Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001470.1 Hibiscus syriacus cultivar Beakdansim tig00002847_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: 1178067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:13814 original size:2 final size:2
Alignment explanation
Indices: 13807--13852 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13797 TTTTACATTG
13807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13849 AT AT
1 AT AT
13853 TATGAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16270 original size:20 final size:21
Alignment explanation
Indices: 16231--16280 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
16221 TTCTCTAAAA
16231 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
16252 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
*
16272 GAT-ATATTA
1 TATAATATTA
16281 AATAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:16311 original size:2 final size:2
Alignment explanation
Indices: 16304--16338 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16294 TGTGAAAATA
16304 AT 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 AT A
16339 AAAGTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18068 original size:20 final size:20
Alignment explanation
Indices: 17967--18330 Score: 429
Period size: 20 Copynumber: 18.4 Consensus size: 20
17957 GATTTTCCAT
* ** *
17967 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
17987 AATCGCAACGCG-A-ACATA
1 AATCGCAACGCGTATCCGTA
18005 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
*
18024 AATCGCAACGTGTATCCGT-
1 AATCGCAACGCGTATCCGTA
**
18043 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
18063 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
18083 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
18103 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
18123 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
18143 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
18163 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
18183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
18203 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
18223 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
18243 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
18263 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
18283 AATCGCAACG-ATAATCCGT-
1 AATCGCAACGCGT-ATCCGTA
* * *
18302 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
18322 AATCACAAC
1 AATCGCAAC
18331 ACTGAAATTT
Statistics
Matches: 300, Mismatches: 34, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
18 14 0.05
19 53 0.18
20 232 0.77
21 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:19050 original size:24 final size:24
Alignment explanation
Indices: 19011--19057 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19001 AAATTTGGTC
19011 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
19035 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
19058 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:21555 original size:19 final size:19
Alignment explanation
Indices: 21533--21852 Score: 351
Period size: 19 Copynumber: 18.4 Consensus size: 19
21523 CGGAAAATAC
*
21533 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21552 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
21566 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
21586 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21619 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21638 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
21652 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21671 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21690 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
21709 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
21723 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
21742 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
21760 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
21774 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21793 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
21807 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21826 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
21845 AATCGCAA
1 AATCGCAA
21853 CGAGATAATC
Statistics
Matches: 258, Mismatches: 12, Indels: 62
0.78 0.04 0.19
Matches are distributed among these distances:
14 56 0.22
15 3 0.01
16 26 0.10
17 15 0.06
18 12 0.05
19 133 0.52
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:21620 original size:33 final size:33
Alignment explanation
Indices: 21533--21833 Score: 225
Period size: 33 Copynumber: 8.8 Consensus size: 33
21523 CGGAAAATAC
* *
21533 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
21566 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
*
21600 AATCGCAATGCGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
21638 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
21671 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
21709 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
21742 AATCGCAATGCGAAATG-AAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
21773 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
21806 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
21834 TGCGAAATGA
Statistics
Matches: 239, Mismatches: 11, Indels: 36
0.84 0.04 0.13
Matches are distributed among these distances:
31 2 0.01
32 17 0.07
33 122 0.51
34 30 0.13
35 12 0.05
36 7 0.03
37 10 0.04
38 39 0.16
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:21863 original size:33 final size:34
Alignment explanation
Indices: 21616--21874 Score: 229
Period size: 33 Copynumber: 7.6 Consensus size: 34
21606 AATGCGAAAT
*
21616 GAAAATCACAATGCGAAATGAAAATCGCAA-CGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
21649 GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
21686 TGAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
* * *
21720 CAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-GCGA
*
21755 AATGAAATCGCAA--CGAAA-G--AATCGCAATGCGAAA
1 GA--AAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
21789 TGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
21822 TGAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
21856 GATAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
21875 TATAAACGCA
Statistics
Matches: 198, Mismatches: 11, Indels: 34
0.81 0.05 0.14
Matches are distributed among these distances:
32 12 0.06
33 115 0.58
34 3 0.02
35 17 0.09
36 5 0.03
37 9 0.05
38 37 0.19
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
Found at i:21890 original size:52 final size:52
Alignment explanation
Indices: 21561--21874 Score: 410
Period size: 52 Copynumber: 6.0 Consensus size: 52
21551 AAATCCCAAC
21561 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
21614 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
21666 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
21716 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AATCGCAATGCGAA
*
21772 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
21821 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
21873 AT
1 AT
21875 TATAAACGCA
Statistics
Matches: 231, Mismatches: 16, Indels: 29
0.84 0.06 0.11
Matches are distributed among these distances:
47 8 0.03
48 1 0.00
49 10 0.04
50 8 0.03
51 33 0.14
52 143 0.62
53 15 0.06
54 2 0.01
55 1 0.00
56 4 0.02
57 5 0.02
58 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:21925 original size:19 final size:19
Alignment explanation
Indices: 21881--21982 Score: 133
Period size: 19 Copynumber: 5.6 Consensus size: 19
21871 AAATTATAAA
21881 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
21900 CCGCATTACGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
21920 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
21936 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
21953 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
21972 CGAATTGCGAT
1 CGCATTGCGAT
21983 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 34 0.47
20 18 0.25
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:21988 original size:19 final size:19
Alignment explanation
Indices: 21947--21990 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21937 GTTGCGATTT
* **
21947 TCATTTCGCATTGCGATTT
1 TCATTTCGAATTGCGATAG
21966 TCATTTCGAATTGCGATAG
1 TCATTTCGAATTGCGATAG
21985 TCATTT
1 TCATTT
21991 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGAATTGCGATAG
Found at i:22108 original size:14 final size:14
Alignment explanation
Indices: 22089--22125 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
22079 CATCAATTAC
22089 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
22103 ACAAATCATCTTTT
1 ACAAATCAACTTTT
22117 ACAAATCAA
1 ACAAATCAA
22126 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:24080 original size:19 final size:19
Alignment explanation
Indices: 24040--24168 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
24030 ATAGTTACTT
* *
24040 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
24060 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
24079 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
24098 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24112 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24131 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
24145 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24164 TCGCA
1 TCGCA
24169 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24119 original size:33 final size:32
Alignment explanation
Indices: 24076--24168 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
24066 CGCGAAACCA
**
24076 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
24108 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
24141 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
24169 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:24166 original size:52 final size:52
Alignment explanation
Indices: 24040--24168 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
24030 ATAGTTACTT
**
24040 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
24092 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
24145 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
24169 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:24186 original size:19 final size:18
Alignment explanation
Indices: 24164--24280 Score: 106
Period size: 18 Copynumber: 6.8 Consensus size: 18
24154 GAAACCAAAA
*
24164 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
24183 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
24199 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
24216 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
*
24232 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCTT
**
24248 TCGCGTTGCGATTTTGGT
1 TCGCGTTGCGATTTTCTT
24266 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
24281 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 8 0.10
18 28 0.35
19 18 0.22
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:24205 original size:14 final size:14
Alignment explanation
Indices: 24186--24242 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
24176 TTTCATTTCG
24186 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
24200 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
24217 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
24233 CGTTGCGATT
1 CGTTGCGATT
24243 TTCATTCGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:24211 original size:33 final size:33
Alignment explanation
Indices: 24169--24296 Score: 150
Period size: 33 Copynumber: 3.8 Consensus size: 33
24159 CAAAATCGCA
24169 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
** *
24202 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
24235 TTGCGATTTTCA-TTCGCGTTGCGATTTTGGTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT--TT--CG
* *
24271 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
24297 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
32 15 0.19
33 40 0.50
34 1 0.01
36 13 0.16
38 11 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:24769 original size:93 final size:93
Alignment explanation
Indices: 24328--24790 Score: 882
Period size: 92 Copynumber: 5.0 Consensus size: 93
24318 GCAAATTGAA
24328 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
24393 GCAGAATTGGCAGCAACCGAAC-AATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
24420 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
24485 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
24513 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
24577 GCAGAATTGGCAGCAACCGAAC-AATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
24604 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
24667 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
24695 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
24760 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
24788 ACT
1 ACT
24791 AAGCAATCTA
Statistics
Matches: 365, Mismatches: 1, Indels: 9
0.97 0.00 0.02
Matches are distributed among these distances:
89 15 0.04
90 36 0.10
91 76 0.21
92 123 0.34
93 115 0.32
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:26507 original size:14 final size:14
Alignment explanation
Indices: 26488--26577 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
26478 TTGAAATGAA
26488 AATCGCAACGAGAG
1 AATCGCAACGAGAG
26502 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
26519 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
26535 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
26554 AATCGCAACGAGAG
1 AATCGCAACGAGAG
26568 AATCGCAACG
1 AATCGCAACG
26578 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:26525 original size:33 final size:33
Alignment explanation
Indices: 26480--26594 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
26470 TCTTTTGGTT
26480 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
26513 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
26546 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
26579 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
26595 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:26526 original size:19 final size:18
Alignment explanation
Indices: 26487--26599 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
26477 GTTGAAATGA
26487 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
26502 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
26519 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
26535 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
26552 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
26568 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
26585 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
26600 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:26630 original size:14 final size:14
Alignment explanation
Indices: 26611--26665 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
26601 TTTGGTTTCG
26611 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26625 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
26644 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26658 CGTTGCGA
1 CGTTGCGA
26666 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:26643 original size:33 final size:33
Alignment explanation
Indices: 26595--26665 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
26585 AAAATCGCAA
**
26595 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
26628 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
26661 TGCGA
1 TGCGA
26666 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:26673 original size:33 final size:33
Alignment explanation
Indices: 26606--26687 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
26596 GCGATTTTGG
***
26606 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
26639 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
26672 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
26688 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:26692 original size:20 final size:20
Alignment explanation
Indices: 26651--26711 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
26641 TCGCGTTGCG
**
26651 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACTTTC
*
26671 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACTTTC
*
26691 ATTTATCTCGTTGCGACTTTC
1 A-TTCTCTCGTTGCGACTTTC
26712 TGCAAATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACTTTC
Found at i:26827 original size:33 final size:33
Alignment explanation
Indices: 26785--26855 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
26775 AATACTAACT
*
26785 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
26818 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
26851 TGAAA
1 TGAAA
26856 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:27087 original size:22 final size:22
Alignment explanation
Indices: 27035--27089 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
27025 TGGTTGTGAG
**
27035 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
27057 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
27079 GGATTTCTTCG
1 GGATTTCTTCG
27090 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:27259 original size:20 final size:20
Alignment explanation
Indices: 27234--27426 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
27224 CTTTAAATAT
27234 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27254 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
27276 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
27295 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
27315 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
27335 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
27355 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
27375 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
27395 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
27415 CGCGTTGCGATT
1 CGCGTTGCGATT
27427 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:27421 original size:60 final size:60
Alignment explanation
Indices: 27234--27426 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
27224 CTTTAAATAT
**
27234 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
27295 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
27355 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
27415 CGCGTTGCGATT
1 CGCGTTGCGATT
27427 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:27507 original size:20 final size:20
Alignment explanation
Indices: 27482--27533 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
27472 AAGAATCGCG
*
27482 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
27502 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
27522 TTGCGATTCTGG
1 TTGCGATTCTGG
27534 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:34193 original size:22 final size:23
Alignment explanation
Indices: 34165--34211 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
34155 TTTTTATTTT
*
34165 TTCTAAAATATATATAT-AAATA
1 TTCTAAAATATAAATATAAAATA
* *
34187 TTCTAAATTTTAAATATAAAATA
1 TTCTAAAATATAAATATAAAATA
34210 TT
1 TT
34212 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TTCTAAAATATAAATATAAAATA
Found at i:36382 original size:12 final size:12
Alignment explanation
Indices: 36365--36415 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
36355 TTTAAAGAGG
36365 TTTTATATTTAA
1 TTTTATATTTAA
36377 TTTTATA-TTATA
1 TTTTATATTTA-A
*
36389 TTTGAT-TTTAA
1 TTTTATATTTAA
36400 TTTTA-ATATTAA
1 TTTTATAT-TTAA
36412 TTTT
1 TTTT
36416 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:36465 original size:14 final size:13
Alignment explanation
Indices: 36396--36466 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 13
36386 ATATTTGATT
36396 TTAATTT-TAATA
1 TTAATTTATAATA
*
36408 TTAATTTTTAA-A
1 TTAATTTATAATA
*
36420 -TAAATTA-AATA
1 TTAATTTATAATA
*
36431 -TAATTTTTAATA
1 TTAATTTATAATA
36443 TT-ATATTATAGATA
1 TTAAT-TTATA-ATA
36457 TTAATTTATA
1 TTAATTTATA
36467 TCATATAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 2 0.04
11 11 0.23
12 14 0.30
13 8 0.17
14 10 0.21
15 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
TTAATTTATAATA
Found at i:36467 original size:19 final size:19
Alignment explanation
Indices: 36437--36486 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
36427 AATATAATTT
* *
36437 TTAATATTATATTATAGATA
1 TTAAT-TTATATCATAGAAA
*
36457 TTAATTTATATCATATAAA
1 TTAATTTATATCATAGAAA
*
36476 TTATTTTATAT
1 TTAATTTATAT
36487 AATATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATTTATATCATAGAAA
Found at i:36491 original size:19 final size:20
Alignment explanation
Indices: 36456--36504 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
36446 TATTATAGAT
* *
36456 ATTAATTTATATCATA-TAA
1 ATTATTTTATATAATATTAA
36475 ATTATTTTATATAATATTAA
1 ATTATTTTATATAATATTAA
36495 A--ATTTTATAT
1 ATTATTTTATAT
36505 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 14 0.52
20 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTTTATATAATATTAA
Found at i:36665 original size:7 final size:7
Alignment explanation
Indices: 36653--36678 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36643 ATTAAGATTT
36653 TAAAATA
1 TAAAATA
36660 TAAAATA
1 TAAAATA
36667 TAAAATA
1 TAAAATA
36674 TAAAA
1 TAAAA
36679 AATTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:37029 original size:31 final size:31
Alignment explanation
Indices: 36992--37051 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
36982 TAGCTGTATT
* *
36992 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
37023 AATTATTTAAGTCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
37052 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:38965 original size:18 final size:18
Alignment explanation
Indices: 38934--38972 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
38924 GTCCCAAAGG
* *
38934 ACTATTTCCTGAAGGACC
1 ACTATATCCCGAAGGACC
38952 ACTATATCCCGAAGGACC
1 ACTATATCCCGAAGGACC
38970 ACT
1 ACT
38973 CCTTAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (18 bp):
ACTATATCCCGAAGGACC
Found at i:43556 original size:32 final size:32
Alignment explanation
Indices: 43520--43601 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
43510 AATTGTTACA
*
43520 CATTATCTAAATGTGACACTAACGCTCATATG
1 CATTATCTAAATGTAACACTAACGCTCATATG
* * * * *
43552 CATTATCTGAATGTAACATTGACTCTGATATG
1 CATTATCTAAATGTAACACTAACGCTCATATG
* *
43584 CATTATCTGAATATAACA
1 CATTATCTAAATGTAACA
43602 TTGACTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CATTATCTAAATGTAACACTAACGCTCATATG
Found at i:43587 original size:16 final size:18
Alignment explanation
Indices: 43557--43609 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 18
43547 ATATGCATTA
*
43557 TCTGAATGTAACATTGAC
1 TCTGAATATAACATTGAC
*
43575 TCTG-ATAT-GCATT-A-
1 TCTGAATATAACATTGAC
43589 TCTGAATATAACATTGAC
1 TCTGAATATAACATTGAC
43607 TCT
1 TCT
43610 AATGTGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 8 0.29
17 4 0.14
18 7 0.25
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (18 bp):
TCTGAATATAACATTGAC
Found at i:43602 original size:32 final size:32
Alignment explanation
Indices: 43547--43627 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
43537 ACTAACGCTC
* *
43547 ATATGCATTATCTGAATGTAACATTGACTCTG
1 ATATGCATTATCTGAATATAACATTGACTCTA
43579 ATATGCATTATCTGAATATAACATTGACTCTA
1 ATATGCATTATCTGAATATAACATTGACTCTA
* * *
43611 ATGTGTATTATTTGAAT
1 ATATGCATTATCTGAAT
43628 GAAACACTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (32 bp):
ATATGCATTATCTGAATATAACATTGACTCTA
Found at i:45398 original size:20 final size:21
Alignment explanation
Indices: 45373--45412 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45363 TTTACACCAA
45373 TTCAT-CCAGTATCGATACTG
1 TTCATCCCAGTATCGATACTG
45393 TTCATCCCAGTATCGATACT
1 TTCATCCCAGTATCGATACT
45413 CGAACCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (21 bp):
TTCATCCCAGTATCGATACTG
Found at i:49333 original size:15 final size:15
Alignment explanation
Indices: 49313--49369 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
49303 AACCGGGTAT
49313 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
49328 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
49345 CGAGTACCCGATTAC
1 CGGGTACCCGATTAC
49360 CGGGTACCCG
1 CGGGTACCCG
49370 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:49357 original size:32 final size:32
Alignment explanation
Indices: 49316--49378 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
49306 CGGGTATCGG
49316 GTACCCGATTACCGGGTACCCGCAAAATCCGA
1 GTACCCGATTACCGGGTACCCGCAAAATCCGA
* *
49348 GTACCCGATTACCGGGTACCCGTAACATCCG
1 GTACCCGATTACCGGGTACCCGCAAAATCCG
49379 GGTCGGGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.17
Consensus pattern (32 bp):
GTACCCGATTACCGGGTACCCGCAAAATCCGA
Found at i:49381 original size:17 final size:16
Alignment explanation
Indices: 49313--49381 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
49303 AACCGGGTAT
**
49313 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
49328 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* **
49345 CGAGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
49360 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
49377 CGGGT
1 CGGGT
49382 CGGGACACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:49455 original size:16 final size:16
Alignment explanation
Indices: 49417--49459 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
49407 ACCCGGAAGT
* *
49417 TCCGGGTACCAGGAAA
1 TCCGGGTACCCGAAAA
49433 T-CGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
49448 TCCGGGTACCCG
1 TCCGGGTACCCG
49460 GATTTGCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:53323 original size:114 final size:113
Alignment explanation
Indices: 53105--53471 Score: 603
Period size: 114 Copynumber: 3.3 Consensus size: 113
53095 TTGTCGGTTT
* *
53105 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* *
53170 CGGCCTATAAATGACTAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
53218 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAATGAAAAAA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAAATGACAAAA
*
53283 CTGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
53332 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* * *
53396 CGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
53444 GTGTCGATACTTTATTATAA-GTATCGAT
1 GTGTCGATACTTTATAAAAATGTATCGAT
53472 ACTTTTGGAA
Statistics
Matches: 238, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
111 7 0.03
112 77 0.32
113 46 0.19
114 108 0.45
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (113 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:53636 original size:182 final size:182
Alignment explanation
Indices: 53329--53761 Score: 749
Period size: 182 Copynumber: 2.4 Consensus size: 182
53319 GGATATATTG
* *
53329 AAAGTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * * * * *
53394 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGATCTAGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
* *
53459 TATAAGTATCGATACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
53511 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
53576 ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
66 ACCGATCTAGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
53641 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
*
53693 AAAGTTTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
53758 ACCG
66 ACCG
53762 GTAAAGAGCT
Statistics
Matches: 238, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 238 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGATCTAGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
Found at i:53772 original size:162 final size:162
Alignment explanation
Indices: 53588--53925 Score: 595
Period size: 162 Copynumber: 2.1 Consensus size: 162
53578 CGATCTCGAA
*
53588 ATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAATGTCGATACTTTATTATAAGTATCGA
* *
53653 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTTTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
53718 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
* * *
53750 ATGACAAAACCGGTAAAGAGCTATCGGATATGTTGAAAATGTTGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAATGTCGATACTTTATTATAAGTATCGA
53815 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
*
53880 TATCGATCCATAACAATATAACAGGTAGAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
* *
53912 ATGAAAAAATCGGT
1 ATGACAAAACCGGT
53926 CTCGAAATGA
Statistics
Matches: 167, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 167 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (162 bp):
ATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAATGTCGATACTTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:54058 original size:25 final size:25
Alignment explanation
Indices: 53988--54052 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
53978 ACTTTATTAT
53988 AAGTATCGACACTTTTGGAATAATA
1 AAGTATCGACACTTTTGGAATAATA
54013 AAGTATCGACACTTTTGGAATAATA
1 AAGTATCGACACTTTTGGAATAATA
*
54038 AAGTATCGATACTTT
1 AAGTATCGACACTTT
54053 CAGAATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (25 bp):
AAGTATCGACACTTTTGGAATAATA
Found at i:54847 original size:23 final size:23
Alignment explanation
Indices: 54818--54865 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
54808 AAATAGGTTA
*
54818 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
54841 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
54864 AT
1 AT
54866 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:55075 original size:14 final size:14
Alignment explanation
Indices: 55056--55082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55046 TTGATTTAAG
55056 AATCAGTTATAGTA
1 AATCAGTTATAGTA
55070 AATCAGTTATAGT
1 AATCAGTTATAGT
55083 CTGTACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
AATCAGTTATAGTA
Found at i:57132 original size:2 final size:2
Alignment explanation
Indices: 57125--57150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57115 ATATTCTTTA
57125 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
57151 TCAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57633 original size:21 final size:21
Alignment explanation
Indices: 57604--57656 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
57594 ATTCTGACTA
*
57604 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTATCCAAAT
* *
57625 TCGCGTTGCGATTATCCTAAT
1 TCGCATTGCGATTATCCAAAT
*
57646 TCGCAATGCGA
1 TCGCATTGCGA
57657 ATACGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTATCCAAAT
Found at i:57667 original size:20 final size:20
Alignment explanation
Indices: 57646--57734 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
57636 TTATCCTAAT
*
57646 TCGCAATGCGAATACGTAAT
1 TCGCAATGCGAATACGTAAA
57666 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
57686 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
57706 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
57726 TCGTAATGC
1 TCGCAATGC
57735 AATTTACGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:57747 original size:20 final size:20
Alignment explanation
Indices: 57646--57749 Score: 108
Period size: 20 Copynumber: 5.2 Consensus size: 20
57636 TTATCCTAAT
*
57646 TCGCAATGCGAA-TACGTAAT
1 TCGCAATGC-AATTACGTAAA
57666 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGC-AATTACGTAAA
*
57686 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGC-AATTACGTAAA
*
57706 TCGCAATGCGATTACGTAAA
1 TCGCAATGCAATTACGTAAA
*
57726 TCGTAATGCAATTTACGT-AA
1 TCGCAATGCAA-TTACGTAAA
57746 TCGC
1 TCGC
57750 GTTGCGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 1 0.01
20 68 0.91
21 6 0.08
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGCAATTACGTAAA
Found at i:57748 original size:40 final size:39
Alignment explanation
Indices: 57631--57773 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 39
57621 AAATTCGCGT
* * *
57631 TGCGATTATCCTAATTCGCAATGCGAATACGTAATTCGCAA
1 TGCGATTA-CGTAAATCGCAACGCGAATACGTAA-TCGCAA
*
57672 TGCGAATACGTAAATCGCAACGCGAATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAACGCGAATACGT-AATCGCAA
* * **
57712 TGCGATTACGTAAATCGTAATGC-AATTTACGTAATCGCGT
1 TGCGATTACGTAAATCGCAACGCGAA--TACGTAATCGCAA
*
57752 TGCGATTTA-GAAAATCGCAACG
1 TGCGA-TTACGTAAATCGCAACG
57774 AGATTCTGAC
Statistics
Matches: 86, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
39 2 0.02
40 67 0.78
41 17 0.20
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (39 bp):
TGCGATTACGTAAATCGCAACGCGAATACGTAATCGCAA
Found at i:58660 original size:24 final size:24
Alignment explanation
Indices: 58627--58686 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
58617 TAGTCAGTAT
*
58627 TCGAAATTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
58651 TCGGACTTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
58675 TCGAATTTTGAT
1 TCGAACTTTGAT
58687 GATTTTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAACTTTGATCTTGGTCAATAC
Found at i:61239 original size:14 final size:14
Alignment explanation
Indices: 61220--61306 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
61210 GGAAATTACT
61220 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
61234 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
61253 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
61267 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
61286 ATCGCAACGAGGGA
1 ATCGCAACGAGAGA
61300 ATCGCAA
1 ATCGCAA
61307 AGCGAAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 26 0.45
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.34
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:61257 original size:19 final size:18
Alignment explanation
Indices: 61233--61331 Score: 79
Period size: 19 Copynumber: 5.7 Consensus size: 18
61223 GCAACGAGAG
61233 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
*
61252 AATCGCAA-CG--A-GAG
1 AATCGCAAGCGAAATGAA
61266 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
**
61285 AATCGCAA-CG--A-GGG
1 AATCGCAAGCGAAATGAA
61299 AATCGCAAAGCGAAATGAA
1 AATCGC-AAGCGAAATGAA
61318 AATCGCAACGCGAA
1 AATCGCAA-GCGAA
61332 TTTAGTTTCG
Statistics
Matches: 63, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
14 17 0.27
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 30 0.48
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
AATCGCAAGCGAAATGAA
Found at i:61257 original size:33 final size:33
Alignment explanation
Indices: 61220--61327 Score: 198
Period size: 33 Copynumber: 3.3 Consensus size: 33
61210 GGAAATTACT
61220 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
61253 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
61286 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
61319 ATCGCAACG
1 ATCGCAACG
61328 CGAATTTAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:61381 original size:33 final size:33
Alignment explanation
Indices: 61337--61416 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
61327 GCGAATTTAG
* * *
61337 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
61370 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
61403 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
61417 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:61382 original size:19 final size:19
Alignment explanation
Indices: 61358--61416 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
61348 GATTTTGTCG
61358 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
61377 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
61391 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
61410 TTGCGAT
1 TTGCGAT
61417 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:61424 original size:19 final size:17
Alignment explanation
Indices: 61366--61416 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
61356 CGTTGCGATT
61366 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
61383 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
61397 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
61416 T
1 T
61417 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:61542 original size:14 final size:14
Alignment explanation
Indices: 61523--61559 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61513 CATCAATTAA
61523 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
61537 ACAAATCATCTTTT
1 ACAAATCAACTTTT
61551 ACAAATCAA
1 ACAAATCAA
61560 TTAAACATTC
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:64855 original size:20 final size:20
Alignment explanation
Indices: 64830--64882 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
64820 GTCTTTTGGT
64830 GCAACGAGAGAATGACTATC
1 GCAACGAGAGAATGACTATC
*
64850 GCAACGCG-GAAATGACTATC
1 GCAACGAGAG-AATGACTATC
64870 GCAACGAGAGAAT
1 GCAACGAGAGAAT
64883 CGCAACGCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (20 bp):
GCAACGAGAGAATGACTATC
Found at i:64929 original size:19 final size:19
Alignment explanation
Indices: 64907--64951 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
64897 AAAATCTCAA
**
64907 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAATTTCGCGT
64926 TGCGATTTTAATTTCGCGT
1 TGCGATTTTAATTTCGCGT
*
64945 TGTGATT
1 TGCGATT
64952 CTCTCGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTAATTTCGCGT
Found at i:64976 original size:21 final size:21
Alignment explanation
Indices: 64950--65028 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
64940 CGCGTTGTGA
*
64950 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
64971 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
64992 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
65012 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
65029 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:65588 original size:20 final size:20
Alignment explanation
Indices: 65563--65714 Score: 90
Period size: 20 Copynumber: 7.5 Consensus size: 20
65553 GCTATGTAAA
65563 TCGCATTGCGATAGT-CATAT
1 TCGCATTGCGAT-GTACATAT
* *
65583 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
* * *
65603 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTACAT-AT
* * *
65624 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
* * ** *
65644 TCACATTGCGATTTATGTAA
1 TCGCATTGCGATGTACATAT
* * * *
65664 TCGCGTTGCGATTTACGTAA
1 TCGCATTGCGATGTACATAT
* * *
65684 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
*
65704 TCGCGTTGCGA
1 TCGCATTGCGA
65715 ATTAGGAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.01
20 99 0.85
21 17 0.15
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTACATAT
Found at i:65630 original size:21 final size:20
Alignment explanation
Indices: 65580--65705 Score: 144
Period size: 20 Copynumber: 6.2 Consensus size: 20
65570 GCGATAGTCA
*
65580 TATTCGCATTGCGATTTACG
1 TATTCACATTGCGATTTACG
* * *
65600 TATTCGCATTGCGATTTTCC
1 TATTCACATTGCGATTTACG
65620 TAATTCACATTGCGATTTACG
1 T-ATTCACATTGCGATTTACG
*
65641 TATTCACATTGCGATTTATG
1 TATTCACATTGCGATTTACG
* * *
65661 TAATCGCGTTGCGATTTACG
1 TATTCACATTGCGATTTACG
* * *
65681 TAATCGCGTTGCGATTTACG
1 TATTCACATTGCGATTTACG
65701 TATTC
1 TATTC
65706 GCGTTGCGAA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 77 0.82
21 17 0.18
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
TATTCACATTGCGATTTACG
Found at i:65756 original size:21 final size:21
Alignment explanation
Indices: 65710--65756 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
65700 GTATTCGCGT
*
65710 TGCGAATTAGGAAAATCGTAA
1 TGCGAATTAGGAAAATCGCAA
*
65731 CGCGAATTTAGG-AAATCGCAA
1 TGCGAA-TTAGGAAAATCGCAA
65752 TGCGA
1 TGCGA
65757 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:70139 original size:21 final size:21
Alignment explanation
Indices: 70110--70151 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
70100 GCCCCGATTC
70110 CCCGCCAAATTCT-TCCACCTA
1 CCCGCCAAATTCTCT-CACCTA
*
70131 CCCGTCAAATTCTCTCACCTA
1 CCCGCCAAATTCTCTCACCTA
70152 TTTCCCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.45, G:0.05, T:0.26
Consensus pattern (21 bp):
CCCGCCAAATTCTCTCACCTA
Found at i:70310 original size:21 final size:21
Alignment explanation
Indices: 70284--70341 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
70274 AAAATTTTTA
70284 TTATTTAAGTAATTAATTATT
1 TTATTTAAGTAATTAATTATT
* * * *
70305 TTATTTTAGTATTTATTTTTT
1 TTATTTAAGTAATTAATTATT
* *
70326 TTATTTGATTAATTAA
1 TTATTTAAGTAATTAA
70342 GTGTAAACTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATTTAAGTAATTAATTATT
Found at i:70529 original size:14 final size:14
Alignment explanation
Indices: 70505--70542 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
70495 ATTATATATT
70505 ATTTAATTTATTAGA
1 ATTT-ATTTATTAGA
*
70520 ATTTATTTATTTGA
1 ATTTATTTATTAGA
70534 ATTTATTTA
1 ATTTATTTA
70543 AATAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
ATTTATTTATTAGA
Found at i:72525 original size:9 final size:9
Alignment explanation
Indices: 72493--72564 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
72483 TTGTTGAAAG
*
72493 TGATGATGA
1 TGATGAGGA
*
72502 CGATGAGGA
1 TGATGAGGA
72511 -GA--AGGA
1 TGATGAGGA
*
72517 GGATGAGGA
1 TGATGAGGA
* **
72526 TGAAGATAA
1 TGATGAGGA
*
72535 TGATGACGA
1 TGATGAGGA
72544 TGATGAGGA
1 TGATGAGGA
*
72553 GGATGAGGA
1 TGATGAGGA
72562 TGA
1 TGA
72565 CGATAATGGG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
8 2 0.04
9 40 0.83
ACGTcount: A:0.38, C:0.03, G:0.42, T:0.18
Consensus pattern (9 bp):
TGATGAGGA
Found at i:72560 original size:36 final size:38
Alignment explanation
Indices: 72495--72572 Score: 115
Period size: 36 Copynumber: 2.1 Consensus size: 38
72485 GTTGAAAGTG
72495 ATGATGACGATGAGGAGAAGGAGGATGAGGATGAAGATA
1 ATGATGACGATGA-GAGAAGGAGGATGAGGATGAAGATA
* *
72534 ATGATGACGATGA-TG-AGGAGGATGAGGATGACGATA
1 ATGATGACGATGAGAGAAGGAGGATGAGGATGAAGATA
72570 ATG
1 ATG
72573 GGGATGAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 23 0.62
37 1 0.03
39 13 0.35
ACGTcount: A:0.38, C:0.04, G:0.40, T:0.18
Consensus pattern (38 bp):
ATGATGACGATGAGAGAAGGAGGATGAGGATGAAGATA
Found at i:72584 original size:24 final size:24
Alignment explanation
Indices: 72536--72585 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
72526 TGAAGATAAT
* *
72536 GATGACGATGATGAGGAGGATGAG
1 GATGACGATAATGAGGAGGAAGAG
* *
72560 GATGACGATAATGGGGATGAAGAG
1 GATGACGATAATGAGGAGGAAGAG
72584 GA
1 GA
72586 ACTGTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.44, T:0.16
Consensus pattern (24 bp):
GATGACGATAATGAGGAGGAAGAG
Found at i:73410 original size:31 final size:32
Alignment explanation
Indices: 73372--73445 Score: 123
Period size: 31 Copynumber: 2.3 Consensus size: 32
73362 TAAGAAAAGT
73372 CTATTTTAGGTGTATGTGTATGC-TTTATTTA
1 CTATTTTAGGTGTATGTGTATGCTTTTATTTA
73403 CTATTTTAGGTGTATGTGTATGCTTTTATTTA
1 CTATTTTAGGTGTATGTGTATGCTTTTATTTA
* *
73435 CTGTTTAAGGT
1 CTATTTTAGGT
73446 CTGTGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 23 0.57
32 17 0.43
ACGTcount: A:0.19, C:0.07, G:0.20, T:0.54
Consensus pattern (32 bp):
CTATTTTAGGTGTATGTGTATGCTTTTATTTA
Found at i:73544 original size:26 final size:27
Alignment explanation
Indices: 73493--73544 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
73483 GGTATGCTTC
*
73493 ATGTCATGTTTAATAGTTTGTTGTTTA
1 ATGTAATGTTTAATAGTTTGTTGTTTA
*
73520 ATGTAATGTTT-ATGGTTTGTTGTTT
1 ATGTAATGTTTAATAGTTTGTTGTTT
73545 TTATAGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (27 bp):
ATGTAATGTTTAATAGTTTGTTGTTTA
Found at i:74513 original size:83 final size:83
Alignment explanation
Indices: 74447--74888 Score: 498
Period size: 83 Copynumber: 5.4 Consensus size: 83
74437 AAATATTTGT
* ** * ** *
74447 CATGTCATAGTGTTCTATCCCATCTTAAATGAAAGACATGTTTCAGGGGAAGCGTTTTCCATTAT
1 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTCAGGGGAAGCATTTTCCATTAT
* * *
74512 TAATCAGAGAATATCTAC
66 TATTCAGAGAATCTCTGC
** * ** **
74530 CATGTCATAGTGTTCCATCCCATCTTAAATGAGAGGCATG-TTCTAGGGGAAGCATTTT-TTTTA
1 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTC-AGGGGAAGCATTTTCCATTA
* *
74593 TTATTTAGAGAATCTCTGT
65 TTATTCAGAGAATCTCTGC
* * * * **
74612 AATGTTATAGTGTTCTATCCCATCCGAAATGAAAGGCGCG-TTCTAGAGGAATTATTTTCCATTA
1 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTC-AGGGGAAGCATTTTCCATTA
*
74676 TTATTCGGAGAATCTCTGC
65 TTATTCAGAGAATCTCTGC
* * * * *
74695 CATGTCATAATGTTCCATCCCATCCGAAATGAAAGGCGCATTCCAAGGGAAACATTTTCCATTAT
1 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTCAGGGGAAGCATTTTCCATTAT
74760 TATTCAGAGAATCTCTGC
66 TATTCAGAGAATCTCTGC
* * * *
74778 CATGTCATAGTGTTCCATCCCATCCAAAATGAAAGGCGCATTTCAGGGAAAGCGTTTTCCATTAT
1 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTCAGGGGAAGCATTTTCCATTAT
* *
74843 TATTC--AGAATCTTTGT
66 TATTCAGAGAATCTCTGC
74859 CATGTCATAGTGTTCCATCCCATCCGAAAT
1 CATGTCATAGTGTTCCATCCCATCCGAAAT
74889 AAAATGTGCA
Statistics
Matches: 308, Mismatches: 48, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
81 38 0.12
82 67 0.22
83 201 0.65
84 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (83 bp):
CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTCAGGGGAAGCATTTTCCATTAT
TATTCAGAGAATCTCTGC
Found at i:78766 original size:47 final size:47
Alignment explanation
Indices: 78697--78792 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
78687 CGACTAAAAC
* * * *
78697 TAAATTTATCATCGCAGCATAGTGAATATCTTACTTTTATTAATATT
1 TAAATTTATCATAGCAACATAGTGAACACCTTACTTTTATTAATATT
* *
78744 TAAATTTATCATAGTAACATAGTGAACACCTTATTTTTATTAATATT
1 TAAATTTATCATAGCAACATAGTGAACACCTTACTTTTATTAATATT
78791 TA
1 TA
78793 TTTTATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (47 bp):
TAAATTTATCATAGCAACATAGTGAACACCTTACTTTTATTAATATT
Found at i:83572 original size:16 final size:16
Alignment explanation
Indices: 83548--83578 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
83538 TTTATTTTAA
83548 TTTAATTTAATATATT
1 TTTAATTTAATATATT
*
83564 TTTATTTTAATATAT
1 TTTAATTTAATATAT
83579 ATTAACTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:83583 original size:26 final size:27
Alignment explanation
Indices: 83538--83592 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
83528 GAGGACTAAC
*
83538 TTTATTTTAATTTAATTTAA-TATATT
1 TTTATTTTAATATAATTTAACTATATT
*
83564 TTTATTTTAATAT-ATATTAACTTTATT
1 TTTATTTTAATATAAT-TTAACTATATT
83591 TT
1 TT
83593 AATAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
27 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTTTAATATAATTTAACTATATT
Found at i:83609 original size:19 final size:21
Alignment explanation
Indices: 83566--83609 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
83556 AATATATTTT
* *
83566 TATTTTAATATATATTAACTT
1 TATTTTAATATATATTAAATA
83587 TATTTTAATA-A-ATTAAATA
1 TATTTTAATATATATTAAATA
83606 TATT
1 TATT
83610 AAAGTAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTAATATATATTAAATA
Found at i:90628 original size:18 final size:16
Alignment explanation
Indices: 90589--90630 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
90579 ACTTTCGTAG
90589 CATTATCA-TATTTAT
1 CATTATCATTATTTAT
*
90604 TATTATCATTATCTCTAT
1 CATTATCATTAT-T-TAT
90622 CATTATCAT
1 CATTATCAT
90631 CGAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 1 0.05
18 11 0.50
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (16 bp):
CATTATCATTATTTAT
Found at i:95829 original size:22 final size:22
Alignment explanation
Indices: 95804--95849 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
95794 TGTCACCACA
**
95804 GCACGTATCATTGCACCGAAGT
1 GCACGTAGAATTGCACCGAAGT
*
95826 GCACGTAGAATTGCACCGTAGT
1 GCACGTAGAATTGCACCGAAGT
95848 GC
1 GC
95850 CCTATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (22 bp):
GCACGTAGAATTGCACCGAAGT
Found at i:99129 original size:62 final size:62
Alignment explanation
Indices: 99052--99168 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
99042 TTCTCCTATG
* *
99052 GGACTATAAGTTGGCATCGGA-ACCAGTGTTGTAAAAAAACAAG-CACCACTATGTTTCCCATA
1 GGACTATAACTTGGCATAGGAGA-CAGTGTTGTAAAAAAA-AAGTCACCACTATGTTTCCCATA
* * * *
99114 GGACTGTAACTTGGCATAGGAGACATTGTTGTCAAAAAATAGTCACCACTATGTT
1 GGACTATAACTTGGCATAGGAGACAGTGTTGTAAAAAAAAAGTCACCACTATGTT
99169 CTTTCGGGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 2 0.04
62 44 0.94
63 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GGACTATAACTTGGCATAGGAGACAGTGTTGTAAAAAAAAAGTCACCACTATGTTTCCCATA
Found at i:108486 original size:24 final size:24
Alignment explanation
Indices: 108452--108503 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
108442 CTTAGCATGT
108452 TAAAAACAAAACTT-AAAATAAAG
1 TAAAAACAAAACTTGAAAATAAAG
108475 TAAAAACGAAAACTTGAAAATAAAG
1 TAAAAAC-AAAACTTGAAAATAAAG
108500 -AAAA
1 TAAAA
108504 GAAGAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.26
24 11 0.41
25 9 0.33
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (24 bp):
TAAAAACAAAACTTGAAAATAAAG
Found at i:111905 original size:15 final size:15
Alignment explanation
Indices: 111885--111914 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111875 TTTTATTTTA
111885 AAATTAAATTAATTT
1 AAATTAAATTAATTT
*
111900 AAATTAAATTGATTT
1 AAATTAAATTAATTT
111915 TTTTCATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTAAATTAATTT
Found at i:113415 original size:30 final size:30
Alignment explanation
Indices: 113379--113442 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
113369 GAAGGACCTG
* *
113379 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
113409 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
113439 TCCA
1 TCCA
113443 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:114234 original size:64 final size:65
Alignment explanation
Indices: 114126--114249 Score: 180
Period size: 64 Copynumber: 1.9 Consensus size: 65
114116 CAATGAATGT
* ** *
114126 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCCATTCGATGTTTTCTATTTAATGGGG
*
114190 ATGCATCGATGCACTCCTTATGCATCAATGCAT-AAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCC-ATTCGATGTTTTCTATTTAA
114250 ATTCATGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 5 0.09
64 41 0.77
65 7 0.13
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCCATTCGATGTTTTCTATTTAATGGGG
Found at i:114258 original size:64 final size:63
Alignment explanation
Indices: 114126--114266 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
114116 CAATGAATGT
* ** * *
114126 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTAATGGGG
1 ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCCATTCGATGTTTTTATTTAAT-GGC
* *
114190 ATGCATCGATGCACTCCTTATGCATCAATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAT-T
1 ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCC-ATTCGATGTTTT-TATTT-AATGG
114253 C
63 C
114254 ATGCATCGATGCA
1 ATGCATCGATGCA
114267 TCTTAAACAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
63 5 0.07
64 54 0.81
65 5 0.07
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCAATGCATAAAATCCATTCGATGTTTTTATTTAATGGC
Found at i:114296 original size:34 final size:34
Alignment explanation
Indices: 114257--114336 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
114247 TAAATTCATG
114257 CATCGATGCATCTTAAACAATTTCTGGTATTTAT
1 CATCGATGCATCTTAAACAATTTCTGGTATTTAT
114291 CATCGATGCATCTTAAACAATTTCTGGTATTTAT
1 CATCGATGCATCTTAAACAATTTCTGGTATTTAT
114325 CATCGATGCATC
1 CATCGATGCATC
114337 GGTGCACAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (34 bp):
CATCGATGCATCTTAAACAATTTCTGGTATTTAT
Found at i:116469 original size:34 final size:35
Alignment explanation
Indices: 116420--116487 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
116410 TGTTCATTTA
116420 AATGATAAACAAACACAAATGAACGAACATAAACG
1 AATGATAAACAAACACAAATGAACGAACATAAACG
* *
116455 AATG-TAAACGAACACAAATGAACGAACGTAAAC
1 AATGATAAACAAACACAAATGAACGAACATAAAC
116488 AAACACAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.12
Consensus pattern (35 bp):
AATGATAAACAAACACAAATGAACGAACATAAACG
Found at i:116524 original size:57 final size:58
Alignment explanation
Indices: 116425--116533 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
116415 ATTTAAATGA
*
116425 TAAACAAACACAAATGAACGAACATAAACGAATGTAAACGAACACAAATGAACGAACG
1 TAAACAAACACAAATAAACGAACATAAACGAATGTAAACGAACACAAATGAACGAACG
* * * *
116483 TAAACAAACAC-AATAAACTAACATAAATG-ATCGTAAGCGAACATAAATGAA
1 TAAACAAACACAAATAAACGAACATAAACGAAT-GTAAACGAACACAAATGAA
116534 AATAGATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 2 0.04
57 32 0.71
58 11 0.24
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14
Consensus pattern (58 bp):
TAAACAAACACAAATAAACGAACATAAACGAATGTAAACGAACACAAATGAACGAACG
Found at i:116737 original size:22 final size:22
Alignment explanation
Indices: 116707--116748 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
116697 CTAAACATAA
116707 ATTAACGAACATAAACGAACAT
1 ATTAACGAACATAAACGAACAT
* * *
116729 ATTACCGAACGTAAATGAAC
1 ATTAACGAACATAAACGAAC
116749 GAACGAGCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (22 bp):
ATTAACGAACATAAACGAACAT
Found at i:117021 original size:14 final size:15
Alignment explanation
Indices: 116993--117024 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
116983 TACGTAACGT
116993 CCGTAACATCCGCAA
1 CCGTAACATCCGCAA
117008 CCGTAACA-CCGCAA
1 CCGTAACATCCGCAA
117022 CCG
1 CCG
117025 CATCCGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.31, C:0.44, G:0.16, T:0.09
Consensus pattern (15 bp):
CCGTAACATCCGCAA
Found at i:119946 original size:2 final size:2
Alignment explanation
Indices: 119939--119983 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
119929 TTAATTATCG
*
119939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119981 TA T
1 TA T
119984 TTTTGTATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:120802 original size:15 final size:15
Alignment explanation
Indices: 120782--120816 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
120772 ATTTAGTCTT
120782 AATTTCAGTAATCTA
1 AATTTCAGTAATCTA
* *
120797 AATTTCTGTAATTTA
1 AATTTCAGTAATCTA
120812 AATTT
1 AATTT
120817 TACAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (15 bp):
AATTTCAGTAATCTA
Found at i:123777 original size:11 final size:11
Alignment explanation
Indices: 123761--123787 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
123751 CGTCATTTTA
123761 TTTTTTTAATT
1 TTTTTTTAATT
123772 TTTTTTTAATT
1 TTTTTTTAATT
123783 TTTTT
1 TTTTT
123788 ATAAAACACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:130613 original size:24 final size:24
Alignment explanation
Indices: 130581--130626 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
130571 AGATGAGGAA
130581 TTAAATTGAAA-TAATTATAAAATG
1 TTAAATTGAAATTAA-TATAAAATG
*
130605 TTAAGTTGAAATTAATATAAAA
1 TTAAATTGAAATTAATATAAAA
130627 GTGGACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (24 bp):
TTAAATTGAAATTAATATAAAATG
Found at i:131633 original size:3 final size:3
Alignment explanation
Indices: 131627--131711 Score: 116
Period size: 3 Copynumber: 27.7 Consensus size: 3
131617 TTTTTACTCA
* * *
131627 TAT TAT TAT TAT TAT TAG TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
131675 TAT TAT TAT TAT TAT TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
131712 CAAACAGACC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:137146 original size:15 final size:15
Alignment explanation
Indices: 137126--137157 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
137116 ATCAATACCT
137126 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
137141 TTTTGCATACATTCA
1 TTTTGCATACATGCA
137156 TT
1 TT
137158 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:144498 original size:10 final size:10
Alignment explanation
Indices: 144483--144567 Score: 81
Period size: 10 Copynumber: 8.7 Consensus size: 10
144473 ATGCTTGAAG
144483 AGAAAAAAAA
1 AGAAAAAAAA
144493 AGAAAAAAAAAA
1 AG--AAAAAAAA
144505 AGAAAAAAAA
1 AGAAAAAAAA
* *
144515 AGAGAGAAAA
1 AGAAAAAAAA
144525 AG---AAAAA
1 AGAAAAAAAA
144532 AGAAAAAAGAA
1 AGAAAAAA-AA
144543 AG--AAAAAA
1 AGAAAAAAAA
*
144551 AGAAAAAAGA
1 AGAAAAAAAA
144561 AGAAAAA
1 AGAAAAA
144568 GGAGGGTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
7 6 0.10
8 4 0.06
9 4 0.06
10 35 0.56
11 4 0.06
12 10 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:144500 original size:7 final size:7
Alignment explanation
Indices: 144488--144566 Score: 80
Period size: 6 Copynumber: 11.9 Consensus size: 7
144478 TGAAGAGAAA
144488 AAAAAAG
1 AAAAAAG
144495 -AAAAA-
1 AAAAAAG
144500 AAAAAAG
1 AAAAAAG
144507 -AAAAA-
1 AAAAAAG
*
144512 AAAAGAG
1 AAAAAAG
144519 AGAAAAAG
1 A-AAAAAG
144527 AAAAAAG
1 AAAAAAG
144534 AAAAAAG
1 AAAAAAG
*
144541 -AAAGA-
1 AAAAAAG
144546 AAAAAAG
1 AAAAAAG
144553 AAAAAAG
1 AAAAAAG
144560 AAGAAAA
1 AA-AAAA
144567 AGGAGGGTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
6 27 0.45
7 23 0.38
8 10 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:144500 original size:12 final size:12
Alignment explanation
Indices: 144480--144567 Score: 97
Period size: 12 Copynumber: 6.8 Consensus size: 12
144470 ATTATGCTTG
*
144480 AAGAGAAAAAAA
1 AAGAAAAAAAAA
144492 AAGAAAAAAAAA
1 AAGAAAAAAAAA
144504 AAGAAAAAAAAA
1 AAGAAAAAAAAA
144516 GAGAGAAAAAGAAAA
1 -A-AGAAAAA-AAAA
144531 AAGAAAAAAGAAA
1 AAGAAAAAA-AAA
144544 GAA-AAAAAGAAAA
1 -AAGAAAAA-AAAA
144557 AAGAAGAAAAA
1 AAGAA-AAAAA
144568 GGAGGGTCAA
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
12 26 0.39
13 23 0.34
14 14 0.21
15 4 0.06
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:144522 original size:26 final size:26
Alignment explanation
Indices: 144480--144567 Score: 119
Period size: 26 Copynumber: 3.4 Consensus size: 26
144470 ATTATGCTTG
*
144480 AAGAGAAAAAAA-AAGAAAAA-AAAA
1 AAGAAAAAAAAAGAAGAAAAAGAAAA
144504 AAGAAAAAAAAAGAGAGAAAAAGAAAA
1 AAGAAAAAAAAAGA-AGAAAAAGAAAA
144531 AAGAAAAAAGAAAGAA-AAAAAGAAAA
1 AAGAAAAAA-AAAGAAGAAAAAGAAAA
*
144557 AAGAAGAAAAA
1 AAGAAAAAAAA
144568 GGAGGGTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.19
25 3 0.05
26 25 0.43
27 14 0.24
28 5 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAAAAGAAGAAAAAGAAAA
Found at i:144545 original size:38 final size:36
Alignment explanation
Indices: 144481--144567 Score: 110
Period size: 34 Copynumber: 2.5 Consensus size: 36
144471 TTATGCTTGA
144481 AGAGAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAG
1 AGAGAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAG
* * *
144517 AGAG-AAAAAGAA-AAAAGAAAAAAGAAAGAAAAA-
1 AGAGAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAG
*
144550 A-AGAAAAAAGAAGAAAAA
1 AGAGAAAAAAAAAGAAAAA
144568 GGAGGGTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 2 0.04
33 9 0.20
34 23 0.51
35 7 0.16
36 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (36 bp):
AGAGAAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAG
Found at i:144567 original size:1 final size:1
Alignment explanation
Indices: 144485--144558 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
144475 GCTTGAAGAG
* * * * * * * * *
144485 AAAAAAAAAGAAAAAAAAAAAGAAAAAAAAAGAGAGAAAAAGAAAAAAGAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
144550 AAGAAAAAA
1 AAAAAAAAA
144559 GAAGAAAAAG
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:146813 original size:113 final size:113
Alignment explanation
Indices: 146611--147607 Score: 1748
Period size: 113 Copynumber: 8.8 Consensus size: 113
146601 CAAAGATTTG
*
146611 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
* **
146676 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
* *
146724 AATCCATCA-TCCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAG
1 AATCCATCACT-TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
146788 GAGGAAGAAGAAGTTCATAACGAGAAGAGCTTGTTCAACCTTATGCTCA
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
146837 AATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
146901 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
65 GAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
*
146950 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAAGGAGAAGAACTCATCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
147015 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
*
147063 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
147128 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
* *
147176 AATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAAGGAGAAGAACTCATCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
147241 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
147289 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
147354 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
*
147402 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCTGAAGG
1 AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
* **
147467 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTATGCTCA
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
* *
147515 AATCCATCA-TTCGATGGATCAGCTTTTCAAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
147579 AAGGAAGAAGAAGTTCATAATGAGAAGAA
65 GAGGAAGAAGAAATTCATAATGAGAAGAA
147608 CTCATCTGAA
Statistics
Matches: 853, Mismatches: 27, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
112 3 0.00
113 848 0.99
114 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (113 bp):
AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGG
AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTCA
Found at i:147603 original size:40 final size:38
Alignment explanation
Indices: 147543--147677 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 38
147533 TCAGCTTTTC
*
147543 AAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 AAGAAGAAGTTCATAATGAGAAGAACTCATCTG-AGAA-G
147583 AAGAAGAAGTTCATAATGAGAAGAACTCATCT--GAAG
1 AAGAAGAAGTTCATAATGAGAAGAACTCATCTGAGAAG
*
147619 AAGAAGAAGTTCATAATGAGAAGAACTCATATGA-AAG
1 AAGAAGAAGTTCATAATGAGAAGAACTCATCTGAGAAG
147656 AAG-A-AA-TTCATAATGAGAAGAA
1 AAGAAGAAGTTCATAATGAGAAGAA
147678 TTTGTTCAAC
Statistics
Matches: 91, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
34 16 0.18
35 2 0.02
36 33 0.36
37 9 0.10
40 31 0.34
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.19
Consensus pattern (38 bp):
AAGAAGAAGTTCATAATGAGAAGAACTCATCTGAGAAG
Found at i:147656 original size:14 final size:16
Alignment explanation
Indices: 147593--147677 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 16
147583 AAGAAGAAGT
147593 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
*
147609 TCATCTGAA-GAAGAAGAAGT
1 TCA--T-AATG-AGAAGAA-C
147629 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
*
147645 TCAT-ATGAAAGAAGAAAT
1 TCATAATG--AGAAG-AAC
147663 TCATAATGAGAAGAA
1 TCATAATGAGAAGAA
147678 TTTGTTCAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
15 3 0.05
16 9 0.16
17 19 0.34
18 10 0.18
19 12 0.21
20 3 0.05
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (16 bp):
TCATAATGAGAAGAAC
Found at i:147759 original size:182 final size:188
Alignment explanation
Indices: 147436--147791 Score: 474
Period size: 182 Copynumber: 1.9 Consensus size: 188
147426 TTTCCAGAGA
* * *
147436 AAGTTCATAATGAGAAGAACTCCTCTGAAGGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATATGAA-GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
147501 CAACCTTATGCTCAAATCCATCATTCGATGGATCAGCTTTTCAAGAGGAAGTTCATAATGAGAAG
65 CAACCTTATGCTCAAATCCATCATTCAATAGATCAACCTTTCAAGAGAAAATTCATAATGAGAAG
* *
147566 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
130 AACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
*
147625 AAGTTCATAATGAGAAGAACTCATATGAA-A-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTC
1 AAGTTCATAATGAGAAGAACTCATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * *
147685 AA-CTTTTGCTTGAATTCATCATTTAATATATCAACCTTT-ATAGAGAAAATTCATAATGAGAAG
66 AACCTTATGCTCAAATCCATCATTCAATAGATCAACCTTTCA-AGAGAAAATTCATAATGAGAAG
*
147748 AATTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAACT
130 AACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAACT
147792 TATTCAACCT
Statistics
Matches: 147, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
181 1 0.01
182 88 0.60
183 23 0.16
184 2 0.01
185 1 0.01
186 4 0.03
187 1 0.01
189 27 0.18
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (188 bp):
AAGTTCATAATGAGAAGAACTCATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTATGCTCAAATCCATCATTCAATAGATCAACCTTTCAAGAGAAAATTCATAATGAGAAGA
ACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
Found at i:148037 original size:3 final size:3
Alignment explanation
Indices: 148031--148113 Score: 112
Period size: 3 Copynumber: 27.0 Consensus size: 3
148021 TTTACTCATT
* *
148031 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
148079 TTA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
148114 CAAACAGACC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 64 0.91
4 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:169211 original size:17 final size:18
Alignment explanation
Indices: 169168--169208 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
169158 AAATTATATT
169168 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
169185 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
169203 ATTAAA
1 AGTAAA
169209 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:169288 original size:10 final size:10
Alignment explanation
Indices: 169250--169289 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
169240 CTTAAACAGA
*
169250 GAGAGTATTT
1 GAGAGAATTT
*
169260 GAGAGAAATT
1 GAGAGAATTT
*
169270 GAGAAAATTT
1 GAGAGAATTT
169280 GAGAGAATTT
1 GAGAGAATTT
169290 AGTGTGATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:178592 original size:3 final size:3
Alignment explanation
Indices: 178584--178660 Score: 92
Period size: 3 Copynumber: 27.3 Consensus size: 3
178574 TTTGGCCGAC
* *
178584 TCT TCT TCT TCT TCT TC- ACT T-T TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
178630 TCT TC- ACT T-T TCT TCT TCT T-T TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
178661 TCTTTCTCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 8 0.13
3 55 0.87
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:178634 original size:37 final size:34
Alignment explanation
Indices: 178584--178683 Score: 148
Period size: 34 Copynumber: 2.9 Consensus size: 34
178574 TTTGGCCGAC
178584 TCTTCTTCTTCTTCTTCACTTTTCTTCTTCTTTT
1 TCTTCTTCTTCTTCTTCACTTTTCTTCTTCTTTT
178618 TCTTCTTCTTCTTCTTCACTTTTCTTCTTC-TTT
1 TCTTCTTCTTCTTCTTCACTTTTCTTCTTCTTTT
*
178651 TCTTCTTCTTTCTTTCTCATCACTTTTATTCTT
1 TCTTCTTC-TTC-TTCT--TCACTTTTCTTCTT
178684 TTCTTATTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
33 11 0.18
34 33 0.54
35 4 0.07
37 13 0.21
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (34 bp):
TCTTCTTCTTCTTCTTCACTTTTCTTCTTCTTTT
Found at i:179589 original size:16 final size:15
Alignment explanation
Indices: 179570--179618 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
179560 GAAGAAAAGT
179570 GAAGAGAAAGAAAGAA
1 GAAGA-AAAGAAAGAA
*
179586 GAAGAAAAGTGAAGAA
1 GAAGAAAAG-AAAGAA
179602 GAAGAAAAGAAA-AA
1 GAAGAAAAGAAAGAA
179616 GAA
1 GAA
179619 TAACAAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 19 0.63
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
GAAGAAAAGAAAGAA
Done.