Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000913.1 Hibiscus syriacus cultivar Beakdansim tig00001818_pilon, 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: 1610646
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1168274 original size:60 final size:60
Alignment explanation
Indices: 1168154--1168275 Score: 133
Period size: 60 Copynumber: 2.0 Consensus size: 60
1168144 TTTGAAAACC
* * ** * *
1168154 AATTTAGAATGAAGGTCATAGTTTGAGGATGAAAATGAATTTTTCAAAATTTTGAGGACT
1 AATTTAGAATGAAGATCATAGTTTAAAAATGAAAATGAATATTTCAAAATTTAGAGGACT
*
1168214 AATTTAGAATGACA-ATCATAGTTTAAAAATGAAATTAGAATATTT-AAAAGTTTAGA-GACT
1 AATTTAGAATGA-AGATCATAGTTTAAAAATGAAAAT-GAATATTTCAAAA-TTTAGAGGACT
1168274 AA
1 AA
1168276 AAGTTATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
60 39 0.75
61 13 0.25
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (60 bp):
AATTTAGAATGAAGATCATAGTTTAAAAATGAAAATGAATATTTCAAAATTTAGAGGACT
Found at i:1169756 original size:17 final size:18
Alignment explanation
Indices: 1169722--1169754 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1169712 TTTTGTTAGT
1169722 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
1169740 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
1169755 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:1179864 original size:17 final size:17
Alignment explanation
Indices: 1179832--1179898 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
1179822 TAGGCTTCAA
1179832 TTGAGCTTCTAAATTTTTT
1 TTGAG-TTC-AAATTTTTT
1179851 TTGAGTTCAAATTTTTT
1 TTGAGTTCAAATTTTTT
*
1179868 TTGAGTTCAAAATTTTT
1 TTGAGTTCAAATTTTTT
*
1179885 TT-AGTTCAAGTTTT
1 TTGAGTTCAAATTTT
1179899 AATATTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.22
17 27 0.60
18 3 0.07
19 5 0.11
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (17 bp):
TTGAGTTCAAATTTTTT
Found at i:1182282 original size:3 final size:3
Alignment explanation
Indices: 1182274--1182318 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
1182264 ATATTTATTA
*
1182274 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AA
1182319 CAAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1182300 original size:22 final size:22
Alignment explanation
Indices: 1182275--1182317 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1182265 TATTTATTAA
1182275 ATAATAATAAT-ATATATAATAT
1 ATAATAATAATAATA-ATAATAT
*
1182297 ATAATATTAATAATAATAATA
1 ATAATAATAATAATAATAATA
1182318 ACAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAATAATAATAATAATAT
Found at i:1182730 original size:75 final size:76
Alignment explanation
Indices: 1182448--1182704 Score: 428
Period size: 76 Copynumber: 3.4 Consensus size: 76
1182438 GAAATGTTGA
* * * *
1182448 AAACATCATGCACTGAAAGG-CTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCA
1 AAACATCATGCACTG-TAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1182512 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
1182524 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGGTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1182589 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1182600 AAACATCATGCACTGTAGGA-TTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1182664 AGGCTTTTTGG
66 AGGCTTTTTGG
1182675 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1182705 TGGGAAATAG
Statistics
Matches: 170, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
75 76 0.45
76 94 0.55
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1182955 original size:76 final size:76
Alignment explanation
Indices: 1182829--1183191 Score: 656
Period size: 76 Copynumber: 4.8 Consensus size: 76
1182819 TCAAAATAAC
*
1182829 AACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1182894 AAGGCTTTGAA
66 AAGGCTTTGAA
1182905 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1182970 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1182981 AACATC-AAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1183045 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1183056 AACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
*
1183121 AAGGCTTTAAA
66 AAGGCTTTGAA
*
1183132 AACATCAAAAAGCTCCCGAAGACTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1183192 TAGGAAATAG
Statistics
Matches: 277, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
75 73 0.26
76 204 0.74
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1183110 original size:151 final size:152
Alignment explanation
Indices: 1182829--1183187 Score: 648
Period size: 151 Copynumber: 2.4 Consensus size: 152
1182819 TCAAAATAAC
* *
1182829 AACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGACCCT
1182894 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
66 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
*
1182959 CAGATGACCCTAAGGCTTTGAA
131 CAGATGACCCTAAGGCTTTAAA
*
1182981 AACATC-AAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGACCCT
* *
1183045 AAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTA
66 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
1183110 CAGATGACCCTAAGGCTTTAAA
131 CAGATGACCCTAAGGCTTTAAA
*
1183132 AACATCAAAAAGCTCCCGAAGACTTTTTGGAAACATCATGCACTGTAGGACTTACA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACA
1183188 GATGTAGGAA
Statistics
Matches: 198, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
151 145 0.73
152 53 0.27
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (152 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGACCCT
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
CAGATGACCCTAAGGCTTTAAA
Found at i:1183888 original size:22 final size:22
Alignment explanation
Indices: 1183863--1183939 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
1183853 CATAAAGCTT
1183863 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1183885 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1183907 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1183929 TCATCTTTGAA
1 TCATCTTTGAA
1183940 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1188172 original size:32 final size:32
Alignment explanation
Indices: 1188131--1188193 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1188121 TGAAGAAATG
*
1188131 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCTCATCTCGTAGAGATACTTCTC
*
1188163 ATTGTTATGCTCATCTCGTAGAGATATTTCT
1 ATTGTTATGCTCATCTCGTAGAGATACTTCT
1188194 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (32 bp):
ATTGTTATGCTCATCTCGTAGAGATACTTCTC
Found at i:1188812 original size:1 final size:1
Alignment explanation
Indices: 1188806--1188891 Score: 109
Period size: 1 Copynumber: 86.0 Consensus size: 1
1188796 AATTTTCCTC
* ** *
1188806 TTTTTTTCTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** *
1188871 TTTTTCCTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
1188892 CCTTCTTCTT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:1188815 original size:8 final size:8
Alignment explanation
Indices: 1188804--1188906 Score: 111
Period size: 8 Copynumber: 12.6 Consensus size: 8
1188794 TCAATTTTCC
1188804 TCTTTTTT
1 TCTTTTTT
1188812 TCTTTTTTT
1 TC-TTTTTT
*
1188821 TTTTTTTT
1 TCTTTTTT
1188829 TCCTTTTTT
1 T-CTTTTTT
1188838 T-TTTTTT
1 TCTTTTTT
1188845 T-TTTTTT
1 TCTTTTTT
*
1188852 TTTTTTTT
1 TCTTTTTT
*
1188860 TTTTTTTT
1 TCTTTTTT
1188868 TCTTTTTT
1 TCTTTTTT
*
1188876 CCTTTTTT
1 TCTTTTTT
1188884 TCTTTTTT
1 TCTTTTTT
*
1188892 CCTTCTTCTT
1 TCTT-TT-TT
1188902 TCTTT
1 TCTTT
1188907 GCTGGATGAG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
7 14 0.17
8 47 0.57
9 17 0.20
10 5 0.06
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TCTTTTTT
Found at i:1188819 original size:7 final size:7
Alignment explanation
Indices: 1188807--1188902 Score: 89
Period size: 6 Copynumber: 14.4 Consensus size: 7
1188797 ATTTTCCTCT
1188807 TTTTTTC
1 TTTTTTC
1188814 -TTTTT-
1 TTTTTTC
1188819 TTTTTT-
1 TTTTTTC
*
1188825 TTTTTCC
1 TTTTTTC
1188832 TTTTTT-
1 TTTTTTC
1188838 TTTTTT-
1 TTTTTTC
1188844 TTTTTT-
1 TTTTTTC
1188850 TTTTTT-
1 TTTTTTC
*
1188856 TTTTTTT
1 TTTTTTC
1188863 TTTTTTC
1 TTTTTTC
1188870 TTTTTTCC
1 TTTTTT-C
1188878 TTTTTTTC
1 -TTTTTTC
1188886 TTTTTTC
1 TTTTTTC
* *
1188893 CTTCTTC
1 TTTTTTC
1188900 TTT
1 TTT
1188903 CTTTGCTGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
6 39 0.50
7 31 0.40
8 2 0.03
9 6 0.08
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:1188838 original size:28 final size:28
Alignment explanation
Indices: 1188798--1188891 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
1188788 CTTGATTCAA
*
1188798 TTTTCCTCTTTTTTTCTTTTTTTTTTTT
1 TTTTCCTTTTTTTTTCTTTTTTTTTTTT
*
1188826 TTTTCCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTCCTTTTTTTTTCTTTTTTTTTTTT
** **
1188854 TTTTTTTTTTTTTTTC-TTTTTTCCTTT
1 TTTTCCTTTTTTTTTCTTTTTTTTTTTT
1188881 TTTT-CTTTTTT
1 TTTTCCTTTTTT
1188892 CCTTCTTCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.10
27 13 0.22
28 39 0.67
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (28 bp):
TTTTCCTTTTTTTTTCTTTTTTTTTTTT
Found at i:1191510 original size:21 final size:21
Alignment explanation
Indices: 1191486--1191525 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1191476 AAAAAGTAAG
1191486 AATACAAAATGAAAATGCACA
1 AATACAAAATGAAAATGCACA
*
1191507 AATACAAAATGTAAATGCA
1 AATACAAAATGAAAATGCA
1191526 TGTATGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AATACAAAATGAAAATGCACA
Found at i:1194648 original size:17 final size:17
Alignment explanation
Indices: 1194618--1194651 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1194608 AATTAAATAT
1194618 ATTACAAATAAAATAAA
1 ATTACAAATAAAATAAA
1194635 ATTA-AAATATAAATAAA
1 ATTACAAATA-AAATAAA
1194652 TAATAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTACAAATAAAATAAA
Found at i:1194648 original size:22 final size:22
Alignment explanation
Indices: 1194623--1194665 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1194613 AATATATTAC
*
1194623 AAATAAAATAA-AATTAAAATAT
1 AAAT-AAATAATAACTAAAATAT
1194645 AAATAAATAATAACTAAAATA
1 AAATAAATAATAACTAAAATA
1194666 AATAATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAATAATAACTAAAATAT
Found at i:1194652 original size:16 final size:17
Alignment explanation
Indices: 1194611--1194652 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1194601 TAATAATAAT
*
1194611 TAAATATATTACAAATA
1 TAAATAAATTACAAATA
1194628 -AAATAAAATTA-AAATA
1 TAAAT-AAATTACAAATA
1194644 TAAATAAAT
1 TAAATAAAT
1194653 AATAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATAAATTACAAATA
Found at i:1196097 original size:3 final size:3
Alignment explanation
Indices: 1196089--1196130 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
1196079 ATATTTATTA
*
1196089 AAT AAT AAT AAT -AT ATAT ATAT AAT ATT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AA
1196131 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 26 0.74
4 7 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1196114 original size:22 final size:20
Alignment explanation
Indices: 1196077--1196123 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
1196067 TTTTTGCTTG
*
1196077 TAATATTTATTAAATAATAA
1 TAATATATATTAAATAATAA
*
1196097 TAATATATATATATAATATTAA
1 TAATATATAT-TA-AATAATAA
1196119 TAATA
1 TAATA
1196124 ATAATAACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 2 0.09
22 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATATATTAAATAATAA
Found at i:1201736 original size:18 final size:20
Alignment explanation
Indices: 1201713--1201752 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1201703 TTAGCATTTT
*
1201713 AAAAAAG-AAATCTTT-TAA
1 AAAAAAGTAAAACTTTATAA
1201731 AAAAAAGTAAAACTTTATAA
1 AAAAAAGTAAAACTTTATAA
1201751 AA
1 AA
1201753 CTAAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAAAAGTAAAACTTTATAA
Found at i:1201889 original size:21 final size:20
Alignment explanation
Indices: 1201847--1201890 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1201837 TAAAAACCCT
*
1201847 AAAAGATACATTTAAGATAA
1 AAAAGATACATTTAAAATAA
1201867 AAAAGATA-ATTCCTAAAATAA
1 AAAAGATACATT--TAAAATAA
1201888 AAA
1 AAA
1201891 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 8 0.38
21 10 0.48
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAAGATACATTTAAAATAA
Found at i:1204024 original size:65 final size:65
Alignment explanation
Indices: 1203891--1204049 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
1203881 GGACCCTTAG
* * *
1203891 TGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
* * * *
1203955 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TA
1 TGCATTGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-
*
1204018 TA
64 GA
*
1204020 TGCATTGATGCATGAAATGCATTCGATGTT
1 TGCATTGATGCATCAAATGCATTCGATGTT
1204050 CAATTTAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 27 0.33
65 52 0.63
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
TGCATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGA
Found at i:1204089 original size:65 final size:64
Alignment explanation
Indices: 1203890--1204099 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
1203880 TGGACCCTTA
* * ** *
1203890 GTGCATTGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * *
1203954 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATTGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1204017 AT-
63 -TG
* * * *
1204019 ATGCATTGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATAGATT
1 GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCAT-GGTT
1204083 G
64 G
* *
1204084 GTGCATCGGTGCATCA
1 GTGCATTGATGCATCA
1204100 CTCTGAAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 48 0.41
65 60 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATTGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1206729 original size:43 final size:43
Alignment explanation
Indices: 1206659--1206757 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
1206649 ACCCGACGGA
* *
1206659 TGCATCGATGCATGACCATGTGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCATGAACATGTGAATCGATGCACATTCAAGGCG
*
1206702 TGCATCGGTGCAT-AACATGATGAATCGATGCACATTCAAAGG-G
1 TGCATCGATGCATGAACATG-TGAATCGATGCACATTC-AAGGCG
*
1206745 ATGCATTGATGCA
1 -TGCATCGATGCA
1206758 CTGTTAAGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
42 5 0.10
43 29 0.60
44 14 0.29
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (43 bp):
TGCATCGATGCATGAACATGTGAATCGATGCACATTCAAGGCG
Found at i:1210628 original size:22 final size:21
Alignment explanation
Indices: 1210586--1210625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1210576 GAGTTTATTT
*
1210586 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1210607 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1210626 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1212591 original size:18 final size:17
Alignment explanation
Indices: 1212537--1212585 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1212527 TTGGACCCTT
* *
1212537 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1212555 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1212573 AGTGCATTCGATG
1 AGTGCA-TCGATG
1212586 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1212755 original size:65 final size:64
Alignment explanation
Indices: 1212557--1212766 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
1212547 TGCACTAAGA
* * ** *
1212557 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
** * *
1212621 GTGCATCGATGCATCAAACACATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1212684 AT-
63 -TG
* * *
1212686 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATAGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCAT-GGTT
1212750 G
64 G
*
1212751 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1212767 CTATGAAAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 47 0.40
65 62 0.53
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1214454 original size:58 final size:55
Alignment explanation
Indices: 1214258--1214465 Score: 229
Period size: 57 Copynumber: 3.6 Consensus size: 55
1214248 CAAAATTTCC
** *
1214258 AAGAAATAAATTCAATTATTTATTTCTTTTTACAAAATAGAATCATACTTGATTCTT
1 AAGAAATAAATTCAACGATTTATTTC-TTTTACAAAATAGAATCATACATGATTC-T
* * *
1214315 AAGAAATAAATTCAACGATTTAATTTCTTTTACAAAACAGAATCATACAAGATTAT
1 AAGAAATAAATTCAACGATTT-ATTTCTTTTACAAAATAGAATCATACATGATTCT
* * * *
1214371 ACGTAAATAAATTCAACAATTTATTTACTTTTACAAAATAGAATCGTCCATGATTTCT
1 AAG-AAATAAATTCAACGATTTATTT-CTTTTACAAAATAGAATCATACATGA-TTCT
*
1214429 AAGAAAATAAATTTGAA-GATTTATTTCCTTTTACAAA
1 AAG-AAATAAA-TTCAACGATTTATTT-CTTTTACAAA
1214466 CCAAAATCAT
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
56 7 0.05
57 82 0.64
58 35 0.27
59 4 0.03
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (55 bp):
AAGAAATAAATTCAACGATTTATTTCTTTTACAAAATAGAATCATACATGATTCT
Found at i:1217197 original size:24 final size:23
Alignment explanation
Indices: 1217153--1217199 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1217143 TAAGATTTAG
**
1217153 AGTTTTCAAAAATCAAACTTGAA
1 AGTTTTCAAAAAGAAAACTTGAA
*
1217176 AGTTTTGAAAAAGAAAATCTTGAA
1 AGTTTTCAAAAAGAAAA-CTTGAA
1217200 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (23 bp):
AGTTTTCAAAAAGAAAACTTGAA
Found at i:1226125 original size:29 final size:30
Alignment explanation
Indices: 1226069--1226133 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1226059 ATGCCTTAGA
* * * *
1226069 AAAATTTGGGGACCATTTCGTAAGTTTT-G
1 AAAATTTGGGGACAAATTCATAAATTTTGG
*
1226098 AAAATTTGGGGATAAATTCATAAATTTTGG
1 AAAATTTGGGGACAAATTCATAAATTTTGG
1226128 AAAATT
1 AAAATT
1226134 GATGAAGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (30 bp):
AAAATTTGGGGACAAATTCATAAATTTTGG
Found at i:1227347 original size:40 final size:40
Alignment explanation
Indices: 1227292--1227373 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1227282 TGCAGGTTTA
1227292 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1227332 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1227372 TA
1 TA
1227374 GCACTACGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1227572 original size:47 final size:45
Alignment explanation
Indices: 1227478--1227603 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1227468 GTAACCATGC
* * *
1227478 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* * *
1227522 AAATAAACTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
*
1227569 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1227604 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.15
46 1 0.01
47 38 0.54
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:1233343 original size:20 final size:20
Alignment explanation
Indices: 1233318--1233365 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1233308 ATGATTAGAT
1233318 TCAAAACTTAT-ATTAAAGTA
1 TCAAAACTTATCA-TAAAGTA
* *
1233338 TCAAAACTTTTCATAAAGTT
1 TCAAAACTTATCATAAAGTA
1233358 TCAAAACT
1 TCAAAACT
1233366 CCCGAAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (20 bp):
TCAAAACTTATCATAAAGTA
Found at i:1233520 original size:71 final size:73
Alignment explanation
Indices: 1233332--1233527 Score: 294
Period size: 72 Copynumber: 2.7 Consensus size: 73
1233322 AACTTATATT
* * *
1233332 AAAGTATCAAAACTTTTCATAAAGTTTCAAAACTCC-CGAAGAGTATCCAAACTGTCCAAAAAAG
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCAAAACTGTCCAAAAAAG
1233396 ATTGCTAA
66 ATTGCTAA
*
1233404 AAAGTATCGAAACTTTTCATAAAGTTTCGAAACTCCT-AAAGAGTATCAAAACTGTCCAAAAAA-
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCAAAACTGTCCAAAAAAG
1233467 ATTGCTAA
66 ATTGCTAA
* *
1233475 AAAGTATCAAAACTTTTCA-AAAGTTTCGAAACTACCTCCAA-AGTATCGAAACT
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACT-CCTCAAAGAGTATCAAAACT
1233528 CCTTAAGAGT
Statistics
Matches: 114, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
70 14 0.12
71 40 0.35
72 60 0.53
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (73 bp):
AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCAAAACTGTCCAAAAAAG
ATTGCTAA
Found at i:1233523 original size:20 final size:18
Alignment explanation
Indices: 1233475--1233546 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
1233465 AAATTGCTAA
* **
1233475 AAAGTATCAAAACTTTTC
1 AAAGTATCGAAACTCCTC
*
1233493 AAAAGTTTCGAAACTACCTCC
1 -AAAGTATCGAAACT-CCT-C
*
1233514 AAAGTATCGAAACTCCTT
1 AAAGTATCGAAACTCCTC
1233532 AAGAGTATCGAAACT
1 AA-AGTATCGAAACT
1233547 TGTCACGCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.05
19 27 0.61
20 14 0.32
21 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAGTATCGAAACTCCTC
Found at i:1235159 original size:21 final size:21
Alignment explanation
Indices: 1235118--1235164 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1235108 ATGACATGAC
* *
1235118 TGCTCATCTTGGTGTCATGGA
1 TGCTCATCTTGGCGCCATGGA
*
1235139 TGCTCATCTTGGCGCCTTGGA
1 TGCTCATCTTGGCGCCATGGA
*
1235160 GGCTC
1 TGCTC
1235165 GTTTCCTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.26, G:0.30, T:0.34
Consensus pattern (21 bp):
TGCTCATCTTGGCGCCATGGA
Found at i:1235516 original size:22 final size:24
Alignment explanation
Indices: 1235452--1235518 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
1235442 TTTTTCAATG
* *
1235452 GATATATTTTGGCCTATTATGTTG
1 GATATATTTTGGCTTATTATGTTC
* * *
1235476 GATATATGTTGGATCATTAT-TTC
1 GATATATTTTGGCTTATTATGTTC
1235499 G-TATATTTTGGCTTATTATG
1 GATATATTTTGGCTTATTATG
1235519 CTCTAATCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
22 15 0.44
23 3 0.09
24 16 0.47
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51
Consensus pattern (24 bp):
GATATATTTTGGCTTATTATGTTC
Found at i:1237675 original size:23 final size:21
Alignment explanation
Indices: 1237637--1237679 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1237627 ATAATTATTT
1237637 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1237658 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1237679 A
1 A
1237680 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1240244 original size:39 final size:38
Alignment explanation
Indices: 1240201--1240327 Score: 106
Period size: 39 Copynumber: 3.5 Consensus size: 38
1240191 AAACAGATTG
*
1240201 CTAAAAAGTATCGAAACTTTTCATAAAGTTTCGAAACTC
1 CTAAAAAGTATCAAAACTTTTCA-AAAGTTTCGAAACTC
* * * * *
1240240 CTAAAGAGTATCAAAAC-TGTCCAAA------AAATTG
1 CTAAAAAGTATCAAAACTTTTCAAAAGTTTCGAAACTC
1240271 CTAAAAAGTATCAAAACTTTTCAAAAGTTTCGAAACTAC
1 CTAAAAAGTATCAAAACTTTTCAAAAGTTTCGAAACT-C
** *
1240310 CTCCAAAGTATCGAAACT
1 CTAAAAAGTATCAAAACT
1240328 CCTTAAGAGT
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
31 20 0.30
32 6 0.09
37 3 0.05
38 7 0.11
39 30 0.45
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (38 bp):
CTAAAAAGTATCAAAACTTTTCAAAAGTTTCGAAACTC
Found at i:1240320 original size:70 final size:73
Alignment explanation
Indices: 1240133--1240327 Score: 276
Period size: 72 Copynumber: 2.7 Consensus size: 73
1240123 AACTTATATT
** * *
1240133 AAAGTATCAAAACTTTTCATAAAGTTTTAAAACTCC-CGAAGAGTATCGAAACTGTCTAAAACAG
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCGAAACTGTCCAAAACAG
1240197 ATTGCTAA
66 ATTGCTAA
* *
1240205 AAAGTATCGAAACTTTTCATAAAGTTTCGAAACTCCT-AAAGAGTATCAAAACTGTCCAAAA-A-
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCGAAACTGTCCAAAACAG
1240267 ATTGCTAA
66 ATTGCTAA
*
1240275 AAAGTATCAAAACTTTTCA-AAAGTTTCGAAACTACCTCCAA-AGTATCGAAACT
1 AAAGTATCAAAACTTTTCATAAAGTTTCGAAACT-CCTCAAAGAGTATCGAAACT
1240328 CCTTAAGAGT
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
69 14 0.13
70 40 0.36
71 3 0.03
72 54 0.49
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (73 bp):
AAAGTATCAAAACTTTTCATAAAGTTTCGAAACTCCTCAAAGAGTATCGAAACTGTCCAAAACAG
ATTGCTAA
Found at i:1240323 original size:20 final size:18
Alignment explanation
Indices: 1240275--1240346 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
1240265 AAATTGCTAA
* **
1240275 AAAGTATCAAAACTTTTC
1 AAAGTATCGAAACTCCTC
*
1240293 AAAAGTTTCGAAACTACCTCC
1 -AAAGTATCGAAACT-CCT-C
*
1240314 AAAGTATCGAAACTCCTT
1 AAAGTATCGAAACTCCTC
1240332 AAGAGTATCGAAACT
1 AA-AGTATCGAAACT
1240347 TGTCACGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 2 0.05
19 27 0.61
20 14 0.32
21 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAGTATCGAAACTCCTC
Found at i:1241970 original size:21 final size:20
Alignment explanation
Indices: 1241926--1241970 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1241916 TGACATGACT
*
1241926 GCTCATCTTGGTGCATGGAT
1 GCTCATCTTGGTGCATGGAG
*
1241946 GCTCATCTTGGTGCCTTGGAG
1 GCTCATCTTGGTG-CATGGAG
1241967 GCTC
1 GCTC
1241971 GTTTCCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.11, C:0.24, G:0.31, T:0.33
Consensus pattern (20 bp):
GCTCATCTTGGTGCATGGAG
Found at i:1242311 original size:22 final size:24
Alignment explanation
Indices: 1242247--1242313 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
1242237 TTTTTCAATG
* *
1242247 GATATATTTTGGCCTATTATGTTG
1 GATATATTTTGGCTTATTATGTTC
* * *
1242271 GATATATGTTGGATCATTAT-TTC
1 GATATATTTTGGCTTATTATGTTC
1242294 G-TATATTTTGGCTTATTATG
1 GATATATTTTGGCTTATTATG
1242314 CTCTAATCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
22 15 0.44
23 3 0.09
24 16 0.47
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.51
Consensus pattern (24 bp):
GATATATTTTGGCTTATTATGTTC
Found at i:1246953 original size:56 final size:56
Alignment explanation
Indices: 1246888--1246993 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 56
1246878 ATCATCCAAC
* * *
1246888 TATAAGATGTTTTTTTTGT-TCTCTTACTATTAAAAGTTACAAAATGATCATTTGAT
1 TATAAGATGTTTTTTTAGTCCCTC-GACTATTAAAAGTTACAAAATGATCATTTGAT
* * *
1246944 TATAGGATGTTTTTTTAGTCCCTCGACTATTAAAAGTTATAAGATGATCA
1 TATAAGATGTTTTTTTAGTCCCTCGACTATTAAAAGTTACAAAATGATCA
1246994 CCTGACTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
56 40 0.93
57 3 0.07
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (56 bp):
TATAAGATGTTTTTTTAGTCCCTCGACTATTAAAAGTTACAAAATGATCATTTGAT
Found at i:1258123 original size:64 final size:65
Alignment explanation
Indices: 1258055--1258211 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 65
1258045 TTGAAGGTGT
* ***
1258055 ATCGATGCA-CAGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCA-ATTAG
1 ATCGATGCATCAGGTAGTGCATCGATGCATC-CCAGTAATAAT-AAAACATCGAATGCATATTA-
1258116 TGC
63 TGC
* * *
1258119 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATCAGGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
*
1258183 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCATCAGGTAGTGCATCGATGCAT
1258212 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 68 0.86
65 10 0.13
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (65 bp):
ATCGATGCATCAGGTAGTGCATCGATGCATCCCAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:1258976 original size:31 final size:31
Alignment explanation
Indices: 1258938--1259002 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1258928 AGAGTCGAGG
*
1258938 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
** *
1258969 GTTTACCTAGGTTCTTTGGGACATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
1259000 GTT
1 GTT
1259003 GTCAAGGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTACGGAACATATGGACA
Found at i:1259013 original size:30 final size:30
Alignment explanation
Indices: 1258958--1259015 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1258948 GTTCTACGGA
*
1258958 ACATATGGACAGTTTACCTAGGTTCTTTGGG
1 ACATATGGACAGTTTA-CAAGGTTCTTTGGG
1258989 ACATATGGACAGTTGT-CAAGGTTCTTT
1 ACATATGGACAGTT-TACAAGGTTCTTT
1259016 ATGACCTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 14 0.56
32 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (30 bp):
ACATATGGACAGTTTACAAGGTTCTTTGGG
Found at i:1263468 original size:30 final size:31
Alignment explanation
Indices: 1263409--1263472 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
1263399 AGATTCTAGG
*
1263409 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
* *
1263440 GTTTACCTAGGTTCT-CGGGACCTATGGACA
1 GTTTACCTAGGTTCTACGGAACATATGGACA
1263470 GTT
1 GTT
1263473 GTCGAGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (31 bp):
GTTTACCTAGGTTCTACGGAACATATGGACA
Found at i:1266422 original size:50 final size:52
Alignment explanation
Indices: 1266335--1266431 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 52
1266325 GTCCCCTGCA
**
1266335 CGCGCTATACGATGATTTGACGCCACGTGGGGTATAGCGC-GCCCCTTAAAC
1 CGCGCTATACGATGAGCTGACGCCACGTGGGGTATAGCGCGGCCCCTTAAAC
* *
1266386 CGCGCTATACGGTGAGCTGACGTCACGT-GGGTATAGCGCGGCCCCT
1 CGCGCTATACGATGAGCTGACGCCACGTGGGGTATAGCGCGGCCCCT
1266432 GCAGTGCACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 11 0.27
51 30 0.73
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.21
Consensus pattern (52 bp):
CGCGCTATACGATGAGCTGACGCCACGTGGGGTATAGCGCGGCCCCTTAAAC
Found at i:1266444 original size:50 final size:50
Alignment explanation
Indices: 1266320--1266475 Score: 135
Period size: 51 Copynumber: 3.1 Consensus size: 50
1266310 TTAGCAGTAA
* **
1266320 AGCGCGTCCCCTGCACGCGCTATACGATGATTTGACGCCACGTGGGGTAT
1 AGCGCGGCCCCTGCACGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
** * *
1266370 AGCGC-GCCCCTTAAACCGCGCTATACGGTGAGCTGACGTCACGT-GGGTAT
1 AGCGCGGCCCC-TGCA-CGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
* * *
1266420 AGCGCGGCCCCTGCAGTGCACTATACTGTAT-ATCTGA---CACGTGGGGTAT
1 AGCGCGGCCCCTGCA-CGCGCTATAC-G-ATGAGCTGACGCCACGTGGGGTAT
1266469 AGCGCGG
1 AGCGCGG
1266476 TGCAGGGGGT
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
48 5 0.06
49 17 0.20
50 28 0.33
51 35 0.41
52 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.21
Consensus pattern (50 bp):
AGCGCGGCCCCTGCACGCGCTATACGATGAGCTGACGCCACGTGGGGTAT
Found at i:1268359 original size:18 final size:18
Alignment explanation
Indices: 1268335--1268375 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1268325 CCCAGCAGCC
1268335 ACCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
*
1268353 GCCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
1268371 ACCGC
1 ACCGC
1268376 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.20
Consensus pattern (18 bp):
ACCGCAGCCATATATGAT
Found at i:1272573 original size:51 final size:50
Alignment explanation
Indices: 1272458--1272578 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 50
1272448 TACAAAACGT
1272458 GGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCAC
1 GGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCAC
** * *
1272508 GGTACCTGCCCCGCGCTATATAAAATTATGTCGGGAGTAAAGGTATAG-CGC
1 GGTACCTGATCCGCGCTATATAAAATTATGTC-AGAGTAAAGGTAT-GTCAC
*
1272559 GGTTCCTGATCCGCGCTATA
1 GGTACCTGATCCGCGCTATA
1272579 CCCCTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 30 0.48
51 31 0.50
52 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (50 bp):
GGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCAC
Found at i:1272665 original size:50 final size:51
Alignment explanation
Indices: 1272590--1272717 Score: 177
Period size: 51 Copynumber: 2.5 Consensus size: 51
1272580 CCCTACGTGG
* * * **
1272590 CGTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
* *
1272640 CGTATAGCGCGGTTCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
*
1272691 CGTATAGCGCGGTACAGAGGGCGCGCT
1 CGTATAGCGCGGTACAGGGGGCGCGCT
1272718 TTACTGCTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 27 0.39
51 42 0.61
ACGTcount: A:0.18, C:0.33, G:0.34, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAC
Found at i:1275970 original size:22 final size:22
Alignment explanation
Indices: 1275942--1275987 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1275932 TGTCCTCCTG
*
1275942 CCCAAACCCAGATGCAACCTTA
1 CCCAAACCCAGATACAACCTTA
1275964 CCCAAACCCAGATACAACCTTA
1 CCCAAACCCAGATACAACCTTA
1275986 CC
1 CC
1275988 ATAGTTACCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.43, G:0.07, T:0.13
Consensus pattern (22 bp):
CCCAAACCCAGATACAACCTTA
Found at i:1280635 original size:17 final size:17
Alignment explanation
Indices: 1280609--1280656 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
1280599 TCGAATTATG
* *
1280609 TATAATTATAATATATA
1 TATAAATATAATATAAA
1280626 TATAAATATAAT-TAAA
1 TATAAATATAATATAAA
1280642 TATAAA-ATAATATAA
1 TATAAATATAATATAA
1280657 TTGTGATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 5 0.18
16 12 0.43
17 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAAATATAATATAAA
Found at i:1280653 original size:20 final size:23
Alignment explanation
Indices: 1280609--1280658 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 23
1280599 TCGAATTATG
*
1280609 TATAATTATAATATATATATAAA
1 TATAATTATAATATATAAATAAA
1280632 TATAATTA-AATATA-AAAT-AA
1 TATAATTATAATATATAAATAAA
1280652 TATAATT
1 TATAATT
1280659 GTGATTACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 3 0.12
22 6 0.23
23 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAATTATAATATATAAATAAA
Found at i:1291513 original size:5 final size:5
Alignment explanation
Indices: 1291503--1291546 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
1291493 TAGATGCCGT
1291503 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCT
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCT
1291547 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CTCTC
Found at i:1293189 original size:182 final size:180
Alignment explanation
Indices: 1292884--1293245 Score: 706
Period size: 182 Copynumber: 2.0 Consensus size: 180
1292874 AATTTATACA
1292884 TAATCTTTTTCCACCCGAATTAATTAATTAAGCCTTGGTTTTTATTCAAAATCACGCGCAATGGC
1 TAATCTTTTTCCACCCGAATTAATTAATTAAGCCTTGGTTTTTATTCAAAATCACGCGCAATGGC
1292949 ATATCTGTAATAACCATCCAAATGAGTGTCATTTTAAAGTAACCATCCAACCAGCTCTTCCGTCT
66 ATATCTGTAATAACCATCCAAATGAGTGTCATTTTAAAGTAACCATCCAACCAGCTCTTCCGTCT
1293014 TTATTTTAAAAACTCAAAAACGGAGAGAAAAGAAATAAAAACAAGTCCAC
131 TTATTTTAAAAACTCAAAAACGGAGAGAAAAGAAATAAAAACAAGTCCAC
1293064 TAATCTTTTTCCACCCGAATTATTATTAATTAAGCCTTGGTTTTTATTCAAAATCACGCGCAATG
1 TAATCTTTTTCCACCCGAATTA--ATTAATTAAGCCTTGGTTTTTATTCAAAATCACGCGCAATG
1293129 GCATATCTGTAATAACCATCCAAATGAGTGTCATTTTAAAGTAACCATCCAACCAGCTCTTCCGT
64 GCATATCTGTAATAACCATCCAAATGAGTGTCATTTTAAAGTAACCATCCAACCAGCTCTTCCGT
1293194 CTTTATTTTAAAAACTCAAAAACGGAGAGAAAAGAAATAAAAACAAGTCCAC
129 CTTTATTTTAAAAACTCAAAAACGGAGAGAAAAGAAATAAAAACAAGTCCAC
1293246 CAAACATAAA
Statistics
Matches: 180, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
180 22 0.12
182 158 0.88
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (180 bp):
TAATCTTTTTCCACCCGAATTAATTAATTAAGCCTTGGTTTTTATTCAAAATCACGCGCAATGGC
ATATCTGTAATAACCATCCAAATGAGTGTCATTTTAAAGTAACCATCCAACCAGCTCTTCCGTCT
TTATTTTAAAAACTCAAAAACGGAGAGAAAAGAAATAAAAACAAGTCCAC
Found at i:1308438 original size:42 final size:42
Alignment explanation
Indices: 1308379--1308462 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1308369 AAGCTGAATA
1308379 TGATTCACTTAGAGTATTTGGGTGTCGATATTTTCCCCATTT
1 TGATTCACTTAGAGTATTTGGGTGTCGATATTTTCCCCATTT
1308421 TGATTCACTTAGAGTATTTGGGTGTCGATATTTTCCCCATTT
1 TGATTCACTTAGAGTATTTGGGTGTCGATATTTTCCCCATTT
1308463 GCAGTCATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (42 bp):
TGATTCACTTAGAGTATTTGGGTGTCGATATTTTCCCCATTT
Found at i:1312042 original size:21 final size:20
Alignment explanation
Indices: 1312018--1312081 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1312008 ATGGATACCC
* *
1312018 ATTTATTCGGTATGGAGACTA
1 ATTT-TTCGGTATAGAGACCA
*
1312039 ATTTTTTGGTATAGAGACCA
1 ATTTTTCGGTATAGAGACCA
*
1312059 A-TTTTCAGTAT-GAAGACCA
1 ATTTTTCGGTATAG-AGACCA
1312078 ATTT
1 ATTT
1312082 CAACACCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.42
20 16 0.44
21 4 0.11
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTTTTCGGTATAGAGACCA
Found at i:1315318 original size:19 final size:18
Alignment explanation
Indices: 1315281--1315317 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1315271 AAATGATAGT
1315281 AGCCAAAATATTTAAAAA
1 AGCCAAAATATTTAAAAA
1315299 AGCCAAAATATTTAAAAA
1 AGCCAAAATATTTAAAAA
1315317 A
1 A
1315318 ATATATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (18 bp):
AGCCAAAATATTTAAAAA
Found at i:1325851 original size:95 final size:96
Alignment explanation
Indices: 1325650--1325872 Score: 222
Period size: 95 Copynumber: 2.3 Consensus size: 96
1325640 AGCAATGGGG
* *
1325650 TATCGATACCATGGTAAGGGTATCGATACCAGTAAAAATATCGAATCTAAATTGGGTATCGATAC
1 TATCGATACCATGGTAAGGGTATCGATACCAGTAAAAATATCGAAGCTAAATTCGGTATCGATAC
* *
1325715 CTAGAGGGGGTATCGGTACCATAGCATAGGAG
66 CTAGAGGGGGTATCGATACCATA-CATAGGAA
* **** * * *
1325747 TATCGATACCATGGTGAGGGTATCGATACCA-T-GCTCTATTGAAGCTAATTTCGGTATTGATAC
1 TATCGATACCATGGTAAGGGTATCGATACCAGTAAAAATATCGAAGCTAAATTCGGTATCGATAC
* *
1325810 ATTA-AGGGGGTATCGATACCCTA-ATAGGGAAA
66 -CTAGAGGGGGTATCGATACCATACATA-GG-AA
* *
1325842 TATCGATACCCTAG-AAGGGGTATCGATACCA
1 TATCGATACCATGGTAA-GGGTATCGATACCA
1325873 AAGGACCAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
93 3 0.03
94 3 0.03
95 66 0.63
96 3 0.03
97 30 0.29
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (96 bp):
TATCGATACCATGGTAAGGGTATCGATACCAGTAAAAATATCGAAGCTAAATTCGGTATCGATAC
CTAGAGGGGGTATCGATACCATACATAGGAA
Found at i:1325867 original size:20 final size:20
Alignment explanation
Indices: 1325816--1325871 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
1325806 ATACATTAAG
1325816 GGGGTATCGATACCCTAATA
1 GGGGTATCGATACCCTAATA
*
1325836 GGGAAATATCGATACCCTAGA-A
1 GGG--GTATCGATACCCTA-ATA
1325858 GGGGTATCGATACC
1 GGGGTATCGATACC
1325872 AAAGGACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 13 0.42
22 17 0.55
23 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (20 bp):
GGGGTATCGATACCCTAATA
Found at i:1326336 original size:57 final size:57
Alignment explanation
Indices: 1326195--1326384 Score: 308
Period size: 57 Copynumber: 3.3 Consensus size: 57
1326185 GTGCAAAATA
*
1326195 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTATGCTAAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCT-AAAATGT
* * * **
1326253 TAAGAAATCATACTAAATGTACGAATTTTAGATAGGGCGTTCCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCTAAAATGT
*
1326310 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCTAAAATGT
1326367 TAAGAAATCATACTAAGT
1 TAAGAAATCATACTAAGT
1326385 TAAGAAATCA
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 76 0.63
58 44 0.37
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCTAAAATGT
Found at i:1326388 original size:18 final size:18
Alignment explanation
Indices: 1326365--1326400 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1326355 ACACTAAAAT
1326365 GTTAAGAAATCATACTAA
1 GTTAAGAAATCATACTAA
1326383 GTTAAGAAATCATACTAA
1 GTTAAGAAATCATACTAA
1326401 ATGTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
GTTAAGAAATCATACTAA
Found at i:1326431 original size:75 final size:75
Alignment explanation
Indices: 1326308--1326460 Score: 288
Period size: 75 Copynumber: 2.0 Consensus size: 75
1326298 ACGCTAAAAT
*
1326308 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
1 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
*
1326373 ATCATACTAA
66 ATCAGACTAA
1326383 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
1 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
1326448 ATCAGACTAA
66 ATCAGACTAA
1326458 GTT
1 GTT
1326461 TATGAATTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (75 bp):
GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
ATCAGACTAA
Found at i:1326471 original size:57 final size:57
Alignment explanation
Indices: 1326383--1327146 Score: 1168
Period size: 57 Copynumber: 13.5 Consensus size: 57
1326373 ATCATACTAA
* * *
1326383 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* * * * * *
1326440 GTTAAGAAATCAGACTAAGTTTATGAATTTCAGATAAGGCATTTCATACGCTAAATT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* *
1326497 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTCATACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* * * * *
1326554 GTTAAGAAATCATATTAAGTTTATGAATTTCAGATAGGGCATTTTGTACGCTAAATT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* * * *
1326611 GTTAAGAAATCGTACTAAATGTATGAACTTCAGTTAGGGCGTTTCGTACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
1326668 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCG-TTCGTACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* *
1326724 GTTAAGAAATCATACTAAGTGTATGAATTTTAGATAGGGCGTTTTGTACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* *
1326781 GTTAAGAAATCATACTAACTGTATGAATTTCAGATA-GGCGTTTCATACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
1326837 G-TAAGAAATCATACT-AGTGTATGAATTTCAGATAGGGCG-TTCGTAC-CGTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGC-TAAAAT
* *
1326891 GTT-AG-AATCATACTAACTGTATGAA-TTCAGATAGGGCGCTTCGTACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
*
1326945 GTTAAGAAATCATACTAACTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* *
1327002 GTTAAGAAATCATACTAAGTGTATGAATTTCAAATAGGGCGTTTCGTACACTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
* **
1327059 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTATCACACGCTAAAAT
1 GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
1327116 GTTAAGAAATCATACTAAGTGTATGAATTTC
1 GTTAAGAAATCATACTAAGTGTATGAATTTC
1327147 TATCTTGGAC
Statistics
Matches: 644, Mismatches: 53, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
53 23 0.04
54 58 0.09
55 22 0.03
56 94 0.15
57 447 0.69
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (57 bp):
GTTAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAT
Found at i:1326494 original size:132 final size:132
Alignment explanation
Indices: 1326251--1326514 Score: 411
Period size: 132 Copynumber: 2.0 Consensus size: 132
1326241 TGCTAAAAAT
* *
1326251 GTTAAGAAATCATACTAAATGTACGAATTTTAGATAGGGCGTTCCGTACGCTAAAATGTTAAGAA
1 GTTAAGAAATCATACTAAATGTACGAATTTCAGATAGGGCGTTCCGTACACTAAAATGTTAAGAA
* * * **
1326316 ATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAAATCATACT
66 ATCAGACTAAGTGTATGAATTTCAGATAAGGCATTTCATACACTAAAATGTTAAGAAATCATACT
1326381 AA
131 AA
* **
1326383 GTTAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTTGTACACTAAAATGTTAAGAA
1 GTTAAGAAATCATACTAAATGTACGAATTTCAGATAGGGCGTTCCGTACACTAAAATGTTAAGAA
* * *
1326448 ATCAGACTAAGTTTATGAATTTCAGATAAGGCATTTCATACGCTAAATTGTTAAGAAATCATACT
66 ATCAGACTAAGTGTATGAATTTCAGATAAGGCATTTCATACACTAAAATGTTAAGAAATCATACT
1326513 AA
131 AA
1326515 ATGTATGAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 119 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (132 bp):
GTTAAGAAATCATACTAAATGTACGAATTTCAGATAGGGCGTTCCGTACACTAAAATGTTAAGAA
ATCAGACTAAGTGTATGAATTTCAGATAAGGCATTTCATACACTAAAATGTTAAGAAATCATACT
AA
Found at i:1329155 original size:27 final size:27
Alignment explanation
Indices: 1329125--1329214 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
1329115 TTCGAACTAA
1329125 TTCGGTTAACCGATCGAACCGAATTAG
1 TTCGGTTAACCGATCGAACCGAATTAG
* *
1329152 TTCGGTTAACCGACCGAATCGAATTAG
1 TTCGGTTAACCGATCGAACCGAATTAG
* *
1329179 TTCGGTTAATTCGGTCGACCACCGAATTAG
1 TTCGGTTAA-CCGATCGA--ACCGAATTAG
1329209 TTCGGT
1 TTCGGT
1329215 CGGTTAACGG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
27 34 0.63
28 5 0.09
30 15 0.28
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (27 bp):
TTCGGTTAACCGATCGAACCGAATTAG
Found at i:1334596 original size:18 final size:18
Alignment explanation
Indices: 1334573--1334607 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1334563 TTTTAAGTTA
1334573 ATGCACGGGTAAATGCTT
1 ATGCACGGGTAAATGCTT
1334591 ATGCACGGGTAAATGCT
1 ATGCACGGGTAAATGCT
1334608 CATTACGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGCACGGGTAAATGCTT
Found at i:1339758 original size:28 final size:30
Alignment explanation
Indices: 1339724--1339855 Score: 89
Period size: 30 Copynumber: 4.4 Consensus size: 30
1339714 TTGGTAATTT
*
1339724 TATTTTAGTCTTTTAA-ATGTT-TTTTTGC
1 TATTTTAGTCCTTTAAGATGTTATTTTTGC
* * *
1339752 TATTTTAGTCCTTTAAGTTTTTATTTTTTC
1 TATTTTAGTCCTTTAAGATGTTATTTTTGC
* *
1339782 TATTTTAGTTCC-TTAAG-TTTCTATTTTTTTC
1 TATTTTAG-TCCTTTAAGATGT-TA-TTTTTGC
* *
1339813 TA-TTTAGTACC-TTAAG-TTTCTATTTTTGT
1 TATTTTAGT-CCTTTAAGATGT-TATTTTTGC
1339842 TATTTTAGTACCTT
1 TATTTTAGT-CCTT
1339856 AAGTTTCTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
28 15 0.17
29 14 0.16
30 48 0.53
31 13 0.14
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.63
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGATGTTATTTTTGC
Found at i:1339877 original size:30 final size:30
Alignment explanation
Indices: 1339744--1339866 Score: 171
Period size: 30 Copynumber: 4.1 Consensus size: 30
1339734 TTTTAAATGT
*
1339744 TTTTTTGCTATTTTAGT-CCTTTAAGTTTTTA
1 TTTTTT-CTATTTTAGTACC-TTAAGTTTCTA
*
1339775 TTTTTTCTATTTTAGTTCCTTAAGTTTCTA
1 TTTTTTCTATTTTAGTACCTTAAGTTTCTA
1339805 TTTTTTTCTA-TTTAGTACCTTAAGTTTCTA
1 -TTTTTTCTATTTTAGTACCTTAAGTTTCTA
1339835 TTTTTGT-TATTTTAGTACCTTAAGTTTCTA
1 TTTTT-TCTATTTTAGTACCTTAAGTTTCTA
1339865 TT
1 TT
1339867 AATCATATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
29 7 0.08
30 62 0.72
31 17 0.20
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTTTTCTATTTTAGTACCTTAAGTTTCTA
Found at i:1357411 original size:16 final size:16
Alignment explanation
Indices: 1357326--1357446 Score: 75
Period size: 16 Copynumber: 7.6 Consensus size: 16
1357316 CCCCAAAACG
* *
1357326 AAAGTAATTTGAATAA
1 AAAGTAATTCGAATCA
* *
1357342 AAAATAATTCGAACCA
1 AAAGTAATTCGAATCA
** *
1357358 AAAACAATTCAAATCA
1 AAAGTAATTCGAATCA
* **
1357374 AAATTAACCCGAAT-A
1 AAAGTAATTCGAATCA
*
1357389 GAAAGTAATTCAAATCA
1 -AAAGTAATTCGAATCA
* *
1357406 AAAGTAATTTGAACCA
1 AAAGTAATTCGAATCA
* *
1357422 AAAGTAACTC-AAACTA
1 AAAGTAATTCGAATC-A
1357438 AAAGTAATT
1 AAAGTAATT
1357447 TGAAATGAAA
Statistics
Matches: 79, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
15 4 0.05
16 74 0.94
17 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.23
Consensus pattern (16 bp):
AAAGTAATTCGAATCA
Found at i:1357426 original size:32 final size:32
Alignment explanation
Indices: 1357326--1357446 Score: 102
Period size: 32 Copynumber: 3.8 Consensus size: 32
1357316 CCCCAAAACG
** * *
1357326 AAAGTAATTTGAATAAAAAATAATTCGAACCA
1 AAAGTAATTCAAATCAAAAGTAATTCGAACCA
** * ** *
1357358 AAAACAATTCAAATCAAAATTAACCCGAA-TA
1 AAAGTAATTCAAATCAAAAGTAATTCGAACCA
*
1357389 GAAAGTAATTCAAATCAAAAGTAATTTGAACCA
1 -AAAGTAATTCAAATCAAAAGTAATTCGAACCA
*
1357422 AAAGTAACTCAAA-CTAAAAGTAATT
1 AAAGTAATTCAAATC-AAAAGTAATT
1357447 TGAAATGAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
31 2 0.03
32 66 0.96
33 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.23
Consensus pattern (32 bp):
AAAGTAATTCAAATCAAAAGTAATTCGAACCA
Found at i:1359903 original size:54 final size:54
Alignment explanation
Indices: 1359817--1360042 Score: 248
Period size: 54 Copynumber: 4.3 Consensus size: 54
1359807 GACTTTCGCA
*
1359817 TAAGGCGAGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
* *
1359871 TAAGGCTTGGGCACGGCTTATTCATCCGGAGCTAACGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
* * * *
1359925 TAAGGCGTGGGCACGGCTTATCCATCCCGAGCT-ACTGCAAAAGAA-TC-TCTACT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAAC-GCAGAAGAAGTCTTC-AGT
* * * * ** * *
1359978 TAAGGCGTGGG-A--ACTTATTCACCCACATCTTTCGCAGAAGAAATATTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
*
1360029 TATGGCGTGGGCAC
1 TAAGGCGTGGGCAC
1360043 ACCATCTATC
Statistics
Matches: 146, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
50 20 0.14
51 14 0.10
52 6 0.04
53 17 0.12
54 89 0.61
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
Found at i:1370800 original size:35 final size:35
Alignment explanation
Indices: 1370746--1370813 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1370736 TATATACATA
* * *
1370746 ATACATTGCCGTATCTGTCATTGCCATTCTTGTTT
1 ATACATTGCCATATATGTCATTACCATTCTTGTTT
*
1370781 ATACATTGCTATATATGTCATTACCATTCTTGT
1 ATACATTGCCATATATGTCATTACCATTCTTGT
1370814 ACATATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (35 bp):
ATACATTGCCATATATGTCATTACCATTCTTGTTT
Found at i:1370840 original size:35 final size:35
Alignment explanation
Indices: 1370746--1370841 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
1370736 TATATACATA
** * * **
1370746 ATACATTGCCGTATCTGTCATTGCCATTCTTGTTT
1 ATACATTGCTATACCTGTCATTACCATTCTTGTAC
**
1370781 ATACATTGCTATATATGTCATTACCATTCTTGTAC
1 ATACATTGCTATACCTGTCATTACCATTCTTGTAC
* * *
1370816 ATATATTGTTATACCTGTCCTTACCA
1 ATACATTGCTATACCTGTCATTACCA
1370842 GAAATGTAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (35 bp):
ATACATTGCTATACCTGTCATTACCATTCTTGTAC
Found at i:1371572 original size:93 final size:93
Alignment explanation
Indices: 1371412--1371582 Score: 236
Period size: 93 Copynumber: 1.8 Consensus size: 93
1371402 ATATATTTTG
* **
1371412 ATATATATCGTTATATTTGTCATTACCAAATAAGTAAATTTTAATTAATATAATACGTATAGTTA
1 ATATATATCGTTATATCTGTCATTACCAAATAAGTAAATTTTAATTAATATAATACGTATAAATA
*
1371477 TGTTTTTATTACTCACGCATCAATTCTT
66 TGTTTTTAATACTCACGCATCAATTCTT
* * * * * *
1371505 ATATATATCGTTATATCTGTTATTATCAAATATGTAGA-TTTAATTAATATAATACATTTTAAAT
1 ATATATATCGTTATATCTGTCATTACCAAATAAGTAAATTTTAATTAATATAATAC-GTATAAAT
1371569 ATGTTTTTAATACT
65 ATGTTTTTAATACT
1371583 TGACAAAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
92 17 0.25
93 50 0.75
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (93 bp):
ATATATATCGTTATATCTGTCATTACCAAATAAGTAAATTTTAATTAATATAATACGTATAAATA
TGTTTTTAATACTCACGCATCAATTCTT
Found at i:1373150 original size:26 final size:26
Alignment explanation
Indices: 1373121--1373185 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
1373111 ATCATCGCAT
1373121 GTTTTGTATTATTCTCTTAATTTGAA
1 GTTTTGTATTATTCTCTTAATTTGAA
1373147 GTTTTGTATTATTCTCTTAATTTGAA
1 GTTTTGTATTATTCTCTTAATTTGAA
*
1373173 GTTTTTTATTATT
1 GTTTTGTATTATT
1373186 TACATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.62
Consensus pattern (26 bp):
GTTTTGTATTATTCTCTTAATTTGAA
Found at i:1380321 original size:99 final size:99
Alignment explanation
Indices: 1380212--1380407 Score: 295
Period size: 99 Copynumber: 2.0 Consensus size: 99
1380202 TATTATATAC
* * * **
1380212 ATACAATAAAGCTTAAGTTATCCCTCTAGAGCAATTAGTTAAACGTTCCGGCTTTATGGATAAGA
1 ATACAATAAAGCTTAAGCTATCCCTCTAAAGAAATTAGTTAAACGCCCCGGCTTTATGGATAAGA
1380277 TTCAGCTAGCCTGAT-AAAGTTGATTATAATATCT
66 TTCAGCTAGCCTGATAAAAG-TGATTATAATATCT
* * * *
1380311 ATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAATGCCCCGGCTTTATGGATAAGA
1 ATACAATAAAGCTTAAGCTATCCCTCTAAAGAAATTAGTTAAACGCCCCGGCTTTATGGATAAGA
1380376 TTCAGCTAGCCTGATAAAAGTGATTATAATAT
66 TTCAGCTAGCCTGATAAAAGTGATTATAATAT
1380408 TGAGTTGTCC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 83 0.95
100 4 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (99 bp):
ATACAATAAAGCTTAAGCTATCCCTCTAAAGAAATTAGTTAAACGCCCCGGCTTTATGGATAAGA
TTCAGCTAGCCTGATAAAAGTGATTATAATATCT
Found at i:1382081 original size:85 final size:85
Alignment explanation
Indices: 1381922--1382409 Score: 575
Period size: 85 Copynumber: 5.8 Consensus size: 85
1381912 CCTATCACAA
* *
1381922 CATAGCTCAAGGCGAGAAGGGATATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACATTCAGCTC
*
1381987 AAGGACATATCAAATTTACAG
65 AAGGGCATATCAAATTTACAG
* * * * * * * *
1382008 CAAATCTCAAGGCGAGAAGGGTTATCTTTCAATAAAAACCTTTGAGTTCAATTACATTCAGCTTA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
1382073 AGGGCATATCAAATCTACAA
66 AGGGCATATCAAATTTACAG
** * * * * * * *
1382093 CATAGCTCAAGTTGAGAAAGGCTATTTGTCAACAAAATCCTTTGAGTTTGATTACATTTAGTTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* * *
1382158 AGGGCATATAAAATCTACAT
66 AGGGCATATCAAATTTACAG
* *
1382178 CATAGCTCAATGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
1382243 AGGCCATATCAAGTTTACAG
66 AGGGCATATCAAATTTACAG
* * * *
1382263 TATAGCTCAAGGCGAGAAGGGCTATTTGTCAACAAAAACCTTCAAGTTCGATTCCATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
**
1382328 AGGGCA-GCCAAATTTACAG
66 AGGGCATATCAAATTTACAG
* ** * * * *
1382347 CATAACTCAAGGCGAGAA-GATTATCTGTCAACAAAAATCTTCGAGTTTGATTCCACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTC
1382410 GATGAAAGCG
Statistics
Matches: 340, Mismatches: 62, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
83 38 0.11
84 26 0.08
85 249 0.73
86 27 0.08
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
AGGGCATATCAAATTTACAG
Found at i:1385115 original size:30 final size:30
Alignment explanation
Indices: 1385081--1385137 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1385071 AAGTTGAAAT
* **
1385081 AAATATATCTTGTTCTTATTTTAACTTAAA
1 AAATATATCTTATTCTTACCTTAACTTAAA
*
1385111 AAATATATTTTATTCTTACCTTAACTT
1 AAATATATCTTATTCTTACCTTAACTT
1385138 TTAAAAACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (30 bp):
AAATATATCTTATTCTTACCTTAACTTAAA
Found at i:1389567 original size:17 final size:18
Alignment explanation
Indices: 1389536--1389572 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1389526 TTTTAGTTAA
*
1389536 AAATATAATCGTAATTTT
1 AAATATAATCATAATTTT
1389554 AAATA-AATCATAATTTT
1 AAATATAATCATAATTTT
1389571 AA
1 AA
1389573 TTTAATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATATAATCATAATTTT
Found at i:1393078 original size:103 final size:103
Alignment explanation
Indices: 1392919--1393184 Score: 304
Period size: 103 Copynumber: 2.6 Consensus size: 103
1392909 AACAACATCG
* * * *
1392919 ATATTGGCATATAACACTAG-ATTACGGGTTACATCCAATATATCGATACCTTTAATGTATCGAT
1 ATATTGACATATAACA-TTGTATTATGGGTTACATCCAATGTATCGATACCTTTAATGTATCGAT
* *
1392983 ACCTAGTAGCCAAGA-TGTACCGGTACACAAGAAGTATCA
65 ACCTAGAAGCCAA-ATTGTACCAGTACACAAGAAGTATCA
* * * * *
1393022 ATATTGACATATAACATTGTATTATGGGTTACATCCGATGTATCAACACCTATAATGTACCGATA
1 ATATTGACATATAACATTGTATTATGGGTTACATCCAATGTATCGATACCTTTAATGTATCGATA
** * * *
1393087 CCTAGAAGTTAAATTGTACTAGTACACTAGAAGTATCG
66 CCTAGAAGCCAAATTGTACCAGTACACAAGAAGTATCA
* * * *
1393125 ATACT-AGCATATAACACTGTATTATGAGTTACGTCCAATGTATCGATACCTTTAATGTAT
1 ATATTGA-CATATAACATTGTATTATGGGTTACATCCAATGTATCGATACCTTTAATGTAT
1393185 TCATTGTTAC
Statistics
Matches: 135, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
102 4 0.03
103 131 0.97
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (103 bp):
ATATTGACATATAACATTGTATTATGGGTTACATCCAATGTATCGATACCTTTAATGTATCGATA
CCTAGAAGCCAAATTGTACCAGTACACAAGAAGTATCA
Found at i:1398049 original size:23 final size:24
Alignment explanation
Indices: 1398002--1398050 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1397992 AAAATTGTGA
* *
1398002 TTTATTTAAAATTATGATTACATT
1 TTTAATTAAAATTATAATTACATT
*
1398026 TTTAATTAAAA-TATAATTATATT
1 TTTAATTAAAATTATAATTACATT
1398049 TT
1 TT
1398051 GAGTACTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAATTAAAATTATAATTACATT
Found at i:1400151 original size:13 final size:13
Alignment explanation
Indices: 1400133--1400163 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1400123 TTGATCGGTC
*
1400133 TGACCCGACCCGT
1 TGACCCGACCCAT
1400146 TGACCCGACCCAT
1 TGACCCGACCCAT
1400159 TGACC
1 TGACC
1400164 GTTAACCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCAT
Found at i:1408866 original size:41 final size:41
Alignment explanation
Indices: 1408809--1408889 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
1408799 ACAGGTTATG
1408809 CAATTATGTTATCCCTTTGAAACTAAACTTGGGATCTCCAA
1 CAATTATGTTATCCCTTTGAAACTAAACTTGGGATCTCCAA
* *
1408850 CAATTATGTTATCCCTTTGAATCTAATCTTGGGATCTCCA
1 CAATTATGTTATCCCTTTGAAACTAAACTTGGGATCTCCA
1408890 GTCAACAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (41 bp):
CAATTATGTTATCCCTTTGAAACTAAACTTGGGATCTCCAA
Found at i:1409479 original size:51 final size:51
Alignment explanation
Indices: 1409403--1409518 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
1409393 TTTAGGACCT
**
1409403 ATTTTCATTTGTTTTGGTAATATGACAATTACATTCTCAAGACACCCCAAC
1 ATTTTCAAGTGTTTTGGTAATATGACAATTACATTCTCAAGACACCCCAAC
*
1409454 ATTTTCAAGTGTTTTGGTAATATGACAATTACCTTCTCAAGACACCCCAAC
1 ATTTTCAAGTGTTTTGGTAATATGACAATTACATTCTCAAGACACCCCAAC
*
1409505 GTTTTCAAGTGTTT
1 ATTTTCAAGTGTTT
1409519 GTATGATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (51 bp):
ATTTTCAAGTGTTTTGGTAATATGACAATTACATTCTCAAGACACCCCAAC
Found at i:1410595 original size:12 final size:10
Alignment explanation
Indices: 1410554--1410594 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1410544 TTTATCACAC
1410554 CAAATTCTCT
1 CAAATTCTCT
1410564 CAAATTCTCT
1 CAAATTCTCT
1410574 -AAATTTCTCT
1 CAAA-TTCTCT
*
1410584 CAAATACTCT
1 CAAATTCTCT
1410594 C
1 C
1410595 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1410917 original size:111 final size:111
Alignment explanation
Indices: 1410718--1410939 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 111
1410708 TGGAAATCAT
* *
1410718 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACGTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1410783 TATTTAGTTGATTTATTATATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
1410829 ATATCTCGACACGTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACGTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1410894 TAATTAGTTGATTCATT-TAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTAT-ATGCATGATTATTAGATTAAGAATTAA
1410940 TTTTTGTAAT
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
110 1 0.01
111 105 0.99
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACGTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
Found at i:1412836 original size:15 final size:15
Alignment explanation
Indices: 1412816--1412862 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1412806 TCAGGACGAC
1412816 GACGATGACGATGAT
1 GACGATGACGATGAT
*
1412831 GACGATGACGATGGT
1 GACGATGACGATGAT
*
1412846 GACGACGACGATGAT
1 GACGATGACGATGAT
1412861 GA
1 GA
1412863 TGACAGCGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.36, T:0.17
Consensus pattern (15 bp):
GACGATGACGATGAT
Found at i:1413740 original size:50 final size:49
Alignment explanation
Indices: 1413679--1413786 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
1413669 GTGGATCAGT
* * * * * * *
1413679 GGGCGCACTATACCCACGTGGCGTCAGATCACCGTATATCGTAGG-GCAGG
1 GGGCGCGCTATA-CCACGAGACGCCAAATCACCATATAACG-AGGTGCAGG
*
1413729 GGGCGCGCTATACCACGAGACGCCAAATCAGCATATAACGAGGTGCAGG
1 GGGCGCGCTATACCACGAGACGCCAAATCACCATATAACGAGGTGCAGG
1413778 GGGCGCGCT
1 GGGCGCGCT
1413787 TTTCTGCTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
48 3 0.06
49 35 0.71
50 11 0.22
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.15
Consensus pattern (49 bp):
GGGCGCGCTATACCACGAGACGCCAAATCACCATATAACGAGGTGCAGG
Found at i:1415289 original size:2 final size:2
Alignment explanation
Indices: 1415282--1415342 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1415272 GTGTAAAGGG
1415282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1415324 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1415343 AAGGTTAGGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1421056 original size:32 final size:32
Alignment explanation
Indices: 1421015--1421079 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1421005 GGCTCAAAGG
1421015 AACCAAAGGTTTTCATTTAAAAAGAAAAAACT
1 AACCAAAGGTTTTCATTTAAAAAGAAAAAACT
1421047 AACCAAAGGTTTTCATTTAAAAAGAAAAAACT
1 AACCAAAGGTTTTCATTTAAAAAGAAAAAACT
1421079 A
1 A
1421080 TCTTTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (32 bp):
AACCAAAGGTTTTCATTTAAAAAGAAAAAACT
Found at i:1424588 original size:185 final size:183
Alignment explanation
Indices: 1424293--1424680 Score: 613
Period size: 185 Copynumber: 2.1 Consensus size: 183
1424283 ATTAAATTTT
1424293 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
*
1424358 TTTAAGATCTAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAA-TT
* *
1424422 TTTATTTTATATTTATATATTATTTAAATTAATTGTAAACTATTTTTTTAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAAC--TTTTTTTAATTAAA
* *
1424478 AAATATTATATATATTATATATAACATATGGGCT-AAGCCTAAACCATTTAAAA-CCTAATTAAT
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAATCC-AATTAAT
* *
1424541 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTGAAAT
64 AATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAAT
1424606 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
* * *
1424661 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1424681 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
182 8 0.04
183 22 0.12
184 4 0.02
185 152 0.80
186 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
Found at i:1425651 original size:25 final size:22
Alignment explanation
Indices: 1425623--1425697 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 22
1425613 AAATATATTT
*
1425623 TATTTTTGTCTTAACTTATTAAATA
1 TATTTTT-TCTTAA-TT-TTAAAAA
1425648 TATTTTATTCTTAATTTTAAAAA
1 TATTTT-TTCTTAATTTTAAAAA
* *
1425671 TATATTTTATTATTATTTTAAAAA
1 TATTTTTTCTTA--ATTTTAAAAA
1425695 TAT
1 TAT
1425698 ATATTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.11
23 11 0.25
24 15 0.34
25 12 0.27
26 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (22 bp):
TATTTTTTCTTAATTTTAAAAA
Found at i:1425670 original size:55 final size:52
Alignment explanation
Indices: 1425607--1425770 Score: 163
Period size: 55 Copynumber: 3.0 Consensus size: 52
1425597 ACATCTTACC
* *
1425607 TTTTAAAAATATATTTTATTTTTGTCTTAACTTATTAAATATATTTTATTCTTAA
1 TTTTAAAAATATATTTTATTATTATCTTAACTTA--AAATATATTTTATTCTT-A
*
1425662 TTTTAAAAATATATTTTATTATTATTTTAA---AAATATATATTTTATTCTTA
1 TTTTAAAAATATATTTTATTATTATCTTAACTTAAA-ATATATTTTATTCTTA
* * *
1425712 TCTCAACTTCAAAATATATTTTATTCTTATCTTAACTTAAAAATATATTTTATTTTTA
1 T-T----TTAAAAATATATTTTATTATTATCTTAACTT-AAAATATATTTTATTCTTA
1425770 T
1 T
1425771 CTAACTTTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
50 4 0.04
51 16 0.17
52 1 0.01
55 52 0.57
58 16 0.17
59 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.56
Consensus pattern (52 bp):
TTTTAAAAATATATTTTATTATTATCTTAACTTAAAATATATTTTATTCTTA
Found at i:1425673 original size:23 final size:23
Alignment explanation
Indices: 1425623--1425697 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 23
1425613 AAATATATTT
*
1425623 TATTTT-TGTCTTAACTTATTAAATA
1 TATTTTAT-TCTTAA-TT-TTAAAAA
1425648 TATTTTATTCTTAATTTTAAAAATA
1 TATTTTATTCTTAATTTT-AAAA-A
*
1425673 TATTTTATTATT-ATTTTAAAAA
1 TATTTTATTCTTAATTTTAAAAA
1425695 TAT
1 TAT
1425698 ATATTTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
22 4 0.09
23 6 0.13
24 10 0.22
25 24 0.53
26 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (23 bp):
TATTTTATTCTTAATTTTAAAAA
Found at i:1425693 original size:24 final size:25
Alignment explanation
Indices: 1425643--1425707 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 25
1425633 TTAACTTATT
*
1425643 AAATATATTTTATTCTTAATTTTAA
1 AAATATATTTTATTATTAATTTTAA
1425668 AAATATATTTTATTATT-ATTTTAA
1 AAATATATTTTATTATTAATTTTAA
*
1425692 AAATATATATT-TTATT
1 AAATATATTTTATTATT
1425708 CTTATCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 5 0.13
24 17 0.45
25 16 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATTTTATTATTAATTTTAA
Found at i:1425729 original size:29 final size:28
Alignment explanation
Indices: 1425609--1425777 Score: 165
Period size: 29 Copynumber: 6.1 Consensus size: 28
1425599 ATCTTACCTT
* *
1425609 TTAAAAATATATTTTATTTTTGTCTTAAC
1 TTAAAAATATATTTTATTCTTATC-TAAC
*
1425638 TTATTAAATATATTTTATTCTTAAT-T---
1 TTA-AAAATATATTTTATTCTT-ATCTAAC
*
1425664 TTAAAAATATATTTTATTATTAT-T---
1 TTAAAAATATATTTTATTCTTATCTAAC
1425688 TTAAAAATATATATTTTATTCTTATCTCAAC
1 TT-AAAA-ATATATTTTATTCTTATCT-AAC
*
1425719 TTCAAAATATATTTTATTCTTATCTTAAC
1 TTAAAAATATATTTTATTCTTATC-TAAC
*
1425748 TTAAAAATATATTTTATTTTTATCTAAC
1 TTAAAAATATATTTTATTCTTATCTAAC
1425776 TT
1 TT
1425778 TATTTTTTAA
Statistics
Matches: 121, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.04
25 20 0.17
26 19 0.16
27 1 0.01
28 6 0.05
29 47 0.39
30 20 0.17
31 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.55
Consensus pattern (28 bp):
TTAAAAATATATTTTATTCTTATCTAAC
Found at i:1428687 original size:14 final size:14
Alignment explanation
Indices: 1428664--1428705 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1428654 TGTCAAAGTC
*
1428664 AATGATTTGACTC-
1 AATGAGTTGACTCG
1428677 AGATGAGTTGACTCG
1 A-ATGAGTTGACTCG
1428692 AATGAGTTGACTCG
1 AATGAGTTGACTCG
1428706 GTCTGGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (14 bp):
AATGAGTTGACTCG
Found at i:1430291 original size:2 final size:2
Alignment explanation
Indices: 1430284--1430343 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1430274 TATTTTAATA
1430284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1430326 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1430344 TAATTTTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1438434 original size:18 final size:18
Alignment explanation
Indices: 1438385--1438436 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1438375 ATTCTAAATG
*
1438385 TTTATAGTTATCAAATGA
1 TTTATAGTTATCAGATGA
1438403 TTT-TCAGTTATCAGATGA
1 TTTAT-AGTTATCAGATGA
1438421 TTTATAGTTATCAGAT
1 TTTATAGTTATCAGAT
1438437 AATTATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (18 bp):
TTTATAGTTATCAGATGA
Found at i:1438611 original size:41 final size:41
Alignment explanation
Indices: 1438566--1438646 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
1438556 AAATGAGTGC
*
1438566 TTATCATTTCAGCTTTGGTACATTCGTGTATCAATGTTCAG
1 TTATCAATTCAGCTTTGGTACATTCGTGTATCAATGTTCAG
1438607 TTATCAATTCAGCTTTGGTACATTCGTGTATCAATGTTCA
1 TTATCAATTCAGCTTTGGTACATTCGTGTATCAATGTTCA
1438647 ACACCAACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (41 bp):
TTATCAATTCAGCTTTGGTACATTCGTGTATCAATGTTCAG
Found at i:1441850 original size:14 final size:14
Alignment explanation
Indices: 1441831--1441879 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1441821 AGTCAACCGT
1441831 TTGACTCGGACAAG
1 TTGACTCGGACAAG
*
1441845 TTGACTCAG-CGAAG
1 TTGACTCGGAC-AAG
* *
1441859 TTGACTCGAACGAG
1 TTGACTCGGACAAG
1441873 TTGACTC
1 TTGACTC
1441880 TGCCGGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (14 bp):
TTGACTCGGACAAG
Found at i:1443520 original size:22 final size:22
Alignment explanation
Indices: 1443495--1443542 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1443485 ATAAGCATTG
* *
1443495 GGAAGGTAAGACACATTAGAGA
1 GGAAAGTAAGACACATTAGAAA
* *
1443517 GGAAAGTTAGACACATTGGAAA
1 GGAAAGTAAGACACATTAGAAA
1443539 GGAA
1 GGAA
1443543 CTTATTCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (22 bp):
GGAAAGTAAGACACATTAGAAA
Found at i:1444153 original size:2 final size:2
Alignment explanation
Indices: 1444142--1444175 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1444132 TGTTATAAAC
1444142 TA TA -A TA TA 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 TA T
1444176 TATTTCAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1444166 original size:28 final size:28
Alignment explanation
Indices: 1444107--1444179 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
1444097 CCGCTTAAAT
* *
1444107 TATAAATTATAATATTATTATATAATGT
1 TATAAACTATAATATTATTATATAATGA
1444135 TATAAACTATAATA-TA-TATATATAT-A
1 TATAAACTATAATATTATTATATA-ATGA
*
1444161 TATATA-TATATATATTATT
1 TATAAACTATA-ATATTATT
1444180 TCAGGTCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 4 0.11
26 14 0.37
27 6 0.16
28 14 0.37
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATAAACTATAATATTATTATATAATGA
Found at i:1445366 original size:24 final size:23
Alignment explanation
Indices: 1445338--1445385 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
1445328 TGTTTTTATA
1445338 TATGTATATATATTTATTTATTTT
1 TATGTATATATATTTA-TTATTTT
*
1445362 TATGTGTATATATTTATTATTTT
1 TATGTATATATATTTATTATTTT
1445385 T
1 T
1445386 CATATTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (23 bp):
TATGTATATATATTTATTATTTT
Found at i:1445430 original size:17 final size:18
Alignment explanation
Indices: 1445408--1445441 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1445398 TTTACTTATT
1445408 TTACTAAATA-ATATATC
1 TTACTAAATATATATATC
*
1445425 TTACTATATATATATAT
1 TTACTAAATATATATAT
1445442 ATTATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
TTACTAAATATATATATC
Found at i:1445511 original size:23 final size:22
Alignment explanation
Indices: 1445480--1445536 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1445470 TTCTTTTACC
*
1445480 TTTTTTTTT-TGTTTATGTTTCT
1 TTTTTTTTTCTGTTTA-GTTTCA
*
1445502 TTTTTATTTTCTTTTTAGTTTCA
1 TTTTT-TTTTCTGTTTAGTTTCA
1445525 TTTTTGTTTTCT
1 TTTTT-TTTTCT
1445537 TCTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 20 0.67
24 5 0.17
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTCTGTTTAGTTTCA
Found at i:1445514 original size:12 final size:12
Alignment explanation
Indices: 1445491--1445585 Score: 52
Period size: 12 Copynumber: 7.7 Consensus size: 12
1445481 TTTTTTTTTG
1445491 TTTATGTTTCTTT
1 TTTAT-TTTCTTT
1445504 TTTATTTTC-TT
1 TTTATTTTCTTT
* *
1445515 TTTAGTTTCATT
1 TTTATTTTCTTT
*
1445527 TTTGTTTTCTTCT
1 TTTATTTTCTT-T
* *
1445540 CTT-TTTT-ATT
1 TTTATTTTCTTT
*
1445550 TTTATTCTTTTTT
1 TTTATT-TTCTTT
*
1445563 TTTCATTTTTTTCGT
1 TTT-ATTTTCTT--T
1445578 TTTATTTT
1 TTTATTTT
1445586 ATGTAGATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
10 3 0.05
11 13 0.20
12 20 0.30
13 18 0.27
14 8 0.12
15 4 0.06
ACGTcount: A:0.08, C:0.09, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTATTTTCTTT
Found at i:1445537 original size:23 final size:24
Alignment explanation
Indices: 1445491--1445572 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 24
1445481 TTTTTTTTTG
*
1445491 TTTATGTTTCTTTTTTATTTTCTT
1 TTTATGTTTCATTTTTATTTTCTT
*
1445515 TTTA-GTTTCATTTTTGTTTTCTT
1 TTTATGTTTCATTTTTATTTTCTT
1445538 CTCTT-T-TTT-ATTTTTA--TTCTT
1 -T-TTATGTTTCATTTTTATTTTCTT
1445559 TTT-T-TTTCATTTTT
1 TTTATGTTTCATTTTT
1445573 TTCGTTTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.12
20 7 0.14
21 5 0.10
23 23 0.45
24 8 0.16
25 2 0.04
ACGTcount: A:0.09, C:0.10, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTATGTTTCATTTTTATTTTCTT
Found at i:1445565 original size:14 final size:14
Alignment explanation
Indices: 1445501--1445574 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
1445491 TTTATGTTTC
1445501 TTTTTTATTTTC--
1 TTTTTTATTTTCAT
*
1445513 -TTTTTAGTTTCAT
1 TTTTTTATTTTCAT
1445526 TTTTGTT-TTCTTC-T
1 TTTT-TTATT-TTCAT
*
1445540 CTTTTTTATTTTTAT
1 -TTTTTTATTTTCAT
1445555 TCTTTTT-TTTTCAT
1 T-TTTTTATTTTCAT
1445569 TTTTTT
1 TTTTTT
1445575 CGTTTTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
11 10 0.20
13 5 0.10
14 17 0.35
15 17 0.35
ACGTcount: A:0.08, C:0.09, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTTCAT
Found at i:1445570 original size:20 final size:19
Alignment explanation
Indices: 1445541--1445587 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1445531 TTTTCTTCTC
1445541 TTTTTTATTTTTATTC-TTT
1 TTTTTTATTTTT-TTCGTTT
1445560 TTTTTTCATTTTTTTCGTTT
1 TTTTTT-ATTTTTTTCGTTT
*
1445580 TATTTTAT
1 TTTTTTAT
1445588 GTAGATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTTATTTTTTTCGTTT
Found at i:1445574 original size:23 final size:21
Alignment explanation
Indices: 1445479--1445574 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 21
1445469 TTTCTTTTAC
* * *
1445479 CTTTTTTTTTTGTTTATGTTT
1 CTTTTTTTTTTCTTTTTTTTT
*
1445500 CTTTTTTATTTTCTTTTTAGTTT
1 CTTTTTT-TTTTCTTTTT-TTTT
* *
1445523 CATTTTTGTTTTCTTCTCTTTTT
1 C-TTTTTTTTTTCTT-TTTTTTT
* *
1445546 -TATTTTTATTCTTTTTTTTT
1 CTTTTTTTTTTCTTTTTTTTT
*
1445566 CATTTTTTT
1 CTTTTTTTT
1445575 CGTTTTATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.10
21 22 0.38
22 8 0.14
23 15 0.26
24 7 0.12
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.79
Consensus pattern (21 bp):
CTTTTTTTTTTCTTTTTTTTT
Found at i:1445584 original size:14 final size:12
Alignment explanation
Indices: 1445482--1445585 Score: 50
Period size: 13 Copynumber: 8.3 Consensus size: 12
1445472 CTTTTACCTT
1445482 TTTTTTTTGTTTA
1 TTTTTTTT-TTTA
*
1445495 TGTTTCTTTTTTA
1 T-TTTTTTTTTTA
*
1445508 -TTTTCTTTTTA
1 TTTTTTTTTTTA
* ** *
1445519 GTTTCATTTTTG
1 TTTTTTTTTTTA
* * *
1445531 TTTTCTTCTCT-
1 TTTTTTTTTTTA
*
1445542 TTTTTATTTTTA
1 TTTTTTTTTTTA
1445554 TTCTTTTTTTTTCA
1 TT-TTTTTTTTT-A
1445568 TTTTTTTCGTTTTA
1 TTTTTTT--TTTTA
1445582 TTTT
1 TTTT
1445586 ATGTAGATTT
Statistics
Matches: 69, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
11 16 0.23
12 17 0.25
13 18 0.26
14 14 0.20
15 4 0.06
ACGTcount: A:0.08, C:0.09, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:1456000 original size:17 final size:17
Alignment explanation
Indices: 1455978--1456015 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1455968 TCGAAGAATA
1455978 AAAAGAA-AAAAGAAAAG
1 AAAAGAACAAAA-AAAAG
1455995 AAAAGAACAAAAAAAAG
1 AAAAGAACAAAAAAAAG
1456012 AAAA
1 AAAA
1456016 ATGTTTAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAGAACAAAAAAAAG
Found at i:1456075 original size:7 final size:6
Alignment explanation
Indices: 1456053--1456105 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
1456043 GCCCTAAATT
*
1456053 AAAA-A AAAAGA AAAAGA ACAAAG- AAAAGAA AAAAGA GAAAATA AAAAGA
1 AAAAGA AAAAGA AAAAGA A-AAAGA AAAAG-A AAAAGA -AAAAGA AAAAGA
1456102 AAAA
1 AAAA
1456106 TAAGGTGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
5 8 0.20
6 19 0.46
7 14 0.34
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAGA
Done.