Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:9119 original size:20 final size:21
Alignment explanation
Indices: 9096--9135 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9086 TATTTTAGGG
*
9096 TTTTTAGTTTAGTT-TTTTTC
1 TTTTCAGTTTAGTTCTTTTTC
*
9116 TTTTCATTTTAGTTCTTTTT
1 TTTTCAGTTTAGTTCTTTTT
9136 ATACTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTCAGTTTAGTTCTTTTTC
Found at i:11440 original size:40 final size:41
Alignment explanation
Indices: 11338--11453 Score: 144
Period size: 41 Copynumber: 2.9 Consensus size: 41
11328 CCAAAAATGA
**
11338 TACACCGGCACCAAGCCTGCTAGGCATAAAGCCTGATAGAG
1 TACACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATAGAG
* **
11379 TACACCGGCATAAAGCCTGCTAGGCATAAAGCTTGATA-CT
1 TACACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATAGAG
* * * *
11419 TCCACCGGCTTAAAGCATGCTAGGCATATAGCCTG
1 TACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
11454 GATATCATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 30 0.46
41 35 0.54
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (41 bp):
TACACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATAGAG
Found at i:24913 original size:21 final size:22
Alignment explanation
Indices: 24883--24930 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
24873 ACCAAACCAG
*
24883 AATTTGATTT-TAACTTTGT-CT
1 AATTTCATTTCTAACTTT-TCCT
24904 AATTTCATTTCTAACTTTTCCT
1 AATTTCATTTCTAACTTTTCCT
24926 AATTT
1 AATTT
24931 TCCGATAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (22 bp):
AATTTCATTTCTAACTTTTCCT
Found at i:26231 original size:29 final size:29
Alignment explanation
Indices: 26189--26244 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
26179 CACCAACCAA
26189 GAAATGCTTATTCAACATTGCATCACAGC
1 GAAATGCTTATTCAACATTGCATCACAGC
26218 GAAATGCTTATTCAACATTGCATCACA
1 GAAATGCTTATTCAACATTGCATCACA
26245 TTCATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (29 bp):
GAAATGCTTATTCAACATTGCATCACAGC
Found at i:26520 original size:30 final size:31
Alignment explanation
Indices: 26484--26545 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
26474 CATCTCAATC
* *
26484 ATTGATAA-CCCCATGCAAAACTTTGTAGTT
1 ATTGATAACCCCCATGCAAAACCTTATAGTT
26514 ATTGATAACCCCCATGCAAAACCTTATAGTT
1 ATTGATAACCCCCATGCAAAACCTTATAGTT
26545 A
1 A
26546 CAAATTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (31 bp):
ATTGATAACCCCCATGCAAAACCTTATAGTT
Found at i:33524 original size:25 final size:25
Alignment explanation
Indices: 33490--33617 Score: 116
Period size: 25 Copynumber: 5.1 Consensus size: 25
33480 TCATTAGGGT
*
33490 TACCGATTTATAGCTCGTAAGAACA
1 TACCGATTTATAGCTCGTAAGAGCA
* *
33515 TACCAATTTATAGCTCGTAAGAGTA
1 TACCGATTTATAGCTCGTAAGAGCA
* *
33540 TACCGATTTATCGCTCGTGAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
* * * *
33565 TACTGATCTT-CAGGTC-AAATGAGCA
1 TACCGAT-TTATAGCTCGTAA-GAGCA
* * *
33590 TACCGATTCACAGCTCGTATGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
33615 TAC
1 TAC
33618 TTGTACATGA
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.02
25 76 0.94
26 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (25 bp):
TACCGATTTATAGCTCGTAAGAGCA
Found at i:47962 original size:150 final size:154
Alignment explanation
Indices: 47713--48060 Score: 375
Period size: 150 Copynumber: 2.3 Consensus size: 154
47703 ATTTGGGTAA
* *
47713 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGATATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--TCATATGATGAGAGGTCCC
* * * ** *
47778 ATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTC
64 ACGTAAGACCATGTCTAGGACATGGCATCGGCACCGAGATGAGAACTCCCATGTAAGACCATATC
* *
47843 TGGGACATGGCGTTGGCACCGAGATG
129 TAGGACATGGCATTGGCACCGAGATG
* * *
47869 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CA-A-GATGAGAGGTCCCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTCATATGATGAGAGGTCCCAC
* * **
47930 GTAAGACCATGTCTAGGACATGGCAT-GAGCACCTATATGAGAACTCTGATGTAAGACCATATCT
66 GTAAGACCATGTCTAGGACATGGCATCG-GCACCGAGATGAGAACTCCCATGTAAGACCATATCT
* ** * *
47994 AGGATATGGCATTGGCA-ATACAAG
130 AGGACATGGCATTGGCACCGAGATG
* * * * * *
48018 AAACATCTCATGTAAGACTATGTCTGGGACATAGCTTTGGCAT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
48061 GTTATATTCA
Statistics
Matches: 161, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
149 39 0.24
150 79 0.49
151 1 0.01
152 1 0.01
155 1 0.01
156 40 0.25
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (154 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTCATATGATGAGAGGTCCCAC
GTAAGACCATGTCTAGGACATGGCATCGGCACCGAGATGAGAACTCCCATGTAAGACCATATCTA
GGACATGGCATTGGCACCGAGATG
Found at i:47971 original size:50 final size:50
Alignment explanation
Indices: 47713--47953 Score: 347
Period size: 50 Copynumber: 4.7 Consensus size: 50
47703 ATTTGGGTAA
* * * *
47713 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGATATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CG--A-GATG
*
47769 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
47819 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
47869 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
47919 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
47954 ATGAGCACCT
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 133 0.76
51 1 0.01
53 1 0.01
55 1 0.01
56 39 0.22
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:47984 original size:50 final size:49
Alignment explanation
Indices: 47713--48010 Score: 317
Period size: 50 Copynumber: 5.8 Consensus size: 49
47703 ATTTGGGTAA
* * *
47713 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGATATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGGCA-C--CG--A-GATG
*
47769 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT-GGCACCGAGATG
*
47819 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGAGATG
* *
47869 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGAGATG
** * * *
47919 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGAGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATG-GCACCGAGATG
** ** * * *
47969 AGAACTCTGATGTAAGACCATATCTAGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGGCA
48011 ATACAAGAAA
Statistics
Matches: 218, Mismatches: 20, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
49 2 0.01
50 171 0.78
51 4 0.02
53 1 0.00
55 2 0.01
56 38 0.17
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGAGATG
Found at i:53350 original size:12 final size:11
Alignment explanation
Indices: 53314--53347 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
53304 GTATTATGAG
53314 TTTGTAAAAAAA
1 TTTG-AAAAAAA
*
53326 TTCGAAAAAAA
1 TTTGAAAAAAA
53337 TTTGAAAAAAA
1 TTTGAAAAAAA
53348 ATTATTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (11 bp):
TTTGAAAAAAA
Found at i:53748 original size:25 final size:21
Alignment explanation
Indices: 53699--53740 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53689 AAAAGCCGAA
53699 GTGAGTGATTGGTGAGATTTT
1 GTGAGTGATTGGTGAGATTTT
*
53720 GTGATTGATTGGTGAGATTTT
1 GTGAGTGATTGGTGAGATTTT
53741 TGTTGTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (21 bp):
GTGAGTGATTGGTGAGATTTT
Found at i:55477 original size:15 final size:14
Alignment explanation
Indices: 55448--55498 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
55438 TCCATTGAGC
55448 GAGA-AAAAGAAAAA
1 GAGAGAAAA-AAAAA
55462 GAGAGAAACAAAAAA
1 GAGAGAAA-AAAAAA
* *
55477 GTGA-AAAGAAAAA
1 GAGAGAAAAAAAAA
55490 GAGAGAAAA
1 GAGAGAAAA
55499 GACTGACGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 11 0.37
16 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (14 bp):
GAGAGAAAAAAAAA
Found at i:55499 original size:15 final size:15
Alignment explanation
Indices: 55448--55500 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 15
55438 TCCATTGAGC
55448 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
55462 GAGAG-AAACAAAAA
1 GAGAGAAAAGAAAAA
*
55476 -AGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
55490 GAGAGAAAAGA
1 GAGAGAAAAGA
55501 CTGACGAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.09
14 20 0.62
15 9 0.28
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:62304 original size:45 final size:46
Alignment explanation
Indices: 62256--62371 Score: 121
Period size: 45 Copynumber: 2.5 Consensus size: 46
62246 ACTCGTTTTC
* ** * *
62256 TTTTCTTTCTTCAATTTCTTTTTTGATTTTCTCTTTTTCACATC-CT
1 TTTTCTTTCTTCAATTTCTTTTTTCATTTTCTCACTCTCAC-TCTCA
** *
62302 TTTTCAATC-TCAATTTCTTTTTTCTTTTTCTCACTCTCACTCTCA
1 TTTTCTTTCTTCAATTTCTTTTTTCATTTTCTCACTCTCACTCTCA
62347 TTTTCTTT-TTCAATTTCTTGTTTTC
1 TTTTCTTTCTTCAATTTCTT-TTTTC
62372 TTTCATGTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
44 2 0.04
45 43 0.75
46 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63
Consensus pattern (46 bp):
TTTTCTTTCTTCAATTTCTTTTTTCATTTTCTCACTCTCACTCTCA
Found at i:62363 original size:12 final size:12
Alignment explanation
Indices: 62348--62419 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
62338 TCACTCTCAT
62348 TTTCTTTTTCAA
1 TTTCTTTTTCAA
62360 TTTCTTGTTTTC--
1 TTTC-T-TTTTCAA
* *
62372 TTTCATGTTC-A
1 TTTCTTTTTCAA
62383 TTTCCTTTTTCAA
1 TTT-CTTTTTCAA
***
62396 TTTCTTTTTGTT
1 TTTCTTTTTCAA
62408 TTTCTTTTTCAA
1 TTTCTTTTTCAA
62420 AAACTGTTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
10 4 0.09
11 3 0.07
12 28 0.62
13 5 0.11
14 5 0.11
ACGTcount: A:0.11, C:0.17, G:0.04, T:0.68
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:64705 original size:18 final size:18
Alignment explanation
Indices: 64684--64719 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64674 GAGGCCTATA
64684 TATATGGTTTGGCCAGCC
1 TATATGGTTTGGCCAGCC
64702 TATATGGTTTGGCCAGCC
1 TATATGGTTTGGCCAGCC
64720 ACGCTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (18 bp):
TATATGGTTTGGCCAGCC
Found at i:99713 original size:53 final size:53
Alignment explanation
Indices: 99650--99756 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
99640 GTAAAAAGTA
*
99650 AAAGAGCGTGAGATCATTCGAGAGAAGAAAAAGCCAAAACGAGCAAAAGCATG
1 AAAGAGCGTGAGATCATTCAAGAGAAGAAAAAGCCAAAACGAGCAAAAGCATG
*
99703 AAAGAGCGTGAGATCATTCAAGAGAAGAAAAAGCCAAAACGAGCAAAATCATG
1 AAAGAGCGTGAGATCATTCAAGAGAAGAAAAAGCCAAAACGAGCAAAAGCATG
99756 A
1 A
99757 GTGGAGTGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.50, C:0.15, G:0.24, T:0.10
Consensus pattern (53 bp):
AAAGAGCGTGAGATCATTCAAGAGAAGAAAAAGCCAAAACGAGCAAAAGCATG
Found at i:100286 original size:12 final size:12
Alignment explanation
Indices: 100269--100307 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
100259 ATCGAAAAAG
100269 AAGAAAATGAGA
1 AAGAAAATGAGA
100281 AAGAAAATGAGAA
1 AAGAAAATGAG-A
*
100294 AAGAAAAAGAGA
1 AAGAAAATGAGA
100306 AA
1 AA
100308 ACCGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (12 bp):
AAGAAAATGAGA
Found at i:100298 original size:13 final size:13
Alignment explanation
Indices: 100269--100308 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
100259 ATCGAAAAAG
100269 AAGAAAATGAG-A
1 AAGAAAATGAGAA
100281 AAGAAAATGAGAA
1 AAGAAAATGAGAA
*
100294 AAGAAAAAGAGAA
1 AAGAAAATGAGAA
100307 AA
1 AA
100309 CCGAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (13 bp):
AAGAAAATGAGAA
Found at i:100316 original size:15 final size:13
Alignment explanation
Indices: 100269--100318 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
100259 ATCGAAAAAG
*
100269 AAGAAAATGAG-A
1 AAGAAAAAGAGAA
*
100281 AAGAAAATGAGAA
1 AAGAAAAAGAGAA
100294 AAGAAAAAGAGAA
1 AAGAAAAAGAGAA
100307 AACCGAAAAAGA
1 AA--GAAAAAGA
100319 AATTGAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.32
13 15 0.44
15 8 0.24
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (13 bp):
AAGAAAAAGAGAA
Found at i:100318 original size:34 final size:35
Alignment explanation
Indices: 100262--100329 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
100252 TAATAAAATC
* *
100262 GAAAAAGAAGAAAATGAGAAAGAAAATG-AGAAAA
1 GAAAAAGAAGAAAACGAAAAAGAAAATGAAGAAAA
*
100296 GAAAAAG-AGAAAACCGAAAAAGAAATTGAAGAAA
1 GAAAAAGAAGAAAA-CGAAAAAGAAAATGAAGAAA
100330 GAAGAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 6 0.21
34 18 0.62
35 5 0.17
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (35 bp):
GAAAAAGAAGAAAACGAAAAAGAAAATGAAGAAAA
Found at i:104411 original size:12 final size:12
Alignment explanation
Indices: 104390--104435 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
104380 ATAGTAGTTT
104390 CTCG-AAAAAAA
1 CTCGAAAAAAAA
104401 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
104413 TTC-AAAAAAAA
1 CTCGAAAAAAAA
* *
104424 TTTGAAAAAAAA
1 CTCGAAAAAAAA
104436 ATTGTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 14 0.45
12 17 0.55
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.15
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:104433 original size:14 final size:14
Alignment explanation
Indices: 104416--104450 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
104406 AAAAAAATTC
104416 AAAAAAAATT-TGA
1 AAAAAAAATTGTGA
104429 AAAAAAAATTGTGA
1 AAAAAAAATTGTGA
104443 AAAAAAAA
1 AAAAAAAA
104451 GAAAGCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTGTGA
Found at i:104445 original size:12 final size:12
Alignment explanation
Indices: 104394--104449 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
104384 TAGTTTCTCG
* *
104394 AAAAAAACTCGA
1 AAAAAAATTTGA
*
104406 AAAAAAA-TTCA
1 AAAAAAATTTGA
104417 AAAAAAATTTGAA
1 AAAAAAATTTG-A
104430 AAAAAAATTGTGA
1 AAAAAAATT-TGA
104443 AAAAAAA
1 AAAAAAA
104450 AGAAAGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
11 9 0.24
12 9 0.24
13 18 0.47
14 2 0.05
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:134312 original size:60 final size:60
Alignment explanation
Indices: 134165--134299 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 60
134155 TTTCTTATTT
*
134165 TCAAGAAAATCAAGAAACCGAATCTTGGTCCAATTTTGCTGTTTCGAGCAATTTCAAGAA
1 TCAAGAAAATCAAGAAACCGAATCTTGGTCCAATTTTGCTATTTCGAGCAATTTCAAGAA
* * * *
134225 TCAAGAAAATTAAGAAACCGAATCTTGGTCCAATTTTGCTATTTGGATCGATTTCAAGAA
1 TCAAGAAAATCAAGAAACCGAATCTTGGTCCAATTTTGCTATTTCGAGCAATTTCAAGAA
134285 TCAAGAAAATCAAGA
1 TCAAGAAAATCAAGA
134300 TTTCAAATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (60 bp):
TCAAGAAAATCAAGAAACCGAATCTTGGTCCAATTTTGCTATTTCGAGCAATTTCAAGAA
Found at i:138623 original size:42 final size:42
Alignment explanation
Indices: 138564--138646 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
138554 AAATTCAAAG
138564 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
* * *
138606 GGATAAGAACACGAGTTCAAATGTTTGAATTTGAAATGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
138647 CACACAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:146040 original size:18 final size:18
Alignment explanation
Indices: 146017--146074 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
146007 TGGAGAAATG
* *
146017 AAAGAAAAAGACATTGAA
1 AAAGAAAAGGAAATTGAA
*
146035 AAAGAAAAGGAAATTGCA
1 AAAGAAAAGGAAATTGAA
146053 AAAGAAAAGGAAATTGAA
1 AAAGAAAAGGAAATTGAA
146071 AAAG
1 AAAG
146075 TGAGTGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.66, C:0.03, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAGAAAAGGAAATTGAA
Found at i:146089 original size:18 final size:18
Alignment explanation
Indices: 146068--146107 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
146058 AAAGGAAATT
* *
146068 GAAAAAGTGAGTGAAAAG
1 GAAAAAGAGAGTGAAAAA
*
146086 GAAAAAGAGATTGAAAAA
1 GAAAAAGAGAGTGAAAAA
146104 GAAA
1 GAAA
146108 TTGAAAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAGTGAAAAA
Found at i:146113 original size:30 final size:29
Alignment explanation
Indices: 146038--146118 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
146028 CATTGAAAAA
* *
146038 GAAAAGGAAATTGCAAAAGAAAAGGAAATT
1 GAAAAAGAAATTG-AAAAGAAAAAGAAATT
** * *
146068 GAAAAAGTGAGTGAAAAGGAAAAAGAGATT
1 GAAAAAGAAATTGAAAA-GAAAAAGAAATT
146098 GAAAAAGAAATTGAAAGAGAA
1 GAAAAAGAAATTGAAA-AGAA
146119 GAAAAAAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 4 0.10
30 35 0.88
31 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.26, T:0.12
Consensus pattern (29 bp):
GAAAAAGAAATTGAAAAGAAAAAGAAATT
Found at i:147853 original size:20 final size:20
Alignment explanation
Indices: 147825--147893 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
147815 TTCCATGTGG
*
147825 TTCAGCTCACTCGAGCTAAA
1 TTCAGCTCACTCGAGCTCAA
*
147845 TTTAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* * *
147865 GTCAGCTCCCACGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
147885 TTCAGCTCA
1 TTCAGCTCA
147894 TTGGGCTCGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:149335 original size:20 final size:20
Alignment explanation
Indices: 149310--149357 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
149300 TCCATGCAGT
*
149310 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACACGAGCTCAAG
*
149330 TCAGCTTC-CACGAGCTCAAT
1 TCAGC-TCACACGAGCTCAAG
149350 TCAGCTCA
1 TCAGCTCA
149358 TTGAGATCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (20 bp):
TCAGCTCACACGAGCTCAAG
Found at i:151993 original size:103 final size:103
Alignment explanation
Indices: 151804--154367 Score: 5049
Period size: 103 Copynumber: 24.9 Consensus size: 103
151794 NNNNNNNNNN
* *
151804 CTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATA
1 CTGATT-CCCCGAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTAGTGATGCTAAGTGCGATA
* * *
151869 TCCACCATATCTTTGAAATG-AAAAGGGGGTTGCTATGTG
64 TCCACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
151908 CTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATAT
1 CTGATT-CCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATAT
151973 CCACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
65 CCACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152012 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152077 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152115 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152180 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152218 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152283 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152321 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152386 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152424 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152489 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152527 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152592 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152630 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152695 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152733 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152798 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152836 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
152901 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
152939 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153004 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153042 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153107 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153145 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153210 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153248 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153313 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153351 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153416 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153454 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153519 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153557 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153622 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153660 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153725 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153763 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153828 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153866 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
153931 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
153969 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
154034 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
154072 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
154137 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
154175 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
154240 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
66 CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
154278 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
1 CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
154343 CACCGTATCTTTGAAATGAAAAATG
66 CACCGTATCTTTGAAATGAAAAATG
154368 AGTTGAAACA
Statistics
Matches: 2454, Mismatches: 5, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
103 2392 0.97
104 62 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (103 bp):
CTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTAGTGATGCTAAGTGCGATATC
CACCGTATCTTTGAAATGAAAAATGGGGTTGCTATGGG
Found at i:152040 original size:26 final size:26
Alignment explanation
Indices: 151998--152049 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
151988 AATGAAAAAT
*
151998 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152024 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152050 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152143 original size:26 final size:26
Alignment explanation
Indices: 152101--152152 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152091 AATGAAAAAT
*
152101 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152127 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152153 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152246 original size:26 final size:26
Alignment explanation
Indices: 152204--152255 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152194 AATGAAAAAT
*
152204 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152230 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152256 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152349 original size:26 final size:26
Alignment explanation
Indices: 152307--152358 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152297 AATGAAAAAT
*
152307 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152333 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152359 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152452 original size:26 final size:26
Alignment explanation
Indices: 152410--152461 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152400 AATGAAAAAT
*
152410 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152436 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152462 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152555 original size:26 final size:26
Alignment explanation
Indices: 152513--152564 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152503 AATGAAAAAT
*
152513 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152539 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152565 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152658 original size:26 final size:26
Alignment explanation
Indices: 152616--152667 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152606 AATGAAAAAT
*
152616 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152642 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152668 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152761 original size:26 final size:26
Alignment explanation
Indices: 152719--152770 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152709 AATGAAAAAT
*
152719 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152745 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152771 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152864 original size:26 final size:26
Alignment explanation
Indices: 152822--152873 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152812 AATGAAAAAT
*
152822 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152848 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152874 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:152967 original size:26 final size:26
Alignment explanation
Indices: 152925--152976 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
152915 AATGAAAAAT
*
152925 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
152951 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
152977 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153070 original size:26 final size:26
Alignment explanation
Indices: 153028--153079 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153018 AATGAAAAAT
*
153028 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153054 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153080 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153173 original size:26 final size:26
Alignment explanation
Indices: 153131--153182 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153121 AATGAAAAAT
*
153131 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153157 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153183 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153276 original size:26 final size:26
Alignment explanation
Indices: 153234--153285 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153224 AATGAAAAAT
*
153234 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153260 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153286 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153379 original size:26 final size:26
Alignment explanation
Indices: 153337--153388 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153327 AATGAAAAAT
*
153337 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153363 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153389 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153482 original size:26 final size:26
Alignment explanation
Indices: 153440--153491 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153430 AATGAAAAAT
*
153440 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153466 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153492 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153585 original size:26 final size:26
Alignment explanation
Indices: 153543--153594 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153533 AATGAAAAAT
*
153543 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153569 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153595 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153688 original size:26 final size:26
Alignment explanation
Indices: 153646--153697 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153636 AATGAAAAAT
*
153646 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153672 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153698 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153791 original size:26 final size:26
Alignment explanation
Indices: 153749--153800 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153739 AATGAAAAAT
*
153749 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153775 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153801 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153894 original size:26 final size:26
Alignment explanation
Indices: 153852--153903 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153842 AATGAAAAAT
*
153852 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153878 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
153904 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:153997 original size:26 final size:26
Alignment explanation
Indices: 153955--154006 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
153945 AATGAAAAAT
*
153955 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
153981 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
154007 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:154100 original size:26 final size:26
Alignment explanation
Indices: 154058--154109 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
154048 AATGAAAAAT
*
154058 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
154084 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
154110 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:154203 original size:26 final size:26
Alignment explanation
Indices: 154161--154212 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
154151 AATGAAAAAT
*
154161 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
154187 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
154213 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:154306 original size:26 final size:26
Alignment explanation
Indices: 154264--154315 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
154254 AATGAAAAAT
*
154264 GGGGTTGCTATGGGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
*
154290 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGGGCTGATTCCCCGA
154316 TTCATTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (26 bp):
GGGGTTGCTAAGGGCTGATTCCCCGA
Found at i:160923 original size:20 final size:20
Alignment explanation
Indices: 160900--160948 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
160890 ACGAGCTCAA
160900 TGAGCTGAATTGAGCTC-ATG
1 TGAGCTGAATTGAGCTCGA-G
*
160920 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
160940 TGAGCTGAA
1 TGAGCTGAA
160949 CCGCATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:162697 original size:18 final size:18
Alignment explanation
Indices: 162671--162710 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
162661 TCTCTTTCAA
* *
162671 TTTCTTTTTCAATCTCTT
1 TTTCCTTTTCAATCACTT
*
162689 TTTCCTTTTCACTCACTT
1 TTTCCTTTTCAATCACTT
162707 TTTC
1 TTTC
162711 AATTTCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCCTTTTCAATCACTT
Found at i:162725 original size:18 final size:18
Alignment explanation
Indices: 162704--162761 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
162694 TTTTCACTCA
*
162704 CTTTTTCAATTTCCTTTT
1 CTTTTTCAATTTCTTTTT
*
162722 CTTTTGCAATTTCTTTTT
1 CTTTTTCAATTTCTTTTT
*
162740 CTTTTTCAATGTCTTTTT
1 CTTTTTCAATTTCTTTTT
162758 CTTT
1 CTTT
162762 CATTTCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.67
Consensus pattern (18 bp):
CTTTTTCAATTTCTTTTT
Found at i:162738 original size:30 final size:29
Alignment explanation
Indices: 162660--162740 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
162650 TTTCTTTTTC
*
162660 TTCTCTTTCAATTTCTTTTTCAATCTCTTT
1 TTCT-TTTCAATTTCTTTTTCAATCTCCTT
* ** *
162690 TTCCTTTTCACTCACTTTTTCAATTTCCTT
1 TT-CTTTTCAATTTCTTTTTCAATCTCCTT
162720 TTCTTTTGCAATTTCTTTTTC
1 TTCTTTT-CAATTTCTTTTTC
162741 TTTTTCAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.12
30 34 0.83
31 2 0.05
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (29 bp):
TTCTTTTCAATTTCTTTTTCAATCTCCTT
Found at i:163872 original size:11 final size:11
Alignment explanation
Indices: 163856--163884 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
163846 CAAAATAAAC
163856 TTTTTTTTGAA
1 TTTTTTTTGAA
163867 TTTTTTTTGAA
1 TTTTTTTTGAA
163878 TTTTTTT
1 TTTTTTT
163885 CACAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:165311 original size:20 final size:20
Alignment explanation
Indices: 165287--165375 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
165277 AAAAGCTCAA
*
165287 TGAGCTGAATTGAGCTCGTG
1 TGAGCTGAATTGAGCTCGAG
* *
165307 GGAGCT-AACTTGAGCTCGAA
1 TGAGCTGAA-TTGAGCTCGAG
* *
165327 TGAGCTGACTTGAGGTCGAG
1 TGAGCTGAATTGAGCTCGAG
165347 TGAGCTGAATTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
165367 TGAGCTGAA
1 TGAGCTGAA
165376 CCGCATGGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 55 0.95
21 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.25
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:166828 original size:10 final size:11
Alignment explanation
Indices: 166798--166826 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
166788 TTTTTAAAAT
166798 TTTTTTTTCAA
1 TTTTTTTTCAA
166809 TTTTTTTTCAA
1 TTTTTTTTCAA
166820 TTTTTTT
1 TTTTTTT
166827 CACAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:166832 original size:23 final size:23
Alignment explanation
Indices: 166786--166832 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
166776 AAATAAACTC
**
166786 TTTTTTTAAAATTTTTTTTTCAA
1 TTTTTTTAAAATTTTTTTCACAA
**
166809 TTTTTTTTCAATTTTTTTCACAA
1 TTTTTTTAAAATTTTTTTCACAA
166832 T
1 T
166833 GACTTACTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTTTAAAATTTTTTTCACAA
Found at i:169428 original size:42 final size:42
Alignment explanation
Indices: 169369--169577 Score: 418
Period size: 42 Copynumber: 5.0 Consensus size: 42
169359 AAAATTCAAA
169369 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
169411 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
169453 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
169495 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
169537 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
169578 CACACATATT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 167 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:172178 original size:14 final size:14
Alignment explanation
Indices: 172159--172187 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
172149 TAATGTGGAC
172159 ACAAATTAAATGAA
1 ACAAATTAAATGAA
172173 ACAAATTAAATGAA
1 ACAAATTAAATGAA
172187 A
1 A
172188 ACTAAACAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
ACAAATTAAATGAA
Found at i:172224 original size:45 final size:43
Alignment explanation
Indices: 172157--172253 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 43
172147 CATAATGTGG
*
172157 ACACAAATTAAATGAAACAAATTAAATGAAAACTAAACAGGAC
1 ACACTAATTAAATGAAACAAATTAAATGAAAACTAAACAGGAC
*
172200 ACACTAATTAACATTGAAAGAAATTAAATGAAAACTAAACAGGAC
1 ACACTAATTAA-A-TGAAACAAATTAAATGAAAACTAAACAGGAC
172245 ACACTAATT
1 ACACTAATT
172254 CGGCTGTGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 10 0.20
44 1 0.02
45 39 0.78
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (43 bp):
ACACTAATTAAATGAAACAAATTAAATGAAAACTAAACAGGAC
Found at i:178056 original size:12 final size:12
Alignment explanation
Indices: 178027--178107 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
178017 TCTTCACTCG
*
178027 TTTCTTTTGCAA
1 TTTCTTTTTCAA
**
178039 ACTCTTTTTCAA
1 TTTCTTTTTCAA
*
178051 TTTCTTTTTCCACTC
1 TTTCTTTTT-CA--A
178066 TTTCTTTTTC--
1 TTTCTTTTTCAA
*
178076 -TTCTCTTTCAA
1 TTTCTTTTTCAA
178087 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
178099 TCTCTTTTT
1 TTTCTTTTT
178108 GCTTTTCACT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 8 0.15
12 34 0.63
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.23, G:0.01, T:0.63
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:178129 original size:16 final size:18
Alignment explanation
Indices: 178092--178129 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
178082 TTCAATTTCT
178092 TTTTCAATCTCTTTTTGC
1 TTTTCAATCTCTTTTTGC
*
178110 TTTTCACTCT-TTTTTG-
1 TTTTCAATCTCTTTTTGC
178126 TTTT
1 TTTT
178130 TGAAATCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTCAATCTCTTTTTGC
Found at i:178192 original size:12 final size:12
Alignment explanation
Indices: 178150--178191 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
178140 TTTTCATCTT
178150 TTTCTTTTTC-A
1 TTTCTTTTTCAA
178161 TTTC--TTTCAA
1 TTTCTTTTTCAA
178171 TTTCTTTTTCAA
1 TTTCTTTTTCAA
178183 TGTTCTTTT
1 T-TTCTTTT
178192 CTCGCTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 4 0.15
12 7 0.26
13 7 0.26
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:181387 original size:24 final size:24
Alignment explanation
Indices: 181363--181409 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
181353 ATACTACTTC
181363 TGAAAAAAACTCAAGAGAGAATTCT
1 TGAAAAAAACTCAA-AGAGAATTCT
* *
181388 TGGAGAAAACTCAAAGAGAATT
1 TGAAAAAAACTCAAAGAGAATT
181410 TTTCACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (24 bp):
TGAAAAAAACTCAAAGAGAATTCT
Found at i:183830 original size:33 final size:34
Alignment explanation
Indices: 183787--183851 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
183777 TTAAACAATT
183787 TAATTACTAACACTTATTTAAGCTGAACTAAAAA
1 TAATTACTAACACTTATTTAAGCTGAACTAAAAA
*
183821 TAATT-CTAACACTTATTTGAGCTGAACTAAA
1 TAATTACTAACACTTATTTAAGCTGAACTAAA
183852 TTTAATAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (34 bp):
TAATTACTAACACTTATTTAAGCTGAACTAAAAA
Found at i:185685 original size:18 final size:18
Alignment explanation
Indices: 185662--185700 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
185652 CTATTTTTGC
185662 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
*
185680 TCTTTTTCGATTTGTTTT
1 TCTTTTTCGATTTCTTTT
185698 TCT
1 TCT
185701 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:188201 original size:16 final size:16
Alignment explanation
Indices: 188162--188203 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
188152 AATGAGCCAT
* *
188162 ATCCATGAATCCAGCC
1 ATCCATGTATTCAGCC
188178 ATCCATGTATTCAGCC
1 ATCCATGTATTCAGCC
*
188194 ATTCATGTAT
1 ATCCATGTAT
188204 ACTCCCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (16 bp):
ATCCATGTATTCAGCC
Found at i:188574 original size:20 final size:20
Alignment explanation
Indices: 188545--188585 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
188535 AAGCTAATTC
*
188545 AATGAGCTGAATTGAGCTCA
1 AATGACCTGAATTGAGCTCA
*
188565 AATGACCTGACTTGAGCTCA
1 AATGACCTGAATTGAGCTCA
188585 A
1 A
188586 GTGAGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
AATGACCTGAATTGAGCTCA
Found at i:190295 original size:12 final size:11
Alignment explanation
Indices: 190278--190327 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
190268 TCACTCTCAT
190278 TTTCTTTTTCGA
1 TTTCTTTTTC-A
*
190290 TTTCTTGTTC-
1 TTTCTTTTTCA
190300 TTT-TTCTTTCA
1 TTTCTT-TTTCA
190311 TTTCTTTTTTCA
1 TTTC-TTTTTCA
190323 TTTCT
1 TTTCT
190328 CGATTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 4 0.12
12 18 0.56
13 2 0.06
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTCTTTTTCA
Found at i:191807 original size:12 final size:12
Alignment explanation
Indices: 191790--191822 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
191780 AAAATCTGAT
191790 TTCAATGTATAA
1 TTCAATGTATAA
191802 TTCAATGTATAA
1 TTCAATGTATAA
191814 TTCAATGTA
1 TTCAATGTA
191823 ATTTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (12 bp):
TTCAATGTATAA
Found at i:212201 original size:17 final size:18
Alignment explanation
Indices: 212179--212214 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
212169 GGAATAAACA
212179 TAGTTAA-TTAAATAAGT
1 TAGTTAATTTAAATAAGT
*
212196 TAGTTAATTTAATTAAGT
1 TAGTTAATTTAAATAAGT
212214 T
1 T
212215 CAGCTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TAGTTAATTTAAATAAGT
Found at i:212390 original size:41 final size:41
Alignment explanation
Indices: 212337--212416 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
212327 CCTAGGACAA
*
212337 ATTTATTAGCTGCTGCTATTTAATTTGTCCAGCTGAATTTG
1 ATTTATTAGCTGCTGCTATTTAATGTGTCCAGCTGAATTTG
* * * *
212378 ATTTATTGGCTGCTGTTGTTTAATGTGTCTAGCTGAATT
1 ATTTATTAGCTGCTGCTATTTAATGTGTCCAGCTGAATT
212417 AATTGTGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (41 bp):
ATTTATTAGCTGCTGCTATTTAATGTGTCCAGCTGAATTTG
Found at i:213733 original size:30 final size:30
Alignment explanation
Indices: 213698--213758 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
213688 CAATTTGTTG
* *
213698 TGAGCT-GAACTAAGCTCCATTTCAGCTCAA
1 TGAGCTCGAA-TAAGCTCAAATTCAGCTCAA
*
213728 TGAGCTCGAATCAGCTCAAATTCAGCTCAA
1 TGAGCTCGAATAAGCTCAAATTCAGCTCAA
213758 T
1 T
213759 TCCATTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (30 bp):
TGAGCTCGAATAAGCTCAAATTCAGCTCAA
Found at i:214007 original size:20 final size:20
Alignment explanation
Indices: 213982--214026 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
213972 TGTCCAACCG
213982 AATTAATTGTGTCTTAA-TTT
1 AATTAATTGTGTC-TAATTTT
214002 AATTAATTGTGTCTAATTTT
1 AATTAATTGTGTCTAATTTT
214022 AATTA
1 AATTA
214027 TGTGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (20 bp):
AATTAATTGTGTCTAATTTT
Found at i:216079 original size:282 final size:283
Alignment explanation
Indices: 215565--216129 Score: 1114
Period size: 282 Copynumber: 2.0 Consensus size: 283
215555 CAATAAGTCT
215565 TCTTGAAACAAAATACGAATTCACGAGAGTGAGACGAGCAGAAAAAGGCACGAGTGGTGAGTACA
1 TCTTGAAACAAAATACGAATTCACGAGAGTGAGACGAGCAGAAAAAGGCACGAGTGGTGAGTACA
215630 TTAGAGCGAGCAAAAGCCATTAAACGAGCGTAAACACGAGTGGAGTGCTATACAATTTTCTTTGC
66 TTAGAGCGAGCAAAAGCCATTAAACGAGCGTAAACACGAGTGGAGTGCTATACAATTTTCTTTGC
215695 GAGTGAAACGTGAGATTTTTGTGGTGAGGTATTTAATTTTTGTTTTGTTTTAACCACTATTCTTT
131 GAGTGAAACGTGAGATTTTTGTGGTGAGGTATTTAATTTTTGTTTTGTTTTAACCACTATTCTTT
215760 TTCAACAATTAAATCATGTCTTGAGAAGAATTCCCTATCGATGAATTTCAATACCTGGTGAACGA
196 TTCAACAATTAAATCATGTCTTGAGAAGAATTCCCTATCGATGAATTTCAATACCTGGTGAACGA
215825 GATGGGCCGGATGTTGGAGGAAA
261 GATGGGCCGGATGTTGGAGGAAA
215848 TCTTGAAAC-AAATACGAATTCACGAGAGTGAGACGAGCAGAAAAAGGCACGAGTGGTGAGTACA
1 TCTTGAAACAAAATACGAATTCACGAGAGTGAGACGAGCAGAAAAAGGCACGAGTGGTGAGTACA
*
215912 TTAGAGCGAGCAAAAGCCATTAAACGGGCGTAAACACGAGTGGAGTGCTATACAATTTTCTTTGC
66 TTAGAGCGAGCAAAAGCCATTAAACGAGCGTAAACACGAGTGGAGTGCTATACAATTTTCTTTGC
215977 GAGTGAAACGTGAGATTTTTGTGGTGAGGTATTTAATTTTTGTTTTGTTTTAACCACTATTCTTT
131 GAGTGAAACGTGAGATTTTTGTGGTGAGGTATTTAATTTTTGTTTTGTTTTAACCACTATTCTTT
216042 TTCAACAATTAAATCATGTCTTGAGAAGAATTCCCTATCGATGAATTTCAATACCTGGTGAACGA
196 TTCAACAATTAAATCATGTCTTGAGAAGAATTCCCTATCGATGAATTTCAATACCTGGTGAACGA
216107 GATGGGCCGGATGTTGGAGGAAA
261 GATGGGCCGGATGTTGGAGGAAA
216130 AACTAAGCCC
Statistics
Matches: 281, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
282 272 0.97
283 9 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (283 bp):
TCTTGAAACAAAATACGAATTCACGAGAGTGAGACGAGCAGAAAAAGGCACGAGTGGTGAGTACA
TTAGAGCGAGCAAAAGCCATTAAACGAGCGTAAACACGAGTGGAGTGCTATACAATTTTCTTTGC
GAGTGAAACGTGAGATTTTTGTGGTGAGGTATTTAATTTTTGTTTTGTTTTAACCACTATTCTTT
TTCAACAATTAAATCATGTCTTGAGAAGAATTCCCTATCGATGAATTTCAATACCTGGTGAACGA
GATGGGCCGGATGTTGGAGGAAA
Found at i:218852 original size:5 final size:6
Alignment explanation
Indices: 218804--218871 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
218794 AATGAAAAAG
** **
218804 AAGAAA AAGAAA AAGAAA GTGAAA AAGAAA AAGAAA GTGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
218852 AA-AAA ATTGCAA AAGAAA AA
1 AAGAAA A-AGAAA AAGAAA AA
218872 TAAATCGAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
5 4 0.08
6 41 0.85
7 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:218876 original size:18 final size:18
Alignment explanation
Indices: 218806--218871 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
218796 TGAAAAAGAA
218806 GAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAAGT
218824 GAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAAGT
* *
218842 GAAAAAGAAAAAAAAATT
1 GAAAAAGAAAAAGAAAGT
*
218860 GCAAAAGAAAAA
1 GAAAAAGAAAAA
218872 TAAATCGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAGT
Found at i:220591 original size:12 final size:14
Alignment explanation
Indices: 220565--220597 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
220555 ACTCATTTTC
220565 TCTTCTTTCTTCAA
1 TCTTCTTTCTTCAA
220579 T-TTCTTT-TTCAA
1 TCTTCTTTCTTCAA
220591 TCTTCTT
1 TCTTCTT
220598 GTCTGTGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 11 0.61
14 1 0.06
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTTCTTTCTTCAA
Found at i:220667 original size:18 final size:20
Alignment explanation
Indices: 220621--220670 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
220611 TCACTCTCAA
220621 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCTCTTTTTCAT
*
220642 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTCTTTTTCAT
*
220661 T-TGTTTTTCT
1 TCTCTTTTTCT
220671 GTCTTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 7 0.26
21 4 0.15
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (20 bp):
TCTCTTTTTCTCTTTTTCAT
Found at i:224553 original size:637 final size:632
Alignment explanation
Indices: 223325--224582 Score: 1686
Period size: 637 Copynumber: 2.0 Consensus size: 632
223315 ATTCTTGGAG
223325 AACTCAAAGAGAATTTTCACTCAACAAAACAAATCTGATTTCAATGTATTCTTCAAGTGTAATGT
1 AACTCAAAGAGAATTTTCACT--ACAAAACAAATCTGATTTCAATGTATTCTTCAAGTGTAATG-
* * *
223390 AATGTGTATAAGGGTGGCTGGCCAAGCCATATATATAGGCCTCCTAACTACTTTCCCAGCCCTAC
63 -ATGTGTATAAAGGTGGCTGGCCAAGCCATACATATAGGCCTCCTAACTACTTTCCCAGCCCTAA
* * * * * * *
223455 TAGGAAAACTTATAAAAAAAACCCTAATTTTAACTTTCAAAGGGGAATTTCGTCCAAGTCCTTTA
127 TAGGAAAACTTATAAAAAAAAACCTAATTTTAAATTTCAAAGGGAAAATTCGGCCAAGGCATTTA
* * *
223520 AATGGGCCTCTTGGACTAAATTTTTACATAATAATTTATTCATAAAGTCTAAAAATTAAAATTCA
192 AATGGGCCTCTTGGACTAAATTTTTACATAAGAATTTAATCATAAAGTCTAAAAATTAAAACTCA
* *
223585 GTATTTAAAGAATTAAATTGGGCCACTTTGACTATTTGGCCTGATTTTCAGCTAAGTCTAATTTA
257 GTATTTAAAGAATTAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTCTAATTTA
* * * *
223650 AACTTCTGTATTGGGCTTGGGACATCTTATTGGGCCTTGTCTTCAAGAACTTGGGCTTGTAATCT
322 AACTTCTGTATTGGGCTTGGAACATCTTATTGGGCCTTGCCTTCAAGAACCTGGGCTTGTAATCC
* * *
223715 GTTCTCTCCCAAAATTGGCTTGTTAATGCTCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGAT
387 GTTCTCTCCCAAAATTGGATTGTTAATGCTCGTAACAGAGATCCAATGCGCCTTAGCTGCAAGAT
* * *
223780 TCGGTTTCTTGGACGAGGATTTGCAAGATTTGAAATATTGATTTTCTTGATTCTTGAAATCGCTC
452 TCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATATTGATTTTCTTGATTCTTGAAATCGCTC
* *
223845 AAAACAACAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAATAAGAAAGTGAATCTTG
517 AAAACAACAAAATTGGACCAAGATTAGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTG
223910 ATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTTTGACTCGTATCAA
582 ATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTTTTTGACTCGTATCAA
* * * *
223961 AACTCAAAGAGAATTTTTCACT-CAATA-AAATCTGATTTCAATGTGTTGTTTAATGTGTAATG-
1 AACTCAAAGAGAA-TTTTCACTACAAAACAAATCTGATTTCAATGTATTCTTCAA-GTGTAATGA
* * * ** *
224023 T-TGTATAAAGGTGGTTGGCCAAGCCATACATATAGGCCTTCTAACTATTTTCCTTGTCCTAATA
64 TGTGTATAAAGGTGGCTGGCCAAGCCATACATATAGGCCTCCTAACTACTTTCCCAGCCCTAATA
*
224087 GGAAAAC-TA-AAAAAAAAACCTAATTATTAAATTT-AGAGGGAAAAATTCGGCCAAGGCATTT-
129 GGAAAACTTATAAAAAAAAACCTAATT-TTAAATTTCAAAGGG-AAAATTCGGCCAAGGCATTTA
* * * *
224148 AATGGG-CTGCTTGGGCTGAATTTTTTTACATAGGCA-TTAATCATAAAGTCTAAAAATT-AAAC
192 AATGGGCCT-CTTGGACT-AA-ATTTTTACATAAGAATTTAATCATAAAGTCTAAAAATTAAAAC
224210 T-AGGTATTTAAAGAATTAAAATTTTACAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAA
254 TCA-GTATTTAAAG------AA--TT--AAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAA
* *
224274 CTAAGTCTCA-TTCAACTTTCT-TGATTGGGCTTGGAACATCTTATTGGGCCTTGCCTTCAAGAA
308 CTAAGTCTAATTTAAAC-TTCTGT-ATTGGGCTTGGAACATCTTATTGGGCCTTGCCTTCAAGAA
* * * *
224337 CCTGGGC-TGTAGTCCGTT-TGCTTCCGAAATT-GATTCGTTGATGCTCGTAACAGAGATCCAAT
371 CCTGGGCTTGTAATCCGTTCT-CTCCCAAAATTGGATT-GTTAATGCTCGTAACAGAGATCCAAT
*
224399 GCGCCTTAGCTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCT
434 GCGCCTTAGCTGCAAGATTCGGTTTCTTGGACCAAGATTTCCAAGATTTGAAATATTGATTTTCT
*
224464 TGATTCTTGAAATCGCTCCAAACAACAAAATTGGACCAAGATTAGGTTTCTTGATTTTCTTGAAA
499 TGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTAGGTTTCTTGATTTTCTTGAAA
* * *
224529 ACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTTGTGTACGTATCTAAGGCCTT
564 ACAAGAAAGTGAATCTTGATTTTCTTTTTCCTTCGTATACGCATCTAAGGCCTT
224583 GGTAATAAAT
Statistics
Matches: 547, Mismatches: 53, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
627 3 0.01
628 47 0.09
629 47 0.09
630 72 0.13
631 1 0.00
633 23 0.04
634 14 0.03
636 19 0.03
637 229 0.42
638 92 0.17
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (632 bp):
AACTCAAAGAGAATTTTCACTACAAAACAAATCTGATTTCAATGTATTCTTCAAGTGTAATGATG
TGTATAAAGGTGGCTGGCCAAGCCATACATATAGGCCTCCTAACTACTTTCCCAGCCCTAATAGG
AAAACTTATAAAAAAAAACCTAATTTTAAATTTCAAAGGGAAAATTCGGCCAAGGCATTTAAATG
GGCCTCTTGGACTAAATTTTTACATAAGAATTTAATCATAAAGTCTAAAAATTAAAACTCAGTAT
TTAAAGAATTAAATTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTCTAATTTAAACT
TCTGTATTGGGCTTGGAACATCTTATTGGGCCTTGCCTTCAAGAACCTGGGCTTGTAATCCGTTC
TCTCCCAAAATTGGATTGTTAATGCTCGTAACAGAGATCCAATGCGCCTTAGCTGCAAGATTCGG
TTTCTTGGACCAAGATTTCCAAGATTTGAAATATTGATTTTCTTGATTCTTGAAATCGCTCAAAA
CAACAAAATTGGACCAAGATTAGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTT
TCTTTTTCCTTCGTATACGCATCTAAGGCCTTTTTGACTCGTATCAA
Found at i:227575 original size:18 final size:20
Alignment explanation
Indices: 227552--227601 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
227542 AACAGAAGAC
227552 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
227570 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
227590 AGTAAAAAGAGA
1 AG-AAAAAGAGA
227602 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:235126 original size:28 final size:28
Alignment explanation
Indices: 235094--235156 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
235084 TCAATCCACA
*
235094 TAGCTTGCCAAAGCTTCTTTAAAGTTCT
1 TAGCTCGCCAAAGCTTCTTTAAAGTTCT
**
235122 TAGCTCGTGAAAGCTTCTTTAAAGTTCT
1 TAGCTCGCCAAAGCTTCTTTAAAGTTCT
235150 TAGCTCG
1 TAGCTCG
235157 TGACCTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (28 bp):
TAGCTCGCCAAAGCTTCTTTAAAGTTCT
Found at i:235157 original size:28 final size:28
Alignment explanation
Indices: 235103--235159 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
235093 ATAGCTTGCC
235103 AAAGCTTCTTTAAAGTTCTTAGCTCGTG
1 AAAGCTTCTTTAAAGTTCTTAGCTCGTG
235131 AAAGCTTCTTTAAAGTTCTTAGCTCGTG
1 AAAGCTTCTTTAAAGTTCTTAGCTCGTG
235159 A
1 A
235160 CCTAGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (28 bp):
AAAGCTTCTTTAAAGTTCTTAGCTCGTG
Found at i:238029 original size:24 final size:26
Alignment explanation
Indices: 237988--238036 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
237978 CACTGAATAT
* *
237988 TTTTTTAATTTTTATTTGATTTCTTA
1 TTTTTCAATTTTTATTTGACTTCTTA
238014 TTTTTCAA-TTTT-TTTGACTTCTT
1 TTTTTCAATTTTTATTTGACTTCTT
238037 CTACTGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 4 0.19
26 7 0.33
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTTCAATTTTTATTTGACTTCTTA
Found at i:240528 original size:50 final size:50
Alignment explanation
Indices: 240374--240539 Score: 235
Period size: 50 Copynumber: 3.3 Consensus size: 50
240364 NNNNNNNNNT
240374 ACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGCCTGC
1 ACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGCCTGC
* * * ** * * *
240424 ACATAGTACTACACACGTGATC-AAAATTATCCGATACGCATAGTAGCCTAC
1 ACATAGTACTACACATGCGACCTATCA-T-TCCGATACACGTAGTAGCCTGC
240475 ACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGCCTGC
1 ACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGCCTGC
240525 ACATAGTACTACACA
1 ACATAGTACTACACA
240540 CATCACCATC
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.02
50 54 0.56
51 39 0.40
52 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.23
Consensus pattern (50 bp):
ACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGCCTGC
Found at i:247858 original size:73 final size:73
Alignment explanation
Indices: 247719--247866 Score: 289
Period size: 72 Copynumber: 2.0 Consensus size: 73
247709 TTTTATATTT
247719 ATTAATTATGAAAAAAAAAATTTTTTACATTAATTACATAATGAGAGAGAACAAATTGAAAGAAA
1 ATTAATTATGAAAAAAAAAATTTTTTACATTAATTACATAATGAGAGAGAACAAATTGAAAGAAA
247784 AAACAAAA
66 AAACAAAA
247792 ATTAATTATG-AAAAAAAAATTTTTTACATTAATTACATAATGAGAGAGAACAAATTGAAAGAAA
1 ATTAATTATGAAAAAAAAAATTTTTTACATTAATTACATAATGAGAGAGAACAAATTGAAAGAAA
247856 AAACAAAA
66 AAACAAAA
247864 ATT
1 ATT
247867 TTATCAATAA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 65 0.87
73 10 0.13
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.27
Consensus pattern (73 bp):
ATTAATTATGAAAAAAAAAATTTTTTACATTAATTACATAATGAGAGAGAACAAATTGAAAGAAA
AAACAAAA
Found at i:249923 original size:86 final size:86
Alignment explanation
Indices: 249778--250035 Score: 480
Period size: 86 Copynumber: 3.0 Consensus size: 86
249768 TGAAAGATAT
*
249778 AACGAAATCATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
1 AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
249843 GTTATCAGCTTCTCCCGACAA
66 GTTATCAGCTTCTCCCGACAA
249864 AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
1 AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
249929 GTTATCAGCTTCTCCCGACAA
66 GTTATCAGCTTCTCCCGACAA
*
249950 AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTCCCAAGGTCGA
1 AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
* *
250015 GCTATCAGCTTCACCCGACAA
66 GTTATCAGCTTCTCCCGACAA
250036 GCTCGGCCTG
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 168 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (86 bp):
AACGAAATTATCACTAAAACAAATTTTGGAACACGATCTACATCAAACATGTGTTCCAAGGTCGA
GTTATCAGCTTCTCCCGACAA
Found at i:250429 original size:22 final size:24
Alignment explanation
Indices: 250390--250436 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
250380 AATTGACATT
*
250390 TTAATATATTATTATTATTAAATA
1 TTAATATAATATTATTATTAAATA
250414 TTAA-ATAATATT-TTATTAAATA
1 TTAATATAATATTATTATTAAATA
250436 T
1 T
250437 AAACTGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATATAATATTATTATTAAATA
Found at i:250528 original size:78 final size:79
Alignment explanation
Indices: 250434--250591 Score: 309
Period size: 78 Copynumber: 2.0 Consensus size: 79
250424 TTTTATTAAA
250434 TATAAACTGCACATTTTATGCCGATGTTAAAATAAACTTCCATTATAATTCAAGTCATCAATTTT
1 TATAAACTGCACATTTTATGCCGATGTTAAAATAAACTTCCATTATAATTCAAGTCATCAATTTT
250499 CGGTTAGACTTTAT
66 CGGTTAGACTTTAT
250513 TATAAACTGC-CATTTTATGCCGATGTTAAAATAAACTTCCATTATAATTCAAGTCATCAATTTT
1 TATAAACTGCACATTTTATGCCGATGTTAAAATAAACTTCCATTATAATTCAAGTCATCAATTTT
250577 CGGTTAGACTTTAT
66 CGGTTAGACTTTAT
250591 T
1 T
250592 GGTATTTCAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.87
79 10 0.13
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (79 bp):
TATAAACTGCACATTTTATGCCGATGTTAAAATAAACTTCCATTATAATTCAAGTCATCAATTTT
CGGTTAGACTTTAT
Found at i:265138 original size:29 final size:29
Alignment explanation
Indices: 265105--265164 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
265095 TAGGAATAGG
*
265105 AAATTCAATTAGGATATCTTAGGTTAATT
1 AAATTCAATTAGGATATCTTAGATTAATT
* * * *
265134 AAATTCCATTAGGTTATTTTTGATTAATT
1 AAATTCAATTAGGATATCTTAGATTAATT
265163 AA
1 AA
265165 TTTTGATTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (29 bp):
AAATTCAATTAGGATATCTTAGATTAATT
Found at i:267649 original size:20 final size:21
Alignment explanation
Indices: 267624--267668 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
267614 AAATAGTGAG
*
267624 AATTTTATTCTCTA-AATATA
1 AATTTTATTCTCTAGAATAAA
*
267644 AATTTTATTTTCTAGAATAAA
1 AATTTTATTCTCTAGAATAAA
267665 AATT
1 AATT
267669 CTACCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTTTATTCTCTAGAATAAA
Found at i:273588 original size:23 final size:23
Alignment explanation
Indices: 273558--273603 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
273548 GAGGGGCAAC
*
273558 TTGTAATATCCCGAAAATTACTA
1 TTGTAATACCCCGAAAATTACTA
273581 TTGTAATACCCCGAAAATTACTA
1 TTGTAATACCCCGAAAATTACTA
273604 CAGTAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
TTGTAATACCCCGAAAATTACTA
Found at i:273609 original size:23 final size:23
Alignment explanation
Indices: 273560--273609 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
273550 GGGGCAACTT
* **
273560 GTAATATCCCGAAAATTACTATT
1 GTAATACCCCGAAAATTACTACA
273583 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
273606 GTAA
1 GTAA
273610 GAAAGTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTACA
Found at i:280542 original size:50 final size:50
Alignment explanation
Indices: 280444--280631 Score: 225
Period size: 50 Copynumber: 3.6 Consensus size: 50
280434 TGTGAGCCAG
280444 TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAGGTCCCA
*
280500 TGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCA
* * * *
280550 TGTAAGACCATGTCTGGGACATGGCTTTGGCAC-CAGGATGAGAGATCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGA-GATGAGAGGTCCCA
** * *
280600 CATAAGACCATGTCTGGGATATGACATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
280632 GTATAGGAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.01
50 84 0.69
53 4 0.03
55 1 0.01
56 31 0.26
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCA
Found at i:282200 original size:23 final size:23
Alignment explanation
Indices: 282166--282216 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
282156 GGGGGAGAAA
*
282166 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
282189 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
282212 AGTAA
1 TGTAA
282217 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:286480 original size:45 final size:44
Alignment explanation
Indices: 286379--286510 Score: 156
Period size: 45 Copynumber: 2.9 Consensus size: 44
286369 GTGTTTCACT
* * * *
286379 TGATGACATAGCATTTTTTAGCTATGGTCTTGCTCACTTTTATCA
1 TGAT-ACATAGCATTTTTCAACTATGGTCTTACTCATTTTTATCA
*
286424 TGATACTATAGCATTTTTCAACTATGGTCTTACTAATTTTTATCA
1 TGATAC-ATAGCATTTTTCAACTATGGTCTTACTCATTTTTATCA
* * * *
286469 TGTTGTCATAGCATCTTTCAACTATTGTCTTACTCATTTTTA
1 TGAT-ACATAGCATTTTTCAACTATGGTCTTACTCATTTTTA
286511 GGAGTATAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
44 2 0.03
45 72 0.96
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.47
Consensus pattern (44 bp):
TGATACATAGCATTTTTCAACTATGGTCTTACTCATTTTTATCA
Found at i:291000 original size:16 final size:16
Alignment explanation
Indices: 290979--291030 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
290969 AATAAAATAT
290979 GATAGATAATTTGATG
1 GATAGATAATTTGATG
290995 GATAGATTAA----ATG
1 GATAGA-TAATTTGATG
291008 GATAGATAATTTGATG
1 GATAGATAATTTGATG
*
291024 GACAGAT
1 GATAGAT
291031 GAAATGGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
12 3 0.10
13 9 0.30
16 15 0.50
17 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (16 bp):
GATAGATAATTTGATG
Found at i:291012 original size:29 final size:29
Alignment explanation
Indices: 290979--291038 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
290969 AATAAAATAT
* *
290979 GATAGATAATTTGATGGATAGATTAAATG
1 GATAGATAATTTGATGGACAGATGAAATG
291008 GATAGATAATTTGATGGACAGATGAAATG
1 GATAGATAATTTGATGGACAGATGAAATG
291037 GA
1 GA
291039 AATTCAGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.02, G:0.27, T:0.30
Consensus pattern (29 bp):
GATAGATAATTTGATGGACAGATGAAATG
Found at i:294386 original size:30 final size:30
Alignment explanation
Indices: 294314--294386 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
294304 TTTTTTGATT
* * *
294314 TTTTTCTTTTGCAATTTATTTTGCAATTTC
1 TTTTTCTTTTTCTATTTATTTTGCAATTTA
* * * * *
294344 TTTGTCGTTTTCTATTTCTTTTTCACTTTA
1 TTTTTCTTTTTCTATTTATTTTGCAATTTA
294374 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
294387 TCTTTTTTGT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.11, C:0.15, G:0.05, T:0.68
Consensus pattern (30 bp):
TTTTTCTTTTTCTATTTATTTTGCAATTTA
Found at i:295210 original size:33 final size:33
Alignment explanation
Indices: 295173--295240 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
295163 GAAATGGTAG
*
295173 AATGAATGGATGATCGGGAATAACAATAAATGA
1 AATGAATGGATGATCGGGAATAACAAGAAATGA
295206 AATGAATGGATGATCGGGAATAACAAGAAATGA
1 AATGAATGGATGATCGGGAATAACAAGAAATGA
295239 AA
1 AA
295241 ACAAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (33 bp):
AATGAATGGATGATCGGGAATAACAAGAAATGA
Found at i:297085 original size:20 final size:20
Alignment explanation
Indices: 297052--297108 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
297042 ATCTAATAAC
297052 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
** *
297071 GAGCTCGTGTGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
297091 GAGCTCGAATGAGCTGAA
1 GAGCTCGAATGAGCTGAA
297109 CCTCATAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:297870 original size:26 final size:26
Alignment explanation
Indices: 297841--297897 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
297831 TACTAAGGGC
* *
297841 AAAATCGTTAAAATTTTATCGGGGGT
1 AAAATCGTCAAAATTTTATCAGGGGT
* * *
297867 AAAATTGTCAAAATTTTGTTAGGGGT
1 AAAATCGTCAAAATTTTATCAGGGGT
297893 AAAAT
1 AAAAT
297898 ATGGATGAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (26 bp):
AAAATCGTCAAAATTTTATCAGGGGT
Found at i:308705 original size:25 final size:25
Alignment explanation
Indices: 308655--308741 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
308645 ATAAGCTGTA
*
308655 AACGGTAAGCTCCTTCAAGATGAAT
1 AACGGTAAGCTCCTCCAAGATGAAT
* * * *
308680 AATGGTAAGCTCCTCCGAGCTTAAT
1 AACGGTAAGCTCCTCCAAGATGAAT
* * *
308705 AACAGTAAGCTCATACC-AGCTGAAT
1 AACGGTAAGCTCCT-CCAAGATGAAT
*
308730 AACAGTAAGCTC
1 AACGGTAAGCTC
308742 ATCAGAGCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 50 0.96
26 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCAAGATGAAT
Found at i:308742 original size:25 final size:25
Alignment explanation
Indices: 308675--308753 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
308665 TCCTTCAAGA
** *
308675 TGAATAATGGTAAGCTCCTCCGAGC
1 TGAATAACAGTAAGCTCATCCGAGC
*
308700 TTAATAACAGTAAGCTCATACC-AGC
1 TGAATAACAGTAAGCTCAT-CCGAGC
*
308725 TGAATAACAGTAAGCTCATCAGAGC
1 TGAATAACAGTAAGCTCATCCGAGC
308750 TGAA
1 TGAA
308754 ATCGATAACC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.93
26 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (25 bp):
TGAATAACAGTAAGCTCATCCGAGC
Found at i:310399 original size:23 final size:24
Alignment explanation
Indices: 310360--310404 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
310350 TAGGTATCTC
* *
310360 AATATTCACAAATTTAATCAATCA
1 AATAATCACAAATTTAAACAATCA
310384 AATAATCACAAA-TTAAACAAT
1 AATAATCACAAATTTAAACAAT
310405 TTATCATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAATCACAAATTTAAACAATCA
Found at i:317871 original size:26 final size:26
Alignment explanation
Indices: 317842--317900 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 26
317832 TAGTTGTTTC
317842 TGTTTATGCCGATTGGTTGATTAACT
1 TGTTTATGCCGATTGGTTGATTAACT
317868 TGTTTATGCCGATTGGTTGATTAACT
1 TGTTTATGCCGATTGGTTGATTAACT
317894 TGATTTA
1 TG-TTTA
317901 ATTTCTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.47
Consensus pattern (26 bp):
TGTTTATGCCGATTGGTTGATTAACT
Found at i:327088 original size:26 final size:26
Alignment explanation
Indices: 327055--327151 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
327045 ACCCTATGAG
*
327055 GGGTATTTCGATCATTTTACCATAC-A
1 GGGTATTTCGATCATTTTACC-TTCGA
* *
327081 GGGTATTTCGGTCATTTTACCCTTCGG
1 GGGTATTTCGATCATTTTA-CCTTCGA
*
327108 GGGTATTTCTG-TCATTTTAACCTTCTA
1 GGGTATTTC-GATCATTTT-ACCTTCGA
*
327135 GGATATTTCGATCATTT
1 GGGTATTTCGATCATTT
327152 ACCCACGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
26 21 0.35
27 37 0.62
28 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (26 bp):
GGGTATTTCGATCATTTTACCTTCGA
Found at i:327153 original size:53 final size:53
Alignment explanation
Indices: 327054--327155 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 53
327044 TACCCTATGA
* *
327054 GGGGTATTTCGATCATTTTACCATACAGGGTATTTCGGTCATTTTACCCTTCG
1 GGGGTATTTCGATCATTTTACCATACAGGATATTTCGATCATTTTACCCTTCG
*
327107 GGGGTATTTCTG-TCATTTTAACC-TTCTAGGATATTTCGATCA-TTTACCC
1 GGGGTATTTC-GATCATTTT-ACCATAC-AGGATATTTCGATCATTTTACCC
327156 ACGAATCGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
53 26 0.60
54 17 0.40
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (53 bp):
GGGGTATTTCGATCATTTTACCATACAGGATATTTCGATCATTTTACCCTTCG
Found at i:331106 original size:33 final size:34
Alignment explanation
Indices: 331069--331140 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
331059 GAGTTAGTTT
* *
331069 ATTAAATTTAGTTCAGCTCAAATAAGTTTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAATGTTAGAA
* *
331102 ATTAATTTTAGTTCAGCTTAAATAAATGTTAGAA
1 ATTAAATTTAGTTCAGCTCAAATAAATGTTAGAA
331136 ATTAA
1 ATTAA
331141 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAATGTTAGAA
Found at i:340335 original size:18 final size:18
Alignment explanation
Indices: 340276--340340 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
340266 CTCGCACTCG
*
340276 TTTTCTTTTTCAATCTTGT
1 TTTTCTTTTTCAAT-TTCT
* * *
340295 TTTGCTTTATCTCACTCTCT
1 TTTTCTTT-T-TCAATTTCT
340315 TTTTCTTTTTCAATTTCT
1 TTTTCTTTTTCAATTTCT
340333 TTTTCTTT
1 TTTTCTTT
340341 CATCTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 15 0.41
19 8 0.22
20 10 0.27
21 4 0.11
ACGTcount: A:0.09, C:0.20, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTCTTTTTCAATTTCT
Found at i:341656 original size:13 final size:13
Alignment explanation
Indices: 341638--341680 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
341628 TGTTGCCAAA
341638 TTCTCTCTTCTCT
1 TTCTCTCTTCTCT
341651 TTCTCTCTT-TCT
1 TTCTCTCTTCTCT
341663 CTTCTCTTCTTCT-T
1 -TTCTC-TCTTCTCT
341677 TTCT
1 TTCT
341681 AGCCGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 18 0.67
14 5 0.19
15 1 0.04
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTCTCTCTTCTCT
Found at i:342037 original size:27 final size:27
Alignment explanation
Indices: 341999--342247 Score: 256
Period size: 27 Copynumber: 9.2 Consensus size: 27
341989 ATCCGTGGGC
* *
341999 AAATGACAGAAATACCCTTGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
342026 AAATGACTGAAATAACCCT-GAAGGGTA
1 AAATGACTGAAAT-ACCCTCGAAGGGTA
* * *
342053 AAAGGACCGAAATACCCTCAAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
** * *
342080 AAATGACCAAAATACCCACGAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
342107 AAATGA-TCGAAATACCCTTGAAGGATA
1 AAATGACT-GAAATACCCTCGAAGGGTA
342134 AAATGA-TCGAAATACCCTCGAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* * *
342161 ACATGA-TCAAAATACCCCCGAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* * *
342188 TAATGATTGAAATACCCCCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
342215 AAATGACTGAAATACCC-CCATAGGGTA
1 AAATGACTGAAATACCCTCGA-AGGGTA
342242 AAATGA
1 AAATGA
342248 TTGTTATACC
Statistics
Matches: 191, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
26 7 0.04
27 178 0.93
28 6 0.03
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:342136 original size:81 final size:79
Alignment explanation
Indices: 341999--342247 Score: 293
Period size: 81 Copynumber: 3.1 Consensus size: 79
341989 ATCCGTGGGC
** *
341999 AAATGACAGAAATACCCTTGAAGGGTAAAATGA-CTGAAATAACCCTGAAGGGTAAAAGGACCGA
1 AAATGACA-AAATACCCACGAAGGGTAAAATGATC-GAAAT-ACCCTGAAGGGTAAAATGACCGA
342063 AATACCCTCAAAGGGTA
63 AATACCCTCAAAGGGTA
* * *
342080 AAATGACCAAAATACCCACGAAAGGTAAAATGATCGAAATACCCTTGAAGGATAAAATGATCGAA
1 AAATGA-CAAAATACCCACGAAGGGTAAAATGATCGAAATACCC-TGAAGGGTAAAATGACCGAA
*
342145 ATACCCTCGAAGGGTA
64 ATACCCTCAAAGGGTA
* * * * * *
342161 ACATGATCAAAATACCCCCGAAGGGTATAATGATTGAAATACCCCCGAAGGGTAAAATGACTGAA
1 AAATGA-CAAAATACCCACGAAGGGTAAAATGATCGAAATA-CCCTGAAGGGTAAAATGACCGAA
* *
342226 ATACCCCCATAGGGTA
64 ATACCCTCAAAGGGTA
342242 AAATGA
1 AAATGA
342248 TTGTTATACC
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
80 4 0.03
81 133 0.93
82 6 0.04
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (79 bp):
AAATGACAAAATACCCACGAAGGGTAAAATGATCGAAATACCCTGAAGGGTAAAATGACCGAAAT
ACCCTCAAAGGGTA
Found at i:344396 original size:27 final size:28
Alignment explanation
Indices: 344333--344397 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
344323 ATCCAGCTAG
* *
344333 AACATATTAAAAATATGTAATAGCTTAA
1 AACATATTAAAAACATGTAATAGATTAA
* * *
344361 AACACATTAAACACATGTACTA-ATTAA
1 AACATATTAAAAACATGTAATAGATTAA
344388 AACATATTAA
1 AACATATTAA
344398 TACTTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (28 bp):
AACATATTAAAAACATGTAATAGATTAA
Done.