Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 196 of 206
Found at i:59285706 original size:14 final size:14
Alignment explanation
Indices: 59285683--59285713 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59285673 TGTCGCGTTC
*
59285683 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
59285697 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
59285711 TTA
1 TTA
59285714 AAACAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:59287461 original size:23 final size:25
Alignment explanation
Indices: 59287409--59287481 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
59287399 AATAATATTA
*
59287409 TTTTAATAGTTTAATATT-AAAGT-
1 TTTTAATACTTTAATATTAAAAGTG
*
59287432 TAATTTAATAC-TT-ATATTAATAGTG
1 T--TTTAATACTTTAATATTAAAAGTG
*
59287457 TTTTATTACTTTAATATTAAAAGTG
1 TTTTAATACTTTAATATTAAAAGTG
59287482 ATTATCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
23 13 0.32
24 8 0.20
25 19 0.47
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (25 bp):
TTTTAATACTTTAATATTAAAAGTG
Found at i:59295209 original size:12 final size:12
Alignment explanation
Indices: 59295192--59295216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59295182 CCCAAAATAT
59295192 AAAATATAAAAC
1 AAAATATAAAAC
59295204 AAAATATAAAAC
1 AAAATATAAAAC
59295216 A
1 A
59295217 TCTGAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATATAAAAC
Found at i:59301081 original size:18 final size:18
Alignment explanation
Indices: 59301058--59301094 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
59301048 TTGGAGAAAG
59301058 ATAATTAATTTGCCCCGA
1 ATAATTAATTTGCCCCGA
59301076 ATAATTAATTTGCCCCGA
1 ATAATTAATTTGCCCCGA
59301094 A
1 A
59301095 GTGAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (18 bp):
ATAATTAATTTGCCCCGA
Found at i:59302066 original size:3 final size:3
Alignment explanation
Indices: 59302001--59302049 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
59301991 GGAGAGTGAC
59302001 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59302049 T
1 T
59302050 TAAGCTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:59310392 original size:11 final size:11
Alignment explanation
Indices: 59310373--59310422 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
59310363 TAAACTAGCC
*
59310373 ATTAATATACA
1 ATTAATATATA
*
59310384 ATTATTATATA
1 ATTAATATATA
59310395 ATATATATATATA
1 AT-TA-ATATATA
59310408 ATTAATATAATA
1 ATTAATAT-ATA
59310420 ATT
1 ATT
59310423 TTATAACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 15 0.45
12 10 0.30
13 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTAATATATA
Found at i:59317296 original size:20 final size:23
Alignment explanation
Indices: 59317251--59317301 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
59317241 GTTTTATGTG
59317251 TATTTTAATGTTTACATATATTAAT
1 TATTTT-AT-TTTACATATATTAAT
59317276 T-TTTTATTTTACAT-T-TTAAT
1 TATTTTATTTTACATATATTAAT
59317296 TATTTT
1 TATTTT
59317302 GTCTTAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.24
21 5 0.20
22 7 0.28
23 2 0.08
24 4 0.16
25 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTTTATTTTACATATATTAAT
Found at i:59318378 original size:13 final size:13
Alignment explanation
Indices: 59318360--59318403 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
59318350 TTTAAATAAA
59318360 CAGTTAATAGAAT
1 CAGTTAATAGAAT
*
59318373 CAGTTAGTCA-AAT
1 CAGTTAAT-AGAAT
*
59318386 CGGTTAATAGAAT
1 CAGTTAATAGAAT
59318399 CAGTT
1 CAGTT
59318404 TCTAACACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (13 bp):
CAGTTAATAGAAT
Found at i:59319947 original size:50 final size:50
Alignment explanation
Indices: 59319900--59319995 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
59319890 CCAAGCCATT
*
59319900 TATCGGGAAGCTCA-AGAGAGCCAAATATCGGGAAGCTCGTGAGAGCCAAA
1 TATCGGGAAGCTCATA-AGAGCCAAATAACGGGAAGCTCGTGAGAGCCAAA
* * *
59319950 TATCTGGATGCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGC
1 TATCGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCGTGAGAGC
59319996 TGTGGTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (50 bp):
TATCGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCGTGAGAGCCAAA
Found at i:59319996 original size:25 final size:25
Alignment explanation
Indices: 59319900--59319995 Score: 120
Period size: 25 Copynumber: 3.8 Consensus size: 25
59319890 CCAAGCCATT
*
59319900 TATCGGGAAGCTCAAGAGAGCCAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
*
59319925 TATCGGGAAGCTCGTGAGAGCCAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
* * * *
59319950 TATCTGGATGCTCATAAGAGCTAAA
1 TATCGGGAAGCTCATGAGAGCCAAA
* *
59319975 TAACGGGAAGCTCGTGAGAGC
1 TATCGGGAAGCTCATGAGAGC
59319996 TGTGGTGTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (25 bp):
TATCGGGAAGCTCATGAGAGCCAAA
Found at i:59320172 original size:22 final size:23
Alignment explanation
Indices: 59320142--59320188 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
59320132 AACTACACAT
*
59320142 TTCACACACATA-ACAATATTCAA
1 TTCACACACATACA-AATATACAA
59320165 TTCA-ACACATACAAATATACAA
1 TTCACACACATACAAATATACAA
59320187 TT
1 TT
59320189 TAGTTATACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (23 bp):
TTCACACACATACAAATATACAA
Found at i:59323882 original size:23 final size:23
Alignment explanation
Indices: 59323854--59323902 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
59323844 AAATTTTCCT
*
59323854 AATA-TTTTTTATAGTTTTTAATA
1 AATATTTTTTTATAATTTTT-ATA
59323877 AATATTTTTTTATAATTTTTATA
1 AATATTTTTTTATAATTTTTATA
59323900 AAT
1 AAT
59323903 TGTTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
AATATTTTTTTATAATTTTTATA
Found at i:59333075 original size:30 final size:29
Alignment explanation
Indices: 59333004--59333107 Score: 118
Period size: 30 Copynumber: 3.3 Consensus size: 29
59332994 TAAAAATTGT
59333004 TAAAAAAATAAGAAATATATAAATTATAAAA
1 TAAAAAAA-AAGAAATATATAAATTA-AAAA
*
59333035 CTTTAAAAAAAAGAACATATATAAATTAAAAA
1 --TAAAAAAAAAGAA-ATATATAAATTAAAAA
* *
59333067 TAAAAAAAAATAGAATATATAAATTGAAAA
1 TAAAAAAAAAGA-AATATATAAATTAAAAA
59333097 TAAAACAAAAA
1 TAAAA-AAAAA
59333108 ATTTAGTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
30 30 0.47
31 6 0.09
32 9 0.14
33 19 0.30
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (29 bp):
TAAAAAAAAAGAAATATATAAATTAAAAA
Found at i:59333576 original size:10 final size:10
Alignment explanation
Indices: 59333553--59333586 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
59333543 TTCTAATTTT
59333553 TTTTTTAAGA
1 TTTTTTAAGA
59333563 -TTTTTAAGA
1 TTTTTTAAGA
*
59333572 TTTTTTAAAA
1 TTTTTTAAGA
59333582 TTTTT
1 TTTTT
59333587 GTAGGAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (10 bp):
TTTTTTAAGA
Found at i:59337621 original size:11 final size:11
Alignment explanation
Indices: 59337566--59337621 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
59337556 TATTCTCTTG
59337566 TTATTTT-TTA
1 TTATTTTATTA
* *
59337576 TTGTTTTATTG
1 TTATTTTATTA
* *
59337587 TCATTTCATTA
1 TTATTTTATTA
* *
59337598 TTATATTACTA
1 TTATTTTATTA
59337609 TTATTTTATTA
1 TTATTTTATTA
59337620 TT
1 TT
59337622 TTTGTTTAGA
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
10 6 0.18
11 27 0.82
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:59338606 original size:12 final size:11
Alignment explanation
Indices: 59338598--59338658 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
59338588 TAAAAAAAGT
59338598 ATTTTAAAAAA
1 ATTTTAAAAAA
59338609 ATTTT---AAA
1 ATTTTAAAAAA
59338617 A--TTAAAAAA
1 ATTTTAAAAAA
*
59338626 ATTTAAAAAAA
1 ATTTTAAAAAA
59338637 GTATTTTAAAAAA
1 --ATTTTAAAAAA
*
59338650 AATTTAAAA
1 ATTTTAAAA
59338659 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
6 2 0.05
8 4 0.10
9 4 0.10
11 20 0.50
13 10 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:59338634 original size:17 final size:17
Alignment explanation
Indices: 59338601--59338634 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59338591 AAAAAGTATT
*
59338601 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAA
59338618 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
59338635 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:59338649 original size:42 final size:41
Alignment explanation
Indices: 59338565--59338707 Score: 196
Period size: 41 Copynumber: 3.4 Consensus size: 41
59338555 CCAAAAAATT
*
59338565 ATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAAA
1 ATTTT-AAAATT-AAA-AAAATTTAAAAAAAGTATTTTAAAAAA
59338609 ATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAAA
1 ATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAAA
* * **
59338650 AATTTAAAATTAAAAAAATTAAAAAAAAAGTATTTTAAAAGT
1 ATTTTAAAATTAAAAAAATT-TAAAAAAAGTATTTTAAAAAA
*
59338692 ATTTTAAAGTTAAAAA
1 ATTTTAAAATTAAAAA
59338708 TAAAAAATAA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
41 45 0.49
42 35 0.38
43 6 0.07
44 5 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (41 bp):
ATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAAA
Found at i:59338689 original size:11 final size:11
Alignment explanation
Indices: 59338675--59338699 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59338665 AAATTAAAAA
59338675 AAAAGTATTTT
1 AAAAGTATTTT
59338686 AAAAGTATTTT
1 AAAAGTATTTT
59338697 AAA
1 AAA
59338700 GTTAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:59338720 original size:13 final size:13
Alignment explanation
Indices: 59338702--59338727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59338692 ATTTTAAAGT
59338702 TAAAAATAAAAAA
1 TAAAAATAAAAAA
59338715 TAAAAATAAAAAA
1 TAAAAATAAAAAA
59338728 ATTTATTATT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:59338748 original size:5 final size:5
Alignment explanation
Indices: 59338738--59338769 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
59338728 ATTTATTATT
59338738 CGGGC CGGGC CGGGC CGGGC CGGGCC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC C
59338770 AAAAAAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.44, G:0.56, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:59340991 original size:7 final size:7
Alignment explanation
Indices: 59340979--59341011 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
59340969 CTTCCAAACA
59340979 CAAAAGC
1 CAAAAGC
59340986 CAAAAGC
1 CAAAAGC
*
59340993 CAAAATC
1 CAAAAGC
59341000 CAAAAGC
1 CAAAAGC
59341007 CAAAA
1 CAAAA
59341012 ACACCTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.27, G:0.09, T:0.03
Consensus pattern (7 bp):
CAAAAGC
Found at i:59347895 original size:20 final size:20
Alignment explanation
Indices: 59347866--59347905 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
59347856 TTCACCTCAT
59347866 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
*
59347886 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
59347906 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:59349868 original size:22 final size:22
Alignment explanation
Indices: 59349843--59349922 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
59349833 ATTCGTTAGC
* * *
59349843 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
59349865 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
*
59349887 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAAA
59349909 CATGAGAGCTTAGT
1 CATGAGAGCTTAGT
59349923 GAGTCTCCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:59354426 original size:2 final size:2
Alignment explanation
Indices: 59354419--59354446 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59354409 ACGTAGTGTT
59354419 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
59354447 CTGTGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:59364845 original size:16 final size:16
Alignment explanation
Indices: 59364808--59364847 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
59364798 TTAATAAAAT
* *
59364808 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
59364824 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
59364840 TAAAATTA
1 TAAAATTA
59364848 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:59364847 original size:22 final size:22
Alignment explanation
Indices: 59364780--59364832 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
59364770 CGTTTTGCAT
* * *
59364780 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
59364802 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
59364824 TAAAATTAA
1 TAAAATTAA
59364833 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:59364932 original size:9 final size:9
Alignment explanation
Indices: 59364920--59364956 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
59364910 TTTATCAAAT
59364920 TATTAATTG
1 TATTAATTG
59364929 TATTAATTG
1 TATTAATTG
59364938 --TTAATTG
1 TATTAATTG
59364945 TATTAATTG
1 TATTAATTG
59364954 TAT
1 TAT
59364957 GGAACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
9 19 0.73
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:59364953 original size:16 final size:16
Alignment explanation
Indices: 59364917--59364954 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
59364907 AAATTTATCA
*
59364917 AATTATTAATTGTATT
1 AATTGTTAATTGTATT
59364933 AATTGTTAATTGTATT
1 AATTGTTAATTGTATT
59364949 AATTGT
1 AATTGT
59364955 ATGGAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (16 bp):
AATTGTTAATTGTATT
Found at i:59365754 original size:2 final size:2
Alignment explanation
Indices: 59365747--59365772 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59365737 NNNNNNNNGA
59365747 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59365773 TCTAAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59366527 original size:202 final size:201
Alignment explanation
Indices: 59366182--59366587 Score: 751
Period size: 202 Copynumber: 2.0 Consensus size: 201
59366172 TTAATTCAAA
*
59366182 CTGTTTCTAAGAAAAAGTAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
1 CTGTTTCTAAGAAAAAGGAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
59366247 ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
66 ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
*
59366312 AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAATAGTG
131 AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAGTG
59366377 GGTAAT
196 GGTAAT
59366383 CTGTTTCTAAGAAAAAGGAAGAATTGTATTAAATATCCTCCATT-AGCATGAATCACTACTGACT
1 CTGTTTCTAAGAAAAAGGAAGAATTGTATT-AATATCCTCCATTGA-CATGAATCACTACTGACT
59366447 CTACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAAC
64 CTACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAAC
* *
59366512 AAAACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCGAATCATCTTGAGAGGTAAAAGAG
129 AAAACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAG
59366577 TGGGTAAT
194 TGGGTAAT
59366585 CTG
1 CTG
59366588 CAGAAAGTGG
Statistics
Matches: 199, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
201 30 0.15
202 169 0.85
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (201 bp):
CTGTTTCTAAGAAAAAGGAAGAATTGTATTAATATCCTCCATTGACATGAATCACTACTGACTCT
ACCCTCTAATATTTTCATAGTATCAACCACTAAATACATGCATAAAACAAAAATTAAGTAAACAA
AACACATCATGCCTGTATGTTTTGTAACTAAAATTAAGCAAATCATCTTGAGAGCTAAAAGAGTG
GGTAAT
Found at i:59369009 original size:22 final size:22
Alignment explanation
Indices: 59368964--59369009 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
59368954 ATAAATTGAG
* *
59368964 AATAACATTAAAACAAGAAGAA
1 AATAACATTAAAACAACAAAAA
* *
59368986 AATAGCATTGAAACAACAAAAA
1 AATAACATTAAAACAACAAAAA
59369008 AA
1 AA
59369010 ACAACAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (22 bp):
AATAACATTAAAACAACAAAAA
Found at i:59371769 original size:28 final size:29
Alignment explanation
Indices: 59371710--59371770 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
59371700 AAAATTGCAG
* *
59371710 AAAAAATTGTAAAATTTATTAAACATTAT
1 AAAAAATTGTAAAATTTATTAAAAATCAT
*
59371739 AAAAAATTG-AACAA-TTATTAAAAATCGT
1 AAAAAATTGTAA-AATTTATTAAAAATCAT
59371767 AAAA
1 AAAA
59371771 TTATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAAATTGTAAAATTTATTAAAAATCAT
Found at i:59371829 original size:18 final size:18
Alignment explanation
Indices: 59371734--59371832 Score: 68
Period size: 18 Copynumber: 5.7 Consensus size: 18
59371724 TTTATTAAAC
59371734 ATTATAAAAAATTGAACA
1 ATTATAAAAAATTGAACA
* *
59371752 ATTATTAAAAATCGTAA-A
1 ATTATAAAAAATTG-AACA
*
59371770 ATTATAATAAA---AA-A
1 ATTATAAAAAATTGAACA
* * *
59371784 ACTGTAAAAATATTAAAC-
1 ATTATAAAAA-ATTGAACA
59371802 ATT-TAGAAAAATTGAACA
1 ATTATA-AAAAATTGAACA
59371820 ATTATAAAAAATT
1 ATTATAAAAAATT
59371833 TAAAAAGTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
17 8 0.13
18 40 0.63
19 4 0.06
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
ATTATAAAAAATTGAACA
Found at i:59371865 original size:18 final size:18
Alignment explanation
Indices: 59371825--59371865 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
59371815 GAACAATTAT
* *
59371825 AAAAAATTTAAAAAGTAG
1 AAAAAATTTAAAAACTAA
*
59371843 TAAAAATTTAAAAACTAA
1 AAAAAATTTAAAAACTAA
59371861 AAAAA
1 AAAAA
59371866 TATATGTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAAATTTAAAAACTAA
Found at i:59371904 original size:29 final size:29
Alignment explanation
Indices: 59371845--59371906 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
59371835 AAAAGTAGTA
**
59371845 AAAATTTAAAAACTAAAAAAATATATGTT
1 AAAATTTAAAAACTAAAAAAATATAAATT
* *
59371874 AAAATTTGAAAATTATAAAAAAT-TAAATT
1 AAAATTTAAAAACTA-AAAAAATATAAATT
59371903 AAAA
1 AAAA
59371907 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATTTAAAAACTAAAAAAATATAAATT
Found at i:59390553 original size:28 final size:29
Alignment explanation
Indices: 59390503--59390557 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
59390493 TTAAAAGTTA
*
59390503 AAAATTTAATTTTTTTTGAATTTTTATTG
1 AAAATATAATTTTTTTTGAATTTTTATTG
59390532 AAAATATAATTTTTTTT-AATTTTTAT
1 AAAATATAATTTTTTTTGAATTTTTAT
59390558 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
AAAATATAATTTTTTTTGAATTTTTATTG
Found at i:59396649 original size:37 final size:37
Alignment explanation
Indices: 59396599--59396673 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
59396589 CCAAGTTGAA
59396599 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
1 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
*
59396636 TACTTATTCCAAATTGTTTAGGAAAAGGATTCTTTTT
1 TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
59396673 T
1 T
59396674 GTTAAGTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (37 bp):
TACTTATTCCAAATTGTTTAGCAAAAGGATTCTTTTT
Found at i:59397846 original size:15 final size:17
Alignment explanation
Indices: 59397816--59397847 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
59397806 ATGTCGCCAA
59397816 TTTTGTACTGTGTTTGT
1 TTTTGTACTGTGTTTGT
59397833 TTTTG-ACT-TGTTTGT
1 TTTTGTACTGTGTTTGT
59397848 GATCCTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (17 bp):
TTTTGTACTGTGTTTGT
Found at i:59402343 original size:7 final size:6
Alignment explanation
Indices: 59402304--59402341 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
59402294 CTTTTTTCCC
*
59402304 AAAA-A AAAA-A AAAAGA AAAAGG AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
59402342 AGGGAACTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:59403133 original size:183 final size:183
Alignment explanation
Indices: 59402821--59403558 Score: 1196
Period size: 183 Copynumber: 4.0 Consensus size: 183
59402811 CTGTCATACC
* * * **
59402821 CTCAGTTGTAGCTGGTTTCAGAGTCAATTCTACACTCGGACTCAGTCTAGGCC-CTTTTGTCTTG
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTC-TTCATCTTG
* *
59402885 TGTCTTGCTATATCTTGGGAAGTGCTG-TGGTTGGTTGGTATGTGCTCCTTGGT-GATGCTGGGG
65 TATCTTGCTATATCTTGGGAAGTGCTGTTGG-TGGTTGGTATGTGCTCCTT-GTCGATGCCGGGG
*
59402948 GTTGTAGTTGCAGTGATTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
128 GTTGTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
59403004 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
59403069 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
* * *
59403134 GTAGTTGCCGTGGTTTGACCTAGTTCATGGTTCTGGACATCTGCCAAATGATA
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
*
59403187 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCAAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
* * *
59403252 ATCTTGCTATATCTAGGGAAGTACTGTTGGTGGTTGGTGTGTGCTCCTTGTCGATGCCGGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
*
59403317 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATAATA
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
59403370 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
1 CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
* *
59403435 ATCTTGCAATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCAGGGGTT
66 ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
* * * * * *
59403500 GTAGTTGCAGTGGTTTGGCCTAGTTCATGGCTT-AAGACCTCTGCCGAATGATC
131 GTAGTTGCAGTGGTTCGACCTAGTTCATGG-TTCAGGACATCTGCCAAATGATA
59403553 CTCAGT
1 CTCAGT
59403559 CTCAGAAGGC
Statistics
Matches: 519, Mismatches: 32, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
182 2 0.00
183 511 0.98
184 6 0.01
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (183 bp):
CTCAGTTGTAGTTGGTTTCAGAGTCAATTCTAAACTCGAACTCAGTCTAGGCCTCTTCATCTTGT
ATCTTGCTATATCTTGGGAAGTGCTGTTGGTGGTTGGTATGTGCTCCTTGTCGATGCCGGGGGTT
GTAGTTGCAGTGGTTCGACCTAGTTCATGGTTCAGGACATCTGCCAAATGATA
Found at i:59404871 original size:259 final size:259
Alignment explanation
Indices: 59404412--59404934 Score: 1010
Period size: 259 Copynumber: 2.0 Consensus size: 259
59404402 CATTATTATT
*
59404412 ATACTCCAAAAAAATGTCAATTCCCTGGATGACGTCTGCCCTTGTCTGGGGAATACTTGTTTCAA
1 ATACTCCAAAAAAATGTCAATTCCCTGGATGACGGCTGCCCTTGTCTGGGGAATACTTGTTTCAA
59404477 TGGCGCGAGTGCCCCGTTGTAAGAAGCATGGATTGCTGCTTTTCGTGGTAGGTTTTCGTCGCCCA
66 TGGCGCGAGTGCCCCGTTGTAAGAAGCATGGATTGCTGCTTTTCGTGGTAGGTTTTCGTCGCCCA
59404542 AAAAAGAGAAGCAGGTCGGTCGTTGCTGTACGACTCATTTTTTTTCTTTGGGGTCGCGCGGCTGT
131 AAAAAGAGAAGCAGGTCGGTCGTTGCTGTACGACTCATTTTTTTTCTTTGGGGTCGCGCGGCTGT
*
59404607 TGAGTGATGTCTTCTAGATTCGAGTATTTATTGGTGAGAGGTAGAAGGGAGGATTAGTAGAGCG
196 TGAGTGATGTCTTCTAGATTCGAGTATTTATTGGTGAGAGGTAAAAGGGAGGATTAGTAGAGCG
59404671 ATACTCCAAAAAAATGTCAATTCCCTGGATGACGGCTGCCCTTGTCTGGGGAATACTTGTTTCAA
1 ATACTCCAAAAAAATGTCAATTCCCTGGATGACGGCTGCCCTTGTCTGGGGAATACTTGTTTCAA
* *
59404736 TGGCGCGAGTGCCCGGTTGTAAGAAGCGTGGATTGCTGCTTTTCGTGGTAGGTTTTCGTCGCCCA
66 TGGCGCGAGTGCCCCGTTGTAAGAAGCATGGATTGCTGCTTTTCGTGGTAGGTTTTCGTCGCCCA
59404801 AAAAAGAGAAGCAGGTCGGTCGTTGCTGTACGACTCATTTTTTTTCTTTGGGGTCGCGCGGCTGT
131 AAAAAGAGAAGCAGGTCGGTCGTTGCTGTACGACTCATTTTTTTTCTTTGGGGTCGCGCGGCTGT
59404866 TGAGTGATGTCTTCTAGATTCGAGTATTTATTGGTGAGAGGTAAAAGGGAGGATTAGTAGAGCG
196 TGAGTGATGTCTTCTAGATTCGAGTATTTATTGGTGAGAGGTAAAAGGGAGGATTAGTAGAGCG
59404930 ATACT
1 ATACT
59404935 GCCGCACCAA
Statistics
Matches: 260, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 260 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (259 bp):
ATACTCCAAAAAAATGTCAATTCCCTGGATGACGGCTGCCCTTGTCTGGGGAATACTTGTTTCAA
TGGCGCGAGTGCCCCGTTGTAAGAAGCATGGATTGCTGCTTTTCGTGGTAGGTTTTCGTCGCCCA
AAAAAGAGAAGCAGGTCGGTCGTTGCTGTACGACTCATTTTTTTTCTTTGGGGTCGCGCGGCTGT
TGAGTGATGTCTTCTAGATTCGAGTATTTATTGGTGAGAGGTAAAAGGGAGGATTAGTAGAGCG
Found at i:59420101 original size:37 final size:37
Alignment explanation
Indices: 59420051--59420123 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
59420041 CATTGTTGTA
59420051 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
1 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
59420088 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTT
1 CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTT
59420124 CTTAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (37 bp):
CCAAAAGAAAGGTCGAGCATTGCAAAAATCCACTTTT
Found at i:59420901 original size:22 final size:22
Alignment explanation
Indices: 59420876--59420925 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
59420866 GTCCAGGTTG
* *
59420876 GGTGTCCTGACATCATATGGCT
1 GGTGTCCTAACATCACATGGCT
*
59420898 GGTGTCGTAACATCACATGGCT
1 GGTGTCCTAACATCACATGGCT
59420920 GGTGTC
1 GGTGTC
59420926 ATCACATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (22 bp):
GGTGTCCTAACATCACATGGCT
Found at i:59420932 original size:22 final size:22
Alignment explanation
Indices: 59420876--59420932 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
59420866 GTCCAGGTTG
* * *
59420876 GGTGTCCTGACATCATATGGCT
1 GGTGTCATAACATCACATGGCT
*
59420898 GGTGTCGTAACATCACATGGCT
1 GGTGTCATAACATCACATGGCT
*
59420920 GGTGTCATCACAT
1 GGTGTCATAACAT
59420933 TGATGTCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (22 bp):
GGTGTCATAACATCACATGGCT
Found at i:59426108 original size:28 final size:27
Alignment explanation
Indices: 59426076--59426134 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
59426066 TGAAGGAGAT
59426076 AAGACAAAGGATTTAATGGCTGAGCTAG
1 AAGACAAAGGATTTAATGGCT-AGCTAG
* * * *
59426104 AAGACTAAGTATTTCATGGCTAGCTTG
1 AAGACAAAGGATTTAATGGCTAGCTAG
59426131 AAGA
1 AAGA
59426135 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
AAGACAAAGGATTTAATGGCTAGCTAG
Found at i:59427445 original size:22 final size:22
Alignment explanation
Indices: 59427420--59427476 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
59427410 CGTCCAGGTT
59427420 TGGTGTCATGACACCACATGGC
1 TGGTGTCATGACACCACATGGC
** * *
59427442 TGGTGTCGCGACATCACTTGGC
1 TGGTGTCATGACACCACATGGC
*
59427464 TGGTGTGATGACA
1 TGGTGTCATGACA
59427477 TTGATTGTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (22 bp):
TGGTGTCATGACACCACATGGC
Found at i:59432447 original size:22 final size:23
Alignment explanation
Indices: 59432421--59432467 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
59432411 TTGTTTCCTT
*
59432421 TTGCTTCTCGATTCTTGTT-CTG
1 TTGCTTCTCAATTCTTGTTGCTG
* *
59432443 TTGCTTGTCAATTTTTGTTGCTG
1 TTGCTTCTCAATTCTTGTTGCTG
59432466 TT
1 TT
59432468 TTTAGAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.06, C:0.17, G:0.19, T:0.57
Consensus pattern (23 bp):
TTGCTTCTCAATTCTTGTTGCTG
Found at i:59437432 original size:50 final size:50
Alignment explanation
Indices: 59437367--59437549 Score: 188
Period size: 50 Copynumber: 3.6 Consensus size: 50
59437357 TTCGATATAT
* * * * *
59437367 GTAGTAGCATTCACATTGTACTACACACGTGATCAAACTTTTCGGTTCAC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTCGGTACAC
* * * *
59437417 GTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCAGTACGC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATC-AAACTATTCGGTACAC
* * * * ***
59437468 ATAGTAGCCTGCACATAGTACTACACATGCGACCTTTC-ATTCAGGTACAC
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTC-GGTACAC
*
59437518 GTAGTAGCCTACACATAGTACTACACACGTGA
1 GTAGTAGCCTGCACATAGTACTACACACGTGA
59437550 CTATCACTTT
Statistics
Matches: 108, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 3 0.03
50 65 0.60
51 40 0.37
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATTCGGTACAC
Found at i:59448154 original size:57 final size:57
Alignment explanation
Indices: 59448049--59448157 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
59448039 TGGTATCCAT
*
59448049 CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTGCTTGGAACTAAAA
1 CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTACTTGGAACTAAAA
* * * *
59448106 CACCGGTACATAGTACCTGGAACTTTAATCGTT-G-ACAACTAGTACTTGGAAC
1 CACCGATACATAGTACATGGAACTGTAATCATTAGCAC-A-TAGTACTTGGAAC
59448158 GCCCTAATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 2 0.04
57 41 0.91
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (57 bp):
CACCGATACATAGTACATGGAACTGTAATCATTAGCACATAGTACTTGGAACTAAAA
Found at i:59450028 original size:67 final size:67
Alignment explanation
Indices: 59449920--59450145 Score: 296
Period size: 67 Copynumber: 3.4 Consensus size: 67
59449910 GAGGTTTAAG
* * *
59449920 GTGTAAGACCATATCTCGACTAT-AGCAACCA-ATAGAGTCCGCCAAGACATTAAATATGGGGTT
1 GTGTAAGACCATAGCTCGACTATGA-CAA-CATGTGGAGTCCGCCAAGACATTAAATATGGGGTT
59449983 ACAT
64 ACAT
*
59449987 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGATATT-AATCATGGGGTTA
1 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAAT-ATGGGGTTA
59450051 CAT
65 CAT
* * * * *
59450054 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCCGTCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAATATGGGGTTAC
59450119 AT
66 AT
* * *
59450121 GGGTAATACCATAGCTCAACTATGA
1 GTGTAAGACCATAGCTCGACTATGA
59450146 TAATAGATAA
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
66 5 0.04
67 132 0.94
68 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (67 bp):
GTGTAAGACCATAGCTCGACTATGACAACATGTGGAGTCCGCCAAGACATTAAATATGGGGTTAC
AT
Found at i:59452786 original size:4 final size:4
Alignment explanation
Indices: 59452777--59452808 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
59452767 ACGAGGAAAA
59452777 ATTT ATTT ATTT ATTT ATTT ATTT ATTAT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATT
59452809 CTTATGGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:59455591 original size:42 final size:42
Alignment explanation
Indices: 59455536--59455638 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
59455526 AACCTGTAAG
* * **
59455536 GGTTGAACGGAAGCTCATCGGAGCTGAACGAAAACCCATAAA
1 GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
* * * *
59455578 GGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACCCATTAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
*
59455620 GGTTAAACAGAAACTCATA
1 GGTTAAACAGAAGCTCATA
59455639 TGAGTTAACA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTGAACGAAAACCCATAAA
Found at i:59460451 original size:57 final size:57
Alignment explanation
Indices: 59460287--59460436 Score: 266
Period size: 57 Copynumber: 2.6 Consensus size: 57
59460277 GGGTGATCCT
**
59460287 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCAAACGGGTG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
59460344 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
*
59460401 ATCTTGATATAGCCCTCCTGAAGAATATGTG-GAAAA
1 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAA
59460437 TGGATTTAGC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
56 5 0.06
57 85 0.94
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (57 bp):
ATCTTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGATCTAACCCGGACGGGTG
Found at i:59462805 original size:2 final size:2
Alignment explanation
Indices: 59462751--59462795 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
59462741 AAACTACATA
59462751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59462793 AT A
1 AT A
59462796 ACATTATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59467068 original size:10 final size:10
Alignment explanation
Indices: 59467052--59467085 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
59467042 TAAAAAATAC
59467052 ATAAATATTT
1 ATAAATATTT
* *
59467062 TTAAATATAT
1 ATAAATATTT
59467072 ATAAATATTT
1 ATAAATATTT
59467082 ATAA
1 ATAA
59467086 TTAGGATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAAATATTT
Found at i:59469779 original size:14 final size:14
Alignment explanation
Indices: 59469760--59469788 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59469750 CTACTATTTC
59469760 ACTATTATGTTATT
1 ACTATTATGTTATT
59469774 ACTATTATGTTATT
1 ACTATTATGTTATT
59469788 A
1 A
59469789 TTGTTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (14 bp):
ACTATTATGTTATT
Found at i:59475296 original size:5 final size:5
Alignment explanation
Indices: 59475286--59475320 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
59475276 AAGTGAGTTG
*
59475286 TTATA TTATA TTATTA TAATA TTATA TTATA TTAT
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTAT
59475321 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:59475310 original size:21 final size:22
Alignment explanation
Indices: 59475286--59475329 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
59475276 AAGTGAGTTG
59475286 TTATATTATATTATTATA-ATA
1 TTATATTATATTATTATATATA
59475307 TTATATTATATTATTATATATA
1 TTATATTATATTATTATATATA
59475329 T
1 T
59475330 AAAGCAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATTATATTATTATATATA
Found at i:59475313 original size:13 final size:13
Alignment explanation
Indices: 59475297--59475331 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
59475287 TATATTATAT
59475297 TATTATAATATTA
1 TATTATAATATTA
*
59475310 TATTATATTATTA
1 TATTATAATATTA
59475323 TATATATAA
1 TAT-TATAA
59475332 AGCAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTATAATATTA
Found at i:59475396 original size:11 final size:11
Alignment explanation
Indices: 59475380--59475405 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59475370 AAATTGAAAC
59475380 GAAACAGGGGA
1 GAAACAGGGGA
59475391 GAAACAGGGGA
1 GAAACAGGGGA
59475402 GAAA
1 GAAA
59475406 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:59475607 original size:12 final size:13
Alignment explanation
Indices: 59475578--59475609 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59475568 TGTAGCTTAT
59475578 ATTGAATTAGTGG
1 ATTGAATTAGTGG
59475591 A-TGAATTAGT-G
1 ATTGAATTAGTGG
59475602 ATTGAATT
1 ATTGAATT
59475610 GATGGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (13 bp):
ATTGAATTAGTGG
Found at i:59476620 original size:25 final size:24
Alignment explanation
Indices: 59476529--59476684 Score: 228
Period size: 24 Copynumber: 6.5 Consensus size: 24
59476519 ACTTTAGCGC
59476529 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
59476553 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
59476577 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
59476601 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
59476626 GCTCTCTGATATTTAGCACGCCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
59476651 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
59476673 GCTCTCTG-TATT
1 GCTCTCTGATATT
59476685 TGTTCCGTAT
Statistics
Matches: 122, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
22 18 0.15
23 2 0.02
24 60 0.49
25 42 0.34
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:59485150 original size:41 final size:41
Alignment explanation
Indices: 59485089--59485170 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
59485079 TGTCTAGTTA
*
59485089 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTCATTTG
1 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
*
59485130 TTGGGATGAAAATAGGTTTTTAATTAAATAAATTTAATTTG
1 TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
59485171 GACTACCACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (41 bp):
TTGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTTG
Found at i:59489704 original size:3 final size:3
Alignment explanation
Indices: 59489696--59489726 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59489686 GCTCTGTGAG
59489696 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
59489727 GTCTGGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:59490504 original size:2 final size:2
Alignment explanation
Indices: 59490497--59490530 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
59490487 ATTTAGTCCT
59490497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59490531 ATTTTGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59491319 original size:9 final size:9
Alignment explanation
Indices: 59491299--59491334 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
59491289 TTTTTAAAAA
59491299 TAAAAATGAT
1 TAAAAAT-AT
59491309 TAAAAATAT
1 TAAAAATAT
59491318 TAAAAATAT
1 TAAAAATAT
59491327 ATAAAAAT
1 -TAAAAAT
59491335 TTTAGTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:59513853 original size:88 final size:88
Alignment explanation
Indices: 59513752--59513922 Score: 206
Period size: 88 Copynumber: 1.9 Consensus size: 88
59513742 TGAAGCCAAT
* * * *
59513752 AATTCTACTTCCCTG-GG-CAGCAGTGGAATAGATTGAAGATTTCAG-A-TCTTGTCTCCCTAAG
1 AATTCTACCTCCCTGTGGTCA-CAGTGGAATACATTGAAG---CCAGTATTCTTATCTCCCTAAG
59513813 CAGTAGTGGAGCAGATCAAAGATGGTG
62 CAGTAGTGGAGCAGATCAAAGATGGTG
* * *
59513840 AATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTATTCTTATCTCCCTAAGCAGT
1 AATTCTACCTCCCTGTGGTCACAGTGGAATACATTGAAGCCAGTATTCTTATCTCCCTAAGCAGT
*
59513905 AGTGGAGCAGATCGAAGA
66 AGTGGAGCAGATCAAAGA
59513923 CCCCAGTCTT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
86 3 0.04
87 1 0.01
88 48 0.68
89 18 0.25
90 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (88 bp):
AATTCTACCTCCCTGTGGTCACAGTGGAATACATTGAAGCCAGTATTCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGATGGTG
Found at i:59513909 original size:132 final size:132
Alignment explanation
Indices: 59513655--59513910 Score: 399
Period size: 132 Copynumber: 1.9 Consensus size: 132
59513645 GTTCCTCCAT
* *
59513655 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGCGGATTTTACCTCC
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCC
**
59513720 CCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGAT
66 CCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTAAGCAGCAGTGGAATAGAT
59513785 TG
131 TG
* *
59513787 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCC
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCC
* * *
59513852 CTGTGGTTACAGTGGAGTACATTGAAGCCAGT-ATTCTTA-TCTCCCTAAGCAGTAGTGGA
66 CCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTC-TACT-TCCCTAAGCAGCAGTGGA
59513911 GCAGATCGAA
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 5 0.04
132 108 0.96
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (132 bp):
AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCC
CCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTAAGCAGCAGTGGAATAGAT
TG
Found at i:59513953 original size:132 final size:132
Alignment explanation
Indices: 59513662--59513957 Score: 355
Period size: 132 Copynumber: 2.2 Consensus size: 132
59513652 CATAAGATTT
** * * *
59513662 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGCGGATTTTACCTCCCCGTGGT
1 CAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCCGTGGT
** * * *
59513727 TACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTAAGCAGCAGTGGAACAGATCGAAGAC
**
59513792 TT
131 CC
* * * *
59513794 CAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCCGTGGT
* * *
59513859 TACAGTGGAGTACATTGAAGCCAGT-ATTCTTA-TCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
66 TACAGTGGAGTACATTGAAGCCAATAATTC-TACT-TCCCTAAGCAGCAGTGGAACAGATCGAAG
59513922 ACCC
129 ACCC
**
59513926 CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 CAGATCTTATCTCCCT-AAGCAGCAGTGGAGCA
59513958 AACAGAAGTA
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
131 16 0.11
132 126 0.89
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (132 bp):
CAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCAAAGATGGCGAATTTTACCTCCCCGTGGT
TACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTAAGCAGCAGTGGAACAGATCGAAGAC
CC
Found at i:59515484 original size:3 final size:3
Alignment explanation
Indices: 59515469--59515525 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
59515459 TACTATGAAT
*
59515469 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59515517 TTA TTA TTA
1 TTA TTA TTA
59515526 CTGTACATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:59515620 original size:16 final size:16
Alignment explanation
Indices: 59515576--59515630 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
59515566 ACTTTTTATA
59515576 TTTATATTTT-TAC-T
1 TTTATATTTTATACAT
*
59515590 TTTCTAATATTTATACAT
1 TTTAT-AT-TTTATACAT
*
59515608 TTTATATTTTATATAT
1 TTTATATTTTATACAT
*
59515624 ATTATAT
1 TTTATAT
59515631 AACATATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 17 0.52
17 5 0.15
18 5 0.15
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATATTTTATACAT
Found at i:59515791 original size:16 final size:16
Alignment explanation
Indices: 59515758--59515791 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59515748 TATTGTACAC
**
59515758 ATATATATGTATTTGA
1 ATATATATGTATGCGA
59515774 ATATATATGTATGCGA
1 ATATATATGTATGCGA
59515790 AT
1 AT
59515792 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:59518926 original size:9 final size:8
Alignment explanation
Indices: 59518909--59518933 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
59518899 CCTGCCCGAT
59518909 AATAAAAA
1 AATAAAAA
59518917 AATAAAAA
1 AATAAAAA
59518925 AATAAAAA
1 AATAAAAA
59518933 A
1 A
59518934 TAGTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:59521960 original size:48 final size:47
Alignment explanation
Indices: 59521902--59522054 Score: 198
Period size: 48 Copynumber: 3.2 Consensus size: 47
59521892 AACAACATTC
59521902 GGACAGCATTAATTTGTACAAAAATGGACAGCATTTAAGCACCAATTT
1 GGACAGCATTAATTTGT-CAAAAATGGACAGCATTTAAGCACCAATTT
* ** * * *
59521950 GGACAACATTAATATACTCAAAAATGGACAGCAATTAATCATCAATTT
1 GGACAGCATTAAT-TTGTCAAAAATGGACAGCATTTAAGCACCAATTT
* * *
59521998 GGACAGCATTAATATGCTCAAAAATGGATAGCATTTAAGCACTAATTT
1 GGACAGCATTAATTTG-TCAAAAATGGACAGCATTTAAGCACCAATTT
59522046 GGACAGCAT
1 GGACAGCAT
59522055 CTTATCATCA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 86 0.98
49 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (47 bp):
GGACAGCATTAATTTGTCAAAAATGGACAGCATTTAAGCACCAATTT
Found at i:59521988 original size:26 final size:25
Alignment explanation
Indices: 59521949--59522032 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
59521939 AGCACCAATT
*
59521949 TGGACAACATTAATATACTCAAAAA
1 TGGACAGCATTAATATACTCAAAAA
* **
59521974 TGGACAGCAATTAAT-CA-TC-AATT
1 TGGACAGC-ATTAATATACTCAAAAA
*
59521997 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATACTCAAAAA
*
59522022 TGGATAGCATT
1 TGGACAGCATT
59522033 TAAGCACTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 6 0.13
23 10 0.22
24 4 0.09
25 20 0.43
26 6 0.13
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (25 bp):
TGGACAGCATTAATATACTCAAAAA
Found at i:59522053 original size:23 final size:23
Alignment explanation
Indices: 59521926--59522054 Score: 73
Period size: 23 Copynumber: 5.4 Consensus size: 23
59521916 TGTACAAAAA
*
59521926 TGGACAGCATTTAAGCACCAATT
1 TGGACAGCATTTAAGCACAAATT
* * **
59521949 TGGACAACATTAATATA-CTCAAAAA
1 TGGACAGCATT--TA-AGCACAAATT
* *
59521974 TGGACAGCAATTAATCATC-AATT
1 TGGACAGCATTTAAGCA-CAAATT
* * **
59521997 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATT--TAAGCACAAATT
* *
59522022 TGGATAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACAAATT
59522045 TGGACAGCAT
1 TGGACAGCAT
59522055 CTTATCATCA
Statistics
Matches: 75, Mismatches: 23, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
22 1 0.01
23 41 0.55
24 2 0.03
25 30 0.40
26 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACAAATT
Found at i:59524685 original size:12 final size:12
Alignment explanation
Indices: 59524670--59524695 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59524660 AATCTTGATG
59524670 AAAATCTGCTTC
1 AAAATCTGCTTC
59524682 AAAATCTGCTTC
1 AAAATCTGCTTC
59524694 AA
1 AA
59524696 TGGTGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAATCTGCTTC
Found at i:59530596 original size:22 final size:23
Alignment explanation
Indices: 59530559--59530601 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
59530549 ACTATTTGGT
*
59530559 AGTTTGACTTTTTTTATATTTAA
1 AGTTTGACCTTTTTTATATTTAA
59530582 AGTTT-ACCTTTTTTATATTT
1 AGTTTGACCTTTTTTATATTT
59530602 GGAATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (23 bp):
AGTTTGACCTTTTTTATATTTAA
Found at i:59530609 original size:22 final size:23
Alignment explanation
Indices: 59530568--59530617 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
59530558 TAGTTTGACT
59530568 TTTTTTATATTTAAAGTTTA-CC
1 TTTTTTATATTTAAAGTTTATCC
*
59530590 TTTTTTATATTTGGAA-TTTATCC
1 TTTTTTATATTT-AAAGTTTATCC
59530613 TTTTT
1 TTTTT
59530618 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTTTATATTTAAAGTTTATCC
Found at i:59541613 original size:9 final size:10
Alignment explanation
Indices: 59541586--59541614 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
59541576 AATCATATCA
59541586 TTTAGAAAAT
1 TTTAGAAAAT
59541596 TTTAGAAAAT
1 TTTAGAAAAT
59541606 TTTA-AAAAT
1 TTTAGAAAAT
59541615 AATTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
TTTAGAAAAT
Found at i:59542607 original size:22 final size:22
Alignment explanation
Indices: 59542579--59542622 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59542569 CAAAAAGAAA
59542579 AAAAAAAGCATTTTTTTTCAAT
1 AAAAAAAGCATTTTTTTTCAAT
59542601 AAAAAAAGCATTTTTTTTCAAT
1 AAAAAAAGCATTTTTTTTCAAT
59542623 CTTGAGATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAAAAAGCATTTTTTTTCAAT
Found at i:59549013 original size:107 final size:106
Alignment explanation
Indices: 59548788--59549058 Score: 314
Period size: 107 Copynumber: 2.5 Consensus size: 106
59548778 TTTTCGAGTA
* * ** *
59548788 TTGGTCTATCAATGGCCGGCACCAAAATACGAAAAAAG-TAAGAAATTTTTTTTTGTGGTGGCCT
1 TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAGTTAA-AAA-AATTTTTGGTGGTGGCCT
* * * **
59548852 GCCAATGGCCGGCACCACCTTTATGGAATTTTTTTTTTATATT
64 ACCAATGGCCAGCAACACCTTTATCAAATTTTTTTTTTATATT
* * * **
59548895 TT-TTCATGTCAATGGCAGGCACTAATATACGAAAAAAGTTAAAAAAAAATTTGGTGGTGGCCTA
1 TTGGTC-TGTCAATGGCCGGCACCAATATACGAAAAAAGTTAAAAAAATTTTTGGTGGTGGCCTA
*
59548959 CCAATGGCCAGCAACACCTTT-TCCAAATTTTTTTTTTTTACTT
65 CCAATGGCCAGCAACACCTTTAT-CAAATTTTTTTTTTATA-TT
*
59549002 TTGGTCTGTCAATGGCCGGCACCAGTATACGAAAAAAGTTTAAAAAAATTTTTGGTG
1 TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAG-TTAAAAAAATTTTTGGTG
59549059 ACAACCTCCA
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
105 1 0.01
106 48 0.35
107 66 0.49
108 21 0.15
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (106 bp):
TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAGTTAAAAAAATTTTTGGTGGTGGCCTAC
CAATGGCCAGCAACACCTTTATCAAATTTTTTTTTTATATT
Found at i:59550617 original size:107 final size:106
Alignment explanation
Indices: 59550456--59550900 Score: 476
Period size: 107 Copynumber: 4.2 Consensus size: 106
59550446 AAATTGTTGT
* * *
59550456 AAAGGTGGTGCCGGCCATTGGTAAGCCACCACCAAAATTTCTTTTTTTATTTTTTTCGTATACTG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTT-TTTTTTTACTTTTTTCGTATACTG
*
59550521 GTGACGACCATTGACAGACCAAAAGTAAAAAAAACATTTGGAA
65 GTGACGACCATTGACAAACCAAAAGTAAAAAAAA-ATTTGGAA
* * *
59550564 AAAGGTAGTGCCGGTCATTGGCAGGCCACCACCCAAATTTTTTTTTTACTTTTTTCGTATACTGG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
* *
59550629 TGCCGACCATTGACAAACCAAAAGTAAAAAAAAAAATTGGAA
66 TGACGACCATTGACAAACCAAAAGT-AAAAAAAAATTTGGAA
* *
59550671 AAAGGTGGTGCCGACCATTGGTAGGCC-CCAACCAAAATTTTTTTTTTAACTTTTTTCGTATACT
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACC-ACCAAAATTTTTTTTTT-ACTTTTTTCGTATACT
* * *** *
59550735 GGTGTCTG-CCATTGACACAA-AAAAAGTAAAAAAAAATTCCCAT
64 GGTGAC-GACCATTGACA-AACCAAAAGTAAAAAAAAATTTGGAA
***** ** *
59550778 AAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAAAAAAAATTTAAACTTTTTTCGTATACTAG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
* *
59550842 TGATTG-CCATTGACACGAA--AAAAGTAAAAAAAAATTCT-CATA
66 TGA-CGACCATTGACA--AACCAAAAGTAAAAAAAAATT-TGGA-A
59550884 AAA-GTGGTGCCGGCCAT
1 AAAGGTGGTGCCGGCCAT
59550901 GGACAGACCA
Statistics
Matches: 291, Mismatches: 36, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
105 62 0.21
106 15 0.05
107 130 0.45
108 81 0.28
109 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (106 bp):
AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
TGACGACCATTGACAAACCAAAAGTAAAAAAAAATTTGGAA
Found at i:59550875 original size:215 final size:214
Alignment explanation
Indices: 59550456--59550875 Score: 512
Period size: 215 Copynumber: 2.0 Consensus size: 214
59550446 AAATTGTTGT
* *
59550456 AAAGGTGGTGCCGGCCATTGGTAAGCCACCACCAAAATTTCTTTTTTTATTTTTTTCGTATACTG
1 AAAGGTGGTGCCGACCATTGGTAAGCCACCACCAAAATTTCTTTTTTTACTTTTTTCGTATACTG
* ** *** *
59550521 GTGACGACCATTGACAGACCAAAAGTAAAAAAAACATTTGGAAAAAGGTAGTGCCGGTCATTGGC
66 GTGACGACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATTGGC
* ***** ** *
59550586 AGGCCACCACCCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCGACCATTGACAAACCAAA
131 AGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACAAA-CAAA
59550651 AGTAAAAAAAAAAATTGGAA
195 AGTAAAAAAAAAAATTGGAA
*
59550671 AAAGGTGGTGCCGACCATTGGTAGGCC-CCAACCAAAATTT-TTTTTTTAACTTTTTTCGTATAC
1 AAAGGTGGTGCCGACCATTGGTAAGCCACC-ACCAAAATTTCTTTTTTT-ACTTTTTTCGTATAC
* * *
59550734 TGGTGTCTG-CCATTGACACAAAAAAAGTAAAAAAAA-ATTCCCATAAAGGTGGTGCCGGCCATT
64 TGGTGAC-GACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATT
**
59550797 GGCAGGCCACCA-CAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGATTG-CCATTGACACGA
128 GGCAGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTG-CCGACCATTGACA--A
59550860 A-AAAAGTAAAAAAAAA
190 ACAAAAGTAAAAAAAAA
59550876 TTCTCATAAA
Statistics
Matches: 175, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
213 50 0.29
214 43 0.25
215 81 0.46
216 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (214 bp):
AAAGGTGGTGCCGACCATTGGTAAGCCACCACCAAAATTTCTTTTTTTACTTTTTTCGTATACTG
GTGACGACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATTGGC
AGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACAAACAAAA
GTAAAAAAAAAAATTGGAA
Found at i:59550900 original size:49 final size:48
Alignment explanation
Indices: 59550847--59550950 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 48
59550837 ACTAGTGATT
* *
59550847 GCCATTGACACGA-AAAAAGTAAAAAAAAATTCTCATAAAAGTGGTGCCG
1 GCCATTGACA-GACAAAAAGTAAAAAAAAATT-GCAAAAAAGTGGTGCCG
* * *
59550896 GCCATGGACAGACCAAAAGTAAAAAAAAATTGGAAAAAAGTGGTGCCG
1 GCCATTGACAGACAAAAAGTAAAAAAAAATTGCAAAAAAGTGGTGCCG
59550944 GCCATTG
1 GCCATTG
59550951 GCAGGCCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 22 0.46
49 26 0.54
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (48 bp):
GCCATTGACAGACAAAAAGTAAAAAAAAATTGCAAAAAAGTGGTGCCG
Found at i:59550920 original size:105 final size:105
Alignment explanation
Indices: 59550718--59550926 Score: 305
Period size: 105 Copynumber: 2.0 Consensus size: 105
59550708 TTTTTTTTTT
* *
59550718 AACTTTTTTCGTATACTGGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAGG
1 AACTTTTTTCGTATACTAGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAAG
* **
59550783 TGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATTTA
66 TGGTGCCGGCCATTGGCAGACCAAAACAAAAAAAAATTTA
* *
59550823 AACTTTTTTCGTATACTAGTGAT-TGCCATTGACACGAAAAAAGTAAAAAAAAATTCTCATAAAA
1 AACTTTTTTCGTATACTAGTG-TCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAA
*
59550887 GTGGTGCCGGCCA-TGGACAGACCAAAAGTAAAAAAAAATT
65 GTGGTGCCGGCCATTGG-CAGACCAAAA-CAAAAAAAAATT
59550927 GGAAAAAAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
104 3 0.03
105 78 0.84
106 12 0.13
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (105 bp):
AACTTTTTTCGTATACTAGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAAG
TGGTGCCGGCCATTGGCAGACCAAAACAAAAAAAAATTTA
Found at i:59551016 original size:151 final size:153
Alignment explanation
Indices: 59550756--59551062 Score: 431
Period size: 151 Copynumber: 2.0 Consensus size: 153
59550746 TTGACACAAA
* *
59550756 AAAAGTAAAAAAAAATTCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATT
1 AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAA-T
* * *
59550821 TAAACTTTTTTCGTATACTAGTGATTGCCATTGACACGAAAAAAGTAAAAAAAAATTCTCATAAA
65 TAAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAA
*
59550886 AGTGGTGCCGGCCATGGACAGACC
130 AGTGGTGCCAGCCATGGACAGACC
**
59550910 AAAAGTAAAAAAAAATT-GGAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAAAA-
1 AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCA-CAAAAAAAAAT
* * * * *
59550973 T-AACTTTTTTCGTATACTGGTGCCTGCTATTGATACGAAAAAAGTAAAAAAAATTTCCCACAAA
65 TAAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAA
* * *
59551037 GGTGGTGCCAGCTATTGACAGACC
130 AGTGGTGCCAGCCATGGACAGACC
59551061 AA
1 AA
59551063 TACCTGAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
151 77 0.57
152 1 0.01
153 31 0.23
154 27 0.20
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATT
AAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAAA
GTGGTGCCAGCCATGGACAGACC
Found at i:59562226 original size:2 final size:2
Alignment explanation
Indices: 59562219--59562244 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59562209 GAAAGAGAAC
59562219 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
59562245 ATGAGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:59568532 original size:20 final size:20
Alignment explanation
Indices: 59568490--59568532 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
59568480 TTAAAATTAG
*
59568490 AAAATATCAAAATTTAGTTT
1 AAAATATCAAAATTTAGTAT
*
59568510 AAAATATTAAAATATTA-TAT
1 AAAATATCAAAAT-TTAGTAT
59568530 AAA
1 AAA
59568533 TCATTACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATATCAAAATTTAGTAT
Found at i:59569497 original size:20 final size:19
Alignment explanation
Indices: 59569450--59569548 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 19
59569440 TGGTGTAGGG
*
59569450 TTAGAAATTTTGGTAAAGTC
1 TTAGAAATATTGGTAAA-TC
** *
59569470 CCATAAATATTGGTAAATC
1 TTAGAAATATTGGTAAATC
*
59569489 TATAGAAATTTTGGTAAATC
1 T-TAGAAATATTGGTAAATC
* * ** *
59569509 GTCAGATATATTAATAAGTCC
1 -TTAGAAATATTGGTAAAT-C
59569530 TTAGAAATATTGGTAAATC
1 TTAGAAATATTGGTAAATC
59569549 GTCGAATGTT
Statistics
Matches: 57, Mismatches: 19, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
19 3 0.05
20 52 0.91
21 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
TTAGAAATATTGGTAAATC
Found at i:59569520 original size:40 final size:40
Alignment explanation
Indices: 59569450--59569585 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
59569440 TGGTGTAGGG
* * *
59569450 TTAGAAATTTTGGTAAAGTC-CCATAAATATTGGTAAAT-C
1 TTAGAAATTTTGGTAAA-TCGTCAGATATATTGGTAAATCC
** *
59569489 TATAGAAATTTTGGTAAATCGTCAGATATATTAATAAGTCC
1 T-TAGAAATTTTGGTAAATCGTCAGATATATTGGTAAATCC
* * *
59569530 TTAGAAATATTGGTAAATCGTC-GAATGTTTTGGTAAATCC
1 TTAGAAATTTTGGTAAATCGTCAG-ATATATTGGTAAATCC
* *
59569570 TTTGAAAATTTGGTAA
1 TTAGAAATTTTGGTAA
59569586 TTGTTAAGAC
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (40 bp):
TTAGAAATTTTGGTAAATCGTCAGATATATTGGTAAATCC
Found at i:59569642 original size:20 final size:21
Alignment explanation
Indices: 59569617--59569741 Score: 93
Period size: 20 Copynumber: 6.2 Consensus size: 21
59569607 TTTAGAAAAT
59569617 TTAGAAATATTGGTAAAAT-A
1 TTAGAAATATTGGTAAAATCA
* *
59569637 TTAGAAATTTTGGTAAAGTCCA
1 TTAGAAATATTGGTAAAAT-CA
* * *
59569659 --ATAAATATTGATAAAATGA
1 TTAGAAATATTGGTAAAATCA
* *
59569678 -TAGAAATTTTGGT-AAATCC
1 TTAGAAATATTGGTAAAATCA
* *
59569697 TTAGAAATGTTGGT-AAATCG
1 TTAGAAATATTGGTAAAATCA
* *
59569717 TTAGATATATTGGTAAATTC-
1 TTAGAAATATTGGTAAAATCA
59569737 TTAGA
1 TTAGA
59569742 TATTTTGATA
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
19 5 0.06
20 73 0.88
21 4 0.05
22 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (21 bp):
TTAGAAATATTGGTAAAATCA
Found at i:59569884 original size:20 final size:20
Alignment explanation
Indices: 59569839--59569926 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 20
59569829 AAAATGATAT
* *
59569839 AAATTTTGGTAACTCATTA-
1 AAATTTTGATAAATCATTAG
*
59569858 AATATTTTGATAAATCCTTAG
1 AA-ATTTTGATAAATCATTAG
*
59569879 AAATTTT-AGTAAATCGTT-G
1 AAATTTTGA-TAAATCATTAG
* * *
59569898 AATATATTGATAAAACAATAG
1 AA-ATTTTGATAAATCATTAG
59569919 AAATTTTG
1 AAATTTTG
59569927 GTAATTGTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.11
20 42 0.78
21 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (20 bp):
AAATTTTGATAAATCATTAG
Found at i:59569902 original size:40 final size:40
Alignment explanation
Indices: 59569821--59569930 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 40
59569811 AGTTTCATAA
* ** * *
59569821 ATATTGGTAAAATGATATAAATTTTGGTAACTCATTAAAT
1 ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
* * ** * * *
59569861 ATTTTGATAAATCCTTAGAAATTTTAGTAAATCGTTGAAT
1 ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
59569901 ATATTGATAAAACAATAGAAATTTTGGTAA
1 ATATTGATAAAACAATAGAAATTTTGGTAA
59569931 TTGTTAAGAC
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (40 bp):
ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
Found at i:59569908 original size:158 final size:158
Alignment explanation
Indices: 59569605--59569910 Score: 388
Period size: 158 Copynumber: 1.9 Consensus size: 158
59569595 CTTCGTATAG
* *
59569605 GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAGAAATTTTGGTAAAGTCCAATAAATATTGA
1 GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAAAAATTATGGTAAAGTCCAATAAATATTGA
* * * * *
59569670 TAAAATGATAGAAATTTTGGTAAATCCTTAGAAATGTTGGTAAATCGTTAGATATATTGGTAAAT
66 TAAAATGATAGAAATTTTGGTAAATCATTAGAAATGTTGATAAATCCTTAGAAATATTAGTAAAT
*
59569735 TCTTAGATATTTTGATAAGGCCATTGAA
131 TCTTAGATATATTGATAAGGCCATTGAA
* * *
59569763 GGTTTAGAAAATTT-GAAAATATTGGTAAAATCTTAAAAATTATGGTGAAGTTTC-ATAAATATT
1 GGTTTAGAAAATTTAG-AAATATTGGTAAAATATTAAAAATTATGGTAAAG-TCCAATAAATATT
* * * * *
59569826 GGTAAAATGATATAAATTTTGGTAACTCATTA-AATATTTTGATAAATCCTTAGAAATTTTAGTA
64 GATAAAATGATAGAAATTTTGGTAAATCATTAGAA-ATGTTGATAAATCCTTAGAAATATTAGTA
59569890 AA-TCGTT-GAATATATTGATAA
128 AATTC-TTAG-ATATATTGATAA
59569911 AACAATAGAA
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
157 6 0.05
158 119 0.94
159 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (158 bp):
GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAAAAATTATGGTAAAGTCCAATAAATATTGA
TAAAATGATAGAAATTTTGGTAAATCATTAGAAATGTTGATAAATCCTTAGAAATATTAGTAAAT
TCTTAGATATATTGATAAGGCCATTGAA
Found at i:59570008 original size:20 final size:19
Alignment explanation
Indices: 59569957--59570011 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
59569947 TGATGTTTAG
*
59569957 AAAATTTGGAAATATTGAT
1 AAAATTTGTAAATATTGAT
* * *
59569976 AAAATTTTATAAATTTTGGT
1 AAAA-TTTGTAAATATTGAT
59569996 AAAATCTTGTAAATAT
1 AAAAT-TTGTAAATAT
59570012 CGGCAAAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAATTTGTAAATATTGAT
Found at i:59571740 original size:25 final size:25
Alignment explanation
Indices: 59571698--59571745 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
59571688 GACATTTTCA
*
59571698 TAATTTCCTAATCAAGTTAGTACAT
1 TAATTTCCTAACCAAGTTAGTACAT
* *
59571723 TAATTTCCTAACCGAGTTGGTAC
1 TAATTTCCTAACCAAGTTAGTAC
59571746 CCGGTTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (25 bp):
TAATTTCCTAACCAAGTTAGTACAT
Found at i:59574641 original size:10 final size:10
Alignment explanation
Indices: 59574626--59574671 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
59574616 TAAATTTGAG
59574626 TATAATTATT
1 TATAATTATT
59574636 TATAATTA-T
1 TATAATTATT
* *
59574645 TATTACT-TT
1 TATAATTATT
*
59574654 GATAATTATT
1 TATAATTATT
59574664 TATAATTA
1 TATAATTA
59574672 AAGTATTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TATAATTATT
Found at i:59576213 original size:16 final size:17
Alignment explanation
Indices: 59576194--59576235 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
59576184 AATCCTTTCA
*
59576194 AAATTTATAT-AATTAT
1 AAATTTATATAAATGAT
*
59576210 AAATTAATATAAATGAT
1 AAATTTATATAAATGAT
*
59576227 AAAATTATA
1 AAATTTATA
59576236 CTTTAGTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTATATAAATGAT
Found at i:59580836 original size:4 final size:4
Alignment explanation
Indices: 59580829--59580879 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
59580819 TTGATTGATT
*
59580829 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GACG
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG
59580877 GAT
1 GAT
59580880 TAAGAAGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.25, C:0.02, G:0.49, T:0.24
Consensus pattern (4 bp):
GATG
Found at i:59587029 original size:21 final size:21
Alignment explanation
Indices: 59587005--59587048 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
59586995 CTTCAACGAA
59587005 AACCCAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
59587026 AACCCAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
59587047 AA
1 AA
59587049 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (21 bp):
AACCCAGAATAAAGATTTTTT
Found at i:59588367 original size:33 final size:33
Alignment explanation
Indices: 59588325--59588392 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
59588315 TAATATATTA
59588325 TTATGGATGGTTTGTGCATGATTTTAACAATTG
1 TTATGGATGGTTTGTGCATGATTTTAACAATTG
59588358 TTATGGATGGTTTGTGCATGATTTTAACAATTG
1 TTATGGATGGTTTGTGCATGATTTTAACAATTG
59588391 TT
1 TT
59588393 TTCTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (33 bp):
TTATGGATGGTTTGTGCATGATTTTAACAATTG
Found at i:59593354 original size:19 final size:19
Alignment explanation
Indices: 59593330--59593404 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
59593320 TTATGTGTGA
59593330 ATATGTGAATTGTGAATTG
1 ATATGTGAATTGTGAATTG
*
59593349 ATATGTGAATTG-GAAATCG
1 ATATGTGAATTGTG-AATTG
* *
59593368 AGATATGAGATT-TGAA--G
1 ATATGTGA-ATTGTGAATTG
59593385 ATATGTGAATATGTGAATTG
1 ATATGTGAAT-TGTGAATTG
59593405 TGTATTGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.05
17 8 0.18
18 5 0.11
19 24 0.55
20 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (19 bp):
ATATGTGAATTGTGAATTG
Found at i:59593700 original size:41 final size:37
Alignment explanation
Indices: 59593652--59593751 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 37
59593642 TCGACCTTGA
59593652 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
59593692 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
59593730 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
59593752 CTTTATTGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 16 0.35
38 11 0.24
40 2 0.04
41 17 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:59595929 original size:23 final size:24
Alignment explanation
Indices: 59595903--59596041 Score: 79
Period size: 23 Copynumber: 5.6 Consensus size: 24
59595893 TAGTGTATGA
59595903 AAATTTAAAATAATAT-TAATAAT
1 AAATTTAAAATAATATATAATAAT
* * *
59595926 AAATTTAGAGTAAT-TATGATAAT
1 AAATTTAAAATAATATATAATAAT
* *
59595949 AAACTAAAAATAATA-ATACATGAA-
1 AAATTTAAAATAATATATA-AT-AAT
** * *
59595973 AAACCTAAAATAATACATATATAAAAA
1 AAATTTAAAATAAT--ATATA-ATAAT
*
59596000 AAACTTTTAAAATAATAATACAATAAT
1 AAA--TTTAAAATAAT-ATATAATAAT
*
59596027 AAATTTATAATAATA
1 AAATTTAAAATAATA
59596042 AGTTTAATTA
Statistics
Matches: 87, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 30 0.34
24 15 0.17
25 12 0.14
26 3 0.03
27 13 0.15
28 4 0.05
29 9 0.10
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (24 bp):
AAATTTAAAATAATATATAATAAT
Found at i:59599772 original size:68 final size:69
Alignment explanation
Indices: 59599641--59599778 Score: 176
Period size: 68 Copynumber: 2.0 Consensus size: 69
59599631 TTCCACCTTT
* *
59599641 TCTTTTAAATGGCATCAAAACATTTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
1 TCTTTCAAATGGCATCAAAACATGTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
59599706 CCAA
66 CCAA
* * *
59599710 TCTTTCAAATGGCATCAAAAC-TAGT-CAATATACTAGTCAAGTCCAACAGAAA-A-CAACCAAT
1 TCTTTCAAATGGCATCAAAACAT-GTCCAAGATACCAATCAAGTCCAA-A-AAATATCAACCAAT
59599771 AAGCCAA
63 AAGCCAA
59599778 T
1 T
59599779 AGTCTATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
68 35 0.57
69 23 0.38
70 3 0.05
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (69 bp):
TCTTTCAAATGGCATCAAAACATGTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
CCAA
Found at i:59603237 original size:21 final size:22
Alignment explanation
Indices: 59603201--59603243 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
59603191 TTTGACCCCC
59603201 TAAAATTATAAAAATTCAATTT
1 TAAAATTATAAAAATTCAATTT
*
59603223 TAAAATTAT-AAAATTCGATTT
1 TAAAATTATAAAAATTCAATTT
59603244 AATCCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATTATAAAAATTCAATTT
Found at i:59604422 original size:57 final size:55
Alignment explanation
Indices: 59604310--59604423 Score: 131
Period size: 57 Copynumber: 2.0 Consensus size: 55
59604300 CCTGCAGAGA
** *
59604310 AGTTGAACACCTTTTAGTTTGCTTATGTATTTTTTTTCCACCATTTGGTTTATTCTT
1 AGTTGAACACCTTTTAGTTTGCTTATGTA--TTTTTTCCACCATTACGTTCATTCTT
* *
59604367 AGTTGAACTCCTTTTAGTAGTCTGCTTATGTA-TTTTTCCTCCATTACGTTCATTCTT
1 AGTTGAACACCTTTTAGT--T-TGCTTATGTATTTTTTCCACCATTACGTTCATTCTT
59604424 GGTCAAACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
57 38 0.78
59 1 0.02
60 10 0.20
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (55 bp):
AGTTGAACACCTTTTAGTTTGCTTATGTATTTTTTCCACCATTACGTTCATTCTT
Found at i:59607300 original size:28 final size:29
Alignment explanation
Indices: 59607269--59607324 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
59607259 TTTAAATAAA
* * *
59607269 AAAATATAT-GACTTAATTTTTAATTTTT
1 AAAATATATGGACTAAAATTTAAATTTTT
59607297 AAAATATATGGACTAAAATTTAAATTTT
1 AAAATATATGGACTAAAATTTAAATTTT
59607325 ATCAAAGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (29 bp):
AAAATATATGGACTAAAATTTAAATTTTT
Found at i:59607325 original size:28 final size:28
Alignment explanation
Indices: 59607269--59607325 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
59607259 TTTAAATAAA
** *
59607269 AAAATATATGACTTAATTTTTAATTTTT
1 AAAATATATGACTTAAAATTTAAATTTT
59607297 AAAATATATGGAC-TAAAATTTAAATTTT
1 AAAATATAT-GACTTAAAATTTAAATTTT
59607325 A
1 A
59607326 TCAAAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (28 bp):
AAAATATATGACTTAAAATTTAAATTTT
Found at i:59608788 original size:21 final size:22
Alignment explanation
Indices: 59608764--59608818 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
59608754 AATAGCGGTG
* *
59608764 GCGGTGAGATTAG-TTACTGTA
1 GCGGTGAGATTAGCATAATGTA
59608785 GCGGTGAGATT-GCATAATGTA
1 GCGGTGAGATTAGCATAATGTA
59608806 GCGGTGAGATTAG
1 GCGGTGAGATTAG
59608819 AAACAATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (22 bp):
GCGGTGAGATTAGCATAATGTA
Found at i:59619029 original size:2 final size:2
Alignment explanation
Indices: 59619022--59619052 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59619012 TGAAAATTAA
59619022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59619053 AACTAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59627091 original size:18 final size:18
Alignment explanation
Indices: 59627070--59627105 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59627060 TAATATTTTA
59627070 AAATAATTAGAATTATTC
1 AAATAATTAGAATTATTC
*
59627088 AAATAATTATAATTATTC
1 AAATAATTAGAATTATTC
59627106 GATCGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATAATTAGAATTATTC
Found at i:59632922 original size:14 final size:15
Alignment explanation
Indices: 59632890--59632922 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59632880 TTTTTTTAAG
*
59632890 AAAATATATAAAATT
1 AAAATATATAAAATA
59632905 AAAAT-TATAAAATA
1 AAAATATATAAAATA
59632919 AAAA
1 AAAA
59632923 ATTAGCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATATAAAATA
Found at i:59634923 original size:17 final size:17
Alignment explanation
Indices: 59634903--59634936 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59634893 GGGAGTTTTC
59634903 GGTAAAAACATACCACA
1 GGTAAAAACATACCACA
59634920 GGTAAAAACATACCACA
1 GGTAAAAACATACCACA
59634937 TTGTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (17 bp):
GGTAAAAACATACCACA
Found at i:59637444 original size:92 final size:92
Alignment explanation
Indices: 59636844--59637405 Score: 863
Period size: 92 Copynumber: 6.1 Consensus size: 92
59636834 ACTGTTTATA
* * * * * *
59636844 GTTATACATTGTCGAAATTGATTTGCATATGAATATAAGTTGTCGAATTGATTTGTATATGATTG
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
*
59636909 TACATTGTTGAAATTAATTTGTATATG
66 TACATTGCTGAAATTAATTTGTATATG
59636936 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
* *
59637001 TACATTGCTTAAATTAATTTGTACATG
66 TACATTGCTGAAATTAATTTGTATATG
* * * *
59637028 GTTATACATTATTGAAATTGAATTGTATATGAATATAAGTTGCCGAATTGATTTGTATATAATTG
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
59637093 TACATTGCTGAAATTAATTTGTATATG
66 TACATTGCTGAAATTAATTTGTATATG
** * * *
59637120 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCATTTATGGTTG
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
59637185 TACATTGCTGAAATTAATTTGTATATG
66 TACATTGCTGAAATTAATTTGTATATG
* *
59637212 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGTCGAATTGATTTTTATATGATTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
* * *
59637277 TATATTGTTGAAATTAATTTGTACATG
66 TACATTGCTGAAATTAATTTGTATATG
* * *
59637304 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTTA
1 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
* *
59637369 TACATTGATGAATTTAATTTGTATATG
66 TACATTGCTGAAATTAATTTGTATATG
*
59637396 ATTATACATT
1 GTTATACATT
59637406 ACCGAACTTG
Statistics
Matches: 429, Mismatches: 41, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 429 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.44
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGTATATGATTA
TACATTGCTGAAATTAATTTGTATATG
Found at i:59638804 original size:2 final size:2
Alignment explanation
Indices: 59638797--59638850 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
59638787 AAACTATTAA
* *
59638797 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT GT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
59638839 AT AT AT AT AT AT
1 AT AT AT AT AT AT
59638851 TTACAAAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:59638822 original size:22 final size:22
Alignment explanation
Indices: 59638772--59638850 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
59638762 AGTGTATGTC
*
59638772 TATATACATAT-TATA-AAACTA
1 TATATATATATATATATAAA-TA
*
59638793 TTAAATATATATATATATAAATA
1 -TATATATATATATATATAAATA
* *
59638816 TATATATATATATATGTAAGTA
1 TATATATATATATATATAAATA
59638838 TATATATATATAT
1 TATATATATATAT
59638851 TTACAAAAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 41 0.82
23 6 0.12
24 3 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (22 bp):
TATATATATATATATATAAATA
Found at i:59638860 original size:24 final size:24
Alignment explanation
Indices: 59638797--59638860 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 24
59638787 AAACTATTAA
*
59638797 ATATATATATATA-TAAA-TATAT
1 ATATATATATATACAAAAGTATAT
**
59638819 ATATATATATAT--GTAAGTATAT
1 ATATATATATATACAAAAGTATAT
*
59638841 ATATATATATTTACAAAAGT
1 ATATATATATATACAAAAGT
59638861 TAAAAATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.06
22 28 0.82
24 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (24 bp):
ATATATATATATACAAAAGTATAT
Done.