Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 13 of 325
Found at i:2925299 original size:17 final size:17
Alignment explanation
Indices: 2925277--2925315 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2925267 TCTCCGGTTG
2925277 TCTCCTCC-TCTTACTTT
1 TCTCCTCCGT-TTACTTT
2925294 TCTCCTCCGTTTACTTT
1 TCTCCTCCGTTTACTTT
*
2925311 CCTCC
1 TCTCC
2925316 GCCTACCGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.05, C:0.44, G:0.03, T:0.49
Consensus pattern (17 bp):
TCTCCTCCGTTTACTTT
Found at i:2928506 original size:3 final size:3
Alignment explanation
Indices: 2928500--2928533 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2928490 TAGAAGAAGC
*
2928500 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2928534 GTTGGACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2934224 original size:2 final size:2
Alignment explanation
Indices: 2934217--2934257 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2934207 AGAACTAAGG
2934217 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
2934258 ATCATTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2934859 original size:11 final size:11
Alignment explanation
Indices: 2934845--2934874 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2934835 TAAAAAACTT
2934845 AATTAAAATAA
1 AATTAAAATAA
2934856 AATTAAAATAA
1 AATTAAAATAA
*
2934867 AAATAAAA
1 AATTAAAA
2934875 GGCATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AATTAAAATAA
Found at i:2939707 original size:32 final size:32
Alignment explanation
Indices: 2939651--2939711 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2939641 AGCTGACACT
** *
2939651 GAACTGTGAACTATGAGCTGCATGCAAGCTGC
1 GAACTGTGAACTACAAGCTACATGCAAGCTGC
*
2939683 GAACTGTGAACTGCAAGCTACATGCAAGC
1 GAACTGTGAACTACAAGCTACATGCAAGC
2939712 AAGTTGCGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (32 bp):
GAACTGTGAACTACAAGCTACATGCAAGCTGC
Found at i:2943126 original size:46 final size:44
Alignment explanation
Indices: 2943026--2943133 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
2943016 TGTCTTTGAC
** * * * *
2943026 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
*
2943070 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
2943116 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2943134 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:2947254 original size:32 final size:32
Alignment explanation
Indices: 2947225--2947285 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2947215 AACCCCTTCG
2947225 CAAA-TTTT-GAAAAATTTTAATTAGACCCTT
1 CAAACTTTTCGAAAAATTTTAATTAGACCCTT
* *
2947255 TAAACTTTTCTAAAAATTTTAATTAGACCCT
1 CAAACTTTTCGAAAAATTTTAATTAGACCCT
2947286 CCCAAGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 4 0.15
32 20 0.74
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (32 bp):
CAAACTTTTCGAAAAATTTTAATTAGACCCTT
Found at i:2950862 original size:31 final size:29
Alignment explanation
Indices: 2950827--2950893 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
2950817 ATATCAAAAT
*
2950827 TATACATCAACTTTGGCTTAATGTGCAATTA
1 TATACATCAACTTT-GATT-ATGTGCAATTA
* * *
2950858 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATCAACTTTGATTATGTGCAATTA
2950887 TATACAT
1 TATACAT
2950894 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
30 3 0.09
31 13 0.41
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (29 bp):
TATACATCAACTTTGATTATGTGCAATTA
Found at i:2955080 original size:39 final size:38
Alignment explanation
Indices: 2955035--2955116 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
2955025 ATGGGTAGAC
***
2955035 GAGAACCTTCCGGCAAGAACAAATGGCTAGCTAGTGGAT
1 GAGAACCTTCCAAAAAGAACAAATGGCTAGCTAGT-GAT
* * *
2955074 GAGAACCTTCCAAAAAGAGCAAGTGGCTAGCTGGTGAT
1 GAGAACCTTCCAAAAAGAACAAATGGCTAGCTAGTGAT
2955112 GAGAA
1 GAGAA
2955117 TGGTCGATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 8 0.22
39 29 0.78
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.17
Consensus pattern (38 bp):
GAGAACCTTCCAAAAAGAACAAATGGCTAGCTAGTGAT
Found at i:2959378 original size:29 final size:29
Alignment explanation
Indices: 2959308--2959378 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2959298 TTTCCTCTTT
* *
2959308 AAAAGTTATCTAAAAACATATTATCCAGAA
1 AAAAATTAT-TAAAAAAATATTATCCAGAA
* ** *
2959338 TAATTTTTTTAAAAAAATATTATCCAGAA
1 AAAAATTATTAAAAAAATATTATCCAGAA
2959367 AAAAATTATTAA
1 AAAAATTATTAA
2959379 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTATTAAAAAAATATTATCCAGAA
Found at i:2964752 original size:31 final size:31
Alignment explanation
Indices: 2964716--2964781 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2964706 TTACAATTCG
*
2964716 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
** *
2964747 GTCACTGAGTTATTTAAAAGTTTTTATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
2964778 GTCA
1 GTCA
2964782 ATAGGCTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (31 bp):
GTCACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:2966195 original size:30 final size:29
Alignment explanation
Indices: 2966161--2966220 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
2966151 TTTTAGCTTT
2966161 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAA-TTTA
* * *
2966191 GGGGCAAAATTGTAACTTTGCAAAATTTA
1 GGGGCAAAAGTGTAAATATGCAAAATTTA
2966220 G
1 G
2966221 ATTTAAGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (29 bp):
GGGGCAAAAGTGTAAATATGCAAAATTTA
Found at i:2970124 original size:16 final size:17
Alignment explanation
Indices: 2970081--2970124 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2970071 AAATTTAAAC
*
2970081 ATTTTATTAAAAATAAT
1 ATTTTATTTAAAATAAT
* *
2970098 ATTTTAATTAAAATTAT
1 ATTTTATTTAAAATAAT
2970115 -TTTTATTTAA
1 ATTTTATTTAA
2970125 TAAATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATTTAAAATAAT
Found at i:2970373 original size:2 final size:2
Alignment explanation
Indices: 2970368--2970398 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2970358 AGAGAGTTGA
*
2970368 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2970399 GCCCGTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2977920 original size:15 final size:15
Alignment explanation
Indices: 2977902--2977936 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2977892 TTCTTCTTTT
*
2977902 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
2977917 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
2977932 TTTTT
1 TTTTT
2977937 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:2977951 original size:16 final size:15
Alignment explanation
Indices: 2977932--2977967 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2977922 TTGGGGTAGG
*
2977932 TTTTTCTTTTTCTTTT
1 TTTTTCTTTGT-TTTT
2977948 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
2977963 TTTTT
1 TTTTT
2977968 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:2978817 original size:30 final size:30
Alignment explanation
Indices: 2978781--2978842 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2978771 TTTTGAAAAA
2978781 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
2978811 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
2978841 CA
1 CA
2978843 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:2978972 original size:13 final size:13
Alignment explanation
Indices: 2978937--2978973 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2978927 ATGAGTTGAT
*
2978937 TTTTGAAAACAGA
1 TTTTGAAAATAGA
*
2978950 ATTTGAAAATAGA
1 TTTTGAAAATAGA
2978963 TTTTGAAAATA
1 TTTTGAAAATA
2978974 CCTCGACATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (13 bp):
TTTTGAAAATAGA
Found at i:2979158 original size:242 final size:249
Alignment explanation
Indices: 2978614--2979203 Score: 756
Period size: 253 Copynumber: 2.4 Consensus size: 249
2978604 AACAGACATT
2978614 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAA-GCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** * * * * **
2978678 TTGATTTTTTG-AAACTTAACTTGAAAAGCAGATTTTGAAAATACCTCGATATGTGACTGGAGGT
66 TTGATTTTTTGAAAACAGAAATTGAAAA-TAGATTTTGAAAATACCTCGACATGTAACCCGAGGT
* * *
2978742 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACT
130 CCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGAATCAACTCAACT
2978807 CTCGCAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAA
195 CTCGCAG-AATT-AAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTG---A
* *
2978867 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
2978932 TTGA-TTTTTGAAAACAGAATTTGAAAATAGATTTTGAAAATACCTCGACATGTAACCCGAGG-C
66 TTGATTTTTTGAAAACAGAAATTGAAAATAGATTTTGAAAATACCTCGACATGTAACCCGAGGTC
* * * *
2978995 CAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAA-AAT-ACCTC-A
131 CAACTCACATCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGAATCAACTCAA
* * * *
2979057 GTGT-G-TG-ATCT-GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG-
193 CTCTCGCAGAAT-TAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGA
* * * * *
2979109 AAAGATAGAAATTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
2979174 TTGATTTTTTGAAAACAGAAATTGAAAATA
66 TTGATTTTTTGAAAACAGAAATTGAAAATA
2979204 CCTCAACGTG
Statistics
Matches: 301, Mismatches: 29, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
242 62 0.21
243 24 0.08
246 9 0.03
247 31 0.10
248 2 0.01
249 1 0.00
250 1 0.00
251 1 0.00
252 28 0.09
253 77 0.26
254 61 0.20
255 4 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (249 bp):
AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAACAGAAATTGAAAATAGATTTTGAAAATACCTCGACATGTAACCCGAGGTC
CAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGAATCAACTCAACTC
TCGCAGAATTAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGA
Found at i:2979160 original size:77 final size:74
Alignment explanation
Indices: 2978991--2979348 Score: 388
Period size: 79 Copynumber: 4.8 Consensus size: 74
2978981 ATGTAACCCG
* * * *
2978991 AGGC-CAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTG--AAAATACCT
* *
2979055 CAGTGTGTGATCTGA
63 CA--GCGTG-TCTCA
* *
2979070 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
*
2979134 GCGCATGAGC-CA
65 GCG--TG-TCTCA
* * *
2979146 AGGGTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
2979210 CGTGTCTTG
66 CGTGTCTCA
** * *
2979219 AGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
2979282 CGTGTC-CA
66 CGTGTCTCA
*
2979290 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAA-ACAGAAATTGAAAA
2979349 ATGGAAATTG
Statistics
Matches: 240, Mismatches: 29, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
71 30 0.12
72 35 0.15
73 30 0.12
74 8 0.03
75 35 0.15
76 12 0.05
77 42 0.17
78 5 0.02
79 43 0.18
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (74 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGTCTCA
Found at i:2979367 original size:89 final size:90
Alignment explanation
Indices: 2979263--2979437 Score: 241
Period size: 92 Copynumber: 2.0 Consensus size: 90
2979253 TTTGAAAACA
* * *
2979263 GAAATTGAAATTACCTC-A-GCGTG-TCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGACGCGTGATCCAAGGCTCAACTCACCTCTCGCAATACGAGTTGA-CT
2979325 TTTTTGA-AAGGCAGAAATTGAAAAATG
65 TTTTTGACAA--CAGAAATTGAAAAATG
* **
2979352 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGCGTGATCCAAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
2979417 TTTTGACAACAGAAATTGAAA
66 TTTTGACAACAGAAATTGAAA
2979438 TTACCTCAGC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 16 0.21
90 13 0.17
91 12 0.16
92 35 0.46
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (90 bp):
GAAATTGAAAATACCTCGACGCGTGATCCAAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
TTTTGACAACAGAAATTGAAAAATG
Found at i:2979475 original size:74 final size:75
Alignment explanation
Indices: 2979352--2979513 Score: 222
Period size: 74 Copynumber: 2.1 Consensus size: 75
2979342 TTGAAAAATG
*
2979352 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
2979417 TTTTGACAACA
65 TTTTGACAACA
* * *
2979428 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
2979491 TTTTGA-AAGGCA
65 TTTTGACAA--CA
*
2979503 AAAATTGAAAA
1 GAAATTGAAAA
2979514 ACGGAAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
73 2 0.03
74 42 0.55
75 12 0.16
76 21 0.27
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACA
Found at i:2979496 original size:165 final size:165
Alignment explanation
Indices: 2979185--2979835 Score: 880
Period size: 165 Copynumber: 3.9 Consensus size: 165
2979175 TGATTTTTTG
* * * ** *
2979185 AAAACAGAAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
*
2979248 TGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCC-AAGGCTCAACTCACCTCTCGC
66 TGACTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGC
2979310 AATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGA
131 AATATGAGTTGA-TTTTTTTGAAAGGCAGAAATTGA
* *
2979346 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* *
2979411 TGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGACTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGC
*
2979476 AATATGAGTTGATTTTTTTGAAAGGCAAAAATTGA
131 AATATGAGTTGATTTTTTTGAAAGGCAGAAATTGA
* * *
2979511 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* *
2979576 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGC
66 TGACTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGC
** *
2979641 AATATGAGTTTTTTTTTTTGAAAGACAGAAATTGA
131 AATATGAGTTGATTTTTTTGAAAGGCAGAAATTGA
* *
2979676 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * * *
2979741 TGATTCTTTCAAAAACATAATAATGAAAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTC
66 TGA--CTTT--------T--T--TGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTC
* *
2979806 AACTCACCTCTCGCAATATGGGCTGATTTT
117 AACTCACCTCTCGCAATATGAGTTGATTTT
2979836 GAAAAAGTAG
Statistics
Matches: 437, Mismatches: 34, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
161 27 0.06
163 31 0.07
165 279 0.64
166 32 0.07
167 3 0.01
175 1 0.00
177 1 0.00
179 63 0.14
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (165 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGACTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTTTTTGAAAGGCAGAAATTGA
Found at i:2979650 original size:74 final size:76
Alignment explanation
Indices: 2979507--2979678 Score: 222
Period size: 74 Copynumber: 2.3 Consensus size: 76
2979497 AAGGCAAAAA
* * * * *
2979507 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGT-ACCTAAGGCTCAACTCACCACTCGCAATAC
2979572 GAGTTGATTTTT
65 GAGTTGATTTTT
* * * *
2979584 TTGACA-ACAGAAATTGAAATTACCTCAGCGTGT-CCTAAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTAAGGCTCAACTCACCACTCGCAATACG
**
2979647 AGTTTTTTTTT
66 AGTTGATTTTT
2979658 TTGAAAGACAGAAATTGAAAA
1 TTGAAAGACAGAAATTGAAAA
2979679 ACGGAAATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
74 40 0.49
75 13 0.16
76 24 0.29
77 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (76 bp):
TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTAAGGCTCAACTCACCACTCGCAATACG
AGTTGATTTTT
Found at i:2979677 original size:14 final size:14
Alignment explanation
Indices: 2979658--2979692 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2979648 GTTTTTTTTT
*
2979658 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
2979672 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
2979686 TTGAAAA
1 TTGAAAA
2979693 TACCTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2979768 original size:91 final size:90
Alignment explanation
Indices: 2979589--2979823 Score: 300
Period size: 90 Copynumber: 2.6 Consensus size: 90
2979579 TTTTTTTGAC
* * * *
2979589 AACAGAAATTGAAATTACCTCAGCGTGT--CCTAAGGCTCAACTCACCTCTCGCAATATGAGTTT
1 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTT
** * * * *
2979652 TTTTTTTTGAAAGACAGAAATTGAAA
66 GATTCTTTCAAAAACAGAAAATG-AA
* *
2979678 AACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAG-TT
1 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTT
*
2979742 GATTCTTTCAAAAACATAATAATGAA
66 GATTCTTTCAAAAACAGAA-AATGAA
2979768 AACAGAAATTGAAAATACCTCGGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATA
1 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
2979824 TGGGCTGATT
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
88 31 0.24
89 25 0.20
90 40 0.31
91 32 0.25
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (90 bp):
AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTT
GATTCTTTCAAAAACAGAAAATGAA
Found at i:2979993 original size:127 final size:127
Alignment explanation
Indices: 2979767--2980081 Score: 576
Period size: 127 Copynumber: 2.5 Consensus size: 127
2979757 ATAATAATGA
* ** * * *
2979767 AAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGGGCTGA
1 AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
2979832 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAC
66 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAC
2979894 AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
2979959 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAC
66 TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAC
2980021 AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
2980082 TTGAAATTAA
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 182 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (127 bp):
AAACAGAAATTGAAATTACCTCATCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGAC
Found at i:2980077 original size:73 final size:70
Alignment explanation
Indices: 2979985--2980177 Score: 235
Period size: 70 Copynumber: 2.7 Consensus size: 70
2979975 ATTAAAAGGT
* * * * * *
2979985 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCATGT
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTGA-AAACAAAAATTAAAAATACCT-AGCATGC
*
2980050 CCTGAGGC
63 CCCGAGGC
** *
2980058 TCAACTCACCTCTCGCAATATGAGTTGAAATT-AAAACAAAAAATTAAAAATACCTAGCGTGCCC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAC-AAAAATTAAAAATACCTAGCATGCCC
2980122 CGAGGC
65 CGAGGC
*
2980128 TCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
2980178 GGCTTAACTC
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
70 44 0.42
71 26 0.25
72 7 0.07
73 27 0.26
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (70 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTAGCATGCCCC
GAGGC
Found at i:2987105 original size:37 final size:38
Alignment explanation
Indices: 2987005--2987106 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 38
2986995 ATATATTTGG
2987005 TAATAATAATA--TAAAATAATAA-TATGTACATAAAAA
1 TAATAATAATATCTAAAATAA-AAGTATGTACATAAAAA
* *
2987041 TACATATATATATATGCATATAATAAAAGTATGTA-ATAATAA
1 TA-ATA-ATA-ATAT-C-TAAAATAAAAGTATGTACATAAAAA
*
2987083 TAATAATAATATCTACAATAAAAG
1 TAATAATAATATCTAAAATAAAAG
2987107 AAAATATTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 7 0.13
40 3 0.05
41 3 0.05
42 10 0.18
43 13 0.24
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (38 bp):
TAATAATAATATCTAAAATAAAAGTATGTACATAAAAA
Found at i:2987931 original size:16 final size:15
Alignment explanation
Indices: 2987912--2987947 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
2987902 TTTCTTCTTT
2987912 TTTTTTTTGGGTTAGG
1 TTTTTTTTGGG-TAGG
2987928 TTTTTTTTGGGTAGG
1 TTTTTTTTGGGTAGG
2987943 TTTTT
1 TTTTT
2987948 CTTTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.06, C:0.00, G:0.28, T:0.67
Consensus pattern (15 bp):
TTTTTTTTGGGTAGG
Found at i:2987962 original size:16 final size:15
Alignment explanation
Indices: 2987943--2987978 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2987933 TTTGGGTAGG
*
2987943 TTTTTCTTTTTCTTTT
1 TTTTTCTTTGT-TTTT
2987959 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
2987974 TTTTT
1 TTTTT
2987979 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:2991143 original size:2 final size:2
Alignment explanation
Indices: 2991090--2991124 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2991080 TAGAAGTGTA
2991090 AT AT AT AT AT 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 AT AT AT AT AT A
2991125 AACAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2993829 original size:12 final size:12
Alignment explanation
Indices: 2993812--2993838 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2993802 ACGTGCAGTT
2993812 GAAACTGTCATC
1 GAAACTGTCATC
2993824 GAAACTGTCATC
1 GAAACTGTCATC
2993836 GAA
1 GAA
2993839 GCTTATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (12 bp):
GAAACTGTCATC
Found at i:2995902 original size:3 final size:3
Alignment explanation
Indices: 2995890--2995922 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2995880 AAAAAAGGAA
*
2995890 AAG AAA AAG AAG AAG AA- AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2995923 TCAAATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2995916 original size:17 final size:17
Alignment explanation
Indices: 2995887--2995922 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2995877 AAAAAAAAAG
2995887 GAAAAGAAAAAGAAGAA
1 GAAAAGAAAAAGAAGAA
*
2995904 GAAAAGAAGAAGAAGAA
1 GAAAAGAAAAAGAAGAA
2995921 GA
1 GA
2995923 TCAAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAGAAGAA
Found at i:3002111 original size:3 final size:3
Alignment explanation
Indices: 3002103--3002197 Score: 70
Period size: 3 Copynumber: 31.0 Consensus size: 3
3002093 TTAATTTTGC
* *
3002103 TAT TAT TAT TAT TA- TAT TAT TGT TACT TAT TAT TAT GTACA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TA-T TAT TAT
* * * *
3002150 T-T ATAC TAT TCT TAA TAT TAT TAT TAT TAT TA- TATT TAC TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
3002195 TAT
1 TAT
3002198 AAATATTAGT
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
2 5 0.07
3 58 0.81
4 9 0.12
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3002115 original size:21 final size:24
Alignment explanation
Indices: 3002091--3002138 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3002081 GTATTTGTAA
3002091 TATTA-ATT-TTGCTA-TTATTAT
1 TATTATATTATTGCTACTTATTAT
*
3002112 TATTATATTATTGTTACTTATTAT
1 TATTATATTATTGCTACTTATTAT
3002136 TAT
1 TAT
3002139 GTACATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 3 0.13
23 5 0.22
24 10 0.43
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TATTATATTATTGCTACTTATTAT
Found at i:3002133 original size:27 final size:25
Alignment explanation
Indices: 3002090--3002198 Score: 87
Period size: 27 Copynumber: 4.1 Consensus size: 25
3002080 AGTATTTGTA
*
3002090 ATATTAATTTTGCTATTATTATTATT
1 ATATT-ATTTTACTATTATTATTATT
*
3002116 ATATTATTGTTACTTATTATTATGTA-C
1 ATATTATT-TTAC-TATTATTAT-TATT
* *
3002143 ATATTATTTATACTATTCTTAATATT
1 ATATTATTT-TACTATTATTATTATT
*
3002169 ATTATTATTATTA-TATTTACTATTATT
1 A-TATTATT-TTACTA-TTATTATTATT
3002196 ATA
1 ATA
3002199 AATATTAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
25 5 0.07
26 21 0.31
27 38 0.57
28 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (25 bp):
ATATTATTTTACTATTATTATTATT
Found at i:3002286 original size:21 final size:24
Alignment explanation
Indices: 3002260--3002310 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
3002250 ATTTTTAACA
*
3002260 TTATTATATTT-A-CTATTA-TAT
1 TTATTATATTTAATATATTATTAT
*
3002281 TTATTATTTTTAATATATTATTAT
1 TTATTATATTTAATATATTATTAT
3002305 TTATTA
1 TTATTA
3002311 CTTTATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 5 0.20
24 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATATTTAATATATTATTAT
Found at i:3002535 original size:3 final size:3
Alignment explanation
Indices: 3002361--3002520 Score: 84
Period size: 3 Copynumber: 54.3 Consensus size: 3
3002351 ATATTTTTAC
*
3002361 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * ** *
3002406 TAT TAT T-T T-T TGT T-T GTAT ATAT TAT TCA- TAC TAT CCT TGT TA-
1 TAT TAT TAT TAT TAT TAT -TAT -TAT TAT T-AT TAT TAT TAT TAT TAT
* * * * *
3002449 TAT TAT TTT TAC CAT TAT TA- CATT TAT TA- TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * *
3002493 TAC TAT CAT TAT CAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3002521 GTGTGTTTTT
Statistics
Matches: 119, Mismatches: 27, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
2 13 0.11
3 97 0.82
4 9 0.08
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3002653 original size:25 final size:25
Alignment explanation
Indices: 3002607--3002661 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
3002597 TTCATACTAT
3002607 TATTAACTATTATATTATTTTTAATA
1 TATTAAC-ATTATATTATTTTTAATA
*
3002633 GTATTAAC-TTATATT-TGTTTTTATA
1 -TATTAACATTATATTAT-TTTTAATA
3002658 TATT
1 TATT
3002662 CTTTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
27 7 0.27
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTAACATTATATTATTTTTAATA
Found at i:3002805 original size:6 final size:6
Alignment explanation
Indices: 3002780--3002815 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3002770 ACATGATTTG
*
3002780 TTTTTA TTTTTC TTTATTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTT
3002816 TTGTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:3011553 original size:16 final size:17
Alignment explanation
Indices: 3011522--3011554 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3011512 TTCATAAGTA
3011522 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
3011539 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
3011555 GTTCCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:3011890 original size:46 final size:45
Alignment explanation
Indices: 3011832--3012197 Score: 471
Period size: 46 Copynumber: 8.0 Consensus size: 45
3011822 TATTTATCTT
* * * * *
3011832 TGTCATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC
1 TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTC
* ***
3011878 TGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTC
1 TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
* ** ** *
3011923 ATGTTACATTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCC
1 -TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
* *
3011969 CGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTA
1 TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTC
* *
3012015 TATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
* *
3012060 ATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTA
1 -TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTC
*
3012107 TGTCATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTC
1 TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
*
3012152 TAATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 T-GTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
3012198 ATTTCAGAAA
Statistics
Matches: 284, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
45 46 0.16
46 235 0.83
47 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (45 bp):
TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
Found at i:3015433 original size:9 final size:8
Alignment explanation
Indices: 3015405--3015429 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3015395 TGGGTTCTTT
3015405 GTTTTCGG
1 GTTTTCGG
3015413 GTTTTCGG
1 GTTTTCGG
3015421 GTTTTCGG
1 GTTTTCGG
3015429 G
1 G
3015430 GTTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTCGG
Found at i:3017811 original size:6 final size:6
Alignment explanation
Indices: 3017796--3017841 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
3017786 AAAACCAAAC
*
3017796 GAAAAA -AAAAA GAAAAA GAAAAA G-GAAA GAAAAGA GAAAGAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAA-AA GAAA
3017842 GGAAGCCACG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.26
6 14 0.41
7 10 0.29
8 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:3017816 original size:17 final size:18
Alignment explanation
Indices: 3017796--3017834 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3017786 AAAACCAAAC
3017796 GAAAAAAAAAAGAAAA-A
1 GAAAAAAAAAAGAAAAGA
**
3017813 GAAAAAGGAAAGAAAAGA
1 GAAAAAAAAAAGAAAAGA
3017831 GAAA
1 GAAA
3017835 GAAGAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAGAAAAGA
Found at i:3017828 original size:22 final size:23
Alignment explanation
Indices: 3017803--3017845 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3017793 AACGAAAAAA
3017803 AAAAGAAAAAGAA-AAAGGAAAG
1 AAAAGAAAAAGAAGAAAGGAAAG
*
3017825 AAAAGAGAAAGAAGAAAGGAA
1 AAAAGAAAAAGAAGAAAGGAA
3017846 GCCACGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAGAAGAAAGGAAAG
Found at i:3024050 original size:60 final size:60
Alignment explanation
Indices: 3023943--3024057 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
3023933 CTCAACAACT
* * * *
3023943 TGAGTACTGGCAGGAGCTGAATGGGAATCTGAACATGCAGTAGCTGGAGAAGAATCAATC
1 TGAGTACTGCCAGGAGCTAAATGGGAATCTGAACAAGCAGTAACTGGAGAAGAATCAATC
* *
3024003 TGAGTATTGCCAGGAGCTAAATGGGAAT-TAGAACAAGTA-TCAACTGGAGAAGAAT
1 TGAGTACTGCCAGGAGCTAAATGGGAATCT-GAACAAGCAGT-AACTGGAGAAGAAT
3024058 GTGGTGTAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.21
Consensus pattern (60 bp):
TGAGTACTGCCAGGAGCTAAATGGGAATCTGAACAAGCAGTAACTGGAGAAGAATCAATC
Found at i:3025677 original size:46 final size:46
Alignment explanation
Indices: 3025516--3025691 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
3025506 TGTAACCCGC
* * * **
3025516 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTCCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
3025562 CCATGAGTGAACTCGGACTCAAATCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
3025612 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
3025655 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3025692 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 62 0.58
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:3025683 original size:93 final size:93
Alignment explanation
Indices: 3025524--3025694 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
3025514 GCCCATAAGT
* * *
3025524 GAACTCGGACTCAACTCAACGAGCTCGGGCGTCCGCATCCATGAGTGAACTCGGACTCAAATCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAAATCAA
3025589 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* ** *
3025617 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAAATCAA
3025682 CGAGTTCGGATGC
66 CGAGTTCGGATGC
3025695 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAAATCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:3034321 original size:17 final size:17
Alignment explanation
Indices: 3034299--3034331 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3034289 TAATTCACTT
3034299 TTCATATACAA-TCAATA
1 TTCATAT-CAATTCAATA
3034316 TTCATATCAATTCAAT
1 TTCATATCAATTCAAT
3034332 TAATCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (17 bp):
TTCATATCAATTCAATA
Found at i:3035182 original size:28 final size:28
Alignment explanation
Indices: 3035147--3035204 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3035137 TTAGTATTTA
3035147 TTTAATTGTTAATAAATTTTATTTTTGG
1 TTTAATTGTTAATAAATTTTATTTTTGG
3035175 TTTAATTGTTAATAAATTTTATTTTTGG
1 TTTAATTGTTAATAAATTTTATTTTTGG
3035203 TT
1 TT
3035205 ACTCGTTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (28 bp):
TTTAATTGTTAATAAATTTTATTTTTGG
Found at i:3035553 original size:7 final size:7
Alignment explanation
Indices: 3035543--3035568 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3035533 ATAAATATTG
3035543 AGGGTTT
1 AGGGTTT
3035550 AGGGTTT
1 AGGGTTT
3035557 AGGGTTT
1 AGGGTTT
3035564 AGGGT
1 AGGGT
3035569 GTAATAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (7 bp):
AGGGTTT
Found at i:3037336 original size:26 final size:26
Alignment explanation
Indices: 3037307--3037440 Score: 223
Period size: 26 Copynumber: 5.2 Consensus size: 26
3037297 TGGTACAAAT
3037307 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
3037333 TGATAATGGATTAAGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3037359 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3037385 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3037411 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3037437 TGAT
1 TGAT
3037441 GGGCATTTCA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 101 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3038952 original size:26 final size:26
Alignment explanation
Indices: 3038923--3038975 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3038913 TTTACAGTTT
3038923 TACCCCTAGTGGATAAATT-ACCGAAA
1 TACCCCTAG-GGATAAATTGACCGAAA
* *
3038949 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3038975 T
1 T
3038976 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3044424 original size:25 final size:26
Alignment explanation
Indices: 3044394--3044523 Score: 205
Period size: 25 Copynumber: 5.2 Consensus size: 26
3044384 TGGTACAAAT
3044394 TGATAATGGGTTAGGT-AATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3044419 TGATAATGGATTA-GTAAATATT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
3044443 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3044469 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3044494 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3044520 TGAT
1 TGAT
3044524 GGGCATTTCA
Statistics
Matches: 96, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
24 16 0.17
25 50 0.52
26 30 0.31
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3044516 original size:51 final size:50
Alignment explanation
Indices: 3044394--3044523 Score: 210
Period size: 51 Copynumber: 2.6 Consensus size: 50
3044384 TGGTACAAAT
3044394 TGATAATGGGTTAGGT-AATGTTCCATGATAATGGATTAGTAAATATTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGTAAATATTCA
*
3044443 TGATAATGGGTTAGGTAAATGTTCCATGATAATGG-TTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTA-GTAAATATT-CA
*
3044494 TGATAATGGTTTAGGTAAATGTTCCATGAT
1 TGATAATGGGTTAGGTAAATGTTCCATGAT
3044524 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
49 19 0.25
50 26 0.34
51 31 0.41
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (50 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGTAAATATTCA
Found at i:3047348 original size:20 final size:20
Alignment explanation
Indices: 3047325--3047364 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3047315 TATATAATTG
*
3047325 TATTTTTATTTTTCAAAAAT
1 TATTATTATTTTTCAAAAAT
*
3047345 TATTATTATTTTTTAAAAAT
1 TATTATTATTTTTCAAAAAT
3047365 ATCTTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTATTTTTCAAAAAT
Found at i:3048836 original size:43 final size:43
Alignment explanation
Indices: 3048685--3048915 Score: 342
Period size: 43 Copynumber: 5.4 Consensus size: 43
3048675 GCGTTTATTG
*
3048685 AGAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGA
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
* * *
3048728 A-AAAGAGCGCCGCTAAAAGCCATGGCCTTCAGCAGCGTTTGA
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
* *
3048770 A-AAAGAGCGCCGCTAAAAGCCATGGCCTTCAGCGGCGTTTGA
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
3048812 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
** *
3048855 AGAAAAAGCGCCGCTAAAAGTGACGGCCTTTAGCGGCGTTTGCA
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTG-A
*
3048899 AG-AAAGGCGCCGCTAAA
1 AGAAAAAGCGCCGCTAAA
3048916 GGCCTTCACT
Statistics
Matches: 175, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
42 79 0.45
43 93 0.53
44 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (43 bp):
AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGA
Found at i:3048837 original size:127 final size:129
Alignment explanation
Indices: 3048685--3048915 Score: 369
Period size: 127 Copynumber: 1.8 Consensus size: 129
3048675 GCGTTTATTG
* *
3048685 AGAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTGAA-AAAGAGCGCCGCTAAAAGCC
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGCC
*
3048749 ATGGCCTTCAGCAGCGTTTG-AA-AAAGAGCGCCGCTAAAAGCCATGGCCTTCAGCGGCGTTTGA
66 ACGGCCTTCAGCAGCGTTTGCAAGAAAG-GCGCCGCTAAAAGCCATGGCCTTCAGCGGCGTTTGA
**
3048812 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGTG
1 AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGCC
* *
3048877 ACGGCCTTTAGCGGCGTTTGCAAGAAAGGCGCCGCTAAA
66 ACGGCCTTCAGCAGCGTTTGCAAGAAAGGCGCCGCTAAA
3048916 GGCCTTCACT
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
127 43 0.46
128 34 0.36
129 13 0.14
130 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (129 bp):
AGAAAAAGCGCCGCTAAAAGCCATGGCCTTTAGCGGCGTTTGAAGAAAAAGCGCCGCTAAAAGCC
ACGGCCTTCAGCAGCGTTTGCAAGAAAGGCGCCGCTAAAAGCCATGGCCTTCAGCGGCGTTTGA
Found at i:3049046 original size:31 final size:31
Alignment explanation
Indices: 3049011--3049077 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
3049001 CTTCCTGCAT
*
3049011 TAAAATCCAACCAAATACAACAAATATAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * * *
3049042 TAAAATGCAGCCAAAAACAATAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAACA
3049073 TAAAA
1 TAAAA
3049078 AATACGACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:3049334 original size:21 final size:20
Alignment explanation
Indices: 3049310--3049362 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3049300 TTTTGCTCTG
3049310 CTCTGCTGCCATCGCTGCTGC
1 CTCTGCT-CCATCGCTGCTGC
*
3049331 CTCTGCCTCCCTCGCTGCTGC
1 CTCTG-CTCCATCGCTGCTGC
*
3049352 CGCTGCCTCCA
1 CTCTG-CTCCA
3049363 CTCTAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.04, C:0.49, G:0.21, T:0.26
Consensus pattern (20 bp):
CTCTGCTCCATCGCTGCTGC
Found at i:3049799 original size:13 final size:14
Alignment explanation
Indices: 3049774--3049802 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3049764 TGATGAATTG
3049774 AATTAAACAATTAT
1 AATTAAACAATTAT
3049788 AATTAAAC-ATTAT
1 AATTAAACAATTAT
3049801 AA
1 AA
3049803 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:3054957 original size:46 final size:46
Alignment explanation
Indices: 3054872--3055002 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 46
3054862 TAAGTTATTT
**
3054872 ATTATGTAAGTTATGTAAAAGCTGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGTATTA--TGTAAGTTATGAAATTTGATCTTTAA
*
3054920 ATTATGTAAGTTATGTATTATGTAAGTTTTGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
* *
3054966 ATTATGTAACTCATGTATTATGTAAGTTATGTAAATT
1 ATTATGTAAGTTATGTATTATGTAAGTTATG-AAATT
3055003 ATGTAAGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
46 53 0.70
47 5 0.07
48 18 0.24
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (46 bp):
ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:3054970 original size:30 final size:30
Alignment explanation
Indices: 3054936--3055108 Score: 165
Period size: 30 Copynumber: 5.5 Consensus size: 30
3054926 TAAGTTATGT
*
3054936 ATTATGTAAGTTTTGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
* * *
3054966 ATTATGTAACTCATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
3055000 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
*
3055030 ATTATGTAAGTTATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
3055064 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
3055094 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
3055109 TATTATGTAA
Statistics
Matches: 118, Mismatches: 9, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
29 6 0.05
30 52 0.44
31 4 0.03
32 8 0.07
33 4 0.03
34 38 0.32
35 6 0.05
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:3055004 original size:64 final size:64
Alignment explanation
Indices: 3054920--3055129 Score: 372
Period size: 64 Copynumber: 3.3 Consensus size: 64
3054910 TGATCTTTAA
* * *
3054920 ATTATGTAAGTTATGT--ATTATGTAAGTTTTGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
3054982 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
3055046 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
3055110 ATTATGTAAGTTATG-AAATT
1 ATTATGTAAGTTATGTAAATT
3055130 TGATCTTTAA
Statistics
Matches: 143, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
62 16 0.11
63 5 0.03
64 122 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.47
Consensus pattern (64 bp):
ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
Found at i:3055050 original size:110 final size:112
Alignment explanation
Indices: 3054852--3055234 Score: 455
Period size: 110 Copynumber: 3.5 Consensus size: 112
3054842 ATAAGTATAA
* * * ***
3054852 TTAAGTTATGTAAGTTATTTATTATGTAAGTTATGTAAAAGCTGTAAGTTATGAAATTTGATCTT
1 TTAAATTATGTAA-CTATATATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTT
* *
3054917 TAAATTATGTAAGTTATGTATTATGTAAGTTTTG-AAATT-TG-ATCT
65 TAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAACT
*
3054962 TTAAATTATGTAACTCATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTT
1 TTAAATTATGTAACT-ATATATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTT
*
3055027 TAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAAGT
65 TAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAACT
* * *
3055075 TATGAAATT-TG-ATCTTTAAATTATGTAAGTTATGT--ATTATGTAAGTTATGAAATTTGATCT
1 T-T-AAATTATGTAACTATATATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCT
* * *
3055136 TTAAATTATGTAACTCATGTATTATGTAAGTTATGTAAATTATGTAAGT
64 TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAACT
* * * *
3055185 TATAAAATT-TG-ATCTTTAAATTATGTAAGTTATGT--TTTATGTAAGTTATG
1 T-T-AAATTATGTAACTATATATTATGTAAGTTATGTAAATTATGTAAGTTATG
3055235 TATTAAATAA
Statistics
Matches: 250, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
109 1 0.00
110 211 0.84
111 5 0.02
112 19 0.08
113 6 0.02
114 3 0.01
115 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (112 bp):
TTAAATTATGTAACTATATATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTT
AAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAACT
Found at i:3055126 original size:46 final size:46
Alignment explanation
Indices: 3055046--3055176 Score: 217
Period size: 46 Copynumber: 2.8 Consensus size: 46
3055036 TAAGTTATGT
3055046 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGT--ATTATGTAAGTTATGAAATTTGATCTTTAA
3055094 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
* *
3055140 ATTATGTAACTCATGTATTATGTAAGTTATGTAAATT
1 ATTATGTAAGTTATGTATTATGTAAGTTATG-AAATT
3055177 ATGTAAGTTA
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
46 59 0.74
47 5 0.06
48 16 0.20
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.47
Consensus pattern (46 bp):
ATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:3055144 original size:30 final size:30
Alignment explanation
Indices: 3055110--3055218 Score: 114
Period size: 30 Copynumber: 3.5 Consensus size: 30
3055100 TAAGTTATGT
3055110 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
* * *
3055140 ATTATGTAACTCATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
*
3055174 ATTATGTAAGTTATAAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
3055204 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
3055219 TTTTATGTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
29 3 0.05
30 32 0.51
31 2 0.03
32 4 0.06
33 2 0.03
34 17 0.27
35 3 0.05
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:3055147 original size:174 final size:174
Alignment explanation
Indices: 3054852--3055236 Score: 698
Period size: 174 Copynumber: 2.2 Consensus size: 174
3054842 ATAAGTATAA
* * *
3054852 TTAAGTTATGTAAGTTATTTATTATGTAAGTTATGTAAAAGCTGTAAGTTATGAAATTTGATCTT
1 TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAAAGATGTAAGTTATGAAATTTGATCTT
*
3054917 TAAATTATGTAAGTTATGTATTATGTAAGTTTTGAAATTTGATCTTTAAATTATGTAACTCATGT
66 TAAATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
*
3054982 ATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCT
131 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCT
**
3055026 TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTT
1 TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAAAGATGTAAGTTATGAAATTTGATCTT
3055091 TAAATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
66 TAAATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
3055156 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCT
131 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCT
*
3055200 TTAAATTATGTAAGTTATGTTTTATGTAAGTTATGTA
1 TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTA
3055237 TTAAATAATA
Statistics
Matches: 203, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 203 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (174 bp):
TTAAATTATGTAAGTTATGTATTATGTAAGTTATGTAAAAGATGTAAGTTATGAAATTTGATCTT
TAAATTATGTAAGTTATGTATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCT
Found at i:3055178 original size:64 final size:63
Alignment explanation
Indices: 3055094--3055236 Score: 234
Period size: 64 Copynumber: 2.3 Consensus size: 63
3055084 TGATCTTTAA
*
3055094 ATTATGTAAGTTATGT-ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGTAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
* *
3055156 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT-AATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
*
3055220 TTTATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
3055237 TTAAATAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
62 16 0.21
63 1 0.01
64 58 0.77
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.48
Consensus pattern (63 bp):
ATTATGTAAGTTATGTAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
Found at i:3056515 original size:25 final size:25
Alignment explanation
Indices: 3056487--3056550 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
3056477 GAGAAGCAAC
3056487 AGAGGGATGCCGACGAAGATGTAGA
1 AGAGGGATGCCGACGAAGATGTAGA
* * * *
3056512 AGAGGGATGTCGATGGAGATGTAGT
1 AGAGGGATGCCGACGAAGATGTAGA
*
3056537 AGAGGGCTGCCGAC
1 AGAGGGATGCCGAC
3056551 AACGATGCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.12, G:0.42, T:0.16
Consensus pattern (25 bp):
AGAGGGATGCCGACGAAGATGTAGA
Found at i:3059083 original size:21 final size:21
Alignment explanation
Indices: 3059024--3059075 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3059014 CACTATATAT
*
3059024 ACCCTAAACCCAAAATAACAA
1 ACCCCAAACCCAAAATAACAA
3059045 ACCCCAAACCCAAAATAACAA
1 ACCCCAAACCCAAAATAACAA
3059066 ACCCCAAACC
1 ACCCCAAACC
3059076 ATGCATAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.54, C:0.40, G:0.00, T:0.06
Consensus pattern (21 bp):
ACCCCAAACCCAAAATAACAA
Found at i:3059535 original size:32 final size:32
Alignment explanation
Indices: 3059499--3059563 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3059489 TGTATGCATT
3059499 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
3059531 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
3059563 T
1 T
3059564 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:3061073 original size:26 final size:26
Alignment explanation
Indices: 3061044--3061096 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3061034 TTTACAATTT
3061044 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
3061070 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3061096 T
1 T
3061097 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3062649 original size:83 final size:83
Alignment explanation
Indices: 3062494--3062733 Score: 299
Period size: 83 Copynumber: 2.9 Consensus size: 83
3062484 TATTGATTAG
* *
3062494 TTTTAGTGGCGTTTTAACAAAAATGCCGTTATTTCTC--CATTTTTAGTGGCGTTTTAGATAAAA
1 TTTTAGTGGCGTTTAAACGAAAATGCCGTTATTTCTCTGC-TTTTTAGTGGCGTTTTAGATAAAA
*
3062557 ACGCCGCTATTTCCCTAGT
65 ACGCCGCTATTTCCCCAGT
* ** *
3062576 TTTTAGTGGCATTTGGACGAAAATGCCGTTATTTCTCTGCTTTTTAGTGGCGTTTTGGATAAAAA
1 TTTTAGTGGCGTTTAAACGAAAATGCCGTTATTTCTCTGCTTTTTAGTGGCGTTTTAGATAAAAA
*
3062641 CGCAGCTATTTCCCCAGT
66 CGCCGCTATTTCCCCAGT
* * *** *
3062659 TTTTAGTGGCGTTTACAA-GAAAACGCCGCTATCGATCTG-TTTGTAGTGGCGTTTTAGATAAAA
1 TTTTAGTGGCGTTTA-AACGAAAATGCCGTTATTTCTCTGCTTTTTAGTGGCGTTTTAGAT-AAA
3062722 AACGCCGCTATT
64 AACGCCGCTATT
3062734 GATATGTTTT
Statistics
Matches: 136, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
82 51 0.38
83 83 0.61
84 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (83 bp):
TTTTAGTGGCGTTTAAACGAAAATGCCGTTATTTCTCTGCTTTTTAGTGGCGTTTTAGATAAAAA
CGCCGCTATTTCCCCAGT
Found at i:3062651 original size:42 final size:41
Alignment explanation
Indices: 3062473--3062775 Score: 258
Period size: 41 Copynumber: 7.4 Consensus size: 41
3062463 GTTTGGTCCT
**
3062473 AAAAACGCCGCTATTGAT-TAG-TTTTAGTGGCGTTTTA-AC
1 AAAAACGCCGCTATTTCTCT-GTTTTTAGTGGCGTTTTAGAC
* * ** *
3062512 AAAAATGCCGTTATTTCTCCATTTTTAGTGGCGTTTTAGAT
1 AAAAACGCCGCTATTTCTCTGTTTTTAGTGGCGTTTTAGAC
* * *
3062553 AAAAACGCCGCTATTTCCCTAGTTTTTAGTGGC-ATTTGGAC
1 AAAAACGCCGCTATTTCTCT-GTTTTTAGTGGCGTTTTAGAC
* * * * *
3062594 GAAAATGCCGTTATTTCTCTGCTTTTTAGTGGCGTTTTGGAT
1 AAAAACGCCGCTATTTCTCTG-TTTTTAGTGGCGTTTTAGAC
* * * *
3062636 AAAAACGCAGCTATTTCCCCAGTTTTTAGTGGCG-TTTACA-
1 AAAAACGCCGCTATTT-CTCTGTTTTTAGTGGCGTTTTAGAC
*** * *
3062676 AGAAAACGCCGCTATCGATCTGTTTGTAGTGGCGTTTTAGATA
1 A-AAAACGCCGCTATTTCTCTGTTTTTAGTGGCGTTTTAGA-C
** * *
3062719 AAAAACGCCGCTATTGATATGTTTTTAGTGGCGGTTTAGAC
1 AAAAACGCCGCTATTTCTCTGTTTTTAGTGGCGTTTTAGAC
3062760 AAAAACGCCGCTATTT
1 AAAAACGCCGCTATTT
3062776 TCATTTTTTT
Statistics
Matches: 210, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
39 14 0.07
40 31 0.15
41 85 0.40
42 76 0.36
43 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (41 bp):
AAAAACGCCGCTATTTCTCTGTTTTTAGTGGCGTTTTAGAC
Found at i:3063446 original size:21 final size:21
Alignment explanation
Indices: 3063380--3063483 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
3063370 GCCCGAAGGC
* * * *
3063380 TGAACAGAACCACATAAGTGC
1 TGAACAGAAACTCATAAGAGT
* * *
3063401 TAAACAGAAACCCATAAGGGT
1 TGAACAGAAACTCATAAGAGT
* *
3063422 TGAACAGAAGCTCATAAGAGA
1 TGAACAGAAACTCATAAGAGT
*
3063443 TGAAC-GAAAACTCATATGAGT
1 TGAACAG-AAACTCATAAGAGT
* * *
3063464 TAAACAGAAGCTCGTAAGAG
1 TGAACAGAAACTCATAAGAG
3063484 CTAAATGGAA
Statistics
Matches: 64, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGAGT
Found at i:3067501 original size:17 final size:17
Alignment explanation
Indices: 3067479--3067512 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3067469 ATTGAAGGTT
3067479 AAAGAGTATGATGTGCC
1 AAAGAGTATGATGTGCC
*
3067496 AAAGAGTGTGATGTGCC
1 AAAGAGTATGATGTGCC
3067513 TAGGGTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (17 bp):
AAAGAGTATGATGTGCC
Found at i:3067729 original size:30 final size:28
Alignment explanation
Indices: 3067683--3067743 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 28
3067673 ACTAATTTTA
3067683 TTGTTAATTTTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTATTATTTTAAAGGCAT
*
3067711 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAA-TTT-TTATTATTTTAAAGGCAT
3067741 TTG
1 TTG
3067744 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
30 20 0.67
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (28 bp):
TTGTTAATTTTTATTATTTTAAAGGCAT
Found at i:3067897 original size:12 final size:12
Alignment explanation
Indices: 3067867--3067899 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3067857 TATATATTTT
3067867 AAAATT-ATATA
1 AAAATTAATATA
3067878 AAAA-TAATATA
1 AAAATTAATATA
3067889 AAAATTAATAT
1 AAAATTAATAT
3067900 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3071274 original size:53 final size:53
Alignment explanation
Indices: 3071133--3071283 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3071123 ACAAGTGTGC
* **
3071133 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
3071186 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
3071239 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
3071284 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:3078789 original size:53 final size:53
Alignment explanation
Indices: 3078648--3078798 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3078638 ACAAGTGTGC
* **
3078648 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
3078701 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
3078754 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
3078799 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:3090331 original size:18 final size:17
Alignment explanation
Indices: 3090308--3090342 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
3090298 GAATAGATTT
3090308 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
3090326 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
3090343 AGCCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:3091008 original size:17 final size:17
Alignment explanation
Indices: 3090986--3091019 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3090976 AGGTTTAGGT
3090986 TTAAAAAATTTAATTAA
1 TTAAAAAATTTAATTAA
**
3091003 TTAAAATTTTTAATTAA
1 TTAAAAAATTTAATTAA
3091020 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAAATTTAATTAA
Found at i:3099464 original size:29 final size:29
Alignment explanation
Indices: 3099430--3099488 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3099420 ATATTATAAA
3099430 AATGTATTAATTATAGAATTTTACGAGTG
1 AATGTATTAATTATAGAATTTTACGAGTG
*
3099459 AATGTATTAATTATAGAATTTTATGAGTG
1 AATGTATTAATTATAGAATTTTACGAGTG
3099488 A
1 A
3099489 TGTTTGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.42
Consensus pattern (29 bp):
AATGTATTAATTATAGAATTTTACGAGTG
Found at i:3100405 original size:23 final size:23
Alignment explanation
Indices: 3100336--3100408 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
3100326 ATTTAAGTTA
*
3100336 TAAAATTTGTTTGGTATATTACT
1 TAAAATTTGGTTGGTATATTACT
**
3100359 TAAAATTAAG--GGTA-AGCTTA--
1 TAAAATTTGGTTGGTATA--TTACT
3100379 TAAAATTTGGTTGGTATATTACT
1 TAAAATTTGGTTGGTATATTACT
3100402 TAAAATT
1 TAAAATT
3100409 AAGGGTAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
20 9 0.24
21 7 0.18
22 7 0.18
23 15 0.39
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (23 bp):
TAAAATTTGGTTGGTATATTACT
Found at i:3100421 original size:21 final size:21
Alignment explanation
Indices: 3100354--3100421 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
3100344 GTTTGGTATA
3100354 TTACTTAAAATTAAGGGTAAG
1 TTACTTAAAATTAAGGGTAAG
**
3100375 CTTA--TAAAATTTGGTTGGTATA-
1 -TTACTTAAAATTAAG--GGTA-AG
3100397 TTACTTAAAATTAAGGGTAAG
1 TTACTTAAAATTAAGGGTAAG
3100418 TTAC
1 TTAC
3100422 AAAAATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
20 9 0.25
21 11 0.31
22 7 0.19
23 9 0.25
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (21 bp):
TTACTTAAAATTAAGGGTAAG
Found at i:3100427 original size:43 final size:42
Alignment explanation
Indices: 3100329--3100425 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 42
3100319 GTTTTGAATT
*
3100329 TAAGTTATAAAATTTGTTTGGTATATTACTTAAAATTAAGGG
1 TAAGTTATAAAATTTGGTTGGTATATTACTTAAAATTAAGGG
3100371 TAAGCTTATAAAATTTGGTTGGTATATTACTTAAAATTAAGGG
1 TAAG-TTATAAAATTTGGTTGGTATATTACTTAAAATTAAGGG
*
3100414 TAAGTTACAAAA
1 TAAGTTATAAAA
3100426 ATATTCACTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 11 0.21
43 41 0.79
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.39
Consensus pattern (42 bp):
TAAGTTATAAAATTTGGTTGGTATATTACTTAAAATTAAGGG
Found at i:3102672 original size:16 final size:15
Alignment explanation
Indices: 3102651--3102684 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3102641 AATTAGTTAA
*
3102651 TTTTAGTTTTTAAACT
1 TTTTAGGTTTTAAA-T
3102667 TTTTAGGTTTTAAAT
1 TTTTAGGTTTTAAAT
3102682 TTT
1 TTT
3102685 AAATTCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (15 bp):
TTTTAGGTTTTAAAT
Found at i:3110282 original size:75 final size:75
Alignment explanation
Indices: 3110159--3110307 Score: 201
Period size: 75 Copynumber: 2.0 Consensus size: 75
3110149 GTGTCTTACA
* * *
3110159 GGACGCGTTTTCAACAGTTTCTTGCAAGACACGTTTTTTATTTTTTTTTTCAAAATCAACCTATG
1 GGACGCGTTTTCAACAGCTTCTTGCAAGACAAGTTTTTTATTTTTTTTTACAAAATCAACCTATG
3110224 TCCTTAAATG
66 TCCTTAAATG
* * * * **
3110234 GGACGCGTTTTCAACGGCTTCTTTCAAGATATATTTTTTTA-TTTTTTTTACAAAATTGACCTAT
1 GGACGCGTTTTCAACAGCTTCTTGCAAGACA-AGTTTTTTATTTTTTTTTACAAAATCAACCTAT
3110298 GTCCTTAAAT
65 GTCCTTAAAT
3110308 ATCCTAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 57 0.89
76 7 0.11
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (75 bp):
GGACGCGTTTTCAACAGCTTCTTGCAAGACAAGTTTTTTATTTTTTTTTACAAAATCAACCTATG
TCCTTAAATG
Found at i:3116275 original size:22 final size:21
Alignment explanation
Indices: 3116234--3116275 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3116224 ATCAGATTGA
*
3116234 TAAACAAAATATATCCAAATC
1 TAAACAAAATAAATCCAAATC
*
3116255 TAAACAAAAATAAATCTAAAT
1 TAAAC-AAAATAAATCCAAAT
3116276 AAATACTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACAAAATAAATCCAAATC
Found at i:3125607 original size:31 final size:31
Alignment explanation
Indices: 3125563--3125635 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
3125553 AAAACTTAAC
* *
3125563 AGTTCAATGACTTAAATAAAAACTTTTGAAT
1 AGTTCAATAACTTAAATAAAAACTTTCGAAT
* *
3125594 AGTTTAATAACTTAAATGAAAACTTTCGAAT
1 AGTTCAATAACTTAAATAAAAACTTTCGAAT
*
3125625 AATTCAATAAC
1 AGTTCAATAAC
3125636 CATTTTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (31 bp):
AGTTCAATAACTTAAATAAAAACTTTCGAAT
Found at i:3126276 original size:22 final size:22
Alignment explanation
Indices: 3126246--3126289 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3126236 TAGTCCTATA
3126246 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
3126268 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
3126290 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:3126335 original size:16 final size:16
Alignment explanation
Indices: 3126313--3126349 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3126303 AATTTTATTT
3126313 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
3126330 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
3126345 TAATA
1 TAATA
3126350 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:3126388 original size:14 final size:14
Alignment explanation
Indices: 3126293--3126401 Score: 50
Period size: 13 Copynumber: 7.6 Consensus size: 14
3126283 AATAAATTAT
3126293 TTAATATTTTAAT-
1 TTAATATTTTAATA
3126306 TT--TATTTTAATA
1 TTAATATTTTAATA
* *
3126318 ATAA-ATTTTAAAA
1 TTAATATTTTAATA
*
3126331 ATAATAATTTTAA-A
1 TTAAT-ATTTTAATA
3126345 -TAATATTATTCACATA
1 TTAATATT-TT-A-ATA
* *
3126361 TTATTGAAAATTTAATA
1 TTA---ATATTTTAATA
3126378 TTAATATTTTAATAA
1 TTAATATTTTAAT-A
*
3126393 TAAATATTT
1 TTAATATTT
3126402 ATTAAAATTA
Statistics
Matches: 75, Mismatches: 7, Indels: 26
0.69 0.06 0.24
Matches are distributed among these distances:
11 9 0.12
12 4 0.05
13 20 0.27
14 10 0.13
15 17 0.23
16 1 0.01
17 8 0.11
18 1 0.01
19 2 0.03
20 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (14 bp):
TTAATATTTTAATA
Found at i:3126400 original size:15 final size:15
Alignment explanation
Indices: 3126371--3126436 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
3126361 TTATTGAAAA
*
3126371 TTTAAT-ATTAATAT
1 TTTAATAATAAATAT
3126385 TTTAATAATAAATATT
1 TTTAATAATAAATA-T
*
3126401 TATTAAAATTATAAATAT
1 T-TT--AATAATAAATAT
* *
3126419 ATTAATAATAAATGT
1 TTTAATAATAAATAT
3126434 TTT
1 TTT
3126437 GTAGTATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.15
15 18 0.44
16 2 0.05
17 4 0.10
18 1 0.02
19 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTAATAATAAATAT
Found at i:3128490 original size:3 final size:3
Alignment explanation
Indices: 3128482--3128523 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3128472 TATTCTTACT
3128482 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3128524 CAAGGTAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3130919 original size:2 final size:2
Alignment explanation
Indices: 3130914--3130945 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3130904 TACACGTAAT
3130914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3130946 GGTCAAATTC
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):
TA
Found at i:3131127 original size:18 final size:18
Alignment explanation
Indices: 3131101--3131135 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3131091 TCGGATCACC
*
3131101 TTTGTTTTAATAAAACAT
1 TTTGGTTTAATAAAACAT
*
3131119 TTTGGTTTACTAAAACA
1 TTTGGTTTAATAAAACA
3131136 ACATTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (18 bp):
TTTGGTTTAATAAAACAT
Found at i:3132949 original size:3 final size:3
Alignment explanation
Indices: 3132941--3132981 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3132931 CTACTTTAAT
3132941 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3132982 GTAGCACCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3133803 original size:64 final size:64
Alignment explanation
Indices: 3133730--3133939 Score: 149
Period size: 64 Copynumber: 3.2 Consensus size: 64
3133720 CTGGGCTAGA
* *
3133730 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
3133794 GCCCATTTCAAAATAC-ATGCAACATCAATAACATATGCAAGCCC--ATTTGGGTAACAGTGGTA
1 GCCCATTTCAGATTACAAT--AA-A-CTAGGCCTTA-GC---CCCTTATTCAGATAACA---GTA
* *
3133856 CTGGGCCA-AA
55 -TGGCCCATAG
*
3133866 GCCCTTTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
3133930 GCCCATTTCA
1 GCCCATTTCA
3133940 AAATACATGC
Statistics
Matches: 102, Mismatches: 28, Indels: 32
0.63 0.17 0.20
Matches are distributed among these distances:
63 8 0.08
64 26 0.25
65 5 0.05
66 1 0.01
67 13 0.13
68 4 0.04
69 14 0.14
70 1 0.01
71 5 0.05
72 17 0.17
73 8 0.08
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTAGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:3133940 original size:136 final size:137
Alignment explanation
Indices: 3133696--3133981 Score: 511
Period size: 136 Copynumber: 2.1 Consensus size: 137
3133686 TATTGGGCCT
** * * *
3133696 AAGCCCATTCAGGTAACAGTGGTACTGGGCTAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTAGGCCTT
3133761 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
3133825 CATATGC
131 CATATGC
3133832 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTAGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTAGGCCTT
*
3133897 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
3133962 CATATGC
131 CATATGC
3133969 AAGCCCATTTGGG
1 AAGCCCATTTGGG
3133982 GAGACTACTC
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 121 0.85
137 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTAGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:3134265 original size:25 final size:27
Alignment explanation
Indices: 3134228--3134281 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
3134218 TCAAACATGC
3134228 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
3134254 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
3134280 AT
1 AT
3134282 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:3135793 original size:26 final size:26
Alignment explanation
Indices: 3135757--3135864 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
3135747 CATGAAATTC
3135757 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3135783 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3135809 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
3135835 TTATCATG-AA-ATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3135859 TTATCA
1 TTATCA
3135865 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
24 20 0.25
25 2 0.03
26 58 0.73
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3135875 original size:10 final size:10
Alignment explanation
Indices: 3135860--3135884 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3135850 CCTAACCTAT
3135860 TATCAATTTG
1 TATCAATTTG
3135870 TATCAATTTG
1 TATCAATTTG
3135880 TATCA
1 TATCA
3135885 CCATAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (10 bp):
TATCAATTTG
Found at i:3136206 original size:3 final size:3
Alignment explanation
Indices: 3136198--3136235 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3136188 GGGCGTTACA
3136198 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3136236 GTGTTGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3136412 original size:23 final size:23
Alignment explanation
Indices: 3136319--3136415 Score: 51
Period size: 23 Copynumber: 4.2 Consensus size: 23
3136309 CAAATGTGTC
*
3136319 TATATTATGTATTATTTTATGTATA
1 TATATTATGTACTATTTTA--TATA
* **
3136344 TATATATATTTA-TACGTTATATA
1 TATAT-TATGTACTATTTTATATA
* * *
3136367 TACTTTTA-ATACTATATT-T-TA
1 TA-TATTATGTACTATTTTATATA
3136388 TATATTATGTA-TATTTTAGTATA
1 TATATTATGTACTATTTTA-TATA
3136411 TATAT
1 TATAT
3136416 ATATTTGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
20 9 0.16
21 6 0.11
22 4 0.07
23 19 0.35
24 2 0.04
25 10 0.18
26 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
TATATTATGTACTATTTTATATA
Found at i:3136635 original size:21 final size:19
Alignment explanation
Indices: 3136599--3136642 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3136589 CTACGTTCTA
*
3136599 TATATATTTTTATATTATG
1 TATATATTTTAATATTATG
3136618 TATATATTTTAA-ATTAT-
1 TATATATTTTAATATTATG
3136635 TATATATT
1 TATATATT
3136643 AAGTATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 5 0.21
19 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATATATTTTAATATTATG
Found at i:3136638 original size:17 final size:18
Alignment explanation
Indices: 3136599--3136642 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3136589 CTACGTTCTA
*
3136599 TATATATTTTTATATTATG
1 TATATA-TTTTAAATTATG
3136618 TATATATTTTAAATTAT-
1 TATATATTTTAAATTATG
3136635 TATATATT
1 TATATATT
3136643 AAGTATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 10 0.42
19 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATATATTTTAAATTATG
Found at i:3136769 original size:15 final size:14
Alignment explanation
Indices: 3136738--3136781 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
3136728 GTTTCTAGTA
*
3136738 TATGTATATATTA-
1 TATGTATTTATTAT
3136751 TATGTATTTATATAT
1 TATGTATTTAT-TAT
3136766 TATGTATATTATTAT
1 TATGTAT-TTATTAT
3136781 T
1 T
3136782 TTTATCATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 11 0.41
16 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATGTATTTATTAT
Found at i:3136775 original size:17 final size:17
Alignment explanation
Indices: 3136735--3136775 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3136725 GTCGTTTCTA
*
3136735 GTATATGTATATATTAT
1 GTATATTTATATATTAT
* *
3136752 ATGTATTTATATATTAT
1 GTATATTTATATATTAT
3136769 GTATATT
1 GTATATT
3136776 ATTATTTTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (17 bp):
GTATATTTATATATTAT
Found at i:3137131 original size:3 final size:3
Alignment explanation
Indices: 3137123--3137158 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3137113 TATCTTTTCC
* *
3137123 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3137159 GTATACGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3138538 original size:26 final size:26
Alignment explanation
Indices: 3138516--3138573 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
3138506 GGAAAAAAAG
*
3138516 TTTAAAACAAATAATATGTAAAATAA
1 TTTAAAACAAATAATATATAAAATAA
* *
3138542 TTTAAGATAAATAATATAT-AAATGAA
1 TTTAAAACAAATAATATATAAAAT-AA
3138568 TTTAAA
1 TTTAAA
3138574 GTAAATGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
TTTAAAACAAATAATATATAAAATAA
Found at i:3138589 original size:26 final size:25
Alignment explanation
Indices: 3138524--3138589 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
3138514 AGTTTAAAAC
3138524 AAATAATATGTAAAATAATTTAAGAT
1 AAATAATATGT-AAATAATTTAAGAT
*
3138550 AAATAATATATAAATGAATTTAA-AGT
1 AAATAATATGTAAAT-AATTTAAGA-T
**
3138576 AAATGTTATGTAAA
1 AAATAATATGTAAA
3138590 AAGAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (25 bp):
AAATAATATGTAAATAATTTAAGAT
Found at i:3138749 original size:26 final size:26
Alignment explanation
Indices: 3138712--3138834 Score: 119
Period size: 26 Copynumber: 4.8 Consensus size: 26
3138702 AATTAATGTA
3138712 AATA-ATAAAACAATTTAAAATGAAT
1 AATACATAAAACAATTTAAAATGAAT
* *
3138737 AATACATAAAACAAAATTAAAATAAAT
1 AATACATAAAAC-AATTTAAAATGAAT
* * * *
3138764 AATATACAAAACAATTTAAAGTGTAT
1 AATACATAAAACAATTTAAAATGAAT
* * *
3138790 AGTATATAAAATAATTTAAAAT-AAT
1 AATACATAAAACAATTTAAAATGAAT
3138815 -ATATC-TAAAACAATTTAAAA
1 AATA-CATAAAACAATTTAAAA
3138835 CAGTTTAATG
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
24 16 0.20
25 6 0.08
26 35 0.44
27 22 0.28
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (26 bp):
AATACATAAAACAATTTAAAATGAAT
Found at i:3138764 original size:27 final size:26
Alignment explanation
Indices: 3138712--3138777 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
3138702 AATTAATGTA
* *
3138712 AATAATAAAAC-AATTTAAAATGAAT
1 AATAATAAAACAAAATTAAAATAAAT
3138737 AATACATAAAACAAAATTAAAATAAAT
1 AATA-ATAAAACAAAATTAAAATAAAT
*
3138764 AATATACAAAACAA
1 AATA-ATAAAACAA
3138778 TTTAAAGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 4 0.11
26 7 0.20
27 24 0.69
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (26 bp):
AATAATAAAACAAAATTAAAATAAAT
Found at i:3138799 original size:53 final size:50
Alignment explanation
Indices: 3138687--3138834 Score: 140
Period size: 53 Copynumber: 2.9 Consensus size: 50
3138677 TTTGAAATTG
* * ** *
3138687 ATAATATATGAAAAAAATTAATGTAA-ATA-ATAAAACAATTTAAAATGA
1 ATAATACATAAAAAAAATTAAAATAATATATCTAAAACAATTTAAAATGA
* *
3138735 ATAATACATAAAACAAAATTAAAATAAATAATATAC-AAAACAATTTAAAGTGT
1 ATAATACATAAAA-AAAATTAAAAT-AAT-ATAT-CTAAAACAATTTAAAATGA
* * * *
3138788 ATAGTATATAAAATAATTTAAAATAATATATCTAAAACAATTTAAAA
1 ATAATACATAAAAAAAATTAAAATAATATATCTAAAACAATTTAAAA
3138835 CAGTTTAATG
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
48 11 0.14
49 10 0.12
50 19 0.23
51 3 0.04
52 12 0.15
53 26 0.32
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (50 bp):
ATAATACATAAAAAAAATTAAAATAATATATCTAAAACAATTTAAAATGA
Found at i:3142870 original size:26 final size:26
Alignment explanation
Indices: 3142835--3142942 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3142825 TGAAATTCCC
3142835 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
3142861 ATCATAGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
3142887 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
3142913 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
3142939 ATCA
1 ATCA
3142943 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Done.