Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 117 of 290
Found at i:39879711 original size:17 final size:17
Alignment explanation
Indices: 39879673--39879710 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
39879663 TCAAATAAGT
*
39879673 AAAAATATATATAAATA
1 AAAAATATATAAAAATA
39879690 AAAAAT-TATAAAAATA
1 AAAAATATATAAAAATA
39879706 AAAAA
1 AAAAA
39879711 AAATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAAATA
Found at i:39891835 original size:12 final size:10
Alignment explanation
Indices: 39891800--39891849 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 10
39891790 CTTAATATTA
39891800 TTTA-AATTT
1 TTTATAATTT
39891809 TTTATTTAA-TT
1 TTTA--TAATTT
39891820 TTTATAATTT
1 TTTATAATTT
39891830 AATTTATAATTT
1 --TTTATAATTT
39891842 TTTATAAT
1 TTTATAAT
39891850 AGTCGGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
9 7 0.20
10 10 0.29
11 6 0.17
12 12 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATAATTT
Found at i:39894261 original size:18 final size:18
Alignment explanation
Indices: 39894234--39894280 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
39894224 TTTAAAAATA
39894234 TTTATGAAAATTTG-GATAT
1 TTTAT-AAAATTTGAGA-AT
*
39894253 TTTATAAAAGTTGAGAAT
1 TTTATAAAATTTGAGAAT
*
39894271 TTTAAAAAAT
1 TTTATAAAAT
39894281 ACTTTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (18 bp):
TTTATAAAATTTGAGAAT
Found at i:39894383 original size:9 final size:9
Alignment explanation
Indices: 39894359--39894392 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39894349 AAACTAATTT
*
39894359 ATTATTTGA
1 ATTATTTAA
*
39894368 ATAATTTAA
1 ATTATTTAA
39894377 ATTATTTAA
1 ATTATTTAA
39894386 ATTATTT
1 ATTATTT
39894393 GAATCGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTATTTAA
Found at i:39895209 original size:26 final size:26
Alignment explanation
Indices: 39895180--39895231 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
39895170 AACAAATGTC
39895180 TTTTTA-TAAAAAATAAAA-AATAATAA
1 TTTTTATTAAAAAA-AAAAGAA-AATAA
39895206 TTTTTATTAAAAAAAAAAGAAAATAA
1 TTTTTATTAAAAAAAAAAGAAAATAA
39895232 CCTAGTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TTTTTATTAAAAAAAAAAGAAAATAA
Found at i:39895777 original size:16 final size:19
Alignment explanation
Indices: 39895743--39895777 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39895733 TTTACATATA
39895743 AATAATATTTTATATTTTT
1 AATAATATTTTATATTTTT
39895762 AATAAT-TTTTA-ATTTT
1 AATAATATTTTATATTTT
39895778 CAGATACGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATAATATTTTATATTTTT
Found at i:39897244 original size:15 final size:15
Alignment explanation
Indices: 39897203--39897245 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
39897193 AATGAGAAAA
39897203 ATAAAAATAAAACAC
1 ATAAAAATAAAACAC
* *
39897218 AT-AAATTTAAACAC
1 ATAAAAATAAAACAC
39897232 ATAAAAATAAAACA
1 ATAAAAATAAAACA
39897246 AATACAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAAATAAAACAC
Found at i:39900856 original size:23 final size:21
Alignment explanation
Indices: 39900814--39900856 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39900804 TTTCATACAC
*
39900814 TATATACTTTAAATTGTTTTG
1 TATATACTTTAAATTATTTTG
*
39900835 TATATATTTCTAAACTTATTTT
1 TATATACTT-TAAA-TTATTTT
39900857 TATGTACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (21 bp):
TATATACTTTAAATTATTTTG
Found at i:39904155 original size:19 final size:19
Alignment explanation
Indices: 39904131--39904182 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
39904121 TTGACCTCTT
39904131 TTTGCATT-CATTTCATCCA
1 TTTGCATTACATTTCAT-CA
39904150 TTTGCATTACATTTCATCA
1 TTTGCATTACATTTCATCA
* *
39904169 TATGCATTAAATTT
1 TTTGCATTACATTT
39904183 TACAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (19 bp):
TTTGCATTACATTTCATCA
Found at i:39915783 original size:34 final size:34
Alignment explanation
Indices: 39915737--39915807 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
39915727 ACAAGTGTGA
39915737 ATTTTGGCTACATGAGGTTGGATTTCTAGGTCAT
1 ATTTTGGCTACATGAGGTTGGATTTCTAGGTCAT
*
39915771 ATTTTGGTTACATGAGGTTGGATTTCTAGGTCAT
1 ATTTTGGCTACATGAGGTTGGATTTCTAGGTCAT
39915805 ATT
1 ATT
39915808 GTTTTAGCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (34 bp):
ATTTTGGCTACATGAGGTTGGATTTCTAGGTCAT
Found at i:39918983 original size:51 final size:51
Alignment explanation
Indices: 39918907--39919020 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
39918897 AGTGACAAGC
* *
39918907 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
39918958 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
39919009 GACAAGTGATAA
1 GACAAGTGATAA
39919021 ATGTGATCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:39920940 original size:44 final size:44
Alignment explanation
Indices: 39920874--39921049 Score: 167
Period size: 44 Copynumber: 4.0 Consensus size: 44
39920864 AATCACCATG
* * *
39920874 GCGAATCTTGTCTCCCTAAAGTTGTAGTGGAACAGATTGAAGCC
1 GCGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGCA
* * *
39920918 GCGAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGTTA
1 GCGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAG-CA
* * *
39920963 -C-AGATCTTATCTCCCTAAAGTTGCAGTGGAATAGATCGAAGATA
1 GCGA-ATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAG-CA
** * * * * *
39921007 GAAAATCTCATTTCCTTGAAGTTGCAGTGGAACAGATTAAAGC
1 GCGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGC
39921050 TATGAGTTAC
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.01
44 77 0.70
45 31 0.28
46 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
GCGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGCA
Found at i:39920992 original size:88 final size:89
Alignment explanation
Indices: 39920878--39921044 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 89
39920868 ACCATGGCGA
* * * * ** *
39920878 ATCTTGTCTCCCTAAAGTTGTAGTGGAACAGATTGAAG-CCGCGAATCTTATCTCCCTGAAGTTG
1 ATCTTATCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGAAAATCTCATCTCCCTGAAGTTG
*
39920942 CAGTGGAATAGATTGAAGTTACAG
66 CAGTGGAACAGATTGAAGTTACAG
* * * *
39920966 ATCTTATCTCCCTAAAGTTGCAGTGGAATAGATCGAAGATAGAAAATCTCATTTCCTTGAAGTTG
1 ATCTTATCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGAAAATCTCATCTCCCTGAAGTTG
39921031 CAGTGGAACAGATT
66 CAGTGGAACAGATT
39921045 AAAGCTATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
88 34 0.52
89 32 0.48
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (89 bp):
ATCTTATCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGAAAATCTCATCTCCCTGAAGTTG
CAGTGGAACAGATTGAAGTTACAG
Found at i:39921327 original size:94 final size:94
Alignment explanation
Indices: 39921153--39921389 Score: 262
Period size: 94 Copynumber: 2.5 Consensus size: 94
39921143 GCTAAAGATA
* * * * *
39921153 GCAAATCTTATCTTTCTGAAGTTGCAGTAGAGCATATTAAAGCTACAAATCCTATACCTCTGAAG
1 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCCTATACCTCTGAAA
* *
39921218 TTGCAGTAGGTCGGATCAAA-TCTATCATG
66 TTGCAGTAGGACGGATCAAAGT-TACCATG
* * * * *
39921247 GCGAATCTTATCTCCCTGACGTTGCGGTAGAGCAGATTGAAGCCACTAATCCTATACC-CGTGAA
1 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCCTATACCTC-TGAA
* * * *
39921311 ATTGTAGTGGGACGGATTAAAGTTACCTTG
65 ATTGCAGTAGGACGGATCAAAGTTACCATG
* * * *
39921341 GCAAATCTTATCTCTCTAAAGTTGTAGTAGAGTAGATTGAAGACACAAA
1 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAA
39921390 CCTTGTCTCC
Statistics
Matches: 116, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
93 1 0.01
94 114 0.98
95 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (94 bp):
GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCACAAATCCTATACCTCTGAAA
TTGCAGTAGGACGGATCAAAGTTACCATG
Found at i:39924342 original size:182 final size:183
Alignment explanation
Indices: 39923955--39924375 Score: 517
Period size: 182 Copynumber: 2.3 Consensus size: 183
39923945 TCATATTTTA
* * * * * * *
39923955 AAGTTTTCCTTTCTTTGTTCCATTACTCTTCTCTGAATCTTCTCTCGTTTTCTCTATTATGTTAT
1 AAGTTTTTCTTTCTTTGTT-CGTTCCTCTTCTTTGACTCTACTCTTGTTTTCTCTATTATGTTAT
39924020 CACGCTCATCAAAACAAAATCAAGTAGAAAAAAAGAAAGAAAGAGGGCAACAACTTGCAATCCAA
65 CACGCTCATCAAAACAAAATCAAGTAGAAAAAAAG-AAGAAAGA-GG--A-AACTTGCAATCCAA
39924085 AATACCATAAAAGAAAGTTGAATGTTAGTATTCCCTTCCTACTCAATAGTCTAACTAGT
125 AATACCATAAAAGAAAGTTGAATGTTAGTATTCCCTTCCTACTCAATAGTCTAACTAGT
** *
39924144 ACCTTTTTATTTCTTTGTCTCGTTCCTCTTCTTTGACTCTACTCTTGTTTTCTCTATTATGTTTA
1 AAGTTTTTCTTTCTTTGT-TCGTTCCTCTTCTTTGACTCTACTCTTGTTTTCTCTATTATG-TTA
* * *
39924209 TCATGCTCATCAAAACAAAATCAAGTA-AAAAAAAG-AGAACGA-G-AACTTTCAATCCAAAATA
64 TCACGCTCATCAAAACAAAATCAAGTAGAAAAAAAGAAGAAAGAGGAAACTTGCAATCCAAAATA
** * * * *
39924270 CTGTAAAAGGAAAGTTGAATGTTAGTATTCCTTTCCTAGTCAATAGTCTAATTGGT
129 CCATAAAA-GAAAGTTGAATGTTAGTATTCCCTTCCTACTCAATAGTCTAACTAGT
* ** *
39924326 AAGTTTTTCTTTCTTTGTTTAGTTCCTCTTCTTCAACTCTACTATTGTTT
1 AAGTTTTTCTTTCTTTG-TTCGTTCCTCTTCTTTGACTCTACTCTTGTTT
39924376 GTTCCGTTCC
Statistics
Matches: 202, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
181 23 0.11
182 84 0.42
183 1 0.00
185 1 0.00
187 6 0.03
189 57 0.28
190 30 0.15
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (183 bp):
AAGTTTTTCTTTCTTTGTTCGTTCCTCTTCTTTGACTCTACTCTTGTTTTCTCTATTATGTTATC
ACGCTCATCAAAACAAAATCAAGTAGAAAAAAAGAAGAAAGAGGAAACTTGCAATCCAAAATACC
ATAAAAGAAAGTTGAATGTTAGTATTCCCTTCCTACTCAATAGTCTAACTAGT
Found at i:39924552 original size:217 final size:216
Alignment explanation
Indices: 39924164--39924585 Score: 682
Period size: 217 Copynumber: 1.9 Consensus size: 216
39924154 TTCTTTGTCT
*
39924164 CGTTCCTCTTCTTTGACTCTACTCTTGTTTTCTCTATTATGTTTATCATGCTCATCAAAACAAAA
1 CGTTCCTCTTCTCTGACTCTACTCTTGTTTTCTCTATTATGTTTATCATGCTCATCAAAACAAAA
* * * ** *
39924229 TCAAGTAAAAAAAAGAGAACGAGAACTTTCAATCCAAAATACTGTAAAAGGAAAGTTGAATGTTA
66 TCAAGTAAAAAAAAAAGAACGACAACTTACAATCCAAAATACCATAAAAGAAAAGTTGAATGTTA
* *
39924294 GTATTCCTTTCCTAGTCAATAGTCTAATTGGTAAGTTTTTCTTTCTTTGTTTAGTTCCTCTTCTT
131 GTATTCCTTTCCTAGTCAATAGTCTAATTGGTAAGTTTTTCTTTCTTTGTCTAGTTCCTCTTCTC
39924359 CAACTCTACTATTGTTTGTTC
196 CAACTCTACTATTGTTTGTTC
* *
39924380 CGTTCCTCTTCTCTGACTCTACTTTTGTTTTCTCTATTATGTTTATCATGCTCATCTAAACAAAA
1 CGTTCCTCTTCTCTGACTCTACTCTTGTTTTCTCTATTATGTTTATCATGCTCATCAAAACAAAA
* * *
39924445 TCAAGTAAAAAAAAAAAGGATGACAACTTACAATCCAAAATACCATAGAAGAAAAGTTGAATGTT
66 TCAAGT-AAAAAAAAAAGAACGACAACTTACAATCCAAAATACCATAAAAGAAAAGTTGAATGTT
* *
39924510 AGTATTCCTTTCCTAGTTAATAGTCTAATTGGTAAGTTTTTCTTTCTTTGTCTCGTTCCTCTTCT
130 AGTATTCCTTTCCTAGTCAATAGTCTAATTGGTAAGTTTTTCTTTCTTTGTCTAGTTCCTCTTCT
*
39924575 CCGACTCTACT
195 CCAACTCTACT
39924586 CTCGTTTTCT
Statistics
Matches: 188, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
216 68 0.36
217 120 0.64
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (216 bp):
CGTTCCTCTTCTCTGACTCTACTCTTGTTTTCTCTATTATGTTTATCATGCTCATCAAAACAAAA
TCAAGTAAAAAAAAAAGAACGACAACTTACAATCCAAAATACCATAAAAGAAAAGTTGAATGTTA
GTATTCCTTTCCTAGTCAATAGTCTAATTGGTAAGTTTTTCTTTCTTTGTCTAGTTCCTCTTCTC
CAACTCTACTATTGTTTGTTC
Found at i:39926048 original size:28 final size:28
Alignment explanation
Indices: 39925995--39926048 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
39925985 TGATTTTATT
* *
39925995 AAAATAAATAAATTCAATGGATAATTAA
1 AAAATAAATAAATTAAATGGAAAATTAA
*
39926023 AAAATAAATAAATTAAATGTAAAATT
1 AAAATAAATAAATTAAATGGAAAATT
39926049 GGAGAAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAATAAATAAATTAAATGGAAAATTAA
Found at i:39926218 original size:24 final size:23
Alignment explanation
Indices: 39926160--39926219 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
39926150 AGTTAAAATG
*
39926160 TATTTAAATT-ATTTTATAATTT
1 TATTTAAATTAATTTTATAATTA
** *
39926182 TGCTTAAATTTAATTTTATGATTAA
1 TATTTAAA-TTAATTTTATAATT-A
39926207 TATTTAAATTAAT
1 TATTTAAATTAAT
39926220 ATAAATGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
24 15 0.52
25 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTTAAATTAATTTTATAATTA
Found at i:39929317 original size:24 final size:24
Alignment explanation
Indices: 39929290--39929337 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
39929280 AAAAAAGAAT
39929290 AGAAAAT-AAAGAAAAAAAGTTAAA
1 AGAAAATAAAAGAAAAAAA-TTAAA
39929314 AGAAAATAAAAGAAAAAAATTAAA
1 AGAAAATAAAAGAAAAAAATTAAA
39929338 TTGATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.12
Consensus pattern (24 bp):
AGAAAATAAAAGAAAAAAATTAAA
Found at i:39939832 original size:84 final size:84
Alignment explanation
Indices: 39939686--39939853 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
39939676 TTCTGGTCTT
*
39939686 AATTTTGATACTGCAACACATGCAACTTAAGCATTATATATACTAAGTTTGCTTATCAATATGGA
1 AATTCTGATACTGCAACACATGCAACTTAAGCATTATATATACTAAGTTTGCTTATCAATATGGA
39939751 CAGTCTTCTAGCACAATAG
66 CAGTCTTCTAGCACAATAG
39939770 AATTCTGATACTGCAACACATGCAACTTAAGCATTATATATACTAAGTTTGCTTATCAATATGGA
1 AATTCTGATACTGCAACACATGCAACTTAAGCATTATATATACTAAGTTTGCTTATCAATATGGA
39939835 CAGTCTTCTAGCACAATAG
66 CAGTCTTCTAGCACAATAG
39939854 CTTAATTTCA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (84 bp):
AATTCTGATACTGCAACACATGCAACTTAAGCATTATATATACTAAGTTTGCTTATCAATATGGA
CAGTCTTCTAGCACAATAG
Found at i:39943789 original size:7 final size:7
Alignment explanation
Indices: 39943777--39943811 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
39943767 TTTGTCACAC
39943777 ACCACCT
1 ACCACCT
39943784 ACCACCT
1 ACCACCT
39943791 ACCACCT
1 ACCACCT
39943798 ACCACC-
1 ACCACCT
39943804 ACC-CCT
1 ACCACCT
39943810 AC
1 AC
39943812 TTTCTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.07
6 5 0.19
7 20 0.74
ACGTcount: A:0.29, C:0.60, G:0.00, T:0.11
Consensus pattern (7 bp):
ACCACCT
Found at i:39947405 original size:80 final size:80
Alignment explanation
Indices: 39947309--39947464 Score: 285
Period size: 80 Copynumber: 1.9 Consensus size: 80
39947299 TGAAATAAAC
*
39947309 TACATGTGTATATGTTATAAGAATTGATGGGTAAAAGAAAACTTAGAAAAAACGCCCATAAAAGA
1 TACATGTGTATATGTTATAAGAATTGATGGGTAAAAGAAAACTTAGAAAAAACGCCCATAAAACA
39947374 ATTTTTGTTTTTTTT
66 ATTTTTGTTTTTTTT
* *
39947389 TACATGTGTATATGTTATAAGAATTGATGGGTAAAAGAAAACTTAGAATAAACGCCTATAAAACA
1 TACATGTGTATATGTTATAAGAATTGATGGGTAAAAGAAAACTTAGAAAAAACGCCCATAAAACA
39947454 ATTTTTGTTTT
66 ATTTTTGTTTT
39947465 AAAAAAAAGA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (80 bp):
TACATGTGTATATGTTATAAGAATTGATGGGTAAAAGAAAACTTAGAAAAAACGCCCATAAAACA
ATTTTTGTTTTTTTT
Found at i:39949761 original size:21 final size:21
Alignment explanation
Indices: 39949735--39949787 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39949725 CAACTCTTTC
*
39949735 GAGCTTCTGTTAAGCTCTTAT
1 GAGCTTCTGTTAAGCTCTTAA
* *
39949756 GTGCTTCTGTTTAGCTCTTAA
1 GAGCTTCTGTTAAGCTCTTAA
39949777 GAGCTTCTGTT
1 GAGCTTCTGTT
39949788 GGCGTGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (21 bp):
GAGCTTCTGTTAAGCTCTTAA
Found at i:39950836 original size:20 final size:20
Alignment explanation
Indices: 39950799--39950837 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39950789 CCTGCAGTCC
* * *
39950799 AAAATTTTCAACTTTTTCCT
1 AAAATTTCCAAATGTTTCCT
39950819 AAAATTTCCAAATGTTTCC
1 AAAATTTCCAAATGTTTCC
39950838 GATTTAGTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATTTCCAAATGTTTCCT
Found at i:39951933 original size:20 final size:18
Alignment explanation
Indices: 39951908--39951944 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
39951898 ATTGCTAAGT
39951908 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
39951928 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
39951945 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:39957564 original size:25 final size:25
Alignment explanation
Indices: 39957511--39957573 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
39957501 TTATTATTTT
*
39957511 AAAATTAAAAATATATAAAAAAATTA
1 AAAATT-AAAATATATAAAAAAATAA
***
39957537 AAAATTAAAATATATAACTTAATAA
1 AAAATTAAAATATATAAAAAAATAA
39957562 AAATATTAAAAT
1 AAA-ATTAAAAT
39957574 CTTTTACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.56
26 14 0.44
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATTAAAATATATAAAAAAATAA
Found at i:39957731 original size:8 final size:8
Alignment explanation
Indices: 39957720--39957761 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
39957710 ATTTTTTAAT
39957720 TTTATATA
1 TTTATATA
39957728 TTTATATA
1 TTTATATA
*
39957736 TTTATAAA
1 TTTATATA
*
39957744 TTTATGTA
1 TTTATATA
39957752 -TTATATA
1 TTTATATA
39957759 TTT
1 TTT
39957762 TAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:39957767 original size:23 final size:24
Alignment explanation
Indices: 39957720--39957765 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39957710 ATTTTTTAAT
39957720 TTTATATATTTATATATTTATAAA
1 TTTATATATTTATATATTTATAAA
*
39957744 TTTATGTA-TTATATATTT-TAAA
1 TTTATATATTTATATATTTATAAA
39957766 ATAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTATATATTTATATATTTATAAA
Found at i:39961730 original size:22 final size:22
Alignment explanation
Indices: 39961704--39961747 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39961694 CTTACAAAAT
39961704 TAATTATTTGGATATTAAGCCA
1 TAATTATTTGGATATTAAGCCA
*
39961726 TAATTATTTGGCTATTAAGCCA
1 TAATTATTTGGATATTAAGCCA
39961748 ATCCAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TAATTATTTGGATATTAAGCCA
Found at i:39962944 original size:19 final size:19
Alignment explanation
Indices: 39962922--39962961 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39962912 GTGATTGAAG
39962922 ATAGGTTTTAGTGACAGGA
1 ATAGGTTTTAGTGACAGGA
*
39962941 ATAGGTTTTGGTGACAGGA
1 ATAGGTTTTAGTGACAGGA
39962960 AT
1 AT
39962962 CAATCAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.33
Consensus pattern (19 bp):
ATAGGTTTTAGTGACAGGA
Found at i:39964795 original size:42 final size:42
Alignment explanation
Indices: 39964736--39964819 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
39964726 GATGGAAAAA
*
39964736 TACCTTTAAAATCTTTAAAATCTGCCCAAATTCCAAATCTAG
1 TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
*
39964778 TACCTTTAAAATCTTTAAAATCCGCCCAAATTTCAAATCTAG
1 TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
39964820 AAATTTAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (42 bp):
TACCTTTAAAATCTTTAAAATCCGCCCAAATTCCAAATCTAG
Found at i:39965810 original size:50 final size:50
Alignment explanation
Indices: 39965751--39965850 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
39965741 CAATGTGAAG
39965751 TTTATAATGCCACTACGTCAACAAAGTAAATATAATTTCCAAACAATTAT
1 TTTATAATGCCACTACGTCAACAAAGTAAATATAATTTCCAAACAATTAT
39965801 TTTATAATGCCACTACGTCAACAAAGTAAATATAATTTCCAAACAATTAT
1 TTTATAATGCCACTACGTCAACAAAGTAAATATAATTTCCAAACAATTAT
39965851 ATGCAATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (50 bp):
TTTATAATGCCACTACGTCAACAAAGTAAATATAATTTCCAAACAATTAT
Found at i:39984170 original size:3 final size:3
Alignment explanation
Indices: 39984162--39984210 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
39984152 TTTTGTTTTC
39984162 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39984210 A
1 A
39984211 GTAGTAGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39984215 original size:3 final size:3
Alignment explanation
Indices: 39984209--39984263 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
39984199 TTATTATTAT
39984209 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
39984257 TAG TAG T
1 TAG TAG T
39984264 TTAGTTAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:39995800 original size:5 final size:6
Alignment explanation
Indices: 39995782--39995816 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
39995772 AATGATCGGG
39995782 AAGAAA AAGAAA AAGAAA AAGAAA AA-AATA AAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAA-A AAGAA
39995817 CATAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.07
6 23 0.85
7 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:39999129 original size:14 final size:14
Alignment explanation
Indices: 39999110--39999142 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39999100 AAATAACATA
39999110 CGAGTTAGGTAAAT
1 CGAGTTAGGTAAAT
39999124 CGAGTTAGGTAAAT
1 CGAGTTAGGTAAAT
39999138 C-AGTT
1 CGAGTT
39999143 TGAACTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (14 bp):
CGAGTTAGGTAAAT
Found at i:40011667 original size:21 final size:21
Alignment explanation
Indices: 40011628--40011667 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40011618 TTTCGAAAAT
40011628 AAATCTATATTTATATTTTTG
1 AAATCTATATTTATATTTTTG
*
40011649 AAATC-ATATTTATTTTTTT
1 AAATCTATATTTATATTTTT
40011668 ATTTCGAATA
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:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
AAATCTATATTTATATTTTTG
Found at i:40011737 original size:13 final size:13
Alignment explanation
Indices: 40011714--40011747 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40011704 TTTTTTTAAA
40011714 TATAA-TATATTT
1 TATAATTATATTT
*
40011726 TATTATTATATTT
1 TATAATTATATTT
40011739 TATAATTAT
1 TATAATTAT
40011748 TTATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATAATTATATTT
Found at i:40011742 original size:20 final size:20
Alignment explanation
Indices: 40011719--40011764 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40011709 TTAAATATAA
*
40011719 TATATTTTA-TTATTATATT
1 TATATTTTATTTATAATATT
*
40011738 T-TATAATTATTTATAATATT
1 TATAT-TTTATTTATAATATT
40011758 TATATTT
1 TATATTT
40011765 AAATTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 11 0.52
21 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTTTATTTATAATATT
Found at i:40012335 original size:25 final size:25
Alignment explanation
Indices: 40012307--40012354 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40012297 TATGAAAAAC
*
40012307 AATTATAATTAACAATAACAAAAGG
1 AATTATAATTAAAAATAACAAAAGG
* * *
40012332 AATTTTATTTAAAAATAATAAAA
1 AATTATAATTAAAAATAACAAAA
40012355 ATAAAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (25 bp):
AATTATAATTAAAAATAACAAAAGG
Found at i:40012862 original size:30 final size:30
Alignment explanation
Indices: 40012828--40012890 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
40012818 ATTTATTTTA
40012828 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
40012858 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
40012888 TTG
1 TTG
40012891 CTTCTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:40014995 original size:16 final size:16
Alignment explanation
Indices: 40014971--40015014 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
40014961 ATTAATATAG
*
40014971 AATTTAAAAT-AATAA
1 AATTAAAAATAAATAA
40014986 TAATTAAAAATAAATAA
1 -AATTAAAAATAAATAA
40015003 AATT-AAAATAAA
1 AATTAAAAATAAA
40015015 CTTAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTAAAAATAAATAA
Found at i:40015659 original size:23 final size:23
Alignment explanation
Indices: 40015629--40015674 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40015619 AAACCCTCGC
40015629 AACAATTCCATCTCATGGATGTG
1 AACAATTCCATCTCATGGATGTG
40015652 AACAATTCCATCTCATGGATGTG
1 AACAATTCCATCTCATGGATGTG
40015675 GAGAATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (23 bp):
AACAATTCCATCTCATGGATGTG
Found at i:40026131 original size:46 final size:46
Alignment explanation
Indices: 40026064--40026284 Score: 370
Period size: 46 Copynumber: 4.8 Consensus size: 46
40026054 TGTAACCCGC
* * * * *
40026064 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
40026110 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40026156 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40026202 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40026248 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40026285 TGCTCAACCA
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 170 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40029451 original size:41 final size:41
Alignment explanation
Indices: 40029398--40029525 Score: 193
Period size: 41 Copynumber: 3.1 Consensus size: 41
40029388 GCAAAAATTG
* *
40029398 AAAAACACAGAGCAATAGCGGCGCTTTTGGCAAAACGCCGCT
1 AAAAAC-CAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
* *
40029440 AAAAACCAGAGCATTAGCGGTGTTTTTGGAAAAACGCCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
* *
40029481 AAAAACCAGAGCATTAGCGTCGCTTTTAGAAAAACGCCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
40029522 AAAA
1 AAAA
40029526 GTCATATAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 72 0.92
42 6 0.08
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAACGCCGCT
Found at i:40029720 original size:14 final size:14
Alignment explanation
Indices: 40029698--40029797 Score: 65
Period size: 14 Copynumber: 6.9 Consensus size: 14
40029688 TTAATTATCA
*
40029698 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
40029712 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
40029726 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
* *
40029740 TTAAGGTTTATGAGT
1 TTATGGTTTAAG-GT
*
40029755 TAACTATGGTTTAAGAT
1 T---TATGGTTTAAGGT
* * *
40029772 ATATAGTTTAGGGT
1 TTATGGTTTAAGGT
*
40029786 TTAAGGTTTAAG
1 TTATGGTTTAAG
40029798 AGTTAACTAG
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
14 50 0.79
15 3 0.05
17 1 0.02
18 9 0.14
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:40029733 original size:21 final size:21
Alignment explanation
Indices: 40029709--40029790 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 21
40029699 TATAGTTTAA
*
40029709 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
* *
40029730 GGTTTAGGGTTTAAGGTTTAT
1 GGTTTAGGGTTTAAGATATAT
*
40029751 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
*
40029776 AGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
40029791 GTTTAAGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 29 0.59
22 3 0.06
24 3 0.06
25 14 0.29
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:40029763 original size:46 final size:46
Alignment explanation
Indices: 40029713--40029806 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
40029703 GTTTAAGGTT
* *
40029713 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
40029759 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
40029805 TA
1 TA
40029807 GTATTTGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
Found at i:40030284 original size:15 final size:15
Alignment explanation
Indices: 40030264--40030301 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40030254 TATCATTAGG
40030264 TTTAAGTAAATTTAC
1 TTTAAGTAAATTTAC
40030279 TTTAAGTAAATTTAC
1 TTTAAGTAAATTTAC
*
40030294 GTTAAGTA
1 TTTAAGTA
40030302 TTTGTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (15 bp):
TTTAAGTAAATTTAC
Found at i:40034813 original size:22 final size:23
Alignment explanation
Indices: 40034771--40034813 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40034761 TTTCAAGAAT
*
40034771 TAAACATAATATAATATTTAACA
1 TAAAAATAATATAATATTTAACA
*
40034794 TAAAAATAA-ATATTATTTAA
1 TAAAAATAATATAATATTTAA
40034814 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATAATATAATATTTAACA
Found at i:40034918 original size:42 final size:43
Alignment explanation
Indices: 40034854--40034988 Score: 191
Period size: 43 Copynumber: 3.2 Consensus size: 43
40034844 GATTTCTAGT
* * *
40034854 GGCGTTTGTGAGAAAAGCGCCACTAAAGGTCCTGGTCTTTAGC
1 GGCGTTTGTTAGAAAAGTGCCACTAAAGGTCATGGTCTTTAGC
*
40034897 GGCGTTT-TTAGAAAAGTGCCACTAAAGGTCATGGTTTTTAGC
1 GGCGTTTGTTAGAAAAGTGCCACTAAAGGTCATGGTCTTTAGC
* * * *
40034939 GGCGTTTGTAAAAAAAGTGCCGCTAAAAGTCATGGTCTTTAGC
1 GGCGTTTGTTAGAAAAGTGCCACTAAAGGTCATGGTCTTTAGC
40034982 GGCGTTT
1 GGCGTTT
40034989 TTTTAAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 38 0.46
43 44 0.54
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
GGCGTTTGTTAGAAAAGTGCCACTAAAGGTCATGGTCTTTAGC
Found at i:40034977 original size:85 final size:85
Alignment explanation
Indices: 40034834--40034990 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
40034824 ATATTTTTTT
* * * * * *
40034834 TAAAGTTCATGATTTCTAGTGGCGTTTGTGAGAAAAGCGCCACTAAAGGTCCTGGTCTTTAGCGG
1 TAAAGGTCATGATTTCTAGCGGCGTTTGTAAAAAAAGCGCCACTAAAAGTCATGGTCTTTAGCGG
40034899 CGTTTTTAGAAAAGTGCCAC
66 CGTTTTTAGAAAAGTGCCAC
* * * *
40034919 TAAAGGTCATGGTTTTTAGCGGCGTTTGTAAAAAAAGTGCCGCTAAAAGTCATGGTCTTTAGCGG
1 TAAAGGTCATGATTTCTAGCGGCGTTTGTAAAAAAAGCGCCACTAAAAGTCATGGTCTTTAGCGG
40034984 CGTTTTT
66 CGTTTTT
40034991 TTAAATAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (85 bp):
TAAAGGTCATGATTTCTAGCGGCGTTTGTAAAAAAAGCGCCACTAAAAGTCATGGTCTTTAGCGG
CGTTTTTAGAAAAGTGCCAC
Found at i:40035998 original size:30 final size:31
Alignment explanation
Indices: 40035964--40036028 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
40035954 AGAAAAATTT
*
40035964 AATAGCTCAATGACTT-AATAAAAACTTTTG
1 AATAGCTCAATGACTTAAATAAAAACTTTCG
* * * *
40035994 AATAGTTTAGTGACTTAAATGAAAACTTTCG
1 AATAGCTCAATGACTTAAATAAAAACTTTCG
40036025 AATA
1 AATA
40036029 ATTTTGTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
AATAGCTCAATGACTTAAATAAAAACTTTCG
Found at i:40036022 original size:31 final size:30
Alignment explanation
Indices: 40035974--40036038 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
40035964 AATAGCTCAA
* *
40035974 TGACTTAATAAAAACTTTTGAATAGTTTAG
1 TGACTTAATAAAAACTTTCGAATAATTTAG
* *
40036004 TGACTTAAATGAAAACTTTCGAATAATTTTG
1 TGACTT-AATAAAAACTTTCGAATAATTTAG
40036035 TGAC
1 TGAC
40036039 CAAATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (30 bp):
TGACTTAATAAAAACTTTCGAATAATTTAG
Found at i:40037014 original size:14 final size:14
Alignment explanation
Indices: 40036995--40037022 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40036985 TAACAACCTT
40036995 TTATTACCATAGTA
1 TTATTACCATAGTA
40037009 TTATTACCATAGTA
1 TTATTACCATAGTA
40037023 AAGAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTATTACCATAGTA
Found at i:40037536 original size:43 final size:43
Alignment explanation
Indices: 40037487--40037618 Score: 203
Period size: 43 Copynumber: 3.1 Consensus size: 43
40037477 TTAAAAAAAT
* *
40037487 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTTTGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCAGCGTTTGTTAGAAAAGC
* * *
40037530 GCCGCTAAAAGCCATGACTTTTAGCAGCGTTTGTTGGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCAGCGTTTGTTAGAAAAGC
*
40037573 GCCGCTAAAAGTCATGGCTTTTAGCTGCGTTTGTTAGAAAA-C
1 GCCGCTAAAAGTCATGGCTTTTAGCAGCGTTTGTTAGAAAAGC
40037615 GCCG
1 GCCG
40037619 TTAGTTTTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 5 0.06
43 76 0.94
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCTTTTAGCAGCGTTTGTTAGAAAAGC
Found at i:40037731 original size:31 final size:31
Alignment explanation
Indices: 40037677--40037757 Score: 65
Period size: 31 Copynumber: 2.6 Consensus size: 31
40037667 TTCCTGCATT
* * * * *
40037677 AAAATCCAACCAAATACAACAAATATAA-TA
1 AAAATACAACCAAAAATAGCAAATATACATA
* * *
40037707 TAAAATGCAGCCAAAAATAGCAAATTTAGCATA
1 -AAAATACAACCAAAAATAGCAAATATA-CATA
40037740 AAAATACAACCAAAAATA
1 AAAATACAACCAAAAATA
40037758 TTAATTCTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
31 21 0.54
32 16 0.41
33 2 0.05
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (31 bp):
AAAATACAACCAAAAATAGCAAATATACATA
Found at i:40038020 original size:21 final size:21
Alignment explanation
Indices: 40037992--40038085 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
40037982 GCTGCCATCA
40037992 CTGCTGCCTCTGCCTCCCTCG
1 CTGCTGCCTCTGCCTCCCTCG
*
40038013 CT-CGTGCCTCTGCCTCCCTTG
1 CTGC-TGCCTCTGCCTCCCTCG
* *
40038034 TTGCTGCCGCTGCCTCCCTCG
1 CTGCTGCCTCTGCCTCCCTCG
*
40038055 CTGCTG-CTGCTGCCTCCCTCT
1 CTGCTGCCT-CTGCCTCCCTCG
40038076 CTGCTGCCTC
1 CTGCTGCCTC
40038086 CGCTCTAAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 2 0.03
21 57 0.92
22 3 0.05
ACGTcount: A:0.00, C:0.49, G:0.20, T:0.31
Consensus pattern (21 bp):
CTGCTGCCTCTGCCTCCCTCG
Found at i:40038063 original size:18 final size:18
Alignment explanation
Indices: 40038036--40038086 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
40038026 CTCCCTTGTT
*
40038036 GCTGCCGCTGCCTCCCTC
1 GCTGCTGCTGCCTCCCTC
*
40038054 GCTGCTGCTG-CTGCCTC
1 GCTGCTGCTGCCTCCCTC
* *
40038071 CCTCTCTGCTGCCTCC
1 GCT-GCTGCTGCCTCC
40038087 GCTCTAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 8 0.31
18 15 0.58
19 3 0.12
ACGTcount: A:0.00, C:0.51, G:0.22, T:0.27
Consensus pattern (18 bp):
GCTGCTGCTGCCTCCCTC
Found at i:40039141 original size:106 final size:106
Alignment explanation
Indices: 40039021--40039232 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
40039011 TAAAATATTG
40039021 TTTTTTTAAAGTGCTTTTATTGTCTCTCCATTTTTTACCCAATGCCTTCTTGATATAATCATCGG
1 TTTTTTTAAAGTGCTTTTATTGTCTCTCCATTTTTTACCCAATGCCTTCTTGATATAATCATCGG
*
40039086 AGACCTCAAAAGCAAATCTCTCCTAAAAAAGCACAAGTTTA
66 AGACCTCAAAAGCAAATCTCTCCTAAAAAAACACAAGTTTA
40039127 TTTTTTTAAAGTGCTTTTATTGTCTCTCCATTTTTTACCCAATGCCTTCTTGATATAATCATCGG
1 TTTTTTTAAAGTGCTTTTATTGTCTCTCCATTTTTTACCCAATGCCTTCTTGATATAATCATCGG
40039192 AGACCTCAAAAGCAAATCTCTCCTAAAAAAACACAAGTTTA
66 AGACCTCAAAAGCAAATCTCTCCTAAAAAAACACAAGTTTA
40039233 GAATGTAAAA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (106 bp):
TTTTTTTAAAGTGCTTTTATTGTCTCTCCATTTTTTACCCAATGCCTTCTTGATATAATCATCGG
AGACCTCAAAAGCAAATCTCTCCTAAAAAAACACAAGTTTA
Found at i:40042578 original size:9 final size:9
Alignment explanation
Indices: 40042557--40042677 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
40042547 TATATATTAC
*
40042557 GTAAGTTAA
1 GTAAGTTAT
40042566 GTAAGCTT-T
1 GTAAG-TTAT
40042575 GTAAGTTAT
1 GTAAGTTAT
40042584 GTAAGTTAT
1 GTAAGTTAT
* *
40042593 GTTA-TGAT
1 GTAAGTTAT
* *
40042601 ATACATTTAT
1 GTA-AGTTAT
**
40042611 GTAAGGCAT
1 GTAAGTTAT
40042620 GTAAGTTAT
1 GTAAGTTAT
* *
40042629 GATATGATAT
1 G-TAAGTTAT
* *
40042639 AT-ATTTAT
1 GTAAGTTAT
40042647 GT-A-TTAT
1 GTAAGTTAT
*
40042654 GTAAGTTGT
1 GTAAGTTAT
40042663 GTAAGTTAT
1 GTAAGTTAT
40042672 GATAAG
1 G-TAAG
40042678 ATATATATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 15
0.70 0.18 0.13
Matches are distributed among these distances:
7 6 0.07
8 12 0.14
9 48 0.58
10 17 0.20
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:40042698 original size:56 final size:56
Alignment explanation
Indices: 40042631--40042862 Score: 348
Period size: 56 Copynumber: 4.2 Consensus size: 56
40042621 TAAGTTATGA
40042631 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
40042687 TATGATATATATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
1 TATGATATATATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* * *
40042744 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
* *
40042800 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTATG-TAAG-T-TAT-TA
1 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
40042852 TATGATATATA
1 TATGATATATA
40042863 ATAAATATTA
Statistics
Matches: 163, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
52 12 0.07
53 3 0.02
54 1 0.01
55 4 0.02
56 91 0.56
57 51 0.31
58 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (56 bp):
TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATT
Found at i:40042760 original size:113 final size:112
Alignment explanation
Indices: 40042631--40042841 Score: 361
Period size: 113 Copynumber: 1.9 Consensus size: 112
40042621 TAAGTTATGA
*
40042631 TATGATATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
40042696 TATTTGGA-GTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
66 TATTT--ATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
* *
40042744 TATGAAATATATTTATGTATTATGTTAGTTGTGTAAGTTATGATATGATATATATTTATGATATA
1 TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
*
40042809 TATTTATGTATTATGTAAGTTTTGTAAGTTATG
66 TATTTATGTATTATGTAAGTTGTGTAAGTTATG
40042842 TAAGTTATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
111 1 0.01
112 25 0.27
113 67 0.72
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (112 bp):
TATGAAATATATTTATGTATTATGTAAGTTGTGTAAGTTATGATAAGATATATATTTATGATATA
TATTTATGTATTATGTAAGTTGTGTAAGTTATGATATGATACATATT
Found at i:40042805 original size:13 final size:13
Alignment explanation
Indices: 40042787--40042816 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40042777 TAAGTTATGA
40042787 TATGATATATATT
1 TATGATATATATT
40042800 TATGATATATATT
1 TATGATATATATT
40042813 TATG
1 TATG
40042817 TATTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:40042836 original size:9 final size:9
Alignment explanation
Indices: 40042819--40042849 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40042809 TATTTATGTA
40042819 TTATGTAAG
1 TTATGTAAG
*
40042828 TTTTGTAAG
1 TTATGTAAG
40042837 TTATGTAAG
1 TTATGTAAG
40042846 TTAT
1 TTAT
40042850 TATATGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40043300 original size:37 final size:37
Alignment explanation
Indices: 40043256--40043346 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 37
40043246 AAATTATATT
*
40043256 AATTGATAAATATTGAAATAT-TG-AAAT-ATATTTAA
1 AATTGATAAATATTGAAATATAAGCAAATCAT-TTTAA
40043291 AATGTTGAT-AA-A-TGAAATATAAGCAAATCATTTTAA
1 AA--TTGATAAATATTGAAATATAAGCAAATCATTTTAA
40043327 AATTGATAAATATTGAAATA
1 AATTGATAAATATTGAAATA
40043347 CATTAAAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
34 13 0.28
35 6 0.13
36 14 0.30
37 14 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (37 bp):
AATTGATAAATATTGAAATATAAGCAAATCATTTTAA
Found at i:40045332 original size:59 final size:59
Alignment explanation
Indices: 40045234--40045363 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
40045224 TTTCAAATTG
** * ** * * *
40045234 GGGAGAAAAGGGTAATTATTTTAGGGTTTTGAATTAGGGAAAATGGGGGGAATAAACTA
1 GGGAGAAGGGGGTAATTATTTTAGGGATTTGAAGAAGGGAAAATGGAGGAAATAAACCA
*
40045293 GGGAGAAGGGGGTGATTATTTTAGGGATTTGAAGAAGGGAAAATGGAGGAAATAAACCA
1 GGGAGAAGGGGGTAATTATTTTAGGGATTTGAAGAAGGGAAAATGGAGGAAATAAACCA
40045352 GGGAGAAGGGGG
1 GGGAGAAGGGGG
40045364 AACTCGGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.37, C:0.02, G:0.39, T:0.22
Consensus pattern (59 bp):
GGGAGAAGGGGGTAATTATTTTAGGGATTTGAAGAAGGGAAAATGGAGGAAATAAACCA
Found at i:40045958 original size:114 final size:116
Alignment explanation
Indices: 40045432--40045970 Score: 517
Period size: 114 Copynumber: 4.7 Consensus size: 116
40045422 TAACATTTGC
* * * * * *
40045432 GGCGTTT-TCACCTAGCGCCGCTAAAGGCAAACCAATTGCGGCATTTTAACAT-AAACGCCACTA
1 GGCGTTTATAACCTAGCGCTGCTAAAGGCAACCCTATTGCGGCGTTTTAACCTAAAACGCCACTA
** * * *
40045495 AAAAAACAAACAAAACGACACCGTTTTGATATAGACAGAATAAACTTTAGT
66 AAAATCCAAACAAAACGACACCGTTTTGATATAAACAAAATAACCTTTAGT
* * * ** * * *
40045546 GGCGTTT-T-TCCGTAGCACCGCTAAAGGCAAATCAATTGCGGCGTTTCACCCTAAAACGCCACT
1 GGCGTTTATAACC-TAGCGCTGCTAAAGGCAACCCTATTGCGGCGTTTTAACCTAAAACGCCACT
* * * *
40045609 AAAAATCCAAA-AAAACGACGA-CGTTTTCATATGAACAGAATAACATTTAGT
65 AAAAATCCAAACAAAACGAC-ACCGTTTTGATATAAACAAAATAACCTTTAGT
* * * * *
40045660 GGCGTTTTATCACCAAGCG-TCGCTAAAGGCGAA-ACTATTCCGGCGTTTTACCCTAAAACGCCA
1 GGCG-TTTATAACCTAGCGCT-GCTAAAGGC-AACCCTATTGCGGCGTTTTAACCTAAAACGCCA
** * * * * * *
40045723 CTAATGAT-CGAATAAAACTACATCGTTTTGATATAAACAAATTAACCATTAGT
63 CTAAAAATCCAAACAAAACGACACCGTTTTGATATAAACAAAATAACCTTTAGT
* * *
40045776 GGCGTTTATAACCTTGCGCTGCTAAA-TCAACCCTATTGTGGCGTTTTAACCTAAAACGCCACTA
1 GGCGTTTATAACCTAGCGCTGCTAAAGGCAACCCTATTGCGGCGTTTTAACCTAAAACGCCACTA
* * * *
40045840 AAAATCCATA-AAAACTACACCGTTTTGATCTAAACAAAATAACCCTTAGT
66 AAAATCCAAACAAAACGACACCGTTTTGATATAAACAAAATAACCTTTAGT
* * *
40045890 GGCGTTTATAACCTTGCGCTGCTAAA-TCAACCCTATTGTGGCGTTTTAACCTAAAACGCCACTA
1 GGCGTTTATAACCTAGCGCTGCTAAAGGCAACCCTATTGCGGCGTTTTAACCTAAAACGCCACTA
* *
40045954 AAAATCTAAAGAAAACG
66 AAAATCCAAACAAAACG
40045971 GTGTCGTCTT
Statistics
Matches: 360, Mismatches: 51, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
113 4 0.01
114 220 0.61
115 51 0.14
116 81 0.22
117 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (116 bp):
GGCGTTTATAACCTAGCGCTGCTAAAGGCAACCCTATTGCGGCGTTTTAACCTAAAACGCCACTA
AAAATCCAAACAAAACGACACCGTTTTGATATAAACAAAATAACCTTTAGT
Found at i:40046848 original size:7 final size:7
Alignment explanation
Indices: 40046836--40046876 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
40046826 AAAGGTTATA
40046836 GTTTAGT
1 GTTTAGT
40046843 GTTTAGT
1 GTTTAGT
40046850 GTTTAGT
1 GTTTAGT
*
40046857 GTTTAGGGG
1 GTTTA--GT
40046866 GTTTAGT
1 GTTTAGT
40046873 GTTT
1 GTTT
40046877 TAGGGGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 24 0.80
9 6 0.20
ACGTcount: A:0.12, C:0.00, G:0.34, T:0.54
Consensus pattern (7 bp):
GTTTAGT
Found at i:40046880 original size:17 final size:16
Alignment explanation
Indices: 40046836--40046882 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 16
40046826 AAAGGTTATA
*
40046836 GTTTAGTGTTTA--GT
1 GTTTAGTGTTTAGGGG
40046850 GTTTAGTGTTTAGGGG
1 GTTTAGTGTTTAGGGG
40046866 GTTTAGTGTTTTAGGGG
1 GTTTAGTG-TTTAGGGG
40046883 TTATAGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.41
16 9 0.31
17 8 0.28
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.49
Consensus pattern (16 bp):
GTTTAGTGTTTAGGGG
Found at i:40046883 original size:16 final size:15
Alignment explanation
Indices: 40046836--40046884 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
40046826 AAAGGTTATA
*
40046836 GTTTAGTGTTTA-GT
1 GTTTAGTGTTTAGGG
40046850 GTTTAGTGTTTAGGGG
1 GTTTAGTGTTTA-GGG
40046866 GTTTAGTGTTTTAGGG
1 GTTTAGTG-TTTAGGG
40046882 GTT
1 GTT
40046885 ATAGATTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.39
16 15 0.48
17 4 0.13
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (15 bp):
GTTTAGTGTTTAGGG
Found at i:40046894 original size:45 final size:45
Alignment explanation
Indices: 40046845--40046930 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
40046835 AGTTTAGTGT
*
40046845 TTAGTGTTTA-GTGTTTAGGGGGTTTAGTGTTTTAGGGGTTATAGA
1 TTAGTGTTTATGT-TTTAGGGGGTTTAGGGTTTTAGGGGTTATAGA
**
40046890 TTAGTGTTTATGTTTTTTGGGGTTTAGGGTTTTAGGGGTTA
1 TTAGTGTTTATGTTTTAGGGGGTTTAGGGTTTTAGGGGTTA
40046931 AATGACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 35 0.95
46 2 0.05
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (45 bp):
TTAGTGTTTATGTTTTAGGGGGTTTAGGGTTTTAGGGGTTATAGA
Found at i:40047046 original size:41 final size:41
Alignment explanation
Indices: 40046937--40047186 Score: 204
Period size: 41 Copynumber: 6.1 Consensus size: 41
40046927 GTTAAATGAC
*** *
40046937 TTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATT-CTTTGGT
1 TTTTAGCGGCGTTTTTGGTAAAA-CGCCGCT-ATTGCTCTGGT
* *** * * *
40046978 TTTTAGTGGCG-TTTTACCAAAAGCGCCACTAATGCTCTGGC
1 TTTTAGCGGCGTTTTTGGTAAAA-CGCCGCTATTGCTCTGGT
* * *
40047019 TTTTAGCGGCGTTTTTGGTAAAACGCCACTATTGCTATGTT
1 TTTTAGCGGCGTTTTTGGTAAAACGCCGCTATTGCTCTGGT
* * * **
40047060 TTTTGGCGGCGTTTTCT-GTAAAACGCCGCTATTTCTATAAT
1 TTTTAGCGGCGTTTT-TGGTAAAACGCCGCTATTGCTCTGGT
* ***
40047101 TTTTAGCGTCGTTTTAACTAAAAACGCCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTTGGT-AAAACGCCGCTATTGCTCTGGT
40047142 TTTTAGCGGCGTTTTTGGTAAAACGCCGCTATTGCTCTGCGT
1 TTTTAGCGGCGTTTTTGGTAAAACGCCGCTATTGCTCTG-GT
40047184 TTT
1 TTT
40047187 ACAATTTTTG
Statistics
Matches: 173, Mismatches: 29, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
40 21 0.12
41 121 0.70
42 31 0.18
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTGGTAAAACGCCGCTATTGCTCTGGT
Found at i:40062179 original size:41 final size:41
Alignment explanation
Indices: 40062132--40062214 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
40062122 TAGCAATTCT
* *
40062132 TAATAGCAGCATCACTCTGGCGTAGTCCTTCTAGCAAACAG
1 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
*
40062173 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAATAAACAG
1 TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
40062214 T
1 T
40062215 CTTTTCAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
TAATAGCAGCAGCACTCTGGCGTAGTCCTTCTAACAAACAG
Found at i:40063337 original size:62 final size:59
Alignment explanation
Indices: 40063228--40063344 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
40063218 ATAACTTTAA
* * * *
40063228 TATTAAATTAATATAATATTTATCTAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCTAGATAAACATTAAATTAAATTTAATATTAAATCT
*
40063287 TATTAAAATAATAGAATGTTTATCATGTAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATC---TAGATAAACATTAAATTAAATTTAATATTAA
40063345 GATAATCATT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
62 29 0.58
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATCTAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:40063370 original size:20 final size:18
Alignment explanation
Indices: 40063323--40063371 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40063313 GTAGATAAAC
40063323 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40063340 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
40063360 ATTAAATTAATA
1 ATTAAATTAATA
40063372 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40066509 original size:32 final size:32
Alignment explanation
Indices: 40066469--40066568 Score: 78
Period size: 32 Copynumber: 3.0 Consensus size: 32
40066459 TCAACTATAA
40066469 TTAA-ACTTAATCACTTTAATATTAAATTAAT
1 TTAATACTTAATCACTTTAATATTAAATTAAT
** * *
40066500 TTAATACTT-ATCAAGATAAATATTAGATTAAAT
1 TTAATACTTAATC-ACTTTAATATTAAATT-AAT
* *
40066533 TTAATATTAAGATAATCTCTTTAATATTAAATTAAT
1 TTAATACT----TAATCACTTTAATATTAAATTAAT
40066569 AAAATACTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
31 7 0.14
32 16 0.31
33 10 0.20
36 3 0.06
37 12 0.24
38 3 0.06
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (32 bp):
TTAATACTTAATCACTTTAATATTAAATTAAT
Found at i:40066555 original size:69 final size:68
Alignment explanation
Indices: 40066476--40066603 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 68
40066466 TAATTAAACT
** *
40066476 TAATCACTTTAATATTAAATTAATTTAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATAC-TATCAAGATAAATATTAAATTAAATTTAATATT
40066541 AAGA
65 AAGA
* * *
40066545 TAATCTCTTTAATATTAAATTAATAAAATACTATCAAGATAAGTATTAAATTTAATTTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTTA
40066604 CTATAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
68 25 0.47
69 28 0.53
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTTAATATTA
AGA
Found at i:40070316 original size:12 final size:12
Alignment explanation
Indices: 40070299--40070330 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40070289 CATGTTATGG
40070299 CACACGGCTTAC
1 CACACGGCTTAC
*
40070311 CACACGGCTTAT
1 CACACGGCTTAC
40070323 CACACGGC
1 CACACGGC
40070331 CATGTGGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.41, G:0.19, T:0.16
Consensus pattern (12 bp):
CACACGGCTTAC
Found at i:40098800 original size:17 final size:17
Alignment explanation
Indices: 40098778--40098812 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40098768 CCTGTCAGAA
40098778 AATTCAATCGACGAAAT
1 AATTCAATCGACGAAAT
*
40098795 AATTCAATCGATGAAAT
1 AATTCAATCGACGAAAT
40098812 A
1 A
40098813 TCGTTTACTA
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:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (17 bp):
AATTCAATCGACGAAAT
Found at i:40100215 original size:19 final size:19
Alignment explanation
Indices: 40100191--40100230 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
40100181 AAAAGAATTA
40100191 TTAAAAATA-TTAAAAATAT
1 TTAAAAATATTTAAAAA-AT
40100210 TTAAAAATATTTAAAAAAT
1 TTAAAAATATTTAAAAAAT
40100229 TT
1 TT
40100231 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATATTTAAAAAAT
Found at i:40100233 original size:10 final size:10
Alignment explanation
Indices: 40100191--40100230 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
40100181 AAAAGAATTA
40100191 TTAAAAATA-
1 TTAAAAATAT
40100200 TTAAAAATAT
1 TTAAAAATAT
40100210 TTAAAAATAT
1 TTAAAAATAT
40100220 TTAAAAA-AT
1 TTAAAAATAT
40100229 TT
1 TT
40100231 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 13 0.43
10 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:40101864 original size:24 final size:24
Alignment explanation
Indices: 40101820--40101866 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40101810 TTGTTGGTGT
* *
40101820 TTTGTGGTCTCTTGTGTTAGGTCA
1 TTTGTGGCCTCTTGTGATAGGTCA
40101844 TTTGTGGCCTCTT-TGGATAGGTC
1 TTTGTGGCCTCTTGT-GATAGGTC
40101867 GGTGGTGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.09, C:0.15, G:0.30, T:0.47
Consensus pattern (24 bp):
TTTGTGGCCTCTTGTGATAGGTCA
Found at i:40103802 original size:3 final size:3
Alignment explanation
Indices: 40103794--40103839 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40103784 TTCTATTCTG
40103794 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40103840 TTCTGTGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40105894 original size:21 final size:22
Alignment explanation
Indices: 40105868--40105908 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40105858 CTCTTTTTTT
40105868 ATTATA-AAAAATTTAAAAAAA
1 ATTATAGAAAAATTTAAAAAAA
*
40105889 ATTATAGAAAAATTTTAAAA
1 ATTATAGAAAAATTTAAAAA
40105909 TATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
ATTATAGAAAAATTTAAAAAAA
Found at i:40106140 original size:20 final size:20
Alignment explanation
Indices: 40106108--40106151 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40106098 TTTTATACTA
40106108 AAAAATATTAAATTCAA-AT
1 AAAAATATTAAATTCAAGAT
* *
40106127 AAAAATTTTAAAATTTAAGAT
1 AAAAATATT-AAATTCAAGAT
40106148 AAAA
1 AAAA
40106152 TTAGTGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATATTAAATTCAAGAT
Found at i:40113881 original size:21 final size:21
Alignment explanation
Indices: 40113828--40113909 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
40113818 AAAAAATTTA
*
40113828 AAAAAT-ATTTTTATACTTTTT
1 AAAAATAATTTTT-TAATTTTT
40113849 -AAAATAA-TTTTTAATTTTT
1 AAAAATAATTTTTTAATTTTT
*
40113868 AAAAATAATTTTTTGATTTTT
1 AAAAATAATTTTTTAATTTTT
**
40113889 ATAAAA-AATTAATTAATTTTT
1 A-AAAATAATTTTTTAATTTTT
40113910 GATGTGGCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.13
20 16 0.31
21 25 0.48
22 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
AAAAATAATTTTTTAATTTTT
Found at i:40114663 original size:5 final size:5
Alignment explanation
Indices: 40114640--40114689 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
40114630 TTATCATGTG
*
40114640 TATA- TATAT ATATTAT TATAT TATAT TAAAT TATAT TATAT TATAT TATA
1 TATAT TATAT -TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
40114690 AGGTTTTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
4 4 0.10
5 30 0.73
6 4 0.10
7 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:40117677 original size:938 final size:938
Alignment explanation
Indices: 40115860--40117736 Score: 3754
Period size: 938 Copynumber: 2.0 Consensus size: 938
40115850 AAGAATTGAG
40115860 AAAGGTTGAGTAATCAGATTACAAGATTAATGAGGATTGATGTTATTGCAAGTTTTACGAGTTTT
1 AAAGGTTGAGTAATCAGATTACAAGATTAATGAGGATTGATGTTATTGCAAGTTTTACGAGTTTT
40115925 ACTAGTCAAAACGAAAGTACTTACTGAGCTATCGATGAGGACACAAATAGGAATGATGAGTTTGA
66 ACTAGTCAAAACGAAAGTACTTACTGAGCTATCGATGAGGACACAAATAGGAATGATGAGTTTGA
40115990 AAATCTAGTAGAGAGAAATGAATTAATCAGAGATCAATTTTGATTCGGGATTCACAAGAAATATT
131 AAATCTAGTAGAGAGAAATGAATTAATCAGAGATCAATTTTGATTCGGGATTCACAAGAAATATT
40116055 TTCAGCAATGAGGAGCAAATATTGTGTAAAGATGATGATGAAAAAGAAAGGGATGAAGAAATTGG
196 TTCAGCAATGAGGAGCAAATATTGTGTAAAGATGATGATGAAAAAGAAAGGGATGAAGAAATTGG
40116120 GAAAAGAAGAAAGAATTCTAATTAGATTTGTAAAGATATTAGAGTCCATATCTAATTAGGTAAGA
261 GAAAAGAAGAAAGAATTCTAATTAGATTTGTAAAGATATTAGAGTCCATATCTAATTAGGTAAGA
40116185 TGAGACTAAATAGCTAGGGCTAACAAATTTTAGAGGGGCAGCATGGTAAATTACCCATATTGCCG
326 TGAGACTAAATAGCTAGGGCTAACAAATTTTAGAGGGGCAGCATGGTAAATTACCCATATTGCCG
40116250 AAATTAAAAGGAAAAAAATAAGGAAGGGTGACATAACTTGAACTTGAAAATGCAAGGGGAAAGTG
391 AAATTAAAAGGAAAAAAATAAGGAAGGGTGACATAACTTGAACTTGAAAATGCAAGGGGAAAGTG
40116315 CACAACTTAACCATTTAGGTTGTTGCCCACTCTTGTTTATTTTCTACTCCATTTAATTTTTGTTT
456 CACAACTTAACCATTTAGGTTGTTGCCCACTCTTGTTTATTTTCTACTCCATTTAATTTTTGTTT
40116380 TAGGGTTGCTTTCATCCTAGTTTGCTAAAAAAAAATAGATAGGAGAGGCATGAATAAAACCTAAG
521 TAGGGTTGCTTTCATCCTAGTTTGCTAAAAAAAAATAGATAGGAGAGGCATGAATAAAACCTAAG
40116445 ATCTCTAGGGAGTGCATTAGCTACATAACCATCAAGTCTGAGTAATTTCTTAGTTATTTATTTCA
586 ATCTCTAGGGAGTGCATTAGCTACATAACCATCAAGTCTGAGTAATTTCTTAGTTATTTATTTCA
40116510 TCTAACCCTATATATTTTTGGGTGTTACAAAAAGTGCAATTTTACTATTTTTGAAAAAGGGCGAA
651 TCTAACCCTATATATTTTTGGGTGTTACAAAAAGTGCAATTTTACTATTTTTGAAAAAGGGCGAA
40116575 ATTTGAAAAAATGTTTTTTTTAATGATTGTGACATGGATATGTATCGATATATGGAGTTGGAAAA
716 ATTTGAAAAAATGTTTTTTTTAATGATTGTGACATGGATATGTATCGATATATGGAGTTGGAAAA
40116640 TTAAGATATGGATTAAATTGAATAAAGTGGAAAAGTATAAAGACTAAAGAGCAATTTTCCCATTT
781 TTAAGATATGGATTAAATTGAATAAAGTGGAAAAGTATAAAGACTAAAGAGCAATTTTCCCATTT
40116705 TATGGAGGAGGGACCTAATGTAAGATTTTTATTTTAAAATGATATTTGGATACACAATGATGATG
846 TATGGAGGAGGGACCTAATGTAAGATTTTTATTTTAAAATGATATTTGGATACACAATGATGATG
40116770 TTAAAACACCTAAGCTCGTGAGTTGTAA
911 TTAAAACACCTAAGCTCGTGAGTTGTAA
40116798 AAAGGTTGAGTAATCAGATTACAAGATTAATGAGGATTGATGTTATTGCAAGTTTTACGAGTTTT
1 AAAGGTTGAGTAATCAGATTACAAGATTAATGAGGATTGATGTTATTGCAAGTTTTACGAGTTTT
40116863 ACTAGTCAAAACGAAAGTACTTACTGAGCTATCGATGAGGACACAAATAGGAATGATGAGTTTGA
66 ACTAGTCAAAACGAAAGTACTTACTGAGCTATCGATGAGGACACAAATAGGAATGATGAGTTTGA
40116928 AAATCTAGTAGAGAGAAATGAATTAATCAGAGATCAATTTTGATTCGGGATTCACAAGAAATATT
131 AAATCTAGTAGAGAGAAATGAATTAATCAGAGATCAATTTTGATTCGGGATTCACAAGAAATATT
40116993 TTCAGCAATGAGGAGCAAATATTGTGTAAAGATGATGATGAAAAAGAAAGGGATGAAGAAATTGG
196 TTCAGCAATGAGGAGCAAATATTGTGTAAAGATGATGATGAAAAAGAAAGGGATGAAGAAATTGG
40117058 GAAAAGAAGAAAGAATTCTAATTAGATTTGTAAAGATATTAGAGTCCATATCTAATTAGGTAAGA
261 GAAAAGAAGAAAGAATTCTAATTAGATTTGTAAAGATATTAGAGTCCATATCTAATTAGGTAAGA
40117123 TGAGACTAAATAGCTAGGGCTAACAAATTTTAGAGGGGCAGCATGGTAAATTACCCATATTGCCG
326 TGAGACTAAATAGCTAGGGCTAACAAATTTTAGAGGGGCAGCATGGTAAATTACCCATATTGCCG
40117188 AAATTAAAAGGAAAAAAATAAGGAAGGGTGACATAACTTGAACTTGAAAATGCAAGGGGAAAGTG
391 AAATTAAAAGGAAAAAAATAAGGAAGGGTGACATAACTTGAACTTGAAAATGCAAGGGGAAAGTG
40117253 CACAACTTAACCATTTAGGTTGTTGCCCACTCTTGTTTATTTTCTACTCCATTTAATTTTTGTTT
456 CACAACTTAACCATTTAGGTTGTTGCCCACTCTTGTTTATTTTCTACTCCATTTAATTTTTGTTT
40117318 TAGGGTTGCTTTCATCCTAGTTTGCTAAAAAAAAATAGATAGGAGAGGCATGAATAAAACCTAAG
521 TAGGGTTGCTTTCATCCTAGTTTGCTAAAAAAAAATAGATAGGAGAGGCATGAATAAAACCTAAG
40117383 ATCTCTAGGGAGTGCATTAGCTACATAACCATCAAGTCTGAGTAATTTCTTAGTTATTTATTTCA
586 ATCTCTAGGGAGTGCATTAGCTACATAACCATCAAGTCTGAGTAATTTCTTAGTTATTTATTTCA
40117448 TCTAACCCTATATATTTTTGGGTGTTACAAAAAGTGCAATTTTACTATTTTTGAAAAAGGGCGAA
651 TCTAACCCTATATATTTTTGGGTGTTACAAAAAGTGCAATTTTACTATTTTTGAAAAAGGGCGAA
40117513 ATTTGAAAAAATGTTTTTTTTAATGATTGTGACATGGATATGTATCGATATATGGAGTTGGAAAA
716 ATTTGAAAAAATGTTTTTTTTAATGATTGTGACATGGATATGTATCGATATATGGAGTTGGAAAA
40117578 TTAAGATATGGATTAAATTGAATAAAGTGGAAAAGTATAAAGACTAAAGAGCAATTTTCCCATTT
781 TTAAGATATGGATTAAATTGAATAAAGTGGAAAAGTATAAAGACTAAAGAGCAATTTTCCCATTT
40117643 TATGGAGGAGGGACCTAATGTAAGATTTTTATTTTAAAATGATATTTGGATACACAATGATGATG
846 TATGGAGGAGGGACCTAATGTAAGATTTTTATTTTAAAATGATATTTGGATACACAATGATGATG
40117708 TTAAAACACCTAAGCTCGTGAGTTGTAA
911 TTAAAACACCTAAGCTCGTGAGTTGTAA
40117736 A
1 A
40117737 GTTTCAAGGA
Statistics
Matches: 939, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
938 939 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (938 bp):
AAAGGTTGAGTAATCAGATTACAAGATTAATGAGGATTGATGTTATTGCAAGTTTTACGAGTTTT
ACTAGTCAAAACGAAAGTACTTACTGAGCTATCGATGAGGACACAAATAGGAATGATGAGTTTGA
AAATCTAGTAGAGAGAAATGAATTAATCAGAGATCAATTTTGATTCGGGATTCACAAGAAATATT
TTCAGCAATGAGGAGCAAATATTGTGTAAAGATGATGATGAAAAAGAAAGGGATGAAGAAATTGG
GAAAAGAAGAAAGAATTCTAATTAGATTTGTAAAGATATTAGAGTCCATATCTAATTAGGTAAGA
TGAGACTAAATAGCTAGGGCTAACAAATTTTAGAGGGGCAGCATGGTAAATTACCCATATTGCCG
AAATTAAAAGGAAAAAAATAAGGAAGGGTGACATAACTTGAACTTGAAAATGCAAGGGGAAAGTG
CACAACTTAACCATTTAGGTTGTTGCCCACTCTTGTTTATTTTCTACTCCATTTAATTTTTGTTT
TAGGGTTGCTTTCATCCTAGTTTGCTAAAAAAAAATAGATAGGAGAGGCATGAATAAAACCTAAG
ATCTCTAGGGAGTGCATTAGCTACATAACCATCAAGTCTGAGTAATTTCTTAGTTATTTATTTCA
TCTAACCCTATATATTTTTGGGTGTTACAAAAAGTGCAATTTTACTATTTTTGAAAAAGGGCGAA
ATTTGAAAAAATGTTTTTTTTAATGATTGTGACATGGATATGTATCGATATATGGAGTTGGAAAA
TTAAGATATGGATTAAATTGAATAAAGTGGAAAAGTATAAAGACTAAAGAGCAATTTTCCCATTT
TATGGAGGAGGGACCTAATGTAAGATTTTTATTTTAAAATGATATTTGGATACACAATGATGATG
TTAAAACACCTAAGCTCGTGAGTTGTAA
Found at i:40117865 original size:34 final size:34
Alignment explanation
Indices: 40117825--40117893 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40117815 AGAAAGGAAA
40117825 AATGTAGAGATTTCTAGAGGAGAGATAAAGTAGG
1 AATGTAGAGATTTCTAGAGGAGAGATAAAGTAGG
40117859 AATGTAGAGATTTCTAGAGGAGAGATAAAGTAGG
1 AATGTAGAGATTTCTAGAGGAGAGATAAAGTAGG
40117893 A
1 A
40117894 CATCAACAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.03, G:0.32, T:0.23
Consensus pattern (34 bp):
AATGTAGAGATTTCTAGAGGAGAGATAAAGTAGG
Found at i:40126882 original size:31 final size:30
Alignment explanation
Indices: 40126841--40126944 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
40126831 TTTTAATAAC
*
40126841 TTAATGTAATATTTATCTAGTTAGA-ATTTTA
1 TTAATTTAATATTTATCT-G-TAGATATTTTA
* **
40126872 TTAATTTAATATTAAT-TG-AGATATTAAA
1 TTAATTTAATATTTATCTGTAGATATTTTA
*
40126900 TTTAATTTAATATTTATCTTGATA-ATATTTTG
1 -TTAATTTAATATTTATC-TG-TAGATATTTTA
40126932 TTAATTTAATATT
1 TTAATTTAATATT
40126945 AATGTCATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 16 0.27
30 1 0.02
31 29 0.49
32 5 0.08
33 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TTAATTTAATATTTATCTGTAGATATTTTA
Found at i:40134620 original size:46 final size:46
Alignment explanation
Indices: 40134568--40134659 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
40134558 TCGTATGTAG
40134568 ATTTTAAGCGTAAGGAGATTGAGTATTCTATAGG-GGACTTCATTTT
1 ATTTTAAGCGTAAGGAGATTGAGTATTCTAT-GGAGGACTTCATTTT
*
40134614 ATTTTAAGCGTAAGGAGATTGAGTATTCTGTGGAGGACTTCATTTT
1 ATTTTAAGCGTAAGGAGATTGAGTATTCTATGGAGGACTTCATTTT
40134660 TCTCAAGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (46 bp):
ATTTTAAGCGTAAGGAGATTGAGTATTCTATGGAGGACTTCATTTT
Found at i:40144998 original size:42 final size:42
Alignment explanation
Indices: 40144935--40145020 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
40144925 AAATGAAGGT
* * *
40144935 AGCAGACTAGCTATTGGCCTCACTAATACGACCATTTTGTTA
1 AGCAGAATAGCTATCGACCTCACTAATACGACCATTTTGTTA
40144977 AGCAGAATAGCTATCGACCTCACTAATACGACCATTTTGTTA
1 AGCAGAATAGCTATCGACCTCACTAATACGACCATTTTGTTA
40145019 AG
1 AG
40145021 TTAAGTTCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (42 bp):
AGCAGAATAGCTATCGACCTCACTAATACGACCATTTTGTTA
Found at i:40145398 original size:92 final size:92
Alignment explanation
Indices: 40145232--40145412 Score: 274
Period size: 92 Copynumber: 2.0 Consensus size: 92
40145222 TAAGCTCATA
* * *
40145232 ATTATTATCGTCGGTTAACCTGACTAGTACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGT
1 ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
* *
40145297 TGGGCTCACAATT-ATTATCGTCGGGTT
66 TAGGATCAC-ATTCATTATCGTCGGGTT
* *
40145324 ATTATTATCGTCGATTAACCTGACTGGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGTGC
1 ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
*
40145389 TAGGATCACATTCATTATTGTCGG
66 TAGGATCACATTCATTATCGTCGG
40145413 TTAATCTGAC
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 3 0.04
92 77 0.96
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (92 bp):
ATTATTATCGTCGATTAACCTGACTAGCACTGGGTGCAATTATTGTTGGTTTATCCAACTAGAGC
TAGGATCACATTCATTATCGTCGGGTT
Found at i:40151136 original size:46 final size:46
Alignment explanation
Indices: 40151084--40151207 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
40151074 AGTGTGCTCT
40151084 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40151130 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
40151176 ATGACA-GAAAATGAGTAAGACCATAGTTGAAA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAA
40151208 AACACTATGG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 1 0.01
46 72 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:40151326 original size:13 final size:13
Alignment explanation
Indices: 40151308--40151337 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40151298 CCGGATGATG
40151308 AATGGTTATATGA
1 AATGGTTATATGA
*
40151321 AATGGTTATGTGA
1 AATGGTTATATGA
40151334 AATG
1 AATG
40151338 CTTACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:40151526 original size:16 final size:17
Alignment explanation
Indices: 40151505--40151537 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40151495 ATTATGGAGC
40151505 ATGAAAT-ATTAATATA
1 ATGAAATGATTAATATA
*
40151521 ATGAAATGATTGATATA
1 ATGAAATGATTAATATA
40151538 TATACTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTAATATA
Found at i:40172950 original size:2 final size:2
Alignment explanation
Indices: 40172943--40172969 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40172933 CTATTACATT
40172943 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 T
40172970 TTTGCGCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40181799 original size:21 final size:22
Alignment explanation
Indices: 40181773--40181829 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
40181763 TAATTCAACC
*
40181773 TTTTATATATATTTT-TTAA-TT
1 TTTTATA-ATATTTTATAAAGTT
40181794 TTTTATAAT-TTTTATAAAGTT
1 TTTTATAATATTTTATAAAGTT
40181815 TTTTATAACTATTTT
1 TTTTATAA-TATTTT
40181830 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 5 0.16
21 17 0.55
22 1 0.03
23 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATAATATTTTATAAAGTT
Found at i:40181802 original size:10 final size:10
Alignment explanation
Indices: 40181773--40181822 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 10
40181763 TAATTCAACC
40181773 TTTTATATATAT
1 TTTTATA-AT-T
40181785 TTTT-TAATT
1 TTTTATAATT
40181794 TTTTATAA-T
1 TTTTATAATT
40181803 TTTTATAAAGTT
1 TTTTAT-AA-TT
40181815 TTTTATAA
1 TTTTATAA
40181823 CTATTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 12 0.35
10 7 0.21
11 4 0.12
12 11 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40182465 original size:146 final size:146
Alignment explanation
Indices: 40182200--40182490 Score: 352
Period size: 146 Copynumber: 2.0 Consensus size: 146
40182190 ATTTAAGTAA
* * * * * *
40182200 AGTTTCTTTTTATTTGGTAAAAGATTAATTTTGGAGAACCGGCGGTTATAGTGTCACTGATCACG
1 AGTTTCTTTTTAGTTAGTAAAAGATTAATTTTGGAGAACCGACAGTTATAGTATCACTGATCACA
* * * **
40182265 TAACGATTGAGAGAGAGACTGGACCACACCCAATCGAGAGTAAAAAGACAATAATCGTCCTAGCA
66 TAACGAATGAGAGAGAGACTGGACAACACACAATCGAGAGTAAAAAGACAATAATCACCCTAGCA
40182330 AAAAGGGCCACATTAG
131 AAAAGGGCCACATTAG
* ** *
40182346 AGTTTCTTTTTAGTTATTAGAAA-ATTAATTTTGGAGAATTGACAGTTATAGTATCAGTGATCAC
1 AGTTTCTTTTTAGTTAGTA-AAAGATTAATTTTGGAGAACCGACAGTTATAGTATCACTGATCAC
* * * * *
40182410 ATAACGAATGAGAGAGAGACTAGG-CAATAGACACTCGAGCGTAAAAAGACCATAATCACCCTAG
65 ATAACGAATGAGAGAGAGACT-GGACAACACACAATCGAGAGTAAAAAGACAATAATCACCCTAG
* *
40182474 CGAAAAGGGCTACATTA
129 CAAAAAGGGCCACATTA
40182491 CATCCCTTTC
Statistics
Matches: 121, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
146 116 0.96
147 5 0.04
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (146 bp):
AGTTTCTTTTTAGTTAGTAAAAGATTAATTTTGGAGAACCGACAGTTATAGTATCACTGATCACA
TAACGAATGAGAGAGAGACTGGACAACACACAATCGAGAGTAAAAAGACAATAATCACCCTAGCA
AAAAGGGCCACATTAG
Found at i:40183104 original size:23 final size:23
Alignment explanation
Indices: 40183078--40183122 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40183068 TACTTTTAGC
40183078 CTTTAATAGCTTTTGCGATAATG
1 CTTTAATAGCTTTTGCGATAATG
*
40183101 CTTTAATAGCTTTTGTGATAAT
1 CTTTAATAGCTTTTGCGATAAT
40183123 AGTACCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.47
Consensus pattern (23 bp):
CTTTAATAGCTTTTGCGATAATG
Found at i:40186665 original size:12 final size:12
Alignment explanation
Indices: 40186644--40186673 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40186634 GAATACGCTG
40186644 AATTAAATTTAA
1 AATTAAATTTAA
*
40186656 AATTACATTTAA
1 AATTAAATTTAA
40186668 AATTAA
1 AATTAA
40186674 CTTGAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:40187749 original size:91 final size:89
Alignment explanation
Indices: 40187637--40187950 Score: 306
Period size: 91 Copynumber: 3.5 Consensus size: 89
40187627 TGAGTGATTT
* *
40187637 TTTTGCACTCAATTG-GATACTTGAACTTTCAAAATGCATAAACAAAATACTCAATCTTTTTCAA
1 TTTTGCACTCAATTGAG-TACTTGAACTTTCAAAATGCATAAA-AAAACACTCAAACTTTTTCAA
* *
40187701 AAAAAAGCAATTAAGCCCTTGCTTTTTC
64 AAAAAA--AATTAAGCCCCTACTTTTTC
* * *
40187729 TTTT-CACTCAATTGAGTACTTGAACTTTTAAAATGCATAAAAAAGGCCCTCAAAC---TT-AAA
1 TTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAA-ACACTCAAACTTTTTCAAA
40187789 AAAAAAA-TAAGCCCCTACTTTTTTC
65 AAAAAAATTAAGCCCCTAC-TTTTTC
* * * *
40187814 TTTTGTACTCAATTGGGTACTTAAAC-TTCAAAATGCATAAAAAAAAGACTCTCAAACTTTTTCA
1 TTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCAT--AAAAAA-ACACTCAAACTTTTTCA
40187878 AAAAAAATTAATTAAGCCCCTACTTTTT-
63 AAAAAAA--AATTAAGCCCCTACTTTTTC
* * * * *
40187906 TTTTACACCCAATT-AGGTACTTGAACTGTCAAAATACATCAAAAA
1 TTTTGCACTCAATTGA-GTACTTGAACTTTCAAAATGCATAAAAAA
40187951 GACCCTTTGA
Statistics
Matches: 186, Mismatches: 21, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
84 9 0.05
85 23 0.12
86 18 0.10
87 23 0.12
88 2 0.01
90 5 0.03
91 53 0.28
92 25 0.13
93 17 0.09
94 11 0.06
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (89 bp):
TTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAACACTCAAACTTTTTCAAAA
AAAAAATTAAGCCCCTACTTTTTC
Found at i:40187879 original size:178 final size:177
Alignment explanation
Indices: 40187637--40187956 Score: 439
Period size: 178 Copynumber: 1.8 Consensus size: 177
40187627 TGAGTGATTT
* * * *
40187637 TTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATAAACAAAATACTCAATCTTTTTCAAA
1 TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAAAGACTCAAACTTTTTCAAA
* * * * * *
40187702 AAAAAGCAATTAAGCCCTTGCTTTTTCTTTT-CACTCAATT-GAGTACTTGAACTTTTAAAATGC
66 AAAAAGCAATTAAGCCCCTACTTTTT-TTTTACACCCAATTAG-GTACTTGAACTGTCAAAATAC
*
40187765 ATAAAAAAGGCCCTCAAACTTAAAAAAAAAATAAGCCCCTACTTTTTTC
129 ATAAAAAAGACCCTCAAACTTAAAAAAAAAATAAGCCCCTACTTTTTTC
* *
40187814 TTTTGTACTCAATTGGGTACTTAAAC-TTCAAAATGCATAAAAAAAAGACTCTCAAACTTTTTCA
1 TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAAAGA--CTCAAACTTTTTCA
**
40187878 AAAAAAATTAATTAAGCCCCTACTTTTTTTTTACACCCAATTAGGTACTTGAACTGTCAAAATAC
64 AAAAAAAGCAATTAAGCCCCTACTTTTTTTTTACACCCAATTAGGTACTTGAACTGTCAAAATAC
*
40187943 ATCAAAAAGACCCT
129 ATAAAAAAGACCCT
40187957 TTGACAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
176 20 0.16
177 27 0.22
178 75 0.61
179 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (177 bp):
TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAAAAGACTCAAACTTTTTCAAA
AAAAAGCAATTAAGCCCCTACTTTTTTTTTACACCCAATTAGGTACTTGAACTGTCAAAATACAT
AAAAAAGACCCTCAAACTTAAAAAAAAAATAAGCCCCTACTTTTTTC
Found at i:40188050 original size:10 final size:10
Alignment explanation
Indices: 40188035--40188137 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
40188025 TGACACATGA
40188035 AAAAAATTAT
1 AAAAAATTAT
40188045 AAAAAA--AT
1 AAAAAATTAT
*
40188053 AAAAAAATA-
1 AAAAAATTAT
40188062 AAAAAATTAT
1 AAAAAATTAT
* *
40188072 TAAAAATTAGA
1 AAAAAATTA-T
*
40188083 AAAAAATGAT
1 AAAAAATTAT
40188093 AAAAAATGTA-
1 AAAAAAT-TAT
* *
40188103 AAAGATTTAT
1 AAAAAATTAT
*
40188113 AAAAAATTGT
1 AAAAAATTAT
**
40188123 AAAATTTTAT
1 AAAAAATTAT
40188133 AAAAA
1 AAAAA
40188138 TCATAAAATG
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
8 8 0.11
9 10 0.14
10 45 0.63
11 8 0.11
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:40188050 original size:11 final size:11
Alignment explanation
Indices: 40188034--40188098 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
40188024 GTGACACATG
40188034 AAAAAAATTAT
1 AAAAAAATTAT
40188045 -AAAAAA--AT
1 AAAAAAATTAT
40188053 -AAAAAA--AT
1 AAAAAAATTAT
40188061 AAAAAAATTAT
1 AAAAAAATTAT
* *
40188072 -TAAAAATTAG
1 AAAAAAATTAT
*
40188082 AAAAAAATGAT
1 AAAAAAATTAT
40188093 AAAAAA
1 AAAAAA
40188099 TGTAAAAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
8 10 0.22
9 6 0.13
10 14 0.31
11 15 0.33
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:40188058 original size:7 final size:8
Alignment explanation
Indices: 40188043--40188068 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40188033 GAAAAAAATT
40188043 ATAAAAAA
1 ATAAAAAA
40188051 ATAAAAAA
1 ATAAAAAA
40188059 ATAAAAAA
1 ATAAAAAA
40188067 AT
1 AT
40188069 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:40188076 original size:27 final size:28
Alignment explanation
Indices: 40188034--40188087 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
40188024 GTGACACATG
40188034 AAAAAAATTATAAAAAAATA-AAAAAAT
1 AAAAAAATTATAAAAAAATAGAAAAAAT
* *
40188061 AAAAAAATTATTAAAAATTAGAAAAAA
1 AAAAAAATTATAAAAAAATAGAAAAAA
40188088 ATGATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (28 bp):
AAAAAAATTATAAAAAAATAGAAAAAAT
Found at i:40188105 original size:20 final size:19
Alignment explanation
Indices: 40188031--40188120 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 19
40188021 GGCGTGACAC
40188031 ATGA-AAAAAATTATAAAAA
1 ATGATAAAAAATTA-AAAAA
*
40188050 A--ATAAAAAAATAAAAAA
1 ATGATAAAAAATTAAAAAA
* *
40188067 ATTATTAAAAATTAGAAAAAA
1 ATGATAAAAAATT--AAAAAA
*
40188088 ATGATAAAAAATGTAAAAGA
1 ATGATAAAAAAT-TAAAAAA
* *
40188108 TTTATAAAAAATT
1 ATGATAAAAAATT
40188121 GTAAAATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
17 7 0.12
18 8 0.14
19 10 0.18
20 15 0.26
21 16 0.28
22 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (19 bp):
ATGATAAAAAATTAAAAAA
Found at i:40188117 original size:21 final size:20
Alignment explanation
Indices: 40188093--40188137 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
40188083 AAAAAATGAT
40188093 AAAAAATGTAAAAGATTTATA
1 AAAAAATGTAAAA-ATTTATA
* *
40188114 AAAAATTGTAAAATTTTATA
1 AAAAAATGTAAAAATTTATA
40188134 AAAA
1 AAAA
40188138 TCATAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAAATGTAAAAATTTATA
Found at i:40188144 original size:19 final size:20
Alignment explanation
Indices: 40188108--40188146 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
40188098 ATGTAAAAGA
**
40188108 TTTATAAAAAATTGTAAAAT
1 TTTATAAAAAATCATAAAAT
40188128 TTTAT-AAAAATCATAAAAT
1 TTTATAAAAAATCATAAAAT
40188147 GCATCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTTATAAAAAATCATAAAAT
Found at i:40188354 original size:20 final size:20
Alignment explanation
Indices: 40188329--40188367 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40188319 TTGGTATGAT
40188329 AATTTTATAATTCTTTTATG
1 AATTTTATAATTCTTTTATG
* *
40188349 AATTTTATATTTTTTTTAT
1 AATTTTATAATTCTTTTAT
40188368 TTTTTTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
AATTTTATAATTCTTTTATG
Found at i:40188401 original size:10 final size:10
Alignment explanation
Indices: 40188388--40188516 Score: 53
Period size: 10 Copynumber: 13.5 Consensus size: 10
40188378 CTTTATAAAA
40188388 TTTTATAATT
1 TTTTATAATT
*
40188398 TTTTCT-ATAT
1 TTTTATAAT-T
*
40188408 TTCTATATATT
1 TTTTATA-ATT
40188419 TTTTAT-A--
1 TTTTATAATT
40188426 TTTTATAATT
1 TTTTATAATT
* *
40188436 TTTAATAA-A
1 TTTTATAATT
40188445 TTTTA-AATT
1 TTTTATAATT
**
40188454 TTTTATTAAAA
1 TTTTA-TAATT
* *
40188465 TTTAATAA-A
1 TTTTATAATT
*
40188474 TTTTATAA-C
1 TTTTATAATT
*
40188483 TTTTATTGA-T
1 TTTTA-TAATT
*
40188493 TTTTAT-TTT
1 TTTTATAATT
40188502 TTTTATAATT
1 TTTTATAATT
40188512 TTTTA
1 TTTTA
40188517 CTACATGTCA
Statistics
Matches: 90, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
7 6 0.07
8 3 0.03
9 33 0.37
10 34 0.38
11 12 0.13
12 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40188409 original size:19 final size:18
Alignment explanation
Indices: 40188387--40188457 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
40188377 GCTTTATAAA
40188387 ATTTTATAATTTTTTCTAT
1 ATTTTATAATTTTTT-TAT
40188406 ATTTCTAT-ATATTTTTTAT
1 ATTT-TATAAT-TTTTTTAT
* *
40188425 ATTTTATAATTTTTAATAA
1 ATTTTATAATTTTT-TTAT
40188444 ATTTTA-AATTTTTT
1 ATTTTATAATTTTTT
40188458 ATTAAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 14 0.31
19 23 0.51
20 8 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTATAATTTTTTTAT
Found at i:40188463 original size:19 final size:19
Alignment explanation
Indices: 40188379--40188469 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 19
40188369 TTTTTACGGC
*
40188379 TTTATAAAATTTTATAATTT
1 TTTATTAAATTTTA-AATTT
* * * *
40188399 TTT-CTATATTTCTATATAT
1 TTTATTAAATTT-TAAATTT
*
40188418 TTT-TTATATTTTATAA-TT
1 TTTATTAAATTTTA-AATTT
*
40188436 TTTAATAAATTTTAAATTT
1 TTTATTAAATTTTAAATTT
*
40188455 TTTATTAAAATTTAA
1 TTTATTAAATTTTAA
40188470 TAAATTTTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
18 8 0.15
19 42 0.76
20 5 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTAAATTTTAAATTT
Found at i:40188497 original size:29 final size:29
Alignment explanation
Indices: 40188426--40188497 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
40188416 ATTTTTTATA
*
40188426 TTTTA-TAATTTTTAATAAATTTTAAATT
1 TTTTATTAATTTTTAATAAATTTTAAATC
**
40188454 TTTTATTAAAATTTAATAAATTTTATAA-C
1 TTTTATTAATTTTTAATAAATTTTA-AATC
*
40188483 TTTTATTGATTTTTA
1 TTTTATTAATTTTTA
40188498 TTTTTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 5 0.14
29 29 0.81
30 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTATTAATTTTTAATAAATTTTAAATC
Found at i:40188513 original size:9 final size:9
Alignment explanation
Indices: 40188388--40188514 Score: 62
Period size: 9 Copynumber: 13.4 Consensus size: 9
40188378 CTTTATAAAA
40188388 TTTTATAATT
1 TTTTATAA-T
*
40188398 TTTTCTATAT
1 TTTTATA-AT
*
40188408 TTCTATATAT
1 TTTTATA-AT
40188418 TTTT-T-AT
1 TTTTATAAT
40188425 ATTTTATAAT
1 -TTTTATAAT
*
40188435 TTTTAATAAA
1 TTTT-ATAAT
40188445 TTTTA-AATT
1 TTTTATAA-T
*
40188454 TTTTATTAAAA
1 TTTTA-T-AAT
* *
40188465 TTTAATAAA
1 TTTTATAAT
*
40188474 TTTTATAAC
1 TTTTATAAT
*
40188483 TTTTATTGAT
1 TTTTA-TAAT
**
40188493 TTTTATTTT
1 TTTTATAAT
40188502 TTTTATAAT
1 TTTTATAAT
40188511 TTTT
1 TTTT
40188515 TACTACATGT
Statistics
Matches: 91, Mismatches: 16, Indels: 21
0.71 0.12 0.16
Matches are distributed among these distances:
7 2 0.02
8 6 0.07
9 40 0.44
10 36 0.40
11 5 0.05
12 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40188685 original size:91 final size:91
Alignment explanation
Indices: 40188576--40188759 Score: 221
Period size: 91 Copynumber: 2.0 Consensus size: 91
40188566 TAATGATCAA
* * * ** *
40188576 AGGGTCTTTTTAATGCATTTTGGCAA-TTCAAGTA-CATAATTGAGTGCAAAAAA-AAGGTATGG
1 AGGGCCTTTTTAATGCATTTT-GAAAGTTCAAGTATC-GAATTGAGTGCAAAAAAGAAAATAAGG
* *
40188638 GCTTAATTGCTTTTTTTTTAAAAAGTTTG
64 GCTTAATT-ATTTTTTTTGAAAAAGTTTG
* *
40188667 AGGGCCTTTTTTATGCATTTTGAAAGTTTAAGTATCGAATTGAGTGCAAAAAAGAAAATAAGGGC
1 AGGGCCTTTTTAATGCATTTTGAAAGTTCAAGTATCGAATTGAGTGCAAAAAAGAAAATAAGGGC
*
40188732 TTAATTATTTTTTTTGAAAAATTTTG
66 TTAATTATTTTTTTTGAAAAAGTTTG
40188758 AG
1 AG
40188760 ACATTTTTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
90 3 0.04
91 61 0.77
92 15 0.19
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.39
Consensus pattern (91 bp):
AGGGCCTTTTTAATGCATTTTGAAAGTTCAAGTATCGAATTGAGTGCAAAAAAGAAAATAAGGGC
TTAATTATTTTTTTTGAAAAAGTTTG
Found at i:40188942 original size:6 final size:6
Alignment explanation
Indices: 40188931--40188956 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40188921 TGAAGATTAA
40188931 TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
40188957 TTGAATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Done.