Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009767.1 Kokia drynarioides strain JFW-HI SEQ_124487, 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: 569295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 111 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9030 original size:25 final size:26
Alignment explanation
Indices: 9002--9056 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
8992 AAAATAGTAA
* *
9002 AAAAATAAATACACTTAAAA-ACATT
1 AAAAATAAATAAACTTAAAATAAATT
*
9027 AAAAATAAATAAATTTAAAATAAATT
1 AAAAATAAATAAACTTAAAATAAATT
9053 AAAA
1 AAAA
9057 TTCTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAATAAATAAACTTAAAATAAATT
Found at i:9155 original size:23 final size:21
Alignment explanation
Indices: 9129--9181 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
9119 TACAATATTC
9129 AAATAATAATAAAAACGACAGTA
1 AAATAATAATAAAAACG-CA-TA
*
9152 AAATAATAGTAAAAACGCATA
1 AAATAATAATAAAAACGCATA
*
9173 AAAAAATAA
1 AAATAATAA
9182 CATCCAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
22 2 0.07
23 16 0.59
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.17
Consensus pattern (21 bp):
AAATAATAATAAAAACGCATA
Found at i:9241 original size:23 final size:24
Alignment explanation
Indices: 9215--9268 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
9205 AAACAATAGC
*
9215 AAAAATAATAAC-AAAACAACAAA
1 AAAAATAAAAACAAAAACAACAAA
**
9238 AAAAA-AAAAACAAAAACAACAGC
1 AAAAATAAAAACAAAAACAACAAA
9261 AAAAATAA
1 AAAAATAA
9269 CACCAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 19 0.73
24 2 0.08
ACGTcount: A:0.80, C:0.13, G:0.02, T:0.06
Consensus pattern (24 bp):
AAAAATAAAAACAAAAACAACAAA
Found at i:12682 original size:72 final size:74
Alignment explanation
Indices: 12517--12769 Score: 312
Period size: 75 Copynumber: 3.4 Consensus size: 74
12507 AAGCTTTTGT
* *
12517 GCCCAGCACTAGTCGGATAATTGACAAATATAAGAAGTGTGCCCAGAACTAGTCAGATAAACTGA
1 GCCCAGCACTAGTCGGATAATCGACGAATATAAGAAGTGTGCCCA-AACTAGTCAGATAAACTGA
*
12582 TGAAGGTTGT
65 TGAAGGTTGC
* * * * *
12592 GCCTAGCGCTAGTCGGATAATCGACGAATATAAGAAGTGTG-CCTAA-TAGTCAGTTAAACTGTT
1 GCCCAGCACTAGTCGGATAATCGACGAATATAAGAAGTGTGCCCAAACTAGTCAGATAAACTGAT
12655 GAAGGTTGC
66 GAAGGTTGC
* * * * * *
12664 GCCCAGCACTAGTTGGATAACCGATGAATATAAGAAGAGTGCCCAACACTAGTCAGATACATTGA
1 GCCCAGCACTAGTCGGATAATCGACGAATATAAGAAGTGTGCCCAA-ACTAGTCAGATAAACTGA
*
12729 CGAAGGTTGC
65 TGAAGGTTGC
* *
12739 GCCCAGCTCTAGTTGGATAAATCGACGAATA
1 GCCCAGCACTAGTCGGAT-AATCGACGAATA
12770 GAATGATGTG
Statistics
Matches: 151, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
72 58 0.38
73 5 0.03
74 3 0.02
75 75 0.50
76 10 0.07
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (74 bp):
GCCCAGCACTAGTCGGATAATCGACGAATATAAGAAGTGTGCCCAAACTAGTCAGATAAACTGAT
GAAGGTTGC
Found at i:15634 original size:9 final size:9
Alignment explanation
Indices: 15620--15667 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
15610 AGCAAATGAT
15620 TTAAAATTA
1 TTAAAATTA
15629 TTAAAATTA
1 TTAAAATTA
15638 TTTTTAAAA-TA
1 ---TTAAAATTA
15649 -TAAAATTA
1 TTAAAATTA
15657 TTAAAATTA
1 TTAAAATTA
15666 TT
1 TT
15668 TTTTGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 19 0.56
11 2 0.06
12 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:15640 original size:19 final size:19
Alignment explanation
Indices: 15613--15667 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
15603 CCACGTCAGC
*
15613 AAATGATTTAAAATTATTA
1 AAATTATTTAAAATTATTA
15632 AAATTATTTTTAAAA-TA-TA
1 AAATTA--TTTAAAATTATTA
15651 AAATTA-TTAAAATTATT
1 AAATTATTTAAAATTATT
15668 TTTTGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
19 13 0.42
20 2 0.06
21 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AAATTATTTAAAATTATTA
Found at i:15652 original size:28 final size:30
Alignment explanation
Indices: 15621--15691 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
15611 GCAAATGATT
15621 TAAAATTATTAAAATTA-TTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
15649 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
15679 TAAAATTCTTAAA
1 TAAAATTATTAAA
15692 TAATTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 17 0.44
29 9 0.23
30 13 0.33
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAATAA
Found at i:15697 original size:29 final size:28
Alignment explanation
Indices: 15621--15698 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
15611 GCAAATGATT
*
15621 TAAAATTATTAAA-ATTATTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTAAAATA
* *
15649 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTAAAAT-A
*
15679 TAAAATTCTTAAATAATTTT
1 TAAAATTATTAAATAATTTT
15699 AATTTTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.24
29 21 0.50
30 11 0.26
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
TAAAATTATTAAATAATTTTTTAAAATA
Found at i:16481 original size:16 final size:16
Alignment explanation
Indices: 16428--16481 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
16418 CAAAAAAATA
*
16428 ATTTTAATAATTTTAT
1 ATTTTAAAAATTTTAT
16444 ATTTTAAAAA---TA-
1 ATTTTAAAAATTTTAT
*
16456 ATTTAAAAAATTTTAT
1 ATTTTAAAAATTTTAT
16472 ATTTTAAAAA
1 ATTTTAAAAA
16482 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 9 0.29
13 2 0.06
15 2 0.06
16 18 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAAATTTTAT
Found at i:16481 original size:29 final size:29
Alignment explanation
Indices: 16399--16497 Score: 146
Period size: 28 Copynumber: 3.4 Consensus size: 29
16389 AATAAAATTA
*
16399 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-TAAAAAATAAT
16430 TTTAATAATTTTATATTTT-AAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
* *
16458 TTAAAAAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
16487 TTTAATAATTT
1 TTTAATAATTT
16498 GAAATCATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
28 26 0.42
29 18 0.29
30 5 0.08
31 13 0.21
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:22043 original size:74 final size:75
Alignment explanation
Indices: 21905--22049 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 75
21895 TTATTCGTCC
*
21905 AGCGCTAGTCGAATAACCATCGAATATAAGAAGTGTGCCAAGCACTAGTCAGATAAACTAACGAA
1 AGCGCTAGTCGAATAACCATCGAATATAACAAGTGTGCCAAGCACTAGTCAGATAAACTAACGAA
21970 GGTTGCGCCT
66 GGTTGCGCCT
* * * * * *
21980 AGCGCTAGTCGGATAATCGAT-GAATATAACAAGTTTTCC-AGCAGTAGTCAGATAAACTGACGA
1 AGCGCTAGTCGAATAA-CCATCGAATATAACAAGTGTGCCAAGCACTAGTCAGATAAACTAACGA
22043 AGGTTGC
65 AGGTTGC
22050 TAGTCGAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 29 0.47
75 30 0.48
76 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (75 bp):
AGCGCTAGTCGAATAACCATCGAATATAACAAGTGTGCCAAGCACTAGTCAGATAAACTAACGAA
GGTTGCGCCT
Found at i:25161 original size:17 final size:17
Alignment explanation
Indices: 25139--25174 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25129 TGGAAGCTAT
25139 GGTTGGAGCATTTCAGC
1 GGTTGGAGCATTTCAGC
25156 GGTTGGAGCATTTCAGC
1 GGTTGGAGCATTTCAGC
25173 GG
1 GG
25175 ATTGCTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.28
Consensus pattern (17 bp):
GGTTGGAGCATTTCAGC
Found at i:38102 original size:22 final size:22
Alignment explanation
Indices: 38075--38116 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38065 GTCACACCCC
*
38075 AATTTTTATTAAGTAGTTAATT
1 AATTTTTATTAAGTAATTAATT
38097 AATTTTTATTAAGTAATTAA
1 AATTTTTATTAAGTAATTAA
38117 GTTAGTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
AATTTTTATTAAGTAATTAATT
Found at i:40325 original size:45 final size:45
Alignment explanation
Indices: 40276--40393 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 45
40266 ATTGACATAA
* * ** *
40276 ATCGTTGCCAAGTAACTTGGGGTAGCAATTTGACATAAGTGAGCT
1 ATCGTTGCCAAGCAACCTGGGGTAGCAATTCAACATAAGTGAGCC
*** * *
40321 ATCGTTGCTGGGCAACCTGGGGTAGGAATTCAATATAAGTGAGCC
1 ATCGTTGCCAAGCAACCTGGGGTAGCAATTCAACATAAGTGAGCC
* * *
40366 ATCGTTGCCAGGCAACCTAGGGTGGCAA
1 ATCGTTGCCAAGCAACCTGGGGTAGCAA
40394 GTCATTGTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (45 bp):
ATCGTTGCCAAGCAACCTGGGGTAGCAATTCAACATAAGTGAGCC
Found at i:40707 original size:19 final size:19
Alignment explanation
Indices: 40685--40751 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
40675 CATGTGGAAT
40685 ATGTGAATATGTGAAATTG
1 ATGTGAATATGTGAAATTG
**
40704 ATGTGAATATGTGCCATTG
1 ATGTGAATATGTGAAATTG
* ** *
40723 ATGTAAATATGAAAAATAG
1 ATGTGAATATGTGAAATTG
40742 ATGTGAATAT
1 ATGTGAATAT
40752 CAAATGTGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (19 bp):
ATGTGAATATGTGAAATTG
Found at i:70123 original size:15 final size:15
Alignment explanation
Indices: 70103--70136 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
70093 ACCATTAAGC
*
70103 CCAAACCTAATTAAA
1 CCAAACCCAATTAAA
*
70118 CCAAACCCAATTGAA
1 CCAAACCCAATTAAA
70133 CCAA
1 CCAA
70137 GTCCAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.32, G:0.03, T:0.15
Consensus pattern (15 bp):
CCAAACCCAATTAAA
Found at i:70256 original size:21 final size:20
Alignment explanation
Indices: 70232--70284 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
70222 TTGTTAATCG
*
70232 TTGACCGTTGACAGTTGACCT
1 TTGACCGTTGACAATTGA-CT
*
70253 TTGACCGTTAACAATTGACT
1 TTGACCGTTGACAATTGACT
*
70273 TTGATCGTTGAC
1 TTGACCGTTGAC
70285 TTTTTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGACCGTTGACAATTGACT
Found at i:71325 original size:22 final size:24
Alignment explanation
Indices: 71297--71348 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
71287 TTACAAATTT
71297 ATATTATTTT-ATTTT-ATTATTA
1 ATATTATTTTGATTTTGATTATTA
71319 ATATTATTTTGATTTTGGATTATTA
1 ATATTATTTTGATTTT-GATTATTA
71344 ATATT
1 ATATT
71349 CTTTGTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.37
23 5 0.19
25 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATATTATTTTGATTTTGATTATTA
Found at i:77320 original size:11 final size:11
Alignment explanation
Indices: 77306--77381 Score: 71
Period size: 11 Copynumber: 6.9 Consensus size: 11
77296 AACCAAGTCA
77306 AACCGTTGACC
1 AACCGTTGACC
*
77317 AACCGTTGATC
1 AACCGTTGACC
* * *
77328 GACCGTTAACT
1 AACCGTTGACC
*
77339 AATCGTTGACC
1 AACCGTTGACC
77350 AACCGTTGACC
1 AACCGTTGACC
** *
77361 AGTCATTGACC
1 AACCGTTGACC
*
77372 GACCGTTGAC
1 AACCGTTGAC
77382 TAGCTGTTGA
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 48 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (11 bp):
AACCGTTGACC
Found at i:77332 original size:22 final size:22
Alignment explanation
Indices: 77307--77381 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
77297 ACCAAGTCAA
* *
77307 ACCGTTGACCAACCGTTGATCG
1 ACCGTTGACCAATCGTTGACCG
* * *
77329 ACCGTTAACTAATCGTTGACCA
1 ACCGTTGACCAATCGTTGACCG
* *
77351 ACCGTTGACCAGTCATTGACCG
1 ACCGTTGACCAATCGTTGACCG
77373 ACCGTTGAC
1 ACCGTTGAC
77382 TAGCTGTTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (22 bp):
ACCGTTGACCAATCGTTGACCG
Found at i:77391 original size:22 final size:23
Alignment explanation
Indices: 77307--77392 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 23
77297 ACCAAGTCAA
* *
77307 ACCGTTGACCAAC-CGTTGATCG
1 ACCGTTGACCAGCTCGTTGACCG
* * * *
77329 ACCGTTAACTA-ATCGTTGACCA
1 ACCGTTGACCAGCTCGTTGACCG
*
77351 ACCGTTGACCAG-TCATTGACCG
1 ACCGTTGACCAGCTCGTTGACCG
*
77373 ACCGTTGACTAGCT-GTTGAC
1 ACCGTTGACCAGCTCGTTGAC
77393 TGTTGACCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
22 49 0.98
23 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (23 bp):
ACCGTTGACCAGCTCGTTGACCG
Found at i:78110 original size:14 final size:15
Alignment explanation
Indices: 78075--78104 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
78065 ATATATATAT
78075 AACCCAATTGAACCA
1 AACCCAATTGAACCA
78090 AACCCAA-TGAACCA
1 AACCCAATTGAACCA
78104 A
1 A
78105 GTCCAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.33, G:0.07, T:0.10
Consensus pattern (15 bp):
AACCCAATTGAACCA
Found at i:78222 original size:14 final size:14
Alignment explanation
Indices: 78196--78250 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
78186 TTAACCAGCC
*
78196 GTTGACTGTTGACT
1 GTTGACCGTTGACT
* *
78210 GTTAACCGTTGACC
1 GTTGACCGTTGACT
*
78224 GTTGACCATTGACT
1 GTTGACCGTTGACT
*
78238 -TTGATCGTTGACT
1 GTTGACCGTTGACT
78251 TTTTCAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (14 bp):
GTTGACCGTTGACT
Found at i:79273 original size:19 final size:21
Alignment explanation
Indices: 79249--79296 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
79239 TACAAATTTA
79249 TATTATTTT-ATTTT-ATTAT
1 TATTATTTTGATTTTGATTAT
79268 TATTATTTTGATTTTGGATTAT
1 TATTATTTTGATTTT-GATTAT
*
79290 TAATATT
1 TATTATT
79297 CTTTGTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 5 0.20
22 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (21 bp):
TATTATTTTGATTTTGATTAT
Found at i:83854 original size:158 final size:158
Alignment explanation
Indices: 83564--83883 Score: 417
Period size: 158 Copynumber: 2.0 Consensus size: 158
83554 CCATATCCTA
** *
83564 TAATGCTCACACAAGCTATGAAATGGGTCTGCTCACACGAGCTGTGGATCGAGATGTTGAGCTAC
1 TAATGCTCACACAAGCTATGAAATGGCCCTGCTCACACAAGCTGTGGATCGAGATGTTGAGCTAC
* * * *
83629 ATAATGCTACTCACACGAGCTGTGGAGAATCCACAATAATTGTCGAATCTCAGCCATCGATAAGA
66 ACAATGCTACTCACACGAGCTGTGCAAAATCCACAATAATTATCGAATCTCAGCCATCGATAAGA
* *
83694 CATCTAAGACCAACACCCTTATAACTTG
131 CATCTAAGACCAACACCCATATAACCTG
* * * *
83722 TAATGCTCACACGAGTTGTGAAATGGCCCTGCTCACACAAGCTGTGCG-TTGAGATGTTGAGCTA
1 TAATGCTCACACAAGCTATGAAATGGCCCTGCTCACACAAGCTGTG-GATCGAGATGTTGAGCTA
* * * ** * * * *
83786 CACAATGTTGCTCACACGAGTTGTGCAAAATCCGTAATAATTATCGGATCTTAGCCATCGGTAGG
65 CACAATGCTACTCACACGAGCTGTGCAAAATCCACAATAATTATCGAATCTCAGCCATCGATAAG
*
83851 ACATCTAAGACCAGCACCCATATAACCTG
130 ACATCTAAGACCAACACCCATATAACCTG
83880 TAAT
1 TAAT
83884 CTCGAAGATG
Statistics
Matches: 138, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
158 137 0.99
159 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (158 bp):
TAATGCTCACACAAGCTATGAAATGGCCCTGCTCACACAAGCTGTGGATCGAGATGTTGAGCTAC
ACAATGCTACTCACACGAGCTGTGCAAAATCCACAATAATTATCGAATCTCAGCCATCGATAAGA
CATCTAAGACCAACACCCATATAACCTG
Found at i:84399 original size:29 final size:28
Alignment explanation
Indices: 84357--84416 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
84347 TTACTATGTC
* *
84357 TTCACTCTAGCCC-TATATTTTCTACTAT
1 TTCACTCTAACCCTTATATTTT-TACCAT
*
84385 TTCACATCTAACCCTTGTATTTTTACCAT
1 TTCAC-TCTAACCCTTATATTTTTACCAT
84414 TTC
1 TTC
84417 CATAAATAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.22, C:0.28, G:0.03, T:0.47
Consensus pattern (28 bp):
TTCACTCTAACCCTTATATTTTTACCAT
Found at i:95075 original size:34 final size:32
Alignment explanation
Indices: 95037--95138 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 32
95027 AAAAGCTTAG
95037 GTACCAAATTAGAAAAAAAAAATATCATGTTTAA
1 GTACCAAATT-GAAAAAAAAAATATCA-GTTTAA
* *
95071 GTACCAAATTG-GATAAAAAA-A--A-TTTAA
1 GTACCAAATTGAAAAAAAAAATATCAGTTTAA
* *
95098 GTACCAAATT-AAAAAAAAAATGTCAAGTTCAA
1 GTACCAAATTGAAAAAAAAAATATC-AGTTTAA
95130 GTACCAAAT
1 GTACCAAAT
95139 ATTATATTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 22 0.39
29 1 0.02
31 2 0.04
32 20 0.36
33 1 0.02
34 10 0.18
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.25
Consensus pattern (32 bp):
GTACCAAATTGAAAAAAAAAATATCAGTTTAA
Found at i:95115 original size:27 final size:27
Alignment explanation
Indices: 94998--95117 Score: 80
Period size: 27 Copynumber: 4.1 Consensus size: 27
94988 TATAATATTT
* *
94998 AAAAAA-TTAAATACCAAATTAAATTTAA
1 AAAAAATTTAAGTACCAAATTAAA--AAA
** *
95026 AAAAAGCTTAGGTACCAAATTAGAAAAAA
1 AAAAAATTTAAGTACCAAATT--AAAAAA
** *
95055 AAAATATCATGTTTAAGTACCAAATTGGATAA
1 AAAA-A--A--TTTAAGTACCAAATTAAAAAA
95087 AAAAAATTTAAGTACCAAATTAAAAAA
1 AAAAAATTTAAGTACCAAATTAAAAAA
95114 AAAA
1 AAAA
95118 TGTCAAGTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
27 22 0.31
28 5 0.07
29 19 0.27
30 1 0.01
31 4 0.06
32 7 0.10
34 13 0.18
ACGTcount: A:0.60, C:0.08, G:0.07, T:0.24
Consensus pattern (27 bp):
AAAAAATTTAAGTACCAAATTAAAAAA
Found at i:95132 original size:59 final size:60
Alignment explanation
Indices: 95023--95138 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
95013 AAATTAAATT
* * * *
95023 TAAAAAAAGCTTAGGTACCAAATTAGAAAAAAAAAATATCATGTTTAAGTACCAAATTGGA
1 TAAAAAAAACTTAAGTACCAAATTA-AAAAAAAAAATATCAAGTTCAAGTACCAAATTGGA
* *
95084 TAAAAAAAATTTAAGTACCAAATT-AAAAAAAAAATGTCAAGTTCAAGTACCAAAT
1 TAAAAAAAACTTAAGTACCAAATTAAAAAAAAAAATATCAAGTTCAAGTACCAAAT
95139 ATTATATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 28 0.57
61 21 0.43
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (60 bp):
TAAAAAAAACTTAAGTACCAAATTAAAAAAAAAAATATCAAGTTCAAGTACCAAATTGGA
Found at i:107829 original size:4 final size:4
Alignment explanation
Indices: 107810--107875 Score: 78
Period size: 4 Copynumber: 16.5 Consensus size: 4
107800 CTGTGTTTTC
* * * * *
107810 ATAT ATAC ATAC ATAT ATAT ATAT ATAT ATGT ATGT ATAT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
107858 GTAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT AT
107876 TCTTCCTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (4 bp):
ATAT
Found at i:107833 original size:6 final size:6
Alignment explanation
Indices: 107810--107875 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
107800 CTGTGTTTTC
* * * * *
107810 ATATAT ACATAC ATATAT ATATAT ATATAT GTATGT ATATAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
107858 GTATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT
107876 TCTTCCTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (6 bp):
ATATAT
Found at i:108817 original size:20 final size:20
Alignment explanation
Indices: 108789--108841 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
108779 TTATATTCTA
* *
108789 TTTTGTTTTTATTTAAGTCC
1 TTTTATTTTTATTTAAATCC
108809 TTTTATTTTT-TATTAAATCC
1 TTTTATTTTTAT-TTAAATCC
108829 TTTTA-TTTTATTT
1 TTTTATTTTTATTT
108842 TTTTAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTATTTTTATTTAAATCC
Found at i:108820 original size:21 final size:20
Alignment explanation
Indices: 108794--108837 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
108784 TTCTATTTTG
*
108794 TTTTTATTTAAGTCCTTTTAT
1 TTTTTA-TTAAATCCTTTTAT
108815 TTTTTATTAAATCCTTTTAT
1 TTTTTATTAAATCCTTTTAT
108835 TTT
1 TTT
108838 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTATTAAATCCTTTTAT
Found at i:108844 original size:27 final size:27
Alignment explanation
Indices: 108814--108880 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
108804 AGTCCTTTTA
* *
108814 TTTTTTATTAAATCCTTTTATTTTATT
1 TTTTTTATTAAACCCTTCTATTTTATT
* * *
108841 TTTTTAAGTTTAACCCTTCTATTTTTTT
1 TTTTTTA-TTAAACCCTTCTATTTTATT
108869 TTTGTTTATTAA
1 TTT-TTTATTAA
108881 TATTTTAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 6 0.19
28 22 0.71
29 3 0.10
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTTTTATTAAACCCTTCTATTTTATT
Found at i:115827 original size:13 final size:14
Alignment explanation
Indices: 115802--115831 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
115792 CACTTAGGTA
115802 TTTGGGTTGTTTAT
1 TTTGGGTTGTTTAT
115816 TTTGGGTT-TTTAT
1 TTTGGGTTGTTTAT
115829 TTT
1 TTT
115832 ATTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (14 bp):
TTTGGGTTGTTTAT
Found at i:122008 original size:26 final size:22
Alignment explanation
Indices: 121948--122049 Score: 159
Period size: 22 Copynumber: 4.6 Consensus size: 22
121938 GATGTATTAT
121948 GCCAATATAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
*
121970 GCCAATATAATTGATTGATTGT
1 GCCAATATAATTGATTGATTGC
121992 GCCAATATAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
* *
122014 ACCAATTTAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
* *
122036 ACTAATATAATTGA
1 GCCAATATAATTGA
122050 ATATTTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
GCCAATATAATTGATTGATTGC
Found at i:125039 original size:25 final size:23
Alignment explanation
Indices: 124998--125043 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
124988 CCAATTAGGA
124998 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
125021 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
125044 TGGATCGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:130316 original size:15 final size:14
Alignment explanation
Indices: 130292--130321 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
130282 GAAATTCCTC
130292 ATAGCAAGGGAGTT
1 ATAGCAAGGGAGTT
130306 ATAGACAAGGGAGTT
1 ATAG-CAAGGGAGTT
130321 A
1 A
130322 CAACAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (14 bp):
ATAGCAAGGGAGTT
Found at i:134676 original size:14 final size:14
Alignment explanation
Indices: 134653--134690 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
134643 CATTTTTGCA
134653 TTTCCTTTTATGT-
1 TTTCCTTTTATGTG
*
134666 TTTCGCTTTTATTTG
1 TTTC-CTTTTATGTG
134681 TTTCCTTTTA
1 TTTCCTTTTA
134691 AATTCTATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATGTG
Found at i:136542 original size:17 final size:17
Alignment explanation
Indices: 136501--136546 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
136491 GGAAAACCCT
136501 GAAGAAGAAGAGGCATAA
1 GAAGAAGAAG-GGCATAA
* * *
136519 CAAGAAGAAGGTCATGA
1 GAAGAAGAAGGGCATAA
136536 GAAGAAGAAGG
1 GAAGAAGAAGG
136547 AAGGAGAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.52, C:0.07, G:0.35, T:0.07
Consensus pattern (17 bp):
GAAGAAGAAGGGCATAA
Found at i:137667 original size:10 final size:11
Alignment explanation
Indices: 137654--137699 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
137644 AAAAATTCAC
137654 AAAAAG-AAAG
1 AAAAAGAAAAG
137664 AAAAAG-AAAG
1 AAAAAGAAAAG
*
137674 AAGAAGAAAAG
1 AAAAAGAAAAG
137685 AGAAAAGAAAAG
1 A-AAAAGAAAAG
137697 AAA
1 AAA
137700 TATATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:143913 original size:22 final size:22
Alignment explanation
Indices: 143888--143967 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
143878 GATGTAATAT
143888 GCCAATATAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
*
143910 GCCAATATAATTAATTGATTGC
1 GCCAATATAATTGATTGATTGC
* *
143932 ACCAATTTAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
*
143954 TCCAATATAATTGA
1 GCCAATATAATTGA
143968 ATATTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
GCCAATATAATTGATTGATTGC
Found at i:146457 original size:42 final size:42
Alignment explanation
Indices: 146398--146481 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
146388 AGGTCCAGTT
*
146398 AGGCAAGTCGCTAGAGCTGAGACTGGTACGGGTGATCAGGGA
1 AGGCAAGTCGCTAGAGCTGAGACTGGTACGGGAGATCAGGGA
146440 AGGCAAGTCGCTAGAGCTGAGACTGGTACGGGAGATCAGGGA
1 AGGCAAGTCGCTAGAGCTGAGACTGGTACGGGAGATCAGGGA
146482 GTTGTTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.40, T:0.15
Consensus pattern (42 bp):
AGGCAAGTCGCTAGAGCTGAGACTGGTACGGGAGATCAGGGA
Found at i:153534 original size:17 final size:15
Alignment explanation
Indices: 153512--153550 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
153502 ATCAACAAGG
*
153512 AAAATAATGAAATAATA
1 AAAATAAT-AAA-AACA
153529 AAAATAATAAAAACA
1 AAAATAATAAAAACA
153544 AAAATAA
1 AAAATAA
153551 AGACTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAATAAAAACA
Found at i:165771 original size:30 final size:29
Alignment explanation
Indices: 165722--165824 Score: 129
Period size: 29 Copynumber: 3.5 Consensus size: 29
165712 AATTAAAATT
165722 TTTTAATAATTTTATTATTTAAAAAAAATAA
1 TTTTAATAATTTTA-TATTT-AAAAAAATAA
*
165753 TTTTAATAATTTTATATTTAAATAAATAA
1 TTTTAATAATTTTATATTTAAAAAAATAA
*
165782 -TTTAA-AATTTTTATATTTTTAAAAAATAA
1 TTTTAATAA-TTTTATA-TTTAAAAAAATAA
*
165811 TTTTAATAAATTTA
1 TTTTAATAATTTTA
165825 AAATCATTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.03
28 12 0.19
29 20 0.31
30 14 0.22
31 16 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTTAATAATTTTATATTTAAAAAAATAA
Found at i:172152 original size:17 final size:17
Alignment explanation
Indices: 172115--172154 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
172105 TTGTAGTATA
**
172115 ATTGTCCCTGCATTTTT
1 ATTGTCCCTGCATTTAC
*
172132 ATTGTCGCTGCATTTAC
1 ATTGTCCCTGCATTTAC
172149 ATTGTC
1 ATTGTC
172155 ATTTCATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (17 bp):
ATTGTCCCTGCATTTAC
Found at i:173317 original size:37 final size:38
Alignment explanation
Indices: 173224--173321 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
173214 ATTTTCGGAA
*
173224 TGCACCCA-AGACTATCACTGCATAAATATTCTTCAAAT
1 TGCACCCAGA-ACTATCGCTGCATAAATATTCTTCAAAT
* * *
173262 TGCATCTAGAACTATCGCTGCATAAGTATTCTTC-AAT
1 TGCACCCAGAACTATCGCTGCATAAATATTCTTCAAAT
*
173299 TGCACCCAGGAA-TGTCGCTGCAT
1 TGCACCCA-GAACTATCGCTGCAT
173322 GAACATATAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 19 0.37
38 31 0.61
39 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (38 bp):
TGCACCCAGAACTATCGCTGCATAAATATTCTTCAAAT
Found at i:176321 original size:23 final size:23
Alignment explanation
Indices: 176295--176362 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
176285 GCCACACGGA
*
176295 CATCACAAAATACGCCACATATG
1 CATCACAAAATACGCCACATAAG
* *
176318 CATCACAGAATAATACACAACATAAG
1 CATCAC--AA-AATACGCCACATAAG
* *
176344 CATCAAAAAATAAGCCACA
1 CATCACAAAATACGCCACA
176363 CATGTAACAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
23 14 0.40
24 2 0.06
25 2 0.06
26 17 0.49
ACGTcount: A:0.51, C:0.26, G:0.07, T:0.15
Consensus pattern (23 bp):
CATCACAAAATACGCCACATAAG
Found at i:176680 original size:21 final size:21
Alignment explanation
Indices: 176637--176687 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
176627 GTGCAGACTC
* * *
176637 CTACCGATATAAGTGATAGTT
1 CTACCGATACAAGTCATACTT
*
176658 CTACCGATACAAGTCTTACTT
1 CTACCGATACAAGTCATACTT
*
176679 CTACTGATA
1 CTACCGATA
176688 GTAAAAACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (21 bp):
CTACCGATACAAGTCATACTT
Found at i:182880 original size:21 final size:21
Alignment explanation
Indices: 182855--182927 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
182845 GTGCAGACTC
182855 CTACCGATACAAGTGATACTT
1 CTACCGATACAAGTGATACTT
* *
182876 TTACCGATACAAATGACT-CTT
1 CTACCGATACAAGTGA-TACTT
* **
182897 CTACTGATACAAGTCTTACTT
1 CTACCGATACAAGTGATACTT
182918 CTACCGATAC
1 CTACCGATAC
182928 TAAAAACTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (21 bp):
CTACCGATACAAGTGATACTT
Found at i:184043 original size:23 final size:23
Alignment explanation
Indices: 184013--184067 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
184003 GTTACAACAC
*
184013 AGGCATCACAGAATACACCACAA
1 AGGCATCACAAAATACACCACAA
184036 AGGCATCACAAAATACACCACAA
1 AGGCATCACAAAATACACCACAA
184059 AGGCATCAC
1 AGGCATCAC
184068 TGAGAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.47, C:0.31, G:0.13, T:0.09
Consensus pattern (23 bp):
AGGCATCACAAAATACACCACAA
Found at i:200081 original size:6 final size:6
Alignment explanation
Indices: 200038--200065 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
200028 AAAAAAATAG
200038 AAAGAA AAAGAA AAAGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG
200066 CAGATCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:204947 original size:20 final size:20
Alignment explanation
Indices: 204919--204987 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
204909 TCCTAAAATG
204919 CAACTAATTTTACTAAAGTA
1 CAACTAATTTTACTAAAGTA
* * *
204939 CAGAC-AATTAT-CTAAAATG
1 CA-ACTAATTTTACTAAAGTA
204958 CAACTAATTTTACTAAAGTA
1 CAACTAATTTTACTAAAGTA
* *
204978 TAAATAATTT
1 CAACTAATTT
204988 AAAACCCTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.05
19 13 0.34
20 21 0.55
21 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (20 bp):
CAACTAATTTTACTAAAGTA
Found at i:204966 original size:19 final size:20
Alignment explanation
Indices: 204911--204974 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
204901 TTTAAAACTC
*
204911 CTAAAATGCAACTAATTTTA
1 CTAAAATGCAACTAATTATA
* *
204931 CTAAAGTACAGAC-AATTAT-
1 CTAAAATGCA-ACTAATTATA
*
204950 CTAAAATGCAACTAATTTTA
1 CTAAAATGCAACTAATTATA
204970 CTAAA
1 CTAAA
204975 GTATAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 18 0.51
21 2 0.06
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (20 bp):
CTAAAATGCAACTAATTATA
Found at i:206246 original size:21 final size:21
Alignment explanation
Indices: 206208--206251 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
206198 GATTTCTATC
* *
206208 GATACAAGTGACAGTTCTACT
1 GATACAAGAGACACTTCTACT
*
206229 GATACAAGAGTCACTTCTACT
1 GATACAAGAGACACTTCTACT
206250 GA
1 GA
206252 ATGAAGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
GATACAAGAGACACTTCTACT
Found at i:217236 original size:40 final size:40
Alignment explanation
Indices: 217192--217273 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
217182 CGCATGATTC
*
217192 AGAGGAAACATAACATGATTTTTACTTTGAAAAATGAGAG
1 AGAGGAAACATAACATGATTTCTACTTTGAAAAATGAGAG
217232 AGAGGAAACATAACATGATTTCTACTTTGAAAAATGAGAG
1 AGAGGAAACATAACATGATTTCTACTTTGAAAAATGAGAG
217272 AG
1 AG
217274 GAGAGTGGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.26
Consensus pattern (40 bp):
AGAGGAAACATAACATGATTTCTACTTTGAAAAATGAGAG
Found at i:222844 original size:18 final size:18
Alignment explanation
Indices: 222821--222856 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
222811 GCAAAGTTTT
222821 GCCATGGAAATTCTAACG
1 GCCATGGAAATTCTAACG
222839 GCCATGGAAATTCTAACG
1 GCCATGGAAATTCTAACG
222857 ATGATGAAGA
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
GCCATGGAAATTCTAACG
Found at i:236775 original size:17 final size:17
Alignment explanation
Indices: 236753--236796 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
236743 TCAGTCACAT
*
236753 AAAAAAAGAGAAAAAGA
1 AAAAAAAAAGAAAAAGA
*
236770 AAAAAAAAAGGAAAAGA
1 AAAAAAAAAGAAAAAGA
236787 AGAAAAAAAA
1 A-AAAAAAAA
236797 TATATGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGA
Found at i:236776 original size:18 final size:18
Alignment explanation
Indices: 236753--236796 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
236743 TCAGTCACAT
236753 AAAAAAAGAGAAAAAGAA-
1 AAAAAAA-AGAAAAAGAAG
*
236771 AAAAAAAAGGAAAAGAAG
1 AAAAAAAAGAAAAAGAAG
236789 AAAAAAAA
1 AAAAAAAA
236797 TATATGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAGAAG
Found at i:236778 original size:20 final size:20
Alignment explanation
Indices: 236753--236796 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
236743 TCAGTCACAT
236753 AAAAAAAGAGAAA-AAGAAAA
1 AAAAAAAGA-AAAGAAGAAAA
*
236773 AAAAAAGGAAAAGAAGAAAA
1 AAAAAAAGAAAAGAAGAAAA
236793 AAAA
1 AAAA
236797 TATATGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAGAAGAAAA
Found at i:242941 original size:24 final size:24
Alignment explanation
Indices: 242914--242969 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
242904 AAGTCTAATT
* *
242914 CTAATCAACGCAAAATGTATTATG
1 CTAATAAACGCAAAATATATTATG
* * *
242938 CTAATAAATGCTAAATATATTATA
1 CTAATAAACGCAAAATATATTATG
*
242962 CTACTAAA
1 CTAATAAA
242970 TCTTTTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (24 bp):
CTAATAAACGCAAAATATATTATG
Found at i:248391 original size:56 final size:56
Alignment explanation
Indices: 248331--248508 Score: 259
Period size: 56 Copynumber: 3.2 Consensus size: 56
248321 TTCCCTTCTA
* * * *
248331 ATTATTTTCCCAAATTTTCTCATACTTTCTCTCTTT-CAGAACACCCACTTTCTCTC
1 ATTATTTTTCCAGATTTTCTCAAACTTTCTCTCTTTCCA-AACACCCATTTTCTCTC
* *
248387 ATTATTTTTCCAGATTTTCTCAGAGTTTCTCTCTTTCCAAACACCCATTTTCTCTC
1 ATTATTTTTCCAGATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
* *
248443 ATTATTTTTCTAGATTTTCTCAAACTTTCTCTCTTTCCAAACACCTATTTTCTCTC
1 ATTATTTTTCCAGATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
*
248499 ATTTTTTTTC
1 ATTATTTTTC
248509 TTTCTTTTCG
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
56 109 0.98
57 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.49
Consensus pattern (56 bp):
ATTATTTTTCCAGATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
Found at i:249646 original size:54 final size:56
Alignment explanation
Indices: 249582--249694 Score: 151
Period size: 56 Copynumber: 2.1 Consensus size: 56
249572 CTATAAAAAT
* * *
249582 GAGAAAATGGGTGT-TTGAAA-AGAGAAAGTCTGAA-AAAATCTGGAAAAATAATAA
1 GAGAAAATGGGTGTATGGAAAGAAAGAAAGTCT-AATAAAATCTGAAAAAATAATAA
* *
249636 GAGAAAATGGGTGTATGGAAAGAAAGAAAGTCTAATAAAATTTGAAAAAATAATTA
1 GAGAAAATGGGTGTATGGAAAGAAAGAAAGTCTAATAAAATCTGAAAAAATAATAA
249692 GAG
1 GAG
249695 GGAAAGAGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 14 0.27
55 7 0.14
56 30 0.59
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (56 bp):
GAGAAAATGGGTGTATGGAAAGAAAGAAAGTCTAATAAAATCTGAAAAAATAATAA
Found at i:251279 original size:24 final size:24
Alignment explanation
Indices: 251252--251352 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
251242 TTAAACTCTG
251252 TCTGGGCTCGAATGAGCTAACTTA
1 TCTGGGCTCGAATGAGCTAACTTA
* *
251276 TCTGGACTCGTAA-GAGCTAACCTA
1 TCTGGGCTCG-AATGAGCTAACTTA
* * *
251300 TCTGGGCTCGTATGAGCTAATTTTG
1 TCTGGGCTCGAATGAGCTAA-CTTA
* * *
251325 TCTAGGCTCGTATGAGCTAAATT-
1 TCTGGGCTCGAATGAGCTAACTTA
251348 TCTGG
1 TCTGG
251353 AAGACTCAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.08
24 37 0.58
25 22 0.34
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (24 bp):
TCTGGGCTCGAATGAGCTAACTTA
Found at i:252593 original size:36 final size:35
Alignment explanation
Indices: 252546--252617 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
252536 AAGATAATAT
* *
252546 ATTTTGTTTAACTTGACTTGCAAGTAATTCTCTTAG
1 ATTTTATTTAACTTGACTTGCAAGCAA-TCTCTTAG
252582 ATTTTATTTAACTTGACTTGCAAGCAATCTCTTAG
1 ATTTTATTTAACTTGACTTGCAAGCAATCTCTTAG
252617 A
1 A
252618 ATTTGGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 9 0.26
36 25 0.74
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (35 bp):
ATTTTATTTAACTTGACTTGCAAGCAATCTCTTAG
Found at i:260768 original size:11 final size:11
Alignment explanation
Indices: 260731--260768 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
260721 TTCACAAAAC
260731 CCTCACAAGAT
1 CCTCACAAGAT
* *
260742 CCTTAC-AGAA
1 CCTCACAAGAT
260752 CCTCACAAGAT
1 CCTCACAAGAT
260763 CCTCAC
1 CCTCAC
260769 CTTTTGCAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.34, C:0.39, G:0.08, T:0.18
Consensus pattern (11 bp):
CCTCACAAGAT
Found at i:265180 original size:31 final size:30
Alignment explanation
Indices: 265119--265181 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
265109 CAACACAACA
*
265119 AATATAAAAATAAAATATTTAAATTATTTT
1 AATATAAAAATAAAATATTAAAATTATTTT
*
265149 AATATAAAAATAATTATATTAAAATGT-TTTT
1 AATATAAAAATAA-AATATTAAAAT-TATTTT
265180 AA
1 AA
265182 ATTATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
31 15 0.52
32 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
AATATAAAAATAAAATATTAAAATTATTTT
Found at i:267688 original size:17 final size:16
Alignment explanation
Indices: 267668--267707 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
267658 CCCAAATAAA
*
267668 TAATAAAATAATAATG
1 TAATAAAATAAAAATG
267684 TTAATAAAAATAAAAATG
1 -TAAT-AAAATAAAAATG
267702 TAATAA
1 TAATAA
267708 TAATTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
TAATAAAATAAAAATG
Found at i:267716 original size:17 final size:18
Alignment explanation
Indices: 267666--267716 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
267656 ATCCCAAATA
*
267666 AATAATAAAATAATAATGTT
1 AATAAT-AATTAA-AATGTT
* *
267686 AATAAAAATAAAAATG-T
1 AATAATAATTAAAATGTT
267703 AATAATAATTAAAA
1 AATAATAATTAAAA
267717 GAACATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 13 0.50
18 4 0.15
19 4 0.15
20 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AATAATAATTAAAATGTT
Found at i:273191 original size:26 final size:28
Alignment explanation
Indices: 273128--273183 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
273118 ATAAATTGTG
273128 ATTATCAATCTGTGAGTGAATCCGTACC
1 ATTATCAATCTGTGAGTGAATCCGTACC
273156 AAATTATCAATCTGTGAGTGAATCCGTA
1 --ATTATCAATCTGTGAGTGAATCCGTA
273184 GCTTTCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (28 bp):
ATTATCAATCTGTGAGTGAATCCGTACC
Found at i:278600 original size:20 final size:21
Alignment explanation
Indices: 278554--278623 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 21
278544 AGTTTGAAAC
* *
278554 AATTTTAAAATCAAGTTAAAAT
1 AATTTTAAACT-AAGTCAAAAT
* *
278576 TATTTTAAAC-ATGTCAAAAT
1 AATTTTAAACTAAGTCAAAAT
*
278596 AA-TTTGAACTAAGTCAAAAT
1 AATTTTAAACTAAGTCAAAAT
*
278616 CATTTTAA
1 AATTTTAA
278624 CACTTCAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
19 6 0.16
20 19 0.51
21 4 0.11
22 8 0.22
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (21 bp):
AATTTTAAACTAAGTCAAAAT
Found at i:280314 original size:31 final size:32
Alignment explanation
Indices: 280279--280378 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 32
280269 AAATAATATT
280279 ATTTTAATAGT-TTAATATTAAATTTAATTTA
1 ATTTTAATAGTATTAATATTAAATTTAATTTA
*
280310 ATTTTAATAGTATT-TTATT-AATTTAATATTA
1 ATTTTAATAGTATTAATATTAAATTTAAT-TTA
** ** *
280341 AAATTGTTA-TCTTAATATTAAATTTAATTTA
1 ATTTTAATAGTATTAATATTAAATTTAATTTA
280372 ATGTTTA
1 AT-TTTA
280379 TCTTGTAGAT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
30 11 0.20
31 31 0.57
32 12 0.22
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (32 bp):
ATTTTAATAGTATTAATATTAAATTTAATTTA
Found at i:280339 original size:11 final size:11
Alignment explanation
Indices: 280289--280341 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
280279 ATTTTAATAG
280289 TTTAATATTAAA
1 TTTAATATT-AA
280301 TTTAAT-TTAA
1 TTTAATATTAA
*
280311 TTTTAATAGT-A
1 -TTTAATATTAA
280322 TTT--TATTAA
1 TTTAATATTAA
280331 TTTAATATTAA
1 TTTAATATTAA
280342 AATTGTTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
8 3 0.09
9 4 0.12
10 5 0.15
11 15 0.44
12 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAATATTAA
Found at i:285282 original size:19 final size:19
Alignment explanation
Indices: 285258--285297 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
285248 ATTAATTTTG
285258 ATCAAGTAAAATT-AAATTA
1 ATCAAGT-AAATTAAAATTA
*
285277 ATCAAGTTAATTAAAATTA
1 ATCAAGTAAATTAAAATTA
285296 AT
1 AT
285298 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
ATCAAGTAAATTAAAATTA
Found at i:285445 original size:20 final size:18
Alignment explanation
Indices: 285380--285472 Score: 64
Period size: 20 Copynumber: 4.9 Consensus size: 18
285370 ATTCCAAAAT
* *
285380 AATATTATTTTAATAATTT
1 AATATTAATTTAAT-ATTA
* *
285399 AATACTTATTTTAATAGTA
1 AATA-TTAATTTAATATTA
**
285418 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
285437 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
285457 AAT-TTAATTTAATATT
1 AATATTAATTTAATATT
285473 TATCTTGATA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 10 0.17
18 2 0.03
19 22 0.37
20 26 0.43
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:301730 original size:5 final size:5
Alignment explanation
Indices: 301694--301720 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
301684 ACACAACAAG
301694 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
301721 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:317247 original size:10 final size:11
Alignment explanation
Indices: 317234--317279 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
317224 AAAAAATCAC
317234 AAAAAG-AAAG
1 AAAAAGAAAAG
317244 AAAAAG-AAAG
1 AAAAAGAAAAG
*
317254 AAGAAGAAAAG
1 AAAAAGAAAAG
317265 AGAAAAGAAAAG
1 A-AAAAGAAAAG
317277 AAA
1 AAA
317280 TATATTGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:332262 original size:30 final size:30
Alignment explanation
Indices: 332226--332298 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
332216 CCTCTGATGG
332226 GTTCTACTGGAACCACAATCAACCATCAAA
1 GTTCTACTGGAACCACAATCAACCATCAAA
332256 GTTCTACTGGAACCACAATCAACCATCAAA
1 GTTCTACTGGAACCACAATCAACCATCAAA
332286 GTTCTACTGGAAC
1 GTTCTACTGGAAC
332299 AAGGGTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (30 bp):
GTTCTACTGGAACCACAATCAACCATCAAA
Found at i:334104 original size:59 final size:59
Alignment explanation
Indices: 334038--334150 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
334028 GTAAAAATAA
* * *
334038 TTTTGGAAAGTTTGGGGGCCAAAT-TCGAAGTTTTAGGAAGTTCGGGGGTTAAATCAAAT
1 TTTTGGAAAGTTTAGGGGCCAAATCT-AAAGTTTTAAGAAGTTCGGGGGTTAAATCAAAT
* *
334097 TTTTGGAAAGTTTAGGGGTCAAATCTAAATTTTTAAGAAGTTCGGGGGTTAAAT
1 TTTTGGAAAGTTTAGGGGCCAAATCTAAAGTTTTAAGAAGTTCGGGGGTTAAAT
334151 TTGAATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 47 0.98
60 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (59 bp):
TTTTGGAAAGTTTAGGGGCCAAATCTAAAGTTTTAAGAAGTTCGGGGGTTAAATCAAAT
Found at i:334107 original size:29 final size:30
Alignment explanation
Indices: 334038--334150 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
334028 GTAAAAATAA
* * *
334038 TTTTGGAAAGTTTGGGGGCCAAATTCGAAGT
1 TTTTGGAAAGTTCGGGGGTCAAA-TCGAAAT
* *
334069 TTTAGG-AAGTTCGGGGGTTAAATC-AAAT
1 TTTTGGAAAGTTCGGGGGTCAAATCGAAAT
** *
334097 TTTTGGAAAGTTTAGGGGTCAAATCTAAAT
1 TTTTGGAAAGTTCGGGGGTCAAATCGAAAT
* *
334127 TTTT-AAGAAGTTCGGGGGTTAAAT
1 TTTTGGA-AAGTTCGGGGGTCAAAT
334151 TTGAATTTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.12
29 18 0.27
30 35 0.53
31 5 0.08
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAGTTCGGGGGTCAAATCGAAAT
Found at i:334129 original size:30 final size:29
Alignment explanation
Indices: 334038--334130 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 29
334028 GTAAAAATAA
* *
334038 TTTTGGAAAGTTTGGGGGCCAAATTCGAAGT
1 TTTTGGAAAGTTTGGGGGTCAAA-TC-AAAT
* * *
334069 TTTAGG-AAGTTCGGGGGTTAAATCAAAT
1 TTTTGGAAAGTTTGGGGGTCAAATCAAAT
*
334097 TTTTGGAAAGTTTAGGGGTCAAATCTAAAT
1 TTTTGGAAAGTTTGGGGGTCAAATC-AAAT
334127 TTTT
1 TTTT
334131 AAGAAGTTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.16
29 17 0.33
30 21 0.41
31 5 0.10
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTTGGGGGTCAAATCAAAT
Found at i:335909 original size:42 final size:42
Alignment explanation
Indices: 335853--336679 Score: 779
Period size: 42 Copynumber: 20.5 Consensus size: 42
335843 TCTTGATTTA
* * * *
335853 GGGGTAAAATATTGGATGGTGGCTTCAATCAGCCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * * *
335895 GGGGTAAAAGATTGGATGATATCTTTAATCTACCCTATTA-C
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* ** * * *
335936 TGGGTAAGTG-TTTGA--ATGGCTTCAATCTGCCCCATGACC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
335975 GGGGTAAAAG-TT-CA-GATGT-TTCAATCTGCCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
336013 GGGGTAAGAGATTGG-TG-TGTCTTCAATCTACCCTC-TAATT
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCC-CATGATC
* * * * *
336053 AGGATAAAAGA-T-CA-GATG-CTTCAATCTACCCCATGGTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
**
336091 GGGGTAAGGGATTGGATGATGTCTTCAATCTGCCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
336133 GAGGTAAAAGATTAGATGATGTCTTCAATCTGCCCTATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
336175 GGGGCAAAAGA-TCG--GATG-CTTCAATCTGCCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
336213 GAGGTAAAAGATTGGATGATGTCTTCAATCTGCCTCATAATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
336255 AGGGTAAAAGATTGGACG--G-CTGCAATCTGCCTCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * **
336294 GGGATAAAATATTGGATGATGTCTTCAATCTGCCTTATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
336336 GGGGTAAAAGATTGG-TG-TGTCTTCAATTTGCCCCATAATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
** * *
336376 GACGTAAGAGATTGGATGATGTCTTCAATCTGCCTCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
336418 AGGCTAAGAGATTGGATG--G-CTTCAATCTACCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
336457 GGGGTAAGAGATTGGATG--G-CTTCAATCTGCCTCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
336496 GGGGTAAGAGATTGGATGATGTCTTCAATTTACCCTC-TGATT
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCC-CATGATC
* * * *
336538 AGGGTAAAAGA-TCG--GATG-CTTCAATCTGTCCCATGGTC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
336576 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATCATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
336618 GGGGTAAAAGATTTGATGATGTCTTCAATATGCCCCATGATC
1 GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
336660 GGGGTAAAAGATCGGATGAT
1 GGGGTAAAAGATTGGATGAT
336680 CAAGGTAAGA
Statistics
Matches: 638, Mismatches: 115, Indels: 64
0.78 0.14 0.08
Matches are distributed among these distances:
37 2 0.00
38 117 0.18
39 137 0.21
40 61 0.10
41 31 0.05
42 289 0.45
43 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (42 bp):
GGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATC
Found at i:336308 original size:81 final size:81
Alignment explanation
Indices: 335853--336677 Score: 714
Period size: 80 Copynumber: 10.2 Consensus size: 81
335843 TCTTGATTTA
* * * *
335853 GGGGTAAAATATTGGATGGTGGCTTCAATCAGCCCCATGATCGGGGTAAAAGATTGGATGATATC
1 GGGGTAAAAGATTGGA---TGGCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTC
* * *
335918 TTTAATCTACC-CTATTA-C
63 TTCAATCTGCCTC-ATGATC
* ** * * * * *
335936 TGGGTAAGTGTTTGAATGGCTTCAATCTGCCCCATGACCGGGGTAAAAG-TT-CA-GATGT-TTC
1 GGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCTTC
*
335997 AATCTGCCCCATGATC
66 AATCTGCCTCATGATC
* * * * *
336013 GGGGTAAGAGATTGG-TGTGTCTTCAATCTACCCTC-TAAT-TAGGATAAAAGA-T-CA-GATG-
1 GGGGTAAAAGATTGGATG-G-CTTCAATCTGCCC-CATGATCGAGG-TAAAAGATTGGATGATGT
* * *
336071 CTTCAATCTACCCCATGGTC
62 CTTCAATCTGCCTCATGATC
** *
336091 GGGGTAAGGGATTGGATGATGTCTTCAATCTGCCCCATGATCGAGGTAAAAGATTAGATGATGTC
1 GGGGTAAAAGATTGGATG--G-CTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTC
336156 TTCAATCTGCC-CTATGATC
63 TTCAATCTGCCTC-ATGATC
* *
336175 GGGGCAAAAGATCGGAT-GCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCTTC
1 GGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCTTC
*
336239 AATCTGCCTCATAATC
66 AATCTGCCTCATGATC
* * * * *
336255 AGGGTAAAAGATTGGACGGCTGCAATCTGCCTCATGATCG-GGATAAAATATTGGATGATGTCTT
1 GGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGATCGAGG-TAAAAGATTGGATGATGTCTT
*
336319 CAATCTGCCTTATGATC
65 CAATCTGCCTCATGATC
* * * *
336336 GGGGTAAAAGATTGG-TGTGTCTTCAATTTGCCCCATAATCGACGTAAGAGATTGGATGATGTCT
1 GGGGTAAAAGATTGGATG-G-CTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCT
336400 TCAATCTGCCTCATGATC
64 TCAATCTGCCTCATGATC
* * * * * *
336418 AGGCTAAGAGATTGGATGGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATG--G-CTTC
1 GGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCTTC
336480 AATCTGCCTCATGATC
66 AATCTGCCTCATGATC
* * * * *
336496 GGGGTAAGAGATTGGATGATGTCTTCAATTTACCCTC-TGAT-TAGGGTAAAAGA-TCG--GATG
1 GGGGTAAAAGATTGGATG--G-CTTCAATCTGCCC-CATGATCGA-GGTAAAAGATTGGATGATG
*
336556 -CTTCAATCTGTCC-CATGGTC
61 TCTTCAATCTG-CCTCATGATC
* * * *
336576 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATCATCGGGGTAAAAGATTTGATGATGTC
1 GGGGTAAAAGATTGGATG--G-CTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTC
* *
336641 TTCAATATGCCCCATGATC
63 TTCAATCTGCCTCATGATC
*
336660 GGGGTAAAAGATCGGATG
1 GGGGTAAAAGATTGGATG
336678 ATCAAGGTAA
Statistics
Matches: 621, Mismatches: 82, Indels: 77
0.80 0.11 0.10
Matches are distributed among these distances:
76 14 0.02
77 20 0.03
78 96 0.15
79 8 0.01
80 195 0.31
81 137 0.22
82 67 0.11
83 24 0.04
84 60 0.10
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (81 bp):
GGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGATGATGTCTTC
AATCTGCCTCATGATC
Found at i:336517 original size:363 final size:360
Alignment explanation
Indices: 335955--336630 Score: 937
Period size: 363 Copynumber: 1.9 Consensus size: 360
335945 GTTTGAATGG
* **
335955 CTTCAATCTGCCCCATGACCGGGGTAAAAGTTCAGATGTTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCCATGACCGGGGTAAAAGTTCAGATGTTTCAATCTGCCCCATAATCGACGTAA
*
336020 GAGATTGGTGTGTCTTCAATCTACCCTCTAATTAGGATAAAAGATCAGATGCTTCAATCTACCCC
66 GAGATTGGTGTGTCTTCAATCTACCCTCTAATCAGGATAAAAGATCAGATGCTTCAATCTACCCC
* *
336085 ATGGTCGGGGTAAGGGATTGGATGATGTCTTCAATCTGCCCCATGATCGAGGTAAAAGATTAGAT
131 ATGATCGGGGTAAGAGATTGGATGA-GTCTTCAATCTGCCCCATGATCGAGGTAAAAGATTAGAT
* *
336150 GATGTCTTCAATCTGCCCTATGATCGGGGCAAAAGATCGGATGCTTCAATCTGCCCCATGATCGA
195 GATGTCTTCAATCTACCCTATGATCAGGGCAAAAGATCGGATGCTTCAATCTGCCCCATGATCGA
*
336215 GGTAAAAGATTGGATGATGTCTTCAATCTGCCTCATAATCAGGGTAAAAGATTGGACGGCTGCAA
260 GGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATAATCAGGGTAAAAGATTGGACGGCTGCAA
336280 TCTGCCTCATGATCGGGATAAAATATTGGATGATGT
325 TCTGCCTCATGATCGGGATAAAATATTGGATGATGT
** * * * *
336316 CTTCAATCTGCCTTATGATCGGGGTAAAAGATT-GGTGTGTCTTCAATTTGCCCCATAATCGACG
1 CTTCAATCTGCCCCATGACCGGGGTAAAAG-TTCAG-ATGT-TTCAATCTGCCCCATAATCGACG
* * * * **
336380 TAAGAGATTGGATGATGTCTTCAATCT-GCCTCATGATCAGGCTAAGAGATTGGATGGCTTCAAT
63 TAAGAGATTGG-TG-TGTCTTCAATCTACCCTC-TAATCAGGATAAAAGATCAGAT-GCTTCAAT
* * *
336444 CTACCCCATGATCGGGGTAAGAGATTGGATG-G-CTTCAATCTGCCTCATGATCGGGGTAAGAGA
124 CTACCCCATGATCGGGGTAAGAGATTGGATGAGTCTTCAATCTGCCCCATGATCGAGGTAAAAGA
* * * * * *
336507 TTGGATGATGTCTTCAATTTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGTCCCAT
189 TTAGATGATGTCTTCAATCTACCCTATGATCAGGGCAAAAGATCGGATGCTTCAATCTGCCCCAT
* * * * *
336572 GGTCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATCATCGGGGTAAAAGATT
254 GATCGAGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATAATCAGGGTAAAAGATT
336631 TGATGATGTC
Statistics
Matches: 273, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
361 28 0.10
362 5 0.02
363 168 0.62
364 7 0.03
365 28 0.10
366 37 0.14
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (360 bp):
CTTCAATCTGCCCCATGACCGGGGTAAAAGTTCAGATGTTTCAATCTGCCCCATAATCGACGTAA
GAGATTGGTGTGTCTTCAATCTACCCTCTAATCAGGATAAAAGATCAGATGCTTCAATCTACCCC
ATGATCGGGGTAAGAGATTGGATGAGTCTTCAATCTGCCCCATGATCGAGGTAAAAGATTAGATG
ATGTCTTCAATCTACCCTATGATCAGGGCAAAAGATCGGATGCTTCAATCTGCCCCATGATCGAG
GTAAAAGATTGGATGATGTCTTCAATCTGCCCCATAATCAGGGTAAAAGATTGGACGGCTGCAAT
CTGCCTCATGATCGGGATAAAATATTGGATGATGT
Found at i:336962 original size:49 final size:49
Alignment explanation
Indices: 336909--337368 Score: 182
Period size: 49 Copynumber: 9.3 Consensus size: 49
336899 AGATTTGTCA
* *
336909 TTGCGGCCTCAATCTTTCCTTTCATATCTCTAAGGTATAAGGTTCGCTG
1 TTGCGGCCTCAATCTTTCCCTTCATATCTCTAAGGTATAAGGTTCGCCG
* * * * * * * * **
336958 TTGCGACTTCAACCTTTCCCTCCATATCTCCAGGGTACAAGATTCATCG
1 TTGCGGCCTCAATCTTTCCCTTCATATCTCTAAGGTATAAGGTTCGCCG
* * * ** *
337007 TTGTGGCCTCAATCCTTT-CCTTCATTTCT-TCATGGTA-CCGGATTCACCG
1 TTGCGGCCTCAAT-CTTTCCCTTCATATCTCT-AAGGTATAAGG-TTCGCCG
** * * * * * * *
337056 TTGTAGCCTCAATCCTT-CTTATCACATCTTCTAAGGCATAGGGTTTGCCA
1 TTGCGGCCTCAATCTTTCCCT-TCATATC-TCTAAGGTATAAGGTTCGCCG
* * *
337106 TTGCGGCCTCAATCTTTCCCTTCATATCT-TCATGGTATCAGATTCGCCG
1 TTGCGGCCTCAATCTTTCCCTTCATATCTCT-AAGGTATAAGGTTCGCCG
* * * * * * * * ***
337155 TTGTGGTCTCAATCCTTCCCATCACATCTTTTAAGGTATAGGGTTTGTTA
1 TTGCGGCCTCAATCTTTCCCTTCATATC-TCTAAGGTATAAGGTTCGCCG
* * ** *
337205 TTGCGGTCC-CAACCTTTCCCTTCATATCT-TCATGGTA-CCGGATTCACCG
1 TTGCGG-CCTCAATCTTTCCCTTCATATCTCT-AAGGTATAAGG-TTCGCCG
* * * * * *
337254 TTGCGGTCTCGATCTTTCCCATCATGTCATCTAAGGTACAAGGCTT-GTCG
1 TTGCGGCCTCAATCTTTCCCTTCATATC-TCTAAGGTATAAGG-TTCGCCG
* * * * * * * * * *
337304 TTGTGGCCTTAACCTTTCCCTTCGTATTTCCAGGGTATCAGATTCGCCA
1 TTGCGGCCTCAATCTTTCCCTTCATATCTCTAAGGTATAAGGTTCGCCG
*
337353 TTACGGCCTCAATCTT
1 TTGCGGCCTCAATCTT
337369 CCTTGTCAAA
Statistics
Matches: 286, Mismatches: 106, Indels: 38
0.67 0.25 0.09
Matches are distributed among these distances:
48 13 0.05
49 170 0.59
50 91 0.32
51 12 0.04
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (49 bp):
TTGCGGCCTCAATCTTTCCCTTCATATCTCTAAGGTATAAGGTTCGCCG
Found at i:337289 original size:99 final size:99
Alignment explanation
Indices: 337011--337326 Score: 366
Period size: 99 Copynumber: 3.2 Consensus size: 99
337001 TCATCGTTGT
* * * *
337011 GGCCTCAATCCTTT-CCTTCATTTCTTCATGGTACCGGATTCACCGTTGTAGCCTCAATCCTTCT
1 GGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGTGGTCTCAATCCTTCC
* *
337075 TATCACATCTTCTAAGGCATAGGGTTTGCCATTGC
65 CATCACATCTTCTAAGGTATAGGGTTTGCCATTGC
* * * *
337110 GGCCTCAATCTTTCCCTTCATATCTTCATGGTATCAGATTCGCCGTTGTGGTCTCAATCCTTCCC
1 GGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGTGGTCTCAATCCTTCCC
* **
337175 ATCACATCTTTTAAGGTATAGGGTTTGTTATTGC
66 ATCACATCTTCTAAGGTATAGGGTTTGCCATTGC
* * *
337209 GGTCC-CAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCGGTCTCGATCTTTCC
1 GG-CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGTGGTCTCAATCCTTCC
** * * * * * * *
337273 CATCATGTCATCTAAGGTACAAGGCTTGTCGTTGT
65 CATCACATCTTCTAAGGTATAGGGTTTGCCATTGC
*
337308 GGCCTTAACCTTTCCCTTC
1 GGCCTCAACCTTTCCCTTC
337327 GTATTTCCAG
Statistics
Matches: 183, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
98 6 0.03
99 175 0.96
100 2 0.01
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (99 bp):
GGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGTGGTCTCAATCCTTCCC
ATCACATCTTCTAAGGTATAGGGTTTGCCATTGC
Found at i:337348 original size:99 final size:99
Alignment explanation
Indices: 337011--337370 Score: 323
Period size: 99 Copynumber: 3.6 Consensus size: 99
337001 TCATCGTTGT
* * * ** * *
337011 GGCCTCAATCCTTT-CCTTCATTTCTTCATGGTACCGGATTCACCGTTGTAGCCTCAATCCTTCT
1 GGCCTCAA-CCTTTCCCTTCATATCTTCATGGTATCAGATTCACCGTTGCGGTCTCAATCCTTCC
* * * * * * *
337075 TATCACATCTTCTAAGGCATAGGGTTTGCCATTGC
65 CATCACATCATCTAAGGTACAAGGCTTGTCATTGC
* * *
337110 GGCCTCAATCTTTCCCTTCATATCTTCATGGTATCAGATTCGCCGTTGTGGTCTCAATCCTTCCC
1 GGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGATTCACCGTTGCGGTCTCAATCCTTCCC
* * * * * *
337175 ATCACATCTTTTAAGGTATAGGGTTTGTTATTGC
66 ATCACATCATCTAAGGTACAAGGCTTGTCATTGC
* * * *
337209 GGTCC-CAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACCGTTGCGGTCTCGATCTTTCC
1 GG-CCTCAACCTTTCCCTTCATATCTTCATGGTATCAGATTCACCGTTGCGGTCTCAATCCTTCC
** * *
337273 CATCATGTCATCTAAGGTACAAGGCTTGTCGTTGT
65 CATCACATCATCTAAGGTACAAGGCTTGTCATTGC
* * * * * * *
337308 GGCCTTAACCTTTCCCTTCGTAT-TTCCAGGGTATCAGATTCGCCATTACGGCCTCAAT-CTTCC
1 GGCCTCAACCTTTCCCTTCATATCTT-CATGGTATCAGATTCACCGTTGCGGTCTCAATCCTTCC
337371 TTGTCAAACC
Statistics
Matches: 216, Mismatches: 41, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
98 12 0.06
99 202 0.94
100 2 0.01
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (99 bp):
GGCCTCAACCTTTCCCTTCATATCTTCATGGTATCAGATTCACCGTTGCGGTCTCAATCCTTCCC
ATCACATCATCTAAGGTACAAGGCTTGTCATTGC
Found at i:343461 original size:30 final size:29
Alignment explanation
Indices: 343420--343593 Score: 152
Period size: 30 Copynumber: 5.8 Consensus size: 29
343410 AAAAATGAAA
* *
343420 TTTTGGAAAGTTTGGTGGCCAAATTCAAAT
1 TTTTGGGAAGTTTGG-GGTCAAATTCAAAT
**
343450 TTTTGGGAAGTTTAGGGGTCAAATTTGAAT
1 TTTTGGGAAGTTT-GGGGTCAAATTCAAAT
**
343480 TTTTGAAAAGTTTGAGGGTCAAA-TCTAAAT
1 TTTTGGGAAGTTTG-GGGTCAAATTC-AAAT
* * *
343510 TTTGGGGAAGTTTGAGGGTTAAATCCAAAT
1 TTTTGGGAAGTTTG-GGGTCAAATTCAAAT
* * *
343540 TTTTTGGAAGTTTGGGGTTTAAATCCAAAT
1 TTTTGGGAAGTTTGGGG-TCAAATTCAAAT
* *
343570 TTTTTGGAAGTTTGAGGGTTAAAT
1 TTTTGGGAAGTTTG-GGGTCAAAT
343594 ATGAATTTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.04
30 112 0.91
31 6 0.05
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (29 bp):
TTTTGGGAAGTTTGGGGTCAAATTCAAAT
Found at i:343601 original size:30 final size:30
Alignment explanation
Indices: 343446--343621 Score: 162
Period size: 30 Copynumber: 5.9 Consensus size: 30
343436 GGCCAAATTC
* * *
343446 AAATTTTTGGGAAGTTT-AGGGGTCAAATTT
1 AAATTTTTTGGAAGTTTGA-GGGTTAAATCT
* * *
343476 GAA-TTTTTGAAAAGTTTGAGGGTCAAATCT
1 AAATTTTTTG-GAAGTTTGAGGGTTAAATCT
** *
343506 AAATTTTGGGGAAGTTTGAGGGTTAAATCC
1 AAATTTTTTGGAAGTTTGAGGGTTAAATCT
*
343536 AAATTTTTTGGAAGTTTG-GGGTTTAAATCC
1 AAATTTTTTGGAAGTTTGAGGG-TTAAATCT
*
343566 AAATTTTTTGGAAGTTTGAGGGTTAAATAT
1 AAATTTTTTGGAAGTTTGAGGGTTAAATCT
* * *
343596 GAA-TTTTTGGACAATTTGGGGGTTAA
1 AAATTTTTTGGA-AGTTTGAGGGTTAA
343622 TATGGAATTT
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.13
30 99 0.80
31 8 0.07
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (30 bp):
AAATTTTTTGGAAGTTTGAGGGTTAAATCT
Found at i:343601 original size:60 final size:58
Alignment explanation
Indices: 343405--343621 Score: 193
Period size: 60 Copynumber: 3.6 Consensus size: 58
343395 AGGAGAAACG
* * * ** *
343405 GGGTCAAAAATGAAATTTTGGAAAGTTTGGTGGCCAAATTCAAATTTTTGGGAAGTTT-A
1 GGGTTAAATATGAATTTTTGG-AAGTTTGG-GGTTAAATCCAAATTTTTGGGAAGTTTGA
* * * * * *
343464 GGGGTCAAATTTGAATTTTTGAAAAGTTTGAGGGTCAAATCTAAATTTTGGGGAAGTTTGA
1 -GGGTTAAATATGAATTTTTG-GAAGTTTG-GGGTTAAATCCAAATTTTTGGGAAGTTTGA
*** *
343525 GGGTTAAATCCAAATTTTTTGGAAGTTTGGGGTTTAAATCCAAATTTTTTGGAAGTTTGA
1 GGGTTAAATATGAA-TTTTTGGAAGTTTGGGG-TTAAATCCAAATTTTTGGGAAGTTTGA
*
343585 GGGTTAAATATGAATTTTTGGACAATTTGGGGGTTAA
1 GGGTTAAATATGAATTTTTGGA-AGTTT-GGGGTTAA
343622 TATGGAATTT
Statistics
Matches: 129, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
59 11 0.09
60 106 0.82
61 12 0.09
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (58 bp):
GGGTTAAATATGAATTTTTGGAAGTTTGGGGTTAAATCCAAATTTTTGGGAAGTTTGA
Found at i:343623 original size:29 final size:30
Alignment explanation
Indices: 343570--343631 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
343560 AAATCCAAAT
*
343570 TTTTTGGAAGTTTGAGGGTTAAATAT-GAA
1 TTTTTGGAAATTTGAGGGTTAAATATGGAA
*
343599 TTTTTGGACAATTTGGGGGTT-AATATGGAA
1 TTTTTGGA-AATTTGAGGGTTAAATATGGAA
343629 TTT
1 TTT
343632 CTAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (30 bp):
TTTTTGGAAATTTGAGGGTTAAATATGGAA
Found at i:345783 original size:22 final size:24
Alignment explanation
Indices: 345756--345803 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
345746 CTATGGAATT
345756 AAATACA-CAATA-TATTTTATTA
1 AAATACATCAATATTATTTTATTA
*
345778 AAATACATCCATATTATTTTATTA
1 AAATACATCAATATTATTTTATTA
345802 AA
1 AA
345804 TTTAACTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATACATCAATATTATTTTATTA
Found at i:347727 original size:47 final size:47
Alignment explanation
Indices: 347594--347706 Score: 174
Period size: 47 Copynumber: 2.4 Consensus size: 47
347584 AAGGAGGAAG
*
347594 AAGTGACAGTTTATCTGCAAAAGTGATGACTTG-TCTGCAATATTATA
1 AAGTGACAGTTTATCTGCAAAAGTGATGACTTGTTC-ACAATATTATA
* * *
347641 AAGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTTCACAATATTATT
1 AAGTGACAGTTTATCTGCAAAAGTGATGACTTGTTCACAATATTATA
347688 AAGTGACAGTTTATCTGCA
1 AAGTGACAGTTTATCTGCA
347707 TTATTGTGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
47 59 0.97
48 2 0.03
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (47 bp):
AAGTGACAGTTTATCTGCAAAAGTGATGACTTGTTCACAATATTATA
Found at i:350961 original size:18 final size:18
Alignment explanation
Indices: 350935--350972 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
350925 AAATAATTTT
*
350935 AATATTAAATAAATAATG
1 AATAGTAAATAAATAATG
*
350953 AATAGTAAATAATTAATG
1 AATAGTAAATAAATAATG
350971 AA
1 AA
350973 AAACATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAGTAAATAAATAATG
Found at i:352804 original size:18 final size:18
Alignment explanation
Indices: 352781--352817 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
352771 TGAGCAAAGA
*
352781 ACTGTTTTAAAAATAGCC
1 ACTGTTTCAAAAATAGCC
352799 ACTGTTTCAAAAATAGCC
1 ACTGTTTCAAAAATAGCC
352817 A
1 A
352818 AGTTATGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (18 bp):
ACTGTTTCAAAAATAGCC
Found at i:373431 original size:23 final size:24
Alignment explanation
Indices: 373394--373453 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
373384 AAAATTACAA
* *
373394 AAAAATTAAATATTTATAAAATTTC-
1 AAAAATT--ATATTTAAAAAAATTCT
*
373419 AAAATTTATATTTAAAAAAATTCT
1 AAAAATTATATTTAAAAAAATTCT
373443 AAAAATTATAT
1 AAAAATTATAT
373454 AAAAAAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 14 0.47
24 10 0.33
25 6 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATTATATTTAAAAAAATTCT
Found at i:373438 original size:24 final size:25
Alignment explanation
Indices: 373394--373454 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
373384 AAAATTACAA
* *
373394 AAAAATTAAATATTTATAAAATT-T
1 AAAAATTATATATTTAAAAAATTCT
*
373418 CAAAATT-TATATTTAAAAAAATTCT
1 AAAAATTATATATTT-AAAAAATTCT
373443 AAAAATTATATA
1 AAAAATTATATA
373455 AAAAAGTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 6 0.20
24 13 0.43
25 7 0.23
26 4 0.13
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAATTATATATTTAAAAAATTCT
Found at i:390020 original size:18 final size:19
Alignment explanation
Indices: 389985--390021 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
389975 GCTATCTTTA
389985 AGTAATTTAAATTGATAAG
1 AGTAATTTAAATTGATAAG
*
390004 AGTATTTTAAATT-ATAAG
1 AGTAATTTAAATTGATAAG
390022 TAATAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
AGTAATTTAAATTGATAAG
Found at i:391380 original size:3 final size:3
Alignment explanation
Indices: 391372--391408 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
391362 TTATATGAAT
*
391372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
391409 AATTTGCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:393608 original size:3 final size:3
Alignment explanation
Indices: 393600--393630 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
393590 TTGATTAAAT
393600 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
393631 AATTTGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:399208 original size:6 final size:7
Alignment explanation
Indices: 399177--399207 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
399167 ATTTAACTTG
*
399177 AAAATTA
1 AAAATAA
399184 AAAATAA
1 AAAATAA
399191 AAAATAA
1 AAAATAA
399198 AAAATAA
1 AAAATAA
399205 AAA
1 AAA
399208 TGAATTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:404827 original size:29 final size:29
Alignment explanation
Indices: 404781--404864 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
404771 GATGAACTGC
404781 CACATATTTT-CCATAAAATGGCCACATAT
1 CACATATTTTGCCA-AAAATGGCCACATAT
*
404810 CACATATTTTGCCAAAAATGGCGACATAT
1 CACATATTTTGCCAAAAATGGCCACATAT
*
404839 CACATATTTTGCC-AAAATGGTCACAT
1 CACATATTTTGCCAAAAATGGCCACAT
404865 CTTCCTCCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
28 11 0.22
29 37 0.73
30 3 0.06
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (29 bp):
CACATATTTTGCCAAAAATGGCCACATAT
Found at i:405042 original size:8 final size:8
Alignment explanation
Indices: 405031--405064 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
405021 CGATATTCAT
405031 ATATCCAC
1 ATATCCAC
405039 ATATCCAC
1 ATATCCAC
405047 ATATCCAC
1 ATATCCAC
*
405055 ATATTCAC
1 ATATCCAC
405063 AT
1 AT
405065 TTTTCACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCCAC
Found at i:411919 original size:28 final size:28
Alignment explanation
Indices: 411866--411920 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
411856 GATGAACTGC
411866 CACATATTTGCCATAAAATGGCCACATAT
1 CACATATTTGCCA-AAAATGGCCACATAT
*
411895 CACATATTTTGCC-AAAATGGTCACAT
1 CACATA-TTTGCCAAAAATGGCCACAT
411921 CTTCCTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 6 0.25
30 6 0.25
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (28 bp):
CACATATTTGCCAAAAATGGCCACATAT
Found at i:420051 original size:37 final size:37
Alignment explanation
Indices: 419613--420039 Score: 556
Period size: 37 Copynumber: 11.6 Consensus size: 37
419603 GACTACTTCA
* * * *
419613 ATGGAAGGCTTACGTCTTGGTTAGACCGTAATGTAAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
*
419650 ATGTAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
*
419687 ATGGAAGGCTTACGTCTCGGTTAGAGCGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
* * * *
419724 ATGGAAGGTTTACATCTCGGA-TAGGGCATAATGTTAT
1 ATGGAAGGCTTACGTCTC-GATTAGAGCGTAATGTTAT
* *
419761 ATGGAAGGTTTACGTCTCG-TTACAGCGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
* *
419797 ATGGAAGGCTTATGTCTCGGTTAGAGCGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
*
419834 ATGGAAGGCTTATGTCTCGATTAGAGCG-AGATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTA-ATGTTAT
*
419871 ATGGAAGGCTTACGTTTCGATTAGAGCGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
*
419908 ATGGAAGGCTTATGTCTCGATTAGAGCG-AGATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTA-ATGTTAT
* * *
419945 ATGAAAGGCTTACGTCTCGACTAGAGTGTAATGTTAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
** * * *
419982 ATAAAAGGCTTACATCTCGGTTAGAGCGTAATGTAAT
1 ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
* *
420019 ATGGAAGGATTACGACTCGAT
1 ATGGAAGGCTTACGTCTCGAT
420040 CAAAGTGTAA
Statistics
Matches: 343, Mismatches: 40, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
36 33 0.10
37 307 0.90
38 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (37 bp):
ATGGAAGGCTTACGTCTCGATTAGAGCGTAATGTTAT
Found at i:433039 original size:16 final size:15
Alignment explanation
Indices: 433007--433045 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
432997 TGATAATAAC
433007 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
433023 TTATTATAATGTATAT
1 TAATTATAAT-TATAT
433039 TAATTAT
1 TAATTAT
433046 TATCAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:435560 original size:10 final size:10
Alignment explanation
Indices: 435541--435581 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
435531 AAAAAAAGAG
435541 AGAGAAAAAA
1 AGAGAAAAAA
*
435551 A-TGAAAAAA
1 AGAGAAAAAA
435560 AGAGAAAAAA
1 AGAGAAAAAA
*
435570 AGA-AAAAGA
1 AGAGAAAAAA
435579 AGA
1 AGA
435582 ATATATCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 16 0.59
10 11 0.41
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:435565 original size:19 final size:19
Alignment explanation
Indices: 435533--435581 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
435523 ATGATGCTAA
435533 AAAAAGAGAGAGAAAAAAATG
1 AAAAAGA-AGAGAAAAAAA-G
435554 AAAAA-AAGAGAAAAAAAG
1 AAAAAGAAGAGAAAAAAAG
435572 AAAAAGAAGA
1 AAAAAGAAGA
435582 ATATATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.22
19 15 0.56
20 1 0.04
21 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAGAAAAAAAG
Found at i:435631 original size:31 final size:32
Alignment explanation
Indices: 435567--435631 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
435557 AAAAGAGAAA
* * *
435567 AAAAGAAAAAGAAGAATATATCATATGTACTC
1 AAAAGAAAAAGAAGAAAAGAGCATATGTACTC
435599 AAAAGAAAAAG-AGAAAAGAGCATGA-GTACTC
1 AAAAGAAAAAGAAGAAAAGAGCAT-ATGTACTC
435630 AA
1 AA
435632 GTTCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.58, C:0.09, G:0.17, T:0.15
Consensus pattern (32 bp):
AAAAGAAAAAGAAGAAAAGAGCATATGTACTC
Found at i:442772 original size:17 final size:17
Alignment explanation
Indices: 442750--442787 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
442740 AAATTAAACA
*
442750 AAAATAAATACTTAATG
1 AAAATAAATAATTAATG
*
442767 AAAATAAATAATTAATT
1 AAAATAAATAATTAATG
442784 AAAA
1 AAAA
442788 ATCGTATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATAAATAATTAATG
Found at i:443140 original size:16 final size:17
Alignment explanation
Indices: 443110--443142 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
443100 TTTTTTATAA
*
443110 TAAACATAAACATAAAG
1 TAAACATAAAAATAAAG
443127 TAAA-ATAAAAATAAAG
1 TAAACATAAAAATAAAG
443143 GAAATAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAACATAAAAATAAAG
Found at i:446081 original size:26 final size:28
Alignment explanation
Indices: 446043--446098 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
446033 GTTAATAAAA
*
446043 TTCTCTTTAAGTTTTCTTTT-TAAGAAT
1 TTCTCTTTAAGTTTTCTTTTAGAAGAAT
*
446070 TTCTC-TTGAGTTTTCTTTTAGAAGAAT
1 TTCTCTTTAAGTTTTCTTTTAGAAGAAT
446097 TT
1 TT
446099 TAACAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (28 bp):
TTCTCTTTAAGTTTTCTTTTAGAAGAAT
Found at i:448628 original size:15 final size:15
Alignment explanation
Indices: 448604--448635 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
448594 TTGGATCCGA
448604 GTCGGGTCAGTTCGG
1 GTCGGGTCAGTTCGG
*
448619 GTCGGTTCAGTTCGG
1 GTCGGGTCAGTTCGG
448634 GT
1 GT
448636 GGATTGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.44, T:0.31
Consensus pattern (15 bp):
GTCGGGTCAGTTCGG
Found at i:460275 original size:13 final size:13
Alignment explanation
Indices: 460257--460281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460247 AAGATAGCCA
460257 GAAGAAGAAGAAT
1 GAAGAAGAAGAAT
460270 GAAGAAGAAGAA
1 GAAGAAGAAGAA
460282 AAATAAGAAG
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:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (13 bp):
GAAGAAGAAGAAT
Found at i:460275 original size:16 final size:15
Alignment explanation
Indices: 460256--460293 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
460246 GAAGATAGCC
*
460256 AGAAGAAGAAGAATGA
1 AGAAGAAGAAAAAT-A
460272 AGAAGAAGAAAAATA
1 AGAAGAAGAAAAATA
460287 AGAAGAA
1 AGAAGAA
460294 AATGACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.05
Consensus pattern (15 bp):
AGAAGAAGAAAAATA
Found at i:460763 original size:19 final size:19
Alignment explanation
Indices: 460739--460783 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
460729 ATAGTTTTCA
*
460739 TGCATTTTTATTTTGTCAT
1 TGCATTTTTATTTTGTCAG
*
460758 TGCATTTTTATTTTGTTAG
1 TGCATTTTTATTTTGTCAG
460777 TGCATTT
1 TGCATTT
460784 CTTTTGTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.09, G:0.13, T:0.62
Consensus pattern (19 bp):
TGCATTTTTATTTTGTCAG
Found at i:461397 original size:15 final size:15
Alignment explanation
Indices: 461365--461413 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
461355 TCAGTCACTT
*
461365 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
*
461380 GAAAAGGAAGAAAAA
1 GAAAAAGAAGAAAAA
461395 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
461410 -AAAA
1 GAAAA
461414 TTATGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.13
15 23 0.77
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:468954 original size:36 final size:36
Alignment explanation
Indices: 468908--468980 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
468898 TGGTTAGAGC
* *
468908 GTGTATTGCTATGAAATTGCTTATGTCTTGGCTAGA
1 GTGTATTGCTACGAAATTGCTTATGTCTCGGCTAGA
* *
468944 GTGTATTGCTACGTAATTGCTTATGTCTCGGTTAGA
1 GTGTATTGCTACGAAATTGCTTATGTCTCGGCTAGA
468980 G
1 G
468981 CGTAATGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (36 bp):
GTGTATTGCTACGAAATTGCTTATGTCTCGGCTAGA
Found at i:473805 original size:18 final size:18
Alignment explanation
Indices: 473782--473823 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
473772 GCAAGCTGAA
* *
473782 GAAGAAGATGAATATCCT
1 GAAGAAGAAGAAGATCCT
*
473800 GAAGAAGAAGAAGATCTT
1 GAAGAAGAAGAAGATCCT
473818 GAAGAA
1 GAAGAA
473824 CACGAGGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (18 bp):
GAAGAAGAAGAAGATCCT
Found at i:477593 original size:18 final size:18
Alignment explanation
Indices: 477567--477616 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
477557 GCAGGCACAT
*
477567 CATGATCAGATGCAATCA
1 CATGCTCAGATGCAATCA
477585 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAATCA
*
477603 CATGCTCATATGCA
1 CATGCTCAGATGCA
477617 GCCACAGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (18 bp):
CATGCTCAGATGCAATCA
Done.