Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 145 of 292
Found at i:43112051 original size:18 final size:18
Alignment explanation
Indices: 43112028--43112063 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43112018 AACTTAATGA
43112028 TATTTATATGATATGATG
1 TATTTATATGATATGATG
43112046 TATTTATATGATATGATG
1 TATTTATATGATATGATG
43112064 ATTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TATTTATATGATATGATG
Found at i:43119489 original size:18 final size:18
Alignment explanation
Indices: 43119466--43119501 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43119456 AACTTAATGA
43119466 TATTTATATGATATGATG
1 TATTTATATGATATGATG
43119484 TATTTATATGATATGATG
1 TATTTATATGATATGATG
43119502 ATTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TATTTATATGATATGATG
Found at i:43125543 original size:42 final size:42
Alignment explanation
Indices: 43125491--43125571 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
43125481 GCAGACACAC
* *
43125491 GGGCGTGTGTCTAGACCGTATGTGACACACGGCCTGGTACAG
1 GGGCATGTGTCTAGACCGTATATGACACACGGCCTGGTACAG
*
43125533 GGGCATGTGTCTAGACCGTGTATGACACACGGCCTGGTA
1 GGGCATGTGTCTAGACCGTATATGACACACGGCCTGGTA
43125572 AACGGAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.22
Consensus pattern (42 bp):
GGGCATGTGTCTAGACCGTATATGACACACGGCCTGGTACAG
Found at i:43125595 original size:42 final size:42
Alignment explanation
Indices: 43125496--43125583 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
43125486 CACACGGGCG
* * ** *
43125496 TGTGTCTAGACCGTATGTGACACACGGCCTGGTACAGGGGCA
1 TGTGTCTAGACCGTGTATGACACACGGCCTGGTACAACGGAA
43125538 TGTGTCTAGACCGTGTATGACACACGGCCTGGTA-AACGGAA
1 TGTGTCTAGACCGTGTATGACACACGGCCTGGTACAACGGAA
43125579 GTGTG
1 -TGTG
43125584 GTTAGGCCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.23
Consensus pattern (42 bp):
TGTGTCTAGACCGTGTATGACACACGGCCTGGTACAACGGAA
Found at i:43130171 original size:28 final size:28
Alignment explanation
Indices: 43130118--43130172 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
43130108 TTATAAAATT
*
43130118 ATTTAAATTTTAACAAAAATATAAAAAC
1 ATTTAAATTTTAACAAAAATAGAAAAAC
** *
43130146 ATTTAAATTTTATTAAAATTAGAAAAA
1 ATTTAAATTTTAACAAAAATAGAAAAA
43130173 AAATTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTTAAATTTTAACAAAAATAGAAAAAC
Found at i:43130184 original size:21 final size:22
Alignment explanation
Indices: 43130155--43130196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
43130145 CATTTAAATT
*
43130155 TTATTAAAAT-TAGAAAAAAAA
1 TTATAAAAATCTAGAAAAAAAA
*
43130176 TTATAAAAATCTTGAAAAAAA
1 TTATAAAAATCTAGAAAAAAA
43130197 TAAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (22 bp):
TTATAAAAATCTAGAAAAAAAA
Found at i:43130516 original size:19 final size:19
Alignment explanation
Indices: 43130492--43130612 Score: 63
Period size: 20 Copynumber: 6.4 Consensus size: 19
43130482 AAAATTTTGT
*
43130492 ATTTTATGATTTTTATAAA
1 ATTTTATAATTTTTATAAA
* *
43130511 ATTTTACAAATTTTTATATA
1 ATTTTA-TAATTTTTATAAA
* ** **
43130531 TTTTTACGATTTTTATATTT
1 ATTTTATAATTTTTATA-AA
* *
43130551 TTTTTCTAATTTTTA-ATAA
1 ATTTTATAATTTTTATA-AA
43130570 ATTTTA-AATATTTTATTAAA
1 ATTTTATAAT-TTTTA-TAAA
*
43130590 ATTTAAT-A-TTTTAT-AA
1 ATTTTATAATTTTTATAAA
43130606 ATTTTAT
1 ATTTTAT
43130613 TGATTTTATT
Statistics
Matches: 80, Mismatches: 16, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
16 8 0.10
17 1 0.01
18 8 0.10
19 26 0.32
20 36 0.45
21 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATAATTTTTATAAA
Found at i:43130525 original size:20 final size:19
Alignment explanation
Indices: 43130500--43130593 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
43130490 GTATTTTATG
43130500 ATTTTTATAAAATTTTACAA
1 ATTTTTATAAAATTTTAC-A
* * *
43130520 ATTTTTATATATTTTTACG
1 ATTTTTATAAAATTTTACA
*** *
43130539 ATTTTTATATTTTTTTTCTA
1 ATTTTTATAAAATTTTAC-A
43130559 ATTTTTA-ATAAATTTTA-A
1 ATTTTTATA-AAATTTTACA
43130577 ATATTTTATTAAAATTT
1 AT-TTTTA-TAAAATTT
43130594 AATATTTTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
18 3 0.05
19 22 0.37
20 33 0.56
21 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:43130599 original size:18 final size:18
Alignment explanation
Indices: 43130557--43130622 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
43130547 ATTTTTTTTC
*
43130557 TAAT-TTTTAATAAATTT
1 TAATATTTTATTAAATTT
*
43130574 TAAATATTTTATTAAAATT
1 T-AATATTTTATTAAATTT
43130593 TAATATTTTA-TAAATTT
1 TAATATTTTATTAAATTT
*
43130610 TATTGATTTTATT
1 TAAT-ATTTTATT
43130623 TTTATAATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.24
18 18 0.44
19 13 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATATTTTATTAAATTT
Found at i:43132545 original size:24 final size:25
Alignment explanation
Indices: 43132518--43132564 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
43132508 ATTTTTTAAT
43132518 TATTAACTTTTATGA-TATAAGAGA
1 TATTAACTTTTATGATTATAAGAGA
* * *
43132542 TATTCATTTTTATTATTATAAGA
1 TATTAACTTTTATGATTATAAGA
43132565 AAAGAGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
TATTAACTTTTATGATTATAAGAGA
Found at i:43135270 original size:18 final size:18
Alignment explanation
Indices: 43135247--43135281 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43135237 AAGAATGAAC
43135247 TTTTTAATTATTTTTCAT
1 TTTTTAATTATTTTTCAT
43135265 TTTTTAATTATTTTTCA
1 TTTTTAATTATTTTTCA
43135282 ATTGGTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTAATTATTTTTCAT
Found at i:43136003 original size:2 final size:2
Alignment explanation
Indices: 43135996--43136024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43135986 TGCGAGTAAG
43135996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43136025 GCGAACACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43137054 original size:46 final size:46
Alignment explanation
Indices: 43136977--43137073 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
43136967 GATAGTAATT
* * * *
43136977 TAAAAAGCCATCAAAATCGGGTCAACCGGATGATAATTTAGTATAG
1 TAAAAAGCCATAAAAATCGAGACAACCGGATGATAAGTTAGTATAG
* * * *
43137023 TAAAAAGCCATAAAAATC-AGACAGCCGGGATGGTAAGTTATTGTAG
1 TAAAAAGCCATAAAAATCGAGACAACC-GGATGATAAGTTAGTATAG
43137069 TAAAA
1 TAAAA
43137074 GTCATCATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 5 0.12
46 37 0.88
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAAAAGCCATAAAAATCGAGACAACCGGATGATAAGTTAGTATAG
Found at i:43138486 original size:2 final size:2
Alignment explanation
Indices: 43138474--43138504 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
43138464 CAATAAAATG
*
43138474 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43138505 CACATAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43140038 original size:138 final size:138
Alignment explanation
Indices: 43139782--43140342 Score: 906
Period size: 138 Copynumber: 4.1 Consensus size: 138
43139772 GAAAACATAG
* *
43139782 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGGATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
** * * * * * *
43139847 AATATAAACCGTTATTTTAATTAATTTCCGTCAAAAGATAAAAGATATAGAAATTAATATTTTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
43139912 TGGAAAGA
131 TGGAAAGA
* * *
43139920 ATATAATTAATATATGAACTTGATTTATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* *
43139985 AATATAAAGAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
43140050 TGGAAAGA
131 TGGAAAGA
43140058 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
* * * *
43140123 AATATAAACAATTATATTAGTTAATTTCAGTCAAAATATAAATGGCATGGAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
43140188 TGGAAAGA
131 TGGAAAGA
*
43140196 GTATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAA-TTTAT
* *
43140261 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTATT
65 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
43140326 TTGAAAAGA
130 TTGGAAAGA
43140335 ATATAATT
1 ATATAATT
43140343 CAATTTTCTA
Statistics
Matches: 389, Mismatches: 33, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
138 310 0.80
139 79 0.20
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAGA
Found at i:43140093 original size:71 final size:71
Alignment explanation
Indices: 43140016--43140232 Score: 177
Period size: 71 Copynumber: 3.1 Consensus size: 71
43140006 TAATTTTGGT
*
43140016 CAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAATGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
43140081 TTCATA
66 TTCATA
* * ** * * * *
43140087 CAAAATATTAATTGTATAT--ATTTTACTGAATT-TATT--AATATAA-ACAATT-ATAT-T--A
1 CAAAATA-TAAATG-ACATGGAAATTAAT--ATTCTTTTGGAA-AGAATATAATTAATATATGAA
* *
43140142 GTTAATTTCAGT-
61 TTTGA-TTCA-TA
* *
43140154 CAAAATATAAATGGCATGGAAATTAATATTCTTTTGGAAAGAGTATAATTAATATATGAATTTGA
1 CAAAATATAAATGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
43140219 TTCATA
66 TTCATA
43140225 CAAAATAT
1 CAAAATAT
43140233 TAATTGTATA
Statistics
Matches: 105, Mismatches: 23, Indels: 36
0.64 0.14 0.22
Matches are distributed among these distances:
65 5 0.05
66 12 0.11
67 18 0.17
68 9 0.09
69 8 0.08
70 9 0.09
71 27 0.26
72 11 0.10
73 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (71 bp):
CAAAATATAAATGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
TTCATA
Found at i:43140161 original size:67 final size:67
Alignment explanation
Indices: 43139949--43140300 Score: 170
Period size: 71 Copynumber: 5.1 Consensus size: 67
43139939 TTGATTTATA
* * **
43139949 CAAAATATTAATTGTATATATTTTACCGAATTTATTAATATAAAGAATTATATTAATTAATTTTG
1 CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACAATTATATTAATTAATTTCA
43140014 GT
66 GT
** * ** * * * *
43140016 CAAAATA-TAAAAG-ACATGGAAATTAAT--ATTCTTTTGGAA-AGAATATAATTAATATATGAA
1 CAAAATATTAATTGTATAT--ATTTTACTGAATT-TATT--AATATAA-ACAATT-ATAT-T-AA
*
43140076 TTTGA-TTCA-T
57 -TTAATTTCAGT
*
43140086 ACAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACAATTATATTAGTTAATTTC
1 -CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACAATTATATTAATTAATTTC
43140151 AGT
65 AGT
* * * * * *** * ** *
43140154 CAAAATATAAATGGCATGGAAATTAATA-TTCTTTTGGA-AAGAGTATAATTAA-TATATGAATT
1 CAAAATATTAATTGTAT--ATATT-TTACTGAATTT--ATTA-A-TATAAACAATTATATTAA-T
*
43140216 TGA-TTCA-T
58 TAATTTCAGT
43140224 ACAAAATATTAATTGTATATATTTTACTGAATTTTATTAATATAAACAATTATATTAATTAATTT
1 -CAAAATATTAATTGTATATATTTTACTGAA-TTTATTAATATAAACAATTATATTAATTAATTT
*
43140289 CGGT
64 CAGT
43140293 CAAAATAT
1 CAAAATAT
43140301 AAAAGACATG
Statistics
Matches: 200, Mismatches: 52, Indels: 65
0.63 0.16 0.21
Matches are distributed among these distances:
65 6 0.03
66 10 0.05
67 43 0.22
68 31 0.16
69 23 0.12
70 16 0.08
71 45 0.22
72 20 0.10
73 6 0.03
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.42
Consensus pattern (67 bp):
CAAAATATTAATTGTATATATTTTACTGAATTTATTAATATAAACAATTATATTAATTAATTTCA
GT
Found at i:43140275 original size:71 final size:71
Alignment explanation
Indices: 43140062--43140275 Score: 187
Period size: 71 Copynumber: 3.1 Consensus size: 71
43140052 GAAAGAATAT
43140062 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAA-TTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTTATTAAT
43140126 ATAAAC
66 ATAAAC
* * * * * ** ** *
43140132 AATT-ATAT-T--AGTTAATTTCAGT-CAAAATATAAATGGCATGGAAATTAAT--ATTCTT-TT
1 AATTAATATATGAATTTGA-TTCA-TACAAAATATTAATTGTATATATTTTACTGAATT-TTATT
* * *
43140189 GGAA-AGAGTAT
63 --AATATA-AAC
43140200 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTTATTAAT
43140265 ATAAAC
66 ATAAAC
43140271 AATTA
1 AATTA
43140276 TATTAATTAA
Statistics
Matches: 102, Mismatches: 26, Indels: 31
0.64 0.16 0.19
Matches are distributed among these distances:
65 1 0.01
66 7 0.07
67 27 0.26
68 9 0.09
69 8 0.08
70 6 0.06
71 31 0.30
72 8 0.08
73 5 0.05
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (71 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTTATTAAT
ATAAAC
Found at i:43140415 original size:75 final size:76
Alignment explanation
Indices: 43140319--43140466 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 76
43140309 TGAAAATTAA
43140319 TATTATTTTGAAAAGAATATAATTCA-ATTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
1 TATTATTTTGAAAAGAATATAATTCATATTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
*
43140383 GAATAATCTTG
66 AAATAATCTTG
* * * *
43140394 TATTCTTTTGAAAATAATATAATTTATTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
1 TATTATTTTGAAAAGAATATAATTCATATTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
43140459 AAATAATC
66 AAATAATC
43140467 ATGAATTTCT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 23 0.34
76 44 0.66
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (76 bp):
TATTATTTTGAAAAGAATATAATTCATATTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
AAATAATCTTG
Found at i:43141039 original size:11 final size:11
Alignment explanation
Indices: 43141023--43141054 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
43141013 TGCCTTTCTA
43141023 TATTTCTCTTG
1 TATTTCTCTTG
43141034 TATTTCTCTTG
1 TATTTCTCTTG
43141045 TATTTCTCTT
1 TATTTCTCTT
43141055 CACATCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.06, T:0.66
Consensus pattern (11 bp):
TATTTCTCTTG
Found at i:43144236 original size:239 final size:239
Alignment explanation
Indices: 43143813--43144295 Score: 950
Period size: 239 Copynumber: 2.0 Consensus size: 239
43143803 TTCGGGTTGT
43143813 CACA-GTAGGTATCGATAGTGGAATATGGGTATCAATATTTTCCTTACACAGTATCGATATGAAA
1 CACACGTAGGTATCGATAGTGGAATATGGGTATCAATATTTTCCTTACACAGTATCGATATGAAA
43143877 AATCAGTACCAAATCAACATTCTATTTCTCGGCTAAAATCAAAACTCAAGAAAATATCAGTACTT
66 AATCAGTACCAAATCAACATTCTATTTCTCGGCTAAAATCAAAACTCAAGAAAATATCAGTACTT
43143942 TTCAAAAATATCAGTAAAAATTACCCCAAGTATCTATACTCGTGATATGGTACCATATCACGATT
131 TTCAAAAATATCAGTAAAAATTACCCCAAGTATCTATACTCGTGATATGGTACCATATCACGATT
43144007 CTGACTTCCTGCACATTTCAAAATCATAGAGGTACCATTTTTAA
196 CTGACTTCCTGCACATTTCAAAATCATAGAGGTACCATTTTTAA
43144051 CACACGTAGGTATCGATAGTGGAATATGGGTATCAATATTTTCCTTACACAGTATCGATATGAAA
1 CACACGTAGGTATCGATAGTGGAATATGGGTATCAATATTTTCCTTACACAGTATCGATATGAAA
*
43144116 AATCAGTACCAAATCAACATTCTATTTGTCGGCTAAAATCAAAACTCAAGAAAATATCAGTACTT
66 AATCAGTACCAAATCAACATTCTATTTCTCGGCTAAAATCAAAACTCAAGAAAATATCAGTACTT
43144181 TTCAAAAATATCAGTAAAAATTACCCCAAGTATCTATACTCGTGATATGGTACCATATCACGATT
131 TTCAAAAATATCAGTAAAAATTACCCCAAGTATCTATACTCGTGATATGGTACCATATCACGATT
43144246 CTGACTTCCTGCACATTTCAAAATCATAGAGGTACCATTTTTAA
196 CTGACTTCCTGCACATTTCAAAATCATAGAGGTACCATTTTTAA
43144290 CACACG
1 CACACG
43144296 AATGCAGATA
Statistics
Matches: 243, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
238 4 0.02
239 239 0.98
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (239 bp):
CACACGTAGGTATCGATAGTGGAATATGGGTATCAATATTTTCCTTACACAGTATCGATATGAAA
AATCAGTACCAAATCAACATTCTATTTCTCGGCTAAAATCAAAACTCAAGAAAATATCAGTACTT
TTCAAAAATATCAGTAAAAATTACCCCAAGTATCTATACTCGTGATATGGTACCATATCACGATT
CTGACTTCCTGCACATTTCAAAATCATAGAGGTACCATTTTTAA
Found at i:43150386 original size:41 final size:41
Alignment explanation
Indices: 43150215--43150374 Score: 168
Period size: 41 Copynumber: 3.9 Consensus size: 41
43150205 GGGTCTAAAT
43150215 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
* * * * *
43150256 CCGAACTTAGTTTCGAAGGGCTTTAGAGCCAGTG-TCATAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
* * **
43150296 CCG-GACTTAGT-TCCGAAGGGCCTTCAAGCCAGTGGTCTAAT--
1 CCGAG-CTTGGTCT-CGAAGGGCTTTTGAGCCAGT-G-CTAATAA
43150337 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
43150375 GAATCAGGCT
Statistics
Matches: 98, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
39 5 0.05
40 32 0.33
41 56 0.57
42 2 0.02
43 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
CCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAA
Found at i:43155297 original size:40 final size:40
Alignment explanation
Indices: 43155214--43155434 Score: 277
Period size: 40 Copynumber: 5.5 Consensus size: 40
43155204 AATCAAGCAT
** ** *
43155214 CTTCGGGGTTTAG-CCGGATATAACCACTCGCACAAA-GC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
43155252 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
43155292 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
43155332 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
43155372 CTT-GGGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
43155413 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
43155435 CATTCGAGTA
Statistics
Matches: 162, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
38 11 0.07
39 22 0.14
40 99 0.61
41 26 0.16
42 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:43165601 original size:34 final size:34
Alignment explanation
Indices: 43165534--43165601 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
43165524 GCTTATATGA
*
43165534 TACTGAAACTGAAATGGGCTAAGGCCCGAACTGC
1 TACTGAAACTGAAATGGGCTAAGGCCAGAACTGC
* * *
43165568 TACTGAAATTGGAATGGGCTTAGGCCTAG-ACTGC
1 TACTGAAACTGAAATGGGCTAAGGCC-AGAACTGC
43165602 ATATGACTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (34 bp):
TACTGAAACTGAAATGGGCTAAGGCCAGAACTGC
Found at i:43166444 original size:21 final size:17
Alignment explanation
Indices: 43166404--43166436 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43166394 GTATACTAAA
43166404 ACTGTAGTAAAACTGAG
1 ACTGTAGTAAAACTGAG
43166421 ACTGTAGTAAAACTGA
1 ACTGTAGTAAAACTGA
43166437 TAGAGACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
ACTGTAGTAAAACTGAG
Found at i:43170886 original size:46 final size:46
Alignment explanation
Indices: 43170833--43171008 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
43170823 TATTTGGGCA
43170833 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
43170879 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
43170924 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
43170972 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43171009 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:43170988 original size:93 final size:93
Alignment explanation
Indices: 43170829--43171000 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
43170819 GGGATATTTG
* *
43170829 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
43170894 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
43170922 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
43170987 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
43171001 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:43175987 original size:21 final size:20
Alignment explanation
Indices: 43175963--43176004 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
43175953 GAAGTTTACG
*
43175963 AGAGATAAATAGAAGATAAAT
1 AGAGATAAATAG-AGACAAAT
43175984 AGAGATAAATAGAGACAAAT
1 AGAGATAAATAGAGACAAAT
43176004 A
1 A
43176005 CTCATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (20 bp):
AGAGATAAATAGAGACAAAT
Found at i:43175991 original size:10 final size:10
Alignment explanation
Indices: 43175963--43176004 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
43175953 GAAGTTTACG
43175963 AGAGATAAAT
1 AGAGATAAAT
43175973 AGAAGATAAAT
1 AG-AGATAAAT
43175984 AGAGATAAAT
1 AGAGATAAAT
*
43175994 AGAGACAAAT
1 AGAGATAAAT
43176004 A
1 A
43176005 CTCATGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (10 bp):
AGAGATAAAT
Found at i:43177571 original size:29 final size:30
Alignment explanation
Indices: 43177514--43177571 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
43177504 TGGAAGGGGA
** * *
43177514 GTAAAAGTTTTGGGGGGAAAGTGAGAAGGG
1 GTAAAAGTTTTGGAAGGAAAGTAAAAAGGG
43177544 GTAAAAGTTTT-GAAGGAAAGTAAAAAGG
1 GTAAAAGTTTTGGAAGGAAAGTAAAAAGG
43177572 TTTGAGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (30 bp):
GTAAAAGTTTTGGAAGGAAAGTAAAAAGGG
Found at i:43177626 original size:9 final size:9
Alignment explanation
Indices: 43177612--43177642 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43177602 TATAGTTTAA
43177612 TATTCGAAT
1 TATTCGAAT
43177621 TATTCGAAT
1 TATTCGAAT
*
43177630 TATTCGATT
1 TATTCGAAT
43177639 TATT
1 TATT
43177643 GAAATTCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43177713 original size:9 final size:9
Alignment explanation
Indices: 43177699--43177731 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
43177689 AATCAAGTTG
43177699 ACTCGAATA
1 ACTCGAATA
*
43177708 ACTCGATTA
1 ACTCGAATA
43177717 ACTCGAATA
1 ACTCGAATA
43177726 ACTCGA
1 ACTCGA
43177732 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:43177722 original size:18 final size:18
Alignment explanation
Indices: 43177699--43177733 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43177689 AATCAAGTTG
43177699 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
43177717 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
43177734 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:43180758 original size:24 final size:24
Alignment explanation
Indices: 43180731--43180781 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
43180721 AATGCTCACA
43180731 TCAAACTATCGACACGAGTCATAG
1 TCAAACTATCGACACGAGTCATAG
*
43180755 TCAAACTGTCGACACGAGTCATAG
1 TCAAACTATCGACACGAGTCATAG
43180779 TCA
1 TCA
43180782 CTTACTTATT
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:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (24 bp):
TCAAACTATCGACACGAGTCATAG
Found at i:43182152 original size:34 final size:35
Alignment explanation
Indices: 43182108--43182181 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
43182098 CAAATAAAAA
43182108 TTACAGCATTATTGCTGTATTATTATCATACCAAC
1 TTACAGCATTATTGCTGTATTATTATCATACCAAC
43182143 TTACA-CATTATTGCTGTATTATTATCATACCAAC
1 TTACAGCATTATTGCTGTATTATTATCATACCAAC
43182177 TTACA
1 TTACA
43182182 TACTTTCAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
34 34 0.87
35 5 0.13
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (35 bp):
TTACAGCATTATTGCTGTATTATTATCATACCAAC
Found at i:43182447 original size:30 final size:30
Alignment explanation
Indices: 43182413--43182473 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43182403 TCCTTAACTC
43182413 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
43182443 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
43182473 A
1 A
43182474 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:43184308 original size:40 final size:40
Alignment explanation
Indices: 43184233--43184309 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
43184223 GTGCATTTAA
* * ** *
43184233 GGGTACCGAAGTACAAAGAGGGGCATGTAATTGCAATCAG
1 GGGTACCAAAGTACAAACAGGGGCACATAAGTGCAATCAG
43184273 GGGTACCAAAGTACAAACAGGGGCACATAAGTGCAAT
1 GGGTACCAAAGTACAAACAGGGGCACATAAGTGCAAT
43184310 AATTCAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.16
Consensus pattern (40 bp):
GGGTACCAAAGTACAAACAGGGGCACATAAGTGCAATCAG
Found at i:43188784 original size:46 final size:46
Alignment explanation
Indices: 43188650--43188865 Score: 150
Period size: 47 Copynumber: 4.6 Consensus size: 46
43188640 TCATTTGTAT
* * *
43188650 GCTAGTGTAAGACATGTCTGGGACATGCAACGACCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGA-GATGAGA
* * * * *
43188696 GCCAGTGTAAGATCATGT-AGGGACATGGCATCGGCATTGAGATGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGAGATGAGA
* *
43188743 TCTAGTGTGAGACATGTCTGGGACATGCATCGACCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATG-AGA
* * * * * * * * * *
43188789 CCCAGTTTAAGACCATGTTTGGGACATGGCGTCGGCCTCAATTACGATA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCGA-GATGAGA
*
43188838 GTTAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGA-CATGTCTGGGACATG
43188866 GCATAGACTT
Statistics
Matches: 131, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
46 46 0.35
47 47 0.36
48 13 0.10
49 25 0.19
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGAGA
Found at i:43191660 original size:12 final size:12
Alignment explanation
Indices: 43191643--43191667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43191633 TTATTAAATG
43191643 AATTAAAAGCCA
1 AATTAAAAGCCA
43191655 AATTAAAAGCCA
1 AATTAAAAGCCA
43191667 A
1 A
43191668 TCTTTGTCCA
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:43192349 original size:25 final size:26
Alignment explanation
Indices: 43192321--43192374 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
43192311 TAAGCATTAA
43192321 ATTATATATGTAAT-AATGCT-TAATT
1 ATTATATATGTAATAAATGCTAT-ATT
* *
43192346 ATTATATTTGTGATAAATGCTATATT
1 ATTATATATGTAATAAATGCTATATT
43192372 ATT
1 ATT
43192375 GAAATGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 12 0.48
27 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (26 bp):
ATTATATATGTAATAAATGCTATATT
Found at i:43195498 original size:20 final size:20
Alignment explanation
Indices: 43195482--43195528 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43195472 GAACCATTTT
43195482 ATCTACTTACTTTCCATTCC
1 ATCTACTTACTTTCCATTCC
* *
43195502 ATTTACTTACTTTACATTCC
1 ATCTACTTACTTTCCATTCC
*
43195522 ATTTACT
1 ATCTACT
43195529 CAACATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (20 bp):
ATCTACTTACTTTCCATTCC
Found at i:43196384 original size:40 final size:39
Alignment explanation
Indices: 43196323--43196503 Score: 157
Period size: 40 Copynumber: 4.5 Consensus size: 39
43196313 CACTGAACTG
* *
43196323 CAAACAGGGGCACT-TATGTGCATTCAAGGGTATCGAAGTA
1 CAAACAGGGGCA-TGTAAGTGCAAT-AAGGGTATCGAAGTA
* * *
43196363 CAAAGAGGGGCATGTAAGTGCAATAAGGGGAATTGAAGTA
1 CAAACAGGGGCATGTAAGTGCAATAA-GGGTATCGAAGTA
* * * *
43196403 CAAACAGGGGCATGTAAGTACAATTAGGGGTATTGAAATA
1 CAAACAGGGGCATGTAAGTGCAA-TAAGGGTATCGAAGTA
* * * * *
43196443 CAAATAGGGGCACGTAAGTGCAATCAGTGGTACCAAAGTA
1 CAAACAGGGGCATGTAAGTGCAATAAG-GGTATCGAAGTA
* * *
43196483 CAAATAAGGGCACGTAAGTGC
1 CAAACAGGGGCATGTAAGTGC
43196504 CATCATTCAA
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
39 5 0.04
40 110 0.94
41 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (39 bp):
CAAACAGGGGCATGTAAGTGCAATAAGGGTATCGAAGTA
Found at i:43196391 original size:20 final size:20
Alignment explanation
Indices: 43196358--43196432 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
43196348 AAGGGTATCG
43196358 AAGTACAA-AGAGGGGCATGT
1 AAGTACAATA-AGGGGCATGT
* *
43196378 AAGTGCAATAAGGGGAAT-T
1 AAGTACAATAAGGGGCATGT
43196397 GAAGTACAA-ACAGGGGCATGT
1 -AAGTACAATA-AGGGGCATGT
*
43196418 AAGTACAATTAGGGG
1 AAGTACAATAAGGGG
43196433 TATTGAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.17
Consensus pattern (20 bp):
AAGTACAATAAGGGGCATGT
Found at i:43196482 original size:80 final size:80
Alignment explanation
Indices: 43196350--43196501 Score: 187
Period size: 80 Copynumber: 1.9 Consensus size: 80
43196340 GTGCATTCAA
* * *** *
43196350 GGGTATCGAAGTACAAAGAGGGGCATGTAAGTGCAATAAGGGGAATTGAAGTACAAACAGGGGCA
1 GGGTATCGAAATACAAAGAGGGGCACGTAAGTGCAATAAGGGGAACCAAAGTACAAACAAGGGCA
*
43196415 TGTAAGTACAATTAG
66 CGTAAGTACAATTAG
* * * * * *
43196430 GGGTATTGAAATACAAATAGGGGCACGTAAGTGCAATCAGTGGTACCAAAGTACAAATAAGGGCA
1 GGGTATCGAAATACAAAGAGGGGCACGTAAGTGCAATAAGGGGAACCAAAGTACAAACAAGGGCA
43196495 CGTAAGT
66 CGTAAGT
43196502 GCCATCATTC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.19
Consensus pattern (80 bp):
GGGTATCGAAATACAAAGAGGGGCACGTAAGTGCAATAAGGGGAACCAAAGTACAAACAAGGGCA
CGTAAGTACAATTAG
Found at i:43204926 original size:45 final size:45
Alignment explanation
Indices: 43204862--43204955 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
43204852 CAAAATGCAC
43204862 TAGTTTAGATTTTAGCTCTTTAGATTTCTCATCATCTGGATTTTA
1 TAGTTTAGATTTTAGCTCTTTAGATTTCTCATCATCTGGATTTTA
*
43204907 TAGTTTAGATTTTAGCTCTTTAGATTTCTCATCATCTGGATTTTC
1 TAGTTTAGATTTTAGCTCTTTAGATTTCTCATCATCTGGATTTTA
43204952 TAGT
1 TAGT
43204956 GTAGGAACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (45 bp):
TAGTTTAGATTTTAGCTCTTTAGATTTCTCATCATCTGGATTTTA
Found at i:43212145 original size:19 final size:19
Alignment explanation
Indices: 43212121--43212182 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
43212111 TAAGATACTT
43212121 TTTTCAAAAATTGATTTGA
1 TTTTCAAAAATTGATTTGA
**
43212140 TTTTC---AA--GATACG-
1 TTTTCAAAAATTGATTTGA
43212153 TTTTCAAAAATTGATTTGA
1 TTTTCAAAAATTGATTTGA
43212172 TTTTCTAAAAA
1 TTTTC-AAAAA
43212183 CCATAGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 13
0.65 0.08 0.27
Matches are distributed among these distances:
13 5 0.16
14 4 0.12
16 4 0.12
18 4 0.12
19 10 0.31
20 5 0.16
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTCAAAAATTGATTTGA
Found at i:43212159 original size:32 final size:33
Alignment explanation
Indices: 43212112--43212176 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
43212102 AAAGATCTCT
*
43212112 AAGATACTTTTTTCAAAAATTGATTTGATTTTC
1 AAGATACTGTTTTCAAAAATTGATTTGATTTTC
43212145 AAGATAC-GTTTTCAAAAATTGATTTGATTTTC
1 AAGATACTGTTTTCAAAAATTGATTTGATTTTC
43212177 TAAAAACCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (33 bp):
AAGATACTGTTTTCAAAAATTGATTTGATTTTC
Found at i:43213826 original size:87 final size:86
Alignment explanation
Indices: 43213670--43213924 Score: 262
Period size: 87 Copynumber: 2.9 Consensus size: 86
43213660 TAACGATGAT
* *
43213670 CATCGAATATGAAAAGGGATAGTTTCGTCTATCGATTATGAAAAGGGATGGTGATGACCATCAAC
1 CATCGATTATGAAAAGGGATAGTTT-GACTATCGATTATGAAAAGGGATGGTGATGACCATCAAC
* *
43213735 TATGAAAAGGGATGGTGACGAC
65 TATGAAAAAGGATGGTGAAGAC
* * * * **
43213757 CATCGATTATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAGGGATAGGT-TTGGCTATTGA
1 CATCGATTATGAAAAGGGATAG-TTTGACTATCGATTATGAAAAGGGAT-GGTGATGACCATCAA
*
43213821 TTATGAAAAAGGATGGTGAAGAC
64 CTATGAAAAAGGATGGTGAAGAC
* * * * * * * * *
43213844 CATCAATAATGAAAAGGGATGGTTTTGACCATCAAATATGAAAAGGGATGATGACGACCATCGGA
1 CATCGATTATGAAAAGGGATAG-TTTGACTATCGATTATGAAAAGGGATGGTGATGACCATC-AA
*
43213909 -TATGAAAAGGGATGGT
64 CTATGAAAAAGGATGGT
43213925 TTCAACCATC
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
86 2 0.01
87 129 0.93
88 8 0.06
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25
Consensus pattern (86 bp):
CATCGATTATGAAAAGGGATAGTTTGACTATCGATTATGAAAAGGGATGGTGATGACCATCAACT
ATGAAAAAGGATGGTGAAGAC
Found at i:43213893 original size:29 final size:29
Alignment explanation
Indices: 43213670--43213934 Score: 207
Period size: 29 Copynumber: 9.1 Consensus size: 29
43213660 TAACGATGAT
* *
43213670 CATCGAATATGAAAAGGGATAGTTTCGTC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
* * *
43213699 TATCGATTATGAAAAGGGATGGTGAT-GAC
1 CATCGAATATGAAAAGGGATGGT-TTCGAC
**
43213728 CATC-AACTATGAAAAGGGATGGTGACGAC
1 CATCGAA-TATGAAAAGGGATGGTTTCGAC
* * *
43213757 CATCGATTATGAAAAGGGATAGCTTT-GGC
1 CATCGAATATGAAAAGGGAT-GGTTTCGAC
* * *
43213786 TATCGATTATGAAAAGGGATAGGTTT-GGC
1 CATCGAATATGAAAAGGGAT-GGTTTCGAC
* * * * ***
43213815 TATTGATTATGAAAAAGGATGGTGAAGAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
*
43213844 CATC-AATAATGAAAAGGGATGGTTTTGAC
1 CATCGAAT-ATGAAAAGGGATGGTTTCGAC
* * **
43213873 CATCAAATATGAAAAGGGATGATGACGAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
* *
43213902 CATCGGATATGAAAAGGGATGGTTTCAAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
43213931 CATC
1 CATC
43213935 ATTCAACACA
Statistics
Matches: 190, Mismatches: 38, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
28 6 0.03
29 177 0.93
30 7 0.04
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATGGTTTCGAC
Found at i:43213935 original size:58 final size:57
Alignment explanation
Indices: 43213664--43213934 Score: 258
Period size: 58 Copynumber: 4.7 Consensus size: 57
43213654 ACGGTGTAAC
* * * *
43213664 GATGATCATCGAATATGAAAAGGGATAGTTTCGTCTATCGATTATGAAAAGGGATGGT
1 GATGACCATC-AATATGAAAAGGGATGGTTTCGACCATCGATTATGAAAAGGGATGGT
** *
43213722 GATGACCATCAACTATGAAAAGGGATGGTGACGACCATCGATTATGAAAAGGGATAGCT
1 GATGACCATCAA-TATGAAAAGGGATGGTTTCGACCATCGATTATGAAAAGGGAT-GGT
* * * * * * * *
43213781 -TTGGCTATCGATTATGAAAAGGGATAGGTTT-GGCTATTGATTATGAAAAAGGATGGT
1 GATGACCATC-AATATGAAAAGGGAT-GGTTTCGACCATCGATTATGAAAAGGGATGGT
* * * * *
43213838 GAAGACCATCAATAATGAAAAGGGATGGTTTTGACCATCAAATATGAAAAGGGATGAT
1 GATGACCATCAAT-ATGAAAAGGGATGGTTTCGACCATCGATTATGAAAAGGGATGGT
* * *
43213896 GACGACCATCGGATATGAAAAGGGATGGTTTCAACCATC
1 GATGACCATC-AATATGAAAAGGGATGGTTTCGACCATC
43213935 ATTCAACACA
Statistics
Matches: 171, Mismatches: 34, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
57 11 0.06
58 152 0.89
59 8 0.05
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.25
Consensus pattern (57 bp):
GATGACCATCAATATGAAAAGGGATGGTTTCGACCATCGATTATGAAAAGGGATGGT
Found at i:43214059 original size:31 final size:31
Alignment explanation
Indices: 43214023--43214086 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
43214013 ATATTCATAA
*
43214023 TTATGAAATGTATGATTTAAGTGATGTTATG
1 TTATGAAATATATGATTTAAGTGATGTTATG
43214054 TTATGAAATATATGATTTAAGTGATGTTATG
1 TTATGAAATATATGATTTAAGTGATGTTATG
43214085 TT
1 TT
43214087 TATGTACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (31 bp):
TTATGAAATATATGATTTAAGTGATGTTATG
Found at i:43221645 original size:40 final size:40
Alignment explanation
Indices: 43221600--43221766 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
43221590 CGGAATATAA
43221600 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
43221640 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
43221680 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
43221720 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
43221759 CCGGATAT
1 CCGGATAT
43221767 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:43221750 original size:80 final size:79
Alignment explanation
Indices: 43221600--43221766 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
43221590 CGGAATATAA
* *
43221600 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
43221665 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
43221680 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
43221742 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
43221759 CCGGATAT
1 CCGGATAT
43221767 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:43222615 original size:17 final size:19
Alignment explanation
Indices: 43222592--43222637 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
43222582 AAGAAGCATG
43222592 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
43222610 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
43222628 AATCATGCTC
1 AATCATGCTC
43222638 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:43229667 original size:40 final size:40
Alignment explanation
Indices: 43229622--43229788 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
43229612 CGGAATATAA
43229622 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
43229662 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
43229702 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
43229742 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
43229781 CCGGATAT
1 CCGGATAT
43229789 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:43229772 original size:80 final size:79
Alignment explanation
Indices: 43229622--43229788 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
43229612 CGGAATATAA
* *
43229622 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
43229687 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
43229702 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
43229764 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
43229781 CCGGATAT
1 CCGGATAT
43229789 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:43230637 original size:17 final size:19
Alignment explanation
Indices: 43230614--43230659 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
43230604 AAGAAGCATG
43230614 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
43230632 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
43230650 AATCATGCTC
1 AATCATGCTC
43230660 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:43234497 original size:25 final size:25
Alignment explanation
Indices: 43234468--43234515 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43234458 TTATAATATG
* * *
43234468 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
43234493 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43234516 GTTTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:43234599 original size:11 final size:11
Alignment explanation
Indices: 43234563--43234618 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
43234553 CATGGTATGT
43234563 ATGATATGCAC
1 ATGATATGCAC
* *
43234574 ATGACATG--T
1 ATGATATGCAC
43234583 ATGATATGCAC
1 ATGATATGCAC
*
43234594 ATGATATG--T
1 ATGATATGCAC
43234603 ATGATATGCAC
1 ATGATATGCAC
43234614 ATGAT
1 ATGAT
43234619 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:43234618 original size:20 final size:20
Alignment explanation
Indices: 43234552--43234618 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
43234542 ATTTTGATAA
*
43234552 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
43234572 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
43234592 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
43234612 ACATGAT
1 ACATGAT
43234619 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:43234694 original size:24 final size:24
Alignment explanation
Indices: 43234667--43234840 Score: 276
Period size: 24 Copynumber: 7.2 Consensus size: 24
43234657 GGAGGAAGTG
43234667 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234691 CAAAAGGGCTTATGCCCCAGCTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234715 CAAAAGGGCTTATGCCCCAGCTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234739 CAAAAGGGCTTATGCCCCAGCTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234763 CAAAAGGGCTTATGCCCTAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234787 TAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
43234811 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
43234835 TAAAAG
1 CAAAAG
43234841 AGGGTAGGCC
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 144 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:43236719 original size:30 final size:30
Alignment explanation
Indices: 43236672--43236823 Score: 182
Period size: 30 Copynumber: 5.1 Consensus size: 30
43236662 AGCTTCGGCT
*
43236672 ATCGATT-ATGTAAAGGGATGGTGACGACC
1 ATCGATTAATGAAAAGGGATGGTGACGACC
*
43236701 ATCGATTAATGGAAAGGGATGGTGACGACC
1 ATCGATTAATGAAAAGGGATGGTGACGACC
* * *
43236731 ATCGATTAATGGAAAGGGTTGGTGATGACC
1 ATCGATTAATGAAAAGGGATGGTGACGACC
* ***
43236761 ATCAATTAATGAAAAGGGATGGTTTTGACC
1 ATCGATTAATGAAAAGGGATGGTGACGACC
* **
43236791 ATCGAAT-ATGAAAAGGGATGGTTTCGACC
1 ATCGATTAATGAAAAGGGATGGTGACGACC
43236820 ATCG
1 ATCG
43236824 TTTAGCACAC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
29 32 0.29
30 79 0.71
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (30 bp):
ATCGATTAATGAAAAGGGATGGTGACGACC
Found at i:43243437 original size:22 final size:22
Alignment explanation
Indices: 43243411--43243455 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
43243401 AGATCAACAC
43243411 AAATAT-AATCACATACATATCA
1 AAATATAAATCACAT-CATATCA
*
43243433 AAATATAAATCTCATCATATCA
1 AAATATAAATCACATCATATCA
43243455 A
1 A
43243456 CCATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAAATCACATCATATCA
Found at i:43243530 original size:18 final size:19
Alignment explanation
Indices: 43243507--43243543 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
43243497 TGAACATGTC
43243507 GATGCATACTTTA-AAAAT
1 GATGCATACTTTATAAAAT
*
43243525 GATGCATATTTTATAAAAT
1 GATGCATACTTTATAAAAT
43243544 TTCCTACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (19 bp):
GATGCATACTTTATAAAAT
Found at i:43255029 original size:40 final size:40
Alignment explanation
Indices: 43254970--43255177 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
43254960 CAATTGAATG
* * * *
43254970 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
43255010 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
43255050 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
43255090 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
43255130 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
43255170 ATATCCGG
1 ATATCCGG
43255178 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:43255108 original size:80 final size:80
Alignment explanation
Indices: 43254971--43255177 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
43254961 AATTGAATGA
* * ** * * *
43254971 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
43255036 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
43255049 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
43255114 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
43255131 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
43255178 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:43265040 original size:118 final size:118
Alignment explanation
Indices: 43264830--43265042 Score: 336
Period size: 118 Copynumber: 1.8 Consensus size: 118
43264820 CGTTACATGC
* * *
43264830 TGTTTGCCGAAGGTATCCAGGTGGACCTGAAAAAGATAGAGGTTATTCTGGAGTGGAAGCAACCT
1 TGTTTGCCGAAGGTATCCAAGTGGACCTGAAAAAGATAGAAGTTATTCTAGAGTGGAAGCAACCT
* *
43264895 AGGAATGTTTCTAAGATTTGGAGTTTTCTCAGTTACGTTTTTGGGTGATGTGG
66 AGGAATGTTTCTAAGATTCGAAGTTTTCTCAGTTACGTTTTTGGGTGATGTGG
* *
43264948 TGTTTGTCGAAGGTATCCAAGTGGACCTGAAAAAGATAGAAGTTATTCTAGAGTGGAAGCAACTT
1 TGTTTGCCGAAGGTATCCAAGTGGACCTGAAAAAGATAGAAGTTATTCTAGAGTGGAAGCAACCT
* * *
43265013 AGGAATGTTTTTGAGATTCGAATTTTTCTC
66 AGGAATGTTTCTAAGATTCGAAGTTTTCTC
43265043 GGTCTAGCAG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 85 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (118 bp):
TGTTTGCCGAAGGTATCCAAGTGGACCTGAAAAAGATAGAAGTTATTCTAGAGTGGAAGCAACCT
AGGAATGTTTCTAAGATTCGAAGTTTTCTCAGTTACGTTTTTGGGTGATGTGG
Found at i:43269082 original size:79 final size:82
Alignment explanation
Indices: 43268945--43269129 Score: 256
Period size: 79 Copynumber: 2.3 Consensus size: 82
43268935 TCGAATGATG
*
43268945 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
43269009 TGTGCGAGTTACTA-AA
66 TGTGCGAGTTACTATAA
* * * **
43269025 TCCGGGTTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT
43269087 TTGTGCGAGTTACTATAA
65 TTGTGCGAGTTACTATAA
*
43269105 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43269130 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.63
80 33 0.35
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATAA
Found at i:43269136 original size:40 final size:40
Alignment explanation
Indices: 43268945--43269129 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
43268935 TCGAATGATG
* * *
43268945 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
43268985 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43269025 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43269064 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43269105 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43269130 AACGAGTAGC
Statistics
Matches: 133, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
39 40 0.30
40 83 0.62
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43269151 original size:79 final size:79
Alignment explanation
Indices: 43268945--43269162 Score: 252
Period size: 79 Copynumber: 2.7 Consensus size: 79
43268935 TCGAATGATG
* *
43268945 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCAT
43269008 TTGTGCGAGTTACTAAA
63 TTGTGCGAGTTACTAAA
* *
43269025 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCAT
43269087 TTGTGCGAGTTACTATAA
63 TTGTGCGAGTTACTA-AA
* **
43269105 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGA-TCCGAAGG
43269163 TACGTGATTC
Statistics
Matches: 119, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
78 1 0.01
79 70 0.59
80 48 0.40
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTG
TGCGAGTTACTAAA
Found at i:43269159 original size:119 final size:119
Alignment explanation
Indices: 43268945--43269162 Score: 282
Period size: 119 Copynumber: 1.8 Consensus size: 119
43268935 TCGAATGATG
*
43268945 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTT
** *
43269010 GTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
66 GAACGAGTTACTAAATCCGGGTTAACTCCGAAGGCATTTGTGCGAGTTACTAAA
* * * * *
43269064 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAACCGGACTAAGAT-CCGAAGGCAT
*
43269127 TTGAACGAG-TAGCTATATCC-GGTTAAACTCCGAAGG
64 TTGAACGAGTTA-CTAAATCCGGGTT-AACTCCGAAGG
43269163 TACGTGATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
118 7 0.08
119 71 0.84
120 7 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAATCCGGGTTAACTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43277266 original size:40 final size:40
Alignment explanation
Indices: 43277075--43277259 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
43277065 TCGAATGATG
* * *
43277075 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
43277115 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
43277155 TCCGCGTTAAGT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43277194 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43277235 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43277260 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 38 0.29
40 81 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43277289 original size:119 final size:119
Alignment explanation
Indices: 43277075--43277292 Score: 282
Period size: 119 Copynumber: 1.8 Consensus size: 119
43277065 TCGAATGATG
*
43277075 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTT
** *
43277140 GTGCGAGTTACTAAATCCGCGTTAAGTCCGAAGGCATTTGTACGAGTTACTAAA
66 GAACGAGTTACTAAATCCGCGTTAACTCCGAAGGCATTTGTACGAGTTACTAAA
* * * * *
43277194 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAACCGGACTAAGAT-CCGAAGGCAT
*
43277257 TTGAACGAG-TAGCTATATCCG-GTTAAACTCCGAAGG
64 TTGAACGAGTTA-CTAAATCCGCGTT-AACTCCGAAGG
43277293 TACGTGATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
118 6 0.07
119 72 0.85
120 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAATCCGCGTTAACTCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:43277290 original size:79 final size:78
Alignment explanation
Indices: 43277075--43277292 Score: 239
Period size: 79 Copynumber: 2.7 Consensus size: 78
43277065 TCGAATGATG
* * *
43277075 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTAG-CTATATCCGG-TTAA-ATCCGAAGGCAT
43277138 TTGTGCGAGTTACTAAA
62 TTGTGCGAGTTACTAAA
* * * *
43277155 TCCGCGTTAAGT-CCGAAGGCATTTGTACGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAG-TAGCTATATCC-GGTTAAAT-CCGAAGGCATT
43277218 TGTGCGAGTTACTATAA
63 TGTGCGAGTTACTA-AA
* *
43277235 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTAGCTATATCCGGTTAAA-TCCGAAGG
43277293 TACGTGATTC
Statistics
Matches: 116, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
78 1 0.01
79 68 0.59
80 47 0.41
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTAGCTATATCCGGTTAAATCCGAAGGCATTTGT
GCGAGTTACTAAA
Found at i:43279324 original size:44 final size:44
Alignment explanation
Indices: 43279206--43279376 Score: 263
Period size: 44 Copynumber: 3.9 Consensus size: 44
43279196 TATACAGTAC
43279206 TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
** *
43279250 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATTTCGGTAAGATAT
1 TATTCGGGCC-TTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* *
43279295 TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAGACAC
1 TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
* *
43279339 TATTCGGGCCTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGA
43279377 ATGAATTCGG
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
43 11 0.09
44 64 0.55
45 41 0.35
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (44 bp):
TATTCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
Found at i:43280005 original size:24 final size:24
Alignment explanation
Indices: 43279973--43280021 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
43279963 GACTTAAGTG
43279973 AATGATATTTTGAAATGTTGATGT
1 AATGATATTTTGAAATGTTGATGT
43279997 AATGATATTTTGAAATGTTGATGT
1 AATGATATTTTGAAATGTTGATGT
43280021 A
1 A
43280022 TATAAGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (24 bp):
AATGATATTTTGAAATGTTGATGT
Found at i:43287418 original size:111 final size:111
Alignment explanation
Indices: 43287224--43287448 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
43287214 TGTGGACAGA
*
43287224 CTCCATGATTAAGTAATTGTAAATTATTAGAACGATGTTTCTGGACATAATTACAATTACTAGAG
1 CTCCATGATTAAGTAATTGTAAATTATTAGAACGATGCTTCTGGACATAATTACAATTACTAGAG
43287289 TCTAATTGTATATGTCCGATTGGTCCCTCTGTTAGCCCAACAAAAG
66 TCTAATTGTATATGTCCGATTGGTCCCTCTGTTAGCCCAACAAAAG
43287335 CTCCATGATTAAGTAATTGTAAATTATTAGAACGATGCTTCTGGACATAATTACAATTACTAGAG
1 CTCCATGATTAAGTAATTGTAAATTATTAGAACGATGCTTCTGGACATAATTACAATTACTAGAG
43287400 TCTAATTGTATATGTCCGATTGGTCCCTCTGTTAGCCCAACAAAAG
66 TCTAATTGTATATGTCCGATTGGTCCCTCTGTTAGCCCAACAAAAG
43287446 CTC
1 CTC
43287449 GATCAGACTA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (111 bp):
CTCCATGATTAAGTAATTGTAAATTATTAGAACGATGCTTCTGGACATAATTACAATTACTAGAG
TCTAATTGTATATGTCCGATTGGTCCCTCTGTTAGCCCAACAAAAG
Found at i:43288156 original size:48 final size:48
Alignment explanation
Indices: 43288085--43288182 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 48
43288075 TATTCCAAAA
*
43288085 TAATATTATTTTAAAAGTTTAATATTAAATTAAATTTAAT-ATTTATCT
1 TAATAGTATTTTAAAAGTTTAATATTAAATTAAATTTAATGA-TTATCT
* * *
43288133 TAATAGTATTTTATTAA-TTTAATATTAAATTTAGTTTAATGATTATCT
1 TAATAGTATTTTA-AAAGTTTAATATTAAATTAAATTTAATGATTATCT
43288181 TA
1 TA
43288183 TAGATAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
48 41 0.93
49 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (48 bp):
TAATAGTATTTTAAAAGTTTAATATTAAATTAAATTTAATGATTATCT
Found at i:43291324 original size:18 final size:18
Alignment explanation
Indices: 43291301--43291346 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
43291291 GAATCATCCC
*
43291301 TCATCCCTCA-TCCTTCA
1 TCATCCCTCAGTCATTCA
43291318 TTCATCCCTCAGTCATTCA
1 -TCATCCCTCAGTCATTCA
43291337 TCATTCCCTC
1 TCA-TCCCTC
43291347 CTCTCTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.17, C:0.43, G:0.02, T:0.37
Consensus pattern (18 bp):
TCATCCCTCAGTCATTCA
Found at i:43298488 original size:17 final size:17
Alignment explanation
Indices: 43298449--43298482 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43298439 GTTGTCGTTG
43298449 CTGCAACCTCTTAGCCA
1 CTGCAACCTCTTAGCCA
*
43298466 CTGCAACCTCTTCGCCA
1 CTGCAACCTCTTAGCCA
43298483 TCGCAAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.44, G:0.12, T:0.24
Consensus pattern (17 bp):
CTGCAACCTCTTAGCCA
Found at i:43304777 original size:40 final size:40
Alignment explanation
Indices: 43304716--43304919 Score: 239
Period size: 40 Copynumber: 5.1 Consensus size: 40
43304706 CGGAATTTAG
* ** *
43304716 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * *
43304756 CCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
43304796 CCGGATATAACCACTCGCACAAATGCCTTCAGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
43304836 CCGGATATAACAACTCGGACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * * * *
43304876 CTGGATATAATC-ACTAGCATAAATGCCTTTGGGGCTTAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAAC
43304916 CCGG
1 CCGG
43304920 GTATCATTCA
Statistics
Matches: 140, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 139 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:43304816 original size:80 final size:80
Alignment explanation
Indices: 43304712--43304923 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 80
43304702 TCTTCGGAAT
* * *
43304712 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTCGCAC
43304776 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * * *
43304791 TTAGCCCGGATATAACCACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAACAACTCGGAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTCGCAC
43304856 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * * * * *
43304871 TTAGCCTGGATATAATCACTAGCATAAATGCCTTTGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
43304924 CATTCAAATG
Statistics
Matches: 116, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 4 0.03
80 112 0.97
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTCGCAC
AAATGCCTTCGGGTC
Found at i:43312194 original size:20 final size:21
Alignment explanation
Indices: 43312169--43312309 Score: 81
Period size: 20 Copynumber: 7.0 Consensus size: 21
43312159 AATCTAACCC
43312169 TATATATTTATTTTAATTATTAT
1 TATATATTTATTTT-A-TATTAT
*
43312192 ATATATATTT-TTTTATATTGT
1 -TATATATTTATTTTATATTAT
* * ***
43312213 TATTTGTTTTATTTT-TAACCT
1 TATAT-ATTTATTTTATATTAT
*
43312234 TAT-T-TTTATATTATA-TA-
1 TATATATTTATTTTATATTAT
43312251 T-TATA-TTATTATTAT-TTAT
1 TATATATTTATT-TTATATTAT
43312270 TATATA-TTA-TTTATATTAT
1 TATATATTTATTTTATATTAT
*
43312289 TAT-TATTTATTATATATTAT
1 TATATATTTATTTTATATTAT
43312309 T
1 T
43312310 TTTCACAAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
16 1 0.01
17 6 0.06
18 19 0.20
19 14 0.15
20 22 0.23
21 14 0.15
22 5 0.05
23 4 0.04
24 9 0.10
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (21 bp):
TATATATTTATTTTATATTAT
Found at i:43312252 original size:7 final size:7
Alignment explanation
Indices: 43312240--43312464 Score: 100
Period size: 7 Copynumber: 32.1 Consensus size: 7
43312230 ACCTTATTTT
43312240 TATATTA
1 TATATTA
43312247 TATA-T-
1 TATATTA
43312252 TATATTA
1 TATATTA
43312259 T-TATTA
1 TATATTA
*
43312265 TTTATTA
1 TATATTA
43312272 TATATTA
1 TATATTA
43312279 TTTATATTA
1 --TATATTA
43312288 T-TATTA
1 TATATTA
*
43312294 TTTATTA
1 TATATTA
43312301 TATATTA
1 TATATTA
*
43312308 T-TTTTCA
1 TATATT-A
* *
43312315 CAAATTA
1 TATATTA
43312322 T-TATTA
1 TATATTA
*
43312328 TTTTCCATTA
1 -TAT--ATTA
43312338 T-TATTTA
1 TATA-TTA
43312345 TATATTA
1 TATATTA
43312352 T-TATTA
1 TATATTA
*
43312358 TATTTTTA
1 TA-TATTA
*
43312366 CTTGTATTA
1 --TATATTA
43312375 TATATT-
1 TATATTA
43312381 TATTAATTA
1 TA-T-ATTA
*
43312390 TTTA-TA
1 TATATTA
*
43312396 TATTTTA
1 TATATTA
43312403 TATATTA
1 TATATTA
*
43312410 T-T-TTT
1 TATATTA
*
43312415 TACA-TA
1 TATATTA
*
43312421 TATACTTT
1 TATA-TTA
43312429 TATATTA
1 TATATTA
43312436 TATATTA
1 TATATTA
43312443 TA-ATTA
1 TATATTA
*
43312449 TTTTATTA
1 -TATATTA
43312457 TATATTA
1 TATATTA
43312464 T
1 T
43312465 TATGTCATTT
Statistics
Matches: 166, Mismatches: 24, Indels: 56
0.67 0.10 0.23
Matches are distributed among these distances:
5 7 0.04
6 43 0.26
7 75 0.45
8 23 0.14
9 13 0.08
10 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTA
Found at i:43312262 original size:3 final size:3
Alignment explanation
Indices: 43312233--43312517 Score: 112
Period size: 3 Copynumber: 90.0 Consensus size: 3
43312223 ATTTTTAACC
*
43312233 TTA TTT TTA -TA TTA TATA TTA -TA TTA TTA TTA TTTA TTA TATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA
* **
43312279 TT- TATA TTA TTA TTA TTTA TTA TATA TTA TTT TTCA CAAA TTA TTA
1 TTA T-TA TTA TTA TTA -TTA TTA T-TA TTA TTA TT-A -TTA TTA TTA
*
43312325 TTA TT- TTCCA TTA TTA TTTA TATA TTA TTA TTA -TA TTT TTA CTT-
1 TTA TTA TT--A TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA -TTA
*
43312369 GTA TTA TATA TTTA TTAA TTA TTTA TATA TT- TTA TATA TTA TT- TT-
1 TTA TTA T-TA -TTA TT-A TTA -TTA T-TA TTA TTA T-TA TTA TTA TTA
* *
43312414 TTA CATA TATA CTT- TTA -TA TTA TATA TTA TAA TTA TT- TTA TTA TATA
1 TTA -TTA T-TA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA
* * *
43312461 TTA TTA TGTCA TT- TTT TTA -TA TTA TTA TACA TTT TTA TCTA TGTA
1 TTA TTA T-T-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA T-TA
43312506 TTA TTA TTA TTA
1 TTA TTA TTA TTA
43312518 AAGGTTTTTA
Statistics
Matches: 219, Mismatches: 22, Indels: 82
0.68 0.07 0.25
Matches are distributed among these distances:
2 26 0.12
3 125 0.57
4 62 0.28
5 6 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43312293 original size:47 final size:46
Alignment explanation
Indices: 43312242--43312488 Score: 166
Period size: 49 Copynumber: 5.1 Consensus size: 46
43312232 CTTATTTTTA
43312242 TATTATATATTATATTATTATTATTTATTATATATTATTTATATTAT
1 TATTATATATTATATTATTATT-TTTATTATATATTATTTATATTAT
*
43312289 TATTATTTATTATA-TATTATTTTTCACAAATTAT-TATTATTT-TCCATTAT
1 TATTATATATTATATTATTATTTTT-----ATTATATATTATTTAT--ATTAT
* *
43312339 TATTTATATATTATTATTA-TATTTTTACTTGTATTATATATTTAT-TAAT
1 TA-TTATATATTA-TATTATTATTTTTA-TTATA-TAT-TATTTATATTAT
* * *
43312388 TATTTATATATTTTATATATTATTTTTTACATATATACT-TTTATATTAT
1 TA-TTATATATTATAT-TATTA-TTTTTA-TTATATATTATTTATATTAT
* * * *
43312437 ATATTATA-ATTATTTTATTATATATTATTATGTCATTTTTTTATATTAT
1 -TATTATATATTATATTATTAT-TTTTATTATAT-A-TTATTTATATTAT
43312486 TAT
1 TAT
43312489 ACATTTTTAT
Statistics
Matches: 161, Mismatches: 15, Indels: 47
0.72 0.07 0.21
Matches are distributed among these distances:
45 3 0.02
46 12 0.07
47 24 0.15
48 21 0.13
49 44 0.27
50 21 0.13
51 24 0.15
52 10 0.06
53 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTATATATTATATTATTATTTTTATTATATATTATTTATATTAT
Found at i:43312357 original size:20 final size:20
Alignment explanation
Indices: 43312233--43312516 Score: 121
Period size: 20 Copynumber: 14.6 Consensus size: 20
43312223 ATTTTTAACC
*
43312233 TTATTTTTATATTATATATTA
1 TTATTATTAT-TTATATATTA
*
43312254 -TATTATTA-TTATTTATTA
1 TTATTATTATTTATATATTA
43312272 -TA-TATTA-TT-TATATTA
1 TTATTATTATTTATATATTA
43312288 TTATTATT-TATTATATATTA
1 TTATTATTAT-TTATATATTA
* ** *
43312308 TTTTTCACAAATTAT-TATTA
1 TTATT-ATTATTTATATATTA
43312328 TTTTCCATTATTATTTATATATTA
1 --TT--ATTATTATTTATATATTA
43312352 TTATTA-TATTT-T-TACTT-
1 TTATTATTATTTATATA-TTA
*
43312369 GTATTATATATTTAT-TA--A
1 TTATTAT-TATTTATATATTA
43312387 TTATTTATATATTTTATATATTA
1 TTA-TTAT-TA-TTTATATATTA
**
43312410 TT-TT-TTACATATATACTT-
1 TTATTATTATTTATATA-TTA
* *
43312428 TTA-TATTATATAT-TATAA
1 TTATTATTATTTATATATTA
43312446 TTATT-TTA-TTATATATTA
1 TTATTATTATTTATATATTA
*
43312464 TTATGTCATT-TTTTTATATTA
1 TTAT-T-ATTATTTATATATTA
* *
43312485 TTATACATT-TTTATCTATGTA
1 TTAT-TATTATTTATATAT-TA
43312506 TTATTATTATT
1 TTATTATTATT
43312517 AAAGGTTTTT
Statistics
Matches: 204, Mismatches: 25, Indels: 68
0.69 0.08 0.23
Matches are distributed among these distances:
16 6 0.03
17 20 0.10
18 45 0.22
19 32 0.16
20 49 0.24
21 32 0.16
22 4 0.02
23 9 0.04
24 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTATTATTTATATATTA
Found at i:43312719 original size:21 final size:20
Alignment explanation
Indices: 43312678--43312716 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43312668 TCTAAACTTA
*
43312678 TATTTATTATATTATATAAT
1 TATTTATTATAATATATAAT
43312698 TATTTCATTATAA-ATATAA
1 TATTT-ATTATAATATATAA
43312717 ATTCTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTATTATAATATATAAT
Found at i:43312811 original size:15 final size:15
Alignment explanation
Indices: 43312769--43312827 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 15
43312759 CCAATATATT
43312769 TTATTTTTTATATAA
1 TTATTTTTTATATAA
43312784 TTATTATTCTTATA-AA
1 TTATT-TT-TTATATAA
43312800 TATATTTTTTATTATATA
1 T-TATTTTTTA-TATA-A
*
43312818 TTATATTTTA
1 TTATTTTTTA
43312828 AATTTATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 8 0.22
16 9 0.24
17 18 0.49
18 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTTTTATATAA
Found at i:43312835 original size:85 final size:84
Alignment explanation
Indices: 43312662--43312827 Score: 198
Period size: 87 Copynumber: 1.9 Consensus size: 84
43312652 ACTTATTTTA
*
43312662 TATTTTTCTAAACTTATATTTATTATATTATATAATTATTTCATTATAAATATAAATTCTTTTAC
1 TATTTTTCTAAACATATATTTATTATATTATATAATTATTTCATTATAAATAT-AATTCTTTTAC
43312727 ATATTTGATATTTTATACAT
65 ATATTTGATATTTTATACAT
*
43312747 TATTTTTCTAAACCAATATATTTTATT-TTTTATATAATTATTATTC-TTATAAATAT-ATT-TT
1 TATTTTTCTAAA-C-ATATA-TTTATTATATTATATAATTA-T-TTCATTATAAATATAATTCTT
*
43312808 TTATTATATATT-ATATTTTA
61 TTA-CATAT-TTGATATTTTA
43312828 AATTTATTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
85 17 0.24
86 16 0.23
87 18 0.25
88 17 0.24
89 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.58
Consensus pattern (84 bp):
TATTTTTCTAAACATATATTTATTATATTATATAATTATTTCATTATAAATATAATTCTTTTACA
TATTTGATATTTTATACAT
Found at i:43312851 original size:26 final size:26
Alignment explanation
Indices: 43312803--43312852 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
43312793 TTATAAATAT
* * * *
43312803 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
43312829 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
43312853 TTTATTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:43313672 original size:3 final size:3
Alignment explanation
Indices: 43313666--43313697 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43313656 TAAAAGTATG
43313666 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
43313698 TCTACAATAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43314516 original size:27 final size:26
Alignment explanation
Indices: 43314467--43314533 Score: 109
Period size: 27 Copynumber: 2.6 Consensus size: 26
43314457 TTTTTTGGGG
43314467 GGGTTAGG-TTTTTTCTTTTTTTTTT
1 GGGTTAGGTTTTTTTCTTTTTTTTTT
43314492 GGGTTAGGTTTTTTTCTTTTTTTTTTT
1 GGGTTAGGTTTTTTTC-TTTTTTTTTT
*
43314519 TGGTTAGGTTTTTTT
1 GGGTTAGGTTTTTTT
43314534 TTTGGGAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 8 0.21
26 7 0.18
27 24 0.62
ACGTcount: A:0.04, C:0.03, G:0.21, T:0.72
Consensus pattern (26 bp):
GGGTTAGGTTTTTTTCTTTTTTTTTT
Found at i:43317341 original size:18 final size:18
Alignment explanation
Indices: 43317318--43317352 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43317308 GAGTTAAACG
*
43317318 AATCAAGTTATTCGAGTT
1 AATCAAGTTACTCGAGTT
43317336 AATCAAGTTACTCGAGT
1 AATCAAGTTACTCGAGT
43317353 CAACTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
AATCAAGTTACTCGAGTT
Found at i:43317429 original size:9 final size:9
Alignment explanation
Indices: 43317402--43317438 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
43317392 TAAGTTTTCG
43317402 AATTCGAAT
1 AATTCGAAT
* *
43317411 AACTCAAAT
1 AATTCGAAT
43317420 AATTCGAAT
1 AATTCGAAT
43317429 AATTCGAAT
1 AATTCGAAT
43317438 A
1 A
43317439 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43317599 original size:14 final size:14
Alignment explanation
Indices: 43317577--43317607 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43317567 CCAAAATCTA
*
43317577 TTTCTCACCAAAAT
1 TTTCCCACCAAAAT
43317591 TTTCCCACCAAAAT
1 TTTCCCACCAAAAT
43317605 TTT
1 TTT
43317608 ACTCTCCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTCCCACCAAAAT
Found at i:43328824 original size:42 final size:42
Alignment explanation
Indices: 43328777--43328883 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
43328767 TATTGGTCTC
*
43328777 GGCACTAAGTGTGCAGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
43328819 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
43328861 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
43328884 ATTGTACAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:43328948 original size:27 final size:28
Alignment explanation
Indices: 43328891--43328960 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
43328881 AAAATTGTAC
**
43328891 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
43328919 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
43328946 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
43328961 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:43343101 original size:28 final size:28
Alignment explanation
Indices: 43343061--43343115 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
43343051 GTTTATGATG
* *
43343061 ATTTGTTCTTCAAGAAGACGTCTGGTTA
1 ATTTGTTCTTCAAGAAAACATCTGGTTA
43343089 ATTTGTTCTTCAAGAAAACATCTGGTT
1 ATTTGTTCTTCAAGAAAACATCTGGTT
43343116 TATGATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (28 bp):
ATTTGTTCTTCAAGAAAACATCTGGTTA
Found at i:43347155 original size:49 final size:50
Alignment explanation
Indices: 43347033--43347164 Score: 153
Period size: 49 Copynumber: 2.7 Consensus size: 50
43347023 TATGAGATGT
*
43347033 GTCAGTGTAAGACCATGTCCGGGACATGGCATCAGCACAAATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAATATGTGAGA
* * ** * * *
43347083 G-CTAGTGTAAGACCATGTTTGGGACATGGCGTTGGCCTCAAGT-T-TGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCAG-CACAAATATGTGAGA
43347132 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
43347165 GGTATTATAC
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 33 0.49
50 30 0.44
51 5 0.07
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAATATGTGAGA
Found at i:43349763 original size:21 final size:21
Alignment explanation
Indices: 43349734--43349777 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
43349724 CTTTTTCCTA
* *
43349734 GAGTGTGAATTGAATTAAATT
1 GAGTATGAAATGAATTAAATT
*
43349755 GAGTATGAAATGGATTAAATT
1 GAGTATGAAATGAATTAAATT
43349776 GA
1 GA
43349778 TGTTAAGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (21 bp):
GAGTATGAAATGAATTAAATT
Found at i:43350260 original size:25 final size:25
Alignment explanation
Indices: 43350218--43350272 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
43350208 AAACGCATCT
*
43350218 ATTTATGAGCGTCCTGATATAGGCTC
1 ATTTGTGAGCGTCCTGATAT-GGCTC
* *
43350244 -TTTGTGAGCTTCTTGATATGGCTC
1 ATTTGTGAGCGTCCTGATATGGCTC
43350268 ATTTG
1 ATTTG
43350273 AACATATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (25 bp):
ATTTGTGAGCGTCCTGATATGGCTC
Found at i:43359102 original size:29 final size:29
Alignment explanation
Indices: 43359047--43359102 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
43359037 AATTAACTTA
**
43359047 AAATTAAAATTTAATTATATTAATACATC
1 AAATTAAAATTTAATTATAACAATACATC
*
43359076 AAATTAAAA-TTAATGTATAACATTACA
1 AAATTAAAATTTAAT-TATAACAATACA
43359103 AATTATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTAAAATTTAATTATAACAATACATC
Found at i:43361033 original size:17 final size:18
Alignment explanation
Indices: 43361005--43361040 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43360995 CTAGGTTTGT
43361005 ATTTGTATTTAGTGATTA
1 ATTTGTATTTAGTGATTA
*
43361023 ATTTG-ATTTAGTGGTTA
1 ATTTGTATTTAGTGATTA
43361040 A
1 A
43361041 GAGTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (18 bp):
ATTTGTATTTAGTGATTA
Found at i:43362252 original size:16 final size:17
Alignment explanation
Indices: 43362222--43362254 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43362212 AACAATTTTT
43362222 TAAAATATTAATTTAATA
1 TAAAATATT-ATTTAATA
43362240 TAAAATATT-TTTAAT
1 TAAAATATTATTTAAT
43362255 TTTATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATATTATTTAATA
Found at i:43363375 original size:15 final size:17
Alignment explanation
Indices: 43363338--43363369 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43363328 ATAATAATAC
43363338 ATAA-TAATATATTATA
1 ATAATTAATATATTATA
43363354 ATAATTAATATATTAT
1 ATAATTAATATATTAT
43363370 GTATTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATTAATATATTATA
Found at i:43363463 original size:26 final size:25
Alignment explanation
Indices: 43363419--43363481 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
43363409 TAATAAAATA
* *
43363419 ATATATTTTATAAGTATTAATATAT
1 ATATATATTATAACTATTAATATAT
*
43363444 ATATATATATATAACTATTATTATAT
1 ATATATAT-TATAACTATTAATATAT
*
43363470 -TATAGATTATAA
1 ATATATATTATAA
43363482 TAAAAGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.15
25 13 0.39
26 15 0.45
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (25 bp):
ATATATATTATAACTATTAATATAT
Found at i:43364645 original size:18 final size:21
Alignment explanation
Indices: 43364609--43364646 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43364599 AATATTATAA
43364609 ATATTATAAAACTATAAAATT
1 ATATTATAAAACTATAAAATT
43364630 ATATTA-AAAA-TA-AAAAT
1 ATATTATAAAACTATAAAAT
43364647 ACTTACCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 2 0.12
20 4 0.24
21 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATTATAAAACTATAAAATT
Found at i:43370747 original size:5 final size:5
Alignment explanation
Indices: 43370734--43370765 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
43370724 AAAACACAAT
*
43370734 TTTTT TTTTG TTTTG TTTTG TTTTG TTTTG TT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
43370766 GATCATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:43372921 original size:20 final size:19
Alignment explanation
Indices: 43372880--43372922 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
43372870 AATAGTGATT
**
43372880 TTTTTAAAAAAAATTTAGA
1 TTTTTAAAAAAAAAATAGA
*
43372899 TTTTTAAAAATAAAAATATA
1 TTTTTAAAAA-AAAAATAGA
43372919 TTTT
1 TTTT
43372923 AGTCATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTTTAAAAAAAAAATAGA
Found at i:43372990 original size:141 final size:144
Alignment explanation
Indices: 43372729--43373035 Score: 435
Period size: 141 Copynumber: 2.1 Consensus size: 144
43372719 AAGTTTTGAT
*
43372729 TTTTTTTAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAAAATATTTTTTAGTCATTTTAAAGA
1 TTTTTTT-AAAA-A-AAA-TTTAGATTTTTAAAAAT-AAAAAATATATTTTAGTCATTTTAAAGA
** * *
43372794 AAAAGTTTAATTTTTTTTAAAACAAAGTTTTGATCTTTTTCAACTACTTCAAAATAAAGTTTTGA
61 AAAAGTTTAATGATTTTTAAAACAAAGTTTTGATCTTTTTAAACTACTTCAAAATAAAGCTTTGA
43372859 TTTTTAAGAAAAATAGTGA
126 TTTTTAAGAAAAATAGTGA
43372878 TTTTTTTAAAAAAAATTTAGATTTTTAAAAAT-AAAAATATATTTTAGTCATTTTAAA-AGAAAA
1 TTTTTTTAAAAAAAATTTAGATTTTTAAAAATAAAAAATATATTTTAGTCATTTTAAAGA-AAAA
* *
43372941 G-TTAA-GATTTTTAAAACAAAGTTTTGATCTTTTTAAACTATTTCGAAATAAAGCTTTGATTTT
65 GTTTAATGATTTTTAAAACAAAGTTTTGATCTTTTTAAACTACTTCAAAATAAAGCTTTGATTTT
* *
43373004 TAAGAAAAGTTGTGA
130 TAAGAAAAATAGTGA
*
43373019 -TTTTTTAAAGAAAATTT
1 TTTTTTTAAAAAAAATTT
43373036 TAATTTTGCA
Statistics
Matches: 147, Mismatches: 10, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
140 16 0.11
141 65 0.44
142 5 0.03
143 29 0.20
145 17 0.12
146 3 0.02
147 1 0.01
148 4 0.03
149 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (144 bp):
TTTTTTTAAAAAAAATTTAGATTTTTAAAAATAAAAAATATATTTTAGTCATTTTAAAGAAAAAG
TTTAATGATTTTTAAAACAAAGTTTTGATCTTTTTAAACTACTTCAAAATAAAGCTTTGATTTTT
AAGAAAAATAGTGA
Found at i:43373041 original size:20 final size:20
Alignment explanation
Indices: 43373000--43373042 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
43372990 AAAGCTTTGA
*
43373000 TTTTTAAGAAAAGTTGTGAT
1 TTTTTAAGAAAAGTTGTAAT
*
43373020 TTTTTAAAGAAAA-TTTTAAT
1 TTTTT-AAGAAAAGTTGTAAT
43373040 TTT
1 TTT
43373043 GCAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTTTAAGAAAAGTTGTAAT
Found at i:43375643 original size:20 final size:21
Alignment explanation
Indices: 43375606--43375653 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
43375596 TAATTTCGTA
*
43375606 TTTTTTTCATTTGTCTTTATT
1 TTTTTTTCATTTGACTTTATT
*
43375627 GTTTTTTT-A-TTGACTTTGTT
1 -TTTTTTTCATTTGACTTTATT
43375647 TTTTTTT
1 TTTTTTT
43375654 TTTGTGTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 9 0.38
21 1 0.04
22 7 0.29
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTTTTTCATTTGACTTTATT
Found at i:43381960 original size:40 final size:39
Alignment explanation
Indices: 43381790--43381971 Score: 183
Period size: 40 Copynumber: 4.6 Consensus size: 39
43381780 ATGATGTCCA
* *
43381790 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGC-AAGTTACTAAATCC
* * *
43381829 GGACTAAGAT-CCAAAGGCATTCGTGCGAGTTACTAAATCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCAAGTTACTAAATCC
*
43381869 GGACTAAGAT-CCGAAGGCATTTATGCAAGTTACTAAATCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCAAGTTACTAAATCC
* *
43381909 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 -GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-AATCC
*
43381949 GAGCTATGTCCCGAAGGCATTTG
1 G-GCTAAGTCCCGAAGGCATTTG
43381972 AACCAGTAGC
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.03
40 107 0.88
41 11 0.09
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAAATCC
Found at i:43381963 original size:80 final size:80
Alignment explanation
Indices: 43381790--43381970 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
43381780 ATGATGTCCA
* *
43381790 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCAAAGGCATTCGTG
1 GGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGACTAAGATCCAAAGGCATTCGTG
43381854 CGAGTTACTAAATCC
66 CGAGTTACTAAATCC
* ** * *
43381869 GGACTAAGAT-CCGAAGGCATTTATGC-AAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTT
1 GG-CTAAG-TCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGACTAAGAT-CCAAAGGCATTC
43381931 GTGCGAGTTACTATAA-CC
63 GTGCGAGTTACTA-AATCC
*
43381949 GAGCTATGTCCCGAAGGCATTT
1 G-GCTAAGTCCCGAAGGCATTT
43381971 GAACCAGTAG
Statistics
Matches: 87, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
79 4 0.05
80 73 0.84
81 10 0.11
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGACTAAGATCCAAAGGCATTCGTG
CGAGTTACTAAATCC
Found at i:43391100 original size:47 final size:47
Alignment explanation
Indices: 43391046--43391178 Score: 221
Period size: 47 Copynumber: 2.8 Consensus size: 47
43391036 ACAATCGAGA
* * * * *
43391046 AGTACCTATACCCTAGTCCGTAGCCAAATCAAGGTAACTTTTCCTGG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGG
43391093 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGG
43391140 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACT
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACT
43391179 CCTCTCAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 81 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGG
Found at i:43391193 original size:94 final size:94
Alignment explanation
Indices: 43391046--43391218 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
43391036 ACAATCGAGA
* * ** ** *
43391046 AGTACCTATACCCTAGTCCGTAGCCAAATCAAGGTAACTTTTCCTGGAGTACCTATACCATGGCC
1 AGTACCTATACCATAGCCCGTAGCCAAATCAAGGTAACTCCTCCTAAAATACCTATACCATGGCC
43391111 CGTAGCCAAATCAAGGTAACTTATCCCGG
66 CGTAGCCAAATCAAGGTAACTTATCCCGG
* **
43391140 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCT-CTCAAAATACCTATGTCATGGC
1 AGTACCTATACCATAGCCCGTAGCCAAATCAAGGTAACTCCTCCT-AAAATACCTATACCATGGC
*
43391204 CTGTAGCCAAATCAA
65 CCGTAGCCAAATCAA
43391219 TGTATTATTC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
93 2 0.03
94 65 0.97
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (94 bp):
AGTACCTATACCATAGCCCGTAGCCAAATCAAGGTAACTCCTCCTAAAATACCTATACCATGGCC
CGTAGCCAAATCAAGGTAACTTATCCCGG
Found at i:43391210 original size:47 final size:47
Alignment explanation
Indices: 43391048--43391218 Score: 180
Period size: 47 Copynumber: 3.6 Consensus size: 47
43391038 AATCGAGAAG
* * * ** *** *
43391048 TACCTATACCCTAGTCCGTAGCCAAATCAAGGTAACTTTTCCTGGAG
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
* ** *
43391095 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGGAG
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
* *
43391142 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCAAAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
** *
43391189 TACCTATGTCATGGCCTGTAGCCAAATCAA
1 TACCTATACCATGGCCCGTAGCCAAATCAA
43391219 TGTATTATTC
Statistics
Matches: 110, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (47 bp):
TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
Found at i:43392517 original size:13 final size:12
Alignment explanation
Indices: 43392498--43392533 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
43392488 AATTGGGCTG
43392498 TTACAGGACCCT
1 TTACAGGACCCT
43392510 TATACAGGACCC-
1 T-TACAGGACCCT
43392522 TTACAGGACCCT
1 TTACAGGACCCT
43392534 GTAGATATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (12 bp):
TTACAGGACCCT
Found at i:43395726 original size:49 final size:49
Alignment explanation
Indices: 43395645--43395828 Score: 260
Period size: 49 Copynumber: 3.7 Consensus size: 49
43395635 TCTATTGTGA
* *
43395645 GGTCACATGTGTAGTACTAAGTGCAGGATACTACGTGTACTGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTGGATAATT
* * **
43395694 GGTCTCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTGGATAA-TT
* * *
43395744 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTGGATAATT
*
43395794 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
43395829 CATACCAAAT
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 73 0.62
50 4 0.03
51 40 0.34
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTGGATAATT
Done.