Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold182
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: 891401
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 40281 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:61 original size:41 final size:41
Alignment explanation
Indices: 1--176 Score: 291
Period size: 41 Copynumber: 4.3 Consensus size: 41
1 CCGCTAAAGCCCAGAACATTAGCGGCGCTTA-ACTAAAAACG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACA-TAAAAACG
* * * *
42 CCACTAAATCCTAGAACATTAGCGGCGCTTAAATAAAAACG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
*
83 CCGCTAAATCCCAGAACATTAGCGGCGCTTACATAAAAACG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
124 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
165 CCGCTAAAGCCC
1 CCGCTAAAGCCC
177 CCGAAAAGTC
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
41 126 0.99
42 1 0.01
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.16
Consensus pattern (41 bp):
CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
Found at i:3918 original size:46 final size:46
Alignment explanation
Indices: 3851--3942 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3841 ATCCTCTCCA
*
3851 TGCCACGTTGATCGACCGATTTACTGTATTACAATGCCTTTTTGGG
1 TGCCACGTTGATCAACCGATTTACTGTATTACAATGCCTTTTTGGG
3897 TGCCACGTTGATCAACCGATTTACTGTATTACAATGCCTTTTTGGG
1 TGCCACGTTGATCAACCGATTTACTGTATTACAATGCCTTTTTGGG
3943 GGATAGCCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (46 bp):
TGCCACGTTGATCAACCGATTTACTGTATTACAATGCCTTTTTGGG
Found at i:4250 original size:25 final size:24
Alignment explanation
Indices: 4212--4259 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
4202 ATTTATTTTC
4212 TTTTTTGTTTCTCTATTTGTTTGA
1 TTTTTTGTTTCTCTATTTGTTTGA
* *
4236 TTTTTTTTTTACTCTTTTTGTTTG
1 TTTTTTGTTT-CTCTATTTGTTTG
4260 GAGTATATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.06, C:0.08, G:0.10, T:0.75
Consensus pattern (24 bp):
TTTTTTGTTTCTCTATTTGTTTGA
Found at i:6346 original size:14 final size:15
Alignment explanation
Indices: 6324--6400 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
6314 CATCCAAACA
6324 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
6338 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
6353 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
6373 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
6387 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
6401 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:6365 original size:20 final size:20
Alignment explanation
Indices: 6340--6379 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6330 AATATTTTCC
*
6340 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
6360 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
6380 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:6385 original size:34 final size:35
Alignment explanation
Indices: 6328--6394 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
6318 CAAACACCAG
*
6328 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
6363 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
6395 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:6401 original size:14 final size:14
Alignment explanation
Indices: 6363--6402 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6353 ACAGAAAAGT
*
6363 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
6377 AAATCATTTTACGG
1 AAAACATTTTACAG
6391 AAAACATTTTAC
1 AAAACATTTTAC
6403 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:7175 original size:20 final size:20
Alignment explanation
Indices: 7150--7203 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
7140 TTAATAGTAT
7150 TTTATTAATTTAATATTAAA
1 TTTATTAATTTAATATTAAA
7170 TTTATT-ATCTTAATATTAAA
1 TTTATTAAT-TTAATATTAAA
7190 -TTA--AATTTAATATT
1 TTTATTAATTTAATATT
7204 TATCTTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.25
18 2 0.06
19 5 0.16
20 17 0.53
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTAATTTAATATTAAA
Found at i:7175 original size:25 final size:25
Alignment explanation
Indices: 7147--7198 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
7137 ATCTTAATAG
*
7147 TATTTTATTAAT-TTAATATTAAATT
1 TATTATATTAATATTAA-ATTAAATT
*
7172 TATTATCTTAATATTAAATTAAATT
1 TATTATATTAATATTAAATTAAATT
7197 TA
1 TA
7199 ATATTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATTAATATTAAATTAAATT
Found at i:7255 original size:12 final size:12
Alignment explanation
Indices: 7238--7262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7228 AATTTAATAG
7238 ATTTAATATTAA
1 ATTTAATATTAA
7250 ATTTAATATTAA
1 ATTTAATATTAA
7262 A
1 A
7263 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:9402 original size:17 final size:16
Alignment explanation
Indices: 9376--9407 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
9366 TTTGGTTACT
9376 TTAATTTTAATTTTTA
1 TTAATTTTAATTTTTA
9392 TTAATTTTTAATTTTT
1 TTAA-TTTTAATTTTT
9408 TTCCCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATTTTAATTTTTA
Found at i:11724 original size:47 final size:47
Alignment explanation
Indices: 11671--11774 Score: 163
Period size: 47 Copynumber: 2.2 Consensus size: 47
11661 GGGTGCACAG
*
11671 CATATTTGCAAATTAAGCAAACCGCCACTTGGTTCGTGATCAAACCA
1 CATATTTGCAAATTAAACAAACCGCCACTTGGTTCGTGATCAAACCA
* * * *
11718 CATATTTGTATATTAAACAAACTGCCACTTGGTTTGTGATCAAACCA
1 CATATTTGCAAATTAAACAAACCGCCACTTGGTTCGTGATCAAACCA
11765 CATATTTGCA
1 CATATTTGCA
11775 GTTACTGCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (47 bp):
CATATTTGCAAATTAAACAAACCGCCACTTGGTTCGTGATCAAACCA
Found at i:14018 original size:25 final size:23
Alignment explanation
Indices: 13982--14031 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
13972 GATATCATAT
*
13982 GTTTTAAGCTTAATTTTTG-GTTG
1 GTTTTAAGCTT-ATTTGTGTGTTG
14005 GTTTTGAATGCTTATTTGTGTGTTG
1 GTTTT-AA-GCTTATTTGTGTGTTG
14030 GT
1 GT
14032 CATATGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 8 0.35
25 10 0.43
ACGTcount: A:0.14, C:0.04, G:0.26, T:0.56
Consensus pattern (23 bp):
GTTTTAAGCTTATTTGTGTGTTG
Found at i:14173 original size:30 final size:30
Alignment explanation
Indices: 14139--14207 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
14129 GTGTATCTCA
* *
14139 GTCGTGTGTGACATAAGGCCATGTGACATG
1 GTCGTGTGTGACATAAGACCAGGTGACATG
*
14169 GTCGTGTGTGACATACGACCAGGTGACATG
1 GTCGTGTGTGACATAAGACCAGGTGACATG
14199 GTCGTGTGT
1 GTCGTGTGT
14208 CCCCTGTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (30 bp):
GTCGTGTGTGACATAAGACCAGGTGACATG
Found at i:15374 original size:12 final size:12
Alignment explanation
Indices: 15357--15382 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15347 GGATGTTATG
15357 ATTGTGAAATGT
1 ATTGTGAAATGT
15369 ATTGTGAAATGT
1 ATTGTGAAATGT
15381 AT
1 AT
15383 GATTGACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
ATTGTGAAATGT
Found at i:15725 original size:25 final size:24
Alignment explanation
Indices: 15688--15740 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
15678 ACATACCACA
*
15688 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTACGAGCGTCCTGATAT-G
* *
15713 GCTCTTTGCGAGCTTCCTGATATG
1 GCTCTTTACGAGCGTCCTGATATG
15737 GCTC
1 GCTC
15741 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.36
Consensus pattern (24 bp):
GCTCTTTACGAGCGTCCTGATATG
Found at i:21895 original size:24 final size:24
Alignment explanation
Indices: 21880--21931 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
21870 AATCAAAGTC
21880 AAATATATTAGGCTAATAAATGCT
1 AAATATATTAGGCTAATAAATGCT
** * *
21904 AAATATATTATACTCATAAATACT
1 AAATATATTAGGCTAATAAATGCT
21928 AAAT
1 AAAT
21932 CTTCTAGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATATTAGGCTAATAAATGCT
Found at i:28915 original size:43 final size:44
Alignment explanation
Indices: 28837--28934 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
28827 ACCATATCCA
* * *
28837 TAATTTAACCTAAAACAATTTATACTTAATAAAATTAATTTTCATT
1 TAATTTAA--TAAAACAATTGATACTTAAAAAAATTAATTTTAATT
* * **
28883 TGATTTAATAAAA-AATTGATATTTAAAAAAATTGTTTTTAATT
1 TAATTTAATAAAACAATTGATACTTAAAAAAATTAATTTTAATT
28926 TAATTTAAT
1 TAATTTAAT
28935 TTAATTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 32 0.73
44 5 0.11
46 7 0.16
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (44 bp):
TAATTTAATAAAACAATTGATACTTAAAAAAATTAATTTTAATT
Found at i:28929 original size:5 final size:5
Alignment explanation
Indices: 28919--28950 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
28909 AAAAATTGTT
28919 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
28951 AATAGGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:29226 original size:22 final size:22
Alignment explanation
Indices: 29184--29226 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29174 AAAAAAATTC
* *
29184 AATTTTATTAAAATTTTTAAAT
1 AATTTTATTAAAATATATAAAT
29206 AATTTT-TTAAAAATATATAAA
1 AATTTTATT-AAAATATATAAA
29227 AATACATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTATTAAAATATATAAAT
Found at i:29337 original size:18 final size:20
Alignment explanation
Indices: 29311--29349 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
29301 ATTTTAGATG
29311 AGTTCAAAA-CTA-AAAAAA
1 AGTTCAAAACCTATAAAAAA
*
29329 AGTTTAAAACCTATAAAAAA
1 AGTTCAAAACCTATAAAAAA
29349 A
1 A
29350 TGTCAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (20 bp):
AGTTCAAAACCTATAAAAAA
Found at i:31072 original size:27 final size:27
Alignment explanation
Indices: 31014--31072 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
31004 AAAATAGTAT
* * *
31014 ATAAATATATAAAAGAACTAAAATTTC
1 ATAAATATATAAAAAAAATAAAATATC
*
31041 ATAAATTTATAAAAAAAATATAAATATC
1 ATAAATATATAAAAAAAATA-AAATATC
31069 -TAAA
1 ATAAA
31073 AGAACTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAAATATATAAAAAAAATAAAATATC
Found at i:31212 original size:27 final size:28
Alignment explanation
Indices: 31175--31232 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
31165 TGTAAAAACT
31175 TTTTATATA-TTTTAAAATTTATTAAAA
1 TTTTATATATTTTTAAAATTTATTAAAA
* * * *
31202 TTTTATTTATTTTTTAATTTTTTTAAAA
1 TTTTATATATTTTTAAAATTTATTAAAA
31230 TTT
1 TTT
31233 ATGTCCACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTATATATTTTTAAAATTTATTAAAA
Found at i:38001 original size:11 final size:10
Alignment explanation
Indices: 37905--38003 Score: 53
Period size: 10 Copynumber: 9.8 Consensus size: 10
37895 TTATAAATTA
37905 TAATAAAAAT
1 TAATAAAAAT
* * *
37915 CTTAGAAATAT
1 -TAATAAAAAT
*
37926 TAAAAAAAAT
1 TAATAAAAAT
*
37936 TAA-AAAAAC
1 TAATAAAAAT
37945 T-ATAAATAAGT
1 TAATAAA-AA-T
37956 T-ATATAAAAT
1 TAATA-AAAAT
*
37966 TACT-AAAAT
1 TAATAAAAAT
*
37975 TATTAAAAAT
1 TAATAAAAAT
37985 TAATAAAAAGT
1 TAATAAAAA-T
*
37996 TTATAAAA
1 TAATAAAA
38004 TAAAAAATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
8 1 0.01
9 17 0.25
10 27 0.39
11 22 0.32
12 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:39707 original size:26 final size:27
Alignment explanation
Indices: 39678--39733 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
39668 AATAAACCAA
*
39678 ATTAATAAATAGAAAAAT-ATTATCTT
1 ATTAACAAATAGAAAAATAATTATCTT
* *
39704 ATTAACAACTAGAAAAATAATTATTTT
1 ATTAACAAATAGAAAAATAATTATCTT
39731 ATT
1 ATT
39734 TTTTAGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTAACAAATAGAAAAATAATTATCTT
Found at i:46512 original size:58 final size:59
Alignment explanation
Indices: 46408--46557 Score: 167
Period size: 58 Copynumber: 2.5 Consensus size: 59
46398 CATTAGAATT
* * * * * * *
46408 TGAACTTTCTTTTTATCCAAGTTAGACCCTAAATTTGGCAATTGTTCTCATATTGAGGCA
1 TGAACTTT-TTTTTATCCAAGTTAGACCTTGAACTTGGCAAATGTTCCCAAATTGAGACA
* * * *
46468 TGAA-TTTTTTTTGTCCAAGTTAGGCCTTGAACTTGGGAAATGTTCCCAAATTGAGACT
1 TGAACTTTTTTTTATCCAAGTTAGACCTTGAACTTGGCAAATGTTCCCAAATTGAGACA
* *
46526 TCAACTTTTTTTTATCCAAGTTAGTCCTTGAA
1 TGAACTTTTTTTTATCCAAGTTAGACCTTGAA
46558 AACCTAAAGT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 43 0.57
59 28 0.37
60 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (59 bp):
TGAACTTTTTTTTATCCAAGTTAGACCTTGAACTTGGCAAATGTTCCCAAATTGAGACA
Found at i:47557 original size:24 final size:24
Alignment explanation
Indices: 47515--47566 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
47505 AATCAAAGTC
** *
47515 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
47539 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
47563 AAAT
1 AAAT
47567 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:51984 original size:24 final size:24
Alignment explanation
Indices: 51938--51989 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
51928 AATCAAAGTC
** *
51938 AAATATATTATGTTAATATATACT
1 AAATATATTATACTAATAAATACT
*
51962 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
51986 AAAT
1 AAAT
51990 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:53176 original size:20 final size:22
Alignment explanation
Indices: 53134--53177 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
53124 AAATATTTTG
*
53134 AATATTTTATTTTAATATTTAAT
1 AATAATTTATTTTAATA-TTAAT
53157 AATAATTTA-TTTAATA-TAAT
1 AATAATTTATTTTAATATTAAT
53177 A
1 A
53178 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATAATTTATTTTAATATTAAT
Found at i:61617 original size:37 final size:37
Alignment explanation
Indices: 61567--61642 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
61557 TTCAAACCAG
61567 AAAGGTTCTTATAGAATATGTTCCCGACATCTATGTT
1 AAAGGTTCTTATAGAATATGTTCCCGACATCTATGTT
61604 AAAGGTTCTTATAGAATATGTTCCCGACATCTATGTT
1 AAAGGTTCTTATAGAATATGTTCCCGACATCTATGTT
61641 AA
1 AA
61643 TCTAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (37 bp):
AAAGGTTCTTATAGAATATGTTCCCGACATCTATGTT
Found at i:64231 original size:35 final size:35
Alignment explanation
Indices: 64192--64268 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
64182 AGTTCACAAG
64192 TTAATTTTTTAAATAATAAAAAACCTAACACTGTA
1 TTAATTTTTTAAATAATAAAAAACCTAACACTGTA
64227 TTAATTTTTTAAATAATAAAAAACCTAACACTGTA
1 TTAATTTTTTAAATAATAAAAAACCTAACACTGTA
*
64262 TTGATTT
1 TTAATTT
64269 AAATAAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (35 bp):
TTAATTTTTTAAATAATAAAAAACCTAACACTGTA
Found at i:66314 original size:16 final size:16
Alignment explanation
Indices: 66295--66328 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
66285 CCAAAAATAA
66295 AAAAACAAAAACCT-AC
1 AAAAA-AAAAACCTGAC
66311 AAAAAAAAAACCTGAC
1 AAAAAAAAAACCTGAC
66327 AA
1 AA
66329 CAGCCTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAACCTGAC
Found at i:66744 original size:22 final size:22
Alignment explanation
Indices: 66719--66784 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 22
66709 ATTGTTTTGG
66719 TAATTTGATGAGAATAGTTTAT
1 TAATTTGATGAGAATAGTTTAT
* *
66741 TAA-TT-A--A-AAAAATTTACT
1 TAATTTGATGAGAATAGTTTA-T
*
66759 AAATTTGATGAGAATAGTTTA-
1 TAATTTGATGAGAATAGTTTAT
66780 TAATT
1 TAATT
66785 ATAATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
17 7 0.22
18 4 0.12
19 2 0.06
20 2 0.06
21 6 0.19
22 4 0.12
23 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (22 bp):
TAATTTGATGAGAATAGTTTAT
Found at i:67129 original size:18 final size:17
Alignment explanation
Indices: 67100--67134 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
67090 GTAATGTTTC
*
67100 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
67117 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
67135 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:67378 original size:27 final size:26
Alignment explanation
Indices: 67324--67387 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
67314 TTTTTTTTAG
* **
67324 AATATTTTGGTAAATAAAAAAATTAT
1 AATAATTTGGTAAATAAAAAAAGGAT
*
67350 AATAATTTGTTAAATAAAAAAAGGGAT
1 AATAATTTGGTAAATAAAAAAA-GGAT
* *
67377 AACATTTTGGT
1 AATAATTTGGT
67388 TATTTTTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (26 bp):
AATAATTTGGTAAATAAAAAAAGGAT
Found at i:70155 original size:31 final size:32
Alignment explanation
Indices: 70114--70176 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
70104 TGGGACAACA
* *
70114 CAATGGGTCACGCCTAGGGAAGAGGCGGCACC
1 CAATGGGTCACACCTAGGGAACAGGCGGCACC
* *
70146 CAAT-GGTCACACCTTGGGCACAGGCGGCACC
1 CAATGGGTCACACCTAGGGAACAGGCGGCACC
70177 ACCAATCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.24, C:0.32, G:0.33, T:0.11
Consensus pattern (32 bp):
CAATGGGTCACACCTAGGGAACAGGCGGCACC
Found at i:70773 original size:25 final size:24
Alignment explanation
Indices: 70728--70776 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
70718 ATATAGTTTT
70728 TATATTATTTATAAAGGTTATAATA
1 TATATTATTTATAAA-GTTATAATA
70753 TATATTATATTATAATA-TTATAAT
1 TATATTAT-TTATAA-AGTTATAAT
70777 TAAACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.68
26 6 0.27
27 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATTATTTATAAAGTTATAATA
Found at i:71725 original size:41 final size:41
Alignment explanation
Indices: 71647--71745 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
71637 CTATATGATT
* *
71647 AGCACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAACG
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
*
71687 AGCACTAAGTGTGCGAAATTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
*
71728 GGCACTAAGTGTGCGAAA
1 AGCACTAAGTGTGCGAAA
71746 CCGAGATCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 15 0.28
41 39 0.72
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
Found at i:76493 original size:33 final size:33
Alignment explanation
Indices: 76409--76493 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 33
76399 TAGTCCAGTC
* *
76409 CCACCACAGTACAATACTTCTCTCGGCCCGTAT
1 CCACCACAGTACAACACTCCTCTCGGCCCGTAT
* * ** * **
76442 CCACTACATTACTTCACTCCTCTTGGGTCGTAT
1 CCACCACAGTACAACACTCCTCTCGGCCCGTAT
76475 CCACCACAGTACAACACTC
1 CCACCACAGTACAACACTC
76494 TTCCCCATAT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.25, C:0.39, G:0.11, T:0.26
Consensus pattern (33 bp):
CCACCACAGTACAACACTCCTCTCGGCCCGTAT
Found at i:76964 original size:62 final size:61
Alignment explanation
Indices: 76886--77053 Score: 246
Period size: 62 Copynumber: 2.7 Consensus size: 61
76876 ATTAATTGCA
* *
76886 ACATTACAACACTAAAACTTGGAACAAACTTTATAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAA-TTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * *
76948 ACATTACAATATTAAAAATTAGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATT-AAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* *
77010 ACATTATAACATTAGAAATTGGAAAAAACTTTGTAATATAAATT
1 ACATTACAACATTA-AAATTGGAACAAACTTTGTAATATAAATT
77054 AAATACATTA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
61 1 0.01
62 90 0.95
63 4 0.04
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (61 bp):
ACATTACAACATTAAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
Found at i:77110 original size:48 final size:48
Alignment explanation
Indices: 76991--77102 Score: 188
Period size: 48 Copynumber: 2.3 Consensus size: 48
76981 TAATATAAAT
* * *
76991 TTTGTTATATAAATTAAATACATTATAACATTAGAAATTGGAAAAAAC
1 TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAAAAAAC
*
77039 TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAACAAAC
1 TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAAAAAAC
77087 TTTGTAATATAAATTA
1 TTTGTAATATAAATTA
77103 GGTACATTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (48 bp):
TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAAAAAAC
Found at i:80437 original size:31 final size:31
Alignment explanation
Indices: 80396--80457 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
80386 TACACCAGAA
*
80396 TGGACTAAGTGGTGCCGCCTATCACTTTGGC
1 TGGACAAAGTGGTGCCGCCTATCACTTTGGC
80427 TGGACAAAGTGGTGCCGCCTATCACTTTGGC
1 TGGACAAAGTGGTGCCGCCTATCACTTTGGC
80458 ACCGCTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (31 bp):
TGGACAAAGTGGTGCCGCCTATCACTTTGGC
Found at i:80850 original size:19 final size:19
Alignment explanation
Indices: 80826--80866 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
80816 TATACACACT
80826 AAATTCCAAGGTTAAGTCA
1 AAATTCCAAGGTTAAGTCA
80845 AAATTCCAAGGTTAAGTCA
1 AAATTCCAAGGTTAAGTCA
80864 AAA
1 AAA
80867 ACTAGCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (19 bp):
AAATTCCAAGGTTAAGTCA
Found at i:84670 original size:29 final size:29
Alignment explanation
Indices: 84638--84697 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
84628 ACAGGACGGA
* * *
84638 TTCTGAAAAAATAGTTTTGAGGGGATGGG
1 TTCTGAAAAAATAATTTTGACGAGATGGG
84667 TTCTGAAAAAATAATTTTGACGAGATGGG
1 TTCTGAAAAAATAATTTTGACGAGATGGG
84696 TT
1 TT
84698 GAGTTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
TTCTGAAAAAATAATTTTGACGAGATGGG
Found at i:87139 original size:110 final size:111
Alignment explanation
Indices: 86931--87151 Score: 426
Period size: 110 Copynumber: 2.0 Consensus size: 111
86921 TAGTGGGTGG
86931 CAAAGGACTAATGTAACCTTATTATATATGTTTAATATATATATATAGGTAAAGGTTAATATAGT
1 CAAAGGACTAATGTAACCTTATTATATATGTTTAATATATATATATAGGTAAAGGTTAATATAGT
86996 AAACTAATAATAAGGTTAATATATGTTTAATATAACAAATTAAAAA
66 AAACTAATAATAAGGTTAATATATGTTTAATATAACAAATTAAAAA
87042 CAAAGGACT-ATGTAACCTTATTATATATGTTTAATATATATATATAGGTAAAGGTTAATATAGT
1 CAAAGGACTAATGTAACCTTATTATATATGTTTAATATATATATATAGGTAAAGGTTAATATAGT
*
87106 AAACTAATAATAAGGTTAATATATGTTTTATATAACAAATTAAAAA
66 AAACTAATAATAAGGTTAATATATGTTTAATATAACAAATTAAAAA
87152 GCCATGTTCT
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 100 0.92
111 9 0.08
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (111 bp):
CAAAGGACTAATGTAACCTTATTATATATGTTTAATATATATATATAGGTAAAGGTTAATATAGT
AAACTAATAATAAGGTTAATATATGTTTAATATAACAAATTAAAAA
Found at i:88069 original size:42 final size:43
Alignment explanation
Indices: 88010--88122 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 43
88000 TGTGTTTTCG
* *
88010 TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGATT-CC
1 TGTAAGACCACGTCTGGGACGTTGGCATCAACATGTGATTACA
*
88052 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGACATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAACATGTGATTACA
*
88095 TGTAAGACCACGTCTGTGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
88123 TGTACGGACT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 35 0.56
43 25 0.40
44 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAACATGTGATTACA
Found at i:102416 original size:26 final size:25
Alignment explanation
Indices: 102373--102421 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
102363 TAGTTATACC
*
102373 AAAATTTCCAACACTATACTAAAACT
1 AAAATTTCAAACACTATA-TAAAACT
102399 AAAATTTCAAAC-CATATATAAAA
1 AAAATTTCAAACAC-TATATAAAA
102422 AATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAATTTCAAACACTATATAAAACT
Found at i:112053 original size:25 final size:25
Alignment explanation
Indices: 112025--112072 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
112015 TGGAATGCTA
112025 TTCTAACAGTGTTTATGAAATAACT
1 TTCTAACAGTGTTTATGAAATAACT
*
112050 TTCTAACAGTTTTTATGAAATAA
1 TTCTAACAGTGTTTATGAAATAA
112073 AGATTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (25 bp):
TTCTAACAGTGTTTATGAAATAACT
Found at i:114103 original size:4 final size:4
Alignment explanation
Indices: 114096--114146 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
114086 GCATGCACGC
114096 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
114144 ATG
1 ATG
114147 AAAATGAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:122088 original size:23 final size:23
Alignment explanation
Indices: 122058--122104 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
122048 CCCCACGCCC
122058 TTTCGGGTTAAGAGGAGTATTTA
1 TTTCGGGTTAAGAGGAGTATTTA
122081 TTTCGGGTTAAGAGGAGTATTTA
1 TTTCGGGTTAAGAGGAGTATTTA
122104 T
1 T
122105 AGGGGCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.40
Consensus pattern (23 bp):
TTTCGGGTTAAGAGGAGTATTTA
Found at i:122599 original size:18 final size:18
Alignment explanation
Indices: 122564--122601 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
122554 ATTATAAAAA
*
122564 ATGTTATAATAATTATAT
1 ATGTTATAATAATAATAT
122582 ATGTTA-AATAATAAATAT
1 ATGTTATAATAAT-AATAT
122600 AT
1 AT
122602 ATATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATGTTATAATAATAATAT
Found at i:125337 original size:24 final size:25
Alignment explanation
Indices: 125294--125348 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
125284 GCTTATTCGG
125294 GCTTAATAACAGAAAACTCATAAGA
1 GCTTAATAACAGAAAACTCATAAGA
* * *
125319 GTTTAA-AACAGAAAGCTCATATGA
1 GCTTAATAACAGAAAACTCATAAGA
125343 GCTTAA
1 GCTTAA
125349 CGGGATAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (25 bp):
GCTTAATAACAGAAAACTCATAAGA
Found at i:125762 original size:18 final size:18
Alignment explanation
Indices: 125739--125799 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
125729 TGGGGCATTA
125739 TCATACATGTGATCAATT
1 TCATACATGTGATCAATT
** *
125757 TCATACATAAG-GC-ATT
1 TCATACATGTGATCAATT
125773 ATCATACATGTGATCAATT
1 -TCATACATGTGATCAATT
125792 TCATACAT
1 TCATACAT
125800 AATTTAGTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 18 0.53
19 3 0.09
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (18 bp):
TCATACATGTGATCAATT
Found at i:125778 original size:35 final size:35
Alignment explanation
Indices: 125732--125801 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
125722 TTATTTTTGG
125732 GGCATTATCATACATGTGATCAATTTCATACATAA
1 GGCATTATCATACATGTGATCAATTTCATACATAA
125767 GGCATTATCATACATGTGATCAATTTCATACATAA
1 GGCATTATCATACATGTGATCAATTTCATACATAA
125802 TTTAGTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (35 bp):
GGCATTATCATACATGTGATCAATTTCATACATAA
Found at i:136754 original size:23 final size:23
Alignment explanation
Indices: 136728--136784 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
136718 TTACAAGTCA
136728 TTATACCAAAATAAGTTTGCTAT
1 TTATACCAAAATAAGTTTGCTAT
136751 TTATACCAAAATAAGTTTGCTAT
1 TTATACCAAAATAAGTTTGCTAT
136774 TTATACCAAAA
1 TTATACCAAAA
136785 CGAGCTGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (23 bp):
TTATACCAAAATAAGTTTGCTAT
Found at i:137322 original size:25 final size:25
Alignment explanation
Indices: 137270--137322 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
137260 CACTCTCTCA
* **
137270 AGCCATATAACAGGAAGCTCATGTG
1 AGCCATATAACAGAAAGCTCATCCG
* *
137295 AGCCATGTAACAGAAAGCTTATCCG
1 AGCCATATAACAGAAAGCTCATCCG
137320 AGC
1 AGC
137323 TTAATACAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (25 bp):
AGCCATATAACAGAAAGCTCATCCG
Found at i:137481 original size:25 final size:25
Alignment explanation
Indices: 137443--137491 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
137433 CAAGCGAGCC
137443 ATATCAGGAAGCTCACAAAGAGCTT
1 ATATCAGGAAGCTCACAAAGAGCTT
* * *
137468 ATATCGGGACGCTCATAAAGAGCT
1 ATATCAGGAAGCTCACAAAGAGCT
137492 ACAGTATGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (25 bp):
ATATCAGGAAGCTCACAAAGAGCTT
Found at i:142540 original size:16 final size:18
Alignment explanation
Indices: 142514--142546 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
142504 TTTAATTAGA
142514 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
142531 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
142547 CCAATTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:155436 original size:13 final size:13
Alignment explanation
Indices: 155403--155438 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
155393 ATAGTGATTT
*
155403 ATTATAATAAATA
1 ATTAAAATAAATA
155416 ATTTAAAATAAATA
1 A-TTAAAATAAATA
155430 ATTAAAATA
1 ATTAAAATA
155439 TCTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTAAAATAAATA
Found at i:170583 original size:44 final size:42
Alignment explanation
Indices: 170482--170584 Score: 100
Period size: 44 Copynumber: 2.3 Consensus size: 42
170472 TATGTAGGTA
* *
170482 TAATAATAATAATAATAATATATTATATGATAAATAAAAAAAT
1 TAATAAT-ATAATAATAATATATAATATGACAAATAAAAAAAT
* * *
170525 TAAAAAAAACTAATAATAATATAGTAATAATG-CAAATAAACAATAT
1 T-AATAATA-TAATAATAATATA-TAAT-ATGACAAATAAA-AAAAT
170571 TAATAATATAATAA
1 TAATAATATAATAA
170585 AAAGAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
43 2 0.04
44 23 0.48
45 15 0.31
46 8 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (42 bp):
TAATAATATAATAATAATATATAATATGACAAATAAAAAAAT
Found at i:171175 original size:12 final size:13
Alignment explanation
Indices: 171150--171183 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
171140 TTCTCTTCTC
*
171150 TTTTGTTATTTTG
1 TTTTGTTTTTTTG
171163 TTTT-TTTTTTTG
1 TTTTGTTTTTTTG
171175 TTTTGTTTT
1 TTTTGTTTT
171184 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTGTTTTTTTG
Found at i:174864 original size:101 final size:101
Alignment explanation
Indices: 174689--174915 Score: 384
Period size: 101 Copynumber: 2.2 Consensus size: 101
174679 GAATTGACGC
* * * *
174689 ATAAGACCATAACTAGGTTATGGCACTATGAACTTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTTA
* *
174754 TATGTAAGACCATAGTTGGGTTATAG-CATTCTGATG
66 TATGTAAGACCATAGCTGGGCTAT-GTCATTCTGATG
174790 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTTA
174855 TATGTAAGACCATAGCTGGGCTATGTCATTCTGATG
66 TATGTAAGACCATAGCTGGGCTATGTCATTCTGATG
174891 ATAAGACCATAACTGGGTTATGACA
1 ATAAGACCATAACTGGGTTATGACA
174916 TTACGAATGT
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
100 1 0.01
101 118 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTTA
TATGTAAGACCATAGCTGGGCTATGTCATTCTGATG
Found at i:174901 original size:33 final size:32
Alignment explanation
Indices: 174755--174917 Score: 112
Period size: 33 Copynumber: 4.9 Consensus size: 32
174745 CAGTGTTTAT
*
174755 ATGTAAGACCATAGTTGGGTTAT-AGCATTCTG
1 ATGTAAGACCATAGCTGGGTTATGA-CATTCTG
* * *
174787 ATGATAAGACCATAACTGGGTTATGACACTATG
1 ATG-TAAGACCATAGCTGGGTTATGACATTCTG
* * * *** * * *
174820 AACGTAAGACCATGGTTGGACCATGGCAATGTTTAT
1 -ATGTAAGACCATAGCTGGGTTATGAC-AT-TCT-G
* *
174856 ATGTAAGACCATAGCTGGGCTATGTCATTCTG
1 ATGTAAGACCATAGCTGGGTTATGACATTCTG
*
174888 ATGATAAGACCATAACTGGGTTATGACATT
1 ATG-TAAGACCATAGCTGGGTTATGACATT
174918 ACGAATGTAA
Statistics
Matches: 98, Mismatches: 26, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
32 6 0.06
33 64 0.65
34 6 0.06
35 22 0.22
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGTTATGACATTCTG
Found at i:174971 original size:24 final size:24
Alignment explanation
Indices: 174921--174971 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
174911 TGACATTACG
*
174921 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACAGAA
*
174945 AATGTAAAGGATGAATTGACAGTA
1 AATGTAAAGGATGAATTGACAGAA
174969 AAT
1 AAT
174972 TACCCAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACAGAA
Found at i:181940 original size:23 final size:25
Alignment explanation
Indices: 181886--181941 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
181876 TAAAAATGAA
181886 AATATATTATTTTATATTATATTTT
1 AATATATTATTTTATATTATATTTT
*
181911 AA-A-ATTATTTTATA-T-TCTTTT
1 AATATATTATTTTATATTATATTTT
181932 AATATATTAT
1 AATATATTAT
181942 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 16 0.57
24 1 0.04
25 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
AATATATTATTTTATATTATATTTT
Found at i:188514 original size:29 final size:30
Alignment explanation
Indices: 188468--188525 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
188458 ATATTGGTTG
* *
188468 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTTGGATTTTTGCTGTTAATGCTGTTC
188498 TGATTTGGA-TTTTGCTGTTAATGCTGTT
1 TGATTTGGATTTTTGCTGTTAATGCTGTT
188526 AATGGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (30 bp):
TGATTTGGATTTTTGCTGTTAATGCTGTTC
Found at i:189257 original size:311 final size:312
Alignment explanation
Indices: 188692--189304 Score: 1185
Period size: 311 Copynumber: 2.0 Consensus size: 312
188682 TATACATGCT
188692 GTAATGGGTCTGTAATTTGTTTTCATTAGTTTGATCATGTCTAATACCGGCAAATGCATATGTCC
1 GTAATGGGTCTGTAATTTGTTTTCATTAGTTTGATCATGTCTAATACCGGCAAATGCATATGTCC
188757 CGAACCTATTACTGGTTATACTAATTTTTTTTTTATTTTTTTAAAACTAATTTGTCATCCCTATT
66 CGAACCTATTACTGGTTATACTAA-TTTTTTTTTATTTTTTTAAAACTAATTTGTCATCCCTATT
*
188822 CCCTACTACCAAGTACCAGCTACCAACCTATTGCCTATGCATGCATTTCTGCTCCAATTCTTACA
130 CCCTACTACCAAGTACCAACTACCAACCTATTGCCTATGCATGCATTTCTGCTCCAATTCTTACA
188887 TTTCCCCATGTTTTCCATTATTTTGGGACCAATGATATAAGATGGTAGCCTTTCCACCAAATATA
195 TTTCCCCATGTTTTCCATTATTTTGGGACCAATGATATAAGATGGTAGCCTTTCCACCAAATATA
188952 TT-CTTTCATTCTTACTATTGTCAGAAAACCACAAGTCTATTTGTTTTCATGAG
260 TTAC-TTCATTCTTACTATTGTCAGAAAACCACAAGTCTATTTGTTTTCATGAG
189005 GTAATGGGTCTGTAATTTGTTTTCATTAGTTTGATCATGTCTAATACCGGCAAATGCATATGTCC
1 GTAATGGGTCTGTAATTTGTTTTCATTAGTTTGATCATGTCTAATACCGGCAAATGCATATGTCC
189070 CGAACCTATTACTGGTTATACTAA-TTTTTTTTATTTTTTTAAAACTAATTTGTCATCCCTATTC
66 CGAACCTATTACTGGTTATACTAATTTTTTTTTATTTTTTTAAAACTAATTTGTCATCCCTATTC
189134 CCTACTACCAAGTACCAACTACCAACCTATTGCCTATGCATGCATTTCTGCTCCAATTCTTACAT
131 CCTACTACCAAGTACCAACTACCAACCTATTGCCTATGCATGCATTTCTGCTCCAATTCTTACAT
189199 TTCCCCATGTTTTCCATTATTTTGGGACCAATGATATAAGATGGTAGCCTTTCCACCAAATATAT
196 TTCCCCATGTTTTCCATTATTTTGGGACCAATGATATAAGATGGTAGCCTTTCCACCAAATATAT
189264 TACTTCATTCTTACTATTGTCAGAAAACCACAAGTCTATTT
261 TACTTCATTCTTACTATTGTCAGAAAACCACAAGTCTATTT
189305 CAGTGTGGAA
Statistics
Matches: 298, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
311 208 0.70
312 1 0.00
313 89 0.30
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.40
Consensus pattern (312 bp):
GTAATGGGTCTGTAATTTGTTTTCATTAGTTTGATCATGTCTAATACCGGCAAATGCATATGTCC
CGAACCTATTACTGGTTATACTAATTTTTTTTTATTTTTTTAAAACTAATTTGTCATCCCTATTC
CCTACTACCAAGTACCAACTACCAACCTATTGCCTATGCATGCATTTCTGCTCCAATTCTTACAT
TTCCCCATGTTTTCCATTATTTTGGGACCAATGATATAAGATGGTAGCCTTTCCACCAAATATAT
TACTTCATTCTTACTATTGTCAGAAAACCACAAGTCTATTTGTTTTCATGAG
Found at i:190111 original size:13 final size:13
Alignment explanation
Indices: 190093--190223 Score: 126
Period size: 13 Copynumber: 10.2 Consensus size: 13
190083 ATTTTTAATG
190093 TAATATACTGTTT
1 TAATATACTGTTT
*
190106 TAATATACTGTTA
1 TAATATACTGTTT
*
190119 TAA-A-A-T-TTG
1 TAATATACTGTTT
190128 TAATATACTGTTT
1 TAATATACTGTTT
*
190141 TAATATACTATTAT
1 TAATATACTGTT-T
* *
190155 AAATATACTTTTT
1 TAATATACTGTTT
* *
190168 TGATATATTGTTT
1 TAATATACTGTTT
190181 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
190195 AAATATATTGTTT
1 TAATATACTGTTT
*
190208 TAATATAATGTTT
1 TAATATACTGTTT
190221 TAA
1 TAA
190224 CTTTTAATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
11 2 0.02
12 2 0.02
13 63 0.66
14 22 0.23
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:190137 original size:35 final size:37
Alignment explanation
Indices: 190091--190199 Score: 141
Period size: 35 Copynumber: 2.9 Consensus size: 37
190081 TAATTTTTAA
190091 TGTAATATACTGTTTTAATATACTGTTATAAA-A-TT
1 TGTAATATACTGTTTTAATATACTGTTATAAATACTT
*
190126 TGTAATATACTGTTTTAATATACTATTATAAATATACTTT
1 TGTAATATACTGTTTTAATATACTGTTAT-AA-ATAC-TT
* * *
190166 TTTGATATATTGTTTTAATATACTGTTATAAATA
1 TGTAATATACTGTTTTAATATACTGTTATAAATA
190200 TATTGTTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
35 28 0.44
36 2 0.03
37 1 0.02
38 4 0.06
39 2 0.03
40 27 0.42
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (37 bp):
TGTAATATACTGTTTTAATATACTGTTATAAATACTT
Found at i:190159 original size:27 final size:26
Alignment explanation
Indices: 190093--190223 Score: 126
Period size: 27 Copynumber: 5.1 Consensus size: 26
190083 ATTTTTAATG
* *
190093 TAATATACTGTTTTAATATACTGTTA
1 TAATATATTGTTTTAATATACTGTTT
*
190119 TAA-A-A-T-TTGTAATATACTGTTT
1 TAATATATTGTTTTAATATACTGTTT
* * * *
190141 TAATATACTATTATAAATATACTTTTT
1 TAATATATTGTT-TTAATATACTGTTT
*
190168 TGATATATTGTTTTAATATACTGTTAT
1 TAATATATTGTTTTAATATACTGTT-T
* *
190195 AAATATATTGTTTTAATATAATGTTT
1 TAATATATTGTTTTAATATACTGTTT
190221 TAA
1 TAA
190224 CTTTTAATAT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
22 17 0.20
23 2 0.02
24 2 0.02
25 2 0.02
26 19 0.22
27 43 0.51
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.52
Consensus pattern (26 bp):
TAATATATTGTTTTAATATACTGTTT
Found at i:190185 original size:40 final size:40
Alignment explanation
Indices: 190093--190223 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
190083 ATTTTTAATG
* *
190093 TAATATACTGTTTTAATATACTGTTATAAA-AT-TTG---
1 TAATATAATGTTTTAATATACTATTATAAATATATTGTTT
*
190128 TAATATACTGTTTTAATATACTATTATAAATATACTT-TTT
1 TAATATAATGTTTTAATATACTATTATAAATATA-TTGTTT
* * *
190168 TGATATATTGTTTTAATATACTGTTATAAATATATTGTTT
1 TAATATAATGTTTTAATATACTATTATAAATATATTGTTT
190208 TAATATAATGTTTTAA
1 TAATATAATGTTTTAA
190224 CTTTTAATAT
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
35 29 0.35
36 2 0.02
38 2 0.02
39 2 0.02
40 48 0.58
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.52
Consensus pattern (40 bp):
TAATATAATGTTTTAATATACTATTATAAATATATTGTTT
Found at i:193753 original size:19 final size:19
Alignment explanation
Indices: 193729--193799 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
193719 AATATTTAAA
193729 TTGACAGTTTTGGTATTAT
1 TTGACAGTTTTGGTATTAT
* * *
193748 TTGACAGTTTTTTTGCAGTTTT
1 TTGACAG--TTTTGGTA-TTAT
193770 TTGACAGTTTTGGTATTAT
1 TTGACAGTTTTGGTATTAT
193789 TTGACAGTTTT
1 TTGACAGTTTT
193800 TTTTGGTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 21 0.49
20 6 0.14
21 6 0.14
22 10 0.23
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.55
Consensus pattern (19 bp):
TTGACAGTTTTGGTATTAT
Found at i:193768 original size:11 final size:12
Alignment explanation
Indices: 193747--193780 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
193737 TTTGGTATTA
193747 TTTGACAGTTTT
1 TTTGACAGTTTT
193759 TTTG-CAG-TTT
1 TTTGACAGTTTT
193769 TTTGACAGTTTT
1 TTTGACAGTTTT
193781 GGTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.35
11 6 0.30
12 7 0.35
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.59
Consensus pattern (12 bp):
TTTGACAGTTTT
Found at i:193769 original size:10 final size:11
Alignment explanation
Indices: 193747--193780 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
193737 TTTGGTATTA
193747 TTTGACAGTTTT
1 TTTGACAG-TTT
193759 TTTG-CAGTTT
1 TTTGACAGTTT
193769 TTTGACAGTTT
1 TTTGACAGTTT
193780 T
1 T
193781 GGTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.15, C:0.09, G:0.18, T:0.59
Consensus pattern (11 bp):
TTTGACAGTTT
Found at i:195514 original size:23 final size:22
Alignment explanation
Indices: 195471--195514 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
195461 TTCTAAGTCG
195471 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
195494 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
195515 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:195627 original size:45 final size:45
Alignment explanation
Indices: 195561--195647 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
195551 CAGATACTTG
* *
195561 GTGGATTCAGCACATAACAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCA
*
195606 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGT
195648 TTGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (45 bp):
GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCA
Found at i:195723 original size:51 final size:51
Alignment explanation
Indices: 195658--195946 Score: 330
Period size: 51 Copynumber: 5.7 Consensus size: 51
195648 TTGGTTCACA
*
195658 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* * * ** * * *
195709 TAGAAGTCTGCACATAGTACTACACACGTGATCAAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* *
195760 TAGTAGCCTGCACATAGTACTACACATGTGACCATTCCCATCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* * * * ** * * *
195811 TAGAAGTCTGCACATAGTACTACTCACGTGATCAAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* * * *
195862 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCA-TCCGGTACACG
*
195912 TAGTAGCCTACACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
195947 CGCTTTCACT
Statistics
Matches: 190, Mismatches: 45, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
49 2 0.01
50 38 0.20
51 150 0.79
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
Found at i:195813 original size:102 final size:101
Alignment explanation
Indices: 195656--195942 Score: 470
Period size: 102 Copynumber: 2.8 Consensus size: 101
195646 GTTTGGTTCA
195656 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGGTACACGTAGAAGTCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATT-CCATCCGGTACACGTAGAAGTCTGCA
195721 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
195758 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTCCCATCCGGTACACGTAGAAGTCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATT-CCATCCGGTACACGTAGAAGTCTGCA
*
195823 CATAGTACTACTCACGTGATCAAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
* * * * *
195860 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TAT-CATTCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCAT-TCCA-TCCGGTACACGTAGAAGTCTGC
195923 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
195943 CCATCGCTTT
Statistics
Matches: 175, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
100 2 0.01
101 38 0.22
102 135 0.77
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATTCCATCCGGTACACGTAGAAGTCTGCAC
ATAGTACTACACACGTGATCAAAACTATCCGGTACG
Found at i:200631 original size:38 final size:38
Alignment explanation
Indices: 200577--200701 Score: 153
Period size: 38 Copynumber: 3.3 Consensus size: 38
200567 CGTTAATTCG
* * * *
200577 GGCTTTGTGCTGGTGATATTTGGGCTCTATGCCTAGCA
1 GGCTTTGTGCTAGTGATATTCGGGCTTTGTGCCTAGCA
* * *
200615 GGCTTTGTGCCAGTGATATTCGAGCTTTGTGTCTAGCA
1 GGCTTTGTGCTAGTGATATTCGGGCTTTGTGCCTAGCA
* *
200653 GGCTTTATG-TAGGTGATATTCGGGCTTTGTGCCTAGTA
1 GGCTTTGTGCTA-GTGATATTCGGGCTTTGTGCCTAGCA
200691 GGCTTTGTGCT
1 GGCTTTGTGCT
200702 GGTGTAATTG
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
37 1 0.01
38 70 0.97
39 1 0.01
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.38
Consensus pattern (38 bp):
GGCTTTGTGCTAGTGATATTCGGGCTTTGTGCCTAGCA
Found at i:224487 original size:12 final size:12
Alignment explanation
Indices: 224470--224499 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
224460 TTGTCGCCCC
224470 CTTTTTTTTTTT
1 CTTTTTTTTTTT
224482 CTTTTTTTTTTT
1 CTTTTTTTTTTT
224494 -TTTTTT
1 CTTTTTT
224500 CTTTCATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:224488 original size:9 final size:9
Alignment explanation
Indices: 224474--224503 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
224464 CGCCCCCTTT
224474 TTTTTTTTC
1 TTTTTTTTC
*
224483 TTTTTTTTT
1 TTTTTTTTC
224492 TTTTTTTTC
1 TTTTTTTTC
224501 TTT
1 TTT
224504 CATCCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:226170 original size:17 final size:17
Alignment explanation
Indices: 226150--226182 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
226140 TGCTTCATTA
226150 TTTTTTATATAATTCTT
1 TTTTTTATATAATTCTT
226167 TTTTTTATATAATTCT
1 TTTTTTATATAATTCT
226183 AATTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTATATAATTCTT
Found at i:226822 original size:3 final size:3
Alignment explanation
Indices: 226816--226843 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
226806 CAACAATTGT
226816 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
226844 CCAAACAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:228943 original size:23 final size:24
Alignment explanation
Indices: 228917--228964 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
228907 TAGATTAAGT
228917 ATTATATTTAAAATT-TTTTGAAA
1 ATTATATTTAAAATTATTTTGAAA
*
228940 ATTATATTTAAAATTATTTTTAAA
1 ATTATATTTAAAATTATTTTGAAA
228964 A
1 A
228965 CATATTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTATATTTAAAATTATTTTGAAA
Found at i:228954 original size:12 final size:12
Alignment explanation
Indices: 228917--228964 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
228907 TAGATTAAGT
228917 ATTATATTTAAA
1 ATTATATTTAAA
228929 ATT-T-TTTGAAA
1 ATTATATTT-AAA
228940 ATTATATTTAAA
1 ATTATATTTAAA
*
228952 ATTATTTTTAAA
1 ATTATATTTAAA
228964 A
1 A
228965 CATATTGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 3 0.09
11 7 0.22
12 19 0.59
13 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATTATATTTAAA
Found at i:228969 original size:23 final size:23
Alignment explanation
Indices: 228920--228975 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
228910 ATTAAGTATT
*
228920 ATATTTAAAATTTTTTGAAAATT
1 ATATTTAAAATTTTTTGAAAATC
*
228943 ATATTTAAAATTATTTTTAAAA-C
1 ATATTTAAAATT-TTTTGAAAATC
228966 ATATTGTAAA
1 ATATT-TAAA
228976 TCAATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATTTAAAATTTTTTGAAAATC
Found at i:230946 original size:14 final size:14
Alignment explanation
Indices: 230927--230968 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
230917 TCTTGATACT
*
230927 TTTTCAGTGGTTTA
1 TTTTCAGTGATTTA
230941 TTTTCAGTGATTTA
1 TTTTCAGTGATTTA
230955 -TTTCA-TGA-TTA
1 TTTTCAGTGATTTA
230966 TTT
1 TTT
230969 AGAAGGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 5 0.19
13 5 0.19
14 13 0.50
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (14 bp):
TTTTCAGTGATTTA
Found at i:234285 original size:6 final size:6
Alignment explanation
Indices: 234250--234281 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
234240 GTAGTCCCCC
*
234250 GTACCA GTACCA GTACCA GTACCA GTCCCA GT
1 GTACCA GTACCA GTACCA GTACCA GTACCA GT
234282 CCCACTACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (6 bp):
GTACCA
Found at i:247246 original size:16 final size:16
Alignment explanation
Indices: 247199--247247 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
247189 TTTTTGAATG
*
247199 AAAAT-TTAA-TATAC
1 AAAATATTAATTATAT
247213 AAAA-ATTAAATTAT-T
1 AAAATATT-AATTATAT
247228 AAAATATTAATTATAT
1 AAAATATTAATTATAT
247244 AAAA
1 AAAA
247248 AAATACGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 6 0.21
15 12 0.41
16 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTAATTATAT
Found at i:250803 original size:20 final size:20
Alignment explanation
Indices: 250778--250825 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
250768 GGGTGACACG
250778 GCCAAGCCACACGCCTGTGT
1 GCCAAGCCACACGCCTGTGT
250798 GCCAAGCCACACGCCTGTGT
1 GCCAAGCCACACGCCTGTGT
250818 GCCAAGCC
1 GCCAAGCC
250826 GTGAGATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.42, G:0.25, T:0.12
Consensus pattern (20 bp):
GCCAAGCCACACGCCTGTGT
Found at i:251970 original size:24 final size:25
Alignment explanation
Indices: 251908--251973 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
251898 GCTTATCCGG
*
251908 GCAATATAACGGGAAGCTCACAAAGA
1 GCAAT-TAACGGGTAGCTCACAAAGA
* *
251934 GTCTA-TAATGGGTAGCTC-CAAAGA
1 G-CAATTAACGGGTAGCTCACAAAGA
251958 GCAATTAACGGGTAGC
1 GCAATTAACGGGTAGC
251974 ACTGGATAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.06
24 17 0.52
25 11 0.33
26 1 0.03
27 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (25 bp):
GCAATTAACGGGTAGCTCACAAAGA
Found at i:252045 original size:26 final size:26
Alignment explanation
Indices: 251911--252076 Score: 107
Period size: 25 Copynumber: 6.7 Consensus size: 26
251901 TATCCGGGCA
*
251911 ATATAACGGGAAGCTCACAAAGAGTC
1 ATATAACGGGAAGCTCACAAAGAGCC
* * *
251937 -TATAATGGGTAGCTC-CAAAGAGCA
1 ATATAACGGGAAGCTCACAAAGAGCC
* ** *
251961 AT-TAACGGGTAG--CACTGGATAGCC
1 ATATAACGGGAAGCTCAC-AAAGAGCC
* **
251985 ATATAACGGGAAGTTCA-AGCGAG-C
1 ATATAACGGGAAGCTCACAAAGAGCC
* *
252009 A-CTAACAGGAAGCTCACAAAGAGCC
1 ATATAACGGGAAGCTCACAAAGAGCC
* *
252034 -TTTAATCGGGAAGCTCACGAAGAGCC
1 ATATAA-CGGGAAGCTCACAAAGAGCC
*
252060 ATATAACGGGACGCTCA
1 ATATAACGGGAAGCTCA
252077 TAAGAGCTGT
Statistics
Matches: 106, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 13 0.12
24 28 0.26
25 30 0.28
26 28 0.26
27 6 0.06
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (26 bp):
ATATAACGGGAAGCTCACAAAGAGCC
Found at i:255000 original size:15 final size:16
Alignment explanation
Indices: 254977--255009 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
254967 ACCAAAAACA
254977 AAAAAAAAAGAA-AAG
1 AAAAAAAAAGAAGAAG
*
254992 AAAAGAAAAGAAGAAG
1 AAAAAAAAAGAAGAAG
255008 AA
1 AA
255010 GCAATGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAG
Found at i:257996 original size:12 final size:12
Alignment explanation
Indices: 257979--258012 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
257969 CACCCTCCCA
257979 AAAAAAAAAACG
1 AAAAAAAAAACG
257991 AAAAAAAAAA-G
1 AAAAAAAAAACG
*
258002 AAAAAAGAAAC
1 AAAAAAAAAAC
258013 TCTAAAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACG
Found at i:267473 original size:4 final size:4
Alignment explanation
Indices: 267466--267550 Score: 52
Period size: 4 Copynumber: 21.5 Consensus size: 4
267456 TCTTTCTCCT
* * * * *
267466 TTTC TTTC CTT- TTTC TTTC TTTC CTTC TCTG TTTC GTTT- TTGC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
* *
267512 GTTC TTTC AATTCC TTT- TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC --TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
267551 ATTTATTTGA
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
3 9 0.15
4 45 0.75
5 3 0.05
6 3 0.05
ACGTcount: A:0.02, C:0.24, G:0.05, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:267956 original size:2 final size:2
Alignment explanation
Indices: 267949--267973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267939 GCTTAAGATG
267949 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
267974 GAAACCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:270098 original size:159 final size:160
Alignment explanation
Indices: 269922--270241 Score: 633
Period size: 159 Copynumber: 2.0 Consensus size: 160
269912 AAAAAAAGGG
269922 TAAAAGATACTAAATAGATAAATAAATAATAAAATAATATATATAATCTATAAAGGGTTGAAATT
1 TAAAAGATACTAAATAGATAAATAAATAATAAAATAATATATATAATCTATAAAGGGTTGAAATT
269987 AAATAAATAAGGGTCAAGTCACAATTTAGACAAAGTTAAGGGATAGATTGTAAAAAAAAAAAGAA
66 AAATAAATAAGGGTCAAGTCACAATTTAGACAAAGTTAAGGGATAGATTGTAAAAAAAAAAAGAA
270052 GAAAAGGCAGAATGAAGGGCCAAAATAAAA
131 GAAAAGGCAGAATGAAGGGCCAAAATAAAA
270082 TAAAAGATAC-AAATAGATAAATAAATAATAAAATAATATATATAATCTATAAAGGGTTGAAATT
1 TAAAAGATACTAAATAGATAAATAAATAATAAAATAATATATATAATCTATAAAGGGTTGAAATT
270146 AAATAAATAAGGGTCAAGTCACAATTTAGACAAAGTTAAGGGATAGATTGTAAAAAAAAAAAGAA
66 AAATAAATAAGGGTCAAGTCACAATTTAGACAAAGTTAAGGGATAGATTGTAAAAAAAAAAAGAA
270211 GAAAAGGCAGAATGAAGGGCCAAAATAAAA
131 GAAAAGGCAGAATGAAGGGCCAAAATAAAA
270241 T
1 T
270242 GAGCGAAAAG
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 150 0.94
160 10 0.06
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (160 bp):
TAAAAGATACTAAATAGATAAATAAATAATAAAATAATATATATAATCTATAAAGGGTTGAAATT
AAATAAATAAGGGTCAAGTCACAATTTAGACAAAGTTAAGGGATAGATTGTAAAAAAAAAAAGAA
GAAAAGGCAGAATGAAGGGCCAAAATAAAA
Found at i:271715 original size:45 final size:45
Alignment explanation
Indices: 271659--272244 Score: 509
Period size: 45 Copynumber: 12.8 Consensus size: 45
271649 TTGTAGCTTT
* * * *
271659 AATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGATGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* * *
271704 AATCTGCTCCACTGCAACTTCAGGGTGATAAGATTCGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* * *
271749 AATCTGCTCCAGTGCAACTTCAGGGAGATGAGATTTG-TAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* * * *
271793 AATCTGCT-CACTACAACTTGAGGGAGATAAGA-TTCACTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGA-TATCTTC
* *
271837 AATCTGTTCCACTAG-AACTTCAGGGAGATAAGATTTGTAACTTATAGCTTT
1 AATCTGCTCCACT-GCAACTTCAGGGAGATAAGATTTG--A--TAT--CTTC
* * * * *
271888 AATCTGTTCCACTGCAACTTCAGGGAAAGAAGATTTGCTATTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* ** * * *
271933 AATCTGTTCCACTATAACTTTAGGGAGATAA-AATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGA-TATCTTC
* * * * *
271978 AATCTGCTCCATTACAACTTCAAGGAGATAAGATTTGCTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* ** *
272023 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTTCTATTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* * * * * *
272068 AATCTACTCCACTACAACTTCAGGGGGATAAGGTTTGTAACTTGTAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--A----TATCTTC
* * *
272119 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* * * * * * *
272164 AATCTACTGCACTGCAACTTCAAGGAGATAAGATTGGTTGT-TTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
* *
272208 AATCTGCTCCACTACAACTTTAGGGAGATAAGATTTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
272245 TTGTAACAAC
Statistics
Matches: 433, Mismatches: 89, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
42 2 0.00
43 20 0.05
44 62 0.14
45 266 0.61
46 5 0.01
47 3 0.01
48 1 0.00
49 2 0.00
50 1 0.00
51 71 0.16
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGATATCTTC
Found at i:272144 original size:96 final size:92
Alignment explanation
Indices: 271604--272243 Score: 488
Period size: 96 Copynumber: 6.9 Consensus size: 92
271594 GGATTTGTCG
* * ** *
271604 CTTCAATCTACTCCACTGCAACTTTAGAGG-GATAAGATTAATAACTTGTAGCTTTAATCTGTTC
1 CTTCAATCTGCTCCACTGCAACTTCAG-GGAGATAAGATT--TGTCTT-TA-CTTCAATCTGTTC
* ** *
271668 CACTGCAACTTTAGGGAAATAAGATTTGATGT
61 CACTGCAACTTCAGGGAAATAAGATTTTCTAT
* * * * *
271700 CTTCAATCTGCTCCACTGCAACTTCAGGGTGATAAGATTCGT-TAT-CTTCAATCTGCTCCAGTG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTTTACTTCAATCTGTTCCACTG
* * * *
271763 CAACTTCAGGGAGATGAGA-TTTGTAG
66 CAACTTCAGGGAAATAAGATTTTCTAT
* * ** *
271789 CTTCAATCTGCT-CACTACAACTTGAGGGAGATAAGA-TTCACTGT-CTTCAATCTGTTCCACTA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTTTACTTCAATCTGTTCCACT-
*
271851 G-AACTTCAGGGAGATAAGATTTGTAACTTAT
65 GCAACTTCAGGGAAATAAGATTT-T--C-TAT
* * * *
271882 AGCTTTAATCTGTTCCACTGCAACTTCAGGGAAAGAAGATTTG-CTATT--TTCAATCTGTTCCA
1 --CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCT-TTACTTCAATCTGTTCCA
** * * * **
271944 CTATAACTTTAGGGAGATAAAATTCACTAT
63 CTGCAACTTCAGGGAAATAAGATTTTCTAT
* * * * * *
271974 CTTCAATCTGCTCCATTACAACTTCAAGGAGATAAGATTTG-CTAT-CTTTAATCTGCTCCACTG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTTTACTTCAATCTGTTCCACTG
272037 CAACTTCAGGGAAATAAGATTTTCTAT
66 CAACTTCAGGGAAATAAGATTTTCTAT
* * * * * *
272064 TTTCAATCTACTCCACTACAACTTCAGGGGGATAAGGTTTGTAACTTGTAGCTTTAATCTGTTCC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT--CTT-TA-CTTCAATCTGTTCC
272129 ACTGCAACTTCAGGGAAATAAGATTTGT-TAT
62 ACTGCAACTTCAGGGAAATAAGATTT-TCTAT
* * * * *
272160 CTTCAATCTACTGCACTGCAACTTCAAGGAGATAAGATTGGT-TGTT--TT-AATCTGCTCCACT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCT-TTACTTCAATCTGTTCCACT
* * *
272221 ACAACTTTAGGGAGATAAGATTT
65 GCAACTTCAGGGAAATAAGATTT
272244 GTTGTAACAA
Statistics
Matches: 444, Mismatches: 77, Indels: 53
0.77 0.13 0.09
Matches are distributed among these distances:
87 1 0.00
88 55 0.12
89 51 0.11
90 140 0.32
92 4 0.01
93 8 0.02
94 2 0.00
95 12 0.03
96 167 0.38
97 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (92 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCTTTACTTCAATCTGTTCCACTG
CAACTTCAGGGAAATAAGATTTTCTAT
Found at i:272185 original size:141 final size:137
Alignment explanation
Indices: 271659--272239 Score: 592
Period size: 141 Copynumber: 4.2 Consensus size: 137
271649 TTGTAGCTTT
* * * *
271659 AATCTGTTCCACTGCAACTTTAGGGAAATAAG-ATTTGA-TGT-CTTCAATCTGCTCCACTGCAA
1 AATCTGCTCCACTACAACTTTAGGGAGATAAGTA-TTCACTGTACTTCAATCTGCTCCACTGCAA
* * * * *
271721 CTTCAGGGTGATAAGATTCGTTATCTTCAATCTGCTCCAGTGCAACTTCAGGGAGATGAGA-TTT
65 CTTCAGGGAGATAAGATTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTT
* **
271785 GTAGCTTC
130 CTATTTTC
* *
271793 AATCTGCT-CACTACAACTTGAGGGAGATAAG-ATTCACTGT-CTTCAATCTGTTCCACTAG-AA
1 AATCTGCTCCACTACAACTTTAGGGAGATAAGTATTCACTGTACTTCAATCTGCTCCACT-GCAA
* * *
271854 CTTCAGGGAGATAAGATTTGTAACTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAAGAA
65 CTTCAGGGAGATAAGATTTG----TTAT--CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAA
*
271919 GATTTGCTATTTTC
124 GATTTTCTATTTTC
* * * * * *
271933 AATCTGTTCCACTATAACTTTAGGGAGATAA-AATTCACTAT-CTTCAATCTGCTCCATTACAAC
1 AATCTGCTCCACTACAACTTTAGGGAGATAAGTATTCACTGTACTTCAATCTGCTCCACTGCAAC
* * *
271996 TTCAAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTTC
66 TTCAGGGAGATAAGATTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTTC
272061 TATTTTC
131 TATTTTC
* * * * * * *
272068 AATCTACTCCACTACAACTTCAGGGGGATAAGGTTTGTAACTTGTAGCTTTAATCTGTTCCACTG
1 AATCTGCTCCACTACAACTTTAGGGAGATAA-GTAT-TCAC-TGTA-CTTCAATCTGCTCCACTG
* * * * *
272133 CAACTTCAGGGAAATAAGATTTGTTATCTTCAATCTACTGCACTGCAACTTCAAGGAGATAAGAT
62 CAACTTCAGGGAGATAAGATTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* *
272198 TGGT-TGTTTT-
127 T-TTCTATTTTC
272208 AATCTGCTCCACTACAACTTTAGGGAGATAAG
1 AATCTGCTCCACTACAACTTTAGGGAGATAAG
272240 ATTTGTTGTA
Statistics
Matches: 372, Mismatches: 56, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
132 3 0.01
133 60 0.16
134 8 0.02
135 72 0.19
137 8 0.02
138 3 0.01
139 34 0.09
140 42 0.11
141 141 0.38
142 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (137 bp):
AATCTGCTCCACTACAACTTTAGGGAGATAAGTATTCACTGTACTTCAATCTGCTCCACTGCAAC
TTCAGGGAGATAAGATTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTTC
TATTTTC
Found at i:287308 original size:84 final size:85
Alignment explanation
Indices: 287147--287309 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 85
287137 ATATGTGTTC
* * * *
287147 TCGTGTAAGACCACGTCTAGGACGATGGCATCGATATATGTGATTACGTGTAAGACCATGTCTAG
1 TCGTATAAGACCACGTCTAGGACGATGGCATCGA-ATATGAGATTACATGTAAGACCACGTCTAG
287212 GACATTAGCATTGTATTTGAT
65 GACATTAGCATTGTATTTGAT
** *
287233 TCGTATAAGACCTTGTCTAGGAC-AGTGGCATCG-ATATGAGA-TAGCATGTAAGACCACGTCTG
1 TCGTATAAGACCACGTCTAGGACGA-TGGCATCGAATATGAGATTA-CATGTAAGACCACGTCTA
*
287295 GGACATTGGCATTGT
64 GGACATTAGCATTGT
287310 TCGATATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
83 2 0.03
84 36 0.54
85 1 0.01
86 28 0.42
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (85 bp):
TCGTATAAGACCACGTCTAGGACGATGGCATCGAATATGAGATTACATGTAAGACCACGTCTAGG
ACATTAGCATTGTATTTGAT
Found at i:289851 original size:27 final size:29
Alignment explanation
Indices: 289808--289870 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
289798 TGAATTTTTG
* *
289808 GTGAAATTGAGAATTT-AGGG-CTAAATT
1 GTGAAATTGAAAATTTAAGGGACTAAAAT
289835 GTGAAATT-AAAATTTTAAGGGACTAAAAT
1 GTGAAATTGAAAA-TTTAAGGGACTAAAAT
*
289864 ATGAAAT
1 GTGAAAT
289871 AAATAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 11 0.37
28 4 0.13
29 12 0.40
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (29 bp):
GTGAAATTGAAAATTTAAGGGACTAAAAT
Found at i:290519 original size:45 final size:45
Alignment explanation
Indices: 290452--290538 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
290442 TGAGTTTTGA
*
290452 ATATATATATATATATACAAGTATAAGTTTTCGAGTTGAATTTAT
1 ATATATATACATATATACAAGTATAAGTTTTCGAGTTGAATTTAT
*
290497 ATATATATACATATATATAAGTATAAGTTTTCGAGTTGAATT
1 ATATATATACATATATACAAGTATAAGTTTTCGAGTTGAATT
290539 AAAGATGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (45 bp):
ATATATATACATATATACAAGTATAAGTTTTCGAGTTGAATTTAT
Found at i:290905 original size:40 final size:40
Alignment explanation
Indices: 290861--291121 Score: 495
Period size: 40 Copynumber: 6.5 Consensus size: 40
290851 GGTTCTGTGC
* *
290861 CTAGCAGGCTTAATGCCGGTGAATTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
290901 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
290941 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
290981 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
291021 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
291061 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
*
291101 CTAGCAGGCTTAATGCCGGTG
1 CTAGCAGGCTTAATGCTGGTG
291122 TTCTGAGTCA
Statistics
Matches: 218, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCTGGTGAGTTTTTCAGACTTAATGT
Found at i:302290 original size:23 final size:23
Alignment explanation
Indices: 302243--302294 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
302233 TTTCTTTATT
302243 TATTTTTTTCTCTGCATTTTCTC
1 TATTTTTTTCTCTGCATTTTCTC
*
302266 TATTATTTTTCTTTGC-TTCTT-TC
1 TATT-TTTTTCTCTGCATT-TTCTC
302289 TATTTT
1 TATTTT
302295 CCATACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 12 0.46
24 12 0.46
ACGTcount: A:0.10, C:0.17, G:0.04, T:0.69
Consensus pattern (23 bp):
TATTTTTTTCTCTGCATTTTCTC
Found at i:303142 original size:24 final size:25
Alignment explanation
Indices: 303087--303142 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
303077 TCATATCTTT
* * *
303087 GAAGTTATTGTGTATTATTATTCTA
1 GAAGTTATTATGCATTATTACTCTA
*
303112 -AAATTATTATGCATTATTACT-TA
1 GAAGTTATTATGCATTATTACTCTA
303135 GAAGTTAT
1 GAAGTTAT
303143 GCTGTATTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (25 bp):
GAAGTTATTATGCATTATTACTCTA
Found at i:306950 original size:27 final size:27
Alignment explanation
Indices: 306920--306975 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
306910 ATTGAAAGAG
306920 ATAGTGGCTACACCGAAGAGGGATGAC
1 ATAGTGGCTACACCGAAGAGGGATGAC
*
306947 ATAGTGGCTACACCGAGGAGGGATGAC
1 ATAGTGGCTACACCGAAGAGGGATGAC
306974 AT
1 AT
306976 CTCGGAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16
Consensus pattern (27 bp):
ATAGTGGCTACACCGAAGAGGGATGAC
Found at i:311931 original size:29 final size:29
Alignment explanation
Indices: 311899--311959 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
311889 TTCGTATGCA
*
311899 TTTTT-GAGCCAGTATTCTTTTATTTCTTT
1 TTTTTCGAGCAAGTATTCTTTTA-TTCTTT
* *
311928 TTTTTCGAGTAATTATTCTTTTATTCTTT
1 TTTTTCGAGCAAGTATTCTTTTATTCTTT
311957 TTT
1 TTT
311960 GCTACATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.66
Consensus pattern (29 bp):
TTTTTCGAGCAAGTATTCTTTTATTCTTT
Found at i:316943 original size:127 final size:127
Alignment explanation
Indices: 316717--317630 Score: 1569
Period size: 127 Copynumber: 7.2 Consensus size: 127
316707 ACTTCAATCC
* * *
316717 TATCTCCCTGAAGTTGCAGTGGAGCAGGCAAAATAAATCAATCCTATCTCCCTGAAGTTGCAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
* * *
316782 GAGTGAATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAAATCGCATCCAGTCT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
*
316844 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
*
316909 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAGTCT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
* *
316971 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTTGAAGTTGCAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
* *
317036 GAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGATCAGATCGCATCCAGTCTT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTC-T
*
317099 TACCT-CCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
*
317163 GAGTGGATTAACATCCAGATCTTATCTTTCTGATGTTACAGAGAGCAGATCGCATCCAGTCT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
* * *
317225 TATCTCCCTGAAGTTGCAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCCTGAAGTTGTAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
* * *
317290 GAATGGATTAACATCCAGATCTTATCTTTTTGAGGTTGCAGAGAGCAGATCGCATCCAGTCT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
* *
317352 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTTGAAGTTGCAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
* *
317417 GAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAGTTT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
*
317479 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACAGCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
*
317544 GAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAGTCT
66 GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
*
317606 TATCTCCCTGAAGTTGCAGTAGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
317631 GGATTAACAT
Statistics
Matches: 744, Mismatches: 41, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
126 5 0.01
127 734 0.99
128 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCAGCG
GAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCAGATCGCATCCAGTCT
Found at i:317275 original size:44 final size:44
Alignment explanation
Indices: 316711--317546 Score: 213
Period size: 44 Copynumber: 19.7 Consensus size: 44
316701 GGTGAAACTT
*
316711 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGGCAAAATAAAT-
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * *
316755 CAATCCTATCTCCCTGAAGTTGCAGCGGAG-TG-A-ATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* ** * **
316797 CAGATCTTATCTTTCTGAGGTTGCA---GAGA-GCA-AATCGCATC
1 CA-ATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAAT-AAATC
* * * *
316838 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAA-C
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * *
316882 CAATCCTATCTCCCTGAAGTTGCAGCGGAG-TG--GATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* ** * **
316924 CAGATCTTATCTTTCTGAGGTTGCA---GAGA-GCAG-ATCGCATC
1 CA-ATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAAT-AAATC
* * * *
316965 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * * * *
317009 CAATCATATCTCCTTGAAGTTGCAGCGGAG-TG--GATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* ** * * **
317051 CAGATCTTATCTTTCT-AAGGTTACA---GAGA-TCAG-ATCGCATC
1 CA-ATCCTATCTCCCTGAA-GTTGCAGTGGAGAGGCAGAAT-AAATC
* * * * *
317092 CAGTCTTTACCT-CCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-
1 CAATC-CTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * *
317136 CAATCCTATCTCCCTGAAGTTGCAGCGGAG-TG--GATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* ** * * **
317178 CAGATCTTATCTTTCTGATGTTACA---GAGA-GCAG-ATCGCATC
1 CA-ATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAAT-AAATC
* *
317219 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCAGAATAAAT-
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * * *
317263 CAATCCTATCTCCCTGAAGTTGTAGCGGA-ATG--GATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* *** * **
317305 CAGATCTTATCTTTTTGAGGTTGCA---GAGA-GCAG-ATCGCATC
1 CA-ATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAAT-AAATC
* * * *
317346 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* * * * *
317390 CAATCATATCTCCTTGAAGTTGCAGCGGAG-TG--GATTAACATC
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAA-ATC
* ** * **
317432 CAGATCTTATCTTTCT-AAGGTTACA---GAGA-GCAG-ATCGCATC
1 CA-ATCCTATCTCCCTGAA-GTTGCAGTGGAGAGGCAGAAT-AAATC
* ** * *
317473 CAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAT-
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG-AGGCAGAATAAATC
* *
317517 CAATCCTATCTCCCTGAAGTTACAGCGGAG
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG
317547 TGGATTAACA
Statistics
Matches: 567, Mismatches: 142, Indels: 166
0.65 0.16 0.19
Matches are distributed among these distances:
40 140 0.25
41 60 0.11
42 25 0.04
43 119 0.21
44 186 0.33
45 29 0.05
46 8 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (44 bp):
CAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGCAGAATAAATC
Found at i:317620 original size:210 final size:210
Alignment explanation
Indices: 317396--317830 Score: 690
Period size: 210 Copynumber: 2.1 Consensus size: 210
317386 AAATCAATCA
* * *
317396 TATCTCCTTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
1 TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
* * * *
317461 GCAGATCGCATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTAT
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTAT
*
317526 CTCCCTGAAGTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCA
131 CTCCCTGAAGTTACAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCA
317591 GATCGCATCCAGTCT
196 GATCGCATCCAGTCT
* * *
317606 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
* * *
317671 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCCTAT
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTAT
* * * *
317736 CTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCA
131 CTCCCTGAAGTTACAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCA
317801 GATCGCATCCAGTCT
196 GATCGCATCCAGTCT
* *
317816 TATTTCTCTGAAGTT
1 TATCTCCCTGAAGTT
317831 ACAGGGGAAC
Statistics
Matches: 205, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
210 205 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (210 bp):
TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTAT
CTCCCTGAAGTTACAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCA
GATCGCATCCAGTCT
Found at i:317739 original size:254 final size:250
Alignment explanation
Indices: 316710--317757 Score: 1238
Period size: 254 Copynumber: 4.1 Consensus size: 250
316700 CGGTGAAACT
*
316710 TCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGGCAAAATAAATCAATCCTATCTCCCTGAAGT
1 TCAATCCTATCTCCCTGAAGTTGCAGTGGAGCA-GCAGAATAAATCAATCCTATCTCCCTGAAGT
* * * *
316775 TGCAGCGGAGTGAATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAAATCGCATCCA
65 TGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCA
* * * * *
316840 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGC
130 GTCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-AGAA-CATCCAATCTTATCTTCCTGAAGTTGC
* ** * * * *
316905 AGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCA
193 AGCAGAGCAGATTAACATCCAGATCTTATCTTTCTGAAGTTACAGAGAGCAGATAGAA
* * * * *
316963 TCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTTGAAG
1 T-CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAATAAATCAATCCTATCTCCCTGAAG
*
317028 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGATCAGATCGCATCC
64 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCC
* * *
317093 AGTCTTTACCT-CCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CAATCCTATCTCCCTGAAG
129 AGTC-TTATCTCCCTGAAGTTGCAGT--AG-AG-CAGAAGAACATCCAATCTTATCTTCCTGAAG
* ** * * *
317155 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGATGTTACAGAGAGCAGATCGCA
189 TTGCAGCAGAGCAGATTAACATCCAGATCTTATCTTTCTGAAGTTACAGAGAGCAGATAGAA
* *
317217 TCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCAGAATAAATCAATCCTATCTCCCTGAAG
1 T-CAATCCTATCTCCCTGAAGTTGCAGTGGAGCA-GCAGAATAAATCAATCCTATCTCCCTGAAG
* * * * *
317282 TTGTAGCGGAATGGATTAACATCCAGATCTTATCTTTTTGAGGTTGCAGAGAGCAGATCGCATCC
64 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCC
*
317347 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CAATCATATC-TCCTTGAAG
129 AGTCTTATCTCCCTGAAGTTGCAGT--AG-AG-CAGAAGAACATCCAATCTTATCTTCC-TGAAG
* ** * *
317409 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCT-AAGGTTACAGAGAGCAGATCGCA
189 TTGCAGCAGAGCAGATTAACATCCAGATCTTATCTTTCTGAA-GTTACAGAGAGCAGATAGAA
* ** *
317471 TCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAG
1 T-CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAG-CAGAATAAATCAATCCTATCTCCCTGAAG
*
317536 TTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCC
64 TTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCC
* ** * *
317601 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGC
129 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGAAGAACATCCA-ATCTTATCTTCCTGAAGTTGC
** *
317666 AG-AGAGCAGA-TCGCATCCAG-TCTTAT-TTCTCTGAAGTTACAGGGGAACAGGCAGA-AGAAA
193 AGCAGAGCAGATTAACATCCAGATCTTATCTT-TCTGAAGTTACA---G-AGA-GCAGATAG-AA
317726 TCAATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 TCAATCCTATCTCCCTGAAGTTGCAGTGGAGC
317758 GGATTAACAT
Statistics
Matches: 717, Mismatches: 54, Indels: 47
0.88 0.07 0.06
Matches are distributed among these distances:
249 2 0.00
250 20 0.03
251 14 0.02
252 9 0.01
253 29 0.04
254 618 0.86
255 14 0.02
256 1 0.00
257 6 0.01
258 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (250 bp):
TCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGCAGAATAAATCAATCCTATCTCCCTGAAGTT
GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAG
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAAGAACATCCAATCTTATCTTCCTGAAGTTGCAGC
AGAGCAGATTAACATCCAGATCTTATCTTTCTGAAGTTACAGAGAGCAGATAGAA
Found at i:317873 original size:381 final size:378
Alignment explanation
Indices: 316711--317883 Score: 1231
Period size: 381 Copynumber: 3.1 Consensus size: 378
316701 GGTGAAACTT
* * *
316711 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGGCAAAATAAATCAATCCTATCTCCCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
* * * *
316776 GCAGCGGAGTGAATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAAATCGCATCCAG
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAG
* * * *
316841 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-ATAA-CATCCAATCCTATCTCCCTGAAGTTGCA
* ** * * * * * * *
316906 GCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGCATCCAGTCT
194 G-AGAGCAGATTAACATCCAGATCTTATCTTTCTGAAGTTACAGACAGCAGATAGAATCCAATCC
*
316971 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTTGAAGTTGCAGCG
258 TATCTCCCTGAAGTTGCAGTGGAGCAG--AGAAGAAATCAATCATATCTCCTTGAAGTTGCAGCA
** * * ** *
317036 GAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGATCAG-A-TCGCATC
321 GAGCAGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGGGAACAGCAGAAGAATC
* * *
317092 CAGTCTTTACCT-CCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGT
1 CAATC-CTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGT
* *
317156 TGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGATGTTACAGAGAGCAGATCGCATCCA
65 TGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCA
317221 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCAGAATAA-AT-CAATCCTATCTCCCTGAAGTT
130 GTCTTATCTCCCTGAAGTTGCAGT--AG-A-GCAGAATAACATCCAATCCTATCTCCCTGAAGTT
* * * * * * * * *
317284 GTAGCG-GAATGGATTAACATCCAGATCTTATCTTTTTGAGGTTGCAGAGAGCAGATCGCATCCA
191 GCAGAGAGCA--GATTAACATCCAGATCTTATCTTTCTGAAGTTACAGACAGCAGATAGAATCCA
* *
317348 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTTGAAGTTGC
254 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAG--AGAAGAAATCAATCATATCTCCTTGAAGTTGC
* ** * * *
317413 AGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACA--G-AGAGCAGATCGCATC
317 AGCAGAGCAGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGGGAACAGCAGA-AGAATC
* **
317473 CAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
*
317538 ACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAG
66 GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAG
* * * ** *
317603 TCTTATCTCCCTGAAGTTGCAGTAGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAG
131 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAATAACATCCA-ATCCTATCTCCCTGAAGTTGCAG
**
317668 AGAGCAGA-TCGCATCCAG-TCTTAT-TTCTCTGAAGTTACAGGGGAACAGGCAGA-AGAAAT-C
195 AGAGCAGATTAACATCCAGATCTTATCTT-TCTGAAGTTACA---G-ACA-GCAGATAG-AATCC
** * * *
317728 AATCCTATCTCCCTGAAGTTGCAGTGGAGC-G-GATTAACATCCAGATCTTATCT-TTCTGAGGT
253 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAGAAGAA-AT-CA-ATCATATCTCCT-TGAAGT
**
317790 TGCAG-AGAGCAGA-TCGCATCCAG-TCTTAT-TTCTCTGAA-GTTACAGGGGAACAGGCAGAAG
314 TGCAGCAGAGCAGATTAACATCCAGATCTTATCTT-TCT-AAGGTTACA-GGGAACA-GCAGAAG
317850 AAAT-
375 -AATC
* * * *
317854 TAATCCTATCTCACTGAAGTTACAGCGGAG
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAG
317884 TGGATTAACA
Statistics
Matches: 693, Mismatches: 65, Indels: 68
0.84 0.08 0.08
Matches are distributed among these distances:
376 4 0.01
377 41 0.06
378 25 0.04
379 17 0.02
380 46 0.07
381 531 0.77
382 19 0.03
383 1 0.00
384 4 0.01
385 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (378 bp):
CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTT
GCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATCCAG
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAATAACATCCAATCCTATCTCCCTGAAGTTGCAGA
GAGCAGATTAACATCCAGATCTTATCTTTCTGAAGTTACAGACAGCAGATAGAATCCAATCCTAT
CTCCCTGAAGTTGCAGTGGAGCAGAGAAGAAATCAATCATATCTCCTTGAAGTTGCAGCAGAGCA
GATTAACATCCAGATCTTATCTTTCTAAGGTTACAGGGAACAGCAGAAGAATC
Found at i:318046 original size:87 final size:86
Alignment explanation
Indices: 316834--318302 Score: 287
Period size: 83 Copynumber: 17.3 Consensus size: 86
316824 GAGCAAATCG
** * * *
316834 CATCCAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACAGAAGAAA-CCAATCCTATCTCCC
1 CATCCAGATCTTATCTTTCTGAAGTTGCAG-GG-GAATGGCAGAAGAAATCCAATCTTATCTCCC
316896 TGAAGTTGCAGCGGAGTGGATTAA
64 TGAAGTTGCAG-GGAGTGGATTAA
* * * * *
316920 CATCCAGATCTTATCTTTCTGAGGTTGCA-GAG-A--GCAGATCG-CATCCAGTCTTATCTCCCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGA-AGAAATCCAATCTTATCTCCCT
* **
316980 GAAGTTGCAGTGGAGCAGACAGAAGAA
65 GAAGTTGCAG-GGAG-TG---GATTAA
* * * * ** * **
317007 -AT-CA-ATCATATC-TCCTTGAAGTTGCAGCGGAGTGG-ATTA-ACATCCAGATCTTATCTTTC
1 CATCCAGATCTTATCTTTC-TGAAGTTGCAGGGGAATGGCAGAAGAAATCCA-ATCTTATCTCCC
* * * **
317066 T-AAGGTTACAGAGA-TCAGA-TCG
64 TGAA-GTTGCAGGGAGT-GGATTAA
* * * * *
317088 CATCCAG-TCTT-TACCTCCTGAAGTTGCAGTGGAGCA-GACAGAAGAAAT-CAATCCTATCTCC
1 CATCCAGATCTTAT-CTTTCTGAAGTTGCAG-GG-GAATGGCAGAAGAAATCCAATCTTATCTCC
317149 CTGAAGTTGCAGCGGAGTGGATTAA
63 CTGAAGTTGCAG-GGAGTGGATTAA
* * * * * *
317174 CATCCAGATCTTATCTTTCTGATGTTACA-GAG-A--GCAGATCG-CATCCAGTCTTATCTCCCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGA-AGAAATCCAATCTTATCTCCCT
* *
317234 GAAGTTGCAGTGGAGCAGGCAGAATAA
65 GAAGTTGCAG-GGAG--TG--GATTAA
* ** * * ** * ***
317261 -AT-CA-ATCCTATCTCCCTGAAGTTGTAGCGGAATGG-ATTA-ACATCCAGATCTTATCTTTTT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAAATCCA-ATCTTATCTCCCT
* * ** **
317321 GAGGTTGCAGAGAGCAGA-TCG
65 GAAGTTGCAGGGAGTGGATTAA
** * * * *
317342 CATCCAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACAGAAGAAAT-CAATCATATCTCCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAG-GG-GAATGGCAGAAGAAATCCAATCTTATCTCCC
317404 TGAAGTTGCAGCGGAGTGGATTAA
64 TGAAGTTGCAG-GGAGTGGATTAA
* * * * * *
317428 CATCCAGATCTTATCTTTCT-AAGGTTACA-GAG-A--GCAGATCG-CATCCAGTTTTATCTCCC
1 CATCCAGATCTTATCTTTCTGAA-GTTGCAGGGGAATGGCAGA-AGAAATCCAATCTTATCTCCC
* **
317487 TGAAGTTGCAGTGGAGCAGACAGAAGAA
64 TGAAGTTGCAG-GGAG-TG---GATTAA
* ** * * * ** * **
317515 -AT-CA-ATCCTATCTCCCTGAAGTTACAGCGGAGTGG-ATTA-ACATCCAGATCTTATCTTTCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAAATCCA-ATCTTATCTCCCT
* * ** **
317575 -AAGGTTACAGAGAGCAGA-TCG
65 GAA-GTTGCAGGGAGTGGATTAA
** ** * ** **
317596 CATCCAG-TCTTATCTCCCTGAAGTTGCAGTAG-A--GCGGATTAACATCCAGATCTTATCTTTC
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAA-ATCCA-ATCTTATCTCCC
* * ** **
317657 TGAGGTTGCAGAGAGCAGA-TCG
64 TGAAGTTGCAGGGAGTGGATTAA
* * *
317679 CATCCAG-TCTTAT-TTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAAT-CAATCCTATCTCCC
1 CATCCAGATCTTATCTT-TCTGAAGTTGCAGGGGAA-TGGCAGAAGAAATCCAATCTTATCTCCC
*
317741 TGAAGTTGCAGTGGAGCGGATTAA
64 TGAAGTTGCAG-GGAGTGGATTAA
* * * * * * *
317765 CATCCAGATCTTATCTTTCTGAGGTTGCA-GAG-A--GCAGATCG-CATCCAGTCTTATTTCTCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGA-AGAAATCCAATCTTATCTCCCT
* ** **
317825 GAAGTTACAGGGGAACAGGCAGAAGA
65 GAAGTTGCA-GGG-AGTGG-ATTA-A
* * * ** * * * ** * **
317851 AAT-TA-ATCCTATCTCACTGAAGTTACAGCGGAGTGG-ATTA-ACATCCAGATCTTATCTTTCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAAATCCA-ATCTTATCTCCCT
* * ** **
317912 GAGGTTGCAGAGAGCAGA-TCG
65 GAAGTTGCAGGGAGTGGATTAA
*
317933 CATCCAG-TCTTAT-TTCTCTGAAGTTGCAGGGGAATCGGCAGAAGAAAT-CAATCCTATCTCCC
1 CATCCAGATCTTATCTT-TCTGAAGTTGCAGGGGAAT-GGCAGAAGAAATCCAATCTTATCTCCC
317995 TGAAGTTGCAGCGGAGTGGATTAA
64 TGAAGTTGCAG-GGAGTGGATTAA
* * * * * * *
318019 CATCCAGATCTTATCTTTCTGAGGTTGCA-GAG-A--GCAGATCG-CATCCAGTCTTATTTCTCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGA-AGAAATCCAATCTTATCTCCCT
* * **
318079 GAAGTTACAGGGGAACATGCAGAAGAA
65 GAAGTTGCA-GGG-A-GTG--GATTAA
* ** * * ** * **
318106 -AT-CA-ATCCTATCTCCCTGAAGTTGCAGCGGAGTGG-ATTA-ACATCCAGATCTTATCTTTCT
1 CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAAATCCA-ATCTTATCTCCCT
* * ** **
318166 GAGGTTGCAGAGAGCAGA-TCG
65 GAAGTTGCAGGGAGTGGATTAA
* *
318187 CATCCAG-TCTTAT-TTCTCTAAAGTTGCAGGGGAATAGGCAGAAGAAAT-CAATCATATCTCCC
1 CATCCAGATCTTATCTT-TCTGAAGTTGCAGGGGAAT-GGCAGAAGAAATCCAATCTTATCTCCC
318249 TGAAGTTGCAGTGGAGTGGATTAA
64 TGAAGTTGCAG-GGAGTGGATTAA
*
318273 CATCCAGATCTTATCTTTCTGAGGTTGCAG
1 CATCCAGATCTTATCTTTCTGAAGTTGCAG
318303 AGAGCAGATC
Statistics
Matches: 978, Mismatches: 275, Indels: 259
0.65 0.18 0.17
Matches are distributed among these distances:
80 1 0.00
81 1 0.00
82 54 0.06
83 298 0.30
84 200 0.20
85 77 0.08
86 126 0.13
87 209 0.21
88 12 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (86 bp):
CATCCAGATCTTATCTTTCTGAAGTTGCAGGGGAATGGCAGAAGAAATCCAATCTTATCTCCCTG
AAGTTGCAGGGAGTGGATTAA
Found at i:318137 original size:591 final size:591
Alignment explanation
Indices: 317015--318215 Score: 1904
Period size: 591 Copynumber: 2.0 Consensus size: 591
317005 AAATCAATCA
* * *
317015 TATCTCCTTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
1 TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
* * * *
317080 TCAGATCGCATCCAGTCTTTACCTCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTAT
66 GCAGATCGCATCCAGTCTTTACCTCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTAT
* *
317145 CTCCCTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGATGTTACAGAGAGCA
131 CTCCCTGAAGTTGCAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCA
* * * *
317210 GATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCAGAATAAATCAATCCTATCTC
196 GATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCCTATCTC
* ** *
317275 CCTGAAGTTGTAGCGGAATGGATTAACATCCAGATCTTATCTTTTTGAGGTTGCAGAGAGCAGAT
261 ACTGAAGTTACAGCGGAATGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGAT
* *
317340 CGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCATATCTCCTT
326 CGCATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCATATCTCCCT
317405 GAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGC
391 GAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGC
* * * *
317470 ATCCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAA
456 ATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTATCTCCCTGAA
317535 GTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATC
521 GTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATC
317600 CAGTCT
586 CAGTCT
* * *
317606 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
** *
317671 GCAGATCGCATCCAGTC-TTATTTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCCTA
66 GCAGATCGCATCCAGTCTTTACCTC-CTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTA
* *
317735 TCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGC
130 TCTCCCTGAAGTTGCAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGC
* * *
317800 AGATCGCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAATTAATCCTATCT
195 AGATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCCTATCT
*
317865 CACTGAAGTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGA
260 CACTGAAGTTACAGCGGAATGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGA
* * * * *
317930 TCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAATC-GGCAGAAGAAATCAATCCTATCTCC
325 TCGCATCCAGTCTTATCTCCCTGAAGTTGCAGGGG-AGCAGACAGAAGAAATCAATCATATCTCC
* *
317994 CTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC
389 CTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATC
* *
318059 GCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACATG-CAGAAGAAATCAATCCTATCTCCCT
454 GCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACA-GACAGAAGAAATCAATCCTATCTCCCT
* * *
318123 GAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGC
518 GAAGTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGC
318188 ATCCAGTCT
583 ATCCAGTCT
* * *
318197 TATTTCTCTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAG
318216 GGGAATAGGC
Statistics
Matches: 557, Mismatches: 50, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
590 5 0.01
591 549 0.99
592 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (591 bp):
TATCTCCCTGAAGTTGCAGCAGAGCGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGA
GCAGATCGCATCCAGTCTTTACCTCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTAT
CTCCCTGAAGTTGCAGCGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTACAGAGAGCA
GATCGCATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCCTATCTC
ACTGAAGTTACAGCGGAATGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGAT
CGCATCCAGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACAGAAGAAATCAATCATATCTCCCT
GAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGC
ATCCAGTCTTATCTCCCTGAAGTTACAGGGGAACAGACAGAAGAAATCAATCCTATCTCCCTGAA
GTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTAAGGTTACAGAGAGCAGATCGCATC
CAGTCT
Found at i:318466 original size:127 final size:127
Alignment explanation
Indices: 317606--318469 Score: 1480
Period size: 127 Copynumber: 6.8 Consensus size: 127
317596 CATCCAGTCT
* *
317606 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
*
317671 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
*
317733 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
* *
317798 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACAGGCAGAAGAAATTAATCC
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
* * *
317860 TATCTCACTGAAGTTACAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
317925 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAATC-GGCAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAA-CAGGCAGAAGAAATCAATCC
*
317987 TATCTCCCTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
* *
318052 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTACAGGGGAACATGCAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
*
318114 TATCTCCCTGAAGTTGCAGCGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
* * *
318179 GCAGATCGCATCCAGTCTTATTTCTCTAAAGTTGCAGGGGAATAGGCAGAAGAAATCAATCA
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
318241 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
318306 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
66 GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
* * * *
318368 TATCTCCCTGAAGTTACAGTGGAGCGGATTAACATCTAGATCTTATATTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
* * * *
318433 GCATG-TCACATCCAGTTTTATCTCCCTGAAGTTGCAG
66 GCA-GATCGCATCCAGTCTTATTTCTCTGAAGTTGCAG
318470 TGGAGCAGAC
Statistics
Matches: 705, Mismatches: 29, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
126 1 0.00
127 702 1.00
128 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
GCAGATCGCATCCAGTCTTATTTCTCTGAAGTTGCAGGGGAACAGGCAGAAGAAATCAATCC
Found at i:319124 original size:7 final size:8
Alignment explanation
Indices: 319085--319127 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
319075 TTTTACTGTT
319085 TTTTTTTG
1 TTTTTTTG
319093 TTATTTTTG
1 TT-TTTTTG
319102 CTTCTCTTTTG
1 -TT-T-TTTTG
319113 TTTTTTTG
1 TTTTTTTG
319121 TTTTTTT
1 TTTTTTT
319128 TCTTTCAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 14 0.45
9 7 0.23
10 5 0.16
11 5 0.16
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.81
Consensus pattern (8 bp):
TTTTTTTG
Found at i:325294 original size:27 final size:26
Alignment explanation
Indices: 325252--325303 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
325242 GTAAAAATGG
* *
325252 TAATGAAGAAATAGTTTAGGTACCAC
1 TAATGAAGAAAAAGTTTAGATACCAC
325278 TAATGACAGAAAAAGTTTAGATACCA
1 TAATGA-AGAAAAAGTTTAGATACCA
325304 ACTTAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (26 bp):
TAATGAAGAAAAAGTTTAGATACCAC
Found at i:328094 original size:10 final size:10
Alignment explanation
Indices: 328079--328209 Score: 51
Period size: 10 Copynumber: 13.3 Consensus size: 10
328069 ATTTAATCCT
328079 TTAAAAATTA
1 TTAAAAATTA
*
328089 TTAAAAATAGA
1 TTAAAAAT-TA
328100 TTAAAAAATTA
1 TT-AAAAATTA
*
328111 TTAGAAATT-
1 TTAAAAATTA
* * *
328120 GTAAACTATTG
1 TTAAA-AATTA
*
328131 TAAAAAATTA
1 TTAAAAATTA
*
328141 -TAAAAATGA
1 TTAAAAATTA
* **
328150 TTATAAACCA
1 TTAAAAATTA
328160 -TAAAATATTA
1 TTAAAA-ATTA
328170 -TAAATAATTA
1 TTAAA-AATTA
*
328180 TTTAAAA-T-
1 TTAAAAATTA
*
328188 TTAAAAACTA
1 TTAAAAATTA
*
328198 GT-AAAATTA
1 TTAAAAATTA
328207 TTA
1 TTA
328210 TATCTTAGAA
Statistics
Matches: 87, Mismatches: 23, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
8 6 0.07
9 23 0.26
10 39 0.45
11 13 0.15
12 6 0.07
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:329230 original size:18 final size:17
Alignment explanation
Indices: 329209--329245 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
329199 TTAATTTTAG
*
329209 TAATTTTATATTGTTTTT
1 TAATTTTATAGT-TTTTT
329227 TAATTTTATAGTTTTTT
1 TAATTTTATAGTTTTTT
329244 TA
1 TA
329246 TAACTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TAATTTTATAGTTTTTT
Done.