Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:561389 original size:20 final size:20
Alignment explanation
Indices: 561364--561477 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
561354 AATTGGGAAA
*
561364 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
561384 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
561405 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
561425 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
* *
561445 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
561465 TTCGCAACGCGAT
1 ATCGCAACGCGAT
561478 TTACATAATC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.78
21 12 0.15
22 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:561490 original size:40 final size:41
Alignment explanation
Indices: 561363--561497 Score: 150
Period size: 40 Copynumber: 3.3 Consensus size: 41
561353 GAATTGGGAA
* * * * *
561363 AATCGCAATGCGATACTTACTATCGCAATGCGATAATACAA
1 AATCGCAACGCGATACTTACTTTCGCAACGCGATATTACAT
* *
561404 AATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC-T
1 AATCGCAACGCGATACTTACTTTCGCAACGCGATA-TTACAT
* *
561445 -TTCGCAACGCGATACTGACTTTCGCAACGCGAT-TTACAT
1 AATCGCAACGCGATACTTACTTTCGCAACGCGATATTACAT
*
561484 AATCGCAATGCGAT
1 AATCGCAACGCGAT
561498 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
38 3 0.04
39 1 0.01
40 41 0.53
41 31 0.40
42 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
AATCGCAACGCGATACTTACTTTCGCAACGCGATATTACAT
Found at i:561693 original size:22 final size:22
Alignment explanation
Indices: 561665--561708 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
561655 CACTCTCTCA
561665 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
561687 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
561709 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:561997 original size:20 final size:20
Alignment explanation
Indices: 561972--562009 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
561962 CGATTCTCTC
561972 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
561992 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
562010 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:563777 original size:18 final size:18
Alignment explanation
Indices: 563742--563787 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
563732 GCTGCCAATC
563742 TGTTTTT-G-TTTGTATT
1 TGTTTTTGGTTTTGTATT
*
563758 TGTTTTTGGTTTTGTTTT
1 TGTTTTTGGTTTTGTATT
563776 TGTCTTTTGGTT
1 TGT-TTTTGGTT
563788 GAAGTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 10 0.38
19 8 0.31
ACGTcount: A:0.02, C:0.02, G:0.22, T:0.74
Consensus pattern (18 bp):
TGTTTTTGGTTTTGTATT
Found at i:563875 original size:20 final size:19
Alignment explanation
Indices: 563841--563906 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
563831 TAGTTTACTT
*
563841 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
563860 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
563880 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
563899 TCGCAACG
1 TCGCAACG
563907 ACAATCGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:563945 original size:14 final size:14
Alignment explanation
Indices: 563895--563950 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
563885 ATGCGAAATG
563895 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
563909 --AATCGCAACACGAA
1 AAAATCGC-A-ACGAC
563923 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
563939 AAAATCGCAACG
1 AAAATCGCAACG
563951 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
12 6 0.18
13 1 0.03
14 15 0.44
16 5 0.15
17 1 0.03
18 6 0.18
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:563955 original size:32 final size:31
Alignment explanation
Indices: 563879--563967 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 31
563869 GGAAATGGCT
*
563879 ATCGCAATGCGAAATGAAAATCGCAACGACA
1 ATCGCAACGCGAAATGAAAATCGCAACGACA
*
563910 ATCGCAACACGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAC--A
563942 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
563968 TGCGATTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 13 0.25
31 14 0.27
32 16 0.31
33 9 0.17
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (31 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACA
Found at i:564003 original size:14 final size:14
Alignment explanation
Indices: 563984--564023 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
563974 TTGTGTTTCG
563984 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
563998 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
564012 CGTTGCGATTTT
1 CGTTGCGATTTT
564024 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:564038 original size:19 final size:19
Alignment explanation
Indices: 564014--564061 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
564004 GATTTTGTCG
564014 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
564033 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
564052 TTGCGATTTT
1 TTGCGATTTT
564062 AAGTTTCGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:566054 original size:19 final size:19
Alignment explanation
Indices: 566030--566278 Score: 410
Period size: 19 Copynumber: 13.6 Consensus size: 19
566020 AAAACAGACT
* *
566030 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
566049 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566068 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566087 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
566101 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566120 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566139 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566158 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566177 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566196 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566215 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566234 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
566253 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
566267 ATCGCAATGCGA
1 ATCGCAATGCGA
566279 TTTTCTCGTT
Statistics
Matches: 220, Mismatches: 2, Indels: 18
0.92 0.01 0.08
Matches are distributed among these distances:
14 22 0.10
15 2 0.01
16 4 0.02
17 4 0.02
18 1 0.00
19 187 0.85
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:566335 original size:20 final size:20
Alignment explanation
Indices: 566278--566335 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
566268 TCGCAATGCG
* *
566278 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
566298 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
566318 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
566336 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:567036 original size:19 final size:19
Alignment explanation
Indices: 567012--567053 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
567002 CTTCAACTAA
567012 AACTGTCATTAAAGAAGTT
1 AACTGTCATTAAAGAAGTT
567031 AACTGTCATTAAAGAAGTT
1 AACTGTCATTAAAGAAGTT
567050 AACT
1 AACT
567054 TATGAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (19 bp):
AACTGTCATTAAAGAAGTT
Found at i:567441 original size:24 final size:24
Alignment explanation
Indices: 567414--567467 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
567404 GTATTCGAAA
* *
567414 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
567438 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
567462 TTTGAT
1 TTTGAT
567468 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:570000 original size:19 final size:19
Alignment explanation
Indices: 569944--570074 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
569934 GGAAATTACT
569944 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
569963 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
569977 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
569996 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
570010 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
570029 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
570043 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
570062 ATCGCAACGCGAA
1 ATCGCAATGCGAA
570075 TTTAATTTCG
Statistics
Matches: 80, Mismatches: 17, Indels: 30
0.63 0.13 0.24
Matches are distributed among these distances:
14 25 0.31
15 3 0.04
16 6 0.08
17 6 0.08
18 3 0.04
19 37 0.46
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:570077 original size:33 final size:33
Alignment explanation
Indices: 569945--570077 Score: 205
Period size: 33 Copynumber: 4.0 Consensus size: 33
569935 GAAATTACTA
* * *
569945 TCGCAATGCGAAATGAAAATCACAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
569978 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
570011 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
570044 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
570077 T
1 T
570078 AATTTCGCGT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 1 0.01
33 93 0.99
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:570253 original size:14 final size:14
Alignment explanation
Indices: 570234--570270 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
570224 CATCAATTAA
570234 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
570248 ACAAATCACCTTTT
1 ACAAATCAACTTTT
570262 ACAAATCAA
1 ACAAATCAA
570271 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:571694 original size:21 final size:21
Alignment explanation
Indices: 571628--571694 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
571618 GTGAATCGGG
*
571628 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
571648 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
571670 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
571691 CTCT
1 CTCT
571695 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:571713 original size:42 final size:42
Alignment explanation
Indices: 571667--571748 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
571657 CGATGACAGT
* * *
571667 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATATG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATATG
* * *
571709 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATA
571749 GGAGAGTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATATG
Found at i:573828 original size:33 final size:33
Alignment explanation
Indices: 573771--573869 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
573761 ACGGGATAAT
*
573771 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
573805 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
573838 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
573870 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:573863 original size:19 final size:19
Alignment explanation
Indices: 573746--573911 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
573736 TCTTTTGGTT
*
573746 GAAATGAAAATCGCAACGG
1 GAAATGAAAATCGCAACGC
*
573765 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
573785 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
573803 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
573819 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
573837 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
573852 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
573872 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
573891 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
573910 GA
1 GA
573912 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:573941 original size:18 final size:18
Alignment explanation
Indices: 573907--573986 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
573897 AAAATCGCAA
*
573907 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
573926 TGCGATTTTATTTCGCGT
1 TGCGATTTTATTTCGCGT
*
573944 TGCGA--TTA--TCTCGT
1 TGCGATTTTATTTCGCGT
*
573958 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
573978 TGCGATTTT
1 TGCGATTTT
573987 CATTCTCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
18 13 0.25
19 12 0.24
20 10 0.20
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.46
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:574523 original size:20 final size:20
Alignment explanation
Indices: 574498--574549 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
574488 CGCTATGTAA
*
574498 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
574518 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
574538 ATCTCGTTGCGA
1 ATCGCGTTGCGA
574550 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:574586 original size:20 final size:20
Alignment explanation
Indices: 574498--574583 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
574488 CGCTATGTAA
* *
574498 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
574518 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
574538 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
574559 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
574579 ATCGC
1 ATCGC
574584 ATTACGATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 39 0.75
21 13 0.25
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:574592 original size:41 final size:41
Alignment explanation
Indices: 574517--574594 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
574507 CGAAAGTCAG
* * * *
574517 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
*
574558 TATCGCATTGCGATAGTAAGTATCGCATTACGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTT
574595 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
Found at i:574610 original size:41 final size:41
Alignment explanation
Indices: 574563--574653 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
574553 TTTATTATCG
574563 CATTGCGATAGTAAGTA-TCGCATTACGATTTTCCCAATTCA
1 CATTGCGAT-GTAAGTATTCGCATTACGATTTTCCCAATTCA
* * ** * *
574604 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CATTGCGATGTAAGTATTCGCATTACGATTTTCCCAATTCA
574645 CATTGCGAT
1 CATTGCGAT
574654 TTTCCCAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (41 bp):
CATTGCGATGTAAGTATTCGCATTACGATTTTCCCAATTCA
Found at i:574614 original size:21 final size:21
Alignment explanation
Indices: 574580--574693 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
574570 ATAGTAAGTA
*
574580 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
574601 TCACGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
574621 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
574642 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
574663 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
574683 TCGCATTGCGA
1 TCGCATTGCGA
574694 ATTGGGAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
20 31 0.41
21 45 0.59
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:574708 original size:62 final size:62
Alignment explanation
Indices: 574579--574708 Score: 188
Period size: 62 Copynumber: 2.1 Consensus size: 62
574569 GATAGTAAGT
* * *
574579 ATCGCATTACGATTTTCCCAATTCACGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAA
1 ATCGCATTACGATTTTCCCAATTCACGTTGCGATTTACTTATTCGCATTGCGAATTGCCAAA
* * * **
574641 TTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTACGATTTTCCCAATTCACGTTGCGATTTACTTATTCGCATTGCGAATTGCCAAA
574703 ATCGCA
1 ATCGCA
574709 ACGATACTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (62 bp):
ATCGCATTACGATTTTCCCAATTCACGTTGCGATTTACTTATTCGCATTGCGAATTGCCAAA
Found at i:574955 original size:30 final size:32
Alignment explanation
Indices: 574921--574988 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
574911 ATAGTTTTTA
574921 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
574951 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
574984 TATTT
1 TATTT
574989 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:579514 original size:21 final size:21
Alignment explanation
Indices: 579488--579529 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
579478 AATAATTAAT
*
579488 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
579509 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
579530 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:585247 original size:14 final size:14
Alignment explanation
Indices: 585222--585263 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
585212 GGGGAAAGAG
585222 AAATATTAAATAAAT
1 AAATA-TAAATAAAT
585237 CAAA-ATAAATAAAT
1 -AAATATAAATAAAT
*
585251 AAATAAAAATAAA
1 AAATATAAATAAA
585264 AATAGATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 17 0.71
15 1 0.04
16 3 0.12
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATAAATAAAT
Found at i:585251 original size:18 final size:18
Alignment explanation
Indices: 585228--585349 Score: 69
Period size: 18 Copynumber: 6.8 Consensus size: 18
585218 AGAGAAATAT
*
585228 TAAATAAATCAAAATAAA
1 TAAATAAATAAAAATAAA
585246 TAAATAAATAAAAAT-AA
1 TAAATAAATAAAAATAAA
*
585263 -AAATAGATCATAAAAAT-AT
1 TAAATA-A--ATAAAAATAAA
*
585282 TAAATAAATATGAAAA-CAA
1 TAAATAAATA--AAAATAAA
*
585301 -AAATAAATAAAAA-ATA
1 TAAATAAATAAAAATAAA
*
585317 TTAATATAATAATAAA-AAA
1 TAAATA-AATAA-AAATAAA
* *
585336 TAGATGAATAAAAA
1 TAAATAAATAAAAA
585350 GATGGGGCGT
Statistics
Matches: 84, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
16 10 0.12
17 13 0.15
18 33 0.39
19 23 0.27
20 5 0.06
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (18 bp):
TAAATAAATAAAAATAAA
Found at i:585287 original size:36 final size:35
Alignment explanation
Indices: 585246--585349 Score: 99
Period size: 36 Copynumber: 2.9 Consensus size: 35
585236 TCAAAATAAA
585246 TAAATAAATAAAAATAAAAATAGATCATAAAAATAT
1 TAAATAAATAAAAATAAAAATAGAT-ATAAAAATAT
* *
585282 TAAATAAATATGAAAACAAAAATAAATA-AAAAATAT
1 TAAATAAATA--AAAATAAAAATAGATATAAAAATAT
*
585318 T-AAT--ATAATAATAAAAAATAGATGAATAAAAA
1 TAAATAAATAAAAAT-AAAAATAGAT--ATAAAAA
585350 GATGGGGCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
31 3 0.05
32 9 0.16
33 3 0.05
34 1 0.02
35 8 0.14
36 19 0.33
37 1 0.02
38 13 0.23
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (35 bp):
TAAATAAATAAAAATAAAAATAGATATAAAAATAT
Found at i:585529 original size:95 final size:95
Alignment explanation
Indices: 585353--585603 Score: 351
Period size: 95 Copynumber: 2.6 Consensus size: 95
585343 ATAAAAAGAT
* * * *
585353 GGGGCGTTTAACAAATTGCTCTAGAGGGATAACTCAATGTCATTGTATAG-ATATTATAATCACC
1 GGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA-G-C-TT-TATTGTATATTATAATCACC
585417 TTTATCAGGCTAGCTGAATATTATCCATAAAATC
62 TTTATCAGGCTAGCTGAATATTATCCATAAAATC
* *
585451 GGGGTGTTTAACCAATTGCTCTAGAGGAACAACTCAAGCCTTATTGTATATTATAATCACCTTTA
1 GGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTA
* * * *
585516 TCAGGCTATCTGAATCTTATCTATAAAGTC
66 TCAGGCTAGCTGAATATTATCCATAAAATC
*
585546 GGGGTATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATATATAAT
1 GGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAAT
585604 ATTATAATCT
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
94 4 0.03
95 93 0.67
96 7 0.05
97 1 0.01
98 33 0.24
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (95 bp):
GGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTTA
TCAGGCTAGCTGAATATTATCCATAAAATC
Found at i:589058 original size:44 final size:45
Alignment explanation
Indices: 588971--589062 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 45
588961 TCAAGTTTTG
*
588971 AAATTACTCTCCCTTACTTTAACACTTCTCCCATTTATCATTTAA
1 AAATTACTCCCCCTTACTTTAACACTTCTCCCATTTATCATTTAA
*
589016 AAATTACTCCCCCTTACTTTAAC-CTTCTCTCATTTATCATTTAA
1 AAATTACTCCCCCTTACTTTAACACTTCTCCCATTTATCATTTAA
589060 AAA
1 AAA
589063 CACTTTTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 23 0.51
45 22 0.49
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (45 bp):
AAATTACTCCCCCTTACTTTAACACTTCTCCCATTTATCATTTAA
Found at i:592846 original size:44 final size:47
Alignment explanation
Indices: 592780--592877 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 47
592770 TTTATTTTCG
592780 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
592827 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
592872 TTTTTG
1 TTTTTG
592878 TGAATAACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 28 0.57
45 12 0.24
46 4 0.08
47 5 0.10
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:600051 original size:15 final size:15
Alignment explanation
Indices: 600031--600060 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
600021 GGGAAGCTAT
600031 TGGGTTTCGTAGTAA
1 TGGGTTTCGTAGTAA
600046 TGGGTTTCGTAGTAA
1 TGGGTTTCGTAGTAA
600061 GCAAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
TGGGTTTCGTAGTAA
Found at i:602559 original size:6 final size:7
Alignment explanation
Indices: 602541--602725 Score: 97
Period size: 7 Copynumber: 26.6 Consensus size: 7
602531 AAATAAAAGA
602541 GAAAAAT
1 GAAAAAT
602548 GAAAAAT
1 GAAAAAT
602555 GAAAAAAAT
1 G--AAAAAT
602564 GAAAAAT
1 GAAAAAT
*
602571 AATAATAAT
1 GA-AA-AAT
602580 -AAAAAT
1 GAAAAAT
602586 GAGAAGAA-
1 GA-AA-AAT
602594 GAAAAA-
1 GAAAAAT
*
602600 GAAGAAAA
1 GAA-AAAT
602608 GAAAAAT
1 GAAAAAT
602615 GAGAAAAAT
1 --GAAAAAT
602624 GAAAAA-
1 GAAAAAT
*
602630 GAGAAA-
1 GAAAAAT
**
602636 -AAAAGG
1 GAAAAAT
602642 GAAAAA-
1 GAAAAAT
*
602648 GAGAAA-
1 GAAAAAT
602654 -AAAAAT
1 GAAAAAT
602660 GAAAAAT
1 GAAAAAT
602667 GAAAAAT
1 GAAAAAT
*
602674 AAAAAAT
1 GAAAAAT
*
602681 AAAAAAT
1 GAAAAAT
*
602688 AAAAAAT
1 GAAAAAT
602695 GAAAAAAAT
1 G--AAAAAT
*
602704 -AAAAAA
1 GAAAAAT
602710 GAAAAA-
1 GAAAAAT
602716 GAAAAA-
1 GAAAAAT
602722 GAAA
1 GAAA
602726 TAAAAGGAGG
Statistics
Matches: 149, Mismatches: 11, Indels: 37
0.76 0.06 0.19
Matches are distributed among these distances:
5 7 0.05
6 33 0.22
7 74 0.50
8 10 0.07
9 25 0.17
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
GAAAAAT
Found at i:602563 original size:9 final size:9
Alignment explanation
Indices: 602549--602709 Score: 64
Period size: 9 Copynumber: 18.4 Consensus size: 9
602539 GAGAAAAATG
602549 AAAAATGAA
1 AAAAATGAA
602558 AAAAATGAA
1 AAAAATGAA
*
602567 AAATAATAATAA
1 AAA-AAT--GAA
*
602579 TAAAAATGAG
1 -AAAAATGAA
*
602589 AAGAA-GAA
1 AAAAATGAA
602597 AAAGAA-GAAAA
1 AAA-AATG--AA
*
602608 GAAAAATGAG
1 -AAAAATGAA
602618 AAAAATGAA
1 AAAAATGAA
*
602627 AAAGA-GAA
1 AAAAATGAA
*
602635 AAAAAGGGAA
1 AAAAA-TGAA
*
602645 AAAGA-GAAA
1 AAAAATG-AA
602654 AAAAATG--
1 AAAAATGAA
602661 AAAAATG--
1 AAAAATGAA
602668 AAAAAT--A
1 AAAAATGAA
602675 AAAAAT--A
1 AAAAATGAA
602682 AAAAAT--A
1 AAAAATGAA
602689 AAAAATGAA
1 AAAAATGAA
602698 AAAAAT-AA
1 AAAAATGAA
602706 AAAA
1 AAAA
602710 GAAAAAGAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
7 33 0.27
8 18 0.15
9 44 0.35
10 13 0.10
11 4 0.03
12 9 0.07
13 3 0.02
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (9 bp):
AAAAATGAA
Found at i:602684 original size:28 final size:29
Alignment explanation
Indices: 602653--602715 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
602643 AAAAAGAGAA
* *
602653 AAAAAATGAAAAATG-AAAAATAAAAAAT
1 AAAAAATAAAAAATGAAAAAATAAAAAAG
602681 AAAAAATAAAAAATGAAAAAAATAAAAAAG
1 AAAAAATAAAAAATG-AAAAAATAAAAAAG
602711 AAAAA
1 AAAAA
602716 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.45
30 17 0.55
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (29 bp):
AAAAAATAAAAAATGAAAAAATAAAAAAG
Found at i:604051 original size:37 final size:36
Alignment explanation
Indices: 603997--604068 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
603987 AAACAGGTCA
603997 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
*
604033 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
604069 TCATTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
Found at i:604364 original size:162 final size:161
Alignment explanation
Indices: 604083--604491 Score: 557
Period size: 162 Copynumber: 2.6 Consensus size: 161
604073 TTTATGAAGA
* *
604083 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGC-GAACACATTTTATGAAGA----TCGAGTCTT
1 TCGAGTTCTATACTCTCTGAA-GAATAGAGAGCAG-ACACATTTTATGAAGATTGTTCGAGTCTT
* * *
604143 ATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAG
64 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAG
604208 AATAGGGAGCGGACCTGTTTATTGAAGATT-TT
129 AATAGGGAGCGGACCTGTTTATTGAAGATTATT
* * * *
604240 TCGAGTTCTATACTCTCTGAAGAAATAGAGAGCAGACTCGTTTTATGGAAGATTGTTCAAGTATT
1 TCGAGTTCTATACTCTCTGAAG-AATAGAGAGCAGACACATTTTAT-GAAGATTGTTCGAGTCTT
* * * * *
604305 ATACTCTCTGAATGAATAGAGAGCAGACACGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGG
64 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAG
*
604370 AATAGGGAGCGGACCTGTTTGTTGAAGATTATT
129 AATAGGGAGCGGACCTGTTTATTGAAGATTATT
604403 T-GAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTT
1 TCGAGTTC-TATACTCTCTGAA-GAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTT
604466 ATACT-TCCTGAAGGAATAGGGAGCAG
64 ATACTCT-CTGAAGGAATAGGGAGCAG
604492 GCTCGTCGTC
Statistics
Matches: 220, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
156 1 0.00
157 38 0.17
158 6 0.03
160 1 0.00
161 40 0.18
162 130 0.59
163 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (161 bp):
TCGAGTTCTATACTCTCTGAAGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTTAT
ACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGAA
TAGGGAGCGGACCTGTTTATTGAAGATTATT
Found at i:604451 original size:55 final size:54
Alignment explanation
Indices: 604083--604491 Score: 373
Period size: 51 Copynumber: 7.6 Consensus size: 54
604073 TTTATGAAGA
*
604083 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGC-GAACACATTTTATGAAG---A-
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAG-ACAC-TTTTATGAAGATTAT
* * * * *
604134 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTAA-A-GAT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTATGAAGATTAT
* * * *
604186 T-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGAAGATTTT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACT-TTTA-TGAAGATTAT
* * * *
604240 TCGAGT-TCTATACTCTCTGAAGAAATAGAGAGCAGACTCGTTTTATGGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACAC-TTTTAT-GAAGATTAT
* * * * *
604296 TCAAGTATTATACTCTCTGAATGAATAGAGAGCAGACACGTTTATTGAAG---A-
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTA-TGAAGATTAT
* *
604347 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGAC-CTGTTTGTTGAAGATTAT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACT-TTT-ATGAAGATTAT
* * * *
604402 TTGAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACAC-TTTTATGAAGATTAT
604457 TCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 TCGAGTCTTATACTCT-CTGAAGGAATAGGGAGCAG
604492 GCTCGTCGTC
Statistics
Matches: 295, Mismatches: 39, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
50 8 0.03
51 113 0.38
52 5 0.02
53 1 0.00
54 4 0.01
55 110 0.37
56 51 0.17
57 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (54 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACTTTTATGAAGATTAT
Found at i:608768 original size:23 final size:23
Alignment explanation
Indices: 608738--608819 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
608728 TTCCCCTGTG
608738 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
608761 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
608784 GGGGGAATCGGTT-CCC-TC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
608804 GGGGGGATCGATTCCC
1 GGGGGAATCGGTTCCC
608820 TCTGCACTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
20 13 0.23
21 4 0.07
22 3 0.05
23 36 0.64
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:615204 original size:18 final size:18
Alignment explanation
Indices: 615181--615216 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
615171 AAATCGAAAG
615181 GAAAAAAAGATAAAAAAA
1 GAAAAAAAGATAAAAAAA
*
615199 GAAAAATAGATAAAAAAA
1 GAAAAAAAGATAAAAAAA
615217 TATTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
GAAAAAAAGATAAAAAAA
Found at i:615234 original size:18 final size:18
Alignment explanation
Indices: 615211--615273 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 18
615201 AAAATAGATA
615211 AAAAAATATTAAATAAAT
1 AAAAAATATTAAATAAAT
*
615229 ATAAAAATA-AAAATAAAT
1 A-AAAAATATTAAATAAAT
615247 AAAAAATATTAATATAGTAAT
1 AAAAAATATTAA-ATA--AAT
615268 AAAAAA
1 AAAAAA
615274 ATAGATGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.18
18 12 0.32
19 10 0.26
21 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAAATATTAAATAAAT
Found at i:615258 original size:36 final size:39
Alignment explanation
Indices: 615190--615276 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 39
615180 GGAAAAAAAG
* *
615190 ATAAAAAAAGAAAAATAGATAAAAAAATATTAA-ATA-A
1 ATAAAAAAATAAAAATAAATAAAAAAATATTAATATAGA
*
615227 ATATAAAAATAAAAATAAAT-AAAAAATATTAATATAGTA
1 ATAAAAAAATAAAAATAAATAAAAAAATATTAATATAG-A
615266 ATAAAAAAATA
1 ATAAAAAAATA
615277 GATGAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.28
37 20 0.47
39 11 0.26
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (39 bp):
ATAAAAAAATAAAAATAAATAAAAAAATATTAATATAGA
Found at i:615285 original size:37 final size:34
Alignment explanation
Indices: 615200--615286 Score: 81
Period size: 37 Copynumber: 2.5 Consensus size: 34
615190 ATAAAAAAAG
615200 AAAAATAGAT-A-AAAAAATATTAAATAAATATA
1 AAAAATAGATAATAAAAAATATTAAATAAATATA
* *
615232 AAAATAAAAATAAATAAAAAATATTAATATAGTAATA-A
1 AAAA-ATAGAT-AATAAAAAATATTAA-ATA--AATATA
615270 AAAAATAGATGAATAAA
1 AAAAATAGAT-AATAAA
615287 GATAAGTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
35 1 0.02
36 12 0.28
37 13 0.30
38 5 0.12
39 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (34 bp):
AAAAATAGATAATAAAAAATATTAAATAAATATA
Found at i:616591 original size:16 final size:16
Alignment explanation
Indices: 616570--616607 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
616560 AAAACTATAT
616570 AATATATATTTTCAAA
1 AATATATATTTTCAAA
* *
616586 AATATATTTTTTTAAA
1 AATATATATTTTCAAA
616602 AATATA
1 AATATA
616608 ATATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATATTTTCAAA
Found at i:616643 original size:14 final size:14
Alignment explanation
Indices: 616610--616643 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
616600 AAAATATAAT
616610 ATATATTTTTAAAA
1 ATATATTTTTAAAA
*
616624 AAATATTTTTAAAA
1 ATATATTTTTAAAA
*
616638 CTATAT
1 ATATAT
616644 AATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTTTTAAAA
Found at i:616725 original size:71 final size:73
Alignment explanation
Indices: 616622--616962 Score: 300
Period size: 71 Copynumber: 4.4 Consensus size: 73
616612 ATATTTTTAA
* *
616622 AAAAATATTTTT-AAAACTATATAATATATATATA-AAAAGGTTTTAAAAACTATATATTATAT-
1 AAAAATGTTTTTAAAAACTATATAATATATATATATAAAAAGTTTTAAAAACTATATATTATATA
616684 AAGTTTTC
66 AAGTTTTC
* *
616692 AAAAATGTTTTTAAAAACTATATAATATATATATATATATTCAAAATATTTTTAAAAACTATATC
1 AAAAATGTTTTTAAAAAC--TAT-ATA-ATATATATATA-T-AAAA-AGTTTTAAAAACTATATA
616757 TTATATATAAGTTTTC
59 TTATATA-AAGTTTTC
* *
616773 AAAAATGTTTTTTAAAAATTATAATATATATATATATATATATATATTAAAAATGTTCTAAAAAC
1 AAAAATG-TTTTT---AA--A-AA-CTATATA-ATATATATATATA--AAAA--GTTTTAAAAAC
616838 TATATATTATTTATAAAGTTTTC
53 TATATATTA--TATAAAGTTTTC
* * * *
616861 -AAAATATTTTAAAAAACTATATAATATATAT-TTTAAAAATGTTTTCAAAACTATATATTATAT
1 AAAAATGTTTTTAAAAACTATATAATATATATATATAAAAA-GTTTTAAAAACTATATATTATAT
**
616924 GTAG-TTT-
65 AAAGTTTTC
*
616931 AAAAATGTTTTAAAAAACTATATAATATATAT
1 AAAAATGTTTTTAAAAACTATATAATATATAT
616963 TTTTTCAAAC
Statistics
Matches: 228, Mismatches: 17, Indels: 51
0.77 0.06 0.17
Matches are distributed among these distances:
70 11 0.05
71 38 0.17
72 5 0.02
73 3 0.01
74 22 0.10
75 15 0.07
77 3 0.01
78 12 0.05
79 27 0.12
80 2 0.01
81 16 0.07
82 5 0.02
83 2 0.01
84 1 0.00
85 4 0.02
86 22 0.10
87 26 0.11
88 10 0.04
89 4 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (73 bp):
AAAAATGTTTTTAAAAACTATATAATATATATATATAAAAAGTTTTAAAAACTATATATTATATA
AAGTTTTC
Found at i:616750 original size:41 final size:39
Alignment explanation
Indices: 616623--617046 Score: 214
Period size: 41 Copynumber: 10.9 Consensus size: 39
616613 TATTTTTAAA
616623 AAAATATTTTT-AAAACTATATA--ATATATATATA---
1 AAAATATTTTTAAAAACTATATATTATATATATATATTC
**
616656 AAAA-GGTTTTAAAAACTATATATTATATA-AGT-T-TTC
1 AAAATATTTTTAAAAACTATATATTATATATA-TATATTC
*
616692 AAAAATGTTTTTAAAAACTATATAATATATATATATATATTC
1 -AAAATATTTTTAAAAACTATAT-AT-TATATATATATATTC
* *
616734 AAAATATTTTTAAAAACTATATCTTATATATA-AGTTTTC
1 AAAATATTTTTAAAAACTATATATTATATATATA-TATTC
* * *
616773 AAAAATGTTTTTTAAAAATTATAATATATATATATATATATATAT
1 -AAAAT-ATTTTTAAAAACTAT-ATAT-TATATATATATAT-T-C
* * * * *
616818 ATTAAAAATGTTCTAAAAACTATATATTATTTATAAAGTTTTC
1 A--AAATAT-TTTTAAAAACTATATATTATATATATA-TATTC
*
616861 AAAATATTTTAAAAAACTATATA--ATATATAT-T-TT-
1 AAAATATTTTTAAAAACTATATATTATATATATATATTC
* * * *
616895 AAAA-ATGTTTTCAAAACTATATATTATATGTA-GT-TTA
1 AAAATAT-TTTTAAAAACTATATATTATATATATATATTC
* * * *
616932 AAAATGTTTTAAAAAACTATATA--ATATATATTTTTTC
1 AAAATATTTTTAAAAACTATATATTATATATATATATTC
*** * *
616969 AAACCGTTTTCTGAAAATTATATATTATAT-T-T-T-TTC
1 AAAATATTTT-TAAAAACTATATATTATATATATATATTC
* *
617005 AAAAACATTTTCAAAAACTATATTATATTACTATATATATAT
1 -AAAATATTTTTAAAAAC--TA-TATATTA-TATATATATAT
617047 ATAATATTAA
Statistics
Matches: 302, Mismatches: 43, Indels: 81
0.71 0.10 0.19
Matches are distributed among these distances:
32 4 0.01
33 17 0.06
34 20 0.07
35 14 0.05
36 18 0.06
37 41 0.14
38 37 0.12
39 22 0.07
40 34 0.11
41 42 0.14
42 7 0.02
43 12 0.04
44 13 0.04
45 7 0.02
46 14 0.05
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (39 bp):
AAAATATTTTTAAAAACTATATATTATATATATATATTC
Found at i:616800 original size:37 final size:37
Alignment explanation
Indices: 616560--617032 Score: 260
Period size: 37 Copynumber: 12.4 Consensus size: 37
616550 AAATGTTTCG
* *
616560 AAAACTATATAATATAT-ATTTTCAAAAATATATTTTTTT
1 AAAACTATATAATATATAATTTTC-AAAA-AT-GTTTTTA
* * *
616599 AAAA--ATATAATATATATTTTTAAAAAAATATTTTT-
1 AAAACTATATAATATATAATTTT-CAAAAATGTTTTTA
* *
616634 AAAACTATATAATATAT-A-TAT-AAAAA-GGTTTTA
1 AAAACTATATAATATATAATTTTCAAAAATGTTTTTA
*
616667 AAAACTATATATTATATAAGTTTTCAAAAATGTTTTTA
1 AAAACTATATAATATATAA-TTTTCAAAAATGTTTTTA
*
616705 AAAACTATATAATATATATATATATATTC-AAAATATTTTTA
1 AAAACTATAT-A-ATATATA-AT-T-TTCAAAAATGTTTTTA
*
616746 AAAACTATATCTTATATATAAGTTTTCAAAAATGTTTTTTAAA
1 AAAACTATA--TAATATATAA-TTTTCAAAAATG-TTTTT--A
* * *
616789 AATTATAATATATATATATATATATATATATTAAAAATG-TTCTA
1 AA--A-ACTATATA-ATATATA-AT-T-T-TCAAAAATGTTTTTA
* * *
616833 AAAACTATATATTATTTATAAAGTTTTC-AAAATATTTTAA
1 AAAACTATATA--ATATAT-AA-TTTTCAAAAATGTTTTTA
*
616873 AAAACTATATAATATAT-ATTTT-AAAAATG-TTTTC
1 AAAACTATATAATATATAATTTTCAAAAATGTTTTTA
* * * *
616907 AAAACTATATATTATATGTAGTTT-AAAAATGTTTTAA
1 AAAACTATATAATATAT-AATTTTCAAAAATGTTTTTA
* ** *
616944 AAAACTATATAATATATATTTTTTC-AAACCGTTTTCTG
1 AAAACTATATAATATATA-ATTTTCAAAAATGTTTT-TA
* * * ** *
616982 AAAATTATATATTATAT-TTTTTCAAAAACATTTTCA
1 AAAACTATATAATATATAATTTTCAAAAATGTTTTTA
*
617018 AAAACTATATTATAT
1 AAAACTATATAATAT
617033 TACTATATAT
Statistics
Matches: 343, Mismatches: 49, Indels: 87
0.72 0.10 0.18
Matches are distributed among these distances:
32 4 0.01
33 21 0.06
34 20 0.06
35 15 0.04
36 37 0.11
37 67 0.20
38 44 0.13
39 13 0.04
40 29 0.08
41 43 0.13
42 12 0.03
43 6 0.02
44 4 0.01
45 9 0.03
46 10 0.03
47 1 0.00
48 8 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAACTATATAATATATAATTTTCAAAAATGTTTTTA
Found at i:616818 original size:88 final size:84
Alignment explanation
Indices: 616639--616891 Score: 290
Period size: 81 Copynumber: 3.0 Consensus size: 84
616629 TTTTTAAAAC
* *
616639 TATATA-ATATATATA-TAAAAAGGTTTTAAAAACTATATAT-TATATAAGTTTTCAAAAATGTT
1 TATATATATATATATATTAAAAA-TTTTTAAAAACTATATTTATATATAAGTTTTCAAAAATGTT
*
616701 TTTAAAAACTAT-ATA-ATA
65 TTTAAAAATTATAATATATA
*
616719 TATATATATATAT-TCA--AAATATTTTTAAAAACTATATCTTATATATAAGTTTTCAAAAATGT
1 TATATATATATATAT-ATTAAAAATTTTTAAAAACTATAT-TTATATATAAGTTTTCAAAAATG-
616781 TTTTTAAAAATTATAATATATA
63 TTTTTAAAAATTATAATATATA
* * *
616803 TATATATATATATATATTAAAAATGTTCTAAAAACTATATATTATTTATAAAGTTTTC-AAAATA
1 TATATATATATATATATTAAAAAT-TTTTAAAAACTATAT-TTATATAT-AAGTTTTCAAAAATG
*
616867 TTTTAAAAAACTATATAATATATA
63 TTTTTAAAAA-T-TATAATATATA
616891 T
1 T
616892 TTTAAAAATG
Statistics
Matches: 149, Mismatches: 10, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
79 15 0.10
80 12 0.08
81 27 0.18
82 13 0.09
83 3 0.02
84 17 0.11
85 1 0.01
86 14 0.09
87 27 0.18
88 20 0.13
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (84 bp):
TATATATATATATATATTAAAAATTTTTAAAAACTATATTTATATATAAGTTTTCAAAAATGTTT
TTAAAAATTATAATATATA
Found at i:616932 original size:36 final size:37
Alignment explanation
Indices: 616801--616962 Score: 172
Period size: 36 Copynumber: 4.4 Consensus size: 37
616791 TTATAATATA
*
616801 TATATATATATATATA-TATTAAAAATGTTCT-AAAAAC
1 TATATAT-TATATATAGT-TTAAAAATGTTTTAAAAAAC
* * *
616838 TATATATTATTTATAAAGTTTTCAAAATATTTTAAAAAAC
1 TATATATTA--TATATAG-TTTAAAAATGTTTTAAAAAAC
* *
616878 TATATA--ATATATATTTTAAAAATGTTTT-CAAAAC
1 TATATATTATATATAGTTTAAAAATGTTTTAAAAAAC
*
616912 TATATATTATATGTAGTTTAAAAATGTTTTAAAAAAC
1 TATATATTATATATAGTTTAAAAATGTTTTAAAAAAC
*
616949 TATATAATATATAT
1 TATATATTATATAT
616963 TTTTTCAAAC
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
34 11 0.11
35 12 0.12
36 27 0.26
37 24 0.23
38 6 0.06
39 10 0.10
40 13 0.13
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATTATATATAGTTTAAAAATGTTTTAAAAAAC
Found at i:617027 original size:36 final size:36
Alignment explanation
Indices: 616803--617027 Score: 158
Period size: 36 Copynumber: 6.1 Consensus size: 36
616793 ATAATATATA
* * *
616803 TATATATATATATATATT-AAAAATGTTCT-AAAAAC
1 TATATAT-TATATTTTTTCAAAAATGTTTTCAAAAAC
* * *
616838 TATATATTATTTATAAAGTTTTC-AAAATATTTTAAAAAAC
1 TATATATTA--TAT---TTTTTCAAAAATGTTTTCAAAAAC
* *
616878 TATATAATATATATTTT-AAAAATGTTTTC-AAAAC
1 TATATATTATATTTTTTCAAAAATGTTTTCAAAAAC
* *
616912 TATATATTATATGTAGTTT-AAAAATGTTTTAAAAAAC
1 TATATATTATAT-T-TTTTCAAAAATGTTTTCAAAAAC
** * *
616949 TATATAATATATATTTTTTC-AAACCGTTTTCTGAAAAT
1 TATAT-AT-TATATTTTTTCAAAAATGTTTTC-AAAAAC
**
616987 TATATATTATATTTTTTCAAAAACATTTTCAAAAAC
1 TATATATTATATTTTTTCAAAAATGTTTTCAAAAAC
617023 TATAT
1 TATAT
617028 TATATTACTA
Statistics
Matches: 152, Mismatches: 22, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
34 18 0.12
35 20 0.13
36 37 0.24
37 32 0.21
38 15 0.10
39 16 0.11
40 14 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATTATATTTTTTCAAAAATGTTTTCAAAAAC
Found at i:617042 original size:239 final size:235
Alignment explanation
Indices: 616623--617059 Score: 543
Period size: 239 Copynumber: 1.9 Consensus size: 235
616613 TATTTTTAAA
*
616623 AAAATATTTTTAAAACTATATAATATATATATAAAAAGGTTTTAAAAACTATATATTATATAAGT
1 AAAATATTTTAAAAACTATATAATATATATATAAAAAGGTTTTAAAAACTATATATTATATAAGT
* *
616688 TTTCAAAAATGTTTTTAAAAACTATATAATATATATATATATATTCAAAATATTTTTAAAAACTA
66 TTTCAAAAATGTTTTAAAAAACTATATAATATATATATATATATTCAAAACATTTTTAAAAACTA
* ** **
616753 TATCTTATATATAAGTTTTCAAAAATGTTTTTTAAAAATTATAATATATATATATATATATATAT
131 TATATTATATAT-A-TTTTCAAAAACATTTTAAAAAAATTATAATATATATATATATA-ATATAT
616818 ATTAAAAATGTTCTAAAAACTATATATTATTTATAAAGTTTTC
193 ATTAAAAATGTTCTAAAAACTATATATTATTTATAAAGTTTTC
* * * *
616861 AAAATATTTTAAAAAACTATATAATATATATTTTAAAAATGTTTTCAAAACTATATATTATATGT
1 AAAATATTTT-AAAAACTATATAATATATA-TATAAAAAGGTTTTAAAAACTATATATTATAT-A
* * *
616926 AG-TTT-AAAAATGTTTTAAAAAACTATATAATATATAT-T-T-T-TTCAAACCGTTTTCTGAAA
63 AGTTTTCAAAAATGTTTTAAAAAACTATATAATATATATATATATATTCAAAACATTTT-TAAAA
* *
616985 ATTATATATTATAT-T-TTTTCAAAAACATTTTCAAAAACTATATTATATTACTATATATATAT-
127 ACTATATATTATATATATTTTCAAAAACATTTT-AAAAA--A-ATTATAATA-TATATATATATA
617047 ATA-ATATTAAAAA
187 ATATATATTAAAAA
617060 ATTAAAATAA
Statistics
Matches: 173, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
232 14 0.08
233 3 0.02
234 10 0.06
235 15 0.09
236 25 0.14
237 12 0.07
238 11 0.06
239 49 0.28
240 32 0.18
241 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (235 bp):
AAAATATTTTAAAAACTATATAATATATATATAAAAAGGTTTTAAAAACTATATATTATATAAGT
TTTCAAAAATGTTTTAAAAAACTATATAATATATATATATATATTCAAAACATTTTTAAAAACTA
TATATTATATATATTTTCAAAAACATTTTAAAAAAATTATAATATATATATATATAATATATATT
AAAAATGTTCTAAAAACTATATATTATTTATAAAGTTTTC
Found at i:636512 original size:17 final size:18
Alignment explanation
Indices: 636490--636523 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
636480 TCAGTCGGTC
636490 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
636507 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
636524 CTAACATCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:646289 original size:2 final size:2
Alignment explanation
Indices: 646282--646335 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
646272 CGTTCAAAAC
646282 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
646323 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
646336 ACTCACCATT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:647923 original size:2 final size:2
Alignment explanation
Indices: 647916--647948 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
647906 GTGGGTTTTA
647916 AT AT AT 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 AT AT AT A
647949 AAAAGGGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:655015 original size:18 final size:17
Alignment explanation
Indices: 654982--655015 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
654972 TTAATACTAA
654982 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
654999 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
655016 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:657713 original size:14 final size:12
Alignment explanation
Indices: 657676--657721 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
657666 GACTTTATCA
*
657676 TTATTAACTATG
1 TTATTAAATATG
657688 TTATTAAATATG
1 TTATTAAATATG
657700 TTATTCATAATATG
1 TTATT-A-AATATG
*
657714 TTTTTAAA
1 TTATTAAA
657722 ATATTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 18 0.60
13 2 0.07
14 10 0.33
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (12 bp):
TTATTAAATATG
Found at i:661586 original size:67 final size:68
Alignment explanation
Indices: 661509--661646 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 68
661499 TAATTATAAA
* * * * *
661509 ATATTTTATTTTAC-TCGCTCATAGTTTTATATTACTCATTTTGGACTTTATTAACATTAACTAT
1 ATATTTTATTTTACATCACTCATAATTTTACATTACTCATTTAGGACTTTATCAACATTAACTAT
*
661573 GTT
66 ATT
* * **
661576 ATATTTTATTTTACAATCACTTATAATTTTACATTACTCGTTTAGGACTTTATCATTATTAACTA
1 ATATTTTATTTTAC-ATCACTCATAATTTTACATTACTCATTTAGGACTTTATCAACATTAACTA
661641 TATT
65 TATT
661645 AT
1 AT
661647 TAAAGATGTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 14 0.24
69 45 0.76
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (68 bp):
ATATTTTATTTTACATCACTCATAATTTTACATTACTCATTTAGGACTTTATCAACATTAACTAT
ATT
Found at i:671760 original size:24 final size:23
Alignment explanation
Indices: 671733--671796 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
671723 TTATTTTGTT
*
671733 AAAATTTTATAAA-TTTATTCTTTC
1 AAAATCTTA-AAATTTTA-TCTTTC
671757 AAAATCTTAAAATTTTATCTTTC
1 AAAATCTTAAAATTTTATCTTTC
** *
671780 TTAAT-ATAAAATTTTAT
1 AAAATCTTAAAATTTTAT
671797 ATTTATCTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 11 0.31
23 12 0.34
24 12 0.34
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATCTTAAAATTTTATCTTTC
Found at i:672262 original size:87 final size:87
Alignment explanation
Indices: 672153--672315 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 87
672143 TTTATCCCTA
*
672153 ATAGGATAATTATTTGAAATGTATATAGGTGTTTTGCAAAACACA-CACCAAGCTATGTTTAATT
1 ATAGGATAATTATTTGAAATGTATATAGGTGTTTTGCAAAACACATCA-CAAGCTATATTTAATT
672217 TATTCTTCATTTGTAAGTTTGGG
65 TATTCTTCATTTGTAAGTTTGGG
* * ** *
672240 ATAGGGTAATTATTTGAAATGTATGTAGGTGTTTTGCATGACACATGACAAGCTATATTTAATTT
1 ATAGGATAATTATTTGAAATGTATATAGGTGTTTTGCAAAACACATCACAAGCTATATTTAATTT
*
672305 ATTTTTCATTT
66 ATTCTTCATTT
672316 TAATCGGTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (87 bp):
ATAGGATAATTATTTGAAATGTATATAGGTGTTTTGCAAAACACATCACAAGCTATATTTAATTT
ATTCTTCATTTGTAAGTTTGGG
Found at i:673536 original size:16 final size:16
Alignment explanation
Indices: 673515--673550 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
673505 TTAAAATATT
673515 TAAATATTTTAAAAAA
1 TAAATATTTTAAAAAA
*
673531 TAAATATTTTGAAAAA
1 TAAATATTTTAAAAAA
673547 TAAA
1 TAAA
673551 CAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAATATTTTAAAAAA
Found at i:674276 original size:24 final size:24
Alignment explanation
Indices: 674218--674282 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
674208 AAATTATCAG
* * *
674218 TATTTTTATTTTTAATATCTTTTTA
1 TATTTTAAGTTTTAA-ATATTTTTA
*
674243 -ATATTCAAGTTTTAAATATTTTTA
1 TAT-TTTAAGTTTTAAATATTTTTA
674267 TATTTTAAGTTTTAAA
1 TATTTTAAGTTTTAAA
674283 CTATGCTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 22 0.67
25 11 0.33
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (24 bp):
TATTTTAAGTTTTAAATATTTTTA
Found at i:675117 original size:29 final size:29
Alignment explanation
Indices: 675085--675148 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
675075 GATTAAAAAT
*
675085 AAAATAAATTAAGAATCAGCCTCTGACCC
1 AAAAAAAATTAAGAATCAGCCTCTGACCC
*
675114 AAAAAAAATTAAGAATCAGCCTCTGACCT
1 AAAAAAAATTAAGAATCAGCCTCTGACCC
675143 AAAAAA
1 AAAAAA
675149 TCAATAACCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.19
Consensus pattern (29 bp):
AAAAAAAATTAAGAATCAGCCTCTGACCC
Found at i:677831 original size:26 final size:26
Alignment explanation
Indices: 677801--677876 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
677791 GGATTTACTT
677801 GTCAATTAAATTATACTTTCATTTTA
1 GTCAATTAAATTATACTTTCATTTTA
677827 GTCAATTAAATTATACTTTCATTTTA
1 GTCAATTAAATTATACTTTCATTTTA
*
677853 GTCAATTAAACTATACTTTC-TTTT
1 GTCAATTAAATTATACTTTCATTTT
677877 GTAAAATCTG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 4 0.08
26 45 0.92
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (26 bp):
GTCAATTAAATTATACTTTCATTTTA
Found at i:682874 original size:24 final size:24
Alignment explanation
Indices: 682845--682894 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
682835 TGGTGGTTGA
*
682845 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
682869 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
682893 TT
1 TT
682895 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:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:683813 original size:17 final size:17
Alignment explanation
Indices: 683779--683811 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
683769 TTTTGCCAGA
683779 GCATTTTATTTTGTTTT
1 GCATTTTATTTTGTTTT
*
683796 GCATTTT-TTTTATTTT
1 GCATTTTATTTTGTTTT
683812 TGTATAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (17 bp):
GCATTTTATTTTGTTTT
Found at i:688405 original size:20 final size:20
Alignment explanation
Indices: 688363--688411 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
688353 TAACTTTTTC
*
688363 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
688383 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
688402 TTTTACCTTT
1 TTTTATCTTT
688412 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:691734 original size:24 final size:24
Alignment explanation
Indices: 691705--691754 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
691695 TGGTGGTTGA
*
691705 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
691729 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
691753 TT
1 TT
691755 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:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:692213 original size:17 final size:16
Alignment explanation
Indices: 692182--692215 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
692172 TACGTGAGGA
692182 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
692198 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
692215 T
1 T
692216 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:692314 original size:8 final size:8
Alignment explanation
Indices: 692301--692325 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
692291 TCCATTTGCT
692301 ACACCATC
1 ACACCATC
692309 ACACCATC
1 ACACCATC
692317 ACACCATC
1 ACACCATC
692325 A
1 A
692326 ATCCGCATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (8 bp):
ACACCATC
Found at i:709171 original size:20 final size:20
Alignment explanation
Indices: 709129--709174 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
709119 ACAATTTCTG
* * * *
709129 TTCGGTGCTGACTAATTCCA
1 TTCGATGCTGACAAATGCAA
709149 TTCGATGCTGACAAATGCAA
1 TTCGATGCTGACAAATGCAA
709169 TTCGAT
1 TTCGAT
709175 ATTGACTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
TTCGATGCTGACAAATGCAA
Found at i:717682 original size:88 final size:88
Alignment explanation
Indices: 717533--717711 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 88
717523 CAATGCTAAT
* * * *
717533 GAGGGATCTAATAAAGCTCATACTAGAAAGCAAGAGAATGGTGCCAACTATAGGAATGAGAGTGG
1 GAGGGACCTAATAAAGCTCATACCAGAAAGCAAGAGAAGGGTGCCAACTATAGGAAGGAGAGTGG
*
717598 AAACTGTAAGAACTTTTGAAGTG
66 AAACTGTAACAACTTTTGAAGTG
717621 GAGGGACCTAATAAAGCTCATACCAGAAAGCAAGAGAAGGGTGCCAACTATAGGAAGGAGAGTGG
1 GAGGGACCTAATAAAGCTCATACCAGAAAGCAAGAGAAGGGTGCCAACTATAGGAAGGAGAGTGG
* *
717686 CAACTGTAACAACTTTTGATGTG
66 AAACTGTAACAACTTTTGAAGTG
717709 GAG
1 GAG
717712 AATACCATTT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (88 bp):
GAGGGACCTAATAAAGCTCATACCAGAAAGCAAGAGAAGGGTGCCAACTATAGGAAGGAGAGTGG
AAACTGTAACAACTTTTGAAGTG
Found at i:718807 original size:62 final size:61
Alignment explanation
Indices: 718708--718893 Score: 300
Period size: 62 Copynumber: 3.0 Consensus size: 61
718698 CTAACCACCT
*
718708 TGGAAGCCTAGGAGAACGACAAGAAAGCCATGAATGATTTAGCTATGGCATTGAATGAAGTG
1 TGGAAGCCTAGGAGAA-GACAAGAAAGCCATGGATGATTTAGCTATGGCATTGAATGAAGTG
*
718770 TGGAAGCCTAGGAGAATGACAAGAAAGCCATGGATGATTTAGCTATGGCTTTGAATGAAGTG
1 TGGAAGCCTAGGAGAA-GACAAGAAAGCCATGGATGATTTAGCTATGGCATTGAATGAAGTG
* * *
718832 TAGAAGCCTAAGAGAAGAACAAGAAAACCATGGATGATTTAGCTATGGCATTGAATGAAGTG
1 TGGAAGCCTAGGAGAAG-ACAAGAAAGCCATGGATGATTTAGCTATGGCATTGAATGAAGTG
718894 ATTATTGAAT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
61 1 0.01
62 115 0.99
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (61 bp):
TGGAAGCCTAGGAGAAGACAAGAAAGCCATGGATGATTTAGCTATGGCATTGAATGAAGTG
Found at i:725309 original size:20 final size:21
Alignment explanation
Indices: 725284--725322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
725274 TTTTGGTTTA
*
725284 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
725304 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
725323 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:734165 original size:63 final size:62
Alignment explanation
Indices: 734061--734187 Score: 182
Period size: 63 Copynumber: 2.0 Consensus size: 62
734051 AAAAAGGGTT
* * * * * *
734061 AATTAATGGTGCGCGTCTAGAGCAAGGAATTTCATGATTCTTTTCAATTAATAAACTTTGAA
1 AATTAATGGTGCGCATATAGAGCAAGAAAGTTCATGATTCTTTTCAATTAAGAAACTCTGAA
*
734123 AATTAATGGTGCGCATATAGAAGCAAGAAAGTTCGTGATTCTTTTCAATTAAGAAACTCTGAA
1 AATTAATGGTGCGCATATAG-AGCAAGAAAGTTCATGATTCTTTTCAATTAAGAAACTCTGAA
734186 AA
1 AA
734188 GCATGCCCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 18 0.32
63 39 0.68
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (62 bp):
AATTAATGGTGCGCATATAGAGCAAGAAAGTTCATGATTCTTTTCAATTAAGAAACTCTGAA
Found at i:743580 original size:34 final size:34
Alignment explanation
Indices: 743541--743654 Score: 149
Period size: 34 Copynumber: 3.4 Consensus size: 34
743531 TTCTAAACTC
* * *
743541 AAATCTTATCCGACCCAAATATAATCTTTAAAAA
1 AAATCTGATCCGACCTAAACATAATCTTTAAAAA
*
743575 AAATCTGATTCGACCTAAACATAATCTTT-AAAA
1 AAATCTGATCCGACCTAAACATAATCTTTAAAAA
* *
743608 AAATTTGATCCGACCTAAACATAATATTTTAAAAA
1 AAATCTGATCCGACCTAAACATAAT-CTTTAAAAA
*
743643 AAGTCTGATCCG
1 AAATCTGATCCG
743655 GGTCAATGAG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
33 27 0.39
34 28 0.41
35 14 0.20
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (34 bp):
AAATCTGATCCGACCTAAACATAATCTTTAAAAA
Found at i:743794 original size:48 final size:48
Alignment explanation
Indices: 743722--743817 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
743712 GATCAAAACT
*
743722 CATAAGATACTAATCCTATACCCGTCCCTAAATGGGATGATCTTGGTG
1 CATAAGATACGAATCCTATACCCGTCCCTAAATGGGATGATCTTGGTG
*
743770 CATAAGATACGAATCCTATGCCCGTCCCTAAATGGGATGATCTTGGTG
1 CATAAGATACGAATCCTATACCCGTCCCTAAATGGGATGATCTTGGTG
743818 AGCATTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (48 bp):
CATAAGATACGAATCCTATACCCGTCCCTAAATGGGATGATCTTGGTG
Found at i:763593 original size:13 final size:14
Alignment explanation
Indices: 763568--763597 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
763558 CATGCAAGTT
763568 TTATTTCTTTATTA
1 TTATTTCTTTATTA
763582 TTATTT-TTTATTA
1 TTATTTCTTTATTA
763595 TTA
1 TTA
763598 ATCCGGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTCTTTATTA
Found at i:767872 original size:47 final size:48
Alignment explanation
Indices: 767803--767901 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 48
767793 TAAATAATAG
767803 ATTATTTAGTAATATCACTA-TTTTACCTCAACAAGTTGATGGATGAA
1 ATTATTTAGTAATATCACTATTTTTACCTCAACAAGTTGATGGATGAA
* **
767850 ATTATTTAGTAATATCCCTATTTTTTTTTTCTCAACAAGTTGATGGATGAA
1 ATTATTTAGTAATATCACTA---TTTTTACCTCAACAAGTTGATGGATGAA
767901 A
1 A
767902 GTCTTATCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
47 19 0.42
51 26 0.58
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (48 bp):
ATTATTTAGTAATATCACTATTTTTACCTCAACAAGTTGATGGATGAA
Found at i:768568 original size:27 final size:28
Alignment explanation
Indices: 768504--768559 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
768494 TGATTATTCA
768504 ACTATCTTTTTTAAAATCATACATAACT
1 ACTATCTTTTTTAAAATCATACATAACT
768532 ACTATCTTTTTTAAAATCATACATAACT
1 ACTATCTTTTTTAAAATCATACATAACT
768560 TTACGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (28 bp):
ACTATCTTTTTTAAAATCATACATAACT
Found at i:771758 original size:31 final size:31
Alignment explanation
Indices: 771694--771761 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
771684 TTAGACACTT
* * *
771694 AAAATAAATATATTATATTAAGAAAATTCTC
1 AAAATAAAAATATAATATTAAGAAAATTATC
*
771725 AAAATAAAAATATAATATTAA-ATAATTTATC
1 AAAATAAAAATATAATATTAAGA-AAATTATC
771756 AAAATA
1 AAAATA
771762 TAACCACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (31 bp):
AAAATAAAAATATAATATTAAGAAAATTATC
Found at i:773352 original size:20 final size:20
Alignment explanation
Indices: 773327--773365 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
773317 CAAAGATTTT
773327 ATAAAAATGTATGATAGTTC
1 ATAAAAATGTATGATAGTTC
773347 ATAAAAATGTATGATAGTT
1 ATAAAAATGTATGATAGTT
773366 GACATTCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (20 bp):
ATAAAAATGTATGATAGTTC
Found at i:773926 original size:2 final size:2
Alignment explanation
Indices: 773919--773952 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
773909 AAAATTTAGG
773919 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
773953 GATTGAGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:775571 original size:17 final size:17
Alignment explanation
Indices: 775539--775589 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
775529 TTTGTGTAAT
775539 TTATATTATAAATTTTAAA
1 TTATATT-T-AATTTTAAA
775558 TTATATTTAATTTTAAA
1 TTATATTTAATTTTAAA
*
775575 ATATATTTTAATTTT
1 TTATA-TTTAATTTT
775590 TTAATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 13 0.43
18 10 0.33
19 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTAATTTTAAA
Found at i:775894 original size:2 final size:2
Alignment explanation
Indices: 775887--775918 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
775877 GATGCTCACG
775887 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
775919 AGCCTTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:779283 original size:41 final size:41
Alignment explanation
Indices: 779238--779315 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
779228 GCTTATACGT
*
779238 GGGTATAGCGCG-CCCCATGATCCGCGCTATATGCCACATAG
1 GGGTATAGCGCGTCCCC-TGATCCGCGCTATACGCCACATAG
*
779279 GGGTATAGCGCGTCTCCTGATCCGCGCTATACGCCAC
1 GGGTATAGCGCGTCCCCTGATCCGCGCTATACGCCAC
779316 GTTTTATCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 31 0.91
42 3 0.09
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (41 bp):
GGGTATAGCGCGTCCCCTGATCCGCGCTATACGCCACATAG
Found at i:784161 original size:103 final size:103
Alignment explanation
Indices: 783982--784190 Score: 373
Period size: 103 Copynumber: 2.0 Consensus size: 103
783972 CTACGCGATT
* *
783982 CTTCGGGACACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTT
1 CTTCGGGACACATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
*
784047 GGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 AGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
*
784085 CTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
1 CTTCGGGACACATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
*
784150 AGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 AGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
784188 CTT
1 CTT
784191 ATGGACATTA
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
CTTCGGGACACATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
AGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
Found at i:784240 original size:23 final size:23
Alignment explanation
Indices: 784207--784274 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
784197 ATTATTATAT
784207 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
784230 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * * *
784253 GTCACTTCGATGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
784275 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:784655 original size:16 final size:16
Alignment explanation
Indices: 784604--784656 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
784594 TGTATGTGAT
784604 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
784622 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
784638 ATATGATATATGTGTG
1 ATATGATATATGTGTG
784654 ATA
1 ATA
784657 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:789403 original size:104 final size:103
Alignment explanation
Indices: 789205--789414 Score: 348
Period size: 104 Copynumber: 2.0 Consensus size: 103
789195 CTACGCGATT
* * *
789205 CTTCGGGACACATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATACTTGATCCTT
1 CTTCGGGACACATATATATTCTTTGGAACACGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
*
789270 GGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 AGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
* *
789308 CTTCGGGACATATATATATTTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATACTTGATCCC
1 CTTCGGGACACATATATA-TTCTTTGGAACACGTGTAAAGTCTGGTGAGACACATACTTGATCCC
*
789373 TAGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
65 TAGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
789412 CTT
1 CTT
789415 ATGGACATTA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
103 16 0.16
104 83 0.84
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (103 bp):
CTTCGGGACACATATATATTCTTTGGAACACGTGTAAAGTCTGGTGAGACACATACTTGATCCCT
AGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
Found at i:789464 original size:23 final size:23
Alignment explanation
Indices: 789431--789498 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
789421 ATTATTATAT
789431 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
789454 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * * *
789477 GTCACTTCGATGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
789499 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:789880 original size:16 final size:16
Alignment explanation
Indices: 789829--789881 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
789819 TGTATGTGAT
789829 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
789847 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
789863 ATATGATATATGTGTG
1 ATATGATATATGTGTG
789879 ATA
1 ATA
789882 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:790421 original size:17 final size:17
Alignment explanation
Indices: 790371--790433 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 17
790361 GGGTGTTACA
*
790371 AAAC-ATCCATAAATTC
1 AAACAATCCACAAATTC
* *
790387 AAACAAAT--TCAAAGTC
1 AAAC-AATCCACAAATTC
790403 AAACAATCCACAAATTC
1 AAACAATCCACAAATTC
*
790420 AAACATTCCA-AAAT
1 AAACAATCCACAAAT
790434 ATCCAAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 3 0.08
16 17 0.46
17 15 0.41
18 2 0.05
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.21
Consensus pattern (17 bp):
AAACAATCCACAAATTC
Found at i:792392 original size:21 final size:22
Alignment explanation
Indices: 792316--792391 Score: 100
Period size: 23 Copynumber: 3.5 Consensus size: 22
792306 CCCAGTGGGT
*
792316 ATCGATTCCCCTAC-AGGGGGA
1 ATCGATTCCCCTTCAAGGGGGA
*
792337 ATCGGTTCCCCTTCAAAGGGGGA
1 ATCGATTCCCCTTC-AAGGGGGA
* *
792360 ATCGGTTCCCCTTCAAGGGGGT
1 ATCGATTCCCCTTCAAGGGGGA
792382 ATCGATTCCC
1 ATCGATTCCC
792392 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 12 0.24
22 16 0.33
23 21 0.43
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.24
Consensus pattern (22 bp):
ATCGATTCCCCTTCAAGGGGGA
Found at i:800508 original size:10 final size:10
Alignment explanation
Indices: 800493--800517 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
800483 CTTAAATAGA
800493 GAGAGTATTT
1 GAGAGTATTT
800503 GAGAGTATTT
1 GAGAGTATTT
800513 GAGAG
1 GAGAG
800518 AATATGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (10 bp):
GAGAGTATTT
Found at i:813902 original size:36 final size:35
Alignment explanation
Indices: 813822--813959 Score: 190
Period size: 35 Copynumber: 3.9 Consensus size: 35
813812 AGATGAACAA
*
813822 TTGAATCGAAAGTG-CTTATGCTTCC-TCCGTTCAC
1 TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTCAC
* *
813856 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
* *
813892 TTGAATCGAAAGTGCCGATGTTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
*
813927 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC
813960 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
34 22 0.24
35 38 0.42
36 31 0.34
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Found at i:813937 original size:71 final size:70
Alignment explanation
Indices: 813822--813964 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 70
813812 AGATGAACAA
**
813822 TTGAATCGAAAGTGCTTATGCTTCCTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCGT
1 TTGAATCGAAAGTGCCGATGCTTCCTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCGT
813887 TCTTC
66 TCTTC
*
813892 TTGAATCGAAAGTGCCGATGTTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCC-TCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
813957 TTCTTC
65 TTCTTC
813963 TT
1 TT
813965 ATTCACCATC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 22 0.32
71 47 0.68
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (70 bp):
TTGAATCGAAAGTGCCGATGCTTCCTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCGT
TCTTC
Found at i:813984 original size:24 final size:23
Alignment explanation
Indices: 813952--814009 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
813942 CGATGCTTCC
*
813952 TTTCGTTCTTCTTATTCACCATCT
1 TTTCTTTCTTCTT-TTCACCATCT
*
813976 TTTCTTTCTTC--TTCACCTTCT
1 TTTCTTTCTTCTTTTCACCATCT
*
813997 TTTATTTCTTCTT
1 TTTCTTTCTTCTT
814010 CATCCTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 19 0.66
24 10 0.34
ACGTcount: A:0.09, C:0.28, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTCTTTCTTCTTTTCACCATCT
Found at i:813990 original size:21 final size:20
Alignment explanation
Indices: 813960--814021 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
813950 CCTTTCGTTC
* *
813960 TTCTTATTCACCATCTTTTCT
1 TTCTTCTTCACC-TCTTTTAT
813981 TTCTTCTTCACCTTCTTTTAT
1 TTCTTCTTCACC-TCTTTTAT
814002 TTCTTCTTCATCCTCTTTTA
1 TTCTTCTTCA-CCTCTTTTA
814022 CAAGGTTCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (20 bp):
TTCTTCTTCACCTCTTTTAT
Found at i:820952 original size:18 final size:18
Alignment explanation
Indices: 820931--820972 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
820921 CCGTCGTCCA
820931 ATTTG-GAAGGTTTATACT
1 ATTTGTGAAGG-TTATACT
* *
820949 ATTTGTTAAGGTTATATT
1 ATTTGTGAAGGTTATACT
820967 ATTTGT
1 ATTTGT
820973 AATCTTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.52
Consensus pattern (18 bp):
ATTTGTGAAGGTTATACT
Found at i:820961 original size:19 final size:18
Alignment explanation
Indices: 820937--820972 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
820927 TCCAATTTGG
820937 AAGGTTTATACTATTTGTT
1 AAGG-TTATACTATTTGTT
*
820956 AAGGTTATATTATTTGT
1 AAGGTTATACTATTTGT
820973 AATCTTACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (18 bp):
AAGGTTATACTATTTGTT
Found at i:821042 original size:5 final size:5
Alignment explanation
Indices: 821032--821074 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
821022 AAATTCTATG
*
821032 ATTTT ATTTT ATTTT ATTTT ATTAGT A-TTT ATTTT AATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT -ATTTT AT
821075 AAAGAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.06
5 24 0.73
6 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:821576 original size:40 final size:40
Alignment explanation
Indices: 821530--821611 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
821520 ATTTTGATAA
821530 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
1 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
821570 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
1 ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
821610 AT
1 AT
821612 AATACGAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (40 bp):
ATTAAAATGACATTTTGAAGATAAGAATAAAATAAACTAC
Found at i:828575 original size:12 final size:12
Alignment explanation
Indices: 828558--828587 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
828548 ATGAATGAAA
828558 GGATCAGTAGAG
1 GGATCAGTAGAG
828570 GGATCAGTAGAG
1 GGATCAGTAGAG
*
828582 GTATCA
1 GGATCA
828588 AGCGTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (12 bp):
GGATCAGTAGAG
Found at i:829588 original size:27 final size:26
Alignment explanation
Indices: 829535--829589 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
829525 CGCGATGTAA
* **
829535 ATTGTGATTGCAATTGTATTATATTT
1 ATTGTGATTACAAACGTATTATATTT
*
829561 ATTGTGATTACAAACGTCATTATCTTT
1 ATTGTGATTACAAACGT-ATTATATTT
829588 AT
1 AT
829590 ATAACGTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (26 bp):
ATTGTGATTACAAACGTATTATATTT
Found at i:833068 original size:18 final size:18
Alignment explanation
Indices: 833044--833090 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
833034 GTCACAACCC
833044 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* * *
833062 TACCCGACCCAACCTGTT
1 GACCCGACCCGACCCGTT
*
833080 GACCCAACCCG
1 GACCCGACCCG
833091 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.49, G:0.17, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:833083 original size:13 final size:13
Alignment explanation
Indices: 833067--833109 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
833057 CCGTTTACCC
*
833067 GACCCAACCTGTT
1 GACCCAACCCGTT
833080 GACCCAACCCGTT
1 GACCCAACCCGTT
*
833093 GACCCGACCCGTT
1 GACCCAACCCGTT
833106 GACC
1 GACC
833110 GTTGACACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:835600 original size:24 final size:23
Alignment explanation
Indices: 835573--835659 Score: 111
Period size: 24 Copynumber: 3.7 Consensus size: 23
835563 ATTTCCGAAT
835573 TGAATTCTGTTCTGATACGTTATC
1 TGAATTCTGTTCTGATAC-TTATC
* *
835597 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTTATC
* *
835620 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATA-CTTATC
*
835644 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
835660 TTCTGATATC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTTATC
Found at i:835610 original size:12 final size:12
Alignment explanation
Indices: 835573--835664 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
835563 ATTTCCGAAT
835573 TGAATTCTGTTC
1 TGAATTCTGTTC
*
835585 TG-ATAC-GTTATC
1 TGAATTCTG-T-TC
835597 TGAATTCTGTTC
1 TGAATTCTGTTC
*
835609 TG-ATTCTGATC
1 TGAATTCTGTTC
*
835620 TGGATTCTGTTC
1 TGAATTCTGTTC
*
835632 TG-ATATCT-TATA
1 TGAAT-TCTGT-TC
*
835644 TGAATTCTGTTT
1 TGAATTCTGTTC
*
835656 TGATTTCTG
1 TGAATTCTG
835665 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
10 1 0.02
11 17 0.27
12 38 0.59
13 7 0.11
14 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.50
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:835627 original size:47 final size:48
Alignment explanation
Indices: 835576--835666 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 48
835566 TCCGAATTGA
*
835576 ATTCTGTTCTGATA-CGTTATCTGAATTCTGTTCTGA-TTCTGATCTGG
1 ATTCTGTTCTGATATC-TTATATGAATTCTGTTCTGATTTCTGATCTGG
*
835623 ATTCTGTTCTGATATCTTATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTTATATGAATTCTGTTCTGATTTCTGAT
835667 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 32 0.80
48 8 0.20
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTTATATGAATTCTGTTCTGATTTCTGATCTGG
Found at i:838595 original size:31 final size:31
Alignment explanation
Indices: 838562--838876 Score: 551
Period size: 31 Copynumber: 10.2 Consensus size: 31
838552 GGTCACAATA
*
838562 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
838593 TAAACTGTTCATATATGTCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
838624 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
838655 TAAACTGTTCATATGTGTCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
838686 TAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
838717 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
838748 TAAACTGTTCATATGCT-CCTTTAAACATATG
1 TAAACTGTTCATATG-TGCCTTTAAACATATG
838779 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
838810 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
838841 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
838872 TAAAC
1 TAAAC
838877 CCTCGACTCT
Statistics
Matches: 271, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
30 1 0.00
31 269 0.99
32 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:838809 original size:16 final size:16
Alignment explanation
Indices: 838788--838872 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
838778 GTAAACTGTT
838788 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
*** *
838804 CATATGTAAATTGT--T
1 CATATGTGCCTT-TAAA
838819 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
838835 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
838850 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
838866 CATATGT
1 CATATGT
838873 AAACCCTCGA
Statistics
Matches: 49, Mismatches: 12, Indels: 16
0.64 0.16 0.21
Matches are distributed among these distances:
13 2 0.04
14 3 0.06
15 16 0.33
16 23 0.47
17 3 0.06
18 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:839494 original size:64 final size:64
Alignment explanation
Indices: 839386--839562 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 64
839376 TAATGAAGGT
* * ** **** **
839386 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-AATATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGT-GTCAATATTAATGGG
* * *
839450 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTACATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTACATTCGATGTGTCAATATTAATGGG
*
839514 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGT
839563 CTTTATTTTA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.03
64 92 0.97
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTGTCAATATTAATGGG
Found at i:839583 original size:64 final size:63
Alignment explanation
Indices: 839449--839610 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 63
839439 ATATTGCTGG
* * *
839449 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTACATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTACATTCGATGTTTCACTATTAAAGA
* * *
839513 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTACATTCGATGT-TTCACTATTAAAGA
** *
839576 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
839611 ATTCAAACAA
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.05
64 79 0.92
65 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTACATTCGATGTTTCACTATTAAAGA
Found at i:842396 original size:23 final size:23
Alignment explanation
Indices: 842354--842426 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
842344 CACCACAGCT
*
842354 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
*
842375 CATATAGAATTGTACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
*** *
842398 CGCGTAGAGTTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
842421 CATATA
1 CATATA
842427 ATAATGTCCA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 32 0.80
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Done.