Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 7 of 276
Found at i:2192606 original size:18 final size:19
Alignment explanation
Indices: 2192571--2192607 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2192561 ATAATTAATA
*
2192571 TAATTTTATGATAATTTTT
1 TAATTTTATGAAAATTTTT
2192590 TAATTTT-TGAAAATTTTT
1 TAATTTTATGAAAATTTTT
2192608 CAGGTCCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TAATTTTATGAAAATTTTT
Found at i:2192838 original size:18 final size:19
Alignment explanation
Indices: 2192817--2192853 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2192807 AGAAATAAAT
2192817 ATATAAAAAATC-AGAAAA
1 ATATAAAAAATCTAGAAAA
*
2192835 ATATATAAAATCTAGAAAA
1 ATATAAAAAATCTAGAAAA
2192854 CAACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
ATATAAAAAATCTAGAAAA
Found at i:2192840 original size:22 final size:21
Alignment explanation
Indices: 2192789--2192841 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2192779 TATGCACATT
* * *
2192789 AAAATAAATATAATAATTAGA
1 AAAATATATATAAAAATCAGA
2192810 AATAA-ATATATAAAAAATCAGA
1 AA-AATATATAT-AAAAATCAGA
2192832 AAAATATATA
1 AAAATATATA
2192842 AAATCTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
AAAATATATATAAAAATCAGA
Found at i:2192942 original size:22 final size:22
Alignment explanation
Indices: 2192917--2192970 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2192907 AAATTAGTTG
*
2192917 AAATTGATAATATTATTACAAA
1 AAATTGATAATATTATAACAAA
* *
2192939 AAATGTGA-AAAATTATAATAAA
1 AAAT-TGATAATATTATAACAAA
2192961 AAATT-ATAAT
1 AAATTGATAAT
2192971 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 19 0.73
23 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATTGATAATATTATAACAAA
Found at i:2192964 original size:13 final size:13
Alignment explanation
Indices: 2192946--2192970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2192936 AAAAAATGTG
2192946 AAAAATTATAATA
1 AAAAATTATAATA
2192959 AAAAATTATAAT
1 AAAAATTATAAT
2192971 TTTTTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTATAATA
Found at i:2193099 original size:18 final size:20
Alignment explanation
Indices: 2193063--2193101 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2193053 AAATTTAAAT
2193063 ACATTTTTCTAATTTTTATA
1 ACATTTTTCTAATTTTTATA
2193083 ACATTTTTC-AA-TTTTATA
1 ACATTTTTCTAATTTTTATA
2193101 A
1 A
2193102 ATTATTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
ACATTTTTCTAATTTTTATA
Found at i:2193659 original size:18 final size:18
Alignment explanation
Indices: 2193632--2193670 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2193622 AAAACAAGAA
*
2193632 TACTCGTCGTTTGATTAT
1 TACTCATCGTTTGATTAT
2193650 TACTCATCGTTTGATTAT
1 TACTCATCGTTTGATTAT
2193668 TAC
1 TAC
2193671 CTAAATCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (18 bp):
TACTCATCGTTTGATTAT
Found at i:2193943 original size:16 final size:18
Alignment explanation
Indices: 2193918--2193961 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
2193908 GGGTAAAAAC
*
2193918 AAAATGATAAT-A-TAAT
1 AAAATAATAATAAGTAAT
2193934 AAAATAATAATAAAGTAAT
1 AAAATAATAAT-AAGTAAT
2193953 AAAATAATA
1 AAAATAATA
2193962 GTAATCGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
18 1 0.04
19 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATAATAATAAGTAAT
Found at i:2196295 original size:917 final size:918
Alignment explanation
Indices: 2194921--2196640 Score: 3273
Period size: 917 Copynumber: 1.9 Consensus size: 918
2194911 CCTTTCAAAT
* *
2194921 CGGAAGGGGGACCTCCCACGACAACGACTAACAGGTAAACAAAAAACCTTTAATTTTTTGTTATA
1 CGGAAGAGGGACCTCCCACGACAACGACTAACAGGTAAACAAAAAACCTTTAATCTTTTGTTATA
2194986 TATTTTTTTATATGTATGTTCTTCAAAAATTAAAAAACAGTAAGGGGACTACCTTTTTTTTTTAA
66 TATTTTTTTATATGTATGTTCTTCAAAAATTAAAAAACAGTAAGGGGACTACC--TTTTTTTTAA
2195051 AAAAAAAATTGTTGTTTTGTTCTTTTGTTGTCTATATTACAACTGGTTTTTGGTTTTTTTATAGC
129 AAAAAAAATTGTTGTTTTGTTCTTTTGTTGTCTATATTACAACTGGTTTTTGGTTTTTTTATAGC
2195116 TTAAGTATATTACAAGATATTACTAATTTTCTTTTTCTGTTTTGCTCATCTTTTTTCTGCTCTCT
194 TTAAGTATATTACAAGATATTACTAATTTTCTTTTTCTGTTTTGCTCATCTTTTTTCTGCTCTCT
*
2195181 GTCTTTTGTTTTTTTTTCTTTTTTGCAGGTGTTCGGGGTGGTTAATGACGTTGGGGATCCACGCC
259 GTCTTTTGTTTTTTTTTCTTTTTTGCAGGTGTTCGGGGTGGTTAACGACGTTGGGGATCCACGCC
* *
2195246 CTTGCCATTTTGGTGAAAGAAGGCAGACGAGGCGTCAAGCTTTGGGTGACACAATTGCTGATGTG
324 CTTGCCATTTTGGTGAAAGAAGGCAGACGAGGCGTCAAGCCTTGGGCGACACAATTGCTGATGTG
*
2195311 GCAGAGGCTATGGCATAGATGGCTTTATGGTTCTAGGGTTTTCTGTTTAGTTTTTAGGTTTTTGG
389 GCAAAGGCTATGGCATAGATGGCTTTATGGTTCTAGGGTTTTCTGTTTAGTTTTTAGGTTTTTGG
2195376 GCTGTTGGGTTAGCATTTGGGCTTGGGTGTATTGGGTTTAGGTTAGCATGTTTGGGTTAGGGTTT
454 GCTGTTGGGTTAGCATTTGGGCTTGGGTGTATTGGGTTTAGGTTAGCATGTTTGGGTTAGGGTTT
2195441 GGGCTTGTAAATGGACTGGACTTTTAATTAATGAGCTTGTTTTTATTTTTGCTTATTTGTTTTTT
519 GGGCTTGTAAATGGACTGGACTTTTAATTAATGAGCTTGTTTTTATTTTTGCTTATTTGTTTTTT
2195506 TGGTCTTTTGGTTTTGGGACGGATAAAATTAGGCCTCCATACCTGCCCCTCTTTGCTCATTGTCG
584 TGGTCTTTTGGTTTTGGGACGGATAAAATTAGGCCTCCATACCTGCCCCTCTTTGCTCATTGTCG
* * *
2195571 TGTAATGAGAAGGGAGTAAAGACTTTAAGGAGGACCAATTTTGTCTGGTCTTGTCGAATCTCGAC
649 TGTAATGAGAAGGGAGCAAAGACTTTAAGGAGGACCAATTTTGTCTGGTCCTATCGAATCTCGAC
2195636 TTCTTTGGTGCTCATCTTTTTCAAGTAGCTCATTCTTTCAATCTATTGGTTACTCTACTTCACTG
714 TTCTTTGGTGCTCATCTTTTTCAAGTAGCTCATTCTTTCAATCTATTGGTTACTCTACTTCACTG
*
2195701 TATCCGGTTCGTTACAAGTTTAGAAATTGCTAAAATTACCCTTTCGAACCCCTTTTACGTGTAGA
779 TATCCGGTTCATTACAAGTTTAGAAATTGCTAAAATTACCCTTTCGAACCCCTTTTACGTGTAGA
2195766 GTCTAGATCCAGGCTTCAAATCCCTAGAAACCCAGTCGAAGTTCAACTAGAAGGCGAGAAACCTT
844 GTCTAGATCCAGGCTTCAAATCCCTAGAAACCCAGTCGAAGTTCAACTAGAAGGCGAGAAACCTT
2195831 TCGGTTTCCC
909 TCGGTTTCCC
**
2195841 CGGAAGAGGGACCTCCCACGATGACGACTAACAGGTAAACAAAAAACCTTTAATCTTTTGTTATA
1 CGGAAGAGGGACCTCCCACGACAACGACTAACAGGTAAACAAAAAACCTTTAATCTTTTGTTATA
2195906 TATTTTTTTATATGTATGTTCTTCAAAAATTAAAAAACAGTAAGGGGACTACC-TTTTTTT-AAA
66 TATTTTTTTATATGTATGTTCTTCAAAAATTAAAAAACAGTAAGGGGACTACCTTTTTTTTAAAA
2195969 AAAAAATTGTTGTTTTGTTCTTTTGTTGTCTATATTACAACTGGTTTTTGGTTTTTTTATAGCTT
131 AAAAAATTGTTGTTTTGTTCTTTTGTTGTCTATATTACAACTGGTTTTTGGTTTTTTTATAGCTT
*
2196034 AAGTATATTACAAGATATTACTAATTTTCTTTTTCTGTTTTGTTCATCTTTTTTCTGCTCTCTGT
196 AAGTATATTACAAGATATTACTAATTTTCTTTTTCTGTTTTGCTCATCTTTTTTCTGCTCTCTGT
2196099 CTTTTGTTTTTTTTTTCTTTTTTGCAGGTGTTCGGGGTGGTTAACGACGTTGGGGATCCACGCCC
261 CTTTTG-TTTTTTTTTCTTTTTTGCAGGTGTTCGGGGTGGTTAACGACGTTGGGGATCCACGCCC
2196164 TTGCCATTTTGGTGAAAGAAGGCAGACGAGGCGTCAAGCCTTGGGCGACACAATTGCTGATGTGG
325 TTGCCATTTTGGTGAAAGAAGGCAGACGAGGCGTCAAGCCTTGGGCGACACAATTGCTGATGTGG
2196229 CAAAGGCTATGGCATAGATGGCTTTATGGTTCTAGGGTTTTCTGTTTAGTTTTTAGGTTTTTGGG
390 CAAAGGCTATGGCATAGATGGCTTTATGGTTCTAGGGTTTTCTGTTTAGTTTTTAGGTTTTTGGG
2196294 CTGTTGGGTTAGCATTTGGGCTTGGGTGTATTGGGTTTAGGTTAGCATGTTTGGGTTAGGGTTTG
455 CTGTTGGGTTAGCATTTGGGCTTGGGTGTATTGGGTTTAGGTTAGCATGTTTGGGTTAGGGTTTG
2196359 GGCTTGTAAATGGACTGGACTTTTAATTAATGAGCTTGTTTTTATTTTTGCTTATTTGTTTTTTT
520 GGCTTGTAAATGGACTGGACTTTTAATTAATGAGCTTGTTTTTATTTTTGCTTATTTGTTTTTTT
2196424 GGTCTTTTGGTTTTGGGACGGATAAAATTAGGCCTCCATACCTGCCCCTCTTTGCTCATTGTCGT
585 GGTCTTTTGGTTTTGGGACGGATAAAATTAGGCCTCCATACCTGCCCCTCTTTGCTCATTGTCGT
2196489 GTAATGAGAAGGGAGCAAAGACTTTAAGGAGGACCAATTTTGTCTGGTCCTATCGAATCTCGACT
650 GTAATGAGAAGGGAGCAAAGACTTTAAGGAGGACCAATTTTGTCTGGTCCTATCGAATCTCGACT
*
2196554 TCTTTGGTGCTCATCTTTTTCAAGTAGCTTATTCTTTCAATCTATTGGTTACTCTACTTCACTGT
715 TCTTTGGTGCTCATCTTTTTCAAGTAGCTCATTCTTTCAATCTATTGGTTACTCTACTTCACTGT
2196619 ATCCGGTTCATTACAAGTTTAG
780 ATCCGGTTCATTACAAGTTTAG
2196641 GAAGGTAGGA
Statistics
Matches: 785, Mismatches: 14, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
916 138 0.18
917 533 0.68
920 114 0.15
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (918 bp):
CGGAAGAGGGACCTCCCACGACAACGACTAACAGGTAAACAAAAAACCTTTAATCTTTTGTTATA
TATTTTTTTATATGTATGTTCTTCAAAAATTAAAAAACAGTAAGGGGACTACCTTTTTTTTAAAA
AAAAAATTGTTGTTTTGTTCTTTTGTTGTCTATATTACAACTGGTTTTTGGTTTTTTTATAGCTT
AAGTATATTACAAGATATTACTAATTTTCTTTTTCTGTTTTGCTCATCTTTTTTCTGCTCTCTGT
CTTTTGTTTTTTTTTCTTTTTTGCAGGTGTTCGGGGTGGTTAACGACGTTGGGGATCCACGCCCT
TGCCATTTTGGTGAAAGAAGGCAGACGAGGCGTCAAGCCTTGGGCGACACAATTGCTGATGTGGC
AAAGGCTATGGCATAGATGGCTTTATGGTTCTAGGGTTTTCTGTTTAGTTTTTAGGTTTTTGGGC
TGTTGGGTTAGCATTTGGGCTTGGGTGTATTGGGTTTAGGTTAGCATGTTTGGGTTAGGGTTTGG
GCTTGTAAATGGACTGGACTTTTAATTAATGAGCTTGTTTTTATTTTTGCTTATTTGTTTTTTTG
GTCTTTTGGTTTTGGGACGGATAAAATTAGGCCTCCATACCTGCCCCTCTTTGCTCATTGTCGTG
TAATGAGAAGGGAGCAAAGACTTTAAGGAGGACCAATTTTGTCTGGTCCTATCGAATCTCGACTT
CTTTGGTGCTCATCTTTTTCAAGTAGCTCATTCTTTCAATCTATTGGTTACTCTACTTCACTGTA
TCCGGTTCATTACAAGTTTAGAAATTGCTAAAATTACCCTTTCGAACCCCTTTTACGTGTAGAGT
CTAGATCCAGGCTTCAAATCCCTAGAAACCCAGTCGAAGTTCAACTAGAAGGCGAGAAACCTTTC
GGTTTCCC
Found at i:2196947 original size:94 final size:93
Alignment explanation
Indices: 2196770--2197711 Score: 728
Period size: 94 Copynumber: 10.2 Consensus size: 93
2196760 TTATCCCTTT
* * * * * * * * * * *
2196770 CACTGCAACTTTAGGAAGATGGGATTTG-A-CTTTATCTGGCTCCATTGCATCTTCAGAGAGATG
1 CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATA
** *
2196833 AGATTTGTTGTTGTAGTTTCATTCTATTC
66 AGATTTGTCATTGTAGTTTCATTCGA-TC
** * *
2196862 CACAACAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCTATTGCAACTTTAGAGG-GAT
1 CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAG-GGAGAT
*
2196926 AAGATTTGTCATAGTAGTTTCATTCCGATC
65 AAGATTTGTCATTGTAGTTTCATT-CGATC
* * * * * * * * ** *
2196956 CACTGTAACTTTAAGGATATAGAATTTGTAGTTTTATCTTACTCTACTGTGA-TTTCAGGGATAT
1 CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTT-AGGGAGAT
** *
2197020 AAGA-TTCACTATTGTAGTTTTATTCCGA-C
65 AAGATTTGTC-ATTGTAGTTTCATT-CGATC
* * * * *** * *
2197049 CTACTGCAACTTCAGGGGTATAGGATTTATAGCTCCATCTTACTCCACTATGACTTCAGGAAGAT
1 C-ACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGAT
* * *
2197114 AAGATTTATCGTTGTAGTTTCATTTTGA-C
65 AAGATTTGTCATTGTAGTTTCA-TTCGATC
* * * *
2197143 TCACTACAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGAT
1 -CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGAT
* *
2197208 AAGATTCG-CAATTGTAGTTTCATTTCGACC
65 AAGATTTGTC-ATTGTAGTTTCA-TTCGATC
*
2197238 CACTGCAACTTCATGGG-TATAGGATTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGAT
1 CACTGCAACTTCA-GGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGAT
**
2197302 AAGATTTACCATTGTAGTTTCATTCCGA-C
65 AAGATTTGTCATTGTAGTTTCATT-CGATC
* * * * *
2197331 CTACTGCAA---C-------TA--ATTTATAGC-TCTATCTTACTCCACTACGACTTTAGAGAGA
1 C-ACTGCAACTTCAGGGATATAGGATTTGTAGCTTC-ATCTTGCTCCACTGCAACTTTAGGGAGA
*
2197383 TAAGATTTGTCATTGTAGTTTCATTCCGACC
64 TAAGATTTGTCATTGTAGTTTCATT-CGATC
* * * *
2197414 CACTGCAACTTCAAGGG-TATAAGACTTGTAGCTTCATCTTGCTCCATTGCATCTTTAGGGAGAT
1 CACTGCAACTTC-AGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGAT
* * * * *
2197478 AAGATTCGTTATTGTAGTTTCAATCCATTT
65 AAGATTTGTCATTGTAGTTTCATTCGA-TC
** * * *
2197508 CACTAAAACTTCAGGGATATAAGATTTGTAGCTTCATCTTGCTCTACTGCATCTTTAGGGAGATA
1 CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATA
* * * *
2197573 AGATTCGCCATTGTAGTTTCATTCCAACC
66 AGATTTGTCATTGTAGTTTCATT-CGATC
* * * * *
2197602 CGCTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAGGTA
1 CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATA
** * * *
2197667 AGA-TTCACTACTGTAGTTTCATTCCAACC
66 AGATTTGTC-ATTGTAGTTTCATT-CGATC
2197696 CACTGCAACTTCAGGG
1 CACTGCAACTTCAGGG
2197712 GGACTAGAAT
Statistics
Matches: 697, Mismatches: 116, Indels: 72
0.79 0.13 0.08
Matches are distributed among these distances:
81 2 0.00
82 65 0.09
83 2 0.00
84 2 0.00
85 1 0.00
91 1 0.00
92 24 0.03
93 24 0.03
94 556 0.80
95 20 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (93 bp):
CACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATA
AGATTTGTCATTGTAGTTTCATTCGATC
Found at i:2197180 original size:44 final size:44
Alignment explanation
Indices: 2197125--2197274 Score: 133
Period size: 44 Copynumber: 3.3 Consensus size: 44
2197115 AGATTTATCG
*
2197125 TTGTAGTTTCATTTTGACTCACTACAACTTCAGGGGTATAGGAT
1 TTGTAGCTTCATTTTGACTCACTACAACTTCAGGGGTATAGGAT
* * *
2197169 TTGTAGCTTCATCTTG-CTCTACTACAACTTTAGGGAG-ATAAGATTCGCAA
1 TTGTAGCTTCATTTTGACTC-ACTACAACTTCAGGG-GTAT-AG----G-AT
* * * * *
2197219 TTGTAGTTTCATTTCGACCCACTGCAACTTCATGGGTATAGGAT
1 TTGTAGCTTCATTTTGACTCACTACAACTTCAGGGGTATAGGAT
2197263 TTGTAGCTTCAT
1 TTGTAGCTTCAT
2197275 CTTGCTCCAC
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.04
44 42 0.51
45 4 0.05
49 4 0.05
50 28 0.34
51 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (44 bp):
TTGTAGCTTCATTTTGACTCACTACAACTTCAGGGGTATAGGAT
Found at i:2197247 original size:50 final size:49
Alignment explanation
Indices: 2197193--2197341 Score: 116
Period size: 50 Copynumber: 3.1 Consensus size: 49
2197183 TGCTCTACTA
2197193 CAACTTTAGGGAGATAAGATTCGCAATTGTAGTTTCATTTCGACCCACTG
1 CAACTTTAGGGAGATAAGATT-GCAATTGTAGTTTCATTTCGACCCACTG
* * * *
2197243 CAACTTCATGG-G-TATAG---G-ATTTGTAGCTTCATCTT-G-CTCCACTG
1 CAACTTTAGGGAGATA-AGATTGCAATTGTAGTTTCAT-TTCGAC-CCACTG
* * * * *
2197287 TAACTTTAGGGAGATAAGATTTACCATTGTAGTTTCATTCCGACCTACTG
1 CAACTTTAGGGAGATAAGA-TTGCAATTGTAGTTTCATTTCGACCCACTG
2197337 CAACT
1 CAACT
2197342 AATTTATAGC
Statistics
Matches: 73, Mismatches: 14, Indels: 24
0.66 0.13 0.22
Matches are distributed among these distances:
43 1 0.01
44 27 0.37
45 6 0.08
46 2 0.03
48 2 0.03
49 4 0.05
50 30 0.41
51 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (49 bp):
CAACTTTAGGGAGATAAGATTGCAATTGTAGTTTCATTTCGACCCACTG
Found at i:2197308 original size:44 final size:44
Alignment explanation
Indices: 2197125--2197308 Score: 126
Period size: 44 Copynumber: 4.0 Consensus size: 44
2197115 AGATTTATCG
* * * * *
2197125 TTGTAGTTTCATTTTGACT-CACTACAACTTCAGGG-GTATAGGAT
1 TTGTAGCTTCATCTTG-CTCCACTGCAACTTTAGGGAG-ATAAGAT
* *
2197169 TTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGA-T
* * * *
2197214 CGCAATTGTAGTTTCAT-TTCGAC-CCACTGCAACTTCATGGG-TATAGGAT
1 -----TTGTAGCTTCATCTT-G-CTCCACTGCAACTTTA-GGGAGATAAGAT
*
2197263 TTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGAT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGAT
2197307 TT
1 TT
2197309 ACCATTGTAG
Statistics
Matches: 110, Mismatches: 16, Indels: 28
0.71 0.10 0.18
Matches are distributed among these distances:
43 6 0.05
44 65 0.59
45 4 0.04
49 3 0.03
50 28 0.25
51 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (44 bp):
TTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGAT
Found at i:2197536 original size:364 final size:364
Alignment explanation
Indices: 2197030--2197705 Score: 971
Period size: 364 Copynumber: 1.9 Consensus size: 364
2197020 AAGATTCACT
* * * * *
2197030 ATTGTAGTTTTATTCCGACCTACTGCAACTTCAGGGGTATAGGATTTATAGCTCCATCTTACTCC
1 ATTGTAGTTTCATTCCGACCCACTGCAACTTCAAGGGTATAAGACTTATAGCTCCATCTTACTCC
* * * ** *
2197095 ACTATGACTTCAGGAAGATAAGATTTATCGTTGTAGTTTCATTTTGACTCACTACAACTTCAGGG
66 ACTATGACTTCAGGAAGATAAGATTCATCATTGTAGTTTCATATCCACTCACTAAAACTTCAGGG
* *
2197160 GTATAGGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATTCGCAATTGTAG
131 ATATAAGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATTCGCAATTGTAG
* * * * *
2197225 TTTCATTTCGACCCACTGCAACTTCATGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGTAA
196 TTTCATTCCAACCCACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTGCAA
* * * *
2197290 CTTTAGGGAGATAAGATTTACCATTGTAGTTTCATTCCGACCTACTGCAACTAATTTATAGCTCT
261 CTTTAGGGAGATAAGATTCACCACTGTAGTTTCATTCCAACCCACTGCAACTAATTTATAGCTCT
2197355 ATCTTACTCCACTACGACTTTAGAGAGATAAGATTTGTC
326 ATCTTACTCCACTACGACTTTAGAGAGATAAGATTTGTC
* * *
2197394 ATTGTAGTTTCATTCCGACCCACTGCAACTTCAAGGGTATAAGACTTGTAGCTTCATCTTGCTCC
1 ATTGTAGTTTCATTCCGACCCACTGCAACTTCAAGGGTATAAGACTTATAGCTCCATCTTACTCC
* * * * *
2197459 A-T-TGCATCTTTAGGGAGATAAGATTCGTTATTGTAGTTTCA-ATCCATTTCACTAAAACTTCA
66 ACTATG-A-CTTCAGGAAGATAAGATTCATCATTGTAGTTTCATATCCA-CTCACTAAAACTTCA
* * *
2197521 GGGATATAAGATTTGTAGCTTCATCTTGCTCTACTGCATCTTTAGGGAGATAAGATTCGCCATTG
128 GGGATATAAGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATTCGCAATTG
*
2197586 TAGTTTCATTCCAACCCGCTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTG
193 TAGTTTCATTCCAACCCACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTG
* * *
2197651 CATCTTTAGGGAGGTAAGATTCACTACTGTAGTTTCATTCCAACCCACTGCAACT
258 CAACTTTAGGGAGATAAGATTCACCACTGTAGTTTCATTCCAACCCACTGCAACT
2197706 TCAGGGGGAC
Statistics
Matches: 272, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
362 2 0.01
363 4 0.01
364 266 0.98
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (364 bp):
ATTGTAGTTTCATTCCGACCCACTGCAACTTCAAGGGTATAAGACTTATAGCTCCATCTTACTCC
ACTATGACTTCAGGAAGATAAGATTCATCATTGTAGTTTCATATCCACTCACTAAAACTTCAGGG
ATATAAGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGGGAGATAAGATTCGCAATTGTAG
TTTCATTCCAACCCACTGCAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTGCAA
CTTTAGGGAGATAAGATTCACCACTGTAGTTTCATTCCAACCCACTGCAACTAATTTATAGCTCT
ATCTTACTCCACTACGACTTTAGAGAGATAAGATTTGTC
Found at i:2197566 original size:270 final size:270
Alignment explanation
Indices: 2197073--2197611 Score: 733
Period size: 270 Copynumber: 2.0 Consensus size: 270
2197063 GGGGTATAGG
* *
2197073 ATTTATAGCTCCATCTTACTCCACTATGACTTCAGGAAGATAAGATTTATCGTTGTAGTTTCATT
1 ATTTATAGCTCCATCTTACTCCACTACGACTTCAGGAAGATAAGATTTATCATTGTAGTTTCATT
** * * * * *
2197138 TTGACTCACTACAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCTACTACAACTTTAGG
66 CCGACCCACTACAACTTCAAGGGTATAAGACTTGTAGCTTCATCTTGCTCCACTACAACTTTAGG
* * ** *
2197203 GAGATAAGATTCGCAATTGTAGTTTCATTTCGACCCACTGCAACTTCATGGGTATAGGATTTGTA
131 GAGATAAGATTCGCAATTGTAGTTTCATATCCACCCACTAAAACTTCATGGGTATAAGATTTGTA
* * * *
2197268 GCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGATTTACCATTGTAGTTTCATTCCGACCT
196 GCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCACCATTGTAGTTTCATTCCAACCC
2197333 ACTGCAACTA
261 ACTGCAACTA
* * *
2197343 ATTTATAGCTCTATCTTACTCCACTACGACTTTA-GAGAGATAAGATTTGTCATTGTAGTTTCAT
1 ATTTATAGCTCCATCTTACTCCACTACGACTTCAGGA-AGATAAGATTTATCATTGTAGTTTCAT
* * * *
2197407 TCCGACCCACTGCAACTTCAAGGGTATAAGACTTGTAGCTTCATCTTGCTCCATTGCATCTTTAG
65 TCCGACCCACTACAACTTCAAGGGTATAAGACTTGTAGCTTCATCTTGCTCCACTACAACTTTAG
** **
2197472 GGAGATAAGATTCGTTATTGTAGTTTCA-ATCCATTTCACTAAAACTTCA-GGGATATAAGATTT
130 GGAGATAAGATTCGCAATTGTAGTTTCATATCCA-CCCACTAAAACTTCATGGG-TATAAGATTT
* * *
2197535 GTAGCTTCATCTTGCTCTACTGCATCTTTAGGGAGATAAGATTCGCCATTGTAGTTTCATTCCAA
193 GTAGCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCACCATTGTAGTTTCATTCCAA
*
2197600 CCCGCTGCAACT
258 CCCACTGCAACT
2197612 TCAGGGGTAT
Statistics
Matches: 233, Mismatches: 33, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
269 8 0.03
270 225 0.97
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (270 bp):
ATTTATAGCTCCATCTTACTCCACTACGACTTCAGGAAGATAAGATTTATCATTGTAGTTTCATT
CCGACCCACTACAACTTCAAGGGTATAAGACTTGTAGCTTCATCTTGCTCCACTACAACTTTAGG
GAGATAAGATTCGCAATTGTAGTTTCATATCCACCCACTAAAACTTCATGGGTATAAGATTTGTA
GCTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCACCATTGTAGTTTCATTCCAACCC
ACTGCAACTA
Found at i:2197574 original size:44 final size:44
Alignment explanation
Indices: 2197432--2197671 Score: 139
Period size: 44 Copynumber: 5.2 Consensus size: 44
2197422 CTTCAAGGGT
* *
2197432 ATAAGACTTGTAGCTTCATCTTGCTCCATTGCATCTTTAGGGAG
1 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAG
* ** * * *
2197476 ATAAGATTCGTTATTGTAGTTTCAATCCATT--T-CACTAAAACTTCAGGGAT
1 ATAAGA-----T-TTGTAGCTTC-AT-C-TTGCTCCACTGCATCTTTAGGGAG
*
2197526 ATAAGATTTGTAGCTTCATCTTGCTCTACTGCATCTTTAGGGAG
1 ATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAG
* *** * * *
2197570 ATAAGATTCGCCATTGTAGTTTCATTCCAAC-CCGCTGCAACTTCAGGG-G
1 ATAAGA-T-----TTGTAGCTTCA-TCTTGCTCCACTGCATCTTTAGGGAG
2197619 TATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAG
1 -ATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAG
*
2197664 GTAAGATT
1 ATAAGATT
2197672 CACTACTGTA
Statistics
Matches: 143, Mismatches: 31, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 6 0.04
44 64 0.45
45 3 0.02
49 2 0.01
50 56 0.39
51 6 0.04
52 1 0.01
53 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (44 bp):
ATAAGATTTGTAGCTTCATCTTGCTCCACTGCATCTTTAGGGAG
Found at i:2197608 original size:50 final size:48
Alignment explanation
Indices: 2197379--2197711 Score: 124
Period size: 50 Copynumber: 7.0 Consensus size: 48
2197369 CGACTTTAGA
* *
2197379 GAGATAAGATTTGTCATTGTAGTTTCATTCCGACCCACTGCAACTTCAAGG
1 GAGATAAGA-TT-CCATTGTAGTTTCATTCCAACCCACTGCAACTTC-AGG
* * *** * * *
2197430 G-TATAAGA---C-TTGTAGCTTCA-TCTTGCTCCATTGCATCTTTAGG
1 GAGATAAGATTCCATTGTAGTTTCATTCCAAC-CCACTGCAACTTCAGG
* * *** **
2197473 GAGATAAGATTCGTTATTGTAGTTTCAATCCATTTCACTAAAACTTCAGG
1 GAGATAAGATTC--CATTGTAGTTTCATTCCAACCCACTGCAACTTCAGG
* * *** * * *
2197523 GATATAAGA-T---TTGTAGCTTCA-TCTTGCTCTACTGCATCTTTAGG
1 GAGATAAGATTCCATTGTAGTTTCATTCCAAC-CCACTGCAACTTCAGG
*
2197567 GAGATAAGATTCGCCATTGTAGTTTCATTCCAACCCGCTGCAACTTCAGG
1 GAGATAAGATT--CCATTGTAGTTTCATTCCAACCCACTGCAACTTCAGG
* *** * *
2197617 G-GTATAAGA-T---TTGTAGCTTCA-TCTTGCTCCACTGCATCTTTAGG
1 GAG-ATAAGATTCCATTGTAGTTTCATTCCAAC-CCACTGCAACTTCAGG
* *
2197661 GAGGTAAGATTCACTACTGTAGTTTCATTCCAACCCACTGCAACTTCAGG
1 GAGATAAGATTC-C-ATTGTAGTTTCATTCCAACCCACTGCAACTTCAGG
2197711 G
1 G
2197712 GGACTAGAAT
Statistics
Matches: 198, Mismatches: 57, Indels: 55
0.64 0.18 0.18
Matches are distributed among these distances:
43 12 0.06
44 83 0.42
45 4 0.02
49 3 0.02
50 87 0.44
51 9 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (48 bp):
GAGATAAGATTCCATTGTAGTTTCATTCCAACCCACTGCAACTTCAGG
Found at i:2202351 original size:41 final size:41
Alignment explanation
Indices: 2202306--2202436 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
2202296 GCATTACGCC
*
2202306 TGCTAGGCTCGGAGCTTGATAATATTCACCAGCTTAAAGCT
1 TGCTAGGCTCGGAGCTCGATAATATTCACCAGCTTAAAGCT
* *** * * *
2202347 TGCTAGCCCTTTAAG-TCCGAT-ATCATTTCACTAGCATT-ACGCC
1 TGCTAG-GCTCGGAGCT-CGATAAT-A-TTCACCAGC-TTAAAGCT
*
2202390 TGCTAGGCTCGGAGCCCGATAATATTCACCAGCTTAAAGCT
1 TGCTAGGCTCGGAGCTCGATAATATTCACCAGCTTAAAGCT
2202431 TGCTAG
1 TGCTAG
2202437 ACCTTTAAGT
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
40 2 0.03
41 26 0.39
42 17 0.26
43 19 0.29
44 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (41 bp):
TGCTAGGCTCGGAGCTCGATAATATTCACCAGCTTAAAGCT
Found at i:2202395 original size:43 final size:42
Alignment explanation
Indices: 2202260--2202479 Score: 148
Period size: 43 Copynumber: 5.2 Consensus size: 42
2202250 CCGGCAATAA
* *
2202260 GCCTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTAC
1 GCCTGCTAG-CCTTTAAGTCCGATATCATTTCACCAGCATTAC
* *** * *
2202303 GCCTGCTAGGCTCGGAG-CTTGATA--ATATTCACCAGC-TTAAA
1 GCCTGCTAGCCTTTAAGTC-CGATATCAT-TTCACCAGCATT-AC
* *
2202344 GCTTGCTAGCCCTTTAAGTCCGATATCATTTCACTAGCATTAC
1 GCCTGCTAG-CCTTTAAGTCCGATATCATTTCACCAGCATTAC
* *** * *
2202387 GCCTGCTAGGCTCGGAGCCCGATA--ATATTCACCAGC-TTAAA
1 GCCTGCTAGCCTTTAAGTCCGATATCAT-TTCACCAGCATT-AC
* * *
2202428 GCTTGCTAGACCTTTAAGTCCTATATCATTTCACCGGCATTAC
1 GCCTGCTAG-CCTTTAAGTCCGATATCATTTCACCAGCATTAC
2202471 GCCTGCTAG
1 GCCTGCTAG
2202480 GCTCAAAGCC
Statistics
Matches: 129, Mismatches: 34, Indels: 28
0.68 0.18 0.15
Matches are distributed among these distances:
40 8 0.06
41 35 0.27
42 34 0.26
43 44 0.34
44 8 0.06
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (42 bp):
GCCTGCTAGCCTTTAAGTCCGATATCATTTCACCAGCATTAC
Found at i:2202490 original size:84 final size:84
Alignment explanation
Indices: 2202258--2202483 Score: 380
Period size: 84 Copynumber: 2.7 Consensus size: 84
2202248 CACCGGCAAT
* **
2202258 AAGCCTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCTT
1 AAGCTTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
2202323 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
* * **
2202342 AAGCTTGCTAGCCCTTTAAGTCCGATATCATTTCACTAGCATTACGCCTGCTAGGCTCGGAGCCC
1 AAGCTTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
2202407 GATAATATTCACCAGCTTA
66 GATAATATTCACCAGCTTA
*
2202426 AAGCTTGCTAGACCTTTAAGTCCTATATCATTTCACCGGCATTACGCCTGCTAGGCTC
1 AAGCTTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTACGCCTGCTAGGCTC
2202484 AAAGCCCAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 131 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (84 bp):
AAGCTTGCTAGACCTTTAAGTCCAATATCATTTCACCGGCATTACGCCTGCTAGGCTCGGAGCCC
GATAATATTCACCAGCTTA
Found at i:2206546 original size:19 final size:20
Alignment explanation
Indices: 2206512--2206566 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
2206502 AACTATGAGG
*
2206512 GTAA-AAAA-AATGATAATA
1 GTAATAAAATAATAATAATA
2206530 -TAATAAAATAATAATAA-A
1 GTAATAAAATAATAATAATA
*
2206548 GTAATAAAATAATAGTAAT
1 GTAATAAAATAATAATAAT
2206567 CGTATTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 3 0.10
18 5 0.16
19 23 0.74
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.27
Consensus pattern (20 bp):
GTAATAAAATAATAATAATA
Found at i:2210983 original size:33 final size:36
Alignment explanation
Indices: 2210946--2211018 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 36
2210936 CTTAGTTATA
* *
2210946 GTCTTTTCA-TTAAA-A-TGCCATAGCCCAACTATG
1 GTCTTTACATTTAAATATTGCCATAGCCCAACAATG
* *
2210979 GTC-TTACATTTAAATATTGCCATGGTCCAACAATG
1 GTCTTTACATTTAAATATTGCCATAGCCCAACAATG
2211014 GTCTT
1 GTCTT
2211019 ATCCGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
32 4 0.12
33 8 0.25
34 1 0.03
35 18 0.56
36 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (36 bp):
GTCTTTACATTTAAATATTGCCATAGCCCAACAATG
Found at i:2222321 original size:39 final size:39
Alignment explanation
Indices: 2222263--2222458 Score: 182
Period size: 39 Copynumber: 5.0 Consensus size: 39
2222253 TTCAGTGATG
* **
2222263 TATATCCGGACTTATGGTCCATAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
2222302 TATATCCGGACTTAGGGTCCGCAGGCTATTTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
2222341 TATATCCGGACTTAAGATCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * * *
2222380 TATGTCCGGGC-TAAAGTCCCGCAGGCTACGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGGAAT
** **
2222419 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGTAAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGG-AAT
2222458 T
1 T
2222459 GGTTTCAAGT
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
38 15 0.11
39 117 0.89
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:2228159 original size:21 final size:23
Alignment explanation
Indices: 2228126--2228183 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
2228116 TAAAGAAATA
* *
2228126 ATATATTTTATAAGTATTA-A-T
1 ATATATATAATAAGTATTATATT
*
2228147 ATATATATAATAATTATTATATT
1 ATATATATAATAAGTATTATATT
*
2228170 ATAGATTATAATAA
1 ATATA-TATAATAA
2228184 AAGATATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 5 0.17
24 8 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
ATATATATAATAAGTATTATATT
Found at i:2229606 original size:18 final size:17
Alignment explanation
Indices: 2229562--2229597 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2229552 CAAGTTTAAT
2229562 AACTAAAAAAGACTGAA
1 AACTAAAAAAGACTGAA
2229579 AACTAAAAAAGACTGAA
1 AACTAAAAAAGACTGAA
2229596 AA
1 AA
2229598 ACTGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (17 bp):
AACTAAAAAAGACTGAA
Found at i:2232496 original size:141 final size:135
Alignment explanation
Indices: 2232312--2232721 Score: 538
Period size: 141 Copynumber: 3.0 Consensus size: 135
2232302 CAGAGGAACT
* * *
2232312 GCAGAATGTCCAC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTTGAACCACA
1 GCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCGAACCACA
* * *
2232375 GATGTCTTTTGCAGCAGAGCAGCATAAGAAATCTAAAATGGCAACAGAAAGTTCTCAAATGCCAC
64 GATGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCAC
2232440 AACTAAC
129 AACTAAC
*
2232447 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCAAAC
1 GCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCGAAC
* ** * * * * *
2232512 CGCAGACATCTTTTGCAACAGAACCGCATAAGAAATCAAAAATGGAAATAGGAAGTTCTGAAATG
60 CACAGATGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATG
*
2232577 CCACAACTAAT
125 CCACAACTAAC
* *
2232588 GCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCGAACCACAGA
1 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCGAACCACAGA
* *
2232653 TGTCTTTTGCAAAAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCACA
66 TGTCTTTTGCAACAGAA-CAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
2232717 ACTAA
130 ACTAA
2232722 TGCCAATGGA
Statistics
Matches: 237, Mismatches: 29, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
135 115 0.49
136 3 0.01
141 118 0.50
142 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (135 bp):
GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCGAACCACAGA
TGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACAA
CTAAC
Found at i:2232703 original size:135 final size:135
Alignment explanation
Indices: 2232311--2232724 Score: 546
Period size: 135 Copynumber: 3.0 Consensus size: 135
2232301 TCAGAGGAAC
* * *
2232311 TGCAGAATGTCCAC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTTGAACCAC
1 TGCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCGAACCAC
* * *
2232374 AGATGTCTTTTGCAGCAG-AGCAGCATAAGAAATCTAAAATGGCAACAGAAAGTTCTCAAATGCC
64 AGATGTCTTTTGCAACAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCC
2232438 ACAACTAA
128 ACAACTAA
* *
2232446 CGCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCAAA
1 TGCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCGAA
* ** * * * * *
2232511 CCGCAGACATCTTTTGCAACAGAACCGCATAAGAAATCAAAAATGGAAATAGGAAGTTCTGAAAT
60 CCACAGATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAAT
2232576 GCCACAACTAA
125 GCCACAACTAA
* *
2232587 TGCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCGAACCACAG
1 TGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCGAACCACAG
* *
2232652 ATGTCTTTTGCAAAAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCACA
66 ATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
2232717 ACTAA
131 ACTAA
2232722 TGC
1 TGC
2232725 CAATGGATTC
Statistics
Matches: 240, Mismatches: 30, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
135 120 0.50
136 2 0.01
141 115 0.48
142 3 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (135 bp):
TGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCGAACCACAG
ATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
ACTAA
Found at i:2245221 original size:15 final size:15
Alignment explanation
Indices: 2245201--2245233 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2245191 ACATAGATTT
*
2245201 ATTCTAAATTGGTTC
1 ATTCTAAATTGGCTC
2245216 ATTCTAAATTGGCTC
1 ATTCTAAATTGGCTC
2245231 ATT
1 ATT
2245234 TACAACATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (15 bp):
ATTCTAAATTGGCTC
Found at i:2247251 original size:24 final size:23
Alignment explanation
Indices: 2247207--2247253 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2247197 TTATGTTTGC
* * *
2247207 TTATTATATAAGTATATTAAATA
1 TTATTATAAAAGTAAAGTAAATA
2247230 TTATTATTAAAAGTAAAGTAAATA
1 TTATTA-TAAAAGTAAAGTAAATA
2247254 AAAAGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TTATTATAAAAGTAAAGTAAATA
Found at i:2247259 original size:16 final size:16
Alignment explanation
Indices: 2247238--2247289 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2247228 TATTATTATT
*
2247238 AAAAGTAAAGTAAATA
1 AAAAGTAAAATAAATA
2247254 AAAAGTAAAATAAAT-
1 AAAAGTAAAATAAATA
* *
2247269 GAAA-TAAAAGAAATGA
1 AAAAGTAAAATAAAT-A
2247285 AAAAG
1 AAAAG
2247290 AGAAACAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 17 0.59
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.15
Consensus pattern (16 bp):
AAAAGTAAAATAAATA
Found at i:2247308 original size:22 final size:21
Alignment explanation
Indices: 2247275--2247315 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2247265 AAATGAAATA
*
2247275 AAAGAAATGAAAAAGAGAAAC
1 AAAGAAACGAAAAAGAGAAAC
*
2247296 AAAGAAAACGAAACAGAGAA
1 AAAG-AAACGAAAAAGAGAA
2247316 GAACACGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.71, C:0.07, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAGAAACGAAAAAGAGAAAC
Found at i:2249242 original size:40 final size:40
Alignment explanation
Indices: 2249198--2249382 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
2249188 GCTACTCATT
* *
2249198 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2249238 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
2249278 CCAATGCCTTCGGG-CTTAG-TCTGAAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
2249317 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2249358 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2249383 CATCATTCGA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 5 0.04
39 26 0.21
40 75 0.62
41 15 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:2249366 original size:79 final size:80
Alignment explanation
Indices: 2249226--2249376 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 80
2249216 AGCCCGGTTA
* * *
2249226 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
2249291 G-CTTAGTCTGAAAT
66 GACTTAGTCTGAAAT
** * *
2249305 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTC
2249368 GGGACTTAG
64 GGGACTTAG
2249377 CCCGGACATC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.05
79 50 0.81
80 9 0.15
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGTCTGAAAT
Found at i:2251388 original size:3 final size:3
Alignment explanation
Indices: 2251382--2251422 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2251372 ATTATTATTA
2251382 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2251423 ATTATGGTAT
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:2251559 original size:22 final size:21
Alignment explanation
Indices: 2251517--2251573 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 21
2251507 TGGAAAAATG
* *
2251517 TATATTGTATTGAAATTGAAT
1 TATATTGAATTGAAATGGAAT
*
2251538 TATATGTGAATTGATATGGAAT
1 TATAT-TGAATTGAAATGGAAT
** *
2251560 CGTATTGAAATGAA
1 TATATTGAATTGAA
2251574 GGGAAAGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (21 bp):
TATATTGAATTGAAATGGAAT
Found at i:2260928 original size:39 final size:40
Alignment explanation
Indices: 2260827--2260981 Score: 165
Period size: 40 Copynumber: 3.9 Consensus size: 40
2260817 TTGAATGATG
* * * *
2260827 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
2260867 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
2260907 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
2260946 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGATGATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GATA
2260982 AGTGTCGTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
39 35 0.36
40 48 0.49
41 13 0.13
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:2260965 original size:79 final size:81
Alignment explanation
Indices: 2260827--2260981 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 81
2260817 TTGAATGATG
* *
2260827 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
2260892 GTGCGA-GATACTAAT
66 GTGCGATGATACTAAT
* * * * **
2260907 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
2260969 TTGTGCGATGATA
64 TTGTGCGATGATA
2260982 AGTGTCGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 1 0.02
79 41 0.64
80 22 0.34
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGATGATACTAAT
Found at i:2261169 original size:39 final size:40
Alignment explanation
Indices: 2261068--2261252 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
2261058 TTGAATGATG
* * * *
2261068 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
2261107 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
2261148 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2261187 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2261226 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
2261253 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 36 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:2261176 original size:241 final size:242
Alignment explanation
Indices: 2260733--2261217 Score: 927
Period size: 241 Copynumber: 2.0 Consensus size: 242
2260723 AATTACAAGA
* *
2260733 ATGATAAGTGTCTTGTGTTTGAGTTTTGCTAACGAAAATGAAATACGAATGTGCCATGATTTATT
1 ATGATAAGTGTC-TGTGTTCGAGTTTTGCTAACGAAAATGAAATACGAATGTGCCATGATTTACT
2260798 GTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGAC
65 GTTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGAC
2260863 CATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCA
130 CATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCA
2260928 TTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCG
195 TTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCG
*
2260976 ATGATAAGTGTC-GTGTTCGAGTTTTGTTAACGAAAATGAAATACGAATGTGCCATGATTTACTG
1 ATGATAAGTGTCTGTGTTCGAGTTTTGCTAACGAAAATGAAATACGAATGTGCCATGATTTACTG
2261040 TTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACC
66 TTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACC
2261105 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCAT
131 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCAT
2261170 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCG
196 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCG
2261217 A
1 A
2261218 GTTACTATAA
Statistics
Matches: 239, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
241 227 0.95
243 12 0.05
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (242 bp):
ATGATAAGTGTCTGTGTTCGAGTTTTGCTAACGAAAATGAAATACGAATGTGCCATGATTTACTG
TTAAATGTGCATGGTTATTTGAATGATGTCCGGGCTAAGTCCCAAAGGCTTTGTGCTAAGTGACC
ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCG
Found at i:2261206 original size:79 final size:81
Alignment explanation
Indices: 2261068--2261252 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
2261058 TTGAATGATG
* * *
2261068 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
2261132 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
2261147 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
2261209 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
2261227 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2261253 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:2261274 original size:79 final size:79
Alignment explanation
Indices: 2261121--2261275 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
2261111 GGACTAAGAT
* * **
2261121 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
2261186 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
2261200 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
2261263 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
2261276 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:2265097 original size:33 final size:34
Alignment explanation
Indices: 2265054--2265119 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
2265044 ACGGTGCATG
*
2265054 CAATAACAGTCTGAGCCTGAGCCCTATTTAGTAT
1 CAATAACAGTCTGAGCCTGAGCCCTATATAGTAT
* * *
2265088 CAAT-ACAGTCTGGGCCTTAGCCTTATATAGTA
1 CAATAACAGTCTGAGCCTGAGCCCTATATAGTA
2265120 ACAGTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (34 bp):
CAATAACAGTCTGAGCCTGAGCCCTATATAGTAT
Found at i:2265500 original size:23 final size:21
Alignment explanation
Indices: 2265468--2265521 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
2265458 GTCTGTGATA
2265468 TGTGAATTTATTCTGTACAGTTTC
1 TGTG-ATTTATT-TGT-CAGTTTC
*
2265492 TGTGATTTAATTTGTCTGTTTC
1 TGTGATTT-ATTTGTCAGTTTC
2265514 TGTG-TTTA
1 TGTGATTTA
2265522 ATTATGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 10 0.36
23 7 0.25
24 7 0.25
ACGTcount: A:0.17, C:0.09, G:0.19, T:0.56
Consensus pattern (21 bp):
TGTGATTTATTTGTCAGTTTC
Found at i:2266074 original size:27 final size:28
Alignment explanation
Indices: 2266044--2266100 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
2266034 ATTTTTGATG
2266044 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
2266071 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
2266100 A
1 A
2266101 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:2268322 original size:42 final size:46
Alignment explanation
Indices: 2268262--2268395 Score: 141
Period size: 49 Copynumber: 2.9 Consensus size: 46
2268252 CTTCGTTTAC
* ** *
2268262 TCGATGCCAAAGTTCAACTATGGTCTTACAC-AT-C-T-TCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACAATACATATCACATA
*
2268304 TCGATGTCATAGCCCAACTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC--AAT-ACATATCACATA
*
2268353 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATC
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-AAT-ACATATC
2268396 TCACTAATGC
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
42 27 0.35
45 2 0.03
47 1 0.01
48 12 0.16
49 35 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (46 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACAATACATATCACATA
Found at i:2268364 original size:49 final size:48
Alignment explanation
Indices: 2268301--2268395 Score: 163
Period size: 49 Copynumber: 2.0 Consensus size: 48
2268291 ACATCTTCAT
*
2268301 ATATCGATGTCATAGCCCAACTATGGTCTTACACGTAATCACATATCAC
1 ATATCGATGCCATAGCCCAACTATGGTCTTACACG-AATCACATATCAC
*
2268350 ATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATC
1 ATATCGATGCCATAGCCCAACTATGGTCTTACACGAATCACATATC
2268396 TCACTAATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 11 0.25
49 33 0.75
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (48 bp):
ATATCGATGCCATAGCCCAACTATGGTCTTACACGAATCACATATCAC
Found at i:2268424 original size:46 final size:47
Alignment explanation
Indices: 2268311--2268426 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 47
2268301 ATATCGATGT
*
2268311 CATAGCCCA-ACTATGGTCTTACACGTAATCACATATCACATATCGATGC
1 CATAGCCCAGA-TACGGTCTTACACGTAATCACATATCACATA-C-ATGC
* * *
2268360 CATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCACTA-ATGC
1 CATAGCCCAGATACGGTCTTACACGTAATCACATATCACA-TACATGC
* *
2268406 CTTATCCCAGATACGGTCTTA
1 CATAGCCCAGATACGGTCTTA
2268427 TACAGTAGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
46 21 0.36
48 13 0.22
49 25 0.42
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (47 bp):
CATAGCCCAGATACGGTCTTACACGTAATCACATATCACATACATGC
Found at i:2268530 original size:31 final size:31
Alignment explanation
Indices: 2268495--2268644 Score: 201
Period size: 31 Copynumber: 4.8 Consensus size: 31
2268485 CTTGTCACTT
* *
2268495 GTAGCCGAAGCTACCACTATTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
2268526 GTAGCCGGAGATACCATTTTTTCACTGATCAG
1 GTAGCCGAAGCTACCA-CTTTTCACTGATCAG
* * *
2268558 GTAGTCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2268589 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2268620 GTAGCCGAAGCTATCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2268645 TGTCATTTGT
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
31 79 0.75
32 26 0.25
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2268718 original size:50 final size:51
Alignment explanation
Indices: 2268620--2268748 Score: 206
Period size: 50 Copynumber: 2.5 Consensus size: 51
2268610 CACTGATCAG
* * *
2268620 GTAGCCGAAGCTATCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
* *
2268671 GTAGTCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
2268721 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
2268749 TGTCATGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 46 0.66
51 24 0.34
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:2271357 original size:27 final size:27
Alignment explanation
Indices: 2271327--2271445 Score: 130
Period size: 27 Copynumber: 4.4 Consensus size: 27
2271317 GGGCATAATC
* *
2271327 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * *
2271354 GTCATTTTACCCTATTGGGGTATTGCG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
2271381 GTCATTTTACCCTATAGGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
2271408 GCCATTTTACTCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
2271435 ATTATTTTACC
1 GTCATTTTACC
2271446 TATTTTGGGG
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:2272652 original size:51 final size:49
Alignment explanation
Indices: 2272532--2272775 Score: 281
Period size: 51 Copynumber: 4.9 Consensus size: 49
2272522 TATTGTGAGG
* * * * * * *
2272532 TCACGTGTGTAGTACTAACTGCAGGCTACTACGTGTACCGGATTATTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAATTGA
*
2272581 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAA-TT-GA
* *
2272632 TCACATGTGTAGTATTAAGTGCAGGCTACTATGCATACCCGATAACTTCGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAA-TT-GA
* * * * *
2272683 TTACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAATTGA
** * *
2272732 TTGCATGTGTAGTACTAAGTGCAGGGTACTATGCGTACCAGATA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATA
2272776 GCTTTGGCTA
Statistics
Matches: 170, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 78 0.46
50 4 0.02
51 88 0.52
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (49 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAATTGA
Found at i:2272711 original size:102 final size:100
Alignment explanation
Indices: 2272532--2272775 Score: 276
Period size: 100 Copynumber: 2.4 Consensus size: 100
2272522 TATTGTGAGG
* * * ** * * * **
2272532 TCACGTGTGTAGTACTAACTGCAGGCTACTACGTGTACCGGATTA-TT-GGTCGCATGTGTAGTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATAACTTCGATTACATGTGTAGTA
*
2272595 CTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 CTAAGTGCAGGCTACTACGCGTACCCGATAA-TT-GA
* *
2272632 TCACATGTGTAGTATTAAGTGCAGGCTACTATGCATACCCGATAACTTCGATTACATGTGTAGTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATAACTTCGATTACATGTGTAGTA
* * *
2272697 CTAAGTGCAGGCTACTACGTGTACCGGATAATTGG
66 CTAAGTGCAGGCTACTACGCGTACCCGATAATTGA
** * *
2272732 TTGCATGTGTAGTACTAAGTGCAGGGTACTATGCGTACCAGATA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATA
2272776 GCTTTGGCTA
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
100 76 0.63
101 4 0.03
102 41 0.34
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTATGCATACCAGATAACTTCGATTACATGTGTAGTA
CTAAGTGCAGGCTACTACGCGTACCCGATAATTGA
Found at i:2274681 original size:52 final size:50
Alignment explanation
Indices: 2274576--2274745 Score: 220
Period size: 52 Copynumber: 3.4 Consensus size: 50
2274566 CAATGGCCAG
* * *
2274576 CACATAGTACCATC-CTTGTAGTCAAAGCTACCTTCTTCACAAAGTGGCCTT
1 CACATAGTACCA-CACTTGGA-CCAAAGCTATCTTCTTCACAAAGTGGCCTT
* *
2274627 CACATAGTACCATACTTGCGACCAAAGCTATCTTTCTTCACAAAGTGGCATT
1 CACATAGTACCACACTTG-GACCAAAGCTATC-TTCTTCACAAAGTGGCCTT
*
2274679 CACATAGTACCACACTTGTGACC-AAGCTATC-TCTTCTCAAAGTGGCCTT
1 CACATAGTACCACACTTG-GACCAAAGCTATCTTCTTCACAAAGTGGCCTT
2274728 CACATAGTACCACACTTG
1 CACATAGTACCACACTTG
2274746 AGTCACTAGT
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
49 34 0.32
51 33 0.31
52 40 0.37
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (50 bp):
CACATAGTACCACACTTGGACCAAAGCTATCTTCTTCACAAAGTGGCCTT
Found at i:2275986 original size:8 final size:8
Alignment explanation
Indices: 2275975--2276007 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
2275965 ATTAAACTAG
2275975 AATAATAA
1 AATAATAA
2275983 AATAATAA
1 AATAATAA
2275991 AATAATAA
1 AATAATAA
2275999 AATAATAA
1 AATAATAA
2276007 A
1 A
2276008 TGATTCTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:2278803 original size:19 final size:20
Alignment explanation
Indices: 2278778--2278863 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2278768 CATCCAAACA
* *
2278778 CCAGAAAAGCAAATCAATTT
1 CCAGAAAAGTAAATCATTTT
2278798 -CAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
*
2278817 CCAAAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
*
2278837 CCAAAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
*
2278857 ACAGAAA
1 CCAGAAA
2278864 TTATTTTTCG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.28
20 43 0.72
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:2282015 original size:23 final size:24
Alignment explanation
Indices: 2281985--2282032 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2281975 TCTTTAAGCT
2281985 ACCAAAAC-ATGC-CAATTCATCAA
1 ACCAAAACTAT-CACAATTCATCAA
*
2282008 ACCAAAACTATCACAATTTATCAA
1 ACCAAAACTATCACAATTCATCAA
2282032 A
1 A
2282033 TTCCAAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.21
Consensus pattern (24 bp):
ACCAAAACTATCACAATTCATCAA
Found at i:2282777 original size:43 final size:42
Alignment explanation
Indices: 2282726--2282878 Score: 159
Period size: 44 Copynumber: 3.6 Consensus size: 42
2282716 GTACAAAGCA
*
2282726 AACGTCCCAGAAGTGGTCTTACATGTAATCAAATATCGATGCC
1 AACGTCCCAGAAGTGGTCTTACACGTAATCAAATA-CGATGCC
* * * *
2282769 -ACTGTCCCAAACAG-GGTCTTACACGAAATCATATACAATGCC
1 AAC-GTCCCAGA-AGTGGTCTTACACGTAATCAAATACGATGCC
*
2282811 AACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATA-GATGCC
1 AACGTCCCAGAAGTGGTCTTACACGT-AA--TCAAATACGATGCC
* *
2282855 AACGTCCCAGACGTAGTCTTACAC
1 AACGTCCCAGAAGTGGTCTTACAC
2282879 AAAATCTCAT
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.28
43 29 0.32
44 30 0.33
45 6 0.07
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
AACGTCCCAGAAGTGGTCTTACACGTAATCAAATACGATGCC
Found at i:2282861 original size:44 final size:43
Alignment explanation
Indices: 2282726--2282878 Score: 172
Period size: 43 Copynumber: 3.6 Consensus size: 43
2282716 GTACAAAGCA
* *
2282726 AACGTCCCAGAAGTGGTCTTACATGT-AATCAAATATCGATGCC
1 AACGTCCCAGACGTGGTCTTACACGTAAATCAAATA-CGATGCC
* * *
2282769 -ACTGTCCCAAACAG-GGTCTTACACG-AAATCATATACAATGCC
1 AAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAAATACGATGCC
2282811 AACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATA-GATGCC
1 AACGTCCCAGACGTGGTCTTACACGTAAA--TCAAATACGATGCC
*
2282855 AACGTCCCAGACGTAGTCTTACAC
1 AACGTCCCAGACGTGGTCTTACAC
2282879 AAAATCTCAT
Statistics
Matches: 93, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.29
43 30 0.32
44 29 0.31
45 6 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
AACGTCCCAGACGTGGTCTTACACGTAAATCAAATACGATGCC
Found at i:2282878 original size:86 final size:84
Alignment explanation
Indices: 2282717--2282884 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 84
2282707 GAAAAGCTCG
*
2282717 TACAAAGCAAACGTCCCAGAAGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAACA
1 TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGTAATCAAATA-CGATGCCACTGTCCCAAACA
* *
2282782 GGGTCTTACACGAAATCATA
65 GAGTCTTACACAAAATCATA
* * * *
2282802 TACAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATA-GATGCCAAC-GTCCCAG
1 TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGT-AA--TCAAATACGATGCC-ACTGTCCCAA
2282865 AC-GTAGTCTTACACAAAATC
62 ACAG-AGTCTTACACAAAATC
2282885 TCATATTGGA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
85 32 0.45
86 30 0.42
87 2 0.03
88 7 0.10
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (84 bp):
TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGTAATCAAATACGATGCCACTGTCCCAAACAG
AGTCTTACACAAAATCATA
Found at i:2290738 original size:43 final size:44
Alignment explanation
Indices: 2290690--2290810 Score: 160
Period size: 43 Copynumber: 2.8 Consensus size: 44
2290680 TGTATACACA
* *
2290690 TGTCCCAGACGTGGTCTTACATGTA-ATCACATATCGATGCC-AC
1 TGTCCCAGACGTGGTCTTACACG-AGAACACATATCGATGCCAAC
*
2290733 TGTCCCAGACAG-CGTCTTACACGAGAACACATATCGATGCCAAC
1 TGTCCCAGAC-GTGGTCTTACACGAGAACACATATCGATGCCAAC
*
2290777 -GTCCCAGACGTGGTCTTACAGGAGAACACATATC
1 TGTCCCAGACGTGGTCTTACACGAGAACACATATC
2290811 AAAAATCCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.03
43 64 0.93
44 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
TGTCCCAGACGTGGTCTTACACGAGAACACATATCGATGCCAAC
Found at i:2302609 original size:23 final size:23
Alignment explanation
Indices: 2302580--2302641 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
2302570 CGTGTCCCTA
2302580 AGCACACGGGCGTGTGCTTTGCC
1 AGCACACGGGCGTGTGCTTTGCC
2302603 AGCACACGGGCGTGTGCTTTGCC
1 AGCACACGGGCGTGTGCTTTGCC
** *
2302626 TCCACACGGGCATGTG
1 AGCACACGGGCGTGTG
2302642 AGGCATAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.21
Consensus pattern (23 bp):
AGCACACGGGCGTGTGCTTTGCC
Found at i:2303834 original size:44 final size:42
Alignment explanation
Indices: 2303692--2303863 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 42
2303682 AGCTCGTACA
* * * * **
2303692 ATGCCAACATCCCAGACGTGGTCTTACATGTAA-TCAAATATAA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATTC--ATATCG
*
2303735 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAA-TCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATTCATAT-CG
* * * *
2303777 ATGCTAATGTCCCAGATATGGTCTTACACGTAAATTTCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAA-TTCATATCG
2303821 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCTCATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAT-TCATATCG
2303864 GAATCCTATG
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
41 4 0.04
42 27 0.25
43 41 0.39
44 29 0.27
45 5 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATTCATATCG
Found at i:2308217 original size:17 final size:17
Alignment explanation
Indices: 2308195--2308228 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2308185 TGTACACCAA
2308195 AAAACTAAAAAAACTTG
1 AAAACTAAAAAAACTTG
*
2308212 AAAACTAAACAAACTTG
1 AAAACTAAAAAAACTTG
2308229 CAAGTAATAT
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:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAACTAAAAAAACTTG
Found at i:2313114 original size:34 final size:34
Alignment explanation
Indices: 2313071--2313140 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2313061 TTTGATTCAC
2313071 TTTATCTATCTCTATCTCTTGCAATTTTAATTCT
1 TTTATCTATCTCTATCTCTTGCAATTTTAATTCT
2313105 TTTATCTATCTCTATCTCTTGCAATTTTAATTCT
1 TTTATCTATCTCTATCTCTTGCAATTTTAATTCT
2313139 TT
1 TT
2313141 GTTTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (34 bp):
TTTATCTATCTCTATCTCTTGCAATTTTAATTCT
Found at i:2315913 original size:30 final size:30
Alignment explanation
Indices: 2315879--2315935 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2315869 CGAGCCTAGA
2315879 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
1 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
* * * *
2315909 GGCAAAATTGTAATTTTGCCAAAGTTT
1 GGCAAAAGTGTAAATATGCAAAAGTTT
2315936 GAGTTAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (30 bp):
GGCAAAAGTGTAAATATGCAAAAGTTTAGG
Found at i:2316718 original size:68 final size:66
Alignment explanation
Indices: 2316646--2316812 Score: 169
Period size: 67 Copynumber: 2.5 Consensus size: 66
2316636 CATCATGTGT
* * * *
2316646 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
2316709 TGTAG
62 TGTAG
** * *
2316714 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
2316779 AG
65 AG
* * *
2316781 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTC
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTC
2316813 ACATCGGTGG
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
64 24 0.28
65 3 0.04
66 13 0.15
67 32 0.38
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:2316751 original size:64 final size:64
Alignment explanation
Indices: 2316670--2316853 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
2316660 AGACATTATG
* * *
2316670 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
2316734 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
2316799 AA
63 AA
* * * *
2316801 AT-TGGCTAGGTCACATCGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
2316854 CGAATTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 20 0.20
67 33 0.34
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:2317284 original size:23 final size:23
Alignment explanation
Indices: 2317254--2317307 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2317244 AATCAGAGAT
2317254 TGAATGAGATATAAAATTAAAGC
1 TGAATGAGATATAAAATTAAAGC
2317277 TGAATGAGATATAAAATTAAAGC
1 TGAATGAGATATAAAATTAAAGC
*
2317300 TTAATGAG
1 TGAATGAG
2317308 TCTATCTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.28
Consensus pattern (23 bp):
TGAATGAGATATAAAATTAAAGC
Found at i:2324407 original size:23 final size:24
Alignment explanation
Indices: 2324377--2324424 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2324367 TCTTTAAGCT
2324377 ACCAAAAC-ATGC-CAATTCATCAA
1 ACCAAAACTAT-CACAATTCATCAA
*
2324400 ACCAAAACTATCACAATTTATCAA
1 ACCAAAACTATCACAATTCATCAA
2324424 A
1 A
2324425 TTCCAAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.21
Consensus pattern (24 bp):
ACCAAAACTATCACAATTCATCAA
Found at i:2325252 original size:44 final size:43
Alignment explanation
Indices: 2325117--2325269 Score: 172
Period size: 43 Copynumber: 3.6 Consensus size: 43
2325107 GTACAAAGCA
* *
2325117 AACGTCCCAGAAGTGGTCTTACATGT-AATCAAATATCGATGCC
1 AACGTCCCAGACGTGGTCTTACACGTAAATCAAATA-CGATGCC
* * *
2325160 -ACTGTCCCAAACAG-GGTCTTACACG-AAATCATATACAATGCC
1 AAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAAATACGATGCC
2325202 AACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATA-GATGCC
1 AACGTCCCAGACGTGGTCTTACACGTAAA--TCAAATACGATGCC
*
2325246 AACGTCCCAGACGTAGTCTTACAC
1 AACGTCCCAGACGTGGTCTTACAC
2325270 AAAATCTCAT
Statistics
Matches: 93, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.29
43 30 0.32
44 29 0.31
45 6 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
AACGTCCCAGACGTGGTCTTACACGTAAATCAAATACGATGCC
Found at i:2325269 original size:86 final size:84
Alignment explanation
Indices: 2325108--2325275 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 84
2325098 GAAAAGCTCG
*
2325108 TACAAAGCAAACGTCCCAGAAGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAACA
1 TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGTAATCAAATA-CGATGCCACTGTCCCAAACA
* *
2325173 GGGTCTTACACGAAATCATA
65 GAGTCTTACACAAAATCATA
* * * *
2325193 TACAATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCTCAAATA-GATGCCAAC-GTCCCAG
1 TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGT-AA--TCAAATACGATGCC-ACTGTCCCAA
2325256 AC-GTAGTCTTACACAAAATC
62 ACAG-AGTCTTACACAAAATC
2325276 TCATATCGGA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
85 32 0.45
86 30 0.42
87 2 0.03
88 7 0.10
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (84 bp):
TACAAAGCAAACGTCCCAGAAGTGGTCTTACACGTAATCAAATACGATGCCACTGTCCCAAACAG
AGTCTTACACAAAATCATA
Found at i:2333126 original size:43 final size:44
Alignment explanation
Indices: 2333078--2333198 Score: 169
Period size: 43 Copynumber: 2.8 Consensus size: 44
2333068 TGTATACACA
*
2333078 TGTCCCAGACGTGGTCTTACATGTA-ATCACATATCGATGCC-AC
1 TGTCCCAGACGTGGTCTTACATG-AGAACACATATCGATGCCAAC
* *
2333121 TGTCCCAGACAG-CGTCTTACACGAGAACACATATCGATGCCAAC
1 TGTCCCAGAC-GTGGTCTTACATGAGAACACATATCGATGCCAAC
2333165 -GTCCCAGACGTGGTCTTACATGAGAACACATATC
1 TGTCCCAGACGTGGTCTTACATGAGAACACATATC
2333199 AAAAATCCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.03
43 64 0.93
44 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (44 bp):
TGTCCCAGACGTGGTCTTACATGAGAACACATATCGATGCCAAC
Found at i:2343762 original size:27 final size:27
Alignment explanation
Indices: 2343732--2343909 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2343722 ATATTGAGTC
* * * *
2343732 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
2343759 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2343786 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
2343814 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
2343841 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
2343868 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2343895 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2343910 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:2343871 original size:82 final size:81
Alignment explanation
Indices: 2343753--2343908 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2343743 TGCTATATAA
* *
2343753 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
2343818 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
2343835 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
2343899 CACTTAGTGC
65 CACTTAGTGC
2343909 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:2345587 original size:87 final size:87
Alignment explanation
Indices: 2345441--2345613 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 87
2345431 TATCACATTT
* *
2345441 TAAAATTTTCTCATCTAACTCCTATTGACTAAATTCACATGCAATTGACTAAATCGAAGCTTGAA
1 TAAAATTTTCTCATATAACTCCTATTGACTAAATTCACATGCAATCGACTAAATCGAAGCTTGAA
2345506 ATTTTCACACATTCATGATTAG
66 ATTTTCACACATTCATGATTAG
*
2345528 TAAAATTTTCTCATATAAGTCCTATTGACTAAATTCACATGCAATCGACTAAATCGAAGCTTGAA
1 TAAAATTTTCTCATATAACTCCTATTGACTAAATTCACATGCAATCGACTAAATCGAAGCTTGAA
2345593 ATTTTCACACATTCATGATTA
66 ATTTTCACACATTCATGATTA
2345614 CATATTCTAG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (87 bp):
TAAAATTTTCTCATATAACTCCTATTGACTAAATTCACATGCAATCGACTAAATCGAAGCTTGAA
ATTTTCACACATTCATGATTAG
Found at i:2345785 original size:45 final size:45
Alignment explanation
Indices: 2345721--2345811 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
2345711 CAACTCTCCC
2345721 TCACTTAAGAAATTTTCGTCCTCGAAAATCTTACCGGTAAATAGG
1 TCACTTAAGAAATTTTCGTCCTCGAAAATCTTACCGGTAAATAGG
2345766 TCACTTAAGAAATTTTCGTCCTCGAAAATCTTACCGGTAAATAGG
1 TCACTTAAGAAATTTTCGTCCTCGAAAATCTTACCGGTAAATAGG
2345811 T
1 T
2345812 TTGGATATCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (45 bp):
TCACTTAAGAAATTTTCGTCCTCGAAAATCTTACCGGTAAATAGG
Found at i:2347728 original size:43 final size:43
Alignment explanation
Indices: 2347667--2347752 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2347657 CAAACTCTTT
2347667 ACCCGATTCGGGTTGCACCAAAATTGGAGCTTCAGTCAAATGA
1 ACCCGATTCGGGTTGCACCAAAATTGGAGCTTCAGTCAAATGA
2347710 ACCCGATTCGGGTTGCACCAAAATTGGAGCTTCAGTCAAATGA
1 ACCCGATTCGGGTTGCACCAAAATTGGAGCTTCAGTCAAATGA
2347753 GTTTTCAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (43 bp):
ACCCGATTCGGGTTGCACCAAAATTGGAGCTTCAGTCAAATGA
Found at i:2351992 original size:27 final size:27
Alignment explanation
Indices: 2351962--2352139 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2351952 ATATTGAGTC
* * * *
2351962 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
2351989 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2352016 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
2352044 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
2352071 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
2352098 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2352125 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2352140 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:2352101 original size:82 final size:81
Alignment explanation
Indices: 2351983--2352138 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2351973 TGCTATATAA
* *
2351983 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
2352048 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
2352065 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
2352129 CACTTAGTGC
65 CACTTAGTGC
2352139 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:2352511 original size:146 final size:144
Alignment explanation
Indices: 2352249--2352539 Score: 555
Period size: 146 Copynumber: 2.0 Consensus size: 144
2352239 CTTTTCTTTT
2352249 CATTCAACAATTTCATCATCACATACGTACATGCATATATATATGTATATTTATTCATTCCATTC
1 CATTCAACAATTTCATCATCACATACGTACATGCATATATATATGTATATTTATTCATTCCATTC
*
2352314 AGCATCAATACATAAACATTATGGCCATTTGAAATAATACCAACTACATGCTTAATGACTTACCT
66 AGCATCAATACATAAACATTATGACCATTTGAAATAATACCAACTACATGCTTAATGACTTACCT
2352379 TGTGTTGGGTAAGA
131 TGTGTTGGGTAAGA
2352393 CATTCAACAATTTCATCATCACATACGTACATGCATATATATATATGTATATTTATTCATTCCAT
1 CATTCAACAATTTCATCATCACATACGTACATGC--ATATATATATGTATATTTATTCATTCCAT
2352458 TCAGCATCAATACATAAACATTATGACCATTTGAAATAATACCAACTACATGCTTAATGACTTAC
64 TCAGCATCAATACATAAACATTATGACCATTTGAAATAATACCAACTACATGCTTAATGACTTAC
2352523 CTTGTGTTGGGTAAGA
129 CTTGTGTTGGGTAAGA
2352539 C
1 C
2352540 GGTTCCAACT
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
144 34 0.24
146 110 0.76
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (144 bp):
CATTCAACAATTTCATCATCACATACGTACATGCATATATATATGTATATTTATTCATTCCATTC
AGCATCAATACATAAACATTATGACCATTTGAAATAATACCAACTACATGCTTAATGACTTACCT
TGTGTTGGGTAAGA
Found at i:2354962 original size:76 final size:76
Alignment explanation
Indices: 2354836--2354988 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
2354826 TCAACATATC
*
2354836 CTCAAGTATCTAAATTACCCGCTCGGATTGACCATCGGTTTGTGGATGAAAAGCGGTGCTAAAAT
1 CTCAAGTATCTAAATTACCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCGGTGCTAAAAT
2354901 GCAGCTTGGTA
66 GCAGCTTGGTA
* * * *
2354912 CTCAAGTATTTGAATTATCCGCTCGGATTGACCATCGGTTTGGGGGTGAAAAGCGGTGCTAAAAT
1 CTCAAGTATCTAAATTACCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCGGTGCTAAAAT
2354977 GCAGCTTGGTA
66 GCAGCTTGGTA
2354988 C
1 C
2354989 CCAAAGCTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (76 bp):
CTCAAGTATCTAAATTACCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCGGTGCTAAAAT
GCAGCTTGGTA
Found at i:2356078 original size:39 final size:40
Alignment explanation
Indices: 2355996--2356092 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 40
2355986 AAATCGACCT
*
2355996 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAAC
** * *
2356036 TCGCACAAATGCCTTCGGG-CTTCGCCCGGAATTATTATC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAAC
2356075 TCGCACAAATGCCTTCGG
1 TCGCACAAATGCCTTCGG
2356093 ATCTTAGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
39 33 0.63
40 19 0.37
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAAC
Found at i:2356332 original size:40 final size:40
Alignment explanation
Indices: 2356286--2356362 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
2356276 TAATAACCGG
* *
2356286 CGAGCCCTAGAAAGCTCCGGACTTCGGTAACATTTCTCGA
1 CGAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCTCGA
* *
2356326 CGAGCCCCAGGAAGCTCCGAACTTCGGTAATATTTCT
1 CGAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCT
2356363 TGGAGGCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
CGAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCTCGA
Found at i:2365211 original size:13 final size:13
Alignment explanation
Indices: 2365193--2365220 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2365183 GTTCAACAGG
2365193 GACACGCCCGTGT
1 GACACGCCCGTGT
2365206 GACACGCCCGTGT
1 GACACGCCCGTGT
2365219 GA
1 GA
2365221 GGTGGCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:2369235 original size:39 final size:39
Alignment explanation
Indices: 2369189--2369296 Score: 162
Period size: 39 Copynumber: 2.8 Consensus size: 39
2369179 GCTTAAAGAC
*
2369189 CCGCAGGCTATATGCTGGAATTATATCCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT
* *
2369228 CCGCAGGCTATGTGCTAGAATTATAACCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT
* * *
2369267 CCGCAGGCTACGTGCTGGAAATATGTCCGG
1 CCGCAGGCTATGTGCTGGAATTATATCCGG
2369297 GCAAAAGTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT
Found at i:2373475 original size:75 final size:75
Alignment explanation
Indices: 2373330--2373475 Score: 177
Period size: 74 Copynumber: 1.9 Consensus size: 75
2373320 AGGGTGGCCC
* * * *
2373330 AAAGTTTAAAATTTTTGCAATTTAGCCATTTGTAGATATACTATGGCCCTCCCAAAAATATACGT
1 AAAGTTTAAAATTGTTGCAATTTACCCATTTGTAGATATACTATAGCCCTCCCAAAAATATACAT
2373395 AGCCTCCCCT
66 AGCCTCCCCT
* * ** * * *
2373405 AAAGTTTAAGATTGTTGCAATTT-CCCCTTTGTATTTATATTGTAGCCCTCCCAAAAATATATAT
1 AAAGTTTAAAATTGTTGCAATTTACCCATTTGTAGATATACTATAGCCCTCCCAAAAATATACAT
2373469 AGGCCTC
66 A-GCCTC
2373476 TCCAATATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 33 0.56
75 26 0.44
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (75 bp):
AAAGTTTAAAATTGTTGCAATTTACCCATTTGTAGATATACTATAGCCCTCCCAAAAATATACAT
AGCCTCCCCT
Found at i:2374046 original size:14 final size:14
Alignment explanation
Indices: 2374027--2374062 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2374017 ATTTGAGATG
2374027 TATTTTTTAGTTAT
1 TATTTTTTAGTTAT
* *
2374041 TATTTTTAATTTAT
1 TATTTTTTAGTTAT
2374055 TATTTTTT
1 TATTTTTT
2374063 GTGTTAAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (14 bp):
TATTTTTTAGTTAT
Found at i:2374265 original size:18 final size:18
Alignment explanation
Indices: 2374242--2374289 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2374232 ATCTTAAAGT
2374242 TTTTTTATAAATAGGAAA
1 TTTTTTATAAATAGGAAA
* **
2374260 TTTTTTAAAAATATTAAA
1 TTTTTTATAAATAGGAAA
*
2374278 ATTTTTATAAAT
1 TTTTTTATAAAT
2374290 TATCCGATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTTTTATAAATAGGAAA
Found at i:2380430 original size:32 final size:32
Alignment explanation
Indices: 2380389--2380452 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2380379 GCTCAAAGTA
* *
2380389 AGTTTTTAAGGGATAATTCTTCATATGGTAGG
1 AGTTTTTAAGGGATAATTCTTAATACGGTAGG
2380421 AGTTTTTAAGGGATAATTCTTAATACGGTAGG
1 AGTTTTTAAGGGATAATTCTTAATACGGTAGG
2380453 CTTGAAAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (32 bp):
AGTTTTTAAGGGATAATTCTTAATACGGTAGG
Found at i:2381872 original size:20 final size:20
Alignment explanation
Indices: 2381847--2381888 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2381837 TTTAAATACT
*
2381847 CTTTTCGGCAAGTATGACTA
1 CTTTTCAGCAAGTATGACTA
2381867 CTTTTCAGCAAGTATGACTA
1 CTTTTCAGCAAGTATGACTA
2381887 CT
1 CT
2381889 ATATTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
CTTTTCAGCAAGTATGACTA
Found at i:2383392 original size:47 final size:48
Alignment explanation
Indices: 2383318--2383589 Score: 180
Period size: 47 Copynumber: 5.9 Consensus size: 48
2383308 GCCATATTAC
* *
2383318 GAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGAT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* **
2383366 GAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-TACAAGAT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGAT
* * * *
2383412 GTG-TC-AGTGTAAGACCATGTTTGGGCCATGGCATCGGCA-TG-GAT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* * * * * * **
2383456 -A-TG-T-GAG-AGGACCATGTCTGGGACATGGCGTCGCCCTTGATTT
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* * *
2383499 CGATAG-TCAATGTAAGACCATGTCTGGGACATGGCATCGAC-TT--GAT
1 -GAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
* * *
2383545 GGATGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT
1 -GA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
2383590 ATACCCTACG
Statistics
Matches: 169, Mismatches: 38, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
41 23 0.14
42 4 0.02
43 1 0.01
44 12 0.07
45 15 0.09
46 25 0.15
47 44 0.26
48 20 0.12
49 25 0.15
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (48 bp):
GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAT
Found at i:2384610 original size:41 final size:41
Alignment explanation
Indices: 2384552--2384630 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
2384542 AGATTTTCAA
2384552 ACACGGGCTGAGACACGGGTGTGT-CGAGGCCGTGTGAGGG
1 ACACGGGCTGAGACACGGGTGTGTGCGAGGCCGTGTGAGGG
* *
2384592 ACACGGGCCTTAGACACGGGTGTGTGCTAGGCCGTGTGA
1 ACACGGG-CTGAGACACGGGTGTGTGCGAGGCCGTGTGA
2384631 AAACCCCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 7 0.20
41 16 0.46
42 12 0.34
ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18
Consensus pattern (41 bp):
ACACGGGCTGAGACACGGGTGTGTGCGAGGCCGTGTGAGGG
Found at i:2384771 original size:21 final size:20
Alignment explanation
Indices: 2384747--2384786 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2384737 ATGTTCAAGT
*
2384747 TCCACACTGGCATGTTGCCCA
1 TCCACACGGGCATG-TGCCCA
*
2384768 TCCATACGGGCATGTGCCC
1 TCCACACGGGCATGTGCCC
2384787 TGTTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (20 bp):
TCCACACGGGCATGTGCCCA
Found at i:2390976 original size:53 final size:52
Alignment explanation
Indices: 2390825--2391025 Score: 159
Period size: 52 Copynumber: 4.0 Consensus size: 52
2390815 TGACGGAAAA
* * * *
2390825 GATGTGATATGTGCTTCCATATAATACCATAGCTGGGCTATGGCATCGGTAC
1 GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
* * **
2390877 AATGTGAT-T-CGAGTTCCCGTATAAGACCATAGT-TGGGCTATGGCATCGGTGT
1 GATGTGATATGTGA-TT-CCGTATAAGACCATA-TCTGGGCTATGGCATCGGTAC
* * *
2390929 GATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATAGCATCAGT--
1 GATGTGAT-ATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
* ** * *
2390980 -ATGT--TATGTGA-TCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGT
1 GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGT
2391026 GTGTGATGTG
Statistics
Matches: 121, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
46 27 0.22
47 6 0.05
48 1 0.01
50 5 0.04
51 3 0.02
52 45 0.37
53 29 0.24
54 3 0.02
55 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (52 bp):
GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
Found at i:2396072 original size:42 final size:42
Alignment explanation
Indices: 2395977--2396074 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 42
2395967 ACGAATCGAT
* *
2395977 TATGGCACTTAGTGTGCGTATCGAGGTAGCTTCAGCTATATA
1 TATGGCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATA
* * *
2396019 -A-AGCACTTAGTGTGCGAATTG-GAATAGCTTCGGCTATATA
1 TATGGCACTTAGTGTGCGAATCGAG-ATAGCTTCAGCTATATA
2396059 TATGGCACTTAGTGTG
1 TATGGCACTTAGTGTG
2396075 TGAGACTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 1 0.02
40 32 0.68
41 2 0.04
42 12 0.26
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TATGGCACTTAGTGTGCGAATCGAGATAGCTTCAGCTATATA
Found at i:2401292 original size:127 final size:127
Alignment explanation
Indices: 2401141--2401372 Score: 306
Period size: 127 Copynumber: 1.8 Consensus size: 127
2401131 TGTGGACGGA
* ** **
2401141 ATTTTAAAGGGATGTTTGATTATTTGGATAAACAGAAA-ATCGAAACCCAACACATTAGGACACG
1 ATTTTAAAGAGAAATTTGATTATTTAAATAAAC-GAAAGATCGAAACCCAACACATTAGGACACG
* * *
2401205 ATTTCC-CAAATTCCCAAACATCAATCATCGCTTTTGTTTTAAAGTTTAGAAAACACGGATGGG
65 A-TCCCTCAAATTCCCAAACATCAAACATCGCCTTTGTTTTAAAGTTTAGAAAACACGGATGGG
* * *
2401268 ATTTTAAAGAGAAATTTGATTATTTAAATAAACGAAAGATCGAAACCCAACACGTTGGGGCACGA
1 ATTTTAAAGAGAAATTTGATTATTTAAATAAACGAAAGATCGAAACCCAACACATTAGGACACGA
* * *
2401333 TCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTA
66 TCCCTCAAATTCCCAAACATCAAACATCGCCTTTGTTTTA
2401373 TAAAGTCGAC
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
126 7 0.08
127 82 0.92
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (127 bp):
ATTTTAAAGAGAAATTTGATTATTTAAATAAACGAAAGATCGAAACCCAACACATTAGGACACGA
TCCCTCAAATTCCCAAACATCAAACATCGCCTTTGTTTTAAAGTTTAGAAAACACGGATGGG
Found at i:2401553 original size:17 final size:17
Alignment explanation
Indices: 2401531--2401564 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2401521 TAATGAATGA
2401531 AAATAATATAAAA-AAAT
1 AAATAA-ATAAAACAAAT
2401548 AAATAAATAAAACAAAT
1 AAATAAATAAAACAAAT
2401565 TAACATACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAATAAAACAAAT
Found at i:2401741 original size:15 final size:15
Alignment explanation
Indices: 2401723--2401765 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
2401713 CTAATGGACA
2401723 ATATGAAATAATAAT
1 ATATGAAATAATAAT
2401738 ATATGAAATAATAAT
1 ATATGAAATAATAAT
*
2401753 ATATTAAATAATA
1 ATATGAAATAATA
2401766 TGAAGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
ATATGAAATAATAAT
Found at i:2402341 original size:50 final size:49
Alignment explanation
Indices: 2402168--2402366 Score: 133
Period size: 50 Copynumber: 4.0 Consensus size: 49
2402158 ATATATATAT
* *
2402168 ATAAAATAGTTTAAGAT-A-AATA--AAAAATA-TTGAAAGTAAATAATAC
1 ATAAAATAGTTTAAAATAATAATATTAAAAA-ACTT-AAAATAAATAATAC
* * * * * *
2402214 GTAAAATAGTTTAAAATAACTAATATATATACAAATTTAAAATGAGTAATAGT
1 ATAAAATAGTTTAAAATAA-TAATAT-TA-AAAAACTTAAAATAAATAATA-C
* *
2402267 TTAAAAT-GATTTAAAATACATAATATGTAAAAAACTTAAAGTAAATAATA-
1 ATAAAATAG-TTTAAAATA-ATAATAT-TAAAAAACTTAAAATAAATAATAC
* * *
2402317 ATAGAATAGTTTAAAATAAGTAATATAAACAAAACTTAAAATATATAATA
1 ATAAAATAGTTTAAAATAA-TAATATTAA-AAAACTTAAAATAAATAATA
2402367 ATGATAAAAC
Statistics
Matches: 120, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
46 15 0.12
47 1 0.01
49 7 0.06
50 38 0.32
51 1 0.01
52 29 0.24
53 28 0.23
54 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.31
Consensus pattern (49 bp):
ATAAAATAGTTTAAAATAATAATATTAAAAAACTTAAAATAAATAATAC
Found at i:2404029 original size:15 final size:16
Alignment explanation
Indices: 2404011--2404040 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2404001 TCTTTATTTA
2404011 TATTTTT-TAATAATT
1 TATTTTTCTAATAATT
2404026 TATTTTTCTAATAAT
1 TATTTTTCTAATAAT
2404041 AATATCCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTCTAATAATT
Found at i:2404032 original size:16 final size:17
Alignment explanation
Indices: 2404006--2404040 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2403996 TATTTTCTTT
*
2404006 ATTTATATTTTTTAATA
1 ATTTATATTTTCTAATA
2404023 ATTTAT-TTTTCTAATA
1 ATTTATATTTTCTAATA
2404039 AT
1 AT
2404041 AATATCCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATATTTTCTAATA
Found at i:2408389 original size:14 final size:14
Alignment explanation
Indices: 2408353--2408395 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2408343 CGTTTGTTTG
*
2408353 CTAATAAAATATTTT
1 CTAA-AAAATAATTT
2408368 CTAAAAAATAATTT
1 CTAAAAAATAATTT
**
2408382 CTGGAAAATAATTT
1 CTAAAAAATAATTT
2408396 ATTTTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (14 bp):
CTAAAAAATAATTT
Found at i:2408526 original size:18 final size:18
Alignment explanation
Indices: 2408500--2408542 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2408490 AAAAACTATT
*
2408500 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
2408518 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
2408536 TTTATAT
1 TTTATAT
2408543 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:2412017 original size:34 final size:34
Alignment explanation
Indices: 2411974--2412080 Score: 121
Period size: 40 Copynumber: 3.1 Consensus size: 34
2411964 CCTTGCGAGA
2411974 AGGAATGAGATTTGCCTGAGAAAGAGAGAAAGAG
1 AGGAATGAGATTTGCCTGAGAAAGAGAGAAAGAG
*
2412008 AGGAATGAGATTGGCCTTTGCCTGAGAAAGAGAGAAAGGG
1 AGGAATGAGA------TTTGCCTGAGAAAGAGAGAAAGAG
*
2412048 AGGAATGAGATTTG-C--AGAAAGAGAGAGAGAG
1 AGGAATGAGATTTGCCTGAGAAAGAGAGAAAGAG
2412079 AG
1 AG
2412081 AAAGAAGATG
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
31 16 0.25
33 1 0.02
34 14 0.22
40 33 0.52
ACGTcount: A:0.41, C:0.07, G:0.37, T:0.15
Consensus pattern (34 bp):
AGGAATGAGATTTGCCTGAGAAAGAGAGAAAGAG
Found at i:2412039 original size:40 final size:40
Alignment explanation
Indices: 2411984--2412059 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
2411974 AGGAATGAGA
2411984 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
1 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
*
2412024 TTTGCCTGAGAAAGAGAGAAAGGGAGGAATGAGATT
1 TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATT
2412060 TGCAGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.36, T:0.18
Consensus pattern (40 bp):
TTTGCCTGAGAAAGAGAGAAAGAGAGGAATGAGATTGGCC
Found at i:2413100 original size:20 final size:21
Alignment explanation
Indices: 2413045--2413100 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
2413035 ATATAAACTT
*
2413045 ATAAATTTTATAAAA-ATCTA
1 ATAAATTTTATAAAATTTCTA
*
2413065 ATAAA-TTTA-AATAATTTGTA
1 ATAAATTTTATAA-AATTTCTA
2413085 A-AAATTTTATAAAATT
1 ATAAATTTTATAAAATT
2413101 AATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.07
19 9 0.30
20 17 0.57
21 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATTTTATAAAATTTCTA
Found at i:2420455 original size:14 final size:14
Alignment explanation
Indices: 2420436--2420462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2420426 TTCAATCGAA
2420436 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
2420450 TCGAGTTAAATTA
1 TCGAGTTAAATTA
2420463 AAAAAAATTA
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:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:2423252 original size:25 final size:24
Alignment explanation
Indices: 2423218--2423270 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
2423208 GAGTTTAAGC
2423218 GAGCCATATCAAGAAGCTCAAAAA
1 GAGCCATATCAAGAAGCTCAAAAA
* * *
2423242 GAGCCTATATCAGGATGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCAAAAA
2423267 GAGC
1 GAGC
2423271 TACTTTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCAAAAA
Found at i:2428709 original size:17 final size:17
Alignment explanation
Indices: 2428689--2428739 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2428679 ACTTTATTAA
2428689 TTTTT-TTTCTTTTCAT
1 TTTTTATTTCTTTTCAT
*
2428705 TTTTTATTTCTTTTCCT
1 TTTTTATTTCTTTTCAT
* *
2428722 TTTTCATCTTCTATTCAT
1 TTTTTAT-TTCTTTTCAT
2428740 ACCCTAACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.17
17 16 0.55
18 8 0.28
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTTCTTTTCAT
Found at i:2429911 original size:30 final size:31
Alignment explanation
Indices: 2429870--2429930 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
2429860 CGATTTAGTT
2429870 GACAGAAAAAAAA-GTTAAGGTACCAATCTAG
1 GACAGAAAAAAAACGTTAA-GTACCAATCTAG
*
2429901 GACA-AAAAAAAACGTTAAGTATCAATCTAG
1 GACAGAAAAAAAACGTTAAGTACCAATCTAG
2429931 AAGAAATGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.18
Consensus pattern (31 bp):
GACAGAAAAAAAACGTTAAGTACCAATCTAG
Found at i:2431244 original size:58 final size:58
Alignment explanation
Indices: 2431155--2431305 Score: 151
Period size: 58 Copynumber: 2.6 Consensus size: 58
2431145 TTATACGCTT
* * * * * * * *
2431155 ATGCCCCAAGATGCAC-CTGTGTGCCAGGATGCACTTCATTTTCCATATATGCGCTTC
1 ATGCGCCAAGATGCACTTTGTGTGCCAAGATGCACTCCATGTGCCAGATATGCACTTC
* ** * *
2431212 GTGCGCCAAGATGCACTTTGTGTGTTAAGATGCAGTCCATGTGCCAGATATGCACTTT
1 ATGCGCCAAGATGCACTTTGTGTGCCAAGATGCACTCCATGTGCCAGATATGCACTTC
* * *
2431270 ATGCGCTAAGATGCATTTTGTGTGCCAGGATGCACT
1 ATGCGCCAAGATGCACTTTGTGTGCCAAGATGCACT
2431306 TTGTGTTTCA
Statistics
Matches: 73, Mismatches: 20, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
57 14 0.19
58 59 0.81
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (58 bp):
ATGCGCCAAGATGCACTTTGTGTGCCAAGATGCACTCCATGTGCCAGATATGCACTTC
Found at i:2431265 original size:39 final size:38
Alignment explanation
Indices: 2431222--2431345 Score: 115
Period size: 38 Copynumber: 3.2 Consensus size: 38
2431212 GTGCGCCAAG
* *
2431222 ATGCACTTTGTGTGTTAAGATGCAGTCCATGTGCCAGAT
1 ATGCACTTTGTGTGTTAAGATGCACTTCATGTGCCAG-T
* * * * ** *
2431261 ATGCACTTTATGCGCTAAGATGCATTTTGTGTGCCAGG
1 ATGCACTTTGTGTGTTAAGATGCACTTCATGTGCCAGT
* *
2431299 ATGCACTTTGTGT-TTCAGGATGTACTTCATGTGCCAGT
1 ATGCACTTTGTGTGTT-AAGATGCACTTCATGTGCCAGT
*
2431337 ATGCGCTTT
1 ATGCACTTT
2431346 ATGCGTCAGG
Statistics
Matches: 66, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
37 1 0.02
38 35 0.53
39 30 0.45
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (38 bp):
ATGCACTTTGTGTGTTAAGATGCACTTCATGTGCCAGT
Found at i:2431317 original size:19 final size:19
Alignment explanation
Indices: 2431251--2431364 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 19
2431241 ATGCAGTCCA
* *
2431251 TGTGCCAGATATGCACTTTA
1 TGTGCCAG-GATGCACTTTG
* * * *
2431271 TGCGCTAAGATGCATTTTG
1 TGTGCCAGGATGCACTTTG
2431290 TGTGCCAGGATGCACTTTG
1 TGTGCCAGGATGCACTTTG
** * **
2431309 TGTTTCAGGATGTACTTCA
1 TGTGCCAGGATGCACTTTG
* * *
2431328 TGTGCCAGTATGCGCTTTA
1 TGTGCCAGGATGCACTTTG
* * *
2431347 TGCGTCAGGATGCGCTTT
1 TGTGCCAGGATGCACTTT
2431365 ACGTGCCAAT
Statistics
Matches: 70, Mismatches: 24, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
19 65 0.93
20 5 0.07
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (19 bp):
TGTGCCAGGATGCACTTTG
Found at i:2431355 original size:38 final size:38
Alignment explanation
Indices: 2431222--2431359 Score: 107
Period size: 38 Copynumber: 3.6 Consensus size: 38
2431212 GTGCGCCAAG
* * * * * *
2431222 ATGCACTTTGTGTGTTAAGATGCAGTCCATGTGCCAGAT
1 ATGCACTTTATGCGTCAGGATGCACTTCATGTGCCAG-T
* * ** *
2431261 ATGCACTTTATGCG-CTAAGATGCATTTTGTGTGCCAGG
1 ATGCACTTTATGCGTC-AGGATGCACTTCATGTGCCAGT
* ** *
2431299 ATGCACTTTGTGTTTCAGGATGTACTTCATGTGCCAGT
1 ATGCACTTTATGCGTCAGGATGCACTTCATGTGCCAGT
*
2431337 ATGCGCTTTATGCGTCAGGATGC
1 ATGCACTTTATGCGTCAGGATGC
2431360 GCTTTACGTG
Statistics
Matches: 75, Mismatches: 22, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
38 45 0.60
39 30 0.40
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (38 bp):
ATGCACTTTATGCGTCAGGATGCACTTCATGTGCCAGT
Found at i:2435718 original size:50 final size:48
Alignment explanation
Indices: 2435595--2435916 Score: 185
Period size: 45 Copynumber: 6.8 Consensus size: 48
2435585 CATGGGTAAG
* * *
2435595 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTTC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
* * *
2435643 GAGGCCAATGCCATGTCCC-GAACATGGTCTTACACTAGCTCTCA-CATAACC
1 G-TGCCGATGCCATGTCCCAG-ACATGGTCTTACACTAGCTATCATC-T--CC
*
2435694 GTGCCGATGCCATGTCCCAGACATGGTTTTACACT-GAC-A-CATCTCAC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTATCATCTC-C
* * * ** * *
2435741 -AGCTGATG-CATGTCTCAGACAT-GTCTTGTACTGGCT-TACGTCT-C
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCC
* * * *
2435785 GAGGCCGATG--ATGTCTCAGACAT-GTCTTACACTAAC-ACTCGTCT-C
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTCC
* * * * * *
2435830 GATGCCGATGCCACGTCCCAGACGTGGTCTTACACTGGCTTTCATAT-T
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
*
2435878 ATGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTA
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTA
2435917 ATACAAGTGA
Statistics
Matches: 214, Mismatches: 38, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
44 9 0.04
45 51 0.24
46 31 0.14
47 24 0.11
48 28 0.13
49 38 0.18
50 30 0.14
51 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCC
Found at i:2436183 original size:20 final size:21
Alignment explanation
Indices: 2436145--2436184 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2436135 TTTCCCCCTG
2436145 TCTTGATTCTGATTTAGAAAT
1 TCTTGATTCTGATTTAGAAAT
2436166 TCTTGA-TCT-ATATTAGAAA
1 TCTTGATTCTGAT-TTAGAAA
2436185 AAAGACACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (21 bp):
TCTTGATTCTGATTTAGAAAT
Found at i:2442675 original size:16 final size:16
Alignment explanation
Indices: 2442651--2442702 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
2442641 TGGTTCACTA
* *
2442651 TAATGGAATAGGGTTG
1 TAATTGAATAGAGTTG
2442667 TAATTGAATAGAGTTG
1 TAATTGAATAGAGTTG
*
2442683 TAATTGAATAGAGCTG
1 TAATTGAATAGAGTTG
2442699 TAAT
1 TAAT
2442703 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.35
Consensus pattern (16 bp):
TAATTGAATAGAGTTG
Found at i:2442970 original size:17 final size:17
Alignment explanation
Indices: 2442948--2442980 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2442938 AATTATTATT
2442948 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
*
2442965 AAATATTATTTAATAA
1 AAATATAATTTAATAA
2442981 CATTCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:2451198 original size:23 final size:20
Alignment explanation
Indices: 2451150--2451191 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2451140 TAGTTTAACA
2451150 AATATTTTCAATAATATGTG
1 AATATTTTCAATAATATGTG
2451170 AATATTTTCAATAATATGTG
1 AATATTTTCAATAATATGTG
2451190 AA
1 AA
2451192 GAATATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (20 bp):
AATATTTTCAATAATATGTG
Found at i:2451226 original size:14 final size:14
Alignment explanation
Indices: 2451195--2451233 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
2451185 ATGTGAAGAA
2451195 TATTATTTAAAA-T
1 TATTATTTAAAATT
2451208 TATTATTTAAAATT
1 TATTATTTAAAATT
2451222 TATTA-TTAAAAT
1 TATTATTTAAAAT
2451234 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTTAAAATT
Done.