Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold885
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1053811
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 99868 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:2112 original size:2 final size:2
Alignment explanation
Indices: 2107--2171 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2097 TCTTTAAAAA
2107 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2149 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
2172 ATATTAAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3221 original size:2 final size:2
Alignment explanation
Indices: 3214--3255 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3204 TAAATTTAAA
3214 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3256 TTCTGCATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5600 original size:21 final size:21
Alignment explanation
Indices: 5517--5602 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
5507 TTTGATTAAA
5517 ATTT-TCTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
* * **
5537 AGTTATGTTGCATGTTGACAT
1 ATTTATCTTGCATGTCAACAT
** *
5558 AACTATCTT-AATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
*
5578 ATTTATCTTGCATTTCAACAT
1 ATTTATCTTGCATGTCAACAT
5599 ATTT
1 ATTT
5603 GATAGAAAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 18 0.36
21 32 0.64
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.44
Consensus pattern (21 bp):
ATTTATCTTGCATGTCAACAT
Found at i:8494 original size:2 final size:2
Alignment explanation
Indices: 8487--8520 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
8477 ATTTCGAACA
*
8487 AT AT AT AT AT AT AT -T AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8521 AAATTGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8506 original size:13 final size:13
Alignment explanation
Indices: 8488--8512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8478 TTTCGAACAA
8488 TATATATATATAT
1 TATATATATATAT
8501 TATATATATATA
1 TATATATATATA
8513 AATATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:9428 original size:21 final size:21
Alignment explanation
Indices: 9404--9450 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
9394 CCCAATCGGT
*
9404 ACGTGATGCCT-TCAATTTGTC
1 ACGTGATG-CTATCAATTTGCC
9425 ACGTGATGCTATCAATTTGCC
1 ACGTGATGCTATCAATTTGCC
9446 ACGTG
1 ACGTG
9451 GTAATGTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (21 bp):
ACGTGATGCTATCAATTTGCC
Found at i:18930 original size:37 final size:37
Alignment explanation
Indices: 18880--18955 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
18870 ATAAAGCCAA
18880 AAAACTTACTTTATTGACTGACCCATGAGCTATGCGT
1 AAAACTTACTTTATTGACTGACCCATGAGCTATGCGT
18917 AAAACTTACTTTATTGACTGACCCATGAGCTATGCGT
1 AAAACTTACTTTATTGACTGACCCATGAGCTATGCGT
18954 AA
1 AA
18956 GCATTCGCTA
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:0.21, G:0.16, T:0.32
Consensus pattern (37 bp):
AAAACTTACTTTATTGACTGACCCATGAGCTATGCGT
Found at i:37472 original size:31 final size:31
Alignment explanation
Indices: 37422--37503 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
37412 ATGCTTCTAA
* *
37422 AGGATCCTATCGGACATGTACCATAA-ATAAG
1 AGGATCTTATTGGACATGTACCA-AAGATAAG
* *
37453 AGGATCTTATTGGATATGTACTAAAGATAAG
1 AGGATCTTATTGGACATGTACCAAAGATAAG
*
37484 AGAAT-TCTATTGGACATGTA
1 AGGATCT-TATTGGACATGTA
37504 TTGTACATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (31 bp):
AGGATCTTATTGGACATGTACCAAAGATAAG
Found at i:37591 original size:25 final size:25
Alignment explanation
Indices: 37557--37780 Score: 412
Period size: 25 Copynumber: 9.0 Consensus size: 25
37547 AAAAAAAGAA
37557 CTTATTGGACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
37582 CTTATTGGACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
*
37607 CTTATTGGACATGAGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
*
37632 CTTATTGGACATGTACTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
37657 CTTATTGGACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
37682 CTTATTGGACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
*
37707 CTTAATGGACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
*
37732 CTTATTGAACATGTGCTGTAGATAT
1 CTTATTGGACATGTGCTGTAGATAT
37757 CTTATTGGACATGTGCTGTAGATA
1 CTTATTGGACATGTGCTGTAGATA
37781 CACTGTAAGA
Statistics
Matches: 191, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 191 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (25 bp):
CTTATTGGACATGTGCTGTAGATAT
Found at i:40315 original size:11 final size:11
Alignment explanation
Indices: 40299--40329 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40289 ATCAATAAAT
40299 AATAACCATTG
1 AATAACCATTG
*
40310 AATAACCTTTG
1 AATAACCATTG
40321 AATAACCAT
1 AATAACCAT
40330 CAAATACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (11 bp):
AATAACCATTG
Found at i:54254 original size:22 final size:22
Alignment explanation
Indices: 54228--54297 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
54218 GGTCGAAGAT
*
54228 GCGAGAGTACGAAGTTGCGAAG
1 GCGAGAGTGCGAAGTTGCGAAG
54250 GCGAGAGTGCGAAGTTGCGAAG
1 GCGAGAGTGCGAAGTTGCGAAG
* * *
54272 GCGAAAGTGCGAAGATGCGACG
1 GCGAGAGTGCGAAGTTGCGAAG
54294 GCGA
1 GCGA
54298 AGCGCAAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.43, T:0.11
Consensus pattern (22 bp):
GCGAGAGTGCGAAGTTGCGAAG
Found at i:54261 original size:8 final size:7
Alignment explanation
Indices: 54221--54291 Score: 56
Period size: 8 Copynumber: 9.4 Consensus size: 7
54211 GCCTTTAGGT
54221 CGAAGATG
1 CGAAG-TG
*
54229 CGAGAGTA
1 CGA-AGTG
54237 CGAAGTTG
1 CGAAG-TG
54245 CGAAG-G
1 CGAAGTG
54251 CGAGAGTG
1 CGA-AGTG
54259 CGAAGTTG
1 CGAAG-TG
54267 CGAAG-G
1 CGAAGTG
54273 CGAAAGTG
1 CG-AAGTG
54281 CGAAGATG
1 CGAAG-TG
54289 CGA
1 CGA
54292 CGGCGAAGCG
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
6 7 0.13
7 12 0.23
8 32 0.60
9 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.41, T:0.13
Consensus pattern (7 bp):
CGAAGTG
Found at i:54275 original size:14 final size:14
Alignment explanation
Indices: 54221--54291 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 14
54211 GCCTTTAGGT
*
54221 CGAAGATGCGAGAGTA
1 CGAAG-TGCGA-AGTG
54237 CGAAGTTGCGAAG-G
1 CGAAG-TGCGAAGTG
54251 CGAGAGTGCGAAGTTG
1 CGA-AGTGCGAAG-TG
54267 CGAAG-GCGAAAGTG
1 CGAAGTGCG-AAGTG
54281 CGAAGATGCGA
1 CGAAG-TGCGA
54292 CGGCGAAGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
14 20 0.43
15 10 0.21
16 17 0.36
ACGTcount: A:0.32, C:0.14, G:0.41, T:0.13
Consensus pattern (14 bp):
CGAAGTGCGAAGTG
Found at i:54298 original size:22 final size:22
Alignment explanation
Indices: 54237--54312 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
54227 TGCGAGAGTA
* *
54237 CGAAGTTGCGAAGGCGAGAGTG
1 CGAAGATGCGAAGGCGAAAGTG
*
54259 CGAAGTTGCGAAGGCGAAAGTG
1 CGAAGATGCGAAGGCGAAAGTG
* *
54281 CGAAGATGCGACGGCG-AAGCG
1 CGAAGATGCGAAGGCGAAAGTG
*
54302 CAAAGATGCGA
1 CGAAGATGCGA
54313 TACTACTTCG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 14 0.29
22 35 0.71
ACGTcount: A:0.32, C:0.17, G:0.41, T:0.11
Consensus pattern (22 bp):
CGAAGATGCGAAGGCGAAAGTG
Found at i:62582 original size:18 final size:18
Alignment explanation
Indices: 62559--62599 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
62549 TAGTTTAAAA
*
62559 TTTGAAAGAGAAATTTGT
1 TTTGAAAGAGAAATTTAT
*
62577 TTTGAAAGAGAGATTTAT
1 TTTGAAAGAGAAATTTAT
62595 TTTGA
1 TTTGA
62600 TTGATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (18 bp):
TTTGAAAGAGAAATTTAT
Found at i:65538 original size:1 final size:1
Alignment explanation
Indices: 65501--65530 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
65491 CAATGCATCA
65501 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
65531 TATCCCCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:66886 original size:18 final size:19
Alignment explanation
Indices: 66844--66890 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
66834 GGTGTCGCCA
* *
66844 CCAGTAGACATTGGTAGCG
1 CCAGTAGACATTAGTAGCC
*
66863 CCAGTAGACA-TAGTATCC
1 CCAGTAGACATTAGTAGCC
66881 CCAGTAGACA
1 CCAGTAGACA
66891 ATGGTGAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (19 bp):
CCAGTAGACATTAGTAGCC
Found at i:66909 original size:37 final size:38
Alignment explanation
Indices: 66844--66915 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
66834 GGTGTCGCCA
* * *
66844 CCAGTAGACATTGGTAGCGCCAGTAGACA-TAGTATCC
1 CCAGTAGACAATGGTAGCACCAGCAGACAGTAGTATCC
66881 CCAGTAGACAATGGTGAG-ACCAGCAGACAGTAGTA
1 CCAGTAGACAATGGT-AGCACCAGCAGACAGTAGTA
66916 GTACCAGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 23 0.77
38 7 0.23
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.18
Consensus pattern (38 bp):
CCAGTAGACAATGGTAGCACCAGCAGACAGTAGTATCC
Found at i:75222 original size:17 final size:17
Alignment explanation
Indices: 75192--75225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
75182 TGAAGTAAAT
**
75192 TGTAAATTTGATAAAAA
1 TGTAAATTAAATAAAAA
75209 TGTAAATTAAATAAAAA
1 TGTAAATTAAATAAAAA
75226 AAGTAAACGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (17 bp):
TGTAAATTAAATAAAAA
Found at i:83322 original size:2 final size:2
Alignment explanation
Indices: 83317--83354 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
83307 AAAGTTCAGG
83317 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
83355 ATTGATACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:91829 original size:2 final size:2
Alignment explanation
Indices: 91822--91849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91812 GGTATCGCCT
91822 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
91850 TTGCTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:99822 original size:2 final size:2
Alignment explanation
Indices: 99817--99848 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
99807 ATATATATGG
99817 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
99849 TATGCTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:120507 original size:10 final size:10
Alignment explanation
Indices: 120492--120525 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
120482 ACTGGAATGA
120492 AAATATTTAT
1 AAATATTTAT
120502 AAATATTTAT
1 AAATATTTAT
*
120512 AAA-ACTTAT
1 AAATATTTAT
120521 AAATA
1 AAATA
120526 CTACGCTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATATTTAT
Found at i:137190 original size:2 final size:2
Alignment explanation
Indices: 137183--137231 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
137173 GGCATACAAA
137183 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
137225 TC TC TC T
1 TC TC TC T
137232 GCGCTAATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:137276 original size:12 final size:14
Alignment explanation
Indices: 137243--137275 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
137233 CGCTAATTCA
137243 TTATATAATGGTTT
1 TTATATAATGGTTT
137257 TTATATAATGGTTT
1 TTATATAATGGTTT
137271 TTATA
1 TTATA
137276 ACATGCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (14 bp):
TTATATAATGGTTT
Found at i:140802 original size:2 final size:2
Alignment explanation
Indices: 140795--140840 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
140785 AGTGTTGAAA
140795 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
140837 AG AG
1 AG AG
140841 TTTATTGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:141417 original size:2 final size:2
Alignment explanation
Indices: 141410--141463 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
141400 TCATAAGAGT
141410 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
141452 TC TC TC TC TC TC
1 TC TC TC TC TC TC
141464 AGTAAGAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:158569 original size:2 final size:2
Alignment explanation
Indices: 158562--158599 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
158552 GGGAGGGAGG
158562 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
158600 ATGTGTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:161732 original size:3 final size:3
Alignment explanation
Indices: 161726--161760 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
161716 ACTCTCTTCT
*
161726 TCC TCC TCC TCC TCC TCC TTC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
161761 ATCATCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:163468 original size:2 final size:2
Alignment explanation
Indices: 163461--163517 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
163451 CGAATTTATT
163461 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
163503 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
163518 CTAGGTAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:168992 original size:17 final size:17
Alignment explanation
Indices: 168970--169017 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
168960 GGATTATCGG
168970 TATATCCAATAGGATTA
1 TATATCCAATAGGATTA
168987 TATAT-CAAT--G--TA
1 TATATCCAATAGGATTA
168999 TATATCCAATAGGATTA
1 TATATCCAATAGGATTA
169016 TA
1 TA
169018 AAAAGGACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 1 0.04
15 1 0.04
16 4 0.15
17 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (17 bp):
TATATCCAATAGGATTA
Found at i:173353 original size:21 final size:21
Alignment explanation
Indices: 173327--173418 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
173317 TTCTGCCACC
*
173327 ACTTGTCAGATAATCATGTCA
1 ACTTGTCAGATAATCATGTCG
** *
173348 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATCATGTCG
* *
173369 ACTTGTCAGATAATTATGTTG
1 ACTTGTCAGATAATCATGTCG
** *
173390 ACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATCATGTCG
*
173411 AATTGTCA
1 ACTTGTCA
173419 CTTATTCACA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATCATGTCG
Found at i:173394 original size:42 final size:42
Alignment explanation
Indices: 173327--173418 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
173317 TTCTGCCACC
173327 ACTTGTCAGATAATCATGTCAACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATAATCATGTCAACTTGTCAGATCTTGATGTCG
* ** *
173369 ACTTGTCAGATAATTATGTTGACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATCATGTCAACTTGTCAGATCTTGATGTCG
*
173411 AATTGTCA
1 ACTTGTCA
173419 CTTATTCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (42 bp):
ACTTGTCAGATAATCATGTCAACTTGTCAGATCTTGATGTCG
Found at i:173522 original size:21 final size:20
Alignment explanation
Indices: 173496--173612 Score: 117
Period size: 21 Copynumber: 5.7 Consensus size: 20
173486 TAATTTTTTT
173496 TCTGACAAGTCGACATAAGTA
1 TCTGACAAGTCGACATAA-TA
*
173517 TCTGACAAGTCGACATTATCA
1 TCTGACAAGTCGACATAAT-A
* * *
173538 TCTGTCAAGTCGACATCATT
1 TCTGACAAGTCGACATAATA
* *
173558 TTTGACATGTCGACATAATA
1 TCTGACAAGTCGACATAATA
* * * *
173578 TCCGAAAAGTCAACATCATTA
1 TCTGACAAGTCGACAT-AATA
173599 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
173613 TTATAATATA
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.36
21 49 0.64
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (20 bp):
TCTGACAAGTCGACATAATA
Found at i:173608 original size:61 final size:63
Alignment explanation
Indices: 173493--173612 Score: 163
Period size: 61 Copynumber: 1.9 Consensus size: 63
173483 TGATAATTTT
* * * * *
173493 TTTTCTGACAAGTCGACATAAGTATCTGACAAGTCGACATTATCATCTGTCAAGTCGACATCA
1 TTTTCTGACAAGTCGACATAAGTATCCGAAAAGTCAACATCATCATCTGACAAGTCGACATCA
* *
173556 TTTT-TGACATGTCGACATAA-TATCCGAAAAGTCAACATCATTATCTGACAAGTCGAC
1 TTTTCTGACAAGTCGACATAAGTATCCGAAAAGTCAACATCATCATCTGACAAGTCGAC
173613 TTATAATATA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 31 0.62
62 15 0.30
63 4 0.08
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (63 bp):
TTTTCTGACAAGTCGACATAAGTATCCGAAAAGTCAACATCATCATCTGACAAGTCGACATCA
Found at i:173699 original size:21 final size:20
Alignment explanation
Indices: 173653--173707 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
173643 AATTTTTTTC
*
173653 TGTCAAATAATTATGTTAACT
1 TGTCAAAT-ATTATGTCAACT
* *
173674 CGTCAAATCATTATGTCGACT
1 TGTCAAAT-ATTATGTCAACT
*
173695 TGTCAGATATTAT
1 TGTCAAATATTAT
173708 AATGACAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
TGTCAAATATTATGTCAACT
Found at i:173868 original size:21 final size:21
Alignment explanation
Indices: 173788--173877 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
173778 TGATAATTTG
* **
173788 CTGACAAGTCAACATAAAGAT
1 CTGACAAGTCGACATAATCAT
* * *
173809 ATGACAAGTTGATATAAAT-AT
1 CTGACAAGTCGACAT-AATCAT
173830 CTGACAAGTCGACATAATCAT
1 CTGACAAGTCGACATAATCAT
* * *
173851 TTGACAAGTC-AGCTTAATTAT
1 CTGACAAGTCGA-CATAATCAT
173872 CTGACA
1 CTGACA
173878 TGTGGTGGCA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.07
21 48 0.89
22 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (21 bp):
CTGACAAGTCGACATAATCAT
Found at i:177529 original size:13 final size:13
Alignment explanation
Indices: 177511--177535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177501 AATTTAATTT
177511 TTTGTTTGTTTTG
1 TTTGTTTGTTTTG
177524 TTTGTTTGTTTT
1 TTTGTTTGTTTT
177536 TATTTATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (13 bp):
TTTGTTTGTTTTG
Found at i:177614 original size:40 final size:40
Alignment explanation
Indices: 177531--177617 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
177521 TTGTTTGTTT
* * *
177531 GTTTTTATTTATTTGGGGGGGGGGGGGGGGGAGGGGGGGG
1 GTTTTTTTTTATTTGGGGGGGGGGGGGGAGGAAGGGGGGG
* * * *
177571 GTTTTTTTTTTTTTGGGGGGGGGGGGGTAGGAAGGTGGTG
1 GTTTTTTTTTATTTGGGGGGGGGGGGGGAGGAAGGGGGGG
177611 GTTTTTT
1 GTTTTTT
177618 GTTGTTGATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.07, C:0.00, G:0.55, T:0.38
Consensus pattern (40 bp):
GTTTTTTTTTATTTGGGGGGGGGGGGGGAGGAAGGGGGGG
Found at i:178443 original size:2 final size:2
Alignment explanation
Indices: 178436--178494 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
178426 GTATGTACGA
178436 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
178478 AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG
178495 TAAATAACAG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:190185 original size:4 final size:4
Alignment explanation
Indices: 190176--190261 Score: 100
Period size: 4 Copynumber: 21.5 Consensus size: 4
190166 ATTGATATCA
* *
190176 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAC AGAC
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * * *
190224 AGAC AGAC AGAC AGAC AGAG ACAG ACAG AGAG AGAG AG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AG
190262 TGTTATTCAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 78 1.00
ACGTcount: A:0.50, C:0.09, G:0.41, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:198622 original size:1 final size:1
Alignment explanation
Indices: 198618--198642 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
198608 TTAGAAAACA
198618 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
198643 ACACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:199276 original size:14 final size:14
Alignment explanation
Indices: 199257--199294 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
199247 CCAAATAATA
199257 TTATTTATTTTATC
1 TTATTTATTTTATC
199271 TTATTTCA-TTTATC
1 TTATTT-ATTTTATC
199285 -TATTTATTTT
1 TTATTTATTTT
199295 TGAGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 8 0.36
14 12 0.55
15 1 0.05
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTATTTTATC
Found at i:199684 original size:2 final size:2
Alignment explanation
Indices: 199677--199720 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
199667 GTGAACCACT
199677 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
199719 GA
1 GA
199721 ATATATAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:202612 original size:21 final size:20
Alignment explanation
Indices: 202588--202808 Score: 179
Period size: 21 Copynumber: 11.1 Consensus size: 20
202578 TGGATATTTC
202588 ATATGAAGATGGTGCTTTATT
1 ATATGAAGATGGTGCTTT-TT
* *
202609 ATATGAATATTGTG-TTTATT
1 ATATGAAGATGGTGCTTT-TT
*
202629 ATATGAAGATGGTCCTTTTT
1 ATATGAAGATGGTGCTTTTT
*
202649 -TATG-TGATGGTGCTTTGTT
1 ATATGAAGATGGTGCTTT-TT
*
202668 ATGTGAAGATGGTGCTTTTTT
1 ATATGAAGATGGTGC-TTTTT
*
202689 ATATGAAGATGGAGCTATTTT
1 ATATGAAGATGGTGCT-TTTT
* *
202710 A-AGTGAAGATGATGGTTTGTT
1 ATA-TGAAGATGGTGCTTT-TT
* * *
202731 ATGTGAAGATGGCGCTATATT
1 ATATGAAGATGGTGCT-TTTT
*
202752 ATATGAAGGTGGTGCTTTTT
1 ATATGAAGATGGTGCTTTTT
* *
202772 -TCTG-TGATGGTGCTTTTT
1 ATATGAAGATGGTGCTTTTT
*
202790 -TAT-ATGATGGTGCTTTTT
1 ATATGAAGATGGTGCTTTTT
202808 A
1 A
202809 ATGTGAAGGG
Statistics
Matches: 161, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
18 38 0.24
19 9 0.06
20 29 0.18
21 81 0.50
22 4 0.02
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (20 bp):
ATATGAAGATGGTGCTTTTT
Found at i:202659 original size:18 final size:18
Alignment explanation
Indices: 202636--202673 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
202626 ATTATATGAA
*
202636 GATGGTCCTTTTTTATGT
1 GATGGTCCTTTGTTATGT
*
202654 GATGGTGCTTTGTTATGT
1 GATGGTCCTTTGTTATGT
202672 GA
1 GA
202674 AGATGGTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.08, G:0.29, T:0.50
Consensus pattern (18 bp):
GATGGTCCTTTGTTATGT
Found at i:202784 original size:18 final size:18
Alignment explanation
Indices: 202761--202807 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
202751 TATATGAAGG
* *
202761 TGGTGCTTTTTTCTGTGA
1 TGGTGCTTTTTTATATGA
202779 TGGTGCTTTTTTATATGA
1 TGGTGCTTTTTTATATGA
202797 TGGTGCTTTTT
1 TGGTGCTTTTT
202808 AATGTGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.57
Consensus pattern (18 bp):
TGGTGCTTTTTTATATGA
Found at i:203533 original size:21 final size:21
Alignment explanation
Indices: 203507--204500 Score: 1016
Period size: 21 Copynumber: 47.4 Consensus size: 21
203497 AAAAACCCCA
*
203507 TCATATAAAAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* *
203528 TCATATAATAAAGCA--TTAT
1 TCATATAATAAAGCACCATCT
*
203547 TCATATAAAAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
203568 TCATATAACAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
203589 TCACATAA-ACAAGCACCATCT
1 TCATATAATA-AAGCACCATCT
* *
203610 TCACATAA-AAAGCAACATCT
1 TCATATAATAAAGCACCATCT
* *
203630 TCATATAAAAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
203651 TCATATTAATAAAGCACCATCT
1 TCATA-TAATAAAGCACCATCT
*
203673 TCATATAATAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
*
203694 TCATATGATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
203715 TCATATAATAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
* *
203736 TCACATGATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
203757 TCATATAATAAAGCACCATCG
1 TCATATAATAAAGCACCATCT
203778 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* * * *
203799 TCACATGAA-ATAACCA-CAGCA
1 TCATAT-AATA-AAGCACCATCT
*
203820 TAATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* *
203841 TCATATAATAAAGCACCTTTT
1 TCATATAATAAAGCACCATCT
* *
203862 TCTTATAATAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
203883 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* * *
203904 TGACATGA-AAT-AACCA-CAGCA
1 T--CAT-ATAATAAAGCACCATCT
* *
203925 TAAAATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
203946 TAATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* *
203967 TCATATAAAAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
* *
203988 TCATATAAAAAAGCACCACCT
1 TCATATAATAAAGCACCATCT
*
204009 TCATATTATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
204030 TCATATAA-AGAAGCACCATCT
1 TCATATAATA-AAGCACCATCT
* * * *
204051 TCACATGAA-ATAACCA-CAGCA
1 TCATAT-AATA-AAGCACCATCT
* *
204072 TAATATAATAAAGCACTATCT
1 TCATATAATAAAGCACCATCT
*
204093 GCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* *
204114 TCATACAATAAAGCATCATCT
1 TCATATAATAAAGCACCATCT
*
204135 TCATAAAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
204156 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
204177 TCATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
** *
204198 TCATATGAA-AAAGCAGGATTT
1 TCATAT-AATAAAGCACCATCT
*
204219 TCATATAAAAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
*
204240 TCACATTAA-AAAGCACCATCT
1 TCATA-TAATAAAGCACCATCT
* *
204261 TCATATAAAAAAGCAGCATCT
1 TCATATAATAAAGCACCATCT
* *
204282 TCATATAAAAAAGCAGCATCT
1 TCATATAATAAAGCACCATCT
**
204303 TCATATAATAAAGCACCGCCT
1 TCATATAATAAAGCACCATCT
* *
204324 TCACATTAATAAAGCACCACCT
1 TCATA-TAATAAAGCACCATCT
* * *
204346 TCGTATAATAAAACACCATTT
1 TCATATAATAAAGCACCATCT
* *
204367 TCATATAATAAAGCACAACCT
1 TCATATAATAAAGCACCATCT
* *
204388 TCATATTATAAGGCACCATCTT
1 TCATATAATAAAGCACCATC-T
* * * *
204410 TACATAAAAT-AACCA-CAGCA
1 T-CATATAATAAAGCACCATCT
*
204430 TAATATAATAAAGCACCATCT
1 TCATATAATAAAGCACCATCT
* * *
204451 TCACATAA-AATAGC-CACAGCA
1 TCATATAATAA-AGCAC-CATCT
* * *
204472 TAATATAATCAAGCAGCATCT
1 TCATATAATAAAGCACCATCT
204493 TCATATAA
1 TCATATAA
204501 ATCAAAGTAC
Statistics
Matches: 810, Mismatches: 131, Indels: 64
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.00
19 26 0.03
20 48 0.06
21 657 0.81
22 65 0.08
23 12 0.01
24 1 0.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (21 bp):
TCATATAATAAAGCACCATCT
Found at i:214837 original size:44 final size:44
Alignment explanation
Indices: 214575--214823 Score: 367
Period size: 44 Copynumber: 5.7 Consensus size: 44
214565 ATTTTCCATC
* *
214575 TTGCTACCATATATTTTTCAACTAT-CAGGTATAAAGTCGTAACA
1 TTGCTACCACATATTTTTCAACTATCCA-GTATAAAGTGGTAACA
*
214619 TTGCTACCACATA-TTTTCAACTATCCAGTATAAAGTGGTAACT
1 TTGCTACCACATATTTTTCAACTATCCAGTATAAAGTGGTAACA
*
214662 TTGCTACCACATATTTTTCAATTATCCAGTATAAAGTGGTAACA
1 TTGCTACCACATATTTTTCAACTATCCAGTATAAAGTGGTAACA
* * * * *
214706 TTTCTACTATATATTTTTCAACTATTCAGTATAAAGTGGTAACT
1 TTGCTACCACATATTTTTCAACTATCCAGTATAAAGTGGTAACA
*
214750 TTGCTACCACATATTTTTCAACTATCCAGTGTAAAGTGGTAACA
1 TTGCTACCACATATTTTTCAACTATCCAGTATAAAGTGGTAACA
* *
214794 TTGCTACCATATATTTTTCATCTATCCAGT
1 TTGCTACCACATATTTTTCAACTATCCAGT
214824 GTAATATCGT
Statistics
Matches: 184, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 38 0.21
44 146 0.79
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (44 bp):
TTGCTACCACATATTTTTCAACTATCCAGTATAAAGTGGTAACA
Found at i:240282 original size:14 final size:14
Alignment explanation
Indices: 240263--240289 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
240253 ACTAAATCGA
240263 TCAATCTCAAAATC
1 TCAATCTCAAAATC
240277 TCAATCTCAAAAT
1 TCAATCTCAAAAT
240290 AGTCTACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
TCAATCTCAAAATC
Found at i:243669 original size:55 final size:53
Alignment explanation
Indices: 243602--243718 Score: 139
Period size: 53 Copynumber: 2.2 Consensus size: 53
243592 GTCAACACTT
* * *
243602 GCAATGACACCAAAATATACAATAT-TAAGGCAATAACTTCAACACTTGCAAAGA-
1 GCAATAACACCAAAATATAC-AT-TGTAA-ACAATAACATCAACACTTGCAAAGAC
* *
243656 GACAATAACACCAAAATATGCATTGTAAACAATAACATCAACACTTGCAACGAC
1 G-CAATAACACCAAAATATACATTGTAAACAATAACATCAACACTTGCAAAGAC
243710 GCAATAACA
1 GCAATAACA
243719 TCAACATGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
53 31 0.56
54 7 0.13
55 17 0.31
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (53 bp):
GCAATAACACCAAAATATACATTGTAAACAATAACATCAACACTTGCAAAGAC
Found at i:243704 original size:27 final size:26
Alignment explanation
Indices: 243632--243724 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
243622 AATATTAAGG
* *
243632 CAATAACTTCAACACTTGCAAAGAGA
1 CAATAACATCAACACTTGCAAAGAAA
* * **
243658 CAATAACACCAA-AATATGCATTGTAAA
1 CAATAACATCAACACT-TGCAAAG-AAA
* **
243685 CAATAACATCAACACTTGCAACGACG
1 CAATAACATCAACACTTGCAAAGAAA
243711 CAATAACATCAACA
1 CAATAACATCAACA
243725 TGTGCAATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
25 2 0.04
26 30 0.58
27 18 0.35
28 2 0.04
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (26 bp):
CAATAACATCAACACTTGCAAAGAAA
Found at i:245035 original size:175 final size:170
Alignment explanation
Indices: 244768--245092 Score: 515
Period size: 175 Copynumber: 1.9 Consensus size: 170
244758 AAAAATAACT
*
244768 AAGTTCAAAAGCTGGTGTTTTCCCATAAATAATCAGAAATCAAAATCCTAGCAATATGCACACCT
1 AAGTTCAAAAGCTGGTGTTTTCCCATAAATAATCAGAAATCAAAATCCTAGCAATATGCACACAT
* *
244833 CTGATATATGTACAATTTATATGCAAAAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTA
66 CTGATATATGTACAATTGATATGCAAAAGAACAACTTCCTATCGTGAAAACTGT---AGGAGTTA
244898 TCCCGTACAATGAGGGTACCCTTTATGCAATATTTTGCCAAAAA
128 T-CCGTACAATGAGGGTACCCTTTATGCAATATTTTGCCAAAAA
* ** * *
244942 AAGTTCAAAAGCTGGTATTTTTTGCATAAATTATCGGAAATCAAAATCCTAGCAATATGCACACA
1 AAGTTCAAAAGCTGGT-GTTTTCCCATAAATAATCAGAAATCAAAATCCTAGCAATATGCACACA
* *
245007 TCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCGTATCGTGAAAACTGTAGGAGTTATC
65 TCTGATATATGTACAATTGATATGCAAAAGAACAACTTCCTATCGTGAAAACTGTAGGAGTTATC
245072 CGTACAATGAGGGTACCCTTT
130 CGTACAATGAGGGTACCCTTT
245093 TGGCAGCCGT
Statistics
Matches: 140, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
171 22 0.16
172 9 0.06
174 16 0.11
175 93 0.66
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (170 bp):
AAGTTCAAAAGCTGGTGTTTTCCCATAAATAATCAGAAATCAAAATCCTAGCAATATGCACACAT
CTGATATATGTACAATTGATATGCAAAAGAACAACTTCCTATCGTGAAAACTGTAGGAGTTATCC
GTACAATGAGGGTACCCTTTATGCAATATTTTGCCAAAAA
Found at i:247394 original size:16 final size:16
Alignment explanation
Indices: 247373--247405 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
247363 TGGGACTCTG
247373 TATCTACCTTAATCCT
1 TATCTACCTTAATCCT
*
247389 TATCTACCTTAGTCCT
1 TATCTACCTTAATCCT
247405 T
1 T
247406 TAATCCTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.30, G:0.03, T:0.45
Consensus pattern (16 bp):
TATCTACCTTAATCCT
Found at i:253288 original size:30 final size:30
Alignment explanation
Indices: 253240--253301 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
253230 TGTAGGACTT
253240 TCTATATATCCAATAGGAGATTTTTATTTCA
1 TCTATATATCCAATAGGAGATTTTT-TTTCA
253271 TCTATATATCC-ATAGGAGATTTTTTTTCA
1 TCTATATATCCAATAGGAGATTTTTTTTCA
253300 TC
1 TC
253302 CCTCGGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 7 0.23
30 13 0.42
31 11 0.35
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.47
Consensus pattern (30 bp):
TCTATATATCCAATAGGAGATTTTTTTTCA
Found at i:254363 original size:30 final size:30
Alignment explanation
Indices: 254315--254376 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
254305 TGTAGGACTT
254315 TCTATATATCCAATAGGAGATTTTTATTTCA
1 TCTATATATCCAATAGGAGATTTTT-TTTCA
254346 TCTATATATCC-ATAGGAGATTTTTTTTCA
1 TCTATATATCCAATAGGAGATTTTTTTTCA
254375 TC
1 TC
254377 CCTCGGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 7 0.23
30 13 0.42
31 11 0.35
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.47
Consensus pattern (30 bp):
TCTATATATCCAATAGGAGATTTTTTTTCA
Found at i:259767 original size:3 final size:3
Alignment explanation
Indices: 259761--259805 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
259751 TTACAATCAC
* * * *
259761 TAT TAT TAT TAA TAT TAC TAT TAT TAT CAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
259806 AATCATTTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:259769 original size:18 final size:18
Alignment explanation
Indices: 259746--259787 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
259736 CCAACTGATG
259746 TATTATTACA-ATCACTAT
1 TATTATTA-ATATCACTAT
*
259764 TATTATTAATATTACTAT
1 TATTATTAATATCACTAT
259782 TATTAT
1 TATTAT
259788 CATTATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTATTAATATCACTAT
Found at i:263530 original size:36 final size:36
Alignment explanation
Indices: 263490--263601 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 36
263480 TTCGTTTGTG
263490 TGCTTTGTAAATAACAATGCAAATACTGTTTGCGTA
1 TGCTTTGTAAATAACAATGCAAATACTGTTTGCGTA
* *
263526 TGCTTTGTAAATAACAATGCCAATACTGTTAAAAATTGTGTA
1 TGCTTTGTAAATAACAATGCAAATACTG-T-----TTGCGTA
*
263568 TGCTTTGTAAATAACAATACAAATACTGTTTGCG
1 TGCTTTGTAAATAACAATGCAAATACTGTTTGCG
263602 ATGGTCTGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
36 31 0.48
37 1 0.02
41 1 0.02
42 32 0.49
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (36 bp):
TGCTTTGTAAATAACAATGCAAATACTGTTTGCGTA
Found at i:276668 original size:2 final size:2
Alignment explanation
Indices: 276663--276758 Score: 178
Period size: 2 Copynumber: 49.0 Consensus size: 2
276653 TGTGTGGATA
276663 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
276704 CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
276745 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
276759 GGTTTGATGG
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 90 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:278615 original size:11 final size:11
Alignment explanation
Indices: 278599--278625 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
278589 GGTGCTCTTT
278599 TTTTTTTTTTC
1 TTTTTTTTTTC
278610 TTTTTTTTTTC
1 TTTTTTTTTTC
278621 TTTTT
1 TTTTT
278626 CATGTCTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:282990 original size:16 final size:16
Alignment explanation
Indices: 282969--282999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
282959 CTGAAGTGGG
282969 ACAGACAGACGGACGA
1 ACAGACAGACGGACGA
*
282985 ACAGACGGACGGACG
1 ACAGACAGACGGACG
283000 GACGCAGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (16 bp):
ACAGACAGACGGACGA
Found at i:295546 original size:2 final size:2
Alignment explanation
Indices: 295539--295594 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
295529 TCGAAATGGA
*
295539 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
295581 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
295595 AGCATTACTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:297190 original size:2 final size:2
Alignment explanation
Indices: 297183--297265 Score: 148
Period size: 2 Copynumber: 41.5 Consensus size: 2
297173 GAATTTTAAA
**
297183 TC TC TC TC AA TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
297225 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
297266 GAGAGAATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:310234 original size:2 final size:2
Alignment explanation
Indices: 310227--310267 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
310217 CAATACACAT
310227 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
310268 NCCACTCGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:310675 original size:467 final size:466
Alignment explanation
Indices: 309799--310735 Score: 1865
Period size: 467 Copynumber: 2.0 Consensus size: 466
309789 TAGACAGAGG
309799 TCTCCACTCGCCGCGTCTTGCTGTCGATGGAGTGGTTTCTATCCCTCTCTACTTTAAGTTTGTCC
1 TCTCCACTCGCCGCGTCTTGCTGTCGATGGAGTGGTTTCTATCCCTCTCTACTTTAAGTTTGTCC
309864 AAAAGCCAAGCGAACTTTAATGATGGCTTTCCGGCCTGTTGCAAAAATAATTCCAGTTTTGTCAT
66 AAAAGCCAAGCGAACTTTAATGATGGCTTTCCGGCCTGTTGCAAAAATAATTCCAGTTTTGTCAT
309929 AGTTATATCCATAAGAAAGTTAAACATTTTTCATATCTTTGGGGGTTTTTTTTTGGATGGGAGTA
131 AGTTATATCCATAAGAAAGTTAAACATTTTTCATATCTTTGGGGGTTTTTTTTTGGATGGGAGTA
309994 TTTCTACATTTCAAATTTTCGAAGAAGCTAACAGCAGTACTTCCTTAATCGTTTTCGTTTTATAG
196 TTTCTACATTTCAAATTTTCGAAGAAGCTAACAGCAGTACTTCCTTAATCGTTTTCGTTTTATAG
310059 ATAAAGGAAACCTTTGATGTGTGAGTCTTTTTCATTGTTGTTTACTTTTCATCTGGTCTCTGTTG
261 ATAAAGGAAACCTTTGATGTGTGAGTCTTTTTCATTGTTGTTTACTTTTCATCTGGTCTCTGTTG
310124 TGAAATCAATAAATATGTTCGTGATGGAGGATATTAATATGAAAGATGAGAACAGATATAACATA
326 TGAAATCAATAAATATGTTCGTGATGGAGGATATTAATATGAAAGATGAGAACAGATATAACATA
310189 ATAACCATAGACAACCGCAGTAATAAATCAATACACATTCTCTCTCTCTCTCTCTCTCTCTCTCT
391 ATAACCATAGACAACCGCAGTAATAAATCAATACACATTCTCTCTCTCTCTCTCTCTCTCTCTCT
310254 CTCTCTCTCTC
456 CTCTCTCTCTC
310265 TCTNCCACTCGCCGCGTCTTGCTGTCGATGGAGTGGTTTCTATCCCTCTCTACTTTAAGTTTGTC
1 TCT-CCACTCGCCGCGTCTTGCTGTCGATGGAGTGGTTTCTATCCCTCTCTACTTTAAGTTTGTC
310330 CAAAAGCCAAGCGAACTTTAATGATGGCTTTCCGGCCTGTTGCAAAAATAATTCCAGTTTTGTCA
65 CAAAAGCCAAGCGAACTTTAATGATGGCTTTCCGGCCTGTTGCAAAAATAATTCCAGTTTTGTCA
310395 TAGTTATATCCATAAGAAAGTTAAACATTTTTCATATCTTTGGGGGTTTTTTTTTGGATGGGAGT
130 TAGTTATATCCATAAGAAAGTTAAACATTTTTCATATCTTTGGGGGTTTTTTTTTGGATGGGAGT
310460 ATTTCTACATTTCAAATTTTCGAAGAAGCTAACAGCAGTACTTCCTTAATCGTTTTCGTTTTATA
195 ATTTCTACATTTCAAATTTTCGAAGAAGCTAACAGCAGTACTTCCTTAATCGTTTTCGTTTTATA
310525 GATAAAGGAAACCTTTGATGTGTGAGTCTTTTTCATTGTTGTTTACTTTTCATCTGGTCTCTGTT
260 GATAAAGGAAACCTTTGATGTGTGAGTCTTTTTCATTGTTGTTTACTTTTCATCTGGTCTCTGTT
310590 GTGAAATCAATAAATATGTTCGTGATGGAGGATATTAATATGAAAGATGAGAACAGATATAACAT
325 GTGAAATCAATAAATATGTTCGTGATGGAGGATATTAATATGAAAGATGAGAACAGATATAACAT
310655 AATAACCATAGACAACCGCAGTAATAAATCAATACACATTCTCTCTCTCTCTCTCTCTCTCTCTC
390 AATAACCATAGACAACCGCAGTAATAAATCAATACACATTCTCTCTCTCTCTCTCTCTCTCTCTC
310720 TCTCTCTCTCTC
455 TCTCTCTCTCTC
310732 TCTC
1 TCTC
310736 TCTCTCTGCG
Statistics
Matches: 470, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
466 4 0.01
467 466 0.99
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (466 bp):
TCTCCACTCGCCGCGTCTTGCTGTCGATGGAGTGGTTTCTATCCCTCTCTACTTTAAGTTTGTCC
AAAAGCCAAGCGAACTTTAATGATGGCTTTCCGGCCTGTTGCAAAAATAATTCCAGTTTTGTCAT
AGTTATATCCATAAGAAAGTTAAACATTTTTCATATCTTTGGGGGTTTTTTTTTGGATGGGAGTA
TTTCTACATTTCAAATTTTCGAAGAAGCTAACAGCAGTACTTCCTTAATCGTTTTCGTTTTATAG
ATAAAGGAAACCTTTGATGTGTGAGTCTTTTTCATTGTTGTTTACTTTTCATCTGGTCTCTGTTG
TGAAATCAATAAATATGTTCGTGATGGAGGATATTAATATGAAAGATGAGAACAGATATAACATA
ATAACCATAGACAACCGCAGTAATAAATCAATACACATTCTCTCTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTC
Found at i:310701 original size:2 final size:2
Alignment explanation
Indices: 310694--310742 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
310684 CAATACACAT
310694 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
310736 TC TC TC T
1 TC TC TC T
310743 GCGTAGAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:316801 original size:16 final size:17
Alignment explanation
Indices: 316782--316817 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
316772 AATAGTAAAC
316782 ATAGTAACC-AGTAACT
1 ATAGTAACCAAGTAACT
316798 ATAGTAACCATAGTAACT
1 ATAGTAACCA-AGTAACT
316816 AT
1 AT
316818 GTAGTAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
ATAGTAACCAAGTAACT
Found at i:316814 original size:9 final size:9
Alignment explanation
Indices: 316773--316814 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
316763 TCAATAACTA
*
316773 ATAGTAAAC
1 ATAGTAACC
316782 ATAGTAACC
1 ATAGTAACC
*
316791 --AGTAACT
1 ATAGTAACC
316798 ATAGTAACC
1 ATAGTAACC
316807 ATAGTAAC
1 ATAGTAAC
316815 TATGTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
7 6 0.21
9 22 0.79
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.24
Consensus pattern (9 bp):
ATAGTAACC
Found at i:319099 original size:15 final size:14
Alignment explanation
Indices: 319079--319113 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
319069 ATCGATGCGG
319079 TTTTTTATTTTTATT
1 TTTTTTATTTTT-TT
319094 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
319108 TTTTTT
1 TTTTTT
319114 GTAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTATTTTTTT
Found at i:320723 original size:12 final size:13
Alignment explanation
Indices: 320706--320734 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
320696 ACGTAGAATC
320706 GGGGGGGAG-GGG
1 GGGGGGGAGAGGG
320718 GGGGGGGAGAGGG
1 GGGGGGGAGAGGG
320731 GGGG
1 GGGG
320735 TNNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.10, C:0.00, G:0.90, T:0.00
Consensus pattern (13 bp):
GGGGGGGAGAGGG
Found at i:322516 original size:18 final size:19
Alignment explanation
Indices: 322493--322528 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
322483 GAATGTTGCC
*
322493 TTTTACCATGTAC-TTTCA
1 TTTTACAATGTACATTTCA
322511 TTTTACAATGTACATTTC
1 TTTTACAATGTACATTTC
322529 TTTGATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTACAATGTACATTTCA
Found at i:323280 original size:18 final size:19
Alignment explanation
Indices: 323257--323292 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
323247 GAATGTTGCC
*
323257 TTTTACCATGTAC-TTTCA
1 TTTTACAATGTACATTTCA
323275 TTTTACAATGTACATTTC
1 TTTTACAATGTACATTTC
323293 TTTGATGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTACAATGTACATTTCA
Found at i:328209 original size:161 final size:160
Alignment explanation
Indices: 327944--328446 Score: 621
Period size: 161 Copynumber: 3.1 Consensus size: 160
327934 AACATCCACT
* ** ** * * * *
327944 AAGAAAATGAACCTAAACTGCAAATATTTGGAATTCTTCTAAGTCCTAGGGCCATAACTCTGTCA
1 AAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGTCG
* *
328009 AAAATTGCTCGATCGTACCCAAAATCAAACTTGACCTAGATATTAT-TTGGATAAACCTGTATAC
66 AAAATTGCTCGATCGTA-CCAATATCAAACTTGACCTAGATATTATCAT-GATAAACCTGTATAC
* * * *
328073 TAAATTTCATATCAATATGTGCAACCTCTGCG
129 CAAATTTCATTTCAATATGTTCATCCTCTGCG
* * *
328105 AAGAAAATGCGCAGAAATTGCAAATAACTGGAATTTTTCTATGTCCAAGAGCCATAACTCTGTCG
1 AAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGTCG
* * ** *
328170 AAAATTGCTCAATCGCACTTTATATCAAACTTGACCTAGATATTATCATAATAAACCTGTATACC
66 AAAATTGCTCGATCGTAC-CAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACC
* * * **
328235 AAATTTCATTTCAGTATGTTCATTCACTATG
130 AAATTTCATTTCAATATGTTCATCCTCTGCG
** *
328266 AAGAAAATGAGTGGAAACTGCAAATAACTGGAATTTCTCTATGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGTCG
* * *
328331 AAAACTGCTCGATTGTAGCCAATATCAAACTTGACCTAGATATTATCATGATTAACCTGTATACC
66 AAAATTGCTCGATCGTA-CCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACC
* *
328396 AAATTTCATTTCAATATGTTCATCTTCTGCA
130 AAATTTCATTTCAATATGTTCATCCTCTGCG
* *
328427 AAGAAAATGAACGGAAACTG
1 AAGAAAATGAGCAGAAACTG
328447 TTGGTGGACC
Statistics
Matches: 288, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
160 1 0.00
161 285 0.99
162 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (160 bp):
AAGAAAATGAGCAGAAACTGCAAATAACTGGAATTTTTCTATGTCCAAGGGCCATAACTCTGTCG
AAAATTGCTCGATCGTACCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCA
AATTTCATTTCAATATGTTCATCCTCTGCG
Found at i:329841 original size:14 final size:14
Alignment explanation
Indices: 329822--329848 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
329812 TGCTAGATAC
329822 ATATAGATATATAT
1 ATATAGATATATAT
329836 ATATAGATATATA
1 ATATAGATATATA
329849 AAAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATAGATATATAT
Found at i:330108 original size:16 final size:16
Alignment explanation
Indices: 330079--330112 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
330069 ATAGGTTCCC
*
330079 ACCAAGTTTAAGAGAA
1 ACCAAATTTAAGAGAA
*
330095 ACCAAATTTTAGAGAA
1 ACCAAATTTAAGAGAA
330111 AC
1 AC
330113 ATTATCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (16 bp):
ACCAAATTTAAGAGAA
Found at i:344197 original size:5 final size:5
Alignment explanation
Indices: 344178--344308 Score: 135
Period size: 5 Copynumber: 25.4 Consensus size: 5
344168 TATAAAATTG
*
344178 CGAAA CGAAA TCGAAA CGAAA CGAAA CGAAA CGAAA TC-AGA CGAAA CGAAA
1 CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA
*
344229 CGAAA C-AAA TCGAAA CGAAA CGAAA TC-AAT CGAAA CGAAA CGAAA TC-AAA
1 CGAAA CGAAA -CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA -CGAAA
*
344279 CGAAA CGAAA TCAAAAA TCGAAA CGAAA CG
1 CGAAA CGAAA -C-GAAA -CGAAA CGAAA CG
344309 GAATTTAAAC
Statistics
Matches: 109, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
4 6 0.06
5 83 0.76
6 15 0.14
7 5 0.05
ACGTcount: A:0.57, C:0.20, G:0.17, T:0.06
Consensus pattern (5 bp):
CGAAA
Found at i:344221 original size:20 final size:20
Alignment explanation
Indices: 344178--344308 Score: 167
Period size: 20 Copynumber: 6.3 Consensus size: 20
344168 TATAAAATTG
344178 CGAAACGAAATCGAAA-CGAAA
1 CGAAACGAAA-CGAAATC-AAA
*
344199 CGAAACGAAACGAAATCAGA
1 CGAAACGAAACGAAATCAAA
344219 CGAAACGAAACGAAA-CAAA
1 CGAAACGAAACGAAATCAAA
*
344238 TCGAAACGAAACGAAATCAAT
1 -CGAAACGAAACGAAATCAAA
344259 CGAAACGAAACGAAATCAAA
1 CGAAACGAAACGAAATCAAA
*
344279 CGAAACGAAATCAAAAATCGAAA
1 CGAAACGAAA-C-GAAATC-AAA
344302 CGAAACG
1 CGAAACG
344309 GAATTTAAAC
Statistics
Matches: 99, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.03
20 66 0.67
21 15 0.15
22 5 0.05
23 10 0.10
ACGTcount: A:0.57, C:0.20, G:0.17, T:0.06
Consensus pattern (20 bp):
CGAAACGAAACGAAATCAAA
Found at i:344552 original size:2 final size:2
Alignment explanation
Indices: 344545--344592 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
344535 CAGACGTTTT
344545 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
344587 GA GA GA
1 GA GA GA
344593 TGCCTTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:345487 original size:2 final size:2
Alignment explanation
Indices: 345480--345512 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
345470 CTTTTAAGGC
345480 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
345513 AAAACGTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:345767 original size:5 final size:5
Alignment explanation
Indices: 345757--345882 Score: 120
Period size: 5 Copynumber: 25.4 Consensus size: 5
345747 GTCTAAATTC
* *
345757 CGTTT CGTTT CGTTT CGATT --TTT GGTTT CGTTT CGTTT -GATTT CGTTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT
* * *
345805 CGTTT CGATT -GATTT TGTTT CGTTT CGATTT -GTGT CGTTT CGTTT CGTTT
1 CGTTT CGTTT CG-TTT CGTTT CGTTT CG-TTT CGTTT CGTTT CGTTT CGTTT
345855 -GATTT CGTTT CGTTT CGATTT CGTTT CG
1 CG-TTT CGTTT CGTTT CG-TTT CGTTT CG
345883 CACTTTACAG
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
3 2 0.02
4 5 0.05
5 84 0.82
6 11 0.11
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.58
Consensus pattern (5 bp):
CGTTT
Found at i:345806 original size:20 final size:20
Alignment explanation
Indices: 345757--345871 Score: 151
Period size: 20 Copynumber: 5.6 Consensus size: 20
345747 GTCTAAATTC
345757 CGTTTCGTTTCGTTTCGATTTTT
1 CGTTTCGTTTCGTTT-GA--TTT
*
345780 GGTTTCGTTTCGTTTGATTT
1 CGTTTCGTTTCGTTTGATTT
*
345800 CGTTTCGTTTCGATTGATTT
1 CGTTTCGTTTCGTTTGATTT
* *
345820 TGTTTCGTTTCGATTTG-TGT
1 CGTTTCGTTTCG-TTTGATTT
345840 CGTTTCGTTTCGTTTGATTT
1 CGTTTCGTTTCGTTTGATTT
345860 CGTTTCGTTTCG
1 CGTTTCGTTTCG
345872 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
19 4 0.05
20 59 0.72
21 3 0.04
22 2 0.02
23 14 0.17
ACGTcount: A:0.05, C:0.15, G:0.22, T:0.58
Consensus pattern (20 bp):
CGTTTCGTTTCGTTTGATTT
Found at i:352860 original size:21 final size:21
Alignment explanation
Indices: 352836--352875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
352826 TTGACATAAC
352836 TATCTTGAATGTCAACATATT
1 TATCTTGAATGTCAACATATT
* *
352857 TATCTTGCATGTCGACATA
1 TATCTTGAATGTCAACATA
352876 ATTAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TATCTTGAATGTCAACATATT
Found at i:353079 original size:21 final size:21
Alignment explanation
Indices: 353055--353111 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
353045 TTTTTCTATC
* *
353055 AAATAAGTCGACATGGAAGAT
1 AAATATGTCGACATGCAAGAT
*
353076 AAATATGTTGACATGCAAGAT
1 AAATATGTCGACATGCAAGAT
**
353097 AGTTATGTCGACATG
1 AAATATGTCGACATG
353112 TTGGTATGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (21 bp):
AAATATGTCGACATGCAAGAT
Found at i:357146 original size:4 final size:4
Alignment explanation
Indices: 357137--357217 Score: 162
Period size: 4 Copynumber: 20.2 Consensus size: 4
357127 AGTGACGAAG
357137 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
357185 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
357218 ATCTAACACA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:358588 original size:4 final size:4
Alignment explanation
Indices: 358579--358653 Score: 150
Period size: 4 Copynumber: 18.8 Consensus size: 4
358569 ATAATTAAAA
358579 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
358627 AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGA
358654 CCATTTTACT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:374175 original size:436 final size:435
Alignment explanation
Indices: 373330--374315 Score: 1426
Period size: 436 Copynumber: 2.3 Consensus size: 435
373320 TCTAGCATTA
** * * * *
373330 ATAACCTTTCACAAAATGGCTCTCATTAAAGGGCTATAGATAAA-AATTTTTAGAGCACTTTGAT
1 ATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGATAAAGAA--TTTAGAGCCCTTTGGT
*
373394 CCCCTAATTTAAGGGGCCAGCCCCTTTTTCTTGGA-ATCAAATGAAAGGACATTTAATTCTGAAA
64 CCCCTAATTTAAGGGGCCAGCCCCTTTTTCTT-GATATCAAATGAAAGGTCATTTAATTCTGAAA
* ** *
373458 ACATTTTGTCAACAAGTGTTTAAAAATTCGTTACTGTTCTGGAGATATATGAGAAAGAATGTTTA
128 AAATTTTGTCAACAAGTGTTTAAAAATTCGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTA
* ** *
373523 AGGGGCCGATCCCTTATCTCCTTATAGGGGCCGTTTGGCGAAATTTTGAAGACTGCATATGGTTA
193 AGGGGCCAATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGACTGCATATGGTTA
** ** *
373588 AGAACATCTTTTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCCGAGATA
258 AGAACATCAATTTGAACAACTTTTCTTCTGTATTGCATAACAAAATAGTTTTCCTTTCCGAGATA
* * *
373653 TGGGTAATCAAAATGTTGGACTTTTGGTCCCTAAAAACCTTTAATTACGTGATACATGACAAAAT
323 TGGGTAATCAAAATGTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAATACATGACAAAAT
* **
373718 CATCTCAGTGCTTGGATACATAACTGTAAGATAAACATATTTGCTTTT
388 CATCTCACTGCTTGGATACATAACTGTAAGATAAACATATTTGCTACT
*
373766 ATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGATCAAAGACTTTAGAGCCCTTTGGTC
1 ATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGAT-AAAGAATTTAGAGCCCTTTGGTC
* *
373831 CCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCT-AAACA
65 CCCTAATTTAAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTGAAA-A
* * *
373895 AATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTT
129 AATTTTG-TCAACAAGTGTTTAAAAATTCGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTA
** *
373960 AGGGGCCAATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGGTTGCATATTGTTA
193 AGGGGCCAATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGACTGCATATGGTTA
* *
374025 AGAACAAT-AATTTGAACAACTTTTCTTCTGTGTTGCATAACAAAATAGTTTTCCTTTCTGAGAT
258 AGAAC-ATCAATTTGAACAACTTTTCTTCTGTATTGCATAACAAAATAGTTTTCCTTTCCGAGAT
* * * *
374089 ATGGGTGATC-GAATTTTGGACTTTTGGCCCCTAAAATCCCTTAATTACGTAATACATGACAAAA
322 ATGGGTAATCAAAATGTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAATACATGACAAAA
*
374153 TCAT-TACACTGCTTGGATACATAACTGTGAGATAAACATATTTGCTACT
387 TCATCT-CACTGCTTGGATACATAACTGTAAGATAAACATATTTGCTACT
* *
374202 ATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGAATTTAGAGCCCTTTGGTT
1 ATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGA-TAAAGAATTTAGAGCCCTTTGGTC
* * *
374267 CCCTAATTTTAGGGGACAGCCCCTTTTTCTTGATATTAAATGAAAGGTC
65 CCCTAATTTAAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTC
374316 TTGTAAATAT
Statistics
Matches: 493, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
435 6 0.01
436 308 0.62
437 176 0.36
438 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (435 bp):
ATAACCTTTCACAAAATATCTCTCAGTAAAGGGCTACAGATAAAGAATTTAGAGCCCTTTGGTCC
CCTAATTTAAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCATTTAATTCTGAAAAAA
TTTTGTCAACAAGTGTTTAAAAATTCGTTACCATTCTGGAGATATATGAGAAAGAAGGTTTAAGG
GGCCAATCCCTTATCTCCTTATAGGGGCCGTTTAACAAAATTTTGAAGACTGCATATGGTTAAGA
ACATCAATTTGAACAACTTTTCTTCTGTATTGCATAACAAAATAGTTTTCCTTTCCGAGATATGG
GTAATCAAAATGTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAATACATGACAAAATCAT
CTCACTGCTTGGATACATAACTGTAAGATAAACATATTTGCTACT
Found at i:380411 original size:186 final size:185
Alignment explanation
Indices: 380097--380467 Score: 733
Period size: 186 Copynumber: 2.0 Consensus size: 185
380087 TTGCATACTA
380097 AATTAGCCATCTGTTTACTTTTATCAACAAACCAATCAGGTGAATGAGTTGCAAGGTATTGTGGG
1 AATTAGCCATCTGTTTACTTTTATCAACAAACCAATCAGGTGAATGAGTTGCAAGGTATTGTGGG
380162 CTACTACAAGTTTCAGTGTATACAAAGCGTATTGAAAATATATACCATTTTGAATTGTCCTTTGG
66 CTACTACAAGTTTCAGTGTATACAAAGCGTATTGAAAATATATACCATTTTGAATTGTCCTTTGG
380227 AAACTCATTTTGAATGATTTTTCAGAATTTAAGAAATTAATATGGACAATTATGT
131 AAACTCATTTTGAATGATTTTTCAGAATTTAAGAAATTAATATGGACAATTATGT
380282 NAATTAGCCATCTGTTTACTTTTATCAACAAACCAATCAGGTGAATGAGTTGCAAGGTATTGTGG
1 -AATTAGCCATCTGTTTACTTTTATCAACAAACCAATCAGGTGAATGAGTTGCAAGGTATTGTGG
380347 GCTACTACAAGTTTCAGTGTATACAAAGCGTATTGAAAATATATACCATTTTGAATTGTCCTTTG
65 GCTACTACAAGTTTCAGTGTATACAAAGCGTATTGAAAATATATACCATTTTGAATTGTCCTTTG
380412 GAAACTCATTTTGAATGATTTTTCAGAATTTAAGAAATTAATATGGACAATTATGT
130 GAAACTCATTTTGAATGATTTTTCAGAATTTAAGAAATTAATATGGACAATTATGT
380468 CTGAACTTCA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (185 bp):
AATTAGCCATCTGTTTACTTTTATCAACAAACCAATCAGGTGAATGAGTTGCAAGGTATTGTGGG
CTACTACAAGTTTCAGTGTATACAAAGCGTATTGAAAATATATACCATTTTGAATTGTCCTTTGG
AAACTCATTTTGAATGATTTTTCAGAATTTAAGAAATTAATATGGACAATTATGT
Found at i:390799 original size:49 final size:49
Alignment explanation
Indices: 390728--390876 Score: 298
Period size: 49 Copynumber: 3.0 Consensus size: 49
390718 AATAATAATA
390728 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
1 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
390777 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
1 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
390826 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
1 AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
390875 AA
1 AA
390877 TAATAAAATA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 100 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (49 bp):
AAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACCTT
Found at i:399297 original size:166 final size:166
Alignment explanation
Indices: 399023--399910 Score: 1379
Period size: 166 Copynumber: 5.3 Consensus size: 166
399013 NNNNNNNNNN
* * * * * *
399023 TTGTGAAATTCATGATCCCCGGGGATAGGGTAGGGCCACAATGGGGGGTTGAAGTTTTACATAGG
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
*
399088 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAAGAAAGCTGAAACT
66 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
399153 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
131 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* *
399189 TTGTGAAATTCATGATCCATGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
399254 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
66 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
399319 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
131 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* *
399355 TTGTGAAAATCATGACCCCTGGTGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
* * * *
399420 AAAATATAAAGTAAATCTTTTAAAATCTTCTTCTCGGAAACTAATCAGCCAGGAAAGCTGAAACT
66 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
*
399485 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAG
131 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* * *
399521 TTATGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGGGT-GTTAAAATTTTAC
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAAT--GGGGGGTCG---AAATTTTAC
*
399585 ATAGAAATACATGTATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGA
61 ATAG---GA-A--TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGA
*
399650 AAGCTGAAACTTGTGTGGAAGCATCCTCA-ATCAGTGTAGATTCAAAG
120 AAGCTGAAACTTGTGTGGAAGCATCCTCAGGT-AGTGTAGATTCAAAG
*
399697 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGG-CACAATGGGGGGTCGAAGTTTTACATAGG
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
*
399761 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTTATCAGCCAGGAAAGCTGAAACT
66 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
* *
399826 TGTGTGGAAGTATCTTCAGGTAGTGTAGATTCAAAG
131 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* * *
399862 TTGTGAAAATCATGATCCATGGGGGTAGGTTGAGGCCAC-ATGGAGGGGT
1 TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGG-GGGGT
399911 GGGGGTGTTA
Statistics
Matches: 666, Mismatches: 40, Indels: 32
0.90 0.05 0.04
Matches are distributed among these distances:
165 129 0.19
166 362 0.54
167 2 0.00
168 8 0.01
170 13 0.02
171 12 0.02
173 8 0.01
174 2 0.00
175 6 0.01
176 124 0.19
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (166 bp):
TTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAATTTTACATAGG
AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
Found at i:402359 original size:2 final size:2
Alignment explanation
Indices: 402352--402402 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
402342 TGTGAGTGTT
402352 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
402394 GA GA GA GA G
1 GA GA GA GA G
402403 GAGTATGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:410691 original size:21 final size:22
Alignment explanation
Indices: 410653--410693 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
410643 AAAATCGGTA
*
410653 AGAAAAAAAAAGGAGAAGAATG
1 AGAAAAAAAAAGCAGAAGAATG
*
410675 AGAAAAAAAAA-CCGAAGAA
1 AGAAAAAAAAAGCAGAAGAA
410694 AAACAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.05, G:0.22, T:0.02
Consensus pattern (22 bp):
AGAAAAAAAAAGCAGAAGAATG
Found at i:410762 original size:59 final size:57
Alignment explanation
Indices: 410699--410851 Score: 263
Period size: 56 Copynumber: 2.7 Consensus size: 57
410689 AAGAAAAACA
*
410699 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAATAAAAAACCTTACAATCACT
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA-AA-AAAAAACATTACAATCACT
*
410758 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT-AAAAAGAAACATTACAATCACT
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAAAAAAAACATTACAATCACT
410814 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA
410852 CATTATTTTT
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
56 51 0.56
57 5 0.05
58 1 0.01
59 34 0.37
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (57 bp):
ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAAAAAAAACATTACAATCACT
Found at i:414045 original size:2 final size:2
Alignment explanation
Indices: 414038--414078 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
414028 GTGCATCCAC
414038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
414079 CTGCAAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:414776 original size:1 final size:1
Alignment explanation
Indices: 414770--414804 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
414760 GATTGTACTT
*
414770 GGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
414805 CACTGTAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:417465 original size:2 final size:2
Alignment explanation
Indices: 417400--417451 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
417390 GAGATTTTTA
417400 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
417442 TC TC TC TC TC
1 TC TC TC TC TC
417452 AATTCTATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:417809 original size:16 final size:17
Alignment explanation
Indices: 417781--417816 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
417771 GTCCTTCTTC
417781 CTTGCGCAAACAAACAT
1 CTTGCGCAAACAAACAT
417798 CTTGCG-AAACAAACAT
1 CTTGCGCAAACAAACAT
417814 CTT
1 CTT
417817 TCATAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (17 bp):
CTTGCGCAAACAAACAT
Found at i:418705 original size:36 final size:36
Alignment explanation
Indices: 418664--418735 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
418654 GTTTAATTAA
418664 ATCATGTTCGTCAAAAGCAGGGTGGGCCATATTGGG
1 ATCATGTTCGTCAAAAGCAGGGTGGGCCATATTGGG
418700 ATCATGTTCGTCAAAAGCAGGGTGGGCCATATTGGG
1 ATCATGTTCGTCAAAAGCAGGGTGGGCCATATTGGG
418736 GGNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (36 bp):
ATCATGTTCGTCAAAAGCAGGGTGGGCCATATTGGG
Found at i:418759 original size:1 final size:1
Alignment explanation
Indices: 418753--418788 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
418743 NNNNNNNNNN
**
418753 GGGGGGGGGGGGGTTGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
418789 CTCGAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.94, T:0.06
Consensus pattern (1 bp):
G
Found at i:437314 original size:25 final size:24
Alignment explanation
Indices: 437279--437325 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
437269 GAGAGATTAG
437279 ATGGGGGATATACACGTGACCAGC
1 ATGGGGGATATACACGTGACCAGC
437303 ATGGGGGAATATACACGTGACCA
1 ATGGGGG-ATATACACGTGACCA
437326 CCATACGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.17
Consensus pattern (24 bp):
ATGGGGGATATACACGTGACCAGC
Found at i:438347 original size:31 final size:31
Alignment explanation
Indices: 438309--438373 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
438299 TGGTGCAGGG
438309 AACAGCTCAGTATGATCTATTGCCCGAGGCC
1 AACAGCTCAGTATGATCTATTGCCCGAGGCC
438340 AACAGCTCAGTATGATCTATTGCCCGAGGCC
1 AACAGCTCAGTATGATCTATTGCCCGAGGCC
438371 AAC
1 AAC
438374 GGCCTCGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (31 bp):
AACAGCTCAGTATGATCTATTGCCCGAGGCC
Found at i:447450 original size:115 final size:119
Alignment explanation
Indices: 447244--447461 Score: 399
Period size: 115 Copynumber: 1.9 Consensus size: 119
447234 ACTGGTACAA
447244 TTAAATGGCAATTTGTTTAGTGTTCTAGCTGTGCTTATTTGTTCTAATATCAGCATCATGACATC
1 TTAAATGGCAATTTGTTTAGTGTTCTA-CTGTGCTTATTTGTTCTAATATCAGCATCATGACATC
447309 TTTCTTATAATCTTTTAAAAACATAAGTATTA-ATATAAACCCAAATCGGCCTCC
65 TTTCTTATAATCTTTTAAAAACATAAGTATTACATATAAACCCAAATCGGCCTCC
447363 TTAAATGGCAATTTGTTTAGTG-T-T-CTGTGCTTATTTGTTCTAATATCAGCATCATGACATCT
1 TTAAATGGCAATTTGTTTAGTGTTCTACTGTGCTTATTTGTTCTAATATCAGCATCATGACATCT
447425 TTCTTATAATCTTTTAAAAACATAAGTATTACATATA
66 TTCTTATAATCTTTTAAAAACATAAGTATTACATATA
447462 TATCTATACA
Statistics
Matches: 98, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
115 69 0.70
116 5 0.05
117 1 0.01
118 1 0.01
119 22 0.22
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (119 bp):
TTAAATGGCAATTTGTTTAGTGTTCTACTGTGCTTATTTGTTCTAATATCAGCATCATGACATCT
TTCTTATAATCTTTTAAAAACATAAGTATTACATATAAACCCAAATCGGCCTCC
Found at i:454424 original size:20 final size:23
Alignment explanation
Indices: 454389--454429 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
454379 CTTTGAAACA
454389 TATACAACTATATTTG-TATAAT
1 TATACAACTATATTTGATATAAT
454411 TATA-AACT-TATTTGATATA
1 TATACAACTATATTTGATATA
454430 CTGTGGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (23 bp):
TATACAACTATATTTGATATAAT
Found at i:460964 original size:18 final size:17
Alignment explanation
Indices: 460941--460975 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
460931 GGAAGTCCTT
460941 TATATAAAATACACTGTA
1 TATATAAAATACA-TGTA
*
460959 TATATAAACTACATGTA
1 TATATAAAATACATGTA
460976 ATAAAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
TATATAAAATACATGTA
Found at i:461834 original size:2 final size:2
Alignment explanation
Indices: 461829--461892 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
461819 AAAATCCCCC
461829 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
461871 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
461893 TAAAGTTTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:463075 original size:2 final size:2
Alignment explanation
Indices: 463068--463128 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
463058 GTAACTGATA
463068 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
463110 AG A- AG AG AG A- AT AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
463129 ATAGACGATA
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:470806 original size:2 final size:2
Alignment explanation
Indices: 470799--470862 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
470789 TACTCACTCA
470799 CT CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
470840 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
470863 ACATAATCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:474209 original size:2 final size:2
Alignment explanation
Indices: 474202--474252 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
474192 TTGCCATCAA
474202 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
474244 CT CT CT CT C
1 CT CT CT CT C
474253 AAAAATAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:475035 original size:72 final size:72
Alignment explanation
Indices: 474946--475125 Score: 272
Period size: 72 Copynumber: 2.5 Consensus size: 72
474936 CATCATTCCT
* **
474946 GGCAGCGTGTCAGCTGGATGGATACATCCTGGGAAGGAATATCTTATCTCCTGATC-AGAATTCA
1 GGCAGCGTGTCAGCTGGATGGATACATCCAGGGAAGGAATATCCCATCTCCTGATCTA-AATTCA
475010 TGACTCCA
65 TGACTCCA
* * *
475018 GGCATCGTGTCAGCTGGATGGATATATCCAGGGAAGGAATATCCCATCTCCTGATCTAAGTTCAT
1 GGCAGCGTGTCAGCTGGATGGATACATCCAGGGAAGGAATATCCCATCTCCTGATCTAAATTCAT
475083 GACTCCA
66 GACTCCA
**
475090 GGCAGCGTGTCAGCTGGATGGATGTATCCAGGGAAG
1 GGCAGCGTGTCAGCTGGATGGATACATCCAGGGAAG
475126 TTATCGAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 98 0.99
73 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (72 bp):
GGCAGCGTGTCAGCTGGATGGATACATCCAGGGAAGGAATATCCCATCTCCTGATCTAAATTCAT
GACTCCA
Found at i:477231 original size:2 final size:2
Alignment explanation
Indices: 477224--477274 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
477214 TCAGATTTAT
* *
477224 TC TC TC TC TC TC TT TC TC TT TC -C TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
477265 TC TC TC TC TC
1 TC TC TC TC TC
477275 ATAATCTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:487483 original size:18 final size:18
Alignment explanation
Indices: 487462--487524 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
487452 TCTTGATTGT
487462 TGTTGTGGTGGGTTTGGG
1 TGTTGTGGTGGGTTTGGG
* *
487480 TGTTGTTGTTGGTTTTGGGG
1 TGTTG-TGGTGGGTTT-GGG
* *
487500 TGGTTGTTGTTGGTTTGGG
1 T-GTTGTGGTGGGTTTGGG
*
487519 AGTTGT
1 TGTTGT
487525 CGTAGTTGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.29
19 11 0.31
20 10 0.29
21 4 0.11
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.51
Consensus pattern (18 bp):
TGTTGTGGTGGGTTTGGG
Found at i:487483 original size:21 final size:20
Alignment explanation
Indices: 487459--487524 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
487449 TTGTCTTGAT
487459 TGTTGTTGTGGTGGGTTTGGG
1 TGTTGTTGT-GTGGGTTTGGG
*
487480 TGTTGTTGT-TGGTTTTGGGG
1 TGTTGTTGTGTGGGTTT-GGG
487500 TGGTTGTTGT-T-GGTTTGGG
1 T-GTTGTTGTGTGGGTTTGGG
*
487519 AGTTGT
1 TGTTGT
487525 CGTAGTTGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 8 0.20
21 18 0.45
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.52
Consensus pattern (20 bp):
TGTTGTTGTGTGGGTTTGGG
Found at i:487610 original size:18 final size:18
Alignment explanation
Indices: 487589--487629 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
487579 CCGAGGAGTA
487589 GTTGTAGTT-GGAGTGGTT
1 GTTGT-GTTAGGAGTGGTT
487607 GTTG-GTTCAGGAGTGGTT
1 GTTGTGTT-AGGAGTGGTT
487625 GTTGT
1 GTTGT
487630 TGGTTTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.15
18 17 0.85
ACGTcount: A:0.10, C:0.02, G:0.44, T:0.44
Consensus pattern (18 bp):
GTTGTGTTAGGAGTGGTT
Found at i:487630 original size:21 final size:21
Alignment explanation
Indices: 487604--487652 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
487594 AGTTGGAGTG
487604 GTTGTTGGTTCAGGAGTGGTT
1 GTTGTTGGTTCAGGAGTGGTT
** *
487625 GTTGTTGGTTTTGGAGTTGTT
1 GTTGTTGGTTCAGGAGTGGTT
487646 GTTGTTG
1 GTTGTTG
487653 TGGTTGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.02, G:0.41, T:0.51
Consensus pattern (21 bp):
GTTGTTGGTTCAGGAGTGGTT
Found at i:487643 original size:15 final size:14
Alignment explanation
Indices: 487625--487695 Score: 63
Period size: 15 Copynumber: 4.8 Consensus size: 14
487615 AGGAGTGGTT
487625 GTTGTTGGTTTTGG
1 GTTGTTGGTTTTGG
487639 AGTTGTT-GTTGTTGTG
1 -GTTGTTGGTT-TTG-G
*
487655 GTTGTTGGTTTCTGT
1 GTTGTTGGTTT-TGG
*
487670 GTTGTTGGTTCTGGG
1 GTTGTTGGTT-TTGG
*
487685 GTCGTTGGTTT
1 GTTGTTGGTTT
487696 CGGTGTAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.09
15 36 0.77
16 7 0.15
ACGTcount: A:0.01, C:0.04, G:0.39, T:0.55
Consensus pattern (14 bp):
GTTGTTGGTTTTGG
Found at i:490375 original size:2 final size:2
Alignment explanation
Indices: 490368--490403 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
490358 ACCCGATTTG
490368 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
490404 GTATAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:492409 original size:63 final size:63
Alignment explanation
Indices: 492337--492470 Score: 259
Period size: 63 Copynumber: 2.1 Consensus size: 63
492327 GATGGAAATA
492337 TATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCCC
1 TATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCCC
492400 TATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCCC
1 TATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCCC
*
492463 TTTTATTA
1 TATTATTA
492471 TTTTTTTTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.18, C:0.19, G:0.13, T:0.49
Consensus pattern (63 bp):
TATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCCC
Found at i:493725 original size:437 final size:437
Alignment explanation
Indices: 492911--494338 Score: 2579
Period size: 437 Copynumber: 3.3 Consensus size: 437
492901 CGTTTGATAA
* * *
492911 CAAGAAAAAGGGGCTGGTCCCTT-AAATAAGGGGCCAAAAGGGCTCTAAAGTCTTTCTCCCATAG
1 CAAGAAAAAGGGGCTGG-CCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAG
492975 CACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATAAA
65 CACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATAAA
*
493040 ACTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAATCCA
130 ACTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCA
493105 AAACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATG
195 AAACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATG
493170 CTTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGA
260 CTTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGA
* * **
493235 TTAGGGGTCGGCCCCTAAAATGTCCTTTCCCAGATAGCTCTTAAACGGCAAAGAATTTCTAAACA
325 TTAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACA
493300 CTTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
390 CTTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
493348 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCTATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
* *
493413 ACTTTACTGAGAAATGTTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTCACTAATAAAA
66 ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATAAAA
**
493478 CTATACATTATAAAAATTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
131 CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
* *
493543 AATTTCGATCGAATATATCTCAAAAAGGACAAATATTTTAAAAAGCAATATAGAATAAAAGATGC
196 AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGC
*
493608 TTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGAT
261 TTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGAT
* *
493673 TAGGGGTCGGCCCCTTAAATATCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
326 TAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
*
493738 TTGTTGTACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
391 TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
493785 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTGTCTTCCATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
* *
493850 ACTTTACTGAGAAATATTTTGTCATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAAA
66 ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATAAAA
493915 CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
131 CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
*
493980 AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGT
196 AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGC
494045 TTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGAT
261 TTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGAT
*
494110 TAGGGGTCGGCCCCTAAAACGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
326 TAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
494175 TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
391 TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
494222 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGACCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
* * * *
494287 ACTTTACTGAAAAATGTTTTGTTATATGTTTAGGAAGCAAAAATGTTCATCT
66 ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCT
494339 CACATTTATT
Statistics
Matches: 949, Mismatches: 41, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
436 5 0.01
437 944 0.99
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (437 bp):
CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATAAAA
CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGC
TTAGAATGATGTTTTAAACAATATTCAATCATAAAATTTTCGTTATCTGGCCCCAATAAGGAGAT
TAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
Found at i:500637 original size:23 final size:21
Alignment explanation
Indices: 500596--500652 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
500586 TCTTTATTGA
*
500596 TCTTCT-TATATTTCCCATGATT
1 TCTTCTATATCTTTCCCATG--T
* *
500618 TCTTTTATATCTTTCGCATGT
1 TCTTCTATATCTTTCCCATGT
500639 TCTTCTATATCTTT
1 TCTTCTATATCTTT
500653 TAGCATATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.47
22 5 0.17
23 11 0.37
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (21 bp):
TCTTCTATATCTTTCCCATGT
Found at i:505662 original size:2 final size:2
Alignment explanation
Indices: 505655--505691 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
505645 GTTTATGTGA
505655 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
505692 GCTATGTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.