Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 4 of 125
Found at i:525763 original size:10 final size:10
Alignment explanation
Indices: 525748--525790 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
525738 AATTTGAGTC
*
525748 TTTTTTCATT
1 TTTTTTTATT
525758 TTTTTTTA--
1 TTTTTTTATT
525766 TTTTTTTATT
1 TTTTTTTATT
525776 TTTTTTTATT
1 TTTTTTTATT
525786 TTTTT
1 TTTTT
525791 CATCCATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.27
10 22 0.73
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:525790 original size:18 final size:18
Alignment explanation
Indices: 525748--525790 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
525738 AATTTGAGTC
*
525748 TTTTTTCATTTTTTTTTA
1 TTTTTTTATTTTTTTTTA
525766 TTTTTTTATTTTTTTTTA
1 TTTTTTTATTTTTTTTTA
525784 TTTTTTT
1 TTTTTTT
525791 CATCCATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTTATTTTTTTTTA
Found at i:528076 original size:21 final size:18
Alignment explanation
Indices: 528029--528082 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 18
528019 ATTTTACATA
528029 ATTGCATGATAATTAATAT
1 ATTGCATGAT-ATTAATAT
528048 ATTTGCATGATATTATATTATT
1 A-TTGCATGATATTA-A-TA-T
*
528070 ATTGCATTATATT
1 ATTGCATGATATT
528083 TTTTGCACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.17
20 10 0.33
21 13 0.43
22 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
ATTGCATGATATTAATAT
Found at i:532748 original size:19 final size:20
Alignment explanation
Indices: 532726--532764 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
532716 TTTTTTGTTA
532726 TTTTAACATTT-TCTTAAAT
1 TTTTAACATTTATCTTAAAT
*
532745 TTTTTACATTTATCTTAAAT
1 TTTTAACATTTATCTTAAAT
532765 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAACATTTATCTTAAAT
Found at i:532888 original size:13 final size:15
Alignment explanation
Indices: 532864--532901 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
532854 ACAAAATTAG
532864 GAATAAAA-ATATAT
1 GAATAAAATATATAT
532878 -AA-AAAATATATAT
1 GAATAAAATATATAT
532891 GAATAAAATAT
1 GAATAAAATAT
532902 CAAGATTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.19
13 8 0.38
14 2 0.10
15 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
GAATAAAATATATAT
Found at i:534607 original size:12 final size:12
Alignment explanation
Indices: 534590--534614 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
534580 TATAAAAATA
534590 AATTTTTTAATT
1 AATTTTTTAATT
534602 AATTTTTTAATT
1 AATTTTTTAATT
534614 A
1 A
534615 TTTAATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTTTAATT
Found at i:538784 original size:17 final size:17
Alignment explanation
Indices: 538762--538797 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
538752 TCAACCCTTT
*
538762 GGCTTGGAGAGAAAGAA
1 GGCTTGGACAGAAAGAA
*
538779 GGCTTGGACAGAAGGAA
1 GGCTTGGACAGAAAGAA
538796 GG
1 GG
538798 TTAATGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.44, T:0.11
Consensus pattern (17 bp):
GGCTTGGACAGAAAGAA
Found at i:551949 original size:22 final size:23
Alignment explanation
Indices: 551921--551975 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
551911 TAATCATTGG
* *
551921 TAACTTAGTAGA-AAATTAGTGA
1 TAACTTAGTAGATAAATTAATAA
*
551943 TAACTTAATA-ATAAATTAATAA
1 TAACTTAGTAGATAAATTAATAA
*
551965 TAATTTAGTAG
1 TAACTTAGTAG
551976 TCAATAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (23 bp):
TAACTTAGTAGATAAATTAATAA
Found at i:552111 original size:22 final size:22
Alignment explanation
Indices: 552085--552251 Score: 138
Period size: 22 Copynumber: 7.6 Consensus size: 22
552075 AATATAGTAC
*
552085 TAAATCAAGGATAACTTAATAA
1 TAAATCAATGATAACTTAATAA
* *
552107 AAAAT-AAGTGATAACTTAGTAA
1 TAAATCAA-TGATAACTTAATAA
* * * * *
552129 TTAATTATTAATAACTTAGTAA
1 TAAATCAATGATAACTTAATAA
*
552151 TAAATCAATTATAACTTAATAA
1 TAAATCAATGATAACTTAATAA
* *
552173 TAAATTAATGATAATTTAATAA
1 TAAATCAATGATAACTTAATAA
* * * * *
552195 TAAATCATTCATAAATTAGTAG
1 TAAATCAATGATAACTTAATAA
* * *
552217 TAAATCATTGAGAAATTAATAA
1 TAAATCAATGATAACTTAATAA
*
552239 TAAATCATTGATA
1 TAAATCAATGATA
552252 GTTTAGTAGT
Statistics
Matches: 117, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
21 2 0.02
22 114 0.97
23 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (22 bp):
TAAATCAATGATAACTTAATAA
Found at i:552164 original size:11 final size:11
Alignment explanation
Indices: 552095--552243 Score: 75
Period size: 11 Copynumber: 13.5 Consensus size: 11
552085 TAAATCAAGG
*
552095 ATAACTTAATA
1 ATAAATTAATA
* *
552106 A-AAAATAAGTG
1 ATAAATTAA-TA
* *
552117 ATAACTTAGTA
1 ATAAATTAATA
* *
552128 ATTAATTATTA
1 ATAAATTAATA
* *
552139 ATAACTTAGTA
1 ATAAATTAATA
* *
552150 ATAAATCAATT
1 ATAAATTAATA
*
552161 ATAACTTAATA
1 ATAAATTAATA
*
552172 ATAAATTAATG
1 ATAAATTAATA
*
552183 ATAATTTAATA
1 ATAAATTAATA
* * *
552194 ATAAATCATTC
1 ATAAATTAATA
*
552205 ATAAATTAGTA
1 ATAAATTAATA
* * * *
552216 GTAAATCATTG
1 ATAAATTAATA
*
552227 AGAAATTAATA
1 ATAAATTAATA
552238 ATAAAT
1 ATAAAT
552244 CATTGATAGT
Statistics
Matches: 95, Mismatches: 41, Indels: 4
0.68 0.29 0.03
Matches are distributed among these distances:
10 5 0.05
11 86 0.91
12 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.36
Consensus pattern (11 bp):
ATAAATTAATA
Found at i:552165 original size:66 final size:66
Alignment explanation
Indices: 552074--552242 Score: 178
Period size: 66 Copynumber: 2.5 Consensus size: 66
552064 TAAATGCATA
* * * *
552074 AAATATAGTACTAAATCAAGGATAACTTAATAA-AAAATAAGTGATAACTTAGTAATTAATTATT
1 AAAT-TAGTAATAAATCAAGGATAACTTAATAATAAAATAA-TGATAACTTAATAATAAATCATT
552138 AAT
64 AAT
* ** * * *
552141 AACTTAGTAATAAATCAATTATAACTTAATAATAAATTAATGATAATTTAATAATAAATCATTCA
1 AAATTAGTAATAAATCAAGGATAACTTAATAATAAAATAATGATAACTTAATAATAAATCATTAA
552206 T
66 T
* ** * *
552207 AAATTAGTAGTAAATCATTGAGAAATTAATAATAAA
1 AAATTAGTAATAAATCAAGGATAACTTAATAATAAA
552243 TCATTGATAG
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
66 76 0.89
67 9 0.11
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (66 bp):
AAATTAGTAATAAATCAAGGATAACTTAATAATAAAATAATGATAACTTAATAATAAATCATTAA
T
Found at i:552251 original size:66 final size:66
Alignment explanation
Indices: 552100--552265 Score: 172
Period size: 66 Copynumber: 2.5 Consensus size: 66
552090 CAAGGATAAC
* * * * * * *
552100 TTAATAAAAAATAAGTGATAACTTAGTAATTAATTATTAATAACTTAGTAATAAATCAATTATAA
1 TTAATAATAAATAAATGATAATTTAGTAATAAATCATTAATAAATTAGTAATAAATCAATTAGAA
*
552165 C
66 A
* * * *
552166 TTAATAATAAATTAATGATAATTTAATAATAAATCATTCATAAATTAGTAGTAAATC-ATTGAGA
1 TTAATAATAAATAAATGATAATTTAGTAATAAATCATTAATAAATTAGTAATAAATCAATT-AGA
552230 AA
65 AA
* * * *
552232 TTAATAATAAATCATTGATAGTTTAGTAGTAAAT
1 TTAATAATAAATAAATGATAATTTAGTAATAAAT
552266 AACTGATAAT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 3 0.04
66 79 0.96
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (66 bp):
TTAATAATAAATAAATGATAATTTAGTAATAAATCATTAATAAATTAGTAATAAATCAATTAGAA
A
Found at i:552280 original size:44 final size:43
Alignment explanation
Indices: 552074--552295 Score: 149
Period size: 44 Copynumber: 5.0 Consensus size: 43
552064 TAAATGCATA
* * * * * *
552074 AAATATAGTACTAAATCAAGGATAACTTAATAAAAAATAAGTGAT
1 AAAT-TAGTAGTAAAT-AATGATAATTTAATAATAAATCATTGAT
* * * * * * *
552119 AACTTAGTAATTAATTATTAATAACTTAGTAATAAATCAATT-AT
1 AAATTAGT-AGTAAATAATGATAATTTAATAATAAATC-ATTGAT
* * * *
552163 AACTTAATAATAAATTAATGATAATTTAATAATAAATCATTCAT
1 AAATTAGTAGTAAA-TAATGATAATTTAATAATAAATCATTGAT
* * *
552207 AAATTAGTAGTAAATCATTGAGAAATTAATAATAAATCATTGAT
1 AAATTAGTAGTAAAT-AATGATAATTTAATAATAAATCATTGAT
** * * *
552251 AGTTTAGTAGTAAATAACTGATAATTTAATTATCAATAATTGAT
1 AAATTAGTAGTAAATAA-TGATAATTTAATAATAAATCATTGAT
552295 A
1 A
552296 CCTTTTTTTA
Statistics
Matches: 139, Mismatches: 32, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
43 9 0.06
44 120 0.86
45 10 0.07
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (43 bp):
AAATTAGTAGTAAATAATGATAATTTAATAATAAATCATTGAT
Found at i:552616 original size:43 final size:41
Alignment explanation
Indices: 552556--552669 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 41
552546 AATGATAGGT
* * *
552556 TAATAAAAATAAGTGATAACTTAGTAGTTAATAATTGATAA
1 TAATAAAAATAAGTGATAACTTAATAGTAAATAAGTGATAA
*
552597 CTAATAATAAATTAA-TGATAACTTAATAGTAAATTAGTGATAA
1 -TAATAA-AAA-TAAGTGATAACTTAATAGTAAATAAGTGATAA
* * *
552640 TAAT--AAATTAGTAATAACTTAATAATAAAT
1 TAATAAAAATAAGTGATAACTTAATAGTAAAT
552670 CAATTTCAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.03
39 20 0.32
42 10 0.16
43 27 0.44
44 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (41 bp):
TAATAAAAATAAGTGATAACTTAATAGTAAATAAGTGATAA
Found at i:552646 original size:17 final size:17
Alignment explanation
Indices: 552620--552656 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
552610 AATGATAACT
* *
552620 TAATAGTAAATTAGTGA
1 TAATAATAAATTAGTAA
552637 TAATAATAAATTAGTAA
1 TAATAATAAATTAGTAA
552654 TAA
1 TAA
552657 CTTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAATAATAAATTAGTAA
Found at i:552711 original size:23 final size:22
Alignment explanation
Indices: 552684--552740 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
552674 TTCAGTTTAA
**
552684 TAGTAATTAATTTATAAACTTAG
1 TAGTAATTAATAAAT-AACTTAG
* *
552707 TAGTAAATCATAAATAACTTAG
1 TAGTAATTAATAAATAACTTAG
552729 TAGTAAATTAAT
1 TAGT-AATTAAT
552741 GATAATTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
TAGTAATTAATAAATAACTTAG
Found at i:552745 original size:22 final size:22
Alignment explanation
Indices: 552537--553329 Score: 117
Period size: 22 Copynumber: 36.0 Consensus size: 22
552527 AACAACCTAT
** *
552537 TAGTAAATTAATGATAGGTTAA
1 TAGTAAATTAATGATAACTTAG
*
552559 TA--AAAATAAGTGATAACTTAG
1 TAGTAAATTAA-TGATAACTTAG
* *
552580 TAGTTAA-TAATTGATAAC-TAA
1 TAGTAAATTAA-TGATAACTTAG
* *
552601 TAATAAATTAATGATAACTTAA
1 TAGTAAATTAATGATAACTTAG
*
552623 TAGTAAATTAGTGATAA--TA-
1 TAGTAAATTAATGATAACTTAG
* * *
552642 -A-TAAATTAGTAATAACTTAA
1 TAGTAAATTAATGATAACTTAG
* * * ** *
552662 TAATAAATCAAT-TTCAGTTTAA
1 TAGTAAATTAATGAT-AACTTAG
*
552684 TAGT-AATTAATTTATAAACTTAG
1 TAGTAAATTAA-TGAT-AACTTAG
552707 TAGTAAATCATAA--ATAACTTAG
1 TAGTAAAT--TAATGATAACTTAG
*
552729 TAGTAAATTAATGATAATTTAG
1 TAGTAAATTAATGATAACTTAG
* * * * * *
552751 TAATTAATCATTGAAAACTTAA
1 TAGTAAATTAATGATAACTTAG
* * *
552773 AAGTAAATCAAT-ATAACTTAATAA
1 TAGTAAATTAATGATAAC-T--TAG
* ** *
552797 TAGTTAACCAATGATAACTTAT
1 TAGTAAATTAATGATAACTTAG
* * *
552819 TAGTAAA-TCATGAATAATTTAA
1 TAGTAAATTAATG-ATAACTTAG
* *
552841 TA-TAAATCAATGATAAGTT-G
1 TAGTAAATTAATGATAACTTAG
* * * *
552861 ATAATGAA-TCATGGTTAACTTAG
1 -TAGTAAATTAAT-GATAACTTAG
* ** * * *
552884 TAATAAATTTGTCATGA-TTGTG
1 TAGTAAATTAATGATAACTT-AG
* * **
552906 TAGTAAA-TAATCAAAAACCAAG
1 TAGTAAATTAAT-GATAACTTAG
* *
552928 TAGTAAATTAATAATAACATAG
1 TAGTAAATTAATGATAACTTAG
** * * *
552950 TAGTAAATGCATAATAACATAA
1 TAGTAAATTAATGATAACTTAG
* * * *
552972 TAATAAATCATTGATAATTTAG
1 TAGTAAATTAATGATAACTTAG
* *
552994 -ATGTAAATTATTGGTAACTTAG
1 TA-GTAAATTAATGATAACTTAG
* * * *
553016 TAGTAAATCACTAATAATTTAG
1 TAGTAAATTAATGATAACTTAG
* * * * *
553038 TTGTAAATCAATAATAATTTAA
1 TAGTAAATTAATGATAACTTAG
* *
553060 TAATAAATGGTTAATCATTGATAACTTTG
1 TAGTAAA---TT-A--A-TGATAACTTAG
* * * *
553089 TAGTAAATCATTGATAAATTAA
1 TAGTAAATTAATGATAACTTAG
* * *
553111 TAGTAAATCAGTTATAACTTTA-
1 TAGTAAATTAATGATAAC-TTAG
** * *
553133 TAACAAATT-ATCAGTAACTTAA
1 TAGTAAATTAATGA-TAACTTAG
* * * *
553155 TAGTAAA-TCATCAATAATTTAA
1 TAGTAAATTAAT-GATAACTTAG
* * * *
553177 TAGTAAATCAGTCAAAACTTAG
1 TAGTAAATTAATGATAACTTAG
* * * *
553199 TAGTAAATTATTAATAAATTAA
1 TAGTAAATTAATGATAACTTAG
* * *
553221 TAGTAAATCAATGCTAATTTAG
1 TAGTAAATTAATGATAACTTAG
* * * *
553243 TAGTAAATCATTAATAATTTAG
1 TAGTAAATTAATGATAACTTAG
* * * * *
553265 TGGTATAA-CATTGATAGCTTAA
1 TAGTA-AATTAATGATAACTTAG
***
553287 TAGTAAATCGTTGATAACATTA-
1 TAGTAAATTAATGATAAC-TTAG
*
553309 TAGTAAATCAATGATAACTTA
1 TAGTAAATTAATGATAACTTA
553330 ATTATTAATC
Statistics
Matches: 566, Mismatches: 154, Indels: 103
0.69 0.19 0.13
Matches are distributed among these distances:
17 13 0.02
18 1 0.00
19 2 0.00
20 11 0.02
21 68 0.12
22 398 0.70
23 31 0.05
24 16 0.03
25 7 0.01
26 5 0.01
28 1 0.00
29 13 0.02
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (22 bp):
TAGTAAATTAATGATAACTTAG
Found at i:553045 original size:66 final size:66
Alignment explanation
Indices: 552931--553264 Score: 223
Period size: 66 Copynumber: 4.9 Consensus size: 66
552921 AACCAAGTAG
* * * ** * *
552931 TAAATTAATAATAACATAGTAGTAAATGCATAATAACATAATAATAAATCATTGATAATTTAGAT
1 TAAATTATTAATAACTTAATAGTAAAT-CATAATAATTTAATAGTAAATCATTAATAATTTAGAT
*
552996 -G
65 AA
** * * * *
552997 TAAATTATTGGTAACTTAGTAGTAAATCACTAATAATTTAGTTGTAAATCAATAATAATTTA-AT
1 TAAATTATTAATAACTTAATAGTAAATCA-TAATAATTTAATAGTAAATCATTAATAATTTAGAT
553061 AA
65 AA
* ** * *
553063 TAAATGGTTAATCATTGATAACTTTGTAGTAAATCATTGATAAATTAATAGTAAATCAGTT-ATA
1 TAAA----T--T-ATTAATAACTTAATAGTAAATCA-TAATAATTTAATAGTAAATCA-TTAATA
553127 ACTTT--ATAA
57 A-TTTAGATAA
* * * * *
553136 CAAATTATCAGTAACTTAATAGTAAATCATCAATAATTTAATAGTAAATCAGTCAA-AACTTAG-
1 TAAATTATTAATAACTTAATAGTAAATCAT-AATAATTTAATAGTAAATCA-TTAATAATTTAGA
*
553199 TAG
64 TAA
* ** *
553202 TAAATTATTAATAAATTAATAGTAAATCAATGCTAATTTAGTAGTAAATCATTAATAATTTAG
1 TAAATTATTAATAACTTAATAGTAAATC-ATAATAATTTAATAGTAAATCATTAATAATTTAG
553265 TGGTATAACA
Statistics
Matches: 211, Mismatches: 40, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
65 10 0.05
66 141 0.67
67 4 0.02
69 1 0.00
70 1 0.00
72 1 0.00
73 49 0.23
74 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (66 bp):
TAAATTATTAATAACTTAATAGTAAATCATAATAATTTAATAGTAAATCATTAATAATTTAGATA
A
Found at i:553128 original size:44 final size:44
Alignment explanation
Indices: 553072--553331 Score: 215
Period size: 44 Copynumber: 5.9 Consensus size: 44
553062 ATAAATGGTT
* * * *
553072 AATCATTGATAACTTTGTAGTAAATCATTGATAAATTAATAGTA
1 AATCATTAATAACTTTATAGTAAATCAATGATAACTTAATAGTA
** * *
553116 AATCAGTT-ATAACTTTATAACAAAT-TATCAGTAACTTAATAGTA
1 AATCA-TTAATAACTTTATAGTAAATCAATGA-TAACTTAATAGTA
* * * * *
553160 AATCATCAATAA-TTTAATAGTAAATCAGTCAAAACTTAGTAGTA
1 AATCATTAATAACTTT-ATAGTAAATCAATGATAACTTAATAGTA
* * * * * *
553204 AATTATTAATAAATTAATAGTAAATCAATGCTAATTTAGTAGTA
1 AATCATTAATAACTTTATAGTAAATCAATGATAACTTAATAGTA
* * *
553248 AATCATTAATAA-TTTAGTGGTATAA-CATTGATAGCTTAATAGTA
1 AATCATTAATAACTTTA-TAGTA-AATCAATGATAACTTAATAGTA
* * *
553292 AATCGTTGATAACATTATAGTAAATCAATGATAACTTAAT
1 AATCATTAATAACTTTATAGTAAATCAATGATAACTTAAT
553332 TATTAATCAT
Statistics
Matches: 170, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
43 11 0.06
44 147 0.86
45 12 0.07
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (44 bp):
AATCATTAATAACTTTATAGTAAATCAATGATAACTTAATAGTA
Found at i:553603 original size:21 final size:21
Alignment explanation
Indices: 553578--553617 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
553568 TATTAAATAT
*
553578 ATAA-TAGCACAAATTTTATCA
1 ATAATTAGCA-AAAGTTTATCA
553599 ATAATTAGCAAAAGTTTAT
1 ATAATTAGCAAAAGTTTAT
553618 TATAAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (21 bp):
ATAATTAGCAAAAGTTTATCA
Found at i:554719 original size:34 final size:34
Alignment explanation
Indices: 554700--554773 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
554690 ATGTGTTTTC
554700 AGAAATGGATTTCCAAGAATACAATGTAATTCTT
1 AGAAATGGATTTCCAAGAATACAATGTAATTCTT
* * *
554734 AGATATGGATTTCTAAGAATACAACGTAATTCTT
1 AGAAATGGATTTCCAAGAATACAATGTAATTCTT
*
554768 AAAAAT
1 AGAAAT
554774 ATATTTTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (34 bp):
AGAAATGGATTTCCAAGAATACAATGTAATTCTT
Found at i:554787 original size:34 final size:34
Alignment explanation
Indices: 554702--554790 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
554692 GTGTTTTCAG
* * * *
554702 AAATGGATTTCCAAGAATACAATGTAATTCTTAG
1 AAATAGATTTCTAAGAATACAACGTAATTCTTAA
* *
554736 ATATGGATTTCTAAGAATACAACGTAATTCTTAA
1 AAATAGATTTCTAAGAATACAACGTAATTCTTAA
* * *
554770 AAATATATTTTTGAGAATACA
1 AAATAGATTTCTAAGAATACA
554791 TTATAATTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (34 bp):
AAATAGATTTCTAAGAATACAACGTAATTCTTAA
Found at i:554914 original size:34 final size:34
Alignment explanation
Indices: 554876--554942 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
554866 CTCAGAATTC
** *
554876 TATTTCTAAAAATACATCATAATTCTTGAAAATA
1 TATTTCTAAAAATACAAAATAATTCTCGAAAATA
*
554910 TATTTCTAAGAATACAAAATAATTCTCGAAAAT
1 TATTTCTAAAAATACAAAATAATTCTCGAAAAT
554943 CCCTATATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (34 bp):
TATTTCTAAAAATACAAAATAATTCTCGAAAATA
Found at i:557849 original size:17 final size:18
Alignment explanation
Indices: 557821--557869 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
557811 AAACATTTTG
*
557821 TATTAATGTTTATTATTTA
1 TATT-ATGTTTATGATTTA
*
557840 TATT-TGTTTATGCTTTA
1 TATTATGTTTATGATTTA
557857 TATTATG-TTATGA
1 TATTATGTTTATGA
557870 GCATGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 20 0.77
18 2 0.08
19 4 0.15
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTATGTTTATGATTTA
Found at i:558039 original size:17 final size:18
Alignment explanation
Indices: 557998--558044 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
557988 ACATAACAAC
557998 ATATAAAATTAGTATGTCA
1 ATATAAAATTAGTA-GTCA
*
558017 ACATAAAATTAGTA-TCA
1 ATATAAAATTAGTAGTCA
558034 ATATAAAATTA
1 ATATAAAATTA
558045 ATTCCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 13 0.50
19 13 0.50
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (18 bp):
ATATAAAATTAGTAGTCA
Found at i:565118 original size:21 final size:21
Alignment explanation
Indices: 565094--565134 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
565084 ATGAGGCAGA
565094 TGATGATGAAGAAGAGGAGGG
1 TGATGATGAAGAAGAGGAGGG
* *
565115 TGATGATGAGGGAGAGGAGG
1 TGATGATGAAGAAGAGGAGG
565135 AAGGGCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.51, T:0.15
Consensus pattern (21 bp):
TGATGATGAAGAAGAGGAGGG
Found at i:568252 original size:20 final size:20
Alignment explanation
Indices: 568229--568266 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
568219 TGGTTGAAAG
568229 GGAGAAAAAATGGTGCTATA
1 GGAGAAAAAATGGTGCTATA
568249 GGAGAAAAAATGGTGCTA
1 GGAGAAAAAATGGTGCTA
568267 ATGAATCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.32, T:0.18
Consensus pattern (20 bp):
GGAGAAAAAATGGTGCTATA
Found at i:570991 original size:9 final size:9
Alignment explanation
Indices: 570977--571006 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
570967 CAACGGCTAG
570977 TTCATATTT
1 TTCATATTT
570986 TTCATATTTT
1 TTCATA-TTT
570996 TTCATATTT
1 TTCATATTT
571005 TT
1 TT
571007 ATCCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (9 bp):
TTCATATTT
Found at i:570998 original size:10 final size:10
Alignment explanation
Indices: 570977--571006 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
570967 CAACGGCTAG
570977 TTCATA-TTT
1 TTCATATTTT
570986 TTCATATTTT
1 TTCATATTTT
570996 TTCATATTTT
1 TTCATATTTT
571006 T
1 T
571007 ATCCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCATATTTT
Found at i:575523 original size:29 final size:29
Alignment explanation
Indices: 575471--575547 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
575461 ATATGTTTGC
* * * *
575471 GTTAGTTATGTCTATTTATGTATATTCGT
1 GTTAGTCATGTCTATTCATATATATTCAT
* *
575500 GTTAGTCATGTCTATTCGTATATATTTAT
1 GTTAGTCATGTCTATTCATATATATTCAT
* *
575529 GTTATTCATGTTTATTCAT
1 GTTAGTCATGTCTATTCAT
575548 GTTGTGTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.22, C:0.09, G:0.14, T:0.55
Consensus pattern (29 bp):
GTTAGTCATGTCTATTCATATATATTCAT
Found at i:575534 original size:19 final size:19
Alignment explanation
Indices: 575483--575535 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
575473 TAGTTATGTC
*
575483 TATTTATGTATATTCGTGT
1 TATTTATGTATATTCGTAT
* * *
575502 TAGTCATGTCTATTCGTAT
1 TATTTATGTATATTCGTAT
575521 ATATTTATGT-TATTC
1 -TATTTATGTATATTC
575536 ATGTTTATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTATGTATATTCGTAT
Found at i:575584 original size:15 final size:14
Alignment explanation
Indices: 575564--575593 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
575554 TTTAAATAGA
575564 TTAATTGTATACGTG
1 TTAATTGTAT-CGTG
575579 TTAATTGTATCGTG
1 TTAATTGTATCGTG
575593 T
1 T
575594 CGTGTATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (14 bp):
TTAATTGTATCGTG
Found at i:576674 original size:5 final size:5
Alignment explanation
Indices: 576666--576692 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
576656 TAAAATAGTT
576666 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
576693 TACTTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:577214 original size:5 final size:6
Alignment explanation
Indices: 577187--577212 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
577177 ATAAACAAAC
577187 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
577213 TATTTGTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:577592 original size:43 final size:43
Alignment explanation
Indices: 577512--577632 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 43
577502 AACAAATTAA
* * *
577512 ACTCCTCTATACAGAGG-TAAACAAATTTAAATTAAGAAATGG
1 ACTCCTCTATACAAAGGCTAAACAACTTTAAAATAAGAAATGG
* *
577554 ACTCCTTTATACAAAGGCTAAATAACTTTAAAATAAGAAATGG
1 ACTCCTCTATACAAAGGCTAAACAACTTTAAAATAAGAAATGG
* * * *
577597 GCTGCTCTATATAAAGACTAAACAACTTTAAAATAA
1 ACTCCTCTATACAAAGGCTAAACAACTTTAAAATAA
577633 ATAACTTTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 15 0.22
43 52 0.78
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (43 bp):
ACTCCTCTATACAAAGGCTAAACAACTTTAAAATAAGAAATGG
Found at i:577638 original size:15 final size:15
Alignment explanation
Indices: 577615--577648 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
577605 ATATAAAGAC
577615 TAAACAACTTTAAAA
1 TAAACAACTTTAAAA
*
577630 TAAATAACTTTAAAA
1 TAAACAACTTTAAAA
577645 TAAA
1 TAAA
577649 AAATGGGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAACAACTTTAAAA
Found at i:577663 original size:58 final size:58
Alignment explanation
Indices: 577572--577689 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 58
577562 ATACAAAGGC
* *
577572 TAAATAACTTTAAAATAAGAAATGGGCTGCTCTATAT-AAAGACTAAACAACTTTAAAA
1 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAG-CTAAACAACTTTAAAA
* *
577630 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAGCTAAATAATTTTAAAA
1 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAGCTAAACAACTTTAAAA
577688 TA
1 TA
577690 TAAAATGGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 51 0.93
59 4 0.07
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (58 bp):
TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAGCTAAACAACTTTAAAA
Found at i:577678 original size:43 final size:43
Alignment explanation
Indices: 577630--577815 Score: 160
Period size: 43 Copynumber: 4.3 Consensus size: 43
577620 AACTTTAAAA
*
577630 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAGC
1 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAAGC
* * * * * * *
577673 TAAATAATTTTAAAATATAAAATGGGTTCCTCTAAATAGAGGC
1 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAAGC
* * * * *
577716 TAAAACAACTTTAAATTAAGAAATGGGCTCCTTTATGCAAAA--
1 T-AAATAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAAGC
* ** * * * * *
577758 TAAACAACTTTAAAATATGAAATGGGCTCATTTATGCACAGGC
1 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAAGC
577801 TAAATAACTTTAAAA
1 TAAATAACTTTAAAA
577816 ACTTTAGATA
Statistics
Matches: 116, Mismatches: 24, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
41 35 0.30
42 1 0.01
43 52 0.45
44 28 0.24
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (43 bp):
TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAAGC
Found at i:577719 original size:101 final size:102
Alignment explanation
Indices: 577537--577730 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 102
577527 GGTAAACAAA
* * * * *
577537 TTTAAATTAAGAAATGGACTCCTTTATACAAAGGCTAAATAACTTTAAAATAAGAAATGGGCTGC
1 TTTAAAATAAAAAATGGACTCCTCTATACAAAAGCTAAATAACTTTAAAATAAGAAATGGGCTCC
*
577602 TCTATATAAAGACT-AAACAACTTTAAAATAAATAAC
66 TCTAAATAAAGACTAAAACAACTTTAAAATAAATAAC
* * * *
577638 TTTAAAATAAAAAATGGGCTCCTCTATATAAAAGCTAAATAATTTTAAAATATA-AAATGGGTTC
1 TTTAAAATAAAAAATGGACTCCTCTATACAAAAGCTAAATAACTTTAAAATA-AGAAATGGGCTC
* *
577702 CTCTAAATAGAGGCTAAAACAACTTTAAA
65 CTCTAAATAAAGACTAAAACAACTTTAAA
577731 TTAAGAAATG
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
101 65 0.82
102 14 0.18
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (102 bp):
TTTAAAATAAAAAATGGACTCCTCTATACAAAAGCTAAATAACTTTAAAATAAGAAATGGGCTCC
TCTAAATAAAGACTAAAACAACTTTAAAATAAATAAC
Found at i:577771 original size:41 final size:41
Alignment explanation
Indices: 577718--577795 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
577708 ATAGAGGCTA
* *
577718 AAACAACTTTAAATTAAGAAATGGGCTCCTTTATGCAAAAT
1 AAACAACTTTAAAATAAGAAATGGGCTCATTTATGCAAAAT
*
577759 AAACAACTTTAAAATATGAAATGGGCTCATTTATGCA
1 AAACAACTTTAAAATAAGAAATGGGCTCATTTATGCA
577796 CAGGCTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (41 bp):
AAACAACTTTAAAATAAGAAATGGGCTCATTTATGCAAAAT
Found at i:577801 original size:85 final size:85
Alignment explanation
Indices: 577630--577815 Score: 194
Period size: 85 Copynumber: 2.2 Consensus size: 85
577620 AACTTTAAAA
* * * *
577630 TAAATAACTTTAAAATAAAAAATGGGCTCCTCTATATAAAAGCTAAATAATTTTAAAATATAAAA
1 TAAACAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAA-CTAAACAACTTTAAAATATAAAA
* * * *
577695 TGGGTTCCTCTAAATAGAGGC
65 TGGGCTCATCTAAACACAGGC
* * * * *
577716 TAAAACAACTTTAAATTAAGAAATGGGCTCCTTTATGCAAAA-TAAACAACTTTAAAATATGAAA
1 T-AAACAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAACTAAACAACTTTAAAATATAAAA
* **
577780 TGGGCTCATTTATGCACAGGC
65 TGGGCTCATCTAAACACAGGC
*
577801 TAAATAACTTTAAAA
1 TAAACAACTTTAAAA
577816 ACTTTAGATA
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
84 12 0.15
85 34 0.42
86 1 0.01
87 34 0.42
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (85 bp):
TAAACAACTTTAAAATAAAAAATGGGCTCCTCTATACAAAACTAAACAACTTTAAAATATAAAAT
GGGCTCATCTAAACACAGGC
Found at i:578190 original size:17 final size:18
Alignment explanation
Indices: 578168--578208 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
578158 CCAAAGGTTC
*
578168 TAGATTCGTAAAA-ATTT
1 TAGATTCGCAAAATATTT
*
578185 TAGATTTGCAAAATATTT
1 TAGATTCGCAAAATATTT
578203 TAGATT
1 TAGATT
578209 ATCAGAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (18 bp):
TAGATTCGCAAAATATTT
Found at i:578329 original size:18 final size:18
Alignment explanation
Indices: 578316--578360 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
578306 CAAAAATTTG
578316 AAAGAATTTTAAAATTCA
1 AAAGAATTTTAAAATTCA
*
578334 AAAGAATTTTCAAATTCA
1 AAAGAATTTTAAAATTCA
578352 AAAGAATTT
1 AAAGAATTT
578361 AAATTCGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAGAATTTTAAAATTCA
Found at i:578523 original size:17 final size:17
Alignment explanation
Indices: 578474--578536 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
578464 GGTTTTCAAG
*
578474 AATTTTAAGTTCACAAA
1 AATTTAAAGTTCACAAA
* * *
578491 AACTTCAGGTTCACAAA
1 AATTTAAAGTTCACAAA
* *
578508 AATTTAAAGTTTACAAG
1 AATTTAAAGTTCACAAA
*
578525 AATTTAAGGTTC
1 AATTTAAAGTTC
578537 GCAGAAATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (17 bp):
AATTTAAAGTTCACAAA
Found at i:578738 original size:65 final size:66
Alignment explanation
Indices: 578657--578794 Score: 167
Period size: 65 Copynumber: 2.1 Consensus size: 66
578647 TTTTGTTAGT
* * *
578657 GATTCACATGCAAAATTCAAA-ATTTCACATTTGAAA-ATTTTATGAATTCACAT-CAAAGGTTT
1 GATTCACCTTCAAAATTCAAATA-TTCACATTTGAAAGATTTTAAGAATTCACATACAAA--TTT
578719 CAAA
63 CAAA
* **
578723 G-TTCACCTTCAAAATTCAAATATTCTCATTTGAAAGATTTTAAGGTTTCACATACAAATTTCAA
1 GATTCACCTTCAAAATTCAAATATTCACATTTGAAAGATTTTAAGAATTCACATACAAATTTCAA
578787 A
66 A
578788 GATTCAC
1 GATTCAC
578795 ATTGGAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
65 37 0.60
66 21 0.34
67 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (66 bp):
GATTCACCTTCAAAATTCAAATATTCACATTTGAAAGATTTTAAGAATTCACATACAAATTTCAA
A
Found at i:585647 original size:30 final size:31
Alignment explanation
Indices: 585611--585672 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 31
585601 GACCTAATCG
*
585611 AAGTTTTTTTTTCA-TTTTATT-TTTAATTTT
1 AAGTTTTTATTTCATTTTTATTATTT-ATTTT
585641 AAGTTTTTATTTCATTTTTATTATTTATTTT
1 AAGTTTTTATTTCATTTTTATTATTTATTTT
585672 A
1 A
585673 TTTTGCTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 13 0.45
31 13 0.45
32 3 0.10
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (31 bp):
AAGTTTTTATTTCATTTTTATTATTTATTTT
Found at i:590484 original size:9 final size:10
Alignment explanation
Indices: 590458--590486 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
590448 ATCAAGTTTT
590458 TATATTTTAA
1 TATATTTTAA
590468 TATATTTTAA
1 TATATTTTAA
590478 T-TATTTTAA
1 TATATTTTAA
590487 CTGATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTTTAA
Found at i:591363 original size:33 final size:34
Alignment explanation
Indices: 591313--591381 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
591303 TACTGTTTAA
*
591313 TTTTTTGTTATAAATTTG-TTGAG-ATTTGTTGGG
1 TTTTTGGTTATAAATTTGCTT-AGTATTTGTTGGG
*
591346 TTTTTGGTTA-AATATTTGCTTAGTTTTTGTTGGG
1 TTTTTGGTTATAA-ATTTGCTTAGTATTTGTTGGG
591380 TT
1 TT
591382 AAATTTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 2 0.06
33 16 0.52
34 13 0.42
ACGTcount: A:0.16, C:0.01, G:0.23, T:0.59
Consensus pattern (34 bp):
TTTTTGGTTATAAATTTGCTTAGTATTTGTTGGG
Found at i:591381 original size:27 final size:27
Alignment explanation
Indices: 591351--591404 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
591341 TTGGGTTTTT
591351 GGTTAAATATTT-GCTTAGTTTTTGTTG
1 GGTTAAATATTTAGCTTA-TTTTTGTTG
* *
591378 GGTTAAATTTTTAGTTTATTTTTGTTG
1 GGTTAAATATTTAGCTTATTTTTGTTG
591405 ATTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.20, T:0.59
Consensus pattern (27 bp):
GGTTAAATATTTAGCTTATTTTTGTTG
Found at i:591481 original size:27 final size:28
Alignment explanation
Indices: 591451--591526 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
591441 TTTTTTTGAA
591451 TTTTTTTTAGTATTGTTGAGT-TTTTTT
1 TTTTTTTTAGTATTGTTGAGTATTTTTT
*
591478 TTTTTTTTTG-ATTTGTTGAGTAATTTTTT
1 TTTTTTTTAGTA-TTGTTGAGT-ATTTTTT
* *
591507 TATTTGTTGAGTATTGTTGA
1 T-TTTTTTTAGTATTGTTGA
591527 AATTTGTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.03
27 18 0.45
29 7 0.17
30 13 0.32
31 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.68
Consensus pattern (28 bp):
TTTTTTTTAGTATTGTTGAGTATTTTTT
Found at i:591506 original size:21 final size:20
Alignment explanation
Indices: 591480--591519 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 20
591470 GTTTTTTTTT
591480 TTTTTTTGATTTGTTGAGTAA
1 TTTTTTT-ATTTGTTGAGTAA
591501 TTTTTTTATTTGTTGAGTA
1 TTTTTTTATTTGTTGAGTA
591520 TTGTTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.65
Consensus pattern (20 bp):
TTTTTTTATTTGTTGAGTAA
Found at i:593534 original size:19 final size:19
Alignment explanation
Indices: 593512--593550 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
593502 CCATCACACT
593512 AGTTGAAGCCCATGACTGC
1 AGTTGAAGCCCATGACTGC
593531 AGTTGAAGCCCATGACTGC
1 AGTTGAAGCCCATGACTGC
593550 A
1 A
593551 TCCATCGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (19 bp):
AGTTGAAGCCCATGACTGC
Found at i:595203 original size:23 final size:23
Alignment explanation
Indices: 595176--595221 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
595166 ATGGAACTAA
595176 TTTTGAACAGATACAATGAACAT
1 TTTTGAACAGATACAATGAACAT
595199 TTTTGAACAGATACAATGAACAT
1 TTTTGAACAGATACAATGAACAT
595222 GATATAAAAC
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:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (23 bp):
TTTTGAACAGATACAATGAACAT
Found at i:607288 original size:3 final size:3
Alignment explanation
Indices: 607280--607322 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
607270 AGTTTGATTG
607280 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
607323 TGAAGTGGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:607308 original size:20 final size:20
Alignment explanation
Indices: 607283--607322 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
607273 TTGATTGATA
607283 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
607303 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
607323 TGAAGTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:608099 original size:52 final size:52
Alignment explanation
Indices: 608010--608166 Score: 174
Period size: 52 Copynumber: 3.0 Consensus size: 52
608000 TGGATAAAAA
* * * * *
608010 GACTTGCAAAAGAAAAATTCCAAGA-GAAAGAGAATTCTTAATAGGTAAATTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAG-ATTCTTAATAGGCAAATTT
*
608062 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAATTT
* * * * * *
608114 GACTTACAGGAGAAGAGA-TCTAAAAGGAGAGAGATTTTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGA-ATTCTAAAAGGAAAGAGATTCTTAATAGGCAAATTT
608166 G
1 G
608167 TATGGTTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 84 0.91
53 8 0.09
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAATTT
Found at i:614374 original size:18 final size:19
Alignment explanation
Indices: 614339--614374 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
614329 CTGAAAGAAT
614339 TTGAATTTTTCGACTACCG
1 TTGAATTTTTCGACTACCG
614358 TTGAATTTTTCGA-TACC
1 TTGAATTTTTCGACTACC
614375 AGAATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (19 bp):
TTGAATTTTTCGACTACCG
Found at i:614733 original size:6 final size:6
Alignment explanation
Indices: 614724--614771 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
614714 TTTTCTTTCG
* *
614724 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TATTGA TTTTTA TGTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTT
614772 TTTAATGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 33 0.89
7 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:615192 original size:19 final size:20
Alignment explanation
Indices: 615154--615194 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
615144 AAGATTGATT
*
615154 TAAACAATGTAAAATAATAA
1 TAAAAAATGTAAAATAATAA
*
615174 TAAAAAATG-AAATTAATAA
1 TAAAAAATGTAAAATAATAA
615193 TA
1 TA
615195 TTTGAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAAATGTAAAATAATAA
Found at i:627584 original size:21 final size:21
Alignment explanation
Indices: 627533--627584 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
627523 TTAAAATAAC
* *
627533 AAAAATAATATTTTTAAAAAAT
1 AAAAATAA-AATTTCAAAAAAT
**
627555 CTAAA-AAAATTTCAAAAAAT
1 AAAAATAAAATTTCAAAAAAT
627575 AAAAATAAAA
1 AAAAATAAAA
627585 ATAAAATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 14 0.61
21 6 0.26
22 3 0.13
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAATTTCAAAAAAT
Found at i:627909 original size:48 final size:48
Alignment explanation
Indices: 627831--627927 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
627821 CAAAATGACG
*
627831 TCGTTTTAGTCTTTATTGAAACAGTGTCGTTTGGGTTTTCACCGTTTA
1 TCGTTTTAGTCTTTATTGAAACAGTATCGTTTGGGTTTTCACCGTTTA
* *
627879 TCGTTTTAGTCTTTATTGAAATAGTATCGTTTTGGTTTTCACCGTTTA
1 TCGTTTTAGTCTTTATTGAAACAGTATCGTTTGGGTTTTCACCGTTTA
627927 T
1 T
627928 ATAAAAGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.51
Consensus pattern (48 bp):
TCGTTTTAGTCTTTATTGAAACAGTATCGTTTGGGTTTTCACCGTTTA
Found at i:629247 original size:50 final size:49
Alignment explanation
Indices: 628971--629301 Score: 260
Period size: 48 Copynumber: 6.8 Consensus size: 49
628961 TAAAATCTGA
* * * * *
628971 AAAAGGCTCTTCTTAGTAGAGGCTCAACAACTTT-AAAATTTTATCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* * * * * * * *
629019 AAAAGGTTCATCTCAGCAGAGGTTTAATAATTTTAAAACT-TTAT-TTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTT-G
* * * * *
629067 AAAA-GCTACTCTTAGCAGAGGTTCAACGACTTT-AAAATCTCATCTTC
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* * ** * * * *
629114 AAAAAGCTCCTATCATTAGAGGCTCAACAA-TTTTAAAATTTTATCTTA
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* * * * * * *
629162 AAAAGGTTTCTCTCAGCAGAAGCTTAACAAATTTAAAAATATCATTTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* *
629211 AAAAGGTCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCATTTTG
1 AAAAGG-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
* *
629261 AAAAAGGGTCATCTCAGCAGAGGCTCAACAACTTTAAAAAT
1 -AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAT
629302 TTTTATTTGT
Statistics
Matches: 221, Mismatches: 53, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
46 4 0.02
47 33 0.15
48 88 0.40
49 23 0.10
50 67 0.30
51 6 0.03
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (49 bp):
AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTG
Found at i:629247 original size:98 final size:100
Alignment explanation
Indices: 629120--629301 Score: 244
Period size: 100 Copynumber: 1.8 Consensus size: 100
629110 CTTCAAAAAG
* * * * *
629120 CTCCTATCATTAGAGGCTCAACAA-TTTTAAAATTTTATCTT-AAAAAGGTTTC-TCTCAGCAGA
1 CTCCTATCAGTAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGG-GTCATCTCAGCAGA
*
629182 AGCTTAACAAATTTAAAAATATCATTTTGAAAAGGT
65 AGCTCAACAAATTTAAAAATATCATTTTGAAAAGGT
* * *
629218 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCATTTTGAAAAAGGGTCATCTCAGCAGAG
1 CTCCTATCAGTAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGGGTCATCTCAGCAGAA
*
629283 GCTCAACAACTTTAAAAAT
66 GCTCAACAAATTTAAAAAT
629302 TTTTATTTGT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
98 22 0.31
99 15 0.21
100 34 0.48
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (100 bp):
CTCCTATCAGTAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGGGTCATCTCAGCAGAA
GCTCAACAAATTTAAAAATATCATTTTGAAAAGGT
Found at i:638821 original size:9 final size:9
Alignment explanation
Indices: 638804--638834 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
638794 ATACAATAAG
*
638804 GGCACCCAA
1 GGCATCCAA
638813 GGCATCCAA
1 GGCATCCAA
638822 GGCATCCAA
1 GGCATCCAA
638831 GGCA
1 GGCA
638835 CCATCCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.35, G:0.26, T:0.06
Consensus pattern (9 bp):
GGCATCCAA
Found at i:641915 original size:2 final size:2
Alignment explanation
Indices: 641904--641935 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
641894 TGAATGTTGT
641904 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
641936 TAAATTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:644946 original size:11 final size:11
Alignment explanation
Indices: 644930--644960 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
644920 TTTGTTAGAA
644930 ATTTTATTAAT
1 ATTTTATTAAT
644941 ATTTTATTAAT
1 ATTTTATTAAT
644952 ATTCTTATT
1 ATT-TTATT
644961 TAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATTAAT
Found at i:645161 original size:19 final size:18
Alignment explanation
Indices: 645137--645182 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
645127 CATTCCTATT
* *
645137 TTTATTACTTATTTTTTAA
1 TTTATTACTCAATTTTT-A
*
645156 TTTATTAATCAATTTTTA
1 TTTATTACTCAATTTTTA
645174 TTTATTACT
1 TTTATTACT
645183 AAAAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTACTCAATTTTTA
Found at i:645600 original size:13 final size:13
Alignment explanation
Indices: 645582--645607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
645572 GTGCGATTCA
645582 GTTCGACGGTTCG
1 GTTCGACGGTTCG
645595 GTTCGACGGTTCG
1 GTTCGACGGTTCG
645608 ATCCAATCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (13 bp):
GTTCGACGGTTCG
Found at i:647004 original size:49 final size:49
Alignment explanation
Indices: 646827--647636 Score: 685
Period size: 49 Copynumber: 16.6 Consensus size: 49
646817 TAAAATATTG
* * * *
646827 AAAAAGCTCCTCTCAACAGAGGCTCTACAACTTTAAAAAATTCTCTATATT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAA-TCTTTATCTT
* * *
646878 GGAAAAAACTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATC-TCATCTG
1 --AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
*
646927 AAAAAGCTCCTATCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * * *
646976 TAAAAGCTCCTCTCAACAGAGGCACAACAACTTT-AAAATC--CATATG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* *
647022 AAAAAGCTCCTCTCAGCAGAGGCTCAGCAACTTTAAAATTCTCTT-T-TT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-TTATCTT
* * *
647070 AAAAAAGCTCCTCTTAGCAGAGGCTCCACAACTTTAAAATTC-TTATCTT
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * *
647119 GAAAAGGGCTCCTCTCAGCAGAGACTCAACAACTTTAAAATTCTCATAT-TG
1 -AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-TTATCTT
* * * * *
647170 GAAAAGCTCCTCTCAGCAGAGGTTCAACAAC-TTAAAAATTTTTTTTTT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * *
647218 GAAAAAGCTCTTCTCAGCAGAAGATCCACAACTTTAAAATTC-TTATCTT
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * *
647267 GAAAAGGGCTCCTCTCAGCAGAGGCTTAACAACTTTAAAATTC-TCATTTT
1 -AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * *
647317 GGAAAAGCTCCTCTCAGCAAAGGCTCAATAACTTT-AAAA--TTCATCTG
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * *
647364 AAAAAGCTCCTCTCAGCAGAGGCTTAACAAC-TTAAAAATTTTTTTTTT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * *
647412 GAAAAAGCTCTTCTCAACAAAGGCTCCACAACTTTAAAATTC-TTATCTT
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * *
647461 GAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTC-TCATCTT
1 -AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* * * * * *
647511 GGAAAAGCTCCTCTCAGCAAAGGCTCAACGA-TTTTAAAA--TTCATCTA
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
* *
647558 AAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTCTT-T-TT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCT-TTATCTT
* * *
647606 GAAAAAGCTCTTCTCAGTAGAGGCTCCACAA
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAA
647637 AAGGGCTCCT
Statistics
Matches: 617, Mismatches: 111, Indels: 62
0.78 0.14 0.08
Matches are distributed among these distances:
45 2 0.00
46 90 0.15
47 58 0.09
48 37 0.06
49 256 0.41
50 135 0.22
51 5 0.01
52 3 0.00
53 31 0.05
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (49 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTTATCTT
Found at i:647182 original size:194 final size:194
Alignment explanation
Indices: 646784--647636 Score: 934
Period size: 194 Copynumber: 4.4 Consensus size: 194
646774 TTAAAAGTTT
* * * *
646784 AAAAGGCTCATCTCAGCAGAGGCTCAATAACTTTAAAA----TATTGAAAAAGCTCCTCTCAACA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCCTTTTGAAAAAGCTCCTCTCAACA
* * **
646845 GAGGCTCTACAACTTTAAAAAATTCTCTATATTGGAAAA-AACTCCTCTCAGCAGAGGCTCAACA
66 GAGGCTCCACAACTTT--AAAATTCT-TATCTT-GAAAAGGGCTCCTCTCAGCAGAGGCTCAACA
* * *
646909 ACTTTAAAA-TCTCATC-TGAAAAAGCTCCTATCAGCAGAGGCTCAACAACTTTAAAAATCT-TT
127 ACTTTAAAATTCTCATCTTG-AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT
*
646971 ATCTT
191 AT-TG
* * * * * *
646976 TAAAAGCTCCTCTCAACAGAGGCACAACAACTTTAAAA-TCCATATGAAAAAGCTCCTCTCAGCA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCCTTTTGAAAAAGCTCCTCTCAACA
* ** * *
647040 GAGGCT-CAGCAACTTTAAAATTCTCT-T-TTTAAAAAAGCTCCTCTTAGCAGAGGCTCCACAAC
66 GAGGCTCCA-CAACTTTAAAATTCT-TATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAAC
* *
647102 TTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGACTCAACAACTTTAAAATTCTCATA
129 TTTAAAATTCTCATCTTGAAAA--GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATA
647167 TTG
192 TTG
* * * ** * *
647170 GAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTAAAAATTTTTTTTTTGAAAAAGCTCTTCTCAG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA--TTCCTTTTGAAAAAGCTCCTCTCAA
* * *
647235 CAGAAGATCCACAACTTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTTAACAAC
64 CAGAGGCTCCACAACTTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAAC
* * * *
647300 TTTAAAATTCTCATTTTGGAAAAGCTCCTCTCAGCAAAGGCTCAATAACTTTAAAA-T-TCAT-C
129 TTTAAAATTCTCATCTT-GAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATAT
647362 TG
193 TG
* * ** *
647364 AAAAAGCTCCTCTCAGCAGAGGCTTAACAACTTAAAAATTTTTTTTTTGAAAAAGCTCTTCTCAA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA--TTCCTTTTGAAAAAGCTCCTCTCAA
*
647429 CAAAGGCTCCACAACTTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAAC
64 CAGAGGCTCCACAACTTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAAC
* * *
647494 TTTAAAATTCTCATCTTGGAAAAGCTCCTCTCAGCAAAGGCTCAACGATTTTAAAATTCATC-TA
129 TTTAAAATTCTCATCTT-GAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTC-TCATA
647558 ---
192 TTG
* * *
647558 AAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTCTTTTTGAAAAAGCTCTTCTCAG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTC-C-TTTTGAAAAAGCTCCTCTCAA
*
647623 TAGAGGCTCCACAA
64 CAGAGGCTCCACAA
647637 AAGGGCTCCT
Statistics
Matches: 573, Mismatches: 65, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
190 4 0.01
191 33 0.06
192 45 0.08
193 12 0.02
194 312 0.54
195 40 0.07
196 3 0.01
197 73 0.13
198 46 0.08
199 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (194 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCCTTTTGAAAAAGCTCCTCTCAACA
GAGGCTCCACAACTTTAAAATTCTTATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTT
TAAAATTCTCATCTTGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATATTG
Found at i:647720 original size:50 final size:49
Alignment explanation
Indices: 647635--647876 Score: 290
Period size: 50 Copynumber: 4.9 Consensus size: 49
647625 GAGGCTCCAC
*
647635 AAAAGGGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTTATCTTG
1 AAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTG
* *
647685 AAAATGGCTTCTCTCAGCAGAGGCTCAATAACTTTAAAATT-TTCATCTTG
1 AAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTT-ATCTTG
* * * * *
647735 AAAAAGCTCATCTCAGCAAAGGTTCAACAACTTTAAAATTCTCT-TTTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCT-TATCTTG
* ** * * *
647784 AAAAAGCTCCTCTCAATAGAGGCTCCACAACTTTTTAAATTATTATCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAAC-TTTAAAATTCTTATCTTG
647834 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCT
1 AAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCT
647877 CATATATTTT
Statistics
Matches: 162, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
49 62 0.38
50 76 0.47
51 24 0.15
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (49 bp):
AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTG
Found at i:647741 original size:128 final size:124
Alignment explanation
Indices: 647517--647750 Score: 333
Period size: 128 Copynumber: 1.9 Consensus size: 124
647507 TCTTGGAAAA
* *
647517 GCTCCTCTCAGCAAAGGCTCAACGATTTTAAAATTCATCTAAAAAAGCTCCTCTCAGCAGAGGCT
1 GCTCCTCTCAGCAAAGGCTCAACAACTTTAAAATTCATCTAAAAAAGCTCCTCTCAGCAGAGGCT
* * *
647582 CAATAACTTTAAAATTCTCTTTTTGAAAAAGCTCTTCTCAGTAGAGGCTCCACAAAAGG
66 CAATAACTTTAAAATTCTCATCTTGAAAAAGCTCATCTCAGTAGAGGCTCCACAAAAGG
* * ** *
647641 GCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTTATCTTGAAAATGGCTTCTCTCAGCAGA
1 GCTCCTCTCAGCAAAGGCTCAACAACTTTAAAATTC--ATC-T-AAAAAAGCTCCTCTCAGCAGA
*
647706 GGCTCAATAACTTTAAAATTTTCATCTTGAAAAAGCTCATCTCAG
62 GGCTCAATAACTTTAAAATTCTCATCTTGAAAAAGCTCATCTCAG
647751 CAAAGGTTCA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
124 32 0.34
126 3 0.03
127 1 0.01
128 59 0.62
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (124 bp):
GCTCCTCTCAGCAAAGGCTCAACAACTTTAAAATTCATCTAAAAAAGCTCCTCTCAGCAGAGGCT
CAATAACTTTAAAATTCTCATCTTGAAAAAGCTCATCTCAGTAGAGGCTCCACAAAAGG
Found at i:647787 original size:177 final size:173
Alignment explanation
Indices: 647462--647813 Score: 526
Period size: 177 Copynumber: 2.0 Consensus size: 173
647452 TCTTATCTTG
647462 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTGGAAAAGCTCCTCTCA
1 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTGGAAAAGCTCCTCTCA
* * * * *
647527 GCAAAGGCTCAACGATTTTAAAATTCATCTAAAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTT
66 GCAAAGGCTCAACAACTTTAAAATTCATCTAAAAAAGCTCATCTCAGCAAAGGCTCAACAACTTT
* *
647592 AAAATTCTCTTTTTGAAAAAGCTCTTCTCAGTAGAGGCTCCAC
131 AAAATTCTCTTTTTGAAAAAGCTCCTCTCAATAGAGGCTCCAC
* * *
647635 AAAAGGGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTTATCTT-GAAAATGGCTTCTCT
1 AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTGGAAAA--GCTCCTCT
* * * *
647699 CAGCAGAGGCTCAATAACTTTAAAATTTTCATCTTGAAAAAGCTCATCTCAGCAAAGGTTCAACA
64 CAGCAAAGGCTCAACAACTTTAAAA--TTCATC-TAAAAAAGCTCATCTCAGCAAAGGCTCAACA
647764 ACTTTAAAATTCTCTTTTTGAAAAAGCTCCTCTCAATAGAGGCTCCAC
126 ACTTTAAAATTCTCTTTTTGAAAAAGCTCCTCTCAATAGAGGCTCCAC
647812 AA
1 AA
647814 CTTTTTAAAT
Statistics
Matches: 160, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
172 5 0.03
173 47 0.29
174 28 0.17
176 6 0.04
177 74 0.46
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (173 bp):
AAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTGGAAAAGCTCCTCTCA
GCAAAGGCTCAACAACTTTAAAATTCATCTAAAAAAGCTCATCTCAGCAAAGGCTCAACAACTTT
AAAATTCTCTTTTTGAAAAAGCTCCTCTCAATAGAGGCTCCAC
Found at i:654469 original size:23 final size:23
Alignment explanation
Indices: 654443--654488 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
654433 GTGGGTGTCC
*
654443 AAAAAGATGACTGAAAATGGGAT
1 AAAAAGATGACTAAAAATGGGAT
654466 AAAAAGATGACTAAAAATGGGAT
1 AAAAAGATGACTAAAAATGGGAT
654489 GGATAAGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.17
Consensus pattern (23 bp):
AAAAAGATGACTAAAAATGGGAT
Found at i:658258 original size:21 final size:22
Alignment explanation
Indices: 658234--658274 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
658224 AATATTTTTT
*
658234 ATTTTTTTA-GTTTTTTTTTAG
1 ATTTTTTTATGTTTTGTTTTAG
658255 ATTTTTTTATGTTTTGTTTT
1 ATTTTTTTATGTTTTGTTTT
658275 GTTTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (22 bp):
ATTTTTTTATGTTTTGTTTTAG
Found at i:658731 original size:21 final size:22
Alignment explanation
Indices: 658701--658751 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
658691 GTGTGTGAGT
*
658701 TTTTTTTTTTTG-TTT-TTTTG
1 TTTTTATTTTTGATTTGTTTTG
658721 CTTTTTATTTTTGATTTGTTTTG
1 -TTTTTATTTTTGATTTGTTTTG
658744 -TTTTATTT
1 TTTTTATTT
658752 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 19 0.70
22 3 0.11
23 5 0.19
ACGTcount: A:0.06, C:0.02, G:0.10, T:0.82
Consensus pattern (22 bp):
TTTTTATTTTTGATTTGTTTTG
Found at i:660094 original size:12 final size:10
Alignment explanation
Indices: 660065--660090 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
660055 AATAATATAT
660065 AAAAAATTCA
1 AAAAAATTCA
660075 AAAAAATTCA
1 AAAAAATTCA
660085 AAAAAA
1 AAAAAA
660091 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:661051 original size:3 final size:3
Alignment explanation
Indices: 661034--661103 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
661024 ACAAGAAATA
661034 AAT AA- AAT AAAT 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
661079 AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
661104 ATAAAAAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:667591 original size:529 final size:518
Alignment explanation
Indices: 666406--667800 Score: 1595
Period size: 529 Copynumber: 2.6 Consensus size: 518
666396 ATTCAATGTA
* * *
666406 GATGATTTTTTTTTTTACACATGGATTACTTAACTTGATGTCACGTGACATTAATTAATGCGAAT
1 GATGGTTTTTTTTTTT--ACATGGATTGCTTAACTTGATGTCACGTGATATTAATTAATGCGAAT
* * *
666471 TAATTATTAGTTTTAAAATACTTAATAAGTAAC-AAATTAATTAAATTAATTTATAAAATTAGCT
64 TAATTATTAGTTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGCT
* *
666535 AGCAAAATTTTTTGAATCATACTATTATTATTTCAATAAAAATGAGATTTTATTTAAATTTGT-T
129 AGCAAAA-TTTTTGAATCATATTATTACTATTTCAATAAAAATGAGATTTTATTTAAATTTGTAT
* * * * * *
666599 TTATTTTCATGATCTAATTTCAAGTATGAATATCCTTTATTTTTTGCAATATTACTAAAAAATAT
193 TT-TTTTTATGATCTAATTCCAAGT-TGAATATCCTTTATTTTTGGCAAAATTAATGAAAAATAT
* * * *
666664 ATGATAATTTAATACAAATTTCAAATTTCAAAACCTAAATAAGTAAATA-ATATCTATTACCGCT
256 ATGATAATTTATTACAAATTTCAAA-TTCAAAACCTAAA-GAGTAAATATATATATATTACCGAT
* * * * * * *
666728 CAAAAATTAATGCAAATAAGAGGTGTTCATGGGTCAGACTAGGTCAAATTCGAATTAGGCTCATG
319 CAAAAATTAATGCAAATAAGAGGTGTTCATGGGTAAGACCAAGCCAAATTAGAATCAAGCTCATG
** ** * * *
666793 ATTGGTATTAATAACTTATATGCTTATCAAAACTTGATTTAGTCCGAAATTTCAAGTCTAAAAAC
384 ATTAATATTAATAACTTATATGCTTATCAAAACCCGATCTAATCCAAAATTTCAAGTCTAAAAAC
* * *
666858 TTTTTCAAGTCCAGTCCAAATCTTATATAAATATATAAAATTAAAACCTTACGTAAAAACAAAAA
449 TTTTTCAAGTCCAGTCCAAATCTTATATAAATATATAAAATCAAAACCTTACATAAAAAAAAAAA
*
666923 ATGTG
514 ATATG
*** * * *
666928 GATGGTTAATTTTTTAACACATGGATTGCTTAACTTGATGTCACGTGTCTATTAATTAATACGAG
1 GATGGTT--TTTTTTTTTACATGGATTGCTTAACTTGATGTCACGTG-ATATTAATTAATGCGAA
666993 TTAATTATTAGTTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGC
63 TTAATTATTAGTTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGC
* * *
667058 TAGCAAAATTTTTGAAATCATATTATTACTATTTGACTAATAATGAGATTTTATTTAAATTTGTA
128 TAGCAAAATTTTTG-AATCATATTATTACTATTTCAATAAAAATGAGATTTTATTTAAATTTGTA
* * *
667123 TTTTTTTTATAATCTAATTCCAAGCTTGAATATCTTTTATATTTGGCAAAATTAATGAAAAATAT
192 TTTTTTTTATGATCTAATTCCAAG-TTGAATATCCTTTATTTTTGGCAAAATTAATGAAAAATAT
* * * *
667188 ATAATAATTTAGTTACAAATTTCAAATTCAGAAACTTAAAGAGTAAATAGTATATAGATTA-CTA
256 ATGATAATTTA-TTACAAATTTCAAATTCA-AAACCTAAAGAGTAAATA-TATATATATTACCGA
* * * *** *
667252 TCCAAAATTAATGCAAATTAGAGGTGTTTATGGGTTAAG-CCAAGCCGGGTTTAG-ATCAAGTTC
318 TCAAAAATTAATGCAAATAAGAGGTGTTCATGGG-TAAGACCAAGCC-AAATTAGAATCAAGCTC
* * * * ** * *
667315 AT-ATTTAATATTAATAACTTATATGTTTGTTC-AAACCCGGTCTAATCTAAAATTTTGAGTTTC
381 ATGA-TTAATATTAATAACTTATATGCTT-ATCAAAACCCGATCTAATCCAAAATTTCAAGTCTA
* * * *
667378 AAAATTTTTTTAAG-CTTAGTCCAAATCTTATATAAATATATAAAAATCAAAACCTTATATAAAA
444 AAAACTTTTTCAAGTC-CAGTCCAAATCTTATATAAATATAT-AAAATCAAAACCTTACAT-AAA
667442 AAGGGAAAAAATCACTATG
506 AA---AAAAAA--A-TATG
* * * *
667461 GATGGTTTTTTTTTTTACATGAATTGCTTAATTTGATGTCGCGTG-TATTAATTAATGCAAATTA
1 GATGGTTTTTTTTTTTACATGGATTGCTTAACTTGATGTCACGTGATATTAATTAATGCGAATTA
*
667525 ATTATTAATTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGCTAG
66 ATTATTAGTTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGCTAG
* * * * *
667590 CAAAATTTTAGGAATCATATTATTACTATTTCATTAAGAATGATATTTTATTTAAATTTGTATTA
131 CAAAATTTT-TGAATCATATTATTACTATTTCAATAAAAATGAGATTTTATTTAAATTTGTATTT
* ** *
667655 TTTTTATGATCCAATTCCAAGTTTGAATATCCTTTATTTTTGGCAACTTTAATGAAAAATATACG
195 TTTTTATGATCTAATTCCAAG-TTGAATATCCTTTATTTTTGGCAAAATTAATGAAAAATATATG
* * * * *
667720 GTAATTTAATTACAAATTTCAAAATTTAAAACCTAAAGAAGTAAATATTATATATATTATCGTTT
259 ATAATTT-ATTACAAATTTC-AAATTCAAAACCTAAAG-AGTAAATA-TATATATATTACCGATC
*
667785 AAAAATTAATACAAAT
320 AAAAATTAATGCAAAT
667801 TAAAGGTATC
Statistics
Matches: 738, Mismatches: 106, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
522 34 0.05
523 52 0.07
524 161 0.22
525 146 0.20
526 31 0.04
527 5 0.01
529 219 0.30
530 31 0.04
531 48 0.07
532 1 0.00
533 10 0.01
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (518 bp):
GATGGTTTTTTTTTTTACATGGATTGCTTAACTTGATGTCACGTGATATTAATTAATGCGAATTA
ATTATTAGTTTTAAAATACTTAATAAATAACAAAATCAATTAAATTAATTTATAAAATTGGCTAG
CAAAATTTTTGAATCATATTATTACTATTTCAATAAAAATGAGATTTTATTTAAATTTGTATTTT
TTTTATGATCTAATTCCAAGTTGAATATCCTTTATTTTTGGCAAAATTAATGAAAAATATATGAT
AATTTATTACAAATTTCAAATTCAAAACCTAAAGAGTAAATATATATATATTACCGATCAAAAAT
TAATGCAAATAAGAGGTGTTCATGGGTAAGACCAAGCCAAATTAGAATCAAGCTCATGATTAATA
TTAATAACTTATATGCTTATCAAAACCCGATCTAATCCAAAATTTCAAGTCTAAAAACTTTTTCA
AGTCCAGTCCAAATCTTATATAAATATATAAAATCAAAACCTTACATAAAAAAAAAAAATATG
Found at i:669622 original size:50 final size:50
Alignment explanation
Indices: 669563--669660 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
669553 TTCTTTTTGT
* *
669563 CATTAATTTGTCACGTATAAATTGATTTGGTCCAATAATTAAAATTTTAG
1 CATTAATTTGTAACGTATAAATTGATTTAGTCCAATAATTAAAATTTTAG
* ** * *
669613 CATTTATTTGTAATTTATAAATTGATTTAGTCTAATAGTTAAAATTTT
1 CATTAATTTGTAACGTATAAATTGATTTAGTCCAATAATTAAAATTTT
669661 TTGCTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (50 bp):
CATTAATTTGTAACGTATAAATTGATTTAGTCCAATAATTAAAATTTTAG
Found at i:671517 original size:15 final size:15
Alignment explanation
Indices: 671497--671526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
671487 TCTTCTACTA
*
671497 CATGGTGGTTGTTTG
1 CATGGTGGCTGTTTG
671512 CATGGTGGCTGTTTG
1 CATGGTGGCTGTTTG
671527 TAAGAGATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.40, T:0.43
Consensus pattern (15 bp):
CATGGTGGCTGTTTG
Found at i:674437 original size:2 final size:2
Alignment explanation
Indices: 674426--674455 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
674416 TGTATGTTAC
674426 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
674456 TAAATTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:675032 original size:9 final size:9
Alignment explanation
Indices: 675008--675049 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
674998 CAATTTGTCC
*
675008 TGTATTATTT
1 TGTATT-TTA
675018 TGTATTTTA
1 TGTATTTTA
675027 TGTATTTTA
1 TGTATTTTA
675036 TGTATTTTA
1 TGTATTTTA
675045 T-TATT
1 TGTATT
675050 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:675041 original size:18 final size:19
Alignment explanation
Indices: 675008--675061 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
674998 CAATTTGTCC
*
675008 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
675027 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
675045 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
675062 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:675525 original size:26 final size:24
Alignment explanation
Indices: 675483--675536 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
675473 CTGGGAGTGA
*
675483 GAAAAATTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTAGAAATTTCTGG
* *
675507 CGAAAATTTTTTCTGGAAATTTCTGG
1 -GAAAAATTTTT-TAGAAATTTCTGG
675533 GAAA
1 GAAA
675537 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (24 bp):
GAAAAATTTTTTAGAAATTTCTGG
Found at i:675670 original size:20 final size:20
Alignment explanation
Indices: 675645--675682 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
675635 ACTTCCGGTG
*
675645 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
675665 AAATTTCCAGAATCCGGC
1 AAATTTCCAGAATCCGGC
675683 ACCGGTGTTC
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:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:676061 original size:13 final size:12
Alignment explanation
Indices: 676026--676075 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
676016 TTTTTTTGAA
676026 TTTT-TTTTATT
1 TTTTATTTTATT
*
676037 TCTTT-GTTTATT
1 T-TTTATTTTATT
676049 TGTTTATTTTATT
1 T-TTTATTTTATT
676062 TTTTATTTTTATT
1 TTTTA-TTTTATT
676075 T
1 T
676076 ATTAGATTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.03
12 17 0.52
13 15 0.45
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:676066 original size:12 final size:12
Alignment explanation
Indices: 676027--676075 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
676017 TTTTTTGAAT
676027 TTTTTTTATTTC
1 TTTTTTTATTTC
* *
676039 TTTGTTTATTTG
1 TTTTTTTATTTC
*
676051 TTTATTTTATTTT
1 TTT-TTTTATTTC
676064 TTATTTTTATTT
1 TT-TTTTTATTT
676076 ATTAGATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 13 0.42
13 17 0.55
14 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTC
Found at i:676228 original size:60 final size:59
Alignment explanation
Indices: 676155--676433 Score: 424
Period size: 60 Copynumber: 4.7 Consensus size: 59
676145 AAAAAATTCT
**
676155 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC
* *
676213 AAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTT-AGAAAT-AAATTTCC
1 -AAA-AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC
*
676273 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCC
676333 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCC
676393 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
676434 CTAAAAAAAA
Statistics
Matches: 209, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
58 43 0.21
59 48 0.23
60 118 0.56
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (59 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTCC
Found at i:676293 original size:118 final size:118
Alignment explanation
Indices: 676155--676446 Score: 434
Period size: 118 Copynumber: 2.5 Consensus size: 118
676145 AAAAAATTCT
**
676155 AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTCCAAAAT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAAATTT-CAAAA-
*
676218 AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTT-AGAAAT-AAATTTCC
63 AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC
676273 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAATTTCAAAAAA
*
676338 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTCC
65 AATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCC
* *
676393 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCT-AAAAAAAAATT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
676447 CATTCTTTCC
Statistics
Matches: 162, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
117 6 0.04
118 93 0.57
119 49 0.30
120 14 0.09
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (118 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTCAAAAAAA
ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTCC
Found at i:678899 original size:20 final size:19
Alignment explanation
Indices: 678853--678900 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
678843 AAATGAAATA
*
678853 ATTTTAAATTTTAAATAAT
1 ATTTTAAATTTTAAACAAT
*
678872 AGTATTAAATTTTAAACAACT
1 A-TTTTAAATTTTAAACAA-T
678893 ATTTTAAA
1 ATTTTAAA
678901 AAGTGTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTTAAATTTTAAACAAT
Found at i:682744 original size:28 final size:28
Alignment explanation
Indices: 682713--682781 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
682703 TAATTATCTG
* *
682713 TTAATAAA-TTTATAATTTAAATATCAGA
1 TTAA-AAATTTTAAAATTTAAATATCACA
*
682741 TTAAAAATTTTTAAAATTTAATTATCACA
1 TTAAAAA-TTTTAAAATTTAAATATCACA
*
682770 TTAAATATTTTA
1 TTAAAAATTTTA
682782 TTATAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 3 0.09
28 9 0.26
29 23 0.66
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (28 bp):
TTAAAAATTTTAAAATTTAAATATCACA
Found at i:682793 original size:31 final size:29
Alignment explanation
Indices: 682721--682798 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
682711 TGTTAATAAA
* *
682721 TTTATAATTTAAATATCAGATTAAAAATT
1 TTTATAATTTAATTATCACATTAAAAATT
* *
682750 TTTAAAATTTAATTATCACATTAAATATTT
1 TTTATAATTTAATTATCACATTAAA-AATT
*
682780 TATTATAATTTAATGATCA
1 T-TTATAATTTAATTATCA
682799 TAACATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 22 0.54
30 4 0.10
31 15 0.37
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTATAATTTAATTATCACATTAAAAATT
Found at i:686112 original size:20 final size:20
Alignment explanation
Indices: 686076--686119 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
686066 TATTTATATA
* *
686076 TATTTAATAAATAAAATTTT
1 TATTAAATAAATAAAATTAT
686096 TATTAAAT-AATATAAATTAT
1 TATTAAATAAATA-AAATTAT
686116 TATT
1 TATT
686120 TTAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAATAAATAAAATTAT
Found at i:686853 original size:2 final size:2
Alignment explanation
Indices: 686848--686872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
686838 ACCAACACGC
686848 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
686873 ACTGCATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:687786 original size:10 final size:10
Alignment explanation
Indices: 687771--687854 Score: 55
Period size: 10 Copynumber: 8.4 Consensus size: 10
687761 GACCTGACAT
*
687771 ATATATGTAC
1 ATATATATAC
687781 ATATATATAC
1 ATATATATAC
* *
687791 ACACAT-TA-
1 ATATATATAC
687799 ATACATATATAC
1 AT--ATATATAC
* *
687811 ATATATACAT
1 ATATATATAC
687821 ATATATATAC
1 ATATATATAC
* *
687831 ACATATACAC
1 ATATATATAC
* *
687841 ACATATATAT
1 ATATATATAC
687851 ATAT
1 ATAT
687855 GTATGTGTGT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
8 1 0.02
9 2 0.04
10 49 0.88
11 2 0.04
12 2 0.04
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (10 bp):
ATATATATAC
Found at i:687808 original size:20 final size:20
Alignment explanation
Indices: 687783--687849 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
687773 ATATGTACAT
687783 ATATATACACACATTA-ATAC
1 ATATATACACACA-TACATAC
* * *
687803 ATATATACATATATACATAT
1 ATATATACACACATACATAC
* *
687823 ATATATACACATATACACAC
1 ATATATACACACATACATAC
687843 ATATATA
1 ATATATA
687850 TATATGTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 2 0.05
20 38 0.95
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATATACACACATACATAC
Found at i:687810 original size:8 final size:8
Alignment explanation
Indices: 687799--687854 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
687789 ACACACATTA
687799 ATACATAT
1 ATACATAT
687807 ATACATAT
1 ATACATAT
687815 ATACATAT
1 ATACATAT
687823 AT--ATAT
1 ATACATAT
*
687829 ACACATAT
1 ATACATAT
* *
687837 ACACACAT
1 ATACATAT
*
687845 ATATATAT
1 ATACATAT
687853 AT
1 AT
687855 GTATGTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 5 0.12
8 36 0.88
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (8 bp):
ATACATAT
Found at i:687828 original size:12 final size:12
Alignment explanation
Indices: 687767--687853 Score: 75
Period size: 12 Copynumber: 7.1 Consensus size: 12
687757 CTTTGACCTG
*
687767 ACATATATATGT
1 ACATATATATAT
*
687779 ACATATATATAC
1 ACATATATATAT
* *
687791 ACACATTAATACAT
1 ACATA-T-ATATAT
* *
687805 ATATACATATAT
1 ACATATATATAT
687817 ACATATATATAT
1 ACATATATATAT
* * *
687829 ACACATATACAC
1 ACATATATATAT
687841 ACATATATATAT
1 ACATATATATAT
687853 A
1 A
687854 TGTATGTGTG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
12 48 0.86
13 1 0.02
14 7 0.12
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.34
Consensus pattern (12 bp):
ACATATATATAT
Found at i:687828 original size:22 final size:22
Alignment explanation
Indices: 687785--687853 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
687775 ATGTACATAT
687785 ATATACACACATTAATACATATATAC
1 ATATACACACA-T-AT--ATATATAC
* * *
687811 ATATATACATATATATATACAC
1 ATATACACACATATATATATAC
687833 ATATACACACATATATATATA
1 ATATACACACATATATATATA
687854 TGTATGTGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 25 0.68
24 2 0.05
25 1 0.03
26 9 0.24
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATACACACATATATATATAC
Found at i:687833 original size:38 final size:40
Alignment explanation
Indices: 687773--687854 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 40
687763 CCTGACATAT
* *
687773 ATATGTACATATATATACACACAT-TA-ATACATATATAC
1 ATATATACATATATATACACACATATACACACATATATAC
* *
687811 ATATATACATATATATATACACATATACACACATATATAT
1 ATATATACATATATATACACACATATACACACATATATAC
687851 ATAT
1 ATAT
687855 GTATGTGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 22 0.58
39 2 0.05
40 14 0.37
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (40 bp):
ATATATACATATATATACACACATATACACACATATATAC
Found at i:689422 original size:74 final size:74
Alignment explanation
Indices: 689333--689474 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
689323 AGCATGTTGC
689333 ATGATGTTGAAAATTTGTCATATATATAACATATGTATGTCATTATCATACTTTATATAACAAAT
1 ATGATGTTGAAAATTTGTCATATATATAACATATGTATGTCATTATCATACTTTATATAACAAAT
689398 TAACGCTGT
66 TAACGCTGT
* * *
689407 ATGATTTTGAAAATTTGTCATATATATAACATATGTATTTCATTATCATATTTTATATAACAAAT
1 ATGATGTTGAAAATTTGTCATATATATAACATATGTATGTCATTATCATACTTTATATAACAAAT
689472 TAA
66 TAA
689475 ATTTAAATCT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.43
Consensus pattern (74 bp):
ATGATGTTGAAAATTTGTCATATATATAACATATGTATGTCATTATCATACTTTATATAACAAAT
TAACGCTGT
Found at i:696989 original size:18 final size:18
Alignment explanation
Indices: 696938--696996 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
696928 AATGTTATGC
*
696938 AAATATATTAATTATCATG
1 AAATATA-TAACTATCATG
* *
696957 CAATA-ATAACAATCATG
1 AAATATATAACTATCATG
696974 TAAATATATAA-TATCATG
1 -AAATATATAACTATCATG
696992 CAAAT
1 -AAAT
696997 CTATTAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 9 0.28
18 15 0.47
19 8 0.25
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (18 bp):
AAATATATAACTATCATG
Found at i:697053 original size:20 final size:20
Alignment explanation
Indices: 697012--697054 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
697002 AATAATTATA
**
697012 CAATAATATAAAAGGCATTG
1 CAATAATATAAAAACCATTG
697032 CAATAATATAAAATACCA-TG
1 CAATAATATAAAA-ACCATTG
697052 CAA
1 CAA
697055 ATATATAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.23
Consensus pattern (20 bp):
CAATAATATAAAAACCATTG
Found at i:697246 original size:24 final size:25
Alignment explanation
Indices: 697219--697275 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
697209 TAAATATATT
697219 AATAATAAT-ACAATCATATAAATA
1 AATAATAATCACAATCATATAAATA
* * *
697243 AATAA-ATTCATAATCATATAATTA
1 AATAATAATCACAATCATATAAATA
697267 AATATATAA
1 AATA-ATAA
697276 ATCATGCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 22 0.85
25 1 0.04
26 1 0.04
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAATAATCACAATCATATAAATA
Found at i:697276 original size:32 final size:32
Alignment explanation
Indices: 697206--697277 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
697196 ATAACCATGC
* *
697206 AAATAAATATATTAATAATAATACAATCATAT
1 AAATAAATAAATTAATAATAATACAATCAAAT
* * * *
697238 AAATAAATAAATTCATAATCATATAATTAAAT
1 AAATAAATAAATTAATAATAATACAATCAAAT
*
697270 ATATAAAT
1 AAATAAAT
697278 CATGCAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATAAATAAATTAATAATAATACAATCAAAT
Found at i:697280 original size:21 final size:22
Alignment explanation
Indices: 697222--697295 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
697212 ATATATTAAT
*
697222 AATA-ATACAATCATATAAATA
1 AATATATACAATCATATAATTA
* *
697243 AATAAATTCATAATCATATAATTA
1 AATATA-T-ACAATCATATAATTA
**
697267 AATATATA-AATCATGCAATTA
1 AATATATACAATCATATAATTA
697288 AATATATA
1 AATATATA
697296 AACATGTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 23 0.51
22 2 0.04
23 2 0.04
24 18 0.40
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (22 bp):
AATATATACAATCATATAATTA
Found at i:697296 original size:21 final size:20
Alignment explanation
Indices: 697262--697301 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
697252 ATAATCATAT
697262 AATTAAATATATAAATCATGC
1 AATTAAATATATAAA-CATGC
697283 AATTAAATATATAAACATG
1 AATTAAATATATAAACATG
697302 TAATAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTAAATATATAAACATGC
Found at i:697427 original size:12 final size:12
Alignment explanation
Indices: 697389--697436 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
697379 AATTAAATAT
*
697389 ATAATCATGCAA
1 ATAATCATACAA
* **
697401 ATAATAATATTA
1 ATAATCATACAA
697413 ATAATCATACAA
1 ATAATCATACAA
*
697425 ATAAACATACAA
1 ATAATCATACAA
697437 TTAAATATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (12 bp):
ATAATCATACAA
Found at i:697440 original size:56 final size:55
Alignment explanation
Indices: 697373--697516 Score: 191
Period size: 55 Copynumber: 2.6 Consensus size: 55
697363 ATGCAATTAG
* *
697373 ACATGCAATTAAATATATAATCATGCAAATAATAATAT-TAATAATCATACAAATAA
1 ACATGCAATTAAATATATAATCATGCAAATAAAAATATAT-A-AACCATACAAATAA
* * *
697429 ACATACAATTAAATATATAATTATGCAAATAAAAATATATAAACCATGCAAATAA
1 ACATGCAATTAAATATATAATCATGCAAATAAAAATATATAAACCATACAAATAA
* * *
697484 ATACGCAATTAAATATATAATCATACAAATAAA
1 ACATGCAATTAAATATATAATCATGCAAATAAA
697517 TATGCAATTA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
55 40 0.52
56 36 0.47
57 1 0.01
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.28
Consensus pattern (55 bp):
ACATGCAATTAAATATATAATCATGCAAATAAAAATATATAAACCATACAAATAA
Found at i:697449 original size:32 final size:31
Alignment explanation
Indices: 697272--697545 Score: 161
Period size: 32 Copynumber: 9.1 Consensus size: 31
697262 AATTAAATAT
* * *
697272 ATAAATCATGCAATTAAATATATAAACATG-TA
1 ATAAAT-ATACAATT-AATATATAATCATGCAA
* *
697304 ATAAACATGCAATTTAATATATGAA-CTATGCAA
1 ATAAATATACAA-TTAATATAT-AATC-ATGCAA
* *
697337 ATAAATATACAATCAAATATATGATCATGCAA
1 ATAAATATACAAT-TAATATATAATCATGCAA
* * * *
697369 TTAGACATGCAATTAAATATATAATCATGCAA
1 ATAAATATACAATT-AATATATAATCATGCAA
* *
697401 AT--A-AT--AA-TATTA-ATAATCATACAA
1 ATAAATATACAATTAATATATAATCATGCAA
* *
697425 ATAAACATACAATTAAATATATAATTATGCAA
1 ATAAATATACAATT-AATATATAATCATGCAA
*
697457 AT--A-A-A-AA-T-ATATA-AACCATGCAA
1 ATAAATATACAATTAATATATAATCATGCAA
** *
697480 ATAAATACGCAATTAAATATATAATCATACAA
1 ATAAATATACAATT-AATATATAATCATGCAA
*
697512 ATAAATATGCAATTAA-ATATAATCATGCAA
1 ATAAATATACAATTAATATATAATCATGCAA
697542 ATAA
1 ATAA
697546 TAATATATAA
Statistics
Matches: 193, Mismatches: 25, Indels: 50
0.72 0.09 0.19
Matches are distributed among these distances:
23 10 0.05
24 18 0.09
25 4 0.02
26 4 0.02
27 6 0.03
28 3 0.02
29 6 0.03
30 20 0.10
31 24 0.12
32 79 0.41
33 19 0.10
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (31 bp):
ATAAATATACAATTAATATATAATCATGCAA
Found at i:697557 original size:14 final size:14
Alignment explanation
Indices: 697540--697587 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
697530 ATAATCATGC
697540 AAATAATAATATAT
1 AAATAATAATATAT
*
697554 AAATAATGCAATCATGT
1 AAATAAT--AAT-ATAT
697571 AAATAATAATATAT
1 AAATAATAATATAT
697585 AAA
1 AAA
697588 CCATGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.45
15 3 0.10
16 3 0.10
17 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:697575 original size:17 final size:15
Alignment explanation
Indices: 697525--697580 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
697515 AATATGCAAT
697525 TAAAT-ATAATCATG
1 TAAATAATAATCATG
* *
697539 CAAATAATAAT-ATA
1 TAAATAATAATCATG
697553 TAAATAATGCAATCATG
1 TAAATAAT--AATCATG
697570 TAAATAATAAT
1 TAAATAATAAT
697581 ATATAAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 13 0.38
15 8 0.24
16 3 0.09
17 10 0.29
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.32
Consensus pattern (15 bp):
TAAATAATAATCATG
Found at i:697585 original size:85 final size:88
Alignment explanation
Indices: 697391--697628 Score: 244
Period size: 85 Copynumber: 2.8 Consensus size: 88
697381 TTAAATATAT
* * *
697391 AATCATGCAAATAATAATAT-TAATAATCATACAAATAAACATACAATTAAATATATAATTATGC
1 AATCATGTAAATAATAATATAT-ATAATCATACAAATAAATATGCAATTAAATATATAATTATGC
*
697455 AAATAAAAATATATAAACCATGCA
65 AAATAAAAATATATAAACAATGCA
** *** *
697479 AAT-AAATACGCAATTAA-ATATATAATCATACAAATAAATATGCAATT-AA-ATATAATCATGC
1 AATCATGTAAATAA-TAATATATATAATCATACAAATAAATATGCAATTAAATATATAATTATGC
* *
697540 AAATAATAATATATAAATAATGC-
65 AAATAAAAATATATAAACAATGCA
* * * *
697563 AATCATGTAAATAATAATATATA-AACCATGC--A-AAATATGCAATTGAATATATAATTATACA
1 AATCATGTAAATAATAATATATATAATCATACAAATAAATATGCAATTAAATATATAATTATGCA
697624 AATAA
66 AATAA
697629 CATGTAGTTA
Statistics
Matches: 123, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
81 12 0.10
82 3 0.02
83 16 0.13
84 12 0.10
85 41 0.33
86 2 0.02
87 30 0.24
88 7 0.06
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (88 bp):
AATCATGTAAATAATAATATATATAATCATACAAATAAATATGCAATTAAATATATAATTATGCA
AATAAAAATATATAAACAATGCA
Found at i:697594 original size:31 final size:31
Alignment explanation
Indices: 697532--697595 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
697522 AATTAAATAT
*
697532 AATCATGCAAATAATAATATATAAATAATGC
1 AATCATGCAAATAATAATATATAAACAATGC
* *
697563 AATCATGTAAATAATAATATATAAACCATGC
1 AATCATGCAAATAATAATATATAAACAATGC
697594 AA
1 AA
697596 AATATGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (31 bp):
AATCATGCAAATAATAATATATAAACAATGC
Found at i:697674 original size:24 final size:24
Alignment explanation
Indices: 697644--697804 Score: 137
Period size: 24 Copynumber: 7.0 Consensus size: 24
697634 AGTTAAATGT
697644 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* *
697668 ATAATCAAGCAATTAAATATATTA
1 ATAATCATGCAAATAAATATATTA
*
697692 ATAATCATGC-AATCAAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
*
697714 TATAATCATAGC-AACAAATATATTA
1 -ATAATCAT-GCAAATAAATATATTA
*
697739 ATAATCA-G---ACAAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
697759 ATAAATCACACAAATAAATATA-T-
1 AT-AATCATGCAAATAAATATATTA
*
697782 -TAATCATGCAAACAAATATATTA
1 ATAATCATGCAAATAAATATATTA
697805 GGCAAATAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
20 14 0.12
21 21 0.19
22 4 0.04
23 16 0.14
24 49 0.43
25 9 0.08
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:697738 original size:71 final size:65
Alignment explanation
Indices: 697637--697804 Score: 189
Period size: 71 Copynumber: 2.5 Consensus size: 65
697627 AACATGTAGT
* * *
697637 TAAATGTATAATCATGCAAATAAATATATTAATAATCAAGCAATTAAATATATTAAT-AATCATG
1 TAAATATATAATCATGCAAACAAATATATTAATAATC-AG--A-CAAATATATTAATAAATCA--
697701 CAATCAAA
60 C-A-CAAA
*
697709 TTAA-ATATAATCATAGC-AACAAATATATTAATAATCAGACAAATATATTAATAAATCACACAA
1 TAAATATATAATCAT-GCAAACAAATATATTAATAATCAGACAAATATATTAATAAATCACACAA
697772 A
65 A
697773 TAAATATATTAATCATGCAAACAAATATATTA
1 TAAATATA-TAATCATGCAAACAAATATATTA
697805 GGCAAATAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
64 7 0.08
65 6 0.07
66 21 0.24
67 12 0.14
68 6 0.07
70 2 0.02
71 27 0.31
72 5 0.06
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (65 bp):
TAAATATATAATCATGCAAACAAATATATTAATAATCAGACAAATATATTAATAAATCACACAAA
Found at i:697750 original size:20 final size:21
Alignment explanation
Indices: 697727--697774 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
697717 AATCATAGCA
*
697727 ACAAATATATTAAT-AATCAG
1 ACAAATATATTAATAAATCAC
697747 ACAAATATATTAATAAATCAC
1 ACAAATATATTAATAAATCAC
697768 ACAAATA
1 ACAAATA
697775 AATATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (21 bp):
ACAAATATATTAATAAATCAC
Found at i:697759 original size:47 final size:46
Alignment explanation
Indices: 697668--697804 Score: 140
Period size: 47 Copynumber: 2.9 Consensus size: 46
697658 AAATATATTA
*
697668 ATAATCAAGCAATTAAATATATTAATAATCATG-C-AATCAAATTAAAT
1 ATAATCAAGCAA-TAAATATATTAATAATCA-GACAAAT-ATATTAAAT
*
697715 ATAATCATAGCAACAAATATATTAATAATCAGACAAATATATT-AAT
1 ATAATCA-AGCAATAAATATATTAATAATCAGACAAATATATTAAAT
* *
697761 A-AATCACA-CAAATAAATATATTAATCATGCAAACAAATATATTA
1 ATAATCA-AGC-AATAAATATATTAATAAT-CAGACAAATATATTA
697805 GGCAAATAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
44 1 0.01
45 22 0.28
46 18 0.23
47 29 0.37
48 8 0.10
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.30
Consensus pattern (46 bp):
ATAATCAAGCAATAAATATATTAATAATCAGACAAATATATTAAAT
Found at i:697786 original size:21 final size:20
Alignment explanation
Indices: 697727--697787 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
697717 AATCATAGCA
* * *
697727 ACAAATATATTAATAATCAG
1 ACAAATAAATTATTAATCAC
* *
697747 ACAAATATATTAATAAATCAC
1 ACAAATAAATT-ATTAATCAC
697768 ACAAATAAATATATTAATCA
1 ACAAATAAAT-TATTAATCA
697788 TGCAAACAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 11 0.32
21 22 0.65
22 1 0.03
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (20 bp):
ACAAATAAATTATTAATCAC
Done.