Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 2 of 295
Found at i:430985 original size:88 final size:88
Alignment explanation
Indices: 430667--431170 Score: 728
Period size: 88 Copynumber: 5.9 Consensus size: 88
430657 TGCTCCAATG
** * * * *
430667 CAACCGATGGAGGCAAGGCTT-TGTCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
** * * * *
430731 GCT-TCTTTAACTAGCTCCA-CTG
66 TTTGTCTTCAACCAGCTCTATC-A
* ** * *
430753 CAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATC
1 CAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATC
430816 -TTTGTCTTCAACCAGCTCTAT--
65 TTTTGTCTTCAACCAGCTCTATCA
430837 CAA-CGAAAGAGGC-AGG-TT-TGT-TTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
430897 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
430920 CAATCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
430985 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
431008 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
431073 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
*
431096 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATTTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
431161 TTTGTCTTCA
66 TTTGTCTTCA
431171 TTGATCTGTC
Statistics
Matches: 389, Mismatches: 16, Indels: 24
0.91 0.04 0.06
Matches are distributed among these distances:
79 1 0.00
80 40 0.10
81 21 0.05
82 3 0.01
83 10 0.03
84 13 0.03
85 4 0.01
86 67 0.17
87 6 0.02
88 224 0.58
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Found at i:431154 original size:44 final size:44
Alignment explanation
Indices: 430765--431156 Score: 188
Period size: 44 Copynumber: 9.1 Consensus size: 44
430755 ATCGATGGAT
*
430765 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAG
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
* * * * * * * *
430808 GCAAGATCTT-TGTCTTCAACCAGC-T--CTATCAACGAAAG-AG
1 GCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
430848 GC-AGG-TT-TGT-TTCGATCTGCTTCGCTGTCAATGTAGGAAG
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
* * * * * ** ** * *
430888 GCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAATCGAAAG-AG
1 GCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAAT-GTAGGAAG
430932 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
* * * * * ** ** * * *
430976 GCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AG
1 GCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGGAAG
431020 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
* * * * * ** ** * * *
431064 GCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AG
1 GCAAGGT-TTGTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGGAAG
*
431108 GCAAGGTTTGTGTCTTCGATTTGCTTCGCTGTCAATGTAGGAAG
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
431152 GCAAG
1 GCAAG
431157 ATCTTTTGTC
Statistics
Matches: 239, Mismatches: 87, Indels: 45
0.64 0.23 0.12
Matches are distributed among these distances:
36 7 0.03
37 6 0.03
39 11 0.05
40 8 0.03
41 10 0.04
42 2 0.01
43 58 0.24
44 95 0.40
45 42 0.18
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (44 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAG
Found at i:436913 original size:4 final size:5
Alignment explanation
Indices: 436886--436914 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
436876 GTGAAACAAT
436886 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
436915 GCACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:437355 original size:26 final size:25
Alignment explanation
Indices: 437326--437390 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
437316 AAAAATAAGC
437326 GTATATGTATATATATAGTACAAAAA
1 GTATATGTATATATATA-TACAAAAA
*
437352 GTATGCATGTA-A-ATATATAGAAAAA
1 GTAT--ATGTATATATATATACAAAAA
*
437377 -TATATTTATATATA
1 GTATATGTATATATA
437391 AAAGAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 6 0.18
25 7 0.21
26 9 0.27
27 1 0.03
28 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (25 bp):
GTATATGTATATATATATACAAAAA
Found at i:437437 original size:9 final size:9
Alignment explanation
Indices: 437423--437488 Score: 54
Period size: 8 Copynumber: 7.7 Consensus size: 9
437413 AAGAGCAGCT
*
437423 ATAATAATG
1 ATAATAATA
437432 ATAATAATA
1 ATAATAATA
437441 ATAATAATA
1 ATAATAATA
437450 CA-AA-AATA
1 -ATAATAATA
437458 ATAAT-ATA
1 ATAATAATA
437466 AT-ATAGA-A
1 ATAATA-ATA
437474 AT-ATAATA
1 ATAATAATA
437482 ATGAATA
1 AT-AATA
437489 GATGAGTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
7 4 0.08
8 20 0.42
9 20 0.42
10 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
ATAATAATA
Found at i:437438 original size:3 final size:3
Alignment explanation
Indices: 437423--437488 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
437413 AAGAGCAGCT
*
437423 ATA ATA ATG ATA ATA ATA ATA ATA ATA CA-A A-A ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
437466 AT- ATA GA-A AT- ATA ATA ATGA ATA
1 ATA ATA -ATA ATA ATA ATA AT-A ATA
437489 GATGAGTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
2 10 0.19
3 38 0.72
4 5 0.09
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:438442 original size:20 final size:20
Alignment explanation
Indices: 438406--438445 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
438396 TCCTATTGTT
438406 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
438426 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
438446 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:453150 original size:19 final size:21
Alignment explanation
Indices: 453122--453164 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
453112 GAATTTAAGT
453122 TTAAAATTTAAAAT-TTAA-A
1 TTAAAATTTAAAATATTAATA
*
453141 TTAAATTTTAAAATATTAATA
1 TTAAAATTTAAAATATTAATA
453162 TTA
1 TTA
453165 CAAGAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 4 0.19
21 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAATTTAAAATATTAATA
Found at i:455148 original size:24 final size:23
Alignment explanation
Indices: 455116--455191 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
455106 TACTGGTGAA
*
455116 GGTGGTGGAGGAGATGGTGGAGGT
1 GGTGATGGAGGAG-TGGTGGAGGT
** * *
455140 GGTGATGGATAAGTAGGTGGCGGG
1 GGTGATGGAGGAGT-GGTGGAGGT
*
455164 GGTGATGGTGGAGGTGG-GGATGGT
1 GGTGATGGAGGA-GTGGTGGA-GGT
455188 GGTG
1 GGTG
455192 GTGGTGGTGG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 3 0.08
24 34 0.87
25 2 0.05
ACGTcount: A:0.16, C:0.01, G:0.61, T:0.22
Consensus pattern (23 bp):
GGTGATGGAGGAGTGGTGGAGGT
Found at i:455173 original size:15 final size:15
Alignment explanation
Indices: 455167--455207 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
455157 TGGCGGGGGT
455167 GATGGTGGAGGTGGG
1 GATGGTGGAGGTGGG
*
455182 GATGGTGGTGGT--G
1 GATGGTGGAGGTGGG
455195 G-TGGTGGAGGTGG
1 GATGGTGGAGGTGG
455208 CTCAATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
15 11 0.50
ACGTcount: A:0.10, C:0.00, G:0.66, T:0.24
Consensus pattern (15 bp):
GATGGTGGAGGTGGG
Found at i:455260 original size:21 final size:21
Alignment explanation
Indices: 455236--455284 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
455226 TGATGGTGGT
* * *
455236 GGTGGTGAGTGAACTGGAGGA
1 GGTGGTGAATAAACAGGAGGA
* *
455257 GGTGGGGAATAAACAGGAGGT
1 GGTGGTGAATAAACAGGAGGA
455278 GGTGGTG
1 GGTGGTG
455285 GTGGTGGAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.53, T:0.18
Consensus pattern (21 bp):
GGTGGTGAATAAACAGGAGGA
Found at i:455491 original size:377 final size:378
Alignment explanation
Indices: 454805--455958 Score: 2283
Period size: 378 Copynumber: 3.1 Consensus size: 378
454795 TACTCCACAC
*
454805 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGGGATGGTGGTGGTGGTGAGTGA
1 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
454870 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
66 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
454935 TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
131 TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
455000 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
196 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
455065 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
261 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
455130 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
326 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
455183 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
1 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
455248 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
66 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
455313 TGGAGGAGGTGAATGTGGT-GGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
131 TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
455377 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
196 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
455442 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
261 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
455507 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
326 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
455560 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
1 ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
455625 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
66 ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
455690 TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
131 TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
455755 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
196 GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
455820 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
261 GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
455885 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
326 TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
*
455938 ATGGAGGTGGTGGTGGTGGAG
1 ATGGTGGTGGTGGTGGTGGAG
455959 AGTAAACTGG
Statistics
Matches: 773, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
377 377 0.49
378 396 0.51
ACGTcount: A:0.22, C:0.05, G:0.52, T:0.22
Consensus pattern (378 bp):
ATGGTGGTGGTGGTGGTGGAGGTGGCTCAATACATGGAGGAGGTGATGGTGGTGGTGGTGAGTGA
ACTGGAGGAGGTGGGGAATAAACAGGAGGTGGTGGTGGTGGTGGAGATAAGTATGGATAAATTGG
TGGAGGAGGTGAATGTGGTGGGGGTGGTGGAGAATGTACAGGAGGTGGCGGTGAATGGTGTGGCG
GTGGCGGGGAGTTATAGTAGTAAGGAACTGGTGGAGGTGGGGAAAACAATGGAGGTGGAGGAGGG
GGTGAATTTGGTGGTGGAGGAGGTGGAGACCTCACACAGTATACTGGTGAAGGTGGTGGAGGAGA
TGGTGGAGGTGGTGATGGATAAGTAGGTGGCGGGGGTGATGGTGGAGGTGGGG
Found at i:455525 original size:24 final size:23
Alignment explanation
Indices: 455493--455568 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
455483 TACTGGTGAA
*
455493 GGTGGTGGAGGAGATGGTGGAGGT
1 GGTGATGGAGGAG-TGGTGGAGGT
** * *
455517 GGTGATGGATAAGTAGGTGGCGGG
1 GGTGATGGAGGAGT-GGTGGAGGT
*
455541 GGTGATGGTGGAGGTGG-GGATGGT
1 GGTGATGGAGGA-GTGGTGGA-GGT
455565 GGTG
1 GGTG
455569 GTGGTGGTGG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 3 0.08
24 34 0.87
25 2 0.05
ACGTcount: A:0.16, C:0.01, G:0.61, T:0.22
Consensus pattern (23 bp):
GGTGATGGAGGAGTGGTGGAGGT
Found at i:455550 original size:15 final size:15
Alignment explanation
Indices: 455544--455584 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
455534 TGGCGGGGGT
455544 GATGGTGGAGGTGGG
1 GATGGTGGAGGTGGG
*
455559 GATGGTGGTGGT--G
1 GATGGTGGAGGTGGG
455572 G-TGGTGGAGGTGG
1 GATGGTGGAGGTGG
455585 CTCAATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
15 11 0.50
ACGTcount: A:0.10, C:0.00, G:0.66, T:0.24
Consensus pattern (15 bp):
GATGGTGGAGGTGGG
Found at i:455637 original size:21 final size:21
Alignment explanation
Indices: 455613--455661 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
455603 TGATGGTGGT
* * *
455613 GGTGGTGAGTGAACTGGAGGA
1 GGTGGTGAATAAACAGGAGGA
* *
455634 GGTGGGGAATAAACAGGAGGT
1 GGTGGTGAATAAACAGGAGGA
455655 GGTGGTG
1 GGTGGTG
455662 GTGGTGGAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.53, T:0.18
Consensus pattern (21 bp):
GGTGGTGAATAAACAGGAGGA
Found at i:455957 original size:15 final size:15
Alignment explanation
Indices: 455919--455993 Score: 57
Period size: 15 Copynumber: 5.0 Consensus size: 15
455909 AGGTGGCGGG
*
455919 GGTGATGGTGGAGGT
1 GGTGGTGGTGGAGGT
*
455934 -G-GG-GATGGAGGT
1 GGTGGTGGTGGAGGT
455946 GGTGGTGGTGGAGAGT
1 GGTGGTGGTGGAG-GT
** *
455962 AAACTGGTGGTGGTGGT
1 --GGTGGTGGTGGAGGT
455979 GGTGGTGGTGGAGGT
1 GGTGGTGGTGGAGGT
455994 CGAGGTGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
12 8 0.18
13 2 0.04
14 3 0.07
15 18 0.40
16 2 0.04
17 2 0.04
18 10 0.22
ACGTcount: A:0.13, C:0.01, G:0.60, T:0.25
Consensus pattern (15 bp):
GGTGGTGGTGGAGGT
Found at i:455971 original size:42 final size:42
Alignment explanation
Indices: 455925--456075 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 42
455915 CGGGGGTGAT
* *
455925 GGTGGAGGTGG-GGATGGAGGTGGTGGTGGTGGAGAGTAAACT
1 GGTGGAGGTGGAGG-TGGAGGTGGTGGTGGAGGAGAGTAAACA
* * * * * * *
455967 GGTGGTGGTGGTGGTGGTGGTGGAGGTCGAGGTGAATAAACA
1 GGTGGAGGTGGAGGTGGAGGTGGTGGTGGAGGAGAGTAAACA
* * * * *
456009 GGTGGAGGTGGAGATGGTGGCGGTGGAGGAGGAGAGTACACA
1 GGTGGAGGTGGAGGTGGAGGTGGTGGTGGAGGAGAGTAAACA
* *
456051 GGTGGCGGCGGAGGTGGAGGTGGTG
1 GGTGGAGGTGGAGGTGGAGGTGGTG
456076 AAGGGGGAGG
Statistics
Matches: 85, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.19, C:0.05, G:0.57, T:0.19
Consensus pattern (42 bp):
GGTGGAGGTGGAGGTGGAGGTGGTGGTGGAGGAGAGTAAACA
Found at i:456042 original size:27 final size:26
Alignment explanation
Indices: 456012--456073 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
456002 ATAAACAGGT
* *
456012 GGAGGTGGAGATGGTGGCGGTGGAGGA
1 GGAGGTGGACA-GGTGGCGGCGGAGGA
** *
456039 GGAGAGTACACAGGTGGCGGCGGAGGT
1 GGAG-GTGGACAGGTGGCGGCGGAGGA
456066 GGAGGTGG
1 GGAGGTGG
456074 TGAAGGGGGA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
26 2 0.07
27 21 0.78
28 4 0.15
ACGTcount: A:0.19, C:0.08, G:0.60, T:0.13
Consensus pattern (26 bp):
GGAGGTGGACAGGTGGCGGCGGAGGA
Found at i:456109 original size:48 final size:48
Alignment explanation
Indices: 456012--456124 Score: 127
Period size: 48 Copynumber: 2.4 Consensus size: 48
456002 ATAAACAGGT
* ** * *
456012 GGAGGTGGAGATGGTGGCGGTGGAGGAGGAGAGTACACAGGTGGCGGC
1 GGAGGTGGAGGTGGTGAAGGGGGAGGAGGAGAGTACACAGGCGGCGGC
* * * *
456060 GGAGGTGGAGGTGGTGAAGGGGGAGGGGGAGAGTATACTGGCGGTGGC
1 GGAGGTGGAGGTGGTGAAGGGGGAGGAGGAGAGTACACAGGCGGCGGC
* *
456108 GGCGGCGGAGGTGGTGA
1 GGAGGTGGAGGTGGTGA
456125 TTGTGGAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.19, C:0.09, G:0.59, T:0.13
Consensus pattern (48 bp):
GGAGGTGGAGGTGGTGAAGGGGGAGGAGGAGAGTACACAGGCGGCGGC
Found at i:459520 original size:14 final size:14
Alignment explanation
Indices: 459501--459527 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
459491 ATTTGTTGGT
459501 TTAAATGAATTTAA
1 TTAAATGAATTTAA
459515 TTAAATGAATTTA
1 TTAAATGAATTTA
459528 TAATTTTATC
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:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TTAAATGAATTTAA
Found at i:460629 original size:14 final size:14
Alignment explanation
Indices: 460606--460639 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
460596 GATAGCCTAG
*
460606 TGGTTTGTCCTAAT
1 TGGTTCGTCCTAAT
460620 TGGTTCGTCCTAAT
1 TGGTTCGTCCTAAT
460634 TGGTTC
1 TGGTTC
460640 AGGTTGAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
TGGTTCGTCCTAAT
Found at i:462227 original size:3 final size:3
Alignment explanation
Indices: 462219--462246 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
462209 TTAACATACT
462219 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
462247 GTTGTTACAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:463669 original size:15 final size:14
Alignment explanation
Indices: 463644--463673 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
463634 TTTCACAAAA
463644 TTTGAAGATTAAAT
1 TTTGAAGATTAAAT
463658 TTTGATAGATTAAAT
1 TTTGA-AGATTAAAT
463673 T
1 T
463674 GGAGGGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTTGAAGATTAAAT
Found at i:469475 original size:45 final size:45
Alignment explanation
Indices: 469287--469481 Score: 282
Period size: 45 Copynumber: 4.3 Consensus size: 45
469277 TCGGCCATGG
* * * * *
469287 TGCTTCATCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
469332 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
469377 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
469422 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
469467 TGCTTCCTTAATTTC
1 TGCTTCCTTAATTTC
469482 ATGCCGTTCA
Statistics
Matches: 135, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:469830 original size:20 final size:20
Alignment explanation
Indices: 469805--469857 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
469795 ACGAGTTAAA
* *
469805 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
469825 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
*
469845 TTGAGCTCAAATG
1 TTGAGCTCGAATG
469858 TTGAACCACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:475788 original size:234 final size:233
Alignment explanation
Indices: 475380--475846 Score: 801
Period size: 234 Copynumber: 2.0 Consensus size: 233
475370 TTCAATGACT
* *
475380 GCTATCGATGCTGTTGTGGCTGAGGATGGTGCGGTTAAGGTGGATCTGAGAGTATTTTTGACTAA
1 GCTATCGATACTGTTGTGGCTGAGGATGGTGCGGTTAAGGTAGATCTGAGAGTATTTTTGACTAA
*
475445 GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGAGGTGATTTTTTGGTGAGT
66 GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGAGGTGATTTCTTGGTGAGT
475510 TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
131 TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
*
475575 GGGCTGGAAACGTTGTTTTCTTGGTGGCAAATAAGAAA
196 GGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
* * *
475613 GCTATCGATACTGTTGTGGCTGAGGCTGGTGTGGTTAAGGTAGATCT-ACGAGTATTTTTTACTA
1 GCTATCGATACTGTTGTGGCTGAGGATGGTGCGGTTAAGGTAGATCTGA-GAGTATTTTTGACTA
* *
475677 AGATTTAGAATTCTTTTGTTTTTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTCTTGGTGA
65 AGA-TTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGAGGTGATTTCTTGGTGA
*
475742 GTTATTAAGGCATTGAGCCATTGGTCTTTTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTT
129 GTTATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTT
* *
475807 AAGGGCTGGAAATGTTGTTTACTTGGTGGCAGATAAGAAA
194 AAGGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
475847 AGTAACGAAT
Statistics
Matches: 220, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
232 1 0.00
233 60 0.27
234 159 0.72
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (233 bp):
GCTATCGATACTGTTGTGGCTGAGGATGGTGCGGTTAAGGTAGATCTGAGAGTATTTTTGACTAA
GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGAGGTGATTTCTTGGTGAGT
TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
GGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
Found at i:483249 original size:29 final size:29
Alignment explanation
Indices: 483217--483283 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
483207 TTCTAATCTT
*
483217 TTTAAATTATTTATTCAAATT-GTTTCAAA
1 TTTAAATTATTTATTCAAATTAATTT-AAA
* * *
483246 TTTAAACTATTTTTTTAAATTAATTTAAA
1 TTTAAATTATTTATTCAAATTAATTTAAA
*
483275 TTCAAATTA
1 TTTAAATTA
483284 AGTATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTAAATTATTTATTCAAATTAATTTAAA
Found at i:484554 original size:40 final size:40
Alignment explanation
Indices: 484481--484559 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
484471 AAATCTAAAG
* * ** *
484481 GTTGAACAATTTGTATGCAAAGAATTAGTAAAAATCAATT
1 GTTGAACAACTTATATGCAAAGAATTACCAAAAACCAATT
484521 GTTGAACAACTTATATGCAATA-AATTACCAAAAACCAAT
1 GTTGAACAACTTATATGCAA-AGAATTACCAAAAACCAAT
484560 AGTTCAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (40 bp):
GTTGAACAACTTATATGCAAAGAATTACCAAAAACCAATT
Found at i:487396 original size:20 final size:20
Alignment explanation
Indices: 487338--487397 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
487328 TTCATTCCAA
487338 TTACTATCTAGAATAATATT
1 TTACTATCTAGAATAATATT
* *
487358 TTACT-T-TTG-A-AGT-TT
1 TTACTATCTAGAATAATATT
487373 TTACTATCTAGAATAATATT
1 TTACTATCTAGAATAATATT
487393 TTACT
1 TTACT
487398 TTTGAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 7 0.23
16 3 0.10
17 3 0.10
18 3 0.10
19 3 0.10
20 12 0.39
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
TTACTATCTAGAATAATATT
Found at i:487416 original size:35 final size:35
Alignment explanation
Indices: 487338--487409 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
487328 TTCATTCCAA
487338 TTACTATCTAGAATAATATTTTACTTTTGAAGTTT
1 TTACTATCTAGAATAATATTTTACTTTTGAAGTTT
487373 TTACTATCTAGAATAATATTTTACTTTTGAAGTTT
1 TTACTATCTAGAATAATATTTTACTTTTGAAGTTT
487408 TT
1 TT
487410 CTTATCTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (35 bp):
TTACTATCTAGAATAATATTTTACTTTTGAAGTTT
Found at i:497912 original size:15 final size:18
Alignment explanation
Indices: 497871--497912 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
497861 ATTACTACAA
497871 TATTAAAATAATATATAT
1 TATTAAAATAATATATAT
*
497889 TATTTAAATAA-AT-TAT
1 TATTAAAATAATATATAT
497905 T-TTAAAAT
1 TATTAAAAT
497913 GGGGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 2 0.09
18 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAAAATAATATATAT
Found at i:498951 original size:15 final size:16
Alignment explanation
Indices: 498926--498955 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
498916 TATTTTAATT
498926 TTTTTTAATTTTTAAA
1 TTTTTTAATTTTTAAA
498942 TTTTTT-ATTTTTAA
1 TTTTTTAATTTTTAA
498956 GTTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTAATTTTTAAA
Found at i:498987 original size:15 final size:15
Alignment explanation
Indices: 498969--499014 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
498959 AAATTTAATC
*
498969 ATTAATCTTTTAAAA
1 ATTAATTTTTTAAAA
498984 ATTAACTTTTTTAAAAA
1 ATTAA-TTTTTT-AAAA
499001 ATT-ATTTTTTAAAA
1 ATTAATTTTTTAAAA
499015 TGGAAGACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.14
15 11 0.39
16 6 0.21
17 7 0.25
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATTTTTTAAAA
Found at i:498997 original size:16 final size:14
Alignment explanation
Indices: 498976--499014 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
498966 ATCATTAATC
498976 TTTTAAAAATTAACTT
1 TTTTAAAAATT-A-TT
498992 TTTTAAAAAATTATT
1 TTTT-AAAAATTATT
499007 TTTTAAAA
1 TTTTAAAA
499015 TGGAAGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 5 0.23
17 7 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTAAAAATTATT
Found at i:502491 original size:12 final size:12
Alignment explanation
Indices: 502474--502498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
502464 ATTTACTGTA
502474 TAAAAAATATTT
1 TAAAAAATATTT
502486 TAAAAAATATTT
1 TAAAAAATATTT
502498 T
1 T
502499 TCAATTGTAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:502613 original size:21 final size:21
Alignment explanation
Indices: 502571--502613 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
502561 ATTAATTCCG
* * *
502571 TTAAACAATAATTGGTATTTT
1 TTAAACAATAAATAGTAATTT
*
502592 TTAAACAATAAATATTAATTT
1 TTAAACAATAAATAGTAATTT
502613 T
1 T
502614 ATTCTAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
TTAAACAATAAATAGTAATTT
Found at i:503554 original size:21 final size:21
Alignment explanation
Indices: 503530--503591 Score: 51
Period size: 24 Copynumber: 3.0 Consensus size: 21
503520 ATTATGAGCT
503530 AAATATATATTAATAAATTTA
1 AAATATATATTAATAAATTTA
*
503551 AAATTTTATATATGAA-AAA--TA
1 AAA---TATATATTAATAAATTTA
*
503572 TAAT-TATATTAATAAATTTA
1 AAATATATATTAATAAATTTA
503592 TACAGTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 13
0.67 0.06 0.27
Matches are distributed among these distances:
17 7 0.22
18 4 0.12
20 2 0.06
21 7 0.22
23 3 0.09
24 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATATATATTAATAAATTTA
Found at i:509626 original size:46 final size:47
Alignment explanation
Indices: 509559--509780 Score: 251
Period size: 46 Copynumber: 4.8 Consensus size: 47
509549 TGTAACCCGC
509559 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGACGTTCGCAT
* *
509605 CCATAGGTGAACTCGGACTCAACTCAACGAGC-TCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGACGTTCGCAT
* * * * *
509651 CCATAGGTGAACTCGGACTCAACTCAACGAG-TTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGACG-TTCGCAT
* * * * * *
509697 ACATTTCA-CGAACTCAGACTCAACTCAACGA-ATTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGCTTCGGACGTTCGCAT
509744 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGA
509781 TGCTCAACCA
Statistics
Matches: 146, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
45 3 0.02
46 110 0.75
47 32 0.22
48 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTTCGGACGTTCGCAT
Found at i:509745 original size:93 final size:93
Alignment explanation
Indices: 509613--509783 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
509603 ATCCATAGGT
* * * * *
509613 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
509678 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
509706 GAACTCAGACTCAACTCAACGAATTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
509771 CGAGTTCGGATGC
66 CGAGTTCGGATGC
509784 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:513010 original size:46 final size:45
Alignment explanation
Indices: 512898--513011 Score: 131
Period size: 46 Copynumber: 2.5 Consensus size: 45
512888 GAATGTTATG
* *
512898 GTGTCTTTCAACCATGGTCTTATTCATTCCCAACTTGATGTCAGA
1 GTGTCTTTCAACCATGGTCTTATTCATTCCCAACGTGATGCCAGA
* ** * *
512943 GTGTCTTTCAACCATGATCTTATTCATT-TTATATCGTGTTGCCATA
1 GTGTCTTTCAACCATGGTCTTATTCATTCCCA-A-CGTGATGCCAGA
*
512989 GTGTCTTTCAACCGTGGTCTTAT
1 GTGTCTTTCAACCATGGTCTTAT
513012 CCGTCTGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 28 0.48
46 29 0.50
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (45 bp):
GTGTCTTTCAACCATGGTCTTATTCATTCCCAACGTGATGCCAGA
Found at i:513052 original size:45 final size:45
Alignment explanation
Indices: 512982--513146 Score: 147
Period size: 45 Copynumber: 3.7 Consensus size: 45
512972 TATATCGTGT
* ** *
512982 TGCCATAGTGTCTTTCAACCGTGGTCTTA-TCCGTCT-GATTCATAA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACT-CG-CTAGAATCATAA
* * *
513027 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGCTAGAATCGTGA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGCTAGAATCATAA
* * * * ****
513072 TGCCATAACGTCTTTCAACTATGAT-TTACTCGTTAAAATTGGGA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGCTAGAATCATAA
*
513116 TGCCATAACGTCTTTCAACTATGGTCTTACT
1 TGCCATAGCGTCTTTCAACTATGGTCTTACT
513147 TGTTTTTGGT
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
44 41 0.40
45 60 0.59
46 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (45 bp):
TGCCATAGCGTCTTTCAACTATGGTCTTACTCGCTAGAATCATAA
Found at i:513118 original size:44 final size:45
Alignment explanation
Indices: 513026--513146 Score: 163
Period size: 44 Copynumber: 2.7 Consensus size: 45
513016 CTGATTCATA
* * * * *
513026 ATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGCTAGAATCGTG
1 ATGCCATAACGTCTTTCAACTATGATCTTACTCGCTAAAATCGGG
* *
513071 ATGCCATAACGTCTTTCAACTATGAT-TTACTCGTTAAAATTGGG
1 ATGCCATAACGTCTTTCAACTATGATCTTACTCGCTAAAATCGGG
*
513115 ATGCCATAACGTCTTTCAACTATGGTCTTACT
1 ATGCCATAACGTCTTTCAACTATGATCTTACT
513147 TGTTTTTGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 39 0.58
45 28 0.42
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (45 bp):
ATGCCATAACGTCTTTCAACTATGATCTTACTCGCTAAAATCGGG
Found at i:513165 original size:45 final size:45
Alignment explanation
Indices: 513069--513190 Score: 126
Period size: 44 Copynumber: 2.7 Consensus size: 45
513059 GCTAGAATCG
* *
513069 TGATGCCATAACGTCTTTCAACTATGAT-TTACTCGTTAAAATTGG--
1 TGATGCCATAACGTCTTTCAACTATGATCTTACTTGTT---TTTGGTA
*
513114 -GATGCCATAACGTCTTTCAACTATGGTCTTACTTGTTTTTGGTA
1 TGATGCCATAACGTCTTTCAACTATGATCTTACTTGTTTTTGGTA
***
513158 TGATGCCAATAGTTTCTTTCAACTATGATCTTA
1 TGATGCC-ATAACGTCTTTCAACTATGATCTTA
513191 TTTAATTCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
42 4 0.06
44 26 0.40
45 14 0.22
46 21 0.32
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAACTATGATCTTACTTGTTTTTGGTA
Found at i:514440 original size:15 final size:17
Alignment explanation
Indices: 514409--514441 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
514399 ATTTATTCGT
514409 TCAAATAACATAAATTA
1 TCAAATAACATAAATTA
514426 TCAAATAA-A-AAATTA
1 TCAAATAACATAAATTA
514441 T
1 T
514442 TATAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
TCAAATAACATAAATTA
Found at i:515799 original size:85 final size:85
Alignment explanation
Indices: 515528--515936 Score: 427
Period size: 85 Copynumber: 4.8 Consensus size: 85
515518 TCTGTTGTTC
* * *
515528 GTATAGGAGGAACAAAATACGATTTATTGAAACTTAAAATGTTCTTTTTTGAAATTATATACATA
1 GTATAGGAGGAACGAAATACGATTTATTGAAACCTAAAATGTTC--TTTTGGAA--AT-T-C--A
* * *
515593 TATATATAGGGATGGTCTTCTCCGGTTC
58 TATATATAGGGATAGTCTACTCCGGTTT
* * * * * * * * *
515621 ATTTAGGAGGAAAGGAGTACGATTTATTGGAACCTAAACTGTTCTTTTGGGAATT-ACATATATA
1 GTATAGGAGGAACGAAATACGATTTATTGAAACCTAAAATGTTCTTTTGGAAATTCATATATATA
*
515685 GGGATAGTCTACTCCAGTTT
66 GGGATAGTCTACTCCGGTTT
* * *
515705 GTATGGGAGGAACGAAATATGATTTATTGGAACCTAAAATGTTCTTTTTGGAAA-TCATATATAT
1 GTATAGGAGGAACGAAATACGATTTATTGAAACCTAAAATGTTC-TTTTGGAAATTCATATATAT
* *
515769 AGGGATAGTCTTCTCTGGTTT
65 AGGGATAGTCTACTCCGGTTT
* * * *
515790 GTATAGGAGGAACGAAATACAATCTATTGAAACATAAAATGTTCTTTTGGAAATTC-TATATCTA
1 GTATAGGAGGAACGAAATACGATTTATTGAAACCTAAAATGTTCTTTTGGAAATTCATATATATA
515854 GGGGATAGTCTACTCCGGTTT
66 -GGGATAGTCTACTCCGGTTT
*
515875 GTATAGGAGTG---G-AATATGATTTATTGAAACCTAAAATGTTCTTTTGGAAATTGCATATATA
1 GTATAGGAG-GAACGAAATACGATTTATTGAAACCTAAAATGTTCTTTTGGAAATT-CATATATA
515936 T
64 T
515937 CGTTTTTGTG
Statistics
Matches: 266, Mismatches: 43, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
82 36 0.14
83 2 0.01
84 83 0.31
85 100 0.38
86 1 0.00
88 1 0.00
89 2 0.01
91 6 0.02
93 35 0.13
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (85 bp):
GTATAGGAGGAACGAAATACGATTTATTGAAACCTAAAATGTTCTTTTGGAAATTCATATATATA
GGGATAGTCTACTCCGGTTT
Found at i:515838 original size:169 final size:171
Alignment explanation
Indices: 515528--515936 Score: 465
Period size: 169 Copynumber: 2.4 Consensus size: 171
515518 TCTGTTGTTC
* * * *
515528 GTATAGGAGGAACAAAATACGATTTATTGAAACTTAAAATGTTCTTTTTTGAAATTATATACATA
1 GTATAGGAGGAACGAAATATGATTTATTGAAACCTAAAATGTTC-TTTTTG-GA--A-ATAC--A
* * * * * * * *
515593 TATATATAGGGATGGTCTTCTCCGGTTCATTTAGGAGGAAAGGAGTACGATTTATTGGAACCTAA
59 TATATATAGGGATAGTCTTCTCCGGTTCATATAGGAGGAAAGAAATACAATCTATTGAAACATAA
* *
515658 ACTGTTCTTTTGGGAATTAC-ATATATA-GGGATAGTCTACTCCAGTTT
124 AATGTTCTTTTGGAAATT-CTATATATAGGGGATAGTCTACTCCAGTTT
* *
515705 GTATGGGAGGAACGAAATATGATTTATTGGAACCTAAAATGTTCTTTTTGGAAAT-CATATATAT
1 GTATAGGAGGAACGAAATATGATTTATTGAAACCTAAAATGTTCTTTTTGGAAATACATATATAT
* ** *
515769 AGGGATAGTCTTCTCTGGTTTGTATAGGAGGAACGAAATACAATCTATTGAAACATAAAATGTTC
66 AGGGATAGTCTTCTCCGGTTCATATAGGAGGAAAGAAATACAATCTATTGAAACATAAAATGTTC
* *
515834 TTTTGGAAATTCTATATCTAGGGGATAGTCTACTCCGGTTT
131 TTTTGGAAATTCTATATATAGGGGATAGTCTACTCCAGTTT
*
515875 GTATAGGAGTG---G-AATATGATTTATTGAAACCTAAAATGTTC-TTTTGGAAATTGCATATAT
1 GTATAGGAG-GAACGAAATATGATTTATTGAAACCTAAAATGTTCTTTTTGGAAA-TACATATAT
515935 AT
64 AT
515937 CGTTTTTGTG
Statistics
Matches: 203, Mismatches: 24, Indels: 19
0.83 0.10 0.08
Matches are distributed among these distances:
166 9 0.04
167 29 0.14
168 11 0.05
169 76 0.37
170 27 0.13
171 2 0.01
172 2 0.01
173 1 0.00
175 1 0.00
176 6 0.03
177 39 0.19
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (171 bp):
GTATAGGAGGAACGAAATATGATTTATTGAAACCTAAAATGTTCTTTTTGGAAATACATATATAT
AGGGATAGTCTTCTCCGGTTCATATAGGAGGAAAGAAATACAATCTATTGAAACATAAAATGTTC
TTTTGGAAATTCTATATATAGGGGATAGTCTACTCCAGTTT
Found at i:524628 original size:21 final size:22
Alignment explanation
Indices: 524602--524646 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
524592 TTCTTCACTG
524602 TTTGTAA-TATTAGAT-TTTGTA
1 TTTGTAAGTATTA-ATCTTTGTA
524623 TTTGTAAGTATTAATCTTTGTA
1 TTTGTAAGTATTAATCTTTGTA
524645 TT
1 TT
524647 ATCTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (22 bp):
TTTGTAAGTATTAATCTTTGTA
Found at i:525035 original size:24 final size:25
Alignment explanation
Indices: 525000--525050 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
524990 GCACATTCTC
* * *
525000 TTAATTTGATATTTATAATTTT-TT
1 TTAATTTAATATCTAAAATTTTATT
525024 TTAATTTAATATCTAAAATTTTATT
1 TTAATTTAATATCTAAAATTTTATT
525049 TT
1 TT
525051 GATCTATCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTAATTTAATATCTAAAATTTTATT
Found at i:526229 original size:18 final size:18
Alignment explanation
Indices: 526206--526242 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
526196 ATATCATCTC
526206 AGCTTAGTATTACTACAT
1 AGCTTAGTATTACTACAT
526224 AGCTTAGTATTACTACAT
1 AGCTTAGTATTACTACAT
526242 A
1 A
526243 ATACTCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
AGCTTAGTATTACTACAT
Found at i:528994 original size:14 final size:14
Alignment explanation
Indices: 528961--528987 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
528951 AATTATGTCA
528961 AATTAAATTACAAG
1 AATTAAATTACAAG
528975 AATTAAATTACAA
1 AATTAAATTACAA
528988 ATTTTAACAT
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:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (14 bp):
AATTAAATTACAAG
Found at i:529523 original size:17 final size:17
Alignment explanation
Indices: 529501--529540 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
529491 GAAAAAGACT
*
529501 ATTTTATCATTATATTA
1 ATTTTATAATTATATTA
*
529518 ATTTTATAATTTTATTA
1 ATTTTATAATTATATTA
*
529535 TTTTTA
1 ATTTTA
529541 AAGGAGTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATAATTATATTA
Found at i:531565 original size:29 final size:25
Alignment explanation
Indices: 531532--531604 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 25
531522 TTTCACTATT
531532 TTAAAAATAAAATATTTAATT-TTTA
1 TTAAAAATAAAATA-TTAATTATTTA
* *
531557 TATAATAAAAAATTAAAATTAATTATTTA
1 T-TAA-AAATAA--AATATTAATTATTTA
531586 TTAAAAATAAAAT-TTAATT
1 TTAAAAATAAAATATTAATT
531605 CAATTTTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
24 6 0.15
25 3 0.08
26 3 0.08
27 10 0.26
28 9 0.23
29 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAAAAATAAAATATTAATTATTTA
Found at i:531609 original size:29 final size:27
Alignment explanation
Indices: 531532--531611 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
531522 TTTCACTATT
*
531532 TTAAAAATAAAA--TATTTAATTTTTA
1 TTAAAAATAAAATTTAATTAATTTTTA
* *
531557 TATAATAA-AAAATTAAAATTAATTATTTA
1 T-TAAAAATAAAATT-TAATTAATT-TTTA
531586 TTAAAAATAAAATTTAATTCAATTTT
1 TTAAAAATAAAATTTAATT-AATTTT
531612 GAGTAACCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
25 5 0.12
26 5 0.12
28 18 0.42
29 15 0.35
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAAAATAAAATTTAATTAATTTTTA
Found at i:533425 original size:51 final size:51
Alignment explanation
Indices: 533361--533462 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
533351 TGAATATGAA
533361 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
1 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
533412 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
1 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
533463 TCTTTTTTAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (51 bp):
GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
Found at i:546591 original size:6 final size:6
Alignment explanation
Indices: 546580--546612 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
546570 CACATGTCAA
546580 AATTTC AATTTC AATTTC AATTTC AATTTC AAT
1 AATTTC AATTTC AATTTC AATTTC AATTTC AAT
546613 GATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTC
Found at i:547792 original size:126 final size:132
Alignment explanation
Indices: 547490--547793 Score: 386
Period size: 126 Copynumber: 2.3 Consensus size: 132
547480 GATTGAACTG
*
547490 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTTCGTTATTTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
* * *
547555 GACGCCTACTACTTAATTTAAGTATTAGGGTTTAGGTTTTAATTCTCAGCTTAACTATTATCCAA
66 GACGCCTA-TACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAA
*
547620 TTC
130 ATC
* * * *
547623 ACTGGTTAATTTTTAACTATAATATTATTATGATTGTTTTTATTGCGTTA-TTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
* * * *
547687 GATG-CT-TAC-T-ACTT-AGTTTTAGGGTTTAGGGTTTAATTCTCAGTTTAACTATTATTAAAA
66 GACGCCTATACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAAA
547747 TC
131 TC
* * * * * *
547749 TTTGGTTAATGTTTAGCTTTATTATGATTGTGACTGTTGTTATTG
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTG
547794 TTTTGTTTTG
Statistics
Matches: 148, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
126 77 0.52
127 3 0.02
128 1 0.01
129 3 0.02
131 2 0.01
132 17 0.11
133 45 0.30
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (132 bp):
ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
GACGCCTATACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAAA
TC
Found at i:559024 original size:23 final size:22
Alignment explanation
Indices: 558973--559029 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
558963 AAGGAGGGGG
*
558973 ATCGATGGTATTTTGAGGAAGA
1 ATCGATTGTATTTTGAGGAAGA
*
558995 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGA-AGA
559018 AGT-GATTGTATT
1 A-TCGATTGTATT
559030 AGAGGGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 17 0.55
23 13 0.42
24 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.37
Consensus pattern (22 bp):
ATCGATTGTATTTTGAGGAAGA
Found at i:559448 original size:23 final size:22
Alignment explanation
Indices: 559397--559453 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
559387 AGGAGGGGGG
*
559397 ATCGATCGTATTTTGAGGAAGA
1 ATCGATTGTATTTTGAGGAAGA
*
559419 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGA-AGA
559442 AGT-GATTGTATT
1 A-TCGATTGTATT
559454 AGAGGGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 17 0.55
23 13 0.42
24 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.37
Consensus pattern (22 bp):
ATCGATTGTATTTTGAGGAAGA
Found at i:560077 original size:40 final size:39
Alignment explanation
Indices: 560033--560124 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
560023 TTTTTTTATG
*
560033 ATAAAAAAAAAGAGAAAAT-AAAGTATGGTTTTAATTAATA
1 ATAAAAAAAAAGAG--AATGAAAGAATGGTTTTAATTAATA
* * **
560073 ATAAAAACAAAATAGTATGAGGGAATGGTTTTAATTAATA
1 ATAAAAA-AAAAGAGAATGAAAGAATGGTTTTAATTAATA
*
560113 ATAAAAACAAAG
1 ATAAAAAAAAAG
560125 TAGCATGGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
39 5 0.12
40 32 0.74
41 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.26
Consensus pattern (39 bp):
ATAAAAAAAAAGAGAATGAAAGAATGGTTTTAATTAATA
Found at i:562311 original size:14 final size:14
Alignment explanation
Indices: 562292--562321 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
562282 AATTTTATAA
*
562292 TTATTTTTATATTT
1 TTATTTATATATTT
562306 TTATTTATATATTT
1 TTATTTATATATTT
562320 TT
1 TT
562322 GAACAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTATATATTT
Found at i:567213 original size:95 final size:95
Alignment explanation
Indices: 567050--567253 Score: 295
Period size: 95 Copynumber: 2.2 Consensus size: 95
567040 AAATTGAAGT
*
567050 TTTATGTATATATTTGATCTACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
1 TTTATGTATATATTTGATCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
* *
567115 TCATATATAAAATTACATATTAAATCAAAG
66 TCATATATAAAATTACACATAAAATCAAAG
* * * * * *
567145 TTTATTTATATATTT-AGTCAACAATAAAAGTTTTATGTGTATATATTATTGCACTAAATTAAAA
1 TTTATGTATATATTTGA-TCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAA
*
567209 TTCATATATAAAATTACACATAAAATTAAAG
65 TTCATATATAAAATTACACATAAAATCAAAG
567240 TTTATGTATA-ATTT
1 TTTATGTATATATTT
567254 TGAGATTTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
94 5 0.05
95 92 0.95
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (95 bp):
TTTATGTATATATTTGATCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
TCATATATAAAATTACACATAAAATCAAAG
Found at i:569499 original size:19 final size:20
Alignment explanation
Indices: 569455--569499 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
569445 GACTTATTTT
569455 ATATCATTTTTAATTATTTAA
1 ATAT-ATTTTTAATTATTTAA
569476 A-ATATTTTT-A-TATTTATA
1 ATATATTTTTAATTATTTA-A
569494 ATATAT
1 ATATAT
569500 AATAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 10 0.45
20 2 0.09
21 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTTTTAATTATTTAA
Found at i:579120 original size:3 final size:3
Alignment explanation
Indices: 579105--579140 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
579095 TAGTTACTAA
*
579105 CAT CAT CAA CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
579141 AGGCCATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:588187 original size:60 final size:60
Alignment explanation
Indices: 587992--588178 Score: 188
Period size: 60 Copynumber: 3.2 Consensus size: 60
587982 CAAGTTTTAG
* *
587992 GTACCTAATTGGACCAAAATAAACTTTGGGTACCAAATTGAACCTTAAAGTCAAGTTCAA
1 GTACCTAATTGGACCAAAATAAACTTTAGGTACCAAATTGAACCTTAAAGCCAAGTTCAA
* ** * * *
588052 GTGCCTAATTGG----AAA-AAACTCTTAGGTACTGATTTGAACCTTGAAGCTAAGCTT-AA
1 GTACCTAATTGGACCAAAATAAACT-TTAGGTACCAAATTGAACCTTAAAGCCAAG-TTCAA
* * * * * *
588108 TTACCTAATTGAACCAAAATAAACTTTTGTTACCAAATTGACCCTTAAAACCAAGTTCAA
1 GTACCTAATTGGACCAAAATAAACTTTAGGTACCAAATTGAACCTTAAAGCCAAGTTCAA
588168 GTACCTAATTG
1 GTACCTAATTG
588179 AGAAAAAATC
Statistics
Matches: 98, Mismatches: 21, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
55 5 0.05
56 37 0.38
57 2 0.02
59 2 0.02
60 47 0.48
61 5 0.05
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (60 bp):
GTACCTAATTGGACCAAAATAAACTTTAGGTACCAAATTGAACCTTAAAGCCAAGTTCAA
Found at i:588191 original size:116 final size:116
Alignment explanation
Indices: 587993--588218 Score: 346
Period size: 116 Copynumber: 1.9 Consensus size: 116
587983 AAGTTTTAGG
* ** *
587993 TACCTAATTGGACCAAAATAAACTTTGGGTACCAAATTGAACCTTAAAGTCAAGTTCAAGTGCCT
1 TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTGAACCTTAAAACCAAGTTCAAGTACCT
* *
588058 AATTGGAAAAAACTCTTAGGTACTGATTTGAACCTTGAAGCTAAGCTTAAT
66 AATTGGAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAGCTTAAT
* * *
588109 TACCTAATTGAACCAAAATAAACTTTTGTTACCAAATTGACCCTTAAAACCAAGTTCAAGTACCT
1 TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTGAACCTTAAAACCAAGTTCAAGTACCT
*
588174 AATTGAGAAAAAA-TCTTAGGTGCCGATTTGAACCTTGAACCTAAG
66 AATTG-GAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAG
588219 TTCATGTACC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 92 0.93
117 7 0.07
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (116 bp):
TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTGAACCTTAAAACCAAGTTCAAGTACCT
AATTGGAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAGCTTAAT
Found at i:590397 original size:25 final size:26
Alignment explanation
Indices: 590346--590398 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
590336 TTTTTTATTT
*
590346 TATTTTAAGTTTATAATATTTTATAA
1 TATTTTAAGTTTATAATATTATATAA
** *
590372 TATTTTATTTTTAT-ATATTATGTAA
1 TATTTTAAGTTTATAATATTATATAA
590397 TA
1 TA
590399 ATTCTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
TATTTTAAGTTTATAATATTATATAA
Found at i:595338 original size:24 final size:24
Alignment explanation
Indices: 595292--595338 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
595282 ACATATTATA
*
595292 AAATATTTAAATATGTATTATATT
1 AAATATTTAAATATGTATAATATT
*
595316 AAATTTTTAAA-ATGATATAATAT
1 AAATATTTAAATATG-TATAATAT
595339 GTTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATATTTAAATATGTATAATATT
Found at i:597355 original size:74 final size:74
Alignment explanation
Indices: 597265--597413 Score: 244
Period size: 74 Copynumber: 2.0 Consensus size: 74
597255 GAAGAACAGT
* * *
597265 ATAGTTTGCGACCAATTTTGTTGTGAGCTTTCCCCATCTTTTGGGTTAATTATATCACACATCCC
1 ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATATTTTGGGTTAATTATAGCACACATCCC
597330 TAGAATATG
66 TAGAATATG
* *
597339 ATAGTTTGGGACCAATTTTGTTGTGAGCTTCCCCCATATTTTGGGTTAATTATAGCACACATTCC
1 ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATATTTTGGGTTAATTATAGCACACATCCC
*
597404 TAGATTATG
66 TAGAATATG
597413 A
1 A
597414 CTTTGATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (74 bp):
ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATATTTTGGGTTAATTATAGCACACATCCC
TAGAATATG
Found at i:598912 original size:47 final size:47
Alignment explanation
Indices: 598843--598937 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
598833 TTGCAGATCA
598843 TATCTCCACTAATCAAGGTACCTTCTTTGTGAATCATACACAACTCT
1 TATCTCCACTAATCAAGGTACCTTCTTTGTGAATCATACACAACTCT
598890 TATCTCCACTAATCAAGGTACCTTCTTTGTGAATCATACACAACTCT
1 TATCTCCACTAATCAAGGTACCTTCTTTGTGAATCATACACAACTCT
598937 T
1 T
598938 CGCAGATATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (47 bp):
TATCTCCACTAATCAAGGTACCTTCTTTGTGAATCATACACAACTCT
Found at i:600676 original size:375 final size:378
Alignment explanation
Indices: 600045--600732 Score: 951
Period size: 375 Copynumber: 1.8 Consensus size: 378
600035 AAAATCTAAC
*
600045 CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTTACA
1 CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTAACA
* * **
600110 GTGAATGAATTACTTATTTTACTAGGATTATATGACAGCTGATGCTTCATTTCATTTGATCTAAT
66 GTGAATGAAATACTAATTTTACTAGGATTATATGA-AGCTGATGCTTCAAGTCATTTGATCTAAT
* *
600175 TCATAAGCTAGTGAAGTTACTTCGGAAATTCTGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
130 TCAT-A--TAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
* * ** * *
600240 TGCATTATGTTTTTTTTTTCATCCAAATGCTGCGTTTTTAATCGCAGCTGAGGCTATGGCATTTG
192 TGCATTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGGCGATGGCATTTG
* * *
600305 CATTAGTTAAAAGGGTGTTGATGTTAAATTCTAATGGACTCTT-CATTTTTGTTGAAGTATACAG
257 CATTAGTT-AAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAG
600369 ATGGATATACGGATATGACTGTAAAAATTTAAAAAAATCTAACCATATCGCCAAGTAA
321 ATGGATATACGGATATGACTGTAAAAATTTAAAAAAATCTAACCATATCGCCAAGTAA
* * **
600427 CATAAATCGAGTTAACTTAGATCAATGGTCA-TGTAGCAAAA-ATTTGTAAACCTGCTCAATTAA
1 CATAAATCAAGTTAACTTAAATCAAT-GAAATTGTAG-AAAATATTTGTAAACCTGCTCAATTAA
* * *
600490 CAGTGTATGAAATACTAATTTTACTAGGATTACTA-G-AGCTGGTGCTTCAAGTCATTTGATCTG
64 CAGTGAATGAAATACTAATTTTACTAGGATTA-TATGAAGCTGATGCTTCAAGTCATTTGATCTA
* * *
600553 GTTCAT-T-GTGCAGTTACTTTGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACT
128 ATTCATATAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACT
* * **
600616 TCATTATGTGTTCTTTTTCATCCAAATGCAATGTTTTTAATCTTAGATG-GGACGATGGCATTTG
193 GCATTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGG-CGATGGCATTTG
* *
600680 CATTAGTTAAAGGGTTTTGATGCTAAATTCTAATAGACTATTGCTTTTTTGTT
257 CATTAGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTT
600733 TGAATTGCTA
Statistics
Matches: 269, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
374 32 0.12
375 120 0.45
376 1 0.00
380 28 0.10
382 80 0.30
383 8 0.03
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (378 bp):
CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTAACA
GTGAATGAAATACTAATTTTACTAGGATTATATGAAGCTGATGCTTCAAGTCATTTGATCTAATT
CATATAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACTGCA
TTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGGCGATGGCATTTGCATT
AGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAGATGGA
TATACGGATATGACTGTAAAAATTTAAAAAAATCTAACCATATCGCCAAGTAA
Found at i:603239 original size:20 final size:20
Alignment explanation
Indices: 603201--603239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
603191 ACTTGTTTAA
* **
603201 AATTTATATTTTTTTAAATT
1 AATTTATATATTTAAAAATT
603221 AATTTATATATTTAAAAAT
1 AATTTATATATTTAAAAAT
603240 AACATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTATATATTTAAAAATT
Found at i:604980 original size:23 final size:24
Alignment explanation
Indices: 604954--605004 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
604944 TTTCTAGATA
* *
604954 ATTTAATATTTATTGGTA-AATAT
1 ATTTAACATTTATTAGTATAATAT
*
604977 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTTATTAGTATAATAT
605001 ATTT
1 ATTT
605005 GACCTACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTTAACATTTATTAGTATAATAT
Found at i:615950 original size:16 final size:16
Alignment explanation
Indices: 615931--615963 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
615921 AGTTTAGGTT
615931 ATTTTGAATTTTGGTC
1 ATTTTGAATTTTGGTC
*
615947 ATTTTGAGTTTTGGTC
1 ATTTTGAATTTTGGTC
615963 A
1 A
615964 CTTCAATTTA
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:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (16 bp):
ATTTTGAATTTTGGTC
Found at i:617663 original size:16 final size:17
Alignment explanation
Indices: 617642--617675 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
617632 TCTATTCAAT
*
617642 TAAAAA-TTCAAAAAAA
1 TAAAAAGTTAAAAAAAA
617658 TAAAAAGTTAAAAAAAA
1 TAAAAAGTTAAAAAAAA
617675 T
1 T
617676 GAACTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAAAGTTAAAAAAAA
Found at i:618723 original size:32 final size:32
Alignment explanation
Indices: 618687--618756 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
618677 ATAAATTGTT
618687 TAAAAAGAATAAAGGTAAAATTGT-AAAAAATA
1 TAAAAAGAA-AAAGGTAAAATTGTAAAAAAATA
** * * *
618719 TAAAAATTAAAAGTTAAATTTTTAAAAAAATA
1 TAAAAAGAAAAAGGTAAAATTGTAAAAAAATA
618751 TAAAAA
1 TAAAAA
618757 TGTATACTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (32 bp):
TAAAAAGAAAAAGGTAAAATTGTAAAAAAATA
Found at i:623564 original size:130 final size:124
Alignment explanation
Indices: 623386--623728 Score: 362
Period size: 125 Copynumber: 2.7 Consensus size: 124
623376 GGTGGATAAT
* * * * ** *
623386 ATTAATAAGTTAGGCAGAAAAGATTTCGGTTTGGATCTACTTTTAATAAATTTGTAGTTACAGTA
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGA-TTTTAATAAATTTACAGTTACAATA
623451 TTTTAATTTTTGAAAAAACAAAGAACCATATAACATGAACCATAAACAACAGTGAAAACAAACAC
65 TTTTAATTTTTGAAAAAACAAAGAACC-----ACATGAACCATAAACAACAGTGAAAACAAACAC
* *
623516 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTTAAATAAATTTACGGTTACAATG
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTT-AATAAATTTACAGTTACAATA
* * * * *
623581 TTTTAGTTTTTGAAAAAGCAAAGAACCGCATGAATCATAAACAACAGTGAAAATAAACAC
65 TTTTAATTTTTGAAAAAACAAAGAACCACATGAACCATAAACAACAGTGAAAACAAACAC
* * * * * * * * * * *
623641 ATCAATAACTTAGACGGATAACATTTTGATTTGGATTGATTTTGAACAAATTTACGGATATAGTA
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTT-AATAAATTTACAGTTACAATA
* *
623706 GTTTAATTTTTAAAAAAAGCAAA
65 TTTTAATTTTTGAAAAAA-CAAA
623729 TCGATTCATA
Statistics
Matches: 181, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
125 97 0.54
126 4 0.02
129 4 0.02
130 76 0.42
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (124 bp):
ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTTAATAAATTTACAGTTACAATAT
TTTAATTTTTGAAAAAACAAAGAACCACATGAACCATAAACAACAGTGAAAACAAACAC
Found at i:625748 original size:18 final size:18
Alignment explanation
Indices: 625697--625751 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
625687 CGTTTATGGC
* *
625697 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGT
625715 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGT
*
625733 ACTGTTCACGTATACAGT
1 ACTATTCACGTATACAGT
625751 A
1 A
625752 GTTGGGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACAGT
Found at i:640642 original size:3 final size:3
Alignment explanation
Indices: 640634--640658 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
640624 TAACAGCAAT
640634 AGC AGC AGC AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC A
640659 TCGTTAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:646383 original size:3 final size:3
Alignment explanation
Indices: 646375--646406 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
646365 TGGCTAAGTT
646375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
646407 CCAAAATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:654978 original size:202 final size:195
Alignment explanation
Indices: 654549--655109 Score: 669
Period size: 198 Copynumber: 2.8 Consensus size: 195
654539 GAAGGAAATA
** *
654549 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATTTGGAAAATGAGATTAGTGGTTTGCTTGG
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAA-TACGAAAACGAGATTAGTGGTTTGCTTGG
** * ** *
654614 CAGAGTAG-AAAAAA-GGGAAGAAATGGATATAGGATGGTGAAAAACCAAAAAAGAACATAAATG
65 CAGAG-AGAAAAAAACAAGAAG-AAT-GAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATG
* * * * *
654677 TTTGAGTGTGTTAGGTAGGGAAGAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCTTTG
127 TTTGAGCGTGTTTGGTA-GGAAAAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCATCG
654742 TCTTC
191 TCTTC
* *
654747 ATTAGCTTTCTTGTTCATAGATAGTAAAGCAAAAATACGAAAACGAGTTTAGTGGTTTGCTTGGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * *
654812 AGAGAGAAAAAAAAACAACAGAAGAATGAACAAAAGATGGTGAAAAACTGAAAAAGAATATGAAT
66 AGAGAG--AAAAAAAC-A-AGAAGAATGAA-ATAGGATGGTGAAAAACTGAAAAAGAACATGAAT
* * * *
654877 GTTTGAGCGTGTTTGGTAGGAAAAAGAATTCTTGTTCATTTAGCTGCATTACAAAAGATTAGCAT
126 GTTTGAGCGTGTTTGGTAGGAAAAA-AATTCTCGCTCACTTAACTGCATTAC-AAAGATTAGCAT
654942 CGTCTTC
189 CGTCTTC
* * *
654949 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGGAAACAAGATTAGTGGTTTGCTTAGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * * * * * *
655014 AGAGTG-AAAAATCTAGAAGAAATGGAATTAGGGTGGTGAAAAACTGAAAAAGAAGATGGATGTT
66 AGAGAGAAAAAAACAAGAAG-AAT-GAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATGTT
655078 TGAGCGTGTTTGGTAGGAAAGAAAATTCTCGC
129 TGAGCGTGTTTGGTAGGAAA-AAAATTCTCGC
655110 ACCTGTTTGT
Statistics
Matches: 312, Mismatches: 39, Indels: 24
0.83 0.10 0.06
Matches are distributed among these distances:
196 2 0.01
197 35 0.11
198 95 0.30
199 17 0.05
200 8 0.03
201 69 0.22
202 86 0.28
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (195 bp):
ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
AGAGAGAAAAAAACAAGAAGAATGAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATGTTTG
AGCGTGTTTGGTAGGAAAAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCATCGTCTTC
Found at i:657838 original size:25 final size:25
Alignment explanation
Indices: 657810--657859 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
657800 ATAAATTCAG
*
657810 TTTAAA-TATTCAAAATTATTATTTA
1 TTTAAATTATTAAAAATT-TTATTTA
*
657835 TTTAAATTTTTAAAAATTTTATTTA
1 TTTAAATTATTAAAAATTTTATTTA
657860 AAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTAAATTATTAAAAATTTTATTTA
Found at i:661099 original size:20 final size:20
Alignment explanation
Indices: 661058--661100 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
661048 ATTATTATAC
*
661058 TAATAAAAAATATTTACAAT
1 TAATAAAAAATATTAACAAT
*
661078 TAATGAAAAAA-ATTAACGAT
1 TAAT-AAAAAATATTAACAAT
661098 TAA
1 TAA
661101 ATTATGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
TAATAAAAAATATTAACAAT
Found at i:667767 original size:21 final size:21
Alignment explanation
Indices: 667725--667769 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
667715 TAAACTCTTG
667725 TTTTTTTAATGAAATCTTATGT
1 TTTTTTTAATGAAATC-TATGT
*
667747 TTTTTTTTATGAAATAC-ATGT
1 TTTTTTTAATGAAAT-CTATGT
667768 TT
1 TT
667770 ACAAGCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 14 0.67
23 1 0.05
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTTTTTAATGAAATCTATGT
Found at i:669107 original size:306 final size:311
Alignment explanation
Indices: 668542--669168 Score: 953
Period size: 306 Copynumber: 2.0 Consensus size: 311
668532 TTTCTCGATT
** * *
668542 TTTTGTTCCTAATTGGAGTCAACGTTGTGATTCAATTCGATTTGACTTGGTTTGCAGCTTTTTTT
1 TTTTGTTGTTAATTGGAGTCAACGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
* *
668607 GGTTAGTGGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACTCGTGCAATAGAGCTTAA
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATT-ATAATACTCATGCAATAGAGCTTAA
* * *
668672 TGCGATTCAATAGTGGAAAAATTAGATGTTTCAAATTCATATTCGAGCTGGAAACTATTGATATT
130 TGCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATT
* *
668737 AGAAGAGGTATGGAAATTTGAACTGTTTTACTTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGT
195 AGAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGT
* * *
668802 TGCAT-AATATACTGGAGCTATT-AAAATATGAGGAAATGGTTTTTCC-TTTG
260 TGCATAAATATACTGGAGCTATTAAAAAT-TAAGGAAATAGTTTTCCCTTTTG
* * * *
668852 TTTTGTTGTTAATTGGAGTTACCTTTGTGATTTAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
1 TTTTGTTGTTAATTGGAGTCAACGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
*
668917 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAA-T-TAATACTCATGGAATAGAGCTTAAT
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTATAATACTCATGCAATAGAGCTTAAT
* * * * *
668980 GCGATTTAATA-TAGAGAAATTAGATGGTTCAAATTCCTATTTAAGCTGGAAATTATTGATATTA
131 GCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATTA
669044 GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTG-TTTGACTTGGTATTTTTGATGTAGGAAGT
196 GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGT-TTTTTGATGTAGGAAGT
669108 TGCATAAATATACTGGAGCTATTAAAAATTAAGGAAATAGTTTTCCCTTTTG
260 TGCATAAATATACTGGAGCTATTAAAAATTAAGGAAATAGTTTTCCCTTTTG
*
669160 TTTTCTTGT
1 TTTTGTTGT
669169 AAAATTGTTA
Statistics
Matches: 288, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
305 11 0.04
306 101 0.35
307 65 0.23
308 17 0.06
309 1 0.00
310 93 0.32
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (311 bp):
TTTTGTTGTTAATTGGAGTCAACGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTATAATACTCATGCAATAGAGCTTAAT
GCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATTA
GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGTT
GCATAAATATACTGGAGCTATTAAAAATTAAGGAAATAGTTTTCCCTTTTG
Found at i:673690 original size:13 final size:14
Alignment explanation
Indices: 673655--673683 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
673645 CTTAAAATTA
673655 TACATAAATTTTGG
1 TACATAAATTTTGG
673669 TACATAAATTTTGG
1 TACATAAATTTTGG
673683 T
1 T
673684 GATAAATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TACATAAATTTTGG
Found at i:673970 original size:29 final size:31
Alignment explanation
Indices: 673924--673985 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
673914 ATATATCTGA
* **
673924 ACCACAATTATAGCTTCACGTATATAATTGC
1 ACCACAATTAAAGCTTCACACATATAATTGC
*
673955 ACCA-AATTAAAG-TTCATACATATAATTGC
1 ACCACAATTAAAGCTTCACACATATAATTGC
673984 AC
1 AC
673986 GTTAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.59
30 7 0.26
31 4 0.15
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (31 bp):
ACCACAATTAAAGCTTCACACATATAATTGC
Found at i:674386 original size:12 final size:11
Alignment explanation
Indices: 674369--674405 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
674359 AATTTAATTA
674369 TATAAATATTT
1 TATAAATATTT
674380 GTATAAA-ATTT
1 -TATAAATATTT
674391 TA-AAATATTT
1 TATAAATATTT
674401 TATAA
1 TATAA
674406 TACAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 8 0.35
11 6 0.26
12 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TATAAATATTT
Found at i:675678 original size:17 final size:18
Alignment explanation
Indices: 675658--675703 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
675648 ATATTAAATT
675658 AAAATAACTA-TTATATAA
1 AAAATAACTATTTA-ATAA
**
675676 AAAATAAGAATTTAAT-A
1 AAAATAACTATTTAATAA
675693 AAAATAACTAT
1 AAAATAACTAT
675704 ATTGGTAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 10 0.43
18 10 0.43
19 3 0.13
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATAACTATTTAATAA
Found at i:679108 original size:25 final size:25
Alignment explanation
Indices: 679074--679124 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
679064 TTCAACAATC
679074 CGATTTGACCCGAATCTAAAACTAA
1 CGATTTGACCCGAATCTAAAACTAA
679099 CGATTTGACCCGAATCTAAAACTAA
1 CGATTTGACCCGAATCTAAAACTAA
679124 C
1 C
679125 TTGGAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (25 bp):
CGATTTGACCCGAATCTAAAACTAA
Found at i:679908 original size:45 final size:46
Alignment explanation
Indices: 679843--679954 Score: 163
Period size: 45 Copynumber: 2.4 Consensus size: 46
679833 GAGGGAGGAC
* * *
679843 TAGTTGGCGGCGGAGCTGCTGCGGTTGGTGGTGGTGT-AGGAGTGT
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGATGGTGTGAGGAGTGG
679888 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGATGGTGTGGAAGGAGTGG
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGATGGTGT-G-AGGAGTGG
*
679936 TAGTTGGCGGCGGATTTGC
1 TAGTTGGCGGCGGAGTTGC
679955 GGTGGATGGC
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 35 0.58
48 25 0.42
ACGTcount: A:0.11, C:0.11, G:0.50, T:0.29
Consensus pattern (46 bp):
TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGATGGTGTGAGGAGTGG
Found at i:679923 original size:48 final size:45
Alignment explanation
Indices: 679843--679954 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 45
679833 GAGGGAGGAC
* * *
679843 TAGTTGGCGGCGGAGCTGCTGCGGTTGGTGGTG-GTGTAGGAGTGT
1 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGTGTG-GAAGGAGTGG
679888 TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGATGGTGTGGAAGGAGTGG
1 TAGTTGGCGGCGGAGTTGCTGCGGTT-G-G-TGGTGTGGAAGGAGTGG
*
679936 TAGTTGGCGGCGGATTTGC
1 TAGTTGGCGGCGGAGTTGC
679955 GGTGGATGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
45 25 0.42
46 1 0.02
47 1 0.02
48 31 0.53
49 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.50, T:0.29
Consensus pattern (45 bp):
TAGTTGGCGGCGGAGTTGCTGCGGTTGGTGGTGTGGAAGGAGTGG
Found at i:683941 original size:27 final size:27
Alignment explanation
Indices: 683903--683955 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
683893 TTTAGGAGAG
683903 GATTAACAAGTAATTTTTCTATTTTTT
1 GATTAACAAGTAATTTTTCTATTTTTT
683930 GATTAACAAGTAATTTTTCTATTTTT
1 GATTAACAAGTAATTTTTCTATTTTT
683956 CTGGGGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.55
Consensus pattern (27 bp):
GATTAACAAGTAATTTTTCTATTTTTT
Found at i:689629 original size:18 final size:18
Alignment explanation
Indices: 689598--689639 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
689588 AATATGCTTG
*
689598 AATT-AAAATGTAAA-TT
1 AATTAAAAATATAAACTT
689614 AAATTAAAAATATAAACTT
1 -AATTAAAAATATAAACTT
689633 AATTAAA
1 AATTAAA
689640 TATTTATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTAAAAATATAAACTT
Found at i:691537 original size:5 final size:5
Alignment explanation
Indices: 691524--691557 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
691514 AGACAATGAT
* *
691524 TATGA TATGG TATGG TATGG TATGG TATGA TATG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATG
691558 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (5 bp):
TATGG
Found at i:691547 original size:15 final size:15
Alignment explanation
Indices: 691519--691561 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
691509 ATTCGAGACA
691519 ATGATTATGATATGGT
1 ATGA-TATGATATGGT
* *
691535 ATGGTATGGTATGGT
1 ATGATATGATATGGT
691550 ATGATATGATAT
1 ATGATATGATAT
691562 ATATATCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (15 bp):
ATGATATGATATGGT
Found at i:698889 original size:21 final size:22
Alignment explanation
Indices: 698860--698906 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
698850 CAGAAGGAGT
*
698860 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
698882 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
698903 GAGT
1 GAGT
698907 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:700437 original size:233 final size:220
Alignment explanation
Indices: 700068--700667 Score: 726
Period size: 220 Copynumber: 2.7 Consensus size: 220
700058 ATGAGGAACG
* * *
700068 CAATGGTTACTTATATGAAACCTTATTCGGTAGGGATAGTCTAATAGGAATGAAATACGACTCAT
1 CAAT-GTTACTTATATGAAACCTTATTCGATAGGGATAGTCTAATAGGAAAGAAATACGATTCAT
* *
700133 CGGTTTGAATGTATACATATAGCTTTTGTGTTTATATAATCGAATCGCTAGTCATATTGAATTGG
65 CGGTTTGAATGTATACATATAGC-TTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGG
* *
700198 ATTGCTATTGTTTCTTGATTTTTATATGAGATTACACATGATTATGTATTTTGAATGGAGGGTTG
129 ATTGCTATTGTTCCGTGA----T-T-T----TT---CATGATTATGTATTTTGAATGGAGGGTTG
* * ** *
700263 TCATTGGATTGGTTTGGTACGAGGAACAGAAATTGAAATGCA
181 TCATTGGATCGGTTCGGTACGACAAACAGAAAGTGAAA--CA
* * *
700305 -AATAGTTACTTATATGAAACCTTATTTGATAGGGTTAGTCTAAGAGGAAAGAAATACGATTCAT
1 CAAT-GTTACTTATATGAAACCTTATTCGATAGGGATAGTCTAATAGGAAAGAAATACGATTCAT
* * *
700369 C-GTTTGATTTTATACATATAGC-TTGTGTTTATATAATCGAATTGTTAGTCATACTGAATTGGA
65 CGGTTTGAATGTATACATATAGCTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGA
*
700432 TTGCTATTGTTCCGTGATTTTTCATGATTATTTATTTTGAATGGAGGGTTGTCATTGGATCGGTT
130 TTGCTATTGTTCCGTGATTTTTCATGATTATGTATTTTGAATGGAGGGTTGTCATTGGATCGGTT
* *
700497 CGGTATGACAAACAGAAAGTGGAACA
195 CGGTACGACAAACAGAAAGTGAAACA
* * *
700523 CAATG---GTTATATGAAACCTTATTCGATAGGGATAGTCTAATAGGAACGAAATACGATTCGTC
1 CAATGTTACTTATATGAAACCTTATTCGATAGGGATAGTCTAATAGGAAAGAAATACGATTCATC
* * * *
700585 GGTTTGAATGTATGCATATAGCTTTTGTATTTATATAATTGAATCGTTAGTCATACTGAACTGGA
66 GGTTTGAATGTATACATATAGC-TTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGA
*
700650 TTGCTATTGTTCTGTGAT
130 TTGCTATTGTTCCGTGAT
700668 CGGGATTGTA
Statistics
Matches: 323, Mismatches: 36, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
215 51 0.16
216 18 0.06
218 57 0.18
219 3 0.01
220 59 0.18
223 2 0.01
227 1 0.00
228 1 0.00
229 1 0.00
233 53 0.16
235 19 0.06
236 58 0.18
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (220 bp):
CAATGTTACTTATATGAAACCTTATTCGATAGGGATAGTCTAATAGGAAAGAAATACGATTCATC
GGTTTGAATGTATACATATAGCTTTGTGTTTATATAATCGAATCGTTAGTCATACTGAATTGGAT
TGCTATTGTTCCGTGATTTTTCATGATTATGTATTTTGAATGGAGGGTTGTCATTGGATCGGTTC
GGTACGACAAACAGAAAGTGAAACA
Found at i:702209 original size:14 final size:14
Alignment explanation
Indices: 702190--702235 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
702180 ATATGAACAC
702190 TTCGGGTTTCAGGT
1 TTCGGGTTTCAGGT
*
702204 TTCGGGTTTCGGGT
1 TTCGGGTTTCAGGT
* *
702218 TTCGAGTTTCAAGT
1 TTCGGGTTTCAGGT
702232 TTCG
1 TTCG
702236 AATTTCGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.09, C:0.15, G:0.33, T:0.43
Consensus pattern (14 bp):
TTCGGGTTTCAGGT
Found at i:702226 original size:21 final size:21
Alignment explanation
Indices: 702190--702250 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
702180 ATATGAACAC
702190 TTCGGGTTTC-AGGTTTCGGGT
1 TTCGGGTTTCGA-GTTTCGGGT
**
702211 TTCGGGTTTCGAGTTTCAAGT
1 TTCGGGTTTCGAGTTTCGGGT
**
702232 TTCGAATTTCGAGTTTCGG
1 TTCGGGTTTCGAGTTTCGG
702251 ATATAACTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.11, C:0.15, G:0.31, T:0.43
Consensus pattern (21 bp):
TTCGGGTTTCGAGTTTCGGGT
Found at i:702236 original size:14 final size:14
Alignment explanation
Indices: 702190--702249 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
702180 ATATGAACAC
* *
702190 TTCGGGTTTCAGGT
1 TTCGAGTTTCAAGT
* **
702204 TTCGGGTTTCGGGT
1 TTCGAGTTTCAAGT
702218 TTCGAGTTTCAAGT
1 TTCGAGTTTCAAGT
* *
702232 TTCGAATTTCGAGT
1 TTCGAGTTTCAAGT
702246 TTCG
1 TTCG
702250 GATATAACTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.43
Consensus pattern (14 bp):
TTCGAGTTTCAAGT
Found at i:704706 original size:17 final size:17
Alignment explanation
Indices: 704662--704710 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
704652 ATCTAGCACG
704662 CAAACTTGAAATGA-TC
1 CAAACTTGAAATGACTC
* **
704678 TAAACTCAAAATGACTC
1 CAAACTTGAAATGACTC
*
704695 CGAACTTGAAATGACT
1 CAAACTTGAAATGACT
704711 TAAGCAAGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (17 bp):
CAAACTTGAAATGACTC
Found at i:705126 original size:7 final size:7
Alignment explanation
Indices: 705114--705138 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
705104 AAGCAAATTA
705114 ACAATGT
1 ACAATGT
705121 ACAATGT
1 ACAATGT
705128 ACAATGT
1 ACAATGT
705135 ACAA
1 ACAA
705139 CGTAAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (7 bp):
ACAATGT
Found at i:709858 original size:47 final size:47
Alignment explanation
Indices: 709755--709858 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 47
709745 AATAGCAAAG
709755 AATTTAAAAAAAATACTAATTACTTTATTTAAACATAGATTACTTGA
1 AATTTAAAAAAAATACTAATTACTTTATTTAAACATAGATTACTTGA
* *
709802 AACTGAAAAAAAATACTAATTACTTTATTTAAACATAGATTACTTGA
1 AATTTAAAAAAAATACTAATTACTTTATTTAAACATAGATTACTTGA
709849 AATTTAAAAA
1 AATTTAAAAA
709859 TTGATATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (47 bp):
AATTTAAAAAAAATACTAATTACTTTATTTAAACATAGATTACTTGA
Found at i:718425 original size:23 final size:23
Alignment explanation
Indices: 718407--718460 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
718397 GGTATACACG
718407 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* **
718430 TACATAATAATAATA-ATGGTAA
1 TACATAATAAAAATATATACTAA
718452 TAC-TAATAA
1 TACATAATAA
718461 TACTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 8 0.29
23 14 0.50
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:718441 original size:3 final size:3
Alignment explanation
Indices: 718410--718480 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
718400 ATACACGTAC
* * * * *
718410 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATG GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
718457 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
718481 CAAGGATATT
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:718960 original size:11 final size:12
Alignment explanation
Indices: 718941--718977 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
718931 AAGAAAAAAA
718941 AAGAGAGAGAGGG
1 AAGAGAGA-AGGG
718954 AAGAGAGAAGGG
1 AAGAGAGAAGGG
718966 -AGAGAGAAGGG
1 AAGAGAGAAGGG
718977 A
1 A
718978 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 4 0.17
13 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:720306 original size:16 final size:16
Alignment explanation
Indices: 720281--720312 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
720271 ATATAAAATT
720281 AATTTAATTTTTGAAA
1 AATTTAATTTTTGAAA
*
720297 AATTTTATTTTTGAAA
1 AATTTAATTTTTGAAA
720313 TAAATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
AATTTAATTTTTGAAA
Found at i:721327 original size:14 final size:14
Alignment explanation
Indices: 721307--721341 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
721297 ATATTCGAAT
721307 TAAATTATATTT-A
1 TAAATTATATTTGA
721320 TCAAATTATATTTGA
1 T-AAATTATATTTGA
721335 TAAATTA
1 TAAATTA
721342 AACGTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 17 0.85
15 2 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
TAAATTATATTTGA
Found at i:725138 original size:18 final size:17
Alignment explanation
Indices: 725115--725151 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
725105 ATAAACCAAA
725115 AAGAAAATAAAATTAACC
1 AAGAAAATAAAATT-ACC
*
725133 AAGAAAATGAAATTACC
1 AAGAAAATAAAATTACC
725150 AA
1 AA
725152 AACTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.65, C:0.11, G:0.08, T:0.16
Consensus pattern (17 bp):
AAGAAAATAAAATTACC
Found at i:727041 original size:37 final size:37
Alignment explanation
Indices: 726991--727069 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
726981 TTATTACGAA
* *
726991 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
727028 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
727065 GTCTT
1 GTCTT
727070 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:727314 original size:47 final size:47
Alignment explanation
Indices: 727188--727508 Score: 426
Period size: 47 Copynumber: 6.6 Consensus size: 47
727178 CCCTTCGGGA
* * * * * *
727188 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
727235 CCTGTCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
727284 CTTATCACATATATACACTCTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
727331 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
727382 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
727429 CTTATCACATATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC------ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
727482 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
727509 TATTCAAATA
Statistics
Matches: 244, Mismatches: 18, Indels: 24
0.85 0.06 0.08
Matches are distributed among these distances:
47 115 0.47
49 39 0.16
51 45 0.18
53 45 0.18
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:727472 original size:100 final size:98
Alignment explanation
Indices: 727188--727508 Score: 511
Period size: 98 Copynumber: 3.3 Consensus size: 98
727178 CCCTTCGGGA
* * * * * * * *
727188 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAT
1 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATAT
727251 ACACTTTCACATTCATCACATCGGCCATTAGGC
66 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
727284 CTTATCACATATATACACTCTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATAT
727349 ACACTTTCACATTCATCACATCGGCCATTAGGC
66 ACACTTTCACATTCATCACATCGGCCATTAGGC
727382 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGCCTTATCAC--ATATATAT
727447 ATACACTTTCACATTCATCACATCGGCCATTAGGC
64 ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
727482 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTCTCACATT
727509 TATTCAAATA
Statistics
Matches: 208, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
96 45 0.22
98 94 0.45
100 69 0.33
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (98 bp):
CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGCCTTATCACATATATATAT
ACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:730838 original size:10 final size:11
Alignment explanation
Indices: 730798--730830 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
730788 ACCAGTAATA
730798 ATTAAATAATTC
1 ATTAAA-AATTC
730810 ATTAAAAATTC
1 ATTAAAAATTC
730821 ATTAAAAATT
1 ATTAAAAATT
730831 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTAAAAATTC
Found at i:737731 original size:149 final size:149
Alignment explanation
Indices: 737504--738100 Score: 948
Period size: 149 Copynumber: 4.0 Consensus size: 149
737494 TCCCACAGCC
* * * *
737504 ACAGGTATCCCTTGTGTTTGATCTTTACTTGCCTAATTGCCTCTTCGCATTGGAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
*
737569 CTCTGTAACTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
*
737634 ATAAATCAAATTATGGAAA
131 ATAAATCAAATGATGGAAA
* * * *
737653 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTTCATCTTCACGCTGAAACTCTTCTGAT
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
*
737718 CTCTGTAATTGTTCTCTAGGACCGACTTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
66 CTCTGTAATTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
737783 ATAAATCAAATGATGGAAA
131 ATAAATCAAATGATGGAAA
* *
737802 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTTTTCACACTGGAACAT-TTATGA
1 ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAAC-TCTTCTGA
* *
737866 TCTCTGTAATTGTTCTCTAGGACCGACTTAAAAAGTACGGGTCTTTCCATGTCAATGGTGATGAT
65 TCTCTGTAATTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGAT
737931 AATAAATCAAATGATGGAAA
130 AATAAATCAAATGATGGAAA
* ** *
737951 ACAGGTATCCCTCGTGTTTGCA-CTTTACTTGTCTGATTATCTCTTCACACTGGAACTCTTCTAA
1 ACAGGTATCCCTCGTGTTTG-ATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGA
*
738015 TCTCTGTAAGTT-TTCTCTAGGACCGACCTAAAAAATACGGGCCTTTCCATGTCAATGGTGATGA
65 TCTCTGTAA-TTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGA
**
738079 TAATAAATCAAACAATGGAAA
129 TAATAAATCAAATGATGGAAA
738100 A
1 A
738101 AGTGCTGATC
Statistics
Matches: 415, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
148 1 0.00
149 410 0.99
150 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (149 bp):
ACAGGTATCCCTCGTGTTTGATCTTTACTTGCCTGATTGCCTCTTCACACTGGAACTCTTCTGAT
CTCTGTAATTGTTCTCTAGGACCGACCTAAAAAATACGGGTCTTTCCATGTCAATGGTGATGATA
ATAAATCAAATGATGGAAA
Found at i:740289 original size:12 final size:12
Alignment explanation
Indices: 740272--740298 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
740262 AAATTTATCC
740272 GAGTTAGAATTA
1 GAGTTAGAATTA
740284 GAGTTAGAATTA
1 GAGTTAGAATTA
740296 GAG
1 GAG
740299 ATGATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (12 bp):
GAGTTAGAATTA
Found at i:741295 original size:3 final size:3
Alignment explanation
Indices: 741287--741319 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
741277 CCGTTCATGG
741287 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
741320 CCGATGAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:741557 original size:12 final size:12
Alignment explanation
Indices: 741540--741564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
741530 TTTTATTATT
741540 TTCAAATTTTGA
1 TTCAAATTTTGA
741552 TTCAAATTTTGA
1 TTCAAATTTTGA
741564 T
1 T
741565 GCGTCGAACA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTCAAATTTTGA
Found at i:749348 original size:19 final size:19
Alignment explanation
Indices: 749335--749371 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
749325 AAAAAGTAAC
749335 AGATGAAATAAAAATAAAA
1 AGATGAAATAAAAATAAAA
749354 AGATGAAATAAAAATAAA
1 AGATGAAATAAAAATAAA
749372 TAACAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (19 bp):
AGATGAAATAAAAATAAAA
Found at i:750292 original size:16 final size:16
Alignment explanation
Indices: 750262--750309 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
750252 GAAAATTAAT
750262 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
750277 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
750294 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
750309 A
1 A
750310 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:750308 original size:11 final size:11
Alignment explanation
Indices: 750253--750323 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
750243 ATAGCTTAAG
*
750253 AAAATTAATAT
1 AAAATTAAAAT
750264 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
750276 AATAA-T-AATT
1 AA-AATTAAAAT
*
750286 AAAAAT-AAAT
1 AAAATTAAAAT
750296 AAAATTAAAAT
1 AAAATTAAAAT
*
750307 AAACTTAAAAT
1 AAAATTAAAAT
*
750318 AGAATT
1 AAAATT
750324 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Done.