Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 164 of 189
Found at i:49252919 original size:15 final size:15
Alignment explanation
Indices: 49252901--49252958 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
49252891 AAAAAAGTAA
*
49252901 AATTTTTAAAATTAT
1 AATTTTGAAAATTAT
* *
49252916 AATTTTGAAAAATAA
1 AATTTTGAAAATTAT
*
49252931 AATTTTTTTAAAATTAT
1 AA--TTTTGAAAATTAT
49252948 AATTTTGAAAA
1 AATTTTGAAAA
49252959 ATAAAAAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 22 0.65
17 12 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTTTGAAAATTAT
Found at i:49252927 original size:16 final size:16
Alignment explanation
Indices: 49252908--49252960 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
49252898 TAAAATTTTT
49252908 AAAATTATAATTTTGA
1 AAAATTATAATTTTGA
* **
49252924 AAAA-TAAAATTTTTTT
1 AAAATTATAA-TTTTGA
49252940 AAAATTATAATTTTGA
1 AAAATTATAATTTTGA
49252956 AAAAT
1 AAAAT
49252961 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
AAAATTATAATTTTGA
Found at i:49252927 original size:32 final size:32
Alignment explanation
Indices: 49252891--49252964 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 32
49252881 CATATTAAAA
49252891 AAAAAAGTAAAA-TTTTTAAAATTATAATTTTG
1 AAAAAA-TAAAATTTTTTAAAATTATAATTTTG
49252923 -AAAAATAAAATTTTTTTAAAATTATAATTTTG
1 AAAAAATAAAA-TTTTTTAAAATTATAATTTTG
49252955 -AAAAATAAAA
1 AAAAAATAAAA
49252965 AATTATTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
30 5 0.12
31 5 0.12
32 30 0.75
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (32 bp):
AAAAAATAAAATTTTTTAAAATTATAATTTTG
Found at i:49252943 original size:17 final size:17
Alignment explanation
Indices: 49252918--49252964 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
49252908 AAAATTATAA
49252918 TTTTGAAAAATAAAATT
1 TTTTGAAAAATAAAATT
* * *
49252935 TTTTTAAAATTATAA--
1 TTTTGAAAAATAAAATT
49252950 TTTTGAAAAATAAAA
1 TTTTGAAAAATAAAA
49252965 AATTATTTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 12 0.50
17 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TTTTGAAAAATAAAATT
Found at i:49253015 original size:20 final size:19
Alignment explanation
Indices: 49252987--49253031 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
49252977 ATTTTTTAAA
* * *
49252987 AAAATTAAATAAAATTTTT
1 AAAATTAAAAAAAAATTCT
49253006 AAAATATAAAAAAAAATTCT
1 AAAAT-TAAAAAAAAATTCT
49253026 AAAATT
1 AAAATT
49253032 TAATGTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAAAAAAAATTCT
Found at i:49253021 original size:21 final size:22
Alignment explanation
Indices: 49252979--49253023 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
49252969 ATTTCATAAT
* *
49252979 TTTTTAAAAAAATTAAATAAAA
1 TTTTTAAAAAAATAAAAAAAAA
*
49253001 TTTTT-AAAATATAAAAAAAAA
1 TTTTTAAAAAAATAAAAAAAAA
49253022 TT
1 TT
49253024 CTAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTTAAAAAAATAAAAAAAAA
Found at i:49253201 original size:25 final size:25
Alignment explanation
Indices: 49253173--49253223 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
49253163 TGACTTGACT
49253173 AGTTCAAAGCAAAT-AAATTATAAAA
1 AGTTCAAAG-AAATAAAATTATAAAA
**
49253198 AGTTCAAAGTTATAAAATTATAAAA
1 AGTTCAAAGAAATAAAATTATAAAA
49253223 A
1 A
49253224 TAAATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (25 bp):
AGTTCAAAGAAATAAAATTATAAAA
Found at i:49253379 original size:25 final size:20
Alignment explanation
Indices: 49253327--49253371 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
49253317 TTTTTAGCCC
49253327 TCAATATTTACATTTTTTTG
1 TCAATATTTACATTTTTTTG
49253347 TCAATATTTACATTTTTTTG
1 TCAATATTTACATTTTTTTG
49253367 TCAAT
1 TCAAT
49253372 CCAATATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (20 bp):
TCAATATTTACATTTTTTTG
Found at i:49257010 original size:23 final size:23
Alignment explanation
Indices: 49256980--49257038 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
49256970 AATCTCTTTA
49256980 GTTTCACTTGATTGTTCTACTAT
1 GTTTCACTTGATTGTTCTACTAT
* ** *
49257003 GTTTCACTTAATTGTTCTGTTGT
1 GTTTCACTTGATTGTTCTACTAT
*
49257026 GTTCCACTTGATT
1 GTTTCACTTGATT
49257039 TCTAAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (23 bp):
GTTTCACTTGATTGTTCTACTAT
Found at i:49259425 original size:72 final size:72
Alignment explanation
Indices: 49259310--49259446 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
49259300 CCAAACAAAT
* * * *
49259310 ATTAAAATTAAATAAAATCTATTTCAGGGTTTGTTCTCACCGTTTAACAGATTTTATTCGATTTT
1 ATTAAAAGTAAATAAAATCTATTTCAGGGTTTATTCTCACCGTTCAACAGATTTTATTCAATTTT
49259375 GTTTGAA
66 GTTTGAA
* * *
49259382 ATTAAAAGTAAATAAAATCTGTTTC-GGGATTTATTC-CTGCCGTTCAACGGATTTTATTCAATT
1 ATTAAAAGTAAATAAAATCTATTTCAGGG-TTTATTCTC-ACCGTTCAACAGATTTTATTCAATT
49259445 TT
64 TT
49259447 TATTTTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 4 0.07
72 52 0.93
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (72 bp):
ATTAAAAGTAAATAAAATCTATTTCAGGGTTTATTCTCACCGTTCAACAGATTTTATTCAATTTT
GTTTGAA
Found at i:49259681 original size:90 final size:89
Alignment explanation
Indices: 49259382--49259960 Score: 539
Period size: 84 Copynumber: 6.7 Consensus size: 89
49259372 TTTGTTTGAA
* * * *
49259382 ATTAAAAGT-AAATAAAATCTGTTTCGGGATTTATTCCTGCCGTTCAACGGATTTTATT-CAATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCAATT
* ** *
49259445 TTTATTTTATTTCCAAAAGGGA-A
66 TTGATTTTATTTCCAAAAACGAGT
* * * * *
49259468 ATTAAAGTT-AAATAAATTCTGTTTCGGGATTTATTCCCGTCGTTCAACAAATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCAATT
*
49259532 TTGATTTTATTTCC-AAAACGAGC
66 TTGATTTTATTTCCAAAAACGAGT
* * *
49259555 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTGTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCAATT
49259620 TTGATTTTATTTCCAAAAAACGAGT
66 TTGATTTTATTTCC-AAAAACGAGT
* * *
49259645 ATTAAAATTAAAATAAAATCTGTTTTGAGATTTATTCCTGCTGTTCAACAGATTTTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCAATT
* *
49259710 TTGATTTTATTTCTAAAAACAAGT
66 TTGATTTTATTTCCAAAAACGAGT
** * * * **
49259734 ATTAAAATTAAAATAAAATCTGTTTCAGAATTTATTCCCGCCGTTTAACAAGATCTTATT-TGA-
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAAC-AGATTTTATTCCAAT
* **
49259797 TTTGATTTTGTTTCCAATTTA-GA--
65 TTTGATTTTATTTCCAA-AAACGAGT
* ** * * * * * **
49259820 ATT-AAATT-AAATTAAATCTGTTCCGAGATCTATTCCCGCCATTTAACAATATTTTATT-TGAT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAAC-AGATTTTATTCCAAT
* *
49259882 TTTG-TTTTGTTTCCAAATTA-GA--
65 TTTGATTTTATTTCCAAA-AACGAGT
* * * * *
49259904 ATT-AAATT-ACATTAAATCTGTTTTGGGATTTATTCCCACCGTTTAACAAATTTTATT
1 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATT
49259961 TTGATTTAAT
Statistics
Matches: 423, Mismatches: 61, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
83 9 0.02
84 100 0.24
85 9 0.02
86 59 0.14
87 26 0.06
88 78 0.18
89 53 0.13
90 89 0.21
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (89 bp):
ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTCCAATT
TTGATTTTATTTCCAAAAACGAGT
Found at i:49259704 original size:178 final size:175
Alignment explanation
Indices: 49259382--49259877 Score: 558
Period size: 178 Copynumber: 2.8 Consensus size: 175
49259372 TTTGTTTGAA
* * *
49259382 ATTAAAAGT-AAATAAAATCTGTTTCGGGATTTATTCCTGCCGTTCAACGGATTTTATTCAATTT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTGTATTCAATTT
* ** * * *
49259446 TTATTTTATTTCCAAAAGGGAAATTAAAGTTAAATAAATTCTGTTTCGGGATTTATTCCCGTCGT
66 TGATTTTATTTCCAAAAACGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGT
* *
49259511 TCAACAAATTTTATTCCAATTTTGATTTTATTTC-CAAAACGAGC
131 TCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
* *
49259555 ATTAAAATTAAAATAAAATCTGTTTTGGGATTTATTCCCACCGTTCAACGGATTGTATTCCAATT
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTGTATT-CAATT
* * *
49259620 TTGATTTTATTTCCAAAAAACGAGTATTAAAATTAAAATAAAATCTGTTTTGAGATTTATTCCTG
65 TTGATTTTATTTCC-AAAAACGA-AATTAAAATT-AAATAAAATCTGTTTCGAGATTTATTCCCG
* *
49259685 -CTGTTCAACAGATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGT
127 TC-GTTCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
* * * * **
49259734 ATTAAAATTAAAATAAAATCTGTTTCAGAATTTATTCCCGCCGTTTAACAAGATCT-TATTTGA-
1 ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAAC-GGAT-TGTATTCAAT
* ** * * * *
49259797 TTTGATTTTGTTTCCAATTTA-G-AATT-AAATTAAATTAAATCTGTTCCGAGATCTATTCCCGC
64 TTTGATTTTATTTCCAA-AAACGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGT
* *
49259859 CATTTAACAATATTTTATT
128 CGTTCAACAA-ATTTTATT
49259878 TGATTTTGTT
Statistics
Matches: 273, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
173 39 0.14
174 59 0.22
175 21 0.08
176 6 0.02
177 12 0.04
178 76 0.28
179 52 0.19
180 7 0.03
181 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (175 bp):
ATTAAAATTAAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTGTATTCAATTT
TGATTTTATTTCCAAAAACGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGT
TCAACAAATTTTATTCCAATTTTGATTTTATTTCTAAAAACAAGC
Found at i:49259994 original size:59 final size:59
Alignment explanation
Indices: 49259908--49260020 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
49259898 ATTAGAATTA
* * *
49259908 AATTACATTAAATCTGTTTTGGGATTTATTCCCACCGTTTAACAAATTTTATTTTGATTT
1 AATTACATTAAATCTGTTTTGGGATTTAATCCCACCGTTGAACAAA-ATTATTTTGATTT
* * **
49259968 AATTACA-TAATTTTGTTTTGGGATTTAATCCTGCCGTTGAACAAAATTATTTT
1 AATTACATTAAATCTGTTTTGGGATTTAATCCCACCGTTGAACAAAATTATTTT
49260021 TGAGTTTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 7 0.15
59 32 0.70
60 7 0.15
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (59 bp):
AATTACATTAAATCTGTTTTGGGATTTAATCCCACCGTTGAACAAAATTATTTTGATTT
Found at i:49260039 original size:59 final size:59
Alignment explanation
Indices: 49259922--49260040 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 59
49259912 ACATTAAATC
* * * *
49259922 TGTTTTGGGATTTATTCCCACCGTTTAACAAATTTTATTTTGATTTAATTACATAATTT
1 TGTTTTGGGATTTAATCCCACCGTTGAACAAATTATATTTTGATTTAATTACAAAATTT
** * *
49259981 TGTTTTGGGATTTAATCCTGCCGTTGAACAAAATTAT-TTTTGAGTTT-GTTTCAAAATTT
1 TGTTTTGGGATTTAATCCCACCGTTGAAC-AAATTATATTTTGA-TTTAATTACAAAATTT
49260040 T
1 T
49260041 AATTCTATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 41 0.82
60 9 0.18
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (59 bp):
TGTTTTGGGATTTAATCCCACCGTTGAACAAATTATATTTTGATTTAATTACAAAATTT
Found at i:49272146 original size:18 final size:18
Alignment explanation
Indices: 49272093--49272151 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
49272083 AATGATTGTT
49272093 GAAAAAGAAATG-GTG--
1 GAAAAAGAAATGAGTGAA
*
49272108 GAAAAAGAAA-GAGAGATA
1 GAAAAAGAAATGAGTGA-A
49272126 GAAAAAGAAATGAGTGAA
1 GAAAAAGAAATGAGTGAA
*
49272144 GAACAAGA
1 GAAAAAGA
49272152 GAGCGTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.33
18 18 0.50
19 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAATGAGTGAA
Found at i:49273217 original size:28 final size:30
Alignment explanation
Indices: 49273167--49273232 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
49273157 ATTTGACAAT
* *
49273167 TTTA-ATATAAATTATTCTATTTATATTTTA
1 TTTATATATAAATAATTCTATTTAT-TTATA
49273197 -TTATATATAAATAATT-T-TTTATTTATA
1 TTTATATATAAATAATTCTATTTATTTATA
49273224 TTTATATAT
1 TTTATATAT
49273233 TTTGTTCGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
28 13 0.41
29 4 0.12
30 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTATATATAAATAATTCTATTTATTTATA
Found at i:49275990 original size:27 final size:27
Alignment explanation
Indices: 49275960--49276236 Score: 301
Period size: 27 Copynumber: 10.3 Consensus size: 27
49275950 GTATTGGGCC
* * * *
49275960 TAAAATGATCGAATTACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAAGG
*
49275987 TAAAATGACCGAAATACCCCCGAAAGG
1 TAAAATGACCGAAATACCCTCGAAAGG
*
49276014 TAAAATGACCGAAATACCC-CTAAATGG
1 TAAAATGACCGAAATACCCTCGAAA-GG
* *
49276041 TAAAATGACTGAAATACCCTCAAAAGG
1 TAAAATGACCGAAATACCCTCGAAAGG
*
49276068 TAAAAAGACCGAAATACCCTCGAAAGG
1 TAAAATGACCGAAATACCCTCGAAAGG
*
49276095 TAAAATGACCGAAATACCCTTGAAAGG
1 TAAAATGACCGAAATACCCTCGAAAGG
* * * *
49276122 TAAAATGACTGAATTACCCTTGAATGG
1 TAAAATGACCGAAATACCCTCGAAAGG
* * *
49276149 TAAAATGATCGAATTACCCTC-AAATGA
1 TAAAATGACCGAAATACCCTCGAAA-GG
* *
49276176 TAAAATGACTGAAATATCCTC-AAATGG
1 TAAAATGACCGAAATACCCTCGAAA-GG
** *
49276203 TAAAATGATTGAAATACCC-CGAAGGG
1 TAAAATGACCGAAATACCCTCGAAAGG
49276229 TAAAATGA
1 TAAAATGA
49276237 TTGTTATACC
Statistics
Matches: 219, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.08
27 198 0.90
28 4 0.02
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAAGG
Found at i:49276441 original size:26 final size:26
Alignment explanation
Indices: 49276412--49276483 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
49276402 TTGCTACATA
*
49276412 TACTGTTACTGGCAGCTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCAT
49276438 TACTGTTACTGGCAGCTTTGTTGCAT
1 TACTGTTACTGGCAGCTTTGTTGCAT
* * *
49276464 CACTATTATTGGCAGCTTTG
1 TACTGTTACTGGCAGCTTTG
49276484 CTGTGATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGTTGCAT
Found at i:49276643 original size:28 final size:28
Alignment explanation
Indices: 49276594--49276659 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
49276584 ATTGCATTGT
* **
49276594 ACTGTTACTGTATTGGGTTAAGACCCAC
1 ACTGTTACTGTAATGGACTAAGACCCAC
* *
49276622 ACTGTTATTGTAATGGACTAAGGCCCAC
1 ACTGTTACTGTAATGGACTAAGACCCAC
49276650 ACTG-TACTGT
1 ACTGTTACTGT
49276660 TACTGTATAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (28 bp):
ACTGTTACTGTAATGGACTAAGACCCAC
Found at i:49277896 original size:25 final size:26
Alignment explanation
Indices: 49277848--49277896 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
49277838 TGTTTTAATT
*
49277848 TATTTTAAAGTTATCTTGTTAGTTAC
1 TATTATAAAGTTATCTTGTTAGTTAC
49277874 TATTATAAA-TTAT-TTGTTCAGTT
1 TATTATAAAGTTATCTTGTT-AGTT
49277897 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (26 bp):
TATTATAAAGTTATCTTGTTAGTTAC
Found at i:49281679 original size:49 final size:48
Alignment explanation
Indices: 49281531--49281729 Score: 274
Period size: 48 Copynumber: 4.1 Consensus size: 48
49281521 TCCAAGGTAC
* * *
49281531 CTAATTTATATTACAAAGTATGTTTCTTGTTTTAATGTTGCAATATAT
1 CTAATTTATATTACAAAGTTTGTTCCTTGTTTTAATGTTGCAATGTAT
* * *
49281579 CTAATTTATATTACAAAGTTTGTTCATCGTTTTAATGTTGTAATGTAT
1 CTAATTTATATTACAAAGTTTGTTCCTTGTTTTAATGTTGCAATGTAT
49281627 CTAATTTATATTACAAAGTTTGTTCCTTTGTTTTAATGTTGCAATGTAT
1 CTAATTTATATTACAAAGTTTGTTCC-TTGTTTTAATGTTGCAATGTAT
* * ** *
49281676 CTAATTTATGTTACAAAGTTTATTCCAAGTTTTAATGTTACAAT-TAAT
1 CTAATTTATATTACAAAGTTTGTTCCTTGTTTTAATGTTGCAATGT-AT
49281724 CTAATT
1 CTAATT
49281730 AAACAAATAC
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.01
48 90 0.67
49 44 0.33
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.49
Consensus pattern (48 bp):
CTAATTTATATTACAAAGTTTGTTCCTTGTTTTAATGTTGCAATGTAT
Found at i:49281696 original size:97 final size:96
Alignment explanation
Indices: 49281531--49281714 Score: 289
Period size: 97 Copynumber: 1.9 Consensus size: 96
49281521 TCCAAGGTAC
*
49281531 CTAATTTATATTACAAAGTATGTTTCTTGTTTTAATGTTGCAATATATCTAATTTATATTACAAA
1 CTAATTTATATTACAAAGTATGTTCCTTGTTTTAATGTTGCAATATATCTAATTTATATTACAAA
* *
49281596 GTTTGTT-CATCGTTTTAATGTTGTAATGTAT
66 GTTTATTCCA-AGTTTTAATGTTGTAATGTAT
* * *
49281627 CTAATTTATATTACAAAGTTTGTTCCTTTGTTTTAATGTTGCAATGTATCTAATTTATGTTACAA
1 CTAATTTATATTACAAAGTATGTTCC-TTGTTTTAATGTTGCAATATATCTAATTTATATTACAA
49281692 AGTTTATTCCAAGTTTTAATGTT
65 AGTTTATTCCAAGTTTTAATGTT
49281715 ACAATTAATC
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 24 0.30
97 54 0.68
98 2 0.03
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.50
Consensus pattern (96 bp):
CTAATTTATATTACAAAGTATGTTCCTTGTTTTAATGTTGCAATATATCTAATTTATATTACAAA
GTTTATTCCAAGTTTTAATGTTGTAATGTAT
Found at i:49283820 original size:12 final size:12
Alignment explanation
Indices: 49283803--49283827 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49283793 CTAAATGTGA
49283803 TACAATAAATTT
1 TACAATAAATTT
49283815 TACAATAAATTT
1 TACAATAAATTT
49283827 T
1 T
49283828 CATTACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TACAATAAATTT
Found at i:49284445 original size:31 final size:31
Alignment explanation
Indices: 49284392--49284463 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
49284382 AACCCCGAAT
*
49284392 ACAACCTCTTAATTTTTTTCAAACACTAAAC
1 ACAACCTCTTAATTTTTTTCAAACACCAAAC
**
49284423 ACAACC-C-TAATTCTTTTCTCAAATTCCAAAC
1 ACAACCTCTTAATT-TTTT-TCAAACACCAAAC
49284454 ACAACCTCTT
1 ACAACCTCTT
49284464 CTCCTTCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.15
30 5 0.15
31 22 0.65
32 1 0.03
33 1 0.03
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (31 bp):
ACAACCTCTTAATTTTTTTCAAACACCAAAC
Found at i:49284499 original size:14 final size:14
Alignment explanation
Indices: 49284460--49284506 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
49284450 AAACACAACC
49284460 TCTTCTCCTTCCTTTT
1 TCTTCT-CTTCC-TTT
*
49284476 TCTCCT-TTCCTTT
1 TCTTCTCTTCCTTT
*
49284489 TCTTCTCTTCCATT
1 TCTTCTCTTCCTTT
49284503 TCTT
1 TCTT
49284507 TTCCTTCCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 8 0.30
14 14 0.52
16 5 0.19
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTCTCTTCCTTT
Found at i:49290439 original size:15 final size:15
Alignment explanation
Indices: 49290421--49290450 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49290411 TATTTACATG
*
49290421 TGATAAATTTTTTAT
1 TGATAAATTTATTAT
49290436 TGATAAATTTATTAT
1 TGATAAATTTATTAT
49290451 AACATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TGATAAATTTATTAT
Found at i:49291337 original size:29 final size:31
Alignment explanation
Indices: 49291283--49291365 Score: 107
Period size: 31 Copynumber: 2.6 Consensus size: 31
49291273 AATCTTAAAA
*
49291283 TTATATATGAACTTTAATTTAATATGT-AATT
1 TTATATATGAATTTTAATTT-ATATGTAAATT
*
49291314 TTATACATGAATTTTAATTT-TATGTAAATT
1 TTATATATGAATTTTAATTTATATGTAAATT
49291344 TATATATATGAATTTTTAATTT
1 T-TATATATGAA-TTTTAATTT
49291366 GATTCAATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.11
30 5 0.11
31 27 0.59
32 9 0.20
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (31 bp):
TTATATATGAATTTTAATTTATATGTAAATT
Found at i:49293387 original size:27 final size:28
Alignment explanation
Indices: 49293336--49293408 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
49293326 TTTTGGGTTT
*
49293336 TTTACAAAAATAT-TATAACTTTTTTTTA
1 TTTACCAAAATATATA-AACTTTTTTTTA
*
49293364 TTTATCAAAATATATAAAC-TTTTTTTA
1 TTTACCAAAATATATAAACTTTTTTTTA
*
49293391 TTTGCCAAAATATATAAA
1 TTTACCAAAATATATAAA
49293409 AAAAAACCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 24 0.60
28 14 0.35
29 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.48
Consensus pattern (28 bp):
TTTACCAAAATATATAAACTTTTTTTTA
Found at i:49293511 original size:27 final size:27
Alignment explanation
Indices: 49293481--49293547 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
49293471 CGCCAATGGT
49293481 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
49293508 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
49293535 ATTGGCGGCACCA
1 ATTGGCGGCACCA
49293548 GTTGGTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:49293617 original size:26 final size:26
Alignment explanation
Indices: 49293588--49293705 Score: 84
Period size: 29 Copynumber: 4.3 Consensus size: 26
49293578 CAGAAGGAGG
49293588 GAAAGAAAAAAAGA-AAGGAAAGGAAA
1 GAAAGAAAAAAAGAGAA-GAAAGGAAA
49293614 GAAAGAAAAGGAAAGGAGAAGAGAAGAGAAA
1 GAAAGAAAA--AAA-GAGAAGA-AAG-GAAA
*
49293645 -AAAGGAAAGAAAGAAGAAGAAAAGGAGAA
1 GAAA-GAAAAAAAG-AGAAG-AAAGGA-AA
*
49293674 GAGAAG-AAAAAAGA-AAGAAA-GAAG
1 GA-AAGAAAAAAAGAGAAGAAAGGAAA
49293698 GAAAGAAA
1 GAAAGAAA
49293706 GGGAAAGGAG
Statistics
Matches: 76, Mismatches: 3, Indels: 28
0.71 0.03 0.26
Matches are distributed among these distances:
23 3 0.04
24 5 0.07
25 2 0.03
26 12 0.16
27 3 0.04
28 7 0.09
29 23 0.30
30 11 0.14
31 10 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (26 bp):
GAAAGAAAAAAAGAGAAGAAAGGAAA
Found at i:49293650 original size:39 final size:40
Alignment explanation
Indices: 49293606--49293742 Score: 164
Period size: 39 Copynumber: 3.5 Consensus size: 40
49293596 AAAAGAAAGG
49293606 AAAGGAAAGAAAGAA-AAGGAAAGGAGAAGAGAAGAGAAA
1 AAAGGAAAGAAAGAAGAAGGAAAGGAGAAGAGAAGAGAAA
*
49293645 AAAGGAAAGAAAGAAGAAGAAAAGGAGAAGAG-A-AGAAA
1 AAAGGAAAGAAAGAAGAAGGAAAGGAGAAGAGAAGAGAAA
*
49293683 AAA-GAAAGAAAGAAGGAAAGAAAGG-GAAAGGAGAAGAGAAA
1 AAAGGAAAGAAAGAA-GAAGGAAAGGAG-AA-GAGAAGAGAAA
*
49293724 AAA--AAAG-AAGAAGAGGGAA
1 AAAGGAAAGAAAGAAGAAGGAA
49293743 GAAAGGAAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
37 12 0.14
38 23 0.26
39 24 0.28
40 20 0.23
41 8 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (40 bp):
AAAGGAAAGAAAGAAGAAGGAAAGGAGAAGAGAAGAGAAA
Found at i:49293666 original size:45 final size:44
Alignment explanation
Indices: 49293588--49293730 Score: 149
Period size: 44 Copynumber: 3.3 Consensus size: 44
49293578 CAGAAGGAGG
*
49293588 GAAAGAAAAAAAGAAAGGAAAGGAAAGAAAGAAAAGGAAAGGAGAAGA
1 GAAAGAAAAAAGGAAA-GAAA-G-AAG-AAGAAAAGGAAAGGAGAAGA
49293636 GAAGAGAAAAAAGGAAAGAAAGAAGAAG---A--AAAGGAGAAGA
1 GAA-AGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGA
*
49293676 G-AAGAAAAAA-GAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGA
1 GAAAGAAAAAAGGAAAGAAAGAA-G-AAGAAAAGGAAAGGAGAAGA
49293720 GAAA-AAAAAAG
1 GAAAGAAAAAAG
49293731 AAGAAGAGGG
Statistics
Matches: 83, Mismatches: 2, Indels: 23
0.77 0.02 0.21
Matches are distributed among these distances:
37 11 0.13
38 9 0.11
39 4 0.05
40 12 0.14
42 1 0.01
44 18 0.22
45 5 0.06
46 3 0.04
47 1 0.01
48 7 0.08
49 12 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (44 bp):
GAAAGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGA
Found at i:49293730 original size:18 final size:18
Alignment explanation
Indices: 49293625--49293738 Score: 68
Period size: 18 Copynumber: 5.7 Consensus size: 18
49293615 AAAGAAAAGG
49293625 AAAGGAGAAGAGAAGAGAAA
1 AAAGGAGAAGAGAA-A-AAA
*
49293645 AAAGGA-AAGAAAGAAGAAGA
1 AAAGGAGAAG--AGAA-AAAA
*
49293665 AAAGGAGAAGAGAAGAAA
1 AAAGGAGAAGAGAAAAAA
*
49293683 AAAGAAAGAAAGAAGGAAAGAAA
1 AAAG-GAG-AAG-A-GAAA-AAA
49293706 GGGAAAGGAGAAGAGAAAAAA
1 ---AAAGGAGAAGAGAAAAAA
*
49293727 AAAGAAGAAGAG
1 AAAGGAGAAGAG
49293739 GGAAGAAAGG
Statistics
Matches: 76, Mismatches: 7, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
18 17 0.22
19 9 0.12
20 17 0.22
21 13 0.17
22 7 0.09
23 4 0.05
24 3 0.04
25 2 0.03
26 4 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGGAGAAGAGAAAAAA
Found at i:49293794 original size:19 final size:19
Alignment explanation
Indices: 49293770--49293807 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49293760 GGAAAAAGGT
49293770 AATTTTATTTATAA-ATTTG
1 AATTTT-TTTATAATATTTG
*
49293789 AATTTTTTTGTAATATTTG
1 AATTTTTTTATAATATTTG
49293808 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AATTTTTTTATAATATTTG
Found at i:49300130 original size:26 final size:26
Alignment explanation
Indices: 49300081--49300133 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
49300071 ACACACTAAA
* *
49300081 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
49300107 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
49300133 A
1 A
49300134 CACACTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:49300185 original size:62 final size:61
Alignment explanation
Indices: 49300053--49300165 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 61
49300043 TTTTTAAAAA
** *
49300053 AATT-ATACTCAAAATAATACACACTAAAATTATTAATTTTATACTACGAATAATATTAAT
1 AATTAATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAAAAATATTAAT
* *
49300113 AATTTTATACTCAAAATAATACACACTTAAATTATTAATTTT-T-CTAAAAAAAA
1 AA-TTAATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAAAAA
49300166 CTAACTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 9 0.19
61 3 0.06
62 35 0.74
ACGTcount: A:0.50, C:0.12, G:0.01, T:0.37
Consensus pattern (61 bp):
AATTAATACTCAAAATAATACACACTAAAATTATTAATTTTATACTAAAAAAAATATTAAT
Found at i:49300320 original size:3 final size:3
Alignment explanation
Indices: 49300312--49300337 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49300302 TCTTCATACT
49300312 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
49300338 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:49300434 original size:19 final size:21
Alignment explanation
Indices: 49300410--49300448 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
49300400 ACTAAAACAA
*
49300410 AAAATATTAA-AA-AATATAC
1 AAAATAATAACAACAATATAC
49300429 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
49300449 ATCAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:49307913 original size:262 final size:262
Alignment explanation
Indices: 49307448--49307952 Score: 947
Period size: 262 Copynumber: 1.9 Consensus size: 262
49307438 GGAAGACATC
*
49307448 TTCAAACTCTGCTAATAGTTGTTGAAAGTCTTCAATGATAACCTACTTAGTCAGTGTTAAAAGTT
1 TTCAAACTCTGCTAATAGTTGTTGAAAGTCTTCAATGATAACCTACTTAGTCAGTGTTAAAAGTG
*
49307513 TCTATTTTCTATTGGTAATGAAACACCCCATATCTGACCTGATCATCGGATTCGAACTGCAAGAT
66 TCTATTTTCTATTGGTAATGAAACACCCCATATCTGACCTGATCATCGGATTCGAACTACAAGAT
49307578 ACTACTTTCAATTATCCAAAATTAATATTCACTGAGTACAAGTATTACGGAAACCAAAAGTCATC
131 ACTACTTTCAATTATCCAAAATTAATATTCACTGAGTACAAGTATTACGGAAACCAAAAGTCATC
*
49307643 AATTTAACCTTGCAATATTCATGATTTTACTTACAATTATATACTTTGCTAATAGTTGTTAAAAG
196 AATTTAACCTTGCAATATTCATGAATTTACTTACAATTATATACTTTGCTAATAGTTGTTAAAAG
49307708 TA
261 TA
49307710 TTCAAACTCTGCTAATAGTTGTTGAAAGTCTTCAATGATAACCTACTTAGTCAGTGTTAAAAGTG
1 TTCAAACTCTGCTAATAGTTGTTGAAAGTCTTCAATGATAACCTACTTAGTCAGTGTTAAAAGTG
* *
49307775 TCTATTTTCTATTGGTAATGAAACACCCCATATCTGACCTGATCATCGGATTTGGACTACAAGAT
66 TCTATTTTCTATTGGTAATGAAACACCCCATATCTGACCTGATCATCGGATTCGAACTACAAGAT
49307840 ACTACTTTCAATTATCCAAAATTAATATTCACTGAGTACAAGTATTACGGAAACCAAAAGTCATC
131 ACTACTTTCAATTATCCAAAATTAATATTCACTGAGTACAAGTATTACGGAAACCAAAAGTCATC
* *
49307905 GATTTAACCTTGCAATATTCATGAATTTACTTCCAATTATATACTTTG
196 AATTTAACCTTGCAATATTCATGAATTTACTTACAATTATATACTTTG
49307953 ATCTAATATA
Statistics
Matches: 236, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
262 236 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (262 bp):
TTCAAACTCTGCTAATAGTTGTTGAAAGTCTTCAATGATAACCTACTTAGTCAGTGTTAAAAGTG
TCTATTTTCTATTGGTAATGAAACACCCCATATCTGACCTGATCATCGGATTCGAACTACAAGAT
ACTACTTTCAATTATCCAAAATTAATATTCACTGAGTACAAGTATTACGGAAACCAAAAGTCATC
AATTTAACCTTGCAATATTCATGAATTTACTTACAATTATATACTTTGCTAATAGTTGTTAAAAG
TA
Found at i:49309225 original size:28 final size:28
Alignment explanation
Indices: 49309191--49309277 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
49309181 AAATCCAACT
*
49309191 TATAAGATAATCCTGACAGATTTCCATA
1 TATAAGATAATCTTGACAGATTTCCATA
* * *
49309219 TATAAGATAATCTTGACAAACTTCCACA
1 TATAAGATAATCTTGACAGATTTCCATA
*
49309247 TATAAGATAATCTTGGCAGACTTT-CATA
1 TATAAGATAATCTTGACAGA-TTTCCATA
49309275 TAT
1 TAT
49309278 CTTTCATAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
28 48 0.96
29 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (28 bp):
TATAAGATAATCTTGACAGATTTCCATA
Found at i:49319433 original size:94 final size:93
Alignment explanation
Indices: 49319381--49319596 Score: 261
Period size: 94 Copynumber: 2.3 Consensus size: 93
49319371 GTTTATTATT
* * * * *
49319381 TTTTAAGAAAAAATCAATTAAATTAGAGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTA
1 TTTTAAGAAAAAATCAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATT-ATAAATTTTA
49319446 AAAATCAAATTAGGGTTTAGAGTTAAGGG
65 AAAATCAAATTAGGGTTTAGAGTTAAGGG
* *
49319475 TTTTAAGGAAAAATCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTTA
1 TTTTAAGAAAAAATCAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAA-TTTTA
* ** * * *
49319540 ATAAATTAGTTTAGGGTTTAGTGTTTAGGAT
65 A-AAATCAAATTAGGGTTTAGAGTTAAGG-G
49319571 TTTTAAGAAAAAAACTCAAATAAATT
1 TTTTAAG-AAAAAA-TCAAATAAATT
49319597 TGGGTTTGGG
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
93 4 0.04
94 54 0.52
95 22 0.21
96 7 0.07
97 5 0.05
98 11 0.11
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (93 bp):
TTTTAAGAAAAAATCAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTAA
AAATCAAATTAGGGTTTAGAGTTAAGGG
Found at i:49320069 original size:126 final size:126
Alignment explanation
Indices: 49319643--49320069 Score: 660
Period size: 126 Copynumber: 3.4 Consensus size: 126
49319633 TTGTTAATTT
* * *
49319643 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTATG-TCTTGAGAAAATAATTTCGAGTAGA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTA-GCCCCTGAAAAAATAATTTCGAGTAGA
* * * *
49319707 CGTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGAATGATGTTTTGTCAGCAGAAGTATTG
65 CGTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
49319769 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAACAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
*
49319834 GTTTCTGAGAAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
** * * * * *
49319895 AAAGAAGCTCCCACGTGGACTTGCTTTTTCTACAGTTGCCCCTAAAAAAATAATTTTGAATAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
* *
49319960 GTTTCTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAATACTG
66 GTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
49320021 AAAGAAGCTCCCACGTGGA-GCGCTTTTGCTACAGTAACCCCTGAAAAAA
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAA
49320070 CTCCCACGCG
Statistics
Matches: 274, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
125 25 0.09
126 249 0.91
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:49320074 original size:42 final size:44
Alignment explanation
Indices: 49320018--49320099 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 44
49320008 AGCAGAAATA
* * *
49320018 CTGAAAGAAGCTCCCACGTGGA-GCGCTTTTGCTACAGTAACCC
1 CTGAAAGAAACTCCCACGCGGACGCACTTTTGCTACAGTAACCC
49320061 CTGAAA-AAACTCCCACGCGGACGCACTTTTGCTACAGTA
1 CTGAAAGAAACTCCCACGCGGACGCACTTTTGCTACAGTA
49320100 GCGCATAGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 13 0.37
43 22 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (44 bp):
CTGAAAGAAACTCCCACGCGGACGCACTTTTGCTACAGTAACCC
Found at i:49323536 original size:21 final size:21
Alignment explanation
Indices: 49323498--49323542 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
49323488 TTGTCCAGCT
* * * *
49323498 TCCAGCGGGGGTTGTGGTTGC
1 TCCAGCGAGGATTCTGGTTCC
49323519 TCCAGCGAGGATTCTGGTTCC
1 TCCAGCGAGGATTCTGGTTCC
49323540 TCC
1 TCC
49323543 GGTAGGGGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.27, G:0.36, T:0.29
Consensus pattern (21 bp):
TCCAGCGAGGATTCTGGTTCC
Found at i:49325454 original size:24 final size:25
Alignment explanation
Indices: 49325417--49325464 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
49325407 AATATTTACG
49325417 ATTTAAAAAATTTTTTAAAAATAAA
1 ATTTAAAAAATTTTTTAAAAATAAA
*
49325442 ATTT-AAAACTTTTTTAAAAATAA
1 ATTTAAAAAATTTTTTAAAAATAA
49325465 TTAACAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAAAAATTTTTTAAAAATAAA
Found at i:49326103 original size:17 final size:16
Alignment explanation
Indices: 49326070--49326104 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
49326060 ATATATGTTT
49326070 ATATTAAATCATATTA
1 ATATTAAATCATATTA
*
49326086 ATATTAATATCATTTTA
1 ATATTAA-ATCATATTA
49326103 AT
1 AT
49326105 TACTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTAAATCATATTA
Found at i:49326511 original size:20 final size:20
Alignment explanation
Indices: 49326486--49326525 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49326476 CCCAAATAAG
49326486 TATATTTCAAATGGGCTGGA
1 TATATTTCAAATGGGCTGGA
*
49326506 TATATTTCAAATGGGTTGGA
1 TATATTTCAAATGGGCTGGA
49326526 AGTACCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (20 bp):
TATATTTCAAATGGGCTGGA
Found at i:49329013 original size:17 final size:18
Alignment explanation
Indices: 49328991--49329025 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
49328981 AGTTCTAATG
*
49328991 TGTGATGA-ATTGTGATA
1 TGTGATGATATTATGATA
49329008 TGTGATGATATTATGATA
1 TGTGATGATATTATGATA
49329026 GGTAATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (18 bp):
TGTGATGATATTATGATA
Found at i:49329939 original size:12 final size:12
Alignment explanation
Indices: 49329924--49329949 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49329914 TAGTTTATAG
49329924 TTATCATTATTA
1 TTATCATTATTA
49329936 TTATCATTATTA
1 TTATCATTATTA
49329948 TT
1 TT
49329950 TTGGGATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:49333828 original size:30 final size:33
Alignment explanation
Indices: 49333781--49333841 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
49333771 TTCAATTTTT
*
49333781 ATATATTATTTTGAA-TTT-TAAAAAATTATAA
1 ATATATTATTTTAAATTTTATAAAAAATTATAA
49333812 ATATA-TATTTTAAATTTTATAAAAAATTAT
1 ATATATTATTTTAAATTTTATAAAAAATTAT
49333842 TTTTAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 8 0.30
32 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (33 bp):
ATATATTATTTTAAATTTTATAAAAAATTATAA
Found at i:49333836 original size:31 final size:32
Alignment explanation
Indices: 49333781--49333841 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
49333771 TTCAATTTTT
*
49333781 ATATATTATTTTGAATTTT-AAAAAATTATAA
1 ATATATTATTTTAAATTTTAAAAAAATTATAA
49333812 ATATA-TATTTTAAATTTTATAAAAAATTAT
1 ATATATTATTTTAAATTTTA-AAAAAATTAT
49333842 TTTTAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
31 5 0.19
32 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
ATATATTATTTTAAATTTTAAAAAAATTATAA
Found at i:49333854 original size:25 final size:24
Alignment explanation
Indices: 49333810--49333868 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
49333800 AAAAAATTAT
49333810 AAATATATATTTTAAATTTTATAAA
1 AAAT-TATATTTTAAATTTTATAAA
*
49333835 AAATTAT-TTTTAAACTTTTTTTAAA
1 AAATTATATTTTAAA--TTTTATAAA
49333860 AAATTATAT
1 AAATTATAT
49333869 ATCTTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 19 0.63
26 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATTATATTTTAAATTTTATAAA
Found at i:49342914 original size:27 final size:27
Alignment explanation
Indices: 49342875--49342946 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
49342865 ATATATTATT
49342875 ATAAAA-AATTAAATATATATAAATAC
1 ATAAAATAATTAAATATATATAAATAC
* * * **
49342901 ATAAAATAACTAAAAATTTATAAATTT
1 ATAAAATAATTAAATATATATAAATAC
*
49342928 ATAAAATATTTAAATATAT
1 ATAAAATAATTAAATATAT
49342947 GAAATCACTA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 6 0.17
27 30 0.83
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAAAATAATTAAATATATATAAATAC
Found at i:49346431 original size:12 final size:12
Alignment explanation
Indices: 49346414--49346460 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
49346404 ATGTATGTAA
49346414 ATTATGTAAGTT
1 ATTATGTAAGTT
49346426 ATTATGTAAG--
1 ATTATGTAAGTT
49346436 -TTATGTAAGTT
1 ATTATGTAAGTT
* *
49346447 ACTATGTAGGTT
1 ATTATGTAAGTT
49346459 AT
1 AT
49346461 GTTCGTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 9 0.31
12 20 0.69
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (12 bp):
ATTATGTAAGTT
Found at i:49346444 original size:9 final size:9
Alignment explanation
Indices: 49346407--49346476 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 9
49346397 AATATTTATG
*
49346407 TATGTAAAT
1 TATGTAAGT
49346416 TATGTAAGTTAT
1 TATGTAAG---T
49346428 TATGTAAGT
1 TATGTAAGT
49346437 TATGTAAGTT
1 TATGTAAG-T
*
49346447 ACTATGTAGGT
1 --TATGTAAGT
**
49346458 TATGTTCGT
1 TATGTAAGT
49346467 TATGTAAGT
1 TATGTAAGT
49346476 T
1 T
49346477 GTGATATGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
9 31 0.63
10 1 0.02
11 1 0.02
12 16 0.33
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TATGTAAGT
Found at i:49346468 original size:21 final size:21
Alignment explanation
Indices: 49346407--49346462 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
49346397 AATATTTATG
* *
49346407 TATGTAAATTATGTAAGTTAT
1 TATGTAAGTTATGTAAGTTAC
49346428 TATGTAAGTTATGTAAGTTAC
1 TATGTAAGTTATGTAAGTTAC
*
49346449 TATGTAGGTTATGT
1 TATGTAAGTTATGT
49346463 TCGTTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
TATGTAAGTTATGTAAGTTAC
Found at i:49346561 original size:91 final size:88
Alignment explanation
Indices: 49346371--49346563 Score: 192
Period size: 91 Copynumber: 2.1 Consensus size: 88
49346361 TAAGTATAAT
* * * *
49346371 TAAGCTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAAGTTATTATGTAAG
1 TAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAACTGATAATGTAAG
* *
49346436 TTATGTAAGTTACTATGTAGGTTATG
66 CTATATAAG-T-CTATGTA-GTTATG
** ** * *
49346462 TTCGTTATGTAAGTTGTGATATGATTAATATTTATGTATGTAAATTATGATATGACTGATAAATT
1 TAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATG-TA--ACTGAT-AATG
49346527 TAAGCTATATAAG-CTATGTA-TTATG
62 TAAGCTATATAAGTCTATGTAGTTATG
49346552 TAAGTTTATGTA
1 TAAG-TTATGTA
49346564 TGTAGGAATA
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
90 7 0.08
91 50 0.60
92 9 0.11
94 4 0.05
95 13 0.16
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (88 bp):
TAAGTTATGTAAGTTAAGATATAATTAATATTTATGTATGTAAATTATGTAACTGATAATGTAAG
CTATATAAGTCTATGTAGTTATG
Found at i:49346594 original size:9 final size:9
Alignment explanation
Indices: 49346580--49346616 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
49346570 AATAAGTATA
*
49346580 ATGTAAGCT
1 ATGTAAGTT
49346589 ATGTAAGTT
1 ATGTAAGTT
49346598 ATGTAAGTT
1 ATGTAAGTT
49346607 ATGTAAGTT
1 ATGTAAGTT
49346616 A
1 A
49346617 AGATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:49346662 original size:39 final size:40
Alignment explanation
Indices: 49346608--49346683 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
49346598 ATGTAAGTTA
* *
49346608 TGTAAGTTAAGATATAATATATATCCCTGTAAGTTATAAG
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
49346648 TGTAA-TTAAGATATAATATACATCCCGGTAAGTTAT
1 TGTAAGTTAAGATATAATATACATCCCGGTAAGTTAT
49346684 GTATTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (40 bp):
TGTAAGTTAAGATATAATATACATCCCGGTAAGTTATAAG
Found at i:49346695 original size:9 final size:9
Alignment explanation
Indices: 49346681--49346778 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
49346671 CCCGGTAAGT
49346681 TATGTATTA
1 TATGTATTA
49346690 TATGTATTA
1 TATGTATTA
*
49346699 TATGTAAGT-
1 TATGT-ATTA
49346708 TATGTAGGTTA
1 TATGTA--TTA
* *
49346719 T-T-AATAA
1 TATGTATTA
49346726 GTTATGTATTA
1 --TATGTATTA
49346737 TATGTATTA
1 TATGTATTA
*
49346746 TATGTAAGT-
1 TATGT-ATTA
*
49346755 TATGTAGGT-
1 TATGTA-TTA
49346764 TATGTATTA
1 TATGTATTA
49346773 TATGTA
1 TATGTA
49346779 GGTTATGTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 54 0.77
10 7 0.10
11 4 0.06
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (9 bp):
TATGTATTA
Found at i:49346705 original size:27 final size:27
Alignment explanation
Indices: 49346675--49346787 Score: 125
Period size: 27 Copynumber: 4.4 Consensus size: 27
49346665 ATACATCCCG
49346675 GTAAGTTATGTATTATATGTATTATAT
1 GTAAGTTATGTATTATATGTATTATAT
**
49346702 GTAAGTTATG---TAGGT-TATTA-A-
1 GTAAGTTATGTATTATATGTATTATAT
49346723 -TAAGTTATGTATTATATGTATTATAT
1 GTAAGTTATGTATTATATGTATTATAT
*
49346749 GTAAGTTATGTAGGT-TATGTATTATAT
1 GTAAGTTATGTA-TTATATGTATTATAT
*
49346776 GTAGGTTATGTA
1 GTAAGTTATGTA
49346788 GGTTATTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
20 9 0.12
22 1 0.01
23 8 0.11
24 8 0.11
25 1 0.01
27 44 0.61
28 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (27 bp):
GTAAGTTATGTATTATATGTATTATAT
Found at i:49346730 original size:47 final size:47
Alignment explanation
Indices: 49346676--49346766 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
49346666 TACATCCCGG
49346676 TAAGTTATGTATTATATGTATTATATGTAAGTTATGTAGGTTATTAA
1 TAAGTTATGTATTATATGTATTATATGTAAGTTATGTAGGTTATTAA
49346723 TAAGTTATGTATTATATGTATTATATGTAAGTTATGTAGGTTAT
1 TAAGTTATGTATTATATGTATTATATGTAAGTTATGTAGGTTAT
49346767 GTATTATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (47 bp):
TAAGTTATGTATTATATGTATTATATGTAAGTTATGTAGGTTATTAA
Found at i:49346779 original size:18 final size:18
Alignment explanation
Indices: 49346690--49346787 Score: 85
Period size: 18 Copynumber: 5.3 Consensus size: 18
49346680 TTATGTATTA
49346690 TATGTATTATATGTAAGT
1 TATGTATTATATGTAAGT
*
49346708 TATGTAGGTTAT-TAATAAGT
1 TATGTA--TTATAT-GTAAGT
*
49346728 TATGTATTATATGT-ATT
1 TATGTATTATATGTAAGT
* *
49346745 ATATGTAAGT-TATGTAGGT
1 -TATGT-ATTATATGTAAGT
*
49346764 TATGTATTATATGTAGGT
1 TATGTATTATATGTAAGT
49346782 TATGTA
1 TATGTA
49346788 GGTTATTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
17 4 0.06
18 41 0.63
19 5 0.08
20 15 0.23
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (18 bp):
TATGTATTATATGTAAGT
Found at i:49346785 original size:9 final size:9
Alignment explanation
Indices: 49346746--49346793 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
49346736 ATATGTATTA
*
49346746 TATGTAAGT
1 TATGTAGGT
49346755 TATGTAGGT
1 TATGTAGGT
*
49346764 TATGTA-TT
1 TATGTAGGT
49346772 ATATGTAGGT
1 -TATGTAGGT
49346782 TATGTAGGT
1 TATGTAGGT
49346791 TAT
1 TAT
49346794 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 1 0.03
9 32 0.94
10 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (9 bp):
TATGTAGGT
Found at i:49347593 original size:18 final size:18
Alignment explanation
Indices: 49347550--49347584 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49347540 CAATCAACTT
49347550 AATA-TAAATTAAATCAA
1 AATATTAAATTAAATCAA
49347567 AATATTAAATTAAA-CAA
1 AATATTAAATTAAATCAA
49347584 A
1 A
49347585 TATGGTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTAAATTAAATCAA
Found at i:49349431 original size:27 final size:29
Alignment explanation
Indices: 49349372--49349432 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 29
49349362 CGATATCTTA
49349372 AAAATTTAAATAATTCTATTATTAGAAAATTT
1 AAAATTTAAATAATTC--TTATTA-AAAATTT
49349404 AAAATTTAAATAATTC-TATT-AAAATTT
1 AAAATTTAAATAATTCTTATTAAAAATTT
49349431 AA
1 AA
49349433 TACTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 9 0.31
29 4 0.14
32 16 0.55
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAATTTAAATAATTCTTATTAAAAATTT
Found at i:49349823 original size:13 final size:14
Alignment explanation
Indices: 49349795--49349828 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
49349785 ACATTAACTA
49349795 TTAACCCCTAAACCC
1 TTAACCCC-AAACCC
49349810 TTAACCCC-AACCC
1 TTAACCCCAAACCC
49349823 TTAACC
1 TTAACC
49349829 ATTAACCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (14 bp):
TTAACCCCAAACCC
Found at i:49349833 original size:35 final size:35
Alignment explanation
Indices: 49349788--49349886 Score: 119
Period size: 35 Copynumber: 2.8 Consensus size: 35
49349778 TCATAAAACA
* *
49349788 TTAACTATTAACCCCTAAACCCTTAACCCCAACCC
1 TTAACCATTAACCCATAAACCCTTAACCCCAACCC
* * *
49349823 TTAACCATTAACCCTTAAACCCTAAACACCAACCC
1 TTAACCATTAACCCATAAACCCTTAACCCCAACCC
* *
49349858 TTAAACCA-TAATCCATAAACCCCTAACCC
1 TT-AACCATTAACCCATAAACCCTTAACCC
49349887 ATATCCCTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 49 0.91
36 5 0.09
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (35 bp):
TTAACCATTAACCCATAAACCCTTAACCCCAACCC
Found at i:49349845 original size:8 final size:7
Alignment explanation
Indices: 49349795--49349904 Score: 55
Period size: 7 Copynumber: 15.6 Consensus size: 7
49349785 ACATTAACTA
49349795 TTAACCCC
1 TTAA-CCC
*
49349803 TAAACCC
1 TTAACCC
49349810 TTAACCC
1 TTAACCC
*
49349817 -CAACCC
1 TTAACCC
*
49349823 TTAACCA
1 TTAACCC
49349830 TTAACCC
1 TTAACCC
49349837 TTAAACCC
1 TT-AACCC
*
49349845 TAAACACC
1 TTAAC-CC
49349853 --AACCC
1 TTAACCC
*
49349858 TTAAACC
1 TTAACCC
* *
49349865 ATAATCCA
1 TTAA-CCC
*
49349873 TAAACCC
1 TTAACCC
*
49349880 CTAACCC
1 TTAACCC
* *
49349887 ATATCCC
1 TTAACCC
*
49349894 TTAAACC
1 TTAACCC
49349901 TTAA
1 TTAA
49349905 ATCATAGAAC
Statistics
Matches: 75, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
5 2 0.03
6 8 0.11
7 51 0.68
8 14 0.19
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (7 bp):
TTAACCC
Found at i:49350047 original size:8 final size:8
Alignment explanation
Indices: 49350034--49350060 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
49350024 ACATTAACTA
49350034 TAAACCCC
1 TAAACCCC
49350042 TAAACCCC
1 TAAACCCC
49350050 TAAACCCC
1 TAAACCCC
49350058 TAA
1 TAA
49350061 CCTCAACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAACCCC
Found at i:49350074 original size:13 final size:13
Alignment explanation
Indices: 49350052--49350086 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
49350042 TAAACCCCTA
* *
49350052 AACCCCTAACCTC
1 AACCCTTAACCCC
49350065 AACCCTTAACCCC
1 AACCCTTAACCCC
49350078 AACCCTTAA
1 AACCCTTAA
49350087 ACCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (13 bp):
AACCCTTAACCCC
Found at i:49350103 original size:22 final size:22
Alignment explanation
Indices: 49350078--49350127 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
49350068 CCTTAACCCC
49350078 AACCCTTAAACCATAAT-CCATA
1 AACCCTTAAACCAT-ATCCCATA
* *
49350100 AACCCTTAACCCATATCCCTTA
1 AACCCTTAAACCATATCCCATA
49350122 AACCCT
1 AACCCT
49350128 AAATTATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (22 bp):
AACCCTTAAACCATATCCCATA
Found at i:49350599 original size:74 final size:75
Alignment explanation
Indices: 49350473--49350625 Score: 186
Period size: 74 Copynumber: 2.1 Consensus size: 75
49350463 GGTTTCTAAT
* * * *
49350473 AAGCGCCACTAACGTCTCTAAAAGCTATATAAAAAAAGACATCATTCTCTTAACAG-TTTGTGGC
1 AAGCGCCACTAAAGTCCCTAAAAGCTAAATAAAAAAAGACATCATTCTCTTAACAGTTTTGCGGC
*
49350537 GTTTTTAGAC
66 GCTTTTAGAC
* * *
49350547 AAGCGCCACTAAAAG-CCCTAAATGCTAAATAAAAAATGACATC-TTTTGCTTAACAGTTTTGCG
1 AAGCGCCACT-AAAGTCCCTAAAAGCTAAATAAAAAAAGACATCATTCT-CTTAACAGTTTTGCG
*
49350610 GCGCTTTTAGAT
64 GCGCTTTTAGAC
49350622 AAGC
1 AAGC
49350626 ACCGCTAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
73 3 0.04
74 42 0.63
75 22 0.33
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (75 bp):
AAGCGCCACTAAAGTCCCTAAAAGCTAAATAAAAAAAGACATCATTCTCTTAACAGTTTTGCGGC
GCTTTTAGAC
Found at i:49350901 original size:114 final size:113
Alignment explanation
Indices: 49350783--49351109 Score: 266
Period size: 114 Copynumber: 2.9 Consensus size: 113
49350773 AAGAAAGCGT
* * *
49350783 CACTAACGTCTCTAAAACCTAAATTAAAAACGACTACGTTTTCTTAACAGTTTTGCGGCGCAT-T
1 CACTAACGTCTCTAAAACCTAAACTAAAAACGAC-ACGTTTTCTTAACAGTTTTGCGACGCTTAT
* * * * * *
49350847 GTTAAAAGCGCCGCTAAATCTTGGCTATTGCGGTATTTTTC-GATAATCGC
65 GAT-AAAGCGCCGCTAAATCTTGACTATTACGGCATTTTTCAG-TAAGCAC
* ** * * * * * *
49350897 CACTATCGTCT-TGAAAAGATAAACGAAAAACGGCAACATTTTCTTAACAATTTCGTGACGCTTA
1 CACTAACGTCTCT-AAAACCTAAACTAAAAACGAC-ACGTTTTCTTAACAGTTTTGCGACGCTTA
* * * * *
49350961 TGATAAAGTGCTGCTAATTCTTGACTGTTACGGCGTTTTTCAGTAAGCAC
64 TGATAAAGCGCCGCTAAATCTTGACTATTACGGCATTTTTCAGTAAGCAC
* * ** *
49351011 CACTAACGTCCCTAAAACCTAAACCT-AAAACGACACCGTTTTCTTAACAGTTTTTACGGTGTTT
1 CACTAACGTCTCTAAAACCTAAA-CTAAAAACGACA-CGTTTTCTTAACAG-TTTTGCGACGCTT
* * * *
49351075 ATGATAAAACGCCGGTAATTCTTGACTATTGCGGC
63 ATGATAAAGCGCCGCTAAATCTTGACTATTACGGC
49351110 GTTTCTAAAG
Statistics
Matches: 162, Mismatches: 44, Indels: 13
0.74 0.20 0.06
Matches are distributed among these distances:
113 2 0.01
114 118 0.73
115 42 0.26
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (113 bp):
CACTAACGTCTCTAAAACCTAAACTAAAAACGACACGTTTTCTTAACAGTTTTGCGACGCTTATG
ATAAAGCGCCGCTAAATCTTGACTATTACGGCATTTTTCAGTAAGCAC
Found at i:49352295 original size:24 final size:24
Alignment explanation
Indices: 49352250--49352296 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
49352240 TTATAATATA
* * *
49352250 AAATATATATGATTATAAAAAATT
1 AAATATATATAAATACAAAAAATT
*
49352274 AAATATATATAAATACATAAAAT
1 AAATATATATAAATACAAAAAAT
49352297 AACTAACAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATATATATAAATACAAAAAATT
Found at i:49352451 original size:25 final size:24
Alignment explanation
Indices: 49352423--49352469 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
49352413 TTTTTATTAA
49352423 TTTATATAATTTAAAATTTTAAACT
1 TTTATAT-ATTTAAAATTTTAAACT
**
49352448 TTTATATATTTTTAATTTTAAA
1 TTTATATATTTAAAATTTTAAA
49352470 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATATATTTAAAATTTTAAACT
Found at i:49352993 original size:22 final size:21
Alignment explanation
Indices: 49352950--49352993 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
49352940 TTTTTGCATC
* *
49352950 TCACAAATAAAGAAAAAAATT
1 TCACAAACAAAAAAAAAAATT
49352971 TCACAAACAAAAAAAAAACATT
1 TCACAAACAAAAAAAAAA-ATT
49352993 T
1 T
49352994 TATTGAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.18
Consensus pattern (21 bp):
TCACAAACAAAAAAAAAAATT
Found at i:49353508 original size:9 final size:9
Alignment explanation
Indices: 49353472--49353510 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
49353462 TAAATTTCAC
49353472 AATTCAAAT
1 AATTCAAAT
*
49353481 AACTCAAAT
1 AATTCAAAT
**
49353490 AATTTGAAT
1 AATTCAAAT
49353499 AATTCAAAT
1 AATTCAAAT
49353508 AAT
1 AAT
49353511 AGATTGATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (9 bp):
AATTCAAAT
Found at i:49353619 original size:20 final size:19
Alignment explanation
Indices: 49353596--49353662 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
49353586 TACAAAATAA
49353596 TTCAAAATAATTTTCAAAAT
1 TTCAAAATAATTTT-AAAAT
49353616 TTCAAAATAAATTTT-AAAT
1 TTCAAAAT-AATTTTAAAAT
*
49353635 TTTAAAAT-ATTTATAAAAAT
1 TTCAAAATAATTT-T-AAAAT
49353655 TTCAAAAT
1 TTCAAAAT
49353663 TTATATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 11 0.27
20 19 0.46
21 6 0.15
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCAAAATAATTTTAAAAT
Found at i:49353688 original size:27 final size:26
Alignment explanation
Indices: 49353644--49353695 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
49353634 TTTTAAAATA
* * *
49353644 TTTATAAAAATTTCAAAATTTATATT
1 TTTAAAAAAATTTAAAAAATTATATT
49353670 TTTAAAAAAATTATAAAAAATTATAT
1 TTTAAAAAAATT-TAAAAAATTATAT
49353696 AAAAAAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTAAAAAAATTTAAAAAATTATATT
Found at i:49354935 original size:20 final size:20
Alignment explanation
Indices: 49354906--49354953 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
49354896 TTTATTTTTA
* *
49354906 ATTTTAATCCACATTTTTATG
1 ATTTT-ATCCACAATTTCATG
*
49354927 GTTTTATCCACAATTTCATG
1 ATTTTATCCACAATTTCATG
49354947 ATTTTAT
1 ATTTTAT
49354954 TTTGTCCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (20 bp):
ATTTTATCCACAATTTCATG
Found at i:49357220 original size:18 final size:19
Alignment explanation
Indices: 49357183--49357229 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
49357173 AATAATTATA
49357183 AAAATATTATTTATTTTTT
1 AAAATATTATTTATTTTTT
*
49357202 AGAATATTATTTA-TTTTT
1 AAAATATTATTTATTTTTT
49357220 AAAATATTAT
1 AAAATATTAT
49357230 CATATTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AAAATATTATTTATTTTTT
Found at i:49364232 original size:20 final size:21
Alignment explanation
Indices: 49364195--49364243 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
49364185 TTAAATACAC
*
49364195 TTATAAAAACTATTATAA-TA
1 TTATAAAAACTATAATAACTA
* * *
49364215 TTATAAAAATTCTAATAACTT
1 TTATAAAAACTATAATAACTA
49364236 TTATAAAA
1 TTATAAAA
49364244 TTAATAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATAAAAACTATAATAACTA
Found at i:49364297 original size:21 final size:22
Alignment explanation
Indices: 49364234--49364297 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
49364224 TTCTAATAAC
*
49364234 TTTTATAAAATTAATAAAACATA
1 TTTTATAAAATTAATATAA-ATA
49364257 TTTTATAAAA--ACATATTAAA-A
1 TTTTATAAAATTA-ATA-TAAATA
*
49364278 TTTTATAAAATTGATATAAA
1 TTTTATAAAATTAATATAAA
49364298 CTTATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
21 16 0.46
22 7 0.20
23 12 0.34
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTATAAAATTAATATAAATA
Found at i:49364316 original size:65 final size:64
Alignment explanation
Indices: 49364195--49364317 Score: 142
Period size: 65 Copynumber: 1.9 Consensus size: 64
49364185 TTAAATACAC
* * * * *
49364195 TTATAAAAACTATTATAATATTATAAAAATTCTAATAACTTTTATAAAATTAATAAAACATATT
1 TTATAAAAACTATTAAAATATTATAAAAATTATAATAACTTATAAAAAAATAATAAAACATATT
* *
49364259 TTATAAAAACATATTAAAATTTTAT-AAAATTGAT-ATAAACTTATAAAAAAATCATAAAA
1 TTATAAAAAC-TATTAAAATATTATAAAAATT-ATAAT-AACTTATAAAAAAATAATAAAA
49364318 ACTTGAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
64 18 0.37
65 31 0.63
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (64 bp):
TTATAAAAACTATTAAAATATTATAAAAATTATAATAACTTATAAAAAAATAATAAAACATATT
Found at i:49364879 original size:10 final size:9
Alignment explanation
Indices: 49364866--49364971 Score: 60
Period size: 10 Copynumber: 11.6 Consensus size: 9
49364856 TTTATCAGAA
49364866 TTTATTAATT
1 TTTA-TAATT
*
49364876 TTTAT-AGT
1 TTTATAATT
49364884 TTTATAATGT
1 TTTATAAT-T
49364894 TTT-TAAGTT
1 TTTATAA-TT
49364903 TTTATAATT
1 TTTATAATT
*
49364912 TTAATAAGTT
1 TTTATAA-TT
* *
49364922 TATATCAAAT
1 TTTAT-AATT
*
49364932 TTAATATATT
1 TTTATA-ATT
49364942 TTTAT-ATT
1 TTTATAATT
*
49364950 TTT-TAATA
1 TTTATAATT
49364958 TTTA-ATATT
1 TTTATA-ATT
49364967 TTTAT
1 TTTAT
49364972 TTTATTATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
7 1 0.01
8 19 0.26
9 24 0.33
10 27 0.37
11 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:49364898 original size:19 final size:19
Alignment explanation
Indices: 49364874--49364910 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
49364864 AATTTATTAA
49364874 TTTTTATAG-TTTTATAATG
1 TTTTTA-AGTTTTTATAATG
49364893 TTTTTAAGTTTTTATAAT
1 TTTTTAAGTTTTTATAAT
49364911 TTTAATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTAAGTTTTTATAATG
Found at i:49364922 original size:27 final size:26
Alignment explanation
Indices: 49364847--49364924 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
49364837 TTTTATAATT
*
49364847 TTTTTATAA-TTTATCAGAATTTATTAA
1 TTTTTATAATTTTAT-A-AGTTTATTAA
*
49364874 TTTTTATAGTTTTATAATGTTT-TTAA
1 TTTTTATAATTTTATAA-GTTTATTAA
49364900 GTTTTTATAATTTTAATAAGTTTAT
1 -TTTTTATAATTTT-ATAAGTTTAT
49364925 ATCAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 5 0.12
27 28 0.65
28 10 0.23
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTTTATAATTTTATAAGTTTATTAA
Found at i:49364936 original size:20 final size:19
Alignment explanation
Indices: 49364897--49364937 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49364887 ATAATGTTTT
* *
49364897 TAAGTTTTTATAATTTTAA
1 TAAGTTTATATAAATTTAA
49364916 TAAGTTTATATCAAATTTAA
1 TAAGTTTATAT-AAATTTAA
49364936 TA
1 TA
49364938 TATTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAGTTTATATAAATTTAA
Found at i:49370494 original size:4 final size:4
Alignment explanation
Indices: 49370485--49370518 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
49370475 AAGTTTTATT
49370485 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
49370519 AATTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:49372899 original size:17 final size:18
Alignment explanation
Indices: 49372862--49372899 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
49372852 GATTGAGAGT
* *
49372862 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
49372880 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
49372897 GAA
1 GAA
49372900 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:49372912 original size:13 final size:12
Alignment explanation
Indices: 49372881--49372935 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
49372871 TGTGAAACAG
*
49372881 AAAAGAAATTGA
1 AAAAGAAGTTGA
49372893 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
49372905 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
49372917 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
49372929 AAAAGAA
1 AAAAGAA
49372936 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:49374301 original size:4 final size:4
Alignment explanation
Indices: 49374292--49374324 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
49374282 AAGTTTTATT
49374292 TTTA TTTA TTTA TTTA TTTA TTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
49374325 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:49378362 original size:9 final size:9
Alignment explanation
Indices: 49378350--49378398 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
49378340 ATATAATATG
49378350 TTATTTGAA
1 TTATTTGAA
*
49378359 TTATTAGAA
1 TTATTTGAA
*
49378368 TTA-TTCAA
1 TTATTTGAA
*
49378376 GTTATTTGAG
1 -TTATTTGAA
49378386 TTATTTGAA
1 TTATTTGAA
49378395 TTAT
1 TTAT
49378399 AAAATTCAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 3 0.09
9 26 0.81
10 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (9 bp):
TTATTTGAA
Found at i:49378417 original size:36 final size:36
Alignment explanation
Indices: 49378349--49378419 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
49378339 TATATAATAT
* *
49378349 GTTATTTGAATTATTAGAATTATTCAAGTTATTTGA
1 GTTATTTGAATTATTAAAATTACTCAAGTTATTTGA
49378385 GTTATTTGAATTA-TAAAATTCAACTCAA-TTATTTG
1 GTTATTTGAATTATTAAAATT--ACTCAAGTTATTTG
49378420 CTTTTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.19
36 20 0.65
37 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (36 bp):
GTTATTTGAATTATTAAAATTACTCAAGTTATTTGA
Found at i:49384327 original size:7 final size:7
Alignment explanation
Indices: 49384315--49384385 Score: 142
Period size: 7 Copynumber: 10.1 Consensus size: 7
49384305 GCGGATTAAG
49384315 AATTCAA
1 AATTCAA
49384322 AATTCAA
1 AATTCAA
49384329 AATTCAA
1 AATTCAA
49384336 AATTCAA
1 AATTCAA
49384343 AATTCAA
1 AATTCAA
49384350 AATTCAA
1 AATTCAA
49384357 AATTCAA
1 AATTCAA
49384364 AATTCAA
1 AATTCAA
49384371 AATTCAA
1 AATTCAA
49384378 AATTCAA
1 AATTCAA
49384385 A
1 A
49384386 TTTGAAGATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AATTCAA
Found at i:49384397 original size:7 final size:7
Alignment explanation
Indices: 49384387--49384430 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
49384377 AAATTCAAAT
49384387 TTGAAGA
1 TTGAAGA
49384394 TTGAAGA
1 TTGAAGA
*
49384401 TTGAAAA
1 TTGAAGA
*
49384408 TTGAAAA
1 TTGAAGA
**
49384415 TTGGGGA
1 TTGAAGA
49384422 TTGAAGA
1 TTGAAGA
49384429 TT
1 TT
49384431 TAGGAAGGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (7 bp):
TTGAAGA
Found at i:49384412 original size:21 final size:21
Alignment explanation
Indices: 49384320--49384426 Score: 70
Period size: 21 Copynumber: 5.1 Consensus size: 21
49384310 TTAAGAATTC
* * * *
49384320 AAAATTCAAAATTCAAAATTC
1 AAAATTGAAAATTGAAGATTG
* * * *
49384341 AAAATTCAAAATTCAAAATTC
1 AAAATTGAAAATTGAAGATTG
* * * *
49384362 AAAATTCAAAATTCAAAATTC
1 AAAATTGAAAATTGAAGATTG
* *
49384383 AAATTTGAAGATTGAAGATTG
1 AAAATTGAAAATTGAAGATTG
**
49384404 AAAATTGAAAATTGGGGATTG
1 AAAATTGAAAATTGAAGATTG
49384425 AA
1 AA
49384427 GATTTAGGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (21 bp):
AAAATTGAAAATTGAAGATTG
Found at i:49389375 original size:10 final size:10
Alignment explanation
Indices: 49389360--49389384 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49389350 CAAATCTAAC
49389360 ATTATGTAAA
1 ATTATGTAAA
49389370 ATTATGTAAA
1 ATTATGTAAA
49389380 ATTAT
1 ATTAT
49389385 TAAGTCCAAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:49389429 original size:55 final size:55
Alignment explanation
Indices: 49389368--49389548 Score: 344
Period size: 55 Copynumber: 3.3 Consensus size: 55
49389358 ACATTATGTA
49389368 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
* *
49389423 AAATTATGCAAAATTATTAAGTCCAAAAATTGTGTTAATGGCTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
49389478 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
49389533 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
49389549 GGTTAGGGTT
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 122 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:49389596 original size:30 final size:29
Alignment explanation
Indices: 49389543--49389794 Score: 375
Period size: 30 Copynumber: 8.6 Consensus size: 29
49389533 AAATTATGTA
*
49389543 AAATTAGGTTAGGGTTAGGGTTTTTATTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
49389572 AAATTAGGTTAGGG-TAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
49389602 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
49389632 AAATTAGGTTAGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
49389661 AAATTAGGTTAGGG-CAGTAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAG--GGTTTTTAATT
*
49389691 AAATTAGGTTAGGG-CAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
*
49389721 AAATTAGGTTAGAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
49389750 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
49389779 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
49389795 TTTAATTAAA
Statistics
Matches: 207, Mismatches: 7, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.02
29 98 0.47
30 101 0.49
31 1 0.00
32 3 0.01
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:49389653 original size:89 final size:87
Alignment explanation
Indices: 49389543--49389795 Score: 393
Period size: 89 Copynumber: 2.9 Consensus size: 87
49389533 AAATTATGTA
*
49389543 AAATTAGGTTAGGGTTAGGGTTTTTATTTAAATTAGGTTAGGGTAGTGGGTTTTTAATTAAATTA
1 AAATTAGGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAGTGGGTTTTTAATTAAATTA
49389608 GGTTAGGGTTTAGGGTTTTTAATT
65 GGTTAGGGTTT-GGGTTTTTAATT
* *
49389632 AAATTAGGTTAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGCAGTAGGTTTTTAATTAAATTA
1 AAATTAGGTTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTAGTGGGTTTTTAATTAAATTA
**
49389697 GGTTAGGGCAGTGGGTTTTTAATT
65 GGTTAGGG-TTTGGGTTTTTAATT
49389721 AAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGT--TAGGGTTTTTAATTAAATT
1 AAATTAGGTTAG-GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAGT-GGGTTTTTAATTAAATT
49389784 AGGTTAGGGTTT
64 AGGTTAGGGTTT
49389796 TTAATTAAAT
Statistics
Matches: 151, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
87 2 0.01
88 27 0.18
89 120 0.79
90 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (87 bp):
AAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAGTGGGTTTTTAATTAAATTAG
GTTAGGGTTTGGGTTTTTAATT
Found at i:49389764 original size:23 final size:23
Alignment explanation
Indices: 49389729--49389809 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 23
49389719 TTAAATTAGG
49389729 TTAGAGTTAGGGTTTTTAATTAAATTA
1 TTAG-GTTAGGGTTTTTAATT-AA--A
49389756 GGTTAGGGTTAGGGTTTTTAATTAAA
1 --TTA-GGTTAGGGTTTTTAATTAAA
49389782 TTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAA
49389805 TTAGG
1 TTAGG
49389810 GTTTTTATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
23 25 0.49
24 3 0.06
26 1 0.02
28 2 0.04
29 19 0.37
30 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTTAATTAAA
Found at i:49389801 original size:18 final size:18
Alignment explanation
Indices: 49389764--49389816 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
49389754 TAGGTTAGGG
49389764 TTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATT-AA--A
49389785 GGTTAGGGTTTTTAATTAAA
1 --TTAGGGTTTTTAATTAAA
49389805 TTAGGGTTTTTA
1 TTAGGGTTTTTA
49389817 TTATATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.40
20 1 0.03
22 2 0.07
23 15 0.50
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:49389923 original size:71 final size:71
Alignment explanation
Indices: 49389815--49389999 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
49389805 TTAGGGTTTT
49389815 TATTATATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTATATCAAATA-AACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
49389880 CTATGCC
65 CTATGCC
* *
49389887 TATTATATCAAATAAACTTCTATTTTATTATTTCAAATAATATCAAAATAACTTGAAAAAATTTC
1 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
49389952 TATGCG
66 TATGCC
* *
49389958 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATA
49390000 AATTTAAATA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 93 0.87
72 14 0.13
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (71 bp):
TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:49389940 original size:35 final size:35
Alignment explanation
Indices: 49389819--49389940 Score: 88
Period size: 36 Copynumber: 3.4 Consensus size: 35
49389809 GGTTTTTATT
* *
49389819 ATATCAAATAGAACTTCTATTTTATTATATCAAATA
1 ATATCAAA-ATAACTTCTATTTTATTATTTCAAATA
* **** ** *
49389855 ATATCAAAATAAC-TCGAAAAAATT-TCTATGCCTATT
1 ATATCAAAATAACTTCTATTTTATTAT-T-T-CAAATA
49389891 ATATC-AAATAAACTTCTATTTTATTATTTCAAATA
1 ATATCAAAAT-AACTTCTATTTTATTATTTCAAATA
49389926 ATATCAAAATAACTT
1 ATATCAAAATAACTT
49389941 GAAAAAATTT
Statistics
Matches: 61, Mismatches: 18, Indels: 15
0.65 0.19 0.16
Matches are distributed among these distances:
33 1 0.02
34 6 0.10
35 22 0.36
36 24 0.39
37 7 0.11
38 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.39
Consensus pattern (35 bp):
ATATCAAAATAACTTCTATTTTATTATTTCAAATA
Found at i:49390428 original size:18 final size:18
Alignment explanation
Indices: 49390401--49390435 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49390391 CGAAAAAGGA
* *
49390401 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
49390419 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
49390436 AAACACACCT
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:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:49391097 original size:7 final size:7
Alignment explanation
Indices: 49391087--49391111 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49391077 TTATATACAT
49391087 AATACTA
1 AATACTA
49391094 AATACTA
1 AATACTA
49391101 AATACTA
1 AATACTA
49391108 AATA
1 AATA
49391112 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:49392206 original size:21 final size:21
Alignment explanation
Indices: 49392179--49392226 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
49392169 GATGAAAATA
49392179 TAAAAAAAT-TAAAATTATTT
1 TAAAAAAATATAAAATTATTT
49392199 TAAAAAAATATAAAATTATTT
1 TAAAAAAATATAAAATTATTT
49392220 TAAAAAA
1 TAAAAAA
49392227 TGAAATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAAATATAAAATTATTT
Found at i:49392283 original size:29 final size:29
Alignment explanation
Indices: 49392251--49392339 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 29
49392241 AATTGAAATT
49392251 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
49392280 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
49392302 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
49392331 AAATTTGGA
1 AAATATGGA
49392340 AGGAAATTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
22 9 0.21
23 4 0.10
24 4 0.10
27 5 0.12
28 4 0.10
29 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:49392287 original size:51 final size:51
Alignment explanation
Indices: 49392228--49392349 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 51
49392218 TTTAAAAAAT
*
49392228 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
49392279 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
49392330 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
49392350 GAGGATTAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 54 0.81
52 13 0.19
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:49392339 original size:12 final size:12
Alignment explanation
Indices: 49392322--49392347 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49392312 TTGAGAGAAT
49392322 TTTGGAAGGAAA
1 TTTGGAAGGAAA
49392334 TTTGGAAGGAAA
1 TTTGGAAGGAAA
49392346 TT
1 TT
49392348 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:49392931 original size:18 final size:17
Alignment explanation
Indices: 49392898--49392950 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
49392888 TTCTAATTTT
49392898 TTTAAAAA-TTATTAAAA
1 TTTAAAAATTTA-TAAAA
49392915 TTTAAATAATTTATAAAA
1 TTTAAA-AATTTATAAAA
*
49392933 TTAAAAAATTTTATAAAA
1 TTTAAAAA-TTTATAAAA
49392951 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 8 0.25
18 21 0.66
19 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAAATTTATAAAA
Found at i:49392955 original size:18 final size:18
Alignment explanation
Indices: 49392924--49392958 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49392914 ATTTAAATAA
*
49392924 TTTATAAAATTAAAAAAT
1 TTTATAAAAATAAAAAAT
49392942 TTTATAAAAATAAAAAA
1 TTTATAAAAATAAAAAA
49392959 AATACATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTATAAAAATAAAAAAT
Found at i:49392957 original size:19 final size:18
Alignment explanation
Indices: 49392924--49392959 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49392914 ATTTAAATAA
*
49392924 TTTATAAAATTAAAAAAT
1 TTTATAAAATAAAAAAAT
49392942 TTTATAAAAATAAAAAAA
1 TTTAT-AAAATAAAAAAA
49392960 ATACATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTATAAAATAAAAAAAT
Found at i:49397010 original size:5 final size:5
Alignment explanation
Indices: 49397000--49397024 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49396990 CATAAACAAG
49397000 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
49397025 TAACGAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:49399728 original size:2 final size:2
Alignment explanation
Indices: 49399721--49399749 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49399711 AAACTTAAAC
49399721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49399750 GCTCCCCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49400406 original size:14 final size:14
Alignment explanation
Indices: 49400387--49400413 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49400377 TGAGTTGACA
49400387 AAAAAAGAAAAAGG
1 AAAAAAGAAAAAGG
49400401 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
49400414 TGGAAACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:49401248 original size:3 final size:3
Alignment explanation
Indices: 49401240--49401265 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49401230 AACCAAGTAT
49401240 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
49401266 TTTTATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:49403331 original size:24 final size:24
Alignment explanation
Indices: 49403307--49403353 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
49403297 AAACTACTTC
49403307 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
**
49403332 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
49403354 TTTCACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Done.