACTATTTATC
128014 CCATAAGCTCGTAAGCCAAAATACTTACCATTTAAATT
1 CCATAAGCTCGTAAGCCAAAATACTTACCATTTAAATT
128052 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCGTAAG---------CCAAAATACTTACCATTTAAATT
128099 CCATAAGCTCGTAAGC
1 CCATAAGCTCGTAAGC
128115 TTATTTTACC
Statistics
Matches: 54, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
38 16 0.30
47 38 0.70
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.31
Consensus pattern (38 bp):
CCATAAGCTCGTAAGCCAAAATACTTACCATTTAAATT
Found at i:128080 original size:47 final size:47
Alignment explanation
Indices: 128029--128164 Score: 206
Period size: 47 Copynumber: 3.0 Consensus size: 47
128019 AGCTCGTAAG
128029 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTA
128076 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTA
* * * * *
128123 CCCATATACTTGCCA-TT--ATTCCAAAAGCTTGTAAGCTTATTT
1 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
128165 GTATGTTTAC
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
44 23 0.27
46 2 0.02
47 59 0.70
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (47 bp):
CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:128313 original size:40 final size:40
Alignment explanation
Indices: 128269--128390 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
128259 ACCGTAGTGC
*
128269 TACACATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
128309 TACACATAAGTTCGTGCCCAACATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
128349 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
128389 TA
1 TA
128391 TAAACCTACA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:133418 original size:13 final size:13
Alignment explanation
Indices: 133400--133433 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
133390 GAAAGCACAC
133400 AGAAAACAAGTGT
1 AGAAAACAAGTGT
133413 AGAAAACAAGTGT
1 AGAAAACAAGTGT
133426 AGAAAACA
1 AGAAAACA
133434 CTTTGAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.59, C:0.09, G:0.21, T:0.12
Consensus pattern (13 bp):
AGAAAACAAGTGT
Found at i:143918 original size:36 final size:36
Alignment explanation
Indices: 143871--143951 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
143861 TTTCTCCAGC
*
143871 TTCAATATCTGTTAAATATGGTGAAATTCATTGCCT
1 TTCAACATCTGTTAAATATGGTGAAATTCATTGCCT
143907 TTCAACATCTGTTAAATATGGTGAAATTCATTGCCT
1 TTCAACATCTGTTAAATATGGTGAAATTCATTGCCT
143943 TTCAACATC
1 TTCAACATC
143952 AAATACAGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (36 bp):
TTCAACATCTGTTAAATATGGTGAAATTCATTGCCT
Found at i:144988 original size:14 final size:14
Alignment explanation
Indices: 144969--144998 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
144959 TTAGATTTGT
*
144969 TTAAAATTACATTA
1 TTAAAAATACATTA
144983 TTAAAAATACATTA
1 TTAAAAATACATTA
144997 TT
1 TT
144999 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:145390 original size:69 final size:69
Alignment explanation
Indices: 145279--145417 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
145269 AGCTTGTCAA
145279 GGGATATGATTGGAAATCCCTTTTCCCGAGATGTGCTCTCAAGATTGATATTCAAAAAGCTTTTG
1 GGGATATGATTGGAAATCCCTTTTCCCGAGATGTGCTCTCAAGATTGATATTCAAAAAGCTTTTG
145344 ACAC
66 ACAC
145348 GGGATATGATTGGAAATCCCTTTTCCCGAGATGTGCTCTCAAGATTGATATTCAAAAAGCTTTTG
1 GGGATATGATTGGAAATCCCTTTTCCCGAGATGTGCTCTCAAGATTGATATTCAAAAAGCTTTTG
145413 ACAC
66 ACAC
145417 G
1 G
145418 TTAAGTTGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (69 bp):
GGGATATGATTGGAAATCCCTTTTCCCGAGATGTGCTCTCAAGATTGATATTCAAAAAGCTTTTG
ACAC
Found at i:147817 original size:17 final size:17
Alignment explanation
Indices: 147795--147828 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
147785 GCCCCTAACT
147795 AAATTTTGTCCAAGCTG
1 AAATTTTGTCCAAGCTG
*
147812 AAATTTTTTCCAAGCTG
1 AAATTTTGTCCAAGCTG
147829 TAAAAGGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (17 bp):
AAATTTTGTCCAAGCTG
Found at i:151835 original size:22 final size:22
Alignment explanation
Indices: 151797--152052 Score: 349
Period size: 22 Copynumber: 11.6 Consensus size: 22
151787 ATATTTTAAA
151797 ATTTATTTTAAAAATATAGATTG
1 ATTTATTTT-AAAATATAGATTG
151820 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
* *
151842 GTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
* *
151864 ATTTATTTTAAAATATGGTTTG
1 ATTTATTTTAAAATATAGATTG
*
151886 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
***
151908 ATTTATTTTAAAATAT-GAAAAA
1 ATTTATTTTAAAATATAG-ATTG
*
151930 AGTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
151952 ATTTATTTTAAAATA-AGGATTG
1 ATTTATTTTAAAATATA-GATTG
151974 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
*
151996 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
152018 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
152040 ATTTATTTTAAAA
1 ATTTATTTTAAAA
152053 AATTTATTAT
Statistics
Matches: 214, Mismatches: 14, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
21 2 0.01
22 201 0.94
23 11 0.05
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATAGATTG
Found at i:152133 original size:31 final size:31
Alignment explanation
Indices: 152076--152134 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
152066 ACTTGTATGG
*
152076 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
152107 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
152135 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:153159 original size:3 final size:3
Alignment explanation
Indices: 153151--153179 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
153141 CTTGACATTT
153151 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
153180 TTGATAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:160586 original size:34 final size:34
Alignment explanation
Indices: 160543--160631 Score: 178
Period size: 34 Copynumber: 2.6 Consensus size: 34
160533 GTCCAATGGG
160543 TTATTTAACTATTTAAATGATTGGTTCGTGCGGA
1 TTATTTAACTATTTAAATGATTGGTTCGTGCGGA
160577 TTATTTAACTATTTAAATGATTGGTTCGTGCGGA
1 TTATTTAACTATTTAAATGATTGGTTCGTGCGGA
160611 TTATTTAACTATTTAAATGAT
1 TTATTTAACTATTTAAATGAT
160632 GTTAATCATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (34 bp):
TTATTTAACTATTTAAATGATTGGTTCGTGCGGA
Found at i:164721 original size:16 final size:16
Alignment explanation
Indices: 164692--164736 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
164682 TGCTCTTGTA
*
164692 AGTTGCTTTAGGTTCG
1 AGTTGCTTTTGGTTCG
*
164708 AGTTGATTTTGGTTCG
1 AGTTGCTTTTGGTTCG
164724 -GATTGCTTTTGGT
1 AG-TTGCTTTTGGT
164737 CCAACTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.11, C:0.09, G:0.31, T:0.49
Consensus pattern (16 bp):
AGTTGCTTTTGGTTCG
Found at i:165332 original size:28 final size:28
Alignment explanation
Indices: 165249--165333 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
165239 CTTCGTGGGG
* * * **
165249 TTCCTTCCGAGCTGGTAAAATGTGCGGA
1 TTCCTTCCGAGCTGGCAAAAGGAGCAAA
*
165277 TTCCGTCCGAGCTGGCAAAAGGCA-CAAA
1 TTCCTTCCGAGCTGGCAAAAGG-AGCAAA
165305 TTCCTTCCGAGCTGGCAAAAGGAGCAAA
1 TTCCTTCCGAGCTGGCAAAAGGAGCAAA
165333 T
1 T
165334 CATAATCCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.02
28 47 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (28 bp):
TTCCTTCCGAGCTGGCAAAAGGAGCAAA
Found at i:166263 original size:21 final size:22
Alignment explanation
Indices: 166226--166266 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
166216 TTAAATATAA
166226 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTATCGATACTCAT
166248 TAAAGG-AGTA-CTGATACTC
1 TAAAGGAAGTATC-GATACTC
166267 TCTGTCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTATCGATACTCAT
Found at i:166315 original size:33 final size:34
Alignment explanation
Indices: 166267--166334 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 34
166257 ACTGATACTC
166267 TCTGTCCTGAGCAGTTTTA-TTTTGCAGAGAATT
1 TCTGTCCTGAGCAGTTTTATTTTTGCAGAGAATT
*
166300 TCTGTCCTG-GACAGTTTTATTTTTGTAGAGAATT
1 TCTGTCCTGAG-CAGTTTTATTTTTGCAGAGAATT
166334 T
1 T
166335 ATCCCCAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 1 0.03
33 17 0.53
34 14 0.44
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (34 bp):
TCTGTCCTGAGCAGTTTTATTTTTGCAGAGAATT
Found at i:186090 original size:43 final size:43
Alignment explanation
Indices: 185780--186223 Score: 256
Period size: 44 Copynumber: 10.3 Consensus size: 43
185770 GGTCCTCATT
* * * * * * *
185780 TTTTTATCTTTATAATTAAGTCT-TTAATTTTTTTAAATCTTAT
1 TTTTTAACTTTATAATTGAGGCTCCTAAGTTTTTT-AATCTCAC
* * * *
185823 TTTTTTACTTTTATAATTGAGG-TCATAA-TATTATTCAATCTTAC
1 TTTTTAAC-TTTATAATTGAGGCTCCTAAGT-TT-TTTAATCTCAC
* * * *
185867 TTTTTTTA-TTTATAATTGAAG-TCTCTAA-TCCTTTTCAATC-CTC
1 -TTTTTAACTTTATAATTGAGGCTC-CTAAGT--TTTTTAATCTCAC
* *
185910 TTTTTACCTTTATAATTGA-GCTCTCTAA-TTTTGTAATCTCAC
1 TTTTTAACTTTATAATTGAGGCTC-CTAAGTTTTTTAATCTCAC
* * *
185952 -TTTTAACTTTATAATTGAGGCT-TTCAAGTTTTTCCAATCTAAC
1 TTTTTAACTTTATAATTGAGGCTCCT-AAGTTTTT-TAATCTCAC
* * * * *
185995 TTTCTACCTTT-TCAATTGAGGCCCCTAAGTTTTTTCAATCTTAA
1 TTTTTAACTTTAT-AATTGAGGCTCCTAAGTTTTTT-AATCTCAC
* *
186039 TATCTAACTTTATAATTGAGGCTCCTAA-TTTTTTAATCTCAC
1 TTTTTAACTTTATAATTGAGGCTCCTAAGTTTTTTAATCTCAC
186081 TTTTTTAACTTTATAATTGAGGC-CCTTAAGTTTTTTTAATCTCAC
1 -TTTTTAACTTTATAATTGAGGCTCC-TAAG-TTTTTTAATCTCAC
* * * * ** *
186126 TTTCTAGCTTTCTAATTGAGGCCCCTAAGTTTTTCGATATCA-
1 TTTTTAACTTTATAATTGAGGCTCCTAAGTTTTTTAATCTCAC
* * * *
186168 ATTATACCTTTATAATTGAGGCTCCT-ATTTTTTTCAATCTCGA-
1 TTTTTAACTTTATAATTGAGGCTCCTAAGTTTTTT-AATCTC-AC
*
186211 TTTATAACTTTAT
1 TTTTTAACTTTAT
186224 TAAGGCCTCT
Statistics
Matches: 322, Mismatches: 53, Indels: 52
0.75 0.12 0.12
Matches are distributed among these distances:
40 1 0.00
41 32 0.10
42 48 0.15
43 101 0.31
44 111 0.34
45 29 0.09
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.50
Consensus pattern (43 bp):
TTTTTAACTTTATAATTGAGGCTCCTAAGTTTTTTAATCTCAC
Found at i:186111 original size:87 final size:86
Alignment explanation
Indices: 185955--186159 Score: 225
Period size: 87 Copynumber: 2.3 Consensus size: 86
185945 ATCTCACTTT
* * *
185955 TAACTTTATAATTGAGGCT-TTCAAGTTTTTCCAATCTAACTTTCTACCTTTTCAATTGAGGCCC
1 TAACTTTATAATTGAGGCTCCT-AA-TTTTT-TAATCTAACTTTCTAACTTTTCAATTGAGGCCC
*
186019 CTAAGTTTTTTCAATCTTAATATC
63 CTAAGTTTTTTCAATCTCAATATC
* * *
186043 TAACTTTATAATTGAGGCTCCTAATTTTTTAATCTCACTTTTTTAACTTTAT-AATTGAGGCCCT
1 TAACTTTATAATTGAGGCTCCTAATTTTTTAATCTAAC-TTTCTAACTTT-TCAATTGAGGCCCC
* * *
186107 TAAGTTTTTTTAATCTCACTTTC
64 TAAGTTTTTTCAATCTCAATATC
* * * *
186130 TAGCTTTCTAATTGAGGCCCCTAAGTTTTT
1 TAACTTTATAATTGAGGCTCCTAATTTTTT
186160 CGATATCAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
86 7 0.07
87 70 0.70
88 22 0.22
89 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (86 bp):
TAACTTTATAATTGAGGCTCCTAATTTTTTAATCTAACTTTCTAACTTTTCAATTGAGGCCCCTA
AGTTTTTTCAATCTCAATATC
Found at i:186122 original size:131 final size:127
Alignment explanation
Indices: 185917--186223 Score: 388
Period size: 129 Copynumber: 2.4 Consensus size: 127
185907 CTCTTTTTAC
* *
185917 CTTTATAATTGA-GCTCTCTAATTTTGTAATCTCACTTTTAACTTTATAATTGAGGCTTTCAAGT
1 CTTTATAATTGAGGCTC-CTAATTTTTTAATCTCACTTTTAACTTTATAATTGAGGCCTTCAAGT
* * *
185981 TTTTCCAATCTAACTTTCTACCTTT-TCAATTGAGGCCCCTAAGTTTTTTCAATCTTAATATCTA
65 TTTTCCAATCTAACTTTCTACCTTTCT-AATTGAGGCCCCTAAG-TTTTTCAATATCAAT-TATA
186045 A
127 A
186046 CTTTATAATTGAGGCTCCTAATTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGCCCTT-AA
1 CTTTATAATTGAGGCTCCTAATTTTTTAATCTCAC--TTTTAACTTTATAATTGAGG-CCTTCAA
** * * * *
186110 GTTTTTTTAATCTCACTTTCTAGCTTTCTAATTGAGGCCCCTAAGTTTTTCGATATCAATTATAC
63 GTTTTTCCAATCTAACTTTCTACCTTTCTAATTGAGGCCCCTAAGTTTTTCAATATCAATTATAA
*
186175 CTTTATAATTGAGGCTCCTATTTTTTTCAATCTCGA-TTTATAACTTTAT
1 CTTTATAATTGAGGCTCCTAATTTTTT-AATCTC-ACTTT-TAACTTTAT
186224 TAAGGCCTCT
Statistics
Matches: 158, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
128 3 0.02
129 67 0.42
130 22 0.14
131 62 0.39
132 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (127 bp):
CTTTATAATTGAGGCTCCTAATTTTTTAATCTCACTTTTAACTTTATAATTGAGGCCTTCAAGTT
TTTCCAATCTAACTTTCTACCTTTCTAATTGAGGCCCCTAAGTTTTTCAATATCAATTATAA
Found at i:187806 original size:2 final size:2
Alignment explanation
Indices: 187799--187843 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
187789 ATTAACAATC
187799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
187841 TA T
1 TA T
187844 GGTTTTGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:193560 original size:19 final size:19
Alignment explanation
Indices: 193533--193575 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
193523 ATGACCAACA
* * *
193533 AATTCGCAACGCGATCTCG
1 AATTTGCAACGCGAACTCC
*
193552 AATTTGCAATGCGAACTCC
1 AATTTGCAACGCGAACTCC
193571 AATTT
1 AATTT
193576 CACAACTCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (19 bp):
AATTTGCAACGCGAACTCC
Found at i:193683 original size:20 final size:20
Alignment explanation
Indices: 193595--193681 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
193585 GTTTCCAAAT
193595 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
193615 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
193635 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
193655 TCGCAACACGAAATTT-TAAT
1 TCGCAACGCG-AATTTGTAAA
193675 TCGCAAC
1 TCGCAAC
193682 ACAGAAGTCA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 59 0.92
21 5 0.08
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:193880 original size:22 final size:22
Alignment explanation
Indices: 193855--193902 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
193845 CTACGGCGAC
193855 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
193877 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
193899 ATCC
1 ATCC
193903 ATCTATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.46, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:196479 original size:21 final size:21
Alignment explanation
Indices: 196455--196526 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
196445 TTTCCTATCG
196455 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTATCATCC
* **
196476 TTCAAGATGCCCCTCCCA-CC
1 TTCAAGAGGCCCCTATCATCC
* *
196496 GTTCAAGAGGCCCCTGTCATCA
1 -TTCAAGAGGCCCCTATCATCC
196518 TTCAAGAGG
1 TTCAAGAGG
196527 TTCCTCCCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.93
22 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTATCATCC
Found at i:196499 original size:42 final size:42
Alignment explanation
Indices: 196453--196546 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
196443 CATTTCCTAT
* *
196453 CGTTCAAGAGGCCCCTATCATCCTTCAAGATGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCAC
* **
196495 CGTTCAAGAGGCCCCTGTCATCATTCAAGAGGTTCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCAC
*
196537 CGTTCGAGAG
1 CGTTCAAGAG
196547 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCAC
Found at i:197965 original size:14 final size:14
Alignment explanation
Indices: 197946--197982 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
197936 CCTTGTGTAA
197946 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
197960 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
197974 TTGATTTGT
1 TTGATTTGT
197983 TTAATAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:198019 original size:78 final size:78
Alignment explanation
Indices: 197885--198038 Score: 227
Period size: 78 Copynumber: 2.0 Consensus size: 78
197875 AAATTGATGT
*
197885 ATTTGTAAAAGTTCATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCCTTGTGTAATTGA
1 ATTTGTAAAAGTTCATTTGTTTAATAGATGAGGAAATAAGAATTATTTTTTCCTTGTGTAATTGA
197950 TTTGTAAAAGTTG
66 TTTGTAAAAGTTG
* * * *** * *
197963 ATTTGTAAAAGTTGATTTGTTTAATAGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTGA
1 ATTTGTAAAAGTTCATTTGTTTAATAGATGAGGAAATAAGAATTATTTTTTCCTTGTGTAATTGA
198028 TTTGTAAAAGT
66 TTTGTAAAAGT
198039 CAAAAATACC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (78 bp):
ATTTGTAAAAGTTCATTTGTTTAATAGATGAGGAAATAAGAATTATTTTTTCCTTGTGTAATTGA
TTTGTAAAAGTTG
Found at i:198135 original size:20 final size:20
Alignment explanation
Indices: 198064--198129 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
198054 AAGGTACAAT
*
198064 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* *
198084 TTCTCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
198104 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
198124 TTCGCA
1 TTCGCA
198130 TTGCGATGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:198164 original size:20 final size:20
Alignment explanation
Indices: 198139--198176 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
198129 ATTGCGATGG
198139 TTGCGAAAGTCAAATTCGCA
1 TTGCGAAAGTCAAATTCGCA
*
198159 TTGCGATAGTCAAATTCG
1 TTGCGAAAGTCAAATTCG
198177 TGTTAGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
TTGCGAAAGTCAAATTCGCA
Found at i:198407 original size:6 final size:6
Alignment explanation
Indices: 198398--198432 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
198388 TTGTGATTAA
**
198398 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
198433 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:200602 original size:24 final size:24
Alignment explanation
Indices: 200568--200621 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
200558 CTGAAACATC
200568 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
200592 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
200616 ATCAAA
1 ATCAAA
200622 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:200635 original size:24 final size:24
Alignment explanation
Indices: 200568--200635 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
200558 CTGAAACATC
* * *
200568 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
200592 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
200616 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
200636 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:201410 original size:14 final size:15
Alignment explanation
Indices: 201373--201411 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
201363 AGAAATCATT
201373 AAAAAATTATATAGA
1 AAAAAATTATATAGA
*
201388 AATAAAATTATGTA-A
1 AA-AAAATTATATAGA
201403 AAAAAATTA
1 AAAAAATTA
201412 GAGATGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAAATTATATAGA
Found at i:201631 original size:20 final size:19
Alignment explanation
Indices: 201581--201646 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
201571 GTGAATTCGA
*
201581 AAATCGAGTTGCGAAAATA-
1 AAATCGAGTTGCG-AATTAG
*
201600 AAATTCGCGTTGCGAATTCAG
1 AAA-TCGAGTTGCGAATT-AG
*
201621 AAATCGAGTTGCTAATTTAG
1 AAATCGAGTTGCGAA-TTAG
201641 AAATCG
1 AAATCG
201647 CATTGTGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.15
20 28 0.72
21 5 0.13
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (19 bp):
AAATCGAGTTGCGAATTAG
Found at i:201657 original size:20 final size:21
Alignment explanation
Indices: 201581--201663 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 21
201571 GTGAATTCGA
**
201581 AAATCGAGTTGC-GAAAATA-
1 AAATCGAGTTGCTGAATTTAG
* *
201600 AAATTCGCGTTGC-GAATTCAG
1 AAA-TCGAGTTGCTGAATTTAG
201621 AAATCGAGTTGCT-AATTTAG
1 AAATCGAGTTGCTGAATTTAG
*
201641 AAATCGCA-TTG-TGAATTTGG
1 AAATCG-AGTTGCTGAATTTAG
201661 AAA
1 AAA
201664 ATCACGCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 4 0.08
20 44 0.85
21 4 0.08
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (21 bp):
AAATCGAGTTGCTGAATTTAG
Found at i:201657 original size:40 final size:40
Alignment explanation
Indices: 201568--201666 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
201558 ACTAAAACCT
201568 ATTGTGAATTCGAAAATCGAGTTGCGAAAATAAAATTCGC
1 ATTGTGAATTCGAAAATCGAGTTGCGAAAATAAAATTCGC
* * * **
201608 GTTGCGAATTC-AGAAATCGAGTTGCTAATTTAGAAA-TCGC
1 ATTGTGAATTCGA-AAATCGAGTTGCGAAAATA-AAATTCGC
*
201648 ATTGTGAATTTGGAAAATC
1 ATTGTGAA-TTCGAAAATC
201667 ACGCGAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.02
40 35 0.74
41 10 0.21
42 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (40 bp):
ATTGTGAATTCGAAAATCGAGTTGCGAAAATAAAATTCGC
Found at i:201948 original size:20 final size:20
Alignment explanation
Indices: 201925--201962 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
201915 TAACAATTCA
201925 ATAAAT-TTAATAATTATTTT
1 ATAAATCTTAA-AATTATTTT
*
201945 ATAATTCTTAAAATTATT
1 ATAAATCTTAAAATTATT
201963 AATAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAATCTTAAAATTATTTT
Found at i:202953 original size:4 final size:4
Alignment explanation
Indices: 202944--202975 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
202934 CTTTCTCTTA
202944 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
202976 ATTGTTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:209188 original size:23 final size:22
Alignment explanation
Indices: 209162--209208 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
209152 ATAAAGTACA
*
209162 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAG-GCTTAT
**
209185 ATAATGTAATAGGTAGGCTTAT
1 ATAACATAATAGGTAGGCTTAT
209207 AT
1 AT
209209 TTACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (22 bp):
ATAACATAATAGGTAGGCTTAT
Found at i:209719 original size:23 final size:23
Alignment explanation
Indices: 209689--209747 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
209679 TACAACTACC
209689 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
209712 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
209735 TATTACATCATAT
1 TATTACATTATAT
209748 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Done.