Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 180 of 218
Found at i:54132965 original size:21 final size:21
Alignment explanation
Indices: 54132939--54132978 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54132929 AACGTGGCAA
54132939 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
54132960 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
54132979 GGTCCAGTTA
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:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:54134618 original size:6 final size:6
Alignment explanation
Indices: 54134609--54134666 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
54134599 ATAGGAATAG
54134609 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
*
54134657 GCATAT GTAT
1 GTATAT GTAT
54134667 CCATATACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:54135832 original size:28 final size:28
Alignment explanation
Indices: 54135800--54135877 Score: 156
Period size: 28 Copynumber: 2.8 Consensus size: 28
54135790 TCTGGATGCG
54135800 GTACTTACCAAAATAGATTAATCTCGTT
1 GTACTTACCAAAATAGATTAATCTCGTT
54135828 GTACTTACCAAAATAGATTAATCTCGTT
1 GTACTTACCAAAATAGATTAATCTCGTT
54135856 GTACTTACCAAAATAGATTAAT
1 GTACTTACCAAAATAGATTAAT
54135878 TTCATGGTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (28 bp):
GTACTTACCAAAATAGATTAATCTCGTT
Found at i:54135887 original size:28 final size:28
Alignment explanation
Indices: 54135799--54135887 Score: 142
Period size: 28 Copynumber: 3.2 Consensus size: 28
54135789 GTCTGGATGC
54135799 GGTACTTACCAAAATAGATTAATCTCGT
1 GGTACTTACCAAAATAGATTAATCTCGT
*
54135827 TGTACTTACCAAAATAGATTAATCTCGT
1 GGTACTTACCAAAATAGATTAATCTCGT
* * *
54135855 TGTACTTACCAAAATAGATTAATTTCAT
1 GGTACTTACCAAAATAGATTAATCTCGT
54135883 GGTAC
1 GGTAC
54135888 GGGTTATCGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (28 bp):
GGTACTTACCAAAATAGATTAATCTCGT
Found at i:54137573 original size:28 final size:25
Alignment explanation
Indices: 54137533--54137586 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 25
54137523 TTGCGTTGAG
54137533 ATTTCGTTATCACTAATGTAATTTTATT
1 ATTTCGTTATCACT-AT-T-ATTTTATT
54137561 ATTTCGTTATCACTATTATTTTATT
1 ATTTCGTTATCACTATTATTTTATT
54137586 A
1 A
54137587 ATCAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 2 0.08
28 14 0.54
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (25 bp):
ATTTCGTTATCACTATTATTTTATT
Found at i:54138521 original size:13 final size:13
Alignment explanation
Indices: 54138503--54138531 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54138493 TCAGTGCGGT
54138503 GTCAGCAAAACGC
1 GTCAGCAAAACGC
54138516 GTCAGCAAAACGC
1 GTCAGCAAAACGC
54138529 GTC
1 GTC
54138532 CTTGGGAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.24, T:0.10
Consensus pattern (13 bp):
GTCAGCAAAACGC
Found at i:54138802 original size:11 final size:11
Alignment explanation
Indices: 54138772--54138835 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
54138762 AAACTAATCC
54138772 TCTCTCAATTAT
1 TCTCTCAATT-T
*
54138784 TTTCTCAATTT
1 TCTCTCAATTT
54138795 TCTCTCAATTT
1 TCTCTCAATTT
*
54138806 GCTCTCAATTT
1 TCTCTCAATTT
* *
54138817 CCT-TCCAAATT
1 TCTCT-CAATTT
54138828 TCTCTCAA
1 TCTCTCAA
54138836 ATCCATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 1 0.02
11 33 0.75
12 10 0.23
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:54139992 original size:7 final size:7
Alignment explanation
Indices: 54139980--54140005 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54139970 TAATCGATTG
54139980 GTATTTA
1 GTATTTA
54139987 GTATTTA
1 GTATTTA
54139994 GTATTTA
1 GTATTTA
54140001 GTATT
1 GTATT
54140006 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:54140568 original size:30 final size:30
Alignment explanation
Indices: 54140502--54140576 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
54140492 GATGACGACG
54140502 CAGGCCCATCAACAAGGCCCAGAAATTCAC
1 CAGGCCCATCAACAAGGCCCAGAAATTCAC
* * * * *
54140532 CCGGCCCATCATC-AGCGCCCATAACTTCAT
1 CAGGCCCATCAACAAG-GCCCAGAAATTCAC
*
54140562 CAGGCCCAGCAACAA
1 CAGGCCCATCAACAA
54140577 TACCGACACA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 2 0.06
30 32 0.91
31 1 0.03
ACGTcount: A:0.32, C:0.40, G:0.16, T:0.12
Consensus pattern (30 bp):
CAGGCCCATCAACAAGGCCCAGAAATTCAC
Found at i:54140685 original size:17 final size:19
Alignment explanation
Indices: 54140653--54140695 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
54140643 TATCAGGTGC
*
54140653 GTATCCTAGCCCCTTA-AT
1 GTATCCTAGACCCTTATAT
54140671 GTATCCTA-ACCCTTATAT
1 GTATCCTAGACCCTTATAT
*
54140689 GTTTCCT
1 GTATCCT
54140696 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
GTATCCTAGACCCTTATAT
Found at i:54141242 original size:21 final size:21
Alignment explanation
Indices: 54141208--54141257 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
54141198 CAAAAACCCT
*
54141208 AACCCTAACTCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54141229 AACTCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
54141250 AACCCTAA
1 AACCCTAA
54141258 ACTAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:54141339 original size:27 final size:25
Alignment explanation
Indices: 54141309--54141391 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 25
54141299 AAACCCTAAC
54141309 AAAAACCCTAACCCTAACCGTTAACTT
1 AAAAACCCTAA-CC-AACCGTTAACTT
*
54141336 AAAAACCCT-A--AACCTTTAACTT
1 AAAAACCCTAACCAACCGTTAACTT
54141358 AAAAACCCT----AACCGTTAACTT
1 AAAAACCCTAACCAACCGTTAACTT
*
54141379 AAAAACCCCAACC
1 AAAAACCCTAACC
54141392 CTTAACATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 19 0.39
22 20 0.41
26 1 0.02
27 9 0.18
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAAACCCTAACCAACCGTTAACTT
Found at i:54141354 original size:22 final size:21
Alignment explanation
Indices: 54141318--54141407 Score: 135
Period size: 21 Copynumber: 4.2 Consensus size: 21
54141308 CAAAAACCCT
54141318 AACCCTAACCGTTAACTTAAA
1 AACCCTAACCGTTAACTTAAA
*
54141339 AACCCTAAACCTTTAACTTAAA
1 AACCCT-AACCGTTAACTTAAA
54141361 AACCCTAACCGTTAACTTAAA
1 AACCCTAACCGTTAACTTAAA
* * *
54141382 AACCCCAACCCTTAACATAAA
1 AACCCTAACCGTTAACTTAAA
54141403 AACCC
1 AACCC
54141408 CATAACCCTA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 43 0.68
22 20 0.32
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.21
Consensus pattern (21 bp):
AACCCTAACCGTTAACTTAAA
Found at i:54141369 original size:43 final size:42
Alignment explanation
Indices: 54141318--54141407 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 42
54141308 CAAAAACCCT
* *
54141318 AACCCTAACCGTTAACTTAAAAACCCTAAACCTTTAACTTAAA
1 AACCCTAACCGTTAACTTAAAAACCC-AAACCCTTAACATAAA
*
54141361 AACCCTAACCGTTAACTTAAAAACCCCAACCCTTAACATAAA
1 AACCCTAACCGTTAACTTAAAAACCCAAACCCTTAACATAAA
54141403 AACCC
1 AACCC
54141408 CATAACCCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 18 0.41
43 26 0.59
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.21
Consensus pattern (42 bp):
AACCCTAACCGTTAACTTAAAAACCCAAACCCTTAACATAAA
Found at i:54150887 original size:23 final size:23
Alignment explanation
Indices: 54150861--54150905 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54150851 GAATTTTTAT
54150861 ATATCTTAAAGATTT-TAAAAATA
1 ATAT-TTAAAGATTTATAAAAATA
* *
54150884 ATATTTATATATTTATAAAAAT
1 ATATTTAAAGATTTATAAAAAT
54150906 TTGAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATTTAAAGATTTATAAAAATA
Found at i:54150914 original size:33 final size:31
Alignment explanation
Indices: 54150855--54150942 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
54150845 AAATTAGAAT
* * * *
54150855 TTTTATATATCT-TAAAGATTTTAAAAATAA
1 TTTTATATATTTATAAAAATTTGAAAAAAAA
54150885 TATTTATATATTTATAAAAATTTGAAAAAAAA
1 T-TTTATATATTTATAAAAATTTGAAAAAAAA
* * *
54150917 TTATATAAATATTATGAAAATTTGAA
1 TTTTATATAT-TTATAAAAATTTGAA
54150943 GATTATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 17 0.35
32 30 0.62
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (31 bp):
TTTTATATATTTATAAAAATTTGAAAAAAAA
Found at i:54155740 original size:36 final size:36
Alignment explanation
Indices: 54155664--54155740 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
54155654 ATATCAAAAG
* * * *
54155664 AATTTGGATTATTAAAATTTAATATTTACATTATTT
1 AATTTGAATTATTAAAATTTAATATTTACATGAATC
* * *
54155700 AATTTGAATTGTTAAAATTTAATGTTTACGTGAATC
1 AATTTGAATTATTAAAATTTAATATTTACATGAATC
54155736 AATTT
1 AATTT
54155741 CAATCTAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (36 bp):
AATTTGAATTATTAAAATTTAATATTTACATGAATC
Found at i:54157628 original size:10 final size:10
Alignment explanation
Indices: 54157613--54157664 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
54157603 GGACTGGAGG
*
54157613 AGAAGAATGA
1 AGAAGAAAGA
54157623 AGAAGAAAGA
1 AGAAGAAAGA
*
54157633 AAAAGAAAGA
1 AGAAGAAAGA
*
54157643 A-AAGGAAAGG
1 AGAA-GAAAGA
54157653 AGAAG-AAGA
1 AGAAGAAAGA
54157662 AGA
1 AGA
54157665 GGGAGGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.22
10 26 0.72
11 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:54159053 original size:105 final size:105
Alignment explanation
Indices: 54158944--54159154 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
54158934 TATAAAATAC
54158944 TACTAATTTTAACTAAATCCTTCTAGATATTGTCTCGGTTGTCATTTTTTTCTTACTTTGTCACT
1 TACTAATTTTAACTAAATCCTTCTAGATATTGTCTCGGTTGTCATTTTTTTCTTACTTTGTCACT
54159009 CGTGTAGTTTCGTTTTACCCTTCCATGGAAACGTGTCTTA
66 CGTGTAGTTTCGTTTTACCCTTCCATGGAAACGTGTCTTA
54159049 TACTAATTTTAACTAAATCCTTCTAGATATTGTCTCGGTTGTCATTTTTTTCTTACTTTGTCACT
1 TACTAATTTTAACTAAATCCTTCTAGATATTGTCTCGGTTGTCATTTTTTTCTTACTTTGTCACT
54159114 CGTGTAGTTTCGTTTTACCCTTCCATGGAAACGTGTCTTA
66 CGTGTAGTTTCGTTTTACCCTTCCATGGAAACGTGTCTTA
54159154 T
1 T
54159155 GATTGTAGAC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (105 bp):
TACTAATTTTAACTAAATCCTTCTAGATATTGTCTCGGTTGTCATTTTTTTCTTACTTTGTCACT
CGTGTAGTTTCGTTTTACCCTTCCATGGAAACGTGTCTTA
Found at i:54165235 original size:40 final size:39
Alignment explanation
Indices: 54165129--54165237 Score: 164
Period size: 39 Copynumber: 2.8 Consensus size: 39
54165119 AGGGTTATCA
* * *
54165129 AAGTACAAACAGAGCACGTATGTGTATTTAGGGGTATTG
1 AAGTACAAACAGAGCACGTATGTGCATTCAGGGGTACTG
*
54165168 AAGTACAAAAAGAGCACGTATGTGCATTCAGGGGTACTG
1 AAGTACAAACAGAGCACGTATGTGCATTCAGGGGTACTG
*
54165207 AAGTACAAACAGAAGCACATATGTGCATTCA
1 AAGTACAAACAG-AGCACGTATGTGCATTCA
54165238 TACAATAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 46 0.73
40 17 0.27
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (39 bp):
AAGTACAAACAGAGCACGTATGTGCATTCAGGGGTACTG
Found at i:54167858 original size:10 final size:10
Alignment explanation
Indices: 54167843--54167867 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54167833 TTTATAATAA
54167843 ATTTTGATTT
1 ATTTTGATTT
54167853 ATTTTGATTT
1 ATTTTGATTT
54167863 ATTTT
1 ATTTT
54167868 CGATAGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
ATTTTGATTT
Found at i:54176696 original size:20 final size:22
Alignment explanation
Indices: 54176654--54176696 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
54176644 CTTGGAAAAT
*
54176654 TTATTGTGTTGAATAGTAGTGG
1 TTATTGTGTTGAATAATAGTGG
*
54176676 TTATTGT-TTTAATAATA-TGG
1 TTATTGTGTTGAATAATAGTGG
54176696 T
1 T
54176697 ATGATGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (22 bp):
TTATTGTGTTGAATAATAGTGG
Found at i:54181218 original size:14 final size:15
Alignment explanation
Indices: 54181179--54181220 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54181169 TTTTAACATA
*
54181179 ATTATTATTAAATAT
1 ATTATAATTAAATAT
54181194 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
54181208 A-TATAATTTAATA
1 ATTATAATTAAATA
54181221 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:54181329 original size:16 final size:16
Alignment explanation
Indices: 54181285--54181331 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
54181275 TACTATAAAA
*
54181285 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
54181301 TATTATT-AAATATAT
1 TATAATTAAAATATAT
54181316 TATAATTAAAATATAT
1 TATAATTAAAATATAT
54181332 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:54181449 original size:16 final size:16
Alignment explanation
Indices: 54181406--54181451 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
54181396 ACTATAAAAG
*
54181406 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
54181422 ATTATT-AAATATATT
1 ATAATTAAAATATATT
54181437 ATAATTAAAATATAT
1 ATAATTAAAATATAT
54181452 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:54181458 original size:14 final size:15
Alignment explanation
Indices: 54181406--54181460 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
54181396 ACTATAAAAG
54181406 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
54181422 ATTATTAAATATATT
1 ATAATTAAATATATT
54181437 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
54181450 ATAATTTAATA
1 ATAATTAAATA
54181461 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:54181511 original size:59 final size:58
Alignment explanation
Indices: 54181208--54181511 Score: 184
Period size: 57 Copynumber: 5.1 Consensus size: 58
54181198 TAATTAAAAT
*
54181208 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCGTA
1 ATATAATTTAATAAAATTCTTAATAAT-AATATTCTTATATGAATTTACTCAAATCATA
* * * * * * *
54181267 ATAT-ATGATACTATAAAATATAATTTAA-CATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAAT-T--CTTAATAATAA-TATTCTTATATGA-ATT-TACTCAAATCA
54181327 T-
57 TA
54181328 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * *
54181387 ATATATGATACTATAA-AAGATAAT-TTAA-CATAATTATTATTAAAT-ATATTATAATTAAA--
1 ATATA--AT--T-TAATAA-A-ATTCTTAATAATAA-TATTCTTATATGA-ATT-TACTCAAATC
54181446 AT-
56 ATA
*
54181448 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAT-AATATTCTTATATGAATTTACTCAAATCATA
54181507 ATATA
1 ATATA
54181512 TGATACTATA
Statistics
Matches: 184, Mismatches: 27, Indels: 68
0.66 0.10 0.24
Matches are distributed among these distances:
55 2 0.01
56 24 0.13
57 30 0.16
58 14 0.08
59 25 0.14
61 20 0.11
62 13 0.07
63 30 0.16
64 24 0.13
65 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAATTCTTAATAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:54181523 original size:61 final size:61
Alignment explanation
Indices: 54181218--54181525 Score: 235
Period size: 61 Copynumber: 5.1 Consensus size: 61
54181208 ATATAATTTA
* *
54181218 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCGTAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * * * * * *
54181279 ATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* *
54181337 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
** * * * * * * * * *
54181399 ATAAAA--GATAATTTAA-C-ATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
54181457 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
54181519 ATAAAAT
1 ATAAAAT
54181526 ATAATTTGAA
Statistics
Matches: 179, Mismatches: 48, Indels: 40
0.67 0.18 0.15
Matches are distributed among these distances:
58 2 0.01
59 67 0.37
60 32 0.18
61 76 0.42
62 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:54181579 original size:120 final size:120
Alignment explanation
Indices: 54181170--54181564 Score: 720
Period size: 120 Copynumber: 3.3 Consensus size: 120
54181160 TTAATCATAT
54181170 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
54181235 CAATATTCTTATATGAATTTACTCAAATCGTAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
54181290 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* *
54181355 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
54181410 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
54181475 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
* *
54181530 TTTGAA-ATAATTAATATTAAATATATTTTAATTAA
1 TTT-AACATAATTATTATTAAATATATTATAATTAA
54181565 TATTAAATAA
Statistics
Matches: 266, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 264 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
Found at i:54187324 original size:23 final size:23
Alignment explanation
Indices: 54187298--54187373 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
54187288 ATAAGTGCAA
54187298 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54187321 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54187344 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54187367 CACTGAT
1 CACTGAT
54187374 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54193969 original size:23 final size:23
Alignment explanation
Indices: 54193943--54194064 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
54193933 ATAAGTGCAA
54193943 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54193966 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54193989 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54194012 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
54194035 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
54194058 CACTGAT
1 CACTGAT
54194065 CAATAACACT
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54196411 original size:36 final size:36
Alignment explanation
Indices: 54196359--54196442 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
54196349 ATATATAATT
* * * * * * *
54196359 ATCACTTTTAAATATTACAATTATATCATTATGTCGA
1 ATCACTTAT-AATATTACAAATACATCAATAGGCCAA
54196396 ATCACTTATAATATTACAAATACATCAATAGGCCAA
1 ATCACTTATAATATTACAAATACATCAATAGGCCAA
54196432 ATCACTTATAA
1 ATCACTTATAA
54196443 GTTCAATTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 32 0.80
37 8 0.20
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (36 bp):
ATCACTTATAATATTACAAATACATCAATAGGCCAA
Found at i:54196715 original size:43 final size:43
Alignment explanation
Indices: 54196648--54196767 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
54196638 CTCGTACAAC
* * * *
54196648 GCCAACGTCCCAGACGTGGTCTTACATGTAATCATATA-TTGAT
1 GCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCGAT
54196691 GCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCGAT
1 GCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCGAT
*
54196734 GCCAACGTCCCAGACGTGGTCTTACACGAAAACA
1 GCCAACGTCCCAGACGTGGTCTTACACGTAAACA
54196768 TATATCGAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.06
43 60 0.90
44 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCGAT
Found at i:54199274 original size:43 final size:43
Alignment explanation
Indices: 54199227--54199432 Score: 162
Period size: 43 Copynumber: 4.8 Consensus size: 43
54199217 GTGTCGCTAA
* *
54199227 CTTTAGTGGCG-TTCTTAGAAAAAACGCCGCTAAAGACCAGGAC
1 CTTTAGTGGCGCTT-TTACAAAAAACACCGCTAAAGACCAGGAC
* *
54199270 CTTTAGTGGCGCTTTTACCACAAACACCGCTAAAGACCAGGAC
1 CTTTAGTGGCGCTTTTACAAAAAACACCGCTAAAGACCAGGAC
* * * * * ** * *
54199313 CTTTAGCGACGCTTTTCCCACAAATGCCACTAAAGACCAAGAC
1 CTTTAGTGGCGCTTTTACAAAAAACACCGCTAAAGACCAGGAC
* * * * * * *
54199356 CTTTAGCGGCACTTTTTCCACAAACGCCGCTAAAGGCCAGGAC
1 CTTTAGTGGCGCTTTTACAAAAAACACCGCTAAAGACCAGGAC
* * * * * *
54199399 CTTTAGCGGCACTTTTCCGACAAACGCCGCTAAA
1 CTTTAGTGGCGCTTTTACAAAAAACACCGCTAAA
54199433 AACATGACTT
Statistics
Matches: 142, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 140 0.99
44 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
CTTTAGTGGCGCTTTTACAAAAAACACCGCTAAAGACCAGGAC
Found at i:54199350 original size:86 final size:86
Alignment explanation
Indices: 54199248--54199432 Score: 262
Period size: 86 Copynumber: 2.2 Consensus size: 86
54199238 TTCTTAGAAA
* * * *
54199248 AAACGCCGCTAAAGACCAGGACCTTTAGTGGCGCTTTTACCACAAACACCGCTAAAGACCAGGAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGACCAGGAC
*
54199313 CTTTAGCGACGCTTTTCCCAC
66 CTTTAGCGACACTTTTCCCAC
* * * *
54199334 AAATGCCACTAAAGACCAAGACCTTTAGCGGCACTTTTTCCACAAACGCCGCTAAAGGCCAGGAC
1 AAACGCCACTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGACCAGGAC
* *
54199399 CTTTAGCGGCACTTTTCCGAC
66 CTTTAGCGACACTTTTCCCAC
*
54199420 AAACGCCGCTAAA
1 AAACGCCACTAAA
54199433 AACATGACTT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (86 bp):
AAACGCCACTAAAGACCAAGACCTTTAGCGGCACTTTTACCACAAACACCGCTAAAGACCAGGAC
CTTTAGCGACACTTTTCCCAC
Found at i:54199656 original size:18 final size:18
Alignment explanation
Indices: 54199633--54199692 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
54199623 TTAAAACAAG
54199633 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
54199651 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
54199668 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
54199686 TTACATT
1 TTACATT
54199693 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:54204940 original size:13 final size:13
Alignment explanation
Indices: 54204922--54204946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54204912 TGTCAATCTA
54204922 TTACATTAATTTG
1 TTACATTAATTTG
54204935 TTACATTAATTT
1 TTACATTAATTT
54204947 ATTTATTTAT
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:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTACATTAATTTG
Found at i:54205443 original size:7 final size:7
Alignment explanation
Indices: 54205427--54205471 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
54205417 CACTAGCTCT
54205427 TAACCCC
1 TAACCCC
*
54205434 TAACCTC
1 TAACCCC
*
54205441 TAACTCC
1 TAACCCC
54205448 TAACCCC
1 TAACCCC
**
54205455 TAACTAC
1 TAACCCC
54205462 TAACCCC
1 TAACCCC
54205469 TAA
1 TAA
54205472 ATCTTATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:54205449 original size:14 final size:14
Alignment explanation
Indices: 54205427--54205471 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
54205417 CACTAGCTCT
* *
54205427 TAACCCCTAACCTC
1 TAACTCCTAACCCC
54205441 TAACTCCTAACCCC
1 TAACTCCTAACCCC
*
54205455 TAACTACTAACCCC
1 TAACTCCTAACCCC
54205469 TAA
1 TAA
54205472 ATCTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACTCCTAACCCC
Found at i:54205451 original size:21 final size:21
Alignment explanation
Indices: 54205427--54205471 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
54205417 CACTAGCTCT
*
54205427 TAACCCCTAACCT-CTAACTCC
1 TAACCCCTAA-CTACTAACCCC
54205448 TAACCCCTAACTACTAACCCC
1 TAACCCCTAACTACTAACCCC
54205469 TAA
1 TAA
54205472 ATCTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (21 bp):
TAACCCCTAACTACTAACCCC
Found at i:54205800 original size:14 final size:14
Alignment explanation
Indices: 54205778--54205814 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54205768 ATCCTAAATT
54205778 AACCATATACCCTA
1 AACCATATACCCTA
*
54205792 AATCATATACCCTA
1 AACCATATACCCTA
54205806 AACCATATA
1 AACCATATA
54205815 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:54206247 original size:41 final size:40
Alignment explanation
Indices: 54206183--54206262 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 40
54206173 TCAAAAATGG
54206183 GCATTAGCGGCGCTTTCAAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTC-AAAAAACGCCGCTAAAGGCCCGA
54206224 GCATTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGC-T-TTCAAAAAACGCCGCTAAAGGCCC
54206263 CAAAAACTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 33 0.89
42 1 0.03
43 3 0.08
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTCAAAAAACGCCGCTAAAGGCCCGA
Found at i:54206432 original size:40 final size:39
Alignment explanation
Indices: 54206303--54206432 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 39
54206293 TAGGCTTGTT
* * * * *
54206303 GCGGCGCTTTTCAAAAAACGCTGTTAATTCTT-ATTTTTA
1 GCGGCG-TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTA
* * **
54206342 GCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGACCTTTA
1 GCGGCGTTTT-TAAAAAGCGCCGCTAATGCTTGATTTTTA
*
54206382 GCGGCGTTTTTAGAAAAGCGCCTCTAATGCTTGATTTTTA
1 GCGGCGTTTTTA-AAAAGCGCCGCTAATGCTTGATTTTTA
*
54206422 GTGGCGTTTTT
1 GCGGCGTTTTT
54206433 TGTCCAAACG
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 4 0.05
39 23 0.31
40 48 0.64
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAGCGCCGCTAATGCTTGATTTTTA
Found at i:54206455 original size:12 final size:12
Alignment explanation
Indices: 54206438--54206463 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54206428 TTTTTTGTCC
54206438 AAACGCCGCTAA
1 AAACGCCGCTAA
54206450 AAACGCCGCTAA
1 AAACGCCGCTAA
54206462 AA
1 AA
54206464 GCCTGTTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:54211444 original size:16 final size:15
Alignment explanation
Indices: 54211423--54211464 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
54211413 CTATTTGCAT
54211423 GTTTAGTGCTTTATGG
1 GTTTAGTGCTTTA-GG
* *
54211439 GTTTAGGGTTTTAGG
1 GTTTAGTGCTTTAGG
54211454 G-TTAGTGCTTT
1 GTTTAGTGCTTT
54211465 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.12, C:0.05, G:0.33, T:0.50
Consensus pattern (15 bp):
GTTTAGTGCTTTAGG
Found at i:54211849 original size:126 final size:126
Alignment explanation
Indices: 54211700--54212473 Score: 953
Period size: 126 Copynumber: 6.2 Consensus size: 126
54211690 AATTTTGTTT
* * * * * *
54211700 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAAAAGGTTCGGAAAAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
* * * * *
54211765 ACGCTTCAAGCAGGATGTACTGTTAGTAAAATTACTGAATAAAGCTCCCACATGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * *
54211826 TTTTTCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAGTTCTG-AAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * * * * *
54211890 ATGTTTCAAGCAGGATACACTATAAGCAAAATTATTGAAAAAAGCTCCCATGTCGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * *
54211951 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTCGA-AAAGACGGTTCTAAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAA-ACGGTTCTGAAAAAATAGTGTCAAA
54212015 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* *
54212077 TTTTTCTACAGTGGTTCCTGAAAAAATAATTTTGA-AAAGACGGTTCTAAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAA-ACGGTTCTGAAAAAATAGTGTCAAA
* * * * *
54212141 AACGCTTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGTTCCCACGTGAAAGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * * *
54212203 TTTTTCTACATTAGTTCTTG-AAAAATAATTTTTAGAAGACGTTTTTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
* * * ** *
54212267 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCACACGTGGGTGATC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * *
54212328 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTCAGAAGACGTTTTTGAAAAAATTGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
* * * * ** ** *
54212393 ATGCTTCAAACAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCATACGTGGGTGCTA
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
54212454 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
54212474 CTTGGCCTTA
Statistics
Matches: 570, Mismatches: 74, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
124 2 0.00
125 208 0.36
126 360 0.63
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:54212229 original size:251 final size:250
Alignment explanation
Indices: 54211700--54212470 Score: 972
Period size: 251 Copynumber: 3.1 Consensus size: 250
54211690 AATTTTGTTT
* * * *
54211700 TTTTTCTACAGTAGTT-TCAGAAAAATTAATTTTGAGAAA-AAGGTTCGGAAAAAATAATGTCAA
1 TTTTTCTACAGTAGTTCT-TGAAAAA-TAATTTTGA-AAAGACGGTTCTGAAAAAATAGTGTCAA
* * * * *
54211763 AAACGCTTCAAGCAGGATGTACTGTTAGTAAAATTACTGAATAAAGCTCCCACATGGACGCTCTT
63 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTT
* * * * *
54211828 TTTCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAATAGTGTCAAAAATG
128 TTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAATAGTGTCAAAAATG
* * * * * *
54211893 TTTCAAGCAGGATACACTATAAGCAAAATTATTGAAAAAAGCTCCCATGTCGATGCTC
193 CTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTCGAAGCTC
* * * *
54211951 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTCGAAAAGACGGTTCTAAAAAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCTTG-AAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAGTGTCAAAA
54212016 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTT
65 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTT
* * *
54212081 TCTACAGTGGTTCCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACGC
130 TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAGTGTCAAAAATGC
* *
54212146 TTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGTTCCCACGT-GAAAGCTC
194 TTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTCG-AAGCTC
* * * * *
54212203 TTTTTCTACATTAGTTCTTGAAAAATAATTTTTAGAAGACGTTTTTGAAAAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCTTGAAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAGTGTCAAAAA
* * * ** *
54212268 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCACACGTGGGTGATCTTTTT
66 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
* * * *
54212333 CTACAGTAGTTCCTGAAAAAATAATTTTCAGAAGACGTTTTTGAAAAAATTGTGTCAAAAATGCT
131 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAGTGTCAAAAATGCT
* * * * ** * ** *
54212398 TCAAACAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCATACGTGGGTGCTA
195 TCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTCGAAGCTC
54212454 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
54212471 CTGCTTGGCC
Statistics
Matches: 451, Mismatches: 63, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
250 3 0.01
251 358 0.79
252 90 0.20
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (250 bp):
TTTTTCTACAGTAGTTCTTGAAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAGTGTCAAAAA
CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAATAGTGTCAAAAATGCTT
CAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTCGAAGCTC
Found at i:54212257 original size:377 final size:377
Alignment explanation
Indices: 54211700--54212473 Score: 1016
Period size: 377 Copynumber: 2.1 Consensus size: 377
54211690 AATTTTGTTT
* * * *
54211700 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAAAAGGTTCGGAAAAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAAAGGTTCGAAAAAAATAATGTCAAAA
* * * * * * * *
54211765 ACGCTTCAAGCAGGATGTACTGTTAGTAAAATTACTGAATAAAGCTCCCACATGGACGCTCTTTT
66 ACGCTTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGAAAGCTCTTTT
* *
54211830 TCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAATAGTGTCAAAAATGTT
131 TCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAATAGTGTCAAAAACGCT
* * * *
54211895 TCAAGCAGGATACACTATAAGCAAAATTATTGAAAAAAGCTCCCATGTCGATGCTCTTTTTCTAC
196 TCAAGCAGGATACACTATAAGCAAAATTACTGAAAAAAGCTCACACGTCGATGATCTTTTTCTAC
54211960 AGTAGTTCCTGAAAAAATAA-TTTCGAAAAGACGGTTCTAAAAAAATAGTGTAAAAAACGCTTCA
261 AGTAGTTCCTGAAAAAATAATTTTC-AAAAGACGGTTCTAAAAAAATAGTGTAAAAAACGCTTCA
* * *
54212024 AGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
325 AACAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTA
* * * *
54212077 TTTTTCTACAGTGGTTCCTGAAAAAATAATTTTGA-AAAGACGGTTCTAAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAA-AAGGTTCGAAAAAAATAATGTCAAA
* *
54212141 AACGCTTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGTTCCCACGTGAAAGCTCTTT
65 AACGCTTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGAAAGCTCTTT
* * * ** *
54212206 TTCTACATTAGTTCTTG-AAAAATAATTTTTAGAAGAC-GTTTTTGAAAAAATAGTGTCAAAAAC
130 TTCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAG-TTCTG-AAAAATAGTGTCAAAAAC
* * * * * * *
54212269 GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCACACGTGGGTGATCTTTTTC
193 GCTTCAAGCAGGATACACTATAAGCAAAATTACTGAAAAAAGCTCACACGTCGATGATCTTTTTC
* * * * * * *
54212334 TACAGTAGTTCCTGAAAAAATAATTTTCAGAAGACGTTTTTGAAAAAATTGTGTCAAAAATGCTT
258 TACAGTAGTTCCTGAAAAAATAATTTTCAAAAGACGGTTCTAAAAAAATAGTGTAAAAAACGCTT
* * * **
54212399 CAAACAGGATGCACTGTCAGCAAAATTACTGAAAAATGGTCATACGTGGGTGCTA
323 CAAACAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTA
54212454 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
54212474 CTTGGCCTTA
Statistics
Matches: 340, Mismatches: 53, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
375 1 0.00
376 25 0.07
377 310 0.91
378 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (377 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAAAGGTTCGAAAAAAATAATGTCAAAA
ACGCTTCAAGCAGAATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGAAAGCTCTTTT
TCTAAAGTAGTTCATGAAAAAATAATTTAGAGAAGACAGTTCTGAAAAATAGTGTCAAAAACGCT
TCAAGCAGGATACACTATAAGCAAAATTACTGAAAAAAGCTCACACGTCGATGATCTTTTTCTAC
AGTAGTTCCTGAAAAAATAATTTTCAAAAGACGGTTCTAAAAAAATAGTGTAAAAAACGCTTCAA
ACAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTA
Found at i:54213874 original size:12 final size:12
Alignment explanation
Indices: 54213857--54213882 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54213847 CAAAACAGGC
54213857 TTTTAGCGGCGT
1 TTTTAGCGGCGT
54213869 TTTTAGCGGCGT
1 TTTTAGCGGCGT
54213881 TT
1 TT
54213883 GGACAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:54213931 original size:39 final size:39
Alignment explanation
Indices: 54213888--54213982 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
54213878 CGTTTGGACA
*
54213888 AAAAACGCCACTAAAATCAAGCATTAGAGGCGCTTTTCT-
1 AAAAACGCCGCTAAAATCAAGCATTAGAGGCGCTTTT-TG
* * *
54213927 AAAAACGCCGCTAAAGGTCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAA-ATCAAGCATTAGAGGCGCTTTTTG
*
54213967 GAAAACGCCGCTAAAA
1 AAAAACGCCGCTAAAA
54213983 ATAAGCGCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 15 0.31
40 33 0.69
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (39 bp):
AAAAACGCCGCTAAAATCAAGCATTAGAGGCGCTTTTTG
Found at i:54214474 original size:14 final size:14
Alignment explanation
Indices: 54214457--54214493 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54214447 GGGTTTAATA
54214457 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
54214471 TATATGATTTAGGG
1 TATATGGTTTAGGG
54214485 TATATGGTT
1 TATATGGTT
54214494 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:54214814 original size:14 final size:14
Alignment explanation
Indices: 54214795--54214840 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
54214785 TAAATAAGAT
*
54214795 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
54214809 TTAGGGGATAGGAG
1 TTAGGGGTTAGGAG
* *
54214823 TTAGAGGTTAGGGG
1 TTAGGGGTTAGGAG
54214837 TTAG
1 TTAG
54214841 AGCTAGTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.46, T:0.30
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:54215337 original size:13 final size:13
Alignment explanation
Indices: 54215319--54215343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54215309 ATAAATAAAT
54215319 AAATTAATGTAAC
1 AAATTAATGTAAC
54215332 AAATTAATGTAA
1 AAATTAATGTAA
54215344 TAGATTGACA
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:54238705 original size:6 final size:6
Alignment explanation
Indices: 54238694--54238729 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
54238684 GGAAACAATC
54238694 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TTT-TT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
54238730 GGGGGGGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTCTT
Found at i:54241865 original size:21 final size:21
Alignment explanation
Indices: 54241837--54241876 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54241827 TATAATTTTG
*
54241837 TAAAAAATT-ATTAAAATTTA
1 TAAAAAATTAAATAAAATTTA
54241857 TAAATAAATTAAATAAAATT
1 TAAA-AAATTAAATAAAATT
54241877 CAAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAAATTAAATAAAATTTA
Found at i:54252084 original size:21 final size:21
Alignment explanation
Indices: 54252060--54252100 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54252050 TCCAATTCAT
54252060 TATCA-ATACACATATATCTAA
1 TATCATATA-ACATATATCTAA
*
54252081 TATCATATAACATATTTCTA
1 TATCATATAACATATATCTA
54252101 TCCATTGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (21 bp):
TATCATATAACATATATCTAA
Found at i:54255016 original size:55 final size:55
Alignment explanation
Indices: 54254956--54255067 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
54254946 TTAGTTAATC
* *
54254956 TTAAATTTATCATTAATAGAAATCATCATCAAAATCTACTAAATACTATTCCAAA
1 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCCAAA
*
54255011 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCTAAA
1 TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCCAAA
54255066 TT
1 TT
54255068 GGTTTATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATTTATCATTAATAGAAATCATCACCAAAATATACTAAATACTATTCCAAA
Found at i:54258641 original size:28 final size:28
Alignment explanation
Indices: 54258588--54258641 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
54258578 GAGAAAATAA
* * *
54258588 TTTAATTAAGTGAATTAATTAAATTTAT
1 TTTAATTAAGTCAAATAAATAAATTTAT
54258616 TTTAATTAA-TCAAATAAATAATATTT
1 TTTAATTAAGTCAAATAAATAA-ATTT
54258642 TGAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (28 bp):
TTTAATTAAGTCAAATAAATAAATTTAT
Found at i:54258746 original size:44 final size:44
Alignment explanation
Indices: 54258683--54258767 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
54258673 AAATTATATG
*
54258683 AATTAATTTAAAGACTAGATAACACATATTAATACATAATATTA
1 AATTAATTTAAAGACTAGATAACACATATTAATACACAATATTA
*
54258727 AATTAGTTTAAAGACTAGATAACACATATTAATACACAATA
1 AATTAATTTAAAGACTAGATAACACATATTAATACACAATA
54258768 CATGAAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.32
Consensus pattern (44 bp):
AATTAATTTAAAGACTAGATAACACATATTAATACACAATATTA
Found at i:54259505 original size:12 final size:13
Alignment explanation
Indices: 54259472--54259503 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54259462 TTTCAAAAGT
*
54259472 ACTTTTTCACGTC
1 ACTTTTTCACATC
54259485 ACTTTTTCACATC
1 ACTTTTTCACATC
54259498 ACTTTT
1 ACTTTT
54259504 CAAAAACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (13 bp):
ACTTTTTCACATC
Found at i:54259521 original size:12 final size:13
Alignment explanation
Indices: 54259497--54259521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54259487 TTTTTCACAT
54259497 CACTTTTCAAAAA
1 CACTTTTCAAAAA
54259510 CACTTTTCAAAA
1 CACTTTTCAAAA
54259522 GCATTGCCAA
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
CACTTTTCAAAAA
Found at i:54262445 original size:17 final size:17
Alignment explanation
Indices: 54262423--54262455 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54262413 AAGGATAGTC
54262423 AGTAGCTGTTAGTCAAG
1 AGTAGCTGTTAGTCAAG
54262440 AGTAGCTGTTAGTCAA
1 AGTAGCTGTTAGTCAA
54262456 AGCTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (17 bp):
AGTAGCTGTTAGTCAAG
Found at i:54265608 original size:22 final size:23
Alignment explanation
Indices: 54265559--54265610 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
54265549 ATTAAAAAAA
* * *
54265559 ACTATTTTTTTGTTGTTTTGCTG
1 ACTATTTTCTTGTTATTTTGCTC
54265582 A-TATTTTCTTGTTATTTT-CTC
1 ACTATTTTCTTGTTATTTTGCTC
54265603 ACTATTTT
1 ACTATTTT
54265611 GCTACCATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 21 0.84
23 1 0.04
ACGTcount: A:0.13, C:0.12, G:0.10, T:0.65
Consensus pattern (23 bp):
ACTATTTTCTTGTTATTTTGCTC
Found at i:54266871 original size:23 final size:21
Alignment explanation
Indices: 54266832--54266876 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54266822 CCAAAAAAAA
*
54266832 TATTAATGTAAAATTATATAT
1 TATTAATATAAAATTATATAT
54266853 TATTAATATATAAATT-TAT-T
1 TATTAATATA-AAATTATATAT
54266873 TATT
1 TATT
54266877 CATTCTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTAATATAAAATTATATAT
Found at i:54275123 original size:15 final size:15
Alignment explanation
Indices: 54275099--54275133 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54275089 AAAACCCTAA
* *
54275099 CCTAAGCCCTAAATT
1 CCTAAACCCTAAATC
54275114 CCTAAACCCTAAATC
1 CCTAAACCCTAAATC
54275129 CCTAA
1 CCTAA
54275134 CTCTTAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (15 bp):
CCTAAACCCTAAATC
Found at i:54275164 original size:22 final size:22
Alignment explanation
Indices: 54275139--54275187 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54275129 CCTAACTCTT
*
54275139 AACCTCTAATGTCTAACCCCTA
1 AACCTCTAATATCTAACCCCTA
* * *
54275161 AACCCCTGATATCTAACCCCTG
1 AACCTCTAATATCTAACCCCTA
54275183 AACCT
1 AACCT
54275188 TAAATCCCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.39, G:0.06, T:0.24
Consensus pattern (22 bp):
AACCTCTAATATCTAACCCCTA
Found at i:54275247 original size:15 final size:15
Alignment explanation
Indices: 54275202--54275248 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
54275192 TCCCAACCCG
54275202 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
* *
54275216 T-AATCCATATTCTC
1 TAAATCCATAATCCC
*
54275230 TAAATCCATACTCCC
1 TAAATCCATAATCCC
54275245 TAAA
1 TAAA
54275249 CCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 15 0.56
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:54275535 original size:14 final size:14
Alignment explanation
Indices: 54275518--54275559 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
54275508 AACCCTTAAA
54275518 CCATAATCCCTAAT
1 CCATAATCCCTAAT
54275532 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
* *
54275547 TCATACTCCCTAA
1 CCATAATCCCTAA
54275560 ACCTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:54275556 original size:15 final size:15
Alignment explanation
Indices: 54275514--54275560 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
54275504 TCTCAACCCT
54275514 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
54275528 T-AATCCATAATCCC
1 TAAATCCATAATCCC
* *
54275542 TAAATTCATACTCCC
1 TAAATCCATAATCCC
54275557 TAAA
1 TAAA
54275561 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.41
15 15 0.52
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:54275582 original size:312 final size:314
Alignment explanation
Indices: 54275035--54275633 Score: 922
Period size: 312 Copynumber: 1.9 Consensus size: 314
54275025 ATCTTTTACA
54275035 ATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCCAAAACCCTAAC
1 ATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCCAAAACCCTAAC
* * *
54275100 CTAAGCCCTAAATTCCTAAACCCTAAATCCCTAACTCTTAACCTCTAATGTCTAACCCCTAAACC
66 CTAACCCCTAAATCCCTAAACCCTAAATCCCTAACTCTTAACCTCTAATATCTAACCCCTAAACC
* * * * * *
54275165 CCTGATATCTAACCCCTGAACCTTAAATCCCAACCCGTAAACCATAATCCCTAATCCATATTCTC
131 CCTAACATATAACCCCTAAACCTTAAATCCCAACCCGTAAACCATAATCCCTAATCCATAATCCC
* *
54275230 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAA-CTGGTCTTAAATCTTAAATTAAT
196 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATC-GGCCTTAAATCTTAAATAAAT
* *
54275294 CATATACCTTAAACTAAAAATCCTAAACAAATTGATTATTATCTCCTTTACAAAT
260 CATATACCCTAAACCAAAAATCCTAAACAAATTGATTATTATCTCCTTTACAAAT
*
54275349 ATTATATAAGAACATATTTAAAATATAAATT-AAAAAATAATTAATCTAAACCCAAAACCTTAA-
1 ATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCCAAAACCCTAAC
* *
54275412 CTCAACCCCTAAATCCCTAAACCCTGAAT-CCTAACTCTTAACC-CATAATATCTAACCCTTAAA
66 CT-AACCCCTAAATCCCTAAACCCTAAATCCCTAACTCTTAACCTC-TAATATCTAACCCCTAAA
* * * *
54275475 CCCCTAACCTATAACCCCTAAATCTTAAATCTCAACCCTTAAACCATAATCCCTAATCCATAATC
129 CCCCTAACATATAACCCCTAAACCTTAAATCCCAACCCGTAAACCATAATCCCTAATCCATAATC
* *
54275540 CCTAAATTCATACTCCCTAAACCTTAAAATA-GTAACTCCTAAATCGGCCTTAAATTTTAAATAA
194 CCTAAATCCATACTCCCTAAACCTTAAAATATG-AACTCCTAAATCGGCCTTAAATCTTAAATAA
54275604 ATCATATACCCTAAACCAAAAATCCTAAAC
258 ATCATATACCCTAAACCAAAAATCCTAAAC
54275634 TATAGTGATA
Statistics
Matches: 259, Mismatches: 22, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
311 2 0.01
312 171 0.66
313 55 0.21
314 31 0.12
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.28
Consensus pattern (314 bp):
ATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCCAAAACCCTAAC
CTAACCCCTAAATCCCTAAACCCTAAATCCCTAACTCTTAACCTCTAATATCTAACCCCTAAACC
CCTAACATATAACCCCTAAACCTTAAATCCCAACCCGTAAACCATAATCCCTAATCCATAATCCC
TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCGGCCTTAAATCTTAAATAAATC
ATATACCCTAAACCAAAAATCCTAAACAAATTGATTATTATCTCCTTTACAAAT
Found at i:54275970 original size:40 final size:41
Alignment explanation
Indices: 54275926--54276065 Score: 165
Period size: 41 Copynumber: 3.4 Consensus size: 41
54275916 GTTTTTTCAG
*
54275926 AAACGCCGCTAAAGCCCCCAGCATTAGCGGCGC-TTTTAAA
1 AAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCATTTTAAA
* * * *
54275966 AAACGCTGCTAAAACACCAAGCATTAGCGGCGCATTTTCAA
1 AAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCATTTTAAA
*** * * **
54276007 AAACGCCGCTAAAGCCTTGAGCATTAGCGGTGCTTTTTTGA
1 AAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCATTTTAAA
54276048 AAACGCCGCTAAAGCCCC
1 AAACGCCGCTAAAGCCCC
54276066 GAAAGGTAAG
Statistics
Matches: 82, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 29 0.35
41 53 0.65
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (41 bp):
AAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCATTTTAAA
Found at i:54278841 original size:23 final size:22
Alignment explanation
Indices: 54278814--54278857 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54278804 CGTTACCTTA
*
54278814 TTTTTGAAA-ACACGAGAAATTT
1 TTTTTTAAAGACACGA-AAATTT
54278836 TTTTTTAAAGACACGAAAATTT
1 TTTTTTAAAGACACGAAAATTT
54278858 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (22 bp):
TTTTTTAAAGACACGAAAATTT
Found at i:54279256 original size:15 final size:15
Alignment explanation
Indices: 54279221--54279260 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
54279211 CACTTTTTTT
54279221 TTCTTTTTTCTCTTC
1 TTCTTTTTTCTCTTC
54279236 TCTCTTTTTTCT-TTCC
1 T-TCTTTTTTCTCTT-C
54279252 TTCTTTTTT
1 TTCTTTTTT
54279261 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCTCTTC
Found at i:54279327 original size:26 final size:26
Alignment explanation
Indices: 54279272--54279326 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
54279262 TTTATTTTTT
**
54279272 CTGCTGGGCTAATGGGCGAACTGGGC
1 CTGCTGGGCTGCTGGGCGAACTGGGC
54279298 CTGCTGGGCTGCTGGG-GAA-TGGG-
1 CTGCTGGGCTGCTGGGCGAACTGGGC
54279321 CTGCTG
1 CTGCTG
54279327 CAGGCCTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 4 0.15
25 3 0.11
26 14 0.52
ACGTcount: A:0.11, C:0.22, G:0.45, T:0.22
Consensus pattern (26 bp):
CTGCTGGGCTGCTGGGCGAACTGGGC
Found at i:54279783 original size:21 final size:20
Alignment explanation
Indices: 54279726--54279782 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
54279716 GGAGGCTCTC
* *
54279726 CTCTTCTTCTCATTTCTCCT
1 CTCTTTTTCTCATTTTTCCT
* *
54279746 CTCTTTCTCTCCTTTTTCCT
1 CTCTTTTTCTCATTTTTCCT
54279766 CTTCTTTTTCTC-TTTTT
1 C-TCTTTTTCTCATTTTT
54279783 TGCAAGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (20 bp):
CTCTTTTTCTCATTTTTCCT
Found at i:54280107 original size:30 final size:29
Alignment explanation
Indices: 54280015--54280137 Score: 149
Period size: 29 Copynumber: 4.2 Consensus size: 29
54280005 GCTGAAATAA
*
54280015 AATTTTGAGAAAG-TTAGGGGTCAAAATGT
1 AATTTT-AAAAAGTTTAGGGGTCAAAATGT
* * *
54280044 AATTTCAAAAAGTTTATGGGTTAAAATGT
1 AATTTTAAAAAGTTTAGGGGTCAAAATGT
* * *
54280073 AATTTTATGAAATTTTAGGGGTCAAAATGC
1 AATTTTA-AAAAGTTTAGGGGTCAAAATGT
*
54280103 AATTTTAAAAAGTTTAGGGGCCAAAATGT
1 AATTTTAAAAAGTTTAGGGGTCAAAATGT
54280132 AATTTT
1 AATTTT
54280138 TTATTTTTTG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 5 0.06
29 49 0.63
30 24 0.31
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
AATTTTAAAAAGTTTAGGGGTCAAAATGT
Found at i:54280430 original size:77 final size:76
Alignment explanation
Indices: 54280337--54281588 Score: 729
Period size: 74 Copynumber: 16.6 Consensus size: 76
54280327 GGAGTGTCGC
* * *
54280337 CCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACAAAAATTTAAATGAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAA-GAAATA
* * *
54280402 CATCGGCATGGT
65 CCTCAGCATGAT
* *
54280414 CCGAGGCTTAACTCACCTCTCGCAATATGTGTTGATTTTTTTGAAAAAAAACAGAAATTTAAAAG
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT---AAAAAACAGAAATTT-AAAG
* *
54280479 AAGTACCTCAGCATGAC
60 AAATACCTCAGCATGAT
* * *
54280496 CCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAAGACAGAAA-TT-AA-AAAT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TAAAAA-ACAGAAATTTAAAGAAAT
*
54280558 ACCTCAGCGTGAT
64 ACCTCAGCATGAT
* * * * *
54280571 CCGAGGCTCAACTCACCT-TTGTATTATGAGTTGATTTTTAAAAAAAAGACCGAAATT-AA-AAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGA---AATTTAAAGAAA
* *
54280633 TACCTCAGCGTGAC
63 TACCTCAGCATGAT
* * * * *
54280647 CCGAGGCTCAACTCACCTCT-GTATTTTGAGTTGA-TTTT-AAAAA-AG--A---GAGGAAATAC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAGAAATAC
* *
54280703 CTCAGCGTGAC
66 CTCAGCATGAT
* * *
54280714 CCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTAAAAAA-AGACATAAATT-AA-A
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAACAG--A-AATTTAAAGA
* *
54280775 AATACCTCAGCGTGAC
61 AATACCTCAGCATGAT
* * * * *
54280791 CCGAGGCTCAACTCACCTCTCGTATTATGAGTTAATTTTAAAAAAGATAGAAA-TT-AA-AAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA-ACAGAAATTTAAAGAAATA
*
54280853 CCTCAGCGTGA-
65 CCTCAGCATGAT
* * * *
54280864 CTCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTT-AAAAA-AG--A---GAGGAAATA
1 C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAGAAATA
* *
54280920 CCTCAGCGTGAC
65 CCTCAGCATGAT
* * *
54280932 CCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTTTTAAAAAGACATAAA-TT-AA-
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTAAAAA-ACAGAAATTTAAAG
* *
54280993 AAATACCTCAGCGTGAC
60 AAATACCTCAGCATGAT
* * * * * * *
54281010 CCGAAGCTCAACTCACCTCTCGTATTATAAGTTAATTTTAAAAAAGATAGAAA-TT-AA-AAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA-ACAGAAATTTAAAGAAATA
* *
54281072 CCTCAGCGTGAC
65 CCTCAGCATGAT
* * * *
54281084 CCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAAGACCGAAATT-AA-AAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGA---AATTTAAAGAAA
*
54281146 TACCTCAGCGTGA-
63 TACCTCAGCATGAT
* * **
54281159 CGCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAAAGACAGAAA-TT-AA-
1 C-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT----TTAAAAA-ACAGAAATTTAAAG
* *
54281220 AAATACCTCAGCGTGAC
60 AAATACCTCAGCATGAT
* * * *
54281237 CCGAGGCTCAATTCACCTCT-GTATTATGAGTTGATTTTTTTTTTTAAAAAGACATAAA-TT-AA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA------TTTTTAAAAA-ACAGAAATTTAAA
* *
54281299 -AAATACCTCAGCGTGAC
59 GAAATACCTCAGCATGAT
* * *
54281316 CCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTAAAAAAGACAGAAA-TT-AA-AAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAA-ACAGAAATTTAAAGAAATA
* *
54281378 CCTCAGCGTGAC
65 CCTCAGCATGAT
* * * *
54281390 CCGAAGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTAAAAAA-AGACATAAATT-AA-A
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAACAG--A-AATTTAAAGA
* *
54281451 AATACCTCAGCGTGAC
61 AATACCTCAGCATGAT
* * * *
54281467 CCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTAAAAAAAAGACCGAAATT-AA-AAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGA---AATTTAAAGAAA
* *
54281528 TACCTCAGCGTGAC
63 TACCTCAGCATGAT
* * * *
54281542 CCGAGGCTCAACTCACCTTTCGTATTATGAGTTGATATTTGAAAAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTAAAAAA
54281589 AACAGAAAGT
Statistics
Matches: 1037, Mismatches: 60, Indels: 155
0.83 0.05 0.12
Matches are distributed among these distances:
66 2 0.00
67 100 0.10
68 2 0.00
69 2 0.00
70 5 0.00
71 11 0.01
72 11 0.01
73 63 0.06
74 189 0.18
75 99 0.10
76 137 0.13
77 177 0.17
78 72 0.07
79 77 0.07
80 23 0.02
81 4 0.00
82 57 0.05
83 6 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (76 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAGAAATAC
CTCAGCATGAT
Found at i:54280640 original size:76 final size:75
Alignment explanation
Indices: 54280336--54281606 Score: 1599
Period size: 77 Copynumber: 16.9 Consensus size: 75
54280326 CGGAGTGTCG
* * * *
54280336 CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACA-A-A-AATTTAAATGA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT-AAAAAAAGACAGAAATT-AA--A
* * * *
54280398 AATACATCGGCATGG
61 AATACCTCAGCGTGA
* * * * *
54280413 TCCGAGGCTTAACTCACCTCTCGCAATATGTGTTGATTTTTTTGAAAAAAA-ACAGAAATTTAAA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA--TTTTT-AAAAAAAGACAGAAA-TT-AA
*
54280477 AGAAGTACCTCAGCATGA
60 A-AA-TACCTCAGCGTGA
54280495 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTTAAAAAAAGACAGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATA
54280559 CCTCAGCGTGA
65 CCTCAGCGTGA
* * *
54280570 TCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTAAAAAAAAGACCGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT-AAAAAAAGACAGAAATTAAAAATA
54280635 CCTCAGCGTGA
65 CCTCAGCGTGA
* **
54280646 CCCGAGGCTCAACTCACCTCTGTATTTTGAGTTGA-TTTT-AAAAAAG--AG--A--GGAAATAC
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATAC
54280703 CTCAGCGTGA
66 CTCAGCGTGA
*
54280713 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTAAAAAAAGACATAAATTAAAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTAAAAAAAGACAGAAATTAAAAAT
54280778 ACCTCAGCGTGA
64 ACCTCAGCGTGA
* *
54280790 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTT-AATTTT-AAAAAAGATAGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATA
54280853 CCTCAGCGTGA
65 CCTCAGCGTGA
* **
54280864 CTCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTT-AAAAAAG--AG--A--GGAAATAC
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATAC
54280921 CTCAGCGTGA
66 CTCAGCGTGA
** *
54280931 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTTTTAAAAAGACATAAATTAAAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA---TTTTTAAAAAAAGACAGAAATTAAAAA
54280996 TACCTCAGCGTGA
63 TACCTCAGCGTGA
* * * *
54281009 CCCGAAGCTCAACTCACCTCTCGTATTATAAGTT-AATTTT-AAAAAAGATAGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATA
54281072 CCTCAGCGTGA
65 CCTCAGCGTGA
*
54281083 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACCGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTT-AAAAAAAGACAGAAATTAAAAATA
54281148 CCTCAGCGTGA
65 CCTCAGCGTGA
* **
54281159 CGCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAAAGACAGAAATTAAAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT--TTAAAAAAAGACAGAAATTAAAAAT
54281224 ACCTCAGCGTGA
64 ACCTCAGCGTGA
* ** *
54281236 CCCGAGGCTCAATTCACCTCTGTATTATGAGTTGATTTTTTTTTTTAAAAAGACATAAATTAAAA
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA----TTTTTAAAAAAAGACAGAAATTAAAA
54281301 ATACCTCAGCGTGA
62 ATACCTCAGCGTGA
54281315 CCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT-AAAAAAGACAGAAATTAAAAATA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATA
54281378 CCTCAGCGTGA
65 CCTCAGCGTGA
* *
54281389 CCCGAAGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTAAAAAAAGACATAAATTAAAAAT
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTAAAAAAAGACAGAAATTAAAAAT
54281454 ACCTCAGCGTGA
64 ACCTCAGCGTGA
* *
54281466 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGACCGAAATTAAAAATAC
1 CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATAC
54281531 CTCAGCGTGA
66 CTCAGCGTGA
* * *
54281541 CCCGAGGCTCAACTCACCTTTCGTATTATGAGTTGATATTTGAAAAAAA-ACAGAAAGTGAAAAA
1 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGAT-TTTTAAAAAAAGACAGAAA-TTAAAAA
54281605 TA
63 TA
54281607 TTTCTTGAAA
Statistics
Matches: 1069, Mismatches: 74, Indels: 102
0.86 0.06 0.08
Matches are distributed among these distances:
67 100 0.09
69 2 0.00
70 4 0.00
71 14 0.01
72 6 0.01
73 56 0.05
74 176 0.16
75 109 0.10
76 163 0.15
77 225 0.21
78 58 0.05
79 87 0.08
80 16 0.01
81 7 0.01
82 46 0.04
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (75 bp):
CCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATAC
CTCAGCGTGA
Found at i:54282484 original size:10 final size:9
Alignment explanation
Indices: 54282481--54282522 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
54282471 TTTTTCTGTT
54282481 TTTTTTTTG
1 TTTTTTTTG
54282490 TTTTTTTCT-
1 TTTTTTT-TG
*
54282499 TGTTTTTTG
1 TTTTTTTTG
54282508 TTATTTTTTG
1 TT-TTTTTTG
54282518 TTTTT
1 TTTTT
54282523 GTTTTTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 1 0.04
9 17 0.61
10 10 0.36
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:54282491 original size:11 final size:11
Alignment explanation
Indices: 54282466--54282529 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
54282456 TCATCTTGAT
54282466 TTTTCTTTTTCTG
1 TTTT-TTTTT-TG
54282479 TTTTTTTTTTG
1 TTTTTTTTTTG
*
54282490 TTTTTTTCTTG
1 TTTTTTTTTTG
54282501 TTTTTTGTTATT-
1 TTTTTT-TT-TTG
*
54282513 TTTTGTTTTTG
1 TTTTTTTTTTG
54282524 TTTTTT
1 TTTTTT
54282530 AGGCATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.05
11 25 0.57
12 11 0.25
13 6 0.14
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:54293899 original size:22 final size:20
Alignment explanation
Indices: 54293865--54293907 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
54293855 CGTTACCTTA
54293865 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
54293886 TTTTTTAAAGACACGAAAATT
1 TTTTTGAAA-ACACGAAAATT
54293907 T
1 T
54293908 CGAAGCCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:54294281 original size:7 final size:7
Alignment explanation
Indices: 54294265--54294331 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
54294255 GGTTACACAC
54294265 TTTT-TT
1 TTTTCTT
54294271 TTTTCTT
1 TTTTCTT
54294278 TTTTCTT
1 TTTTCTT
54294285 TTTTCTCT
1 TTTTCT-T
*
54294293 TATCTCTT
1 T-TTTCTT
54294301 TTTTC--
1 TTTTCTT
*
54294306 TTTCCTT
1 TTTTCTT
*
54294313 CTTT-TT
1 TTTTCTT
54294319 TTTTCTT
1 TTTTCTT
54294326 TTTTCT
1 TTTTCT
54294332 GTTGGGCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
5 4 0.08
6 9 0.18
7 28 0.57
8 4 0.08
9 4 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:54294288 original size:14 final size:14
Alignment explanation
Indices: 54294265--54294331 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 14
54294255 GGTTACACAC
54294265 TTTT-TTTTTTCTT
1 TTTTCTTTTTTCTT
54294278 TTTTCTTTTTTCTCT
1 TTTTCTTTTTTCT-T
*
54294293 TATCTCTTTTTTC--
1 T-TTTCTTTTTTCTT
* *
54294306 TTTCCTTCTTT-TT
1 TTTTCTTTTTTCTT
54294319 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
54294332 GTTGGGCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.17
13 14 0.33
14 9 0.21
15 2 0.05
16 10 0.24
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:54294404 original size:13 final size:14
Alignment explanation
Indices: 54294378--54294408 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
54294368 TGGGGAATGG
54294378 GCTGCTGCAGGCCT
1 GCTGCTGCAGGCCT
54294392 GCTGCTG-AGGCCT
1 GCTGCTGCAGGCCT
54294405 GCTG
1 GCTG
54294409 GATTGGGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.06, C:0.32, G:0.39, T:0.23
Consensus pattern (14 bp):
GCTGCTGCAGGCCT
Found at i:54294840 original size:20 final size:20
Alignment explanation
Indices: 54294784--54294842 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
54294774 TCGGAGGCTC
*
54294784 TCCTCTTC-TTCT-TCTTTC
1 TCCTCTTCTTTCTCTCTTTT
54294802 TCCTC-TCTTTCTCTCCTTTT
1 TCCTCTTCTTTCTCT-CTTTT
*
54294822 TCCTCTTCTTTTTCTCTTTT
1 TCCTCTTCTTTCTCTCTTTT
54294842 T
1 T
54294843 TGCAAGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.06
18 9 0.26
19 1 0.03
20 15 0.43
21 8 0.23
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TCCTCTTCTTTCTCTCTTTT
Found at i:54295111 original size:30 final size:29
Alignment explanation
Indices: 54295077--54295200 Score: 124
Period size: 29 Copynumber: 4.2 Consensus size: 29
54295067 GCTGAAACAA
*
54295077 AATTTTGAGAAAGTTTA-GGGTTCAAAATGT
1 AATTTT-AAAAAGTTTAGGGGTT-AAAATGT
* * * *
54295107 AATTTGAAAAAGTTTATGGATTAAAATAT
1 AATTTTAAAAAGTTTAGGGGTTAAAATGT
* * * *
54295136 AATTTTATGAAATTTTAGGGGTCAAAATGA
1 AATTTTA-AAAAGTTTAGGGGTTAAAATGT
*
54295166 AATTTTAAAAAATTTAGGGGTTAAAATGT
1 AATTTTAAAAAGTTTAGGGGTTAAAATGT
54295195 AATTTT
1 AATTTT
54295201 TTATTTTTTG
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
29 45 0.59
30 31 0.41
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.39
Consensus pattern (29 bp):
AATTTTAAAAAGTTTAGGGGTTAAAATGT
Found at i:54295140 original size:59 final size:59
Alignment explanation
Indices: 54295077--54295200 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
54295067 GCTGAAACAA
* * * *
54295077 AATTTTGA-GAAAGTTTAGGGTTCAAAATGTAATTTGAAAAAGTTTATGGATTAAAATAT
1 AATTTT-ATGAAAGTTTAGGGGTCAAAATGAAATTTGAAAAAATTTAGGGATTAAAATAT
* * * *
54295136 AATTTTATGAAATTTTAGGGGTCAAAATGAAATTTTAAAAAATTTAGGGGTTAAAATGT
1 AATTTTATGAAAGTTTAGGGGTCAAAATGAAATTTGAAAAAATTTAGGGATTAAAATAT
54295195 AATTTT
1 AATTTT
54295201 TTATTTTTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 1 0.02
59 55 0.98
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.39
Consensus pattern (59 bp):
AATTTTATGAAAGTTTAGGGGTCAAAATGAAATTTGAAAAAATTTAGGGATTAAAATAT
Found at i:54299399 original size:7 final size:7
Alignment explanation
Indices: 54299387--54299414 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54299377 ATGATGATTT
54299387 TTTTATA
1 TTTTATA
54299394 TTTTATA
1 TTTTATA
54299401 TTTTATA
1 TTTTATA
54299408 TTTTATA
1 TTTTATA
54299415 AATTAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:54302082 original size:19 final size:18
Alignment explanation
Indices: 54302058--54302121 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
54302048 TGCAAAACTA
54302058 AAAAAAATTTAAAATTTAT
1 AAAAAAATTTAAAATTT-T
*
54302077 AAAAAATATTTATAATTGTT
1 AAAAAA-ATTTAAAATT-TT
54302097 -AAAAAATTCTAAAATGTTTT
1 AAAAAAATT-TAAAA--TTTT
54302117 AAAAA
1 AAAAA
54302122 TAACATATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 3 0.08
19 15 0.41
20 12 0.32
21 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAAAATTTAAAATTTT
Found at i:54302103 original size:20 final size:20
Alignment explanation
Indices: 54302056--54302121 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
54302046 AGTGCAAAAC
*
54302056 TAAAAAAAATTTAAAATTTA
1 TAAAAAATATTTAAAATTTA
*
54302076 TAAAAAATATTTATAATTGT-
1 TAAAAAATATTTAAAATT-TA
* *
54302096 TAAAAAAT-TCTAAAATGTTT
1 TAAAAAATATTTAAAAT-TTA
54302116 TAAAAA
1 TAAAAA
54302122 TAACATATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 7 0.18
20 31 0.79
21 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAAATATTTAAAATTTA
Found at i:54302259 original size:19 final size:18
Alignment explanation
Indices: 54302234--54302306 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
54302224 GGATGACTTC
54302234 AAAATTATAAAAAAATTT
1 AAAATTATAAAAAAATTT
*
54302252 AGAAATTAT-AAAAGATATT
1 A-AAATTATAAAAAAAT-TT
*
54302271 AATAATTATTAAAAAATTAT
1 AA-AATTATAAAAAAATT-T
54302291 AAAAATTACTAAAAAA
1 -AAAATTA-TAAAAAA
54302307 TTAAAATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 8 0.18
19 17 0.38
20 12 0.27
21 8 0.18
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAATTATAAAAAAATTT
Found at i:54302297 original size:20 final size:20
Alignment explanation
Indices: 54302234--54302309 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
54302224 GGATGACTTC
*
54302234 AAAATTATAAAAAAATT-TA
1 AAAATTATTAAAAAATTATA
* *
54302253 GAAATTA-TAAAAGA-TATTA
1 AAAATTATTAAAAAATTA-TA
*
54302272 ATAATTATTAAAAAATTATA
1 AAAATTATTAAAAAATTATA
*
54302292 AAAATTACTAAAAAATTA
1 AAAATTATTAAAAAATTA
54302310 AAATGTGAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
17 1 0.02
18 5 0.11
19 13 0.29
20 24 0.53
21 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATTATTAAAAAATTATA
Found at i:54302305 original size:11 final size:10
Alignment explanation
Indices: 54302234--54302309 Score: 61
Period size: 11 Copynumber: 7.7 Consensus size: 10
54302224 GGATGACTTC
54302234 AAAATTATAAA
1 AAAATTAT-AA
54302245 AAAATT-T-A
1 AAAATTATAA
*
54302253 GAAATTATAA
1 AAAATTATAA
* *
54302263 AAGA-TATTA
1 AAAATTATAA
*
54302272 ATAATTATTAA
1 AAAATTA-TAA
54302283 AAAATTAT-A
1 AAAATTATAA
54302292 AAAATTACTAA
1 AAAATTA-TAA
54302303 AAAATTA
1 AAAATTA
54302310 AAATGTGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.12
9 15 0.29
10 8 0.16
11 22 0.43
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:54302369 original size:18 final size:20
Alignment explanation
Indices: 54302333--54302384 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
54302323 CTCAAAGAAG
54302333 TATTTAATATTTTTAATAAT
1 TATTTAATATTTTTAATAAT
54302353 TATTTAA-ATTTTT-ATAAT
1 TATTTAATATTTTTAATAAT
**
54302371 TATAAAATATTTTT
1 TATTTAATATTTTT
54302385 TTCCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 10 0.34
19 12 0.41
20 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAATATTTTTAATAAT
Found at i:54303477 original size:28 final size:29
Alignment explanation
Indices: 54303440--54303502 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
54303430 ACTTAATGGA
*
54303440 TTATTATTTTGGAT-TACTATTTGTTGATG
1 TTATTATTTT-GATGTAATATTTGTTGATG
*
54303469 TTATT-TTTTTATGTAATATTTGTTGATG
1 TTATTATTTTGATGTAATATTTGTTGATG
54303497 TTATTA
1 TTATTA
54303503 ATATTACGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 23 0.77
29 5 0.17
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (29 bp):
TTATTATTTTGATGTAATATTTGTTGATG
Found at i:54303497 original size:15 final size:13
Alignment explanation
Indices: 54303457--54303501 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
54303447 TTTGGATTAC
54303457 TATTTGTTGATGT
1 TATTTGTTGATGT
* *
54303470 TATTTTTTTATGT
1 TATTTGTTGATGT
54303483 AATATTTGTTGATGT
1 --TATTTGTTGATGT
54303498 TATT
1 TATT
54303502 AATATTACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
TATTTGTTGATGT
Found at i:54305880 original size:24 final size:24
Alignment explanation
Indices: 54305852--54305903 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
54305842 TTAGTAAGTC
* *
54305852 AAATAAACTATGCAAATAAATGCT
1 AAATAAACTATACAAATAAATACT
* * *
54305876 AAATATATTATACTAATAAATACT
1 AAATAAACTATACAAATAAATACT
54305900 AAAT
1 AAAT
54305904 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACAAATAAATACT
Found at i:54307314 original size:12 final size:12
Alignment explanation
Indices: 54307279--54307321 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
54307269 CTGAAGTAGT
*
54307279 TGATACTAATTGA
1 TGATAATAATT-A
54307292 TGAATAA-AATTA
1 TG-ATAATAATTA
54307304 TGATAATAATTA
1 TGATAATAATTA
54307316 TGATAA
1 TGATAA
54307322 AAGAGATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.15
12 14 0.52
13 6 0.22
14 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (12 bp):
TGATAATAATTA
Found at i:54308725 original size:18 final size:18
Alignment explanation
Indices: 54308672--54308728 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 18
54308662 GCGTTAATTT
* * *
54308672 ATTTTTAAAAAAATTATAG
1 ATTTATAAAAATATTA-AA
*
54308691 ATTTGTAAAACATTATTAAA
1 ATTTATAAAA-A-TATTAAA
54308711 ATTTATAAAAATATTAAA
1 ATTTATAAAAATATTAAA
54308729 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.22
19 10 0.31
20 11 0.34
21 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTTATAAAAATATTAAA
Found at i:54309252 original size:11 final size:10
Alignment explanation
Indices: 54309248--54309291 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
54309238 TTTTTATTAA
*
54309248 TTTTTAATTT
1 TTTTTAAATT
*
54309258 TTTTTAACTT
1 TTTTTAAATT
54309268 TTTTTAATATT
1 TTTTTAA-ATT
54309279 TTTTATAAATT
1 TTTT-TAAATT
54309290 TT
1 TT
54309292 AATAATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 16 0.53
11 11 0.37
12 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:54309261 original size:10 final size:10
Alignment explanation
Indices: 54309248--54309283 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54309238 TTTTTATTAA
54309248 TTTTTAATTT
1 TTTTTAATTT
*
54309258 TTTTTAACTT
1 TTTTTAATTT
*
54309268 TTTTTAATAT
1 TTTTTAATTT
54309278 TTTTTA
1 TTTTTA
54309284 TAAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:54309261 original size:20 final size:20
Alignment explanation
Indices: 54309238--54309295 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54309228 TTTTAGATGG
*
54309238 TTTTTATTAATTTTTAATTT
1 TTTTTATTAATTTTTAATAT
54309258 TTTTTAACTT--TTTTTAATAT
1 TTTTT-A-TTAATTTTTAATAT
*
54309278 TTTTTA-TAAATTTTAATA
1 TTTTTATTAATTTTTAATA
54309296 ATGTTTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 1 0.03
19 9 0.28
20 19 0.59
21 1 0.03
22 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTATTAATTTTTAATAT
Found at i:54309311 original size:19 final size:19
Alignment explanation
Indices: 54309269--54309310 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
54309259 TTTTAACTTT
* *
54309269 TTTTAATATTTTTTATAAA
1 TTTTAATATGTTTTACAAA
54309288 TTTTAATAATGTTTTACAAA
1 TTTTAAT-ATGTTTTACAAA
54309308 TTT
1 TTT
54309311 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTAATATGTTTTACAAA
Found at i:54311979 original size:26 final size:26
Alignment explanation
Indices: 54311943--54312009 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
54311933 AAAACAAGTA
* *
54311943 TTGAGCTGGTGGTTATGTAGTAGGCC
1 TTGAGCCGGTGGTTATGTAGCAGGCC
*
54311969 TTGAGCCGGTGGTTATTTAGCAGGCC
1 TTGAGCCGGTGGTTATGTAGCAGGCC
* * *
54311995 TCGAGTCAGTGGTTA
1 TTGAGCCGGTGGTTA
54312010 GCAGGCTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.16, C:0.15, G:0.36, T:0.33
Consensus pattern (26 bp):
TTGAGCCGGTGGTTATGTAGCAGGCC
Found at i:54313187 original size:29 final size:29
Alignment explanation
Indices: 54313155--54313255 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
54313145 CACGGGCTGT
* *
54313155 CACACGGTCGTGTACCACACACGGTCTCC
1 CACACGGCCGTGTGCCACACACGGTCTCC
* * * *
54313184 CACATGACCGTGTGCCACATATGGTCTCC
1 CACACGGCCGTGTGCCACACACGGTCTCC
* **
54313213 CACATC-GTCGTGTGGAACACACGGTCTCC
1 CACA-CGGCCGTGTGCCACACACGGTCTCC
54313242 CACACGGCCGTGTG
1 CACACGGCCGTGTG
54313256 GTTGTTTGAT
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
28 1 0.02
29 55 0.98
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (29 bp):
CACACGGCCGTGTGCCACACACGGTCTCC
Found at i:54316109 original size:3 final size:3
Alignment explanation
Indices: 54316101--54316156 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
54316091 AAATTAGTTA
54316101 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54316149 AAT AAT AA
1 AAT AAT AA
54316157 AAGGATAGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54316491 original size:31 final size:31
Alignment explanation
Indices: 54316456--54316515 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
54316446 AGGAAAATTA
*
54316456 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTCAATCCTAATAAAACTCTTT
54316487 CAAGAGTAATTCAATCCTAATAAAACTCT
1 CAAGAGTAATTCAATCCTAATAAAACTCT
54316516 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.30
Consensus pattern (31 bp):
CAAGAGTAATTCAATCCTAATAAAACTCTTT
Found at i:54322074 original size:12 final size:12
Alignment explanation
Indices: 54322056--54322085 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54322046 AGGTAGGCAA
54322056 CTTTTTTTTGCG
1 CTTTTTTTTGCG
*
54322068 GTTTTTTTTGCG
1 CTTTTTTTTGCG
54322080 CTTTTT
1 CTTTTT
54322086 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.70
Consensus pattern (12 bp):
CTTTTTTTTGCG
Found at i:54327578 original size:41 final size:41
Alignment explanation
Indices: 54327528--54327796 Score: 360
Period size: 41 Copynumber: 6.6 Consensus size: 41
54327518 TTAAACAGGT
* * * * *
54327528 TCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
54327569 TCATCGGCACTTAGCCTGCTAGGCTTATAGCCTAATCCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
54327610 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
54327651 TCACCGGCACTTAGCCCGCTAGGCTTATAGCCCGTTTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
54327692 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * *
54327732 TTCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGA
1 -TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
54327774 TCACTGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGG
54327797 TTTTAAAACC
Statistics
Matches: 198, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 197 0.99
42 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:54330656 original size:21 final size:21
Alignment explanation
Indices: 54330632--54330674 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54330622 CATGAGATTA
*
54330632 TAGGATTTCAACAATTCATTG
1 TAGGATTTCAAAAATTCATTG
54330653 TAGGATTTCAAAAATTCATTG
1 TAGGATTTCAAAAATTCATTG
54330674 T
1 T
54330675 GTTTCTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
TAGGATTTCAAAAATTCATTG
Found at i:54335057 original size:27 final size:27
Alignment explanation
Indices: 54335026--54335089 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
54335016 TATAAAATAT
*
54335026 ACAGTCATTTTATAACAT-AGGGGCATA
1 ACAGTCATTTTACAACATGA-GGGCATA
* *
54335053 ACAGTCATTTTACCACGTGAGGGCATA
1 ACAGTCATTTTACAACATGAGGGCATA
54335080 ACAGTCATTT
1 ACAGTCATTT
54335090 CATATCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (27 bp):
ACAGTCATTTTACAACATGAGGGCATA
Found at i:54343001 original size:13 final size:13
Alignment explanation
Indices: 54342985--54343012 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54342975 TTATGTGGAA
54342985 ATTAGACCATTAT
1 ATTAGACCATTAT
54342998 ATTAGACCATTAT
1 ATTAGACCATTAT
54343011 AT
1 AT
54343013 GTTATATATA
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:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTAGACCATTAT
Found at i:54344711 original size:41 final size:41
Alignment explanation
Indices: 54344644--54344914 Score: 434
Period size: 41 Copynumber: 6.6 Consensus size: 41
54344634 CTATACGTCA
* *
54344644 AGCAGGCTAAGTGTCGGTGATTTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
*
54344685 AGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
**
54344726 AGCAGGCTAAGTGCTAGTGATCTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
*
54344767 AGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
* *
54344808 AGAAAGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
* *
54344849 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
*
54344890 AGCAGGCTATGTGCCGGTGAATCTG
1 AGCAGGCTAAGTGCCGGTG-ATCTG
54344915 TTAAATTAAG
Statistics
Matches: 212, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
41 207 0.98
42 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (41 bp):
AGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCT
Found at i:54363205 original size:90 final size:90
Alignment explanation
Indices: 54363052--54363232 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
54363042 CACATTTTGA
54363052 CATGAGCATTCTTTTGTCATTTCACACATTAATAAGAGCATTCGTGTGTTTGTCTTTTGTGTCAA
1 CATGAGCATTCTTTTGTCATTTCACACATTAATAAGAGCATTCGTGTGTTTGTCTTTTGTGTCAA
54363117 AATGCTTTTTAAATGTAAAAAAGAC
66 AATGCTTTTTAAATGTAAAAAAGAC
54363142 CATGAGCATTCTTTTGTCATTTCACACATTAATAAGAGCATTCGTGTGTTTGTCTTTTGTGTCAA
1 CATGAGCATTCTTTTGTCATTTCACACATTAATAAGAGCATTCGTGTGTTTGTCTTTTGTGTCAA
54363207 AATGCTTTTTAAATGTAAAAAAGAC
66 AATGCTTTTTAAATGTAAAAAAGAC
54363232 C
1 C
54363233 CCAATTATTC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (90 bp):
CATGAGCATTCTTTTGTCATTTCACACATTAATAAGAGCATTCGTGTGTTTGTCTTTTGTGTCAA
AATGCTTTTTAAATGTAAAAAAGAC
Found at i:54365566 original size:24 final size:22
Alignment explanation
Indices: 54365522--54365566 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
54365512 TTTAATTTAA
* *
54365522 AAAATAAAAAAAACATTTTTTG
1 AAAATAAAAAAAAAATGTTTTG
54365544 AAAATGAAAATAAAAAATGTTTT
1 AAAAT-AAAA-AAAAAATGTTTT
54365567 CAGAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 4 0.21
24 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (22 bp):
AAAATAAAAAAAAAATGTTTTG
Found at i:54374281 original size:19 final size:20
Alignment explanation
Indices: 54374257--54374294 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
54374247 AAGTGCTTAC
54374257 ATGTGTAGTT-AATCAATAG
1 ATGTGTAGTTAAATCAATAG
*
54374276 ATGTGTGGTTAAATCAATA
1 ATGTGTAGTTAAATCAATA
54374295 CCCAAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (20 bp):
ATGTGTAGTTAAATCAATAG
Found at i:54378804 original size:15 final size:15
Alignment explanation
Indices: 54378781--54378815 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
54378771 AATAAATACT
*
54378781 AAACTTACATAAACA
1 AAACGTACATAAACA
54378796 AAACGTACATAAACA
1 AAACGTACATAAACA
54378811 AAACG
1 AAACG
54378816 CCATTTTCTA
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:0.60, C:0.20, G:0.06, T:0.14
Consensus pattern (15 bp):
AAACGTACATAAACA
Found at i:54379220 original size:64 final size:63
Alignment explanation
Indices: 54379146--54379271 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
54379136 GGATTATTTG
* * ***
54379146 TGAAAATACAAATACCATAATACAATACATTATTAATAGTTCAGGTACCAAATTAAACATTTTA
1 TGAAAATACAAATACCATAATAAAACACA-TATTAATAGTTCAAACACCAAATTAAACATTTTA
* * *
54379210 TGAAAGTACAAATACCATAATAAAACACATATTGATAGTTCAAACACCATATTAAACATTTT
1 TGAAAATACAAATACCATAATAAAACACATATTAATAGTTCAAACACCAAATTAAACATTTT
54379272 CAATACTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
63 28 0.52
64 26 0.48
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (63 bp):
TGAAAATACAAATACCATAATAAAACACATATTAATAGTTCAAACACCAAATTAAACATTTTA
Found at i:54379226 original size:31 final size:32
Alignment explanation
Indices: 54379191--54379271 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 32
54379181 ATAGTTCAGG
54379191 TACCAAATTAAACATTTTA-TGAAAGTACAAA
1 TACCAAATTAAACATTTTATTGAAAGTACAAA
* ** * *
54379222 TACCATAATAAAACA-CATATTGATAGTTCAAA
1 TACCA-AATTAAACATTTTATTGAAAGTACAAA
* *
54379254 CACCATATTAAACATTTT
1 TACCAAATTAAACATTTT
54379272 CAATACTACA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (32 bp):
TACCAAATTAAACATTTTATTGAAAGTACAAA
Found at i:54379236 original size:32 final size:33
Alignment explanation
Indices: 54379146--54379236 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 33
54379136 GGATTATTTG
*
54379146 TGAAAATACAAATACCATAATACAATACATTATTA
1 TGAAAGTACAAATACCATAATA-AA-ACATTATTA
* * ** *
54379181 --ATAGTTCAGGTACCA-AATTAAACATT-TTA
1 TGAAAGTACAAATACCATAATAAAACATTATTA
54379210 TGAAAGTACAAATACCATAATAAAACA
1 TGAAAGTACAAATACCATAATAAAACA
54379237 CATATTGATA
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
29 3 0.07
30 5 0.12
31 13 0.31
32 11 0.26
33 10 0.24
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (33 bp):
TGAAAGTACAAATACCATAATAAAACATTATTA
Done.