Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008371.1 Hibiscus syriacus cultivar Beakdansim tig00111127_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: 546649
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:210725 original size:32 final size:32
Alignment explanation
Indices: 210676--210749 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
210666 GCAACGAGAA
**
210676 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGC-ACGAGAGAATCGCAACGCGAAACC
210709 AAAATCGCACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCACGAGAGAATCGCAACGCGAAACC
210741 AAAATCGCA
1 AAAATCGCA
210750 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.08
Consensus pattern (32 bp):
AAAATCGCACGAGAGAATCGCAACGCGAAACC
Found at i:210801 original size:21 final size:21
Alignment explanation
Indices: 210775--210836 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
210765 CGCGTTGCGA
210775 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
210796 TTCTCTCGTTGCGA-CGTCA-
1 TTCTCTCGTTGCGATTTTCAT
210815 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
210836 T
1 T
210837 CAACCAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 14 0.40
20 6 0.17
21 15 0.43
ACGTcount: A:0.10, C:0.26, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:210818 original size:19 final size:20
Alignment explanation
Indices: 210774--210829 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
210764 TCGCGTTGCG
**
210774 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATCGTC
210794 ATTTCTCTCGTTGCGA-CGTC
1 A-TTCTCTCGTTGCGATCGTC
210814 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
210830 TTTCATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
21 14 0.44
ACGTcount: A:0.11, C:0.27, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATCGTC
Found at i:212731 original size:88 final size:92
Alignment explanation
Indices: 212502--212800 Score: 460
Period size: 89 Copynumber: 3.4 Consensus size: 92
212492 ATTGCTTAGT
*
212502 AATTTATTC-GTTGCTGCCAATTCTGCT-AACTGTGTATTC-TTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
* *
212564 TCTTTGTTTTGCCTTTTGTTGAAAGTA
66 TCTTTGTTTTGTCTTTGGTTGAAAGTA
212591 AATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-AGTATTT-
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
212652 T-TTTGTTTTGTCTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTGGTTGAAAGTA
*
212678 AATTTGTTCGGTTTGCTGCCAATT-TGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTATTT
1 AATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTT
212742 GTCTTTG-TTTGTCTTTTGGTTGAAAGT-
65 GTCTTTGTTTTGTC-TTTGGTTGAAAGTA
212769 AATTTGTTCGGTTGCTGCC-ATTCTGCTAAACT
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
212801 AATACCCCTG
Statistics
Matches: 196, Mismatches: 4, Indels: 19
0.89 0.02 0.09
Matches are distributed among these distances:
87 32 0.16
88 30 0.15
89 50 0.26
90 38 0.19
91 29 0.15
92 17 0.09
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (92 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTGGTTGAAAGTA
Found at i:212931 original size:14 final size:14
Alignment explanation
Indices: 212912--212968 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
212902 ACAAACTTAA
212912 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
212926 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
212945 AATCGCAACGACAG
1 AATCGCAACGAGAG
212959 AATCGCAACG
1 AATCGCAACG
212969 CGAAAACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:212984 original size:20 final size:19
Alignment explanation
Indices: 212926--213017 Score: 71
Period size: 14 Copynumber: 5.4 Consensus size: 19
212916 GCAACGAGAG
**
212926 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
212945 AATCGCAA--CG--A-CAG
1 AATCGCAACGCGAAACCAA
212959 AATCGCAACGCGAAAACCAA
1 AATCGCAACGCG-AAACCAA
212979 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
212993 AATCGCAACGCGAAACC-A
1 AATCGCAACGCGAAACCAA
213011 AATCGCA
1 AATCGCA
213018 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 2 0.03
18 11 0.19
19 10 0.17
20 10 0.17
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:212986 original size:34 final size:33
Alignment explanation
Indices: 212910--213017 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
212900 ACACAAACTT
* **
212910 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
212943 AAAATCGCAACGACAGAATCGCAACGCGAAAACC
1 AAAATCGCAACGACAGAATCGCAACGCG-AAACC
*
212977 AAAATCGCAACGACAAAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
213010 -AAATCGCA
1 AAAATCGCA
213018 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
32 8 0.11
33 32 0.46
34 30 0.43
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:213040 original size:19 final size:19
Alignment explanation
Indices: 213013--213166 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
213003 CGAAACCAAA
*
213013 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
213032 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
213046 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
213065 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
213081 T--CATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
213098 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
213117 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
213136 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
213156 TCGTGTTGCGA
1 TCGCGTTGCGA
213167 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.17
16 8 0.07
17 8 0.07
19 61 0.57
20 12 0.11
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:213060 original size:33 final size:33
Alignment explanation
Indices: 213018--213148 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
213008 CCAAATCGCA
213018 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
213051 TTGCGATTTTCATTTCGCATTGCGATTCTGTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
213084 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
213122 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
213149 TTAAGTTTCG
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 55 0.65
35 1 0.01
36 1 0.01
38 28 0.33
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:214576 original size:64 final size:65
Alignment explanation
Indices: 214487--214618 Score: 257
Period size: 64 Copynumber: 2.0 Consensus size: 65
214477 ATTCTGGATG
214487 CGATCAATTATTGGACTCGTTCTGGAAACAAGAAGCCAAAGAAGCTCAATTACAGTTATTAGAGA
1 CGATCAATTATTGGACTCGTTCTGGAAACAAGAAGCCAAAGAAGCTCAATTACAGTTATTAGAGA
214552 CGATCAATTATT-GACTCGTTCTGGAAACAAGAAGCCAAAGAAGCTCAATTACAGTTATTAGAGA
1 CGATCAATTATTGGACTCGTTCTGGAAACAAGAAGCCAAAGAAGCTCAATTACAGTTATTAGAGA
214616 CGA
1 CGA
214619 GTTAAGACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 55 0.82
65 12 0.18
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (65 bp):
CGATCAATTATTGGACTCGTTCTGGAAACAAGAAGCCAAAGAAGCTCAATTACAGTTATTAGAGA
Found at i:215269 original size:14 final size:14
Alignment explanation
Indices: 215250--215285 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
215240 ATTGTTTAAT
215250 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
215264 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
215278 TGATTTGT
1 TGATTTGT
215286 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:215521 original size:20 final size:19
Alignment explanation
Indices: 215476--215664 Score: 187
Period size: 19 Copynumber: 10.7 Consensus size: 19
215466 AACGAGAGAA
*
215476 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
215495 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
215514 TCCGCATTGCGA--TTC---
1 T-CGCATTGCGATTTTCATT
*
215529 TC-CGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
215547 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
215566 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
215583 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
215600 TCGCATTTCGATTTTCATT
1 TCGCATTGCGATTTTCATT
215619 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
215637 T-G--TTGGGA-TTTCATT
1 TCGCATTGCGATTTTCATT
215652 TCGCATTGCGATT
1 TCGCATTGCGATT
215665 CTCTCGTTGC
Statistics
Matches: 141, Mismatches: 9, Indels: 40
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.09
14 12 0.09
15 5 0.04
16 7 0.05
17 6 0.04
18 14 0.10
19 50 0.35
20 35 0.25
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:215612 original size:53 final size:53
Alignment explanation
Indices: 215482--215664 Score: 309
Period size: 52 Copynumber: 3.5 Consensus size: 53
215472 AGAATCGCAA
215482 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-CGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
215534 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
215587 TGCGATTTTCATTTCGCATTTCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
215640 TGGGA-TTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
215665 CTCTCGTTGC
Statistics
Matches: 125, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
52 68 0.54
53 56 0.45
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:218176 original size:24 final size:24
Alignment explanation
Indices: 218142--218195 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
218132 CTGAAACATC
*
218142 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAG
*
218166 ATCAAAGTCCGGATATTGACCAAG
1 ATCAAAATCCGGATATTGACCAAG
218190 ATCAAA
1 ATCAAA
218196 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAG
Found at i:218209 original size:24 final size:24
Alignment explanation
Indices: 218158--218209 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
218148 ATCCGTGTAT
* * *
218158 TGACCAATATCAAAGTCCGGATAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
218182 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
218206 TGAC
1 TGAC
218210 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:218901 original size:20 final size:20
Alignment explanation
Indices: 218873--219085 Score: 194
Period size: 20 Copynumber: 10.4 Consensus size: 20
218863 AAATTTCAGT
* * *
218873 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
218893 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
218913 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
218933 GTTGCGATTTACGGATTATTACGC
1 GTTGCGATTTACGG---ATT-CGC
* *
218957 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
218977 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
218997 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
219017 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
219037 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
219057 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
219077 GTTGCGATT
1 GTTGCGATT
219086 CTTTAAAATC
Statistics
Matches: 163, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
20 142 0.87
21 3 0.02
23 3 0.02
24 15 0.09
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:219138 original size:21 final size:20
Alignment explanation
Indices: 219053--219150 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
219043 ATTTATGTGT
* *
219053 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
219073 TCGCGTTGCGATTCTTTAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
219094 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
219115 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
219136 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
219151 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:219146 original size:42 final size:43
Alignment explanation
Indices: 219053--219151 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
219043 ATTTATGTGT
* *
219053 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTTAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
219094 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
219136 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
219152 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:220717 original size:2 final size:2
Alignment explanation
Indices: 220710--220736 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
220700 AAGTTACCCT
220710 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
220737 CGGAAAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:221124 original size:11 final size:11
Alignment explanation
Indices: 221108--221132 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
221098 ACATATTGTA
221108 TTACTTTTATG
1 TTACTTTTATG
221119 TTACTTTTATG
1 TTACTTTTATG
221130 TTA
1 TTA
221133 TAATAGCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (11 bp):
TTACTTTTATG
Found at i:229206 original size:20 final size:20
Alignment explanation
Indices: 229177--229228 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
229167 CGTTGGATCT
*
229177 AAAGTATCGAAACT-TTAATG
1 AAAGTTTCGAAACTCTTAA-G
*
229197 AAAGTTTCGAAACTCTTGAG
1 AAAGTTTCGAAACTCTTAAG
*
229217 ATAGTTTCGAAA
1 AAAGTTTCGAAA
229229 TTATTGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAG
Found at i:233862 original size:639 final size:640
Alignment explanation
Indices: 232642--233924 Score: 2496
Period size: 639 Copynumber: 2.0 Consensus size: 640
232632 AAGGGATCTC
232642 GGATCAATATTGTATTTACTGCAGATCACTCTTTTCCTCTACCACGACTCTTTCTTATTTACAAA
1 GGATCAATATTGTATTTACTGCAGATCACTCTTTTCCTCTACCACGACTCTTTCTTATTTACAAA
*
232707 TTTCCACACTCATTTACCCAAAAGCGCTCGATTCATTAAAATCAAGTCTGTGATTCCAAGCCCCC
66 TTTCCACACTCATTTACCCAAAAGCGCCCGATTCATTAAAATCAAGTCTGTGATTCCAAG-CCCC
232772 CCCAACTCCTTTGGTATGAAAACAGAAGGTCATTTCACCCAATGGATCTTCTCAACCGAATTCCC
130 CCCAACTCCTTTGGTATGAAAACAGAAGGTCATTTCACCCAATGGATCTTCTCAACCGAATTCCC
232837 CTATAGGAACTTAGCCATAATAGAATTTAACCTTCTTATAATACATTACGACATTCTAAACATAG
195 CTATAGGAACTTAGCCATAATAGAATTTAACCTTCTTATAATACATTACGACATTCTAAACATAG
232902 ACAAGAAGTAAATCGGCAATAAACATAAAACTGATTTTACCAATACCACTCTTCCTGATATGGAG
260 ACAAGAAGTAAATCGGCAATAAACATAAAACTGATTTTACCAATACCACTCTTCCTGATATGGAG
232967 AGGGAGGTTGCCTTCCAACCTGCCAACTTTTTATACAATCTCTGGACGGCGAGCTCCCATAATGC
325 AGGGAGGTTGCCTTCCAACCTGCCAACTTTTTATACAATCTCTGGACGGCGAGCTCCCATAATGC
233032 AACCAAATTCTTTTTCACCCCCAAAGGAAGGCCAAGGTACTCCGTCAGGAAGGCACCCACCGCAC
390 AACCAAATTCTTTTTCACCCCCAAAGGAAGGCCAAGGTACTCCGTCAGGAAGGCACCCACCGCAC
233097 AACCAATTGAGGCTGCCCACTTCTCCAAGACAACAACTTCTACATTAATCCCAAACATCATACTC
455 AACCAATTGAGGCTGCCCACTTCTCCAAGACAACAACTTCTACATTAATCCCAAACATCATACTC
233162 TTAGACATATTCAATTGTAAACCAAATATCAATTAAAAAATGACAAACCCTATTTTACATTCTTC
520 TTAGACATATTCAATTGTAAACCAAATATCAATTAAAAAATGACAAACCCTATTTTACATTCTTC
233227 AACTTCTCAATGGATGCATTACAAAAAATTAGCAAGTCGTCTGCGAACTGTAAATG
585 AACTTCTCAATGGATGCATTACAAAAAATTAGCAAGTCGTCTGCGAACTGTAAATG
*
233283 GGATCAATATTGTATTTACTGTAGATCACTCTTTTCCTCTACCACGACTCTTTCTTATTTACAAA
1 GGATCAATATTGTATTTACTGCAGATCACTCTTTTCCTCTACCACGACTCTTTCTTATTTACAAA
233348 TTTCCACACTCATTTACCCAAAAGCGCCCGATTCATTAAAATCAAGTCTGTGATTCCAAG-CCCC
66 TTTCCACACTCATTTACCCAAAAGCGCCCGATTCATTAAAATCAAGTCTGTGATTCCAAGCCCCC
233412 CCAACTCCTTTGGTATGAAAACAGAAGGTCATTTCACCCAATGGATCTTCTCAACCGAATTCCCC
131 CCAACTCCTTTGGTATGAAAACAGAAGGTCATTTCACCCAATGGATCTTCTCAACCGAATTCCCC
233477 TATAGGAACTTAGCCATAATAGAATTTAACCTTCTTATAATACATTACGACATTCTAAACATAGA
196 TATAGGAACTTAGCCATAATAGAATTTAACCTTCTTATAATACATTACGACATTCTAAACATAGA
233542 CAAGAAGTAAATCGGCAATAAACATAAAACTGATTTTACCAATACCACTCTTCCTGATATGGAGA
261 CAAGAAGTAAATCGGCAATAAACATAAAACTGATTTTACCAATACCACTCTTCCTGATATGGAGA
*
233607 GGGAGGTTGCCTTCTAACCTGCCAACTTTTTATACAATCTCTGGACGGCGAGCTCCCATAATGCA
326 GGGAGGTTGCCTTCCAACCTGCCAACTTTTTATACAATCTCTGGACGGCGAGCTCCCATAATGCA
*
233672 ACCAAATTCTTTTTCACCCCCAAAGGAAGGCCAAGGTACTCCGTCAGGAAGGCACCCATCGCACA
391 ACCAAATTCTTTTTCACCCCCAAAGGAAGGCCAAGGTACTCCGTCAGGAAGGCACCCACCGCACA
233737 ACCAATTGAGGCTGCCCACTTCTCCAAGACAACAACTTCTACATTAATCCCAAACATCATACTCT
456 ACCAATTGAGGCTGCCCACTTCTCCAAGACAACAACTTCTACATTAATCCCAAACATCATACTCT
*
233802 TAGACATATTCAATTGTAAACCAAATATCAATTCAAAAATGACAAACCCTATTTTACATTCTTCA
521 TAGACATATTCAATTGTAAACCAAATATCAATTAAAAAATGACAAACCCTATTTTACATTCTTCA
*
233867 ACTTCTCAATTGATGCATTACAAAAAATTAGCAAGTCGTCTGCGAACTGTAAATG
586 ACTTCTCAATGGATGCATTACAAAAAATTAGCAAGTCGTCTGCGAACTGTAAATG
233922 GGA
1 GGA
233925 CATCAAGAAA
Statistics
Matches: 636, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
639 513 0.81
641 123 0.19
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (640 bp):
GGATCAATATTGTATTTACTGCAGATCACTCTTTTCCTCTACCACGACTCTTTCTTATTTACAAA
TTTCCACACTCATTTACCCAAAAGCGCCCGATTCATTAAAATCAAGTCTGTGATTCCAAGCCCCC
CCAACTCCTTTGGTATGAAAACAGAAGGTCATTTCACCCAATGGATCTTCTCAACCGAATTCCCC
TATAGGAACTTAGCCATAATAGAATTTAACCTTCTTATAATACATTACGACATTCTAAACATAGA
CAAGAAGTAAATCGGCAATAAACATAAAACTGATTTTACCAATACCACTCTTCCTGATATGGAGA
GGGAGGTTGCCTTCCAACCTGCCAACTTTTTATACAATCTCTGGACGGCGAGCTCCCATAATGCA
ACCAAATTCTTTTTCACCCCCAAAGGAAGGCCAAGGTACTCCGTCAGGAAGGCACCCACCGCACA
ACCAATTGAGGCTGCCCACTTCTCCAAGACAACAACTTCTACATTAATCCCAAACATCATACTCT
TAGACATATTCAATTGTAAACCAAATATCAATTAAAAAATGACAAACCCTATTTTACATTCTTCA
ACTTCTCAATGGATGCATTACAAAAAATTAGCAAGTCGTCTGCGAACTGTAAATG
Found at i:239597 original size:20 final size:21
Alignment explanation
Indices: 239560--239599 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
239550 AGTCGTTGGG
*
239560 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCAATACTAT
*
239581 GCCT-ATGGTATTAATACTA
1 GCCTGATGGTATCAATACTA
239600 CTATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:240344 original size:55 final size:55
Alignment explanation
Indices: 240260--240370 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
240250 AAGACTTAAT
240260 TTCCTTAATTAAAGTACTAAAAAACACCGAAGATAGACTAGGCAACTGGTCTCAA
1 TTCCTTAATTAAAGTACTAAAAAACACCGAAGATAGACTAGGCAACTGGTCTCAA
240315 TTCCTTAATTAAAGTACTAAAAAACACCGAAGATAGACTAGGCAACTGGTCTCAA
1 TTCCTTAATTAAAGTACTAAAAAACACCGAAGATAGACTAGGCAACTGGTCTCAA
240370 T
1 T
240371 CCACTGCATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (55 bp):
TTCCTTAATTAAAGTACTAAAAAACACCGAAGATAGACTAGGCAACTGGTCTCAA
Found at i:251522 original size:20 final size:20
Alignment explanation
Indices: 251493--251542 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
251483 TATAAGCATC
* *
251493 ACAAGGTACACGAACCTAAT
1 ACAAGATACACGAACCCAAT
251513 ACAAGATACACGAACCCAAT
1 ACAAGATACACGAACCCAAT
*
251533 ACTAGATACA
1 ACAAGATACA
251543 ACATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (20 bp):
ACAAGATACACGAACCCAAT
Found at i:252885 original size:2 final size:2
Alignment explanation
Indices: 252880--252908 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
252870 ACACGTATCT
252880 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
252909 AATCTCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:256052 original size:30 final size:31
Alignment explanation
Indices: 256012--256070 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
256002 CTGCTACTTG
256012 ATAGTACTCTGCTAGTAACTATACTAGTTAT
1 ATAGTACTCTGCTAGTAACTATACTAGTTAT
*
256043 ATAGT-CTCTGCTAGTAACTATGCTAGTT
1 ATAGTACTCTGCTAGTAACTATACTAGTT
256071 CTTGATAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (31 bp):
ATAGTACTCTGCTAGTAACTATACTAGTTAT
Found at i:256813 original size:29 final size:29
Alignment explanation
Indices: 256779--256837 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
256769 CCTAAATTAA
256779 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
256808 TTTGATGTCATTGCTTACATTAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
256837 T
1 T
256838 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:261474 original size:29 final size:29
Alignment explanation
Indices: 261440--261498 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
261430 CCTAAATTAC
261440 TTTGATGTCATTGCT-TACATCAATTTAGT
1 TTTGATGTCATTGCTAT-CATCAATTTAGT
261469 TTTGATGTCATTGCTATCATCAATTTAGT
1 TTTGATGTCATTGCTATCATCAATTTAGT
261498 T
1 T
261499 AGGAGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTATCATCAATTTAGT
Found at i:276566 original size:23 final size:22
Alignment explanation
Indices: 276542--276586 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
276532 CTTCGATATT
276542 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
276566 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
276587 TTTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:278036 original size:3 final size:3
Alignment explanation
Indices: 278028--278088 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
278018 AATTATTTTT
* *
278028 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
278073 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
278089 TATAGTTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:278099 original size:12 final size:12
Alignment explanation
Indices: 278028--278099 Score: 92
Period size: 12 Copynumber: 6.0 Consensus size: 12
278018 AATTATTTTT
*
278028 TAATAATAATAA
1 TAATAATTATAA
278040 TAATAA-TATATA
1 TAATAATTATA-A
278052 TAATAATTATAA
1 TAATAATTATAA
278064 TAATAATTATAA
1 TAATAATTATAA
*
278076 TAATAATAATAA
1 TAATAATTATAA
* *
278088 TTATAGTTATAA
1 TAATAATTATAA
278100 AAAAATTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
11 3 0.06
12 46 0.87
13 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:280917 original size:17 final size:15
Alignment explanation
Indices: 280889--280930 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
280879 AAAATAACTC
*
280889 ATTAATAATATTTTT
1 ATTAAAAATATTTTT
280904 ATATATAAAATA-TTTT
1 AT-TA-AAAATATTTTT
280920 ATTAAAAATAT
1 ATTAAAAATAT
280931 ATTATCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 8 0.35
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAAAATATTTTT
Found at i:281052 original size:20 final size:18
Alignment explanation
Indices: 281009--281049 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
280999 CTAAAAGAAT
281009 ATTAAAAAAATATTAGTA
1 ATTAAAAAAATATTAGTA
281027 ATTAAAATAAATTATTAAGTA
1 ATTAAAA-AAA-TATT-AGTA
281048 AT
1 AT
281050 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 4 0.20
21 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
ATTAAAAAAATATTAGTA
Found at i:287034 original size:21 final size:21
Alignment explanation
Indices: 287010--287051 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
287000 TAATAGAAAT
*
287010 GTTAAAAA-AATTAATGTTTTA
1 GTTAAAAATAA-TAATATTTTA
287031 GTTAAAAATAATAATATTTTA
1 GTTAAAAATAATAATATTTTA
287052 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
GTTAAAAATAATAATATTTTA
Found at i:287302 original size:30 final size:30
Alignment explanation
Indices: 287266--287370 Score: 106
Period size: 30 Copynumber: 3.4 Consensus size: 30
287256 TAATTTAATT
287266 TTAATTTAATTTTTAACTTTTATATAAAA-A
1 TTAATTTAA-TTTTAACTTTTATATAAAATA
* *
287296 TTAATTTAATTTTATGC-TCTATATAAAATA
1 TTAATTTAATTTTA-ACTTTTATATAAAATA
* * *
287326 TTAATTTAACTTTAATTTTTTATTTAAAATA
1 TTAATTTAATTTTAA-CTTTTATATAAAATA
*
287357 TCAATTTAAATTTT
1 TTAATTT-AATTTT
287371 GTATCCAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
29 15 0.25
30 24 0.39
31 17 0.28
32 5 0.08
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (30 bp):
TTAATTTAATTTTAACTTTTATATAAAATA
Found at i:287357 original size:31 final size:30
Alignment explanation
Indices: 287266--287365 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
287256 TAATTTAATT
287266 TTAATTTAATTTTTAA-CTTTTATATAAAA-A
1 TTAATTTAA--TTTAATCTTTTATATAAAATA
* *
287296 TTAATTTAATTTTATGC-TCTATATAAAATA
1 TTAATTTAATTTAAT-CTTTTATATAAAATA
* *
287326 TTAATTTAACTTTAATTTTTTATTTAAAATA
1 TTAATTTAA-TTTAATCTTTTATATAAAATA
*
287357 TCAATTTAA
1 TTAATTTAA
287366 ATTTTGTATC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
28 4 0.07
29 10 0.17
30 20 0.34
31 24 0.41
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (30 bp):
TTAATTTAATTTAATCTTTTATATAAAATA
Found at i:288636 original size:31 final size:31
Alignment explanation
Indices: 288591--288702 Score: 111
Period size: 31 Copynumber: 3.7 Consensus size: 31
288581 TAGATTCAGG
* * *
288591 GATCAAATTGATATTTTATATAAAGTTTAGA
1 GATCAAATTAATATTTTATTTAAAATTTAGA
* *
288622 GATTAAATTAATATTTTATTTAAATTTTA-A
1 GATCAAATTAATATTTTATTTAAAATTTAGA
* * *
288652 GGTCAAATTAGTATTTTGTTTAAAATTTAGA
1 GATCAAATTAATATTTTATTTAAAATTTAGA
* * *
288683 AATCAAGTTAA-AATTTATTT
1 GATCAAATTAATATTTTATTT
288703 TTACTAAAGT
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 32 0.49
31 33 0.51
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (31 bp):
GATCAAATTAATATTTTATTTAAAATTTAGA
Found at i:289488 original size:14 final size:14
Alignment explanation
Indices: 289471--289499 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
289461 ATCATTTTAC
289471 GGTGTTTGGATGAT
1 GGTGTTTGGATGAT
289485 GGTGTTTGGATGAT
1 GGTGTTTGGATGAT
289499 G
1 G
289500 TTGTGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (14 bp):
GGTGTTTGGATGAT
Found at i:289597 original size:21 final size:20
Alignment explanation
Indices: 289572--289644 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
289562 TGTACAATAA
289572 ATAATATTATTTATTTAAAAT
1 ATAATATTATTTATTT-AAAT
*
289593 ATAATAATA-TTATTTATAA-
1 ATAATATTATTTATTTA-AAT
*
289612 A-AATATTATAATAATTT--AT
1 ATAATATTAT--TTATTTAAAT
289631 ATAATATTATTTAT
1 ATAATATTATTTAT
289645 GTCAATATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
18 10 0.24
19 3 0.07
20 16 0.38
21 13 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATATTATTTATTTAAAT
Found at i:289600 original size:24 final size:23
Alignment explanation
Indices: 289567--289631 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
289557 CATCATGTAC
*
289567 AATA-AATAATATTATTTATTTAA
1 AATATAATAATATTATTTA-TAAA
289590 AATATAATAATATTATTTATAAA
1 AATATAATAATATTATTTATAAA
*
289613 AATATTATAATA--ATTTATA
1 AATATAATAATATTATTTATA
289632 TAATATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.18
23 18 0.46
24 14 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATAATAATATTATTTATAAA
Found at i:289622 original size:11 final size:11
Alignment explanation
Indices: 289590--289640 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
289580 ATTTATTTAA
*
289590 AATATAATAAT
1 AATATTATAAT
* *
289601 ATTATTTATAAA
1 AATA-TTATAAT
289613 AATATTATAAT
1 AATATTATAAT
289624 AAT-TTAT-AT
1 AATATTATAAT
289633 AATATTAT
1 AATATTAT
289641 TTATGTCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 5 0.15
10 8 0.24
11 12 0.36
12 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATATTATAAT
Found at i:289641 original size:23 final size:25
Alignment explanation
Indices: 289571--289686 Score: 66
Period size: 24 Copynumber: 4.7 Consensus size: 25
289561 ATGTACAATA
**
289571 AATAATATTATTTATTTAAA-A-TAT
1 AATAATATTA-TTATAAAAATATTAT
289595 AATAATATTATTTATAAAAATATTAT
1 AATAATATTA-TTATAAAAATATTAT
* *
289621 AATAAT-TTA-TATAATATTATT-T
1 AATAATATTATTATAAAAATATTAT
* * *
289643 ATGTCAATATTATTATGAACATATTAT
1 A-AT-AATATTATTATAAAAATATTAT
289670 -ATATATAATT-TTATAAA
1 AATA-AT-ATTATTATAAA
289687 TAAAATATTA
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
22 2 0.03
23 11 0.15
24 22 0.31
25 16 0.22
26 20 0.28
27 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AATAATATTATTATAAAAATATTAT
Found at i:289642 original size:14 final size:14
Alignment explanation
Indices: 289572--289697 Score: 53
Period size: 14 Copynumber: 9.7 Consensus size: 14
289562 TGTACAATAA
289572 ATAATATTATTTAT
1 ATAATATTATTTAT
* *
289586 TTAA-A--ATATA-
1 ATAATATTATTTAT
289596 ATAATATTATTTAT
1 ATAATATTATTTAT
*
289610 A-AA-A--ATAT-T
1 ATAATATTATTTAT
289619 ATAATA--ATTTAT
1 ATAATATTATTTAT
289631 ATAATATTATTTAT
1 ATAATATTATTTAT
*
289645 GTCAATATTA-TTAT
1 AT-AATATTATTTAT
*
289659 GA-ACATATTATATAT
1 -ATA-ATATTATTTAT
* **
289674 ATAATTTTATAAAT
1 ATAATATTATTTAT
*
289688 AAAATATTAT
1 ATAATATTAT
289698 GATTATTATA
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
9 2 0.02
10 8 0.09
11 9 0.11
12 8 0.09
13 8 0.09
14 39 0.46
15 11 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
ATAATATTATTTAT
Found at i:290850 original size:21 final size:20
Alignment explanation
Indices: 290826--290864 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
290816 CACTAGAATT
*
290826 TTAAAGGTTATAAAATAATAA
1 TTAAACGTT-TAAAATAATAA
*
290847 TTAAACGTTTTAAATAAT
1 TTAAACGTTTAAAATAAT
290865 TATAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
TTAAACGTTTAAAATAATAA
Found at i:290874 original size:11 final size:11
Alignment explanation
Indices: 290858--290905 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
290848 TAAACGTTTT
290858 AAATAATTATA
1 AAATAATTATA
* *
290869 AAATAATCATT
1 AAATAATTATA
*
290880 AAATTATTATA
1 AAATAATTATA
*
290891 AAATAATTATT
1 AAATAATTATA
290902 AAAT
1 AAAT
290906 TTATGAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATAATTATA
Found at i:290888 original size:22 final size:22
Alignment explanation
Indices: 290856--290906 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
290846 ATTAAACGTT
*
290856 TTAAATAATTATAAAATAATCA
1 TTAAATTATTATAAAATAATCA
*
290878 TTAAATTATTATAAAATAATTA
1 TTAAATTATTATAAAATAATCA
290900 TTAAATT
1 TTAAATT
290907 TATGAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAATTATTATAAAATAATCA
Found at i:295260 original size:56 final size:56
Alignment explanation
Indices: 295195--295307 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
295185 TGCGTAGTGC
*
295195 ACACTTGTTTGAATTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
295251 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
295307 A
1 A
295308 ATTTTAGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (56 bp):
ACACTTGTTTGAACTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCT
Found at i:300281 original size:56 final size:56
Alignment explanation
Indices: 300193--300303 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
300183 CGGAGTGCAC
* *
300193 ACTTGTTTGAATTTATTCTGATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTAT
1 ACTTGTTTGAACTTATTCTAATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTAT
*
300249 ACTTGTTTGAACTTATTCTAATTTGAATTGTTATGTGGTGGTTTTGTAACTGCTA
1 ACTTGTTTGAACTTATTCTAATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTA
300304 ATTTTAGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (56 bp):
ACTTGTTTGAACTTATTCTAATTTGAACTGTTATGTGGTGGTTTTGTAACTGCTAT
Found at i:303178 original size:2 final size:2
Alignment explanation
Indices: 303171--303225 Score: 69
Period size: 2 Copynumber: 27.5 Consensus size: 2
303161 ATGGGAGCAA
*
303171 AT AT AT AT AT AT AT AT AT A- AT CAT AT AT AC AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
303212 CAT AT AT AT AT AT A
1 -AT AT AT AT AT AT A
303226 ATTATTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 2 0.04
2 41 0.87
3 4 0.09
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:303198 original size:20 final size:20
Alignment explanation
Indices: 303173--303225 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
303163 GGGAGCAAAT
303173 ATATATATATATATATAATC
1 ATATATATATATATATAATC
*
303193 ATATATACATATATATAATC
1 ATATATATATATATATAATC
303213 ATATATATATATA
1 ATATATATATATA
303226 ATTATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATATATATATAATC
Found at i:303425 original size:7 final size:7
Alignment explanation
Indices: 303413--303440 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
303403 AATCTTACTA
303413 TGTAAAT
1 TGTAAAT
303420 TGTAAAT
1 TGTAAAT
303427 TGTAAAT
1 TGTAAAT
303434 TGTAAAT
1 TGTAAAT
303441 GAAAGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TGTAAAT
Found at i:307140 original size:21 final size:21
Alignment explanation
Indices: 307102--307142 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
307092 AAACTTTTAT
307102 AACATATAAAAACTTATTCAA
1 AACATATAAAAACTTATTCAA
*
307123 AACATTTACAAAAC-TATTCA
1 AACATATA-AAAACTTATTCA
307143 GAGCTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (21 bp):
AACATATAAAAACTTATTCAA
Found at i:308432 original size:24 final size:20
Alignment explanation
Indices: 308379--308436 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
308369 TTTCCCTTGA
*
308379 AGTGCATCGATGCATTCCAC
1 AGTGCATCGATGCATTCAAC
308399 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC---AAC
308422 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
308437 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:308501 original size:64 final size:64
Alignment explanation
Indices: 308424--308561 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 64
308414 TCTTTAACAT
*
308424 GTGCATCGATGCACTACC-CATGCATCGATACAC-AAAT-CACCTTCGATGTTTTCA-TTTTAAG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACTAAATGCA--TTCGATGTTTCCATTTTTAA-
308485 GGG
62 GGG
* * * *
308488 GTGCATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTCATGCATCGATACACTAAATGCATTCGATGTTTCCATTTTTAAGGG
308552 GTGCATCGAT
1 GTGCATCGAT
308562 ATACTCTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
63 2 0.03
64 52 0.80
65 9 0.14
66 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACTAAATGCATTCGATGTTTCCATTTTTAAGGG
Found at i:310000 original size:21 final size:21
Alignment explanation
Indices: 309971--310010 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
309961 ACCAATCTTC
*
309971 ATTGCATCCTCATAACTTTAG
1 ATTGAATCCTCATAACTTTAG
309992 ATTGAATCCTCATAACTTT
1 ATTGAATCCTCATAACTTT
310011 GGTAACCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTGAATCCTCATAACTTTAG
Found at i:311253 original size:2 final size:2
Alignment explanation
Indices: 311246--311273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
311236 GTCACAAAAC
311246 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
311274 CACATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:316187 original size:20 final size:21
Alignment explanation
Indices: 316153--316194 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
316143 AGCTTTTCGC
316153 TTATGCATTTCGATTTTATTA
1 TTATGCATTTCGATTTTATTA
* *
316174 TTATGTATTT-GATTTTTTTA
1 TTATGCATTTCGATTTTATTA
316194 T
1 T
316195 AAAAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.21, C:0.05, G:0.10, T:0.64
Consensus pattern (21 bp):
TTATGCATTTCGATTTTATTA
Found at i:321975 original size:43 final size:43
Alignment explanation
Indices: 321914--321999 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
321904 TTGCTAAAAG
321914 AAGAATCCTACTTTAACTAATAGCTTGTATCTTTATGATGGTT
1 AAGAATCCTACTTTAACTAATAGCTTGTATCTTTATGATGGTT
321957 AAGAATCCTACTTTAACTAATAGCTTGTATCTTTATGATGGTT
1 AAGAATCCTACTTTAACTAATAGCTTGTATCTTTATGATGGTT
322000 TTACTGAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (43 bp):
AAGAATCCTACTTTAACTAATAGCTTGTATCTTTATGATGGTT
Found at i:332012 original size:12 final size:12
Alignment explanation
Indices: 331995--332019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
331985 CCCACAACCA
331995 ACCTGTAGTATT
1 ACCTGTAGTATT
332007 ACCTGTAGTATT
1 ACCTGTAGTATT
332019 A
1 A
332020 TTCACCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
ACCTGTAGTATT
Found at i:361558 original size:20 final size:19
Alignment explanation
Indices: 361533--361573 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
361523 TCGTTTTTAA
361533 TAAAAAGAAATTTGCAATTT
1 TAAAAAGAAATTT-CAATTT
* *
361553 TAAAAATATATTTCAATTT
1 TAAAAAGAAATTTCAATTT
361572 TA
1 TA
361574 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TAAAAAGAAATTTCAATTT
Found at i:366028 original size:27 final size:28
Alignment explanation
Indices: 365975--366033 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
365965 TGAAATTCAA
* *
365975 TTTATTTTATTAATTATATAATTATAT-
1 TTTATTTTAATAATTATATAATAATATC
*
366002 TTTATTTTAATAATT-TAATACTAATATC
1 TTTATTTTAATAATTAT-ATAATAATATC
366030 TTTA
1 TTTA
366034 AAAAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 22 0.81
28 4 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTATTTTAATAATTATATAATAATATC
Found at i:369842 original size:256 final size:251
Alignment explanation
Indices: 369324--369930 Score: 835
Period size: 256 Copynumber: 2.4 Consensus size: 251
369314 TTTATTCATA
*
369324 TATTGAATAAAAATATTTTTTTATTATTTCGGT--TCGGGTTTCTAATTCATATATGT-GAGTCG
1 TATTGAATAAAAATATTTTTTTATTATTTCGGTCGTC-GGTTTCTAATTCATATAT-TCGGGTCG
*
369386 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTAAGTGTGATATTCGGGTCGGGT
64 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTAAGTGTGATATTAGGGTC-GG-
* *
369451 CGAGCTCGGGTTTACGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTACATATTT
127 CGAGCTCGGGTTTACGGTGAAAAATACCCGACCCGAAAAAATATATAATGTTACCTTACATATTT
* *
369516 AGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCTAATTAAGTCATTGTTTT
192 AGGAATAATTACAATAATACCCCTC-ATATATAATTTTTTTTCCAATTAAATCATTGTTTT
369577 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGATCGGATTTCTAATTCATATATTCGGG
1 TATTGAATAAAAAT-ATTTTTTTATTATTTC-GGTC-G-TCGG-TTTCTAATTCATATATTCGGG
* * *
369642 TCGGGTCGGGTGAAACTTTATTTTGATCGGGTCAGGTCGGGTTTTTTTTAAGTGTGATATTAGGG
61 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC--G-ATTTTTTAAGTGTGATATTAGGG
*
369707 TC-G-G-G-TCGGGTTTA-GTGTGAAAAATACCCGACCCGACCCAAAAAATATATAATGTTATCT
123 TCGGCGAGCTCGGGTTTACG-GTGAAAAATACCCGACCCG----AAAAAATATATAATGTTACCT
*
369767 TATATATTTAGGAATAATTACAATAATACCCCTC-TATAT-ATTTTTTTTCCAATTAAATCATTG
183 TACATATTTAGGAATAATTACAATAATACCCCTCATATATAATTTTTTTTCCAATTAAATCATTG
369830 -TTT
248 TTTT
369833 TATTGAATAAAAATATATTTTTTATTATTTCAGGTCG--GGTTTCTAATTCATATATTCGGGTCG
1 TATTGAATAAAAATAT-TTTTTTATTATTTC-GGTCGTCGGTTTCTAATTCATATATTCGGGTCG
*
369896 GGTCGGGTGAAACTTTACTTTGGTCGGGTCGGGTC
64 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
369931 TCGGATGGAG
Statistics
Matches: 322, Mismatches: 15, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
251 56 0.17
252 2 0.01
253 14 0.04
254 16 0.05
255 7 0.02
256 63 0.20
257 23 0.07
258 9 0.03
259 56 0.17
260 52 0.16
261 1 0.00
262 23 0.07
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (251 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGTCGTCGGTTTCTAATTCATATATTCGGGTCGGG
TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTAAGTGTGATATTAGGGTCGGCGAG
CTCGGGTTTACGGTGAAAAATACCCGACCCGAAAAAATATATAATGTTACCTTACATATTTAGGA
ATAATTACAATAATACCCCTCATATATAATTTTTTTTCCAATTAAATCATTGTTTT
Found at i:372265 original size:19 final size:19
Alignment explanation
Indices: 372241--372278 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
372231 ATGGTATGTA
372241 ATCTTCTTTCAGTGTTTCT
1 ATCTTCTTTCAGTGTTTCT
372260 ATCTTCTTTCAGTGTTTCT
1 ATCTTCTTTCAGTGTTTCT
372279 CTATGGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.58
Consensus pattern (19 bp):
ATCTTCTTTCAGTGTTTCT
Found at i:377817 original size:20 final size:21
Alignment explanation
Indices: 377790--377849 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 21
377780 TATTTCCGCA
377790 TCCTTCTCTCTGCAAAGAACC
1 TCCTTCTCTCTGCAAAGAACC
377811 T-CTTCTCTCTGCAAAGAACC
1 TCCTTCTCTCTGCAAAGAACC
*
377831 TCCTTCTCTC-GCAATGAAC
1 TCCTTCTCTCTGCAAAGAAC
377850 ACCTTCAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 28 0.76
21 9 0.24
ACGTcount: A:0.23, C:0.37, G:0.10, T:0.30
Consensus pattern (21 bp):
TCCTTCTCTCTGCAAAGAACC
Found at i:379944 original size:21 final size:21
Alignment explanation
Indices: 379918--379964 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
379908 ACTATCGCAA
379918 TGCGATTTT-CCAATTTCGAAT
1 TGCGATTTTCCCAA-TTCGAAT
*
379939 TGCGATTTTCCCAATTCGCAT
1 TGCGATTTTCCCAATTCGAAT
379960 TGCGA
1 TGCGA
379965 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TGCGATTTTCCCAATTCGAAT
Found at i:379983 original size:20 final size:21
Alignment explanation
Indices: 379954--380005 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
379944 TTTTCCCAAT
* *
379954 TCGCATTGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
379974 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
379995 TCGCAATGCGA
1 TCGCAATGCGA
380006 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:379984 original size:41 final size:41
Alignment explanation
Indices: 379939--380148 Score: 113
Period size: 41 Copynumber: 5.1 Consensus size: 41
379929 AATTTCGAAT
* *
379939 TGCGATTTTCCCAATTCGCATTGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
379980 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
380021 TGCAATTTTCCTAATTCGCATTACGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
380062 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
** *** * * *
380103 CCCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
380144 TGCGA
1 TGCGA
380149 ATACGTAAAT
Statistics
Matches: 121, Mismatches: 41, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
39 2 0.02
40 25 0.21
41 92 0.76
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:380049 original size:21 final size:21
Alignment explanation
Indices: 380025--380081 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
380015 TCGCAATGCA
*
380025 ATTTTCCTAATTCGCATTACG
1 ATTTTCATAATTCGCATTACG
* * * *
380046 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTACG
380066 ATTTTCATAATTCGCA
1 ATTTTCATAATTCGCA
380082 ATGCGAATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTACG
Found at i:380086 original size:21 final size:21
Alignment explanation
Indices: 380015--380087 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
380005 ATACTGACTA
* *
380015 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * * *
380036 TCGCATTACGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
380056 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
380077 TCGCAATGCGA
1 TCGCAATGCGA
380088 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:380102 original size:20 final size:20
Alignment explanation
Indices: 380077--380168 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
380067 TTTTCATAAT
380077 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** * *
380097 TCGCAACCCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
380117 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
380138 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
380158 TCGCAATGCGA
1 TCGCAATGCGA
380169 TTTACATAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 42 0.70
21 18 0.30
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:380157 original size:41 final size:40
Alignment explanation
Indices: 380077--380168 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
380067 TTTTCATAAT
* *
380077 TCGCAATGCGAATACGTAAATCGCAACCCGATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACCCGAATAAGTAAA
* ** *
380117 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACCCGAATAAGTAAA
380158 TCGCAATGCGA
1 TCGCAATGCGA
380169 TTTACATAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 12 0.27
41 33 0.73
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACCCGAATAAGTAAA
Found at i:380736 original size:19 final size:20
Alignment explanation
Indices: 380694--380747 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
380684 TAGTTTCGAG
*
380694 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACACGGA
**
380714 AATGACTATCGCAACAC-GA
1 AATGAAAATCGCAACACGGA
380733 AATGAAAATCGCAAC
1 AATGAAAATCGCAAC
380748 GAGATAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACACGGA
Found at i:380815 original size:14 final size:14
Alignment explanation
Indices: 380796--380851 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
380786 TTTCATTTCA
380796 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
380810 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
380829 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
380843 CGTTGCGAT
1 CGTTGCGAT
380852 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:380821 original size:33 final size:33
Alignment explanation
Indices: 380779--380860 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
380769 CAAAATCGCA
380779 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
380812 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
**
380845 TTGCGATAGTCATTTC
1 TTGCGATTTTCATTTC
380861 CGCATTGCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:381743 original size:12 final size:12
Alignment explanation
Indices: 381726--381750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
381716 TCTTCGGGGA
381726 CTTTTTCTTCTT
1 CTTTTTCTTCTT
381738 CTTTTTCTTCTT
1 CTTTTTCTTCTT
381750 C
1 C
381751 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:381952 original size:24 final size:24
Alignment explanation
Indices: 381925--381978 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
381915 CTGAAACACC
*
381925 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* * *
381949 ATCACAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
381973 ATCAAA
1 ATCAAA
381979 TTTCGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:382748 original size:20 final size:20
Alignment explanation
Indices: 382723--382809 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
382713 TGTATTATCT
* *
382723 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
* *
382743 CATTGCGAAAATCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
382763 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
382783 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
382803 C-TTGCGA
1 CGTTGCGA
382810 TTTTGTATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 6 0.10
20 54 0.90
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:382830 original size:21 final size:21
Alignment explanation
Indices: 382798--382916 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 21
382788 CGAAAGTCAG
382798 TATCGC-TTGCGATTTTGTAT
1 TATCGCATTGCGATTTTGTAT
* * *
382818 TATCGCGTTGCGA--TAGTCAG
1 TATCGCATTGCGATTTTGT-AT
**
382838 TATCGCATTGCGATTTTCCA-
1 TATCGCATTGCGATTTTGTAT
*
382858 AATTCGCATTGCGATTTTGTAT
1 TA-TCGCATTGCGATTTTGTAT
* * *
382880 TATCGCGTTGCGA--TAGTCAG
1 TATCGCATTGCGATTTTGT-AT
382900 TATCGCATTGCGATTTT
1 TATCGCATTGCGATTTT
382917 CCAAATTCGT
Statistics
Matches: 75, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
19 6 0.08
20 33 0.44
21 33 0.44
22 3 0.04
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
TATCGCATTGCGATTTTGTAT
Found at i:382870 original size:41 final size:40
Alignment explanation
Indices: 382779--382872 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
382769 GAAAGTCAGA
* ** *
382779 ATCGCGTTGCGAAAGTCAGTATCGCTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCTTGCGATTTTCAAAT
382819 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGC-TTGCGATTTT-CAAAT
*
382861 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
382873 TTTGTATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 24 0.51
41 21 0.45
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
ATCGCGTTGCGATAGTCAGTATCGCTTGCGATTTTCAAAT
Found at i:382890 original size:62 final size:62
Alignment explanation
Indices: 382800--382936 Score: 258
Period size: 62 Copynumber: 2.2 Consensus size: 62
382790 AAAGTCAGTA
382800 TCGC-TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
382861 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
*
382923 TCGTATTGCGATTT
1 TCGCATTGCGATTT
382937 ATTTATTCGC
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 4 0.05
62 70 0.95
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:382967 original size:62 final size:62
Alignment explanation
Indices: 382800--382968 Score: 191
Period size: 62 Copynumber: 2.7 Consensus size: 62
382790 AAAGTCAGTA
* * **
382800 TCGC-TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCATTGCGATAGGCAAAATCGCATTGCGATTTTCCAAAT
* * **
382861 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCATTGCGATAGGCAAAATCGCATTGCGATTTTCCAAAT
* * * *
382923 TCGTATTGCGA-TTTAT-TTATTCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCGATTTTGTATTA-TCGCATTGCG-ATAGGCAAAATCGCA
382969 ACGCGAAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
60 3 0.03
61 17 0.18
62 77 0.79
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCATTGCGATAGGCAAAATCGCATTGCGATTTTCCAAAT
Found at i:382995 original size:21 final size:22
Alignment explanation
Indices: 382943--382995 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
382933 ATTTATTTAT
382943 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
382964 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
382985 TCGCATTGCGA
1 TCGCATTGCGA
382996 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:384277 original size:18 final size:18
Alignment explanation
Indices: 384254--384289 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
384244 GTTCTTAAGG
*
384254 AGTGGTCCTTCAGGACAT
1 AGTGGTCATTCAGGACAT
*
384272 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCAGGACAT
384290 TTCTACGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCATTCAGGACAT
Found at i:386138 original size:15 final size:15
Alignment explanation
Indices: 386118--386148 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
386108 CCGATGATCA
*
386118 ACCAGGTTTCTGGTG
1 ACCAGGTTTCCGGTG
386133 ACCAGGTTTCCGGTG
1 ACCAGGTTTCCGGTG
386148 A
1 A
386149 GATCCGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (15 bp):
ACCAGGTTTCCGGTG
Found at i:394529 original size:18 final size:17
Alignment explanation
Indices: 394508--394543 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
394498 TCTCGGTCAC
394508 TGATTCTTAGGGAGTTGT
1 TGATTCTTAGGGA-TTGT
*
394526 TGATTTTTAGGGATTGT
1 TGATTCTTAGGGATTGT
394543 T
1 T
394544 TCCTTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.03, G:0.31, T:0.50
Consensus pattern (17 bp):
TGATTCTTAGGGATTGT
Found at i:400354 original size:19 final size:20
Alignment explanation
Indices: 400321--400359 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
400311 AGCAACAGAA
*
400321 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
400341 TAAAAAT-ATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
400360 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:400402 original size:20 final size:21
Alignment explanation
Indices: 400373--400412 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
400363 TAATAGAATA
*
400373 AAAAATTGATTCTATCTAATT
1 AAAAATTGATCCTATCTAATT
400394 AAAAA-TGATCCTATCTAAT
1 AAAAATTGATCCTATCTAAT
400413 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAATTGATCCTATCTAATT
Found at i:400421 original size:53 final size:52
Alignment explanation
Indices: 400317--400518 Score: 345
Period size: 53 Copynumber: 3.9 Consensus size: 52
400307 AATTAGCAAC
400317 AGAATAAAAA-TGATTCTATCTAATTAAAAAT-ATCCTATCTAATAACTAAT
1 AGAATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
400367 AGAATAAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
400420 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
400473 AGAATAAAAATTGATTCTATCTAATTAAAACTGATCTTATCTAATA
1 AGAATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATA
400519 TTTAATTTAG
Statistics
Matches: 145, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
50 5 0.03
51 5 0.03
52 59 0.41
53 76 0.52
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (52 bp):
AGAATAAAAATTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:400445 original size:105 final size:103
Alignment explanation
Indices: 400317--400518 Score: 352
Period size: 105 Copynumber: 1.9 Consensus size: 103
400307 AATTAGCAAC
400317 AGAATAAAAATGATTCTATCTAATTAAAAAT-ATCCTATCTAATAACTAATAGAATAAAAAATTG
1 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAAT-AAAAATTG
400381 ATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
65 ATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
400420 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAATAAAAATT
1 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAATAAAAATT
* *
400485 GATTCTATCTAATTAAAACTGATCTTATCTAATA
64 GATTCTATCTAATTAAAAATGATCCTATCTAATA
400519 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 5 0.05
104 5 0.05
105 60 0.64
106 24 0.26
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (103 bp):
AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAGAATAAAAATTGA
TTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:400455 original size:20 final size:21
Alignment explanation
Indices: 400426--400465 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
400416 TAATAGAATA
*
400426 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
400447 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
400466 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:405079 original size:20 final size:20
Alignment explanation
Indices: 405054--405093 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
405044 AGCAACAGAA
*
405054 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
405074 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
405094 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:405136 original size:20 final size:21
Alignment explanation
Indices: 405107--405146 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
405097 TAATAGAATA
405107 AAAAACTGAT-TCTATCTAATT
1 AAAAACTGATCT-TATCTAATT
405128 AAAAA-TGATCTTATCTAAT
1 AAAAACTGATCTTATCTAAT
405147 AACTAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAACTGATCTTATCTAATT
Found at i:405188 original size:20 final size:20
Alignment explanation
Indices: 405160--405198 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
405150 TAATAGAATA
*
405160 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
*
405180 AAAATTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
405199 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:405189 original size:52 final size:52
Alignment explanation
Indices: 405050--405199 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
405040 AATTAGCAAC
405050 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
405101 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCTTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
405154 AGAATAAAAACTGATTCTATCTAATTAAAATTGATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
405200 TTTAATTTAG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.47
53 45 0.48
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:410326 original size:6 final size:6
Alignment explanation
Indices: 410312--410354 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
410302 TCAAGGAAAT
*
410312 TAAAAA TAAAGA TAAAGA TAAAGA TAACAAAGA TAAAGA TAAA
1 TAAAGA TAAAGA TAAAGA TAAAGA T---AAAGA TAAAGA TAAA
410355 ATACAATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 27 0.82
9 6 0.18
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (6 bp):
TAAAGA
Found at i:410345 original size:15 final size:15
Alignment explanation
Indices: 410325--410353 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
410315 AAATAAAGAT
410325 AAAGATAAAGATAAC
1 AAAGATAAAGATAAC
410340 AAAGATAAAGATAA
1 AAAGATAAAGATAA
410354 AATACAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAGATAAAGATAAC
Found at i:410413 original size:13 final size:13
Alignment explanation
Indices: 410395--410421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
410385 CATAGTTGAA
410395 CAGTCTTCGTATG
1 CAGTCTTCGTATG
410408 CAGTCTTCGTATG
1 CAGTCTTCGTATG
410421 C
1 C
410422 GTGTTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (13 bp):
CAGTCTTCGTATG
Found at i:420412 original size:29 final size:30
Alignment explanation
Indices: 420348--420418 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
420338 AATTTATTTG
*
420348 TTATTATTATGAGTCTAATTTTCCAGTACT
1 TTATTATTATGAGTCTAATTTTCCAATACT
* *
420378 TT-TTATTA-GAAGTCTATTTTTTCAATA-T
1 TTATTATTATG-AGTCTAATTTTCCAATACT
420406 TTATTATTATGAG
1 TTATTATTATGAG
420419 CATACTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 4 0.11
29 28 0.80
30 3 0.09
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (30 bp):
TTATTATTATGAGTCTAATTTTCCAATACT
Found at i:423261 original size:20 final size:20
Alignment explanation
Indices: 423213--423261 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
423203 CAAAATTCGC
*
423213 GTTGCGAATTTGAAAACTGG
1 GTTGCGAATTTGAAAACTGA
*
423233 GTTACGAATTTGAAAACTGA
1 GTTGCGAATTTGAAAACTGA
*
423253 GTTGTGAAT
1 GTTGCGAAT
423262 AGTTGTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAAACTGA
Found at i:423287 original size:98 final size:98
Alignment explanation
Indices: 423139--423329 Score: 303
Period size: 98 Copynumber: 1.9 Consensus size: 98
423129 ATTCGCGTTC
*
423139 CGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACTTATATCGGTAATTAGCGTTGCGAA-AA
1 CGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAATAA
423203 CAAAATTCGCGTTGCGAATTTGAAAACTGGGTTA
66 CAAAA-TCGCGTTGCGAATTTGAAAACTGGGTTA
* * * **
423237 CGAATTTGAAAACTGAGTTGTGAATAGTTGTGTTTACCTATATCGTTAATTAGCGTTGTGAATTT
1 CGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAATAA
*
423302 GAAAATCGCGTTGCGAATTTGAAAACTG
66 CAAAATCGCGTTGCGAATTTGAAAACTG
423330 AGTTGTGAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
98 81 0.95
99 4 0.05
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (98 bp):
CGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAATAA
CAAAATCGCGTTGCGAATTTGAAAACTGGGTTA
Found at i:423300 original size:78 final size:78
Alignment explanation
Indices: 423206--423417 Score: 291
Period size: 78 Copynumber: 2.7 Consensus size: 78
423196 GCGAAAACAA
* *
423206 AATTCGCGTTGCGAATTTGAAAA-CTGGGTTACGAATTTGAAAACTGAGTTGTGAATAGTTGTGT
1 AATTAGCGTTGCGAATTTGAAAATC-GCGTTACGAATTTGAAAACTGAGTTGTGAATAGTTGTGT
*
423270 TTACCTATATCGTT
65 TTACCTATATCGGT
* *
423284 AATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAATTTGAAAACTGAGTTGTGAATAGTTGTGTT
1 AATTAGCGTTGCGAATTTGAAAATCGCGTTACGAATTTGAAAACTGAGTTGTGAATAGTTGTGTT
423349 TACCTATATCGGT
66 TACCTATATCGGT
* * * * * * *
423362 AATTAGCGATACGAATTTGGAGAATCGCGTTGCGAATTTGGAAAGTGTGTTGTGAA
1 AATTAGCGTTGCGAATTT-GAAAATCGCGTTACGAATTTGAAAACTGAGTTGTGAA
423418 ATTGGAGTTC
Statistics
Matches: 120, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 86 0.72
79 34 0.28
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (78 bp):
AATTAGCGTTGCGAATTTGAAAATCGCGTTACGAATTTGAAAACTGAGTTGTGAATAGTTGTGTT
TACCTATATCGGT
Found at i:423314 original size:20 final size:20
Alignment explanation
Indices: 423289--423339 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
423279 TCGTTAATTA
423289 GCGTTGTGAATTTGAAAA-T
1 GCGTTGTGAATTTGAAAACT
*
423308 CGCGTTGCGAATTTGAAAACT
1 -GCGTTGTGAATTTGAAAACT
*
423329 GAGTTGTGAAT
1 GCGTTGTGAAT
423340 AGTTGTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.33
Consensus pattern (20 bp):
GCGTTGTGAATTTGAAAACT
Found at i:423399 original size:21 final size:21
Alignment explanation
Indices: 423373--423440 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
423363 ATTAGCGATA
423373 CGAATTTGGAGAATCGCGTTG
1 CGAATTTGGAGAATCGCGTTG
*
423394 CGAATTTGGA-AAGT-GTGTTG
1 CGAATTTGGAGAA-TCGCGTTG
* * *
423414 TGAAATTGGAG-TTCGCGTTG
1 CGAATTTGGAGAATCGCGTTG
423434 CGAATTT
1 CGAATTT
423441 TTTGGTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
19 1 0.03
20 25 0.68
21 11 0.30
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (21 bp):
CGAATTTGGAGAATCGCGTTG
Found at i:423637 original size:21 final size:20
Alignment explanation
Indices: 423611--423687 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 20
423601 AAAACGAAAT
423611 TCGCGTTGCGAATTTAGAGAA
1 TCGCGTTGCGAATTT-GAGAA
*
423632 TCGCGTTGCAAATTTG-GAA
1 TCGCGTTGCGAATTTGAGAA
* * *
423651 ACTGTGTTGCGAAATTG-GAGA
1 TC-GCGTTGCGAATTTGAGA-A
423672 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
423688 TTGGTTATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.09
20 26 0.57
21 16 0.35
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGAGAA
Found at i:424413 original size:39 final size:39
Alignment explanation
Indices: 424367--424461 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
424357 GACTCCTATG
* *
424367 CTTTGTGCACAGGGTGAGTTCTTATTGCAAGCTCCTCAA
1 CTTTGTGCACAGGGTAAGTCCTTATTGCAAGCTCCTCAA
* * **
424406 CTTTGTGCATAGGGTAAGTCCTTATTGCATGCTCCTCTG
1 CTTTGTGCACAGGGTAAGTCCTTATTGCAAGCTCCTCAA
*
424445 TTTTGTGCACAGGGTAA
1 CTTTGTGCACAGGGTAA
424462 ACCTTACCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (39 bp):
CTTTGTGCACAGGGTAAGTCCTTATTGCAAGCTCCTCAA
Found at i:426890 original size:16 final size:16
Alignment explanation
Indices: 426871--426904 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
426861 CAATATACGA
426871 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
426887 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
426903 AT
1 AT
426905 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:426979 original size:16 final size:18
Alignment explanation
Indices: 426948--426980 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
426938 ATTAATGTAA
426948 GAATCATTTATATTTTTT
1 GAATCATTTATATTTTTT
426966 GAAT-ATTT-TATTTTT
1 GAATCATTTATATTTTT
426981 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
GAATCATTTATATTTTTT
Found at i:427653 original size:130 final size:130
Alignment explanation
Indices: 427449--427696 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
427439 AATTTTCTTC
* *
427449 TAATTAGGTGGTGACACGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
427514 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
427579 TAATTAGGTGGTGACATGTGTCACCAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
427644 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGATCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
427697 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:428143 original size:35 final size:35
Alignment explanation
Indices: 428093--428168 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
428083 AATTGAATTT
* *
428093 AATTGAATTATTTTGGAATTTAGGGTTTAGAATAA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
* *
428128 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
428163 AATTGA
1 AATTGA
428169 TGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
Found at i:435825 original size:22 final size:23
Alignment explanation
Indices: 435799--435865 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 23
435789 AACGCAAAAA
435799 TATTATAATAAAAATATATAA-T
1 TATTATAATAAAAATATATAATT
* *
435821 TATTA-CATAGGAAATATATTAATT
1 TATTATAATA-AAAATATA-TAATT
*
435845 TAAACTATAATAAAAATATAT
1 T--ATTATAATAAAAATATAT
435866 TTTATAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
21 3 0.09
22 12 0.35
23 3 0.09
24 2 0.06
25 1 0.03
26 10 0.29
27 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (23 bp):
TATTATAATAAAAATATATAATT
Found at i:439124 original size:20 final size:22
Alignment explanation
Indices: 439099--439138 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
439089 AGTCGTATAT
439099 AGCCG-TTGGGGA-TGTTTTGG
1 AGCCGTTTGGGGATTGTTTTGG
439119 AGCCGTTTGGGGATTGTTTT
1 AGCCGTTTGGGGATTGTTTT
439139 TCTGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (22 bp):
AGCCGTTTGGGGATTGTTTTGG
Found at i:439370 original size:20 final size:20
Alignment explanation
Indices: 439325--439370 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
439315 TGTTCATTAA
* *
439325 TATTCAAACAGTATCGGTAT
1 TATTCAAACAGTATCAGTAC
* *
439345 TGTTCACACAGTATCAGTAC
1 TATTCAAACAGTATCAGTAC
439365 TATTCA
1 TATTCA
439371 TATAATACAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
TATTCAAACAGTATCAGTAC
Found at i:441698 original size:20 final size:20
Alignment explanation
Indices: 441673--441728 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
441663 GTGAAAGTTG
441673 TCCCGAAGGACCTATGTATA
1 TCCCGAAGGACCTATGTATA
* * *
441693 TCCCGAAGGATCTCTGTATG
1 TCCCGAAGGACCTATGTATA
* *
441713 TCTCGAAAGACCTATG
1 TCCCGAAGGACCTATG
441729 AACCCTCGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
TCCCGAAGGACCTATGTATA
Found at i:456043 original size:20 final size:20
Alignment explanation
Indices: 456018--456073 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
456008 GTGAAAGTTG
456018 TCCCGAAGGACCTATGTATA
1 TCCCGAAGGACCTATGTATA
* * *
456038 TCCCGAAGGATCTCTGTATG
1 TCCCGAAGGACCTATGTATA
* *
456058 TCTCGAAAGACCTATG
1 TCCCGAAGGACCTATG
456074 AACCCTCGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
TCCCGAAGGACCTATGTATA
Found at i:456877 original size:65 final size:64
Alignment explanation
Indices: 456808--456930 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
456798 ACATAAATCT
** * * *
456808 CATTCGATGTTTATATTTTAAGGGGAGTGCATCGATGCACTACTTGCACATCGATACACTGATAG
1 CATTCGACATTTATATTTTAA-AGGAGTGCATCGATACACTACATGCACATCGATACACTGATAG
* * **
456873 CATTCGACATTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCGACATTTATATTTTAAAGGAGTGCATCGATACACTACATGCACATCGATACAC
456931 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
64 31 0.63
65 18 0.37
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
CATTCGACATTTATATTTTAAAGGAGTGCATCGATACACTACATGCACATCGATACACTGATAG
Found at i:459539 original size:15 final size:15
Alignment explanation
Indices: 459519--459555 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
459509 CGCCCTGCAT
459519 CCGCCCCGTATCCAC
1 CCGCCCCGTATCCAC
**
459534 CCGCCCCGTATCTGC
1 CCGCCCCGTATCCAC
459549 CCGCCCC
1 CCGCCCC
459556 ACATCCGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.62, G:0.16, T:0.14
Consensus pattern (15 bp):
CCGCCCCGTATCCAC
Found at i:463744 original size:3 final size:3
Alignment explanation
Indices: 463736--463814 Score: 74
Period size: 3 Copynumber: 26.3 Consensus size: 3
463726 TTAAATAAGA
* * * *
463736 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT ATT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
463782 AAT AAAT AAT AAT AAT AAT -AT AAT AAT -AT AAT A
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
463815 TATATATAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 47 0.76
4 9 0.15
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:463785 original size:37 final size:35
Alignment explanation
Indices: 463735--463851 Score: 69
Period size: 37 Copynumber: 3.2 Consensus size: 35
463725 ATTAAATAAG
*
463735 AAATAATAATAATAAATAAAATAATTACAATA-ATAAT
1 AAATAATAATAAT-AATATAATAA-TA-AATATATAAT
* *
463772 AAATGATATTAATAA-ATAATAAT-AATAATATAAT
1 AAATAATAATAATAATATAATAATAAAT-ATATAAT
** * *
463806 AATATAATATATATATAAATATTTTAAAAAACATATAAT
1 AA-ATAATA-ATA-AT-AATATAATAATAAATATATAAT
*
463845 ATATAAT
1 AAATAAT
463852 TTCCAAAATG
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
32 3 0.05
33 1 0.02
34 8 0.13
35 11 0.18
36 4 0.06
37 13 0.21
38 7 0.11
39 13 0.21
40 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (35 bp):
AAATAATAATAATAATATAATAATAAATATATAAT
Found at i:463812 original size:13 final size:14
Alignment explanation
Indices: 463736--463816 Score: 91
Period size: 13 Copynumber: 6.1 Consensus size: 14
463726 TTAAATAAGA
463736 AATAATAATAATA-
1 AATAATAATAATAT
*
463749 AATAA-AATAATTAC
1 AATAATAATAA-TAT
463763 AATAATAATAA-AT
1 AATAATAATAATAT
* *
463776 GATATTAATAA-AT
1 AATAATAATAATAT
463789 AATAATAATAATAT
1 AATAATAATAATAT
463803 AATAAT-ATAATAT
1 AATAATAATAATAT
463816 A
1 A
463817 TATATAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.08
13 36 0.61
14 13 0.22
15 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (14 bp):
AATAATAATAATAT
Done.