Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold15
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: 4011073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11440 characters in sequence are not A, C, G, or T
File 6 of 25
Found at i:847386 original size:13 final size:13
Alignment explanation
Indices: 847368--847392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
847358 CAAAAAAATA
847368 TGTATCGATACAT
1 TGTATCGATACAT
847381 TGTATCGATACA
1 TGTATCGATACA
847393 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:850435 original size:33 final size:33
Alignment explanation
Indices: 850398--850466 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
850388 GAAAATATAC
*
850398 AAAAAA-TATAAAAATCAAAAGAGAAAT-AAAAGA
1 AAAAAATTA-AAAAAT-AAAAGAAAAATCAAAAGA
*
850431 AAAAAATTAAAAAATAAAAGAAAAATCAAATGA
1 AAAAAATTAAAAAATAAAAGAAAAATCAAAAGA
850464 AAA
1 AAA
850467 TCCAAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 20 0.62
34 2 0.06
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (33 bp):
AAAAAATTAAAAAATAAAAGAAAAATCAAAAGA
Found at i:850465 original size:12 final size:11
Alignment explanation
Indices: 850407--850466 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
850397 CAAAAAATAT
850407 AAAAATCAAAAG
1 AAAAAT-AAAAG
*
850419 AGAAATAAAAG
1 AAAAATAAAAG
*
850430 AAAAA-AATTA-
1 AAAAATAA-AAG
850440 AAAAATAAAAG
1 AAAAATAAAAG
*
850451 AAAAATCAAATG
1 AAAAAT-AAAAG
850463 AAAA
1 AAAA
850467 TCCAAAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.21
11 18 0.46
12 13 0.33
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:854507 original size:21 final size:21
Alignment explanation
Indices: 854478--854522 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
854468 AAGTTTTTAT
*
854478 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
854498 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
854520 TTT
1 TTT
854523 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:856440 original size:32 final size:30
Alignment explanation
Indices: 856404--856462 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
856394 GAAATCAAAT
856404 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
856436 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
856463 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:856761 original size:13 final size:13
Alignment explanation
Indices: 856743--856768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
856733 AATTTTTTTG
856743 TGTATCGATACAT
1 TGTATCGATACAT
856756 TGTATCGATACAT
1 TGTATCGATACAT
856769 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:856779 original size:32 final size:34
Alignment explanation
Indices: 856722--856786 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
856712 TACAAGCCAA
*
856722 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
856756 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
856787 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:860577 original size:19 final size:20
Alignment explanation
Indices: 860553--860605 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
860543 ATTGATACAA
*
860553 TGTATCGATACATGCTC-TT
1 TGTATCGATACATGCTCAAT
*
860572 TGTATCGATACATACTCAAT
1 TGTATCGATACATGCTCAAT
*
860592 TGTATTGATACATG
1 TGTATCGATACATG
860606 AAACTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:860582 original size:32 final size:33
Alignment explanation
Indices: 860519--860583 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
860509 ACATATCCAG
* *
860519 ATGTATCGATACATTATGCTTTGTATTGATACA
1 ATGTATCGATACATGATGCTTTGTATCGATACA
*
860552 ATGTATCGATACATGCT-CTTTGTATCGATACA
1 ATGTATCGATACATGATGCTTTGTATCGATACA
860584 TACTCAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
ATGTATCGATACATGATGCTTTGTATCGATACA
Found at i:860668 original size:13 final size:13
Alignment explanation
Indices: 860650--860679 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
860640 GATACATGGG
*
860650 ACATTGTATTGAT
1 ACATTGTATCGAT
860663 ACATTGTATCGAT
1 ACATTGTATCGAT
860676 ACAT
1 ACAT
860680 GATGAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:873814 original size:980 final size:980
Alignment explanation
Indices: 871909--874851 Score: 5701
Period size: 980 Copynumber: 3.0 Consensus size: 980
871899 TTTGGTTTAG
871909 TGTTCAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACAT
1 TGTTCAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACAT
*
871974 CAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCTGGCTATGTCTCTA
66 CAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGGCTATGTCTCTA
872039 CAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTAG
131 CAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTAG
872104 GATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTACT
196 GATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTACT
*
872169 CCAAGTAGAGATAGATGAGGGCGTATTATGGGCAGTAGCACAGTTCTGGAACCCAGCCTACCGAT
261 CCAAGTAGAGATAGATGAGGGCATATTATGGGCAGTAGCACAGTTCTGGAACCCAGCCTACCGAT
872234 CTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACATA
326 CTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACATA
872299 GAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATTG
391 GAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATTG
872364 GCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATGA
456 GCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATGA
*
872429 GTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAATGTGCAAG
521 GTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAAG
872494 ATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCTA
586 ATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCTA
872559 TCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGAG
651 TCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGAG
872624 ACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGCT
716 ACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGCT
*
872689 CCTCCAAGTTTGGCTCATTAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAATT
781 CCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAATT
872754 CTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGATA
846 CTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGATA
872819 GAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCC-CTAGG
911 GAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTC-AGG
872883 CAATCA
975 CAATCA
872889 TGTTCCA-CAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACA
1 TGTT-CAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACA
*
872953 TCAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGACTATGTCTCT
65 TCAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGGCTATGTCTCT
*
873018 ACAATGCTTGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTA
130 ACAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTA
873083 GGATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTAC
195 GGATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTAC
*
873148 TCCAAGTAGAGATAGATGAGGGCATATTATGGGTAGTAGCACAGTTCTGGAACCCAGCCTACCGA
260 TCCAAGTAGAGATAGATGAGGGCATATTATGGGCAGTAGCACAGTTCTGGAACCCAGCCTACCGA
873213 TCTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACAT
325 TCTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACAT
*
873278 AGAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCATCCTTTAAGAAAAGATT
390 AGAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATT
873343 GGCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATG
455 GGCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATG
873408 AGTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAA
520 AGTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAA
873473 GATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCT
585 GATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCT
* *
873538 ATCATTGCAAATTGTTTCTCCAGATTATGATGTAATATAAATCCTACCTCAACCATCATTACGGA
650 ATCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGA
873603 GACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGC
715 GACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGC
873668 TCCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAAT
780 TCCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAAT
873733 TCTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGAT
845 TCTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGAT
873798 AGAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTCAGG
910 AGAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTCAGG
873863 CAATCA
975 CAATCA
873869 TGTTCAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACAT
1 TGTTCAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACAT
873934 CAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGGCTATGTCTCTA
66 CAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGGCTATGTCTCTA
873999 CAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTAG
131 CAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTAG
*
874064 GATAGTTGGGATAATAATGACAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTACT
196 GATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTACT
* *
874129 CCAAGTAGAGATAGATGAGGGCATATTATGGGCAGTAGCACAGTTTTGGAACCCAGCCTACCAAT
261 CCAAGTAGAGATAGATGAGGGCATATTATGGGCAGTAGCACAGTTCTGGAACCCAGCCTACCGAT
874194 CTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACATA
326 CTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACATA
874259 GAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATTG
391 GAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATTG
874324 GCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATGA
456 GCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATGA
874389 GTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAAG
521 GTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAAG
874454 ATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCTA
586 ATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCTA
874519 TCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGAG
651 TCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGAG
*
874584 ACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTAGGTGTGCTCTGCT
716 ACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGCT
*
874649 CCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTTTGAGGAAATACAACTTTCTTTTTAATT
781 CCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAATT
* *
874714 CTGGTTCCCTCTCTAAAATTCTCAAGGAAAAATAGCCTCAGAGTAGGTCCGAAGAACAATGGATA
846 CTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGATA
874779 GAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTCAGGC
911 GAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTCAGGC
874844 AATCA
976 AATCA
874849 TGT
1 TGT
874852 ACAGATGTGG
Statistics
Matches: 1937, Mismatches: 23, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
979 2 0.00
980 1932 1.00
981 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (980 bp):
TGTTCAGCAAGGGGCATTATCAAGGAGCAGTAAACTGTTACTACCCTTGAGTCATTCGAGAACAT
CAGAGCATGGTCAAAAAATCACCAATGCCAAGATAGAGATATCTTGAAGCCCGGCTATGTCTCTA
CAATGCATGAACAGGTCAAAATTGGGTTTCGACAGAATGATTGGCGAGAGCTAAAGTGTATCTAG
GATAGTTGGGATAATAATGAGAAAGATGCGATCACCAAAAGGTATGGCGACATTACTCTCTTACT
CCAAGTAGAGATAGATGAGGGCATATTATGGGCAGTAGCACAGTTCTGGAACCCAGCCTACCGAT
CTTTTACTTTCAACCAAGAAGACTTGGCTCTTTCTATTGATGAATACATAGTGTTGCTCAACATA
GAAAAAACCAAGTTTGATAGAGTATATTGCAAGACTCTTGGTCCCCACCCTTTAAGAAAAGATTG
GCACAAATCGTCGGGGCTACTGAAGCATGGATACAAGAACACATTAAGGTCAAAAGGAATCATGA
GTGCATTTCTTGGAGTAGTTTGAAGGAAGCCATGGCAAATCTTACCGATCAGAAGAAAGTGCAAG
ATGTCTATGCTTTGGAATTTATGGTTTGGTTATGTTCCCAAAGACTCTTGGCTATATAGAAGCTA
TCATTGCAAATTGTTTCTCCAGATTATGTTGTAATATAAATCCTGCCTCAACCATCATTACGGAG
ACCATAAGAGCCCCCAGTTATTGCAAAAAGATAGGAACGAGAAGATTCATTGGGTGTGCTCTGCT
CCTCCAAGTTTGGCTCATCAGCTATCTCTATGATAGTCTGAGGAAATACAACTTTCTTTTTAATT
CTGGTTCCCTCTCTAAAATTCTCGAGGAAAAATAGCCTCAGAGTAAGTCCGAAGAACAATGGATA
GAAATGTTTTGGAATCTCAAAAGTGAAGAAGTGACATGGAAGGCTTTATGGATGTTCCCTCAGGC
AATCA
Found at i:875350 original size:13 final size:13
Alignment explanation
Indices: 875332--875356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
875322 CATAAAGTGT
875332 TGTATCGATACAA
1 TGTATCGATACAA
875345 TGTATCGATACA
1 TGTATCGATACA
875357 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:875354 original size:33 final size:33
Alignment explanation
Indices: 875312--875378 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
875302 TTCAACGATT
875312 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
875345 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
875378 T
1 T
875379 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:875437 original size:13 final size:13
Alignment explanation
Indices: 875419--875443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
875409 ATCACTTAAA
875419 TGTATCGATACAT
1 TGTATCGATACAT
875432 TGTATCGATACA
1 TGTATCGATACA
875444 CTGATCTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:875508 original size:52 final size:52
Alignment explanation
Indices: 875452--875580 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
875442 CACTGATCTG
*
875452 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
875504 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
875556 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
875581 TCATATTTCA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:879725 original size:10 final size:10
Alignment explanation
Indices: 879710--879736 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
879700 TGCTAACTAA
879710 GTTTTTGTTT
1 GTTTTTGTTT
879720 GTTTTTGTTT
1 GTTTTTGTTT
879730 GTTTTTG
1 GTTTTTG
879737 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:889430 original size:1 final size:1
Alignment explanation
Indices: 889424--889517 Score: 80
Period size: 1 Copynumber: 94.0 Consensus size: 1
889414 GGCGTCCTCC
* ** * * * *
889424 AAAAAAACAAAAAAAAATGAAAAAAACAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
889489 CAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
889518 GGGGGTCCGG
Statistics
Matches: 70, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (1 bp):
A
Found at i:889439 original size:10 final size:10
Alignment explanation
Indices: 889424--889517 Score: 97
Period size: 10 Copynumber: 9.5 Consensus size: 10
889414 GGCGTCCTCC
889424 AAAAAAACAA
1 AAAAAAACAA
**
889434 AAAAAAA-TG
1 AAAAAAACAA
889443 AAAAAAACAA
1 AAAAAAACAA
889453 AAAAAAA-AA
1 AAAAAAACAA
889462 AACAAAAA-AA
1 AA-AAAAACAA
889472 ACAAAAAA-AA
1 A-AAAAAACAA
*
889482 ACAAAAACAA
1 AAAAAAACAA
889492 TAAAAAAACAA
1 -AAAAAAACAA
*
889503 ACAAAAACAA
1 AAAAAAACAA
889513 AAAAA
1 AAAAA
889518 GGGGGTCCGG
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 16 0.23
10 45 0.63
11 10 0.14
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:889448 original size:19 final size:17
Alignment explanation
Indices: 889424--889517 Score: 109
Period size: 17 Copynumber: 5.4 Consensus size: 17
889414 GGCGTCCTCC
889424 AAAAAAACAAAAAAAAA
1 AAAAAAACAAAAAAAAA
889441 TGAAAAAAACAAAAAAAAA
1 --AAAAAAACAAAAAAAAA
* *
889460 AAAACAA-AAAAAACAA
1 AAAAAAACAAAAAAAAA
* *
889476 AAAAAAACAAAAACAAT
1 AAAAAAACAAAAAAAAA
*
889493 AAAAAAACAAACAAAAAC
1 AAAAAAACAAA-AAAAAA
889511 AAAAAAA
1 AAAAAAA
889518 GGGGGTCCGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
16 14 0.22
17 23 0.35
18 11 0.17
19 17 0.26
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAA
Found at i:889454 original size:14 final size:14
Alignment explanation
Indices: 889424--889517 Score: 93
Period size: 15 Copynumber: 6.4 Consensus size: 14
889414 GGCGTCCTCC
889424 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
*
889438 AAATGAAAA-AAACAA
1 AAA--AAAACAAAAAA
*
889453 AAAAAAA-AAAACA
1 AAAAAAACAAAAAA
889466 AAAAAAACAAAAAAA
1 AAAAAAAC-AAAAAA
889481 AACAAAAACAATAAAA
1 AA-AAAAACAA-AAAA
*
889497 AAACAAACAAAAACA
1 AAAAAAACAAAAA-A
889512 AAAAAA
1 AAAAAA
889518 GGGGGTCCGG
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
13 15 0.22
14 6 0.09
15 30 0.45
16 16 0.24
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.02
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:889462 original size:27 final size:26
Alignment explanation
Indices: 889423--889517 Score: 106
Period size: 25 Copynumber: 3.7 Consensus size: 26
889413 CGGCGTCCTC
*
889423 CAAAAAAACAAAAAAAAATGAAAAAAA
1 CAAAAAAAAAAAAAAAAAT-AAAAAAA
*
889450 C--AAAAAAAAAAAAACA-AAAAAAA
1 CAAAAAAAAAAAAAAAAATAAAAAAA
*
889473 CAAAAAAAAACAAAAACAATAAAAAAA
1 CAAAAAAAAA-AAAAAAAATAAAAAAA
* *
889500 CAAACAAAAACAAAAAAA
1 CAAAAAAAAAAAAAAAAA
889518 GGGGGTCCGG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
23 8 0.14
25 20 0.35
26 12 0.21
27 17 0.30
ACGTcount: A:0.86, C:0.11, G:0.01, T:0.02
Consensus pattern (26 bp):
CAAAAAAAAAAAAAAAAATAAAAAAA
Found at i:891015 original size:30 final size:29
Alignment explanation
Indices: 890960--891242 Score: 162
Period size: 30 Copynumber: 9.6 Consensus size: 29
890950 TCACCCTTCA
*
890960 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
890989 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ***
891018 AAAAGCCCACAAGTTAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* **
891046 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
* * * * * *
891076 GAAGCCCACAAGTCGGCGGCCTCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* * * *
891105 AAAGCTCACAACTCTA-TAGCACTCTTTTTCTTTT
1 AAAGCCCACAAGTC-AGTGGCA----TTTT-TTTC
* * ***
891139 TAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*** *
891168 AAAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *** *
891197 AAAGCCCACGAGTCAGTGGCA-ACCTTTA
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
891225 AAAGCCCACAAGTCAGTG
1 AAAGCCCACAAGTCAGTG
891243 ATGCAAACCT
Statistics
Matches: 199, Mismatches: 43, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
27 19 0.10
28 47 0.24
29 54 0.27
30 59 0.30
33 4 0.02
34 16 0.08
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTC
Found at i:891210 original size:28 final size:28
Alignment explanation
Indices: 891140--891266 Score: 164
Period size: 28 Copynumber: 4.3 Consensus size: 28
891130 TTTTCTTTTT
* *
891140 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
891170 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
891198 AAGCCCACGAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
891226 AAGCCCACAAGTCAGTGATGCAAACCTCTCAA
1 AAGCCCACAAGTCAGTG--GC-AACCT-TTAA
891258 AAGCCCACA
1 AAGCCCACA
891267 CAAGTTGGTG
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
28 45 0.51
29 3 0.03
30 23 0.26
31 5 0.06
32 12 0.14
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:891428 original size:42 final size:42
Alignment explanation
Indices: 891364--891446 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
891354 CCTTCATATT
*
891364 TAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACCA
1 TAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACCA
* *
891406 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 TAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
891447 TTTTCCATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
TAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACCA
Found at i:891554 original size:55 final size:54
Alignment explanation
Indices: 891406--891556 Score: 180
Period size: 55 Copynumber: 2.8 Consensus size: 54
891396 ATTGGCACCA
*
891406 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCATCTT
* * ** *
891458 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCTTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTC-CATCTT
* * * * *
891513 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTT
891557 ATCACTTTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 34 0.43
53 1 0.01
54 5 0.06
55 40 0.50
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCATCTT
Found at i:892387 original size:13 final size:13
Alignment explanation
Indices: 892369--892393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
892359 CATAAAGTGT
892369 TGTATCGATACAA
1 TGTATCGATACAA
892382 TGTATCGATACA
1 TGTATCGATACA
892394 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:892391 original size:33 final size:33
Alignment explanation
Indices: 892349--892415 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
892339 TTCAACGATT
892349 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
892382 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
892415 T
1 T
892416 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:892474 original size:13 final size:13
Alignment explanation
Indices: 892456--892480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
892446 ATCACTTAAA
892456 TGTATCGATACAT
1 TGTATCGATACAT
892469 TGTATCGATACA
1 TGTATCGATACA
892481 CTGATCTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:892545 original size:52 final size:52
Alignment explanation
Indices: 892489--892617 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
892479 CACTGATCTG
*
892489 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
892541 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
892593 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
892618 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:902210 original size:13 final size:13
Alignment explanation
Indices: 902192--902216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
902182 CATTGCACAT
902192 TGTATCGATACAA
1 TGTATCGATACAA
902205 TGTATCGATACA
1 TGTATCGATACA
902217 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:902214 original size:33 final size:33
Alignment explanation
Indices: 902172--902236 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
902162 TACCACTATC
* *
902172 TGTATCGATACATTGCA-CATTGTATCGATACAA
1 TGTATCGATACA-TGAAGAATTGTATCGATACAA
902205 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATGAAGAATTGTATCGATACA
902237 TTATCCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATACAA
Found at i:903831 original size:3 final size:3
Alignment explanation
Indices: 903816--903849 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
903806 AACCATCAAA
* *
903816 GAT GAT GAA GAT GAT GAT AAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
903850 TTGACTCGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:911033 original size:13 final size:13
Alignment explanation
Indices: 911015--911039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
911005 CATTGCACAT
911015 TGTATCGATACAA
1 TGTATCGATACAA
911028 TGTATCGATACA
1 TGTATCGATACA
911040 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:911039 original size:33 final size:33
Alignment explanation
Indices: 910995--911059 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
910985 TACCACTATT
* *
910995 TGTATCCATACATTGCA-CATTGTATCGATACAA
1 TGTATCCATACA-TGAAGAATTGTATCGATACAA
*
911028 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCCATACATGAAGAATTGTATCGATACA
911060 TTGTCCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCCATACATGAAGAATTGTATCGATACAA
Found at i:917429 original size:52 final size:52
Alignment explanation
Indices: 917281--917409 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
917271 CGAAATATGA
* *
917281 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
917333 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
917385 AAATTTGCTTGCATGTATCGATACA
1 AAATTTGCTTGCATGTATCGATACA
917410 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:917436 original size:13 final size:13
Alignment explanation
Indices: 917418--917442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
917408 CAAAGATCAG
917418 TGTATCGATACAA
1 TGTATCGATACAA
917431 TGTATCGATACA
1 TGTATCGATACA
917443 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:917509 original size:19 final size:18
Alignment explanation
Indices: 917485--917579 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
917475 TAGCTTATAT
917485 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
917504 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
917517 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
917536 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
917549 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
917568 TGTATCGATACA
1 TGTATCGATACA
917580 TTGTTGAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 2 0.03
19 34 0.53
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:917522 original size:13 final size:13
Alignment explanation
Indices: 917504--917560 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
917494 ACAAAACTTA
917504 TGTATCGATACAT
1 TGTATCGATACAT
917517 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
917535 ATGTATCGATACAT
1 -TGTATCGATACAT
917549 TGTATCGATACA
1 TGTATCGATACA
917561 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:917524 original size:32 final size:32
Alignment explanation
Indices: 917483--917583 Score: 193
Period size: 32 Copynumber: 3.2 Consensus size: 32
917473 AGTAGCTTAT
*
917483 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
917515 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
917547 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
917579 ATTGT
1 ATTGT
917584 TGAAATTCAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:918145 original size:20 final size:20
Alignment explanation
Indices: 918122--918183 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
918112 TGCTTTGTAT
918122 TGATACATTGTATCGATACA
1 TGATACATTGTATCGATACA
*
918142 TGAT-CTTTGTATCGATACA
1 TGATACATTGTATCGATACA
* *
918161 TG-CACAATTGTATCAATACA
1 TGATAC-ATTGTATCGATACA
918181 TGA
1 TGA
918184 AACTGGTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:918159 original size:32 final size:33
Alignment explanation
Indices: 918097--918161 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
918087 CATATCCAGA
*
918097 TGTATCGATACATAATGCTTTGTATTGATACAT
1 TGTATCGATACATAATGCTTTGTATCGATACAT
*
918130 TGTATCGATACATGAT-CTTTGTATCGATACAT
1 TGTATCGATACATAATGCTTTGTATCGATACAT
918162 GCACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAATGCTTTGTATCGATACAT
Found at i:919890 original size:15 final size:15
Alignment explanation
Indices: 919870--919904 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
919860 AACCATCAAA
919870 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
919885 GATGATGATGATAAT
1 GATGATGAAGATAAT
919900 GATGA
1 GATGA
919905 AGTAGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:924232 original size:21 final size:21
Alignment explanation
Indices: 924207--924246 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
924197 CTAACGATTC
*
924207 ATTTTTCAAATTTCTTCAAAT
1 ATTTTTCAAATTTCATCAAAT
924228 ATTTTTCAAATTTCATCAA
1 ATTTTTCAAATTTCATCAA
924247 TTTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTTCAAATTTCATCAAAT
Found at i:926014 original size:26 final size:25
Alignment explanation
Indices: 925985--926047 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
925975 GAACAAATAA
925985 AAAGTATTTTTTATAAAAAGAGGGAG
1 AAAG-ATTTTTTATAAAAAGAGGGAG
* **
926011 AAAGAATTTTTTTTATTAAGAGGGAG
1 AAAG-ATTTTTTATAAAAAGAGGGAG
926037 AAA-ATTTTTTA
1 AAAGATTTTTTA
926048 AGGGAGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 7 0.22
26 25 0.78
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (25 bp):
AAAGATTTTTTATAAAAAGAGGGAG
Found at i:926673 original size:20 final size:19
Alignment explanation
Indices: 926582--926674 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 19
926572 ACTCTTGAAG
*
926582 GTATCGATACAT-ATCCAGAT
1 GTATCGATACATGAT-CA-TT
* *
926602 GTATCGATACATAATGCTTT
1 GTATCGATACATGAT-CATT
926622 GTATCGATACATGATCATT
1 GTATCGATACATGATCATT
926641 GTATCGATACATGCA-CAATT
1 GTATCGATACATG-ATC-ATT
926661 GTATCGATACATGA
1 GTATCGATACATGA
926675 AACTGGCAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
19 18 0.28
20 44 0.68
21 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (19 bp):
GTATCGATACATGATCATT
Found at i:927383 original size:13 final size:13
Alignment explanation
Indices: 927365--927392 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
927355 CATTATTCAA
927365 TGTATCGATACAT
1 TGTATCGATACAT
927378 TGTATCGATACAT
1 TGTATCGATACAT
927391 TG
1 TG
927393 AATAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:927389 original size:33 final size:33
Alignment explanation
Indices: 927345--927410 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
927335 GCTAAGGAAA
*
927345 TGTATCAATACATT-ATTCAATGTATCGATACAT
1 TGTATCAATACATTGAAT-AATGTATCGATACAT
*
927378 TGTATCGATACATTGAATAATGTATCGATACAT
1 TGTATCAATACATTGAATAATGTATCGATACAT
927411 CATTCTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
TGTATCAATACATTGAATAATGTATCGATACAT
Found at i:937788 original size:20 final size:20
Alignment explanation
Indices: 937763--937880 Score: 103
Period size: 20 Copynumber: 5.8 Consensus size: 20
937753 TTTTAACTAG
937763 ATGTATCGATACATTGAACA
1 ATGTATCGATACATTGAACA
* *
937783 ATGTATCGATACATCTGGGTAGA
1 ATGTATCGATACAT-T--GAACA
* * *
937806 ATATATCGATATATTGAAGA
1 ATGTATCGATACATTGAACA
* * * *
937826 ATGTATCGACACATTCATCC
1 ATGTATCGATACATTGAACA
937846 ATGTATCGATACATTGGAA-A
1 ATGTATCGATACATT-GAACA
*
937866 ATGTATTGATACATT
1 ATGTATCGATACATT
937881 TGGGTAAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
20 59 0.77
21 2 0.03
22 1 0.01
23 15 0.19
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAACA
Found at i:943379 original size:28 final size:26
Alignment explanation
Indices: 943348--943415 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
943338 CAATCTTCAA
*
943348 TGGAATCAAGAAAAGTGCCAATCGCTAG
1 TGGAATCAAGAAAAGTG-CAATC-CCAG
* *
943376 TGGAATCAGGACAAATTGCAATCCCAG
1 TGGAATCAAGA-AAAGTGCAATCCCAG
*
943403 TAGAATCAAGAAA
1 TGGAATCAAGAAA
943416 CTTGCAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.06
27 12 0.35
28 15 0.44
29 5 0.15
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (26 bp):
TGGAATCAAGAAAAGTGCAATCCCAG
Found at i:944078 original size:33 final size:34
Alignment explanation
Indices: 944033--944108 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
944023 TCATCCTTTT
* *
944033 AAGCCCACACAAGTTGGTGGCATC-TTTTCTTAA
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTAA
* *
944066 AAGCCCATACAAGTCGGTGGCACCTTTTTCTTTA
1 AAGCCCACACAAGTCGGTGGCACCTTTTTCTTAA
944100 AAGCCCACA
1 AAGCCCACA
944109 ACTACGTGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (34 bp):
AAGCCCACACAAGTCGGTGGCACCTTTTTCTTAA
Found at i:944281 original size:32 final size:32
Alignment explanation
Indices: 944163--944281 Score: 114
Period size: 32 Copynumber: 3.7 Consensus size: 32
944153 TCATCCTTCT
* *
944163 AAGCCCACATAAGTTGGTGGC-ACTTTTTCTCAA
1 AAGCCCACACAAGTTGGTGGCAAC--CTTCTCAA
* * * * * *
944196 AAGCCCACAAAAGCTGGTGGTAATCTTCCCCA
1 AAGCCCACACAAGTTGGTGGCAACCTTCTCAA
* *
944228 AAGCCCACACAAGTCGATGGCAACCTTCTCAA
1 AAGCCCACACAAGTTGGTGGCAACCTTCTCAA
*
944260 AAGCCCACACAAGTTAGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
944282 TCCCCTTCCA
Statistics
Matches: 67, Mismatches: 18, Indels: 3
0.76 0.20 0.03
Matches are distributed among these distances:
32 48 0.72
33 18 0.27
34 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.20
Consensus pattern (32 bp):
AAGCCCACACAAGTTGGTGGCAACCTTCTCAA
Found at i:944485 original size:52 final size:52
Alignment explanation
Indices: 944429--944988 Score: 376
Period size: 52 Copynumber: 10.8 Consensus size: 52
944419 ACTGGCCCCA
* * **
944429 AATCAGCATA-TGAGCACTTTCTTTATCTTTCAGTCCAATGTCATTGGCCTTG
1 AATCAGCATATTG-GCACTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* * *
944481 AATCAGCATATTGGCACTCATC-TCATTTTTAAGTCCAATGTTGCTGGCCTTG
1 AATCAGCATATTGGCACT-TTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
** * * * *
944533 AATTGGCATATTGGCACTTT-TGTCATC-TTAAGTCTAATATCGCTAGCCCTG
1 AATCAGCATATTGGCACTTTCT-TCATCTTTAAGTCCAATGTCGCTGGCCTTG
* * * *
944584 AATCGGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCGTTGGCCTTG
1 AATCAGCATATTGGCACTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* * * * * ** *
944636 AATCAACACATTGGAACTTAT-TTCATTTTTACGTCCAATGTTACTGGCCCTG
1 AATCAGCATATTGGCACTT-TCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* * * * * * *
944688 AATCGGCACATTGGCACCTTTGTT-ATC-TTAAATCTAATATCGCTAGCCTTG
1 AATCAGCATATTGGCA-CTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
** * * *
944739 AATCAATATATTAGCACTTTTTTCATCTTTAAGTCCAATGTCGCTGGTCTTG
1 AATCAGCATATTGGCACTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* *
944791 AATCAGCACATTGGCACTCATC-TCAAT-TTTAAGTCCAATGTCGCTGGCCTTG
1 AATCAGCATATTGGCACT-TTCTTC-ATCTTTAAGTCCAATGTCGCTGGCCTTG
* * * * *** * * *
944843 AATCGGCACATTAGCACCTTT-GTCATC-TTAAGTTTGATATCGCTAGCCTTC
1 AATCAGCATATTGGCA-CTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
* * * ** * * *
944894 AATTAGCATATTAGCACTTT-TATCAT-TCTTAAGCCCAATGTCATTAGCCCTA
1 AATCAGCATATTGGCACTTTCT-TCATCT-TTAAGTCCAATGTCGCTGGCCTTG
* *
944946 AATCAGCACATTGGCA--TTCTTCTAGTCTTTAAGCCCAATGTCG
1 AATCAGCATATTGGCACTTTCTTC-A-TCTTTAAGTCCAATGTCG
944989 TTGACCCTGA
Statistics
Matches: 393, Mismatches: 92, Indels: 46
0.74 0.17 0.09
Matches are distributed among these distances:
50 14 0.04
51 112 0.28
52 251 0.64
53 16 0.04
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (52 bp):
AATCAGCATATTGGCACTTTCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
Found at i:944622 original size:103 final size:102
Alignment explanation
Indices: 944479--944935 Score: 348
Period size: 103 Copynumber: 4.4 Consensus size: 102
944469 TCATTGGCCT
* * *** *
944479 TGAATCAGCATATTGGCACTCATC-TCATTTTTAAGTCCAATGTTGCTGGCCTTGAATTGGCATA
1 TGAATCAGCATATTGGCACT-TTCTTCA-TTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACA
* *
944543 TTGGCACTTTTGTCATCTTAAGTCTAATATCGCTAGCCC
64 TTAGCACTTTTGTCATCTTAAGTCCAATATCGCTAGCCC
* * * *
944582 TGAATCGGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAACACAT
1 TGAATCAGCATATTGGCACTTTCTTCAT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACAT
* * * * * ** *
944647 TGGAACTTATT-TCATTTTTACGTCCAATGTTACTGGCCC
65 TAGCACTT-TTGTCA-TCTTAAGTCCAATATCGCTAGCCC
* * * * * * * * * *
944686 TGAATCGGCACATTGGCACCTTTGTT-ATCTTAAATCTAATATCGCTAGCCTTGAATCAATATAT
1 TGAATCAGCATATTGGCA-CTTTCTTCATTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACAT
* * * * *
944750 TAGCACTTTTTTCATCTTTAAGTCCAATGTCGCTGGTCT
65 TAGCACTTTTGTCATC-TTAAGTCCAATATCGCTAGCCC
* * **
944789 TGAATCAGCACATTGGCACTCATC-TCAATTTTAAGTCCAATGTCGCTGGCCTTGAATCGGCACA
1 TGAATCAGCATATTGGCACT-TTCTTC-ATTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACA
* *** *
944853 TTAGCACCTTTGTCATCTTAAGTTTGATATCGCTAGCCT
64 TTAGCACTTTTGTCATCTTAAGTCCAATATCGCTAGCCC
* * * *
944892 TCAATTAGCATATTAGCACTTT-TATCATTCTTAAGCCCAATGTC
1 TGAATCAGCATATTGGCACTTTCT-TCATT-TTAAGTCCAATGTC
944936 ATTAGCCCTA
Statistics
Matches: 277, Mismatches: 64, Indels: 26
0.75 0.17 0.07
Matches are distributed among these distances:
102 13 0.05
103 178 0.64
104 80 0.29
105 6 0.02
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (102 bp):
TGAATCAGCATATTGGCACTTTCTTCATTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATT
AGCACTTTTGTCATCTTAAGTCCAATATCGCTAGCCC
Found at i:944690 original size:155 final size:155
Alignment explanation
Indices: 944429--944961 Score: 701
Period size: 155 Copynumber: 3.4 Consensus size: 155
944419 ACTGGCCCCA
* * * * *
944429 AATCAGCATATGAGCACTTTCTTTATCTTTCAGTCCAATGTCATTGGCCTTGAATCAGCATATTG
1 AATCAGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTG
* * *
944494 GCACTCATCTCATTTTTAAGTCCAATGTTGCTGGCCTTGAATTGGCATATTGGCACTTTTGTCAT
66 GCACTCATCTCATTTTTAAGTCCAATGTTGCTGGCCTTGAATCGGCACATTGGCACCTTTGTCAT
*
944559 CTTAAGTCTAATATCGCTAGCCCTG
131 CTTAAGTCTAATATCGCTAGCCTTG
* * *
944584 AATCGGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTG
1 AATCAGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTG
* * * * * * *
944649 GAACTTATTTCATTTTTACGTCCAATGTTACTGGCCCTGAATCGGCACATTGGCACCTTTGTTAT
66 GCACTCATCTCATTTTTAAGTCCAATGTTGCTGGCCTTGAATCGGCACATTGGCACCTTTGTCAT
*
944714 CTTAAATCTAATATCGCTAGCCTTG
131 CTTAAGTCTAATATCGCTAGCCTTG
** * * ** *
944739 AATCAATATATTAGCACTTTTTTCATCTTTAAGTCCAATGTCGCTGGTCTTGAATCAGCACATTG
1 AATCAGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTG
* * *
944804 GCACTCATCTCAATTTTAAGTCCAATGTCGCTGGCCTTGAATCGGCACATTAGCACCTTTGTCAT
66 GCACTCATCTCATTTTTAAGTCCAATGTTGCTGGCCTTGAATCGGCACATTGGCACCTTTGTCAT
* * *
944869 CTTAAGTTTGATATCGCTAGCCTTC
131 CTTAAGTCTAATATCGCTAGCCTTG
* * * *
944894 AATTAGCATATTAGCACTTT-TATCAT-TCTTAAGCCCAATGTCATTAGCCCTAAATCAGCACAT
1 AATCAGCATATTAGCACTTTCT-TCATCT-TTAAGCCCAATGTCATTGGCCTTGAATCAGCACAT
944957 TGGCA
64 TGGCA
944962 TTCTTCTAGT
Statistics
Matches: 324, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
154 2 0.01
155 322 0.99
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (155 bp):
AATCAGCATATTAGCACTTTCTTCATCTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTG
GCACTCATCTCATTTTTAAGTCCAATGTTGCTGGCCTTGAATCGGCACATTGGCACCTTTGTCAT
CTTAAGTCTAATATCGCTAGCCTTG
Found at i:945618 original size:20 final size:20
Alignment explanation
Indices: 945595--945632 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
945585 AAAAGTAATG
*
945595 AAAAAATAGAAAAATAAATA
1 AAAAAAGAGAAAAATAAATA
*
945615 AAAAAAGATAAAAATAAA
1 AAAAAAGAGAAAAATAAA
945633 ACAACTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAAAAGAGAAAAATAAATA
Found at i:949183 original size:20 final size:20
Alignment explanation
Indices: 949157--949212 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
949147 TAAAAAGACA
*
949157 AAATGTATCGATACATTGA-
1 AAATGTATCGATACATTCAT
*
949176 AGAATGTATAGATACATTCAT
1 A-AATGTATCGATACATTCAT
*
949197 ACATGTATCGATACAT
1 AAATGTATCGATACAT
949213 CTGGGTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACATTCAT
Found at i:950304 original size:28 final size:27
Alignment explanation
Indices: 950262--950320 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
950252 GGTCTTGGTA
*
950262 ATATTTGCATTTTATTTTTTATAT-TAT
1 ATATTTGCATTTTA-TATTTATATCTAT
950289 CATATTTGC-TTGTTATATTTATATCTAT
1 -ATATTTGCATT-TTATATTTATATCTAT
950317 ATAT
1 ATAT
950321 ATATTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (27 bp):
ATATTTGCATTTTATATTTATATCTAT
Found at i:955156 original size:22 final size:22
Alignment explanation
Indices: 955117--955158 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
955107 TCTCACTGAG
*
955117 GAGCTAAACTCATGGAAGGATA
1 GAGCTAAACTAATGGAAGGATA
955139 GAGCTCAAACTAAT-GAAGGA
1 GAGCT-AAACTAATGGAAGGA
955159 AAATTCACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (22 bp):
GAGCTAAACTAATGGAAGGATA
Found at i:959583 original size:19 final size:19
Alignment explanation
Indices: 959559--959658 Score: 98
Period size: 19 Copynumber: 5.9 Consensus size: 19
959549 AATTCAACAA
959559 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
959578 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
959593 --TATATCGATACATAAGT
1 TTTGTATCGATACATAAGT
959610 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
959625 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
959642 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
959659 TTAGCTACTG
Statistics
Matches: 67, Mismatches: 2, Indels: 24
0.72 0.02 0.26
Matches are distributed among these distances:
13 21 0.31
15 4 0.06
17 4 0.06
19 38 0.57
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:959604 original size:32 final size:32
Alignment explanation
Indices: 959563--959655 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
959553 CAACAATTTG
959563 TATCGATACATAAGTTTTGTATCGATACAATA
1 TATCGATACATAAGTTTTGTATCGATACAATA
*
959595 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGTTTTGTATCGATACAATA
*
959627 TATCGATACATAAGTATTGTATCGATACA
1 TATCGATACATAAGTTTTGTATCGATACA
959656 TAATTAGCTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TATCGATACATAAGTTTTGTATCGATACAATA
Found at i:959630 original size:13 final size:13
Alignment explanation
Indices: 959612--959636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
959602 ACATAAGTTT
959612 TGTATCGATACAA
1 TGTATCGATACAA
959625 TGTATCGATACA
1 TGTATCGATACA
959637 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:959716 original size:13 final size:13
Alignment explanation
Indices: 959698--959723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
959688 CATTTTTCTG
959698 TGTATCGATACAT
1 TGTATCGATACAT
959711 TGTATCGATACAT
1 TGTATCGATACAT
959724 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:959720 original size:33 final size:33
Alignment explanation
Indices: 959678--959744 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
959668 GCCAAGGAAA
***
959678 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
959711 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
959744 T
1 T
959745 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:962247 original size:28 final size:27
Alignment explanation
Indices: 962180--962248 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
962170 CTTCACAATC
**
962180 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
962207 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
962235 GGGGATACTCCAAC
1 GGGGATACTCCAAC
962249 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:962290 original size:107 final size:105
Alignment explanation
Indices: 962125--962517 Score: 323
Period size: 107 Copynumber: 3.7 Consensus size: 105
962115 TTCTATAATC
* *
962125 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGATACTC
1 GGGGATACTCCAACTCCGGTTTTA-TTCC--AAAAACACCAATTT-TTCACAATCGGGGATACTC
962190 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
62 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* *
962235 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGGTTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
* * ** * * * * *** * *
962299 ATCCCGATTTTATTTTC---AAAACACTATTTTCCTTTAAT-C--
64 ACCCCG--TTAATCATCGGGGATACTCCA-ACCCCGTTATTCCGA
* * * *
962338 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATGCTCCAA
1 GGGGATACTCCAACTCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
962403 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* * * * *** * * *
962446 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
962511 CCCGTTA
66 CCCGTTA
962518 TTTTCGAAGG
Statistics
Matches: 217, Mismatches: 51, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
101 2 0.01
102 3 0.01
103 44 0.20
104 19 0.09
105 9 0.04
106 9 0.04
107 79 0.36
108 23 0.11
109 7 0.03
110 22 0.10
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:962310 original size:52 final size:51
Alignment explanation
Indices: 962235--962403 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 51
962225 TTATTTCCGA
*
962235 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGATTTTATC-CTAAAACACTAATTTTTCCACAATC
** **
962287 GGGGATACTCCAA-TCCCGATTTTATTTTCAAAACACT-A-TTTTCCTTTAATC
1 GGGGATACTCCAACT-CCGATTTTATCCT-AAAACACTAATTTTTCC-ACAATC
* * *
962338 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGATTTTA--TCCTAAAACACTAATTTTTCCACAATC
* *
962390 GAGGATGCTCCAAC
1 GGGGATACTCCAAC
962404 CTCGTTATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
50 6 0.06
51 29 0.31
52 53 0.56
53 3 0.03
54 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATCCTAAAACACTAATTTTTCCACAATC
Found at i:974028 original size:91 final size:90
Alignment explanation
Indices: 973912--974092 Score: 290
Period size: 91 Copynumber: 2.0 Consensus size: 90
973902 TACAATTCAT
* * *
973912 AATGTATCGATACATGCATTTAAAATTTATAGCCATTGGGCTCGATGTATCGATACATTTCCCCT
1 AATGTATCAATACATGCATTTAAAATTTATAGCCATTGGGCTCAATGTATCGATACACTTCCCC-
*
973977 ATGTATCAATACTAAGTGAGTTTTAG
65 ATGTATCAATACTAAGTAAGTTTTAG
* *
974003 AATGTATCAATACATGCATTTAAAATTTATAGCCGTTGGGCTCAATGTTTCGATACACTTCCCCA
1 AATGTATCAATACATGCATTTAAAATTTATAGCCATTGGGCTCAATGTATCGATACACTTCCCCA
*
974068 TGTATCAATACTGAGTAAGTTTTAG
66 TGTATCAATACTAAGTAAGTTTTAG
974093 CTACTGCTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 24 0.29
91 59 0.71
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (90 bp):
AATGTATCAATACATGCATTTAAAATTTATAGCCATTGGGCTCAATGTATCGATACACTTCCCCA
TGTATCAATACTAAGTAAGTTTTAG
Found at i:974169 original size:32 final size:33
Alignment explanation
Indices: 974128--974191 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
974118 CAATTCAGTG
974128 TGTATCGATACCAA-AAACATGTATCGATATAA
1 TGTATCGATACCAAGAAACATGTATCGATATAA
* * *
974160 TGTATCGATACTAAGCAATATGTATCGATATA
1 TGTATCGATACCAAGAAACATGTATCGATATA
974192 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCGATACCAAGAAACATGTATCGATATAA
Found at i:974304 original size:22 final size:21
Alignment explanation
Indices: 974270--974311 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
974260 ACTTTGGATT
974270 ATTTTTACTTTGAAAACATATG
1 ATTTTTACTTTGAAAA-ATATG
974292 ATTTATTAC-TTGAAAAATAT
1 ATTT-TTACTTTGAAAAATAT
974312 TTATACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTTTTACTTTGAAAAATATG
Found at i:975515 original size:17 final size:16
Alignment explanation
Indices: 975488--975542 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
975478 CTCATAATGC
975488 AAAAATATTTAAAAATTG
1 AAAAAT-TTT-AAAATTG
975506 AAAAATTTT--AATTG
1 AAAAATTTTAAAATTG
**
975520 TTAAATTTTAAGAATTG
1 AAAAATTTTAA-AATTG
975537 AAAAAT
1 AAAAAT
975543 AAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 12 0.40
17 12 0.40
18 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (16 bp):
AAAAATTTTAAAATTG
Found at i:976256 original size:15 final size:14
Alignment explanation
Indices: 976207--976254 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
976197 TTTTAAAATT
976207 TTTTTAAATTTAAAA
1 TTTTTAAA-TTAAAA
976222 TTTTTAAATTAAAA
1 TTTTTAAATTAAAA
976236 TTTTTAAATTAAAA
1 TTTTTAAATTAAAA
976250 TTTTT
1 TTTTT
976255 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 25 0.76
15 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTAAATTAAAA
Found at i:982668 original size:16 final size:16
Alignment explanation
Indices: 982647--982677 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
982637 TTTCGTTGAT
982647 TTTAATTAAATTTAAA
1 TTTAATTAAATTTAAA
*
982663 TTTAATTTAATTTAA
1 TTTAATTAAATTTAA
982678 GTTGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATTAAATTTAAA
Found at i:982741 original size:16 final size:16
Alignment explanation
Indices: 982722--982774 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
982712 ATTAAAATAC
982722 AAAATGATTTAAATTT
1 AAAATGATTTAAATTT
*
982738 AAAATGATTAAAATTT
1 AAAATGATTTAAATTT
* *
982754 AAAATGATCTAAATTC
1 AAAATGATTTAAATTT
982770 AAAAT
1 AAAAT
982775 AATCTCGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (16 bp):
AAAATGATTTAAATTT
Found at i:982750 original size:32 final size:32
Alignment explanation
Indices: 982712--982774 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
982702 AAATTAATTT
* *
982712 ATTAAAATACAAAATGATTTAAATTTAAAATG
1 ATTAAAATACAAAATGATCTAAATTCAAAATG
**
982744 ATTAAAATTTAAAATGATCTAAATTCAAAAT
1 ATTAAAATACAAAATGATCTAAATTCAAAAT
982775 AATCTCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (32 bp):
ATTAAAATACAAAATGATCTAAATTCAAAATG
Found at i:982779 original size:16 final size:16
Alignment explanation
Indices: 982716--982779 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
982706 TAATTTATTA
* *
982716 AAATACAAAATGATTT
1 AAATTCAAAATGATCT
*
982732 AAATTTAAAATGAT-T
1 AAATTCAAAATGATCT
*
982747 AAAATTTAAAATGATCT
1 -AAATTCAAAATGATCT
*
982764 AAATTCAAAATAATCT
1 AAATTCAAAATGATCT
982780 CGAATAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 1 0.02
16 40 0.95
17 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (16 bp):
AAATTCAAAATGATCT
Found at i:983274 original size:25 final size:24
Alignment explanation
Indices: 983246--983304 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
983236 TAGAAGTAAG
* **
983246 AAATTTAATAAAAATTTACATGCAA
1 AAATTTAAT-AAAATATACATAAAA
*
983271 AAATTCTAATTAAATATACATAAAA
1 AAATT-TAATAAAATATACATAAAA
983296 AAATTTAAT
1 AAATTTAAT
983305 GAGAAAGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 21 0.72
26 4 0.14
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATTTAATAAAATATACATAAAA
Found at i:985737 original size:150 final size:150
Alignment explanation
Indices: 985466--985917 Score: 895
Period size: 150 Copynumber: 3.0 Consensus size: 150
985456 AGTCTAAAGG
*
985466 AAGTCTAAAAAATGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
1 AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
985531 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
66 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
985596 ATCTGAATTTATTTCTGGTT
131 ATCTGAATTTATTTCTGGTT
985616 AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
1 AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
985681 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
66 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
985746 ATCTGAATTTATTTCTGGTT
131 ATCTGAATTTATTTCTGGTT
985766 AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
1 AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
985831 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
66 ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
985896 ATCTGAATTTATTTCTGGTT
131 ATCTGAATTTATTTCTGGTT
985916 AA
1 AA
985918 TTCGAGGGTT
Statistics
Matches: 301, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 301 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (150 bp):
AAGTCTAAAAAAGGTTTCAAGGCTGATCGAGATTATACAGAGGCATCGGAATGTCTCAGGATGAA
ACCTAAGAAAATAACTCAAATCAACCCATAACCAAAAACAGGGGACAACATCGCGTTATCCCACT
ATCTGAATTTATTTCTGGTT
Found at i:988210 original size:21 final size:20
Alignment explanation
Indices: 988166--988216 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
988156 ATATGAAATA
* *
988166 TATCAATACATTCTCTTTTG
1 TATCAATACATTCACTTATG
*
988186 TATCCATACATTCACTTAATG
1 TATCAATACATTCACTT-ATG
*
988207 TATCGATACA
1 TATCAATACA
988217 ATTTATAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (20 bp):
TATCAATACATTCACTTATG
Found at i:988838 original size:21 final size:21
Alignment explanation
Indices: 988809--988857 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
988799 TGTATTTTTT
*
988809 AAAAA-ACAAAAACAAAACAA
1 AAAAATACAAAAACAAAAAAA
*
988829 AAAAATACAAACACAAAAAAA
1 AAAAATACAAAAACAAAAAAA
988850 ACAAAATA
1 A-AAAATA
988858 AAACTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 14 0.56
22 6 0.24
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (21 bp):
AAAAATACAAAAACAAAAAAA
Found at i:988846 original size:15 final size:14
Alignment explanation
Indices: 988811--988854 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
988801 TATTTTTTAA
988811 AAAACAAAAACAAAAC
1 AAAA-AAAAAC-AAAC
*
988827 AAAAAAATACAAAC
1 AAAAAAAAACAAAC
988841 ACAAAAAAAACAAA
1 A-AAAAAAAACAAA
988855 ATAAAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.20
15 16 0.64
16 4 0.16
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (14 bp):
AAAAAAAAACAAAC
Found at i:989545 original size:26 final size:26
Alignment explanation
Indices: 989492--989546 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
989482 ACAATATTTT
* *
989492 AATTTTGATAAAAGATCATAGGAAAA
1 AATTTTAATAAAAGATCATAGAAAAA
*
989518 AATTTTAATAAAAGATGATA-AAATAA
1 AATTTTAATAAAAGATCATAGAAA-AA
989544 AAT
1 AAT
989547 AATAAGTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (26 bp):
AATTTTAATAAAAGATCATAGAAAAA
Found at i:994243 original size:40 final size:40
Alignment explanation
Indices: 994184--994275 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 40
994174 TTTTCTTTCT
994184 CCCTTAACTAAAGTAATTTTAACAAAATT-CGTACATTCTCC
1 CCCTTAACTAAAGTAATTTTAACAAAATTACG--CATTCTCC
* *
994225 CCCTTAA-T-AAGATAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAACTAAAG-TAATTTTAACAAAATTACGCATTCTCC
* *
994264 CCTTTTACTAAA
1 CCCTTAACTAAA
994276 AAAAATCTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
39 16 0.37
40 16 0.37
41 11 0.26
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (40 bp):
CCCTTAACTAAAGTAATTTTAACAAAATTACGCATTCTCC
Found at i:995985 original size:21 final size:22
Alignment explanation
Indices: 995951--995991 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
995941 GCTGGTTTTG
995951 ATGAAAAACGAAGTAATTTGAA
1 ATGAAAAACGAAGTAATTTGAA
*
995973 ATGAAAAAC-AAGTATTTTG
1 ATGAAAAACGAAGTAATTTG
995992 CAAAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (22 bp):
ATGAAAAACGAAGTAATTTGAA
Found at i:998232 original size:15 final size:15
Alignment explanation
Indices: 998212--998242 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
998202 ATTTCGTTTG
*
998212 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
998227 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
998242 G
1 G
998243 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1002330 original size:19 final size:20
Alignment explanation
Indices: 1002290--1002333 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1002280 TACAAGCCAA
**
1002290 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
1002310 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
1002329 TGTAT
1 TGTAT
1002334 TGATGCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:1003288 original size:28 final size:28
Alignment explanation
Indices: 1003237--1003323 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
1003227 AATCAATGTT
*
1003237 TTGAAAATAAAACTGGGTTGGAGTATTCCC
1 TTGAAAAT--AACGGGGTTGGAGTATTCCC
1003267 TTGAAAATAACGGGGTTGGAGTA-TCCC
1 TTGAAAATAACGGGGTTGGAGTATTCCC
* * *
1003294 TTCAAAAATAACGGGGATGGAGTATCCCC
1 TT-GAAAATAACGGGGTTGGAGTATTCCC
1003323 T
1 T
1003324 CAAAAAATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 6 0.12
28 33 0.65
29 4 0.08
30 8 0.16
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (28 bp):
TTGAAAATAACGGGGTTGGAGTATTCCC
Found at i:1003326 original size:28 final size:28
Alignment explanation
Indices: 1003255--1003329 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
1003245 AAAACTGGGT
* ** *
1003255 TGGAGTATTCCCTTGAAAATAACGGGGT
1 TGGAGTATCCCCTCAAAAATAACGGGGA
*
1003283 TGGAGTATCCCTTCAAAAATAACGGGGA
1 TGGAGTATCCCCTCAAAAATAACGGGGA
1003311 TGGAGTATCCCCTCAAAAA
1 TGGAGTATCCCCTCAAAAA
1003330 ATCAGTGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (28 bp):
TGGAGTATCCCCTCAAAAATAACGGGGA
Found at i:1003444 original size:79 final size:75
Alignment explanation
Indices: 1003280--1003475 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 75
1003270 AAAATAACGG
* *
1003280 GGTTGGAGTATCCCTTCAAAAATAACGGGGATGGAGTATCCCCTCAAAAAATCAGTGTTTTGGAA
1 GGTTGGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCCCTCAAAAAATCAGTGTTTTGGAA
* * *
1003345 ATAATACCGG
66 AAAAAACCGA
* * * ** *
1003355 GGTTGAAGTATCCTTTCAGAAATAACGGGGTTGGAATATCCCCGATTGTGAAAAAT-TGATGTTT
1 GGTTGGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCCC---T-CAAAAAATCAG-TGTTT
*
1003419 TGGAAAAAAAATCGA
61 TGGAAAAAAAACCGA
*
1003434 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCC
1003476 TTTAAAAATA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
75 38 0.38
78 2 0.02
79 60 0.60
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (75 bp):
GGTTGGAGTATCCCTTCAGAAATAACGGGGTTGGAGTATCCCCTCAAAAAATCAGTGTTTTGGAA
AAAAAACCGA
Found at i:1003466 original size:28 final size:28
Alignment explanation
Indices: 1003434--1003502 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
1003424 AAAAAATCGA
* *
1003434 GGTTGGAGTATCCCCTCAGAAATAACGG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
* * *
1003462 GGTTGGAGTATCCCTTTAAAAATAATAG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
1003490 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1003503 ATGATTATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAAAAATAACAG
Found at i:1003493 original size:107 final size:108
Alignment explanation
Indices: 1003347--1003580 Score: 294
Period size: 107 Copynumber: 2.2 Consensus size: 108
1003337 TTTTGGAAAT
* * * * * *
1003347 AATACCGGGGTTGAAGTAT-CCTTTCAGAAATAACGGGGTTGGAATATCCCCGATTGTGAAAAAT
1 AATAACGGGGTTGGAGTATCCCTTTCAAAAATAACAGGGTTGGAATATCCACGATTATGAAAAAT
**
1003411 TGATGTTTTGGAAAAAAAATCGA-GGTTGGAGTATCCCCTCAGA
66 CAATGTTTTGGAAAAAAAAT-GAGGGTTGGAGTATCCCCTCAGA
* * *
1003454 AATAACGGGGTTGGAGTATCCCTTT-AAAAATAATAGGGTTGGAGTATCCATGATTATGAAAAAT
1 AATAACGGGGTTGGAGTATCCCTTTCAAAAATAACAGGGTTGGAATATCCACGATTATGAAAAAT
* * * *
1003518 CAATGTTTTGGAAATAAAATTAGGGTTGGTGTATCCCCTCGGA
66 CAATGTTTTGGAAAAAAAATGAGGGTTGGAGTATCCCCTCAGA
*
1003561 AATAATGGGGTTGGAGTATC
1 AATAACGGGGTTGGAGTATC
1003581 TCTGATTGTG
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
106 1 0.01
107 103 0.94
108 5 0.05
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (108 bp):
AATAACGGGGTTGGAGTATCCCTTTCAAAAATAACAGGGTTGGAATATCCACGATTATGAAAAAT
CAATGTTTTGGAAAAAAAATGAGGGTTGGAGTATCCCCTCAGA
Found at i:1003544 original size:79 final size:78
Alignment explanation
Indices: 1003461--1003975 Score: 454
Period size: 79 Copynumber: 6.5 Consensus size: 78
1003451 AGAAATAACG
* * * *
1003461 GGGTTGGAGTATCCCTTTAAAAATAATAGGGTTGGAGTATCCATGATTATGAAAAATCAATGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCC-CGATTATGAAAAATCGATGTTT
1003526 TGGAAATAAAATTA
65 TGGAAATAAAATTA
* ** * * *
1003540 GGGTTGGTGTATCCCCTCGGAAATAATGGGGTTGGAGTATCTCTGATTGTGAAAAATCGATGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATC-CCGATTATGAAAAATCGATGTTT
* * *
1003605 T-AAAAAAAAATCA
65 TGGAAATAAAATTA
* * ** * * *
1003618 AGGTTGAAGTATCCCCTCGGAAATAACAGGGTTAGAGTATCTCCGATCATGAAAAATCGATGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATC-CCGATTATGAAAAATCGATGTTT
* *
1003683 TGAAAATAAAA-TC
65 TGGAAATAAAATTA
* * * * * *
1003696 GAGGTTGGTGTATCCCCTAAAAAAGAAT-GGAGTTGGAGTATCCCCGATTGTAAAAAATCGTTGT
1 G-GGTTGGAGTATCCCCTCAAAAATAATAGG-GTTGGAGTAT-CCCGATTATGAAAAATCGATGT
*
1003760 TTTGGAAATAAAAAT-
63 TTTGGAAATAAAATTA
* * * * * *
1003775 GGAGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCTCCAATAATGAAAAATTGATGTT
1 GG-GTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATC-CCGATTATGAAAAATCGATGTT
1003840 TTGGAAATAAAATT-
64 TTGGAAATAAAATTA
* * * * *
1003854 GAGGTTGGTGTATCCCCTAAAAAAGAAT-GGAGTTGGAGTATCCCCGATTGTGAAAAATC-ATTA
1 G-GGTTGGAGTATCCCCTCAAAAATAATAGG-GTTGGAGTAT-CCCGATTATGAAAAATCGA-TG
1003917 TTTTGGAAATAAAA--A
62 TTTTGGAAATAAAATTA
* * *
1003932 CGAAGTTAGAGTATCTCCTCAAAAATAATAGGGTTGGAGTATCC
1 -G-GGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCC
1003976 TCTCGAAAAT
Statistics
Matches: 353, Mismatches: 67, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
78 75 0.21
79 269 0.76
80 9 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCCCGATTATGAAAAATCGATGTTTT
GGAAATAAAATTA
Found at i:1003851 original size:158 final size:157
Alignment explanation
Indices: 1003467--1003974 Score: 639
Period size: 158 Copynumber: 3.2 Consensus size: 157
1003457 AACGGGGTTG
* * * * *
1003467 GAGTATCCCTTTAAAAATAATAGGGTTGGAGTA--TCCATGATTATGAAAAATCAATGTTTTGGA
1 GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCTCCA--ATAATGAAAAATCGATGTTTTGGA
* *** * * * *
1003530 AATAAAATTAGGGTTGGTGTATCCCCTCGGAAATAATGGGGTTGGAGTATCTCTGATTGTGAAAA
64 AATAAAATGA-GGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAA
* * *
1003595 ATCGATGTTTT--AAAAAAAAATCAAGGTT-
128 ATCGTTGTTTTGGAAATAAAAATGAA-GTTA
** * * * *
1003623 GAAGTATCCCCTCGGAAATAACAGGGTTAGAGTATCTCCGATCATGAAAAATCGATGTTTTGAAA
1 G-AGTATCCCCTCAAAAATAACAGGGTTGGAGTATCTCCAATAATGAAAAATCGATGTTTTGGAA
*
1003688 ATAAAATCGAGGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTAAAAAA
65 ATAAAAT-GAGGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAAA
*
1003753 TCGTTGTTTTGGAAATAAAAATGGAGTTA
129 TCGTTGTTTTGGAAATAAAAATGAAGTTA
* *
1003782 GAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCTCCAATAATGAAAAATTGATGTTTTGGAAA
1 GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCTCCAATAATGAAAAATCGATGTTTTGGAAA
1003847 TAAAATTGAGGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAAAT
66 TAAAA-TGAGGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAAAT
* * *
1003912 CATTATTTTGGAAATAAAAACGAAGTTA
130 CGTTGTTTTGGAAATAAAAATGAAGTTA
* *
1003940 GAGTATCTCCTCAAAAATAATAGGGTTGGAGTATC
1 GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATC
1003975 CTCTCGAAAA
Statistics
Matches: 307, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
156 1 0.00
157 111 0.36
158 180 0.59
159 15 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (157 bp):
GAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCTCCAATAATGAAAAATCGATGTTTTGGAAA
TAAAATGAGGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAAATC
GTTGTTTTGGAAATAAAAATGAAGTTA
Found at i:1003967 original size:107 final size:105
Alignment explanation
Indices: 1003856--1004190 Score: 379
Period size: 107 Copynumber: 3.1 Consensus size: 105
1003846 ATAAAATTGA
* * * * * *
1003856 GGTTGGTGTATCCCCTAAAAAAGAATGGAGTTGGAGTATCCCCGATTGTGAAAAATCATTATTTT
1 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGA-TGTTTT
* * *
1003921 GGAAATAAAAACGAAGTTAGAGTATCTCCTCAAAAATAATAG
65 GGAAATAAAAACGAGGTTGGAGTATC-CCTCGAAAATAATAG
* **
1003963 GGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAA-TGATGTTTT
* *
1004028 GAAAATAAAACCGAGGTTGGAGTATCCCTTCGAAAATAAT-G
65 GGAAATAAAAACGAGGTTGGAGTATCCC-TCGAAAATAATAG
* * ** * *
1004069 AGATTAGAGTATCTTCTAAAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTT
1 -GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGT-GAAAAATGATGTTT
* *
1004134 TGGAAAT-AAAACGGGGGTTGGAGTATCCCCTCGAAAATAACA-
64 TGGAAATAAAAAC-GAGGTTGGAGTAT-CCCTCGAAAATAATAG
1004176 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1004191 GATTGTGAAA
Statistics
Matches: 192, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
106 18 0.09
107 164 0.85
108 10 0.05
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (105 bp):
GGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGATGTTTTG
GAAATAAAAACGAGGTTGGAGTATCCCTCGAAAATAATAG
Found at i:1003973 original size:28 final size:28
Alignment explanation
Indices: 1003940--1004003 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1003930 AACGAAGTTA
*
1003940 GAGTAT-CTCCTCAAAAATAATAGGGTTG
1 GAGTATCCT-CTCAAAAATAACAGGGTTG
* *
1003968 GAGTATCCTCTCGAAAATAACGGGGTTG
1 GAGTATCCTCTCAAAAATAACAGGGTTG
1003996 GAGTATCC
1 GAGTATCC
1004004 CCGATTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
GAGTATCCTCTCAAAAATAACAGGGTTG
Found at i:1004049 original size:51 final size:51
Alignment explanation
Indices: 1003988--1004163 Score: 153
Period size: 51 Copynumber: 3.4 Consensus size: 51
1003978 TCGAAAATAA
1003988 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAAC
* *** * *
1004039 CGAGGTTGGAGTATCCCTTCGAAAAT-AATGAGATTAGA-GTATCTTCTAAAA-AATAA-
1 CGGGGTTGGAGTATCCC--CGATTGTGAA--AAATT-GATGT-T-TT-GAAAATAA-AAC
* * *
1004095 CGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAAC
*
1004146 GGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1004164 TCGAAAATAA
Statistics
Matches: 95, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
50 5 0.05
51 36 0.38
52 5 0.05
53 10 0.11
54 10 0.11
55 4 0.04
56 19 0.20
57 6 0.06
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAAC
Found at i:1004158 original size:79 final size:79
Alignment explanation
Indices: 1004088--1004502 Score: 506
Period size: 78 Copynumber: 5.3 Consensus size: 79
1004078 TATCTTCTAA
1004088 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAA-CGGGGGT
1 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATC-GGGGT
1004152 TGGAGTATCCCCTCG
65 TGGAGTATCCCCTCG
* * *
1004167 AAAATAAC-AGGTTGGAGTATCCCCGATTGTGAAAAATT-AGTGTTTTGGAAATAAAA-CTGGGG
1 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGA-TGTTTTGGAAATAAAATC-GGGG
*
1004229 TTGGAGTATCCCCTTG
64 TTGGAGTATCCCCTCG
* *
1004245 AAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTT-GAAATAAAATCGAGGTT
1 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGTT
* **
1004309 AGAGTATCCTTTCG
66 GGAGTATCCCCTCG
* ** * ** * * **
1004323 AAAATAACAGGGTTAAAGTAT-ATCCGATCAT-GAAAAATGATGTTTTAGAAATAAAATCAAGGT
1 AAAATAACGGGGTTGGAGTATCCT-CGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGT
1004386 TGGTA-TATCCCCTCG
65 TGG-AGTATCCCCTCG
* * * *
1004401 AAAATAATGGGGTTGGAGTAT-CTCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGT
1 AAAATAACGGGGTTGGAGTATCCT-CGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGT
1004465 TGGAGTATCCCCTCG
65 TGGAGTATCCCCTCG
1004480 AAAATAACGGGGTTGGAGTATCC
1 AAAATAACGGGGTTGGAGTATCC
1004503 CCTCAGAAAT
Statistics
Matches: 290, Mismatches: 36, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
77 16 0.06
78 170 0.59
79 102 0.35
80 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (79 bp):
AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGTT
GGAGTATCCCCTCG
Found at i:1004272 original size:157 final size:156
Alignment explanation
Indices: 1004088--1004504 Score: 547
Period size: 157 Copynumber: 2.7 Consensus size: 156
1004078 TATCTTCTAA
1004088 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAA-CGGGGGT
1 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATC-GGGGT
** * *
1004152 TGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAA
65 TGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCCGATCATGAAAAATGA-TGTTTTAGAA
** *
1004217 ATAAAA-CTGGGGTTGG-AGTATCCCCTTG
129 ATAAAATC-AAGGTTGGTA-TATCCCCTCG
* *
1004245 AAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTT-GAAATAAAATCGAGGTT
1 AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGTT
* ** ** **
1004309 AGAGTATCCTTTCGAAAATAACAGGGTTAAAGTATATCCGATCATGAAAAATGATGTTTTAGAAA
66 GGAGTATCCCCTCGAAAATAACA-GGTTGGAGTATCCCCGATCATGAAAAATGATGTTTTAGAAA
1004374 TAAAATCAAGGTTGGTATATCCCCTCG
130 TAAAATCAAGGTTGGTATATCCCCTCG
* * * *
1004401 AAAATAATGGGGTTGGAGTAT-CTCCGATTATGAAAAATCGATGTTTTGGAAATAAAATCGGGGT
1 AAAATAACGGGGTTGGAGTATCCT-CGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGT
*
1004465 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
65 TGGAGTATCCCCTCGAAAATAAC-AGGTTGGAGTATCCCC
1004505 TCAGAAATAA
Statistics
Matches: 223, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
155 2 0.01
156 103 0.46
157 118 0.53
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (156 bp):
AAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATTGATGTTTTGGAAATAAAATCGGGGTT
GGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCCCGATCATGAAAAATGATGTTTTAGAAAT
AAAATCAAGGTTGGTATATCCCCTCG
Found at i:1004492 original size:28 final size:28
Alignment explanation
Indices: 1004459--1004530 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
1004449 GAAATAAAAT
1004459 CGGGGTTGGAGTATCCCCTC-GAAAATAA
1 CGGGGTTGGAGTATCCCCTCAG-AAATAA
1004487 CGGGGTTGGAGTATCCCCTCAGAAATAA
1 CGGGGTTGGAGTATCCCCTCAGAAATAA
* *
1004515 CGGGATTAGAGTATCC
1 CGGGGTTGGAGTATCC
1004531 TCAATCATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAA
Found at i:1004502 original size:107 final size:107
Alignment explanation
Indices: 1004383--1004607 Score: 276
Period size: 107 Copynumber: 2.1 Consensus size: 107
1004373 ATAAAATCAA
* * * * * *
1004383 GGTTGGTA-TATCCCCTC-GAAAATAATGGGGTTGGAGTAT-CTCCGATTATGAAAAATCGATGT
1 GGTTGG-AGTATCCCCTCAG-AAATAACGGGATTAGAGTATCCT-CAATCATGAAAAATCGATAT
* * * *
1004445 TTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGG
63 TTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGG
*
1004490 GGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCTCAATCATGAAAAATTGATATTTT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCTCAATCATGAAAAATCGATATTTT
* *
1004555 AGAAATAAAACCAGGGTTGGTGTATCCCCTCAAAAATAATGG
66 AGAAATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGG
*
1004597 GATTGGAGTAT
1 GGTTGGAGTAT
1004608 TCCCGATGGT
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
106 1 0.01
107 97 0.96
108 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (107 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCTCAATCATGAAAAATCGATATTTT
AGAAATAAAACCAGGGTTGGAGTATCCCCTCAAAAATAACGG
Found at i:1004624 original size:79 final size:79
Alignment explanation
Indices: 1004489--1004643 Score: 197
Period size: 79 Copynumber: 2.0 Consensus size: 79
1004479 GAAAATAACG
* *
1004489 GGGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCTCAATCATGAAAAAT-TGATATT
1 GGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTATCCTCAATCATGAAAAATCAG-TATT
1004553 TTAGAAATAAAACCA
65 TTAGAAATAAAACCA
* * * * ** *
1004568 GGGTTGGTGTATCCCCTCAAAAATAATGGGATTGGAGTATTCC-CGATGGTGGAAAATCAGTATT
1 GGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTA-TCCTCAATCATGAAAAATCAGTATT
1004632 TTAGAAATAAAA
65 TTAGAAATAAAA
1004644 ACATCAATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 61 0.94
80 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCAAAAATAACGGGATTAGAGTATCCTCAATCATGAAAAATCAGTATTT
TAGAAATAAAACCA
Found at i:1007060 original size:30 final size:30
Alignment explanation
Indices: 1007019--1007093 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
1007009 ATATATTGAG
* *
1007019 AAATATATCGATACCTCTAGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
* * *
1007049 GAATGTATCGATATATCTGGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
1007079 AAATGTATCGATACA
1 AAATGTATCGATACA
1007094 ATGAAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATGTATCGATACATCTAGGTAAAACCCA
Found at i:1009341 original size:30 final size:30
Alignment explanation
Indices: 1009300--1009374 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
1009290 ATATATTGAG
* *
1009300 AAATATATCGATACCTCTAGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
* * *
1009330 GAATGTATCGATATATCTGGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
1009360 AAATGTATCGATACA
1 AAATGTATCGATACA
1009375 ATGAAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATGTATCGATACATCTAGGTAAAACCCA
Found at i:1011622 original size:30 final size:30
Alignment explanation
Indices: 1011581--1011655 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
1011571 ATATATTGAG
* *
1011581 AAATATATCGATACCTCTAGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
* * *
1011611 GAATGTATCGATATATCTGGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
1011641 AAATGTATCGATACA
1 AAATGTATCGATACA
1011656 ATGAAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATGTATCGATACATCTAGGTAAAACCCA
Found at i:1011975 original size:53 final size:53
Alignment explanation
Indices: 1011917--1012030 Score: 228
Period size: 53 Copynumber: 2.2 Consensus size: 53
1011907 ACCCCGAACT
1011917 CATTTCTTATCAAAAAATTACAAATTATACCTTCACAAAAAGGGAATTTCATG
1 CATTTCTTATCAAAAAATTACAAATTATACCTTCACAAAAAGGGAATTTCATG
1011970 CATTTCTTATCAAAAAATTACAAATTATACCTTCACAAAAAGGGAATTTCATG
1 CATTTCTTATCAAAAAATTACAAATTATACCTTCACAAAAAGGGAATTTCATG
1012023 CATTTCTT
1 CATTTCTT
1012031 GGGAAAAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (53 bp):
CATTTCTTATCAAAAAATTACAAATTATACCTTCACAAAAAGGGAATTTCATG
Found at i:1013956 original size:30 final size:30
Alignment explanation
Indices: 1013915--1013989 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
1013905 ATATATTGAG
* *
1013915 AAATATATCGATACCTCTAGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
* * *
1013945 GAATGTATCGATATATCTGGGTAAAACCCA
1 AAATGTATCGATACATCTAGGTAAAACCCA
1013975 AAATGTATCGATACA
1 AAATGTATCGATACA
1013990 ATGAAGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATGTATCGATACATCTAGGTAAAACCCA
Found at i:1017390 original size:79 final size:78
Alignment explanation
Indices: 1017170--1017390 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 78
1017160 CGAGTGGATA
*
1017170 TCCAACCCT-GCTTTTA-TTCTCAAAACAC-AGATTTTTCACAATCAAGGATACTCTAA-CCTCG
1 TCCAACCCTAG-TTTTATTTC-CAAAACACTA-ATTTTTCACAAT-TAGGATACTCTAATCCT-G
* *
1017231 TTATTTTCAAGGGGATAG
61 TTATTTTCAAGGGAATAC
* * * * *
1017249 TTCAACCCTAGTTTTATTTCTAAAATA-TCGATTTTTCACAATTAGGAATACTCTAATTCTGTTA
1 TCCAACCCTAGTTTTATTTCCAAAACACT-AATTTTTCACAATTAGG-ATACTCTAATCCTGTTA
*
1017313 TTTTTAAGGGAATAC
64 TTTTCAAGGGAATAC
* * *
1017328 TCCTA-CCTCAGTTTTATTTCCAAAACACTAATTTTTCATAATTGAGGATACTCCAATCCTGTT
1 TCCAACCCT-AGTTTTATTTCCAAAACACTAATTTTTCACAATT-AGGATACTCTAATCCTGTT
1017391 TGTTAGCTCA
Statistics
Matches: 116, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
78 6 0.05
79 100 0.86
80 10 0.09
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (78 bp):
TCCAACCCTAGTTTTATTTCCAAAACACTAATTTTTCACAATTAGGATACTCTAATCCTGTTATT
TTCAAGGGAATAC
Found at i:1017679 original size:34 final size:35
Alignment explanation
Indices: 1017641--1017707 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
1017631 CCTTACAACA
1017641 CTATC-TTTC-AAGACTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGACTAAGATAG-AACCTCTCTCT
*
1017675 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGACTAAGATAGAACCTCTC
1017708 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGACTAAGATAGAACCTCTCTCT
Found at i:1018212 original size:13 final size:13
Alignment explanation
Indices: 1018177--1018215 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1018167 ACTATTTATG
*
1018177 ATGTATCGAGACA
1 ATGTATCGATACA
*
1018190 CTGTATCGATACA
1 ATGTATCGATACA
1018203 ATGTATCGATACA
1 ATGTATCGATACA
1018216 TGAATAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1018281 original size:21 final size:22
Alignment explanation
Indices: 1018225--1018304 Score: 117
Period size: 21 Copynumber: 3.6 Consensus size: 22
1018215 ATGAATAGTT
* *
1018225 ATGAACAGTGATTTTTAACGATAC
1 ATGAACAGTGA--TGTATCGATAC
1018249 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1018271 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1018292 ATGAACAGTGATG
1 ATGAACAGTGATG
1018305 AATAGTGATG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 21 0.40
22 21 0.40
24 11 0.21
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1018311 original size:10 final size:10
Alignment explanation
Indices: 1018292--1018322 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1018282 GTATCGATAC
1018292 ATGAACAGTG
1 ATGAACAGTG
*
1018302 ATGAATAGTG
1 ATGAACAGTG
1018312 ATGAACAGTG
1 ATGAACAGTG
1018322 A
1 A
1018323 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1018410 original size:53 final size:53
Alignment explanation
Indices: 1018346--1018482 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1018336 CTACTACCAA
*
1018346 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1018399 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1018452 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1018483 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1018515 original size:20 final size:20
Alignment explanation
Indices: 1018452--1018522 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1018442 GCCAATGTCC
**
1018452 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1018472 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1018492 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1018512 TGTATCGATAC
1 TGTATCGATAC
1018523 TTTTCAGCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1018588 original size:21 final size:21
Alignment explanation
Indices: 1018562--1018602 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1018552 GTCAACCTTG
1018562 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1018583 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1018603 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1019170 original size:79 final size:79
Alignment explanation
Indices: 1018805--1019568 Score: 688
Period size: 79 Copynumber: 9.7 Consensus size: 79
1018795 TCCTAACACT
* * * * * * * * *
1018805 GTTATTTTTGAGGAGATACTCTAACCTCGATTTTATTTTCAAAATACCAATTTTCCACAATTGGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
1018870 GATACTCCAACCCC
66 GATACTCCAACCCC
* * * ** **
1018884 ATTATTTTCGAGAGGATAGTCCAACCTAG-TTTTA-TTCTCAAAACACCGA-TTTTCACAATCGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTC-CAAAACACTAATTTTTCACAATCGG
* * *
1018946 GGATGCTCTAACCTC
65 GGATACTCCAACCCC
* * * * * *
1018961 GTTA-TTTCTAAGGGGATACTCCAACCCTGGTTTTATTTCCAAAATATTGATTTTTCACAATCGG
1 GTTATTTTC-GAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGG
* ***
1019025 GGAT-CTCTAATTTC
65 GGATACTCCAACCCC
* * ** * *
1019039 ATTATTTCCGAGGGGATACTCCAACCAAG-TTTTATTTTCAAAACACCAATTTTTCACAATCGGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
* *
1019103 GATACTCCAATCTC
66 GATACTCCAACCCC
* * **
1019117 GTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAATACTAATTTTTCACAATTAGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
1019182 GATACTCCAACCCC
66 GATACTCCAACCCC
* * * * *
1019196 GTTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACTAATTTTTTATAATCAGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
**
1019261 GATACTCCAACCTT
66 GATACTCCAACCCC
* * * * * * *
1019275 GTTATTTTCTAAGGGATACTCCAACACCGGTTTTATTTCCAAAATACTAATTTTTCATAATTGGG
1 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
*
1019340 GATACTCCAACACC
66 GATACTCCAACCCC
* * * *
1019354 GTTATTTTCGAGGAGATACTCCAACCCC-AGTTTTATTTTCAAAACACTGATTTTTCACAATCGA
1 GTTATTTTCGAGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACTAATTTTTCACAATCGG
* *
1019418 AGATACTCCGACCCC
65 GGATACTCCAACCCC
* * * * * * * *
1019433 TTTA-TTTCTGAGGGGATACTCCAA-CCTGGTTTTATTTCTAAAACA-TCGATTTTCCACCATTG
1 GTTATTTTC-GAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACT-AATTTTTCACAATCG
* *
1019495 GGGATACTCCATCACC
64 GGGATACTCCAACCCC
* * * *
1019511 GTTA-TTTCTGAGGGGATACTTCGACCCC-ATTTTTATCTCCAAAATACTAAATTTTTCA
1 GTTATTTTC-GAGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACT-AATTTTTCA
1019569 TTGGAAGATG
Statistics
Matches: 559, Mismatches: 111, Indels: 29
0.80 0.16 0.04
Matches are distributed among these distances:
76 4 0.01
77 77 0.14
78 151 0.27
79 319 0.57
80 8 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (79 bp):
GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGG
GATACTCCAACCCC
Found at i:1021604 original size:4 final size:4
Alignment explanation
Indices: 1021595--1021633 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
1021585 TTTTGAGGTG
*
1021595 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1021634 TGTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1028360 original size:31 final size:30
Alignment explanation
Indices: 1028315--1028374 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1028305 ATCTAGCTTG
*
1028315 TTTTTCCTTATTTTCTCTCTTTTTCTTTTCT
1 TTTTTCCTTATTTTCTCCCTTTTT-TTTTCT
* *
1028346 TTTTTCTTTTTTTTCTCCCTTTTTTTTTC
1 TTTTTCCTTATTTTCTCCCTTTTTTTTTC
1028375 CTACTTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTCCTTATTTTCTCCCTTTTTTTTTCT
Found at i:1028383 original size:31 final size:31
Alignment explanation
Indices: 1028325--1028383 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1028315 TTTTTCCTTA
* **
1028325 TTTTCTCTCTTTTTCTTTTCTTTTTTCTTTT
1 TTTTCTCCCTTTTTCTTTTCTACTTTCTTTT
1028356 TTTTCTCCCTTTTT-TTTTCCTACTTTCT
1 TTTTCTCCCTTTTTCTTTT-CTACTTTCT
1028384 AAAGCTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTCTCCCTTTTTCTTTTCTACTTTCTTTT
Found at i:1030470 original size:47 final size:47
Alignment explanation
Indices: 1030409--1031466 Score: 795
Period size: 47 Copynumber: 22.7 Consensus size: 47
1030399 TGACTAGAAT
* *
1030409 TAACGCCAATACAGTCAAATGAGGGTGAGAAAAGTTTGACCAAGCCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * *
1030456 TAATGCTAATACAGTCAAACGAGGGTG-GAAAAAGTTTGACCAGGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
* * *
1030503 TAATGCCAATATAGTCAAATGAGGGTG-GAAAAAGTTTGACCAAGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
* * * * *
1030550 TAA-ACCAATATAATTAAACAAGGGT--GAAAAGTTTGACCAAGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * * ** *
1030594 AAATGCCAATACAGTCAAACGAGGGTAAGAAAAAGTTTGACTGAGCCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
* * * * *
1030642 CAACGCTAATACAATCAAACGAGGGTGAAAAAGAGTTTGACCAAG-AC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
* * * * * *
1030689 TAACACCAATATAGTCAAACAAGGGTGA-AAAGACTTTGACTAGGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
** * *
1030736 TAACGTTAATACAGTCAAACAAGGGT--GAAAGGTTTGACCAAGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * * * **
1030781 TAATGCTAATATAGTCAAACGAGGGTGAAAAAGAGTTTGA-C-AGGAC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
* * * *
1030827 TAACACCAATACAGTCAAACAAGGGTGAGAAAAAGTTT-AACTAGATCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAG-TCC
*** ** ** **
1030875 TAACATTAATAC-GTCAAATAAAAGTGAGAAAAAGTTTGA-C-AGGAC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
*** *
1030920 TAACATTAAT-CAGTCAAACGAGGGTG-GAAAAGTTTGACCAAATCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * ** *
1030965 CAATGCCAATACAGTCAAGTGAGGGTGA-AAAGTGTTTGACTC-AGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGAC-CAAGTCC
* * ** *
1031012 TAACGCCAATATAGTCAAACGAGGGTGAGAAAAAGTTTGATCGGGCCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
* * * * *
1031060 TAATGCCAATACAATCAAACGAGGGTTAAAAAGAGTTTGACCAAG-AC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
* * * * * *
1031107 TAACACCAATAAAGTCAAACAAGGGT-AAAAAGAGTTTGACTAGGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
* * *
1031154 TAACGCTAATACAG-CAAATGAGGGT--GAAAAGTTTGACTAAGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * * * *
1031198 TAACGCTAATATAGTCAAACGAGGGTGAAAAAGAGTTTGGCCAAG-AC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAA-AGTTTGACCAAGTCC
* * *
1031245 TAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTTGACC-AGATCC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAG-TCC
* **
1031293 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAAGTTTGA-CTAGGAC
1 TAACGCCAATACAGTCAAACGAGGGTGAG-AAAAGTTTGACCAAGTCC
** * * * * * *
1031340 TAATACTAATATAGTCAAACGAGGGTGAAAAAAGTTTAACTAAGTCT
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* * * * *
1031387 TAACACCAATACAATCAAACGAGGATGAAAAAAGTTTGACCAGGTCC
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
* *
1031434 TAATGCCAATACAGTCAAATGAGGGTGA-AAAAG
1 TAACGCCAATACAGTCAAACGAGGGTGAGAAAAG
1031467 AGTTGGTGAA
Statistics
Matches: 810, Mismatches: 164, Indels: 75
0.77 0.16 0.07
Matches are distributed among these distances:
43 10 0.01
44 50 0.06
45 93 0.11
46 126 0.16
47 366 0.45
48 162 0.20
49 3 0.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (47 bp):
TAACGCCAATACAGTCAAACGAGGGTGAGAAAAGTTTGACCAAGTCC
Found at i:1030838 original size:233 final size:232
Alignment explanation
Indices: 1030395--1031470 Score: 999
Period size: 233 Copynumber: 4.6 Consensus size: 232
1030385 TGATGAAACG
* * * * * * *
1030395 AGTTTGACTAGAATTAACGCCAATACAGTCAAATGAGGGTGAGAAAAGTTTGACCAAGCCCTAAT
1 AGTTTGACTAG-ACTAACACTAATACAGTCAAACGAGGGTGAAAAAAGTTTGACCAAG-ACTAAC
* *
1030460 GCTAATACAGTCAAACGAGGGTGGAAAA-AGTTTGACCAGGTCCTAATGCCAATATAGTCAAATG
64 ACTAATACAGTCAAACGAGGGT-GAAAAGA-TTTGACCAGGTCCTAATGCCAATACAGTCAAATG
* * *
1030524 AGGGTGGAAAA-AGTTTGACCAAGTCCTAA-ACCAATATAATTAAACAAGGGT--G-AAAAGTTT
127 AGGGT-GAAAAGAGTTTGACCAAGTCCTAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTT
* * *
1030584 GACCAAGTCCAA-ATGCCAATACAGTCAAACGAGGGTAAGAAAA
191 GACCAGGACTAACA--CCAATACAGTCAAACGAGGGTAAGAAAA
* * * *
1030627 AGTTTGACTGAGCCCCAACGCTAATACAATCAAACGAGGGTGAAAAAGAGTTTGACCAAGACTAA
1 AGTTTGACT-AG-ACTAACACTAATACAGTCAAACGAGGGTGAAAAA-AGTTTGACCAAGACTAA
* * * * * ** **
1030692 CACCAATATAGTCAAACAAGGGTGAAAAGACTTTGACTAGGTCCTAACGTTAATACAGTCAAACA
63 CACTAATACAGTCAAACGAGGGTGAAAAGA-TTTGACCAGGTCCTAATGCCAATACAGTCAAATG
* *
1030757 AGGGTG-AAAG-GTTTGACCAAGTCCTAATGCTAATATAGTCAAACGAGGGTGA-AAAAGAGTTT
127 AGGGTGAAAAGAGTTTGACCAAGTCCTAATGCCAATATAGTCAAACAAGGGTGAGAAAA-AGTTT
* *
1030819 GA-CAGGACTAACACCAATACAGTCAAACAAGGGTGAGAAAA
191 GACCAGGACTAACACCAATACAGTCAAACGAGGGTAAGAAAA
* * ** ** *
1030860 AGTTTAACTAGATCCTAACATTAATAC-GTCAAATAAAAGTGAGAAAAAGTTTGA-CAGGACTAA
1 AGTTTGACTAGA--CTAACACTAATACAGTCAAACGAGGGTGA-AAAAAGTTTGACCAAGACTAA
* ** * *
1030923 CATTAAT-CAGTCAAACGAGGGTGGAAAAG-TTTGACCAAATCCCAATGCCAATACAGTCAAGTG
63 CACTAATACAGTCAAACGAGGGT-GAAAAGATTTGACCAGGTCCTAATGCCAATACAGTCAAATG
* * *
1030986 AGGGTGAAAAGTGTTTGACTC-AGTCCTAACGCCAATATAGTCAAACGAGGGTGAGAAAAAGTTT
127 AGGGTGAAAAGAGTTTGAC-CAAGTCCTAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTT
* * * ** * *
1031050 GATCGGGCCCTAATGCCAATACAATCAAACGAGGGTTAA-AAAG
191 GACCAGG-ACTAACACCAATACAGTCAAACGAGGG-TAAGAAAA
* * * * * * *
1031093 AGTTTGACCAAGACTAACACCAATAAAGTCAAACAAGGGT-AAAAAGAGTTTGACTAGGTCCTAA
1 AGTTTGA-CTAGACTAACACTAATACAGTCAAACGAGGGTGAAAAA-AGTTTGACCAAG-ACTAA
* * * * * * * *
1031157 CGCTAATACAG-CAAATGAGGGTGAAAAG-TTTGACTAAGTCCTAACGCTAATATAGTCAAACGA
63 CACTAATACAGTCAAACGAGGGTGAAAAGATTTGACCAGGTCCTAATGCCAATACAGTCAAATGA
* *
1031220 GGGTGAAAAAGAGTTTGGCCAAG-ACTAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTTG
128 GGGTG-AAAAGAGTTTGACCAAGTCCTAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTTG
* *
1031284 ACCA-GATCCTAACGCCAATACAGTCAAACGAGGGTGAGAAAA
192 ACCAGGA--CTAACACCAATACAGTCAAACGAGGGTAAGAAAA
* * * * *
1031326 AGTTTGACTAGGACTAATACTAATATAGTCAAACGAGGGTGAAAAAAGTTTAACTAAGTCTTAAC
1 AGTTTGACTA-GACTAACACTAATACAGTCAAACGAGGGTGAAAAAAGTTTGACCAAGAC-TAAC
* * * *
1031391 ACCAATACAATCAAACGAGGATGAAAAAAGTTTGACCAGGTCCTAATGCCAATACAGTCAAATGA
64 ACTAATACAGTCAAACGAGGGTGAAAAGA-TTTGACCAGGTCCTAATGCCAATACAGTCAAATGA
1031456 GGGTGAAAAAGAGTT
128 GGGTG-AAAAGAGTT
1031471 GGTGAAGATT
Statistics
Matches: 686, Mismatches: 120, Indels: 72
0.78 0.14 0.08
Matches are distributed among these distances:
229 30 0.04
230 17 0.02
231 88 0.13
232 83 0.12
233 335 0.49
234 78 0.11
235 11 0.02
236 44 0.06
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (232 bp):
AGTTTGACTAGACTAACACTAATACAGTCAAACGAGGGTGAAAAAAGTTTGACCAAGACTAACAC
TAATACAGTCAAACGAGGGTGAAAAGATTTGACCAGGTCCTAATGCCAATACAGTCAAATGAGGG
TGAAAAGAGTTTGACCAAGTCCTAATGCCAATATAGTCAAACAAGGGTGAGAAAAAGTTTGACCA
GGACTAACACCAATACAGTCAAACGAGGGTAAGAAAA
Found at i:1031045 original size:185 final size:182
Alignment explanation
Indices: 1030413--1031423 Score: 641
Period size: 186 Copynumber: 5.4 Consensus size: 182
1030403 TAGAATTAAC
* * *
1030413 GCCAATACAGTCAAATGAGGGTGAGAAAAGTTTGACCAAGCCCTAATGCTAATACAGTCAAACGA
1 GCCAATACAGTCAAACGAGGGTGA-AAAAGTTTGACC-AGCCCTAACGCCAATACAGTCAAACGA
* * * *
1030478 GGGTG-GAAAAAGTTTGACCAGGTCCTAATGCCAAT-ATAGTCAAATGAGGGTG-GAAAAAGTTT
64 GGGTGAGAAAAAGTTTAACAAGATCCTAA---CAATAATAGTCAAATAAGGGTGAGAAAAAGTTT
* * * *
1030540 GACCAAGTCCTAAACCAAT-AT-AATTAAACAAGGGTGAAAAGTTTGACCAAGTCCAAAT
126 GA-CAAGGCCT-AA-CATTAATCAGTCAAACAAGGGTGAAAAGTTTGACCAAGTCCAAAT
* * * *
1030598 GCCAATACAGTCAAACGAGGGTAAGAAAAAGTTTGACTGAGCCCCAACGCTAATACAATCAAACG
1 GCCAATACAGTCAAACGAGGGT--GAAAAAGTTTGAC-CAGCCCTAACGCCAATACAGTCAAACG
* * * *
1030663 AGGGTGA-AAAAGAGTTTGACCAAGA--CTAACACCA-ATATAGTCAAACAAGGGTGA-AAAGAC
63 AGGGTGAGAAAA-AGTTT-AACAAGATCCTAACA--ATA-ATAGTCAAATAAGGGTGAGAAAAAG
* * * *
1030723 TTTGACTAGGTCCTAACGTTAATACAGTCAAACAAGGGTGAAAGGTTTGACCAAGTCCTAAT
123 TTTGACAAGG-CCTAACATTAAT-CAGTCAAACAAGGGTGAAAAGTTTGACCAAGTCCAAAT
* * ** * *
1030785 GCTAATATAGTCAAACGAGGGTGAAAAAGAGTTTGA-CAGGACTAACACCAATACAGTCAAACAA
1 GCCAATACAGTCAAACGAGGGTG-AAAA-AGTTTGACCAGCCCTAACGCCAATACAGTCAAACGA
* * **
1030849 GGGTGAGAAAAAGTTTAACTAGATCCTAACATTAATACGTCAAATAAAAGTGAGAAAAAGTTTGA
64 GGGTGAGAAAAAGTTTAACAAGATCCTAACAATAATA-GTCAAATAAGGGTGAGAAAAAGTTTGA
* * * *
1030914 C-AGGACTAACATTAATCAGTCAAACGAGGGTGGAAAAGTTTGACCAAATCCCAAT
128 CAAGGCCTAACATTAATCAGTCAAACAAGGGT-GAAAAGTTTGACCAAGTCCAAAT
** * * *
1030969 GCCAATACAGTCAAGTGAGGGTGAAAAGTGTTTGACTCAGTCCTAACGCCAATATAGTCAAACGA
1 GCCAATACAGTCAAACGAGGGTGAAAA-AGTTTGAC-CAGCCCTAACGCCAATACAGTCAAACGA
* * ** ** *
1031034 GGGTGAGAAAAAGTTTGATC-GGGCCCTAATGCCAATACA-A-TCAAACGAGGGTTA-AAAAGAG
64 GGGTGAGAAAAAGTTT-AACAAGATCCTAA---CAATA-ATAGTCAAATAAGGGTGAGAAAA-AG
* ** * * * * * *
1031095 TTTGACCAA-GACTAACACCAATAAAGTCAAACAAGGGTAAAAAGAGTTTGACTAGGTCCTAAC
123 TTTGA-CAAGGCCTAACATTAAT-CAGTCAAACAAGGGT-GAAA-AGTTTGACCAAGTCCAAAT
* * * * * *
1031158 GCTAATACAG-CAAATGAGGGTG-AAAAGTTTGACTAAGTCCTAACGCTAATATAGTCAAACGAG
1 GCCAATACAGTCAAACGAGGGTGAAAAAGTTTGAC-CAGCCCTAACGCCAATACAGTCAAACGAG
** *
1031221 GGTGA-AAAAGAGTTTGGCCAAGA--CTAATGCCAAT-ATAGTCAAACAAGGGTGAGAAAAAGTT
65 GGTGAGAAAA-AGTTT-AACAAGATCCTAA---CAATAATAGTCAAATAAGGGTGAGAAAAAGTT
* * *** * * ** *
1031282 TGACCAGATCCTAACGCCAATACAGTCAAACGAGGGTGAGAAAAAGTTTGA-CTAGGACTAAT
125 TGACAAG-GCCTAACATTAAT-CAGTCAAACAAGGGT--G-AAAAGTTTGACCAAGTCCAAAT
* * * * * * * * *
1031344 ACTAATATAGTCAAACGAGGGTGAAAAAAGTTTAACTAAGTCTTAACACCAATACAATCAAACGA
1 GCCAATACAGTCAAACGAGGGTG-AAAAAGTTTGAC-CAGCCCTAACGCCAATACAGTCAAACGA
*
1031409 GGATGA-AAAAAGTTT
64 GGGTGAGAAAAAGTTT
1031424 GACCAGGTCC
Statistics
Matches: 668, Mismatches: 110, Indels: 93
0.77 0.13 0.11
Matches are distributed among these distances:
183 28 0.04
184 62 0.09
185 160 0.24
186 205 0.31
187 102 0.15
188 44 0.07
189 67 0.10
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (182 bp):
GCCAATACAGTCAAACGAGGGTGAAAAAGTTTGACCAGCCCTAACGCCAATACAGTCAAACGAGG
GTGAGAAAAAGTTTAACAAGATCCTAACAATAATAGTCAAATAAGGGTGAGAAAAAGTTTGACAA
GGCCTAACATTAATCAGTCAAACAAGGGTGAAAAGTTTGACCAAGTCCAAAT
Done.