Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015262.1 Kokia drynarioides strain JFW-HI SEQ_130307, 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: 411148
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 200 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9991 original size:17 final size:17
Alignment explanation
Indices: 9969--10003 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
9959 GTCCGGTAAG
9969 TTCGTATGGTTAAATTC
1 TTCGTATGGTTAAATTC
9986 TTCGTATGGTTAAATTC
1 TTCGTATGGTTAAATTC
10003 T
1 T
10004 AACTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (17 bp):
TTCGTATGGTTAAATTC
Found at i:10200 original size:51 final size:50
Alignment explanation
Indices: 10124--10352 Score: 232
Period size: 51 Copynumber: 4.5 Consensus size: 50
10114 CGAAAGGGTT
* *
10124 CGATGACTAAGAGTCATCGTGAGTAAATGAATCCTTTACAAATTAGAAGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTA-AAGTC
* * *
10175 CGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTAAAAGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT-AAAGTC
* * * *
10226 CGATGACTAAGTGTCATTGTGAGTAAATGAATCCATGATGAATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAA-GTC
** * *
10277 CGATGACTCTGTGTCATCGTGAGT--ATGAATTCCTATACGGAA-CAAGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTAC-GAATTAA-A-GTC
*
10328 CAATGACTATA-TGTCATCGTGAGTA
1 CGATGACTA-AGTGTCATCGTGAGTA
10353 TTAAATGAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
49 5 0.03
50 9 0.06
51 133 0.90
52 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (50 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAGTC
Found at i:10300 original size:102 final size:101
Alignment explanation
Indices: 10121--10317 Score: 263
Period size: 102 Copynumber: 1.9 Consensus size: 101
10111 AAACGAAAGG
* *
10121 GTTCGATGACTAAGAGTCATCGTGAGTAAATGAATCCTTTACAAATTAGAAGTCCGATGACTAAG
1 GTTCGATGACTAAGAGTCATCGTGAGTAAATGAATCCATGACAAATTAGAAGTCCGATGACTAAG
*
10186 TGTCATCATGAGTAAATGAA-TCCTTTACGGATTAAAA
66 TGTCATCATGAGT--ATGAATTCCTATACGGATTAAAA
* * ** **
10223 GTTCGATGACTAAGTGTCATTGTGAGTAAATGAATCCATGATGAATTA-AAGGTCCGATGACTCT
1 GTTCGATGACTAAGAGTCATCGTGAGTAAATGAATCCATGACAAATTAGAA-GTCCGATGACTAA
*
10287 GTGTCATCGTGAGTATGAATTCCTATACGGA
65 GTGTCATCATGAGTATGAATTCCTATACGGA
10318 ACAAGAGGTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 5 0.06
101 12 0.14
102 66 0.80
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (101 bp):
GTTCGATGACTAAGAGTCATCGTGAGTAAATGAATCCATGACAAATTAGAAGTCCGATGACTAAG
TGTCATCATGAGTATGAATTCCTATACGGATTAAAA
Found at i:11098 original size:21 final size:21
Alignment explanation
Indices: 11071--11130 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
11061 TAAATGCATG
*
11071 ACATGTATCGGTAGAAATTAT
1 ACATGTATCGGTAGAAATAAT
* *
11092 ACTTGTATCGGTAGAACTAAT
1 ACATGTATCGGTAGAAATAAT
* *
11113 ACAGGTACCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
11131 CTGCATTGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (21 bp):
ACATGTATCGGTAGAAATAAT
Found at i:12809 original size:43 final size:43
Alignment explanation
Indices: 12724--12815 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
12714 AAGCTTTGGG
* **
12724 ATGAGAATTTATATTAAAGGAAGACTCATGTCTCGAGTTGAGC
1 ATGAGAATTTATATTAAAGGAAGACTCATGTCTCAAAATGAGC
*
12767 ATGAGAATTTATATTAAAGGAAGATTCATGTCTCAAAATGAGC
1 ATGAGAATTTATATTAAAGGAAGACTCATGTCTCAAAATGAGC
*
12810 GTGAGA
1 ATGAGA
12816 TTTGTTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (43 bp):
ATGAGAATTTATATTAAAGGAAGACTCATGTCTCAAAATGAGC
Found at i:12884 original size:40 final size:40
Alignment explanation
Indices: 12827--12922 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
12817 TTGTTTTTAT
* *
12827 AAAGGAAGACTTATGACTCGGTAGAGCATAAGAGTGATTA
1 AAAGGAAGACTTATGACTCGGTAAAGCATAAGAGTAATTA
* * *
12867 AAAGGAAGACTTGTGACTCGGTAAAGCATAAGATTAATTC
1 AAAGGAAGACTTATGACTCGGTAAAGCATAAGAGTAATTA
12907 AAAGGAAGACTTATGA
1 AAAGGAAGACTTATGA
12923 ACCTATGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (40 bp):
AAAGGAAGACTTATGACTCGGTAAAGCATAAGAGTAATTA
Found at i:15382 original size:24 final size:24
Alignment explanation
Indices: 15346--15395 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15336 TTCATACAAT
* * *
15346 TTTTTTTAATTTTAAATATTTTTA
1 TTTTTATAATTTTAAAAATATTTA
*
15370 TTTTTATATTTTTAAAAATATTTA
1 TTTTTATAATTTTAAAAATATTTA
15394 TT
1 TT
15396 AATATGACAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTATAATTTTAAAAATATTTA
Found at i:19209 original size:28 final size:28
Alignment explanation
Indices: 19177--19234 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
19167 GAGTTAAATA
19177 TTTAATAA-TATTATTTTAATTCATAATT
1 TTTAA-AATTATTATTTTAATTCATAATT
*
19205 TTTAAAATTATTATTTTAATTTATAATT
1 TTTAAAATTATTATTTTAATTCATAATT
19233 TT
1 TT
19235 AATTGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTAAAATTATTATTTTAATTCATAATT
Found at i:19769 original size:12 final size:12
Alignment explanation
Indices: 19747--19805 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
19737 TTTGGTTCTG
*
19747 TTTTTGCTGTTA
1 TTTTTGTTGTTA
* *
19759 TTATTGTTGTTG
1 TTTTTGTTGTTA
*
19771 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
19783 TTTTTGTTATT-
1 TTTTTGTTGTTA
19794 TTTGTTGTTGTT
1 TTT-TTGTTGTT
19806 TTGATTTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 3 0.08
12 34 0.92
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.71
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:19769 original size:21 final size:22
Alignment explanation
Indices: 19745--19802 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
19735 ATTTTGGTTC
19745 TGTTTTTGCTGTTATTATTGTTGT
1 TGTTTTTGCTGTTATTA-T-TTGT
19769 TGTTTTTGCTGTTATT-TTTGT
1 TGTTTTTGCTGTTATTATTTGT
* *
19790 TATTTTTGTTGTT
1 TGTTTTTGCTGTT
19803 GTTTTGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 15 0.47
22 1 0.03
24 16 0.50
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.71
Consensus pattern (22 bp):
TGTTTTTGCTGTTATTATTTGT
Found at i:19772 original size:24 final size:24
Alignment explanation
Indices: 19745--19790 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
19735 ATTTTGGTTC
19745 TGTTTTTGCTGTTATTATTGTTGT
1 TGTTTTTGCTGTTATTATTGTTGT
*
19769 TGTTTTTGCTGTTATTTTTGTT
1 TGTTTTTGCTGTTATTATTGTT
19791 ATTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.70
Consensus pattern (24 bp):
TGTTTTTGCTGTTATTATTGTTGT
Found at i:19781 original size:33 final size:33
Alignment explanation
Indices: 19744--19807 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
19734 TATTTTGGTT
19744 CTGTT-TTTGCTGTTATTATTGTTGTTGTTTTTG
1 CTGTTATTT-CTGTTATTATTGTTGTTGTTTTTG
* *
19777 CTGTTATTTTTGTTATTTTTGTTGTTGTTTT
1 CTGTTATTTCTGTTATTATTGTTGTTGTTTT
19808 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.06, C:0.05, G:0.19, T:0.70
Consensus pattern (33 bp):
CTGTTATTTCTGTTATTATTGTTGTTGTTTTTG
Found at i:19807 original size:21 final size:21
Alignment explanation
Indices: 19747--19807 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
19737 TTTGGTTCTG
*
19747 TTTTTGCTGTTATTATTGTTGTTG
1 TTTTTGCTGTTA-T-TT-TTGTTA
19771 TTTTTGCTGTTATTTTTGTTA
1 TTTTTGCTGTTATTTTTGTTA
* *
19792 TTTTTGTTGTTGTTTT
1 TTTTTGCTGTTATTTT
19808 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.56
22 2 0.06
23 1 0.03
24 12 0.35
ACGTcount: A:0.07, C:0.03, G:0.18, T:0.72
Consensus pattern (21 bp):
TTTTTGCTGTTATTTTTGTTA
Found at i:19826 original size:33 final size:33
Alignment explanation
Indices: 19756--19829 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
19746 GTTTTTGCTG
* * *
19756 TTATTATTGTTGTTGTTTTTGCTGTTATTTTTG
1 TTATTTTTGTTGTTGTTTTTGATGTTATTTTTA
* *
19789 TTATTTTTGTTGTTG-TTTTGATTTTTTTTTATA
1 TTATTTTTGTTGTTGTTTTTGATGTTATTTT-TA
19822 TTATTTTT
1 TTATTTTT
19830 TAAGCGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.11, C:0.01, G:0.14, T:0.74
Consensus pattern (33 bp):
TTATTTTTGTTGTTGTTTTTGATGTTATTTTTA
Found at i:19830 original size:23 final size:23
Alignment explanation
Indices: 19804--19873 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
19794 TTTGTTGTTG
19804 TTTTGATTTTTTTTTATATTATT
1 TTTTGATTTTTTTTTATATTATT
****
19827 TTTT-AAGCGTTTTTACTATTATT
1 TTTTGATTTTTTTTTA-TATTATT
* *
19850 TCGTTG-TTTTTTTTAATATTATT
1 T-TTTGATTTTTTTTTATATTATT
19873 T
1 T
19874 GAATATTGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
22 7 0.21
23 20 0.59
24 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTTGATTTTTTTTTATATTATT
Found at i:23794 original size:23 final size:23
Alignment explanation
Indices: 23763--23978 Score: 324
Period size: 23 Copynumber: 9.4 Consensus size: 23
23753 TCTTATATCC
23763 GTGCTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
23786 ATGCTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
*
23809 GTGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
*
23832 GTGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
23855 ATGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTT
*
23878 GTGCTCAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* *
23901 ATGCTAAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
* * *
23924 GTGTTTAAATATTAATATAATTT
1 GTGCTTAAATATTAATGTGATTT
*
23947 ATGCTTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTT
23970 GTGCTTAAA
1 GTGCTTAAA
23979 GAATTAAGAT
Statistics
Matches: 170, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 170 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (23 bp):
GTGCTTAAATATTAATGTGATTT
Found at i:24153 original size:3 final size:3
Alignment explanation
Indices: 24145--24181 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
24135 TACAAATAGG
24145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
24182 GTGGATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:33616 original size:21 final size:21
Alignment explanation
Indices: 33603--33645 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33593 AAGGAGAAGG
33603 AAGAAGAAGAGAAGAATGAAA
1 AAGAAGAAGAGAAGAATGAAA
33624 AAGAAGAAGAGAATGAAATGAA
1 AAGAAGAAGAGAA-G-AATGAA
33646 GGAACCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (21 bp):
AAGAAGAAGAGAAGAATGAAA
Found at i:33627 original size:18 final size:18
Alignment explanation
Indices: 33591--33641 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
33581 GATAACCAAC
* *
33591 AGAAGGAGAAGGAAGAAGA
1 AGAA-GAGAATGAAAAAGA
33610 AG-AGAAGAATGAAAAAGA
1 AGAAG-AGAATGAAAAAGA
33628 AGAAGAGAATGAAA
1 AGAAGAGAATGAAA
33642 TGAAGGAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 23 0.82
19 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
AGAAGAGAATGAAAAAGA
Found at i:39447 original size:17 final size:17
Alignment explanation
Indices: 39424--39463 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39414 TATAATTTTT
39424 AAATATAAA-ATTTAAA
1 AAATATAAATATTTAAA
*
39440 ATAATATAAATATTTTAA
1 A-AATATAAATATTTAAA
39458 AAATAT
1 AAATAT
39464 TAACAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATAAATATTTAAA
Found at i:44196 original size:4 final size:4
Alignment explanation
Indices: 44178--44218 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
44168 TTTGAAAGAA
*
44178 AAAT AAAC AAA- AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
44219 AAGAAAGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:44204 original size:12 final size:12
Alignment explanation
Indices: 44178--44218 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
44168 TTTGAAAGAA
*
44178 AAATAAACAAA-
1 AAATAAATAAAT
44189 AAATAAATAAAT
1 AAATAAATAAAT
44201 AAATAAATAAAT
1 AAATAAATAAAT
44213 -AATAAA
1 AAATAAA
44219 AAGAAAGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:48580 original size:30 final size:30
Alignment explanation
Indices: 48557--48928 Score: 302
Period size: 30 Copynumber: 12.6 Consensus size: 30
48547 CCCTATTTTA
*
48557 TCTAAAAATTATATTTTGACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
* ***
48587 T-TAAAAAATCACATTTTGACTTTTAAACTT
1 TCT-AAAAATTACATTTTGACCCCTAAACTT
* *
48617 TCTAAAAATCACATTTTGACCCC-AAATTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
* * *
48646 ATCT-AAAATTATATTTTAACCCTTAAACTT
1 -TCTAAAAATTACATTTTGACCCCTAAACTT
* * *
48676 TCTAAAAAATATATTTTAACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
* *
48706 TCTAAGAATAACATTTTGACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
*
48736 CTCT-AAAATTACATTTTGACCCTTAAACTTT
1 -TCTAAAAATTACATTTTGACCCCTAAAC-TT
48767 TCT-AAAATTACATTTTGACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
* * * *
48796 TTTTAAAACTACA-TTTAACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCTAAACTT
* * *
48825 T-TCCAAAATTATATTTTAACCCCTAAACTT
1 TCT-AAAAATTACATTTTGACCCCTAAACTT
* * *
48855 CTCT-AAAATTATGATTTT-TCCCC-AAAC-A
1 -TCTAAAAATTA-CATTTTGACCCCTAAACTT
* *
48883 TCCAAAAATTACCATTTT-A-CCCTAAAATT
1 TCTAAAAATTA-CATTTTGACCCCTAAACTT
* **
48912 TCCAAAAAACACATTTT
1 TCTAAAAATTACATTTT
48929 CAACCTCAAA
Statistics
Matches: 284, Mismatches: 42, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.02
28 22 0.08
29 64 0.23
30 180 0.63
31 12 0.04
32 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
TCTAAAAATTACATTTTGACCCCTAAACTT
Found at i:48705 original size:89 final size:90
Alignment explanation
Indices: 48553--48862 Score: 353
Period size: 89 Copynumber: 3.4 Consensus size: 90
48543 AAGCCCCTAT
* ***
48553 TTTATCTAAAAATTATATTTTGACCCCTAAACTTT-TAAAAAATCACATTTTGACTTTTAAACTT
1 TTTATCT-AAAATTATATTTTAACCCCTAAACTTTCTAAAAAAT-ACATTTTGACCCCTAAACTT
48617 TCTAAAAATCACATTTTGACCCC-AAA
64 TCTAAAAATCACATTTTGACCCCTAAA
* * *
48643 TTTATCTAAAATTATATTTTAACCCTTAAACTTTCTAAAAAATATATTTTAACCCCTAAACTTTC
1 TTTATCTAAAATTATATTTTAACCCCTAAACTTTCTAAAAAATACATTTTGACCCCTAAACTTTC
* *
48708 TAAGAATAACATTTTGACCCCTAAA
66 TAAAAATCACATTTTGACCCCTAAA
* * * * * *
48733 CTTCTCTAAAATTACATTTTGACCCTTAAACTTTTCT-AAAATTACATTTTGACCCCTAAACTTT
1 TTTATCTAAAATTATATTTTAACCCCTAAAC-TTTCTAAAAAATACATTTTGACCCCTAAACTTT
* * *
48797 TTTAAAA-CTACA-TTTAACCCCTAAA
65 CTAAAAATC-ACATTTTGACCCCTAAA
*
48822 CTTT-TCCAAAATTATATTTTAACCCCTAAACTTCTCTAAAA
1 -TTTATCTAAAATTATATTTTAACCCCTAAACTT-TCTAAAA
48863 TTATGATTTT
Statistics
Matches: 187, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
88 2 0.01
89 99 0.53
90 81 0.43
91 5 0.03
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (90 bp):
TTTATCTAAAATTATATTTTAACCCCTAAACTTTCTAAAAAATACATTTTGACCCCTAAACTTTC
TAAAAATCACATTTTGACCCCTAAA
Found at i:48744 original size:119 final size:119
Alignment explanation
Indices: 48557--48863 Score: 354
Period size: 119 Copynumber: 2.6 Consensus size: 119
48547 CCCTATTTTA
* * * ***
48557 TCTAAAAATTATATTTTGACCCCTAAACTTT-TAAAAAATCACATTTTGACTTTTAAACTT-TCT
1 TCTAAAAAATATATTTTAACCCCTAAACTTTCT--AAAATAACATTTTGACCCCTAAACTTCTCT
* *
48620 AAAAATCACATTTTGACCC-CAAA-TTTATCTAAAATTATATTTTAACCCTTAAACTT
64 -AAAATCACATTTTGACCCTCAAACTTT-TCTAAAATTACATTTTAACCCCTAAACTT
48676 TCTAAAAAATATATTTTAACCCCTAAACTTTCTAAGAATAACATTTTGACCCCTAAACTTCTCTA
1 TCTAAAAAATATATTTTAACCCCTAAACTTTCTAA-AATAACATTTTGACCCCTAAACTTCTCTA
* * *
48741 AAATTACATTTTGACCCTTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTT
65 AAATCACATTTTGACCCTCAAACTTTTCTAAAATTACATTTTAACCCCTAAACTT
* * * * * * * *
48796 TTTTAAAACTACA-TTTAACCCCTAAACTTTTCCAAAATTATATTTTAACCCCTAAACTTCTCTA
1 TCTAAAAAATATATTTTAACCCCTAAAC-TTTCTAAAATAACATTTTGACCCCTAAACTTCTCTA
48860 AAAT
65 AAAT
48864 TATGATTTTT
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
118 2 0.01
119 110 0.67
120 48 0.29
121 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (119 bp):
TCTAAAAAATATATTTTAACCCCTAAACTTTCTAAAATAACATTTTGACCCCTAAACTTCTCTAA
AATCACATTTTGACCCTCAAACTTTTCTAAAATTACATTTTAACCCCTAAACTT
Found at i:48985 original size:28 final size:29
Alignment explanation
Indices: 48924--48999 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
48914 CAAAAAACAC
* *
48924 ATTTTCAACCTCAAATTTTCCAAAAGTTTG
1 ATTTTGAACCCCAAATTTTCCAAAAG-TTG
*
48954 A-TTT-AATCCCAAATTTTCCTAAAA-TTG
1 ATTTTGAACCCCAAATTTTCC-AAAAGTTG
48981 CATTTTGAACCCCAAATTT
1 -ATTTTGAACCCCAAATTT
49000 CTTGAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 3 0.08
28 14 0.36
29 10 0.26
30 12 0.31
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
ATTTTGAACCCCAAATTTTCCAAAAGTTG
Found at i:53223 original size:14 final size:14
Alignment explanation
Indices: 53204--53230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53194 AAATTTTGAA
53204 AAAAAAAATAAAAG
1 AAAAAAAATAAAAG
53218 AAAAAAAATAAAA
1 AAAAAAAATAAAA
53231 TCCTACAAAG
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:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (14 bp):
AAAAAAAATAAAAG
Found at i:54497 original size:88 final size:88
Alignment explanation
Indices: 54395--54570 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
54385 TTGGTCAGAT
54395 ACATTTTGGCTTTTAATCATGATGTCAAATTCTTACTTCTTGTTCAGTGGCTATTGATTATTGGT
1 ACATTTTGGCTTTTAATCATGATGTCAAATTCTTACTTCTTGTTCAGTGGCTATTGATTATTGGT
54460 TGTTGCGACTCCTTGCTGATGTA
66 TGTTGCGACTCCTTGCTGATGTA
54483 ACATTTTGGCTTTTAATCATGATGTCAAATTCTTACTTCTTGTTCAGTGGCTATTGATTATTGGT
1 ACATTTTGGCTTTTAATCATGATGTCAAATTCTTACTTCTTGTTCAGTGGCTATTGATTATTGGT
54548 TGTTGCGACTCCTTGCTGATGTA
66 TGTTGCGACTCCTTGCTGATGTA
54571 GTTTATCCTT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (88 bp):
ACATTTTGGCTTTTAATCATGATGTCAAATTCTTACTTCTTGTTCAGTGGCTATTGATTATTGGT
TGTTGCGACTCCTTGCTGATGTA
Found at i:56679 original size:38 final size:38
Alignment explanation
Indices: 56628--56703 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
56618 ACAGTAAATG
56628 CCTTTTACATGTATTTGCCAAGCTATCGAAACTCAATA
1 CCTTTTACATGTATTTGCCAAGCTATCGAAACTCAATA
56666 CCTTTTACATGTATTTGCCAAGCTATCGAAACTCAATA
1 CCTTTTACATGTATTTGCCAAGCTATCGAAACTCAATA
56704 AGGCCATGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (38 bp):
CCTTTTACATGTATTTGCCAAGCTATCGAAACTCAATA
Found at i:61924 original size:25 final size:25
Alignment explanation
Indices: 61890--61939 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
61880 GTGCCAGTTT
61890 TTTGGGAATTTTTTAGAAGATAATA
1 TTTGGGAATTTTTTAGAAGATAATA
61915 TTTGGGAATTTTTTAGAAGATAATA
1 TTTGGGAATTTTTTAGAAGATAATA
61940 ACTTGTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTGGGAATTTTTTAGAAGATAATA
Found at i:65381 original size:21 final size:21
Alignment explanation
Indices: 65357--65398 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
65347 ATTTAGGCCC
65357 TTTATAATTTATAAAATTTTA
1 TTTATAATTTATAAAATTTTA
65378 TTTATAATTTATAAAATTTTA
1 TTTATAATTTATAAAATTTTA
65399 AATTAGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATAATTTATAAAATTTTA
Found at i:69611 original size:29 final size:28
Alignment explanation
Indices: 69578--69684 Score: 144
Period size: 29 Copynumber: 3.7 Consensus size: 28
69568 TAAATGATTT
69578 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATT-AAATTATTTTTTAAAATA
**
69607 TAAAAATT-TTAAATTATTTTTTTTAATA
1 T-AAAATTATTAAATTATTTTTTAAAATA
*
69635 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATT-AAATTATTTTTTAAAAT-A
69665 TAAAATTATTAAATTATTTT
1 TAAAATTATTAAATTATTTT
69685 AATTTTCAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
27 6 0.09
28 19 0.27
29 28 0.40
30 17 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TAAAATTATTAAATTATTTTTTAAAATA
Found at i:70344 original size:6 final size:6
Alignment explanation
Indices: 70328--70375 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
70318 CAGAAGAACG
*
70328 ATTAGA TTTAGA ATTAGA ATTAGA ATTAGA ATTCTCAGA ATTAGA ATT
1 ATTAGA ATTAGA ATTAGA ATTAGA ATTAGA A-T-T-AGA ATTAGA ATT
70376 CTTGCCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 29 0.78
7 2 0.05
8 2 0.05
9 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (6 bp):
ATTAGA
Found at i:71843 original size:17 final size:17
Alignment explanation
Indices: 71821--71878 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
71811 TTGATTGACA
71821 TTTATTGTCATTATT-AT
1 TTTATTGT-ATTATTAAT
*
71838 TTTATTGTGTTATTAAT
1 TTTATTGTATTATTAAT
*
71855 TTTATT-TATTTAATTTAT
1 TTTATTGTA-TT-ATTAAT
71873 TTTATT
1 TTTATT
71879 CATGTATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 6 0.17
17 18 0.51
18 11 0.31
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTATTGTATTATTAAT
Found at i:71864 original size:4 final size:4
Alignment explanation
Indices: 71855--71908 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
71845 TGTTATTAAT
* * *
71855 TTTA TTTA TTTAA TTTA TTTTA TTCA TGTA TTGTT TTTA TTTA TTTA TTTA
1 TTTA TTTA TTT-A TTTA -TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA
71906 TTT
1 TTT
71909 TGTCATTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 30 0.73
5 11 0.27
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:75987 original size:21 final size:21
Alignment explanation
Indices: 75961--76012 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
75951 GTGTAGATTA
*
75961 CTACCGATACAAGTGACAGTT
1 CTACCGATACAAGTCACAGTT
* **
75982 CTACCGATACATGTCTTAGTT
1 CTACCGATACAAGTCACAGTT
76003 CTACCGATAC
1 CTACCGATAC
76013 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCACAGTT
Found at i:76711 original size:40 final size:40
Alignment explanation
Indices: 76662--76758 Score: 160
Period size: 40 Copynumber: 2.5 Consensus size: 40
76652 AAGTCCATGT
* *
76662 GTCTT-CCTTTTAACAATCTTATGTTCTACCGAGTTATAA
1 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
76701 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
1 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
*
76741 GTCTTCCTTTTTAACAAT
1 GTCTTCCCTTTTAACAAT
76759 ATTCTCACGC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 5 0.09
40 49 0.91
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (40 bp):
GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
Found at i:82793 original size:15 final size:15
Alignment explanation
Indices: 82773--82815 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
82763 GGGTTTTTTT
82773 TTGGGCTCGAACAAA
1 TTGGGCTCGAACAAA
82788 TTGGGCTCGAACAAA
1 TTGGGCTCGAACAAA
*
82803 TTGGGCTCCAACA
1 TTGGGCTCGAACA
82816 GTTACCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (15 bp):
TTGGGCTCGAACAAA
Found at i:83377 original size:39 final size:39
Alignment explanation
Indices: 83302--83427 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 39
83292 GTTTTGTATG
* * * * *
83302 GGGGTAAGAGATTGGATGGTTTTGATTTGCCTCATGATT
1 GGGGTAAGAGATCGGATGGTTGTAATTTACCTCATGATC
83341 GGGGTAAGAGATCGGATGGTTGTAATTTACAC-CATGATC
1 GGGGTAAGAGATCGGATGGTTGTAATTTAC-CTCATGATC
* * * * *
83380 GAGGTAAGAGATTGGTTGACGGTTGTAATTTGCCTTATGATC
1 GGGGTAAGAGA-TCG--GATGGTTGTAATTTACCTCATGATC
83422 GGGGTA
1 GGGGTA
83428 GCAGATTGGT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 42 0.59
40 3 0.04
41 1 0.01
42 25 0.35
ACGTcount: A:0.24, C:0.10, G:0.33, T:0.33
Consensus pattern (39 bp):
GGGGTAAGAGATCGGATGGTTGTAATTTACCTCATGATC
Found at i:83581 original size:78 final size:77
Alignment explanation
Indices: 83452--84000 Score: 550
Period size: 78 Copynumber: 7.1 Consensus size: 77
83442 TGTAATCTAT
* * * * ** *
83452 GAGATTGG-TCGATGGTGATCTACCCCAAGCTCGAGGTAAAAGATTGGATGGTTGCAATCTTTCT
1 GAGATTGGCT-GATGGTGATCT-GCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCC
* * *
83516 TAGGTTAGGGGAAA
64 TAGGCTCGGGGTAA
*
83530 GAGATTGGCTGATGGTGATCTGCTCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAATCTACCCT
1 GAGATTGGCTGATGGTGATCTGC-CCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCT
* *
83595 AGGGTCGAGGTAA
65 AGGCTCGGGGTAA
* * * * * * *
83608 GAGATTGGTTGATGGTGATCTGCCTCAAACTCGGGGTAAAAGATCGGATGGTTGTAATTTGCCCA
1 GAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCT
*
83673 AGACTCGGGGTAA
65 AGGCTCGGGGTAA
* * *
83686 GAGATT-GTTGATGGTGATCTGCCCTAAGCTCGTGGTAAAAGATCGGATGGCTGCAATCT-GCCT
1 GAGATTGGCTGATGGTGATCTGCCC-AAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCT
*
83749 CAGGCTCGAGGTAA
65 -AGGCTCGGGGTAA
* * * * * * * *
83763 GATATT-GCTTATGGTGATTTACCTTAGGCTCGGGGTAAAAGATCAGATGGCTGCAATCTACCCC
1 GAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCT
*
83827 AAGCTCGGGGTAA
65 AGGCTCGGGGTAA
* * * * * *
83840 GAGATTAGCTGATGGTGATCTGTCCAAGGCTCGGGCTAAAAGATTGGATGGCTACAATCTGCCCT
1 GAGATTGGCTGATGGTGATCTGCCCAA-GCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCT
*
83905 AGACTCGGGGTAA
65 AGGCTCGGGGTAA
** *
83918 GAGATTGGCTGATGGTGATCTGTCCCAAGCTAAGGGTAAAAGATCGGATGGCTGCAAGCTATCCC
1 GAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTA-CCC
* * *
83983 -ATGATCGGCGTAA
64 TAGGCTCGGGGTAA
83996 GAGAT
1 GAGAT
84001 CGAAATCTTC
Statistics
Matches: 391, Mismatches: 69, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
76 3 0.01
77 125 0.32
78 255 0.65
79 8 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (77 bp):
GAGATTGGCTGATGGTGATCTGCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCTA
GGCTCGGGGTAA
Found at i:83679 original size:39 final size:38
Alignment explanation
Indices: 83547--83968 Score: 181
Period size: 39 Copynumber: 10.9 Consensus size: 38
83537 GCTGATGGTG
*
83547 ATCTGCTCCAAGCTCGGGGTAAAAGATCGGATGGTTGCA
1 ATCTGC-CCAAGCTCGGGGTAAAAGATCGGATGGTTGTA
* * * * * * * * * *
83586 ATCTACCCTAGGGTCGAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCC-AAGCTCGGGGTAAAAGATCGGATGGTTGTA
*
83625 ATCTGCCTCAAACTCGGGGTAAAAGATCGGATGGTTGTA
1 ATCTGCC-CAAGCTCGGGGTAAAAGATCGGATGGTTGTA
* * *
83664 ATTTGCCCAAGACTCGGGGTAAGAGATTGTTGATGG-TG--
1 ATCTGCCCAAG-CTCGGGGTAAAAGATCG--GATGGTTGTA
* * *
83702 ATCTGCCCTAAGCTCGTGGTAAAAGATCGGATGGCTGCA
1 ATCTGCCC-AAGCTCGGGGTAAAAGATCGGATGGTTGTA
* * * * **
83741 ATCTGCCTCAGGCTCGAGGTAAGATATTGCTTATGG-TG--
1 ATCTGCC-CAAGCTCGGGGTAAAAGA-T-CGGATGGTTGTA
* * * * * * *
83779 ATTTACCTTAGGCTCGGGGTAAAAGATCAGATGGCTGCA
1 ATCTGCC-CAAGCTCGGGGTAAAAGATCGGATGGTTGTA
* * ** * * * *
83818 ATCTACCCCAAGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCT-GCCCAAGCTCGGGGTAAAAGATCGGATGGTTGTA
* * * * **
83857 ATCTGTCCAAGGCTCGGGCTAAAAGATTGGATGGCTACA
1 ATCTGCCCAA-GCTCGGGGTAAAAGATCGGATGGTTGTA
* * * * * * *
83896 ATCTGCCCTAGACTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCAAG-CTCGGGGTAAAAGATCGGATGGTTGTA
**
83935 ATCTGTCCCAAGCTAAGGGTAAAAGATCGGATGG
1 ATCTG-CCCAAGCTCGGGGTAAAAGATCGGATGG
83969 CTGCAAGCTA
Statistics
Matches: 278, Mismatches: 86, Indels: 38
0.69 0.21 0.09
Matches are distributed among these distances:
36 10 0.04
37 5 0.02
38 51 0.18
39 188 0.68
40 14 0.05
41 10 0.04
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (38 bp):
ATCTGCCCAAGCTCGGGGTAAAAGATCGGATGGTTGTA
Found at i:84327 original size:49 final size:50
Alignment explanation
Indices: 84243--84367 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
84233 GGTATAAAAC
* * ** * * *
84243 TCGTCGTTGTGACCTCAATCTTTCCTGTCATATTTT-TAAGGTACTGGGT
1 TCGTCGTTGCGACCTCAACCTTTCCCATCACATTTTCCAAGGTACCGGGT
*
84292 TCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCCAAGGTACCGGGT
1 TCGTCGTTGCGACCTCAACCTTTCCCATCACATTTTCCAAGGTACCGGGT
** * *
84342 TTATCGTTACGACCTCAACTTTTCCC
1 TCGTCGTTGCGACCTCAACCTTTCCC
84368 TTCAAATCTT
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 30 0.48
50 32 0.52
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.37
Consensus pattern (50 bp):
TCGTCGTTGCGACCTCAACCTTTCCCATCACATTTTCCAAGGTACCGGGT
Found at i:100210 original size:81 final size:81
Alignment explanation
Indices: 100066--100258 Score: 269
Period size: 81 Copynumber: 2.4 Consensus size: 81
100056 TGAGTGATTT
** * * * *
100066 ACGATGCTGCTTGCATAAGTTGATGAGAATCCACAACATATGTGAGACCTCAGCTATCGCTACGG
1 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
100131 TCTATATCACCCGCTC
66 TCTATATCACCCGCTC
* * *
100147 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATTTGAGACCTCAACCATCTCTACGT
1 ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
* * *
100212 TTTATATCACTCGCTT
66 TCTATATCACCCGCTC
*
100228 ACGATGCTGCTCACACAAGCTAATGAGAATC
1 ACGATGCTGCTCACACAAGCTGATGAGAATC
100259 TGCAACGTAT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 99 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (81 bp):
ACGATGCTGCTCACACAAGCTGATGAGAATCCACAACATATGTGAGACCTCAACCATCGCTACGG
TCTATATCACCCGCTC
Found at i:102211 original size:13 final size:14
Alignment explanation
Indices: 102194--102233 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
102184 AGCAAACATT
102194 TTTTTCTTCTTTTC
1 TTTTTCTTCTTTTC
102208 -TTTTC-TCTTTTC
1 TTTTTCTTCTTTTC
102220 TTTTTCTTTCTTTT
1 TTTTTC-TTCTTTT
102234 TCTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
15 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTCTTTTC
Found at i:102226 original size:23 final size:24
Alignment explanation
Indices: 102190--102250 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
102180 TTATAGCAAA
102190 CATTTT-TTTCTTCTTT-TCTTTTCT
1 CATTTTCTTT-TTCTTTCT-TTTTCT
102214 C-TTTTCTTTTTCTTTCTTTTTCT
1 CATTTTCTTTTTCTTTCTTTTTCT
102237 CATTTTCCTTTTTC
1 CATTTT-CTTTTTC
102251 AAGTGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
23 17 0.52
24 9 0.27
25 7 0.21
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (24 bp):
CATTTTCTTTTTCTTTCTTTTTCT
Found at i:102248 original size:30 final size:29
Alignment explanation
Indices: 102192--102248 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
102182 ATAGCAAACA
102192 TTTTTTTCTTCTTTTCTTTTCTCTTTTCT
1 TTTTTTTCTTCTTTTCTTTTCTCTTTTCT
102221 TTTTCTTTCTT-TTTCTCATTTTC-CTTTT
1 TTTT-TTTCTTCTTT-TC-TTTTCTCTTTT
102249 TCAAGTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTTTCTTCTTTTCTTTTCTCTTTTCT
Found at i:117076 original size:27 final size:27
Alignment explanation
Indices: 117024--117076 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
117014 CTAGAATATG
* *
117024 CCACAAAGGTTATCCTTGTGATGTTCA
1 CCACAAAGGCTATCCTTGTCATGTTCA
*
117051 CCACTAAGGCTATCCTT-TCATAGTTC
1 CCACAAAGGCTATCCTTGTCAT-GTTC
117077 GCCATGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (27 bp):
CCACAAAGGCTATCCTTGTCATGTTCA
Found at i:117148 original size:22 final size:23
Alignment explanation
Indices: 117087--117182 Score: 122
Period size: 23 Copynumber: 4.2 Consensus size: 23
117077 GCCATGAAGA
*
117087 CCATTCTTTGTTTGCCACAAAGG
1 CCATTCATTGTTTGCCACAAAGG
* * *
117110 CCAATCACTGGTTGCCACAAAGG
1 CCATTCATTGTTTGCCACAAAGG
*
117133 CCATTCATTG-TTGCCACAAATG
1 CCATTCATTGTTTGCCACAAAGG
* *
117155 CCATTCATTGTTTGCCACCAAGA
1 CCATTCATTGTTTGCCACAAAGG
117178 CCATT
1 CCATT
117183 AATTCCTATC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
22 21 0.34
23 41 0.66
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (23 bp):
CCATTCATTGTTTGCCACAAAGG
Found at i:117170 original size:45 final size:46
Alignment explanation
Indices: 117083--117182 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 46
117073 GTTCGCCATG
*
117083 AAGACCATTCTTTGTTTGCCACAAAGGCCAATCACTGGTTGCCACA
1 AAGACCATTCATTGTTTGCCACAAAGGCCAATCACTGGTTGCCACA
* * * * * *
117129 AAGGCCATTCATTG-TTGCCACAAATGCCATTCATTGTTTGCCACC
1 AAGACCATTCATTGTTTGCCACAAAGGCCAATCACTGGTTGCCACA
117174 AAGACCATT
1 AAGACCATT
117183 AATTCCTATC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
45 34 0.74
46 12 0.26
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (46 bp):
AAGACCATTCATTGTTTGCCACAAAGGCCAATCACTGGTTGCCACA
Found at i:127102 original size:43 final size:42
Alignment explanation
Indices: 127038--127138 Score: 148
Period size: 43 Copynumber: 2.4 Consensus size: 42
127028 ATATATACAT
*
127038 GGAAGACTCATGTCTCAGGATGAGCATGAGATTATGTTTAAAA
1 GGAAGACTCATGACTCAGGATGAGCATGAGATTATGTTT-AAA
* *
127081 GGAAGACTCGTGACTCGGGATGAGCATGAGATTATGTTTAAA
1 GGAAGACTCATGACTCAGGATGAGCATGAGATTATGTTTAAA
* *
127123 GGAAGAATTATGACTC
1 GGAAGACTCATGACTC
127139 GGTTGTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 16 0.31
43 36 0.69
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.27
Consensus pattern (42 bp):
GGAAGACTCATGACTCAGGATGAGCATGAGATTATGTTTAAA
Found at i:135540 original size:17 final size:17
Alignment explanation
Indices: 135518--135574 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
135508 TAATTATTCC
*
135518 TGCATTATTAATGTCAT
1 TGCATTATTATTGTCAT
* *
135535 TGCATTTTTATTGTCAC
1 TGCATTATTATTGTCAT
*
135552 TGCATCTA-CATTGTCAT
1 TGCAT-TATTATTGTCAT
135569 TGCATT
1 TGCATT
135575 TCCATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
TGCATTATTATTGTCAT
Found at i:139859 original size:17 final size:17
Alignment explanation
Indices: 139837--139871 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
139827 AATCTAGTTT
139837 ATGTATTAGTCAGTTGC
1 ATGTATTAGTCAGTTGC
139854 ATGTATTAGTCAGTTGC
1 ATGTATTAGTCAGTTGC
139871 A
1 A
139872 GGTTGTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (17 bp):
ATGTATTAGTCAGTTGC
Found at i:153323 original size:7 final size:7
Alignment explanation
Indices: 153311--153344 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
153301 CAGGTCCTTC
153311 TCTTCTT
1 TCTTCTT
153318 TCTTCTT
1 TCTTCTT
153325 TCTTCTT
1 TCTTCTT
153332 TCTTCTT
1 TCTTCTT
153339 T-TTCTT
1 TCTTCTT
153345 CCTCTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TCTTCTT
Found at i:159248 original size:5 final size:5
Alignment explanation
Indices: 159238--159299 Score: 55
Period size: 5 Copynumber: 13.4 Consensus size: 5
159228 TATAAACATA
**
159238 TTCTT TTCTT TTCTT TTCTT TTCCC TT-TT TT-TT TTCTT TT-TCT TTC-T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT-T TTCTT
159285 TTCTT TT-TT TT-TT TT
1 TTCTT TTCTT TTCTT TT
159300 TGACTGAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
4 19 0.39
5 30 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTCTT
Found at i:159283 original size:28 final size:27
Alignment explanation
Indices: 159241--159299 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
159231 AAACATATTC
159241 TTTTCTTTTCTTTTCTTTTCCCTTTTTT
1 TTTTCTTTTCTTTTC-TTTCCCTTTTTT
**
159269 TTTTCTTTT-TCTTTCTTTCTTTTTTTT
1 TTTTCTTTTCT-TTTCTTTCCCTTTTTT
159296 TTTT
1 TTTT
159300 TGACTGAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTCTTTTCTTTTCTTTCCCTTTTTT
Found at i:160346 original size:14 final size:14
Alignment explanation
Indices: 160327--160367 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
160317 TAAAAATTTC
160327 TTCCTTCTCTCTTT
1 TTCCTTCTCTCTTT
*
160341 TTCCTTCT-TCCTT
1 TTCCTTCTCTCTTT
*
160354 TTCCTCCTC-CTTT
1 TTCCTTCTCTCTTT
160367 T
1 T
160368 CTTCTTTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TTCCTTCTCTCTTT
Found at i:160366 original size:12 final size:13
Alignment explanation
Indices: 160327--160368 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
160317 TAAAAATTTC
*
160327 TTCCTTCTCTCTTT
1 TTCCTTC-CTCCTT
*
160341 TTCCTTCTTCCTT
1 TTCCTTCCTCCTT
160354 TTCC-TCCTCCTT
1 TTCCTTCCTCCTT
160366 TTC
1 TTC
160369 TTCTTTCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 8 0.32
14 7 0.28
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCCTTCCTCCTT
Found at i:160381 original size:24 final size:26
Alignment explanation
Indices: 160325--160383 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
160315 AATAAAAATT
*
160325 TCTTCCTTCTCTCTTTTTCCTTCTTCC
1 TCTTCC-TCTCTCCTTTTCCTTCTTCC
* *
160352 TTTTCCTC-CTCCTTTT-CTTCTTTC
1 TCTTCCTCTCTCCTTTTCCTTCTTCC
160376 TCTTCCTC
1 TCTTCCTC
160384 AATACCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 14 0.50
25 7 0.25
26 2 0.07
27 5 0.18
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (26 bp):
TCTTCCTCTCTCCTTTTCCTTCTTCC
Found at i:162130 original size:9 final size:9
Alignment explanation
Indices: 162118--162146 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
162108 ATTTCAGCAA
162118 TTTTTCTTT
1 TTTTTCTTT
162127 TTTTTC-TT
1 TTTTTCTTT
162135 TTTTTCTTT
1 TTTTTCTTT
162144 TTT
1 TTT
162147 GTTTTTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:186108 original size:15 final size:14
Alignment explanation
Indices: 186082--186120 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
186072 ACAAAGAATG
* *
186082 TAAAACAAAACAAG
1 TAAAAGAAAACAAA
186096 TAAAAGTAAAACAAA
1 TAAAAG-AAAACAAA
186111 TAAAAGAAAA
1 TAAAAGAAAA
186121 TGTAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (14 bp):
TAAAAGAAAACAAA
Found at i:186120 original size:20 final size:21
Alignment explanation
Indices: 186078--186127 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
186068 TTCTACAAAG
*
186078 AATGTAAAACAAAACAAGTAA
1 AATGTAAAACAAAAAAAGTAA
186099 AA-GTAAAACAAATAAAAG-AA
1 AATGTAAAACAAA-AAAAGTAA
186119 AATGTAAAA
1 AATGTAAAA
186128 ATGCACTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.70, C:0.06, G:0.10, T:0.14
Consensus pattern (21 bp):
AATGTAAAACAAAAAAAGTAA
Found at i:197210 original size:18 final size:18
Alignment explanation
Indices: 197187--197240 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
197177 ACGACAAAAA
197187 CTTCCTCTTT-TTCTTCTT
1 CTTCCT-TTTCTTCTTCTT
197205 CTTCCTTTTCTTCTTCTT
1 CTTCCTTTTCTTCTTCTT
* *
197223 CTTTCCCTTCCTTCTTCT
1 C-TTCCTTTTCTTCTTCT
197241 CCTCGATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 3 0.09
18 15 0.47
19 14 0.44
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
CTTCCTTTTCTTCTTCTT
Found at i:197213 original size:15 final size:15
Alignment explanation
Indices: 197195--197223 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
197185 AACTTCCTCT
197195 TTTTCTTCTTCTTCC
1 TTTTCTTCTTCTTCC
197210 TTTTCTTCTTCTTC
1 TTTTCTTCTTCTTC
197224 TTTCCCTTCC
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTCTTCTTCTTCC
Found at i:219189 original size:13 final size:13
Alignment explanation
Indices: 219173--219200 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
219163 ATAGGACTTA
219173 GATGTCGACTAAG
1 GATGTCGACTAAG
219186 GATGTCGACTAAG
1 GATGTCGACTAAG
219199 GA
1 GA
219201 CTAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (13 bp):
GATGTCGACTAAG
Found at i:219541 original size:99 final size:99
Alignment explanation
Indices: 219374--220055 Score: 670
Period size: 99 Copynumber: 6.9 Consensus size: 99
219364 TCGCAACAGT
* * * * * *
219374 GAATCTGATACCCTGGAA-ATACGAAGGGAAAGG-TGAGGTCTCAAAGGCGAACCCTGTACCTTA
1 GAATCCGATACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTA
* *
219437 AAAGATGTGATGGGAAGGATTGAGGCCGCAATGAC
65 GAAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
219472 GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAG
1 GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAG
* **
219537 AAGATGTGATGGGAAGGATTGAGGCCACAACGGT
66 AAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
* * * * * *
219571 AAATTCGATACTATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGTGAACCCTGTACCCTAG
1 GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAG
* *
219636 AAGATGTGATGGGAAAGATTAAGGCCGCAACGAC
66 AAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
* * * * * * ** * *
219670 GAATCTGGTACTATGAAGATATAAACGGAAAGGTTGAGGTCAT-AAC-GACAAACTTGTACCTTA
1 GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGG-CCTCAACGGTGAACCCTGTACCTTA
* * *
219733 GAAGATGTAATGGGAAAGATTGAGGCTGCAAC-A-
65 GAAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
* * * *
219766 GTAAATCTGATACCATGAAGATATGAAGGGAAAGGTTAAGGCCGT-AACGGTGAACCTTATACCT
1 G--AATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC-TCAACGGTGAACCCTGTACCT
* * * *
219830 TAGAAGATATGATAGGAAGGATTGAGGTCGTAAC-AGC
63 TAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGA-C
* * * *
219867 GAATCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGG-CAAACCTAGTACCTTA
1 GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCT-GTACCTTA
* * **
219931 G-AGACGTGATGGGAAAGATCAAGGCCGCAACGAC
65 GAAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
* * * ** * *
219965 GGAT-CTAGTACCATAGAA-ATATAAAGGGGAAAGGTTGAGGCAGCAACGGTGAACCTTGTACCC
1 GAATCCGA-TACCAT-GAAGATATGAA-GGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCT
**
220028 TAGAA-ACATGATGGGAAGGATTGAGGCC
63 TAGAAGATGTGATGGGAAGGATTGAGGCC
220056 ATAACGGCGA
Statistics
Matches: 482, Mismatches: 85, Indels: 33
0.80 0.14 0.05
Matches are distributed among these distances:
96 1 0.00
97 6 0.01
98 146 0.30
99 322 0.67
100 6 0.01
101 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (99 bp):
GAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAG
AAGATGTGATGGGAAGGATTGAGGCCGCAACGAC
Found at i:219790 original size:197 final size:196
Alignment explanation
Indices: 219354--220055 Score: 731
Period size: 197 Copynumber: 3.6 Consensus size: 196
219344 TTTGACAGGG
* * * * * * * *
219354 AAGATTAAGGTCGCAACAGTGAATCTGATACCCTGGAAATACGAAGGGAAAGG-TGAGGTCTCAA
1 AAGATTGAGGCCGCAACAGTAAATCTGATACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAA
* * * * * * *
219418 AGGCGAACCCTGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAATGACGAATCCGATAC
66 CGGTGAACCCTGTACCCTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGACGAATCCGGTAC
* ** * *
219483 CATGAAGATATGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAGAAGATGTGATG
131 CATGAAGATATGAAGGGAAAGGTTGAGGCAT-AAC-GACAAACTTGTACCTTAGAAGATGTGATG
219548 GGA
194 GGA
* * * *
219551 AGGATTGAGGCCACAACGGTAAAT-TCGATACTAT-GAAGATATGAAGGGAAAGGTTGAGGCCGC
1 AAGATTGAGGCCGCAACAGTAAATCT-GATACCATAGAA-ATATGAAGGGAAAGGTTGAGGCCGC
* * * * *
219614 AATGGTGAACCCTGTACCCTAGAAGATGTGATGGGAAAGATTAAGGCCGCAACGACGAATCTGGT
64 AACGGTGAACCCTGTACCCTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGACGAATCCGGT
* * * *
219679 ACTATGAAGATATAAACGGAAAGGTTGAGGTCATAACGACAAACTTGTACCTTAGAAGATGTAAT
129 ACCATGAAGATATGAAGGGAAAGGTTGAGG-CATAACGACAAACTTGTACCTTAGAAGATGTGAT
219744 GGGA
193 GGGA
* * *
219748 AAGATTGAGGCTGCAACAGTAAATCTGATACCAT-GAAGATATGAAGGGAAAGGTTAAGGCCGTA
1 AAGATTGAGGCCGCAACAGTAAATCTGATACCATAGAA-ATATGAAGGGAAAGGTTGAGGCCGCA
* * * * * *
219812 ACGGTGAACCTTATACCTTAGAAGATATGATAGGAAGGATTGAGGTCGTAAC-AGCGAATCCGGT
65 ACGGTGAACCCTGTACCCTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGA-CGAATCCGGT
** * * *
219876 ACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAACCTAGTACCTTAG-AGACGTGA
129 ACCATGAAGATATGAAGGGAAAGGTTGAGG-CATAACGACAAA-CTTGTACCTTAGAAGATGTGA
219940 TGGGA
192 TGGGA
** * * *
219945 AAGATCAAGGCCGCAAC-G-ACGGATCT-AGTACCATAGAAATATAAAGGGGAAAGGTTGAGGCA
1 AAGATTGAGGCCGCAACAGTA--AATCTGA-TACCATAGAAATATGAA-GGGAAAGGTTGAGGCC
* *
220007 GCAACGGTGAACCTTGTACCCTAGAA-ACATGATGGGAAGGATTGAGGCC
62 GCAACGGTGAACCCTGTACCCTAGAAGATATGATGGGAAGGATTGAGGCC
220056 ATAACGGCGA
Statistics
Matches: 423, Mismatches: 70, Indels: 24
0.82 0.14 0.05
Matches are distributed among these distances:
195 1 0.00
196 7 0.02
197 268 0.63
198 145 0.34
199 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.19
Consensus pattern (196 bp):
AAGATTGAGGCCGCAACAGTAAATCTGATACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAA
CGGTGAACCCTGTACCCTAGAAGATATGATGGGAAGGATTGAGGCCGCAACGACGAATCCGGTAC
CATGAAGATATGAAGGGAAAGGTTGAGGCATAACGACAAACTTGTACCTTAGAAGATGTGATGGG
A
Found at i:219888 original size:296 final size:295
Alignment explanation
Indices: 219428--220004 Score: 786
Period size: 296 Copynumber: 1.9 Consensus size: 295
219418 AGGCGAACCC
* * *
219428 TGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCGCAATGACGAATCCGATACCATGAAGATA
1 TGTACCTTAAAAGATGTAATGGGAAAGATTGAGGCCGCAAAGAC-AATCCGATACCATGAAGATA
* * * *
219493 TGAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAGAAGATGTGATGGGAAGGATTG
65 TGAAGGGAAAGGTTAAGGCCTCAACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGATTG
* * * * * *
219558 AGGCCACAACGGTAAATTCGATACTATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGTGAA
130 AGGCCACAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGG-CAA
* * * * *
219623 CCCT-GTACCCTAGAAGATGTGATGGGAAAGATTAAGGCCGCAACGACGAATCTGGTACTAT-GA
194 ACCTAGTACCCTAG-AGACGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCATAGA
219686 AGATATAAA-CGGAAAGGTTGAGGTCATAACGACAAACT
258 A-ATATAAAGCGGAAAGGTTGAGGTCATAACGACAAACT
* * *
219724 TGTACCTTAGAAGATGTAATGGGAAAGATTGAGGCTGCAACAGTA-AATCTGATACCATGAAGAT
1 TGTACCTTAAAAGATGTAATGGGAAAGATTGAGGCCGCAA-AG-ACAATCCGATACCATGAAGAT
*
219788 ATGAAGGGAAAGGTTAAGGCCGT-AACGGTGAACCTTATACCTTAGAAGATATGATAGGAAGGAT
64 ATGAAGGGAAAGGTTAAGGCC-TCAACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGAT
* ** * *
219852 TGAGGTCGTAACAGCGAATCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCA
128 TGAGGCCACAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCA
* *
219917 AACCTAGTACCTTAGAGACGTGATGGGAAAGATCAAGGCCGCAACGACGGATCTAGTACCATAGA
193 AACCTAGTACCCTAGAGACGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCATAGA
*
219982 AATATAAAGGGGAAAGGTTGAGG
258 AATATAAAGCGGAAAGGTTGAGG
220005 CAGCAACGGT
Statistics
Matches: 245, Mismatches: 30, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
295 54 0.22
296 188 0.77
297 2 0.01
298 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (295 bp):
TGTACCTTAAAAGATGTAATGGGAAAGATTGAGGCCGCAAAGACAATCCGATACCATGAAGATAT
GAAGGGAAAGGTTAAGGCCTCAACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGATTGA
GGCCACAACAGCAAATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCAAAC
CTAGTACCCTAGAGACGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCATAGAAAT
ATAAAGCGGAAAGGTTGAGGTCATAACGACAAACT
Found at i:219927 original size:49 final size:48
Alignment explanation
Indices: 219396--220013 Score: 293
Period size: 49 Copynumber: 12.5 Consensus size: 48
219386 CTGGAAATAC
* * * * * * *
219396 GAAGGGAAAGG-TGAGGTCTCAAAGGCGAACCCTGTACCTTAAAAGATGT
1 GAAGGGAAAGGTTGAGGCCGCAACGGC-AAACCTGTACCAT-GAAGATAT
* * * *
219445 GATGGG-AAGGATTGAGGCCGCAATGACGAATCC-GATACCATGAAGATAT
1 GAAGGGAAAGG-TTGAGGCCGCAACGGC-AAACCTG-TACCATGAAGATAT
* * * * *
219494 GAAGGGAAAGGTTGAGGCCTCAACGGTGAACCCTGTACCTTAGAAGATGT
1 GAAGGGAAAGGTTGAGGCCGCAACGG-CAAACCTGTACCAT-GAAGATAT
* * * * *
219544 GATGGG-AAGGATTGAGGCCACAACGGTAAA-TTCGATACTATGAAGATAT
1 GAAGGGAAAGG-TTGAGGCCGCAACGGCAAACCT-G-TACCATGAAGATAT
* * * * *
219593 GAAGGGAAAGGTTGAGGCCGCAATGGTGAACCCTGTACCCTAGAAGATGT
1 GAAGGGAAAGGTTGAGGCCGCAACGG-CAAACCTGTACCAT-GAAGATAT
* * * * * * *
219643 GATGGGAAAGATTAAGGCCGCAACGACGAATCTGGTACTATGAAGATAT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCT-GTACCATGAAGATAT
* * * ** * * * *
219692 AAACGGAAAGGTTGAGGTCATAACGACAAACTTGTACCTTAGAAGATGT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCTGTACCAT-GAAGATAT
* * * * *
219741 -AATGGGAAAGATTGAGGCTGCAACAGTAAATCTGATACCATGAAGATAT
1 GAA-GGGAAAGGTTGAGGCCGCAACGGCAAACCTG-TACCATGAAGATAT
* * ** * *
219790 GAAGGGAAAGGTTAAGGCCGTAACGGTGAACCTTATACCTTAGAAGATAT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACC-TGTACCAT-GAAGATAT
* * * * *
219840 GATA-GG-AAGGATTGAGGTCGTAACAGCGAATCCGGTACCATGAAGATAT
1 GA-AGGGAAAGG-TTGAGGCCGCAACGGC-AAACCTGTACCATGAAGATAT
* **
219889 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCTAGTACC-TTAGAGACGT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCT-GTACCATGA-AGATAT
* * ** * ** *
219938 GATGGGAAAGATCAAGGCCGCAACGACGGATCTAGTACCATAGAA-ATAT
1 GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCT-GTACCAT-GAAGATAT
* *
219987 AAAGGGGAAAGGTTGAGGCAGCAACGG
1 GAA-GGGAAAGGTTGAGGCCGCAACGG
220014 TGAACCTTGT
Statistics
Matches: 421, Mismatches: 117, Indels: 61
0.70 0.20 0.10
Matches are distributed among these distances:
48 19 0.05
49 239 0.57
50 157 0.37
51 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (48 bp):
GAAGGGAAAGGTTGAGGCCGCAACGGCAAACCTGTACCATGAAGATAT
Found at i:220110 original size:296 final size:293
Alignment explanation
Indices: 219444--220115 Score: 771
Period size: 296 Copynumber: 2.3 Consensus size: 293
219434 TTAAAAGATG
* * **
219444 TGATGGGAAGGATTGAGGCCGCAATGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTTGA
1 TGATGGGAAGGATTGAGGCCGCAACGGCGAATTTGATACCATGAAGATATGAAGGGAAAGGTTGA
* * * * * *
219509 GGCCTCAACGGTGAACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCACAACGGTAAA
66 GGCGT-AACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGATTGAGGCCACAACAGCAAA
* * * * *
219574 TTCGATACTATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGTGAACCCTGTACCCTAGAAG
130 TCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTCAAACCTGTACCCTAGAAG
* * * *
219639 ATGTGATGGGAAAGATTAAGGCCGCAACGACGAATCTGGTACTATGAAGATATAAACGGAAAGGT
195 ACGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCATGAAGATATAAACGGAAAGGT
* * *
219704 TGAGGTCATAACGACAAACTTGTACCTTAGAAGA
260 TGAGGTCACAACGACAAACTTGTACCCTAGAACA
* * * ** *
219738 TGTAATGGGAAAGATTGAGGCTGCAACAGTAAATCTGATACCATGAAGATATGAAGGGAAAGGTT
1 TG--ATGGGAAGGATTGAGGCCGCAACGGCGAATTTGATACCATGAAGATATGAAGGGAAAGGTT
* * * ** *
219803 AAGGCCGTAACGGTGAACCTTATACCTTAGAAGATATGATAGGAAGGATTGAGGTCGTAACAGCG
64 GAGG-CGTAACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGATTGAGGCCACAACAGCA
* *
219868 AATCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGG-CAAACCTAGTACCTTAG
128 AATCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTCAAACCT-GTACCCTAG
* *
219932 -AGACGTGATGGGAAAGATCAAGGCCGCAACGACGGATCTAGTACCATAGAA-ATATAAAGGGGA
192 AAGACGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCAT-GAAGATATAAA-CGGA
** *
219995 AAGGTTGAGG-CAGCAACGGTGAACCTTGTACCCTAGAAACA
255 AAGGTTGAGGTCA-CAAC-GACAAACTTGTACCCTAG-AACA
** * * *
220036 TGATGGGAAGGATTGAGGCCATAACGGCGAATTTGGA-ACCATAAAGATTTG-AGGAGAAAGATT
1 TGATGGGAAGGATTGAGGCCGCAACGGCGAATTT-GATACCATGAAGATATGAAGG-GAAAGGTT
220099 GAGGTCGTAACGGTGAA
64 GAGG-CGTAACGGTGAA
220116 TTTGAAACCA
Statistics
Matches: 315, Mismatches: 52, Indels: 20
0.81 0.13 0.05
Matches are distributed among these distances:
294 2 0.01
295 59 0.19
296 231 0.73
297 18 0.06
298 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (293 bp):
TGATGGGAAGGATTGAGGCCGCAACGGCGAATTTGATACCATGAAGATATGAAGGGAAAGGTTGA
GGCGTAACGGTGAACCCTATACCTTAGAAGATATGATAGGAAGGATTGAGGCCACAACAGCAAAT
CCGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTCAAACCTGTACCCTAGAAGA
CGTGATGGGAAAGATCAAGGCCGCAACGACGAATCTAGTACCATGAAGATATAAACGGAAAGGTT
GAGGTCACAACGACAAACTTGTACCCTAGAACA
Found at i:220582 original size:114 final size:114
Alignment explanation
Indices: 220390--220661 Score: 332
Period size: 114 Copynumber: 2.4 Consensus size: 114
220380 AGCGGAATGG
* * *
220390 AGTGAAACTTCAAAT-CTCATCTTCCTGGTGAGGTATAGATAACTAGGTCAAAACAGTATGTTAA
1 AGTGAGACTTCAAATCCT-ATCTTCCTGGTGAGGTATAGAGAAGTAGGTCAAAACAGTATGTTAA
* * *
220454 ATCAAAATAACGAAGCCGAGCTCAACATCC-TAGAGGATACAGTGGAGTGG
65 ATCAAAACAACGAAGCCGAGCTCAACATCCTTA-AGGATACAGTAGAGTGA
* * * * * * *
220504 GGTGAGGCTTCAAATCCTATCTTCCTGATGAGGTATAGAGAAGTAGGTCAAGATAGTTTGTTGAA
1 AGTGAGACTTCAAATCCTATCTTCCTGGTGAGGTATAGAGAAGTAGGTCAAAACAGTATGTTAAA
* * * *
220569 TCAAAACAGCGAAGTCGAGCTCAACGTCCTTAAGGATATAGTAGAGTGA
66 TCAAAACAACGAAGCCGAGCTCAACATCCTTAAGGATACAGTAGAGTGA
* * *
220618 AGTGAGATTTCAAATCCCATCTTCCTGGTGAGGTACAGAGAAGT
1 AGTGAGACTTCAAATCCTATCTTCCTGGTGAGGTATAGAGAAGT
220662 GGTTTAAAAC
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
114 129 0.97
115 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (114 bp):
AGTGAGACTTCAAATCCTATCTTCCTGGTGAGGTATAGAGAAGTAGGTCAAAACAGTATGTTAAA
TCAAAACAACGAAGCCGAGCTCAACATCCTTAAGGATACAGTAGAGTGA
Found at i:226704 original size:22 final size:23
Alignment explanation
Indices: 226654--226701 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
226644 ATAAAATTAT
* * *
226654 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAAAAATAAAAAA
226676 TAAATATTTAAAAAAATAAAAAA
1 TAAATATTTAAAAAAATAAAAAA
226699 TAA
1 TAA
226702 TATGAGCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAATATTTAAAAAAATAAAAAA
Found at i:227124 original size:2 final size:2
Alignment explanation
Indices: 227117--227148 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
227107 CACATTCATT
*
227117 CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
227149 TATACATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:227153 original size:12 final size:12
Alignment explanation
Indices: 227117--227154 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
227107 CACATTCATT
*
227117 CACACACACACA
1 CACACACACATA
227129 CACACACACATA
1 CACACACACATA
*
227141 CACACACATATA
1 CACACACACATA
227153 CA
1 CA
227155 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.42, G:0.00, T:0.08
Consensus pattern (12 bp):
CACACACACATA
Found at i:227280 original size:36 final size:36
Alignment explanation
Indices: 227230--227311 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
227220 ACTTTACAAT
227230 CCCAAAATAATATAATAATATAAAATAAACTAAAAC
1 CCCAAAATAATATAATAATATAAAATAAACTAAAAC
* * * *
227266 CCTAAAATAATATAATAATATAAAATGAATTGAAAC
1 CCCAAAATAATATAATAATATAAAATAAACTAAAAC
227302 CCCAAAATAA
1 CCCAAAATAA
227312 CTTATACGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.61, C:0.13, G:0.02, T:0.23
Consensus pattern (36 bp):
CCCAAAATAATATAATAATATAAAATAAACTAAAAC
Found at i:234725 original size:16 final size:16
Alignment explanation
Indices: 234686--234716 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
234676 ATTTTGATTT
234686 TTACTTTTTTTTTCTA
1 TTACTTTTTTTTTCTA
234702 TTACTTTTTTTTTCT
1 TTACTTTTTTTTTCT
234717 TTAAGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTACTTTTTTTTTCTA
Found at i:239191 original size:40 final size:39
Alignment explanation
Indices: 239113--239250 Score: 179
Period size: 40 Copynumber: 3.5 Consensus size: 39
239103 TTTCATTGTT
* * * *
239113 ATCCTTTTCGACCTTTGT-ATTAATATCATTTCGAATAAC
1 ATCCTTTTCAACCTTT-TCATTGATATCCTTTCGGATAAC
239152 ATCCTTTTCAACCTTTTCACTTGATATCCTTTCGGATAAC
1 ATCCTTTTCAACCTTTTCA-TTGATATCCTTTCGGATAAC
* * *
239192 ATCATTTTCAACCATTTCATTTGATATCCTTTTGGATAAC
1 ATCCTTTTCAACCTTTTCA-TTGATATCCTTTCGGATAAC
239232 ATCCTTTTCAACCTTTTCA
1 ATCCTTTTCAACCTTTTCA
239251 AGAATTCGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 16 0.18
40 70 0.80
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (39 bp):
ATCCTTTTCAACCTTTTCATTGATATCCTTTCGGATAAC
Found at i:239410 original size:4 final size:4
Alignment explanation
Indices: 239396--239561 Score: 89
Period size: 4 Copynumber: 41.5 Consensus size: 4
239386 ATCATGTATG
* * * * * * * *
239396 TATA TACA TATA TATA CACA TGTA TGTA TATA CATA TATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * *
239444 TACA TGTA TGTA TGTA TACA TACA TATA TATA TACA TATA TATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * * *
239492 CATG TATA TATG TATA TATA CATG TATA TATG TATA CACA TATA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
239540 TGTA TGTA TATA TATA TATA TA
1 TATA TATA TATA TATA TATA TA
239562 AATTAGTCTT
Statistics
Matches: 122, Mismatches: 40, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
4 122 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (4 bp):
TATA
Found at i:239442 original size:26 final size:26
Alignment explanation
Indices: 239384--239561 Score: 132
Period size: 26 Copynumber: 7.0 Consensus size: 26
239374 ACAATCTTAA
239384 ACAT-CATGTATGTATATACATATAT
1 ACATACATGTATGTATATACATATAT
* *
239409 ATACACATGTATGTATATACATATAT
1 ACATACATGTATGTATATACATATAT
* * *
239435 ACATACATATACATGTATGT--ATGTAT
1 ACATACATGT--ATGTATATACATATAT
* * * *
239461 ACATACATATATATATACATATATAT
1 ACATACATGTATGTATATACATATAT
**
239487 ACATACATGTA--TATATGTATATAT
1 ACATACATGTATGTATATACATATAT
** * *
239511 ACATGTATATATGTATACACATATAT
1 ACATACATGTATGTATATACATATAT
** * *
239537 ACATGTATGTATATATATATATATA
1 ACATACATGTATGTATATACATATA
239562 AATTAGTCTT
Statistics
Matches: 122, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
24 24 0.20
25 2 0.02
26 89 0.73
28 7 0.06
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (26 bp):
ACATACATGTATGTATATACATATAT
Found at i:239554 original size:46 final size:46
Alignment explanation
Indices: 239422--239557 Score: 173
Period size: 46 Copynumber: 3.0 Consensus size: 46
239412 CACATGTATG
* * *
239422 TATATACATATATACATACATATACATGTATGTATGTATACATACA
1 TATATATATATATACATATATATACATGTATGTATGTATATATACA
* * * *
239468 TATATATATACATATATATACATACATGTATATATGTATATATACA
1 TATATATATATATACATATATATACATGTATGTATGTATATATACA
* * * *
239514 TGTATATATGTATACACATATATACATGTATGTATATATATATA
1 TATATATATATATACATATATATACATGTATGTATGTATATATA
239558 TATAAATTAG
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (46 bp):
TATATATATATATACATATATATACATGTATGTATGTATATATACA
Found at i:239558 original size:50 final size:49
Alignment explanation
Indices: 239392--239561 Score: 171
Period size: 50 Copynumber: 3.4 Consensus size: 49
239382 AAACATCATG
* * *
239392 TATGTATATACATATATATACA-CATGTATGTATATACATATATACATACA
1 TATGTATATATATATATATACATCATATATGTATACACATATATACAT--A
** * * * * *
239442 TATACATGTATGTATGTATACATACATATATATATACATATATATACATA
1 TATGTATATATATATATATACAT-CATATATGTATACACATATATACATA
* * * *
239492 CATGTATATATGTATATATACATGTATATATGTATACACATATATACATG
1 TATGTATATATATATATATACAT-CATATATGTATACACATATATACATA
239542 TATGTATATATATATATATA
1 TATGTATATATATATATATA
239562 AATTAGTCTT
Statistics
Matches: 96, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
50 75 0.78
52 21 0.22
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (49 bp):
TATGTATATATATATATATACATCATATATGTATACACATATATACATA
Found at i:240305 original size:3 final size:3
Alignment explanation
Indices: 240297--240326 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
240287 TTTACTTACT
240297 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
240327 AAACACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:245152 original size:24 final size:24
Alignment explanation
Indices: 245084--245155 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
245074 GGATGAGATA
*
245084 TCGACCTTTTCATTGCTATCATTT
1 TCGACCTTTTCATTGCTATCCTTT
*
245108 TCAACCTTTTCATTGCTATCCTTT
1 TCGACCTTTTCATTGCTATCCTTT
* *
245132 TCGACCTTTTTATTGATATCCTTT
1 TCGACCTTTTCATTGCTATCCTTT
245156 CGAATAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.25, G:0.07, T:0.51
Consensus pattern (24 bp):
TCGACCTTTTCATTGCTATCCTTT
Found at i:245203 original size:40 final size:39
Alignment explanation
Indices: 245125--245222 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 39
245115 TTTCATTGCT
*
245125 ATCCTTTTCGACCTTTTTATTGATATCCTTTCGAATAAC
1 ATCCTTTTCGACCTTTTCATTGATATCCTTTCGAATAAC
*
245164 ATCCTTTTCAACCTTTTCATTTGATATCCTTTC-AGATAAC
1 ATCCTTTTCGACCTTTTCA-TTGATATCCTTTCGA-ATAAC
245204 ATCCTTTTCGACCTTTTCA
1 ATCCTTTTCGACCTTTTCA
245223 AGAATTCGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 18 0.33
40 36 0.67
ACGTcount: A:0.22, C:0.26, G:0.06, T:0.46
Consensus pattern (39 bp):
ATCCTTTTCGACCTTTTCATTGATATCCTTTCGAATAAC
Found at i:245379 original size:4 final size:4
Alignment explanation
Indices: 245365--245403 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
245355 AGCATCAATG
* *
245365 CATA AATA CATA CATA CAT- CATA CATG CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
245404 TATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:248890 original size:17 final size:18
Alignment explanation
Indices: 248862--248895 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
248852 TTTTCAATTG
248862 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
248880 TAATTAA-TTAAAATTT
1 TAATTAATTTAAAATTT
248896 ATTTTCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:249349 original size:8 final size:8
Alignment explanation
Indices: 249331--249381 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
249321 CAAAGACTCT
249331 ATTTT-TA
1 ATTTTATA
249338 ATTTTATA
1 ATTTTATA
249346 ATTTTATA
1 ATTTTATA
249354 ATTTTATA
1 ATTTTATA
249362 A-TTTATA
1 ATTTTATA
*
249369 GTTTTCATA
1 ATTTT-ATA
249378 ATTT
1 ATTT
249382 AATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 11 0.28
8 22 0.56
9 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (8 bp):
ATTTTATA
Found at i:249355 original size:16 final size:16
Alignment explanation
Indices: 249331--249381 Score: 70
Period size: 15 Copynumber: 3.2 Consensus size: 16
249321 CAAAGACTCT
249331 ATTTT-TAATTTTATA
1 ATTTTATAATTTTATA
249346 ATTTTATAATTTTATA
1 ATTTTATAATTTTATA
*
249362 A-TTTATAGTTTTCATA
1 ATTTTATAATTTT-ATA
249378 ATTT
1 ATTT
249382 AATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 15 0.47
16 15 0.47
17 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTTTATAATTTTATA
Found at i:249440 original size:23 final size:22
Alignment explanation
Indices: 249333--249447 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 22
249323 AAGACTCTAT
*
249333 TTTTAATTTTATAATTTTAT-AA
1 TTTTAATTTTAT-ATTTCATAAA
*
249355 TTTTATAATTTATAGTTTTCAT-AA
1 TTTTA-ATTTTATA--TTTCATAAA
249379 -TTTAA-TTTA-ATTTCATAAAAAA
1 TTTTAATTTTATATTTCAT---AAA
249401 TGATTTAATTTTATATTTCTATAAA
1 T--TTTAATTTTATATTTC-ATAAA
249426 TTTTATATTTT-TATTTCATAAA
1 TTTTA-ATTTTATATTTCATAAA
249448 AAAAAATTAA
Statistics
Matches: 77, Mismatches: 2, Indels: 28
0.72 0.02 0.26
Matches are distributed among these distances:
18 6 0.08
20 1 0.01
21 4 0.05
22 14 0.18
23 20 0.26
24 12 0.16
25 9 0.12
26 4 0.05
27 5 0.06
28 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTAATTTTATATTTCATAAA
Found at i:253056 original size:48 final size:47
Alignment explanation
Indices: 252977--253070 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 47
252967 GAGAATTATG
*
252977 AAGACATCTTATTAAATCATAATAAACATATAAAACAAAATATATTGT
1 AAGACATCTTATTAAATCAAAATAAACATAT-AAACAAAATATATTGT
* * *
253025 AAGACATCTTATTAAATCAAAATGAATATATAAAGAAAATATATTG
1 AAGACATCTTATTAAATCAAAATAAACATATAAACAAAATATATTG
253071 CCTCGACTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 14 0.33
48 28 0.67
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (47 bp):
AAGACATCTTATTAAATCAAAATAAACATATAAACAAAATATATTGT
Found at i:258209 original size:17 final size:18
Alignment explanation
Indices: 258170--258212 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
258160 AATAAATATT
* *
258170 ATTATTTATATTTAATGT
1 ATTATTTATATTGAATGG
*
258188 TTTATTTATA-TGAATGG
1 ATTATTTATATTGAATGG
258205 ATTATTTA
1 ATTATTTA
258213 ATTAGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTATTTATATTGAATGG
Found at i:266393 original size:22 final size:22
Alignment explanation
Indices: 266358--266404 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
266348 GGTATTGATA
** *
266358 TTTTTATACGAGTATCAATATT
1 TTTTTATAAAAGTATCAATAAT
*
266380 TTTTTATAAAAGTATCGATAAT
1 TTTTTATAAAAGTATCAATAAT
266402 TTT
1 TTT
266405 AAACCAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTTATAAAAGTATCAATAAT
Found at i:266589 original size:4 final size:4
Alignment explanation
Indices: 266580--266626 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
266570 AGATGTATGA
* * *
266580 AAAT AAAT AAAT AAAA AAAT AAAT GAAT AAAT AAAT AATT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
266627 GTCAAAGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:272254 original size:17 final size:18
Alignment explanation
Indices: 272234--272275 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
272224 ACTACAATGC
272234 AAATGTACTAACAAAT-A
1 AAATGTACTAACAAATAA
* * *
272251 AAATGCAGTGACAAATAA
1 AAATGTACTAACAAATAA
272269 AAATGTA
1 AAATGTA
272276 ATGACAAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (18 bp):
AAATGTACTAACAAATAA
Found at i:272273 original size:18 final size:18
Alignment explanation
Indices: 272244--272287 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
272234 AAATGTACTA
*
272244 ACAAAT-AAAATGCAGTG
1 ACAAATAAAAATGCAATG
*
272261 ACAAATAAAAATGTAATG
1 ACAAATAAAAATGCAATG
*
272279 ACAAGTAAA
1 ACAAATAAA
272288 TGCTATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:286464 original size:24 final size:24
Alignment explanation
Indices: 286437--286499 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
286427 ACCATTTTGA
* * *
286437 GCTCGTAAGAGCTAACTATTCTGG
1 GCTCGTAAGAGCTAACCATCCTAG
286461 GCTCGTAAGAGCTAACCATCCTAG
1 GCTCGTAAGAGCTAACCATCCTAG
*
286485 GCTCGTGAGAGCTAA
1 GCTCGTAAGAGCTAA
286500 TGTTGTCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (24 bp):
GCTCGTAAGAGCTAACCATCCTAG
Found at i:291705 original size:24 final size:23
Alignment explanation
Indices: 291678--291752 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
291668 GTTATTAAAT
291678 ATATTATTTACACTTATATTTTAA
1 ATATTATTTA-ACTTATATTTTAA
** *
291702 ATATT-TTT--GGT-TA-TTAAA
1 ATATTATTTAACTTATATTTTAA
291720 TATATTATTTATACTTATATTTTAA
1 -ATATTATTTA-ACTTATATTTTAA
291745 ATATTATT
1 ATATTATT
291753 GGTTTAGGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
18 4 0.11
19 7 0.18
20 4 0.11
23 4 0.11
24 15 0.39
25 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
ATATTATTTAACTTATATTTTAA
Found at i:291715 original size:43 final size:43
Alignment explanation
Indices: 291668--291756 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
291658 TGCTATTTAT
*
291668 GTTATTAAATATATTATTTACACTTATATTTTAAATATTTTTG
1 GTTATTAAATATATTATTTACACTTATATTTTAAATATTATTG
*
291711 GTTATTAAATATATTATTTATACTTATATTTTAAATATTATTG
1 GTTATTAAATATATTATTTACACTTATATTTTAAATATTATTG
291754 GTT
1 GTT
291757 TAGGGAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (43 bp):
GTTATTAAATATATTATTTACACTTATATTTTAAATATTATTG
Found at i:293247 original size:20 final size:20
Alignment explanation
Indices: 293167--293253 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
293157 GGCCGGGAGC
* *
293167 TATTTTGACTTGTTTGAAAAA
1 TATTTTGACATGTTT-AAAAT
* *
293188 TATTTTG-CAAGTGTTCAAAT
1 TATTTTGACATGT-TTAAAAT
* * *
293208 GATTTTGACTTAG-TTCAAAT
1 TATTTTGACAT-GTTTAAAAT
293228 TATTTTGACATGTTTAAAAT
1 TATTTTGACATGTTTAAAAT
*
293248 CATTTT
1 TATTTT
293254 AGCGTGATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.02
20 39 0.76
21 10 0.20
22 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (20 bp):
TATTTTGACATGTTTAAAAT
Found at i:303912 original size:23 final size:23
Alignment explanation
Indices: 303884--304216 Score: 432
Period size: 23 Copynumber: 14.3 Consensus size: 23
303874 AGTGTAAGTG
*
303884 TGTGTTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
303907 TTTGTTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
303930 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
303953 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* * * *
303976 TATGCTTGAATATTAATATGGTT
1 TGTGCTTAAATATTAATGTGATT
*
303999 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
**
304022 TGTGCTTAATATATTAATACGATT
1 TGTGCTTAA-ATATTAATGTGATT
* *
304046 TGTGCTCAAATATTAATGTGACT
1 TGTGCTTAAATATTAATGTGATT
* *
304069 TATGCTTAAATATTGATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
304092 TATGCTTAAAAATATTAATGTGGTT
1 TGTGCTT--AAATATTAATGTGATT
304117 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
304140 TGTGCTTAAATATTACTATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
304163 TTTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
304186 TGTACTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
304209 TGTGCTTA
1 TGTGCTTA
304217 CAGAATTAAG
Statistics
Matches: 270, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
23 230 0.85
24 20 0.07
25 20 0.07
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (23 bp):
TGTGCTTAAATATTAATGTGATT
Found at i:305338 original size:21 final size:21
Alignment explanation
Indices: 305297--305369 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
305287 GGAGTTTTTA
305297 GTATCAGTAGAAGTAAG--ACTT
1 GTATCAGTAGAAG--AGTCACTT
305318 GTATCAGTAGAAGAGTCACTT
1 GTATCAGTAGAAGAGTCACTT
** *
305339 GTATTGGTAGAATTA-TCACTT
1 GTATCAGTAGAA-GAGTCACTT
*
305360 GTATCGGTAG
1 GTATCAGTAG
305370 GAGTCTGGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
21 42 0.93
22 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCAGTAGAAGAGTCACTT
Found at i:317059 original size:23 final size:23
Alignment explanation
Indices: 317033--317379 Score: 340
Period size: 23 Copynumber: 15.6 Consensus size: 23
317023 GTGTTCTTAT
* *
317033 ATTTATGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
* * *
317056 ATTTATGATTAAATATTAATGTA
1 ATTTGTGCTTAAATATTAATGTG
* * *
317079 ATTTGTGCTTAAGTATTAATATT
1 ATTTGTGCTTAAATATTAATGTG
*
317102 ATTTTTGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
* *
317125 CCTTT-TGTTTAAATATTAATGTG
1 -ATTTGTGCTTAAATATTAATGTG
* *
317148 A--CGTGTTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
**
317169 ATTTGTATTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
*
317192 CTTTGTGCTT-AA-ATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
* *
317213 ATTTATGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
* **
317236 ATATGTGCTTAAATATTAATGCA
1 ATTTGTGCTTAAATATTAATGTG
**
317259 ATTTGTGCTTAAATATTAATGCA
1 ATTTGTGCTTAAATATTAATGTG
*
317282 ATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
*
317305 ATTTGTGCTCAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
*
317328 A-------TTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
* * *
317344 ATTTATGATTAAATATTAACGTG
1 ATTTGTGCTTAAATATTAATGTG
317367 ATTTGTGCTTAAA
1 ATTTGTGCTTAAA
317380 GAATTAAGAT
Statistics
Matches: 270, Mismatches: 41, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
16 14 0.05
21 36 0.13
22 4 0.01
23 213 0.79
24 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
ATTTGTGCTTAAATATTAATGTG
Found at i:317201 original size:90 final size:88
Alignment explanation
Indices: 317033--317379 Score: 321
Period size: 90 Copynumber: 3.9 Consensus size: 88
317023 GTGTTCTTAT
* * * *
317033 ATTTATGCTTAAATATTAATATGATTTATGATTAAATATTAATGTAATTTGTGCTTAAGTATTAA
1 ATTTATGCTTAAATATTAATGTGA---GTG-TTAAATATTAATGTAATTTGTACTTAAATATTAA
* * *
317098 TATTATTTTTGCTTAAATATTAATGTG
62 TGTGATTTGTGCTTAAATATTAATGTG
* * * *
317125 CCTTT-TGTTTAAATATTAATGTGACGTGTTTAAATATTAATGTGATTTGTATTTAAATATTAAT
1 -ATTTATGCTTAAATATTAATGTGA-GTG-TTAAATATTAATGTAATTTGTACTTAAATATTAAT
*
317189 GTGCTTTGTGCTT-AA-ATTAATGTG
63 GTGATTTGTGCTTAAATATTAATGTG
* * *
317213 ATTTATGCTTAAATATTAATATGATATGTGCTTAAATATTAATGCAATTTGTGCTTAAATATTAA
1 ATTTATGCTTAAATATTAATGTG--A-GTG-TTAAATATTAATGTAATTTGTACTTAAATATTAA
** *
317278 TGCAATTTGTGCTTAAATATTAATATG
62 TGTGATTTGTGCTTAAATATTAATGTG
* * * * * *
317305 ATTTGTGCTCAAATATTAATGTGA---TTAAATATTAATATGATTTATGA-TTAAATATTAACGT
1 ATTTATGCTTAAATATTAATGTGAGTGTTAAATATTAATGTAATTTGT-ACTTAAATATTAATGT
317366 GATTTGTGCTTAAA
65 GATTTGTGCTTAAA
317380 GAATTAAGAT
Statistics
Matches: 210, Mismatches: 38, Indels: 20
0.78 0.14 0.07
Matches are distributed among these distances:
85 42 0.20
87 3 0.01
88 25 0.12
89 2 0.01
90 88 0.42
91 2 0.01
92 45 0.21
93 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (88 bp):
ATTTATGCTTAAATATTAATGTGAGTGTTAAATATTAATGTAATTTGTACTTAAATATTAATGTG
ATTTGTGCTTAAATATTAATGTG
Found at i:317334 original size:16 final size:16
Alignment explanation
Indices: 317315--317346 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
317305 ATTTGTGCTC
*
317315 AAATATTAATGTGATT
1 AAATATTAATATGATT
317331 AAATATTAATATGATT
1 AAATATTAATATGATT
317347 TATGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
AAATATTAATATGATT
Found at i:317344 original size:39 final size:39
Alignment explanation
Indices: 317285--317369 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
317275 TAATGCAATT
* * *
317285 TGTGCTTAAATATTAATATGATTTGTGCTCAAATATTAA
1 TGTGATTAAATATTAATATGATTTATGATCAAATATTAA
*
317324 TGTGATTAAATATTAATATGATTTATGATTAAATATTAA
1 TGTGATTAAATATTAATATGATTTATGATCAAATATTAA
*
317363 CGTGATT
1 TGTGATT
317370 TGTGCTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.45
Consensus pattern (39 bp):
TGTGATTAAATATTAATATGATTTATGATCAAATATTAA
Found at i:332255 original size:14 final size:14
Alignment explanation
Indices: 332210--332252 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
332200 TAAAATTTAA
*
332210 GTTTAAGATTAAAGG
1 GTTTAAGATT-ATGG
332225 GTTTAAGATTATGG
1 GTTTAAGATTATGG
332239 GTTTAAGATT-TGG
1 GTTTAAGATTATGG
332252 G
1 G
332253 GTTATAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 4 0.15
14 13 0.48
15 10 0.37
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (14 bp):
GTTTAAGATTATGG
Found at i:334552 original size:21 final size:21
Alignment explanation
Indices: 334528--334573 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
334518 TATCATGAAT
* *
334528 AGTGGAGTCAAGTCCATAAAC
1 AGTGGAATCAAATCCATAAAC
* *
334549 AGTGGAATCAAATTCATGAAC
1 AGTGGAATCAAATCCATAAAC
334570 AGTG
1 AGTG
334574 ATTATGTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (21 bp):
AGTGGAATCAAATCCATAAAC
Found at i:338510 original size:25 final size:24
Alignment explanation
Indices: 338461--338510 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
338451 ATTTTTTTTA
* *
338461 TTTTTTTAATTATAATATAATTAT
1 TTTTTTTAATTATAATAAAAATAT
338485 TTTTATTTAA-TATTAATAAAAATAT
1 TTTT-TTTAATTA-TAATAAAAATAT
338510 T
1 T
338511 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTTTAATTATAATAAAAATAT
Found at i:340177 original size:5 final size:5
Alignment explanation
Indices: 340167--340196 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
340157 TTTTGTATAT
340167 TGATG TGATG TGATG TGATG TGATG TGATG
1 TGATG TGATG TGATG TGATG TGATG TGATG
340197 ATATTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGATG
Found at i:345503 original size:10 final size:10
Alignment explanation
Indices: 345484--345528 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
345474 CATTTTTAAA
*
345484 TAAAATTTAT
1 TAAAAATTAT
345494 TAAAAATTAT
1 TAAAAATTAT
* *
345504 AAAAAAGTAT
1 TAAAAATTAT
*
345514 TAAAAATAAT
1 TAAAAATTAT
345524 TAAAA
1 TAAAA
345529 TTGTAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:350669 original size:34 final size:34
Alignment explanation
Indices: 350627--350702 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
350617 CATAAACTAA
* *
350627 ACCCAAATATTTTAAATTTTTTACCTTTTATCTT
1 ACCCAAATATTTTAAAATTTTTACCTTTTACCTT
*
350661 ACCTAAATATTTTAAAATTTTTACCTTTTACCTT
1 ACCCAAATATTTTAAAATTTTTACCTTTTACCTT
350695 ACCCAAAT
1 ACCCAAAT
350703 GCTGTTTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (34 bp):
ACCCAAATATTTTAAAATTTTTACCTTTTACCTT
Found at i:351471 original size:29 final size:29
Alignment explanation
Indices: 351438--351515 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
351428 TCACTAGATT
351438 GAACTGATTATATGT-ATACTATTGTATGC
1 GAACTGATTATATGTGA-ACTATTGTATGC
* *
351467 GAACTGATCATATGTGAACTATTGTATGT
1 GAACTGATTATATGTGAACTATTGTATGC
*
351496 GAACTGATTATGTGTGAACT
1 GAACTGATTATATGTGAACT
351516 GTTATCTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (29 bp):
GAACTGATTATATGTGAACTATTGTATGC
Found at i:351485 original size:15 final size:15
Alignment explanation
Indices: 351437--351520 Score: 86
Period size: 15 Copynumber: 5.8 Consensus size: 15
351427 ATCACTAGAT
351437 TGAACTGATTATATG
1 TGAACTGATTATATG
*
351452 T-ATACT-ATTGTATG
1 TGA-ACTGATTATATG
* *
351466 CGAACTGATCATATG
1 TGAACTGATTATATG
*
351481 TGAACT-ATTGTATG
1 TGAACTGATTATATG
*
351495 TGAACTGATTATGTG
1 TGAACTGATTATATG
351510 TGAACTG-TTAT
1 TGAACTGATTAT
351521 CTATGATCTA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
14 27 0.48
15 29 0.52
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (15 bp):
TGAACTGATTATATG
Found at i:352273 original size:13 final size:14
Alignment explanation
Indices: 352255--352285 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
352245 GTCAATGCAA
352255 TCAAA-GTTAAATG
1 TCAAAGGTTAAATG
352268 TCAAAGGTTAAATG
1 TCAAAGGTTAAATG
352282 TCAA
1 TCAA
352286 TGTACTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (14 bp):
TCAAAGGTTAAATG
Found at i:360225 original size:23 final size:23
Alignment explanation
Indices: 360192--360236 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
360182 AACCTATTCC
*
360192 TAATTTTTTGAAAGTAGACAAAA
1 TAATTTCTTGAAAGTAGACAAAA
360215 TAATTTCTTGAAAGTAGACAAA
1 TAATTTCTTGAAAGTAGACAAA
360237 GGTATAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (23 bp):
TAATTTCTTGAAAGTAGACAAAA
Found at i:360543 original size:21 final size:21
Alignment explanation
Indices: 360517--360558 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
360507 TAGAAATAAT
360517 CCTTTGATATTCTTTATCATG
1 CCTTTGATATTCTTTATCATG
360538 CCTTTGATATTCTTTATCATG
1 CCTTTGATATTCTTTATCATG
360559 GACTTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (21 bp):
CCTTTGATATTCTTTATCATG
Found at i:372931 original size:8 final size:9
Alignment explanation
Indices: 372909--372933 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
372899 GTATGTTGAA
372909 TAAAAAGTG
1 TAAAAAGTG
372918 TAAAAAGTG
1 TAAAAAGTG
372927 TAAAAAG
1 TAAAAAG
372934 GTTCTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (9 bp):
TAAAAAGTG
Found at i:387595 original size:18 final size:19
Alignment explanation
Indices: 387555--387596 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
387545 TTTTTTCTTC
**
387555 TTTTCTTTCTCTTTTATTT
1 TTTTCTTTCTCTTTTATGA
*
387574 TTTTCTTTCT-TTTTCTGA
1 TTTTCTTTCTCTTTTATGA
387592 TTTTC
1 TTTTC
387597 CTTTTCTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCTTTCTCTTTTATGA
Found at i:388484 original size:72 final size:72
Alignment explanation
Indices: 388367--388502 Score: 272
Period size: 72 Copynumber: 1.9 Consensus size: 72
388357 CTCCCGAGAT
388367 GTGTGATTCCTTGAGGTAATTCGATCTTTTTGTAGCAAAATACGATCAAATGGATGAACCAAAGA
1 GTGTGATTCCTTGAGGTAATTCGATCTTTTTGTAGCAAAATACGATCAAATGGATGAACCAAAGA
388432 TGGCCGA
66 TGGCCGA
388439 GTGTGATTCCTTGAGGTAATTCGATCTTTTTGTAGCAAAATACGATCAAATGGATGAACCAAAG
1 GTGTGATTCCTTGAGGTAATTCGATCTTTTTGTAGCAAAATACGATCAAATGGATGAACCAAAG
388503 TTGGTCGAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (72 bp):
GTGTGATTCCTTGAGGTAATTCGATCTTTTTGTAGCAAAATACGATCAAATGGATGAACCAAAGA
TGGCCGA
Found at i:389739 original size:9 final size:9
Alignment explanation
Indices: 389717--389759 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
389707 AAAATTATTT
389717 TTAAAA-TA
1 TTAAAATTA
389725 -TAAAATTA
1 TTAAAATTA
389733 TTAAAATTAA
1 TTAAAATT-A
389743 TTTAAAATTA
1 -TTAAAATTA
389753 TTAAAAT
1 TTAAAAT
389760 CAATATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 14 0.45
10 2 0.06
11 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TTAAAATTA
Found at i:390475 original size:9 final size:9
Alignment explanation
Indices: 390461--390503 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 9
390451 CAAATTTTTT
390461 TTTTAATAA
1 TTTTAATAA
390470 TTTTAAGTTAA
1 TTTTAA--TAA
390481 TTTTAAAATAA
1 TTTT--AATAA
390492 TTTTAATAA
1 TTTTAATAA
390501 TTT
1 TTT
390504 AAAAAGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 14 0.47
11 14 0.47
13 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TTTTAATAA
Done.