Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 135 of 216
Found at i:42899049 original size:35 final size:36
Alignment explanation
Indices: 42898993--42899099 Score: 112
Period size: 35 Copynumber: 3.1 Consensus size: 36
42898983 TACTCTCTGT
* * * * *
42898993 TTGGCGTG-TTTCAGTTTGACTAGCTCTTATGAGTA
1 TTGGCATGTTTTCGGTTGGACTAACTCTTATGAGCA
* *
42899028 TTGGCAT-TTTTCGGTTGGACTATCTCTTATGTGCA
1 TTGGCATGTTTTCGGTTGGACTAACTCTTATGAGCA
* *
42899063 TTGGCATGTTTT-GGTTGGACTAACTCTTGTGAACA
1 TTGGCATGTTTTCGGTTGGACTAACTCTTATGAGCA
42899098 TT
1 TT
42899100 TGGTGTGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
35 56 0.93
36 4 0.07
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (36 bp):
TTGGCATGTTTTCGGTTGGACTAACTCTTATGAGCA
Found at i:42905702 original size:96 final size:96
Alignment explanation
Indices: 42905528--42905707 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
42905518 ATGCTGCTCC
* * * *
42905528 CACAAGCTATCGAGTATCCACAACTAATGTCGGACCTCAACCATCGATAGGACATTCAAGACCAG
1 CACAAGCTATCGAGTATCCACAACTAATGCCGAAACTCAACCACCGATAGGACATTCAAGACCAG
* *
42905593 CATCAGAACCATGGTAACCTGGGTCTGCTTA
66 CACCAGAAACATGGTAACCTGGGTCTGCTTA
* * * * * *
42905624 CACAAGCTGTTGAGTATCCGCAACTAATGCCGAAACTCAGCCACCGGTAGGACATTCAAGACTAG
1 CACAAGCTATCGAGTATCCACAACTAATGCCGAAACTCAACCACCGATAGGACATTCAAGACCAG
* *
42905689 TACCCGAAACATGGTAACC
66 CACCAGAAACATGGTAACC
42905708 GTAATGACAT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (96 bp):
CACAAGCTATCGAGTATCCACAACTAATGCCGAAACTCAACCACCGATAGGACATTCAAGACCAG
CACCAGAAACATGGTAACCTGGGTCTGCTTA
Found at i:42909150 original size:20 final size:20
Alignment explanation
Indices: 42909125--42909173 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
42909115 AAAAACAAAT
*
42909125 TTACAAATAAATATAAAAAA
1 TTACAAAAAAATATAAAAAA
42909145 TTACAAACAAAAATATAAAAAA
1 TTAC-AA-AAAAATATAAAAAA
42909167 TTACAAA
1 TTACAAA
42909174 CATTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 17 0.65
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (20 bp):
TTACAAAAAAATATAAAAAA
Found at i:42909161 original size:22 final size:22
Alignment explanation
Indices: 42909133--42909175 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42909123 ATTTACAAAT
42909133 AAATATAAAAAATTACAAACAA
1 AAATATAAAAAATTACAAACAA
42909155 AAATATAAAAAATTACAAACA
1 AAATATAAAAAATTACAAACA
42909176 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATATAAAAAATTACAAACAA
Found at i:42909194 original size:10 final size:9
Alignment explanation
Indices: 42909153--42909254 Score: 56
Period size: 9 Copynumber: 11.7 Consensus size: 9
42909143 AATTACAAAC
42909153 AAAAA-TAT
1 AAAAATTAT
*
42909161 AAAAAATTAC
1 -AAAAATTAT
*
42909171 AAACATTAT
1 AAAAATTAT
42909180 AAAAATTATT
1 AAAAATTA-T
42909190 AAAAA-TAT
1 AAAAATTAT
42909198 -AAAATTAT
1 AAAAATTAT
* *
42909206 --AAACTAC
1 AAAAATTAT
**
42909213 AAAAAAAAT
1 AAAAATTAT
42909222 ATAAAA--AT
1 A-AAAATTAT
42909230 AAAAATTACT
1 AAAAATTA-T
*
42909240 AAAAATTTT
1 AAAAATTAT
42909249 AAAAAT
1 AAAAAT
42909255 CACATTTACT
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
7 13 0.18
8 7 0.09
9 34 0.46
10 20 0.27
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:42909198 original size:18 final size:18
Alignment explanation
Indices: 42909153--42909205 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
42909143 AATTACAAAC
42909153 AAAAATATAAAAA--ATT
1 AAAAATATAAAAATTATT
42909169 ACAAACATTATAAAAATTATT
1 A-AAA-A-TATAAAAATTATT
42909190 AAAAATAT-AAAATTAT
1 AAAAATATAAAAATTAT
42909206 AAACTACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 11 0.34
18 4 0.12
19 9 0.28
20 3 0.09
21 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATAAAAATTATT
Found at i:42909243 original size:24 final size:24
Alignment explanation
Indices: 42909178--42909254 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 24
42909168 TACAAACATT
*
42909178 ATAAAAATTATTAAAAATATAAAA
1 ATAAAAATTACTAAAAATATAAAA
* * * *
42909202 TTATAAACTACAAAAAAAATATAAAA
1 ATAAAAATTAC--TAAAAATATAAAA
*
42909228 ATAAAAATTACTAAAAATTTTAAAA
1 ATAAAAATTACTAAAAA-TATAAAA
42909253 AT
1 AT
42909255 CACATTTACT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
24 12 0.30
25 8 0.20
26 20 0.50
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
ATAAAAATTACTAAAAATATAAAA
Found at i:42909243 original size:26 final size:26
Alignment explanation
Indices: 42909178--42909244 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
42909168 TACAAACATT
*
42909178 ATAAAAATTA-T-TAAAAATATAAAA
1 ATAAAAATTACTAAAAAAATATAAAA
* * * *
42909202 TTATAAACTACAAAAAAAATATAAAA
1 ATAAAAATTACTAAAAAAATATAAAA
42909228 ATAAAAATTACTAAAAA
1 ATAAAAATTACTAAAAA
42909245 TTTTAAAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 7 0.22
26 25 0.78
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
ATAAAAATTACTAAAAAAATATAAAA
Found at i:42910089 original size:28 final size:28
Alignment explanation
Indices: 42910049--42910109 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
42910039 TTTTACTATT
*
42910049 TTTTACAATATTTTATAATTTCTAATAA
1 TTTTACAACATTTTATAATTTCTAATAA
*
42910077 TTTTACAACATTTTATAATTTCTAATAT
1 TTTTACAACATTTTATAATTTCTAATAA
42910105 TTTTA
1 TTTTA
42910110 TAATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTACAACATTTTATAATTTCTAATAA
Found at i:42915419 original size:90 final size:90
Alignment explanation
Indices: 42915266--42915564 Score: 356
Period size: 90 Copynumber: 3.3 Consensus size: 90
42915256 ACTACTATTC
* * **
42915266 AAAATGTTCGTATTATTTTTGTATCCGTAAATC-AATTTTAGTCCGTATTATTTGTTGGTCGAAT
1 AAAATGTTTGTATTATCTTTGTATATGTAAA-CAAATTTTAGTCCGTATTATTTGTTGGTCGAAT
42915330 TTTATATTTTCGTATATCAGTTTTGT
65 TTTATATTTTCGTATATCAGTTTTGT
* * **
42915356 AAAATGTTTGTATTATCTTTGGATATGTAAA-AATATTTTAGACCGTATTATTTGCCGGTCGAAT
1 AAAATGTTTGTATTATCTTTGTATATGTAAACAA-ATTTTAGTCCGTATTATTTGTTGGTCGAAT
* *
42915420 TTTATATTTTCGTATATCAATTTTCT
65 TTTATATTTTCGTATATCAGTTTTGT
* * * *
42915446 AAAATGTTCGTATTATTTTTGTATATGTAAATCAAA-TTTAGTCGGTATTATTTATTGGTCGAAT
1 AAAATGTTTGTATTATCTTTGTATATGTAAA-CAAATTTTAGTCCGTATTATTTGTTGGTCGAAT
* *
42915510 TATATATTTTCATATA-CTAGTTTTGT
65 TTTATATTTTCGTATATC-AGTTTTGT
* * *
42915536 AGAATTTTTGTATTTTC-TTGTATATGTAA
1 AAAATGTTTGTATTATCTTTGTATATGTAA
42915565 TTTTTTTTGT
Statistics
Matches: 177, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
89 14 0.08
90 160 0.90
91 1 0.01
92 2 0.01
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (90 bp):
AAAATGTTTGTATTATCTTTGTATATGTAAACAAATTTTAGTCCGTATTATTTGTTGGTCGAATT
TTATATTTTCGTATATCAGTTTTGT
Found at i:42918928 original size:42 final size:42
Alignment explanation
Indices: 42918815--42918973 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 42
42918805 GGCTCGTACA
* * * *
42918815 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCATAT-ACG
*
42918858 ATGCC-ACTGTCCTAGACATGGTCTTACACGTAATCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCATATACG
* * *
42918900 ACGCCAACGTCCCAGACATGGTCTTACACATAAATC-TCAAACCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCAT-ATA-CG
*
42918944 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
42918974 ATATCACATT
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
42 31 0.31
43 41 0.41
44 29 0.29
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCATATACG
Found at i:42918973 original size:86 final size:85
Alignment explanation
Indices: 42918817--42918973 Score: 201
Period size: 86 Copynumber: 1.8 Consensus size: 85
42918807 CTCGTACAAT
* * ** *
42918817 GCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTGTCCTAGACATGGTCT
1 GCCAACGTCCCAGACATGGTCTTACACATAATCAAATAACGATGCCACTGTCCCAGACATGGTCT
42918882 TACACGTAATCATATACGAC
66 TACACGTAATCATATACGAC
* * *
42918902 GCCAACGTCCCAGACATGGTCTTACACATAAATCTCAA-ACCGATGCCAAC-GTCCCAGACGTGG
1 GCCAACGTCCCAGACATGGTCTTACACAT-AATC-AAATAACGATGCC-ACTGTCCCAGACATGG
42918965 TCTTACACG
63 TCTTACACG
42918974 ATATCACATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
85 25 0.41
86 32 0.52
87 4 0.07
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (85 bp):
GCCAACGTCCCAGACATGGTCTTACACATAATCAAATAACGATGCCACTGTCCCAGACATGGTCT
TACACGTAATCATATACGAC
Found at i:42919529 original size:18 final size:20
Alignment explanation
Indices: 42919492--42919530 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42919482 TTTCATTTTC
*
42919492 AATTCAACCCAAAATACTCA
1 AATTCAACCAAAAATACTCA
42919512 AATTC-ACCAAAAAT-CTCA
1 AATTCAACCAAAAATACTCA
42919530 A
1 A
42919531 TACAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (20 bp):
AATTCAACCAAAAATACTCA
Found at i:42921261 original size:38 final size:38
Alignment explanation
Indices: 42921218--42921326 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 38
42921208 TGCTGAAGTA
* * *
42921218 AGCCACTTATAGGCCATGGCCTGACACGACCTGAAGCC
1 AGCCACTTATAGGCCAAGGCCTGACATGACCTGAAACC
*
42921256 AGCCACTTAGT-GGCCAAGGCCTGACATAACCTGAAACC
1 AGCCACTTA-TAGGCCAAGGCCTGACATGACCTGAAACC
* * *
42921294 -GATCATTTAAAGGCCAAGGCCTGACATGACCTG
1 AG-CCACTTATAGGCCAAGGCCTGACATGACCTG
42921327 CAGCTTATCC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 58 0.97
39 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.17
Consensus pattern (38 bp):
AGCCACTTATAGGCCAAGGCCTGACATGACCTGAAACC
Found at i:42921435 original size:46 final size:48
Alignment explanation
Indices: 42921376--42921471 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 48
42921366 ATTCACTTAA
*
42921376 TATATAATGTTAAATTTAATTA-TTATTTTTT-AATTACATGCTATTTT
1 TATATAATGTTAAATTT-ATTATTTATTTTTTCAATTAAATGCTATTTT
* * *
42921423 TATA-AATTTTAAATTTATTATTTGTTTTTTCAATTAAATGTTATTTT
1 TATATAATGTTAAATTTATTATTTATTTTTTCAATTAAATGCTATTTT
42921470 TA
1 TA
42921472 AATTAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 4 0.09
46 19 0.44
47 20 0.47
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (48 bp):
TATATAATGTTAAATTTATTATTTATTTTTTCAATTAAATGCTATTTT
Found at i:42921469 original size:18 final size:17
Alignment explanation
Indices: 42921448--42921538 Score: 71
Period size: 18 Copynumber: 5.2 Consensus size: 17
42921438 TATTATTTGT
42921448 TTTTTCAATTAAATGTTA
1 TTTTTCAATTAAAT-TTA
*
42921466 TTTTTAAATTAAATTTA
1 TTTTTCAATTAAATTTA
* *
42921483 --TTGC-ATTAAATTGA
1 TTTTTCAATTAAATTTA
* *
42921497 TTTATCATTTAAATATTTA
1 TTTTTCAATT-AA-ATTTA
42921516 TTTTTTCAATTAAATTATA
1 -TTTTTCAATTAAATT-TA
42921535 TTTT
1 TTTT
42921539 AAATATTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
14 9 0.16
15 2 0.04
16 2 0.04
17 5 0.09
18 22 0.39
19 8 0.14
20 8 0.14
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTTCAATTAAATTTA
Found at i:42921525 original size:69 final size:64
Alignment explanation
Indices: 42921441--42921573 Score: 178
Period size: 69 Copynumber: 2.0 Consensus size: 64
42921431 TTAAATTTAT
* *
42921441 TATTTGTTTTTTCAATTAAATGT-TATTTTTAAATTAAATTTATTGCATTAAATTGATTTATCAT
1 TATTTATTTTTTCAATTAAAT-TATA-TTTTAAA-T--ATTTATTGCATTAAATTGA-TAATCAT
42921505 TTAAA
60 TTAAA
*
42921510 TATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCTTTAAATTGATAATCATTTAAA
1 TATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCATTAAATTGATAATCATTTAAA
42921574 AGTTATATCT
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
64 11 0.18
65 18 0.30
67 1 0.02
68 8 0.13
69 22 0.37
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (64 bp):
TATTTATTTTTTCAATTAAATTATATTTTAAATATTTATTGCATTAAATTGATAATCATTTAAA
Found at i:42921572 original size:32 final size:32
Alignment explanation
Indices: 42921478--42921573 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
42921468 TTTAAATTAA
*
42921478 ATTTATTGCATTAAATTGATTTATCATTTAAAT
1 ATTTATTGCTTTAAATTGA-TTATCATTTAAAT
* * *
42921511 ATTTATT-TTTTCAATTAAATTAT-ATTTTAAAT
1 ATTTATTGCTTTAAATT-GATTATCA-TTTAAAT
*
42921543 ATTTATTGCTTTAAATTGATAATCATTTAAA
1 ATTTATTGCTTTAAATTGATTATCATTTAAA
42921574 AGTTATATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 1 0.02
32 34 0.67
33 16 0.31
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (32 bp):
ATTTATTGCTTTAAATTGATTATCATTTAAAT
Found at i:42923861 original size:55 final size:54
Alignment explanation
Indices: 42923755--42923937 Score: 237
Period size: 55 Copynumber: 3.4 Consensus size: 54
42923745 GAGGTGCTAA
* * *
42923755 CCATCAGTGTCCCAGCACACAATTTTTTTTTAAAATCTGGTACAAGGGTGCTCG
1 CCATCAATGTCCCAACACCCAATTTTTTTTTAAAATCTGGTACAAGGGTGCTCG
* *
42923809 CCATCAATGTCCCAACACCCAATTTTTTTTTAAAAATATGGTACAAGGGTGCTAG
1 CCATCAATGTCCCAACACCCAATTTTTTTTT-AAAATCTGGTACAAGGGTGCTCG
* **
42923864 CCATCAATGTCCCAGCACCCAAAATTTTTTT--AATCTGGTACAAGGGTG-TCG
1 CCATCAATGTCCCAACACCCAATTTTTTTTTAAAATCTGGTACAAGGGTGCTCG
* *
42923915 ACCATTAGTGTCCCAACACCCAA
1 -CCATCAATGTCCCAACACCCAA
42923938 AAAAAATATT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
51 2 0.02
52 35 0.31
54 28 0.25
55 49 0.43
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (54 bp):
CCATCAATGTCCCAACACCCAATTTTTTTTTAAAATCTGGTACAAGGGTGCTCG
Found at i:42927491 original size:18 final size:18
Alignment explanation
Indices: 42927460--42927494 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42927450 AAGCCAGAGG
**
42927460 AGGAACATGTTTGGGTGA
1 AGGAACATCCTTGGGTGA
42927478 AGGAACATCCTTGGGTG
1 AGGAACATCCTTGGGTG
42927495 TCAGAAAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (18 bp):
AGGAACATCCTTGGGTGA
Found at i:42945083 original size:15 final size:14
Alignment explanation
Indices: 42945063--42945109 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
42945053 CATTTTTAAA
42945063 ATTTTCTATTATTTT
1 ATTTTCTATT-TTTT
*
42945078 ATTTTCTTTGTTTTT
1 ATTTTCTAT-TTTTT
42945093 AGTTTT-TATTTTTT
1 A-TTTTCTATTTTTT
42945107 ATT
1 ATT
42945110 GCATGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 6 0.21
15 15 0.54
16 5 0.18
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (14 bp):
ATTTTCTATTTTTT
Found at i:42954708 original size:6 final size:6
Alignment explanation
Indices: 42954693--42954738 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
42954683 ACAATGGAGA
*
42954693 GGGTAG GGGTAC GGGTAC GGGTAC GGGTAC GGGTAC GGGTAC GGGT
1 GGGTAC GGGTAC GGGTAC GGGTAC GGGTAC GGGTAC GGGTAC GGGT
42954739 GGGGTGGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.17
Consensus pattern (6 bp):
GGGTAC
Found at i:42958745 original size:19 final size:20
Alignment explanation
Indices: 42958721--42958766 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
42958711 TGTTATATTT
* *
42958721 TGATTAATTAAGTAAAATC-
1 TGATTAATTAAGAAAAAACA
42958740 TGATTAATTAAGAAAAAACA
1 TGATTAATTAAGAAAAAACA
42958760 TGATTAA
1 TGATTAA
42958767 ATAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (20 bp):
TGATTAATTAAGAAAAAACA
Found at i:42970199 original size:4 final size:4
Alignment explanation
Indices: 42970190--42970221 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
42970180 TTTGACTAAA
42970190 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
1 TGAT TGAT TGAT TGAT TGAT TGAT TGAT TGAT
42970222 ATTGTCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGAT
Found at i:42981535 original size:18 final size:18
Alignment explanation
Indices: 42981508--42981546 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42981498 TTGTTCCATT
*
42981508 CATGACAAGTCAACATAC
1 CATGAAAAGTCAACATAC
42981526 CATGAAAAGTCAACATAC
1 CATGAAAAGTCAACATAC
42981544 CAT
1 CAT
42981547 ATTTTACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (18 bp):
CATGAAAAGTCAACATAC
Found at i:42983207 original size:47 final size:47
Alignment explanation
Indices: 42983136--42983284 Score: 203
Period size: 47 Copynumber: 3.2 Consensus size: 47
42983126 GGAAGAAGTG
* * * *
42983136 GTTTATCTACAAAAGTGGTAGCTTGTTCACAATTTTATAAAGTCGTA
1 GTTTATCTACAAAAGTGGTGGCTTGTCCACAATTTTATTAAGTGGTA
*
42983183 GTTTATCTACAAAAGTGGTGGCTTGTCCACAAATTTATTAAGTGGTA
1 GTTTATCTACAAAAGTGGTGGCTTGTCCACAATTTTATTAAGTGGTA
**
42983230 GTTTATCTGA-AAAAGTGGTGATTTGTCCAC-ATTATTATTAAGTGGTA
1 GTTTATCT-ACAAAAGTGGTGGCTTGTCCACAATT-TTATTAAGTGGTA
42983277 GTTTATCT
1 GTTTATCT
42983285 GCATTACTGT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 2 0.02
47 89 0.97
48 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (47 bp):
GTTTATCTACAAAAGTGGTGGCTTGTCCACAATTTTATTAAGTGGTA
Found at i:42987764 original size:47 final size:47
Alignment explanation
Indices: 42987685--42987937 Score: 289
Period size: 47 Copynumber: 5.4 Consensus size: 47
42987675 TGGAGGAAGT
* * * *
42987685 AGTGGCAGTTTATCTACAAAAGTGGT-AGCTTGTCTAGAGTATTATAA
1 AGTGGCAGTTTATCTGCAAAAGTGGTGA-CTTGTCCACAATATTATAA
* *
42987732 AGTGACAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATTTTATTAA
1 AGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATATTA-TAA
* *
42987780 A-TGGCAGTTTATTTGCAAAAGTGG-GAGCTTGTCCACCATATTATAA
1 AGTGGCAGTTTATCTGCAAAAGTGGTGA-CTTGTCCACAATATTATAA
* * * * *
42987826 AGTGGCAGTTTATTTGCAAAAGTGGTGGCTTGTCCACAATTTTTTTA
1 AGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATATTATAA
* * *
42987873 AGTGGCAGTTTATTTGCAAAAGCT-GTGGCTTGTCCACAATATTATTA
1 AGTGGCAGTTTATCTGCAAAAG-TGGTGACTTGTCCACAATATTATAA
*
42987920 AGTGGTAGTTTATCTGCA
1 AGTGGCAGTTTATCTGCA
42987938 TTATTGTGAT
Statistics
Matches: 181, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
46 6 0.03
47 168 0.93
48 7 0.04
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (47 bp):
AGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATATTATAA
Found at i:42987848 original size:94 final size:94
Alignment explanation
Indices: 42987687--42987937 Score: 351
Period size: 94 Copynumber: 2.7 Consensus size: 94
42987677 GAGGAAGTAG
* * * * * * *
42987687 TGGCAGTTTATCTACAAAAGTGGTAGCTTGTCTAGAGTATTATAAAGTGACAGTTTATCTGCAAA
1 TGGCAGTTTATTTGCAAAAGTGGGAGCTTGTCCACAATATTATAAAGTGGCAGTTTATCTGCAAA
42987752 AGTGGTGACTTGTCCACAATTTTATTAAA
66 AGTGGTGACTTGTCCACAATTTTATTAAA
* *
42987781 TGGCAGTTTATTTGCAAAAGTGGGAGCTTGTCCACCATATTATAAAGTGGCAGTTTATTTGCAAA
1 TGGCAGTTTATTTGCAAAAGTGGGAGCTTGTCCACAATATTATAAAGTGGCAGTTTATCTGCAAA
* * *
42987846 AGTGGTGGCTTGTCCACAATTTTTTTAAG
66 AGTGGTGACTTGTCCACAATTTTATTAAA
* * *
42987875 TGGCAGTTTATTTGCAAAAGCTGTG-GCTTGTCCACAATATTATTAAGTGGTAGTTTATCTGCA
1 TGGCAGTTTATTTGCAAAAG-TGGGAGCTTGTCCACAATATTATAAAGTGGCAGTTTATCTGCA
42987938 TTATTGTGAT
Statistics
Matches: 139, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
94 136 0.98
95 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (94 bp):
TGGCAGTTTATTTGCAAAAGTGGGAGCTTGTCCACAATATTATAAAGTGGCAGTTTATCTGCAAA
AGTGGTGACTTGTCCACAATTTTATTAAA
Found at i:42991254 original size:7 final size:7
Alignment explanation
Indices: 42991242--42991271 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
42991232 AATACCATCA
42991242 ATATGTG
1 ATATGTG
42991249 ATATGTG
1 ATATGTG
*
42991256 ATTTGTG
1 ATATGTG
42991263 ATATGTG
1 ATATGTG
42991270 AT
1 AT
42991272 GATGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
ATATGTG
Found at i:42993062 original size:69 final size:70
Alignment explanation
Indices: 42992946--42993079 Score: 216
Period size: 69 Copynumber: 1.9 Consensus size: 70
42992936 TAGTTTATTA
* * * * *
42992946 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
42993011 CTTAG
66 CTTAG
42993016 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
42993080 TTATGTGCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 36 0.61
70 23 0.39
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:42994617 original size:47 final size:47
Alignment explanation
Indices: 42994564--42994796 Score: 322
Period size: 47 Copynumber: 5.0 Consensus size: 47
42994554 TTAGGATTTT
** *
42994564 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
42994611 ATGTGATGAATGTGAGCATTCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
42994658 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
42994705 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
42994752 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
42994797 TAGTGTGAAA
Statistics
Matches: 161, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 161 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:42994680 original size:94 final size:94
Alignment explanation
Indices: 42994564--42994796 Score: 385
Period size: 94 Copynumber: 2.5 Consensus size: 94
42994554 TTAGGATTTT
* * **
42994564 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
* *
42994629 TTCATATGTGTGATAAGGCTGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
42994658 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
42994723 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * *
42994752 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGC
42994797 TAGTGTGAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 130 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.28
Consensus pattern (94 bp):
ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
TGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:42994760 original size:25 final size:25
Alignment explanation
Indices: 42994685--42994760 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
42994675 ATGTATATAT
42994685 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
42994710 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
42994732 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
42994757 GTGA
1 GTGA
42994761 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:42995009 original size:37 final size:37
Alignment explanation
Indices: 42994959--42995064 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
42994949 GGAAATATAT
*
42994959 TCCGGGTGAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGAGTATG
* *
42994996 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGAGTATG
* * * * *
42995033 CCCAGGTAAGACCCAATAACTTCGTGTGGAGA
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGA
42995065 TTTCGTTCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGAGTATG
Found at i:42996390 original size:40 final size:40
Alignment explanation
Indices: 42996336--42996658 Score: 452
Period size: 40 Copynumber: 8.1 Consensus size: 40
42996326 AGAATTGAGA
* * *
42996336 GTGATATATCCGGGCTAAATCCCGAAGAGTATTCGTGCTA
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
42996376 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* * *
42996416 GTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGAGTTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
** * *
42996456 GTTTTATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTA
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
*
42996496 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* * *
42996536 GTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCGAGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* * **
42996576 GTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCGAACTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* *
42996616 GTG-T-TATCCGGGCTAAGTCTCGAAGAGCATTCATGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
42996654 GTGAT
1 GTGAT
42996659 GTGTATTCGG
Statistics
Matches: 256, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
38 32 0.12
39 2 0.01
40 222 0.87
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
Found at i:42996670 original size:120 final size:120
Alignment explanation
Indices: 42996340--42996656 Score: 512
Period size: 120 Copynumber: 2.7 Consensus size: 120
42996330 TTGAGAGTGA
* *
42996340 TATATCCGGGCTAAATCCCGAAGAGTATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
* * *
42996405 CATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGAGTTGGTTT
66 CATTCATGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGAGCTGGTGT
*
42996460 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
*
42996525 CATTCATGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCGAGCTGGTGT
66 CATTCATGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGAGCTGGTGT
* ** * *
42996580 TATATCCGGGCTAGGTCCCGAAGAGCATTCGAACTGGTG-T-TATCCGGGCTAAGTCTCGAAGAG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
42996643 CATTCATGCTGGTG
66 CATTCATGCTGGTG
42996657 ATGTGTATTC
Statistics
Matches: 184, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
118 36 0.20
119 1 0.01
120 147 0.80
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAG
CATTCATGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCATTCGAGCTGGTGT
Found at i:42999079 original size:69 final size:70
Alignment explanation
Indices: 42998947--42999079 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 70
42998937 TAGTTTATTA
* * * * *
42998947 CTAATTAATTTGCTGCTATAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
42999012 CTTAG
66 CTTAG
*
42999017 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
42999080 GTTATGTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 35 0.61
70 22 0.39
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:43000620 original size:47 final size:47
Alignment explanation
Indices: 43000566--43000892 Score: 465
Period size: 47 Copynumber: 7.0 Consensus size: 47
43000556 TTAGGATTTT
** * *
43000566 ATGTGATGAATGTGAATGTGTATATATGTGATACGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
43000613 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
43000660 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
43000707 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
43000754 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
43000801 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
43000848 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
43000893 TAGTGTGAAA
Statistics
Matches: 246, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 246 1.00
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:43000900 original size:94 final size:94
Alignment explanation
Indices: 43000566--43000892 Score: 573
Period size: 94 Copynumber: 3.5 Consensus size: 94
43000556 TTAGGATTTT
* * ** *
43000566 ATGTGATGAATGTGAATGTGTATATATGTGATACGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
*
43000631 TGCATATGTGTGATAAGGCTGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
43000660 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
43000725 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
43000754 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
43000819 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * *
43000848 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGC
43000893 TAGTGTGAAA
Statistics
Matches: 224, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 224 1.00
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.27
Consensus pattern (94 bp):
ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
TGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:43001161 original size:37 final size:37
Alignment explanation
Indices: 43001063--43001163 Score: 157
Period size: 37 Copynumber: 2.7 Consensus size: 37
43001053 ATTCCAGGTG
* * *
43001063 AGACCCGATGACTACGTGTGGAGAGTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTTTGCCCGGGTA
43001100 AGACCCGATGACTACGTGTGGAGATTTTGCCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTTTGCCCGGGTA
* *
43001137 AGACCCGATAACTTCGTGTGGAGATTT
1 AGACCCGATGACTACGTGTGGAGATTT
43001164 CGTCCGAGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTTTGCCCGGGTA
Found at i:43002167 original size:19 final size:19
Alignment explanation
Indices: 43002143--43002181 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43002133 AACTCATGAA
43002143 GTATGTATTTTAATCTAAG
1 GTATGTATTTTAATCTAAG
43002162 GTATGTATTTTAATCTAAG
1 GTATGTATTTTAATCTAAG
43002181 G
1 G
43002182 AATTGTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (19 bp):
GTATGTATTTTAATCTAAG
Found at i:43012923 original size:12 final size:13
Alignment explanation
Indices: 43012903--43012929 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43012893 ATGTCATACC
43012903 AAAATTTTTAATA
1 AAAATTTTTAATA
43012916 AAAATTTTTAATA
1 AAAATTTTTAATA
43012929 A
1 A
43012930 TGTTAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTTTAATA
Found at i:43013389 original size:16 final size:15
Alignment explanation
Indices: 43013358--43013398 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
43013348 CCCTATTTTT
*
43013358 AAATAATTTTAAAAA
1 AAATTATTTTAAAAA
43013373 AAATTATTTTAAAAA
1 AAATTATTTTAAAAA
43013388 AAA--ATTTTAAA
1 AAATTATTTTAAA
43013399 CCGTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 8 0.32
15 17 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATTTTAAAAA
Found at i:43014496 original size:7 final size:7
Alignment explanation
Indices: 43014484--43014516 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
43014474 TAGTCGATTG
43014484 GTATTTA
1 GTATTTA
43014491 GTATTTA
1 GTATTTA
43014498 GTATTTA
1 GTATTTA
43014505 GTATTTA
1 GTATTTA
43014512 GTATT
1 GTATT
43014517 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:43015172 original size:18 final size:18
Alignment explanation
Indices: 43015145--43015184 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43015135 CAGGTGCGTT
* *
43015145 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
43015163 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
43015181 TCCT
1 TCCT
43015185 TTTTCCGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:43015777 original size:27 final size:27
Alignment explanation
Indices: 43015736--43015787 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
43015726 ACAAAACTTA
43015736 AACCCTTAACCTAAAAACCCTAACCGT
1 AACCCTTAACCTAAAAACCCTAACCGT
*
43015763 AACCCTTAACTTAAAAACCCTAACC
1 AACCCTTAACCTAAAAACCCTAACC
43015788 CTTAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.19
Consensus pattern (27 bp):
AACCCTTAACCTAAAAACCCTAACCGT
Found at i:43015809 original size:22 final size:22
Alignment explanation
Indices: 43015734--43016423 Score: 796
Period size: 22 Copynumber: 31.8 Consensus size: 22
43015724 TGACAAAACT
*
43015734 TAAACCCTTAACCTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
43015756 TAACCGTAACCCTTAACTTAAAAACCC
1 T-A----AACCCTTAACTTAAAAACCC
* *
43015783 T-AACCCTTAAATTAAAAACCA
1 TAAACCCTTAACTTAAAAACCC
*
43015804 TAAACCCTTAACTTAAAAACCA
1 TAAACCCTTAACTTAAAAACCC
*
43015826 TAAACCCTTAACCTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
43015848 T-AACTCTTAACTTAAAAATCC
1 TAAACCCTTAACTTAAAAACCC
* *
43015869 TAAATCTTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
43015891 TAAACCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
43015913 TAAA-CCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
43015934 T-AACCTTTAACTT-AGAACCC
1 TAAACCCTTAACTTAAAAACCC
*
43015954 TAACCCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
43015976 TAAACCCTTAAATTAAAAACCT
1 TAAACCCTTAACTTAAAAACCC
43015998 TAAACCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
43016020 T-AACACTTAACTT-AAAACCC
1 TAAACCCTTAACTTAAAAACCC
* * *
43016040 TAAATCATTAACTTAAAAATCC
1 TAAACCCTTAACTTAAAAACCC
* *
43016062 T-AACCCTTAACTTAAAAATCA
1 TAAACCCTTAACTTAAAAACCC
* *
43016083 TAACCCCTTAACTTAAAAACCT
1 TAAACCCTTAACTTAAAAACCC
* *
43016105 TAAACCCTTAAATTAAAAACCA
1 TAAACCCTTAACTTAAAAACCC
*
43016127 TAAACCCTTAACTTAAAAAGCC
1 TAAACCCTTAACTTAAAAACCC
* *
43016149 TAAACTCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCC
**
43016171 TAAACAATTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* * *
43016193 TAACCCCTTAACTTTAAAACCT
1 TAAACCCTTAACTTAAAAACCC
*
43016215 TAAACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
43016237 TAAACCCTTAAATTAAAAATCC
1 TAAACCCTTAACTTAAAAACCC
*
43016259 TAAACCCTTAACTTAAAAAACC
1 TAAACCCTTAACTTAAAAACCC
**
43016281 T-AACCCTTAACTTTCAAACCC
1 TAAACCCTTAACTTAAAAACCC
***
43016302 TAAACCCTTAACTTAAAAATTG
1 TAAACCCTTAACTTAAAAACCC
*
43016324 T-AACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* * * *
43016345 TAAACTCTTAACTT-TAAATCG
1 TAAACCCTTAACTTAAAAACCC
* *
43016366 T-AACCCTTAAATAAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
43016387 T-AACACTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
43016408 T-AACCCTTAACTTAAA
1 TAAACCCTTAACTTAAA
43016424 TATAATTTGA
Statistics
Matches: 565, Mismatches: 87, Indels: 33
0.82 0.13 0.05
Matches are distributed among these distances:
20 26 0.05
21 188 0.33
22 330 0.58
23 1 0.00
27 20 0.04
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (22 bp):
TAAACCCTTAACTTAAAAACCC
Found at i:43020027 original size:127 final size:124
Alignment explanation
Indices: 43019620--43020161 Score: 692
Period size: 126 Copynumber: 4.3 Consensus size: 124
43019610 TGTCCATGTG
* * *
43019620 GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAGCG-ATTTTATACTATTTGCTC
1 GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCTC
* * * *
43019684 AAAAACGTCAAGTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAAGTGCTTCCACGA
66 AGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCATCCACGA
* *
43019743 GGACGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTGCAGCGTTTTTTTATACTATTTG
1 GG-CGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTGAAGCG-TTTTTTAAACTATTTG
* * * * * *
43019807 CTTAGAAACGTCAACTCGAAATTATTTTTTCAGGACCTACTGTAGCAAAAGCACGTCCACGTG
63 CTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCATCCACG-A
* * *
43019870 GGCACGATTTTACAAATTCTTCTCATAAAGCATCTTGCTTGAAGCGTTTTTTTAAACTATTTGCT
1 GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCG-TTTTTTAAACTATTTGCT
*
43019935 CAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCATCCACGA
65 CAGAAACGTCAACTCAAAATTATTT-TTCCAGGACCTACTGTAGCAAAAGCGCATCCACGA
* * *
43019996 CGGCGCTATTTCACAAATTATTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTAAACTATTTACT
1 -GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCT
* * * * * *
43020061 CAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTTTAGCAAAAGTGCGTACACGTG
65 CAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCATCCACG-A
* * * * * *
43020122 GGCGTGACTTCAAAAATCCTTCTGATAAATCATCCTGCTT
1 GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
43020162 TGATTTTATC
Statistics
Matches: 365, Mismatches: 45, Indels: 16
0.86 0.11 0.04
Matches are distributed among these distances:
123 4 0.01
124 39 0.11
125 61 0.17
126 186 0.51
127 75 0.21
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (124 bp):
GGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGTTTTTTAAACTATTTGCTC
AGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCATCCACGA
Found at i:43020079 original size:252 final size:250
Alignment explanation
Indices: 43019594--43020160 Score: 780
Period size: 252 Copynumber: 2.3 Consensus size: 250
43019584 CCAAACATGA
* * * *
43019594 TACTGTAGCAAAAACGTGTCCATGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* * *
43019659 AGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAGTCAAAATTATTTTTCCAGGACCTACTGT
66 AGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTGT
* * * *
43019724 AGCAAAAGTGCTTCCACGAGGACGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAGC
131 AGCAAAAGCGCATCCACGAGGACGCGATTTCACAAATTATTCTCAAATAGCATCCTGCTTGAAGC
* * * *
43019789 GTTTTTTTATACTATTTGCTTAGAAACGTCAACTCGAAATTATTTTTTCAGGACC
196 GTTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACC
* * *
43019844 TACTGTAGCAAAAGCACGTCCACGTGGGCACGATTTTACAAATTCTTCTCATAAAGCATCTTGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* * *
43019909 TGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAAC
66 AGAAGCG--ATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGACCAAC
*
43019974 TGTAGCAAAAGCGCATCCACGACGG-CGCTATTTCACAAATTATTCTCATAA-AGCATCCTGCTT
128 TGTAGCAAAAGCGCATCCACGA-GGACGCGATTTCACAAATTATTCTCA-AATAGCATCCTGCTT
43020037 GAAGCG-TTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACC
191 GAAGCGTTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACC
* * * ** * * * * *
43020096 TACTTTAGCAAAAGTGCGTACACGTGGGCGTGACTTCAAAAATCCTTCTGATAAATCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
43020161 TTGATTTTAT
Statistics
Matches: 277, Mismatches: 35, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
250 64 0.23
252 139 0.50
253 70 0.25
254 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (250 bp):
TACTGTAGCAAAAGCGCGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
AGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTGT
AGCAAAAGCGCATCCACGAGGACGCGATTTCACAAATTATTCTCAAATAGCATCCTGCTTGAAGC
GTTTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACC
Found at i:43020291 original size:9 final size:9
Alignment explanation
Indices: 43020277--43020314 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
43020267 TTTTTTCTCC
43020277 AAAAATCCT
1 AAAAATCCT
43020286 AAAAATCCT
1 AAAAATCCT
43020295 AAAAA-CTCT
1 AAAAATC-CT
43020304 AAAAATCCT
1 AAAAATCCT
43020313 AA
1 AA
43020315 CCTGGGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 1 0.04
9 25 0.93
10 1 0.04
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATCCT
Found at i:43021713 original size:15 final size:15
Alignment explanation
Indices: 43021693--43021721 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43021683 CAAGATTGTA
43021693 GCTTTAAATTGAATC
1 GCTTTAAATTGAATC
43021708 GCTTTAAATTGAAT
1 GCTTTAAATTGAAT
43021722 TGAGTTGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (15 bp):
GCTTTAAATTGAATC
Found at i:43026284 original size:19 final size:19
Alignment explanation
Indices: 43026260--43026299 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43026250 TGAGATTCAG
* *
43026260 ATATATTTTTTTTGATGGA
1 ATATATATTTTTTAATGGA
43026279 ATATATATTTTTTAATGGA
1 ATATATATTTTTTAATGGA
43026298 AT
1 AT
43026300 TTTATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
ATATATATTTTTTAATGGA
Found at i:43030268 original size:3 final size:3
Alignment explanation
Indices: 43030262--43030292 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
43030252 CAACCACAAC
43030262 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
43030293 CGATGATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:43031477 original size:17 final size:18
Alignment explanation
Indices: 43031455--43031488 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43031445 TCATTCGATT
*
43031455 ACAGATCAAAA-TCATAG
1 ACAGATAAAAATTCATAG
43031472 ACAGATAAAAATTCATA
1 ACAGATAAAAATTCATA
43031489 CTGTAGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.21
Consensus pattern (18 bp):
ACAGATAAAAATTCATAG
Found at i:43033249 original size:20 final size:21
Alignment explanation
Indices: 43033201--43033250 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
43033191 GACAATGGGA
43033201 CTATGTCTCAAGACATTAACCC
1 CTATGTCTCAAGACA-TAACCC
*
43033223 CTATGTCTCAAGACA-AAGCC
1 CTATGTCTCAAGACATAACCC
*
43033243 TTATGTCT
1 CTATGTCT
43033251 TTGAAACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 11 0.42
22 15 0.58
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (21 bp):
CTATGTCTCAAGACATAACCC
Found at i:43058412 original size:24 final size:24
Alignment explanation
Indices: 43058380--43058430 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
43058370 CTGGTTAAGG
*
43058380 TTCATTGTCCGCTTTTAGGGATCT
1 TTCATTGTCCGCTTCTAGGGATCT
43058404 TTCATTGTCCGCTTCTAGGGATCT
1 TTCATTGTCCGCTTCTAGGGATCT
43058428 TTC
1 TTC
43058431 TTGAATACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (24 bp):
TTCATTGTCCGCTTCTAGGGATCT
Found at i:43061009 original size:12 final size:12
Alignment explanation
Indices: 43060984--43061024 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
43060974 AGAAAAAGGA
*
43060984 AAAACAAAAGACT
1 AAAACTAAA-ACT
43060997 AAAACTAAAACT
1 AAAACTAAAACT
43061009 AAAACTAAAACT
1 AAAACTAAAACT
43061021 AAAA
1 AAAA
43061025 AGAAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.71, C:0.15, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAACTAAAACT
Found at i:43061017 original size:18 final size:19
Alignment explanation
Indices: 43060984--43061024 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
43060974 AGAAAAAGGA
43060984 AAAACAAAAGACTAAAACT
1 AAAACAAAAGACTAAAACT
*
43061003 AAAACTAAA-ACTAAAACT
1 AAAACAAAAGACTAAAACT
43061021 AAAA
1 AAAA
43061025 AGAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.71, C:0.15, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAACAAAAGACTAAAACT
Found at i:43061030 original size:18 final size:18
Alignment explanation
Indices: 43060994--43061030 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43060984 AAAACAAAAG
**
43060994 ACTAAAACTAAAACTAAA
1 ACTAAAACTAAAAAGAAA
43061012 ACTAAAACTAAAAAGAAA
1 ACTAAAACTAAAAAGAAA
43061030 A
1 A
43061031 TTATACAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.14, G:0.03, T:0.14
Consensus pattern (18 bp):
ACTAAAACTAAAAAGAAA
Found at i:43065652 original size:53 final size:52
Alignment explanation
Indices: 43065594--43065744 Score: 116
Period size: 53 Copynumber: 3.1 Consensus size: 52
43065584 TTACATAAGC
*
43065594 AATGAATGCTTAGTAAGCTCGTATAAACGTAAAACATAATATTTCATTTTAAT
1 AATGAATGCTTAGTAAGCTCGTATAAAC-TAAAACATAATATTACATTTTAAT
* * *
43065647 AATGAA--CTTTA-TAAG---G--TAAA-TATAA-GT-A-ATTACA--TAAGA-
1 AATGAATGC-TTAGTAAGCTCGTATAAACTAAAACATAATATTACATTTTA-AT
*
43065686 AATGAATGCTTAGTAAGCTCGTATAAACTTAAAACATAATATTCCATTTTAAT
1 AATGAATGCTTAGTAAGCTCGTATAAAC-TAAAACATAATATTACATTTTAAT
43065739 AATGAA
1 AATGAA
43065745 CTTTATAAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 36
0.62 0.07 0.31
Matches are distributed among these distances:
39 8 0.11
40 4 0.06
41 10 0.14
42 1 0.01
43 1 0.01
44 5 0.07
46 8 0.11
48 5 0.07
49 1 0.01
50 1 0.01
51 10 0.14
52 4 0.06
53 14 0.19
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (52 bp):
AATGAATGCTTAGTAAGCTCGTATAAACTAAAACATAATATTACATTTTAAT
Found at i:43065721 original size:92 final size:92
Alignment explanation
Indices: 43065578--43065763 Score: 345
Period size: 92 Copynumber: 2.0 Consensus size: 92
43065568 AAGTAAAAGA
* *
43065578 AAGTAATTACATAAGCAATGAATGCTTAGTAAGCTCGTATAAACGTAAAACATAATATTTCATTT
1 AAGTAATTACATAAGAAATGAATGCTTAGTAAGCTCGTATAAACGTAAAACATAATATTCCATTT
43065643 TAATAATGAACTTTATAAGGTAAATAT
66 TAATAATGAACTTTATAAGGTAAATAT
*
43065670 AAGTAATTACATAAGAAATGAATGCTTAGTAAGCTCGTATAAACTTAAAACATAATATTCCATTT
1 AAGTAATTACATAAGAAATGAATGCTTAGTAAGCTCGTATAAACGTAAAACATAATATTCCATTT
43065735 TAATAATGAACTTTATAAGGTAAATAT
66 TAATAATGAACTTTATAAGGTAAATAT
43065762 AA
1 AA
43065764 ACCTATACCA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (92 bp):
AAGTAATTACATAAGAAATGAATGCTTAGTAAGCTCGTATAAACGTAAAACATAATATTCCATTT
TAATAATGAACTTTATAAGGTAAATAT
Found at i:43066499 original size:6 final size:6
Alignment explanation
Indices: 43066490--43066515 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43066480 AACCATAACC
43066490 TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TT
43066516 ACATCGTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:43075256 original size:22 final size:22
Alignment explanation
Indices: 43075231--43075284 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
43075221 ACATTTAGGG
43075231 CTTAATGTCGTGACACAAGACA
1 CTTAATGTCGTGACACAAGACA
43075253 CTTAATGTCGTGACACAAGACA
1 CTTAATGTCGTGACACAAGACA
*
43075275 CTTAGTGTCG
1 CTTAATGTCG
43075285 CGACTTCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (22 bp):
CTTAATGTCGTGACACAAGACA
Found at i:43076227 original size:18 final size:18
Alignment explanation
Indices: 43076206--43076243 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43076196 CCAAATATAC
43076206 ATTCTAAATCAATCATCA
1 ATTCTAAATCAATCATCA
43076224 ATTCTAAATCAATCATCA
1 ATTCTAAATCAATCATCA
43076242 AT
1 AT
43076244 ATACCTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTCTAAATCAATCATCA
Found at i:43080040 original size:19 final size:19
Alignment explanation
Indices: 43080016--43080071 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
43080006 GTAGTAGAAA
43080016 TTTATTTTCTAGAATAAAT
1 TTTATTTTCTAGAATAAAT
*
43080035 TTTATTTTCTGGAATAAAT
1 TTTATTTTCTAGAATAAAT
*
43080054 TCTATTTTCTATGAATAA
1 TTTATTTTCTA-GAATAA
43080072 CAATTTTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTATTTTCTAGAATAAAT
Found at i:43083674 original size:22 final size:22
Alignment explanation
Indices: 43083631--43083675 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43083621 ATATTTTTGC
* ***
43083631 ATACTAATAAATTTTGTTATAT
1 ATACTAATAAAATTTAAAATAT
43083653 ATACTAATAAAATTTAAAATAT
1 ATACTAATAAAATTTAAAATAT
43083675 A
1 A
43083676 AAGGACCACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
ATACTAATAAAATTTAAAATAT
Found at i:43090538 original size:21 final size:20
Alignment explanation
Indices: 43090498--43090546 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
43090488 AATTTCAATG
*
43090498 TCAAGGAAGGAACAAGATGA
1 TCAAGCAAGGAACAAGATGA
43090518 CTCAAGCAA-GAACAAGAATGA
1 -TCAAGCAAGGAACAAG-ATGA
*
43090539 TGAAGCAA
1 TCAAGCAA
43090547 AAGATAGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.51, C:0.14, G:0.24, T:0.10
Consensus pattern (20 bp):
TCAAGCAAGGAACAAGATGA
Found at i:43099069 original size:9 final size:10
Alignment explanation
Indices: 43099058--43099119 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
43099048 GGTATAAATA
43099058 AATAAATAA-
1 AATAAATAAT
*
43099067 AATGCAATAAT
1 AAT-AAATAAT
43099078 AATAATGATAAT
1 AATAA--ATAAT
43099090 AAT-AATAAT
1 AATAAATAAT
43099099 AATAAATTCAAT
1 AATAAA-T-AAT
43099111 AATAAATAA
1 AATAAATAA
43099120 AATGACAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 11 0.25
10 10 0.23
11 6 0.14
12 17 0.39
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:43099115 original size:3 final size:3
Alignment explanation
Indices: 43099072--43099103 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
43099062 AATAAAATGC
*
43099072 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43099104 ATTCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43100693 original size:175 final size:170
Alignment explanation
Indices: 43100389--43100794 Score: 573
Period size: 175 Copynumber: 2.4 Consensus size: 170
43100379 TGCAGCAACT
*
43100389 TCAGGGAGATAGGATTA-TCGGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATAAGATCTAAA
1 TCAGGGAGATAGGATTACT-GGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTAAA
*
43100453 ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACACGATTTACTCTGCTGTAA
65 ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACACGATTTACTCTACTGTAA
* *
43100518 CTTTAGAGAGATAAGATCCTTCGTTTTAATCCGTTCCACTGTAATC
130 CTTCAGAGAGATAAGAT-C--C--TTTAATCCGCTCCACTGTAATC
* * *
43100564 TCAGGGAGATAGGATTACTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAA
1 TCAGGGAGATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTAAAA
** ***
43100629 TTCTTTGGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGATGTGATCTT-CTCTACTGTAA
66 TTCTTCAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACACGAT-TTACTCTACTGTAA
*
43100693 CTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATC
130 CTTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATC
* ** **
43100734 TCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 TCAGGGAGATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
43100795 CTGGCTTCAA
Statistics
Matches: 209, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
170 74 0.35
172 1 0.00
174 1 0.00
175 130 0.62
176 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (170 bp):
TCAGGGAGATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTAAAA
TTCTTCAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACACGATTTACTCTACTGTAAC
TTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATC
Found at i:43100838 original size:44 final size:43
Alignment explanation
Indices: 43100389--43100838 Score: 201
Period size: 44 Copynumber: 10.4 Consensus size: 43
43100379 TGCAGCAACT
* * * * *
43100389 TCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCGCTATAATC
1 TCAGGGAGATAAGA-TCTCTGCTTCAATCTGCTCCACTGTAATC
* * * **
43100433 TCAGGGAGATAAGATCTAAAATTCTTCAGTCTATTCCACTGTAATC
1 TCAGGGAGATAAGATCT---CTGCTTCAATCTGCTCCACTGTAATC
* * * * * **
43100479 TCAGGGAAATAAGA-C-CTGAC-ACGATTTACTCTGCTGTAA-C
1 TCAGGGAGATAAGATCTCTG-CTTCAATCTGCTCCACTGTAATC
* * * * * *
43100519 TTTAGAGAGATAAGATC-CTTCGTTTTAATCCGTTCCACTGTAATC
1 -TCAGGGAGATAAGATCTC-T-GCTTCAATCTGCTCCACTGTAATC
* *
43100564 TCAGGGAGATAGGAT-TACTGGCTTCAATCTGCTCCACTGTAACC
1 TCAGGGAGATAAGATCT-CT-GCTTCAATCTGCTCCACTGTAATC
* * *** **
43100608 TCAGGGAGATAAGATCTGAAATTCTTTGGTCTATTCCACTGTAATC
1 TCAGGGAGATAAGATCT---CTGCTTCAATCTGCTCCACTGTAATC
* * * * *
43100654 TCAGGGAAATAAGA-C-CTGATGT-GATCTTCTCTACTGTAA-C
1 TCAGGGAGATAAGATCTCTGCT-TCAATCTGCTCCACTGTAATC
* * *
43100694 TTCAGAGAGATAAGATC-CT--TT-AATCCGCTCCATTGTAATC
1 -TCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCACTGTAATC
* * * ** *
43100734 TCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCGCTGTAATC
1 TCAGGGAGATAAGATCT-CT-GCTTCAATCTGCTCCACTGTAATC
* *
43100778 TCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACC
1 TCAGGGAGATAAGATCTCT-GCTTCAATCTGCTCCACTGTAATC
43100822 TCAGGGAGATAAGATCT
1 TCAGGGAGATAAGATCT
43100839 GAAATTCTTT
Statistics
Matches: 300, Mismatches: 80, Indels: 52
0.69 0.19 0.12
Matches are distributed among these distances:
39 25 0.08
40 6 0.02
41 51 0.17
42 7 0.02
43 5 0.02
44 137 0.46
45 6 0.02
46 61 0.20
47 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
TCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCACTGTAATC
Found at i:43100877 original size:45 final size:44
Alignment explanation
Indices: 43100556--43100880 Score: 185
Period size: 44 Copynumber: 7.5 Consensus size: 44
43100546 ATCCGTTCCA
* * ** *
43100556 CTGTAATCTCAGGGAGATAGGAT-TACTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTA-TGTCTTTGATCTGCTCCG
* * ** *
43100600 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTTGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---ATGTCTTTGATCTGCTCCG
* * * **
43100646 CTGTAATCTCAGGGAAATAAGACCTGATG----TGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCT-ATGTCTTTGATCTGCTCCG
* * * *
43100687 CTGTAA-CTTCAGAGAGATAAGATC-----CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCG
* * * *
43100726 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTA-TGTCTTTGATCTGCTCCG
* * **
43100770 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCG
* * *
43100814 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTTGGTCTGTTCC-
1 CTGTAATCTCAGGGAGATAAGATCT---ATGTCTTTGATCTGCTCCG
43100859 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
43100881 CCTGTATAAT
Statistics
Matches: 215, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
39 25 0.12
40 2 0.01
41 27 0.13
44 93 0.43
45 23 0.11
46 42 0.20
47 2 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTGCTCCG
Found at i:43113484 original size:9 final size:10
Alignment explanation
Indices: 43113473--43113534 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
43113463 GGTATAAATA
43113473 AATAAATAA-
1 AATAAATAAT
*
43113482 AATGCAATAAT
1 AAT-AAATAAT
43113493 AATAATGATAAT
1 AATAA--ATAAT
43113505 AAT-AATAAT
1 AATAAATAAT
43113514 AATAAATTCAAT
1 AATAAA-T-AAT
43113526 AATAAATAA
1 AATAAATAA
43113535 AATGACAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 11 0.25
10 10 0.23
11 6 0.14
12 17 0.39
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:43113530 original size:3 final size:3
Alignment explanation
Indices: 43113487--43113518 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
43113477 AATAAAATGC
*
43113487 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43113519 ATTCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43115519 original size:27 final size:27
Alignment explanation
Indices: 43115488--43115665 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43115478 TAAATTGTAC
43115488 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43115515 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43115541 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43115569 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43115597 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43115624 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43115651 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43115666 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43115602 original size:82 final size:81
Alignment explanation
Indices: 43115489--43115644 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43115479 AAATTGTACA
* *
43115489 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43115553 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43115570 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43115635 TGCGAGTTGA
65 TGCGAATTGA
43115645 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43115656 original size:82 final size:81
Alignment explanation
Indices: 43115485--43115665 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43115475 GATTAAATTG
* *
43115485 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43115550 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43115566 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43115630 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43115648 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43115666 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43124015 original size:17 final size:17
Alignment explanation
Indices: 43123993--43124035 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
43123983 TTCTAATTAA
43123993 TTTATATATTTTAAAAT
1 TTTATATATTTTAAAAT
* *
43124010 TTTATAAATTTTTAAAT
1 TTTATATATTTTAAAAT
43124027 TTTATATAT
1 TTTATATAT
43124036 GCCGCGTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTTTAAAAT
Found at i:43124018 original size:9 final size:9
Alignment explanation
Indices: 43123993--43124032 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
43123983 TTCTAATTAA
*
43123993 TTTATATAT
1 TTTATAAAT
43124002 TTTA-AAAT
1 TTTATAAAT
43124010 TTTATAAAT
1 TTTATAAAT
43124019 TTT-TAAAT
1 TTTATAAAT
43124027 TTTATA
1 TTTATA
43124033 TATGCCGCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTATAAAT
Found at i:43124693 original size:114 final size:112
Alignment explanation
Indices: 43124492--43124769 Score: 468
Period size: 113 Copynumber: 2.5 Consensus size: 112
43124482 AAAAAAAATT
* * * *
43124492 AAAAAAATTTTGGGTGATGGCCTGTCAATGGCCGACACCCAATATACAGTACAAAAAAAATTTAT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAATTTAT
43124557 TTTTTTTCATGTCAGAATCAGATATAAAAATACGAAAAAAATTTTAAA
66 TTTTTTTCATGTCAGAATCAGATATAAAAATACGAAAAAAATTTT-AA
*
43124605 AAAAAAATTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAATTTTA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAA-TTTA
*
43124670 TTTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTTTAA
65 TTTTTTTTCATGTCAGAATCAGATATAAAAATACGAAAAAAATTTTAA
*
43124718 AAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACATTACA
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
43124770 TTTTTTTCGT
Statistics
Matches: 156, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
112 43 0.28
113 64 0.41
114 49 0.31
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (112 bp):
AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAATTTAT
TTTTTTTCATGTCAGAATCAGATATAAAAATACGAAAAAAATTTTAA
Found at i:43124991 original size:113 final size:113
Alignment explanation
Indices: 43124769--43124982 Score: 376
Period size: 113 Copynumber: 1.9 Consensus size: 113
43124759 TACACATTAC
43124769 ATTTTTTTCGTATTTTTAAATCTGATTCTGACACGAAAAAAATAAAAATAAAATTTGTACTCTGT
1 ATTTTTTTCGTATTTTTAAATCTGATTCTGACACGAAAAAAATAAAAATAAAATTTGTACTCTGT
43124834 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTAAA
66 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTAAA
* ** *
43124882 ATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAA-AATTTTTGTACTGTG
1 ATTTTTTTCGTATTTTTAAATCTGATTCTGACACG-AAAAAAATAAAAATAAAATTTGTACTCTG
43124946 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
65 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
43124983 TTTTTTTTTT
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 83 0.86
114 13 0.14
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (113 bp):
ATTTTTTTCGTATTTTTAAATCTGATTCTGACACGAAAAAAATAAAAATAAAATTTGTACTCTGT
ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTAAA
Found at i:43125752 original size:19 final size:20
Alignment explanation
Indices: 43125716--43125753 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43125706 TATTTTTTTA
* *
43125716 AATTTAAAATCATTAAAATT
1 AATTAAAAATCATAAAAATT
43125736 AATTAAAAAT-ATAAAAAT
1 AATTAAAAATCATAAAAAT
43125754 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTAAAAATCATAAAAATT
Found at i:43127672 original size:60 final size:59
Alignment explanation
Indices: 43127633--43127765 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 59
43127623 AATGTATTTT
* * *
43127633 TTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAA
1 TTTTTG-TGTTTATAATTATTTTAAAATTAATTTATTAGT-ATTTAGGATAATGTTATAAA
*
43127694 TTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAA-GTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGT-ATTTAGGA-TAATGTTATAAA
*
43127754 TTATTGTGTTTA
1 TTTTTGTGTTTA
43127766 ATTTAGTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 57 0.88
61 8 0.12
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (59 bp):
TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTATTTAGGATAATGTTATAAA
Found at i:43127910 original size:39 final size:39
Alignment explanation
Indices: 43127845--43128011 Score: 234
Period size: 39 Copynumber: 4.4 Consensus size: 39
43127835 CATAACTAGC
* * *
43127845 TTTTTTA-ATC-ATATAATTGCTATTAACTCATTTAATT
1 TTTTTTATATCAACATAGTTGCTGTTAACTCATTTAATT
43127882 TTTTTTATATCAACATAGTTGCTGTTAACTCATTT-ATT
1 TTTTTTATATCAACATAGTTGCTGTTAACTCATTTAATT
* *
43127920 TATTTTTATATCAACATAGTTGTTGTTAACTCATTTAAAT
1 T-TTTTTATATCAACATAGTTGCTGTTAACTCATTTAATT
* *
43127960 TTTTTTATATCAATATAGTTGCTGTTAACTTATTTAA-T
1 TTTTTTATATCAACATAGTTGCTGTTAACTCATTTAATT
43127998 TTTTTTATATCAAC
1 TTTTTTATATCAAC
43128012 TTGGATATCA
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
37 7 0.06
38 21 0.18
39 86 0.74
40 3 0.03
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (39 bp):
TTTTTTATATCAACATAGTTGCTGTTAACTCATTTAATT
Found at i:43128309 original size:15 final size:15
Alignment explanation
Indices: 43128289--43128328 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
43128279 GGGATATTGA
*
43128289 TAATTTTATATAATG
1 TAATTTTATAAAATG
43128304 TAATTTTTATAAAATG
1 TAA-TTTTATAAAATG
43128320 TAATTTTAT
1 TAATTTTAT
43128329 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
TAATTTTATAAAATG
Found at i:43128530 original size:52 final size:51
Alignment explanation
Indices: 43128467--43128576 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 51
43128457 TTATTAAACG
43128467 AAAAAAATTTAATATAAAAAATTAATTCGCGCCTGTCAAATA-AACGCAATT
1 AAAAAAATTTAATATAAAAAATTAATTCGCGCCTGTCAAATAGAA-GCAATT
* * *
43128518 AAAAAAATTTTAATATAAAAAATTAATTTGCGCCTGTCAGATAGAAGCGATT
1 AAAAAAA-TTTAATATAAAAAATTAATTCGCGCCTGTCAAATAGAAGCAATT
43128570 AAAAAAA
1 AAAAAAA
43128577 ACATACTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
51 7 0.13
52 45 0.83
53 2 0.04
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (51 bp):
AAAAAAATTTAATATAAAAAATTAATTCGCGCCTGTCAAATAGAAGCAATT
Found at i:43131323 original size:44 final size:44
Alignment explanation
Indices: 43131260--43131350 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
43131250 AACTTTATTT
* *
43131260 TTAGTTTACCACTTAAACTCTGATTATTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
* *
43131304 TTAGTTTCCCATTTAAACTCTAATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
43131348 TTA
1 TTA
43131351 TTTGACCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
Found at i:43134136 original size:3 final size:3
Alignment explanation
Indices: 43134128--43134168 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
43134118 TAATTCCCAC
* *
43134128 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
43134169 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:43135254 original size:9 final size:9
Alignment explanation
Indices: 43135240--43135289 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
43135230 CATTTGAATA
43135240 AATAATTAT
1 AATAATTAT
43135249 AATAATTAT
1 AATAATTAT
43135258 AATAATTAT
1 AATAATTAT
43135267 -ATACA-TAT
1 AATA-ATTAT
*
43135275 AATATTTAT
1 AATAATTAT
43135284 ATATAA
1 A-ATAA
43135290 CTTAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 6 0.17
9 26 0.74
10 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:43137105 original size:20 final size:21
Alignment explanation
Indices: 43137054--43137106 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 21
43137044 AAATCATTGC
43137054 AATATATGTAAAAA-TAATTT
1 AATATATGTAAAAATTAATTT
* *
43137074 AA-A-ATATAAAAATTTA-TT
1 AATATATGTAAAAATTAATTT
43137092 AATATATGTAAAAAT
1 AATATATGTAAAAAT
43137107 AACTTTTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.44
19 4 0.15
20 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AATATATGTAAAAATTAATTT
Found at i:43137220 original size:20 final size:20
Alignment explanation
Indices: 43137195--43137234 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43137185 AATATTTTCT
*
43137195 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43137215 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43137235 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43137237 original size:34 final size:35
Alignment explanation
Indices: 43137183--43137249 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43137173 CAAACACCAG
* *
43137183 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43137218 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43137250 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43139651 original size:29 final size:29
Alignment explanation
Indices: 43139615--43139674 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
43139605 TAATAATATT
43139615 TTAATATTAAATTTAATTTAAT-ACTTATC
1 TTAATATTAAATTTAATTTAATGA-TTATC
43139644 TTAATATTAAATTTAATTTAATGATTATC
1 TTAATATTAAATTTAATTTAATGATTATC
43139673 TT
1 TT
43139675 GTAGATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAATATTAAATTTAATTTAATGATTATC
Found at i:43141744 original size:19 final size:20
Alignment explanation
Indices: 43141691--43141745 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
43141681 ATTTTGGAAA
*
43141691 TTTTAAATTTTTTTTGAATT
1 TTTTAAAATTTTTTTGAATT
* * *
43141711 TTTAAAAATTATTTT-ATTT
1 TTTTAAAATTTTTTTGAATT
43141730 TTTTAAAATTTTTTTG
1 TTTTAAAATTTTTTTG
43141746 TGAGAGAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTAAAATTTTTTTGAATT
Found at i:43151028 original size:15 final size:14
Alignment explanation
Indices: 43150995--43151040 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
43150985 TAATTAATAA
43150995 TATAT-TTTTTAAT
1 TATATCTTTTTAAT
43151008 TA-ATCTTTTTAAT
1 TATATCTTTTTAAT
*
43151021 TAATATCTCTTTTATT
1 T-ATATCT-TTTTAAT
43151037 TATA
1 TATA
43151041 AAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 11 0.39
14 1 0.04
15 7 0.25
16 7 0.25
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATCTTTTTAAT
Found at i:43151831 original size:60 final size:61
Alignment explanation
Indices: 43151721--43151908 Score: 204
Period size: 61 Copynumber: 3.1 Consensus size: 61
43151711 TTAATATAAC
* ** *
43151721 ATTTGATACTTGAACTTGAC-ACTTTTTCCTAAATTAGTACCTAAACCTTTTTTT-GGCTCA
1 ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAA-CTTTTTTTAGGCTCA
* * * *
43151781 ATTTGGTACTTGAAATTGACTTTTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAACTTTTTTTAGGCTCA
* * * * *
43151842 ATTTGGTACTTGAACTTGAAATTTTTTTT-CT-ACTTGGCACCTAAGCTTTTTTTTAGGTTCA
1 ATTTGGTACTTGAACTTG-ACTTTTTTTTCCTAAATTGGTACCTAAAC-TTTTTTTAGGCTCA
43151903 ATTTGG
1 ATTTGG
43151909 CACCTAAAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
60 38 0.35
61 62 0.57
62 9 0.08
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (61 bp):
ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAACTTTTTTTAGGCTCA
Found at i:43151844 original size:61 final size:60
Alignment explanation
Indices: 43151721--43151894 Score: 201
Period size: 60 Copynumber: 2.9 Consensus size: 60
43151711 TTAATATAAC
* ** * *
43151721 ATTTGATACTTGAACTTGAC-ACTTTTTCCTAAATTAGTACCTAAACCTTTTTTTGGCTCA
1 ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAA-CTTTTTTTGGCCCA
* *
43151781 ATTTGGTACTTGAAATTGACTTTTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAACTTTTTTT-GGCCCA
* * * *
43151842 ATTTGGTACTTGAACTTGAAATTTTTTTT-CT-ACTTGGCACCTAAGCTTTTTTT
1 ATTTGGTACTTGAACTTG-ACTTTTTTTTCCTAAATTGGTACCTAAACTTTTTTT
43151895 TAGGTTCAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 45 0.45
61 45 0.45
62 9 0.09
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (60 bp):
ATTTGGTACTTGAACTTGACTTTTTTTTCCTAAATTGGTACCTAAACTTTTTTTGGCCCA
Found at i:43151857 original size:29 final size:28
Alignment explanation
Indices: 43151767--43151858 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
43151757 GTACCTAAAC
*
43151767 CTTTTTTTGGCTCAATTTGGTACTTGAAATTGA
1 CTTTTTTTGGCCCAATTTGGTACTTG--A---A
* * * *
43151800 CTTTTTTT-TCCTAATTTGGTACCTAAA
1 CTTTTTTTGGCCCAATTTGGTACTTGAA
43151827 CTTTTTTTGGGCCCAATTTGGTACTTGAA
1 CTTTTTTT-GGCCCAATTTGGTACTTGAA
43151856 CTT
1 CTT
43151859 GAAATTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 9 0.19
29 18 0.38
30 1 0.02
32 12 0.25
33 8 0.17
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (28 bp):
CTTTTTTTGGCCCAATTTGGTACTTGAA
Found at i:43152316 original size:60 final size:60
Alignment explanation
Indices: 43152252--43152383 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
43152242 AAACATTTGA
** * *
43152252 CAAGTACCAAATCGAACAAAAAAAAAGATTAGGTACCAAATTAGGAAAAAGAGTTAAGTT
1 CAAGTACCAAATCGAACAAAAAAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTT
* **** * *
43152312 CAAGTACCAAATTGAACTCCCAAAAAGATTAAATACCAACTTAAGAAAAAGTGTCAAGTT
1 CAAGTACCAAATCGAACAAAAAAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTT
* *
43152372 TAGGTACCAAAT
1 CAAGTACCAAAT
43152384 TGGACCAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.20
Consensus pattern (60 bp):
CAAGTACCAAATCGAACAAAAAAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTT
Found at i:43152384 original size:60 final size:60
Alignment explanation
Indices: 43152273--43152385 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
43152263 TCGAACAAAA
** * *
43152273 AAAAAGATTAGGTACCAAATTAGGAAAAAGAGTTAAGTTCAAGTACCAAATTGAACTCCC
1 AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACTCCC
* * * *
43152333 AAAAAGATTAAATACCAACTTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTG
1 AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTG
43152386 GACCAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (60 bp):
AAAAAGATTAAATACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACTCCC
Found at i:43152972 original size:17 final size:17
Alignment explanation
Indices: 43152928--43152977 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
43152918 AATTATTTGA
43152928 TATTAATTAAAAATGAAT
1 TATTAATTAAAAAT-AAT
* * *
43152946 TA-AAAATAAAAATATT
1 TATTAATTAAAAATAAT
43152962 TATTAATTAAAAATAA
1 TATTAATTAAAAATAA
43152978 AAAAACTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TATTAATTAAAAATAAT
Found at i:43158845 original size:13 final size:13
Alignment explanation
Indices: 43158829--43158853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43158819 AAAATTAATA
43158829 AACCCAATTACCC
1 AACCCAATTACCC
43158842 AACCCAATTACC
1 AACCCAATTACC
43158854 ATTTACCAAC
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:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCAATTACCC
Found at i:43159240 original size:22 final size:20
Alignment explanation
Indices: 43159205--43159248 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
43159195 TTAAAGATTG
43159205 AAACTTTTTATTTAGCTGTTC
1 AAACTTTTTATTTA-CTGTTC
*
43159226 AAACTTTTTATTTTACTTTTC
1 AAACTTTTTA-TTTACTGTTC
43159247 AA
1 AA
43159249 CTTGGACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.55
Consensus pattern (20 bp):
AAACTTTTTATTTACTGTTC
Found at i:43162500 original size:20 final size:20
Alignment explanation
Indices: 43162477--43162613 Score: 85
Period size: 20 Copynumber: 7.3 Consensus size: 20
43162467 TATGTGTTAA
43162477 TTTTAAGACTTATGTAATGT
1 TTTTAAGACTTATGTAATGT
* * *
43162497 TTTT-A-A-TTATATAGTGA
1 TTTTAAGACTTATGTAATGT
* *
43162514 TTTAAAGGCTTATGTAATGT
1 TTTTAAGACTTATGTAATGT
* *
43162534 TTTT-A-A-TTATGTAGTGA
1 TTTTAAGACTTATGTAATGT
**
43162551 TTCAAAGACTTATGTAATGT
1 TTTTAAGACTTATGTAATGT
* *
43162571 TTTT-AG--TTATGTAGTGA
1 TTTTAAGACTTATGTAATGT
** *
43162588 TTCAAAGACTTATGTAATTT
1 TTTTAAGACTTATGTAATGT
43162608 TTTTAA
1 TTTTAA
43162614 TTATGTAGTG
Statistics
Matches: 81, Mismatches: 27, Indels: 18
0.64 0.21 0.14
Matches are distributed among these distances:
17 33 0.41
18 5 0.06
19 5 0.06
20 38 0.47
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (20 bp):
TTTTAAGACTTATGTAATGT
Found at i:43162506 original size:17 final size:17
Alignment explanation
Indices: 43162486--43162620 Score: 63
Period size: 17 Copynumber: 7.4 Consensus size: 17
43162476 ATTTTAAGAC
43162486 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* * * *
43162503 TTATATAGTGATTTAAA
1 TTATGTAATGTTTTTAA
43162520 GGCTTATGTAATGTTTTTAA
1 ---TTATGTAATGTTTTTAA
* ***
43162540 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
43162559 CTTATGTAATGTTTTTAG
1 -TTATGTAATGTTTTTAA
* ***
43162577 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
43162596 CTTATGTAATTTTTTTAA
1 -TTATGTAATGTTTTTAA
43162614 TTATGTA
1 TTATGTA
43162621 GTGATTTAAA
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
17 38 0.46
18 7 0.09
19 7 0.09
20 30 0.37
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:43162526 original size:37 final size:37
Alignment explanation
Indices: 43162459--43162630 Score: 247
Period size: 37 Copynumber: 4.6 Consensus size: 37
43162449 AAAGACTTAC
* * *
43162459 TTTTCAATTATGT-GTTAATTTTAAGACTTATGTAATG
1 TTTTTAATTATGTAG-TGATTTAAAGACTTATGTAATG
* *
43162496 TTTTTAATTATATAGTGATTTAAAGGCTTATGTAATG
1 TTTTTAATTATGTAGTGATTTAAAGACTTATGTAATG
*
43162533 TTTTTAATTATGTAGTGATTCAAAGACTTATGTAATG
1 TTTTTAATTATGTAGTGATTTAAAGACTTATGTAATG
* * *
43162570 TTTTTAGTTATGTAGTGATTCAAAGACTTATGTAATT
1 TTTTTAATTATGTAGTGATTTAAAGACTTATGTAATG
43162607 TTTTTAATTATGTAGTGATTTAAA
1 TTTTTAATTATGTAGTGATTTAAA
43162631 TCGGTTAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
37 121 0.99
38 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (37 bp):
TTTTTAATTATGTAGTGATTTAAAGACTTATGTAATG
Found at i:43162665 original size:8 final size:9
Alignment explanation
Indices: 43162626--43162664 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
43162616 ATGTAGTGAT
43162626 TTAAATCGG
1 TTAAATCGG
43162635 TTAAATCGG
1 TTAAATCGG
43162644 TTAAATCGG
1 TTAAATCGG
43162653 TT-AATCGG
1 TTAAATCGG
43162661 TTAA
1 TTAA
43162665 TTTTTAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (9 bp):
TTAAATCGG
Found at i:43163023 original size:20 final size:22
Alignment explanation
Indices: 43162982--43163028 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
43162972 ACATCTTCCT
43162982 ATTTTTTGGTATTCTCTAAT-A
1 ATTTTTTGGTATTCTCTAATAA
*
43163003 ATTTTTT-GTAGTTC-CTCATAA
1 ATTTTTTGGTA-TTCTCTAATAA
43163024 ATTTT
1 ATTTT
43163029 GGTACATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (22 bp):
ATTTTTTGGTATTCTCTAATAA
Found at i:43163060 original size:20 final size:20
Alignment explanation
Indices: 43163000--43163061 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
43162990 GTATTCTCTA
* ** *
43163000 ATAATTTTTTGTAGTTCCTC
1 ATAATTTTTGGTAAATCCTT
* * *
43163020 ATAAATTTTGGTACATTCTT
1 ATAATTTTTGGTAAATCCTT
43163040 ATAATTTTTGGTAAATCCTT
1 ATAATTTTTGGTAAATCCTT
43163060 AT
1 AT
43163062 TTTCTTTTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (20 bp):
ATAATTTTTGGTAAATCCTT
Found at i:43163342 original size:20 final size:20
Alignment explanation
Indices: 43163290--43163404 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
43163280 GTTTTGGAAA
**
43163290 TTCCTCATAA-TTTTGGTTT
1 TTCCTCATAATTTTTGGTAC
* * * *
43163309 TTCTTCGTATTTTTTGGTAT
1 TTCCTCATAATTTTTGGTAC
*
43163329 TTCCTCATAATTTTTGATAC
1 TTCCTCATAATTTTTGGTAC
* * *
43163349 ATCCTCGTAAGTTTTGGTAC
1 TTCCTCATAATTTTTGGTAC
* *
43163369 TTCCTCATAAATCTTGGTAC
1 TTCCTCATAATTTTTGGTAC
*
43163389 TTCCTCATAGTTTTTG
1 TTCCTCATAATTTTTG
43163405 ATGCTTTCTT
Statistics
Matches: 75, Mismatches: 20, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
19 7 0.09
20 68 0.91
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.51
Consensus pattern (20 bp):
TTCCTCATAATTTTTGGTAC
Found at i:43163394 original size:40 final size:40
Alignment explanation
Indices: 43163277--43163402 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 40
43163267 TTTATACATC
* ** *
43163277 TAAGTTTTGGAAATTCCTCAT-AATTTTGGTTTTTCTTCG
1 TAAGTTTTGGTAATTCCTCATAAATTTTGGTACTTCCTCG
** * * * *
43163316 TATTTTTTGGTATTTCCTCATAATTTTTGATACATCCTCG
1 TAAGTTTTGGTAATTCCTCATAAATTTTGGTACTTCCTCG
* * *
43163356 TAAGTTTTGGTACTTCCTCATAAATCTTGGTACTTCCTCA
1 TAAGTTTTGGTAATTCCTCATAAATTTTGGTACTTCCTCG
43163396 T-AGTTTT
1 TAAGTTTT
43163403 TGATGCTTTC
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
39 23 0.34
40 45 0.66
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.50
Consensus pattern (40 bp):
TAAGTTTTGGTAATTCCTCATAAATTTTGGTACTTCCTCG
Found at i:43163733 original size:20 final size:20
Alignment explanation
Indices: 43163710--43163927 Score: 84
Period size: 20 Copynumber: 10.8 Consensus size: 20
43163700 TTAGTATTAT
43163710 CTCATAATTTTTGGTATTTC
1 CTCATAATTTTTGGTATTTC
* * *
43163730 CTCATATTTTTTTTTGTATTCC
1 CTCATA--ATTTTTGGTATTTC
* * *
43163752 CTTATAATTTTTGATACTTC
1 CTCATAATTTTTGGTATTTC
* *
43163772 CTCAAAATTTTTTGGTACTT-
1 CTCATAA-TTTTTGGTATTTC
* * *
43163792 AT-AT-TTTTTTGATATTTC
1 CTCATAATTTTTGGTATTTC
* * **
43163810 CTCAAAATTTTTGATGGTTC
1 CTCATAATTTTTGGTATTTC
** * *
43163830 CTCATTTTTTTTGGCACTTTTT
1 CTCATAATTTTTGGTA--TTTC
* * * *
43163852 TTCAT-TTTTTTTGTATTTT
1 CTCATAATTTTTGGTATTTC
** *
43163871 CTCATAATTTTTTATATTCC
1 CTCATAATTTTTGGTATTTC
* * *
43163891 CTCACAATTTTTGTTACTTC
1 CTCATAATTTTTGGTATTTC
* *
43163911 CTCATATTTTTTAGTAT
1 CTCATAATTTTTGGTAT
43163928 ACCTATTTTT
Statistics
Matches: 141, Mismatches: 48, Indels: 18
0.68 0.23 0.09
Matches are distributed among these distances:
17 10 0.07
18 1 0.01
19 10 0.07
20 79 0.56
21 19 0.13
22 22 0.16
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (20 bp):
CTCATAATTTTTGGTATTTC
Found at i:43163748 original size:22 final size:22
Alignment explanation
Indices: 43163710--43163763 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
43163700 TTAGTATTAT
*
43163710 CTCATAA--TTTTTGGTATTTC
1 CTCATAATTTTTTTGGTATTCC
* *
43163730 CTCATATTTTTTTTTGTATTCC
1 CTCATAATTTTTTTGGTATTCC
*
43163752 CTTATAATTTTT
1 CTCATAATTTTT
43163764 GATACTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 6 0.22
22 21 0.78
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.61
Consensus pattern (22 bp):
CTCATAATTTTTTTGGTATTCC
Found at i:43163783 original size:21 final size:21
Alignment explanation
Indices: 43163759--43163821 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
43163749 TCCCTTATAA
43163759 TTTTTGATACTTCCTCAAAAT
1 TTTTTGATACTTCCTCAAAAT
* * *
43163780 TTTTTGGTAC-T--T-ATATT
1 TTTTTGATACTTCCTCAAAAT
*
43163797 TTTTTGATATTTCCTCAAAAT
1 TTTTTGATACTTCCTCAAAAT
43163818 TTTT
1 TTTT
43163822 GATGGTTCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
17 11 0.35
18 2 0.06
20 2 0.06
21 16 0.52
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTGATACTTCCTCAAAAT
Found at i:43163838 original size:38 final size:38
Alignment explanation
Indices: 43163759--43163840 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
43163749 TCCCTTATAA
* *
43163759 TTTTTGATACTTCCTCAAAATTTTTTGGTACTTATATT
1 TTTTTGATACTTCCTCAAAATTTTTTGGTACCTACATT
* *
43163797 TTTTTGATATTTCCTCAAAATTTTTGATGGTTCCT-CATT
1 TTTTTGATACTTCCTCAAAATTTTT--TGGTACCTACATT
43163836 TTTTT
1 TTTTT
43163841 TGGCACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 24 0.63
39 8 0.21
40 6 0.16
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (38 bp):
TTTTTGATACTTCCTCAAAATTTTTTGGTACCTACATT
Found at i:43164189 original size:21 final size:20
Alignment explanation
Indices: 43164165--43164231 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
43164155 AATATCATAA
43164165 TTTTTTATATTCCCTCATATT
1 TTTTTTATATT-CCTCATATT
* *
43164186 TTTTGGTACT-TT-CTAATATT
1 TTTT-TTA-TATTCCTCATATT
*
43164206 TTTTTTGTACTTCCTCATATT
1 TTTTTTATA-TTCCTCATATT
43164227 TTTTT
1 TTTTT
43164232 GTATTACCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 13 0.36
21 16 0.44
22 4 0.11
23 1 0.03
ACGTcount: A:0.16, C:0.15, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTTATATTCCTCATATT
Found at i:43164204 original size:20 final size:20
Alignment explanation
Indices: 43164181--43164252 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
43164171 ATATTCCCTC
*
43164181 ATATTTTTTGGTACTTTCTA
1 ATATTTTTTGGTACTTCCTA
* *
43164201 ATATTTTTTTTGTACTTCCTC
1 ATA-TTTTTTGGTACTTCCTA
* *
43164222 ATATTTTTTTGTA-TTACCTT
1 ATATTTTTTGGTACTT-CCTA
*
43164242 ATAATTTTTGG
1 ATATTTTTTGG
43164253 AGTGCTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.05
20 25 0.57
21 17 0.39
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (20 bp):
ATATTTTTTGGTACTTCCTA
Found at i:43164250 original size:21 final size:20
Alignment explanation
Indices: 43164159--43164234 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
43164149 TAATAAAATA
* *
43164159 TCATAATTTTTTATA-TTCCC
1 TCATATTTTTTTGTACTT-CC
* *
43164179 TCATATTTTTTGGTACTTTC
1 TCATATTTTTTTGTACTTCC
*
43164199 TAATATTTTTTTTGTACTTCC
1 TCATA-TTTTTTTGTACTTCC
43164220 TCATATTTTTTTGTA
1 TCATATTTTTTTGTA
43164235 TTACCTTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 27 0.59
21 19 0.41
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (20 bp):
TCATATTTTTTTGTACTTCC
Found at i:43164250 original size:41 final size:41
Alignment explanation
Indices: 43164161--43164250 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 41
43164151 ATAAAATATC
*
43164161 ATAA-TTTTTTATATTCCCTCATATTTTTTGGTACTTTCTA
1 ATAATTTTTTTATATTCCCTCATATTTTTTGGTACTTCCTA
* * * *
43164201 ATATTTTTTTTGTACTT-CCTCATATTTTTTTGTA-TTACCTT
1 ATAATTTTTTTATA-TTCCCTCATATTTTTTGGTACTT-CCTA
43164242 ATAATTTTT
1 ATAATTTTT
43164251 GGAGTGCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
40 5 0.12
41 34 0.83
42 2 0.05
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.61
Consensus pattern (41 bp):
ATAATTTTTTTATATTCCCTCATATTTTTTGGTACTTCCTA
Found at i:43168003 original size:23 final size:22
Alignment explanation
Indices: 43167960--43168003 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
43167950 TTTCAAGTCA
43167960 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
43167983 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
43168004 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Done.