Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 68 of 187
Found at i:19918134 original size:22 final size:22
Alignment explanation
Indices: 19918109--19918150 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19918099 TCATTGACAG
19918109 AATTCTC-AATCTCTTTCTCTCT
1 AATTCTCTAA-CTCTTTCTCTCT
*
19918131 AATTCTCTCACTCTTTCTCT
1 AATTCTCTAACTCTTTCTCT
19918151 TTGTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTCTCTAACTCTTTCTCTCT
Found at i:19920275 original size:21 final size:23
Alignment explanation
Indices: 19920249--19920291 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
19920239 AGTTTATGTG
19920249 TATATTT-AATA-AAAAATTGTA
1 TATATTTAAATAGAAAAATTGTA
19920270 TATATTTACAATAGAAAAATTG
1 TATATTTA-AATAGAAAAATTG
19920292 GTGGCGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (23 bp):
TATATTTAAATAGAAAAATTGTA
Found at i:19929347 original size:51 final size:51
Alignment explanation
Indices: 19929250--19929365 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
19929240 TTATAAAACT
** *
19929250 TATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATA-AA
1 TATATA-ATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
* * *
19929301 TATATACATATAAAATATATTCATGCATTTACAAAAAAAATG-AAATATATAA
1 TATATA-ATATAAAATACA-TAATGCATTTACAAAAAAAAGGAAAATATATAA
*
19929353 -GTATAATATAAAA
1 TATATAATATAAAA
19929366 CGTGGAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 8 0.15
51 28 0.51
52 19 0.35
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (51 bp):
TATATAATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
Found at i:19929905 original size:20 final size:22
Alignment explanation
Indices: 19929866--19929906 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
19929856 ATTTTTTTAA
*
19929866 AATCGTAAATAAGTAAAAAAAT
1 AATCGTAAATAAGAAAAAAAAT
19929888 AATCG-AAA-AAGAAAAAAAA
1 AATCGTAAATAAGAAAAAAAA
19929907 GAAAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (22 bp):
AATCGTAAATAAGAAAAAAAAT
Found at i:19931155 original size:20 final size:20
Alignment explanation
Indices: 19931118--19931167 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 20
19931108 CCGGCTTATT
19931118 TTTTAATAAATATTAAAAAATTA
1 TTTTAA-AAATA-TAAAAAA-TA
19931141 TTTTAAAAATA-AAAAAATA
1 TTTTAAAAATATAAAAAATA
19931160 TTTTAAAA
1 TTTTAAAA
19931168 GTATTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 6 0.22
22 5 0.19
23 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAAATATAAAAAATA
Found at i:19931161 original size:30 final size:30
Alignment explanation
Indices: 19931125--19931186 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
19931115 ATTTTTTAAT
*
19931125 AAATATTAAAAAATTATTTTAAAAATAAAA
1 AAATATTAAAAAAGTATTTTAAAAATAAAA
** *
19931155 AAATATTTTAAAAGTATTTTAAAATTAAAA
1 AAATATTAAAAAAGTATTTTAAAAATAAAA
19931185 AA
1 AA
19931187 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATATTAAAAAAGTATTTTAAAAATAAAA
Found at i:19933075 original size:43 final size:44
Alignment explanation
Indices: 19932994--19933082 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
19932984 TTTTTTTTTC
* * * * *
19932994 TTTCTAATTTAGATCTAAGGATTCAAATAGGTTGGAATTTTATT
1 TTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAATTTTATT
*
19933038 TTTCTAATTTA-ATATTAGGATTCAAAAAAGATAGAATTTTATT
1 TTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAATTTTATT
19933081 TT
1 TT
19933083 ATTTTTTCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (44 bp):
TTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAATTTTATT
Found at i:19933151 original size:33 final size:33
Alignment explanation
Indices: 19933085--19933152 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
19933075 TTTATTTTAT
* *
19933085 TTTTTCTAATTTAGATCTTAGGATTTAGATAGG
1 TTTTTCTAATTTAGAACTTAGGATTCAGATAGG
*
19933118 TTTTTCTCATTTAGAACTTAGGATTCA-ATTAGG
1 TTTTTCTAATTTAGAACTTAGGATTCAGA-TAGG
19933151 TT
1 TT
19933153 AAAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (33 bp):
TTTTTCTAATTTAGAACTTAGGATTCAGATAGG
Found at i:19937368 original size:2 final size:2
Alignment explanation
Indices: 19937363--19937390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19937353 ACACACACAC
19937363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19937391 GATAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19938603 original size:18 final size:17
Alignment explanation
Indices: 19938580--19938623 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
19938570 AATTTATAAA
19938580 AAAATATTAA-AAATTATG
1 AAAATATTAATAAA--ATG
19938598 AAAATATATAATAAAATG
1 AAAATAT-TAATAAAATG
19938616 AAAATATT
1 AAAATATT
19938624 TAGATGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 3 0.12
20 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATATTAATAAAATG
Found at i:19942923 original size:14 final size:14
Alignment explanation
Indices: 19942885--19942927 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
19942875 CAAAATGTAC
19942885 AATATAATTAAA-T
1 AATATAATTAAATT
19942898 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
19942913 AA-ATAATTTAATT
1 AATATAATTAAATT
19942926 AA
1 AA
19942928 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:19943084 original size:12 final size:12
Alignment explanation
Indices: 19943067--19943091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19943057 TTATGTAACT
19943067 AAGTTACAAATA
1 AAGTTACAAATA
19943079 AAGTTACAAATA
1 AAGTTACAAATA
19943091 A
1 A
19943092 TAGTACTTGA
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:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAGTTACAAATA
Found at i:19945238 original size:21 final size:20
Alignment explanation
Indices: 19945212--19945250 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19945202 TTATTTTTAT
19945212 TTATATATAAGAAATATAAAA
1 TTATAT-TAAGAAATATAAAA
*
19945233 TTATATTTAGAAATATAA
1 TTATATTAAGAAATATAA
19945251 GCAACTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTATATTAAGAAATATAAAA
Found at i:19945767 original size:10 final size:10
Alignment explanation
Indices: 19945752--19945793 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
19945742 ATGAAATTTT
19945752 TAAATAATAA
1 TAAATAATAA
19945762 TAAATAATAA
1 TAAATAATAA
19945772 -ATAATAAATAA
1 TA-AAT-AATAA
19945783 TAAATAATAA
1 TAAATAATAA
19945793 T
1 T
19945794 CATTATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.03
10 19 0.66
11 8 0.28
12 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAATAATAA
Found at i:19945808 original size:7 final size:7
Alignment explanation
Indices: 19945757--19945792 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
19945747 ATTTTTAAAT
19945757 AATAATA
1 AATAATA
19945764 AATAATA
1 AATAATA
19945771 AATAATA
1 AATAATA
19945778 AATAATA
1 AATAATA
19945785 AATAATA
1 AATAATA
19945792 A
1 A
19945793 TCATTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:19947204 original size:9 final size:9
Alignment explanation
Indices: 19947192--19947316 Score: 78
Period size: 9 Copynumber: 13.6 Consensus size: 9
19947182 AAAAAAAAGT
19947192 TAAAAATTA
1 TAAAAATTA
19947201 T-AAAATTGA
1 TAAAAATT-A
*
19947210 TAGAAAATCA
1 TA-AAAATTA
19947220 TAAAAATTA
1 TAAAAATTA
* *
19947229 CAAATATATA
1 TAAAAAT-TA
* *
19947239 TATAATTTA
1 TAAAAATTA
19947248 TTAAAAA-T-
1 -TAAAAATTA
19947256 TAAAAA-TA
1 TAAAAATTA
** *
19947264 TAGAAACGTG
1 TA-AAAATTA
19947274 TAAAAATTA
1 TAAAAATTA
*
19947283 TAAAAAGTA
1 TAAAAATTA
19947292 TAGAAAATTA
1 TA-AAAATTA
19947302 TAAAAATATA
1 TAAAAAT-TA
19947312 TAAAA
1 TAAAA
19947317 GTTTAAATTC
Statistics
Matches: 89, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
7 7 0.08
8 8 0.09
9 39 0.44
10 30 0.34
11 5 0.06
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:19947225 original size:28 final size:26
Alignment explanation
Indices: 19947192--19947316 Score: 108
Period size: 28 Copynumber: 4.5 Consensus size: 26
19947182 AAAAAAAAGT
*
19947192 TAAAAATTATAAAATTGATAGAAAATCA
1 TAAAAATTATAAAA-T-ATAGAAAATTA
* * *
19947220 TAAAAATTACAAATATATATATAATTTA
1 TAAAAATTATAAA-ATATAGA-AAATTA
** *
19947248 TTAAAAATTA-AAAATATAGAAACGTG
1 -TAAAAATTATAAAATATAGAAAATTA
19947274 TAAAAATTATAAAAAGTATAGAAAATTA
1 TAAAAATTAT-AAAA-TATAGAAAATTA
19947302 TAAAAATATATAAAA
1 TAAAAAT-TATAAAA
19947317 GTTTAAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
25 9 0.11
26 3 0.04
27 14 0.18
28 40 0.51
29 13 0.16
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (26 bp):
TAAAAATTATAAAATATAGAAAATTA
Found at i:19947284 original size:19 final size:18
Alignment explanation
Indices: 19947192--19947316 Score: 66
Period size: 19 Copynumber: 6.8 Consensus size: 18
19947182 AAAAAAAAGT
*
19947192 TAAAAATTAT-AAAATTGA
1 TAAAAAGTATAAAAATT-A
19947210 TAGAAAA-TCATAAAAATTA
1 TA-AAAAGT-ATAAAAATTA
* * *
19947229 CAAATATA-TATATAATTTA
1 TAAA-A-AGTATAAAAATTA
19947248 TTAAAAA-T-TAAAAA-TA
1 -TAAAAAGTATAAAAATTA
* *
19947264 TAGAAACGTGTAAAAATTA
1 TA-AAAAGTATAAAAATTA
19947283 TAAAAAGTATAGAAAATTA
1 TAAAAAGTATA-AAAATTA
19947302 TAAAAA-TATATAAAA
1 TAAAAAGTATA-AAAA
19947317 GTTTAAATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.02
16 5 0.06
17 5 0.06
18 28 0.33
19 35 0.41
20 11 0.13
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (18 bp):
TAAAAAGTATAAAAATTA
Found at i:19947298 original size:10 final size:9
Alignment explanation
Indices: 19947256--19947323 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
19947246 TATTAAAAAT
19947256 TAAAAA-TA
1 TAAAAAGTA
* *
19947264 TAGAAACGTG
1 TA-AAAAGTA
*
19947274 TAAAAATTA
1 TAAAAAGTA
19947283 TAAAAAGTA
1 TAAAAAGTA
*
19947292 TAGAAAATTA
1 TA-AAAAGTA
19947302 TAAAAA-TA
1 TAAAAAGTA
*
19947310 TATAAAAGTT
1 TA-AAAAGTA
19947320 TAAA
1 TAAA
19947324 TTCTTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 6 0.13
9 27 0.57
10 14 0.30
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (9 bp):
TAAAAAGTA
Found at i:19948082 original size:22 final size:22
Alignment explanation
Indices: 19948053--19948104 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
19948043 ATTGTTTAAT
*
19948053 TAGGGTTTAAGGTTTATTAAAG
1 TAGGGTTTAAGGTTAATTAAAG
* * *
19948075 TATGGTTTAGGGTTAATTAAAT
1 TAGGGTTTAAGGTTAATTAAAG
19948097 TAGGGTTT
1 TAGGGTTT
19948105 TAGCATTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (22 bp):
TAGGGTTTAAGGTTAATTAAAG
Found at i:19948284 original size:29 final size:29
Alignment explanation
Indices: 19948251--19948318 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
19948241 TTAAGTGTTC
* *
19948251 TGAAAAAATAATTTTGACGAGATGGGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
19948280 TGAAAAAATAATTTTGACAAGATGAGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
19948309 TGAAAAAATA
1 TGAAAAAATA
19948319 TCCCAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.32
Consensus pattern (29 bp):
TGAAAAAATAATTTTGACAAGATGAGTTT
Found at i:19950299 original size:17 final size:17
Alignment explanation
Indices: 19950277--19950310 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19950267 ACATGCCTTG
19950277 GTATAGCAAGGCATTGA
1 GTATAGCAAGGCATTGA
19950294 GTATAGCAAGGCATTGA
1 GTATAGCAAGGCATTGA
19950311 TAGCAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (17 bp):
GTATAGCAAGGCATTGA
Found at i:19950315 original size:14 final size:16
Alignment explanation
Indices: 19950277--19950316 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
19950267 ACATGCCTTG
19950277 GTATAGCAAGGCATTGA
1 GTATAGCAAGGCATT-A
19950294 GTATAGCAAGGCATT-
1 GTATAGCAAGGCATTA
19950309 G-ATAGCAA
1 GTATAGCAA
19950317 ATCAGAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 1 0.04
17 15 0.65
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (16 bp):
GTATAGCAAGGCATTA
Found at i:19951673 original size:19 final size:18
Alignment explanation
Indices: 19951624--19951679 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
19951614 ATACTAAGTT
19951624 AAAATATAACAGTAAA-A
1 AAAATATAACAGTAAATA
19951641 TAAAA-A-AA-A-TAAATA
1 -AAAATATAACAGTAAATA
19951656 AAAATATAACAGTGAAATA
1 AAAATATAACAGT-AAATA
19951675 AAAAT
1 AAAAT
19951680 TTAAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 8 0.25
15 3 0.09
16 4 0.12
17 2 0.06
18 5 0.16
19 10 0.31
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAATATAACAGTAAATA
Found at i:19951902 original size:11 final size:11
Alignment explanation
Indices: 19951888--19951929 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
19951878 TATTAGAGAA
19951888 TTTGAGAGATT
1 TTTGAGAGATT
19951899 TTTGAGAG-TT
1 TTTGAGAGATT
* *
19951909 GATTGAGAAATT
1 -TTTGAGAGATT
19951921 TTTGAGAGA
1 TTTGAGAGA
19951930 ATTGTGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (11 bp):
TTTGAGAGATT
Found at i:19951937 original size:22 final size:22
Alignment explanation
Indices: 19951874--19951941 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
19951864 TTTAGGAAAA
*
19951874 AAATTATT-AGAGAATT-TGAG
1 AAATTTTTGAGAGAATTGTGAG
*
19951894 AGATTTTTGAGAG--TTGATTGAG
1 AAATTTTTGAGAGAATTG--TGAG
19951916 AAATTTTTGAGAGAATTGTGAG
1 AAATTTTTGAGAGAATTGTGAG
19951938 AAAT
1 AAAT
19951942 GTGAGTGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 4 0.10
22 24 0.62
24 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (22 bp):
AAATTTTTGAGAGAATTGTGAG
Found at i:19952442 original size:28 final size:28
Alignment explanation
Indices: 19952400--19952453 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
19952390 AGTATAATGA
*
19952400 TAAAATTATACTTTACCCCCTTAAAGTT
1 TAAAATTATACTTTAACCCCTTAAAGTT
19952428 TAAAATT-TACTTTTAACCCCTTAAAG
1 TAAAATTATAC-TTTAACCCCTTAAAG
19952454 CAGTTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (28 bp):
TAAAATTATACTTTAACCCCTTAAAGTT
Found at i:19953074 original size:5 final size:5
Alignment explanation
Indices: 19953064--19953089 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19953054 TGAGCATTCG
19953064 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
19953090 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:19953881 original size:31 final size:30
Alignment explanation
Indices: 19953846--19953905 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
19953836 GGAGGTGGGA
*
19953846 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
19953877 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
19953906 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:19954134 original size:9 final size:9
Alignment explanation
Indices: 19954120--19954156 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19954110 TATAGTTTGA
19954120 TATTCGAAT
1 TATTCGAAT
19954129 TATTCGAAT
1 TATTCGAAT
*
19954138 TATTCGAGT
1 TATTCGAAT
19954147 TATTCGAAT
1 TATTCGAAT
19954156 T
1 T
19954157 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19958979 original size:15 final size:15
Alignment explanation
Indices: 19958950--19958984 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19958940 AGCTCTATTT
19958950 TAATT-ATATTAAGA
1 TAATTAATATTAAGA
*
19958964 TAATTAATATTGAGA
1 TAATTAATATTAAGA
19958979 TAATTA
1 TAATTA
19958985 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:19975506 original size:28 final size:29
Alignment explanation
Indices: 19975453--19975518 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
19975443 TAAATGGTTT
* *
19975453 TTTTATTAATTTTTAAATTTTATTTA-AAA
1 TTTTA-TAAATTTTAAAATTTATTTACAAA
19975482 TTTTATAAATTTTAATAATTT-TTTACAAA
1 TTTTATAAATTTTAA-AATTTATTTACAAA
19975511 -TTTATAAA
1 TTTTATAAA
19975519 AAAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATAAATTTTAAAATTTATTTACAAA
Found at i:19980329 original size:25 final size:27
Alignment explanation
Indices: 19980300--19980363 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
19980290 TATATTTGTT
19980300 TTTTTATACATATAA-TTAATTT-TATA
1 TTTTTATA-ATATAAGTTAATTTATATA
19980326 TTTTTATAA-A-AAGTTAATTTATATA
1 TTTTTATAATATAAGTTAATTTATATA
19980351 TTTTTATATATAT
1 TTTTTATA-ATAT
19980364 GTATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATAAGTTAATTTATATA
Found at i:19980376 original size:27 final size:27
Alignment explanation
Indices: 19980345--19980403 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
19980335 AAAGTTAATT
*
19980345 TATATATTTTTATA-TATATGTATGAA
1 TATATATTTTTATACTATACGTATGAA
* *
19980371 TA-ATATTTTTTTTACTATACGTATGTA
1 TATATA-TTTTTATACTATACGTATGAA
19980398 TATATA
1 TATATA
19980404 ATAATACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.11
26 9 0.33
27 12 0.44
28 3 0.11
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (27 bp):
TATATATTTTTATACTATACGTATGAA
Found at i:19992866 original size:44 final size:43
Alignment explanation
Indices: 19992796--19993037 Score: 202
Period size: 44 Copynumber: 5.6 Consensus size: 43
19992786 GGAGATGGCA
* *
19992796 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAG-CGAT
* * * * **
19992840 AATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGCGAT
* * * * *
19992883 AGATCTTATCTCTCTGAAGTTGCGGTAGAGTGGATCGTAA-C-A-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTG-AAGCGAT
* * **
19992925 AGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAG-CGAT
* * * **
19992969 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGCGAT
* *
19993012 GGATCTTATCTCTCTGAAGTTGCAGT
1 -AATCTTATCTCCCTGAAGTTGCAGT
19993038 AGAGTGAATC
Statistics
Matches: 153, Mismatches: 38, Indels: 14
0.75 0.19 0.07
Matches are distributed among these distances:
40 2 0.01
41 28 0.18
42 2 0.01
43 7 0.05
44 112 0.73
45 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGCGAT
Found at i:19992987 original size:129 final size:129
Alignment explanation
Indices: 19992798--19993086 Score: 497
Period size: 129 Copynumber: 2.2 Consensus size: 129
19992788 AGATGGCAAA
*
19992798 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCTTGAAGTTGTA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
* * *
19992863 GTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCGGTAGAGTGGATCGTAACAAG
66 GTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
*
19992927 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
* * *
19992992 GTGGAGCGGATTAAAGTAATGGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCATCAGG
66 GTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
*
19993056 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
19993087 CTGAGTAAGC
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 150 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (129 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTA
GTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
Found at i:19996645 original size:28 final size:29
Alignment explanation
Indices: 19996553--19996730 Score: 173
Period size: 29 Copynumber: 6.2 Consensus size: 29
19996543 AAGGTCTCGA
* *
19996553 GCCACTGGTTTTCCAAATTTTACAATTTT
1 GCCACTGGTTTTCCAGATTTTACAGTTTT
* ** * *
19996582 GTCACTAATTTTCCAAATTTTATAGTTTT
1 GCCACTGGTTTTCCAGATTTTACAGTTTT
*
19996611 GCCACT-GTTATTCCAGATTTT-CAGTTCT
1 GCCACTGGTT-TTCCAGATTTTACAGTTTT
* * *
19996639 GCCACTGGTTTTCCAAATTTTACAATTCT
1 GCCACTGGTTTTCCAGATTTTACAGTTTT
* * * *
19996668 ACCACT-ATTATTCCAGATTTTAAAATTTT
1 GCCACTGGTT-TTCCAGATTTTACAGTTTT
*
19996697 TCCACTGGTTTTCCAGATTTTACAGTTTT
1 GCCACTGGTTTTCCAGATTTTACAGTTTT
19996726 GCCAC
1 GCCAC
19996731 ACTTCTTCAA
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
28 25 0.20
29 95 0.78
30 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (29 bp):
GCCACTGGTTTTCCAGATTTTACAGTTTT
Found at i:19996673 original size:57 final size:58
Alignment explanation
Indices: 19996563--19996720 Score: 165
Period size: 57 Copynumber: 2.7 Consensus size: 58
19996553 GCCACTGGTT
* * * * ** * * * * *
19996563 TTCCAAATTTTACAATTTTGTCACTAATTTTCCAAATTTTATAGTTTTGCCACTGTTA
1 TTCCAGATTTTAAAATTCTGCCACTGGTTTTCCAAATTTTACAATTCTACCACTATTA
* *
19996621 TTCCAGATTTT-CAGTTCTGCCACTGGTTTTCCAAATTTTACAATTCTACCACTATTA
1 TTCCAGATTTTAAAATTCTGCCACTGGTTTTCCAAATTTTACAATTCTACCACTATTA
* * *
19996678 TTCCAGATTTTAAAATTTTTCCACTGGTTTTCCAGATTTTACA
1 TTCCAGATTTTAAAATTCTGCCACTGGTTTTCCAAATTTTACA
19996721 GTTTTGCCAC
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
57 47 0.57
58 36 0.43
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (58 bp):
TTCCAGATTTTAAAATTCTGCCACTGGTTTTCCAAATTTTACAATTCTACCACTATTA
Found at i:19996702 original size:86 final size:87
Alignment explanation
Indices: 19996553--19996730 Score: 245
Period size: 86 Copynumber: 2.1 Consensus size: 87
19996543 AAGGTCTCGA
* ** * *
19996553 GCCACTGGTTTTCCAAATTTTACAATTTTGTCACTAATTTTCCAAATTTTATAGTTTTGCCACT-
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTAATTTTCCAAATTTTAAAATTTTGCCACTG
19996617 GTTATTCCAGATTTT-CAGTTCT
66 GTT-TTCCAGATTTTACAGTTCT
* *
19996639 GCCACTGGTTTTCCAAATTTTACAATTCTACCACT-ATTATTCCAGATTTTAAAATTTTTCCACT
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTAATT-TTCCAAATTTTAAAATTTTGCCACT
*
19996703 GGTTTTCCAGATTTTACAGTTTT
65 GGTTTTCCAGATTTTACAGTTCT
19996726 GCCAC
1 GCCAC
19996731 ACTTCTTCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 3 0.04
86 64 0.79
87 14 0.17
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (87 bp):
GCCACTGGTTTTCCAAATTTTACAATTCTACCACTAATTTTCCAAATTTTAAAATTTTGCCACTG
GTTTTCCAGATTTTACAGTTCT
Found at i:20000030 original size:12 final size:12
Alignment explanation
Indices: 20000013--20000038 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20000003 TTCATGAATC
20000013 AAATTACATATT
1 AAATTACATATT
20000025 AAATTACATATT
1 AAATTACATATT
20000037 AA
1 AA
20000039 CTTTAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTACATATT
Found at i:20000245 original size:18 final size:19
Alignment explanation
Indices: 20000205--20000245 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20000195 TAAAATTCAT
*
20000205 ATTTATTTATTGGATATAG
1 ATTTATGTATTGGATATAG
20000224 ATTTATGTA-TGGAGTATA-
1 ATTTATGTATTGGA-TATAG
20000242 ATTT
1 ATTT
20000246 TTTTTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
ATTTATGTATTGGATATAG
Found at i:20000688 original size:14 final size:14
Alignment explanation
Indices: 20000650--20000678 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20000640 TAATAACATA
20000650 ATAAATTA-TTAAT
1 ATAAATTATTTAAT
20000663 ATAAATTATTTAAT
1 ATAAATTATTTAAT
20000677 AT
1 AT
20000679 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATTATTTAAT
Found at i:20003619 original size:16 final size:19
Alignment explanation
Indices: 20003595--20003633 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
20003585 AGGAAAATTT
20003595 TATAGAAA-T-AAAAAATA
1 TATAGAAATTCAAAAAATA
20003612 TATA-AAATTCAAAAAATA
1 TATAGAAATTCAAAAAATA
20003630 TATA
1 TATA
20003634 TACTTATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 5 0.25
18 12 0.60
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
TATAGAAATTCAAAAAATA
Found at i:20003719 original size:17 final size:17
Alignment explanation
Indices: 20003689--20003737 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
20003679 AAAAAACTTT
20003689 ATATAAAAAGTTAAAAG
1 ATATAAAAAGTTAAAAG
* * *
20003706 ATATATAAATTTAAAAA
1 ATATAAAAAGTTAAAAG
*
20003723 ATAAAAAAAG-TAAAA
1 ATATAAAAAGTTAAAA
20003738 ATTCAAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
ATATAAAAAGTTAAAAG
Found at i:20003869 original size:23 final size:22
Alignment explanation
Indices: 20003833--20003898 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
20003823 AAATTATATA
20003833 CAAT-TATATGAAATTAAAAAATT
1 CAATATATAT-AAATTAAAAAA-T
20003856 CAATATATATAAATTTAAAAAAT
1 CAATATATATAAA-TTAAAAAAT
* * *
20003879 AAAAATATTTAAATTAAAAA
1 CAATATATATAAATTAAAAA
20003899 TTGATCAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 7 0.18
23 18 0.47
24 13 0.34
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (22 bp):
CAATATATATAAATTAAAAAAT
Found at i:20003873 original size:24 final size:23
Alignment explanation
Indices: 20003833--20003878 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
20003823 AAATTATATA
20003833 CAATTATATGAAATTAAAAAATT
1 CAATTATATGAAATTAAAAAATT
20003856 CAATATATAT-AAATTTAAAAAAT
1 CAAT-TATATGAAA-TTAAAAAAT
20003879 AAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
CAATTATATGAAATTAAAAAATT
Found at i:20004167 original size:21 final size:21
Alignment explanation
Indices: 20004143--20004184 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20004133 ATCTTTTCTA
*
20004143 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
20004164 AAGTTAAAAGGCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
20004185 TCGTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:20009518 original size:25 final size:26
Alignment explanation
Indices: 20009464--20009518 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
20009454 ATGATTTATA
* *
20009464 ACATCAACCATTAAGTCATTTTGCAAG
1 ACATCAAACATGAAGTCA-TTTGCAAG
20009491 ACATCAAACATGAAGTCA-TTGCAAG
1 ACATCAAACATGAAGTCATTTGCAAG
20009516 ACA
1 ACA
20009519 GAACTTCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 10 0.38
27 16 0.62
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (26 bp):
ACATCAAACATGAAGTCATTTGCAAG
Found at i:20015180 original size:17 final size:17
Alignment explanation
Indices: 20015158--20015194 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20015148 AAGAACATTT
20015158 AAAATTAATATTAAA-TA
1 AAAATTAA-ATTAAACTA
20015175 AAAATTAAATTAAACTA
1 AAAATTAAATTAAACTA
20015192 AAA
1 AAA
20015195 TAAAAATCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAATTAAACTA
Found at i:20015195 original size:16 final size:16
Alignment explanation
Indices: 20015157--20015195 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20015147 TAAGAACATT
20015157 TAAAATTAATATTAAA
1 TAAAATTAATATTAAA
20015173 TAAAAATTAA-ATTAAA
1 T-AAAATTAATATTAAA
20015189 CTAAAAT
1 -TAAAAT
20015196 AAAAATCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATTAATATTAAA
Found at i:20026877 original size:22 final size:22
Alignment explanation
Indices: 20026832--20026877 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20026822 ACTAATCGAC
* **
20026832 ATGTTGCAACAGGGGGAGTTGA
1 ATGTTGCAACAGAGGGAGCAGA
*
20026854 ATGTTGCAACATAGGGAGCAGA
1 ATGTTGCAACAGAGGGAGCAGA
20026876 AT
1 AT
20026878 AGCATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.35, T:0.22
Consensus pattern (22 bp):
ATGTTGCAACAGAGGGAGCAGA
Found at i:20029212 original size:31 final size:31
Alignment explanation
Indices: 20029160--20029221 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
20029150 TATATGGAGG
* *
20029160 AGACGAACCGCTCTTCTACTATATTAACAAT
1 AGACAAACCGCTCTTCCACTATATTAACAAT
*
20029191 AGACAAACCTCTCTTCCACTATATTAACAAT
1 AGACAAACCGCTCTTCCACTATATTAACAAT
20029222 CCCACTGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (31 bp):
AGACAAACCGCTCTTCCACTATATTAACAAT
Found at i:20060405 original size:22 final size:21
Alignment explanation
Indices: 20060380--20060423 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
20060370 TGATAAACTT
20060380 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
20060402 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
20060423 T
1 T
20060424 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:20067483 original size:21 final size:21
Alignment explanation
Indices: 20067441--20067482 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20067431 AATCCTCTCG
20067441 TAAACTATTAAATCTAATTTT
1 TAAACTATTAAATCTAATTTT
* *
20067462 TAAA-TATTAAATTTCATTTT
1 TAAACTATTAAATCTAATTTT
20067482 T
1 T
20067483 TCTAGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAACTATTAAATCTAATTTT
Found at i:20069629 original size:18 final size:17
Alignment explanation
Indices: 20069602--20069635 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
20069592 TAACAGACTT
20069602 ATTCACCAAGCCTTTAG
1 ATTCACCAAGCCTTTAG
20069619 ATTCAACCAAGCCTTTA
1 ATTC-ACCAAGCCTTTA
20069636 AATTTGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (17 bp):
ATTCACCAAGCCTTTAG
Found at i:20073891 original size:17 final size:17
Alignment explanation
Indices: 20073869--20073903 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20073859 ACTAGTTGGA
20073869 TTAGAAATTGATCAGGG
1 TTAGAAATTGATCAGGG
*
20073886 TTAGAAATTGATTAGGG
1 TTAGAAATTGATCAGGG
20073903 T
1 T
20073904 ATCAAATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (17 bp):
TTAGAAATTGATCAGGG
Found at i:20077111 original size:5 final size:5
Alignment explanation
Indices: 20077097--20077126 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
20077087 AAGTAAACAA
20077097 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
20077127 AGAAATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20077132 original size:10 final size:10
Alignment explanation
Indices: 20077090--20077151 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 10
20077080 TTGTAGAAAG
20077090 TAAACAAAAAA
1 TAAA-AAAAAA
20077101 TAAAAATAAAA
1 TAAAAA-AAAA
*
20077112 TAAAATAAAA
1 TAAAAAAAAA
*
20077122 TAAAAAGAAATG
1 TAAAAA-AAA-A
20077134 TAAAACAAAAAA
1 T-AAA-AAAAAA
20077146 TAAAAA
1 TAAAAA
20077152 GGAAGAGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 13 0.31
11 19 0.45
12 2 0.05
13 6 0.14
14 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:20079824 original size:44 final size:44
Alignment explanation
Indices: 20079774--20079863 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
20079764 GTTAAAATAA
* * * * * *
20079774 AATAGAAGTTGTGATAATTATACATTTAAAAATAATTATAATTT
1 AATAGAAATAGTGAGAATTACACATTTAAAAATAAATAGAATTT
20079818 AATAGAAATAGTGAGAATTACACATTTAAAAATAAATAGAATTT
1 AATAGAAATAGTGAGAATTACACATTTAAAAATAAATAGAATTT
20079862 AA
1 AA
20079864 ATTACAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (44 bp):
AATAGAAATAGTGAGAATTACACATTTAAAAATAAATAGAATTT
Found at i:20080128 original size:44 final size:45
Alignment explanation
Indices: 20080056--20080146 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
20080046 AAAGTTGGAA
* * *
20080056 AATAGAAGTTTGTCATAATTATAAATTTAAAAATAATTATAATTT
1 AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
20080101 AATAGAAG-TTATAATAATTA-AACATTTAAAAATAATTAGAATTT
1 AATAGAAGTTTATAATAATTATAA-ATTTAAAAATAATTAGAATTT
20080145 AA
1 AA
20080147 ATTATTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 2 0.05
44 32 0.76
45 8 0.19
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (45 bp):
AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
Found at i:20080146 original size:17 final size:18
Alignment explanation
Indices: 20080113--20080147 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20080103 TAGAAGTTAT
20080113 AATAATTAAACATTTAAA
1 AATAATTAAACATTTAAA
*
20080131 AATAATTAGA-ATTTAAA
1 AATAATTAAACATTTAAA
20080148 TTATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATTAAACATTTAAA
Found at i:20081125 original size:20 final size:21
Alignment explanation
Indices: 20081061--20081152 Score: 59
Period size: 20 Copynumber: 4.6 Consensus size: 21
20081051 AACTTATTAT
* * *
20081061 TTTTGAAATTATTT-TAATTA
1 TTTTAAAATTTTTTATAAATA
* *
20081081 TTTT-AACTTTTTTATATAT-
1 TTTTAAAATTTTTTATAAATA
* *
20081100 TCTTTAGAATTTTTTATGAA-A
1 T-TTTAAAATTTTTTATAAATA
* *
20081121 TTTTATAA-TTGTTATAAATA
1 TTTTAAAATTTTTTATAAATA
20081141 TTTTAAAATTTT
1 TTTTAAAATTTT
20081153 GAATTTTTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
19 16 0.30
20 24 0.45
21 13 0.25
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTAAAATTTTTTATAAATA
Found at i:20081311 original size:18 final size:18
Alignment explanation
Indices: 20081288--20081328 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20081278 TCACCAATCT
*
20081288 ATTATTCAAGTTGTTTGA
1 ATTATTCAAGTTATTTGA
**
20081306 ATTATTTGAGTTATTTGA
1 ATTATTCAAGTTATTTGA
20081324 ATTAT
1 ATTAT
20081329 AAAATTCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (18 bp):
ATTATTCAAGTTATTTGA
Found at i:20082804 original size:17 final size:17
Alignment explanation
Indices: 20082782--20082820 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20082772 ACTTTATTGT
20082782 ATTTATTAATT-AATATA
1 ATTTATT-ATTAAATATA
*
20082799 ATTTATTATTAAATTTA
1 ATTTATTATTAAATATA
20082816 ATTTA
1 ATTTA
20082821 ATAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTATTAAATATA
Found at i:20093637 original size:25 final size:27
Alignment explanation
Indices: 20093580--20093638 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
20093570 CTATGAAAAA
* *
20093580 AAAACTAAACACAAATAAAATTAATAAT
1 AAAA-TAAACACAAATAAAATTAAGAAC
20093608 AAAATAAACA-AAA-AAAATTAAGAAC
1 AAAATAAACACAAATAAAATTAAGAAC
*
20093633 GAAATA
1 AAAATA
20093639 GAAGTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.54
26 3 0.11
27 6 0.21
28 4 0.14
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.17
Consensus pattern (27 bp):
AAAATAAACACAAATAAAATTAAGAAC
Found at i:20097228 original size:16 final size:15
Alignment explanation
Indices: 20097203--20097232 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20097193 ATTAAGTTAA
20097203 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
20097218 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
20097233 ATGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:20112762 original size:37 final size:37
Alignment explanation
Indices: 20112712--20112788 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
20112702 ATGGCCAAAG
20112712 ACCAATCATGGGATGATTTTAATCACATGCTCATTTT
1 ACCAATCATGGGATGATTTTAATCACATGCTCATTTT
20112749 ACCAATCATGGGATGATTTTAATCACATGCTCATTTT
1 ACCAATCATGGGATGATTTTAATCACATGCTCATTTT
20112786 ACC
1 ACC
20112789 CTACTTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (37 bp):
ACCAATCATGGGATGATTTTAATCACATGCTCATTTT
Found at i:20112784 original size:17 final size:17
Alignment explanation
Indices: 20112727--20112786 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
20112717 TCATGGGATG
20112727 ATTTTAATCACATGCTC
1 ATTTTAATCACATGCTC
* * *
20112744 ATTTT-ACCAATCATGGGATG
1 ATTTTAATC-A-CAT--GCTC
20112764 ATTTTAATCACATGCTC
1 ATTTTAATCACATGCTC
20112781 ATTTTA
1 ATTTTA
20112787 CCCTACTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 2 0.06
17 14 0.44
18 3 0.09
19 3 0.09
20 8 0.25
21 2 0.06
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (17 bp):
ATTTTAATCACATGCTC
Found at i:20125521 original size:28 final size:30
Alignment explanation
Indices: 20125466--20125522 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
20125456 ATACGGCCGG
*
20125466 ACACATGGGCATGTGACTTGGCCATGTGAA
1 ACACATGGGCATGTGACATGGCCATGTGAA
* *
20125496 ACACAT-GGCTTG-GACATGGCCGTGTGA
1 ACACATGGGCATGTGACATGGCCATGTGA
20125523 GGCTATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.54
29 5 0.21
30 6 0.25
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (30 bp):
ACACATGGGCATGTGACATGGCCATGTGAA
Found at i:20132525 original size:11 final size:11
Alignment explanation
Indices: 20132509--20132551 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
20132499 GTTTTAATTA
20132509 AATAAAATATT
1 AATAAAATATT
20132520 AAT-AAATATCT
1 AATAAAATAT-T
20132531 AATTAAAATATT
1 AA-TAAAATATT
20132543 AATAAAATA
1 AATAAAATA
20132552 ATATTTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.21
11 13 0.45
12 4 0.14
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:20136871 original size:31 final size:31
Alignment explanation
Indices: 20136835--20136906 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
20136825 GTTTTTAAAG
*
20136835 GTGTACAATTGAAGC-AAAATTAAAGTTTTAT
1 GTGTACAATTG-ACCTAAAATTAAAGTTTTAT
*
20136866 GTGTACACA-TGACCTATAATTAAAGTTTTAT
1 GTGTACA-ATTGACCTAAAATTAAAGTTTTAT
* *
20136897 ATGTATAATT
1 GTGTACAATT
20136907 ACATCAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 3 0.09
31 30 0.88
32 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (31 bp):
GTGTACAATTGACCTAAAATTAAAGTTTTAT
Found at i:20145218 original size:25 final size:25
Alignment explanation
Indices: 20145170--20145218 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20145160 CTAGGCTAAC
* *
20145170 TAGAGTTTAAGTGAGAAACTAAAAA
1 TAGAGTTTAACTGAGAAACGAAAAA
20145195 TAGAGTTTAACTGAGAGAA-GAAAA
1 TAGAGTTTAACTGAGA-AACGAAAA
20145219 CTAAAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (25 bp):
TAGAGTTTAACTGAGAAACGAAAAA
Found at i:20146819 original size:27 final size:27
Alignment explanation
Indices: 20146788--20146845 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
20146778 ATGATAATGA
20146788 ATTTAAA-TTATTTTATTAGTT-TTTTAT
1 ATTTAAATTTA-TTTATT-GTTATTTTAT
* *
20146815 ATTTATATTTATTTATTGTTATTTTTT
1 ATTTAAATTTATTTATTGTTATTTTAT
20146842 ATTT
1 ATTT
20146846 TAGCTACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 21 0.78
28 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (27 bp):
ATTTAAATTTATTTATTGTTATTTTAT
Found at i:20148515 original size:18 final size:18
Alignment explanation
Indices: 20148475--20148517 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20148465 GTTCAAGGTG
20148475 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
20148493 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
20148511 TAATTAA
1 TAATTAA
20148518 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:20167362 original size:4 final size:4
Alignment explanation
Indices: 20167353--20167403 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
20167343 TACTAGTCTC
20167353 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
20167401 TAT
1 TAT
20167404 CATATTTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:20169143 original size:45 final size:45
Alignment explanation
Indices: 20169074--20169163 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
20169064 TTGTTCACTA
*
20169074 AAATACACTCACAAAATACATTCCACGATGAACAGACAAGTGCTC
1 AAATACACTCACAAAATACATTCCACAATGAACAGACAAGTGCTC
* *
20169119 AAATACACTCACAAAATACGTTCCACAATGAATAGACAAGTGCTC
1 AAATACACTCACAAAATACATTCCACAATGAACAGACAAGTGCTC
20169164 TCAATACTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (45 bp):
AAATACACTCACAAAATACATTCCACAATGAACAGACAAGTGCTC
Found at i:20175527 original size:26 final size:26
Alignment explanation
Indices: 20175494--20175579 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
20175484 GAACAAGTGT
*
20175494 TTATTTAGTAGGCTTTGAGCTGGTGA
1 TTATTTAGCAGGCTTTGAGCTGGTGA
* *
20175520 TTACTTAGCAGGCTATGAGCTGGT-A
1 TTATTTAGCAGGCTTTGAGCTGGTGA
** *
20175545 CTTATTTAGCAGGCTTTGAGCCAGTGT
1 -TTATTTAGCAGGCTTTGAGCTGGTGA
20175572 TTATTTAG
1 TTATTTAG
20175580 TAGGTACTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.02
26 49 0.98
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.40
Consensus pattern (26 bp):
TTATTTAGCAGGCTTTGAGCTGGTGA
Found at i:20180804 original size:14 final size:15
Alignment explanation
Indices: 20180780--20180808 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20180770 CAATTATTTA
20180780 ATTTAAAAATTAATT
1 ATTTAAAAATTAATT
20180795 ATTT-AAAATTAATT
1 ATTTAAAAATTAATT
20180809 TAATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAAAAATTAATT
Found at i:20186260 original size:7 final size:7
Alignment explanation
Indices: 20186248--20186298 Score: 102
Period size: 7 Copynumber: 7.3 Consensus size: 7
20186238 CATGTCGGAC
20186248 AGTAGGG
1 AGTAGGG
20186255 AGTAGGG
1 AGTAGGG
20186262 AGTAGGG
1 AGTAGGG
20186269 AGTAGGG
1 AGTAGGG
20186276 AGTAGGG
1 AGTAGGG
20186283 AGTAGGG
1 AGTAGGG
20186290 AGTAGGG
1 AGTAGGG
20186297 AG
1 AG
20186299 GAGAGATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
AGTAGGG
Found at i:20187849 original size:26 final size:26
Alignment explanation
Indices: 20187818--20187871 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
20187808 GCCCAAATCA
*
20187818 AATAAATAAACAAAATATAA-AAAAAT
1 AATAAATAAA-AAAATAAAACAAAAAT
20187844 AATAAATAAAAAAATAAAACAAAAAT
1 AATAAATAAAAAAATAAAACAAAAAT
20187870 AA
1 AA
20187872 AGTTATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (26 bp):
AATAAATAAAAAAATAAAACAAAAAT
Found at i:20188783 original size:16 final size:16
Alignment explanation
Indices: 20188758--20188799 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
20188748 CGATGACCCA
*
20188758 ACCCGAGCGTGGCCAG
1 ACCCGCGCGTGGCCAG
20188774 ACCCGCGCGTGGCCAG
1 ACCCGCGCGTGGCCAG
20188790 ACCCGCGCGT
1 ACCCGCGCGT
20188800 TTTGGTCTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.36, T:0.07
Consensus pattern (16 bp):
ACCCGCGCGTGGCCAG
Found at i:20189738 original size:18 final size:18
Alignment explanation
Indices: 20189710--20189750 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20189700 TGATGTGAGC
20189710 TTATTGTCTTATGTGTAT
1 TTATTGTCTTATGTGTAT
*
20189728 TGTATTG-CTTATTTGTAT
1 T-TATTGTCTTATGTGTAT
20189746 TTATT
1 TTATT
20189751 AATTATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTATTGTCTTATGTGTAT
Found at i:20201443 original size:44 final size:44
Alignment explanation
Indices: 20201389--20201486 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
20201379 CAAGAGTGAG
* *
20201389 GGAGCAGATTGAAGCCAAAAATCTTATCTCCCTG-AGATTACAGT
1 GGAGCAGATTGAAGCCAAAAATCCTATCTCCCTGAAG-TTACAAT
* * *
20201433 GGAGCAGATTGAAGCCGATAATCCTATCTCCTTGAAGTTACAAT
1 GGAGCAGATTGAAGCCAAAAATCCTATCTCCCTGAAGTTACAAT
*
20201477 GGAGCGGATT
1 GGAGCAGATT
20201487 AAAATAAAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
GGAGCAGATTGAAGCCAAAAATCCTATCTCCCTGAAGTTACAAT
Found at i:20201663 original size:44 final size:44
Alignment explanation
Indices: 20201597--20201719 Score: 185
Period size: 44 Copynumber: 2.8 Consensus size: 44
20201587 GAAAATGGTG
20201597 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGA-
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCC-GAT
* *
20201641 AATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCGAT
* * *
20201685 AATCCTATCTCCTTGAGGTTACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
20201720 AAAATAAAGG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
43 2 0.03
44 69 0.97
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCGAT
Found at i:20201751 original size:88 final size:88
Alignment explanation
Indices: 20201597--20201762 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
20201587 GAAAATGGTG
* ** *
20201597 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTA
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAAACAGAAATCTTATCTCCCTAAAATTA
*
20201662 CAGTGGAGCAGATTGAAGCCGAT
66 CAGTAGAGCAGATTGAAGCCGAT
* * * *
20201685 AATCCTATCTCCTTGAGGTTACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTAAAAT
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAAACAGAA--ATCTTATCTCCCTAAAAT
*
20201748 TACAGTAGAGTAGAT
64 TACAGTAGAGCAGAT
20201763 CACATCAGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
86 2 0.03
87 3 0.05
88 61 0.92
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (88 bp):
AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAAACAGAAATCTTATCTCCCTAAAATTA
CAGTAGAGCAGATTGAAGCCGAT
Found at i:20201802 original size:233 final size:233
Alignment explanation
Indices: 20201389--20202120 Score: 1293
Period size: 233 Copynumber: 3.1 Consensus size: 233
20201379 CAAGAGTGAG
* *
20201389 GGAGCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGATAA
1 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAA
* *
20201454 TCCTATCTCCTTGAAGTTACAATGGAGCGGATTAAAATAAAGGATATTATCTCTCTAAAATTACA
66 TCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTACA
* *
20201519 GTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTAGAATAGACCGAAGAATTCCTA
131 GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCTA
*
20201584 ATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGT
196 ATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGT
20201622 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAA
1 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAA
*
20201687 TCCTATCTCCTTGAGGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTACA
66 TCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTACA
*
20201752 GTAGAGTAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCTA
131 GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCTA
*
20201817 ATCGAAAATGGTGAATCTTATCTTCTTGAGGTTACAGT
196 ATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGT
* * *
20201855 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTAGAGTATATTGAAGCCGATAA
1 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAA
* *
20201920 TCCTATATCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAATTACA
66 TCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTACA
*
20201985 GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAACTCCTA
131 GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCTA
* *
20202050 ATCGAAAATGGTGAATATTATCTCCTTGAGGTTACAAT
196 ATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGT
*
20202088 GGAGCAAATTGAAGCCAGAAATCTTATCTCCCT
1 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCT
20202121 GCGGTATAGC
Statistics
Matches: 477, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 477 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (233 bp):
GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCGATAA
TCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTACA
GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCTA
ATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGT
Found at i:20201896 original size:44 final size:43
Alignment explanation
Indices: 20201830--20201952 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 43
20201820 GAAAATGGTG
* *
20201830 AATCTTATCTTCTTGAGGTTACAGTGGAGCAGATTGAAGCCAGA-
1 AATCTTATCTCCTT-AAGTTACAGTGGAGCAGATTGAAGCC-GAT
* * * *
20201874 AATCTTATCTCCCTAAGATTACAGTAGAGTATATTGAAGCCGAT
1 AATCTTATCTCCTTAAG-TTACAGTGGAGCAGATTGAAGCCGAT
* * *
20201918 AATCCTATATCCTTGAAGTTACAGTGGAGCGGATT
1 AATCTTATCTCCTT-AAGTTACAGTGGAGCAGATT
20201953 AAAATAAAGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 4 0.06
44 56 0.89
45 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCTTAAGTTACAGTGGAGCAGATTGAAGCCGAT
Found at i:20202555 original size:23 final size:24
Alignment explanation
Indices: 20202524--20202569 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
20202514 TGCCCGGCCC
20202524 AAATCAAATAAAAAA-ACAAAATAT
1 AAATCAAATAAAAAATA-AAAATAT
20202548 AAAT-AAATAAAAAATAAAAATA
1 AAATCAAATAAAAAATAAAAATA
20202570 AAGTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (24 bp):
AAATCAAATAAAAAATAAAAATAT
Found at i:20202559 original size:15 final size:15
Alignment explanation
Indices: 20202529--20202567 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20202519 GGCCCAAATC
20202529 AAATAAAAAAACAAA
1 AAATAAAAAAACAAA
* * *
20202544 ATATAAATAAATAAA
1 AAATAAAAAAACAAA
20202559 AAATAAAAA
1 AAATAAAAA
20202568 TAAAGTTATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATAAAAAAACAAA
Found at i:20202693 original size:26 final size:27
Alignment explanation
Indices: 20202652--20202702 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
20202642 CAAACAGATC
*
20202652 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
20202679 CCAAA-ACCCAATTAACCTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
20202703 GCTAATGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:20203468 original size:16 final size:16
Alignment explanation
Indices: 20203447--20203489 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
20203437 CCGATGACCT
20203447 GACCCGAGCGTGGCCA
1 GACCCGAGCGTGGCCA
*
20203463 GACCCGTGCGTGGCCA
1 GACCCGAGCGTGGCCA
*
20203479 GACCCGCGCGT
1 GACCCGAGCGT
20203490 TTTGGTCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.40, G:0.37, T:0.09
Consensus pattern (16 bp):
GACCCGAGCGTGGCCA
Found at i:20204184 original size:14 final size:14
Alignment explanation
Indices: 20204165--20204191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20204155 ATATGGATAT
20204165 ACTATTTTTATTAA
1 ACTATTTTTATTAA
20204179 ACTATTTTTATTA
1 ACTATTTTTATTA
20204192 TACATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTATTTTTATTAA
Found at i:20208523 original size:18 final size:19
Alignment explanation
Indices: 20208500--20208537 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
20208490 CTTATTAATT
*
20208500 TAATAATTAAAT-AACATA
1 TAATAAATAAATAAACATA
*
20208518 TAATAAATAATTAAACATA
1 TAATAAATAAATAAACATA
20208537 T
1 T
20208538 TGTTTGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAAATAAATAAACATA
Found at i:20214052 original size:23 final size:24
Alignment explanation
Indices: 20214017--20214061 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
20214007 GATTTTTCAC
*
20214017 ATCATTTAAATAA-AATAAAAATT
1 ATCATTTAAATAATAAAAAAAATT
**
20214040 ATCATTTTTATAATAAAAAAAA
1 ATCATTTAAATAATAAAAAAAA
20214062 GGTTTAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
ATCATTTAAATAATAAAAAAAATT
Found at i:20224556 original size:25 final size:25
Alignment explanation
Indices: 20224509--20224556 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20224499 AAATACTATA
*
20224509 AAAAATTTTAAAAATATTTTTTCGT
1 AAAAATTTTAAAAATATCTTTTCGT
*
20224534 AAAACTTTTCAAAAATA-CTTTTC
1 AAAAATTTT-AAAAATATCTTTTC
20224557 AACTTCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAATTTTAAAAATATCTTTTCGT
Found at i:20232389 original size:3 final size:3
Alignment explanation
Indices: 20232381--20232461 Score: 126
Period size: 3 Copynumber: 27.0 Consensus size: 3
20232371 TTCTTTGCAG
* * * *
20232381 TAT TAT TAT TGT TGT TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20232429 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20232462 ATAAAACAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:20242000 original size:11 final size:11
Alignment explanation
Indices: 20241964--20242002 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
20241954 TAAATAGTAA
*
20241964 TTTATTAATAT
1 TTTAATAATAT
20241975 TTTAATGAGATAT
1 TTTAAT-A-ATAT
20241988 TTTAATAATAT
1 TTTAATAATAT
20241999 TTTA
1 TTTA
20242003 TTTAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 2 0.08
13 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:20243204 original size:2 final size:2
Alignment explanation
Indices: 20243199--20243223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20243189 CAATATATGA
20243199 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20243224 GTAGATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20245251 original size:16 final size:16
Alignment explanation
Indices: 20245211--20245259 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
20245201 TAACAATATG
20245211 AATAATAATATAATAA-
1 AATAA-AATATAATAAT
*
20245227 AA-CAAATATAATAAT
1 AATAAAATATAATAAT
*
20245242 AATAAAATATGATAAT
1 AATAAAATATAATAAT
20245258 AA
1 AA
20245260 AAATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 15 0.54
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAAAATATAATAAT
Found at i:20245276 original size:14 final size:15
Alignment explanation
Indices: 20245217--20245276 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
20245207 TATGAATAAT
20245217 AATATAATAAAAC-A
1 AATATAATAAAACAA
*
20245231 AATATAATAATAATAA
1 AATATAATAA-AACAA
* *
20245247 AATATGATAATA-AA
1 AATATAATAAAACAA
20245261 AATA-AATAAAACAA
1 AATATAATAAAACAA
20245275 AA
1 AA
20245277 AAGAAAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.13
14 20 0.53
15 3 0.08
16 10 0.26
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (15 bp):
AATATAATAAAACAA
Found at i:20247419 original size:12 final size:12
Alignment explanation
Indices: 20247374--20247419 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
20247364 TTTTTCTCTT
*
20247374 TTTTA-TTTTAA
1 TTTTATTTTTCA
*
20247385 TTATATTTTTCA
1 TTTTATTTTTCA
20247397 TTTT-TTCTTTCA
1 TTTTATT-TTTCA
20247409 TTTTATTTTTC
1 TTTTATTTTTC
20247420 CAATTTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.21
12 21 0.72
13 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:20255508 original size:3 final size:3
Alignment explanation
Indices: 20255502--20255526 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20255492 GTTGCCCTCT
20255502 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
20255527 CATGTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:20258883 original size:30 final size:31
Alignment explanation
Indices: 20258847--20258904 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
20258837 AAAAATCAAG
*
20258847 AAAATTAACATCACAAAC-AAAATCCATTAA
1 AAAATTAACATAACAAACAAAAATCCATTAA
20258877 AAAATTAACATAACAAACAAAAATCCAT
1 AAAATTAACATAACAAACAAAAATCCAT
20258905 CAATCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (31 bp):
AAAATTAACATAACAAACAAAAATCCATTAA
Found at i:20260723 original size:21 final size:21
Alignment explanation
Indices: 20260694--20260733 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20260684 CAACAAAAAA
20260694 AAAGCCTTTACCAAGAATACT
1 AAAGCCTTTACCAAGAATACT
* *
20260715 AAAGGCTTTTCCAAGAATA
1 AAAGCCTTTACCAAGAATA
20260734 GCAAGAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAGCCTTTACCAAGAATACT
Found at i:20261263 original size:22 final size:22
Alignment explanation
Indices: 20261237--20261278 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20261227 AATGTTAATT
*
20261237 TAAT-AAACAAAGGTAAATAAAA
1 TAATAAAACAAAAG-AAATAAAA
20261259 TAATAAAACAAAAGAAATAA
1 TAATAAAACAAAAGAAATAA
20261279 TCATCAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (22 bp):
TAATAAAACAAAAGAAATAAAA
Found at i:20261377 original size:58 final size:59
Alignment explanation
Indices: 20261271--20261389 Score: 195
Period size: 58 Copynumber: 2.0 Consensus size: 59
20261261 ATAAAACAAA
* * * *
20261271 AGAAATAATCATCAGTTTCTTTATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTCTTCAATTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
20261330 AGAAAGAATCATCAGCTTCTTCAATTT-TTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTCTTCAATTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
20261388 AG
1 AG
20261390 TCTCCAAGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 33 0.59
59 23 0.41
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (59 bp):
AGAAAGAATCATCAGCTTCTTCAATTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
Found at i:20268709 original size:10 final size:10
Alignment explanation
Indices: 20268687--20268726 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
20268677 ACTGGACATT
20268687 TATTTATTATA
1 TATTTA-TATA
*
20268698 TATATATATA
1 TATTTATATA
*
20268708 TATTTTTATA
1 TATTTATATA
20268718 TATTTATAT
1 TATTTATAT
20268727 TTGATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATATA
Found at i:20268719 original size:16 final size:16
Alignment explanation
Indices: 20268698--20268728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20268688 ATTTATTATA
20268698 TATATATATATATTTT
1 TATATATATATATTTT
*
20268714 TATATATTTATATTT
1 TATATATATATATTT
20268729 GATTTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATATATATATTTT
Found at i:20268735 original size:20 final size:20
Alignment explanation
Indices: 20268687--20268726 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20268677 ACTGGACATT
20268687 TATTTATTATATATATATATA
1 TATTT-TTATATATATATATA
*
20268708 TATTTTTATATATTTATAT
1 TATTTTTATATATATATAT
20268727 TTGATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATATATATATATA
Found at i:20270323 original size:15 final size:17
Alignment explanation
Indices: 20270288--20270326 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20270278 AAGTTGATTT
*
20270288 TTTTTTTAGATTTGAGC
1 TTTTTTAAGATTTGAGC
20270305 TTTTTTAAG-TTTGAG-
1 TTTTTTAAGATTTGAGC
20270320 TTTTTTA
1 TTTTTTA
20270327 TATTCGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTTTAAGATTTGAGC
Found at i:20279296 original size:4 final size:4
Alignment explanation
Indices: 20279287--20279330 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
20279277 TTATTCTATT
* * * *
20279287 TTTA TTTA TTTA TTTA TGTA TTCA TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
20279331 CTCTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:20279409 original size:12 final size:12
Alignment explanation
Indices: 20279389--20279432 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
20279379 CATTTTATTA
20279389 TTATTGTTGTTG
1 TTATTGTTGTTG
* **
20279401 TTGTTGTTGCGG
1 TTATTGTTGTTG
20279413 TTATTGTTGTTG
1 TTATTGTTGTTG
20279425 TTATTGTT
1 TTATTGTT
20279433 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.02, G:0.27, T:0.64
Consensus pattern (12 bp):
TTATTGTTGTTG
Found at i:20296767 original size:21 final size:19
Alignment explanation
Indices: 20296741--20296779 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
20296731 TTTGCCCTGG
20296741 CCCAAAAACAAATATAAAAAA
1 CCCAAAAA-AAA-ATAAAAAA
*
20296762 CCCAAATAAAAATAAAAA
1 CCCAAAAAAAAATAAAAA
20296780 CAGTCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.72, C:0.18, G:0.00, T:0.10
Consensus pattern (19 bp):
CCCAAAAAAAAATAAAAAA
Found at i:20300646 original size:4 final size:4
Alignment explanation
Indices: 20300637--20300690 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
20300627 TATTATTCTA
* * *
20300637 TATT TATT TATT TATT TATT TATT TATG TATT CATT CATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
*
20300685 TCTT TA
1 TATT TA
20300691 CTCTTTTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:20311620 original size:2 final size:2
Alignment explanation
Indices: 20311613--20311644 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20311603 AGAATTTAGA
20311613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20311645 TCAAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20319055 original size:24 final size:26
Alignment explanation
Indices: 20319008--20319056 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
20318998 TGTATCACAT
**
20319008 TATTATTTAAAAATTTTATTTTTTTG
1 TATTATTTAAAAATTTTACATTTTTG
20319034 TATT-TTT-AAAATTTTACATTTTT
1 TATTATTTAAAAATTTTACATTTTT
20319057 AAGTAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 3 0.14
26 4 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTATTTAAAAATTTTACATTTTTG
Found at i:20321498 original size:12 final size:13
Alignment explanation
Indices: 20321481--20321509 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20321471 TTGTCCAGGA
20321481 AAAAGAAAA-TTC
1 AAAAGAAAAGTTC
20321493 AAAAGAAAAGTTC
1 AAAAGAAAAGTTC
20321506 AAAA
1 AAAA
20321510 ATTGATTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAAGAAAAGTTC
Found at i:20327288 original size:33 final size:33
Alignment explanation
Indices: 20327246--20327312 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
20327236 TAATTAAAAA
20327246 TATATTTTCATCCCAACAACTAGACATCCAAGT
1 TATATTTTCATCCCAACAACTAGACATCCAAGT
20327279 TATATTTTCATCCCAACAACTAGACATCCAAGT
1 TATATTTTCATCCCAACAACTAGACATCCAAGT
20327312 T
1 T
20327313 GGCATTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (33 bp):
TATATTTTCATCCCAACAACTAGACATCCAAGT
Found at i:20330792 original size:34 final size:30
Alignment explanation
Indices: 20330741--20330805 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 30
20330731 ATCTCATTAT
20330741 TAAATAAAATAAAAAAA-TAGTAAATAATTTA
1 TAAATAAAATAAAAAAATTA-TAAAT-ATTTA
20330772 TAAATAATAATTAAATAAAATTATAAATATTTA
1 TAAATAA-AA-TAAA-AAAATTATAAATATTTA
20330805 T
1 T
20330806 TTACAAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
31 7 0.23
32 2 0.07
33 10 0.33
34 9 0.30
35 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
TAAATAAAATAAAAAAATTATAAATATTTA
Found at i:20335737 original size:12 final size:12
Alignment explanation
Indices: 20335720--20335744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20335710 AACACTCCTC
20335720 GCCCATCTCGTT
1 GCCCATCTCGTT
20335732 GCCCATCTCGTT
1 GCCCATCTCGTT
20335744 G
1 G
20335745 TACAATACAA
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:0.08, C:0.40, G:0.20, T:0.32
Consensus pattern (12 bp):
GCCCATCTCGTT
Done.