Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 125 of 173
Found at i:38275027 original size:18 final size:18
Alignment explanation
Indices: 38274979--38275033 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
38274969 TCATTTTGGC
*
38274979 TTTGATTTTGAT-TTTGAT
1 TTTGATTTTGATCTTT-TT
38274997 TTTGATTTT--TCTTTTT
1 TTTGATTTTGATCTTTTT
38275013 TTTGATTTTGATCTTTTT
1 TTTGATTTTGATCTTTTT
38275031 TTT
1 TTT
38275034 TGGATTGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 11 0.33
17 3 0.09
18 19 0.58
ACGTcount: A:0.11, C:0.04, G:0.11, T:0.75
Consensus pattern (18 bp):
TTTGATTTTGATCTTTTT
Found at i:38275044 original size:19 final size:19
Alignment explanation
Indices: 38275008--38275045 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38274998 TTGATTTTTC
*
38275008 TTTTTTTTGATTTTGATCT
1 TTTTTTTTGATTTGGATCT
38275027 TTTTTTTTGGA-TTGGATCT
1 TTTTTTTT-GATTTGGATCT
38275046 GAACCCATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (19 bp):
TTTTTTTTGATTTGGATCT
Found at i:38289192 original size:3 final size:3
Alignment explanation
Indices: 38289184--38289208 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38289174 TCGTTGCATC
38289184 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
38289209 TGTAGTGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:38291943 original size:3 final size:3
Alignment explanation
Indices: 38291935--38291982 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
38291925 AGTCCCCATT
*
38291935 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38291983 CTACTACTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:38292193 original size:12 final size:12
Alignment explanation
Indices: 38292176--38292204 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38292166 TATGCATACC
38292176 TACATATTTTAA
1 TACATATTTTAA
38292188 TACATATTTTAA
1 TACATATTTTAA
38292200 TACAT
1 TACAT
38292205 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:38293597 original size:39 final size:41
Alignment explanation
Indices: 38293496--38293599 Score: 99
Period size: 44 Copynumber: 2.5 Consensus size: 41
38293486 GGTTCGCTGT
*
38293496 AATGGAATAGA-GGTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
38293536 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
38293580 AATGGAAT-GATGTTGTAATA
1 AATGGAATAGATGCTGTAATA
38293600 ACATAAGGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 7 0.13
40 9 0.17
41 2 0.04
42 2 0.04
43 3 0.06
44 22 0.41
45 9 0.17
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:38293904 original size:59 final size:59
Alignment explanation
Indices: 38293709--38293906 Score: 185
Period size: 59 Copynumber: 3.4 Consensus size: 59
38293699 TATTAATATA
* * *
38293709 AATAATAAATAATTTAAT--CATAT--TTTAACATAATTATTATTAAATATAATTTAAT
1 AATAATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
* * * * * * **
38293764 AAAAATATATAATTTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAAT
1 AATAATATATAATTTAATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAAT
* *
38293825 CATAATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
1 AATAATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
38293884 AATAATATATAATTTAATAAAAT
1 AATAATATATAATTTAATAAAAT
38293907 TCAATATAAT
Statistics
Matches: 108, Mismatches: 23, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
55 16 0.15
57 1 0.01
58 4 0.04
59 38 0.35
60 15 0.14
61 31 0.29
62 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (59 bp):
AATAATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
Found at i:38293987 original size:117 final size:119
Alignment explanation
Indices: 38293738--38293972 Score: 384
Period size: 117 Copynumber: 2.0 Consensus size: 119
38293728 ATATTTTAAC
*
38293738 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
1 ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATTAAATAT
* *
38293803 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAA
65 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTAAA
* * *
38293858 ATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTC-AATA-TAATTATT
1 ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTAAATATT
*
38293921 CTTATATGAATTTACTAAAGTCATAATATATAATACTATAAAAAATAATGTA
66 CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTA
38293973 TAATCTACTT
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
117 56 0.51
118 4 0.04
120 50 0.45
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (119 bp):
ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTAAATATT
CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTAAA
Found at i:38293989 original size:120 final size:119
Alignment explanation
Indices: 38293732--38293969 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 119
38293722 TTAATCATAT
*
38293732 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
*
38293797 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
*
38293852 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
* *
38293915 ATTATTCTTATATGAATTTACTAAAGTCATAATATATAATACTATAAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
38293969 T
1 T
38293970 GTATAATCTA
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
117 54 0.48
118 4 0.04
120 55 0.49
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
Found at i:38295431 original size:49 final size:49
Alignment explanation
Indices: 38295359--38295462 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
38295349 AGAAAAAAAC
* * *
38295359 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
38295408 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
*
38295457 ATATTA
1 AAATTA
38295463 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:38305371 original size:87 final size:88
Alignment explanation
Indices: 38305197--38305372 Score: 309
Period size: 87 Copynumber: 2.0 Consensus size: 88
38305187 AGCGCTATCG
*
38305197 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTCTTTTTTTTAGTCTACCATCTTCAG
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
38305262 TTCGATTAGAATGGGTGAGAAGA
66 TTCGATTAGAATGGGTGAGAAGA
* *
38305285 TGCGTTGAGCAAAATTCCTAACCATCAATGCAAATGCTC-ATTTTTTTTAGTCTACCTTCTTCAG
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
*
38305349 TTCGATTGGAATGGGTGAGAAGA
66 TTCGATTAGAATGGGTGAGAAGA
38305372 T
1 T
38305373 TTCTTTTTGA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
87 46 0.55
88 38 0.45
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (88 bp):
TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
TTCGATTAGAATGGGTGAGAAGA
Found at i:38307100 original size:16 final size:16
Alignment explanation
Indices: 38307076--38307126 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
38307066 TGAATTACTA
38307076 ATTATAGCTCTATTCC
1 ATTATAGCTCTATTCC
* * *
38307092 ATTACAGCTTTATTAC
1 ATTATAGCTCTATTCC
*
38307108 ATTATAACTCTATTCC
1 ATTATAGCTCTATTCC
38307124 ATT
1 ATT
38307127 CTCCCTAACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTATAGCTCTATTCC
Found at i:38307405 original size:14 final size:14
Alignment explanation
Indices: 38307386--38307414 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38307376 GGATTATTAT
38307386 TAAAAATAATTTAA
1 TAAAAATAATTTAA
38307400 TAAAAATAATTTAA
1 TAAAAATAATTTAA
38307414 T
1 T
38307415 CATATTTTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATAATTTAA
Found at i:38307862 original size:42 final size:45
Alignment explanation
Indices: 38307786--38307887 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 45
38307776 GCCCATTTTT
* * * *
38307786 AAAATAAATATTAAAAAATTATTTTAAAAATAAAAAA-AAATA-AA
1 AAAATATATATT-TAAAAGTATTTTAAAAATAAAAAATAAAAATAA
* *
38307830 AAAATTTAT-TTTAAAAGTATTTTAAAATTAAAAAATAAAAATAA
1 AAAATATATATTTAAAAGTATTTTAAAAATAAAAAATAAAAATAA
38307874 AAAATATATATTTA
1 AAAATATATATTTA
38307888 TTATATTCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 21 0.44
43 6 0.12
44 17 0.35
45 4 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (45 bp):
AAAATATATATTTAAAAGTATTTTAAAAATAAAAAATAAAAATAA
Found at i:38329279 original size:31 final size:31
Alignment explanation
Indices: 38329230--38329303 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
38329220 ATTTAAACAA
* * *
38329230 AAAACATAAAAATTTAAAAATTATAATT-TTT
1 AAAATATAAAAA-TTAAAAATAAAAATTCTTT
38329261 AAAATATATAAAATTAAAAATAAAAATTCTTT
1 AAAATATA-AAAATTAAAAATAAAAATTCTTT
38329293 AAAAT-TAAAAA
1 AAAATATAAAAA
38329304 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 4 0.11
31 22 0.58
32 12 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAATTAAAAATAAAAATTCTTT
Found at i:38340548 original size:24 final size:25
Alignment explanation
Indices: 38340515--38340569 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
38340505 AACTGAAATA
*
38340515 AAAATTTAAAACCTAGA-AAAAGAG
1 AAAATCTAAAACCTAGACAAAAGAG
* *
38340539 AAAATCTAAAGCCTAGATCGAAAGAG
1 AAAATCTAAAACCTAGA-CAAAAGAG
38340565 AAAAT
1 AAAAT
38340570 TATACATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 15 0.58
26 11 0.42
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (25 bp):
AAAATCTAAAACCTAGACAAAAGAG
Found at i:38344023 original size:23 final size:23
Alignment explanation
Indices: 38343997--38344042 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38343987 ACAAACAACA
38343997 AATAATCTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
38344020 AATAATCTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
38344043 TCTAACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAATCTACTATTACTCCTACT
Found at i:38345078 original size:21 final size:21
Alignment explanation
Indices: 38345040--38345080 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38345030 ACCAATCCAT
*
38345040 TTTAACATATTTTCAAGATAG
1 TTTAACATATTATCAAGATAG
38345061 TTTAACATATTCAT-AAGATA
1 TTTAACATATT-ATCAAGATA
38345081 ACCTCATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTAACATATTATCAAGATAG
Found at i:38345340 original size:24 final size:24
Alignment explanation
Indices: 38345310--38345357 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
38345300 GGTAAGCACT
38345310 TTGTGCTTAGTAAGCTCGTGTAAC
1 TTGTGCTTAGTAAGCTCGTGTAAC
*
38345334 TTGTGCTTAGTAAGCTTGTGTAAC
1 TTGTGCTTAGTAAGCTCGTGTAAC
38345358 AAGAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (24 bp):
TTGTGCTTAGTAAGCTCGTGTAAC
Found at i:38348579 original size:18 final size:17
Alignment explanation
Indices: 38348532--38348579 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
38348522 ACAAAAGAAG
*
38348532 ATTTAGAGGTTCTAAAA
1 ATTTAGAGGTTTTAAAA
38348549 AGTTTAGA-GTTTTAAAA
1 A-TTTAGAGGTTTTAAAA
38348566 ATTTAGAGGATTTT
1 ATTTAGAGG-TTTT
38348580 GAGACAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 11 0.41
18 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (17 bp):
ATTTAGAGGTTTTAAAA
Found at i:38357146 original size:22 final size:22
Alignment explanation
Indices: 38357120--38357174 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
38357110 TACATAGGTG
38357120 ATGTCGAGACACACCAGGTCCT
1 ATGTCGAGACACACCAGGTCCT
*
38357142 GTGTC-ATGACACACCAGGTCCT
1 ATGTCGA-GACACACCAGGTCCT
*
38357164 ATGTCGCGACA
1 ATGTCGAGACA
38357175 TCGATGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (22 bp):
ATGTCGAGACACACCAGGTCCT
Found at i:38358427 original size:39 final size:39
Alignment explanation
Indices: 38358384--38358460 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
38358374 TCCACGTTAC
* *
38358384 ATTGTGTTGTCACA-CTATTGATTTGATGATTGCTTCCAT
1 ATTGTCTTGTCACATC-ATTGATTTGATGATTACTTCCAT
* *
38358423 ATTGTCTTGTTACATCATTGATTTGATGGTTACTTCCA
1 ATTGTCTTGTCACATCATTGATTTGATGATTACTTCCA
38358461 AGTTGCAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (39 bp):
ATTGTCTTGTCACATCATTGATTTGATGATTACTTCCAT
Found at i:38360433 original size:17 final size:15
Alignment explanation
Indices: 38360409--38360458 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
38360399 TTTTTTTTAA
38360409 TTTTAAAATACTTTT
1 TTTTAAAATACTTTT
* *
38360424 TTTTAAAAAATTTTT
1 TTTTAAAATACTTTT
38360439 AATTTTAAAATACTTTT
1 --TTTTAAAATACTTTT
38360456 TTT
1 TTT
38360459 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 16 0.55
17 13 0.45
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAAAATACTTTT
Found at i:38363866 original size:19 final size:18
Alignment explanation
Indices: 38363794--38363866 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
38363784 ACTTCTATAT
38363794 ATTTTATAATTCTTTTACTA
1 ATTTTATAATT-TTTTAC-A
* **
38363814 TTTTTATAAAATTTTACAA
1 ATTTTATAATTTTTTAC-A
* *
38363833 ATTTTATATTTTTTTACG
1 ATTTTATAATTTTTTACA
38363851 ATTTTATAATCTTTTT
1 ATTTTATAAT-TTTTT
38363867 CTAATTATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
18 9 0.21
19 25 0.60
20 8 0.19
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTTTTACA
Found at i:38363917 original size:10 final size:10
Alignment explanation
Indices: 38363901--38363954 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
38363891 TTTCTTATAT
38363901 TTTTTATTAA
1 TTTTTATTAA
*
38363911 ATTTTA-TAA
1 TTTTTATTAA
*
38363920 TTTTTATTGA
1 TTTTTATTAA
38363930 TTTTTATT--
1 TTTTTATTAA
*
38363938 TTTTTATCAA
1 TTTTTATTAA
38363948 TTTTTAT
1 TTTTTAT
38363955 CACATGTCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 22 0.59
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:38363923 original size:19 final size:19
Alignment explanation
Indices: 38363890--38363954 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
38363880 AAAATTAAAT
38363890 ATTTCTTATATTTTTTATTA
1 ATTT-TTATATTTTTTATTA
* * *
38363910 AATTTTATAATTTTTATTG
1 ATTTTTATATTTTTTATTA
*
38363929 ATTTTTAT-TTTTTTATCA
1 ATTTTTATATTTTTTATTA
38363947 ATTTTTAT
1 ATTTTTAT
38363955 CACATGTCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.39
19 20 0.53
20 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTTTATATTTTTTATTA
Found at i:38363956 original size:10 final size:9
Alignment explanation
Indices: 38363890--38363954 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
38363880 AAAATTAAAT
38363890 ATTTCTTATA
1 ATTT-TTATA
*
38363900 TTTTTTATTA
1 ATTTTTA-TA
*
38363910 AATTTTATA
1 ATTTTTATA
*
38363919 ATTTTTATTG
1 ATTTTTA-TA
38363929 ATTTTTAT-
1 ATTTTTATA
*
38363937 TTTTTTATCA
1 ATTTTTAT-A
38363947 ATTTTTAT
1 ATTTTTAT
38363955 CACATGTCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
8 7 0.16
9 12 0.27
10 25 0.57
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTTATA
Found at i:38366753 original size:15 final size:15
Alignment explanation
Indices: 38366711--38366778 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
38366701 CCAATTCGAC
* *
38366711 TAATTTTTTGAAAAT
1 TAATTATTTGAAAAA
**
38366726 TAATT-TTACAAAAA
1 TAATTATTTGAAAAA
38366740 TAATTATTTGAAAAA
1 TAATTATTTGAAAAA
* *
38366755 AAATTATTTTTAAAAA
1 TAATTA-TTTGAAAAA
38366771 -AATTATTT
1 TAATTATTT
38366779 TTTAAAAAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 14 0.32
15 22 0.50
16 8 0.18
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (15 bp):
TAATTATTTGAAAAA
Found at i:38366756 original size:18 final size:16
Alignment explanation
Indices: 38366735--38366800 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
38366725 TTAATTTTAC
38366735 AAAAATAATTATTTGAAA
1 AAAAATAATT-TTT-AAA
*
38366753 AAAAATTATTTTTAAA
1 AAAAATAATTTTTAAA
* *
38366769 AAAATTATTTTTTAAA
1 AAAAATAATTTTTAAA
*
38366785 AAGTAAATAAATTTTA
1 AA--AAATAATTTTTA
38366801 TTTCCAGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 18 0.46
17 3 0.08
18 18 0.46
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAAAATAATTTTTAAA
Found at i:38366766 original size:33 final size:32
Alignment explanation
Indices: 38366721--38366800 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
38366711 TAATTTTTTG
*
38366721 AAAATTAATTTTACAAAAATAATTATTTGAAAA
1 AAAATTAATTTTAAAAAAATAATT-TTTGAAAA
* * *
38366754 AAAATTATTTTTAAAAAAATTATTTTTTAAAA
1 AAAATTAATTTTAAAAAAATAATTTTTGAAAA
*
38366786 AGTAAATAAATTTTA
1 A--AAATTAATTTTA
38366801 TTTCCAGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 8 0.21
33 21 0.54
34 10 0.26
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (32 bp):
AAAATTAATTTTAAAAAAATAATTTTTGAAAA
Found at i:38366779 original size:15 final size:15
Alignment explanation
Indices: 38366721--38366786 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 15
38366711 TAATTTTTTG
*
38366721 AAAATTAATTTTACAAA
1 AAAATT-ATTTT-TAAA
**
38366738 AATAATTATTTGAAAA
1 AA-AATTATTTTTAAA
38366754 AAAATTATTTTTAAA
1 AAAATTATTTTTAAA
38366769 AAAATTATTTTTTAAA
1 AAAATTA-TTTTTAAA
38366785 AA
1 AA
38366787 GTAAATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
15 18 0.42
16 15 0.35
17 6 0.14
18 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AAAATTATTTTTAAA
Found at i:38368639 original size:24 final size:23
Alignment explanation
Indices: 38368612--38368705 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 23
38368602 AGCGTCCAGT
38368612 TATTAGCTCTCATGAGCATCTCGA
1 TATTAGCTCTCATGAGCATC-CGA
* * *
38368636 TATTGGCTCTCTTGAGCTTCCTGA
1 TATTAGCTCTCATGAGCATCC-GA
* * *
38368660 TATTTGGCTCTCATGAGCTTCCCA
1 TA-TTAGCTCTCATGAGCATCCGA
* *
38368684 TTAATAGCTCTTATGAGCATCC
1 -TATTAGCTCTCATGAGCATCC
38368706 CGATTGGTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 1 0.02
24 37 0.64
25 20 0.34
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (23 bp):
TATTAGCTCTCATGAGCATCCGA
Found at i:38368676 original size:25 final size:25
Alignment explanation
Indices: 38368612--38368681 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
38368602 AGCGTCCAGT
* *
38368612 TATTAGCTCTCATGAGCAT-CTCGA
1 TATTGGCTCTCATGAGCTTCCTCGA
*
38368636 TATTGGCTCTCTTGAGCTTCCT-GA
1 TATTGGCTCTCATGAGCTTCCTCGA
38368660 TATTTGGCTCTCATGAGCTTCC
1 TA-TTGGCTCTCATGAGCTTCC
38368682 CATTAATAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.39
Consensus pattern (25 bp):
TATTGGCTCTCATGAGCTTCCTCGA
Found at i:38368806 original size:24 final size:25
Alignment explanation
Indices: 38368752--38368883 Score: 96
Period size: 24 Copynumber: 5.4 Consensus size: 25
38368742 CGCAGCTTTT
* * *
38368752 ATGAGCGTCCTAATATTTGGCT-TT
1 ATGAGCTTCCTGATATTTGGCTCTC
38368776 ATGAGCTTCCTGA-ATTTGGCTCTC
1 ATGAGCTTCCTGATATTTGGCTCTC
*
38368800 ATGAGCTTTCTG-T-TTATGGCTCGT-
1 ATGAGCTTCCTGATATT-TGGCTC-TC
* * *
38368824 ATGAGCTTCCTGATAATTAGCTCAC
1 ATGAGCTTCCTGATATTTGGCTCTC
* * * *
38368849 AAGAGCTTCCTGTTATATAGCTCAT-
1 ATGAGCTTCCTGATATTTGGCTC-TC
38368874 ATGAGCTTCC
1 ATGAGCTTCC
38368884 CGTTTTATGG
Statistics
Matches: 86, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
23 10 0.12
24 40 0.47
25 35 0.41
26 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCTGATATTTGGCTCTC
Found at i:38368827 original size:48 final size:50
Alignment explanation
Indices: 38368775--38368883 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 50
38368765 TATTTGGCTT
* * * * * * *
38368775 TATGAGCTTCCTGA-ATTTGGCTCTCATGAGCTTTCTGTT-TATGGCTCG
1 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
38368823 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
38368873 TATGAGCTTCC
1 TATGAGCTTCC
38368884 CGTTTTATGG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 14 0.27
49 20 0.38
50 18 0.35
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (50 bp):
TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
Found at i:38368896 original size:25 final size:25
Alignment explanation
Indices: 38368775--38368896 Score: 92
Period size: 25 Copynumber: 5.0 Consensus size: 25
38368765 TATTTGGCTT
**
38368775 TATGAGCTTCCTGAATT-TGGCTC-
1 TATGAGCTTCCTGTTTTATGGCTCA
* *
38368798 TCATGAGCTTTCTG-TTTATGGCTCG
1 T-ATGAGCTTCCTGTTTTATGGCTCA
*
38368823 TATGAGCTTCCTGATAATTA--GCTCA
1 TATGAGCTTCCTG-T-TTTATGGCTCA
* * * *
38368848 CAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGTTTTATGGCTCA
*
38368873 TATGAGCTTCCCGTTTTATGGCTC
1 TATGAGCTTCCTGTTTTATGGCTC
38368897 GAAAGAGTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
23 5 0.06
24 29 0.38
25 40 0.52
27 3 0.04
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (25 bp):
TATGAGCTTCCTGTTTTATGGCTCA
Found at i:38373123 original size:76 final size:75
Alignment explanation
Indices: 38373022--38373268 Score: 305
Period size: 76 Copynumber: 3.3 Consensus size: 75
38373012 AGGACGTATA
* *
38373022 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGACACAAATCTTTATCGGTTAATCCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGG-CACAAATCTTTATCGGTTAATCCGA
*
38373087 CTAGTGTTGGG
65 CTAGTGCTGGG
* * * ** *
38373098 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGGCATAAATCTTTATTAGTTAATCCGG
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTT-GGCACAAATCTTTATCGGTTAATCCGA
* *
38373163 CTAGTACTAGG
65 CTAGTGCTGGG
* * * * *
38373174 CGCACATTTAATATCGTCGGTTTATCCGACTAGTGCTAGGCGCAAATCTTTGTCGGTTAATTCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTG-TTGGCACAAATCTTTATCGGTTAATCCGA
38373239 CTAGTGCTGGG
65 CTAGTGCTGGG
* *
38373250 TACACATTTAGTATCGTCG
1 CACACATTTAATATCGTCG
38373269 ATTGATCTGA
Statistics
Matches: 142, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
76 139 0.98
77 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (75 bp):
CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGCACAAATCTTTATCGGTTAATCCGAC
TAGTGCTGGG
Found at i:38373132 original size:40 final size:39
Alignment explanation
Indices: 38373022--38373268 Score: 138
Period size: 36 Copynumber: 6.5 Consensus size: 39
38373012 AGGACGTATA
* * *
38373022 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGA
1 CACAAATTTAATA-TGTCGGTTTATCCGACTAGTGTTGGG
*
38373062 CACAAATCTT--TA--TCGGTTAATCCGACTAGTGTTGGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* *
38373098 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * ** *
38373138 CATAAATCTT--TAT-T-AGTTAATCCGGCTAGTACTAGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * * *
38373174 CGCACATTTAATATCGTCGGTTTATCCGACTAGTGCTAGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * *
38373214 CGCAAATCT--T-TGTCGGTTAATTCGACTAGTGCTGGG
1 CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * *
38373250 TACACATTTAGTATCGTCG
1 CACAAATTTAATAT-GTCG
38373269 ATTGATCTGA
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
35 4 0.03
36 73 0.46
37 7 0.04
38 2 0.01
39 7 0.04
40 62 0.39
41 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (39 bp):
CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
Found at i:38374801 original size:17 final size:17
Alignment explanation
Indices: 38374781--38374815 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38374771 GTAAAAAAAT
* *
38374781 GATAAAAGTATAATTTA
1 GATAAAAATAGAATTTA
38374798 GATAAAAATAGAATTTA
1 GATAAAAATAGAATTTA
38374815 G
1 G
38374816 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
GATAAAAATAGAATTTA
Found at i:38374905 original size:13 final size:13
Alignment explanation
Indices: 38374889--38374915 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38374879 AGCAGAGAAT
38374889 TGTGAGAAATGTG
1 TGTGAGAAATGTG
38374902 TGTGAGAAATGTG
1 TGTGAGAAATGTG
38374915 T
1 T
38374916 TGGGGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGAGAAATGTG
Found at i:38376987 original size:9 final size:9
Alignment explanation
Indices: 38376952--38377027 Score: 57
Period size: 9 Copynumber: 8.1 Consensus size: 9
38376942 TTTTACTCAT
38376952 TTTTAAATAA
1 TTTTAAA-AA
**
38376962 TTTTAATGA
1 TTTTAAAAA
38376971 TTTT-AAAA
1 TTTTAAAAA
38376979 TTTTAAAAA
1 TTTTAAAAA
38376988 TAAATTT-AAAA
1 T---TTTAAAAA
**
38376999 TTCTTTGAAA
1 TT-TTAAAAA
38377009 TTTTAAAAA
1 TTTTAAAAA
38377018 TTTTAAAAA
1 TTTTAAAAA
38377027 T
1 T
38377028 AATTAAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
8 7 0.13
9 27 0.51
10 11 0.21
11 5 0.09
12 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:38381611 original size:18 final size:18
Alignment explanation
Indices: 38381590--38381656 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
38381580 TAAAAATTAT
*
38381590 AAAAAATTTTATTTTTTA
1 AAAAAATTATATTTTTTA
38381608 AAAAAATTATATTTTTTTA
1 AAAAAATTATA-TTTTTTA
*
38381627 TTAAAAATTATATTTTTTA
1 -AAAAAATTATATTTTTTA
*
38381646 AAAATATTATA
1 AAAAAATTATA
38381657 AATTTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.44
19 14 0.33
20 10 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAAAAATTATATTTTTTA
Found at i:38381633 original size:38 final size:38
Alignment explanation
Indices: 38381568--38381671 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 38
38381558 TAAAATTATA
* ** * *
38381568 TTAAAAAAATCATAAA-AATTATAAAAAATTTTATTTT
1 TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
**
38381605 TTAAAAAAATTATATTTTTTTATTAAAAATTATATTTT
1 TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
*
38381643 TTAAAAATATTATAAATTTTTATTAAAAA
1 TTAAAAAAATTATAAATTTTTATTAAAAA
38381672 ATATCAATAC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
37 13 0.23
38 43 0.77
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
Found at i:38381661 original size:20 final size:18
Alignment explanation
Indices: 38381589--38381664 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 18
38381579 ATAAAAATTA
*
38381589 TAAAAAATT-TTATTTTT
1 TAAAAAATTATAATTTTT
*
38381606 TAAAAAAATTATATTTTTT
1 T-AAAAAATTATAATTTTT
38381625 TATTAAAAATTAT-ATTTTT
1 TA--AAAAATTATAATTTTT
*
38381644 TAAAAATATTATAAATTTT
1 TAAAAA-ATTATAATTTTT
38381663 TA
1 TA
38381665 TTAAAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.10
18 14 0.29
19 21 0.43
20 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAAAATTATAATTTTT
Found at i:38387429 original size:26 final size:25
Alignment explanation
Indices: 38387386--38387445 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
38387376 TTTACCCCCA
*
38387386 GTAAAATTTGAAAATTTTACCCTTG
1 GTAAAATTTGAAAATTTTACCATTG
** * *
38387411 GTAAAATCTTGATGATTTTTCTATTG
1 GTAAAAT-TTGAAAATTTTACCATTG
38387437 GTAAAATTT
1 GTAAAATTT
38387446 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (25 bp):
GTAAAATTTGAAAATTTTACCATTG
Found at i:38392423 original size:26 final size:26
Alignment explanation
Indices: 38392394--38392455 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
38392384 TATCCCCAAC
*
38392394 AAAATTTTGACAATTTTACCCTTGAT
1 AAAATTTTGACAATTTTACCCCTGAT
* * * *
38392420 AAAATTTTAACGATTTTGCCCCTGGT
1 AAAATTTTGACAATTTTACCCCTGAT
38392446 AAAATTTTGA
1 AAAATTTTGA
38392456 GAAAATATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTGAT
Found at i:38393588 original size:31 final size:30
Alignment explanation
Indices: 38393553--38393617 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
38393543 TTATTTAATA
38393553 CATTAAAGAAAGTGAGTTTATGATAATTATT
1 CATTAAA-AAAGTGAGTTTATGATAATTATT
* *
38393584 CATT--AATATTGAGTTTATGATAATTATT
1 CATTAAAAAAGTGAGTTTATGATAATTATT
38393612 CATTAA
1 CATTAA
38393618 TATTAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 25 0.83
29 1 0.03
31 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (30 bp):
CATTAAAAAAGTGAGTTTATGATAATTATT
Found at i:38393596 original size:28 final size:28
Alignment explanation
Indices: 38393565--38393621 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
38393555 TTAAAGAAAG
38393565 TGAGTTTATGATAATTATTCATTAATAT
1 TGAGTTTATGATAATTATTCATTAATAT
38393593 TGAGTTTATGATAATTATTCATTAATAT
1 TGAGTTTATGATAATTATTCATTAATAT
38393621 T
1 T
38393622 AAATGTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (28 bp):
TGAGTTTATGATAATTATTCATTAATAT
Found at i:38394445 original size:30 final size:29
Alignment explanation
Indices: 38394402--38394483 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 29
38394392 TAGGGTCTAG
* *
38394402 GGGTTCTAAAAAAATAATATTGACGAGTT
1 GGGTTCTAAAAAAATAATTTTGACGAGAT
* *
38394431 GGGTTCTAAAAAAAATAATTTTTATGAGAT
1 GGGTTCT-AAAAAAATAATTTTGACGAGAT
*
38394461 GGGTTCTAAAGAAATAATTTTGA
1 GGGTTCTAAAAAAATAATTTTGA
38394484 AGAAAAAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 21 0.46
30 25 0.54
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
GGGTTCTAAAAAAATAATTTTGACGAGAT
Found at i:38400909 original size:25 final size:25
Alignment explanation
Indices: 38400881--38400942 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
38400871 TCATTATACA
38400881 GCTCACATGAGCTTCCCG-TTATAT
1 GCTCACATGAGCTTCCCGTTTATAT
*
38400905 GGCTCGA-AAGAGCTTCCCGTTTATAT
1 -GCTC-ACATGAGCTTCCCGTTTATAT
38400931 GCTCACATGAGC
1 GCTCACATGAGC
38400943 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 24 0.75
26 7 0.22
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (25 bp):
GCTCACATGAGCTTCCCGTTTATAT
Found at i:38401134 original size:62 final size:62
Alignment explanation
Indices: 38401063--38401192 Score: 260
Period size: 62 Copynumber: 2.1 Consensus size: 62
38401053 TAGGAGTACG
38401063 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
1 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
38401125 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
1 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
38401187 AAATGA
1 AAATGA
38401193 GATGAAAGAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (62 bp):
AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
Found at i:38405935 original size:19 final size:18
Alignment explanation
Indices: 38405910--38405954 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
38405900 ACGAATTGTA
* *
38405910 TATTTTTTTCTCTTATTT
1 TATTTTTTTCTATTATTC
*
38405928 TCATTTTTATCTATTATTC
1 T-ATTTTTTTCTATTATTC
38405947 TATTTTTT
1 TATTTTTT
38405955 CGAAGGAGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTTTTTCTATTATTC
Found at i:38406798 original size:3 final size:3
Alignment explanation
Indices: 38406711--38406779 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
38406701 CCTTTTTGTG
* * *
38406711 TTA TTT TTA TTA TTA TTAA TTA GT- TTA ATA TT- TTCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* *
38406756 TTA TTA TCA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
38406780 CTACTACTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
2 3 0.06
3 44 0.85
4 5 0.10
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:38409692 original size:13 final size:13
Alignment explanation
Indices: 38409674--38409702 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38409664 TTAAATTACG
38409674 ATGTGATTAAATC
1 ATGTGATTAAATC
38409687 ATGTGATTAAATC
1 ATGTGATTAAATC
38409700 ATG
1 ATG
38409703 CTCTATGTGT
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:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (13 bp):
ATGTGATTAAATC
Found at i:38410052 original size:39 final size:39
Alignment explanation
Indices: 38409831--38410052 Score: 239
Period size: 40 Copynumber: 5.6 Consensus size: 39
38409821 TTGAATGCTG
* * * * * *
38409831 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
38409871 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
38409911 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
38409951 TCCGGGTTAAGTCCCGAAGGCATCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
38409990 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
38410029 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
38410053 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 74 0.47
40 75 0.47
41 9 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:38410076 original size:78 final size:79
Alignment explanation
Indices: 38409906--38410087 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 79
38409896 GTGCGAGATA
* * *
38409906 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
**
38409971 CATCGTGCGAGTTG
66 CATCGTGCGAGGAG
* * * *
38409985 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
38410049 CAT-TTGAACGAGGAG
66 CATCGTG--CGAGGAG
* *
38410064 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
38410088 TACGTGATTT
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.02
78 47 0.54
79 38 0.44
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATCGTGCGAGGAG
Found at i:38417921 original size:39 final size:39
Alignment explanation
Indices: 38417718--38417939 Score: 223
Period size: 40 Copynumber: 5.6 Consensus size: 39
38417708 TTGAATGCTG
* * * * * *
38417718 TCCGGGCTAAGT-CCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
38417757 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
38417797 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
38417837 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
38417877 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
38417916 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
38417940 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 48 0.30
40 101 0.64
41 9 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:38417959 original size:79 final size:80
Alignment explanation
Indices: 38417792--38417974 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
38417782 GTGCGAGATA
* * *
38417792 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
38417857 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
38417872 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
38417936 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
38417951 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
38417975 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:38421267 original size:26 final size:26
Alignment explanation
Indices: 38421218--38421267 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
38421208 AATTGGAAAG
* *
38421218 TTAAATAATAAAATATGATAATTTAA
1 TTAAATAAGAAAATATCATAATTTAA
*
38421244 TTAAATAAGAAAATATCATCATTT
1 TTAAATAAGAAAATATCATAATTT
38421268 TATATCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
TTAAATAAGAAAATATCATAATTTAA
Found at i:38422400 original size:25 final size:25
Alignment explanation
Indices: 38422378--38422434 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
38422368 ATTGGCTCGT
38422378 AAGAGCTTCCCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCAC
* * ** *
38422403 ATGAGTTTCCCGTTATATGGCTCAA
1 AAGAGCTTCCCGTTATACAGCTCAC
38422428 AAGAGCT
1 AAGAGCT
38422435 ACTCGTTTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (25 bp):
AAGAGCTTCCCGTTATACAGCTCAC
Found at i:38423878 original size:23 final size:23
Alignment explanation
Indices: 38423852--38423944 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
38423842 AGCGTCCAGT
38423852 TATTAGCTCTCATGAGCATCCGA
1 TATTAGCTCTCATGAGCATCCGA
* * *
38423875 TATTGGCTCTCTTGAGCTTCCTGA
1 TATTAGCTCTCATGAGCATCC-GA
* * *
38423899 TATTTGGCTCTCATGAGCTTCCCA
1 TA-TTAGCTCTCATGAGCATCCGA
* *
38423923 TTAATAGCTCTTATGAGCATCC
1 -TATTAGCTCTCATGAGCATCC
38423945 CGATTGGTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 18 0.31
24 20 0.34
25 20 0.34
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (23 bp):
TATTAGCTCTCATGAGCATCCGA
Found at i:38423905 original size:25 final size:23
Alignment explanation
Indices: 38423852--38423920 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 23
38423842 AGCGTCCAGT
* *
38423852 TATTAGCTCTCATGAGCATCCGA
1 TATTGGCTCTCATGAGCTTCCGA
*
38423875 TATTGGCTCTCTTGAGCTTCCTGA
1 TATTGGCTCTCATGAGCTTCC-GA
38423899 TATTTGGCTCTCATGAGCTTCC
1 TA-TTGGCTCTCATGAGCTTCC
38423921 CATTAATAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 18 0.45
24 4 0.10
25 18 0.45
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (23 bp):
TATTGGCTCTCATGAGCTTCCGA
Found at i:38424045 original size:23 final size:21
Alignment explanation
Indices: 38424005--38424075 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 21
38423995 GCGTCCTAAT
*
38424005 ATTTGGCTTTATGAGCTTCTG
1 ATTTGGCTCTATGAGCTTCTG
38424026 AATTTGGCTCTCATGAGCTTTCTG
1 -ATTTGGCTCT-ATGAGC-TTCTG
*
38424050 TTTATGGCTCGTATGAGCTTCCTG
1 ATT-TGGCTC-TATGAGCTT-CTG
38424074 AT
1 AT
38424076 AATTAGCTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.22
23 10 0.24
24 21 0.51
25 1 0.02
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (21 bp):
ATTTGGCTCTATGAGCTTCTG
Found at i:38424121 original size:50 final size:48
Alignment explanation
Indices: 38424014--38424121 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 48
38424004 TATTTGGCTT
* * * * * * *
38424014 TATGAGCTT-CTGAATTTGGCTCTCATGAGCTTTCTGTTTATGGCTCG
1 TATGAGCTTCCTGAAATTAGCTCACAAGAGCTTCCTGTTTATAGCTCA
38424061 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGA-AATTAGCTCACAAGAGCTTCCTGTT-TATAGCTCA
38424111 TATGAGCTTCC
1 TATGAGCTTCC
38424122 CGTTTTATGG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 9 0.18
48 4 0.08
49 20 0.39
50 18 0.35
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (48 bp):
TATGAGCTTCCTGAAATTAGCTCACAAGAGCTTCCTGTTTATAGCTCA
Found at i:38424134 original size:25 final size:25
Alignment explanation
Indices: 38424014--38424134 Score: 83
Period size: 25 Copynumber: 5.0 Consensus size: 25
38424004 TATTTGGCTT
**
38424014 TATGAGCTT-CTGAATT-TGGCTC-
1 TATGAGCTTCCTGTTTTATGGCTCA
* *
38424036 TCATGAGCTTTCTG-TTTATGGCTCG
1 T-ATGAGCTTCCTGTTTTATGGCTCA
*
38424061 TATGAGCTTCCTGATAATTA--GCTCA
1 TATGAGCTTCCTG-T-TTTATGGCTCA
* * * *
38424086 CAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGTTTTATGGCTCA
*
38424111 TATGAGCTTCCCGTTTTATGGCTC
1 TATGAGCTTCCTGTTTTATGGCTC
38424135 GAAAGAGTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
22 1 0.01
23 12 0.16
24 21 0.27
25 40 0.52
27 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (25 bp):
TATGAGCTTCCTGTTTTATGGCTCA
Found at i:38428359 original size:76 final size:76
Alignment explanation
Indices: 38428258--38428504 Score: 323
Period size: 76 Copynumber: 3.2 Consensus size: 76
38428248 AGGACGTATA
* * *
38428258 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGACACAAATCTTTATCGGTTAATCCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
*
38428323 CTAGTGTTGGG
66 CTAGTGCTGGG
* * * ** *
38428334 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGGCATAAATCTTTATTAGTTAATCCGG
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
* *
38428399 CTAGTACTAGG
66 CTAGTGCTGGG
* * * * *
38428410 CGCACATTTAATATCGTCGGTTTATCCGACTAGTGCTGGGCGCAAATCTTTGTCGGTTAATTCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
38428475 CTAGTGCTGGG
66 CTAGTGCTGGG
* *
38428486 TACACATTTAGTATCGTCG
1 CACACATTTAATATCGTCG
38428505 ATTGATCTGA
Statistics
Matches: 143, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 143 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (76 bp):
CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
CTAGTGCTGGG
Found at i:38428368 original size:40 final size:39
Alignment explanation
Indices: 38428258--38428504 Score: 147
Period size: 36 Copynumber: 6.5 Consensus size: 39
38428248 AGGACGTATA
* * *
38428258 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGA
1 CACAAATTTAATA-TGTCGGTTTATCCGACTAGTGTTGGG
*
38428298 CACAAATCTT--TA--TCGGTTAATCCGACTAGTGTTGGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* *
38428334 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * ** *
38428374 CATAAATCTT--TAT-T-AGTTAATCCGGCTAGTACTAGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * *
38428410 CGCACATTTAATATCGTCGGTTTATCCGACTAGTGCTGGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * *
38428450 CGCAAATCT--T-TGTCGGTTAATTCGACTAGTGCTGGG
1 CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * *
38428486 TACACATTTAGTATCGTCG
1 CACAAATTTAATAT-GTCG
38428505 ATTGATCTGA
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
35 4 0.03
36 74 0.47
37 7 0.04
38 2 0.01
39 7 0.04
40 61 0.38
41 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (39 bp):
CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
Found at i:38430038 original size:17 final size:17
Alignment explanation
Indices: 38430018--38430052 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38430008 GTAAAAAAAT
* *
38430018 GATAAAAGTATAATTTA
1 GATAAAAATAGAATTTA
38430035 GATAAAAATAGAATTTA
1 GATAAAAATAGAATTTA
38430052 G
1 G
38430053 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
GATAAAAATAGAATTTA
Found at i:38430142 original size:13 final size:13
Alignment explanation
Indices: 38430126--38430152 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38430116 AGCAGAGAAT
38430126 TGTGAGAAATGTG
1 TGTGAGAAATGTG
38430139 TGTGAGAAATGTG
1 TGTGAGAAATGTG
38430152 T
1 T
38430153 TGGGGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGAGAAATGTG
Found at i:38432224 original size:9 final size:9
Alignment explanation
Indices: 38432189--38432264 Score: 57
Period size: 9 Copynumber: 8.1 Consensus size: 9
38432179 TTTTACTCAT
38432189 TTTTAAATAA
1 TTTTAAA-AA
*
38432199 TTTTAATAA
1 TTTTAAAAA
38432208 TTTT-AAAA
1 TTTTAAAAA
38432216 TTTTAAAAA
1 TTTTAAAAA
38432225 TAAATTT-AAAA
1 T---TTTAAAAA
**
38432236 TTCTTTGAAA
1 TT-TTAAAAA
38432246 TTTTAAAAA
1 TTTTAAAAA
*
38432255 ATTTAAAAA
1 TTTTAAAAA
38432264 T
1 T
38432265 AATTAAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
8 8 0.15
9 26 0.49
10 11 0.21
11 5 0.09
12 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:38435490 original size:20 final size:21
Alignment explanation
Indices: 38435465--38435503 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38435455 AAACTGACTT
*
38435465 TTGAAAAGCT-TTTGTTTGGC
1 TTGAAAAACTATTTGTTTGGC
38435485 TTGAAAAACTATTTGTTTG
1 TTGAAAAACTATTTGTTTG
38435504 CAATTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (21 bp):
TTGAAAAACTATTTGTTTGGC
Found at i:38442242 original size:6 final size:6
Alignment explanation
Indices: 38442231--38442270 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
38442221 AAATTTTAAA
38442231 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
38442271 TAGTATGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:38442375 original size:19 final size:20
Alignment explanation
Indices: 38442351--38442396 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
38442341 ATATTCTTTA
*
38442351 GAATTTTTATAAA-TATTTT
1 GAATTTTTAAAAATTATTTT
38442370 GAATTTTTAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
38442390 -AATTTTT
1 GAATTTTT
38442397 TATTGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:38445087 original size:18 final size:18
Alignment explanation
Indices: 38445030--38445087 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 18
38445020 GTTTTTTTAA
38445030 TGTTTTTTGCTTAGAAAAT
1 TGTTTTTT-CTTAGAAAAT
*
38445049 TGTTTTTTTATTCAAAGAAAAT
1 TG-TTTTTTCTT---AGAAAAT
38445071 TGTTTTTTCTTAGAAAA
1 TGTTTTTTCTTAGAAAA
38445088 GATGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 6 0.18
21 8 0.24
22 9 0.27
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (18 bp):
TGTTTTTTCTTAGAAAAT
Found at i:38445542 original size:33 final size:33
Alignment explanation
Indices: 38445478--38445553 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
38445468 TGACTATTGA
* * * **
38445478 GGAGGGTGATGTTGAAGGGGTGGAAGTTGATGG
1 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
38445511 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
1 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
* *
38445544 TGATGGTGAT
1 GGAGGGTGAT
38445554 CTAGAAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.01, G:0.49, T:0.24
Consensus pattern (33 bp):
GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
Found at i:38446875 original size:34 final size:34
Alignment explanation
Indices: 38446832--38446900 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
38446822 TGGAGGAAGT
38446832 TAGAGAAATCTTATGAGTGATTTCTAGCAGATTG
1 TAGAGAAATCTTATGAGTGATTTCTAGCAGATTG
38446866 TAGAGAAATCTTATGAGTGATTTCTAGCAGATTG
1 TAGAGAAATCTTATGAGTGATTTCTAGCAGATTG
38446900 T
1 T
38446901 GAAGTGCACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (34 bp):
TAGAGAAATCTTATGAGTGATTTCTAGCAGATTG
Found at i:38448681 original size:16 final size:16
Alignment explanation
Indices: 38448660--38448698 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38448650 GTTTTTGACT
38448660 TGTATAGCATGAATAG
1 TGTATAGCATGAATAG
** *
38448676 TGTATAGGGTGAATGG
1 TGTATAGCATGAATAG
38448692 TGTATAG
1 TGTATAG
38448699 ACTAATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (16 bp):
TGTATAGCATGAATAG
Found at i:38449089 original size:212 final size:210
Alignment explanation
Indices: 38448722--38449137 Score: 674
Period size: 212 Copynumber: 2.0 Consensus size: 210
38448712 TTTTGTAAAG
* * *
38448722 TACATTTATCCAAATTGCAAAGGGGAAATCATATGCTTAAATGATCAAATTTGTCTTTTTAGTCT
1 TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTCT
* *
38448787 TATGTTTATTGTCACTGCATTATTTATTAAGCTAAATTAAATTAGGCATAAACAATAAATATTAG
66 TATGTTTATTGTCACTGCATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTAG
* *
38448852 CCATTACTTCCAAGCATTATGTTAAATTACATAAAAAAAACAACCAATATTAGTTAATCAACATT
131 CCATTACTTCCAAGCATAATGTTAAATTACAT--AAAAAACAACCAATATTAGTCAATCAACATT
38448917 TGCAACTGCTAGCTGCA
194 TGCAACTGCTAGCTGCA
*
38448934 TACATTTATCTAAATCGCAATA-GGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTC
1 TACATTTATCCAAATCGCAA-AGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTC
*
38448998 TTATGTTTATTGTTACTGCATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATT-
65 TTATGTTTATTGTCACTGCATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTA
* *
38449062 GATCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTTGTCAATCAACATT
130 G-CCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTAGTCAATCAACATT
*
38449127 TGTAACTGCTA
194 TGCAACTGCTA
38449138 ATTGCATATG
Statistics
Matches: 190, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
210 39 0.21
211 1 0.01
212 149 0.78
213 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (210 bp):
TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTCT
TATGTTTATTGTCACTGCATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATTAG
CCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTAGTCAATCAACATTTG
CAACTGCTAGCTGCA
Found at i:38451764 original size:31 final size:30
Alignment explanation
Indices: 38451720--38451780 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
38451710 AGGCAAATTG
38451720 CAAGAGTTTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTTTGAATCCTAATAAAAACTCTTT
38451749 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGT--TTGAATCCTAATAAAAACTCTTT
38451781 AAAATTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 7 0.24
31 12 0.41
32 10 0.34
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (30 bp):
CAAGAGTTTGAATCCTAATAAAAACTCTTT
Found at i:38456027 original size:34 final size:32
Alignment explanation
Indices: 38455984--38456058 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
38455974 AGGTAGGCAA
*
38455984 CTTTTTTTTTGCAGTTTTTTTTTTGCGCTTTTTG
1 CTTTTTTTTTGC-G-GTTTTTTTTGCGCTTTTTG
38456018 CTTTTTTTTTGCGGTTTTTTTTGCGCTTTTTG
1 CTTTTTTTTTGCGGTTTTTTTTGCGCTTTTTG
38456050 CTTTTTTTT
1 CTTTTTTTT
38456059 AAGAATAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 27 0.68
33 1 0.03
34 12 0.30
ACGTcount: A:0.01, C:0.12, G:0.15, T:0.72
Consensus pattern (32 bp):
CTTTTTTTTTGCGGTTTTTTTTGCGCTTTTTG
Found at i:38456056 original size:20 final size:20
Alignment explanation
Indices: 38455999--38456036 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38455989 TTTTTGCAGT
38455999 TTTTTTTTTGCGCTTTTTGC
1 TTTTTTTTTGCGCTTTTTGC
*
38456019 TTTTTTTTTGCGGTTTTT
1 TTTTTTTTTGCGCTTTTT
38456037 TTTGCGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.16, T:0.74
Consensus pattern (20 bp):
TTTTTTTTTGCGCTTTTTGC
Found at i:38458300 original size:22 final size:23
Alignment explanation
Indices: 38458275--38458319 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38458265 AACACAATTC
38458275 ATAAAAAAT-TGAAAAATATAAA
1 ATAAAAAATATGAAAAATATAAA
* *
38458297 ATAAAAAGTATGAAAATTATAAA
1 ATAAAAAATATGAAAAATATAAA
38458320 TTTTTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (23 bp):
ATAAAAAATATGAAAAATATAAA
Found at i:38469947 original size:35 final size:35
Alignment explanation
Indices: 38469907--38469987 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
38469897 GAGAGCGATT
38469907 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
38469942 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
38469977 GAGCAATACAT
1 GAGCAATACAT
38469988 AATTGAATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (35 bp):
GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
Found at i:38479942 original size:153 final size:153
Alignment explanation
Indices: 38479769--38480055 Score: 468
Period size: 153 Copynumber: 1.9 Consensus size: 153
38479759 TATTTAAATG
*
38479769 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTTTTAAAAGCACTTTTTGA
1 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
** * *
38479834 CAACAATACT-AACACTTAAATCTTAAACTGAACTTTTCAAAACTACTTCTCAAAATCATTTTTC
66 CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTTCTCAAAATCACTTTT-
38479898 TAAAATACTTTTTAAAATAGGCAT
130 TAAAATACTTTTTAAAATAGGCAT
* * *
38479922 TTTATTTGTTACTTTATAACACCATGTCTAAAATGAGCATTTTATTTCTTAAAATCACTTTTTGA
1 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
* *
38479987 CAGCAATATTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTTCTCAAAATCACTTTTT
66 CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTTCTCAAAATCACTTTTT
38480052 AAAA
131 AAAA
38480056 GCAGTTTATC
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
153 74 0.60
154 49 0.40
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (153 bp):
TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTTCTCAAAATCACTTTTT
AAAATACTTTTTAAAATAGGCAT
Found at i:38480407 original size:2 final size:2
Alignment explanation
Indices: 38480402--38480433 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38480392 CCCACTTACT
38480402 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38480434 ACACACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:38483101 original size:31 final size:31
Alignment explanation
Indices: 38483066--38483128 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
38483056 ATATACTTGG
38483066 CTATATGCCTTTACTAGAGTAGCCTCACTAT
1 CTATATGCCTTTACTAGAGTAGCCTCACTAT
38483097 CTATATGCCTTTACTAGAGTAGCCTCACTAT
1 CTATATGCCTTTACTAGAGTAGCCTCACTAT
38483128 C
1 C
38483129 ACAACAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (31 bp):
CTATATGCCTTTACTAGAGTAGCCTCACTAT
Found at i:38484743 original size:54 final size:52
Alignment explanation
Indices: 38484632--38484786 Score: 186
Period size: 54 Copynumber: 2.9 Consensus size: 52
38484622 CATCTCCTAA
* *
38484632 GGTATTTTGGTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGC
1 GGTATTTTGGTCATTTTATCCTATGGGGTATTTCG-TCATTTTACCTTATAGC
* *
38484685 GGTATTTCGATCATTTTATCCTATGAGGGTATTTCAGTCATTTTACCTTATGAG-
1 GGTATTTTGGTCATTTTATCCTATG-GGGTATTTC-GTCATTTTACCTTAT-AGC
* * *
38484739 GGTATTTTGGTCATTTTATCTTATGGCGGTATTTTTGTTATTTTACCT
1 GGTATTTTGGTCATTTTATCCTATGG-GGTA-TTTCGTCATTTTACCT
38484787 ATTTTAAGGT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
53 23 0.26
54 59 0.67
55 6 0.07
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (52 bp):
GGTATTTTGGTCATTTTATCCTATGGGGTATTTCGTCATTTTACCTTATAGC
Found at i:38484763 original size:27 final size:27
Alignment explanation
Indices: 38484632--38484756 Score: 164
Period size: 27 Copynumber: 4.7 Consensus size: 27
38484622 CATCTCCTAA
*
38484632 GGTATTTTGGTCATTTTACCCTATG-G
1 GGTATTTCGGTCATTTTACCCTATGAG
*
38484658 GGTATTTCGATCATTTTACCCTAT-AG
1 GGTATTTCGGTCATTTTACCCTATGAG
* *
38484684 CGGTATTTCGATCATTTTATCCTATGAG
1 -GGTATTTCGGTCATTTTACCCTATGAG
* *
38484712 GGTATTTCAGTCATTTTACCTTATGAG
1 GGTATTTCGGTCATTTTACCCTATGAG
*
38484739 GGTATTTTGGTCATTTTA
1 GGTATTTCGGTCATTTTA
38484757 TCTTATGGCG
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 23 0.26
27 62 0.71
28 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (27 bp):
GGTATTTCGGTCATTTTACCCTATGAG
Found at i:38484773 original size:27 final size:26
Alignment explanation
Indices: 38484632--38484772 Score: 156
Period size: 27 Copynumber: 5.3 Consensus size: 26
38484622 CATCTCCTAA
*
38484632 GGTATTTTGGTCATTTTACCCTATGG
1 GGTATTTCGGTCATTTTACCCTATGG
* *
38484658 GGTATTTCGATCATTTTACCCTATAGC
1 GGTATTTCGGTCATTTTACCCTAT-GG
* *
38484685 GGTATTTCGATCATTTTATCCTATGAG
1 GGTATTTCGGTCATTTTACCCTATG-G
* *
38484712 GGTATTTCAGTCATTTTACCTTATGAG
1 GGTATTTCGGTCATTTTACCCTATG-G
* * *
38484739 GGTATTTTGGTCATTTTATCTTATGG
1 GGTATTTCGGTCATTTTACCCTATGG
38484765 CGGTATTT
1 -GGTATTT
38484773 TTGTTATTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
26 24 0.24
27 76 0.76
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (26 bp):
GGTATTTCGGTCATTTTACCCTATGG
Found at i:38487415 original size:36 final size:37
Alignment explanation
Indices: 38487366--38487461 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
38487356 GTCTCCAATT
* * *
38487366 TCACATTTTAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
38487402 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
*
38487440 TCA-ATATTCATTTCAATTTCAC
1 TCACA-ATTCAATTCAATTTCAC
38487462 ACATATATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
36 12 0.24
37 27 0.54
38 11 0.22
ACGTcount: A:0.31, C:0.23, G:0.01, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:38490162 original size:20 final size:20
Alignment explanation
Indices: 38490124--38490165 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
38490114 AAATAAACAC
**
38490124 ATAACTATTTATTTAATATT
1 ATAACTATTTAAATAATATT
*
38490144 ATAACTATTTAAATGATATT
1 ATAACTATTTAAATAATATT
38490164 AT
1 AT
38490166 TTAAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAACTATTTAAATAATATT
Found at i:38493590 original size:4 final size:4
Alignment explanation
Indices: 38493576--38493626 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
38493566 GATGCACCTG
*
38493576 CATA AATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
38493624 CAT
1 CAT
38493627 GATCATCTTG
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:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:38498751 original size:24 final size:24
Alignment explanation
Indices: 38498723--38498771 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
38498713 ACATAACTTA
38498723 CCATTTCATTTGCATAATATAAAG
1 CCATTTCATTTGCATAATATAAAG
38498747 CCATTTCATTTGCATAATATAAAG
1 CCATTTCATTTGCATAATATAAAG
38498771 C
1 C
38498772 ATAAGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (24 bp):
CCATTTCATTTGCATAATATAAAG
Found at i:38508447 original size:16 final size:17
Alignment explanation
Indices: 38508428--38508459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38508418 TTAGGGAAGA
38508428 GAAATAA-TAGTTGGAT
1 GAAATAATTAGTTGGAT
38508444 GAAATAATTAGTTGGA
1 GAAATAATTAGTTGGA
38508460 ATAGATCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (17 bp):
GAAATAATTAGTTGGAT
Found at i:38516630 original size:41 final size:41
Alignment explanation
Indices: 38516573--38516719 Score: 231
Period size: 41 Copynumber: 3.6 Consensus size: 41
38516563 AGTAAGATGA
* *
38516573 TTCAGACTTTAAGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
* *
38516614 TTCAGACTTTTCGTCTAGCAGGCTTGATGCCAGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
* *
38516655 TTTAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
*
38516696 TTCTGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
38516720 AATTGCTGGT
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
Found at i:38517168 original size:21 final size:21
Alignment explanation
Indices: 38517144--38517194 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
38517134 ATGCATTTGG
*
38517144 ATATATACAGGTGATAAATAC
1 ATATATACAAGTGATAAATAC
* * * *
38517165 ATATACACAATTGATACATAT
1 ATATATACAAGTGATAAATAC
38517186 ATATATACA
1 ATATATACA
38517195 CAGAGATATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (21 bp):
ATATATACAAGTGATAAATAC
Found at i:38519601 original size:22 final size:22
Alignment explanation
Indices: 38519575--38519616 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38519565 AATACGAGAA
38519575 AATATGGAACTAAAAAGAAATG
1 AATATGGAACTAAAAAGAAATG
*
38519597 AATATGGAACTAAGAAGAAA
1 AATATGGAACTAAAAAGAAA
38519617 AGTTGTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (22 bp):
AATATGGAACTAAAAAGAAATG
Found at i:38520247 original size:22 final size:22
Alignment explanation
Indices: 38520220--38520261 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
38520210 CAAAAGAATA
38520220 ATGATATAAACGTTTATCAATG
1 ATGATATAAACGTTTATCAATG
38520242 ATGATATAAACGTTTATCAA
1 ATGATATAAACGTTTATCAA
38520262 ACTCGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
ATGATATAAACGTTTATCAATG
Found at i:38521411 original size:4 final size:4
Alignment explanation
Indices: 38521402--38521557 Score: 60
Period size: 4 Copynumber: 37.5 Consensus size: 4
38521392 GGGAAAGGAG
* *
38521402 AAGA AAGA AAGA AAGAA AATGA AAGGA GAGGG AAGA AAG- AA-A AAGA
1 AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA AAGA
* *
38521448 AGGA AAGAA AAGGA AAGGA GAAGA AA-A AAGA AAGAA AACGA AGGA AAGAA
1 AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAG-A AA-GA AAGA AAG-A
**
38521498 AAGGA AAGGA GAAGA AA-A AA-A AAGA AAG- AAG- AAG- AAG- AAGA GGGA
1 AA-GA AA-GA -AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
38521543 AAGAA AAGA AAGA AA
1 AAG-A AAGA AAGA AA
38521558 AAAAAGGTAA
Statistics
Matches: 122, Mismatches: 13, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
3 25 0.20
4 48 0.39
5 40 0.33
6 9 0.07
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:38521453 original size:10 final size:11
Alignment explanation
Indices: 38521433--38521556 Score: 90
Period size: 10 Copynumber: 12.3 Consensus size: 11
38521423 AAAGGAGAGG
*
38521433 GAAGAAAGAAA
1 GAAGAAGGAAA
38521444 -AAGAAGGAAA
1 GAAGAAGGAAA
38521454 GAA-AAGGAAA
1 GAAGAAGGAAA
*
38521464 GGAGAA-GAAA
1 GAAGAAGGAAA
* *
38521474 AAAGAAAGAAA
1 GAAGAAGGAAA
*
38521485 -ACGAAGGAAA
1 GAAGAAGGAAA
38521495 GAA-AAGGAAA
1 GAAGAAGGAAA
*
38521505 GGAGAA-GAAA
1 GAAGAAGGAAA
* *
38521515 -AAAAAAGAAA
1 GAAGAAGGAAA
38521525 GAAGAA-G-AA
1 GAAGAAGGAAA
*
38521534 GAAGAGGGAAA
1 GAAGAAGGAAA
38521545 GAA-AA-GAAA
1 GAAGAAGGAAA
38521554 GAA
1 GAA
38521557 AAAAAAGGTA
Statistics
Matches: 91, Mismatches: 13, Indels: 20
0.73 0.10 0.16
Matches are distributed among these distances:
9 17 0.19
10 54 0.59
11 20 0.22
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAA
Found at i:38521473 original size:20 final size:20
Alignment explanation
Indices: 38521410--38521558 Score: 105
Period size: 20 Copynumber: 7.5 Consensus size: 20
38521400 AGAAGAAAGA
*
38521410 AAGAAAGAAAATGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
* * *
38521430 AGGGAAG-AAA-GAAA-AAG
1 AAGAAAGAAAAGGAAAGGAG
38521447 AAGGAAAGAAAAGGAAAGGAG
1 AA-GAAAGAAAAGGAAAGGAG
* *
38521468 AAGAAAAAAGAAAGAAA--ACG
1 AAGAAAGAA-AAGGAAAGGA-G
38521488 AAGGAAAGAAAAGGAAAGGAG
1 AA-GAAAGAAAAGGAAAGGAG
* * *
38521509 AAGAAAAAAAAAGAAAGAAG
1 AAGAAAGAAAAGGAAAGGAG
* *
38521529 AAG-AAGAAGAGGGAAA-GAA
1 AAGAAAGAA-AAGGAAAGGAG
38521548 AAGAAAGAAAA
1 AAGAAAGAAAA
38521559 AAAAGGTAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 23
0.70 0.13 0.16
Matches are distributed among these distances:
17 3 0.03
18 8 0.08
19 16 0.16
20 52 0.53
21 19 0.19
22 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAAGGAG
Found at i:38521491 original size:41 final size:41
Alignment explanation
Indices: 38521400--38521531 Score: 173
Period size: 41 Copynumber: 3.3 Consensus size: 41
38521390 GAGGGAAAGG
* * **
38521400 AGAAGAAAGAAAGAAAGAAAATGAAAGGAG-AG--GGAAGAA
1 AGAA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
38521439 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
*
38521480 AGAAAACGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAA-AA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
38521520 AGAAAGAAGAAG
1 AGAAA-AAGAAG
38521532 AAGAAGAGGG
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
38 23 0.28
39 6 0.07
40 7 0.08
41 47 0.57
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (41 bp):
AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
Found at i:38522470 original size:317 final size:317
Alignment explanation
Indices: 38521890--38523095 Score: 1653
Period size: 317 Copynumber: 3.9 Consensus size: 317
38521880 AAAATGGTAT
* * * *
38521890 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
1 ATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* * *
38521955 AATTAAAAATTATGGTATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAATGGCTGA
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGA
* * * *
38522020 AGTAAGAGTGTTTTACTAAATTTTTTAAAAGTTTAGAAATAATTAATACAAATATTTCAAACAAA
131 AGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAAA
38522085 ATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA
196 ATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA
*
38522150 TTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGTTTTTTTTTACACTAAATTA
261 TTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTA
*
38522207 ATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATTTAAAATTATAA
1 ATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
38522272 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAAC-AATGGGCCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAAT-GGCCG
38522336 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
130 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
*
38522401 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTCATTGAAAGTAATAAA
195 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
* * *
38522466 ATTCGAGAAAATAATACAAGCAAAAGACAGGAATAAGGGTTTTTTTTACACTAAATTA
260 ATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTA
*
38522524 ATTTTAAAAACACACTAAATTCATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
1 ATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* * *
38522589 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATAAGAATAAAGGGCCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAACAAATGGCCG
38522654 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
130 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
* * *
38522719 AATGTATTGAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAA
195 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
* * *
38522784 ATTCGGGAAAATTATACGAGTAAAGGGCAGGAATAAAAGGGTTTTTTTTACACTAAA-T-
260 ATTCGAGAAAATAATACGAGCAAAGGGCAGGAAT--AAGGGTTTTTTTTACACTAAATTA
* * * * * *
38522842 -TTTTAAAAATTTATATTGAAAGTAATAAAATTCAGAA-ATAAT----T----T--T-TAAAAAT
1 ATTTTAAAAA--CACACT-AAATTAATAAATTTCA-AACATAATGCACTGAAATAATGTAAAATT
* * * *
38522894 ACAAAAATA-ATATT-T--T-TTTTATTGAAAGTAATAAAATTCGG-GAAAAAATACGAACAAAT
62 ATAAAATTAGAAATTATGATATTTT-TT-AAAGTAATAAAATGCGGAGAAAAAATACGAACAAAT
* * * * * *
38522953 GGCCGAAATAAGGGTTTTTTACTAATTTTTTTTGAAAAA---AGAAATAATTAATAC----ACTT
125 GGCCGAAGTAAGAGTCTTTTACTAA-ATTTTTT-AAAAATTCAGAAATAATGAATACAAATATTT
* * * * *
38523011 CAAACATAATGTAATAAAATAATGTAAAATAATAAAATACGAAATTAATATATTTTTATTGAAAG
188 CAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAG
38523076 TAATAAAATTC-AGGAAAATA
253 TAATAAAATTCGA-GAAAATA
38523096 GTATAAATAA
Statistics
Matches: 816, Mismatches: 59, Indels: 46
0.89 0.06 0.05
Matches are distributed among these distances:
299 80 0.10
303 14 0.02
304 40 0.05
305 10 0.01
306 21 0.03
307 1 0.00
308 4 0.00
309 13 0.02
310 1 0.00
312 1 0.00
316 4 0.00
317 410 0.50
318 170 0.21
319 6 0.01
320 39 0.05
321 2 0.00
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (317 bp):
ATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAATACGAACAAATGGCCGA
AGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAAA
ATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA
TTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAATTA
Found at i:38522892 original size:21 final size:22
Alignment explanation
Indices: 38522868--38522909 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
38522858 TGAAAGTAAT
* *
38522868 AAAATTCAGAAATAAT-TTTTA
1 AAAATACAAAAATAATATTTTA
38522889 AAAATACAAAAATAATATTTT
1 AAAATACAAAAATAATATTTT
38522910 TTTTATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATACAAAAATAATATTTTA
Found at i:38525588 original size:42 final size:38
Alignment explanation
Indices: 38525527--38525652 Score: 114
Period size: 40 Copynumber: 3.1 Consensus size: 38
38525517 ACTAACACAA
38525527 TAACAATAATAAT-AGTTTTATACTCAAAATAATACTAAC
1 TAACAATAATAATAAGTTTT-TACT-AAAATAATACTAAC
38525566 TAACAATAATAATTAGAG-TTTTACTAAAAATAATAACTAAC
1 TAACAATAATAA-TA-AGTTTTTACT-AAAATAAT-ACTAAC
* * *
38525607 -CATAATAATAATACTAGTTTTTTACTAACAATAATACTAAG
1 TAACAATAATAATA--AG-TTTTTACTAA-AATAATACTAAC
38525648 TAACA
1 TAACA
38525653 TCTAAACCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
39 14 0.20
40 24 0.34
41 16 0.23
42 17 0.24
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (38 bp):
TAACAATAATAATAAGTTTTTACTAAAATAATACTAAC
Found at i:38525950 original size:27 final size:27
Alignment explanation
Indices: 38525912--38525972 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
38525902 ATAACACGAG
38525912 TGGTGCCGCCTATAGG-AAAGGCACCTT
1 TGGTGCCGCCTAT-GGAAAAGGCACCTT
38525939 TGGTGCCGCCTATGGAAAAGGCACCTT
1 TGGTGCCGCCTATGGAAAAGGCACCTT
38525966 TGGTGCC
1 TGGTGCC
38525973 ACCTGTCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (27 bp):
TGGTGCCGCCTATGGAAAAGGCACCTT
Found at i:38528644 original size:15 final size:15
Alignment explanation
Indices: 38528614--38528642 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38528604 ACTATTAATA
38528614 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
38528629 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
38528643 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:38529404 original size:20 final size:20
Alignment explanation
Indices: 38529379--38529416 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38529369 TTTAATATTA
38529379 ACAATTAAAATAAATAAAGT
1 ACAATTAAAATAAATAAAGT
*
38529399 ACAATTAAAATAATTAAA
1 ACAATTAAAATAAATAAA
38529417 AATATTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAATTAAAATAAATAAAGT
Found at i:38542209 original size:50 final size:47
Alignment explanation
Indices: 38542118--38542244 Score: 119
Period size: 50 Copynumber: 2.6 Consensus size: 47
38542108 GGGGGTCTTA
* * *
38542118 TGAAAGGTAATAAAAGCCCTACTCTCAGATGAATGGGGGGAGACTTC
1 TGAAAGGTAATAAAAGCCCTACTCCCAAATGAATGGAGGGAGACTTC
* * * *
38542165 TGAAAGGTAATAATAATGACCTTACTCCCAAATGCATGGAGGGAGGCTTA
1 TGAAAGGTAATAA-AA-G-CCCTACTCCCAAATGAATGGAGGGAGACTTC
* *
38542215 TGGAAGGTGGTAATAAAAGCCCTATTCCCA
1 T-GAA--AGGTAATAAAAGCCCTACTCCCA
38542245 GACGCATAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
47 13 0.20
48 2 0.03
49 1 0.02
50 34 0.53
51 4 0.06
52 2 0.03
53 8 0.12
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (47 bp):
TGAAAGGTAATAAAAGCCCTACTCCCAAATGAATGGAGGGAGACTTC
Found at i:38543421 original size:17 final size:16
Alignment explanation
Indices: 38543399--38543433 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
38543389 CATGAATCGC
38543399 TGGTCTAATATACATCA
1 TGGTCTAATATAC-TCA
38543416 TGGTCTAATATACTCA
1 TGGTCTAATATACTCA
38543432 TG
1 TG
38543434 AACAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (16 bp):
TGGTCTAATATACTCA
Found at i:38547213 original size:43 final size:43
Alignment explanation
Indices: 38547152--38547238 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
38547142 ATTCGATGTA
38547152 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
1 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
38547195 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
1 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
38547238 T
1 T
38547239 ATGAAATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (43 bp):
TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
Found at i:38562280 original size:18 final size:18
Alignment explanation
Indices: 38562237--38562284 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
38562227 GGATTGTTCG
*
38562237 TCGCCATATTTGGATTGC
1 TCGCCATATTTGGACTGC
*
38562255 TCGTCATATTTGGACTG-
1 TCGCCATATTTGGACTGC
38562272 TCCGCCATATTTG
1 T-CGCCATATTTG
38562285 ATAGTTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (18 bp):
TCGCCATATTTGGACTGC
Found at i:38567289 original size:13 final size:13
Alignment explanation
Indices: 38567271--38567295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38567261 TAATTTATAT
38567271 GTGTGAAAATTTC
1 GTGTGAAAATTTC
38567284 GTGTGAAAATTT
1 GTGTGAAAATTT
38567296 TATTGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:38569653 original size:43 final size:43
Alignment explanation
Indices: 38569588--38569748 Score: 250
Period size: 43 Copynumber: 3.7 Consensus size: 43
38569578 GATATGATTT
38569588 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
* *
38569631 CGTGTAAGACCACGTCTAGGATGTTGGCATCAACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
*
38569674 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
* * * **
38569717 CGTGTAAAACCATGTTTGGGACATTGGCATCG
1 CGTGTAAGACCACGTCTGGGATGTTGGCATCG
38569749 TATTTGATTC
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 109 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
Found at i:38573266 original size:20 final size:20
Alignment explanation
Indices: 38573228--38573266 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38573218 ATTTTAACTA
*
38573228 CTTAATTAACTTAATTTAAC
1 CTTAATTAACTTAAATTAAC
38573248 CTTAATTAA-TTAAAATTAA
1 CTTAATTAACTT-AAATTAA
38573267 TCACCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
CTTAATTAACTTAAATTAAC
Found at i:38574968 original size:24 final size:24
Alignment explanation
Indices: 38574940--38574987 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38574930 ATTAGGAGAT
38574940 GGTGAATGATGATGACTTTTCCAC
1 GGTGAATGATGATGACTTTTCCAC
38574964 GGTGAATGATGATGACTTTTCCAC
1 GGTGAATGATGATGACTTTTCCAC
38574988 TAAGTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
GGTGAATGATGATGACTTTTCCAC
Found at i:38574996 original size:24 final size:24
Alignment explanation
Indices: 38574943--38574997 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
38574933 AGGAGATGGT
**
38574943 GAATGATGATGACTTTTCCACGGT
1 GAATGATGATGACTTTTCCACGAA
*
38574967 GAATGATGATGACTTTTCCACTAA
1 GAATGATGATGACTTTTCCACGAA
*
38574991 GTATGAT
1 GAATGAT
38574998 TAATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (24 bp):
GAATGATGATGACTTTTCCACGAA
Found at i:38577502 original size:14 final size:14
Alignment explanation
Indices: 38577483--38577509 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38577473 AAAGGGGATG
38577483 AAATCAGTGTAAAA
1 AAATCAGTGTAAAA
38577497 AAATCAGTGTAAA
1 AAATCAGTGTAAA
38577510 GAGAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
AAATCAGTGTAAAA
Found at i:38578373 original size:24 final size:24
Alignment explanation
Indices: 38578344--38578593 Score: 155
Period size: 24 Copynumber: 10.7 Consensus size: 24
38578334 GTTTATTGTA
*
38578344 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
38578368 TTTTATTATTTGT-AATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
* *
38578391 TATTATTATTTTAAATTCATCGT-
1 TATTATTATTTTAAATTTATCATG
**
38578414 TAACATTATTTTAAATTTATCATG
1 TATTATTATTTTAAATTTATCATG
*
38578438 TA-TATTTATTTCAAATTTATCAT-
1 TATTA-TTATTTTAAATTTATCATG
* * *
38578461 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* ** *
38578483 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
38578507 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * * *
38578530 CA-AAAT-TTTTAAATTTTAT-ATA
1 TATTATTATTTTAAA-TTTATCATG
* *
38578552 TATTATTATTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
38578576 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
38578594 ATTCAATTCA
Statistics
Matches: 175, Mismatches: 34, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.11
22 13 0.07
23 48 0.27
24 80 0.46
25 13 0.07
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:38578433 original size:46 final size:46
Alignment explanation
Indices: 38578348--38578568 Score: 55
Period size: 45 Copynumber: 4.8 Consensus size: 46
38578338 ATTGTATATT
* * * * * **
38578348 ATTATTTTAGATTTATCATGTTTTATTATTTGT-AATTTATCAATATT
1 ATTATTTTAAATTTATCA-ATATTATTATTT-TAAATTCATCATTAAC
* ** ** *
38578395 ATTATTTTAAATTCATCGTTAACATTATTTTAAATTTATCATGTATA-
1 ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCAT-TA-AC
* * * * * *
38578442 TTTATTTCAAATTTATCATTAATA-T-TTTTAAATTTATTA-TATAC
1 ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCATTA-AC
** * * * *
38578486 TATTATTTTGGATTTATCACGTATGATTATTCTAGAATT-ATCATCAA-
1 -ATTATTTTAAATTTATCA-ATATTATTATTTTA-AATTCATCATTAAC
*
38578533 AAT-TTTTAAATTTTAT-ATATATTATTATTTTAAATT
1 ATTATTTTAAA-TTTATCA-ATATTATTATTTTAAATT
38578569 TATTATATAT
Statistics
Matches: 131, Mismatches: 32, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
43 4 0.03
44 4 0.03
45 45 0.34
46 28 0.21
47 37 0.28
48 8 0.06
49 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (46 bp):
ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCATTAAC
Done.