Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009596.1 Hibiscus syriacus cultivar Beakdansim tig00116975_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: 1846166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:968697 original size:14 final size:14
Alignment explanation
Indices: 968678--968736 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
968668 TTTGGTTTCG
968678 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
968692 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
968709 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
968725 CGTTGCGATTTT
1 CGTTGCGATTTT
968737 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:968704 original size:33 final size:33
Alignment explanation
Indices: 968662--968785 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
968652 AAAATCGCAA
*
968662 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
968695 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
968728 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* * *
968761 TGCAATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
968786 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:968716 original size:19 final size:18
Alignment explanation
Indices: 968662--968753 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
968652 AAAATCGCAA
968662 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
968681 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
968695 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
968714 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
968728 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
968747 TGCGATT
1 TGCGATT
968754 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:968949 original size:83 final size:87
Alignment explanation
Indices: 968833--969105 Score: 315
Period size: 93 Copynumber: 3.1 Consensus size: 87
968823 ATGGATTGCA
* *
968833 TTAC-TTCAACCAATAGACAAAACAAAGACAAATAATGACTT-CAG-G-G-TA-TTAGTTTAGCA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAAT-ACTTACAGTGAGATACATAGTTTAGCA
968892 GAATTGGCAGCAACCGAACAAAT
65 GAATTGGCAGCAACCGAACAAAT
* *
968915 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACATAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAATACTT-ACAGTG----AG-ATACATAGTT
968980 TAGCAGAATTGGCAGCAACCGAACAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
* * *
969008 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAATACTT-ACAGTG----AG-ATACATAGTT
*
969073 TAGCAGAATTGGCAGCAACCGAATAAAT
60 TAGCAGAATTGGCAGCAACCGAACAAAT
969101 TTACT
1 TTACT
969106 AAGCAATCTA
Statistics
Matches: 173, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
82 7 0.04
83 30 0.17
84 3 0.02
85 1 0.01
90 1 0.01
92 2 0.01
93 129 0.75
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (87 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATAATACTTACAGTGAGATACATAGTTTAGCAG
AATTGGCAGCAACCGAACAAAT
Found at i:969041 original size:93 final size:93
Alignment explanation
Indices: 968882--969105 Score: 430
Period size: 93 Copynumber: 2.4 Consensus size: 93
968872 TTCAGGGTAT
968882 TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
1 TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
968947 ATACTATTTCACAGTGTTAAAGAATACA
66 ATACTATTTCACAGTGTTAAAGAATACA
968975 TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
1 TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
969040 ATACTATTTCACAGTGTTAAAGAATACA
66 ATACTATTTCACAGTGTTAAAGAATACA
* *
969068 CAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
969106 AAGCAATCTA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (93 bp):
TAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
ATACTATTTCACAGTGTTAAAGAATACA
Found at i:970813 original size:20 final size:20
Alignment explanation
Indices: 970782--970845 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
970772 TTTTGGTTGA
970782 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
970802 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
970822 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
970843 AAT
1 AAT
970846 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:970834 original size:21 final size:21
Alignment explanation
Indices: 970780--970844 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
970770 TCTTTTGGTT
970780 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
970801 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
970821 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
970842 GAA
1 GAA
970845 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:970848 original size:14 final size:14
Alignment explanation
Indices: 970829--970885 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
970819 GAGAAATGAA
970829 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
970843 AATCGCAACGCGAAATAAA
1 AATCGCAA--CG--A-GAG
970862 AATCGCAACGAGAG
1 AATCGCAACGAGAG
970876 AATCGCAACG
1 AATCGCAACG
970886 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:970864 original size:33 final size:33
Alignment explanation
Indices: 970780--970902 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
970770 TCTTTTGGTT
*
970780 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
970821 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
970854 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
970887 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
970903 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
33 48 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:970867 original size:19 final size:19
Alignment explanation
Indices: 970780--970907 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
970770 TCTTTTGGTT
*
970780 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
970799 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
970821 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
970838 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
970854 GAAATAAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
970871 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
970887 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
970906 GA
1 GA
970908 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
14 19 0.23
15 2 0.02
16 4 0.05
17 3 0.04
18 2 0.02
19 25 0.30
20 12 0.15
21 11 0.13
22 4 0.05
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:970938 original size:14 final size:14
Alignment explanation
Indices: 970919--970975 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
970909 TTTGGTTTCG
970919 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
970933 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
970952 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
970966 CGTTGCGATT
1 CGTTGCGATT
970976 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:970951 original size:33 final size:33
Alignment explanation
Indices: 970903--970982 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
970893 AAAATCGCAA
**
970903 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
970936 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
970969 TGCGATTTTCATTT
1 TGCGATTTTCATTT
970983 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:970988 original size:21 final size:21
Alignment explanation
Indices: 970963--971036 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
970953 GTTGCGATTC
970963 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
970984 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
971005 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
971026 TCTCGTTGCGA
1 TCTCGTTGCGA
971037 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:971158 original size:33 final size:33
Alignment explanation
Indices: 971116--971186 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
971106 AATACTAACT
971116 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
971149 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
971182 TGAAA
1 TGAAA
971187 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:971591 original size:20 final size:20
Alignment explanation
Indices: 971566--971758 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
971556 CTTTAAAAAT
971566 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
971586 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
971606 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
971627 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
971647 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
971667 CGCGTTGCGATTCACGGATA
1 CGCGTTGCGATTTACGGATA
*
971687 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
971707 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
971727 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
971747 CGCGTTGCGATT
1 CGCGTTGCGATT
971759 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:972390 original size:84 final size:84
Alignment explanation
Indices: 972269--972437 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
972259 CCCTCTTTAC
* *
972269 ACATTCTTGTGTTAATAAAGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATG
1 ACATTCTTGTGTTAATAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCAATAAATG
*
972334 AAGCATGTGACATAAACAA
66 AAACATGTGACATAAACAA
* * *
972353 ACATTCTTGTGTTAATAAAGATATGACAAAGACGAAAAAGACAAACAGTTTTTGTCCAATAAATG
1 ACATTCTTGTGTTAATAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCAATAAATG
972418 AAACATGTGACATAAACAA
66 AAACATGTGACATAAACAA
972437 A
1 A
972438 AATATATCTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (84 bp):
ACATTCTTGTGTTAATAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCAATAAATG
AAACATGTGACATAAACAA
Found at i:972457 original size:17 final size:17
Alignment explanation
Indices: 972435--972469 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
972425 TGACATAAAC
*
972435 AAAAATATATCTGATAA
1 AAAAATATATCCGATAA
972452 AAAAATATATCCGATAA
1 AAAAATATATCCGATAA
972469 A
1 A
972470 TTTTACTTTT
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:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAATATATCCGATAA
Found at i:972854 original size:19 final size:19
Alignment explanation
Indices: 972830--972873 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
972820 TACAAATATT
972830 AAAAAATCAGAAAAAATT-C
1 AAAAAATCAG-AAAAATTAC
**
972849 AAAAAATTTGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
972868 AAAAAA
1 AAAAAA
972874 ATTAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:972912 original size:25 final size:25
Alignment explanation
Indices: 972884--972936 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
972874 ATTAATATGA
*
972884 TTATTTATC-TAATTTAAATATATTT
1 TTATCTATCTTAATTT-AATATATTT
972909 TTATCTATCTTATAATTTAATATATTT
1 TTATCTATC-T-TAATTTAATATATTT
972936 T
1 T
972937 AACTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATCTATCTTAATTTAATATATTT
Found at i:973294 original size:12 final size:12
Alignment explanation
Indices: 973277--973304 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
973267 CTGATAAAAT
973277 TTTGGGACAAAG
1 TTTGGGACAAAG
973289 TTTGGGACAAAG
1 TTTGGGACAAAG
973301 TTTG
1 TTTG
973305 AGCTGTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (12 bp):
TTTGGGACAAAG
Found at i:983237 original size:6 final size:6
Alignment explanation
Indices: 983226--983250 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
983216 AACACGTATT
983226 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
983251 GCCGAGCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:986565 original size:19 final size:20
Alignment explanation
Indices: 986527--986566 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
986517 AAACCATTCA
986527 GGGGGGAATCGGTACCTCCTTG
1 GGGGGGAATCGGT--CTCCTTG
986549 GGGGGGAATCGGT-TCCTT
1 GGGGGGAATCGGTCTCCTT
986567 CTGAGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.20, G:0.42, T:0.25
Consensus pattern (20 bp):
GGGGGGAATCGGTCTCCTTG
Found at i:988635 original size:21 final size:21
Alignment explanation
Indices: 988565--988646 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
988555 CAGAACCCCA
*
988565 GGGGGTATCGATTCCC-C-TG
1 GGGGGAATCGATTCCCTCATG
* **
988584 TGGGAGGAATCGGTTCCCCATCAAA
1 -GGG-GGAATCGATT-CCC-TCATG
988609 GGGGGAATCGATTCCCTCATG
1 GGGGGAATCGATTCCCTCATG
988630 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
988647 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 15 0.30
21 16 0.32
22 6 0.12
23 9 0.18
24 4 0.08
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCATG
Found at i:988638 original size:20 final size:20
Alignment explanation
Indices: 988609--988646 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
988599 CCCCATCAAA
988609 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
988629 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
988647 TGCACCAAAA
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:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:997321 original size:24 final size:24
Alignment explanation
Indices: 997294--997343 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
997284 TGGTGGTTGA
*
997294 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
997318 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
997342 TT
1 TT
997344 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:998702 original size:24 final size:24
Alignment explanation
Indices: 998625--998703 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
998615 GTCTAAACTC
* **
998625 CAAAGTAACAATCCACAAATTTAT
1 CAAACTAACAATCCACAAATAAAT
* * *
998649 CAAACTAATAA--CA-TATTAAAAT
1 CAAACTAACAATCCACAAAT-AAAT
998671 CAAA-TAACAATCCACAAATAAAT
1 CAAACTAACAATCCACAAATAAAT
998694 CAAACTAACA
1 CAAACTAACA
998704 TATTAAAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 7 0.17
22 8 0.20
23 10 0.24
24 16 0.39
ACGTcount: A:0.57, C:0.20, G:0.01, T:0.22
Consensus pattern (24 bp):
CAAACTAACAATCCACAAATAAAT
Found at i:999869 original size:2 final size:2
Alignment explanation
Indices: 999825--999853 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
999815 ATATCTCTAG
999825 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
999854 TTTGCTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1010823 original size:21 final size:20
Alignment explanation
Indices: 1010786--1010824 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1010776 TTATCTCCAT
**
1010786 TAGAGAAGAAATTGCTGAAA
1 TAGAGAAGAAAAGGCTGAAA
1010806 TAGAGAATGAAAAGGCTGA
1 TAGAGAA-GAAAAGGCTGA
1010825 TATCCACAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.49, C:0.05, G:0.28, T:0.18
Consensus pattern (20 bp):
TAGAGAAGAAAAGGCTGAAA
Found at i:1015930 original size:13 final size:13
Alignment explanation
Indices: 1015912--1015955 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1015902 ATAAATAATA
*
1015912 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
1015925 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
1015938 AAACAACTACAAT
1 AAAAAACTACAAT
1015951 AAAAA
1 AAAAA
1015956 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:1018086 original size:24 final size:24
Alignment explanation
Indices: 1018016--1018086 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1018006 CAATCTTATA
* * *
1018016 TGGCACTACAGTGC-ATTTCTACT
1 TGGCACTTCGGTGCAATTTCTACG
* *
1018039 TGCCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
1018063 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
1018087 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:1019261 original size:33 final size:33
Alignment explanation
Indices: 1019210--1019273 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1019200 CTCCAGGAGA
* * *
1019210 GGTCATAAAACTCTGTGAAGGTGGCGTCGGCGG
1 GGTCATAAAACTCGGTGAAGGCGGCGGCGGCGG
1019243 GGTCATAAAA-TCAGGTGAAGGCGGCGGCGGC
1 GGTCATAAAACTC-GGTGAAGGCGGCGGCGGC
1019274 ATCTAGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.23, C:0.19, G:0.41, T:0.17
Consensus pattern (33 bp):
GGTCATAAAACTCGGTGAAGGCGGCGGCGGCGG
Found at i:1020948 original size:16 final size:16
Alignment explanation
Indices: 1020924--1020977 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1020914 TATATCTGTA
* *
1020924 AAAAAATTAATTAAAT
1 AAAATATTAAATAAAT
1020940 AAAATATTAAATAAAT
1 AAAATATTAAATAAAT
* **
1020956 TAAATACAAAAT-AAT
1 AAAATATTAAATAAAT
1020971 AAAATAT
1 AAAATAT
1020978 AATAAAATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:1020979 original size:10 final size:10
Alignment explanation
Indices: 1020937--1020988 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
1020927 AAATTAATTA
1020937 AATAAAATATT
1 AATAAAATA-T
*
1020948 AAATAAATTA-
1 -AATAAAATAT
1020958 AATACAAA-AT
1 AATA-AAATAT
1020968 AATAAAATAT
1 AATAAAATAT
1020978 AATAAAATAT
1 AATAAAATAT
1020988 A
1 A
1020989 CCTTAGACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.23
10 19 0.54
12 8 0.23
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAAATAT
Found at i:1021301 original size:29 final size:31
Alignment explanation
Indices: 1021259--1021327 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
1021249 AAGGTTGTTA
* * *
1021259 GATCAGGAATTATAGT-CTGAACGGTG-TCT
1 GATCGGGAAATATAGTGCTGAACGGTGATAT
* *
1021288 GATCGGGAAATATATTGCTTAACGGTGATAT
1 GATCGGGAAATATAGTGCTGAACGGTGATAT
1021319 -ATCGGGAAA
1 GATCGGGAAA
1021328 ATCGCCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 13 0.39
30 18 0.55
31 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (31 bp):
GATCGGGAAATATAGTGCTGAACGGTGATAT
Found at i:1023802 original size:20 final size:20
Alignment explanation
Indices: 1023777--1023852 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
1023767 ACTGTAGATT
1023777 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1023797 ATCGCAACGCGTAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1023817 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
1023837 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
1023853 CAACGCGAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1025737 original size:30 final size:30
Alignment explanation
Indices: 1025691--1025762 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1025681 TGTTTTCTGG
*
1025691 TTGGT-GGTGGTCGTCCAGTGGTCTGTGCT
1 TTGGTGGGTGGTTGTCCAGTGGTCTGTGCT
1025720 TTGGTGGGTGGTTGTCCAGTGGTCTGTGCT
1 TTGGTGGGTGGTTGTCCAGTGGTCTGTGCT
1025750 TTGGTGGGTGGTT
1 TTGGTGGGTGGTT
1025763 TCTGTCTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.03, C:0.12, G:0.44, T:0.40
Consensus pattern (30 bp):
TTGGTGGGTGGTTGTCCAGTGGTCTGTGCT
Found at i:1026752 original size:23 final size:23
Alignment explanation
Indices: 1026726--1026792 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1026716 CCACAACTCA
1026726 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
1026749 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
1026772 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
1026793 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:1026979 original size:103 final size:103
Alignment explanation
Indices: 1026808--1027025 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1026798 TAATGTCCAT
* *
1026808 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1026873 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
*
1026911 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1026976 GACTTCACACATGTTCCAAAAAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
1027014 AAGGACCACATA
1 AAGGACCACATA
1027026 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
Found at i:1027836 original size:19 final size:19
Alignment explanation
Indices: 1027812--1027862 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1027802 TTCCCCATCG
1027812 GTGCATCGATGCACTACTT
1 GTGCATCGATGCACTACTT
1027831 GTGCATCGATGCACTACTT
1 GTGCATCGATGCACTACTT
*
1027850 GTGCATCGGTGCA
1 GTGCATCGATGCA
1027863 TAAAATACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCACTACTT
Found at i:1027904 original size:64 final size:63
Alignment explanation
Indices: 1027831--1027986 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 63
1027821 TGCACTACTT
* * * ** *
1027831 GTGCATCGATGCACTACTTGTGCATCGGTGCATAAAATACATTCGATGTTTGTT-TATTACTGG
1 GTGCATCGATGCACTACTTGTGCATCGATGCACAAAATACATTCGATGTTT-TTAGATTAAAGA
* * * * *
1027894 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTTAGATTAAAGA
1 G-TGCATCGATGCACT-ACTTGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAGA
1027958 GTGCATCGATGCACTACTTGTGCATCGAT
1 GTGCATCGATGCACTACTTGTGCATCGAT
1027987 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
63 28 0.37
64 48 0.63
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAGA
Found at i:1029543 original size:21 final size:21
Alignment explanation
Indices: 1029519--1029561 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1029509 CTTGAAGTGG
1029519 TGTACTTTGTTCCTCTTTATA
1 TGTACTTTGTTCCTCTTTATA
1029540 TGTACTTTGTTCCTCTTTATA
1 TGTACTTTGTTCCTCTTTATA
1029561 T
1 T
1029562 AAAGTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.09, T:0.58
Consensus pattern (21 bp):
TGTACTTTGTTCCTCTTTATA
Found at i:1031478 original size:24 final size:26
Alignment explanation
Indices: 1031451--1031504 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
1031441 AAAAATAATA
1031451 TATTCTAT-TTAAT-TAATAATAAA-T
1 TATT-TATGTTAATCTAATAATAAAGT
*
1031475 TA-TTATGTTAGTCTAATAATAAAGT
1 TATTTATGTTAATCTAATAATAAAGT
1031500 TATTT
1 TATTT
1031505 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.12
23 5 0.20
24 12 0.48
25 3 0.12
26 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (26 bp):
TATTTATGTTAATCTAATAATAAAGT
Found at i:1040689 original size:18 final size:19
Alignment explanation
Indices: 1040653--1040690 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1040643 TAGTACCTAA
*
1040653 ATAAACTATATATATACAC
1 ATAAACTATATATACACAC
*
1040672 ATAAA-TATATGTACACAC
1 ATAAACTATATATACACAC
1040690 A
1 A
1040691 GCATATCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (19 bp):
ATAAACTATATATACACAC
Found at i:1043638 original size:14 final size:14
Alignment explanation
Indices: 1043619--1043655 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1043609 TCACGATTAA
1043619 TGATATTTATATAT
1 TGATATTTATATAT
1043633 TGATATTTAT-TAT
1 TGATATTTATATAT
*
1043646 T-ATTTTTATA
1 TGATATTTATA
1043656 AAATATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 7 0.33
13 4 0.19
14 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (14 bp):
TGATATTTATATAT
Found at i:1054733 original size:3 final size:3
Alignment explanation
Indices: 1054725--1054751 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1054715 ATTAATAAAA
1054725 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1054752 GTAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1056410 original size:31 final size:31
Alignment explanation
Indices: 1056374--1056438 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1056364 ATAAACATAT
1056374 ATATTATTACAATTAATTAGTAGAATAAAAA
1 ATATTATTACAATTAATTAGTAGAATAAAAA
1056405 ATATTATTACAATTAATTAGTAGAATAAAAA
1 ATATTATTACAATTAATTAGTAGAATAAAAA
1056436 ATA
1 ATA
1056439 AATTATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (31 bp):
ATATTATTACAATTAATTAGTAGAATAAAAA
Found at i:1057285 original size:73 final size:72
Alignment explanation
Indices: 1057153--1057295 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 72
1057143 TTTTAAGTTT
* * * *
1057153 AATAATTAAAAAATATTTTTAAACATACTTTTTATTTCAAATACTCTAAAATATGGTAATTTAGT
1 AATAATTAAAAAATATTTTTAAACATACTTTTTATTTAAAAAACTCAAAAATATGGTAATTCAGT
1057218 GGGCCTC
66 GGGCCTC
* *
1057225 AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCAAAAATATTGTAATTCAG
1 AATAATTAAAAAATATTTTTAAACAT-ACTTTTTATTTAAAAAACTCAAAAATATGGTAATTCAG
1057290 TGGGCC
65 TGGGCC
1057296 CCATTTTAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 26 0.41
73 38 0.59
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (72 bp):
AATAATTAAAAAATATTTTTAAACATACTTTTTATTTAAAAAACTCAAAAATATGGTAATTCAGT
GGGCCTC
Found at i:1061440 original size:14 final size:14
Alignment explanation
Indices: 1061423--1061466 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
1061413 TGCAAACATC
1061423 ATTCTTATCAATTT
1 ATTCTTATCAATTT
**
1061437 ATTCTTATCAAAAT
1 ATTCTTATCAATTT
1061451 ATTCTTATCAATTT
1 ATTCTTATCAATTT
1061465 AT
1 AT
1061467 GATGTTTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTCTTATCAATTT
Found at i:1068239 original size:31 final size:31
Alignment explanation
Indices: 1068196--1068260 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1068186 CACAGATTCT
* *
1068196 GAAGAACCTAGGTAAACAACCCATATGTCTC
1 GAAGAACATAGGTAAACAACCCATATGTCCC
**
1068227 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAACCCATATGTCCC
1068258 GAA
1 GAA
1068261 AACTATATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAACCCATATGTCCC
Found at i:1068592 original size:24 final size:23
Alignment explanation
Indices: 1068565--1068611 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1068555 TCACATAGCA
1068565 TATAAACTTATACATATA-TTCATG
1 TATAAAC-T-TACATATATTTCATG
*
1068589 TATATACTTACATATATTTCATG
1 TATAAACTTACATATATTTCATG
1068612 ATCAACGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 7 0.33
24 6 0.29
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (23 bp):
TATAAACTTACATATATTTCATG
Found at i:1088586 original size:16 final size:18
Alignment explanation
Indices: 1088550--1088586 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1088540 GTTACGTAAA
*
1088550 TATTACAAATTATATTAT
1 TATTACAAATAATATTAT
1088568 TATTA-AAATAATA-TAT
1 TATTACAAATAATATTAT
1088584 TAT
1 TAT
1088587 ATTATAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTACAAATAATATTAT
Found at i:1088629 original size:15 final size:16
Alignment explanation
Indices: 1088609--1088638 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1088599 TGTATTTAAT
1088609 AATATTAAAA-ATTAG
1 AATATTAAAATATTAG
1088624 AATATTAAAATATTA
1 AATATTAAAATATTA
1088639 AATTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATATTAAAATATTAG
Found at i:1090200 original size:2 final size:2
Alignment explanation
Indices: 1090195--1090226 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1090185 TCTCTCTCTC
1090195 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1090227 TAATTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1094397 original size:27 final size:27
Alignment explanation
Indices: 1094367--1094448 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
1094357 CTGAAAATAT
1094367 AAAAAAATTAAAATATATATTAATTTA
1 AAAAAAATTAAAATATATATTAATTTA
** *
1094394 AAAAATCTAAAAATATATATTAATTT-
1 AAAAAAATTAAAATATATATTAATTTA
1094420 --AAAAATCTAAAATATATATTAATTTA
1 AAAAAAAT-TAAAATATATATTAATTTA
1094446 AAA
1 AAA
1094449 CTGGTAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 4 0.09
25 17 0.38
27 23 0.51
28 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAAAAATTAAAATATATATTAATTTA
Found at i:1094409 original size:25 final size:26
Alignment explanation
Indices: 1094368--1094448 Score: 139
Period size: 25 Copynumber: 3.2 Consensus size: 26
1094358 TGAAAATATA
1094368 AAAAAAT-TAAAATATATATTAATTT
1 AAAAAATCTAAAATATATATTAATTT
1094393 AAAAAATCTAAAAATATATATTAATTT
1 AAAAAATCT-AAAATATATATTAATTT
1094420 -AAAAATCTAAAATATATATTAATTT
1 AAAAAATCTAAAATATATATTAATTT
1094445 AAAA
1 AAAA
1094449 CTGGTAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
25 24 0.45
26 12 0.23
27 17 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAAAATCTAAAATATATATTAATTT
Found at i:1094492 original size:6 final size:6
Alignment explanation
Indices: 1094481--1094521 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1094471 TATCCGATTC
* * *
1094481 CTTCCG CTTCCG CTTCCA CTTCCG CTTCCA CTTCCG TTTCC
1 CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCC
1094522 TCTACTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.49, G:0.10, T:0.37
Consensus pattern (6 bp):
CTTCCG
Found at i:1094502 original size:12 final size:12
Alignment explanation
Indices: 1094481--1094521 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1094471 TATCCGATTC
*
1094481 CTTCCGCTTCCG
1 CTTCCACTTCCG
1094493 CTTCCACTTCCG
1 CTTCCACTTCCG
1094505 CTTCCACTTCCG
1 CTTCCACTTCCG
*
1094517 TTTCC
1 CTTCC
1094522 TCTACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.05, C:0.49, G:0.10, T:0.37
Consensus pattern (12 bp):
CTTCCACTTCCG
Found at i:1094521 original size:18 final size:18
Alignment explanation
Indices: 1094481--1094515 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1094471 TATCCGATTC
*
1094481 CTTCCGCTTCCGCTTCCA
1 CTTCCGCTTCCACTTCCA
1094499 CTTCCGCTTCCACTTCC
1 CTTCCGCTTCCACTTCC
1094516 GTTTCCTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.51, G:0.09, T:0.34
Consensus pattern (18 bp):
CTTCCGCTTCCACTTCCA
Found at i:1094971 original size:20 final size:20
Alignment explanation
Indices: 1094948--1094995 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1094938 GGAATGTAAA
1094948 ATTACCAGTGAGAATAAAAG
1 ATTACCAGTGAGAATAAAAG
*
1094968 ATTACCAGTGGGAATAAAAG
1 ATTACCAGTGAGAATAAAAG
1094988 ATTACCAG
1 ATTACCAG
1094996 AGAATAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (20 bp):
ATTACCAGTGAGAATAAAAG
Found at i:1100442 original size:17 final size:17
Alignment explanation
Indices: 1100420--1100453 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1100410 TATTAAAATT
*
1100420 ATATTATTTTGATAAAA
1 ATATTATTTTAATAAAA
1100437 ATATTATTTTAATAAAA
1 ATATTATTTTAATAAAA
1100454 TTATCGAAAG
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATTATTTTAATAAAA
Found at i:1104549 original size:64 final size:63
Alignment explanation
Indices: 1104464--1104624 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
1104454 TTGTTTAAGG
* * *
1104464 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAAAAGAAAACATCGAATAAGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAAGATTTA
* * * * *
1104528 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAAGATTTA
*
1104592 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGTAGTGCATCGATGCAT
1104625 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 60 0.71
65 23 0.27
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATATGTAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAAGATTTA
Found at i:1106178 original size:149 final size:149
Alignment explanation
Indices: 1105991--1106294 Score: 536
Period size: 149 Copynumber: 2.0 Consensus size: 149
1105981 GAGTCGAGGG
* *
1105991 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
1106056 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1106121 TATGGCACTTTGGTGCAAT
131 TATGGCACTTCGGTGCAAT
* * *
1106140 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1106205 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGATATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1106270 TATGGCACTTCGGTGCAAT
131 TATGGCACTTCGGTGCAAT
*
1106289 TATACG
1 TCTACG
1106295 AGCTGTGGTG
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTTCGGTGCAAT
Found at i:1109671 original size:64 final size:63
Alignment explanation
Indices: 1109586--1109746 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
1109576 TTGTTTAAGG
* * *
1109586 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
1109650 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
1109714 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGTAGTGCATCGATGCAT
1109747 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 61 0.72
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATATGTAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1123860 original size:10 final size:10
Alignment explanation
Indices: 1123845--1123940 Score: 57
Period size: 10 Copynumber: 8.9 Consensus size: 10
1123835 ATGACACTTT
*
1123845 ATATAATTCA
1 ATATAATTAA
1123855 ATATAACTATAA
1 ATATAA-T-TAA
*
1123867 ATGTAATTAA
1 ATATAATTAA
*
1123877 GTATATAATTCA
1 --ATATAATTAA
1123889 ATATAACTATAA
1 ATATAA-T-TAA
*
1123901 ATGTAATTAA
1 ATATAATTAA
* * *
1123911 GTCTAATTAT
1 ATATAATTAA
*
1123921 ATAGAATTTAA
1 ATATAA-TTAA
1123932 ATATAATTA
1 ATATAATTA
1123941 TACAATTATT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
10 31 0.48
11 12 0.18
12 22 0.34
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (10 bp):
ATATAATTAA
Found at i:1123882 original size:34 final size:34
Alignment explanation
Indices: 1123844--1123912 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1123834 AATGACACTT
1123844 TATATAATTCAATATAACTATAAATGTAATTAAG
1 TATATAATTCAATATAACTATAAATGTAATTAAG
1123878 TATATAATTCAATATAACTATAAATGTAATTAAG
1 TATATAATTCAATATAACTATAAATGTAATTAAG
1123912 T
1 T
1123913 CTAATTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (34 bp):
TATATAATTCAATATAACTATAAATGTAATTAAG
Found at i:1124176 original size:13 final size:15
Alignment explanation
Indices: 1124140--1124178 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1124130 TTAAATCGAA
*
1124140 CTATTAAACTTTAAT
1 CTATAAAACTTTAAT
1124155 CTATAAAACTTTAAT
1 CTATAAAACTTTAAT
1124170 -T-TAAAACTT
1 CTATAAAACTT
1124179 AGTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (15 bp):
CTATAAAACTTTAAT
Found at i:1130285 original size:18 final size:19
Alignment explanation
Indices: 1130254--1130306 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
1130244 TATTTGGTTC
*
1130254 ACGGAATGTAAGATTATCG
1 ACGGAATATAAGATTATCG
1130273 ACGGAA-ATAAGATTATCG
1 ACGGAATATAAGATTATCG
*
1130291 ACGGAATATAACATTA
1 ACGGAATATAAGATTA
1130307 CCTAACACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (19 bp):
ACGGAATATAAGATTATCG
Found at i:1130557 original size:36 final size:37
Alignment explanation
Indices: 1130484--1130557 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
1130474 TACTATAATT
**
1130484 AATTTATATATTTTCTTTAAAAAAATTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAAATTAAAAACATAA
* *
1130521 AATTTATATAATTTT-TTT-ACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAAATTAAAAACATAA
1130557 A
1 A
1130558 TATATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 15 0.47
37 12 0.38
38 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAAATTAAAAACATAA
Found at i:1131257 original size:38 final size:38
Alignment explanation
Indices: 1131202--1131326 Score: 153
Period size: 39 Copynumber: 3.3 Consensus size: 38
1131192 AACCAAGAAA
* * *
1131202 ACCATATG-AAACATTGCCAGTGTATGTATCGGCATGC
1 ACCAAATGAAAACATTGCCAGTGTATCTATTGGCATGC
* ** *
1131239 TCCAAATGAAAACATTGCCAACGTATCCATTGGCATGC
1 ACCAAATGAAAACATTGCCAGTGTATCTATTGGCATGC
*
1131277 ACCAAAATGAAAACATTGCCAGTGTATCTATTGGAATGC
1 ACC-AAATGAAAACATTGCCAGTGTATCTATTGGCATGC
1131316 ACCAAACTGAA
1 ACCAAA-TGAA
1131327 CGTTTCACAT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 6 0.08
38 29 0.40
39 38 0.52
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (38 bp):
ACCAAATGAAAACATTGCCAGTGTATCTATTGGCATGC
Found at i:1135612 original size:18 final size:19
Alignment explanation
Indices: 1135589--1135631 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1135579 CAATAATCCT
*
1135589 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
*
1135607 ATTCCCACTGATAATTTTAC
1 ATT-CCACTGATAATCTTAC
1135627 ATTCC
1 ATTCC
1135632 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:1136639 original size:18 final size:18
Alignment explanation
Indices: 1136604--1136645 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1136594 GGTTGTCATT
*
1136604 TTTGTTTTATTTCTTTCC
1 TTTGTTTTATTTCCTTCC
1136622 TTTGTTTTA-TTCACTTCC
1 TTTGTTTTATTTC-CTTCC
*
1136640 ATTGTT
1 TTTGTT
1136646 CTTTCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTGTTTTATTTCCTTCC
Found at i:1140105 original size:39 final size:39
Alignment explanation
Indices: 1140051--1140128 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1140041 TGGTGGTTCT
1140051 ACGTTACGGGCTCAATGGCTCTCCCCCGAAGTCACTGGA
1 ACGTTACGGGCTCAATGGCTCTCCCCCGAAGTCACTGGA
1140090 ACGTTACGGGCTCAATGGCTCTCCCCCGAAGTCACTGGA
1 ACGTTACGGGCTCAATGGCTCTCCCCCGAAGTCACTGGA
1140129 GGAGATCGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (39 bp):
ACGTTACGGGCTCAATGGCTCTCCCCCGAAGTCACTGGA
Found at i:1142555 original size:183 final size:184
Alignment explanation
Indices: 1142236--1142622 Score: 611
Period size: 183 Copynumber: 2.1 Consensus size: 184
1142226 TTTTCTAATT
* * * *
1142236 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
* *
1142300 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATATAAGTTTAAAAGTTATT
* * *
1142365 GGATCTTAAATTATTAATTGGGGTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGGGTTTAAATGATTTGGG-TTGAACCCATATGTTA
1142419 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
* *
1142483 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATATAATTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATATAAGTTTAAAAGTTAT
* *
1142547 TAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAACTCATATGTTA
130 TAGATCTTAAATTATTAATTGGGGTTTAAATGATTTGGGTTGAACCCATATGTTA
1142602 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1142623 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 2 0.01
183 121 0.64
184 65 0.35
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATATAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGGGTTTAAATGATTTGGGTTGAACCCATATGTTA
Found at i:1144686 original size:12 final size:12
Alignment explanation
Indices: 1144669--1144693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1144659 TAAAATGTAA
1144669 ATATATGTATAT
1 ATATATGTATAT
1144681 ATATATGTATAT
1 ATATATGTATAT
1144693 A
1 A
1144694 ATTATATAAT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:1145325 original size:84 final size:83
Alignment explanation
Indices: 1145121--1145795 Score: 772
Period size: 84 Copynumber: 8.1 Consensus size: 83
1145111 GAGCAGACAA
* * * * * * * * * *
1145121 TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCCTCGGAGCTGAGTG
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCT-TGAGCTGAGCG
* * **
1145186 GAATCGAACTCGGGGGTC--
64 TAGTCGAACTCGAAGGTCTT
* * * * *
1145204 TT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAACGATGTGCCGTTGAGCTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGT
*
1145267 AGTCGAACTCAAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
* * * *
1145286 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAACTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGT
1145351 AGTCGAACTCGAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
* * *
1145370 TGGTTGGCATATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGT
*
1145435 AGTCGAACTCAAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
* * **
1145454 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGT
1145519 AGTCGAACTCGAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
* * * *
1145538 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCG
* **
1145603 TAATCGAACTCGGGGGTC--
64 TAGTCGAACTCGAAGGTCTT
* * *
1145621 -T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGT
*
1145684 AGTCGAACTCAAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
* * **
1145703 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGT
1 TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGT
1145768 AGTCGAACTCGAAGGTCTT
65 AGTCGAACTCGAAGGTCTT
*
1145787 TGGTTGGCA
1 TTGTTGGCA
1145796 CGATTCCCTT
Statistics
Matches: 507, Mismatches: 69, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
80 48 0.09
81 83 0.16
82 4 0.01
83 11 0.02
84 333 0.66
85 28 0.06
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTA
GTCGAACTCGAAGGTCTT
Found at i:1146094 original size:106 final size:106
Alignment explanation
Indices: 1145909--1147305 Score: 2261
Period size: 106 Copynumber: 13.3 Consensus size: 106
1145899 GTATTGTTCC
* ** * * *
1145909 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
* *
1145973 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG-CATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
1146015 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146080 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1146121 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146186 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1146227 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146292 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1146333 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146398 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1146439 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146504 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1146545 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146598 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1146639 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146704 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1146745 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146810 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1146851 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146916 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1146957 GAGTCAAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1147021 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1147062 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1147127 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1147168 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* **
1147232 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTATGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
1147274 GA-TTCAAGATCCTTCGTTGAGAAGCTGAAATT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1147306 TACTCTCGAG
Statistics
Matches: 1211, Mismatches: 64, Indels: 33
0.93 0.05 0.03
Matches are distributed among these distances:
94 87 0.07
95 3 0.00
96 2 0.00
99 1 0.00
101 1 0.00
104 2 0.00
105 176 0.15
106 937 0.77
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1146574 original size:43 final size:43
Alignment explanation
Indices: 1146513--1146668 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
1146503 ACCAGCGGTC
1146513 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
1146556 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
1146606 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1146650 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1146669 ATTGGCTCTG
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 40 0.48
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.26
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1147107 original size:211 final size:211
Alignment explanation
Indices: 1146571--1147305 Score: 1247
Period size: 211 Copynumber: 3.5 Consensus size: 211
1146561 GTTGTGAAGT
*
1146571 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1146636 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
* *
1146701 CAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1146766 GAAGTTGAAATTGGCTC
195 GAAGTTGAAATTGGCTC
* * *
1146783 TGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * * *
1146848 CTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGA
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
* *
1146913 CAACCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAAATATCCTTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
*
1146978 GAAGCTGAAATTGGCTC
195 GAAGTTGAAATTGGCTC
1146995 TGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1147060 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGAC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGAC
1147125 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
131 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
1147190 AAGTTGAAATTGGCTC
196 AAGTTGAAATTGGCTC
* **
1147206 TGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTATGTTGTC
1 TGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* * * *
1147271 TTGGA-TTCAAGATCCTTCGTTGAGAAGCTGAAATT
66 -TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1147306 TACTCTCGAG
Statistics
Matches: 489, Mismatches: 32, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
211 277 0.57
212 212 0.43
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (211 bp):
TGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGAC
AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
AAGTTGAAATTGGCTC
Found at i:1150474 original size:18 final size:19
Alignment explanation
Indices: 1150433--1150477 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1150423 AGTTAATGTG
1150433 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1150452 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1150470 AATGCAAA
1 AATGCAAA
1150478 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1153449 original size:12 final size:12
Alignment explanation
Indices: 1153432--1153456 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1153422 TAAAATGTAA
1153432 ATATATGTATAT
1 ATATATGTATAT
1153444 ATATATGTATAT
1 ATATATGTATAT
1153456 A
1 A
1153457 ATTATATAAT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:1159581 original size:23 final size:20
Alignment explanation
Indices: 1159531--1159587 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
1159521 TTATCTTTAA
*
1159531 ATCTTTAAATATTATAAAAT
1 ATCTTTAATTATTATAAAAT
**
1159551 ATGATTAATTTATTATAAAAAAT
1 ATCTTTAA-TTATTAT--AAAAT
1159574 ATCTTTAAATTATT
1 ATCTTT-AATTATT
1159588 TTTAAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
23 14 0.50
24 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
ATCTTTAATTATTATAAAAT
Found at i:1161712 original size:21 final size:20
Alignment explanation
Indices: 1161626--1161783 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1161616 AAATGACCAA
**
1161626 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1161645 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1161665 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1161685 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1161706 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1161727 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1161747 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1161768 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1161784 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1161776 original size:20 final size:20
Alignment explanation
Indices: 1161751--1162061 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
1161741 GATTTTCAAT
* *
1161751 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1161771 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1161791 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1161811 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1161831 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1161851 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1161871 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1161891 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1161912 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1161932 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1161952 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1161972 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1161992 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1162012 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
1162032 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1162052 AATCGCAACG
1 AATCGCAACG
1162062 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1161796 original size:40 final size:40
Alignment explanation
Indices: 1161751--1162140 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
1161741 GATTTTCAAT
* ** * * *
1161751 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
1161791 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
1161831 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1161871 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
1161912 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1161952 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
1161992 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
1162032 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
1162072 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
1162112 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
1162141 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:1162068 original size:20 final size:19
Alignment explanation
Indices: 1161789--1162140 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
1161779 CGCGAACACA
1161789 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1161809 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
1161829 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
1161849 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1161869 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
1161889 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
1161909 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
1161930 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
1161950 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1161970 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1161990 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1162010 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
1162030 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1162050 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1162070 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1162090 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1162110 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1162130 TAAATCACAAC
1 TAAATCGCAAC
1162141 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:1162856 original size:24 final size:24
Alignment explanation
Indices: 1162817--1162863 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1162807 AAATTTGGTC
1162817 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1162841 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1162864 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1165363 original size:19 final size:19
Alignment explanation
Indices: 1165341--1165594 Score: 307
Period size: 19 Copynumber: 14.4 Consensus size: 19
1165331 CGGAAAATAC
*
1165341 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1165360 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1165374 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
*
1165393 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1165407 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1165426 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1165445 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1165459 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1165478 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1165497 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
1165516 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1165535 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1165549 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1165568 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1165587 AATCGCAA
1 AATCGCAA
1165595 CGAGATAATC
Statistics
Matches: 205, Mismatches: 8, Indels: 44
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.00
14 39 0.19
15 1 0.00
16 12 0.06
17 10 0.05
18 2 0.01
19 137 0.67
20 3 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1165396 original size:33 final size:34
Alignment explanation
Indices: 1165341--1165594 Score: 218
Period size: 33 Copynumber: 7.2 Consensus size: 34
1165331 CGGAAAATAC
* *
1165341 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
* *
1165374 AATCGCAATGCGGAAATG-AAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACAATGAA
1165407 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* * * *
1165445 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAACAATGAA
*
1165478 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
*
1165516 AATCGCAATGCGAAATGAAAATCGCAACGAA--AG
1 AATCGCAATGCGAAATGAAAATCGCAAC-AATGAA
1165549 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
1165587 AATCGCAA
1 AATCGCAA
1165595 CGAGATAATC
Statistics
Matches: 180, Mismatches: 19, Indels: 39
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.01
32 12 0.07
33 88 0.49
34 7 0.04
35 4 0.02
36 3 0.02
37 1 0.01
38 57 0.32
39 6 0.03
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:1165595 original size:52 final size:55
Alignment explanation
Indices: 1165341--1165616 Score: 297
Period size: 52 Copynumber: 5.3 Consensus size: 55
1165331 CGGAAAATAC
* *
1165341 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATGA
*
1165393 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
1165445 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
1165497 AATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
1165549 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
1165601 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1165617 TATAAACGCA
Statistics
Matches: 206, Mismatches: 6, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 1 0.00
50 2 0.01
51 6 0.03
52 150 0.73
54 3 0.01
55 5 0.02
56 1 0.00
57 28 0.14
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:1165713 original size:19 final size:19
Alignment explanation
Indices: 1165623--1165705 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
1165613 AAATTATAAA
1165623 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1165642 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1165662 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1165678 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1165695 CGCATTGCGAT
1 CGCATTGCGAT
1165706 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1165831 original size:14 final size:14
Alignment explanation
Indices: 1165812--1165848 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1165802 CATCAATTAC
1165812 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1165826 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1165840 ACAAATCAA
1 ACAAATCAA
1165849 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:1167819 original size:14 final size:14
Alignment explanation
Indices: 1167800--1167856 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1167790 GCGAAATGAA
*
1167800 AATCGCAACGACAG
1 AATCGCAACGAAAG
1167814 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1167831 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1167847 AATCGCAACG
1 AATCGCAACG
1167857 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:1167827 original size:33 final size:33
Alignment explanation
Indices: 1167781--1167873 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1167771 GCGAAACCAA
*
1167781 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1167814 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1167847 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1167874 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:1167838 original size:19 final size:19
Alignment explanation
Indices: 1167744--1167878 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1167734 TAGTTTACTT
* *
1167744 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1167764 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1167783 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1167802 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1167816 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1167835 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1167849 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1167868 TCGCAATGCGA
1 TCGCAACGCGA
1167879 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:1167896 original size:19 final size:19
Alignment explanation
Indices: 1167874--1168002 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1167864 AAAATCGCAA
1167874 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1167893 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1167907 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1167926 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1167940 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1167959 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1167978 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1167998 TGCGA
1 TGCGA
1168003 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:1167916 original size:33 final size:33
Alignment explanation
Indices: 1167874--1167965 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1167864 AAAATCGCAA
1167874 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1167907 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1167940 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1167966 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:1168113 original size:17 final size:17
Alignment explanation
Indices: 1168091--1168123 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1168081 AATACTATTT
1168091 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
1168108 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
1168124 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:1168217 original size:92 final size:93
Alignment explanation
Indices: 1168046--1168424 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
1168036 TTGAATGGAT
1168046 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1168111 AGTTTAACAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1168139 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1168203 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1168231 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1168295 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1168323 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1168388 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1168416 AAATTTACT
1 AAATTTACT
1168425 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 183 0.65
93 100 0.35
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1168375 original size:185 final size:185
Alignment explanation
Indices: 1168046--1168424 Score: 724
Period size: 185 Copynumber: 2.0 Consensus size: 185
1168036 TTGAATGGAT
1168046 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1168111 AGTTTAACAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAACAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1168176 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1168231 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1168295 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAACAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1168360 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1168416 AAATTTACT
1 AAATTTACT
1168425 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 91 0.48
185 100 0.52
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAACAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1170150 original size:14 final size:14
Alignment explanation
Indices: 1170131--1170220 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1170121 TTGAAATGAA
1170131 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1170145 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1170162 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1170178 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1170197 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1170211 AATCGCAACG
1 AATCGCAACG
1170221 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:1170168 original size:33 final size:33
Alignment explanation
Indices: 1170123--1170237 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1170113 TCTTTTGGTT
1170123 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1170156 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1170189 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1170222 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1170238 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:1170169 original size:19 final size:18
Alignment explanation
Indices: 1170130--1170242 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1170120 GTTGAAATGA
1170130 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1170145 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1170162 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1170178 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1170195 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1170211 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1170228 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1170243 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:1170273 original size:14 final size:14
Alignment explanation
Indices: 1170254--1170308 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1170244 TTTGGTTTCG
1170254 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1170268 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1170287 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1170301 CGTTGCGA
1 CGTTGCGA
1170309 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:1170286 original size:33 final size:33
Alignment explanation
Indices: 1170238--1170308 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1170228 AAAATCGCAA
**
1170238 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1170271 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1170304 TGCGA
1 TGCGA
1170309 CAGTCATTCT
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:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1170316 original size:33 final size:33
Alignment explanation
Indices: 1170249--1170330 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1170239 GCGATTTTGG
***
1170249 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1170282 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1170315 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1170331 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:1170335 original size:20 final size:20
Alignment explanation
Indices: 1170261--1170349 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1170251 TCGCGTTGCG
1170261 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1170281 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1170294 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1170314 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1170334 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1170350 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:1170471 original size:33 final size:33
Alignment explanation
Indices: 1170429--1170499 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1170419 AATACTAACT
*
1170429 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1170462 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1170495 TGAAA
1 TGAAA
1170500 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:1170733 original size:22 final size:22
Alignment explanation
Indices: 1170681--1170735 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1170671 TGGTTGTGAG
**
1170681 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1170703 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1170725 GGATTTCTTCG
1 GGATTTCTTCG
1170736 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:1170906 original size:20 final size:20
Alignment explanation
Indices: 1170881--1171073 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1170871 CTTTAAATAT
1170881 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1170901 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1170923 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1170942 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1170962 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1170982 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1171002 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1171022 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1171042 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1171062 CGCGTTGCGATT
1 CGCGTTGCGATT
1171074 ATTGAAAATC
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:1171068 original size:60 final size:60
Alignment explanation
Indices: 1170881--1171073 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1170871 CTTTAAATAT
**
1170881 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1170942 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1171002 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1171062 CGCGTTGCGATT
1 CGCGTTGCGATT
1171074 ATTGAAAATC
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:1176924 original size:26 final size:26
Alignment explanation
Indices: 1176863--1176925 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
1176853 AGTGAACATC
*
1176863 ACACACTAAAATATATTATTAATGTG
1 ACACACTGAAATATATTATTAATGTG
*
1176889 ACACATTGAAATATATTATTAATGTG
1 ACACACTGAAATATATTATTAATGTG
*
1176915 ACATACTGAAA
1 ACACACTGAAA
1176926 CACATCACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (26 bp):
ACACACTGAAATATATTATTAATGTG
Found at i:1177953 original size:18 final size:19
Alignment explanation
Indices: 1177930--1177966 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1177920 TATACCAATC
1177930 TTAAACAAATA-ATTTTTT
1 TTAAACAAATAGATTTTTT
*
1177948 TTAAACAATTAGATTTTTT
1 TTAAACAAATAGATTTTTT
1177967 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAAACAAATAGATTTTTT
Found at i:1179037 original size:17 final size:19
Alignment explanation
Indices: 1179015--1179051 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1179005 CCATGAACGT
1179015 AAAGTTA-AAAAA-AATAA
1 AAAGTTAGAAAAACAATAA
1179032 AAAGTTAGAAAAACAATAA
1 AAAGTTAGAAAAACAATAA
1179051 A
1 A
1179052 TATCGATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAGTTAGAAAAACAATAA
Found at i:1191070 original size:21 final size:21
Alignment explanation
Indices: 1191045--1191088 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1191035 AATTTAGTTA
1191045 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
*
1191066 ATTAGTTTGTTAGTTTAAATT
1 ATTAGTTTGTTAGTATAAATT
1191087 AT
1 AT
1191089 ATTATATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1191098 original size:28 final size:28
Alignment explanation
Indices: 1191065--1191118 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1191055 TAGTATAAAT
1191065 TATTAGTTTGTTAGTTTAAATTATATTA
1 TATTAGTTTGTTAGTTTAAATTATATTA
*
1191093 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTTAAATTATAT
1191119 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAATTATATTA
Found at i:1191626 original size:17 final size:17
Alignment explanation
Indices: 1191604--1191662 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
1191594 TTTATTCCCA
1191604 TTTAAAAAAATATTTTG
1 TTTAAAAAAATATTTTG
* *
1191621 TTTAAAAATATTTAGTGTTG
1 TTTAAAAA-A-ATA-TTTTG
**
1191641 TTTTTAAAAATATTTTG
1 TTTAAAAAAATATTTTG
1191658 TTTAA
1 TTTAA
1191663 TTTACATTAG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 15 0.48
18 3 0.10
19 3 0.10
20 10 0.32
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTAAAAAAATATTTTG
Found at i:1194538 original size:11 final size:11
Alignment explanation
Indices: 1194517--1194564 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
1194507 TTTGTTAATA
1194517 ATTATATGATTT
1 ATTA-ATGATTT
1194529 ATTAATGATTT
1 ATTAATGATTT
1194540 GATAATAATGATTT
1 -AT--TAATGATTT
*
1194554 AATAATGATTT
1 ATTAATGATTT
1194565 TAATATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 16 0.50
12 6 0.19
13 1 0.03
14 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (11 bp):
ATTAATGATTT
Found at i:1194550 original size:14 final size:14
Alignment explanation
Indices: 1194511--1194559 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1194501 ATAGGATTTG
1194511 TTAATAATTATATGAT
1 TTAATAA-TA-ATGAT
1194527 TT-AT--TAATGAT
1 TTAATAATAATGAT
*
1194538 TTGATAATAATGAT
1 TTAATAATAATGAT
1194552 TTAATAAT
1 TTAATAAT
1194560 GATTTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 7 0.24
12 4 0.14
14 14 0.48
15 2 0.07
16 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (14 bp):
TTAATAATAATGAT
Found at i:1194620 original size:26 final size:26
Alignment explanation
Indices: 1194591--1194660 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
1194581 GATGATTTAG
1194591 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1194617 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
*
1194643 TAATAATTTGATAATAAT
1 TAATGATTTGATAATAAT
1194661 GATTTAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:1194693 original size:14 final size:13
Alignment explanation
Indices: 1194522--1194691 Score: 98
Period size: 14 Copynumber: 13.7 Consensus size: 13
1194512 TAATAATTAT
1194522 ATGATTTAT--TA
1 ATGATTTATAATA
1194533 ATGATTTGATAATA
1 ATGATTT-ATAATA
1194547 ATGA-TT-TAATA
1 ATGATTTATAATA
1194558 ATGATTT-TAATA
1 ATGATTTATAATA
* * * * * *
1194570 TTTA-ATGTACTG
1 ATGATTTATAATA
*
1194582 ATGA-TT-TAGTA
1 ATGATTTATAATA
1194593 ATGATTTGATAATA
1 ATGATTT-ATAATA
*
1194607 ATCA-TTATAATA
1 ATGATTTATAATA
1194619 ATGATTTAGTAATA
1 ATGATTTA-TAATA
*
1194633 ATCA-TTATAATA
1 ATGATTTATAATA
*
1194645 ATAATTTGATAATA
1 ATGATTT-ATAATA
1194659 ATGATTTAGTAAT-
1 ATGATTTA-TAATA
1194672 -T-A-TTATTAATA
1 ATGATTTA-TAATA
1194683 ATGATTTAT
1 ATGATTTAT
1194692 TATTAATATT
Statistics
Matches: 125, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
10 7 0.06
11 25 0.20
12 38 0.30
13 15 0.12
14 40 0.32
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (13 bp):
ATGATTTATAATA
Done.