Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015252.1 Kokia drynarioides strain JFW-HI SEQ_130297, 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: 344124
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 305 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:415 original size:51 final size:51
Alignment explanation
Indices: 360--460 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 51
350 AGCAGGGGCG
360 AAAAAACAAAATAAAATTGTA-ATTTTTATAATAATAAAAATATAATTTTTA
1 AAAAAACAAAATAAAATTGTATATTTTTA-AATAATAAAAATATAATTTTTA
** * * * *
411 AAAAATTAAATTAAAATTTTATTATTTTTAAATGATTAAAATATAATTTT
1 AAAAAACAAAATAAAATTGTA-TATTTTTAAATAATAAAAATATAATTTT
461 ATCTTTATCA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 17 0.40
52 18 0.43
53 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (51 bp):
AAAAAACAAAATAAAATTGTATATTTTTAAATAATAAAAATATAATTTTTA
Found at i:428 original size:22 final size:23
Alignment explanation
Indices: 380--430 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
370 ATAAAATTGT
* *
380 AATTTTTATAATAATAAAAATAT
1 AATTTTTATAAAAATAAAAATAA
* *
403 AATTTTTA-AAAAATTAAATTAA
1 AATTTTTATAAAAATAAAAATAA
425 AATTTT
1 AATTTT
431 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTTTATAAAAATAAAAATAA
Found at i:438 original size:30 final size:30
Alignment explanation
Indices: 404--462 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
394 TAAAAATATA
*
404 ATTTTTAAAAAATTAAATTAAAATTTTATT
1 ATTTTTAAAAAATTAAAATAAAATTTTATT
** *
434 ATTTTTAAATGATTAAAATATAATTTTAT
1 ATTTTTAAAAAATTAAAATAAAATTTTAT
463 CTTTATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTTTAAAAAATTAAAATAAAATTTTATT
Found at i:797 original size:13 final size:13
Alignment explanation
Indices: 779--803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
769 TTAATACTTT
779 ATTAATTTGAAAA
1 ATTAATTTGAAAA
792 ATTAATTTGAAA
1 ATTAATTTGAAA
804 TTAAATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTAATTTGAAAA
Found at i:11835 original size:16 final size:18
Alignment explanation
Indices: 11814--11856 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
11804 GTACACATTA
11814 TTTTTTACAAT-TA-AAT
1 TTTTTTACAATATATAAT
*
11830 TTTTTTAAAATAATATAAT
1 TTTTTTACAAT-ATATAAT
11849 TTTTTTAC
1 TTTTTTAC
11857 TATAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
18 2 0.09
19 10 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTTACAATATATAAT
Found at i:12829 original size:30 final size:31
Alignment explanation
Indices: 12765--12835 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
12755 ACAACGAGAG
* * *
12765 GACTATTTTGTCACTTTTCTATAACTTTAGT
1 GACTATTTTGCCACATTTCTATAACTTGAGT
*
12796 GACTATTTTGCCACATTTCTA-AAGTTGAGT
1 GACTATTTTGCCACATTTCTATAACTTGAGT
*
12826 GACTGTTTTG
1 GACTATTTTG
12836 TTAAACGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (31 bp):
GACTATTTTGCCACATTTCTATAACTTGAGT
Found at i:12989 original size:30 final size:31
Alignment explanation
Indices: 12930--12989 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
12920 GGAAAAGGAC
*
12930 TGTTTTGTCACATTTTTAAAAGTTGAGGGAT
1 TGTTTTGTCACATTTTTAAAAGTTAAGGGAT
*
12961 TGTTTTGTCACA-TTTTCAAAGTTAAGGGA
1 TGTTTTGTCACATTTTTAAAAGTTAAGGGA
12990 CTGAAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (31 bp):
TGTTTTGTCACATTTTTAAAAGTTAAGGGAT
Found at i:13787 original size:23 final size:23
Alignment explanation
Indices: 13757--13816 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
13747 CATCACTTCA
13757 GTGCTTCATGTTATAGCACATTT-
1 GTGCTTCATGTTATAGCAC-TTTG
13780 GTGCTTCATGTTATAGCACTTTG
1 GTGCTTCATGTTATAGCACTTTG
*
13803 GTGTTTCATGTTAT
1 GTGCTTCATGTTAT
13817 CCGATATGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (23 bp):
GTGCTTCATGTTATAGCACTTTG
Found at i:20906 original size:14 final size:14
Alignment explanation
Indices: 20887--20916 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20877 CATTGACTTT
*
20887 TTGATCGTTGACCA
1 TTGATCATTGACCA
20901 TTGATCATTGACCA
1 TTGATCATTGACCA
20915 TT
1 TT
20917 TTGAGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (14 bp):
TTGATCATTGACCA
Found at i:23322 original size:3 final size:3
Alignment explanation
Indices: 23314--23362 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
23304 TGGGAAAAAT
23314 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23362 A
1 A
23363 AACTTGTGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:27533 original size:14 final size:14
Alignment explanation
Indices: 27502--27595 Score: 59
Period size: 14 Copynumber: 6.8 Consensus size: 14
27492 CGAACCCACT
*
27502 TTGACCATTAACCCG
1 TTGACCATTGA-CCG
27517 TTGACCATTGACCG
1 TTGACCATTGACCG
***
27531 TTGATTGTTGA-C-
1 TTGACCATTGACCG
* *
27543 TTGATCATTGATCG
1 TTGACCATTGACCG
*
27557 TTGA-CAGTTGACAG
1 TTGACCA-TTGACCG
** *
27571 TTGACCGCTGATCG
1 TTGACCATTGACCG
27585 TTGACCATTGA
1 TTGACCATTGA
27596 TCATTGACCG
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
12 9 0.15
13 4 0.07
14 37 0.61
15 11 0.18
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (14 bp):
TTGACCATTGACCG
Found at i:27566 original size:26 final size:26
Alignment explanation
Indices: 27517--27568 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
27507 CATTAACCCG
**
27517 TTGACCATTGACCGTTGATTGTTGAC
1 TTGACCATTGACCGTTGACAGTTGAC
* *
27543 TTGATCATTGATCGTTGACAGTTGAC
1 TTGACCATTGACCGTTGACAGTTGAC
27569 AGTTGACCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (26 bp):
TTGACCATTGACCGTTGACAGTTGAC
Found at i:27583 original size:28 final size:28
Alignment explanation
Indices: 27551--27605 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
27541 ACTTGATCAT
27551 TGATCGTTGA-CAGTTGA-CAGTTGACCGC
1 TGATCGTTGACCA-TTGATCA-TTGACCGC
27579 TGATCGTTGACCATTGATCATTGACCG
1 TGATCGTTGACCATTGATCATTGACCG
27606 TTACTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (28 bp):
TGATCGTTGACCATTGATCATTGACCGC
Found at i:27596 original size:14 final size:14
Alignment explanation
Indices: 27515--27604 Score: 62
Period size: 14 Copynumber: 6.6 Consensus size: 14
27505 ACCATTAACC
*
27515 CGTTGACCATTGAC
1 CGTTGACCATTGAT
***
27529 CGTTGATTGTTGA-
1 CGTTGACCATTGAT
*
27542 C-TTGATCATTGAT
1 CGTTGACCATTGAT
27555 CGTTGA-CAGTTGA-
1 CGTTGACCA-TTGAT
**
27568 CAGTTGACCGCTGAT
1 C-GTTGACCATTGAT
27583 CGTTGACCATTGAT
1 CGTTGACCATTGAT
*
27597 CATTGACC
1 CGTTGACC
27605 GTTACTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 9 0.15
13 5 0.08
14 44 0.73
15 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (14 bp):
CGTTGACCATTGAT
Found at i:27607 original size:21 final size:21
Alignment explanation
Indices: 27515--27607 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
27505 ACCATTAACC
* *
27515 CGTTGACCATTGACCGTTGAT
1 CGTTGACCGTTGACCATTGAT
* *
27536 TGTTGA-C-TTGATCATTGAT
1 CGTTGACCGTTGACCATTGAT
* *
27555 CGTTGACAGTTGA-CAGTTGAC
1 CGTTGACCGTTGACCA-TTGAT
* *
27576 CGCTGATCGTTGACCATTGAT
1 CGTTGACCGTTGACCATTGAT
*
27597 CATTGACCGTT
1 CGTTGACCGTT
27608 ACTTTTTAGG
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 15 0.27
20 3 0.05
21 35 0.64
22 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
CGTTGACCGTTGACCATTGAT
Found at i:29161 original size:18 final size:17
Alignment explanation
Indices: 29121--29168 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
29111 GATACATCAG
*
29121 GTTGCGTCGACATCGTC
1 GTTGCGTCGACATCGTA
*
29138 GATTGCGTCGACATTGGTA
1 G-TTGCGTCGACA-TCGTA
*
29157 GTTGCATCGACA
1 GTTGCGTCGACA
29169 ATTTTGGCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (17 bp):
GTTGCGTCGACATCGTA
Found at i:38332 original size:20 final size:20
Alignment explanation
Indices: 38309--38366 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
38299 TACAAAGGAA
*
38309 AAAGCATAAATACTTTTAGC
1 AAAGTATAAATACTTTTAGC
* *
38329 AAAGTATATATACTTTTAGT
1 AAAGTATAAATACTTTTAGC
* *
38349 GAAGTATAGATACTTTTA
1 AAAGTATAAATACTTTTA
38367 AAAAAGAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAGTATAAATACTTTTAGC
Found at i:40058 original size:24 final size:24
Alignment explanation
Indices: 40031--40085 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
40021 GATGGGGGTA
* *
40031 GAATTTGTGTCTGCATCTATATCT
1 GAATCTGTGTCTACATCTATATCT
* *
40055 GAATCTGTGTCTACATTTGTATCT
1 GAATCTGTGTCTACATCTATATCT
40079 GAATCTG
1 GAATCTG
40086 AATATGTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
GAATCTGTGTCTACATCTATATCT
Found at i:47057 original size:6 final size:6
Alignment explanation
Indices: 47046--47078 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47036 ATGTTTGTTG
*
47046 AATGAA AATGAA AATAAA AATGAA AATGAA AAT
1 AATGAA AATGAA AATGAA AATGAA AATGAA AAT
47079 TTATTACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (6 bp):
AATGAA
Found at i:55776 original size:18 final size:20
Alignment explanation
Indices: 55739--55784 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
55729 ATAGTTTGCA
55739 TGCATTTTTATTTATTGTCAC
1 TGCA-TTTTATTTATTGTCAC
*
55760 TGCATTTTA-TT-TTGTCAT
1 TGCATTTTATTTATTGTCAC
55778 TGCATTT
1 TGCATTT
55785 CTTTTGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 5 0.21
21 4 0.17
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (20 bp):
TGCATTTTATTTATTGTCAC
Found at i:59609 original size:63 final size:63
Alignment explanation
Indices: 59531--59657 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
59521 TAGAACCTTG
59531 CGCATCGACGATGTAGTCACGAAAAATGGTACTTGGGATAGGGATCGCCTTGCCTATCTTGTC
1 CGCATCGACGATGTAGTCACGAAAAATGGTACTTGGGATAGGGATCGCCTTGCCTATCTTGTC
59594 CGCATCGACGATGTAGTCACGAAAAATGGTACTTGGGATAGGGATCGCCTTGCCTATCTTGTC
1 CGCATCGACGATGTAGTCACGAAAAATGGTACTTGGGATAGGGATCGCCTTGCCTATCTTGTC
59657 C
1 C
59658 CATGGAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (63 bp):
CGCATCGACGATGTAGTCACGAAAAATGGTACTTGGGATAGGGATCGCCTTGCCTATCTTGTC
Found at i:64101 original size:36 final size:36
Alignment explanation
Indices: 64054--64153 Score: 146
Period size: 37 Copynumber: 2.8 Consensus size: 36
64044 TAGTAATAGG
64054 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* *
64090 CATGATCTTTGGGGTCAATAAGGAGTAAAATGAGCAT
1 CATGACCTTT-GGGTCAATAGGGAGTAAAATGAGCAT
* * *
64127 CATGACCTTTGGTTCAACAGGAAGTAA
1 CATGACCTTTGGGTCAATAGGGAGTAA
64154 GCATGAACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 22 0.39
37 34 0.61
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:64165 original size:28 final size:28
Alignment explanation
Indices: 64127--64181 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
64117 AAATGAGCAT
* *
64127 CATGACCTTTGGTTCAAC-AGGAAGTAAG
1 CATGAACTTTGGGTCAACAAGG-AGTAAG
64155 CATGAACTTTGGGTCAACAAGGAGTAA
1 CATGAACTTTGGGTCAACAAGGAGTAA
64182 ATCAGATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (28 bp):
CATGAACTTTGGGTCAACAAGGAGTAAG
Found at i:70354 original size:10 final size:10
Alignment explanation
Indices: 70339--70387 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
70329 TTTTTTGGTC
70339 AAAATATATA
1 AAAATATATA
70349 AAAATATAT-
1 AAAATATATA
*
70358 AAAAT-CATA
1 AAAATATATA
*
70367 AAAATTTATA
1 AAAATATATA
*
70377 AATATATATA
1 AAAATATATA
70387 A
1 A
70388 TATAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 2 0.06
9 10 0.30
10 21 0.64
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATATA
Found at i:70379 original size:8 final size:8
Alignment explanation
Indices: 70344--70399 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
70334 TGGTCAAAAT
*
70344 ATATAAAA
1 ATATATAA
70352 ATATATAAA
1 ATATAT-AA
*
70361 ATCATAAAA
1 AT-ATATAA
*
70370 ATTTATAA
1 ATATATAA
70378 ATATATATA
1 ATATATA-A
70387 ATATA-AA
1 ATATATAA
70394 ATATAT
1 ATATAT
70400 TCTAATGGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.15
8 16 0.41
9 14 0.36
10 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAA
Found at i:70446 original size:15 final size:15
Alignment explanation
Indices: 70423--70499 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
70413 GTAAGAAATG
*
70423 TTATTAAAATTTATA
1 TTATAAAAATTTATA
70438 TTATAAAAA-TTATTA
1 TTATAAAAATTTA-TA
* *
70453 TATATTACAAATATATA
1 T-TA-TAAAAATTTATA
* * *
70470 ATATAAAAATATATG
1 TTATAAAAATTTATA
70485 TTATAAAAATTTATA
1 TTATAAAAATTTATA
70500 AATATAACAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 3 0.06
15 33 0.67
16 4 0.08
17 7 0.14
18 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
TTATAAAAATTTATA
Found at i:71952 original size:15 final size:15
Alignment explanation
Indices: 71932--71962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71922 TATGAAGGGT
71932 ATTAATCTAAATTAA
1 ATTAATCTAAATTAA
*
71947 ATTAATCTAAGTTAA
1 ATTAATCTAAATTAA
71962 A
1 A
71963 AATAAAAATA
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:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTAATCTAAATTAA
Found at i:79858 original size:15 final size:15
Alignment explanation
Indices: 79838--79880 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
79828 TATAAGAGTT
*
79838 AAATTTTAGATTTTA
1 AAATTTAAGATTTTA
79853 AAATTTGAA-ATTTTTA
1 AAATTT-AAGA-TTTTA
79869 AAATTTAAGATT
1 AAATTTAAGATT
79881 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (15 bp):
AAATTTAAGATTTTA
Found at i:80428 original size:18 final size:18
Alignment explanation
Indices: 80405--80446 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
80395 TTCGATCAAG
*
80405 TTGACTAATC-CAATCGGT
1 TTGACTAA-CACAATCAGT
80423 TTGACTAACACAATCAGT
1 TTGACTAACACAATCAGT
80441 TTGACT
1 TTGACT
80447 GGTTCATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (18 bp):
TTGACTAACACAATCAGT
Found at i:80938 original size:22 final size:22
Alignment explanation
Indices: 80913--80957 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
80903 GCTTCATCAG
80913 TCTGTTTCCCCATCAATCACAC
1 TCTGTTTCCCCATCAATCACAC
80935 TCTGTTTCCCCATCAATCACAC
1 TCTGTTTCCCCATCAATCACAC
80957 T
1 T
80958 GCCAAGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.40, G:0.04, T:0.33
Consensus pattern (22 bp):
TCTGTTTCCCCATCAATCACAC
Found at i:82812 original size:42 final size:42
Alignment explanation
Indices: 82764--82844 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
82754 ACGTGTTATA
82764 ACTAGTATAAATATTTAATTTTATTGTTATAATAAATCATAC
1 ACTAGTATAAATATTTAATTTTATTGTTATAATAAATCATAC
82806 ACTAGTATAAATATTTAATTTTATTGTTATAATAAATCA
1 ACTAGTATAAATATTTAATTTTATTGTTATAATAAATCA
82845 AATATATGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (42 bp):
ACTAGTATAAATATTTAATTTTATTGTTATAATAAATCATAC
Found at i:87988 original size:42 final size:42
Alignment explanation
Indices: 87923--88141 Score: 330
Period size: 42 Copynumber: 5.2 Consensus size: 42
87913 GAGTCATAAT
* * * *
87923 TCTTCCTTTAATCATATTTTTATTCTCATTCCGAGACATGAG
1 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
* * *
87965 TCTTCCTTTAATAATAATCTTATTCTCATCCCGAGACATGAC
1 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
*
88007 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAC
1 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
*
88049 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATAAG
1 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
* * *
88091 TCTTCCTTTAGTCATAATCTCATTTTCATCTCGAGACATGAG
1 TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
88133 TCTTCCTTT
1 TCTTCCTTT
88142 TTATACATCA
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 164 1.00
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.40
Consensus pattern (42 bp):
TCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATGAG
Found at i:91664 original size:42 final size:42
Alignment explanation
Indices: 91617--91707 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
91607 CATTGCCAAC
91617 ATAGGAAGGTGTGGTTAGTGTGAGCATTTGAGTCTTTGATAA
1 ATAGGAAGGTGTGGTTAGTGTGAGCATTTGAGTCTTTGATAA
91659 ATAGGAAGGTGTGGTTAGTGTGAGCATTTGAGTCTTTGATAA
1 ATAGGAAGGTGTGGTTAGTGTGAGCATTTGAGTCTTTGATAA
91701 ATAGGAA
1 ATAGGAA
91708 AGTTAAGGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (42 bp):
ATAGGAAGGTGTGGTTAGTGTGAGCATTTGAGTCTTTGATAA
Found at i:94213 original size:2 final size:2
Alignment explanation
Indices: 94206--94235 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
94196 TACAGCTGCT
94206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
94236 GTTATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95044 original size:37 final size:37
Alignment explanation
Indices: 95016--95095 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
95006 ATTTTCGGAA
*
95016 TGCACCCAAGACTGTCGCTACATAAATATTCTTCAAT
1 TGCACCCAAGACTATCGCTACATAAATATTCTTCAAT
* * * *
95053 TGCATCCAGGACTATCGCTACATAAGTATTGTTCAAT
1 TGCACCCAAGACTATCGCTACATAAATATTCTTCAAT
95090 TGCACC
1 TGCACC
95096 TAAAAATGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (37 bp):
TGCACCCAAGACTATCGCTACATAAATATTCTTCAAT
Found at i:95108 original size:37 final size:37
Alignment explanation
Indices: 95028--95108 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
95018 CACCCAAGAC
** *
95028 TGTCGCTACATAAATATTCTTCAATTGCATCCAGGAC
1 TGTCGCTACATAAATATTCTTCAATTGCATCCAAAAA
* * *
95065 TATCGCTACATAAGTATTGTTCAATTGCA-CCTAAAAA
1 TGTCGCTACATAAATATTCTTCAATTGCATCC-AAAAA
95102 TGTCGCT
1 TGTCGCT
95109 GCATGAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
TGTCGCTACATAAATATTCTTCAATTGCATCCAAAAA
Found at i:95138 original size:26 final size:26
Alignment explanation
Indices: 95102--95154 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
95092 CACCTAAAAA
* *
95102 TGTCGCTGCATGAACATGTCTAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
*
95128 TGTCACTGCATGAACGTGTCCAGAAT
1 TGTCACTGCATGAACATGTCCAGAAT
95154 T
1 T
95155 ACGCCTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTCCAGAAT
Found at i:124269 original size:16 final size:16
Alignment explanation
Indices: 124248--124278 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
124238 ATGGAATGTT
*
124248 GGCAAGGTTTTAAAGG
1 GGCAAGGTTTGAAAGG
124264 GGCAAGGTTTGAAAG
1 GGCAAGGTTTGAAAG
124279 TGAAGTGGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.39, T:0.23
Consensus pattern (16 bp):
GGCAAGGTTTGAAAGG
Found at i:124624 original size:43 final size:42
Alignment explanation
Indices: 124564--124646 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
124554 AGTATGTGCG
* * *
124564 GGAGTTAGTGAAGTCATGCTTCAAATTTTGGGTTTGAGCGTA
1 GGAGTTAGTGAACTCATGCTTCAAATTTTAGATTTGAGCGTA
124606 GGAGTTCAGTGAACTCATGCTTCAAATTTTAGATTTGAGCG
1 GGAGTT-AGTGAACTCATGCTTCAAATTTTAGATTTGAGCG
124647 AGAAGGAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 6 0.16
43 31 0.84
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (42 bp):
GGAGTTAGTGAACTCATGCTTCAAATTTTAGATTTGAGCGTA
Found at i:131339 original size:24 final size:23
Alignment explanation
Indices: 131290--131339 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
131280 TAAAGTAGGT
* *
131290 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
131313 TATATTATGATTTTTGCTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
131337 TAT
1 TAT
131340 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:131418 original size:57 final size:58
Alignment explanation
Indices: 131331--131465 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 58
131321 GATTTTTGCT
* * *
131331 AATTCATATTTTAATAATAATTATATTAAAA-ATTTATTAAATTATATATTATT-TTATTA
1 AATT-ATA-TTTAATAATAAATATAGTAAAATA-TAATTAAATTATATATTATTATTATTA
* *
131390 AATTGTATTTAATAATAAATA-AGGTAAAATATAATTAAATTATTTATTATTATTATTA
1 AATTATATTTAATAATAAATATA-GTAAAATATAATTAAATTATATATTATTATTATTA
131448 AATTATATTTAATAATAA
1 AATTATATTTAATAATAA
131466 TCTTATTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
56 1 0.01
57 36 0.54
58 26 0.39
59 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (58 bp):
AATTATATTTAATAATAAATATAGTAAAATATAATTAAATTATATATTATTATTATTA
Found at i:131476 original size:58 final size:56
Alignment explanation
Indices: 131331--131482 Score: 171
Period size: 58 Copynumber: 2.6 Consensus size: 56
131321 GATTTTTGCT
*
131331 AATTCATATTTTAATAATAATTATATTAAAA-ATTTATTAAATTATATATTATTTTATTA
1 AATT-ATA-TTTAATAATAATT-TATTAAAATA-TAATTAAATTATATATTATTTTATTA
* * * * *
131390 AATTGTATTTAATAATAAATAAGGTAAAATATAATTAAATTATTTATTATTATTATTA
1 AATTATATTTAATAATAATTTA-TTAAAATATAATTAAATTATATATTATT-TTATTA
*
131448 AATTATATTTAATAATAATCTTATTAAAATTTAAT
1 AATTATATTTAATAATAAT-TTATTAAAATATAAT
131483 AACAATAATC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 35 0.45
58 36 0.46
59 6 0.08
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (56 bp):
AATTATATTTAATAATAATTTATTAAAATATAATTAAATTATATATTATTTTATTA
Found at i:134750 original size:198 final size:204
Alignment explanation
Indices: 134373--135024 Score: 657
Period size: 198 Copynumber: 3.2 Consensus size: 204
134363 CCACAAAATA
* * * ** * * * * *
134373 ATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAACCAAGCTCGCGCACGATGTGAGC
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCAAAGTAAAC
* * * * * * * * * *
134438 -AAGTCTTCAAATCC-CAGCTTCCTGATG-ACACACCGAGAAGCAGATCGGAGCAATAAATAGTT
66 AAAATCTTCGAACCCACAACTTCCTGA-GAAGATACTGAAAAGCAGGTC-GAACAAT-AA-AGTT
* *
134500 AGCTTCCTGATGAGATACGGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGG
127 AGCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
* *
134565 ATTGAAACGAACA
192 ATTGAAACAAACG
* * *
134578 ATGCGGTCGTCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCGACA-T-GA
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTC-AAAGTAAA
* * *
134641 GAAAATCTTCGAA-CCACAAC-TCCTTGATG-AGATACTGAGAAGC-GTGTCG-A-AGT-AA-TT
65 CAAAATCTTCGAACCCACAACTTCC-TGA-GAAGATACTGAAAAGCAG-GTCGAACAATAAAGTT
* *
134698 AGCTTCCTAATGAGATACAGAGAAGTAGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGG
127 AGCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
*
134763 ATTAAAACAAACG
192 ATTGAAACAAACG
* * * * * *
134776 ACGCGATCATCTTCCTAATGAGATATTGAGAAGAAGACCAAATCGAACCCATGCTCAAAGTAAAC
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCAAAGTAAAC
* *
134841 AAAATCTTCGAACCCCCAGCTTCCTGAGAAGATACTGAAAAGCAGGTCGAAACAATACAAGGTTA
66 AAAATCTTCGAACCCACAACTTCCTGAGAAGATACTGAAAAGCAGGTCG-AACAATA-AA-GTTA
* * * * * * *
134906 GCTTCCTGATGAGATACTGAGAAGT-GAACCAAACTCGTATTCCTGATGAGGTATAGAGAAGTGA
128 GCTTCCTGATGAGATACAGAGAAGTAG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
134970 ATTGAAACAAACG
192 ATTGAAACAAACG
*
134983 ATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
135025 TCGATAAAAC
Statistics
Matches: 370, Mismatches: 58, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
197 2 0.01
198 123 0.33
199 15 0.04
200 26 0.07
201 4 0.01
202 3 0.01
203 2 0.01
204 7 0.02
205 82 0.22
206 1 0.00
207 105 0.28
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (204 bp):
ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGCTCAAAGTAAAC
AAAATCTTCGAACCCACAACTTCCTGAGAAGATACTGAAAAGCAGGTCGAACAATAAAGTTAGCT
TCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
AAACAAACG
Found at i:135287 original size:17 final size:17
Alignment explanation
Indices: 135263--135319 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
135253 TTGGAAATTG
135263 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
135280 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
135297 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
135314 AATTTA
1 AATTTA
135320 GAAAAGTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:136256 original size:21 final size:23
Alignment explanation
Indices: 136226--136267 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
136216 GGGGAAAACC
*
136226 GTTTGGATCTAG-GCTAGATCTG
1 GTTTGGATCTAGACCTAGATCTG
136248 GTTT-GATCTAGACCTAGATC
1 GTTTGGATCTAGACCTAGATC
136268 CGTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (23 bp):
GTTTGGATCTAGACCTAGATCTG
Found at i:136272 original size:21 final size:21
Alignment explanation
Indices: 136224--136272 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
136214 AAGGGGAAAA
*
136224 CCGTTTGGATCTAGGCTAGAT
1 CCGTTTGGATCTAGCCTAGAT
*
136245 CTGGTTT-GATCTAGACCTAGAT
1 C-CGTTTGGATCTAG-CCTAGAT
136267 CCGTTT
1 CCGTTT
136273 TTTTAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (21 bp):
CCGTTTGGATCTAGCCTAGAT
Found at i:137172 original size:61 final size:60
Alignment explanation
Indices: 137070--137397 Score: 416
Period size: 61 Copynumber: 5.5 Consensus size: 60
137060 GAGGTCCCTA
* * *
137070 AACCTTCTGAAAATTACCATTTTAACCCCGAATTTCCAAAAATCCCATTTTTTTTACCCCG
1 AACCTTCTAAAAATTACCATTTT-ACCCCGAACTTCCAAAAATCCCATTTTTTTGACCCCG
* * *
137131 AACCTTCTAAAAATTACCATTTTACTCCCGAACTTCAAAAAATCCCATTTTTTTTACCTCG
1 AACCTTCTAAAAATTACCATTTTAC-CCCGAACTTCCAAAAATCCCATTTTTTTGACCCCG
* * *
137192 AACCTTCTAAAAATGACCATTTTACCCCCGAACTTCCAAAAATCCCA--ATTTTGACCTCG
1 AACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTTTGACCCCG
* *
137251 AACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTTTGACTCCG
1 AACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTTTGACCCCG
* * *
137311 AACCTTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCA--TTTTTGACTCTG
1 AACC-TTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTTTGACCCCG
* *
137371 AACCTTC-CAAAACTACCATTTTACCCC
1 AACCTTCTAAAAATTACCATTTTACCCC
137398 CCCGTGCATC
Statistics
Matches: 243, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
57 1 0.00
58 16 0.07
59 58 0.24
60 33 0.14
61 134 0.55
62 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (60 bp):
AACCTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTTTGACCCCG
Found at i:137297 original size:120 final size:119
Alignment explanation
Indices: 137070--137398 Score: 448
Period size: 120 Copynumber: 2.7 Consensus size: 119
137060 GAGGTCCCTA
* * * * * *
137070 AACCTTCTGAAAATTACCATTTTAACCCCGAATTTCCAAAAATCCCATTTTTTTTACCCCGAACC
1 AACCTTCTAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTGACCTCGAACC
* * *
137135 TTCTAAAAATTACCATTTTACTCCCGAACTTCAAAAAATCCCATTTTTTTTAC-CTCG
64 TTCTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCA-TTTTTTGACTC-CG
* *
137192 AACCTTCTAAAAATGACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCTCGAACCTT
1 AACCTTCTAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
*
137257 CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTGACTCCG
66 CTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTTTGACTCCG
*
137311 AACCTTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CTCTGAACC
1 AACC-TTCTAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTC-GAACC
* *
137375 TTC-CAAAACTACCATTTTACCCCC
64 TTCTAAAAATTACCATTTTACCCCC
137399 CCGTGCATCC
Statistics
Matches: 188, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
119 36 0.19
120 109 0.58
122 43 0.23
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (119 bp):
AACCTTCTAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
CTAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTTTGACTCCG
Found at i:140049 original size:32 final size:32
Alignment explanation
Indices: 140008--140116 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 32
139998 AAATATTTTT
140008 ATAAGATAAATATGATTTTGATTGTATTGTTA
1 ATAAGATAAATATGATTTTGATTGTATTGTTA
** * *
140040 ATAAGATAAATACTTTGATAGGGTGAGTG-ACTGTTA
1 ATAAGATAAATA---TGAT--TTTGATTGTATTGTTA
* *
140076 ATAA-A-AAATA-GTTTTTAATTGTATTGTTA
1 ATAAGATAAATATGATTTTGATTGTATTGTTA
140105 ATAAGATAAATA
1 ATAAGATAAATA
140117 CAATTTAAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
28 4 0.07
29 10 0.17
30 3 0.05
31 5 0.08
32 12 0.20
34 5 0.08
35 5 0.08
36 10 0.17
37 5 0.08
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (32 bp):
ATAAGATAAATATGATTTTGATTGTATTGTTA
Found at i:148312 original size:8 final size:9
Alignment explanation
Indices: 148288--148313 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
148278 AAGGTTCAAA
148288 AAGAAAAAG
1 AAGAAAAAG
148297 AAGAAAAAG
1 AAGAAAAAG
148306 AAGAAAAA
1 AAGAAAAA
148314 AATATGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:168128 original size:96 final size:96
Alignment explanation
Indices: 167947--168128 Score: 219
Period size: 96 Copynumber: 1.9 Consensus size: 96
167937 AAGAATATCT
** *
167947 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGA
* ** *
168012 TAAGGAAACATTGTCTCGATTAAGGGTATTC
66 TAAAGAAACATTACCCCGATTAAGGGTATTC
*
168043 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC-GAAACTCGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA-TCGA
*
168106 A-ATAAA-AGAATATTACCCCGATT
63 AGATAAAGA-AACATTACCCCGATT
168129 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
95 3 0.04
96 65 0.89
97 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGA
TAAAGAAACATTACCCCGATTAAGGGTATTC
Found at i:168525 original size:30 final size:29
Alignment explanation
Indices: 168479--168700 Score: 265
Period size: 29 Copynumber: 7.6 Consensus size: 29
168469 ATCCGAGGGG
*
168479 AAAAATGTAATTTTTGGAAGTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGGGGTC
*
168508 AAAAATGGATTTTTTTGGAAGTTTGAGGGT-
1 AAAAATGGA-ATTTTTGGAAGTTTG-GGGTC
168538 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTT-GGGGTC
*
168568 AAAAATGGAATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAG-TTTGGGGTC
*
168598 -AAAATGGAATTTTTTGAA-TTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTT-G-GGGTC
**
168626 AAAAATGGAATTTTTGGAAGTTTCCAGGTC
1 AAAAATGGAATTTTTGGAAGTTT-GGGGTC
* *
168656 GAAAATGGAATTTTTGGAAGTTCGGGGGT-
1 AAAAATGGAATTTTTGGAAGTT-TGGGGTC
168685 AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
168701 AATAGTTTAG
Statistics
Matches: 168, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.02
29 81 0.48
30 77 0.46
31 7 0.04
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGTC
Found at i:168536 original size:59 final size:58
Alignment explanation
Indices: 168473--168700 Score: 284
Period size: 59 Copynumber: 3.9 Consensus size: 58
168463 TTGGTCATCC
* *
168473 GAGGGGAAAAATGTAATTTTTGGAAGTTT-GGGGTCAAAAATGGATTTTTTTGGAAGTTT
1 GAGGGGAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGA-ATTTTTGGAAGTTT
*
168532 GAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GAGGGGAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTT
* ** *
168591 TAGGGTCAAAATGGAATTTTTTGAA-TTTCGAGGGTAAAAATGGAATTTTTGGAAGTTT
1 GAGGGGAAAAATGGAATTTTTGGAAGTTTCG-GGGTAAAAATGGAATTTTTGGAAGTTT
* *
168649 CCAGGTCG-AAAATGGAATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTG
1 -GAGG-GGAAAAATGGAATTTTTGGAAGTTTC-GGGGTAAAAATGGAATTTTTG
168701 AATAGTTTAG
Statistics
Matches: 153, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
58 28 0.18
59 109 0.71
60 16 0.10
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (58 bp):
GAGGGGAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:170644 original size:18 final size:17
Alignment explanation
Indices: 170621--170727 Score: 115
Period size: 17 Copynumber: 6.2 Consensus size: 17
170611 TATAATAAGT
170621 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
170639 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
**
170656 TTTAAATTTTAAAGCAAA
1 TTTAAA-TTTAAAATAAA
170674 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
170691 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
170708 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
170725 TTT
1 TTT
170728 TAGAATGAGT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
17 49 0.67
18 24 0.33
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:170662 original size:35 final size:34
Alignment explanation
Indices: 170621--170727 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 34
170611 TATAATAAGT
* *
170621 TTTAAATTTAAATATAAATCTAAATTTATATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTTAAAATAAA
** *
170656 TTTAAATTTTAAAGCAAATTTAAATTTAAAATAAA
1 TTTAAA-TTTAAAATAAATCTAAATTTAAAATAAA
* * * **
170691 TTTATATTCAAAATAAATTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
170725 TTT
1 TTT
170728 TAGAATGAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
34 26 0.43
35 28 0.47
36 6 0.10
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
Found at i:170668 original size:7 final size:6
Alignment explanation
Indices: 170621--170712 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
170611 TATAATAAGT
* * *
170621 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * *
170669 -GCAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
170713 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 44 0.69
7 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:170674 original size:29 final size:29
Alignment explanation
Indices: 170622--170677 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
170612 ATAATAAGTT
*
170622 TTAAATTTAAATATAAATCTAAATTTATA
1 TTAAATTTAAATATAAAGCTAAATTTATA
*
170651 TTAAATTTAAATTTTAAAGC-AAATTTA
1 TTAAATTTAAA-TATAAAGCTAAATTTA
170678 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TTAAATTTAAATATAAAGCTAAATTTATA
Found at i:171492 original size:118 final size:119
Alignment explanation
Indices: 171161--171533 Score: 577
Period size: 118 Copynumber: 3.1 Consensus size: 119
171151 TCACTTCCCC
* * * * * * *
171161 GTATTTCATCGGGAAGCTAACCGTTTTATTACTTCGACTTACTTCTCAGTATCTCATCAAGAAGC
1 GTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGC
* *
171226 TGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTTA
65 TAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
* * * * * *
171281 GTATCTCATTAAGAAGCTAACCTTTTATCGCTTCAACCTGCTTCTCACTGTCTCATCAGGAAACT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT
* *
171346 AGGGTTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGATCTTCTTCTCA
66 AGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
171400 GTATCTCATCAGGAAGCTAACC-TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT
171464 AGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
66 AGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
171518 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
171534 ATGACCATGT
Statistics
Matches: 228, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
118 106 0.46
119 104 0.46
120 18 0.08
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (119 bp):
GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT
AGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
Found at i:171761 original size:205 final size:205
Alignment explanation
Indices: 171393--171949 Score: 963
Period size: 205 Copynumber: 2.7 Consensus size: 205
171383 ATTTGATCTT
171393 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
*
171457 GGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
* * * * * *
171522 CTCATCAGGAAGATGACCATGTCGTTTTTTTCAATTTGCTTTTCTGTATCTCATTAGGAAGATGA
131 CTCATCAGGAAGATGACCACGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACGA
171587 ATTTGGTCCA
196 ATTTGGTCCA
*
171597 CTTCTCAGTAGCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
*
171662 GGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
**
171727 CTCATCAGGAAGATGACTGCGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCACGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACGA
171792 ATTTGGTCCA
196 ATTTGGTCCA
*
171802 CTTCTCAGTATCTCATCAGGAAGCTAATCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
* * * *
171867 GGAAGTTGGGGTTCAAAGATTTGCTCACATCGAGCATAGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
171932 CTCATCAGGAAGATGACC
131 CTCATCAGGAAGATGACC
171950 GCTTCGTTCG
Statistics
Matches: 333, Mismatches: 19, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
204 28 0.08
205 305 0.92
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (205 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
CTCATCAGGAAGATGACCACGTCATTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACGA
ATTTGGTCCA
Found at i:183059 original size:96 final size:96
Alignment explanation
Indices: 182880--183062 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
182870 GGGAAAAAGA
* ** **
182880 TATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCAGAATC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCAAATATTTCAGAATC
**
182945 GAAGATAAGGAAACATTGCCTCAATTAAGGG
66 GAAGATAAAAAAACATTGCCTCAATTAAGGG
* * *
182976 TATTCGATTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTTGA-AAC
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGC-CAAATATTTCAGAA-
*
183040 TCGAA-ATAAAAAAATATTGCCTC
64 TCGAAGATAAAAAAACATTGCCTC
183063 GATTTTAAAG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
96 62 0.84
97 12 0.16
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (96 bp):
TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCAAATATTTCAGAATC
GAAGATAAAAAAACATTGCCTCAATTAAGGG
Found at i:183365 original size:58 final size:60
Alignment explanation
Indices: 183270--183405 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 60
183260 ATCGGAGTTG
* * * * *
183270 AAAATGAGACTTTTTGGATACTTGGAGGGGCAAAAGGGTGATTTTGGGAAATTCGAGGTTA
1 AAAATGA-AATTTTTAGATACTTGGAGGGGCAAAAGGGTAATTTTGAGAAATTCGAGGTCA
* ** *
183331 AAAATGAAATTTTTAGATA-TTGG-GGGGTAAAAGGGTAATTTTGAGAGTTTCGAGGTCG
1 AAAATGAAATTTTTAGATACTTGGAGGGGCAAAAGGGTAATTTTGAGAAATTCGAGGTCA
* *
183389 AAAATGGAGTTTTTAGA
1 AAAATGAAATTTTTAGA
183406 CATCCCGGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 43 0.67
59 4 0.06
60 10 0.16
61 7 0.11
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (60 bp):
AAAATGAAATTTTTAGATACTTGGAGGGGCAAAAGGGTAATTTTGAGAAATTCGAGGTCA
Found at i:183478 original size:29 final size:29
Alignment explanation
Indices: 183417--183602 Score: 243
Period size: 29 Copynumber: 6.4 Consensus size: 29
183407 ATCCCGGGGG
* * * *
183417 AAAATGTAATTTTTGAAAGTTTGA-GGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
183445 AAAATGGAATTTTTGGAAGTTCGACTGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
183474 AAAATGGAATTTTTTGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
183502 AAAATGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGG-TA
*
183532 AAAATGGAATTTTTGGAAGTTTCGA-GGTT
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
183561 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
183590 AAAATGGAATTTT
1 AAAATGGAATTTT
183603 AGAATAGTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
28 50 0.36
29 64 0.46
30 21 0.15
31 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:183566 original size:87 final size:86
Alignment explanation
Indices: 183417--183612 Score: 270
Period size: 87 Copynumber: 2.3 Consensus size: 86
183407 ATCCCGGGGG
* * *
183417 AAAATGTAATTTTTGAAAGTTTGAGGTCAAAATGGAATTTTTGGAAGTTCGACTGTAAAAATGGA
1 AAAATGGAATTTTTGAAAGTTTGAGGTAAAAATGGAATTTTTGGAAGTTCGACGGTAAAAATGGA
*
183482 ATTTTTTGAAGTTCGAGGGT-
66 ATTTTTGGAAGTTCGAGGGTA
* * *
183502 AAAATGGAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTCGA-GGTTAAAAT
1 AAAATGGAATTTTTGAAAGTTTGA-GG-TAAAAATGGAATTTTTGGAAG-TTCGACGGTAAAAAT
183566 GGAATTTTTGGAAGTTCGAGGGTA
63 GGAATTTTTGGAAGTTCGAGGGTA
*
183590 AAAATGGAATTTTAGAATAGTTT
1 AAAATGGAATTTTTGAA-AGTTT
183613 AGGGACCTCC
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
85 21 0.22
86 2 0.02
87 49 0.51
88 20 0.21
89 5 0.05
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (86 bp):
AAAATGGAATTTTTGAAAGTTTGAGGTAAAAATGGAATTTTTGGAAGTTCGACGGTAAAAATGGA
ATTTTTGGAAGTTCGAGGGTA
Found at i:185504 original size:18 final size:17
Alignment explanation
Indices: 185462--185502 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
185452 TATAGTAAGT
*
185462 TTTAAATTTAAATATAAA
1 TTTAAATTTATAT-TAAA
*
185480 TCTAAATTTATATTAAA
1 TTTAAATTTATATTAAA
185497 TTTAAA
1 TTTAAA
185503 ATAAACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:185524 original size:22 final size:22
Alignment explanation
Indices: 185469--185524 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
185459 AGTTTTAAAT
* *
185469 TTAAATATAAATCTAAATTTATA
1 TTAAATATAAA-ATAAACTTATA
*
185492 TTAAATTTAAAATAAACTTATA
1 TTAAATATAAAATAAACTTATA
185514 TTCAAA-ATAAA
1 TT-AAATATAAA
185525 TTTAACCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAATATAAAATAAACTTATA
Found at i:210179 original size:165 final size:165
Alignment explanation
Indices: 209907--210234 Score: 611
Period size: 165 Copynumber: 2.0 Consensus size: 165
209897 TATTAAATGA
**
209907 AAATGTTAAAATATGTCTTTTTAAATAATTGAATTTTTAAATATTTTTTAATTGTATTAAGGAAT
1 AAATGTTAAAATATGTCTTTTTAAATAATTGAATTTTTAAATATTTGGTAATTGTATTAAGGAAT
*
209972 GATTGTAGAATCATCATCAAGTCAAGCAGCATTAAGATATCTTGTGGAGCTCTCATTTTGATGAA
66 AATTGTAGAATCATCATCAAGTCAAGCAGCATTAAGATATCTTGTGGAGCTCTCATTTTGATGAA
210037 AGTTAAAAAAACTGACAGTCTATATATTCTGTAAG
131 AGTTAAAAAAACTGACAGTCTATATATTCTGTAAG
210072 AAATGTTAAAATATGTCTTTTTAAATAATTGAATTTTTAAATATTTGGTAATTGTATTAAGGAAT
1 AAATGTTAAAATATGTCTTTTTAAATAATTGAATTTTTAAATATTTGGTAATTGTATTAAGGAAT
*
210137 AATTGTAGAATCATCATCAAGTCAAGTAGCATTAAGATATCTTGTGGAGCTCTCATTTTGATGAA
66 AATTGTAGAATCATCATCAAGTCAAGCAGCATTAAGATATCTTGTGGAGCTCTCATTTTGATGAA
*
210202 ATTTAAAAAAACTGACAGTCTATATATTCTGTA
131 AGTTAAAAAAACTGACAGTCTATATATTCTGTA
210235 GGGTTCAATA
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 158 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (165 bp):
AAATGTTAAAATATGTCTTTTTAAATAATTGAATTTTTAAATATTTGGTAATTGTATTAAGGAAT
AATTGTAGAATCATCATCAAGTCAAGCAGCATTAAGATATCTTGTGGAGCTCTCATTTTGATGAA
AGTTAAAAAAACTGACAGTCTATATATTCTGTAAG
Found at i:215825 original size:20 final size:20
Alignment explanation
Indices: 215802--215844 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
215792 TTCTTTTTTA
215802 TTAATGTTGGAACCTTTTCT
1 TTAATGTTGGAACCTTTTCT
215822 TTAATGTTGGAACCTTTTCT
1 TTAATGTTGGAACCTTTTCT
215842 TTA
1 TTA
215845 TGAAGAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (20 bp):
TTAATGTTGGAACCTTTTCT
Found at i:215929 original size:34 final size:34
Alignment explanation
Indices: 215865--215930 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
215855 AGCTTGGTTG
* *
215865 GGGGGTTGATTTTAGGGTTTTTTTGCCATTGATT
1 GGGGGTTGATTTTAAGGTTTTCTTGCCATTGATT
215899 GGGGGTTGATTTTAAGG-TTTCTTGCTCATTGA
1 GGGGGTTGATTTTAAGGTTTTCTTGC-CATTGA
215931 CCAATCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.14, C:0.08, G:0.32, T:0.47
Consensus pattern (34 bp):
GGGGGTTGATTTTAAGGTTTTCTTGCCATTGATT
Found at i:216943 original size:11 final size:11
Alignment explanation
Indices: 216927--217005 Score: 63
Period size: 11 Copynumber: 7.0 Consensus size: 11
216917 CTAAACTCAT
216927 TTTTAAATTTA
1 TTTTAAATTTA
216938 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
216950 ATTT-ATTTTAA
1 TTTTAAATTT-A
*
216961 GTTTAAATTTA
1 TTTTAAATTTA
*
216972 TTTTCAATTTAA
1 TTTTAAATTT-A
*
216984 ATTT-AATTTA
1 TTTTAAATTTA
216994 TTTTTAAATTTA
1 -TTTTAAATTTA
217006 AATTCATTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
10 1 0.02
11 36 0.65
12 18 0.33
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:216948 original size:6 final size:6
Alignment explanation
Indices: 216928--217066 Score: 96
Period size: 6 Copynumber: 24.2 Consensus size: 6
216918 TAAACTCATT
* * * *
216928 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * *
216973 TTTCAA TTTAAA TTT-AA TTTATT TTTAAA TTTAAA -TT-CA TTCTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
* **
217019 TTCAAA TTTATT TTTAAA TTTAAA TTT--A TTCTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA
217066 T
1 T
217067 GTCCAAAAAT
Statistics
Matches: 101, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
4 4 0.04
5 21 0.21
6 71 0.70
7 5 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:216950 original size:17 final size:17
Alignment explanation
Indices: 216928--217063 Score: 146
Period size: 17 Copynumber: 7.6 Consensus size: 17
216918 TAAACTCATT
216928 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
216945 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
216962 TTTAAATTTATTTTCAA
1 TTTAAATTTATTTTAAA
216979 TTTAAATTTAATTTATTTTTAAA
1 TTT--A---AATTTA-TTTTAAA
* * *
217002 TTTAAATTCATTCTAAG
1 TTTAAATTTATTTTAAA
*
217019 TTCAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
217037 TTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAA
217054 TTTAAATTTA
1 TTTAAATTTA
217064 AATGTCCAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
17 63 0.64
18 19 0.19
19 1 0.01
21 1 0.01
22 6 0.06
23 9 0.09
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:216954 original size:23 final size:23
Alignment explanation
Indices: 216939--217066 Score: 86
Period size: 23 Copynumber: 5.6 Consensus size: 23
216929 TTAAATTTAT
* *
216939 TTTAAATTTAAATTTATTTTAAG
1 TTTAAATTTAAATTTAATTTAAA
*
216962 TTTAAATTT-ATTTTCAATTTAAA
1 TTTAAATTTAAATTT-AATTTAAA
**
216985 TTT-AATTTATTTTTAAATTTAAA
1 TTTAAATTTAAATTT-AATTTAAA
* * * **
217008 -TT-CATTCTAAGTTCAAATTTATT
1 TTTAAATT-TAAATT-TAATTTAAA
217031 TTTAAATTTAAATTT-ATTCTAAA
1 TTTAAATTTAAATTTAATT-TAAA
217054 TTTAAATTTAAAT
1 TTTAAATTTAAAT
217067 GTCCAAAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
22 17 0.21
23 55 0.67
24 7 0.09
25 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:216967 original size:34 final size:35
Alignment explanation
Indices: 216928--217063 Score: 159
Period size: 35 Copynumber: 3.8 Consensus size: 35
216918 TAAACTCATT
* *
216928 TTTAAATTTATTTTAAATTTAAATTTA-TTTTAAG
1 TTTAAATTTATTCTAAATTTAAATTTATTTTTAAA
216962 TTTAAATTTATTTTCAATTTAAATTT-AATTTATTTTTAAA
1 TTTAAATTTA--TTC----TAAATTTAAATTTATTTTTAAA
* * *
217002 TTTAAATTCATTCTAAGTTCAAATTTATTTTTAAA
1 TTTAAATTTATTCTAAATTTAAATTTATTTTTAAA
217037 TTTAAATTTATTCTAAATTTAAATTTA
1 TTTAAATTTATTCTAAATTTAAATTTA
217064 AATGTCCAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
34 15 0.17
35 38 0.44
36 2 0.02
38 3 0.03
39 6 0.07
40 22 0.26
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTCTAAATTTAAATTTATTTTTAAA
Found at i:218647 original size:29 final size:29
Alignment explanation
Indices: 218604--218940 Score: 256
Period size: 29 Copynumber: 11.5 Consensus size: 29
218594 AAATCACATT
* *
218604 TCAAACTTTTCAAAAATTACATTTTTTCCC
1 TCAAAC-TTCCAAAAATTACATTTTTGCCC
* *
218634 TCGAACTTCCAAAAAATACA-TTTTGCCC
1 TCAAACTTCCAAAAATTACATTTTTGCCC
* * *
218662 TTAAACTTCCAAAAATCACATTTTTACCC
1 TCAAACTTCCAAAAATTACATTTTTGCCC
218691 -CTAAACTT-CATAAAATTTACATTTTTGCCC
1 TC-AAACTTCCA-AAAA-TTACATTTTTGCCC
* * * * *
218721 TCGAACTTCTCAAAAATAATAATTTT-ACC
1 TCAAACTTC-CAAAAATTACATTTTTGCCC
* * *
218750 TTAAACTTCCAAAAATCACATTTTTACCC
1 TCAAACTTCCAAAAATTACATTTTTGCCC
* *
218779 CCAAACTTTTCCAAAATTTACATTTTTGCCC
1 TCAAAC--TTCCAAAAATTACATTTTTGCCC
*
218810 TTAAACTTCC-AAAATTCACATTTTTGCCC
1 TCAAACTTCCAAAAATT-ACATTTTTGCCC
* * *
218839 TCGAACATCCAAAAATTACCA-TTTTACCC
1 TCAAACTTCCAAAAATTA-CATTTTTGCCC
** *
218868 TTGAACATCC-AAAATTACCATTTTTGCCC
1 TCAAACTTCCAAAAATTA-CATTTTTGCCC
* * * **
218897 TCAAATTTCTAAAAATCACATTTTTAACC
1 TCAAACTTCCAAAAATTACATTTTTGCCC
*
218926 TCAAATTTTCCAAAA
1 TCAAA-CTTCCAAAA
218941 GTTCAATTTT
Statistics
Matches: 245, Mismatches: 46, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
28 53 0.22
29 110 0.45
30 51 0.21
31 29 0.12
32 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
TCAAACTTCCAAAAATTACATTTTTGCCC
Found at i:218669 original size:58 final size:57
Alignment explanation
Indices: 218604--218940 Score: 286
Period size: 58 Copynumber: 5.8 Consensus size: 57
218594 AAATCACATT
* ** *
218604 TCAAACTTTTCAAAAATTACATTTTTTCCCTCGAACTTCCAAAAAATACA-TTTTGCCC
1 TCAAAC-TTTCAAAAATTACATTTTTACCCTTAAACTTCC-AAAATTACATTTTTGCCC
* * * * *
218662 TTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCATAAAATTTACATTTTTGCCC
1 TCAAACTTTCAAAAATTACATTTTTACCCTTAAACTTC-CAAAA-TTACATTTTTGCCC
* * * * * *
218721 TCGAACTTCTCAAAAATAATAATTTTA-CCTTAAACTTCCAAAAATCACATTTTTACCC
1 TCAAACTT-TCAAAAATTACATTTTTACCCTTAAACTTCC-AAAATTACATTTTTGCCC
* * *
218779 CCAAACTTTTCCAAAATTTACATTTTTGCCCTTAAACTTCCAAAATTCACATTTTTGCCC
1 TCAAAC-TTT-CAAAAATTACATTTTTACCCTTAAACTTCCAAAATT-ACATTTTTGCCC
* * * * *
218839 TCGAACATCCAAAAATTACCA-TTTTACCCTTGAACATCCAAAATTACCATTTTTGCCC
1 TCAAACTTTCAAAAATTA-CATTTTTACCCTTAAACTTCCAAAATTA-CATTTTTGCCC
* * * *
218897 TCAAA-TTTCTAAAAATCACATTTTTAACCTCAAATTTTCCAAAA
1 TCAAACTTTC-AAAAATTACATTTTTACCCTTAAA-CTTCCAAAA
218941 GTTCAATTTT
Statistics
Matches: 220, Mismatches: 45, Indels: 27
0.75 0.15 0.09
Matches are distributed among these distances:
57 35 0.16
58 87 0.40
59 57 0.26
60 41 0.19
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
TCAAACTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAATTACATTTTTGCCC
Found at i:218722 original size:87 final size:86
Alignment explanation
Indices: 218616--218920 Score: 309
Period size: 89 Copynumber: 3.5 Consensus size: 86
218606 AAACTTTTCA
*
218616 AAAATTACATTTTTTCCCTCGAACTTCCAAAAAAT-ACATTTTGCCCTTAAACTTCCAAAAATCA
1 AAAATTACATTTTTGCCCTCGAACTTCCAAAAAATCACATTTTGCCCTTAAACTTCCAAAAATCA
*
218680 CATTTTTACCCCTAAACTTCAT
66 CATTTTTACCCCTAAACTTC-C
*
218702 AAAATTTACATTTTTGCCCTCGAACTTCTCAAAAATAAT-A-ATTTT-ACCTTAAACTTCCAAAA
1 AAAA-TTACATTTTTGCCCTCGAACTTC-C-AAAA-AATCACATTTTGCCCTTAAACTTCCAAAA
*
218764 ATCACATTTTTACCCCCAAACTTTTCC
62 ATCACATTTTTACCCCTAAAC--TTCC
** * ** *
218791 AAAATTTACATTTTTGCCCTTAAACTTCC-AAAATTCACATTTTTGCCCTCGAACATCCAAAAAT
1 AAAA-TTACATTTTTGCCCTCGAACTTCCAAAAAATCACA-TTTTGCCCTTAAACTTCCAAAAAT
* * * *
218855 TACCA-TTTTACCCTTGAACATCC
64 CA-CATTTTTACCCCTAAACTTCC
* * *
218878 AAAATTACCATTTTTGCCCTC-AAATTTCTAAAAATCACATTTT
1 AAAATTA-CATTTTTGCCCTCGAACTTCCAAAAAATCACATTTT
218921 TAACCTCAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
85 2 0.01
86 20 0.11
87 51 0.27
88 42 0.23
89 62 0.33
90 9 0.05
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (86 bp):
AAAATTACATTTTTGCCCTCGAACTTCCAAAAAATCACATTTTGCCCTTAAACTTCCAAAAATCA
CATTTTTACCCCTAAACTTCC
Found at i:218776 original size:88 final size:88
Alignment explanation
Indices: 218605--218823 Score: 304
Period size: 88 Copynumber: 2.5 Consensus size: 88
218595 AATCACATTT
* *
218605 CAAACTTTTCAAAAA-TTACATTTTTTCCCTCGAACTTCC-AAAAAATACATTTTGCCCTTAAAC
1 CAAAC-TTTCAAAAATTTACATTTTTGCCCTCGAACTTCCAAAAAAATACATTTTGACCTTAAAC
218668 TTCCAAAAATCACATTTTTACCCC
65 TTCCAAAAATCACATTTTTACCCC
*
218692 TAAAC-TTCATAAAATTTACATTTTTGCCCTCGAACTTCTCAAAAATAATA-ATTTT-ACCTTAA
1 CAAACTTTCA-AAAATTTACATTTTTGCCCTCGAACTTC-CAAAAA-AATACATTTTGACCTTAA
218754 ACTTCCAAAAATCACATTTTTACCCC
63 ACTTCCAAAAATCACATTTTTACCCC
* **
218780 CAAACTTTTCCAAAATTTACATTTTTGCCCTTAAACTTCCAAAA
1 CAAAC-TTTCAAAAATTTACATTTTTGCCCTCGAACTTCCAAAA
218824 TTCACATTTT
Statistics
Matches: 118, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
85 4 0.03
86 4 0.03
87 26 0.22
88 42 0.36
89 35 0.30
90 7 0.06
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (88 bp):
CAAACTTTCAAAAATTTACATTTTTGCCCTCGAACTTCCAAAAAAATACATTTTGACCTTAAACT
TCCAAAAATCACATTTTTACCCC
Found at i:218890 original size:118 final size:119
Alignment explanation
Indices: 218668--218922 Score: 313
Period size: 118 Copynumber: 2.2 Consensus size: 119
218658 GCCCTTAAAC
* * *
218668 TTCCAAAAATCACATTTTTACCCCTAAACTTCATAAAATTTACATTTTTGCCCTCGAACTTCTCA
1 TTCCAAAAATCACATTTTTACCCCTAAACTTCACAAAATTCACATTTTTGCCCTCGAACATCTCA
* *
218733 AAAATAATAATTTTACCTTAAACTTCCAAAAATCACATTTTTACCCCCAAACTT
66 AAAATAACAATTTTACCTTAAACATCCAAAAATCACATTTTTACCCCCAAACTT
* * * *
218787 TTCCAAAATTTACATTTTTGCCCTTAAACTTC-CAAAATTCACATTTTTGCCCTCGAACATC-CA
1 TTCCAAAAATCACATTTTTACCCCTAAACTTCACAAAATTCACATTTTTGCCCTCGAACATCTCA
* * * * * *
218850 AAAATTACCATTTTACCCTTGAACATCC-AAAATTACCATTTTTGCCCTCAAA--T
66 AAAATAACAATTTTA-CCTTAAACATCCAAAAATCA-CATTTTTACCCCCAAACTT
*
218903 TTCTAAAAATCACATTTTTA
1 TTCCAAAAATCACATTTTTA
218923 ACCTCAAATT
Statistics
Matches: 115, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
116 17 0.15
117 20 0.17
118 50 0.43
119 28 0.24
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (119 bp):
TTCCAAAAATCACATTTTTACCCCTAAACTTCACAAAATTCACATTTTTGCCCTCGAACATCTCA
AAAATAACAATTTTACCTTAAACATCCAAAAATCACATTTTTACCCCCAAACTT
Found at i:218950 original size:29 final size:30
Alignment explanation
Indices: 218918--218991 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
218908 AAAATCACAT
*
218918 TTTTAA-CCTCAAATTTTCC-AAAAGTTCAA
1 TTTTAATCC-CAAATTTACCAAAAAGTTCAA
*
218947 TTTTAATCCCAAATTTACCAAAAATTTCAA
1 TTTTAATCCCAAATTTACCAAAAAGTTCAA
*
218977 TTTTGATCCCAAATT
1 TTTTAATCCCAAATT
218992 CCTCGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (30 bp):
TTTTAATCCCAAATTTACCAAAAAGTTCAA
Found at i:219001 original size:30 final size:29
Alignment explanation
Indices: 218937--219028 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
218927 CAAATTTTCC
* *
218937 AAAAGTTCAATTTTAATCCCAAATTTACCA
1 AAAATTTCAATTTTAATCCCAAA-TTCCCA
* *
218967 AAAATTTCAATTTTGATCCCAAATTCCTCG
1 AAAATTTCAATTTTAATCCCAAATTCC-CA
* * *
218997 AAAATTAC-GTTTTCATCCCAAATTCTCCA
1 AAAATTTCAATTTTAATCCCAAATTC-CCA
219026 AAA
1 AAA
219029 CTCCATTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 22 0.42
30 30 0.58
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTTCAATTTTAATCCCAAATTCCCA
Found at i:219255 original size:48 final size:48
Alignment explanation
Indices: 219199--219295 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
219189 TCGTTATTAG
219199 CTGCTCATTCATATTTAAATTACATGTTCATTTTCAAAATTACTTTTA
1 CTGCTCATTCATATTTAAATTACATGTTCATTTTCAAAATTACTTTTA
*
219247 CTGCTCATTCATATTTAAATTACATGTTCATTTTCAAAATTATTTTTA
1 CTGCTCATTCATATTTAAATTACATGTTCATTTTCAAAATTACTTTTA
219295 C
1 C
219296 ATATAAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (48 bp):
CTGCTCATTCATATTTAAATTACATGTTCATTTTCAAAATTACTTTTA
Found at i:228275 original size:5 final size:5
Alignment explanation
Indices: 228242--228291 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
228232 CCCATTGTTT
*
228242 TTTTA TTTTT TATTTA TTTT- TTATTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA T-TTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTT
228292 TCGTCATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 2 0.05
5 32 0.80
6 6 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:229293 original size:8 final size:8
Alignment explanation
Indices: 229282--229325 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
229272 AAAAGGTCCG
229282 AAAAGAAA
1 AAAAGAAA
229290 AAAAGAGAA
1 AAAAGA-AA
229299 AAAA-AAA
1 AAAAGAAA
*
229306 AAGAGAAA
1 AAAAGAAA
229314 AAGAAGAAA
1 AA-AAGAAA
229323 AAA
1 AAA
229326 TAGTTGCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 5 0.16
8 13 0.42
9 13 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:229306 original size:14 final size:14
Alignment explanation
Indices: 229281--229315 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
229271 CAAAAGGTCC
229281 GAAAAGAAAAAAAGA
1 GAAAA-AAAAAAAGA
229296 GAAAAAAAAAAAGA
1 GAAAAAAAAAAAGA
229310 GAAAAA
1 GAAAAA
229316 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAGA
Found at i:229307 original size:22 final size:23
Alignment explanation
Indices: 229282--229325 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
229272 AAAAGGTCCG
229282 AAAAGAAAAAAAG-AGAAAAAAA
1 AAAAGAAAAAAAGAAGAAAAAAA
*
229304 AAAAGAGAAAAAGAAGAAAAAA
1 AAAAGAAAAAAAGAAGAAAAAA
229326 TAGTTGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAAGAAGAAAAAAA
Found at i:230110 original size:23 final size:23
Alignment explanation
Indices: 230056--230102 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
230046 TGACGTGACA
* *
230056 TCCATTCAGCAGCTTCTAGAAGG
1 TCCAGTCAGCAGCATCTAGAAGG
230079 TCCAGTCAGCAGCATCTAGAAGG
1 TCCAGTCAGCAGCATCTAGAAGG
230102 T
1 T
230103 GTAGTCAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCATCTAGAAGG
Found at i:234463 original size:10 final size:9
Alignment explanation
Indices: 234448--234479 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
234438 TACAAACAGC
234448 AAAAAAAAG
1 AAAAAAAAG
234457 AAAAAAAAG
1 AAAAAAAAG
234466 AAAAAAAAG
1 AAAAAAAAG
234475 CAAAA
1 -AAAA
234480 GGTTCGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:246731 original size:78 final size:77
Alignment explanation
Indices: 246644--247021 Score: 264
Period size: 78 Copynumber: 4.8 Consensus size: 77
246634 GAAGATTCTG
* * * * * *
246644 ATCTCTTACCTCGAGTTTAGGGCGGATCACAATCATCAGATCTTTTACCCTGAGCTTGGGACAGA
1 ATCTTTTACCTCGAGATT-GGGCAGATTACAATCGTCAGATCTTTTACCCCGAGCTTGGGACAGA
*
246709 TCACCATCAGCCA
65 TCACCATCAACCA
* * * *
246722 ATCTTTTACC-CTGAGACTGAGGCATATTACAGTCGTCTA-ATCTTTTACCCCGAACTTGGGACA
1 ATCTTTTACCTC-GAGATTG-GGCAGATTACAATCGTC-AGATCTTTTACCCCGAGCTTGGGACA
*
246785 AATCACCATCAACCA
63 GATCACCATCAACCA
* * ** *
246800 ATCTTTTACCTCGAGCTTGGGGCAGATTGCAA-CTGTTTGATCTTTTACCCCGAGCCT-GGAGCA
1 ATCTTTTACCTCGAGATT-GGGCAGATTACAATC-GTCAGATCTTTTACCCCGAGCTTGGGA-CA
*
246863 GATCACTATCAACCA
63 GATCACCATCAACCA
* * ** * * * ** * *
246878 ATCTTTTACC-CCAAACCTAAGGCAAATTGCAGTCGTTTGATCTTTTACCCCGAGCCTGGGGCAG
1 ATCTTTTACCTCGAGA--TTGGGCAGATTACAATCGTCAGATCTTTTACCCCGAGCTTGGGACAG
* *
246942 ATCACCATCAGCCG
64 ATCACCATCAACCA
* ** * * * * *
246956 ATCTTTTACCTAGAGCCTGAGGCAGATCACTATCAGCCA-ATCTCTTACCCCGAGCTTGGGGCAG
1 ATCTTTTACCTCGAGATTG-GGCAGATTACAATC-GTCAGATCTTTTACCCCGAGCTTGGGACAG
247020 AT
64 AT
247022 TGTAACCGTC
Statistics
Matches: 234, Mismatches: 51, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
77 8 0.03
78 217 0.93
79 9 0.04
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (77 bp):
ATCTTTTACCTCGAGATTGGGCAGATTACAATCGTCAGATCTTTTACCCCGAGCTTGGGACAGAT
CACCATCAACCA
Found at i:247035 original size:78 final size:78
Alignment explanation
Indices: 246953--247101 Score: 219
Period size: 78 Copynumber: 1.9 Consensus size: 78
246943 TCACCATCAG
* * * *
246953 CCGATCTTTTACCTAGAGCCT-GAGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGGGG
1 CCGATCTCTTACCTAGACCCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCATGGGG
247017 CAGATTGTAACCGT
65 CAGATTGTAACCGT
* * *
247031 CCGATCTCTTACCTTGACCCTAGGGCAGATCACCATCAGCTAATCTCTTACCCCGATCATGGGGC
1 CCGATCTCTTACCTAGACCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCATGGGGC
247096 AGATTG
66 AGATTG
247102 CAGTCATTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 62 0.98
79 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (78 bp):
CCGATCTCTTACCTAGACCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCATGGGGC
AGATTGTAACCGT
Found at i:247037 original size:117 final size:117
Alignment explanation
Indices: 246838--247070 Score: 270
Period size: 117 Copynumber: 2.0 Consensus size: 117
246828 GCAACTGTTT
* *
246838 GATCTTTTACCCCGAGCCTGGAGCAGATCACTATCAACCAATCTTTTACCCCAAACCTAAGGCAA
1 GATCTTTTACCCAGAGCCTGGAGCAGATCACTATCAACCAATCTCTTACCCCAAACCTAAGGCAA
** ** * * *
246903 ATTGCAGTCGTTTGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCC
66 ATTGCAACCGTCCGATCTCTTACCCCGACCCTAGGGCAGATCACCATCAGCC
* * * * * **
246955 GATCTTTTACCTAGAGCCT-GAGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
1 GATCTTTTACCCAGAGCCTGGA-GCAGATCACTATCAACCAATCTCTTACCCCAAACCTAAGGCA
* * **
247019 GATTGTAACCGTCCGATCTCTTACCTTGACCCTAGGGCAGATCACCATCAGC
65 AATTGCAACCGTCCGATCTCTTACCCCGACCCTAGGGCAGATCACCATCAGC
247071 TAATCTCTTA
Statistics
Matches: 95, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
116 2 0.02
117 93 0.98
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (117 bp):
GATCTTTTACCCAGAGCCTGGAGCAGATCACTATCAACCAATCTCTTACCCCAAACCTAAGGCAA
ATTGCAACCGTCCGATCTCTTACCCCGACCCTAGGGCAGATCACCATCAGCC
Found at i:247096 original size:39 final size:39
Alignment explanation
Indices: 246683--247099 Score: 171
Period size: 39 Copynumber: 10.7 Consensus size: 39
246673 CAATCATCAG
* * * *
246683 ATCTTTTACCCTGAGCTTGGGACAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * * * *
246722 ATCTTTTACCCTGAGACTGAGGCATATTA-CAGTC-GTCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAG-CCA
* * * * * *
246761 ATCTTTTACCCCGAACTTGGGACAAATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * ** * * ***
246800 ATCTTTTACCTCGAGCTTGGGGCAGAT-TGCAACTGTTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-CCA
* * * *
246839 ATCTTTTACCCCGAGCCTGGAGCAGATCACTATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * ** * ** ***
246878 ATCTTTTACCCCAAACCTAAGGCAAAT-TGCAGTC-GTTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAG-CCA
* *
246917 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* ** * *
246956 ATCTTTTACCTAGAGCCTGAGGCAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* *** * * *
246995 ATCTCTTACCCCGAGCTTGGGGCAGAT-TGTAACCGTCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-CCA
** * * *
247034 ATCTCTTACCTTGACCCTAGGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* *
247073 ATCTCTTACCCCGATCATGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
247100 TGCAGTCATT
Statistics
Matches: 271, Mismatches: 95, Indels: 24
0.69 0.24 0.06
Matches are distributed among these distances:
38 11 0.04
39 250 0.92
40 10 0.04
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:247506 original size:11 final size:11
Alignment explanation
Indices: 247490--247546 Score: 71
Period size: 11 Copynumber: 5.0 Consensus size: 11
247480 TTAAACCCAT
247490 TTTTAAATTTA
1 TTTTAAATTTA
247501 TTTTAAATTTAA
1 TTTTAAATTT-A
*
247513 ATTT-AATTTAA
1 TTTTAAATTT-A
247524 TTTTAAATTTA
1 TTTTAAATTTA
247535 TTTTTAAATTTA
1 -TTTTAAATTTA
247547 AATTCATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
11 21 0.51
12 20 0.49
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:247511 original size:6 final size:6
Alignment explanation
Indices: 247491--247625 Score: 111
Period size: 6 Copynumber: 23.2 Consensus size: 6
247481 TAAACCCATT
* * **
247491 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAT TTTAAA TTTATT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * **
247537 TTTAAA TTTAAA -TT-CA TTCTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
247584 TTTATT TTTAAA TTTAAA TTT--T TTCTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA T
247626 GTCCAAAATT
Statistics
Matches: 99, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
4 3 0.03
5 13 0.13
6 79 0.80
7 4 0.04
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:247511 original size:17 final size:17
Alignment explanation
Indices: 247491--247622 Score: 176
Period size: 17 Copynumber: 7.6 Consensus size: 17
247481 TAAACCCATT
247491 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
247508 TTTAAATTTAATTTAAT
1 TTTAAATTTATTTTAAA
247525 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* * *
247543 TTTAAATTCATTCTAAG
1 TTTAAATTTATTTTAAA
247560 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
247578 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
247596 TTTAAATTT-TTTCTAAA
1 TTTAAATTTATTT-TAAA
247613 TTTAAATTTA
1 TTTAAATTTA
247623 AATGTCCAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
16 3 0.03
17 52 0.51
18 46 0.46
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:247527 original size:35 final size:35
Alignment explanation
Indices: 247490--247623 Score: 184
Period size: 35 Copynumber: 3.9 Consensus size: 35
247480 TTAAACCCAT
247490 TTTTAAATTTA-TTTTAAATTTAAATTTAATTTAA
1 TTTTAAATTTATTTTTAAATTTAAATTTAATTTAA
*
247524 TTTTAAATTTATTTTTAAATTTAAA-TTCATTCTAA
1 TTTTAAATTTATTTTTAAATTTAAATTTAATT-TAA
* *
247559 GTTTAAATTTATTTTTAAATTTAAATTTATTTTTAA
1 TTTTAAATTTATTTTTAAATTTAAATTTA-ATTTAA
* *
247595 ATTTAAATTT-TTTCTAAATTTAAATTTAA
1 TTTTAAATTTATTTTTAAATTTAAATTTAA
247624 ATGTCCAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
34 16 0.18
35 57 0.64
36 14 0.16
37 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTTAAATTTATTTTTAAATTTAAATTTAATTTAA
Found at i:249191 original size:29 final size:28
Alignment explanation
Indices: 249149--249513 Score: 275
Period size: 29 Copynumber: 12.5 Consensus size: 28
249139 CTAAATTATC
* *
249149 CAAAAATCACATTTTGACCCCAAACTTTT
1 CAAAAATTACATTTTTACCCCAAAC-TTT
* *
249178 CAAAAATTACATTTTTGCCCCTGAACTTT
1 CAAAAATTACATTTTTACCCC-AAACTTT
* * * *
249207 CAAAAATTACATTTTTGCTCTCGAACTTC
1 CAAAAATTACATTTTTAC-CCCAAACTTT
*
249236 CAAAAATCACATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTTACCC-CAAACTT-T
249266 CAAAAATTACATTTTTACCCCCAAACTTCT
1 CAAAAATTACATTTTTA-CCCCAAACTT-T
* *
249296 CAAAAATTACATTTTT-CTCTCGAACTTT
1 CAAAAATTACATTTTTAC-CCCAAACTTT
* **
249324 CAAAAATCACATTTTTACCCTCAAACTAC
1 CAAAAATTACATTTTTACCC-CAAACTTT
* * *
249353 CCAAAATCACATTTTTTACCCCCGAACTTCT
1 CAAAAATTACA-TTTTTA-CCCCAAACTT-T
* *
249384 AAAAAATTACATTTTTACCCTAAAC-TT
1 CAAAAATTACATTTTTACCCCAAACTTT
* * *
249411 CCAAAATCACATTTTAACCCCCAAACTTTT
1 CAAAAATTACATTTTTA-CCCCAAAC-TTT
* ** *
249441 CCAAAAATTACATTTTTTCCCTGGAACTTC
1 -CAAAAATTACATTTTTACCC-CAAACTTT
* * * *
249471 CAAAAATCACATTTTTTCCTCAAATTTT
1 CAAAAATTACATTTTTACCCCAAACTTT
** *
249499 TGAAAATCACATTTT
1 CAAAAATTACATTTT
249514 CAACCTCAAA
Statistics
Matches: 272, Mismatches: 48, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
27 14 0.05
28 44 0.16
29 114 0.42
30 70 0.26
31 30 0.11
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCAAACTTT
Found at i:249274 original size:88 final size:88
Alignment explanation
Indices: 249147--249486 Score: 431
Period size: 88 Copynumber: 3.9 Consensus size: 88
249137 CCCTAAATTA
* * * *
249147 TCCAAAAATCACATTTTGACCC-CAAACTTTTCAAAAATTACATTTTTGCCCCTGAACTT-TCAA
1 TCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCTCAA
249210 AAATTACATTTTTGCTCTCGAACT
66 AAATTACATTTTT-CTCTCGAACT
*
249234 TCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCCAAACTTCTCAA
1 TCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCTCAA
249299 AAATTACATTTTTCTCTCGAACT
66 AAATTACATTTTTCTCTCGAACT
* * * * *
249322 TTCAAAAATCACATTTTTACCCTCAAACTAC-CCAAAATCACATTTTTTACCCCCGAACTTCTAA
1 TCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACA-TTTTTACCCCCGAACTTCTCA
* *
249386 AAAATTACATTTTTACCCT-AAACT
65 AAAATTACATTTTT-CTCTCGAACT
* * * * **
249410 TCC-AAAATCACATTTTAACCCCCAAACTTTTCCAAAAATTACATTTTTTCCCTGGAACTTC-CA
1 TCCAAAAATCACATTTTTACCCTCAAACTTCT-CAAAAATTACATTTTTACCCCCGAACTTCTCA
*
249473 AAAATCACATTTTT
65 AAAATTACATTTTT
249487 TCCTCAAATT
Statistics
Matches: 222, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
87 67 0.30
88 126 0.57
89 29 0.13
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (88 bp):
TCCAAAAATCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCTCAA
AAATTACATTTTTCTCTCGAACT
Found at i:249423 original size:58 final size:58
Alignment explanation
Indices: 249149--249486 Score: 369
Period size: 58 Copynumber: 5.8 Consensus size: 58
249139 CTAAATTATC
* * * * * *
249149 CAAAAATCACATTTTGACCC-CAAACTTTTCAAAAATTACATTTTTGCCCCTGAACTTT
1 CAAAAATTACATTTTTACCCTCAAAC-TTCCAAAAATCACATTTTTACCCCCGAACTTT
* * * * *
249207 CAAAAATTACATTTTTGCTCTCGAACTTCCAAAAATCACATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCCGAACTT-T
* * * *
249266 CAAAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACATTTTT-CTCTCGAACTTT
1 CAAAAATTACATTTTTACCCTCAAACTTC-CAAAAATCACATTTTTACCCCCGAACTTT
* * *
249324 CAAAAATCACATTTTTACCCTCAAACTACCCAAAATCACATTTTTTACCCCCGAACTTCT
1 CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACA-TTTTTACCCCCGAACTT-T
* * *
249384 AAAAAATTACATTTTTACCCT-AAACTTCC-AAAATCACATTTTAACCCCCAAACTTTT
1 CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCCGAAC-TTT
* **
249441 CCAAAAATTACATTTTTTCCCTGGAACTTCCAAAAATCACATTTTT
1 -CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTT
249487 TCCTCAAATT
Statistics
Matches: 236, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
57 23 0.10
58 103 0.44
59 62 0.26
60 48 0.20
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCCGAACTTT
Found at i:249487 original size:88 final size:88
Alignment explanation
Indices: 249151--249533 Score: 408
Period size: 88 Copynumber: 4.4 Consensus size: 88
249141 AAATTATCCA
* * *
249151 AAAATCACATTTTGACCC-CAAACTTTT-CAAAAATTACATTTTTGCCCCTGAACTT-TCAAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAAATTACATTTTTTCCCCCGAACTTCTCAAAAA
* *
249213 TTACATTTTTGCTCTCGAACTTCC
66 TTACATTTTT-CCCTCAAACTTCC
* * * *
249237 AAAAATCACATTTTTACCCTCAAACTTCT-CAAAAATTACATTTTTACCCCCAAACTTCTCAAAA
1 -AAAATCACATTTTAACCCTCAAACTTTTCCAAAAATTACATTTTTTCCCCCGAACTTCTCAAAA
* * *
249301 ATTACATTTTTCTCTCGAACTTTCA
65 ATTACATTTTTCCCTCAAAC-TTCC
* * * * *
249326 AAAATCACATTTTTACCCTCAAAC--TACCCAAAATCACATTTTTTACCCCCGAACTTCTAAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAAATTACATTTTTT-CCCCCGAACTTCTCAAAA
249389 ATTACATTTTTACCCT-AAACTTCC
65 ATTACATTTTT-CCCTCAAACTTCC
* **
249413 AAAATCACATTTTAACCCCCAAACTTTTCCAAAAATTACATTTTTTCCCTGGAACTTC-CAAAAA
1 AAAATCACATTTTAACCCTCAAACTTTTCCAAAAATTACATTTTTTCCCCCGAACTTCTCAAAAA
* * * **
249477 TCACATTTTTTCCTCAAATTTTTG
66 TTACATTTTTCCCTCAAA-CTTCC
249501 AAAATCACATTTTCAA-CCTCAAA-TTTTCCAAAA
1 AAAATCACATTTT-AACCCTCAAACTTTTCCAAAA
249534 GTTCAATTTT
Statistics
Matches: 255, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
86 3 0.01
87 83 0.33
88 127 0.50
89 42 0.16
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (88 bp):
AAAATCACATTTTAACCCTCAAACTTTTCCAAAAATTACATTTTTTCCCCCGAACTTCTCAAAAA
TTACATTTTTCCCTCAAACTTCC
Found at i:249527 original size:28 final size:28
Alignment explanation
Indices: 249473--249527 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
249463 GGAACTTCCA
**
249473 AAAATCACATTTTTTCCTCAAATTTTTG
1 AAAATCACATTTTAACCTCAAATTTTTG
249501 AAAATCACATTTTCAACCTCAAATTTT
1 AAAATCACATTTT-AACCTCAAATTTT
249528 CCAAAAGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (28 bp):
AAAATCACATTTTAACCTCAAATTTTTG
Found at i:249533 original size:29 final size:28
Alignment explanation
Indices: 249409--249562 Score: 107
Period size: 29 Copynumber: 5.3 Consensus size: 28
249399 TACCCTAAAC
*
249409 TTCCAAAATCACATTTTAACCCCCAAACTT
1 TTCCAAAATCACATTTTAA-CCTCAAA-TT
* ** ** *
249439 TTCCAAAAATTACATTTTTTCCCTGGAA-C
1 TTCC-AAAATCACA-TTTTAACCTCAAATT
**
249468 TTCCAAAAATCACATTTTTTCCTCAAATT
1 TTCC-AAAATCACATTTTAACCTCAAATT
**
249497 TTTGAAAATCACATTTTCAACCTCAAATT
1 TTCCAAAATCACATTTT-AACCTCAAATT
249526 TTCCAAAAGTTCA-ATTTTAATCCT-AAATT
1 TTCCAAAA--TCACATTTTAA-CCTCAAATT
249555 TTCCAAAA
1 TTCCAAAA
249563 ATTTCAATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
28 23 0.23
29 45 0.45
30 12 0.12
31 15 0.15
32 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (28 bp):
TTCCAAAATCACATTTTAACCTCAAATT
Found at i:249569 original size:30 final size:29
Alignment explanation
Indices: 249521--249578 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
249511 TTTCAACCTC
249521 AAATTTTCCAAAAGTTCAATTTTAATCCT
1 AAATTTTCCAAAAGTTCAATTTTAATCCT
* *
249550 AAATTTTCCAAAAATTTCAATTTTGATCC
1 AAATTTTCC-AAAAGTTCAATTTTAATCC
249579 CCAAATTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (29 bp):
AAATTTTCCAAAAGTTCAATTTTAATCCT
Found at i:256867 original size:13 final size:13
Alignment explanation
Indices: 256849--256874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256839 ATGCATTAGC
256849 TAAAAATAAAAAA
1 TAAAAATAAAAAA
256862 TAAAAATAAAAAA
1 TAAAAATAAAAAA
256875 AACTTTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:259991 original size:58 final size:57
Alignment explanation
Indices: 259856--259996 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 57
259846 ATTTAATAAC
* * * * *
259856 AATAATAATTATATTAAAAAAGTTATTAAATTATATATTATTTTATTATATTGTATTT
1 AATAATAATTATATTAAAATA-TAATTAAATTATATATTATTTTATCAAATTATATTT
* *
259914 AATAATAATTATGTTAAAATATAATTAAATTATTTATTATTTTTATCAAATTATATTT
1 AATAATAATTATATTAAAATATAATTAAATTATATATTA-TTTTATCAAATTATATTT
*
259972 AATAATAA-TATTATTAAAATTTAAT
1 AATAATAATTA-TATTAAAATATAAT
259997 AACAATAATC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
57 18 0.25
58 54 0.75
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (57 bp):
AATAATAATTATATTAAAATATAATTAAATTATATATTATTTTATCAAATTATATTT
Found at i:260352 original size:21 final size:21
Alignment explanation
Indices: 260328--260370 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
260318 GTTCAATTTG
260328 TTTTATATT-TTTGTAATATAT
1 TTTTATATTATTTGT-ATATAT
*
260349 TTTTATTTTATTTGTATATAT
1 TTTTATATTATTTGTATATAT
260370 T
1 T
260371 ATATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATATTATTTGTATATAT
Found at i:260380 original size:22 final size:22
Alignment explanation
Indices: 260337--260381 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
260327 GTTTTATATT
* *
260337 TTTGTAATATATTTTTATTTTA
1 TTTGTAATATATTTATAATTTA
260359 TTTGT-ATATATTATATAATTTA
1 TTTGTAATATATT-TATAATTTA
260381 T
1 T
260382 ATCACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTGTAATATATTTATAATTTA
Found at i:261453 original size:31 final size:32
Alignment explanation
Indices: 261418--261478 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
261408 TTTTCAAATT
261418 ATTTAAAAAATCTTTTTATTTT-TAT-TTTTGA
1 ATTTAAAAAAT-TTTTTATTTTATATATTTTGA
* *
261449 ATTTAAAGAGTTTTTTATTTTATATATTTT
1 ATTTAAAAAATTTTTTATTTTATATATTTT
261479 TAAAATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 12 0.46
32 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (32 bp):
ATTTAAAAAATTTTTTATTTTATATATTTTGA
Found at i:261512 original size:18 final size:17
Alignment explanation
Indices: 261465--261513 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
261455 AGAGTTTTTT
*
261465 ATTTTATATATTTTTAAA
1 ATTTTAT-TTTTTTTAAA
*
261483 ATATGTATTTTTTTTAAA
1 AT-TTTATTTTTTTTAAA
261501 ATTTTATGTTTTT
1 ATTTTAT-TTTTT
261514 GTTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTATTTTTTTTAAA
Found at i:261518 original size:20 final size:21
Alignment explanation
Indices: 261484--261522 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
261474 ATTTTTAAAA
*
261484 TATGTATTTTTTTTAAAATTT
1 TATGTATTTTGTTTAAAATTT
261505 TATGT-TTTTGTTTAAAAT
1 TATGTATTTTGTTTAAAAT
261523 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TATGTATTTTGTTTAAAATTT
Found at i:268556 original size:36 final size:36
Alignment explanation
Indices: 268516--268589 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
268506 CAAACTAATT
268516 ACTCTACAATTAAAAATATTGAATTATCTAGTATCA
1 ACTCTACAATTAAAAATATTGAATTATCTAGTATCA
268552 ACTCTACAATTAAAAATATTGAATTATCTAGTATCA
1 ACTCTACAATTAAAAATATTGAATTATCTAGTATCA
268588 AC
1 AC
268590 CAAAATTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (36 bp):
ACTCTACAATTAAAAATATTGAATTATCTAGTATCA
Found at i:274759 original size:24 final size:24
Alignment explanation
Indices: 274732--274818 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
274722 ATATCATTTA
274732 ATATTATATATTTTATTATAATAT
1 ATATTATATATTTTATTATAATAT
274756 ATATTATAATAATATTTATATATAATAGTAGT
1 ATATTAT-AT-AT-TTTAT-TAT-A-A-TA-T
274788 ATATTATATATTACTTATTAT--TAT
1 ATATTATATATT--TTATTATAATAT
274812 ATATTAT
1 ATATTAT
274819 TGTTTATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 2 0.04
27 5 0.09
28 3 0.06
29 2 0.04
30 6 0.11
31 8 0.15
32 8 0.15
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATTATATATTTTATTATAATAT
Found at i:274992 original size:15 final size:15
Alignment explanation
Indices: 274972--275028 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
274962 ACTATATAGT
274972 TTATTATAATTAATA
1 TTATTATAATTAATA
*
274987 TTATTATAATAGTTATA
1 TTATTATAAT--TAATA
275004 TATATTAT-ATTATTATA
1 T-TATTATAATTA--ATA
275021 TTATTATA
1 TTATTATA
275029 TTATCATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 11 0.32
16 6 0.18
17 11 0.32
18 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATTATAATTAATA
Found at i:275019 original size:8 final size:8
Alignment explanation
Indices: 274972--275032 Score: 72
Period size: 8 Copynumber: 7.5 Consensus size: 8
274962 ACTATATAGT
274972 TTATTATA
1 TTATTATA
274980 --ATTAATA
1 TTATT-ATA
274987 TTATTATA
1 TTATTATA
*
274995 ATAGTTATA
1 TTA-TTATA
275004 TATATTATA
1 T-TATTATA
275013 TTATTATA
1 TTATTATA
275021 TTATTATA
1 TTATTATA
275029 TTAT
1 TTAT
275033 CATTAAAGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 24 0.52
9 14 0.30
10 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
TTATTATA
Found at i:275073 original size:16 final size:17
Alignment explanation
Indices: 275054--275086 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
275044 AATTTTATAG
275054 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
275070 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
275087 TACATCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:278309 original size:15 final size:15
Alignment explanation
Indices: 278291--278406 Score: 79
Period size: 15 Copynumber: 7.3 Consensus size: 15
278281 GGCGGAGCCA
278291 AAGAAGGAAGAACCC
1 AAGAAGGAAGAACCC
* * *
278306 AAGAAAGAGGACGAGCCA
1 AAG--A-AGGAAGAACCC
*
278324 AAGAAAGAAGAACCC
1 AAGAAGGAAGAACCC
**
278339 AAGAAGGAAGAAGAGCAG
1 AAGAAGGAAG-A-A-CCC
* * *
278357 AAGAAAGAAGAGCCT
1 AAGAAGGAAGAACCC
*
278372 AAGAAGGAAGAACCA
1 AAGAAGGAAGAACCC
*
278387 AAAAAGGAAGAACCC
1 AAGAAGGAAGAACCC
278402 AAGAA
1 AAGAA
278407 AGAGGAAGAG
Statistics
Matches: 75, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
15 49 0.65
16 2 0.03
17 3 0.04
18 21 0.28
ACGTcount: A:0.57, C:0.15, G:0.28, T:0.01
Consensus pattern (15 bp):
AAGAAGGAAGAACCC
Found at i:278322 original size:33 final size:33
Alignment explanation
Indices: 278285--278430 Score: 149
Period size: 33 Copynumber: 4.5 Consensus size: 33
278275 GAAGAAGGCG
*
278285 GAGCCAAAGAAGGAAGAACCCAAGAAAGAGGAC
1 GAGCCAAAGAAGGAAGAACCCAAGAAAGAGGAA
* * *
278318 GAGCCAAAGAAAGAAGAACCCAAGAAGGAAGAA
1 GAGCCAAAGAAGGAAGAACCCAAGAAAGAGGAA
* * *
278351 GAG-CAGAAGAAAGAAGAGCCTAAG--A-AGGAA
1 GAGCCA-AAGAAGGAAGAACCCAAGAAAGAGGAA
* *
278381 GAACCAAAAAAGGAAGAACCCAAGAAAGAGGAA
1 GAGCCAAAGAAGGAAGAACCCAAGAAAGAGGAA
*
278414 GAG-AAGAAGAAGGAAGA
1 GAGCCA-AAGAAGGAAGA
278431 GGAGAAAAAG
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
30 20 0.22
31 2 0.02
32 4 0.04
33 65 0.71
ACGTcount: A:0.56, C:0.13, G:0.30, T:0.01
Consensus pattern (33 bp):
GAGCCAAAGAAGGAAGAACCCAAGAAAGAGGAA
Found at i:278349 original size:18 final size:18
Alignment explanation
Indices: 278328--278383 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
278318 GAGCCAAAGA
278328 AAGAAGAACCCAAGAAGG
1 AAGAAGAACCCAAGAAGG
* *
278346 AAGAAG-A-GC-AGAAGA
1 AAGAAGAACCCAAGAAGG
* *
278361 AAGAAGAGCCTAAGAAGG
1 AAGAAGAACCCAAGAAGG
278379 AAGAA
1 AAGAA
278384 CCAAAAAAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 11 0.38
16 1 0.03
17 1 0.03
18 16 0.55
ACGTcount: A:0.57, C:0.11, G:0.30, T:0.02
Consensus pattern (18 bp):
AAGAAGAACCCAAGAAGG
Found at i:278415 original size:48 final size:48
Alignment explanation
Indices: 278288--278430 Score: 157
Period size: 48 Copynumber: 3.0 Consensus size: 48
278278 GAAGGCGGAG
* *
278288 CCAAAGAAGGAAGAACCCAAGAAAGAGGACGAGCCAAAGAAAGAAGAA
1 CCAAAGAAGGAAGAACCCAAGAAAGAGGAAGAGCCAAAGAAGGAAGAA
* ** * *
278336 CCCAAGAAGGAAGAAGAGC-AG-AAGAAAGAAGAGCCTAAGAAGGAAGAA
1 CCAAAGAAGGAAGAA-CCCAAGAAAG-AGGAAGAGCCAAAGAAGGAAGAA
* *
278384 CCAAAAAAGGAAGAACCCAAGAAAGAGGAAGAG-AAGAAGAAGGAAGA
1 CCAAAGAAGGAAGAACCCAAGAAAGAGGAAGAGCCA-AAGAAGGAAGA
278431 GGAGAAAAAG
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
47 4 0.05
48 68 0.89
49 4 0.05
ACGTcount: A:0.57, C:0.13, G:0.29, T:0.01
Consensus pattern (48 bp):
CCAAAGAAGGAAGAACCCAAGAAAGAGGAAGAGCCAAAGAAGGAAGAA
Found at i:282474 original size:18 final size:18
Alignment explanation
Indices: 282453--282487 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
282443 TAAATTTAAC
*
282453 TTTATTATAAGATTATTT
1 TTTATTACAAGATTATTT
*
282471 TTTATTACATGATTATT
1 TTTATTACAAGATTATT
282488 AAATGAGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTATTACAAGATTATTT
Found at i:284552 original size:2 final size:2
Alignment explanation
Indices: 284545--284583 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
284535 GATACTTGGA
284545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
284584 ATTCTGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.