Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 64 of 373
Found at i:19304343 original size:9 final size:10
Alignment explanation
Indices: 19304296--19304362 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 10
19304286 TATTTTCCTA
19304296 TATATTTATAT
1 TATATTT-TAT
19304307 TATATTTTAT
1 TATATTTTAT
19304317 TATATAACATTTAT
1 TATAT----TTTAT
19304331 TATATTTTAT
1 TATATTTTAT
*
19304341 ATATATATTACT
1 -TATATTTTA-T
*
19304353 TATCTTTTAT
1 TATATTTTAT
19304363 ATGTTATGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
10 14 0.30
11 22 0.47
12 1 0.02
14 10 0.21
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATTTTAT
Found at i:19304683 original size:7 final size:7
Alignment explanation
Indices: 19304671--19304696 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19304661 AAATTTTTGT
19304671 TATTATA
1 TATTATA
19304678 TATTATA
1 TATTATA
19304685 TATTATA
1 TATTATA
19304692 TATTA
1 TATTA
19304697 AATACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:19326812 original size:206 final size:206
Alignment explanation
Indices: 19326450--19327171 Score: 1032
Period size: 206 Copynumber: 3.5 Consensus size: 206
19326440 GCAGATCTGG
*
19326450 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT
* * * * * *
19326515 GATTTGG-TTTCCGCGTGCTTACGCTAAAGCAAATCTAAGATGATTTAGTATCTTTGTATTGTTA
65 GATTTGGCTTT-CACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA
* *
19326579 GAGAATAGATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCCAACCT
129 GAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCCAACCT
19326644 TCAGATGTTTATA
194 TCAGATGTTTATA
* * *
19326657 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
** * * *
19326722 ATTTGGCTTTCACGAACTTATGTTGAAGCAAATCTAAGATGATTTGGCATCTGTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
19326787 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCCAACCTTC
131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCCAACCTTC
*
19326852 AGATGTTTGTA
196 AGATGTTTATA
* * * *
19326863 CTGAAGCAGATCCAAAATGATTTGGTATCCTTGTGCTTACAAGGACCAAATCGAAGACATAGATG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
* *
19326928 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAAA
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* * * * * * *
19326993 GAACAAATCAAATTTTGGCATTTCCATATTCGACAGAGAGTAGACACATAGCAGATCTAACTTTC
131 GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCCAACCTTC
* * *
19327058 AGACGATTAGA
196 AGATGTTTATA
* * * * * * *
19327069 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGGTCATAAGAAGCAAATCGAACACATAACAG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
*
19327134 ATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAG
66 ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAG
19327172 CATCTCTGTA
Statistics
Matches: 463, Mismatches: 51, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
206 453 0.98
207 10 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGTAGACACATAGCAGATCCAACCTTC
AGATGTTTATA
Found at i:19328921 original size:9 final size:10
Alignment explanation
Indices: 19328874--19328938 Score: 51
Period size: 11 Copynumber: 6.0 Consensus size: 10
19328864 TATTTTCCTA
19328874 TATATTTATAT
1 TATATTT-TAT
19328885 TATATTTTAT
1 TATATTTTAT
19328895 TATATAACATTTAT
1 TATAT----TTTAT
19328909 TATATTTTA-
1 TATATTTTAT
*
19328918 TATATATTACT
1 TATATTTTA-T
*
19328929 TATCTTTTAT
1 TATATTTTAT
19328939 ATGTTAGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
9 8 0.18
10 13 0.29
11 14 0.31
14 10 0.22
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTTTAT
Found at i:19334653 original size:53 final size:54
Alignment explanation
Indices: 19334589--19334792 Score: 250
Period size: 55 Copynumber: 3.8 Consensus size: 54
19334579 CTTTTTGAAA
* * * *
19334589 TTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAAC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAAC
* **
19334642 TTACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAAC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AAC
* * * * *
19334697 TCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAAC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAAC
* *
19334751 TTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
19334793 ATCTTACCAA
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 41 0.32
54 42 0.32
55 43 0.33
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
TTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAAC
Found at i:19334780 original size:54 final size:54
Alignment explanation
Indices: 19334596--19334798 Score: 248
Period size: 54 Copynumber: 3.8 Consensus size: 54
19334586 AAATTACCAT
* * * * *
19334596 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTTACCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAGAACTTATCAA
* ** * *
19334649 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCC-TTACCTTATAG-AACTTATCAA
* *
19334704 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAGAACTTATCAA
* *
19334758 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTA
1 TGCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTA
19334799 CCAAATGTCA
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 35 0.27
54 47 0.36
55 43 0.33
56 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGATATCCTTACCTTATAGAACTTATCAA
Found at i:19341352 original size:55 final size:55
Alignment explanation
Indices: 19341275--19341433 Score: 216
Period size: 55 Copynumber: 2.9 Consensus size: 55
19341265 TTACGTGGTA
*
19341275 TTTGCCTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGA-GACC
1 TTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATGACC
* * * **
19341328 TTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTGCATGATTTCC
1 TTTGCCTTATAG-AACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATGACC
* *
19341384 -TTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGAT
1 TTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGAT
19341434 ATCCTTATCT
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
53 10 0.11
54 36 0.39
55 44 0.48
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (55 bp):
TTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATGACC
Found at i:19341432 original size:54 final size:54
Alignment explanation
Indices: 19341279--19341445 Score: 221
Period size: 54 Copynumber: 3.1 Consensus size: 54
19341269 GTGGTATTTG
* * *
19341279 CCTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGAGA-CCTTTG
1 CCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC-TTA
* * * *
19341332 CCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTGCATGATTTCCTTA
1 CCTTATAG-AACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTA
*
19341387 CCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTA
1 CCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTA
*
19341441 TCTTA
1 CCTTA
19341446 CCAAATGCCA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
53 6 0.06
54 46 0.47
55 44 0.45
56 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (54 bp):
CCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTA
Found at i:19341477 original size:47 final size:47
Alignment explanation
Indices: 19341422--19341539 Score: 200
Period size: 47 Copynumber: 2.5 Consensus size: 47
19341412 CCTTGGCATG
* *
19341422 GTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATA
1 GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
* *
19341469 GTCTTACATGGTATCCTTGTCTTACTAAATGCCATGTTCCAAACATG
1 GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
19341516 GTCTTACATGGTATCCTTGTCTTA
1 GTCTTACATGGTATCCTTGTCTTA
19341540 GTGTCAATGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (47 bp):
GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
Found at i:19344775 original size:34 final size:34
Alignment explanation
Indices: 19344723--19344790 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
19344713 ATAGTCAAAT
*
19344723 GCAGTCTGGGCCTAAGCCCATTTCAGTTTCAGTA
1 GCAGTCTGAGCCTAAGCCCATTTCAGTTTCAGTA
* *
19344757 GCAGTTTGAGCCTTAGCCCATTTCAGTTTCAGTA
1 GCAGTCTGAGCCTAAGCCCATTTCAGTTTCAGTA
19344791 TTAGATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (34 bp):
GCAGTCTGAGCCTAAGCCCATTTCAGTTTCAGTA
Found at i:19346290 original size:29 final size:28
Alignment explanation
Indices: 19346245--19346361 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 28
19346235 TTGCCCATCT
19346245 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGG-CCATCAGGCCCAATTCA
19346274 CATTCATATGGCTCATCAGGCCCAATTCA
1 CATTCATATGGC-CATCAGGCCCAATTCA
* * *
19346303 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCC-ATCAGGCCCAATTCA
* * * * *
19346332 CCTTTATATGGTCCGTTAGGCCCAAATCA
1 CATTCATATGG-CCATCAGGCCCAATTCA
19346361 C
1 C
19346362 CTTATATTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
28 2 0.03
29 74 0.95
30 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (28 bp):
CATTCATATGGCCATCAGGCCCAATTCA
Found at i:19346593 original size:8 final size:8
Alignment explanation
Indices: 19346577--19346612 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
19346567 GCAGCCAATC
19346577 TTTCGGCT
1 TTTCGGCT
*
19346585 TTTCAGCT
1 TTTCGGCT
*
19346593 TTTCGGCA
1 TTTCGGCT
19346601 TTTCGGCT
1 TTTCGGCT
19346609 TTTC
1 TTTC
19346613 AACTTTTGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (8 bp):
TTTCGGCT
Found at i:19354333 original size:35 final size:35
Alignment explanation
Indices: 19354291--19354360 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
19354281 AATTATAAAG
19354291 AATGATTCAAAATATGTCCAGTTGGCAAATTATAT
1 AATGATTCAAAATATGTCCAGTTGGCAAATTATAT
19354326 AATGATTCAAAATATGTCCAGTTGGCAAATTATAT
1 AATGATTCAAAATATGTCCAGTTGGCAAATTATAT
19354361 GTTTTCACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (35 bp):
AATGATTCAAAATATGTCCAGTTGGCAAATTATAT
Found at i:19354362 original size:20 final size:20
Alignment explanation
Indices: 19354302--19354362 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
19354292 ATGATTCAAA
19354302 ATATGTCCAGTTGGCAAATT
1 ATATGTCCAGTTGGCAAATT
* *
19354322 ATATAAT-GA-TT--CAAA--
1 ATAT-GTCCAGTTGGCAAATT
19354337 ATATGTCCAGTTGGCAAATT
1 ATATGTCCAGTTGGCAAATT
19354357 ATATGT
1 ATATGT
19354363 TTTCACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 2 0.07
17 4 0.13
18 4 0.13
19 2 0.07
20 11 0.37
21 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (20 bp):
ATATGTCCAGTTGGCAAATT
Found at i:19361539 original size:29 final size:29
Alignment explanation
Indices: 19361507--19361562 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19361497 AAGTCTAAAA
*
19361507 AAAGAAAGGCTCATAATATCTCTCTAATT
1 AAAGAAAGACTCATAATATCTCTCTAATT
* * *
19361536 AAAGAAAGATTCCTAATATTTCTCTAA
1 AAAGAAAGACTCATAATATCTCTCTAA
19361563 AATATTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAGAAAGACTCATAATATCTCTCTAATT
Found at i:19363793 original size:6 final size:6
Alignment explanation
Indices: 19363772--19363813 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
19363762 ATTTAGTCAT
19363772 TTTTTA TTTTAATA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTT--TA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
19363814 GTTTAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 28 0.82
8 6 0.18
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:19366234 original size:40 final size:40
Alignment explanation
Indices: 19366189--19366333 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
19366179 CAAGCATAAT
* *
19366189 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCACACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCACACAAA
* *
19366229 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCATACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCACACAAA
* * *
19366269 TGCCTTCGGGTCTTAGCCCGGATAAAATC-ACT-AGCATAAA
1 TGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTCA-CACAAA
*
19366309 TGCCTTCGGGACTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATAT
19366334 CATTCAAATG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.02
40 88 0.94
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATAGCAACTCACACAAA
Found at i:19368441 original size:41 final size:41
Alignment explanation
Indices: 19368384--19368464 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
19368374 AAATTGTGTC
*
19368384 TGTGTGCTTCAACCCTTAACTAAACTTTAGTAAGGGTAGTA
1 TGTGTGCTTCAACCCTTAACTAAACTTTAGTAAGGATAGTA
* *
19368425 TGTGTGCTTCAACCCTTGACTAAGCTTTAGTAAGGATAGT
1 TGTGTGCTTCAACCCTTAACTAAACTTTAGTAAGGATAGT
19368465 TAAGACTCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
TGTGTGCTTCAACCCTTAACTAAACTTTAGTAAGGATAGTA
Found at i:19372527 original size:30 final size:30
Alignment explanation
Indices: 19372497--19372623 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
19372487 ATGACTTGGG
* * *
19372497 CACATGACTGTGTGGGACACACAACCTGGG
1 CACATGACCGTGTGGGACACACGACCTGGA
* * ** *
19372527 CACTTGGCTATGTGGGACACACGGCCTGGA
1 CACATGACCGTGTGGGACACACGACCTGGA
* **
19372557 CACA-CAGCCGTGTGGGACGTACGACCTGGA
1 CACATGA-CCGTGTGGGACACACGACCTGGA
** *
19372587 CACATGACCGTGTGGGATGCACGGCCTGGA
1 CACATGACCGTGTGGGACACACGACCTGGA
19372617 CACATGA
1 CACATGA
19372624 TCATGTGGTA
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
30 76 0.99
31 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.17
Consensus pattern (30 bp):
CACATGACCGTGTGGGACACACGACCTGGA
Found at i:19372979 original size:12 final size:12
Alignment explanation
Indices: 19372964--19373051 Score: 74
Period size: 12 Copynumber: 7.5 Consensus size: 12
19372954 TTACTTTTAC
*
19372964 TTTTACTTTTGT
1 TTTTATTTTTGT
*
19372976 TTTTGTTTTTGTT
1 TTTTATTTTTG-T
19372989 TTTTATTTTTGT
1 TTTTATTTTTGT
* **
19373001 TTTTGTTTTTAC
1 TTTTATTTTTGT
*
19373013 TTTT-GTTTTGT
1 TTTTATTTTTGT
*
19373024 TTTTGTTTTTGT
1 TTTTATTTTTGT
*
19373036 TTTT-TCTTT-T
1 TTTTATTTTTGT
19373046 TTTTAT
1 TTTTAT
19373052 ATATTATTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.08
11 13 0.21
12 33 0.53
13 11 0.18
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTGT
Found at i:19372993 original size:31 final size:31
Alignment explanation
Indices: 19372958--19373021 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
19372948 TAATTTTTAC
**
19372958 TTTTACTTTTACTTTTGTTTTTGTTTTTGTT
1 TTTTACTTTTACTTTTGTTTTTACTTTTGTT
* **
19372989 TTTTATTTTTGTTTTTGTTTTTACTTTTGTT
1 TTTTACTTTTACTTTTGTTTTTACTTTTGTT
19373020 TT
1 TT
19373022 GTTTTTGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.06, C:0.05, G:0.09, T:0.80
Consensus pattern (31 bp):
TTTTACTTTTACTTTTGTTTTTACTTTTGTT
Found at i:19373046 original size:6 final size:6
Alignment explanation
Indices: 19372970--19373039 Score: 97
Period size: 6 Copynumber: 11.7 Consensus size: 6
19372960 TTACTTTTAC
* **
19372970 TTTTGT TTTTGT TTTTGTT TTTTAT TTTTGT TTTTGT TTTTAC TTTTG-
1 TTTTGT TTTTGT TTTTG-T TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
19373018 TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTT
19373040 TCTTTTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 5 0.09
6 47 0.82
7 5 0.09
ACGTcount: A:0.03, C:0.01, G:0.13, T:0.83
Consensus pattern (6 bp):
TTTTGT
Found at i:19375614 original size:29 final size:28
Alignment explanation
Indices: 19375582--19375639 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
19375572 ATTTAGCCCT
19375582 ATATT-TATTTTTTTATATATATTTTTTAC
1 ATATTATATTTTTTTATAT-T-TTTTTTAC
19375611 ATATTGATATTTTTTTATATTTTTTTTAC
1 ATATT-ATATTTTTTTATATTTTTTTTAC
19375640 TTTACTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 13 0.48
30 1 0.04
31 13 0.48
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (28 bp):
ATATTATATTTTTTTATATTTTTTTTAC
Found at i:19375744 original size:14 final size:14
Alignment explanation
Indices: 19375710--19375749 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
19375700 TTTCACAAAT
19375710 TATTATTATTGTTTTA
1 TATTATTA-T-TTTTA
*
19375726 CATTATTATTTTTA
1 TATTATTATTTTTA
19375740 TATTATTATT
1 TATTATTATT
19375750 ATATCTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 1 0.05
16 7 0.32
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTTA
Found at i:19375934 original size:12 final size:11
Alignment explanation
Indices: 19375917--19375983 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 11
19375907 ATATATATCA
19375917 TATATTATCTAT
1 TATATTAT-TAT
19375929 TATATTATATAT
1 TATATTAT-TAT
19375941 TATCTATTA-TAT
1 TA--TATTATTAT
19375953 TAT-TTATGT-T
1 TATATTAT-TAT
19375963 TATATTATTCAT
1 TATATTATT-AT
19375975 TATATTATT
1 TATATTATT
19375984 TAAAATTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
9 3 0.06
10 6 0.13
11 5 0.11
12 28 0.60
14 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (11 bp):
TATATTATTAT
Found at i:19375938 original size:19 final size:19
Alignment explanation
Indices: 19375910--19375955 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
19375900 TTATGTCATA
*
19375910 TATATCATATATTATCTAT
1 TATATTATATATTATCTAT
19375929 TATATTATATATTATCTAT
1 TATATTATATATTATCTAT
19375948 TATATTAT
1 TATATTAT
19375956 TTATGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATATTATCTAT
Found at i:19376206 original size:22 final size:21
Alignment explanation
Indices: 19376154--19376207 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
19376144 AAACAATATA
*
19376154 TTTTATATA-ATTATTATTAT
1 TTTTATATATTTTATTATTAT
* *
19376174 TTTATAAATATTTTGTTATTAT
1 TTT-TATATATTTTATTATTAT
19376196 GTTTTATATATT
1 -TTTTATATATT
19376208 GTATAGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 5 0.19
22 16 0.59
23 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTATATATTTTATTATTAT
Found at i:19376459 original size:33 final size:32
Alignment explanation
Indices: 19376390--19376464 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
19376380 ATTGATATTG
*
19376390 TATTATT-CTTTTTTGGTATGTCATGCATTAT
1 TATTATTACTTTTTTGGTATATCATGCATTAT
19376421 T-TTATTACTTTTTT-GTATATCATGCATTATT
1 TATTATTACTTTTTTGGTATATCATGCATTA-T
19376452 TAATTATTACTTT
1 T-ATTATTACTTT
19376465 GTATATTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 19 0.49
31 10 0.26
33 10 0.26
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.60
Consensus pattern (32 bp):
TATTATTACTTTTTTGGTATATCATGCATTAT
Found at i:19380036 original size:15 final size:15
Alignment explanation
Indices: 19380000--19380049 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
19379990 CGATATCCTT
19380000 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
19380014 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
*
19380030 TTT-CATCACAT-CA
1 TTTGCATCTCATGCA
19380043 TTTGCAT
1 TTTGCAT
19380050 TTAAAGTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:19383055 original size:27 final size:27
Alignment explanation
Indices: 19383015--19383155 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
19383005 AGGAAGCGTC
*
19383015 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
19383042 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
19383068 CCTGGTGGTTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
19383096 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
19383123 CTGGTGGCTCTGCCACAA-TATCTATAT
1 CTGGTGGCTCTGCCACAATTATCT-GAT
19383150 CTGGTG
1 CTGGTG
19383156 ACTTCATCAC
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
26 10 0.10
27 85 0.86
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:19383094 original size:54 final size:54
Alignment explanation
Indices: 19383012--19383155 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
19383002 TGGAGGAAGC
19383012 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
*
19383066 GTCCTGGTGGTTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* * *
19383120 GTTCTGGTGGCTCTGCCACAA-TATCTATATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCT-GATCTGGTG
19383156 ACTTCATCAC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 79 0.94
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:19383167 original size:81 final size:79
Alignment explanation
Indices: 19383015--19383173 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 79
19383005 AGGAAGCGTC
* *
19383015 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGTTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATCCTGGTGCTTAT
19383080 GCCACAATTATCTGAT
66 -CCACAA-TATCTGAT
* * *
19383096 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTATATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGTGGCTCTGCCACATATATCTAT-CCTGGTG-CT
19383159 TCAT-CACAATATCTG
63 T-ATCCACAATATCTG
19383174 GCAGCCTCGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
80 15 0.22
81 50 0.72
82 2 0.03
83 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (79 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATCCTGGTGCTTAT
CCACAATATCTGAT
Found at i:19394141 original size:24 final size:24
Alignment explanation
Indices: 19394092--19394152 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
19394082 TAGATATAAA
* *
19394092 AAAAAATA-TTACATAATAAGTGT
1 AAAAAATACATACATAATAAATGT
19394115 AAAAAATACATACATAATATAAT-T
1 AAAAAATACATACATAATA-AATGT
19394139 AAAATATATACATA
1 AAAA-A-ATACATA
19394153 AGATAACATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.25
24 14 0.44
25 3 0.09
26 7 0.22
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (24 bp):
AAAAAATACATACATAATAAATGT
Found at i:19394149 original size:22 final size:22
Alignment explanation
Indices: 19394117--19394158 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19394107 ATAAGTGTAA
*
19394117 AAAATACATACATAATATAATT
1 AAAATACATACATAAGATAATT
*
19394139 AAAATATATACATAAGATAA
1 AAAATACATACATAAGATAA
19394159 CATGTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATACATACATAAGATAATT
Found at i:19394216 original size:25 final size:25
Alignment explanation
Indices: 19394180--19394314 Score: 95
Period size: 25 Copynumber: 5.6 Consensus size: 25
19394170 AAATATATAT
*
19394180 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
19394205 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
19394230 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
19394254 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* * *
19394276 AATATATATATAATATAATGTT-AAG
1 -ATATATACATAATATAGTATTAAAG
*
19394301 AAATATA-ATAATAT
1 ATATATACATAATAT
19394315 CAAAAAAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 21 0.24
24 23 0.26
25 38 0.44
26 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:19394826 original size:30 final size:30
Alignment explanation
Indices: 19394790--19394917 Score: 202
Period size: 30 Copynumber: 4.3 Consensus size: 30
19394780 AGGTACAAGT
*
19394790 GGTGGTGGAACAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
19394820 GGTGGTGGAGCAAGTGTGGCTAGTGGTGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
* * *
19394850 AGTGGTGGAGCAAGTGTAGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
19394880 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
19394910 GGTGGTGG
1 GGTGGTGG
19394918 CAAAGGCTAG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.19, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:19402539 original size:16 final size:16
Alignment explanation
Indices: 19402514--19402565 Score: 70
Period size: 15 Copynumber: 3.2 Consensus size: 16
19402504 AACTTAGCCC
*
19402514 TATATTTATTTTTTTA
1 TATATATATTTTTTTA
19402530 TATATATA-TTTTTTA
1 TATATATATTTTTTTA
19402545 TATATTGATATTTTTTTA
1 TATA-T-ATATTTTTTTA
19402563 TAT
1 TAT
19402566 TTTTTTACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 11 0.34
16 8 0.25
17 3 0.09
18 10 0.31
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TATATATATTTTTTTA
Found at i:19402832 original size:99 final size:98
Alignment explanation
Indices: 19402729--19403135 Score: 237
Period size: 99 Copynumber: 4.1 Consensus size: 98
19402719 TTCTTACATA
19402729 TATATTTTCGTTATTTTATATTATATCTATTATATTTTTTATTTCCTATATATATTTAAATTATA
1 TATATTTTCGTTATTTTATATTATATCTATTATATTTTTTATTTCCTATATATATTTAAATTATA
*
19402794 TTTTATTATATAACATTTATTGTGTTTTTATTTT
66 TTTTATTATATAACATTTATT-TGTTTTTATATT
* * * * ** ** * * *
19402828 TATA-TTACCTT-TTTATGTCATATATATC-A-TATATTATCAATTATATTATTTATGTTTATAT
1 TATATTTTCGTTATTT-TAT-AT-TATATCTATTATATTTTTTATT-TCCTATATATATTTAAAT
* * * ** *
19402889 TATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTA-AAT
62 TA-T-ATTTTATTATATAACA-TTT---ATTTGT-TTTTATATT
** * * * * *
19402932 TATA-TTT--TTAACTCATATTATACACATATTAAATTATTTTATAT--TATAT-TATTCTTACA
1 TATATTTTCGTTATTTTATATTATA-TC-TATTATATT-TTTTATTTCCTATATATA-T-TTAAA
** * * * *
19402991 -TATATATTTATTA-ATTATTTATTTATATTATTCTTACATA
61 TTATAT-TTTATTATA-TA-ACATTTAT-TTGTTTTTATATT
19403031 TATATTTTCGTTATTTTATATTATATCTATTATATTTTTTATTTCCTATATATATTTAAATTATA
1 TATATTTTCGTTATTTTATATTATATCTATTATATTTTTTATTTCCTATATATATTTAAATTATA
*
19403096 TTTTATTATATAACATTTATTGTGTTTTTATTTT
66 TTTTATTATATAACATTTATT-TGTTTTTATATT
19403130 TATATT
1 TATATT
19403136 ACCTTTTTAT
Statistics
Matches: 220, Mismatches: 55, Indels: 66
0.65 0.16 0.19
Matches are distributed among these distances:
97 3 0.01
98 23 0.10
99 56 0.25
100 37 0.17
101 42 0.19
102 28 0.13
103 6 0.03
104 16 0.07
105 9 0.04
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (98 bp):
TATATTTTCGTTATTTTATATTATATCTATTATATTTTTTATTTCCTATATATATTTAAATTATA
TTTTATTATATAACATTTATTTGTTTTTATATT
Found at i:19402973 original size:5 final size:5
Alignment explanation
Indices: 19402957--19403106 Score: 53
Period size: 5 Copynumber: 29.8 Consensus size: 5
19402947 TATTATACAC
* * * *
19402957 ATATT AAATT ATTTT ATATT ATATT ATTCTT ACATAT ATATT -TATT A-ATT
1 ATATT ATATT ATATT ATATT ATATT A-TATT ATAT-T ATATT ATATT ATATT
* * * * *
19403007 AT-TT AT-TT ATATT ATTCTT ACATAT ATATT TTCGTT ATTTT ATATT
1 ATATT ATATT ATATT A-TATT ATAT-T ATATT AT-ATT ATATT ATATT
* * * *
19403053 ATA-T CTATT ATATT -TTTT AT-TT CCTATAT ATATTT AAATT ATATT
1 ATATT ATATT ATATT ATATT ATATT -ATAT-T ATA-TT ATATT ATATT
*
19403098 TTATT ATAT
1 ATATT ATAT
19403107 AACATTTATT
Statistics
Matches: 105, Mismatches: 26, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
4 24 0.23
5 54 0.51
6 25 0.24
7 2 0.02
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:19403009 original size:302 final size:302
Alignment explanation
Indices: 19402689--19403283 Score: 1190
Period size: 302 Copynumber: 2.0 Consensus size: 302
19402679 TTACTTGTAT
19402689 TATATATTTATTAATTATTTATTTATATTATTCTTACATATATATTTTCGTTATTTTATATTATA
1 TATATATTTATTAATTATTTATTTATATTATTCTTACATATATATTTTCGTTATTTTATATTATA
19402754 TCTATTATATTTTTTATTTCCTATATATATTTAAATTATATTTTATTATATAACATTTATTGTGT
66 TCTATTATATTTTTTATTTCCTATATATATTTAAATTATATTTTATTATATAACATTTATTGTGT
19402819 TTTTATTTTTATATTACCTTTTTATGTCATATATATCATATATTATCAATTATATTATTTATGTT
131 TTTTATTTTTATATTACCTTTTTATGTCATATATATCATATATTATCAATTATATTATTTATGTT
19402884 TATATTATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTAAATTATATTTTTAACTCATA
196 TATATTATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTAAATTATATTTTTAACTCATA
19402949 TTATACACATATTAAATTATTTTATATTATATTATTCTTACA
261 TTATACACATATTAAATTATTTTATATTATATTATTCTTACA
19402991 TATATATTTATTAATTATTTATTTATATTATTCTTACATATATATTTTCGTTATTTTATATTATA
1 TATATATTTATTAATTATTTATTTATATTATTCTTACATATATATTTTCGTTATTTTATATTATA
19403056 TCTATTATATTTTTTATTTCCTATATATATTTAAATTATATTTTATTATATAACATTTATTGTGT
66 TCTATTATATTTTTTATTTCCTATATATATTTAAATTATATTTTATTATATAACATTTATTGTGT
19403121 TTTTATTTTTATATTACCTTTTTATGTCATATATATCATATATTATCAATTATATTATTTATGTT
131 TTTTATTTTTATATTACCTTTTTATGTCATATATATCATATATTATCAATTATATTATTTATGTT
19403186 TATATTATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTAAATTATATTTTTAACTCATA
196 TATATTATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTAAATTATATTTTTAACTCATA
19403251 TTATACACATATTAAATTATTTTATATTATATT
261 TTATACACATATTAAATTATTTTATATTATATT
19403284 TATTATGTAT
Statistics
Matches: 293, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
302 293 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (302 bp):
TATATATTTATTAATTATTTATTTATATTATTCTTACATATATATTTTCGTTATTTTATATTATA
TCTATTATATTTTTTATTTCCTATATATATTTAAATTATATTTTATTATATAACATTTATTGTGT
TTTTATTTTTATATTACCTTTTTATGTCATATATATCATATATTATCAATTATATTATTTATGTT
TATATTATTCATTATATTATTTAAAATTTTAAAATTTGTAAATTAAATTATATTTTTAACTCATA
TTATACACATATTAAATTATTTTATATTATATTATTCTTACA
Found at i:19403020 original size:38 final size:41
Alignment explanation
Indices: 19402958--19403061 Score: 139
Period size: 38 Copynumber: 2.7 Consensus size: 41
19402948 ATTATACACA
19402958 TATTAAATTATTTTATATTATATTATTCTTACATATATATT
1 TATTAAATTATTTTATATTATATTATTCTTACATATATATT
19402999 TATT-AATTA-TTTAT-TTATATTATTCTTACATATATA-T
1 TATTAAATTATTTTATATTATATTATTCTTACATATATATT
**
19403036 T-TT-CGTTATTTTATATTATATCTATT
1 TATTAAATTATTTTATATTATAT-TATT
19403062 ATATTTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
36 5 0.09
37 7 0.12
38 28 0.48
39 9 0.16
40 5 0.09
41 4 0.07
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.61
Consensus pattern (41 bp):
TATTAAATTATTTTATATTATATTATTCTTACATATATATT
Found at i:19403193 original size:99 final size:99
Alignment explanation
Indices: 19402783--19403193 Score: 270
Period size: 99 Copynumber: 4.1 Consensus size: 99
19402773 CCTATATATA
19402783 TTTAAATTATATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGTCA
1 TTTAAATTATATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGTCA
19402848 TATATATCATATATTATCAATTATATTATTTATG
66 TATATATCATATATTATCAATTATATTATTTATG
* * * * **** * ** * ** **
19402882 TTTATATTATTCATTATATTATTTAAAATTT-TAAAATTTGTA-AATTAAATTATATTTTTAACT
1 TTTAAATTA-T-ATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGT
* * *
19402945 CATAT-TATACACATATTAAATTATTTTATATTATATTAT-
64 CATATATAT-CATATATT--ATCA-ATTATATTAT-TTATG
* * * * * *
19402984 TCTTACA-TATATATTTATTA-AT--TATTTATT-T-ATATTATTCTTACATATATA-TTTTCGT
1 T-TTAAATTATAT-TTTATTATATAACATTTATTGTGTTTTTATT-TT-TATAT-TACCTTT--T
* * * ** ** * *
19403042 TATTTTATATTATATCTATTATATTTTTTATT-TCCTATATATA
59 TATGTCATA-TATATC-A-TATATTATCAATTATATTATTTATG
19403085 TTTAAATTATATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGTCA
1 TTTAAATTATATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGTCA
19403150 TATATATCATATATTATCAATTATATTATTTATG
66 TATATATCATATATTATCAATTATATTATTTATG
*
19403184 TTTATATTAT
1 TTTAAATTAT
19403194 TCATTATATT
Statistics
Matches: 224, Mismatches: 59, Indels: 58
0.66 0.17 0.17
Matches are distributed among these distances:
97 3 0.01
98 17 0.08
99 53 0.24
100 36 0.16
101 48 0.21
102 23 0.10
103 26 0.12
104 7 0.03
105 11 0.05
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (99 bp):
TTTAAATTATATTTTATTATATAACATTTATTGTGTTTTTATTTTTATATTACCTTTTTATGTCA
TATATATCATATATTATCAATTATATTATTTATG
Found at i:19403681 original size:33 final size:32
Alignment explanation
Indices: 19403612--19403686 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
19403602 ATTGATATTG
*
19403612 TATTATT-CTTTTTTGGTATGTCATGCATTAT
1 TATTATTACTTTTTTGGTATATCATGCATTAT
19403643 T-TTATTACTTTTTT-GTATATCATGCATTATT
1 TATTATTACTTTTTTGGTATATCATGCATTA-T
19403674 TAATTATTACTTT
1 T-ATTATTACTTT
19403687 GTATGTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 19 0.49
31 10 0.26
33 10 0.26
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.60
Consensus pattern (32 bp):
TATTATTACTTTTTTGGTATATCATGCATTAT
Found at i:19409260 original size:24 final size:24
Alignment explanation
Indices: 19409233--19409284 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
19409223 TAGTTTAACC
*
19409233 ATATTTTAACATAATTATTATTAA
1 ATATTTTAACATAATAATTATTAA
19409257 ATATTTTAACATAATAATTATTAA
1 ATATTTTAACATAATAATTATTAA
19409281 ATAT
1 ATAT
19409285 AATAGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTTAACATAATAATTATTAA
Found at i:19414410 original size:37 final size:37
Alignment explanation
Indices: 19414347--19414455 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
19414337 AGCTCAGATG
* * *
19414347 AAATCTCCACACGAAGTTATCTGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
19414384 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
19414421 TAATCTCCACACGTAATCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
19414456 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:19414656 original size:48 final size:48
Alignment explanation
Indices: 19414597--19414981 Score: 644
Period size: 48 Copynumber: 8.0 Consensus size: 48
19414587 TATACACACG
* * * *
19414597 TCTCCTACATATTTCACACTAGCCCTTCGGCTTTACCACATATACGTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
19414645 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
* ** *
19414693 TCTCATATATATTTCACATTAGCCATTCGGCTTTATAAGATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
19414741 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
19414789 TCTCATACATATTTCACATTAGTCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
* *
19414837 TCGCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACCTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
19414885 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACCTA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
*
19414933 TCTCATACATATTTCACATTAGCCATTCGGTTTTACCACATATACATA
1 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
19414981 T
1 T
19414982 ATTTATCTTG
Statistics
Matches: 318, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 318 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
Found at i:19419103 original size:16 final size:16
Alignment explanation
Indices: 19419082--19419115 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19419072 CTTCCACTTT
19419082 TTCCAACTATTTGTTG
1 TTCCAACTATTTGTTG
19419098 TTCCAACTATTTGTTG
1 TTCCAACTATTTGTTG
19419114 TT
1 TT
19419116 GGTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (16 bp):
TTCCAACTATTTGTTG
Found at i:19425253 original size:228 final size:228
Alignment explanation
Indices: 19424836--19425280 Score: 543
Period size: 228 Copynumber: 1.9 Consensus size: 228
19424826 CCTTGTGGTT
* * * * *
19424836 GGCCATGTAACTCATTGTTCATCAATTTGGGGCCATATAGGCAAGGCATACGGCCATGTGTCTAG
1 GGCCATGTAACTCATTGTTCATCAATTTAGGGACACATAGGCAAGGCACACGGCCATGTATCTAG
* * * * *
19424901 GCCGTGTGTGGCAATATTAGTGCAGAGTTCGAGGGGCAACAGACATGGGCGTGTGTGTCTGGGCG
66 GCCGCGTGTGGCAATATTAGTGCAAAGTTCGACGAGCAACAGACACGGGCG-GTGTGTCTGGGCG
*** * *
19424966 TGTAACTCATTATTTGTGGTACAAAACCACACGGCTAGGGACACGAGCGTGTTCCCAGGCCATAT
130 AACAACTCATTATTTGTGGTACAAAACCACACGGCTAGGGACACGAGCATGTACCCAGGCCATAT
* *
19425031 GAGTCACATAGCCAGGGACACGAGCTTGTGTCTA
195 AAGTCACACAGCCAGGGACACGAGCTTGTGTCTA
* * * * * ** *
19425065 GGCCGTGTAACTCATTGTTCATCAATTTAGGGATACATGGGCAAGGTACATGGCTGTGTATCTTG
1 GGCCATGTAACTCATTGTTCATCAATTTAGGGACACATAGGCAAGGCACACGGCCATGTATCTAG
* *
19425130 GCCGCGTGTGGCCATATTAGTGCAAAGTTCGCACGAGTAAC-GTACACGGGC-GTGTGTCTGGGC
66 GCCGCGTGTGGCAATATTAGTGCAAAGTTCG-ACGAGCAACAG-ACACGGGCGGTGTGTCTGGGC
* * * * *
19425193 GAACAACTTATTGTTTGTGGTACAAAACCACATGGCTAGGGACACGGGCATGTACCCAGGCCGTA
129 GAACAACTCATTATTTGTGGTACAAAACCACACGGCTAGGGACACGAGCATGTACCCAGGCCATA
* *
19425258 TAAGTCACACGGGCAGGGACACG
194 TAAGTCACACAGCCAGGGACACG
19425281 GACGTGTGTC
Statistics
Matches: 180, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
228 86 0.48
229 81 0.45
230 13 0.07
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (228 bp):
GGCCATGTAACTCATTGTTCATCAATTTAGGGACACATAGGCAAGGCACACGGCCATGTATCTAG
GCCGCGTGTGGCAATATTAGTGCAAAGTTCGACGAGCAACAGACACGGGCGGTGTGTCTGGGCGA
ACAACTCATTATTTGTGGTACAAAACCACACGGCTAGGGACACGAGCATGTACCCAGGCCATATA
AGTCACACAGCCAGGGACACGAGCTTGTGTCTA
Found at i:19430563 original size:7 final size:6
Alignment explanation
Indices: 19430548--19430579 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
19430538 CATTTCTAGG
19430548 TCATTT TCATTTT TCATTT TCATTT TCATTT T
1 TCATTT TCA-TTT TCATTT TCATTT TCATTT T
19430580 AGAGAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TCATTT
Found at i:19430611 original size:57 final size:57
Alignment explanation
Indices: 19430550--19430684 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 57
19430540 TTTCTAGGTC
*
19430550 ATTTTCATTTTTCATTTTCATTTTCATTTTAGAGAAAACCATATTCATTTCCAAATG
1 ATTTTCATTTTTCATTTTCATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATG
* * * * *
19430607 ATTTT-ATTTCTCCATTTTTATTTTTATTTTGGAGGAAACCATAATCATTTCCAAATG
1 ATTTTCATTT-TTCATTTTCATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATG
19430664 -TTTATCATTTTTACATTTTCA
1 ATTT-TCATTTTT-CATTTTCA
19430685 CCATTTTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
56 7 0.11
57 48 0.73
58 11 0.17
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (57 bp):
ATTTTCATTTTTCATTTTCATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATG
Found at i:19432944 original size:8 final size:8
Alignment explanation
Indices: 19432919--19432970 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
19432909 CAATGATGTG
*
19432919 AATAATAA
1 AATATTAA
19432927 AATATATAA
1 AATAT-TAA
19432936 AATATT-A
1 AATATTAA
19432943 AATATTAA
1 AATATTAA
*
19432951 AATATCAA
1 AATATTAA
*
19432959 AATATTAG
1 AATATTAA
19432967 AATA
1 AATA
19432971 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (8 bp):
AATATTAA
Found at i:19432951 original size:24 final size:24
Alignment explanation
Indices: 19432918--19432974 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
19432908 ACAATGATGT
*
19432918 GAATAATAAAATATATAAAATATTA
1 GAATAATAAAATAT-CAAAATATTA
*
19432943 -AATATTAAAATATCAAAATATTA
1 GAATAATAAAATATCAAAATATTA
19432966 GAATAATAA
1 GAATAATAA
19432975 TAATTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
GAATAATAAAATATCAAAATATTA
Found at i:19433154 original size:25 final size:25
Alignment explanation
Indices: 19433120--19433184 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
19433110 CGTGATAATA
*
19433120 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAGTG
19433145 TTAAAAATATATACATAATATA--G
1 TTAAAAATATATACATAATATAGTG
*
19433168 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
19433185 GATAACATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
25 21 0.55
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATATATACATAATATAGTG
Found at i:19433343 original size:23 final size:25
Alignment explanation
Indices: 19433214--19433345 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 25
19433204 TATATATATA
19433214 AATA-ATATAATATAATATT-AAAG
1 AATATATATAATATAATATTAAAAG
* *
19433237 -ATATATA-AATAAAATAGTATAAAAT
1 AATATATATAATATAATA-T-TAAAAG
*
19433262 ATATATATACGTAATATAGA-ATT-TAA-
1 A-ATATATA--TAATATA-ATATTAAAAG
**
19433288 AATATACCT-A-AT-ATATTAAAAG
1 AATATATATAATATAATATTAAAAG
*
19433310 AATATATATAATATAATATTAAGA-
1 AATATATATAATATAATATTAAAAG
19433334 AATATA-ATAATA
1 AATATATATAATA
19433346 ACAAAAAAAG
Statistics
Matches: 83, Mismatches: 10, Indels: 32
0.66 0.08 0.26
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 4 0.05
22 19 0.23
23 12 0.14
24 9 0.11
25 16 0.19
26 1 0.01
27 9 0.11
28 1 0.01
29 1 0.01
30 6 0.07
31 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (25 bp):
AATATATATAATATAATATTAAAAG
Found at i:19433985 original size:30 final size:30
Alignment explanation
Indices: 19433835--19434009 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
19433825 TAGGTACAAG
* *
19433835 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
19433865 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
19433895 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
19433925 TGGTGGTGGAAAATGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
19433955 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
19433985 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
19434010 TGAGAAAAGT
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
29 2 0.02
30 127 0.98
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:19434892 original size:73 final size:73
Alignment explanation
Indices: 19434722--19435234 Score: 535
Period size: 73 Copynumber: 6.8 Consensus size: 73
19434712 TGTGAACCCA
* * *
19434722 AGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAAATACCTCAG
*
19434787 CGTGTCCTG
65 CGTGTCCCG
*
19434796 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAAATACCTCAGC
19434861 GTGTCCCG
66 GTGTCCCG
* * * *
19434869 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTATTTTTTTGAAATTAAAACACAAAAATCGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTG----A--TTTTTG-----ACAA-ACAGAAATTGA
* * *
19434934 CAATTCCTCAGCGTGCCCCG
54 AAATACCTCAGCGTGTCCCG
* * *
19434954 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAAATACCTCAGC
* *
19435019 ATGTCCTG
66 GTGTCCCG
*
19435027 AGGCTCAACGCACCTCTCGCAATATGAGTTGA-TTTTGACAAACAGAAACAAAATTGAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAG-----AAATTGAAAATACC
***
19435091 TCAGCACGTGAGTCG
61 TCAG--CGTGTCCCG
* * * * * *
19435106 AGGCTCAACTCACTTCTTGCAATATGAATTGATTTTTTTGAC-AATAGAAATTGCAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGACAAACAGAAATTGAAAATACCTCA
*
19435170 GCATGTCCCG
64 GCGTGTCCCG
* * *
19435180 AGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAA
19435235 CACAAAAATT
Statistics
Matches: 366, Mismatches: 50, Indels: 47
0.79 0.11 0.10
Matches are distributed among these distances:
72 19 0.05
73 115 0.31
74 85 0.23
76 16 0.04
77 18 0.05
79 44 0.12
81 5 0.01
82 7 0.02
84 3 0.01
85 54 0.15
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAAATACCTCAGC
GTGTCCCG
Found at i:19435299 original size:87 final size:87
Alignment explanation
Indices: 19435153--19435317 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
19435143 TTGACAATAG
* *
19435153 AAATTGCAATTACCTCAGCATGTCCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTG
1 AAATTGCAATTACCTCAGCATGCCCCGAGGCTCAACTCACATATCGCAATATGAGTTGATTTTTG
*
19435218 AAAAACATAAATTGAAACACAA
66 AAAAACAGAAATTGAAACACAA
* *
19435240 AAATTGACAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTT
1 AAATTG-CAATTACCTCAGCATGCCCCGAGGCTCAACTCACATATCGCAATATGAGTTGATTTTT
19435304 GAAAAACAGAAATT
65 GAAAAACAGAAATT
19435318 TAAAAATACC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
87 69 0.96
88 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (87 bp):
AAATTGCAATTACCTCAGCATGCCCCGAGGCTCAACTCACATATCGCAATATGAGTTGATTTTTG
AAAAACAGAAATTGAAACACAA
Found at i:19435404 original size:14 final size:14
Alignment explanation
Indices: 19435385--19435413 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19435375 TTTTTTTACG
19435385 AACAGAAATTGAAA
1 AACAGAAATTGAAA
19435399 AACAGAAATTGAAA
1 AACAGAAATTGAAA
19435413 A
1 A
19435414 GACCTCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:19435458 original size:92 final size:91
Alignment explanation
Indices: 19435302--19435469 Score: 259
Period size: 92 Copynumber: 1.8 Consensus size: 91
19435292 GAGTTGATTT
* * *
19435302 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTCTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCATATCCTGAGGCTCAACTCACCTCTCGCAATATG
19435367 AGTTGATTTTTTTTTACGAACAGAAA
66 AGTTGATTTTTTTTTACGAACAGAAA
*
19435393 TTGAAAAACAGAAA-TTGAAAAGACCTCAGCATATGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCATAT---CCTGAGGCTCAACTCACCTCTCGCAAT
19435456 ATGAGTTGATTTTT
63 ATGAGTTGATTTTT
19435470 GACAAACAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
90 16 0.23
91 14 0.20
92 38 0.54
93 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (91 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCATATCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTTTTACGAACAGAAA
Found at i:19435516 original size:239 final size:237
Alignment explanation
Indices: 19434695--19436315 Score: 2124
Period size: 239 Copynumber: 6.9 Consensus size: 237
19434685 AAAGTAGATT
* * * *
19434695 TTGAAAATACCTC-GACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTT
1 TTGAAAAGACCTCAG-CATGTG-AGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * *
19434759 GAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
64 GACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
19434824 TTGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCA
128 TTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
* * *
19434888 CAATATGAGTTGATTTATTTTTT-----TGAAATTAAAACACAAAAA
193 CAATATGAGTTGATTT-TTTTTTACAACAGAAATTGAAA-ACAGAAA
* * ** ** *
19434930 TCGACAATTCCTCAGC--GTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* * * *
19434993 AAAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACGCACCTCTCGCAATATGAGTTG
66 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * *
19435058 A-TTTTGACAAACAGAAACAAAATTGAAAATACCTCAGCACGTGAGT-C-GAGGCTCAACTCACT
131 ATTTTTGAAAAACAG----AAATTTAAAAATACCTCAG--CGT--GTCCTGAGGCTCAACTCACC
* * * *
19435120 TCTTGCAATATGAATTGA-TTTTTTTGACAATAGAAATTG----C---AA
188 TCTCGCAATATGAGTTGATTTTTTTTTACAACAGAAATTGAAAACAGAAA
* *
19435162 TT------ACCTCAGCATGT--CCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* * * *
19435219 AAAACATAAATTGAAACACAAAAATTGACAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTAT
66 CAAACAGAAATTG--------AAA-T-----TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCT
*
19435284 CGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTCTCCTGAGGCTCAA
117 CGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAA
19435349 CTCACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAACAGAAA
182 CTCACCTCTCGCAATATGAGTTGATTTTTTTTTAC-AACAGAAATTG-AAAACAGAAA
*
19435407 TTGAAAAGACCTCAGCATATGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
19435472 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
66 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19435537 ATTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
131 A-TTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
19435602 ATATGAGTTGA-TTTTTTTTACGAACAGAAATTGAAGAACAGAAA
195 ATATGAGTTGATTTTTTTTTAC-AACAGAAATTGAA-AACAGAAA
*
19435646 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAAGATGAGTTGATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
19435711 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT
66 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19435776 ATTTTTG-AAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
131 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
19435840 TATGAGTTGATTTTTTTTT---AC-------G--AACAGAAA
196 TATGAGTTGATTTTTTTTTACAACAGAAATTGAAAACAGAAA
* *
19435870 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAGTTAATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
19435935 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
66 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19436000 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
131 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
19436065 TATGAGTTGA-TTTTTTTTACGAACAGAAATTGAAGAACAGAAA
196 TATGAGTTGATTTTTTTTTAC-AACAGAAATTGAA-AACAGAAA
* *
19436108 ATGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGA
1 TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* *
19436173 CAAACAGAAATTGAAATTACCTCAGTGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTG
66 CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * * *
19436238 ATTTTTGACAAACA-AAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAA
131 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
19436302 TATGAGTTGATTTT
196 TATGAGTTGATTTT
19436316 GAAAAACAAA
Statistics
Matches: 1253, Mismatches: 62, Indels: 139
0.86 0.04 0.10
Matches are distributed among these distances:
224 149 0.12
225 67 0.05
226 60 0.05
227 1 0.00
228 4 0.00
230 13 0.01
231 52 0.04
232 53 0.04
233 4 0.00
234 9 0.01
235 66 0.05
236 12 0.01
237 182 0.15
238 167 0.13
239 207 0.17
240 123 0.10
241 12 0.01
242 1 0.00
244 1 0.00
245 7 0.01
251 11 0.01
253 52 0.04
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (237 bp):
TTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
CAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTTTTTACAACAGAAATTGAAAACAGAAA
Found at i:19435525 original size:73 final size:73
Alignment explanation
Indices: 19435393--19435636 Score: 335
Period size: 75 Copynumber: 3.3 Consensus size: 73
19435383 CGAACAGAAA
* * * **
19435393 TTGAAAAACAGAAATTGAAAAGACCTCAGCATATGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGACAAACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
19435458 GAGTTGATTT
64 GAGTTGATTT
*
19435468 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
19435533 GTTGATTTT
66 GTTGA-TTT
* * *
19435542 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGACAAACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
19435607 AGTTGATTTTT
65 AGTTGA--TTT
* *
19435618 TTTACGAACAGAAATTGAA
1 TTGACAAACAGAAATTGAA
19435637 GAACAGAAAT
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
73 37 0.24
74 16 0.11
75 84 0.55
76 15 0.10
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:19435642 original size:14 final size:14
Alignment explanation
Indices: 19435623--19435650 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19435613 TTTTTTTTAC
19435623 GAACAGAAATTGAA
1 GAACAGAAATTGAA
19435637 GAACAGAAATTGAA
1 GAACAGAAATTGAA
19435651 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:19435699 original size:91 final size:88
Alignment explanation
Indices: 19435542--19435726 Score: 248
Period size: 91 Copynumber: 2.1 Consensus size: 88
19435532 AGTTGATTTT
* * *
19435542 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAAGATG
* *
19435607 AGTTGATTTTTTTTACGAACAGAAA
66 AGTTGA--TTTTTGACAAACAGAAA
* *
19435632 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAG
19435695 ATGAGTTGATTTTTGACAAACAGAAA
63 ATGAGTTGATTTTTGACAAACAGAAA
19435721 TTGAAA
1 TTGAAA
19435727 TTACCTCAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
89 34 0.40
90 13 0.15
91 35 0.42
92 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAAGATG
AGTTGATTTTTGACAAACAGAAA
Found at i:19435763 original size:73 final size:73
Alignment explanation
Indices: 19435638--19436098 Score: 627
Period size: 73 Copynumber: 6.2 Consensus size: 73
19435628 GAAATTGAAG
* ** *
19435638 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAAGATGAGTTG
1 AACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19435703 ATTTTTGACA
64 ATTTTTGACA
* *
19435713 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
19435778 TTTTGA-A
66 TTTTGACA
* *
19435785 AACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
19435850 TTTTTTTTTACG
65 ---TTTTTGACA
* ** * *
19435862 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAGTTA
1 AACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
19435927 ATTTTTGACA
64 ATTTTTGACA
*
19435937 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
19436002 TTTTGAAA
66 TTTTGACA
* *
19436010 AACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
19436075 TTTTTTTTACG
65 --TTTTTGACA
19436086 AACAGAAATTGAA
1 AACAGAAATTGAA
19436099 GAACAGAAAA
Statistics
Matches: 341, Mismatches: 35, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
72 9 0.03
73 147 0.43
74 53 0.16
75 55 0.16
76 34 0.10
77 8 0.02
78 35 0.10
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGACA
Found at i:19436081 original size:224 final size:224
Alignment explanation
Indices: 19435637--19436315 Score: 1110
Period size: 224 Copynumber: 3.0 Consensus size: 224
19435627 AGAAATTGAA
*
19435637 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAAGATGAGTT
1 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
19435702 GATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
66 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
*
19435767 TATGAGTTTATTTTTG-AAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
131 TATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
19435831 CTCTCGCAATATGAGTTGATTTTTTTTTAC
196 CTCTCGCAATATGAGTTGA-TTTTTTTTAC
*
19435861 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAGTT
1 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
19435926 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
66 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
19435991 TATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
131 TATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
19436056 CTCTCGCAATATGAGTTGATTTTTTTTAC
196 CTCTCGCAATATGAGTTGATTTTTTTTAC
19436085 GAACAGAAATTGAAGAACAGAAAATGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTC
1 GAACAGAAA-T-------------TGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTC
*
19436150 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGTGTGTCCCGAGGCTCAA
52 TCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
* * * * *
19436215 CTCACCTTTCGCAATATGAGTTGATTTTTGACAAACA-AAAATTGAAATTACCTCAGCGTGTCCT
117 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCT
*
19436279 GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
182 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
19436316 GAAAAACAAA
Statistics
Matches: 428, Mismatches: 12, Indels: 17
0.94 0.03 0.04
Matches are distributed among these distances:
224 161 0.38
225 68 0.16
237 60 0.14
238 139 0.32
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (224 bp):
GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTTTTTTAC
Found at i:19436185 original size:462 final size:463
Alignment explanation
Indices: 19434696--19436315 Score: 2113
Period size: 462 Copynumber: 3.4 Consensus size: 463
19434686 AAGTAGATTT
* *
19434696 TGAAAATACCTC-GACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTG
1 TGAAAAGACCTCAG-CATGTG-ACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTG
* * *
19434760 AAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
64 AAAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
19434825 TGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCAC
128 TGATTTTTGACAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
** * * * ** **
19434889 AATATGAGTTGATTTATTTTTTTGAAATTAAAACACAAAAATCGACAATTCCTCAGC--GTGCCC
193 AATATGAGTTG----ATTTTTTT----TTACGA-ACAGAAATTGAAAAGACCTCAGCATGTGAGC
* *
19434952 CGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCA
249 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCA
* * * * *
19435017 GCATGTCCTGAGGCTCAACGCACCTCTCGCAATATGAGTTGA-TTTTGACAAACAGAAACAAAAT
314 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG----AAATT
* * * *
19435081 TGAAAATACCTCAGCACGTGAGT-C-GAGGCTCAACTCACTTCTTGCAATATGAATTGATTTTTT
375 TAAAAATACCTCAG--CGT--GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
19435144 TGAC-AATAGAAATT---G--C----AA
436 TTACGAACAGAAATTGAAGAACAGAAAA
*
19435162 T-----TACCTCAGCATGT--CCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAA
1 TGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAA
* * *
19435220 AAACATAAATTGAAACACAAAAATTGACAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTATC
66 AAACAGAAATTG--------AAA-T-----TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
* *
19435285 GCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTCTCCTGAGGCTCAAC
117 GCAATATGAGTTGATTTTTGACAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAAC
19435350 TCACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAACAGAAATTGAAAAG
182 TCACCTCTCGCAATATGAGTTGATTTTTTTTT----AC-------G---AACAGAAATTGAAAAG
*
19435415 ACCTCAGCATATGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGA
233 ACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGA
19435480 AATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG
298 AATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG
19435545 AAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
362 AAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
19435610 TGATTTTTTTTACGAACAGAAATTGAAGAACAGAAAT
427 TGATTTTTTTTACGAACAGAAATTGAAGAACAGAAAA
* * * *
19435647 TGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAAGATGAGTTGATTTTTGAC
1 TGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAA
*
19435712 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTA
66 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
19435777 TTTTTGA-AAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
131 TTTTTGACAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
19435841 ATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACT
196 ATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACT
* *
19435906 CACCTCTCACAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
261 CACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
19435971 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCG
326 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCG
19436036 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTGAAGA
391 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTGAAGA
19436101 ACAGAAAA
456 ACAGAAAA
* * * *
19436109 TGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAC
1 TGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAA
* *
19436174 AAACAGAAATTGAAATTACCTCAGTGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGA
66 AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
19436239 TTTTTGACAAACA-AAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAAT
131 TTTTTGACAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
19436303 ATGAGTTGATTTT
196 ATGAGTTGATTTT
19436316 GAAAAACAAA
Statistics
Matches: 1040, Mismatches: 60, Indels: 112
0.86 0.05 0.09
Matches are distributed among these distances:
457 2 0.00
458 51 0.05
461 11 0.01
462 300 0.29
463 141 0.14
464 2 0.00
465 3 0.00
466 2 0.00
468 9 0.01
471 62 0.06
472 50 0.05
473 4 0.00
474 1 0.00
475 42 0.04
476 9 0.01
477 109 0.10
478 54 0.05
479 106 0.10
481 13 0.01
483 1 0.00
484 3 0.00
485 2 0.00
490 12 0.01
492 51 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (463 bp):
TGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAA
AAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGACAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCG
TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTGAAGA
ACAGAAAA
Found at i:19436354 original size:72 final size:73
Alignment explanation
Indices: 19436133--19436387 Score: 395
Period size: 73 Copynumber: 3.5 Consensus size: 73
19436123 CATGTGAGCC
* *
19436133 GAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
* *
19436198 TGTGTCCC
66 CGTGTCCT
*
19436206 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
19436271 CGTGTCCT
66 CGTGTCCT
* * * * *
19436279 GAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGTACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
*
19436343 CGTGTCTT
66 CGTGTCCT
*
19436351 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
19436388 CCTTGAAAAG
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
72 65 0.39
73 102 0.61
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (73 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
CGTGTCCT
Found at i:19444669 original size:12 final size:12
Alignment explanation
Indices: 19444649--19444684 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
19444639 TGGGATATGC
*
19444649 AATGTATGAATG
1 AATGCATGAATG
19444661 AATGCATGAATG
1 AATGCATGAATG
19444673 AATGCATGAATG
1 AATGCATGAATG
19444685 TCAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:19451507 original size:19 final size:20
Alignment explanation
Indices: 19451466--19451508 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19451456 AAGTTAGTTT
* *
19451466 TTTTTTTCAAAATAATTTTA
1 TTTTTTTCAAAATAATATAA
19451486 TTTTTTTCAAAA-AATATAA
1 TTTTTTTCAAAATAATATAA
19451505 TTTT
1 TTTT
19451509 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTTTCAAAATAATATAA
Found at i:19451669 original size:3 final size:3
Alignment explanation
Indices: 19451661--19451701 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
19451651 GAAAAGCACA
19451661 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19451702 CAACGTGTCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19453700 original size:14 final size:15
Alignment explanation
Indices: 19453681--19453712 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19453671 TTATTATGTG
19453681 ATAATAA-AAAATTA
1 ATAATAACAAAATTA
19453695 ATAATAACAAAATTA
1 ATAATAACAAAATTA
19453710 ATA
1 ATA
19453713 TTAATTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACAAAATTA
Found at i:19461224 original size:14 final size:15
Alignment explanation
Indices: 19461193--19461225 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19461183 ATAAAAAATG
*
19461193 ATATTTATTATTAGT
1 ATATTTATTATTAAT
19461208 ATATTTA-TATTAAT
1 ATATTTATTATTAAT
19461222 ATAT
1 ATAT
19461226 ATTTCTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:19463193 original size:19 final size:18
Alignment explanation
Indices: 19463171--19463218 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
19463161 ATTAATAATT
19463171 AATTTTTTAAAATATAAA
1 AATTTTTTAAAATATAAA
* **
19463189 AA-ATTCAAAAATATAAA
1 AATTTTTTAAAATATAAA
19463206 AATTATTTTAAAA
1 AATT-TTTTAAAA
19463219 AATTGAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
17 14 0.64
18 2 0.09
19 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTTTTAAAATATAAA
Found at i:19463227 original size:29 final size:29
Alignment explanation
Indices: 19463185--19463241 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
19463175 TTTTAAAATA
19463185 TAAAAAATTCAAAAATATAAAAATTATTT
1 TAAAAAATTCAAAAATATAAAAATTATTT
* * * *
19463214 TAAAAAATTGAAAATTATTAAACTTATT
1 TAAAAAATTCAAAAATATAAAAATTATT
19463242 AAAAAGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAAAAATTCAAAAATATAAAAATTATTT
Found at i:19465457 original size:22 final size:21
Alignment explanation
Indices: 19465432--19465507 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
19465422 GGGAGGTTAA
*
19465432 ACACTCGTGTGAAGAAGGGCAC
1 ACACCCGTGTGAAG-AGGGCAC
*
19465454 ACACCCATGTGAAGAGAGGCAC
1 ACACCCGTGTGAAGAG-GGCAC
*
19465476 ACAGCCGTGTGAAG-GAGGCAC
1 ACACCCGTGTGAAGAG-GGCAC
*
19465497 ACGCCCGTGTG
1 ACACCCGTGTG
19465508 GACCAGGGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.38
22 29 0.62
ACGTcount: A:0.29, C:0.26, G:0.33, T:0.12
Consensus pattern (21 bp):
ACACCCGTGTGAAGAGGGCAC
Found at i:19470949 original size:26 final size:26
Alignment explanation
Indices: 19470898--19470961 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
19470888 GCCCAAACCC
* *
19470898 ATGAGGTCGTAGACTGAGCTTGCATG
1 ATGAGATCGTAGACTGAGCTTACATG
*
19470924 ATGGGATCGTAGACTGAG-TTCACATG
1 ATGAGATCGTAGACTGAGCTT-ACATG
*
19470950 ATGATATCGTAG
1 ATGAGATCGTAG
19470962 GCTAAGCTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (26 bp):
ATGAGATCGTAGACTGAGCTTACATG
Found at i:19477150 original size:20 final size:21
Alignment explanation
Indices: 19477125--19477164 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19477115 TGGGCTAAGT
*
19477125 ATGAT-GTTTAAGCATGATAA
1 ATGATGGTTTAAGAATGATAA
19477145 ATGATGGTTTAAGAATGATA
1 ATGATGGTTTAAGAATGATA
19477165 TGTTATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (21 bp):
ATGATGGTTTAAGAATGATAA
Found at i:19478811 original size:45 final size:45
Alignment explanation
Indices: 19478699--19478872 Score: 194
Period size: 45 Copynumber: 3.9 Consensus size: 45
19478689 CGAATTCACC
* * * *
19478699 CACCGGCATT-TTGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATTT
1 CACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGT-ATCT
* * * * *
19478741 CACCAGCGTTATAGCCTGCTAGGCTCGAAGGCCCAAATAGTATCT
1 CACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATCT
*
19478786 CATCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATCT
* * *
19478831 CACCGGCGTCATAGCCTACTAGGCTCAAAGGCTCGAATAGTA
1 CACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTA
19478873 CCGTACGATA
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
42 8 0.07
43 17 0.15
44 4 0.04
45 83 0.73
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (45 bp):
CACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:19482000 original size:43 final size:44
Alignment explanation
Indices: 19481925--19482017 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
19481915 CTTAATATAT
***
19481925 ATAATAATATTTCATGCAAATATAACTTAAAAT-AACAACATAA
1 ATAATAATATTTCATGCAAATATAAAAAAAAATAAACAACATAA
*
19481968 ATAATCAAT-TTTCATGCAAATATAAAAAAAAATAAATAACATAA
1 ATAAT-AATATTTCATGCAAATATAAAAAAAAATAAACAACATAA
19482012 A-AATAA
1 ATAATAA
19482018 CAAATAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 2 0.05
43 29 0.66
44 13 0.30
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (44 bp):
ATAATAATATTTCATGCAAATATAAAAAAAAATAAACAACATAA
Found at i:19482423 original size:12 final size:12
Alignment explanation
Indices: 19482406--19482455 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
19482396 AAATTATACA
19482406 TAATATAATAAG
1 TAATATAATAAG
19482418 TAATATAA-AA-
1 TAATATAATAAG
*
19482428 TAAAAT-ATAAG
1 TAATATAATAAG
*
19482439 TAATATAATAAA
1 TAATATAATAAG
19482451 TAATA
1 TAATA
19482456 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 1 0.03
10 7 0.22
11 7 0.22
12 17 0.53
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
TAATATAATAAG
Found at i:19484251 original size:45 final size:45
Alignment explanation
Indices: 19484202--19484617 Score: 153
Period size: 45 Copynumber: 9.2 Consensus size: 45
19484192 TAAATCTATC
*
19484202 ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGGTCTACT
1 ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGATCTACT
* * * * * * * *
19484247 ATCTTCAATCTACTCCCCG-TCT-AATATA-GAGAGGCCAAATCTA-T
1 ATCTTCGATCTACT--TCGATGTAAACACACGA-ATGTCAGATCTACT
* *
19484291 CATCTTCGATCTGCTTCGATGTAAACACACGAATGTCAGATCTGCT
1 -ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGATCTACT
* * * * * * * **
19484337 ATCTTCGATCTGCTCCCCG-TCT-AATACA-GAGACGCCAAAT-TTGT
1 ATCTTCGATCTACT--TCGATGTAAACACACGA-ATGTCAGATCTACT
* * * *
19484381 CATCTTCGATCTGCTTTGATGTAATCACACGAATGTCAGATCTGCT
1 -ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGATCTACT
* * * * * * * *
19484427 ATCTTCGATCTGCTCCCCG-TCT-AATACA-GAGACGCCAAATCT-GT
1 ATCTTCGATCTACT--TCGATGTAAACACACGA-ATGTCAGATCTACT
* * *
19484471 CATCTTCGATC-AGCTTTGATATAAACACACGAATGTCAGATCTGCT
1 -ATCTTCGATCTA-CTTCGATGTAAACACACGAATGTCAGATCTACT
* * ** * * * * * *
19484517 ATCTTCAATCTGC-TCCCTGTCTAATACA-GAGACGCCAAATCT-GT
1 ATCTTCGATCTACTTCGATGT-AAACACACGA-ATGTCAGATCTACT
* *
19484561 CATCTTCGATCTACTTCGATATAAACACACGAATGTTAGATCTACT
1 -ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGATCTACT
19484607 ATCTTCGATCT
1 ATCTTCGATCT
19484618 GCTCTTCGTC
Statistics
Matches: 260, Mismatches: 79, Indels: 64
0.65 0.20 0.16
Matches are distributed among these distances:
43 4 0.02
44 22 0.08
45 206 0.79
46 23 0.09
47 5 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (45 bp):
ATCTTCGATCTACTTCGATGTAAACACACGAATGTCAGATCTACT
Found at i:19484310 original size:90 final size:90
Alignment explanation
Indices: 19484157--19484699 Score: 798
Period size: 90 Copynumber: 6.0 Consensus size: 90
19484147 TCATGCTGAA
* * * * * * *
19484157 ATCTTTGATCTGCTCCTCGCCTAATACAGAGATGCTAAATCTATCATCTTCGATCTACTTCGATG
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
* *
19484222 TAAACACACGAATGTCAGGTCTACT
66 TAAACACACGAATGTCAGATCTGCT
* * * * *
19484247 ATCTTCAATCTACTCCCCGTCTAATATAGAGAGGCCAAATCTATCATCTTCGATCTGCTTCGATG
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
19484312 TAAACACACGAATGTCAGATCTGCT
66 TAAACACACGAATGTCAGATCTGCT
* *
19484337 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATTTGTCATCTTCGATCTGCTTTGATG
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
*
19484402 TAATCACACGAATGTCAGATCTGCT
66 TAAACACACGAATGTCAGATCTGCT
* * *
19484427 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCAGCTTTGATA
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
19484492 TAAACACACGAATGTCAGATCTGCT
66 TAAACACACGAATGTCAGATCTGCT
* * * *
19484517 ATCTTCAATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTACTTCGATA
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
* *
19484582 TAAACACACGAATGTTAGATCTACT
66 TAAACACACGAATGTCAGATCTGCT
** * * *
19484607 ATCTTCGATCTGCTCTTCGTCTAATACAAAGACGCCAAATTTGTCATCTTTGATCTGCTTCGATG
1 ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
*
19484672 TAAACACACGAATGTCAGACCTGCT
66 TAAACACACGAATGTCAGATCTGCT
19484697 ATC
1 ATC
19484700 GGCAAGAGGA
Statistics
Matches: 411, Mismatches: 42, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 411 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (90 bp):
ATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATG
TAAACACACGAATGTCAGATCTGCT
Found at i:19484656 original size:45 final size:45
Alignment explanation
Indices: 19484264--19484665 Score: 172
Period size: 45 Copynumber: 8.9 Consensus size: 45
19484254 ATCTACTCCC
* * * *
19484264 CGTCTAATATAGAGAGGCCAAATCTATCATCTTCGATCTG--CTT
1 CGTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCTCTT
* * * * * **
19484307 CGATGTAA-ACACACGAATGTCAGATCTG-CTATCTTCGATCTGCTCCC
1 CG-TCTAATACA-AAG-ACGCCAAATCTGTC-ATCTTCGATCTGCTCTT
* *
19484354 CGTCTAATACAGAGACGCCAAATTTGTCATCTTCGATCTGCT-TT
1 CGTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCTCTT
* * * * * **
19484398 -GATGTAAT-CACACGAATGTCAGATCTG-CTATCTTCGATCTGCTCCC
1 CG-TCTAATACA-AAG-ACGCCAAATCTGTC-ATCTTCGATCTGCTCTT
* *
19484444 CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCAGCT-TT
1 CGTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCTCTT
* * * * * * *
19484488 -GATATAA-ACACACGAATGTCAGATCTG-CTATCTTCAATCTGCTC-C
1 CG-TCTAATACA-AAG-ACGCCAAATCTGTC-ATCTTCGATCTGCTCTT
* *
19484533 CTGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCT--ACTT
1 C-GTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCTCTT
* * * ** * *
19484577 CGATATAA-ACACACGAATGTTAGATCT-ACTATCTTCGATCTGCTCTT
1 CG-TCTAATACA-AAG-ACGCCAAATCTGTC-ATCTTCGATCTGCTCTT
* *
19484624 CGTCTAATACAAAGACGCCAAATTTGTCATCTTTGATCTGCT
1 CGTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCT
19484666 TCGATGTAAA
Statistics
Matches: 252, Mismatches: 73, Indels: 66
0.64 0.19 0.17
Matches are distributed among these distances:
43 16 0.06
44 26 0.10
45 163 0.65
46 26 0.10
47 21 0.08
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (45 bp):
CGTCTAATACAAAGACGCCAAATCTGTCATCTTCGATCTGCTCTT
Found at i:19493204 original size:27 final size:27
Alignment explanation
Indices: 19493126--19493204 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
19493116 CATGGCTGCT
* *
19493126 AGAACAGATAA-TGTGACAGAGTCACC
1 AGAACAGATAATTGTGGCAGAGCCACC
*
19493152 AGAACAGATAATTGTGGCAGAACCACC
1 AGAACAGATAATTGTGGCAGAGCCACC
* *
19493179 AGATCAGATAATTGTGGCATAGCCAC
1 AGAACAGATAATTGTGGCAGAGCCAC
19493205 TAGGACGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 11 0.24
27 35 0.76
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (27 bp):
AGAACAGATAATTGTGGCAGAGCCACC
Found at i:19493355 original size:26 final size:27
Alignment explanation
Indices: 19493326--19493385 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
19493316 GGGTATAATG
*
19493326 GTAATTTT-ACACCTAAGGGTATATC-A
1 GTAATTTTCACACATAAGGGTAT-TCAA
* *
19493352 GTAATTTTCATACATAGGGGTATTCAA
1 GTAATTTTCACACATAAGGGTATTCAA
19493379 GTAATTT
1 GTAATTT
19493386 CACTATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (27 bp):
GTAATTTTCACACATAAGGGTATTCAA
Found at i:19500224 original size:41 final size:43
Alignment explanation
Indices: 19500177--19500266 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
19500167 TGAATATAAC
* * *
19500177 AATATAAATT-ACATAA-AATATATATAAT-AATATTTCATGCA
1 AATATAAATTAAAATAACAACATAAATAATCAAT-TTTCATGCA
*
19500218 AATATAACTTAAAATAACAACATAAATAATCAATTTTCATGCA
1 AATATAAATTAAAATAACAACATAAATAATCAATTTTCATGCA
19500261 AATATA
1 AATATA
19500267 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 9 0.21
42 5 0.12
43 25 0.60
44 3 0.07
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (43 bp):
AATATAAATTAAAATAACAACATAAATAATCAATTTTCATGCA
Found at i:19500283 original size:43 final size:42
Alignment explanation
Indices: 19500200--19500291 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
19500190 TAAAATATAT
*
19500200 ATAATAATATTTCATGCAAATATAACTTAAAATAACAACATAA
1 ATAATAATATTTCATGCAAATATAAC-AAAAATAACAACATAA
*
19500243 ATAATCAAT-TTTCATGCAAATATATA-AAAAATAAATAACATAA
1 ATAAT-AATATTTCATGCAAATATA-ACAAAAAT-AACAACATAA
19500286 A-AATAA
1 ATAATAA
19500292 CAAATAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 2 0.05
42 8 0.18
43 30 0.68
44 4 0.09
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (42 bp):
ATAATAATATTTCATGCAAATATAACAAAAATAACAACATAA
Found at i:19500730 original size:21 final size:21
Alignment explanation
Indices: 19500688--19500746 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
19500678 ACATAATATA
*
19500688 ATAAGTAATATATATTAA-AAT
1 ATAAGTAATATA-ATAAATAAT
19500709 ATAAGTAATATAATAAATAAT
1 ATAAGTAATATAATAAATAAT
* *
19500730 ACAA--AATAAAATAAATA
1 ATAAGTAATATAATAAATA
19500747 TTTTTTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.35
20 4 0.12
21 18 0.53
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (21 bp):
ATAAGTAATATAATAAATAAT
Found at i:19506798 original size:16 final size:18
Alignment explanation
Indices: 19506779--19506811 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
19506769 CATACTAGAT
19506779 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
19506795 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
19506812 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:19507439 original size:45 final size:45
Alignment explanation
Indices: 19507339--19507509 Score: 242
Period size: 45 Copynumber: 3.9 Consensus size: 45
19507329 ATTCATCCAT
* * *
19507339 CGGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATTTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCAC
* *
19507381 CGGTATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
19507426 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
* *
19507471 CGGCATCATAGCCTGCTAGGCTCAAAGGCCCAAATAGTA
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
19507510 CCGTACGATA
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
42 6 0.05
43 17 0.14
44 5 0.04
45 89 0.75
46 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (45 bp):
CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
Found at i:19510223 original size:14 final size:15
Alignment explanation
Indices: 19510190--19510227 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
19510180 TGCACTATCA
*
19510190 ATAAAATTCACATGTT
1 ATAAAATT-ACATATT
19510206 ATAAAATT-CATATT
1 ATAAAATTACATATT
19510220 ATAAAATT
1 ATAAAATT
19510228 TATTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
16 8 0.38
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAAATTACATATT
Found at i:19510807 original size:24 final size:24
Alignment explanation
Indices: 19510776--19510823 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19510766 ATATACATAG
19510776 TATTAAGCATTCAAAAATAATCTA
1 TATTAAGCATTCAAAAATAATCTA
19510800 TATTAAGCATTCAAAAATAATCTA
1 TATTAAGCATTCAAAAATAATCTA
19510824 ACTTATCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
TATTAAGCATTCAAAAATAATCTA
Found at i:19524115 original size:31 final size:31
Alignment explanation
Indices: 19524056--19524115 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19524046 TAATTTCTAA
**
19524056 GTTATTATTATAAGGGTAAAAATGTAAAATG
1 GTTATTATTATAAGGGTAAAAAAATAAAATG
*
19524087 GTTATTATTATAA-GTTAAATAAAATAAAA
1 GTTATTATTATAAGGGTAAA-AAAATAAAA
19524116 CAAATAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (31 bp):
GTTATTATTATAAGGGTAAAAAAATAAAATG
Found at i:19524989 original size:23 final size:23
Alignment explanation
Indices: 19524935--19524994 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
19524925 CAGCTCATTG
* *
19524935 GAGCTTACCGATTTAGCTCAAAA
1 GAGCTTACTGATTCAGCTCAAAA
* *
19524958 AAGCTTACTGATTCAGCTCGAAA
1 GAGCTTACTGATTCAGCTCAAAA
19524981 GAGCTTACTG-TTCA
1 GAGCTTACTGATTCA
19524995 TCAGCTGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (23 bp):
GAGCTTACTGATTCAGCTCAAAA
Found at i:19531099 original size:31 final size:31
Alignment explanation
Indices: 19531040--19531099 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19531030 TGATTTATAA
* **
19531040 GTTATTATTATAAGGGTAAAAATGTAAAATG
1 GTTATTATTATAAGGATAAAAAAATAAAATG
19531071 GTTATTATTATAA-GATAAATAAAATAAAA
1 GTTATTATTATAAGGATAAA-AAAATAAAA
19531100 CAAATAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (31 bp):
GTTATTATTATAAGGATAAAAAAATAAAATG
Found at i:19531982 original size:23 final size:22
Alignment explanation
Indices: 19531956--19532024 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
19531946 GTACTCACCA
*
19531956 CAGCTCGTAAGAGCTTACTGTTT
1 CAGCTC-TAAGAGCTTACCGTTT
** *
19531979 CAGCTCATTGGAGCTTACCGATT
1 CAGCTC-TAAGAGCTTACCGTTT
*
19532002 CAGCTCAATAGAGCTTACCGTTT
1 CAGCTCTA-AGAGCTTACCGTTT
19532025 TTAGCTCAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
CAGCTCTAAGAGCTTACCGTTT
Found at i:19532035 original size:24 final size:23
Alignment explanation
Indices: 19531965--19532043 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
19531955 ACAGCTCGTA
* *
19531965 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACCGTTTCAGCTCAAT
* *
19531988 GGAGCTTACCGATTCAGCTCAAT
1 AGAGCTTACCGTTTCAGCTCAAT
*
19532011 AGAGCTTACCGTTTTTAGCTCAAT
1 AGAGCTTACCG-TTTCAGCTCAAT
*
19532035 AAAGCTTAC
1 AGAGCTTAC
19532044 TATTCATCAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 29 0.62
24 18 0.38
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTCAAT
Found at i:19532930 original size:12 final size:12
Alignment explanation
Indices: 19532897--19532930 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19532887 ATTTTTGTCT
*
19532897 ACACGGGCAGAG
1 ACACGGGCATAG
19532909 ACACGGGCATAG
1 ACACGGGCATAG
*
19532921 ACATGGGCAT
1 ACACGGGCAT
19532931 CTGTCTCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.35, T:0.09
Consensus pattern (12 bp):
ACACGGGCATAG
Found at i:19535632 original size:47 final size:47
Alignment explanation
Indices: 19535563--19535656 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
19535553 GTATTTTCCC
*
19535563 CAACATCCGTTGTTAGAAAATGTGCCCATATTGTAGTAAACATGTAA
1 CAACACCCGTTGTTAGAAAATGTGCCCATATTGTAGTAAACATGTAA
*
19535610 CAACACCCGTTGTTGGAAAATGTGCCCATATTGTAGTAAACATGTAA
1 CAACACCCGTTGTTAGAAAATGTGCCCATATTGTAGTAAACATGTAA
19535657 TTATTTTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (47 bp):
CAACACCCGTTGTTAGAAAATGTGCCCATATTGTAGTAAACATGTAA
Found at i:19535739 original size:15 final size:15
Alignment explanation
Indices: 19535719--19535748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19535709 TTCACTATTA
*
19535719 TGTCTTTTGTATTTT
1 TGTCTTTTCTATTTT
19535734 TGTCTTTTCTATTTT
1 TGTCTTTTCTATTTT
19535749 GCATACATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTCTATTTT
Found at i:19537589 original size:42 final size:43
Alignment explanation
Indices: 19537468--19537620 Score: 134
Period size: 43 Copynumber: 3.6 Consensus size: 43
19537458 TTCCGAGGTG
* * ** * * *
19537468 TGATATCATGTAAGACCACGTCTGGGACTTTGGCATCGACTAGA
1 TGATTTCATGTAAGACCATGTCTAAGACATCGGCATCGA-TATA
* **
19537512 -AATTTACATGTAAGACCATGTCTGGGACATCGGCATC-ATATA
1 TGATTT-CATGTAAGACCATGTCTAAGACATCGGCATCGATATA
*
19537554 TGATTTCATGTAAGAACC-TGTCTAAGACAGT-GGCATCGATATT
1 TGATTTCATGTAAG-ACCATGTCTAAGACA-TCGGCATCGATATA
*
19537597 TGATTACATGTAAGACCATGTCTA
1 TGATTTCATGTAAGACCATGTCTA
19537621 GGATGTTGGT
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
42 29 0.32
43 35 0.38
44 28 0.30
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (43 bp):
TGATTTCATGTAAGACCATGTCTAAGACATCGGCATCGATATA
Found at i:19537610 original size:43 final size:42
Alignment explanation
Indices: 19537515--19537620 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
19537505 GACTAGAAAT
**
19537515 TTACATGTAAGACCATGTCTGGGACATCGGCATCATATATGA
1 TTACATGTAAGACCATGTCTAAGACATCGGCATCATATATGA
* *
19537557 TTTCATGTAAGAACC-TGTCTAAGACAGT-GGCATCGATATTTGA
1 TTACATGTAAG-ACCATGTCTAAGACA-TCGGCATC-ATATATGA
19537600 TTACATGTAAGACCATGTCTA
1 TTACATGTAAGACCATGTCTA
19537621 GGATGTTGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
42 28 0.51
43 27 0.49
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTAAGACATCGGCATCATATATGA
Found at i:19543650 original size:18 final size:18
Alignment explanation
Indices: 19543627--19543670 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
19543617 TTTGTGATCA
19543627 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
19543645 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
19543663 ATATTGAA
1 AAATTGAA
19543671 TTGAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:19543652 original size:12 final size:12
Alignment explanation
Indices: 19543627--19543670 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
19543617 TTTGTGATCA
19543627 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
19543639 AAAGTGAAATTG
1 AAATTGAAAGTG
19543651 AAATTGAAAGTG
1 AAATTGAAAGTG
*
19543663 ATATTGAA
1 AAATTGAA
19543671 TTGAGAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:19550244 original size:18 final size:20
Alignment explanation
Indices: 19550221--19550267 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
19550211 TCTATTATCT
*
19550221 ATTATTATTA-AATTAAATA
1 ATTATTATAATAATTAAATA
19550240 A-TATT-TAATAATTAAATA
1 ATTATTATAATAATTAAATA
19550258 ATTATTATAA
1 ATTATTATAA
19550268 GATTTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 5 0.21
20 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTATAATAATTAAATA
Found at i:19550393 original size:21 final size:21
Alignment explanation
Indices: 19550369--19550409 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19550359 ATTTTATTTA
* *
19550369 ATTAGTAAATAGATATTTATT
1 ATTAGTAAAAAAATATTTATT
*
19550390 ATTATTAAAAAAATATTTAT
1 ATTAGTAAAAAAATATTTAT
19550410 GAGATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTAGTAAAAAAATATTTATT
Found at i:19551381 original size:18 final size:18
Alignment explanation
Indices: 19551358--19551401 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
19551348 TTTGTGATCA
19551358 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
19551376 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
19551394 ATATTGAA
1 AAATTGAA
19551402 TTGAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:19551383 original size:12 final size:12
Alignment explanation
Indices: 19551358--19551401 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
19551348 TTTGTGATCA
19551358 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
19551370 AAAGTGAAATTG
1 AAATTGAAAGTG
19551382 AAATTGAAAGTG
1 AAATTGAAAGTG
*
19551394 ATATTGAA
1 AAATTGAA
19551402 TTGAGAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:19553433 original size:31 final size:31
Alignment explanation
Indices: 19553372--19553507 Score: 127
Period size: 31 Copynumber: 4.4 Consensus size: 31
19553362 AAAAAAAGCC
* * *
19553372 TAGGTATCAAATTAGGAAAAAAAATGTCAAGTT
1 TAGGTACCAAATTAGG--AAAAAGTATCAAGTT
*
19553405 TAGGTACTAAATTAGGAAAAAGTATCAAGTT
1 TAGGTACCAAATTAGGAAAAAGTATCAAGTT
* * *
19553436 CAGGTACCGAATT-GGACCAAAA--A-AAAGTT
1 TAGGTACCAAATTAGGA--AAAAGTATCAAGTT
* *
19553465 TATGTACCAAATTAGGAAAAAGTATCAAATT
1 TAGGTACCAAATTAGGAAAAAGTATCAAGTT
19553496 TAGGTACCAAAT
1 TAGGTACCAAAT
19553508 ATTATATTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
28 4 0.05
29 15 0.18
30 8 0.10
31 38 0.46
32 4 0.05
33 14 0.17
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (31 bp):
TAGGTACCAAATTAGGAAAAAGTATCAAGTT
Found at i:19555972 original size:30 final size:30
Alignment explanation
Indices: 19555938--19555997 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19555928 ACTTAACAAG
*
19555938 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
19555968 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
19555998 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:19556944 original size:20 final size:20
Alignment explanation
Indices: 19556919--19556962 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19556909 GAGTTTTTTT
19556919 TATATT-TTTAAATTTTATTA
1 TATATTCTTT-AATTTTATTA
* *
19556939 TATATTCTTTAGTTTTATTT
1 TATATTCTTTAATTTTATTA
19556959 TATA
1 TATA
19556963 AATTTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TATATTCTTTAATTTTATTA
Found at i:19558475 original size:29 final size:29
Alignment explanation
Indices: 19558433--19558497 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
19558423 ACTCATCGAT
19558433 CACACGGTCGTGTATCGCCACACAGCCTC
1 CACACGGTCGTGTATCGCCACACAGCCTC
19558462 CACACGGTCGTGTATCGCCACACAGCCTC
1 CACACGGTCGTGTATCGCCACACAGCCTC
19558491 CACACGG
1 CACACGG
19558498 ATAGTCCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.22, C:0.42, G:0.22, T:0.15
Consensus pattern (29 bp):
CACACGGTCGTGTATCGCCACACAGCCTC
Found at i:19560633 original size:38 final size:40
Alignment explanation
Indices: 19560527--19560789 Score: 317
Period size: 40 Copynumber: 6.7 Consensus size: 40
19560517 TTGAATGATG
* * *
19560527 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
19560567 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
19560607 TCCGGGCTAAG-CCCGAA-GCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
19560645 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
19560684 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
*
19560724 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AA
* *
19560765 -CCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19560790 AACGAGGAGC
Statistics
Matches: 202, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
38 38 0.19
39 34 0.17
40 117 0.58
41 12 0.06
42 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:19560807 original size:80 final size:80
Alignment explanation
Indices: 19560527--19560822 Score: 270
Period size: 80 Copynumber: 3.8 Consensus size: 80
19560517 TTGAATGATG
** * * * **
19560527 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCAT
*
19560590 TTGTGCGAGA-TACTAAT
64 TTGTGCGA-ATTACTAAA
** * *
19560607 TCCGGGCTAAG-CCCGAA-GCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATT
*
19560668 TGTGCGAGTTACTAAA
65 TGTGCGAATTACTAAA
* ** *
19560684 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTT
19560749 GTGCGAATTACTATAA
66 GTGCGAATTACTA-AA
* * * * *
19560765 -CCGGGCTATGTCCTGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
19560823 TACGTGATTT
Statistics
Matches: 186, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
77 34 0.18
78 24 0.13
79 57 0.31
80 69 0.37
81 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTT
GTGCGAATTACTAAA
Found at i:19566652 original size:23 final size:23
Alignment explanation
Indices: 19566624--19566691 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
19566614 TATAAACACC
*
19566624 AATTAATTATTTAATCATTATTT
1 AATTAATTATTTAATAATTATTT
* * *
19566647 AATTAATTTTTTATATAAATA-CT
1 AATTAATTATTTA-ATAATTATTT
* *
19566670 AATTAATTATTAAATTATTATT
1 AATTAATTATTTAATAATTATT
19566692 AGAGACTCAA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
22 5 0.15
23 24 0.71
24 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTAATTATTTAATAATTATTT
Found at i:19569421 original size:14 final size:15
Alignment explanation
Indices: 19569402--19569434 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19569392 TCCTCCCTTA
*
19569402 AAAATTTTTTCCT-C
1 AAAATTTTTACCTAC
19569416 AAAATTTTTACCTAC
1 AAAATTTTTACCTAC
19569431 AAAA
1 AAAA
19569435 AGGTTAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTTTTACCTAC
Found at i:19575174 original size:50 final size:50
Alignment explanation
Indices: 19575056--19575231 Score: 187
Period size: 50 Copynumber: 3.5 Consensus size: 50
19575046 CTGGTACGCA
**
19575056 TAGTAGCCTGCACTTAGTACTACACA--TGCAACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTG-AACCAACAGTCTAATACACG
* *
19575105 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGAAC-CAACAGTCTAATACACG
* *** *** * *
19575155 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGAAC-CAACAGTCTAATACACG
19575206 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
19575232 TGCGACCTCG
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 26 0.24
50 45 0.41
51 38 0.35
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGAACCAACAGTCTAATACACG
Found at i:19575229 original size:101 final size:99
Alignment explanation
Indices: 19575056--19575240 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 99
19575046 CTGGTACGCA
* *
19575056 TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
19575121 GTACTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* *** *
19575155 TAGTAGCCTGCACTTAGTACTACACACGTG-ATCACAATTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACA--TGCAAC-CAACAGTCGGGTACACATAGTAGCCTGCAC
*
19575219 TTAGTACTACACATGCGACCTC
63 TTAGTACTACACACGCGACCTC
19575241 GCAATAGATC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 26 0.35
100 2 0.03
101 46 0.62
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:19586034 original size:17 final size:17
Alignment explanation
Indices: 19585984--19586034 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
19585974 TGGAAACATG
*
19585984 ATCTTCGAAGATATGCA
1 ATCTTAGAAGATATGCA
*
19586001 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGCA
19586020 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
19586035 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:19586034 original size:22 final size:23
Alignment explanation
Indices: 19586006--19586050 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19585996 ATGCAATCTT
19586006 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
19586028 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
19586051 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Done.