Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012038.1 Kokia drynarioides strain JFW-HI SEQ_127036, 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: 380274
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 148 characters in sequence are not A, C, G, or T
Found at i:2040 original size:22 final size:22
Alignment explanation
Indices: 1998--2041 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1988 CGAATAAACC
* *
1998 AAATAAACTTTATTTCTGTAGA
1 AAATAAACTTAATTACTGTAGA
2020 AAATAAACTTAATATAC-GTAGA
1 AAATAAACTTAAT-TACTGTAGA
2042 CTGAAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (22 bp):
AAATAAACTTAATTACTGTAGA
Found at i:5564 original size:40 final size:40
Alignment explanation
Indices: 5520--5599 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5510 TAGAATCAAA
5520 CTTAAAATTAAATTCCTTAAACATGCATCAATTTAACATG
1 CTTAAAATTAAATTCCTTAAACATGCATCAATTTAACATG
5560 CTTAAAATTAAATTCCTTAAACATGCATCAATTTAACATG
1 CTTAAAATTAAATTCCTTAAACATGCATCAATTTAACATG
5600 AATTTACATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (40 bp):
CTTAAAATTAAATTCCTTAAACATGCATCAATTTAACATG
Found at i:10575 original size:4 final size:4
Alignment explanation
Indices: 10566--10610 Score: 63
Period size: 4 Copynumber: 11.0 Consensus size: 4
10556 TTTTACAATG
* *
10566 TAAA TAAA TAAA TAAG TAAA TAAA TAAA GTAAC TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA
10611 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
4 33 0.92
5 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:10604 original size:17 final size:16
Alignment explanation
Indices: 10566--10610 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
10556 TTTTACAATG
*
10566 TAAATAAATAAATAAG
1 TAAATAAATAAATAAC
10582 TAAATAAATAAAGTAAC
1 TAAATAAATAAA-TAAC
10599 TAAATAAATAAA
1 TAAATAAATAAA
10611 ATATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (16 bp):
TAAATAAATAAATAAC
Found at i:11221 original size:17 final size:18
Alignment explanation
Indices: 11180--11221 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
11170 TAGACAAACA
11180 AATTTTTAAATTTTAATG
1 AATTTTTAAATTTTAATG
* **
11198 AAATTTT-AATTTTTTTG
1 AATTTTTAAATTTTAATG
11215 AATTTTT
1 AATTTTT
11222 GCATACTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
AATTTTTAAATTTTAATG
Found at i:11291 original size:27 final size:27
Alignment explanation
Indices: 11252--11318 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
11242 AAATAGATTT
* *
11252 TTTTTTTACTTTTCTAAGTTTTTATGA
1 TTTTTTTATTTTTCTAAGTTTTTATAA
**
11279 TTTTTTTATTTTTCTATTTTTTTATAA
1 TTTTTTTATTTTTCTAAGTTTTTATAA
* *
11306 TTTTATGATTTTT
1 TTTTTTTATTTTT
11319 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTTTTATTTTTCTAAGTTTTTATAA
Found at i:11326 original size:27 final size:27
Alignment explanation
Indices: 11261--11327 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
11251 TTTTTTTTAC
** * * *
11261 TTTTCTAAGTTTTTATGATTTTTTTAT
1 TTTTCTATTTTTTTATAATTTTATGAT
11288 TTTTCTATTTTTTTATAATTTTATGATT
1 TTTTCTATTTTTTTATAATTTTATGA-T
*
11316 TTTTTTATTTTT
1 TTTTCTATTTTT
11328 AAATATTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTCTATTTTTTTATAATTTTATGAT
Found at i:27846 original size:27 final size:27
Alignment explanation
Indices: 27787--27852 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
27777 AATTATCATC
* * *
27787 TTTTTATTATCCCAACGGACTATCCCG
1 TTTTTATTGTCCCAACGGACTACCCCA
** *
27814 CGTTTATTGTCCCGACGGACTACCCCA
1 TTTTTATTGTCCCAACGGACTACCCCA
27841 TTTTTATTGTCC
1 TTTTTATTGTCC
27853 TAACAAACTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (27 bp):
TTTTTATTGTCCCAACGGACTACCCCA
Found at i:30278 original size:67 final size:67
Alignment explanation
Indices: 29994--30280 Score: 315
Period size: 67 Copynumber: 4.3 Consensus size: 67
29984 AGGTGTTACA
* * * * * **
29994 TATGATCTTACACATTATACCTCATGTTTAATGTCCTAGTGGACTTTCTATGTTGACATATTCGA
1 TATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATAGCCGA
30059 AC
66 AC
* * * * *
30061 TATGGTCTTACACATTATACCCTATGTTTAATGTCTTGGCGGACTCT-TAATGTTGCCATAGTCA
1 TATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGTGGACTCTCT-ATGTTGCCATAGCCG
30125 AAC
65 AAC
* * * *
30128 TATGGTCTTACACATTATATCCGATGTTTAATGTCCTGGTGAACTCTCTATGTTGCCATAGCTGA
1 TATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATAGCCGA
30193 AC
66 AC
* * * * ** *
30195 TACGATCTTAAACATTATTCCCCATGTTTAATGTTATGGAGGACTCTCTATGTTGCCATAGCCGA
1 TATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATAGCCGA
*
30260 GC
66 AC
* **
30262 TATGGCCTTAGGCATTATA
1 TATGGTCTTACACATTATA
30281 ACTCTTTACA
Statistics
Matches: 182, Mismatches: 36, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
66 1 0.01
67 180 0.99
68 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (67 bp):
TATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATAGCCGA
AC
Found at i:31465 original size:14 final size:15
Alignment explanation
Indices: 31432--31464 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
31422 TAGGTTTTTT
31432 GTTTTAGGTTTAAGG
1 GTTTTAGGTTTAAGG
31447 GTTTTA-GTTT-AGG
1 GTTTTAGGTTTAAGG
31460 GTTTT
1 GTTTT
31465 TTGGGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (15 bp):
GTTTTAGGTTTAAGG
Found at i:31598 original size:18 final size:18
Alignment explanation
Indices: 31575--31610 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31565 TGCTCAGAGA
31575 CACATTTCTTTTGCTGTG
1 CACATTTCTTTTGCTGTG
*
31593 CACATTTCTTTTGTTGTG
1 CACATTTCTTTTGCTGTG
31611 TTAGGATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (18 bp):
CACATTTCTTTTGCTGTG
Found at i:36842 original size:23 final size:24
Alignment explanation
Indices: 36811--36857 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
36801 CAAATCAGAA
36811 AAATATCTC-TAGAG-ATTTTCTG
1 AAATATCTCTTAGAGAATTTTCTG
36833 AAATAATCTCTTTAGAGAATTTTCT
1 AAAT-ATCTC-TTAGAGAATTTTCT
36858 CTTAAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 5 0.24
25 5 0.24
26 7 0.33
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (24 bp):
AAATATCTCTTAGAGAATTTTCTG
Found at i:37064 original size:62 final size:57
Alignment explanation
Indices: 36961--37084 Score: 158
Period size: 62 Copynumber: 2.1 Consensus size: 57
36951 AATATTGAAT
* * *
36961 TAATATAATATTTATCAAGATAAAAACTAGATTAAATTTAATATTAAATCTTATTAAAA
1 TAATAGAATATTTATCAAGATAAAAACTAAATTAAAGTTAATATTAAA--TTATTAAAA
* *
37020 TAATAGAATATTTATCTATAAGATAAACATTAAATTAAAGTTAATATTAAATTATTAAAA
1 TAATAGAATATTTATC---AAGATAAAAACTAAATTAAAGTTAATATTAAATTATTAAAA
37080 TAATA
1 TAATA
37085 TTATTTTGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
59 15 0.26
60 14 0.25
62 28 0.49
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (57 bp):
TAATAGAATATTTATCAAGATAAAAACTAAATTAAAGTTAATATTAAATTATTAAAA
Found at i:41551 original size:18 final size:18
Alignment explanation
Indices: 41521--41679 Score: 104
Period size: 18 Copynumber: 8.7 Consensus size: 18
41511 CGGAAGGAAT
* *
41521 AGCATACTAGCTCATTTG
1 AGCATACTGGCTCGTTTG
*
41539 AGTATACTGGCTCGTTTG
1 AGCATACTGGCTCGTTTG
* *
41557 AGCATACAGGTTCGTTTG
1 AGCATACTGGCTCGTTTG
* *
41575 AGCACACCGGCTCGTTTG
1 AGCATACTGGCTCGTTTG
* * *
41593 AGCATACTGACTTGTTTA
1 AGCATACTGGCTCGTTTG
** *
41611 AGCATA-TCGATTCGTTGG
1 AGCATACT-GGCTCGTTTG
* * *
41629 AGCATACTAGCTTGTTAG
1 AGCATACTGGCTCGTTTG
* * **
41647 AGCAACACTGGCTCATAAG
1 AGC-ATACTGGCTCGTTTG
41666 AGCGATACTGGCTC
1 AGC-ATACTGGCTC
41680 ATAAGACTGA
Statistics
Matches: 108, Mismatches: 30, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
17 1 0.01
18 84 0.78
19 23 0.21
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:41650 original size:54 final size:54
Alignment explanation
Indices: 41521--41650 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
41511 CGGAAGGAAT
* * * * * *
41521 AGCATACTAGCTCATTTGAGTATACTGGCTCGTTTGAGCATACAGGTTCGTTTG
1 AGCATACTAGCTCGTTTGAGCATACTGACTCGTTTAAGCATACAGATTCGTTGG
* ** *
41575 AGCACACCGGCTCGTTTGAGCATACTGACTTGTTTAAGCATATC-GATTCGTTGG
1 AGCATACTAGCTCGTTTGAGCATACTGACTCGTTTAAGCATA-CAGATTCGTTGG
* *
41629 AGCATACTAGCTTGTTAGAGCA
1 AGCATACTAGCTCGTTTGAGCA
41651 ACACTGGCTC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
54 59 0.98
55 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (54 bp):
AGCATACTAGCTCGTTTGAGCATACTGACTCGTTTAAGCATACAGATTCGTTGG
Found at i:41698 original size:19 final size:19
Alignment explanation
Indices: 41657--41706 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
41647 AGCAACACTG
*
41657 GCTCATAAGAGCGATACTG
1 GCTCATAAGAGCGATACTA
*
41676 GCTCATAAGA-CTGATATTA
1 GCTCATAAGAGC-GATACTA
*
41695 GCTCGTAAGAGC
1 GCTCATAAGAGC
41707 AATATACTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
GCTCATAAGAGCGATACTA
Found at i:41766 original size:26 final size:26
Alignment explanation
Indices: 41696--41766 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
41686 CTGATATTAG
* *
41696 CTCGTAAGAGCAATATACTGCACTGG
1 CTCGTAAGAGCGATATACTGCACTGA
* * * *
41722 CTCGTAAGAGTGACATACTGTATTGA
1 CTCGTAAGAGCGATATACTGCACTGA
*
41748 CTCGTAAGAGCGATTTACT
1 CTCGTAAGAGCGATATACT
41767 AACTGGGATC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (26 bp):
CTCGTAAGAGCGATATACTGCACTGA
Found at i:50982 original size:95 final size:94
Alignment explanation
Indices: 50833--51006 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 94
50823 TCTTTTCTTC
* *
50833 TTTTAGGGTAGCATGTTTTTAATAGTTAATAAGAAGAATTAGTTATTTCGATTGTTCTAAAATTC
1 TTTTAGGGTAGCATGTTTTTAATAGTTAATAAGAAGAATTAGATATTTCCATTGTTCTAAAATTC
50898 AAATAGTTAATAAGTAGAATTAGTTCTCT
66 AAATAGTTAATAAGTAGAATTAGTTCTCT
*
50927 TTTTAGGGTAGCATGTTTTTGAGTAGTTAACT-AGAAGAATTAGATATTTCCATTGTTCTAAAAT
1 TTTTAGGGTAGCATGTTTTT-AATAGTTAA-TAAGAAGAATTAGATATTTCCATTGTTCTAAAAT
50991 TCAAATAGTTAATAAG
64 TCAAATAGTTAATAAG
51007 ATTCTCATTC
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
94 20 0.27
95 54 0.72
96 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (94 bp):
TTTTAGGGTAGCATGTTTTTAATAGTTAATAAGAAGAATTAGATATTTCCATTGTTCTAAAATTC
AAATAGTTAATAAGTAGAATTAGTTCTCT
Found at i:55021 original size:44 final size:44
Alignment explanation
Indices: 54969--55055 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
54959 AACAAGATCA
*
54969 GCCTTTTTAAACAACTTATAGTCAAATACTTGAAAGATTGAAAT
1 GCCTTTTTAAACAACTTATAGTCAAATACTTGAAAGATAGAAAT
*
55013 GCCTTTTTAAACAACTTATAGTCAATTACTTGAAAGATAGAAA
1 GCCTTTTTAAACAACTTATAGTCAAATACTTGAAAGATAGAAA
55056 AAAATTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (44 bp):
GCCTTTTTAAACAACTTATAGTCAAATACTTGAAAGATAGAAAT
Found at i:55165 original size:261 final size:261
Alignment explanation
Indices: 54651--55149 Score: 668
Period size: 261 Copynumber: 1.9 Consensus size: 261
54641 AGGGTCGAAG
* * *
54651 GAAAATCGAATTGGTAGTGTTTGATGCGATGAAGTGGCTATAATAGCAATAATATAAGCCTTTTT
1 GAAAATCAAATTGGTAGTGTTTGATGCGATGAAGTGGCTATAATAGCAACAAGATAAGCCTTTTT
* ** **
54716 AAACAACTTATAGTCAAATACTTGAAAGATTGAGATACCTTTTGTTCAGGAGTGAGTAAAATTTG
66 AAACAACTTATAGTCAAATACTTGAAAGATTGAAATACCTTTTGTAAACAAGTGAGTAAAATTTG
* * * * * *
54781 ATTCAACTCGAAAAAAATTTAAATTTTGAATTATTTGAATTGAGTTAATCGAGTCAACTCAAATT
131 ATTAAAATAGAAAAAAATTTAAATTTCGAATTATTCGAATCGAGTTAATCGAGTCAACTCAAATT
*
54846 ATTTTCCGAATTTCGAGTTCGAATCGAATTTATTTTTCGAATTCGAATAATACGAATAATTTGAA
196 ATTTTCCGAATTTCGAGTTCGAATCGAATTTATTTTTCAAATTCGAATAATACGAATAATTTGAA
54911 A
261 A
* *
54912 GAAAATCAAATTGGTAGTGTTTGCTGC-AGTGAAGTGGCTATAATAGCAACAAGATCAGCCTTTT
1 GAAAATCAAATTGGTAGTGTTTGATGCGA-TGAAGTGGCTATAATAGCAACAAGATAAGCCTTTT
* * * *
54976 TAAACAACTTATAGTCAAATACTTGAAAGATTGAAATGCCTTTT-TAAACAACTTA-TAGTCAA-
65 TAAACAACTTATAGTCAAATACTTGAAAGATTGAAATACCTTTTGTAAACAAGTGAGTA--AAAT
*
55038 TT-ACTTGAAAGATAGAAAAAAATTTAAATTTCGAATTATTCGAATCGAGTTAATCGAGTCAATT
128 TTGA-TT-AAA-ATAGAAAAAAATTTAAATTTCGAATTATTCGAATCGAGTTAATCGAGTCAACT
* * * *
55102 CGAATT-TTTTTCGAATTTCGAGTTCGAATTGAGTTTATTTTTCAAATT
190 CAAATTATTTTCCGAATTTCGAGTTCGAATCGAATTTATTTTTCAAATT
55150 TTAATAACTC
Statistics
Matches: 206, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
259 3 0.01
260 10 0.05
261 141 0.68
262 52 0.25
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (261 bp):
GAAAATCAAATTGGTAGTGTTTGATGCGATGAAGTGGCTATAATAGCAACAAGATAAGCCTTTTT
AAACAACTTATAGTCAAATACTTGAAAGATTGAAATACCTTTTGTAAACAAGTGAGTAAAATTTG
ATTAAAATAGAAAAAAATTTAAATTTCGAATTATTCGAATCGAGTTAATCGAGTCAACTCAAATT
ATTTTCCGAATTTCGAGTTCGAATCGAATTTATTTTTCAAATTCGAATAATACGAATAATTTGAA
A
Found at i:56287 original size:56 final size:54
Alignment explanation
Indices: 56213--56349 Score: 150
Period size: 56 Copynumber: 2.5 Consensus size: 54
56203 TCAGTTAAAG
* * * *
56213 TTTTTTGGGTTATCGTGTACTAGGTGCTTGACACCCCTTTATCT-GAAAAAAAGTTA
1 TTTTTTGGGATGTCGTGTACTAGGTGATCGACACCCCTTTAT-TAG-AAAAAA-TTA
* * * *
56269 TTTTTTGGGATGTCGTGTACCAAGTTATCGACACCCCTTTGTTAGAAAAAATTA
1 TTTTTTGGGATGTCGTGTACTAGGTGATCGACACCCCTTTATTAGAAAAAATTA
*
56323 TTATTTTTGGATGTCGTGTACTAGGTG
1 TT-TTTTGGGATGTCGTGTACTAGGTG
56350 GCCAACACCC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
54 5 0.07
55 27 0.40
56 35 0.52
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (54 bp):
TTTTTTGGGATGTCGTGTACTAGGTGATCGACACCCCTTTATTAGAAAAAATTA
Found at i:56358 original size:55 final size:55
Alignment explanation
Indices: 56213--56360 Score: 140
Period size: 55 Copynumber: 2.7 Consensus size: 55
56203 TCAGTTAAAG
* * *
56213 TTTTTTGGGTTATCGTGTACTAGGTGCTTGACACCCCTTTATCTGAAAAAAAGTTA
1 TTTTTTGGGATGTCGTGTACTAGGTGC-CGACACCCCTTTATCTGAAAAAAAGTTA
* * ** *
56269 TTTTTTGGGATGTCGTGTACCAAGTTATCGACACCCCTTTGT-T-AGAAAAAA-TTA
1 TTTTTTGGGATGTCGTGTA-CTAGGTGCCGACACCCCTTTATCTGA-AAAAAAGTTA
* *
56323 TTATTTTTGGATGTCGTGTACTAGGTGGCCAACACCCC
1 TT-TTTTGGGATGTCGTGTACTAGGT-GCCGACACCCC
56361 ATCATCTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
54 10 0.14
55 31 0.42
56 29 0.39
57 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (55 bp):
TTTTTTGGGATGTCGTGTACTAGGTGCCGACACCCCTTTATCTGAAAAAAAGTTA
Found at i:56542 original size:18 final size:17
Alignment explanation
Indices: 56515--56548 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56505 GAGGAGGAAG
56515 CAAATATTGTTGAGTGCC
1 CAAATATTGTT-AGTGCC
*
56533 CAAATTTTGTTAGTGC
1 CAAATATTGTTAGTGC
56549 ACGTTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (17 bp):
CAAATATTGTTAGTGCC
Found at i:58598 original size:14 final size:14
Alignment explanation
Indices: 58579--58622 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
58569 TGTAATTTAA
58579 ATTTAATTGTATCC
1 ATTTAATTGTATCC
58593 ATTTAATTGTATCC
1 ATTTAATTGTATCC
58607 ATTTAA-TGTATTCC
1 ATTTAATTGTA-TCC
58621 AT
1 AT
58623 GCATGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTAATTGTATCC
Found at i:62389 original size:37 final size:37
Alignment explanation
Indices: 62348--62459 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 37
62338 ACATAGTCTA
62348 ATTACATCGGCATGAAGCCTGCTAGGCACATAGCCCG
1 ATTACATCGGCATGAAGCCTGCTAGGCACATAGCCCG
* * * *
62385 ATTACATCGGTACGAAACCTGCTAGGCACATAGCCCA
1 ATTACATCGGCATGAAGCCTGCTAGGCACATAGCCCG
* * * *
62422 AATACACCGGCATGGAGCCTACTAGGCACATAGCCCG
1 ATTACATCGGCATGAAGCCTGCTAGGCACATAGCCCG
62459 A
1 A
62460 ATTTTTAGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (37 bp):
ATTACATCGGCATGAAGCCTGCTAGGCACATAGCCCG
Found at i:77840 original size:52 final size:52
Alignment explanation
Indices: 77778--77906 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
77768 TTCTCATTTA
*
77778 ATACTCACGATGACACATTGTCATC-GAACCACATAATCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCACATAATCCGTAAAGGAATCAT
* * * *
77830 ATACTCACGATGACATATAGTCATCAGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCACATAATCCGTAAAGGAATCAT
77882 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
77907 TAAGGATTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
52 69 0.99
53 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCACATAATCCGTAAAGGAATCAT
Found at i:77963 original size:88 final size:88
Alignment explanation
Indices: 77820--77994 Score: 269
Period size: 88 Copynumber: 2.0 Consensus size: 88
77810 ATAATCCGTA
* * *
77820 AAGGAATCATATACTCACGATGACATATAGTCATCAGACCTCATAATTCGTAAAGGATTCATATA
1 AAGGAATCATATACTCACGATGACACATAGTCATCAGACCTCATAATCCGGAAAGGATTCATATA
*
77885 CTCACGATGACACATAGTCATCT
66 CTCACGATGACACATAATCATCT
* * * *
77908 AAGGATTCATATACTCATGATGACACATAGTTATCGGACCTCATAATCCGGAAAGGATTCATATA
1 AAGGAATCATATACTCACGATGACACATAGTCATCAGACCTCATAATCCGGAAAGGATTCATATA
*
77973 CTCATGATGACACATAATCATC
66 CTCACGATGACACATAATCATC
77995 GGACCTCATA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (88 bp):
AAGGAATCATATACTCACGATGACACATAGTCATCAGACCTCATAATCCGGAAAGGATTCATATA
CTCACGATGACACATAATCATCT
Found at i:77970 original size:52 final size:52
Alignment explanation
Indices: 77908--78104 Score: 295
Period size: 52 Copynumber: 3.8 Consensus size: 52
77898 ATAGTCATCT
* * *
77908 AAGGATTCATATACTCATGATGACACATAGTTATCGGACCTCATAATCCGGA
1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA
* *
77960 AAGGATTCATATACTCATGATGACACATAATCATCGGACCTCATAATCCGTA
1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA
* * * *
78012 AAGAATTCATATACTCACGATGATACATAGTCATCAGACCTTATAATCCGTA
1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA
* *
78064 AATGATTCATATACTCACGATGACACATAGTCATCGAACCT
1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCT
78105 TTTTCATTTA
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 131 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA
Found at i:78030 original size:140 final size:140
Alignment explanation
Indices: 77778--78046 Score: 412
Period size: 140 Copynumber: 1.9 Consensus size: 140
77768 TTCTCATTTA
* *
77778 ATACTCACGATGACACATTGTCATCGAACCACATAATCCGTAAAGGAATCATATACTCACGATGA
1 ATACTCACGATGACACATAGTCATCGAACCACATAATCCGGAAAGGAATCATATACTCACGATGA
* * * *
77843 CATATAGTCATCAGACCTCATAATTCGTAAAGGATTCATATACTCACGATGACACATAGTCATCT
66 CACATAATCATCAGACCTCATAATCCGTAAAGAATTCATATACTCACGATGACACATAGTCATCT
77908 AAGGATTCAT
131 AAGGATTCAT
* * * * * *
77918 ATACTCATGATGACACATAGTTATCGGACCTCATAATCCGGAAAGGATTCATATACTCATGATGA
1 ATACTCACGATGACACATAGTCATCGAACCACATAATCCGGAAAGGAATCATATACTCACGATGA
* *
77983 CACATAATCATCGGACCTCATAATCCGTAAAGAATTCATATACTCACGATGATACATAGTCATC
66 CACATAATCATCAGACCTCATAATCCGTAAAGAATTCATATACTCACGATGACACATAGTCATC
78047 AGACCTTATA
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (140 bp):
ATACTCACGATGACACATAGTCATCGAACCACATAATCCGGAAAGGAATCATATACTCACGATGA
CACATAATCATCAGACCTCATAATCCGTAAAGAATTCATATACTCACGATGACACATAGTCATCT
AAGGATTCAT
Found at i:84854 original size:37 final size:37
Alignment explanation
Indices: 84803--84898 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
84793 CGGCACAAAG
*
84803 GCCTGCTAGACACATAGCCCGATTACACCAG-CACGAA
1 GCCTGCTAGGCACATAGCCCGATTACA-CAGACACGAA
**
84840 GCCTGCTAGGCACATAGCTTGATTACACAGACACGAA
1 GCCTGCTAGGCACATAGCCCGATTACACAGACACGAA
*
84877 GCTTGCTAGGCACATAGCCCGA
1 GCCTGCTAGGCACATAGCCCGA
84899 ATTTCTTAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 3 0.06
37 49 0.94
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (37 bp):
GCCTGCTAGGCACATAGCCCGATTACACAGACACGAA
Found at i:93609 original size:42 final size:42
Alignment explanation
Indices: 93563--93779 Score: 124
Period size: 42 Copynumber: 5.2 Consensus size: 42
93553 AGTCTTACTT
* *
93563 TTTAAACATAATCTAATGCTCATTCCGAGTCATGAGTCTTCC
1 TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCC
* * * * * * *
93605 TTTAATCTTATTCTCATTCTCATCCCAAGACACGAGTCTTCC
1 TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCC
* * *
93647 TTTAATCATATTCTCATTCTCA-TCCTGAGACATGAG---TCC
1 TTTAAACATAATCTCATGCTCATTCC-GAGACATGAGTCTTCC
* * ** * * *
93686 -TTAAAAAT-ATGCTCATGCTCGTTTTGAGCCACGAGTATTCC
1 TTTAAACATAAT-CTCATGCTCATTCCGAGACATGAGTCTTCC
* * * *
93727 ATT-CATATAAGTTCTCATGCTCAATCCGAGACATGAGTCTTCC
1 TTTAAACATAA--TCTCATGCTCATTCCGAGACATGAGTCTTCC
*
93770 ATTTATACAT
1 -TTTAAACAT
93780 CAATTGTCTC
Statistics
Matches: 129, Mismatches: 34, Indels: 21
0.70 0.18 0.11
Matches are distributed among these distances:
37 1 0.01
38 22 0.17
39 4 0.03
41 8 0.06
42 65 0.50
43 23 0.18
44 3 0.02
45 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (42 bp):
TTTAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCC
Found at i:115370 original size:37 final size:36
Alignment explanation
Indices: 115313--115529 Score: 254
Period size: 37 Copynumber: 5.9 Consensus size: 36
115303 ATTCTTGAAT
* * *
115313 CACCGGCACAAAGGCCTGCTAGACACATAGTTCGATTA
1 CACCGGCACGAA-GCCTGCTAGGCACATAG-CCGATTA
*
115351 CACCGGCATGAAGCCTGCTAGGCACATAGCCTGATTA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCC-GATTA
*
115388 TACCGGCACGAAGCCTGCTAGGCACATAGCCTGATTA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCC-GATTA
* * * *
115425 CACTGGCACGAAGTCTGCTAGGCACATAGCCCAAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAG-CCGATTA
* * *
115462 CACCAGCACGAAGCCTGCTAGGCACATTGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAG-CCGATTA
* *
115499 CACCGACACAAAGCCTGCTAGGCACATAGCC
1 CACCGGCACGAAGCCTGCTAGGCACATAGCC
115530 TGAATTTCTT
Statistics
Matches: 157, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
36 3 0.02
37 142 0.90
38 12 0.08
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (36 bp):
CACCGGCACGAAGCCTGCTAGGCACATAGCCGATTA
Found at i:118400 original size:70 final size:69
Alignment explanation
Indices: 118321--118466 Score: 172
Period size: 70 Copynumber: 2.1 Consensus size: 69
118311 GTCACTAGTT
* ** * *
118321 ATTCTTTCATTCTTATCCAATTTAACAAATGTTTCATTT-ATACTCA-ATC-TACATAATTAATC
1 ATTCATTCATTCTTATCCAATTTAACAAACATTT--TTTCATACTCATACCATAC--AATCAATC
118383 ATTCTTAA
62 ATTCTTAA
* *
118391 ATTCATTCATTCTTGTCCAATTTGACAAACATTTTTTCATACTCATACCATACAATCAATCATTC
1 ATTCATTCATTCTTATCCAATTTAACAAACATTTTTTCATACTCATACCATACAATCAATCATTC
118456 TTAA
66 TTAA
118460 ATTCATT
1 ATTCATT
118467 TTGTTTTGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
68 3 0.05
69 29 0.44
70 31 0.47
71 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.44
Consensus pattern (69 bp):
ATTCATTCATTCTTATCCAATTTAACAAACATTTTTTCATACTCATACCATACAATCAATCATTC
TTAA
Found at i:119600 original size:109 final size:110
Alignment explanation
Indices: 119426--119651 Score: 391
Period size: 109 Copynumber: 2.1 Consensus size: 110
119416 ATTTTAGCTA
119426 AAGTTGAACCTAGAAAAGTGCACTTTTAGGGTTACTTCAAACAAGTTGTTAGGCTTCATGGTCAG
1 AAGTT-AACCTAGAAAAGTGCACTTTTAGGGTTACTTCAAACAAGTTGTTAGGCTTCATGGTCAG
*
119491 CAAGAGAGGAATTGAGATCGATCTAGATAAGGTCAAGGTCATATAG
65 CAAGAGAGGAATTGAGATCGATCCAGATAAGGTCAAGGTCATATAG
* * **
119537 -AGTTAACCTAGTAAAGTGCACTTTTGGGGTTACTTCAGGCAAGTTGTTAGGCTTCATGGTCAGC
1 AAGTTAACCTAGAAAAGTGCACTTTTAGGGTTACTTCAAACAAGTTGTTAGGCTTCATGGTCAGC
119601 AAGAGAGGAATTGAGATCGATCCAGATAAGGTCAAGGTCATATAG
66 AAGAGAGGAATTGAGATCGATCCAGATAAGGTCAAGGTCATATAG
119646 AAGTTA
1 AAGTTA
119652 CCACCACCCT
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
109 100 0.92
110 9 0.08
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (110 bp):
AAGTTAACCTAGAAAAGTGCACTTTTAGGGTTACTTCAAACAAGTTGTTAGGCTTCATGGTCAGC
AAGAGAGGAATTGAGATCGATCCAGATAAGGTCAAGGTCATATAG
Found at i:121419 original size:158 final size:158
Alignment explanation
Indices: 121195--121510 Score: 596
Period size: 158 Copynumber: 2.0 Consensus size: 158
121185 CTTCTCCGTG
*
121195 GCCTTTTTCTATGTATGGCATGGATGTTATCGGACCAATTTCACCAAAGGCTTTTAATGGGCATA
1 GCCTTTTTCTATGTAGGGCATGGATGTTATCGGACCAATTTCACCAAAGGCTTTTAATGGGCATA
121260 GGTTCATCTTTATGGTTATTGACTATTTCACCAAGTGGGTGGAAGCTACTTCTTACGCCTGTAAC
66 GGTTCATCTTTATGGTTATTGACTATTTCACCAAGTGGGTGGAAGCTACTTCTTACGCCTGTAAC
* *
121325 ACTCGAAACTCAAAACTATTGCCGATTA
131 ACCCGAAACTCAAAACTATTACCGATTA
*
121353 GCCTTTTTCTATGTGGGGCATGGATGTTATCGGACCAATTTCACCAAAGGCTTTTAATGGGCATA
1 GCCTTTTTCTATGTAGGGCATGGATGTTATCGGACCAATTTCACCAAAGGCTTTTAATGGGCATA
121418 GGTTCATCTTTATGGTTATTGACTATTTCACCAAGTGGGTGGAAGCTACTTCTTACGCCTGTAAC
66 GGTTCATCTTTATGGTTATTGACTATTTCACCAAGTGGGTGGAAGCTACTTCTTACGCCTGTAAC
121483 ACCCGAAACTCAAAACTATTACCGATTA
131 ACCCGAAACTCAAAACTATTACCGATTA
121511 AGGGCCCGAT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (158 bp):
GCCTTTTTCTATGTAGGGCATGGATGTTATCGGACCAATTTCACCAAAGGCTTTTAATGGGCATA
GGTTCATCTTTATGGTTATTGACTATTTCACCAAGTGGGTGGAAGCTACTTCTTACGCCTGTAAC
ACCCGAAACTCAAAACTATTACCGATTA
Found at i:122608 original size:52 final size:52
Alignment explanation
Indices: 122530--122659 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
122520 CATTTCGTTT
* *
122530 AATACTCATAAAGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAATCA
1 AATACTCATAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCA
* *
122582 AATACTCATAATGACACATAATCATCGGACCTCATAATCCGTAAAGGATTCA
1 AATACTCATAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCA
* *
122634 TATACTCACAATGACACATAGTCATC
1 AATACTCATAATGACACATAGTCATC
122660 AAACCTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.25
Consensus pattern (52 bp):
AATACTCATAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCA
Found at i:129721 original size:52 final size:52
Alignment explanation
Indices: 129643--129829 Score: 275
Period size: 52 Copynumber: 3.6 Consensus size: 52
129633 ATTTCAATTA
* * * *
129643 ATACTCACAATGACATATAGTCATCGGACCTCTTAATCCGTAAAAGAATCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * **
129695 ATACTCACGATGACACACAGTCATCGGACCTCATAATTAGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
129747 ATACTCATAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
129799 ATACTCACAATGACACATAATCATCAGACCT
1 ATACTCACAATGACACATAGTCATCGGACCT
129830 TTTTCATTTA
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 119 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (52 bp):
ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:132812 original size:46 final size:46
Alignment explanation
Indices: 132678--133246 Score: 638
Period size: 46 Copynumber: 12.6 Consensus size: 46
132668 GAAGTTACAT
* * ** *
132678 CACCATCCAATATTCTACCCCTAAATTTAGAAAGGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* ** *
132724 CA--A-CCAATCTTTTACTCCT-AATTTAGAGAGGCAGATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * * *
132766 CACTATCCAATGTTTTACCCCTAAATCTAGAGGGGCAGATTGAAG-
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * * *
132811 --CCATCCAATCTTTTATCCC-AAATCCAGAGGGGTAGATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* *
132854 CACCATCCAATTTTTTACCCTTAAATCCAGAGAGGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * * *
132900 CATCATCCAATCTTTTGCCCCTAAATCTAGAGAGGCAAATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * * ** * *
132946 CACCATCAAATCTTTAATCTTTAAATCCAAAGGGGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* *
132992 CACCATCCAATCTTTTAACCCTAAATCCAGA-AGGGCAGACTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGA-GGCAGATTGAAGC
* * *
133038 CACCATCCAATCTTTTACCCCTAAATCTAAAGAGGTAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * *
133084 CATCATCCAATCTTTTACTCCT-AATCCAGAG-GGTAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
*
133128 CACCATCCAATCTTTTACCCTTAAATCCAGAGAGGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* * * * *
133174 CACAATCCAACCTTTTACCCCTAAATACAGAGCGGCAAATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
* *
133220 CACCATTCAATCTTTTGCCCCTAAATC
1 CACCATCCAATCTTTTACCCCTAAATC
133247 TAAAGGGGAA
Statistics
Matches: 440, Mismatches: 71, Indels: 24
0.82 0.13 0.04
Matches are distributed among these distances:
42 43 0.10
43 29 0.07
44 34 0.08
45 46 0.10
46 287 0.65
47 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (46 bp):
CACCATCCAATCTTTTACCCCTAAATCCAGAGAGGCAGATTGAAGC
Found at i:133161 original size:274 final size:268
Alignment explanation
Indices: 132711--133234 Score: 747
Period size: 274 Copynumber: 1.9 Consensus size: 268
132701 AATTTAGAAA
** * *
132711 GGCAGATTGAAGCCAACCAATCTTTTACTCCTAATTTAGAGAGGCAGATTAAAGCCACTATCCAA
1 GGCAGATTGAAGCCAACCAATCTTTTACTCCTAATCCAGAGAGGCAGACTAAAGCCACCATCCAA
* * *
132776 TGTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCATCCAATCTTTTATCCCAAATCCAGAGG
66 TCTTTTACCCCTAAATCTAAAGAGGCAGATTGAAGCCATCCAATCTTTTATCCCAAATCCAGAGG
*
132841 GGTAGATTAAAGCCACCATCCAATTTTTTACCCTTAAATCCAGAGAGGCAGATTGAAGCCATC-A
131 GGTAGATTAAAGCCACCATCCAATCTTTTACCCTTAAATCCAGAGAGGCAGATTGAAGCCA-CAA
* *
132905 TCCAATCTTTTGCCCCTAAAT-CTAGAGAGGCAAATTGAAGCCACCA-TCAAATCTTTAATCTTT
195 TCCAACCTTTTACCCCTAAATAC-AGAGAGGCAAATTGAAGCCACCATTC-AATCTTTAATCTTT
132968 AAATCCAAAGG
258 AAATCCAAAGG
*
132979 GGCAGATTGAAGCCACCATCCAATCTTTTAAC-CCTAAATCCAGA-AGGGCAGACTGAAGCCACC
1 GGCAGATTGAAGCCA--A-CCAATCTTTT-ACTCCT-AATCCAGAGA-GGCAGACTAAAGCCACC
* *
133042 ATCCAATCTTTTACCCCTAAATCTAAAGAGGTAGATTGAAGCCATCATCCAATCTTTTA-CTCCT
60 ATCCAATCTTTTACCCCTAAATCTAAAGAGGCAGATTGAAG-C--CATCCAATCTTTTATC-CCA
*
133106 AATCCAGA-GGGTAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCCAGAGAGGCAGATTG
121 AATCCAGAGGGGTAGATTAAAGCCACCATCCAATCTTTTACCCTTAAATCCAGAGAGGCAGATTG
*
133170 AAGCCACAATCCAACCTTTTACCCCTAAATACAGAGCGGCAAATTGAAGCCACCATTCAATCTTT
186 AAGCCACAATCCAACCTTTTACCCCTAAATACAGAGAGGCAAATTGAAGCCACCATTCAATCTTT
133235 TGCCCCTAAA
Statistics
Matches: 228, Mismatches: 15, Indels: 20
0.87 0.06 0.08
Matches are distributed among these distances:
268 15 0.07
270 1 0.00
271 14 0.06
272 59 0.26
273 2 0.01
274 110 0.48
275 27 0.12
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (268 bp):
GGCAGATTGAAGCCAACCAATCTTTTACTCCTAATCCAGAGAGGCAGACTAAAGCCACCATCCAA
TCTTTTACCCCTAAATCTAAAGAGGCAGATTGAAGCCATCCAATCTTTTATCCCAAATCCAGAGG
GGTAGATTAAAGCCACCATCCAATCTTTTACCCTTAAATCCAGAGAGGCAGATTGAAGCCACAAT
CCAACCTTTTACCCCTAAATACAGAGAGGCAAATTGAAGCCACCATTCAATCTTTAATCTTTAAA
TCCAAAGG
Found at i:133620 original size:10 final size:11
Alignment explanation
Indices: 133596--133625 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
133586 CCCAAATATA
133596 AAAATAAATCC
1 AAAATAAATCC
133607 AAAATAAA-CC
1 AAAATAAATCC
133617 AAAATAAAT
1 AAAATAAAT
133626 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAATCC
Found at i:135860 original size:46 final size:46
Alignment explanation
Indices: 135749--136042 Score: 308
Period size: 46 Copynumber: 6.4 Consensus size: 46
135739 ACTAATTCAA
* *
135749 AGGGGTAGATTGAAGCCACCATCCAATCTTTTA-CCTCT-AATCCAG
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCT-TAAATCTAG
* * *
135794 AGGGGCAGATTGAAGTCACCATCCAATATTATACCCTTAAATCTAG
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCTAG
* * *
135840 AGAGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAAT-TCAG
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCT-AG
* * * *
135886 AGGGGCAGATTGAAGTCATCATCTAATCTTTTACCCGTAAATCTAG
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCTAG
* * * * * * *
135932 AGGGACAGATTAAAGCCCCCATCTAACCTTTTACACTTAAATAC-AA
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAAT-CTAG
* * *
135978 AGGGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCTAT
1 AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCTAG
* * *
136024 AGGGACAAAGTGAAGCCAC
1 AGGGGCAGATTGAAGCCAC
136043 ATACACAACT
Statistics
Matches: 204, Mismatches: 39, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
45 32 0.16
46 170 0.83
47 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (46 bp):
AGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCTAG
Found at i:135928 original size:92 final size:91
Alignment explanation
Indices: 135751--136027 Score: 349
Period size: 92 Copynumber: 3.0 Consensus size: 91
135741 TAATTCAAAG
* *
135751 GGGTAGATTGAAGCCACCATCCAATCTTTTACCTCT-AATCCAGAGGGGCAGATTGAAGTCACCA
1 GGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATACAGAGGGGCAGATTGAAGTCACCA
* * *
135815 TCCAATATTATACCCTTAAATCTAGA
66 TCCAATCTTTTACCCCTAAATCTAGA
* *
135841 GAGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATTCAGAGGGGCAGATTGAAGTCATC
1 G-GGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATACAGAGGGGCAGATTGAAGTCACC
* *
135906 ATCTAATCTTTTACCCGTAAATCTAGA
65 ATCCAATCTTTTACCCCTAAATCTAGA
* * * * * * * * * *
135933 GGGACAGATTAAAGCCCCCATCTAACCTTTTACACTTAAATACAAAGGGGTAGATTGAAGCCACC
1 GGG-TAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATACAGAGGGGCAGATTGAAGTCACC
*
135998 ATCCAATCTTTTACCCCTAAATCTATA
65 ATCCAATCTTTTACCCCTAAATCTAGA
136025 GGG
1 GGG
136028 ACAAAGTGAA
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 36 0.22
92 125 0.77
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (91 bp):
GGGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATACAGAGGGGCAGATTGAAGTCACCA
TCCAATCTTTTACCCCTAAATCTAGA
Found at i:135989 original size:138 final size:137
Alignment explanation
Indices: 135742--136019 Score: 362
Period size: 138 Copynumber: 2.0 Consensus size: 137
135732 TTTGACAACT
* * *
135742 AATTCAAAGGGGTAGATTGAAGCCACCATCCAATCTTTTACCTCTAATCCAGAGGGGCAGATTGA
1 AATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAATCCAGAGGGACAGATTAA
* * * *
135807 AGTCACCATCCAATATTATACCCTTAAATCTAGAGAGGTAGATTGAAGCCACCATCCAATCTTTT
66 AGCCACCATCCAACATTATACACTTAAATCTAAAGAGGTAGATTGAAGCCACCATCCAATCTTTT
135872 ACCCCTA
131 ACCCCTA
* * * * *
135879 AATTCAGAGGGGCAGATTGAAGTCATCATCTAATCTTTTACC-CGTAAATCTAGAGGGACAGATT
1 AATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTC-T-AATCCAGAGGGACAGATT
* * * * *
135943 AAAGCCCCCATCTAACCTTTTACACTTAAATAC-AAAGGGGTAGATTGAAGCCACCATCCAATCT
64 AAAGCCACCATCCAACATTATACACTTAAAT-CTAAAGAGGTAGATTGAAGCCACCATCCAATCT
136007 TTTACCCCTA
128 TTTACCCCTA
136017 AAT
1 AAT
136020 CTATAGGGAC
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
136 1 0.01
137 38 0.31
138 81 0.67
139 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (137 bp):
AATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCTCTAATCCAGAGGGACAGATTAA
AGCCACCATCCAACATTATACACTTAAATCTAAAGAGGTAGATTGAAGCCACCATCCAATCTTTT
ACCCCTA
Found at i:138750 original size:45 final size:44
Alignment explanation
Indices: 138682--138982 Score: 300
Period size: 45 Copynumber: 6.6 Consensus size: 44
138672 GTTTCAATAG
*
138682 CTAATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
1 CTAAATCAAA-GGGCAGATTGAAGCCACCATCCAATCTTTTACCC
* * * *
138727 CTAATTCATAGGTGCAGAATGAAGCCACCATCCAATCTTATACCC
1 CTAAATCAAAGG-GCAGATTGAAGCCACCATCCAATCTTTTACCC
* * *
138772 CTAAATCAAGTGGGATAGATTGAAGCCACCATTCAATCTTTTA-CC
1 CTAAATCAA-AGGG-CAGATTGAAGCCACCATCCAATCTTTTACCC
* * *
138817 CTAAATCTAAAGAAGCAGATTGAAGCCACCGTCAAATCTTTTACCC
1 CTAAATC-AAAG-GGCAGATTGAAGCCACCATCCAATCTTTTACCC
* *
138863 CTAAATCTAGAA-GGCAAATTGAAGCCACCATCCAACCTTTTACCC
1 CTAAATC-A-AAGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
* * * * * *
138908 TTAAATTCAGAAGGGTAGATTAAATCAACCATCAAATCTTTTACCC
1 CTAAA-TCA-AAGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
*
138954 CTAAATCAAGAGGGGTAGATTGAAGCCAC
1 CTAAATCAA-A-GGGCAGATTGAAGCCAC
138983 ACATACAACT
Statistics
Matches: 212, Mismatches: 33, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
44 3 0.01
45 121 0.57
46 86 0.41
47 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (44 bp):
CTAAATCAAAGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
Found at i:138855 original size:91 final size:90
Alignment explanation
Indices: 138697--138982 Score: 319
Period size: 91 Copynumber: 3.1 Consensus size: 90
138687 TCAAAGGGGC
* * * * *
138697 AGATTGAAGCCACCATCCAATCTTTTACCCCTAATTC-ATAGGTGCAGAATGAAGCCACCATCCA
1 AGATTGAAGCCACCATCCAATCTTTTA-CCCTAAATCTA-AAGAGCAGATTGAAGCCACCATCAA
* *
138761 ATCTTATACCCCTAAATCAAGTGGGAT
64 ATCTTTTACCCCTAAATCAAGAGGGAT
* *
138788 AGATTGAAGCCACCATTCAATCTTTTACCCTAAATCTAAAGAAGCAGATTGAAGCCACCGTCAAA
1 AGATTGAAGCCACCATCCAATCTTTTACCCTAAATCTAAAG-AGCAGATTGAAGCCACCATCAAA
* *
138853 TCTTTTACCCCTAAATCTAGAAGGCA-
65 TCTTTTACCCCTAAATCAAG-AGGGAT
* * * * * *
138879 A-ATTGAAGCCACCATCCAACCTTTTACCCTTAAAT-TCAGAAGGGTAGATTAAATCAACCATCA
1 AGATTGAAGCCACCATCCAATCTTTTACCC-TAAATCT-A-AAGAGCAGATTGAAGCCACCATCA
*
138942 AATCTTTTACCCCTAAATCAAGAGGGGT
63 AATCTTTTACCCCTAAATCAAGAGGGAT
138970 AGATTGAAGCCAC
1 AGATTGAAGCCAC
138983 ACATACAACT
Statistics
Matches: 165, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
90 40 0.24
91 108 0.65
92 17 0.10
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (90 bp):
AGATTGAAGCCACCATCCAATCTTTTACCCTAAATCTAAAGAGCAGATTGAAGCCACCATCAAAT
CTTTTACCCCTAAATCAAGAGGGAT
Found at i:138939 original size:136 final size:137
Alignment explanation
Indices: 138695--138982 Score: 340
Period size: 136 Copynumber: 2.1 Consensus size: 137
138685 ATTCAAAGGG
* *
138695 GCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATTCATAGGTGCAGAATGAAGCCACCATCC
1 GCAGATTGAAGCCACCATCAAATCTTTTACCCCTAAATCATAGGTGCAGAATGAAGCCACCATCC
* * * *
138760 AATCTTATACCCCTAAATCAAGTGGGATAGATTGAAGCCACCATTC-AATCTTTTA-CCCTAAAT
66 AACCTTATACCCCTAAATCAAGAGGGATAGATTAAAGCAACCA-TCAAATCTTTTACCCCTAAAT
138823 CTAA-AGAA
130 C-AAGAGAA
*
138831 GCAGATTGAAGCCACCGTCAAATCTTTTACCCCTAAATC-TAGAAG-GCA-AATTGAAGCCACCA
1 GCAGATTGAAGCCACCATCAAATCTTTTACCCCTAAATCATAG--GTGCAGAA-TGAAGCCACCA
* * *
138893 TCCAACCTTTTACCCTTAAATTC-AGAAGGG-TAGATTAAATCAACCATCAAATCTTTTACCCCT
63 TCCAACCTTATACCCCTAAA-TCAAG-AGGGATAGATTAAAGCAACCATCAAATCTTTTACCCCT
**
138956 AAATCAAGAGGG
126 AAATCAAGAGAA
*
138968 GTAGATTGAAGCCAC
1 GCAGATTGAAGCCAC
138983 ACATACAACT
Statistics
Matches: 131, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
135 7 0.05
136 93 0.71
137 31 0.24
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (137 bp):
GCAGATTGAAGCCACCATCAAATCTTTTACCCCTAAATCATAGGTGCAGAATGAAGCCACCATCC
AACCTTATACCCCTAAATCAAGAGGGATAGATTAAAGCAACCATCAAATCTTTTACCCCTAAATC
AAGAGAA
Found at i:141732 original size:46 final size:45
Alignment explanation
Indices: 141622--141957 Score: 264
Period size: 46 Copynumber: 7.4 Consensus size: 45
141612 TAATTTAGAA
* *
141622 GGGCAGATTGAAGCCACCATCTAATCTTTCACCCCT-AATCCAAAG
1 GGGCAGATTGAAGCCACCATCCAATCTTT-ACCCCTAAATCAAAAG
* * * * *
141667 GGGTAGATTAAAGTCACCATCCAATCTTATATCCTTAAATCAAAAG
1 GGGCAGATTGAAGCCACCATCCAATCTT-TACCCCTAAATCAAAAG
* ** ** *
141713 GGGCAGGTTGAAGCCACCATCCAATCTTTTTCCCTAAATTTAGAG
1 GGGCAGATTGAAGCCACCATCCAATCTTTACCCCTAAATCAAAAG
* * * * ** *
141758 AGGTAGATTGAAGACATCATATAATCTCTTACCCCTAAATCAAGAG
1 GGGCAGATTGAAGCCACCATCCAATCT-TTACCCCTAAATCAAAAG
* * * *
141804 GGGCATATTGAAGTCACCGTACAATCTTTTACCCCTAAAT-ATAAAG
1 GGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTAAATCA-AAAG
* * * * * * *
141850 GGGAAGATTAAAGCCACTATCCAACCTTTTACCCTTAAATCCAGAG
1 GGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTAAATCAAAAG
* * * * *
141896 GGGTA-ATTGAACCCATCATCCAATCTTTTACTCCTAAATCAATAG
1 GGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTAAATCAAAAG
141941 GGGCAGATTGAAGCCAC
1 GGGCAGATTGAAGCCAC
141958 ACACACAACT
Statistics
Matches: 225, Mismatches: 59, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
45 96 0.43
46 128 0.57
47 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (45 bp):
GGGCAGATTGAAGCCACCATCCAATCTTTACCCCTAAATCAAAAG
Found at i:141784 original size:91 final size:91
Alignment explanation
Indices: 141622--141935 Score: 247
Period size: 91 Copynumber: 3.4 Consensus size: 91
141612 TAATTTAGAA
* * * *
141622 GGGCAGATTGAAGCCACCATCTAATCTTTCACCCCT-AATCCAAAGGGGTAGATTAAAGTCACCA
1 GGGCAGATTGAAGCCACCATCCAATCTTT-TCCCCTAAATCCAAAGAGGTAGATTAAAGACACCA
* * *
141686 TCCAATCT-TATATCCTTAAATCAAAAG
65 TACAATCTCT-TACCCCTAAATCAAAAG
* * ** * * *
141713 GGGCAGGTTGAAGCCACCATCCAATCTTTTTCCCTAAATTTAGAGAGGTAGATTGAAGACATCAT
1 GGGCAGATTGAAGCCACCATCCAATCTTTTCCCCTAAATCCAAAGAGGTAGATTAAAGACACCAT
* *
141778 ATAATCTCTTACCCCTAAATCAAGAG
66 ACAATCTCTTACCCCTAAATCAAAAG
* * * * ** * * * *
141804 GGGCATATTGAAGTCACCGTACAATCTTTTACCCCTAAATATAAAGGGGAAGATTAAAGCCACTA
1 GGGCAGATTGAAGCCACCATCCAATCTTTT-CCCCTAAATCCAAAGAGGTAGATTAAAGACACCA
* * * * * *
141869 TCCAACCTTTTACCCTTAAATCCAGAG
65 TACAATCTCTTACCCCTAAATCAAAAG
* * * *
141896 GGGTA-ATTGAACCCATCATCCAATCTTTTACTCCTAAATC
1 GGGCAGATTGAAGCCACCATCCAATCTTTT-CCCCTAAATC
141936 AATAGGGGCA
Statistics
Matches: 176, Mismatches: 44, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
90 4 0.02
91 121 0.69
92 51 0.29
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (91 bp):
GGGCAGATTGAAGCCACCATCCAATCTTTTCCCCTAAATCCAAAGAGGTAGATTAAAGACACCAT
ACAATCTCTTACCCCTAAATCAAAAG
Found at i:141864 original size:137 final size:136
Alignment explanation
Indices: 141613--141975 Score: 367
Period size: 137 Copynumber: 2.6 Consensus size: 136
141603 TTCGACAACT
* * *
141613 AATTTAGA-AGGGCAGATTGAAGCCACCATCTAATCTTTCACCCCT-AATCCAAAGGGGTAGATT
1 AATTTAGAGA-GGTAGATTGAAGCCATCATCTAATCTTT-ACCCCTAAAT-CAAAGGGGCAGATT
* * * * * * * *
141676 AAAGTCACCATCCAATCTTATATCCTTAAATCAAAAGGGGCAGGTTGAAGCCACCATCCAATCTT
63 GAAGTCACCATACAATCTTATACCCCTAAATCAAAAGGGGAAGATTAAAGCCACCATCCAACCTT
*
141741 TTTCCC-TA
128 TTACCCTTA
* * *
141749 AATTTAGAGAGGTAGATTGAAGACATCATATAATCTCTTACCCCTAAATCAAGAGGGGCATATTG
1 AATTTAGAGAGGTAGATTGAAGCCATCATCTAATCT-TTACCCCTAAATCAA-AGGGGCAGATTG
* * *
141814 AAGTCACCGTACAATCTTTTACCCCTAAAT-ATAAAGGGGAAGATTAAAGCCACTATCCAACCTT
64 AAGTCACCATACAATCTTATACCCCTAAATCA-AAAGGGGAAGATTAAAGCCACCATCCAACCTT
141878 TTACCCTTA
128 TTACCCTTA
** * * * *
141887 AATCCAGAGGGGTA-ATTGAACCCATCATCCAATCTTTTACTCCTAAATCAATAGGGGCAGATTG
1 AATTTAGAGAGGTAGATTGAAGCCATCATCTAATC-TTTACCCCTAAATCAA-AGGGGCAGATTG
* *
141951 AAGCCACACACACAACTCTTATACC
64 AAGTCAC-CATACAA-TCTTATACC
141976 TTAAAAACTA
Statistics
Matches: 186, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
136 40 0.22
137 119 0.64
138 19 0.10
139 8 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (136 bp):
AATTTAGAGAGGTAGATTGAAGCCATCATCTAATCTTTACCCCTAAATCAAAGGGGCAGATTGAA
GTCACCATACAATCTTATACCCCTAAATCAAAAGGGGAAGATTAAAGCCACCATCCAACCTTTTA
CCCTTA
Found at i:145768 original size:46 final size:45
Alignment explanation
Indices: 145650--145949 Score: 282
Period size: 46 Copynumber: 6.6 Consensus size: 45
145640 TTCGACAGCT
* *
145650 AATC-AGAAGGGCAGATTGAAGCCACCATCCAATCTTCCACCCCT-
1 AATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTT-TACCCCTA
* *
145694 AATCCAGAGGGGTAGATTGAAGCCACCATCCAATCTTATACCCCTA
1 AATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTT-TACCCCTA
* * *
145740 AATCAATAGGGGCAAATTGAAGCCACCATCTAATCTTTTACCCCTA
1 AATCAAGAGGGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTA
* * * * ** *
145786 AATCTAGAGAGGCAGATTGAAGCTATCATATAATCGCTTACCCCTA
1 AATCAAGAGGGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTA
* * * * *
145832 AATCCAA-AGGGGCATATTAAAGTCACCGTACAATCTTTTACCCCTA
1 AAT-CAAGAGGGGCAGATTGAAGCCACCATCCAATC-TTTACCCCTA
* * * * * *
145878 AATCCAGAGGAGAAAATTGAGGCCACTATCCAATCTTTAACCCCTA
1 AATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTT-ACCCCTA
*
145924 AATCAAGAGGGGTAGATTGAAGCCAC
1 AATCAAGAGGGGCAGATTGAAGCCAC
145950 ACACAACTTT
Statistics
Matches: 206, Mismatches: 44, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
44 4 0.02
45 41 0.20
46 157 0.76
47 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (45 bp):
AATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTACCCCTA
Found at i:145913 original size:138 final size:137
Alignment explanation
Indices: 145688--145946 Score: 338
Period size: 138 Copynumber: 1.9 Consensus size: 137
145678 CCAATCTTCC
* * * * * * *
145688 ACCCCTAATCCAGAGGGGTAGATTGAAGCCACCATCCAATCTTATACCCCTAAATCAATAGGGGC
1 ACCCCTAATCCAAAGGGGCAGATTAAAGCCACCATACAATCTTATACCCCTAAATCAAGAGGAGA
* * *
145753 AAATTGAAGCCACCATCTAATCTTTTACCCCTAAATCTAGAGAGGCAGATTGAAGCTATCATATA
66 AAATTGAAGCCACCATCCAATCTTTAACCCCTAAATCAAGAGAGGCAGATTGAAGCTATCATATA
145818 ATCGCTT
131 ATCGCTT
* * * * *
145825 ACCCCTAAATCCAAAGGGGCATATTAAAGTCACCGTACAATCTTTTACCCCTAAATCCAGAGGAG
1 ACCCCT-AATCCAAAGGGGCAGATTAAAGCCACCATACAATCTTATACCCCTAAATCAAGAGGAG
* * * *
145890 AAAATTGAGGCCACTATCCAATCTTTAACCCCTAAATCAAGAGGGGTAGATTGAAGC
65 AAAATTGAAGCCACCATCCAATCTTTAACCCCTAAATCAAGAGAGGCAGATTGAAGC
145947 CACACACAAC
Statistics
Matches: 102, Mismatches: 19, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
137 6 0.06
138 96 0.94
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (137 bp):
ACCCCTAATCCAAAGGGGCAGATTAAAGCCACCATACAATCTTATACCCCTAAATCAAGAGGAGA
AAATTGAAGCCACCATCCAATCTTTAACCCCTAAATCAAGAGAGGCAGATTGAAGCTATCATATA
ATCGCTT
Found at i:147905 original size:520 final size:520
Alignment explanation
Indices: 146922--147965 Score: 2007
Period size: 520 Copynumber: 2.0 Consensus size: 520
146912 TTGAGTGTAG
146922 CCACTGACGATGGCCTCCGAGTAATCAACATTCATGAGAGCCTCATCAAAAAAGGGGAAAACAAA
1 CCACTGACGATGGCCTCCGAGTAATCAACATTCATGAGAGCCTCATCAAAAAAGGGGAAAACAAA
*
146987 AGAGTTTCTTTTTTGAAAACCCTAAAAGATGAGGGTTTTCATTTTTAGGGACTTAAGATTGGATC
66 AGAGTTTCTTTTTTGAAAACCCTAAAAGACGAGGGTTTTCATTTTTAGGGACTTAAGATTGGATC
147052 TAGTGGATTTCGATCCTAGATCTGAATTTTGGGTTAGAAAGGGTTGAAATGTCTTTTGAAGATCT
131 TAGTGGATTTCGATCCTAGATCTGAATTTTGGGTTAGAAAGGGTTGAAATGTCTTTTGAAGATCT
* * *
147117 TAGCCACCATATGTGACGGTCACTGTCGTCGATGACAGTGACCAACGGTGATGCTCACAGCGGGG
196 TAGCCACCATATGTGACGGTCACTGTCATCGATAACAGTGACCAACGGAGATGCTCACAGCGGGG
147182 CAAATATAGGTTCCTTAATTGGATTTGGGACCCAAAGAGAGGAAAAAAGGAAAGATGAGAGGTTT
261 CAAATATAGGTTCCTTAATTGGATTTGGGACCCAAAGAGAGGAAAAAAGGAAAGATGAGAGGTTT
147247 TTTTAAAAGGGGCAAGGGAAATGAATTTTTTTGTTAAAAAATTGGATTATATAGCCCCCATTAAA
326 TTTTAAAAGGGGCAAGGGAAATGAATTTTTTTGTTAAAAAATTGGATTATATAGCCCCCATTAAA
*
147312 TGGCACCACTTTGGGCAAACTCTAATGGCCTCAAAATGATGTCGTTTTGAACTTCAACCTGAATA
391 TGGCACCACTTTGGGCAAACTCTAATGGCCTCAAAATGATGTCATTTTGAACTTCAACCTGAATA
147377 CCCGACCCGATCACAAGGGGATCCGCGTGTTTTCATAAAATGGTTTATTTATTTTCGTAGTCCTT
456 CCCGACCCGATCACAAGGGGATCCGCGTGTTTTCATAAAATGGTTTATTTATTTTCGTAGTCCTT
147442 CCACTGACGATGGCCTCCGAGTAATCAACATTCATGAGAGCCTCATCAAAAAAGGGGAAAACAAA
1 CCACTGACGATGGCCTCCGAGTAATCAACATTCATGAGAGCCTCATCAAAAAAGGGGAAAACAAA
147507 AGAGTTTCTTTTTTGAAAACCCTAAAAGACGAGGGTTTTCATTTTTAGGGACTTAAGATTGGATC
66 AGAGTTTCTTTTTTGAAAACCCTAAAAGACGAGGGTTTTCATTTTTAGGGACTTAAGATTGGATC
*
147572 TAGTGGATTTCGATCCTAGATCTGGATTTTGGGTTAGAAAGGGTTGAAATGTCTTTTGAAGATCT
131 TAGTGGATTTCGATCCTAGATCTGAATTTTGGGTTAGAAAGGGTTGAAATGTCTTTTGAAGATCT
* *
147637 TAGCCACCATATGTGACGGTCACTGTCATCGATAACGGTGACCAACGGAGATGCTCACGGCGGGG
196 TAGCCACCATATGTGACGGTCACTGTCATCGATAACAGTGACCAACGGAGATGCTCACAGCGGGG
147702 CAAATATAGGTTCCTTAATTGGATTTGGGACCCAAAGAGAGGAAAAAAGGAAAGATGAGAGGTTT
261 CAAATATAGGTTCCTTAATTGGATTTGGGACCCAAAGAGAGGAAAAAAGGAAAGATGAGAGGTTT
147767 TTTTAAAAGGGGCAAGGGAAATGAATTTTTTTGTTAAAAAATTGGATTATATAGCCCCCATTAAA
326 TTTTAAAAGGGGCAAGGGAAATGAATTTTTTTGTTAAAAAATTGGATTATATAGCCCCCATTAAA
147832 TGGCACCACTTTGGGCAAACTCTAATGGCCTCAAAATGATGTCATTTTGAACTTCAACCTGAATA
391 TGGCACCACTTTGGGCAAACTCTAATGGCCTCAAAATGATGTCATTTTGAACTTCAACCTGAATA
*
147897 CTCGACCCGATCACAAGGGGATCCGCGTGTTTTCATAAAATGGTTTATTTATTTTCGTAGTCCTT
456 CCCGACCCGATCACAAGGGGATCCGCGTGTTTTCATAAAATGGTTTATTTATTTTCGTAGTCCTT
147962 CCAC
1 CCAC
147966 ATTTTAAGAG
Statistics
Matches: 515, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
520 515 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (520 bp):
CCACTGACGATGGCCTCCGAGTAATCAACATTCATGAGAGCCTCATCAAAAAAGGGGAAAACAAA
AGAGTTTCTTTTTTGAAAACCCTAAAAGACGAGGGTTTTCATTTTTAGGGACTTAAGATTGGATC
TAGTGGATTTCGATCCTAGATCTGAATTTTGGGTTAGAAAGGGTTGAAATGTCTTTTGAAGATCT
TAGCCACCATATGTGACGGTCACTGTCATCGATAACAGTGACCAACGGAGATGCTCACAGCGGGG
CAAATATAGGTTCCTTAATTGGATTTGGGACCCAAAGAGAGGAAAAAAGGAAAGATGAGAGGTTT
TTTTAAAAGGGGCAAGGGAAATGAATTTTTTTGTTAAAAAATTGGATTATATAGCCCCCATTAAA
TGGCACCACTTTGGGCAAACTCTAATGGCCTCAAAATGATGTCATTTTGAACTTCAACCTGAATA
CCCGACCCGATCACAAGGGGATCCGCGTGTTTTCATAAAATGGTTTATTTATTTTCGTAGTCCTT
Found at i:151458 original size:28 final size:28
Alignment explanation
Indices: 151420--151474 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
151410 AAATGAGCAT
151420 CATGACCTTTGGGTCAAC-AGGAAGTAAG
1 CATGACCTTTGGGTCAACAAGG-AGTAAG
*
151448 CATGACCTTTGGGTTAACAAGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
151475 ATCGAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:154551 original size:19 final size:19
Alignment explanation
Indices: 154527--154564 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
154517 GTTAAATTGA
154527 AAGTTTTTAGCTTAAGGGC
1 AAGTTTTTAGCTTAAGGGC
154546 AAGTTTTTAGCTTAAGGGC
1 AAGTTTTTAGCTTAAGGGC
154565 TAAATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (19 bp):
AAGTTTTTAGCTTAAGGGC
Found at i:155111 original size:34 final size:34
Alignment explanation
Indices: 155064--155142 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
155054 CAGTGTTTTG
*
155064 GTGTGTT--ATGGACTAGCTCTTA-CGAGCATTTA
1 GTGTGTTGGATGGACTAGCTCTTATC-AACATTTA
* *
155096 TTGTGTTGGATGGACTAGCTCTTATCAACATTTG
1 GTGTGTTGGATGGACTAGCTCTTATCAACATTTA
155130 GTGTGTTGGATGG
1 GTGTGTTGGATGG
155143 TTAGCCGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 6 0.15
34 33 0.82
35 1 0.03
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (34 bp):
GTGTGTTGGATGGACTAGCTCTTATCAACATTTA
Found at i:155310 original size:26 final size:26
Alignment explanation
Indices: 155271--155335 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
155261 GAGTTGTGAT
* *
155271 TGATAGGAATTCTAATAATAACCTTG
1 TGATAGGAACTCTAATAATAACCTTA
*
155297 TGATAGGAACTCTATTAATAACCTTA
1 TGATAGGAACTCTAATAATAACCTTA
*
155323 TGAGAGGAACTCT
1 TGATAGGAACTCT
155336 GTTTATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (26 bp):
TGATAGGAACTCTAATAATAACCTTA
Found at i:161475 original size:136 final size:140
Alignment explanation
Indices: 161222--161520 Score: 385
Period size: 137 Copynumber: 2.1 Consensus size: 140
161212 AAATCTATTT
* * * *
161222 AATTCTATTTTTTAATTTAAATTTATTGCTTTAAATTCAAATGAACTAATTATTTTTTCTTTCGA
1 AATTCTATTTTTTAATTTAAATATATTACTTTAAATTCAAATGAACTAATTATTTTATCTTTCAA
* * * *
161287 TGAAATTCTATTTTTTTTAAATTTAAATGTATTGCCTTAAATTGATTTATTCTTTAATTA-T-TT
66 TCAAATTCTATTTTTTTTAAATTTAAATATATTGCCTTAAATTAACTTATTCTTTAATTATTATT
161350 -TTTTAATTA
131 CTTTTAATTA
* * ***
161359 AATTCTATTTTTTAATTTAAATATATTACTTTAAATTGATTTATTCTCTAATTA-TTTATCTTTC
1 AATTCTATTTTTTAATTTAAATATATTACTTTAAATTCA--AATGAACTAATTATTTTATCTTTC
*
161423 AATCAAATTCTA-TTTTTTT-AATTTAAATATATTGCTTTAAATTAACTTATTCTTTAATTATTT
64 AATCAAATTCTATTTTTTTTAAATTTAAATATATTGCCTTAAATTAACTTATTCTTTAATTA-TT
161486 ATTCTTTTAATTA
128 ATTCTTTTAATTA
161499 AATTCTATTTACTTTAATTTAA
1 AATTCTATTT--TTTAATTTAA
161521 TTTGTTGCTT
Statistics
Matches: 140, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
136 37 0.26
137 43 0.31
138 20 0.14
139 11 0.08
140 19 0.14
142 10 0.07
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (140 bp):
AATTCTATTTTTTAATTTAAATATATTACTTTAAATTCAAATGAACTAATTATTTTATCTTTCAA
TCAAATTCTATTTTTTTTAAATTTAAATATATTGCCTTAAATTAACTTATTCTTTAATTATTATT
CTTTTAATTA
Found at i:161494 original size:16 final size:15
Alignment explanation
Indices: 161326--161498 Score: 57
Period size: 18 Copynumber: 10.3 Consensus size: 15
161316 TATTGCCTTA
161326 AATTGATTTATTCTTT
1 AATT-ATTTATTCTTT
161342 AATTA-TT-TT-TTT
1 AATTATTTATTCTTT
*
161354 AATTAAATTCTATTTTTT
1 AATT--ATT-TATTCTTT
*
161372 AATTTAAATATATTACTTT
1 AA-TT--ATTTATT-CTTT
*
161391 AAATTGATTTATTCTCT
1 -AATT-ATTTATTCTTT
161408 AATTATTTA-TCTTT
1 AATTATTTATTCTTT
* *
161422 CAATCAAATTCTATTTTTTT
1 -AAT--TATT-TA-TTCTTT
*
161442 AATTTAAATATATTGCTTT
1 AA-TT--ATTTATT-CTTT
*
161461 AAATTAACTTATTCTTT
1 -AATT-ATTTATTCTTT
161478 AATTATTTATTCTTTT
1 AATTATTTATTC-TTT
161494 AATTA
1 AATTA
161499 AATTCTATTT
Statistics
Matches: 122, Mismatches: 14, Indels: 42
0.69 0.08 0.24
Matches are distributed among these distances:
12 7 0.06
13 2 0.02
14 7 0.06
15 17 0.14
16 21 0.17
17 12 0.10
18 25 0.20
19 20 0.16
20 11 0.09
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (15 bp):
AATTATTTATTCTTT
Found at i:161533 original size:71 final size:70
Alignment explanation
Indices: 161222--161536 Score: 342
Period size: 70 Copynumber: 4.5 Consensus size: 70
161212 AAATCTATTT
* * * * *
161222 AATTCTATTTTTTAATTTAAATTTATTGCTTTAAATTCAAATGA-AC--TAATTATTTTTTCTTT
1 AATTCTATTTTTTAATTTAAATATATTGCTTTAAATT-AATTTATTCTTTAATTATTTATTCTTT
* *
161284 CGATGA
65 CAATTA
* * *
161290 AATTCTATTTTTTTTAAATTTAAATGTATTGCCTTAAATTGATTTATTCTTTAATTA-TT-TT-T
1 AATTCTA--TTTTTT-AATTTAAATATATTGCTTTAAATTAATTTATTCTTTAATTATTTATTCT
161352 TT-AATTA
63 TTCAATTA
* * *
161359 AATTCTATTTTTTAATTTAAATATATTACTTTAAATTGATTTATTCTCTAATTATTTA-TCTTTC
1 AATTCTATTTTTTAATTTAAATATATTGCTTTAAATTAATTTATTCTTTAATTATTTATTCTTTC
*
161423 AATCA
66 AATTA
*
161428 AATTCTATTTTTTTAATTTAAATATATTGCTTTAAATTAACTTATTCTTTAATTATTTATTCTTT
1 AATTCTA-TTTTTTAATTTAAATATATTGCTTTAAATTAATTTATTCTTTAATTATTTATTCTTT
*
161493 TAATTA
65 CAATTA
* *
161499 AATTCTATTTACTTTAATTT-AATTTGTTGCTTTAAATT
1 AATTCTATTT--TTTAATTTAAATATATTGCTTTAAATT
161537 TATCTAGGGA
Statistics
Matches: 212, Mismatches: 21, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
66 37 0.17
67 9 0.04
68 10 0.05
69 21 0.10
70 62 0.29
71 57 0.27
72 10 0.05
73 6 0.03
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (70 bp):
AATTCTATTTTTTAATTTAAATATATTGCTTTAAATTAATTTATTCTTTAATTATTTATTCTTTC
AATTA
Found at i:161996 original size:18 final size:18
Alignment explanation
Indices: 161965--162000 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
161955 AATTTAAAGG
161965 AATAAATTTAAATTAAAA
1 AATAAATTTAAATTAAAA
161983 AATAGAATTT-AATTAAAA
1 AATA-AATTTAAATTAAAA
162001 GAAGACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATAAATTTAAATTAAAA
Found at i:164217 original size:46 final size:46
Alignment explanation
Indices: 164150--164242 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
164140 TGTTTAGTGA
164150 GTAAGGCTTGTCGCACATCTTTTCCACTCGTATAAAATTTGTGAAC
1 GTAAGGCTTGTCGCACATCTTTTCCACTCGTATAAAATTTGTGAAC
164196 GTAAGGCTTGTCGCACATCTTTTCCACTCGTATAAAATTTGTGAAC
1 GTAAGGCTTGTCGCACATCTTTTCCACTCGTATAAAATTTGTGAAC
164242 G
1 G
164243 ACTCTTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (46 bp):
GTAAGGCTTGTCGCACATCTTTTCCACTCGTATAAAATTTGTGAAC
Found at i:170434 original size:12 final size:12
Alignment explanation
Indices: 170399--170437 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
170389 ATAAATACAA
*
170399 TATAAATCAACC
1 TATAAATCAGCC
* *
170411 TATTAATTAGCC
1 TATAAATCAGCC
170423 TATAAATCAGCC
1 TATAAATCAGCC
170435 TAT
1 TAT
170438 GATTCTGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (12 bp):
TATAAATCAGCC
Found at i:175254 original size:18 final size:17
Alignment explanation
Indices: 175226--175260 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
175216 AGTAAAAAAT
*
175226 TTAAAGTATTTTATTTA
1 TTAAAGTATTTAATTTA
175243 TTAAATGTATTTAATTTA
1 TTAAA-GTATTTAATTTA
175261 CTGAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TTAAAGTATTTAATTTA
Found at i:183684 original size:47 final size:47
Alignment explanation
Indices: 183631--183730 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 47
183621 TTATAAGGGA
*** *
183631 AATAAAAACCTAATATAATAGGGA-AAATAAGTAAAACTAAAACTCTT
1 AATAAAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTC-T
* *
183678 AAT-AAAACCTGATATAATAAAAATAAATAAATAAATCTAAAACTCT
1 AATAAAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTCT
183724 AA-AAAAA
1 AATAAAAA
183731 GCGTCCATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
46 23 0.51
47 22 0.49
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (47 bp):
AATAAAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTCT
Found at i:183687 original size:46 final size:47
Alignment explanation
Indices: 183635--183723 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 47
183625 AAGGGAAATA
*** *
183635 AAAACCTAATATAATAGGGA-AAATAAGTAAAACTAAAACTCTTAAT
1 AAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTCTTAAT
* *
183681 AAAACCTGATATAATAAAAATAAATAAATAAATCTAAAACTCT
1 AAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTCT
183724 AAAAAAAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 16 0.44
47 20 0.56
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (47 bp):
AAAACCTAATATAATAAAAATAAATAAATAAAACTAAAACTCTTAAT
Found at i:195309 original size:63 final size:63
Alignment explanation
Indices: 195185--195326 Score: 169
Period size: 63 Copynumber: 2.3 Consensus size: 63
195175 TGCACATTCT
* * *
195185 TTTCCTGCACCAATACAATGATAACTAATTTATTTTACACAAGCATAACAACACGCACAATCA
1 TTTCCTGCACCAACACAATGATAACTAATTCATTTTACACAAGCATAACAACACACACAATCA
* * * * * **
195248 TTTCCTGCACCAACATAGTGATCACTAATTCATTTTACACAAGCATCACAGCACATGCAATCA
1 TTTCCTGCACCAACACAATGATAACTAATTCATTTTACACAAGCATAACAACACACACAATCA
*
195311 -TTCCATGCACCGACAC
1 TTTCC-TGCACCAACAC
195327 CTTCTCTAGG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 4 0.06
63 62 0.94
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (63 bp):
TTTCCTGCACCAACACAATGATAACTAATTCATTTTACACAAGCATAACAACACACACAATCA
Found at i:197021 original size:25 final size:21
Alignment explanation
Indices: 196999--197040 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
196989 ATTTATAGCT
196999 AATGTAAATAAAAAACTAAATAG
1 AATG-AAATAAAAAA-TAAATAG
*
197022 AATGAAATAATAAATAAAT
1 AATGAAATAAAAAATAAAT
197041 GGATTTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (21 bp):
AATGAAATAAAAAATAAATAG
Found at i:197485 original size:34 final size:34
Alignment explanation
Indices: 197442--197519 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
197432 GTGAACTCAT
*
197442 GGAAAATTAAACATAGATTATTAAATAAATTGTA
1 GGAAAATTAAACATAGATTATTAAAAAAATTGTA
*
197476 GGAAAATTAAACATAGATTGTTAAAAAAATTGTA
1 GGAAAATTAAACATAGATTATTAAAAAAATTGTA
197510 GGAAAATTAA
1 GGAAAATTAA
197520 GGTAGGCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (34 bp):
GGAAAATTAAACATAGATTATTAAAAAAATTGTA
Found at i:198093 original size:50 final size:52
Alignment explanation
Indices: 198012--198155 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 52
198002 AGAAATGTAA
* *
198012 GGTGAATGTTTAGCAGGCCTT-GA-CC-AGTGAATGTTTAGCAAGCTTTAAGCC
1 GGTGAATGTTTAGCAAG-CTTCGAGCCGA-TGAATGTTTAGCAAGCCTTAAGCC
* * * *
198063 GGTGACT-TTTAG-AGGCTTCGAGCCGATGAATGTTTAGCAGGCCTTGAGCC
1 GGTGAATGTTTAGCAAGCTTCGAGCCGATGAATGTTTAGCAAGCCTTAAGCC
* *
198113 GGTGAATGTTTAGCAAGCTTTGAGCCGATGAATGTTTAACAAG
1 GGTGAATGTTTAGCAAGCTTCGAGCCGATGAATGTTTAGCAAG
198156 AACTATGTAC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
48 3 0.04
49 5 0.06
50 34 0.43
51 12 0.15
52 25 0.32
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (52 bp):
GGTGAATGTTTAGCAAGCTTCGAGCCGATGAATGTTTAGCAAGCCTTAAGCC
Found at i:198111 original size:26 final size:26
Alignment explanation
Indices: 198014--198150 Score: 149
Period size: 26 Copynumber: 5.4 Consensus size: 26
198004 AAATGTAAGG
198014 TGAATGTTTAGCAGGCCTTGA-CC-A
1 TGAATGTTTAGCAGGCCTTGAGCCGA
* * * *
198038 GTGAATGTTTAGCAAGCTTTAAGCCGG
1 -TGAATGTTTAGCAGGCCTTGAGCCGA
*
198065 TGACT-TTTAG-AGG-CTTCGAGCCGA
1 TGAATGTTTAGCAGGCCTT-GAGCCGA
*
198089 TGAATGTTTAGCAGGCCTTGAGCCGG
1 TGAATGTTTAGCAGGCCTTGAGCCGA
* *
198115 TGAATGTTTAGCAAGCTTTGAGCCGA
1 TGAATGTTTAGCAGGCCTTGAGCCGA
198141 TGAATGTTTA
1 TGAATGTTTA
198151 ACAAGAACTA
Statistics
Matches: 92, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.02
24 11 0.12
25 28 0.30
26 48 0.52
27 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (26 bp):
TGAATGTTTAGCAGGCCTTGAGCCGA
Found at i:202640 original size:123 final size:122
Alignment explanation
Indices: 202322--202688 Score: 585
Period size: 122 Copynumber: 3.0 Consensus size: 122
202312 AATGTTTTCG
202322 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTT-ATCAAACCTTC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAAT-AAACCTTC
*
202386 CATATATTTCTTTAAAGGAA-ATTTTCCATTTTAATATGAGATATTATATAAAAGGAAA
65 CATATATTTCTCTAAAGGAATA-TTTCCATTTTAATATGAGATATTATATAAAAGGAAA
202444 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
* *
202509 ATATATTTCTCTAAGGGAATATTTCCATTTTAATATGATATATTATATAAAAGGAAA
66 ATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
* * * *
202566 TTGAATATTAAAAACATGGAAGTTAATATCATTTTGGAAATGATATAATATTTTAATAAACCTTC
1 TTAAATATT-AAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* * * * *
202631 CATATATTTCTCTAAAAGTATATTTCTATTTTAATATGAGATATTAAATAAAAAGAAA
65 CATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
202689 ATATAGCAAA
Statistics
Matches: 228, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
122 122 0.54
123 106 0.46
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (122 bp):
TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
ATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
Found at i:212438 original size:122 final size:122
Alignment explanation
Indices: 212302--212545 Score: 346
Period size: 122 Copynumber: 2.0 Consensus size: 122
212292 AATGATTCCG
* *
212302 TTAAATATTAAAACATAGAAATTAATATCCTTTTGGAAA-TGATATAATGTTTTAACAAATCTTC
1 TTAAATATTAAAACATAGAAATTAATATCCTGTTGGAAAGT-ATATAATGTTTTAACAAACCTTC
* * * *
212366 CATATATTTCTTTAAAGGAAAATTTCCATTTTTATATGAGATATTATATAAAAGGAAA
65 CATATATTTCTCTAAAGGAAAATTTCCATTTTAATATGAGATATTAAATAAAAAGAAA
* * **
212424 TTAAATATTAAAACATGGAAGTTAATATCCTGTTGGAAAGTATATAATGTTTTAGTAAACCTTCC
1 TTAAATATTAAAACATAGAAATTAATATCCTGTTGGAAAGTATATAATGTTTTAACAAACCTTCC
* * * *
212489 ATCTATTTCTCTAAGGGAATATTTCTATTTTAATATGAGATATTAAATAAAAAGAAA
66 ATATATTTCTCTAAAGGAAAATTTCCATTTTAATATGAGATATTAAATAAAAAGAAA
212546 AGATAGCAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
122 106 0.99
123 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (122 bp):
TTAAATATTAAAACATAGAAATTAATATCCTGTTGGAAAGTATATAATGTTTTAACAAACCTTCC
ATATATTTCTCTAAAGGAAAATTTCCATTTTAATATGAGATATTAAATAAAAAGAAA
Found at i:224019 original size:24 final size:24
Alignment explanation
Indices: 223962--224019 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
223952 GGGTTATAGA
223962 AAATGAAATTAAAATAGCAATCCAC
1 AAAT-AAATTAAAATAGCAATCCAC
* *
223987 -AATAGAATTATAATCAG-AATTCAC
1 AAATA-AATTAAAAT-AGCAATCCAC
224011 AAATAAATT
1 AAATAAATT
224020 CTCGATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.04
24 21 0.75
25 6 0.21
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATAAATTAAAATAGCAATCCAC
Found at i:232321 original size:9 final size:9
Alignment explanation
Indices: 232307--232377 Score: 56
Period size: 9 Copynumber: 7.9 Consensus size: 9
232297 GAATAGCCCC
232307 ATTAATAAT
1 ATTAATAAT
232316 ATTAATAACT
1 ATTAATAA-T
* *
232326 GTT-TTAAT
1 ATTAATAAT
232334 GA-TAATAAT
1 -ATTAATAAT
*
232343 AATAATAAT
1 ATTAATAAT
*
232352 AATAATAAT
1 ATTAATAAT
*
232361 ATTAATTAT
1 ATTAATAAT
*
232370 TTTAATAA
1 ATTAATAA
232378 AAAAAAGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 3 0.06
9 44 0.88
10 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (9 bp):
ATTAATAAT
Found at i:232343 original size:3 final size:3
Alignment explanation
Indices: 232330--232366 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
232320 ATAACTGTTT
* *
232330 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
232367 TATTTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:232806 original size:65 final size:65
Alignment explanation
Indices: 232693--232826 Score: 196
Period size: 65 Copynumber: 2.1 Consensus size: 65
232683 GGTACCACCA
* * * *
232693 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAGGCGCGTGAAGCGGAGCCAC
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
* * * *
232758 GGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAGGCGCGTGCAGCGAAGCCAC
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
232823 GGTG
1 GGTG
232827 GTCGGACGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.15
Consensus pattern (65 bp):
GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
Found at i:233525 original size:29 final size:29
Alignment explanation
Indices: 233492--233651 Score: 133
Period size: 29 Copynumber: 5.5 Consensus size: 29
233482 CAAATTTTTG
*
233492 AAAATTCCATTTTTACCCCCGTACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
** * * *
233521 AAAATTCCATTTTTGACCCCAAAAATTTCG
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
* *
233551 AAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* **** *
233580 AAAATTCCTTTTTTGACCTAAAAACTTTC-
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
* * *
233609 AAAATTCTATTTTTAACCCCGATCTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
*
233638 GAAATTCCATTTTT
1 AAAATTCCATTTTT
233652 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 31, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
28 7 0.07
29 59 0.61
30 31 0.32
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCGAACTTCCA
Found at i:233536 original size:58 final size:56
Alignment explanation
Indices: 233464--233651 Score: 207
Period size: 58 Copynumber: 3.2 Consensus size: 56
233454 CAAACTTTTG
*
233464 AAAATTCCA-TTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTCCA
1 AAAATTCCATTTTTGA-CCCAAAATTTTGAAAATTCCATTTTTACCCCCG-ACTTCCA
* * *
233521 AAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGA-CCC-AAAATTTTGAAAATTCCATTTTTACCCCCG-ACTTCCA
* * * * * *
233580 AAAATTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCA
1 AAAATTCCATTTTTGACC-CAAAATTTTGAAAATTCCATTTTTACCCCCGA-CTTCCA
*
233638 GAAATTCCATTTTT
1 AAAATTCCATTTTT
233652 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
57 10 0.09
58 52 0.47
59 48 0.44
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (56 bp):
AAAATTCCATTTTTGACCCAAAATTTTGAAAATTCCATTTTTACCCCCGACTTCCA
Found at i:233568 original size:59 final size:57
Alignment explanation
Indices: 233464--233651 Score: 213
Period size: 59 Copynumber: 3.2 Consensus size: 57
233454 CAAACTTTTG
* * *
233464 AAAATTCCA-TTTTGATCCC-AAATTTTTGAAAATTCCATTTTTACCCCCGTACTTCCA
1 AAAATTCCATTTTTGA-CCCAAAAATTTCGAAAATTTCATTTTTACCCCCG-ACTTCCA
*
233521 AAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGA-CCCAAAAATTTCGAAAATTTCATTTTTACCCCCG-ACTTCCA
* * *
233580 AAAATTCCTTTTTTGACCTAAAAACTTTC-AAAA-TTCTATTTTTAACCCCGATCTTCCA
1 AAAATTCCATTTTTGACCCAAAAA-TTTCGAAAATTTC-ATTTTTACCCCCGA-CTTCCA
*
233638 GAAATTCCATTTTT
1 AAAATTCCATTTTT
233652 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
57 13 0.11
58 49 0.43
59 52 0.46
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCCAAAAATTTCGAAAATTTCATTTTTACCCCCGACTTCCA
Found at i:233799 original size:65 final size:65
Alignment explanation
Indices: 233686--233819 Score: 196
Period size: 65 Copynumber: 2.1 Consensus size: 65
233676 GGTACCACCA
* * * *
233686 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAGGCGCGTGAAGCGGAGCCAC
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
* * * *
233751 GGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAGGCGCGTGCAGCGAAGCCAC
1 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
233816 GGTG
1 GGTG
233820 GTCGGACGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.15
Consensus pattern (65 bp):
GGTGACGGACGTCGAAGCATGGTGGTCACGCGCATCGATCGACAAGGCGCGTGAAGCGAAGCCAC
Found at i:234518 original size:29 final size:29
Alignment explanation
Indices: 234485--234893 Score: 197
Period size: 29 Copynumber: 14.0 Consensus size: 29
234475 CAAATTTTTG
*
234485 AAAATTCCATTTTTACCCCCGTACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
** * * *
234514 AAAATTCCATTTTTGACCCCAAAAATTTCG
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
* *
234544 AAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* **** *
234573 AAAATTCCTTTTTTGACCTAAAAACTTTC-
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
* * *
234602 AAAATTCTATTTTTAACCCCGATCTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* * **
234631 GAAATTCCATTTTTTA-CCTCGAAACTT-TT
1 AAAATTCCA-TTTTTACCCCCG-AACTTCCA
** * *
234660 AAAATTATATTTTTACCCTCGATCTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
*
234689 AAAATTCCATTTTTGA-CCCCGAAACCTCCA
1 AAAATTCCATTTTT-ACCCCCG-AACTTCCA
* * *
234719 AAAATTACATTTTTACCCTCGAACCTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* * * ** **
234748 AAACTTCCATATTTAAGCCCAAAACTTTAA
1 AAAATTCCAT-TTTTACCCCCGAACTTCCA
* * *
234778 AAAATACCA-TTTTACCCTCTGGA-TGTCCA
1 AAAATTCCATTTTTACCC-CCGAACT-TCCA
* * * * *
234807 AAAACTCTATTTTCGA-CCTCGAAAC-TCTA
1 AAAATTCCATTTT-TACCCCCG-AACTTCCA
* * *
234836 AAAATTCCATTTTTACTCCTGAA-TGTCTA
1 AAAATTCCATTTTTACCCCCGAACT-TCCA
* *
234865 AAAATTCCATCTTTTAACCTCGAACTTCC
1 AAAATTCCAT-TTTTACCCCCGAACTTCC
234894 CCAAAGCTAC
Statistics
Matches: 272, Mismatches: 86, Indels: 43
0.68 0.21 0.11
Matches are distributed among these distances:
28 27 0.10
29 143 0.53
30 100 0.37
31 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCGAACTTCCA
Found at i:234600 original size:993 final size:983
Alignment explanation
Indices: 232674--234644 Score: 3852
Period size: 993 Copynumber: 2.0 Consensus size: 983
232664 NNNNNNNNNN
232674 AGCCACGCGGGTACCACCAGGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAG
1 AGCCACGCGGGTACCACCAGGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAG
232739 GCGCGTGAAGCGGAGCCACGGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAG
66 GCGCGTGAAGCGGAGCCACGGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAG
232804 GCGCGTGCAGCGAAGCCACGGTGGTCGGACGGCTTGGAGTGTCGGCCAAAAGGAGTGTATGAGAG
131 GCGCGTGCAGCGAAGCCACGGTGGTCGGACGGCTTGGAGTGTCGGCCAAAAGGAGTGTATGAGAG
232869 GTTTTTTGGAAGAGGATCTTTTTTTTTTTGAAAAGGGTAAAAAATGAAATTTTTTTTTAAGAAAT
196 GTTTTTTGGAAGAGGATCTTTTTTTTTTTGAAAAGGGTAAAAAATGAAATTTTTTTTTAAGAAAT
232934 AACCTATTTATAGCCATCCAAAACGGTGTCGTTTTGGCATGGCTTCAGAATGCTCAAAACGACGC
261 AACCTATTTATAGCCATCCAAAACGGTGTCGTTTTGGCATGGCTTCAGAATGCTCAAAACGACGC
232999 CGTTTCACTTCATAACCCATGGCCGACCCGAATTCGACCCGACCCACCTGAAAGATCCGCGTGTT
326 CGTTTCACTTCATAACCCATGGCCGACCCGAATTCGACCCGACCCACCTGAAAGATCCGCGTGTT
233064 TTTGAGAAAAGGGATATTTCTGCATTTGGTCCTTTCGCATTTTTTGATTGCTTCAATCAGGTCTT
391 TTTGAGAAAAGGGATATTTCTGCATTTGGTCCTTTCGCATTTTTTGATTGCTTCAATCAGGTCTT
233129 TTTTGTACTTTTAATTAATTTAAATTGGCCCAATAATTTTTCAATGCTTTTCAATTTAGTCCCTT
456 TTTTGTACTTTTAATTAATTTAAATTGGCCCAATAATTTTTCAATGCTTTTCAATTTAGTCCCTT
233194 GACCTTTTGAAATCATCAGGAGCTGCCACGTGTCTTTGTTTTGGTTCATTTATACAAACGATCCC
521 GACCTTTTGAAATCATCAGGAGCTGCCACGTGTCTTTGTTTTGGTTCATTTATACAAACGATCCC
233259 TTTTATTTTTAATTTGTTTTAATTTAATCCTAAAATCAAGTCCTGTTTAATTACAAAATTGACCC
586 TTTTATTTTTAATTTGTTTTAATTTAATCCTAAAATCAAGTCCTGTTTAATTACAAAATTGACCC
233324 AAAATTTTTTCATGGTTTTCAAATTAGTCCTTTGATTTCAGGATGCTCGGGGGGCTACCACGTGT
651 AAAATTTTTTCATGGTTTTCAAATTAGTCCTTTGATTTCAGGATGCTCGGGGGGCTACCACGTGT
233389 CATTTCTTTCTGGTTTTATTGCCTTGAAGGTCCTTAAACTGTCTAAAAATTATATTTTTTACCCC
716 CATTTCTTTCTGGTTTTATTGCCTTGAAGGTCCTTAAACTGTCTAAAAATTATATTTTTTACCCC
233454 CAAACTTTTGAAAATTCCATTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTC
781 CAAACTTTTGAAAATTCCATTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTC
233519 CAAAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAA
846 CAAAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAA
233584 TTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCAGAAATTCCATT
911 TTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCAGAAATTCCATT
233649 TTTNNNNNNNNNNGGAAC
976 TTT----------GGAAC
233667 AGCCACGCGGGTACCACCAGGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAG
1 AGCCACGCGGGTACCACCAGGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAG
233732 GCGCGTGAAGCGGAGCCACGGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAG
66 GCGCGTGAAGCGGAGCCACGGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAG
233797 GCGCGTGCAGCGAAGCCACGGTGGTCGGACGGCTTGGAGTGTCGGCCAAAAGGAGTGTATGAGAG
131 GCGCGTGCAGCGAAGCCACGGTGGTCGGACGGCTTGGAGTGTCGGCCAAAAGGAGTGTATGAGAG
233862 GTTTTTTGGAAGAGGATCTTTTTTTTTTTGAAAAGGGTAAAAAATGAAATTTTTTTTTAAGAAAT
196 GTTTTTTGGAAGAGGATCTTTTTTTTTTTGAAAAGGGTAAAAAATGAAATTTTTTTTTAAGAAAT
233927 AACCTATTTATAGCCATCCAAAACGGTGTCGTTTTGGCATGGCTTCAGAATGCTCAAAACGACGC
261 AACCTATTTATAGCCATCCAAAACGGTGTCGTTTTGGCATGGCTTCAGAATGCTCAAAACGACGC
233992 CGTTTCACTTCATAACCCATGGCCGACCCGAATTCGACCCGACCCACCTGAAAGATCCGCGTGTT
326 CGTTTCACTTCATAACCCATGGCCGACCCGAATTCGACCCGACCCACCTGAAAGATCCGCGTGTT
234057 TTTGAGAAAAGGGATATTTCTGCATTTGGTCCTTTCGCATTTTTTGATTGCTTCAATCAGGTCTT
391 TTTGAGAAAAGGGATATTTCTGCATTTGGTCCTTTCGCATTTTTTGATTGCTTCAATCAGGTCTT
234122 TTTTGTACTTTTAATTAATTTAAATTGGCCCAATAATTTTTCAATGCTTTTCAATTTAGTCCCTT
456 TTTTGTACTTTTAATTAATTTAAATTGGCCCAATAATTTTTCAATGCTTTTCAATTTAGTCCCTT
234187 GACCTTTTGAAATCATCAGGAGCTGCCACGTGTCTTTGTTTTGGTTCATTTATACAAACGATCCC
521 GACCTTTTGAAATCATCAGGAGCTGCCACGTGTCTTTGTTTTGGTTCATTTATACAAACGATCCC
234252 TTTTATTTTTAATTTGTTTTAATTTAATCCTAAAATCAAGTCCTGTTTAATTACAAAATTGACCC
586 TTTTATTTTTAATTTGTTTTAATTTAATCCTAAAATCAAGTCCTGTTTAATTACAAAATTGACCC
234317 AAAATTTTTTCATGGTTTTCAAATTAGTCCTTTGATTTCAGGATGCTCGGGGGGCTACCACGTGT
651 AAAATTTTTTCATGGTTTTCAAATTAGTCCTTTGATTTCAGGATGCTCGGGGGGCTACCACGTGT
234382 CATTTCTTTCTGGTTTTATTGCCTTGAAGGTCCTTAAACTGTCTAAAAATTATATTTTTTACCCC
716 CATTTCTTTCTGGTTTTATTGCCTTGAAGGTCCTTAAACTGTCTAAAAATTATATTTTTTACCCC
234447 CAAACTTTTGAAAATTCCATTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTC
781 CAAACTTTTGAAAATTCCATTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTC
234512 CAAAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAA
846 CAAAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAA
234577 TTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCAGAAATTCCATT
911 TTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCAGAAATTCCATT
234642 TTT
976 TTT
234645 TACCTCGAAA
Statistics
Matches: 978, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
993 978 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (983 bp):
AGCCACGCGGGTACCACCAGGTGACGGACGTCGAAGCATGGTGGTCACGCGCGTCGGTCGACGAG
GCGCGTGAAGCGGAGCCACGGTGACGGACGTTGAAGTATGGTGGTCACGCGCATCGATTGACAAG
GCGCGTGCAGCGAAGCCACGGTGGTCGGACGGCTTGGAGTGTCGGCCAAAAGGAGTGTATGAGAG
GTTTTTTGGAAGAGGATCTTTTTTTTTTTGAAAAGGGTAAAAAATGAAATTTTTTTTTAAGAAAT
AACCTATTTATAGCCATCCAAAACGGTGTCGTTTTGGCATGGCTTCAGAATGCTCAAAACGACGC
CGTTTCACTTCATAACCCATGGCCGACCCGAATTCGACCCGACCCACCTGAAAGATCCGCGTGTT
TTTGAGAAAAGGGATATTTCTGCATTTGGTCCTTTCGCATTTTTTGATTGCTTCAATCAGGTCTT
TTTTGTACTTTTAATTAATTTAAATTGGCCCAATAATTTTTCAATGCTTTTCAATTTAGTCCCTT
GACCTTTTGAAATCATCAGGAGCTGCCACGTGTCTTTGTTTTGGTTCATTTATACAAACGATCCC
TTTTATTTTTAATTTGTTTTAATTTAATCCTAAAATCAAGTCCTGTTTAATTACAAAATTGACCC
AAAATTTTTTCATGGTTTTCAAATTAGTCCTTTGATTTCAGGATGCTCGGGGGGCTACCACGTGT
CATTTCTTTCTGGTTTTATTGCCTTGAAGGTCCTTAAACTGTCTAAAAATTATATTTTTTACCCC
CAAACTTTTGAAAATTCCATTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCGTACTTC
CAAAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAA
TTCCTTTTTTGACCTAAAAACTTTCAAAATTCTATTTTTAACCCCGATCTTCCAGAAATTCCATT
TTTGGAAC
Found at i:234712 original size:58 final size:58
Alignment explanation
Indices: 234457--234851 Score: 334
Period size: 59 Copynumber: 6.8 Consensus size: 58
234447 CAAACTTTTG
* ** * * *
234457 AAAATTCCA-TTTTGATCCCAAATTTTTGAAAATTCCATTTTTACCCCCG-TACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTACATTTTTACCCTCGAT-CTTCCA
* * * *
234514 AAAATTCCATTTTTGACCCCAAAAATTTCGAAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTT-AAAAATTACATTTTTACCCTCGATCTTCCA
* ** *
234573 AAAATTCCTTTTTTGACCTAAAAACTTTCAAAATT-CTATTTTTAACCC-CGATCTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTAC-ATTTTT-ACCCTCGATCTTCCA
* * * * * *
234631 GAAATTCCATTTTTTACCTCGAAACTTTTAAAATTATATTTTTACCCTCGATCTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTACATTTTTACCCTCGATCTTCCA
* ** * *
234689 AAAATTCCATTTTTGACCCCGAAACCTCCAAAAATTACATTTTTACCCTCGAACCTCCA
1 AAAATTCCATTTTTGACCCC-AAAACTTTAAAAATTACATTTTTACCCTCGATCTTCCA
* * * * * *
234748 AAACTTCCATATTTAAGCCCAAAACTTTAAAAAATACCA-TTTTACCCTCTGGAT-GTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTA-CATTTTTACCCTC--GATCTTCCA
* * * * * * *
234807 AAAACTCTATTTTCGACCTCGAAACTCTAAAAATTCCATTTTTAC
1 AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTACATTTTTAC
234852 TCCTGAATGT
Statistics
Matches: 274, Mismatches: 52, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
57 14 0.05
58 122 0.45
59 136 0.50
60 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCAAAACTTTAAAAATTACATTTTTACCCTCGATCTTCCA
Found at i:234781 original size:59 final size:57
Alignment explanation
Indices: 234425--234879 Score: 330
Period size: 58 Copynumber: 7.8 Consensus size: 57
234415 TTAAACTGTC
* * * *** **
234425 TAAAAATTATATTTTTTACCCCCAAACTTTTGAAAATTCCA-TTTTGATCCCAAATTTT
1 TAAAAATTACA-TTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCAAAACTT
* * * * *
234483 TGAAAATTCCATTTTTACCCCCGTACTTCCAAAAATTCCATTTTTGACCCCAAAAATT
1 TAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCAAAACTT
* * * *
234541 TCGAAAATTTCATTTTTACCCTCGAACTTCCAAAAATTCCTTTTTTGACCTAAAAACTT
1 T-AAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CAAAACTT
* * * * *
234600 TCAAAATT-CTATTTTTAACCC-CGATCTTCCAGAAATTCCATTTTTTACCTCGAAACTT
1 TAAAAATTAC-ATTTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CAAAACTT
* * * * *
234658 TTAAAATTATATTTTTACCCTCGATCTTCCAAAAATTCCATTTTTGACCCCGAAACCTC
1 TAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCC-AAAACTT
* * * * *
234717 CAAAAATTACATTTTTACCCTCGAACCTCCAAAACTTCCATATTTAAGCCCAAAACTT
1 TAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCAAAACTT
* * * * * * *
234775 TAAAAAATACCA-TTTTACCCTCTGGA-TGTCCAAAAACTCTATTTTCGACCTCGAAACTC
1 TAAAAATTA-CATTTTTACCCTC-GAACT-TCCAAAAATTCCATTTTTGACC-CAAAACTT
* *
234834 TAAAAATTCCATTTTTACTCCT-GAA-TGTCTAAAAATTCCATCTTTT
1 TAAAAATTACATTTTTAC-CCTCGAACT-TCCAAAAATTCCAT-TTTT
234880 AACCTCGAAC
Statistics
Matches: 320, Mismatches: 61, Indels: 31
0.78 0.15 0.08
Matches are distributed among these distances:
57 29 0.09
58 147 0.46
59 141 0.44
60 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (57 bp):
TAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCAAAACTT
Found at i:235309 original size:96 final size:95
Alignment explanation
Indices: 235184--235357 Score: 260
Period size: 96 Copynumber: 1.8 Consensus size: 95
235174 GTAATATTCT
* **
235184 TTTATTTCGAGTTTCGAAATTTGTGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCAAAATA
1 TTTATTTCGAGTTTCGAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCAAAATA
235249 ATCGAATACCCTTAATCGAGGTAACGTTTC
66 ATCGAATACCCTTAATCGAGGTAACGTTTC
* * *
235279 TTTATCTTCGA-TTTTGAAATATTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGA
1 TTTAT-TTCGAGTTTCGAAAT-TTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCAAAA
*
235343 TAATCGAATGCCCTT
64 TAATCGAATACCCTT
235358 TTCCAAATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
95 13 0.19
96 57 0.81
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (95 bp):
TTTATTTCGAGTTTCGAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCAAAATA
ATCGAATACCCTTAATCGAGGTAACGTTTC
Found at i:246268 original size:26 final size:28
Alignment explanation
Indices: 246213--246270 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
246203 CAATTTTCAA
* *
246213 TTAATGATTGTTTTCTTTGACCCTCTTT
1 TTAATGATTGTTTCCTTCGACCCTCTTT
*
246241 TTAAT-ATTGTTTCCTTCGATCCTCTTT
1 TTAATGATTGTTTCCTTCGACCCTCTTT
246268 TTA
1 TTA
246271 TAGAATTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.57
Consensus pattern (28 bp):
TTAATGATTGTTTCCTTCGACCCTCTTT
Found at i:247155 original size:206 final size:205
Alignment explanation
Indices: 246771--247156 Score: 513
Period size: 206 Copynumber: 1.9 Consensus size: 205
246761 AGATACTGAG
* * * *
246771 TCAAACCCACGCTTGATGTAAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGCA
1 TCAAACCCACACTCGATGTAAGCAAATCCTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCA
* ** * *
246836 GGTTGAAGCAATAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCT
66 GGTTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACTGAGAAGTAAACCAAATCCATCTTCCT
** * ** * *
246901 GATGAGGTATAGAGAAGCGGATTGAAGCGAATGACGCGGTCATCTTCCTGATGAGATACATAGAA
131 GATGAGACACAGAGAAGCGGATCAAAACGAATGACACGGTCATCTTCCTGATGAGATACATAGAA
246966 GAAGACCAAA
196 GAAGACCAAA
* * *
246976 TCAAACCCACACTCGATGTGAGCAAATCCTCGGACCCCAGCTTCCTGATGAGATACTGAGAAGCA
1 TCAAACCCACACTCGATGTAAGCAAATCCTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCA
* **
247041 GGTTGAAGTAATAAAATGGTTAGCTTCCTAATGCGATACTGAGAAGTAAACCAAATCCATCTTCC
66 GGTTGAAGCAATAAAA-GGTTAGCTTCCTAATGAAATACTGAGAAGTAAACCAAATCCATCTTCC
* * * *
247106 TGATGAGACACAGAGAAGTGGATCAAAAC-AAGTGATATGGTCGTCTTCCTG
130 TGATGAGACACAGAGAAGCGGATCAAAACGAA-TGACACGGTCATCTTCCTG
247157 TTGAAAGACT
Statistics
Matches: 153, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
205 75 0.49
206 78 0.51
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (205 bp):
TCAAACCCACACTCGATGTAAGCAAATCCTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCA
GGTTGAAGCAATAAAAGGTTAGCTTCCTAATGAAATACTGAGAAGTAAACCAAATCCATCTTCCT
GATGAGACACAGAGAAGCGGATCAAAACGAATGACACGGTCATCTTCCTGATGAGATACATAGAA
GAAGACCAAA
Found at i:247665 original size:27 final size:26
Alignment explanation
Indices: 247621--247671 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
247611 ACGGGCCCGA
247621 TCCTAACAACCCAAATGACCCAAATT
1 TCCTAACAACCCAAATGACCCAAATT
247647 TCCTAA-AACACCTAAATGACCCAAA
1 TCCTAACAAC-CC-AAATGACCCAAA
247672 GTCAGCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 8 0.35
27 12 0.52
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.18
Consensus pattern (26 bp):
TCCTAACAACCCAAATGACCCAAATT
Found at i:248354 original size:27 final size:27
Alignment explanation
Indices: 248324--248375 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
248314 AAAACCCCAT
*
248324 TAATAAT-ATAAATAATTGTTTTAATGA
1 TAATAATAAT-AATAATTATTTTAATGA
*
248351 TAATAATAATACTAATTATTTTAAT
1 TAATAATAATAATAATTATTTTAAT
248376 AAAAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TAATAATAATAATAATTATTTTAATGA
Found at i:249444 original size:29 final size:29
Alignment explanation
Indices: 249401--249625 Score: 131
Period size: 29 Copynumber: 7.8 Consensus size: 29
249391 GAAGGTCCCT
* * *
249401 AAACTATCTAAAAATTACAATTTTGCCCCC
1 AAACT-TCCAAAAATTCCAATTTTGCCCCA
249431 AAACTTCCAAAAATT-CAATTTTGACCCCA
1 AAACTTCCAAAAATTCCAATTTTG-CCCCA
* ** * *
249460 AAATTTCTGAAAATTCCATTTTTACCCC-
1 AAACTTCCAAAAATTCCAATTTTGCCCCA
** * * *
249488 GTACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCAATTTT-GCCCCA
* *
249518 AAACTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCAATTTTGCCC-CA
* *
249547 AAACTT--AAAAAATCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCAATTTTG-CCCCA
* * * *
249575 AAACTTTC-AAAATTCTATTTTTACCCTC-
1 AAACTTCCAAAAATTCCAATTTTGCCC-CA
* * *
249603 GATCTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCAATTTT
249626 AACCTCGAAA
Statistics
Matches: 159, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
27 15 0.09
28 43 0.27
29 69 0.43
30 32 0.20
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCAATTTTGCCCCA
Found at i:249449 original size:28 final size:28
Alignment explanation
Indices: 249401--249624 Score: 130
Period size: 28 Copynumber: 7.8 Consensus size: 28
249391 GAAGGTCCCT
* *
249401 AAACTATCTAAAAATTACAATTTTGCCCCC
1 AAACT-TCCAAAAATT-CAATTTTACCCCC
*
249431 AAACTTCCAAAAATTCAATTTTGACCCCA
1 AAACTTCCAAAAATTCAATTTT-ACCCCC
* ** *
249460 AAATTTCTGAAAATTCCATTTTTA-CCCC
1 AAACTTCCAAAAATT-CAATTTTACCCCC
** * **
249488 GTACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATT-CAATTTT-ACCCCC
* *
249518 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATT-CAATTTTACCCCC
* * * *
249547 AAACTT-AAAAAATCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCAATTTT-ACCCCC
* * *
249575 AAACTTTC-AAAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTC-AATTTTACCCCC
* * *
249603 GATCTTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCAATTTT
249625 TAACCTCGAA
Statistics
Matches: 155, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
27 7 0.05
28 63 0.41
29 51 0.33
30 34 0.22
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
AAACTTCCAAAAATTCAATTTTACCCCC
Found at i:249559 original size:58 final size:59
Alignment explanation
Indices: 249397--249833 Score: 326
Period size: 58 Copynumber: 7.5 Consensus size: 59
249387 CCCTGAAGGT
* * * * * * *
249397 CCCT-AAACTATCTAAAAATTACAATTTTGCCCCCAAACTTCCAAAAATT-CAATTTTGA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* * ** * *
249455 CCCCAAAATTTCTGAAAATTCCATTTTTACCC-CGTACTTCCAAAAATTCCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* *
249513 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTT--AAAAAATCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* * * *
249570 CCCCAAAACTTTC-AAAATTCTATTTTTACCCTCGATCTTCCAAAAATTCCATTTTT-A
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* * * * * * **
249627 ACCTCGAAACTTTC-AATATTCTATTTTTACCC-CTGATCTTTTAAAAATTCCATTTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTGA
* * * * * *
249686 CCCTAAAACCTCAAAAAATTACATTTTTACCCTCGAACCTCCAAAACTTCCATATTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
* * * * * * * *
249745 -CCTCGAAACTTTCAAAAAATGCCA-TTTTACCCCCCGGA-TGTCCAAAAACTCTATTTTCGA
1 CCCT-AAAAC-TTCCAAAAATTCCATTTTTA-CCCTCGAACT-TCCAAAAATTCCATTTTTGA
*
249805 -CCTCAAAAC-TCTAAAAATTCCATTTTTAC
1 CCCT-AAAACTTCCAAAAATTCCATTTTTAC
249834 TCCTGAATGT
Statistics
Matches: 305, Mismatches: 59, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
56 23 0.08
57 44 0.14
58 136 0.45
59 61 0.20
60 41 0.13
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
Found at i:249610 original size:115 final size:113
Alignment explanation
Indices: 249397--249777 Score: 335
Period size: 115 Copynumber: 3.3 Consensus size: 113
249387 CCCTGAAGGT
* * ** * * *
249397 CCCTAAACTATCTAAAAATTACAATTTTGCCCCCAAACTTCCAAAAATTCAATTTTGACCCCAAA
1 CCCTAAACT-TCCAAAAATT-CCATTTTTACCCCAAACTT-AAAAAATCCATTTTTGACCCCAAA
*
249462 A-TTTCTGAAAATTCCATTTTTACCC-CG-TACTTCCAAAAATTCCATTTTTAA
63 ACTTTC-AAAAATT-CATTTTTACCCTCGAT-CTTCCAAAAATTCCATTTTTAA
249513 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTAAAAAATCCATTTTTGACCCCAAAA
1 CCCT-AAACTTCCAAAAATTCCATTTTTACCC-CAAACTTAAAAAATCCATTTTTGACCCCAAAA
249578 CTTTC-AAAATTCTATTTTTACCCTCGATCTTCCAAAAATTCCATTTTTAA
64 CTTTCAAAAATTC-ATTTTTACCCTCGATCTTCCAAAAATTCCATTTTTAA
* * * * * * * *
249628 CCTCGAAACTTTC-AATATTCTATTTTTACCCCTGATCTTTTAAAAATTCCATTTTTGACCCTAA
1 CC-CTAAACTTCCAAAAATTCCATTTTTACCCC-AAAC--TTAAAAAATCCATTTTTGACCCCAA
* * * * * *
249692 AAC-CTCAAAAAATTACATTTTTACCCTCGAACCTCCAAAACTTCCATATTTGA
62 AACTTTC-AAAAATT-CATTTTTACCCTCGATCTTCCAAAAATTCCATTTTTAA
* * *
249745 CCTCGAAACTTTCAAAAAATGCCA-TTTTACCCC
1 CC-CTAAAC-TTCCAAAAATTCCATTTTTACCCC
249778 CCGGATGTCC
Statistics
Matches: 224, Mismatches: 26, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
113 2 0.01
114 34 0.15
115 66 0.29
116 52 0.23
117 52 0.23
118 12 0.05
119 6 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (113 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCCCAAACTTAAAAAATCCATTTTTGACCCCAAAACT
TTCAAAAATTCATTTTTACCCTCGATCTTCCAAAAATTCCATTTTTAA
Found at i:249626 original size:29 final size:29
Alignment explanation
Indices: 249432--249874 Score: 252
Period size: 29 Copynumber: 15.2 Consensus size: 29
249422 TTTGCCCCCA
* * *
249432 AACTTCCAAAAATTCAATTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* **
249461 AATTTCTGAAAATTCCATTTTTACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* **
249489 TACTTCCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
249519 AACTTCCAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
249548 AACTT--AAAAAATCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
* *
249576 AACTTTC-AAAATTCTATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
249604 ATCTTCCAAAAATTCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
249633 AAACTTTC-AATATTCTATTTTTACCC-CTG
1 -AACTTCCAAAAATTCCATTTTTACCCTC-G
* ** **
249662 ATCTTTTAAAAATTCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
249692 AACCTCAAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
249721 AACCTCCAAAACTTCCATATTTGA-CCTCG
1 AACTTCCAAAAATTCCAT-TTTTACCCTCG
* * *
249750 AAACTTTCAAAAAATGCCA-TTTTACCCCCCG
1 -AAC-TTCCAAAAATTCCATTTTTA-CCCTCG
* * * * *
249781 GA-TGTCCAAAAACTCTATTTTCGA-CCTCAA
1 AACT-TCCAAAAATTCCATTTT-TACCCTC-G
*
249811 AAC-TCTAAAAATTCCATTTTTACTCCT-G
1 AACTTCCAAAAATTCCATTTTTAC-CCTCG
* *
249839 AA-TGT-CTAAAATTCCATCTTTTAACCTCG
1 AACT-TCCAAAAATTCCAT-TTTTACCCTCG
249868 AACTTCC
1 AACTTCC
249875 CCAAAGCTAC
Statistics
Matches: 316, Mismatches: 67, Indels: 61
0.71 0.15 0.14
Matches are distributed among these distances:
27 15 0.05
28 60 0.19
29 162 0.51
30 64 0.20
31 15 0.05
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:250290 original size:96 final size:95
Alignment explanation
Indices: 250166--250339 Score: 269
Period size: 96 Copynumber: 1.8 Consensus size: 95
250156 GTAATATTCT
* **
250166 TTTATTTCGAGTTTCGAAATTTGTGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCGAAATA
1 TTTATTTCGAGTTTCGAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATA
250231 ATCGAATACCCTTAACCGAGGCAACGTTTC
66 ATCGAATACCCTTAACCGAGGCAACGTTTC
* *
250261 TTTATCTTCGA-TTTTGAAATATTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGA
1 TTTAT-TTCGAGTTTCGAAAT-TTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAA
*
250325 TAATCGAATGCCCTT
64 TAATCGAATACCCTT
250340 TTCCCAAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
95 13 0.18
96 58 0.82
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (95 bp):
TTTATTTCGAGTTTCGAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATA
ATCGAATACCCTTAACCGAGGCAACGTTTC
Found at i:263154 original size:2 final size:2
Alignment explanation
Indices: 263147--263174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
263137 TACAATCGCT
263147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
263175 AGAGATAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:270136 original size:122 final size:122
Alignment explanation
Indices: 269997--270362 Score: 572
Period size: 122 Copynumber: 3.0 Consensus size: 122
269987 AATGATTTCG
* *
269997 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAACAAACCTTCC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCC
*
270062 ATATATATT-TTTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
66 ATATAT-TTCTATAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
* *
270119 TTAAATATTAAATCATGGAAGTTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTCC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCC
* * *
270184 ATATATTTCTCTAAGGGAATATTTCCATTTTAATATGAGATATTATATGAAAGGAAA
66 ATATATTTCTATAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
* **
270241 TTGAATATTAAAACATAAAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCC
* * * * *
270306 ATATATTTCTATAAAGGGATATTTTCATTTCAATATGAGATATTAAATAAAAAGAAA
66 ATATATTTCTATAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
270363 ATATAGCAGA
Statistics
Matches: 224, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 2 0.01
122 222 0.99
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (122 bp):
TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCC
ATATATTTCTATAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
Found at i:272480 original size:122 final size:123
Alignment explanation
Indices: 272351--272707 Score: 547
Period size: 122 Copynumber: 2.9 Consensus size: 123
272341 ATCAGTACTC
* * * *
272351 AACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAACAAACCTTCCATATATTTTTT
1 AACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATATATTTCTA
*
272416 TAAAGGAATATTTCCATTTTAATATGAGATAGTATATAAAAGAAAATTAAATATT-AA
66 TAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTAAATATTAAA
272473 AACATGGAAGTTAATATCCTTTT-GAAAATGATATAATGTTTTAATAAACCTTCCATATATTTCT
1 AACATGGAAGTTAATATCCTTTTGGAAAA-GATATAATGTTTTAATAAACCTTCCATATATTTCT
* * * *
272537 CTAAAGGAATATTTCCATTTTAATATGAGATATTATATGAAAGGAAATTGAATATTAAA
65 ATAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTAAATATTAAA
** *
272596 AACATAAAAGTTAATATCCTTTTGGAAAAGATTTAATGTTTTAATAAACCTTCCATATATTTCTA
1 AACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATATATTTCTA
* * *
272661 TAAAGGAATATTTTCATTTCAATATGAGATATTAAATAAAAAGAAAA
66 TAAAGGAATATTTCCATTTTAATATGAGATATTATAT-AAAAGAAAA
272708 GATAGCAGAA
Statistics
Matches: 214, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
121 4 0.02
122 107 0.50
123 91 0.43
124 12 0.06
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (123 bp):
AACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCATATATTTCTA
TAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGAAAATTAAATATTAAA
Found at i:275887 original size:5 final size:5
Alignment explanation
Indices: 275879--275903 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
275869 CAAAATATGA
275879 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
275904 TGTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:278957 original size:17 final size:17
Alignment explanation
Indices: 278924--278957 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
278914 TGAAGTGTTT
278924 TTGAATAAAATTTAAAA
1 TTGAATAAAATTTAAAA
278941 TTGAA-AAAATTTGAAAA
1 TTGAATAAAATTT-AAAA
278958 ATGATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (17 bp):
TTGAATAAAATTTAAAA
Found at i:281855 original size:20 final size:21
Alignment explanation
Indices: 281826--281878 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
281816 AACTTTTTTC
*
281826 TTTTATTTTC-CCCCAAAAAT
1 TTTTACTTTCTCCCCAAAAAT
*
281846 TTTTACTTTCTCCTCAAAAA-
1 TTTTACTTTCTCCCCAAAAAT
*
281866 GTTTACTTCTCTC
1 TTTTACTT-TCTC
281879 GAACCACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.25, C:0.26, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTACTTTCTCCCCAAAAAT
Found at i:281876 original size:73 final size:73
Alignment explanation
Indices: 281773--281927 Score: 188
Period size: 73 Copynumber: 2.1 Consensus size: 73
281763 CCCTCAAACC
* * * * *
281773 CTTTTACTTTCACCCAAAAATTTTATTTCTCCTCAAACCAC-CAAACTTTTTT-CTTTTATTTTC
1 CTTTTACTTTCACCCAAAAAGTTTACTTCT-CTCAAACCACAAAAACTTTTTTCCTGTTACTTTC
281836 CCCCAAAAA
65 CCCCAAAAA
* * *
281845 TTTTTACTTTCTCCTCAAAAAGTTTACTTCTCTCGAACCACAAAAACTTTTTTCCTGTTACTTTC
1 CTTTTACTTTCACC-CAAAAAGTTTACTTCTCTCAAACCACAAAAACTTTTTTCCTGTTACTTTC
*
281910 CCCCCAAAA
65 CCCCAAAAA
*
281919 CTTTCACTT
1 CTTTTACTT
281928 CCCCTAACTC
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 21 0.30
73 24 0.35
74 24 0.35
ACGTcount: A:0.27, C:0.30, G:0.02, T:0.41
Consensus pattern (73 bp):
CTTTTACTTTCACCCAAAAAGTTTACTTCTCTCAAACCACAAAAACTTTTTTCCTGTTACTTTCC
CCCAAAAA
Found at i:309442 original size:14 final size:14
Alignment explanation
Indices: 309423--309456 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
309413 TCCTAAAAAT
*
309423 GGAGAAATAATGAA
1 GGAGAAATAAGGAA
309437 GGAGAAATAAGGAA
1 GGAGAAATAAGGAA
309451 GTGAGA
1 G-GAGA
309457 TGGAGTGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (14 bp):
GGAGAAATAAGGAA
Found at i:311058 original size:12 final size:13
Alignment explanation
Indices: 311041--311070 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
311031 CAATTCTTTC
311041 CTTTTATTTT-TG
1 CTTTTATTTTATG
311053 CTTTTATTTTATG
1 CTTTTATTTTATG
311066 CTTTT
1 CTTTT
311071 CAAAACCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (13 bp):
CTTTTATTTTATG
Found at i:324012 original size:14 final size:14
Alignment explanation
Indices: 323989--324026 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
323979 CACTTTTGTA
323989 TTTCCTTTTATCT-
1 TTTCCTTTTATCTG
*
324002 TTTCACTTTTATTTG
1 TTTC-CTTTTATCTG
324017 TTTCCTTTTA
1 TTTCCTTTTA
324027 AATTCTATGC
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:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATCTG
Found at i:335706 original size:11 final size:12
Alignment explanation
Indices: 335690--335722 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
335680 GACACATGGT
335690 CGTGTCTTGA-C
1 CGTGTCTTGACC
335701 CGTGTCTTGACC
1 CGTGTCTTGACC
335713 CGTGTGCTTG
1 CGTGT-CTTG
335723 CCCATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 6 0.30
13 4 0.20
ACGTcount: A:0.06, C:0.27, G:0.30, T:0.36
Consensus pattern (12 bp):
CGTGTCTTGACC
Found at i:358064 original size:28 final size:29
Alignment explanation
Indices: 358023--358086 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
358013 CGTAAATGAT
*
358023 AGGAAAGTCTTTGTGGTTGATTCTGTTAA
1 AGGAAAGTCTTTGTGCTTGATTCTGTTAA
* *
358052 AGGAAA-TCTTTGTGCTTGATTTTGTTCA
1 AGGAAAGTCTTTGTGCTTGATTCTGTTAA
358080 A-GAAAGT
1 AGGAAAGT
358087 GTTTATGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 21 0.68
29 6 0.19
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (29 bp):
AGGAAAGTCTTTGTGCTTGATTCTGTTAA
Found at i:365103 original size:19 final size:20
Alignment explanation
Indices: 365078--365121 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
365068 GAAATAGTTA
*
365078 AAAAAATCAAAATTTTATTT
1 AAAAATTCAAAATTTTATTT
* *
365098 AAAAATTTAAAATTTTCTTT
1 AAAAATTCAAAATTTTATTT
365118 AAAA
1 AAAA
365122 TTACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTCAAAATTTTATTT
Found at i:365171 original size:146 final size:150
Alignment explanation
Indices: 364893--365536 Score: 754
Period size: 146 Copynumber: 4.4 Consensus size: 150
364883 AAAACAGTAC
* * *
364893 TTTACTTTAAAATT-AAAACTTTTATTTCAAAATAATTAAAAAAAATCAAAATTTTGTTTAAAAT
1 TTTACTTAAAAATTCAAAACTTTTATTTCGAAATAATT-AAAAAAATCAAAATTTTGTTTAAAAA
* *
364957 TTTAAACTTTTTCTTTAAAATCACT-AAAAATAGATTTTTATTTTTTTAAAAAAAT-TAAAC--T
65 TTTAAACTTTTTCTTTAAAATTACTAAAAAACAGA-TTTTA-TTTTTT-AAAAAATCTAAACTTT
* *
365018 -T-TTTTTTAATGAAAATCACTAC
127 CTCTTTTTTAAAGAAAATCACTAT
* *
365040 TTTACTTAAAAATTCAAAA-TTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAAT
1 TTTACTTAAAAATTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAATTTTGTTTAAAAAT
* * *
365104 TTAAA-ATTTTCTTTAAAATTACTAAAAAA-AAACTTTTATTTTTT-AAAAATCT-AA-TTTTTC
66 TTAAACTTTTTCTTTAAAATTACTAAAAAACAGA-TTTTATTTTTTAAAAAATCTAAACTTTCTC
*
365164 TTATTTTAATGAAAATCACTAT
130 TT-TTTTAAAGAAAATCACTAT
* * * *
365186 TTTAGTTAGAAATTC-AAACTTTTATTTCGAAATAGTT--AAAAATCATAATTTTGTTTAAAAAT
1 TTTACTTAAAAATTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAATTTTGTTTAAAAAT
* * * *
365248 TTAAATTTTTTCTTTAAAATTATTAAAAATATATATTTTA-TTTTT-AAAAATCTAAACTTTCTC
66 TTAAACTTTTTCTTTAAAATTACTAAAAA-ACAGATTTTATTTTTTAAAAAATCTAAACTTTCTC
365311 TTTTTTAAAGAAAATCACTAT
130 TTTTTTAAAGAAAATCACTAT
* * *
365332 TTTACTTAAAAA-TCAAAACTTTTATTTCGATATAATTAAAAAAAAACAAAATTTTGCTTAAAAA
1 TTTACTTAAAAATTCAAAACTTTTATTTCGAAATAATT-AAAAAAATCAAAATTTTGTTTAAAAA
* *
365396 TTTAAAC-TTTTCTTTAAAATGACTAAAAAACAGATTTTATTTTTTAAAAAAACTAAACTTTCTC
65 TTTAAACTTTTTCTTTAAAATTACTAAAAAACAGATTTTATTTTTTAAAAAATCTAAACTTTCTC
** *
365460 TTTTTTAAAGAATTTTACTAT
130 TTTTTTAAAGAAAATCACTAT
* * * *
365481 TTTTCTTAAAAA-TCAAAACTTTTATTTCGAAATTATTTTAAAAAATAAAAACTTTT
1 TTTACTTAAAAATTCAAAACTTTTATTTCGAAA-TAATTAAAAAAATCAAAA-TTTT
365537 CCCAAAATCA
Statistics
Matches: 434, Mismatches: 41, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
142 8 0.02
143 2 0.00
144 35 0.08
145 64 0.15
146 140 0.32
147 46 0.11
148 29 0.07
149 102 0.24
150 8 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (150 bp):
TTTACTTAAAAATTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAATTTTGTTTAAAAAT
TTAAACTTTTTCTTTAAAATTACTAAAAAACAGATTTTATTTTTTAAAAAATCTAAACTTTCTCT
TTTTTAAAGAAAATCACTAT
Found at i:365274 original size:30 final size:30
Alignment explanation
Indices: 365240--365296 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
365230 ATAATTTTGT
*
365240 TTAAAAATTTAAATTTT-TTCTTTAAAATTA
1 TTAAAAATATAAATTTTATT-TTTAAAATTA
*
365270 TTAAAAATATATATTTTATTTTTAAAA
1 TTAAAAATATAAATTTTATTTTTAAAA
365297 ATCTAAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
TTAAAAATATAAATTTTATTTTTAAAATTA
Found at i:365436 original size:293 final size:290
Alignment explanation
Indices: 364893--365536 Score: 782
Period size: 293 Copynumber: 2.2 Consensus size: 290
364883 AAAACAGTAC
* * *
364893 TTTACTTTAAAATTAAAACTTTTATTTCAAAATAATTAAAAAAAATCAAAATTTTGTTTAAAATT
1 TTTAC-TTAAAATTCAAACTTTTATTTCGAAATAATT--AAAAAATCAAAATTTTGTTTAAAAAT
364958 TTAAACTTTTTCTTTAAAATCACTAAAAATAGATTTTTATTTTTTTAAAAAAATTAAACTTTTTT
63 TTAAACTTTTTCTTTAAAATCACTAAAAATAGATTTTTA-TTTTTT-AAAAAATTAAACTTTTTT
* * *
365023 TTAATGAAAATCACTACTTTACTTAAAAATTCAAAATTTTATTTCGAAATAGTTAAAAAAATCAA
126 TTAAAGAAAATCACTACTTTACTTAAAAATTCAAAATTTTATTTCGAAATAATTAAAAAAAACAA
* *
365088 AATTTTATTTAAAAATTTAAAATTTTCTTTAAAATTACTAAAAAAAAACTTTTATTTTTT-AAAA
191 AATTTTACTTAAAAATTTAAAATTTTCTTTAAAATGACTAAAAAAAAACTTTTATTTTTTAAAAA
* * *
365152 ATCT-AA-TTTTTCTTATTTTAATGAAAATCACTAT
256 AACTAAACTTTCTCTT-TTTTAAAGAAAATCACTAT
* * *
365186 TTTAGTTAGAAATTCAAACTTTTATTTCGAAATAGTT-AAAAATCATAATTTTGTTTAAAAATTT
1 TTTACTTA-AAATTCAAACTTTTATTTCGAAATAATTAAAAAATCAAAATTTTGTTTAAAAATTT
* * * *
365250 AAATTTTTTCTTTAAAATTATTAAAAATATATATTTTA-TTTTT-AAAAATCTAAACTTTCTCTT
65 AAACTTTTTCTTTAAAATCACTAAAAATAGAT-TTTTATTTTTTAAAAAAT-TAAAC--T-T-TT
* *
365313 TTTTAAAGAAAATCACTATTTTACTTAAAAA-TCAAAACTTTTATTTCGATATAATTAAAAAAAA
124 TTTTAAAGAAAATCACTACTTTACTTAAAAATTCAAAA-TTTTATTTCGAAATAATT-AAAAAAA
* * *
365377 ACAAAATTTTGCTTAAAAATTTAAACTTTTCTTTAAAATGACTAAAAAACAGA-TTTTATTTTTT
187 ACAAAATTTTACTTAAAAATTTAAAATTTTCTTTAAAATGACTAAAAAA-AAACTTTTATTTTTT
** *
365441 AAAAAAACTAAACTTTCTCTTTTTTAAAGAATTTTACTAT
251 AAAAAAACTAAACTTTCTCTTTTTTAAAGAAAATCACTAT
* * * *
365481 TTTTCTTAAAAATCAAAACTTTTATTTCGAAATTATTTTAAAAAATAAAAACTTTT
1 TTTACTTAAAATTC-AAACTTTTATTTCGAAA-TA-ATTAAAAAATCAAAA-TTTT
365537 CCCAAAATCA
Statistics
Matches: 301, Mismatches: 32, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
287 6 0.02
288 5 0.02
289 5 0.02
290 54 0.18
291 12 0.04
292 50 0.17
293 91 0.30
294 14 0.05
295 40 0.13
296 9 0.03
297 2 0.01
298 9 0.03
299 4 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (290 bp):
TTTACTTAAAATTCAAACTTTTATTTCGAAATAATTAAAAAATCAAAATTTTGTTTAAAAATTTA
AACTTTTTCTTTAAAATCACTAAAAATAGATTTTTATTTTTTAAAAAATTAAACTTTTTTTTAAA
GAAAATCACTACTTTACTTAAAAATTCAAAATTTTATTTCGAAATAATTAAAAAAAACAAAATTT
TACTTAAAAATTTAAAATTTTCTTTAAAATGACTAAAAAAAAACTTTTATTTTTTAAAAAAACTA
AACTTTCTCTTTTTTAAAGAAAATCACTAT
Found at i:365956 original size:3 final size:3
Alignment explanation
Indices: 365948--365996 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
365938 AAACCCTAAA
* * *
365948 AAT AAT AAT AAT AATT AAT ACT AAT AAT AAT AGT AAT GAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
365994 AAT
1 AAT
365997 TTGGACCCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:368324 original size:42 final size:42
Alignment explanation
Indices: 368265--368344 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
368255 TCACATGGTT
368265 TGAGACACAACCATGTGTACCAAGTCAGTGAGTTACACAGTC
1 TGAGACACAACCATGTGTACCAAGTCAGTGAGTTACACAGTC
* *
368307 TGAGACACGACCATGTGTTCCAAGTCAGTGAGTTACAC
1 TGAGACACAACCATGTGTACCAAGTCAGTGAGTTACAC
368345 GAACTAGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (42 bp):
TGAGACACAACCATGTGTACCAAGTCAGTGAGTTACACAGTC
Found at i:373032 original size:24 final size:23
Alignment explanation
Indices: 372983--373032 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
372973 TAAAATAGGT
*
372983 TATATATTATTTTTATAATATTA
1 TATATATTATTTTTATAATATCA
*
373006 TATATTTTGATTTTTATTAAT-TCA
1 TATATATT-ATTTTTA-TAATATCA
373030 TAT
1 TAT
373033 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 12 0.52
25 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TATATATTATTTTTATAATATCA
Found at i:373093 original size:59 final size:57
Alignment explanation
Indices: 373015--373170 Score: 154
Period size: 59 Copynumber: 2.7 Consensus size: 57
373005 ATATATTTTG
* *
373015 ATTTTTATTAATTCATATTTTAATAATAATTATATTAAGA-ATGCTATTAATTCATATATT
1 ATTTTTATTAATTTATA-TTTAATAATAATTATATTAA-ATATG--ATTAAATCATATATT
* * * * *
373075 A-TTTTATTAATTTGTATTTAAGATTAATTATGTTACAATATGATTAAATCATTTATT
1 ATTTTTATTAATTTATATTTAATAATAATTATATTA-AATATGATTAAATCATATATT
** *
373132 ATTTTTTATTAAAATATATTTAATAATAATTTTATTAAA
1 A-TTTTTATTAATTTATATTTAATAATAATTATATTAAA
373171 ATTTAATAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
57 14 0.18
58 19 0.24
59 44 0.56
60 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (57 bp):
ATTTTTATTAATTTATATTTAATAATAATTATATTAAATATGATTAAATCATATATT
Found at i:373367 original size:16 final size:16
Alignment explanation
Indices: 373346--373392 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
373336 TAATTGCAAT
373346 TCTATTTCATTACAAC
1 TCTATTTCATTACAAC
* * *
373362 TCTATTTTATTATATC
1 TCTATTTCATTACAAC
*
373378 TCTATTCCA-TACAAC
1 TCTATTTCATTACAAC
373393 CTTATTCCAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (16 bp):
TCTATTTCATTACAAC
Found at i:379840 original size:25 final size:22
Alignment explanation
Indices: 379774--379871 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 22
379764 CGAAGTACTT
379774 AACAGTAAGCACACA-AGTGCTGGGG
1 AACAG-AAGCACACACAGTGCT---G
*
379799 AAACAGTAAGCACACACAATGCTAGG
1 -AACAG-AAGCACACACAGTGCT--G
*
379825 TAATAGAAGCACACACAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
379848 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
379870 AA
1 AA
379872 TAGTAAGTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
22 23 0.35
23 1 0.02
25 15 0.23
26 21 0.32
27 5 0.08
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:379871 original size:22 final size:25
Alignment explanation
Indices: 379774--379869 Score: 103
Period size: 26 Copynumber: 3.9 Consensus size: 25
379764 CGAAGTACTT
379774 AACAGTAAGCACACA-AGTGCTGGGGA
1 AACAGTAAGCACACACAGTGCT--GGA
* *
379800 AACAGTAAGCACACACAATGCTAGGT
1 AACAGTAAGCACACACAGTGCT-GGA
*
379826 AATAG-AAGCACACACAGTGCT-G-
1 AACAGTAAGCACACACAGTGCTGGA
379848 AACAG-AAGCACACACAGTGCTG
1 AACAGTAAGCACACACAGTGCTG
379870 AATAGTAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
22 20 0.32
23 1 0.02
25 15 0.24
26 21 0.34
27 5 0.08
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (25 bp):
AACAGTAAGCACACACAGTGCTGGA
Found at i:379980 original size:24 final size:26
Alignment explanation
Indices: 379942--379989 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
379932 TCTACATGGG
379942 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
379968 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
379990 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.